Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold421
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: 14441
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:210 original size:42 final size:42
Alignment explanation
Indices: 125--331 Score: 187
Period size: 41 Copynumber: 5.0 Consensus size: 42
115 ACAAAAGTTC
* * * *
125 GCGGCGTTTTTAGAAAAAAACTCCGCTAAAGACCACG-TCTTTA
1 GCGGCGTTTTT--TAAAAAACGCCGCTAAAGACCAGGACCTTTA
* * *
168 GCAGCGTTTTTTAAAAAGCGCCGCTAAAGACCTGGACCTTTA
1 GCGGCGTTTTTTAAAAAACGCCGCTAAAGACCAGGACCTTTA
* * *
210 GCGGCG-CTCTTAAAAAACGCC-CCAAAGACCAGGACCTTTA
1 GCGGCGTTTTTTAAAAAACGCCGCTAAAGACCAGGACCTTTA
* * *
250 GCGGTAC-TTCTTAAAAAAACGCCGC-AAAGATCAGGA-CTTTA
1 GCGG--CGTTTTTTAAAAAACGCCGCTAAAGACCAGGACCTTTA
*
291 GCGGCGTTTTTTATAAAA-GCGCGCTAAAGACCA-GACCTTTA
1 GCGGCGTTTTTTAAAAAACGC-CGCTAAAGACCAGGACCTTTA
332 AAAACAAAAA
Statistics
Matches: 133, Mismatches: 22, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
39 3 0.02
40 35 0.26
41 52 0.39
42 32 0.24
43 11 0.08
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (42 bp):
GCGGCGTTTTTTAAAAAACGCCGCTAAAGACCAGGACCTTTA
Found at i:389 original size:40 final size:42
Alignment explanation
Indices: 345--534 Score: 295
Period size: 41 Copynumber: 4.7 Consensus size: 42
335 ACAAAAAGGA
345 TAGCGGCGCTTTTATAAAAAACGCCGCTA-AGACCTG-AC-TT
1 TAGCGGCGCTTTT-TAAAAAACGCCGCTATAGACCTGAACTTT
*
385 TAGCGGCGC-TTTTATAAAACGCCGCTATAGACCTG-ACTTT
1 TAGCGGCGCTTTTTAAAAAACGCCGCTATAGACCTGAACTTT
425 TAGCGGCGCTTTTTAAAAAACGCCGCTATAGACCTGAAC-TT
1 TAGCGGCGCTTTTTAAAAAACGCCGCTATAGACCTGAACTTT
*
466 TAGCGGCGCTTTTTAAAAAA-GCCGCTATAGACCTGTACTTT
1 TAGCGGCGCTTTTTAAAAAACGCCGCTATAGACCTGAACTTT
*
507 TAGCGGCGTTTTTTAAAAAACGCCGCTA
1 TAGCGGCGCTTTTTAAAAAACGCCGCTA
535 ATTTGCCCAG
Statistics
Matches: 140, Mismatches: 4, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
38 14 0.10
39 12 0.09
40 37 0.26
41 68 0.49
42 9 0.06
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (42 bp):
TAGCGGCGCTTTTTAAAAAACGCCGCTATAGACCTGAACTTT
Found at i:406 original size:177 final size:178
Alignment explanation
Indices: 166--498 Score: 424
Period size: 177 Copynumber: 1.9 Consensus size: 178
156 ACCACGTCTT
* *
166 TAGCAGCGTTTTTTAAAAAGCGCCGCTAAAGACCTGGACCTTTAGCGGCGCTCTTAAAAAACGCC
1 TAGCAGCGTTTTATAAAAAACGCCGCTAAAGACCTGGACCTTTAGCGGCGCTCTTAAAAAACGCC
* * *
231 -CCAAAGACCAGGACCTTTAGCGGTACTTCTTAAAAAAACGCCGC-AAAGATCAGGACTTTAGCG
66 GCCAAAGACC-GGACCTTTAGCGGCACTT-TTAAAAAAACGCCGCTAAAGACCAGAACTTTAGCG
* *
294 GCGTTTTTTATAAAAGCGCGCTAAAGACCAGACCTTTAAAAACAAAAAGGA
129 GCGCTTTTTAAAAAAGC-CGCTAAAGACCAGACCTTTAAAAACAAAAAGGA
* * *
345 TAGCGGCGCTTTTATAAAAAACGCCGCT-AAGACCT-GA-CTTTAGCGGCGCTTTTATAAAACGC
1 TAGCAGCG-TTTTATAAAAAACGCCGCTAAAGACCTGGACCTTTAGCGGCGCTCTTAAAAAACGC
* * * * * * * *
407 CGCTATAGACCTGACTTTTAGCGGCGCTTTTTAAAAAACGCCGCTATAGACCTGAACTTTAGCGG
65 CGCCAAAGACCGGACCTTTAGCGGCACTTTTAAAAAAACGCCGCTAAAGACCAGAACTTTAGCGG
*
472 CGCTTTTTAAAAAAGCCGCTATAGACC
130 CGCTTTTTAAAAAAGCCGCTAAAGACC
499 TGTACTTTTA
Statistics
Matches: 132, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
