Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1485
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: 33924
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:1116 original size:28 final size:29
Alignment explanation
Indices: 1083--1144 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
1073 TACAAAATTC
1083 TAAAAATTAAAAAT-TAAATGAAAGT-AGA
1 TAAAAATTAAAAATATAAAT-AAAGTGAGA
**
1111 TAAAAATTTCAAATATAAATAAAGTGAGA
1 TAAAAATTAAAAATATAAATAAAGTGAGA
*
1140 GAAAA
1 TAAAA
1145 TGAGGGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (29 bp):
TAAAAATTAAAAATATAAATAAAGTGAGA
Found at i:2585 original size:23 final size:25
Alignment explanation
Indices: 2549--2597 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
2539 AGAATAAAAA
*
2549 AATAACATCTTAATTT-AAATAATT
1 AATAACATCTTAATTTGAAAAAATT
*
2573 AATAA-ATTTTAATTTGAAAAAATT
1 AATAACATCTTAATTTGAAAAAATT
2597 A
1 A
2598 TTTTGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (25 bp):
AATAACATCTTAATTTGAAAAAATT
Found at i:10449 original size:89 final size:86
Alignment explanation
Indices: 10311--10537 Score: 222
Period size: 88 Copynumber: 2.6 Consensus size: 86
10301 TCCCTCTTTT
* * * * * * * * * *
10311 TTTTTTTTTACACTCAATTGAGCACTTAAACTTTTAAAATGTATCAAAAATATCTTTA-CACTTC
1 TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCAT-AAAAAAACCTTAATCACTTC
10375 TTCAAAAAAAGCAATTAAACCCCCC
65 TTCAAAAAAA-CAATT-AA-CCCCC
*** *
10400 TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAACCTTAATTTTTTTT
1 TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAACCTTAATCACTTCT
* * *
10465 TCAAAGAAACAATTAAGCCTC
66 TCAAAAAAACAATTAACCCCC
**
10486 TATTTTTTCCCCACTCAATTTGGGTACTTGAACTTTCATAATGCATAAAAAA
1 T-TTTTTTTTCCACTCAA-TTGGGTACTTGAACTTTCATAATGCATAAAAAA
10538 GGCCTTAAAT
Statistics
Matches: 116, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
86 4 0.03
87 16 0.14
88 48 0.41
89 48 0.41
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.38
Consensus pattern (86 bp):
TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAACCTTAATCACTTCT
TCAAAAAAACAATTAACCCCC
Found at i:10509 original size:88 final size:87
Alignment explanation
Indices: 10409--10571 Score: 267
Period size: 88 Copynumber: 1.9 Consensus size: 87
10399 CTTTTTTTTT
*
10409 CCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAA-ACCTTAATTTTTTTTTCAAAGAA
1 CCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAGACCTTAA-ATTTTTTTCAAA-AA
10473 A-CAATTAAGCCTCTATTTTTTCC
64 AGCAATTAAGCCTCTATTTTTTCC
*
10496 CCACTCAATTTGGGTACTTGAACTTTCATAATGCATAAAAAAGGCCTTAAATTTTTTTCAAAAAA
1 CCACTCAA-TTGGGTACTTGAACTTTCATAATGCATAAAAAAGACCTTAAATTTTTTTCAAAAAA
10561 GCAATTAAGCC
65 GCAATTAAGCC
10572 CCTACTCTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
87 11 0.15
88 54 0.76
89 6 0.08
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (87 bp):
CCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAGACCTTAAATTTTTTTCAAAAAAG
CAATTAAGCCTCTATTTTTTCC
Found at i:10647 original size:19 final size:20
Alignment explanation
Indices: 10603--10654 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
10593 AAAAAGAATC
*
10603 ATAAAAATAATAAATTTTAG
1 ATAAAAATATTAAATTTTAG
*
10623 AAAAAAATATTAAATTTTA-
1 ATAAAAATATTAAATTTTAG
10642 ATAAAAAT-TTAAA
1 ATAAAAATATTAAA
10655 AACTTATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 5 0.17
19 7 0.24
20 17 0.59
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAAATATTAAATTTTAG
Found at i:11032 original size:55 final size:55
Alignment explanation
Indices: 10972--11114 Score: 166
Period size: 55 Copynumber: 2.6 Consensus size: 55
10962 TTCTTATGAC
* *
