Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold377
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: 247558
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
File 2 of 2
Found at i:168688 original size:13 final size:13
Alignment explanation
Indices: 168670--168694 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
168660 ACATTATGCT
168670 TTGTATCGATACA
1 TTGTATCGATACA
168683 TTGTATCGATAC
1 TTGTATCGATAC
168695 GTGCTCATTG
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:168705 original size:19 final size:20
Alignment explanation
Indices: 168681--168736 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
168671 TGTATCGATA
* *
168681 CATTGTATCGATACGT-GCT
1 CATTGTATCGATACATGGAT
168700 CATTGTATCGATACATGGAT
1 CATTGTATCGATACATGGAT
*
168720 AATTGTATCGATACATG
1 CATTGTATCGATACATG
168737 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:168812 original size:21 final size:21
Alignment explanation
Indices: 168765--168819 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
168755 CTACCACTAT
168765 TTGTATCGATACATAGGACAA
1 TTGTATCGATACATAGGACAA
*
168786 -TGTATCGATACATGATG-CAA
1 TTGTATCGATACAT-AGGACAA
168806 TTGTATCGATACAT
1 TTGTATCGATACAT
168820 TGCTTGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACATAGGACAA
Found at i:168977 original size:20 final size:20
Alignment explanation
Indices: 168954--169025 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
168944 CACACCCAGA
*
168954 TGTATCGATACATTA-TGCTT
1 TGTATCGATACATTACT-CAT
168974 TGTATCGATACA-TACTCAT
1 TGTATCGATACATTACTCAT
* *
168993 TGTATCGATACATGGAC-AAT
1 TGTATCGATACAT-TACTCAT
169013 TGTATCGATACAT
1 TGTATCGATACAT
169026 GAGATTGGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.35
20 28 0.61
21 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTACTCAT
Found at i:169026 original size:20 final size:20
Alignment explanation
Indices: 168973--169027 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
168963 ACATTATGCT
*
168973 TTGTATCGATACAT-ACTCA
1 TTGTATCGATACATGACTAA
168992 TTGTATCGATACATGGAC-AA
1 TTGTATCGATACAT-GACTAA
169012 TTGTATCGATACATGA
1 TTGTATCGATACATGA
169028 GATTGGCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 16 0.48
20 15 0.45
21 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGACTAA
Found at i:169094 original size:13 final size:13
Alignment explanation
Indices: 169076--169124 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
169066 CATAGGACAA
169076 TGTATCGATACAT
1 TGTATCGATACAT
169089 TGTATCGATACA-
1 TGTATCGATACAT
169101 TG-ATC-A-A-AT
1 TGTATCGATACAT
169110 TGTATCGATACAT
1 TGTATCGATACAT
169123 TG
1 TG
169125 CTTGTAACCG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 16 0.52
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:169097 original size:33 final size:34
Alignment explanation
Indices: 169055--169124 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
169045 CTACCACTAT
169055 TTGTATCGATACATAGGA-C-AA-TGTATCGATACA
1 TTGTATCGATACAT--GATCAAATTGTATCGATACA
169088 TTGTATCGATACATGATCAAATTGTATCGATACA
1 TTGTATCGATACATGATCAAATTGTATCGATACA
169122 TTG
1 TTG
169125 CTTGTAACCG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
31 2 0.06
32 1 0.03
33 16 0.47
34 15 0.44
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGATCAAATTGTATCGATACA
Found at i:177748 original size:13 final size:13
Alignment explanation
Indices: 177730--177756 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
177720 ACATTATGCT
177730 TTGTATCGATACA
1 TTGTATCGATACA
177743 TTGTATCGATACA
1 TTGTATCGATACA
177756 T
1 T
177757 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:177786 original size:20 final size:19
Alignment explanation
Indices: 177740--177796 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
177730 TTGTATCGAT
177740 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
177759 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
177778 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
177797 AGATTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:177870 original size:33 final size:34
Alignment explanation
Indices: 177825--177893 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
177815 CAACCACTGT
*
177825 TTGTATCGATACATGA-GAGAA-TGTATCGATACA
1 TTGTATCGATACATGATGA-AATTGTATCAATACA
*
177858 TTGTATCTATACATGATGAAATTGTATCAATACA
1 TTGTATCGATACATGATGAAATTGTATCAATACA
177892 TT
1 TT
177894 TCTTGTAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (34 bp):
TTGTATCGATACATGATGAAATTGTATCAATACA
Found at i:181485 original size:21 final size:21
Alignment explanation
Indices: 181461--181501 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
181451 TTTTATGTCA
*
181461 TGTTCATCCCACTTTTCTTCT
1 TGTTCATCCCACTCTTCTTCT
181482 TGTTCATCCCACTCTTCTTC
1 TGTTCATCCCACTCTTCTTC
181502 CTTCTTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.37, G:0.05, T:0.49
Consensus pattern (21 bp):
TGTTCATCCCACTCTTCTTCT
Found at i:183344 original size:51 final size:51
Alignment explanation
Indices: 183277--183396 Score: 150
Period size: 51 Copynumber: 2.4 Consensus size: 51
183267 TTGAAAATAA
* * * * *
183277 CGGGGTTGAAGTATCCCCGATTGTGAAAAATCGATGTTCTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTCTAGAAATAAAAC
* * * *
183328 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATACAGC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTCTAGAAATAAAAC
*
183379 CGGAGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
183397 TCGGAAATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTCTAGAAATAAAAC
Found at i:185759 original size:13 final size:13
Alignment explanation
Indices: 185741--185770 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
185731 GTAAACCCAG
185741 AATGTATCCATAC
1 AATGTATCCATAC
*
185754 AATGTATCGATAC
1 AATGTATCCATAC
185767 AATG
1 AATG
185771 AAAAATGTAT
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:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCCATAC
Found at i:185762 original size:62 final size:63
Alignment explanation
Indices: 185692--185817 Score: 211
Period size: 62 Copynumber: 2.0 Consensus size: 63
185682 AAAATGCTTG
*
185692 AATGTATCGATACATTGAAAAATGTATCAATACATCT-GG-GTAAACCCAGAATGTATCCATAC
1 AATGTATCGATACAATGAAAAATGTATCAATACATCTAGGCG-AAACCCAGAATGTATCCATAC
*
185754 AATGTATCGATACAATGAAAAATGTATCAATACATCTAGGCGAAACCCAGAATGTATCGATAC
1 AATGTATCGATACAATGAAAAATGTATCAATACATCTAGGCGAAACCCAGAATGTATCCATAC
185817 A
1 A
185818 GATTGTGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 36 0.60
63 23 0.38
64 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (63 bp):
AATGTATCGATACAATGAAAAATGTATCAATACATCTAGGCGAAACCCAGAATGTATCCATAC
Found at i:186459 original size:62 final size:62
Alignment explanation
Indices: 186386--186704 Score: 495
Period size: 62 Copynumber: 5.2 Consensus size: 62
186376 CTCCTTGGGA
* * * **
186386 ACTAG-AAGGTGCCACCAACTTATATGGGCTTTGCAAGGAGAAA-GCATCCTGCTCTTTGAGG
1 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCATCCTGCTCTTTGAGG
* * *
186447 AC-ATGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGG
1 ACTA-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
186509 ACTAGAAAAGTGCCACCAACTTGTGT-GGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
1 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
* *
