Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold878
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: 47833
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Found at i:3421 original size:40 final size:39
Alignment explanation
Indices: 3292--3474 Score: 158
Period size: 40 Copynumber: 4.6 Consensus size: 39
3282 GTACTCATTC
* *
3292 AATGCCTTC-GGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA--ATAATAACTCGCACA
** *
3331 AATGCCTTCGGGACTTAACCCGGAATTGGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAA-TAATAACTCGCACA
*
3371 AAGGCCTTCGGGACTTAACCCGGAATAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATAATAACTCGCACA
* ** * * *
3410 AATACCTTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACA
1 AATGCC-TTCGGGA-CTTAACCCGGA-ATAATAAC-TCGCACA
*
3452 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3475 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
39 28 0.24
40 71 0.60
41 11 0.09
42 8 0.07
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATAATAACTCGCACA
Found at i:3434 original size:80 final size:79
Alignment explanation
Indices: 3295--3474 Score: 183
Period size: 80 Copynumber: 2.3 Consensus size: 79
3285 CTCATTCAAT
* * *
3295 GCCTTC-GGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGA-ATT
1 GCCTTCGGGACTTAACCCGGA-TATAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATA-T
* *
3358 GGT-A-TCTCGCACAAA
64 AGTCACT-TAGCACAAA
**
3373 GGCCTTCGGGACTTAACCCGGA-ATAATAACTCGCACAAATACCTTTC-GGATCTTAGTCCGGAT
1 -GCCTTCGGGACTTAACCCGGATATAA-AACTCGCACAAATACC-TTCGGGA-CTTAACCCGGAT
3436 ATAGTCACTTAGCACAAA
62 ATAGTCACTTAGCACAAA
*
3454 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
3475 CAGCATTCAA
Statistics
Matches: 86, Mismatches: 8, Indels: 13
0.80 0.07 0.12
Matches are distributed among these distances:
78 3 0.03
79 23 0.27
80 49 0.57
81 10 0.12
82 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
GCCTTCGGGACTTAACCCGGATATAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATATAG
TCACTTAGCACAAA
Found at i:8470 original size:40 final size:40
Alignment explanation
Indices: 8386--8569 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
8376 TTGAATGCTG
* * * *
8386 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
8425 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * **
8466 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACCAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
8506 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
8546 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
8570 GAATGAGTTA
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 110 0.91
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:8590 original size:39 final size:39
Alignment explanation
Indices: 8466--8616 Score: 117
Period size: 40 Copynumber: 3.8 Consensus size: 39
8456 AGTTATTAAT
* ** * * *
8466 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATAC-CAAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
** *
8506 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
8546 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
8586 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
8617 GAGCTATATC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 29 0.31
40 64 0.69
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:11546 original size:39 final size:40
Alignment explanation
Indices: 11436--11653 Score: 327
Period size: 40 Copynumber: 5.5 Consensus size: 40
11426 GAGGACTATA
* *
11436 TCCGGGTTAAGTCCCGCAGGCATTCATGCTGGTTGTTATT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATT
*
11476 TCCGGGTTAAGTCTCGAAGGCATTCGTGCTGGTTGTTATT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATT
11516 TCCGGGTTAAGTCCC-AAGGCATTCGTGCTGGTTGTTATT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATT
*
11555 TCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGCTA-T
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATT
* **
11594 TCC-GGTTAAGT-CCGAAGGCATTTGTGCTGGTTGTTACA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATT
* *
11632 TCCGGGCTAAATCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCA
11654 ATTGGGTTGG
Statistics
Matches: 164, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
37 23 0.14
38 11 0.07
39 49 0.30
40 81 0.49
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.33
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATT
Found at i:11573 original size:79 final size:78
Alignment explanation
Indices: 11431--11653 Score: 322
Period size: 79 Copynumber: 2.8 Consensus size: 78
11421 CAATTGAGGA
* * *
11431 CTATATCCGGGTTAAGTCCCGCAGGCATTCATGCTGGTTGTTATTTCCGGGTTAAGTCTCGAAGG
1 CTAT-TCCGGGTTAAGTCCC-AAGGCATTCGTGCTGGTTGTTATTTCCGGGTTAAGTCCCGAAGG
11496 CATTCGTGCTGGTTG
64 CATTCGTGCTGGTTG
*
11511 TTATTTCCGGGTTAAGTCCCAAGGCATTCGTGCTGGTTGTTATTTCCGGGTTAAGTCCCGAAGGC
1 CTA-TTCCGGGTTAAGTCCCAAGGCATTCGTGCTGGTTGTTATTTCCGGGTTAAGTCCCGAAGGC
11576 ATTCGTGCTGGTTG
65 ATTCGTGCTGGTTG
* * ** * *
11590 CTATTCC-GGTTAAGTCCGAAGGCATTTGTGCTGGTTGTTACATCCGGGCTAAATCCCGAAGGCA
1 CTATTCCGGGTTAAGTCCCAAGGCATTCGTGCTGGTTGTTATTTCCGGGTTAAGTCCCGAAGGCA
11654 ATTGGGTTGG
Statistics
Matches: 131, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
77 51 0.39
78 4 0.03
79 58 0.44
80 17 0.13
81 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (78 bp):
CTATTCCGGGTTAAGTCCCAAGGCATTCGTGCTGGTTGTTATTTCCGGGTTAAGTCCCGAAGGCA
TTCGTGCTGGTTG
Found at i:19548 original size:40 final size:40
Alignment explanation
Indices: 19493--19670 Score: 277