10972 TTTATAAAATTTTATAATTTTT-TATATTTCTAT-ATATTTTTTAAATTTTTAAATT
1 TTTATAAAATTTTATAATTTTTATATATTT-TATAATAATTTTT-AATATTTAAATT
* * *
11027 TTTATAAAATTTTACAATTTTTATATATTTTTTAATAATTTTTAATATTTGAATT
1 TTTATAAAATTTTATAATTTTTATATATTTTATAATAATTTTTAATATTTAAATT
* * *
11082 TTTATTAAAATTTAATAA-TATTATAGATTTTAT
1 TTTA-TAAAATTTTATAATTTTTATATATTTTAT
11115 TGATTTTAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
55 49 0.65
56 26 0.35
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (55 bp):
TTTATAAAATTTTATAATTTTTATATATTTTATAATAATTTTTAATATTTAAATT
Found at i:11036 original size:19 final size:19
Alignment explanation
Indices: 10972--11061 Score: 66
Period size: 19 Copynumber: 4.8 Consensus size: 19
10962 TTCTTATGAC
10972 TTTATAAAA-TTTTATAATT
1 TTTATAAAATTTTTA-AATT
* *
10991 TTT-T-ATATTTCTATATATT
1 TTTATAAAATTT-T-TAAATT
11010 TTT-T-AAATTTTTAAATT
1 TTTATAAAATTTTTAAATT
11027 TTTATAAAA-TTTTACAATT
1 TTTATAAAATTTTTA-AATT
* *
11046 TTTATATATTTTTTAA
1 TTTATAAAATTTTTAA
11062 TAATTTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
17 10 0.17
18 10 0.17
19 31 0.53
20 7 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATAAAATTTTTAAATT
Found at i:11056 original size:10 final size:10
Alignment explanation
Indices: 10981--11076 Score: 73
Period size: 9 Copynumber: 10.2 Consensus size: 10
10971 CTTTATAAAA
10981 TTTTATA-AT
1 TTTTATATAT
10990 TTTT-TATAT
1 TTTTATATAT
*
10999 TTCTATATAT
1 TTTTATATAT
*
11009 TTTT-TAAAT
1 TTTTATATAT
11018 TTTTA-A-AT
1 TTTTATATAT
* *
11026 TTTTATAAAA
1 TTTTATATAT
*
11036 TTTTACA-AT
1 TTTTATATAT
11045 TTTTATATAT
1 TTTTATATAT
11055 TTTT-TAATAAT
1 TTTTAT-AT-AT
11066 TTTTA-ATAT
1 TTTTATATAT
11075 TT
1 TT
11077 GAATTTTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
8 9 0.13
9 31 0.44
10 25 0.35
11 6 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Found at i:11058 original size:11 final size:10
Alignment explanation
Indices: 10988--11076 Score: 57
Period size: 10 Copynumber: 9.4 Consensus size: 10
10978 AAATTTTATA
10988 ATTTTTT-AT
1 ATTTTTTAAT
*
10997 A-TTTCTATAT
1 ATTTTTTA-AT
11007 ATTTTTTAA-
1 ATTTTTTAAT
11016 A-TTTTTAA-
1 ATTTTTTAAT
*
11024 ATTTTTATAAA
1 ATTTTT-TAAT
**
11035 ATTTTACAAT
1 ATTTTTTAAT
*
11045 -TTTTAT-AT
1 ATTTTTTAAT
11053 ATTTTTTAAT
1 ATTTTTTAAT
*
11063 AATTTTTAAT
1 ATTTTTTAAT
11073 ATTT
1 ATTT
11077 GAATTTTTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
8 14 0.22
9 16 0.25
10 23 0.37
11 10 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTTAAT
Found at i:11101 original size:28 final size:27
Alignment explanation
Indices: 11023--11103 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 27
11013 TAAATTTTTA
* *
11023 AATTTTTA-TAAAATTTTACAAT-TTTT
1 AATTTTTATTAAAA-TTTATAATATTTG
*
11049 ATATATTTT-TTAATAATTTTTAATATTTG
1 A-AT-TTTTATTAA-AATTTATAATATTTG
11078 AATTTTTATTAAAATTTAATAATATT
1 AATTTTTATTAAAATTT-ATAATATT
11104 ATAGATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
26 1 0.02
27 11 0.25
28 26 0.59
29 6 0.14
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (27 bp):
AATTTTTATTAAAATTTATAATATTTG
Found at i:12813 original size:28 final size:29
Alignment explanation
Indices: 12780--12841 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
12770 TACAAAATTC
12780 TAAAAATTAAAAAT-TAAATGAAAGT-AGA
1 TAAAAATTAAAAATATAAAT-AAAGTGAGA
**
12808 TAAAAATTTCAAATATAAATAAAGTGAGA
1 TAAAAATTAAAAATATAAATAAAGTGAGA
*
12837 GAAAA
1 TAAAA
12842 TGAGGAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (29 bp):
TAAAAATTAAAAATATAAATAAAGTGAGA
Found at i:14759 original size:62 final size:61
Alignment explanation
Indices: 14684--14808 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 61
