Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3618
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: 48769
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2165 original size:16 final size:17
Alignment explanation
Indices: 2144--2184 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
2134 CTTCTTCTTC
2144 TTTTTTCAC-AAATTTT
1 TTTTTTCACGAAATTTT
2160 TTTTTTCACGAAATTTT
1 TTTTTTCACGAAATTTT
2177 TTTTTTCA
1 TTTTTTCA
2185 ACTTGATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTTTCACGAAATTTT
Found at i:3903 original size:16 final size:15
Alignment explanation
Indices: 3878--3915 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
3868 ATGCAATATA
3878 TTTTTTTTTTCAATT
1 TTTTTTTTTTCAATT
*
3893 TTTTTTCTTTTCGATT
1 TTTTTT-TTTTCAATT
3909 TTTTTTT
1 TTTTTTT
3916 GAAAACTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTCAATT
Found at i:7938 original size:26 final size:27
Alignment explanation
Indices: 7909--7959 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
7899 ACAAGTGAGG
7909 AAAAAGAAAAAGAGA-TGAAAAAGAGC
1 AAAAAGAAAAAGAGAGTGAAAAAGAGC
* **
7935 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAGTGAAAAAGA
7960 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAGTGAAAAAGAGC
Found at i:9591 original size:327 final size:327
Alignment explanation
Indices: 8997--9654 Score: 1210
Period size: 327 Copynumber: 2.0 Consensus size: 327
8987 TTTTTGAGGA
8997 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAAATAAA
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAAATAAA
*
9062 GATTCACTTTCTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGT
66 GATTCACTTTCTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGC
* *
9127 GTTTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATCT
**
9192 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGTGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCATCAACGACCCAATTTCGGTAGGAGATGGAT
* *
9257 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCTAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCAAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
9322 AT
326 AT
*
9324 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAG-AAAATCAA
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAAATAAA
*
9388 GATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAG
66 GATTCACTTTC-TGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAG
9453 CGATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATC
130 CGATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATC
*
9518 TTGTAGCCAAAGCGCGTTGGATCTCCATTACGAGCATCAACGACCCAATTTCGGTAGGAGATGGA
195 TTGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCATCAACGACCCAATTTCGGTAGGAGATGGA
9583 TCACAAGCCCAAATTCTTAAAGGCAAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCA
260 TCACAAGCCCAAATTCTTAAAGGCAAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCA
9648 TAT
325 TAT
9651 GATA
1 GATA
9655 TTCTTGTTTG
Statistics
Matches: 320, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
326 18 0.06
327 302 0.94
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (327 bp):
GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAAATAAA
GATTCACTTTCTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGC
GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATCT
TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCATCAACGACCCAATTTCGGTAGGAGATGGAT
CACAAGCCCAAATTCTTAAAGGCAAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
AT
Found at i:11653 original size:9 final size:9
Alignment explanation
Indices: 11641--11668 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11631 CCAAGATTTC
11641 AAATCTTGG
1 AAATCTTGG
11650 AAATCTTGG
1 AAATCTTGG
11659 AAATCTTGG
1 AAATCTTGG
11668 A
1 A
11669 TTACAAGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (9 bp):
AAATCTTGG
Found at i:14412 original size:29 final size:29
Alignment explanation
Indices: 14375--14447 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
14365 TTAGATATTA
* *
14375 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
14404 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
14433 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
14448 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:20398 original size:10 final size:10
Alignment explanation
