Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1185
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: 37880
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Found at i:1059 original size:26 final size:26
Alignment explanation
Indices: 1030--1109 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
1020 CTGTGATCAG
1030 GTGTAGTACTAAGTGCAGGCTACTAC
1 GTGTAGTACTAAGTGCAGGCTACTAC
*
1056 GTGTA-T-C-AA-TGGTTAGG-T-C-AC
1 GTGTAGTACTAAGT-G-CAGGCTACTAC
1077 GTGTGTAGTACTAAGTGCAGGCTACTAC
1 --GTGTAGTACTAAGTGCAGGCTACTAC
1105 GTGTA
1 GTGTA
1110 CCGGATATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 22
0.63 0.03 0.34
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 9 0.22
24 5 0.12
25 5 0.12
26 14 0.34
27 2 0.05
28 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (26 bp):
GTGTAGTACTAAGTGCAGGCTACTAC
Found at i:1149 original size:48 final size:48
Alignment explanation
Indices: 974--1151 Score: 191
Period size: 48 Copynumber: 3.7 Consensus size: 48
964 TCTATTGTGA
* * * *
974 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGAAAACT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATATT
* * *
1022 -GT-GATCAGGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AATGGTT
1 GGTCG--CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAAT-ATT
* * *
1070 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATATT
1 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATATT
* *
1119 GGTCGCATGTGTAGTACTATGTGTAGGCTACTA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1152 TGCTTACCAG
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
46 1 0.01
47 4 0.04
48 62 0.58
49 35 0.33
50 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (48 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATATT
Found at i:3405 original size:15 final size:15
Alignment explanation
Indices: 3385--3421 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3375 TCGTATCTTA
3385 GGTTTCTTTACTCTG
1 GGTTTCTTTACTCTG
*
3400 GGTTTCTTTATTCTG
1 GGTTTCTTTACTCTG
3415 GGTTTCT
1 GGTTTCT
3422 CTATCTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (15 bp):
GGTTTCTTTACTCTG
Found at i:5197 original size:26 final size:26
Alignment explanation
Indices: 5168--5247 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
5158 TGTGATCAGT
5168 GTGTAGTACTAAGTGCAGGCTACTAC
1 GTGTAGTACTAAGTGCAGGCTACTAC
*
5194 GTGTA-T-C-AA-TGGTTAGG-T-C-AC
1 GTGTAGTACTAAGT-G-CAGGCTACTAC
5215 GTGTGTAGTACTAAGTGCAGGCTACTAC
1 --GTGTAGTACTAAGTGCAGGCTACTAC
5243 GTGTA
1 GTGTA
5248 CCGGATAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 22
0.63 0.03 0.34
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 9 0.22
24 5 0.12
25 5 0.12
26 14 0.34
27 2 0.05
28 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (26 bp):
GTGTAGTACTAAGTGCAGGCTACTAC
Found at i:5269 original size:49 final size:48
Alignment explanation
Indices: 5110--5290 Score: 186
Period size: 49 Copynumber: 3.7 Consensus size: 48
5100 TCTATTGTGA
* * * *
5110 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGATAATT
* * **
5159 -GT-GATCAGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAATGGTT
1 GGTCG--CA-TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATT
* *
5208 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GATAATT
* *
5258 GGTCGCATGTGTAGTACTATGTGTAGGCTACTA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
5291 TGCGTACCAG
Statistics
Matches: 107, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
47 1 0.01
48 2 0.02
49 67 0.63
50 35 0.33
51 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (48 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATT
Found at i:7663 original size:15 final size:15
Alignment explanation
