Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold139
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: 1720190
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4798 characters in sequence are not A, C, G, or T
File 4 of 11
Found at i:504968 original size:20 final size:21
Alignment explanation
Indices: 504945--504998 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
504935 ACAATTAGGC
504945 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
* *
504965 ATGTATTGATACATTTACTAT
1 ATGTATCGATACATTCACTAT
*
504986 TTGTATCGATACA
1 ATGTATCGATACA
504999 AATTATAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:505662 original size:61 final size:61
Alignment explanation
Indices: 505484--506163 Score: 528
Period size: 61 Copynumber: 11.0 Consensus size: 61
505474 TGAAGTAGAT
* * * * *
505484 AGGTGCCACCAACTTCTGTGGGCTTTAAGATA-GAAAGGA-GTCTTAG-TCTTTGAGGACTAAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAA-A-AGGAAAAGACATCCT-GCTCTTTAAGGACT-AAA
* * * * *
505546 AGGAGTGCCACCAATTTTTTTGGGCTTTTAAAAAGAAAAAAAGACATCCTGCTCTTTAAGGATTA
1 A-G-GTGCCACCAACTTGTGTGGGC-TTT-AAAAG--GAAAAGACATCCTGCTCTTTAAGGACTA
505611 AA
60 AA
* * *
505613 AGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGACATCCTGCTCTTTAAAGACCAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTGCTCTTTAAGGACTAAA
* * * *
505674 A---CCCACCAACTTGTGTGGGCTTTGAAAGAAAAAGGCAT-CTGCTCTTTGAA-GACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTGCTCTTT-AAGGACTAAA
* * * * *
505731 AGGTGCCA-CTACTTGTGTGGGCTTTAAAAGAAAAAAAGAAAGTGTCTTGCTCTTTGAGGACTAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAG--GAAAAGACA---TCCTGCTCTTTAAGGACTAA
505795 A
61 A
* * * *
505796 AGGCGCCACTAACTTGTGTGGACTTTGAAAGGAGAAAG-CATCCTGCTCTTTCAA-GACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGACATCCTGCTCTTT-AAGGACTAAA
* * * * ** * *
505857 AAGTGCCACCAGCTTGTGTGGGCTTT-TAAGGGAAAG-TTTCTTACTCTTTGAA-GACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTGCTCTTT-AAGGACTAAA
** * ****
505916 AAATGCCACCAACTTGTGTGGGCTTCAAAAGGAAAAGTTGGCCTGCTCTTTAAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTGCTCTTTAAGGACTAAA
* * *
505977 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTGCTCTTTAAGGACTAAA
* * ** * * * **
506038 AAGTGCCATCGGCTTCTGTGGGCTTT-TAAGGGAAAG-TGTCCTGCTCTTTAAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTGCTCTTTAAGGACTAAA
* * * *
506097 AGGTACCACCAACTTGTGTGTGCTTTAAAAGAAAAAGGAAAGTGTCCTGCTCTTTAAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GACA---TCCTGCTCTTTAAGGACTAAA
506162 AG
1 AG
506164 AATAAAAGGT
Statistics
Matches: 500, Mismatches: 86, Indels: 61
0.77 0.13 0.09
Matches are distributed among these distances:
57 16 0.03
58 36 0.07
59 105 0.21
60 31 0.06
61 164 0.33
62 2 0.00
63 5 0.01
64 26 0.05
65 71 0.14
66 21 0.04
67 10 0.02
68 13 0.03
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (61 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTGCTCTTTAAGGACTAAA
Found at i:506023 original size:181 final size:181
Alignment explanation
Indices: 505530--506163 Score: 679
Period size: 181 Copynumber: 3.4 Consensus size: 181
505520 GGAGTCTTAG
* * * * * **
505530 TCTTTGAGGACTAAAAAGGAGTGCCACCAATTTTTTTGGGCTTTTAAAAAGAAAAAAAGACATCC
1 TCTTTGAAGACT-AAAA-G-GTGCCACCAACTTGTGTGGGC-TTT-AAAAGAAAAAGAG-TGTCC
* *
505595 TGCTCTTTAAGGATTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGACATCCTGCT
60 TGCTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCT
* * * * ** *
505660 CTTTAAAGAC-CAAAA--CCCACCAACTTGTGTGGGCTTTGAAAGAAAAAGGCATCTGC
125 CTTTAAAGACTAAAAAGTGCCACCAGCTTGTGTGGGCTTT-TAAGGGAAA-GTATCTGC
* *
505716 TCTTTGAAGACTAAAAGGTGCCA-CTACTTGTGTGGGCTTTAAAAGAAAAAAAGAAAGTGTCTTG
1 TCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG--AAAAAG--AGTGTCCTG
* * * *
505780 CTCTTTGAGGACTAAAAGGCGCCACTAACTTGTGTGGACTTTGAAAGGAGAAA-GCATCCTGCTC
62 CTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AAAGGCATCCTGCTC
* * *
505844 TTTCAAGACTAAAAAGTGCCACCAGCTTGTGTGGGCTTTTAAGGGAAAGTTTCTTAC
126 TTTAAAGACTAAAAAGTGCCACCAGCTTGTGTGGGCTTTTAAGGGAAAGTATC-TGC
** * * * *
505901 TCTTTGAAGACTAAAAAATGCCACCAACTTGTGTGGGCTTCAAAAGGAAAAG-TTGGCCTGCTCT
1 TCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGAGTGTCCTGCTCT
* * *
505965 TTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGA
66 TTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCTCTTTAA
* * * * *
506030 GGACTAAAAAGTGCCATCGGCTTCTGTGGGCTTTTAAGGGAAAGTGTCCTGC
131 AGACTAAAAAGTGCCACCAGCTTGTGTGGGCTTTTAAGGGAAAGTAT-CTGC
* *
506082 TCTTT-AAGGACTAAAAGGTACCACCAACTTGTGTGTGCTTTAAAAGAAAAAGGAAAGTGTCCTG
1 TCTTTGAA-GACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA-G--AGTGTCCTG
506146 CTCTTTAAGGACTAAAAG
62 CTCTTTAAGGACTAAAAG
506164 AATAAAAGGT
Statistics
Matches: 377, Mismatches: 54, Indels: 35
0.81 0.12 0.08
Matches are distributed among these distances:
180 10 0.03
181 152 0.40
182 17 0.05
183 72 0.19
184 18 0.05
185 57 0.15
186 51 0.14
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (181 bp):
TCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGAGTGTCCTGCTCT
TTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCTCTTTAA
AGACTAAAAAGTGCCACCAGCTTGTGTGGGCTTTTAAGGGAAAGTATCTGC
Found at i:506134 original size:120 final size:121
Alignment explanation
Indices: 505484--506162 Score: 558
Period size: 120 Copynumber: 5.5 Consensus size: 121
505474 TGAAGTAGAT
* * *
505484 AGGTGCCACCAACTTCTGTGGGCTTTAAGATA-G-AAAGGAGTCTTAG-TCTTTGAGGACTAAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAA-A-AGGAAAAGGTGTCCT-GCTCTTTGAGGACT-AAA
* * * * * ** *
505546 AGGAGTGCCACCAATTTTTTTGGGCTTTTAAAAAGAAAAAAAGACATCCTGCTCTTTAAGGATTA
62 A--AGTGCCACCAACTTGTGTGGGC-TTT-GAAAG--GAAAAG-TGTCCTGCTCTTTAAGGACTA
505611 AA
120 AA
* *** * * *
505613 AGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGACATCCTGCTCTTTAAAGAC-CAAAA--
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGT
* *
505675 CCCACCAACTTGTGTGGGCTTTGAAAGAAAAAG-G-CATCTGCTCTTTGAA-GACTAAA
66 GCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGTGTC--CTGCTCTTT-AAGGACTAAA
* * *
505731 AGGTGCCA-CTACTTGTGTGGGCTTTAAAAGAAAAAAAGAAAGTGTCTTGCTCTTTGAGGACTAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAG--GAAAAG---GTGTCCTGCTCTTTGAGGACTAA
* * * * **
505795 AAGGCGCCACTAACTTGTGTGGACTTTGAAAGGAGAAAGCATCCTGCTCTTTCAA-GACTAAA
61 AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AAAGTGTCCTGCTCTTT-AAGGACTAAA
* * * * * * * * *
505857 AAGTGCCACCAGCTTGTGTGGGCTTT-TAAGGGAAA-GTTTCTTACTCTTTGAAGACTAAAAAAT
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGT
** *
505920 GCCACCAACTTGTGTGGGCTTCAAAAGGAAAAGTTGGCCTGCTCTTTAAGGACTAAA
66 GCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG-TGTCCTGCTCTTTAAGGACTAAA
*
505977 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGT
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGT
* ** * * *
506042 GCCATCGGCTTCTGTGGGCTTT-TAAGGGAAAGTGTCCTGCTCTTTAAGGACTAAA
66 GCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGTGTCCTGCTCTTTAAGGACTAAA
* * * *
506097 AGGTACCACCAACTTGTGTGTGCTTTAAAAGAAAAAGGAAAGTGTCCTGCTCTTTAAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-G---GTGTCCTGCTCTTTGAGGACTAAA
506162 A
62 A
506163 GAATAAAAGG
Statistics
Matches: 449, Mismatches: 75, Indels: 57
0.77 0.13 0.10
Matches are distributed among these distances:
116 1 0.00
117 20 0.04
118 23 0.05
119 19 0.04
120 143 0.32
121 20 0.04
122 56 0.12
123 18 0.04
124 26 0.06
125 26 0.06
126 32 0.07
127 19 0.04
128 4 0.01
129 42 0.09
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (121 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGT
GCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGTGTCCTGCTCTTTAAGGACTAAA
Found at i:518522 original size:51 final size:49
Alignment explanation
Indices: 518399--518522 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 49
518389 TTTTGGTTGT
* * *
518399 AAAAACGGGGTTAGAGTATCTTTGATGGTGAAAAATCGATATTTTAAAA
1 AAAAATGGGGTTAGAGTATCCTAGATGGTGAAAAATCGATATTTTAAAA
* * * *
518448 ATAAAATCGAGGTTGGAGCATCCTAGATGGTGAAAAATCGATATTTTGGAAAC
1 A-AAAAT-GGGGTTAGAGTATCCTAGATGGTGAAAAATCGATATTTT--AAAA
518501 AAAAATGGGGTTAGAGTATCCT
1 AAAAATGGGGTTAGAGTATCCT
518523 TTCAAAAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
49 1 0.02
50 4 0.07
51 47 0.77
52 5 0.08
53 4 0.07
