Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007218.1 Corchorus capsularis cultivar CVL-1 contig07239, whole genome shotgun sequence
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: 159756
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1518 original size:22 final size:22
Alignment explanation
Indices: 1493--1735 Score: 104
Period size: 22 Copynumber: 11.1 Consensus size: 22
1483 TTCCAACATA
*
1493 GAAATATTGATAACCACACTGT
1 GAAATATTGATAACCACACTAT
* * *
1515 GAAA-ATTTAATAACCTCATTAT
1 GAAATA-TTGATAACCACACTAT
* * *
1537 GATAT-TTCAATAACCTAC-CTGT
1 GAAATATT-GATAACC-ACACTAT
* * *
1559 GAAA-ATTTGATAATCATACTGT
1 GAAATA-TTGATAACCACACTAT
* *
1581 GAAATTTTGATAAACACACTAT
1 GAAATATTGATAACCACACTAT
* ** * *
1603 GAAATTTTGATAACTTCAGTGT
1 GAAATATTGATAACCACACTAT
* * * *
1625 GAAATTTTGATAATCTCCCTAT
1 GAAATATTGATAACCACACTAT
* *
1647 GAAATTTTGATAATCACACTAT
1 GAAATATTGATAACCACACTAT
* **
1669 -AAA-ATTGGTAACTGCACTAT
1 GAAATATTGATAACCACACTAT
*
1689 GAAA-ACTTTGATAACCACACCAT
1 GAAATA--TTGATAACCACACTAT
* * * *
1712 AAAATTTTGATAACCTCCCTAT
1 GAAATATTGATAACCACACTAT
1734 GA
1 GA
1736 GAATGAAACT
Statistics
Matches: 166, Mismatches: 43, Indels: 24
0.71 0.18 0.10
Matches are distributed among these distances:
20 12 0.07
21 11 0.07
22 125 0.75
23 18 0.11
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
GAAATATTGATAACCACACTAT
Found at i:1604 original size:66 final size:66
Alignment explanation
Indices: 1494--1674 Score: 168
Period size: 66 Copynumber: 2.7 Consensus size: 66
1484 TCCAACATAG
* * * * * * * *
1494 AAATATTGATAACCACACTGTGAAAATTTAATAACCTCATTATGATATTTCAATAACCTAC-CTG
1 AAAT-TTGATAATCATACTGTGAAATTTTGATAAACACACTATGAAATTTCAATAA-CTACACTG
1558 TGA
64 TGA
** * *
1561 AAATTTGATAATCATACTGTGAAATTTTGATAAACACACTATGAAATTTTGATAACTTCAGTGTG
1 AAATTTGATAATCATACTGTGAAATTTTGATAAACACACTATGAAATTTCAATAACTACACTGTG
1626 A
66 A
* * * * *
1627 AATTTTGATAATC-TCCCTATGAAATTTTGATAATCACACTATAAAATT
1 AAATTTGATAATCAT-ACTGTGAAATTTTGATAAACACACTATGAAATT
1675 GGTAACTGCA
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
65 4 0.04
66 87 0.92
67 4 0.04
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (66 bp):
AAATTTGATAATCATACTGTGAAATTTTGATAAACACACTATGAAATTTCAATAACTACACTGTG
A
Found at i:1674 original size:44 final size:43
Alignment explanation
Indices: 1558--1735 Score: 146
Period size: 44 Copynumber: 4.1 Consensus size: 43
1548 AACCTACCTG
* * * * *
1558 TGAAAATTTGATAATCATACTGTGAAATTTTGATAAACACACTA
1 TGAAATTTTGATAATCACACTATAAAATTTTGAT-AACTCACTA
* * * * *
1602 TGAAATTTTGATAA-CTTCAGTGTGAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAATC-ACACTATAAAATTTTGATAA-CTCACTA
*
1646 TGAAATTTTGATAATCACACTATAAAA--TTGGTAACTGCACTA
1 TGAAATTTTGATAATCACACTATAAAATTTTGATAACT-CACTA
* * * *
1688 TGAAAACTTTGATAACCACACCATAAAATTTTGATAACCTCCCTA
1 TG-AAATTTTGATAATCACACTATAAAATTTTGATAA-CTCACTA
1733 TGA
1 TGA
1736 GAATGAAACT
Statistics
Matches: 109, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
41 2 0.02
42 12 0.11
43 25 0.23
44 55 0.50
45 13 0.12
46 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (43 bp):
TGAAATTTTGATAATCACACTATAAAATTTTGATAACTCACTA
Found at i:1874 original size:22 final size:22
Alignment explanation
Indices: 1846--2008 Score: 93
Period size: 22 Copynumber: 7.4 Consensus size: 22
1836 TTCCCTCCCC
*
1846 ATGAAATTTTGTTAACCTTCTT
1 ATGAAATTTTGATAACCTTCTT
* *
1868 ATGAAATTTTGATAA-ATCACATT
1 ATGAAATTTTGATAACCT-TC-TT
* * *
1891 ATAAAATTTTCGATAACTTTCAT
1 ATGAAATTTT-GATAACCTTCTT
* * *
1914 ATGAAATATT--TAACCTCCCT
1 ATGAAATTTTGATAACCTTCTT
* * *
1934 AAGAAATTTTGGTAACCTTCTA
1 ATGAAATTTTGATAACCTTCTT
* *
1956 ACT-AAATTTTGATAA-CTACACT
1 A-TGAAATTTTGATAACCTTC-TT
* * *
1978 ATGAAGTTTTGATAATCTTCAT
1 ATGAAATTTTGATAACCTTCTT
2000 ATGAAATTT
1 ATGAAATTT
2009 CGGTAACCAC
Statistics
Matches: 105, Mismatches: 26, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
20 15 0.14
21 5 0.05
22 55 0.52
23 23 0.22
24 6 0.06
25 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTTCTT
Found at i:2016 original size:88 final size:88
Alignment explanation
Indices: 1839--2006 Score: 218
Period size: 88 Copynumber: 1.9 Consensus size: 88
1829 TGATAAATTC
* * * *
1839 CCTCCCCATGAAATTTTGTTAACCTTCTTATGAAATTTTGATAAATCACATTATAAAATTTTCGA
1 CCTCCCCAAGAAATTTTGGTAACCTTCTAATGAAATTTTGATAAATCACACTATAAAATTTTCGA
1904 TAACTTTCATATGAAATATTTAA
66 TAACTTTCATATGAAATATTTAA
* * * *
1927 CCTCCCTAAGAAATTTTGGTAACCTTCTAACT-AAATTTTGATAACT-ACACTATGAAGTTTT-G
1 CCTCCCCAAGAAATTTTGGTAACCTTCTAA-TGAAATTTTGATAAATCACACTATAAAATTTTCG
1989 ATAA-TCTTCATATGAAAT
65 ATAACT-TTCATATGAAAT
2007 TTCGGTAACC
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
85 1 0.01
86 17 0.24
87 12 0.17
88 39 0.56
89 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (88 bp):
CCTCCCCAAGAAATTTTGGTAACCTTCTAATGAAATTTTGATAAATCACACTATAAAATTTTCGA
TAACTTTCATATGAAATATTTAA
Found at i:2052 original size:44 final size:43
Alignment explanation
Indices: 1936--2052 Score: 117
Period size: 44 Copynumber: 2.7 Consensus size: 43
1926 ACCTCCCTAA
* * * * *
1936 GAAATTTTGGTAACCTTCTAACTAAATTTTGATAACTACACTAT
1 GAAATTTTGATAATCTTCTAAGT-AATTTCGATAACCACACTAT
* * * *
1980 GAAGTTTTGATAATCTTCATATGAAATTTCGGTAACCACACTAT
1 GAAATTTTGATAATCTTC-TAAGTAATTTCGATAACCACACTAT
*
2024 TAAATTTTGATAATCTTGCTAAGTAATTT
1 GAAATTTTGATAATCTT-CTAAGTAATTT
2053 TGGTTGATTG
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
44 55 0.95
45 3 0.05
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (43 bp):
GAAATTTTGATAATCTTCTAAGTAATTTCGATAACCACACTAT
Found at i:4990 original size:2 final size:2
Alignment explanation
Indices: 4983--5022 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4973 TGAAGAAGTG
4983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5023 CAGTTTTGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6872 original size:18 final size:19
Alignment explanation
Indices: 6849--6885 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6839 ATGCACCTCG
6849 AAGTTTTA-TTTTGTGTCA
1 AAGTTTTATTTTTGTGTCA
6867 AAGTTTTATTTTTGTGTCA
1 AAGTTTTATTTTTGTGTCA
6886 TGTTGCACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.57
Consensus pattern (19 bp):
AAGTTTTATTTTTGTGTCA
Found at i:8954 original size:5 final size:5
Alignment explanation
Indices: 8944--8968 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
8934 TATTGGTGTA
8944 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
8969 AATAGCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:9445 original size:27 final size:27
Alignment explanation
Indices: 9415--9472 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
9405 TCTTTTTCCT
*
9415 ATTTAAACCTGGATTTACACATCAAGA
1 ATTTAAACCTGGATTTACACATAAAGA
** * * *
9442 ATTTGGACTTGGGTTTACACATAAAGG
1 ATTTAAACCTGGATTTACACATAAAGA
9469 ATTT
1 ATTT
9473 GCACTTGCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (27 bp):
ATTTAAACCTGGATTTACACATAAAGA
Found at i:9473 original size:27 final size:27
Alignment explanation
Indices: 9428--9479 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
9418 TAAACCTGGA
* *
9428 TTTACACATCAAGAATTTGGACTTGGG
1 TTTACACATAAAGAATTTGCACTTGGG
*
9455 TTTACACATAAAGGATTTGCACTTG
1 TTTACACATAAAGAATTTGCACTTG
9480 CAACTCTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (27 bp):
TTTACACATAAAGAATTTGCACTTGGG
Found at i:9618 original size:27 final size:27
Alignment explanation
Indices: 9588--9645 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
9578 TCTTTTTCCT
*
9588 ATTTAGACTTGGATTTACACATTAAGA
1 ATTTAGACTTGGATTTACACATGAAGA
* * * *
9615 ATTTGGATTTGGGTTTACACATGAAGG
1 ATTTAGACTTGGATTTACACATGAAGA
9642 ATTT
1 ATTT
9646 GCACTTGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
ATTTAGACTTGGATTTACACATGAAGA
Found at i:9682 original size:173 final size:174
Alignment explanation
Indices: 9393--9742 Score: 603
Period size: 173 Copynumber: 2.0 Consensus size: 174
9383 CTATGCTTGC
9393 GGTGCATGCATTTCTTTTTCCTATTTAAACCTGGATTTACACATCAAGAATTTGGACTTGGGTTT
1 GGTGCATGCATTTCTTTTTCCTATTTAAACCTGGATTTACACATCAAGAATTTGGACTTGGGTTT
*
9458 ACACATAAAGGATTTGCACTTGCAACTCTTAAACACATAGGAGAAAAGAC-AAAATAGCTTAGTT
66 ACACATAAAGGATTTGCACTTGCAACTCTTAAACACATAAGAGAAAAGACAAAAATAGCTTAGTT
* *
9522 ATCTCAATTCTATTGAAAACTAAATTGGGGTTTTTAGTAATTTT
131 ATCTCAATTCTAGTGAAAACCAAATTGGGGTTTTTAGTAATTTT
* * * *
9566 GGTGCATGCATTTCTTTTTCCTATTTAGACTTGGATTTACACATTAAGAATTTGGATTTGGGTTT
1 GGTGCATGCATTTCTTTTTCCTATTTAAACCTGGATTTACACATCAAGAATTTGGACTTGGGTTT
* *
9631 ACACATGAAGGATTTGCACTTGCAACTCTTAAACACATAAGAGAAAAGACAAAAATAGGTTAGTT
66 ACACATAAAGGATTTGCACTTGCAACTCTTAAACACATAAGAGAAAAGACAAAAATAGCTTAGTT
*
9696 ATCTCAATTCTGGTGAAAACCAAATTGGGGTTTTTAGTAATTTT
131 ATCTCAATTCTAGTGAAAACCAAATTGGGGTTTTTAGTAATTTT
9740 GGT
1 GGT
9743 AGGGTAAGGA
Statistics
Matches: 166, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
173 109 0.66
174 57 0.34
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (174 bp):
GGTGCATGCATTTCTTTTTCCTATTTAAACCTGGATTTACACATCAAGAATTTGGACTTGGGTTT
ACACATAAAGGATTTGCACTTGCAACTCTTAAACACATAAGAGAAAAGACAAAAATAGCTTAGTT
ATCTCAATTCTAGTGAAAACCAAATTGGGGTTTTTAGTAATTTT
Found at i:12262 original size:670 final size:658
Alignment explanation
Indices: 10365--14553 Score: 3129
