Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1388
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: 16732
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Found at i:3760 original size:27 final size:27
Alignment explanation
Indices: 3722--3783 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
3712 CCAAGATCTT
** *
3722 CATGTTTAGTGTCCTTACGGGCTATCC
1 CATGTTTAGTGTCCCAACGGACTATCC
*
3749 CATGTTTAGTGTCCCAATGGACTATCC
1 CATGTTTAGTGTCCCAACGGACTATCC
3776 CATGTTTA
1 CATGTTTA
3784 ATATTTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (27 bp):
CATGTTTAGTGTCCCAACGGACTATCC
Found at i:3819 original size:27 final size:27
Alignment explanation
Indices: 3768--3819 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3758 TGTCCCAATG
*
3768 GACTATCCCATGTTTAATATTTTGTTA
1 GACTATCCCATGTTTAATATCTTGTTA
* * *
3795 GACTATCTCATGTTTGATGTCTTGT
1 GACTATCCCATGTTTAATATCTTGT
3820 CAGTCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.48
Consensus pattern (27 bp):
GACTATCCCATGTTTAATATCTTGTTA
Found at i:3827 original size:27 final size:27
Alignment explanation
Indices: 3768--3827 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
3758 TGTCCCAATG
* *
3768 GACTATCCCATGTTTAATATTTTGTTA
1 GACTATCCCATGTTTAATATCTTGTCA
* * *
3795 GACTATCTCATGTTTGATGTCTTGTCA
1 GACTATCCCATGTTTAATATCTTGTCA
*
3822 GTCTAT
1 GACTAT
3828 TTATGATGCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.47
Consensus pattern (27 bp):
GACTATCCCATGTTTAATATCTTGTCA
Found at i:6555 original size:47 final size:47
Alignment explanation
Indices: 6477--6931 Score: 750
Period size: 47 Copynumber: 9.6 Consensus size: 47
6467 CCCTTCGGGA
* * * * * *
6477 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6524 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6571 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTATGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6618 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6665 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6714 CTAATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6761 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6810 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6856 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6903 CTTATCACATATATATACGCTTTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
6932 TATTCAAATA
Statistics
Matches: 386, Mismatches: 15, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
46 46 0.12
47 229 0.59
49 111 0.29
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:6706 original size:96 final size:96
Alignment explanation
Indices: 6477--6931 Score: 753
Period size: 96 Copynumber: 4.8 Consensus size: 96
6467 CCCTTCGGGA
* * * * * * *
6477 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
6540 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
6571 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTATGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
6634 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
6665 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTAATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
6730 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
6761 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
6826 ACTTTCACATTCATCACATCGGCCATTAGG-
66 ACTTTCACATTCATCACATCGGCCATTAGGC
6856 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
*
6919 ACGCTTTCACATT
64 ACACTTTCACATT
6932 TATTCAAATA
Statistics
Matches: 343, Mismatches: 12, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
93 48 0.14
94 91 0.27
95 26 0.08
96 178 0.52
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:6733 original size:143 final size:142
Alignment explanation
Indices: 6477--6931 Score: 754
Period size: 143 Copynumber: 3.2 Consensus size: 142
6467 CCCTTCGGGA
* * * * * * * *
6477 CTTATCAC-ATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
6541 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
66 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
*
6606 CGGCCATTATGC
131 CGGCCATTAGGC
6618 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATA
*
6682 CACTTTCACATTCATCACATCGGCCATTAGGCCTAATCACATATATACACTTTCACATTCATCAC
64 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
6747 ATCGGCCATTAGGC
129 ATCGGCCATTAGGC
6761 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
6826 ACTTTCACATTCATCACATCGGCCATTAGG-CTTATCACATATATACACTTTCACATTCATCACA
65 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
6890 TCGGCCATTAGGC
130 TCGGCCATTAGGC
*
6903 CTTATCACATATATATACGCTTTCACATT
1 CTTATCACA-ATATATACACTTTCACATT
6932 TATTCAAATA
Statistics
Matches: 298, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
141 47 0.16
142 74 0.25
143 130 0.44
145 47 0.16
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (142 bp):
CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGC
Found at i:11347 original size:39 final size:40
Alignment explanation
Indices: 11193--11386 Score: 250