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (49 bp):
AAAAATGGGGTTAGAGTATCCTAGATGGTGAAAAATCGATATTTTAAAA
Found at i:518542 original size:28 final size:29
Alignment explanation
Indices: 518508--518576 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
518498 AACAAAAATG
518508 GGGTTAGAGTATCCTT-TCAAAAATAACA
1 GGGTTAGAGTATCCTTCTCAAAAATAACA
* * *
518536 GGGTTAGAAT-TTCTTCTCGAAAATAACA
1 GGGTTAGAGTATCCTTCTCAAAAATAACA
* *
518564 AGGTCAGAGTATC
1 GGGTTAGAGTATC
518577 GCCAAGGGTG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 4 0.12
28 27 0.84
29 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.29
Consensus pattern (29 bp):
GGGTTAGAGTATCCTTCTCAAAAATAACA
Found at i:518748 original size:79 final size:79
Alignment explanation
Indices: 518550--518748 Score: 222
Period size: 79 Copynumber: 2.5 Consensus size: 79
518540 TAGAATTTCT
* * * * ***
518550 TCTCGAAAATAACAAGGTCAGAGTATCGCCAAGGGTGAAAATTTGATAGTTTGAAAATAAAATTG
1 TCTC-AAAATAACAGGGTTAGAGTATCCCCAATGGTGAAAATTTGATAGTTTGAAAATAAAAACA
*
518615 GGGTTAAAGTATTCC
65 GAGTTAAAGTATTCC
* * *
518630 -CTCAGAAATAACAGGGTTTGAGTATCCTCAATGGTGAAAATTTGATATTTTGAAAATAAAAACA
1 TCTCA-AAATAACAGGGTTAGAGTATCCCCAATGGTGAAAATTTGATAGTTTGAAAATAAAAACA
**
518694 GAGTTGGAGTA-TCC
65 GAGTTAAAGTATTCC
* *
518708 TCTCAAAATAACAGGGTTGGAGTATCCCCGATGGTGGAAAA
1 TCTCAAAATAACAGGGTTAGAGTATCCCCAATGGT-GAAAA
518749 AAATCAATAT
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
78 31 0.31
79 69 0.69
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (79 bp):
TCTCAAAATAACAGGGTTAGAGTATCCCCAATGGTGAAAATTTGATAGTTTGAAAATAAAAACAG
AGTTAAAGTATTCC
Found at i:523713 original size:97 final size:98
Alignment explanation
Indices: 523564--523798 Score: 323
Period size: 97 Copynumber: 2.4 Consensus size: 98
523554 CGAGGATACT
* * *
523564 CTAACCCTATTCCTCCGAGGGGATACTCGAACCCCGCTTTTAAATACATCAAAGTTTAAATCTTA
1 CTAACCCTATTCCTCCGAGGGGATACTCCAACCCTGCTTTTAAACACATCAAAGTTTAAATCTTA
*
523629 TTCACACTTAAATTGTCATCATCGGGGACA-CC
66 TTCACACTTAAATTGTCATCATCGAGGACATCC
* *
523661 CTAACCCTATTCCTCTGAGGGGATACTCCAACCCTGCTTTTAAACACTTCAAAGTTTAAATCTTA
1 CTAACCCTATTCCTCCGAGGGGATACTCCAACCCTGCTTTTAAACACATCAAAGTTTAAATCTTA
** *
523726 TTCTTACTTAAATTGTCATCATCGAGGACATTC
66 TTCACACTTAAATTGTCATCATCGAGGACATCC
* ** *
523759 C-AACCCCATTCCTCCGAGAAGATACTCTAA-CCTCGCTTTT
1 CTAACCCTATTCCTCCGAGGGGATACTCCAACCCT-GCTTTT
523799 CAATAAAAAA
Statistics
Matches: 122, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
96 3 0.02
97 117 0.96
98 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (98 bp):
CTAACCCTATTCCTCCGAGGGGATACTCCAACCCTGCTTTTAAACACATCAAAGTTTAAATCTTA
TTCACACTTAAATTGTCATCATCGAGGACATCC
Found at i:527292 original size:13 final size:13
Alignment explanation
Indices: 527274--527299 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
527264 TACAGCAAGT
527274 ATGTATCGATACA
1 ATGTATCGATACA
527287 ATGTATCGATACA
1 ATGTATCGATACA
527300 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:529550 original size:21 final size:21
Alignment explanation
Indices: 529517--529561 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
529507 TTGCAAGTTG
*
529517 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
529539 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
529559 AAA
1 AAA
529562 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:531384 original size:15 final size:15
Alignment explanation
Indices: 531364--531394 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
531354 TAAAAATGTC
*
531364 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
531379 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
531394 C
1 C
531395 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:533477 original size:20 final size:20
Alignment explanation
Indices: 533452--533518 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
533442 AGAAATTCAA
533452 TGTATCGATACATTTTTCTT
1 TGTATCGATACATTTTTCTT
533472 TGTATCGATACA-------T
1 TGTATCGATACATTTTTCTT
533485 TGTATCGATACATTTTTCTT
1 TGTATCGATACATTTTTCTT
533505 TGTATCGATACATT
1 TGTATCGATACATT
533519 GTATCGATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.32
20 27 0.68
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (20 bp):
TGTATCGATACATTTTTCTT
Found at i:533489 original size:13 final size:13
Alignment explanation
Indices: 533471--533542 Score: 93
Period size: 13 Copynumber: 6.0 Consensus size: 13
533461 ACATTTTTCT
533471 TTGTATCGATACA
1 TTGTATCGATACA
533484 TTGTATCGATACA
1 TTGTATCGATACA
*
533497 TT-T-T---T-CT
1 TTGTATCGATACA
533504 TTGTATCGATACA
1 TTGTATCGATACA
533517 TTGTATCGATACA
1 TTGTATCGATACA
533530 TTGTATCGATACA
1 TTGTATCGATACA
533543 GGGTGATTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
9 1 0.02
11 1 0.02
12 2 0.04
13 42 0.82
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:533494 original size:33 final size:33
Alignment explanation
Indices: 533452--533531 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
533442 AGAAATTCAA
533452 TGTATCGATACATTTTTCTTTGTATCGATACAT
1 TGTATCGATACATTTTTCTTTGTATCGATACAT
533485 TGTATCGATACATTTTTCTTTGTATCGATACAT
1 TGTATCGATACATTTTTCTTTGTATCGATACAT
533518 TGTATCGATACATT
1 TGTATCGATACATT
533532 GTATCGATAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (33 bp):
TGTATCGATACATTTTTCTTTGTATCGATACAT
Found at i:536116 original size:13 final size:13
Alignment explanation
Indices: 536098--536123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
536088 TACAGCAAGT
536098 ATGTATCGATACA
1 ATGTATCGATACA
536111 ATGTATCGATACA
1 ATGTATCGATACA
536124 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:538913 original size:18 final size:20
Alignment explanation
Indices: 538890--538927 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
538880 TTCATATTTT
538890 AAAAACCTT-TT-TTTAAAA
1 AAAAACCTTCTTCTTTAAAA
*
538908 AAAAACTTTCTTCTTTAAAA
1 AAAAACCTTCTTCTTTAAAA
538928 CTTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAACCTTCTTCTTTAAAA
Found at i:542746 original size:20 final size:21
Alignment explanation
Indices: 542713--542751 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
542703 GAGAGAAAAT
*
542713 AATATTCTAGAATATCTAAGA
1 AATATTCTAAAATATCTAAGA
542734 AATA-TCTAAAATATCTAA
1 AATATTCTAAAATATCTAA
542752 AATGTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (21 bp):
AATATTCTAAAATATCTAAGA
Found at i:546891 original size:103 final size:104
Alignment explanation
Indices: 546699--546922 Score: 262
Period size: 103 Copynumber: 2.2 Consensus size: 104
546689 ATTTTTTATT
* * *
546699 CATAGGGATACTCCAA-CCTCGACCTTTTAAGGGGATACTCCAACCCCGCTCTTCGAAATTTGTC
1 CATAGGGATACTCCAACCCTCGACCTTTTAAAGAGATACTCCAACCCCGCTCTTAGAAATTTGTC
*
546763 AAGATTTGAACTTTTCCTTAGTCAAAATCATTT-ATCATC
66 AAGATTTAAACTTTTCCTTAGTC-AAATCATTTGATCATC
* ** *
546802 CATGGGGATACTCCAACCCT-GACCTTTTAAAGAGATACTCCAACCTTGCTTTTTAG-AA-TTGT
1 CATAGGGATACTCCAACCCTCGACCTTTTAAAGAGATACTCCAACCCCGC-TCTTAGAAATTTGT
* *
546864 CAAGATTTAAAACTTTTCCTTTA-TCAAATTATTTGGTCATC
65 CAAGATTT-AAACTTTTCC-TTAGTCAAATCATTTGATCATC
* *
546905 CGTAGGGATATTCCAACC
1 CATAGGGATACTCCAACC
546923 TCATCTTTCC
Statistics
Matches: 103, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
102 20 0.19
103 73 0.71
104 10 0.10
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (104 bp):
CATAGGGATACTCCAACCCTCGACCTTTTAAAGAGATACTCCAACCCCGCTCTTAGAAATTTGTC
AAGATTTAAACTTTTCCTTAGTCAAATCATTTGATCATC
Found at i:552464 original size:19 final size:19
Alignment explanation
Indices: 552420--552475 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
552410 TAGCTACTTT
**
552420 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
552440 CATGTACCGATACAATGAA
1 CATGTATCGATACAATGAA
*
552459 CATGTATCAATACAATG
1 CATGTATCGATACAATG
552476 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:554859 original size:22 final size:21
Alignment explanation
Indices: 554824--554873 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
554814 TCTGTTGATG
*
554824 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
554844 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
554865 AATTTGAAG
1 ATTTTGAAG
554874 AAAATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:554870 original size:21 final size:22
Alignment explanation
Indices: 554831--554873 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
554821 ATGATTTTGA
* *
