Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1344
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: 50373
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:425 original size:15 final size:16
Alignment explanation
Indices: 394--426 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
384 TGTTATTTTT
*
394 TTTCTGCTTCTTTCAA
1 TTTCTGCTTCTTGCAA
410 TTTCTG-TTCTTGCAA
1 TTTCTGCTTCTTGCAA
425 TT
1 TT
427 AAATTTCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.12, C:0.21, G:0.09, T:0.58
Consensus pattern (16 bp):
TTTCTGCTTCTTGCAA
Found at i:6571 original size:42 final size:42
Alignment explanation
Indices: 6516--6634 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
6506 TTCTTCTCTC
* *
6516 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
6558 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
6600 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
6635 TTGTGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:6575 original size:12 final size:11
Alignment explanation
Indices: 6549--6624 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
6539 TCTATTATCT
*
6549 CTCCTGTCTCTC
1 CTCCTATCTC-C
6561 CTCCTATCATCC
1 CTCCTATC-TCC
6573 CTCCTATCT--
1 CTCCTATCTCC
*
6582 CTACTATCT--
1 CTCCTATCTCC
*
6591 CTCCTGTCTCTC
1 CTCCTATCTC-C
6603 CTCCTATCATCC
1 CTCCTATC-TCC
*
6615 CTCCTCTCTC
1 CTCCTATCTC
6625 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:6576 original size:24 final size:24
Alignment explanation
Indices: 6540--6625 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
6530 CCTCCTCTCT
* *
6540 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
6564 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
6585 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
6606 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
6626 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:6600 original size:18 final size:18
Alignment explanation
Indices: 6531--6601 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
6521 CCTGTCATCC
* *
6531 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
6549 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
6571 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
6591 CTCCTGTCTCT
1 CTCCTGTCTCT
6602 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:9927 original size:12 final size:11
Alignment explanation
Indices: 9905--9980 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
9895 ATAGAAAGAA
*
9905 GAGAGAGGAGG
1 GAGATAGGAGG
9916 GATGATAGGAGG
1 GA-GATAGGAGG
*
9928 AGAGACAGGA--
1 -GAGATAGGAGG
*
9938 GAGATAGTA--
1 GAGATAGGAGG
9947 GAGATAGGAGG
1 GAGATAGGAGG
9958 GATGATAGGAGG
1 GA-GATAGGAGG
*
9970 AGAGACAGGAG
1 -GAGATAGGAG
9981 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:9937 original size:24 final size:24
Alignment explanation
Indices: 9904--9989 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
9894 AATAGAAAGA
*
9904 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
9928 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
9946 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
9970 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
9990 AGAGTGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:9963 original size:42 final size:42
Alignment explanation
Indices: 9904--10013 Score: 177
Period size: 42 Copynumber: 2.6 Consensus size: 42
9894 AATAGAAAGA
* *
9904 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGT
1 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
9946 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
9988 AGAGAGT-GGAGGGATGACAGGAGGAG
1 AGAGA-TAGGAGGGATGATAGGAGGAG
