Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 51 of 163
Found at i:12699113 original size:99 final size:99
Alignment explanation
Indices: 12699010--12699585 Score: 367
Period size: 99 Copynumber: 5.8 Consensus size: 99
12699000 TCAAATTCGT
* * * *** *
12699010 CGTTGCGACCTCAATCC-TTCCCATCACATTTTCTAAGGTACGGGGATCGTTGTTGCAGCCCCAA
1 CGTTGCGACCTCAA-CCTTTCCCATCACATCTTCTTAGGTACCGGGATCACCGTTACAGCCCCAA
* * * *
12699074 CCTTTCCCTTCATATCTCCGTTGTATCGGGTTTAC
65 CCTTTCCCTTCATATCTCCATGGTACCGGGTTCAC
* * * * *
12699109 CGTTGCGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTACCGGGTTCACCGTTACGGCCTCAAC
1 CGTTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGATCACCGTTACAGCCCCAAC
* *
12699174 CTTTCCCTTCGTATCTTCATGGTACCGGGTTCAC
66 CTTTCCCTTCATATCTCCATGGTACCGGGTTCAC
* ** * **
12699208 CGTTGC-AGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTTGCCATTACAGCCTTAA
1 CGTTGCGA-CCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGATCACCGTTACAGCCCCAA
* * * ** *
12699272 TCC-TTCCCTTCCTCTCTTCATGGTACTAGGTTCGC
65 -CCTTTCCCTTCATATCTCCATGGTACCGGGTTCAC
* * * * * * * * * **
12699307 TGTTGCGGCCTCAACTTTTCCCATCATATCTTCTTAGGTATCAGGCTCGCCGTTGA-GGCCTTAA
1 CGTTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGATCACCGTT-ACAGCCCCAA
* * *** *
12699371 CCTTTCTCTTTGAT-TCTTTGTGGTACCGGGTTCGC
65 CCTTTC-CCTTCATATCTCCATGGTACCGGGTTCAC
* * * * **** *
12699406 TGTTGTGGCCTCAACCTTTCCCATCACAT-TTTTTAAGGTACC-GGATTCACCGTCGTGGCCTCA
1 CGTTGCGACCTCAACCTTTCCCATCACATCTTCTT-AGGTACCGGGA-TCACCGTTACAGCCCCA
* * * * * **
12699469 GTCC-TTCCCTTCATCTCTTCATGTTACTGGGTTCGT
64 -ACCTTTCCCTTCATATCTCCATGGTACCGGGTTCAC
* ** * * * * **
12699505 CGTTACGGGCTCAACATTTCCCATCACATCTTCTTAGGTATCGGGTTCATCGTTACAGCCTTAAC
1 CGTTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGATCACCGTTACAGCCCCAAC
*
12699570 CTTTCCCTTCACATCT
66 CTTTCCCTTCATATCT
12699586 TTTAAGGTAT
Statistics
Matches: 380, Mismatches: 82, Indels: 30
0.77 0.17 0.06
Matches are distributed among these distances:
98 17 0.04
99 348 0.92
100 15 0.04
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.35
Consensus pattern (99 bp):
CGTTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGATCACCGTTACAGCCCCAAC
CTTTCCCTTCATATCTCCATGGTACCGGGTTCAC
Found at i:12699168 original size:50 final size:50
Alignment explanation
Indices: 12698954--12699623 Score: 384
Period size: 50 Copynumber: 13.5 Consensus size: 50
12698944 TTTTCTGTTA
* ** * * * * *
12698954 GGTTCGTCGTTGCGGCCTCAACCTTTCCTTTTATATCTTCAT-GGTATCA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
** * * * * *
12699003 AATTCGTCGTTGCGACCTCAATCC-TTCCCATCACATTTTCTAAGGTACGG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTTAGGTACCG
* ** * * * * * *
12699053 GGATCGTTGTTGCAGCCCCAACCTTTCCCTTCATATCTCCGTT--GTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC-TTAGGTACCG
** *
12699102 GGTTTACCGTTGCGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* * * ** *
12699152 GGTTCACCGTTACGGCCTCAACCTTTCCCTTCGTATCTTCAT-GGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* *
12699201 GGTTCACCGTTGCAGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* * * * * * **
12699251 GGTTTGCCATTACAGCCTTAATCC-TTCCCTTC-C-TC-TCTTCATGGTACTA
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTT-A-GGTACCG
* * * * *
12699300 GGTTCGCTGTTGCGGCCTCAACTTTTCCCATCATATCTTCTTAGGTATCA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* * * ** * *
12699350 GGCTCGCCGTTGAGGCCTTAACCTTTCTCTTTGA-TTCTT-TGT-GGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTC-CCATCACATCTTCT-TAGGTACCG
* * *
12699399 GGTTCGCTGTTGTGGCCTCAACCTTTCCCATCACAT-TTTTTAAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT-AGGTACCG
* * * * * * * * *
12699449 GATTCACCGTCGTGGCCTCAGTCC-TTCCCTTCATC-TCTTCAT-GTTACTG
1 GGTTCGCCGTTGCGGCCTCA-ACCTTTCCCATCA-CATCTTCTTAGGTACCG
* * * * *
12699498 GGTTCGTCGTTACGGGCTCAACATTTCCCATCACATCTTCTTAGGTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
** * * * * *
12699548 GGTTCATCGTTACAGCCTTAACCTTTCCCTTCACATCTT-TTAAGGTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT-AGGTACCG
* *
12699598 GATTCGCTGTTGCGGCCTCAATCCTT
1 GGTTCGCCGTTGCGGCCTCAA-CCTT
12699624 CCTTGTCAAA
Statistics
Matches: 468, Mismatches: 125, Indels: 54
0.72 0.19 0.08
Matches are distributed among these distances:
47 4 0.01
48 14 0.03
49 200 0.43
50 227 0.49
51 19 0.04
52 4 0.01
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.36
Consensus pattern (50 bp):
GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
Found at i:12699314 original size:198 final size:198
Alignment explanation
Indices: 12699109--12699579 Score: 563
Period size: 198 Copynumber: 2.4 Consensus size: 198
12699099 TCGGGTTTAC
* * * *
12699109 CGTTGCGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTACCGGGTTCACCGTTACGGCCTCAAC
1 CGTTGCGGCCTCAACATTTCCCATCACATCTTCTTAGGTATCGGGTTCACCGTTACGGCCTTAAC
12699174 CTTTCCCTTCG-TATCTTCATGGTACCGGGTTCACCGTTGCAGCCTCAACCTTTCCCATCACATC
66 CTTTCCCTTCGAT-TCTTCATGGTACCGGGTTCACCGTTGCAGCCTCAACCTTTCCCATCACAT-
* ** * * *
12699238 TTCTT-AGGTACCGGGTTTGCCATTACAGCCTTAATCCTTCCCTTCCTCTCTTCATGGTACTAGG
129 TTCTTAAGGTACCGGATTCACCATCACAGCCTCAATCCTTCCCTTCATCTCTTCATGGTACTAGG
12699302 TTCG-
194 TTCGT
* * * * *
12699306 CTGTTGCGGCCTCAACTTTTCCCATCATATCTTCTTAGGTATCAGGCTCGCCGTTGA-GGCCTTA
1 C-GTTGCGGCCTCAACATTTCCCATCACATCTTCTTAGGTATCGGGTTCACCGTT-ACGGCCTTA
* * ** * * **
12699370 ACCTTTCTCTTTGATTCTTTGTGGTACCGGGTTCGCTGTTGTGGCCTCAACCTTTCCCATCACAT
64 ACCTTTCCCTTCGATTCTTCATGGTACCGGGTTCACCGTTGCAGCCTCAACCTTTCCCATCACAT
* * *** * * *
12699435 TTTTTAAGGTACCGGATTCACCGTCGTGGCCTCAGTCCTTCCCTTCATCTCTTCATGTTACTGGG
129 TTCTTAAGGTACCGGATTCACCATCACAGCCTCAATCCTTCCCTTCATCTCTTCATGGTACTAGG
12699500 TTCGT
194 TTCGT
* * * *
12699505 CGTTACGGGCTCAACATTTCCCATCACATCTTCTTAGGTATCGGGTTCATCGTTACAGCCTTAAC
1 CGTTGCGGCCTCAACATTTCCCATCACATCTTCTTAGGTATCGGGTTCACCGTTACGGCCTTAAC
12699570 CTTTCCCTTC
66 CTTTCCCTTC
12699580 ACATCTTTTA
Statistics
Matches: 227, Mismatches: 41, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
197 6 0.03
198 218 0.96
199 3 0.01
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (198 bp):
CGTTGCGGCCTCAACATTTCCCATCACATCTTCTTAGGTATCGGGTTCACCGTTACGGCCTTAAC
CTTTCCCTTCGATTCTTCATGGTACCGGGTTCACCGTTGCAGCCTCAACCTTTCCCATCACATTT
CTTAAGGTACCGGATTCACCATCACAGCCTCAATCCTTCCCTTCATCTCTTCATGGTACTAGGTT
CGT
Found at i:12708193 original size:30 final size:32
Alignment explanation
Indices: 12708134--12708196 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
12708124 ATATTCGAGG
*
12708134 AATTTGGGGATCAAAATTGAAATTTTTGGAAA
1 AATTTGGGGATCAAAATTGAAACTTTTGGAAA
*
12708166 AATTT-GGGATTAAAATTG-AACTTTTGGAAA
1 AATTTGGGGATCAAAATTGAAACTTTTGGAAA
12708196 A
1 A
12708197 TTGGAGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 12 0.41
31 12 0.41
32 5 0.17
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (32 bp):
AATTTGGGGATCAAAATTGAAACTTTTGGAAA
Found at i:12708249 original size:29 final size:28
Alignment explanation
Indices: 12708208--12708546 Score: 150
Period size: 29 Copynumber: 11.5 Consensus size: 28
12708198 TGGAGGTCGA
*
12708208 AAAATGTGATTTTTGGAAATTTGAGGGC
1 AAAATGTAATTTTTGGAAATTTGAGGGC
** * * *
12708236 AAAATGATAATTTTTGGATGTTCGGGGGT
1 AAAATG-TAATTTTTGGAAATTTGAGGGC
12708265 AAAATGGTAATTTTT--AAATGTTCGAGGGC
1 AAAAT-GTAATTTTTGGAAAT-TT-GAGGGC
**
12708294 AAAATGGTAATTTTTGGATGTTT-AGAGGC
1 AAAAT-GTAATTTTTGGAAATTTGAG-GGC
*
12708323 AAAATGGTAA-TTTTGGAAGAGTTTG-GGGTG
1 AAAAT-GTAATTTTTGGAA-A-TTTGAGGG-C
* * * *
12708353 AAAATGTGATTTTAGAAAAGTTTGAGGGTT
1 AAAATGTAATTTTTGGAAA-TTTGAGGG-C
** * *
12708383 AAAAAATAATTTTGGAGAAATTTGAGGGTT
1 AAAATGTAATTTTTG-GAAATTTGAGGG-C
* **
12708413 AAAATGTAATTTTTGGAAAATTTAAGGTT
1 AAAATGTAATTTTTGG-AAATTTGAGGGC
* * * * *
12708442 AAAATTTCATTTTTGAGAAGTTTTAAGGGTT
1 AAAATGTAATTTTTG-GAA-ATTTGAGGG-C
* * * *
12708473 AAAATATGATTTTTGGGAAGTTTAAGGGTC
1 AAAATGTAATTTTT-GGAAATTTGAGGG-C
* *
12708503 AAAATGTAA-TTTTGGAAAGTTTAAGAGTC
1 AAAATGTAATTTTTGGAAA-TTTGAG-GGC
*
12708532 AAAATGTGATTTTTG
1 AAAATGTAATTTTTG
12708547 AGAAGTTCGA
Statistics
Matches: 246, Mismatches: 43, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
27 2 0.01
28 20 0.08
29 108 0.44
30 94 0.38
31 21 0.09
32 1 0.00
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAATTTGAGGGC
Found at i:12708394 original size:59 final size:59
Alignment explanation
Indices: 12708330--12708638 Score: 193
Period size: 59 Copynumber: 5.2 Consensus size: 59
12708320 GGCAAAATGG
* *
12708330 TAATTTTGGAAGAGTTT-GGGGTGAAAATGTGATTTTAGAAAAGTTTGAGGGTTAAAAAA
1 TAATTTTGGAAGAGTTTAGGGGTTAAAATGTGATTTTAGAAAAGTTT-AGGGTTAAAATA
* * * * *
12708389 TAATTTTGG-AGAAATTT-GAGGGTTAAAATGTAATTTTTGGAAAA-TTTAAGGTTAAAATT
1 TAATTTTGGAAG-AGTTTAG-GGGTTAAAATGTGA-TTTTAGAAAAGTTTAGGGTTAAAATA
* * * * * ** * *
12708448 TCATTTTTGAGAAG-TTTTAAGGGTTAAAATATGATTTTTGGGAAGTTTAAGGGTCAAAATG
1 T-AATTTTG-GAAGAGTTTAGGGGTTAAAATGTGATTTTAGAAAAGTTT-AGGGTTAAAATA
* * * * * * * * *
12708509 TAATTTTGGAA-AGTTTAAGAGTCAAAATGTGATTTTTGAGAAG-TTCGATGTTCAAATG
1 TAATTTTGGAAGAGTTTAGGGGTTAAAATGTGATTTTAGAAAAGTTTAG-GGTTAAAATA
* * ** *
12708567 TAATTTTGGAA-ATGTTTGGGGGTTAAGATGCAATTTTAGAAAAGTTTAGGAGTCAAAATA
1 TAATTTTGGAAGA-GTTTAGGGGTTAAAATGTGATTTTAGAAAAGTTTAGG-GTTAAAATA
12708627 TAATTTTTGGAA
1 TAA-TTTTGGAA
12708639 AATTCAAGGA
Statistics
Matches: 193, Mismatches: 42, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
57 1 0.01
58 23 0.12
59 82 0.42
60 57 0.30
61 28 0.15
62 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (59 bp):
TAATTTTGGAAGAGTTTAGGGGTTAAAATGTGATTTTAGAAAAGTTTAGGGTTAAAATA
Found at i:12708476 original size:90 final size:90
Alignment explanation
Indices: 12708322--12708553 Score: 247
Period size: 90 Copynumber: 2.6 Consensus size: 90
12708312 TGTTTAGAGG
* * * * * * * *
12708322 CAAAATGGTAATTTTGGAAGAGTTT-GGGGTGAAAATGTGATTTTAGAAAAG-TTTGAGGGTTAA
1 CAAAAT-GTAATTTTGGAA-AATTTAAGAGTCAAAATGTCATTTTTGAGAAGTTTTAAGGGTTAA
*
12708385 AAAAT-AATTTTGGAGAAATTTGAGGGT
64 AAAATGAATTTTGG-GAAATTTAAGGGT
* * *
12708412 TAAAATGTAATTTTTGGAAAATTTAAG-GTTAAAATTTCATTTTTGAGAAGTTTTAAGGGTTAAA
1 CAAAATGTAA-TTTTGGAAAATTTAAGAGTCAAAATGTCATTTTTGAGAAGTTTTAAGGGTTAAA
* * *
12708476 ATATGATTTTTGGGAAGTTTAAGGGT
65 AAATGAATTTTGGGAAATTTAAGGGT
* *
12708502 CAAAATGTAATTTTGGAAAGTTTAAGAGTCAAAATGTGATTTTTGAGAAGTT
1 CAAAATGTAATTTTGGAAAATTTAAGAGTCAAAATGTCATTTTTGAGAAGTT
12708554 CGATGTTCAA
Statistics
Matches: 119, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
89 41 0.34
90 71 0.60
91 7 0.06
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.38
Consensus pattern (90 bp):
CAAAATGTAATTTTGGAAAATTTAAGAGTCAAAATGTCATTTTTGAGAAGTTTTAAGGGTTAAAA
AATGAATTTTGGGAAATTTAAGGGT
Found at i:12708553 original size:30 final size:30
Alignment explanation
Indices: 12708294--12708635 Score: 193
Period size: 30 Copynumber: 11.5 Consensus size: 30
12708284 GTTCGAGGGC
* *
12708294 AAAATGGTAATTTTTG-GATGTTT-AGAGG-C
1 AAAAT-GTAATTTTTGAGAAGTTTAAG-GGTT
* * *
12708323 AAAATGGTAATTTTGGA-AGAGTTT-GGGGTG
1 AAAAT-GTAATTTTTGAGA-AGTTTAAGGGTT
* * * *
12708353 AAAATGTGATTTTAGAAAAGTTTGAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
** * * *
12708383 AAAAAATAATTTTGGAGAAATTTGAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
*
12708413 AAAATGTAATTTTTG-GAAAATTTAA-GGTT
1 AAAATGTAATTTTTGAG-AAGTTTAAGGGTT
* *
12708442 AAAATTTCATTTTTGAGAAGTTTTAAGGGTT
1 AAAATGTAATTTTTGAGAAG-TTTAAGGGTT
* * * *
12708473 AAAATATGATTTTTGGGAAGTTTAAGGGTC
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
* * *
12708503 AAAATGTAATTTTGGA-AAGTTTAAGAGTC
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
* ** *
12708532 AAAATGTGATTTTTGAGAAGTTCGA-TGTT
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
* * **
12708561 CAAATGTAATTTTGGA-AATGTTTGGGGGTT
1 AAAATGTAATTTTTGAGAA-GTTTAAGGGTT
* * * * *
12708591 AAGATGCAATTTTAGAAAAGTTT-AGGAGTC
1 AAAATGTAATTTTTGAGAAGTTTAAGG-GTT
*
12708621 AAAATATAATTTTTG
1 AAAATGTAATTTTTG
12708636 GAAAATTCAA
Statistics
Matches: 247, Mismatches: 52, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
28 2 0.01
29 99 0.40
30 123 0.50
31 23 0.09
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTTAAGGGTT
Found at i:12711065 original size:60 final size:59
Alignment explanation
Indices: 12711001--12711173 Score: 199
Period size: 60 Copynumber: 2.9 Consensus size: 59
12710991 CTAAAAATGG
*
12711001 TATTTTGACCCCAAAACTTTTTGAAAATTACATTTTGACCGCTAAACTATTCCAAAATTA
1 TATTTTGACCCCAAAACTTTTT-AAAATTACATTTTGACCCCTAAACTATTCCAAAATTA
* * * * *
12711061 TATTTTAACCCTAAAAGTTTTTATAAATTACACTTTAACCCCTAAAC-ATTTCCAAAATTA
1 TATTTTGACCCCAAAACTTTTTA-AAATTACATTTTGACCCCTAAACTA-TTCCAAAATTA
* ***
12711121 CATTTTGACCCCAAAACTTCCCAAAATTACATTTTTG-CCCCTAAACT-TTCCAA
1 TATTTTGACCCCAAAACTTTTTAAAATTACA-TTTTGACCCCTAAACTATTCCAA
12711174 GACTCCATTT
Statistics
Matches: 94, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
58 6 0.06
59 19 0.20
60 69 0.73
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (59 bp):
TATTTTGACCCCAAAACTTTTTAAAATTACATTTTGACCCCTAAACTATTCCAAAATTA
Found at i:12711152 original size:29 final size:29
Alignment explanation
Indices: 12711002--12711173 Score: 157
Period size: 30 Copynumber: 5.8 Consensus size: 29
12710992 TAAAAATGGT
**
12711002 ATTTTGACCCCAAAACTTTTTGAAAATTAC
1 ATTTTGACCCCAAAAC-TTTCCAAAATTAC
* * *
12711032 ATTTTGACCGCTAAACTATTCCAAAATTAT
1 ATTTTGACCCCAAAACT-TTCCAAAATTAC
* * * **
12711062 ATTTTAACCCTAAAAGTTTTTATAAATTAC
1 ATTTTGACCCCAAAACTTTCCA-AAATTAC
* * *
12711092 ACTTTAACCCCTAAACATTTCCAAAATTAC
1 ATTTTGACCCCAAAAC-TTTCCAAAATTAC
*
12711122 ATTTTGACCCCAAAACTTCCCAAAATTAC
1 ATTTTGACCCCAAAACTTTCCAAAATTAC
*
12711151 ATTTTTG-CCCCTAAACTTTCCAA
1 A-TTTTGACCCCAAAACTTTCCAA
12711174 GACTCCATTT
Statistics
Matches: 113, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
29 31 0.27
30 78 0.69
31 4 0.04
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (29 bp):
