Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 122 of 187
Found at i:36220095 original size:16 final size:16
Alignment explanation
Indices: 36220074--36220125 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
36220064 AATGCATAAC
36220074 TTCCAAGAACTCAATT
1 TTCCAAGAACTCAATT
* *
36220090 TTCCAATGCA-T-AA-C
1 TTCCAA-GAACTCAATT
36220104 TTCCAAGAACTCAATT
1 TTCCAAGAACTCAATT
36220120 TTCCAA
1 TTCCAA
36220126 TCTTTCTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
13 2 0.07
14 7 0.25
15 4 0.14
16 13 0.46
17 2 0.07
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.31
Consensus pattern (16 bp):
TTCCAAGAACTCAATT
Found at i:36220098 original size:30 final size:30
Alignment explanation
Indices: 36220064--36220126 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
36220054 ACAAGAAAGA
36220064 AATGCATAACTTCCAAGAACTCAATTTTCC
1 AATGCATAACTTCCAAGAACTCAATTTTCC
36220094 AATGCATAACTTCCAAGAACTCAATTTTCC
1 AATGCATAACTTCCAAGAACTCAATTTTCC
36220124 AAT
1 AAT
36220127 CTTTCTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.30
Consensus pattern (30 bp):
AATGCATAACTTCCAAGAACTCAATTTTCC
Found at i:36220912 original size:6 final size:6
Alignment explanation
Indices: 36220898--36220929 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
36220888 GGCAATGTTG
*
36220898 CTAAAA CTAACA CTAACA CTAACA CTAACA CT
1 CTAACA CTAACA CTAACA CTAACA CTAACA CT
36220930 TCCACATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (6 bp):
CTAACA
Found at i:36226138 original size:3 final size:3
Alignment explanation
Indices: 36226130--36226179 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
36226120 CATGAAGTGC
*
36226130 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
36226178 AT
1 AT
36226180 GTACAAGAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:36228516 original size:45 final size:45
Alignment explanation
Indices: 36228427--36228583 Score: 190
Period size: 45 Copynumber: 3.4 Consensus size: 45
36228417 TTATAAAATC
**
36228427 AAATAATTATTTCGAATATCATTATTATTTTTATATGT-ATAATATTTT
1 AAATAATTATTTC-AA-AT-ACCATTATTTTTATATGTGA-AATATTTT
* *
36228475 AAATAATTATTCCAAATACCATTATTTTTATATGTGAAATATTTC
1 AAATAATTATTTCAAATACCATTATTTTTATATGTGAAATATTTT
* * * * *
36228520 AATTAACTATTTCAAATATCACTATTATTATATGTGAAATATTTT
1 AAATAATTATTTCAAATACCATTATTTTTATATGTGAAATATTTT
36228565 AAATAATTATTTCAAATAC
1 AAATAATTATTTCAAATAC
36228584 ACACACAAAA
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
45 77 0.82
46 3 0.03
47 2 0.02
48 12 0.13
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (45 bp):
AAATAATTATTTCAAATACCATTATTTTTATATGTGAAATATTTT
Found at i:36229653 original size:27 final size:28
Alignment explanation
Indices: 36229601--36229653 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
36229591 AGTTAATAAA
*
36229601 TTCTCTTTGAGTTTTTCTTTTCAAGAAT
1 TTCTCTTTGAGTTTTTCTTTACAAGAAT
*
36229629 TTCTC-TTGAGTATTTT-TTTAGAAGA
1 TTCTCTTTGAGT-TTTTCTTTACAAGA
36229654 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (28 bp):
TTCTCTTTGAGTTTTTCTTTACAAGAAT
Found at i:36232143 original size:27 final size:27
Alignment explanation
Indices: 36232106--36232194 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 27
36232096 GGATCAAAAT
* *
36232106 ATACCCCTGTAGGGTAAAATAACTGTA
1 ATACCCCTGTAGGGTAAAATGACCGTA
36232133 ATACCCCTGTAGGGTAAAATGACCGTA
1 ATACCCCTGTAGGGTAAAATGACCGTA
* *
36232160 ATACCTCTGTAAGGTAAAATGACCGTA
1 ATACCCCTGTAGGGTAAAATGACCGTA
*
36232187 ATGCCCCT
1 ATACCCCT
36232195 CGAGGTTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (27 bp):
ATACCCCTGTAGGGTAAAATGACCGTA
Found at i:36232204 original size:27 final size:26
Alignment explanation
Indices: 36232106--36232207 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 26
36232096 GGATCAAAAT
* *
36232106 ATACCCCTGTAGGGTAAAATAACTGTA
1 ATACCCCTGTA-GGTAAAATGACCGTA
36232133 ATACCCCTGTAGGGTAAAATGACCGTA
1 ATACCCCTGTA-GGTAAAATGACCGTA
*
36232160 ATACCTCTGTAAGGTAAAATGACCGTA
1 ATACCCCTGT-AGGTAAAATGACCGTA
* *
36232187 ATGCCCCTCG-AGGTTAAATGA
1 ATACCCCT-GTAGGTAAAATGA
36232208 TTGATTTGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 10 0.15
27 55 0.82
28 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (26 bp):
ATACCCCTGTAGGTAAAATGACCGTA
Found at i:36232282 original size:24 final size:23
Alignment explanation
Indices: 36232200--36232307 Score: 135
Period size: 23 Copynumber: 4.6 Consensus size: 23
36232190 CCCCTCGAGG
*
36232200 TTAAATGATTGATTTGTCTGTGG
1 TTAAATGATTGATTTGTCTGTGT
36232223 TTAAATGATTGATTTGTCTGTGT
1 TTAAATGATTGATTTGTCTGTGT
36232246 TTAAATGATTGATTTGTCTGTGT
1 TTAAATGATTGATTTGTCTGTGT
** * *
36232269 TTGGTATGACTGATTTGTTTGTGAT
1 TT-AAATGATTGATTTGTCTGTG-T
* *
36232294 TTGAATGACTGATT
1 TTAAATGATTGATT
36232308 CTGAGCATGG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
23 47 0.61
24 27 0.35
25 3 0.04
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (23 bp):
TTAAATGATTGATTTGTCTGTGT
Found at i:36232552 original size:32 final size:32
Alignment explanation
Indices: 36232479--36232713 Score: 184
Period size: 32 Copynumber: 7.4 Consensus size: 32
36232469 GTTGTGATGC
* * *
36232479 TACTGATGGCTTTGTGCTGGTCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
36232511 TGCTAATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * * * *
36232543 TACCGATGGCTATGTACTGATAATTTTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * * *
36232575 TATTGATGGCTGTGTGCCGATAATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * *
36232607 TATTGATGGATTTGTACAGATCATGTTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * *
36232639 TACTGATGGCTATGTGCCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
36232671 TACTGATGGCTTTGTGCCAATCACATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
36232702 TACTTATGGCTT
1 TACTGATGGCTT
36232714 GTAGTCATTC
Statistics
Matches: 158, Mismatches: 45, Indels: 1
0.77 0.22 0.00
Matches are distributed among these distances:
31 11 0.07
32 147 0.93
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:36232685 original size:64 final size:64
Alignment explanation
Indices: 36232476--36232685 Score: 233
Period size: 64 Copynumber: 3.3 Consensus size: 64
36232466 TTTGTTGTGA
* * * * * *
36232476 TGCTACTGATGGCTTTGTGCTGGTCATAG-TACCGTTGCTAATGGCTTTGTGCCGATCATATTAC
1 TGCTACTGATGGCTTTGTACTGATCAT-GTTACCGTTACTGATGGCTATGTGCCGATCATATCAC
* * * * * * * * * *
36232540 CGTTACCGATGGCTATGTACTGATAATTTTACTGTTATTGATGGCTGTGTGCCGATAATATCAC
1 TGCTACTGATGGCTTTGTACTGATCATGTTACCGTTACTGATGGCTATGTGCCGATCATATCAC
* * *
36232604 TGCTATTGATGGATTTGTACAGATCATGTTACCGTTACTGATGGCTATGTGCCGATCATATCAC
1 TGCTACTGATGGCTTTGTACTGATCATGTTACCGTTACTGATGGCTATGTGCCGATCATATCAC
36232668 TGCTACTGATGGCTTTGT
1 TGCTACTGATGGCTTTGT
36232686 GCCAATCACA
Statistics
Matches: 115, Mismatches: 30, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
64 115 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTACTGATCATGTTACCGTTACTGATGGCTATGTGCCGATCATATCAC
Found at i:36232730 original size:22 final size:21
Alignment explanation
Indices: 36232705--36232769 Score: 51
Period size: 22 Copynumber: 3.0 Consensus size: 21
36232695 ATTACTGTAC
36232705 TTATGGCTTGTAGTCATTCTGT
1 TTATGGCTT-TAGTCATTCTGT
* * *
36232727 TTATAGCTTATAG-CTATCCTAT
1 TTATGGCTT-TAGTC-ATTCTGT
*
36232749 TTATGACTCTTAGTCATTCTG
1 TTATGGCT-TTAGTCATTCTG
36232770 ACTACTAGCA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 1 0.03
22 29 0.91
23 2 0.06
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (21 bp):
TTATGGCTTTAGTCATTCTGT
Found at i:36234377 original size:34 final size:33
Alignment explanation
Indices: 36234308--36234378 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
36234298 TTTTGATTTT
* *
36234308 ATATATGTTTTGGAAATATGACATTTTAATTTG
1 ATATATGTTTTGGAAATATGACATTCTAATCTG
* * * *
36234341 ATATATGTTTTTGATAATGTGTCATTCTGATCTG
1 ATATATGTTTTGGA-AATATGACATTCTAATCTG
36234375 ATAT
1 ATAT
36234379 CCATACATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (33 bp):
ATATATGTTTTGGAAATATGACATTCTAATCTG
Found at i:36236547 original size:96 final size:96
Alignment explanation
Indices: 36236368--36236547 Score: 227
Period size: 96 Copynumber: 1.9 Consensus size: 96
36236358 AACTGATGTT
* * * ** *
36236368 TCACCTATTGTGAAATGTTATTGGTGTAGTTCAAAAGATCATGAGGGTTACGGATGTCCAATTAA
1 TCACCTATTGTGAAATGTTATTGGTGTAGCTCAAAAGATCATAAAGGTTACCAATGCCCAATTAA
36236433 ATATCCAAATAGAGAGAATACGATTGAGCTA
66 ATATCCAAATAGAGAGAATACGATTGAGCTA
* * * * *
36236464 TCACCTTTTGTGTAATTTTATTGGTGTAGCTCAAACGATTATAAAGGTT-CCAATGCCCAATTAA
1 TCACCTATTGTGAAATGTTATTGGTGTAGCTCAAAAGATCATAAAGGTTACCAATGCCCAATTAA
* *
36236528 ATATCTAACTAGAGAAGAAT
66 ATATCCAAATAGAG-AGAAT
36236548 GTAAGTATGA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
95 24 0.34
96 46 0.66
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (96 bp):
TCACCTATTGTGAAATGTTATTGGTGTAGCTCAAAAGATCATAAAGGTTACCAATGCCCAATTAA
ATATCCAAATAGAGAGAATACGATTGAGCTA
Found at i:36240199 original size:299 final size:299
Alignment explanation
Indices: 36239661--36240261 Score: 1130
Period size: 299 Copynumber: 2.0 Consensus size: 299
36239651 ACTAGGGACT
36239661 ATAACACCTTATACCTATCCCGGTCGCTGAGCCCGAATATCAGGATGCCATACCACCGTCTCATG
1 ATAACACCTTATACCTATCCCGGTCGCTGAGCCCGAATATCAGGATGCCATACCACCGTCTCATG
*
36239726 TCATACACAACAATTAAAAGCTCATTCTCAATGAAACGTCTTCCATTTTAGTATTCGTATAGGTT
66 TCATACACAACAATTAAAAGCTCATTCTCAATGAAACATCTTCCATTTTAGTATTCGTATAGGTT
36239791 TTAAGTCAATCTTACTTTTAAGTTATCATTGTTACATGATAAACATGCATCAGATAGTCTTATAA
131 TTAAGTCAATCTTACTTTTAAGTTATCATTGTTACATGATAAACATGCATCAGATAGTCTTATAA
* *
36239856 CAATAGTTTAACATGCATATGGTCTGTTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
196 CAATAGTTTAACATGCATAAGGTCTATTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
*
36239921 CTAGAATATGGGTACCAATATTTCTCTCAAGTGGTATCG
261 CTAGAACATGGGTACCAATATTTCTCTCAAGTGGTATCG
*
36239960 ATAACACCTTATACCTATCCCGGTCGCTGAGCTCGAATATCAGGATGCCATACCACCGTCTCATG
