Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold557
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: 46130
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:9402 original size:23 final size:22
Alignment explanation
Indices: 9371--9413 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
9361 CCGCTCAAAA
9371 TACATAATA-TATACATAAATTT
1 TACATAATAGTA-ACATAAATTT
9393 TACATTAATAGTAACATAAAT
1 TACA-TAATAGTAACATAAAT
9414 GTTAACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (22 bp):
TACATAATAGTAACATAAATTT
Found at i:14500 original size:27 final size:27
Alignment explanation
Indices: 14470--14647 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
14460 ATATTGAGTC
* * * *
14470 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
14497 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
14524 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
14552 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
14579 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
14606 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
14633 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
14648 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:14609 original size:82 final size:81
Alignment explanation
Indices: 14491--14646 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
14481 TGCTATATAA
* *
14491 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
14556 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
14573 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
14637 CACTTAGTGC
65 CACTTAGTGC
14647 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:22528 original size:27 final size:27
Alignment explanation
Indices: 22498--22675 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
22488 ATATTGAGTC
* * * *
22498 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
22525 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
22552 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
22580 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
22607 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
22634 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
22661 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
22676 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:22637 original size:82 final size:81
Alignment explanation
Indices: 22519--22674 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
22509 TGCTATATAA
* *
22519 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
22584 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
22601 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
22665 CACTTAGTGC
65 CACTTAGTGC
22675 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28224 original size:20 final size:20
Alignment explanation
Indices: 28199--28248 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
28189 TGGCTTAAAA
28199 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
28219 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
28236 GTGGTAGTGGATT
1 TTGGTAGTGGATT
28249 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:32850 original size:20 final size:20
Alignment explanation
Indices: 32825--32874 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
32815 TGGCTTAAAA
32825 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
32845 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
32862 GTGGTAGTGGATT
1 TTGGTAGTGGATT
32875 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:34099 original size:20 final size:19
Alignment explanation
Indices: 34060--34099 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
34050 AAATAGTGAG
*
34060 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGAATA
*
34079 AATTCTATTTTCTGAGAATA
1 AATT-TATTTTCTAAGAATA
34099 A
1 A
34100 CAATTCCGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:35544 original size:23 final size:22
Alignment explanation
Indices: 35513--35555 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
35503 TGGCTCAAAA
35513 TACATAATA-TATACATAAATTT
1 TACATAATAGTA-ACATAAATTT
35535 TACATTAATAGTAACATAAAT
1 TACA-TAATAGTAACATAAAT
35556 GTTAACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (22 bp):
TACATAATAGTAACATAAATTT
Done.