Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1640
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: 55387
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:2382 original size:38 final size:39
Alignment explanation
Indices: 2306--2544 Score: 212
Period size: 38 Copynumber: 6.5 Consensus size: 39
2296 AGCATGATTA
** * *
2306 CTCTTCGGGTTTAGCACGGATATATTACTAGCACGAATG
1 CTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATG
*
2345 CTCTTCGGAACTTAGCCCGGATA-CTCA-TAGCACGAATG
1 CTCTTCGG-ACTTAGCCCGGATATATCACTAGCACGAATG
2383 CTC-TCGGACTTAG-CCGGATATATCACTAGCACGAATG
1 CTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATG
2420 CTCTTCGGACTTAGCCCGGAT-TATC-CTAG---G-ATG
1 CTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATG
*
2453 CTC-TCGGACTTAG--C--ATACAT--C-AGCACGAATG
1 CTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATG
* * *
2484 CTCTTCGGATCTTAGTCCGGATATGGTCACTTAGCAC-AAAG
1 CTCTTCGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAATG
2525 C-CTTCGGGACTTAGCCCGGA
1 CTCTTC-GGACTTAGCCCGGA
2545 CATCATTCAA
Statistics
Matches: 167, Mismatches: 11, Indels: 43
0.76 0.05 0.19
Matches are distributed among these distances:
27 2 0.01
28 3 0.02
29 2 0.01
30 2 0.01
31 6 0.04
32 15 0.09
33 11 0.07
34 1 0.01
35 8 0.05
36 9 0.05
37 25 0.15
38 29 0.17
39 16 0.10
40 26 0.16
41 7 0.04
42 5 0.03
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (39 bp):
CTCTTCGGACTTAGCCCGGATATATCACTAGCACGAATG
Found at i:2413 original size:75 final size:69
Alignment explanation
Indices: 2316--2507 Score: 225
Period size: 75 Copynumber: 2.7 Consensus size: 69
2306 CTCTTCGGGT
2316 TTAGCACGGATATATTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACTCATAGCACGAA
1 TTAGC-CGGATATA-TACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA-TCATAG---G-A
2381 TGCTCTCGGAC
59 TGCTCTCGGAC
*
2392 TTAGCCGGATATATCACTAGCACGAATGCTCTTCGG-ACTTAGCCCGGATTATCCTAGGATGCTC
1 TTAGCCGGATATAT-ACTAGCACGAATGCTCTTCGGAACTTAGCCCGGA-TATCATAGGATGCTC
2456 TCGGAC
64 TCGGAC
* * *
2462 TTAG-C--ATACAT-C-AGCACGAATGCTCTTCGGATCTTAGTCCGGATAT
1 TTAGCCGGATATATACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATAT
2508 GGTCACTTAG
Statistics
Matches: 109, Mismatches: 4, Indels: 18
0.83 0.03 0.14
Matches are distributed among these distances:
64 21 0.19
65 11 0.10
67 5 0.05
69 1 0.01
70 16 0.15
71 1 0.01
74 18 0.17
75 31 0.28
76 5 0.05
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (69 bp):
TTAGCCGGATATATACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATCATAGGATGCTCTC
GGAC
Found at i:2888 original size:29 final size:29
Alignment explanation
Indices: 2849--2927 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
2839 CTTAATAATC
*
2849 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
2879 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
2908 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
2928 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:2970 original size:43 final size:43
Alignment explanation
Indices: 2909--3011 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
2899 TGCATTTCAA
2909 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
2952 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
2995 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
3012 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:4923 original size:37 final size:37
Alignment explanation
Indices: 4873--4951 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
4863 TTATTACGAA
* *
4873 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
4910 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
4947 GTCTT
1 GTCTT
4952 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:5234 original size:47 final size:47
Alignment explanation
Indices: 5070--5480 Score: 745
Period size: 47 Copynumber: 8.7 Consensus size: 47
5060 CCCTTCGGGA
* *
5070 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5117 C-TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5163 CTTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 C-TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5211 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5258 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5305 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5352 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5399 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5446 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
5481 AGAATCCTAA
Statistics
Matches: 355, Mismatches: 6, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
46 44 0.12
47 266 0.75
48 45 0.13
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:10986 original size:17 final size:18
Alignment explanation
Indices: 10951--10999 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
10941 AATTATACGT
* * *
10951 TTTATTTTTTATTATATA
1 TTTATTTTTAAATACATA
10969 -TTATTTTTAAATACATA
1 TTTATTTTTAAATACATA
10986 TTTATATTTTAAAT
1 TTTAT-TTTTAAAT