1 ATAACACCTTATACCTATCCCGGTCGCTGAGCCCGAATATCAGGATGCCATACCACCGTCTCATG
* *
36240025 TCATACACAACAATTAAAAGCTTATTCTCAATGAAACATCTTTCATTTTAGTATTCGTATAGGTT
66 TCATACACAACAATTAAAAGCTCATTCTCAATGAAACATCTTCCATTTTAGTATTCGTATAGGTT
*
36240090 TTAAGTCAATCTTACTTTTAAGTTATCATTGTTACATGCTAAACATGCATCAGATAGTCTTATAA
131 TTAAGTCAATCTTACTTTTAAGTTATCATTGTTACATGATAAACATGCATCAGATAGTCTTATAA
36240155 CAATAGTTTAACATGCATAAGGTCTATTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
196 CAATAGTTTAACATGCATAAGGTCTATTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
36240220 CTAGAACATGGGTACCAATATTTCTCTCAAGTGGTATCG
261 CTAGAACATGGGTACCAATATTTCTCTCAAGTGGTATCG
36240259 ATA
1 ATA
36240262 CCGCTTGGAA
Statistics
Matches: 294, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
299 294 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (299 bp):
ATAACACCTTATACCTATCCCGGTCGCTGAGCCCGAATATCAGGATGCCATACCACCGTCTCATG
TCATACACAACAATTAAAAGCTCATTCTCAATGAAACATCTTCCATTTTAGTATTCGTATAGGTT
TTAAGTCAATCTTACTTTTAAGTTATCATTGTTACATGATAAACATGCATCAGATAGTCTTATAA
CAATAGTTTAACATGCATAAGGTCTATTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
CTAGAACATGGGTACCAATATTTCTCTCAAGTGGTATCG
Found at i:36242639 original size:19 final size:19
Alignment explanation
Indices: 36242617--36242654 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
36242607 TCAATCATCC
36242617 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
36242636 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
36242655 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:36245817 original size:17 final size:17
Alignment explanation
Indices: 36245795--36245828 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
36245785 CTTAGGAGCG
36245795 AGTATCAACTTAATACC
1 AGTATCAACTTAATACC
36245812 AGTATCAACTTAATACC
1 AGTATCAACTTAATACC
36245829 TAAGTCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (17 bp):
AGTATCAACTTAATACC
Found at i:36256881 original size:38 final size:39
Alignment explanation
Indices: 36256825--36256898 Score: 141
Period size: 38 Copynumber: 1.9 Consensus size: 39
36256815 AGCTAAGAAA
36256825 ATCATAAACAAATCATATACATACATACCATCCCTATAT
1 ATCATAAACAAATCATATACATACATACCATCCCTATAT
36256864 ATCA-AAACAAATCATATACATACATACCATCCCTA
1 ATCATAAACAAATCATATACATACATACCATCCCTA
36256899 CATTTATCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 31 0.89
39 4 0.11
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (39 bp):
ATCATAAACAAATCATATACATACATACCATCCCTATAT
Found at i:36257344 original size:20 final size:20
Alignment explanation
Indices: 36257319--36257424 Score: 90
Period size: 20 Copynumber: 5.3 Consensus size: 20
36257309 TAAATGTGTT
36257319 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * *
36257339 CAGGGGCA-CGTATGTGCAAT
1 CAGGGGTACCG-AAGTACAAA
* *
36257359 CACGGGTACCGAAGTATAAA
1 CAGGGGTACCGAAGTACAAA
** * *
36257379 CAAGGGG-ACATATGTGCAAA
1 C-AGGGGTACCGAAGTACAAA
36257399 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
36257419 CAGGGG
1 CAGGGG
36257425 CACGTATGTG
Statistics
Matches: 62, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
19 7 0.11
20 49 0.79
21 6 0.10
ACGTcount: A:0.36, C:0.19, G:0.32, T:0.13
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:36257366 original size:40 final size:40
Alignment explanation
Indices: 36257322--36257440 Score: 186
Period size: 40 Copynumber: 3.0 Consensus size: 40
36257312 ATGTGTTCAG
36257322 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCAC
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCAC
* * * *
36257362 GGGTACCGAAGTATAAACAAGGGG-ACATATGTGCAAACAG
1 GGGTACCGAAGTACAAAC-AGGGGCACGTATGTGCAATCAC
36257402 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCA
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCA
36257441 TGCAATAATT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 5 0.07
40 60 0.86
41 5 0.07
ACGTcount: A:0.35, C:0.19, G:0.30, T:0.15
Consensus pattern (40 bp):
GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCAC
Found at i:36260050 original size:22 final size:22
Alignment explanation
Indices: 36260007--36260071 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
36259997 TGCCAGTAGT
* *
36260007 CAGAATGGCTA-AGAGCCGTAAA
1 CAGAATAGCTACA-AGCCATAAA
* * *
36260029 CAGGATAGCTATAAGCTATAAA
1 CAGAATAGCTACAAGCCATAAA
*
36260051 CAGAATGGCTACAAGCCATAA
1 CAGAATAGCTACAAGCCATAA
36260072 GTACAGTAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (22 bp):
CAGAATAGCTACAAGCCATAAA
Found at i:36260118 original size:32 final size:32
Alignment explanation
Indices: 36260063--36260390 Score: 408
Period size: 32 Copynumber: 10.3 Consensus size: 32
36260053 GAATGGCTAC
* *
36260063 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
36260094 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* ** ** *
36260126 CAGCCATCAACAATGGTAATATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
36260158 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
36260190 AAGCCATCAGTAATGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
36260222 AAGCCATCCGTAAC-GATATTATGATCGGCACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
** * *
36260254 AAGCCATCAGTAATGGTAATATAATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
36260286 AAGCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
36260318 AAGCCATCAGTAACAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
36260350 AAGCCATCAATAACAGTAATATGATCAGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
36260382 AAGCCATCA
1 AAGCCATCA
36260391 TTAGCATCGC
Statistics
Matches: 258, Mismatches: 36, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
31 11 0.04
32 246 0.95
33 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:36260448 original size:26 final size:26
Alignment explanation
Indices: 36260396--36260449 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
36260386 CATCATTAGC
* *
36260396 ATCGCAGCAAAGCTGCCAGCAGCAGT
1 ATCGCAACAAAGCTGCCAGCAACAGT
* *
36260422 ATCGCAACAAAGCTGCCAGTAATAGT
1 ATCGCAACAAAGCTGCCAGCAACAGT
36260448 AT
1 AT
36260450 ATGTGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (26 bp):
ATCGCAACAAAGCTGCCAGCAACAGT
Found at i:36260467 original size:27 final size:27
Alignment explanation
Indices: 36260437--36260500 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
36260427 AACAAAGCTG
*
36260437 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
36260464 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
36260491 CCAGT-ACAGT
1 CCAGTAACAGT
36260501 ACTTCCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.21
27 25 0.74
28 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:36260697 original size:27 final size:27
Alignment explanation
Indices: 36260667--36260798 Score: 194
Period size: 27 Copynumber: 4.9 Consensus size: 27
36260657 GGTATTACGA
36260667 TCATTTTACCCTACAGGGGCATTACAG
1 TCATTTTACCCTACAGGGGCATTACAG
* * *
36260694 TCATTTTACCTTACAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGCATTACAG
*
36260721 TCATTTTATCCTACAGGGGCATTACAG
1 TCATTTTACCCTACAGGGGCATTACAG
*
36260748 TCATTTTACCCTATAGGGGCATTACAG
1 TCATTTTACCCTACAGGGGCATTACAG
* *
36260775 TCA-TTTACCTTACAGGGGTATTAC
1 TCATTTTACCCTACAGGGGCATTAC
36260799 GATTATTTTA
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 18 0.19
27 75 0.81
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCATTACAG
Found at i:36262904 original size:30 final size:28
Alignment explanation
Indices: 36262870--36262925 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
36262860 TCATAATGAA
* *
36262870 ATATATTTAATATATTTTTATTATATAATT
1 ATATAATTAATAT-TTTAT-TTATATAATT
36262900 ATATAATTAATATTTTATTTATATAA
1 ATATAATTAATATTTTATTTATATAA
36262926 ATAAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 4 0.17
30 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATATAATTAATATTTTATTTATATAATT
Found at i:36265452 original size:51 final size:50
Alignment explanation
Indices: 36265268--36265612 Score: 343
Period size: 51 Copynumber: 6.8 Consensus size: 50
36265258 ACTTTTATCA
* * * * *
36265268 TTCGATACACGTAGTAGCCTTCACATAGTACTACAAACATGATCAAGTTT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTT
* * * *
36265318 TTCGGTTCACGTATTAGCCTTCACATAGTACTACATACGTGATCAAG-TT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTT
* *
36265367 TTACGGTTCACGTAGTAGCCTTTACATAGTACTACACACGTGACCAAAGCTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTT
* * * * *
36265419 TTTGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACC-ATCATT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TT
* * *
36265469 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTT
* * ** * * ***
36265521 CTCGGTACACATTCTAGCCTTCACTTAGTACTACACATGTGACCATTATT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTT
* * *
36265571 TATCGATACACGTAGTAGCCTTCACACAATACTACACACGTG
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTG
36265613 TTCATCGATA
Statistics
Matches: 242, Mismatches: 45, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
49 6 0.02
50 86 0.36
51 142 0.59
52 6 0.02
53 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTT
Found at i:36265489 original size:102 final size:102
Alignment explanation
Indices: 36265269--36265612 Score: 433
Period size: 102 Copynumber: 3.4 Consensus size: 102
36265259 CTTTTATCAT
* * * * * * *
36265269 TCGATACACGTAGTAGCCTTCACATAGTACTACAAACATGATC-AAG-TTTTTCGGTTCACGTAT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTT-GGTACACATAC
* * * * ***
36265332 TAGCCTTCACATAGTACTACATACGTGATCAAGTTTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * * *
36265370 -CGGTTCACGTAGTAGCCTTTACATAGTACTACACACGTGACCAAAGCTTTTTGGTACACATAGT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTTGGTACACATACT
36265434 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * *
36265471 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTCT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTTGGTACACATACT
*
36265536 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
*
36265573 TCGATACACGTAGTAGCCTTCACACAATACTACACACGTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
36265613 TTCATCGATA
Statistics
Matches: 214, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
100 36 0.17
101 42 0.20
102 136 0.64
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (102 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTTGGTACACATACT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:36271668 original size:16 final size:16
Alignment explanation
Indices: 36271647--36271708 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
36271637 ACCATGTTAA
36271647 TAGAAAGCATTTTTTG
1 TAGAAAGCATTTTTTG
*
36271663 TAGAAACCATTTTTT-
1 TAGAAAGCATTTTTTG
* * **
36271678 CAAAAAATATTTTTTTG
1 TAGAAAGCA-TTTTTTG
36271695 TAGAAAGCATTTTT
1 TAGAAAGCATTTTT
36271709 CATAAAGCAC
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
15 5 0.14
16 25 0.71
17 5 0.14
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (16 bp):
TAGAAAGCATTTTTTG
Found at i:36288209 original size:27 final size:26
Alignment explanation
Indices: 36288179--36288253 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 26
36288169 AAAACAACCA
*
36288179 TCAAAATAAGAAAAATCAAAATATAGT-
1 TCAAAATAA-AAAAATCAAAAGA-AGTC
36288206 TCAAAATCAAAATAAA--ATAAAGAAGTC
1 TCAAAAT-AAAA-AAATCA-AAAGAAGTC
36288233 TCACAAATAAAAAAATCAAAA
1 TCA-AAATAAAAAAATCAAAA
36288254 ATCAAAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
26 7 0.17
27 23 0.57
28 10 0.25
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (26 bp):
TCAAAATAAAAAAATCAAAAGAAGTC
Found at i:36295493 original size:44 final size:44
Alignment explanation
Indices: 36295443--36295530 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
36295433 CACCAAATCG
*
36295443 GGATAACCTCCTCAATCCCATAATATTCTCCTAAAATCACTCCA
1 GGATAACCTCCCCAATCCCATAATATTCTCCTAAAATCACTCCA
*
36295487 GGATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTCCA
1 GGATAACCTCCCCAATCCCATAATATTCTCCTAAAATCACTCCA
36295531 ACCTTCCCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.33, C:0.36, G:0.05, T:0.26
Consensus pattern (44 bp):
GGATAACCTCCCCAATCCCATAATATTCTCCTAAAATCACTCCA
Found at i:36296578 original size:143 final size:143
Alignment explanation
Indices: 36296317--36296578 Score: 339
Period size: 143 Copynumber: 1.8 Consensus size: 143
36296307 TCGATTTGTT
* * * *
36296317 CGACTAGCGCTGGATGCAACTTTCGTCAGTTTATCTAACTAGTGTTGGGCACACATTCGTCGGTT
1 CGACTAGCGCTGGATACAACTTTCGTCAGTTTATCTAACTAGTGCTGGGCACACAATCGTCGGTA
* * *
36296382 TATCCGACTAGCACTGGGTGAAAACATCGTTGGTTTATCCAACTAGAGTTGGGCTCACTATTGAT
66 TAACCGACTAGCACTGGGTCAAAACATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTATTGAT
36296447 TTTTTGGTATATC
131 TTTTTGGTATATC
* * * *
36296460 CGACTAGCGCTGGGTACAACTTTTGAT-AGTTTATCTAACTAGTGCTGGGCACATAATCGTTGGT
1 CGACTAGCGCTGGATACAACTTTCG-TCAGTTTATCTAACTAGTGCTGGGCACACAATCGTCGGT
* * * * * *
36296524 ATAACTGACTAGCATTGGG-CACAATCATCTTTGGTTTGTCCAACTTGAGCTGGGC
65 ATAACCGACTAGCACTGGGTCA-AAACATCGTTGGTTTATCCAACTAGAGCTGGGC
36296579 ACATAAACAT
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
142 1 0.01
143 98 0.98
144 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (143 bp):
CGACTAGCGCTGGATACAACTTTCGTCAGTTTATCTAACTAGTGCTGGGCACACAATCGTCGGTA
TAACCGACTAGCACTGGGTCAAAACATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTATTGAT
TTTTTGGTATATC
Found at i:36298159 original size:3 final size:3
Alignment explanation
Indices: 36298151--36298237 Score: 69
Period size: 3 Copynumber: 30.0 Consensus size: 3
36298141 CATCCAACAA
* *
36298151 AAT AAT AAT AAT AAT AA- AAGT AAT AAT AA- AAA AAT -AT GAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
* *
36298194 AAT AAT AACT AAA AAT AAT AA- AAG AAT AAGT AA- AAT AA- AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
36298238 TAAATAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
2 12 0.17
3 50 0.71
4 8 0.11
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:36298236 original size:35 final size:35
Alignment explanation
Indices: 36298154--36298241 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 35
36298144 CCAACAAAAT
* *
36298154 AATAATAATAA-TAAAAGTAATAATAAAAAAATATGAT
1 AATAATAATAACT-AAA--AATAATAAAAAAATAAGAA
*
36298191 AATAATAATAACTAAAAATAATAAAAGAATAAGTAA
1 AATAATAATAACTAAAAATAATAAAAAAATAAG-AA
*
36298227 AATAA-AATAATTAAA
1 AATAATAATAACTAAA
36298242 TAAAAATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
35 24 0.53
36 6 0.13
37 14 0.31
38 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (35 bp):
AATAATAATAACTAAAAATAATAAAAAAATAAGAA
Found at i:36298252 original size:25 final size:25
Alignment explanation
Indices: 36298205--36298252 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
36298195 ATAATAACTA
*
36298205 AAAATAATAAAAGAATAAGTAAAAT
1 AAAATAATAAAAGAAAAAGTAAAAT
* * *
36298230 AAAATAATTAAATAAAAATTAAA
1 AAAATAATAAAAGAAAAAGTAAA
36298253 TAGAAGAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAATAATAAAAGAAAAAGTAAAAT
Found at i:36298450 original size:22 final size:23
Alignment explanation
Indices: 36298410--36298453 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
36298400 AGGGAAGAAT
*
36298410 GGGGAAGGTGGGGACGAGAGGAA
1 GGGGAAGGTAGGGACGAGAGGAA
*
36298433 GGGGAAGG-AGGGATGAGAGGA
1 GGGGAAGGTAGGGACGAGAGGA
36298454 GATCGAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.32, C:0.02, G:0.61, T:0.05
Consensus pattern (23 bp):
GGGGAAGGTAGGGACGAGAGGAA
Found at i:36308083 original size:51 final size:50
Alignment explanation
Indices: 36307997--36308338 Score: 361
Period size: 51 Copynumber: 6.7 Consensus size: 50
36307987 TATTGATGAA
*
36307997 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATTGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-ATTGT
* * * * * * * *
36308048 CACATGTCTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAA-ATATT-GT
* * *
36308099 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-ATTGT
* * * *
36308150 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGA-AAAGTTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TATT-GT
* *
36308201 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-TTG-T
* * *
36308252 CACGTGTGTAGTACTATGTGAAAGCTACTACGTGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-TTG-T
*
36308302 CACGTGTGTAGTACTATGTGGAGGCTACTACGTGTAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTAT
36308339 TGAATGATAA
Statistics
Matches: 243, Mismatches: 39, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
50 48 0.20
51 193 0.79
52 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGT
Found at i:36308173 original size:102 final size:101
Alignment explanation
Indices: 36307997--36308335 Score: 450
Period size: 102 Copynumber: 3.3 Consensus size: 101
36307987 TATTGATGAA
* * * *
36307997 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATTGTCACATGTCTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
*
36308062 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTTTGGT
* *
36308099 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
36308164 TAAGTGAAGGCTACTATGTGTATCGAAAAGTTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* *
36308201 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-AACTTGATCACGTGTGTAGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA--TGGTCACATGTGTAGT
* * * * * *
36308264 ACTATGTGAAAGCTACTACGTGAACCGTAAAAC-TTGAT
64 ACTAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
*
36308302 CACGTGTGTAGTACTATGTGGAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
36308336 TATTGAATGA
Statistics
Matches: 213, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
100 1 0.00
101 41 0.19
102 170 0.80
103 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTTGGT
Found at i:36308256 original size:153 final size:152
Alignment explanation
Indices: 36307992--36308338 Score: 412
Period size: 153 Copynumber: 2.3 Consensus size: 152
36307982 TAAGGTATTG
* * *
36307992 ATGAACACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATTGTCACATGTCT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATTGTCACATGTCT
* * * * * * *
36308057 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAG
66 AGTACTAAGTGAAGGCTACAACGTGAACCGAAAAACTTTGATCACGTGTGTAGTACTATGTGAAA
* **
36308122 GCTACTACGTGAATCGATAAATG
131 GCTACTACGTGAACCG-TAAAAC
* * * * *
36308145 ATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGA-AAAGT-TTTGGTCACGTGT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TAATT-GTCACATGT
* * * *
36308208 GTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAAAC-TTGATCACGTGTGTAGTACTATGTG
64 CTAGTACTAAGTGAAGGCTACAACGTGAACCG-AAAAACTTTGATCACGTGTGTAGTACTATGTG
36308272 AAAGCTACTACGTGAACCGTAAAAC
128 AAAGCTACTACGTGAACCGTAAAAC
* * *
36308297 TTGATCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTAT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTAT
36308339 TGAATGATAA
Statistics
Matches: 163, Mismatches: 28, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
152 45 0.28
153 114 0.70
154 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (152 bp):
ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATTGTCACATGTCT
AGTACTAAGTGAAGGCTACAACGTGAACCGAAAAACTTTGATCACGTGTGTAGTACTATGTGAAA
GCTACTACGTGAACCGTAAAAC
Found at i:36320098 original size:26 final size:26
Alignment explanation
Indices: 36320069--36320122 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
36320059 GGCCAAAGAA
36320069 TAGGGAAAGAACCTCATGTTATCTAC
1 TAGGGAAAGAACCTCATGTTATCTAC
*
36320095 TAGGGAAAGAGCCTCATGTTATCTAC
1 TAGGGAAAGAACCTCATGTTATCTAC
36320121 TA
1 TA
36320123 TGCTTCGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (26 bp):
TAGGGAAAGAACCTCATGTTATCTAC
Found at i:36320650 original size:15 final size:15
Alignment explanation
