Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold96_ERROPOS106852
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: 106852
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:11507 original size:46 final size:44
Alignment explanation
Indices: 11441--11808 Score: 203
Period size: 44 Copynumber: 8.5 Consensus size: 44
11431 ATTATACAGG
*
11441 TCTTATCT-CCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* *
11486 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAG--A
* * * * * *
11530 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * *
11569 TCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGATTCAGA
* *
11610 TCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* * ** ****
11656 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * *
11700 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCA-GA
* * * * **
11743 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA-ATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGATTCA-GA
* *
11787 TCTTATCTCTCTGAGGTTACAG
1 TCTTATCTCCCTGAGATTACAG
11809 CAGAGTAGAT
Statistics
Matches: 251, Mismatches: 51, Indels: 43
0.73 0.15 0.12
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 23 0.09
40 1 0.00
41 28 0.11
42 6 0.02
43 32 0.13
44 90 0.36
45 9 0.04
46 60 0.24
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
Found at i:11750 original size:87 final size:87
Alignment explanation
Indices: 11659--11820 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
11649 TTTCAGATCT
* * * *
11659 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAGC
*
11723 GGAGCAGATCGAAGACACTATCC
65 AGAGCAGATCGAAGACACTATCC
* * * *
11746 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
*
11811 GAGTAGATCG
66 GAGCAGATCG
11821 CATCAAGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 62 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAGACACTATCC
Found at i:11924 original size:218 final size:214
Alignment explanation
Indices: 11483--11924 Score: 473
Period size: 218 Copynumber: 2.0 Consensus size: 214
11473 AAAGAATTTC
* * *
11483 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
* *
11548 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
* * * * * * *
11613 TATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAG
131 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATATAAGAGCGTATCTCCCTAAAGTTACAG
* *** *
11678 TGGAGCAGATTGAAGCCAG
196 CGGAGCAGACAAAAGACAG
*
11697 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGA-T
* * * *
11760 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATC
65 TACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATC
* * * *
11825 AAGTCTTATTTCCCTGAAGA-TGCAGTGGAACAGACTGAAA-ACA-ATAAG-GCGTGTCTCCCTA
125 AAGTCTTATCTCCCTG-AGATTACAGTGGAACAGAC-CAAAGA-ATATAAGAGCGTATCTCCCTA
** * *
11886 AAGTTGTAGCGGAGCGGACAAAAGATAG
187 AAGTTACAGCGGAGCAGACAAAAGACAG
*
11914 TGATTCTTATC
1 AGA-TCTTATC
11925 ATGTCTAATC
Statistics
Matches: 187, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
212 1 0.01
213 28 0.15
214 43 0.23
217 29 0.16
218 79 0.42
219 7 0.04
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (214 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATATAAGAGCGTATCTCCCTAAAGTTACAG
CGGAGCAGACAAAAGACAG
Found at i:13675 original size:22 final size:23
Alignment explanation
Indices: 13650--13695 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
13640 ATAATTGCTT
13650 TTATAGATATATACATATA-TTA
1 TTATAGATATATACATATACTTA
* * *
13672 TTATATATTTTTACATATACTTA
1 TTATAGATATATACATATACTTA
13695 T
1 T
