Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold883
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: 48084
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Found at i:182 original size:23 final size:23
Alignment explanation
Indices: 156--200 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
146 CCTTGATCAG
156 CTCCTAAATTCC-TCCCTTATCTA
1 CTCCTAAA-TCCATCCCTTATCTA
179 CTCCTAAATCCTATCCCTTATC
1 CTCCTAAATCC-ATCCCTTATC
201 AATCATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.22, C:0.40, G:0.00, T:0.38
Consensus pattern (23 bp):
CTCCTAAATCCATCCCTTATCTA
Found at i:209 original size:23 final size:24
Alignment explanation
Indices: 168--213 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
158 CCTAAATTCC
* *
168 TCCCTTATCTACTCCTAAATCCTA
1 TCCCTTATCTAATCATAAATCCTA
192 TCCCTTATC-AATCATAAATCCT
1 TCCCTTATCTAATCATAAATCCT
214 CTCCTGACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.37
Consensus pattern (24 bp):
TCCCTTATCTAATCATAAATCCTA
Found at i:6088 original size:48 final size:48
Alignment explanation
Indices: 6015--6427 Score: 361
Period size: 48 Copynumber: 8.6 Consensus size: 48
6005 TATGTATGCT
*
6015 AGTGTAAGACCATGTCTGGGACATGGCATCCGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* * * *** * * *
6063 AGTGTAGGATCATGTCTGGGGCATGGCATCGGCGTTGA-TATGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACATTATGAGAGCC
* * * * * *
6111 AGTGTAAGACCATGCCTAGGACATGGCATCAGTCATATTATAAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* * *** * * *
6159 AATGTAAGACCATGTTTGGGACATGGCATCGGCGTTGATT-TGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACATTATGAGAGCC
* *
6207 AGTGTAAGACCATGTCTGGGAGATGGCATCAGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* * *
6255 AGTGTTAGACCATGTCTGGGACATGTCATCGGCCACATTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* * *
6303 ATTGTAAAACCATGTCTGGGACATGGCATC-G--ACATTGAGATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT---ATGAGAGCC
* * * * * * *
6351 AGTGTAAGACCATGTCTAGGATATGGCATTGACCTCGA-CATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATTATGAGAGCC
* *
6399 AGTGTAAGACCATATCTGGGATATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
6428 TGGCAATTTA
Statistics
Matches: 286, Mismatches: 68, Indels: 22
0.76 0.18 0.06
Matches are distributed among these distances:
45 5 0.02
47 5 0.02
48 270 0.94
49 4 0.01
51 1 0.00
52 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
Found at i:6173 original size:96 final size:96
Alignment explanation
Indices: 6002--6427 Score: 473
Period size: 96 Copynumber: 4.4 Consensus size: 96
5992 GACAATTGGG
* *
6002 TGATATGTATGCTAGTGTAAGACCATGTCTGGGACATGGCATCCGCCACATTATGAGAGCCAGTG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCCAGTG
* * *
6067 TAGGATCATGTCTGGGGCATGGCATCGGCGT
66 TAAGACCATGTCTGGGACATGGCATCGGCGT
* * * * * *
6098 TGATATGTGTGCTAGTGTAAGACCATGCCTAGGACATGGCATCAGTCATATTATAAGAGCCAATG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCCAGTG
*
6163 TAAGACCATGTTTGGGACATGGCATCGGCGT
66 TAAGACCATGTCTGGGACATGGCATCGGCGT
* *
6194 TGATTTGTGTGCTAGTGTAAGACCATGTCTGGGAGATGGCATCAGCCACATTATGAGAGCCAGTG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCCAGTG
* * *
6259 TTAGACCATGTCTGGGACATGTCATCGGC-C
66 TAAGACCATGTCTGGGACATGGCATCGGCGT
** * * * * *
6289 ACATTATGAGAGCTATTGTAAAACCATGTCTGGGACATGGCATC-G--ACATTGAGATGAGAGCT
1 TGA-TATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATT---ATGAGAGCC
* * * * *
6351 AGTGTAAGACCATGTCTAGGATATGGCATTGACCT
62 AGTGTAAGACCATGTCTGGGACATGGCATCGGCGT
* * * * * *
6386 CGACATGTGAGCCAGTGTAAGACCATATCTGGGATATGGCAT
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCAT
6428 TGGCAATTTA
Statistics
Matches: 276, Mismatches: 49, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
93 5 0.02
95 2 0.01
96 268 0.97
97 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (96 bp):
TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCCAGTG
TAAGACCATGTCTGGGACATGGCATCGGCGT
Found at i:6445 original size:33 final size:32
Alignment explanation
Indices: 6403--6469 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
6393 TGAGCCAGTG
*
6403 TAAGACCATATCTGG-GATATGGCATTGGCAATT
1 TAAGACCATATC-GGTGATAT-GCATCGGCAATT
6436 TAAGACCATATCGGTGATATGCATCGGCAATT
1 TAAGACCATATCGGTGATATGCATCGGCAATT
6468 TA
1 TA
6470 CCCTCTAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (32 bp):
TAAGACCATATCGGTGATATGCATCGGCAATT
Found at i:9568 original size:24 final size:24
Alignment explanation
Indices: 9541--9587 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
9531 TTGTCAGGAG
* *
9541 AGGATTTATGAGTTGATAAGGGAT
1 AGGATTTAGGAGTAGATAAGGGAT
9565 AGGATTTAGGAGTAGATAAGGGA
1 AGGATTTAGGAGTAGATAAGGGA
9588 GGAAATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (24 bp):
AGGATTTAGGAGTAGATAAGGGAT
Found at i:11042 original size:27 final size:28
Alignment explanation