Period size: 670 Copynumber: 6.3 Consensus size: 658
10355 AAAAATGACT
* * * * * ***
10365 CGAAAGATTT-TTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGA-CATAAAA
1 CGAAAG-TTTATTTCTCAATTTTTAGCCAAAATACTCATAAAAATTATATAATT-TATCGCCAAA
* * * * *
10428 AAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTCTTCCTATTTTTTTCTGAATTAATTTCCAA
64 AAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCTAA
* *
10493 TTAAATCGAGATAAGATTCAGATGCTCGTA-AAAACAAATCCTTAAATCCAA-AGTGGCTGAGAT
129 TTAAATCGAAACAAGATTCAGATGCT--TATAAAACAAATCCTTAAATCCAATA-TGGCTGAGAT
* * ** * *
10556 TTGGTTAGATGAATATAGAAATTTCAAGGAGTCTTGATGTC-AAAAATCATGCAAAAGTGAGTCG
191 TTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCG-CAAAAAATCATGCAAAACTGA-ACG
* * * * *
10620 GGTCTCAGAACGCGTTTTTAGCCGAAAACAA--TGATGGTA-GTACACGATTTTGGCTAAAATTT
254 GGGCCCAGAACGCGTTTTTAGCC-AAAAAAACGTGATGATATGTACACGATTTCGGCTAAAATTT
* * * * * *
10682 TACAAAAATTTACCGAAATA-TTTTTCTCAATTTTTAG-TCACAATACTCATAAAAAATATATAA
318 T-GAAAAATTGACCGAAAGATTTTTTCTCAATTTTTGGCT-AAAATACTCATAAAATATATATAA
* ** * * * *
10745 TTCAACGTCATGAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTCCTTCTTCTTTTTTA
381 TTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTT-TAATATCGTTTTT-CAT-AT-TTTTCT-
* * *** * *
10810 CAAATTAATTTCTGATTAAATCGAAATTTGATTCAAATGCTCATAAAAACAAATCCTTATATCCA
441 -GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCA
* * * ** * * * *
10875 ATGTGGCT-AAGAGTTGGTTAGATG-A-ATAGACATTTCAATAAGTTTTGCCACCAAAAATCATG
505 ATGTGGCTGAA-ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATG
* * * * ** * * * *
10937 CAAAACTAACCCAGGGCCCCGGAATGCGTTTTTAGC-CTAAAAACCGT-CA-TGGTACATGATTT
569 CAAAACTGAGCCAGGG-CCCAGAACGCGTTTTTAGCAAAAAAAACGGTGGATTGTTACACGATTT
* *
10999 C-ATCTAAAATTTTGTAAATATTGATC
633 CGA-CTAAAATTTTGCAAAAATTGATC
* * * * * * *
11025 C-AAACTATTTTTTCTCAAATTTTAGCCACAATACTCAT-AAAATATATATAATTCAACGCCCAA
1 CGAAAGT-TTATTTCTCAATTTTTAGCCAAAATACTCATAAAAAT-TATATAATTTATCGCCAAA
* * * * *
11088 AAGATTGGAGGACTTTTCATGCTTTTAATATCGTTTTT-C-ATATATTT-TGAATTAATTTCTAA
64 AAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCTAA
* * * * * *
11150 TCAAATCGAAACAAGATTTAGATGCTCGTA-AAAACAAATACTTAAATTCAATGTGGCTAAGATT
129 TTAAATCGAAACAAGATTCAGATGCT--TATAAAACAAATCCTTAAATCCAATATGGCTGAGATT
** * *
11214 TGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCAAAAAATCAAGCGAAACT-AAGTCGG
192 TGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAA--CGG
* * * * *
11278 GGCCCCGAAATGCGTTTTTAGCC--AAAAAC-T-ATGATGTCGTACATGATTTCAGCTAAAATTT
255 GGCCCAG-AACGCGTTTTTAGCCAAAAAAACGTGATGATAT-GTACACGATTTCGGCTAAAATTT
* * * * * * *
11339 TGCAAGAAA-TGACCCAAAAAATTTTCCTCGATTTTTGGCTAAAATACTTACAAAATATATATAA
318 TG-AA-AAATTGACCGAAAGATTTTTTCTCAATTTTTGGCTAAAATACTCATAAAATATATATAA
* * * *
11403 TTTAACGCCAAAAAGATTGGAGGACTTTTCACGCCTTTAATATCGTTTTTCATATTATTCTGAAT
381 TTCAACGCCAAAAAGATTGAAGGGCTTTTCACG-CTTTAATATCGTTTTTCATATTTTTCTGAAT
* * * *
11468 TAATTTCTAATTAAATGGATACAAGATTCAGATGCTCATAAAAA-AAATTCTTAAATCCAATGTA
445 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATGTG
* * * *
11532 GCTGAAATTTGATTAGATGAATATGGATATCTCAAAGAGTC-CTAGCGCCAAAAATCATGCAAAA
510 GCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGA-CGCCAAAAATCATGCAAAA
* * * *
11596 CTTAGGCAGAGCCTCAGAACGCGTTTTTAGACAAAAAAAACGGTGGATTGTTACACGATTTCAAC
574 CTGAGCCAGGGCC-CAGAACGCGTTTTTAG-CAAAAAAAACGGTGGATTGTTACACGATTTCGAC
*
11661 TTAAATTTTGCAAAAATTGATC
637 TAAAATTTTGCAAAAATTGATC
* * *
11683 CGAAAGTTAATTACTCAATTTTTAGCCACAATACTCATAAAAATTATATAATTTATCGCCAAAAA
1 CGAAAGTTTATTTCTCAATTTTTAGCCAAAATACTCATAAAAATTATATAATTTATCGCCAAAAA
* ** * * *
11748 GATTGAAGGGCTTTTCATACTTCTAATATCGTTTTTCCTATTATTTTCTGAATTAATTTTTATTT
66 GATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCTAATT
*** **
11813 AAATCGAAACATA-ATTCAGATGCTTATTTTA-AAATCCTTAAATTTAATATGGCTGAGATTTTG
131 AAATCGAAACA-AGATTCAGATGCTTATAAAACAAATCCTTAAATCCAATATGGCTGAGA-TTTG
* * * * *
11876 -TTTGATGAATATCGATATTTCTAGGAGT-TTCGGCGCCAAAAATCATGCAACACTGAACGAGGG
194 ATTAGATGAATATAGATATTTCAAGGAGTCTT-GGCGCAAAAAATCATGCAAAACTGAACG-GGG
* * *
11939 TCCCGGAACTCGTTTTTAGCCAAAAAAAATCGTGACTTTGACTATTGTACACGATTTCGGCTAAT
257 -CCCAGAACGCGTTTTTAGCC-AAAAAAA-CGTGA---TGA-TA-TGTACACGATTTCGGCTAAA
* * * * *
12004 ATTATGCCAAAATTGACCGGAAATATTTTTTCTCAATTTTTGTCTAAAATAATCATAAAATATAT
314 ATTTTG-AAAAATTGACC-GAAAGATTTTTTCTCAATTTTTGGCTAAAATACTCATAAAATATAT
* * * * *
12069 ATAATTCAACTCCAAAAACATTGGAGGACTTTTCATGCTTTAAATATCGTTTTTCATATTTTTCT
377 ATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTT-AATATCGTTTTTCATATTTTTCT
* * * **
12134 GAATTAATTTCTAATTAAATCGAAATAAGTTTCAGATGCTCGTAAAAAC-AATCCTTAAATGTAA
441 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAA
*
12198 TGTGGCTGAAATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCAAAAATCATGCA
506 TGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCA
* * * * * * *
12263 AAACTGAGTC-GGGGCGA-AACGCGTTTTTAGCAATAAACATGATGG-TTAGTATA-A-GATTTC
571 AAACTGAGCCAGGGCCCAGAACGCGTTTTTAGCAAAAAAAACGGTGGATT-GT-TACACGATTTC
* * *
12323 GGCTAAAATTCTACAAAAAAATT-A-C
634 GACTAAAATTTTGC--AAAAATTGATC
* * * * *
12348 CTGGAAATTTTTTTTCTCAATTTTTGGCTAAAATACTCACGAAATAA--ATATAATTTAAT-GCC
1 C--GAAAGTTTATTTCTCAATTTTTAGCCAAAATACTCA-TAAA-AATTATATAATTT-ATCGCC
* * * ** * *
12410 AAAAATATT-AGAGGACTTTTCACGCTTTTCATATCGTTTTTAATA-TTTTTTCTTAATAAATTT
61 AAAAAGATTGA-AGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTT
* * ** * *
12473 CTAATTAAATCGAAA-ATGGATTCA-AGTGCTTGTAAAAACAAATCCTTAAATGTAATGTAGCTG
125 CTAATTAAATCGAAACA-AGATTCAGA-TGCTTAT-AAAACAAATCCTTAAATCCAATATGGCTG
* * * * * *
12536 AGATTTGATAAGATAAATATGGATATCTCAAGGAGTCTTGGCACAAAAAAACATGCAAAACTGAC
187 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGA-
* * * * * * * *
12601 CCGGAGCCCTAAAACGCGTTTTTAGTC-AAAAACCATAATAATTAT-TACACGATTTCGGCTAAA
251 ACGGGGCCC-AGAACGCGTTTTTAGCCAAAAAAACGTGATGA-TATGTACACGATTTCGGCTAAA
* * * *
12664 ATTTTGTAAAAATTAACCTAAAAGA-TATTTCATTAATTTTTGGCTAAAATACTCATAAAA-ATA
314 ATTTTG-AAAAATTGACC-GAAAGATTTTTTC-TCAATTTTTGGCTAAAATACTCATAAAATATA
* * * * * * *
12727 TATAATTCAACGACAAAAATATTGAAGTGTTTTTTACGCTTCTAATATCGTTTTTCCTACTATTT
376 TATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTT-TAATATCGTTTTTCATA-TTTTT
* * * *
12792 CTGAATTAATTTCTAATTAAATTGAAACAAGATTTAGATGTTCATAAAAACAAATTCTTAAATCC
439 CTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCC
* * * ** *
12857 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTTGGTGACAAAAATCATG
504 AATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATG
* * *
12922 CAAAACTGA-CCCGGAGTCCCGGAACGCGTTTTTAGCAACAACAAAAAAAATTAAAAAAAAAC-C
569 CAAAACTGAGCCAGG-G-CCCAGAACGCGTTTTTAG------C-----------AAAAAAAACGG
* * * * *
12985 TCGTGATGGTT-CACAATTTCGGCTAATATTTTACAAAAATTGA-C
615 T-G-GATTGTTACACGATTTCGACTAAAATTTTGCAAAAATTGATC
* * * * * *
13029 CCAAAATATTATTTTTCCATTTTTAGCCACAATACTCATAAAAA-TATATAATTTAAT-GCAAAA
1 CGAAAGT-TTATTTCTCAATTTTTAGCCAAAATACTCATAAAAATTATATAATTT-ATCGCCAAA
* * * *
13092 AAGATTGAAGGGCCTTTCACGCTTCTAATATAGTTTTTCCTATTTTTTTC-GAATTAGTTTCTAA
64 AAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCTAA
* * *
13156 TTAAATCGAAACATGATTCAGATGCTTGT------AA-----AAA--C-A-ATGACTGAGATTTG
129 TTAAATCGAAACAAGATTCAGATGCTTATAAAACAAATCCTTAAATCCAATATGGCTGAGATTTG
* ** *
13206 GTTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCAAAAAATCATGCAAAACTGAACCGGGCC
194 ATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAA-CGGGGC
* * * * *
13271 CCATAACGCGTTTTTAGTCAAAAAAAAAACTGTGATGAATTAT-TACATGATTTTGGCTAAAACT
258 CCAGAACGCGTTTTTAG-C--CAAAAAAAC-GTGATG-A-TATGTACACGATTTCGGCTAAAATT
* * * * *
13335 TTGCAAATATTGACCCAAAAGATATTTTCTCAATTTTTAGCTACAATACTCATAAAATATATATA
317 TTG-AAAAATTGA-CCGAAAGATTTTTTCTCAATTTTTGGCTAAAATACTCATAAAATATATATA
* * * * * *
13400 ATTCAAAGCCAAAAAAATTGAAGGGTTTTTCAGGCTTTTGATATTGTTTTTCATATTTTTTTCTG
380 ATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGC-TTTAATATCGTTTTTCATA--TTTTTCTG
* * *
13465 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATTCAAT
442 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAAT
** * * * ** *
13530 GCAGCTAAAATTTTG-TTAGATGAATATAGATATTTTAAGGAGTTTCGGTGCCAAAAATCATTCA
507 GTGGCTGAAA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCA
* * * * *
13594 AAACTGAACC-GGGACCCCGAAACGCATTTTTATCAAAAAAAAACTGT-GA-TGTAACGTACACG
571 AAACTGAGCCAGGG-CCCAG-AACGCGTTTTTAGC-AAAAAAAACGGTGGATTGT----TACACG
* * *
13656 ATTTTGACTAAAATTTTGCCAAAAAAAATGACTAA
629 ATTTCGACTAAAATTTTG-C--AAAAATTGA-T-C
** * * * *
13691 AAAAAG-TT-TTCCTCAATTTTT-GCATAAAATACTCAT-AAAATATATATAATTTAACACCAAA
1 CGAAAGTTTATTTCTCAATTTTTAGC-CAAAATACTCATAAAAAT-TATATAATTTATCGCCAAA
* * *
13752 AAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCTTATTTTTTTCTGAATTAATTTCTAA
64 AAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCTAA
* * * * *
13817 TTAAATCGAAATAAGATTCAGATG-TTCGTAAAATCAAATTCTTAAATCCAATGTGGCTAAGATT
129 TTAAATCGAAACAAGATTCAGATGCTT-ATAAAA-CAAATCCTTAAATCCAATATGGCTGAGATT
* * * * * *
13881 TGATTAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAATTGAGCCGAG
192 TGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGA-ACGGG
* * * *
13946 GCCCCGAAACGCATTGTT--CC-AAAAAACTGTGATGGTTAT-TACACGATTTCGGCTAAAATTT
256 GCCCAG-AACGCGTTTTTAGCCAAAAAAAC-GTGAT-GATATGTACACGATTTCGGCTAAAATTT