13696 ACACATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATAGATATATACATATACTTA
Found at i:13703 original size:22 final size:22
Alignment explanation
Indices: 13661--13705 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
13651 TATAGATATA
* *
13661 TACATATATTATTATATATTTT
1 TACATATATTATTACACATTTT
13683 TACATATACTTA-TACACATTTT
1 TACATATA-TTATTACACATTTT
13705 T
1 T
13706 TTTGTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (22 bp):
TACATATATTATTACACATTTT
Found at i:13826 original size:24 final size:24
Alignment explanation
Indices: 13799--13853 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
13789 ATTTCTAACC
13799 TTTATAAATATATAAATACATATT
1 TTTATAAATATATAAATACATATT
* * **
13823 TTTACATATATATATGTACATATT
1 TTTATAAATATATAAATACATATT
13847 TTATATA
1 TT-TATA
13854 TTTTATAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTATAAATATATAAATACATATT
Found at i:18719 original size:19 final size:20
Alignment explanation
Indices: 18695--18738 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
18685 TCAAAACACT
*
18695 AGAAAAATAGATCATTTT-C
1 AGAAAAATAAATCATTTTCC
*
18714 AGAAAAGTAAATCATTTTCC
1 AGAAAAATAAATCATTTTCC
18734 AGAAA
1 AGAAA
18739 TTATTTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.27
Consensus pattern (20 bp):
AGAAAAATAAATCATTTTCC
Found at i:21899 original size:3 final size:3
Alignment explanation
Indices: 21893--21931 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
21883 TATCAAATTA
* *
21893 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21932 TCTCTTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:23577 original size:16 final size:16
Alignment explanation
Indices: 23556--23607 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
23546 GGGCCAAAAG
23556 AAAATTAGAAGGATGA
1 AAAATTAGAAGGATGA
*
23572 AAAATT-GAAGGGT-A
1 AAAATTAGAAGGATGA
*
23586 GAAAACTAGAAGGATGA
1 -AAAATTAGAAGGATGA
23603 AAAAT
1 AAAAT
23608 ATTATTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 11 0.38
16 16 0.55
17 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.25, T:0.17
Consensus pattern (16 bp):
AAAATTAGAAGGATGA
Found at i:25332 original size:20 final size:19
Alignment explanation
Indices: 25269--25333 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
25259 AGTGAATTTT
*
25269 TTTAAAAAAAATAATTATAT
1 TTTAAAAAAAATAA-TATAA
* *
25289 TTTGAAAGAAAGATAATTTAA
1 TTT-AAA-AAAAATAATATAA
*
25310 TTTAAATAAAATAATAATAA
1 TTTAAAAAAAATAAT-ATAA
25330 TTTA
1 TTTA
25334 TTGGTTTCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 7 0.19
20 13 0.36
21 9 0.25
22 7 0.19
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTAAAAAAAATAATATAA
Found at i:29721 original size:26 final size:25
Alignment explanation
Indices: 29692--29743 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
29682 TAATAAAATG
*
29692 ATAAA-ACAAAATAAATAAAAAGGTAA
1 ATAAATACAAAACAAA-AAAAA-GTAA
*
29718 ATAAATAGAAAACAAAAAAAAGTAA
1 ATAAATACAAAACAAAAAAAAGTAA
29743 A
1 A
29744 AGGGGTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 5 0.22
26 10 0.43
27 8 0.35
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (25 bp):
ATAAATACAAAACAAAAAAAAGTAA
Found at i:30117 original size:3 final size:3
Alignment explanation
Indices: 30014--30098 Score: 77
Period size: 3 Copynumber: 28.7 Consensus size: 3
30004 ATGGTTTAAA
* * * *
30014 AAT AAT AAT GAT AAT AAA AAT AAA AAT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
30062 AAT GAAT -AT AAAT AAT AGT AA- AAG AA- AAT AAT AAT AA
1 AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
30099 AATTAACTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.09
