Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold56
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: 1793205
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 19648 characters in sequence are not A, C, G, or T
File 3 of 11
Found at i:341901 original size:61 final size:61
Alignment explanation
Indices: 341798--342551 Score: 685
Period size: 61 Copynumber: 12.5 Consensus size: 61
341788 AAAATGAGAG
* * *
341798 AGGCGTTCTGCTCTTTGAGGACTAGAAGG-GTCCACCAGCTTGTGTGGGCTTTAAAAAGAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTG-CCACCAGCTTGTGTGGGCTTTAAAAGGAAA
* * * ** * *
341859 ATGCATCATGCTCTTTGAGGACTAAAAGGTGCCATTAGCTTGTGTGGCCTTTTAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAA
* ** * * *
341920 A--TGTTTTACTCTTTGAGGA-TAGAAGGTGCCACC-GACTTGTGTGAGCTTTAAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAG-CTTGTGTGGGCTTTAAAAGGAAA
* * * * * *
341978 AGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACTAGTTTGTTTAAGCCTTT-AAAGG-AA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGT-GGGCTTTAAAAGGAAA
* * * * *
342038 A-GTGTCCTGCTCTTTAAGGACTAAAAGGTGCCACC-GACTTGTATGGGCTTTAAAAAGAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAG-CTTGTGTGGGCTTTAAAAGGAAA
* * * * *
342098 AGGTGTCCTGCTCTTTGAGGATTGAAAGGTGCCACTAGCTTGTGTGGGCTTTTAAAGG-AA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAA
* * * * * * * * * * *
342158 A-GTGTCTTACTCTTTAAAGACTAGAAGGTACCATC-GACTTGTGTAGGATTTAAAAGGAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAG-CTTGTGTGGGCTTTAAAAGGAAA
* * * *
342218 AGGCGTCCTGCTCTTTGAGGACTTAAAGGTGCCACCAACTTGTATGGGCTTTGAAA-GAAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAA-A
* * *
342279 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCTACCAACTAGTGTGGGCTTTGAAAA-GAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTT-AAAAGGAAA
* * ** ** *
342340 AGGCGTCTTGCTCTTAGAGGACTAAAAGGTGCCACCAAATTGTGTAAGCTTTAAAAGGGAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAA
* * * * * * *
342401 AGACGTCCTGCTCTTTAAGGACTAAAAGCTGCCACCAACTTGTATGGGCTTTGAAAGGAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAA
* * * *
342462 AGGCGTCCTACTCTTTGAGGACTGAAAA-ATGCCACCAACTTGTGTGAGCTTTGAAAA-GAAA
1 AGGCGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAGCTTGTGTGGGCTTT-AAAAGGAAA
* *
342523 AGGCATCTTGCTCTTTGAGGACTAAAAGG
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGG
342552 ATAAAAGGTT
Statistics
Matches: 554, Mismatches: 117, Indels: 44
0.77 0.16 0.06
Matches are distributed among these distances:
57 1 0.00
58 39 0.07
59 93 0.17
60 32 0.06
61 369 0.67
62 20 0.04
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (61 bp):
AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAA
Found at i:343549 original size:11 final size:11
Alignment explanation
Indices: 343535--343575 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
343525 TTTTTCTTTC
343535 TTTTTTTGGTT
1 TTTTTTTGGTT
**
343546 TTTTTTTTATT
1 TTTTTTTGGTT
343557 TTTTTGTTGGTT
1 TTTTT-TTGGTT
343569 TTTTTTT
1 TTTTTTT
343576 AAGAAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.85
Consensus pattern (11 bp):
TTTTTTTGGTT
Found at i:343549 original size:20 final size:20
Alignment explanation
Indices: 343524--343562 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
343514 GGTTCTTTTC
*
343524 TTTTTTCTTTCTTTTTTTGG
1 TTTTTTCTTTATTTTTTTGG
*
343544 TTTTTTTTTTATTTTTTTG
1 TTTTTTCTTTATTTTTTTG
343563 TTGGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.85
Consensus pattern (20 bp):
TTTTTTCTTTATTTTTTTGG
Found at i:343561 original size:23 final size:24
Alignment explanation
Indices: 343519--343575 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
343509 AAGCAGGTTC
* *
343519 TTTTCTTTTTTCTTTCTTTTTTTGG
1 TTTT-TTTTTTATTTCTTTTGTTGG
343544 TTTTTTTTTTATTT-TTTTGTTGG
1 TTTTTTTTTTATTTCTTTTGTTGG
343567 TTTTTTTTT
1 TTTTTTTTT
343576 AAGAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 17 0.57
24 9 0.30
25 4 0.13
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (24 bp):
TTTTTTTTTTATTTCTTTTGTTGG
Found at i:352253 original size:28 final size:27
Alignment explanation
Indices: 352192--352273 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 27
352182 TTTTGGAGAT
*
352192 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAAC-GGGTTGGAGT-ATCCC-CGATGA
*
352220 AGTAACAGGGTTGGAGTATCCCCGATGA
1 AATAAC-GGGTTGGAGTATCCCCGATGA
352248 AATAACGAGGTTGGAGTATCCCCGAT
1 AATAACG-GGTTGGAGTATCCCCGAT
352274 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.04
27 5 0.11
28 40 0.85
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (27 bp):
AATAACGGGTTGGAGTATCCCCGATGA
Found at i:352317 original size:52 final size:51
Alignment explanation
Indices: 352256--352592 Score: 245
Period size: 51 Copynumber: 6.4 Consensus size: 51
352246 GAAATAACGA
352256 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTA-TTTTGGAAATAAAATCGG
* ** * * * *
352308 TGTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTAGTATTTTGGAAATAAAATCGG
* * * *
352360 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTGGAAATAAAATCGG
* **** * *
352411 GGTTGGAGTATCCCC--TTG-AAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTGTGAAA-AA-----TT--AGTATTTTGGA-AATAAAATCGG
* * * *
352466 GGTTGGAGTGTCCCCAATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATT--AGTATTTTGGAAATAAAATCGG
* * * *
352520 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGA-AAAATTAGTATTTTGGAAATAAAATCGG
* *
352571 AGTTGGAATATCCCCGATTGTG
1 GGTTGGAGTATCCCCGATTGTG
352593 GAGAATTGAG
Statistics
Matches: 221, Mismatches: 46, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
48 3 0.01
49 4 0.02
51 77 0.35
52 54 0.24
53 27 0.12
54 22 0.10
55 17 0.08
56 7 0.03
57 5 0.02
58 4 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTGGAAATAAAATCGG
Found at i:352471 original size:27 final size:27
Alignment explanation
Indices: 352408--352480 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
352398 GAAATAAAGT
352408 CGGGGTTGGAGTATCCCCTTGAAAATAA
1 CGGGGTTGGAGTATCCCC-TGAAAATAA
* *
352436 CGGGGTTGGAGTATCCCC-GATGATTAA
1 CGGGGTTGGAGTATCCCCTGA-AAATAA
*
352463 CGGGGTTGGAGTGTCCCC
1 CGGGGTTGGAGTATCCCC
352481 AATTGTGAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 2 0.05
27 21 0.51
28 18 0.44
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCTGAAAATAA
Found at i:352556 original size:211 final size:211
Alignment explanation
Indices: 352197--352589 Score: 592
Period size: 211 Copynumber: 1.9 Consensus size: 211
352187 GAGATAATAA
* * * *
352197 CGGGGTTGGAGTGTTCCCTCGGAAGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
1 CGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
* *
352262 AGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATT
66 AGTATCCCCAATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
* * *
352327 AAAGAAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT
131 AAAGAAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
352392 ATTTTGGAAATAAAGT
196 ATTTTGGAAATAAAGT
* * * *
352408 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGG
1 CGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
* * *
352472 AGTGTCCCCAATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA
66 AGTATCCCCAATTGTGAA-AAATTAGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA
* *
352537 TTATAG-AAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
129 TTAAAGAAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATT
352590 GTGGAGAATT
Statistics
Matches: 162, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
210 28 0.17
211 94 0.58
212 40 0.25
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (211 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
AGTATCCCCAATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
AAAGAAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
ATTTTGGAAATAAAGT
Found at i:354966 original size:33 final size:33
Alignment explanation
Indices: 354928--354994 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
354918 AAAATTTCCA
***
354928 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
354961 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
354994 A
1 A
354995 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:354967 original size:13 final size:13
Alignment explanation
Indices: 354949--354974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
354939 ACAAAGATCC
354949 ATGTATCGATACA
1 ATGTATCGATACA
354962 ATGTATCGATACA
1 ATGTATCGATACA
354975 CAGAAAAATG
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:355038 original size:19 final size:18
Alignment explanation
Indices: 355014--355078 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
355004 CAGTAGCTAA
355014 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
355033 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
355048 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
355065 TTATGTATCGATAC
1 TTATGTATCGATAC
355079 TTTCATTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:355054 original size:13 final size:13
Alignment explanation
Indices: 355036--355060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
355026 ACAATACTTA
355036 TGTATCGATACAT
1 TGTATCGATACAT
355049 TGTATCGATACA
1 TGTATCGATACA
355061 AAACTTATGT
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:355058 original size:32 final size:32
Alignment explanation
Indices: 355017--355078 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
355007 TAGCTAATTA
*
355017 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
355049 TGTATCGATACAAAACTTATGTATCGATAC
1 TGTATCGATACAAAACTTATGTATCGATAC
355079 TTTCATTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:355823 original size:55 final size:54
Alignment explanation
Indices: 355730--356396 Score: 802
Period size: 55 Copynumber: 12.0 Consensus size: 54
355720 ATAAAGTGTA
* * * *
355730 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
**
355785 TCCTATTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
355840 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
355895 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
355950 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
356005 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
356060 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
356115 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
356170 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * **
356229 TCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG---GTG
** * * **
356286 GGCTCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGGCA
1 TCCT-GCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT---GAAAGGTG
* * * ** *
356344 TCCCGTTCTTTGAGGACTGGAAAATGCCACCAACTCATGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
356397 AAAAGGCATC
Statistics
Matches: 542, Mismatches: 43, Indels: 54
0.85 0.07 0.08
Matches are distributed among these distances:
53 3 0.01
54 44 0.08
55 340 0.63
56 18 0.03
57 15 0.03
58 67 0.12
59 47 0.09
60 3 0.01
61 5 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:355915 original size:26 final size:26
Alignment explanation
Indices: 355886--356030 Score: 75
Period size: 26 Copynumber: 5.3 Consensus size: 26
355876 GTGTGGGCTT
355886 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
355912 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
* *
355939 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
* ** *
355967 TGGAAA-ATG-CCACCAACTTGTGTGGG-C
1 T-GAAAGGTGTCCTGC-TCTT-TG-GGGAC
355994 TTTGAAAGGTGTCCTGCTCTTTGGGGAC