554831 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
554853 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
554874 AAAATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:559449 original size:13 final size:13
Alignment explanation
Indices: 559431--559458 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
559421 ATACAAAGAT
559431 CAATGTATCGATA
1 CAATGTATCGATA
559444 CAATGTATCGATA
1 CAATGTATCGATA
559457 CA
1 CA
559459 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:562126 original size:13 final size:13
Alignment explanation
Indices: 562108--562132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
562098 CAATTCAACA
562108 TGTATCGATACAT
1 TGTATCGATACAT
562121 TGTATCGATACA
1 TGTATCGATACA
562133 ATATGCCATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:562202 original size:13 final size:13
Alignment explanation
Indices: 562184--562208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
562174 ACCAGTTTCA
562184 TGTATCGATACAT
1 TGTATCGATACAT
562197 TGTATCGATACA
1 TGTATCGATACA
562209 AACCATAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:567394 original size:3 final size:3
Alignment explanation
Indices: 567386--567413 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
567376 TCAACCATCA
567386 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
567414 AGTTGACTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:571790 original size:20 final size:21
Alignment explanation
Indices: 571765--571804 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
571755 AATTTCCCAG
571765 AATGTATCGATACAT-TGAAT
1 AATGTATCGATACATCTGAAT
571785 AATGTATCGATACATCTGAA
1 AATGTATCGATACATCTGAA
571805 AAATCTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (21 bp):
AATGTATCGATACATCTGAAT
Found at i:578449 original size:79 final size:78
Alignment explanation
Indices: 578358--578689 Score: 271
Period size: 79 Copynumber: 4.2 Consensus size: 78
578348 TTCATCCTTA
* * * *
578358 AAGGGTACTCCAACCTCGTCTCTCCGAGAGGATGTTCTAACCCCACTTTTCTTACAAAAAATCTT
1 AAGGGTACTCCAA-CTCGTCTCTCCAAGAGGATATTCTAACCCTATTTTTCTTACAAAAAATCTT
578423 GAATTTACATTCTC
65 GAATTTACATTCTC
* * * * * * *
578437 TAGGGTAATCCAACTCTATCTCTCTAA-AGGGATACTCCAATCCTATTTTTCTTACAAAAAATCT
1 AAGGGTACTCCAACTC-GTCTCTCCAAGA-GGATATTCTAACCCTATTTTTCTTACAAAAAATCT
*
578501 TGAATTTACATTATC
64 TGAATTTACATTCTC
* * * * * *
578516 AAGGATACTGCAACTTGATCTCTCTAAGAGGATACTT-TATCCCTATTTTTCTTACGAAAAATCT
1 AAGGGTACTCCAACTCG-TCTCTCCAAGAGGATA-TTCTAACCCTATTTTTCTTACAAAAAATCT
578580 TGAATTTACATTCTC
64 TGAATTTACATTCTC
* * * * * * *
578595 GAA-AGTTCTCCAACTCCATCTCTCTACG-GAGATACTTC-AACCCCATTTTTCTTAAAAAAAAA
1 -AAGGGTACTCCAACT-CGTCTCTCCAAGAG-GATA-TTCTAACCCTATTTTTCTT--ACAAAAA
*
578657 ATCATGAATTTACATTCTC
60 ATCTTGAATTTACATTCTC
*
578676 -AGGGATACTTCAAC
1 AAGGG-TACTCCAAC
578690 CTTATCTCTC
Statistics
Matches: 201, Mismatches: 39, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
78 5 0.02
79 161 0.80
80 5 0.02
81 30 0.15
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (78 bp):
AAGGGTACTCCAACTCGTCTCTCCAAGAGGATATTCTAACCCTATTTTTCTTACAAAAAATCTTG
AATTTACATTCTC
Found at i:578643 original size:158 final size:159
Alignment explanation
Indices: 578404--578699 Score: 400
Period size: 158 Copynumber: 1.9 Consensus size: 159
578394 CTAACCCCAC
* ** *
578404 TTTTCTTACAAAAAATCTTGAATTTACATTCTCTAGGGTAATCCAACTCTATCTCTCTAAAGGGA
1 TTTTCTTACAAAAAATCTTGAATTTACATTCTCGAAAGTAATCCAACTCCATCTCTCTAAAGGGA
* * * *
578469 TACTCCAATCCTATTTTTCTT-ACAAAAAATCTTGAATTTACATTATCAAGGATACTGCAA-CTT
66 TACTCCAACCCCATTTTTCTTAAAAAAAAATCATGAATTTACATTATCAAGGATACTGCAACCTT
578532 GATCTCTCTAAGAGGATACTTTATCCCTAT
131 -ATCTCTCTAAGAGGATACTTTATCCCTAT
* ** *
578562 TTTTCTTACGAAAAATCTTGAATTTACATTCTCGAAAGTTCTCCAACTCCATCTCTCT-ACGGAG
1 TTTTCTTACAAAAAATCTTGAATTTACATTCTCGAAAGTAATCCAACTCCATCTCTCTAAAGG-G
* * * *
578626 ATACTTCAACCCCATTTTTCTTAAAAAAAAAATCATGAATTTACATTCTCAGGGATACTTCAACC
65 ATACTCCAACCCCATTTTTCTT-AAAAAAAAATCATGAATTTACATTATCAAGGATACTGCAACC
578691 TTATCTCTC
129 TTATCTCTC
578700 CAAAAGGGGA
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
157 3 0.03
158 71 0.60
160 41 0.35
161 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (159 bp):
TTTTCTTACAAAAAATCTTGAATTTACATTCTCGAAAGTAATCCAACTCCATCTCTCTAAAGGGA
TACTCCAACCCCATTTTTCTTAAAAAAAAATCATGAATTTACATTATCAAGGATACTGCAACCTT
ATCTCTCTAAGAGGATACTTTATCCCTAT
Found at i:586558 original size:13 final size:13
Alignment explanation
Indices: 586540--586564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
586530 GCATAAGTGT
586540 TGTATCGATACAA
1 TGTATCGATACAA
586553 TGTATCGATACA
1 TGTATCGATACA
586565 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:586558 original size:32 final size:32
Alignment explanation
Indices: 586521--586591 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
586511 TTCAACAATT
*
586521 TGTATCGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
586553 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
586585 TGTATCG
1 TGTATCG
586592 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:586577 original size:19 final size:19
Alignment explanation
Indices: 586519--586583 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
586509 ATTTCAACAA
*
586519 TTTGTATCGATGCATAAGT
1 TTTGTATCGATACATAAGT
*
586538 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
586553 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
586570 TTTGTATCGATACA
1 TTTGTATCGATACA
586584 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:592379 original size:17 final size:17
Alignment explanation
Indices: 592356--592389 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
592346 AAATAAATGT
*
592356 AAAAAAAGGAGTGATTTG
1 AAAAAAA-GAGAGATTTG
592374 AAAAAAAGAGAGATTT
1 AAAAAAAGAGAGATTT
592390 TTTTTGGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.21
Consensus pattern (17 bp):
AAAAAAAGAGAGATTTG
Found at i:593892 original size:79 final size:78
Alignment explanation
Indices: 593775--594113 Score: 298
Period size: 79 Copynumber: 4.3 Consensus size: 78
593765 TTTATCCTTA
* * * *
593775 AAGGATACTCCAACTTCATCTCTCCAAGAGGATGCTCTAACCACATATTTCTTACAAAAAATCTT
1 AAGGGTACTCCAACTTCATCTCTCTAAGAGGATACTCTAACC-CATTTTTCTTACAAAAAATCTT
* *
593840 AAATTTACATTTTC
65 GAATTTACATTATC
* * * *
593854 AAGGGCACTCCAAC-TCTATCTCTCTAA-AGGGATACTCTAATCTCATTTTTCCTACAAAAACTC
1 AAGGGTACTCCAACTTC-ATCTCTCTAAGA-GGATACTCTAA-CCCATTTTTCTTACAAAAAATC
593917 TTGAATTTACATTATC
63 TTGAATTTACATTATC
* * * * * * *
593933 AAGGGTACTGCAACTTGATCTCTTTGAGAGGATACTTTATCCCTATTTTTCTTACGAAAAATCTT
1 AAGGGTACTCCAACTTCATCTCTCTAAGAGGATACTCTAACCC-ATTTTTCTTACAAAAAATCTT
*
593998 GAATTTACATTCTC
65 GAATTTACATTATC
* * * * *
594012 GAA-AGTTCTCCAACTCCATCCCTCTACG-GAGATACT-TCAATCCCATTTTTCTTA-AAAAAAT
1 -AAGGGTACTCCAACTTCATCTCTCTAAGAG-GATACTCT-AA-CCCATTTTTCTTACAAAAAAT
*
594073 CTTGAATTTACATTCTC
62 CTTGAATTTACATTATC
*
594090 -AGGGATACTTCAACCTT-ATCTCTC
1 AAGGG-TACTCCAA-CTTCATCTCTC
594114 CAAAAAGGGA
Statistics
Matches: 209, Mismatches: 38, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
76 1 0.00
77 1 0.00
78 42 0.20
79 157 0.75
80 8 0.04
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (78 bp):
AAGGGTACTCCAACTTCATCTCTCTAAGAGGATACTCTAACCCATTTTTCTTACAAAAAATCTTG
AATTTACATTATC
Found at i:594059 original size:158 final size:157
Alignment explanation
Indices: 593822--594112 Score: 367
Period size: 158 Copynumber: 1.8 Consensus size: 157
593812 TAACCACATA
* * * *
593822 TTTCTTACAAAAAATCTTAAATTTACATTTTCAAGGGCACTCCAACTCTATCTCTCTAAAGGGAT
1 TTTCTTACAAAAAATCTTAAATTTACATTCTCAAGAGCACTCCAACTCCATCCCTCTAAAGGGAT
* *
593887 ACTCTAATCTCATTTTTCCTACAAAAACTCTTGAATTTACATTATCAAGGG-TACTGCAA-CTTG
66 ACTCTAATCCCATTTTTCCTA-AAAAAATCTTGAATTTACATTATC-AGGGATACTGCAACCTT-
593950 ATCTCTTTGAGAGGATACTTTATCCCTATT
128 ATCTCTTTGAGAGGATACTTTATCCCTATT
* * ** *
593980 TTTCTTACGAAAAATCTTGAATTTACATTCTCGAA-AGTTCTCCAACTCCATCCCTCT-ACGGAG
1 TTTCTTACAAAAAATCTTAAATTTACATTCTC-AAGAGCACTCCAACTCCATCCCTCTAAAGG-G
* * *
594043 ATACT-TCAATCCCATTTTTCTTAAAAAAATCTTGAATTTACATTCTCAGGGATACTTCAACCTT
64 ATACTCT-AATCCCATTTTTCCTAAAAAAATCTTGAATTTACATTATCAGGGATACTGCAACCTT
594107 ATCTCT
128 ATCTCT
594113 CCAAAAAGGG
Statistics
Matches: 114, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
156 4 0.04
157 39 0.34
158 69 0.61