186570 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTGAAAAGGAAAAGGCGTCCTGCTCTTTGAGG
1 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
186632 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
1 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
186694 ACTA-AAAAGTG
1 ACTAGAAAAGTG
186705 AAAGGAGAAA
Statistics
Matches: 241, Mismatches: 12, Indels: 10
0.92 0.05 0.04
Matches are distributed among these distances:
60 1 0.00
61 73 0.30
62 166 0.69
63 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (62 bp):
ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
Found at i:186593 original size:123 final size:124
Alignment explanation
Indices: 186386--186704 Score: 513
Period size: 123 Copynumber: 2.6 Consensus size: 124
186376 CTCCTTGGGA
* * * **
186386 ACTAG-AAGGTGCCACCAACTTATATGGGCTTTGCAAGGAGAAA-GCATCCTGCTCTTTGAGGAC
1 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCATCCTGCTCTTTGAGGAC
* * *
186449 -ATGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGG
65 TA-GAAAAGTGCCACCAACTTGTGTGGGCTTGAAAAGGAAAAGGCGTCCTGCTCTTTGAGG
186509 ACTAGAAAAGTGCCACCAACTTGTGT-GGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT
1 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT
186573 AGAAAAGTGCCACCAACTTGTGTGGGCTTGAAAAGGAAAAGGCGTCCTGCTCTTTGAGG
66 AGAAAAGTGCCACCAACTTGTGTGGGCTTGAAAAGGAAAAGGCGTCCTGCTCTTTGAGG
186632 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT
1 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT
186697 A-AAAAGTG
66 AGAAAAGTG
186705 AAAGGAGAAA
Statistics
Matches: 184, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
122 3 0.02
123 124 0.67
124 57 0.31
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (124 bp):
ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT
AGAAAAGTGCCACCAACTTGTGTGGGCTTGAAAAGGAAAAGGCGTCCTGCTCTTTGAGG
Found at i:187683 original size:13 final size:12
Alignment explanation
Indices: 187649--187700 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
187639 CTTAAGCAGG
187649 TTCTTTTTTTTT
1 TTCTTTTTTTTT
* *
187661 CTCTATTTTTTT
1 TTCTTTTTTTTT
187673 TTCTTTGTTTTGTT
1 TTCTTT-TTTT-TT
187687 TT-TTTGTTTTTT
1 TTCTTT-TTTTTT
187699 TT
1 TT
187701 AAAAAGAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 18 0.53
13 12 0.35
14 4 0.12
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.85
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:187683 original size:14 final size:14
Alignment explanation
Indices: 187652--187700 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
187642 AAGCAGGTTC
* *
187652 TTTTTTTTTCTCTA
1 TTTTTTTTTCTTTG
187666 TTTTTTTTTCTTTG
1 TTTTTTTTTCTTTG
*
187680 TTTTGTTTT-TTTG
1 TTTTTTTTTCTTTG
187693 TTTTTTTT
1 TTTTTTTT
187701 AAAAAGAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.02, C:0.06, G:0.06, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Found at i:202594 original size:13 final size:13
Alignment explanation
Indices: 202576--202605 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
202566 GCAAACCCAG
*
202576 AATGTATCGATAC
1 AATGTATCAATAC
202589 AATGTATCAATAC
1 AATGTATCAATAC
202602 AATG
1 AATG
202606 AACAATGTAT
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:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:202624 original size:62 final size:63
Alignment explanation
Indices: 202527--202655 Score: 179
Period size: 62 Copynumber: 2.1 Consensus size: 63
202517 AAAATGCTTG
* * * * *
202527 AATGTATCGATACATTAAAAAATGTATTGATACATCT-GGGCAAACCCAGAATGTATCGATAC
1 AATGTATCAATACAATAAAAAATGTATCGATACATCTAAGGAAAACCCAGAATGTATCGATAC
* * *
202589 AATGTATCAATACAATGAACAATGTATCGATACATCTAAGTAAAACCCAGAATGTATCGATAC
1 AATGTATCAATACAATAAAAAATGTATCGATACATCTAAGGAAAACCCAGAATGTATCGATAC
202652 AATG
1 AATG
202656 AACAATGTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
62 32 0.55
63 26 0.45
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (63 bp):
AATGTATCAATACAATAAAAAATGTATCGATACATCTAAGGAAAACCCAGAATGTATCGATAC
Found at i:205022 original size:78 final size:78
Alignment explanation
Indices: 204856--205026 Score: 175
Period size: 78 Copynumber: 2.2 Consensus size: 78
204846 ATTTCATTTG
* * ** **
204856 TTATCAAGTCTTTTAGGGTTATTAAGATGCTTTCATGCCAAAGGTATACTTTTAGGGTATTTTAG
1 TTATCAAGTCTTTTAGGGTTATCAAAAAACTTTCATGCCAAAGGTATACTTTTAGGGTAGGTTAG
*
204921 TAATTTTACCTCA
66 TAATTTCACCTCA
* * * * * *
204934 -AAGCTGAGTCTTTTAGGGTTATCAAAAAACTTTTATGTCAAAGGTGTA-TTTTAGGGATAGGTT
1 TTATC-AAGTCTTTTAGGGTTATCAAAAAACTTTCATGCCAAAGGTATACTTTTAGGG-TAGGTT
* *
204997 AGTCATTTCATCTCA
64 AGTAATTTCACCTCA
205012 TTATCAAGTCTTTTA
1 TTATCAAGTCTTTTA
205027 CAACTACTGA
Statistics
Matches: 72, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
77 10 0.14
78 60 0.83
79 2 0.03
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (78 bp):
TTATCAAGTCTTTTAGGGTTATCAAAAAACTTTCATGCCAAAGGTATACTTTTAGGGTAGGTTAG
TAATTTCACCTCA
Found at i:207354 original size:21 final size:20
Alignment explanation
Indices: 207303--207343 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
207293 AACAACATTT
*
207303 TGCCAAAATGTATTGATACA
1 TGCCACAATGTATTGATACA
*
207323 TGCCATTAATGTATTGATACA
1 TGCCA-CAATGTATTGATACA
207344 ATGTCCCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
TGCCACAATGTATTGATACA
Found at i:207547 original size:51 final size:50
Alignment explanation
Indices: 207381--207567 Score: 196
Period size: 51 Copynumber: 3.7 Consensus size: 50
207371 TTTCACAATT
* * **
207381 TGTATCGATACATTCTTCATTGTAACGATACATTCTAAGTTTTACCCAGA
1 TGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTTACCCAGA
* * * *
207431 TGTATCAATACATTTTTTTATTGTATCAAGACATTCTGGGTTTTACCCAGA
1 TGTATCGATACA-TTTTTCATTGTATCGATACATTCTGGGTTTTACCCAGA
* * * * * * *
207482 TGTGTTGATTCATTTTTCATTGTTTTGATATATTTTGGGTTTTAACCCAGA
1 TGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTT-ACCCAGA
*
207533 TGTATCGATACATTTCTCAATT-TATCGATACATTC
1 TGTATCGATACATTTTTC-ATTGTATCGATACATTC
207568 AGGAATTTTT
Statistics
Matches: 107, Mismatches: 27, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
50 35 0.33
51 69 0.64
52 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.44
Consensus pattern (50 bp):
TGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTTACCCAGA
Found at i:209664 original size:79 final size:77
Alignment explanation
Indices: 209529--209729 Score: 201
Period size: 79 Copynumber: 2.6 Consensus size: 77
209519 TTTTCATCTC
* ** * *
209529 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACA-TTATTTTTTTGCCATCGAGGATACC-CTA
1 GGGGATACTCTAACCCCAGTTTTATTTCTAAAACACCGA--TTTTCGCCATCAAGGATACCTC-A
209592 ACCCCGTTATTTTCGT-
63 ACCCCGTTA-TTTC-TA
* * * *
209608 GGGGATACTCTAACCCCAGCTTTATTTCTAAAACACCGATTTTCGATCATTAAGGATACTTCAAC
1 GGGGATACTCTAACCCCAGTTTTATTTCTAAAACACCGATTTTCG-CCATCAAGGATACCTCAAC
*
209673 CTCGTTATTTCTAA
65 CCCGTTATTTCT-A
* * *
209687 GGAGATACTCTTACCCCAATTTTATTTCTAAAACACCGATTTT
1 GGGGATACTCTAACCCCAGTTTTATTTCTAAAACACCGATTTT
209730 TCACCAGAGG
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
77 1 0.01
78 9 0.09
79 91 0.88
80 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (77 bp):
GGGGATACTCTAACCCCAGTTTTATTTCTAAAACACCGATTTTCGCCATCAAGGATACCTCAACC
CCGTTATTTCTA
Found at i:209823 original size:78 final size:78
Alignment explanation
Indices: 209736--210140 Score: 369
Period size: 79 Copynumber: 5.2 Consensus size: 78