* * *
14007 TGTAAAAATTGACCCGAAAGATATTTCCTCAATTTCTGGCTAAAATACTCATAAAA-ACTATAT-
318 TG-AAAAATTGA-CCGAAAGATTTTTTCTCAATTTTTGGCTAAAATACTCATAAAATA-TATATA
** * * *
14070 ATTCAACTTCAAAAAGATTGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCCTA-TTTTCGTCG
380 ATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTT-TAATATCGTTTTTCATATTTTTC-T-G
*
14134 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT--TAAAAA-AAATCTTTAAATCCAAT
442 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAAT
* * * * * * *
14196 GTGGCTGAGATTTGATTAAATGAATA-AGATATTTTATGTATTCTCGGA-GCCAAAGATCATGCA
507 GTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-GACGCCAAAAATCATGCA
* * * * * * *
14259 AAAATGAGGCAGGTCTCC-GAAACGTGTTTTTAGC-CAAAAACCGTGATGG-TTAAGTTAGTATA
571 AAACTGAGCCAGGGC-CCAG-AACGCGTTTTTAGCAAAAAAAACG-G-TGGATT--G-T--TACA
* * * *
14321 TGATTTCGGCTAAAATTTTCCAAAAGTTGA-C
627 CGATTTCGACTAAAATTTTGCAAAAATTGATC
* * * * *** * * * *
14352 ATGAAAGATTT-CTCCTCAATTTTTTTGCTGGAATACTTATAAAAA-TATATAATTCAACACCAA
1 -CGAAAG-TTTATTTCTCAA-TTTTTAGCCAAAATACTCATAAAAATTATATAATTTATCGCCAA
* ** * * * *
14415 AAAGATTGGAGTCCTTTTCACGCTTTTAATATCGTATTT-CT-TATTTTTCTAAATTAATTTCTA
63 AAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCTA
* * * * *
14478 ATTAAATCGAAACAAGATTCAGATGATCGTA-AAAACAAATTCTTCAATCCAATGTTGCTGAGAT
128 ATTAAATCGAAACAAGATTCAGATG--CTTATAAAACAAATCCTTAAATCCAATATGGCTGAGAT
*
14542 TTGGTTAGATGA
191 TTGATTAGATGA
14554 TGTAAAGTAT
Statistics
Matches: 2837, Mismatches: 506, Indels: 370
0.76 0.14 0.10
Matches are distributed among these distances:
651 2 0.00
652 33 0.01
653 45 0.02
654 62 0.02
655 15 0.01
656 29 0.01
657 157 0.06
658 216 0.08
659 194 0.07
660 256 0.09
661 152 0.05
662 113 0.04
663 78 0.03
664 86 0.03
665 95 0.03
666 111 0.04
667 143 0.05
668 162 0.06
669 145 0.05
670 393 0.14
671 84 0.03
672 15 0.01
673 4 0.00
675 2 0.00
676 1 0.00
677 67 0.02
678 11 0.00
679 91 0.03
680 42 0.01
681 12 0.00
682 20 0.01
683 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (658 bp):
CGAAAGTTTATTTCTCAATTTTTAGCCAAAATACTCATAAAAATTATATAATTTATCGCCAAAAA
GATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCTAATT
AAATCGAAACAAGATTCAGATGCTTATAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGAT
TAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACGGGGCCCA
GAACGCGTTTTTAGCCAAAAAAACGTGATGATATGTACACGATTTCGGCTAAAATTTTGAAAAAT
TGACCGAAAGATTTTTTCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACGCCA
AAAAGATTGAAGGGCTTTTCACGCTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAAT
TAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAAATTTG
ATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCCAGGGC
CCAGAACGCGTTTTTAGCAAAAAAAACGGTGGATTGTTACACGATTTCGACTAAAATTTTGCAAA
AATTGATC
Found at i:14330 original size:332 final size:330
Alignment explanation
Indices: 10355--14553 Score: 3181
Period size: 331 Copynumber: 12.6 Consensus size: 330
10345 TCATGATGGT
* *
10355 AAAAA-TGACTCGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCAT-AAAAATATATAATTC
* *** * * * *
10419 GACATAAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTCTTCCTATTTTTTTCTGAATT
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTA-TTTTTTCTGAATT
* * * *
10484 AATTTCCAATTAAATCGAGATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCT--TAAAAACAAATCCTTAAATCCAATGTGG
* * * * *
10549 CTGAGATTTGGTTAGATGAATATAGAAATTTCAAGGAGTCT-TGATGTCAAAAATCATGCAAAAG
192 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGA-GCCAAAAATCATGCAAAAC
* * * ** *
10613 TGAGTC-GGGTCTC-AGAACGCGTTTTTAGCCGAAAACAATGATG---GTAGTACACGATTTTGG
256 TGAGCCAGGG-CCCGA-AACGCGTTTTTAGCCAAAAACCGTGATGTAAGTAGTACACGATTTCGG
*
10673 CTAAAATTTTAC
319 CTAAAATTTTGC
* * * * *
10685 AAAAATTTA-CCGAAATAT-TTTTCTCAATTTTTAG-TCACAATACTCATAAAAAATATATAATT
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCT-AAAATACTCAT-AAAAATATATAATT
* ** * * * * *
10747 CAACGTCATGAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTCCTTCTTCTTTTTTACA
64 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCC-TATT-TTTTCT--G
* *** * *
10812 AATTAATTTCTGATTAAATCGAAATTTGATTCAAATGCTCATAAAAACAAATCCTTATATCCAAT
125 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT--TAAAAACAAATCCTTAAATCCAAT
* * * * ** * * *
10877 GTGGCTAAGAGTTGGTTAGATG-A-ATAGACATTTCAATAAGTTTTGCCA-CCAAAAATCATGCA
188 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCG-GAGCCAAAAATCATGCA
* * * * * *
10939 AAACTAACCCAGGGCCCCGGAATGCGTTTTTAGCCTAAAAACCGTCA--T--G--GTACATGATT
252 AAACTGAGCCAGGG-CCCGAAACGCGTTTTTAGCC-AAAAACCGTGATGTAAGTAGTACACGATT
** *
10998 TCATCTAAAATTTTGT
315 TCGGCTAAAATTTTGC
* * * * * * * * *
11014 AAATATTGATCC-AAACTATTTTTTCTCAAATTTTAGCCACAATACTCATAAAATATATATAATT
1 AAAAATTGACCCGAAA-GATATTTCCTCAATTTTTGGCTAAAATACTCATAAAA-ATATATAATT
* * * * * *
11078 CAACGCCCAAAAGATTGGAGGACTTTTCATGCTTTTAATATCGTTTTTCATA-TATTT-TGAATT
64 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCTGAATT
* * * *
11141 AATTTCTAATCAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATACTTAAATTCAATGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCT--TAAAAACAAATCCTTAAATCCAATGTGG
* * * * * *
11206 CTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCAAAAAATCAAGCGAAACT
192 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACT
* * * * * * * *
11271 AAGTCGGGGCCCCGAAATGCGTTTTTAGCCAAAAA-C-T-ATG-ATGTCGTACATGATTTCAGCT
257 GAGCCAGGG-CCCGAAACGCGTTTTTAGCCAAAAACCGTGATGTAAGTAGTACACGATTTCGGCT
11332 AAAATTTTGC
321 AAAATTTTGC
* * * * *
11342 AAGAAA-TGACCCAAAAAAT-TTTCCTCGATTTTTGGCTAAAATACTTACAAAATATATATAATT
1 AA-AAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAA-ATATATAATT
* * * * * *
11405 TAACGCCAAAAAGATTGGAGGACTTTTCACGCCTTTAATATCGTTTTTCATA-TTATTCTGAATT
64 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCTGAATT
* * * *
11469 AATTTCTAATTAAATGGATACAAGATTCAGATGCTCATAAAAA-AAATTCTTAAATCCAATGTAG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCT--TAAAAACAAATCCTTAAATCCAATGTGG
* * * * * *
11533 CTGAAATTTGATTAGATGAATATGGATATCTCAAAGAGTC-CTAGCGCCAAAAATCATGCAAAAC
192 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-GGAGCCAAAAATCATGCAAAAC
* * * * *
11597 TTAGGCAGAGCCTC-AGAACGCGTTTTTAGACAAAAAAAACGGTGGAT-T--GT--TACACGATT
256 TGAGCCAGGGCC-CGA-AACGCGTTTTTAG-C--CAAAAACCGT-GATGTAAGTAGTACACGATT
** *
11656 TCAACTTAAATTTTGC
315 TCGGCTAAAATTTTGC
* * * * * * * *
11672 AAAAATTGATCCGAAAGTTAATTACTCAATTTTTAGCCACAATACTCATAAAAATTATATAATTT
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAA-TATATAATTC
* ** *
11737 ATCGCCAAAAAGATTGAAGGGCTTTTCATACTTCTAATATCGTTTTTCCTATTATTTTCTGAATT
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATT-TTTTCTGAATT
* * *** ** *
11802 AATTTTTATTTAAATCGAAACATA-ATTCAGATGCTTATTTTA-AAATCCTTAAATTTAATATGG
129 AATTTCTAATTAAATCGAAACA-AGATTCAGATGCTTA-AAAACAAATCCTTAAATCCAATGTGG
* * * * * *
11865 CTGAGATTTTG-TTTGATGAATATCGATATTTCTAGGAGTTTCGGCGCCAAAAATCATGCAACAC
192 CTGAGA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAAC
* * * * * * * *
11929 TGAACGAGGGTCCCGGAACTCGTTTTTAGCCAAAAAAAATCGTGACTTTGACTATTGTACACGAT
256 TGAGCCAGGG-CCCGAAACGCGTTTTTAGCC---AAAAACCGTGA-TGTAAGTA--GTACACGAT
* *
11994 TTCGGCTAATATTATGC
314 TTCGGCTAAAATTTTGC
* * * * * * *
12011 CAAAATTGACCGGAAATATTTTTTCTCAATTTTTGTCTAAAATAATCATAAAATATATATAATTC
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAA-ATATATAATTC
* * * * * * *
12076 AACTCCAAAAACATTGGAGGACTTTTCATGCTTTAAATATCGTTTTTCATA-TTTTTCTGAATTA
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCTGAATTA
* * **
12140 ATTTCTAATTAAATCGAAATAAGTTTCAGATGCTCGTAAAAAC-AATCCTTAAATGTAATGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCT--TAAAAACAAATCCTTAAATCCAATGTGGC
* *
12204 TGAAATTTGATTAGATGAATATAGATATTTGAAGGAGTCTC-GACGCCAAAAATCATGCAAAACT
193 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGA-GCCAAAAATCATGCAAAACT
* * * *
12268 GAGTC-GGG-GCGAAACGCGTTTTTAG-CAATAAA-CATGATGGTTAGTA-TA-A-GATTTCGGC
257 GAGCCAGGGCCCGAAACGCGTTTTTAGCCAA-AAACCGTGAT-GTAAGTAGTACACGATTTCGGC
* *
12326 TAAAATTCTAC
320 TAAAATTTTGC
* ** * * *
12337 AAAAAAATT-ACCTGGAAATTTTTTTTCTCAATTTTTGGCTAAAATACTCACGAAATAA-ATATA
1 --AAAAATTGACC-CGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCA-TAAA-AATATATA
* * * * * ** *
12400 ATTTAATGCCAAAAATATT-AGAGGACTTTTCACGCTTTTCATATCGTTTTTAATATTTTTTCTT
61 ATTCAACGCCAAAAAGATTGA-AGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCTG
* * **
12464 AATAAATTTCTAATTAAATCGAAA-ATGGATTCA-AGTGCTTGTAAAAACAAATCCTTAAATGTA
125 AATTAATTTCTAATTAAATCGAAACA-AGATTCAGA-TGC-T-TAAAAACAAATCCTTAAATCCA
* * * * * * * *
12527 ATGTAGCTGAGATTTGATAAGATAAATATGGATATCTCAAGGAGTCTTGGCA-CAAAAAAACATG
186 ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGG-AGCCAAAAATCATG
* * * * * * *
12591 CAAAACTGA-CCCGGAGCCCTAAAACGCGTTTTTAGTCAAAAACCAT-A-ATAATTATTACACGA
250 CAAAACTGAGCCAGG-GCCC-GAAACGCGTTTTTAGCCAAAAACCGTGATGTAAGTAGTACACGA
*
12653 TTTCGGCTAAAATTTTGT
313 TTTCGGCTAAAATTTTGC
* ** * *
12671 AAAAATTAACCTAAAAGATATTTCATTAATTTTTGGCTAAAATACTCATAAAAATATATAATTCA
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATATAATTCA
* * * * * * * *
12736 ACGACAAAAATATTGAAGTGTTTTTTACGCTTCTAATATCGTTTTTCCTACTATTTCTGAATTAA
66 ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCTGAATTAA
* * * *
12801 TTTCTAATTAAATTGAAACAAGATTTAGATGTTCATAAAAACAAATTCTTAAATCCAATGTGGCT
131 TTTCTAATTAAATCGAAACAAGATTCAGATG--CTTAAAAACAAATCCTTAAATCCAATGTGGCT
* * * *
12866 GAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTTGGTGACAAAAATCATGCAAAACTGA
194 GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGA
* * *** * ***
12931 -CCCGGAGTCCCGGAACGCGTTTTTAGCAACAACAAAAAAAATTAAAAAAAAACCTCGTGATGGT
259 GCCAGG-G-CCCGAAACGCGTTTTTAG---C--C-AAAAACCGT--GATGTAA----GT-A--GT
* * * *
12995 TCACAATTTCGGCTAATATTTTAC
307 ACACGATTTCGGCTAAAATTTTGC
* * * * * * * *
13019 AAAAATTGACCCAAAATATTATTT-TTCCATTTTTAGCCACAATACTCATAAAAATATATAATTT
1 AAAAATTGACCCGAAAGA-TATTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATATAATTC
* * * * *
13083 AATGCAAAAAAGATTGAAGGGCCTTTCACGCTTCTAATATAGTTTTTCCTATTTTTT-TCGAATT
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCT-GAATT
* * ** *
13147 AGTTTCTAATTAAATCGAAACATGATTCAGATGCTT-----GTAA-----AAA--CAA--TGACT
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTTAAAAACAAATCCTTAAATCCAATGTGGCT
* * * *
13198 GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCAAAAAATCATGCAAAACTGA
194 GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGA
* * * * * * * *
13263 ACC-GGGCCCCATAACGCGTTTTTAGTCAAAAAAAAAACTGTGATG-AATTATTACATGATTTTG
259 GCCAGGGCCCGA-AACGCGTTTTTAG-C----CAAAAACCGTGATGTAAGTAGTACACGATTTCG
*
13326 GCTAAAACTTTGC
318 GCTAAAATTTTGC
* * * * *
13339 AAATATTGACCCAAAAGATATTTTCTCAATTTTTAGCTACAATACTCATAAAATATATATAATTC
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAA-ATATATAATTC
* * * * * * *
13404 AAAGCCAAAAAAATTGAAGGGTTTTTCAGGCTTTTGATATTGTTTTTCATATTTTTTTCTGAATT
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTA-TTTTTTCTGAATT
* * **
13469 AATTTCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATTCAATGCAG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATG--CTTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * *
13534 CTAAAATTTTG-TTAGATGAATATAGATATTTTAAGGAGTTTCGGTGCCAAAAATCATTCAAAAC
192 CTGAGA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAAC
* * * * * *
13598 TGAACC-GGGACCCCGAAACGCATTTTTATCAAAAAAAAACTGTGATGTAA--CGTACACGATTT
256 TGAGCCAGGG--CCCGAAACGCGTTTTTAGC---CAAAAACCGTGATGTAAGTAGTACACGATTT
* *
13660 TGACTAAAATTTTGCC
316 CGGCTAAAATTTTG-C
* *** *
13676 AAAAAAAATGACTAAAAAAAGT-TTTCCTCAATTTTT-GCATAAAATACTCATAAAATATATATA
1 --AAAAATTGACCCGAAAGA-TATTTCCTCAATTTTTGGC-TAAAATACTCATAAAA-ATATATA
* * * * *
13739 ATTTAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCTTATTTTTTTCTG
61 ATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTA-TTTTTTCTG
* * * *
13804 AATTAATTTCTAATTAAATCGAAATAAGATTCAGATGTTCGTAAAATCAAATTCTTAAATCCAAT
125 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATG--CTTAAAAACAAATCCTTAAATCCAAT
* * * * *
13869 GTGGCTAAGATTTGATTAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAA
188 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAA
* * * * * *
13934 AATTGAGCCGAGGCCCCGAAACGCATTGTT--CCAAAAAACTGTGATG---GTTATTACACGATT
253 AACTGAGCC-AGGGCCCGAAACGCGTTTTTAGCC-AAAAACCGTGATGTAAG-TAGTACACGATT
*
13994 TCGGCTAAAATTTTGT
315 TCGGCTAAAATTTTGC
*
14010 AAAAATTGACCCGAAAGATATTTCCTCAATTTCTGGCTAAAATACTCATAAAAACTATAT-ATTC
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAA-TATATAATTC
** * *
14074 AACTTCAAAAAGATTGAAGGGCTTTTGACG-TTTCTAATATCGTTTTTCCTATTTTCGTC-GAAT
65 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTCCTATTTT-TTCTGAAT
*
14137 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTAAAAA-AAATCTTTAAATCCAATGTGGC
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTAAAAACAAATCCTTAAATCCAATGTGGC
* * * * * * *
14201 TGAGATTTGATTAAATGAATA-AGATATTTTATGTATTCTCGGAGCCAAAGATCATGCAAAAATG
193 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTG
* * * * *
14265 AGGCAGGTCTCCGAAACGTGTTTTTAGCCAAAAACCGTGATGGTTAAGTTAGTATATGATTTCGG
258 AGCCAGGGC-CCGAAACGCGTTTTTAGCCAAAAACCGTGAT-G-TAAG-TAGTACACGATTTCGG
*
14330 CTAAAATTTTCC
319 CTAAAATTTTGC
* ** * ** *
14342 AAAAGTTGACATGAAAGAT-TTCTCCTCAATTTTTTTGCTGGAATACTTATAAAAATATATAATT
1 AAAAATTGACCCGAAAGATATT-TCCTCAA-TTTTTGGCTAAAATACTCATAAAAATATATAATT
* * ** * * *
14406 CAACACCAAAAAGATTGGAGTCCTTTTCACGCTTTTAATATCGTATTTCTTA-TTTTTCTAAATT
64 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCTGAATT
* * * *
14470 AATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATTCTTCAATCCAATGTTG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATG--CTTAAAAACAAATCCTTAAATCCAATGTGG
*
14535 CTGAGATTTGGTTAGATGA
192 CTGAGATTTGATTAGATGA
14554 TGTAAAGTAT
Statistics
Matches: 3136, Mismatches: 551, Indels: 359
0.78 0.14 0.09
Matches are distributed among these distances:
319 5 0.00
320 60 0.02
321 51 0.02
322 43 0.01
323 3 0.00
324 3 0.00
325 79 0.03
326 76 0.02
327 293 0.09
328 186 0.06
329 175 0.06
330 235 0.07
331 452 0.14
332 432 0.14
333 137 0.04
334 43 0.01
335 84 0.03
336 29 0.01
337 73 0.02
338 141 0.04
339 364 0.12
340 7 0.00
341 7 0.00
345 1 0.00
346 3 0.00
347 1 0.00
348 148 0.05
349 5 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (330 bp):
AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATATAATTCA
ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCTGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTTAAAAACAAATCCTTAAATCCAATGTGGCTGA
GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGAGC
CAGGGCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGTAAGTAGTACACGATTTCGGCTAAAAT
TTTGC
Found at i:15144 original size:13 final size:13
Alignment explanation
Indices: 15126--15150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15116 TTCAATGTTC
15126 TAAATATTATTTA
1 TAAATATTATTTA
15139 TAAATATTATTT
1 TAAATATTATTT
15151 GGAATTCCAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:15610 original size:21 final size:23
Alignment explanation
Indices: 15584--15626 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
15574 AATAGTAAGA
15584 TAAGATAAGATA-G-TAAGATTG
1 TAAGATAAGATATGATAAGATTG
15605 TAAGATAAGATATGATAAGATT
1 TAAGATAAGATATGATAAGATT
15627 TGCTAGGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.30
Consensus pattern (23 bp):
TAAGATAAGATATGATAAGATTG
Found at i:23883 original size:22 final size:22
Alignment explanation
Indices: 23858--24023 Score: 115
Period size: 22 Copynumber: 7.6 Consensus size: 22
23848 TCCCATTATT
23858 AAATTTTGATAACCTTTCTATG
1 AAATTTTGATAACCTTTCTATG
* ** *
23880 AAATTTTAATAACGATACTATG
1 AAATTTTGATAACCTTTCTATG
* * *
23902 AAATTTCGAGAACCTTTTTAT-
1 AAATTTTGATAACCTTTCTATG
**
23923 AAATTTTTTTAACC-TTCTTATG
1 AAATTTTGATAACCTTTC-TATG
* ** *
23945 AAATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACCTTTCTATG
***
23967 AAATTTTGA-AGACCTCAATATG
1 AAATTTTGATA-ACCTTTCTATG
* *
23989 AAATTTTGATAA-CTTCCCAATG
1 AAATTTTGATAACCTT-TCTATG
24011 AAATTTTGATAAC
1 AAATTTTGATAAC
24024 GAACACTATG
Statistics
Matches: 109, Mismatches: 28, Indels: 13
0.73 0.19 0.09
Matches are distributed among these distances:
20 2 0.02
21 16 0.15
22 89 0.82
23 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTTTCTATG
Found at i:23907 original size:44 final size:43
Alignment explanation
Indices: 23858--24048 Score: 118
Period size: 44 Copynumber: 4.3 Consensus size: 43
23848 TCCCATTATT
*
23858 AAATTTTGATAACCTTTCTATGAAATTTTAATAACGATACTATG
1 AAATTTTGATAACCTTCCTATGAAATTTTAATAAC-ATACTATG
* * ** ** * *
23902 AAATTTCGAGAACCTTTTTAT-AAATTTTTTTAACCTTCTTATG
1 AAATTTTGATAACCTTCCTATGAAATTTTAATAACATAC-TATG
* * * * * *
23945 AAATTTTGTTAACCTCCCTAAGAAATTTTGAA-GACCTCAATATG
1 AAATTTTGATAACCTTCCTATGAAATTTT-AATAACAT-ACTATG
* * *
23989 AAATTTTGATAA-CTTCCCAATGAAATTTTGATAACGAACACTATG
1 AAATTTTGATAACCTT-CCTATGAAATTTTAATAAC--ATACTATG
* *
24034 AGATGTTGATAACCT
1 AAATTTTGATAACCT
24049 CTATATGATA
Statistics
Matches: 108, Mismatches: 30, Indels: 16
0.70 0.19 0.10
Matches are distributed among these distances:
42 2 0.02
43 32 0.30
44 57 0.53
45 15 0.14
46 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (43 bp):
AAATTTTGATAACCTTCCTATGAAATTTTAATAACATACTATG
Found at i:23959 original size:43 final size:45
Alignment explanation
Indices: 23853--23973 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 45
23843 TATGATCCCA
*
23853 TTATTAAATTTTGATAACCTTTCTATGAAATTTTAATAACGATAC
1 TTATGAAATTTTGATAACCTTTCTATGAAATTTTAATAACGATAC
* * * ** * *
23898 -TATGAAATTTCGAGAACCTTTTTAT-AAATTTTTTTAAC-CTTC
1 TTATGAAATTTTGATAACCTTTCTATGAAATTTTAATAACGATAC
* ** *
23940 TTATGAAATTTTGTTAACCTCCCTAAGAAATTTT
1 TTATGAAATTTTGATAACCTTTCTATGAAATTTT
23974 GAAGACCTCA
Statistics
Matches: 59, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
42 2 0.03
43 29 0.49
44 28 0.47
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.45
Consensus pattern (45 bp):
TTATGAAATTTTGATAACCTTTCTATGAAATTTTAATAACGATAC
Found at i:24146 original size:22 final size:22
Alignment explanation
Indices: 24112--24224 Score: 66
Period size: 22 Copynumber: 5.0 Consensus size: 22
24102 TGTTAGTAAT
* * *
24112 CACACTCTTAAATTTTGATAAT
1 CACACTATGAAATTTTGATAAA
* * *
24134 CACATTATGAAATTGTAATAAA
1 CACACTATGAAATTTTGATAAA
* *
24156 CTCGCTATGAAATTTTGATAAA
1 CACACTATGAAATTTTGATAAA
* **
24178 TCTTC-CTACAAAATTTTGATAAA
1 -C-ACACTATGAAATTTTGATAAA
* * *
24201 CTTCCCTATAAAATTTTGATAAA
