Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2395
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: 84528
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:12801 original size:21 final size:21
Alignment explanation
Indices: 12754--12804 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
12744 ATATGAATAT
* *
12754 ATATTTTACATTAATATGTTTA
1 ATATTTT-TATTAAAATGTTTA
*
12776 A-ATTTTTATTAAAATTTTTA
1 ATATTTTTATTAAAATGTTTA
12796 ATATTTTTA
1 ATATTTTTA
12805 AAAGATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 12 0.48
21 12 0.48
22 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATTTTTATTAAAATGTTTA
Found at i:13207 original size:2 final size:2
Alignment explanation
Indices: 13200--13224 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13190 AATCATCTAC
13200 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 T
13225 TTCCGTAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14720 original size:21 final size:18
Alignment explanation
Indices: 14687--14732 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 18
14677 TTATTTTGAA
14687 ATATTATTTAAATTTATTTAT
1 ATATT-TTTAAA--TATTTAT
14708 ATATTTTTAAAATATTTAT
1 ATATTTTT-AAATATTTAT
14727 ATATTT
1 ATATTT
14733 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.54
20 3 0.12
21 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTTTAAATATTTAT
Found at i:14877 original size:81 final size:80
Alignment explanation
Indices: 14784--14934 Score: 239
Period size: 81 Copynumber: 1.9 Consensus size: 80
14774 CATCCCTTAA
* *
14784 ATATATATATGCAAATTAAAATTTTAAAATTATAAATATTTGATATAAAAAATTTTTAAACATTA
1 ATATATACATGCAAATTAAAATTTTAAAATTATAAATATTTAATAT-AAAAATTTTTAAACATTA
14849 AATAAACATGAAAAAT
65 AATAAACATGAAAAAT
* ** *
14865 ATATATACATGCAAATTAAAATTTTAAATTTATAAATATTTAATATCCAAATTTTTAAACATTGA
1 ATATATACATGCAAATTAAAATTTTAAAATTATAAATATTTAATATAAAAATTTTTAAACATTAA
14930 ATAAA
66 ATAAA
14935 TAAAATAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
80 21 0.33
81 43 0.67
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (80 bp):
ATATATACATGCAAATTAAAATTTTAAAATTATAAATATTTAATATAAAAATTTTTAAACATTAA
ATAAACATGAAAAAT
Found at i:16788 original size:12 final size:12
Alignment explanation
Indices: 16771--16796 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16761 ATATAATAAA
16771 ATAAAATATTTT
1 ATAAAATATTTT
16783 ATAAAATATTTT
1 ATAAAATATTTT
16795 AT
1 AT
16797 CAATATAATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAAAATATTTT
Found at i:21284 original size:44 final size:45
Alignment explanation
Indices: 21221--21309 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 45
21211 CATCAAATCG
21221 ATAGGCATTTACTGAGCGCAAGAGGGTTACTGG-ATGAACCATCT
1 ATAGGCATTTACTGAGCGCAAGAGGGTTACTGGAATGAACCATCT
21265 ATAGGCATTTACTGAGCGCAAGAGGGTTACTGGAATGAACCATCT
1 ATAGGCATTTACTGAGCGCAAGAGGGTTACTGGAATGAACCATCT
21310 GAATTAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 33 0.75
45 11 0.25
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (45 bp):
ATAGGCATTTACTGAGCGCAAGAGGGTTACTGGAATGAACCATCT
Found at i:24409 original size:37 final size:38
Alignment explanation
Indices: 24277--24409 Score: 105
Period size: 38 Copynumber: 3.5 Consensus size: 38
24267 TTGTGTTATC
* * * *
24277 AGTTAA-AATTAATGCTTTTTGTTTC-AAGCCGTGCTACT
1 AGTTAAGAA-TAATGGTTTTTATTTCGAA-CCATGCCACT
*
24315 AGTTAAGATTAATGGTTTTTATTTCGAACCATGCCA-T