ATTTTGACCCCAAAACTTTCCAAAATTAC
Found at i:12711644 original size:96 final size:96
Alignment explanation
Indices: 12711479--12711660 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 96
12711469 AAAACTTTAA
* ** * * * **
12711479 AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAACCTTTGCGCCTTAACTTACTAGGTGCGATT
1 AATCGAGGCAATATTCTTTTATTTCGAGTTATGAAAATTTACGCCTTAACTCACTAGGTGCAACC
12711544 TTTCTTCAAATCGAAATAATCGAATATCCTT
66 TTTCTTCAAATCGAAATAATCGAATATCCTT
* *
12711575 AATCGAGGCAATGTT-TTCTTATCTTC-AGTTATGAAAATTTACGCCTTAACTCACTAGGTGTAA
1 AATCGAGGCAATATTCTT-TTAT-TTCGAGTTATGAAAATTTACGCCTTAACTCACTAGGTGCAA
*
12711638 CCTTTCTTCAAATCGAGATAATC
64 CCTTTCTTCAAATCGAAATAATC
12711661 AAACACCCTT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
95 2 0.03
96 68 0.93
97 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATTTCGAGTTATGAAAATTTACGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAATATCCTT
Found at i:12715806 original size:10 final size:10
Alignment explanation
Indices: 12715791--12715828 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
12715781 ATGTGTTATC
12715791 AAAAAAAAAG
1 AAAAAAAAAG
12715801 AAAAAAAAAG
1 AAAAAAAAAG
*
12715811 AGAAAAAAAG
1 AAAAAAAAAG
12715821 AAGAAAAA
1 AA-AAAAA
12715829 GGTCAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:12715807 original size:11 final size:11
Alignment explanation
Indices: 12715791--12715828 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
12715781 ATGTGTTATC
12715791 AAAAAAAAAGA
1 AAAAAAAAAGA
12715802 AAAAAAAAGAGA
1 AAAAAAAA-AGA
*
12715814 AAAAAAGAAGA
1 AAAAAAAAAGA
12715825 AAAA
1 AAAA
12715829 GGTCAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:12716723 original size:13 final size:13
Alignment explanation
Indices: 12716698--12716757 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
12716688 TTCAATGAAT
12716698 AAAAG-AAAAGAA
1 AAAAGAAAAAGAA
*
12716710 AAAAGAAGAAGAA
1 AAAAGAAAAAGAA
12716723 AAACA-AAAAAGAA
1 AAA-AGAAAAAGAA
*
12716736 AATAAAAAAAAG-A
1 AA-AAGAAAAAGAA
12716749 AAAAGAAAA
1 AAAAGAAAA
12716758 GGAGAGGTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 11 0.27
13 22 0.54
14 8 0.20
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:12716730 original size:19 final size:18
Alignment explanation
Indices: 12716700--12716755 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
12716690 CAATGAATAA
*
12716700 AAGAAAAGAAAAAAGAAG
1 AAGAAAAAAAAAAAGAAG
12716718 AAGAAAAACAAAAAAGAA-
1 AAGAAAAA-AAAAAAGAAG
*
12716736 AATAAAAAAAAGAAA-AAG
1 AAGAAAAAAAA-AAAGAAG
12716754 AA
1 AA
12716756 AAGGAGAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 5 0.15
18 19 0.58
19 9 0.27
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAAAAAAGAAG
Found at i:12717826 original size:101 final size:101
Alignment explanation
Indices: 12717664--12717930 Score: 399
Period size: 101 Copynumber: 2.6 Consensus size: 101
12717654 AAGACATGAT
12717664 GGGAAAGATCTAAGACCGCGACGGTAGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAG
1 GGGAAAGATCTAAGACCGCGACGGTAGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAG
* * *
12717729 TTACAACAGTAGATCGTGTACCTCAGAAGACACAAC
66 TCACAACAGCAGACCGTGTACCTCAGAAGACACAAC
* * * *
12717765 GGGAAAGATCTAAGACCGCGACGGTAGATCCAGTATCACAAAAAGATAAAAGGGAAAGGTCTAAA
1 GGGAAAGATCTAAGACCGCGACGGTAGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAG
* * *
12717830 TCGCAACGGCAGACCGTGTACCTCAGAAGACACGAC
66 TCACAACAGCAGACCGTGTACCTCAGAAGACACAAC
* * * * *
12717866 GGGAAAGATCTAAGACTGCAACGGCAGATCCAGTACCGCAAAAAGACAGAAGGGAAAGATCTAAG
1 GGGAAAGATCTAAGACCGCGACGGTAGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAG
12717931 CTGTAACGGC
Statistics
Matches: 147, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 147 1.00
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.13
Consensus pattern (101 bp):
GGGAAAGATCTAAGACCGCGACGGTAGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAG
TCACAACAGCAGACCGTGTACCTCAGAAGACACAAC
Found at i:12717939 original size:101 final size:101
Alignment explanation
Indices: 12717651--12718086 Score: 397
Period size: 101 Copynumber: 4.4 Consensus size: 101
12717641 GTCTCAACAC
* * *
12717651 CAGAAGACATGATGGGAAAGATCTAAGACCGCGACGGTAGATCCAGTACCGCAAAAAGACAAAAG
1 CAGAAGACACGACGGGAAAGATCTAAGACCGCGACGGCAGATCCAGTACCGCAAAAAGACAAAAG
* * * * * *
12717716 GGAAAGGTCTAAGTTACAACAGTAGATCGTGTACCT
66 GGAAAGATCTAAGCTGCAACGGCAGACCGTGTACCT
* * * * *
12717752 CAGAAGACACAACGGGAAAGATCTAAGACCGCGACGGTAGATCCAGTATCACAAAAAGATAAAAG
1 CAGAAGACACGACGGGAAAGATCTAAGACCGCGACGGCAGATCCAGTACCGCAAAAAGACAAAAG
* *
12717817 GGAAAGGTCTAA-ATCGCAACGGCAGACCGTGTACCT
66 GGAAAGATCTAAGCT-GCAACGGCAGACCGTGTACCT
* * *
12717853 CAGAAGACACGACGGGAAAGATCTAAGACTGCAACGGCAGATCCAGTACCGCAAAAAGACAGAAG
1 CAGAAGACACGACGGGAAAGATCTAAGACCGCGACGGCAGATCCAGTACCGCAAAAAGACAAAAG
* * * *
12717918 GGAAAGATCTAAGCTGTAACGGCGGATCC-AGTACCA
66 GGAAAGATCTAAGCTGCAACGGCAGA-CCGTGTACCT
* * * ** * * *
12717954 CA-AAAACATGAAGACAAAGATCTAAG-CCGCGACGGCGGATCCAGTATCC-C--GAAGACATGA
1 CAGAAGACACGACGGGAAAGATCTAAGACCGCGACGGCAGATCCAGTA-CCGCAAAAAGACA-AA
* * ** * *
12718014 AGGGAAAGATCTAAGCCGCGACGGTGGATCC-AGTACCA
64 AGGGAAAGATCTAAGCTGCAACGGCAGA-CCGTGTACCT
* * *
12718052 C-GAAGACATGAAGAGAAAGATCTAAG-CCGCGACGG
1 CAGAAGACACGACGGGAAAGATCTAAGACCGCGACGG
12718087 TGGATCCCGT
Statistics
Matches: 289, Mismatches: 40, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
97 6 0.02
98 68 0.24
99 18 0.06
100 22 0.08
101 172 0.60
102 3 0.01
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (101 bp):
CAGAAGACACGACGGGAAAGATCTAAGACCGCGACGGCAGATCCAGTACCGCAAAAAGACAAAAG
GGAAAGATCTAAGCTGCAACGGCAGACCGTGTACCT
Found at i:12718113 original size:49 final size:49
Alignment explanation
Indices: 12717649--12718119 Score: 315
Period size: 49 Copynumber: 9.5 Consensus size: 49
12717639 AGGTCTCAAC
* **
12717649 ACCA-GAAGACATGATGGGAAAGATCTAAGACCGCGACGGTAGATCCAGT
1 ACCACGAAGACATGAAGGGAAAGATCTAAG-CCGCGACGGCGGATCCAGT
** * * *** * * ** **
12717698 ACCGCAAAAAGACA-AAAGGGAAAGGTCTAAGTTACAACAGTAGATCGTGT
1 A-C-CACGAAGACATGAAGGGAAAGATCTAAGCCGCGACGGCGGATCCAGT
* * **
12717748 ACCTCAGAAGACA-CAACGGGAAAGATCTAAGACCGCGACGGTAGATCCAGT
1 ACCAC-GAAGACATGAA-GGGAAAGATCTAAG-CCGCGACGGCGGATCCAGT
* * * * * * ** * * *
12717799 ATCACAAAAAGATAAAAGGGAAAGGTCTAAATCGCAACGGCAGA-CCGTGT
1 ACCACGAAGACAT-GAAGGGAAAGATCTAAGCCGCGACGGCGGATCC-AGT
* * * * * *
12717849 ACCTCAGAAGACACGACGGGAAAGATCTAAGACTGCAACGGCAGATCCAGT
1 ACCAC-GAAGACATGAAGGGAAAGATCTAAG-CCGCGACGGCGGATCCAGT
** * **
12717900 ACCGCAAAAAGACA-GAAGGGAAAGATCTAAGCTGTAACGGCGGATCCAGT
1 A-C-CACGAAGACATGAAGGGAAAGATCTAAGCCGCGACGGCGGATCCAGT
* * **
12717950 ACCACAAAAACATGAAGACAAAGATCTAAGCCGCGACGGCGGATCCAGT
1 ACCACGAAGACATGAAGGGAAAGATCTAAGCCGCGACGGCGGATCCAGT
*
12717999 ATCC-CGAAGACATGAAGGGAAAGATCTAAGCCGCGACGGTGGATCCAGT
1 A-CCACGAAGACATGAAGGGAAAGATCTAAGCCGCGACGGCGGATCCAGT
* * *
12718048 ACCACGAAGACATGAAGAGAAAGATCTAAGCCGCGACGGTGGATCCCGT
1 ACCACGAAGACATGAAGGGAAAGATCTAAGCCGCGACGGCGGATCCAGT
**
12718097 ACCACGAAGATTTGAAGGGAAAG
1 ACCACGAAGACATGAAGGGAAAG
12718120 GTTTAAGTCG
Statistics
Matches: 334, Mismatches: 71, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
48 11 0.03
49 149 0.45
50 79 0.24
51 77 0.23
52 17 0.05
53 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.13
Consensus pattern (49 bp):
ACCACGAAGACATGAAGGGAAAGATCTAAGCCGCGACGGCGGATCCAGT
Found at i:12718160 original size:98 final size:97
Alignment explanation
Indices: 12717868--12718148 Score: 235
Period size: 98 Copynumber: 2.9 Consensus size: 97
12717858 GACACGACGG
* * * *
12717868 GAAAGATCTAAGACTGCAACGGCAGATCCAGTA-CCGCAAAAAGACA-GAAGGGAAAGATCTAAG
1 GAAAGATCTAAG-CCGCGACGGCGGATCCAGTATCC-C--GAAGACATGAAGGGAAAGATCTAAG
* * * * * * *
12717931 CTGTAACGGCGGATCCAGTACCACAAAAACATGAAGA
62 CCGCAACAGCGAACCCAGGACCAC-GAAACATGAAGA
*
12717968 CAAAGATCTAAGCCGCGACGGCGGATCCAGTATCCCGAAGACATGAAGGGAAAGATCTAAGCCGC
1 GAAAGATCTAAGCCGCGACGGCGGATCCAGTATCCCGAAGACATGAAGGGAAAGATCTAAGCCGC
* * * * * *
12718033 GACGGTGGATCCAGTACCACGAAGACATGAAGA
66 AACAGCGAACCCAGGACCACGAA-ACATGAAGA
* * ** * * *
12718066 GAAAGATCTAAGCCGCGACGGTGGATCCCGTA-CCACGAAGATTTGAAGGGAAAGGTTTAAGTCG
1 GAAAGATCTAAGCCGCGACGGCGGATCCAGTATCC-CGAAGACATGAAGGGAAAGATCTAAGCCG
* *
12718130 CAATAGCGAACCCGGGACC
65 CAACAGCGAACCCAGGACC
12718149 TTAGAAACAT
Statistics
Matches: 151, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
97 10 0.07
98 110 0.73
99 18 0.12
100 13 0.09
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.13
Consensus pattern (97 bp):
GAAAGATCTAAGCCGCGACGGCGGATCCAGTATCCCGAAGACATGAAGGGAAAGATCTAAGCCGC
AACAGCGAACCCAGGACCACGAAACATGAAGA
Found at i:12718438 original size:39 final size:39
Alignment explanation
Indices: 12718317--12718455 Score: 131
Period size: 39 Copynumber: 3.6 Consensus size: 39
12718307 TGTTAATCTC
* * * *
12718317 TTACCCTGAGCTAGGGGCAGATTG-AAGCCATTTGATCTT
1 TTACCCCGAGCTTGGGGCAGATTGTAA-CCATCTGATCCT
* ** * * **
12718356 TTACCCCGAGCCTGGGGCAGATCATCATCGA-CCAAT-CT
1 TTACCCCGAGCTTGGGGCAGATTGT-AACCATCTGATCCT
12718394 CTTACCCCGAGCTTGGGGCAGATTGTAACCATCTGATCCT
1 -TTACCCCGAGCTTGGGGCAGATTGTAACCATCTGATCCT
12718434 TTACCCCGAGCTTGGGGCAGAT
1 TTACCCCGAGCTTGGGGCAGAT
12718456 CACCAAACTC
Statistics
Matches: 77, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
38 4 0.05
39 68 0.88
40 4 0.05
41 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (39 bp):
TTACCCCGAGCTTGGGGCAGATTGTAACCATCTGATCCT
Found at i:12718440 original size:78 final size:78
Alignment explanation
Indices: 12718311--12718457 Score: 233
Period size: 78 Copynumber: 1.9 Consensus size: 78
12718301 TGAAGATGTT
* * *
12718311 AATCTCTTACCCTGAGCTAGGGGCAGATTGAAGCCATTTGATCTTTTACCCCGAGCCTGGGGCAG
1 AATCTCTTACCCCGAGCTAGGGGCAGATTGAAGCCATCTGATCCTTTACCCCGAGCCTGGGGCAG
12718376 ATCATCATCGACC
66 ATCATCATCGACC
* *
12718389 AATCTCTTACCCCGAGCTTGGGGCAGATTGTAA-CCATCTGATCCTTTACCCCGAGCTTGGGGCA
1 AATCTCTTACCCCGAGCTAGGGGCAGATTG-AAGCCATCTGATCCTTTACCCCGAGCCTGGGGCA
12718453 GATCA
65 GATCA
12718458 CCAAACTCCA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 61 0.97
79 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (78 bp):
AATCTCTTACCCCGAGCTAGGGGCAGATTGAAGCCATCTGATCCTTTACCCCGAGCCTGGGGCAG
ATCATCATCGACC
Found at i:12718477 original size:39 final size:39
Alignment explanation
Indices: 12718356--12718481 Score: 107
Period size: 39 Copynumber: 3.2 Consensus size: 39
12718346 ATTTGATCTT
* * *
12718356 TTACCCCGAGCCTGGGGCAGATCATC-ATCGA-CCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCACCAAAC-ATCCAATC-C
*** * **
12718395 TTACCCCGAGCTTGGGGCAGAT-TGTAACCATCTGATCC
1 TTACCCCGAGCTTGGGGCAGATCACCAAACATCCAATCC
12718433 TTTACCCCGAGCTTGGGGCAGATCACCAAAC-TCCAATACC
1 -TTACCCCGAGCTTGGGGCAGATCACCAAACATCCAAT-CC
12718473 TTACCCCGA
1 TTACCCCGA
12718482 TCACGGGGTA
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
38 2 0.03
39 62 0.90
40 5 0.07
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (39 bp):
TTACCCCGAGCTTGGGGCAGATCACCAAACATCCAATCC
Found at i:12718495 original size:78 final size:78
Alignment explanation
Indices: 12718311--12718496 Score: 209
Period size: 78 Copynumber: 2.4 Consensus size: 78
12718301 TGAAGATGTT
* * *
12718311 AATCTCTTACCCTGAGCTA-GGGGCAGATTGAAGCCATTTGATCTTTTACCCCGAGCCTGGGGCA
1 AATCTCTTACCCCGAGC-ACGGGGCAGATTGAAGCCATCTGATCCTTTACCCCGAGCCTGGGGCA
* *
12718375 GATCATCATCGACC
65 GATCACCAACGACC
** *
12718389 AATCTCTTACCCCGAGCTTGGGGCAGATTGTAA-CCATCTGATCCTTTACCCCGAGCTTGGGGCA
1 AATCTCTTACCCCGAGCACGGGGCAGATTG-AAGCCATCTGATCCTTTACCCCGAGCCTGGGGCA
*
12718453 GATCACCAAAC-TCC
65 GATCACC-AACGACC
* *
12718467 AATAC-CTTACCCCGATCACGGGGTAGATTG
1 AAT-CTCTTACCCCGAGCACGGGGCAGATTG
12718497 CGATTATACA
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 87 0.95
79 5 0.05
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.25
Consensus pattern (78 bp):
AATCTCTTACCCCGAGCACGGGGCAGATTGAAGCCATCTGATCCTTTACCCCGAGCCTGGGGCAG
ATCACCAACGACC
Found at i:12718905 original size:205 final size:206
Alignment explanation
Indices: 12718563--12718964 Score: 610
Period size: 205 Copynumber: 2.0 Consensus size: 206
12718553 CCAACTCGAC
* * * * * *
12718563 GCTCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATAAGATATTGAGAAGCAGGCCGAAGCA
1 GCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGCCAAAGCA
* ** *
12718628 ATAAAATGGTTAGCTTTCTGGTGAGATACAGAAAAGTGGACCAAATTTGTCTTCCTGAGGAGATC
66 ATAAAATGGTTAGCTTCCTAATGAGATACAGAAAAGTGGACCAAATTCGTCTTCCTGAGGAGATC
12718693 CAGAGAAGCGAATTAAAACAAGTGATGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAA
131 CAGAGAAGCGAATTAAAACAAGTGATGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAA
12718758 ATCAAACCCAA
196 ATCAAACCCAA
* * * *
12718769 GCTCAATGCGAGCAAATCTTTGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCAAAGCA
1 GCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGCCAAAGCA
*
12718834 ATAAAATGGTTAG-TTCCTAATGAGATACTA-AGAAGTGGACCAAATTCGTCTTCCTGAGGAGAT
66 ATAAAATGGTTAGCTTCCTAATGAGATAC-AGAAAAGTGGACCAAATTCGTCTTCCTGAGGAGAT
* * **
12718897 CTAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGTGGACCA
130 CCAGAGAAGCGAATTAAAACAAGTGATGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCA
12718962 AAT
195 AAT
12718965 TCGTCTTCCT
Statistics
Matches: 176, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
205 107 0.61
206 69 0.39
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (206 bp):
GCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGCCAAAGCA
ATAAAATGGTTAGCTTCCTAATGAGATACAGAAAAGTGGACCAAATTCGTCTTCCTGAGGAGATC
CAGAGAAGCGAATTAAAACAAGTGATGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAA
ATCAAACCCAA
Found at i:12718953 original size:49 final size:49
Alignment explanation
Indices: 12718882--12719040 Score: 121
Period size: 49 Copynumber: 3.5 Consensus size: 49
12718872 ACCAAATTCG
*