176 24 0.18
177 68 0.52
178 9 0.07
179 14 0.11
180 17 0.13
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (178 bp):
TAGCAGCGTTTTATAAAAAACGCCGCTAAAGACCTGGACCTTTAGCGGCGCTCTTAAAAAACGCC
GCCAAAGACCGGACCTTTAGCGGCACTTTTAAAAAAACGCCGCTAAAGACCAGAACTTTAGCGGC
GCTTTTTAAAAAAGCCGCTAAAGACCAGACCTTTAAAAACAAAAAGGA
Found at i:492 original size:81 final size:80
Alignment explanation
Indices: 345--535 Score: 314
Period size: 81 Copynumber: 2.4 Consensus size: 80
335 ACAAAAAGGA
*
345 TAGCGGCGCTTTTATAAAAAACGCCGCTAAGACCTGACTTTAGCGGCGCTTTTATAAAACGCCGC
1 TAGCGGCGCTTTT-TAAAAAACGCCGCTAAGACCTGACTTTAGCGGCGCTTTTATAAAAAGCCGC
410 TATAGACCTG-ACTTT
65 TATAGACCTGTACTTT
425 TAGCGGCGCTTTTTAAAAAACGCCGCTATAGACCTGAACTTTAGCGGCGCTTTT-TAAAAAAGCC
1 TAGCGGCGCTTTTTAAAAAACGCCGCTA-AGACCTG-ACTTTAGCGGCGCTTTTAT-AAAAAGCC
489 GCTATAGACCTGTACTTT
63 GCTATAGACCTGTACTTT
*
507 TAGCGGCGTTTTTTAAAAAACGCCGCTAA
1 TAGCGGCGCTTTTTAAAAAACGCCGCTAA
536 TTTGCCCAGT
Statistics
Matches: 105, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
79 15 0.14
80 21 0.20
81 37 0.35
82 32 0.30
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (80 bp):
TAGCGGCGCTTTTTAAAAAACGCCGCTAAGACCTGACTTTAGCGGCGCTTTTATAAAAAGCCGCT
ATAGACCTGTACTTT
Found at i:843 original size:19 final size:20
Alignment explanation
Indices: 819--865 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
809 TATTTCTGTT
819 CTGCTCCGCCT-CCTCGCTG
1 CTGCTCCGCCTCCCTCGCTG
838 CTGCT-CGCCTCCCTCGCTG
1 CTGCTCCGCCTCCCTCGCTG
*
857 CTGCCCCGC
1 CTGCTCCGC
866 TCTAAGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 5 0.20
19 17 0.68
20 3 0.12
ACGTcount: A:0.00, C:0.55, G:0.21, T:0.23
Consensus pattern (20 bp):
CTGCTCCGCCTCCCTCGCTG
Found at i:1452 original size:18 final size:18
Alignment explanation
Indices: 1420--1457 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1410 TACAATATAG
1420 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
1439 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
1456 TA
1 TA
1458 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:8859 original size:132 final size:133
Alignment explanation
Indices: 8621--8871 Score: 486
Period size: 132 Copynumber: 1.9 Consensus size: 133
8611 GAATTCAACA
*
8621 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACAAA
8686 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
8751 ATT
131 ATT
8754 ATATAAAACGTGAGCAACAAGACAGC-ATAAACTCTTAAATCAATCTAAGTCCACACTAAACAAA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACAAA
8818 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
8872 GGAATCACCA
Statistics
Matches: 117, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
132 91 0.78
133 26 0.22
ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20
Consensus pattern (133 bp):
ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACAAA
TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
ATT
Found at i:12269 original size:10 final size:10
Alignment explanation
Indices: 12221--12269 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
12211 ACCACTTTTC
