Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1200
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: 44661
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Found at i:4102 original size:47 final size:47
Alignment explanation
Indices: 4048--4461 Score: 706
Period size: 47 Copynumber: 8.7 Consensus size: 47
4038 TTAGGATTCT
* * *
4048 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
4095 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
4142 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
4189 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
4236 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
4285 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
4334 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
4381 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT-ATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
4427 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
4462 TCCCGAAGGG
Statistics
Matches: 357, Mismatches: 7, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
46 39 0.11
47 222 0.62
49 96 0.27
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:4394 original size:192 final size:189
Alignment explanation
Indices: 4069--4461 Score: 709
Period size: 192 Copynumber: 2.1 Consensus size: 189
4059 GTGAACATGC
*
4069 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
4134 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
66 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
* *
4199 TGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
131 TGTGAAAGTGTATATATGTGATAAGGCCT-ATGGCCAACGTGATGAATGTGAAAGTGTAT
4259 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGC
4324 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
64 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
4389 AATGTGAAAGTGTATATATGTGATAAGGCCTATGGCCAACGTGATGGATGTGAAAGTGTAT
129 AATGTGAAAGTGTATATATGTGATAAGGCCTATGGCCAACGTGATGAATGTGAAAGTGTAT
4450 A-A-ATGTGATAAG
1 ATATATGTGATAAG
4462 TCCCGAAGGG
Statistics
Matches: 197, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
189 10 0.05
190 46 0.23
191 28 0.14
192 113 0.57
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (189 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
TGTGAAAGTGTATATATGTGATAAGGCCTATGGCCAACGTGATGAATGTGAAAGTGTAT
Found at i:4635 original size:36 final size:37
Alignment explanation
Indices: 4580--4657 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
4570 CCGAGCTCTA
* *
4580 AAGACCCGATGACTACGTGTGG-GATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
4616 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
4653 AAGAC
1 AAGAC
4658 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:6096 original size:78 final size:80
Alignment explanation
Indices: 5870--6137 Score: 436
Period size: 78 Copynumber: 3.4 Consensus size: 80
5860 GAGAATTGAG
5870 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
5935 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
5950 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
6014 -AGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
* * **
6028 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATATAT-C-GTCTAAACCCCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
6091 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
* * * *
6106 GGTGTTATATCCGGGCTAGGTCTCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
6138 ATCATGCTGG
Statistics
Matches: 177, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
77 9 0.05
78 77 0.44
79 70 0.40
80 21 0.12
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
AAGAGCATTCGTGCT
Found at i:6149 original size:40 final size:40
Alignment explanation
Indices: 5870--6137 Score: 436
Period size: 40 Copynumber: 6.8 Consensus size: 40
5860 GAGAATTGAG
5870 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
5910 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
5950 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
5989 AGTGATATATCCGGGCTAAGTCCCG-AGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
6028 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* **
6068 AGTGATATAT-C-GTCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
6106 GGTGTTATATCCGGGCTAGGTCTCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
6138 ATCATGCTGG
Statistics