12718882 TCTTCCTGAGGAGA-TCTAGAGAAGCGAATTAAAACAAGTGATGCGGTCA
1 TCTTCCTGAGGAGACACT-GAGAAGCGAATTAAAACAAGTGATGCGGTCA
* ** * *
12718931 TCTTCCTGATGAGACACTGAGAA--G---TGGACCAA---AT----TCG
1 TCTTCCTGAGGAGACACTGAGAAGCGAATTAAAACAAGTGATGCGGTCA
* *
12718968 TCTTCCTGAGAAGATC-CAGAGAAGCGAATTAAAACAAGTGATGCGGTCA
1 TCTTCCTGAGGAGA-CACTGAGAAGCGAATTAAAACAAGTGATGCGGTCA
*
12719017 TCTTCCTGATGAGACACTGAGAAG
1 TCTTCCTGAGGAGACACTGAGAAG
12719041 AAGACCAAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 30
0.63 0.13 0.24
Matches are distributed among these distances:
37 20 0.25
38 1 0.01
39 1 0.01
41 2 0.03
42 5 0.06
44 5 0.06
45 2 0.03
47 1 0.01
48 1 0.01
49 39 0.49
50 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (49 bp):
TCTTCCTGAGGAGACACTGAGAAGCGAATTAAAACAAGTGATGCGGTCA
Found at i:12718992 original size:86 final size:86
Alignment explanation
Indices: 12718847--12719050 Score: 345
Period size: 86 Copynumber: 2.4 Consensus size: 86
12718837 AAATGGTTAG
* * * * *
12718847 TTCCTAATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCTAGAGAAGCGAATT
1 TTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGAAGATCCAGAGAAGCGAATT
12718912 AAAACAAGTGATGCGGTCATC
66 AAAACAAGTGATGCGGTCATC
12718933 TTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGAAGATCCAGAGAAGCGAATT
1 TTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGAAGATCCAGAGAAGCGAATT
12718998 AAAACAAGTGATGCGGTCATC
66 AAAACAAGTGATGCGGTCATC
**
12719019 TTCCTGATGAGACACTGAGAAGAAGACCAAAT
1 TTCCTGATGAGACACTGAGAAGTGGACCAAAT
12719051 CAAACCCAGG
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 111 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (86 bp):
TTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGAAGATCCAGAGAAGCGAATT
AAAACAAGTGATGCGGTCATC
Found at i:12719656 original size:17 final size:17
Alignment explanation
Indices: 12719636--12719682 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
12719626 CAATCTTAAT
12719636 TTTAAATTTA-TTGTAAG
1 TTTAAATTTATTTG-AAG
** *
12719653 TTTAAGCTTATTTGGAG
1 TTTAAATTTATTTGAAG
12719670 TTTAAATTTATTT
1 TTTAAATTTATTT
12719683 TAAATTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTGAAG
Found at i:12719697 original size:17 final size:18
Alignment explanation
Indices: 12719677--12719710 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12719667 GAGTTTAAAT
12719677 TTATTTT-AAATTAAAAA
1 TTATTTTCAAATTAAAAA
*
12719694 TTATTTTCGAATTAAAA
1 TTATTTTCAAATTAAAA
12719711 TTTTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TTATTTTCAAATTAAAAA
Found at i:12721380 original size:30 final size:30
Alignment explanation
Indices: 12721344--12721417 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
12721334 TAGAAACGGT
*
12721344 ATTTTGACCCTAAAAATTTTTGAAAATTAC
1 ATTTTGACCCTAAAAATTTTTCAAAATTAC
*
12721374 ATTTTGACCTCT--AAATTTTTCCAAATTAC
1 ATTTTGACC-CTAAAAATTTTTCAAAATTAC
*
12721403 ATTTTGACCCCAAAA
1 ATTTTGACCCTAAAA
12721418 CTTTCTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.03
29 24 0.63
30 11 0.29
31 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.39
Consensus pattern (30 bp):
ATTTTGACCCTAAAAATTTTTCAAAATTAC
Found at i:12721432 original size:30 final size:29
Alignment explanation
Indices: 12721344--12721452 Score: 94
Period size: 30 Copynumber: 3.7 Consensus size: 29
12721334 TAGAAACGGT
* * *
12721344 ATTTTGACCCTAAAAATTTTTGAAAATTAC
1 ATTTTGACCCCAAAACTTTCT-AAAATTAC
* * * *
12721374 ATTTTGACCTCTAAA-TTTTTCCAAATTAC
1 ATTTTGACCCCAAAACTTTCT-AAAATTAC
12721403 ATTTTGACCCCAAAACTTTCTATAAATTAC
1 ATTTTGACCCCAAAACTTTCTA-AAATTAC
* * *
12721433 ACTTTAACCCCTAAACTTTC
1 ATTTTGACCCCAAAACTTTC
12721453 CAAGACTCCA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
29 25 0.38
30 40 0.62
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (29 bp):
ATTTTGACCCCAAAACTTTCTAAAATTAC
Found at i:12721447 original size:59 final size:58
Alignment explanation
Indices: 12721344--12721455 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 58
12721334 TAGAAACGGT
* * * * * *
12721344 ATTTTGACCCTAAAAATTTTTGAAAATTACATTTTGACCTCTAAATTTTTCCAAATTAC
1 ATTTTGACCCCAAAAATTTCTGAAAATTACACTTTAACCCCTAAA-CTTTCCAAATTAC
*
12721403 ATTTTGACCCCAAAACTTTCT-ATAAATTACACTTTAACCCCTAAACTTTCCAA
1 ATTTTGACCCCAAAAATTTCTGA-AAATTACACTTTAACCCCTAAACTTTCCAA
12721456 GACTCCATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
58 8 0.18
59 37 0.82
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (58 bp):
ATTTTGACCCCAAAAATTTCTGAAAATTACACTTTAACCCCTAAACTTTCCAAATTAC
Found at i:12721514 original size:29 final size:29
Alignment explanation
Indices: 12721481--12721560 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
12721471 CCCCGATTTC
12721481 ACCAAAAATTACCATTTTACCCTAAACTTT
1 ACCAAAAATTACCATTTTACCC-AAACTTT
* ** *
12721511 -CC-AAAATT-CTATTTTTAACCCCGATTTT
1 ACCAAAAATTACCA-TTTT-ACCCAAACTTT
12721539 ACCAAAAATTACCATTTTACCC
1 ACCAAAAATTACCATTTTACCC
12721561 CCGAAAGTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
27 2 0.05
28 14 0.35
29 12 0.30
30 10 0.25
31 2 0.05
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.35
Consensus pattern (29 bp):
ACCAAAAATTACCATTTTACCCAAACTTT
Found at i:12721543 original size:58 final size:59
Alignment explanation
Indices: 12721441--12721560 Score: 197
Period size: 58 Copynumber: 2.1 Consensus size: 59
12721431 ACACTTTAAC
*
12721441 CCCTAAACTTTCCAAGACTCCATTTTTTAACCCCGATTTCACCAAAAATTACCATTTTA
1 CCCTAAACTTTCCAAAACTCCATTTTTTAACCCCGATTTCACCAAAAATTACCATTTTA
* * *
12721500 CCCTAAACTTTCCAAAATTCTA-TTTTTAACCCCGATTTTACCAAAAATTACCATTTTA
1 CCCTAAACTTTCCAAAACTCCATTTTTTAACCCCGATTTCACCAAAAATTACCATTTTA
12721558 CCC
1 CCC
12721561 CCGAAAGTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 38 0.67
59 19 0.33
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.35
Consensus pattern (59 bp):
CCCTAAACTTTCCAAAACTCCATTTTTTAACCCCGATTTCACCAAAAATTACCATTTTA
Found at i:12721561 original size:29 final size:30
Alignment explanation
Indices: 12721465--12721564 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
12721455 AGACTCCATT
*
12721465 TTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTAACCCCGATTTTACCAAAAATTACCA
** * *
12721495 TTTT-ACCCTAAACTTT-CC-AAAATT-CTA
1 TTTTAACCC-CGATTTTACCAAAAATTACCA
12721522 TTTTTAACCCCGATTTTACCAAAAATTACCA
1 -TTTTAACCCCGATTTTACCAAAAATTACCA
*
12721553 TTTTACCCCCGA
1 TTTTAACCCCGA
12721565 AAGTCTAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
27 2 0.04
28 14 0.26
29 12 0.22
30 24 0.44
31 2 0.04
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (30 bp):
TTTTAACCCCGATTTTACCAAAAATTACCA
Found at i:12721575 original size:58 final size:58
Alignment explanation
Indices: 12721464--12721584 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 58
12721454 AAGACTCCAT
* *
12721464 TTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTAAACTTTCCAAAATT-CTA
1 TTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCGAAAC-GTCCAAAATTACTA
* *
12721522 TTTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCCGAAA-GTCTAAAATTACTA
1 TTTTTAACCCCGATTTCACCAAAAATTACCATTTTA--CCCGAAACGTCCAAAATTACTA
12721581 TTTT
1 TTTT
12721585 GCCCCCCGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
58 43 0.77
59 7 0.12
60 6 0.11
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
TTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCGAAACGTCCAAAATTACTA
Found at i:12722603 original size:29 final size:28
Alignment explanation
Indices: 12722571--12722626 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
12722561 TTGATTTTTT
* *
12722571 AAATCTATTTTTCCTTTCTTTTTTATTTA
1 AAATCTATTTTT-ATTTATTTTTTATTTA
12722600 AAATCTATTTTTATTTATTTTTTATTT
1 AAATCTATTTTTATTTATTTTTTATTT
12722627 TTTTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (28 bp):
AAATCTATTTTTATTTATTTTTTATTTA
Found at i:12722621 original size:11 final size:10
Alignment explanation
Indices: 12722607--12722640 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
12722597 TTAAAATCTA
12722607 TTTTTATTTAT
1 TTTTTATTT-T
12722618 TTTTTATTTT
1 TTTTTATTTT
12722628 TTTATTATTTT
1 TTT-TTATTTT
12722639 TT
1 TT
12722641 AAAGAACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:12723647 original size:17 final size:17
Alignment explanation
Indices: 12723621--12723684 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
12723611 ACTTTCAAAT
12723621 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
12723638 TTTAAGTTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
12723655 TTTAAACTTAAAACAAA
1 TTTAAATTTAAAATAAA
* *
12723672 TATAAAATTAAAA
1 TTTAAATTTAAAA
12723685 ATTGGGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:12728342 original size:21 final size:21
Alignment explanation
Indices: 12728318--12728391 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
12728308 AGTGCAGACC
*
12728318 TCTACCGATACAAGTGACAGT
1 TCTACCGATACAAGTGACACT
* *
12728339 TCTACCGATACAATTGACTCT
1 TCTACCGATACAAGTGACACT
* ***
12728360 TCTACCGAAACAAGTCTTACT
1 TCTACCGATACAAGTGACACT
12728381 TCTACCGATAC
1 TCTACCGATAC
12728392 TAAAAACTTC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTGACACT
Found at i:12729176 original size:52 final size:52
Alignment explanation
Indices: 12729095--12729439 Score: 363
Period size: 52 Copynumber: 6.6 Consensus size: 52
12729085 TTTCCTTTAG
* * * * *
12729095 TACTCACGATAACACATAGTCATTGGACCTCACAATCCGTAAAGGATTTACA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
* * * *
12729147 TACTCACGATGACACGTAGTCATCAGACCTCATAATCCATAAAGGATTCATA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
* * ** * *
12729199 TACTCACGATGACACGTAGTCATCGGACATCATAAT-TTTACA-GATTCATA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
* * *
12729249 TACTCACGATAACACACAATCATCGGACCTCATAATCCGTAAAAGATTCAGATTCAGA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAG-----GATTCAGA
* * *
12729307 TACTCACGATGACACACAGTGATCGGACCTCATAATCCGTAAAAGATTCAGA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
* ** *
12729359 TACTTACGATGACACATAGTCATCAGG-CCTCATAATCTATAAAGGATTTAGA
1 TACTCACGATGACACATAGTCATC-GGACCTCATAATCCGTAAAGGATTCAGA
* *
12729411 TACTCATGATGACACATAGTTATCGGACC
1 TACTCACGATGACACATAGTCATCGGACC
12729440 CTTTTACATT
Statistics
Matches: 247, Mismatches: 36, Indels: 20
0.82 0.12 0.07
Matches are distributed among these distances:
50 39 0.16
51 6 0.02
52 153 0.62
53 2 0.01
57 3 0.01
58 44 0.18
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (52 bp):
TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
Found at i:12729332 original size:58 final size:58
Alignment explanation
Indices: 12729239--12729359 Score: 206
Period size: 58 Copynumber: 2.1 Consensus size: 58
12729229 CATAATTTTA
*
12729239 CAGATTCATATACTCACGATAACACACAATCATCGGACCTCATAATCCGTAAAAGATT
1 CAGATTCAGATACTCACGATAACACACAATCATCGGACCTCATAATCCGTAAAAGATT
* * *
12729297 CAGATTCAGATACTCACGATGACACACAGTGATCGGACCTCATAATCCGTAAAAGATT
1 CAGATTCAGATACTCACGATAACACACAATCATCGGACCTCATAATCCGTAAAAGATT
12729355 CAGAT
1 CAGAT
12729360 ACTTACGATG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (58 bp):
CAGATTCAGATACTCACGATAACACACAATCATCGGACCTCATAATCCGTAAAAGATT
Found at i:12729394 original size:160 final size:154
Alignment explanation
Indices: 12729095--12729382 Score: 387
Period size: 160 Copynumber: 1.8 Consensus size: 154
12729085 TTTCCTTTAG
* * * *
12729095 TACTCACGATAACACATAGTCATTGGACCTCACAATCCGTAAAGGATTTACATACTCACGATGAC
1 TACTCACGATAACACACAATCATCGGACCTCACAATCCGTAAAGGATTCACATACTCACGATGAC
** * * *
12729160 ACGTAGTCATCAGACCTCATAATCCATAAAGGATTCATATACTCACGATGACACGTAGTCATCGG
66 ACACAGTCATCAGACCTCATAATCCATAAAAGATTCAGATACTCACGATGACACATAGTCATCGG
12729225 ACATCATAATTTTACAGATTCATA
131 ACATCATAATTTTACAGATTCATA
* *
12729249 TACTCACGATAACACACAATCATCGGACCTCATAATCCGTAAAAGATTCAGATTCAGATACTCAC
1 TACTCACGATAACACACAATCATCGGACCTCACAATCCGT-AAAG-----GATTCACATACTCAC
* * * *
12729314 GATGACACACAGTGATCGGACCTCATAATCCGTAAAAGATTCAGATACTTACGATGACACATAGT
60 GATGACACACAGTCATCAGACCTCATAATCCATAAAAGATTCAGATACTCACGATGACACATAGT
12729379 CATC
125 CATC
12729383 AGGCCTCATA
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
154 36 0.32
155 4 0.04
160 73 0.65
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (154 bp):
TACTCACGATAACACACAATCATCGGACCTCACAATCCGTAAAGGATTCACATACTCACGATGAC
ACACAGTCATCAGACCTCATAATCCATAAAAGATTCAGATACTCACGATGACACATAGTCATCGG
ACATCATAATTTTACAGATTCATA
Found at i:12746845 original size:14 final size:14
Alignment explanation
Indices: 12746826--12746852 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12746816 AGGAGGCTTA
12746826 TTTCTTTTCTTTTT
1 TTTCTTTTCTTTTT
12746840 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
12746853 AAACAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTCTTTTCTTTTT
Found at i:12746898 original size:29 final size:28
Alignment explanation
Indices: 12746836--12746899 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
12746826 TTTCTTTTCT
* **
12746836 TTTTTTTCTTTTCTTTTAAACAAGTATG
1 TTTTTTTCTTCTCTTTTAAACAAACATG
12746864 TGTTTTTTCTTCTCTTTTAAATTCAAACA-G
1 T-TTTTTTCTTCTCTTTTAAA--CAAACATG
12746894 TTTTTT
1 TTTTTT
12746900 AAAATAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 23 0.77
30 2 0.07
31 4 0.13
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.61
Consensus pattern (28 bp):
TTTTTTTCTTCTCTTTTAAACAAACATG
Found at i:12753619 original size:31 final size:31
Alignment explanation
Indices: 12753584--12753652 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
12753574 CTTAACAACC
**
12753584 TAATGACTTAAATGATTACTT-TCAAATAATT
1 TAATGACTTAAATGAAAACTTCT-AAATAATT
12753615 TAATGACTTAAATGAAAACTTCTAAATAATT
1 TAATGACTTAAATGAAAACTTCTAAATAATT
12753646 TAATGAC
1 TAATGAC
12753653 CATTTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (31 bp):
TAATGACTTAAATGAAAACTTCTAAATAATT
Found at i:12755744 original size:20 final size:20
