Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1994
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: 49085
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:75 original size:28 final size:28
Alignment explanation
Indices: 1--226 Score: 215
Period size: 28 Copynumber: 7.9 Consensus size: 28
*
1 GGCTCTGAAAAGTATGCCATTCTTGACTTG-G
1 GGCTCTG-AAAGGATGCCA--C-TGACTTGTG
* *
32 GGCTCTGAAAGCATGCCACTAACTTGTG
1 GGCTCTGAAAGGATGCCACTGACTTGTG
* *
60 GACTCTGAAAGGATGCCACTAACTTGTG
1 GGCTCTGAAAGGATGCCACTGACTTGTG
*
88 GGCTCTGAAAGGATGCCACTGACTTATG
1 GGCTCTGAAAGGATGCCACTGACTTGTG
* * ** *
116 GGCTCTTAAAGGGTTTCATTGACTTGTG
1 GGCTCTGAAAGGATGCCACTGACTTGTG
* * *
144 GGCTTTGAAAGGGTGCCATTGACTTGTG
1 GGCTCTGAAAGGATGCCACTGACTTGTG
* *
172 GGCTTTGAAAAGG-TACCACTGACTTGTG
1 GGCTCTG-AAAGGATGCCACTGACTTGTG
200 GGCT-TCGAAAAGGGATGCCACTGACTT
1 GGCTCT-G-AAA-GGATGCCACTGACTT
227 AAGGGTTCTA
Statistics
Matches: 170, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
27 7 0.04
28 128 0.75
29 7 0.04
30 21 0.12
31 7 0.04
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (28 bp):
GGCTCTGAAAGGATGCCACTGACTTGTG
Found at i:7338 original size:15 final size:15
Alignment explanation
Indices: 7299--7343 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
7289 GTGTATCAAC
*
7299 GATTTTGTGGTGGGT
1 GATTTTGTGGTGGAT
* **
7314 AATTAGGTGGTGGAT
1 GATTTTGTGGTGGAT
7329 GATTTTGTGGTGGAT
1 GATTTTGTGGTGGAT
7344 TTGGTGGAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (15 bp):
GATTTTGTGGTGGAT
Found at i:12998 original size:27 final size:27
Alignment explanation
Indices: 12960--13033 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
12950 TTGATTGAAA
12960 AATGGGGTTAGAGTATCCCCTCAGAGG
1 AATGGGGTTAGAGTATCCCCTCAGAGG
*
12987 AATGGGGTTAGAGTATCCCCTCGGAGG
1 AATGGGGTTAGAGTATCCCCTCAGAGG
* * *
13014 AATAGGGTTGGAGTGTCCCC
1 AATGGGGTTAGAGTATCCCC
13034 AATGATGACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (27 bp):
AATGGGGTTAGAGTATCCCCTCAGAGG
Found at i:15797 original size:80 final size:80
Alignment explanation
Indices: 15543--15790 Score: 243
Period size: 80 Copynumber: 3.1 Consensus size: 80
15533 GAATTTTAGT
* * * * ** * *
15543 GTAAAAATGGGGTTAGAGTATACCTTTAGAGATGGTAGGGTTTGAA-TATCCCCAAAGGTGAAAA
1 GTAAAAATGAGGTTGGAGTATCCCCTCGGAGATGGTAGGG-TTAAAGTATCCTCAAAGGTGAAAA
* *** *
15607 ATTCAATGTTTTGGAG
65 TTTTGGTGTTTTGGAA
*
15623 GTAAAAATGAGGTTGGAGTATCCCCTCGGAGATGGTAGGGTTAAAGTATCTTCAAAGGTGAAAAT
1 GTAAAAATGAGGTTGGAGTATCCCCTCGGAGATGGTAGGGTTAAAGTATCCTCAAAGGTGAAAAT
15688 TTTGGTGTTTT-GATA
66 TTTGGTGTTTTGGA-A
* * * * ** *
15703 GTAAAAATGAGGTTGGAGTATCCCCTTGGATATGGTGGGGTTGGAA-TATCC-CTGGAGTTGAAA
1 GTAAAAATGAGGTTGGAGTATCCCCTCGGAGATGGTAGGGTT-AAAGTATCCTC-AAAGGTGAAA
15766 ATTTTGGTGTTTTGGAA
64 ATTTTGGTGTTTTGGAA
15783 GTAAAAAT
1 GTAAAAAT
15791 TGGGTTGAAG
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
79 7 0.05
80 130 0.92
81 4 0.03
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (80 bp):
GTAAAAATGAGGTTGGAGTATCCCCTCGGAGATGGTAGGGTTAAAGTATCCTCAAAGGTGAAAAT
TTTGGTGTTTTGGAA
Found at i:18009 original size:52 final size:52
Alignment explanation
Indices: 17924--18048 Score: 232
Period size: 52 Copynumber: 2.4 Consensus size: 52
17914 ATATGAAAAG
*
17924 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
17976 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
18028 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
18049 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:18061 original size:52 final size:51
Alignment explanation
Indices: 17924--18068 Score: 220
Period size: 52 Copynumber: 2.8 Consensus size: 51
17914 ATATGAAAAG
17924 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
17976 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
