Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3669
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: 32455
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Found at i:2600 original size:27 final size:27
Alignment explanation
Indices: 2570--2747 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
2560 ATATTGAGTC
* * *
2570 CGCACACTCAGTGCTATATAATCCACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
2597 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
2624 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
2652 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
2679 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
2706 CGCACACTTAGTGCAACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
2733 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2748 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:2709 original size:82 final size:81
Alignment explanation
Indices: 2596--2746 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 81
2586 TATAATCCAC
* * *
2596 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGCCAAA-TCGCACACTT
2661 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* **
2678 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGCCAAATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGCCAAATCGCACACTT
2742 AGTGC
65 AGTGC
2747 TGTACAATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGCCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Found at i:7366 original size:28 final size:28
Alignment explanation
Indices: 7326--7434 Score: 114
Period size: 28 Copynumber: 3.9 Consensus size: 28
7316 GGAAGCGTTC
*
7326 TGGTGGCTCTGCCACAAATATCTGTTTT
1 TGGTGACTCTGCCACAAATATCTGTTTT
* * *
7354 TGGTGGCTCTGCCAGAAATATCTATTTT
1 TGGTGACTCTGCCACAAATATCTGTTTT
* * *
7382 TGGTGAC-CTTGCCACAATTATCTGTATC
1 TGGTGACTC-TGCCACAAATATCTGTTTT
* *
7410 TGGTGACTCTGTCAC-AGTATCTGTT
1 TGGTGACTCTGCCACAAATATCTGTT
7435 CTGGTAGCCA
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
27 9 0.13
28 58 0.85
29 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (28 bp):
TGGTGACTCTGCCACAAATATCTGTTTT
Found at i:11495 original size:28 final size:27
Alignment explanation
Indices: 11437--11551 Score: 135
Period size: 28 Copynumber: 4.2 Consensus size: 27
11427 GAAGGAAGCG
*
11437 TTCTGGTGGCTCTGCCACAATATCTGT
1 TTCTGGTGGCTCTGCCACAATATCTAT
*
11464 TTCTAGTGGCTCTGCCACAAATATCTAT
1 TTCTGGTGGCTCTGCCAC-AATATCTAT
11492 TTCTGGTGGC-CTTGCCACAATTATCTAT
1 TTCTGGTGGCTC-TGCCACAA-TATCTAT
* * * *
11520 ATCTGGTGACTCTGTCACAGTATCTA-
1 TTCTGGTGGCTCTGCCACAATATCTAT
11546 TTCTGG
1 TTCTGG
11552 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
26 5 0.07
27 26 0.34
28 44 0.58
29 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (27 bp):
TTCTGGTGGCTCTGCCACAATATCTAT
Found at i:11544 original size:55 final size:54
Alignment explanation
Indices: 11437--11551 Score: 135
Period size: 55 Copynumber: 2.1 Consensus size: 54
11427 GAAGGAAGCG
* * *
11437 TTCTGGTGGCTCTGCCACAATATCTGTTTCTAGTGGCTCTGCCACAAATATCTA
1 TTCTGGTGGCTCTGCCACAATATCTATATCTAGTGACTCTGCCACAAATATCTA
* * *
11491 TTTCTGGTGGC-CTTGCCACAATTATCTATATCTGGTGACTCTGTCAC-AGTATCTA
1 -TTCTGGTGGCTC-TGCCACAA-TATCTATATCTAGTGACTCTGCCACAAATATCTA
11546 TTCTGG
1 TTCTGG
11552 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
54 7 0.13
55 25 0.48
56 20 0.38
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (54 bp):
TTCTGGTGGCTCTGCCACAATATCTATATCTAGTGACTCTGCCACAAATATCTA
Found at i:14310 original size:18 final size:17
Alignment explanation
Indices: 14289--14343 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
14279 ACAATTCTTT
14289 TCTCTTCTTCTTTTCTCC
1 TCTCTTCTTCTTTTCT-C
14307 TCTCTT-TATCTATTT-TC
1 TCTCTTCT-TCT-TTTCTC
14324 TCTTCTTCTTCTTTTC-C
1 TC-TCTTCTTCTTTTCTC
14341 TCT
1 TCT
14344 ATAGCGAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
16 1 0.03
17 10 0.31
18 17 0.53
19 4 0.12
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.64
Consensus pattern (17 bp):
TCTCTTCTTCTTTTCTC
Found at i:15607 original size:28 final size:28
Alignment explanation
Indices: 15567--15732 Score: 195
Period size: 28 Copynumber: 6.2 Consensus size: 28
15557 GGTGGAAGCG
*
15567 TTCTGGAGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
15595 TTCTGGTGGCTCTG-C-C----ATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
15617 TTCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