Alignment explanation
Indices: 12755721--12755759 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12755711 ATTCAAATAA
12755721 TATATTATAATTTAAAATTT
1 TATATTATAATTTAAAATTT
* *
12755741 TATATTATATTTTTAAATT
1 TATATTATAATTTAAAATT
12755760 AATAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTATAATTTAAAATTT
Found at i:12770881 original size:11 final size:11
Alignment explanation
Indices: 12770815--12770921 Score: 76
Period size: 9 Copynumber: 10.6 Consensus size: 11
12770805 CCACATTAGC
*
12770815 AAATGATTTTA
1 AAATTATTTTA
12770826 AAATTA--TTA
1 AAATTATTTTA
12770835 AAATTATTTTTA
1 AAATTA-TTTTA
* *
12770847 AAA--AATATA
1 AAATTATTTTA
*
12770856 AAATTA--TTG
1 AAATTATTTTA
12770865 AAATTATTTTA
1 AAATTATTTTA
12770876 AAATTATTTTTA
1 AAATTA-TTTTA
12770888 AAA-TA---TA
1 AAATTATTTTA
12770895 AAATTA--TTA
1 AAATTATTTTA
12770904 AAATTATTTTA
1 AAATTATTTTA
12770915 AAATTAT
1 AAATTAT
12770922 AATCATTATC
Statistics
Matches: 78, Mismatches: 6, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
7 5 0.06
8 2 0.03
9 30 0.38
10 1 0.01
11 26 0.33
12 14 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:12770891 original size:39 final size:40
Alignment explanation
Indices: 12770823--12770921 Score: 159
Period size: 39 Copynumber: 2.5 Consensus size: 40
12770813 GCAAATGATT
12770823 TTAAAATTA--TTAAAATTATTTTTAAAAAATATAAAATTA
1 TTAAAATTATTTTAAAATTATTTTT-AAAAATATAAAATTA
*
12770862 TTGAAATTATTTTAAAATTATTTTT-AAAATATAAAATTA
1 TTAAAATTATTTTAAAATTATTTTTAAAAATATAAAATTA
12770901 TTAAAATTATTTTAAAATTAT
1 TTAAAATTATTTTAAAATTAT
12770922 AATCATTATC
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
39 42 0.75
41 14 0.25
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (40 bp):
TTAAAATTATTTTAAAATTATTTTTAAAAATATAAAATTA
Found at i:12770930 original size:20 final size:20
Alignment explanation
Indices: 12770815--12770921 Score: 75
Period size: 20 Copynumber: 5.3 Consensus size: 20
12770805 CCACATTAGC
*
12770815 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
12770835 AAATTATTTTTAAAA-AATATA
1 AAATTA-TTTTAAAATTAT-TA
*
12770856 AAATTA--TTGAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
12770876 AAATTATTTTTAAAA-TA-TA
1 AAATTA-TTTTAAAATTATTA
12770895 AAATTA--TTAAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
12770915 AAATTAT
1 AAATTAT
12770922 AATCATTATC
Statistics
Matches: 69, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
16 6 0.09
17 2 0.03
18 5 0.07
19 9 0.13
20 23 0.33
21 17 0.25
22 2 0.03
23 5 0.07
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:12771598 original size:14 final size:15
Alignment explanation
Indices: 12771575--12771610 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12771565 AAAAATAAGA
12771575 GGAA-GGGGAAGG-G
1 GGAAGGGGGAAGGAG
12771588 GGAAGGGGGAAGGAG
1 GGAAGGGGGAAGGAG
12771603 GGAAGGGG
1 GGAAGGGG
12771611 AAAAAACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 8 0.38
15 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (15 bp):
GGAAGGGGGAAGGAG
Found at i:12771605 original size:8 final size:7
Alignment explanation
Indices: 12771575--12771610 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
12771565 AAAAATAAGA
12771575 GGAA-GG
1 GGAAGGG
12771581 GGAAGGG
1 GGAAGGG
12771588 GGAAGGG
1 GGAAGGG
12771595 GGAAGGAG
1 GGAAGG-G
12771603 GGAAGGG
1 GGAAGGG
12771610 G
1 G
12771611 AAAAAACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 4 0.14
7 17 0.61
8 7 0.25
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (7 bp):
GGAAGGG
Found at i:12771650 original size:9 final size:9
Alignment explanation
Indices: 12771636--12771722 Score: 54
Period size: 9 Copynumber: 10.8 Consensus size: 9
12771626 AATGATGATG
12771636 ATTTTAATA
1 ATTTTAATA
12771645 ATTTT-AT-
1 ATTTTAATA
12771652 ATTTTAA-A
1 ATTTTAATA
12771660 A----AATA
1 ATTTTAATA
12771665 ATTTTAAAATA
1 ATTTT--AATA
12771676 ATTTTAATA
1 ATTTTAATA
12771685 ATTTT-AT-
1 ATTTTAATA
12771692 ATTTTAA-A
1 ATTTTAATA
**
12771700 A--AAAATA
1 ATTTTAATA
12771707 ATTTTAATA
1 ATTTTAATA
12771716 ATTTTAA
1 ATTTTAA
12771723 ATCATTTGCT
Statistics
Matches: 60, Mismatches: 4, Indels: 28
0.65 0.04 0.30
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
6 2 0.03
7 12 0.20
8 8 0.13
9 25 0.42
11 9 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATTTTAATA
Found at i:12771675 original size:11 final size:11
Alignment explanation
Indices: 12771659--12771690 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12771649 TATATTTTAA
12771659 AAAATAATTTT
1 AAAATAATTTT
12771670 AAAATAATTTT
1 AAAATAATTTT
12771681 --AATAATTTT
1 AAAATAATTTT
12771690 A
1 A
12771691 TATTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:12771691 original size:40 final size:39
Alignment explanation
Indices: 12771636--12771722 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 39
12771626 AATGATGATG
12771636 ATTTTAATAATTTTATATTTT-AAAAAATAATTTTAAAATA
1 ATTTTAATAATTTTATATTTTAAAAAAATAATTTT--AATA
12771676 ATTTTAATAATTTTATATTTTAAAAAAAATAATTTTAATA
1 ATTTTAATAATTTTATATTTT-AAAAAAATAATTTTAATA
12771716 ATTTTAA
1 ATTTTAA
12771723 ATCATTTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
40 32 0.71
42 13 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (39 bp):
ATTTTAATAATTTTATATTTTAAAAAAATAATTTTAATA
Found at i:12772616 original size:9 final size:9
Alignment explanation
Indices: 12772602--12772635 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
12772592 CAAACTTTGA
12772602 TTTCTTCTT
1 TTTCTTCTT
12772611 TTTCTTCTT
1 TTTCTTCTT
12772620 TTTC-TCTT
1 TTTCTTCTT
*
12772628 CTTCTTCT
1 TTTCTTCT
12772636 ACCACCCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:12772692 original size:82 final size:82
Alignment explanation
Indices: 12772512--12772758 Score: 401
Period size: 85 Copynumber: 3.0 Consensus size: 82
12772502 ACAATCACTT
* *
12772512 AACTTTGATTTCTTCTTTTTCTTTTTCTCTTCTTCTTCTACCACCCAGCTAAGGTTCTTCTATTG
1 AACTTTGATTTCTTCTTTTTCTTTTTCTCTTCTTCTTCTACCACCCAACTAAGGTTCTTCAATTG
*
12772577 GGATTGTGTAAATGACA
66 GGATTGTTTAAATGACA
12772594 AACTTTGATTTCTTCTTTTTCTTCTTTTTCTCTTCTTCTTCTACCACCCAACTAAGGTTCTTCAA
1 AACTTTGATTTCTTC--TTT-TTCTTTTTCTCTTCTTCTTCTACCACCCAACTAAGGTTCTTCAA
*
12772659 TTGAGATTGTTTAAATGACA
63 TTGGGATTGTTTAAATGACA
*
12772679 AACTTTGATTTCTTCTTTTTC-TTTT-TC-TCTTCTTCTACCACCCAACTAGGGTTCTTCAATTG
1 AACTTTGATTTCTTCTTTTTCTTTTTCTCTTCTTCTTCTACCACCCAACTAAGGTTCTTCAATTG
12772741 GGATTGTTTAAATGACA
66 GGATTGTTTAAATGACA
12772758 A
1 A
12772759 CATAGACGCC
Statistics
Matches: 156, Mismatches: 6, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
79 51 0.33
80 2 0.01
81 4 0.03
82 18 0.12
83 3 0.02
84 3 0.02
85 75 0.48
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.47
Consensus pattern (82 bp):
AACTTTGATTTCTTCTTTTTCTTTTTCTCTTCTTCTTCTACCACCCAACTAAGGTTCTTCAATTG
GGATTGTTTAAATGACA
Found at i:12772746 original size:79 final size:76
Alignment explanation
Indices: 12772611--12772758 Score: 242
Period size: 79 Copynumber: 1.9 Consensus size: 76
12772601 ATTTCTTCTT
12772611 TTTCTTCTTTTTCTCTTCTTCTTCTACCACCCAACTAAGGTTCTTCAATTGAGATTGTTTAAATG
1 TTTCTTCTTTTTCTCTTCTTCTTCTACCACCCAACTAAGGTTCTTCAATTGAGATTGTTTAAATG
12772676 ACAAACTTTGA
66 ACAAACTTTGA
* * *
12772687 TTTCTTCTTTTTCTTTTTCTCTTCTTCTACCACCCAACTAGGGTTCTTCAATTGGGATTGTTTAA
1 TTTCTTCTTTTTC--TCT-TCTTCTTCTACCACCCAACTAAGGTTCTTCAATTGAGATTGTTTAA
12772752 ATGACAA
63 ATGACAA
12772759 CATAGACGCC
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
76 13 0.20
78 2 0.03
79 51 0.77
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (76 bp):
TTTCTTCTTTTTCTCTTCTTCTTCTACCACCCAACTAAGGTTCTTCAATTGAGATTGTTTAAATG
ACAAACTTTGA
Found at i:12776520 original size:17 final size:16
Alignment explanation
Indices: 12776495--12776538 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
12776485 AAATATTTTT
12776495 TAAAAATATAATAAATC
1 TAAAAATATAA-AAATC
* *
12776512 TAAATATATAAAAATT
1 TAAAAATATAAAAATC
12776528 TAAAAA-ATAAA
1 TAAAAATATAAA
12776539 GTGTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 5 0.21
16 9 0.38
17 10 0.42
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAATATAAAAATC
Found at i:12777570 original size:20 final size:18
Alignment explanation
Indices: 12777543--12777581 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
12777533 AATATATTGT
12777543 ATTTTTATATGTTTTTTAA
1 ATTTTTATAT-TTTTTTAA
12777562 ATTTATTATATTTTTTTAA
1 ATTT-TTATATTTTTTTAA
12777581 A
1 A
12777582 GATTTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTTTTATATTTTTTTAA
Found at i:12777588 original size:18 final size:19
Alignment explanation
Indices: 12777546--12777588 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12777536 ATATTGTATT
**
12777546 TTTATATGTTTTTTAAATT
1 TTTATATGTTTTTTAAAGA
12777565 TATTATAT-TTTTTTAAAGA
1 T-TTATATGTTTTTTAAAGA
12777584 TTTAT
1 TTTAT
12777589 GTATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 11 0.52
20 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTATATGTTTTTTAAAGA
Found at i:12779282 original size:14 final size:14
Alignment explanation
Indices: 12779263--12779289 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12779253 TAAAAAATAA
12779263 ATATAAATATAAAT
1 ATATAAATATAAAT
12779277 ATATAAATATAAA
1 ATATAAATATAAA
12779290 GTCTATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAAATATAAAT
Found at i:12780575 original size:15 final size:16
Alignment explanation
Indices: 12780557--12780589 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12780547 GGGTTTGGAC
*
12780557 TTGGTTCAA-TTGGGT
1 TTGGTTAAATTTGGGT
12780572 TTGGTTAAATTTGGGT
1 TTGGTTAAATTTGGGT
12780588 TT
1 TT
12780590 AAAAGGGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.15, C:0.03, G:0.30, T:0.52
Consensus pattern (16 bp):
TTGGTTAAATTTGGGT
Found at i:12783559 original size:26 final size:26
Alignment explanation
Indices: 12783530--12783581 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12783520 AGCTAAACCC
12783530 AAAAAACTACAAATCTCAAAAACATT
1 AAAAAACTACAAATCTCAAAAACATT
12783556 AAAAAACTACAAATCTCAAAAACATT
1 AAAAAACTACAAATCTCAAAAACATT
12783582 CTTAGGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (26 bp):
AAAAAACTACAAATCTCAAAAACATT
Found at i:12790567 original size:21 final size:20
Alignment explanation
Indices: 12790533--12790571 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
12790523 GACCAAATTC
12790533 TCATCACAAATAACCAATAGA
1 TCATCACAAATAA-CAATAGA
* *
12790554 TCATCACGAGTAACAATA
1 TCATCACAAATAACAATA
12790572 TCAACACGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.21
Consensus pattern (20 bp):
TCATCACAAATAACAATAGA
Found at i:12798055 original size:24 final size:23
Alignment explanation
Indices: 12798023--12798067 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
12798013 TTAATATATG
*
12798023 AAATATTAATTTTAAATATTTCT
1 AAATATTAATATTAAATATTTCT
*
12798046 AAATAATTAATATTAATTATTT
1 AAAT-ATTAATATTAAATATTT
12798068 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTCT
Found at i:12798073 original size:24 final size:23
Alignment explanation
Indices: 12798023--12798078 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
12798013 TTAATATATG
* **
12798023 AAATATTAATTTTAAATATTTCT
1 AAATATTAATATTAAATATTTAA
*
12798046 AAATAATTAATATTAATTATTTAA
1 AAAT-ATTAATATTAAATATTTAA
12798070 AAAT-TTAAT
1 AAATATTAAT
12798079 TAGATTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 5 0.18
23 4 0.14
24 19 0.68
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTAA
Found at i:12799933 original size:72 final size:71
Alignment explanation
Indices: 12799830--12800012 Score: 303
Period size: 72 Copynumber: 2.5 Consensus size: 71
12799820 AACAAATTTT
*
12799830 ATATCCAAAATCAAATATAAACAACTATTGATAAAACTAAAATACACATAAATAAGTAGAACATA
1 ATATCCAAAATCAAACATAAACAACTATTGATAAAACTAAAATACACATAAATAAGTAGAACATA
12799895 AATTCA
66 AATTCA
* * * *
12799901 ATATCCAAGAACCAAACATAAACAACTATTGATAAAATTAGATTACACATAAATAAGTAGAACAT
1 ATATCCAA-AATCAAACATAAACAACTATTGATAAAACTAAAATACACATAAATAAGTAGAACAT
12799966 AAATTCA
65 AAATTCA
12799973 ATATCCAAAAATCAAACATAAACAACTATTGATAAAACTA
1 ATATCC-AAAATCAAACATAAACAACTATTGATAAAACTA
12800013 GTTTAGCATT
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
71 8 0.08
72 93 0.90
73 2 0.02
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.23
Consensus pattern (71 bp):
ATATCCAAAATCAAACATAAACAACTATTGATAAAACTAAAATACACATAAATAAGTAGAACATA
AATTCA
Found at i:12805589 original size:29 final size:32
Alignment explanation
Indices: 12805533--12805774 Score: 198
Period size: 30 Copynumber: 8.1 Consensus size: 32
12805523 TTTTATTTAA
12805533 AAAAATT-A-ATTTTGACCCTTAAACTTTTC-
1 AAAAATTCACATTTTGACCCTTAAACTTTTCT
*
12805562 AAAAATTCA-ATTTTGACCCTCAAA-TTTTCT
1 AAAAATTCACATTTTGACCCTTAAACTTTTCT
* * * *
12805592 AAAAATTTGA-TTTTTGACTCC-TGAAC-TTTCA
1 AAAAA-TTCACATTTTGAC-CCTTAAACTTTTCT
* * * *
12805623 AAAAAGTCACA-TTTGTCCCTAAAACTTTTGT
1 AAAAATTCACATTTTGACCCTTAAACTTTTCT
* *
12805654 -AAAATT-ACATTTTAACCCTTAAGC-TTTCT
1 AAAAATTCACATTTTGACCCTTAAACTTTTCT
*
12805683 AAAAATTCA-ATTTTGACCC-CAAA-TTTTCT
1 AAAAATTCACATTTTGACCCTTAAACTTTTCT
* * *
12805712 AAAAA-TCACATTTTAACCCTTAAACTTTCCA
1 AAAAATTCACATTTTGACCCTTAAACTTTTCT
12805743 AAAAATT-ACATTTTGACCC-TAAACTTTT-T
1 AAAAATTCACATTTTGACCCTTAAACTTTTCT
12805772 AAA
1 AAA
12805775 TATCACAATT
Statistics
Matches: 167, Mismatches: 30, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
28 3 0.02
29 45 0.27
30 71 0.43
31 45 0.27
32 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (32 bp):
AAAAATTCACATTTTGACCCTTAAACTTTTCT
Found at i:12805780 original size:60 final size:60
Alignment explanation
Indices: 12805533--12805790 Score: 235
Period size: 60 Copynumber: 4.3 Consensus size: 60
12805523 TTTTATTTAA
* * *
12805533 AAAAATTA-ATTTTGACCCTTAAACTTTTC-AAAAATTCAATTTTGACCCTCAAATTTTCT
1 AAAAATCACATTTTAACCCTTAAAC-TTTCAAAAAATTCAATTTTGACCCTAAAATTTTCT
