Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3513
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: 44865
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:2681 original size:39 final size:40
Alignment explanation
Indices: 2636--2820 Score: 187
Period size: 40 Copynumber: 4.7 Consensus size: 40
2626 GCTCCTCGTT
* * * *
2636 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
2676 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
2715 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * * *
2755 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
2796 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
2821 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 36 0.30
40 75 0.61
41 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:2725 original size:79 final size:80
Alignment explanation
Indices: 2638--2820 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
2628 TCCTCGTTCA
* * *
2638 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGA-CTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGGCCTTC-GGATCTTAACCCGGA
* * *
2701 TTTAATGAC-TCGCAC
65 TATAATCACTTAGCAC
* * * **
2716 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGGCCTTCGGATCTTAACCCGGA
*
2781 TATATTCACTTAGCAC
65 TATAATCACTTAGCAC
*
2797 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
2821 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 37 0.43
80 45 0.52
81 5 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGGCCTTCGGATCTTAACCCGGAT
ATAATCACTTAGCAC
Found at i:2829 original size:41 final size:41
Alignment explanation
Indices: 2752--2829 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2742 TTAGTATCTC
* * *
2752 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2793 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2830 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:10153 original size:39 final size:40
Alignment explanation
Indices: 10108--10292 Score: 187
Period size: 40 Copynumber: 4.7 Consensus size: 40
10098 GCTCCTCGTT
* * * *
10108 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
10148 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
10187 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * * *
10227 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
10268 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
10293 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 36 0.30
40 75 0.61
41 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:10197 original size:79 final size:80
Alignment explanation
Indices: 10110--10292 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
10100 TCCTCGTTCA
* * *
10110 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGA-CTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGGCCTTC-GGATCTTAACCCGGA
* * *
10173 TTTAATGAC-TCGCAC
65 TATAATCACTTAGCAC
* * * **
10188 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGGCCTTCGGATCTTAACCCGGA
*
10253 TATATTCACTTAGCAC
65 TATAATCACTTAGCAC
*
10269 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
10293 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 37 0.43
80 45 0.52
81 5 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGGCCTTCGGATCTTAACCCGGAT
ATAATCACTTAGCAC
Found at i:10301 original size:41 final size:41
Alignment explanation
Indices: 10224--10301 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
10214 TTAGTATCTC
* * *
10224 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
10265 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
10302 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:18631 original size:55 final size:53
Alignment explanation
Indices: 18505--18701 Score: 151
Period size: 55 Copynumber: 3.7 Consensus size: 53
18495 AGGGTTTAAG
* * * * * * * * * *
18505 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCAACAAGGTAAG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTAC-ATAAGGCAAA
* * **
18559 GAAATCATGTAAGACCATGTCAAGACATGGCTTTGATAAACTACTATAAGGCAAA
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGAT-AACTAC-ATAAGGCAAA
* * * * * * * *
18614 GATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGCAAG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTACATAAGGCAAA
**
18667 GATACCACATAAGACCATGTCAAGACATGGCAATG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATG
18702 GTAAGTTTAA
Statistics
