Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2393_ERROPOS410500
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: 99999
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2611 original size:42 final size:42
Alignment explanation
Indices: 2515--2674 Score: 155
Period size: 42 Copynumber: 3.8 Consensus size: 42
2505 ACCATACCAG
* **
2515 TGCCATATCCTAGATATGGTCTTACA-TGAGATCTC-G-TACGA
1 TGCCATATCCCAGATATGGTCTTACACAAAG-TCTCAGATA-GA
* * * * *
2556 TGCCAATAGCCCAGCTATGGTATTACACAAAGTCTCATATTGA
1 TGCC-ATATCCCAGATATGGTCTTACACAAAGTCTCAGATAGA
* *
2599 TGCCATATCCCAGATATGGTCTTACACGAAGTCTTAGATAGA
1 TGCCATATCCCAGATATGGTCTTACACAAAGTCTCAGATAGA
* * *
2641 TGTCATATACCAGATATGGTCTTACACATAGTCT
1 TGCCATATCCCAGATATGGTCTTACACAAAGTCT
2675 TAGTAACCCT
Statistics
Matches: 96, Mismatches: 19, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
41 4 0.04
42 83 0.86
43 8 0.08
44 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (42 bp):
TGCCATATCCCAGATATGGTCTTACACAAAGTCTCAGATAGA
Found at i:2659 original size:84 final size:83
Alignment explanation
Indices: 2515--2674 Score: 191
Period size: 84 Copynumber: 1.9 Consensus size: 83
2505 ACCATACCAG
* * * *
2515 TGCCATATCCTAGATATGGTCTTACATGAGATCTCGTACGATGCCAATAGCCCAGCTATGGTATT
1 TGCCATATCCCAGATATGGTCTTACACGAGATCTAGTACGATGCCAATA-CCCAGATATGGTATT
2580 ACACAAAGTCTCATATTGA
65 ACACAAAGTCTCATATTGA
*
2599 TGCCATATCCCAGATATGGTCTTACACGA-AGTCTTAGATA-GATGTCATATA-CCAGATATGGT
1 TGCCATATCCCAGATATGGTCTTACACGAGA-TC-TAG-TACGATGCCA-ATACCCAGATATGGT
* *
2661 CTTACACATAGTCT
62 ATTACACAAAGTCT
2675 TAGTAACCCT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
83 1 0.02
84 51 0.78
85 8 0.12
86 5 0.08
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (83 bp):
TGCCATATCCCAGATATGGTCTTACACGAGATCTAGTACGATGCCAATACCCAGATATGGTATTA
CACAAAGTCTCATATTGA
Found at i:8837 original size:27 final size:27
Alignment explanation
Indices: 8803--9010 Score: 233
Period size: 27 Copynumber: 7.7 Consensus size: 27
8793 TGGATAAGTT
8803 GTAGAATTACCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAAG
** *
8830 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAAG
** *
8857 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAAG
** *
8884 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAAG
*
8911 GTAGAATTACCGAAATACCCCTAT-AG
1 GTAGAATTACCGAAATACCCCTGTAAG
** *
8937 GATAGAATTACTAAAATACCCTTGTAAG
1 G-TAGAATTACCGAAATACCCCTGTAAG
*
8965 GTCA-AAATACCGAAATACCCCTGT-AG
1 GT-AGAATTACCGAAATACCCCTGTAAG
*
8991 GATAGAATTACCGAGATACC
1 G-TAGAATTACCGAAATACC
9011 TTCGTGGGGT
Statistics
Matches: 159, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
26 6 0.04
27 149 0.94
28 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAAG
Found at i:8879 original size:54 final size:54
Alignment explanation
Indices: 8803--9000 Score: 283
Period size: 54 Copynumber: 3.7 Consensus size: 54
8793 TGGATAAGTT
8803 GTAGAATTACCGAAATACCCCTGTAAGG-TAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGT-AGGATAGAATTATTGAAATACCCCTGTAGG
** *
8857 GTAGAATTATTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGGATAGAATTATTGAAATACCCCTGTAGG
* * * * *
8911 GTAGAATTACCGAAATACCCCTATAGGATAGAATTACTAAAATACCCTTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGGATAGAATTATTGAAATACCCCTGTAGG
*
8965 GTCA-AAATACCGAAATACCCCTGTAGGATAGAATTA
1 GT-AGAATTACCGAAATACCCCTGTAGGATAGAATTA
9001 CCGAGATACC
Statistics
Matches: 130, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
53 3 0.02
54 126 0.97
55 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (54 bp):
GTAGAATTACCGAAATACCCCTGTAGGATAGAATTATTGAAATACCCCTGTAGG
Found at i:8943 original size:81 final size:81
Alignment explanation
Indices: 8803--9010 Score: 274
Period size: 81 Copynumber: 2.6 Consensus size: 81
8793 TGGATAAGTT
* ** * * *
8803 GTAGAATTACCGAAATACCCCTGTAAGGTAGAATTATTGAAATACCCCTGTAGGGTAGAATTATT
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTACT
* *
8868 GAAATACCCCTGTAGG
66 AAAATACCCCTGTAAG
**
8884 GTAGAATTATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTACT
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTACT
*
8949 AAAATACCCTTGTAAG
66 AAAATACCCCTGTAAG
* * *
8965 GTCA-AAATACCGAAATACCCCTGTAGGATAGAATTACCGAGATACC
1 GT-AGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACC
9011 TTCGTGGGGT
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 109 0.99
82 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (81 bp):
GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTACT
AAAATACCCCTGTAAG
Found at i:13714 original size:41 final size:41
Alignment explanation
Indices: 13669--13750 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
13659 GACTCGATTT
13669 GGGTAATTGTGAATAGGTTGACCAAATCTGCTCATTTCATA
1 GGGTAATTGTGAATAGGTTGACCAAATCTGCTCATTTCATA
*
13710 GGGTAATTGTGGATAGGTTGACCAAATCTGCTCATTTCATA
1 GGGTAATTGTGAATAGGTTGACCAAATCTGCTCATTTCATA
13751 CCTGTCCGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (41 bp):
GGGTAATTGTGAATAGGTTGACCAAATCTGCTCATTTCATA
Found at i:18579 original size:27 final size:27
Alignment explanation
Indices: 18449--18576 Score: 175
Period size: 27 Copynumber: 4.7 Consensus size: 27
18439 TAGATAAGTT
18449 GTAGAATTACCGAAATACCCATGTAGG
1 GTAGAATTACCGAAATACCCATGTAGG
** * *
18476 GTAGAATTATTGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCATGTAGG
**
18503 GTAGAATTATTGAAATACCCATGTAGG
1 GTAGAATTACCGAAATACCCATGTAGG
*
18530 GTAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCATGTAGG
* *
18557 GTAGAATTACAGAGATACCC
1 GTAGAATTACCGAAATACCC
18577 TTGCGGGGTA
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCATGTAGG
Found at i:18585 original size:27 final size:27
Alignment explanation
Indices: 18449--18593 Score: 164
Period size: 27 Copynumber: 5.4 Consensus size: 27
18439 TAGATAAGTT
* *
18449 GTAGAATTACCGAAATACCCATGTAGG
1 GTAGAATTACAGAAATACCCTTGTAGG
** * *
18476 GTAGAATTATTGAAATACCCCTATAGG
1 GTAGAATTACAGAAATACCCTTGTAGG
** *
18503 GTAGAATTATTGAAATACCCATGTAGG
1 GTAGAATTACAGAAATACCCTTGTAGG
*
18530 GTAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACAGAAATACCCTTGTAGG
* **
18557 GTAGAATTACAGAGATACCCTTGCGGG
1 GTAGAATTACAGAAATACCCTTGTAGG
*
18584 GTAAAATTAC
1 GTAGAATTAC
18594 TATTTTGCCC
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 104 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (27 bp):
GTAGAATTACAGAAATACCCTTGTAGG
Found at i:20775 original size:35 final size:36
Alignment explanation
Indices: 20715--20802 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 36
20705 CTTGGCCCAT
* *
20715 TGCAGTAACAGTAAACAATAAAGTAACAGT-AATAG
1 TGCAGTAATAGTAAACAATAAAGTAACAATAAATAG
* *
20750 TGCATTAATAGTAAACAATACAGTAACAATAAATAG
1 TGCAGTAATAGTAAACAATAAAGTAACAATAAATAG
* *
20786 TGTAGTAATAATAAACA
1 TGCAGTAATAGTAAACA
20803 GTATGCAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 26 0.58
36 19 0.42
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (36 bp):
TGCAGTAATAGTAAACAATAAAGTAACAATAAATAG
Found at i:21301 original size:27 final size:27
Alignment explanation
Indices: 21125--21300 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21115 ACAAAGGAGT
* * *
21125 AAAACAGTCATCTTACCAT-AAAAGGGC
1 AAAACAGTCATTTTACC-TCATAAGGGA
* *
21152 AAAACAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACCTCATAAGGGA
* *
21179 AAAACAGTGATTTTACCTCATAAAGGA
1 AAAACAGTCATTTTACCTCATAAGGGA
*
21206 AAAACAGTGATTTTACCTCATAAGGGA
1 AAAACAGTCATTTTACCTCATAAGGGA
* *
21233 AAAATAGTCATTTTACCTCATAAGGGC
1 AAAACAGTCATTTTACCTCATAAGGGA
*
21260 AAAACAGTCA-TTTA-TTCCATAAGGGA
1 AAAACAGTCATTTTACCT-CATAAGGGA
*
21286 AAAAAAGTCATTTTA
1 AAAACAGTCATTTTA
21301 TCGATTAAGG
Statistics
Matches: 131, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
25 1 0.01
26 21 0.16
27 109 0.83
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (27 bp):
AAAACAGTCATTTTACCTCATAAGGGA
Found at i:21448 original size:17 final size:17
Alignment explanation
Indices: 21422--21468 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
21412 TACGGGCCCA
21422 TGTG-GGCCCACATGTC
1 TGTGTGGCCCACATGTC
21438 TGTGTGGCCCACATGTC
1 TGTGTGGCCCACATGTC
21455 TGTGTGGCCCACAT
1 TGTGTGGCCCACAT
