Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2342
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: 51282
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Found at i:3943 original size:28 final size:28
Alignment explanation
Indices: 3881--4002 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
3871 ATATTAAGTC
*
3881 CGCACACTCA-TGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
3907 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
3935 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
3963 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
3992 CGCACACTTAG
1 CGCACACTTAG
4003 CGCCAATCTC
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
26 9 0.10
27 12 0.14
28 49 0.57
29 16 0.19
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:12088 original size:29 final size:29
Alignment explanation
Indices: 12025--12092 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
12015 TAATCAACCG
*
12025 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
12054 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
12083 CGCACACTTA
1 CGCACACTTA
12093 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:12235 original size:29 final size:29
Alignment explanation
Indices: 12201--12272 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
12191 ATCAACCGCG
* * *
12201 CACACTTAGTGCCATGCACTTTAAACTCA
1 CACACTTAGTGCCATACAATTTAAACCCA
** *
12230 CACACTTAGTGCTGTACAATTTAAACCCG
1 CACACTTAGTGCCATACAATTTAAACCCA
12259 CACACTTAGTGCCA
1 CACACTTAGTGCCA
12273 ATCTCATGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.26
Consensus pattern (29 bp):
CACACTTAGTGCCATACAATTTAAACCCA
Found at i:12263 original size:174 final size:173
Alignment explanation
Indices: 11915--12266 Score: 589
Period size: 174 Copynumber: 2.0 Consensus size: 173
11905 AACTCAAGGT
* *
11915 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
11980 GAAAATATATATTGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGTA
66 GAAAATATATATTGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGCA
* ***
12045 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 CTTTAAACTCACACACTTAGTGCCATACATTTCAAACCCGCAC
12088 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
12153 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATT-GGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
**
12218 ACTTTAAACTCACACACTTAGTGCTGTACAATTT-AAACCCGCAC
130 ACTTTAAACTCACACACTTAGTGCCATAC-ATTTCAAACCCGCAC
12262 ACTTA
1 ACTTA
12267 GTGCCAATCT
Statistics
Matches: 167, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
173 76 0.46
174 87 0.52
175 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (173 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGCA
CTTTAAACTCACACACTTAGTGCCATACATTTCAAACCCGCAC
Found at i:15457 original size:27 final size:27
Alignment explanation
Indices: 15426--15611 Score: 230
Period size: 27 Copynumber: 6.9 Consensus size: 27
15416 AAATTACTGA
*
15426 AATACCCTTGTAGGGTAAAATGACCGT
1 AATACCCCTGTAGGGTAAAATGACCGT
* *
15453 GATACCCCTATAGGGTAAAATGACCGT
1 AATACCCCTGTAGGGTAAAATGACCGT
* **
15480 AATACCCATGTAGGGTAAAATGTTCGT
1 AATACCCCTGTAGGGTAAAATGACCGT
15507 AA-AGCCCCTGTAGGGTAAAATGACCGT
1 AATA-CCCCTGTAGGGTAAAATGACCGT
* * *
15534 AATGCCCCTGTAGGGTAAAATGAACAT
1 AATACCCCTGTAGGGTAAAATGACCGT
* * *
15561 AATGCCCTTGTAGGGTAAAATGACTGT
1 AATACCCCTGTAGGGTAAAATGACCGT
* *
15588 AATACCCCTATATGGTAAAATGAC
1 AATACCCCTGTAGGGTAAAATGAC
15612 GATTATGCCC
Statistics
Matches: 135, Mismatches: 22, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 1 0.01
27 134 0.99
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAATGACCGT
Found at i:15804 original size:27 final size:27
Alignment explanation
Indices: 15747--15830 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
15737 ATAGAAGAAG
* *
15747 TACTG-TACTGGTGACTATGTCAC-AT
1 TACTGATACTGGTGGCTATGCCACAAT
* *
15772 TCACTGTTGCTGGTGGCTATGCCACAAT
1 T-ACTGATACTGGTGGCTATGCCACAAT
* * *
15800 TACTGATACTGGTGGCTTTGCGACACT
1 TACTGATACTGGTGGCTATGCCACAAT
15827 TACT
1 TACT
15831 ATTCTGGCAG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 40 0.83
28 3 0.06
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (27 bp):
TACTGATACTGGTGGCTATGCCACAAT
Found at i:18349 original size:43 final size:43
Alignment explanation
Indices: 18301--18383 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
18291 ATGTTAATTA
*
18301 TATGCTTAACATTAATAAATGTAGTTTGTAAATTTTAACTTTG
1 TATGCTTAACATTAATAAATGTAGTTTATAAATTTTAACTTTG
*
18344 TATGCTTAACATTAATAAATGTAGTTTATAAGTTTTAACT
1 TATGCTTAACATTAATAAATGTAGTTTATAAATTTTAACT
18384 CATGTTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (43 bp):
TATGCTTAACATTAATAAATGTAGTTTATAAATTTTAACTTTG
Found at i:18711 original size:23 final size:23
Alignment explanation
Indices: 18685--18730 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
18675 ATTGAGTATG
