Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1439
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: 97703
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1401 original size:67 final size:68
Alignment explanation
Indices: 1283--1426 Score: 156
Period size: 67 Copynumber: 2.1 Consensus size: 68
1273 TATTTGTATA
* ** * *
1283 TAAATTAAAAGTTAAAATTTTTTTGAATATATATTAAAGATAACTAGTTTATTTAAATACAA-AA
1 TAAATTAAAAGTTAAAAGTTTTTTGAATATATACAAAAGATAACTAGTTTATCTAAATAAAATAA
*
1347 TTT
66 TTC
1350 TAAATTAAAAGTTAAAAAGTTTTTT-ACATATA-ACAAAAG-TATAC-AGATTTATCTAAATAAA
1 TAAATTAAAAGTT-AAAAGTTTTTTGA-ATATATACAAAAGATA-ACTAG-TTTATCTAAATAAA
1411 ATAATTC
62 ATAATTC
1418 TAAA-TAAAA
1 TAAATTAAAA
1427 TAGTAAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
66 4 0.06
67 39 0.59
68 23 0.35
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (68 bp):
TAAATTAAAAGTTAAAAGTTTTTTGAATATATACAAAAGATAACTAGTTTATCTAAATAAAATAA
TTC
Found at i:4842 original size:2 final size:2
Alignment explanation
Indices: 4798--4829 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4788 CTATAAGTGG
*
4798 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4830 CAAACTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5692 original size:16 final size:16
Alignment explanation
Indices: 5671--5703 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5661 AAAATTATTA
5671 ACTTAAACCTAAAATG
1 ACTTAAACCTAAAATG
*
5687 ACTTAAATCTAAAATG
1 ACTTAAACCTAAAATG
5703 A
1 A
5704 TTCGAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (16 bp):
ACTTAAACCTAAAATG
Found at i:7427 original size:19 final size:17
Alignment explanation
Indices: 7403--7441 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
7393 TTTTAAGTAA
*
7403 ATTTTTATTATAATATGTT
1 ATTTTTAATAT-ATAT-TT
7422 ATTTTTAATATATATTT
1 ATTTTTAATATATATTT
7439 ATT
1 ATT
7442 AAAATCTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTTAATATATATTT
Found at i:9050 original size:16 final size:15
Alignment explanation
Indices: 9029--9134 Score: 76
Period size: 16 Copynumber: 6.9 Consensus size: 15
9019 TTACATTAAA
9029 TTTAATTTTAAAATTT
1 TTTAATTTT-AAATTT
9045 TTTAA-TTTAAA-TT
1 TTTAATTTTAAATTT
9058 TTT-ATATTTAAATTAT
1 TTTAAT-TTTAAATT-T
*
9074 TTTAAATTTAAATATAT
1 TTTAATTTTAAAT-T-T
* *
9091 TTAAATTTATAATTTT
1 TTTAATTT-TAAATTT
* *
9107 TTTAATATTGAA-TT
1 TTTAATTTTAAATTT
*
9121 TTTAATTTTTAATT
1 TTTAATTTTAAATT
9135 AAATTCAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
12 1 0.01
13 5 0.07
14 21 0.29
15 7 0.10
16 23 0.32
17 11 0.15
18 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (15 bp):
TTTAATTTTAAATTT
Found at i:9134 original size:30 final size:30
Alignment explanation
Indices: 9029--9134 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 30
9019 TTACATTAAA
*
9029 TTTAATTTTAAAATTTTTTAAT-TTAAATT
1 TTTAATTTTAAATTTTTTTAATATTAAATT
*
9058 TTT-ATATTTAAATTATTTTAA-ATTTAAATAT
1 TTTAAT-TTTAAATTTTTTTAATA-TTAAAT-T
* *
9089 ATTTAAATTTATAATTTTTTTAATATTGAATT
1 -TTTAATTTTA-AATTTTTTTAATATTAAATT
*
9121 TTTAATTTTTAATT
1 TTTAATTTTAAATT
9135 AAATTCAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
28 2 0.03
29 16 0.26
30 10 0.16
31 9 0.15
32 8 0.13
33 16 0.26
34 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTAATTTTAAATTTTTTTAATATTAAATT
Found at i:9145 original size:63 final size:61
Alignment explanation
Indices: 9028--9146 Score: 141
Period size: 63 Copynumber: 1.9 Consensus size: 61
9018 TTTACATTAA
* **
9028 ATTTAATTTTAAAATTTTTTAATTTAAATTTTTATATTTAAATTATTTTAAATTTAAATAT
1 ATTTAAATTTAAAATTTTTTAATTTAAATTTTTATATTTAAATTAAATTAAATTTAAATAT
* * * *
9089 ATTTAAATTTATAATTTTTTTAATATTGAATTTTTA-ATTTTTAATTAAATTCAATTTA
1 ATTTAAATTTA-AAATTTTTTAAT-TTAAATTTTTATA-TTTAAATTAAATTAAATTTA
9147 GAGGGCTTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
61 10 0.21
62 12 0.25
63 26 0.54
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (61 bp):
ATTTAAATTTAAAATTTTTTAATTTAAATTTTTATATTTAAATTAAATTAAATTTAAATAT
Found at i:13163 original size:29 final size:30
Alignment explanation
Indices: 13131--13188 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
13121 TTCAACATTT
*
13131 TAGGAACCTTTT-TGT-AATTTTAGAAAATA
1 TAGGAA-CTTTTGTGTAAATATTAGAAAATA
*
13160 TAGGGACTTTTGTGTAAATATTAGAAAAT
1 TAGGAACTTTTGTGTAAATATTAGAAAAT
13189 TTTTCTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 8 0.32
30 12 0.48
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (30 bp):
TAGGAACTTTTGTGTAAATATTAGAAAATA
Found at i:17484 original size:21 final size:20
Alignment explanation
Indices: 17447--17509 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
17437 CTCTTAAATG
*
17447 TGATTAATCTTT-TTAAAAA
1 TGATCAATCTTTCTTAAAAA
* *
17466 GTTATCAATTTTTCTTAAAATA
1 -TGATCAATCTTTCTTAAAA-A
*
17488 TGATTAATCTTTCTTAAAAA
1 TGATCAATCTTTCTTAAAAA
17508 TG
1 TG
17510 TATACCACTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 12 0.34
21 22 0.63
22 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (20 bp):
TGATCAATCTTTCTTAAAAA
Found at i:17672 original size:18 final size:19
Alignment explanation
Indices: 17632--17674 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
17622 TATTTTTATT
*
17632 TAAATTTTTTAAATATTAGA
1 TAAA-TTTTTAAATATTAAA
17652 TAAATTTTTAAAT-TTAAA
1 TAAATTTTTAAATATTAAA
17670 TAAAT
1 TAAAT
17675 AATTCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 9 0.41
20 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TAAATTTTTAAATATTAAA
Found at i:18826 original size:4 final size:4
Alignment explanation
Indices: 18799--18841 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
18789 AAACCATCTC
* * * *
18799 ATAT ATAC ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
18842 GTCTTTAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:18834 original size:12 final size:12
Alignment explanation
Indices: 18799--18841 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
18789 AAACCATCTC
*
18799 ATATATACATAC
1 ATATATACATAT
*
18811 ATACATACATAT
1 ATATATACATAT
*
18823 ATATATATATAT
1 ATATATACATAT
18835 ATATATA
1 ATATATA