209726 TTTTTCACCA
* * * *
209736 GAGGGGATACTCTAACCCCAGTTTTATTTCTAAAATATCGA-CTTCCAAAATCGGGGATAC-CTC
1 GAGGGGATACTCTAACCCC-GTTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTC-C
* *
209799 AACCCTATTATTTTT
64 AACCCTGTTATTTTC
** * * * **
209814 GAGGGGATACTCTAACCTTGGTTTTATTTTTGAAACATTGATTTTTCATC-ATTTGGGATACTCC
1 GAGGGGATACTCTAACC-CCGTTTTATTTCTAAAACATCGATTTTTCA-CAATCGGGGATACTCC
209878 AA-CCTCGTTATTTTC
64 AACCCT-GTTATTTTC
* ** * *
209893 GAGGGGAAACTCTAACCCTAATTTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCA
1 GAGGGGATACTCTAACCC-CGTTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCA
209958 ACCCTGTTA-TTTC
65 ACCCTGTTATTTTC
* *
209971 GGAGGAGATACT-TCAACCCCGATTTTATTTTTAAAACA-CTGATTTTTCACAATCGGGGATACT
1 -GAGGGGATACTCT-AACCCCG-TTTTATTTCTAAAACATC-GATTTTTCACAATCGGGGATACT
* *
210034 TCAACCCCGTTATTTTC
62 CCAACCCTGTTATTTTC
* * * * * **
210051 GAGGGGATACTCAAACCTCGATTTTATTTC-CAAACACCGATTTTTCACCATCAAGGATACTCCA
1 GAGGGGATACTCTAACCCCG-TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCA
210115 ACCCTGTTA-TTTC
65 ACCCTGTTATTTTC
*
210128 TGAGAGGATACTC
1 -GAGGGGATACTC
210141 CGAAGGAATA
Statistics
Matches: 267, Mismatches: 44, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
77 4 0.01
78 90 0.34
79 165 0.62
80 8 0.03
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (78 bp):
GAGGGGATACTCTAACCCCGTTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAA
CCCTGTTATTTTC
Found at i:210030 original size:158 final size:158
Alignment explanation
Indices: 209736--210140 Score: 455
Period size: 158 Copynumber: 2.6 Consensus size: 158
209726 TTTTTCACCA
* * * * * * *
209736 GAGGGGATACTCTAACCCCAGTTTTATTTCTAAAATATCGA-CTTCCAAAATCGGGGATAC-CTC
1 GAGGGGATACTCTAACCCTAATTTTATTTCCAAAACATCGATTTTTCACAATCGGGGATACTC-C
* ** * ** * * *
209799 AACCCTATTATTTTTGAGGGGATACTCTAACCTTGGTTTTATTTTTGAAACATTGATTTTTCATC
65 AACCCTGTTATTTCGGAGGAGATACTCTAACCCCGATTTTATTTTTAAAACACTGATTTTTCATC
** *
209864 ATTTGGGATACTCCAACCTCGTTATTTTC
130 ATCGGGGATACTCCAACCCCGTTATTTTC
* *
209893 GAGGGGAAACTCTAACCCTAATTTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCA
1 GAGGGGATACTCTAACCCTAATTTTATTTCCAAAACATCGATTTTTCACAATCGGGGATACTCCA
209958 ACCCTGTTATTTCGGAGGAGATACT-TCAACCCCGATTTTATTTTTAAAACACTGATTTTTCA-C
66 ACCCTGTTATTTCGGAGGAGATACTCT-AACCCCGATTTTATTTTTAAAACACTGATTTTTCATC
*
210021 AATCGGGGATACTTCAACCCCGTTATTTTC
130 -ATCGGGGATACTCCAACCCCGTTATTTTC
* * * * **
210051 GAGGGGATACTC-AAACCTCGATTTTATTTCC-AAACACCGATTTTTCACCATCAAGGATACTCC
1 GAGGGGATACTCTAACCCT-AATTTTATTTCCAAAACATCGATTTTTCACAATCGGGGATACTCC
*
210114 AACCCTGTTATTTCTGA-GAGGATACTC
65 AACCCTGTTATTTCGGAGGA-GATACTC
210141 CGAAGGAATA
Statistics
Matches: 210, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
156 2 0.01
157 91 0.43
158 116 0.55
159 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (158 bp):
GAGGGGATACTCTAACCCTAATTTTATTTCCAAAACATCGATTTTTCACAATCGGGGATACTCCA
ACCCTGTTATTTCGGAGGAGATACTCTAACCCCGATTTTATTTTTAAAACACTGATTTTTCATCA
TCGGGGATACTCCAACCCCGTTATTTTC
Found at i:216288 original size:62 final size:62
Alignment explanation
Indices: 216219--217372 Score: 1177
Period size: 62 Copynumber: 18.9 Consensus size: 62
216209 ACAAAACACA
* * *
216219 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCGCAAAAAGTAGGACACC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * **
216281 TTTTTCTTTTCAAAGCTCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACATC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * * * ** *
216343 TTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAAGTCTTTAAGGACCAGGACGTC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * *
216405 -TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTCTAGTCCTCAAAGAGTAAGAC-AC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * *
216466 TTTTT-TTTT-AAAG-CCACACGAGTTGGTGGCAACTTTGAGTCCTTAAAGAGTAGGATGCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * *
216525 TTTTTTCTTTTCAAAGCCTACAC----T-GTGGCACATTTTTAGTCCTCAAAGAGCAGG--GCG
1 -TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-CTTTTAGTCCTCAAAGAGTAGGACGCC
* * * * * *
216582 TTTTTCCTTTTTAAAGGCCATACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGTC
1 TTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * * **
216645 -TTTTCTTTT-AAAGCCCACACAAGTTGGTGACACATTTTAGTCCTTAAAGAGTAGGACATC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * *
216705 TTTTTCTTTTCAAAGCCCACACGAGTTTGTGGCATCCTTTT-GTCCTCAAAGAGCAGGACACC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * **
216767 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCATCC-TTTAGTCCTCAAAAAGTATGAGGTA
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * * * *
216829 TTTTTCTTTTCGAAGCCTATACGAGTTAGTGGCACCCTTTAGCCCTCAAAGAGTAGGACGCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * *
216891 TTTTTCTTTTCAAAGCACATATGAGTTGGTGGCATCCTTTT-GTCCTCAAAGAGTAGGATGCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * * *
216953 TTTTTC-TTTCAAAGCCCACACGAGTTGGTGACACCCTTTAGTCTTTAAAGAGCAGGACGCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * * * *
217014 -TTTTCTTTTCAAAACTCACACGAGTTGGTGGTATCC-TTTAGTCCTCAAAAAGTAGGATGCT
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * * *
217075 TTTTTCTTTTTAAAGCCCACACGAGTTGGTAGCACCCTTTAGTCCTCAAAGAGCAGGATG-C
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * * *
217136 TTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT-GATCCTCAAAGAGCAAGATGCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAG-TCCTCAAAGAGTAGGACGCC
* ** * * * *
217198 TTTTTCTTTTGAAAGCCCACATAAGTTGGTGGCACCCTTTAGTCCTCAAAAAGTAAGACACC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * * * * * *
217260 TTTTTCTTTTCAAAACCTACACAAATTGGTGACACCCTTTAGTCCTCAAAGAATAGGATGCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
* * * *
217322 -TTTTCTTTTCAAAG-CCACACAAGTTGATGGCACCCTTTAGTCCGCAAAGAG
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAG
217373 CAAGAAACCT
Statistics
Matches: 919, Mismatches: 143, Indels: 62
0.82 0.13 0.06
Matches are distributed among these distances:
56 5 0.01
57 15 0.02
58 25 0.03
59 37 0.04
60 95 0.10
61 234 0.25
62 491 0.53
63 17 0.02
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (62 bp):
TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
Found at i:217394 original size:124 final size:123
Alignment explanation
Indices: 216219--217383 Score: 1132
Period size: 123 Copynumber: 9.5 Consensus size: 123
216209 ACAAAACACA
* * * * *
216219 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCGCAAAAAGTAGGACACCTTT
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCTTT
* * *
216284 TTCTTTTCAAAGCTCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACAT-C
66 TTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGG--ATGC
* * * * * * **
216343 TTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTTAAGTCTTTAAGGACCAGGACGTC-T
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT-AGTCCTCAAAGAGCAAGACACCTT
* **
216406 TTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTCTAGTCCTCAAAGAGTAAGACAC
65 TTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTT-TAGTCCTCAAAGAGTAGGATGC
* * * * **
216466 TTTTT-TTTT-AAAG-CCACACGAGTTGGTGGCA-ACTTTGAGTCCTTAAAGAGTAGGATGCCTT
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT-AGTCCTCAAAGAGCAAGACACC-T
* ** *
