Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold656
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: 53281
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2066 original size:20 final size:20
Alignment explanation
Indices: 2043--2089 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2033 GGGTTAAGAT
*
2043 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
2063 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
2083 TGAGCTG
1 TGAGCTG
2090 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:3809 original size:48 final size:47
Alignment explanation
Indices: 3754--3859 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 47
3744 TTGTCTTTTC
*
3754 TTTCTTTTTCAATTT--TCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCATCTC-TTTT--TCACATCCTTT-TTCAATCTCAA
*
3802 TTTCTTTTTCGATTTCATTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCA-TCTCTTTTTCACATCCTTTTTCAATCTCAA
3850 TTTCTTTTTC
1 TTTCTTTTTC
3860 CATGACACTC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
48 40 0.77
49 4 0.08
50 4 0.08
51 4 0.08
ACGTcount: A:0.15, C:0.25, G:0.02, T:0.58
Consensus pattern (47 bp):
TTTCTTTTTCAATTTCATCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:3858 original size:18 final size:17
Alignment explanation
Indices: 3791--3919 Score: 61
Period size: 18 Copynumber: 7.4 Consensus size: 17
3781 CACACTTTTG
3791 TTCAATCTCAATTTCTTT
1 TTCAATCTC-ATTTCTTT
* *
3809 TTCGATTTCATTCTCTTT
1 TTCAATCTCATT-TCTTT
*
3827 TTC-A---CA-TCCTTT
1 TTCAATCTCATTTCTTT
3839 TTCAATCTCAATTTCTTT
1 TTCAATCTC-ATTTCTTT
* *
3857 TTCCATGACACTCGTTTCTTT
1 TT-CA--A-TCTCATTTCTTT
* * *
3878 TACACTCTCGTTTCTTT
1 TTCAATCTCATTTCTTT
*
3895 CTTCAATCTCACTCTCTTT
1 -TTCAATCTCA-TTTCTTT
3914 TTCAAT
1 TTCAAT
3920 TTCTTGTTCC
Statistics
Matches: 85, Mismatches: 13, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
12 7 0.08
13 2 0.02
14 2 0.02
16 1 0.01
17 16 0.19
18 35 0.41
19 8 0.09
20 2 0.02
21 9 0.11
22 3 0.04
ACGTcount: A:0.17, C:0.27, G:0.03, T:0.53
Consensus pattern (17 bp):
TTCAATCTCATTTCTTT
Found at i:4897 original size:9 final size:9
Alignment explanation
Indices: 4881--4918 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
4871 GACTTTTCAC
4881 TTTT-TTTT
1 TTTTCTTTT
4889 TTTTCTTTT
1 TTTTCTTTT
*
4898 TTTACTTTT
1 TTTTCTTTT
4907 TTTTCTTTT
1 TTTTCTTTT
4916 TTT
1 TTT
4919 GCTCACTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 4 0.15
9 23 0.85
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:4904 original size:22 final size:21
Alignment explanation
Indices: 4874--4937 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
4864 CTCACAAGAC
4874 TTTTCACTTTTTTTTTTTTCTT
1 TTTTCACTTTTTTTTTTTT-TT
*
4896 TTTTTACTTTTTTTTCTTTTTT
1 TTTTCACTTTTTTTT-TTTTTT
** *
4918 TGCTCACTTCTTTTTTTTTT
1 TTTTCACTTTTTTTTTTTTT
4938 GAATTTCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.14
22 27 0.75
23 4 0.11
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCACTTTTTTTTTTTTTT
Found at i:6487 original size:20 final size:20
Alignment explanation
Indices: 6464--6510 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
6454 GGGTTAAGAT
*
6464 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
6484 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
6504 TGAGCTG
1 TGAGCTG
6511 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:8119 original size:12 final size:12
Alignment explanation
Indices: 8102--8136 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
8092 AGGAAATTTG
8102 AAAAAAAAATTC
1 AAAAAAAAATTC
8114 AAAAAAAAATTC
1 AAAAAAAAATTC
8126 AAAAAAAAATT
1 AAAAAAAAATT
8137 TTGAAGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:12684 original size:30 final size:30
Alignment explanation
Indices: 12650--12730 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
12640 TAAACTAAAA
12650 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
12680 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
12710 TGAGCTAAGGTTTAGCTCGTG
1 TGAGCTAAGCTTTAGCTCGTG
12731 TGATACGAGC
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
29 2 0.05
30 32 0.86
31 3 0.08
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:16658 original size:12 final size:13
Alignment explanation
Indices: 16636--16664 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16626 AAGTTTTATT
16636 TTTATTTTATTTA
1 TTTATTTTATTTA
16649 TTTA-TTTATTTA
1 TTTATTTTATTTA
16661 TTTA
1 TTTA
16665 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:19754 original size:12 final size:12
Alignment explanation
Indices: 19738--19769 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19728 TTTCTTTTTG
19738 CTTTTCAAAGGC
1 CTTTTCAAAGGC
*
19750 TTTTTCAAAGGC
1 CTTTTCAAAGGC
19762 CTTTTCAA
1 CTTTTCAA
19770 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (12 bp):
CTTTTCAAAGGC
Found at i:22762 original size:30 final size:30
Alignment explanation
Indices: 22728--22825 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
22718 AGCTCACTCC
22728 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
22758 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
22788 CAGCTCAACTTTAGCTCACGAGCTAAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCT-AAACCT
22819 TAGCTCA
1 TAGCTCA
22826 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.79
31 10 0.19
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:28671 original size:30 final size:30
Alignment explanation
Indices: 28637--28733 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
28627 AGCTCACTCC
28637 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
