Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 92 of 135
Found at i:28669567 original size:18 final size:18
Alignment explanation
Indices: 28669544--28669589 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28669534 ATTGCATTTG
** *
28669544 TTTTTATACTTTTATATT
1 TTTTTATAAATTTATAAT
28669562 TTTTTATAAATTTATAAT
1 TTTTTATAAATTTATAAT
28669580 TTTTTA-AAAT
1 TTTTTATAAAT
28669590 AATAATAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTATAAATTTATAAT
Found at i:28669568 original size:10 final size:10
Alignment explanation
Indices: 28669480--28669569 Score: 51
Period size: 10 Copynumber: 8.9 Consensus size: 10
28669470 TGCTTTTTAA
28669480 TTTTTTATAT
1 TTTTTTATAT
* *
28669490 ATTTATATA-
1 TTTTTTATAT
*
28669499 TTTTTTA-GT
1 TTTTTTATAT
28669508 TTTTTTATAAT
1 TTTTTTAT-AT
28669519 TTTTTATATAT
1 TTTTT-TATAT
* **
28669530 TTTAATTGCAT
1 TTT-TTTATAT
28669541 TTGTTTT-TAT
1 TT-TTTTATAT
**
28669551 ACTTTTATAT
1 TTTTTTATAT
28669561 TTTTTTATA
1 TTTTTTATA
28669570 AATTTATAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
9 16 0.28
10 19 0.33
11 18 0.31
12 5 0.09
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.70
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:28671422 original size:17 final size:18
Alignment explanation
Indices: 28671381--28671425 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
28671371 TAAGTTGGGT
*
28671381 TTTAAATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
* *
28671399 ATTAAATTTACTT-TAAG
1 TTTAAATTTACTTCTAAA
28671416 TTTAAATTTA
1 TTTAAATTTA
28671426 AATTCATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:28671452 original size:30 final size:30
Alignment explanation
Indices: 28671416--28671473 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
28671406 TTACTTTAAG
* *
28671416 TTTAAATTT-AAATTCATTTTTAAATTTAGT
1 TTTAAATTTGAAA-TAATTTTAAAATTTAGT
28671446 TTTAAATTTGAAATAATTTTAAAATTTA
1 TTTAAATTTGAAATAATTTTAAAATTTA
28671474 AAATTAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTAAATTTGAAATAATTTTAAAATTTAGT
Found at i:28673437 original size:29 final size:30
Alignment explanation
Indices: 28673404--28673600 Score: 223
Period size: 30 Copynumber: 6.7 Consensus size: 30
28673394 CCCTAAATTG
* *
28673404 TCCAAAAATTACGTTTTTACCCTC-GAACT
1 TCCAAAAATTACATTTTTACCCTCAAAACT
28673433 TCCAAAAATTACATTTTTAACCCT-AAAACT
1 TCCAAAAATTACATTTTT-ACCCTCAAAACT
*
28673463 TCCAAAAATTACATTTTTAACCTCAAAACT
1 TCCAAAAATTACATTTTTACCCTCAAAACT
28673493 TCCAAAAATTACA-TTTTACCC-CTAAAA-T
1 TCCAAAAATTACATTTTTACCCTC-AAAACT
*
28673521 TCTAAAAATTACATTTTTGACCC-CAAAACT
1 TCCAAAAATTACATTTTT-ACCCTCAAAACT
* ** *
28673551 TCCAAAAAATATGTTTTTACCC-CAAAATT
1 TCCAAAAATTACATTTTTACCCTCAAAACT
28673580 TCC-AAAATTACCA-TTTTACCC
1 TCCAAAAATTA-CATTTTTACCC
28673601 CCGAGAGTCC
Statistics
Matches: 147, Mismatches: 13, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
28 28 0.19
29 53 0.36
30 66 0.45
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.34
Consensus pattern (30 bp):
TCCAAAAATTACATTTTTACCCTCAAAACT
Found at i:28673549 original size:58 final size:59
Alignment explanation
Indices: 28673404--28673601 Score: 228
Period size: 58 Copynumber: 3.4 Consensus size: 59
28673394 CCCTAAATTG
* *
28673404 TCCAAAAATTACGTTTTTACCCTC-GAACTTCCAAAAATTACATTTTTAACCCTAAAACT
1 TCCAAAAATTACATTTTTACCC-CAAAACTTCCAAAAATTACATTTTTAACCCTAAAACT
* *
28673463 TCCAAAAATTACATTTTTAACCTCAAAACTTCCAAAAATTACA-TTTTACCCCTAAAA-T
1 TCCAAAAATTACATTTTT-ACCCCAAAACTTCCAAAAATTACATTTTTAACCCTAAAACT
* * ** * *
28673521 TCTAAAAATTACATTTTTGACCCCAAAACTTCCAAAAAATATGTTTTT-ACCCCAAAATT
1 TCCAAAAATTACATTTTT-ACCCCAAAACTTCCAAAAATTACATTTTTAACCCTAAAACT
28673580 TCC-AAAATTACCA-TTTTACCCC
1 TCCAAAAATTA-CATTTTTACCCC
28673602 CGAGAGTCCC
Statistics
Matches: 121, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
57 5 0.04
58 56 0.46
59 40 0.33
60 20 0.17
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTACATTTTTACCCCAAAACTTCCAAAAATTACATTTTTAACCCTAAAACT
Found at i:28673602 original size:29 final size:29
Alignment explanation
Indices: 28673404--28673631 Score: 189
Period size: 29 Copynumber: 7.8 Consensus size: 29
28673394 CCCTAAATTG
* * *
28673404 TCCAAAAATTACGTTTTTACCCTC-GAACT
1 TCCAAAAATTAC-ATTTTACCCCCAAAACT
* *
28673433 TCCAAAAATTACATTTTTAACCCTAAAACT
1 TCCAAAAATTACA-TTTTACCCCCAAAACT
* *
28673463 TCCAAAAATTACATTTTTAACCTCAAAACT
1 TCCAAAAATTACA-TTTTACCCCCAAAACT
*
28673493 TCCAAAAATTACATTTTACCCCTAAAA-T
1 TCCAAAAATTACATTTTACCCCCAAAACT
*
28673521 TCTAAAAATTACATTTTTGA-CCCCAAAACT
1 TCCAAAAATTACA-TTTT-ACCCCCAAAACT
* ** *
28673551 TCCAAAAAATATGTTTTTA-CCCCAAAATT
1 TCCAAAAATTA-CATTTTACCCCCAAAACT
* * *
28673580 TCC-AAAATTACCATTTTACCCCCGAGA-G
1 TCCAAAAATTA-CATTTTACCCCCAAAACT
*
28673608 TCCCAAAATTACCATTTTACCCCC
1 TCCAAAAATTA-CATTTTACCCCC
28673632 GAGCATCCAA
Statistics
Matches: 167, Mismatches: 24, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
28 27 0.16
29 80 0.48
30 60 0.36
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACATTTTACCCCCAAAACT
Found at i:28673642 original size:28 final size:28
Alignment explanation
Indices: 28673580--28673643 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 28
28673570 CCCCAAAATT
28673580 TCCAAAATTACCATTTTACCCCCGAGAG
1 TCCAAAATTACCATTTTACCCCCGAGAG
28673608 TCCCAAAATTACCATTTTACCCCCGAGCA-
1 T-CCAAAATTACCATTTTACCCCCGAG-AG
28673637 TCCAAAA
1 TCCAAAA
28673644 AGTATCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 7 0.21
29 26 0.76
30 1 0.03
ACGTcount: A:0.34, C:0.34, G:0.08, T:0.23
Consensus pattern (28 bp):
TCCAAAATTACCATTTTACCCCCGAGAG
Found at i:28673644 original size:29 final size:29
Alignment explanation
Indices: 28673583--28673663 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
28673573 CAAAATTTCC
*
28673583 AAAATTACCATTTTACCCCCGAGAGTCCC
1 AAAATTACCATTTTACCCCCGAGAGTCCA
28673612 AAAATTACCATTTTACCCCCGAGCA-TCCA
1 AAAATTACCATTTTACCCCCGAG-AGTCCA
* * *
28673641 AAAAGTATCATTTTTAACCCCGA
1 AAAATTACCA-TTTTACCCCCGA
28673664 TTGCATCGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 34 0.74
30 12 0.26
ACGTcount: A:0.35, C:0.31, G:0.09, T:0.26
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAGAGTCCA
Found at i:28675384 original size:119 final size:119
Alignment explanation
Indices: 28675173--28675409 Score: 465
Period size: 119 Copynumber: 2.0 Consensus size: 119
28675163 TCTTTATAAT
28675173 CATTTTCATCTACCGTAATCAAATTTGTCCACCATAATCAAATTTGTTATTAACTTTAATCACCT
1 CATTTTCATCTACCGTAATCAAATTTGTCCACCATAATCAAATTTGTTATTAACTTTAATCACCT
28675238 CATAATTTATTTATCAATCTTTTATATACGGTTAACTTCTTTACTTGCTTAGTC
66 CATAATTTATTTATCAATCTTTTATATACGGTTAACTTCTTTACTTGCTTAGTC
28675292 CATTTTCATCTACCGTAATCAAATTTGTCCACCATAATCAAATTTGTTATTAACTTTAATCACCT
1 CATTTTCATCTACCGTAATCAAATTTGTCCACCATAATCAAATTTGTTATTAACTTTAATCACCT
*
28675357 CATAATTTATTTATCAATCTTTTATATACGGTTAGCTTCTTTACTTGCTTAGT
66 CATAATTTATTTATCAATCTTTTATATACGGTTAACTTCTTTACTTGCTTAGT
28675410 TGCTTCAATT
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 117 1.00
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (119 bp):
CATTTTCATCTACCGTAATCAAATTTGTCCACCATAATCAAATTTGTTATTAACTTTAATCACCT
CATAATTTATTTATCAATCTTTTATATACGGTTAACTTCTTTACTTGCTTAGTC
Found at i:28676397 original size:20 final size:20
Alignment explanation
Indices: 28676374--28676412 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28676364 ATAATTTTAA
28676374 TATTAAA-TTAGATTTAATAC
1 TATTAAATTTA-ATTTAATAC
28676394 TATTAAATTTAATTTAATA
1 TATTAAATTTAATTTAATA
28676413 TTAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATTAAATTTAATTTAATAC
Found at i:28683091 original size:27 final size:29
Alignment explanation
Indices: 28683025--28683091 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
28683015 TTGCATTATG
*
28683025 TCATTAATGGCTATTATATATCTCTCCTTTA
1 TCATTATTGGCTATTATATA-CTCTCC-TTA
28683056 TCATTATTGGCTATTATATA-TCTCC-TA
1 TCATTATTGGCTATTATATACTCTCCTTA
28683083 TCATTATTG
1 TCATTATTG
28683092 CCATGACTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 11 0.31
29 5 0.14
31 19 0.54
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.49
Consensus pattern (29 bp):
TCATTATTGGCTATTATATACTCTCCTTA
Found at i:28686192 original size:20 final size:20
Alignment explanation
Indices: 28686131--28686184 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
28686121 CTTTTTCAAC
*
28686131 AAAAATTACAAAATAATTT-TC
1 AAAAATT-CAAAAT-ATTTATA
*
28686152 GAAAATTCAAAATATTTATA
1 AAAAATTCAAAATATTTATA
*
28686172 AAAAATTCCAAAT
1 AAAAATTCAAAAT
28686185 TTTCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.64
21 6 0.21
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAATTCAAAATATTTATA
Found at i:28687175 original size:123 final size:123
Alignment explanation
Indices: 28686956--28687202 Score: 485
Period size: 123 Copynumber: 2.0 Consensus size: 123
28686946 TCCAAGTTTT
28686956 TTTTACACAAATTGTGGTTTCCAAATAGACCTTAAATAAAATCATCAAACATTTTTTTTCTCTTT
1 TTTTACACAAATTGTGGTTTCCAAATAGACCTTAAATAAAATCATCAAACATTTTTTTTCTCTTT
28687021 CACCAAAACCTTCTTCAAGTCTATCGCAATGCCTCTCTTCTTTTGAATTTCTAACTAG
66 CACCAAAACCTTCTTCAAGTCTATCGCAATGCCTCTCTTCTTTTGAATTTCTAACTAG
28687079 TTTTACACAAATTGTGGTTTCCAAATAGACCTTAAATAAAATCATCAAACATTTTTTTTCTCTTT
1 TTTTACACAAATTGTGGTTTCCAAATAGACCTTAAATAAAATCATCAAACATTTTTTTTCTCTTT
*
28687144 CACCAAAACCTTCTTCAAGTTTATCGCAATGCCTCTCTTCTTTTGAATTTCTAACTAG
66 CACCAAAACCTTCTTCAAGTCTATCGCAATGCCTCTCTTCTTTTGAATTTCTAACTAG
28687202 T
1 T
28687203 GTCATGGGGT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (123 bp):
TTTTACACAAATTGTGGTTTCCAAATAGACCTTAAATAAAATCATCAAACATTTTTTTTCTCTTT
CACCAAAACCTTCTTCAAGTCTATCGCAATGCCTCTCTTCTTTTGAATTTCTAACTAG
Found at i:28690878 original size:71 final size:71
Alignment explanation
Indices: 28690785--28690924 Score: 199
Period size: 71 Copynumber: 2.0 Consensus size: 71
28690775 CTTAATGAAC
* ** *
28690785 TATCGGTAGAAGTACAGGGGAAATGAGAACTTAGCTACTAACTTGAGTTGTTTCGGAACAACTCA
1 TATCGGTAAAAGTACAAAGGAAAAGAGAACTTAGCTACTAACTTGAGTTGTTTCGGAACAACTCA
28690850 ACAAAG
66 ACAAAG
* * * * *
28690856 TATCGGTAAAAGTTCAAAGGAAAAGATATCTTGGCTACTGACTTGAGTTGTTTCGGAACAACTCA
1 TATCGGTAAAAGTACAAAGGAAAAGAGAACTTAGCTACTAACTTGAGTTGTTTCGGAACAACTCA
28690921 ACAA
66 ACAA
28690925 TGCATTGGTA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (71 bp):
TATCGGTAAAAGTACAAAGGAAAAGAGAACTTAGCTACTAACTTGAGTTGTTTCGGAACAACTCA
ACAAAG
Found at i:28690980 original size:71 final size:71
Alignment explanation
Indices: 28690818--28690973 Score: 240
Period size: 71 Copynumber: 2.2 Consensus size: 71
28690808 TGAGAACTTA
*
28690818 GCTACTAACTTGAGTTGTTTCGGAACAACTCAACAAAGTATCGGTAAAAGTTCAAAGGAAAAGAT
1 GCTACTAACTTGAGTTGTTTCGGAACAACTCAACAAAGCATCGGTAAAAGTTCAAAGGAAAAGAT
28690883 ATCTTG
66 ATCTTG
* * * * * * *
28690889 GCTACTGACTTGAGTTGTTTCGGAACAACTCAACAATGCATTGGTAGATGTTTAAGGGAAAAGAT
1 GCTACTAACTTGAGTTGTTTCGGAACAACTCAACAAAGCATCGGTAAAAGTTCAAAGGAAAAGAT
28690954 ATCTTG
66 ATCTTG
28690960 GCTACTAACTTGAG
1 GCTACTAACTTGAG
28690974 AGGTTTCAGT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 76 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (71 bp):
GCTACTAACTTGAGTTGTTTCGGAACAACTCAACAAAGCATCGGTAAAAGTTCAAAGGAAAAGAT
ATCTTG
Found at i:28704186 original size:13 final size:13
Alignment explanation
Indices: 28704154--28704185 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28704144 TCAAATAGCG
28704154 AATAAAATAAATA
1 AATAAAATAAATA
28704167 AATAAAATAAAT-
1 AATAAAATAAATA
28704179 AATAAAA
1 AATAAAA
28704186 AAGAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:28712866 original size:23 final size:24
Alignment explanation
Indices: 28712840--28712885 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
28712830 AAATAGATAT
*
28712840 TAATTAATG-AGGAATATA-AATAG
1 TAATAAATGTAGGAA-ATACAATAG
28712863 TAATAAATGTAGGAAATACAATA
1 TAATAAATGTAGGAAATACAATA
28712886 TGAGAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.28
Consensus pattern (24 bp):
TAATAAATGTAGGAAATACAATAG
Found at i:28714315 original size:50 final size:50
Alignment explanation
Indices: 28714214--28714885 Score: 561
Period size: 50 Copynumber: 13.5 Consensus size: 50
28714204 TTGTTGTTTG
* * * **
28714214 AATCTGCCCCTCT-CAGCTTTATGGGTATAAGA-TCTA-CTTTCGTAAATTC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTC-ACCTTT-GCAGCTTC
** * * * * * *
28714263 AATCTGCCTTTTTATAGCTTTAGGGGTGTAAGATTCCCCATTGCGGCATC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
* * *
28714313 AATCTGCCCTTCTACAGCTTTAGGGGTGTACGATTCGCCTTTGCAGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
** * * * *
28714363 AATCTATCCCTCTATAGCTTTAGGGGTATATGATTCGCCTTTGCAGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
* *
28714413 AATCTGCCCCTCTACAGCTTTAGTGGTGTAAGATTCACCTTTACAGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
* * * ***
28714463 AATCTGCCCCTCTACAGCTTTAGAGATATAAGATTCACCTTTATGGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
* * * * *