216527 TTTTCTTTTCAAAGCCTACAC----T-GTGGCACATTTTTAGTCCTCAAAGAGCAGG--GC
64 TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC-CCTTTAGTCCTCAAAGAGTAGGATGC
* * * * * * **
216581 GTTTTTCCTTTTTAAAGGCCATACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGTC-
1 -TTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCT
* ** *
216645 TTTTCTTTT-AAAGCCCACACAAGTTGGTGACACATTTTAGTCCTTAAAGAGTAGGACAT-C
64 TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGG--ATGC
* * * *
216705 TTTTTCTTTTCAAAGCCCACACGAGTTTGTGGCATCCTTTTGTCCTCAAAGAGCAGGACACCTTT
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCTTT
* * * * * *
216770 TTCTTTTCAAAGCCCACACGAGTTGGTGGCATCCTTTAGTCCTCAAAAAGTATGAGGTA
66 TTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG-C
* * * * * * * *
216829 TTTTTCTTTTCGAAGCCTATACGAGTTAGTGGCACCCTTTAGCCCTCAAAGAGTAGGACGCCTTT
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCTTT
* * ** * *
216894 TTCTTTTCAAAGCACATATGAGTTGGTGGCATCCTTTTGTCCTCAAAGAGTAGGATGCC
66 TTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG-C
* * * * *
216953 TTTTTC-TTTCAAAGCCCACACGAGTTGGTGACACCCTTTAGTCTTTAAAGAGCAGGACGCC-TT
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCTTT
* * * * * *
217016 TTCTTTTCAAAACTCACACGAGTTGGTGGTATCCTTTAGTCCTCAAAAAGTAGGATGC
66 TTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATGC
* * * **
217074 TTTTTTCTTTTTAAAGCCCACACGAGTTGGTAGCACCCTTTAGTCCTCAAAGAGCAGGA-TGCTT
1 -TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCTT
* * * *
217138 TTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT-GATCCTCAAAGAGCAAGATGCC
65 TTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTAG-TCCTCAAAGAGTAGGATG-C
* ** * *
217198 TTTTTCTTTTGAAAGCCCACATAAGTTGGTGGCACCCTTTAGTCCTCAAAAAGTAAGACACCTTT
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCTTT
* * * * *
217263 TTCTTTTCAAAACCTACACAAATTGGTGACACCCTTTAGTCCTCAAAGAATAGGATGC
66 TTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATGC
* * * * *
217321 CTTTTCTTTTCAAAG-CCACACAAGTTGATGGCACCCTTTAGTCCGCAAAGAGCAAGAAACCTT
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCTT
217384 ATCTTTTTTT
Statistics
Matches: 870, Mismatches: 139, Indels: 66
0.81 0.13 0.06
Matches are distributed among these distances:
115 1 0.00
116 5 0.01
117 33 0.04
118 16 0.02
119 4 0.00
120 71 0.08
121 28 0.03
122 181 0.21
123 266 0.31
124 264 0.30
125 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (123 bp):
TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCTTT
TTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATGC
Found at i:217435 original size:42 final size:41
Alignment explanation
Indices: 217388--217628 Score: 202
Period size: 42 Copynumber: 5.7 Consensus size: 41
217378 AACCTTATCT
* * *
217388 TTTTTTCCTTTGTCCTCGAAGAGCGGGATGTAATTTATTTCC
1 TTTTTTCCTTTGTCCTCAAAGAGCAGGA-GCAATTTATTTCC
*
217430 TTTTTTTCCTTTGTCCTCAAAGAGCAGGA-CACATTTCGTTCTCC
1 -TTTTTTCCTTTGTCCTCAAAGAGCAGGAGCA-ATTT-ATT-TCC
* *
217474 -TTTTTCCTTTATCCTCAAAGAGTAGGA-CACATTTCATTTCC
1 TTTTTTCCTTTGTCCTCAAAGAGCAGGAGCA-ATTT-ATTTCC
** * *
217515 TTATTTTCTCTTTGTCCTCAAAGAATAGGATGTACTTTATTT-C
1 TT-TTTTC-CTTTGTCCTCAAAGAGCAGGA-GCAATTTATTTCC
* * *
217558 TTTTTCTCCTTTGTCCTCAAAGAGCAGGGCGCACTTGATTTCC
1 TTTTT-TCCTTTGTCCTCAAAGAGCA-GGAGCAATTTATTTCC
* * *
217601 TTTATTCTTTTGTCCTCGAAGAGCAGGA
1 TTTTTTCCTTTGTCCTCAAAGAGCAGGA
217629 CGCATTCTTT
Statistics
Matches: 167, Mismatches: 20, Indels: 24
0.79 0.09 0.11
Matches are distributed among these distances:
41 6 0.04
42 86 0.51
43 45 0.27
44 26 0.16
45 3 0.02
46 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.42
Consensus pattern (41 bp):
TTTTTTCCTTTGTCCTCAAAGAGCAGGAGCAATTTATTTCC
Found at i:217642 original size:128 final size:128
Alignment explanation
Indices: 217390--217634 Score: 316
Period size: 128 Copynumber: 1.9 Consensus size: 128
217380 CCTTATCTTT
* * * *
217390 TTTTCCTTTGTCCTCGAAGAGCGGGATGTAATTTATTTCCTTTTTTTCCTTTGTCCTCAAAGAGC
1 TTTTCCTTTGTCCTCAAAGAACAGGATGTAATTTATTTCCTTTTTCTCCTTTGTCCTCAAAGAGC
* *
217455 AGGACACATTTCGTTCTCCTTTTTCCTTTATCCTCAAAGAGTAGGACACATTTCATTTCCTTA
66 AGGACACACTTCGTTCTCCTTTTTCCTTTATCCTCAAAGAGCAGGACACATTTCATTTCCTTA
* *
217518 TTTTCTCTTTGTCCTCAAAGAATAGGATGTACTTTATTT-CTTTTTCTCCTTTGTCCTCAAAGAG
1 TTTTC-CTTTGTCCTCAAAGAACAGGATGTAATTTATTTCCTTTTTCTCCTTTGTCCTCAAAGAG
* * * * * *
217582 CAGGGCGCACTT-GATT-TCCTTTATTCTTTTGTCCTCGAAGAGCAGGACGCATT
65 CAGGACACACTTCG-TTCTCCTTT-TTCCTTTATCCTCAAAGAGCAGGACACATT
217635 CTTTTTCCCT
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
127 7 0.07
128 65 0.65
129 28 0.28
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.42
Consensus pattern (128 bp):
TTTTCCTTTGTCCTCAAAGAACAGGATGTAATTTATTTCCTTTTTCTCCTTTGTCCTCAAAGAGC
AGGACACACTTCGTTCTCCTTTTTCCTTTATCCTCAAAGAGCAGGACACATTTCATTTCCTTA
Found at i:217682 original size:42 final size:43
Alignment explanation
Indices: 217633--217750 Score: 121
Period size: 47 Copynumber: 2.7 Consensus size: 43
217623 GCAGGACGCA
* *
217633 TTCTTTTTCCCTTTGTCCTCAAAGAGCAAAACACTTTTCTTTTTC
1 TTCTTTTTCCCTTTGTCCTCAAAGAGCAAAACACATTTC--GTTC
* * * *
217678 TTTTTTTTTTCCCTTTGTCCTTAAGGAGCAAAACCCATTTCGTTC
1 --TTCTTTTTCCCTTTGTCCTCAAAGAGCAAAACACATTTCGTTC
* *
217723 TCCTTTTT-CCTTTGTCCTCGAAGAGCAA
1 TTCTTTTTCCCTTTGTCCTCAAAGAGCAA
217751 GACATACTCT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 17 0.28
43 6 0.10
45 3 0.05
47 34 0.57
ACGTcount: A:0.19, C:0.26, G:0.10, T:0.45
Consensus pattern (43 bp):
TTCTTTTTCCCTTTGTCCTCAAAGAGCAAAACACATTTCGTTC
Found at i:217730 original size:47 final size:47
Alignment explanation
Indices: 217636--217730 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
217626 GGACGCATTC
* * * *
217636 TTTTTCCCTTTGTCCTCAAAGAGCAAAACACTTTTCTTTTTCTTTTT
1 TTTTTCCCTTTGTCCTCAAAGAGCAAAACACATTTCGTTCTCCTTTT
* * *
217683 TTTTTCCCTTTGTCCTTAAGGAGCAAAACCCATTTCGTTCTCCTTTT
1 TTTTTCCCTTTGTCCTCAAAGAGCAAAACACATTTCGTTCTCCTTTT
217730 T
1 T
217731 CCTTTGTCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.18, C:0.25, G:0.08, T:0.48
Consensus pattern (47 bp):
TTTTTCCCTTTGTCCTCAAAGAGCAAAACACATTTCGTTCTCCTTTT
Found at i:218455 original size:50 final size:51
Alignment explanation
Indices: 218379--218513 Score: 195
Period size: 50 Copynumber: 2.7 Consensus size: 51
218369 TTTCATAATT
* * * *
218379 TGTATCGATACATTCTTCATTGTATCGATACCTTTTTG-GTTTTACCCAGA
1 TGTATCGATACATTTTTCATTGTATCGATACCATTCTGAGTTTAACCCAGA
* *
218429 TGTATTGATACATTTTTCATTATATCGATA-CATTCTGAGTTTAACCCAGA
1 TGTATCGATACATTTTTCATTGTATCGATACCATTCTGAGTTTAACCCAGA
218479 TGTATCGATACATTTTTCATTGTATCGATA-CATTC
1 TGTATCGATACATTTTTCATTGTATCGATACCATTC
218514 AGGCATTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
49 5 0.07
50 71 0.93
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (51 bp):
TGTATCGATACATTTTTCATTGTATCGATACCATTCTGAGTTTAACCCAGA
Found at i:220934 original size:78 final size:78
Alignment explanation
Indices: 220815--221113 Score: 316
Period size: 79 Copynumber: 3.8 Consensus size: 78
220805 TTTTCTCGGA
* *
220815 GATACTCTAATCCC-GGTTTTATTTCTAAAACATTGATTTTCCACCATCGAGATACTCCAACCCC
1 GATACTCTAA-CCCAGATTTTATTTCTAAAACATCGATTTTCCACCATCGAGATACTCCAACCCC
220879 GTTATTTTCGAGGG
65 GTTATTTTCGAGGG
* *
220893 GATACTCTAACTCCAG-TTTTATTTCCAAAACA-CTGATTTTCCACCATCGAGGATACTCCAAAC
1 GATACTCTAAC-CCAGATTTTATTTCTAAAACATC-GATTTTCCACCATCGA-GATACTCCAACC
