Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2339
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: 54204
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1876 original size:23 final size:23
Alignment explanation
Indices: 1844--1887 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1834 GATTGAGAGT
1844 GAAAAAGAATT-GAAGAAAGAAGA
1 GAAAAAGAATTAGAA-AAAGAAGA
*
1867 GAAAATGAATTAGAAAAAGAA
1 GAAAAAGAATTAGAAAAAGAA
1888 ACAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (23 bp):
GAAAAAGAATTAGAAAAAGAAGA
Found at i:6809 original size:30 final size:30
Alignment explanation
Indices: 6775--6857 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 30
6765 TAAACTAAAA
* *
6775 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
6805 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
*
6835 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGATTTAGCTCGTGAG
6858 TTGAAAATGA
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:10711 original size:30 final size:31
Alignment explanation
Indices: 10668--10750 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
10658 CTTTTGTTTC
*
10668 AATTTCTTTTTCA-TCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCATTC-TCTTTTTCAATCTCA
10699 AATTTC-TTTTCATTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATTCTCTTTTTCAATCTCA
* * * *
10728 ATTTTATTTTTCTTTTTCTTTTT
1 AATTTCTTTTTCATTCTCTTTTT
10751 TCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.09
30 33 0.73
31 8 0.18
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.65
Consensus pattern (31 bp):
AATTTCTTTTTCATTCTCTTTTTCAATCTCA
Found at i:10768 original size:12 final size:12
Alignment explanation
Indices: 10753--10783 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
10743 TTCTTTTTTC
10753 TTTTCAAAGGCT
1 TTTTCAAAGGCT
10765 TTTTCAAAGGCT
1 TTTTCAAAGGCT
10777 TTTTCAA
1 TTTTCAA
10784 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:10853 original size:6 final size:5
Alignment explanation
Indices: 10831--10888 Score: 57
Period size: 5 Copynumber: 11.0 Consensus size: 5
10821 CTCTTGCCTC
10831 TCTTT TCTTT T-TATT TCATTT TCTTT T-TTCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTT-T TCTTT T-C-TTT TCTTT
10879 TCTTT TCTTT
1 TCTTT TCTTT
10889 GTTTTCTCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
4 3 0.07
5 30 0.65
6 8 0.17
7 5 0.11
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:10854 original size:16 final size:14
Alignment explanation
Indices: 10831--10895 Score: 67
Period size: 16 Copynumber: 4.2 Consensus size: 14
10821 CTCTTGCCTC
10831 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
10846 TCATTTTCTTTTTTCT
1 TC-TTTTCTTTTTT-T
10862 TCTTTTGCTTTTTCTTT
1 TCTTTT-C-TTTT-TTT
*
10879 TCTTTTCTTTGTTT
1 TCTTTTCTTTTTTT
10893 TCT
1 TCT
10896 CTTTACAAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
14 6 0.14
15 10 0.23
16 15 0.34
17 11 0.25
18 2 0.05
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:10889 original size:21 final size:21
Alignment explanation
Indices: 10831--10899 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
10821 CTCTTGCCTC
* *
10831 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
10852 TCTTTT-TTCTTCTTTTGCTTTT
1 TCTTTTCTT-TTC-TTTGCTTTT
10874 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
10894 CTCTTT
1 -TCTTT
10900 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 6 0.15
21 17 0.41
22 15 0.37
23 3 0.07
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:12977 original size:17 final size:17
Alignment explanation
Indices: 12936--12978 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
12926 TGCACTTAAG
12936 CCATTCATGCATTCTAT
1 CCATTCATGCATTCTAT
12953 -CATCTCATGCATT-TGAT
1 CCAT-TCATGCATTCT-AT
12970 CCATTCATG
1 CCATTCATG
12979 GACTAGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 16 0.70
18 3 0.13
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (17 bp):
CCATTCATGCATTCTAT
Found at i:13397 original size:30 final size:30
Alignment explanation
Indices: 13363--13459 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
13353 TAAACTAAAA
13363 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
13393 TGAGCTGAGGC-TAAACTCCTAAGCTAAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
13423 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
13453 TGAGCTA
1 TGAGCTA
13460 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.83
31 7 0.13
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:19410 original size:14 final size:14
Alignment explanation
Indices: 19363--19410 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
19353 GTACGAATGG
*
19363 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
19377 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
19391 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
19405 ATTGGT
1 AATGGT
19411 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:20865 original size:20 final size:20
Alignment explanation
Indices: 20819--20865 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20809 AGCTCGTTTC
*
20819 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
20839 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
20859 CAGCTCA
1 CAGCTCA
20866 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:22631 original size:20 final size:20
Alignment explanation
Indices: 22608--22654 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
22598 GGGTTAAGAT
*
22608 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