28714513 AATCTGCCCCTCTATAGCTTTAGCGGTGTAGGATTCACCTTTAC-GACTTT
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAG-CTTC
* * * *
28714563 AATCTGACCCTCTACAAG-TTTAGAGGTGTACGATTCACCTTTGCGGCTTC
1 AATCTGCCCCTCTAC-AGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
* * * * *
28714613 AATCTGCCCCTCTACAACTTTAGGGGAGTACGATTCATCTTTAC-GACTTC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAG-CTTC
* ** * * **
28714663 AATCTGTCCCCTATA-A-CTTTAAAGGTATACGATTTGCCTTTGCAGCTTC
1 AATCTG-CCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
* * * * * * *
28714712 AATCTACCCCTCTACAACTTTAGGGATGTACGATTCGCCTTTACGGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
* *** * * **
28714762 AATCTGCCCCTTTTTTGCTTTAGGGGTGTACGATTCGCCTTTGTGGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
* ** * **
28714812 AATATGCCCCTCTTTAGCTTTAGGGTTGTAAGATTTGCCTTTGCAGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
*
28714862 AATTTGCCCCTCTACTA-CTTTAGG
1 AATCTGCCCCTCTAC-AGCTTTAGG
28714886 ATTTGGTGTG
Statistics
Matches: 513, Mismatches: 97, Indels: 25
0.81 0.15 0.04
Matches are distributed among these distances:
48 7 0.01
49 42 0.08
50 448 0.87
51 16 0.03
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (50 bp):
AATCTGCCCCTCTACAGCTTTAGGGGTGTAAGATTCACCTTTGCAGCTTC
Found at i:28714386 original size:100 final size:100
Alignment explanation
Indices: 28714260--28714884 Score: 630
Period size: 100 Copynumber: 6.3 Consensus size: 100
28714250 CTTTCGTAAA
** * * * * * * * *
28714260 TTCAATCTGCCTTTTTATAGCTTTAGGGGTGTAAGATTCCCCATTGCGGCATCAATCTGCCCTTC
1 TTCAATCTGCCCCTCTATAGCTTTAGAGGTATACGATTCGCCTTTGCGGCTTCAATCTGCCCCTC
* *
28714325 TACAGCTTTAGGGGTGTACGATTCGCCTTTGCAGC
66 TACAGCTTTAGGGGTGTACGATTCACCTTTACAGC
** * * *
28714360 TTCAATCTATCCCTCTATAGCTTTAGGGGTATATGATTCGCCTTTGCAGCTTCAATCTGCCCCTC
1 TTCAATCTGCCCCTCTATAGCTTTAGAGGTATACGATTCGCCTTTGCGGCTTCAATCTGCCCCTC
* *
28714425 TACAGCTTTAGTGGTGTAAGATTCACCTTTACAGC
66 TACAGCTTTAGGGGTGTACGATTCACCTTTACAGC
* * * * **
28714460 TTCAATCTGCCCCTCTACAGCTTTAGAGATATAAGATTCACCTTTATGGCTTCAATCTGCCCCTC
1 TTCAATCTGCCCCTCTATAGCTTTAGAGGTATACGATTCGCCTTTGCGGCTTCAATCTGCCCCTC
* * *
28714525 TATAGCTTTAGCGGTGTAGGATTCACCTTTAC-GAC
66 TACAGCTTTAGGGGTGTACGATTCACCTTTACAG-C
* * * * *
28714560 TTTAATCTGACCCTCTACAAG-TTTAGAGGTGTACGATTCACCTTTGCGGCTTCAATCTGCCCCT
1 TTCAATCTGCCCCTCTA-TAGCTTTAGAGGTATACGATTCGCCTTTGCGGCTTCAATCTGCCCCT
* * *
28714624 CTACAACTTTAGGGGAGTACGATTCATCTTTAC-GAC
65 CTACAGCTTTAGGGGTGTACGATTCACCTTTACAG-C
* * * * * *
28714660 TTCAATCTGTCCC-CTATAACTTTAAAGGTATACGATTTGCCTTTGCAGCTTCAATCTACCCCTC
1 TTCAATCTGCCCCTCTATAGCTTTAGAGGTATACGATTCGCCTTTGCGGCTTCAATCTGCCCCTC
* * * *
28714724 TACAACTTTAGGGATGTACGATTCGCCTTTACGGC
66 TACAGCTTTAGGGGTGTACGATTCACCTTTACAGC
* * * * * * *
28714759 TTCAATCTGCCCCTTTTTTGCTTTAGGGGTGTACGATTCGCCTTTGTGGCTTCAATATGCCCCTC
1 TTCAATCTGCCCCTCTATAGCTTTAGAGGTATACGATTCGCCTTTGCGGCTTCAATCTGCCCCTC
** * * ** *
28714824 TTTAGCTTTAGGGTTGTAAGATTTGCCTTTGCAGC
66 TACAGCTTTAGGGGTGTACGATTCACCTTTACAGC
*
28714859 TTCAATTTGCCCCTCTACTA-CTTTAG
1 TTCAATCTGCCCCTCTA-TAGCTTTAG
28714885 GATTTGGTGT
Statistics
Matches: 437, Mismatches: 82, Indels: 12
0.82 0.15 0.02
Matches are distributed among these distances:
98 1 0.00
99 83 0.19
100 350 0.80
101 3 0.01
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (100 bp):
TTCAATCTGCCCCTCTATAGCTTTAGAGGTATACGATTCGCCTTTGCGGCTTCAATCTGCCCCTC
TACAGCTTTAGGGGTGTACGATTCACCTTTACAGC
Found at i:28714504 original size:150 final size:149
Alignment explanation
Indices: 28714214--28714885 Score: 638
Period size: 150 Copynumber: 4.5 Consensus size: 149
28714204 TTGTTGTTTG
* * ** * ** ** *
28714214 AATCTGCCCCTCT-CAGCTTTATGGGTATAAGA-TCTACTTTCGTAAATTCAATCTGCCTTTTTA
1 AATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCGCCTTT-GCAGCTTCAATCTGCCCCTCTA
* * * * * * *
28714277 TAGCTTTAGGGGTGTAAGATTCCCCATTGCGGCATCAATCTGCCCTTCTACAGCTTTAGGGGTGT
65 CAGCTTTA-GGGTGTAAGATTCACCTTTACGGCTTCAATCTGCCCCTCTACAGCTTTAGGGATGT
* * *
28714342 ACGATTCGCCTTTGCAGCTTC
129 ACGATTCACCTTTACGGCTTC
** *
28714363 AATCTATCCCTCTATAGCTTTAGGGGTATATGATTCGCCTTTGCAGCTTCAATCTGCCCCTCTAC
1 AATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCGCCTTTGCAGCTTCAATCTGCCCCTCTAC
* * *
28714428 AGCTTTAGTGGTGTAAGATTCACCTTTACAGCTTCAATCTGCCCCTCTACAGCTTTAGAGATATA
66 AGCTTTAG-GGTGTAAGATTCACCTTTACGGCTTCAATCTGCCCCTCTACAGCTTTAGGGATGTA
* *
28714493 AGATTCACCTTTATGGCTTC
130 CGATTCACCTTTACGGCTTC
* * * * * * *
28714513 AATCTGCCCCTCTATAGCTTTAGCGGTGTAGGATTCACCTTTAC-GACTTTAATCTGACCCTCTA
1 AATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCGCCTTTGCAG-CTTCAATCTGCCCCTCTA
* * *
28714577 CAAG-TTTAGAGGTGTACGATTCACCTTTGCGGCTTCAATCTGCCCCTCTACAACTTTAGGGGA-
65 C-AGCTTTAG-GGTGTAAGATTCACCTTTACGGCTTCAATCTGCCCCTCTACAGCTTTA-GGGAT
* *
28714640 GTACGATTCATCTTTACGACTTC
127 GTACGATTCACCTTTACGGCTTC
* * ** * * *
28714663 AATCTGTCCC-CTATAACTTTAAAGGTATACGATTTGCCTTTGCAGCTTCAATCTACCCCTCTAC
1 AATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCGCCTTTGCAGCTTCAATCTGCCCCTCTAC
* * * * *** *
28714727 AACTTTAGGGATGTACGATTCGCCTTTACGGCTTCAATCTGCCCCTTTTTTGCTTTAGGGGTGTA
66 AGCTTTAGGG-TGTAAGATTCACCTTTACGGCTTCAATCTGCCCCTCTACAGCTTTAGGGATGTA
* **
28714792 CGATTCGCCTTTGTGGCTTC
130 CGATTCACCTTTACGGCTTC
* * * * * *
28714812 AATATGCCCCTCTTTAGCTTTAGGGTTGTAAGATTTGCCTTTGCAGCTTCAATTTGCCCCTCTAC
1 AATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCGCCTTTGCAGCTTCAATCTGCCCCTCTAC
28714877 TA-CTTTAGG
66 -AGCTTTAGG
28714886 ATTTGGTGTG
Statistics
Matches: 426, Mismatches: 85, Indels: 23
0.80 0.16 0.04
Matches are distributed among these distances:
148 6 0.01
149 124 0.29
150 284 0.67
151 12 0.03
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (149 bp):
AATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCGCCTTTGCAGCTTCAATCTGCCCCTCTAC
AGCTTTAGGGTGTAAGATTCACCTTTACGGCTTCAATCTGCCCCTCTACAGCTTTAGGGATGTAC
GATTCACCTTTACGGCTTC
Found at i:28715935 original size:62 final size:62
Alignment explanation
Indices: 28715859--28715988 Score: 215
Period size: 62 Copynumber: 2.1 Consensus size: 62
28715849 CTCCCTTTTC
* *
28715859 TTTTTGCCAATTTGAGCCGCCCTTTACAGGTTTTCAACTCAAACTTTTGAGTTTTGAGAGTT
1 TTTTTTCCAATTTGAGCCGCCCTTTACAGGTTTTCAAATCAAACTTTTGAGTTTTGAGAGTT
* * *
28715921 TTTTTTCCAGTTTGAGCCGCCCTTTGCGGGTTTTCAAATCAAACTTTTGAGTTTTGAGAGTT
1 TTTTTTCCAATTTGAGCCGCCCTTTACAGGTTTTCAAATCAAACTTTTGAGTTTTGAGAGTT
28715983 TTTTTT
1 TTTTTT
28715989 AGGCAAAGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (62 bp):
TTTTTTCCAATTTGAGCCGCCCTTTACAGGTTTTCAAATCAAACTTTTGAGTTTTGAGAGTT
Found at i:28727473 original size:15 final size:15
Alignment explanation
Indices: 28727453--28727487 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
28727443 TCTCAACCTG
28727453 GCTCTCTAACAACTT
1 GCTCTCTAACAACTT
28727468 GCTCTCTAACAACTT
1 GCTCTCTAACAACTT
*
28727483 ACTCT
1 GCTCT
28727488 TTATGGCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.34, G:0.06, T:0.34
Consensus pattern (15 bp):
GCTCTCTAACAACTT
Found at i:28730460 original size:5 final size:5
Alignment explanation
Indices: 28730450--28730474 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28730440 ATTAAAACAC
28730450 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
28730475 TCATGATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:28730933 original size:15 final size:15
Alignment explanation
Indices: 28730915--28730960 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
28730905 AAATGTCATG
28730915 AAAATAAATAACAACA
1 AAAATAAATAACAA-A
*
28730931 AAAATAAA-CACACAA
1 AAAATAAATAACA-AA
28730946 AAAATAAATAA-AAA
1 AAAATAAATAACAAA
28730960 A
1 A
28730961 TTAAATGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 3 0.12
15 13 0.50
16 10 0.38
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAATAAATAACAAA
Found at i:28731986 original size:17 final size:19
Alignment explanation
Indices: 28731957--28731993 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28731947 GTAAAAACAA
28731957 TTGGGTCTTA-TTTTTATT
1 TTGGGTCTTATTTTTTATT
28731975 TTGGGT-TTATTTTTTATT
1 TTGGGTCTTATTTTTTATT
28731993 T
1 T
28731994 ATTGGTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.11, C:0.03, G:0.16, T:0.70
Consensus pattern (19 bp):
TTGGGTCTTATTTTTTATT
Found at i:28738467 original size:51 final size:51
Alignment explanation
Indices: 28738389--28738588 Score: 283
Period size: 51 Copynumber: 3.9 Consensus size: 51
28738379 TAAACGAAAG
*
28738389 GGTCCGATGACTAAGTGTTATCGTGAGTAAATGAATCCTTTACGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
* *
28738440 GGTCCGATGACTAAGGGTCATCTTGAGTAAATGAATCCTTTACGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
* * * * * *
28738491 GGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGAATTAAG
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
* * *
28738542 GGTCCGATGACTTAGTGTCATCGTGAGTATATGAATTCCTATACGGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGA
28738589 ACAAGGGGTC
Statistics
Matches: 129, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
51 123 0.95
52 6 0.05
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
Found at i:28755653 original size:50 final size:50
Alignment explanation
Indices: 28755578--28755673 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
28755568 AAAGGAGAAC
* ** *
28755578 CTAACACGATCATTCTGATTTTGAATAGCAGATGAGCTTAAACGTTTTGT
1 CTAACACGATCAATCTGATCCTGAATAGCAGACGAGCTTAAACGTTTTGT
* * *
28755628 CTAACTCGATCAATCTGATCCTGAATAGCTGGCGAGCTTAAACGTT
1 CTAACACGATCAATCTGATCCTGAATAGCAGACGAGCTTAAACGTT
28755674 CTATAGTCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (50 bp):
CTAACACGATCAATCTGATCCTGAATAGCAGACGAGCTTAAACGTTTTGT
Found at i:28770389 original size:15 final size:15
Alignment explanation
Indices: 28770358--28770405 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
28770348 AAATCTCCCA
28770358 ATCTTCATAG-TATTC
1 ATCTTCATAGATA-TC
28770373 ATCTTCATAGATATC
1 ATCTTCATAGATATC
* * *
28770388 ATCCTCGTAGATGTC
1 ATCTTCATAGATATC
28770403 ATC
1 ATC
28770406 ATCGTAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 27 0.93
16 2 0.07
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (15 bp):
ATCTTCATAGATATC
Found at i:28772583 original size:71 final size:71
Alignment explanation
Indices: 28772507--28772691 Score: 246
Period size: 71 Copynumber: 2.6 Consensus size: 71
28772497 ATGAAGTACA
* * * * *
28772507 GGTAGAAGTACAGGGGAAAGGAGACCTTAGCTACTGACTTGAGTTGTTTCT-GAACAACACAACA
1 GGTAGAAGTTCAGGGGAAAAGATATCTTGGCTACTGACTTGAGTTGTTT-TGGAACAACACAACA
28772571 AAGTATC
65 AAGTATC
* * *
28772578 GGTAGAAGTTCAGGGGAAAAGATATTTTGGCGACTGACTTGAGTTGTTTTGGAACAACTCAACAA
1 GGTAGAAGTTCAGGGGAAAAGATATCTTGGCTACTGACTTGAGTTGTTTTGGAACAACACAACAA
*
28772643 TGTATC
66 AGTATC
* * *
28772649 AGTAGATGTTCAAGGGAAAAGATATCTTGGCTACTGACTTGAG
1 GGTAGAAGTTCAGGGGAAAAGATATCTTGGCTACTGACTTGAG
28772692 AGGTTTCAGT
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
70 1 0.01
71 98 0.99
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (71 bp):
GGTAGAAGTTCAGGGGAAAAGATATCTTGGCTACTGACTTGAGTTGTTTTGGAACAACACAACAA
AGTATC
Found at i:28777691 original size:59 final size:59
Alignment explanation
Indices: 28777618--28777991 Score: 477
Period size: 59 Copynumber: 6.3 Consensus size: 59
28777608 TGACTTTAAA
* * *
28777618 GGGTAAAAAT-GTAATTTTTGGTGAAATTGGGGTCAAAAATGGGATTTTAGGAAA-TTCGG
1 GGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTT-GGAAAGTTTGG
** * *
28777677 GGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAGTGGGATTTTGGAAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTGG
* * *
28777736 GGGTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGTGATTTAGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTGG
* *
28777794 GGATAAAATGGTAA-TTTTGGTGAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTGG
* * * * *
28777853 GGGTAAAAAGGTAATTTTTGGTGAAAATCAGAGTTAAAAATGGTATTTTGGAAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTGG
* * * * * *
28777913 GGGCAAAATGGTAATTTTTGGTAAAATCGGGGTTAAGAATGGTATTTGGGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTGG
28777972 GGGTAAAATGGTAATTTTTG
1 GGGTAAAATGGTAATTTTTG
28777992 AACAGTCAAG
Statistics
Matches: 279, Mismatches: 32, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
58 70 0.25
59 149 0.53
60 60 0.22
ACGTcount: A:0.33, C:0.02, G:0.32, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTGG
Found at i:28777762 original size:117 final size:118
Alignment explanation
Indices: 28777617--28777991 Score: 501
Period size: 117 Copynumber: 3.2 Consensus size: 118
28777607 TTGACTTTAA
*
28777617 AGGGTAAAAAT-GTAATTTTTGGTGAAATTGGGGTCAAAAATGGGATTTTAGGAAA-TTCGGGGG
1 AGGGT-AAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTAGGAAAGTTCGGGGG
**
28777680 TAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAGTGGGATTTTGGAAAGTTTG
65 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAA-TGGGATTTTGGAAAGTTTG
* * *