* *
220956 TCGTTATTTTAGAGGG
63 CCGTTATTTTCGAGGG
* * * * * * * * *
220972 GATACTTTAACCCTGATTTTATTTCTTAAACGTCGATTTTTCATCTTCGGGGATACTTCAACCCC
1 GATACTCTAACCCAGATTTTATTTCTAAAACATCGATTTTCCACCATC-GAGATACTCCAACCCC
* * * **
221037 GCTATTTCCAAGAA
65 GTTATTTTCGAGGG
* * *
221051 GATACTCCAACCCAGATTTTATTTCTAAAACATCGATTTTTCACCATTGGAGATACTCCAACC
1 GATACTCTAACCCAGATTTTATTTCTAAAACATCGATTTTCCACCA-TCGAGATACTCCAACC
221114 TCGGTTTTAT
Statistics
Matches: 180, Mismatches: 33, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
77 1 0.01
78 46 0.26
79 130 0.72
80 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (78 bp):
GATACTCTAACCCAGATTTTATTTCTAAAACATCGATTTTCCACCATCGAGATACTCCAACCCCG
TTATTTTCGAGGG
Found at i:220992 original size:79 final size:78
Alignment explanation
Indices: 220815--220996 Score: 251
Period size: 78 Copynumber: 2.3 Consensus size: 78
220805 TTTTCTCGGA
* * * *
220815 GATACTCTAA-TCCCGGTTTTATTTCTAAAACATTGATTTTCCACCATCGAGATACTCCAACCCC
1 GATACTCTAACT-CCAGTTTTATTTCCAAAACACTGATTTTCCACCATCGAGATACTCCAAACCC
*
220879 GTTATTTTCGAGGG
65 GTTATTTTAGAGGG
*
220893 GATACTCTAACTCCAGTTTTATTTCCAAAACACTGATTTTCCACCATCGAGGATACTCCAAACTC
1 GATACTCTAACTCCAGTTTTATTTCCAAAACACTGATTTTCCACCATCGA-GATACTCCAAACCC
220958 GTTATTTTAGAGGG
65 GTTATTTTAGAGGG
* *
220972 GATACTTTAAC-CCTGATTTTATTTC
1 GATACTCTAACTCCAG-TTTTATTTC
220997 TTAAACGTCG
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
78 48 0.52
79 45 0.48
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (78 bp):
GATACTCTAACTCCAGTTTTATTTCCAAAACACTGATTTTCCACCATCGAGATACTCCAAACCCG
TTATTTTAGAGGG
Found at i:221280 original size:78 final size:78
Alignment explanation
Indices: 221102--221500 Score: 418
Period size: 78 Copynumber: 5.1 Consensus size: 78
221092 CACCATTGGA
* * * * *
221102 GATACTCCAACCTCGGTTTTATTTCTAAAACATC-A-ATTTCACAATCGAGGATACTCTAACCCC
1 GATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCG-GGATACTCCAACCCC
*
221165 GTTATTTTCAAAGG
65 GTTATTTTCGAAGG
* ** *
221179 GATACTCTAACCCCGATTTTATTTCTAAAACATCTATTTTTCATTATCTGGGATACTCAAACCCC
1 GATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATC-GGGATACTCCAACCCC
221244 GTTATTTT-GAAGG
65 GTTATTTTCGAAGG
* * * *
221257 GATACTCTAACCCCGGTTTTATTTCTAAAACATTGATTTTTCATAATCAGGGATACTCCAACCTC
1 GATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATC-GGGATACTCCAACCCC
* *
221322 ATTA-TTTCGGAAGA
65 GTTATTTTC-GAAGG
* *
221336 GATACT-TAAACCCCGATTTTATTTCTAAAACAAT-GATTTTTCCCCAATCGAAGATACTCCAAC
1 GATACTCT-AACCCCGATTTTATTTCTAAAAC-ATCGATTTTT-CACAATCG-GGATACTCCAAC
*
221399 CCCGTTATTTTCGAGGG
62 CCCGTTATTTTCGAAGG
*** * * * *
221416 GATACTCTAACCTTAATTTTATTTC-CAAACATCGATTTTTCACCATCGGGGATAGTCTAACCCC
1 GATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATC-GGGATACTCCAACCCC
221480 GTTATTTTCG-AGAG
65 GTTATTTTCGAAG-G
221494 GATACTC
1 GATACTC
221501 CAAAGGAATA
Statistics
Matches: 273, Mismatches: 35, Indels: 27
0.81 0.10 0.08
Matches are distributed among these distances:
77 35 0.13
78 104 0.38
79 82 0.30
80 47 0.17
81 5 0.02
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (78 bp):
GATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGATACTCCAACCCCG
TTATTTTCGAAGG
Found at i:221498 original size:158 final size:157
Alignment explanation
Indices: 221118--221500 Score: 424
Period size: 158 Copynumber: 2.4 Consensus size: 157
221108 CCAACCTCGG
* * *
221118 TTTTATTTCTAAAACATC-A-ATTTCACAATCGAGGATACTCTAACCCCGTTATTTTC-AAAGGG
1 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCTAACCCCGTTATTTTCGAGA-GG
* ** *
221180 ATACTCTAACCCCGATTTTATTTCTAAAACATCTATTTTTCATTATCTGGGATACTCAAACCCCG
65 ATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCTGAGATACTCAAACCCCG
**
221245 TTATTTTGAAGGGATACTCTAACCCCGG
130 TTATTTTGAAGGGATACTCTAACCCCAA
* * * * * *
221273 TTTTATTTCTAAAACATTGATTTTTCATAATCAGGGATACTCCAACCTCATTA-TTTCG-GAAGA
1 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCTAACCCCGTTATTTTCGAG-AG-
* *
221336 GATACT-TAAACCCCGATTTTATTTCTAAAACAAT-GATTTTTCCCCAATC-GAAGATACTCCAA
64 GATACTCT-AACCCCGATTTTATTTCTAAAAC-ATCGATTTTT-CACAATCTG-AGATACTCAAA
* **
221398 CCCCGTTATTTTCGAGGGGATACTCTAACCTTAA
125 CCCCGTTATTTT-GAAGGGATACTCTAACCCCAA
* * *
221432 TTTTATTTC-CAAACATCGATTTTTCACCATCGGGGATAGTCTAACCCCGTTATTTTCGAGAGGA
1 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCTAACCCCGTTATTTTCGAGAGGA
221496 TACTC
66 TACTC
221501 CAAAGGAATA
Statistics
Matches: 186, Mismatches: 29, Indels: 22
0.78 0.12 0.09
Matches are distributed among these distances:
155 17 0.09
156 7 0.04
157 62 0.33
158 67 0.36
159 32 0.17
160 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.36
Consensus pattern (157 bp):
TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCTAACCCCGTTATTTTCGAGAGGA
TACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCTGAGATACTCAAACCCCGT
TATTTTGAAGGGATACTCTAACCCCAA
Found at i:225014 original size:20 final size:20
Alignment explanation
Indices: 224991--225040 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
224981 CGCTCCTATC
224991 CATCGATACATTTTATAAAG
1 CATCGATACATTTTATAAAG
225011 CATCGATACATTTTATAAAG
1 CATCGATACATTTTATAAAG
*
225031 TATCGATACA
1 CATCGATACA
225041 ATGCATTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (20 bp):
CATCGATACATTTTATAAAG
Found at i:226077 original size:20 final size:21
Alignment explanation
Indices: 226052--226090 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
226042 ATTAAAAAAT
*
226052 TATTTTTAT-TTTAAATTTTA
1 TATTTTTATAATTAAATTTTA
226072 TATTTTTATAATTAAATTT
1 TATTTTTATAATTAAATTT
226091 AAATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTTATAATTAAATTTTA
Found at i:226467 original size:13 final size:13
Alignment explanation
Indices: 226451--226497 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
226441 TTTTTATATT
*
226451 AATATTTTTAATA
1 AATATTTATAATA
226464 AATATTTATAATA
1 AATATTTATAATA
* *
226477 ATTAATTATAAT-
1 AATATTTATAATA
226489 AATATTTAT
1 AATATTTAT
226498 TATATTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 7 0.24
13 22 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATATTTATAATA
Found at i:226874 original size:15 final size:15
Alignment explanation
Indices: 226856--226913 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
226846 ATTTAAATGC
*
226856 ATATATTTTATATTT
1 ATATTTTTTATATTT
226871 ATATTTTATTATTATTT
1 ATATTTT-TTA-TATTT
*
226888 AT-TTTATTTATATAT
1 ATATTT-TTTATATTT
226903 ATATTTTTTAT
1 ATATTTTTTAT
226914 CAATTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 17 0.46
16 12 0.32
17 8 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATTTTTTATATTT
Found at i:226875 original size:13 final size:14
Alignment explanation
Indices: 226856--226902 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
226846 ATTTAAATGC
226856 ATATATTTTATATT
1 ATATATTTTATATT
226870 -TATATTTTATTATT
1 ATATATTTTA-TATT
*
226884 ATTTATTTTAT-TT
1 ATATATTTTATATT
226897 ATATAT
1 ATATAT
226903 ATATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 16 0.55
14 5 0.17
15 8 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATATATTTTATATT
Found at i:226930 original size:6 final size:6
Alignment explanation
Indices: 226919--226951 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
226909 TTTATCAATT
226919 ATATAA ATATAA ATAT-A ATATAAA ATATAA ATA
1 ATATAA ATATAA ATATAA ATAT-AA ATATAA ATA