Indices: 36320630--36320661 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
36320620 CGACGGTTTA
36320630 TAGCAGAAACAGAGG
1 TAGCAGAAACAGAGG
36320645 TAGCAGAAACAGAGG
1 TAGCAGAAACAGAGG
36320660 TA
1 TA
36320662 CAGTCTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.31, T:0.09
Consensus pattern (15 bp):
TAGCAGAAACAGAGG
Found at i:36322134 original size:25 final size:25
Alignment explanation
Indices: 36322078--36322137 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
36322068 AAAAAAACAT
* *
36322078 TTTAATTTTCCTATTATTATTATTA
1 TTTATTTTTACTATTATTATTATTA
36322103 TTTATTTTTACTATT-TTATT-TTA
1 TTTATTTTTACTATTATTATTATTA
36322126 TTTTCATTTTTA
1 -TTT-ATTTTTA
36322138 TTTTTACACG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 3 0.10
24 8 0.26
25 20 0.65
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTATTTTTACTATTATTATTATTA
Found at i:36322140 original size:6 final size:6
Alignment explanation
Indices: 36322091--36322143 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
36322081 AATTTTCCTA
* *
36322091 TTATTA TTATTAT TTATTT TTACTATT TTA-TT TTATTT TCATTT TTATTT
1 TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTATTT TTATTT TTATTT
36322141 TTA
1 TTA
36322144 CACGAAACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 5 0.12
6 24 0.60
7 6 0.15
8 5 0.12
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (6 bp):
TTATTT
Found at i:36322142 original size:18 final size:20
Alignment explanation
Indices: 36322092--36322143 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
36322082 ATTTTCCTAT
*
36322092 TATTATTATTATTTATTTTTAC
1 TATT-TTATT-TTTATTTTCAC
36322114 TATTTTA-TTTTATTTTCA-
1 TATTTTATTTTTATTTTCAC
36322132 T-TTTTATTTTTA
1 TATTTTATTTTTA
36322144 CACGAAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.18
18 6 0.21
19 9 0.32
20 1 0.04
21 3 0.11
22 4 0.14
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTTTATTTTTATTTTCAC
Found at i:36333721 original size:21 final size:20
Alignment explanation
Indices: 36333692--36333734 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
36333682 TTTATTATCT
*
36333692 ATTGTATATTATTTATAAACAC
1 ATTGTATA-TATTT-TAAAAAC
36333714 ATTG-ATATATTTTAAAAAC
1 ATTGTATATATTTTAAAAAC
36333733 AT
1 AT
36333735 AATTTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 3 0.15
22 4 0.20
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTGTATATATTTTAAAAAC
Found at i:36337577 original size:26 final size:25
Alignment explanation
Indices: 36337531--36337579 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
36337521 ATCGATGTAT
* *
36337531 AAATAAATTGTATTGTGATAAAACA
1 AAATAAATTATATTGTAATAAAACA
*
36337556 AAATAAATATATATTTTAATAAAA
1 AAATAAAT-TATATTGTAATAAAA
36337580 TGTTTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (25 bp):
AAATAAATTATATTGTAATAAAACA
Found at i:36342119 original size:39 final size:40
Alignment explanation
Indices: 36342074--36342245 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
36342064 GCTCCTCGTT
* * *
36342074 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
36342114 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
36342153 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * *
36342193 CAAAGGCCTTCGGGGCTTAACCCAGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCC-GGATTTAGTAACTCGCA
36342233 CAAATGCCTTCGG
1 CAAATGCCTTCGG
36342246 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.30
40 78 0.66
41 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:36342174 original size:40 final size:39
Alignment explanation
Indices: 36342076--36342298 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
36342066 TCCTCGTTCA
* * * *
36342076 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
36342115 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
36342154 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * * *
36342194 AAAGGCCTTCGGGGCTTAACCCAGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCC-GGATTTAGTAACTCGCAC
** * * * *
36342234 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
36342275 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
36342299 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
39 41 0.26
40 101 0.65
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:36342307 original size:41 final size:41
Alignment explanation
Indices: 36342230--36342307 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
36342220 TTTGTATCTC
* * *
36342230 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
36342271 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
36342308 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:36362817 original size:17 final size:19
Alignment explanation
Indices: 36362778--36362821 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
36362768 CTTTCATTTT
*
36362778 ATATATTTACAATTGATAT
1 ATATATTTACAATTGATAC
*
36362797 ATATATTTA-GATT-ATAC
1 ATATATTTACAATTGATAC
36362814 ATATATTT
1 ATATATTT
36362822 CTTGAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 11 0.48
18 3 0.13
19 9 0.39
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
ATATATTTACAATTGATAC
Found at i:36363987 original size:6 final size:6
Alignment explanation
Indices: 36363976--36364003 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
36363966 GATTGATTGC
36363976 CTGATT CTGATT CTGATT CTGATT CTGA
1 CTGATT CTGATT CTGATT CTGATT CTGA
36364004 CTATGACCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (6 bp):
CTGATT
Found at i:36365989 original size:18 final size:17
Alignment explanation
Indices: 36365956--36365989 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
36365946 AAATATGACG
*
36365956 TAAAAATTTAAAAAATC
1 TAAAAAATTAAAAAATC
36365973 TAAAAAATTATAAAAAT
1 TAAAAAATTA-AAAAAT
36365990 TTCTCAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATTAAAAAATC
Found at i:36366024 original size:23 final size:22
Alignment explanation
Indices: 36365982--36366023 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
36365972 CTAAAAAATT
*
36365982 ATAAAAATTTCTCAAATTTTAA
1 ATAAAAAATTCTCAAATTTTAA
36366004 ATAAAAAATTCT-AAACTTTT
1 ATAAAAAATTCTCAAA-TTTT
36366024 TTAATGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAAAAATTCTCAAATTTTAA
Found at i:36366362 original size:24 final size:24
Alignment explanation
Indices: 36366335--36366382 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
36366325 AAATTAGTAA
36366335 GTCAAATAAACTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
* *
36366359 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
36366383 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
GTCAAATAAACTATACTAATAAAT
Found at i:36368328 original size:24 final size:24
Alignment explanation
Indices: 36368301--36368348 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
36368291 AAATTAGTAA
36368301 GTCAAATAAACTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
* *
36368325 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
36368349 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
GTCAAATAAACTATACTAATAAAT
Found at i:36370981 original size:24 final size:23
Alignment explanation
Indices: 36370943--36370995 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
36370933 TGAAATAAAA
* *
36370943 TAAAAATAGTGATAATCATATATT
1 TAAAAATAATGATAATCAT-TAAT
* *
36370967 TAAAAATAATTATAATTATTAAT
1 TAAAAATAATGATAATCATTAAT
36370990 TAAAAA
1 TAAAAA
36370996 ACTATGCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
TAAAAATAATGATAATCATTAAT
Found at i:36377091 original size:19 final size:20
Alignment explanation
Indices: 36377059--36377098 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
36377049 GTGGTAAAAT
36377059 TAAAGTTCTATTAATGCAAA
1 TAAAGTTCTATTAATGCAAA
36377079 TAAAGTT-TATTAATGCAAA
1 TAAAGTTCTATTAATGCAAA
36377098 T
1 T
36377099 GCTAGGGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
TAAAGTTCTATTAATGCAAA
Found at i:36378747 original size:21 final size:22
Alignment explanation
Indices: 36378731--36378777 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
36378721 GTATTTTTAT
36378731 TTTTTAA-AATTTAATTTATAA
1 TTTTTAAGAATTTAATTTATAA
* *
36378752 TTTTTAAGAATTT-TTTTAAAA
1 TTTTTAAGAATTTAATTTATAA
36378773 TTTTT
1 TTTTT
36378778 TTCATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTAAGAATTTAATTTATAA
Found at i:36378767 original size:12 final size:11
Alignment explanation
Indices: 36378730--36378794 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
36378720 TGTATTTTTA
36378730 TTTTTTAAAAT
1 TTTTTTAAAAT
* *
36378741 TTAATTTATAA-
1 TT-TTTTAAAAT
36378752 -TTTTTAAGAAT
1 TTTTTTAA-AAT
36378763 TTTTTTAAAAT
1 TTTTTTAAAAT
* *
36378774 TTTTTTCATAT
1 TTTTTTAAAAT
36378785 TTTTTTAAAA
1 TTTTTTAAAA
36378795 AATAAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
9 4 0.10
10 3 0.07
11 22 0.52
12 13 0.31
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:36380130 original size:11 final size:12
Alignment explanation
Indices: 36380112--36380140 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
36380102 GCATTAAGGT
36380112 TATTTTATTTTA
1 TATTTTATTTTA
36380124 T-TTTTATTTTA
1 TATTTTATTTTA
36380135 TATTTT
1 TATTTT
36380141 TGATGTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TATTTTATTTTA
Found at i:36386738 original size:50 final size:50
Alignment explanation
Indices: 36386620--36387115 Score: 442
Period size: 50 Copynumber: 9.7 Consensus size: 50
36386610 GGATGAGATA
* *
36386620 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAAAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTC
*
36386676 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * * *
36386726 TCATGTAAGACCATGTCTAGGACATGGCGTTGGCACTGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * * * * **
36386776 TCC-CGTAAGACTATGTCTGGGACATGGCATAGGCACCTATATGAGAACTC
1 -CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * * *
36386826 CCATGTAAGACCATGTTTGGGATATGGCATTGGCATCATTAAGATTATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-GATGAGAGGTC
* * *
36386882 CCATGTAAGACCATGTTTGGGACATGACATTGGCACCGAGATGAGAAGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* *
36386932 TCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
** * * * * **
36386982 CCCCGTAAGACCATGTATGGGATATGGCA-TGGACACCTATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGG-CACCGAGATGAGAGGTC
* * * * * * * **
36387032 CCATGTAAGACCATATCTGGGATATGACATTAGCA--GTACAAGAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTC
* * *
36387081 CCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
36387116 TGTTATATTC
Statistics
Matches: 364, Mismatches: 65, Indels: 29
0.79 0.14 0.06
Matches are distributed among these distances:
49 40 0.11
50 236 0.65
51 6 0.02
53 3 0.01
55 3 0.01
56 76 0.21
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
Found at i:36386915 original size:156 final size:156
Alignment explanation
Indices: 36386716--36387011 Score: 421
Period size: 156 Copynumber: 1.9 Consensus size: 156
36386706 TGGCACCGAG
* * * * * *
36386716 ATGAGAGGTCTCATGTAAGACCATGTCTAGGACATGGCGTTGGCACTGAGATGAGAGGTCTCCCG
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGACATTGGCACCGAGATGAGAAGTCTCACG
* * * * *
36386781 TAAGACTATGTCTGGGACATGGCATAGGCACCTATATGAGAACTCCCATGTAAGACCATGTTTGG
66 TAAGACCATGTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCACGTAAGACCATGTATGG
36386846 GATATGGCATTGGCATCATTAAGATT
131 GATATGGCATTGGCATCATTAAGATT
* * *
36386872 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGACATTGGCACCGAGATGAGAAGTCTCATG
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGACATTGGCACCGAGATGAGAAGTCTCACG
* * ** *
36386937 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATGG
66 TAAGACCATGTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCACGTAAGACCATGTATGG
36387002 GATATGGCAT
131 GATATGGCAT
36387012 GGACACCTAT
Statistics
Matches: 121, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
156 121 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (156 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGACATTGGCACCGAGATGAGAAGTCTCACG
TAAGACCATGTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCACGTAAGACCATGTATGG
GATATGGCATTGGCATCATTAAGATT
Found at i:36386975 original size:206 final size:206
Alignment explanation
Indices: 36386620--36387062 Score: 726
Period size: 206 Copynumber: 2.2 Consensus size: 206
36386610 GGATGAGATA
* *
36386620 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAAAGGTCCCATGTAAG
1 CCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTAAGATTATGAAAGGTCCCATGTAAG
* * *
36386685 ACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCATGTAAGACCATGTCTAGGACA
66 ACCATGTCTGGGACATGACATTGGCACCGAGATGAGAAGTCTCATGTAAGACCATGTCTAGGACA
* * * *
36386750 TGGCGTTGGCACTGAGATGAGAGGTCTCCCGTAAGACTATGTCTGGGACATGGCATAGG-CACCT
131 TGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGCAT-GGACACCT
36386814 ATATGAGAACTC
195 ATATGAGAACTC
* *
36386826 CCATGTAAGACCATGTTTGGGATATGGCATTGGCATCATTAAGATTATGAGAGGTCCCATGTAAG
1 CCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTAAGATTATGAAAGGTCCCATGTAAG
* *
36386891 ACCATGTTTGGGACATGACATTGGCACCGAGATGAGAAGTCTCATGTAAGACCATGTCTGGGACA
66 ACCATGTCTGGGACATGACATTGGCACCGAGATGAGAAGTCTCATGTAAGACCATGTCTAGGACA
*
36386956 TGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATGGGATATGGCATGGACACCTA
131 TGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATGGACACCTA
36387021 TATGAGAACTC
196 TATGAGAACTC
* *
36387032 CCATGTAAGACCATATCTGGGATATGACATT
1 CCATGTAAGACCATGTCTGGGATATGGCATT
36387063 AGCAGTACAA
Statistics
Matches: 219, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
205 2 0.01
206 217 0.99
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (206 bp):
CCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTAAGATTATGAAAGGTCCCATGTAAG
ACCATGTCTGGGACATGACATTGGCACCGAGATGAGAAGTCTCATGTAAGACCATGTCTAGGACA
TGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATGGACACCTA
TATGAGAACTC
Found at i:36389436 original size:30 final size:30
Alignment explanation
Indices: 36389371--36389456 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 30
36389361 CACGAGAATA
* **
36389371 AGTTGCTCACACAAGCTGACAATATTTCAG
1 AGTTGCTCACACAAGCTGACATTATAACAG
* *
36389401 GGTTGCTCACACAAGCTGACATTGTAACAG
1 AGTTGCTCACACAAGCTGACATTATAACAG
* *
36389431 AGTTGCTTACATAAGCTGACATTATA
1 AGTTGCTCACACAAGCTGACATTATA
36389457 TCGAGATTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (30 bp):
AGTTGCTCACACAAGCTGACATTATAACAG
Found at i:36394818 original size:11 final size:11
Alignment explanation
Indices: 36394802--36394827 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
36394792 ATACCAAATG
36394802 TAAAAAATAAA
1 TAAAAAATAAA
36394813 TAAAAAATAAA
1 TAAAAAATAAA
36394824 TAAA
1 TAAA
36394828 TGGCAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:36395773 original size:16 final size:16
Alignment explanation
Indices: 36395752--36395784 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36395742 TTTAAAAGAT
36395752 TTGAAA-GAAAACTCAA
1 TTGAAATGAAAA-TCAA
36395768 TTGAAATGAAAATCAA
1 TTGAAATGAAAATCAA
36395784 T
1 T
36395785 GCCGAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (16 bp):
TTGAAATGAAAATCAA
Found at i:36403006 original size:17 final size:16
Alignment explanation
Indices: 36402982--36403013 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
36402972 TTTTTTTATT
36402982 TTTCTTATTTATTTAA
1 TTTCTTATTTATTTAA
36402998 TTTCGTTATTTATTTA
1 TTTC-TTATTTATTTA
36403014 TTTTTATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTCTTATTTATTTAA
Found at i:36405959 original size:50 final size:50
Alignment explanation
Indices: 36405860--36406047 Score: 178
Period size: 50 Copynumber: 3.6 Consensus size: 50
36405850 AAAGAGATCC
*
36405860 CATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATGAGAGGTCA
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACCA---AG---ATGAGAGGTCA
* * *
36405916 CATGTAAGACCATGTCTAGGACATGGCGTTGGCACCAAGATGAGAGGTCA
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATGAGAGGTCA
** * * * * ** *
36405966 CCCGTAAGACCATGTCTGGGACATGTCATGGGCACCTATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATGAGAGGTCA
* * *
36406016 CATGTAAGACCCTATCTGGGATATGACATTGG
1 CATGTAAGACCATGTCTGGGACATGACATTGG
36406048 TAGTTCAAGA
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 75 0.68
53 2 0.02
56 33 0.30
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATGAGAGGTCA
Found at i:36413794 original size:35 final size:35
Alignment explanation
Indices: 36413695--36413795 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 35
36413685 ATTTATTGAT
* * * *
36413695 ATTCTGATTCGCATGTTGAGCATGCTATTATTCTG
1 ATTCTGATTCGCATGTTAAGCATGCCATTGTTCTA
* * * *
36413730 ATTCTGATTCACTTGTTAAGCTTGTCATTGTTCTA
1 ATTCTGATTCGCATGTTAAGCATGCCATTGTTCTA
* *
36413765 ATTCTGATTCGCATATTAAACATGCCATTGT
1 ATTCTGATTCGCATGTTAAGCATGCCATTGT
36413796 GATAAATCGT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.44
Consensus pattern (35 bp):
ATTCTGATTCGCATGTTAAGCATGCCATTGTTCTA
Found at i:36415045 original size:11 final size:11
Alignment explanation
Indices: 36415016--36415048 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
36415006 AGTGAAAAAG
36415016 AAAAGTGAG-A
1 AAAAGTGAGAA
36415026 AAAAGTGAGAA
1 AAAAGTGAGAA
*
36415037 AAAAATGAGAA
1 AAAAGTGAGAA
36415048 A
1 A
36415049 TTCCAGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (11 bp):
AAAAGTGAGAA
Found at i:36415277 original size:101 final size:102
Alignment explanation
Indices: 36415157--36415341 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
36415147 AAAGTGATGG
* *
36415157 TCACGTGTGTAGTAGTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
36415220 ACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
* * *
36415258 TCACGTGTGTAGTACTATGTGCAGGCTACTTCGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
* *
36415323 TTATGTGTAGGCTACTATG
66 CTATGTGCAGGCTACTATG
36415342 TGAACCAGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 38 0.51
102 33 0.44
103 4 0.05
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
Found at i:36415283 original size:51 final size:50
Alignment explanation
Indices: 36415157--36415339 Score: 172
Period size: 51 Copynumber: 3.6 Consensus size: 50
36415147 AAAGTGATGG
* * *
36415157 TCACGTGTGTAGTAGTATGTGCAGGCTACTACGTGTACCAGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGAATGATAGA
* * * * *
36415207 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACC-GAATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGAAT-G-ATAGA
* * * * *
36415258 TCACGTGTGTAGTACTATGTGCAGGCTACTTCGTGTATCGGATAGTGAT-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGA-A-TGATAGA
* * *
36415309 TCACATGTGTAGTATTATGTGTAGGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
36415340 TGTGAACCAG
Statistics
Matches: 108, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
49 4 0.04
50 35 0.32
51 63 0.58
52 3 0.03
53 2 0.02
54 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGAATGATAGA
Found at i:36419617 original size:21 final size:21
Alignment explanation
Indices: 36419579--36419618 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36419569 ATTATAGCAA
*
36419579 CTCAAAACATGATTAAACAAG
1 CTCAAAACATGATAAAACAAG
36419600 CTCAAAACATG-TCAAAACA
1 CTCAAAACATGAT-AAAACA
36419619 TCTATCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.23, G:0.07, T:0.17
Consensus pattern (21 bp):
CTCAAAACATGATAAAACAAG
Found at i:36423571 original size:3 final size:3
Alignment explanation
Indices: 36423556--36423585 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
36423546 TGTCCATGGA
*
36423556 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36423586 GGAAAATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:36426542 original size:22 final size:22