28777735 AGGGTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGTGA-TTTAGGAAAGTTTGGGGAT
1 AGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTAGGAAAGTTCGGGGGT
28777798 AAAATGGTAA-TTTTGGTGAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTG
66 AAAATGGTAATTTTTGGTG-AAATCGGGGTT-AAAATGGGATTTTGGAAAGTTTG
* ** * *
28777852 AGGGTAAAAAGGTAATTTTTGGTGAAAATCAGAGTTAAAAATGGTATTTT-GGAAAGTTCGGGGG
1 AGGGTAAAATGGTAATTTTTGGTG-AAATTGGGGTTAAAAATGGGATTTTAGGAAAGTTCGGGGG
* * * * *
28777916 CAAAATGGTAATTTTTGGTAAAATCGGGGTTAAGAATGGTATTTGGGGAAGTTTG
65 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAA-AATGGGATTTTGGAAAGTTTG
*
28777971 GGGGTAAAATGGTAATTTTTG
1 AGGGTAAAATGGTAATTTTTG
28777992 AACAGTCAAG
Statistics
Matches: 227, Mismatches: 21, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
116 17 0.07
117 91 0.40
118 23 0.10
119 86 0.38
120 10 0.04
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.33
Consensus pattern (118 bp):
AGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTAGGAAAGTTCGGGGGT
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAGTTTG
Found at i:28777983 original size:28 final size:28
Alignment explanation
Indices: 28777653--28777989 Score: 152
Period size: 29 Copynumber: 11.5 Consensus size: 28
28777643 ATTGGGGTCA
*
28777653 AAAATGGGATTTTAGGAAA-TTCGGGGGT
1 AAAATGGTATTTT-GGAAAGTTCGGGGGT
* *
28777681 AAAATGGTAATTTTTGGTGAAA-TT-AGGGTT
1 AAAATGGT-A-TTTT-G-GAAAGTTCGGGGGT
* * *
28777711 AAAAGTGGGATTTTGGAAAGTTTGAGGGT
1 AAAA-TGGTATTTTGGAAAGTTCGGGGGT
*
28777740 AAAATGGTAATTTTGGTGAAA-TT-GGGGTT
1 AAAATGGT-ATTTT-G-GAAAGTTCGGGGGT
* * *
28777769 AAAAAT-GTGATTTAGGAAAGTTTGGGGAT
1 -AAAATGGT-ATTTTGGAAAGTTCGGGGGT
* *
28777798 AAAATGGTAATTTTGGTGAAA-ATCGGGGTT
1 AAAATGGT-ATTTT-G-GAAAGTTCGGGGGT
* * *
28777828 AAAAATGGGATTTTGGAAAGTTTGAGGGT
1 -AAAATGGTATTTTGGAAAGTTCGGGGGT
* * * * *
28777857 AAAAAGGTAATTTTTGGTGAAA-ATCAGAGTT
1 AAAATGGT-A-TTTT-G-GAAAGTTCGGGGGT
*
28777888 AAAAATGGTATTTTGGAAAGTTCGGGGGC
1 -AAAATGGTATTTTGGAAAGTTCGGGGGT
* *
28777917 AAAATGGTAATTTTTGGTAAA-ATCGGGGTT
1 AAAATGGT-A-TTTTGG-AAAGTTCGGGGGT
* * *
28777947 AAGAATGGTATTTGGGGAAGTTTGGGGGT
1 AA-AATGGTATTTTGGAAAGTTCGGGGGT
28777976 AAAATGGTAATTTT
1 AAAATGGT-ATTTT
28777990 TGAACAGTCA
Statistics
Matches: 233, Mismatches: 47, Indels: 57
0.69 0.14 0.17
Matches are distributed among these distances:
27 8 0.03
28 51 0.22
29 68 0.29
30 57 0.24
31 38 0.16
32 11 0.05
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (28 bp):
AAAATGGTATTTTGGAAAGTTCGGGGGT
Found at i:28780750 original size:200 final size:200
Alignment explanation
Indices: 28780415--28781218 Score: 1274
Period size: 200 Copynumber: 4.0 Consensus size: 200
28780405 CGCAATTATC
* *
28780415 TGTTTTAATTCACTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCAT
1 TGTTTTGATTCACTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCAT
* *
28780480 CAGGAAGCTAACCTTTTTATTGCTTCGTCCTGCTTCTCAGCAT-T-TCATCAAGAAGTCC-GGTT
66 CAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCA--ATGTCTCATCAGGAAG-CCGGGTT
* *
28780542 CAAAGATTTGCTCGCATTAAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACC
128 CGAAGATTTGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACC
28780607 GCCTCGCT
193 GCCTCGCT
* *
28780615 TGTTTTGATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTATATCTCAT
1 TGTTTTGATTCACTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCAT
*
28780680 CAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCCGGGTTCGA
66 CAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCCGGGTTCGA
* *
28780745 AGATTTGCTCGCATTGAGTGTTGAGTTGGTATTCTTCTCTATATCTCATCAGGAAGATGACCGCC
131 AGATTTGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCC
28780810 TCGCT
196 TCGCT
* *
28780815 TGTTTTGATTCGCTTCTCTGGATCTCCTCAAGAAGACGAATCTGGTCCACTTCTCTGTATCTCAT
1 TGTTTTGATTCACTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCAT
*
28780880 CAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTTCGA
66 CAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCCGGGTTCGA
* * * *
28780945 AGATTTGCTCTCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACTGCA
131 AGATTTGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCC
28781010 TCTG-T
196 TC-GCT
* * * * * *
28781015 TGTTTTTATTTACTTTTTTGGATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTGTATCTCAT
1 TGTTTTGATTCACTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCAT
* * **
28781080 TAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTTAATGTCTCATCAGGAAGTTGGGTTCGA
66 CAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCCGGGTTCGA
* *
28781145 AGATTTGCTCGCATTGAGCATTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATCACCGCC
131 AGATTTGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCC
28781210 TCGCT
196 TCGCT
28781215 TGTT
1 TGTT
28781219 GAACTACTCC
Statistics
Matches: 561, Mismatches: 38, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
198 1 0.00
199 4 0.01
200 555 0.99
201 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (200 bp):
TGTTTTGATTCACTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCAT
CAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCCGGGTTCGA
AGATTTGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCC
TCGCT
Found at i:28793401 original size:59 final size:60
Alignment explanation
Indices: 28793333--28793594 Score: 338
Period size: 59 Copynumber: 4.4 Consensus size: 60
28793323 TTGACTTTCG
*
28793333 GGGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAAGTGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
* *
28793392 GGGGTAAAATGGTAA-TTTTGGTGAAAATCGGGGTT-AAAATGGGATTTTAGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGTGAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
* * * * *
28793449 GAGGGTAAAAGGGAGGGTAATATTTGGTGAAAATCAGGGTTAAAAATGGTATTTTGGAATGTTTA
1 G-GGGT-AAA---ATGGTAATTTTTGGTGAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
* *
28793514 GGGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAAATGGTATTTGGGAAAGTTT-
1 GGGGTAAAATGGTAATTTTTGGTGAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
28793572 GAGGGTAAAATGGTAATTTTTGG
1 G-GGGTAAAATGGTAATTTTTGG
28793595 ACAGTCCAGG
Statistics
Matches: 178, Mismatches: 15, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
57 3 0.02
58 30 0.17
59 81 0.46
60 14 0.08
62 6 0.03
63 21 0.12
64 20 0.11
65 3 0.02
ACGTcount: A:0.32, C:0.02, G:0.33, T:0.33
Consensus pattern (60 bp):
GGGGTAAAATGGTAATTTTTGGTGAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
Found at i:28793503 original size:122 final size:122
Alignment explanation
Indices: 28793343--28793581 Score: 365
Period size: 122 Copynumber: 2.0 Consensus size: 122
28793333 GGGGTAAAAT
* * *
28793343 GGTAATTTTTGGTGAAATCGGGGTTAAAAGTGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAA-
1 GGTAATATTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAAT
*
28793407 TTTTGGTGAAAATCGGGGTT-AAAATGGGATTTTAGAAAGTTCGAGGGTAAAAGGGAG
66 TTTTGGTG-AAATCGGGGTTAAAAATGGGATTTGAGAAAGTTCGAGGGTAAAAGGGAG
* *
28793464 GGTAATATTTGGTGAAAATCAGGGTTAAAAATGGTATTTTGGAATGTTTAGGGGTAAAATGGTAA
1 GGTAATATTTGGTG-AAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAA
* * *
28793529 TTTTTGGTGAAATCGGGGTTAAAAATGGTATTTGGGAAAGTTTGAGGGTAAAA
65 TTTTTGGTGAAATCGGGGTTAAAAATGGGATTTGAGAAAGTTCGAGGGTAAAA
28793582 TGGTAATTTT
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
121 13 0.12
122 57 0.54
123 36 0.34
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.32
Consensus pattern (122 bp):
GGTAATATTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAAT
TTTTGGTGAAATCGGGGTTAAAAATGGGATTTGAGAAAGTTCGAGGGTAAAAGGGAG
Found at i:28793581 original size:28 final size:28
Alignment explanation
Indices: 28793491--28793586 Score: 74
Period size: 28 Copynumber: 3.3 Consensus size: 28
28793481 ATCAGGGTTA
* *
28793491 AAAATGGTATTTTGGAATGTTT-AGGGGT
1 AAAATGGTATTTGGGAAAGTTTGA-GGGT
*
28793519 AAAATGGTAATTTTTGGTGAAA--TCG-GGGTT
1 AAAATGGT-A--TTTGG-GAAAGTTTGAGGG-T
28793549 AAAAATGGTATTTGGGAAAGTTTGAGGGT
1 -AAAATGGTATTTGGGAAAGTTTGAGGGT
28793578 AAAATGGTA
1 AAAATGGTA
28793587 ATTTTTGGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
27 4 0.07
28 22 0.41
29 7 0.13
30 6 0.11
31 12 0.22
32 3 0.06
ACGTcount: A:0.33, C:0.01, G:0.31, T:0.34
Consensus pattern (28 bp):
AAAATGGTATTTGGGAAAGTTTGAGGGT
Found at i:28795631 original size:26 final size:26
Alignment explanation
Indices: 28795587--28795645 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
28795577 TTTTCATTAG
* *
28795587 ATTTAAATTCATTTCAAATATT-TTAA
1 ATTTAAATTAATTTCAAAT-TTAATAA
28795613 ATTTAAATTGAATTT-AAATTTAATAA
1 ATTTAAATT-AATTTCAAATTTAATAA
28795639 ATTTAAA
1 ATTTAAA
28795646 CCTAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 2 0.07
26 23 0.79
27 4 0.14
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTTAAATTAATTTCAAATTTAATAA
Found at i:28800772 original size:2 final size:2
Alignment explanation
Indices: 28800765--28800802 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28800755 TCACTATCTG
28800765 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28800803 TGATTAACTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28808029 original size:23 final size:22
Alignment explanation
Indices: 28807989--28808039 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28807979 TTTAAATTGT
* *
28807989 AATTTTTACAATACTAAAAATAA
1 AATTTTTAAAAAACT-AAAATAA
* *
28808012 AATTTTTAAAAAATTAAACTAA
1 AATTTTTAAAAAACTAAAATAA
28808034 AATTTT
1 AATTTT
28808040 ATATTTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTTTTAAAAAACTAAAATAA
Found at i:28808826 original size:17 final size:17
Alignment explanation
Indices: 28808771--28808827 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
28808761 TTTACTTGAA
*
28808771 AAAAAGTACTTTTCTCTC
1 AAAAA-TACTTTTATCTC
*
28808789 AAAAATAAC--TTAT-TT
1 AAAAAT-ACTTTTATCTC
28808804 AAAAATACTTTTATCTC
1 AAAAATACTTTTATCTC
28808821 AAAAATA
1 AAAAATA
28808828 TTTCTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 2 0.06
15 7 0.22
16 7 0.22
17 9 0.28
18 7 0.22
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (17 bp):
AAAAATACTTTTATCTC
Found at i:28819869 original size:7 final size:7
Alignment explanation
Indices: 28819857--28819894 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
28819847 TTTATTATTA
28819857 ACTGCAC
1 ACTGCAC
28819864 ACTGCAC
1 ACTGCAC
28819871 ACTGCAC
1 ACTGCAC
28819878 ACTGCAC
1 ACTGCAC
28819885 ACTGCAC
1 ACTGCAC
28819892 ACT
1 ACT
28819895 TCAGCTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.29, C:0.42, G:0.13, T:0.16
Consensus pattern (7 bp):
ACTGCAC
Found at i:28821174 original size:15 final size:16
Alignment explanation
Indices: 28821156--28821192 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28821146 TATATTACCA
*
28821156 TATTTA-ATATTTATT
1 TATTTATATATTTATG
28821171 TA-TTATATATTTATG
1 TATTTATATATTTATG
28821186 TATTTAT
1 TATTTAT
28821193 TACCGATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 12 0.63
16 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TATTTATATATTTATG
Found at i:28821599 original size:10 final size:11
Alignment explanation
Indices: 28821574--28821615 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
28821564 TGGTCTTTAA
28821574 AGATCTAGTCT
1 AGATCTAGTCT
*
28821585 AGATCTA-TTT
1 AGATCTAGTCT
*
28821595 AGATCTAGACCT
1 AGATCTAG-TCT
28821607 AGATCTAGT
1 AGATCTAGT
28821616 TTTTAAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 9 0.36
11 7 0.28
12 9 0.36
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (11 bp):
AGATCTAGTCT
Found at i:28822317 original size:29 final size:29
Alignment explanation
Indices: 28822276--28822435 Score: 135
Period size: 30 Copynumber: 5.4 Consensus size: 29
28822266 TATTTTGTTT
* * * *
28822276 AAAAATTATATTTTGACCCTTGAACTTCTC
1 AAAAA-TACATTTTGACCCCTAAACTTTTC
* *
28822306 AAAAATACATTTTGACTCCTAAATTTTTCC
1 AAAAATACATTTTGACCCCTAAACTTTT-C
* *
28822336 AAAATTACATTTTTACCCCTAAAC-TTTC
1 AAAAATACATTTTGACCCCTAAACTTTTC
* *
28822364 CAAAATACATTTTTACCCCTAAACTTTTC
1 AAAAATACATTTTGACCCCTAAACTTTTC
* * *
28822393 AAAAATCTCGTTTTGA-CCCTCGAACTTTTC
1 AAAAAT-ACATTTTGACCCCT-AAACTTTTC
* *
28822423 AAAATTATATTTT
1 AAAAATACATTTT
28822436 TCCCCTCGAA
Statistics
Matches: 105, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
28 23 0.22
29 37 0.35
30 45 0.43
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (29 bp):
AAAAATACATTTTGACCCCTAAACTTTTC
Found at i:28822381 original size:28 final size:28
Alignment explanation
Indices: 28822298--28822396 Score: 126
Period size: 28 Copynumber: 3.4 Consensus size: 28
28822288 TTGACCCTTG
* * *
28822298 AACTTCTCAAAAATACATTTTGACTCCTA
1 AACTT-TCCAAAATACATTTTTACCCCTA
*
28822327 AATTTTTCCAAAATTACATTTTTACCCCTA
1 AA-CTTTCCAAAA-TACATTTTTACCCCTA
28822357 AACTTTCCAAAATACATTTTTACCCCTA
1 AACTTTCCAAAATACATTTTTACCCCTA
*
28822385 AACTTTTCAAAA
1 AACTTTCCAAAA
28822397 ATCTCGTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
