Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1196
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: 40149
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:3331 original size:20 final size:19
Alignment explanation
Indices: 3308--3372 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
3298 AAGCTCAAAC
3308 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
3328 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
3348 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
3368 GAGCT
1 GAGCT
3373 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:3592 original size:40 final size:42
Alignment explanation
Indices: 3522--3609 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 42
3512 TTGCTCAATA
* *
3522 TCTTTTCTCTCTTCAGACTCAATTTCTTTTTC-TTCTCACAT
1 TCTTTTCACTCTTCAGACTCAATCTCTTTTTCTTTCTCACAT
* * * *
3563 TCTTTTCACTC-TCAGTCTCGATCTCTTTTTCTTTTTCACTT
1 TCTTTTCACTCTTCAGACTCAATCTCTTTTTCTTTCTCACAT
3604 TCTTTT
1 TCTTTT
3610 TCAATTTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 17 0.43
41 23 0.57
ACGTcount: A:0.11, C:0.28, G:0.03, T:0.57
Consensus pattern (42 bp):
TCTTTTCACTCTTCAGACTCAATCTCTTTTTCTTTCTCACAT
Found at i:3605 original size:12 final size:12
Alignment explanation
Indices: 3590--3624 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
3580 TCGATCTCTT
*
3590 TTTCTTTTTCAC
1 TTTCTTTTTCAA
3602 TTTCTTTTTCAA
1 TTTCTTTTTCAA
3614 TTTCATTTTTC
1 TTTC-TTTTTC
3625 TTTTTCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:3609 original size:18 final size:19
Alignment explanation
Indices: 3586--3631 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
3576 AGTCTCGATC
*
3586 TCTTTTTCTTTTTCA-CTT
1 TCTTTTTCTATTTCATCTT
* *
3604 TCTTTTTCAATTTCATTTT
1 TCTTTTTCTATTTCATCTT
3623 TCTTTTTCT
1 TCTTTTTCT
3632 CATTCTCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.72
Consensus pattern (19 bp):
TCTTTTTCTATTTCATCTT
Found at i:6286 original size:20 final size:20
Alignment explanation
Indices: 6240--6277 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6230 AGCTGAAAAG
6240 AAGCT-AAATCAAGCTCAAAT
1 AAGCTGAAA-CAAGCTCAAAT
6260 AAGCTGAAACAAGCTCAA
1 AAGCTGAAACAAGCTCAA
6278 GTGAGCTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.50, C:0.21, G:0.13, T:0.16
Consensus pattern (20 bp):
AAGCTGAAACAAGCTCAAAT
Found at i:9355 original size:21 final size:21
Alignment explanation
Indices: 9310--9372 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
9300 TTTGAACCAT
* *
9310 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
9332 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
9353 TACCATTTCGTACC-ATTCCA
1 TACCATTTCGTACCAATTCCA
9373 AATACCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.16
21 19 0.51
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:9368 original size:10 final size:10
Alignment explanation
Indices: 9330--9369 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
9320 TACCAAATAC
9330 CATACCATTT
1 CATACCATTT
*
9340 CATACCAATTC
1 CATACC-ATTT
9351 CATACCATTT
1 CATACCATTT
*
9361 CGTACCATT
1 CATACCATT
9370 CCAAATACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.35
Consensus pattern (10 bp):
CATACCATTT
Found at i:12570 original size:22 final size:22
Alignment explanation
Indices: 12519--12584 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
12509 GGTATTTGGG
* *
12519 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
12540 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
12562 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
12585 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:15709 original size:22 final size:22
Alignment explanation
Indices: 15681--15724 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15671 TTTTGAACCA
15681 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
15703 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
15725 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:17664 original size:17 final size:17
Alignment explanation
Indices: 17639--17692 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
17629 TCTCTTTTCA
*
17639 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
17656 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
17673 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
17690 TTC
1 TTC
17693 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:19894 original size:20 final size:19
Alignment explanation
Indices: 19871--19935 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
19861 AAGCTCAAAC
19871 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
19891 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
19911 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
19931 GAGCT
1 GAGCT
19936 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:21737 original size:33 final size:33
Alignment explanation
Indices: 21699--21761 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21689 GATTACTCAC
21699 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
21732 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21762 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:21807 original size:14 final size:14
Alignment explanation
Indices: 21758--21814 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
21748 TCAAGCTCTC
21758 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
21771 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
21785 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
21799 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
21813 TT
1 TT
21815 CTCTCAGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:21837 original size:12 final size:12
