Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold399
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: 184626
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 2
Found at i:139384 original size:227 final size:226
Alignment explanation
Indices: 138983--139435 Score: 622
Period size: 227 Copynumber: 2.0 Consensus size: 226
138973 TCCGGGGTCA
* * *
138983 AAGCCGACAGGCAAACTAAGGAAAAGAAAGTCTCCGAGGTCAAAGCCGACAAGCAGACTAAGGGT
1 AAGCCGACAAGCAAACTAAGGAAAAGAAAGTCTCCGAGGACAAAGCCGACAAGCAGACTAAGGGA
* * * * *
139048 AGGAAAGTCTCCGAGGTCAAAGTCGACAGGCAGACTAAGGGTAGGAAAGTCTCCAAGGACGAAGC
66 AGGAAAGTCTCCGAGGTCAAAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCC-AGGACAAAGC
*
139113 CGACAGGCAGACTAAGAGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGGGAAGGA
130 CGACAGGCAGACTAAGAGAAAGAAAGTCTCCAGGGACAAAGCCGACAGGCAGACTAAGGGAAGGA
* *
139178 AAGTCTCCAGGGACGAAGCCAACAGGCAGACG
195 AAGTCTCCAGGGACAAAGCCAACAAGCAGACG
* * * *
139210 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCC-AGGGACGAAGCCGACAAGCAGACTAAGGG
1 AAGCCGACAAGCAAACTAAGGAAAAGAAAGTCTCCGA-GGACAAAGCCGACAAGCAGACTAAGGG
*
139274 AAGGAAAGTCTCCGGGGTCAAAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCC-GGAGTCAAA
65 AAGGAAAGTCTCCGAGGTCAAAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGA--CAAA
* * * * * * *
139338 GCTGACAGGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCAAAGCCGATAGGCAGACTAAGGGTAG
128 GCCGACAGGCAGACTAAGAGAAAGAAAGTCTCCAGGGACAAAGCCGACAGGCAGACTAAGGGAAG
* * *
139403 GAAAGTCTCCGGGGTCAAAGCCGACAAGCAGAC
193 GAAAGTCTCCAGGGACAAAGCCAACAAGCAGAC
139436 TAAGGGAAAA
Statistics
Matches: 197, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
225 3 0.02
226 1 0.01
227 193 0.98
ACGTcount: A:0.37, C:0.21, G:0.32, T:0.09
Consensus pattern (226 bp):
AAGCCGACAAGCAAACTAAGGAAAAGAAAGTCTCCGAGGACAAAGCCGACAAGCAGACTAAGGGA
AGGAAAGTCTCCGAGGTCAAAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGACAAAGCC
GACAGGCAGACTAAGAGAAAGAAAGTCTCCAGGGACAAAGCCGACAGGCAGACTAAGGGAAGGAA
AGTCTCCAGGGACAAAGCCAACAAGCAGACG
Found at i:153159 original size:20 final size:20
Alignment explanation
Indices: 153134--153194 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
153124 CCCATCATTT
153134 CATGTTTTCTACAAGCTTCA
1 CATGTTTTCTACAAGCTTCA
*
153154 CATGTTTTCTACATGCTTCA
1 CATGTTTTCTACAAGCTTCA
153174 CATGTTTTCTACAAGCTTCA
1 CATGTTTTCTACAAGCTTCA
153194 C
1 C
153195 GTGATGGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.41
Consensus pattern (20 bp):
CATGTTTTCTACAAGCTTCA
Found at i:157474 original size:50 final size:50
Alignment explanation
Indices: 157387--157582 Score: 302
Period size: 50 Copynumber: 3.9 Consensus size: 50
157377 TTTGGTGGTT
* *
157387 TTCACCAACCTTTGACAATAGAGAGAGTTGACCATAATTGTTGACTATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTATTGACTATTC
* * * *
157437 TTCACTAACCTTTGACAATCGAGAAAGGTGACTATAATTATTGACTATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTATTGACTATTC
* *
157487 TTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTATTGACTATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTATTGACTATTC
* *
157537 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTTTTGACT
1 TTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTATTGACT
157583 TTAAGCAACT
Statistics
Matches: 132, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 132 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (50 bp):
TTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTATTGACTATTC
Found at i:159870 original size:2 final size:2
Alignment explanation
Indices: 159863--159901 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
159853 TGCAAAGACC
159863 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
159902 CTACAAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:160431 original size:2 final size:2
Alignment explanation
Indices: 160420--160462 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
160410 AACCCTTTCA
160420 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160461 AT
1 AT
160463 CATTGGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:160662 original size:2 final size:2
Alignment explanation
Indices: 160655--160695 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
160645 ATTTTATCAT
*
160655 TA TA TA TA TA TA TA TT TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
160696 AAGTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:160671 original size:23 final size:23
Alignment explanation
Indices: 160645--160692 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
160635 CTGTTTTTGA
160645 ATTT-TATCATTATATATATATAT
1 ATTTATAT-ATTATATATATATAT
160668 ATTTATATATTATATATATATAT
1 ATTTATATATTATATATATATAT
160691 AT
1 AT
160693 ATAAAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTATATATTATATATATATAT
Found at i:161059 original size:29 final size:28
Alignment explanation
Indices: 160993--161060 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
160983 TAATATTTTA
160993 TTATACTAAATAAACATTAACAATTAAT
