Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2502
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: 16138
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Found at i:439 original size:20 final size:20
Alignment explanation
Indices: 392--462 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
382 AAAAAGACAT
*
392 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
411 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
432 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
452 AATGTATCGAT
1 AATGTATCGAT
463 CTACATCAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1119 original size:28 final size:28
Alignment explanation
Indices: 1069--2184 Score: 1052
Period size: 29 Copynumber: 38.6 Consensus size: 28
1059 CACCAACTCG
* *
1069 TGTGGGCTTTGAAAAGAGTGCCACTAAACT
1 TGTGGGCTTTG-AAAGGGTGCCACT-GACT
1099 TGT-GGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1126 TGTGGGCTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
** *
1155 TGTGGGCTTTGAAAAGATTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1184 TGTGGGCTTTGAAAAGAGTACCACTGAC-
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1212 TGT-GGCTTTGAAAGGGTGCCACTGACAT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
* * *
1240 CGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1269 TGCGGGCTTTGAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1297 TGT-GGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1324 TGTGGTCTTTGAAAAGAGTTGCCACTGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
1354 TGTGGGCTTTGACAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1382 TGTGGGCTTTGTGAAAGGGTGCCACTAACTT
1 TGTGGGC-TT-TGAAAGGGTGCCACTGAC-T
*
1413 TGTGGTGCTTTGAAAGGGTGCCACTTACT
1 TGTGG-GCTTTGAAAGGGTGCCACTGACT
1442 TGCGTGGGCTTTGAAAAGGGTGCCACTGAC-
1 T--GTGGGCTTTG-AAAGGGTGCCACTGACT
1472 TGTGGGC-TTGAAA-GG-GCCACTGATTAGCT
1 TGTGGGCTTTGAAAGGGTGCCACTG---A-CT
* * * * *
1501 GGTGGGCTTTGAAAAAAGTTACCACCGACT
1 TGTGGGCTTTG--AAAGGGTGCCACTGACT
*
1531 CGTGTGGGCTTTGAAAAGAGTGCCACTGGACT
1 --TGTGGGCTTTG-AAAGGGTGCCACT-GACT
1563 TGTGGGTCTTTGAAAGGGGTGCCACTGACT
1 TGTGGG-CTTTGAAA-GGGTGCCACTGACT
*
1593 TGTGGGCTTTGAAAGGGGGTGCCACTGTCT
1 TGTGGGCTTTGAAA--GGGTGCCACTGACT
* * *
1623 TGTGAGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
1652 TGTGGGCTTTAAAAGGGTGTGCCACTAATTT
1 TGTGGGCTTTGAAA-GG-GTGCCACTGA-CT
1683 TGCGTGGGCTTTGAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
1713 TGTGGGGCTTTGAAAGGGTGCCACTGACT
1 TGT-GGGCTTTGAAAGGGTGCCACTGACT
* *
1742 TGT-GACTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1770 TGTGGGCTTTGAAA-GGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1797 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1825 CGT-GGC-TTG-AATGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1850 TGTGGGCTTTGAATGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1878 CGTGGGCTTTGAAA-AGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1905 TGCGTGGGCTTTTAAAAGGAGTGCCACTACTGACTT
1 T--GTGGGC-TTTGAAAGG-GTG-C-C-ACTGAC-T
1941 ATGTGGGCTTTGAAAGGGTTGCCCACTGACT
1 -TGTGGGCTTTGAAAGGG-TG-CCACTGACT
*
1972 TGTTGGGCTTTG-AAGAGTGCCACTGACT
1 TG-TGGGCTTTGAAAGGGTGCCACTGACT
* * *
2000 TGTGGGCTTCG-CAGGGT-TC-CTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2025 TGTGGGCTTCGAAAGGGTGCCACTGATTCCT
1 TGTGGGCTTTGAAAGGGTGCCACTGA---CT
* *
2056 TATTGGGCATTG-AAGGGTGCC-CTGACT
1 T-GTGGGCTTTGAAAGGGTGCCACTGACT
*
2083 TGTGGGCTTTGAAAGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
2111 TGT-GGCTTTGAAAGGGTGCCACTCTGACT
1 TGTGGGCTTTGAAAGGGTGCCA--CTGACT
* *
2140 TGTGGGC-TTGAAAAAGAGTGCCACTGATT
1 TGTGGGCTTTG--AAAGGGTGCCACTGACT
2169 TGTGGGCTTTGAAAGG
1 TGTGGGCTTTGAAAGG
2185 AATGATAATT
Statistics
Matches: 923, Mismatches: 91, Indels: 146
0.80 0.08 0.13
Matches are distributed among these distances:
24 7 0.01
25 35 0.04
26 37 0.04
27 132 0.14
28 166 0.18
29 204 0.22
30 161 0.17
31 97 0.11
32 37 0.04
33 16 0.02
34 18 0.02
35 11 0.01
36 1 0.00
37 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:1947 original size:35 final size:33