Period size: 40 Copynumber: 4.5 Consensus size: 40
19483 ACTATATCCT
*
19493 GGTTAAGTCCCGAAGGCATTCATGCTGGTTGTTATTTCCG
1 GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATTTCCG
*
19533 GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATTTTCG
1 GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATTTCCG
*
19573 GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGCTATTTCCG
1 GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATTTCCG
**
19613 GGTTAAGTCCCGAAGGCATTTC-TGCTGGTTGTTACATCCG
1 GGTTAAGTCCCGAAGGCA-TTCGTGCTGGTTGTTATTTCCG
* *
19653 GGCTAAATCCCGAAGGCA
1 GGTTAAGTCCCGAAGGCA
19671 ATTGGGTTGG
Statistics
Matches: 128, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 125 0.98
41 3 0.02
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (40 bp):
GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATTTCCG
Found at i:23255 original size:47 final size:43
Alignment explanation
Indices: 23203--23300 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 43
23193 TCTAGGATGT
*
23203 TGGCATCGATTTATATATGGTTACGTGTAAGACCATGTCTGGGACA-
1 TGGCATCGA-TTAT-T-TGATT-CGTGTAAGACCATGTCTGGGACAG
*
23249 TCGGCATCG--TATTTGATTCGTGTAAGACCCTGTCTGGGACAG
1 T-GGCATCGATTATTTGATTCGTGTAAGACCATGTCTGGGACAG
23291 TGGCATCGAT
1 TGGCATCGAT
23301 ATGAGATAGC
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
41 29 0.63
42 5 0.11
43 1 0.02
44 3 0.07
46 1 0.02
47 7 0.15
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (43 bp):
TGGCATCGATTATTTGATTCGTGTAAGACCATGTCTGGGACAG
Found at i:30961 original size:47 final size:45
Alignment explanation
Indices: 30846--30971 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
30836 TAAGATTTCA
30846 ATATATATGTTTTCGAGTAAGACCACGTCTGGGATGTTGGCATCG
1 ATATATATGTTTTCGAGTAAGACCACGTCTGGGATGTTGGCATCG
* * *
30891 ATATATGTGTTTTCAAGTAAGACCACGTCTGGGATGTTGGCATTG
1 ATATATATGTTTTCGAGTAAGACCACGTCTGGGATGTTGGCATCG
* * * *
30936 ATTTATATATGGTTACGTGTAAGACCATGTCTGGGA
1 A--TATATATGTTTTCGAGTAAGACCACGTCTGGGA
30972 CATCAGCATT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
45 43 0.61
47 27 0.39
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.35
Consensus pattern (45 bp):
ATATATATGTTTTCGAGTAAGACCACGTCTGGGATGTTGGCATCG
Found at i:32911 original size:16 final size:15
Alignment explanation
Indices: 32886--32919 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
32876 AAAGTTGATA
*
32886 ATAATTAATATATATT
1 ATAATAAATATA-ATT
32902 ATAATAAATATAATT
1 ATAATAAATATAATT
32917 ATA
1 ATA
32920 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:37967 original size:34 final size:33
Alignment explanation
Indices: 37907--37971 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
37897 ATTTCAGTTG
*
37907 GGGCCTTAGCCCATTACAGTATCAGTATCAGTGT
1 GGGCCTGAGCCCATTACAGTATCAGTA-CAGTGT
37941 GGGCCTGAGCCCATCT-CAGTGA-CAGTACAGT
1 GGGCCTGAGCCCAT-TACAGT-ATCAGTACAGT
37972 TCAGATATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 4 0.14
34 22 0.79
35 2 0.07
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (33 bp):
GGGCCTGAGCCCATTACAGTATCAGTACAGTGT
Found at i:41206 original size:27 final size:27
Alignment explanation
Indices: 41175--41352 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 27
41165 TAAATTGTAC
41175 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* **
41202 TGCACTAAGTGTGCGAAATGA--ATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41227 GATGCACTAAGTGTGCGAATTGACCATGC
1 -A-GCACTAAGTGTGCGATTTGACTATGT
*
41256 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41284 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41311 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41338 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41353 GACTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.03
27 99 0.77
28 23 0.18
29 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41316 original size:82 final size:81
Alignment explanation
Indices: 41176--41331 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 81
41166 AAATTGTACA
* *
41176 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATGTGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAACGTGATGCACTAAGTGT
41241 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
**
41257 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGT-A-GCACTAAG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGA--ACGTGATGCACTAAG
*
41320 TGTGCGAGTTGA
63 TGTGCGAATTGA
41332 TTATATAGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
81 15 0.22
82 48 0.72
83 1 0.01
84 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAACGTGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41343 original size:82 final size:81
Alignment explanation
Indices: 41172--41352 Score: 222
Period size: 82 Copynumber: 2.2 Consensus size: 81
41162 GATTAAATTG
* *
41172 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATGTGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAACGTGATGCACTAA
41237 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * **
41253 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGT-A-GCAC
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGA--ACGTGATGCAC
* **
41316 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
41335 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41353 GACTCAATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
81 17 0.20
82 63 0.75
83 1 0.01
84 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAACGTGATGCACTAA
GTGTGCGAATTGACCA
Done.