1 TTATACTAAATAAACATTAACAATTAAT
** **
161021 TTGCACCTAAATAAA-ATCTAACTTTTAAT
1 TTATA-CTAAATAAACAT-TAACAATTAAT
161050 TTATATCTAAA
1 TTATA-CTAAA
161061 CAAATCTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.38
Consensus pattern (28 bp):
TTATACTAAATAAACATTAACAATTAAT
Found at i:165116 original size:27 final size:28
Alignment explanation
Indices: 165065--165120 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
165055 TTGCAAATAA
* *
165065 TGAATTGAATCTTCATGATTAATCTCTT
1 TGAATTGAATCTTCATCAATAATCTCTT
*
165093 TGAATT-AATCTTCATCAATGATCTCTT
1 TGAATTGAATCTTCATCAATAATCTCTT
165120 T
1 T
165121 AGAAGAGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (28 bp):
TGAATTGAATCTTCATCAATAATCTCTT
Found at i:170935 original size:19 final size:16
Alignment explanation
Indices: 170896--170930 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
170886 CCGTATTTGC
170896 AATGTATTCTAGTAAT
1 AATGTATTCTAGTAAT
170912 AATGTATTCTAGTAAT
1 AATGTATTCTAGTAAT
170928 AAT
1 AAT
170931 AATGTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (16 bp):
AATGTATTCTAGTAAT
Found at i:173002 original size:29 final size:30
Alignment explanation
Indices: 172970--173030 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
172960 CAATAAACAG
* **
172970 TAACATTTAACTTGTATTTAAATAAA-TTT
1 TAACATTTAACTTATACCTAAATAAACTTT
*
172999 TAACTTTTAACTTATACCTAAATAAACTTT
1 TAACATTTAACTTATACCTAAATAAACTTT
173029 TA
1 TA
173031 GTGTAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (30 bp):
TAACATTTAACTTATACCTAAATAAACTTT
Found at i:173081 original size:21 final size:21
Alignment explanation
Indices: 173046--173097 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
173036 AATTAATATT
*
173046 TTATTTGAAATAATAAAAAA-
1 TTATTTAAAATAATAAAAAAC
173066 TTATTTAAATATAATAAAAAAC
1 TTATTTAAA-ATAATAAAAAAC
173088 TTATTTAAAA
1 TTATTTAAAA
173098 ATTAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 8 0.28
21 12 0.41
22 9 0.31
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TTATTTAAAATAATAAAAAAC
Found at i:173190 original size:2 final size:2
Alignment explanation
Indices: 173185--173215 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
173175 ATAATGAAGG
173185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
173216 ATTCCTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:173559 original size:43 final size:43
Alignment explanation
Indices: 173502--173612 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 43
173492 TAAACACCAT
*
173502 TAAATTTGAATATTTAGTAGCATTTATAGC-TTAAAAACGTCAC
1 TAAATTTGAATATTTAGTAGCATTTATA-CATCAAAAACGTCAC
* * * * *
173545 TAAATTT-ATGTATTTAGCAGCGTTTATACATCGAAAATGTCAC
1 TAAATTTGA-ATATTTAGTAGCATTTATACATCAAAAACGTCAC
*
173588 TAAATTTGAATATTTAGTGGCATTT
1 TAAATTTGAATATTTAGTAGCATTT
173613 TAATTTATGA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
42 2 0.04
43 52 0.95
44 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (43 bp):
TAAATTTGAATATTTAGTAGCATTTATACATCAAAAACGTCAC
Found at i:173645 original size:42 final size:42
Alignment explanation
Indices: 173599--173691 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
173589 AAATTTGAAT
* * *
173599 ATTTAGTGGCATTTT-AATTTATGAATGCCGTTAAATATATAA
1 ATTTAGTGGCATTTTGAA-ATATAAATACCGTTAAATATATAA
* * *
173641 ATTTAGTGGCGTTTTGAAATATAAATACCGTTAAATTTTTAA
1 ATTTAGTGGCATTTTGAAATATAAATACCGTTAAATATATAA
173683 ATTTAGTGG
1 ATTTAGTGG
173692 TGTTTATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.43
Consensus pattern (42 bp):
ATTTAGTGGCATTTTGAAATATAAATACCGTTAAATATATAA
Found at i:178987 original size:2 final size:2
Alignment explanation
Indices: 178980--179012 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
178970 AGGATTTTCA
178980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
179013 AAACAAGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:180679 original size:36 final size:36
Alignment explanation
Indices: 180632--180706 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
180622 GAATTTTAGT
*
180632 AATATTTTGAATCAAATAAGGTCATCTTATGATAAA
1 AATATTTTGAATCAAATAAGGTCATCTTATGACAAA
*
180668 AATATTTTGAATCAAATAAGGTCATTTTATGACAAA
1 AATATTTTGAATCAAATAAGGTCATCTTATGACAAA
180704 AAT
1 AAT
180707 CTTAGATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (36 bp):
AATATTTTGAATCAAATAAGGTCATCTTATGACAAA
Found at i:180694 original size:20 final size:20
Alignment explanation
Indices: 180635--180695 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
180625 TTTTAGTAAT
180635 ATTTTGAATCAAATAAGGTC
1 ATTTTGAATCAAATAAGGTC
180655 ATCTTATG-AT-AAA-AA--T-
1 AT-TT-TGAATCAAATAAGGTC
180671 ATTTTGAATCAAATAAGGTC
1 ATTTTGAATCAAATAAGGTC
180691 ATTTT
1 ATTTT
180696 ATGACAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 16
0.67 0.00 0.33
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 5 0.15
17 3 0.09
19 3 0.09
20 10 0.30
21 4 0.12
22 2 0.06
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.39
Consensus pattern (20 bp):
ATTTTGAATCAAATAAGGTC
Done.