10014 GAGAGAAGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
42 63 0.98
43 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.47, T:0.10
Consensus pattern (42 bp):
AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:15610 original size:22 final size:22
Alignment explanation
Indices: 15585--15628 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
15575 ATGGGCCTAT
15585 TGTTTAGGATTTCAGATTATGA
1 TGTTTAGGATTTCAGATTATGA
15607 TGTTTAGGATTTCAGATTATGA
1 TGTTTAGGATTTCAGATTATGA
15629 ATAAGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (22 bp):
TGTTTAGGATTTCAGATTATGA
Found at i:17415 original size:12 final size:12
Alignment explanation
Indices: 17393--17437 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
17383 AGAGAAAGAA
*
17393 GAGATAAGA-GG
1 GAGATAGGAGGG
17404 GATGATAGGAGGG
1 GA-GATAGGAGGG
17417 GAGATAGGAGGG
1 GAGATAGGAGGG
17429 GAGATAGGA
1 GAGATAGGA
17438 TAGATAGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 2 0.06
12 25 0.81
13 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.51, T:0.11
Consensus pattern (12 bp):
GAGATAGGAGGG
Found at i:17456 original size:42 final size:42
Alignment explanation
Indices: 17383--17513 Score: 145
Period size: 42 Copynumber: 3.0 Consensus size: 42
17373 TTGCCGTCAA
* * **
17383 AGAGAAAGAAGAGATAAGAGGGATGATAGGAGGGGAGATAGGAGG
1 AGAGATAGAAGAGATAATA--GA-GATAGGAGGGATGATAGGAGG
* * * * *
17428 GGAGATAGGATAGATAGTTGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAATAGAGATAGGAGGGATGATAGGAGG
*
17470 AGAGATAGAAGAGATAATAGAGAGAGGAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAATAGAGATAGGAGGGATGATAGGAGG
17512 AG
1 AG
17514 GACGGAAGAA
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
42 57 0.80
43 2 0.03
45 12 0.17
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (42 bp):
AGAGATAGAAGAGATAATAGAGATAGGAGGGATGATAGGAGG
Found at i:17476 original size:12 final size:11
Alignment explanation
Indices: 17393--17477 Score: 61
Period size: 12 Copynumber: 7.6 Consensus size: 11
17383 AGAGAAAGAA
*
17393 GAGATAAGAGG
1 GAGATAGGAGG
17404 GATGATAGGAGGG
1 GA-GATAGGA-GG
17417 GAGATAGGAGGG
1 GAGATAGGA-GG
17429 GAGATAGGA--
1 GAGATAGGAGG
* **
17438 TAGATA-G-TT
1 GAGATAGGAGG
17447 GAGATAGGAGG
1 GAGATAGGAGG
17458 GATGATAGGAGG
1 GA-GATAGGAGG
17470 AGAGATAG
1 -GAGATAG
17478 AAGAGATAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
8 1 0.02
9 10 0.16
10 1 0.02
11 4 0.07
12 39 0.64
13 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.47, T:0.15
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:22475 original size:64 final size:64
Alignment explanation
Indices: 22374--22529 Score: 294
Period size: 64 Copynumber: 2.4 Consensus size: 64
22364 GAGGGATTGG
* *
22374 AAGGAATTGGAGGTCTAATCACTAGGGATCAACACCTATTTCCAACCTTCTTATAATCCTTTGC
1 AAGGAATTGGAGGTCCAATGACTAGGGATCAACACCTATTTCCAACCTTCTTATAATCCTTTGC
22438 AAGGAATTGGAGGTCCAATGACTAGGGATCAACACCTATTTCCAACCTTCTTATAATCCTTTGC
1 AAGGAATTGGAGGTCCAATGACTAGGGATCAACACCTATTTCCAACCTTCTTATAATCCTTTGC
22502 AAGGAATTGGAGGTCCAATGACTAGGGA
1 AAGGAATTGGAGGTCCAATGACTAGGGA
22530 AGACTAAATG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 90 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (64 bp):
AAGGAATTGGAGGTCCAATGACTAGGGATCAACACCTATTTCCAACCTTCTTATAATCCTTTGC
Found at i:40572 original size:223 final size:219
Alignment explanation
Indices: 40179--40617 Score: 666
Period size: 223 Copynumber: 2.0 Consensus size: 219
40169 AACGTCAAGG
* *
40179 ATAAAAAAGTCACCTAAAGAGCCCTGTCGGTGTTCCTTTAGTCAATTGTATATAGATGTAGAGAC
1 ATAAAAAAGTCACCTAAAGAGCCCTGTCGGTGTTCCCTTAGTCAATTATATATAGATGTAGAGAC
* * *
40244 TACACTTGTGTACCGCTCTTGGGATTATGGGGAAGTACCAGTTATGCTTCTCTATTGGTATTGAG