159 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (157 bp):
TTTCTTACAAAAAATCTTAAATTTACATTCTCAAGAGCACTCCAACTCCATCCCTCTAAAGGGAT
ACTCTAATCCCATTTTTCCTAAAAAAATCTTGAATTTACATTATCAGGGATACTGCAACCTTATC
TCTTTGAGAGGATACTTTATCCCTATT
Found at i:600091 original size:48 final size:48
Alignment explanation
Indices: 600020--600117 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
600010 AAGAAAAAGA
600020 TATTTTAATTGTACAAGTATATGTTGATGATATTATTTTTGGTGCTAC
1 TATTTTAATTGTACAAGTATATGTTGATGATATTATTTTTGGTGCTAC
600068 TATTTTAATTGTACAAGTATATGTTGATGATATTATTTTTGGTGCTAC
1 TATTTTAATTGTACAAGTATATGTTGATGATATTATTTTTGGTGCTAC
600116 TA
1 TA
600118 ATGAATCCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (48 bp):
TATTTTAATTGTACAAGTATATGTTGATGATATTATTTTTGGTGCTAC
Found at i:601454 original size:13 final size:13
Alignment explanation
Indices: 601438--601464 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
601428 ATACAATGTT
601438 CTTTGTATCGATA
1 CTTTGTATCGATA
601451 CTTTGTATCGATA
1 CTTTGTATCGATA
601464 C
1 C
601465 ATGGGTTACT
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:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (13 bp):
CTTTGTATCGATA
Found at i:603937 original size:19 final size:19
Alignment explanation
Indices: 603903--603958 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
603893 TGTATCAATA
* * *
603903 CATTGTATCAAAACATGTT
1 CATTGTATCGATACATGCT
*
603922 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
*
603941 CAATTCTATCGATACATG
1 C-ATTGTATCGATACATG
603959 AAACTAGCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:604025 original size:13 final size:13
Alignment explanation
Indices: 604007--604031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
603997 CATGGGACAT
604007 TGTATCGATACAA
1 TGTATCGATACAA
604020 TGTATCGATACA
1 TGTATCGATACA
604032 TGAAGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:606027 original size:13 final size:13
Alignment explanation
Indices: 606009--606033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
605999 AATATTGCTT
606009 TGTATCGATACAA
1 TGTATCGATACAA
606022 TGTATCGATACA
1 TGTATCGATACA
606034 TGTTTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:606138 original size:13 final size:13
Alignment explanation
Indices: 606120--606149 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
606110 GATACACGGG
*
606120 ACATTGTATTGAT
1 ACATTGTATCGAT
606133 ACATTGTATCGAT
1 ACATTGTATCGAT
606146 ACAT
1 ACAT
606150 AGTGAAAAGT
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:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:608209 original size:15 final size:15
Alignment explanation
Indices: 608184--608219 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
608174 GAATAAATCA
*
608184 AAAATTGTTGAAAAT
1 AAAATTCTTGAAAAT
*
608199 GAAATTCTTGAAAAT
1 AAAATTCTTGAAAAT
608214 AAAATT
1 AAAATT
608220 ATCAAACTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (15 bp):
AAAATTCTTGAAAAT
Found at i:612626 original size:52 final size:52
Alignment explanation
Indices: 612548--612748 Score: 323
Period size: 52 Copynumber: 3.9 Consensus size: 52
612538 CGAAATATGA
*
612548 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
612600 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
612652 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
612704 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
612749 ATGTATCGAT
Statistics
Matches: 139, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
51 2 0.01
52 137 0.99
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:612755 original size:13 final size:13
Alignment explanation
Indices: 612737--612761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
612727 CAAAGATCAG
612737 TGTATCGATACAA
1 TGTATCGATACAA
612750 TGTATCGATACA
1 TGTATCGATACA
612762 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:612842 original size:13 final size:13
Alignment explanation
Indices: 612824--612848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
612814 CAAAAAAACA
612824 TGTATCGATACAT
1 TGTATCGATACAT
612837 TGTATCGATACA
1 TGTATCGATACA
612849 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:612947 original size:21 final size:21
Alignment explanation
Indices: 612906--612947 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
612896 GTTGGGACCT
*
612906 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
612927 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
612948 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:613862 original size:171 final size:171
Alignment explanation
Indices: 613666--613992 Score: 573
Period size: 171 Copynumber: 1.9 Consensus size: 171
613656 TTTTAGAGAT
* * *
613666 GATGAAGGTGCTAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGAAGATGAGAAAA
*
613731 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
613796 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
613837 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGAAGATGAGAAAA
* *
613902 GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
*
613967 TGTCAATGTGCTGATTCAAGGCCAGC
131 TGTCAACGTGCTGATTCAAGGCCAGC
613993 GATATTAGAC
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
171 147 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:613883 original size:49 final size:49
Alignment explanation
Indices: 613737--613895 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
613727 AAAAGTGATA
* * * * *
613737 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
613788 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
613841 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
613890 ATGATG
1 AAGATG
613896 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
49 45 0.53
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:614081 original size:66 final size:66
Alignment explanation
Indices: 613975--614103 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 66
613965 GATGTCAATG
613975 TGCTGATTCAAGGCCAGCGATATTAGACTTAAAAGTGCCAATGTGCTAATTCAAGGCCAGCTAAT
1 TGCTGATTCAAGGCCAGCGATATTAGACTTAAAAGTGCCAATGTGCTAATTCAAGGCCAGCTAAT
614040 A
66 A
* *
614041 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTA
1 TGCTGATTCAAGGCCAGCGATATTAGACTTAAAAGTGCCAATGTGCTAATTCAAGGCCAGCTA
614104 CATTGGACTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (66 bp):
TGCTGATTCAAGGCCAGCGATATTAGACTTAAAAGTGCCAATGTGCTAATTCAAGGCCAGCTAAT
A
Found at i:614147 original size:49 final size:49
Alignment explanation
Indices: 614041--614310 Score: 381
Period size: 49 Copynumber: 5.6 Consensus size: 49
614031 CCAGCTAATA
* *
614041 TGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAA-GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATG
*
614084 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATG
* *
614133 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATG
* *
614182 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATG
* * *
614231 TGCTGATTCAAGGCCAGCTATATTGGATTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATG
* * *
614280 TGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTA
614311 GAAGGGTTGC
Statistics
Matches: 209, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
43 28 0.13
47 1 0.00
48 2 0.01
49 178 0.85
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATG
Found at i:614354 original size:33 final size:35
Alignment explanation
Indices: 614310--614379 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
614300 TATTGGGCTT
*
614310 AGAAGGGTTGCCACCTACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
614344 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
614378 AG
1 AG
614380 GGAGAAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.36, T:0.27
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:614434 original size:35 final size:34
Alignment explanation
Indices: 614364--614516 Score: 168
Period size: 34 Copynumber: 4.4 Consensus size: 34
614354 CACCGACTTG
* * *
614364 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGT
1 TGTGGGCTTTA-AAAGGAAAAAAG-TGCCACGGAGT
*
614400 TGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAA-GGAAAAA-AGTGCCACGGAGT
614435 TGTGGGCTTTAAAAGG-AAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAAGTGCCACGGAGT
* * *
614468 TATGGGCTTTGAAAA-GAAGAACGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAAGTGCCACGGAGT
614502 TGTGGGCTTTGAAAA
1 TGTGGGCTTT-AAAA
614517 AGATGCCACT
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
33 23 0.22
34 39 0.38
35 27 0.26
36 14 0.14
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (34 bp):
TGTGGGCTTTAAAAGGAAAAAAGTGCCACGGAGT
Found at i:614533 original size:29 final size:29
Alignment explanation
Indices: 614415--614540 Score: 119
Period size: 33 Copynumber: 4.0 Consensus size: 29
614405 ACTTAAAAGG
614415 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAGA-TGCCACGGAGTTGTGGGCTTT
*
614445 AAAAGGAAAAAG-TGCCACGGAGTTATGGGCTTT
1 -----GAAAAAGATGCCACGGAGTTGTGGGCTTT
614478 GAAAAGAAGAACGTGCCACGGAGTTGTGGGCTTT
1 G-AAA-AAG-A--TGCCACGGAGTTGTGGGCTTT
* *
614512 GAAAAAGATGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACGGAGTTGTGGGCTTT
614541 TGAAGGGTAA
Statistics
Matches: 81, Mismatches: 4, Indels: 18
0.79 0.04 0.17
Matches are distributed among these distances:
28 1 0.01
29 22 0.27
30 3 0.04
31 1 0.01
32 3 0.04
33 23 0.28
34 21 0.26
35 7 0.09
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (29 bp):
GAAAAAGATGCCACGGAGTTGTGGGCTTT
Found at i:615987 original size:1 final size:1
Alignment explanation
Indices: 615983--616100 Score: 56
Period size: 1 Copynumber: 118.0 Consensus size: 1
615973 CCGGACCCCC
* * * * * * * ** **
615983 TTTTTTTTGTTTGTTTTATTATTGTTTTTTGTTGTTTTTTTTTTTTTTTTTGGTTTTTCATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * ** ** **
616048 TGGTTTTTTTTTTCTTTTGGTTTTTCATTTTTTTTTTCGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
616101 GGAGGACGCC
Statistics
Matches: 86, Mismatches: 31, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 86 1.00
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.83
Consensus pattern (1 bp):
T
Found at i:616013 original size:22 final size:19
Alignment explanation
Indices: 615983--616100 Score: 93
Period size: 18 Copynumber: 6.3 Consensus size: 19
615973 CCGGACCCCC
615983 TTTTTTTTGTTTGTTTTATT
1 TTTTTTTTGTTTGTTTT-TT
616003 ATTGTTTTTTG-TTGTTTTTT
1 -TT-TTTTTTGTTTGTTTTTT
*
616023 TTTTTTTT-TTTGGTTTTT
1 TTTTTTTTGTTTGTTTTTT
** *
616041 CATTTTTTGGTT-TTTTTT
1 TTTTTTTTGTTTGTTTTTT
* * *
616059 TTCTTTTGGTTT-TTCATTT
1 TTTTTTTTGTTTGTT-TTTT
*
616078 TTTTTTTCGTTT-TTTTTT
1 TTTTTTTTGTTTGTTTTTT
616096 TTTTT
1 TTTTT
616101 GGAGGACGCC
Statistics
Matches: 79, Mismatches: 14, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
18 42 0.53
19 19 0.24
20 2 0.03
21 9 0.11
22 7 0.09
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.83
Consensus pattern (19 bp):
TTTTTTTTGTTTGTTTTTT
Found at i:616056 original size:10 final size:9
Alignment explanation
Indices: 615986--616100 Score: 69
Period size: 8 Copynumber: 12.7 Consensus size: 9
615976 GACCCCCTTT
615986 TTTTTGTTTG
1 TTTTT-TTTG
615996 TTTTATTATTG
1 TTTT-TT-TTG
616007 TTTTTTGTTG
1 TTTTTT-TTG
616017 TTTTTTTT-
1 TTTTTTTTG
616025 TTTTTTTT-
1 TTTTTTTTG
** *
616033 TGGTTTTTC
1 TTTTTTTTG
* *
616042 ATTTTTTGG
1 TTTTTTTTG
616051 TTTTTTTT-
1 TTTTTTTTG
* *
616059 TTCTTTTGG
1 TTTTTTTTG
616068 TTTTTCATTT-
1 TTTTT--TTTG
*
616078 TTTTTTTCG
1 TTTTTTTTG
616087 TTTTTTTT-
1 TTTTTTTTG
616095 TTTTTT
1 TTTTTT
616101 GGAGGACGCC
Statistics
Matches: 82, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
8 28 0.34
9 23 0.28
10 21 0.26
11 10 0.12
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.83
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:616060 original size:32 final size:32
Alignment explanation
Indices: 616019--616099 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
616009 TTTTGTTGTT
616019 TTTTTTTTTTTTTTTGGTTTTTCATTTTTTGG
1 TTTTTTTTTTTTTTTGGTTTTTCATTTTTTGG
* **
616051 TTTTTTTTTTCTTTTGGTTTTTCATTTTTTTT
1 TTTTTTTTTTTTTTTGGTTTTTCATTTTTTGG
616083 TTCGTTTTTTTTTTTTT
1 TT--TTTTTTTTTTTTT
616100 TGGAGGACGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 31 0.72
34 12 0.28
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (32 bp):
TTTTTTTTTTTTTTTGGTTTTTCATTTTTTGG
Found at i:616083 original size:12 final size:11
Alignment explanation
Indices: 615983--616100 Score: 62
Period size: 12 Copynumber: 10.2 Consensus size: 11
615973 CCGGACCCCC
*
615983 TTTTTTTTGTT
1 TTTTTTTTCTT
* *
615994 TGTTTTATTATT
1 T-TTTTTTTCTT
*
616006 GTTTTTTGTTGTT
1 -TTTTTT-TTCTT
616019 TTTTTTTT-TT
1 TTTTTTTTCTT
616029 TTTTTGGTTT-TT
1 TTTTT--TTTCTT
* **
616041 CATTTTTTGGTT
1 -TTTTTTTTCTT
616053 TTTTTTTTCTT
1 TTTTTTTTCTT
*
616064 TTGGTTTTTCATT
1 TT-TTTTTTC-TT
616077 TTTTTTTTCGTT
1 TTTTTTTTC-TT
616089 TTTTTTTT-TT
1 TTTTTTTTCTT
616099 TT
1 TT
616101 GGAGGACGCC
Statistics
Matches: 86, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
10 11 0.13
11 15 0.17
12 47 0.55
13 13 0.15
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:616096 original size:25 final size:23
Alignment explanation
Indices: 615983--616100 Score: 82
Period size: 21 Copynumber: 5.0 Consensus size: 23
615973 CCGGACCCCC
* * *
615983 TTTTTTTT-GTTTGTTTTATTAT
1 TTTTTTTTCGTTTTTTTTTTTTT
* *
616005 TGTTTTTT-G-TTGTTTTTTTTT
1 TTTTTTTTCGTTTTTTTTTTTTT
*
616026 TTTTTTTTGGTTTTTCATTTTTTGGTT
1 TTTTTTTTCGTTTTT--TTTTTT--TT
**
616053 TTTTTTTTC-TTTTGGTTTTTCATT
1 TTTTTTTTCGTTTT--TTTTTTTTT
616077 TTTTTTTTCGTTTTTTTTTTTTT
1 TTTTTTTTCGTTTTTTTTTTTTT
616100 T
1 T
616101 GGAGGACGCC
Statistics
Matches: 77, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
21 17 0.22
22 9 0.12
23 11 0.14
24 11 0.14
25 10 0.13
26 8 0.10
27 10 0.13
28 1 0.01
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.83
Consensus pattern (23 bp):
TTTTTTTTCGTTTTTTTTTTTTT
Found at i:625804 original size:10 final size:10
Alignment explanation
Indices: 625789--625815 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
625779 ATGTATCAAG
625789 CAAAAACAAA
1 CAAAAACAAA
625799 CAAAAACAAA
1 CAAAAACAAA
625809 CAAAAAC
1 CAAAAAC
625816 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:630031 original size:52 final size:51
Alignment explanation
Indices: 629953--630101 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
629943 CGAAATATGA
629953 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
630005 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
630057 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
630102 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:630108 original size:13 final size:13
Alignment explanation
Indices: 630090--630114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
630080 CAAAGATCAG
630090 TGTATCGATACAA
1 TGTATCGATACAA
630103 TGTATCGATACA
1 TGTATCGATACA
630115 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:630572 original size:13 final size:13
Alignment explanation
Indices: 630554--630579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
630544 TACAGCAAGT
630554 ATGTATCGATACA
1 ATGTATCGATACA
630567 ATGTATCGATACA
1 ATGTATCGATACA
630580 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:633727 original size:19 final size:19
Alignment explanation
Indices: 633705--633821 Score: 92
Period size: 19 Copynumber: 5.7 Consensus size: 19
633695 CGGACCCCCT
*
633705 TTTTTGTTTGTTTTTTTTG
1 TTTTTGTTTTTTTTTTTTG
*
633724 TTTTTGTTTTTTTTTTTTT
1 TTTTTGTTTTTTTTTTTTG
*
633743 TTTTTTTTTTTTTTTTTTGG
1 TTTTTGTTTTTTTTTTTT-G
* *
633763 TTTCATTTTTGGTTTTTTTTTTC
1 TTT--TTGTT--TTTTTTTTTTG
*
633786 TTTTGGTTTTCAGTTTTTTTTCG
1 TTTTTGTTTT---TTTTTTTT-G
633809 TTTTT-TTTTTTTT
1 TTTTTGTTTTTTTT
633822 GGAGACGCCG
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
19 40 0.50
20 3 0.04
21 3 0.04
22 17 0.21
23 7 0.09
24 10 0.12
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (19 bp):
TTTTTGTTTTTTTTTTTTG
Found at i:633729 original size:6 final size:6
Alignment explanation
Indices: 633705--633795 Score: 66
Period size: 6 Copynumber: 15.7 Consensus size: 6
633695 CGGACCCCCT
*
633705 TTTTTG TTTGTTT TTTTTG TTTTTG TTTTT- TTTTT- TTTTT- TTTTT-
1 TTTTTG TTT-TTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
* * ** * *
633750 TTTTTT TTTTTG GTTTCA TTTTTGG TTTTT- TTTTTC TTTTGG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTT-G TTTTTG TTTTTG TTTTTG TTTT
633796 CAGTTTTTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
5 25 0.36
6 35 0.50
7 10 0.14
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:633780 original size:1 final size:1
Alignment explanation
Indices: 633704--633760 Score: 78