18685 GTTGATCAAGTTATGCTTAACAT
1 GTTGATCAAGTTATGCTTAACAT
18708 GTTGATCAAGTTATGCTTAACAT
1 GTTGATCAAGTTATGCTTAACAT
18731 ATAAGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (23 bp):
GTTGATCAAGTTATGCTTAACAT
Found at i:21240 original size:28 final size:29
Alignment explanation
Indices: 21203--21269 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
21193 AAGTCTACAT
*
21203 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* *
21231 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
21260 ACATTCATAT
1 ACATTCATAT
21270 TCATGCTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:21503 original size:8 final size:8
Alignment explanation
Indices: 21492--21522 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
21482 TTGGCTTTTT
21492 GGCATTTC
1 GGCATTTC
21500 GGCATTTC
1 GGCATTTC
21508 GGCATTTC
1 GGCATTTC
*
21516 GGGATTT
1 GGCATTT
21523 GCCGATCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.19, G:0.29, T:0.39
Consensus pattern (8 bp):
GGCATTTC
Found at i:24685 original size:43 final size:43
Alignment explanation
Indices: 24624--24855 Score: 342
Period size: 43 Copynumber: 5.4 Consensus size: 43
24614 ACATATCATT
* *
24624 TCACCGGCATTACGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* * *
24667 TCACCGGCATTACGCCTGCTAGGCATGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* * *
24710 ACACCGGCACGAAGCTTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
24753 TCACTGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
24796 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATATA-A
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
24838 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
24856 GGGATTCATC
Statistics
Matches: 174, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 15 0.09
42 2 0.01
43 157 0.90
ACGTcount: A:0.29, C:0.33, G:0.24, T:0.14
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:24898 original size:38 final size:38
Alignment explanation
Indices: 24827--24910 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
24817 GGCACGAAGG
*
24827 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTCAT
1 CCCGAATATAATACCAGCACAAGGCCTGCGGGATTCAT
* * * *
24865 CCCGGATATAATACCAGCACGAAGG-CTGTGGGATTTAA
1 CCCGAATATAATACCAGCAC-AAGGCCTGCGGGATTCAT
24903 CCCGAATA
1 CCCGAATA
24911 CATATCAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 36 0.92
39 3 0.08
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACAAGGCCTGCGGGATTCAT
Found at i:32526 original size:40 final size:40
Alignment explanation
Indices: 32442--32662 Score: 202
Period size: 40 Copynumber: 5.5 Consensus size: 40
32432 TTGAATGCTG
* * *
32442 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
** * *
32481 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
32522 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
32562 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAT
**
32602 TCCGGGTTAAGTCCCGAAGGCA-TTGTATGAGTTACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
32640 AACCGGGCTATGTCCCGAAGGCA
1 -TCCGGGTTAAGTCCCGAAGGCA
32663 CTTGAACAAG
Statistics
Matches: 151, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 29 0.19
40 111 0.74
41 10 0.07
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:39744 original size:29 final size:29
Alignment explanation
Indices: 39681--39748 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
39671 TAATCAACCG
39681 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
39710 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
39739 CGCACACTTA
1 CGCACACTTA
39749 CCTTTTTCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:39868 original size:175 final size:174
Alignment explanation
Indices: 39570--39898 Score: 613
Period size: 175 Copynumber: 1.9 Consensus size: 174
39560 AACTCAAGGT
* *
39570 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
39635 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
39700 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
39744 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
1 ACTTACC-TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
39809 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
65 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
* *
39874 TACTTTAAACTCGCACACTTAGTGC
130 CACTTTAAACTCACACACTTAGTGC
39899 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
174 7 0.05
175 143 0.95
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:39890 original size:29 final size:30
Alignment explanation
Indices: 39851--39929 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
39841 CTTAATAATC
39851 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
39881 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
39910 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39930 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Done.