Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2310
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: 38948
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:695 original size:12 final size:12
Alignment explanation
Indices: 678--702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
668 ACAATTTTTG
678 TGTATCGATACA
1 TGTATCGATACA
690 TGTATCGATACA
1 TGTATCGATACA
702 T
1 T
703 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:696 original size:31 final size:31
Alignment explanation
Indices: 658--720 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
648 TTACAAGCCA
**
658 ATGTATCGATACAATTTTTG-TGTATCGATAC
1 ATGTATCGATAC-ATACTTGCTGTATCGATAC
689 ATGTATCGATACATACTTGCTGTATCGATAC
1 ATGTATCGATACATACTTGCTGTATCGATAC
720 A
1 A
721 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (31 bp):
ATGTATCGATACATACTTGCTGTATCGATAC
Found at i:767 original size:21 final size:21
Alignment explanation
Indices: 741--815 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
731 CTGCCAAGAA
*
741 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
762 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
782 ATGTA-CGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
802 ATGTATCGATACAT
1 ATGTATCGATACAT
816 TGCAACATGT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 8 0.19
20 13 0.30
21 22 0.51
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:797 original size:40 final size:41
Alignment explanation
Indices: 741--833 Score: 170
Period size: 40 Copynumber: 2.3 Consensus size: 41
731 CTGCCAAGAA
*
741 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
782 ATGTA-CGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
822 ATGTATCGATAC
1 ATGTATCGATAC
834 TTTGAGTTGT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 39 0.78
41 11 0.22
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:824 original size:20 final size:20
Alignment explanation
Indices: 762--833 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
752 CATCTTTTTT
762 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
782 ATGTA-CGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
802 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
822 ATGTATCGATAC
1 ATGTATCGATAC
834 TTTGAGTTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 8 0.19
20 26 0.62
21 8 0.19
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1466 original size:16 final size:16
Alignment explanation
Indices: 1435--1480 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
1425 TCTCCCTTTG
1435 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC--TTAAAAAA
1453 TCTCCCCCTTAAAAAA
1 TCTCCCCCTTAAAAAA
1469 TCTCCCCCTTAA
1 TCTCCCCCTTAA
1481 TCAAGTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 20 0.71
18 8 0.29
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.28
Consensus pattern (16 bp):
TCTCCCCCTTAAAAAA
Found at i:2994 original size:20 final size:20
Alignment explanation
Indices: 2969--3006 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2959 TTTAGTAGAA
2969 ATAATATTT-TAATAATTATT
1 ATAATATTTAT-ATAATTATT
2989 ATAATATTTATATAATTA
1 ATAATATTTATATAATTA
3007 ATGTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAATATTTATATAATTATT
Found at i:3042 original size:28 final size:27
Alignment explanation
Indices: 3011--3071 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
3001 TAATTAATGT
3011 TTTAATAATAAATA-AATTATTTTAAGTA
1 TTTAATAATAAATATAA-TATTTT-AGTA
*
3039 TTTAAT-ATCAATATAATATTTTAGTA
1 TTTAATAATAAATATAATATTTTAGTA
*
3065 TTAAATA
1 TTTAATA
3072 TTATTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 9 0.31
27 12 0.41
28 8 0.28
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
TTTAATAATAAATATAATATTTTAGTA