226952 GATATACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:226970 original size:24 final size:25
Alignment explanation
Indices: 226915--226970 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
226905 ATTTTTTATC
* *
226915 AATTATATAAATATAAATATAATAT
1 AATTATATAAATAGAAATACAATAT
* *
226940 AA-AATATAAATAGATATACAAT-T
1 AATTATATAAATAGAAATACAATAT
226963 AATTATAT
1 AATTATAT
226971 TTAAATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 3 0.12
24 20 0.80
25 2 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
AATTATATAAATAGAAATACAATAT
Found at i:227039 original size:5 final size:5
Alignment explanation
Indices: 226976--227051 Score: 50
Period size: 5 Copynumber: 15.2 Consensus size: 5
226966 TATATTTAAA
* * * *
226976 TATAT TAAAT TATAT T-TAT TTTAT TATTT TAATAT T-TAT TAAAT T-TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT T-ATAT TATAT TATAT TATAT
* *
227024 CATATT TATAT TATATT TATAT CATAT T
1 TATA-T TATAT TATA-T TATAT TATAT T
227052 TAAAATTATT
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
4 10 0.19
5 31 0.57
6 13 0.24
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:227041 original size:11 final size:11
Alignment explanation
Indices: 226964--227053 Score: 54
Period size: 11 Copynumber: 8.9 Consensus size: 11
226954 TATACAATTA
226964 ATTATATTTA-
1 ATTATATTTAT
* *
226974 AATATA-TTAA
1 ATTATATTTAT
226984 ATTATATTTAT
1 ATTATATTTAT
226995 -TT-TA-TTAT
1 ATTATATTTAT
*
227003 TTTA-ATATT-T
1 ATTATAT-TTAT
*
227013 ATTA-AATT-T
1 ATTATATTTAT
*
227022 ATCATATTTAT
1 ATTATATTTAT
227033 ATTATATTTAT
1 ATTATATTTAT
*
227044 ATCATATTTA
1 ATTATATTTA
227054 AAATTATTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
8 4 0.06
9 14 0.22
10 20 0.32
11 25 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:227550 original size:17 final size:17
Alignment explanation
Indices: 227523--227566 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
227513 AATTAATTAT
*
227523 TAATTATTTTATTA-AA
1 TAATAATTTTATTAGAA
227539 TATATAATTTTATTATGAA
1 TA-ATAATTTTATTA-GAA
227558 TAATAATTT
1 TAATAATTT
227567 AACTAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 11 0.46
18 7 0.29
19 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TAATAATTTTATTAGAA
Found at i:231441 original size:21 final size:21
Alignment explanation
Indices: 231415--231472 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
231405 AAAAAATTCA
231415 AATGTATCAATACATTTGTAG
1 AATGTATCAATACATTTGTAG
*
231436 AATGTATCAATACATTTGTGG
1 AATGTATCAATACATTTGTAG
*
231457 AATGTATCGATACATT
1 AATGTATCAATACATT
231473 CTACAAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (21 bp):
AATGTATCAATACATTTGTAG
Found at i:231551 original size:19 final size:19
Alignment explanation
Indices: 231527--231594 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
231517 AATTCAACAA
231527 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
231546 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
231561 --TGTATCAATACATAAGT
1 TTTGTATCGATACATAAGT
*
231578 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
231595 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:231572 original size:32 final size:32
Alignment explanation
Indices: 231529--231591 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
231519 TTCAACAATT
* *
231529 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACATAAGTATTGTATCGATACAA
231561 TGTATCAATACATAAGTATTGTATCGATACA
1 TGTATCAATACATAAGTATTGTATCGATACA
231592 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTATTGTATCGATACAA
Found at i:234274 original size:52 final size:52
Alignment explanation
Indices: 234156--234378 Score: 202
Period size: 52 Copynumber: 4.3 Consensus size: 52
234146 TTATTTCTGA
* ** * * ***
234156 GGGGATACTCCAACCCTGACTTTATTTTCAAAATATTGATTTTTC-ACAATC
1 GGGGATACTCCAACCCCGGTTTTATTCTCAAAACACCAATTTTTCTACAATC
*
234207 GGGGATACTCCAACCCCGGTTTTATTGCT-AAAACACTAATTTTTCTACAATC
1 GGGGATACTCCAACCCCGGTTTTATT-CTCAAAACACCAATTTTTCTACAATC
** * **
234259 GGGGATACTTTAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTCTCAAAACACCAATTTTT-CTACAATC
** * * *
234312 GGGGATACTCCAATTCTGATTTTATT-TCCAAAAATACCAATTTTTC-ACAATC
1 GGGGATACTCCAACCCCGGTTTTATTCT-C-AAAACACCAATTTTTCTACAATC
*
234364 GAGGATACTCCAACC
1 GGGGATACTCCAACC
234379 TCGTTATCTC
Statistics
Matches: 141, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
51 37 0.26
52 62 0.44
53 28 0.20
54 14 0.10
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTCTCAAAACACCAATTTTTCTACAATC
Found at i:234400 original size:28 final size:29
Alignment explanation
Indices: 234366--234465 Score: 111
Period size: 28 Copynumber: 3.6 Consensus size: 29
234356 TCACAATCGA
*
234366 GGATACTCCAACCTCGTTATC-TCATCG-GG
1 GGATACTCCAACCCCGTTATCTTC--CGAGG
234395 GG-TACTCCAACCCCGTTA-CTTCCGAGG
1 GGATACTCCAACCCCGTTATCTTCCGAGG
* *
234422 GGATACTCCAACCCCGTTAT-TTTCGAAG
1 GGATACTCCAACCCCGTTATCTTCCGAGG
*
234450 GGATACTCCAATCCCG
1 GGATACTCCAACCCCG
234466 ATTTTTTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.03
27 5 0.08
28 54 0.86
29 2 0.03
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (29 bp):
GGATACTCCAACCCCGTTATCTTCCGAGG
Found at i:235891 original size:20 final size:19
Alignment explanation
Indices: 235862--235936 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
235852 AAAAAGACAT
235862 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
235881 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
235902 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
235922 AATGTATCGATACAT
1 AATGTATCGATACAT
235937 CTAGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:235919 original size:40 final size:39
Alignment explanation
Indices: 235859--235936 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
235849 GGTAAAAAGA
*
235859 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
235898 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
235937 CTAGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:236557 original size:28 final size:28
Alignment explanation
Indices: 236520--237942 Score: 644
Period size: 28 Copynumber: 49.2 Consensus size: 28
236510 CACTAACTTC
*
236520 TGTGGGCTTT-AAAGAGACGCCACTGACT
1 TGTGGGCTTTGAAA-AGATGCCACTGACT
* * * *
236548 TGTTGGCTTTGAAAGGATGCCACTAATT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * * * *
236576 TATGGGCTTTGGAAGGCTGCCACTGAGT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
236604 CGTGGGCTTTGAAAAGTTGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
236632 CGTGGGCTTTGAAAAGTTGCCACTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
236660 TGTGGGCTTGGAAAAGATACCATTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
*
236688 TGTGGGCTTTGAAAAGATGCCACCGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
236716 TGTGGACATTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * **
236744 TGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 TGTGGGCTTTGAAA--AGATGCCACTGAC-T
* *
236775 GTGTGGGCTTTGAAATGAGTTACCA-TCGA-T
1 -TGTGGGCTTTGAAA--AGATGCCACT-GACT
* * * **
236805 TGTGTGAGCTTTCAAATGGGTTGCCACCAACTT
1 TGTG-G-GCTTTGAAA--AGATGCCACTGAC-T
* *
236838 GTGTGGGCTTTGAAATAGGTTGCCAC-CAGCTT
1 -TGTGGGCTTTGAAA-A-GATGCCACTGA-C-T
* * **
236870 GTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA--AGATGCCACTGAC-T