12221 ATATATATTT
1 ATATATATTT
*
12231 ATAT-TATAT
1 ATATATATTT
12240 -TA-ATATTT
1 ATATATATTT
* *
12248 AAAAATATTT
1 ATATATATTT
12258 ATATATATTT
1 ATATATATTT
12268 AT
1 AT
12270 CTTATATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
8 6 0.19
9 5 0.16
10 20 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATATATTT
Found at i:12276 original size:15 final size:15
Alignment explanation
Indices: 12256--12286 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12246 TTAAAAATAT
*
12256 TTATATATATTTATC
1 TTATATACATTTATC
12271 TTATATACATTTATC
1 TTATATACATTTATC
12286 T
1 T
12287 CTAAATTAAA
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:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:13451 original size:40 final size:41
Alignment explanation
Indices: 13313--13570 Score: 344
Period size: 41 Copynumber: 6.4 Consensus size: 41
13303 GGTTATGGGA
*
13313 TTTTTAGCGGCGTTTTACCAAAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACC-CAAAGCGCCGCTAATGCTCTGG
* *
13355 TTTTTAGTGACGTTTTACCCAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGG
* * *
13396 TTTTTAGCGGTGTTTTACCCAAAGCGCTGCTAATGCCCT-G
1 TTTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGG
*** * *
13436 TTTTTAGCGGCGTTTTATAGAAAGCACCGCTAATACTCTGG
1 TTTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGG
* *
13477 TTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAAT-ATCTGG
1 TTTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGG
*
13517 TTTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCT-G
1 TTTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGG
*
13557 -TTTTAGTGGCGTTT
1 TTTTTAGCGGCGTTT
13571 CAGTAAAAAA
Statistics
Matches: 190, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
39 13 0.07
40 71 0.37
41 89 0.47
42 17 0.09
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.35
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGG
Found at i:13460 original size:81 final size:82
Alignment explanation
Indices: 13313--13570 Score: 353
Period size: 81 Copynumber: 3.2 Consensus size: 82
13303 GGTTATGGGA
* * *
13313 TTTTTAGCGGCGTTTTACCAAAAAGCGCCGCTAATGCTCTGGTTTTTAGTGACGTTTTACCCAAA
1 TTTTTAGCGGCGTTTTACC-AAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAA
13378 GCGCCGCTAATGCTCTGG
65 GCGCCGCTAATGCTCTGG
* * * * **
13396 TTTTTAGCGGTGTTTTACCCAAAGCGCTGCTAATGCCCT-GTTTTTAGCGGCGTTTTATAGAAAG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAG
* *
13460 CACCGCTAATACTCTGG
66 CGCCGCTAATGCTCTGG
* *
13477 TTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAAT-ATCTGGTTTTTAGCGGCGTTTTACCGAAAG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAG
13541 CGCCGCTAATGCTCT-G
66 CGCCGCTAATGCTCTGG
*
13557 -TTTTAGTGGCGTTT
1 TTTTTAGCGGCGTTT
13571 CAGTAAAAAA
Statistics
Matches: 153, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
79 13 0.08
80 3 0.02
81 102 0.67
82 17 0.11
83 18 0.12
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.35
Consensus pattern (82 bp):
TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAG
CGCCGCTAATGCTCTGG
Done.