14674 AAATGTTTAG
*
14684 TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTGAACTATCAATATG-TGTTATTATTA
1 TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTAAACTATCAATA-GATGTT-TTATTA
* * *
14746 TGGTACATGTACTTTGAAAATGTTTAATGTGGTACCTAAACTATCAATAGATGTTTTATTA
1 TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTAAACTATCAATAGATGTTTTATTA
14807 TG
1 TG
14809 ATACTTGGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 9 0.16
62 49 0.84
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.40
Consensus pattern (61 bp):
TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTAAACTATCAATAGATGTTTTATTA
Found at i:23121 original size:15 final size:16
Alignment explanation
Indices: 23090--23122 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23080 GACAAAACCT
23090 AAAATAAAATCAAATC
1 AAAATAAAATCAAATC
*
23106 AAAATTAAAT-AAATC
1 AAAATAAAATCAAATC
23121 AA
1 AA
23123 TTAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAAATCAAATC
Found at i:23126 original size:13 final size:14
Alignment explanation
Indices: 23094--23145 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 14
23084 AAACCTAAAA
23094 TAAAATCAAATCAAAAT
1 TAAAAT-AAATC--AAT
23111 T-AAATAAATCAAT
1 TAAAATAAATCAAT
*
23124 TAAAATAAAT-AAC
1 TAAAATAAATCAAT
23137 TAAAATAAA
1 TAAAATAAA
23146 AAATAAATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 15 0.45
14 8 0.24
15 5 0.15
16 4 0.12
17 1 0.03
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAAATAAATCAAT
Found at i:26065 original size:15 final size:16
Alignment explanation
Indices: 26045--26081 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
26035 ACCCATAGAA
*
26045 TATTTTTTT-ATTTTT
1 TATTTTTTTCATATTT
26060 TATTTTTTTCATATTT
1 TATTTTTTTCATATTT
26076 TATTTT
1 TATTTT
26082 ATTTTTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
TATTTTTTTCATATTT
Found at i:26068 original size:16 final size:16
Alignment explanation
Indices: 26047--26086 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
26037 CCATAGAATA
*
26047 TTTTTTTATTTTTTAT
1 TTTTTTTATATTTTAT
*
26063 TTTTTTCATATTTTAT
1 TTTTTTTATATTTTAT
26079 TTTATTTT
1 TTT-TTTT
26087 TTCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTATATTTTAT
Found at i:27987 original size:86 final size:88
Alignment explanation
Indices: 27892--28081 Score: 201
Period size: 90 Copynumber: 2.2 Consensus size: 88
27882 AAACTTTTTA
* * * *
27892 AATGTATCAAAAATATCTT-TACACTTCTT-AAAAAAAGCAATTAAATTCC-TA-TTTTTTT-CT
1 AATGCATCAAAAAGATCTTATACACTTCTTCAAAAAAA-CAATT-AA-GCCTTATTTTTTTTCCC
*
27952 GCTCAATTGGGTACTTGAACTTTCAT
63 ACTCAATTGGGTACTTGAACTTTCAT
**** * *
27978 AATGCATCAAAAAGATCTTAATTTTTTTTTTCAAAGAAACAATTAAGCCTTTATTTTTTTTCCCA
1 AATGCATCAAAAAGATCTT-ATACACTTCTTCAAAAAAACAATTAAGCC-TTATTTTTTTTCCCA
28043 CTCAATTGGGTACTTGAACTTTCAT
64 CTCAATTGGGTACTTGAACTTTCAT
28068 AATGCATCAAAAAG
1 AATGCATCAAAAAG
28082 GCCTTAAATT
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
86 19 0.22
87 2 0.02
88 12 0.14
89 13 0.15
90 40 0.47
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (88 bp):
AATGCATCAAAAAGATCTTATACACTTCTTCAAAAAAACAATTAAGCCTTATTTTTTTTCCCACT
CAATTGGGTACTTGAACTTTCAT
Found at i:28555 original size:29 final size:29
Alignment explanation
Indices: 28522--28618 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
28512 TTACATTTTG
*
28522 TATAATTTTCTTATGACTT-TATAAAATTT
1 TATAATTTTCTTAT-AATTCTATAAAATTT
* * *
28551 TATAATTTTTTTATAATTCTATATATTTT
1 TATAATTTTCTTATAATTCTATAAAATTT
* * *
28580 TATAATTTTTTTAAAATTTTTATAAAATTT
1 TATAATTTTCTTATAA-TTCTATAAAATTT
* *
28610 CACAATTTT
1 TATAATTTT
28619 TATAAATTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
