Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3210
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: 37348
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:736 original size:27 final size:26
Alignment explanation
Indices: 696--746 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
686 CGCTGCAATC
* *
696 TGGTGGCTTCGCCACATATATCTGTTT
1 TGGTGGCCTAGCCACA-ATATCTGTTT
723 TGGTGGCCTAGCCACAATATCTGT
1 TGGTGGCCTAGCCACAATATCTGT
747 ATCTGACTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (26 bp):
TGGTGGCCTAGCCACAATATCTGTTT
Found at i:742 original size:67 final size:67
Alignment explanation
Indices: 608--745 Score: 204
Period size: 67 Copynumber: 2.1 Consensus size: 67
598 GAGGAAGCAT
* * *
608 TCTGGCAGCCTCGATGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCAAAA
1 TCTGGCAGCCTCGATGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACCTAGCCAAAA
673 TA
66 TA
* * * * *
675 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTTTGGTGGCCTAGCCACAA
1 TCTGGCAGCCTCGATGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACCTAGCCAAAA
740 TA
66 TA
742 TCTG
1 TCTG
746 TATCTGACTT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (67 bp):
TCTGGCAGCCTCGATGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACCTAGCCAAAA
TA
Found at i:3756 original size:50 final size:49
Alignment explanation
Indices: 3634--3809 Score: 190
Period size: 50 Copynumber: 3.5 Consensus size: 49
3624 TGAGGTCGCA
* * * ** * *
3634 TGTGTAGTACTAAGTGCTGGCTACTATGCGTGCCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAA-TT-GGTCACG
* ** *
3685 TGTGTAGTACTAAGTGCAGGCTACTGCGTGTATCAGATGGTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT-GGTCACG
* * * *
3735 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATTGGTCACG
3784 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
3810 TGCGTACCAG
Statistics
Matches: 104, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
49 29 0.28
50 44 0.42
51 31 0.30
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATTGGTCACG
Found at i:6584 original size:16 final size:15
Alignment explanation
Indices: 6546--6584 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
6536 TGGATTCTCG
*
6546 TATCATGGATTTCTT
1 TATCTTGGATTTCTT
6561 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
6576 TATTCTTGG
1 TA-TCTTGG
6585 CTTCTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:9158 original size:26 final size:26
Alignment explanation
Indices: 9079--9159 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
9069 TCGATCACGT
*
9079 GTGTAGTACTAAGTGCAGGCTACTAC
1 GTGTAGTACTAAGTGTAGGCTACTAC
* **
9105 GTGTA-T-C-AAATGGTTAGG-T-CATGT
1 GTGTAGTACTAAGT-G-TAGGCTAC-TAC
9129 GTGTAGTACTAAGTGTAGGCTACTAC
1 GTGTAGTACTAAGTGTAGGCTACTAC
9155 GTGTA
1 GTGTA
9160 CCGGATATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 16
0.63 0.11 0.25
Matches are distributed among these distances:
23 4 0.10
24 9 0.22
25 9 0.22
26 14 0.35
27 4 0.10
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (26 bp):
GTGTAGTACTAAGTGTAGGCTACTAC
Found at i:9210 original size:49 final size:50
Alignment explanation
Indices: 9019--9215 Score: 189
Period size: 50 Copynumber: 3.9 Consensus size: 50
9009 ATCTATTGTG
* * * * *
9019 AGGTCGCATGTGTAGTACTAAGTGCTGGCTACTATGCGTGCCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA-TT
* * * * * * **
9070 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
** * * *
9120 AGGTCATGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGAT-ATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * *
9169 TGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
9216 GCTTTCGCTA
Statistics
Matches: 116, Mismatches: 29, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
49 40 0.34
50 41 0.35
51 35 0.30
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:13624 original size:25 final size:25
Alignment explanation
Indices: 13590--13640 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
13580 ATTAACCAAA
13590 CTCATACTAAACATGCCAAAATAAG
1 CTCATACTAAACATGCCAAAATAAG
13615 CTCATACTAAACATGCCAAAATAAG
1 CTCATACTAAACATGCCAAAATAAG
13640 C
1 C
13641 CATTCCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.25, G:0.08, T:0.20
Consensus pattern (25 bp):
CTCATACTAAACATGCCAAAATAAG
Found at i:26105 original size:54 final size:55
Alignment explanation
Indices: 26011--26151 Score: 171
Period size: 55 Copynumber: 2.6 Consensus size: 55
26001 AGCATGGCTG
* * * * * *
26011 CCAGA-ACAGATATTGTGACAGAGTCACTAGATACAGATA-TTGTGATAGAGTCA
1 CCAGATACAGATATTGTGGCAGAGCCACCAGAAACAAATATTTGTGATAGAGCCA
* *
26064 CCAGATACAAATATTGTGGCAGAGCCACCAGAAACAAATATTTGTGGTAGAGCCA
1 CCAGATACAGATATTGTGGCAGAGCCACCAGAAACAAATATTTGTGATAGAGCCA
*
26119 CCATAT-CAGATAATTGTGGCAGAGCCACCAGAA
1 CCAGATACAGAT-ATTGTGGCAGAGCCACCAGAA
26152 CGCTTCCTCC
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