*** * * * * *
12805592 AAAAATTTGATTTTTGACTCC-TGAACTTTCAAAAAAGTCACA-TTTGTCCCTAAAACTTTTGT
1 AAAAATCACA-TTTTAAC-CCTTAAACTTTCAAAAAATTCA-ATTTTGACCCTAAAA-TTTTCT
* * * *
12805654 -AAAATTACATTTTAACCCTTAAGCTTTCTAAAAATTCAATTTTGACCC-CAAATTTTCT
1 AAAAATCACATTTTAACCCTTAAACTTTCAAAAAATTCAATTTTGACCCTAAAATTTTCT
*
12805712 AAAAATCACATTTTAACCCTTAAACTTTCCAAAAAATT-ACATTTTGACCCTAAACTTTT-T
1 AAAAATCACATTTTAACCCTTAAACTTT-CAAAAAATTCA-ATTTTGACCCTAAAATTTTCT
* *
12805772 AAATATCACAATTTAACCC
1 AAAAATCACATTTTAACCC
12805791 CAAATTCTCC
Statistics
Matches: 164, Mismatches: 23, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
58 5 0.03
59 39 0.24
60 69 0.42
61 43 0.26
62 8 0.05
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (60 bp):
AAAAATCACATTTTAACCCTTAAACTTTCAAAAAATTCAATTTTGACCCTAAAATTTTCT
Found at i:12809027 original size:29 final size:29
Alignment explanation
Indices: 12808993--12809051 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
12808983 AATGACATTA
**
12808993 CAAAATATGGAGAAGAGATTGAATGAAAG
1 CAAAATATGGAGAAGAGATCAAATGAAAG
12809022 CAAAATATGGAGAAGAGATCAAATGAAAG
1 CAAAATATGGAGAAGAGATCAAATGAAAG
12809051 C
1 C
12809052 TTTTGGCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.07, G:0.25, T:0.15
Consensus pattern (29 bp):
CAAAATATGGAGAAGAGATCAAATGAAAG
Found at i:12814544 original size:99 final size:99
Alignment explanation
Indices: 12814321--12814886 Score: 572
Period size: 99 Copynumber: 5.7 Consensus size: 99
12814311 AGGTTTGGCA
* * * * * *
12814321 GGAAAGGATTGAGGCCGCAATGGCGAA-TCCGGTACCTTAGAAGATGT-AATAGGAAAGGTTAAG
1 GGAAAGG-TTAAGGCCGCAACGGCGAACT-CGGTACCAT-GAAGATATGAA-GGGAAAGGTTGAG
* * * * * *
12814384 GCCGCAACGGTGAACTCAGTAACAT-GAAGA-GATGAAG
62 GCCGCAACGGCGAACCCGGTACCTTAGAAGATG-TGATG
* * * **
12814421 GGAAAGGTTGAGGTCGTAACGGCGAACTCGGTACCATGAAGAGGTGAAGGGAAAGGTTGAGGCCG
1 GGAAAGGTTAAGGCCGCAACGGCGAACTCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCG
* *
12814486 CAACGGTGAACCCGGTACCTTAAAAGATGTGATG
66 CAACGGCGAACCCGGTACCTTAGAAGATGTGATG
* *
12814520 GGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCATGAAGAGATGAAGGGAAAGGTTGAGGCCG
1 GGAAAGGTTAAGGCCGCAACGGCGAACTCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCG
*
12814585 CAACAGCGAACCCGGTACCTTAGAAGATGTGATG
66 CAACGGCGAACCCGGTACCTTAGAAGATGTGATG
* * * *
12814619 GGACAGGTTAAAGCCGCAACGACGAACTCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCG
1 GGAAAGGTTAAGGCCGCAACGGCGAACTCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCG
* * * *
12814684 CAACGACGAACTCGGTATCTTAGAAGATATGATG
66 CAACGGCGAACCCGGTACCTTAGAAGATGTGATG
* * * * * * * *
12814718 GGAAAGGTTGAGGCCACAATGGCGAAC-CTAGTACCATAAAGATTTGAAAGG-AAGGATTGAGGT
1 GGAAAGGTTAAGGCCGCAACGGCGAACTC-GGTACCATGAAGATATGAAGGGAAAGG-TTGAGGC
** * *
12814781 TACGACGGCGAATCCGGTACCTT-GAAAGATGTGATG
64 CGCAACGGCGAACCCGGTACCTTAG-AAGATGTGATG
* * * *
12814817 GGAAAGGTTGAA-GCTGCAATGACGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCC
1 GGAAAGGTT-AAGGCCGCAACGGCGAACTCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCC
*
12814881 ACAACG
65 GCAACG
12814887 ATGAACCTAA
Statistics
Matches: 393, Mismatches: 63, Indels: 21
0.82 0.13 0.04
Matches are distributed among these distances:
98 45 0.11
99 333 0.85
100 15 0.04
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.17
Consensus pattern (99 bp):
GGAAAGGTTAAGGCCGCAACGGCGAACTCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCG
CAACGGCGAACCCGGTACCTTAGAAGATGTGATG
Found at i:12814601 original size:148 final size:149
Alignment explanation
Indices: 12814321--12814886 Score: 602
Period size: 148 Copynumber: 3.8 Consensus size: 149
12814311 AGGTTTGGCA
* * * * *
12814321 GGAAAGGATTGAGGCCGCAATGGCGAATCCGGTACCTTAGAAGATGTAATAGGAAAGGTTAAGGC
1 GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAAGGTTAAGGC
** * * * * ** *
12814386 CGCAACGGTGAACTCAGTAACATGAAGAGATGAAGGGAAAGGTTGAGGTCGTAACGGCGAACTCG
66 CGCAACGACGAACCCGGTACCATGAAGAGATGAAGGGAAAGGTTGAGGCCACAACGGCGAACCCG
*
12814451 GTACCATGAAGAGGTGAAG
131 GTACCATGAAGATGTGAAG
*
12814470 GGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCTTAAAAGATGTGATGGGAAAGGTTAAGGC
1 GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAAGGTTAAGGC
* * *
12814534 CGCAACGGCGAACCCGGTACCATGAAGAGATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCG
66 CGCAACGACGAACCCGGTACCATGAAGAGATGAAGGGAAAGGTTGAGGCCACAACGGCGAACCCG
* *
12814599 GTACCTTAGAAGATGTGATG
131 GTACCAT-GAAGATGTGAAG
* * * * * * * * * * *
12814619 GGACAGG-TTAAAGCCGCAACGACGAACTCGATACCAT-GAAGATATGAAGGGAAAGGTTGAGGC
1 GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAAGGTTAAGGC
* * * * * * *
12814682 CGCAACGACGAACTCGGTATCTTAGAAGATATGATGGGAAAGGTTGAGGCCACAATGGCGAACCT
66 CGCAACGACGAACCCGGTACCAT-GAAGAGATGAAGGGAAAGGTTGAGGCCACAACGGCGAACCC
* * * *
12814747 AGTACCATAAAGATTTGAAA
130 GGTACCATGAAGATGTGAAG
*** * * *
12814767 GG-AAGGATTGAGGTTACGACGGCGAATCCGGTACCTTGAAAGATGTGATGGGAAAGGTTGAA-G
1 GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAAGGTT-AAGG
* * *
12814830 CTGCAATGACGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAACG
65 CCGCAACGACGAACCCGGTACCATGAAGAGATGAAGGGAAAGGTTGAGGCCACAACG
12814887 ATGAACCTAA
Statistics
Matches: 344, Mismatches: 68, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
147 3 0.01
148 215 0.62
149 125 0.36
150 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.17
Consensus pattern (149 bp):
GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAAGGTTAAGGC
CGCAACGACGAACCCGGTACCATGAAGAGATGAAGGGAAAGGTTGAGGCCACAACGGCGAACCCG
GTACCATGAAGATGTGAAG
Found at i:12814893 original size:49 final size:49
Alignment explanation
Indices: 12814321--12814886 Score: 524
Period size: 49 Copynumber: 11.4 Consensus size: 49
12814311 AGGTTTGGCA
* * * * *
12814321 GGAAAGGATTGAGGCCGCAATGGCGAATCCGGTACCTTAGAAGATGT-AATA
1 GGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCAT-GAAGATATGAA-G
* * * * * *
12814372 GGAAAGGTTAAGGCCGCAACGGTGAACTCAGTAACATGAAGAGATGAAG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAG
* * * **
12814421 GGAAAGGTTGAGGTCGTAACGGCGAACTCGGTACCATGAAGAGGTGAAG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAG
* * * * *
12814470 GGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAAAAGATGTGATG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-GAAGATATGAAG
* *
12814520 GGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCATGAAGAGATGAAG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAG
* * * *
12814569 GGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCTTAGAAGATGTGATG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-GAAGATATGAAG
* * * * * *
12814619 GGACAGGTTAAAGCCGCAACGACGAACTCGATACCATGAAGATATGAAG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAG
* * * * *
12814668 GGAAAGGTTGAGGCCGCAACGACGAACTCGGTATCTTAGAAGATATGATG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-GAAGATATGAAG
* * ** * * *
12814718 GGAAAGGTTGAGGCCACAATGGCGAACCTAGTACCATAAAGATTTGAAA
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAG
*** * * * * *
12814767 GG-AAGGATTGAGGTTACGACGGCGAATCCGGTACCTTGAAAGATGTGATG
1 GGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCATG-AAGATATGAAG
* * * *
12814817 GGAAAGGTTGAAGCTGCAATGACGAACCCGGTACCATGAAGATATGAAG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAG
*
12814866 GGAAAGGTTGAGGCCACAACG
1 GGAAAGGTTGAGGCCGCAACG
12814887 ATGAACCTAA
Statistics
Matches: 414, Mismatches: 94, Indels: 16
0.79 0.18 0.03
Matches are distributed among these distances:
48 4 0.01
49 221 0.53
50 178 0.43
51 11 0.03
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.17
Consensus pattern (49 bp):
GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAG
Found at i:12817197 original size:29 final size:30
Alignment explanation
Indices: 12817084--12817285 Score: 189
Period size: 30 Copynumber: 6.8 Consensus size: 30
12817074 GTTTTATTTA
** *
12817084 AAAAATTTGATTTTAACCCCTAAACTTTCT
1 AAAAATTACATTTTGACCCCTAAACTTTCT
** * * * *
12817114 AAAAATTTGATCTTAACCCTTAAACTTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCT
* *
12817144 AAAAATCTA-ATTTTGACCCTTAAACTTTCAA
1 AAAAAT-TACATTTTGACCCCTAAACTTTC-T
*
12817175 AAAAATCACA-TTTGACCCC-AAACATTT-T
1 AAAAATTACATTTTGACCCCTAAAC-TTTCT
*
12817203 AAAAATTACATTTTTACCCCTAAACTTTCT
1 AAAAATTACATTTTGACCCCTAAACTTTCT
*
12817233 AAAAATTACATTTTAACCCCTAAACTTTCT
1 AAAAATTACATTTTGACCCCTAAACTTTCT
* **
12817263 AGAAATTTGATTTTGA-CCCTAAA
1 AAAAATTACATTTTGACCCCTAAA
12817286 TTTTTTGAAA
Statistics
Matches: 148, Mismatches: 17, Indels: 15
0.82 0.09 0.08
Matches are distributed among these distances:
28 9 0.06
29 22 0.15
30 109 0.74
31 8 0.05
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCTAAACTTTCT
Found at i:12817297 original size:59 final size:58
Alignment explanation
Indices: 12817084--12817373 Score: 185
Period size: 59 Copynumber: 4.9 Consensus size: 58
12817074 GTTTTATTTA
* ** * * *
12817084 AAAAATTTGATTTTAACCCCTAAACTTTCTAAAAATTTGATCTTAACCCTTAAACTTTCC
1 AAAAATTTGATTTTAA-CCCTAAATTTTCTAAAAATTACATTTTAACCCCTAAACTTT-T
* * * * * * *
12817144 AAAAATCTAATTTTGACCCTTAAACTTTCAAAAAAATCACA-TTTGACCCC-AAACATTTT
1 AAAAATTTGATTTTAACCC-TAAATTTTC-TAAAAATTACATTTTAACCCCTAAAC-TTTT
** * *
12817203 AAAAATTACATTTTTACCCCTAAACTTTCTAAAAATTACATTTTAACCCCTAAACTTTCT
1 AAAAATTTGA-TTTTAACCCTAAATTTTCTAAAAATTACATTTTAACCCCTAAACTTT-T
* * * * * * * * * *
12817263 AGAAATTTGATTTTGACCCTAAATTTTTTGAAAATCAAATTTTAAGCCTTGAAGTTTT
1 AAAAATTTGATTTTAACCCTAAATTTTCTAAAAATTACATTTTAACCCCTAAACTTTT
* * *
12817321 CAAAAATTAT-ATTTTAACCCAAAATTTT-TCCAAAATTACATTTTGA-CCCTAAA
1 -AAAAATT-TGATTTTAACCCTAAATTTTCT-AAAAATTACATTTTAACCCCTAAA
12817374 ACCTTCCTAA
Statistics
Matches: 178, Mismatches: 42, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
58 16 0.09
59 104 0.58
60 51 0.29
61 7 0.04
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (58 bp):
AAAAATTTGATTTTAACCCTAAATTTTCTAAAAATTACATTTTAACCCCTAAACTTTT
Found at i:12817297 original size:89 final size:88
Alignment explanation
Indices: 12817084--12817373 Score: 217
Period size: 89 Copynumber: 3.3 Consensus size: 88
12817074 GTTTTATTTA
* * ** *
12817084 AAAAATTTGATTTTAACCCCTAAACTTTCTAAAAATTTGATCTTAACCCTTAAACTTTCCAAAAA
1 AAAAATTTGATTTTGA-CCCTAAACTTTTTAAAAATTACATCTTAACCCCTAAACTTTCCAAAAA
* *
12817149 TCTAATTTTGACCCTTAAACTTTC
65 TCTAATTTTAACCCCTAAACTTTC
** * * * * * * *
12817173 AAAAAAATCACATTTGACCCCAAACATTTTAAAAATTACATTTTTACCCCTAAACTTTCTAAAAA
1 AAAAATTTGA-TTTTGACCCTAAACTTTTTAAAAATTACATCTTAACCCCTAAACTTTCCAAAAA
12817238 T-TACATTTTAACCCCTAAACTTTC
65 TCTA-ATTTTAACCCCTAAACTTTC
* * * * * * * * * * *
12817262 TAGAAATTTGATTTTGACCCTAAATTTTTTGAAAATCAAATTTTAAGCCTTGAAGTTTTCAAAAA
1 -AAAAATTTGATTTTGACCCTAAACTTTTTAAAAATTACATCTTAACCCCTAAACTTTCCAAAAA
* *
12817327 T-TATATTTTAA-CCCAAAATTTTTC
65 TCTA-ATTTTAACCCCTAAA-CTTTC
* **
12817351 CAAAATTACATTTTGACCCTAAA
1 AAAAATTTGATTTTGACCCTAAA
12817374 ACCTTCCTAA
Statistics
Matches: 156, Mismatches: 41, Indels: 9
0.76 0.20 0.04
Matches are distributed among these distances:
88 27 0.17
89 119 0.76
90 10 0.06
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (88 bp):
AAAAATTTGATTTTGACCCTAAACTTTTTAAAAATTACATCTTAACCCCTAAACTTTCCAAAAAT
CTAATTTTAACCCCTAAACTTTC
Found at i:12817423 original size:29 final size:29
Alignment explanation
Indices: 12817101--12817432 Score: 159
Period size: 30 Copynumber: 11.2 Consensus size: 29
12817091 TGATTTTAAC
* *** * *
12817101 CCCTAAACTTTCTAAAAATTTGATCTTAA
1 CCCTAAACTTTTTAAAAATCACATTTTGA
**
12817130 CCCTTAAACTTTCCAAAAATCTA-ATTTTGA
1 CCC-TAAACTTTTTAAAAATC-ACATTTTGA
**
12817160 CCCTTAAACTTTCAAAAAAATCACA-TTTGA
1 CCC-TAAACTTT-TTAAAAATCACATTTTGA
* * * *
12817190 CCCCAAACATTTTAAAAATTACATTTTTA
1 CCCTAAACTTTTTAAAAATCACATTTTGA
* * *
12817219 CCCCTAAACTTTCTAAAAATTACATTTTAA
1 -CCCTAAACTTTTTAAAAATCACATTTTGA
* * ***
12817249 CCCCTAAACTTTCTAGAAATTTGATTTTGA
1 -CCCTAAACTTTTTAAAAATCACATTTTGA
* * * *
12817279 CCCTAAATTTTTTGAAAATCAAATTTTAA
1 CCCTAAACTTTTTAAAAATCACATTTTGA
* * * * * * *
12817308 GCCTTGAAGTTTTCAAAAATTATATTTTAA
1 -CCCTAAACTTTTTAAAAATCACATTTTGA
* * *
12817338 CCC-AAAATTTTTCCAAAATTACATTTTGA
1 CCCTAAACTTTTT-AAAAATCACATTTTGA
** ** *
12817367 CCCTAAAACCTTCCT-AAAGCCATATTTTGA
1 CCCT-AAA-CTTTTTAAAAATCACATTTTGA
* *
12817397 CACTAAACTTTTTAAAAATCACATTTTAA
1 CCCTAAACTTTTTAAAAATCACATTTTGA
12817426 CCCTAAA
1 CCCTAAA
12817433 TTCTTCGAAA
Statistics
Matches: 233, Mismatches: 58, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
28 19 0.08
29 72 0.31
30 128 0.55
31 11 0.05
32 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTTTTAAAAATCACATTTTGA
Found at i:12819959 original size:20 final size:19
Alignment explanation
Indices: 12819897--12819952 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
12819887 CACTCTCTCA
*
12819897 ATAAAAATTGCAAATTAATTT
1 ATAAAAATT-CAAAAT-ATTT
12819918 -TCAAAAATTCAAAATATTT
1 AT-AAAAATTCAAAATATTT
12819937 ATAAAAATTTCAAAAT
1 ATAAAAA-TTCAAAAT
12819953 TTATATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 9 0.29
20 15 0.48
21 7 0.23
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAAAATTCAAAATATTT
Found at i:12819969 original size:18 final size:18
Alignment explanation
Indices: 12819920--12819957 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12819910 ATTAATTTTC
12819920 AAAAA-TTCAAAATATTTAT
1 AAAAATTTC-AAA-ATTTAT
12819939 AAAAATTTCAAAATTTAT
1 AAAAATTTCAAAATTTAT
12819957 A
1 A
12819958 TATATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATTTCAAAATTTAT
Found at i:12819980 original size:10 final size:10
Alignment explanation
Indices: 12819967--12820021 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
12819957 ATATATTTTA
12819967 AAAAAATTAT
1 AAAAAATTAT
12819977 AAAAAA-TAT
1 AAAAAATTAT
12819986 ATAAAAATATAT
1 A-AAAAAT-TAT
12819998 AAAGAAATTA-
1 AAA-AAATTAT
* *
12820008 AAAATATTCT
1 AAAAAATTAT