Period size: 1 Copynumber: 57.0 Consensus size: 1
633694 CCGGACCCCC
* * * *
633704 TTTTTTGTTTGTTTTTTTTGTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
633761 GGTTTCATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:633814 original size:12 final size:12
Alignment explanation
Indices: 633717--633818 Score: 72
Period size: 12 Copynumber: 8.8 Consensus size: 12
633707 TTTGTTTGTT
*
633717 TTTTTTGTTTTTG
1 TTTTTT-TTTTCG
633730 TTTTTTTTTT--
1 TTTTTTTTTTCG
*
633740 TTTTTTTTTT-T
1 TTTTTTTTTTCG
*
633751 TTTTTTTTTTGG
1 TTTTTTTTTTCG
** *
633763 TTTCATTTTTGG
1 TTTTTTTTTTCG
633775 TTTTTTTTTTC-
1 TTTTTTTTTTCG
**
633786 TTTTGGTTTTCAG
1 TTTTTTTTTTC-G
633799 --TTTTTTTTCG
1 TTTTTTTTTTCG
633809 TTTTTTTTTT
1 TTTTTTTTTT
633819 TTTGGAGACG
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 11 0.15
11 26 0.36
12 30 0.41
13 6 0.08
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTCG
Found at i:633822 original size:32 final size:31
Alignment explanation
Indices: 633704--633823 Score: 118
Period size: 32 Copynumber: 3.8 Consensus size: 31
633694 CCGGACCCCC
* **
633704 TTTTTTGTTTGTTTTTTTTGTTTTTGTTTTTTTT
1 TTTTTT-TTTGTTTTTTTT-TTTTTG-GTTTTCA
*
633738 TTTTTTTTTTTTTTTTTTTTTTTGG-TTTCA
1 TTTTTTTTTGTTTTTTTTTTTTTGGTTTTCA
** *
633768 TTTTTGGTT-TTTTTTTTCTTTTGGTTTTCA
1 TTTTTTTTTGTTTTTTTTTTTTTGGTTTTCA
*
633798 GTTTTTTTTCGTTTTTTTTTTTTTGG
1 -TTTTTTTTTGTTTTTTTTTTTTTGG
633824 AGACGCCGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
29 14 0.19
30 15 0.21
31 6 0.08
32 20 0.28
33 11 0.15
34 6 0.08
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.83
Consensus pattern (31 bp):
TTTTTTTTTGTTTTTTTTTTTTTGGTTTTCA
Found at i:643519 original size:10 final size:10
Alignment explanation
Indices: 643504--643530 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
643494 ATGTATCAAG
643504 CAAAAACAAA
1 CAAAAACAAA
643514 CAAAAACAAA
1 CAAAAACAAA
643524 CAAAAAC
1 CAAAAAC
643531 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:647745 original size:52 final size:52
Alignment explanation
Indices: 647667--647867 Score: 323
Period size: 52 Copynumber: 3.9 Consensus size: 52
647657 CGAAATATGA
*
647667 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
647719 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
647771 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
647823 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
647868 ATGTATCGAT
Statistics
Matches: 139, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
51 2 0.01
52 137 0.99
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:647874 original size:13 final size:13
Alignment explanation
Indices: 647856--647880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
647846 CAAAGATCAG
647856 TGTATCGATACAA
1 TGTATCGATACAA
647869 TGTATCGATACA
1 TGTATCGATACA
647881 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:647961 original size:13 final size:13
Alignment explanation
Indices: 647943--647967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
647933 CAAAAAAACA
647943 TGTATCGATACAT
1 TGTATCGATACAT
647956 TGTATCGATACA
1 TGTATCGATACA
647968 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:648066 original size:21 final size:21
Alignment explanation
Indices: 648025--648066 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
648015 GTTGGGACCT
*
648025 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
648046 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
648067 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:648404 original size:20 final size:19
Alignment explanation
Indices: 648349--648404 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
648339 AAAACCCTTA
*
648349 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
648369 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
648389 AATGTATCGATACATG
1 AAAGTATCGATACATG
648405 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:648492 original size:13 final size:13
Alignment explanation
Indices: 648474--648499 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
648464 TACACCAAGT
648474 ATGTATCGATACA
1 ATGTATCGATACA
648487 ATGTATCGATACA
1 ATGTATCGATACA
648500 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:652588 original size:15 final size:15
Alignment explanation
Indices: 652568--652598 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
652558 TAAAAATGTC
*
652568 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
652583 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
652598 C
1 C
652599 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:654700 original size:13 final size:13
Alignment explanation
Indices: 654682--654719 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
654672 CATTTTTCTT
654682 TGTATCGATACAA
1 TGTATCGATACAA
*
654695 TGTATCGATACAC
1 TGTATCGATACAA
654708 TGTATCGATACA
1 TGTATCGATACA
654720 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:654874 original size:20 final size:20
Alignment explanation
Indices: 654831--654876 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
654821 AAATCTTTTG
654831 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
654852 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
654872 CAAAA
1 CAAAA
654877 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:657007 original size:13 final size:13
Alignment explanation
Indices: 656989--657014 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
656979 TACACCAAGT
656989 ATGTATCGATACA
1 ATGTATCGATACA
657002 ATGTATCGATACA
1 ATGTATCGATACA
657015 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:657012 original size:32 final size:33
Alignment explanation
Indices: 656971--657034 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
656961 TAGCCAAACT
* **
656971 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
657003 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
657035 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:660624 original size:26 final size:26
Alignment explanation
Indices: 660573--660624 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
660563 ACTTTGTTTG
* *
660573 TATGATTTTGTGTTTTTGTGATTTTT
1 TATGATTGTGTGTTTTTGTGAATTTT
*
660599 TATGATTGTGT-TTATTTGTTAATTTT
1 TATGATTGTGTGTT-TTTGTGAATTTT
660625 GATTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.15, C:0.00, G:0.17, T:0.67
Consensus pattern (26 bp):
TATGATTGTGTGTTTTTGTGAATTTT
Found at i:662753 original size:22 final size:22
Alignment explanation
Indices: 662726--662796 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
662716 AAACAAAAAA
*
662726 GGGGAAAAAAATTTTTATTAAG
1 GGGGAAGAAAATTTTTATTAAG
662748 GGGGAAGAAAATTTTTATTAAG
1 GGGGAAGAAAATTTTTATTAAG
* *
662770 AGGG-AGAAAATTTTTAATTAAA
1 GGGGAAGAAAATTTTT-ATTAAG
662792 GGGGA
1 GGGGA
662797 GTTATAATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 11 0.26
22 32 0.74
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.30
Consensus pattern (22 bp):
GGGGAAGAAAATTTTTATTAAG
Found at i:664269 original size:78 final size:79
Alignment explanation
Indices: 664122--664321 Score: 257
Period size: 78 Copynumber: 2.5 Consensus size: 79
664112 GTCTCTCCGA
*
664122 CTAACCCCATTTTT-TTTTACAAAAAATCTTGAATTTACATTCTCAAGGGTACTCTAACTCTATC
1 CTAATCCCATTTTTCTTTT--AAAAAATCTTGAATTTACATTCTCAAGGGTACTCTAACTCTATC
*
664186 TCTCTAA-AAGATACT
64 CCTCTAAGAAGATACT
664201 CTAATCCCATTTTTCTTTTAAAAAATCTTGAATTTACATTCTCAAGGGTACTGC-AACT-TGATC
1 CTAATCCCATTTTTCTTTTAAAAAATCTTGAATTTACATTCTCAAGGGTACT-CTAACTCT-ATC
664264 CCTCTAAGAAGATACT
64 CCTCTAAGAAGATACT
* * ***
664280 -TTATCCCTGTTTTTCTTACGAAAAATCTTGAATTTACATTCT
1 CTAATCCC-ATTTTTCTTTTAAAAAATCTTGAATTTACATTCT
664322 AGAAAGTTCT
Statistics
Matches: 109, Mismatches: 7, Indels: 10
0.87 0.06 0.08
Matches are distributed among these distances:
77 1 0.01
78 52 0.48
79 52 0.48
80 4 0.04
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (79 bp):
CTAATCCCATTTTTCTTTTAAAAAATCTTGAATTTACATTCTCAAGGGTACTCTAACTCTATCCC
TCTAAGAAGATACT
Found at i:666506 original size:13 final size:13
Alignment explanation
Indices: 666488--666520 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
666478 TACATGGGAT
666488 ATTGTATTAATAC
1 ATTGTATTAATAC
666501 ATTGTATTAATAC
1 ATTGTATTAATAC
666514 ATTGTAT
1 ATTGTAT
666521 CGATACATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (13 bp):
