Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1310
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: 16551
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:396 original size:16 final size:17
Alignment explanation
Indices: 366--412 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
356 AACATAATCA
*
366 ATATTATAATGACAATG
1 ATATTATAATAACAATG
383 ATATT-TAATAACAAT-
1 ATATTATAATAACAATG
* *
398 ATAATATAAGAACAA
1 ATATTATAATAACAA
413 GTTTAATGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 17 0.65
17 5 0.19
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (17 bp):
ATATTATAATAACAATG
Found at i:2759 original size:12 final size:12
Alignment explanation
Indices: 2744--2774 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2734 TTTCTTTTGC
2744 TTTTCAAAGGCT
1 TTTTCAAAGGCT
2756 TTTTCAAAGGCT
1 TTTTCAAAGGCT
2768 TTTTCAA
1 TTTTCAA
2775 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:2850 original size:6 final size:6
Alignment explanation
Indices: 2834--2883 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
2824 TTTCTTTTTA
*
2834 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
2883 T
1 T
2884 ATTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:2880 original size:37 final size:37
Alignment explanation
Indices: 2823--2893 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
2813 CTTGCCTCTC
2823 TTTTCTTTTTATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTATTTCATTTTCTTTATT-TTCTCTTGCT
*
2860 TTTTCTTTTTCTTTTC-TTTTCTTTATTTTCTCTT
1 TTTTCTTTTT-ATTTCATTTTCTTTATTTTCTCTT
2894 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTATTTCATTTTCTTTATTTTCTCTTGCT
Found at i:3769 original size:21 final size:22
Alignment explanation
Indices: 3745--3790 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
3735 TTTTATATAC
3745 TTCGATTTTTTTT-AATTTTTT
1 TTCGATTTTTTTTAAATTTTTT
3766 TTCGATTTTTTTTAAAATTTTTT
1 TTCGATTTTTTTT-AAATTTTTT
3789 TT
1 TT
3791 TCGAATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.57
23 10 0.43
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (22 bp):
TTCGATTTTTTTTAAATTTTTT
Found at i:5525 original size:30 final size:30
Alignment explanation
Indices: 5491--5587 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
5481 AAAACTAAAA
5491 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
5521 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
5551 TGAGCTAAGCTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
5580 ATGAGCTA
1 -TGAGCTA
5588 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 45 0.87
31 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:13156 original size:27 final size:27
Alignment explanation
Indices: 13126--13303 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
13116 ATATTGAGCC
* *
13126 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
13153 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
13180 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*** ** *
13208 CGCACACTTAGTGCCGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
13235 CGCACTCTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
13262 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
13289 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
13304 GTACAATTTA
Statistics
Matches: 117, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
26 2 0.02
27 93 0.79
28 22 0.19
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:13238 original size:55 final size:54
Alignment explanation
Indices: 13126--13303 Score: 150
Period size: 54 Copynumber: 3.3 Consensus size: 54
13116 ATATTGAGCC
* * *
13126 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
* * * *
13180 CGCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTG-C-CGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCCACGTA--ATCAAAT
* * ** * *
13235 CGCACTCTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAAC-AAAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACGTAA-TCA-AAT
13289 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
13304 GTACAATTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
53 5 0.05
54 52 0.53
55 40 0.41
56 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
Done.