Alignment explanation
Indices: 36426510--36426552 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
36426500 TACACACGCA
*
36426510 AATATTTTTTAAAAAATATTTT
1 AATATTATTTAAAAAATATTTT
*
36426532 AATATTATTTAAAATATATTT
1 AATATTATTTAAAAAATATTT
36426553 CATTATCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTATTTAAAAAATATTTT
Found at i:36431866 original size:57 final size:57
Alignment explanation
Indices: 36431772--36431931 Score: 248
Period size: 57 Copynumber: 2.8 Consensus size: 57
36431762 GCATGTAACA
* *
36431772 CTTAGAGACAACTCTCACTTCACCAGTTCGCAACTCCATCTCAGTTCACATGCAATG
1 CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTCAGTTCACATGCAATG
* * * * *
36431829 CTTAGAGACAGCTCGCACTTCACCAGTTTGTATCTCCATCTCTGTTCACATGCAATG
1 CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTCAGTTCACATGCAATG
*
36431886 CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTTAGTT
1 CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTCAGTT
36431932 TCCAAGCTCT
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 91 1.00
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.29
Consensus pattern (57 bp):
CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTCAGTTCACATGCAATG
Found at i:36437202 original size:99 final size:99
Alignment explanation
Indices: 36436805--36437200 Score: 693
Period size: 99 Copynumber: 4.0 Consensus size: 99
36436795 AATATTTTAA
* * *
36436805 AAATTTTAAAATATATATTATTACAAAGTACATAAAAATTAAAAACAAAAACAAGAAGTACACGT
1 AAATTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAGTACACGT
36436870 GGTTGCCATGCGGGCTGCCATATTTAAAAATTTT
66 GGTTGCCATGCGGGCTGCCATATTTAAAAATTTT
36436904 AAATTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAGTACACGT
1 AAATTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAGTACACGT
*
36436969 GGTTGCCATGCGGGCTGCCATATTTAAAAATTTA
66 GGTTGCCATGCGGGCTGCCATATTTAAAAATTTT
* *
36437003 AAATTTTAAAATATATATTATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAGTACACGT
1 AAATTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAGTACACGT
36437068 GGTTGCCATGCGGGCTGCCATATTTAAAAATTTT
66 GGTTGCCATGCGGGCTGCCATATTTAAAAATTTT
* *
36437102 AAATTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACATGAAGTACATGT
1 AAATTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAGTACACGT
* *
36437167 AGGTTGCCATGCGGGCTGTCATATTTCAAAATTT
66 -GGTTGCCATGCGGGCTGCCATATTTAAAAATTT
36437201 AATGTTTTAG
Statistics
Matches: 283, Mismatches: 13, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
99 252 0.89
100 31 0.11
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.29
Consensus pattern (99 bp):
AAATTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAGTACACGT
GGTTGCCATGCGGGCTGCCATATTTAAAAATTTT
Found at i:36437279 original size:31 final size:31
Alignment explanation
Indices: 36437241--36437303 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
36437231 ATAATTCAAT
*
36437241 TCTTTTTT-AAAGATTGATGGTCAAATTTAAC
1 TCTTTTTTAAAAGATTGA-GATCAAATTTAAC
*
36437272 TCTTTTTTAAAAGCTTGAGATCAAATTTAAC
1 TCTTTTTTAAAAGATTGAGATCAAATTTAAC
36437303 T
1 T
36437304 AAAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (31 bp):
TCTTTTTTAAAAGATTGAGATCAAATTTAAC
Found at i:36442756 original size:78 final size:76
Alignment explanation
Indices: 36442674--36442910 Score: 384
Period size: 76 Copynumber: 3.1 Consensus size: 76
36442664 TTTAAATACA
*
36442674 AAGTTGACTATTTAAATTGTAAAAAAAACAACATAAAATTGATAAATAAAATGACAACAAATTCA
1 AAGTTGACTATTTAAATTG-AAAAAAAA-AACATAAAATTGATAAATAAAATGGCAACAAATTCA
36442739 TTACATAAATATG
64 TTACATAAATATG
*
36442752 AAGTTGACTATTTAAATTGAAAAAAAAATCATAAAATTGATAAATAAAATGGCAACAAATTCATT
1 AAGTTGACTATTTAAATTGAAAAAAAAAACATAAAATTGATAAATAAAATGGCAACAAATTCATT
36442817 ACATAAATATG
66 ACATAAATATG
* * * *
36442828 AAGTTGACTATTTAAATCGAAAAAAATAAATCATAAAATTGATAAATAAAATGGGAAAAAAATCA
1 AAGTTGACTATTTAAATTGAAAAAAA-AAA-CATAAAATTGATAAATAAAATGGCAACAAATTCA
36442893 TTACATAAATATG
64 TTACATAAATATG
36442906 AAGTT
1 AAGTT
36442911 ATTTATATTA
Statistics
Matches: 150, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
76 72 0.48
77 10 0.07
78 68 0.45
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (76 bp):
AAGTTGACTATTTAAATTGAAAAAAAAAACATAAAATTGATAAATAAAATGGCAACAAATTCATT
ACATAAATATG
Found at i:36442808 original size:76 final size:77
Alignment explanation
Indices: 36442674--36442910 Score: 388
Period size: 78 Copynumber: 3.1 Consensus size: 77
36442664 TTTAAATACA
*
36442674 AAGTTGACTATTTAAATTGTAAAAAAAACAA-CATAAAATTGATAAATAAAATGACAACAAATTC
1 AAGTTGACTATTTAAATTG-AAAAAAAA-AATCATAAAATTGATAAATAAAATGGCAACAAATTC
36442738 ATTACATAAATATG
64 ATTACATAAATATG
36442752 AAGTTGACTATTTAAATTG-AAAAAAAAATCATAAAATTGATAAATAAAATGGCAACAAATTCAT
1 AAGTTGACTATTTAAATTGAAAAAAAAAATCATAAAATTGATAAATAAAATGGCAACAAATTCAT
36442816 TACATAAATATG
66 TACATAAATATG
* * * *
36442828 AAGTTGACTATTTAAATCGAAAAAAATAAATCATAAAATTGATAAATAAAATGGGAAAAAAATCA
1 AAGTTGACTATTTAAATTGAAAAAAA-AAATCATAAAATTGATAAATAAAATGGCAACAAATTCA
36442893 TTACATAAATATG
65 TTACATAAATATG
36442906 AAGTT
1 AAGTT
36442911 ATTTATATTA
Statistics
Matches: 151, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
75 2 0.01
76 71 0.47
77 6 0.04
78 72 0.48
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (77 bp):
AAGTTGACTATTTAAATTGAAAAAAAAAATCATAAAATTGATAAATAAAATGGCAACAAATTCAT
TACATAAATATG
Found at i:36443137 original size:33 final size:33
Alignment explanation
Indices: 36443095--36443158 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
36443085 ATGAACTTGA
*
36443095 GCCGGGAGAAGTGGTGTACGACGGTGGATACGG
1 GCCGGGAGAAGTGGAGTACGACGGTGGATACGG
36443128 GCCGGGAGAAGTGGAGTACGACGGTGGATAC
1 GCCGGGAGAAGTGGAGTACGACGGTGGATAC
36443159 AGGTTGGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.16, G:0.47, T:0.14
Consensus pattern (33 bp):
GCCGGGAGAAGTGGAGTACGACGGTGGATACGG
Found at i:36443174 original size:33 final size:33
Alignment explanation
Indices: 36443095--36443179 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
36443085 ATGAACTTGA
* * *
36443095 GCCGGGAGAAGTGGTGTACGACGGTGGATACGG
1 GCCGGAAGAAGTGGAGTACGACGGTGGATACAG
*
36443128 GCCGGGAGAAGTGGAGTACGACGGTGGATACAG
1 GCCGGAAGAAGTGGAGTACGACGGTGGATACAG
** *
36443161 GTTGGAAGGAGTGGAGTAC
1 GCCGGAAGAAGTGGAGTAC
36443180 TGAGTTGGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.25, C:0.13, G:0.47, T:0.15
Consensus pattern (33 bp):
GCCGGAAGAAGTGGAGTACGACGGTGGATACAG
Found at i:36443350 original size:12 final size:12
Alignment explanation
Indices: 36443333--36443371 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
36443323 TGTAGTTCCA
36443333 GCTCTACCTCCG
1 GCTCTACCTCCG
* *
36443345 GCTCTAGCTCTG
1 GCTCTACCTCCG
*
36443357 GCTCTGCCTCCG
1 GCTCTACCTCCG
36443369 GCT
1 GCT
36443372 ATGGTGCATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.05, C:0.44, G:0.23, T:0.28
Consensus pattern (12 bp):
GCTCTACCTCCG
Found at i:36447858 original size:24 final size:24
Alignment explanation
Indices: 36447826--36447877 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
36447816 TCGTGTAATG
36447826 ATGCACATGAACTTAGCAAGTTCT
1 ATGCACATGAACTTAGCAAGTTCT
36447850 ATGCACATGAACTTAGCAAGTTCT
1 ATGCACATGAACTTAGCAAGTTCT
36447874 ATGC
1 ATGC
36447878 TTTTTATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (24 bp):
ATGCACATGAACTTAGCAAGTTCT
Found at i:36448189 original size:29 final size:29
Alignment explanation
Indices: 36448075--36448235 Score: 137
Period size: 29 Copynumber: 5.4 Consensus size: 29
36448065 TTTGCATGAT
36448075 CATATAGGCTCGCATGTACCTAGGGTTCACATGG
1 CATATAGGCTCGCATGTACCTAGGGTT--C---G
* *
36448109 CATATAGGCAT-GCATGCT-CTTAGGGATCG
1 CATATAGGC-TCGCATG-TACCTAGGGTTCG
* * * **
36448138 CATAAAGGCTCGTAAGTTTCTAGGGTTCG
1 CATATAGGCTCGCATGTACCTAGGGTTCG
*
36448167 CACATAGGCTCGCATGTACCTAGGGTTCG
1 CATATAGGCTCGCATGTACCTAGGGTTCG
* * * *
36448196 CATGTAGGGTCGCATGTACCTAAGGTTCA
1 CATATAGGCTCGCATGTACCTAGGGTTCG
36448225 CATATAGGCTC
1 CATATAGGCTC
36448236 ACATAATTCT
Statistics
Matches: 102, Mismatches: 21, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
28 2 0.02
29 76 0.75
32 1 0.01
34 21 0.21
35 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (29 bp):
CATATAGGCTCGCATGTACCTAGGGTTCG
Found at i:36448296 original size:36 final size:36
Alignment explanation
Indices: 36448255--36448331 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
36448245 TAGGGTTCTT
* * * *
36448255 ATATAATCAACATATGGTTCGCATAACATGACTTGC
1 ATATAATAAACACATGGTTCACATAACATGACTCGC
* *
36448291 ATATAATAAACACATGGTTCACATATCATGGCTCGC
1 ATATAATAAACACATGGTTCACATAACATGACTCGC
36448327 ATATA
1 ATATA
36448332 GATTCAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (36 bp):
ATATAATAAACACATGGTTCACATAACATGACTCGC
Found at i:36449711 original size:31 final size:30
Alignment explanation
Indices: 36449676--36449753 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
36449666 ATGCTCAAAT
*
36449676 CAATTCAACAATGTATATTC-ATATA-CGAA
1 CAATTCAACAATGTATA-TCGATATACCCAA
** *
36449705 TCCAATTCAGGAATGAATATCGATATACCCAA
1 --CAATTCAACAATGTATATCGATATACCCAA
36449737 CAATTCAACAATGTATA
1 CAATTCAACAATGTATA
36449754 ACTATTCACG
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
30 16 0.42
31 19 0.50
32 3 0.08
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (30 bp):
CAATTCAACAATGTATATCGATATACCCAA
Found at i:36449991 original size:31 final size:31
Alignment explanation
Indices: 36449922--36449992 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
36449912 TATACCAAAC
* * *
36449922 AATTCAGCAATGTATAACCATACACGAATCA
1 AATTCGGCAATATATAACCATACACAAATCA
* *
36449953 AGA-TCGGCAATATATAATCATACACAAATTA
1 A-ATTCGGCAATATATAACCATACACAAATCA
36449984 AATTCGGCA
1 AATTCGGCA
36449993 TCCTATATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 1 0.03
31 31 0.94
32 1 0.03
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (31 bp):
AATTCGGCAATATATAACCATACACAAATCA
Found at i:36449996 original size:184 final size:184
