Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_5986
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: 8866
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Found at i:643 original size:27 final size:27
Alignment explanation
Indices: 612--787 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
602 TAAATTGTAC
612 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* **
639 TGCACTAAGTGTGCGAAATGA--ATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
663 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
691 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
719 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
746 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
773 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
788 GGCTCAATAT
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
25 22 0.17
27 83 0.65
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:673 original size:52 final size:54
Alignment explanation
Indices: 612--762 Score: 182
Period size: 55 Copynumber: 2.8 Consensus size: 54
602 TAAATTGTAC
*
612 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AATGA-ATG-
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGACATGT
* * ** **
663 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGAC-ATGT
* *
719 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAG
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAG
763 TTGATTATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
51 1 0.01
52 38 0.46
53 3 0.04
55 40 0.48
56 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGACATGT
Found at i:798 original size:27 final size:27
Alignment explanation
Indices: 692--798 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
682 TGACCATGCG
* * * *
692 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
720 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
747 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
774 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
799 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:2304 original size:43 final size:41
Alignment explanation
Indices: 2269--2352 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
2259 TCTTATATGT
*
2269 AATCAAATATCGATGCCACTATCCCAGATAGGGTCTTACACGA
1 AATCAAATA--GATGCCAATATCCCAGATAGGGTCTTACACGA
* *
2312 AATCAAATAGATGCCAATGTCCCAGA-CGTGGTCTTACACGA
1 AATCAAATAGATGCCAATATCCCAGATAG-GGTCTTACACGA
2353 TAACTCATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 1 0.03
41 27 0.73
43 9 0.24
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (41 bp):
AATCAAATAGATGCCAATATCCCAGATAGGGTCTTACACGA
Found at i:2337 original size:41 final size:42
Alignment explanation
Indices: 2238--2352 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
2228 AGCTCGTACA
* * * *
2238 ATGCCAACGTCCCAGACGTGGTCTTATATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATA-CG
* * *
2281 ATGCCACTATCCCAGATAG-GGTCTTACACGAAATCAAATA-G
1 ATGCCAATGTCCCAGA-CGTGGTCTTACACGAAATCAAATACG
2322 ATGCCAATGTCCCAGACGTGGTCTTACACGA
1 ATGCCAATGTCCCAGACGTGGTCTTACACGA
2353 TAACTCATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
40 1 0.02
41 27 0.45
43 31 0.52
44 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATACG
Found at i:4444 original size:29 final size:28
Alignment explanation
Indices: 4387--4442 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
4377 TTTTAATTAA
* * *
4387 ATGTGAATTATATATGCTGAATTGAAAT
1 ATGTAAATTATATATGCCGAAGTGAAAT
4415 ATGTAAATGTATATATGCCGAACGTGAA
1 ATGTAAAT-TATATATGCCGAA-GTGAA
4443 TAAGCTTGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 7 0.30
29 12 0.52
30 4 0.17
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (28 bp):
ATGTAAATTATATATGCCGAAGTGAAAT
Found at i:4677 original size:55 final size:55
Alignment explanation
Indices: 4582--4686 Score: 144
Period size: 55 Copynumber: 1.9 Consensus size: 55
4572 ACCATGGCAT
*
4582 CGATATATGTGTGTAAGTAAGACCACGTTTATACGTTGGCATCGATATGTGACTC
1 CGATATATGTGTGTAAGTAAGACCACGTTTAGACGTTGGCATCGATATGTGACTC
*
4637 CGATATATGT-TGTGAGTAAGACC-CTGTTTGAGACAG-TGGCATCGATATGT
1 CGATATATGTGTGTAAGTAAGACCAC-GTTT-AGAC-GTTGGCATCGATATGT
