Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold738
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: 8012
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:2298 original size:18 final size:17
Alignment explanation
Indices: 2273--2342 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
2263 CTTCTTCCCC
2273 CTTTTTTTTTCTTTCTT
1 CTTTTTTTTTCTTTCTT
* *
2290 CTCTTTTTTTCCTTCTT
1 CTTTTTTTTTCTTTCTT
* *
2307 CTTTCTTTTT-GTT-TT
1 CTTTTTTTTTCTTTCTT
*
2322 CTTTTTGTTTTCTTTTTT
1 CTTTTT-TTTTCTTTCTT
2340 CTT
1 CTT
2343 CTTCTTTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
15 7 0.16
16 6 0.14
17 25 0.58
18 5 0.12
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.79
Consensus pattern (17 bp):
CTTTTTTTTTCTTTCTT
Found at i:2298 original size:21 final size:20
Alignment explanation
Indices: 2274--2349 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 20
2264 TTCTTCCCCC
2274 TTTTTTT-TTCTTTCTTCTCT
1 TTTTTTTCTTCTTTCTT-TCT
*
2294 TTTTTTCCTTC-TTCTTTCTT
1 TTTTTTTCTTCTTTCTTTC-T
*
2314 TTTGTTTTCTT-TTTGTTTTCT
1 TTT-TTTTCTTCTTT-CTTTCT
2335 TTTTTCTTCTTCTTT
1 TTTTT-TTCTTCTTT
2350 TCAAACCCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 2 0.04
20 17 0.37
21 20 0.43
22 7 0.15
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTTTCTTCTTTCTTTCT
Found at i:2322 original size:11 final size:11
Alignment explanation
Indices: 2308--2338 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2298 TTCCTTCTTC
2308 TTTCTTTTTGT
1 TTTCTTTTTGT
2319 TTTCTTTTTGT
1 TTTCTTTTTGT
2330 TTTCTTTTT
1 TTTCTTTTT
2339 TCTTCTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTGT
Found at i:2338 original size:39 final size:38
Alignment explanation
Indices: 2273--2349 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
2263 CTTCTTCCCC
2273 CTTTTTTTTTCTTTCTTCTCTTTTTTTCCTTCTTCTTT
1 CTTTTTTTTTCTTTCTTCTCTTTTTTTCCTTCTTCTTT
* * *
2311 CTTTTTGTTTTCTTT-TTGTTTTCTTTTTTCTTCTTCTTT
1 CTTTTT-TTTTCTTTCTTCTCTT-TTTTTCCTTCTTCTTT
2350 TCAAACCCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 11 0.32
39 23 0.68
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (38 bp):
CTTTTTTTTTCTTTCTTCTCTTTTTTTCCTTCTTCTTT
Found at i:2350 original size:11 final size:10
Alignment explanation
Indices: 2273--2351 Score: 56
Period size: 10 Copynumber: 7.8 Consensus size: 10
2263 CTTCTTCCCC
*
2273 CTTTTTTTTT
1 CTTTTTTCTT
2283 CTTTCTTCTCTT
1 CTTT-TT-TCTT
*
2295 -TTTTTCCTT
1 CTTTTTTCTT
*
2304 CTTCTTTCTT
1 CTTTTTTCTT
*
2314 -TTTGTT-TT
1 CTTTTTTCTT
*
2322 CTTTTTGTTTT
1 CTTTTT-TCTT
2333 CTTTTTTCTT
1 CTTTTTTCTT
2343 CTTCTTTTC
1 CTT-TTTTC
2352 AAACCCTAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
8 2 0.04
9 11 0.20
10 20 0.37
11 18 0.33
12 3 0.06
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:2351 original size:18 final size:17
Alignment explanation
Indices: 2274--2350 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 17
2264 TTCTTCCCCC
2274 TTTTTTTTTCTTTCTTCT
