Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3414
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: 50784
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1461 original size:12 final size:11
Alignment explanation
Indices: 1419--1458 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
1409 TAGTTTCTTC
1419 AAAAAAATTCA
1 AAAAAAATTCA
1430 AAAAAAATTCA
1 AAAAAAATTCA
1441 AAAAAAATTCA
1 AAAAAAATTCA
1452 AAAAAAA
1 AAAAAAA
1459 ATTGGTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:1520 original size:15 final size:15
Alignment explanation
Indices: 1500--1537 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1490 TATCAAGTTG
1500 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
1515 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
1530 AAAAAAAA
1 AAAAAAAA
1538 AGAAGAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (15 bp):
AAAAAAAATTCGTGA
Found at i:16894 original size:18 final size:18
Alignment explanation
Indices: 16871--16906 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
16861 AAACCCTAGA
16871 ATTCTTT-TAAATCTAATT
1 ATTCTTTGT-AATCTAATT
16889 ATTCTTTGTAATCTAATT
1 ATTCTTTGTAATCTAATT
16907 TTTTAATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTCTTTGTAATCTAATT
Found at i:18200 original size:34 final size:34
Alignment explanation
Indices: 18162--18253 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 34
18152 TAAAGTCATG
18162 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
*
18196 CATTA---AA--TT-AAGTTAAGTT-AGTTT--A-
1 CATTATGTAACTTTCATGTT-AGTTAAGTTTGCAT
*
18221 -ATTATGTAACTTTCATGTTAGTTAAATTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
18254 TTCAAAACCA
Statistics
Matches: 44, Mismatches: 3, Indels: 23
0.63 0.04 0.33
Matches are distributed among these distances:
24 4 0.09
26 1 0.02
27 2 0.05
28 9 0.20
29 12 0.27
30 8 0.18
31 2 0.05
32 1 0.02
34 5 0.11
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.47
Consensus pattern (34 bp):
CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
Found at i:19589 original size:11 final size:12
Alignment explanation
Indices: 19568--19616 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
19558 ATAGTAGTTT
19568 CTCGAAAAAAAA
1 CTCGAAAAAAAA
19580 CTCGAAAAAAAAA
1 CTCG-AAAAAAAA
* *
19593 TTCAAAAAAAAA
1 CTCGAAAAAAAA
*
19605 TTCGAAAAAAAA
1 CTCGAAAAAAAA
19617 ACTAGTTTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 23 0.70
13 10 0.30
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.12
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:19590 original size:13 final size:13
Alignment explanation
Indices: 19568--19619 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
19558 ATAGTAGTTT
19568 CTCG-AAAAAAAA
1 CTCGAAAAAAAAA
19580 CTCGAAAAAAAAA
1 CTCGAAAAAAAAA
*
19593 TTC-AAAAAAAAA
1 CTCGAAAAAAAAA
*
19605 TTCGAAAAAAAAA
1 CTCGAAAAAAAAA
19618 CT
1 CT
19620 AGTTTCCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
12 16 0.44
13 20 0.56
ACGTcount: A:0.67, C:0.13, G:0.06, T:0.13
Consensus pattern (13 bp):
CTCGAAAAAAAAA
Found at i:19676 original size:13 final size:13
Alignment explanation
Indices: 19658--19708 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
19648 TATCAAGTTG
19658 TGAAAAAAAATTT
1 TGAAAAAAAATTT
*
19671 TGAAAAAAAAAATTG
1 TG--AAAAAAAATTT
*