Alignment explanation
Indices: 1908--1982 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 33
1898 ATTGACTTGC
1908 GTGGGCTTTTAAAAGGAG-TGCCACTACTGACTTAT
1 GTGGGCTTTTAAAAGG-GTTGCC-C-ACTGACTTAT
* *
1943 GTGGGC-TTTGAAAGGGTTGCCCACTGACTTGT
1 GTGGGCTTTTAAAAGGGTTGCCCACTGACTTAT
1975 -TGGGCTTT
1 GTGGGCTTT
1983 GAAGAGTGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
31 5 0.14
32 11 0.31
33 2 0.06
34 12 0.33
35 6 0.17
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (33 bp):
GTGGGCTTTTAAAAGGGTTGCCCACTGACTTAT
Found at i:3423 original size:13 final size:11
Alignment explanation
Indices: 3396--3462 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 11
3386 GACCCTTCTA
3396 TTTTTTTGCTATT
1 TTTTTTTG-T-TT
3409 TTTTCTTGTGTTT
1 TTTT-TT-TGTTT
3422 TTTTTTTGTTTT
1 TTTTTTTG-TTT
3434 TTTGTTTTGTTT
1 TTT-TTTTGTTT
*
3446 CTTTTTTTATTT
1 -TTTTTTTGTTT
3458 TTTTT
1 TTTTT
3463 GGGGTGTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
11 7 0.15
12 18 0.38
13 18 0.38
14 3 0.06
15 2 0.04
ACGTcount: A:0.03, C:0.04, G:0.09, T:0.84
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:3434 original size:24 final size:25
Alignment explanation
Indices: 3396--3461 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
3386 GACCCTTCTA
3396 TTTTTTTGCTATTTTTTCTTGTGTTT-
1 TTTTTTTG-T-TTTTTTCTTGTGTTTC
* *
3422 TTTTTTTGTTTTTTTGTTTTGTTTC
1 TTTTTTTGTTTTTTTCTTGTGTTTC
*
3447 TTTTTTTATTTTTTT
1 TTTTTTTGTTTTTTT
3462 TGGGGTGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.36
25 15 0.42
26 8 0.22
ACGTcount: A:0.03, C:0.05, G:0.09, T:0.83
Consensus pattern (25 bp):
TTTTTTTGTTTTTTTCTTGTGTTTC
Found at i:3435 original size:8 final size:8
Alignment explanation
Indices: 3422--3461 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
3412 TCTTGTGTTT
3422 TTTTTTTG
1 TTTTTTTG
3430 TTTTTTTG
1 TTTTTTTG
*
3438 TTTTGTTTC
1 TTTT-TTTG
*
3447 TTTTTTTA
1 TTTTTTTG
3455 TTTTTTT
1 TTTTTTT
3462 TGGGGTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.76
9 7 0.24
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:13231 original size:11 final size:11
Alignment explanation
Indices: 13215--13247 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
13205 TAGGGAAAAA
13215 GGTTTTTTTTT
1 GGTTTTTTTTT
13226 GGTTTTTTTTT
1 GGTTTTTTTTT
*
13237 TGTTTTTTTTT
1 GGTTTTTTTTT
13248 CTTTCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
GGTTTTTTTTT
Found at i:13234 original size:12 final size:11
Alignment explanation
Indices: 13216--13260 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
13206 AGGGAAAAAG
*
13216 GTTTTTTTTTG
1 GTTTTTTTTTT
13227 GTTTTTTTTTT
1 GTTTTTTTTTT
13238 GTTTTTTTTTCT
1 GTTTTTTTTT-T
13250 -TTCTTTTTTTT
1 GTT-TTTTTTTT
13261 AGGATTAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 23 0.74
12 8 0.26
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:13245 original size:14 final size:14
Alignment explanation
Indices: 13228--13260 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13218 TTTTTTTTGG
*
13228 TTTTTTT-TTTGTT
1 TTTTTTTCTTTCTT
13241 TTTTTTTCTTTCTT
1 TTTTTTTCTTTCTT
13255 TTTTTT
1 TTTTTT
13261 AGGATTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (14 bp):
TTTTTTTCTTTCTT
Found at i:13256 original size:22 final size:22
Alignment explanation
Indices: 13216--13259 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
13206 AGGGAAAAAG
*
13216 GTTTTTTTTTGGTTTTTTTTTT
1 GTTTTTTTTTGCTTTTTTTTTT
13238 GTTTTTTTTT-CTTTCTTTTTTT
1 GTTTTTTTTTGCTTT-TTTTTTT
13260 TAGGATTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (22 bp):
GTTTTTTTTTGCTTTTTTTTTT
Found at i:15523 original size:22 final size:23
Alignment explanation
Indices: 15481--15536 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
15471 TGGACATGTT
*
15481 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACACAATAAA
15504 AAAAATGCATGAAAC-CAATAAA
1 AAAAATGCATGAAACACAATAAA
15526 AAAAATGCATG
1 AAAAATGCATG
15537 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (23 bp):
AAAAATGCATGAAACACAATAAA
Done.