Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2885
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: 54014
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:2089 original size:39 final size:40
Alignment explanation
Indices: 1995--2204 Score: 242
Period size: 39 Copynumber: 5.4 Consensus size: 40
1985 TACTCGCCTC
* * *
1995 AATGCCTTCGGGAC-TAGTCCGGATATAGTAATTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACA
*
2034 AATG-C-TCGGGACTTAGCCCGGATATA-TAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACA
2071 AATGCCTTCGGGACTTAGCCCGGA-ATTAGT-ACTAGCACA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTAGCACA
* * *
2110 AATGCCTTCGGGACTTAGCCTGAAT-TAGTCACTAGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACA
* *
2149 AATTGCCTTCGGGACTTAGCCCCGA-ATTAGTCACTAGCACA
1 AA-TGCCTTCGGGACTTAGCCCGGATA-TAGTAACTAGCACA
2190 AA--CCTTCGGGACTTA
1 AATGCCTTCGGGACTTA
2205 ACCCCTTATC
Statistics
Matches: 153, Mismatches: 8, Indels: 21
0.84 0.04 0.12
Matches are distributed among these distances:
37 21 0.14
38 32 0.21
39 64 0.42
40 20 0.13
41 16 0.10
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACA
Found at i:10038 original size:40 final size:40
Alignment explanation
Indices: 10001--10219 Score: 359
Period size: 40 Copynumber: 5.5 Consensus size: 40
9991 GCTACTCGCT
* * *
10001 CAAATGCCTTCGGGACTTAGTCCGG-ATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCA
* *
10041 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
10081 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
*
10121 CAAATGCCTTCGGGACTTAGCCTGGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
*
10161 CAAATGCCTTCGGGACTTAGCCCAGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
10201 CAAATGCCTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
10220 ACCCCGTTAT
Statistics
Matches: 172, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 170 0.99
41 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
Found at i:14363 original size:46 final size:46
Alignment explanation
Indices: 14310--14446 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
14300 TATATATACA
* * * * *
14310 CATCTCATACATATCTCACTTTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
14356 CATCTCATACACGTTTCGCATAAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
14402 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
14447 ATACATGTTC
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:14481 original size:47 final size:47
Alignment explanation
Indices: 14420--14661 Score: 340
Period size: 47 Copynumber: 5.1 Consensus size: 47
14410 ACACATTTCG
* *
14420 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* *
14467 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* **
14514 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
*
14561 CATTGGCCATTCGGCCTTATCACACATTTATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CACA--TATATACATGTTCACATTCATCA
* * **
14612 CATTTGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
14659 CAT
1 CAT
14662 AAAATCCTAA
Statistics
Matches: 176, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
47 131 0.74
49 7 0.04
51 38 0.22
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
Found at i:14548 original size:94 final size:96
Alignment explanation
Indices: 14420--14661 Score: 344
Period size: 98 Copynumber: 2.5 Consensus size: 96
14410 ACACATTTCG
*
14420 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
14485 AT-CTCA-TATATGCATGTTCACATTCATCA
66 ATACACATTATATACAGGTTCACATTCATCA
* * **
14514 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
14579 ATCACACATTTATATACAGGTTCACATTCATCA
66 AT-ACACA-TTATATACAGGTTCACATTCATCA
* * **
14612 CATTTGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CATTAGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACAT
14662 AAAATCCTAA
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
94 62 0.48
96 3 0.02
98 64 0.50
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (96 bp):
CATTAGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATACACATTATATACAGGTTCACATTCATCA
Found at i:14588 original size:24 final size:24
Alignment explanation
Indices: 14512--14588 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
14502 TCACATTCAT
14512 CACATTGGCCATTCGGCCTTATCA
1 CACATTGGCCATTCGGCCTTATCA
** * *
14536 CACATACG-CATGTTC--ACAT-TCA
1 CACATTGGCCA--TTCGGCCTTATCA
14558 TCACATTGGCCATTCGGCCTTATCA
1 -CACATTGGCCATTCGGCCTTATCA
14583 CACATT
1 CACATT
14589 TATATACAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 6 0.16
23 10 0.26
24 16 0.42
25 6 0.16
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (24 bp):
CACATTGGCCATTCGGCCTTATCA
Found at i:18060 original size:40 final size:40
Alignment explanation
Indices: 18014--18758 Score: 1067
Period size: 40 Copynumber: 18.9 Consensus size: 40
18004 GAATACACAT
* *
18014 CACCAGCATGAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18054 CACCAGCTCGAATGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18094 CACCAGCTCGAATGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
18134 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18174 CACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18214 CACCAGCACAAATGCTCTTCGGGACTTAGCCCGGATATAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
18254 CACTAGCACGAATGCTCTTAGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* ** * *
18294 CACCAGCTCGAATGCTCAACAGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
18334 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18374 CACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
18414 CACCAGCTCGAATGCTCTTTGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18454 CACCAGCTCGAATGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18494 CACCAGCACGAATGCTCTTC--G----AG---AGATATAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18525 CACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18565 CACCAGCTCGAATGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18605 CACCAGCTCGAATGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
18645 CACCAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
18685 CACTAGCACGAATACTCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
18725 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGG
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGG
18759 GTATCTAACT
Statistics
Matches: 634, Mismatches: 62, Indels: 18
0.89 0.09 0.03
Matches are distributed among these distances:
31 25 0.04
33 1 0.00
34 2 0.00
37 2 0.00
38 1 0.00
40 603 0.95
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:18533 original size:31 final size:31
Alignment explanation
Indices: 18487--18548 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
18477 ACCTAGCCCG
18487 GATATAACACCAGCACGAATGCTCTTCGAGA
1 GATATAACACCAGCACGAATGCTCTTCGAGA
* *
18518 GATATATCACTAGCACGAATGCTCTTCGAGA
1 GATATAACACCAGCACGAATGCTCTTCGAGA
18549 CTTAGCCCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (31 bp):
GATATAACACCAGCACGAATGCTCTTCGAGA
Found at i:20305 original size:46 final size:46
Alignment explanation
Indices: 20252--20388 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
20242 TATATATACA
* * * * *
20252 CATCTCATACATATCTCACTTTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
20298 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
20344 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
20389 ATACATGTTC
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:20423 original size:47 final size:47
Alignment explanation
Indices: 20362--20603 Score: 313
Period size: 47 Copynumber: 5.1 Consensus size: 47
20352 ACACATTTCG
* *
20362 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* *
20409 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* **
20456 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* *
20503 CATTGGCCATTCGGCCTTATCACACATATATATACAGGTTCACATTCATTA
1 CATTGGCCATTCGGCCTTAT--CAC--ATATATACATGTTCACATTCATCA
* * * * **
20554 CATTTGTCATTCGTCCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