21469 AGTCCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 4 0.13
17 26 0.87
ACGTcount: A:0.13, C:0.30, G:0.30, T:0.28
Consensus pattern (17 bp):
TGTGTGGCCCACATGTC
Found at i:32128 original size:18 final size:18
Alignment explanation
Indices: 32071--32157 Score: 88
Period size: 18 Copynumber: 4.9 Consensus size: 18
32061 CTTGGCCCAT
*
32071 TGCAGTAACAGT-AACAG
1 TGCAGTAATAGTAAACAG
* *
32088 TGCAGTAACAGT-AACAA
1 TGCAGTAATAGTAAACAG
** *
32105 CACAGTAATAGCAAACAG
1 TGCAGTAATAGTAAACAG
*
32123 TGCAGTAACAGTAAACAG
1 TGCAGTAATAGTAAACAG
*
32141 TGCAATAATAGTAAACA
1 TGCAGTAATAGTAAACA
32158 ATATGCAAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
17 24 0.42
18 33 0.58
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.17
Consensus pattern (18 bp):
TGCAGTAATAGTAAACAG
Found at i:32610 original size:80 final size:81
Alignment explanation
Indices: 32471--32683 Score: 227
Period size: 80 Copynumber: 2.6 Consensus size: 81
32461 AACATACATA
* * * * * * *
32471 CATAGGGGTAAAACAATCATCTTACCAT-AAAAAGCGCAAAACAGTCATCTTACCACAT-AAGAG
1 CATAAGGGAAAAACAATCATTTTACC-TCATAACG-GCAAAAAAGTCATTTTACCACATAAAG-G
*
32534 CAAAAAAATGATTTTACCT
63 CAAAAAAATCATTTTACCT
* * *
32553 CATAAGGGCAAAACAATGATTTTACCTCATAACGG-AAAAAAGTCATTTTACCTCATAAAGGCAA
1 CATAAGGGAAAAACAATCATTTTACCTCATAACGGCAAAAAAGTCATTTTACCACATAAAGGCAA
*
32617 AAAAGTCATTTTACCT
66 AAAAATCATTTTACCT
* * *
32633 CATAAGGGAAAAATAGTCATTTTACCTCATAAGGGCAAAACAA-TCATTTTA
1 CATAAGGGAAAAACAATCATTTTACCTCATAACGGCAAAA-AAGTCATTTTA
32684 TGCCATAAGT
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
80 66 0.59
81 17 0.15
82 28 0.25
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.25
Consensus pattern (81 bp):
CATAAGGGAAAAACAATCATTTTACCTCATAACGGCAAAAAAGTCATTTTACCACATAAAGGCAA
AAAAATCATTTTACCT
Found at i:32691 original size:54 final size:54
Alignment explanation
Indices: 32506--32710 Score: 238
Period size: 54 Copynumber: 3.8 Consensus size: 54
32496 CATAAAAAGC
* * * * * *
32506 GCAAAACAGTCATCTTACCACATAAGAGCAAAAA-AATGATTTTACCTCATAAGG
1 GCAAAACAATCATTTTACCTCATAAG-GGAAAAATAGTCATTTTACCTCATAAGG
* * *
32560 GCAAAACAATGATTTTACCTCATAACGGAAAAA-AGTCATTTTACCTCATAAAG
1 GCAAAACAATCATTTTACCTCATAAGGGAAAAATAGTCATTTTACCTCATAAGG
32613 GCAAAA-AAGTCATTTTACCTCATAAGGGAAAAATAGTCATTTTACCTCATAAGG
1 GCAAAACAA-TCATTTTACCTCATAAGGGAAAAATAGTCATTTTACCTCATAAGG
* * * *
32667 GCAAAACAATCATTTTATGC-CATAAGTGCAAAATAGTTATTTTA
1 GCAAAACAATCATTTTA-CCTCATAAGGGAAAAATAGTCATTTTA
32711 TCGATTATGG
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
52 2 0.02
53 51 0.39
54 75 0.57
55 3 0.02
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (54 bp):
GCAAAACAATCATTTTACCTCATAAGGGAAAAATAGTCATTTTACCTCATAAGG
Found at i:32692 original size:27 final size:26
Alignment explanation
Indices: 32506--32683 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 26
32496 CATAAAAAGC
* * * *
32506 GCAAAACAGTCATCTTACCACATAAGA
1 GCAAAA-AATCATTTTACCTCATAAGG
*
32533 GCAAAAAAATGATTTTACCTCATAAGG
1 GC-AAAAAATCATTTTACCTCATAAGG
* *
32560 GCAAAACAATGATTTTACCTCATAACG
1 GCAAAA-AATCATTTTACCTCATAAGG
*
32587 G-AAAAAAGTCATTTTACCTCATAAAG
1 GCAAAAAA-TCATTTTACCTCATAAGG
32613 GCAAAAAAGTCATTTTACCTCATAAGG
1 GCAAAAAA-TCATTTTACCTCATAAGG
32640 G-AAAAATAGTCATTTTACCTCATAAGG
1 GCAAAAA-A-TCATTTTACCTCATAAGG
32667 GCAAAACAATCATTTTA
1 GCAAAA-AATCATTTTA
32684 TGCCATAAGT
Statistics
Matches: 135, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.01
26 30 0.22
27 93 0.69
28 9 0.07
29 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (26 bp):
GCAAAAAATCATTTTACCTCATAAGG
Found at i:32708 original size:27 final size:28
Alignment explanation
Indices: 32506--32712 Score: 178
Period size: 27 Copynumber: 7.7 Consensus size: 28
32496 CATAAAAAGC
* * * *
32506 GCAAAACAGTCATCTTA-CCACATAAGA
1 GCAAAATAGTCATTTTATCCTCATAAGG
* * *
32533 GCAAAAAAATGATTTTA-CCTCATAAGG
1 GCAAAATAGTCATTTTATCCTCATAAGG
* * * *
32560 GCAAAACAATGATTTTA-CCTCATAACG
1 GCAAAATAGTCATTTTATCCTCATAAGG
* *
32587 G-AAAAAAGTCATTTTA-CCTCATAAAG
1 GCAAAATAGTCATTTTATCCTCATAAGG
*
32613 GCAAAAAAGTCATTTTA-CCTCATAAGG