28 27 0.44
29 17 0.27
30 18 0.29
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.37
Consensus pattern (28 bp):
AACTTTCCAAAATACATTTTTACCCCTA
Found at i:28822419 original size:58 final size:58
Alignment explanation
Indices: 28822276--28822441 Score: 167
Period size: 58 Copynumber: 2.8 Consensus size: 58
28822266 TATTTTGTTT
* * * * * *
28822276 AAAAATTATATTTTGACCCTTGAACTTCTCAAAAATACATTTTGACTCCTAAATTTTTC
1 AAAAATTACATTTTGACCCTCGAACTT-TCCAAAATACATTTTTACCCCTAAACTTTTC
* * *
28822335 CAAAATTACATTTTTACCC-CTAAACTTTCCAAAATACATTTTTACCCCTAAACTTTTC
1 AAAAATTACATTTTGACCCTC-GAACTTTCCAAAATACATTTTTACCCCTAAACTTTTC
* * *
28822393 AAAAATCT-CGTTTTGACCCTCGAACTTTTCAAAATTATATTTTT-CCCCT
1 AAAAAT-TACATTTTGACCCTCGAACTTTCCAAAA-TACATTTTTACCCCT
28822442 CGAACATCCA
Statistics
Matches: 88, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
58 57 0.65
59 31 0.35
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (58 bp):
AAAAATTACATTTTGACCCTCGAACTTTCCAAAATACATTTTTACCCCTAAACTTTTC
Found at i:28822523 original size:30 final size:30
Alignment explanation
Indices: 28822475--28822553 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
28822465 TACCCTCCAA
28822475 TTTCCAAAAA-TC-ACATTTTAGACCTCAAAT
1 TTTCCAAAAATTCTA-ATTTTAGACCT-AAAT
* ** *
28822505 TTTCCAAAAGTT-TAATTTTATTCCTAATT
1 TTTCCAAAAATTCTAATTTTAGACCTAAAT
28822534 TTTCCAAAAATTCTAATTTT
1 TTTCCAAAAATTCTAATTTT
28822554 GATCCCCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
29 14 0.34
30 25 0.61
31 2 0.05
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTCCAAAAATTCTAATTTTAGACCTAAAT
Found at i:28828840 original size:37 final size:36
Alignment explanation
Indices: 28828790--28828869 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 36
28828780 TATTTTGCCT
* *
28828790 AAAAAAATGAGATGAAAA-TCCGCAAAGGGCGTCTTA
1 AAAAAAATAAGATGAAAACT-CGCAAAGGGCGTATTA
*
28828826 AAAAAAATTAAGATGAAAACTCGCAAAGGGTGTATTA
1 AAAAAAA-TAAGATGAAAACTCGCAAAGGGCGTATTA
28828863 AAAAAAA
1 AAAAAAA
28828870 AGATCGAGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
36 7 0.18
37 31 0.79
38 1 0.03
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (36 bp):
AAAAAAATAAGATGAAAACTCGCAAAGGGCGTATTA
Found at i:28829821 original size:49 final size:49
Alignment explanation
Indices: 28829734--28829854 Score: 127
Period size: 49 Copynumber: 2.4 Consensus size: 49
28829724 GAGAACCTAG
* *
28829734 TACCATGAAGAGATAAAGGGAAAGGTTAAGGCCTCAACGACAAACCCGA
1 TACCATGAAGATATGAAGGGAAAGGTTAAGGCCTCAACGACAAACCCGA
* * * * * *
28829783 TACCATGAAGATACGAAGGGAAAGGTTGAGG-TTGCAACGGCGAACCCGG
1 TACCATGAAGATATGAAGGGAAAGGTTAAGGCCT-CAACGACAAACCCGA
* *
28829832 TACCTAAGAAGATGTGAAGGGAA
1 TACC-ATGAAGATATGAAGGGAA
28829855 GGATTGAAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.02
49 43 0.73
50 15 0.25
ACGTcount: A:0.39, C:0.17, G:0.30, T:0.14
Consensus pattern (49 bp):
TACCATGAAGATATGAAGGGAAAGGTTAAGGCCTCAACGACAAACCCGA
Found at i:28829872 original size:50 final size:49
Alignment explanation
Indices: 28829749--28830510 Score: 324
Period size: 50 Copynumber: 15.3 Consensus size: 49
28829739 TGAAGAGATA
* ** * * * **
28829749 AAGGGAAAGGTTAAGGCCTCAACGACAAACCCGATACC-ATGAAGATACG
1 AAGGG-AAGGTTGAGGCAGCAACGGCGAACCCGATACCTAAGAAGATGTG
** *
28829798 AAGGGAAAGGTTGAGGTTGCAACGGCGAACCCGGTACCTAAGAAGATGTG
1 AAGGG-AAGGTTGAGGCAGCAACGGCGAACCCGATACCTAAGAAGATGTG
* * * *** *
28829848 AAGGGAAGGATTGAAGCAGGAACGGTGAGTTCGATACCTTAA-AAGATGCG
1 AAGGGAAGG-TTGAGGCAGCAACGGCGAACCCGATACC-TAAGAAGATGTG
* * * * *
28829898 ATGAGAAAGGTTGAGGCCA-TAACGGCGAACCCGGTACCTAAGAAGACGTG
1 AAG-GGAAGGTTGAGG-CAGCAACGGCGAACCCGATACCTAAGAAGATGTG
* * * * *
28829948 ATGGGAAAGGTTGAGGCCGCAATGACGAACTCGATACC-ATA-AAGA-GATG
1 AAGGG-AAGGTTGAGGCAGCAACGGCGAACCCGATACCTA-AGAAGATG-TG
* * * * * *
28829997 AAGGGAAGGATTGAGGTC-GCAAAGGCCAATCTGATACTTTAGAAGATGTG
1 AAGGGAAGG-TTGAGG-CAGCAACGGCGAACCCGATACCTAAGAAGATGTG
* * *
28830047 ATGGGAAAGGTTGAGGCTGCAACGACGAACCCGATACCTAAGAAGATGTG
1 AAGGG-AAGGTTGAGGCAGCAACGGCGAACCCGATACCTAAGAAGATGTG
* * *** *
28830097 AAGGGAAGGATTGAAGCCA-CAACGGTGAGTTCGGTACCTTAA-AAGAT-TCG
1 AAGGGAAGG-TTG-AGGCAGCAACGGCGAACCCGATACC-TAAGAAGATGT-G
* * * * * * * * **
28830147 ATGGGAAAGGTTGAGCCCGTAACAGCGAATCCGGTACCTAAAAAGACATG
1 AAGGG-AAGGTTGAGGCAGCAACGGCGAACCCGATACCTAAGAAGATGTG
* * * * * *
28830197 ATGGGAAAGGCTGAGGCCA-CAATGGTGAACCCGGTACC-ATGAAGA-GATG
1 AAGGG-AAGGTTGAGG-CAGCAACGGCGAACCCGATACCTAAGAAGATG-TG
* * * * * *
28830246 AAGGGAAGGATGGAGCCCA-CGATGGCGAAACCGATACCTTAA-AAGATGAG
1 AAGGGAAGG-TTGAG-GCAGCAACGGCGAACCCGATACC-TAAGAAGATGTG
* * ** *
28830296 ATGGGAAAGGTTGAGGCCGCAACAGGCGAAGTCGATACC-ATGAAGA-GATG
1 AAGGG-AAGGTTGAGGCAGCAAC-GGCGAACCCGATACCTAAGAAGATG-TG
** *
28830346 AAGGGAAAGGTTGAGGCAGCAACGGTTAACCCGATACCTAAGAAGATGCG
1 AAGGG-AAGGTTGAGGCAGCAACGGCGAACCCGATACCTAAGAAGATGTG
* * * * *
28830396 ATGGGAAAGGTTGAGGCCGCAATGGCAAACCC-AGTACC-ACAG-AGATATG
1 AAGGG-AAGGTTGAGGCAGCAACGGCGAACCCGA-TACCTA-AGAAGATGTG
* * * *
28830445 AAGGGAAAGGTTGAGGCCGTAACGGTGAACCC-AGTACCTCAGAAGATGTG
1 AAGGG-AAGGTTGAGGCAGCAACGGCGAACCCGA-TACCTAAGAAGATGTG
* *
28830495 ATGGGAAAGATTGAGG
1 AAGGG-AAGGTTGAGG
28830511 TCGTAACGGT
Statistics
Matches: 543, Mismatches: 127, Indels: 85
0.72 0.17 0.11
Matches are distributed among these distances:
48 9 0.02
49 171 0.31
50 316 0.58
51 47 0.09
ACGTcount: A:0.35, C:0.17, G:0.32, T:0.16
Consensus pattern (49 bp):
AAGGGAAGGTTGAGGCAGCAACGGCGAACCCGATACCTAAGAAGATGTG
Found at i:28830084 original size:199 final size:198
Alignment explanation
Indices: 28829648--28830094 Score: 452
Period size: 199 Copynumber: 2.3 Consensus size: 198
28829638 CATGAAGAGA
* * * * *
28829648 TGAAGGGAAGAATTGAGGCTGCAACAACTAATTCGATACCTTAAAAGATGTGATGGGAAAAGTAG
1 TGAAGGGAAGGATTGAGGCTGCAACGACGAATTCGATACCTTAAAAGATGCGATGAGAAAAGTAG
* * * * *
28829713 AGGTCGCAACGGAGAACCTAGTACCATGAAGAGATAAAGGGAAAGGTTAAGGCCTCAACGACAAA
66 AGGCCACAACGGAGAACCCAGTACCAAGAAGAGATAAAGGGAAAGGTTAAGGCCGCAACGACAAA
* * * * * *
28829778 CCCGATACCATGAAGATACGAAGGGAAAGGTTGAGGTTGCAACGGCGAACCCGGTACCTAAGAAG
131 CCCGATACCATAAAGAGACGAAGGGAAAGGTTGAGGTCGCAAAGGCCAACCCGATACCTAAGAAG
28829843 ATG
196 ATG
* * * ** * * *
28829846 TGAAGGGAAGGATTGAAGCAGGAACGGTGAGTTCGATACCTTAAAAGATGCGATGAGAAAGGTTG
1 TGAAGGGAAGGATTGAGGCTGCAACGACGAATTCGATACCTTAAAAGATGCGATGAGAAAAGTAG
* * * * * * * *
28829911 AGGCCATAACGGCGAACCCGGTACCTAAGAAGACG-TGATGGGAAAGGTTGAGGCCGCAATGACG
66 AGGCCACAACGGAGAACCCAGTACC-AAGAAGA-GATAAAGGGAAAGGTTAAGGCCGCAACGACA
* * * * * *
28829975 AACTCGATACCATAAAGAGATGAAGGG-AAGGATTGAGGTCGCAAAGGCCAATCTGATACTTTAG
129 AACCCGATACCATAAAGAGACGAAGGGAAAGG-TTGAGGTCGCAAAGGCCAACCCGATACCTAAG
28830039 AAGATG
193 AAGATG
* **
28830045 TGATGGGAAAGG-TTGAGGCTGCAACGACGAACCCGATACC-TAAGAAGATG
1 TGAAGGG-AAGGATTGAGGCTGCAACGACGAATTCGATACCTTAA-AAGATG
28830095 TGAAGGGAAG
Statistics
Matches: 197, Mismatches: 47, Indels: 9
0.78 0.19 0.04
Matches are distributed among these distances:
198 78 0.40
199 114 0.58
200 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.17
Consensus pattern (198 bp):
TGAAGGGAAGGATTGAGGCTGCAACGACGAATTCGATACCTTAAAAGATGCGATGAGAAAAGTAG
AGGCCACAACGGAGAACCCAGTACCAAGAAGAGATAAAGGGAAAGGTTAAGGCCGCAACGACAAA
CCCGATACCATAAAGAGACGAAGGGAAAGGTTGAGGTCGCAAAGGCCAACCCGATACCTAAGAAG
ATG
Found at i:28830097 original size:249 final size:249
Alignment explanation
Indices: 28829800--28830463 Score: 802
Period size: 249 Copynumber: 2.7 Consensus size: 249
28829790 AAGATACGAA
* *
28829800 GGGAAAGGTTGAGGTTGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAGGATTGAAGC
1 GGGAAAGGTTGAGGCTGCAACGGCGAACCCGATACCTAAGAAGATGTGAAGGGAAGGATTGAAGC
* * *
28829865 AGGAACGGTGAGTTCGATACCTTAAAAGATGCGATGAGAAAGGTTGAGGCCATAACGGCGAACCC
66 AGCAACGGTGAGTTCGATACCTTAAAAGATGCGATGGGAAAGGTTGAGGCCGTAACGGCGAACCC
* *
28829930 GGTACCTAAGAAGACGTGATGGGAAAGGTTGAGGCCGCAATGACGAACTCGATACCATAAAGAGA
131 GGTACCTAAGAAGACATGATGGGAAAGGTTGAGGCCGCAATGACGAACCCGATACCATAAAGAGA
* ** * * * * * *
28829995 TGAAGGGAAGGATTGAGGTCGCAAAGGCCAATCTGATACTTTAGAAGATGTGAT
196 TGAAGGGAAGGATGGAGCCCACAAAGGCCAAACCGATACCTTAAAAGATGAGAT
*
28830049 GGGAAAGGTTGAGGCTGCAACGACGAACCCGATACCTAAGAAGATGTGAAGGGAAGGATTGAAGC
1 GGGAAAGGTTGAGGCTGCAACGGCGAACCCGATACCTAAGAAGATGTGAAGGGAAGGATTGAAG-
* * * * *
28830114 CA-CAACGGTGAGTTCGGTACCTTAAAAGATTCGATGGGAAAGGTTGAGCCCGTAACAGCGAATC
65 CAGCAACGGTGAGTTCGATACCTTAAAAGATGCGATGGGAAAGGTTGAGGCCGTAACGGCGAACC
* * * ** * *
28830178 CGGTACCTAAAAAGACATGATGGGAAAGGCTGAGGCCACAATGGTGAACCCGGTACCATGAAGAG
130 CGGTACCTAAGAAGACATGATGGGAAAGGTTGAGGCCGCAATGACGAACCCGATACCATAAAGAG
* * *
28830243 ATGAAGGGAAGGATGGAGCCCACGATGGCGAAACCGATACCTTAAAAGATGAGAT
195 ATGAAGGGAAGGATGGAGCCCACAAAGGCCAAACCGATACCTTAAAAGATGAGAT
* ** *
28830298 GGGAAAGGTTGAGGCCGCAACAGGCGAAGTCGATACC-ATGAAGA-GATGAAGGGAAAGG-TTGA
1 GGGAAAGGTTGAGGCTGCAAC-GGCGAACCCGATACCTAAGAAGATG-TGAAGGG-AAGGATTGA
* * *** * * *
28830360 GGCAGCAACGGTTAACCCGATACC-TAAGAAGATGCGATGGGAAAGGTTGAGGCCGCAATGGCAA
63 AGCAGCAACGGTGAGTTCGATACCTTAA-AAGATGCGATGGGAAAGGTTGAGGCCGTAACGGCGA
* * *
28830424 ACCCAGTACC-ACAG-AGATATGAAGGGAAAGGTTGAGGCCG
127 ACCCGGTACCTA-AGAAGACATGATGGGAAAGGTTGAGGCCG
28830464 TAACGGTGAA
Statistics
Matches: 352, Mismatches: 56, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
248 29 0.08
249 305 0.87
250 18 0.05
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (249 bp):
GGGAAAGGTTGAGGCTGCAACGGCGAACCCGATACCTAAGAAGATGTGAAGGGAAGGATTGAAGC
AGCAACGGTGAGTTCGATACCTTAAAAGATGCGATGGGAAAGGTTGAGGCCGTAACGGCGAACCC
GGTACCTAAGAAGACATGATGGGAAAGGTTGAGGCCGCAATGACGAACCCGATACCATAAAGAGA
TGAAGGGAAGGATGGAGCCCACAAAGGCCAAACCGATACCTTAAAAGATGAGAT
Found at i:28830483 original size:99 final size:100
Alignment explanation
Indices: 28829611--28830510 Score: 394
Period size: 99 Copynumber: 9.1 Consensus size: 100
28829601 ACAAGGAAGC
* * *
28829611 TTGAGGCCGCAAC-GGCAAACCC-AGTACCATGAAGAGATGAAGGG-AAGAATTGAGGCTGCAAC
1 TTGAGGCCGCAACAGGCAAACCCGA-TACCAAGAAGAGATGAAGGGAAAG-GTTGAGGCAGCAAC
** ** * *
28829673 AACT-AATTCGATACCTTAA-AAGATGTGATGGGAAAAG
64 -GGTGAACCCGATACC-TAAGAAGATGAGATGGGAAAGG
* * * * * * **
28829710 TAGAGGTCGCAAC-GG-AGAA-CCTAGTACCATGAAGAGATAAAGGGAAAGGTTAAGGCCTCAAC
1 TTGAGGCCGCAACAGGCA-AACCCGA-TACCAAGAAGAGATGAAGGGAAAGGTTGAGGCAGCAAC
*** * *
28829772 GACAAACCCGATACC-ATGAAGAT-ACGAAGGGAAAGG
64 GGTGAACCCGATACCTAAGAAGATGA-GATGGGAAAGG
** * * * *
28829808 TTGAGGTTGCAAC-GGCGAACCCGGTACCTAAGAAGATG-TGAAGGG-AAGGATTGAAGCAGGAA
1 TTGAGGCCGCAACAGGCAAACCCGATACC-AAGAAGA-GATGAAGGGAAAGG-TTGAGGCAGCAA
*** * *
28829870 CGGTGAGTTCGATACCTTAA-AAGATGCGATGAGAAAGG
63 CGGTGAACCCGATACC-TAAGAAGATGAGATGGGAAAGG
** * * * * *
28829908 TTGAGGCCATAAC-GGCGAACCCGGTACCTAAGAAGACG-TGATGGGAAAGGTTGAGGCCGCAAT
1 TTGAGGCCGCAACAGGCAAACCCGATACC-AAGAAGA-GATGAAGGGAAAGGTTGAGGCAGCAAC
** *
28829971 GACGAACTCGATACCATAA-AGAGATGA-A-GGG-AAGG
64 GGTGAACCCGATACC-TAAGA-AGATGAGATGGGAAAGG
* * * * ** * *
28830006 ATTGAGGTCGCAA-AGGCCAATCTGATACTTTAGAAGATG-TGATGGGAAAGGTTGAGGCTGCAA
1 -TTGAGGCCGCAACAGGCAAACCCGATAC-CAAGAAGA-GATGAAGGGAAAGGTTGAGGCAGCAA
** * *
28830069 CGACGAACCCGATACCTAAGAAGATGTGAAGGG-AAGG
63 CGGTGAACCCGATACCTAAGAAGATGAGATGGGAAAGG
* * ** *** * * * * * *
28830106 ATTGAAGCCACAAC-GGTGAGTTCGGTACCTTAA-AAGA-TTCGATGGGAAAGGTTGAGCCCGTA
1 -TTGAGGCCGCAACAGGCAAACCCGATACC--AAGAAGAGAT-GAAGGGAAAGGTTGAGGCAGCA
* * * * * *
28830168 ACAGCGAATCCGGTACCTAAAAAGA-CATGATGGGAAAGG
62 ACGGTGAACCCGATACCTAAGAAGATGA-GATGGGAAAGG
* * * ** * * * * * *
28830207 CTGAGGCCACAA-TGGTGAACCCGGTACCATGAAGAGATGAAGGG-AAGGATGGAGCCCA-CGAT
1 TTGAGGCCGCAACAGGCAAACCCGATACCAAGAAGAGATGAAGGGAAAGG-TTGAG-GCAGCAAC
* *
28830269 GGCGAAACCGATACCTTAA-AAGATGAGATGGGAAAGG
64 GGTGAACCCGATACC-TAAGAAGATGAGATGGGAAAGG
* ** *
28830306 TTGAGGCCGCAACAGGCGAAGTCGATACCATGAAGAGATGAAGGGAAAGGTTGAGGCAGCAACGG
1 TTGAGGCCGCAACAGGCAAACCCGATACCAAGAAGAGATGAAGGGAAAGGTTGAGGCAGCAACGG
* *
28830371 TTAACCCGATACCTAAGAAGATGCGATGGGAAAGG
66 TGAACCCGATACCTAAGAAGATGAGATGGGAAAGG
* * * *
28830406 TTGAGGCCGCAA-TGGCAAACCC-AGTACCACAG-AGATATGAAGGGAAAGGTTGAGGCCGTAAC
1 TTGAGGCCGCAACAGGCAAACCCGA-TACCA-AGAAGAGATGAAGGGAAAGGTTGAGGCAGCAAC
* * *
28830468 GGTGAACCC-AGTACCTCAGAAGATGTGATGGGAAAGA
64 GGTGAACCCGA-TACCTAAGAAGATGAGATGGGAAAGG
28830505 TTGAGG
1 TTGAGG
28830511 TCGTAACGGT
Statistics
Matches: 623, Mismatches: 135, Indels: 86
0.74 0.16 0.10
Matches are distributed among these distances:
97 1 0.00
98 59 0.09
99 285 0.46
100 259 0.42
101 19 0.03
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.16
Consensus pattern (100 bp):
TTGAGGCCGCAACAGGCAAACCCGATACCAAGAAGAGATGAAGGGAAAGGTTGAGGCAGCAACGG
TGAACCCGATACCTAAGAAGATGAGATGGGAAAGG
Found at i:28830533 original size:99 final size:99
Alignment explanation
Indices: 28830280--28830671 Score: 357
Period size: 99 Copynumber: 4.0 Consensus size: 99
28830270 GCGAAACCGA
* * * * * *
28830280 TACCTTAA-AAGATGAGATGGGAAAGGTTGAGGCCGCAACAGGCGAAGTCGATACCATGAAGAGA
1 TACC-TAAGAAGATGCGATGGGAAAGATTGAGGCCGCAAC-GGCGAATTCAATACCAAGAAGATA
*
28830344 TGAAGGGAAAGGTTGAGGCAGCAACGGTTAACCC-G