Period size: 40 Copynumber: 4.9 Consensus size: 40
11183 CGAATACACG
* * * * *
11193 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * ** * *
11233 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
11273 TCACTAGC--GAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
11311 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
11350 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
11387 TTAGTAACTC
Statistics
Matches: 135, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
38 33 0.24
39 38 0.28
40 64 0.47
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:11405 original size:40 final size:39
Alignment explanation
Indices: 11206--11502 Score: 245
Period size: 40 Copynumber: 7.6 Consensus size: 39
11196 CCAGCATGAT
* * * *
11206 TGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCAC-AA
** * *
11246 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGC-GAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACAA
* * *
11284 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCA-CAA
* *
11324 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCA-CAA
* * *
11363 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACAA
*
11403 TGC-CTTCGGG-CTTAGCCCGGA-ATTAGT-ATCTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATA-TA-TCA-CTAGCAC-AA
* *
11442 TG--CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACAA
*
11481 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
11503 CATCATTCGA
Statistics
Matches: 217, Mismatches: 25, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
37 3 0.01
38 58 0.27
39 65 0.30
40 81 0.37
41 10 0.05
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACAA
Found at i:11417 original size:117 final size:118
Alignment explanation
Indices: 11193--11423 Score: 279
Period size: 117 Copynumber: 2.0 Consensus size: 118
11183 CGAATACACG
* * *
11193 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGG
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGA
* * *
11258 TTTAGCACGGATATATCACTAGCGAATGCTCTTCGGAACTTAGCCCGGATACA
66 CTTAGCACGGATATATAACTAGCCAATGCTCTTCGGAACTTAGCCCGGATACA
* * * * * *
11311 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGA
* * * *
11375 CTTAGCCCGGATTTAGTAACTCGCACAATGC-CTTCGG-GCTTAGCCCGGA
66 CTTAGCACGGATATA-TAACTAGC-CAATGCTCTTCGGAACTTAGCCCGGA
11424 ATTAGTATCT
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
117 59 0.62
118 31 0.33
119 5 0.05
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (118 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGA
CTTAGCACGGATATATAACTAGCCAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:11429 original size:38 final size:39
Alignment explanation
Indices: 11361--11502 Score: 148
Period size: 38 Copynumber: 3.6 Consensus size: 39
11351 CACTAGCATG
*
11361 AATGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
1 AATGC-CTTCGGGACTTAGCCCGGAATTAGTAACTCGCAC
*
11401 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCAC
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCAC
* * * *
11439 AAATG-CTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCAC
*
11479 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
11503 CATCATTCGA
Statistics
Matches: 85, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
37 2 0.02
38 30 0.35
39 27 0.32
40 23 0.27
41 3 0.04
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCAC
Found at i:11848 original size:29 final size:29
Alignment explanation
Indices: 11809--11887 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
11799 CTTAATAATC
*
11809 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
11839 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
11868 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
11888 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:12013 original size:43 final size:43
Alignment explanation
Indices: 11869--12012 Score: 265
Period size: 43 Copynumber: 3.4 Consensus size: 43
11859 TGCATTTCAA
11869 GCCCGCACACTTAGTGCCAATCTCACAACC-TGAACACTTA-T
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
11910 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
11953 GCCCGCACACTTAGTGCTAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
11996 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
12013 TGAAAACCAA
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
41 30 0.30
42 10 0.10
43 60 0.60
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:13509 original size:47 final size:47
Alignment explanation
Indices: 13431--13600 Score: 250
Period size: 47 Copynumber: 3.6 Consensus size: 47
13421 CCCTTCGGGA
* * * * * *
13431 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
13478 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13525 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13572 CTTATCACATATATATACACTTTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
13601 ATTCAAATAT
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
47 92 0.83
49 19 0.17
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.