18842 GTCTTTAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATACATAT
Found at i:19751 original size:16 final size:16
Alignment explanation
Indices: 19725--19757 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19715 ACATGTCTCA
19725 TTTATTTTTTAAATATT
1 TTTATTTTTTAAA-ATT
19742 TTTA-TTTTTAAAATT
1 TTTATTTTTTAAAATT
19757 T
1 T
19758 ACATTAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTTTTTAAAATT
Found at i:23905 original size:61 final size:61
Alignment explanation
Indices: 23840--23975 Score: 193
Period size: 61 Copynumber: 2.2 Consensus size: 61
23830 CAGCAACGTT
* * *
23840 GGGCTTAAAGATGCGAAGAATGATAAAGGTGCCAATATGCT-AATACACGGCCAGCAATATC
1 GGGCTTAAAGATGAGAAGAATGATAAAGGTGCCAATATACTGAAT-CAAGGCCAGCAATATC
* * * *
23901 GGGCTTGAAGATGAGAAGAATGATAAGGGTGCCAATATACTGACTCAAGGCCAGCAATATT
1 GGGCTTAAAGATGAGAAGAATGATAAAGGTGCCAATATACTGAATCAAGGCCAGCAATATC
23962 GGGCTTAAAGATGA
1 GGGCTTAAAGATGA
23976 TAAAAGTGCC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
61 64 0.97
62 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (61 bp):
GGGCTTAAAGATGAGAAGAATGATAAAGGTGCCAATATACTGAATCAAGGCCAGCAATATC
Found at i:24001 original size:52 final size:52
Alignment explanation
Indices: 23929--24126 Score: 225
Period size: 52 Copynumber: 3.8 Consensus size: 52
23919 AATGATAAGG
* * * *
23929 GTGCCAATATACTGACTCAAGGCCAGCAATATTGGGCTTAAAGATGATAAAA
1 GTGCCAATATACTGATTCAAGGCCAGCAACATTGGACTTAAAGATGACAAAA
* * * ** * *
23981 GTGCCAATGTACTGATTCAAGGCTAGCGACATTACACTTAAAGATGGCAAAG
1 GTGCCAATATACTGATTCAAGGCCAGCAACATTGGACTTAAAGATGACAAAA
* *
24033 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAA
1 GTGCCAATATACTGATTCAAGGCCAGCAACATTGGACTTAAAGATGACAAAA
* * * * * *
24085 GAGCCAATATGCTAATTTAAGGCCAGTAATATTGGACTTAAA
1 GTGCCAATATACTGATTCAAGGCCAGCAACATTGGACTTAAA
24127 AGTGTCAACG
Statistics
Matches: 122, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 122 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (52 bp):
GTGCCAATATACTGATTCAAGGCCAGCAACATTGGACTTAAAGATGACAAAA
Found at i:24167 original size:43 final size:43
Alignment explanation
Indices: 24119--24200 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
24109 AGTAATATTG
*
24119 GACTTAAAAGTGTCAACGTGCTGATTCAAGCCCAGCAATGTTC
1 GACTTAAAAGTGCCAACGTGCTGATTCAAGCCCAGCAATGTTC
* * * *
24162 GACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCAAT
1 GACTTAAAAGTGCCAACGTGCTGATTCAAGCCCAGCAAT
24201 AAGGGACTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
GACTTAAAAGTGCCAACGTGCTGATTCAAGCCCAGCAATGTTC
Found at i:24355 original size:33 final size:33
Alignment explanation
Indices: 24316--24425 Score: 159
Period size: 33 Copynumber: 3.4 Consensus size: 33
24306 TTGGGCTTAG
24316 AAGGGTTACCACCGACTTGTGTGGGCTTTAGAA
1 AAGGGTTACCACCGACTTGTGTGGGCTTTAGAA
* * *
24349 AAGGGTTGCCATCGACTTGTGTGGGTTTTAGAA
1 AAGGGTTACCACCGACTTGTGTGGGCTTTAGAA
* *
24382 AAGGGTTGCCACCGACTTGTGTGGGCTTTA-TA
1 AAGGGTTACCACCGACTTGTGTGGGCTTTAGAA
*
24414 AGGGGTTACCAC
1 AAGGGTTACCAC
24426 GGTGTTGTGG
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
32 11 0.16
33 58 0.84
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (33 bp):
AAGGGTTACCACCGACTTGTGTGGGCTTTAGAA
Found at i:24450 original size:27 final size:27
Alignment explanation
Indices: 24420--24473 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
24410 TATAAGGGGT
* * *
24420 TACCACGGTGTTGTGGACTTAAAAGGG
1 TACCACGGAGTTATGGAATTAAAAGGG
*
24447 TACCATGGAGTTATGGAATTAAAAGGG
1 TACCACGGAGTTATGGAATTAAAAGGG
24474 AAAGATGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.26
Consensus pattern (27 bp):
TACCACGGAGTTATGGAATTAAAAGGG
Found at i:24501 original size:32 final size:32
Alignment explanation
Indices: 24449--25157 Score: 507
Period size: 32 Copynumber: 21.6 Consensus size: 32
24439 TAAAAGGGTA
* * *
24449 CCATGGAGTTATGGAATTAAAAGGGAAAGATG
1 CCATGGAGTTGTGGACTTAAAAGGAAAAGATG
*
24481 CCATGGAATTGTGGACTTAAAAGGAAAAGATG
1 CCATGGAGTTGTGGACTTAAAAGGAAAAGATG
* * * *
24513 CCACGAAGTTGTGGACTTAAAAAGAAAAAAGGTG
1 CCATGGAGTTGTGGACTT-AAAAG-GAAAAGATG
** * *
24547 TAACGGAGTTGTAGG-CTTTAAAAGGAAAAAAGTG
1 CCATGGAGTTGT-GGAC-TTAAAAGGAAAAGA-TG
* * *
24581 CCATGAAGTTGTGGACTTAAAAGGGAAAGATA
1 CCATGGAGTTGTGGACTTAAAAGGAAAAGATG
* *** *
24613 TCACAAAGTTGTGGACTTAAAA-GAAAAGGATA
1 CCATGGAGTTGTGGACTTAAAAGGAAAA-GATG
* ** *
24645 TCGCGGAGTTGTGGACTTAAAAGGGAAAAAGGTG
1 CCATGGAGTTGTGGACTTAAAA-GG-AAAAGATG
*** * * * *
24679 CCGCAGAGTTTTGGGCTTTAAAAAGAAAAATATG
1 CCATGGAGTTGTGGAC-TT-AAAAGGAAAAGATG
* *
24713 CCACGGAGTTGTGAACTTAAAAAGG-AAAGATG
1 CCATGGAGTTGTGGACTT-AAAAGGAAAAGATG
* *
24745 CTATGGAGTTGTGGACTTAAAAGGAAAAGATA
1 CCATGGAGTTGTGGACTTAAAAGGAAAAGATG
24777 CCATGGAGTTGTGGACTTAAAAGGAAAAGATG
1 CCATGGAGTTGTGGACTTAAAAGGAAAAGATG
** * * *
24809 CCACAGAGTTGT-GAGCTTTAAAAAGAAAAGGGTA
1 CCATGGAGTTGTGGA-C-TTAAAAGGAAAA-GATG
* * *
24843 TCACGAAGTTGTGGACTTAAAAGGAAAAGATG
1 CCATGGAGTTGTGGACTTAAAAGGAAAAGATG
* *
24875 CCATGGAGTTGTGGACTTAAAAAGAAATGATG
1 CCATGGAGTTGTGGACTTAAAAGGAAAAGATG
*
24907 CCATGGAGTTGTGGACTTAAAAAGGAAAAGGGTG
1 CCATGGAGTTGTGGACTT-AAAAGGAAAA-GATG
* * ** * * *
24941 CCACGGTGTTGTGGGTTTTAAAAAGAAAAAATTA
1 CCATGGAGTTGT-GGACTTAAAAGGAAAAGA-TG
24975 CCATGGAGTTGTGGACTTAAAAGGGAAAA-ATG
1 CCATGGAGTTGTGGACTTAAAA-GGAAAAGATG
* * *
25007 CC-TCAGAGTTATGGACTTAAAAGGAAAGGATG
1 CCAT-GGAGTTGTGGACTTAAAAGGAAAAGATG
* * *
25039 TCACGGAGTTGTGGACTTAAAAGAGAAAAAGGTG
1 CCATGGAGTTGTGGACTTAAAAG-G-AAAAGATG
* * * * *
25073 TCACGAAGTTGTGGGATTTAAAAAGAAAAAGATG
1 CCATGGAGTTGT-GGACTT-AAAAGGAAAAGATG
* * *
25107 CCACGAAGTTGTGGACTTAAATGGGAAAATG-TG
1 CCATGGAGTTGTGGACTTAAA-AGGAAAA-GATG
*
25140 CCACT-GAGTCGTGGACTT
1 CCA-TGGAGTTGTGGACTT
25158 TTAGGAAATG
Statistics
Matches: 541, Mismatches: 104, Indels: 63
0.76 0.15 0.09
Matches are distributed among these distances:
31 18 0.03
32 244 0.45
33 97 0.18
34 151 0.28
35 22 0.04
36 9 0.02
ACGTcount: A:0.39, C:0.10, G:0.29, T:0.23
Consensus pattern (32 bp):
CCATGGAGTTGTGGACTTAAAAGGAAAAGATG
Found at i:24606 original size:132 final size:132
Alignment explanation
Indices: 24455--25134 Score: 753