1 --TGAAAGGTGTCCTGCTCTTTGGGGAC
356022 TGAAAGGTG
1 TGAAAGGTG
356031 CCACCAACTT
Statistics
Matches: 85, Mismatches: 18, Indels: 32
0.63 0.13 0.24
Matches are distributed among these distances:
25 6 0.07
26 26 0.31
27 13 0.15
28 20 0.24
29 14 0.16
30 6 0.07
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:371583 original size:33 final size:33
Alignment explanation
Indices: 371545--371611 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
371535 AAAATTTCCA
***
371545 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
371578 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
371611 A
1 A
371612 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:371584 original size:13 final size:13
Alignment explanation
Indices: 371566--371591 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
371556 ACAAAGATCC
371566 ATGTATCGATACA
1 ATGTATCGATACA
371579 ATGTATCGATACA
1 ATGTATCGATACA
371592 CAGAAAAATG
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:371655 original size:19 final size:18
Alignment explanation
Indices: 371631--371695 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
371621 CAGTAGCTAA
371631 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
371650 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
371665 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
371682 TTATGTATCGATAC
1 TTATGTATCGATAC
371696 TTTCATTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:371671 original size:13 final size:13
Alignment explanation
Indices: 371653--371677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
371643 ACAATACTTA
371653 TGTATCGATACAT
1 TGTATCGATACAT
371666 TGTATCGATACA
1 TGTATCGATACA
371678 AAACTTATGT
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:371675 original size:32 final size:32
Alignment explanation
Indices: 371634--371695 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
371624 TAGCTAATTA
*
371634 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
371666 TGTATCGATACAAAACTTATGTATCGATAC
1 TGTATCGATACAAAACTTATGTATCGATAC
371696 TTTCATTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:372089 original size:33 final size:33
Alignment explanation
Indices: 372052--372133 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
372042 TAGCCCTTAA
*
372052 AGAGAAAGAAGAGATAGGAGGGATGATAGAAGG
1 AGAGATAGAAGAGATAGGAGGGATGATAGAAGG
* *
372085 AGAGATAGTAGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAGGAGGGATGATAGAAGG
*
372118 AGAGATAGGAGAGATA
1 AGAGATAGAAGAGATA
372134 ATAGAGAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.12
Consensus pattern (33 bp):
AGAGATAGAAGAGATAGGAGGGATGATAGAAGG
Found at i:372091 original size:12 final size:12
Alignment explanation
Indices: 372061--372128 Score: 65
Period size: 12 Copynumber: 5.9 Consensus size: 12
372051 AAGAGAAAGA
372061 AGAGATAGGAGG
1 AGAGATAGGAGG
*
372073 -GATGATAGAAGG
1 AGA-GATAGGAGG
*
372085 AGAGAT---AGT
1 AGAGATAGGAGG
372094 AGAGATAGGAGG
1 AGAGATAGGAGG
372106 -GATGATAGGAGG
1 AGA-GATAGGAGG
372118 AGAGATAGGAG
1 AGAGATAGGAG
372129 AGATAATAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
9 8 0.17
11 4 0.09
12 30 0.65
13 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.46, T:0.13
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:372129 original size:42 final size:42
Alignment explanation
Indices: 372082--372162 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
372072 GGATGATAGA
* * * *
372082 AGGAGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGAT
1 AGGAGAGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAT
372124 AGGAGAGATAATAGAGAGAGGAAGGATGACAGGAGGAGA
1 AGGAGAGATAATAGAGAGAGGAAGGATGACAGGAGGAGA
372163 AGAGAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.43, C:0.01, G:0.44, T:0.11
Consensus pattern (42 bp):
AGGAGAGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAT
Found at i:372137 original size:12 final size:12
Alignment explanation
Indices: 372064--372142 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
372054 AGAAAGAAGA
*
372064 GATAGGAGGGAT
1 GATAGGAGAGAT
*
372076 GATAGAAGGAGA-
1 GATAGGA-GAGAT
*
372088 GATA-G-TAGA-
1 GATAGGAGAGAT
*
372097 GATAGGAGGGAT
1 GATAGGAGAGAT
372109 GATAGGAGGAGA-
1 GATAGGA-GAGAT
372121 GATAGGAGAGAT
1 GATAGGAGAGAT
*
372133 AATA-GAGAGA
1 GATAGGAGAGA
372143 GGAAGGATGA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
9 7 0.13
10 1 0.02
11 12 0.23
12 27 0.51
13 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:372175 original size:42 final size:42
Alignment explanation
Indices: 372087--372175 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
372077 ATAGAAGGAG
* * * * * * *
372087 AGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGGAG
1 AGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAGAGAAA
372129 AGATAATAGAGAGAGGAAGGATGACAGGAGGAGA-AGAGAAAA
1 AGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAGAG-AAA
372171 AGATA
1 AGATA
372176 GAAGAGTGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 3 0.08
42 36 0.92
ACGTcount: A:0.47, C:0.01, G:0.40, T:0.11
Consensus pattern (42 bp):
AGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAGAGAAA
Found at i:375787 original size:10 final size:10
Alignment explanation
Indices: 375774--375844 Score: 72
Period size: 10 Copynumber: 7.0 Consensus size: 10
375764 TTTCACTGTC
375774 CATCACTATT
1 CATCACTATT
375784 CATCACTATT
1 CATCACTATT
375794 CATCACTATT
1 CATCACTATT
* * *
375804 CATGTATCGATA
1 CAT-CA-CTATT
*
375816 CATCACTGTT
1 CATCACTATT
*
375826 CATCACTGTT
1 CATCACTATT
375836 CA-CACTATT
1 CATCACTATT
375845 TAATAAAAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
9 6 0.12
10 37 0.73
11 2 0.04
12 6 0.12
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.38
Consensus pattern (10 bp):
CATCACTATT
Found at i:380411 original size:21 final size:19
Alignment explanation
Indices: 380377--380416 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
380367 CTAACAAAAA
*
380377 AATGGGTATTTTTAGGAAG
1 AATGGGTATTTTTAAGAAG
380396 AATGGGTAGTTTTTTAAGAAG
1 AATGGGTA--TTTTTAAGAAG
380417 TAAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.38
Consensus pattern (19 bp):
AATGGGTATTTTTAAGAAG
Found at i:381771 original size:2 final size:2
Alignment explanation
Indices: 381766--381806 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
381756 ATATATATAT
381766 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
381807 CAATAGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:382074 original size:23 final size:23
Alignment explanation
Indices: 382048--382094 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
382038 ATGTATAGAC
*
382048 AATTTAGGCTTATTTATAAAATT
1 AATTTAGACTTATTTATAAAATT
*
382071 AATTTAGACTTATTTATGAAATT
1 AATTTAGACTTATTTATAAAATT
382094 A
1 A
382095 TTATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (23 bp):
AATTTAGACTTATTTATAAAATT
Found at i:382414 original size:24 final size:23
Alignment explanation
Indices: 382387--382454 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 23
382377 ATTTTTTAAA
*
382387 AAATAAAATATAAAAAAATAATAT
1 AAAT-AAATATAAAAAATTAATAT
* *
382411 AAAT-ATTATATAAAATTAATAT
1 AAATAAATATAAAAAATTAATAT
382433 AAATTTAAA-ATAAAAAATTAAT
1 AAA--TAAATATAAAAAATTAAT
382455 TTTTTTACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 18 0.50
24 17 0.47
25 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATAAATATAAAAAATTAATAT
Found at i:382423 original size:11 final size:12
Alignment explanation
Indices: 382405--382446 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
382395 TATAAAAAAA
382405 TAATATAAATAT
1 TAATATAAATAT
382417 T-ATATAAA-AT
1 TAATATAAATAT
382427 TAATATAAAT-T
1 TAATATAAATAT
*
382438 TAAAATAAA
1 TAATATAAA
382447 AAATTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 3 0.11
11 23 0.85
12 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATATAAATAT
Found at i:382576 original size:23 final size:22
Alignment explanation
Indices: 382543--382598 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
382533 TATGTTTGAC
382543 ATAAGAAAAATAACATGAACATA
1 ATAA-AAAAATAACATGAACATA
* *
382566 ATACAAAAAATAACTTGAACATG
1 ATA-AAAAAATAACATGAACATA
382589 ATAAAAAAAT
1 ATAAAAAAAT
382599 TATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 7 0.23
23 22 0.73
24 1 0.03
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (22 bp):
ATAAAAAAATAACATGAACATA
Found at i:382644 original size:23 final size:25
Alignment explanation
Indices: 382612--382660 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
382602 ATAAAAAAAA
382612 TTCATATCATAT-TT-ATATTATTT
1 TTCATATCATATATTCATATTATTT
*
382635 TTCATTTCATATATTCATATTATTT
1 TTCATATCATATATTCATATTATTT
382660 T
1 T
382661 AATAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.48
24 2 0.09
25 10 0.43
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (25 bp):
TTCATATCATATATTCATATTATTT
Found at i:383053 original size:28 final size:29
Alignment explanation
Indices: 382995--383060 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
382985 TATCTTCGAC
* *
382995 TAAAACAATAATATTTTGATAAATTATTT
1 TAAAATAATAATATTTTAATAAATTATTT
383024 TAAAATAATAATA-TTTAAT-AATTAGTTT
1 TAAAATAATAATATTTTAATAAATTA-TTT
383052 TATAAATAA
1 TA-AAATAA
383061 GTGTAGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 5 0.15
28 10 0.30
29 18 0.55
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (29 bp):
TAAAATAATAATATTTTAATAAATTATTT
Found at i:385497 original size:12 final size:14
Alignment explanation
Indices: 385467--385504 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
385457 CGTGAGTAAA
*
385467 AATAAAAATATTTT
1 AATAAAATTATTTT
385481 AAT-AAATTATTTT
1 AATAAAATTATTTT
385494 -ATAAAATTATT
1 AATAAAATTATT
385505 ATTGAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 2 0.09
13 17 0.77
14 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAAAATTATTTT
Found at i:386045 original size:15 final size:15
Alignment explanation
Indices: 386015--386057 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
386005 AGACTTAAAT
386015 AAATTAATAAAAATTA
1 AAATTAA-AAAAATTA
*
386031 AAATTAAAAATATTA
1 AAATTAAAAAAATTA
* *
386046 TATTTAAAAAAA
1 AAATTAAAAAAA
386058 AATTACCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTAAAAAAATTA
Found at i:389458 original size:21 final size:21
Alignment explanation
Indices: 389429--389471 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
389419 GCTATTGCCA
*
389429 ACAAAATGTATCGATACATTC
1 ACAAAATGTATCAATACATTC
* *
389450 ACAAGATGTATTAATACATTC
1 ACAAAATGTATCAATACATTC
389471 A
1 A
389472 ATCCTTAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.30
Consensus pattern (21 bp):
ACAAAATGTATCAATACATTC
Found at i:390600 original size:20 final size:20
Alignment explanation
Indices: 390575--390648 Score: 107
Period size: 20 Copynumber: 3.7 Consensus size: 20
390565 GTTTGGGAGA
*
390575 ATGTATCGATACAATTCTTT
1 ATGTATCGATACAATTCTTC
390595 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTTC
390615 ATGTATCGATACAATGTGC--C
1 ATGTATCGATACAAT-T-CTTC
390635 ATGTATCGATACAA
1 ATGTATCGATACAA
390649 ATAGTGGTAG
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
20 49 0.96
21 1 0.02
22 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCTTC
Found at i:390721 original size:19 final size:19
Alignment explanation
Indices: 390676--390746 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
390666 ACTGCCAGTT
390676 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAA-TGA