22628 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
22648 TGAGCTG
1 TGAGCTG
22655 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:24375 original size:48 final size:48
Alignment explanation
Indices: 24323--24428 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
24313 TTGTCTTTTC
*
24323 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
24371 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
24419 TTTCTTTTTC
1 TTTCTTTTTC
24429 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:25532 original size:15 final size:16
Alignment explanation
Indices: 25514--25546 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25504 TTTTTTTCCC
25514 TTTTTTT-AAAATTTT
1 TTTTTTTCAAAATTTT
*
25529 TTTTTTTCTAAATTTT
1 TTTTTTTCAAAATTTT
25545 TT
1 TT
25547 CTCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTTCAAAATTTT
Found at i:27067 original size:20 final size:20
Alignment explanation
Indices: 27044--27090 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
27034 GGGTTAAGAT
27044 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
* *
27064 TGAGTTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
27084 TGAGCTG
1 TGAGCTG
27091 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.32
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTTGAG
Found at i:28321 original size:10 final size:10
Alignment explanation
Indices: 28273--28321 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
28263 TACTCCTTCA
*
28273 AGCTCAAATT
1 AGCTCAACTT
* *
28283 AGCTCAAATC
1 AGCTCAACTT
28293 AGCTCAACTT
1 AGCTCAACTT
*
28303 CAACTCAACTT
1 -AGCTCAACTT
28314 AGCTCAAC
1 AGCTCAAC
28322 GAGCTCGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.37, C:0.31, G:0.08, T:0.24
Consensus pattern (10 bp):
AGCTCAACTT
Found at i:36731 original size:6 final size:6
Alignment explanation
Indices: 36720--36755 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
36710 TGCAATGCTG
36720 ATAAAA AT-AAA AT-AAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT
36756 TCAATTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:36736 original size:11 final size:11
Alignment explanation
Indices: 36720--36753 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
36710 TGCAATGCTG
36720 ATAAAAATAAA
1 ATAAAAATAAA
36731 AT-AAAATAAAA
1 ATAAAAAT-AAA
36742 ATAAAAATAAA
1 ATAAAAATAAA
36753 A
1 A
36754 ATTCAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:41319 original size:18 final size:20
Alignment explanation
Indices: 41264--41319 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 20
41254 TTTCAATCTC
41264 ATCACTCATTTCTTTTTCTTTGA
1 ATCACTCA--TCTTTTTCTTT-A
41287 ATCACTC-TCTCTTTT-TTT-
1 ATCACTCATCT-TTTTCTTTA
41305 ATCACTCATCTTTTT
1 ATCACTCATCTTTTT
41320 GTTTTTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
18 11 0.35
19 3 0.10
20 6 0.19
21 4 0.13
23 7 0.23
ACGTcount: A:0.16, C:0.25, G:0.02, T:0.57
Consensus pattern (20 bp):
ATCACTCATCTTTTTCTTTA
Found at i:43570 original size:14 final size:13
Alignment explanation
Indices: 43550--43599 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
43540 AGACCGTATG
43550 CAATTTTTTTTTT
1 CAATTTTTTTTTT
43563 CAAATTTTTTTTTT
1 C-AATTTTTTTTTT
*
43577 -GATTTTTTTTTT
1 CAATTTTTTTTTT
*
43589 CGATTTTTTTT
1 CAATTTTTTTT
43600 GAATCTACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
12 11 0.32
13 11 0.32
14 12 0.35
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:43581 original size:12 final size:13
Alignment explanation
Indices: 43552--43599 Score: 71
Period size: 12 Copynumber: 3.7 Consensus size: 13
43542 ACCGTATGCA
*
43552 ATTTTTTTTTTCAA
1 ATTTTTTTTTTC-G
43566 ATTTTTTTTTT-G
1 ATTTTTTTTTTCG
43578 ATTTTTTTTTTCG
1 ATTTTTTTTTTCG
43591 ATTTTTTTT
1 ATTTTTTTT
43600 GAATCTACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 11 0.34
13 10 0.31
14 11 0.34
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.79
Consensus pattern (13 bp):
ATTTTTTTTTTCG
Found at i:45623 original size:14 final size:14
Alignment explanation
Indices: 45604--45643 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
45594 AGAATGGAAT
*
45604 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
45618 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
45632 GATATGAACAAA
1 GGTAGGAACAAA
45644 TTGGTCAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:47988 original size:23 final size:22
Alignment explanation
Indices: 47936--47988 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
47926 TCCACGTCTT
*
47936 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
47958 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
47981 TTTCTTTT
1 TTTCTTTT
47989 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:52509 original size:15 final size:15
Alignment explanation
Indices: 52491--52520 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52481 AATGAATAAA
52491 TATATAAAATGAAAT
1 TATATAAAATGAAAT
*
52506 TATATTAAATGAAAT
1 TATATAAAATGAAAT
52521 GGGTGATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
TATATAAAATGAAAT
Found at i:53247 original size:29 final size:30
Alignment explanation
Indices: 53203--53275 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
53193 AGTTTTACCC
53203 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
53233 AGCT-GTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
53262 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
53276 TGGCTTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 4 0.11
29 21 0.55
30 13 0.34
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Done.