4687 TATTACATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
53 1 0.02
54 16 0.36
55 27 0.60
56 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (55 bp):
CGATATATGTGTGTAAGTAAGACCACGTTTAGACGTTGGCATCGATATGTGACTC
Found at i:8502 original size:37 final size:40
Alignment explanation
Indices: 8421--8653 Score: 179
Period size: 37 Copynumber: 5.8 Consensus size: 40
8411 GAATAGTAAG
*
8421 GCCTAATGGCCGATGTGA-GAATGTGAAAGTGTATTATATGATAA
1 GCCTAATGGCCGATGTGATG-A--TGAAAGTGTA--AAATGATAA
8465 GCCTAATGG-CGATGTGAT-ATGAAAGTG-AAAATGATAA
1 GCCTAATGGCCGATGTGATGATGAAAGTGTAAAATGATAA
*
8502 GGCC-AATGGCCGATGTGATGAATG-AAGTGT-ATAT-ATAAA
1 -GCCTAATGGCCGATGTGATG-ATGAAAGTGTAAAATGAT-AA
* *
8541 GGC-AAT-GCCGATGTGA-GAGTGAAAGTGTAATAGTGA-AA
1 GCCTAATGGCCGATGTGATGA-TGAAAGTGTAA-AATGATAA
8579 GCCT-ATGGCCGATGTGATGAATGTGAAAGTGTATAATATGATAA
1 GCCTAATGGCCGATGTGATG-A--TGAAAGTGTA-AA-ATGATAA
*
8623 GGCTAATGGCCGATGT-ATGATGTAAAGTGTA
1 GCCTAATGGCCGATGTGATGATG-AAAGTGTA
8654 TATAAGGGCC
Statistics
Matches: 159, Mismatches: 8, Indels: 46
0.75 0.04 0.22
Matches are distributed among these distances:
35 1 0.01
36 3 0.02
37 29 0.18
38 26 0.16
39 22 0.14
40 13 0.08
41 3 0.02
42 21 0.13
43 13 0.08
44 17 0.11
45 11 0.07
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.27
Consensus pattern (40 bp):
GCCTAATGGCCGATGTGATGATGAAAGTGTAAAATGATAA
Found at i:8587 original size:76 final size:79
Alignment explanation
Indices: 8411--8651 Score: 257
Period size: 76 Copynumber: 3.0 Consensus size: 79
8401 TAATGAAAAA
* * *
8411 GAATAGT-AAGGCCTAATGGCCGATGTGA-GAATGTGAAAGTGTATTATATGATAAGCCTAATGG
1 GAATAGTGAAAGCCT-ATGGCCGATGTGATGAA-GTGAAAGTGTA-TATATGATAAGGCTAATGC
*
8474 CGATGTGATATGAAAGT
63 CGATGTGAGATGAAAGT
* *
8491 GAA-AATGATAAGGCCAATGGCCGATGTGATGAA-TG-AAGTGTATATAT-A-AAGGC-AATGCC
1 GAATAGTGA-AA-GCCTATGGCCGATGTGATGAAGTGAAAGTGTATATATGATAAGGCTAATGCC
8550 GATGTGAGAGTGAAAGT
64 GATGTGAGA-TGAAAGT
8567 GTAATAGTGAAAGCCTATGGCCGATGTGATGAATGTGAAAGTGTATAATATGATAAGGCTAATGG
1 G-AATAGTGAAAGCCTATGGCCGATGTGATGAA-GTGAAAGTGTAT-ATATGATAAGGCTAAT-G
8632 CCGATGT-ATGATGTAAAGT
62 CCGATGTGA-GATG-AAAGT
8651 G
1 G
8652 TATATAAGGG
Statistics
Matches: 136, Mismatches: 8, Indels: 30
0.78 0.05 0.17
Matches are distributed among these distances:
75 13 0.10
76 32 0.24
77 5 0.04
78 11 0.08
79 17 0.12
80 10 0.07
81 15 0.11
82 11 0.08
83 6 0.04
84 16 0.12
ACGTcount: A:0.36, C:0.09, G:0.29, T:0.26
Consensus pattern (79 bp):
GAATAGTGAAAGCCTATGGCCGATGTGATGAAGTGAAAGTGTATATATGATAAGGCTAATGCCGA
TGTGAGATGAAAGT
Found at i:8631 original size:121 final size:116
Alignment explanation
Indices: 8429--8657 Score: 290
Period size: 121 Copynumber: 1.9 Consensus size: 116
8419 AGGCCTAATG
8429 GCCGATGTGAGAATGTGAAAGTGTATTATATGATAAGCCTAATGGCGATGTGATATGAAAGTGAA
1 GCCGATGTGAGAATGTGAAAGTGTA-TATATGATAAGCCTAATGGCGATGTGATATGAAAGTGAA
8494 AATGATAAGGCCAATGGCCGATGTGATGAATG-AAGTGTATATATAAAGGCAAT
65 AATGATAAGGCCAATGGCCGATGT-ATG-ATGAAAGTGTATATATAAAGGCAAT
8547 GCCGATGTGAG-A-GTGAAAGTGTA-ATAGTGA-AAGCCT-ATGGCCGATGTGATGAATGTGAAA
1 GCCGATGTGAGAATGTGAAAGTGTATATA-TGATAAGCCTAATGG-CGATGTGAT--A--TGAAA
*
8607 GTGTATAATATGATAAGGCTAATGGCCGATGTATGATGTAAAGTGTATATA
60 GTG-A-AA-ATGATAAGGCCAATGGCCGATGTATGATG-AAAGTGTATATA
8658 AGGGCCTAAT
Statistics
Matches: 99, Mismatches: 1, Indels: 19
0.83 0.01 0.16
Matches are distributed among these distances:
113 4 0.04
114 18 0.18
115 3 0.03
116 12 0.12
117 1 0.01
118 19 0.19
119 4 0.04
120 5 0.05
121 33 0.33
ACGTcount: A:0.36, C:0.08, G:0.29, T:0.27
Consensus pattern (116 bp):
GCCGATGTGAGAATGTGAAAGTGTATATATGATAAGCCTAATGGCGATGTGATATGAAAGTGAAA
ATGATAAGGCCAATGGCCGATGTATGATGAAAGTGTATATATAAAGGCAAT
Found at i:8808 original size:37 final size:37
Alignment explanation
Indices: 8758--8829 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
8748 AATGGTGAAA
*
8758 GATAACTTCGTGTGGAGATTATGTCTGGGTAAGACCC
1 GATAACTTCGTGTGGAGATTATGTCCGGGTAAGACCC
8795 GATAACTTCGTGTGGAGATTATGTCCGGGTAAGAC
1 GATAACTTCGTGTGGAGATTATGTCCGGGTAAGAC
8830 TTCGTAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.29
Consensus pattern (37 bp):
GATAACTTCGTGTGGAGATTATGTCCGGGTAAGACCC
Done.