Period size: 132 Copynumber: 5.2 Consensus size: 132
24445 GGTACCATGG
* * * *
24455 AGTTATGGAATTAAAAGGGAAAGATGCCATGGAATTGTGGACTTAAAAGGAAAAGATGCCACGAA
1 AGTTGTGGACTTAAAAGGGAAAGATGCCATGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGA
** * * *
24520 GTTGTGGACTTAAAAAGAAAAAAGGTGTAACGGAGTTGTAGGCTTTAAAAGGAAAAAAGTGCCAT
66 GTTGTGGACTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCAC
24585 GA
131 GA
** *** ** *
24587 AGTTGTGGACTTAAAAGGGAAAGATATCACAAAGTTGTGGACTTAAAA-GAAAAGGATATCGCGG
1 AGTTGTGGACTTAAAAGGGAAAGATGCCATGGAGTTGTGGACTTAAAAGGAAAA-GATGCCACGG
* * * * *
24651 AGTTGTGGACTTAAAAGGGAAAAAGGTGCCGCAGAGTTTTGGGCTTTAAAAAGAAAAATA-TGCC
65 AGTTGTGGACTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA-AGTGCC
*
24715 ACGG
129 ACGA
* * * * *
24719 AGTTGTGAACTTAAAAAGGAAAGATGCTATGGAGTTGTGGACTTAAAAGGAAAAGATACCATGGA
1 AGTTGTGGACTTAAAAGGGAAAGATGCCATGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGA
* * * * ** **
24784 GTTGTGGACTT-AAAAG-GAAAAGATGCCACAGAGTTGTGAGCTTTAAAAAGAAAAGGGTATCAC
66 GTTGTGGACTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCAC
24847 GA
131 GA
* * * *
24849 AGTTGTGGACTTAAAAGGAAAAGATGCCATGGAGTTGTGGACTTAAAAAGAAATGATGCCATGGA
1 AGTTGTGGACTTAAAAGGGAAAGATGCCATGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGA
* * * * * * *
24914 GTTGTGGACTTAAAAAGGAAAAGGGTGCCACGGTGTTGTGGGTTTTAAAAAGAAAAAATTACCAT
66 GTTGTGGACTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCAC
*
24979 GG
131 GA
* * * * *
24981 AGTTGTGGACTTAAAAGGGAAAAATGCC-TCAGAGTTATGGACTTAAAAGGAAAGGATGTCACGG
1 AGTTGTGGACTTAAAAGGGAAAGATGCCAT-GGAGTTGTGGACTTAAAAGGAAAAGATGCCACGG
* * *
25045 AGTTGTGGACTT-AAAAGAGAAAAAGGTGTCACGAAGTTGTGGGATTTAAAAAG-AAAAAGATGC
65 AGTTGTGGACTTAAAAAGA-AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAG-TGC
25108 CACGA
128 CACGA
*
25113 AGTTGTGGACTTAAATGGGAAA
1 AGTTGTGGACTTAAAAGGGAAA
25135 ATGTGCCACT
Statistics
Matches: 455, Mismatches: 84, Indels: 18
0.82 0.15 0.03
Matches are distributed among these distances:
130 107 0.24
131 25 0.05
132 317 0.70
133 6 0.01
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (132 bp):
AGTTGTGGACTTAAAAGGGAAAGATGCCATGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGA
GTTGTGGACTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCAC
GA
Found at i:24859 original size:98 final size:97
Alignment explanation
Indices: 24440--25127 Score: 622
Period size: 98 Copynumber: 7.0 Consensus size: 97
24430 TTGTGGACTT
* * * * * *
24440 AAAAGGGTACCATGGAGTTATGGAATTAAAAGGGAAAGATGCCATGGAATTGTGGACTTAAAAGG
1 AAAAGGGTATCACGGAGTTGTGGACTTAAAAGGAAAAGATGCCATGGAGTTGTGGACTTAAAAGG
24505 AAAAGATGCCAC-GAAGTTGTGGACTTAAAAAG
66 AAAAGATGCCACAG-AGTTGTGGACTTAAAAAG
* * * * *
24537 AAAAAAGGTGTAACGGAGTTGTAGG-CTTTAAAAGGAAAAAAGTGCCATGAAGTTGTGGACTTAA
1 -AAAAGGGTATCACGGAGTTGT-GGAC-TTAAAAGGAAAAGA-TGCCATGGAGTTGTGGACTTAA
* ** *
24601 AAGGGAAAGATATCACAAAGTTGTGGACTT-AAAAG
62 AAGGAAAAGATGCCACAGAGTTGTGGACTTAAAAAG
* * * *** * *
24636 AAAAGGATATCGCGGAGTTGTGGACTTAAAAGGGAAAAAGGTGCCGCAGAGTTTTGGGCTTTAAA
1 AAAAGGGTATCACGGAGTTGTGGACTTAAAA-GG-AAAAGATGCCATGGAGTTGTGGAC-TT-AA
* * * *
24701 AAGAAAAATATGCCACGGAGTTGTGAACTTAAAAAG
62 AAGGAAAAGATGCCACAGAGTTGTGGACTTAAAAAG
* * *
24737 GAAA--G-ATGCTATGGAGTTGTGGACTTAAAAGGAAAAGATACCATGGAGTTGTGGACTTAAAA
1 AAAAGGGTAT-C-ACGGAGTTGTGGACTTAAAAGGAAAAGATGCCATGGAGTTGTGGACTTAAAA
24799 GGAAAAGATGCCACAGAGTTGT-GAGCTTTAAAAAG
64 GGAAAAGATGCCACAGAGTTGTGGA-C-TTAAAAAG
* *
24834 AAAAGGGTATCACGAAGTTGTGGACTTAAAAGGAAAAGATGCCATGGAGTTGTGGACTTAAAAAG
1 AAAAGGGTATCACGGAGTTGTGGACTTAAAAGGAAAAGATGCCATGGAGTTGTGGACTTAAAAGG
* **
24899 AAATGATGCCATGGAGTTGTGGACTTAAAAAGG
66 AAAAGATGCCACAGAGTTGTGGACTTAAAAA-G
** * ** * * *
24932 AAAAGGGTGCCACGGTGTTGTGGGTTTTAAAAAGAAAAAATTACCATGGAGTTGTGGACTTAAAA
1 AAAAGGGTATCACGGAGTTGT-GGACTTAAAAGGAAAAGA-TGCCATGGAGTTGTGGACTTAAAA
* *
24997 GGGAAAA-ATGCCTCAGAGTTATGGACTT-AAAAG
64 -GGAAAAGATGCCACAGAGTTGTGGACTTAAAAAG
* * * * * * * *
25030 GAAAGGATGTCACGGAGTTGTGGACTTAAAAGAGAAAAAGGTGTCACGAAGTTGTGGGATTTAAA
1 AAAAGGGTATCACGGAGTTGTGGACTTAAAAG-G-AAAAGATGCCATGGAGTTGT-GGACTT-AA
*
25095 AAGAAAAAGATGCCAC-GAAGTTGTGGACTTAAA
62 AAGGAAAAGATGCCACAG-AGTTGTGGACTTAAA
25128 TGGGAAAATG
Statistics
Matches: 470, Mismatches: 91, Indels: 55
0.76 0.15 0.09
Matches are distributed among these distances:
95 1 0.00
96 24 0.05
97 36 0.08
98 180 0.38
99 65 0.14
100 150 0.32
101 14 0.03
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (97 bp):
AAAAGGGTATCACGGAGTTGTGGACTTAAAAGGAAAAGATGCCATGGAGTTGTGGACTTAAAAGG
AAAAGATGCCACAGAGTTGTGGACTTAAAAAG
Found at i:29909 original size:51 final size:51
Alignment explanation
Indices: 29805--29930 Score: 193
Period size: 51 Copynumber: 2.5 Consensus size: 51
29795 AAAAGTCACA
* *
29805 TTTTTACCCAAATATATCGATACA--TTTCAATGTATCGTTACATTCTGTC
1 TTTTTACCCAAATATATCGATACATTTTTCAATGTATCGATACATTCTATC
*
29854 TTTTTACCCAAATATATCGATACATTTTTTAATGTATCGATACATTCTATC
1 TTTTTACCCAAATATATCGATACATTTTTCAATGTATCGATACATTCTATC
* *
29905 TTTTTACCCAGATGTATCGATACATT
1 TTTTTACCCAAATATATCGATACATT
29931 GATCTAGTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
49 24 0.34
51 46 0.66
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (51 bp):
TTTTTACCCAAATATATCGATACATTTTTCAATGTATCGATACATTCTATC
Found at i:30832 original size:20 final size:22
Alignment explanation
Indices: 30792--30839 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
30782 TAGCCTTTGA
*
30792 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
30814 CCATGCA-TTTTTAAC-ATG-T
1 CCATGCATTTTTTAACTATGTT
30833 CCA-GCAT
1 CCATGCAT
30840 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 3 0.12
21 7 0.29
22 7 0.29
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:36388 original size:21 final size:20
Alignment explanation
Indices: 36351--36391 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
36341 GAGATGTTGG
36351 ACATACTAAAAGTGCATGAA
1 ACATACTAAAAGTGCATGAA
36371 ACATATCTCAAAA-TGCATGAA
1 ACATA-CT-AAAAGTGCATGAA
36392 CATGGGCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (20 bp):
ACATACTAAAAGTGCATGAA
Found at i:37930 original size:43 final size:43
