Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3016
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: 58099
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4968 original size:11 final size:11
Alignment explanation
Indices: 4947--4981 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
4937 GGAGAGAATT
4947 TTTGTTCATCC
1 TTTGTTCATCC
4958 TTT-TCTCATCC
1 TTTGT-TCATCC
4969 TTTGTTCATCC
1 TTTGTTCATCC
4980 TT
1 TT
4982 GGCCAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.05
11 20 0.91
12 1 0.05
ACGTcount: A:0.09, C:0.29, G:0.06, T:0.57
Consensus pattern (11 bp):
TTTGTTCATCC
Found at i:6021 original size:39 final size:39
Alignment explanation
Indices: 5978--6145 Score: 152
Period size: 39 Copynumber: 4.3 Consensus size: 39
5968 CGACTAAGAT
5978 CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAA-TTCCGGGTTAAGTC
* *
6017 CCGAAGGCCTTTGTGCGAGATACTAAATCC-GGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AATTCCGGGTTAAGTC
*
6056 CCGAAGGCATTCGTGCGAGTTATTA-AATT-CGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAG--A-TACAATTCCGGGTTAAGTC
* * ** * *
6096 CCGAA-GCA-TTGTGTGAGTTACTAAAACCGGGCTATGT-
1 CCGAAGGCATTTGTGCGAGATAC-AATTCCGGGTTAAGTC
6133 CCGAAGGCATTTG
1 CCGAAGGCATTTG
6146 AACGAGAGCT
Statistics
Matches: 106, Mismatches: 12, Indels: 22
0.76 0.09 0.16
Matches are distributed among these distances:
35 2 0.02
37 7 0.07
38 25 0.24
39 50 0.47
40 19 0.18
41 1 0.01
42 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAATTCCGGGTTAAGTC
Found at i:6060 original size:78 final size:77
Alignment explanation
Indices: 5971--6145 Score: 194
Period size: 78 Copynumber: 2.2 Consensus size: 77
5961 ATATATCCGA
* *
5971 CTAAGATCCGAAGGCATTTGTGCGAGATA-CAAGTTCCGGGTTAAG-CCCGAAGGCCTTTGTGCG
1 CTAAG-TCCGAAGGCATTTGTGCGAGATATCAAATT-CGGGTTAAGTCCCGAA-G-CATTGTGCG
*
6034 AGATACTAAATCC-GG
62 AGATACTAAAACCGGG
* * * * * *
6049 TTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATTCGGGTTAAGTCCCGAAGCATTGTGTGAGT
1 CTAAGT-CCGAAGGCATTTGTGCGAGATATCAAATTCGGGTTAAGTCCCGAAGCATTGTGCGAGA
6114 TACTAAAACCGGG
65 TACTAAAACCGGG
*
6127 CTATGTCCGAAGGCATTTG
1 CTAAGTCCGAAGGCATTTG
6146 AACGAGAGCT
Statistics
Matches: 81, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
77 31 0.38
78 40 0.49
79 10 0.12
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (77 bp):
CTAAGTCCGAAGGCATTTGTGCGAGATATCAAATTCGGGTTAAGTCCCGAAGCATTGTGCGAGAT
ACTAAAACCGGG
Found at i:6143 original size:38 final size:40
Alignment explanation
Indices: 5927--6143 Score: 137
Period size: 39 Copynumber: 5.6 Consensus size: 40
5917 TGAATGCTGT
* * * * * *
5927 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAAA
* * * **
5967 CC-GACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGTT
1 CCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA-AA
* * * * *
6006 CCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAA
* * *
6045 CC-GGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAA
* * *
6084 TCGGGTTAAGTCCCGAA-GCATT-GTGTGAGTTACTAAAA
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAA
*
6122 CCGGGCTATGT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
6144 TGAACGAGAG
Statistics
Matches: 146, Mismatches: 22, Indels: 20
0.78 0.12 0.11
Matches are distributed among these distances:
37 5 0.03
38 34 0.23
39 76 0.52
40 31 0.21
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAA
Found at i:15393 original size:39 final size:40
Alignment explanation
Indices: 15348--15572 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
15338 GCTCCTCGTT
* * * *
15348 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
15388 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
15427 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
15467 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
15507 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
15548 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
15573 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:15581 original size:41 final size:41
Alignment explanation
Indices: 15504--15581 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
15494 CTTGTATCTC
* * *
15504 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
15545 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
15582 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:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:22906 original size:39 final size:40
Alignment explanation
Indices: 22861--23083 Score: 240
Period size: 40 Copynumber: 5.7 Consensus size: 40
22851 GCTCCTCGTT
* * * *
22861 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
22901 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
22940 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
22980 CAAAGGCCTTCGGG-CTTAACCCGGAATT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
23018 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
23059 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
23084 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
37 2 0.01
38 20 0.13
39 57 0.36
40 67 0.43
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:22964 original size:79 final size:78
Alignment explanation
Indices: 22861--23083 Score: 252
Period size: 79 Copynumber: 2.8 Consensus size: 78
22851 GCTCCTCGTT
* * *
22861 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
*
22926 TTTAATAACTCGCA
66 ATT-ATAACTCGCA
* * * *
22940 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAA-GCCTTCGGGACTTAACCCGG
* *
23004 AATTGTATCTCGCA
65 AATTATAACTCGCA
* * * * * *
23018 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CACAAAGCCTTCGGGACTTAACCCG
23082 GA
64 GA
23084 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
77 3 0.03
78 42 0.35
79 66 0.55
80 9 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
ATTATAACTCGCA
Found at i:23092 original size:41 final size:41
Alignment explanation
Indices: 23015--23092 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
23005 ATTGTATCTC
* * *
23015 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
23056 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
23093 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:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:25445 original size:46 final size:45
Alignment explanation
Indices: 25392--25525 Score: 173