Found at i:3277 original size:7 final size:7
Alignment explanation
Indices: 3265--3292 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3255 TAAAATTTTA
3265 TTAAAAT
1 TTAAAAT
3272 TTAAAAT
1 TTAAAAT
3279 TTAAAAT
1 TTAAAAT
3286 TTAAAAT
1 TTAAAAT
3293 AATTTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TTAAAAT
Found at i:3758 original size:12 final size:13
Alignment explanation
Indices: 3733--3757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3723 TTTCACAAAA
3733 AAAATAATTTTTT
1 AAAATAATTTTTT
3746 AAAATAATTTTT
1 AAAATAATTTTT
3758 ATATTTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATAATTTTTT
Found at i:4135 original size:18 final size:18
Alignment explanation
Indices: 4095--4137 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4085 AATAAATAGT
*
4095 AAATTA-TTGATATAATA
1 AAATTATTTAATATAATA
**
4112 TTATTATTTAATATAATA
1 AAATTATTTAATATAATA
4130 AAATTATT
1 AAATTATT
4138 ATTTTAATAG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AAATTATTTAATATAATA
Found at i:4135 original size:21 final size:22
Alignment explanation
Indices: 4106--4146 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4096 AATTATTGAT
*
4106 ATAATATTATTA-TTTAATATA
1 ATAAAATTATTATTTTAATATA
4127 ATAAAATTATTATTTTAATA
1 ATAAAATTATTATTTTAATA
4147 GTAAACTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAAAATTATTATTTTAATATA
Found at i:4324 original size:17 final size:17
Alignment explanation
Indices: 4284--4336 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
4274 TAATCGAAAT
*
4284 AATATTTTAAAAATTATTAT
1 AATATTTT-AAAATT-TT-G
4304 AATA-TTTAAATATTTTG
1 AATATTTTAAA-ATTTTG
4321 AATATTTTAAAATTTT
1 AATATTTTAAAATTTT
4337 TATATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 9 0.30
18 11 0.37
19 6 0.20
20 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATATTTTAAAATTTTG
Found at i:4425 original size:14 final size:14
Alignment explanation
Indices: 4398--4437 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4388 ATATCATATT
4398 TTAATATT-AAATA
1 TTAATATTAAAATA
*
4411 TTATTATTAAAATA
1 TTAATATTAAAATA
*
4425 TTAATATGAAAAT
1 TTAATATTAAAAT
4438 TAATAGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
TTAATATTAAAATA
Found at i:4747 original size:23 final size:22
Alignment explanation
Indices: 4690--4748 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
4680 ATAATAATAA
*
4690 TAATAATAATAATATTTTTATAT
1 TAATATTAAT-ATATTTTTATAT
*
4713 TAATATTTATATATTTTTATAAT
1 TAATATTAATATATTTTTAT-AT
4736 TAAT-TTAAATATA
1 TAATATT-AATATA
4749 ATATTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATTAATATATTTTTATAT
Found at i:4751 original size:34 final size:33
Alignment explanation
Indices: 4713--4779 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
4703 ATTTTTATAT
* *
4713 TAATATTTATATATTTTTATAAT-TAATTTAAATA
1 TAATATTT-T-TATTATTACAATATAATTTAAATA
4747 TAATATTTTTATTATTACAATAATAATTTAAAT
1 TAATATTTTTATTATTACAAT-ATAATTTAAAT
4780 CAGACAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.34
33 1 0.03
34 18 0.62
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
TAATATTTTTATTATTACAATATAATTTAAATA
Found at i:14210 original size:350 final size:350
Alignment explanation
Indices: 13565--14252 Score: 1331
Period size: 350 Copynumber: 2.0 Consensus size: 350
13555 TGCATTCTTA
*
13565 CATAGATCCTGATGGTTTAGTTAGGTTTCCAAGGCAAGCCATGTATTCATATGCTCAATGAGCTG
1 CATAGATCCTGATGGTTTAGTTAGGTTCCCAAGGCAAGCCATGTATTCATATGCTCAATGAGCTG
13630 TTGCTAGGTTAAAATCCTGATGATTTTATTTCCTTTGTAAATCTTATTATTAATTTACTCCACCT
66 TTGCTAGGTTAAAATCCTGATGATTTTATTTCCTTTGTAAATCTTATTATTAATTTACTCCACCT
13695 TTAGGCACCTGCCAAGAGTCACATAGCAGGGAGTGTTTTTTACTGACTGTAAGGTTACTAAATGA
131 TTAGGCACCTGCCAAGAGTCACATAGCAGGGAGTGTTTTTTACTGACTGTAAGGTTACTAAATGA