1 AGTTAAGAATAATGGTTTTTATTTCGAACCATGCCACT
* * * *
24352 TGATTGAA-AATAGTGATTTTTA-TTCGAACTATGCCACT
1 AG-TT-AAGAATAATGGTTTTTATTTCGAACCATGCCACT
*
24390 AGTTTAGAATAATGGTTTTT
1 AGTTAAGAATAATGGTTTTT
24410 GTGATATCTT
Statistics
Matches: 75, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
36 1 0.01
37 28 0.37
38 41 0.55
39 5 0.07
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (38 bp):
AGTTAAGAATAATGGTTTTTATTTCGAACCATGCCACT
Found at i:24582 original size:25 final size:25
Alignment explanation
Indices: 24548--24608 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
24538 ATGATTTGAA
24548 ATAATATGATTAGTTCTGTTAT-TT
1 ATAATATGATTAGTTCTGTTATCTT
* * *
24572 GATAATCTGATTCGTTTTGTTATCTT
1 -ATAATATGATTAGTTCTGTTATCTT
*
24598 ATAATTTGATT
1 ATAATATGATT
24609 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (25 bp):
ATAATATGATTAGTTCTGTTATCTT
Found at i:26726 original size:308 final size:306
Alignment explanation
Indices: 25993--27125 Score: 1930
Period size: 300 Copynumber: 3.7 Consensus size: 306
25983 TATTTTTTGA
* * * *
25993 TTTTTTTCTTCATGATTGATGTTGTCTTAAATTGTGTTAAAAAGTCAAAAATTTTACCCAAGTTT
1 TTTTTTTCTTCATGATGGATGTTGTCTTAAATTGTGTTAAAAAGTAAAAAATTTTACCAAAATTT
26058 CCACACGTCTTTGTTTCAACTTTCTTATGTTTGATTCCTTCCTTAATTATATATGTCTATCAATC
66 CCACACGTCTTTGTTTCAACTTTCTTATGTTTGATTCCTTCCTTAATTATATATGTCTATCAATC
26123 ATTCTCAAACTTGCAAATTTTTTTCCAATTTAATTTAGAAGTATTCTTTGGGTCGAAGCTAATGA
131 ATTCTCAAACTTGC-AATTTTTTTCCAATTTAATTTAGAAGTATTCTTTGGGTCGAAGCTAATGA
26188 CTTATATATATATATATATTTATATTATGTTGGGAATTTTAAAAAGGAAACATATTTATATGTGA
195 CTTATATATATATATATATTTATATTATGTTGGGAATTTTAAAAAGGAAACATATTTATATGTGA
* *
26253 TCAATATAAAATTAACTCTTATAAATAAGAGATAATATTTATCAGA-
260 TCAATATAAAATTAACTCATATAAATAAGAGATAATATTTACCAGAT
*
26299 TTTTTTTCTTCATGATGGATGTTGTCTTAAATTGTGTTAAAAAGTCAAAAATTTTACCAAAATTT
1 TTTTTTTCTTCATGATGGATGTTGTCTTAAATTGTGTTAAAAAGTAAAAAATTTTACCAAAATTT
*
26364 CCAGACGTCTTTGTTTCAACTTTCTTATGTTTGATTCCTTCCTTAA-T-TATATGTCTATCAATC
66 CCACACGTCTTTGTTTCAACTTTCTTATGTTTGATTCCTTCCTTAATTATATATGTCTATCAATC
26427 ATTCTCAAACTTGCAATTTTTTTCCAATTTAATTTAGAAGTATTCTTTGGGTCGAAGCTAATGAC
131 ATTCTCAAACTTGCAATTTTTTTCCAATTTAATTTAGAAGTATTCTTTGGGTCGAAGCTAATGAC
26492 TTATATATATATATATATATATTTATATTATGTTGGGAATTTTAAAAAGGAAACATATTTATATG
196 ---T-TATATATATATATATATTTATATTATGTTGGGAATTTTAAAAAGGAAACATATTTATATG
26557 TGATCAATATAAAATTAACTCATATAAATAAGAGATAATATTTACCAGAT
257 TGATCAATATAAAATTAACTCATATAAATAAGAGATAATATTTACCAGAT
*
26607 TTTTTTTCTTCAGGATGGATGTTGTCTTAAATTGTGTTAAAAAGTAAAAAATTTTACCAAAATTT
1 TTTTTTTCTTCATGATGGATGTTGTCTTAAATTGTGTTAAAAAGTAAAAAATTTTACCAAAATTT
*
26672 CCACACATCTTTGTTTCAACTTTCTTATGTTTGATTCCTTCCTTAA-T-TATATGTCTATCAATC
66 CCACACGTCTTTGTTTCAACTTTCTTATGTTTGATTCCTTCCTTAATTATATATGTCTATCAATC
*
26735 ATTCTCAAACTTGCAATTTTTTTTTTCAATTTAATTTAGAAGTATTCTTTGGGTCGAAGCTAATG
131 ATTCTCAAACTTGCAA--TTTTTTTCCAATTTAATTTAGAAGTATTCTTTGGGTCGAAGCTAATG
* * * *
26800 AC---T-TGTGTATATATA--TATATTATGTTGGCAATTTTAAAAAAGAAACATATTTATATGTG
194 ACTTATATATATATATATATTTATATTATGTTGGGAATTTTAAAAAGGAAACATATTTATATGTG
*
26859 ATCAATATAAAATTAACTCATATAAATAAGAGATAATATTTACTAGAT
259 ATCAATATAAAATTAACTCATATAAATAAGAGATAATATTTACCAGAT
* *
26907 TTTTTTTCTTCAAGATGGATGTTGTCTTAAATTGTTTTAAAAAGTAAAAAATTTTACCAAAATTT
1 TTTTTTTCTTCATGATGGATGTTGTCTTAAATTGTGTTAAAAAGTAAAAAATTTTACCAAAATTT
26972 CCACACGTCTTTGTTTCAACTTTCTTATGTTTGATTCCTTCCTTAATTATATATGTCTATCAATC