Indices: 11002--11087 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 28
10992 AGGAAGCGTC
* * *
11002 CTGGTGGCTATGCCACAATTTTTTG-AT
1 CTGGTGGCTCTGCCACAATTATCTGTAT
*
11029 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTGTAT
* * *
11057 CTGGTGACTCTGTCAC-ATTCTCTGT-T
1 CTGGTGGCTCTGCCACAATTATCTGTAT
11083 CTGGT
1 CTGGT
11088 AGCCATGCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.12
27 29 0.57
28 16 0.31
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACAATTATCTGTAT
Found at i:11067 original size:28 final size:27
Alignment explanation
Indices: 11027--11087 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
11017 CAATTTTTTG
*
11027 ATCTGGTGGCTCTGCCACGATTATCTGT
1 ATCTGGTGACTCTGCCAC-ATTATCTGT
* *
11055 ATCTGGTGACTCTGTCACATTCTCTGT
1 ATCTGGTGACTCTGCCACATTATCTGT
11082 -TCTGGT
1 ATCTGGT
11088 AGCCATGCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 6 0.20
27 8 0.27
28 16 0.53
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.39
Consensus pattern (27 bp):
ATCTGGTGACTCTGCCACATTATCTGT
Found at i:12163 original size:11 final size:10
Alignment explanation
Indices: 12135--12168 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12125 AGCCTGTAAG
12135 TATTCTGAAT
1 TATTCTGAAT
*
12145 TTTTCTGAAT
1 TATTCTGAAT
12155 ATATTCTGAAT
1 -TATTCTGAAT
12166 TAT
1 TAT
12169 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:17338 original size:23 final size:23
Alignment explanation
Indices: 17307--17369 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 23
17297 AAAGTCTGTC
*
17307 AGGAGAGGATTTAGGAGTTGATA
1 AGGATAGGATTTAGGAGTTGATA
17330 AGGATAGGATTTAGGAGTTGATA
1 AGGATAGGATTTAGGAGTTGATA
17353 AGGGATA-GATTTAGGAG
1 A-GGATAGGATTTAGGAG
17370 CAGAAAGGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 33 0.87
24 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (23 bp):
AGGATAGGATTTAGGAGTTGATA
Found at i:18834 original size:27 final size:27
Alignment explanation
Indices: 18794--18905 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
18784 AGGAAGCGTC
*
18794 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
18821 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
18848 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
18876 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
18902 CTGG
1 CTGG
18906 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:18900 original size:54 final size:54
Alignment explanation
Indices: 18794--18905 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
18784 AGGAAGCGTC
* *
18794 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
18848 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
18902 CTGG
1 CTGG
18906 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:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:40253 original size:28 final size:28
Alignment explanation
Indices: 40193--40367 Score: 273
Period size: 28 Copynumber: 6.3 Consensus size: 28
40183 TTAAGTCCGT
*
40193 ACACTCAGTGCTATATAATC-AACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
40220 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
*
40248 ACACTTAGTGCTACAT-ATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
40275 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
40303 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
* * * *
40331 ACACTTAGTGCTGTACAATTTAAACCCGC
1 ACACTTAGTGCTATATAA-TCAAACTCGC
40360 ACACTTAG
1 ACACTTAG
40368 CGCCAATCTC
Statistics
Matches: 138, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
27 45 0.33
28 77 0.56
29 16 0.12
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (28 bp):
ACACTTAGTGCTATATAATCAAACTCGC
Found at i:40260 original size:55 final size:56
Alignment explanation
Indices: 40193--40367 Score: 273
Period size: 55 Copynumber: 3.1 Consensus size: 56
40183 TTAAGTCCGT
*
40193 ACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACTCGC
*
40248 ACACTTAGTGCTACAT-ATCAAACTCGCACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACTCGC
* * * *
40303 ACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGC
1 ACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAA-TCAAACTCGC
40360 ACACTTAG
1 ACACTTAG
40368 CGCCAATCTC
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
54 3 0.03
55 64 0.58
56 27 0.25
57 16 0.15
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (56 bp):
ACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACTCGC
Found at i:41693 original size:17 final size:17
Alignment explanation
Indices: 41642--41693 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
41632 TCCTTCTTCC
41642 TCCCTTATTTTATTCA-
1 TCCCTTATTTTATTCAT
* * * *
41658 TCCTTTTTTTTTTTAAT
1 TCCCTTATTTTATTCAT
*
41675 TCCCTTCTTTTATTCAT
1 TCCCTTATTTTATTCAT
41692 TC
1 TC
41694 TTAATTTACT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (17 bp):
TCCCTTATTTTATTCAT
Done.