12820018 AAAA
1 AAAA
12820022 TAATAATTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 8 0.21
10 18 0.47
11 4 0.11
12 8 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:12819996 original size:19 final size:19
Alignment explanation
Indices: 12819968--12820014 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
12819958 TATATTTTAA
*
12819968 AAAAAT-TATAAAAAATATAT
1 AAAAATATATAAAGAA-AT-T
12819988 AAAAATATATAAAGAAATT
1 AAAAATATATAAAGAAATT
12820007 AAAAATAT
1 AAAAATAT
12820015 TCTAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 8 0.32
21 8 0.32
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAATATATAAAGAAATT
Found at i:12820005 original size:12 final size:11
Alignment explanation
Indices: 12819967--12820005 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
12819957 ATATATTTTA
12819967 AAAAAAT-TAT
1 AAAAAATATAT
12819977 AAAAAATATAT
1 AAAAAATATAT
12819988 -AAAAATATAT
1 AAAAAATATAT
12819998 AAAGAAAT
1 AAA-AAAT
12820006 TAAAAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 17 0.65
11 5 0.19
12 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AAAAAATATAT
Found at i:12820124 original size:16 final size:16
Alignment explanation
Indices: 12820105--12820135 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12820095 TTGAAAAAGT
12820105 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
12820121 TTTCAAATTTATATG
1 TTTCAAATATATATG
12820136 CTCTAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:12827592 original size:30 final size:30
Alignment explanation
Indices: 12827556--12827613 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
12827546 CAATTTAACA
* *
12827556 AACAAATGCTTCTAAAATAGTAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
12827586 AACAAATGCCTCTAAAATAATAACAAAA
1 AACAAATGCCTCTAAAATAATAACAAAA
12827614 GTATTATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:12827658 original size:14 final size:14
Alignment explanation
Indices: 12827639--12827665 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12827629 AAAACAATAA
12827639 CAACATAATAGTAG
1 CAACATAATAGTAG
12827653 CAACATAATAGTA
1 CAACATAATAGTA
12827666 AAATTGTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
CAACATAATAGTAG
Found at i:12829401 original size:18 final size:17
Alignment explanation
Indices: 12829377--12829418 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
12829367 AAAGTTCAAC
12829377 TTATATATATATATCAAT
1 TTATATATATATAT-AAT
* *
12829395 TTTTATATATTTATAAT
1 TTATATATATATATAAT
12829412 TTATATA
1 TTATATA
12829419 ACCTAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATATATATATATAAT
Found at i:12829533 original size:13 final size:14
Alignment explanation
Indices: 12829503--12829540 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
12829493 CAAAAGGAAG
12829503 AAAATT-ATATTAT
1 AAAATTAATATTAT
*
12829516 TAAATTAATATTA-
1 AAAATTAATATTAT
12829529 AAAATTAATATT
1 AAAATTAATATT
12829541 TTAATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAATTAATATTAT
Found at i:12829627 original size:19 final size:19
Alignment explanation
Indices: 12829603--12829639 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
12829593 AGTCATAGTG
12829603 ATATTGAAATAGACTATGA
1 ATATTGAAATAGACTATGA
12829622 ATATTGAAATAGACTATG
1 ATATTGAAATAGACTATG
12829640 TATTCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
ATATTGAAATAGACTATGA
Found at i:12831629 original size:52 final size:52
Alignment explanation
Indices: 12831536--12831770 Score: 337
Period size: 52 Copynumber: 4.5 Consensus size: 52
12831526 CATTTAATAT
* * * * *
12831536 TCACGATTACACAAAGTCATCGGACCTTA-AATCCGTAAAAGGATCCATATGC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAGGATTCATATAC
* * * *
12831588 TCACGATGACACATGGTTATCGGGCCTCATAATCCGTAAAGGATTCATACAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
*
12831640 TCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
* *
12831692 TCACGATGACACATAGTCATCAGACCTCATAATCTGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
*
12831744 TCACGATGACACATAATCATCGGACCT
1 TCACGATGACACATAGTCATCGGACCT
12831771 TTTTGCATTT
Statistics
Matches: 163, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
52 156 0.96
53 7 0.04
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (52 bp):
TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
Found at i:12836496 original size:52 final size:52
Alignment explanation
Indices: 12836399--12836638 Score: 340
Period size: 52 Copynumber: 4.6 Consensus size: 52
12836389 TTCCCATTTA
* * * * *
12836399 ATACTCACGATGACACAAAGTCATCAGACCTTA-AATACGTAAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAGGATTCAT
* * *
12836451 ATGCTCACGATGACACATGGTCATC-GAGCCTCATAATCCGTAAAGGGTTCAT
1 ATACTCACGATGACACATAGTCATCGGA-CCTCATAATCCGTAAAGGATTCAT
* * *
12836503 ATACTCACGATGACGCATAGTCATTGGACCTCATAATCCGTAAAGGGGTTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAA-GGATTCAT
12836556 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
12836608 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
12836639 TTTTGCATTT
Statistics
Matches: 170, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.01
52 110 0.65
53 58 0.34
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:12836580 original size:105 final size:104
Alignment explanation
Indices: 12836399--12836638 Score: 347
Period size: 105 Copynumber: 2.3 Consensus size: 104
12836389 TTCCCATTTA
* * * *
12836399 ATACTCACGATGACACAAAGTCATCAGACCTTAAATACGTAAAAGGATCCATATGCTCACGATGA
1 ATACTCACGATGACACATAGTCATCGGACCTCAAATACGTAAAAGGATCCATATACTCACGATGA
* *
12836464 CACATGGTCATC-GAGCCTCATAATCCGTAAAGGGTTCAT
66 CACATAGTCATCGGA-CCTCATAATCCGTAAAGGATTCAT
* * * * * *
12836503 ATACTCACGATGACGCATAGTCATTGGACCTCATAATCCGTAAAGGGGTTCATATACTCACGATG
1 ATACTCACGATGACACATAGTCATCGGACCTCA-AATACGTAAAAGGATCCATATACTCACGATG
12836568 ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
65 ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
12836608 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
12836639 TTTTGCATTT
Statistics
Matches: 120, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
104 28 0.23
105 90 0.75
106 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (104 bp):
ATACTCACGATGACACATAGTCATCGGACCTCAAATACGTAAAAGGATCCATATACTCACGATGA
CACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:12840354 original size:24 final size:24
Alignment explanation
Indices: 12840327--12840377 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
12840317 CTCCAATGGA
12840327 AGAAAGAAGAACAAAGTCTTTTAG
1 AGAAAGAAGAACAAAGTCTTTTAG
* *
12840351 AGAAAGGAGAACGAAGTCTTTTAG
1 AGAAAGAAGAACAAAGTCTTTTAG
12840375 AGA
1 AGA
12840378 TATGTTAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.25, T:0.20
Consensus pattern (24 bp):
AGAAAGAAGAACAAAGTCTTTTAG
Found at i:12842149 original size:371 final size:372
Alignment explanation
Indices: 12841463--12842201 Score: 1273
Period size: 371 Copynumber: 2.0 Consensus size: 372
12841453 GCAAATTGGT
* *
12841463 TACAAAAAGTGATTGGTAAATGTATTGATAGTGCCAGAGCGCTTTTATCCCGAAAATATTAATAT
1 TACAAAAAGCGATTGGTAAATGTATTGATAGTGCCAGAGCGCTTTTATCCCGAAAAGATTAATAT
** * *
12841528 CGGATAACATTCTTCTTGCTTATGAACTTATTCACACTTTCAGACAAAAACGTTATGGGAGGAAA
66 CAAATAACATTCTTCTTGCTTACGAACTTATTCACACTTTCAGACAAAAACGTTATAGGAGGAAA
* ** *
12841593 GGATTTATGGCTGCAAAACTTGATGTGAGTAAGGCATACAATCGTGTGGAGTGGAACTTCATTTG
131 GGATTTATGGCTACAAAACTTGACATGAGTAAGGCATACAATCATGTGGAGTGGAACTTCATTTG
** *
12841658 AGATGTTATGCTCAAAATGGGTTTCAAAGAGGAATGGGTGAAGTGCATTATGTAGTGTATCACAA
196 AGATGTTATGCTCAAAATGGGTTTCAAAGAGGAATGGGTGAAGCACATTATGCAGTGTATCACAA
* *
12841723 AGGTCTCTTGCTCGGTAAATGTAAATGGTAAGAGTGGTCAATTATTTCCTCTAAGGAGAGTGCTT
261 AGGTCTCTTGCTCGGCAAATGTAAATGGTAAGAGTGGTCAATTATTTCATCTAAGGAGAGTGCTT
*
12841788 CGTCAAGGTGACCCTCTCAGCCTCTTCC-TTTCCTAATGTACAGCGA
326 CGTCAAGGTGACCCTCTCAGCCTATTCCTTTTCCTAATGTACAGCGA
* *
12841834 TACAAAAAGCGATTGGTAAATGTATTGATAGTGTCAGAGCGCTTTTATCCCGGAAAGATTAATAT
1 TACAAAAAGCGATTGGTAAATGTATTGATAGTGCCAGAGCGCTTTTATCCCGAAAAGATTAATAT
*
12841899 CAAATAACATTCTTCTTGCTTACGAACTTATTCACACTTTTAGACAAAAACGTTATAGGAGGAAA
66 CAAATAACATTCTTCTTGCTTACGAACTTATTCACACTTTCAGACAAAAACGTTATAGGAGGAAA
* *
12841964 GGATTTATGGCTACAAAACTTGACATGAGTAAGGCATACAATCATGTGGAGTTGAACTTTATTTG
131 GGATTTATGGCTACAAAACTTGACATGAGTAAGGCATACAATCATGTGGAGTGGAACTTCATTTG
12842029 AGATGTTATGCTCAAAATGGGTTTCAAAGAGGAATGGGTGAAGCACATTATGCAGTGTATCACAA
196 AGATGTTATGCTCAAAATGGGTTTCAAAGAGGAATGGGTGAAGCACATTATGCAGTGTATCACAA
*
12842094 TGGTCTCTTGCTCGGCAAATGTAAATGGTAAGAGTGGTCAATTATTTCATCTAAGGAGAGTGCTT
261 AGGTCTCTTGCTCGGCAAATGTAAATGGTAAGAGTGGTCAATTATTTCATCTAAGGAGAGTGCTT
12842159 CGTCAAGGTGACCCTCTCAGCCTATTCCTTTTCCTAATGTACA
326 CGTCAAGGTGACCCTCTCAGCCTATTCCTTTTCCTAATGTACA
12842202 ACGAAGGTTT
Statistics
Matches: 345, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
371 331 0.96
372 14 0.04
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (372 bp):
TACAAAAAGCGATTGGTAAATGTATTGATAGTGCCAGAGCGCTTTTATCCCGAAAAGATTAATAT
CAAATAACATTCTTCTTGCTTACGAACTTATTCACACTTTCAGACAAAAACGTTATAGGAGGAAA
GGATTTATGGCTACAAAACTTGACATGAGTAAGGCATACAATCATGTGGAGTGGAACTTCATTTG
AGATGTTATGCTCAAAATGGGTTTCAAAGAGGAATGGGTGAAGCACATTATGCAGTGTATCACAA
AGGTCTCTTGCTCGGCAAATGTAAATGGTAAGAGTGGTCAATTATTTCATCTAAGGAGAGTGCTT
CGTCAAGGTGACCCTCTCAGCCTATTCCTTTTCCTAATGTACAGCGA
Found at i:12850113 original size:21 final size:21
Alignment explanation
Indices: 12850084--12850123 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12850074 TAATTAATAT
*
12850084 TTTAATAATTTAATCGTTGAA
1 TTTAATAATATAATCGTTGAA
* *
12850105 TTTATTAATATAATTGTTG
1 TTTAATAATATAATCGTTG
12850124 GGGATCAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTAATAATATAATCGTTGAA
Found at i:12855357 original size:2 final size:2
Alignment explanation
Indices: 12855352--12855395 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12855342 GGGTTTTTGT
12855352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12855394 TA
1 TA
12855396 AAATATGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12855724 original size:26 final size:26
Alignment explanation
Indices: 12855671--12855725 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12855661 CCATATCCTT
* **
12855671 ATATCCTACAACTTCTTTCTTCTTCC
1 ATATCCTACAACTTATTTCTTCACCC
* *
12855697 ATATTCTACAATTTATTTCTTCACCC
1 ATATCCTACAACTTATTTCTTCACCC
12855723 ATA
1 ATA
12855726 AATGGTTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATCCTACAACTTATTTCTTCACCC
Found at i:12856457 original size:145 final size:145
Alignment explanation
Indices: 12856186--12856457 Score: 341
Period size: 145 Copynumber: 1.9 Consensus size: 145
12856176 CTCCAAAGAT
* * * ***
12856186 TCTAAACAAATCAAAACAATGCATTGGCCAAGCCTTGACACTGTGGCATCGGTACAACTCCTGGT
1 TCTAAACAAATCAAAACAATGCAGTGGCCAAGCCTTGACACTATGGCATCGATACAACTCCCAAT
* * *** ** * *
12856251 CGTACCAATACAAGTCCCCGCTACTATAGATAATTACATTCTGTTTGATTTGTTACGAAACCAGA
66 CGTACCAATACAAGTCCCCGCTACTATAGATAATGACATTCAGTCAAATACGTAAAGAAACCAGA
12856316 TGGATCAAATAAAAG
131 TGGATCAAATAAAAG
* *
12856331 TCTAAACAAATCAAAACAATGCAGTGGTCAAGCCTTGACATTATGGCATCGATACAACTCCCAAT
1 TCTAAACAAATCAAAACAATGCAGTGGCCAAGCCTTGACACTATGGCATCGATACAACTCCCAAT
* *
12856396 TGTACCAATACAAGTCCCCGCTACTATAGATAA-GACATTCAAGTCAAATGACG-AAATAAACC
66 CGTACCAATACAAGTCCCCGCTACTATAGATAATGACATTC-AGTCAAAT-ACGTAAAGAAACC
12856458 TTGACTAATG
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
144 6 0.06
145 99 0.93
146 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (145 bp):
TCTAAACAAATCAAAACAATGCAGTGGCCAAGCCTTGACACTATGGCATCGATACAACTCCCAAT
CGTACCAATACAAGTCCCCGCTACTATAGATAATGACATTCAGTCAAATACGTAAAGAAACCAGA
TGGATCAAATAAAAG
Found at i:12857773 original size:27 final size:27
Alignment explanation
Indices: 12857739--12857819 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 27
12857729 ATATCAAATC
*
12857739 ATTT-AAATATATTTATTATTTTTAAA
1 ATTTAAAATATATTTATTATTATTAAA
*
12857765 ATTTAAAATAT-TTTATGTATAATT-AA
1 ATTTAAAATATATTTAT-TATTATTAAA
12857791 ATTTACAAATA-ATTTATTAATTATTAAA
1 ATTTA-AAATATATTTATT-ATTATTAAA
12857819 A
1 A
12857820 AGTACTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 17 0.37
27 26 0.57
28 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
ATTTAAAATATATTTATTATTATTAAA
Found at i:12862260 original size:41 final size:39
Alignment explanation
Indices: 12862184--12862261 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 39
12862174 ACATGTAAAC
12862184 TTGAACTATTTTTTTTGCTAATTTTTTTGCATATAAATTA
1 TTGAACTATTTTTTTTGCTAATTTTTTTG-ATATAAATTA
*
12862224 TTGAACTATTACTTTTTTGTTAATTTTTTATG-TATAAA
1 TTGAACTATT--TTTTTTGCTAATTTTTT-TGATATAAA
12862262 ATGCAAATCC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
40 10 0.29
41 6 0.18
42 16 0.47
43 2 0.06
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (39 bp):
TTGAACTATTTTTTTTGCTAATTTTTTTGATATAAATTA
Found at i:12864285 original size:6 final size:6
Alignment explanation
Indices: 12864274--12864301 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12864264 GACAAAAGTA
12864274 GGAAAG GGAAAG GGAAAG GGAAAG GGAA
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAA
12864302 GGTTGATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GGAAAG
Found at i:12868366 original size:701 final size:694
Alignment explanation
Indices: 12866980--12869936 Score: 2884
Period size: 701 Copynumber: 4.2 Consensus size: 694
12866970 TTTGTGGCAA
* * * * *
12866980 TTGTTTATCTGTGTGGCAAAATGGAACCATGAAGAGTTAAGTCAAATACTATTAATTTCAACACT
1 TTGTTTATCTATGTGGCAAAATGGAACCGTGAAGAGTTAAGCCAAATACTATTACTTTCAACACC
* * * *
12867045 TGGATTGATGCCTACTATAAGCTTCGTCAACTTCATTATGACTTATTTATTTGCGA-CAAAATGA
66 TGGATTGATGCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTG-GAGCAAAATGA
* * * * *
12867109 TGAAGATAGGTTTTCAACCTGCTGTTTTATCGGATGTGGGCTTGAGTTCTTAGGTTGGTTTCCTT