19686 TGAAAAAAAA-AT
1 TGAAAAAAAATTT
19698 TGAGAAAAAAA
1 TGA-AAAAAAA
19709 AGAGAGCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 3 0.09
13 17 0.53
15 12 0.38
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.20
Consensus pattern (13 bp):
TGAAAAAAAATTT
Found at i:19679 original size:14 final size:14
Alignment explanation
Indices: 19655--19709 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
19645 GGATATCAAG
19655 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
*
19668 TTTTGAAAAAAAAAA
1 TTGTG-AAAAAAAAA
19683 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
*
19697 TTGAGAAAAAAAA
1 TTGTGAAAAAAAA
19710 GAGAGCTAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.11
14 21 0.57
15 12 0.32
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.22
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:19680 original size:15 final size:15
Alignment explanation
Indices: 19660--19709 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
19650 TCAAGTTGTG
*
19660 AAAAAAAATTTTGAA
1 AAAAAAAATTGTGAA
19675 AAAAAAAATTGTG-A
1 AAAAAAAATTGTGAA
*
19689 AAAAAAAATTGAGAA
1 AAAAAAAATTGTGAA
19704 AAAAAA
1 AAAAAA
19710 GAGAGCTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (15 bp):
AAAAAAAATTGTGAA
Found at i:24861 original size:326 final size:326
Alignment explanation
Indices: 24268--24906 Score: 825
Period size: 326 Copynumber: 2.0 Consensus size: 326
24258 AAATGATAGA
* * * *
24268 GGGTTGCGAGCGGATCAAGATTGAGTTGTCAAGTCACGGAAAACTCTTACGAAAACTCTGAACGA
1 GGGTTGCGAGCGGACCAAGATCGAGTTGTCAAGTCACGGAAAACTCCTACGAAAACTCTAAACGA
* * * * * * **
24333 ATGGATCTGAAACGAAACAGAGAATTAATATTAGATTCGATTAGATCTAAAAATGAAAATTCCCA
66 ATGGATCTGAAACGAAACAGAAAATTAAGATTACAATCAATTAGATCTAAAAACGAAAACACCCA
* * * *
24398 AATCAAGAAAGGAACAGCAAGGATCAAACACACTTAGGGATGACTAATCTTGGAAGCCAAGAACA
131 AATCAAGAAAAGAACAGCAAGAATCAAAAACACTTAGGAATGACTAATCTTGGAAGCCAAGAACA
*** * * * * *
24463 CGAGATTGCGTTCAAGGTAGGCTCCAATCTGTCGAATCTGAAAAGAATAACACAAAACAGCAAGT
196 CGAGATTAAATTCAAGATAGGCTCCAAACAGCCGAATCTGAAAAGAAGAACACAAAACAGCAAGT
* * *
24528 TAATTTCAAAAAAACTCAGCAGATCACGAAATTAACTAGATTTAGGGTTTGGAAGGTTGATCTAG
261 TAATTTCAAAAAAACTCAGCAAATCACGAAATCAACTAGATCTAGGGTTTGGAAGGTTGATCTAG
24593 G
326 G
* * * * * *
24594 GGGTTGCGCGTGGACCAAGATCGAGTTGTCAAGTCAGGGCAAACTCCTACTAAAACTCTAAACGC
1 GGGTTGCGAGCGGACCAAGATCGAGTTGTCAAGTCACGGAAAACTCCTACGAAAACTCTAAACGA
* ** * *
24659 TTGGATCTGAAACGAAACAGAAAATTCGGCTTACAATCAATTAGATCT-GAAACGAAAACACCCA
66 ATGGATCTGAAACGAAACAGAAAATTAAGATTACAATCAATTAGATCTAAAAACGAAAACACCCA
* * * *
24723 AATCAATAAAAGATCAGCCAAGAATTAAAAACACTTATGAAT-AGCTAATCTTGGAAGCCAAGAA
131 AATCAAGAAAAGAACAG-CAAGAATCAAAAACACTTAGGAATGA-CTAATCTTGGAAGCCAAGAA
* *
24787 CACG-GAATTAAATTCAAGATAGGTTCCAAACAGCCGAATCTGAAAAGAGGAACACAAAACAGCA
194 CACGAG-ATTAAATTCAAGATAGGCTCCAAACAGCCGAATCTGAAAAGAAGAACACAAAACAGCA
*
24851 AGTTAATTTCAAAAAAACTCAGCAAATCACGAAATCAATTAGATCTAGGGTTTGGA
258 AGTTAATTTCAAAAAAACTCAGCAAATCACGAAATCAACTAGATCTAGGGTTTGGA
24907 CGGCAATAAA
Statistics
Matches: 265, Mismatches: 45, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
325 28 0.11
326 237 0.89
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (326 bp):
GGGTTGCGAGCGGACCAAGATCGAGTTGTCAAGTCACGGAAAACTCCTACGAAAACTCTAAACGA
ATGGATCTGAAACGAAACAGAAAATTAAGATTACAATCAATTAGATCTAAAAACGAAAACACCCA