1 GCAAAATAGTCATTTTATCCTCATAAGG
*
32640 GAAAAATAGTCATTTTA-CCTCATAAGG
1 GCAAAATAGTCATTTTATCCTCATAAGG
* * * *
32667 GCAAAACAATCATTTTATGC-CATAAGT
1 GCAAAATAGTCATTTTATCCTCATAAGG
*
32694 GCAAAATAGTTATTTTATC
1 GCAAAATAGTCATTTTATC
32713 GATTATGGGT
Statistics
Matches: 154, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 22 0.14
27 131 0.85
28 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.28
Consensus pattern (28 bp):
GCAAAATAGTCATTTTATCCTCATAAGG
Found at i:37823 original size:12 final size:12
Alignment explanation
Indices: 37806--37831 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37796 CACTCTCTCA
37806 TTTTCATTTCCC
1 TTTTCATTTCCC
37818 TTTTCATTTCCC
1 TTTTCATTTCCC
37830 TT
1 TT
37832 ACATAGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTCATTTCCC
Found at i:51424 original size:30 final size:30
Alignment explanation
Indices: 51388--51448 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
51378 TTCCCGAGCC
51388 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * *
51418 TAGGGGAAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
51448 T
1 T
51449 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:53191 original size:37 final size:37
Alignment explanation
Indices: 53141--53219 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
53131 TTATTACGAA
* * *
53141 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
53178 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
53215 GTCTT
1 GTCTT
53220 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:53413 original size:49 final size:47
Alignment explanation
Indices: 53336--53444 Score: 182
Period size: 49 Copynumber: 2.3 Consensus size: 47
53326 GCCCTTCGGG
53336 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATATAC
*
53386 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
53433 ACTTTCACATTC
1 ACTTTCACATTC
53445 TCAAAGTAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
47 20 0.34
49 34 0.59
50 4 0.07
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.32
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
Found at i:53762 original size:24 final size:23
Alignment explanation
Indices: 53714--53771 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
53704 TAATCAAACA
53714 TTATTATATATATATCATATCATT
1 TTATTAT-TATATATCATATCATT
*
53738 TTATTATTAT-TATCATTATTTATT
1 TTATTATTATATATCA-TA-TCATT
53762 TTATT-TTATA
1 TTATTATTATA
53772 CTTTTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 9 0.30
24 16 0.53
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATATATCATATCATT
Found at i:56932 original size:40 final size:41
Alignment explanation
Indices: 56902--57242 Score: 373
Period size: 40 Copynumber: 8.5 Consensus size: 41
56892 AGCATGATTA
* * *
56902 CTCTTCGGGAAC-TAGCCCGGATATAACACCAGCACGAATG
1 CTCTTCGGGAACTTAGCCCGGATACATCACTAGCACGAATG
* ** * *
56942 CTCTTTGGG-GTTTAGCACGGATATATCACTAGCACGAATG
1 CTCTTCGGGAACTTAGCCCGGATACATCACTAGCACGAATG
56982 CTCTTC-GGAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGAACTTAGCCCGGATACATCACTAGCACGAATG
57022 CTCTTC-GGAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGAACTTAGCCCGGATACATCACTAGCACGAATG
* *
57062 CTCTTC-GGAACTTTGCCCGGATACATCACTAGCATGAATG
1 CTCTTCGGGAACTTAGCCCGGATACATCACTAGCACGAATG
* *
57102 CTCTTCGGG-ACTTAGCCCGGATACATCGCTAGCATGAATG
1 CTCTTCGGGAACTTAGCCCGGATACATCACTAGCACGAATG
** * * *
57142 CTCTTCGGG-ACTTAGCCCGGATTTAGTAACTCGCACCAATG
1 CTCTTCGGGAACTTAGCCCGGATACA-TCACTAGCACGAATG
* * ** *
57183 C-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AAAG
1 CTCTTCGGGAACTTAGCCCGGATA-CATCAC-TAGCACGAATG
57223 C-CTTCGGG-ACTTAGCCCGGA
1 CTCTTCGGGAACTTAGCCCGGA
57243 CATCGTTCGA
Statistics
Matches: 261, Mismatches: 32, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
39 4 0.02
40 237 0.91
41 20 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (41 bp):
CTCTTCGGGAACTTAGCCCGGATACATCACTAGCACGAATG
Found at i:57587 original size:29 final size:29
Alignment explanation
Indices: 57548--57626 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