64 TGAAGGGAAAGGTTGAGGCAGCAACGGTGAACCCAG
* * * ** *
28830379 ATACCTAAGAAGATGCGATGGGAAAGGTTGAGGCCGCAATGGCAAACCCAGTACCACAG-AGATA
1 -TACCTAAGAAGATGCGATGGGAAAGATTGAGGCCGCAACGGCGAATTCAATACCA-AGAAGATA
* *
28830443 TGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCAG
64 TGAAGGGAAAGGTTGAGGCAGCAACGGTGAACCCAG
* * * * * *
28830479 TACCTCAGAAGATGTGATGGGAAAGATTGAGGTCGTAACGGTGAATTCAATACCATGAAGATA--
1 TACCTAAGAAGATGCGATGGGAAAGATTGAGGCCGCAACGGCGAATTCAATACCAAGAAGATATG
* * * * ** *
28830542 AAGGGAAAGGATGATGCTGGAACGACGAACCTAG
66 AAGGGAAAGGTTGAGGCAGCAACGGTGAACCCAG
* * ** *
28830576 TACCTTAA-AAGATGCGATGGGAAGGATTGAGGTCGCAACAACGAATTCGATACCATA-AAGATA
1 TACC-TAAGAAGATGCGATGGGAAAGATTGAGGCCGCAACGGCGAATTCAATACCA-AGAAGATA
* * *
28830639 TGAAGGGAAAGGTTGAGGCTGCAATGGCGAACC
64 TGAAGGGAAAGGTTGAGGCAGCAACGGTGAACC
28830672 TAACACTTTA
Statistics
Matches: 239, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
97 77 0.32
98 3 0.01
99 124 0.52
100 35 0.15
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.17
Consensus pattern (99 bp):
TACCTAAGAAGATGCGATGGGAAAGATTGAGGCCGCAACGGCGAATTCAATACCAAGAAGATATG
AAGGGAAAGGTTGAGGCAGCAACGGTGAACCCAG
Found at i:28832957 original size:29 final size:29
Alignment explanation
Indices: 28832920--28833110 Score: 110
Period size: 29 Copynumber: 6.7 Consensus size: 29
28832910 ACCTCGAATT
*
28832920 TTTCC-AAAATTACATTTTTACCCTTAAC
1 TTTCCAAAAATTACATTTTTACCCTGAAC
* *
28832948 TTTCCAAAAATCACATTTTAACCCTCGAAC
1 TTTCCAAAAATTACATTTTTACCCT-GAAC
* *
28832978 TTT-CTAAAATTACATTTTTTCCCTCGAAC
1 TTTCCAAAAATTACATTTTTACCCT-GAAC
* * * *
28833007 -ATCTAAAAATTACCA-TTTTCCCCCGAAC
1 TTTCCAAAAATTA-CATTTTTACCCTGAAC
* * *
28833035 -ATCCAAAAATTACCATTTTTCCCCTAAAC
1 TTTCCAAAAATTA-CATTTTTACCCTGAAC
* * * * *
28833064 -ATCTAAAAGTTACCA-TTTTGCCCTTCAA-
1 TTTCCAAAAATTA-CATTTTTACCC-TGAAC
*
28833092 TTTCCAAAAATCACATTTT
1 TTTCCAAAAATTACATTTT
28833111 CGACCTCAAA
Statistics
Matches: 132, Mismatches: 23, Indels: 15
0.78 0.14 0.09
Matches are distributed among these distances:
28 33 0.25
29 91 0.69
30 8 0.06
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
TTTCCAAAAATTACATTTTTACCCTGAAC
Found at i:28832981 original size:30 final size:30
Alignment explanation
Indices: 28832894--28833006 Score: 99
Period size: 29 Copynumber: 3.9 Consensus size: 30
28832884 CTAAACTTCT
* * * *
28832894 CAAATATCAAATTTTGA-CCTCGAATTTTTC
1 CAAAAATCACATTTTTACCCTCGAA-CTTTC
* *
28832924 C-AAAATTACATTTTTACCCT-TAACTTTC
1 CAAAAATCACATTTTTACCCTCGAACTTTC
*
28832952 CAAAAATCACATTTTAACCCTCGAACTTT-
1 CAAAAATCACATTTTTACCCTCGAACTTTC
* * *
28832981 CTAAAATTACATTTTTTCCCTCGAAC
1 CAAAAATCACATTTTTACCCTCGAAC
28833007 ATCTAAAAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
28 5 0.07
29 52 0.78
30 10 0.15
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (30 bp):
CAAAAATCACATTTTTACCCTCGAACTTTC
Found at i:28833015 original size:58 final size:56
Alignment explanation
Indices: 28832865--28833110 Score: 167
Period size: 58 Copynumber: 4.2 Consensus size: 56
28832855 TGTTTTATTT
* * * * * *
28832865 AAAAATTACATTTTGACCCCTAAACTTCTCAAATATCA-AATTTTGACCTCGAATTTTTC
1 AAAAATTACATTTTTA-CCCTAAACATCT-AAAAATCACCATTTT-CCCTCGAA-CTTTC
* * * *
28832924 CAAAATTACATTTTTACCCTTAACTTTCCAAAAATCA-CATTTTAACCCTCGAACTTTC
1 AAAAATTACATTTTTACCCTAAAC-ATCTAAAAATCACCATTTT--CCCTCGAACTTTC
* * * * * * *
28832982 TAAAATTACATTTTTTCCCTCGAACATCTAAAAATTACCATTTTCCCCCGAACATCC
1 AAAAATTACATTTTTACCCT-AAACATCTAAAAATCACCATTTTCCCTCGAACTTTC
* * *
28833039 AAAAATTACCATTTTTCCCCTAAACATCTAAAAGTTACCATTTTGCCCTTC-AA-TTTCC
1 AAAAATTA-CATTTTTACCCTAAACATCTAAAAATCACCATTTT-CCC-TCGAACTTT-C
*
28833097 AAAAATCACATTTT
1 AAAAATTACATTTT
28833111 CGACCTCAAA
Statistics
Matches: 153, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
57 45 0.29
58 74 0.48
59 34 0.22
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (56 bp):
AAAAATTACATTTTTACCCTAAACATCTAAAAATCACCATTTTCCCTCGAACTTTC
Found at i:28833025 original size:28 final size:29
Alignment explanation
Indices: 28832969--28833087 Score: 129
Period size: 29 Copynumber: 4.1 Consensus size: 29
28832959 CACATTTTAA
*
28832969 CCCTCGAACTTTCT-AAAATTA-CATTTTTT
1 CCCTCGAAC-ATCTAAAAATTACCA-TTTTT
28832998 CCCTCGAACATCTAAAAATTACCA-TTTT
1 CCCTCGAACATCTAAAAATTACCATTTTT
* *
28833026 CCCCCGAACATCCAAAAATTACCATTTTT
1 CCCTCGAACATCTAAAAATTACCATTTTT
* * *
28833055 CCC-CTAAACATCTAAAAGTTACCATTTTG
1 CCCTC-GAACATCTAAAAATTACCATTTTT
28833084 CCCT
1 CCCT
28833088 TCAATTTCCA
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
28 30 0.38
29 46 0.59
30 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (29 bp):
CCCTCGAACATCTAAAAATTACCATTTTT
Found at i:28839529 original size:21 final size:21
Alignment explanation
Indices: 28839505--28839562 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
28839495 TAGAAGTAAG
* **
28839505 ACTTGTTTCGATAGATGAGTC
1 ACTTGTATCGATAGAACAGTC
* *
28839526 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGATAGAACAGTC
28839547 ACTTGTATCGATAGAA
1 ACTTGTATCGATAGAA
28839563 GTTTATACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (21 bp):
ACTTGTATCGATAGAACAGTC
Found at i:28847341 original size:41 final size:40
Alignment explanation
Indices: 28847296--28847387 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 40
28847286 ACAACATTTT
*
28847296 TAGCGGCGTTTGGACAAAAAACGCTACAAAAGGTAAAACAA
1 TAGCGGCGTTTGGAC-AAAAACGCCACAAAAGGTAAAACAA
* *** * * *
28847337 TAGCGACGTTTTTTCATAAACGCCGCAAAAGGTAAAGCAA
1 TAGCGGCGTTTGGACAAAAACGCCACAAAAGGTAAAACAA
*
28847377 TAGTGGCGTTT
1 TAGCGGCGTTT
28847388 ATAAGAAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
40 30 0.73
41 11 0.27
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (40 bp):
TAGCGGCGTTTGGACAAAAACGCCACAAAAGGTAAAACAA
Found at i:28847443 original size:41 final size:41
Alignment explanation
Indices: 28847372--28847628 Score: 300
Period size: 41 Copynumber: 6.2 Consensus size: 41
28847362 CAAAAGGTAA
* * * *
28847372 AGCAATAGTGGCGTTTATAAGAAAAACGCCGCTAAAGATCAG
1 AGCATTAGCGGCGTTTATGAG-AAAGCGCCGCTAAAGATCAG
*
28847414 AGCATTAGCGGCGTTTATGTGAAAGCGCCGCTAAA-AGTCAG
1 AGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGA-TCAG
* * *
28847455 AGCATTAGCGGCGTTTATGATAAAGCGCTGCTAAAGATCGG
1 AGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAG
** * * *
28847496 AGCATTAGCGATGTTTATGAGAAAGCGCCGTTAAAGGTCGG
1 AGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAG
* * ** * *
28847537 AGCATTAACGGCGTTTATGAGAAAGCGTCATTAAAGGTCAA
1 AGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAG
* *
28847578 AGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGTTCAA
1 AGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAG
28847619 AGCATTAGCG
1 AGCATTAGCG
28847629 ACGCTTTCTC
Statistics
Matches: 186, Mismatches: 27, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
40 1 0.01
41 167 0.90
42 18 0.10
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (41 bp):
AGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAG
Found at i:28847525 original size:123 final size:124
Alignment explanation
Indices: 28847384--28847629 Score: 332
Period size: 123 Copynumber: 2.0 Consensus size: 124
28847374 CAATAGTGGC
* * *
28847384 GTTTATAAGAAAAACGCCGCTAAAGATCAGAGCATTAGCGGCGTTTATGTGAAAGCGCCGCTAAA
1 GTTTATAAGAAAAACGCCGCTAAAGATCAGAGCATTAACGGCGTTTATGAGAAAGCGCCACTAAA
* * * **
28847449 AGTCAGAGCATTAGCGGCGTTTATGATAAAGCGCTGCTAAAGATCGGAGCATTAGCGAT
66 AGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAAAGCATTAGCGAT
* * * * * * *
28847508 GTTTATGAG-AAAGCGCCGTTAAAGGTCGGAGCATTAACGGCGTTTATGAGAAAGCGTCATTAAA
1 GTTTATAAGAAAAACGCCGCTAAAGATCAGAGCATTAACGGCGTTTATGAGAAAGCGCCACTAAA
* *
28847572 GGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGTTCAAAGCATTAGCGA
66 AGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAAAGCATTAGCGA
28847630 CGCTTTCTCA
Statistics
Matches: 105, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
123 97 0.92
124 8 0.08
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (124 bp):
GTTTATAAGAAAAACGCCGCTAAAGATCAGAGCATTAACGGCGTTTATGAGAAAGCGCCACTAAA
AGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAAAGCATTAGCGAT
Found at i:28847650 original size:41 final size:41
Alignment explanation
Indices: 28847324--28847656 Score: 188
Period size: 41 Copynumber: 8.1 Consensus size: 41
28847314 AAACGCTACA
* * * * * *
28847324 AAAGGT-AAAACAATAGCGACGTTTTTTCATAAA-CGCCGCA
1 AAAGGTCAAAGCATTAGCGACG-TTTATCAGAAAGCACCGCT
* * * * * *
28847364 AAAGGT-AAAGCAATAGTGGCGTTTATAAGAAAAACGCCGCT
1 AAAGGTCAAAGCATTAGCGACGTTTATCAG-AAAGCACCGCT
* * * ** *
28847405 AAAGATCAGAGCATTAGCGGCGTTTATGTGAAAGCGCCGCT
1 AAAGGTCAAAGCATTAGCGACGTTTATCAGAAAGCACCGCT
* * * * * * *
28847446 AAAAGTCAGAGCATTAGCGGCGTTTATGATAAAGCGCTGCT
1 AAAGGTCAAAGCATTAGCGACGTTTATCAGAAAGCACCGCT
* ** * * * *
28847487 AAAGATCGGAGCATTAGCGATGTTTATGAGAAAGCGCCGTT
1 AAAGGTCAAAGCATTAGCGACGTTTATCAGAAAGCACCGCT
** * * * ** **
28847528 AAAGGTCGGAGCATTAACGGCGTTTATGAGAAAGCGTCATT
1 AAAGGTCAAAGCATTAGCGACGTTTATCAGAAAGCACCGCT
* * *
28847569 AAAGGTCAAAGCATTAGCGGCGTTTATGAGAAAGCGCCGCT
1 AAAGGTCAAAGCATTAGCGACGTTTATCAGAAAGCACCGCT
* * *
28847610 AAAGTTCAAAGCATTAGCGACGCTTTCTCATAAA-CACCGCT
1 AAAGGTCAAAGCATTAGCGACG-TTTATCAGAAAGCACCGCT
28847651 AAAGGT
1 AAAGGT
28847657 TAAGCAATAG
Statistics
Matches: 243, Mismatches: 46, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
39 5 0.02
40 21 0.09
41 191 0.79
42 26 0.11
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (41 bp):
AAAGGTCAAAGCATTAGCGACGTTTATCAGAAAGCACCGCT
Found at i:28847654 original size:123 final size:122
Alignment explanation
Indices: 28847395--28847656 Score: 326
Period size: 123 Copynumber: 2.1 Consensus size: 122
28847385 TTTATAAGAA
* * * * *
28847395 AAACGCCGCTAAAGATCAGAGCATTAGCGGCGTTTATGTGAAAGCGCCGCTAAAAGTCAGAGCAT
1 AAACGCCGCTAAAGGTCAGAGCATTAACGGCGTTTATGAGAAAGCGCCACTAAAAGTCAAAGCAT
* * ** * *
28847460 TAGCGGCGTTTATGATAAAGCGCTGCTAAAGATCGGAGCATTAGCGATGTTTATGAG
66 TAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAAAGCATTAGCGACGTTTATCAG
* * * * *
28847517 AAAGCGCCGTTAAAGGTCGGAGCATTAACGGCGTTTATGAGAAAGCGTCATTAAAGGTCAAAGCA
1 AAA-CGCCGCTAAAGGTCAGAGCATTAACGGCGTTTATGAGAAAGCGCCACTAAAAGTCAAAGCA
* * *
28847582 TTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGTTCAAAGCATTAGCGACGCTTTCTCAT
65 TTAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAAAGCATTAGCGACG-TTTATCAG
*
28847641 AAACACCGCTAAAGGT
1 AAACGCCGCTAAAGGT
28847657 TAAGCAATAG
Statistics
Matches: 117, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
122 3 0.03
123 106 0.91
124 8 0.07
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (122 bp):
AAACGCCGCTAAAGGTCAGAGCATTAACGGCGTTTATGAGAAAGCGCCACTAAAAGTCAAAGCAT
TAGCGGCGTTTATGAGAAAGCGCCGCTAAAGATCAAAGCATTAGCGACGTTTATCAG
Found at i:28851007 original size:43 final size:43
Alignment explanation
Indices: 28850956--28851134 Score: 191
Period size: 43 Copynumber: 4.2 Consensus size: 43
28850946 GTTAATGTTG
* *
28850956 GCGGCGTTTGTGGGAAAAACGCCGCTAAAGAACATGTTCTATA
1 GCGGCGTTTGTGGGAAAAACGTCGCTAAAGAACATGGTCTATA
* *
28850999 GCGGCGTTTGTGGGAAAAACGTCGCTAAAGATCATGGTCTTTA
1 GCGGCGTTTGTGGGAAAAACGTCGCTAAAGAACATGGTCTATA
* * * *** * *
28851042 GCGGTGTTTGTGAGAGACGTGTCGTTAAAGAACATGGTCTTTA
1 GCGGCGTTTGTGGGAAAAACGTCGCTAAAGAACATGGTCTATA
* * *
28851085 GTGGCGTTTGTGGGAAAAACG-C-CTAAAGACCATGTTCTATA
1 GCGGCGTTTGTGGGAAAAACGTCGCTAAAGAACATGGTCTATA
**
28851126 ATGGCGTTT
1 GCGGCGTTT
28851135 TTTCACATAA
Statistics
Matches: 112, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
41 23 0.21
42 1 0.01
43 88 0.79
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTGTGGGAAAAACGTCGCTAAAGAACATGGTCTATA
Found at i:28852197 original size:23 final size:24
Alignment explanation
Indices: 28852171--28852218 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
28852161 TAGAAATTTC
28852171 AATCTTTAA-AAATTTGAT-TTTGT
1 AATC-TTAAGAAATTTGATGTTTGT
28852194 AATCTTAAGAAATTTGATGTTTGT
1 AATCTTAAGAAATTTGATGTTTGT
28852218 A
1 A
28852219 CGTGTGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.17
23 13 0.57
24 6 0.26
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.48
Consensus pattern (24 bp):
AATCTTAAGAAATTTGATGTTTGT
Found at i:28856044 original size:24 final size:24
Alignment explanation
Indices: 28856017--28856135 Score: 130
Period size: 24 Copynumber: 5.0 Consensus size: 24
28856007 ACATGTATGA
*
28856017 GTAAACGTATATAAGCTGACGAGT
1 GTAAACGTATATAAGCTGACGAGC
* ** *
28856041 GTAAACGTGTGCAAGCTGATGAGC
1 GTAAACGTATATAAGCTGACGAGC
* *
28856065 ATAAACGTATATAAGTTGACGAGC
1 GTAAACGTATATAAGCTGACGAGC
* **
28856089 GTAAACGTGTGCAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGC
* *
28856113 GTAAACGTAAATATGCTGACGAG
1 GTAAACGTATATAAGCTGACGAG
28856136 TGAAAATGTG
Statistics
Matches: 74, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (24 bp):
GTAAACGTATATAAGCTGACGAGC
Found at i:28856085 original size:48 final size:48
Alignment explanation