Matches: 212, Mismatches: 12, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
38 31 0.15
39 80 0.38
40 101 0.48
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:10170 original size:49 final size:49
Alignment explanation
Indices: 10052--10449 Score: 668
Period size: 49 Copynumber: 8.3 Consensus size: 49
10042 GTGAACATGC
*
10052 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
10099 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
10148 ATATATGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
10197 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
10246 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTTTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
10295 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
10342 ATATCTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * *
10389 ATATATGTGATAAGGCCTAATAGCCAACGTGATGGATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
10438 A-A-ATGTGATAAG
1 ATATATGTGATAAG
10450 TCCCGAAGGG
Statistics
Matches: 336, Mismatches: 11, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
47 143 0.43
48 1 0.00
49 192 0.57
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.30
Consensus pattern (49 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:10624 original size:37 final size:37
Alignment explanation
Indices: 10568--10646 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
10558 CCGAGCTCTA
* * * *
10568 AAGACCCGATGACTACGTGTGGGGATTTTTTTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTTCGGGT
* *
10605 AAGATCCGATAACTTCGTGTGGAGATTATGTTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTTCGGGT
10642 AAGAC
1 AAGAC
10647 TTCGTAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTTCGGGT
Found at i:16428 original size:28 final size:28
Alignment explanation
Indices: 16388--16506 Score: 132
Period size: 28 Copynumber: 4.2 Consensus size: 28
16378 ATTGCATGAC
* *
16388 TATGAGTGTGATTGGGCCTGACGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* **
16416 TATGAAGGTGATTGGGCCAAATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
16444 TATGAATGTGATTGGG-CTCGATGGGCCA
1 TATGAATGTGATTGGGCCT-GATGGGCCA
* * *
16472 TATAAATGAGATTGGGCCTAAATGGGCCA
1 TATGAATGTGATTGGGCCT-GATGGGCCA
*
16501 AATGAA
1 TATGAA
16507 GAAGTATGGA
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
27 1 0.01
28 60 0.80
29 14 0.19
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATGGGCCA
Found at i:16454 original size:56 final size:57
Alignment explanation
Indices: 16388--16506 Score: 161
Period size: 56 Copynumber: 2.1 Consensus size: 57
16378 ATTGCATGAC
* * *
16388 TATGAGTGTGATTGGGC-CTGACGGGCCATATGAAGGTGATTGGGCC-AAATGGGCCA
1 TATGAATGTGATTGGGCTC-GACGGGCCATATAAAGGAGATTGGGCCTAAATGGGCCA
* *
16444 TATGAATGTGATTGGGCTCGATGGGCCATATAAATGAGATTGGGCCTAAATGGGCCA
1 TATGAATGTGATTGGGCTCGACGGGCCATATAAAGGAGATTGGGCCTAAATGGGCCA
*
16501 AATGAA
1 TATGAA
16507 GAAGTATGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 39 0.71
57 16 0.29
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (57 bp):
TATGAATGTGATTGGGCTCGACGGGCCATATAAAGGAGATTGGGCCTAAATGGGCCA
Found at i:16551 original size:27 final size:27
Alignment explanation
Indices: 16513--16564 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
16503 TGAAGAAGTA
* *
16513 TGGATTTGTTAGTGTTTAGTAAGGGTT
1 TGGATTTGTTAGTGCTTAATAAGGGTT
16540 TGGATTTGTTAGTGCTTAATAAGGG
1 TGGATTTGTTAGTGCTTAATAAGGG
16565 GTTGTGGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (27 bp):
TGGATTTGTTAGTGCTTAATAAGGGTT
Found at i:20902 original size:46 final size:46
Alignment explanation
Indices: 20834--21009 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
20824 TGTAACCCGC
* * *
20834 CCATAAGCGAAATCGGTCTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
20880 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCG---GAC--GTTCGCAT
* * * *
20930 -C-TCA-CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
20973 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
21010 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 2 0.02
46 60 0.57
47 25 0.24
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:21028 original size:46 final size:44
Alignment explanation
Indices: 20885--21028 Score: 114
Period size: 46 Copynumber: 3.1 Consensus size: 44
20875 CGCATCCATA
* *
20885 AGTGAACTCGGACTCAACTCAACGAGCTCGAATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * * *
20932 CA-CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
20978 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
21024 AGTGA
1 AGTGA
21029 CATGTCACTT
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.42
47 28 0.37
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:24703 original size:27 final size:27
Alignment explanation
Indices: 24667--24914 Score: 343
Period size: 27 Copynumber: 9.2 Consensus size: 27
24657 AGAGGTCGTT
* *
24667 AAATGACCGTAATGCCTCTGTAGAGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
24694 AAATAACCGTAATGCTCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
24721 AAATGACCGTGATGCCCTTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * * *
24748 AAATGACTGTAATACCCCTATAGAGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
24775 AAACGACCGTAATGCCCCTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
24802 AAATGACCGTAATGCCACTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
24829 AAATGATCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
24856 AAATGACCATAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
24883 AAATGACCGTAATACCCCTGTATGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
24910 AAATG
1 AAATG
24915 TCGATTATGC
Statistics
Matches: 193, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 193 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (27 bp):
AAATGACCGTAATGCCCCTGTAGGGTA
Found at i:25143 original size:27 final size:27
Alignment explanation
Indices: 25057--25143 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
25047 GGAAGTTTTG
* * *
25057 TACTGGTGACTATGTCACATTCACTGT
1 TACTGGTGGCTATGCCACATTTACTGT
* * **
25084 TACTGGTGGCTATGCCACAATTATTAA
1 TACTGGTGGCTATGCCACATTTACTGT
*
25111 TACTGGTGGCTTTGCCACATTTACTGT
1 TACTGGTGGCTATGCCACATTTACTGT
*
25138 TTCTGG
1 TACTGG
25144 CAGCTATGTT
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (27 bp):
TACTGGTGGCTATGCCACATTTACTGT
Found at i:25379 original size:33 final size:33
Alignment explanation
Indices: 25327--25433 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
25317 ATAAGGCTAG
*
25327 GGCCCAGATTGTACAGATACTGAATAGGGCTTA
1 GGCCCAGATTGTACTGATACTGAATAGGGCTTA
*
25360 GGCCTAGATTGTACTGATACTGAATAGGGCTTA
1 GGCCCAGATTGTACTGATACTGAATAGGGCTTA
*
25393 GGCCCAGATTGTACTAATACTGAATAGGGCTTA
1 GGCCCAGATTGTACTGATACTGAATAGGGCTTA
25426 GGCCCAGA
1 GGCCCAGA
25434 CTATGTTATT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 70 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (33 bp):
GGCCCAGATTGTACTGATACTGAATAGGGCTTA
Found at i:33485 original size:30 final size:30
Alignment explanation
Indices: 33449--33508 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
33439 TTCTCGAGCC
*
33449 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
33479 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
33509 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:37123 original size:39 final size:39
Alignment explanation
Indices: 37059--37177 Score: 159
Period size: 39 Copynumber: 3.1 Consensus size: 39
37049 TGTGAATATA
* *
37059 TATACGCGAGAACTATATCCGGACTTCAGGTCCGCAGGC
1 TATAAGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
*
37098 TATAAGCGAGAATTATATTCC-GACTTCATGTCCGCAGGC
1 TATAAGCGAGAATTATA-TCCGGACTTCAGGTCCGCAGGC
* * * *
37137 TATATGCTAGAATTATATCCTGACTTTAGGTCCGCAGGC
1 TATAAGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
37176 TA
1 TA
37178 CGTGCTGGAC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
38 3 0.04
39 65 0.92
40 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (39 bp):
TATAAGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
Found at i:37193 original size:39 final size:38
Alignment explanation
Indices: 37086--37202 Score: 101
Period size: 39 Copynumber: 3.0 Consensus size: 38
37076 TCCGGACTTC
* * * * * *
37086 AGGTCCGCAGGCTATAAGCGAGAATTATATTCCGACTTC
1 AGGTCCGCAGGCTACATGCTAGAATTATA-TCTGAATTT
* * *
37125 ATGTCCGCAGGCTATATGCTAGAATTATATCCTGACTTT
1 AGGTCCGCAGGCTACATGCTAGAATTATAT-CTGAATTT
* *
37164 AGGTCCGCAGGCTACGTGCTGGACA-TATATCTGAATTT
1 AGGTCCGCAGGCTACATGCTAGA-ATTATATCTGAATTT
37202 A
1 A
37203 AAGTCTTGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
38 9 0.14
39 56 0.85
40 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (38 bp):
AGGTCCGCAGGCTACATGCTAGAATTATATCTGAATTT
Done.