Alignment explanation
Indices: 37877--38023 Score: 147
Period size: 43 Copynumber: 3.3 Consensus size: 43
37867 AATTAGTAAA
*
37877 CACTTTATTTGGTTAATAATTATTAATCTTAGAAATTAAAATT
1 CACTATATTTGGTTAATAATTATTAATCTTAGAAATTAAAATT
* * * *
37920 CACTATATTTGGTGTTACTGAA-AATCTAATATTATTATAATTAGTAAA--
1 CACTATATTT-G-GTTAAT-AATTAT-TAATCTTA-GA-AATTA--AAATT
*
37968 CACTTTATTTGGTTAATAATTATTAATCTTAGAAATTAAAATT
1 CACTATATTTGGTTAATAATTATTAATCTTAGAAATTAAAATT
38011 CACTATATTTGGT
1 CACTATATTTGGT
38024 GTTACTGAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
41 3 0.04
43 26 0.32
44 2 0.02
45 16 0.20
46 16 0.20
47 2 0.02
48 14 0.17
50 3 0.04
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (43 bp):
CACTATATTTGGTTAATAATTATTAATCTTAGAAATTAAAATT
Found at i:37967 original size:91 final size:91
Alignment explanation
Indices: 37865--38046 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
37855 CTCATCACTC
37865 ATAATTAGTAAACACTTTATTTGGTTAATAATTATTAATCTTAGAAATTAAAATTCACTATATTT
1 ATAATTAGTAAACACTTTATTTGGTTAATAATTATTAATCTTAGAAATTAAAATTCACTATATTT
37930 GGTGTTACTGAAAATCTAATATTATT
66 GGTGTTACTGAAAATCTAATATTATT
37956 ATAATTAGTAAACACTTTATTTGGTTAATAATTATTAATCTTAGAAATTAAAATTCACTATATTT
1 ATAATTAGTAAACACTTTATTTGGTTAATAATTATTAATCTTAGAAATTAAAATTCACTATATTT
38021 GGTGTTACTGAAAATCTAATATTATT
66 GGTGTTACTGAAAATCTAATATTATT
38047 TTGTTCAAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.44
Consensus pattern (91 bp):
ATAATTAGTAAACACTTTATTTGGTTAATAATTATTAATCTTAGAAATTAAAATTCACTATATTT
GGTGTTACTGAAAATCTAATATTATT
Found at i:41429 original size:31 final size:29
Alignment explanation
Indices: 41377--41445 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
41367 AGATGATTAG
41377 GGTGAAACCTAATAGTCAAAAGAATGACCAA
1 GGTGAAACCTAATAGTCAAAAG-ATGA-CAA
* *
41408 GGTGAAACCTTA-AGTCAAAAAGGTGACAA
1 GGTGAAACCTAATAGTC-AAAAGATGACAA
41437 GAGTGAAAC
1 G-GTGAAAC
41446 TCAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 4 0.12
30 14 0.41
31 16 0.47
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.16
Consensus pattern (29 bp):
GGTGAAACCTAATAGTCAAAAGATGACAA
Found at i:44435 original size:103 final size:103
Alignment explanation
Indices: 44322--44529 Score: 362
Period size: 104 Copynumber: 2.0 Consensus size: 103
44312 CCTAAATACA
*
44322 ACATTAAAAAATTATAATACAAAGACCAAAAATATTTAATAAAAAATAAAAGTTTGTTGGACTAA
1 ACATTAAAAAATTATAATACAAAGACCAAAAAAATTTAATAAAAAATAAAAGTTTGTTGGACTAA
* *
44387 GTTATAAGAGCCTAGTAAATTATTGCATTAAGAGTAAAC
66 -TTATAAGAGCCCAATAAATTATTGCATTAAGAGTAAAC
*
44426 ACATTAAAAAATTATAATACAAAGACCAAAAAAATTTAATAAAAAATAAAATTTTGTTGGACTAA
1 ACATTAAAAAATTATAATACAAAGACCAAAAAAATTTAATAAAAAATAAAAGTTTGTTGGACTAA
*
44491 TTATAAGAGCCCAATAGATTATTGCATTAAGAGTAAAC
66 TTATAAGAGCCCAATAAATTATTGCATTAAGAGTAAAC
44529 A
1 A
44530 GTTATTTATA
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
103 36 0.36
104 63 0.64
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (103 bp):
ACATTAAAAAATTATAATACAAAGACCAAAAAAATTTAATAAAAAATAAAAGTTTGTTGGACTAA
TTATAAGAGCCCAATAAATTATTGCATTAAGAGTAAAC
Found at i:45102 original size:16 final size:16
Alignment explanation
Indices: 45091--45137 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
45081 ACTTAAACTT
45091 ATTTAAATTTAAAATA
1 ATTTAAATTTAAAATA
* *
45107 ATTTAAATGTGAAA-A
1 ATTTAAATTTAAAATA
*
45122 AGTTAATATTTAAAAT
1 ATTTAA-ATTTAAAAT
45138 GATTCGAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTTAAATTTAAAATA
Found at i:45257 original size:17 final size:16
Alignment explanation
Indices: 45223--45285 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
45213 TAAAAATATA
45223 TAAACTCAAAATAATT
1 TAAACTCAAAATAATT
*
45239 TAAACTCTAAATAAATT
1 TAAACTCAAAAT-AATT
* *
45256 TAAGCTTAAAATAA-T
1 TAAACTCAAAATAATT
*
45271 TAAAATCTAAAATAA
1 TAAACTC-AAAATAA
45286 ACTAAATCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 5 0.13
16 20 0.53
17 13 0.34
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.32
Consensus pattern (16 bp):
TAAACTCAAAATAATT
Found at i:46389 original size:17 final size:19
Alignment explanation
Indices: 46367--46415 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
46357 TTATATATTT
46367 TTATTTTAAAAA-A-TTAA
1 TTATTTTAAAAACACTTAA
46384 TTATTTTAAAAAGCACTTAA
1 TTATTTTAAAAA-CACTTAA
46404 TT-TTTTAAAAAC
1 TTATTTTAAAAAC
46416 TATCATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 12 0.41
18 1 0.03
19 10 0.34
20 6 0.21
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (19 bp):
TTATTTTAAAAACACTTAA
Found at i:46510 original size:18 final size:18
Alignment explanation
Indices: 46483--46524 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
46473 TTATTCATTA
*
46483 ATATTTTTTAAATATAT-
1 ATATTTTTTAAAAATATC
46500 ATATATTTTTAAAAATATC
1 ATAT-TTTTTAAAAATATC
46519 ATATTT
1 ATATTT
46525 CTTATTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTTTTTAAAAATATC
Found at i:47103 original size:18 final size:19
Alignment explanation
Indices: 47082--47123 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
47072 TTAATGAAAC
47082 TAATTAAT-TTTTTTTTTA
1 TAATTAATATTTTTTTTTA
*
47100 TAATTAATATTTTTTTTTG
1 TAATTAATATTTTTTTTTA
47119 TAATT
1 TAATT
47124 TTACATTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TAATTAATATTTTTTTTTA
Found at i:47176 original size:18 final size:18
Alignment explanation
Indices: 47145--47199 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
47135 TACTAAATTA
47145 AATT-TTTATA-TAAAAT
1 AATTATTTATATTAAAAT
47161 AATTATTTATATTAAAAT
1 AATTATTTATATTAAAAT
47179 AATATATTTAATATTTAAAAT
1 AAT-TATTT-ATA-TTAAAAT
47200 TTATTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 9 0.26
19 5 0.15
20 3 0.09
21 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTATTTATATTAAAAT
Found at i:47432 original size:3 final size:3
Alignment explanation
Indices: 47419--47467 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
47409 CACTGTTGCT
47419 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47466 TT
1 TT
47468 GTTGTTTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:47642 original size:11 final size:11