Matches: 112, Mismatches: 30, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 39 0.35
54 33 0.29
55 40 0.36
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (53 bp):
GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTACATAAGGCAAA
Found at i:18684 original size:53 final size:54
Alignment explanation
Indices: 18502--18725 Score: 193
Period size: 53 Copynumber: 4.2 Consensus size: 54
18492 ATTAGGGTTT
* * * *
18502 AAGGATACCA-AGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCAACAAGGT
1 AAGGATACCATA-TAAGACCATGCCAAGACATGGCAATGGTAAGTTCAATAAGGC
* * * * ** * * * *
18556 AAGGAAATCATGTAAGACCATGTCAAGACATGGCTTTGATAAACTACTATAAGGC
1 AAGGATACCATATAAGACCATGCCAAGACATGGCAATGGT-AAGTTCAATAAGGC
* * * * *
18611 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTC-ATAAGGC
1 AAGGATACCATATAAGACCATGCCAAGACATGGCAATGGTAAGTTCAATAAGGC
* * * * *
18664 AAGGATACCACATAAGACCATGTCAAGACATGGCAATGGTAAGTTTAAAAAGGA
1 AAGGATACCATATAAGACCATGCCAAGACATGGCAATGGTAAGTTCAATAAGGC
18718 AAGG-TACC
1 AAGGATACC
18726 CGTGTATCCT
Statistics
Matches: 133, Mismatches: 34, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
53 49 0.37
54 44 0.33
55 40 0.30
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.20
Consensus pattern (54 bp):
AAGGATACCATATAAGACCATGCCAAGACATGGCAATGGTAAGTTCAATAAGGC
Found at i:24846 original size:91 final size:89
Alignment explanation
Indices: 24716--24913 Score: 252
Period size: 91 Copynumber: 2.2 Consensus size: 89
24706 ACTTGAAAAT
* *
24716 AAAAGCAATTAAGCCCCTCCTCATTTTTTGCACTTAATTGAGCACTTAAACTTTTAAAATGCATC
1 AAAAGCAATTAAGCCCCTCCTCATTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGCATC
* *
24781 AAAAAAGGCCCTCAAACTTCTTCAA
66 -AAAAAGACCCTCAAAATTCTTCAA
* * ** * * *
24806 AAAATGCAATTAAGCCCTTGCTTTTTTTTTTCACTCAATTGGGTACTTAAACTTTCAAAATGCAT
1 AAAA-GCAATTAAGCCCCTCCTCATTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGCAT
*
24871 CAAAAAGACCCTCAAAATTTTTCAA
65 CAAAAAGACCCTCAAAATTCTTCAA
* *
24896 AAAAGTAATTAAACCCCT
1 AAAAGCAATTAAGCCCCT
24914 ACTCTTATTA
Statistics
Matches: 92, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
89 11 0.12
90 29 0.32
91 52 0.57
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (89 bp):
AAAAGCAATTAAGCCCCTCCTCATTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGCATC
AAAAAGACCCTCAAAATTCTTCAA
Found at i:24973 original size:22 final size:21
Alignment explanation
Indices: 24923--24979 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
24913 TACTCTTATT
24923 AAAAATAGAA-AAAAATTATAA
1 AAAAATA-AATAAAAATTATAA
* *
24944 AAATAATAAATAAAAATTTTTAG
1 AAA-AATAAATAAAAA-TTATAA
*
24967 AAAAATAATTAAA
1 AAAAATAAATAAA
24980 TTTTAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 5 0.17
22 18 0.60
23 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (21 bp):
AAAAATAAATAAAAATTATAA
Found at i:24990 original size:18 final size:19
Alignment explanation
Indices: 24947--24995 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
24937 ATTATAAAAA
24947 TAATAAATAA--AAATTTT
1 TAATAAATAATTAAATTTT
*
24964 TAGAAAAATAATTAAA-TTT
1 TA-ATAAATAATTAAATTTT
24983 TAATAAAT-ATTAA
1 TAATAAATAATTAA
24996 CAAATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 7 0.26
18 12 0.44
19 5 0.19
20 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAATAAATAATTAAATTTT
Found at i:25157 original size:18 final size:18
Alignment explanation
Indices: 25134--25176 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
25124 GACATTGGCG
25134 AAAAATGATAAAAAAAAT
1 AAAAATGATAAAAAAAAT
* * *
25152 AAAAATTATAGAAAAATT
1 AAAAATGATAAAAAAAAT
25170 AAAAATG
1 AAAAATG
25177 TTTTTTTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAAAATGATAAAAAAAAT
Found at i:25295 original size:19 final size:18
Alignment explanation
Indices: 25273--25383 Score: 64
Period size: 19 Copynumber: 5.9 Consensus size: 18
25263 AATTTTAATT
* *
25273 TTTTTTATATTTCTATATA
1 TTTTATATATTT-TTTATA
*
25292 TTTTATA-ATTTTTTACGA
1 TTTTATATATTTTTTA-TA
*
25310 TTTTTATATATTTTTTCTAA
1 -TTTTATATATTTTTTAT-A
* *
25330 TTTTTATATATTTTCTAAA
1 -TTTTATATATTTTTTATA
* *
25349 TTTTAATAAATTTTTAATA
1 TTTT-ATATATTTTTTATA
* *
25368 -TTTAAATTTTTTTTAT
1 TTTTATATATTTTTTAT
25384 TAAAATTTAA
Statistics
Matches: 71, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
17 12 0.17
18 12 0.17
19 24 0.34
20 23 0.32
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTTATATATTTTTTATA
Found at i:25324 original size:20 final size:20
Alignment explanation
Indices: 25282--25343 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
25272 TTTTTTTATA
25282 TTTCTATATATTTTATA-ATTT
1 TTTCTA-AT-TTTTATATATTT
*
25303 TTTAC-GATTTTTATATATTT
1 TTT-CTAATTTTTATATATTT
25323 TTTCTAATTTTTATATATTT
1 TTTCTAATTTTTATATATTT
25343 T
1 T
25344 CTAAATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 8 0.22
20 24 0.67
21 3 0.08
22 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTCTAATTTTTATATATTT
Found at i:25337 original size:18 final size:18
Alignment explanation
Indices: 25282--25353 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 18
25272 TTTTTTTATA
25282 TTTCTATATATTTTATAATTT
1 TTTCTA-AT-TTTTAT-ATTT
* *
25303 TTTACGATTTTTATATATTT
1 TTT-CTAATTTT-TATATTT
*
25323 TTTCTAATTTTTATATAT
1 TTTCTAATTTTTATATTT
*
25341 TTTCTAAATTTTA
1 TTTCTAATTTTTA
25354 ATAAATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 18 0.42
19 6 0.14
20 10 0.23
21 7 0.16
22 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (18 bp):
TTTCTAATTTTTATATTT
Found at i:25370 original size:9 final size:9
Alignment explanation
Indices: 25256--25370 Score: 58
Period size: 10 Copynumber: 12.3 Consensus size: 9
25246 TTCTTACCAC
25256 TTTTTAA-A
1 TTTTTAATA
* *
25264 ATTTTAATT
1 TTTTTAATA
*
25273 TTTTTTATA
1 TTTTTAATA
*
25282 TTTCTATATA
1 TTTTTA-ATA
25292 TTTTATAAT-
1 TTTT-TAATA
**
25301 TTTTTACGA
1 TTTTTAATA
25310 TTTTTATATA
1 TTTTTA-ATA
**
25320 TTTTTTCTAA
1 TTTTTAAT-A
25330 TTTTTATATA
1 TTTTTA-ATA
25340 TTTTCTAA-A
1 TTTT-TAATA
25349 -TTTTAATAAA
1 TTTTTAAT--A
25359 TTTTTAATA
1 TTTTTAATA
25368 TTT
1 TTT
25371 AAATTTTTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 23
0.67 0.14 0.19
Matches are distributed among these distances:
7 3 0.04
8 11 0.14
9 26 0.33
10 27 0.34
11 12 0.15
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTTAATA
Found at i:25375 original size:15 final size:15
Alignment explanation
Indices: 25355--25402 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
25345 TAAATTTTAA
25355 TAAATTTTTAATATT
1 TAAATTTTTAATATT
**
25370 TAAATTTTTTTTATT
1 TAAATTTTTAATATT
* *
25385 AAAATTTAATAATATT
1 TAAATTT-TTAATATT
25401 TA
1 TA
25403 TAGATTTTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAAATTTTTAATATT
Found at i:25555 original size:93 final size:97
Alignment explanation
Indices: 25458--25636 Score: 260
Period size: 97 Copynumber: 1.9 Consensus size: 97
25448 TAATAAAAGC
* * *
25458 AAGGCTTAATT-TTTTTTT-TAA-GTTTGA-GGTTTTTTTTATGCATTTTAAAAGTTCAAGTACC
1 AAGGCTTAATTCTTTTTTTAGAAGGTTTGATGGCTTTTTTTATGCATTGTAAAAGTTCAAGTACC
*
25519 C-AATTAAGTGCAAAAAAAAAACAAAAAAAATA
66 CAAATGAA-TGCAAAAAAAAAACAAAAAAAATA
* *
25551 AAGGCTTAATTCTTTTTTTAGAAGGTTTGATGGCTTTTTTTATGTATTGTGAAAGTTCAAGTACC
1 AAGGCTTAATTCTTTTTTTAGAAGGTTTGATGGCTTTTTTTATGCATTGTAAAAGTTCAAGTACC
25616 CAAATGAATGCAAAAAAAAAA
66 CAAATGAATGCAAAAAAAAAA
25637 AAAGCAGCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
93 11 0.15
94 7 0.09
95 2 0.03
96 6 0.08
97 44 0.59
98 5 0.07
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (97 bp):
AAGGCTTAATTCTTTTTTTAGAAGGTTTGATGGCTTTTTTTATGCATTGTAAAAGTTCAAGTACC
CAAATGAATGCAAAAAAAAAACAAAAAAAATA
Found at i:26644 original size:23 final size:23
Alignment explanation
Indices: 26617--26663 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
26607 CTTTATACTT
26617 ACAACTTACTATTCATATACCAC
1 ACAACTTACTATTCATATACCAC
26640 ACAACTTACTATTCATATACCAC
1 ACAACTTACTATTCATATACCAC
26663 A
1 A
26664 TACAGGCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (23 bp):
ACAACTTACTATTCATATACCAC
Found at i:27952 original size:57 final size:59
Alignment explanation
Indices: 27854--27974 Score: 174
Period size: 58 Copynumber: 2.1 Consensus size: 59
27844 TAGAAATGGC
* *
27854 GAAAATGGAGAAATGAGAAACATTTGGAAACAAATGTGG-TTTTCTCTAAAATGAAAAA
1 GAAAATGGAGAAATGAGAAACATTTGAAAACAAATGTGGTTTTTCTCCAAAATGAAAAA
* ** *
27912 GAAAATGGAGAAATG-GAAATATTTGAAAATGAATGTGGTTTTTTTCCAAAATGAAAAA
1 GAAAATGGAGAAATGAGAAACATTTGAAAACAAATGTGGTTTTTCTCCAAAATGAAAAA
27970 GAAAA
1 GAAAA
27975 AGAAAAATGA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 19 0.34
58 37 0.66
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (59 bp):
GAAAATGGAGAAATGAGAAACATTTGAAAACAAATGTGGTTTTTCTCCAAAATGAAAAA
Found at i:28000 original size:58 final size:57
Alignment explanation