1 C-ACACTATGAAATTTTGATAAA
24224 C
1 C
24225 TTCTCTATGA
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
22 37 0.50
23 35 0.47
24 2 0.03
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (22 bp):
CACACTATGAAATTTTGATAAA
Found at i:24232 original size:23 final size:22
Alignment explanation
Indices: 24151--24237 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 22
24141 TGAAATTGTA
*
24151 ATAAAC-TCGCTATGAAATTTTG
1 ATAAACTTC-CTATAAAATTTTG
*
24173 ATAAATCTTCCTACAAAATTTTG
1 ATAAA-CTTCCTATAAAATTTTG
24196 ATAAACTTCCCTATAAAATTTTG
1 ATAAACTT-CCTATAAAATTTTG
*
24219 ATAAACTTCTCTATGAAAT
1 ATAAACTTC-CTATAAAAT
24238 CTTGTAACTA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.16
23 46 0.81
24 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (22 bp):
ATAAACTTCCTATAAAATTTTG
Found at i:24298 original size:22 final size:21
Alignment explanation
Indices: 24250--24299 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
24240 TGTAACTACA
*
24250 AATTTTGATAACCTCCCTATG
1 AATTTTGATAACCTCACTATG
* * *
24271 ATTTTTTATAACCTCATTATGG
1 AATTTTGATAACCTCACTAT-G
24293 AATTTTG
1 AATTTTG
24300 TTAGACTAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (21 bp):
AATTTTGATAACCTCACTATG
Found at i:24572 original size:12 final size:12
Alignment explanation
Indices: 24542--24584 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
24532 AAGCCCGCCC
24542 AAAAAATGAAAA
1 AAAAAATGAAAA
24554 AACAAAATGAAAA
1 AA-AAAATGAAAA
*
24567 AAAAAAAGAAAA
1 AAAAAATGAAAA
24579 GAAAAA
1 -AAAAA
24585 GGATCAGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:24582 original size:17 final size:18
Alignment explanation
Indices: 24550--24584 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24540 CCAAAAAATG
24550 AAAAAACAAAATGAAAAA
1 AAAAAACAAAATGAAAAA
*
24568 AAAAAAGAAAA-GAAAAA
1 AAAAAACAAAATGAAAAA
24585 GGATCAGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.86, C:0.03, G:0.09, T:0.03
Consensus pattern (18 bp):
AAAAAACAAAATGAAAAA
Found at i:24656 original size:7 final size:7
Alignment explanation
Indices: 24646--24685 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
24636 TCTCTCTCCT
24646 CTTCTTC
1 CTTCTTC
24653 CTTCTTC
1 CTTCTTC
*
24660 CTTCTTG
1 CTTCTTC
*
24667 CTTCTTG
1 CTTCTTC
24674 CTTCTTC
1 CTTCTTC
24681 CTTCT
1 CTTCT
24686 CCACCACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.00, C:0.38, G:0.05, T:0.57
Consensus pattern (7 bp):
CTTCTTC
Found at i:24670 original size:21 final size:21
Alignment explanation
Indices: 24646--24685 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
24636 TCTCTCTCCT
24646 CTTCTTCCTTCTTCCTTCTTG
1 CTTCTTCCTTCTTCCTTCTTG
*
24667 CTTCTTGCTTCTTCCTTCT
1 CTTCTTCCTTCTTCCTTCT
24686 CCACCACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.38, G:0.05, T:0.57
Consensus pattern (21 bp):
CTTCTTCCTTCTTCCTTCTTG
Found at i:25445 original size:18 final size:19
Alignment explanation
Indices: 25417--25464 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
25407 GCATCGTGGG
*
25417 TTTTTTCTTTTAGTT-TT-
1 TTTTTTTTTTTAGTTATTC
*
25434 TTTTTTTTTTTTGTTATTC
1 TTTTTTTTTTTAGTTATTC
*
25453 TTTTGTTTTTTA
1 TTTTTTTTTTTA
25465 AATTTGGGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 13 0.52
18 2 0.08
19 10 0.40
ACGTcount: A:0.06, C:0.04, G:0.06, T:0.83
Consensus pattern (19 bp):
TTTTTTTTTTTAGTTATTC
Found at i:25859 original size:20 final size:20
Alignment explanation
Indices: 25834--25884 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
25824 ATCTTCATAA
25834 GAAATTTTGATATCCTCCCT
1 GAAATTTTGATATCCTCCCT
* *
25854 GAAATTTTGAGATCTTCCCT
1 GAAATTTTGATATCCTCCCT
*
25874 AAAATTTTGAT
1 GAAATTTTGAT
25885 TACTCCATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (20 bp):
GAAATTTTGATATCCTCCCT
Found at i:26271 original size:22 final size:21
Alignment explanation
Indices: 26242--26378 Score: 90
Period size: 22 Copynumber: 6.4 Consensus size: 21
26232 AAATTGAGAC
26242 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
*
26263 TTTTGATAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
**
26285 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
26307 TATTTG-TAACCTC--ATGAAA
1 T-TTTGATAACCTCATATGAAA
* *
26326 -TTTGTTAAACCACACTATGAAA
1 TTTTGAT-AACCTCA-TATGAAA
*
26348 TTCTT-ATAACCTTGC-TATGACA
1 TT-TTGATAACC-T-CATATGAAA
26370 TTTTGATAA
1 TTTTGATAA
26379 TCTCTTTGAT
Statistics
Matches: 94, Mismatches: 8, Indels: 27
0.73 0.06 0.21
Matches are distributed among these distances:
17 4 0.04
18 1 0.01
19 11 0.12
21 9 0.10
22 59 0.63
23 7 0.07
24 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:26707 original size:31 final size:29
Alignment explanation
Indices: 26644--26707 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
26634 TGACAATTTA
**
26644 GAAATATGTTTTAAAAAAGGGTACAATTG
1 GAAATATGTTTTAAAAAAGGGTACAACCG
*
26673 GAAATATGTTTTAAAAATAAGGGTATAACCG
1 GAAATATGTTTT-AAAA-AAGGGTACAACCG
26704 GAAA
1 GAAA
26708 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 12 0.40
30 4 0.13
31 14 0.47
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (29 bp):
GAAATATGTTTTAAAAAAGGGTACAACCG
Found at i:27065 original size:41 final size:40
Alignment explanation
Indices: 27006--27083 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
26996 GTCCTTCCTA
*
27006 ATAATTAAGGAAACAAATTAAATTCAGGTTTAGTCCCCCTG
1 ATAATTAAGGAAACAAATTAAATCCAGGTTTAG-CCCCCTG
*
27047 ATAATTAA-GATAAGAAATTAAATCCAGGTTTAGCCCC
1 ATAATTAAGGA-AACAAATTAAATCCAGGTTTAGCCCC
27084 TAGTTATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 6 0.18
41 28 0.82
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (40 bp):
ATAATTAAGGAAACAAATTAAATCCAGGTTTAGCCCCCTG
Found at i:34358 original size:9 final size:9
Alignment explanation
Indices: 34344--34368 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
34334 ATGACCTGAT
34344 TGATGAAGC
1 TGATGAAGC
34353 TGATGAAGC
1 TGATGAAGC
34362 TGATGAA
1 TGATGAA
34369 CCATGGAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (9 bp):
TGATGAAGC
Found at i:42690 original size:2 final size:2
Alignment explanation
Indices: 42683--42708 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42673 TTATAATAAC
42683 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42709 GCATACGCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43273 original size:25 final size:24
Alignment explanation
Indices: 43245--43291 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
43235 AATATATAGT
*
43245 TTTTGATATCTGAA-ATTATAAAAAA
1 TTTTGA-ATCCGAATATT-TAAAAAA
43270 TTTTGAATCCGAATATTTAAAA
1 TTTTGAATCCGAATATTTAAAA
43292 TTAAGAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (24 bp):
TTTTGAATCCGAATATTTAAAAAA
Found at i:43927 original size:19 final size:19
Alignment explanation
Indices: 43895--43943 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
43885 AGTTATTAAA
43895 TTATTATT-AATACACAAC
1 TTATTATTAAATACACAAC
*
43913 TTATTATTAAATACACAAT
1 TTATTATTAAATACACAAC
43932 TTATTA-TAAATA
1 TTATTATTAAATA
43944 TGTTCGATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATTATTAAATACACAAC
Found at i:47515 original size:13 final size:13
Alignment explanation
Indices: 47497--47527 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
47487 TGGGGAAGAA
47497 AAAAAAACAAAAC
1 AAAAAAACAAAAC
47510 AAAAAAACAAAAC
1 AAAAAAACAAAAC
47523 AAAAA
1 AAAAA
47528 CAATGGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:48086 original size:16 final size:16
Alignment explanation
Indices: 48065--48097 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
48055 GTCATGTTTT
48065 CCCTTTGACCAGTTAG
1 CCCTTTGACCAGTTAG
48081 CCCTTTGACCAGTTAG
1 CCCTTTGACCAGTTAG
48097 C
1 C
48098 GAGGTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.30
Consensus pattern (16 bp):
CCCTTTGACCAGTTAG
Found at i:55146 original size:3 final size:3
Alignment explanation
Indices: 55140--55170 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
55130 GCAAAAACAA
55140 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
55171 GAAAGAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:58265 original size:3 final size:3
Alignment explanation
Indices: 58257--58290 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
58247 TTATTTTCTT
58257 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
58291 CAACAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:67619 original size:8 final size:8
Alignment explanation
Indices: 67608--67645 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
67598 TATATATCTC
67608 CCATGAGG
1 CCATGAGG
67616 CCATGAGG
1 CCATGAGG
67624 CCATGAGG
1 CCATGAGG
67632 CCATGAGG
1 CCATGAGG
67640 CCATGA
1 CCATGA
67646 CAATATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.13
Consensus pattern (8 bp):
CCATGAGG
Found at i:72443 original size:30 final size:31
Alignment explanation
Indices: 72378--72436 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
72368 ATGGAAATAA
72378 TTTGATGTACCTTGTTTTCTCTTTTTCTACT
1 TTTGATGTACCTTGTTTTCTCTTTTTCTACT
72409 TTTGATGTACCCCTTGTTTT-T-TTTTTCT
1 TTTGATGTA--CCTTGTTTTCTCTTTTTCT
72437 TTTTTGAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 16 0.62
32 1 0.04
33 9 0.35
ACGTcount: A:0.08, C:0.19, G:0.10, T:0.63
Consensus pattern (31 bp):