66 TACACTTGTGTACCGCTCTTGGGATTATGGGGAAGTACCAGTTATGCTCCACTATTAGTATTGAG
** * *
40309 TCAGTTCCAGGGCCATCAATTCATCCTGTTCTTTGAAGACTTGGGACATTGGGATTT-TGAAATG
131 TCAGTTCCAGGGCCATCAATTCATCCCATTCTTCGAAGACTTGCGACATTGGGATTTATG--AT-
40373 GAGAGCCCAATTATAAAGCAAAAGTCGAC
193 --GAGCCCAATTATAAAGCAAAAGTCGAC
** *
40402 ATAAAAAAGTCACCTGGAGAGCCTTGTCGGTGTTCCCTTAGTCAATTATATATAGATGTAGAGAC
1 ATAAAAAAGTCACCTAAAGAGCCCTGTCGGTGTTCCCTTAGTCAATTATATATAGATGTAGAGAC
*
40467 TACACTTGTGTACCGCTTTTGGGATTATGGGGAAGTACCAGTTATGCTCCACTATTAGTATTGAG
66 TACACTTGTGTACCGCTCTTGGGATTATGGGGAAGTACCAGTTATGCTCCACTATTAGTATTGAG
* * *
40532 TCAGTTCCAGTGTCAGT-AATTCATCCCATTCTTCGAAGACTTGCGATATTGGGATTTATGATGA
131 TCAGTTCCAGGGCCA-TCAATTCATCCCATTCTTCGAAGACTTGCGACATTGGGATTTATGATGA
40596 GCCCAATTATAAAGCAAAAGTC
195 GCCCAATTATAAAGCAAAAGTC
40618 TAGATAGCTT
Statistics
Matches: 198, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
219 24 0.12
222 2 0.01
223 169 0.85
224 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (219 bp):
ATAAAAAAGTCACCTAAAGAGCCCTGTCGGTGTTCCCTTAGTCAATTATATATAGATGTAGAGAC
TACACTTGTGTACCGCTCTTGGGATTATGGGGAAGTACCAGTTATGCTCCACTATTAGTATTGAG
TCAGTTCCAGGGCCATCAATTCATCCCATTCTTCGAAGACTTGCGACATTGGGATTTATGATGAG
CCCAATTATAAAGCAAAAGTCGAC
Found at i:45911 original size:9 final size:9
Alignment explanation
Indices: 45899--45959 Score: 74
Period size: 9 Copynumber: 7.1 Consensus size: 9
45889 CTCTCTCTAT
45899 TATCTCTCC
1 TATCTCTCC
45908 TATCTCTCC
1 TATCTCTCC
*
45917 T-TCTAT-C
1 TATCTCTCC
*
45924 -ATCCCTCC
1 TATCTCTCC
*
45932 TATCTCTAC
1 TATCTCTCC
45941 TATCTCTCC
1 TATCTCTCC
45950 TATCTCTCC
1 TATCTCTCC
45959 T
1 T
45960 CCTATCATCC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.09
8 5 0.12
9 34 0.79
ACGTcount: A:0.13, C:0.43, G:0.00, T:0.44
Consensus pattern (9 bp):
TATCTCTCC
Found at i:45913 original size:18 final size:18
Alignment explanation
Indices: 45886--45956 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
45876 CCTGTCATCA
*
45886 CTCCTCTCTCTATTATCT
1 CTCCTATCTCTATTATCT
*
45904 CTCCTATCTCTCCTTCTATCAT
1 CTCCTATCTCT--AT-TATC-T
*
45926 CCCTCCTATCTCTACTATCT
1 --CTCCTATCTCTATTATCT
45946 CTCCTATCTCT
1 CTCCTATCTCT
45957 CCTCCTATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 21 0.49
20 2 0.05
21 8 0.19
22 1 0.02
24 11 0.26
ACGTcount: A:0.13, C:0.42, G:0.00, T:0.45
Consensus pattern (18 bp):
CTCCTATCTCTATTATCT
Found at i:45917 original size:42 final size:42
Alignment explanation
Indices: 45870--45978 Score: 155
Period size: 42 Copynumber: 2.6 Consensus size: 42
45860 CTTCTTCTCT
* * *
45870 TCTCCTCCTGTCATCACTCCTCTCTCTATTATCTCTCCTATC
1 TCTCCTCCTATCATCACTCCTATCTCTACTATCTCTCCTATC
* *
45912 TCTCCTTCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
1 TCTCCTCCTATCATCACTCCTATCTCTACTATCTCTCCTATC
* *
45954 TCTCCTCCTATCATCCCTCTTATCT
1 TCTCCTCCTATCATCACTCCTATCT
45979 ATTCTTTCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.13, C:0.43, G:0.01, T:0.43
Consensus pattern (42 bp):
TCTCCTCCTATCATCACTCCTATCTCTACTATCTCTCCTATC
Found at i:45931 original size:24 final size:24
Alignment explanation
Indices: 45894--45978 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 24
45884 CACTCCTCTC
* *
45894 TCTATTATCTCTCCTATCTCTCCT
1 TCTATCATCCCTCCTATCTCTCCT
45918 TCTATCATCCCTCCTA--TCT-CT
1 TCTATCATCCCTCCTATCTCTCCT
*
45939 ACTATC-T--CTCCTATCTCTCCT
1 TCTATCATCCCTCCTATCTCTCCT
* *
45960 CCTATCATCCCTCTTATCT
1 TCTATCATCCCTCCTATCT
45979 ATTCTTTCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
18 6 0.12
20 4 0.08
21 14 0.28
22 4 0.08
24 22 0.44
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (24 bp):
TCTATCATCCCTCCTATCTCTCCT
Done.