66 CCACACGTCTTTGTTTCAACTTTCTTATGTTTGATTCCTTCCTTAATTATATATGTCTATCAATC
27037 ATTCTCAAACTTGCAATTTTTTTCCAATTTAATTTAGAAGTATTCTTTGGGTCGAAGCTAA-GAA
131 ATTCTCAAACTTGCAATTTTTTTCCAATTTAATTTAGAAGTATTCTTTGGGTCGAAGCTAATG-A
* *
27101 CTTGTATATATATATATATATATAT
195 CTTATATATATATATATATTTATAT
27126 ATATATATAT
Statistics
Matches: 789, Mismatches: 22, Indels: 32
0.94 0.03 0.04
Matches are distributed among these distances:
299 1 0.00
300 243 0.31
301 1 0.00
302 42 0.05
303 53 0.07
304 40 0.05
305 1 0.00
306 113 0.14
307 107 0.14
308 140 0.18
310 48 0.06
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (306 bp):
TTTTTTTCTTCATGATGGATGTTGTCTTAAATTGTGTTAAAAAGTAAAAAATTTTACCAAAATTT
CCACACGTCTTTGTTTCAACTTTCTTATGTTTGATTCCTTCCTTAATTATATATGTCTATCAATC
ATTCTCAAACTTGCAATTTTTTTCCAATTTAATTTAGAAGTATTCTTTGGGTCGAAGCTAATGAC
TTATATATATATATATATTTATATTATGTTGGGAATTTTAAAAAGGAAACATATTTATATGTGAT
CAATATAAAATTAACTCATATAAATAAGAGATAATATTTACCAGAT
Found at i:27112 original size:2 final size:2
Alignment explanation
Indices: 27105--27149 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
27095 TAAGAACTTG
*
27105 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27147 TA T
1 TA T
27150 TATGTTGGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27632 original size:18 final size:18
Alignment explanation
Indices: 27569--27632 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 18
27559 AACCTAATTG
27569 TGCAAAACAAATATATTA
1 TGCAAAACAAATATATTA
27587 TGCAATATA-AAACTAT-TTA
1 TGCAA-A-ACAAA-TATATTA
27606 CCTTGCAAAACAAATATATTA
1 ---TGCAAAACAAATATATTA
27627 TGCAAA
1 TGCAAA
27633 TTAATACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
18 11 0.29
19 7 0.18
20 8 0.21
21 7 0.18
22 5 0.13
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (18 bp):
TGCAAAACAAATATATTA
Found at i:28832 original size:2 final size:2
Alignment explanation
Indices: 28827--28856 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28817 GTGTTTAGGG
28827 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
28857 TCTCTTAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29745 original size:18 final size:18
Alignment explanation
Indices: 29684--29745 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 18
29674 AATCTAAATG
29684 TGCAAAACAAATATATTA
1 TGCAAAACAAATATATTA
*
29702 TGCAATAA-AACTAT-TTACA
1 TGCAA-AACAAATATATT--A
29721 TTGCAAAACAAATATATTA
1 -TGCAAAACAAATATATTA
29740 TGCAAA
1 TGCAAA
29746 TTCATACTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
17 2 0.06
18 16 0.44
19 6 0.17
20 10 0.28
21 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (18 bp):
TGCAAAACAAATATATTA
Found at i:30992 original size:2 final size:2
Alignment explanation
Indices: 30985--31023 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
30975 TTTTGAGATT
*
30985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31024 TCTCCCTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:32696 original size:15 final size:14
Alignment explanation
Indices: 32656--32698 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
32646 AGAATTACTG
* *
32656 TTTAATTAATAAAT
1 TTTAATTAAAAAAA
*
32670 TTTTATTAAAAAAA
1 TTTAATTAAAAAAA
*
32684 TTTAATTATAAAAA
1 TTTAATTAAAAAAA
32698 T
1 T
32699 ATATAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTAATTAAAAAAA
Found at i:33052 original size:22 final size:21
Alignment explanation
Indices: 33021--33069 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