* *
236902 GTGTGGGCTTTGAAATAGGTTGCCAC-CAGCTT
1 -TGTGGGCTTTGAAA-A-GATGCCACTGA-C-T
* * ** *
236934 GTGTGGGCTTTGAAATGGGTTGCCACCAATTT
1 -TGTGGGCTTTGAAA--AGATGCCACTGA-CT
* *
236966 GTGTGGGCTTTCAAATGAGTGCCACTGACT
1 -TGTGGGCTTTGAAAAGA-TGCCACTGACT
*
236996 TGCGTGGGCTTT-AAAAGGATACCACTGACT
1 T--GTGGGCTTTGAAAA-GATGCCACTGACT
** *
237026 CATGGGCTTT-AAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
* *
237054 TGTGGGCTTTGAAAGGGTGCCACTGA-T
1 TGTGGGCTTTGAAAAGATGCCACTGACT
237081 TCGTGGGCTTTGAAAAGAATGCCACTGACT
1 T-GTGGGCTTTGAAAAG-ATGCCACTGACT
** * *
237111 CATGGGCTTTGGAAAAGATACCATTGACT
1 TGTGGGCTTT-GAAAAGATGCCACTGACT
* *
237140 TGTGGGCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
* *
237170 CATGTGGGCTTTGAAAGGATGCCACTAACT
1 --TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
237200 TATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
237228 TATGGGCTTTGAAAAGTGTTGCCACCGACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
* * *
237258 CGTGGACTTTGAAATGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
237286 TGTGGGCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
237316 CGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 --TGTGGGCTTTGAAAAGA-TGCCACTGACT
* *
237347 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
237375 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
*
237403 TGTGGGCTTTGAAAAGTGTTGCCACTGACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
* * * **
237433 CGTGGGCTTTGAAATGATGGGCTTTGA--
1 TGTGGGCTTTGAAAAGAT-GCCACTGACT
*** ** * *
237460 AAAGGG--TTG---CCAT-CGACT--CG
1 TGTGGGCTTTGAAAAGATGCCACTGACT
*
237480 TGTGGGCTTTGAAAAGAGTTCCACTGACT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACT
* * *
237509 TGTGGGCTTTGAAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
237537 TGTGGGCTTT-AAAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAAA-GATGCCACTGACT
* * * *
237565 TGTGGGCTTTGAAATTGGTTGCAACCGACTT
1 TGTGGGCTTTGAAA--AGATGCCACTGAC-T
* * * **
237596 ATGTGGGCTTTCAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA--AGATGCCACTGAC-T
* *
237628 GTGTGGGCTTTGAAATAGGTTGCCACCGACTT
1 -TGTGGGCTTTGAAA-A-GATGCCACTGAC-T
*
237660 GTGTGGGCTTT-AAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAA-GATGCCACTGACT
* *
237689 TGTGGGC-TTAAAAAGGATGCCAC-GAAGT
1 TGTGGGCTTTGAAAA-GATGCCACTG-ACT
** * * *
237717 TGTGAAC-TT-AAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAA-GATGCCACTGACT
* * * *
237744 TGTGGACTTT-AAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAA-GATGCCACTGACT
* * * *
237772 TGTGGACTTT-AAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAA-GATGCCACTGACT
* * * *
237800 TGTGGACTTT-AAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAA-GATGCCACTGACT
* * * * *
237828 TGTGGACTTT-AAAGGGTACCAC-GCAGT
1 TGTGGGCTTTGAAAAGATGCCACTG-ACT
* * *
237855 TGTGGAC-TT-AAAACGATGCCACGGAAT
1 TGTGGGCTTTGAAAA-GATGCCACTGACT
* * * *
237882 TGTGGACTTT-AAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAA-GATGCCACTGACT
* * *
237910 TGTGGACTTT-AAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAA-GATGCCACTGACT
237938 TGTGG
1 TGTGG
237943 ACTTAAAAGA
Statistics
Matches: 1147, Mismatches: 178, Indels: 140
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.00
22 5 0.00
25 4 0.00
26 7 0.01
27 70 0.06
28 553 0.48
29 87 0.08
30 132 0.12
31 52 0.05
32 225 0.20
33 4 0.00
34 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGATGCCACTGACT
Found at i:236598 original size:56 final size:56
Alignment explanation
Indices: 236520--237942 Score: 799
Period size: 56 Copynumber: 24.6 Consensus size: 56
236510 CACTAACTTC
** * * *
236520 TGTGGGCTTT-AAAGAGACGCCACTGACTTGTTGGCTTTGAAAGGATGCCACTAATT
1 TGTGGGCTTTGAAAG-GTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * * *
236576 TATGGGCTTTGGAAGGCTGCCACTGAGTCGTGGGCTTTGAAAAGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * * *
236632 CGTGGGCTTTGAAAAGTTGCCACTAACTTGTGGGCTTGGAAAAGATACCATTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
236688 TGTGGGCTTTGAAAAGATGCCACCGACTTGTGGACATTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
** * *
236744 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGAGTTACCA-TCGA-T
1 TGTGGGCTTTGAAA--GGTTGCCACTGAC-T-TGTGGGCTTTGAAA-G-GATGCCACT-GACT
* ** * *
236805 TGTGTGAGCTTTCAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTTGCCAC-CAGCT
1 TGTG-G-GCTTTGAAA--GGTTGCCACTGAC-T-TGTGGGCTTTG-AA-AGGATGCCACTGA-C-
236869 T
56 T
** * *
236870 GTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTTGCCAC-CAGCTT
1 -TGTGGGCTTTGAAA--GGTTGCCACTGAC-T-TGTGGGCTTTG-AA-AGGATGCCACTGA-C-T
** * * *
236934 GTGTGGGCTTTGAAATGGGTTGCCACCAATTTGTGTGGGCTTTCAAATGAGTGCCACTGACT
1 -TGTGGGCTTTGAAA--GGTTGCCACTGA-CT-TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * ** * *
236996 TGCGTGGGCTTTAAAAGGATACCACTGACTCATGGGCTTT-AAAAGAGTGCCACTAACT
1 T--GTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
237054 TGTGGGCTTTGAAAGGGTGCCACTGA-TTCGTGGGCTTTGAAAAGAATGCCACTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTT-GTGGGCTTTG-AAAGGATGCCACTGACT
** * * * * * *
237111 CATGGGCTTTGGAAAAGATACCATTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGGCTTT-GAAAGGTTGCCACTGACTTGTGGGCTTTG-AAA-GGATGCCACTGACT
* * * *
237170 CATGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTGACT
1 --TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
237228 TATGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGACTTTGAAATGATGCCACTGACT
1 TGTGGGCTTTG-AAAG-GTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* *
237286 TGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAA-GGTTGCCACTGACT--TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
237347 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
237403 TGTGGGCTTTGAAAAGTGTTGCCACTGACTCGTGGGCTTTGAAATGATG-----GGCT
1 TGTGGGCTTTG-AAAG-GTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
237456 T-T--G----AAAAGGGTTGCCA-TCGACTCGTGTGGGCTTTGAAAAGAGTTCCACTGACT
1 TGTGGGCTTTGAAA-GGTTGCCACT-GACT--TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * * *
237509 TGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGGCTTTAAAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * **
237565 TGTGGGCTTTGAAATTGGTTGCAACCGACTTATGTGGGCTTTCAAATGGGTTGCCACCAACTT
1 TGTGGGCTTTGAAA--GGTTGCCACTGAC-T-TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* * *
237628 GTGTGGGCTTTGAAATAGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTG-AA-AGGTTGCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACTGACT
** * * ** * * * *
237689 TGTGGGCTTAAAAAGGATGCCAC-GAAGTTGTGAAC-TTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGTTGCCACTG-ACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * * * * * *
237744 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * * * * *
237800 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTACCAC-GCAGT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTG-ACT
* * * * * * * * * * *
237855 TGTGGAC-TTAAAACGATGCCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
237910 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGG
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGG
237943 ACTTAAAAGA
Statistics
Matches: 1142, Mismatches: 152, Indels: 146
0.79 0.11 0.10
Matches are distributed among these distances:
44 1 0.00
45 14 0.01