Indices: 28856018--28856137 Score: 186
Period size: 48 Copynumber: 2.5 Consensus size: 48
28856008 CATGTATGAG
*
28856018 TAAACGTATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGATGAGCA
1 TAAACGTATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGACGAGCA
* * *
28856066 TAAACGTATATAAGTTGACGAGCGTAAACGTGTGCAAGCTGACGAGCG
1 TAAACGTATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGACGAGCA
* *
28856114 TAAACGTAAATATGCTGACGAGTG
1 TAAACGTATATAAGCTGACGAGTG
28856138 AAAATGTGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (48 bp):
TAAACGTATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGACGAGCA
Found at i:28859142 original size:30 final size:31
Alignment explanation
Indices: 28859106--28859171 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
28859096 GCAAATGATT
28859106 TTAAAATTATTTTTTAAAAATA-TAAAATTA
1 TTAAAATTATTTTTTAAAAATATTAAAATTA
*
28859136 TTAAAATTATTTTTTTAAAATATTAAAATTA
1 TTAAAATTATTTTTTAAAAATATTAAAATTA
28859167 TTAAA
1 TTAAA
28859172 TAATTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 21 0.62
31 13 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TTAAAATTATTTTTTAAAAATATTAAAATTA
Found at i:28859153 original size:31 final size:30
Alignment explanation
Indices: 28859106--28859171 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 30
28859096 GCAAATGATT
28859106 TTAAAATTATTTTTTAAAA-ATATAAAATTA
1 TTAAAATTATTTTTTAAAATAT-TAAAATTA
28859136 TTAAAATTATTTTTTTAAAATATTAAAATTA
1 TTAAAATTA-TTTTTTAAAATATTAAAATTA
28859167 TTAAA
1 TTAAA
28859172 TAATTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 9 0.26
31 23 0.68
32 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAAAATTATTTTTTAAAATATTAAAATTA
Found at i:28859155 original size:14 final size:14
Alignment explanation
Indices: 28859104--28859156 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
28859094 CAGCAAATGA
28859104 TTTTAAAATTATTT
1 TTTTAAAATTATTT
* **
28859118 TTTAAAAATATAAAAT
1 TTTTAAAAT-T-ATTT
*
28859134 TATTAAAATTATTT
1 TTTTAAAATTATTT
28859148 TTTTAAAAT
1 TTTTAAAAT
28859157 ATTAAAATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
14 18 0.62
15 2 0.07
16 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAAAATTATTT
Found at i:28863970 original size:58 final size:60
Alignment explanation
Indices: 28863875--28863990 Score: 182
Period size: 58 Copynumber: 1.9 Consensus size: 60
28863865 TTTGGATGTT
*
28863875 ATTAAATTATATATTTTTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATG
1 ATTAAATTATATA-TTTTATTATTATTAAATTATATTTAATAATAATTATATTAAAATATG
* *
28863936 ATTAAATTAT-TA-TTTATTATTATTAAATTGTATTTAATAATAATTCTATTAAAAT
1 ATTAAATTATATATTTTATTATTATTAAATTATATTTAATAATAATTATATTAAAAT
28863991 TTAATAACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 40 0.77
60 2 0.04
61 10 0.19
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (60 bp):
ATTAAATTATATATTTTATTATTATTAAATTATATTTAATAATAATTATATTAAAATATG
Found at i:28864198 original size:15 final size:15
Alignment explanation
Indices: 28864160--28864207 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
28864150 GAATTATTAT
* *
28864160 TTCAGCTCTATTCCA
1 TTCAGTTCTATTCAA
*
28864175 TTACAGTTCTATTTAA
1 TT-CAGTTCTATTCAA
28864191 TTCAGTTCTATTCAA
1 TTCAGTTCTATTCAA
28864206 TT
1 TT
28864208 GCAACTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (15 bp):
TTCAGTTCTATTCAA
Found at i:28864382 original size:23 final size:23
Alignment explanation
Indices: 28864332--28864383 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
28864322 AAAATTCAAA
28864332 TAAATTATAAATTTTAAAATATT
1 TAAATTATAAATTTTAAAATATT
* * *
28864355 AAAATTA-AAATATTTTAAATTTT
1 TAAATTATAAAT-TTTAAAATATT
28864378 TAAATT
1 TAAATT
28864384 TTAATTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATTATAAATTTTAAAATATT
Found at i:28865136 original size:72 final size:71
Alignment explanation
Indices: 28865009--28865145 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 71
28864999 CTGTCTTTTC
* * ** * * *
28865009 AAAAAACAAAAGAAAACAGTGACTCTCAACACCCTTCATTTTCTTTTATATTAAAGTATTAAAAA
1 AAAAAAAAAAAGAAAACAGAGACTCTCAACACCCTTCATTTTCCCTCAAAATAAAGTATTAAAAA
28865074 TGGAAA
66 TGGAAA
* *
28865080 AAAAAAAAAAAGAAAACGAGAGATTCTCAACACTCTTCATTTTCCCTCAAAATAAAGTATTAAAA
1 AAAAAAAAAAAGAAAAC-AGAGACTCTCAACACCCTTCATTTTCCCTCAAAATAAAGTATTAAAA
28865145 A
65 A
28865146 AAAAAAAGAC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
71 16 0.29
72 40 0.71
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (71 bp):
AAAAAAAAAAAGAAAACAGAGACTCTCAACACCCTTCATTTTCCCTCAAAATAAAGTATTAAAAA
TGGAAA
Found at i:28865163 original size:59 final size:60
Alignment explanation
Indices: 28865081--28865203 Score: 176
Period size: 59 Copynumber: 2.1 Consensus size: 60
28865071 AAATGGAAAA
* *
28865081 AAAAAAAAAAGAAAACGAGAGATTCTCAACACTCTTCATTTTCCCTCAAAATAAAGTATT
1 AAAAAAAAAAGAAAACGAAAGATTCTCAACACCCTTCATTTTCCCTCAAAATAAAGTATT
* * * **
28865141 AAAAAAAAAA-AAGACGAAAGATTTTCAACACCCTTCATTTTCCCTCAAATTAGGGTATT
1 AAAAAAAAAAGAAAACGAAAGATTCTCAACACCCTTCATTTTCCCTCAAAATAAAGTATT
28865200 AAAA
1 AAAA
28865204 TAATAGGAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
59 46 0.82
60 10 0.18
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (60 bp):
AAAAAAAAAAGAAAACGAAAGATTCTCAACACCCTTCATTTTCCCTCAAAATAAAGTATT
Found at i:28866517 original size:17 final size:17
Alignment explanation
Indices: 28866469--28866517 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
28866459 AAACATCTTG
*
28866469 TTTAACAATATTTTTAT
1 TTTAAAAATATTTTTAT
*
28866486 TTTAAAATTAATTTTTA-
1 TTTAAAAAT-ATTTTTAT
*
28866503 TTTAAAAATACTTTT
1 TTTAAAAATATTTTT
28866518 GAGAAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 5 0.19
17 15 0.56
18 7 0.26
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAAAATATTTTTAT
Found at i:28866926 original size:18 final size:18
Alignment explanation
Indices: 28866904--28866968 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
28866894 TCATCCAGAT
28866904 TGGCGAGCTCACATAAAG
1 TGGCGAGCTCACATAAAG
* * * ** *
28866922 GGGCGAGTTCATAGCAAT
1 TGGCGAGCTCACATAAAG
*
28866940 TGACGAGCTCACATAAAG
1 TGGCGAGCTCACATAAAG
28866958 TGGCGAGCTCA
1 TGGCGAGCTCA
28866969 TTAATTTTGG
Statistics
Matches: 33, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.18
Consensus pattern (18 bp):
TGGCGAGCTCACATAAAG
Found at i:28868032 original size:12 final size:12
Alignment explanation
Indices: 28868015--28868080 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
28868005 ATTATGAAAT
28868015 ATAATTTAATAA
1 ATAATTTAATAA
*
28868027 ATAATTTAAT-C
1 ATAATTTAATAA
* *
28868038 ATATTTTAACATA
1 ATAATTTAATA-A
*
28868051 ATTA-TTAATAA
1 ATAATTTAATAA
28868062 ATACAATTTAATAA
1 AT--AATTTAATAA
28868076 ATAAT
1 ATAAT
28868081 ATATTATTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
11 11 0.27
12 18 0.44
13 3 0.07
14 9 0.22
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATTTAATAA
Found at i:28876388 original size:3 final size:3
Alignment explanation
Indices: 28876380--28876428 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
28876370 ACACACACAC
28876380 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
28876428 A
1 A
28876429 AGATTCAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:28877975 original size:30 final size:30
Alignment explanation
Indices: 28877941--28878002 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
28877931 ACTTATTTTA
**
28877941 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACCATTTTAGAGGCAT
*
28877971 TTGTTAGTTTTGTTACCATTTTAGAGGCAT
1 TTGTTAATTTTGTTACCATTTTAGAGGCAT
28878001 TT
1 TT
28878003 ATTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.55
Consensus pattern (30 bp):
TTGTTAATTTTGTTACCATTTTAGAGGCAT
Found at i:28880945 original size:24 final size:27
Alignment explanation
Indices: 28880893--28880948 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
28880883 GTTTGGATTA
28880893 TTTTTTTTATTTTAATTTTGGTTCAAGCT
1 TTTTTTTTATTTTAATTTT-GTT-AAGCT
28880922 TTTTTTTTATTTT-ATTTT-TT-AGCT
1 TTTTTTTTATTTTAATTTTGTTAAGCT
28880946 TTT
1 TTT
28880949 ACTTTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.26
26 2 0.07
28 5 0.19
29 13 0.48
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.73
Consensus pattern (27 bp):
TTTTTTTTATTTTAATTTTGTTAAGCT
Found at i:28884814 original size:29 final size:29
Alignment explanation
Indices: 28884782--28885035 Score: 181
Period size: 30 Copynumber: 8.6 Consensus size: 29
28884772 AGTTTCAGAT
*
28884782 AATTT-AGGATTAAAATGTAATTTTGGAA
1 AATTTGAGGGTTAAAATGTAATTTTGGAA
* * * *
28884810 GAATTCGAGGGTCAAAAGGTAATTTTATGAA
1 -AATTTGAGGGTTAAAATGTAATTTT-GGAA
* * * * *
28884841 AGTTT-AGGCTCAAAATGTGATTTTTGAA
1 AATTTGAGGGTTAAAATGTAATTTTGGAA
* * * *
28884869 AGGTTT-AAGGTTAAAATGTGATTTTAAGAA
1 A-ATTTGAGGGTTAAAATGTAATTTT-GGAA
*
28884899 ATTTTGAGGGTTAAAATGTAATTTTGGAGA
1 AATTTGAGGGTTAAAATGTAATTTTGGA-A
* * * *
28884929 AGTTTGGGGGTTAAAATATGATTTTGGAA
1 AATTTGAGGGTTAAAATGTAATTTTGGAA
* *
28884958 AAGTTTGGGGGATAAAATGTAATTTTGGAAA
1 AA-TTTGAGGGTTAAAATGTAATTTTGG-AA
* * *
28884989 AATTTGAGGGTGAAATTGTGATTTTGGAA
1 AATTTGAGGGTTAAAATGTAATTTTGGAA
* *
28885018 AGGTTTGGGGGTTAAAAT
1 A-ATTTGAGGGTTAAAAT
28885036 ATAGTTTTAA
Statistics
Matches: 181, Mismatches: 35, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
28 5 0.03
29 50 0.28
30 119 0.66
31 7 0.04
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
AATTTGAGGGTTAAAATGTAATTTTGGAA
Found at i:28884951 original size:60 final size:59
Alignment explanation
Indices: 28884791--28885035 Score: 219
Period size: 60 Copynumber: 4.1 Consensus size: 59
28884781 TAATTTAGGA
* * * * * *
28884791 TTAAAATGTAATTTTGGAAGAA-TTCGAGGGTCAAAAGGTAATTTTATGAAAGTTT-AGGC
1 TTAAAATGTAATTTTGG-AGAAGTTTGAGGGTTAAAATGTGATTTT-GGAAAGTTTGAGGG
* * * * * *
28884850 TCAAAATGTGATTTTTGA-AAGGTTT-AAGGTTAAAATGTGATTTTAAGAAATTTTGAGGG
1 TTAAAATGTAATTTTGGAGAA-GTTTGAGGGTTAAAATGTGATTTT-GGAAAGTTTGAGGG
* * *
28884909 TTAAAATGTAATTTTGGAGAAGTTTGGGGGTTAAAATATGATTTTGGAAAAGTTTGGGGG
1 TTAAAATGTAATTTTGGAGAAGTTTGAGGGTTAAAATGTGATTTTGG-AAAGTTTGAGGG
* * * * * *
28884969 ATAAAATGTAATTTTGGAAAAATTTGAGGGTGAAATTGTGATTTTGGAAAGGTTTGGGGG
1 TTAAAATGTAATTTTGGAGAAGTTTGAGGGTTAAAATGTGATTTTGGAAA-GTTTGAGGG
28885029 TTAAAAT
1 TTAAAAT
28885036 ATAGTTTTAA
Statistics
Matches: 151, Mismatches: 28, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
57 2 0.01
58 24 0.16
59 42 0.28
60 83 0.55
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (59 bp):
TTAAAATGTAATTTTGGAGAAGTTTGAGGGTTAAAATGTGATTTTGGAAAGTTTGAGGG
Found at i:28888641 original size:30 final size:30
Alignment explanation
Indices: 28888607--28888760 Score: 168
Period size: 30 Copynumber: 5.2 Consensus size: 30
28888597 ATTCTCTTTA
* *
28888607 AAAATCACATTTTAACCCATAAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
* * *
28888637 AAAATTACATTTTGACCCCTAAATTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
*
28888667 AAAATTTCATTTTAACCCTTAAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
* * * * * *
28888697 AAAATTATATTTTGATCTTTAAACTTCTCT
1 AAAATTACATTTTAACCCTTAAACTTTTCC
*
28888727 AAAATTACATTTTAACCC-CAAACTTCTT-C
1 AAAATTACATTTTAACCCTTAAACTT-TTCC
28888756 AAAAT
1 AAAAT
28888761 CACGTTTTGA
Statistics
Matches: 101, Mismatches: 22, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
29 11 0.11
30 90 0.89
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAACTTTTCC
Found at i:28888690 original size:60 final size:59
Alignment explanation
Indices: 28888607--28888826 Score: 194
Period size: 60 Copynumber: 3.7 Consensus size: 59
28888597 ATTCTCTTTA
* * *
28888607 AAAATCACATTTTAACCCATAAACTTTTCCAAAATTACATTTTGACCCCTAAATTTTTCC
1 AAAATTACATTTTAACCC-TAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTCTCC
* * * ** *
28888667 AAAATTTCATTTTAACCCTTAAACTTTTCCAAAATTATATTTTGATCTTTAAACTTCTCT
1 AAAATTACATTTTAACCC-TAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTCTCC
* * * * * *
28888727 AAAATTACATTTTAACCCCAAACTTCTT-CAAAATCACGTTTTGACTCC-GAACTTCTTC
1 AAAATTACATTTTAACCCTAAACTT-TTCCAAAATTACATTTTGACCCCTAAACTTCTCC
** * * * *
28888785 AAAATCGCATTTTGA-CCTCGAGCTTTCCCAAAATTACATTTT
1 AAAATTACATTTTAACCCT-AAACTTTTCCAAAATTACATTTT
28888827 CATCTCCAAA
Statistics
Matches: 126, Mismatches: 31, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
57 3 0.02
58 35 0.28
59 19 0.15
60 69 0.55
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (59 bp):
AAAATTACATTTTAACCCTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTCTCC
Found at i:28888759 original size:29 final size:30
Alignment explanation
Indices: 28888607--28888857 Score: 140
Period size: 30 Copynumber: 8.4 Consensus size: 30
28888597 ATTCTCTTTA
* *
28888607 AAAATCACATTTTAACCCATAAACTT-TTCC
1 AAAATTACATTTTAACCC-CAAACTTCTTCC
* *
28888637 AAAATTACATTTTGACCCCTAAA-TTTTTCC
1 AAAATTACATTTTAACCCC-AAACTTCTTCC
* *
28888667 AAAATTTCATTTTAACCCTTAAACTT-TTCC
1 AAAATTACATTTTAACCC-CAAACTTCTTCC
* * *** *