Alignment explanation
Indices: 36449721--36450235 Score: 766
Period size: 184 Copynumber: 2.8 Consensus size: 184
36449711 TCAGGAATGA
* * * * *
36449721 ATATCGATATACCCAACAATTCAACAATGTATAACTATTCACGAATCAAGATCGGCAATATATAA
1 ATATCCATATACCAAACAATTCAGCAATGTATAACCATACACGAATCAAGATCGGCAATATATAA
* *
36449786 TCAGACACAAATCAAATTCAGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
66 TCAAACACAAATCAAATTCGGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
36449851 AGTACGAATTAATTTCAACAATGTACAACCCTGTACGAATCAAGTCAGCAACTT
131 AGTACGAATTAATTTCAACAATGTACAACCCTGTACGAATCAAGTCAGCAACTT
36449905 ATATCCATATACCAAACAATTCAGCAATGTATAACCATACACGAATCAAGATCGGCAATATATAA
1 ATATCCATATACCAAACAATTCAGCAATGTATAACCATACACGAATCAAGATCGGCAATATATAA
* *
36449970 TCATACACAAATTAAATTCGGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
66 TCAAACACAAATCAAATTCGGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
* ** *
36450035 AGTACGAATTAATTTTAGTAATGTACAACCCTGTATGAATCAAGTCAGCAACTT
131 AGTACGAATTAATTTCAACAATGTACAACCCTGTACGAATCAAGTCAGCAACTT
* * ** *
36450089 ATATCCATATACCAAATAATTC-GACAATGTATAACCATACACGAATCAAGTTCGATAATGTATA
1 ATATCCATATACCAAACAATTCAG-CAATGTATAACCATACACGAATCAAGATCGGCAATATATA
* * * * *
36450153 ATCAAATACAAATCCAATTCGGCATCCTATATACAT-AACAAATTCAATATCGCCAATATATAAC
65 ATCAAACACAAATCAAATTCGGCATCCTATATTCATAAAC-AATTCACTATCGACAATATATAAC
*
36450217 CATGTAC-AAGTTAATTTCA
129 CAAGTACGAA-TTAATTTCA
36450236 GCAAGGTAAA
Statistics
Matches: 302, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
183 6 0.02
184 296 0.98
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (184 bp):
ATATCCATATACCAAACAATTCAGCAATGTATAACCATACACGAATCAAGATCGGCAATATATAA
TCAAACACAAATCAAATTCGGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
AGTACGAATTAATTTCAACAATGTACAACCCTGTACGAATCAAGTCAGCAACTT
Found at i:36464770 original size:16 final size:16
Alignment explanation
Indices: 36464745--36464775 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36464735 AACAAAAAGA
*
36464745 TTTACGGAAACAATTG
1 TTTACAGAAACAATTG
36464761 TTTACAGAAACAATT
1 TTTACAGAAACAATT
36464776 TTTTTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (16 bp):
TTTACAGAAACAATTG
Found at i:36468809 original size:102 final size:102
Alignment explanation
Indices: 36468687--36468892 Score: 376
Period size: 102 Copynumber: 2.0 Consensus size: 102
36468677 TCTTTTCTTT
*
36468687 TTAGGTCTGCATATGATTTTTTTCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATT
1 TTAGGTCTGCATATGATTTTTGTCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATT
* * *
36468752 TTTTCTTCGGTTTCTTGTACTAACTCAGGACCCATTA
66 TTGTCTTCAGTTTCCTGTACTAACTCAGGACCCATTA
36468789 TTAGGTCTGCATATGATTTTTGTCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATT
1 TTAGGTCTGCATATGATTTTTGTCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATT
36468854 TTGTCTTCAGTTTCCTGTACTAACTCAGGACCCATTA
66 TTGTCTTCAGTTTCCTGTACTAACTCAGGACCCATTA
36468891 TT
1 TT
36468893 TTTCTTTCTT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (102 bp):
TTAGGTCTGCATATGATTTTTGTCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATT
TTGTCTTCAGTTTCCTGTACTAACTCAGGACCCATTA
Found at i:36472811 original size:43 final size:43
Alignment explanation
Indices: 36472641--36472812 Score: 129
Period size: 43 Copynumber: 4.0 Consensus size: 43
36472631 CATAGGATTC
* * * * * *
36472641 CGATATGTGATTACGTGTAAGACCACGTTTGGCACTTTGGCAT
1 CGATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
* * * *
36472684 TGAT-TTACGATTTACATGTAAGACCATGTCTGGGACATTGGCAT
1 CGATATT-TGATTT-CATGTAAGACCACGTCTGGGACGTTGGCAT
** * * *
36472728 C-ATATAAGAGTTCGTGTAAGACC-C-TGCCGAGGACAG-TGGCAT
1 CGATATTTGATTTCATGTAAGACCACGT-CTG-GGAC-GTTGGCAT
36472770 CGATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
36472813 TGAATGAGCT
Statistics
Matches: 97, Mismatches: 22, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 23 0.24
43 41 0.42
44 29 0.30
45 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
CGATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:36476476 original size:29 final size:30
Alignment explanation
Indices: 36476426--36476489 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
36476416 CTATTGTTCA
36476426 CAATATATCTATTTAAATTTAT-TTTATTTT
1 CAATATATCTATTTAAATTTATATTT-TTTT
*
36476456 CAATATAT-TA-TTATATGTTATATTTTTTT
1 CAATATATCTATTTAAAT-TTATATTTTTTT
*
36476485 GAATA
1 CAATA
36476490 AAAATAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.17
29 14 0.47
30 11 0.37
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (30 bp):
CAATATATCTATTTAAATTTATATTTTTTT
Found at i:36477095 original size:61 final size:61
Alignment explanation
Indices: 36476930--36477101 Score: 181
Period size: 61 Copynumber: 2.8 Consensus size: 61
36476920 TATCAATTTG
* * * * *
36476930 ATTCTAAA-TCTAAACAA-TTCAACAAATTTAAACTTTAATGTTAAAAAAATTTGTCATTTTA
1 ATTC-AAATTCTAAA-AATTTCAATAAATTTAATCTCTAATGTTTACAAAATTTGTCATTTTA
* ** * *
36476991 GTTTTAATTC-AAAAATGATCAATAAATTTAATC-CTCAATGTTTACAAAATTTTTCATTTTA
1 ATTCAAATTCTAAAAAT-TTCAATAAATTTAATCTCT-AATGTTTACAAAATTTGTCATTTTA
*
36477052 ATTCAAATTCTAAAAATTTCAATAAATTTAATCTCTAACGTTTACAAAAT
1 ATTCAAATTCTAAAAATTTCAATAAATTTAATCTCTAATGTTTACAAAAT
36477102 GACATTTTGA
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
59 2 0.02
60 6 0.07
61 74 0.82
62 8 0.09
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (61 bp):
ATTCAAATTCTAAAAATTTCAATAAATTTAATCTCTAATGTTTACAAAATTTGTCATTTTA
Found at i:36482745 original size:3 final size:3
Alignment explanation
Indices: 36482737--36482762 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36482727 TGTAGTCTCT
36482737 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
36482763 GATTTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:36487283 original size:29 final size:27
Alignment explanation
Indices: 36487265--36487334 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
36487255 ATATTAAGTC
36487265 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
36487292 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
36487320 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
36487335 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:36487328 original size:28 final size:28
Alignment explanation
Indices: 36487265--36487362 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
36487255 ATATTAAGTC
*
36487265 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
36487292 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
36487320 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
36487349 CGCACACTTAGTGC
1 CGCACACTTAGTGC
36487363 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:36492087 original size:143 final size:144
Alignment explanation
Indices: 36491829--36492122 Score: 518
Period size: 143 Copynumber: 2.0 Consensus size: 144
36491819 GATATGGTTG
* * *
36491829 ATCAAGATAGGATTTGTCCTTCCTACATAATGGGAGCAATATCTTAGGCCTCTTGATTGAGTGAG
1 ATCAAGATAGGATTTGTCCCTCCTACATAATGGGAGCAATATCTTAGGCCTCTAGATGGAGTGAG
36491894 ACTAGAAATGCATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTA-TTTTTTTATTAT
66 ACTAGAAATGCATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTATTTTTTTTATTAT
36491958 AGTCTACACAGAAT
131 AGTCTACACAGAAT
* *
36491972 ATCAAGATAGGATTTGTCCCTCCTACATAATGGGAGGAATATTTTAGGCCTCTAGATGGAGTGAG
1 ATCAAGATAGGATTTGTCCCTCCTACATAATGGGAGCAATATCTTAGGCCTCTAGATGGAGTGAG
* *
36492037 ACTAGAAATGGATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTATTTTTTTTATTGT
66 ACTAGAAATGCATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTATTTTTTTTATTAT
36492102 AGTCTACACAGAAT
131 AGTCTACACAGAAT
36492116 ATCAAGA
1 ATCAAGA
36492123 AATATGAGAT
Statistics
Matches: 143, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
143 111 0.78
144 32 0.22
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (144 bp):
ATCAAGATAGGATTTGTCCCTCCTACATAATGGGAGCAATATCTTAGGCCTCTAGATGGAGTGAG
ACTAGAAATGCATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTATTTTTTTTATTAT
AGTCTACACAGAAT
Found at i:36500316 original size:39 final size:39
Alignment explanation
Indices: 36500262--36500340 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
36500252 AAAGTTCAAG
36500262 ATAATTTCGTTGTTCATTCTTTGACTAAGTGGATTATGT
1 ATAATTTCGTTGTTCATTCTTTGACTAAGTGGATTATGT
*
36500301 ATAATTTCGTTGTTCATTCTTTGACTGAGTGGATTATGT
1 ATAATTTCGTTGTTCATTCTTTGACTAAGTGGATTATGT
36500340 A
1 A
36500341 GAGGCTGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (39 bp):
ATAATTTCGTTGTTCATTCTTTGACTAAGTGGATTATGT
Found at i:36511393 original size:25 final size:25
Alignment explanation
Indices: 36511347--36511420 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
36511337 AGATAACACG
* *
36511347 CCACAAA-GCTTTCAAGTG-AATTCG
1 CCACAAAGGCTTTCCA-TGAAATTCA
*
36511371 CCACAGAGGCTTTCCATGAAATTCA
1 CCACAAAGGCTTTCCATGAAATTCA
* * *
36511396 CCATAAAGGTTTTTCATGAAATTCA
1 CCACAAAGGCTTTCCATGAAATTCA
36511421 TGTTTACTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 8 0.20
25 33 0.80
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (25 bp):
CCACAAAGGCTTTCCATGAAATTCA
Found at i:36512291 original size:16 final size:17
Alignment explanation
Indices: 36512270--36512305 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
36512260 TCAATCATCC
36512270 CTCATCCCTCATCC-CT
1 CTCATCCCTCATCCTCT
*
36512286 CTCATCTCTCATCCTCT
1 CTCATCCCTCATCCTCT
36512303 CTC
1 CTC
36512306 TCAACTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.36
Consensus pattern (17 bp):
CTCATCCCTCATCCTCT
Found at i:36515630 original size:42 final size:42
Alignment explanation
Indices: 36515571--36515653 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
36515561 GAAGGAAAGA
*
36515571 TCGAGGATGTTTTGGTAAGAGTTGATAAATTTATTTTTCCTG
1 TCGAGGATGTTTTGGTAAGAGTCGATAAATTTATTTTTCCTG
36515613 TCGAGGATGTTTTGGTAAGAGTCGATAAATTTATTTTTCCT
1 TCGAGGATGTTTTGGTAAGAGTCGATAAATTTATTTTTCCT
