Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2478
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: 13697
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:385 original size:30 final size:29
Alignment explanation
Indices: 320--388 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
310 TAATCAACCG
320 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
349 CACACACTTAGTGGCCATGCA-TTTCAAGTT
1 CGCACACTTAGT-GCCATGCACTTT-AAACT
379 CGCACACTTA
1 CGCACACTTA
389 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.41
30 20 0.59
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:498 original size:172 final size:175
Alignment explanation
Indices: 210--534 Score: 550
Period size: 172 Copynumber: 1.9 Consensus size: 175
200 AACTCAAGGT
* * *
210 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTGCACCCTTCATGTAAATTATTTATAG
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTGCACCCTTAATGTAAATTAATTATAG
*
275 AAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGT-GCCATGC
66 AAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGGCCATGC
339 ACTTTAAACTCACACACTTAGTGGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGGCCATGCATTTCAAGTTCGCAC
*
384 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCA-CCTTAATGTAAA-TAATT-TA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGT-GCACCCTTAATGTAAATTAATTATA
446 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGGCCATG
65 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGGCCATG
* *
511 TACTTTAAACTCGCACACTTAGTG
130 CACTTTAAACTCACACACTTAGTG
535 CTGTACAATT
Statistics
Matches: 142, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
172 59 0.42
173 32 0.23
174 48 0.34
175 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (175 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTGCACCCTTAATGTAAATTAATTATAG
AAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGGCCATGC
ACTTTAAACTCACACACTTAGTGGCCATGCATTTCAAGTTCGCAC
Found at i:556 original size:29 final size:28
Alignment explanation
Indices: 487--564 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 28
477 CTTAATAATC
487 AACCACGCACACTTAGTGGCCATGTACTTTA
1 AACC-CGCACACTTAGT-G-CATGTACTTTA
*
518 AACTCGCACACTTAGTGC-TGTACAATTTA
1 AACCCGCACACTTAGTGCATGTAC--TTTA
547 AACCCGCACACTTAGTGC
1 AACCCGCACACTTAGTGC
565 CAATCTCATG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 22 0.51
30 12 0.28
31 3 0.07
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (28 bp):
AACCCGCACACTTAGTGCATGTACTTTA
Found at i:2617 original size:11 final size:11
Alignment explanation
Indices: 2601--2643 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
2591 GTAGATTCAA
2601 AAAAAAAATCG
1 AAAAAAAATCG
*
2612 AAAAAAAAAATCA
1 --AAAAAAAATCG
*
2625 AAAAAAAATTG
1 AAAAAAAATCG
2636 AAAAAAAA
1 AAAAAAAA
2644 ATTTGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.09
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:2617 original size:13 final size:13
Alignment explanation
Indices: 2599--2659 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
2589 TTGTAGATTC
2599 AAAAAAAAAATCG
1 AAAAAAAAAATCG
2612 AAAAAAAAAATC-
1 AAAAAAAAAATCG
*
2624 -AAAAAAAAATTG
1 AAAAAAAAAATCG
* *
2636 AAAAAAAAATTTG
1 AAAAAAAAAATCG
2649 AAAAAAAAAAT
1 AAAAAAAAAAT
2660 TGCATACGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 10 0.23
13 33 0.77
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (13 bp):
AAAAAAAAAATCG
Found at i:9222 original size:29 final size:27
Alignment explanation
Indices: 9181--9246 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
9171 TTTTTCGCTT
*