46 1 0.00
47 15 0.01
48 1 0.00
50 1 0.00
52 1 0.00
53 8 0.01
54 29 0.03
55 90 0.08
56 318 0.28
57 62 0.05
58 177 0.15
59 51 0.04
60 80 0.07
61 47 0.04
62 31 0.03
63 65 0.06
64 140 0.12
65 5 0.00
66 5 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:236785 original size:32 final size:32
Alignment explanation
Indices: 236744--237007 Score: 370
Period size: 32 Copynumber: 8.3 Consensus size: 32
236734 GCCACTGACT
236744 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * * *
236776 TGTGGGCTTTGAAATGAGTTACCATCGA-TTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
236807 TGTGAGCTTTCAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
236839 TGTGGGCTTTGAAATAGGTTGCCACCAGCTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
236871 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
236903 TGTGGGCTTTGAAATAGGTTGCCACCAGCTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
236935 TGTGGGCTTTGAAATGGGTTGCCACCAATTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * **
236967 TGTGGGCTTTCAAATGAG-TGCCACTGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
236998 CGTGGGCTTT
1 TGTGGGCTTT
237008 AAAAGGATAC
Statistics
Matches: 204, Mismatches: 27, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
31 44 0.22
32 160 0.78
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (32 bp):
TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
Found at i:237469 original size:45 final size:46
Alignment explanation
Indices: 237405--237493 Score: 137
Period size: 45 Copynumber: 1.9 Consensus size: 46
237395 CACTGACTTG
*
237405 TGGGCTTTGAAAAGTGTTGCCA-CTGACTC-GTGGGCTTTGAAATGA
1 TGGGCTTTGAAAAGGGTTGCCATC-GACTCGGTGGGCTTTGAAATGA
237450 TGGGCTTTGAAAAGGGTTGCCATCGACTCGTGTGGGCTTTGAAA
1 TGGGCTTTGAAAAGGGTTGCCATCGACTCG-GTGGGCTTTGAAA
237494 AGAGTTCCAC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
45 26 0.65
46 1 0.03
47 13 0.32
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (46 bp):
TGGGCTTTGAAAAGGGTTGCCATCGACTCGGTGGGCTTTGAAATGA
Found at i:237793 original size:83 final size:83
Alignment explanation
Indices: 237661--237951 Score: 426
Period size: 83 Copynumber: 3.5 Consensus size: 83
237651 CACCGACTTG
* * * * *
237661 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGATGCCACGAAGTTGTGAAC-T
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGATGCCACGAAGTTGTGGACTT
*
237725 TAAAAGGGTGCCACAGAGT
65 TAAAAGGGTGCCACGGAGT
* *
237744 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGAAGTTGTGGACTT
237809 TAAAAGGGTGCCACGGAGT
65 TAAAAGGGTGCCACGGAGT
* * *
237828 TGTGGACTTT-AAAGGGTACCACGCAGTTGTGGACTTAAAACGATGCCACGGAA-TTGTGGACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCAC-GAAGTTGTGGACTT
237891 TAAAAGGGTGCCACGGAGT
65 TAAAAGGGTGCCACGGAGT
*
237910 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
237952 AAAATGCCAC
Statistics
Matches: 187, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
82 52 0.28
83 104 0.56
84 31 0.17
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (83 bp):
TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTT
AAAAGGGTGCCACGGAGT
Found at i:237943 original size:56 final size:56
Alignment explanation
Indices: 237661--237951 Score: 428
Period size: 55 Copynumber: 5.3 Consensus size: 56
237651 CACCGACTTG
* * * * * *
237661 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGATGCCACGAAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
* * *
237717 TGTGAAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
*
237772 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
* * * *
237828 TGTGGACTTT-AAAGGGTACCACGCAGTTGTGGAC-TTAAAACGATGCCACGGAAT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
237882 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
237938 TGTGGAC-TTAAAAG
1 TGTGGACTTTAAAAG
237952 AAAATGCCAC
Statistics
Matches: 213, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
54 27 0.13
55 99 0.46
56 87 0.41
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (56 bp):
TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
Found at i:239012 original size:13 final size:13
Alignment explanation
Indices: 238994--239027 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
238984 AGGGTCAAAA
238994 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
239007 GG-TTTTTTTTTT
1 GGTTTTTTTTTTT
239019 -GTTTTTTTT
1 GGTTTTTTTT
239028 CTTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 17 0.85
13 2 0.10
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
GGTTTTTTTTTTT
Found at i:239014 original size:12 final size:11
Alignment explanation
Indices: 238997--239036 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
238987 GTCAAAAGGT
238997 TTTTTTTTTTGG
1 TTTTTTTTTT-G
239009 TTTTTTTTTTG
1 TTTTTTTTTTG
*
239020 TTTTTTTTCT-
1 TTTTTTTTTTG
239030 TTTTTTT
1 TTTTTTT
239037 AGGTGAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 7 0.26
11 10 0.37
12 10 0.37
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:239337 original size:23 final size:24
Alignment explanation
Indices: 239311--239356 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
239301 TGCTTTTGCA
239311 CTTTTGCTTTTCA-TTTTTTTGTG
1 CTTTTGCTTTTCACTTTTTTTGTG
*
239334 CTTTTGCTTTTGACTTTTTTTGT
1 CTTTTGCTTTTCACTTTTTTTGT
239357 CATTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.70
Consensus pattern (24 bp):
CTTTTGCTTTTCACTTTTTTTGTG
Found at i:239352 original size:14 final size:13
Alignment explanation
Indices: 239298--239351 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
239288 TCCCTTTTTA
239298 TTTTGCTTTTGCAC
1 TTTTGCTTTTG-AC
*
239312 TTTTGCTTTTCA-
1 TTTTGCTTTTGAC
239324 TTTT--TTTGTG-C
1 TTTTGCTTT-TGAC
239335 TTTTGCTTTTGAC
1 TTTTGCTTTTGAC
239348 TTTT
1 TTTT
239352 TTTGTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
10 3 0.09
11 5 0.15
12 6 0.18
13 9 0.27
14 10 0.30
ACGTcount: A:0.06, C:0.15, G:0.13, T:0.67
Consensus pattern (13 bp):
TTTTGCTTTTGAC
Found at i:239362 original size:24 final size:23
Alignment explanation
Indices: 239304--239362 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
239294 TTTATTTTGC
239304 TTTTG-CACTTTTGCTTTTCATTT
1 TTTTGTCA-TTTTGCTTTTCATTT
*
239327 TTTTGTGC-TTTTGCTTTTGACTTT
1 TTTTGT-CATTTTGCTTTTCA-TTT
239351 TTTTGTCATTTT
1 TTTTGTCATTTT
239363 AAAGGGAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 17 0.55
24 13 0.42
25 1 0.03
ACGTcount: A:0.07, C:0.14, G:0.12, T:0.68
Consensus pattern (23 bp):
TTTTGTCATTTTGCTTTTCATTT
Found at i:246426 original size:20 final size:19
Alignment explanation
Indices: 246395--246469 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
246385 AAAAAGACAT
*
246395 AATGTCTCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
246414 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
246435 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
246455 AATGTATCGATACAT
1 AATGTATCGATACAT
246470 CTAGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:246463 original size:40 final size:39
Alignment explanation
Indices: 246392--246469 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
246382 GGTAAAAAGA
* *
246392 CATAATGTCTCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
246431 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
246470 CTAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Done.