13760 TGGATCTTCGAGTACATCTCAAATGAACTATTAATCCTTAGTCGATGGTGCCATTGTTGCCAACT
196 TGGATCTTCGAGTACATCTCAAATGAACTATTAATCCTTAGTCGATGGTGCCATTGTTGCCAACT
13825 TTGGATCCAAATATCCTTCTACACCTTCCCGATTCTGAATAATTTATCCCATGGCAAGAATTGTA
261 TTGGATCCAAATATCCTTCTACACCTTCCCGATTCTGAATAATTTATCCCATGGCAAGAATTGTA
13890 TTCCAACTAGAGCAAGCCATGTATT
326 TTCCAACTAGAGCAAGCCATGTATT
13915 CATAGATCCTGATGGTTTAGTTAGGTTCCCAAGGCAAGCCATGTATTCATATGCTCAATGAGCTG
1 CATAGATCCTGATGGTTTAGTTAGGTTCCCAAGGCAAGCCATGTATTCATATGCTCAATGAGCTG
13980 TTGCTAGGTTAAAATCCTGATGATTTTATTTCCTTTGTAAATCTTATTATTAATTTACTCCACCT
66 TTGCTAGGTTAAAATCCTGATGATTTTATTTCCTTTGTAAATCTTATTATTAATTTACTCCACCT
* *
14045 TTAGGTACCTGCCAAGAGTCACATAGCAGGGAGTGTTTTTTCCTGACTGTAAGGTTACTAAATGA
131 TTAGGCACCTGCCAAGAGTCACATAGCAGGGAGTGTTTTTTACTGACTGTAAGGTTACTAAATGA
*
14110 TGGATCTTCGAGTACATCTCAAATGAACTGTTAATCCTTAGTCGATGGTGCCATTGTTGCCAACT
196 TGGATCTTCGAGTACATCTCAAATGAACTATTAATCCTTAGTCGATGGTGCCATTGTTGCCAACT
*
14175 TTGGATCCAAATATCCTTCTACACCTTCTCGATTCTGAATAATTTATCCCATGGCAAGAATTGTA
261 TTGGATCCAAATATCCTTCTACACCTTCCCGATTCTGAATAATTTATCCCATGGCAAGAATTGTA
14240 TTCCAACTAGAGC
326 TTCCAACTAGAGC
14253 TAGAATGTGC
Statistics
Matches: 333, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
350 333 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (350 bp):
CATAGATCCTGATGGTTTAGTTAGGTTCCCAAGGCAAGCCATGTATTCATATGCTCAATGAGCTG
TTGCTAGGTTAAAATCCTGATGATTTTATTTCCTTTGTAAATCTTATTATTAATTTACTCCACCT
TTAGGCACCTGCCAAGAGTCACATAGCAGGGAGTGTTTTTTACTGACTGTAAGGTTACTAAATGA
TGGATCTTCGAGTACATCTCAAATGAACTATTAATCCTTAGTCGATGGTGCCATTGTTGCCAACT
TTGGATCCAAATATCCTTCTACACCTTCCCGATTCTGAATAATTTATCCCATGGCAAGAATTGTA
TTCCAACTAGAGCAAGCCATGTATT
Found at i:21947 original size:13 final size:13
Alignment explanation
Indices: 21929--21955 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21919 ACATATTGCT
21929 TTGTATTGATACA
1 TTGTATTGATACA
21942 TTGTATTGATACA
1 TTGTATTGATACA
21955 T
1 T
21956 GTTCTTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:23645 original size:3 final size:3
Alignment explanation
Indices: 23637--23673 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
23627 TCAACCATCA
* *
23637 ATG ATG ATG AAG ACG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
23674 AGTTGACTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.32, T:0.27
Consensus pattern (3 bp):
ATG
Found at i:30149 original size:24 final size:23
Alignment explanation
Indices: 30121--30179 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 23
30111 ATTAATTTTC
30121 TTATTAAAGGGGAGAACGA-AAATA
1 TTATTAAAGGGGAG-A-GATAAATA
*
30145 TTATT-AA-GGGAGAGATAAATT
1 TTATTAAAGGGGAGAGATAAATA
*
30166 TTATTAAGGGGGAG
1 TTATTAAAGGGGAG
30180 TTACATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 2 0.07
21 10 0.33
22 6 0.20
23 7 0.23
24 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.29, T:0.27
Consensus pattern (23 bp):
TTATTAAAGGGGAGAGATAAATA
Found at i:30827 original size:20 final size:19
Alignment explanation
Indices: 30804--30854 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
30794 TGCACCCAGA
30804 TGTATCGATACATATTGCTT
1 TGTATCGATACATATT-CTT
*
30824 TGTATCGATACATGTTCTT
1 TGTATCGATACATATTCTT
*
30843 GGTATCGATACA
1 TGTATCGATACA
30855 CACTAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (19 bp):
TGTATCGATACATATTCTT
Found at i:30849 original size:19 final size:20
Alignment explanation
Indices: 30805--30854 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
30795 GCACCCAGAT
*
30805 GTATCGATACATATTGCTTT
1 GTATCGATACATATTGCTTG
*
30825 GTATCGATACATGTT-CTTG
1 GTATCGATACATATTGCTTG
30844 GTATCGATACA
1 GTATCGATACA
30855 CACTAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (20 bp):
GTATCGATACATATTGCTTG
Done.