Alignment explanation
Indices: 47628--47673 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
47618 TTTATATTAT
*
47628 ATTATGATTTA
1 ATTATTATTTA
47639 ATTATT-TTT-
1 ATTATTATTTA
47648 A-TATTATTTA
1 ATTATTATTTA
*
47658 ATTATTTTTTA
1 ATTATTATTTA
47669 ATTAT
1 ATTAT
47674 ATTATGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 4 0.13
11 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
ATTATTATTTA
Found at i:47683 original size:21 final size:20
Alignment explanation
Indices: 47634--47673 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
47624 TTATATTATG
47634 ATTTAATTA-TTTTTATATT
1 ATTTAATTATTTTTTATATT
47653 ATTTAATTATTTTTTA-ATT
1 ATTTAATTATTTTTTATATT
47672 AT
1 AT
47674 ATTATGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTAATTATTTTTTATATT
Found at i:48332 original size:22 final size:21
Alignment explanation
Indices: 48277--48332 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
48267 ACATTTCGAC
* *
48277 AATACTTTATATTCCATATAT
1 AATATTTTATTTTCCATATAT
48298 AATATTTTATTTTCCATCATA-
1 AATATTTTATTTTCCAT-ATAT
*
48319 AATACTTTTGTTTT
1 AATA-TTTTATTTT
48333 TTTAAACAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (21 bp):
AATATTTTATTTTCCATATAT
Found at i:48642 original size:4 final size:4
Alignment explanation
Indices: 48623--48707 Score: 98
Period size: 4 Copynumber: 21.2 Consensus size: 4
48613 ATAATGTGTA
* * * * *
48623 ATAT ATAC ATAC ATAT ATAT ATAT ATAT TTAT ACAT ACAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
48671 ATAT ATAT ATTT ATAC ATAC ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
48708 ATCTGTTATT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:48663 original size:30 final size:30
Alignment explanation
Indices: 48627--48707 Score: 153
Period size: 30 Copynumber: 2.7 Consensus size: 30
48617 TGTGTAATAT
*
48627 ATACATACATATATATATATATATTTATAC
1 ATACATATATATATATATATATATTTATAC
48657 ATACATATATATATATATATATATTTATAC
1 ATACATATATATATATATATATATTTATAC
48687 ATACATATATATATATATATA
1 ATACATATATATATATATATA
48708 ATCTGTTATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (30 bp):
ATACATATATATATATATATATATTTATAC
Found at i:52880 original size:20 final size:20
Alignment explanation
Indices: 52855--52909 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
52845 TTTTAACTAG
*
52855 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATCGAAAA
52875 ATGTATCGATACATCGAAAA
1 ATGTATCGATACATCGAAAA
*
52895 ATGTATCGATGCATC
1 ATGTATCGATACATC
52910 TGGGTAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACATCGAAAA
Found at i:53666 original size:18 final size:19
Alignment explanation
Indices: 53641--53686 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
53631 ACAAGTCTAA
53641 TCCAAAAATTTCTAC-TTT
1 TCCAAAAATTTCTACATTT
* *
53659 TTCAAAAATTTTTACATTT
1 TCCAAAAATTTCTACATTT
53678 TCCAAAAAT
1 TCCAAAAAT
53687 CATTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.43
Consensus pattern (19 bp):
TCCAAAAATTTCTACATTT
Found at i:62183 original size:2 final size:2
Alignment explanation
Indices: 62176--62206 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62166 TGTTTATTAC
62176 TA TA 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 TA TA T
62207 GTACGTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62646 original size:3 final size:3
Alignment explanation
Indices: 62640--62666 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
62630 CAACAACAAC
62640 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
62667 TTTAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:62733 original size:22 final size:22
Alignment explanation
Indices: 62687--62733 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
62677 GATAAAATTA
* * * *
62687 AATTTAAAGTTTAACTTTCTTT
1 AATTTAAAATTTAAATTTATAT
62709 AATTTAAAATTTAAATTTATAT
1 AATTTAAAATTTAAATTTATAT
62731 AAT
1 AAT
62734 CGATTAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTTAAAATTTAAATTTATAT
Found at i:62979 original size:20 final size:20
Alignment explanation
Indices: 62954--63001 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
62944 ATATTATTTT
62954 AATATTATA-ATAATATTTAA
1 AATATTATATAT-ATATTTAA
*
62974 AATATTATATATTTATTTAA
1 AATATTATATATATATTTAA
*
62994 AATTTTAT
1 AATATTAT
63002 CACATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATATTATATATATATTTAA
Found at i:63040 original size:6 final size:6
Alignment explanation
Indices: 63012--63067 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
63002 CACATTAATA
** *
63012 ATTTAT -TTTAT ATAAAT -TTTAT ATTTAT ATTTAT ATTTTAT ATTAAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT A-TTTAT ATTTAT
63059 -TTTAT ATTT
1 ATTTAT ATTT
63068 TTCATGTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 12 0.30
6 22 0.55
7 6 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:63066 original size:11 final size:11
Alignment explanation
Indices: 63016--63066 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
63006 TTAATAATTT
*
63016 ATTTTATATAA
1 ATTTTATATTA
*
63027 ATTTTATATTT
1 ATTTTATATTA
*
63038 ATATT-TA-T-
1 ATTTTATATTA
63046 ATTTTATATTA
1 ATTTTATATTA
63057 ATTTTATATT
1 ATTTTATATT
63067 TTTCATGTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 4 0.12
9 3 0.09
10 3 0.09
11 23 0.70
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTATATTA
Found at i:63069 original size:19 final size:19
Alignment explanation
Indices: 63027--63068 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
63017 TTTTATATAA
*
63027 ATTTTATATTTATATTTAT
1 ATTTTATATTAATATTTAT
63046 ATTTTATATTAAT-TTTAT
1 ATTTTATATTAATATTTAT
63064 ATTTT
1 ATTTT
63069 TCATGTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTATATTAATATTTAT
Found at i:64718 original size:5 final size:5
Alignment explanation
Indices: 64710--64747 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
64700 AAAGGAAAAA
64710 AGAAG AGAAG AGAAG AGAAG AG-AG AG-AG AGGAAG AGAA
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG A-GAAG AGAA
64748 AAATAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 7 0.23
