Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2704
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: 28692
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Found at i:4986 original size:27 final size:27
Alignment explanation
Indices: 4956--5067 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
4946 AGGAAGCGTC
*
4956 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
4983 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
5010 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
5038 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
5064 CTGG
1 CTGG
5068 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:5062 original size:54 final size:54
Alignment explanation
Indices: 4956--5067 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
4946 AGGAAGCGTC
* *
4956 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
5010 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
5064 CTGG
1 CTGG
5068 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:11571 original size:40 final size:40
Alignment explanation
Indices: 11509--11712 Score: 276
Period size: 40 Copynumber: 5.2 Consensus size: 40
11499 AAACCAAGTA
* * *
11509 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCACTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCACACAAATG
* *
11548 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
11588 CCTTCGGGACTTAGCCC-GATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
11627 CCTTCGGGACTTAGCCCGGATATAGTAACT-AGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCA-CACAAATG
*
11667 CCTTCGGGACTTAGCCCGGA-ATTAGTCACT-AGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCA-CACAAATG
11707 CCTTCG
1 CCTTCG
11713 TTATCATCCG
Statistics
Matches: 152, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
39 52 0.34
40 100 0.66
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
Found at i:11640 original size:79 final size:78
Alignment explanation
Indices: 11509--11712 Score: 286
Period size: 79 Copynumber: 2.6 Consensus size: 78
11499 AAACCAAGTA
* * * *
11509 CCTTCGGGATTTAACCGGATATAGCTACTCACTCAAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCCGATATAG-TACTCACACAAATGCCTTCGGGACTTAGCCCGGATATAGT
* *
11574 AGCTCGCACAAATG
65 AACTAGCACAAATG
11588 CCTTCGGGACTTAGCCCGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCCGATATAGT-ACTCACACAAATGCCTTCGGGACTTAGCCCGGATATAGT
11653 AACTAGCACAAATG
65 AACTAGCACAAATG
11667 CCTTCGGGACTTAGCCCGGA-ATTAGTCACT-AGCACAAATGCCTTCG
1 CCTTCGGGACTTAGCCC-GATA-TAGT-ACTCA-CACAAATGCCTTCG
11713 TTATCATCCG
Statistics
Matches: 114, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
78 1 0.01
79 90 0.79
80 23 0.20
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCCGATATAGTACTCACACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
ACTAGCACAAATG
Found at i:16299 original size:27 final size:27
Alignment explanation
Indices: 16258--16363 Score: 117
Period size: 27 Copynumber: 3.9 Consensus size: 27
16248 AGGAAGCGTC
*
16258 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* *
16285 CTAGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
16312 CTGGTGGCTCTGCTACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* *
16340 CTGGTGACTCTGTCAC-ATTATCTG
1 CTGGTGGCTCTGCCACAATTATCTG
16364 TCCTAGCAGC
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
26 3 0.05
27 46 0.70
28 17 0.26
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:16364 original size:54 final size:54
Alignment explanation
Indices: 16258--16364 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
16248 AGGAAGCGTC
* *
16258 CTGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTT
* * * * *
16312 CTGGTGGCTCTGCTACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTAGTGACTCTGCCACATATATCTGT
16365 CCTAGCAGCC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 28 0.62
55 17 0.38
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTT
Found at i:19452 original size:39 final size:40
Alignment explanation
Indices: 19407--19631 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
19397 GCTCCTCGTT
* * * *
19407 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
19447 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
19486 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
19526 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
19566 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
19607 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
19632 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
39 37 0.24
40 104 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:19500 original size:40 final size:38
Alignment explanation
Indices: 19374--19631 Score: 200
Period size: 40 Copynumber: 6.5 Consensus size: 38
19364 AAATCACGTA
* * *
19374 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCG--CACAATG
* * * *
19413 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAATG
*
19452 CCTTCGGGACTTAACCCGGATTTAATGACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCAC-AATG
*
19492 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCAC-AATG
* *
19532 CCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCAC-AATG
** * * * *
19572 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAATG
*
19612 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
19632 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 28, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.01
39 50 0.28
40 116 0.64
41 12 0.07
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (38 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAATG
Found at i:19640 original size:41 final size:41
Alignment explanation
Indices: 19563--19640 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
19553 CTTGTATCTC
* * *
19563 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
19604 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
19641 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:26990 original size:28 final size:30
Alignment explanation
Indices: 26949--27040 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 30
26939 GGTTTTAGTA
*
26949 ACTCACAC-AATGCCTTCGGGACTTAACCC
1 ACTCGCACGAATGCCTTCGGGACTTAACCC
26978 -CTCGCACG-ATGCCTTCGGGACTTAACCC
1 ACTCGCACGAATGCCTTCGGGACTTAACCC
27006 GGATAACTCGCACGAATGCCTTCGGGACTTAACCC
1 -----ACTCGCACGAATGCCTTCGGGACTTAACCC
27041 GGATTTATCT
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
28 26 0.48
34 8 0.15
35 20 0.37
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.21
Consensus pattern (30 bp):
ACTCGCACGAATGCCTTCGGGACTTAACCC
Found at i:27095 original size:39 final size:38
Alignment explanation
Indices: 26978--27159 Score: 175
Period size: 40 Copynumber: 4.8 Consensus size: 38
26968 GACTTAACCC
*
26978 CTCGCAC-GATGCCTTCGGGACTTAACCCGGA-TA-A-
1 CTCGCACAAATGCCTTCGGGACTTAACCCGGATTATAT
*
27012 CTCGCACGAATGCCTTCGGGACTTAACCCGGATT-TAT
1 CTCGCACAAATGCCTTCGGGACTTAACCCGGATTATAT
*
27049 CTCGCACAAAGGCCTTCGGG-CTTAACCCGGAATTAGTAT
1 CTCGCACAAATGCCTTCGGGACTTAACCCGG-ATTA-TAT
**
27088 CTCGCACAAATGCCTTC-GGATCTTAGTCCGGA-TATATT
1 CTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTATA-T
* *
27126 CACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 --C-TCGCACAAATGCCTTCGGGACTTAACCCGGA
27160 CAGCATTCAA
Statistics
Matches: 126, Mismatches: 8, Indels: 22
0.81 0.05 0.14
Matches are distributed among these distances:
34 7 0.06
35 23 0.18
36 12 0.10
37 23 0.18
38 5 0.04
39 20 0.16
40 25 0.20
41 11 0.09
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (38 bp):
CTCGCACAAATGCCTTCGGGACTTAACCCGGATTATAT
Found at i:27168 original size:41 final size:41
Alignment explanation
Indices: 27091--27168 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
27081 TTAGTATCTC
* * *
27091 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
27132 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
27169 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.