Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2442
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: 10515
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Found at i:309 original size:34 final size:34
Alignment explanation
Indices: 263--480 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
253 GTAAAAACCA
*
263 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
297 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
331 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
365 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
398 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
432 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
465 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
481 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:377 original size:68 final size:67
Alignment explanation
Indices: 261--480 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
251 TGGTAAAAAC
* * *
261 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
326 AT
66 AT
* * *
328 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
393 AAT
65 AAT
* * * * * *
396 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
461 AT
66 AT
463 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
481 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:4573 original size:19 final size:19
Alignment explanation
Indices: 4546--4608 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
4536 TCACGTGTAC
* *
4546 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
4565 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
4584 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
4603 AGTACC
1 AGTACC
4609 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:4959 original size:34 final size:34
Alignment explanation
Indices: 4913--5128 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
4903 GTAAAAACCA
*
4913 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
4947 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
4981 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
5015 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
5048 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
5082 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
5115 CCATTTAATCAACA
1 CCATTTAATCAACA
5129 GCTGTCTCTT
Statistics
Matches: 160, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 43 0.27
34 115 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:5027 original size:68 final size:67
Alignment explanation
Indices: 4911--5128 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
4901 TGGTAAAAAC
* * *
4911 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
4976 AT
66 AT
* * *
4978 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
5043 AAT
65 AAT
* * * * * *
5046 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
5111 AT
66 AT
5113 CACCATTTAATCAACA
1 CACCATTTAATCAACA
5129 GCTGTCTCTT
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:5450 original size:24 final size:25
Alignment explanation
Indices: 5421--5475 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
5411 TAAGGTTTAA
*
5421 ATTTTTAGTATCTTATTTAA-TATAT
1 ATTTTTA-TATCTTAATTAATTATAT
* *
5446 ATTTTTATATTTTAATTAATTATTT
1 ATTTTTATATCTTAATTAATTATAT
5471 ATTTT
1 ATTTT
5476 ATTAGAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTTATATCTTAATTAATTATAT
Found at i:6962 original size:23 final size:23
Alignment explanation
Indices: 6935--6979 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6925 GAAGAAAAAA
*
6935 TTTATCCTTTTA-TATCATATATT
1 TTTATACTTTTATTAT-ATATATT
*
6958 TTTATATTTTTATTATATATAT
1 TTTATACTTTTATTATATATAT
6980 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTATACTTTTATTATATATATT
Found at i:6988 original size:25 final size:24
Alignment explanation
Indices: 6944--7017 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
6934 ATTTATCCTT
*
6944 TTATATCATATATTTTTATATTTTTA
1 TTATAT-ATATA-TATTATATTTTTA
6970 TTATATATATATATATATATTATTT-
1 TTATATATATATAT-TATATT-TTTA
* *
6995 TTATGTATATA-GTTATATTTTTA
1 TTATATATATATATTATATTTTTA
7018 AAAAAATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
22 3 0.07
23 6 0.14
24 3 0.07
25 21 0.50
26 9 0.21
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (24 bp):
TTATATATATATATTATATTTTTA
Found at i:8439 original size:2 final size:2
Alignment explanation
Indices: 8432--8472 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
8422 CTTTTTGCAA
*
8432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8473 ACACAAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8716 original size:20 final size:20
Alignment explanation
Indices: 8668--8716 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
8658 TATACTTGAA
*
8668 TATACATAAAATAATTATTT
1 TATAAATAAAATAATTATTT
* *
8688 TATACATAAAATAAATTTTTT
1 TATAAATAAAAT-AATTATTT
8709 TA-AAATAA
1 TATAAATAA
8717 TATTAATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
TATAAATAAAATAATTATTT
Done.