5 21 0.68
6 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:65715 original size:20 final size:19
Alignment explanation
Indices: 65686--65723 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
65676 AAAGAAAAAT
65686 AATTAAAAACATTATAATTC
1 AATTAAAAACATTA-AATTC
*
65706 AATTAGAAACATTAAATT
1 AATTAAAAACATTAAATT
65724 TCCAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (19 bp):
AATTAAAAACATTAAATTC
Found at i:77462 original size:13 final size:13
Alignment explanation
Indices: 77444--77468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77434 CATAAAATGT
77444 TGTATCGATACAA
1 TGTATCGATACAA
77457 TGTATCGATACA
1 TGTATCGATACA
77469 TATTTTTTTG
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:77550 original size:13 final size:13
Alignment explanation
Indices: 77532--77556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77522 ATTACTCAAA
77532 TGTATCGATACAT
1 TGTATCGATACAT
77545 TGTATCGATACA
1 TGTATCGATACA
77557 CTGATCTTTG
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:77607 original size:52 final size:53
Alignment explanation
Indices: 77545--77681 Score: 165
Period size: 52 Copynumber: 2.6 Consensus size: 53
77535 ATCGATACAT
*** * *
77545 TGTATCGATACACTGAT-CTTTGTATCGATACGTGCAGGCAAATTTG-CCTAGA
1 TGTATCGATACACTGATAAAATATATCGATACATGCAGGCAAATTTGTCC-AGA
*
77597 TGTATCGATACA-TTATAAAATATATCGATACATGCAGGCAAATTTGTCCAGA
1 TGTATCGATACACTGATAAAATATATCGATACATGCAGGCAAATTTGTCCAGA
* *
77649 TGTATCGATACACT-ATTAAATGTATCGATACAT
1 TGTATCGATACACTGATAAAATATATCGATACAT
77682 ACAAGCAACT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
51 3 0.04
52 68 0.92
53 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (53 bp):
TGTATCGATACACTGATAAAATATATCGATACATGCAGGCAAATTTGTCCAGA
Found at i:84639 original size:11 final size:11
Alignment explanation
Indices: 84616--84649 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
84606 AAAAGTAAAC
84616 ACAAAAAACAAA
1 ACAAAAAA-AAA
84628 ACAAAAAAAAA
1 ACAAAAAAAAA
84639 ACCAAAAAAAA
1 A-CAAAAAAAA
84650 GTGCAAAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:85883 original size:31 final size:31
Alignment explanation
Indices: 85845--86020 Score: 198
Period size: 31 Copynumber: 5.7 Consensus size: 31
85835 ATACTTTTTT
*
85845 AAAGTCCACGACTTAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
85876 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* *
85907 AAAGTCCACGACTCAGTGGC-ATCCTTTTCTTT
1 AAAGTCCACGACTCAGTGGCAAT-CTCTTC-TC
*
85939 AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
* *
85969 AAAGTCCACGACTCAGTGGC-ATTTTTTCTTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTC-TC
* * *
86000 AAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
86021 CTCTTAAGCC
Statistics
Matches: 130, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
30 30 0.23
31 77 0.59
32 23 0.18
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:85925 original size:62 final size:62
Alignment explanation
Indices: 85845--86020 Score: 232
Period size: 62 Copynumber: 2.8 Consensus size: 62
85835 ATACTTTTTT
* *
85845 AAAGTCCACGACTTAGTGGCAATCTCTTC-TCAAAGTCCACGACTCAGTGGCAATCTCTG-CTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTTCAAAGTCCACGACTCAGTGGCAAT-TCTGTCTC
* *
85907 AAAGTCCACGACTCAGTGGCATCCTTTTCTTTAAAGTCCACGACTCAGTGGC-ATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCAT-CTTTTCTTCAAAGTCCACGACTCAGTGGCAATTCTGTCTC
* * * *
85969 AAAGTCCACGACTCAGTGGCATTTTTTCTTCAAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCA
86021 CTCTTAAGCC
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
61 29 0.29
62 51 0.50
63 21 0.21
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (62 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCAATTCTGTCTC
Found at i:86002 original size:93 final size:94
Alignment explanation
Indices: 85842--86020 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 94
85832 CAAATACTTT
*
85842 TTTAAAGTCCACGACTTAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 TTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
* *
85907 AAAGTCCACGACTCAGTGGCATCCTTTTC
66 AAAGCCCACAACTCAGTGGCATCCTTTTC
* * * *
85936 TTTAAAGTCCACGACTCAGTGGC-AT-TTTGTCTCAAAGTCCACGACTCAGTGGC-ATTTTTTCT
1 TTTAAAGTCCACGACTCAGTGGCAATCTCT-TCTCAAAGTCCACGACTCAGTGGCAATCTCTGC-
*
85998 TCAAAGCCCACAACTCCGTGGCA
64 TCAAAGCCCACAACTCAGTGGCA
86021 CTCTTAAGCC
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
92 7 0.09
93 46 0.61
94 22 0.29
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (94 bp):
TTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
AAAGCCCACAACTCAGTGGCATCCTTTTC
Found at i:86087 original size:34 final size:33
Alignment explanation
Indices: 86044--86542 Score: 524
Period size: 34 Copynumber: 15.0 Consensus size: 33
86034 TCTGTGGCAC
* *
86044 TCTTTTCAAAGCCCACAACTCTGTGGCACCTTCT
1 TCTTTT-AAAGCCCACAACTCCGTGGCACCTTTT
* *
86078 TCTTTTCAAAGCCCACGACTCCGTGGCA-C--TC
1 TCTTTT-AAAGCCCACAACTCCGTGGCACCTTTT
*
86109 T-TTTTAAAGCCCACAACTCCGTGGCACCTTCT
1 TCTTTTAAAGCCCACAACTCCGTGGCACCTTTT
86141 TCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTT
1 TCTTTT-AAAGCCCACAACTCCGTGGCAC-CTTTT
* *
86176 TCCTTCT-AAGCCCACAACTCTGTGGCACTTCTTTT
1 T-CTTTTAAAGCCCACAACTCCGTGGCAC--CTTTT
86211 T-TTTTAAAGCCCACAACTCCGTGGCACC----
1 TCTTTTAAAGCCCACAACTCCGTGGCACCTTTT
*
86239 -CTTTT-AAGCCCACAACTCCGTGGCACTTTTT
1 TCTTTTAAAGCCCACAACTCCGTGGCACCTTTT
*
86270 TCATCTTT-AAGTCCACAACTCCGTGGCACCTTTT
1 TC-T-TTTAAAGCCCACAACTCCGTGGCACCTTTT
*
86304 TCTGTTTAAAGCCCACAACTCCGTGGCACTTTTT
1 TCT-TTTAAAGCCCACAACTCCGTGGCACCTTTT
* * *
86338 TCTTTTTAAGCCTACAACTCCGTGGCACTTTTT
1 TCTTTTAAAGCCCACAACTCCGTGGCACCTTTT
* *
86371 TCATCTTT-AAGTCCACAACTCTGTGGCACCTTTT
1 TC-T-TTTAAAGCCCACAACTCCGTGGCACCTTTT
*
86405 TCTGTTTAAAGCCCACAACTCCATGGCACTCTTTT
1 TCT-TTTAAAGCCCACAACTCCGTGGCAC-CTTTT
*
86440 TCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTT
1 T--CTTTT-AAAGCCCACAACTCCGTGGCACCTTTT
*
86476 TCTTTTAAAGCCCACAACTCCATGGCACTCTTTT
1 TCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTT
* * *
86510 TCCCTTTT-AAGTCCACAACTCCATGGCATCTTT
