Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1584
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: 49688
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2291 original size:25 final size:25
Alignment explanation
Indices: 2257--2306 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2247 CAATTGGTAA
*
2257 GTTTAAGTTCTTTATACAAGTCATAT
1 GTTTAAGTTCCTTATACAAG-CATAT
*
2283 GTTT-AGTTCCTTATACGAGCATAT
1 GTTTAAGTTCCTTATACAAGCATAT
2307 TAGCACTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 13 0.59
26 4 0.18
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (25 bp):
GTTTAAGTTCCTTATACAAGCATAT
Found at i:5826 original size:22 final size:23
Alignment explanation
Indices: 5801--5843 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5791 TTTGATTCAT
*
5801 CTTTTTC-CTATTTTTTTTTGAA
1 CTTTTTCTCTACTTTTTTTTGAA
*
5823 CTTTTTCTCTGCTTTTTTTTG
1 CTTTTTCTCTACTTTTTTTTG
5844 CATAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.07, C:0.16, G:0.07, T:0.70
Consensus pattern (23 bp):
CTTTTTCTCTACTTTTTTTTGAA
Found at i:6891 original size:10 final size:10
Alignment explanation
Indices: 6876--6901 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6866 AATAAATAAG
6876 TTAATTTAGC
1 TTAATTTAGC
6886 TTAATTTAGC
1 TTAATTTAGC
6896 TTAATT
1 TTAATT
6902 CTACAGCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (10 bp):
TTAATTTAGC
Found at i:21654 original size:20 final size:19
Alignment explanation
Indices: 21631--21695 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
21621 AAGCTCAAAC
21631 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
21651 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
21671 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
21691 GAGCT
1 GAGCT
21696 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:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:26955 original size:29 final size:29
Alignment explanation
Indices: 26921--26993 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
26911 ATGTATTAGT
* *
26921 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
26950 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
26979 TTAGGACATATTTAA
1 TTAGGACATATTTAA
26994 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:29098 original size:14 final size:14
Alignment explanation
Indices: 29079--29120 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
29069 TAGTTTAATG
29079 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
*
29093 ATTTTTATTTATTT
1 ATTTTTATTTTTTT
29107 ATTTCTTAGTTTTT
1 ATTT-TTA-TTTTT
29121 AAGTTAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.71
15 3 0.12
16 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:29686 original size:14 final size:15
Alignment explanation
Indices: 29667--29703 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
29657 TTATTGATGC
29667 TTAAATTAAG-TTCT
1 TTAAATTAAGCTTCT
*
29681 TTAAATTATGCTTCT
1 TTAAATTAAGCTTCT
29696 TT-AATTAA
1 TTAAATTAA
29704 ACTAGTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (15 bp):
TTAAATTAAGCTTCT
Found at i:30612 original size:11 final size:11
Alignment explanation
Indices: 30596--30653 Score: 89
Period size: 11 Copynumber: 5.0 Consensus size: 11
30586 TAGTAGTTTC
30596 TTCAAAAAAAA
1 TTCAAAAAAAA
30607 TTCAAAAAAAAAA
1 TTC--AAAAAAAA
30620 TTCAAAAAAAAA
1 TTC-AAAAAAAA
30632 TTCAAAAAAAA
1 TTCAAAAAAAA
30643 TTCAAAAAAAA
1 TTCAAAAAAAA
30654 AATTGGTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
11 22 0.49
12 12 0.27
13 11 0.24
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:30657 original size:13 final size:12
Alignment explanation
Indices: 30599--30654 Score: 96
Period size: 12 Copynumber: 4.7 Consensus size: 12
30589 TAGTTTCTTC
30599 AAAAAAAATTCAA
1 AAAAAAAATTC-A
30612 AAAAAAAATTCA
1 AAAAAAAATTCA
30624 AAAAAAAATTC-
1 AAAAAAAATTCA
30635 AAAAAAAATTCA
1 AAAAAAAATTCA
30647 AAAAAAAA
1 AAAAAAAA
30655 ATTGGTTTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.26
12 20 0.48
13 11 0.26
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:30713 original size:14 final size:15
Alignment explanation
Indices: 30694--30732 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
30684 GATATCAAGT
30694 TGAAAAAAAA-ATCG
1 TGAAAAAAAATATCG
*
30708 TGAAAAAAAATTTTCG
1 TGAAAAAAAA-TATCG
30724 TGAAAAAAA
1 TGAAAAAAA
30733 GAAGCTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
16 12 0.55
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (15 bp):
TGAAAAAAAATATCG
Found at i:36867 original size:15 final size:15
Alignment explanation
Indices: 36847--36901 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
36837 ACTCTCCTCA
*