390695 TGCATGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
*
390715 TCATGTATCGATACAAAGCA
1 TCATGTATCGATACAATG-A
*
390735 TAATGTATCGAT
1 TCATGTATCGAT
390747 TCATTGGGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.40
20 28 0.60
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:393310 original size:154 final size:152
Alignment explanation
Indices: 392897--393339 Score: 454
Period size: 155 Copynumber: 2.9 Consensus size: 152
392887 GAAAACATCA
* **
392897 TAAAAAGGCGAACCTATCCTAAATGTAAACACTTGGCATAAAAGTGACTGGGTGACTACCTA--A
1 TAAAAAGGCAAACCTATCCTAAATGT-AAC-CTTGGCATAAAAGTGACTTAGTGACTACCTAGGA
* * * * * *
392960 ---GCTTTTAGGAAAAATTACCAAAATACCCTAGAGGTATACCTTTGACGTGAAAGTATCCCGAT
64 CTCGGTTTTAAGAAAAATTACCAAAATACCCT-TAGGTATACCTTCGACATGAAAGTATCCAGAT
* *
393022 AACTCTAAAGGAGTCAAAATGATTG
128 AACTCTAAAGGAGACAAAAGGATTG
* * * * **
393047 TAAAAAGGCAAACCTATCCTAAATGTAGACCCATAGCATAAAATTGACCTAGTGACTATGTAGGA
1 TAAAAAGGCAAACCTATCCTAAATGTA-A-CCTTGGCATAAAAGTGACTTAGTGACTACCTAGGA
* * *
393112 CTCGGTTTTAAAAAAAATTACCAAAATACTCCTAAGGTATACCTTCGACATGAACGTATCCA-AG
64 CTCGGTTTTAAGAAAAATTACCAAAATAC-CCTTAGGTATACCTTCGACATGAAAGTATCCAGA-
*
393176 TAAC-CTTAAGG-GACATGAAAGGATTG
127 TAACTCTAAAGGAGACA--AAAGGATTG
**
393202 TAAAAAGGCAAACCTATCCTAAATGTAACCTTTGGCATAAAAGCAACTTAGTGACTACCTAGGAC
1 TAAAAAGGCAAACCTATCCTAAATGTAACC-TTGGCATAAAAGTGACTTAGTGACTACCTAGGAC
** * **
393267 TCGGTTTTAAGAAAAATTATTAAAATGCCCTTAGGATATACCTTCGATGTGAAAGTATCCCA-AT
65 TCGGTTTTAAGAAAAATTACCAAAATACCCTTAGG-TATACCTTCGACATGAAAGTAT-CCAGAT
*
393331 AACTTTAAA
128 AACTCTAAA
393340 AAACACGAAA
Statistics
Matches: 240, Mismatches: 38, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
149 1 0.00
150 49 0.20
151 1 0.00
152 1 0.00
153 11 0.05
154 81 0.34
155 93 0.39
156 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (152 bp):
TAAAAAGGCAAACCTATCCTAAATGTAACCTTGGCATAAAAGTGACTTAGTGACTACCTAGGACT
CGGTTTTAAGAAAAATTACCAAAATACCCTTAGGTATACCTTCGACATGAAAGTATCCAGATAAC
TCTAAAGGAGACAAAAGGATTG
Found at i:393568 original size:29 final size:28
Alignment explanation
Indices: 393432--393574 Score: 117
Period size: 29 Copynumber: 5.0 Consensus size: 28
393422 CTACTAAGTT
* * ** *
393432 CCTAGACTTTCCAAAATTACACATTGAT
1 CCTAAACTTTTCAAAATTACATGTTGAC
* * *
393460 CCTGAACTTTTTAAAATTATACT-TTGATC
1 CCTAAACTTTTCAAAATTACA-TGTTGA-C
* * *
393489 CCTAAACTTTTTAAAATTACACGTTAAC
1 CCTAAACTTTTCAAAATTACATGTTGAC
* * *
393517 CCCAATCTTTTCAAAATTTCATGTTGAC
1 CCTAAACTTTTCAAAATTACATGTTGAC
*
393545 TCCTAAAATTTTCAAAATTACATGTTGAC
1 -CCTAAACTTTTCAAAATTACATGTTGAC
393574 C
1 C
393575 TCAAAATGGC
Statistics
Matches: 90, Mismatches: 21, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
28 44 0.49
29 46 0.51
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (28 bp):
CCTAAACTTTTCAAAATTACATGTTGAC
Found at i:395263 original size:6 final size:6
Alignment explanation
Indices: 395211--395274 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
395201 ACTAGTTAAC
* * *
395211 AAATATA AAA-TA AAA-TA AAATAA AAATTTCA AAATTA AGA-GA AAATTA
1 AAAT-TA AAATTA AAATTA AAATTA AAA-TT-A AAATTA AAATTA AAATTA
395259 AAATTA AAATTA AAAT
1 AAATTA AAATTA AAAT
395275 ATTTATCATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
5 13 0.28
6 24 0.51
7 6 0.13
8 4 0.09
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.27
Consensus pattern (6 bp):
AAATTA
Found at i:396697 original size:66 final size:66
Alignment explanation
Indices: 396590--397098 Score: 418
Period size: 66 Copynumber: 7.7 Consensus size: 66
396580 AAGTGAGACA
* * * * * *
396590 TAAGTC-AGAAAGAAGTTAACTAGGGCAAAACCGTAACGTCAACTAAAAGGTGACAAGGG-AAAA
1 TAAGTCGA-AAAGAGGTTGACTAGGGCGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAA
396653 GCC
65 -CC
** * * * * * *
396656 TAAGTTTAAAAGTGGTTGACCAGGGCGAAACCATCATGTCAACTAAAA-ATCAACTAAAAGG--A
1 TAAGTCGAAAAGAGGTTGACTAGGGCGAAACCATCACGTCAACTAAAAGGT-GACT--AGGGCAA
*
396718 AAGC
63 AACC
* * * * *
396722 TAAGTAGAAAAGAGGTTGACTAGGGTGAAACCATAATGTCAACTAAAAGGTGATTAGGGCAAAAC
1 TAAGTCGAAAAGAGGTTGACTAGGGCGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
396787 C
66 C
* * * * * * *
396788 TAGGTCGAGAAGAGGTTAATTAGGGTGAAACCATC-CTGTTAACTAAAAGGTGACTAGGGCACAA
1 TAAGTCGAAAAGAGGTTGACTAGGGCGAAACCATCAC-GTCAACTAAAAGGTGACTAGGGCAAAA
*
396852 CA
65 CC
* ** ** * * ** *
396854 TAAGTTGAATGGAGGTTGACTAGGGAAAAACCATCACATCAACTAAAAAGTGACTAATGCGAAAC
1 TAAGTCGAAAAGAGGTTGACTAGGGCGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
396919 C
66 C
* * * ** * * * * * * *
396920 TAAGTTGAAAAGAGATTAAAAAAGGTGGAACCATCACGTCAAGTAATAGGTGACTAGGGCAATAT
1 TAAGTCGAAAAGAGGTTGACTAGGGCGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
396985 C
66 C
* * *
396986 TAAGTCGAAAGGAGGTTGACTAGGGCGAAACCATCACATCAAGTAAAAGGTGACTAGGGCAAAAC
1 TAAGTCGAAAAGAGGTTGACTAGGGCGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
397051 C
66 C
* * *
397052 TAAGTCGAAAGGATGTTGACTAGGGCAAAACCATCACGTCAACTAAA
1 TAAGTCGAAAAGAGGTTGACTAGGGCGAAACCATCACGTCAACTAAA
397099 GGTTGACCAG
Statistics
Matches: 345, Mismatches: 89, Indels: 18
0.76 0.20 0.04
Matches are distributed among these distances:
64 3 0.01
65 1 0.00
66 332 0.96
67 6 0.02
68 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.19
Consensus pattern (66 bp):
TAAGTCGAAAAGAGGTTGACTAGGGCGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
C
Found at i:396780 original size:34 final size:33
Alignment explanation
Indices: 396742--396846 Score: 79
Period size: 34 Copynumber: 3.2 Consensus size: 33
396732 AGAGGTTGAC
396742 TAGGGTGAAACCATAATGTCAACTAAAAGGTGAT
1 TAGGGTGAAACCAT-ATGTCAACTAAAAGGTGAT
** * * * * *
396776 TAGGGCAAAACC-TAGGTCGA-GAAGAGGTTAAT
1 TAGGGTGAAACCATATGTCAACTAAAAGG-TGAT
* * *
396808 TAGGGTGAAACCATCCTGTTAACTAAAAGGTGAC
1 TAGGGTGAAACCAT-ATGTCAACTAAAAGGTGAT
396842 TAGGG
1 TAGGG
396847 CACAACATAA
Statistics
Matches: 50, Mismatches: 17, Indels: 8
0.67 0.23 0.11
Matches are distributed among these distances:
31 5 0.10
32 18 0.36
33 2 0.04
34 20 0.40
35 5 0.10
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (33 bp):
TAGGGTGAAACCATATGTCAACTAAAAGGTGAT
Found at i:397043 original size:34 final size:34
Alignment explanation
Indices: 397002--397151 Score: 123
Period size: 34 Copynumber: 4.5 Consensus size: 34
396992 GAAAGGAGGT
* *
397002 TGACTAGGGCGAAACCATCACATCAAGTAAAAGG
1 TGACTAGGGCAAAACCATCACATCAACTAAAAGG
* * *
397036 TGACTAGGGCAAAACC-T-A-AGTCGAA--AGGATGT
1 TGACTAGGGCAAAACCATCACA-TC-AACTA-AAAGG
*
397068 TGACTAGGGCAAAACCATCACGTCAACT-AAAGG
1 TGACTAGGGCAAAACCATCACATCAACTAAAAGG
* * * *
397101 TTGACCAGGGTAGAACCATCACATCAACTAATAGG
1 -TGACTAGGGCAAAACCATCACATCAACTAAAAGG
*
397136 CGACTAGGGCAAAACC
1 TGACTAGGGCAAAACC
397152 TAAGTTGAAA
Statistics
Matches: 89, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
31 2 0.02
32 21 0.24
33 8 0.09
34 54 0.61
35 4 0.04
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (34 bp):
TGACTAGGGCAAAACCATCACATCAACTAAAAGG
Found at i:397081 original size:32 final size:31
Alignment explanation
Indices: 396970--397083 Score: 99
Period size: 32 Copynumber: 3.5 Consensus size: 31
396960 AAGTAATAGG
* *
396970 TGACTAGGGCAATATCTAAGTCGAAAGGAGGT
1 TGACTAGGGCAAAACCTAAGTCGAAAGGA-GT
* *
397002 TGACTAGGGCGAAACCATCACA-TCAAGTAAA--AGG
1 TGACTAGGGCAAAACC-T-A-AGTC--G-AAAGGAGT
397036 TGACTAGGGCAAAACCTAAGTCGAAAGGATGT
1 TGACTAGGGCAAAACCTAAGTCGAAAGGA-GT
397068 TGACTAGGGCAAAACC
1 TGACTAGGGCAAAACC
397084 ATCACGTCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
29 3 0.05
30 1 0.02
31 2 0.03
32 33 0.50
33 2 0.03
34 19 0.29
35 2 0.03
36 1 0.02
37 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (31 bp):
TGACTAGGGCAAAACCTAAGTCGAAAGGAGT
Found at i:397145 original size:166 final size:167
Alignment explanation
Indices: 396947--397268 Score: 459
Period size: 166 Copynumber: 1.9 Consensus size: 167
396937 AAAAAAGGTG
* * * * * * * *
396947 GAACCATCACGTCAAGTAATAGGTGACTAGGGCAATATCTAAGTCGAAAGGAGGTTGACTAGGGC
1 GAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGAC
* * * *
397012 GAAACCATCACATCAAGTAAAAGGTGACTAGGGCAAAACCTAAGTCGAAAGGATG-TTGACTAGG
66 GAAACCATCACATCAACTAAAAGGTGACTAAGGCAAAACCTAAGTC-AAAAGACGATTGACTAGG
397076 GCAAAACCATCACGTCAACTAA-AGGTTGACCAGGGTA
130 GCAAAACCATCACGTCAACTAATAGGTTGACCAGGGTA
* * *
397113 GAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAAGAGGTTGATTAAGAT
1 GAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGAC
* *
397178 GAAACCATCCCATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCAAAAGACGATTGACTAGGG
66 GAAACCATCACATCAACTAAAAGGTGACTAAGGCAAAACCTAAGTCAAAAGACGATTGACTAGGG
*
397243 CGAAACCATCACGTCAACTAATAGGT
131 CAAAACCATCACGTCAACTAATAGGT
397269 GACTACAACG
Statistics
Matches: 136, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
165 6 0.04
166 126 0.93
167 4 0.03
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (167 bp):
GAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGAC
GAAACCATCACATCAACTAAAAGGTGACTAAGGCAAAACCTAAGTCAAAAGACGATTGACTAGGG
CAAAACCATCACGTCAACTAATAGGTTGACCAGGGTA
Found at i:397183 original size:100 final size:101
Alignment explanation
Indices: 397014--397202 Score: 254
Period size: 100 Copynumber: 1.9 Consensus size: 101
397004 ACTAGGGCGA
* * * * * *
397014 AACCATCACATCAAGTAAAAGGTGACTAGGGCAAAACCTAAGTCGAAAGGATGTTGACTAGGGCA
1 AACCATCACATCAACTAAAAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGACA
*
397079 AAACCATCACGTCAACTAA-AGGTTGACCAGGGTAG
66 AAACCATCACATCAACTAATAGGTTGACCAGGGTAG
* * * **
397114 AACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAAGAGGTTGATTAAGATG
1 AACCATCACATCAACTAAAAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGACA
*
397179 AAACCATCCCATCAACTAATAGGT
66 AAACCATCACATCAACTAATAGGT
397203 GACTAAGGCA
Statistics
Matches: 75, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
100 71 0.95
101 4 0.05
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (101 bp):
AACCATCACATCAACTAAAAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGACA
AAACCATCACATCAACTAATAGGTTGACCAGGGTAG
Found at i:397318 original size:232 final size:232
Alignment explanation
Indices: 396866--397329 Score: 547
Period size: 232 Copynumber: 2.0 Consensus size: 232
396856 AGTTGAATGG
* * * *
396866 AGGTTGACTAGGGAAAAACCATCACATCAACTAAAAAGTGACTAATGCGAAACCTAAGTTGAAAA
1 AGGTTGACCAGGGAAAAACCATCACATCAACTAAAAAGCGACTAAGGCAAAACCTAAGTTGAAAA
* * * * * * *
396931 GAGATTAAAAAAGGTGGAACCATCACGTCAAGTAATAGGTGACTAGGGCAATATCTAAGTCGAAA
66 GAGATTAAAAAAGATGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
* * * *** *
396996 GGAGGTTGACTAGGGCGAAACCATCACATCAAGTAAAAGGTGACTAGGGCAAAACCTAAGTCGAA
131 AGAGATTGACTAGGGCGAAACCATCACATCAACTAAAAGGTGACTACAACAAAACATAAGTCGAA
* * * *
397061 AGGATGTTGACTAGGGCAAAACCATCACGTCAACTAA
196 AAGAGGCTGACCAGGGCAAAACCATCACGTCAACTAA
* * * * *
397098 AGGTTGACCAGGGTAGAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAA
1 AGGTTGACCAGGGAAAAACCATCACATCAACTAAAAAGCGACTAAGGCAAAACCTAAGTTGAAAA
* * ** *
397163 GAGGTTGATTAAGATGAAACCATCCCATCAACTAATAGGTGACTAAGGCAAAACCTAAGTC-AAA
66 GAGATTAAAAAAGATGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
* * *
397227 AGACGATTGACTAGGGCGAAACCATCACGTCAACTAATAGGTGACTACAACGGAAACATAAG-CT
131 AGA-GATTGACTAGGGCGAAACCATCACATCAACTAAAAGGTGACTACAAC-AAAACATAAGTC-
* *
397291 GAAAAGAGGCTGACCA-GGTAGAACCATCACGTCAACTAA
193 GAAAAGAGGCTGACCAGGGCAAAACCATCACGTCAACTAA
397330 TAAGTGACTA
Statistics
Matches: 192, Mismatches: 37, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
231 5 0.03
232 167 0.87
233 20 0.10
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (232 bp):