130 TGAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCTT
** * * * * * *
12867174 GTTTAGATTTTAGGTGAATTTTGGATTTAGCCTAGGTTTGTTTTAGATTAGTTGCTTGCTTATAC
195 GTTGGGCTTTTAGGTGAATTTTTGATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTTGTTTATAC
* * * * * * *
12867239 TTTG-TTTTTTTGTTTTTTGGTC-AGATCCATTTTATTTATAAAAATCGT-AGATTTTTAATTGT
260 TTTGTTTTTTTTGTTTTTTGGCCAAG-CCCACTTTATTTATAAAAGTC-TCAGGTTTTTACTTCT
* *
12867301 GCATGTGCAAAAACCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAA-GATATGTTTTTTT
323 -TATGTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAATG-TAT-TTTTTTT
* * * * * * * * * *
12867365 TATTTTAGAGGGCCTTAGTCTTAGCAACCCCTCCTCCTATAAATGTTTCACATGTTTTCTCTCAT
385 AATTTTAGGGGGCC-TAGTCTTGGC-AGCCCTCCTCATATATATGTGT-ACCTATTTTCTCTAAT
* *
12867430 CTTCATCAATCCCTATATTTCTTTCTTTGCTTCTATTTCTTCTCTTGTTTTTCTCTACTTCTCTT
447 CTTCATCAATCCCTAT-TTTCTTTCTTTGCTTCTCTTTCTTCTCTTATTTTTCTCTACTTCTCTT
* * * * *
12867495 GCAATGGGCAAGCCTTTTTTCTTTCGTT-TCACATCACCCTTTTATTTTAACCACATTACTACAA
511 GCAATGGGCAAGCCTTTTTTATTTCGTTATC-CTTCACCCTATTATTTTAACAATATTACTACAA
* * * *
12867559 AAGTTTTTAACATTTTTGAAAATTCAAACAAGATATGTAAAAACCCATATCCTAACCTTACAACT
575 AAGTTTTTGATATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCCTAACCTCACAACT
* *
12867624 TTTAAATTCAATCAGAAATTAGCAGAACATGCTAGCAAGCACCAGTATGCCACAG
640 TTTTAATTCAATCAGAAATTAGCAGAACATGCTAGCAAGCACTAGTATGCCACAG
* * * * * * *
12867679 TTGTTTATCTGTGTGGCAAAATGGAATCGTCAAGAGTTAAACCAAATATTGTTACTTTCACCACC
1 TTGTTTATCTATGTGGCAAAATGGAACCGTGAAGAGTTAAGCCAAATACTATTACTTTCAACACC
* * ** *
12867744 TAGATTGATGCCTATTGTAAATTTCATCAACTTGATTATGACTTATTTCTTTGGAGCAAAATGAT
66 TGGATTGATGCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGAGCAAAATGAT
* * * *
12867809 GAAGATAAGTTTTCAACTTACTATTTTATCGAAGGTGGGCTTGCGTTCTTAGGTTGGTGTCCTTG
131 GAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCTTG
* * * *
12867874 TTGGGCTTTTAGTTGAATTTTTGGATTTAGCCTAAGCTTGTTTTAGATTTGCTGCTTGTTTATAC
196 TTGGGCTTTTAGGTGAATTTTT-GATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTTGTTTATAC
* *
12867939 TTTGTTCTATTTTTATTTTTTGGCCAAGCACACTTTATTTAT-AAAGTCTCAGGTTTTTACTTCT
260 TTTGTT-T-TTTTTGTTTTTTGGCCAAGCCCACTTTATTTATAAAAGTCTCAGGTTTTTACTTCT
* * * * *
12868003 ATATATACAAAAAGCTAAAATGATTGAATTAATTAATGTAATGAAATTCAATGCATTTTTTTTAA
323 -TATGTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAATGTATTTTTTTTAA
*
12868068 TTTTAGGGGTGCCTAGTTCATGGCAGCCC-CCTCATATATATGCTGTACCTATTTTCTCTAATCT
387 TTTTAGGGG-GCCTAG-TCTTGGCAGCCCTCCTCATATATATG-TGTACCTATTTTCTCTAATCT
** * * * *
12868132 TCATCAATCCCTATTTCTCTTTCTCCGTTTCTCTTTCATATCTTACTTTTTCTCTACTTCTTTTG
449 TCATCAATCCCTATTT-TCTTTCTTTGCTTCTCTTTCTTCTCTTA-TTTTTCTCTACTTCTCTTG
* * * * * *
12868197 CAATGTGTAAGCATTTTTTATTTTGTTATCCTTCACCCTCTTATTTTAGCAATATTACTACAAAA
512 CAATGGGCAAGCCTTTTTTATTTCGTTATCCTTCACCCTATTATTTTAACAATATTACTACAAAA
** * *
12868262 AATTTTGATATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCTTAGCCTCACAACTTT
577 GTTTTTGATATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCCTAACCTCACAACTTT
* * *
12868327 TTAATTCAATAAAAAATTAGCAGAACATGCTAGCAAGCACTAGTATGTCACAG
642 TTAATTCAATCAGAAATTAGCAGAACATGCTAGCAAGCACTAGTATGCCACAG
* *
12868380 TTGTTTATCTATATGGCAAAATGGAACCGTGGAA-AGTTAAGTCAAATACTATTACTTTCAACAC
1 TTGTTTATCTATGTGGCAAAATGGAACCGT-GAAGAGTTAAGCCAAATACTATTACTTTCAACAC
* * *
12868444 TTGGATTAATCCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGG-GACAAAATG
65 CTGGATTGATGCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGAG-CAAAATG
* * * *
12868508 ATGAAGATATGTTTTCAACTTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTCGATGTCCT
129 ATGAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCT
* * * * *
12868573 TGTTGGGGTTTTAGGTGAATTTTTTATTTAGCCTAGGCTTGTTTAAAATTAGCTGTTTGGTTATA
194 TGTTGGGCTTTTAGGTGAATTTTTGATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTTGTTTATA
* * * * *
12868638 C--T-TTTTTTTTGTTTTTTGGCTCGA-CCCACTTTATTTATAAAACTCTCATGTTTTTATTTAT
259 CTTTGTTTTTTTTGTTTTTTGGC-CAAGCCCACTTTATTTATAAAAGTCTCAGGTTTTTACTT-C
* *
12868699 TTATGTGCAAAAAGCTAAAAGAATTGAATTAATTAAAGTAATGAAATTCAAGTGTTTTTTTTTTA
322 TTATGTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAA-TGTATTTTTTTTA
* * * * * * *
12868764 ATTTTAGGGGGCCTGGGTCTTGCCAGCCCTTCCCCTTATATATGTTGCACCTATTTTCTCTTATT
386 ATTTTAGGGGGCCT-AGTCTTGGCAGCCC-TCCTCATATATATG-TGTACCTATTTTCTCTAATC
* * * * *
12868829 TTTATCAATCTCTATTTTTTTTCTTTGCTTCTCTTTCTTCTATTAATTTTCTCTACTTCTCTTGC
448 TTCATCAATCCCTATTTTCTTTCTTTGCTTCTCTTTCTTCTCTTATTTTTCTCTACTTCTCTTGC
** * * *
12868894 AATGGGCAAGCCTTCATTATTTCGTCTA-ACTTCACCCTATTATTTTAATATTATTACTACAAAA
513 AATGGGCAAGCCTTTTTTATTTCGT-TATCCTTCACCCTATTATTTTAACAATATTACTACAAAA
* * * *
12868958 GTTTTTGATATATTTGAAAATTCAAATAAGATATGTAAAAACCAATATCCTAACCTCAAAATTTT
577 GTTTTTGATATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCCTAACCTCACAACTTT
* * * * * * *
12869023 TTAATTCAATCAGAAATTAGAAGAACATACCACCAAGCATTAGCATGCTACAG
642 TTAATTCAATCAGAAATTAGCAGAACATGCTAGCAAGCACTAGTATGCCACAG
* * * * * * *
12869076 TTGTATATTTTATGTGGCAAAATGGAATCGTGGAGAGTTAAGCCAAATATTGTTACTTTTAACAC
1 TTGTTTA-TCTATGTGGCAAAATGGAACCGTGAAGAGTTAAGCCAAATACTATTACTTTCAACAC
* * * * *
12869141 CTGGATTGATGCCTA-TCGTAAGCTTCGTCAACTTAATTATGACTTATTTGTTTGGGGTAAAAGG
65 CTGGATTGATGCCTACT-GTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGAGCAAAATG
* * ** *
12869205 ATGAAGATAAGTTTTTAACCTACTGTTTTATCGGACGTAAGCTTGGGTTCTTAGGTTTGTGTCCT
129 ATGAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCT
* * * * * * *
12869270 TGTTGGGCTTTTAGGTAAATTTTTTATTTTGTCTAGGATTGTTTTAAATTAGTTGCTTATTTTAT
194 TGTTGGGCTTTTAGGTGAATTTTTGATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTT-GTTTAT
* ** * *
12869335 ACTTTGTTTTTTTTTGTTTTCTGATCAGGCCCACTTTATTTATAAAAGTCTCAGGTTTTAAC-TC
258 ACTTTG-TTTTTTTTGTTTTTTGGCCAAGCCCACTTTATTTATAAAAGTCTCAGGTTTTTACTTC
* ** * *
12869399 TTTTGTGC--AAA---AAAAGGATTGAATTAATTAATTTAATGAAATTTAAGGTATTTTTTTTAA
322 TTATGTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAATGTATTTTTTTTAA
* * * * * * * * *
12869459 TTTTAGCCGAGCATGGGTCATGCCAACTCTTCC-CTTTATATATGTTGCAACTATTTTCTCTCAT
387 TTTTAG-GGGGCCT-AGTCTTGGCAGC-CCTCCTC-ATATATATG-TG-------------T-A-
** *
12869523 CTTCATCAATTCTTGTTTTTCTTTCTCTGCTTCTCTTTCTTTATCAATCCCTATTTTTCTTTCTC
432 C--C-T--A------------TTT-TCT-CTAATC-TTC---ATCAATCCCTA-TTTTCTTTCTT
* * ** * *
12869588 TACTTCTTTGCTTCTCTTTCTCTTCATGCTTTTGTCTACTTCTCTTATAATGGGCAAGTCTTATT
473 TGCTTC--T-CTT-TC-TTCTCTT-AT--TTTTCTCTACTTCTCTTGCAATGGGCAAGCCTTTTT
* * * * * * * * *
12869653 TATTTCGTT-TCACTACACCTTTTTATTTTAACAACATTATTACAAAAGTTTTTAACATTGTCGA
530 TATTTCGTTATC-CTTCACCCTATTATTTTAACAATATTACTACAAAAGTTTTTGATATTTTTGA
* * * * *
12869717 AAATTTAAACAAGATATGTAAAAACTCGTATCCTAACCTCACAACTTTTAAATTCAATCAGAAAT
594 AAATTCAAATAAGATATGTAAAAACCCATATCCTAACCTCACAACTTTTTAATTCAATCAGAAAT
* * * * * *
12869782 TAGAAAAACATGCTAGCAAGCACCAATATGTCACAA
659 TAGCAGAACATGCTAGCAAGCACTAGTATGCCACAG
* ** *
12869818 TTGTTTATCTGTGTGGCAAAATGGAACCGTGGTGAGTTAAGTCAAATACTATTACTTTCAACACC
1 TTGTTTATCTATGTGGCAAAATGGAACCGTGAAGAGTTAAGCCAAATACTATTACTTTCAACACC
* * * * * *
12869883 TGGATTGATGTCTAATGTAAGCTTCATCATCTTAATTATGGCTTATCTGTTTGG
66 TGGATTGATGCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGG
12869937 GGCTGTAACA
Statistics
Matches: 1861, Mismatches: 310, Indels: 132
0.81 0.13 0.06
Matches are distributed among these distances:
694 19 0.01
695 88 0.05
696 257 0.14
697 253 0.14
698 56 0.03
699 185 0.10
700 146 0.08
701 391 0.21
702 119 0.06
703 26 0.01
704 2 0.00
709 1 0.00
710 1 0.00
712 1 0.00
713 1 0.00
715 1 0.00
727 3 0.00
728 3 0.00
729 4 0.00
730 2 0.00
733 10 0.01
734 14 0.01
736 1 0.00
737 3 0.00
738 2 0.00
739 6 0.00
740 1 0.00
741 98 0.05
742 167 0.09
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (694 bp):
TTGTTTATCTATGTGGCAAAATGGAACCGTGAAGAGTTAAGCCAAATACTATTACTTTCAACACC
TGGATTGATGCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGAGCAAAATGAT
GAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCTTG
TTGGGCTTTTAGGTGAATTTTTGATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTTGTTTATACT
TTGTTTTTTTTGTTTTTTGGCCAAGCCCACTTTATTTATAAAAGTCTCAGGTTTTTACTTCTTAT
GTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAATGTATTTTTTTTAATTTT
AGGGGGCCTAGTCTTGGCAGCCCTCCTCATATATATGTGTACCTATTTTCTCTAATCTTCATCAA
TCCCTATTTTCTTTCTTTGCTTCTCTTTCTTCTCTTATTTTTCTCTACTTCTCTTGCAATGGGCA
AGCCTTTTTTATTTCGTTATCCTTCACCCTATTATTTTAACAATATTACTACAAAAGTTTTTGAT
ATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCCTAACCTCACAACTTTTTAATTCAA
TCAGAAATTAGCAGAACATGCTAGCAAGCACTAGTATGCCACAG
Found at i:12869050 original size:696 final size:695
Alignment explanation
Indices: 12866980--12869563 Score: 2916
Period size: 701 Copynumber: 3.7 Consensus size: 695
12866970 TTTGTGGCAA
* * * * *
12866980 TTGTTTATCTGTGTGGCAAAATGGAACCATGAAGAGTTAAGTCAAATACTATTAATTTCAACACT
1 TTGTTTATCTATGTGGCAAAATGGAACCGTGAAGAGTTAAGCCAAATACTATTACTTTCAACACC
* * * * *
12867045 TGGATTGATGCCTACTATAAGCTTCGTCAACTTCATTATGACTTATTTATTTGCGACAAAATGAT
66 TGGATTGATGCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGGACAAAATGAT
* * * * *
12867110 GAAGATAGGTTTTCAACCTGCTGTTTTATCGGATGTGGGCTTGAGTTCTTAGGTTGGTTTCCTTG
131 GAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCTTG
** * * * * * *
12867175 TTTAGATTTTAGGTGAATTTTGGATTTAGCCTAGGTTTGTTTTAGATTAGTTGCTTGCTTATACT
196 TTGGGCTTTTAGGTGAATTTTTGATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTTGTTTATACT
* * * * *
12867240 TTGT-TTTTTTGTTTTTTGG-TCAGATCCATTTTATTTATAAAAATCGT-AGATTTTTAATTGTG
261 TT-TCTTTTTTGTTTTTTGGCTCAGACCCACTTTATTTATAAAAGTC-TCAG-TTTTTAATTCTT
* * * *
12867302 CATGTGCAAAAACCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAAG-ATATGTTTTTTTT
323 TATGTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAAGTGTAT-TTTTTTTA
* ** * * * * * *
12867366 ATTTTAGAGGGCCTTAGTCTTAG-CAACCCCTCCTCC-TATAAATGTTTCACATGTTTTCTCTCA
387 ATTTTAGGGGGCCTGGGTCAT-GCCAACCCTTCC-CCTTATATATGTTGCACCTATTTTCTCTCA
* * *
12867429 TCTTCATCAATCCCTATATTTCTTTCTTTGCTTCTATTTCTTCTCTTGTTTTTCTCTACTTCTCT
450 TCTTCATCAATCCCTAT-TTTCTTTCTCTGCTTCTCTTTCTTCTCTTATTTTTCTCTACTTCTCT
* * * * *
12867494 TGCAATGGGCAAGCCTTTTTTCTTTCGTTTCACATCACCCTTTTATTTTAACCACATTACTACAA
514 TGCAATGGGCAAGCCTTTTTTATTTCG-TTAACTTCACCCTATTATTTTAA-CATATTACTACAA
* * * *
12867559 AAGTTTTTAACATTTTTGAAAATTCAAACAAGATATGTAAAAACCCATATCCTAACCTTACAACT
577 AAGTTTTTGATATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCCTAACCTCACAACT
* *
12867624 TTTAAATTCAATCAGAAATTAGCAGAACATGCTAGCAAGCACCAGTATGCCACAG
642 TTTTAATTCAATCAGAAATTAGCAGAACATGCTAGCAAGCACTAGTATG-CACAG
* * * * * * *
12867679 TTGTTTATCTGTGTGGCAAAATGGAATCGTCAAGAGTTAAACCAAATATTGTTACTTTCACCACC
1 TTGTTTATCTATGTGGCAAAATGGAACCGTGAAGAGTTAAGCCAAATACTATTACTTTCAACACC
* * ** *
12867744 TAGATTGATGCCTATTGTAAATTTCATCAACTTGATTATGACTTATTTCTTT-GGAGCAAAATGA
66 TGGATTGATGCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGGA-CAAAATGA
* * * *
12867808 TGAAGATAAGTTTTCAACTTACTATTTTATCGAAGGTGGGCTTGCGTTCTTAGGTTGGTGTCCTT
130 TGAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCTT
* * * *
12867873 GTTGGGCTTTTAGTTGAATTTTTGGATTTAGCCTAAGCTTGTTTTAGATTTGCTGCTTGTTTATA
195 GTTGGGCTTTTAGGTGAATTTTT-GATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTTGTTTATA
* * *
12867938 CTTTGTTCTATTTTTATTTTTTGGC-CA-AGCACACTTTATTTAT-AAAGTCTCAGGTTTTTACT
259 C-TT-TTCT-TTTTTGTTTTTTGGCTCAGA-CCCACTTTATTTATAAAAGTCTCA-GTTTTTAAT
* * * * * *
12868000 TCTATATATACAAAAAGCTAAAATGATTGAATTAATTAATGTAATGAAATTCAA-TGCATTTTTT
319 TCTTTATGTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAAGTGTATTTTTT
* * * * * * * *
12868064 TTAATTTTAGGGGTGCCTAGTTCATGGCAGCCC--CCTCATATATATGCTGTACCTATTTTCTCT
384 TTAATTTTAGGGG-GCCTGGGTCATGCCAACCCTTCCCCTTATATATGTTGCACCTATTTTCTCT
* * * * *
12868127 AATCTTCATCAATCCCTATTTCTCTTTCTCCGTTTCTCTTTCATATCTTACTTTTTCTCTACTTC
448 CATCTTCATCAATCCCTATTT-TCTTTCTCTGCTTCTCTTTCTTCTCTTA-TTTTTCTCTACTTC
* * * * * * * *
12868192 TTTTGCAATGTGTAAGCATTTTTTATTTTGTTATCCTTCACCCTCTTATTTTAGCAATATTACTA
511 TCTTGCAATGGGCAAGCCTTTTTTATTTCGTTA-ACTTCACCCTATTATTTTAAC-ATATTACTA
** * *
12868257 CAAAAAATTTTGATATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCTTAGCCTCACA
574 CAAAAGTTTTTGATATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCCTAACCTCACA
* *
12868322 ACTTTTTAATTCAATAAAAAATTAGCAGAACATGCTAGCAAGCACTAGTATGTCACAG
639 ACTTTTTAATTCAATCAGAAATTAGCAGAACATGCTAGCAAGCACTAGTATG-CACAG
* *
12868380 TTGTTTATCTATATGGCAAAATGGAACCGTGGAA-AGTTAAGTCAAATACTATTACTTTCAACAC
1 TTGTTTATCTATGTGGCAAAATGGAACCGT-GAAGAGTTAAGCCAAATACTATTACTTTCAACAC
* * *
12868444 TTGGATTAATCCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGGACAAAATGA
65 CTGGATTGATGCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGGACAAAATGA
* * * *
12868509 TGAAGATATGTTTTCAACTTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTCGATGTCCTT
130 TGAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCTT
* * * * *
12868574 GTTGGGGTTTTAGGTGAATTTTTTATTTAGCCTAGGCTTGTTTAAAATTAGCTGTTTGGTTATAC
195 GTTGGGCTTTTAGGTGAATTTTTGATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTTGTTTATAC
* * *
12868639 -TTT-TTTTTTGTTTTTTGGCTC-GACCCACTTTATTTATAAAACTCTCATGTTTTTATTTATTT
260 TTTTCTTTTTTGTTTTTTGGCTCAGACCCACTTTATTTATAAAAGTCTCA-GTTTTTAATTCTTT
* *
12868701 ATGTGCAAAAAGCTAAAAGAATTGAATTAATTAAAGTAATGAAATTCAAGTGTTTTTTTTTTAAT
324 ATGTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAAGTGTATTTTTTTTAAT
* * * *
12868766 TTTAGGGGGCCTGGGTCTTGCCAGCCCTTCCCCTTATATATGTTGCACCTATTTTCTCTTATTTT
389 TTTAGGGGGCCTGGGTCATGCCAACCCTTCCCCTTATATATGTTGCACCTATTTTCTCTCATCTT
* * * * * *
12868831 TATCAATCTCTATTTTTTTTCTTTGCTTCTCTTTCTTCTATTAATTTTCTCTACTTCTCTTGCAA
454 CATCAATCCCTATTTTCTTTCTCTGCTTCTCTTTCTTCTCTTATTTTTCTCTACTTCTCTTGCAA
** *
12868896 TGGGCAAGCCTTCATTATTTCGTCTAACTTCACCCTATTATTTTAATATTATTACTACAAAAGTT
519 TGGGCAAGCCTTTTTTATTTCGT-TAACTTCACCCTATTATTTTAACA-TATTACTACAAAAGTT
