Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1161
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: 81604
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:23754 original size:30 final size:30
Alignment explanation
Indices: 23711--23783 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
23701 TTACGGAAGA
23711 AGGAGCG-AAAGCCACTCGACTGGTTGGAG
1 AGGAGCGAAAAGCCACTCGACTGGTTGGAG
23740 AGGAGCGAAAAGCCACTCGACTGGTTGGAG
1 AGGAGCGAAAAGCCACTCGACTGGTTGGAG
23770 AGGAGCGAAAAGCC
1 AGGAGCGAAAAGCC
23784 GCTTTTTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 7 0.16
30 36 0.84
ACGTcount: A:0.32, C:0.21, G:0.37, T:0.11
Consensus pattern (30 bp):
AGGAGCGAAAAGCCACTCGACTGGTTGGAG
Found at i:67567 original size:79 final size:79
Alignment explanation
Indices: 67424--67774 Score: 366
Period size: 79 Copynumber: 4.4 Consensus size: 79
67414 TATTTTGGAG
* * * * ** * * *
67424 ATAAAATCGGGGCTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCTCCGATTATCAAAAA
1 ATAAAATCAGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAA
*
67489 TCAATGTTTTGGAA
66 TCAATGTTTTGAAA
* * * * * *
67503 ATAAAA-CTAGGGTTGGAGTATCCCCTCGAAAATAATGGGGTCAAAGTGTCCCCCATTGTGAAAA
1 ATAAAATC-AGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAA
67567 ATCAATGTTTTGAAA
65 ATCAATGTTTTGAAA
* * * * * *
67582 ATAAAA-CCGGGATTAAAATATCCCCTC-AGAAATAACGGGGTTGGAGTATCTCCGATTGTGGAA
1 ATAAAATCAGGG-TTAGAGTATCCCCTCGA-AAATAACGGGGTTAGAGTATCCCCGATTGTGAAA
* *
67645 AATCGATGTTTTGGAA
64 AATCAATGTTTTGAAA
* * *
67661 ATAAAATCAGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTAGAGTATTCTCGATTGTGAAAAA
1 ATAAAATCAGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAA
**
67726 TCGGTGTTTTGAAA
66 TCAATGTTTTGAAA
* * *
67740 ATAAAATCGGGGTTAGAGTATCCTCTCGGAAATAA
1 ATAAAATCAGGGTTAGAGTATCCCCTCGAAAATAA
67775 AAACATGAAT
Statistics
Matches: 225, Mismatches: 42, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
78 5 0.02
79 215 0.96
80 5 0.02
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (79 bp):
ATAAAATCAGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAA
TCAATGTTTTGAAA
Found at i:67719 original size:158 final size:158
Alignment explanation
Indices: 67442--67774 Score: 425
Period size: 158 Copynumber: 2.1 Consensus size: 158
67432 GGGGCTGGAG
*
67442 TATCCCCTCAAAAATAACAAGGTTAGAGTATCTCCGATTATCAAAAATCAATGTTTTGGAAATAA
1 TATCCCCTCAGAAATAACAAGGTTAGAGTATCTCCGATTATCAAAAATCAATGTTTTGGAAATAA
* ** *
67507 AACTAGGGTTGGAGTATCCCCTCGAAAATAATGGGGTCAAAGTGTCCCCCATTGTGAAAAATCAA
66 AACTAGGGTTAGAGTATCCCCTCGAAAATAACAGGGTCAAAGTATCCCCCATTGTGAAAAATCAA
67572 TGTTTTGAAAATAAAACCGGGATTAAAA
131 TGTTTTGAAAATAAAACCGGGATTAAAA
** * * ** *
67600 TATCCCCTCAGAAATAACGGGGTTGGAGTATCTCCGATTGTGGAAAATCGATGTTTTGGAAATAA
1 TATCCCCTCAGAAATAACAAGGTTAGAGTATCTCCGATTATCAAAAATCAATGTTTTGGAAATAA
* * * * * *
67665 AA-TCAGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTAGAGTATTCTCGATTGTGAAAAATCG
66 AACT-AGGGTTAGAGTATCCCCTCGAAAATAACAGGGTCAAAGTATCCCCCATTGTGAAAAATCA
* * * * *
67729 GTGTTTTGAAAATAAAATCGGGGTTAGAG
130 ATGTTTTGAAAATAAAACCGGGATTAAAA
* *
67758 TATCCTCTCGGAAATAA
1 TATCCCCTCAGAAATAA
67775 AAACATGAAT
Statistics
Matches: 149, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
157 1 0.01
158 148 0.99
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (158 bp):
TATCCCCTCAGAAATAACAAGGTTAGAGTATCTCCGATTATCAAAAATCAATGTTTTGGAAATAA
AACTAGGGTTAGAGTATCCCCTCGAAAATAACAGGGTCAAAGTATCCCCCATTGTGAAAAATCAA
TGTTTTGAAAATAAAACCGGGATTAAAA
Found at i:73586 original size:21 final size:21
Alignment explanation
Indices: 73553--73602 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
73543 TTGCAAGTTG
*
73553 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
73575 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
73596 AAATAAA
1 AAATAAA
73603 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:75420 original size:15 final size:15
Alignment explanation
Indices: 75400--75430 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
75390 TAAAAATGTC
*
75400 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
75415 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
75430 C
1 C
75431 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:77528 original size:13 final size:13
Alignment explanation
Indices: 77510--77560 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
77500 CATTTTTCTT
*
77510 TGTATCGATACAA
1 TGTATCGATACAC
77523 TGTATCGATACAC
1 TGTATCGATACAC
*
77536 TATATCGATACAC
1 TGTATCGATACAC
77549 TGTATCGATACA
1 TGTATCGATACA
77561 GGGGGATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:79212 original size:23 final size:21
Alignment explanation
Indices: 79170--79213 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
79160 GTTTAAAGTT
**
79170 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
79191 TTTGCATTGTACTTTGAATTTTA
1 TTTGC-TTG-ACTTTGAATTTTA
79214 ATCTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:80037 original size:20 final size:19
Alignment explanation
Indices: 79983--80038 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
79973 AAAACCCTTA
*
79983 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
80003 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
80023 AATGTATCGATACATG
1 AAAGTATCGATACATG
80039 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:80109 original size:19 final size:19
Alignment explanation
Indices: 80085--80153 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 19
80075 GGCAGTAGCC
80085 AAATATGTATCGATACACA
1 AAATATGTATCGATACACA
80104 AAATATGTATCGAT--AC-
1 AAATATGTATCGATACACA
80120 --A-ATGTATCGATACACA
1 AAATATGTATCGATACACA
*
80136 AAAAATTGTATCGATACA
1 AAATA-TGTATCGATACA
80154 TTGGCTTGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.23
14 1 0.02
15 2 0.05
17 2 0.05
18 1 0.02
19 15 0.35
20 12 0.28
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (19 bp):
AAATATGTATCGATACACA
Found at i:80126 original size:13 final size:13
Alignment explanation
Indices: 80108--80133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
80098 TACACAAAAT
80108 ATGTATCGATACA
1 ATGTATCGATACA
80121 ATGTATCGATACA
1 ATGTATCGATACA
80134 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:80130 original size:32 final size:33
Alignment explanation
Indices: 80089--80153 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
80079 GTAGCCAAAT
*
80089 ATGTATCGATACACAAAATA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
80121 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
80154 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Done.