33011 GTTAATATTT
*
33021 AAATAATAAAAAATATTATAA
1 AAATAATAAAAAATAATATAA
* *
33042 AAATATATAAATATTAATATAA
1 AAATA-ATAAAAAATAATATAA
33064 AAATAA
1 AAATAA
33070 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAATAAAAAATAATATAA
Found at i:35950 original size:4 final size:4
Alignment explanation
Indices: 35941--35969 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
35931 AATAACTTTG
35941 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
35970 TATTATTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:37441 original size:23 final size:25
Alignment explanation
Indices: 37407--37476 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
37397 AATAAAAATT
37407 AGCCACCAA-TTTTGACAAACAACA
1 AGCCACCAATTTTTGACAAACAACA
*
37431 AGCCA-CAATTTTTGACAAACAAAA
1 AGCCACCAATTTTTGACAAACAACA
37455 AGAAACCACC-ATTTTTGACAAA
1 AG---CCACCAATTTTTGACAAA
37477 TACAAAGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 3 0.08
24 21 0.52
27 15 0.38
28 1 0.03
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.20
Consensus pattern (25 bp):
AGCCACCAATTTTTGACAAACAACA
Found at i:37471 original size:27 final size:27
Alignment explanation
Indices: 37409--37505 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
37399 TAAAAATTAG
* *
37409 CCACCAATTTTGACAAACAACAAG---
1 CCACCATTTTTGACAAACAAAAAGAAA
*
37433 CCACAATTTTTGACAAACAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAGAAA
* *
37460 CCACCATTTTTGACAAATACAAAGTAAA
1 CCACCATTTTTGACAAACAAAAAG-AAA
*
37488 -CACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
37506 CATGGTGGCT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.34
27 37 0.61
28 3 0.05
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGAAA
Found at i:37524 original size:24 final size:25
Alignment explanation
Indices: 37493--37550 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
37483 GTAAACACCA
*
37493 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
37517 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
37543 TTGTTGAC
1 TTGTTGAC
37551 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:42030 original size:24 final size:24
Alignment explanation
Indices: 42003--42079 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 24
41993 AATAAAAATT
*
42003 AGCCACCAATTTTGACAAATAATA
1 AGCCACCAATTTTGACAAATAAAA
*
42027 AGCCA-CAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAATAAAA
*
42051 AGAAACCACCATTTTTGACAAATACAAA
1 AG---CCACCAATTTTGACAAATA-AAA
42079 A
1 A
42080 TAAACACCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
23 3 0.07
24 20 0.47
27 14 0.33
28 6 0.14
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAATAAAA
Found at i:42066 original size:27 final size:27
Alignment explanation
Indices: 42005--42101 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
41995 TAAAAATTAG
* * *
42005 CCACCAATTTTGACAAATAATAAG---
1 CCACCATTTTTGACAAACAAAAAGAAA
*
42029 CCACAATTTTTGACAAACAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAGAAA
* *
42056 CCACCATTTTTGACAAATACAAAATAAA
1 CCACCATTTTTGACAAACA-AAAAGAAA
*
42084 -CACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
42102 CATGGTGGCT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
24 20 0.33
27 33 0.55
28 7 0.12
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.23
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGAAA
Found at i:42120 original size:24 final size:25