9181 TTTCTTTTCCAATTTT-TTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
9210 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
9237 TTTCTTTTTC
1 TTTCTTTTTC
9247 TCTCACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
29 15 0.44
30 5 0.15
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:9230 original size:12 final size:12
Alignment explanation
Indices: 9206--9336 Score: 54
Period size: 12 Copynumber: 10.9 Consensus size: 12
9196 TTTTTCATTC
9206 TCAATTTCTTTT
1 TCAATTTCTTTT
9218 TCAATTTTCTTTTCT
1 TCAA-TTTC-TTT-T
*
9233 TCATTTTCTTTT
1 TCAATTTCTTTT
** **
9245 TCTCTCACTTTT
1 TCAATTTCTTTT
*
9257 TCGATTTCTTTT
1 TCAATTTCTTTT
* **
9269 TC-TTTTGCAATT
1 TCAATTT-CTTTT
**
9281 TCTTTTTCTTTT
1 TCAATTTCTTTT
**
9293 TCGTTTTCTTTT
1 TCAATTTCTTTT
* *
9305 T--GTTT-TCTT
1 TCAATTTCTTTT
9314 TCAATTTCTTTT
1 TCAATTTCTTTT
*
9326 TCAATCTCTTT
1 TCAATTTCTTT
9337 CTCCTTTTCT
Statistics
Matches: 91, Mismatches: 20, Indels: 16
0.72 0.16 0.13
Matches are distributed among these distances:
9 4 0.04
10 3 0.03
11 6 0.07
12 56 0.62
13 11 0.12
14 7 0.08
15 4 0.04
ACGTcount: A:0.10, C:0.19, G:0.03, T:0.68
Consensus pattern (12 bp):
TCAATTTCTTTT
Found at i:9305 original size:18 final size:18
Alignment explanation
Indices: 9196--9310 Score: 79
Period size: 18 Copynumber: 6.2 Consensus size: 18
9186 TTTCCAATTT
* **
9196 TTTTTCATTCTCAATTTC
1 TTTTTCATTTTCTTTTTC
9214 TTTTTCAATTTTCTTTTCTTC
1 TTTTTC-ATTTTC-TTT-TTC
* * * **
9235 ATTTTCTTTTTCTCTCAC
1 TTTTTCATTTTCTTTTTC
9253 TTTTTCGA-TTTCTTTTTC
1 TTTTTC-ATTTTCTTTTTC
* *
9271 TTTTGCAATTTCTTTTTC
1 TTTTTCATTTTCTTTTTC
* *
9289 TTTTTCGTTTTCTTTTTG
1 TTTTTCATTTTCTTTTTC
9307 TTTT
1 TTTT
9311 CTTTCAATTT
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
17 1 0.01
18 52 0.70
19 7 0.09
20 6 0.08
21 8 0.11
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTTCATTTTCTTTTTC
Found at i:9327 original size:6 final size:6
Alignment explanation
Indices: 9210--9314 Score: 68
Period size: 6 Copynumber: 17.2 Consensus size: 6
9200 TCATTCTCAA
* * * ** **
9210 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** * *
9261 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
9308 TTTCTT T
1 TTTCTT T
9315 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 25, Indels: 6
0.70 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 55 0.77
7 9 0.13
8 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:10402 original size:10 final size:10
Alignment explanation
Indices: 10374--10412 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
10364 TTGTCACTTC
**
10374 TTTTTTTTCC
1 TTTTTTTTGA
10384 TTTTTTTTGA
1 TTTTTTTTGA
10394 TTTTTTTTGAA
1 TTTTTTTTG-A
10405 TTTTTTTT
1 TTTTTTTT
10413 TGAATTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:10413 original size:12 final size:12
Alignment explanation
Indices: 10384--10419 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
10374 TTTTTTTTCC
10384 TTTTTTTTG-A-
1 TTTTTTTTGAAT
10394 TTTTTTTTGAAT
1 TTTTTTTTGAAT
10406 TTTTTTTTGAAT
1 TTTTTTTTGAAT
10418 TT
1 TT
10420 CTTCTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
12 14 0.58
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:11981 original size:30 final size:30
Alignment explanation
Indices: 11947--12043 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
11937 TAAACTAAAA
11947 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
11977 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
12007 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
12037 TGAGCTA
1 TGAGCTA
12044 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Done.