Indices: 27886--28003 Score: 141
Period size: 58 Copynumber: 2.1 Consensus size: 57
27876 TTTGGAAACA
* * * * *
27886 AATGTGGTTTTCTCTAAAATGAAAAAGAAAATGGAGAAATGGAAATATTTGAAAATG
1 AATGTGGTTTTCTCCAAAATGAAAAAGAAAATAGAAAAATGAAAATACTTGAAAATG
*
27943 AATGTGGTTTTTTTCCAAAATGAAAAAGAAAA-AGAAAAATGAAAATGACCTTG-AAATG
1 AATGTGG-TTTTCTCCAAAATGAAAAAGAAAATAGAAAAATGAAAAT-A-CTTGAAAATG
28001 AAT
1 AAT
28004 TTATGGTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
57 18 0.35
58 31 0.60
59 3 0.06
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (57 bp):
AATGTGGTTTTCTCCAAAATGAAAAAGAAAATAGAAAAATGAAAATACTTGAAAATG
Found at i:28989 original size:30 final size:31
Alignment explanation
Indices: 28934--28995 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
28924 TGGCACATGA
28934 TATGTCGTAATTTGATATAAAAAAATAGACT
1 TATGTCGTAATTTGATATAAAAAAATAGACT
28965 TATGTCGTAATTTGATAT-AAAAAATAGACT
1 TATGTCGTAATTTGATATAAAAAAATAGACT
28995 T
1 T
28996 TCCTATTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (31 bp):
TATGTCGTAATTTGATATAAAAAAATAGACT
Found at i:31045 original size:40 final size:40
Alignment explanation
Indices: 30981--31124 Score: 191
Period size: 40 Copynumber: 3.6 Consensus size: 40
30971 CTAGCTCGTG
* * * *
30981 GCCTGCGGGTCTCT-AGCCCGGATAGCATTCTAGCACAAA
1 GCCTGCGGGTCTTTAAGCCCGGATAGCATTCCAGCATATA
* *
31020 ACCTGTGGGTCTTTAAGCCCGGATAGCATTCCAGCATATA
1 GCCTGCGGGTCTTTAAGCCCGGATAGCATTCCAGCATATA
** *
31060 GCCTGTAGGTCTTTAAGCCCGGATAACATTCCAGCATATA
1 GCCTGCGGGTCTTTAAGCCCGGATAGCATTCCAGCATATA
*
31100 GCCTACGGGTCTTTAAGCCCGGATA
1 GCCTGCGGGTCTTTAAGCCCGGATA
31125 CAATTCCTCA
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 11 0.12
40 81 0.88
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTGCGGGTCTTTAAGCCCGGATAGCATTCCAGCATATA
Found at i:36621 original size:46 final size:46
Alignment explanation
Indices: 36554--36724 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
36544 AACCCGCCCC
* *
36554 TAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
* *
36600 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
36648 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
36693 TAAGTGAACTTGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
36725 AATGCTCAAC
Statistics
Matches: 103, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 2 0.02
46 57 0.55
47 28 0.27
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:36667 original size:93 final size:93
Alignment explanation
Indices: 36559--36729 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
36549 GCCCCTAAGT
* *
36559 GAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
36624 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGAATGCCTAGTTACATTTCAC
* * *
36652 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
36717 CGAGTTCGAATGC
66 CGAGTTCGAATGC
36730 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGAATGCCTAGTTACATTTCAC
Found at i:37182 original size:30 final size:30
Alignment explanation
Indices: 37148--37207 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
37138 ATTTAATACG
37148 AACTTTGGA-AAAATTACACTTTTGCCCCTA
1 AACTTT-GACAAAATTACACTTTTGCCCCTA
* *
37178 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
37208 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:41560 original size:45 final size:46
Alignment explanation
Indices: 41496--41670 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
41486 TGTAACCCGC
*
41496 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* *
41541 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* *
41591 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
41634 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
41671 TGCTCAACAT
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 36 0.32
46 29 0.26
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:41661 original size:93 final size:92
Alignment explanation
Indices: 41503--41673 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 92
41493 CGCCCATAAG
*
41503 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41568 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
41595 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41660 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
41674 TCAACATCCT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 28 0.37
93 48 0.63
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Done.