TTTGATGTACCTTGTTTTCTCTTTTTCTACT
Found at i:72707 original size:5 final size:6
Alignment explanation
Indices: 72695--72720 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
72685 CTATCCTAAT
72695 AAGAAA AAGAAA AAGAAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AA
72721 CAAAGGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:72778 original size:15 final size:17
Alignment explanation
Indices: 72741--72781 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
72731 TTTTCTTTAA
*
72741 AGAAAAAAAAAAGATAG
1 AGAAAGAAAAAAGATAG
*
72758 ATAAAGAAAAAA-A-AG
1 AGAAAGAAAAAAGATAG
72773 AGAAAGAAA
1 AGAAAGAAA
72782 GGTTAATAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 10 0.48
16 1 0.05
17 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (17 bp):
AGAAAGAAAAAAGATAG
Found at i:85543 original size:17 final size:17
Alignment explanation
Indices: 85517--85553 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
85507 TCCCCCTCAT
85517 GGTACCAGGTAGCATGA
1 GGTACCAGGTAGCATGA
*
85534 GGTACTAGGTAGCATGA
1 GGTACCAGGTAGCATGA
85551 GGT
1 GGT
85554 GCTGGATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.14, G:0.38, T:0.22
Consensus pattern (17 bp):
GGTACCAGGTAGCATGA
Found at i:88354 original size:12 final size:12
Alignment explanation
Indices: 88322--88360 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
88312 ATGGAATTAA
88322 ATATCCGTCGAT
1 ATATCCGTCGAT
88334 AT-T---TCGAT
1 ATATCCGTCGAT
88342 ATATCCGTCGAT
1 ATATCCGTCGAT
88354 ATATCCG
1 ATATCCG
88361 ATATCTGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
11 1 0.04
12 14 0.61
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:88493 original size:10 final size:10
Alignment explanation
Indices: 88471--88509 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
88461 AAATCTCGAT
*
88471 ATATCCGTAA
1 ATATCCATAA
88481 ATATCCATAA
1 ATATCCATAA
*
88491 ATATCCGTAA
1 ATATCCATAA
88501 ATATCCATA
1 ATATCCATA
88510 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (10 bp):
ATATCCATAA
Found at i:88494 original size:20 final size:20
Alignment explanation
Indices: 88471--88509 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
88461 AAATCTCGAT
88471 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
88491 ATATCCGTAAATATCCATA
1 ATATCCGTAAATATCCATA
88510 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:89352 original size:13 final size:13
Alignment explanation
Indices: 89334--89358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89324 TTCGCAGTAC
89334 AAAAAATAAAAAT
1 AAAAAATAAAAAT
89347 AAAAAATAAAAA
1 AAAAAATAAAAA
89359 AATGTCTACA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:89538 original size:12 final size:12
Alignment explanation
Indices: 89521--89559 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
89511 CATCGATACC
89521 TCGATATATCCG
1 TCGATATATCCG
89533 TCGATATATCCG
1 TCGATATATCCG
89545 TTCGATATATCCG
1 -TCGATATATCCG
89558 TC
1 TC
89560 AATACCTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 14 0.54
13 12 0.46
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:89551 original size:13 final size:13
Alignment explanation
Indices: 89521--89558 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
89511 CATCGATACC
89521 TCGATATATCCG-
1 TCGATATATCCGT
89533 TCGATATATCCGT
1 TCGATATATCCGT
89546 TCGATATATCCGT
1 TCGATATATCCGT
89559 CAATACCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:90362 original size:2 final size:2
Alignment explanation
Indices: 90355--90381 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
90345 GCTGGGAGGT
90355 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
90382 GTATGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:93710 original size:16 final size:15
Alignment explanation
Indices: 93660--93710 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
93650 GTGTGTATTC
93660 TTTTTCCTTCTTGAGG
1 TTTTTCC-TCTTGAGG
93676 ATTTTTCC-CATTG-GG
1 -TTTTTCCTC-TTGAGG
93691 TTTTTCCTCTTGAAGG
1 TTTTTCCTCTTG-AGG
93707 TTTT
1 TTTT
93711 AACGAGACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 10 0.33
15 4 0.13
16 9 0.30
17 7 0.23
ACGTcount: A:0.10, C:0.18, G:0.18, T:0.55
Consensus pattern (15 bp):
TTTTTCCTCTTGAGG
Found at i:98458 original size:440 final size:425
Alignment explanation
Indices: 97636--98706 Score: 1341
Period size: 440 Copynumber: 2.5 Consensus size: 425
97626 ATCTAGATAA
* * ** * * *
97636 AAAATTATATGATATTAAATAGACCATCAATTGAAACCATAAAATTCCAGAAGCATTTTTTAAAA
1 AAAATTATATGATATTAAATAGACCAGCAATCGAAACCACCAAATTTCGGAAGCATTTTTTTAAA
* * * *
97701 TTGAAACATAAAAATTTGCTTTTGAATCTTTCATGAAAGTTGTAGATCATGAAATTACTTTTTAA
66 TTGAAACAT-AAAATTTGCTTTTGAGT-TTTTATGAAAGTTGTAGAACATGAAATTACCTTTTAA
* * * **
97766 TAGACACCTAAATTACCTTAATCAGACAAATTGAAAAAAAAAATTTAAGCGTAAAATCGTGTAAG
129 TAGACACCTGAATCACCTTAATCAGACAAATAGAAAAAAAAAAAATAAGCGTAAAATCGTGTAAG
** * * *
97831 ATAGGATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAGTATGAGGGTCGTTTGATAAATAATA
194 ATAAAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTTGATAAATAATA
* * *
97896 CAAATAAAAAAATGTTTGTTGGAGATCTTGAAATATAAAAATTCCTTTTTGAACCATTTATGAAA
259 CAAATAAAAAAATGTTTGTTGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCATTAATGAAA
* * * *
97961 CCCGTAGATCAAATTTAGCTTTCAGGTCCTTCATGAAAGTCGTATATCATACAATAACCTTTTAA
324 CCCATAGATCAAATTTAGCTTTCAGATCCTTCAAGAAAGTCGTACATCATACAATAACCTTTTAA
* *
98026 CCGATACTTGAATAACTTTAATCGAACATGTGGATCG
389 CCGACACTTGAATAACTTTAATCGAACATGTGAATCG
* *
98063 AAAATTATATGATATTAAATAGACCAGCAATCGAAACCACCAAATTTGGGAAGCATTTTTTTTAA
1 AAAATTATATGATATTAAATAGACCAGCAATCGAAACCACCAAATTTCGGAAGCATTTTTTTAAA
* *
98128 TTGAAACACATAAATTTGACTTTTGAGTTATTTAAGAAAGTTGTAGAACATGAAATTACCTTTTA
66 TTGAAACATA-AAATTTG-CTTTTGAGTT-TTTATGAAAGTTGTAGAACATGAAATTACCTTTTA
* * * *
98193 ATAGGATATCTGAATCATCTTAATCAGGCAAATAGAACAAAAAAAAAAATAGAGCTGAAGATAAA
128 ATA-GACACCTGAATCACCTTAATCAGACAAATAG-A-AAAAAAAAAAATA-AGC----G-TAAA
98258 ATCGAT-TAAGATAAAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTT
184 ATCG-TGTAAGATAAAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTT
*
98322 GATAAATAAT-CAAAATAAGAAAATGTTTGTTGATGGAGATCTTGAAACATAAAAATTCCCTTTT
248 GATAAATAATAC-AAATAAAAAAATGTTTG-T--TGGAGATCTTGAAACATAAAAATTCCCTTTT
* * *
98386 GAACCCTTAATGAAACTCATATATCAAATTTAGCTTTC-GTATCCTTCAAGAAAGTCGTACATCA
309 GAACCATTAATGAAACCCATAGATCAAATTTAGCTTTCAG-ATCCTTCAAGAAAGTCGTACATCA
* *
98450 TGCAATAACCTTTTAACCGACACTTGAATAACTTTAATCGGACATGTGAATCG
373 TACAATAACCTTTTAACCGACACTTGAATAACTTTAATCGAACATGTGAATCG
* * *
98503 AAAATTATATAATATTATATAGACC-GACAATCGAAACCACCAAATTTCGGAAGCATTTTTTTGA
1 AAAATTATATGATATTAAATAGACCAG-CAATCGAAACCACCAAATTTCGGAAGCATTTTTTTAA
** *
98567 ATTGAAACATAAAAATAGGCTTTTGAGTCCTTTATGAAAGTTGTA-AATCATGAAATTACCTTTT
65 ATTGAAACAT-AAAATTTGCTTTTGAGT-TTTTATGAAAGTTGTAGAA-CATGAAATTACCTTTT
* *
98631 AATAGACACCTGAATCACCTTAATTCA-ACAAATA-AAAGAAATAAAGATGAAGCGCT-AAATCG
127 AATAGACACCTGAATCACCTTAA-TCAGACAAATAGAAA-AAAAAAAAAT-AAGCG-TAAAATCG
*
98693 AT-TAAGATAGAATT
188 -TGTAAGATAAAATT
98707 TTTAGAGGAT
Statistics
Matches: 558, Mismatches: 61, Indels: 46
0.84 0.09 0.07
Matches are distributed among these distances:
426 1 0.00
427 72 0.13
428 42 0.08
429 24 0.04
430 1 0.00
431 30 0.05
432 5 0.01
435 2 0.00
436 14 0.03
437 88 0.16
438 26 0.05
439 48 0.09
440 204 0.37
441 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (425 bp):
AAAATTATATGATATTAAATAGACCAGCAATCGAAACCACCAAATTTCGGAAGCATTTTTTTAAA
TTGAAACATAAAATTTGCTTTTGAGTTTTTATGAAAGTTGTAGAACATGAAATTACCTTTTAATA
GACACCTGAATCACCTTAATCAGACAAATAGAAAAAAAAAAAATAAGCGTAAAATCGTGTAAGAT
AAAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTTGATAAATAATACA
AATAAAAAAATGTTTGTTGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCATTAATGAAACC
CATAGATCAAATTTAGCTTTCAGATCCTTCAAGAAAGTCGTACATCATACAATAACCTTTTAACC
GACACTTGAATAACTTTAATCGAACATGTGAATCG
Found at i:99049 original size:3 final size:3
Alignment explanation
Indices: 99041--99100 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
99031 CTTCTTACTC
* *
99041 TTA TTA TTA -TA TAA TTA TTA TTA TTA TTA TCA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
99086 TTA -TA TTA TATA TTA
1 TTA TTA TTA T-TA TTA
99101 ATTAATTATA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:99083 original size:16 final size:15
Alignment explanation
Indices: 99045--99131 Score: 83
Period size: 15 Copynumber: 5.7 Consensus size: 15
99035 TTACTCTTAT
99045 TATTATATAATTATTA
1 TATTATAT-ATTATTA
*
99061 TTATTAT-TATCATTA
1 -TATTATATATTATTA
99076 TA-TAT-TATTATTA
1 TATTATATATTATTA
99089 TATTATATATTAATTA
1 TATTATATATT-ATTA
99105 -ATTATATATATATTTA
1 TATTATATAT-TA-TTA
99121 TATATATATAT
1 TAT-TATATAT
99132 ATGTATTTGT
Statistics
Matches: 61, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
13 12 0.20
14 5 0.08
15 20 0.33
16 9 0.15
17 8 0.13
18 7 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATATATTATTA
Found at i:99094 original size:8 final size:8
Alignment explanation
Indices: 99042--99138 Score: 62
Period size: 8 Copynumber: 11.9 Consensus size: 8
99032 TTCTTACTCT
99042 TATTATTA
1 TATTATTA
*
99050 TATAATTA
1 TATTATTA
99058 TTATTATTA
1 -TATTATTA
*
99067 TTATCATTA
1 -TATTATTA
99076 TA-TA-T-
1 TATTATTA
99081 TATTATTA
