Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1729
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: 44368
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Found at i:1888 original size:40 final size:40
Alignment explanation
Indices: 1834--1968 Score: 172
Period size: 40 Copynumber: 3.5 Consensus size: 40
1824 TGGATGATAA
*
1834 CCGGGCT-AGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCAAGTGACTA-TAT
* *
1873 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCAAGTGACTATAT
* *
1913 CCGGGCTAAGTCCCGAAGGCATTTGTGC--GAG-CTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCAAGTGACTATAT
*
1950 CCGGGCTATGTCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
1969 ATTCGAGCGA
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
37 24 0.27
38 1 0.01
39 8 0.09
40 55 0.62
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGCGCAAGTGACTATAT
Found at i:4224 original size:27 final size:27
Alignment explanation
Indices: 4136--4312 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
4126 ATATTAAGTC
* * *
4136 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
4163 -GCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
4190 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
4217 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
4244 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
4271 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
4298 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
4313 GTACAATTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 19 0.15
27 89 0.69
28 21 0.16
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:4247 original size:54 final size:54
Alignment explanation
Indices: 4136--4312 Score: 223
Period size: 54 Copynumber: 3.3 Consensus size: 54
4126 ATATTAAGTC
* * *
4136 CGCACACTCAGTGCTATATAATCAACT-GCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
4190 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
4244 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
4298 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
4313 GTACAATTTA
Statistics
Matches: 106, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.01
54 84 0.79
55 21 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:12381 original size:27 final size:27
Alignment explanation
Indices: 12351--12528 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12341 ATATTAAGTC
* * *
12351 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
12378 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
12406 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
12433 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
12460 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
12487 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
12514 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12529 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:12435 original size:55 final size:54
Alignment explanation
Indices: 12351--12528 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
12341 ATATTAAGTC
* * *
12351 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
12406 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
12460 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
12514 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12529 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:12517 original size:81 final size:82
Alignment explanation
Indices: 12372--12527 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
12362 TGCTATATAA
* *
12372 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
12437 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
12454 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
12517 ACACTTAGTGC
65 ACACTTAGTGC
12528 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:20620 original size:27 final size:26
Alignment explanation
Indices: 20603--20776 Score: 156
Period size: 27 Copynumber: 6.6 Consensus size: 26
20593 ATATTAAGTC
* *
20603 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATAT-ATCAAAT
20630 CGCACACTTAGTGC-ATA-ATCAAAT
1 CGCACACTTAGTGCTATATATCAAAT
* *
20654 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTATATA-TCAAAT
*** * *
20681 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATAT-ATCAAAT
**
20708 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTAT-ATA-TCAAAT
* *
20735 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTATATA-TCAAAT
20762 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20777 GTACAATTTA
Statistics
Matches: 123, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
24 20 0.16
25 2 0.02
26 4 0.03
27 96 0.78
28 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (26 bp):
CGCACACTTAGTGCTATATATCAAAT
Found at i:20738 original size:54 final size:54
Alignment explanation
Indices: 20603--20776 Score: 212
Period size: 54 Copynumber: 3.3 Consensus size: 54
20593 ATATTAAGTC
* * * *
20603 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTG---CATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
20654 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
20708 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
20762 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20777 GTACAATTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
51 37 0.35
53 1 0.01
54 67 0.64
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:20765 original size:81 final size:78
Alignment explanation
Indices: 20624--20775 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 78
20614 TGCTATATAA
* *