Indices: 7643--7679 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
7633 TCGTATCTTA
7643 GGTTTCTTTACTCTG
1 GGTTTCTTTACTCTG
*
7658 GGTTTCTTTATTCTG
1 GGTTTCTTTACTCTG
7673 GGTTTCT
1 GGTTTCT
7680 CTATCTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (15 bp):
GGTTTCTTTACTCTG
Found at i:9498 original size:49 final size:51
Alignment explanation
Indices: 9368--9500 Score: 157
Period size: 51 Copynumber: 2.6 Consensus size: 51
9358 TCTATTGTGA
*
9368 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTAACCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTAACCGAAAACTGT
* * * *
9419 GATCAG-GTGTGTAGTACTAAGTGCAGGCTACTACGTGT-ACCGGATAA-T-T
1 GGTC-GCATGTGTAGTACTAAGTGCAGGCTACTACGCGTAACC-GAAAACTGT
* *
9468 GGTCGCATGTGTAGTACTATGTGTAGGCTACTA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
9501 TGCTTACCAG
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
48 1 0.01
49 28 0.40
50 4 0.06
51 36 0.51
52 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTAACCGAAAACTGT
Found at i:11880 original size:15 final size:15
Alignment explanation
Indices: 11860--11896 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
11850 TCGTATCTTA
11860 GGTTTCTTTACTCTG
1 GGTTTCTTTACTCTG
*
11875 GGTTTCTTTATTCTG
1 GGTTTCTTTACTCTG
11890 GGTTTCT
1 GGTTTCT
11897 CTATCTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (15 bp):
GGTTTCTTTACTCTG
Found at i:13657 original size:50 final size:49
Alignment explanation
Indices: 13587--13724 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 49
13577 TATTGTGAGG
13587 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC-GAAAACTGTGA
1 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGGAAAA-T-TGA
* * * * *
13637 TCAG-GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
1 TC-GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGGAAAATTGA
* * *
13686 TCGCATGTGTAGTACTATGTGTAGGCTACTATGCTTACC
1 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
13725 AGATAGCTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
48 1 0.01
49 33 0.45
50 35 0.47
51 5 0.07
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (49 bp):
TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGGAAAATTGA
Found at i:16089 original size:15 final size:15
Alignment explanation
Indices: 16069--16105 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
16059 TCGTATCTTA
16069 GGTTTCTTTACTCTG
1 GGTTTCTTTACTCTG
*
16084 GGTTTCTTTATTCTG
1 GGTTTCTTTACTCTG
16099 GGTTTCT
1 GGTTTCT
16106 CTATCTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (15 bp):
GGTTTCTTTACTCTG
Found at i:17928 original size:49 final size:51
Alignment explanation
Indices: 17798--17930 Score: 157
Period size: 51 Copynumber: 2.6 Consensus size: 51
17788 TCTATTGTGA
*
17798 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTAACCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTAACCGAAAACTGT
* * * *
17849 GATCAG-GTGTGTAGTACTAAGTGCAGGCTACTACGTGT-ACCGGATAA-T-T
1 GGTC-GCATGTGTAGTACTAAGTGCAGGCTACTACGCGTAACC-GAAAACTGT
* *
17898 GGTCGCATGTGTAGTACTATGTGTAGGCTACTA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
17931 TGCTTACCAG
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
48 1 0.01
49 28 0.40
50 4 0.06
51 36 0.51
52 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTAACCGAAAACTGT
Found at i:20303 original size:15 final size:15
Alignment explanation
Indices: 20283--20319 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
20273 TCGTATCTTA
20283 GGTTTCTTTACTCTG
1 GGTTTCTTTACTCTG
*
20298 GGTTTCTTTATTCTG
1 GGTTTCTTTACTCTG
20313 GGTTTCT
1 GGTTTCT
20320 CTATCTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (15 bp):
GGTTTCTTTACTCTG
Found at i:22098 original size:26 final size:26