18028 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
18069 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:18075 original size:13 final size:13
Alignment explanation
Indices: 18057--18081 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18047 CAAAGATCAG
18057 TGTATCGATACAA
1 TGTATCGATACAA
18070 TGTATCGATACA
1 TGTATCGATACA
18082 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:18148 original size:19 final size:18
Alignment explanation
Indices: 18124--18221 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
18114 TAGCTTAAAT
18124 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
18143 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
18156 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
18175 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
18188 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
18208 TGTATCGATACAAA
1 TGTATCGATACAAA
18222 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:18161 original size:13 final size:13
Alignment explanation
Indices: 18143--18199 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
18133 ACAAAACTTA
18143 TGTATCGATACAT
1 TGTATCGATACAT
18156 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
18174 ATGTATCGATACAT
1 -TGTATCGATACAT
18188 TGTATCGATACA
1 TGTATCGATACA
18200 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:18163 original size:32 final size:32
Alignment explanation
Indices: 18122--18219 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
18112 AGTAGCTTAA
*
18122 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
18154 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
18186 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
18219 A
1 A
18220 AATCGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:20882 original size:80 final size:79
Alignment explanation
Indices: 20750--20906 Score: 242
Period size: 80 Copynumber: 2.0 Consensus size: 79
20740 TATAATAAGC
* * *
20750 ATAAGCCTGAATTTGTTTCAAATACATCCTACCACATGAGGCCTACTTAGGCTGCCTTCTAGCAT
1 ATAAGCCTGAATTTGTTTCAAATACATCCTACCACATGAGGCCTAATTAGGCTGCCTTCTAACAC
20815 CTAGCTTAAGAACA
66 CTAGCTTAAGAACA
* * *
20829 ATAAGCCTGAAATTTGTTTCAAATACATCCTATCATATGAGGCTTAATTAGGCTGCCTTCTAACA
1 ATAAGCCTG-AATTTGTTTCAAATACATCCTACCACATGAGGCCTAATTAGGCTGCCTTCTAACA
*
20894 CCTGGCTTAAGAA
65 CCTAGCTTAAGAA
20907 TAATTCCTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 9 0.13
80 61 0.87
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (79 bp):
ATAAGCCTGAATTTGTTTCAAATACATCCTACCACATGAGGCCTAATTAGGCTGCCTTCTAACAC
CTAGCTTAAGAACA
Found at i:21634 original size:79 final size:78
Alignment explanation
Indices: 21490--21644 Score: 267
Period size: 79 Copynumber: 2.0 Consensus size: 78
21480 CTATGCAACT
*
21490 CTTAGATCAGTTAGGTGGTAACTCTTACCTAAATGCAATGTATGCATTTTGCCTAACAACCACTT
1 CTTAGATCAGTTAGGTGGTAACTCTTACCTAAATGCAATGTATGCATTTCGCCTAACAACCACTT
21555 CCAATACTATACG
66 CCAATACTATACG
*
21568 CTTAGATCAGTTTAGGTGGTAACTCTTTGCCTAAATGCAATGTATGCATTTCGCCT-ACAACCAC
1 CTTAGATCAG-TTAGGTGGTAACTC-TTACCTAAATGCAATGTATGCATTTCGCCTAACAACCAC
21632 TTCCAATACTATA
64 TTCCAATACTATA
21645 ACGATCAACT
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
78 10 0.14
79 35 0.48
80 28 0.38
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (78 bp):
CTTAGATCAGTTAGGTGGTAACTCTTACCTAAATGCAATGTATGCATTTCGCCTAACAACCACTT
CCAATACTATACG
Found at i:23423 original size:13 final size:13
Alignment explanation
Indices: 23405--23435 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23395 CAATTCAATC
23405 ATGTATCGAGACA
1 ATGTATCGAGACA
*
23418 ATGTATCGATACA
1 ATGTATCGAGACA
23431 ATGTA
1 ATGTA
23436 CCATGTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (13 bp):
ATGTATCGAGACA
Found at i:23538 original size:13 final size:13
Alignment explanation