3 56 0.84
4 5 0.07
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:38353 original size:37 final size:37
Alignment explanation
Indices: 38303--38378 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
38293 AGATAGAGGA
38303 ATGCAAAGAAGACATATCTGAACCCTTCATTGAATCT
1 ATGCAAAGAAGACATATCTGAACCCTTCATTGAATCT
38340 ATGCAAAGAAGACATATCTGAACCCTTCATTGAATCT
1 ATGCAAAGAAGACATATCTGAACCCTTCATTGAATCT
38377 AT
1 AT
38379 CTTTATGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (37 bp):
ATGCAAAGAAGACATATCTGAACCCTTCATTGAATCT
Found at i:40566 original size:23 final size:24
Alignment explanation
Indices: 40536--40596 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 24
40526 GTTTAGAATT
* *
40536 AAAACTTAATATATATTCATATC-
1 AAAACTTAATATATATTCAAAGCA
*
40559 AAAACTTAAT-T-TATTGAAAGCA
1 AAAACTTAATATATATTCAAAGCA
40581 AAAACTTAATATATAT
1 AAAACTTAATATATAT
40597 ATCACGAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 7 0.22
22 11 0.34
23 11 0.34
24 3 0.09
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (24 bp):
AAAACTTAATATATATTCAAAGCA
Found at i:44226 original size:24 final size:24
Alignment explanation
Indices: 44199--44244 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
44189 TTAAACAAAA
*
44199 TAATTTAAAAAGTACTTTTTAATG
1 TAATTTAAAAACTACTTTTTAATG
*
44223 TAATTTAAAAACTATTTTTTAA
1 TAATTTAAAAACTACTTTTTAA
44245 AAAATTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (24 bp):
TAATTTAAAAACTACTTTTTAATG
Found at i:46783 original size:10 final size:10
Alignment explanation
Indices: 46768--46793 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
46758 GCAGAGCCTT
46768 TGAAGGTCGA
1 TGAAGGTCGA
46778 TGAAGGTCGA
1 TGAAGGTCGA
46788 TGAAGG
1 TGAAGG
46794 GGATGGGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.42, T:0.19
Consensus pattern (10 bp):
TGAAGGTCGA
Found at i:49475 original size:22 final size:22
Alignment explanation
Indices: 49447--49510 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
49437 AAACCGCTAG
49447 TAATAGTATGCAGTACAA-CTGC
1 TAATAGTATGCAG-ACAAGCTGC
* *
49469 TAATAGTTTGTAGACAAGCTGC
1 TAATAGTATGCAGACAAGCTGC
*
49491 TAGTAAGT-TGCAGACAAGCT
1 TAAT-AGTATGCAGACAAGCT
49511 ACTAGTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.11
22 29 0.81
23 3 0.08
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (22 bp):
TAATAGTATGCAGACAAGCTGC
Found at i:49515 original size:22 final size:22
Alignment explanation
Indices: 49480--49523 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
49470 AATAGTTTGT
* *
49480 AGACAAGCTGCTAGTAAGTTGC
1 AGACAAGCTACTAGTAAATTGC
49502 AGACAAGCTACTAGTAAATTGC
1 AGACAAGCTACTAGTAAATTGC
49524 GATAAGTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (22 bp):
AGACAAGCTACTAGTAAATTGC
Found at i:55173 original size:4 final size:4
Alignment explanation
Indices: 55164--55208 Score: 81
Period size: 4 Copynumber: 11.2 Consensus size: 4
55154 CTATTCTAAC
*
55164 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AAAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
55209 TTTTCTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:56344 original size:21 final size:21
Alignment explanation
Indices: 56293--56344 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
56283 CTTGAATCTC
*
56293 AAACCCAAAATCACGAACCCT
1 AAACCCAAAATCACAAACCCT
* * * * *
56314 GAATCTAAAATCTCAAATCCT
1 AAACCCAAAATCACAAACCCT
56335 AAACCCAAAA
1 AAACCCAAAA
56345 AACCTATAAC
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.31, G:0.04, T:0.15
Consensus pattern (21 bp):