ATTGTATTAATAC
Found at i:666526 original size:13 final size:13
Alignment explanation
Indices: 666488--666528 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
666478 TACATGGGAT
*
666488 ATTGTATTAATAC
1 ATTGTATCAATAC
*
666501 ATTGTATTAATAC
1 ATTGTATCAATAC
*
666514 ATTGTATCGATAC
1 ATTGTATCAATAC
666527 AT
1 AT
666529 AGTGAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (13 bp):
ATTGTATCAATAC
Found at i:670606 original size:2 final size:2
Alignment explanation
Indices: 670601--670643 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
670591 AATGCGTGTG
670601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
670643 T
1 T
670644 TTCATCTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:670750 original size:22 final size:24
Alignment explanation
Indices: 670691--670750 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 24
670681 GCCTCACATG
670691 ATAATATTAAATATAATTTTATAAAT
1 ATAATA-T-AATATAATTTTATAAAT
*
670717 ATAA-A-AAAATAATTTTA-AAA-
1 ATAATATAATATAATTTTATAAAT
670737 ATAATATAATATAA
1 ATAATATAATATAA
670751 ATAAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 4 0.13
21 4 0.13
22 17 0.57
25 1 0.03
26 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAATATAATATAATTTTATAAAT
Found at i:670780 original size:32 final size:30
Alignment explanation
Indices: 670713--670780 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
670703 ATAATTTTAT
*
670713 AAATATAAAAAAATAATTTTAAAAATAATA
1 AAATATAAAAAAAAAATTTTAAAAATAATA
* *
670743 TAATATAAATAAAAAAATTTTAAAAATTGATA
1 AAATATAAA-AAAAAAATTTTAAAAA-TAATA
670775 AAATAT
1 AAATAT
670781 GATTATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 8 0.25
31 15 0.47
32 9 0.28
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (30 bp):
AAATATAAAAAAAAAATTTTAAAAATAATA
Found at i:670835 original size:28 final size:28
Alignment explanation
Indices: 670803--670857 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
670793 TTTAAATTTA
*
670803 TATAA-ATATTAAATATTTTAAATATAAT
1 TATAATATATTAAATA-TATAAATATAAT
*
670831 TATAATATTTTAAATATATAAATATAA
1 TATAATATATTAAATATATAAATATAA
670858 ACAAACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TATAATATATTAAATATATAAATATAAT
Found at i:670850 original size:22 final size:20
Alignment explanation
Indices: 670810--670848 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
670800 TTATATAAAT
670810 ATTA-AATATTTTAAATATA
1 ATTATAATATTTTAAATATA
670829 ATTATAATATTTTAAATATA
1 ATTATAATATTTTAAATATA
670849 TAAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTATAATATTTTAAATATA
Found at i:670856 original size:22 final size:21
Alignment explanation
Indices: 670801--670857 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
670791 CATTTAAATT
670801 TATATAAATATTAAATATTTTAA
1 TATATAAATA-T-AATATTTTAA
*
670824 -ATATAATTATAATATTTTAAA
1 TATATAAATATAATATTTT-AA
670845 TATATAAATATAA
1 TATATAAATATAA
670858 ACAAACAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 8 0.27
21 3 0.10
22 19 0.63
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATAAATATAATATTTTAA
Found at i:672287 original size:2 final size:2
Alignment explanation
Indices: 672251--672278 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
672241 TTAAATAAAC
672251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
672279 CAGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:673021 original size:8 final size:8
Alignment explanation
Indices: 673010--673034 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
673000 AAACCAAAAC
673010 AGAAAAGA
1 AGAAAAGA
673018 AGAAAAGA
1 AGAAAAGA
673026 AGAAAAGA
1 AGAAAAGA
673034 A
1 A
673035 AAACCCAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:683748 original size:26 final size:28
Alignment explanation
Indices: 683719--683774 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
683709 TATTTATAAA
683719 AATAAATAAAATA-TGAAAATAAA-ATT
1 AATAAATAAAATATTGAAAATAAATATT
* * *
683745 AATACATGAAATATTTAAAATAAATATT
1 AATAAATAAAATATTGAAAATAAATATT
683773 AA
1 AA
683775 ATACTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 9 0.36
28 5 0.20
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (28 bp):
AATAAATAAAATATTGAAAATAAATATT
Found at i:686273 original size:30 final size:28
Alignment explanation
Indices: 686216--686336 Score: 111
Period size: 30 Copynumber: 4.2 Consensus size: 28
686206 CTAGATAAGC
*
686216 ATTTATAATTTT-A-TTATATTTAAATAA
1 ATTT-TAATTTTAATTTATATTCAAATAA
*
686243 ATTTCTAATATTTAATTTGTATTCAAATAA
1 ATTT-TAAT-TTTAATTTATATTCAAATAA
* * * *
686273 ATCTTTAATTTTTATCTTTTATTCAGATAC
1 AT-TTTAATTTTAAT-TTATATTCAAATAA
*
686303 ATTTTAATTTTTAATTTATATTTAAATAA
1 ATTTTAA-TTTTAATTTATATTCAAATAA
686332 ATTTT
1 ATTTT
686337 TAACATAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
27 8 0.11
28 3 0.04
29 26 0.34
30 37 0.49
31 2 0.03
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (28 bp):
ATTTTAATTTTAATTTATATTCAAATAA
Found at i:686421 original size:30 final size:30
Alignment explanation
Indices: 686361--686421 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
686351 TTTTATTTTA
** *
686361 AATAAAATGTTATTTAAGTACAAATCAAAT
1 AATAAAAACTTATTTAAGCACAAATCAAAT
*
686391 AATAAAAACTTATTTGAGCACAATAT-AAAT
1 AATAAAAACTTATTTAAGCACAA-ATCAAAT
686421 A
1 A
686422 TACGCACTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.31
Consensus pattern (30 bp):
AATAAAAACTTATTTAAGCACAAATCAAAT
Found at i:686710 original size:31 final size:31
Alignment explanation
Indices: 686666--686741 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
686656 ATCTTCTAGA
686666 TATATAT-ATATAAATAAATATTTATAAGGT
1 TATATATGATATAAATAAATATTTATAAGGT
686696 TATATATGATATAAATAAATATTTATAAGGT
1 TATATATGATATAAATAAATATTTATAAGGT
686727 TATATATGATATAAA
1 TATATATGATATAAA
686742 AAAAATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 7 0.16
31 38 0.84
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (31 bp):
TATATATGATATAAATAAATATTTATAAGGT
Found at i:688027 original size:36 final size:36
Alignment explanation
Indices: 687971--688047 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
687961 TAGAATCTGG
*
687971 AGAGGTGGTATTTAGCAAATATGCATCCTATCCTTA
1 AGAGGTGGCATTTAGCAAATATGCATCCTATCCTTA
* * **
688007 AGAGTTGGCATTTAGGAAATATGCATCCTATTTTTA
1 AGAGGTGGCATTTAGCAAATATGCATCCTATCCTTA
688043 AGAGG
1 AGAGG
688048 GGGCCATGTA
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:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (36 bp):
AGAGGTGGCATTTAGCAAATATGCATCCTATCCTTA
Found at i:690133 original size:3 final size:3
Alignment explanation
Indices: 690125--690153 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
690115 TGACGAGTAC
690125 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
690154 AGAAGAGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:690531 original size:27 final size:29
Alignment explanation
Indices: 690491--690551 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
690481 GATAACATTT
690491 TATATTTTGAAATA-TTATATATATAT-A
1 TATATTTTGAAATATTTATATATATATAA
* *
690518 TATATTTT-ATAATATTTGTATATCTATAA
1 TATATTTTGA-AATATTTATATATATATAA
690547 TATAT
1 TATAT
690552 ATATTAAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 12 0.41
28 10 0.34
29 6 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (29 bp):
TATATTTTGAAATATTTATATATATATAA
Found at i:691358 original size:17 final size:17
Alignment explanation
Indices: 691332--691373 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
691322 TATATATTAG
*
691332 TATATATTAAAATCATA
1 TATATTTTAAAATCATA
* *
691349 TATATTTTAATATTATA
1 TATATTTTAAAATCATA
691366 TATATTTT
1 TATATTTT
691374 TTATTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTTTAAAATCATA
Found at i:691370 original size:19 final size:19
Alignment explanation
Indices: 691346--691388 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
691336 TATTAAAATC
691346 ATATATATTTTAATATTAT
1 ATATATATTTTAATATTAT
* *
691365 ATATAT-TTTTTATTTTAT
1 ATATATATTTTAATATTAT
691383 AT-TATA
1 ATATATA
691389 CATAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATATATTTTAATATTAT
Found at i:691668 original size:2 final size:2
Alignment explanation
Indices: 691663--691705 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
691653 ATGTGTGTAT
691663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
