Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1511
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: 37337
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Found at i:12585 original size:93 final size:93
Alignment explanation
Indices: 12472--12643 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
12462 CGCCCATAAG
* *
12472 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
12537 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
12565 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
12630 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
12644 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:12640 original size:46 final size:46
Alignment explanation
Indices: 12465--12640 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
12455 TGTAACCCGC
* * *
12465 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
12511 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
12561 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
12604 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
12641 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:19648 original size:92 final size:93
Alignment explanation
Indices: 19520--19690 Score: 299
Period size: 92 Copynumber: 1.8 Consensus size: 93
19510 CGCCCATAAG
* *
19520 CGAACTCGGACTAAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTAAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19585 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
19613 CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTAAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19677 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
19691 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 67 0.91
93 7 0.09
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTAAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:19687 original size:46 final size:46
Alignment explanation
Indices: 19513--19687 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
19503 TGTAACCCGC
* * * *
19513 CCATAAGCGAACTCGGACTAAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
19559 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
19609 -C-TCA-CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
19651 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
19688 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
43 2 0.02
44 2 0.02
45 6 0.06
46 77 0.71
47 6 0.06
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:23150 original size:29 final size:29
Alignment explanation
Indices: 23114--23214 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 29
23104 TGGCCCATCT
*
23114 CATTCATA-GGACCCATCAGGCCGAATTCA
1 CATTCATATGG-CCCATCAGGCCCAATTCA
23143 CATTCATATGGCCCATCAGGCCCAATTCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
* * * *
23172 AATTCATATGGCCTATTAGGCCCAAATCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
* *
23201 CCTTTATATGGCCC
1 CATTCATATGGCCC
23215 GTTAGGCCGA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 60 0.97
30 2 0.03
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.26
Consensus pattern (29 bp):
CATTCATATGGCCCATCAGGCCCAATTCA
Found at i:23219 original size:29 final size:29
Alignment explanation
Indices: 23125--23237 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 29
23115 ATTCATAGGA
* * * * *
23125 CCCATCAGGCCGAATTCACATTCATATGG
1 CCCATTAGGCCCAAATCACCTTTATATGG
* * ** *
23154 CCCATCAGGCCCAATTCAAATTCATATGG
1 CCCATTAGGCCCAAATCACCTTTATATGG
*
23183 CCTATTAGGCCCAAATCACCTTTATATGG
1 CCCATTAGGCCCAAATCACCTTTATATGG
* *
23212 CCCGTTAGGCCGAAATCACC-TTATAT
1 CCCATTAGGCCCAAATCACCTTTATAT
23238 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 6 0.08
29 67 0.92
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
CCCATTAGGCCCAAATCACCTTTATATGG
Found at i:23484 original size:16 final size:16
Alignment explanation
Indices: 23465--23499 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
23455 CTTTTCAGTA
*
23465 TTTCGACTTTTTGGCT
1 TTTCGACTTTTCGGCT
23481 TTTCGACTTTTCGGCT
1 TTTCGACTTTTCGGCT
23497 TTT
1 TTT
23500 ACCAATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.20, G:0.17, T:0.57
Consensus pattern (16 bp):
TTTCGACTTTTCGGCT
Found at i:23492 original size:24 final size:24
Alignment explanation
Indices: 23449--23499 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
23439 GTAGCCAAAC
*
23449 TTTTGGCTTTTCAGTATTTCGACT
1 TTTTGGCTTTTCACTATTTCGACT
*
23473 TTTTGGCTTTTCGACT-TTTCGGCT
1 TTTTGGCTTTTC-ACTATTTCGACT
23497 TTT
1 TTT
23500 ACCAATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.08, C:0.18, G:0.18, T:0.57
Consensus pattern (24 bp):
TTTTGGCTTTTCACTATTTCGACT
Found at i:25041 original size:18 final size:19
Alignment explanation
Indices: 25015--25055 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
25005 GGCCTCTCAG
25015 CGGTAGCTG-ACCACC-CCT
1 CGGTAGCTGTA-CACCACCT
*
25033 CGGTGGCTGTACACCACCT
1 CGGTAGCTGTACACCACCT
25052 CGGT
1 CGGT
25056 CCACGACTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.15, C:0.39, G:0.27, T:0.20
Consensus pattern (19 bp):
CGGTAGCTGTACACCACCT
Found at i:27660 original size:29 final size:29
Alignment explanation
Indices: 27626--27726 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 29
27616 TTGCCCATCT
*
27626 CATTCATA-GGACCCATCAGGCCGAATTCA
1 CATTCATATGG-CCCATCAGGCCCAATTCA
*
27655 CATTCATATGGCTCATCAGGCCCAATTCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
* * *
27684 CATTCATATGGCCTATTAGGCCCAAATCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
* *
27713 CCTTTATATGGCCC
1 CATTCATATGGCCC
27727 GTTAGGCCGA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 60 0.97
30 2 0.03
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CATTCATATGGCCCATCAGGCCCAATTCA
Found at i:27731 original size:29 final size:29
Alignment explanation
Indices: 27628--27745 Score: 112
Period size: 29 Copynumber: 4.1 Consensus size: 29
27618 GCCCATCTCA
* * * *
27628 TTCATA-GGACCCATCAGGCCGAATTCACA
1 TTCATATGG-CCCATTAGGCCCAAATCACC
* * * *
27657 TTCATATGGCTCATCAGGCCCAATTCACA
1 TTCATATGGCCCATTAGGCCCAAATCACC
*
27686 TTCATATGGCCTATTAGGCCCAAATCACC
1 TTCATATGGCCCATTAGGCCCAAATCACC
* * *
27715 TTTATATGGCCCGTTAGGCCGAAATCACC
1 TTCATATGGCCCATTAGGCCCAAATCACC
27744 TT
1 TT
27746 GTATTCATGC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (29 bp):
TTCATATGGCCCATTAGGCCCAAATCACC
Found at i:28172 original size:93 final size:93
Alignment explanation
Indices: 28058--28229 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
28048 CGCCCATAAG
* *
28058 CGAACTCGGACTAAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTAAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28123 ACGAGTTCGGATGCCTACTTACATCTCA
66 ACGAGTTCGGATGCCTACTTACATCTCA
* *
28151 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTAAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28216 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28230 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTAAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTACTTACATCTCA
Found at i:28226 original size:46 final size:46
Alignment explanation
Indices: 28051--28226 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
28041 TGTAACCCGC
* * * *
28051 CCATAAGCGAACTCGGACTAAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28097 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTACTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28147 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28190 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28227 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28245 original size:46 final size:46
Alignment explanation
Indices: 28100--28238 Score: 151
Period size: 47 Copynumber: 3.0 Consensus size: 46
28090 TTCGCATCCA
*
28100 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTACTTACATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAAC---CATC
* * * * *
28148 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
28193 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
28239 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 3 0.04
50 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:35702 original size:93 final size:93
Alignment explanation
Indices: 35590--35761 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
35580 CGCCCATAAG
*
35590 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
35654 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
35683 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
35748 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
35762 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:35756 original size:46 final size:46
Alignment explanation
Indices: 35583--35758 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
35573 TGTAACCCGC
* *
35583 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
35629 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
35679 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
35722 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
35759 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.