Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2891
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: 35145
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:9391 original size:15 final size:15
Alignment explanation
Indices: 9371--9425 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
9361 ACTCTCCTCA
*
9371 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
9386 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
9401 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
9415 TTCTTTT-TCTC
1 TTCTTTTCTCTC
9426 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:11484 original size:17 final size:17
Alignment explanation
Indices: 11450--11484 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11440 ACTTCTCTTT
*
11450 TTTTTTTTAATTCCGAA
1 TTTTTTTTAATACCGAA
*
11467 TTTTTTTTAATACTGAA
1 TTTTTTTTAATACCGAA
11484 T
1 T
11485 ACACAAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTTTTAATACCGAA
Found at i:14765 original size:48 final size:48
Alignment explanation
Indices: 14710--14994 Score: 525
Period size: 48 Copynumber: 5.9 Consensus size: 48
14700 TATATATGTG
* *
14710 TGTGGTAAAGCTGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
14758 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
14806 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
14854 TGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
14902 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
14950 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGATATGT
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGT
14995 GTATATTGTG
Statistics
Matches: 231, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 231 1.00
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
Found at i:15184 original size:37 final size:37
Alignment explanation
Indices: 15134--15231 Score: 169
Period size: 37 Copynumber: 2.6 Consensus size: 37
15124 AATATATTCT
15134 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
* *
15171 GGGTAAGACCCGATGACTACGTATGGAGATTTTGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
*
15208 GGGTAAGACCCGATAACTACGTGT
1 GGGTAAGACCCGATGACTACGTGT
15232 AGGGACTATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
Found at i:16563 original size:40 final size:40
Alignment explanation
Indices: 16509--16785 Score: 405
Period size: 40 Copynumber: 7.0 Consensus size: 40
16499 ATTGAGAGTT
*
16509 ATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
* *
16549 TTATGTCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
* * *
16589 TTATGTCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
* * *
16629 TTATGTCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
* * *
16669 ATATATCTGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
*
16709 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
*
16749 ATATATCCGGGCTAA-ACCTCGAAG-GCATTCGTGCTGG
1 ATATATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCTGG
16786 AATTATGAGG
Statistics
Matches: 224, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 14 0.06
40 210 0.94
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (40 bp):
ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
Found at i:16861 original size:29 final size:29
Alignment explanation
Indices: 16791--16923 Score: 121
Period size: 29 Copynumber: 4.7 Consensus size: 29
16781 GCTGGAATTA
* * *
16791 TGAGGCACTGTGTGTGCAAGTTC-TTCAAT
1 TGAGGCACTATGTGTGCGAGTTCGGT-AAT
* *
16820 CGA-GCGCTATGTGTGCGAGATT-GGTAAT
1 TGAGGCACTATGTGTGCGAG-TTCGGTAAT
**
16848 TGAGGCACTATGTGTGCGAGTTCTTTAAT
1 TGAGGCACTATGTGTGCGAGTTCGGTAAT
**
16877 TGAGGCACTATGTGTGCGAGTTCTATAAT
1 TGAGGCACTATGTGTGCGAGTTCGGTAAT
* *
16906 CGA-GCGCTATGTGTGCGA
1 TGAGGCACTATGTGTGCGA
16924 AATCAGTCAG
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
28 34 0.39
29 54 0.61
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (29 bp):
TGAGGCACTATGTGTGCGAGTTCGGTAAT
Found at i:16916 original size:57 final size:57
Alignment explanation
Indices: 16792--16923 Score: 151
Period size: 57 Copynumber: 2.3 Consensus size: 57
16782 CTGGAATTAT
* * * * *
16792 GAGGCACTGTGTGTGCAAGTTCTTCAATCGAGCGCTATGTGTGCGAGATTGGTAATT
1 GAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGATAATC
* * *
16849 GAGGCACTATGTGTGCGAGTTCTTTAATTGAGGCACTATGTGTGCGAG-TTCTATAATC
1 GAGGCACTATGTGTGCGAGTTCTTCAATCGA-GCACTATGTGTGCGAGATT-GATAATC
*
16907 GA-GCGCTATGTGTGCGA
1 GAGGCACTATGTGTGCGA
16924 AATCAGTCAG
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 43 0.67
58 21 0.33
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (57 bp):
GAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGATAATC
Found at i:17836 original size:4 final size:4
Alignment explanation
Indices: 17827--17854 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
17817 TTAAACTAAG
17827 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
17855 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:21842 original size:48 final size:48
Alignment explanation
Indices: 21417--21842 Score: 771
Period size: 48 Copynumber: 8.9 Consensus size: 48
21407 CAAGATAAAT
* * *
21417 ATATATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
21465 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
21513 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
21561 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
21609 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
21657 ATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
21705 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
21753 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
21801 ATATGTATATGTGGTAAATCCGAATGGCTAGTGTGAAATATG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATG
21843 AAGGAGATGT
Statistics
Matches: 369, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 369 1.00
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:22091 original size:37 final size:37
Alignment explanation
Indices: 21991--22093 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
21981 GGAAATATAT
*
21991 TCCGGGTAAGACCCGATGACTACGTGCGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
22028 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
22065 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
22094 GGACTATTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.23
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:27339 original size:46 final size:46
Alignment explanation
Indices: 27272--27441 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 46
27262 AACCCGCCCC
* *
27272 TAAGTGAACTCGGACTCAACTCAACAAGCTCAGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCATTCGCATCCA
* *
27318 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GG-ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCATTCGC-A--TCCA
* * *
27364 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCATTCGCATCCA
*
27411 TAAGTGAACTCGGACTCAACTCAATGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
27442 GGATGCTCAA
Statistics
Matches: 103, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 4 0.04
46 57 0.55
47 29 0.28
48 3 0.03
49 4 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCATTCGCATCCA
Found at i:27389 original size:93 final size:93
Alignment explanation
Indices: 27277--27447 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
27267 GCCCCTAAGT
*
27277 GAACTCGGACTCAACTCAACAAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27342 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
27370 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
27435 TGAGTTCGGATGC
66 CGAGTTCGGATGC
27448 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:34409 original size:46 final size:44
Alignment explanation
Indices: 34307--34432 Score: 191
Period size: 46 Copynumber: 2.8 Consensus size: 44
34297 AACCCGCCCC
* *
34307 TAAGTGAACTCGGACTCAACTCAACGAGCTGGGTGTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTGGATGTCGCATCCA
34351 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAT-TCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTT-GG--ATGTCGCATCCA
34397 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGATG
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTGGATG
34433 CTCAACCATC
Statistics
Matches: 75, Mismatches: 2, Indels: 9
0.87 0.02 0.10
Matches are distributed among these distances:
44 31 0.41
45 2 0.03
46 39 0.52
47 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.22
Consensus pattern (44 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTGGATGTCGCATCCA
Found at i:34449 original size:46 final size:45
Alignment explanation
Indices: 34309--34449 Score: 137
Period size: 46 Copynumber: 3.1 Consensus size: 45
34299 CCCGCCCCTA
* * *
34309 AGTGAACTCGGACTCAACTCAACGAG-CTGGGTG-TC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTTGGATGCTCACCATCC-T
* *** *
34352 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTTGGATGCTCACCATCC-T
34398 AAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTTGGATGCTC-ACCATCCT
34445 AGTGA
1 AGTGA
34450 CATGTCACTT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
44 26 0.31
45 2 0.02
46 49 0.59
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTTGGATGCTCACCATCCT
Done.