691705 T
1 T
691706 GAGAAGTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:692088 original size:21 final size:21
Alignment explanation
Indices: 692053--692108 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
692043 AACCCTTAAT
* * **
692053 TGTATCCATACAATCTTGTCA
1 TGTATCAATATAATCTTAACA
**
692074 TGTATTGATATAATCTTAACA
1 TGTATCAATATAATCTTAACA
692095 TGTATCAATATAAT
1 TGTATCAATATAAT
692109 GGGTTGTAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (21 bp):
TGTATCAATATAATCTTAACA
Found at i:692935 original size:19 final size:19
Alignment explanation
Indices: 692907--692962 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
692897 TTGTATCGAT
* *
692907 ACATTTTATCGATACATGT
1 ACATTGTATCGATACATGA
*
692926 TCATTGTATCGATACATGA
1 ACATTGTATCGATACATGA
*
692945 ACAAATGTATCGATACAT
1 AC-ATTGTATCGATACAT
692963 AAAATTGGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:692938 original size:32 final size:33
Alignment explanation
Indices: 692880--692942 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
692870 CTTTCAGGTG
*
692880 TATCGATACATTATGCTTTGTATCGATACATTT
1 TATCGATACATTATGCATTGTATCGATACATTT
692913 TATCGATACATGT-T-CATTGTATCGATACAT
1 TATCGATACAT-TATGCATTGTATCGATACAT
692943 GAACAAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (33 bp):
TATCGATACATTATGCATTGTATCGATACATTT
Found at i:694670 original size:3 final size:3
Alignment explanation
Indices: 694657--694687 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
694647 AGACGACGAA
*
694657 GAT GAT AAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
694688 TTGACTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:696611 original size:21 final size:21
Alignment explanation
Indices: 696585--696636 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
696575 AGCCCATGAA
696585 TCATGCATTTTGAGCTATGCT
1 TCATGCATTTTGAGCTATGCT
696606 TCATGCATTTTGAGCTATGCT
1 TCATGCATTTTGAGCTATGCT
696627 TCATGCATTT
1 TCATGCATTT
696637 ATAGCATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (21 bp):
TCATGCATTTTGAGCTATGCT
Found at i:705227 original size:20 final size:20
Alignment explanation
Indices: 705204--705256 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
705194 CACTTTCAGA
*
705204 TGTATAGATACATTATGCTT
1 TGTATCGATACATTATGCTT
705224 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
705244 TGTATCGATACAT
1 TGTATCGATACAT
705257 GTTCATTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:705292 original size:20 final size:19
Alignment explanation
Indices: 705244--705295 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
705234 CATTATGCTT
** *
705244 TGTATCGATACATGTTCAT
1 TGTATCGATACATGAACAA
*
705263 TGTATTGATACATGAACAAA
1 TGTATCGATACATGAAC-AA
705283 TGTATCGATACAT
1 TGTATCGATACAT
705296 AAAATTGGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGAACAA
Found at i:705364 original size:13 final size:13
Alignment explanation
Indices: 705346--705370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
705336 CATTGCACAT
705346 TGTATCGATACAA
1 TGTATCGATACAA
705359 TGTATCGATACA
1 TGTATCGATACA
705371 TGAAGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:705368 original size:33 final size:33
Alignment explanation
Indices: 705326--705390 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
705316 TACCACTATT
* *
705326 TGTATCGATACATTGCA-CATTGTATCGATACAA
1 TGTATCGATACA-TGAAGAATTGTATCGATACAA
705359 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCGATACATGAAGAATTGTATCGATACA
705391 TTGTCCCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGAAGAATTGTATCGATACAA
Found at i:714947 original size:22 final size:22
Alignment explanation
Indices: 714922--714972 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
714912 TTTACTTGTA
* *
714922 AAATTTTTGGGGAAATTTTCTC
1 AAATTTCTAGGGAAATTTTCTC
714944 AAATTTCTAGGGAAATTTTCTC
1 AAATTTCTAGGGAAATTTTCTC
714966 AAATTTC
1 AAATTTC
714973 AAGCATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (22 bp):
AAATTTCTAGGGAAATTTTCTC
Found at i:715462 original size:134 final size:136
Alignment explanation
Indices: 715200--715481 Score: 335
Period size: 134 Copynumber: 2.1 Consensus size: 136
715190 TCAAAAATTC
*
715200 ATTCATTTTAATGAGTTTTTGATTTTTTTCCTTGAAATTTTCTTGTTTTCAAAATGTAGAGTTTT
1 ATTCATTTTAATGAGTTTTTGATATTTTTCCTTGAAA-TTTCTTGTTTTCAAAATGTAGAGTTTT
* * *
715265 TAACTCCATAAATATTTTTGGGAGATTTTTCTTAGTTTTTAATTTTTAAAATTGATCAAATATCA
65 TAACTCCATAAATATTTTCGGGAGATTTTTCTTAGTTTTTAAATTTTAAAATTCATCAAATATCA
715330 ATATTTA
130 ATATTTA
* * *
715337 ATTCATTTTCATGCGTTTTTGATATTTTTCCTTG-AA-TTGTT-TTTTCAAAA--TACGAAG-TT
1 ATTCATTTTAATGAGTTTTTGATATTTTTCCTTGAAATTTCTTGTTTTCAAAATGTA-G-AGTTT
* * * * *
715396 TTATGCTCCGTAAATGTTTTCGGGAAGATTTTT-TTAGGTTTTTAAATTTTAGAATTCTTCAAAT
64 TTA-ACTCCATAAATATTTTCGGG-AGATTTTTCTTA-GTTTTTAAATTTTAAAATTCATCAAAT
*
715460 ATCACTATTTA
126 ATCAATATTTA
*
715471 ATTCATATTAA
1 ATTCATTTTAA
715482 ATCATTTTTG
Statistics
Matches: 125, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
131 2 0.02
132 6 0.05
133 30 0.24
134 54 0.43
136 2 0.02
137 31 0.25
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.51
Consensus pattern (136 bp):
ATTCATTTTAATGAGTTTTTGATATTTTTCCTTGAAATTTCTTGTTTTCAAAATGTAGAGTTTTT
AACTCCATAAATATTTTCGGGAGATTTTTCTTAGTTTTTAAATTTTAAAATTCATCAAATATCAA
TATTTA
Found at i:716011 original size:20 final size:20
Alignment explanation
Indices: 715986--716023 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
715976 TACCTCTGTC
715986 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
*
716006 TGTATCGATACATTGTAC
1 TGTATCGATACATGGTAC
716024 CAATACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGGTACAA
Found at i:718292 original size:21 final size:20
Alignment explanation
Indices: 718258--718300 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
718248 TATTAAAAAG
*
718258 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
718279 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
718299 TT
1 TT
718301 TGCTTGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:718299 original size:20 final size:21
Alignment explanation
Indices: 718258--718300 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
718248 TATTAAAAAG
*
718258 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
718279 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
718299 TT
1 TT
718301 TGCTTGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:722416 original size:13 final size:13
Alignment explanation
Indices: 722398--722422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
722388 AGATTGCACA
722398 GTATCGATACATT
1 GTATCGATACATT
722411 GTATCGATACAT
1 GTATCGATACAT
722423 GACTAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:722435 original size:20 final size:20
Alignment explanation
Indices: 722410--722461 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
722400 ATCGATACAT
**
722410 TGTATCGATACATGACTAAA
1 TGTATCGATACATGAAAAAA
*
722430 TGTATCGATACTTGAAAAAA
1 TGTATCGATACATGAAAAAA
722450 TGTATCGATACA
1 TGTATCGATACA
722462 GGTAATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:722455 original size:53 final size:52
Alignment explanation
Indices: 722398--722547 Score: 137
Period size: 53 Copynumber: 2.8 Consensus size: 52
722388 AGATTGCACA
* **
722398 GTATCGATACATTGTATCGATACATGACTAAATGTATCGATACTTGAAAAAAT
1 GTATCGATACATTGTATTGATACATGACTAAATGTATCGATAC-ACAAAAAAT
* * * *
722451 GTATCGATACA-GGTAATTG--GCA-GTAGCTAAATTTGTATCGATACACATAATAT
1 GTATCGATACATTGT-ATTGATACATG-A-CTAAA--TGTATCGATACACAAAAAAT
* *
722504 GTATCGATACATTGTATTGATACATCACAAAATGTATCGATACA
1 GTATCGATACATTGTATTGATACATGACTAAATGTATCGATACA
722548 TTGGCTTGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
50 1 0.01
51 3 0.04
52 19 0.25
53 34 0.44
54 17 0.22
55 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (52 bp):
GTATCGATACATTGTATTGATACATGACTAAATGTATCGATACACAAAAAAT
Found at i:722544 original size:33 final size:32
Alignment explanation
Indices: 722483--722550 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
722473 GTAGCTAAAT
* *
722483 TTGTATCGATACACATAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
722515 TTGTATTGATACATCACAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
722548 TTG
1 TTG
722551 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Done.