1 T--CTTTTAAAGCCCACAACTCCGTGGCACCTTT
86543 CTCCCTTCCT
Statistics
Matches: 403, Mismatches: 34, Indels: 56
0.82 0.07 0.11
Matches are distributed among these distances:
27 21 0.05
28 4 0.01
29 20 0.05
30 5 0.01
31 1 0.00
32 3 0.01
33 68 0.17
34 201 0.50
35 40 0.10
36 17 0.04
37 23 0.06
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (33 bp):
TCTTTTAAAGCCCACAACTCCGTGGCACCTTTT
Found at i:86251 original size:27 final size:28
Alignment explanation
Indices: 86000--86332 Score: 149
Period size: 34 Copynumber: 10.8 Consensus size: 28
85990 TTTTTTCTTC
*
86000 AAAGCCCACAACTCCGTGGCA--CTCTT
1 AAAGCCCACAACTCCGTGGCACCCTTTT
* * *
86026 -AAG--C-CGACTCTGTGGCACTCTTTT
1 AAAGCCCACAACTCCGTGGCACCCTTTT
*
86050 CAAAGCCCACAACTCTGTGGCACCTTCTTCTTTT
1 -AAAGCCCACAACTCCGTGGCA-C--C--CTTTT
* *
86084 CAAAGCCCACGACTCCGTGGCACTCTTTTT
1 -AAAGCCCACAACTCCGTGGCAC-CCTTTT
86114 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 AAAGCCCACAACTCCGTGGCA-C--C--CTTTT
*
86147 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCTT
1 -AAAGCCCACAACTCCGTGGCAC-C--CTT--TT
* * *
86181 CTAAGCCCACAACTCTGTGGCACTTCTTTTTTTTT
1 -AAAGCCCACAACTCCGTGGCAC--C----CTTTT
86216 AAAGCCCACAACTCCGTGGCACCCTTTT
1 AAAGCCCACAACTCCGTGGCACCCTTTT
**
86244 -AAGCCCACAACTCCGTGGCACTTTTTT
1 AAAGCCCACAACTCCGTGGCACCCTTTT
*
86271 CATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTT
1 -A-----AAGCCCACAACTCCGTGGCACC-----CT-TTT
86311 AAAGCCCACAACTCCGTGGCAC
1 AAAGCCCACAACTCCGTGGCAC
86333 TTTTTTCTTT
Statistics
Matches: 250, Mismatches: 22, Indels: 62
0.75 0.07 0.19
Matches are distributed among these distances:
22 11 0.04
23 1 0.00
24 4 0.02
25 3 0.01
26 3 0.01
27 25 0.10
28 5 0.02
29 32 0.13
30 6 0.02
31 2 0.01
32 9 0.04
33 6 0.02
34 129 0.52
35 4 0.02
37 5 0.02
39 2 0.01
40 3 0.01
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.30
Consensus pattern (28 bp):
AAAGCCCACAACTCCGTGGCACCCTTTT
Found at i:86382 original size:101 final size:102
Alignment explanation
Indices: 86044--86542 Score: 563
Period size: 101 Copynumber: 5.0 Consensus size: 102
86034 TCTGTGGCAC
* * * *
86044 TCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCT-TTTCAAAGCCCACGACTCCGTGGCACT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTCTTT--AAGCCCACAACTCCGTGGCACT
* *
86108 C----T-T-TTTAAAGCCCACAACTCCGTGGCACCTTCT
64 CTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTTTTT
*
86141 TCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTC-CTTCTAAGCCCACAACTCTGTGGCACT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACT-TTTTTCTCTT-TAAGCCCACAACTCCGTGGCAC-
86205 TCTTTTT-T-TTTAAAGCCCACAACTCCGTGGCAC-----
63 TCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTTTTT
* *
86238 CCTTTT--AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCAC-C
1 TCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC-TCTTTAAGCCCACAACTCCGTGGCACTC
86300 TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTTTTT
65 TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTTTTT
* * * *
86338 TCTTTT-TAAGCCTACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCTGTGGCAC-C
1 TCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC-TCTTTAAGCCCACAACTCCGTGGCACTC
*
86401 TTTTTCTGTTTAAAGCCCACAACTCCATGGCACTCTTTT
65 TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACT-TTTT
*
86440 TCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCT-TTTAAAGCCCACAACTCCATGGCAC
1 T--CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTCTTT-AAGCCCACAACTCCGTGGCAC
** * * *
86504 TCTTTTTCCCTTTTAAGTCCACAACTCCATGGCATCTTT
63 TCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCA-CTTT
86543 CTCCCTTCCT
Statistics
Matches: 356, Mismatches: 21, Indels: 42
0.85 0.05 0.10
Matches are distributed among these distances:
93 6 0.02
94 7 0.02
95 67 0.19
96 3 0.01
97 52 0.15
98 9 0.03
99 1 0.00
100 5 0.01
101 87 0.24
102 32 0.09
103 3 0.01
104 24 0.07
105 58 0.16
106 2 0.01
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (102 bp):
TCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAGCCCACAACTCCGTGGCACTCT
TTTTCTGTTTAAAGCCCACAACTCCGTGGCACTTTTT
Found at i:86583 original size:104 final size:102
Alignment explanation
Indices: 86244--86595 Score: 263
Period size: 101 Copynumber: 3.4 Consensus size: 102
86234 GCACCCTTTT
* * * * **
86244 AAGCCCACAACTCCGTGGCACT-TTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTG
1 AAGCCCACAACTCCGTGGCACTCTTCTT-A-C--AAAGCCCACAACTCCATGGCACCTTTTTCCC
* * **
86308 TTTAAAGCCCACAACTCCGTGGCACT-TTT-T-TCTT-TTT
62 TTTAAAGCCCACAACTCCATGGCACTCTTTCTCCCTTCTCA
* * * * ** **
86345 AAGCCTACAACTCCGTGGCACT-TTTTTCATCTTTAAGTCCACAACTCTGTGGCACCTTTTTCTG
1 AAGCCCACAACTCCGTGGCACTCTTCTT-A-C--AAAGCCCACAACTCCATGGCACCTTTTTCCC
* *
86409 TTTAAAGCCCACAACTCCATGGCACTCTTTTTCCCTTTTCA
62 TTTAAAGCCCACAACTCCATGGCACTCTTTCTCCCTTCTCA
* **
86450 AAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCATGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCAC--TCTTCTTACAAAGCCCACAACTCCATGGCAC-CTTTTTCCCT
* *
86515 TTTAAGTCCACAACTCCATGGCA-TCTTTCTCCCTTC-CTA
63 TTAAAGCCCACAACTCCATGGCACTCTTTCTCCCTTCTC-A
* *
86554 AAGCCCACACAAGTCGGTGGCAAC-CTTCTTACAAAGCCCACA
1 AAG-CC-CACAACTCCGTGGC-ACTCTTCTTACAAAGCCCACA
86596 CAAGTCGGTG
Statistics
Matches: 214, Mismatches: 25, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
101 87 0.41
102 3 0.01
103 2 0.01
104 51 0.24
105 52 0.24
106 12 0.06
107 3 0.01
108 4 0.02
ACGTcount: A:0.22, C:0.33, G:0.12, T:0.33
Consensus pattern (102 bp):
AAGCCCACAACTCCGTGGCACTCTTCTTACAAAGCCCACAACTCCATGGCACCTTTTTCCCTTTA
AAGCCCACAACTCCATGGCACTCTTTCTCCCTTCTCA
Found at i:86590 original size:33 final size:34
Alignment explanation
Indices: 86553--86616 Score: 121
Period size: 33 Copynumber: 1.9 Consensus size: 34
86543 CTCCCTTCCT
86553 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTTAC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTAC
86586 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
86617 AAGCCCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 24 0.80
34 6 0.20