AGGTTGACCAGGGAAAAACCATCACATCAACTAAAAAGCGACTAAGGCAAAACCTAAGTTGAAAA
GAGATTAAAAAAGATGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
AGAGATTGACTAGGGCGAAACCATCACATCAACTAAAAGGTGACTACAACAAAACATAAGTCGAA
AAGAGGCTGACCAGGGCAAAACCATCACGTCAACTAA
Found at i:397384 original size:198 final size:197
Alignment explanation
Indices: 397102--397668 Score: 631
Period size: 198 Copynumber: 2.9 Consensus size: 197
397092 AACTAAAGGT
* ** * * *
397102 TGACCAGGGTAGAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAAGAGG
1 TGACCAGGGTAGAACCATCACGTCAACTAATAGGCGACTAGAACGAAACCTAAGTCGAAAGGAGG
* * *
397167 TTGATTAAGATGAAACCATCCCATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCAAAAGACG
66 TTGACTAAG-TGAAACCATCACATCAACTAATAGGTGACTAGGGCAAAACCTAAGTCAAAAGA-G
* * * *
397232 ATTGACTAGGGCGAAACCATCACGTCAACTAATAGGTGACTACAACG-GAAACATAAG-CTGAAA
129 GTTGACCAGGGTGAAACCATCACGTCAACTAATAGGTGACTA-AACGTGAAACACAAGTC-GAAA
397295 AGAGGC
192 AGAGGC
* * **
397301 TGACCA-GGTAGAACCATCACGTCAACTAATAAGTGACTAGATTGAAACCTAAGTCGAAAGGAGG
1 TGACCAGGGTAGAACCATCACGTCAACTAATAGGCGACTAGAACGAAACCTAAGTCGAAAGGAGG
* * * * ** * * *
397365 TTGACTAGAGTGGAACCATCATATCAACTACTAGGTGACTCGGGTGAAACATAACTCAAAAAAAG
66 TTGACTA-AGTGAAACCATCACATCAACTAATAGGTGACTAGGGCAAAACCTAAGTC-AAAAGAG
* * ** * *
397430 GTTGACCAAGATGAAACCATCACGTCAACTAATAGGTGACT-AGGGTGAAACCCAAGTCGAAACG
129 GTTGACCAGGGTGAAACCATCACGTCAACTAATAGGTGACTAAACGTGAAACACAAGTCGAAAAG
*
397494 AGGT
194 AGGC
* * *
397498 TGACCAGGGTAAAACCATCACGTCAACTAATAGGGGACTA-AACGAAACCTAAGTCGAAAGAAGG
1 TGACCAGGGTAGAACCATCACGTCAACTAATAGGCGACTAGAACGAAACCTAAGTCGAAAGGAGG
* * * * *
397562 TTGACCAAGGTAAAACCATCACGTCAACTAATATGTGACTAGGGCAAAACCTAAGTCGAAAGGAG
66 TTGACTAA-GTGAAACCATCACATCAACTAATAGGTGACTAGGGCAAAACCTAAGTC-AAAAGAG
* * *
397627 GTTGACCAGAGTGAAACCATCATGTCAACTAATAGGAGACTA
129 GTTGACCAGGGTGAAACCATCACGTCAACTAATAGGTGACTA
397669 GGGCAAAATC
Statistics
Matches: 303, Mismatches: 58, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
196 3 0.01
197 127 0.42
198 160 0.53
199 13 0.04
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (197 bp):
TGACCAGGGTAGAACCATCACGTCAACTAATAGGCGACTAGAACGAAACCTAAGTCGAAAGGAGG
TTGACTAAGTGAAACCATCACATCAACTAATAGGTGACTAGGGCAAAACCTAAGTCAAAAGAGGT
TGACCAGGGTGAAACCATCACGTCAACTAATAGGTGACTAAACGTGAAACACAAGTCGAAAAGAG
GC
Found at i:397384 original size:298 final size:298
Alignment explanation
Indices: 396828--397394 Score: 637
Period size: 298 Copynumber: 1.9 Consensus size: 298
396818 CCATCCTGTT
* * ** *
396828 AACTAAAAGGTGACTAGGGCACAACATAAGTTGAATGGAGGTTGACTAGGGAAAAACCATCACAT
1 AACTAAAAGGCGACTAGGGCAAAACATAAGTTGAAAAGAGGTTGACTAGAGAAAAACCATCACAT
* * * * *
396893 CAACTAAAAAGTGACTAATGCGAAACCTAAGTTGAAAAGAGATTAAAAAAGGTGGAACCATCACG
66 CAACTAAAAAGTGACTAAGGCAAAACCTAAGTTCAAAAGAGATTAAAAAAGGCGAAACCATCACG
* * * * * *
396958 TCAAGTAATAGGTGACTAGGGCAATATCTAAGTCGAAAGGAGGTTGACTAGGGCGAAACCATCAC
131 TCAACTAATAGGTGACTACGGCAATATCTAAGTCGAAAAGAGGCTGACCAGGGAGAAACCATCAC
* * * *
397023 ATCAAGTAAAAGGTGACTAGGGCAAAACCTAAGTCGAAAGGATGTTGACTAGGGCAAAACCATCA
196 ATCAACTAAAAGGTGACTAGAGCAAAACCTAAGTCGAAAGGAGGTTGACTAGAGCAAAACCATCA
*
397088 CGTCAACTAAAGGTTGACCAGGGTAGAACCATCACATC
261 CATCAACTAAAGGTTGACCAGGGTAGAACCATCACATC
* * * * *
397126 AACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAAGAGGTTGATTA-AGATGAAACCATCCCA
1 AACTAAAAGGCGACTAGGGCAAAACATAAGTTGAAAAGAGGTTGACTAGAGA-AAAACCATCACA
* * * ** *
397190 TCAACTAATAGGTGACTAAGGCAAAACCTAAG-TCAAAAGACGATTGACTAGGGCGAAACCATCA
65 TCAACTAAAAAGTGACTAAGGCAAAACCTAAGTTCAAAAGA-GATTAAAAAAGGCGAAACCATCA
*
397254 CGTCAACTAATAGGTGACTACAACGG-AA-A-CATAAG-CTGAAAAGAGGCTGACCAGGTAG-AA
129 CGTCAACTAATAGGTGACT---ACGGCAATATC-TAAGTC-GAAAAGAGGCTGACCAGGGAGAAA
* *** ***
397314 CCATCACGTCAACTAATAA-GTGACTAGATTGAAACCTAAGTCGAAAGGAGGTTGACTAGAGTGG
189 CCATCACATCAACTAA-AAGGTGACTAGAGCAAAACCTAAGTCGAAAGGAGGTTGACTAGAGCAA
*
397378 AACCATCATATCAACTA
253 AACCATCACATCAACTA
397395 CTAGGTGACT
Statistics
Matches: 220, Mismatches: 41, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
297 9 0.04
298 183 0.83
299 23 0.10
300 2 0.01
301 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (298 bp):
AACTAAAAGGCGACTAGGGCAAAACATAAGTTGAAAAGAGGTTGACTAGAGAAAAACCATCACAT
CAACTAAAAAGTGACTAAGGCAAAACCTAAGTTCAAAAGAGATTAAAAAAGGCGAAACCATCACG
TCAACTAATAGGTGACTACGGCAATATCTAAGTCGAAAAGAGGCTGACCAGGGAGAAACCATCAC
ATCAACTAAAAGGTGACTAGAGCAAAACCTAAGTCGAAAGGAGGTTGACTAGAGCAAAACCATCA
CATCAACTAAAGGTTGACCAGGGTAGAACCATCACATC
Found at i:397676 original size:66 final size:66
Alignment explanation
Indices: 397098--397672 Score: 549
Period size: 66 Copynumber: 8.7 Consensus size: 66
397088 CGTCAACTAA
* * * * *
397098 AGGTTGACCAGGGT-AGAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAA
1 AGGTTGACCAGAGTGA-AACCATCACGTCAACTAATAGGTGACTAGGGCGAAACCTAAGTCGAAA
397162 AG
65 AG
** * * * *
397164 AGGTTGATTA-AGATGAAACCATCCCATCAACTAATAGGTGACTAAGGCAAAACCTAAGTC-AAA
1 AGGTTGACCAGAG-TGAAACCATCACGTCAACTAATAGGTGACTAGGGCGAAACCTAAGTCGAAA
397227 AG
65 AG
* * * * *** *
397229 ACGATTGACTAGGGCGAAACCATCACGTCAACTAATAGGTGACTACAACGGAAACATAAG-CTGA
1 A-GGTTGACCAGAGTGAAACCATCACGTCAACTAATAGGTGACTAGGGC-GAAACCTAAGTC-GA
397293 AAAG
63 AAAG
* * ***
397297 AGGCTGACCAG-GT-AGAACCATCACGTCAACTAATAAGTGACTAGATTGAAACCTAAGTCGAAA
1 AGGTTGACCAGAGTGA-AACCATCACGTCAACTAATAGGTGACTAGGGCGAAACCTAAGTCGAAA
*
397360 GG
65 AG
* * ** * * * * * *
397362 AGGTTGACTAGAGTGGAACCATCATATCAACTACTAGGTGACTCGGGTGAAACATAACTCAAAAA
1 AGGTTGACCAGAGTGAAACCATCACGTCAACTAATAGGTGACTAGGGCGAAACCTAAGTCGAAAA
*
397427 A
66 G
* *
397428 AGGTTGACCA-AGATGAAACCATCACGTCAACTAATAGGTGACTAGGGTGAAACCCAAGTCGAAA
1 AGGTTGACCAGAG-TGAAACCATCACGTCAACTAATAGGTGACTAGGGCGAAACCTAAGTCGAAA
*
397492 CG
65 AG
* * * **
397494 AGGTTGACCAGGGTAAAACCATCACGTCAACTAATAGGGGACTA-AACGAAACCTAAGTCG-AAA
1 AGGTTGACCAGAGTGAAACCATCACGTCAACTAATAGGTGACTAGGGCGAAACCTAAGTCGAAAA
397557 G
66 G
* * *
397558 AAGGTTGACCA-AGGTAAAACCATCACGTCAACTAATATGTGACTAGGGCAAAACCTAAGTCGAA
1 -AGGTTGACCAGA-GTGAAACCATCACGTCAACTAATAGGTGACTAGGGCGAAACCTAAGTCGAA
*
397622 AGG
64 AAG
* *
397625 AGGTTGACCAGAGTGAAACCATCATGTCAACTAATAGGAGACTAGGGC
1 AGGTTGACCAGAGTGAAACCATCACGTCAACTAATAGGTGACTAGGGC
397673 AAAATCATCA
Statistics
Matches: 417, Mismatches: 74, Indels: 36
0.79 0.14 0.07
Matches are distributed among these distances:
64 3 0.01
65 85 0.20
66 301 0.72
67 22 0.05
68 6 0.01
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.18
Consensus pattern (66 bp):
AGGTTGACCAGAGTGAAACCATCACGTCAACTAATAGGTGACTAGGGCGAAACCTAAGTCGAAAA
G
Found at i:397737 original size:66 final size:65
Alignment explanation
Indices: 397664--398160 Score: 254
Period size: 66 Copynumber: 7.7 Consensus size: 65
397654 ACTAATAGGA
* * *
397664 GACTAGGGCAAAATCATCACATCAACTAATAAGTGACTAGGGCAAAGCCAAAGTCGAAAGGAGGT
1 GACTAGGGCAAAATCATCACGTCAACTAATAGGCGACTAGGGCAAA-CCAAAGTCGAAAGGAGGT
397729 T
65 T
* * * * * * *
397730 GATTAGGGTAGAACCATCACGTTAACTAATAGGCGACTAGGGTGAAACCTAAGTCGAAAGGAGGT
1 GACTAGGGCAAAATCATCACGTCAACTAATAGGCGACTAGGG-CAAACCAAAGTCGAAAGGAGGT
397795 T
65 T
* ** * *
397796 GACTAGGGCAAAATCATCACGTCAACTAATAGGGGACTAGGGCAAAACGTAAGTCAAAAGAAGGT
1 GACTAGGGCAAAATCATCACGTCAACTAATAGGCGACTAGGGC-AAACCAAAGTCGAAAGGAGGT
397861 T
65 T
* * ** * * * * * * *
397862 GACCAAGGTGAAACCATTACAT-GACT-A-A---GAC----G-AAGCCTAAG-CTATAAGGAGGT
1 GACTAGGGCAAAATCATCACGTCAACTAATAGGCGACTAGGGCAAACCAAAGTCGA-AAGGAGGT
397915 T
65 T
* * * * * *
397916 GACCGAGGTG--AAACCATCACATCAACTAAGAGGTGACTAGCGCGAAACC-AAGTCGAAAGGAG
1 GA-CTAGG-GCAAAATCATCACGTCAACTAATAGGCGACTAGGGC-AAACCAAAGTCGAAAGGAG
397978 GTT
63 GTT
* * * * * * * ** *
397981 CACTAGGGCAAAACCATCACGTCTACTGATAGGGGACTAGGGCAAAACCTAAACT-AAAATAACG
1 GACTAGGGCAAAATCATCACGTCAACTAATAGGCGACTAGGGC-AAACC-AAAGTCGAAAGGAGG
398045 TT
64 TT
* * * * * * ** * *
398047 GACTAGGGAAAAACCATCATGTCAACTAATAGGCAACAAAGGCGAAACTTAAGTCAAAAAGAGGT
1 GACTAGGGCAAAATCATCACGTCAACTAATAGGCGACTAGGGC-AAACCAAAGTCGAAAGGAGGT
398112 T
65 T
* * * * *
398113 GA-TCGAGGCAAAACCATCATGTCAACTAATAGGTGACTAAGGCGAAAC
1 GACTAG-GGCAAAATCATCACGTCAACTAATAGGCGACTAGGGC-AAAC
398161 ATAAGTGAAA
Statistics
Matches: 334, Mismatches: 73, Indels: 48
0.73 0.16 0.11
Matches are distributed among these distances:
53 2 0.01
54 28 0.08
55 6 0.02
56 3 0.01
57 1 0.00
60 6 0.02
63 2 0.01
64 6 0.02
65 53 0.16
66 221 0.66
67 6 0.02
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (65 bp):
GACTAGGGCAAAATCATCACGTCAACTAATAGGCGACTAGGGCAAACCAAAGTCGAAAGGAGGTT
Found at i:397757 original size:100 final size:100
Alignment explanation
Indices: 397573--397771 Score: 283
Period size: 100 Copynumber: 2.0 Consensus size: 100
397563 TGACCAAGGT
* * *
397573 AAAACCATCACGTCAACTAATATGTGACTAGGGCAAAACCTAAGTCGAAAGGAGGTTGACCAGAG
1 AAAACCATCACATCAACTAATAAGTGACTAGGGCAAAACCAAAGTCGAAAGGAGGTTGACCAGAG
*
397638 TGAAACCATCATGTCAACTAATAGGAGACTAGGGC
66 TGAAACCATCACGTCAACTAATAGGAGACTAGGGC
* * ** *
397673 AAAATCATCACATCAACTAATAAGTGACTAGGGCAAAGCCAAAGTCGAAAGGAGGTTGATTAGGG
1 AAAACCATCACATCAACTAATAAGTGACTAGGGCAAAACCAAAGTCGAAAGGAGGTTGACCAGAG
* *
397738 T-AGAACCATCACGTTAACTAATAGGCGACTAGGG
66 TGA-AACCATCACGTCAACTAATAGGAGACTAGGG
397772 TGAAACCTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 1 0.01
100 86 0.99
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (100 bp):
AAAACCATCACATCAACTAATAAGTGACTAGGGCAAAACCAAAGTCGAAAGGAGGTTGACCAGAG
TGAAACCATCACGTCAACTAATAGGAGACTAGGGC
Found at i:398310 original size:66 final size:66
Alignment explanation
Indices: 398240--398464 Score: 164
Period size: 64 Copynumber: 3.4 Consensus size: 66
398230 ATTTGAGAAA
* *
398240 AGGTTGACCAAGGT-AGAATC-ATCATAA-TAACTAATAGGTGACTAAGGTGAAA-CCTAAGTCA
1 AGGTTGACCAAGGTGA-AATCGAT-A-AAGTAACAAAT-GGTGACTAAGATGAAATCCTAAGTCA
398301 AAAAG
62 AAAAG
* *
398306 AGGTTGACCTAGGTGAAATCGATAAAGTTAACAAATGGTGACTAAGATGAAATCCTAAGTCGACA
1 AGGTTGACCAAGGTGAAATCGATAAAG-TAACAAATGGTGACTAAGATGAAATCCTAAGTC-AAA
*
398371 TAG
64 AAG
* * * * * *
398374 -GGTTGATC-AGG-G-CATCGATATAGTTAACAAATAGTGTCT-AGAATGAAAACCTAAGTCGAA
1 AGGTTGACCAAGGTGAAATCGATAAAG-TAACAAATGGTGACTAAG-ATGAAATCCTAAGTC-AA
*
398434 ATAG
63 AAAG
** *
398438 -GGTTGACCAAGGCAAAACCGATAAAGT
1 AGGTTGACCAAGGTGAAATCGATAAAGT
398465 CAATAGATGA
Statistics
Matches: 132, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
63 2 0.02
64 50 0.38
65 6 0.05
66 37 0.28
67 33 0.25
68 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (66 bp):
AGGTTGACCAAGGTGAAATCGATAAAGTAACAAATGGTGACTAAGATGAAATCCTAAGTCAAAAA
G
Found at i:398402 original size:64 final size:64
Alignment explanation
Indices: 398323--398443 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 64
398313 CCTAGGTGAA
* * *
398323 ATCGATAAAGTTAACAAATGGTGACTA-AGATGAAATCCTAAGTCGACATAGGGTTGATCAGGGC
1 ATCGATAAAGTTAACAAATAGTGACTAGA-ATGAAAACCTAAGTCGAAATAGGGTTGATCAGGGC
* *
398387 ATCGATATAGTTAACAAATAGTGTCTAGAATGAAAACCTAAGTCGAAATAGGGTTGA
1 ATCGATAAAGTTAACAAATAGTGACTAGAATGAAAACCTAAGTCGAAATAGGGTTGA
398444 CCAAGGCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 50 0.98
65 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (64 bp):
ATCGATAAAGTTAACAAATAGTGACTAGAATGAAAACCTAAGTCGAAATAGGGTTGATCAGGGC
Found at i:399657 original size:21 final size:21
Alignment explanation
Indices: 399631--399685 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
399621 GTTACAAGCA
*
399631 ATGTATCGATACAATT-TCATC
1 ATGTATCGATACAATTGT-ACC
399652 ATGTATCGATAC-ATTGTACC
1 ATGTATCGATACAATTGTACC
*
399672 ATATATCGATACAA
1 ATGTATCGATACAA
399686 ATAGTGATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACAATTGTACC
Found at i:399759 original size:19 final size:20
Alignment explanation