* * * *
12868961 TTTGATATATTTGAAAATTCAAATAAGATATGTAAAAACCAATATCCTAACCTCAAAATTTTTTA
582 TTTGATATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCCTAACCTCACAACTTTTTA
* * * * * *
12869026 ATTCAATCAGAAATTAGAAGAACATACCACCAAGCATTAGCATGCTACAG
647 ATTCAATCAGAAATTAGCAGAACATGCTAGCAAGCACTAGTATGC-ACAG
* * * * * * *
12869076 TTGTATATTTTATGTGGCAAAATGGAATCGTGGAGAGTTAAGCCAAATATTGTTACTTTTAACAC
1 TTGTTTA-TCTATGTGGCAAAATGGAACCGTGAAGAGTTAAGCCAAATACTATTACTTTCAACAC
* * ** *
12869141 CTGGATTGATGCCTA-TCGTAAGCTTCGTCAACTTAATTATGACTTATTTGTTTGGGGTAAAAGG
65 CTGGATTGATGCCTACT-GTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGGACAAAATG
* * ** *
12869205 ATGAAGATAAGTTTTTAACCTACTGTTTTATCGGACGTAAGCTTGGGTTCTTAGGTTTGTGTCCT
129 ATGAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCT
* * * * * * *
12869270 TGTTGGGCTTTTAGGTAAATTTTTTATTTTGTCTAGGATTGTTTTAAATTAGTTGCTTATTTTAT
194 TGTTGGGCTTTTAGGTGAATTTTTGATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTT-GTTTAT
* * * * * *
12869335 ACTTTGTTTTTTTTTGTTTTCT-GATCAGGCCCACTTTATTTATAAAAGTCTCAGGTTTTAACTC
258 AC-TT-TTCTTTTTTGTTTTTTGGCTCAGACCCACTTTATTTATAAAAGTCTCAGTTTTTAATTC
** *
12869399 TTT-TGTGC--AAA---AAAAGGATTGAATTAATTAATTTAATGAAATTTAAG-GTATTTTTTTT
321 TTTATGTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAAGTGTATTTTTTTT
* * * * * *
12869457 AATTTTAGCCGAGCATGGGTCATGCCAACTCTTCCCTTTATATATGTTGCAACTATTTTCTCTCA
386 AATTTTAG-GGGGCCTGGGTCATGCCAACCCTTCCCCTTATATATGTTGCACCTATTTTCTCTCA
* * *
12869522 TCTTCATCAATTCTTGTTTTTCTTTCTCTGCTTCTCTTTCTT
450 TCTTCATCAATCCCT-ATTTTCTTTCTCTGCTTCTCTTTCTT
12869564 TATCAATCCC
Statistics
Matches: 1586, Mismatches: 259, Indels: 83
0.82 0.13 0.04
Matches are distributed among these distances:
694 18 0.01
695 118 0.07
696 280 0.18
697 252 0.16
698 55 0.03
699 185 0.12
700 141 0.09
701 393 0.25
702 117 0.07
703 27 0.02
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (695 bp):
TTGTTTATCTATGTGGCAAAATGGAACCGTGAAGAGTTAAGCCAAATACTATTACTTTCAACACC
TGGATTGATGCCTACTGTAAGCTTCATCAACTTGATTATGACTTATTTGTTTGGGACAAAATGAT
GAAGATAAGTTTTCAACCTACTGTTTTATCGGAGGTGGGCTTGGGTTCTTAGGTTGGTGTCCTTG
TTGGGCTTTTAGGTGAATTTTTGATTTAGCCTAGGCTTGTTTTAAATTAGCTGCTTGTTTATACT
TTTCTTTTTTGTTTTTTGGCTCAGACCCACTTTATTTATAAAAGTCTCAGTTTTTAATTCTTTAT
GTGCAAAAAGCTAAAAGGATTGAATTAATTAAAGTAATGAAATTCAAGTGTATTTTTTTTAATTT
TAGGGGGCCTGGGTCATGCCAACCCTTCCCCTTATATATGTTGCACCTATTTTCTCTCATCTTCA
TCAATCCCTATTTTCTTTCTCTGCTTCTCTTTCTTCTCTTATTTTTCTCTACTTCTCTTGCAATG
GGCAAGCCTTTTTTATTTCGTTAACTTCACCCTATTATTTTAACATATTACTACAAAAGTTTTTG
ATATTTTTGAAAATTCAAATAAGATATGTAAAAACCCATATCCTAACCTCACAACTTTTTAATTC
AATCAGAAATTAGCAGAACATGCTAGCAAGCACTAGTATGCACAG
Found at i:12869570 original size:38 final size:38
Alignment explanation
Indices: 12869522--12869594 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
12869512 TTTTCTCTCA
* * * *
12869522 TCTTCATCAATTCTTGTTTTTCTTTCTCTGCTTCTCTT
1 TCTTCATCAATCCCTATTTTTCTTTCTCTACTTCTCTT
*
12869560 TCTTTATCAATCCCTATTTTTCTTTCTCTACTTCT
1 TCTTCATCAATCCCTATTTTTCTTTCTCTACTTCT
12869595 TTGCTTCTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.11, C:0.27, G:0.03, T:0.59
Consensus pattern (38 bp):
TCTTCATCAATCCCTATTTTTCTTTCTCTACTTCTCTT
Found at i:12871173 original size:42 final size:42
Alignment explanation
Indices: 12871036--12871219 Score: 219
Period size: 42 Copynumber: 4.4 Consensus size: 42
12871026 TGTATAAATA
** * *
12871036 GAAGACTCATGTCTCGGGATGAGCGTGAGATTATGTTTAAATT
1 GAAGACTCATGTCTCGAAAAGAGCGTGAGATTATGTTTAAA-G
* * * **
12871079 GAAGACTCGTGACTCGAAAAGAGCATGAGACAATG-TTAAAG
1 GAAGACTCATGTCTCGAAAAGAGCGTGAGATTATGTTTAAAG
*
12871120 GAAGACTCATGTCTCGAAAAAAGCGTGAGATTATGTTTAAAG
1 GAAGACTCATGTCTCGAAAAGAGCGTGAGATTATGTTTAAAG
*
12871162 GAATACTCATGTCTC-AGAAAGAGCGTGAGATTATGTTTAAAG
1 GAAGACTCATGTCTCGA-AAAGAGCGTGAGATTATGTTTAAAG
* *
12871204 GAAGATTTATGTCTCG
1 GAAGACTCATGTCTCG
12871220 GTAGAGTATA
Statistics
Matches: 118, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
41 30 0.25
42 61 0.52
43 27 0.23
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (42 bp):
GAAGACTCATGTCTCGAAAAGAGCGTGAGATTATGTTTAAAG
Found at i:12871246 original size:41 final size:41
Alignment explanation
Indices: 12871200--12871294 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
12871190 GATTATGTTT
* * *
12871200 AAAGGAAGATTTATGT-CTCGGT-AGAGTATAAGATTATTTAA
1 AAAGGAAGATTTAT-TACTCGATGA-AGCATAAGATCATTTAA
* *
12871241 AAAGGAAGACTTATTACTCGATGAAGCATAAGATCGTTTAA
1 AAAGGAAGATTTATTACTCGATGAAGCATAAGATCATTTAA
*
12871282 AGAGGAAGATTTA
1 AAAGGAAGATTTA
12871295 CAACTCTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
40 1 0.02
41 43 0.96
42 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (41 bp):
AAAGGAAGATTTATTACTCGATGAAGCATAAGATCATTTAA
Found at i:12875262 original size:41 final size:38
Alignment explanation
Indices: 12875162--12875265 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
12875152 TTCGAAGCAA
* *
12875162 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** * ** *
12875199 TAAAGTGGTACCCAATACCTCATCGAACCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
12875237 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
12875266 CTCAAGGTCG
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
37 20 0.40
38 11 0.22
40 2 0.04
41 17 0.34
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:12875362 original size:24 final size:23
Alignment explanation
Indices: 12875335--12875380 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12875325 TCAGCCCGGC
*
12875335 TAATTAATAGGGACTTTCAATTTA
1 TAATTAATA-GCACTTTCAATTTA
* *
12875359 TAATTCATATCACTTTCAATTT
1 TAATTAATAGCACTTTCAATTT
12875381 CAATTTCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (23 bp):
TAATTAATAGCACTTTCAATTTA
Found at i:12875413 original size:14 final size:13
Alignment explanation
Indices: 12875391--12875431 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
12875381 CAATTTCACT
12875391 TATTAAATATAAA
1 TATTAAATATAAA
12875404 TATCT-AA-ATAAA
1 TAT-TAAATATAAA
12875416 TATTAAATAATAAA
1 TATTAAAT-ATAAA
12875430 TA
1 TA
12875432 ATTTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 1 0.04
12 10 0.42
13 5 0.21
14 8 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:12875429 original size:18 final size:18
Alignment explanation
Indices: 12875394--12875432 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12875384 TTTCACTTAT
*
12875394 TAAATATAAATATCTAAA
1 TAAATATAAATATATAAA
12875412 TAAATATTAAATA-ATAAA
1 TAAATA-TAAATATATAAA
12875430 TAA
1 TAA
12875433 TTTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATATAAATATATAAA
Found at i:12880935 original size:21 final size:21
Alignment explanation
Indices: 12880909--12880961 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12880899 GAGTTTTTAA
**
12880909 TATCGGTAGAAGCATGTCTTG
1 TATCGGTAGAAGCAACTCTTG
* *
12880930 TTTCGGTAGAAGTAACTCTTG
1 TATCGGTAGAAGCAACTCTTG
12880951 TATCGGTAGAA
1 TATCGGTAGAA
12880962 CCATCTCAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (21 bp):
TATCGGTAGAAGCAACTCTTG
Found at i:12894309 original size:24 final size:23
Alignment explanation
Indices: 12894277--12894327 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
12894267 AAAACTACAC
* *
12894277 AAATCTGTCAGTGTAAATGTAATA
1 AAATCTGTCAGAGCAAAT-TAATA
12894301 TAAAT-TGTCAGAGCAAATTAATA
1 -AAATCTGTCAGAGCAAATTAATA
12894324 AAAT
1 AAAT
12894328 ATGAATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 5 0.21
24 11 0.46
25 4 0.17
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (23 bp):
AAATCTGTCAGAGCAAATTAATA
Found at i:12895886 original size:51 final size:51
Alignment explanation
Indices: 12895810--12895912 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
12895800 CTGCGACCAT
* *
12895810 AGCCCACTAGTGATAAGCCTCGTCCTTCAGTAGTGACGCAATACACCTTAC
1 AGCCCACCAGTGATAAGCCTCGTCCTTCAGTAGTGACGCAACACACCTTAC
*
12895861 AGCCCACCAGTGATAAGCCTCGTCCTTCAGTAGTGACGCAGCACACCTTAC
1 AGCCCACCAGTGATAAGCCTCGTCCTTCAGTAGTGACGCAACACACCTTAC
12895912 A
1 A
12895913 AAGTCTTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.21
Consensus pattern (51 bp):
AGCCCACCAGTGATAAGCCTCGTCCTTCAGTAGTGACGCAACACACCTTAC
Found at i:12897562 original size:61 final size:60
Alignment explanation
Indices: 12897423--12897662 Score: 338
Period size: 61 Copynumber: 4.0 Consensus size: 60
12897413 GTTTCACTTG
* * * * * * *
12897423 CATTTATTACTCACGATGACACAAAGTCATCGGACCT-TTGTTTGCATTGAAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCGTATAGGAACTCATTT
12897482 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTT-CGTATAGGAACTCATTT
* * *
12897543 CATTTAATACTCACAATGACATATAGTCATCGGATCTCTTGTTTCGTATAAGAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTG-TTCGTATAGGAACTCATTT
* *
12897604 CATTTAATACTCACGATGACATATAATCATCGGACCTCTTGCTTCGTATAGGAATTCAT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTG-TTCGTATAGGAACTCAT
12897663 ATACTCATGA
Statistics
Matches: 162, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
59 34 0.21
60 5 0.03
61 121 0.75
62 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (60 bp):
CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCGTATAGGAACTCATTT
Found at i:12903867 original size:24 final size:24
Alignment explanation
Indices: 12903826--12903872 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12903816 AAAACTACAC
* *
12903826 AAATCTGTCAGTGTAAATGTAATAT
1 AAATCTGTCAGAGCAAAT-TAATAT
12903851 AAAT-TGTCAGAGCAAATTAATA
1 AAATCTGTCAGAGCAAATTAATA
12903873 AAAGATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (24 bp):
AAATCTGTCAGAGCAAATTAATAT
Found at i:12906791 original size:17 final size:16
Alignment explanation
Indices: 12906771--12906817 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
12906761 ATATACATTA
12906771 AATTTTA-ATTTTAATTT
1 AATTTTATATTTT-A-TT
12906788 AATTTTTATATTTTATT
1 AA-TTTTATATTTTATT
12906805 AATTTTATTATTT
1 AATTTTA-TATTT
12906818 ATATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.19
17 11 0.41
18 6 0.22
19 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTTATATTTTATT
Found at i:12906794 original size:18 final size:17
Alignment explanation
Indices: 12906767--12906810 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
12906757 ATTAATATAC
*
12906767 ATTAAATTTTA-ATTTT
1 ATTAATTTTTATATTTT
12906783 AATTTAATTTTTATATTTT
1 -A-TTAATTTTTATATTTT
12906802 ATTAATTTT
1 ATTAATTTT
12906811 ATTATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.38
18 10 0.42
19 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTAATTTTTATATTTT
Found at i:12906818 original size:23 final size:23
Alignment explanation
Indices: 12906776--12906839 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
12906766 CATTAAATTT
* *
12906776 TAATTTTAATTTAATT-TTTATA
1 TAATATTAATTTTATTATTTATA
**
12906798 TTTTATTAATTTTATTATTTATA
1 TAATATTAATTTTATTATTTATA
12906821 TAATATT-ATTTTAATTATT
1 TAATATTAATTTT-ATTATT
12906840 GACGTGACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TAATATTAATTTTATTATTTATA
Found at i:12919986 original size:29 final size:28
Alignment explanation
Indices: 12919916--12920109 Score: 110
Period size: 29 Copynumber: 6.5 Consensus size: 28
12919906 TTAATATAGT
12919916 ATTTGGTACCTAAACTTGTCACTTTTT--TCTA
1 ATTTGGTACCTAAACTT-T---TTTTTGATC-A
*
12919947 ATTTGGTACTTAAACTTTTTTTTGACTCA
1 ATTTGGTACCTAAACTTTTTTTTGA-TCA
* * *
12919976 ATTTGGTACTTGAACTTGACATTTTTT-ATTA
1 ATTTGGTACCTAAACTT----TTTTTTGATCA
* *
12920007 ATTTGATACCTAAACTTTTTTTGGATCCA
1 ATTTGGTACCTAAACTTTTTTTTGAT-CA
* *
12920036 ATTTGGTACCTGAACTTGACATTTTTT-TTCTA
1 ATTTGGTACCTAAACTT----TTTTTTGATC-A
*
12920068 ATTTGGTACCTAAAC-TTTTTTAGATTCA
1 ATTTGGTACCTAAACTTTTTTTTGA-TCA
*
12920096 ATTTAGTACCTAAA
1 ATTTGGTACCTAAA
12920110 TTTATTAAAT
Statistics
Matches: 131, Mismatches: 16, Indels: 35
0.72 0.09 0.19
Matches are distributed among these distances:
27 15 0.11
28 16 0.12
29 35 0.27
30 3 0.02
31 34 0.26
32 17 0.13
33 11 0.08
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (28 bp):
ATTTGGTACCTAAACTTTTTTTTGATCA
Found at i:12920078 original size:61 final size:61
Alignment explanation
Indices: 12919916--12920106 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 61
12919906 TTAATATAGT
* * * * *
12919916 ATTTGGTACCTAAACTTGTCA-CTTTTTTCTAATTTGGTACTTAAACTTTTTTTTGA-CTCA
1 ATTTGGTACCTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGATC-CA
* * * *
12919976 ATTTGGTACTTGAACTTGACATTTTTTAT-TAATTTGATACCTAAACTTTTTTTGGATCCA
1 ATTTGGTACCTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGATCCA
*
12920036 ATTTGGTACCTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAAC-TTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGATCCA
*
12920096 ATTTAGTACCT
1 ATTTGGTACCT
12920107 AAATTTATTA
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
60 92 0.81
61 22 0.19
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (61 bp):
ATTTGGTACCTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGATCCA
Found at i:12920291 original size:31 final size:31
Alignment explanation
Indices: 12920256--12920388 Score: 91
Period size: 31 Copynumber: 4.4 Consensus size: 31
12920246 AAAAAAAATT
12920256 AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
1 AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
** *
12920287 AAGTACCAAATT-GGATCCCAA-A---AAGTTG
1 AAGTACCAAATTAGGA--AAAAGAGTCAAGTTC
** * *
12920315 AAGTACCAAATTAAAAAAAAAGTGTCAAGTTT
1 AAGTACCAAATT-AGGAAAAAGAGTCAAGTTC
* *
12920347 AGGTACCAAATTA-GAAAAAAATGTCAAGTTC
1 AAGTACCAAATTAGGAAAAAGA-GTCAAGTTC
12920378 ATA-TACCAAAT
1 A-AGTACCAAAT
12920389 GTTATATTAA
Statistics
Matches: 77, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
28 19 0.25
30 9 0.12
31 31 0.40
32 18 0.23
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.23
Consensus pattern (31 bp):
AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
Done.