AAACCCAAAATCACAAACCCT
Found at i:56418 original size:21 final size:20
Alignment explanation
Indices: 56372--56419 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
56362 ATTAAACCTT
*
56372 AAACCCCAAACTCTTAACTC
1 AAACCCCAAACTCTAAACTC
* *
56392 ATAACCTCAAACTCTAAATTCC
1 A-AACCCCAAACTCTAAACT-C
56414 AAACCC
1 AAACCC
56420 TTGAACTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 19 0.86
22 2 0.09
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.21
Consensus pattern (20 bp):
AAACCCCAAACTCTAAACTC
Found at i:58491 original size:26 final size:26
Alignment explanation
Indices: 58448--58498 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
58438 ATATATAATT
58448 TTATCACAAAAATAAATATTATTTAA
1 TTATCACAAAAATAAATATTATTTAA
* * *
58474 TTATCATAAAGATTAATATTATTTA
1 TTATCACAAAAATAAATATTATTTA
58499 TCATAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (26 bp):
TTATCACAAAAATAAATATTATTTAA
Found at i:60286 original size:19 final size:19
Alignment explanation
Indices: 60259--60313 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 19
60249 TGGGTGCCCT
* *
60259 TACGCATTGCTTCAAAGGC
1 TACGAATTGCTTCAAAAGC
*
60278 TACGAATTGTTGTACAAAAGC
1 TACGAATTGCT-T-CAAAAGC
*
60299 CACGAATTGCTTCAA
1 TACGAATTGCTTCAA
60314 TTTTCCCTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 12 0.41
20 2 0.07
21 15 0.52
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (19 bp):
TACGAATTGCTTCAAAAGC
Found at i:61545 original size:21 final size:21
Alignment explanation
Indices: 61519--61559 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
61509 ACTTCTATTG
61519 TTCCTCATATATCCTTTGTTC
1 TTCCTCATATATCCTTTGTTC
61540 TTCCTCATATATCCTTTGTT
1 TTCCTCATATATCCTTTGTT
61560 GAAAGGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.27, G:0.05, T:0.54
Consensus pattern (21 bp):
TTCCTCATATATCCTTTGTTC
Found at i:66601 original size:46 final size:46
Alignment explanation
Indices: 66549--66722 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 46
66539 TTTGGGCATT
*
66549 CGAACTCGTTGAGCTGAGTCCGAGTTCACTTATGGATGCGAACATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATC
* * * *
66595 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGATATGTA-ACTAAGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGAA-CATC
* *
66642 CGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAA-AGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA-TC
* * *
66688 CGAGCTCGTTGATTTGA-TCCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGT-CCGAGTTCACTTATGG
66723 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
45 3 0.03
46 63 0.59
47 39 0.37
48 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATC
Found at i:66711 original size:93 final size:93
Alignment explanation
Indices: 66544--66715 Score: 258
Period size: 93 Copynumber: 1.8 Consensus size: 93
66534 GGATATTTGG
* * *
66544 GCATTCGAACTCGTTGAGCTGAGTCCGAGTTCACTTATGGATGCGAACATCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGCTGAGTCCGAGTTCACTCATGGATGCGAACACCCGAACTCGTTGAGT
66609 TGAGTCCGAGTTCGTGATATGTAACTAA
66 TGAGTCCGAGTTCGTGATATGTAACTAA
* * *
66637 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAA-AGCCCGAGCTCGTTGAT
1 GCATCCGAACTCGTTGAGCTGAGTCCGAGTTCACTCATGGATGCGAACA-CCCGAACTCGTTGAG
66701 TTGA-TCCCGAGTTCG
65 TTGAGT-CCGAGTTCG
66716 CTTATGGGCG
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGCTGAGTCCGAGTTCACTCATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGATATGTAACTAA
Found at i:68286 original size:33 final size:33
Alignment explanation
Indices: 68212--68305 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