Indices: 399713--399769 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
399703 ACTGCCAATC
*
399713 TCATGTATCGATACAAT-TG
1 TCATGTATCGATACAATGAG
399732 TCCATGTATCGATACAATGAG
1 T-CATGTATCGATACAATGAG
*
399753 T-ATGTATCGATATAATG
1 TCATGTATCGATACAATG
399770 TATCGATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.47
20 16 0.47
21 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (20 bp):
TCATGTATCGATACAATGAG
Found at i:399772 original size:13 final size:13
Alignment explanation
Indices: 399754--399780 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
399744 TACAATGAGT
399754 ATGTATCGATATA
1 ATGTATCGATATA
399767 ATGTATCGATATA
1 ATGTATCGATATA
399780 A
1 A
399781 AGCATAATGT
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:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:400389 original size:23 final size:24
Alignment explanation
Indices: 400350--400396 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
400340 AGAATTTCTT
*
400350 CTCTTTAAAAATTTCTCCCCCTTA
1 CTCTTTAAAAATATCTCCCCCTTA
400374 CTCTTTAAAAA-ATCTCCCCCTTA
1 CTCTTTAAAAATATCTCCCCCTTA
400397 ATCAAAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (24 bp):
CTCTTTAAAAATATCTCCCCCTTA
Found at i:404144 original size:21 final size:21
Alignment explanation
Indices: 404111--404160 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
404101 TTGCAAGTTG
*
404111 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
404133 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
404154 AAATAAA
1 AAATAAA
404161 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:405978 original size:15 final size:15
Alignment explanation
Indices: 405958--405988 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
405948 TAAAAATGTC
*
405958 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
405973 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
405988 C
1 C
405989 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:408080 original size:13 final size:13
Alignment explanation
Indices: 408062--408100 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
408052 ACATTTTTCT
408062 TTGTATCGATACA
1 TTGTATCGATACA
408075 TTGTATCGATACA
1 TTGTATCGATACA
408088 TTGTATCGATACA
1 TTGTATCGATACA
408101 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:408264 original size:20 final size:20
Alignment explanation
Indices: 408221--408266 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
408211 AAATCTTTTG
408221 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
408242 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
408262 CAAAA
1 CAAAA
408267 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:411968 original size:13 final size:13
Alignment explanation
Indices: 411950--411975 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
411940 CAATTTTTTG
411950 TGTATCGATACAT
1 TGTATCGATACAT
411963 TGTATCGATACAT
1 TGTATCGATACAT
411976 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:412762 original size:78 final size:78
Alignment explanation
Indices: 412633--412787 Score: 292
Period size: 78 Copynumber: 2.0 Consensus size: 78
412623 ATTTGTACAT
* *
412633 TCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTTCCCCCGTTTATTAATTAATCT
1 TCTCCCCCTTAATAAGGTAATTCACACATTCTCTCCTTTATCTTCCCCCGTTTATTAATAAATCT
412698 CCCCCTTAATCAC
66 CCCCCTTAATCAC
412711 TCTCCCCCTTAATAAGGTAATTCACACATTCTCTCCTTTATCTTCCCCCGTTTATTAATAAATCT
1 TCTCCCCCTTAATAAGGTAATTCACACATTCTCTCCTTTATCTTCCCCCGTTTATTAATAAATCT
412776 CCCCCTTAATCA
66 CCCCCTTAATCA
412788 AGTAATTCAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.23, C:0.34, G:0.05, T:0.38
Consensus pattern (78 bp):
TCTCCCCCTTAATAAGGTAATTCACACATTCTCTCCTTTATCTTCCCCCGTTTATTAATAAATCT
CCCCCTTAATCAC
Found at i:414616 original size:13 final size:13
Alignment explanation
Indices: 414598--414649 Score: 104
Period size: 13 Copynumber: 4.0 Consensus size: 13
414588 ATAATCACCC
414598 TGTATCGATACAA
1 TGTATCGATACAA
414611 TGTATCGATACAA
1 TGTATCGATACAA
414624 TGTATCGATACAA
1 TGTATCGATACAA
414637 TGTATCGATACAA
1 TGTATCGATACAA
414650 AGAAAAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:416747 original size:15 final size:15
Alignment explanation
Indices: 416727--416757 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
416717 ATTTCGTTTG
*
416727 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
416742 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
416757 G
1 G
416758 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:418607 original size:21 final size:21
Alignment explanation
Indices: 418561--418605 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
418551 AAGTTTTCAT
418561 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
418581 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
418603 TTT
1 TTT
418606 CAACTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:420842 original size:13 final size:13
Alignment explanation
Indices: 420824--420849 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
420814 CAATTTTTTG
420824 TGTATCGATACAT
1 TGTATCGATACAT
420837 TGTATCGATACAT
1 TGTATCGATACAT
420850 ACTCGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:421585 original size:13 final size:13
Alignment explanation
Indices: 421562--421603 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
421552 AAATAGTACC
*
421562 CAATATATCGATA
1 CAATGTATCGATA
*
421575 CAGTGTATCGATA
1 CAATGTATCGATA
*
421588 CAATGTATTGATA
1 CAATGTATCGATA
421601 CAA
1 CAA
421604 GGAATATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:428636 original size:52 final size:52
Alignment explanation
Indices: 428551--428675 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
428541 ATATGAAAAG
* *
428551 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
428603 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
428655 TTACCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
428676 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:428688 original size:52 final size:51
Alignment explanation
Indices: 428556--428695 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 51
428546 AAAAGTTGCT
*
428556 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTACC
* *
428608 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTACC
*
428660 TGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TGCATGTATCGATACATTA-AT-AGTGTATCGATACA
428696 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTACC
Found at i:428702 original size:13 final size:13
Alignment explanation
Indices: 428684--428708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
428674 CAAAGATCAG
428684 TGTATCGATACAA
1 TGTATCGATACAA
428697 TGTATCGATACA
1 TGTATCGATACA
428709 TTTGAGTAAT
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:428776 original size:20 final size:20
Alignment explanation
Indices: 428747--428804 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
428737 GCAGTAGCTT
428747 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
428766 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
428786 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
428805 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:432390 original size:75 final size:76
Alignment explanation
Indices: 432234--432545 Score: 305
Period size: 76 Copynumber: 4.1 Consensus size: 76
432224 ACATAGTGGA
* * ** * * *
432234 GAATATGTGGTTTCTAAAATTTTTATCAACAACTAAAATA-AATTGATAATAGGTTTGAAGGAAA
1 GAATATATGATTTCTAAAATTTCCATCAACAACTAAAA-ACAACTGATAACATG-TTGAAGGAAA
432298 -GAACATGATGGG
64 GGAACATGATGGG
*
432310 GAATATATGATTTCTAAAATTTTCATCAACAA-TAAAAACCAACTGATAACATGTTGAAGGAAAG
1 GAATATATGATTTCTAAAATTTCCATCAACAACTAAAAA-CAACTGATAACATGTTGAAGGAAAG
432374 GAACAT-ATGGG
65 GAACATGATGGG
* * * * * *
432385 GAATATATGATTTCTAAAGTTTCCCTTAACAACT-GAAACAAACTGATAACATGCTAAAGGAAAG
1 GAATATATGATTTCTAAAATTTCCATCAACAACTAAAAAC-AACTGATAACATGTTGAAGGAAAG
*
432449 GAACATGATGAG
65 GAACATGATGGG
* * * * * * * *
432461 GAATA-AGTGATTTCTAAAATTTCCATCAACAGC-CAAAGCAAGTTGATAACAGGCTAAAGGCAA
1 GAATATA-TGATTTCTAAAATTTCCATCAACAACTAAAAACAA-CTGATAACATGTTGAAGGAAA
*
432524 TGAACATGATGGG
64 GGAACATGATGGG
432537 GAATATATG
1 GAATATATG
432546 GTTCTGTAAT
Statistics
Matches: 201, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
74 2 0.01
75 82 0.41
76 116 0.58
77 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (76 bp):
GAATATATGATTTCTAAAATTTCCATCAACAACTAAAAACAACTGATAACATGTTGAAGGAAAGG
AACATGATGGG
Found at i:432583 original size:76 final size:75
Alignment explanation
Indices: 432291--432618 Score: 295
Period size: 76 Copynumber: 4.3 Consensus size: 75
432281 AATAGGTTTG
* * * *
432291 AAGGAAA-GAACATGATGGGGAATATATGATTTCTAAAATTTTCATCAACAATAAAAACCAACTG
1 AAGGAAAGGAACATGATGGGGAATATATGATTTCTAAAATTTCCATCAACAGT-GAAACAAACTG
* *
432355 ATAACATGTTG
65 ATAACATGCTA
* * * *
432366 AAGGAAAGGAACAT-ATGGGGAATATATGATTTCTAAAGTTTCCCTTAACAACTGAAACAAACTG
1 AAGGAAAGGAACATGATGGGGAATATATGATTTCTAAAATTTCCATCAAC-AGTGAAACAAACTG
432430 ATAACATGCTA
65 ATAACATGCTA
* ** **
432441 AAGGAAAGGAACATGATGAGGAATA-AGTGATTTCTAAAATTTCCATCAACAGCCAAAGCAAGTT
1 AAGGAAAGGAACATGATGGGGAATATA-TGATTTCTAAAATTTCCATCAACAGTGAAA-CAAACT
*
432505 GATAACAGGCTA
64 GATAACATGCTA
* * * * * * * *
432517 AAGGCAATGAACATGATGGGGAATATATG-GTTCTGTAATTTTTCATTAACAGTGGAAACAAATT
1 AAGGAAAGGAACATGATGGGGAATATATGATTTCT-AAAATTTCCATCAACAGT-GAAACAAACT
* *
432581 GATGACAAGCTA
64 GATAACATGCTA
* * * * *
432593 AAGTAGACGATCATGATAGGGAATAT
1 AAGGAAAGGAACATGATGGGGAATAT
432619 GTAGTTTTGA
Statistics
Matches: 207, Mismatches: 38, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
75 79 0.38
76 124 0.60
77 4 0.02
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (75 bp):
AAGGAAAGGAACATGATGGGGAATATATGATTTCTAAAATTTCCATCAACAGTGAAACAAACTGA
TAACATGCTA
Found at i:434010 original size:17 final size:17
Alignment explanation
Indices: 433988--434022 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
433978 AAAGAGAGGG
*
433988 AAAAAACTAGACCAACA
1 AAAAAACTAAACCAACA
*
434005 AAAAAATTAAACCAACA
1 AAAAAACTAAACCAACA
434022 A
1 A
434023 CCTTTATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.20, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAAAACTAAACCAACA
Found at i:435241 original size:50 final size:51
Alignment explanation
Indices: 435178--435294 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
435168 ATTTTCGAGG
* * *
435178 GGATACTCTAACCCCGATTTTA-TTCCAAAAAAATGATTTTCCATAATCGA
1 GGATACTCCAACCCCGATTTTATTTCCAAAAAAATAATTTTCCACAATCGA
*
435228 GGATACTCCAACCCCGATTTTATTTCCAAAAAACTAATTTTCCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTCCAAAAAAATAATTTTCCACAATCGA
435279 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
435295 TTATCTCCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 21 0.34
51 41 0.66
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.28
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAAAAATAATTTTCCACAATCGA
Found at i:435478 original size:132 final size:130
Alignment explanation
Indices: 435228--435503 Score: 329
Period size: 132 Copynumber: 2.1 Consensus size: 130
435218 CCATAATCGA
435228 GGATACTCCAACCCCGATTTTATTTCCAAAAAACTAATTTTCCACAATCGAGGATACTCCAACCC
1 GGATACTCCAACCCCGATTTTATTTCCAAAAAACTAATTTTCCACAATCGAGGATACTCCAACCC
* * *
435293 CGTTATCTCCGAGGGGATACTCCAATCCCAATTTTATTTTTAAAACATTGATTTTCTACCATTAG
66 CGTTATCTCCGAGAGGATACTCCAATCCCAATTTTATTTTCAAAACATCGATTTTCTACCATTAG
* * ** * * * * *
435358 GGATACTCCAACCTCGGTTTTATTTCCAAACCACTGATTTTTTCATAATCGGGGATACTCTAACC
1 GGATACTCCAACCCCGATTTTATTTCCAAAAAACT-AATTTTCCACAATCGAGGATACTCCAACC