1 TTTTTTTTTC-TTCTTCT
2292 CTTTTTTTCCTTCTTCTTTCT
1 -TTTTTTT--TTCTTC-TTCT
* * *
2313 TTTTGTTTTCTTTTTGT
1 TTTTTTTTTCTTCTTCT
2330 TTTCTTTTTTCTTCTTCT
1 TTT-TTTTTTCTTCTTCT
2348 TTT
1 TTT
2351 CAAACCCTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.12
18 19 0.40
19 7 0.15
20 9 0.19
21 7 0.15
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTCTTCTTCT
Found at i:2886 original size:28 final size:28
Alignment explanation
Indices: 2824--2954 Score: 129
Period size: 28 Copynumber: 4.5 Consensus size: 28
2814 TTCTAGGGAA
* * *
2824 AAAATATAATTTTAGAAAAAAATTAGGGTT
1 AAAATGTAATTTTAG--GAAAATTAGGGGT
2854 AAAATGTAATTTTAGGAAAATTAGGGGT
1 AAAATGTAATTTTAGGAAAATTAGGGGT
*
2882 CAAATGTAATTTTA-GAAAAGTTAGGGGTT
1 AAAATGTAATTTTAGGAAAA-TTAGGGG-T
* * *
2911 AAAATATAATTTTAGGAAAGTTGGGGGT
1 AAAATGTAATTTTAGGAAAATTAGGGGT
*
2939 CAAAATATAAATTTTA
1 -AAAATGT-AATTTTA
2955 AGTTTTTTAT
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
27 5 0.06
28 32 0.36
29 26 0.30
30 25 0.28
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTAGGAAAATTAGGGGT
Found at i:2924 original size:29 final size:29
Alignment explanation
Indices: 2824--2954 Score: 142
Period size: 29 Copynumber: 4.5 Consensus size: 29
2814 TTCTAGGGAA
*
2824 AAAATATAATTTTAGAAAAAAATTA-GGGTT
1 AAAATATAATTTTAG--AAAAGTTAGGGGTT
*
2854 AAAATGTAATTTTAGGAAAA-TTAGGGG-T
1 AAAATATAATTTTA-GAAAAGTTAGGGGTT
* *
2882 CAAATGTAATTTTAGAAAAGTTAGGGGTT
1 AAAATATAATTTTAGAAAAGTTAGGGGTT
* * *
2911 AAAATATAATTTTAGGAAAGTTGGGGGTC
1 AAAATATAATTTTAGAAAAGTTAGGGGTT
2940 AAAATATAAATTTTA
1 AAAATAT-AATTTTA
2955 AGTTTTTTAT
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.06
28 24 0.27
29 39 0.44
30 20 0.22
31 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.34
Consensus pattern (29 bp):
AAAATATAATTTTAGAAAAGTTAGGGGTT
Found at i:2924 original size:57 final size:57
Alignment explanation
Indices: 2825--2954 Score: 172
Period size: 57 Copynumber: 2.2 Consensus size: 57
2815 TCTAGGGAAA
*
2825 AAATATAATTTTAGAAAAAAATTAGGGTTAAAATGTAATTTTAGGAAAATTAGGGGTC
1 AAATATAATTTTAG-AAAAAATTAGGGTTAAAATATAATTTTAGGAAAATTAGGGGTC
* * * *
2883 AAATGTAATTTTAG-AAAAGTTAGGGGTTAAAATATAATTTTAGGAAAGTTGGGGGTC
1 AAATATAATTTTAGAAAAAATTA-GGGTTAAAATATAATTTTAGGAAAATTAGGGGTC
2940 AAAATATAAATTTTA
1 -AAATAT-AATTTTA
2955 AGTTTTTTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
56 7 0.11
57 31 0.49
58 18 0.29
59 7 0.11
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.34
Consensus pattern (57 bp):
AAATATAATTTTAGAAAAAATTAGGGTTAAAATATAATTTTAGGAAAATTAGGGGTC
Found at i:5998 original size:19 final size:19
Alignment explanation
Indices: 5974--6012 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5964 TGTCACTTTC
5974 CATCTCAACACATCTGAAT
1 CATCTCAACACATCTGAAT
5993 CATCTCAACACATCTGAAT
1 CATCTCAACACATCTGAAT
6012 C
1 C
6013 TCTAGCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26
Consensus pattern (19 bp):
CATCTCAACACATCTGAAT
Done.