Indices: 23484--23543 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
23474 TGCTAGTTTC
* *
23484 ATGTATCGAGACC
1 ATGTATCGATACA
23497 ATGTATCGATACA
1 ATGTATCGATACA
23510 ATG-ATC-AT---
1 ATGTATCGATACA
23518 AT-TATCGATACA
1 ATGTATCGATACA
23530 ATGTATCGATACA
1 ATGTATCGATACA
23543 A
1 A
23544 GCATAATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
8 5 0.13
9 2 0.05
11 2 0.05
12 5 0.13
13 25 0.64
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:31457 original size:20 final size:20
Alignment explanation
Indices: 31432--31485 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
31422 GTTACAAGCA
* *
31432 ATGTATCAATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
*
31452 ATGTATCGACACAATGTACC
1 ATGTATCGATACAATGTACC
31472 ATGTATCGATACAA
1 ATGTATCGATACAA
31486 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:31558 original size:19 final size:18
Alignment explanation
Indices: 31513--31570 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
31503 ACTGCCAGTT
31513 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
*
31532 TCCATGTATTGATACAATG
1 T-CATGTATCGATACAATG
31551 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
31570 T
1 T
31571 ATCGATACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.54
20 15 0.43
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:31572 original size:13 final size:13
Alignment explanation
Indices: 31554--31580 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31544 TACAATGATC
31554 ATGTATCGATACA
1 ATGTATCGATACA
31567 ATGTATCGATACA
1 ATGTATCGATACA
31580 A
1 A
31581 AGGATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:31596 original size:33 final size:32
Alignment explanation
Indices: 31535--31598 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
31525 ACAATTGTCC
* * *
31535 ATGTATTGATACAATGATCATGTATCGATACA
1 ATGTATCGATACAAGGATAATGTATCGATACA
31567 ATGTATCGATACAAAGGATAATGTATCGATAC
1 ATGTATCGATAC-AAGGATAATGTATCGATAC
31599 TTCTGGGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACAAGGATAATGTATCGATACA
Found at i:38917 original size:20 final size:21
Alignment explanation
Indices: 38892--38942 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
38882 TTCAAGCATC
*
38892 TATCGATACATTCACTTA-TG
1 TATCGATACATTAACTTATTG
* *
38912 TGTCGATATATTAACTTATTG
1 TATCGATACATTAACTTATTG
38933 TATCGATACA
1 TATCGATACA
38943 AATTGTAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (21 bp):
TATCGATACATTAACTTATTG
Found at i:41932 original size:33 final size:32
Alignment explanation
Indices: 41870--41942 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
41860 ATAGCCGTTT
41870 GAAACAATGTATCGATACAATTCATCATGTATC
1 GAAACAATGTATCGATACAATTCA-CATGTATC
*
41903 GAAACATTGTATCGATACAATGTGC-CATGTATC
1 GAAACAATGTATCGATACAAT-T-CACATGTATC
*
41936 GATACAA
1 GAAACAA
41943 ACAGTGGTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 33 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (32 bp):
GAAACAATGTATCGATACAATTCACATGTATC
Found at i:42015 original size:19 final size:20
Alignment explanation
Indices: 41971--42016 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41961 CTGCCAGTTT
* **
41971 CATGTATCGATACAATTGTC
1 CATGTATCGACACAATTGAA
41991 CATGTATCGACACAA-TGAA
1 CATGTATCGACACAATTGAA
42010 CATGTAT
1 CATGTAT
42017 TGATACAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGACACAATTGAA
Found at i:47083 original size:33 final size:32
Alignment explanation
Indices: 47041--47104 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
47031 TGCAAGCCAA
**
47041 TGTATCGATACATTTTTTGGTGTATCAATACAT
1 TGTATCGATACATACTTT-GTGTATCAATACAT
*
47074 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCAATACA
47105 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCAATACAT
Done.