28667 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
28697 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
*
28727 TTGCTCA
1 TAGCTCA
28734 TTTTAATTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:30193 original size:5 final size:5
Alignment explanation
Indices: 30177--30252 Score: 68
Period size: 6 Copynumber: 14.6 Consensus size: 5
30167 TCTTGTAAAG
*
30177 AGAAA A-AAA AGAAA AGAAA AGAAAA AGCAAA AGCAAA AGCAAA AGAAG
1 AGAAA AGAAA AGAAA AGAAA AG-AAA AG-AAA AG-AAA AG-AAA AGAAA
30225 A-AAA AGAAAA AGAAA TA-AAA AGAAA AGA
1 AGAAA AG-AAA AGAAA -AGAAA AGAAA AGA
30253 GAGGCAAGAG
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
4 8 0.13
5 26 0.42
6 28 0.45
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.01
Consensus pattern (5 bp):
AGAAA
Found at i:30252 original size:15 final size:16
Alignment explanation
Indices: 30173--30250 Score: 72
Period size: 15 Copynumber: 4.9 Consensus size: 16
30163 ACATTCTTGT
*
30173 AAAGAGAAA-AAAAAG
1 AAAGAAAAAGAAAAAG
30188 AAA-AGAAAAGAAAAAG
1 AAAGA-AAAAGAAAAAG
* *
30204 CAAAAGCAAAAGCAAAAG
1 --AAAGAAAAAGAAAAAG
30222 -AAGAAAAAGAAAAAG
1 AAAGAAAAAGAAAAAG
*
30237 AAATAAAAAGAAAA
1 AAAGAAAAAGAAAA
30251 GAGAGGCAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 1 0.02
15 19 0.37
16 18 0.35
18 13 0.25
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.01
Consensus pattern (16 bp):
AAAGAAAAAGAAAAAG
Found at i:30360 original size:30 final size:31
Alignment explanation
Indices: 30326--30396 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
30316 AAAGCAAAAA
*
30326 GAAAAAGAAA-ATGAGATTGAAAAAG-AGAAC
1 GAAAAAGAAATATGAGAGTGAAAAAGAAG-AC
* *
30356 G-AAAAGAAATTTGAGAGTGAAAAAGAAGAT
1 GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
30386 GAAAAAGAAAT
1 GAAAAAGAAAT
30397 TGAAACAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.23
30 16 0.46
31 11 0.31
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.13
Consensus pattern (31 bp):
GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
Found at i:32533 original size:30 final size:30
Alignment explanation
Indices: 32499--32595 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
32489 AGCTCACTCC
32499 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
32529 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
32559 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
32589 TAGCTCA
1 TAGCTCA
32596 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:38806 original size:30 final size:31
Alignment explanation
Indices: 38712--38806 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 31
38702 TAAACTAAAA
* *
38712 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAAGT
* * * * *
38742 TGAGCTGAGGCTAAACTCCTAAGCTG-AAGT
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAAGT
*
38772 TGAGCTAAGGTTTAGCTCGTAAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAAGT
38802 TGAGC
1 TGAGC
38807 GAGGAGTGAG
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (31 bp):
TGAGCTAAGGTTTAGCTCGTAAGCTGAAAGT
Found at i:41388 original size:22 final size:22
Alignment explanation
Indices: 41360--41403 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41350 TTTTGAACCA
41360 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41382 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41404 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:42523 original size:15 final size:15
Alignment explanation
Indices: 42503--42536 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
42493 GTTCAACGAA
*
42503 GAGGCCAACGCAATC
1 GAGGCCAACGAAATC
42518 GAGGCCAACGAAATC
1 GAGGCCAACGAAATC
42533 GAGG
1 GAGG
42537 GAGGTTCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.32, T:0.06
Consensus pattern (15 bp):
GAGGCCAACGAAATC
Found at i:43930 original size:22 final size:22
Alignment explanation
Indices: 43903--43950 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43893 CAATCTTTGG
*
43903 AGAATTTGAAAGA-ACTGAAAA
1 AGAAATTGAAAGAGACTGAAAA
* *
43924 AGAAATTGAGAGAGAGTGAAAA
1 AGAAATTGAAAGAGACTGAAAA
43946 AGAAA
1 AGAAA
43951 AGAAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (22 bp):
AGAAATTGAAAGAGACTGAAAA
Found at i:43999 original size:20 final size:20
Alignment explanation
Indices: 43974--44015 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
43964 AAAAGAAAAG
43974 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
43994 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
44014 AA
1 AA
44016 CACAAGAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.31, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:49669 original size:13 final size:13
Alignment explanation
Indices: 49653--49678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49643 TTTTTTTCGA
49653 TTTTTTTGAATTT
1 TTTTTTTGAATTT
49666 TTTTTTTGAATTT
1 TTTTTTTGAATTT
49679 CTTCTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TTTTTTTGAATTT
Found at i:49772 original size:12 final size:12
Alignment explanation
Indices: 49757--49785 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
49747 CCAACTCAAA
49757 TTTTTTTGA-TT
1 TTTTTTTGACTT
49768 TTTTTTTGACTT
1 TTTTTTTGACTT
49780 TTTTTT
1 TTTTTT
49786 ACATTACGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTTGACTT
Found at i:52077 original size:22 final size:22
Alignment explanation
Indices: 52049--52092 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
52039 TTTTGAACCA
52049 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
52071 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
52093 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Done.