1 TATTATTA
99089 TATTA-TA
1 TATTATTA
99096 TATTAATTA
1 TATT-ATTA
99105 -ATTA-TA
1 TATTATTA
99111 TATATATTTA
1 TAT-TA-TTA
99121 TATATATATA
1 TAT-TAT-TA
99131 TATGTATT
1 TAT-TATT
99139 TGTATAATTG
Statistics
Matches: 73, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
5 2 0.03
6 5 0.07
7 11 0.15
8 20 0.27
9 19 0.26
10 16 0.22
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (8 bp):
TATTATTA
Found at i:99130 original size:20 final size:19
Alignment explanation
Indices: 99044--99139 Score: 71
Period size: 19 Copynumber: 5.1 Consensus size: 19
99034 CTTACTCTTA
99044 TTATTATATA-AT-TAT-T
1 TTATTATATATATATATAT
99060 ATTATTAT-TATCAT-TATAT
1 -TTATTATATAT-ATATATAT
99079 ATTATTAT-TATATTATATAT
1 -TTATTATATATA-TATATAT
*
99099 TAATTA-ATTATATATATAT
1 TTATTATA-TATATATATAT
*
99118 TTATATATATATATATGTAT
1 TTAT-TATATATATATATAT
99138 TT
1 TT
99140 GTATAATTGT
Statistics
Matches: 67, Mismatches: 3, Indels: 15
0.79 0.04 0.18
Matches are distributed among these distances:
16 2 0.03
17 7 0.10
18 6 0.09
19 28 0.42
20 23 0.34
21 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (19 bp):
TTATTATATATATATATAT
Found at i:102759 original size:23 final size:21
Alignment explanation
Indices: 102733--102830 Score: 80
Period size: 23 Copynumber: 4.6 Consensus size: 21
102723 GATACTTGGC
102733 TCGAGCTCGACTCGATACTCGTA
1 TCGAGCT--ACTCGATACTCGTA
*
102756 TCGAGCTACTCGA-GCTCG-A
1 TCGAGCTACTCGATACTCGTA
* *
102775 TCGAG-TA-TCGATTA-TGAGAA
1 TCGAGCTACTCGA-TACT-CGTA
102795 TCGAGCTCGACTCGATACTCGTA
1 TCGAGCT--ACTCGATACTCGTA
102818 TCGAGCTACTCGA
1 TCGAGCTACTCGA
102831 GCTCGATCGG
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
17 4 0.07
18 3 0.05
19 7 0.11
20 10 0.16
21 13 0.21
23 19 0.31
24 5 0.08
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (21 bp):
TCGAGCTACTCGATACTCGTA
Found at i:102773 original size:32 final size:32
Alignment explanation
Indices: 102732--102836 Score: 139
Period size: 32 Copynumber: 3.3 Consensus size: 32
102722 CGATACTTGG
102732 CTCGAGCTCGACTCGATACTCGTATCGAGCTA
1 CTCGAGCTCGACTCGATACTCGTATCGAGCTA
102764 CTCGAGCTCGA-TCGAGTA-TCGATTAT-GAG--A
1 CTCGAGCTCGACTCGA-TACTCG--TATCGAGCTA
*
102794 ATCGAGCTCGACTCGATACTCGTATCGAGCTA
1 CTCGAGCTCGACTCGATACTCGTATCGAGCTA
102826 CTCGAGCTCGA
1 CTCGAGCTCGA
102837 TCGGTAAGCT
Statistics
Matches: 63, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
29 3 0.05
30 16 0.25
31 14 0.22
32 27 0.43
33 3 0.05
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (32 bp):
CTCGAGCTCGACTCGATACTCGTATCGAGCTA
Found at i:103080 original size:16 final size:17
Alignment explanation
Indices: 103061--103093 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
103051 CCCAAATTAA
103061 TTTT-GGACTAAATGTT
1 TTTTGGGACTAAATGTT
*
103077 TTTTGGGATTAAATGTT
1 TTTTGGGACTAAATGTT
103094 AAAACTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.52
Consensus pattern (17 bp):
TTTTGGGACTAAATGTT
Found at i:104937 original size:2 final size:2
Alignment explanation
Indices: 104871--104919 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
104861 TGTTATCTAC
* *
104871 TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
104913 TA TA TA T
1 TA TA TA T
104920 CTATCTATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:106420 original size:36 final size:36
Alignment explanation
Indices: 106377--106447 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
106367 AGGGTTAAAT
106377 ATAGGGTTAGATTAGGAAATTTAACACTAAAATTAA
1 ATAGGGTTAGATTAGGAAATTTAACACTAAAATTAA
*
106413 ATAGGGTTAGATTAGGAAATTTAATACTAAAATTA
1 ATAGGGTTAGATTAGGAAATTTAACACTAAAATTA
106448 GTTAGTTAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.32
Consensus pattern (36 bp):
ATAGGGTTAGATTAGGAAATTTAACACTAAAATTAA
Found at i:107333 original size:18 final size:17
Alignment explanation
Indices: 107297--107339 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
107287 CGGAGTAAAA
*
107297 TATTATTTTATAGAGAT
1 TATTAATTTATAGAGAT
*
107314 TATTAATTTATCGAG--
1 TATTAATTTATAGAGAT
107329 TATTAATTTAT
1 TATTAATTTAT
107340 GGAGGTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
17 13 0.54
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (17 bp):
TATTAATTTATAGAGAT
Found at i:107412 original size:17 final size:17
Alignment explanation
Indices: 107398--107435 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
107388 ATAGTAGTAG
107398 TAATATTTTATTAGTGA
1 TAATATTTTATTAGTGA
*
107415 TAATATTTTATTTGTGA
1 TAATATTTTATTAGTGA
107432 TAAT
1 TAAT
107436 GAAGGGTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (17 bp):
TAATATTTTATTAGTGA
Found at i:110095 original size:131 final size:131
Alignment explanation
Indices: 109861--110121 Score: 486
Period size: 131 Copynumber: 2.0 Consensus size: 131
109851 ACGTATTTCT
* *
109861 CATGAGAAACATTGGTTTTCATTTAAGGATTCCCTAATTTGTAAAAATTTGCCAAGTATGTGTTC
1 CATGAGAAACATTGGTTTTCATTTAAGGATTCCCTAATTTGTAAAAATTTGCCAAGCATATGTTC
* *
109926 TAAATTTGTTGGAATTGTTTATTTTGATCCTTGTTTGAGAAAATCTTAAAACGTTTAGTCCTTAT
66 TAAATTTGTTGGAATTGTGTATTTTGATCCTTGTTTGAGAAAATCTTAAAACGTTTAATCCTTAT
109991 G
131 G
109992 CATGAGAAACATTGGTTTTCATTTAAGGATTCCCTAATTTGTAAAAATTTGCCAAGCATATGTTC
1 CATGAGAAACATTGGTTTTCATTTAAGGATTCCCTAATTTGTAAAAATTTGCCAAGCATATGTTC
110057 TAAATTTGTTGGAATTGTGTATTTTGATCCTTGTTTGAGAAAATCTTAAAACGTTTAATCCTTAT
66 TAAATTTGTTGGAATTGTGTATTTTGATCCTTGTTTGAGAAAATCTTAAAACGTTTAATCCTTAT
110122 TTGAGCATTT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 126 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (131 bp):
CATGAGAAACATTGGTTTTCATTTAAGGATTCCCTAATTTGTAAAAATTTGCCAAGCATATGTTC
TAAATTTGTTGGAATTGTGTATTTTGATCCTTGTTTGAGAAAATCTTAAAACGTTTAATCCTTAT
G
Found at i:111869 original size:25 final size:26
Alignment explanation
Indices: 111836--111887 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
111826 GAGCAAAGTC
111836 TCCAAGGAGAATTATTA-AAAGAAGA
1 TCCAAGGAGAATTATTACAAAGAAGA
* *
111861 TCCACGGAGGATTATTATCAAAGAAGA
1 TCCAAGGAGAATTATTA-CAAAGAAGA
111888 AGATCCAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
27 8 0.35
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (26 bp):
TCCAAGGAGAATTATTACAAAGAAGA
Found at i:112077 original size:47 final size:47
Alignment explanation
Indices: 112002--112091 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 47
111992 AAGTCATCAA
* * * *
112002 ATTATCAATTTAAGATCAAGTCGCCAAGACTCTTGAATCAAATTATC
1 ATTAACAATTCAAGATCAAGTCACCAAGACCCTTGAATCAAATTATC
* *
112049 ATTAACAATTCAATATCAAGTCATCAAGACCCTTGAATCAAAT
1 ATTAACAATTCAAGATCAAGTCACCAAGACCCTTGAATCAAAT
112092 CAAACTCTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (47 bp):
ATTAACAATTCAAGATCAAGTCACCAAGACCCTTGAATCAAATTATC
Found at i:112130 original size:13 final size:13
Alignment explanation
Indices: 112100--112128 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
112090 ATCAAACTCT
112100 CAAATCCTTGAAG
1 CAAATCCTTGAAG
112113 CAAAT-CTTGAAG
1 CAAATCCTTGAAG
112125 CAAA
1 CAAA
112129 ATTTTGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (13 bp):
CAAATCCTTGAAG
Found at i:113369 original size:31 final size:31
Alignment explanation
Indices: 113321--113479 Score: 146
Period size: 31 Copynumber: 5.5 Consensus size: 31
113311 GGTGTCCGAC
*
113321 GTGGCACGCCACGTGTACCAAAAAGTGACAA
1 GTGGCACGCCACATGTACCAAAAAGTGACAA
*
113352 GTGGCACCCCACATGTACCAAAAAGT--C--
1 GTGGCACGCCACATGTACCAAAAAGTGACAA
113379 GT-----GCCACATGTACC-AAAAGTGAC-A
1 GTGGCACGCCACATGTACCAAAAAGTGACAA
* *
113403 -TGTCACGCCACGTGTACCAAAAAGTGACACA
1 GTGGCACGCCACATGTACCAAAAAGTGACA-A
* * *
113434 -TGTCACGCCACGTGTACCAAAAAGTGACAC
1 GTGGCACGCCACATGTACCAAAAAGTGACAA
*
113464 GTGGCATGCCACATGT
1 GTGGCACGCCACATGT
113480 TTCAAAAATG
Statistics
Matches: 108, Mismatches: 8, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.06
22 11 0.10
23 2 0.02
27 2 0.02
28 11 0.10
29 10 0.09
31 66 0.61
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.16
Consensus pattern (31 bp):
GTGGCACGCCACATGTACCAAAAAGTGACAA
Found at i:113486 original size:31 final size:31
Alignment explanation
Indices: 113380--113505 Score: 134
Period size: 31 Copynumber: 4.2 Consensus size: 31
113370 CAAAAAGTCG
*
113380 TGCCACATGTACC-AAAAGTG--ACATGTCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
* * *
113408 CGCCACGTGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
* * *
113439 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
** *
113470 TGCCACATGTTTCAAAAA-TGGCACATGGCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
113500 TGCCAC
1 TGCCAC
113506 GTGCACAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
28 11 0.13
29 7 0.08
30 16 0.19
31 51 0.60
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACATGGCA
Found at i:113505 original size:61 final size:59
Alignment explanation
Indices: 113380--113516 Score: 143
Period size: 61 Copynumber: 2.3 Consensus size: 59
113370 CAAAAAGTCG
* * * *
113380 TGCCACATGTACCAAAAGTGACATGTCACGCCACGTGTACCAAAAAGTGACACATGTCA
1 TGCCACGTGTACCAAAAGTGACATGGCACGCCACATGTACCAAAAAGTGACACATGGCA
* * ** *
113439 CGCCACGTGTACCAAAAAGTGACACGTGGCATGCCACATGTTTCAAAAA-TGGCACATGGCA
1 TGCCACGTGTACC-AAAAGTGACA--TGGCACGCCACATGTACCAAAAAGTGACACATGGCA
*
113500 TGCCACGTGCA-CAAAAG
1 TGCCACGTGTACCAAAAG
113517 GATACATGCC