20601 CAT
1 CAT
20604 AAAATCCTAA
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
47 131 0.76
49 5 0.03
51 36 0.21
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
Found at i:21273 original size:21 final size:21
Alignment explanation
Indices: 21248--21288 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21238 AAATTTTATC
*
21248 TTATAACCATTTTTTAAAAAA
1 TTATAACCATTTTCTAAAAAA
**
21269 TTATAATGATTTTCTAAAAA
1 TTATAACCATTTTCTAAAAA
21289 CAGAATAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (21 bp):
TTATAACCATTTTCTAAAAAA
Found at i:25087 original size:37 final size:37
Alignment explanation
Indices: 25046--25123 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
25036 CAAAGCTACC
*
25046 TTTTTATTTCTTAACTCTTTTGTTTCTCGAGCTAAGA
1 TTTTTATTTCTTAACTCTTTTGTTTCCCGAGCTAAGA
*
25083 TTTTTATTTCTTAACTCTTTTGTTTCCCGAGCTAATA
1 TTTTTATTTCTTAACTCTTTTGTTTCCCGAGCTAAGA
25120 TTTT
1 TTTT
25124 GATTGGTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.18, C:0.17, G:0.09, T:0.56
Consensus pattern (37 bp):
TTTTTATTTCTTAACTCTTTTGTTTCCCGAGCTAAGA
Found at i:27095 original size:27 final size:27
Alignment explanation
Indices: 27034--27095 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
27024 CTATCATAGA
* * * *
27034 AACAGTATCAGGTGGCCTTAGCCCATT
1 AACAGAATTAGGTGGCCTAAGCCCAAT
*
27061 AACGGAATTAGGTGGGCCTAAGCCCAAT
1 AACAGAATTAGGT-GGCCTAAGCCCAAT
27089 -ACAGAAT
1 AACAGAAT
27096 CAGTATCAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (27 bp):
AACAGAATTAGGTGGCCTAAGCCCAAT
Found at i:42419 original size:28 final size:28
Alignment explanation
Indices: 42346--42435 Score: 126
Period size: 28 Copynumber: 3.2 Consensus size: 28
42336 AGGAAGCATC
42346 CTGGTGGCTCTGCCACAAATATCTGTTT
1 CTGGTGGCTCTGCCACAAATATCTGTTT
*
42374 CTGGTGGCTCTACCACAAATATCTGTTT
1 CTGGTGGCTCTGCCACAAATATCTGTTT
* ** * *
42402 CTGGTGGCCCTGGGACAATTATCTGTAT
1 CTGGTGGCTCTGCCACAAATATCTGTTT
42430 CTGGTG
1 CTGGTG
42436 ACTATGACAG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACAAATATCTGTTT
Found at i:49041 original size:24 final size:24
Alignment explanation
Indices: 49009--49055 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
48999 TGGTGGCCGA
49009 TGCTTTGAGTCGTAAAGCACTGTT
1 TGCTTTGAGTCGTAAAGCACTGTT
49033 TGCTTTGAGTCGTAAAGCACTGT
1 TGCTTTGAGTCGTAAAGCACTGT
49056 CTGTTTCGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (24 bp):
TGCTTTGAGTCGTAAAGCACTGTT
Found at i:51611 original size:40 final size:40
Alignment explanation
Indices: 51498--51667 Score: 191
Period size: 39 Copynumber: 4.3 Consensus size: 40
51488 TCCTCGTTCA
* * * * *
51498 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
51537 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
51577 AATGCCTTC-GGACTTAACCCGGCTTTAATAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAT-AACTCGCACG
* * * *
51617 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
51657 AAGGCCTTCGG
1 AATGCCTTCGG
51668 ATCTTAGTCC
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
39 49 0.45
40 43 0.39
41 18 0.16
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:51640 original size:80 final size:78
Alignment explanation
Indices: 51496--51673 Score: 203
Period size: 80 Copynumber: 2.2 Consensus size: 78
51486 GCTCCTCGTT
* * * * * *
51496 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACCATGCCTTCGGGACGTAACCCGGA
1 CAAATGCCTTC-GGACTTAACCCGGCTTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGA
51561 TTTAACAACTCGCA
65 TTTAACAACTCGCA
* * *
51575 CGAATGCCTTCGGACTTAACCCGGCTTTAATAAACTCGCACGAATGCCCTCGGGACTTAACCCGG
1 CAAATGCCTTCGGACTTAACCCGGCTTTAAT-AACTCACAC-AATGCCCTCGGGACGTAACCCGG
** *
51640 ATTTAGTATCTCGCA
64 ATTTAACAACTCGCA
*
51655 CAAAGGCCTTCGGATCTTA
1 CAAATGCCTTCGGA-CTTA
51674 GTCCGGATAT
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.20
79 18 0.22
80 44 0.54
81 4 0.05
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (78 bp):
CAAATGCCTTCGGACTTAACCCGGCTTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGAT
TTAACAACTCGCA
Done.