28888697 AAAATTATATTTTGATCTTTAAACTTC-TCT
1 AAAATTACATTTT-AACCCCAAACTTCTTCC
28888727 AAAATTACATTTTAACCCCAAACTTCTT-C
1 AAAATTACATTTTAACCCCAAACTTCTTCC
* * * * *
28888756 AAAATCACGTTTTGACTCCGAACTTCTT-C
1 AAAATTACATTTTAACCCCAAACTTCTTCC
** * * * * *
28888785 AAAATCGCATTTTGACCTCGAGCTT-TCCC
1 AAAATTACATTTTAACCCCAAACTTCTTCC
* *
28888814 AAAATTACATTTTCATCTCCAAAACTT-TTCC
1 AAAATTACATTTT-AAC-CCCAAACTTCTTCC
**
28888845 AATTTTACATTTT
1 AAAATTACATTTT
28888858 GATCCCATAG
Statistics
Matches: 171, Mismatches: 40, Indels: 19
0.74 0.17 0.08
Matches are distributed among these distances:
28 1 0.01
29 67 0.39
30 80 0.47
31 23 0.13
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAACTTCTTCC
Found at i:28895839 original size:14 final size:13
Alignment explanation
Indices: 28895818--28895847 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28895808 GGCTTTGTGT
*
28895818 AATTTTAAAGGAA
1 AATTTTTAAGGAA
28895831 AATTTTTAAGGAA
1 AATTTTTAAGGAA
28895844 AATT
1 AATT
28895848 CGTCCCCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
AATTTTTAAGGAA
Found at i:28896290 original size:153 final size:153
Alignment explanation
Indices: 28896086--28896387 Score: 462
Period size: 153 Copynumber: 2.0 Consensus size: 153
28896076 TAATTATAAG
* *
28896086 ATTGAAGAGTGTTTTGAAAACTTTTGAAAAGGATATCCGATTTGCATGAATTACGAAAATCACAC
1 ATTGAAGAGTGTTTCGAAAACTTTTGAAAAGGATATCCGATTCGCATGAATTACGAAAATCACAC
* *
28896151 TTAACACGTTAAAGCGCGATTCCTCGAAGTTTTTACACGAAAGGACATTGCCTCGTTTTAAAATT
66 TTAACACGTTAAAGCGCGATTCCTCGAAGTTTTCACACGAAAGGACATTGCCTCGCTTTAAAATT
*
28896216 ATTTGTGATATAGATATATAAAA
131 ATTTGTAATATAGATATATAAAA
* ** **
28896239 ATTGAAG-GATGTTTCGGAAACTTTTGAAGTGGATATTTGATTCGCATGAATTACGAAAATCACA
1 ATTGAAGAG-TGTTTCGAAAACTTTTGAAAAGGATATCCGATTCGCATGAATTACGAAAATCACA
* ** *
28896303 CTTAGCACGTTAAAGCGCGATTTTTCGAAGTTTTCACACGACAGGACATTGCCTCGCTTTAAAAT
65 CTTAACACGTTAAAGCGCGATTCCTCGAAGTTTTCACACGAAAGGACATTGCCTCGCTTTAAAAT
28896368 TATTTGTAATATAGATATAT
130 TATTTGTAATATAGATATAT
28896388 GTTTTGAGAA
Statistics
Matches: 134, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
152 1 0.01
153 133 0.99
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (153 bp):
ATTGAAGAGTGTTTCGAAAACTTTTGAAAAGGATATCCGATTCGCATGAATTACGAAAATCACAC
TTAACACGTTAAAGCGCGATTCCTCGAAGTTTTCACACGAAAGGACATTGCCTCGCTTTAAAATT
ATTTGTAATATAGATATATAAAA
Found at i:28897010 original size:59 final size:59
Alignment explanation
Indices: 28896938--28897494 Score: 659
Period size: 59 Copynumber: 9.5 Consensus size: 59
28896928 TGAGGTTAAG
*
28896938 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTT
* * *
28896997 AAAAAT-GAGATTTTGGAAAATTTTGGGGGTAAAAATGGTAATTTTAGGTGAAATCGAGGTT
1 AAAAATGGA-ATTTTGG-AAAGTTTAGGGGT-AAAATGGTAATTTTGGGTGAAATCGAGGTT
* *
28897058 AAAAATGGAATTTTGAAAAG-TTCGAGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTT
1 AAAAATGGAATTTTGGAAAGTTTAG-GGGTAAAATGGTAATTTTGGGTGAAATCGAGGTT
* * *
28897117 AAAAATAGG-ATTTTGGAAAGTTT-GAGGGTAAAACGGTAATTTTGGGTGAAATTGGGGTT
1 AAAAAT-GGAATTTTGGAAAGTTTAG-GGGTAAAATGGTAATTTTGGGTGAAATCGAGGTT
* * *
28897176 AAAAATGGGA-TTTGGAAAGTTTAGGGAT-AAATGGTAATTTT-TGTGAAATCGAGGTT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTT
* * * *
28897232 AAAAATGGAATTTAGGAAAGTTTATGGGTAAAACGGTAATTTTAGGTGAAATCGAGGTT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTT
* * *
28897291 AAAAATGGAATTTTGAAAAGTTT-GAGGGTAAAATGGTAATTTTGGGTAAAATTTG-GGTT
1 AAAAATGGAATTTTGGAAAGTTTAG-GGGTAAAATGGTAATTTTGGGTGAAA-TCGAGGTT
* * * * * *
28897350 AGAAATGGGATTTTGGAAAGTTTGAGGGGT-AAACGGTAATTTTAGGTGAAATCGGGGTC
1 AAAAATGGAATTTTGGAAAGTTT-AGGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTT
* * * * * *
28897409 AAAAATGAAATTTTAGAAAGTTTGGGGGTAAAATAGTAATTTTGGGTGGAATCAAGGTT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTT
* *
28897468 TAAAATGGAATTTTTGAAAGTTT-GGGG
1 AAAAATGGAATTTTGGAAAGTTTAGGGG
28897495 ACTAGAGAGT
Statistics
Matches: 428, Mismatches: 52, Indels: 37
0.83 0.10 0.07
Matches are distributed among these distances:
56 21 0.05
57 27 0.06
58 42 0.10
59 266 0.62
60 28 0.07
61 42 0.10
62 2 0.00
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.32
Consensus pattern (59 bp):
AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTT
Found at i:28897158 original size:29 final size:29
Alignment explanation
Indices: 28896939--28897453 Score: 180
Period size: 30 Copynumber: 17.6 Consensus size: 29
28896929 GAGGTTAAGA
28896939 AAAATGG-AATTTTGGAAAGTTT-AGGGGT
1 AAAATGGTAATTTTGGAAAGTTTGA-GGGT
* *
28896967 AAAATGGTAATTTTTGGTGAAA--TCGAGGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTTGAGGGT
* *
28896997 AAAAAT-G-AGATTTTGGAAAATTTTGGGGGT
1 -AAAATGGTA-ATTTTGG-AAAGTTTGAGGGT
* *
28897027 AAAAATGGTAATTTTAGGTGAAA--TCGAGGTT
1 -AAAATGGTAATTTT--G-GAAAGTTTGAGGGT
* *
28897058 AAAAATGG-AATTTTGAAAAGTTCGAGGGT
1 -AAAATGGTAATTTTGGAAAGTTTGAGGGT
* *
28897087 AAAATGGTAATTTTGGGTGAAA--TCGAGGTT
1 AAAATGGTAATTTT--G-GAAAGTTTGAGGGT
28897117 AAAAATAGG--ATTTTGGAAAGTTTGAGGGT
1 -AAAAT-GGTAATTTTGGAAAGTTTGAGGGT
*
28897146 AAAACGGTAATTTTGGGTGAAA--TTG-GGGTT
1 AAAATGGTAATTTT--G-GAAAGTTTGAGGG-T
*
28897176 AAAAATGG-GA-TTTGGAAAGTTT-AGGG-
1 -AAAATGGTAATTTTGGAAAGTTTGAGGGT
* *
28897202 ATAAATGGTAATTTTTGTGAAA--TCGAGGTT
1 A-AAATGGTAA-TTTTG-GAAAGTTTGAGGGT
*
28897232 AAAAATGG-AATTTAGGAAAGTTT-ATGGGT
1 -AAAATGGTAATTTTGGAAAGTTTGA-GGGT
* * *
28897261 AAAACGGTAATTTTAGGTGAAA--TCGAGGTT
1 AAAATGGTAATTTT--G-GAAAGTTTGAGGGT
*
28897291 AAAAATGG-AATTTTGAAAAGTTTGAGGGT
1 -AAAATGGTAATTTTGGAAAGTTTGAGGGT
* *
28897320 AAAATGGTAATTTTGGGTAAAATTTG-GGTT
1 AAAATGGTAATTTT-GG-AAAGTTTGAGGGT
*
28897350 AGAAATGG-GATTTTGGAAAGTTTGAGGGGT
1 A-AAATGGTAATTTTGGAAAGTTTGA-GGGT
* *
28897380 -AAACGGTAATTTTAGGTGAAA--TCG-GGGT
1 AAAATGGTAATTTT--G-GAAAGTTTGAGGGT
* * *
28897408 CAAAAAT-GAAATTTTAGAAAGTTTGGGGGT
1 --AAAATGGTAATTTTGGAAAGTTTGAGGGT
*
28897438 AAAATAGTAATTTTGG
1 AAAATGGTAATTTTGG
28897454 GTGGAATCAA
Statistics
Matches: 370, Mismatches: 46, Indels: 141
0.66 0.08 0.25
Matches are distributed among these distances:
25 1 0.00
26 10 0.03
27 23 0.06
28 70 0.19
29 84 0.23
30 90 0.24
31 65 0.18
32 22 0.06
33 4 0.01
34 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTTGAGGGT
Found at i:28897320 original size:233 final size:236
Alignment explanation
Indices: 28896938--28897494 Score: 797
Period size: 233 Copynumber: 2.4 Consensus size: 236
28896928 TGAGGTTAAG
28896938 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT-GTGAAATCGAGGTTAAAAAT
* *
28897003 -GAGATTTTGGAAAATTTTGGGGGTAAAAATGGTAATTTTAGGTGAAATCGAGGTTAAAAATGGA
65 GGA-ATTTTGGAAAGTTTT-GGGGTAAAAACGGTAATTTTAGGTGAAATCGAGGTTAAAAATGGA
*
28897067 ATTTTGAAAAGTTCGAGGGTAAAATGGTAATTTTGGGTGAAA-TCGAGGTTAAAAATAGGATTTT
128 ATTTTGAAAAGTTCGAGGGTAAAATGGTAATTTTGGGTAAAATTCG-GGTTAAAAATAGGATTTT
* * *
28897131 GGAAAGTTTGA-GGGTAAAACGGTAATTTTGGGTGAAATTGGGGTT
192 GGAAAGTTTGAGGGGT-AAACGGTAATTTTAGGTGAAATCGGGGTC
* *
28897176 AAAAATGGGA-TTTGGAAAGTTTAGGGAT-AAATGGTAATTTTTGTGAAATCGAGGTTAAAAATG
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGTGAAATCGAGGTTAAAAATG
*
28897239 GAATTTAGGAAAGTTTAT-GGGT-AAAACGGTAATTTTAGGTGAAATCGAGGTTAAAAATGGAAT
66 GAATTTTGGAAAGTTT-TGGGGTAAAAACGGTAATTTTAGGTGAAATCGAGGTTAAAAATGGAAT
* * * *
28897302 TTTGAAAAGTTTGAGGGTAAAATGGTAATTTTGGGTAAAATTTGGGTTAGAAATGGGATTTTGGA
130 TTTGAAAAGTTCGAGGGTAAAATGGTAATTTTGGGTAAAATTCGGGTTAAAAATAGGATTTTGGA
28897367 AAGTTTGAGGGGTAAACGGTAATTTTAGGTGAAATCGGGGTC
195 AAGTTTGAGGGGTAAACGGTAATTTTAGGTGAAATCGGGGTC
* * * * * * * *
28897409 AAAAATGAAATTTTAGAAAGTTTGGGGGTAAAATAGTAATTTTGGGTGGAATCAAGGTTTAAAAT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTT-TGTGAAATCGAGGTTAAAAAT
*
28897474 GGAATTTTTGAAAG-TTTGGGG
65 GGAATTTTGGAAAGTTTTGGGG
28897495 ACTAGAGAGT
Statistics
Matches: 286, Mismatches: 25, Indels: 19
0.87 0.08 0.06
Matches are distributed among these distances:
233 139 0.49
234 26 0.09
235 49 0.17
236 46 0.16
237 17 0.06
238 9 0.03
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.32
Consensus pattern (236 bp):
AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGTGAAATCGAGGTTAAAAATG
GAATTTTGGAAAGTTTTGGGGTAAAAACGGTAATTTTAGGTGAAATCGAGGTTAAAAATGGAATT
TTGAAAAGTTCGAGGGTAAAATGGTAATTTTGGGTAAAATTCGGGTTAAAAATAGGATTTTGGAA
AGTTTGAGGGGTAAACGGTAATTTTAGGTGAAATCGGGGTC
Found at i:28899474 original size:17 final size:17
Alignment explanation
Indices: 28899454--28899498 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
28899444 TTTTAAATGT
28899454 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
28899471 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
*
28899487 ATTTAAAATTAA
1 ATTTAAATTTAA
28899499 TTCAAACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:28899500 original size:27 final size:27
Alignment explanation
Indices: 28899438--28899500 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28899428 TTTAAGTTTC
* **
28899438 AAATTATTTTAAATGTATTTAAATTTA
1 AAATTAATTTAAATGTAAATAAATTTA
** *
28899465 AAACAAATTTAAATTTAAATAAATTTA
1 AAATTAATTTAAATGTAAATAAATTTA
28899492 AAATTAATT
1 AAATTAATT
28899501 CAAACTCAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
AAATTAATTTAAATGTAAATAAATTTA
Found at i:28899795 original size:3 final size:3
Alignment explanation
Indices: 28899789--28899822 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
28899779 ACCTAAAAAA
28899789 AAG AAG AAG AAG AAG AA- AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
28899823 AAAGGAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28899807 original size:17 final size:17
Alignment explanation
Indices: 28899787--28899824 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
28899777 TCACCTAAAA
28899787 AAAAGAAGAAGAAGAAG
1 AAAAGAAGAAGAAGAAG
28899804 AAAAGAAGAAGAAGAAG
1 AAAAGAAGAAGAAGAAG
28899821 AAAA
1 AAAA
28899825 AGGAGAGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAGAAGAAGAAGAAG
Found at i:28899811 original size:14 final size:14
Alignment explanation
Indices: 28899792--28899819 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28899782 TAAAAAAAAG
28899792 AAGAAGAAGAAGAA
1 AAGAAGAAGAAGAA
28899806 AAGAAGAAGAAGAA
1 AAGAAGAAGAAGAA
28899820 GAAAAAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAAGAA
Found at i:28900962 original size:49 final size:48
Alignment explanation
Indices: 28900857--28900967 Score: 132
Period size: 49 Copynumber: 2.3 Consensus size: 48
28900847 GACGGTAAAT
* * * * **
28900857 CCGATACCATAAAGCTGTGATGGAAAGGTTGTGGCCATAATGGTGAAC
1 CCGATACCATGAAGCTATGATGGAAAGGTTGAGGCCACAATGGCAAAC
* *
28900905 CCGCTACCATGAAGCTATGATGGGAAAGGTTGAGGCCGCAATGGCAAAC
1 CCGATACCATGAAGCTATGAT-GGAAAGGTTGAGGCCACAATGGCAAAC
*
28900954 TCGATACCATGAAG
1 CCGATACCATGAAG
28900968 AGTTGAAGGA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
48 18 0.35
49 34 0.65
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.20
Consensus pattern (48 bp):
CCGATACCATGAAGCTATGATGGAAAGGTTGAGGCCACAATGGCAAAC
Found at i:28901332 original size:39 final size:38
Alignment explanation
Indices: 28901284--28901867 Score: 247
Period size: 39 Copynumber: 15.0 Consensus size: 38
28901274 TAGTCATCCG
* *
28901284 ATCTTTTACCCCGAGCCTAAGGTAGATTATCATCATTCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTA-CATCATTCA
* * * * *
28901323 ATCTCTTACCCCAAGCCTAGGGCAGATTACAGCCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACA-TCATTCA
* * * * * *
28901362 ATCTTTTACCCCGAGCTTGGGGTAGATCACCCTCAGTCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTA-CATCATTCA
* * ** *
28901401 ATCTCTTACCCCGAGCCT-GAGGTAGATTGCAACCACCCG
1 ATCTCTTACCCCGAGCCTAG-GGTAGATTAC-ATCATTCA
* * * * * **
28901440 ATCTTTTACCCCGAGCTTGGGGCAGATCACTATCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTAC-ATCATTCA
* * * *
28901479 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATTCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACA-TCATTCA
* * * * * *
28901518 ATCTTTTACCCCGACCCTAGGGCATATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTA-CATCATTCA
** * * *
28901557 ATCTCTTACCTTGAG-CTTGAGGTAGATTGTA-ACCATTCG
1 ATCTCTTACCCCGAGCCTAG-GGTAGA-T-TACATCATTCA
* * * *
28901596 ATCTTTTACCCCGAGCATAGGGTAGATCACAATCAATCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTAC-ATCATTCA
* * * ** * *
28901635 ATCTCTTACCTCGAGCTTGGGGTAGATTGTAGTCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACA-TCATTCA
* * *** * **
28901674 ACCTTTTACCCCGAGCCTAGAACAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTA-CATCATTCA
* * * * * * *
28901713 ATCTCTTACCCCGAGCTTGGGGCAAATTGCAGCCATTCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACA-TCATTCA
* * * * * *
28901752 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTA-CATCATTCA
* * * * * * *
28901791 ATCTCTTACCCCGATCATGGGGCAGATTGCAGCCATCCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACA-TCATTCA
* * *
28901830 ATCTCTTACCCCGATCATAGGGCAGATTACAGTCATTC
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACA-TCATTC
28901868 GAAGCAATAA
Statistics