Alignment explanation
Indices: 22069--22149 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
22059 GTGATCAGGT
22069 GTGTAGTACTAAGTGCAGGCTACTAC
1 GTGTAGTACTAAGTGCAGGCTACTAC
* *
22095 GTGTA-T-C-AAATGGTTAGG-T-C-AC
1 GTGTAGTACTAAGT-G-CAGGCTACTAC
22117 GTGTGTAGTACTAAGTGCAGGCTACTAC
1 --GTGTAGTACTAAGTGCAGGCTACTAC
22145 GTGTA
1 GTGTA
22150 CCGGATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 20
0.63 0.06 0.31
Matches are distributed among these distances:
22 2 0.05
23 4 0.10
24 8 0.20
25 8 0.20
26 13 0.32
27 4 0.10
28 2 0.05
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (26 bp):
GTGTAGTACTAAGTGCAGGCTACTAC
Found at i:24543 original size:15 final size:15
Alignment explanation
Indices: 24523--24559 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
24513 TCGTATCTTA
24523 GGTTTCTTTACTCTG
1 GGTTTCTTTACTCTG
*
24538 GGTTTCTTTATTCTG
1 GGTTTCTTTACTCTG
24553 GGTTTCT
1 GGTTTCT
24560 CTATCTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (15 bp):
GGTTTCTTTACTCTG
Found at i:26339 original size:26 final size:26
Alignment explanation
Indices: 26310--26390 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
26300 GTGATCAGGT
26310 GTGTAGTACTAAGTGCAGGCTACTAC
1 GTGTAGTACTAAGTGCAGGCTACTAC
* *
26336 GTGTA-T-C-AAATGGTTAGG-T-C-AC
1 GTGTAGTACTAAGT-G-CAGGCTACTAC
26358 GTGTGTAGTACTAAGTGCAGGCTACTAC
1 --GTGTAGTACTAAGTGCAGGCTACTAC
26386 GTGTA
1 GTGTA
26391 CCGGATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 20
0.63 0.06 0.31
Matches are distributed among these distances:
22 2 0.05
23 4 0.10
24 8 0.20
25 8 0.20
26 13 0.32
27 4 0.10
28 2 0.05
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (26 bp):
GTGTAGTACTAAGTGCAGGCTACTAC
Found at i:26441 original size:49 final size:49
Alignment explanation
Indices: 26251--26446 Score: 196
Period size: 50 Copynumber: 3.9 Consensus size: 49
26241 TCTATTGTGA
* * *
26251 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA-T-T
* * * * * **
26302 GATCAG-GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
1 GGTC-GCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * * *
26351 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * *
26401 GGTCGCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCAGATA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
26447 GCTTTGGCTA
Statistics
Matches: 118, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
49 40 0.34
50 42 0.36
51 35 0.30
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.29
Consensus pattern (49 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:28778 original size:15 final size:15
Alignment explanation
Indices: 28758--28794 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
28748 TCGTATCTTA
28758 GGTTTCTTTACTCTG
1 GGTTTCTTTACTCTG
*
28773 GGTTTCTTTATTCTG
1 GGTTTCTTTACTCTG
28788 GGTTTCT
1 GGTTTCT
28795 CTATCTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (15 bp):
GGTTTCTTTACTCTG
Found at i:33028 original size:14 final size:14
Alignment explanation
Indices: 33009--33043 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
32999 TCGTATCTTA
33009 GGTTTCTTTACTCT
1 GGTTTCTTTACTCT
*
33023 GGTTTCTTTATTCT
1 GGTTTCTTTACTCT
*
33037 GGGTTCT
1 GGTTTCT
33044 CTATCTTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.17, G:0.20, T:0.57
Consensus pattern (14 bp):
GGTTTCTTTACTCT
Found at i:37195 original size:17 final size:17
Alignment explanation
Indices: 37164--37196 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
37154 TCGTATCTTA
37164 GGTTTCTCTTTATTCTG
1 GGTTTCTCTTTATTCTG
37181 GGTTT-TCTTTGATTCT
1 GGTTTCTCTTT-ATTCT
37197 TTCGAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.15, G:0.18, T:0.61
Consensus pattern (17 bp):
GGTTTCTCTTTATTCTG
Done.