** * * ***
435423 TCTTTTATTTCCTAGAGGATACTCCAA-CTCTGGTTTTATTTTCAAAACATCGATTTTCTACCAT
65 -CCGTTATCTCCGAGAGGATACTCCAATC-CCAATTTTATTTTCAAAACATCGATTTTCTACCAT
*
435487 TGG
128 TAG
*
435490 GGATACTCTAACCC
1 GGATACTCCAACCC
435504 TGTTATTTTC
Statistics
Matches: 121, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
130 31 0.26
131 25 0.21
132 65 0.54
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (130 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAAAACTAATTTTCCACAATCGAGGATACTCCAACCC
CGTTATCTCCGAGAGGATACTCCAATCCCAATTTTATTTTCAAAACATCGATTTTCTACCATTAG
Found at i:435718 original size:159 final size:157
Alignment explanation
Indices: 435356--435750 Score: 485
Period size: 160 Copynumber: 2.5 Consensus size: 157
435346 TTCTACCATT
* * * * * *
435356 AGGGATACTCCAACCTCGGTTTTATTTCCAAACCACTGATTTTTTCATAATCGGGGATACTCTAA
1 AGGGATACTCCAACCTCGGTTTTATTTCCAAAACA-TCAATTTTTCACAATTGGGGATACTCCAA
** * *
435421 CCTCTTTTATTTCCTAGAGGATACTCCAACTCTGGTTTTATTTTCAAAACATCGATTTTCTACCA
65 CC-CCGTTATTTCCTAGAGGATACTCCAACCCCGGTTTTATTTTCAAAACATCGATTTTCTACCA
* **
435486 TTGGGGATACTCTAACCCTGTTATTTTCG
129 TTGGGGATACTCCAACCCCATTATTTTCG
* * * *
435515 AGGGGATACTCCAACCTCAGTTTTATTTCCAAAAAAACCTATTTTTCACAATTGGGGATACTCCA
1 A-GGGATACTCCAACCTCGGTTTTATTTCC-AAAACATCAATTTTTCACAATTGGGGATACTCCA
*
435580 ACCCCGTTATTTCCTAG-GGAATGCTCCAACCCCGGTTTTA-TTTCTAAAACATCGATTTTCTAC
64 ACCCCGTTATTTCCTAGAGG-ATACTCCAACCCCGGTTTTATTTTC-AAAACATCGATTTTCTAC
435643 CATTTGGGGATACTCCAACCCCATTATTTTCG
127 CA-TTGGGGATACTCCAACCCCATTATTTTCG
*
435675 AGGGCATACTCCAA-CTCCGGTTTTACTTT-CAAAACATCAA-TTTTCTACCATTGGGGATACTC
1 AGGG-ATACTCCAACCT-CGGTTTTA-TTTCCAAAACATCAATTTTTC-ACAATTGGGGATACTC
435737 CAACCCCGTTATTT
62 CAACCCCGTTATTT
435751 TTGAGGGGGT
Statistics
Matches: 204, Mismatches: 23, Indels: 18
0.83 0.09 0.07
Matches are distributed among these distances:
158 11 0.05
159 91 0.45
160 95 0.47
161 7 0.03
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (157 bp):
AGGGATACTCCAACCTCGGTTTTATTTCCAAAACATCAATTTTTCACAATTGGGGATACTCCAAC
CCCGTTATTTCCTAGAGGATACTCCAACCCCGGTTTTATTTTCAAAACATCGATTTTCTACCATT
GGGGATACTCCAACCCCATTATTTTCG
Found at i:435787 original size:79 final size:79
Alignment explanation
Indices: 435357--435787 Score: 438
Period size: 80 Copynumber: 5.4 Consensus size: 79
435347 TCTACCATTA
* * * ** * *
435357 GGGATACTCCAACCTCGGTTTTATTTCCAAACCA-CTGATTTTTTCATAATCGGGGATACTCTAA
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACATC-GATTTTCT-ACCATTGGGGATACTCCAA
** * *
435421 CCTCTTTTATTTCCTAG
64 CC-CCGTTATTTTCGAG
* * * * *
435438 AGGATACTCCAACTCTGGTTTTATTTTCAAAACATCGATTTTCTACCATTGGGGATACTCTAACC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTACCATTGGGGATACTCCAACC
*
435503 CTGTTATTTTCGAG
66 CCGTTATTTTCGAG
* * * * * *
435517 GGGATACTCCAACCTCAGTTTTATTTCCAAAAAAACCTATTTT-TCACAATTGGGGATACTCCAA
1 GGGATACTCCAACCCCGGTTTTATTTCC-AAAACATCGATTTTCT-ACCATTGGGGATACTCCAA
* *
435581 CCCCGTTATTTCCTAG
64 CCCCGTTATTTTCGAG
* * *
435597 GGAATGCTCCAACCCCGGTTTTATTTCTAAAACATCGATTTTCTACCATTTGGGGATACTCCAAC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTACCA-TTGGGGATACTCCAAC
*
435662 CCCATTATTTTCGAG
65 CCCGTTATTTTCGAG
* * *
435677 GGCATACTCCAACTCCGGTTTTACTTT-CAAAACATCAATTTTCTACCATTGGGGATACTCCAAC
1 GGGATACTCCAACCCCGGTTTTA-TTTCCAAAACATCGATTTTCTACCATTGGGGATACTCCAAC
*
435741 CCCGTTATTTTTGAG
65 CCCGTTATTTTCGAG
* * *
435756 GGGGTACT-CAGACCCCGTTTTTATCTCCAAAA
1 GGGATACTCCA-ACCCCGGTTTTATTTCCAAAA
435788 TATTAAATTT
Statistics
Matches: 291, Mismatches: 51, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
78 4 0.01
79 98 0.34
80 150 0.52
81 38 0.13
82 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (79 bp):
GGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTACCATTGGGGATACTCCAACC
CCGTTATTTTCGAG
Found at i:437839 original size:4 final size:4
Alignment explanation
Indices: 437830--437860 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
437820 TTTTAAGGTG
*
437830 TTTA TTTA TTTA TTTA TTCA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
437861 TGTTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:443131 original size:13 final size:13
Alignment explanation
Indices: 443113--443138 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
443103 CTATTTATGA
443113 TGTATCGATACAC
1 TGTATCGATACAC
443126 TGTATCGATACAC
1 TGTATCGATACAC
443139 ACAAATATGT
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:443261 original size:21 final size:21
Alignment explanation
Indices: 443235--443276 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
443225 CCTATGAAAC
443235 AGTGATGTATCGATACATGAA
1 AGTGATGTATCGATACATGAA
443256 AGTGATGTATCGATACATGAA
1 AGTGATGTATCGATACATGAA
443277 CAGTTATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
AGTGATGTATCGATACATGAA
Found at i:443390 original size:53 final size:53
Alignment explanation
Indices: 443326--443462 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
443316 CTACTTTCAA
443326 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
443379 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
443432 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
443463 TATGCAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:443495 original size:20 final size:20
Alignment explanation
Indices: 443432--443502 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
443422 GCCAATGTCC
**
443432 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
443452 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
443472 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
443492 TGTATCGATAC
1 TGTATCGATAC
443503 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:443566 original size:21 final size:21
Alignment explanation
Indices: 443542--443582 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
443532 GTCAACCTTG
443542 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
443563 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
443583 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:445242 original size:13 final size:13
Alignment explanation
Indices: 445224--445248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
445214 ACTGAAGCAA
445224 TGTATCGATACAT
1 TGTATCGATACAT
445237 TGTATCGATACA
1 TGTATCGATACA
445249 ATCTGGAAAA
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:449028 original size:13 final size:13
Alignment explanation
Indices: 449010--449035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
449000 CTATTTATGA
449010 TGTATCGATACAC
1 TGTATCGATACAC
449023 TGTATCGATACAC
1 TGTATCGATACAC
449036 ACAAATATGT
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:449158 original size:21 final size:21
Alignment explanation
Indices: 449132--449173 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
449122 CCTATGAAAC
449132 AGTGATGTATCGATACATGAA
1 AGTGATGTATCGATACATGAA
449153 AGTGATGTATCGATACATGAA
1 AGTGATGTATCGATACATGAA
449174 CAGTTATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
AGTGATGTATCGATACATGAA
Found at i:449339 original size:20 final size:20
Alignment explanation
Indices: 449276--449346 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
449266 GCCAATGACC
**
449276 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
449296 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
449316 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
449336 TGTATCGATAC
1 TGTATCGATAC
449347 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:452485 original size:22 final size:22
Alignment explanation
Indices: 452460--452501 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
452450 GCTTTGATTA
*
452460 AGGGAGAGATTTTTTAAAGAGT
1 AGGGAGAGAATTTTTAAAGAGT
*
452482 AGGGGGAGAATTTTTAAAGA
1 AGGGAGAGAATTTTTAAAGA
452502 AAGAATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (22 bp):
AGGGAGAGAATTTTTAAAGAGT
Found at i:472416 original size:1 final size:1
Alignment explanation
Indices: 472405--472515 Score: 87
Period size: 1 Copynumber: 111.0 Consensus size: 1
472395 CAAGGTGGGT
* * * * * * * * *
472405 GGGGGGCGGGGGGGGGGCGGGAGGGTGGGGGGGGGCGGGGGGGGGGGGGGCGTGGGGGCGGGGGT
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
* * * * * *
472470 GGCGCGGGGCGGGGGGCGGGGGGGGGGCGGGGGGCGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
472516 CTGGCACAAG
Statistics
Matches: 80, Mismatches: 30, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.01, C:0.10, G:0.86, T:0.03
Consensus pattern (1 bp):
G
Found at i:472436 original size:18 final size:17
Alignment explanation
Indices: 472405--472514 Score: 114
Period size: 18 Copynumber: 5.9 Consensus size: 17
472395 CAAGGTGGGT
472405 GGGGGGCGGGGGGGGGGC
1 GGGGGG-GGGGGGGGGGC
*
472423 GGGAGGGTGGGGGGGGGC
1 GGG-GGGGGGGGGGGGGC
472441 GGGGGGGGGGGGGGCGTG-
1 GGGGGGGGGGGGGG-G-GC
472459 GGGGCGGGGGTGGCGCGGGGC
1 GGGG-GGGGG-GG-G-GGGGC
472480 GGGGGGCGGGGGGGGGGC
1 GGGGGG-GGGGGGGGGGC
472498 GGGGGGCGGGGGGGGGG
1 GGGGGG-GGGGGGGGGG
472515 GCTGGCACAA
Statistics
Matches: 81, Mismatches: 2, Indels: 18
0.80 0.02 0.18
Matches are distributed among these distances:
17 10 0.12
18 43 0.53
19 10 0.12
20 7 0.09
21 9 0.11
22 2 0.02
ACGTcount: A:0.01, C:0.10, G:0.86, T:0.03
Consensus pattern (17 bp):
GGGGGGGGGGGGGGGGC
Found at i:474661 original size:32 final size:32
Alignment explanation
Indices: 474620--474682 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
474610 TTTCACTGTT
*
474620 CATCACTATTCATCACTGTTCATGTATCGATA
1 CATCACTATTCATCACCGTTCATGTATCGATA
474652 CATCACTATTCATCACCGTTCATGTATCGAT
1 CATCACTATTCATCACCGTTCATGTATCGAT
474683 GTATTATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (32 bp):
CATCACTATTCATCACCGTTCATGTATCGATA
Found at i:476361 original size:13 final size:13
Alignment explanation
Indices: 476338--476379 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
476328 AAATAGTACC
*
476338 CAATATATCGATA
1 CAATGTATCGATA
*
476351 CAGTGTATCGATA
1 CAATGTATCGATA
*
476364 CAATGTATTGATA
1 CAATGTATCGATA
476377 CAA
1 CAA
476380 GGAATATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:478280 original size:724 final size:724
Alignment explanation
Indices: 476894--478343 Score: 2828
Period size: 724 Copynumber: 2.0 Consensus size: 724
476884 ATTCTATTAC
476894 AACATCCCCTTTTTGCACATGATGTCTAATAAAGTGATGTCTAATTTCAATGTGCTTAGTCCTAG
1 AACATCCCCTTTTTGCACATGATGTCTAATAAAGTGATGTCTAATTTCAATGTGCTTAGTCCTAG
*
476959 AATGTTGTACCGGATTTTTAGTGAGACAAATTGCACTAGCATTGTCACATTTAATAGGAATATGA
66 AATGTTGTACCGAATTTTTAGTGAGACAAATTGCACTAGCATTGTCACATTTAATAGGAATATGA
477024 TCTATGGTATTGCCAAAATCCTCTAATAGTTGTTTTATCCACAATACTTGTGCACAACAACTACC
131 TCTATGGTATTGCCAAAATCCTCTAATAGTTGTTTTATCCACAATACTTGTGCACAACAACTACC
477089 TACGGATATGTATTTCGCTTCGGTTGTGGATAAAGCAACACTATTTTGTTTCTTAAAAAACCATG
196 TACGGATATGTATTTCGCTTCGGTTGTGGATAAAGCAACACTATTTTGTTTCTTAAAAAACCATG
477154 ATATGAGCATAGTTTCAAAGAATTGACAAGTACTAGAAGTGCTCTTTCTATCTATTTTACAACCA
261 ATATGAGCATAGTTTCAAAGAATTGACAAGTACTAGAAGTGCTCTTTCTATCTATTTTACAACCA
*
477219 CCAAAATCCGCATCCGAGTAAGCATGTAAAGCTAGGGAGGATTCTTTAGGGTACCATAAACCTAG
326 CCAAAATCCACATCCGAGTAAGCATGTAAAGCTAGGGAGGATTCTTTAGGGTACCATAAACCTAG
*
477284 ATTTGGAGTGTCTCGTAAATATCTAAAAATTCTTTTTACGGCAAGTAAATGAGACTCCCTAGGTG
391 ATTTGGAGTGTCTCGTAAATATCTAAAAATTCTTTTTACGGCAAGTAAATGAGACACCCTAGGTG
477349 CAGATTGAAAACGGGCACATAGGCATACACTAAACATAATATCCGGTCTACTAGCAGTAAGATAT
456 CAGATTGAAAACGGGCACATAGGCATACACTAAACATAATATCCGGTCTACTAGCAGTAAGATAT
477414 AACAATGAACCAATTATAGACCTATAGAGTTTAGTGTCGATAATGTTACCTCCTTCATCCTTTTC
521 AACAATGAACCAATTATAGACCTATAGAGTTTAGTGTCGATAATGTTACCTCCTTCATCCTTTTC