Matches: 399, Mismatches: 128, Indels: 36
0.71 0.23 0.06
Matches are distributed among these distances:
37 1 0.00
38 14 0.04
39 373 0.93
40 10 0.03
41 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCCTAGGGTAGATTACATCATTCA
Found at i:28901360 original size:78 final size:78
Alignment explanation
Indices: 28901278--28901856 Score: 645
Period size: 78 Copynumber: 7.4 Consensus size: 78
28901268 AGATCATAGT
* * * * * * *
28901278 CATCCGATCTTTTACCCCGAGCCTAAGGTAGATTATCATCATTCAATCTCTTACCCCAAGCCTAG
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGG
*
28901343 GGCAGATTACAGC
66 GGCAGATTGCAGC
* * * * *
28901356 CATCCGATCTTTTACCCCGAGCTTGGGGTAGATCACCCTCAGTCAATCTCTTACCCCGAGCCTGA
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGG
* *
28901421 GGTAGATTGCAAC
66 GGCAGATTGCAGC
* * * * * *
28901434 CACCCGATCTTTTACCCCGAGCTTGGGGCAGATCACTATCAGCCAATCTCTTACCCCGAGCCTAG
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGG
28901499 GGCAGATTGCAGC
66 GGCAGATTGCAGC
* * * ** * *
28901512 CATTCGATCTTTTACCCCGACCCTAGGGCATATCACCATCAGTCAATCTCTTACCTTGAGCTTGA
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGG
* * *
28901577 GGTAGATTGTAAC
66 GGCAGATTGCAGC
* * * * * * *
28901590 CATTCGATCTTTTACCCCGAGCATAGGGTAGATCACAATCAATCAATCTCTTACCTCGAGCTTGG
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGG
* * *
28901655 GGTAGATTGTAGT
66 GGCAGATTGCAGC
* ** ** *
28901668 CATCCGACCTTTTACCCCGAGCCTAGAACAGATCACCATCAACCAATCTCTTACCCCGAGCTTGG
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGG
*
28901733 GGCAAATTGCAGC
66 GGCAGATTGCAGC
* * * * *
28901746 CATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGATCATGG
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGG
28901811 GGCAGATTGCAGC
66 GGCAGATTGCAGC
* * * *
28901824 CATCCAATCTCTTACCCCGATCATAGGGCAGAT
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGAT
28901857 TACAGTCATT
Statistics
Matches: 423, Mismatches: 78, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 423 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (78 bp):
CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGG
GGCAGATTGCAGC
Found at i:28911272 original size:13 final size:13
Alignment explanation
Indices: 28911254--28911278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28911244 AAACATGTTT
28911254 ATTAATTAAAAAC
1 ATTAATTAAAAAC
28911267 ATTAATTAAAAA
1 ATTAATTAAAAA
28911279 TTAAACTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:28911289 original size:57 final size:59
Alignment explanation
Indices: 28911210--28911343 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 59
28911200 TGAACGAGCT
* * *
28911210 ATTAATTAAAAA-TAAAATTAAAAAA-CTTGAAAAAAAACATG-TTTA-TTAATTAAAAAC
1 ATTAATTAAAAATTAAACTAAAAAAATCTTG-AAAAAAA-ATGATTAACTTAATTAAAAAC
* *
28911267 ATTAATTAAAAATTAAACTAAAAAAATCTTGAAACAAAATGAATTAACTTAATTAAAAGC
1 ATTAATTAAAAATTAAACTAAAAAAATCTTGAAAAAAAATG-ATTAACTTAATTAAAAAC
*
28911327 ATTAATTAAAAAGTAAA
1 ATTAATTAAAAATTAAA
28911344 AAATAGAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
57 15 0.23
58 17 0.26
59 7 0.11
60 27 0.41
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.29
Consensus pattern (59 bp):
ATTAATTAAAAATTAAACTAAAAAAATCTTGAAAAAAAATGATTAACTTAATTAAAAAC
Found at i:28913193 original size:17 final size:18
Alignment explanation
Indices: 28913168--28913203 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28913158 AGTTTATAGC
*
28913168 ATATGTAAT-TAAATATT
1 ATATATAATGTAAATATT
28913185 ATATATAATGTAAATATT
1 ATATATAATGTAAATATT
28913203 A
1 A
28913204 AAATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATATAATGTAAATATT
Found at i:28913811 original size:16 final size:16
Alignment explanation
Indices: 28913773--28913815 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
28913763 TTTAACTTAA
*
28913773 ATATTTTAT-TTATTT
1 ATATTATATATTATTT
*
28913788 A-ATCATATATTATTT
1 ATATTATATATTATTT
28913803 ATATTATATATTA
1 ATATTATATATTA
28913816 GTATTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 8 0.35
16 10 0.43
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATATATTATTT
Found at i:28917041 original size:71 final size:71
Alignment explanation
Indices: 28916925--28917069 Score: 245
Period size: 71 Copynumber: 2.0 Consensus size: 71
28916915 CCCTGCTAAA
*
28916925 ATAACATCTCAACATCCCCCAATTCCATCCACCAGCAACAGTAACAAACTCCAACACTTTCACTT
1 ATAACATCTCAACATCCCCCAATTCCATCCACCAACAACAGTAACAAACTCCAACACTTTCACTT
28916990 TCTCCT
66 TCTCCT
* ***
28916996 ATAACATCTCAACATCCCCCAATTCCATCCACCAATAACAGTAACAAACTTTGACACTTTCACTT
1 ATAACATCTCAACATCCCCCAATTCCATCCACCAACAACAGTAACAAACTCCAACACTTTCACTT
28917061 TCTCCT
66 TCTCCT
28917067 ATA
1 ATA
28917070 CTGCTGTCCC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (71 bp):
ATAACATCTCAACATCCCCCAATTCCATCCACCAACAACAGTAACAAACTCCAACACTTTCACTT
TCTCCT
Found at i:28924873 original size:27 final size:27
Alignment explanation
Indices: 28924843--28924937 Score: 77
Period size: 28 Copynumber: 3.5 Consensus size: 27
28924833 GGTTGTCGCA
28924843 AAGGCTTCATTTTCAAAGATTGCCACG
1 AAGGCTTCATTTTCAAAGATTGCCACG
* ** **
28924870 AAGGCTTTCTTTTTCATAAG-TCCCCATA
1 AAGGC-TTCATTTTCA-AAGATTGCCACG
* *
28924898 AAGGCTTCCATTTT-AGAGATTGCCGCG
1 AAGGCTT-CATTTTCAAAGATTGCCACG
*
28924925 AAGGCTTCCTTTT
1 AAGGCTTCATTTT
28924938 TCATAGGTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
26 7 0.14
27 18 0.35
28 23 0.45
29 3 0.06
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (27 bp):
AAGGCTTCATTTTCAAAGATTGCCACG
Found at i:28924952 original size:55 final size:55
Alignment explanation
Indices: 28924842--28924954 Score: 156
Period size: 55 Copynumber: 2.1 Consensus size: 55
28924832 AGGTTGTCGC
* *
28924842 AAAGGCTTCATTTTCAAAGATTGCCACGAAGGCTTTCTTTTTCATAAGTCCCCAT
1 AAAGGCTTCATTTTCAAAGATTGCCACGAAGGCTTCCTTTTTCATAAGTCACCAT
* * * *
28924897 AAAGGCTTCCATTTT-AGAGATTGCCGCGAAGGCTTCCTTTTTCATAGGTTACCAT
1 AAAGGCTT-CATTTTCAAAGATTGCCACGAAGGCTTCCTTTTTCATAAGTCACCAT
28924952 AAA
1 AAA
28924955 TGTTTTTCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
55 45 0.88
56 6 0.12
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (55 bp):
AAAGGCTTCATTTTCAAAGATTGCCACGAAGGCTTCCTTTTTCATAAGTCACCAT
Found at i:28925009 original size:28 final size:28
Alignment explanation
Indices: 28924962--28925133 Score: 123
Period size: 28 Copynumber: 6.2 Consensus size: 28
28924952 AAATGTTTTT
* ** *
28924962 CTTTCAAAGGTTCATAACAAAGACTATC
1 CTTTCAGAGGTTCACCACAAAGACTTTC
*
28924990 CTTTCAGAGGTTCACCACAAAGGCTTTC
1 CTTTCAGAGGTTCACCACAAAGACTTTC
* * *
28925018 TTTTTAGAGGTTCGCCACAAAGACTTTTC
1 CTTTCAGAGGTTCACCACAAAGAC-TTTC
* * * *
28925047 C-TTCAGAGGCTCGCCACAAAGGCTTTT
1 CTTTCAGAGGTTCACCACAAAGACTTTC
* * * *
28925074 GTTTTATAGGTTCA-CACAAAGGCTTTC
1 CTTTCAGAGGTTCACCACAAAGACTTTC
* * ** * *
28925101 CTTTTAAAGGTTTGCCATAAAGGCTTTC
1 CTTTCAGAGGTTCACCACAAAGACTTTC
28925129 CTTTC
1 CTTTC
28925134 CTAATTTTTT
Statistics
Matches: 115, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
27 25 0.22
28 86 0.75
29 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (28 bp):
CTTTCAGAGGTTCACCACAAAGACTTTC
Found at i:28925052 original size:56 final size:54
Alignment explanation
Indices: 28924969--28925103 Score: 155
Period size: 56 Copynumber: 2.4 Consensus size: 54
28924959 TTTCTTTCAA
* * *
28924969 AGGTTCATAACAAAGACTATCCTTTCAGAGGTTCACCACAAAGGCTTTCT-TTTTAG
1 AGGTTCA-CACAAAGACTTTCC-TTCAGAGGCTCACCACAAAGGCTTT-TGTTTTAG
* * *
28925025 AGGTTCGCCACAAAGACTTTTCCTTCAGAGGCTCGCCACAAAGGCTTTTGTTTTAT
1 AGGTTC-ACACAAAGAC-TTTCCTTCAGAGGCTCACCACAAAGGCTTTTGTTTTAG
*
28925081 AGGTTCACACAAAGGCTTTCCTT
1 AGGTTCACACAAAGACTTTCCTT
28925104 TTAAAGGTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
54 7 0.10
55 9 0.13
56 48 0.71
57 4 0.06
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (54 bp):
AGGTTCACACAAAGACTTTCCTTCAGAGGCTCACCACAAAGGCTTTTGTTTTAG
Found at i:28928651 original size:16 final size:18
Alignment explanation
Indices: 28928616--28928653 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
28928606 AATTTACATG
*
28928616 AAATATTGATTTTTAGCA
1 AAATATTGATTTTTAACA
28928634 AAATA-TGA-TTTTAACA
1 AAATATTGATTTTTAACA
28928650 AAAT
1 AAAT
28928654 GGTTCATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (18 bp):
AAATATTGATTTTTAACA
Found at i:28946133 original size:19 final size:19
Alignment explanation
Indices: 28946106--28946158 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
28946096 TCAAAAATCT
28946106 GTTTTTGTTGAAGTTTTGG
1 GTTTTTGTTGAAGTTTTGG
* *
28946125 GTTTGTGTTGAAGTTTTTG
1 GTTTTTGTTGAAGTTTTGG
*
28946144 GTTTTTGCTGAAGTT
1 GTTTTTGTTGAAGTT
28946159 AAGAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.11, C:0.02, G:0.30, T:0.57
Consensus pattern (19 bp):
GTTTTTGTTGAAGTTTTGG
Found at i:28956285 original size:6 final size:6
Alignment explanation
Indices: 28956274--28956303 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28956264 ATTTATTTTC
*
28956274 TATTAA TATTAA TATAAA TATTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA
28956304 AATTTAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TATTAA
Found at i:28959348 original size:23 final size:22
Alignment explanation
Indices: 28959322--28959365 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
28959312 AAAATATTTT
*
28959322 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
28959345 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
28959366 TTATTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:28961858 original size:51 final size:51
Alignment explanation
Indices: 28961777--28962043 Score: 417
Period size: 51 Copynumber: 5.2 Consensus size: 51
28961767 GCTATAAACG
*
28961777 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
28961829 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
28961880 AAAGATCCGATGACTAAATGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
28961931 AAAGATCCGATGACTAAATGTCATCGTGAGTAACTGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * *
28961982 AGAGGTCCGATGTCTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
28962033 AAAGGTTCGAT
1 AAAGGTCCGAT
28962044 AACAATATGT
Statistics
Matches: 201, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
51 197 0.98
52 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:28969184 original size:51 final size:51
Alignment explanation
Indices: 28969103--28969339 Score: 323
Period size: 51 Copynumber: 4.6 Consensus size: 51
28969093 GCTATAAACG
*
28969103 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
28969155 AAAGGTCCGATGATTAAGTGTCATTGTGAGTAAATGAATCTTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
28969206 AAAGATCCAATGACTAAATGTCATCGTCAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
28969257 AAAAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
28969308 AAAGGTCCGATGACCATA-TGTCATCATGAGTA
1 AAAGGTCCGATGACTA-AGTGTCATCGTGAGTA
28969340 TTAAATGAAA
Statistics
Matches: 162, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
51 157 0.97
52 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:28982923 original size:14 final size:14
Alignment explanation
Indices: 28982904--28982930 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28982894 TTTGTTATTC
28982904 ACATATTTTGGTTA
1 ACATATTTTGGTTA
28982918 ACATATTTTGGTT
1 ACATATTTTGGTT
28982931 TAGGGTTATT
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:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
ACATATTTTGGTTA
Found at i:28983272 original size:7 final size:7
Alignment explanation
Indices: 28983260--28983284 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28983250 ATATTGTTTA
28983260 TATTGTT
1 TATTGTT
28983267 TATTGTT
1 TATTGTT
28983274 TATTGTT
1 TATTGTT
28983281 TATT
1 TATT
28983285 TGACATGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (7 bp):
TATTGTT
Found at i:28983588 original size:33 final size:33
Alignment explanation
Indices: 28983563--28983663 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
28983553 TTGCATGTGT
28983563 TGTATTAAATGTTTGTTTCTGGTTTGATAGTGA
1 TGTATTAAATGTTTGTTTCTGGTTTGATAGTGA
* * *
28983596 TGTATTAAAAGTTTTTTTTTGGTTTGATAGTGA
1 TGTATTAAATGTTTGTTTCTGGTTTGATAGTGA
* *
28983629 TGTATTAAATGTTTGTTTGTGGTCTGATAGTGA
1 TGTATTAAATGTTTGTTTCTGGTTTGATAGTGA
28983662 TG
1 TG
28983664 AGTAATTTGT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.22, C:0.02, G:0.25, T:0.51
Consensus pattern (33 bp):
TGTATTAAATGTTTGTTTCTGGTTTGATAGTGA
Found at i:28985434 original size:10 final size:11
Alignment explanation
Indices: 28985404--28985445 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
28985394 AAGTTACCCT
28985404 TTTTAATATTA
1 TTTTAATATTA
*
28985415 TTTTGTATATT-
1 TTTT-AATATTA
28985426 TTTTAATATTA
1 TTTTAATATTA
*
28985437 TTTTCATAT
1 TTTTAATAT
28985446 GCTGTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 5 0.19
11 16 0.62
12 5 0.19
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (11 bp):
TTTTAATATTA
Done.