36847 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
36862 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
36877 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
36891 TTCTTTT-TCTC
1 TTCTTTTCTCTC
36902 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:40467 original size:7 final size:7
Alignment explanation
Indices: 40455--40484 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
40445 GATTGAGAGT
40455 GAAAGAA
1 GAAAGAA
40462 GAAAGAA
1 GAAAGAA
40469 GAAAGAA
1 GAAAGAA
40476 -AAAGAA
1 GAAAGAA
40482 GAA
1 GAA
40485 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Found at i:40481 original size:20 final size:20
Alignment explanation
Indices: 40456--40520 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
40446 ATTGAGAGTG
40456 AAAGAAGAAAGAAGAAAGAA
1 AAAGAAGAAAGAAGAAAGAA
*
40476 AAAGAAGAAGAAAAGAAA-AA
1 AAAGAAGAA-AGAAGAAAGAA
** *
40496 TTAGAA-AAAGAAACAAAGAA
1 AAAGAAGAAAG-AAGAAAGAA
40516 AAAGA
1 AAAGA
40521 CGTGGAAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.03
19 7 0.20
20 20 0.57
21 7 0.20
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (20 bp):
AAAGAAGAAAGAAGAAAGAA
Found at i:40483 original size:23 final size:25
Alignment explanation
Indices: 40457--40507 Score: 54
Period size: 23 Copynumber: 2.1 Consensus size: 25
40447 TTGAGAGTGA
*
40457 AAGAAG-AAAGAAGAAAGA-AAA-AG
1 AAGAAGAAAAGAA-AAATAGAAAAAG
40480 AAGAAGAAAAGAAAAATTAGAAAAAG
1 AAGAAGAAAAGAAAAA-TAGAAAAAG
40506 AA
1 AA
40508 ACAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
23 9 0.39
24 7 0.30
25 3 0.13
26 4 0.17
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.04
Consensus pattern (25 bp):
AAGAAGAAAAGAAAAATAGAAAAAG
Found at i:40501 original size:17 final size:16
Alignment explanation
Indices: 40464--40520 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 16
40454 TGAAAGAAGA
40464 AAGAAGAAAGAAAAAG
1 AAGAAGAAAGAAAAAG
*
40480 AAGAAGAAAAGAAAAAT
1 AAGAAG-AAAGAAAAAG
* *
40497 TAGAA-AAAGAAACA-
1 AAGAAGAAAGAAAAAG
40511 AAGAA-AAAGA
1 AAGAAGAAAGA
40521 CGTGGAAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 9 0.25
15 8 0.22
16 6 0.17
17 13 0.36
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (16 bp):
AAGAAGAAAGAAAAAG
Found at i:40515 original size:14 final size:13
Alignment explanation
Indices: 40456--40520 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 13
40446 ATTGAGAGTG
*
40456 AAAGAAGAAAGAAG
1 AAAGAA-AAAGAAA
40470 AAAGAAAAAG-AA
1 AAAGAAAAAGAAA
*
40482 GAAG-AAAAGAAA
1 AAAGAAAAAGAAA
40494 AATTAGAAAAAGAAA
1 AA--AGAAAAAGAAA
40509 CAAAGAAAAAGA
1 -AAAGAAAAAGA
40521 CGTGGAAAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
11 5 0.12
12 7 0.16
13 4 0.09
14 17 0.40
15 8 0.19
16 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:41868 original size:6 final size:6
Alignment explanation
Indices: 41857--41882 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41847 AAGTTGTAAG
41857 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
41883 ATTTATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:44661 original size:23 final size:22
Alignment explanation
Indices: 44610--44661 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
44600 CCTCGTCTTT
*
44610 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
44632 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
44655 TTCTTTT
1 TTCTTTT
44662 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:44670 original size:12 final size:12
Alignment explanation
Indices: 44619--44673 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
44609 TTTCTTTTGT
44619 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
44632 -TCATTTTC-TC
1 TTCTTTTTCAAC
44642 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
44655 TTCTTTTTCAAT
1 TTCTTTTTCAAC
44667 TTCTTTT
1 TTCTTTT
44674 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:44680 original size:17 final size:18
Alignment explanation
Indices: 44655--44692 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
44645 TTTCTTCAAC
* *
44655 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
44672 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
44690 TTC
1 TTC
44693 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:48303 original size:15 final size:14
Alignment explanation
Indices: 48267--48321 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
48257 TCTATTGAGC
48267 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
48281 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
48295 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
48310 GAAAGAAAAGAA
1 GAGA-AAAAGAA
48322 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Done.