Alignment explanation
Indices: 42089--42146 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
42079 ATAAACACCA
* *
42089 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGACTT
42113 TTGTTGACAAACACAAAGGGTGACTT
1 TTGTTGACAAACAC-AAGGGTGACTT
42139 TTGTTGAC
1 TTGTTGAC
42147 TAACCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGACTT
Found at i:46226 original size:97 final size:98
Alignment explanation
Indices: 46046--46241 Score: 261
Period size: 97 Copynumber: 2.0 Consensus size: 98
46036 AATATTGTGA
* * * *
46046 ATGAATATTAGTGTATTTAAATTTTTAAATTTTAAATAAATATTTAATTTAAAAACAATTAATAA
1 ATGAATATTAGTGTATTTAAACTCTTAAATTTTAAATAAACATTCAATTTAAAAACAATTAATAA
* * **
46111 TATTTAAGGTGGTGTATTATATTTTTGTGCTAT
66 AATTGAAGGTGGCATATTATATTTTTGTGCTAT
* **
46144 ATGAATATTAGTGTATTT-AACTCTTAAATTTTAAATAAACATTCAATTTAAAATCAATTGGTAA
1 ATGAATATTAGTGTATTTAAACTCTTAAATTTTAAATAAACATTCAATTTAAAAACAATTAATAA
*
46208 AAGTTGAA-GTGGCATATTATATTTTTGTGTTAT
66 AA-TTGAAGGTGGCATATTATATTTTTGTGCTAT
46241 A
1 A
46242 GTAACGTAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
97 63 0.74
98 22 0.26
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.45
Consensus pattern (98 bp):
ATGAATATTAGTGTATTTAAACTCTTAAATTTTAAATAAACATTCAATTTAAAAACAATTAATAA
AATTGAAGGTGGCATATTATATTTTTGTGCTAT
Found at i:46711 original size:2 final size:2
Alignment explanation
Indices: 46704--46737 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46694 TTGACTAAAA
46704 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
46738 CTGTAGGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50093 original size:17 final size:17
Alignment explanation
Indices: 50073--50105 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
50063 TTTTGGTACG
*
50073 TTGTTTATTATGTCTTT
1 TTGTTTATCATGTCTTT
50090 TTGTTTATCATGTCTT
1 TTGTTTATCATGTCTT
50106 ATAGACAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.67
Consensus pattern (17 bp):
TTGTTTATCATGTCTTT
Found at i:56035 original size:20 final size:20
Alignment explanation
Indices: 55997--56035 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55987 AAATATTAAT
* **
55997 ATAAAAATAATTTTTAAATA
1 ATAAAAATAACTTACAAATA
56017 ATAAAAATAACTTACAAAT
1 ATAAAAATAACTTACAAAT
56036 CAAATCAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAAATAACTTACAAATA
Found at i:59823 original size:3 final size:3
Alignment explanation
Indices: 59815--59859 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
59805 ATTTTAAAAT
59815 TTA 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
59860 CTACTACTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:66129 original size:37 final size:37
Alignment explanation
Indices: 66079--66197 Score: 139
Period size: 37 Copynumber: 3.2 Consensus size: 37
66069 GGTAGGTTAG
* * * *
66079 AACAAAAATCACTATTTTTACCGGTGGCACGGGTTGA
1 AACAAAAATCACTATTCTTATCGGTGGCACGGATCGA
* * * *
66116 AACAAAAATCACTATTCTTATTGGCGACACGGATCGG
1 AACAAAAATCACTATTCTTATCGGTGGCACGGATCGA
* * *
66153 GACAAAAATCACTATTCTTATCGGTGGCACAGATCAA
1 AACAAAAATCACTATTCTTATCGGTGGCACGGATCGA
66190 AACAAAAA
1 AACAAAAA
66198 CTATTATTCT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (37 bp):
AACAAAAATCACTATTCTTATCGGTGGCACGGATCGA
Found at i:69430 original size:37 final size:37
Alignment explanation
Indices: 69288--69430 Score: 150
Period size: 37 Copynumber: 3.8 Consensus size: 37
69278 GCATAGGTTA
*
