Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold318
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: 30738
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:1141 original size:27 final size:27
Alignment explanation
Indices: 1104--1306 Score: 239
Period size: 27 Copynumber: 7.6 Consensus size: 27
1094 TAAATTGTAC
1104 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
1131 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
1158 TGCACTAAGTGTGCGAAATGA-AATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1183 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
1211 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
1238 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1265 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
1292 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
1307 GACTCAATAT
Statistics
Matches: 153, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
26 22 0.14
27 131 0.86
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:1243 original size:80 final size:80
Alignment explanation
Indices: 1105--1253 Score: 235
Period size: 80 Copynumber: 1.9 Consensus size: 80
1095 AAATTGTACA
* * * * *
1105 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTTGCACTAAGTGT
1 GCACTAAGTGTGCGAATTGACCATGCAGCACTAAGTGTGCGAGTTGACCATGTAGCACTAAGTGT
1170 GCGAAATGAAATGAT
66 GCGAAATGAAATGAT
* *
1185 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGT
1 GCACTAAGTGTGCGAATTGACCATGCAGCACTAAGTGTGCGAGTTGACCATGTAGCACTAAGTGT
1250 GCGA
66 GCGA
1254 TTTGATTACG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (80 bp):
GCACTAAGTGTGCGAATTGACCATGCAGCACTAAGTGTGCGAGTTGACCATGTAGCACTAAGTGT
GCGAAATGAAATGAT
Found at i:9295 original size:27 final size:27
Alignment explanation
Indices: 9258--9461 Score: 232
Period size: 27 Copynumber: 7.6 Consensus size: 27
9248 TAAATTGTAC
*
9258 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
9285 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * **
9312 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
*
9338 ATGCACTAAGTGTGCGAATTGACCATGT
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
9366 GGCACTAAGTGTGCGAGATTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
9394 AGCACTAAGTGTGCG-ATTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
9420 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
9447 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
9462 GACTCAATAT
Statistics
Matches: 154, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
26 25 0.16
27 106 0.69
28 23 0.15
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:17131 original size:27 final size:27
Alignment explanation
Indices: 17114--17264 Score: 142
Period size: 27 Copynumber: 5.6 Consensus size: 27
17104 ATATTAAGTC
17114 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
17141 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
17169 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
17196 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
17223 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
17250 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
17265 GTACAATTTA
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.01
27 81 0.74
28 27 0.25
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:17198 original size:55 final size:55
Alignment explanation
Indices: 17114--17264 Score: 207
Period size: 55 Copynumber: 2.8 Consensus size: 55
17104 ATATTAAGTC
* * *
17114 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTA-CATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTATCATAATC-AACT
* **
17169 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTATCATAATCAACT
* *
17223 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
17265 GTACAATTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
54 42 0.49
55 44 0.51
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTATCATAATCAACT
Found at i:25045 original size:27 final size:27
Alignment explanation
Indices: 25015--25165 Score: 194
Period size: 27 Copynumber: 5.6 Consensus size: 27
25005 ATATTGAGTC
* * *
25015 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
25042 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
25069 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
* * **
25096 CGCACACTTAGTGCATTCATATTCATTT
1 CGCACACTTAGTGC-TACATAATCAAAT
* *
25124 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
25151 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25166 GTACAATTTA
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 85 0.79
28 23 0.21
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:25143 original size:55 final size:54
Alignment explanation
Indices: 25015--25165 Score: 212
Period size: 55 Copynumber: 2.8 Consensus size: 54
25005 ATATTGAGTC
* * *
25015 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAAT
* * **
25069 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCATTCATATTCATTT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC-TACATAATCAAAT
* *
25124 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
25166 GTACAATTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 39 0.45
55 48 0.55
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAAT
Found at i:29354 original size:27 final size:27
Alignment explanation
Indices: 29316--29367 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
29306 GATAATAGAA
*
29316 AAAAGGAAATAGAAGAGGAGGAAAAAG
1 AAAAGGAAATAGAAGAAGAGGAAAAAG
*
29343 AAAA-GAAGATAGGAGAAGAGGAAAA
1 AAAAGGAA-ATAGAAGAAGAGGAAAA
29368 GATCGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (27 bp):
AAAAGGAAATAGAAGAAGAGGAAAAAG
Found at i:29709 original size:14 final size:14
Alignment explanation
Indices: 29686--29715 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29676 GGGAGATAGG
29686 AAGGAAAAGGGGAA
1 AAGGAAAAGGGGAA
*
29700 AAGGATAAGGGGAA
1 AAGGAAAAGGGGAA
29714 AA
1 AA
29716 TTGGAATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (14 bp):
AAGGAAAAGGGGAA
Done.