Alignment explanation
Indices: 21836--21890 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
21826 TCGATTTCTT
*
21836 TTTCTTTTTCAT
1 TTTCTTTTTCAA
*
21848 TTTCTTTTT--G
1 TTTCTTTTTCAA
*
21858 TTT-TCTTTCAA
1 TTTCTTTTTCAA
21869 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
21881 TCTCTTTTTC
1 TTTCTTTTTC
21891 CTTTTCTCGC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 4 0.11
10 3 0.09
11 3 0.09
12 25 0.71
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:21878 original size:6 final size:6
Alignment explanation
Indices: 21776--21865 Score: 56
Period size: 6 Copynumber: 14.7 Consensus size: 6
21766 TCTTTTTTCG
* * * ** *
21776 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA GTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * *
21827 CGATTT CTTTTT CTTTTT CATTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
21866 CAATTTCTTT
Statistics
Matches: 60, Mismatches: 21, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
5 4 0.07
6 44 0.73
7 9 0.15
8 3 0.05
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:22935 original size:12 final size:12
Alignment explanation
Indices: 22920--22946 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
22910 TTTTTTTCAC
22920 TTTTTTTTGAAT
1 TTTTTTTTGAAT
22932 TTTTTTTTGAAT
1 TTTTTTTTGAAT
22944 TTT
1 TTT
22947 GATTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:22946 original size:11 final size:11
Alignment explanation
Indices: 22908--22946 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22898 TTTTTGCTCG
*
22908 ATTTTTTTTCA
1 ATTTTTTTTGA
*
22919 CTTTTTTTTGA
1 ATTTTTTTTGA
22930 ATTTTTTTTTGA
1 A-TTTTTTTTGA
22942 ATTTT
1 ATTTT
22947 GATTTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:26531 original size:22 final size:22
Alignment explanation
Indices: 26480--26545 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
26470 GGTATTTGGG
* *
26480 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
26501 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
26523 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
26546 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:30063 original size:30 final size:30
Alignment explanation
Indices: 30029--30125 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
30019 TAAACTAAAA
30029 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
30059 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
30089 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
30118 ATGAGCTA
1 -TGAGCTA
30126 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:32292 original size:12 final size:12
Alignment explanation
Indices: 32277--32307 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
32267 TTCTTTTTGC
32277 TTTTCAAAGGCT
1 TTTTCAAAGGCT
32289 TTTTCAAAGGCT
1 TTTTCAAAGGCT
32301 TTTTCAA
1 TTTTCAA
32308 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:32384 original size:6 final size:6
Alignment explanation
Indices: 32368--32417 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
32358 TTTCTTTTTA
*
32368 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
32417 T
1 T
32418 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:32400 original size:37 final size:37
Alignment explanation
Indices: 32357--32427 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
32347 CTTGCCTCTC
32357 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
32394 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
32428 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:32428 original size:16 final size:16
Alignment explanation
Indices: 32353--32413 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
32343 GCCTCTTGCC
*
32353 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
32369 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
32385 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
32401 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
32414 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:33345 original size:11 final size:10
Alignment explanation
Indices: 33330--33366 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
33320 TTTTAACTCG
33330 ATTTTTTTTC
1 ATTTTTTTTC
*
33340 ACTTTTTTT-
1 ATTTTTTTTC
33349 -TTTTTTTTC
1 ATTTTTTTTC
33358 ATTTTTTTT
1 ATTTTTTTT
33367 TGAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.30
10 16 0.70
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (10 bp):
ATTTTTTTTC
Found at i:33352 original size:18 final size:17
Alignment explanation
Indices: 33331--33367 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
33321 TTTAACTCGA
33331 TTTTTTTTCACTTTTTTT
1 TTTTTTTTCA-TTTTTTT
33349 TTTTTTTTCATTTTTTT
1 TTTTTTTTCATTTTTTT
33366 TT
1 TT
33368 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTTCATTTTTTT
Found at i:33362 original size:12 final size:12
Alignment explanation
Indices: 33347--33386 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
33337 TTCACTTTTT
**
33347 TTTTTTTTTTCA
1 TTTTTTTTTGAA
33359 TTTTTTTTTGAA
1 TTTTTTTTTGAA
33371 TTTTTTTTCTGAA
1 TTTTTTTT-TGAA
33384 TTT
1 TTT
33387 CTTCTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:35128 original size:30 final size:30
Alignment explanation
Indices: 35094--35190 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
35084 TAAACTAAAA
35094 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
35124 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
35154 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
35183 ATGAGCTA
1 -TGAGCTA
35191 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Done.