69288 AAACAAAAACTACTATTCTAATCCGGTGGCAC-GGTTTG
1 AAACAAAAAC-ACTATTCTTA-CCGGTGGCACTGGTTTG
*
69326 AAACAAAAACTATTATTCTTACCGGTGGCA-TGGTTTG
1 AAACAAAAAC-ACTATTCTTACCGGTGGCACTGGTTTG
* * *
69363 GAACAAAAAC-CGTTATTCTTACAGATGGCACTGG-TTG
1 AAACAAAAACAC--TATTCTTACCGGTGGCACTGGTTTG
*
69400 AAACAAATATCACTATTCTTACCGGTGGCAC
1 AAACAAA-AACACTATTCTTACCGGTGGCAC
69431 GAATGTGGAC
Statistics
Matches: 89, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
37 64 0.72
38 24 0.27
39 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (37 bp):
AAACAAAAACACTATTCTTACCGGTGGCACTGGTTTG
Found at i:69443 original size:74 final size:75
Alignment explanation
Indices: 69314--69476 Score: 183
Period size: 74 Copynumber: 2.2 Consensus size: 75
69304 TCTAATCCGG
* * * * *
69314 TGGCAC-GGTTTGAAACAAAAACTATTATTCTTACCGGTGGCATGGTTTGGAACAAAAACCGTTA
1 TGGCACTGG-TTGAAACAAAAACTACTATTCTTACCGGTGGCACGATGTGGAACAAAAACCATTA
*
69378 TTCTT-ACAGA
65 ATCTTAACAGA
*
69388 TGGCACTGGTTGAAACAAATA-TCACTATTCTTACCGGTGGCACGAATGTGG-ACAAAAACCATT
1 TGGCACTGGTTGAAACAAAAACT-ACTATTCTTACCGGTGGCACG-ATGTGGAACAAAAACCATT
* *
69451 AATCTTAACTGG
64 AATCTTAACAGA
69463 TGGCA-TGGTTGAAA
1 TGGCACTGGTTGAAA
69477 TTGGTTTCTA
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
73 1 0.01
74 61 0.80
75 14 0.18
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (75 bp):
TGGCACTGGTTGAAACAAAAACTACTATTCTTACCGGTGGCACGATGTGGAACAAAAACCATTAA
TCTTAACAGA
Found at i:74082 original size:19 final size:19
Alignment explanation
Indices: 74042--74090 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
74032 ATAAAAATAT
* *
74042 TATAAAATATATTTTTTTAA
1 TATAAAA-ATAATTTTTAAA
74062 TATAAAAATAATTTTTAAA
1 TATAAAAATAATTTTTAAA
74081 TA-AAAAATAA
1 TATAAAAATAA
74091 ACTTACAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 8 0.30
19 12 0.44
20 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATAAAAATAATTTTTAAA
Found at i:75058 original size:6 final size:6
Alignment explanation
Indices: 75047--75131 Score: 100
Period size: 6 Copynumber: 13.7 Consensus size: 6
75037 CAATAGAGCA
*
75047 AAGACT AAGACTT AAGACTT AAGACT AAGACT AAGACT AAAGACT AGGACT
1 AAGACT AAGAC-T AAGAC-T AAGACT AAGACT AAGACT -AAGACT AAGACT
* *
75098 AAGACT AAGAAC- AATACA AAGACT AAGACT AAGA
1 AAGACT AAG-ACT AAGACT AAGACT AAGACT AAGA
75132 ACCATACAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
5 2 0.03
6 47 0.67
7 21 0.30
ACGTcount: A:0.52, C:0.15, G:0.16, T:0.16
Consensus pattern (6 bp):
AAGACT
Found at i:75126 original size:24 final size:24
Alignment explanation
Indices: 75067--75140 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
75057 CTTAAGACTT
* *
75067 AAGACTAAGACTAAG-ACTAAAGACT
1 AAGACTAAGACTAAGAAC--AATACA
*
75092 AGGACTAAGACTAAGAACAATACA
1 AAGACTAAGACTAAGAACAATACA
*
75116 AAGACTAAGACTAAGAACCATACA
1 AAGACTAAGACTAAGAACAATACA
75140 A
1 A
75141 GTGACATTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 27 0.63
25 14 0.33
26 2 0.05
ACGTcount: A:0.54, C:0.18, G:0.15, T:0.14
Consensus pattern (24 bp):
AAGACTAAGACTAAGAACAATACA
Found at i:84398 original size:21 final size:21
Alignment explanation
Indices: 84374--84415 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
84364 GTGATAAAAG
84374 CTTCTTATGAGATGATTATCC
1 CTTCTTATGAGATGATTATCC
84395 CTTCTTATGAGATGATTATCC
1 CTTCTTATGAGATGATTATCC
84416 TTCGTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (21 bp):
CTTCTTATGAGATGATTATCC
Done.