11000 CCGTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 14 0.54
18 4 0.15
19 8 0.31
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATTTTTAAATACATA
Found at i:14221 original size:75 final size:75
Alignment explanation
Indices: 14135--14278 Score: 252
Period size: 75 Copynumber: 1.9 Consensus size: 75
14125 CCTGGCACAC
14135 GGGCGTGTGACTTGGCCGTGTGACATCAATTTGTTCATGCATTGCAAAACAGAGAGTTACACGGG
1 GGGCGTGTGACTTGGCCGTGTGACATCAATTTGTTCATGCATTGCAAAACAGAGAGTTACACGGG
14200 TTAGCGACAT
66 TTAGCGACAT
* * * *
14210 GGGCGTGTGACTTGGTCGTGTGACATCAATTTGTTTATGCATTGCAAAATAGAGAGTTACACGGT
1 GGGCGTGTGACTTGGCCGTGTGACATCAATTTGTTCATGCATTGCAAAACAGAGAGTTACACGGG
14275 TTAG
66 TTAG
14279 GGATATAGGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (75 bp):
GGGCGTGTGACTTGGCCGTGTGACATCAATTTGTTCATGCATTGCAAAACAGAGAGTTACACGGG
TTAGCGACAT
Found at i:16144 original size:25 final size:25
Alignment explanation
Indices: 16116--16205 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
16106 GGTTATAGAT
*
16116 TTCAGCTCATATGAGCTTATTGTTA
1 TTCAGCTCATAAGAGCTTATTGTTA
* *
16141 TTCAGTTCAGAAGAGCTTATTGTTA
1 TTCAGCTCATAAGAGCTTATTGTTA
* ****
16166 TTTAGCTCGGGGGAGCTTATTGTT-
1 TTCAGCTCATAAGAGCTTATTGTTA
*
16190 TACAGCTCATAAGAGC
1 TTCAGCTCATAAGAGC
16206 ATACTGATTC
Statistics
Matches: 51, Mismatches: 14, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
24 10 0.20
25 41 0.80
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (25 bp):
TTCAGCTCATAAGAGCTTATTGTTA
Found at i:17957 original size:42 final size:42
Alignment explanation
Indices: 17909--18075 Score: 156
Period size: 42 Copynumber: 3.9 Consensus size: 42
17899 ATTAGGGTTA
*
17909 ATGAGATTACGTATAAGACCATATCTGGGATATGGCATCGAT
1 ATGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGAT
* * * *
17951 TTGAGATTTCGTGTAAGACCATGTCTGGGACATGGCATCGAT
1 ATGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGAT
* * * *
17993 ACGAGA-CATCGTGTAAGACCATAGCTGGGCTATCGGCATCGAT
1 ATGAGATTA-CGTGTAAGACCATATCTGGGATAT-GGCATCGAT
* ** * * *
18036 ATTTGTGATCCCATGTAAGACCATGTCTAGGATATGGCAT
1 A--TGAGATTACGTGTAAGACCATATCTGGGATATGGCAT
18076 TGGCATCTCA
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
42 61 0.62
43 10 0.10
44 5 0.05
45 22 0.22
46 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (42 bp):
ATGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGAT
Found at i:20423 original size:21 final size:21
Alignment explanation
Indices: 20399--20460 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
20389 ATCATATTTT
20399 ATGTGTGTTTGATATGGTAGA
1 ATGTGTGTTTGATATGGTAGA
* * **
20420 ATGT-T-TATCATAT--T-TT
1 ATGTGTGTTTGATATGGTAGA
20436 ATGTGTGTTTGATATGGTAGA
1 ATGTGTGTTTGATATGGTAGA
20457 ATGT
1 ATGT
20461 TGTAAAGTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 10
0.61 0.17 0.22
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 6 0.21
19 6 0.21
20 2 0.07
21 8 0.29
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (21 bp):
ATGTGTGTTTGATATGGTAGA
Found at i:20431 original size:37 final size:37
Alignment explanation
Indices: 20387--20461 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
20377 ATATGTTGCC
20387 TTATCATATTTTATGTGTGTTTGATATGGTAGAATGT
1 TTATCATATTTTATGTGTGTTTGATATGGTAGAATGT
20424 TTATCATATTTTATGTGTGTTTGATATGGTAGAATGT
1 TTATCATATTTTATGTGTGTTTGATATGGTAGAATGT
20461 T
1 T
20462 GTAAAGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.52
Consensus pattern (37 bp):
TTATCATATTTTATGTGTGTTTGATATGGTAGAATGT
Found at i:47225 original size:27 final size:26
Alignment explanation
Indices: 47160--47230 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 26
47150 CACACCTTAG
* *
47160 CTTTATGAGCATCTCGATTAAAGGTT
1 CTTTATGAGCTTCTCGATTAAAGGCT
* * *
47186 CTTTGTGAACTTCT-TATTAAATTGGCT
1 CTTTATGAGCTTCTCGATTAAA--GGCT
*
47213 CTTTATGAGCTTCCCGAT
1 CTTTATGAGCTTCTCGAT
47231 AATGCTCACT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
25 6 0.18
26 11 0.33
27 14 0.42
28 2 0.06
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (26 bp):
CTTTATGAGCTTCTCGATTAAAGGCT
Found at i:47271 original size:23 final size:23
Alignment explanation
Indices: 47219--47278 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
47209 GGCTCTTTAT
* * *
47219 GAGCTTCCCGATAATGCTCACTT
1 GAGCTTCCAGATATTGCTCACTG
*
47242 GAACTTCCAGATATTGCT-ATCTG
1 GAGCTTCCAGATATTGCTCA-CTG
*
47265 GAGCTTCCTGATAT
1 GAGCTTCCAGATAT
47279 AGTTTTTTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (23 bp):
GAGCTTCCAGATATTGCTCACTG
Found at i:52810 original size:43 final size:43
Alignment explanation
Indices: 52762--52845 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
52752 AAATCGTACA
*
52762 ATGCCAACGTCCCAGACATGGTCTTACATATAGC-CACATATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACATATA-CACACATATCG
**
52805 ATGCCATTGTCCCAGACAGGGTCTTACATATACACACATAT
1 ATGCCAACGTCCCAGACAGGGTCTTACATATACACACATAT
52846 AGGAATCACA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACATATACACACATATCG
Done.