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 16 0.25
60 11 0.17
61 19 0.30
62 18 0.28
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (59 bp):
TGCCACGTGTACCAAAAGTGACATGGCACGCCACATGTACCAAAAAGTGACACATGGCA
Found at i:118329 original size:15 final size:15
Alignment explanation
Indices: 118295--118329 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
118285 TTATATAAGT
118295 TATTAATTTAAAAAA
1 TATTAATTTAAAAAA
*
118310 T-TTAATTTAAAAAC
1 TATTAATTTAAAAAA
118324 TATTAA
1 TATTAA
118330 CTTATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TATTAATTTAAAAAA
Found at i:122162 original size:30 final size:30
Alignment explanation
Indices: 122126--122201 Score: 152
Period size: 30 Copynumber: 2.5 Consensus size: 30
122116 GTCCATTAAA
122126 CAAGAAAATGGGGACAAGCCAAAAGGCTTT
1 CAAGAAAATGGGGACAAGCCAAAAGGCTTT
122156 CAAGAAAATGGGGACAAGCCAAAAGGCTTT
1 CAAGAAAATGGGGACAAGCCAAAAGGCTTT
122186 CAAGAAAATGGGGACA
1 CAAGAAAATGGGGACA
122202 GTCCATTAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.45, C:0.16, G:0.28, T:0.12
Consensus pattern (30 bp):
CAAGAAAATGGGGACAAGCCAAAAGGCTTT
Found at i:123870 original size:124 final size:124
Alignment explanation
Indices: 123742--124005 Score: 478
Period size: 124 Copynumber: 2.1 Consensus size: 124
123732 CCTTTGAAAT
123742 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAAAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAAAGTTTTTA
*
123807 GTAGAATCAAACTATATATTGAAAATTTTTAATATATCCAAGTTTTTAATGAAAAAAAA
66 GTAGAATCAAACTATATATTGAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAAAA
*
123866 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAAAGTTTTTA
* *
123931 GTAGAATCAAACTATATATTGAAAAATTTTAATATATCCAAGTTTTTAATGAAAAATAG
66 GTAGAATCAAACTATATATTGAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAAAA
123990 T--AATGGTAAAAATAAA
1 TAAAATGGTAAAAATAAA
124006 CTTTTAAATT
Statistics
Matches: 136, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
122 15 0.11
124 121 0.89
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (124 bp):
TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAAAGTTTTTA
GTAGAATCAAACTATATATTGAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAAAA
Found at i:124030 original size:149 final size:151
Alignment explanation
Indices: 123866--124156 Score: 523
Period size: 149 Copynumber: 1.9 Consensus size: 151
123856 TGAAAAAAAA
* * *
123866 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATCAAACGAAAATAGAGTTTTCA
* *
123931 GTAGAATCAAACTATATATTGAAAAATTTTAATATATCCAAGTTTTTAATGAAAAATAGT-AA-T
66 GTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATAAAAAATAGTAAATT
123994 GGTAAAAATAAACTTTTAAAT
131 GGTAAAAATAAACTTTTAAAT
124015 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATCAAACGAAAATAGAGTTTTCA
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATCAAACGAAAATAGAGTTTTCA
124080 GTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATAAAAAATAGTAAATT
66 GTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATAAAAAATAGTAAATT
124145 GGTAAAAATAAA
131 GGTAAAAATAAA
124157 GTAATTATAG
Statistics
Matches: 135, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
149 120 0.89
150 2 0.01
151 13 0.10
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (151 bp):
TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATCAAACGAAAATAGAGTTTTCA
GTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATAAAAAATAGTAAATT
GGTAAAAATAAACTTTTAAAT
Found at i:134670 original size:14 final size:13
Alignment explanation
Indices: 134646--134692 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
134636 AGGTTACAAT
*
134646 TTTAGAACATTTA
1 TTTATAACATTTA
134659 TTATATAACATTTA
1 TT-TATAACATTTA
134673 TGTTATAACATTGTA
1 T-TTATAACATT-TA
134688 TTTAT
1 TTTAT
134693 GTGAAATAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.07
14 24 0.80
15 4 0.13
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (13 bp):
TTTATAACATTTA
Found at i:139734 original size:22 final size:21
Alignment explanation
Indices: 139690--139734 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
139680 TAACTTGTTA
*
139690 TTAAAATTTTTAATTTTATTT
1 TTAAAATTTTTAATTTGATTT
139711 TTAAATATTTTT-ATTTGATATT
1 TTAAA-ATTTTTAATTTGAT-TT
139733 TT
1 TT
139735 TTATAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTAAAATTTTTAATTTGATTT
Found at i:142501 original size:12 final size:12
Alignment explanation
Indices: 142468--142501 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
142458 GTGGCTTTTT
142468 TTTTCTTTTTCA
1 TTTTCTTTTTCA
* *
142480 TTTTCCTTTTCC
1 TTTTCTTTTTCA
142492 TTTTCTTTTT
1 TTTTCTTTTT
142502 TTTTCTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:145702 original size:121 final size:121
Alignment explanation
Indices: 145554--145798 Score: 490
Period size: 121 Copynumber: 2.0 Consensus size: 121
145544 AGACCACAAA
145554 ATATCATTGAAGCATAGTCTATAAATTATAAGACAATTAGGTCCACCAACCATAGTTGATAAGTC
1 ATATCATTGAAGCATAGTCTATAAATTATAAGACAATTAGGTCCACCAACCATAGTTGATAAGTC
145619 ATAACATAAATTCTATAGAATACAAAACCCTTATATACTAACAAAGTCCATAAGCT
66 ATAACATAAATTCTATAGAATACAAAACCCTTATATACTAACAAAGTCCATAAGCT
145675 ATATCATTGAAGCATAGTCTATAAATTATAAGACAATTAGGTCCACCAACCATAGTTGATAAGTC
1 ATATCATTGAAGCATAGTCTATAAATTATAAGACAATTAGGTCCACCAACCATAGTTGATAAGTC
145740 ATAACATAAATTCTATAGAATACAAAACCCTTATATACTAACAAAGTCCATAAGCT
66 ATAACATAAATTCTATAGAATACAAAACCCTTATATACTAACAAAGTCCATAAGCT
145796 ATA
1 ATA
145799 ACATATAAGT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 124 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (121 bp):
ATATCATTGAAGCATAGTCTATAAATTATAAGACAATTAGGTCCACCAACCATAGTTGATAAGTC
ATAACATAAATTCTATAGAATACAAAACCCTTATATACTAACAAAGTCCATAAGCT
Found at i:147220 original size:33 final size:33
Alignment explanation
Indices: 147183--147251 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
147173 GAACTTGAAA
*
147183 AAAAAAAAGAGATAATTAAGCCGTTTTAGATAG
1 AAAAAAAAGAGATAATTAAGCCATTTTAGATAG
*
147216 AAAAAGAAGAGATAATTAAGCCATTTTAGATAG
1 AAAAAAAAGAGATAATTAAGCCATTTTAGATAG
147249 AAA
1 AAA
147252 TTGATACGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (33 bp):
AAAAAAAAGAGATAATTAAGCCATTTTAGATAG
Found at i:147817 original size:3 final size:3
Alignment explanation
Indices: 147803--147835 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
147793 AACTGACCTA
147803 ATT ATAT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT AT
147836 ATGTAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:149655 original size:15 final size:15
Alignment explanation
Indices: 149616--149654 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
149606 ATAATCTCTA
149616 AGCCAATATATTTTG
1 AGCCAATATATTTTG
149631 AGCCAATATATTTTG
1 AGCCAATATATTTTG
149646 A-CC-ATATAT
1 AGCCAATATAT
149655 AATTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 6 0.25
14 2 0.08
15 16 0.67
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (15 bp):
AGCCAATATATTTTG
Found at i:150967 original size:105 final size:104
Alignment explanation
Indices: 150747--150972 Score: 308
Period size: 105 Copynumber: 2.2 Consensus size: 104
150737 TTGAAACATG
* * * * *
150747 AAACTTAAGTATTCATCAATTAATACTGGCTCCGAGTTCGCTGTCAACGCTGCCACTTTTTCAAA
1 AAACTGAAGTTTTCATCAATTAATACTGCCTCCGAGTTCGCTGTCAACACTGCCACTTTTTAAAA
150812 GTGAACACTTGGAGTTTTAGTCGATTAATACTAAAACTA
66 GTGAACACTTGGAGTTTTAGTCGATTAATACTAAAACTA
* ** *
150851 AAACTGGAGTTTTCATTGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCACTTTTTTAAA
1 AAACTGAAGTTTTCATCAATTAATACTGCCTCCGAGTTCGCTGTCAACACTGCCAC-TTTTTAAA
* * * ** *
150916 AGTGGAGACTTGGAGTTTTAGTCGATTAATATTGGAATTA
65 AGTGAACACTTGGAGTTTTAGTCGATTAATACTAAAACTA
150956 AAACTGAAGTTTTCATC
1 AAACTGAAGTTTTCATC
150973 GACTAAAACT
Statistics
Matches: 104, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
104 48 0.46
105 56 0.54
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (104 bp):
AAACTGAAGTTTTCATCAATTAATACTGCCTCCGAGTTCGCTGTCAACACTGCCACTTTTTAAAA
GTGAACACTTGGAGTTTTAGTCGATTAATACTAAAACTA
Found at i:156080 original size:82 final size:82
Alignment explanation
Indices: 155933--156093 Score: 243
Period size: 82 Copynumber: 2.0 Consensus size: 82
155923 GGCGCACTTC
* * *
155933 TCCCGCCATTAGTATGTCTCAGATTTTGTTTCTAGTAGAGACAGTTGTTGAGACGAGTAAGTAGA
1 TCCCGCCAATAGTACGTCTCAGATTATGTTTCTAGTAGAGACAGTTGTTGAGACGAGTAAGTAGA
*
155998 GACATTTTTTGAAACGT
66 GACATTCTTTGAAACGT
* * *
156015 TCCCGCCAATAGTACGTCTCAGCTTATGTTTGTAAGTGGAGACAGTTGTTGAGACGAGTAA-TAG
1 TCCCGCCAATAGTACGTCTCAGATTATGTTTCT-AGTAGAGACAGTTGTTGAGACGAGTAAGTAG
156079 AGACATTCTTTGAAA
65 AGACATTCTTTGAAA
156094 TGTACTATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
82 45 0.63
83 26 0.37
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (82 bp):
TCCCGCCAATAGTACGTCTCAGATTATGTTTCTAGTAGAGACAGTTGTTGAGACGAGTAAGTAGA
GACATTCTTTGAAACGT
Found at i:157494 original size:22 final size:21
Alignment explanation
Indices: 157449--157494 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
157439 GGAAATTTAA
* * *
157449 AAGTTACATTAATCTACTCCT
1 AAGTTACATCAAACTAATCCT
157470 AAGTTACATCAAGACTAATCCT
1 AAGTTACATCAA-ACTAATCCT
157492 AAG
1 AAG
157495 AGATAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (21 bp):
AAGTTACATCAAACTAATCCT
Done.