57538 CTTAATAATC
*
57548 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
57578 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
57607 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
57627 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:57656 original size:43 final size:43
Alignment explanation
Indices: 57608--57753 Score: 283
Period size: 43 Copynumber: 3.4 Consensus size: 43
57598 TGCATTTCAA
*
57608 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
57651 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
57694 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
57737 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
57754 TGAAAACCAA
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 102 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:59665 original size:37 final size:37
Alignment explanation
Indices: 59615--59693 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
59605 TTATTACGAA
* * *
59615 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
59652 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
59689 GTCTT
1 GTCTT
59694 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:59887 original size:49 final size:47
Alignment explanation
Indices: 59810--59918 Score: 182
Period size: 49 Copynumber: 2.3 Consensus size: 47
59800 GCCCTTCGGG
59810 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATATAC
*
59860 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
59907 ACTTTCACATTC
1 ACTTTCACATTC
59919 TCAAAGTAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
47 20 0.34
49 34 0.59
50 4 0.07
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.32
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
Found at i:60237 original size:24 final size:23
Alignment explanation
Indices: 60189--60246 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
60179 TAATCAAACA
60189 TTATTATATATATATCATATCATT
1 TTATTAT-TATATATCATATCATT
*
60213 TTATTATTAT-TATCATTATTTATT
1 TTATTATTATATATCA-TA-TCATT
60237 TTATT-TTATA
1 TTATTATTATA
60247 CTTTTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 9 0.30
24 16 0.53
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATATATCATATCATT
Found at i:62693 original size:68 final size:66
Alignment explanation
Indices: 62621--62806 Score: 182
Period size: 67 Copynumber: 2.8 Consensus size: 66
62611 CATCATGTGT
* *
62621 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATAG-GTGATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCAT-GCGTGATACTAGTGAAGGACACC
62683 ATGTAG
61 ATGTAG
* * *
62689 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGGTTCTAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACTA-GTGAAGGACACCATGT
62754 AG
65 AG
* * * * * *
62756 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATGGGTGGTACTGAGTG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACT-AGTG
62807 TTCACCATGT
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
63 1 0.01
64 24 0.23
65 3 0.03
66 28 0.27
67 34 0.33
68 13 0.13
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.23
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACTAGTGAAGGACACCATGTA
G
Found at i:69134 original size:16 final size:17
Alignment explanation
Indices: 69103--69135 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
69093 TTCATAAGTA
69103 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
69120 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
69136 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:69690 original size:46 final size:46
Alignment explanation
Indices: 69421--69694 Score: 343
Period size: 46 Copynumber: 6.0 Consensus size: 46
69411 TTTGACATGA
* * * * * *
69421 TGCCATAGTGTCTTTAAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT
* * * *
69467 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* * * * * *
69513 TGCCAAGGTATCTTTCATCCATGGTCTTATTCATTTCCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
69559 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *
69605 TACCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *
69651 TGCCATGGTATCTTTCAACCATGGTGTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
69695 AGAACACACT
Statistics
Matches: 205, Mismatches: 22, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
45 4 0.02
46 201 0.98
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
Found at i:70112 original size:273 final size:273
Alignment explanation
Indices: 69625--70152 Score: 966
Period size: 273 Copynumber: 1.9 Consensus size: 273
69615 TCTTTCAACC
* **
69625 ATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTGTTACACATTTCAT
1 ATGGTCTTACACATTTCATATCAGGTAGCCATGGTATCTTTCAACCATGGACTTACACATTTCAT
* *
69690 ATCAGAGAACACACTCCCGCGAACCTCATCCTTATAGTGGGATTACCAGTCCAGGCTAAATCCCC
66 ATCAGAGAACACACTCCCGCGAACCTCATCCTTATACTGGAATTACCAGTCCAGGCTAAATCCCC
* *
69755 TGTAATATAAACTCATAGAGTATTGTCGGGATTACCAGTCCAGGCTAAATCCCTTGCAACGACAA
131 TGTAATATAAACTCATAGAGTATTGTCAGGATTACCAGTCCAGGCTAAATCCCCTGCAACGACAA
69820 TTACTCTAATGAGCTTGGATCTGAATTACCAGTCCAGGCTAAATTTAGACCCTGATTCGGATTAC
196 TTACTCTAATGAGCTTGGATCTGAATTACCAGTCCAGGCTAAATTTAGACCCTGATTCGGATTAC
69885 CCGTCCGGGCTAA
261 CCGTCCGGGCTAA
69898 ATGGTCTTACACATTTCATATCAGGTAGCCATGGTATCTTTCAACCATGGACTTACACATTTCAT
1 ATGGTCTTACACATTTCATATCAGGTAGCCATGGTATCTTTCAACCATGGACTTACACATTTCAT
* *
69963 ATTAGAGAGCACACTCCCGCGAACCTCATCCTTATACTGGAATTACCAGTCCAGGCTAAATCCCC
66 ATCAGAGAACACACTCCCGCGAACCTCATCCTTATACTGGAATTACCAGTCCAGGCTAAATCCCC
*
70028 TGTAATGTAAACTCATAGAGTATTGTCAGGATTACCAGTCCAGGCTAAATCCCCTGCAACGACAA
131 TGTAATATAAACTCATAGAGTATTGTCAGGATTACCAGTCCAGGCTAAATCCCCTGCAACGACAA
70093 TTACTCTAATGAGCTTGGATCTGAATTACCAGTCCAGGCTAAATTTAGACCCTGATTCGG
196 TTACTCTAATGAGCTTGGATCTGAATTACCAGTCCAGGCTAAATTTAGACCCTGATTCGG
70153 GAGGGCTATA
Statistics
Matches: 245, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
273 245 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (273 bp):
ATGGTCTTACACATTTCATATCAGGTAGCCATGGTATCTTTCAACCATGGACTTACACATTTCAT
ATCAGAGAACACACTCCCGCGAACCTCATCCTTATACTGGAATTACCAGTCCAGGCTAAATCCCC
TGTAATATAAACTCATAGAGTATTGTCAGGATTACCAGTCCAGGCTAAATCCCCTGCAACGACAA
TTACTCTAATGAGCTTGGATCTGAATTACCAGTCCAGGCTAAATTTAGACCCTGATTCGGATTAC
CCGTCCGGGCTAA
Found at i:71597 original size:47 final size:47
Alignment explanation
Indices: 71543--71633 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
71533 TTTCTATTTC
*
71543 TTGAATCCAACTTGATATTCTTGCTCCCCATCATCTTCTTGCTATAT
1 TTGAATCCAACTTGATATTCTTGCTCCCCATCATCTCCTTGCTATAT
*
71590 TTGAATCCAACTTGATATTCTTGCTCCCGATCATCTCCTTGCTA
1 TTGAATCCAACTTGATATTCTTGCTCCCCATCATCTCCTTGCTA
71634 CCTTTCTCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.21, C:0.29, G:0.10, T:0.41
Consensus pattern (47 bp):
TTGAATCCAACTTGATATTCTTGCTCCCCATCATCTCCTTGCTATAT
Found at i:76694 original size:11 final size:11
Alignment explanation
Indices: 76678--76708 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
76668 GTTTTTTACG
76678 ATTTGATTTTT
1 ATTTGATTTTT
76689 ATTTGATTTTT
1 ATTTGATTTTT
*
76700 ATTTAATTT
1 ATTTGATTT
76709 CTAACCTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (11 bp):
ATTTGATTTTT
Found at i:76760 original size:3 final size:3
Alignment explanation
Indices: 76745--76778 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
76735 TTTTTTCTCT
*
76745 TTA TTA CTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
76779 CTTTAGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:80892 original size:27 final size:27
Alignment explanation
Indices: 80862--81250 Score: 268
Period size: 27 Copynumber: 14.4 Consensus size: 27
80852 AGAATTACTG
* **
80862 AAATACCCTTGGTTTACAAAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
* * *
80889 AAATACCCTCGATTAGCAAAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
* * *
80916 AAATACCCCTGGTTTGTATAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
* * *
80943 AAATA-CCTCTGATTTGTGAAATTATCG
1 AAATACCCT-TGATTTGTAAAATTACCA
* ** *
80970 AAATACCCTCGACCTG-AAAATTACCG
1 AAATACCCTTGATTTGTAAAATTACCA
* * ** *
80996 AAATTCCTTTGACCTATAAAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
* * *