68202 CTTTGTCTTG
* *
68212 TGTTTACTATCCTAGCGGACGTATCTATGTTCTA
1 TGTTTACTATCCTAGCGGAC-TATCTCTGTTCAA
** * *
68246 TACTTACTATCCTAGTGGACCATCTCTGTTCAA
1 TGTTTACTATCCTAGCGGACTATCTCTGTTCAA
*
68279 TGTTTACTATCCCAGCGGACTATCTCT
1 TGTTTACTATCCTAGCGGACTATCTCT
68306 ATGGATGCCG
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 32 0.65
34 17 0.35
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (33 bp):
TGTTTACTATCCTAGCGGACTATCTCTGTTCAA
Found at i:71783 original size:2 final size:2
Alignment explanation
Indices: 71778--71805 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
71768 TTTCATTTTC
71778 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
71806 CATTAGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73933 original size:31 final size:31
Alignment explanation
Indices: 73895--73953 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
73885 CAGCCCAGTG
73895 ACTTAAATAAAAAT-TATCAAATAATTTATTA
1 ACTTAAATAAAAATAT-TCAAATAATTTATTA
*
73926 ACTTAAATAAAAATATTTAAATAATTTA
1 ACTTAAATAAAAATATTCAAATAATTTA
73954 ATTACCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (31 bp):
ACTTAAATAAAAATATTCAAATAATTTATTA
Found at i:82606 original size:87 final size:88
Alignment explanation
Indices: 82467--82655 Score: 290
Period size: 87 Copynumber: 2.2 Consensus size: 88
82457 AATTGCAATA
* *
82467 ATTATCGACTTCATAAGAACATATGGAAAAAATATATGTGCTAAAAGCCTAAAATCAAATCCTCC
1 ATTATCAAATTCATAAGAACATATGGAAAAAATATATGTGCTAAAAGCCTAAAATCAAATCCTCC
* *
82532 AAAAGTCACAAGACTTTTTTATT
66 AAAAGGCACAAGACTTTTTCATT
*
82555 ATTATCAAATTCATAAGAACATAT-GAAAAAATATGTGTGCTAAAAGCCTAAAATCAAATCCTCC
1 ATTATCAAATTCATAAGAACATATGGAAAAAATATATGTGCTAAAAGCCTAAAATCAAATCCTCC
* * *
82619 TAAAGGCATAATACTTTTTCATT
66 AAAAGGCACAAGACTTTTTCATT
*
82642 AATATCAAATTCAT
1 ATTATCAAATTCAT
82656 TGATCATAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 70 0.76
88 22 0.24
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (88 bp):
ATTATCAAATTCATAAGAACATATGGAAAAAATATATGTGCTAAAAGCCTAAAATCAAATCCTCC
AAAAGGCACAAGACTTTTTCATT
Found at i:89979 original size:26 final size:26
Alignment explanation
Indices: 89950--90057 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
89940 CGATACAAAT
89950 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
89976 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
90002 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
90028 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
90054 TGAT
1 TGAT
90058 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:96217 original size:21 final size:21
Alignment explanation
Indices: 96188--96228 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
96178 AATAATAATA
96188 ATTTAAAATTTCATT-AAAAAC
1 ATTTAAAATTT-ATTCAAAAAC
*
96209 ATTTTAAATTTATTCAAAAA
1 ATTTAAAATTTATTCAAAAA
96229 TAGAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAAAATTTATTCAAAAAC
Found at i:100856 original size:32 final size:32
Alignment explanation
Indices: 100820--100943 Score: 221
Period size: 32 Copynumber: 3.9 Consensus size: 32
100810 AATAAAAGTC
*
100820 CTCTTGCTTGATGTGAGTTTTAAATATTAACA
1 CTCTTGCTTGATGTGAGTTTTACATATTAACA
100852 CTCTTGCTTGATGTGAGTTTTACATATTAACA
1 CTCTTGCTTGATGTGAGTTTTACATATTAACA
*
100884 CGCTTGCTTGATGTGAGTTTTACATATTAACA
1 CTCTTGCTTGATGTGAGTTTTACATATTAACA
*
100916 CTCTTGCTTGATATGAGTTTTACATATT
1 CTCTTGCTTGATGTGAGTTTTACATATT
100944 TGTTAATTTT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 88 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (32 bp):
CTCTTGCTTGATGTGAGTTTTACATATTAACA
Done.