Indices: 20383--20420 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
20373 TGTAGATTCA
20383 AAAAAAATCG
1 AAAAAAATCG
20393 AAAAAAAATCG
1 -AAAAAAATCG
*
20404 AAAAAAATTG
1 AAAAAAATCG
20414 AAAAAAA
1 AAAAAAA
20421 AATTTGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (10 bp):
AAAAAAATCG
Found at i:20433 original size:11 final size:11
Alignment explanation
Indices: 20382--20421 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
20372 TTGTAGATTC
20382 AAAAAAAATCG
1 AAAAAAAATCG
20393 AAAAAAAATCG
1 AAAAAAAATCG
*
20404 -AAAAAAATTG
1 AAAAAAAATCG
20414 AAAAAAAA
1 AAAAAAAA
20422 ATTTGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:20436 original size:13 final size:13
Alignment explanation
Indices: 20404--20437 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
20394 AAAAAAATCG
20404 AAAAAAA-TTGAA
1 AAAAAAATTTGAA
20416 AAAAAAATTTGAA
1 AAAAAAATTTGAA
20429 AAAAAAATT
1 AAAAAAATT
20438 GCATACGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (13 bp):
AAAAAAATTTGAA
Found at i:28814 original size:11 final size:11
Alignment explanation
Indices: 28800--28840 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
28790 AAAATTTTTC
*
28800 TTTTTTCAATTT
1 TTTTTTCGA-TT
28812 TTTTTCTCGATT
1 TTTTT-TCGATT
28824 TTTTTTCGATT
1 TTTTTTCGATT
28835 TTTTTT
1 TTTTTT
28841 TTGAATCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 12 0.44
12 12 0.44
13 3 0.11
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTTTTCGATT
Found at i:30349 original size:20 final size:19
Alignment explanation
Indices: 30326--30390 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
30316 AAGCTCAAAC
30326 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
30346 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
30366 AAGCTTATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
30386 GAGCT
1 GAGCT
30391 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:36031 original size:11 final size:10
Alignment explanation
Indices: 36006--36066 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
35996 ACCAATAAAA
36006 TAAA-TGAGC
1 TAAATTGAGC
*
36015 TGAATTGTAGC
1 TAAATTG-AGC
36026 TAAATTGAGC
1 TAAATTGAGC
**
36036 TCGATTGAGC
1 TAAATTGAGC
36046 TGAAA-TGAGC
1 T-AAATTGAGC
*
36056 TCAATTGAGC
1 TAAATTGAGC
36066 T
1 T
36067 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:36067 original size:20 final size:20
Alignment explanation
Indices: 36007--36067 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
35997 CCAATAAAAT
*
36007 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
36027 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
36048 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
36068 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:39884 original size:15 final size:15
Alignment explanation
Indices: 39866--39899 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39856 AAAGGAGTTC
39866 AAAAAAAA-TCAAAA
1 AAAAAAAATTCAAAA
39880 TAAAAAAAATTCAAAA
1 -AAAAAAAATTCAAAA
39896 AAAA
1 AAAA
39900 TTGAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAAAATTCAAAA
Found at i:39885 original size:16 final size:15
Alignment explanation
Indices: 39866--39899 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
39856 AAAGGAGTTC
39866 AAAAAAAATCAAAATA
1 AAAAAAAATCAAAA-A
*
39882 AAAAAAATTCAAAAA
1 AAAAAAAATCAAAAA
39897 AAA
1 AAA
39900 TTGAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAAAATCAAAAA
Found at i:39892 original size:26 final size:27
Alignment explanation
Indices: 39863--39915 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
39853 AAAAAAGGAG
*
39863 TTCAAAAAAAA-TCAAAATAAAAAAAA
1 TTCAAAAAAAATTCAAAAGAAAAAAAA
*
39889 TTCAAAAAAAATTGAAAAGAAAAAAAA
1 TTCAAAAAAAATTCAAAAGAAAAAAAA
39916 ATTGCATACG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (27 bp):
TTCAAAAAAAATTCAAAAGAAAAAAAA
Found at i:39912 original size:28 final size:26
Alignment explanation
Indices: 39863--39918 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
39853 AAAAAAGGAG
*
39863 TTCAAAAAAAATCAAAATAAAAAAAA
1 TTCAAAAAAAATCAAAAAAAAAAAAA
*
39889 TTCAAAAAAAATTGAAAAGAAAAAAAAA
1 TTCAAAAAAAA-TCAAAA-AAAAAAAAA
39917 TT
1 TT
39919 GCATACGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 11 0.42
27 5 0.19
28 10 0.38
ACGTcount: A:0.73, C:0.05, G:0.04, T:0.18
Consensus pattern (26 bp):
TTCAAAAAAAATCAAAAAAAAAAAAA
Done.