81023 AAATACCCTCGACTTGTAAAATTACCG
1 AAATACCCTTGATTTGTAAAATTACCA
* *
81050 AAATACCCTCGATTTGTAAAATTTCCA
1 AAATACCCTTGATTTGTAAAATTACCA
* **
81077 AAATACGCC-TGATTTGGAAAATTACTG
1 AAATAC-CCTTGATTTGTAAAATTACCA
* *
81104 AAATACCATTGATTTAG-AAAATTACAA
1 AAATACCCTTGATTT-GTAAAATTACCA
* * *
81131 AAATACCCCTGATTTATAGAATTA-CA
1 AAATACCCTTGATTTGTAAAATTACCA
** *
81157 GAAATACCCTTGACTTTCAAAAATTACTA
1 -AAATACCCTTGA-TTTGTAAAATTACCA
** * **
81186 AAATATCATTTG-TTTGCAAAATTACTG
1 AAATA-CCCTTGATTTGTAAAATTACCA
* * *
81213 AAATACCCTTGGTTTGTAGATTTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
*
81240 AAACACCCTTG
1 AAATACCCTTG
81251 TAGGGTGAAA
Statistics
Matches: 284, Mismatches: 66, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
26 28 0.10
27 231 0.81
28 20 0.07
29 5 0.02
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATACCCTTGATTTGTAAAATTACCA
Found at i:81248 original size:82 final size:81
Alignment explanation
Indices: 81013--81250 Score: 209
Period size: 82 Copynumber: 2.9 Consensus size: 81
81003 TTTGACCTAT
* * * * * * *
81013 AAAATTACCAAAATACCCTCGACTT-GTAAAATTACCGAAATACCCTCGATTTGTAAAATTT-CC
1 AAAATTACTAAAATACCATTGATTTAG-AAAATTACAGAAATACCCTTGATTTGT-AGATTTACC
**
81076 AAAATACGCC-TGATTTGG
64 AAAATAC-CCTTGATTTCA
* * * * *
81094 AAAATTACTGAAATACCATTGATTTAGAAAATTACAAAAATACCCCTGATTTATAGAATTA-CAG
1 AAAATTACTAAAATACCATTGATTTAGAAAATTACAGAAATACCCTTGATTTGTAGATTTACCA-
81158 AAATACCCTTGACTTTCA
65 AAATACCCTTGA-TTTCA
* * *
81176 AAAATTACTAAAATATCATTTG-TTT-GCAAAATTACTGAAATACCCTTGGTTTGTAGATTTACC
1 AAAATTACTAAAATACCA-TTGATTTAG-AAAATTACAGAAATACCCTTGATTTGTAGATTTACC
*
81239 AAAACACCCTTG
64 AAAATACCCTTG
81251 TAGGGTGAAA
Statistics
Matches: 126, Mismatches: 23, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
80 8 0.06
81 52 0.41
82 61 0.48
83 5 0.04
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (81 bp):
AAAATTACTAAAATACCATTGATTTAGAAAATTACAGAAATACCCTTGATTTGTAGATTTACCAA
AATACCCTTGATTTCA
Found at i:82726 original size:83 final size:83
Alignment explanation
Indices: 82590--82749 Score: 239
Period size: 83 Copynumber: 1.9 Consensus size: 83
82580 TGGCCAAAGG
* *
82590 TTTTAAATAGTAAGAAGGGTTTTCAATGAGAACACGCTTTTCAAAAAACACTTCAATGTGACACG
1 TTTTAAATAGTAAGAAGGATTTTCAATGAGAACACGCTTTTCAAAAAACACTTCAAAGTGACACG
82655 CAAGATTTCGGCCATAAA
66 CAAGATTTCGGCCATAAA
* * * **
82673 TTTTAAATAGTAAGAAGGATTTTCAATGAGAACATGGTTTTCGAAAATTACTTCAAAGTGACACG
1 TTTTAAATAGTAAGAAGGATTTTCAATGAGAACACGCTTTTCAAAAAACACTTCAAAGTGACACG
* *
82738 CCAGGTTTCGGC
66 CAAGATTTCGGC
82750 TATAGTGTCT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (83 bp):
TTTTAAATAGTAAGAAGGATTTTCAATGAGAACACGCTTTTCAAAAAACACTTCAAAGTGACACG
CAAGATTTCGGCCATAAA
Found at i:96797 original size:5 final size:5
Alignment explanation
Indices: 96787--96811 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
96777 AGTAATAATA
96787 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
96812 GCAAGGAAAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:99204 original size:41 final size:41
Alignment explanation
Indices: 99145--99267 Score: 201
Period size: 41 Copynumber: 3.0 Consensus size: 41
99135 AAAAGCCACC
* *
99145 GGTGGATCCAAGATCGTCAAGCAACCATGCGATCCTTAATT
1 GGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAATT
* *
99186 GTTGGATCCACGATCGTCAAGCAACCATGCGATTCTCAATT
1 GGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAATT
*
99227 GGTGGATCCACGATCGTCAAGCAACTATGCGATCCTCAATT
1 GGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAATT
99268 TCTTCCTTCG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (41 bp):
GGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAATT
Found at i:99557 original size:27 final size:27
Alignment explanation
Indices: 99527--99579 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
99517 CGTAAATCTA
99527 CAAACCAATAGTA-TTTTGATAATTTTG
1 CAAACCAATAGTATTTTTG-TAATTTTG
*
99554 CAAACCAATGGTATTTTTGTAATTTT
1 CAAACCAATAGTATTTTTGTAATTTT
99580 TGAAAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (27 bp):
CAAACCAATAGTATTTTTGTAATTTTG