53 5 0.07
54 32 0.43
55 38 0.51
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (55 bp):
CCAGATACAGATATTGTGGCAGAGCCACCAGAAACAAATATTTGTGATAGAGCCA
Found at i:26117 original size:28 final size:27
Alignment explanation
Indices: 26011--26151 Score: 124
Period size: 27 Copynumber: 5.2 Consensus size: 27
26001 AGCATGGCTG
* * *
26011 CCAG-AACAGATATTGTGACAGAGTCA
1 CCAGAAACAAATATTGTGGCAGAGCCA
* * * ** *
26037 CTAGATACAGATATTGTGATAGAGTCA
1 CCAGAAACAAATATTGTGGCAGAGCCA
*
26064 CCAGATACAAATATTGTGGCAGAGCCA
1 CCAGAAACAAATATTGTGGCAGAGCCA
*
26091 CCAGAAACAAATATTTGTGGTAGAGCCA
1 CCAGAAACAAATA-TTGTGGCAGAGCCA
* * *
26119 CCA-TATCAGATAATTGTGGCAGAGCCA
1 CCAGAAACAAAT-ATTGTGGCAGAGCCA
26146 CCAGAA
1 CCAGAA
26152 CGCTTCCTCC
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
26 3 0.03
27 75 0.78
28 18 0.19
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (27 bp):
CCAGAAACAAATATTGTGGCAGAGCCA
Found at i:29720 original size:27 final size:27
Alignment explanation
Indices: 29682--29786 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 27
29672 GCCACTCCGC
** *
29682 TACAAATATTGTGATAGAGTCACCAGA
1 TACAAATATTGTGGCAGAGCCACCAGA
29709 TACAAATATTGTGGCAGAGCCACCAGA
1 TACAAATATTGTGGCAGAGCCACCAGA
* *
29736 AACAGATATTTGTGGCAGAGCCACCAGA
1 TACAAATA-TTGTGGCAGAGCCACCAGA
* *
29764 T-CAGATAATTGTAGCAGAGCCAC
1 TACAAAT-ATTGTGGCAGAGCCAC
29787 TAGAATGCTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
27 49 0.71
28 20 0.29
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (27 bp):
TACAAATATTGTGGCAGAGCCACCAGA
Found at i:30960 original size:27 final size:27
Alignment explanation
Indices: 30923--31031 Score: 141
Period size: 27 Copynumber: 4.0 Consensus size: 27
30913 AGCATGGCTG
* *
30923 CCAGA-ACAGATATTGTGACAGAGTCA
1 CCAGATACAGATATTGTGGCAGAGCCA
*
30949 CCAGATACAGATATTGTGGTAGAGCCA
1 CCAGATACAGATATTGTGGCAGAGCCA
*
30976 CCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATA-TTGTGGCAGAGCCA
*
31004 CCAGAT-CAGATAATTGTAGCAGAGCCA
1 CCAGATACAGAT-ATTGTGGCAGAGCCA
31031 C
1 C
31032 TAGAATGCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.07
27 49 0.67
28 19 0.26
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
CCAGATACAGATATTGTGGCAGAGCCA
Found at i:31006 original size:55 final size:54
Alignment explanation
Indices: 30923--31036 Score: 151
Period size: 55 Copynumber: 2.1 Consensus size: 54
30913 AGCATGGCTG
* * *
30923 CCAG-AACAGATATTGTGACAGAGTCACCAGATACAGAT-ATTGTGGTAGAGCCA
1 CCAGAAACAGATATTGTGACAGAGCCACCAGAT-CAGATAATTGTAGCAGAGCCA
*
30976 CCAGAAACAGATATTTGTGGCAGAGCCACCAGATCAGATAATTGTAGCAGAGCCA
1 CCAGAAACAGATA-TTGTGACAGAGCCACCAGATCAGATAATTGTAGCAGAGCCA
*
31031 CTAGAA
1 CCAGAA
31037 TGCTTCCTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
53 4 0.08
54 13 0.25
55 36 0.68
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (54 bp):
CCAGAAACAGATATTGTGACAGAGCCACCAGATCAGATAATTGTAGCAGAGCCA
Found at i:33307 original size:42 final size:42
Alignment explanation
Indices: 33198--33349 Score: 130
Period size: 42 Copynumber: 3.5 Consensus size: 42
33188 ATGCCAATGT
* * **
33198 CATATCCCAGATATGGTCTTACATGGGATCACATA-TATCGATGTC
1 CATATCCCAGACATGGTCTTACACGAAAT--C-TAGTATCGATG-C
* * **
33243 GATAGCCCAG-CTATGGTCTTACACGATGTCCT-GTATCGATGC
1 CATATCCCAGAC-ATGGTCTTACACGAAAT-CTAGTATCGATGC
* *
33285 CATGTCCCAGACATGGTGTTACACGAAATCTAGTATCGATGC
1 CATATCCCAGACATGGTCTTACACGAAATCTAGTATCGATGC
*
33327 CATATCCCAGATATGGTCTTACA
1 CATATCCCAGACATGGTCTTACA
33350 AAAAATTGCA
Statistics
Matches: 86, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
41 2 0.02
42 52 0.60
43 10 0.12
44 1 0.01
45 21 0.24
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (42 bp):
CATATCCCAGACATGGTCTTACACGAAATCTAGTATCGATGC
Found at i:36453 original size:27 final size:26
Alignment explanation
Indices: 36413--36524 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
36403 AGGAAGCGTC
*
36413 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
36440 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
36467 CTGGTGGCTCTACCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
36495 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
36521 CTGG
1 CTGG
36525 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 7 0.09
27 51 0.69
28 16 0.22
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:36517 original size:54 final size:54
Alignment explanation
Indices: 36413--36524 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
36403 AGGAAGCGTC
* *
36413 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATACCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
36467 CTGGTGGCTCTACCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATACCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
36521 CTGG
1 CTGG
36525 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATACCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Done.