20624 TCAACTCGCACACTTAGTGCATAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCACACT
1 TCAACTCGCACACTTAGTGCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACT
20689 TAGTGCCGCATGG
66 TAGTGCCGCATGG
* **
20702 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCAT-A-A-TCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
20767 ACTTAGTGC
63 ACTTAGTGC
20776 TGTACAATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
78 21 0.32
79 1 0.02
80 1 0.02
81 43 0.65
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (78 bp):
TCAACTCGCACACTTAGTGCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACT
TAGTGCCGCATGG
Found at i:26365 original size:42 final size:42
Alignment explanation
Indices: 26319--26455 Score: 168
Period size: 42 Copynumber: 3.3 Consensus size: 42
26309 TCTTAAACGG
*
26319 GGTCTTCCACGGAATAAGATACGATGCCGATGTCCCAGACAT
1 GGTCTTACACGGAATAAGATACGATGCCGATGTCCCAGACAT
** * *
26361 GGTCTTACAC-GACATTGGATACGATGCCAATGTCGCAGACAT
1 GGTCTTACACGGA-ATAAGATACGATGCCGATGTCCCAGACAT
* * * * *
26403 GGTCTTACATGAAATCAGATATGATGCTGATGTCCCAGACAT
1 GGTCTTACACGGAATAAGATACGATGCCGATGTCCCAGACAT
26445 GGTCTTACACG
1 GGTCTTACACG
26456 TAAATCTCAA
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
41 2 0.03
42 76 0.96
43 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGGAATAAGATACGATGCCGATGTCCCAGACAT
Found at i:33425 original size:29 final size:29
Alignment explanation
Indices: 33392--33465 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
33382 GTTGTGAGAT
* *
33392 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
33421 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
33450 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
33466 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:38336 original size:47 final size:45
Alignment explanation
Indices: 38269--38432 Score: 153
Period size: 47 Copynumber: 3.6 Consensus size: 45
38259 ATTATGGGCT
* *
38269 AGTGTAAGACATGTCCGGGACAT-GCATCAGCTACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCAGCTACA--ATGAGAGTC
* * *
38315 AGTGTAAGACCATGTCTGGGACATGGCATC-G--A-AACGAGTGTT
1 AGTGTAAGA-CATGTCTGGGACATGGCATCAGCTACAATGAGAGTC
* *
38357 AGTGTAAGACATGCCTGGGACAT-GCAT-AGGCTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGGCATCA-GCTAC-A-ATGAGAGTC
38403 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACATGGCATC
38433 GACATGAAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
40 4 0.04
41 14 0.15
42 14 0.15
43 1 0.01
44 1 0.01
45 2 0.02
46 23 0.24
47 27 0.28
48 9 0.09
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGGCATCAGCTACAATGAGAGTC
Found at i:38366 original size:42 final size:46
Alignment explanation
Indices: 38314--38479 Score: 157
Period size: 47 Copynumber: 3.7 Consensus size: 46
38304 TTATGAGAGC
38314 CAGTGTAAGACCATGTCTGGGACATGGCATCGAAACGAG-TG-T-T
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGAAACGAGATGATAT
* * **
38357 -AGTGTAAGA-CATGCCTGGGACAT-GCATAGGCTACGAGATGATAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCAT-CGAAACGAGATGATA-T
* * * *
38402 CAGTGTAAGACCATGTCTGGGACATGGCATCGACATGAAAT-ATGAG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGAAACGAGATGAT-AT
* *
38448 CTAGTGTGAGACCGTGTCTGGGACATGGCATC
1 C-AGTGTAAGACCATGTCTGGGACATGGCATC
38480 AACATCTTAC
Statistics
Matches: 100, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
40 4 0.04
41 19 0.19
42 11 0.11
43 1 0.01
45 1 0.01
46 12 0.12
47 48 0.48
48 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (46 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGAAACGAGATGATAT
Found at i:38417 original size:88 final size:88
Alignment explanation
Indices: 38268--38434 Score: 259
Period size: 88 Copynumber: 1.9 Consensus size: 88
38258 TATTATGGGC
*
38268 TAGTGTAAGACATGTCCGGGACATGCATCAGCTACATTATGAGAGCCAGTGTAAGACCATGTCTG
1 TAGTGTAAGACATGTCCGGGACATGCATCAGCTACATGATGAGAGCCAGTGTAAGACCATGTCTG
38333 GGACATGGCATCGAAACGAGTGT
66 GGACATGGCATCGAAACGAGTGT
* *
38356 TAGTGTAAGACATG-CCTGGGACATGCAT-AGGCTACGA-GATGATAGTCAGTGTAAGACCATGT
1 TAGTGTAAGACATGTCC-GGGACATGCATCA-GCTAC-ATGATGAGAGCCAGTGTAAGACCATGT
38418 CTGGGACATGGCATCGA
63 CTGGGACATGGCATCGA
38435 CATGAAATAT
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
87 3 0.04
88 69 0.95
89 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (88 bp):
TAGTGTAAGACATGTCCGGGACATGCATCAGCTACATGATGAGAGCCAGTGTAAGACCATGTCTG
GGACATGGCATCGAAACGAGTGT
Found at i:38454 original size:47 final size:46
Alignment explanation
Indices: 38261--38484 Score: 141
Period size: 47 Copynumber: 4.9 Consensus size: 46
38251 TATGGGTTAT
* * *
38261 TATGGGCTAGTGTAAGA-CATGTCCGGGACAT-GCATC-AGC-TACAT
1 TATGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-CATA-AA
* *
38305 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG--A-AAC
1 TAT--GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATAAA
* * * * * *
38350 GA-GTGTTAGTGTAAGA-CATGCCTGGGACAT-GCATAGGC-TACGAGA
1 TATGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATA--A-A
38395 TGAT-AG-TCAGTGTAAGACCATGTCTGGGACATGGCATCGACATGAAA
1 T-ATGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACAT-AAA
* * *
38442 TATGAGCTAGTGTGAGACCGTGTCTGGGACATGGCATCAACAT
1 TATGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAT
38485 CTTACCCACG
Statistics
Matches: 140, Mismatches: 19, Indels: 39
0.71 0.10 0.20
Matches are distributed among these distances:
40 5 0.04
41 13 0.09
42 12 0.09
44 4 0.03
45 3 0.02
46 26 0.19
47 62 0.44
48 13 0.09
49 1 0.01
50 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.23
Consensus pattern (46 bp):
TATGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATAAA
Done.