AATCAAGAAAAGAACAGCAAGAATCAAAAACACTTAGGAATGACTAATCTTGGAAGCCAAGAACA
CGAGATTAAATTCAAGATAGGCTCCAAACAGCCGAATCTGAAAAGAAGAACACAAAACAGCAAGT
TAATTTCAAAAAAACTCAGCAAATCACGAAATCAACTAGATCTAGGGTTTGGAAGGTTGATCTAG
G
Found at i:25020 original size:35 final size:35
Alignment explanation
Indices: 24974--25042 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
24964 CCGAATAGAA
24974 TCTTGAAGGTTGAACAGGGCTGGAGAGGCGACAAT
1 TCTTGAAGGTTGAACAGGGCTGGAGAGGCGACAAT
*
25009 TCTTGAAGGTTGAATAGGGCTGGAGAGGCGACAA
1 TCTTGAAGGTTGAACAGGGCTGGAGAGGCGACAA
25043 GAGAGTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.13, G:0.38, T:0.20
Consensus pattern (35 bp):
TCTTGAAGGTTGAACAGGGCTGGAGAGGCGACAAT
Found at i:31177 original size:18 final size:18
Alignment explanation
Indices: 31154--31188 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31144 TTTTTCCTTT
31154 TCAATTTCTTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
31172 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
31189 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:32198 original size:30 final size:30
Alignment explanation
Indices: 32164--32220 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
32154 TCGATTTTTT
*
32164 TTCTCACTTTTTTTTTGAATTTTTTTAACA
1 TTCTCACTCTTTTTTTGAATTTTTTTAACA
*
32194 TTCTCTCTCTTTTTTTGAATTTTTTTA
1 TTCTCACTCTTTTTTTGAATTTTTTTA
32221 TAATTTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.16, C:0.14, G:0.04, T:0.67
Consensus pattern (30 bp):
TTCTCACTCTTTTTTTGAATTTTTTTAACA
Found at i:39730 original size:21 final size:21
Alignment explanation
Indices: 39704--39766 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
39694 TTGGTATTTG
39704 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
39725 GGAATTGGTATGAAGTGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
39746 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
39767 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:43617 original size:12 final size:12
Alignment explanation
Indices: 43597--43655 Score: 84
Period size: 12 Copynumber: 5.0 Consensus size: 12
43587 TACTAGTTTC
*
43597 TTCAAAAAAAAT
1 TTCAAAAAAAAA
*
43609 TTGAAAAAAAAA
1 TTCAAAAAAAAA
43621 TTCAAAAAAAAA
1 TTCAAAAAAAAA
43633 -TCAAAAAAAAA
1 TTCAAAAAAAAA
*
43644 TTGAAAAAAAAA
1 TTCAAAAAAAAA
43656 GAGAGCTAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
11 11 0.26
12 31 0.74
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:43627 original size:11 final size:11
Alignment explanation
Indices: 43597--43654 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 11
43587 TACTAGTTTC
43597 TTCAAAAAAAA
1 TTCAAAAAAAA
*
43608 TTTGAAAAAAAAA
1 -TT-CAAAAAAAA
43621 TTCAAAAAAAA
1 TTCAAAAAAAA
*
43632 ATCAAAAAAAAA
1 TTC-AAAAAAAA
*
43644 TTGAAAAAAAA
1 TTCAAAAAAAA
43655 AGAGAGCTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 18 0.46
12 13 0.33
13 8 0.21
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.17
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:44605 original size:10 final size:11
Alignment explanation
Indices: 44579--44605 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
44569 AGAGACGAGA
44579 GAAAAAGAAAC
1 GAAAAAGAAAC
44590 GAAAAAGAAAC
1 GAAAAAGAAAC
44601 GAAAA
1 GAAAA
44606 TTGAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAC
Done.