ACGTcount: A:0.30, C:0.34, G:0.19, T:0.17
Consensus pattern (34 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTTAC
Found at i:86682 original size:49 final size:49
Alignment explanation
Indices: 86616--87002 Score: 395
Period size: 49 Copynumber: 8.0 Consensus size: 49
86606 GCAACCCTTC
*
86616 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * *
86665 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
86714 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * *
86757 TAAG-CCTGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
86806 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
86849 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TTT-ATCTT
* * * *
86901 CAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * * * *
86956 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
87003 ACTTTTCTCA
Statistics
Matches: 287, Mismatches: 31, Indels: 40
0.80 0.09 0.11
Matches are distributed among these distances:
42 2 0.01
43 75 0.26
44 2 0.01
48 2 0.01
49 119 0.41
50 3 0.01
51 2 0.01
52 38 0.13
53 2 0.01
54 5 0.02
55 37 0.13
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:86774 original size:43 final size:43
Alignment explanation
Indices: 86711--86892 Score: 240
Period size: 43 Copynumber: 4.1 Consensus size: 43
86701 GCATCTTCAT
* *
86711 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* *
86754 CTTTAAG-CCTGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCA----C
* *
86801 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
86846 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
86889 CTTT
1 CTTT
86893 TTCATCTTCA
Statistics
Matches: 121, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
42 2 0.02
43 80 0.66
45 1 0.01
47 1 0.01
49 35 0.29
50 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:86795 original size:92 final size:92
Alignment explanation
Indices: 86662--86945 Score: 453
Period size: 92 Copynumber: 3.0 Consensus size: 92
86652 GCACCTTTAT
86662 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
86727 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
86754 CTTTAAG-CCTGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
86818 AGCTGGCCTTGAATCAGCACATTGGCAC
65 AGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
86846 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTTCAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA---TCTTCATCTTTAAGTCCAAT
* *
86911 ATAGCTGGCCTTGAATCAGCACATTGACATC
63 GTAGCTGGCCTTGAATCAGCACATTGGCA-C
86942 CTTT
1 CTTT
86946 TTCTCATCTT
Statistics
Matches: 178, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
91 2 0.01
92 125 0.70
93 2 0.01
95 44 0.25
96 5 0.03
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:86981 original size:55 final size:52
Alignment explanation
Indices: 86846--86983 Score: 177
Period size: 52 Copynumber: 2.6 Consensus size: 52
86836 ACATTGGCAC
* *
86846 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTTCAT
* *
86898 CTTCAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA-CC-TTTT-TCAT
* * * *
86953 CTTTAAGCCCAATATCGTTGGCCATGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
86984 ACATATTGGC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
52 38 0.52
53 2 0.03
54 4 0.05
55 29 0.40
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTTCAT
Found at i:87886 original size:13 final size:13
Alignment explanation
Indices: 87868--87892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87858 CATAAAATGT
87868 TGTATCGATACAA
1 TGTATCGATACAA
87881 TGTATCGATACA
1 TGTATCGATACA
87893 TATTTTTTTG
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:87974 original size:13 final size:13
Alignment explanation
Indices: 87956--87980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87946 ATTACTCAAA
87956 TGTATCGATACAT
1 TGTATCGATACAT
87969 TGTATCGATACA
1 TGTATCGATACA
87981 CTGATCTTTG
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:88031 original size:52 final size:53
Alignment explanation
Indices: 87969--88105 Score: 199
Period size: 52 Copynumber: 2.6 Consensus size: 53
87959 ATCGATACAT
*** *
87969 TGTATCGATACACTGAT-CTTTGTATCGATACGTGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
88021 TGTATCGATACA-TTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
88073 TGTATCGATACACT-ATTAAATGTATCGATACAT
1 TGTATCGATACACTGATAAAATGTATCGATACAT
88106 ACAAGCAACT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
51 3 0.04
52 73 0.95
53 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (53 bp):
TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:96012 original size:20 final size:20
Alignment explanation
Indices: 95985--96039 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
95975 AAAAGGATAG
* *
95985 AATGTATCGATACATTCATA
1 AATGTATCGATACATTAAAA
** *
96005 CGTGTATCAATACATTAAAA
1 AATGTATCGATACATTAAAA
96025 AATGTATCGATACAT
1 AATGTATCGATACAT
96040 CTAGGTAACA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:97276 original size:30 final size:30
Alignment explanation
Indices: 97136--97365 Score: 106
Period size: 30 Copynumber: 7.7 Consensus size: 30
97126 CGTTGGCAAA
97136 CCTCTTTCAAAAGCCCACAAGTCAG-GGCA-
1 CCTC-TTCAAAAGCCCACAAGTCAGTGGCAT
* * * * *
97165 CC-CTTTAAAAGTCCCATAAGTTAATGGTA-
1 CCTCTTCAAAAG-CCCACAAGTCAGTGGCAT
* * * * *
97194 ACT-TTCATAAGCTCACGAGTCAGAGGCAT
1 CCTCTTCAAAAGCCCACAAGTCAGTGGCAT
* * * *
97223 CCT-TCCATAA-CGACACCAGTCAGTGGCAT
1 CCTCTTCAAAAGC-CCACAAGTCAGTGGCAT
97252 CCTTCTTC-AAAGCCCACAAGTCAGTGGCACT
1 CC-TCTTCAAAAGCCCACAAGTCAGTGGCA-T
* * *
97283 CCTCTT---AAGCCTACATAAGTCGGTGGCCAA
1 CCTCTTCAAAAGCC--CACAAGTCAGTGG-CAT
*
97313 CCTCTCTCATAAAGCCCACAAGTCAGTTGGCAG
1 CCTCT-TCA-AAAGCCCACAAGTCAG-TGGCAT
97346 CC-CTTTCAAAAGCCCACAAG
1 CCTC-TTCAAAAGCCCACAAG
97366 GGTCCAAAAA
Statistics
Matches: 152, Mismatches: 30, Indels: 36
0.70 0.14 0.17
Matches are distributed among these distances:
27 7 0.05
28 26 0.17
29 36 0.24
30 37 0.24
31 21 0.14
32 4 0.03
33 13 0.09
34 3 0.02
35 5 0.03
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (30 bp):
CCTCTTCAAAAGCCCACAAGTCAGTGGCAT
Done.