36515654 ACTGATTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.45
Consensus pattern (42 bp):
TCGAGGATGTTTTGGTAAGAGTCGATAAATTTATTTTTCCTG
Found at i:36518692 original size:7 final size:7
Alignment explanation
Indices: 36518680--36518709 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
36518670 ACTTTTTCAA
36518680 TCATCCC
1 TCATCCC
36518687 TCATCCC
1 TCATCCC
36518694 TCATCCC
1 TCATCCC
36518701 TCATCCC
1 TCATCCC
36518708 TC
1 TC
36518710 TCATCTCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.57, G:0.00, T:0.30
Consensus pattern (7 bp):
TCATCCC
Found at i:36522265 original size:15 final size:14
Alignment explanation
Indices: 36522245--36522279 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
36522235 ACAGATATGA
36522245 TTTTTATTTTTATTT
1 TTTTTA-TTTTATTT
36522260 TTTTTATTTTATTT
1 TTTTTATTTTATTT
36522274 TCTTTT
1 T-TTTT
36522280 TAGGTTGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTATTTTATTT
Found at i:36524648 original size:81 final size:81
Alignment explanation
Indices: 36524513--36524711 Score: 229
Period size: 81 Copynumber: 2.5 Consensus size: 81
36524503 GGAAAGGATG
* * * * * ** *
36524513 CCTATGTGGCTCAAGATGAAAGGAACGTCTTTATGGTGAATCATGAAAAGGTAGTCTTTGTGGCA
1 CCTATGTGGCACAAAATGAAAGGAACGCCTTTGTGGCGAATCATGAAAAGGTAGTCCCTATGGCA
36524578 AACCCTGCAATAATAA
66 AACCCTGCAATAATAA
* * * *
36524594 CCTATATGGCACAATATGAAAGGAACGCCTTTGTGGCGAATTATGAAAGGGTAGTCCCTATGGCA
1 CCTATGTGGCACAAAATGAAAGGAACGCCTTTGTGGCGAATCATGAAAAGGTAGTCCCTATGGCA
* *
36524659 AACCCTGCAATGATCA
66 AACCCTGCAATAATAA
* * *
36524675 CCTTTGTGGCGA-AAAATGAAAGGAATGCATTTGTGGC
1 CCTATGTGGC-ACAAAATGAAAGGAACGCCTTTGTGGC
36524712 AAACTCCATA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
81 98 0.99
82 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (81 bp):
CCTATGTGGCACAAAATGAAAGGAACGCCTTTGTGGCGAATCATGAAAAGGTAGTCCCTATGGCA
AACCCTGCAATAATAA
Found at i:36529047 original size:29 final size:30
Alignment explanation
Indices: 36528987--36529047 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
36528977 GCCTTTTAAA
* * **
36528987 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACAACCAAAATTT
36529017 AATATTTACAAAAAGAG-CAACCAAAATTT
1 AATATTTACAAAAAGAGACAACCAAAATTT
36529046 AA
1 AA
36529048 AAATAATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAACCAAAATTT
Found at i:36536436 original size:16 final size:16
Alignment explanation
Indices: 36536417--36536458 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
36536407 ATTAATTTGG
36536417 ATTAAAATTAAAATTA
1 ATTAAAATTAAAATTA
*
36536433 ATT-ATATTATAAATTA
1 ATTAAAATTA-AAATTA
36536449 A-TAAAATTAA
1 ATTAAAATTAA
36536459 TTTGGACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAAATTAAAATTA
Found at i:36539841 original size:20 final size:20
Alignment explanation
Indices: 36539816--36539863 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
36539806 TATCATCATA
36539816 ACAGATACCCTTCTTGACAT
1 ACAGATACCCTTCTTGACAT
36539836 ACAGATACCCTTCTTGACAT
1 ACAGATACCCTTCTTGACAT
36539856 ACAGATAC
1 ACAGATAC
36539864 ACATCTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.27
Consensus pattern (20 bp):
ACAGATACCCTTCTTGACAT
Found at i:36542270 original size:40 final size:40
Alignment explanation
Indices: 36542214--36542303 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
36542204 AGGGGCACCA
* ** *
36542214 AAGTGCAAACATAGGCATTATTGTACAATCATAGGCATCG
1 AAGTGCAAACAGAGGCACGATTGTACAATCAAAGGCATCG
* * **
36542254 AAGTGCAAATAGAGGCACGATTGTGCAATCAAAGTTATCG
1 AAGTGCAAACAGAGGCACGATTGTACAATCAAAGGCATCG
36542294 AAGTGCAAAC
1 AAGTGCAAAC
36542304 TTGTACAAGC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (40 bp):
AAGTGCAAACAGAGGCACGATTGTACAATCAAAGGCATCG
Found at i:36555350 original size:19 final size:20
Alignment explanation
Indices: 36555326--36555367 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
36555316 CAAACACCAG
*
36555326 AAAAGTAAATTA-TTTTCAA
1 AAAAGTAAATCATTTTTCAA
36555345 AAAAGTAAATCATTTTTCAA
1 AAAAGTAAATCATTTTTCAA
36555365 AAA
1 AAA
36555368 TTATTTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAAGTAAATCATTTTTCAA
Found at i:36556195 original size:59 final size:59
Alignment explanation
Indices: 36556132--36556326 Score: 203
Period size: 59 Copynumber: 3.3 Consensus size: 59
36556122 TTGACTAGTG
36556132 TTACAA-AATAATAATA-AGAAAACATCAAGTTTG-T-TTTACTAATCAAATGTTAGATTCTA
1 TTACAACAATAATAATACA-AAAA-AT-AA-TTTGATATTTACTAATCAAATGTTAGATTCTA
**
36556191 TTACAACAAT--TAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTCTA
1 TTACAACAATAATAATACAAAAAATAATTTGAT--ATTTACTAATCAAATGTTAGATTCTA
** *
36556250 TTACAACAAT--TAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTA
1 TTACAACAATAATAATACAAAAAATAATTTGAT--ATTTACTAATCAAATGTTAGATTCTA
36556309 TTACAACAAT--TAATACAA
1 TTACAACAATAATAATACAA
36556327 TTAACAATTA
Statistics
Matches: 127, Mismatches: 3, Indels: 12
0.89 0.02 0.08
Matches are distributed among these distances:
55 4 0.03
56 3 0.02
57 2 0.02
58 7 0.06
59 108 0.85
60 3 0.02
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (59 bp):
TTACAACAATAATAATACAAAAAATAATTTGATATTTACTAATCAAATGTTAGATTCTA
Found at i:36556327 original size:59 final size:59
Alignment explanation
Indices: 36556166--36556335 Score: 322
Period size: 59 Copynumber: 2.9 Consensus size: 59
36556156 TCAAGTTTGT
36556166 TTTACTAATCAAATGTTAGATTCTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTCTATTACAACAATTAATACAATTAATAATTTGATAAA
36556225 TTTACTAATCAAATGTTAGATTCTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTCTATTACAACAATTAATACAATTAATAATTTGATAAA
* *
36556284 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTCTATTACAACAATTAATACAATTAATAATT
36556336 AATAATTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTCTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:36556367 original size:16 final size:16
Alignment explanation
Indices: 36556346--36556387 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
36556336 AATAATTTGA
*
36556346 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
36556362 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
36556378 TAGTTTTAAT
1 TAATTTTAAT
36556388 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:36556371 original size:22 final size:23
Alignment explanation
Indices: 36556361--36556416 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
36556351 TTACTAACAA
* * *
36556361 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
36556383 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
36556406 TTAATTTTAAT
1 TTAATTTTAAT
36556417 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:36559123 original size:29 final size:28
Alignment explanation
Indices: 36559090--36559145 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
36559080 CTTTGCTCCT
36559090 AATAATGTTA-CTTCCAAGATTTGAAACCC
1 AATAATGTTACCTT-CAAGATTT-AAACCC
*
36559119 AATAATGTTACCTTCAATATTTAAACC
1 AATAATGTTACCTTCAAGATTTAAACC
36559146 TATATTCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 17 0.68
30 3 0.12
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (28 bp):
AATAATGTTACCTTCAAGATTTAAACCC
Found at i:36559357 original size:14 final size:14
Alignment explanation
Indices: 36559320--36559363 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
36559310 GAATTTAAAT
36559320 ATAAATATAATTACA
1 ATAAATATAATTA-A
*
36559335 ATAAATATATTTAA
1 ATAAATATAATTAA
*
36559349 ATAACTATAATTAA
1 ATAAATATAATTAA
36559363 A
1 A
36559364 ATTAATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAATATAATTAA
Found at i:36559404 original size:25 final size:25
Alignment explanation
Indices: 36559324--36559407 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
36559314 TTAAATATAA
* *
36559324 ATATAATTACAATAAATATATTTAAAT
1 ATATAATTA-AATTAATA-ATTAAAAT
** *
36559351 AACTATAATTAAAATTAATTGTTATAAT
1 -A-TATAATT-AAATTAATAATTAAAAT
36559379 ATATAATTAAATTAATAATTAAAAT
1 ATATAATTAAATTAATAATTAAAAT
36559404 ATAT
1 ATAT
36559408 TTAACCTCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
25 18 0.39
26 7 0.15
27 1 0.02
28 6 0.13
29 13 0.28
30 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (25 bp):
ATATAATTAAATTAATAATTAAAAT
Found at i:36559866 original size:36 final size:36
Alignment explanation
Indices: 36559824--36559894 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
36559814 TATTTTTAAA
* *
36559824 ATTTTTTTTTTGAAATATAAAGAGTTTATTTATTTAT
1 ATTTTTTATTTGAAAAAT-AAGAGTTTATTTATTTAT
* * *
36559861 ATTTTTTATTTTAAAAATATGATTTTATTTATTT
1 ATTTTTTATTTGAAAAATAAGAGTTTATTTATTT
36559895 TTAAAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 14 0.48
37 15 0.52
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (36 bp):
ATTTTTTATTTGAAAAATAAGAGTTTATTTATTTAT
Found at i:36560683 original size:30 final size:30
Alignment explanation
Indices: 36560630--36560696 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
36560620 AAGCATATTT
36560630 TTTAAAA-TAAAAATTATAAAAAATAAACTC
1 TTTAAAATTAAAAATTATAAAAAATAAA-TC
* *
36560660 TTTAAAATTCAAAAA-TAT-AAAAATTAATT
1 TTTAAAATT-AAAAATTATAAAAAATAAATC
36560689 TTTAAAAT
1 TTTAAAAT
36560697 ATATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 9 0.27
30 15 0.45
31 4 0.12
32 5 0.15
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (30 bp):
TTTAAAATTAAAAATTATAAAAAATAAATC
Found at i:36560705 original size:31 final size:33
Alignment explanation
Indices: 36560636--36560705 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 33
36560626 ATTTTTTAAA
36560636 ATAAAAATTATAAAAAATAAACTCTTTAAAATT
1 ATAAAAATTATAAAAAATAAACTCTTTAAAATT
* * *
36560669 -CAAAAA-TAT-AAAAATTAA-TTTTTAAAATAT
1 ATAAAAATTATAAAAAATAAACTCTTTAAAAT-T
36560699 ATAAAAA
1 ATAAAAA
36560706 AATTCTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
29 9 0.29
30 9 0.29
31 8 0.26
32 5 0.16
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (33 bp):
ATAAAAATTATAAAAAATAAACTCTTTAAAATT
Done.