*
15645 TTCTGGTGGCTCTGCCACAAATATCTAT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
15673 TTTTGGTGGCCCTGCCACAATTATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * * *
15701 ATCTGGTGACTCTGTCAC-AGTATCTG-
1 TTCTGGTGGCTCTGCCACAAATATCTGT
15727 TTCTGG
1 TTCTGG
15733 CAACCATGCT
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
22 20 0.17
23 1 0.01
24 1 0.01
26 6 0.05
27 8 0.07
28 83 0.70
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:15614 original size:22 final size:22
Alignment explanation
Indices: 15589--15661 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 22
15579 TGCCACAAAT
15589 ATCTGTTTCTGGTGGCTCTGCC
1 ATCTGTTTCTGGTGGCTCTGCC
15611 ATCTGTTTCTGGTGGCTCTGCCAC
1 ATCTGTTTCTGGTGGCTCTG-C-C
15635 AAATATCTGTTTCTGGTGGCTCTGCC
1 ----ATCTGTTTCTGGTGGCTCTGCC
15661 A
1 A
15662 CAAATATCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
22 21 0.47
23 1 0.02
24 1 0.02
26 1 0.02
27 1 0.02
28 20 0.44
ACGTcount: A:0.11, C:0.26, G:0.25, T:0.38
Consensus pattern (22 bp):
ATCTGTTTCTGGTGGCTCTGCC
Found at i:15642 original size:50 final size:50
Alignment explanation
Indices: 15567--15661 Score: 181
Period size: 50 Copynumber: 1.9 Consensus size: 50
15557 GGTGGAAGCG
15567 TTCTGGAGGCTCTGCCACAAATATCTGTTTCTGGTGGCTCTGCCATCTGT
1 TTCTGGAGGCTCTGCCACAAATATCTGTTTCTGGTGGCTCTGCCATCTGT
*
15617 TTCTGGTGGCTCTGCCACAAATATCTGTTTCTGGTGGCTCTGCCA
1 TTCTGGAGGCTCTGCCACAAATATCTGTTTCTGGTGGCTCTGCCA
15662 CAAATATCTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.36
Consensus pattern (50 bp):
TTCTGGAGGCTCTGCCACAAATATCTGTTTCTGGTGGCTCTGCCATCTGT
Found at i:18505 original size:18 final size:18
Alignment explanation
Indices: 18479--18534 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
18469 TTCTGACAAG
*
18479 TCTTTTCTCTTATTCTTT
1 TCTTCTCTCTTATTCTTT
*
18497 TCTTCTCTCTTCA-TCTAT
1 TCTTCTCTCTT-ATTCTTT
*
18515 T-TTCTCTTCTTCTTCTTT
1 TCTTCTC-TCTTATTCTTT
18533 TC
1 TC
18535 CTCTATAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 5 0.17
18 24 0.80
19 1 0.03
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (18 bp):
TCTTCTCTCTTATTCTTT
Found at i:19804 original size:28 final size:28
Alignment explanation
Indices: 19764--19879 Score: 155
Period size: 28 Copynumber: 4.2 Consensus size: 28
19754 GGAGGAAGCG
*
19764 TTCTGGAGGCTCTGCCACAAATATCTAT
1 TTCTGGTGGCTCTGCCACAAATATCTAT
19792 TTCTGGTGGCTCTGCCACAAATATCTAT
1 TTCTGGTGGCTCTGCCACAAATATCTAT
* *
19820 TTCTGGTGGCCCTGCCACAATTATCTAT
1 TTCTGGTGGCTCTGCCACAAATATCTAT
* * * *
19848 ATCTGGTGACTCTGTCAC-AGTATCTA-
1 TTCTGGTGGCTCTGCCACAAATATCTAT
19874 TTCTGG
1 TTCTGG
19880 CAGCCATGTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 5 0.06
27 7 0.09
28 67 0.85
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTAT
Found at i:22559 original size:40 final size:40
Alignment explanation
Indices: 22476--22695 Score: 223
Period size: 40 Copynumber: 5.5 Consensus size: 40
22466 ACCCAAGTAT
** * *
22476 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
22514 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
22554 CTTCGGGACTTAGCTCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
22594 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGT
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*** * * * *
22634 CTTCAAATCTTAGTCCGTATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
22674 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
22696 CATTCGAATA
Statistics
Matches: 146, Mismatches: 31, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
37 1 0.01
38 11 0.08
39 16 0.11
40 117 0.80
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:30604 original size:40 final size:40
Alignment explanation
Indices: 30521--30739 Score: 259
Period size: 40 Copynumber: 5.5 Consensus size: 40
30511 ACCCAAGTAT
** * *
30521 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
30559 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
30599 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
30639 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
30679 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
30719 CTTC-GGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
30740 CATTCGAATA
Statistics
Matches: 155, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 30 0.19
40 112 0.72
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Done.