Found at i:99580 original size:28 final size:28
Alignment explanation
Indices: 99527--99607 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
99517 CGTAAATCTA
*
99527 CAAACCAATAGTA-TTTTGATAA-TTTTG
1 CAAACCAATGGTATTTTTG-TAATTTTTG
99554 CAAACCAATGGTATTTTTGTAATTTTTG
1 CAAACCAATGGTATTTTTGTAATTTTTG
** *
99582 -AAAGTTAAGGGTATTTTTGTAATTTT
1 CAAA-CCAATGGTATTTTTGTAATTTT
99608 CTAAATCAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 18 0.38
28 29 0.62
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (28 bp):
CAAACCAATGGTATTTTTGTAATTTTTG
Found at i:99598 original size:27 final size:27
Alignment explanation
Indices: 99540--99874 Score: 181
Period size: 27 Copynumber: 12.4 Consensus size: 27
99530 ACCAATAGTA
* *
99540 TTTTGATAATTTTGC-AAACCAATGGTAT
1 TTTTG-TAATTTT-CTAAATCAAGGGTAT
*
99568 TTTTGTAATTTT-TGAAAGTTAAGGGTAT
1 TTTTGTAATTTTCT-AAA-TCAAGGGTAT
*
99596 TTTTGTAATTTTCTAAATCAGGGGTAT
1 TTTTGTAATTTTCTAAATCAAGGGTAT
* *
99623 TTCTGTAATTTTCCAAATCAAAGGG-AT
1 TTTTGTAATTTTCTAAATC-AAGGGTAT
*** * * *
99650 TTCAATAATTTTAC-AAGTCGAGAGTAT
1 TTTTGTAATTTT-CTAAATCAAGGGTAT
** ** *
99677 TTCGGTAATTTTAC-AGGTCGAGGGTAT
1 TTTTGTAATTTT-CTAAATCAAGGGTAT
*
99704 TTTGGTAA-TTTCATAAATCAAGGGTAT
1 TTTTGTAATTTTC-TAAATCAAGGGTAT
* *
99731 TTTGGTAATTTTAC-AAATCAGGGGTAT
1 TTTTGTAATTTT-CTAAATCAAGGGTAT
* *
99758 TTTGGTAATTTTAC-AAAGT-AGGGGTAT
1 TTTTGTAATTTT-CTAAA-TCAAGGGTAT
*
99785 TTTGGTAATTTTGCT-AATCAAGGGTA-
1 TTTTGTAATTTT-CTAAATCAAGGGTAT
** * *
99811 TTCAGTAATTTTGTAAACCAAGGGTA-
1 TTTTGTAATTTTCTAAATCAAGGGTAT
** * *
99837 TTCAGTAATTTTGTAAACCAAGGGTAT
1 TTTTGTAATTTTCTAAATCAAGGGTAT
**
99864 TTCAGTAATTT
1 TTTTGTAATTT
99875 ACCCTATAGG
Statistics
Matches: 263, Mismatches: 28, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
25 2 0.01
26 53 0.20
27 170 0.65
28 36 0.14
29 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (27 bp):
TTTTGTAATTTTCTAAATCAAGGGTAT
Found at i:99703 original size:81 final size:80
Alignment explanation
Indices: 99615--99822 Score: 219
Period size: 81 Copynumber: 2.6 Consensus size: 80
99605 TTTCTAAATC
* *
99615 AGGGGTATTTCT-GTAATTTTCCAAATCAAAGGGATTTCAATAATTTTACAAGTC-GAGAGTATT
1 AGGGGTATTT-TGGTAATTTTCCAAATC-AAGGGATTTCAGTAATTTTACAAATCAG-GAGTATT
*
99678 TCGGTAATTTTAC-AGGT
63 TCGGTAATTTTACAAAGT
* * ** *
99695 CGAGGGTATTTTGGTAA-TTTCATAAATCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTATT
1 AG-GGGTATTTTGGTAATTTTC-CAAATCAAGGG-ATTTCAGTAATTTTACAAATCAGGAGTATT
*
99759 TTGGTAATTTTACAAAGT
63 TCGGTAATTTTACAAAGT
* *
99777 AGGGGTATTTTGGTAATTTTGCTAATCAAGGG-TATTCAGTAATTTT
1 AGGGGTATTTTGGTAATTTTCCAAATCAAGGGAT-TTCAGTAATTTT
99823 GTAAACCAAG
Statistics
Matches: 105, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
79 1 0.01
80 21 0.20
81 75 0.71
82 8 0.08
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.40
Consensus pattern (80 bp):
AGGGGTATTTTGGTAATTTTCCAAATCAAGGGATTTCAGTAATTTTACAAATCAGGAGTATTTCG
GTAATTTTACAAAGT
Found at i:99823 original size:26 final size:26
Alignment explanation
Indices: 99789--99874 Score: 138
Period size: 26 Copynumber: 3.3 Consensus size: 26
99779 GGGTATTTTG
*
99789 GTAATTTTGCT-AATCAAGGGTATTCA
1 GTAATTTTG-TAAACCAAGGGTATTCA
99815 GTAATTTTGTAAACCAAGGGTATTCA
1 GTAATTTTGTAAACCAAGGGTATTCA
99841 GTAATTTTGTAAACCAAGGGTATTTCA
1 GTAATTTTGTAAACCAAGGGTA-TTCA
99868 GTAATTT
1 GTAATTT
99875 ACCCTATAGG
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
25 1 0.02
26 45 0.79
27 11 0.19
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (26 bp):
GTAATTTTGTAAACCAAGGGTATTCA
Found at i:99918 original size:27 final size:26
Alignment explanation
Indices: 99855--99918 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
99845 TTTTGTAAAC
99855 CAAGGGTATTTCAGTAATTTACCCTA
1 CAAGGGTATTTCAGTAATTTACCCTA
* ** *
99881 -TAGGAAAATTTCAGTAATTGTACCTTA
1 CAAGG-GTATTTCAGTAATT-TACCCTA
99908 CAAGGGTATTT
1 CAAGGGTATTT
99919 TAGAAATCCT
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
25 3 0.11
26 12 0.43
27 10 0.36
28 3 0.11
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (26 bp):
CAAGGGTATTTCAGTAATTTACCCTA
Done.