Period size: 43 Copynumber: 3.0 Consensus size: 45
25382 GGAGAGATGT
25392 TAGGATATTAGTATAAGATATTATCTTTTAGCAATTTGATTCCTAA
1 TAGGATATTA-TATAAGATATTATCTTTTAGCAATTTGATTCCTAA
* * *
25438 TAGGATA-T-TATAAGATATTATCTCTTAGCAATTTGTTTTCTAA
1 TAGGATATTATATAAGATATTATCTTTTAGCAATTTGATTCCTAA
* * * *
25481 TAGGATATTATTTTAGGATATTATCTTTTCGTAATTTGATTCCTA
1 TAGGATATTA-TATAAGATATTATCTTTTAGCAATTTGATTCCTA
25526 CGTAACTACT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 39 0.52
44 1 0.01
45 1 0.01
46 34 0.45
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (45 bp):
TAGGATATTATATAAGATATTATCTTTTAGCAATTTGATTCCTAA
Found at i:25887 original size:11 final size:9
Alignment explanation
Indices: 25857--25882 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
25847 TTCCATGGAA
25857 TTTTTTAAT
1 TTTTTTAAT
25866 TTTTTTAAT
1 TTTTTTAAT
25875 TTTTTTAA
1 TTTTTTAA
25883 AATTTAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:45660 original size:26 final size:26
Alignment explanation
Indices: 45631--45709 Score: 158
Period size: 26 Copynumber: 3.0 Consensus size: 26
45621 CACCTTTATC
45631 AAATGTTAAATAAATCAACAATTCAT
1 AAATGTTAAATAAATCAACAATTCAT
45657 AAATGTTAAATAAATCAACAATTCAT
1 AAATGTTAAATAAATCAACAATTCAT
45683 AAATGTTAAATAAATCAACAATTCAT
1 AAATGTTAAATAAATCAACAATTCAT
45709 A
1 A
45710 CTCCAAATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.30
Consensus pattern (26 bp):
AAATGTTAAATAAATCAACAATTCAT
Found at i:52098 original size:47 final size:47
Alignment explanation
Indices: 52044--52494 Score: 632
Period size: 47 Copynumber: 9.4 Consensus size: 47
52034 CAGCCAAGAG
* *
52044 AGTGTATGTATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
52091 AGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTA--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
52140 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
52191 AGTGTATGTATATATGTATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTA--TATATGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
52241 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
52288 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
52335 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
52382 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * *
52429 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
52476 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
52495 TCCCGAAGGC
Statistics
Matches: 371, Mismatches: 24, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
47 232 0.63
48 6 0.02
49 48 0.13
50 38 0.10
51 43 0.12
53 4 0.01
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:52666 original size:37 final size:37
Alignment explanation
Indices: 52611--52688 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
52601 CCGAGCTCTA
* * *
52611 AAGA-CCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
52647 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
52684 AAGAC
1 AAGAC
52689 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 4 0.11
37 33 0.89
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54600 original size:43 final size:43
Alignment explanation
Indices: 54536--54678 Score: 265
Period size: 43 Copynumber: 3.4 Consensus size: 43
54526 TTGGTTTTCA
54536 GCACTAAGTGT-CGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
54578 GCACTAAGTGTGCGGGCAATAAGTGTT--CGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
54619 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
54662 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
54679 TTGAAATGCA
Statistics
Matches: 98, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
41 41 0.42
42 11 0.11
43 46 0.47
ACGTcount: A:0.22, C:0.15, G:0.36, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:54695 original size:29 final size:29
Alignment explanation
Indices: 54660--54733 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
54650 GTTGTGAGAT
* *
54660 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
54689 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
54718 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54734 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:55202 original size:79 final size:79
Alignment explanation
Indices: 55080--55274 Score: 243
Period size: 79 Copynumber: 2.5 Consensus size: 79
55070 CTAAGTGACC
* *
55080 ATATCC-GGCTAAG-TCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCG-AGAGC
1 ATATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAA-ACCCGAAGAGC
55142 ATTCATGCTAGTGAT
65 ATTCATGCTAGTGAT
* * *
55157 GTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAACCCGAAGAGCA
1 ATATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAACCCGAAGAGCA
* * *
55222 TTCGTGCTGGTGTT
66 TTCATGCTAGTGAT
* * * * *
55236 ATGTCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 ATATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGA
55275 CGTGTATTCG
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
77 5 0.05
78 11 0.11
79 84 0.84
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
ATATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAACCCGAAGAGCA
TTCATGCTAGTGAT
Found at i:55270 original size:40 final size:40
Alignment explanation
Indices: 55043--55274 Score: 260
Period size: 39 Copynumber: 5.9 Consensus size: 40
55033 TTGAATGATG
** *
55043 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
*
55083 TCC-GGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
*
55121 TCCGGGCTAAGTCCCG-AGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
55160 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * * * *
55200 TCCGTGCTAA-ACCCGAAGAGCATTCGTGCTGGTGTTATG
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
55239 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
55275 CGTGTATTCG
Statistics
Matches: 167, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 11 0.07
39 93 0.56
40 63 0.38
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:55467 original size:25 final size:25
Alignment explanation
Indices: 55437--55487 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
55427 TGTGTATAAC
55437 GAATGAATAAGA-GCACTATGTGTGT
1 GAATG-ATAAGAGGCACTATGTGTGT
* *
55462 GAATGATTAGAGGCACTGTGTGTGT
1 GAATGATAAGAGGCACTATGTGTGT
55487 G
1 G
55488 CGAATTCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.29
Consensus pattern (25 bp):
GAATGATAAGAGGCACTATGTGTGT
Done.