477479 AAGCTTTGTTGAAGTACTCATAAGAGTTTCACATGGTTTGACTTGATCCATTTGAAATCTTTTGA
586 AAGCTTTGTTGAAGTACTCATAAGAGTTTCACATGGTTTGACTTGATCCATTTGAAATCTTTTGA
477544 GTAGCTCCTTTGTGTATTTCACTTAATTGATGAAGATCCCGTCTTTTGTTTGCTTCAGTTGAAGT
651 GTAGCTCCTTTGTGTATTTCACTTAATTGATGAAGATCCCGTCTTTTGTTTGCTTCAGTTGAAGT
477609 CCTAAAAAG
716 CCTAAAAAG
477618 AACATCCCCTTTTTGCACATGATGTCTAATAAAGTGATGTCTAATTTCAATGTGCTTAGTCCTAG
1 AACATCCCCTTTTTGCACATGATGTCTAATAAAGTGATGTCTAATTTCAATGTGCTTAGTCCTAG
477683 AATGTTGTACCGAATTTTTAGTGAGACAAATTGCACTAGCATTGTCACATTTAATAGGAATATGA
66 AATGTTGTACCGAATTTTTAGTGAGACAAATTGCACTAGCATTGTCACATTTAATAGGAATATGA
*
477748 TCTATGGTATTGCCAAAATCCTCTAATTGTTGTTTTATCCACAATACTTGTGCACAACAACTACC
131 TCTATGGTATTGCCAAAATCCTCTAATAGTTGTTTTATCCACAATACTTGTGCACAACAACTACC
*
477813 TACGGATATGTATTTCGCTTCGGTTGTGGATAAAGCAACACTATTTTGTTTCTTGAAAAACCATG
196 TACGGATATGTATTTCGCTTCGGTTGTGGATAAAGCAACACTATTTTGTTTCTTAAAAAACCATG
477878 ATATGAGCATAGTTTCAAAGAATTGACAAGTACTAGAAGTGCTCTTTCTATCTATTTTACAACCA
261 ATATGAGCATAGTTTCAAAGAATTGACAAGTACTAGAAGTGCTCTTTCTATCTATTTTACAACCA
477943 CCAAAATCCACATCCGAGTAAGCATGTAAAGCTAGGGAGGATTCTTTAGGGTACCATAAACCTAG
326 CCAAAATCCACATCCGAGTAAGCATGTAAAGCTAGGGAGGATTCTTTAGGGTACCATAAACCTAG
*
478008 GTTTGGAGTGTCTCGTAAATATCTAAAAATTCTTTTTACGGCAAGTAAATGAGACACCCTAGGTG
391 ATTTGGAGTGTCTCGTAAATATCTAAAAATTCTTTTTACGGCAAGTAAATGAGACACCCTAGGTG
*
478073 CGGATTGAAAACGGGCACATAGGCATACACTAAACATAATATCCGGTCTACTAGCAGTAAGATAT
456 CAGATTGAAAACGGGCACATAGGCATACACTAAACATAATATCCGGTCTACTAGCAGTAAGATAT
478138 AACAATGAACCAATTATAGACCTATAGAGTTTAGTGTCGATAATGTTACCTCCTTCATCCTTTTC
521 AACAATGAACCAATTATAGACCTATAGAGTTTAGTGTCGATAATGTTACCTCCTTCATCCTTTTC
*
478203 AAGCTTTGTTGAAGTACTCATCAGAGTTTCACATGGTTTGACTTGATCCATTTGAAATCTTTTGA
586 AAGCTTTGTTGAAGTACTCATAAGAGTTTCACATGGTTTGACTTGATCCATTTGAAATCTTTTGA
478268 GTAGCTCCTTTGTGTATTTCACTTAATTGATGAAGATCCCGTCTTTTGTTTGCTTCAGTTGAAGT
651 GTAGCTCCTTTGTGTATTTCACTTAATTGATGAAGATCCCGTCTTTTGTTTGCTTCAGTTGAAGT
478333 CCTAAAAAG
716 CCTAAAAAG
478342 AA
1 AA
478344 TGCTAATTCT
Statistics
Matches: 718, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
724 718 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (724 bp):
AACATCCCCTTTTTGCACATGATGTCTAATAAAGTGATGTCTAATTTCAATGTGCTTAGTCCTAG
AATGTTGTACCGAATTTTTAGTGAGACAAATTGCACTAGCATTGTCACATTTAATAGGAATATGA
TCTATGGTATTGCCAAAATCCTCTAATAGTTGTTTTATCCACAATACTTGTGCACAACAACTACC
TACGGATATGTATTTCGCTTCGGTTGTGGATAAAGCAACACTATTTTGTTTCTTAAAAAACCATG
ATATGAGCATAGTTTCAAAGAATTGACAAGTACTAGAAGTGCTCTTTCTATCTATTTTACAACCA
CCAAAATCCACATCCGAGTAAGCATGTAAAGCTAGGGAGGATTCTTTAGGGTACCATAAACCTAG
ATTTGGAGTGTCTCGTAAATATCTAAAAATTCTTTTTACGGCAAGTAAATGAGACACCCTAGGTG
CAGATTGAAAACGGGCACATAGGCATACACTAAACATAATATCCGGTCTACTAGCAGTAAGATAT
AACAATGAACCAATTATAGACCTATAGAGTTTAGTGTCGATAATGTTACCTCCTTCATCCTTTTC
AAGCTTTGTTGAAGTACTCATAAGAGTTTCACATGGTTTGACTTGATCCATTTGAAATCTTTTGA
GTAGCTCCTTTGTGTATTTCACTTAATTGATGAAGATCCCGTCTTTTGTTTGCTTCAGTTGAAGT
CCTAAAAAG
Found at i:484175 original size:76 final size:76
Alignment explanation
Indices: 484093--484362 Score: 350
Period size: 76 Copynumber: 3.6 Consensus size: 76
484083 TGGAGAAGAT
* **
484093 GAACATAGTGGAGAATATATGGTTTCTAAAATTTTTATCAACAATAAAAACCAACTGATAACAGG
1 GAACATAGTGGAGAATATATGATTTCTAAAATTTCCATCAACAATAAAAACCAACTGATAACAGG
484158 TTGAAGGAAAG
66 TTGAAGGAAAG
* **
484169 GAACATAGTGGAGAATATATGGTTTCTAAAATTTTTATCAACAATAAAAACCAACTGATAACAGG
1 GAACATAGTGGAGAATATATGATTTCTAAAATTTCCATCAACAATAAAAACCAACTGATAACAGG
484234 TTGAAGGAAAG
66 TTGAAGGAAAG
* * * * * * *
484245 GAACATA-TGGGGAATATATGATTTCTAAAGTTTCCCTTAACAACT-GAAACAAACTGATAACAT
1 GAACATAGTGGAGAATATATGATTTCTAAAATTTCCATCAACAA-TAAAAACCAACTGATAACAG
*
484308 GCTGAAGGAAAG
65 GTTGAAGGAAAG
*
484320 GAACAT-GAT-GAGGAATATGTGATTTCTAAAATTTCCATCAACA
1 GAACATAG-TGGA-GAATATATGATTTCTAAAATTTCCATCAACA
484363 GCCAAAGCAA
Statistics
Matches: 174, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
75 62 0.36
76 112 0.64
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (76 bp):
GAACATAGTGGAGAATATATGATTTCTAAAATTTCCATCAACAATAAAAACCAACTGATAACAGG
TTGAAGGAAAG
Found at i:484287 original size:151 final size:151
Alignment explanation
Indices: 484093--484416 Score: 350
Period size: 151 Copynumber: 2.1 Consensus size: 151
484083 TGGAGAAGAT
* * ** *
484093 GAACATAGTGGAGAATATATGGTTTCTAAAATTTTTATCAACAA-TAAAAACCAACTGATAACAG
1 GAACATA-TGGGGAATATATGATTTCTAAAATTTCCATCAACAACT-AAAACAAACTGATAACAG
* * ** *
484157 GTTGAAGGAAAGGAACAT-AGTG-GAGAATATATGGTTTCTAAAATTTTTATCAACAATAAAAAC
64 GCTGAAGGAAAGGAACATGA-TGAG-GAATATATGATTTCTAAAATTTCCATCAAC-AGAAAAAC
* *
484220 CAA-CTGATAACAGGTTGAAGGAAAG
126 CAAGCTGATAACAGGCTAAAGGAAAG
* * * * *
484245 GAACATATGGGGAATATATGATTTCTAAAGTTTCCCTTAACAACTGAAACAAACTGATAACATGC
1 GAACATATGGGGAATATATGATTTCTAAAATTTCCATCAACAACTAAAACAAACTGATAACAGGC
* ** * *
484310 TGAAGGAAAGGAACATGATGAGGAATATGTGATTTCTAAAATTTCCATCAACAGCCAAAGCAAGT
66 TGAAGGAAAGGAACATGATGAGGAATATATGATTTCTAAAATTTCCATCAACAGAAAAACCAAGC
* *
484375 TGATAACAGGCTAAAGGCAAT
131 TGATAACAGGCTAAAGGAAAG
484396 GAACATGATGGGGAATATATG
1 GAACAT-ATGGGGAATATATG
484417 GTTCTGTAAT
Statistics
Matches: 143, Mismatches: 24, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
150 7 0.05
151 112 0.78
152 24 0.17
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (151 bp):
GAACATATGGGGAATATATGATTTCTAAAATTTCCATCAACAACTAAAACAAACTGATAACAGGC
TGAAGGAAAGGAACATGATGAGGAATATATGATTTCTAAAATTTCCATCAACAGAAAAACCAAGC
TGATAACAGGCTAAAGGAAAG
Found at i:484304 original size:75 final size:76
Alignment explanation
Indices: 484105--484416 Score: 335
Period size: 76 Copynumber: 4.1 Consensus size: 76
484095 ACATAGTGGA
* ** * *
484105 GAATATATGGTTTCTAAAATTTTTATCAACAA-TAAAAACCAACTGATAACAGGTTGAAGGAAAG
1 GAATATATGATTTCTAAAATTTCCATCAACAACT-AAAACAAACTGATAACAGGCTGAAGGAAAG
*
484169 GAACAT-AGTGGA
65 GAACATGA-TGGG
* ** * *
484181 GAATATATGGTTTCTAAAATTTTTATCAACAA-TAAAAACCAACTGATAACAGGTTGAAGGAAAG
1 GAATATATGATTTCTAAAATTTCCATCAACAACT-AAAACAAACTGATAACAGGCTGAAGGAAAG
484245 GAACAT-ATGGG
65 GAACATGATGGG
* * * * *
484256 GAATATATGATTTCTAAAGTTTCCCTTAACAACTGAAACAAACTGATAACATGCTGAAGGAAAGG
1 GAATATATGATTTCTAAAATTTCCATCAACAACTAAAACAAACTGATAACAGGCTGAAGGAAAGG
*
484321 AACATGATGAG
66 AACATGATGGG
* * * * ** * * *
484332 GAATATGTGATTTCTAAAATTTCCATCAACAGCCAAAGCAAGTTGATAACAGGCTAAAGGCAATG
1 GAATATATGATTTCTAAAATTTCCATCAACAACTAAAACAAACTGATAACAGGCTGAAGGAAAGG
484397 AACATGATGGG
66 AACATGATGGG
484408 GAATATATG
1 GAATATATG
484417 GTTCTGTAAT
Statistics
Matches: 206, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
75 61 0.30
76 145 0.70
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (76 bp):
GAATATATGATTTCTAAAATTTCCATCAACAACTAAAACAAACTGATAACAGGCTGAAGGAAAGG
AACATGATGGG
Found at i:485879 original size:17 final size:17
Alignment explanation
Indices: 485857--485891 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
485847 AAAGAGAGGG
485857 AAAAAACTAGACCAACA
1 AAAAAACTAGACCAACA
485874 AAAAAACTAGACCAACA
1 AAAAAACTAGACCAACA
485891 A
1 A
485892 CCTTTATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.23, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAAACTAGACCAACA
Found at i:487108 original size:50 final size:51
Alignment explanation
Indices: 487043--487161 Score: 186
Period size: 51 Copynumber: 2.4 Consensus size: 51
487033 TTATTTCCGA
* * *
487043 GGGGATACTCTAACCCCGATTTTATT-CCAAAAAAATGATTTTCCATAATC
1 GGGGATACTCCAACCCCGATTTTATTCCCAAAAAAATAATTTTCCACAATC
*
487093 GGGGATACTCCAACCCCGATTTTATTCCCAAAAAACTAATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTCCCAAAAAAATAATTTTCCACAATC
*
487144 GAGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
487162 TTATCTCCGA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
50 25 0.40
51 38 0.60
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTCCCAAAAAAATAATTTTCCACAATC
Found at i:487346 original size:132 final size:130
Alignment explanation
Indices: 487094--487370 Score: 313
Period size: 132 Copynumber: 2.1 Consensus size: 130
487084 TCCATAATCG
487094 GGGATACTCCAACCCCGATTTTATTCCCAAAAAACTAATTTTCCACAATCGAGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTCCCAAAAAACTAATTTTCCACAATCGAGGATACTCCAACC
* * * *
487159 CCGTTATCTCCGAGGGGATACTCCAATCCCAATTTTATTTTTAAAAGATTGATTTTCTACCATTA
66 CCGTTATCTCCGAGAGGATACTCCAATCCCAATTTTATTTTCAAAACATCGATTTTCTACCATTA
* * * ** * * * * *
487224 GGGATACTCCAACCTCGGTTTTATTTCCAAACCACTGATTTTTTCATAATCGGGGATACTCTAAC
1 GGGATACTCCAACCCCGATTTTATTCCCAAAAAACT-AATTTTCCACAATCGAGGATACTCCAAC
** * * ***
487289 CTCTTTTATTTCCTAGAGGATACTCCAA-CTCTGGTTTTATTTTCAAAACATCGATTTTCTACCA
65 C-CCGTTATCTCCGAGAGGATACTCCAATC-CCAATTTTATTTTCAAAACATCGATTTTCTACCA
*
487353 TTG
128 TTA
*
487356 GGGATACTCTAACCC
1 GGGATACTCCAACCC
487371 TGTTATTTTC
Statistics
Matches: 120, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
130 31 0.26
131 25 0.21
132 64 0.53
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (130 bp):
GGGATACTCCAACCCCGATTTTATTCCCAAAAAACTAATTTTCCACAATCGAGGATACTCCAACC
CCGTTATCTCCGAGAGGATACTCCAATCCCAATTTTATTTTCAAAACATCGATTTTCTACCATTA
Found at i:487408 original size:160 final size:160
Alignment explanation
Indices: 487224--487617 Score: 480
Period size: 160 Copynumber: 2.5 Consensus size: 160
487214 TCTACCATTA
** *
487224 GGGATACTCCAACCTCGGTTTTATTTCC-AAACCA-CTGATTTTTTCATAATCGGGGATACTCTA
1 GGGATACTCCAACCTCGGTTTTATTTCCAAAAAAACCT-A-TTTTTCACAATCGGGGATACTCTA
** * * *
487287 ACCTCTTTTATTTCCTAGAGG-ATACTCCAACTCTGGTTTTATTTTCAAAACATCGATTTTCTAC
64 ACC-CCGTTATTTCCTAG-GGAATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTAC
* **
487351 CA-TTGGGGATACTCTAACCCTGTTATTTTCGAG
127 CATTTGGGGATACTCCAACCCCATTATTTTCGAG
*
487384 GGGATACTCCAACCTCGGTTTTATTTCCAAAAAAACCTATTTTTCACAATTGGGGATACTCTAAC
1 GGGATACTCCAACCTCGGTTTTATTTCCAAAAAAACCTATTTTTCACAATCGGGGATACTCTAAC
*
487449 CCCGTTATTTCCTAGGGAATGCTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTACCATT
66 CCCGTTATTTCCTAGGGAATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTACCATT
487514 TGGGGATACTCCAACCCCATTATTTTCGAG
131 TGGGGATACTCCAACCCCATTATTTTCGAG
* * * * * * * *
487544 GGCATACTCCAA-CTCCGATTTTACTTT-C-AAAACATC-AATTTTCTACCATTGGGGATACTCC
1 GGGATACTCCAACCT-CGGTTTTA-TTTCCAAAAAAACCTATTTTTC-ACAATCGGGGATACTCT
487605 AACCCCGTTATTT
63 AACCCCGTTATTT
487618 TTGAGGGGTA
Statistics
Matches: 207, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
158 8 0.04
159 89 0.43
160 100 0.48
161 8 0.04
162 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (160 bp):
GGGATACTCCAACCTCGGTTTTATTTCCAAAAAAACCTATTTTTCACAATCGGGGATACTCTAAC
CCCGTTATTTCCTAGGGAATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTACCATT
TGGGGATACTCCAACCCCATTATTTTCGAG
Found at i:487440 original size:80 final size:79
Alignment explanation
Indices: 487224--487653 Score: 433
Period size: 80 Copynumber: 5.4 Consensus size: 79
487214 TCTACCATTA
* * * *
487224 GGGATACTCCAACCTCGGTTTTATTTCCAAACCA-CTGATTTTTTCATAATCGGGGATACTCTAA
1 GGGATACTCCAACCTCGGTTTTATTTCCAAAACATC-GATTTTCT-ACAATTGGGGATACTCTAA
** * *
487288 CCTCTTTTATTTCCTAG
64 CC-CCGTTATTTTCGAG
* * *
487305 AGGATACTCCAA-CTCTGGTTTTATTTTCAAAACATCGATTTTCTACCATTGGGGATACTCTAAC
1 GGGATACTCCAACCTC-GGTTTTATTTCCAAAACATCGATTTTCTACAATTGGGGATACTCTAAC
*
487369 CCTGTTATTTTCGAG
65 CCCGTTATTTTCGAG
* * *
487384 GGGATACTCCAACCTCGGTTTTATTTCCAAAAAAACCTATTTT-TCACAATTGGGGATACTCTAA
1 GGGATACTCCAACCTCGGTTTTATTTCC-AAAACATCGATTTTCT-ACAATTGGGGATACTCTAA
* *
487448 CCCCGTTATTTCCTAG
64 CCCCGTTATTTTCGAG
* * * * *
487464 GGAATGCTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTACCATTTGGGGATACTCCAAC
1 GGGATACTCCAACCTCGGTTTTATTTCCAAAACATCGATTTTCTA-CAATTGGGGATACTCTAAC
*
487529 CCCATTATTTTCGAG
65 CCCGTTATTTTCGAG
* * * * *
487544 GGCATACTCCAA-CTCCGATTTTACTTT-CAAAACATCAATTTTCTACCATTGGGGATACTCCAA
1 GGGATACTCCAACCT-CGGTTTTA-TTTCCAAAACATCGATTTTCTACAATTGGGGATACTCTAA
*
487607 CCCCGTTATTTTTGAG
64 CCCCGTTATTTTCGAG
* * *
487623 GGG-TACT-CAGACCCCGTTTTTATCTCCAAAA
1 GGGATACTCCA-ACCTCGGTTTTATTTCCAAAA
487654 TATTAAATTT
Statistics
Matches: 294, Mismatches: 43, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
77 4 0.01
78 17 0.06
79 80 0.27
80 155 0.53
81 37 0.13
82 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (79 bp):
GGGATACTCCAACCTCGGTTTTATTTCCAAAACATCGATTTTCTACAATTGGGGATACTCTAACC
CCGTTATTTTCGAG
Found at i:487664 original size:159 final size:159
Alignment explanation
Indices: 487223--487664 Score: 418
Period size: 159 Copynumber: 2.8 Consensus size: 159
487213 TTCTACCATT
* ** * * * * *
487223 AGGG-ATACTCCAACCTCGGTTTTATTTCC-AAACCACTGATTTTTTCATAATCGGGGATACTCT
1 AGGGCATACTCCAACCTCGATTTTATTTCCAAAAAAAC-CAATTTTTCACAATTGGGGATACTCC
** * * * * **
487286 AACCTCTTTTATTTCCTAGAGG-ATACTCCAACTCTGGTTTTATTTTCAAAACATCGATTTTCTA
65 AACC-CCGTTATTTCCTAG-GGAATACTCCAACCCCGGTTTTATCTCCAAAACATAAATTTTCTA
* **
487350 CCATTGGGGATACTCTAACCCTGTTATTTTCG
128 CCATTGGGGATACTCCAACCCCATTATTTTCG
* * * *
487382 AGGGGATACTCCAACCTCGGTTTTATTTCCAAAAAAACCTATTTTTCACAATTGGGGATACTCTA
1 AGGGCATACTCCAACCTCGATTTTATTTCCAAAAAAACCAATTTTTCACAATTGGGGATACTCCA
* * **
487447 ACCCCGTTATTTCCTAGGGAATGCTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTACCA
66 ACCCCGTTATTTCCTAGGGAATACTCCAACCCCGGTTTTATCTCCAAAACATAAATTTTCTACCA
487512 TTTGGGGATACTCCAACCCCATTATTTTCG
131 -TTGGGGATACTCCAACCCCATTATTTTCG
* * *
487542 AGGGCATACTCCAA-CTCCGATTTTACTTT-C-AAAACATCAA-TTTTCTACCATTGGGGATACT
1 AGGGCATACTCCAACCT-CGATTTTA-TTTCCAAAAAAACCAATTTTTC-ACAATTGGGGATACT
* * * *
487603 CCAACCCCGTTATTT-TTGAGGG-GTACT-CAGACCCCGTTTTTATCTCCAAAATATTAAATTTT
63 CCAACCCCGTTATTTCCT-AGGGAATACTCCA-ACCCCGGTTTTATCTCCAAAACA-TAAATTTT
487665 TCATCAAGAG
Statistics
Matches: 242, Mismatches: 31, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
157 2 0.01
158 31 0.13
159 104 0.43
160 97 0.40
161 8 0.03
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (159 bp):
AGGGCATACTCCAACCTCGATTTTATTTCCAAAAAAACCAATTTTTCACAATTGGGGATACTCCA
ACCCCGTTATTTCCTAGGGAATACTCCAACCCCGGTTTTATCTCCAAAACATAAATTTTCTACCA
TTGGGGATACTCCAACCCCATTATTTTCG
Found at i:489687 original size:4 final size:4
Alignment explanation
Indices: 489678--489708 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
489668 TTTTAAGGTG
*
489678 TTTA TTTA TTTA TTTA TTCA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
489709 TGTTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:496817 original size:10 final size:10
Alignment explanation
Indices: 496802--496864 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
496792 ACATCGATAC
*
496802 ATGAACGGTG
1 ATGAACAGTG
496812 ATGAACAGTG
1 ATGAACAGTG
* *
496822 ATGTATC-GATAC
1 ATG-AACAG-T-G
496834 ATGAACAGTG
1 ATGAACAGTG
*
496844 ATGAATAGTG
1 ATGAACAGTG
496854 ATGAACAGTG
1 ATGAACAGTG
496864 A
1 A
496865 AAATGAGATT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
10 32 0.76
11 6 0.14
12 4 0.10
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.24
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:496835 original size:32 final size:32
Alignment explanation
Indices: 496794--496856 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
496784 TTCATAATAC
*
496794 ATCGATACATGAACGGTGATGAACAGTGATGT
1 ATCGATACATGAACAGTGATGAACAGTGATGT
*
496826 ATCGATACATGAACAGTGATGAATAGTGATG
1 ATCGATACATGAACAGTGATGAACAGTGATG
496857 AACAGTGAAA
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:0.11, G:0.27, T:0.25
Consensus pattern (32 bp):
ATCGATACATGAACAGTGATGAACAGTGATGT
Found at i:500143 original size:52 final size:51
Alignment explanation
Indices: 500063--500181 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 51
500053 AAAAGTTGCT
*
500063 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
500115 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
500166 TGCATGTATCGATACA
1 TGCATGTATCGATACA
500182 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 20 0.31
52 44 0.69
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:500208 original size:13 final size:13
Alignment explanation
Indices: 500190--500214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
500180 CAAAGATCAG
500190 TGTATCGATACAA
1 TGTATCGATACAA
500203 TGTATCGATACA
1 TGTATCGATACA
500215 TTTGAGTAAT
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:500292 original size:33 final size:33
Alignment explanation
Indices: 500255--500321 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
500245 AGTAGCTTAA
500255 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
500288 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
500321 A
1 A
500322 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:500295 original size:13 final size:13
Alignment explanation
Indices: 500277--500301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
500267 CAAAAAAATA
500277 TGTATCGATACAT
1 TGTATCGATACAT
500290 TGTATCGATACA
1 TGTATCGATACA
500302 ACATTTTATG
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:504900 original size:12 final size:11
Alignment explanation
Indices: 504866--504923 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
504856 ACATTCCTTT
*
504866 AAAAAAAACAA
1 AAAAAAAAGAA
*
504877 AACACAAAA-AA
1 AA-AAAAAAGAA
*
504888 AAACAAAAGAA
1 AAAAAAAAGAA
504899 AACAAAAAAGAA
1 AA-AAAAAAGAA
504911 AAAAAAAAGAA
1 AAAAAAAAGAA
504922 AA
1 AA
504924 GAACCTGCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 6 0.14
11 21 0.50
12 15 0.36
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:504900 original size:28 final size:29
Alignment explanation
Indices: 504869--504926 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
504859 TTCCTTTAAA
* *
504869 AAAAACAAAACA-CAAAAAAAAACAAAAG
1 AAAAACAAAAAAGAAAAAAAAAACAAAAG
*
504897 -AAAACAAAAAAGAAAAAAAAAAGAAAAG
1 AAAAACAAAAAAGAAAAAAAAAACAAAAG
504925 AA
1 AA
504927 CCTGCTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 10 0.40
28 14 0.56
29 1 0.04
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (29 bp):
AAAAACAAAAAAGAAAAAAAAAACAAAAG
Found at i:504905 original size:17 final size:15
Alignment explanation
Indices: 504866--504923 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 15
504856 ACATTCCTTT
504866 AAAAAAAACAAAACACA
1 AAAAAAAACAAAA-A-A
504883 AAAAAAAACAAAAGAA
1 AAAAAAAACAAAA-AA
*
504899 AACAAAAAAGAAAAAA
1 AA-AAAAAACAAAAAA
504915 AAAAGAAAA
1 AAAA-AAAA
504924 GAACCTGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
15 2 0.05
16 11 0.30
17 24 0.65
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (15 bp):
AAAAAAAACAAAAAA
Found at i:505996 original size:61 final size:60
Alignment explanation
Indices: 505897--506470 Score: 808
Period size: 61 Copynumber: 9.4 Consensus size: 60
505887 AAACTTTTAT
* * *
505897 CCTTTTAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAAAGCAGGACA-CCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* **
505958 CCTTTCAGTCCTCAAAAAGTAGGATGCCTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAAAGCAGGACACCTTTCC-TTTTAAAGCCCACACAAGTTGGTGGCA
* *
506019 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTTCAGTCCTCAAAAAGCAGGACACC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
506080 CCTTTCAGTCCTTAAAAAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTTCAGTCCTCAAAAAGCAGGACACC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* ** ** *
506141 CCTTTTAGTCCTCAAAAAATAGGATGCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAAAGCAGGACACCTTTCC-TTTTAAAGCCCACACAAGTTGGTGGCA
* *
506202 CCTTTCAGTCCTCAAAGAGCAGGACACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAAAGCAGGACAC-CTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
506263 CCTTTCAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTTCAGTCCTCAAAAAGCAGGACACC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
506324 CCTTTCAGTCCTCAAAGAGCAGGAC-CTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAAAGCAGGACAC-C-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
506385 CCTTTCAGTCCCCAAAAAGCAAGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTA
1 CCTTTCAGTCCTCAAAAAGCAGGACAC-CTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
506446 CCTTCCAGTCCTCAAAGAGCAGGAC
1 CCTTTCAGTCCTCAAAAAGCAGGAC
506471 GCATTTTATT
Statistics
Matches: 465, Mismatches: 41, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
60 12 0.03
61 440 0.95
62 13 0.03
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (60 bp):
CCTTTCAGTCCTCAAAAAGCAGGACACCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:506222 original size:183 final size:183
Alignment explanation
Indices: 505897--506470 Score: 936
Period size: 183 Copynumber: 3.1 Consensus size: 183
505887 AAACTTTTAT
* * * *
505897 CCTTTTAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 CCTTTCAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
*
505962 TCAGTCCTCAAAAAGTAGGATGCCTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAG
66 TCAGTCCTCAAAAAGTAGGATGCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAG
* *
506027 TCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCA
131 TCCTCAAAGAGCAGGACACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
506080 CCTTTCAGTCCTTAAAAAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
1 CCTTTCAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
* *
506145 TTAGTCCTCAAAAAATAGGATGCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAG
66 TCAGTCCTCAAAAAGTAGGATGCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAG
506210 TCCTCAAAGAGCAGGACACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
131 TCCTCAAAGAGCAGGACACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
506263 CCTTTCAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
1 CCTTTCAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
* *
506328 TCAGTCCTCAAAGAGCAGGACCT-CTTTTCC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
66 TCAGTCCTCAAAAAGTAGGA--TGCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
506391 AGTCCCCAAAAAGCAAGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTA
129 AGTCCTCAAAGAGCAGGACACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
506446 CCTTCCAGTCCTCAAAGAGCAGGAC
1 CCTTTCAGTCCTCAAAAAGCAGGAC
506471 GCATTTTATT
Statistics
Matches: 365, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
183 357 0.98
184 7 0.02
185 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (183 bp):
CCTTTCAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
TCAGTCCTCAAAAAGTAGGATGCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAG
TCCTCAAAGAGCAGGACACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:509525 original size:50 final size:50
Alignment explanation
Indices: 509420--509535 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 50
509410 TTTCCGAAGG
* * * * *
509420 GATACTCTAATCCCCGGTTTTATTCCAAAAAAATGATTTTCCATAAACAGG
1 GATACTCCAA-CCCCGGTTGTATTCCAAAAAAATAATTTTCCACAAACAGA
* * *
509471 GATACTCCAACCCCGGTTGTATTCCAAAAAACTAATTTTTCACAATC-GAA
1 GATACTCCAACCCCGGTTGTATTCCAAAAAAATAATTTTCCACAAACAG-A
*
509521 GATACTTCAACCCCG
1 GATACTCCAACCCCG
509536 TTATCTATGA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
49 1 0.02
50 45 0.82
51 9 0.16
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (50 bp):
GATACTCCAACCCCGGTTGTATTCCAAAAAAATAATTTTCCACAAACAGA
Done.