28 3 0.05
29 36 0.64
30 17 0.30
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (29 bp):
TATAATTTTCTTATAATTCTATAAAATTT
Found at i:28564 original size:11 final size:11
Alignment explanation
Indices: 28548--28600 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
28538 CTTTATAAAA
28548 TTTTATAATTT
1 TTTTATAATTT
28559 TTTTATAA---
1 TTTTATAATTT
* *
28567 TTCTAT-ATAT
1 TTTTATAATTT
28577 TTTTATAATTT
1 TTTTATAATTT
*
28588 TTTTAAAATTT
1 TTTTATAATTT
28599 TT
1 TT
28601 ATAAAATTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 1 0.03
8 5 0.15
10 5 0.15
11 23 0.68
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:28605 original size:11 final size:11
Alignment explanation
Indices: 28539--28642 Score: 50
Period size: 11 Copynumber: 10.4 Consensus size: 11
28529 TTCTTATGAC
28539 TTTATAAAA-T
1 TTTATAAAATT
28549 TTTAT--AATT
1 TTTATAAAATT
* *
28558 TTTTTATAA-T
1 TTTATAAAATT
* *
28568 TCTAT-ATATT
1 TTTATAAAATT
28578 TTTAT--AATT
1 TTTATAAAATT
*
28587 TTTTTAAAATT
1 TTTATAAAATT
28598 TTTATAAAA--
1 TTTATAAAATT
* *
28607 TTT-CACAATT
1 TTTATAAAATT
*
28617 TTTATAAATTT
1 TTTATAAAATT
28628 TTTA-ATAAATT
1 TTTATA-AAATT
28639 TTTA
1 TTTA
28643 ATATTTGAAT
Statistics
Matches: 69, Mismatches: 15, Indels: 19
0.67 0.15 0.18
Matches are distributed among these distances:
8 5 0.07
9 16 0.23
10 18 0.26
11 30 0.43
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTATAAAATT
Found at i:28628 original size:10 final size:10
Alignment explanation
Indices: 28539--28642 Score: 72
Period size: 10 Copynumber: 10.4 Consensus size: 10
28529 TTCTTATGAC
*
28539 TTTATAAAAT
1 TTTATAAATT
28549 TTTAT-AATT
1 TTTATAAATT
*
28558 TTTTTATAA-T
1 TTTATA-AATT
* *
28568 TCTATATATT
1 TTTATAAATT
28578 TTTAT-AATT
1 TTTATAAATT
*
28587 TTTTTAAAATT
1 TTTAT-AAATT
*
28598 TTTATAAAAT
1 TTTATAAATT
* *
28608 TTCA-CAATT
1 TTTATAAATT
28617 TTTATAAATTT
1 TTTATAAA-TT
28628 TTTAATAAATT
1 TTT-ATAAATT
28639 TTTA
1 TTTA
28643 ATATTTGAAT
Statistics
Matches: 71, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
9 21 0.30
10 25 0.35
11 20 0.28
12 5 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTATAAATT
Found at i:28639 original size:30 final size:30
Alignment explanation
Indices: 28539--28636 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
28529 TTCTTATGAC
* * * *
28539 TTTATAAAATTTTATAATTTTTTTATAA-T
1 TTTATAAAATTTCACAATTTTTATAAAATT
* * * * * *
28568 TCTATATATTTTTATAATTTTTTTAAAATT
1 TTTATAAAATTTCACAATTTTTATAAAATT
*
28598 TTTATAAAATTTCACAATTTTTATAAATTT
1 TTTATAAAATTTCACAATTTTTATAAAATT
28628 TTTAATAAA
1 TTT-ATAAA
28637 TTTTTAATAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 24 0.43
30 27 0.48
31 5 0.09
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTATAAAATTTCACAATTTTTATAAAATT
Found at i:33461 original size:18 final size:18
Alignment explanation
Indices: 33438--33491 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
33428 TTTCTAAAAA
*
33438 AAAATTCTAATTTTTAAT
1 AAAATTTTAATTTTTAAT
*
33456 AAAATTTGTTAATTTTTATT
1 AAAA-TT-TTAATTTTTAAT
33476 AAAATTTTAATGTTTT
1 AAAATTTTAAT-TTTT
33492 CCTAAAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 9 0.29
19 8 0.26
20 14 0.45
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
AAAATTTTAATTTTTAAT
Found at i:33468 original size:20 final size:20
Alignment explanation
Indices: 33445--33482 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
33435 AAAAAAATTC
33445 TAATTTTTAATAAAATTTGT
1 TAATTTTTAATAAAATTTGT
*
33465 TAATTTTTATTAAAATTT
1 TAATTTTTAATAAAATTT
33483 TAATGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TAATTTTTAATAAAATTTGT
Done.