Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1184
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: 53496
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Found at i:5297 original size:47 final size:47
Alignment explanation
Indices: 5219--5780 Score: 818
Period size: 47 Copynumber: 11.6 Consensus size: 47
5209 CCCTTCGGGA
* * * * * * *
5219 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5266 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5313 CTTATCACATATATACACTTTCACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATAT--A---T---ACACTTTCACATTCATCACATCGGCCATTAGGC
5370 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5417 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5466 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5513 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCGTTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5562 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5609 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5656 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5705 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5754 ATTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
5781 TATTCAAATA
Statistics
Matches: 475, Mismatches: 24, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
47 237 0.50
49 189 0.40
50 1 0.00
51 1 0.00
53 1 0.00
54 1 0.00
55 4 0.01
57 41 0.09
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:5453 original size:96 final size:96
Alignment explanation
Indices: 5337--5780 Score: 793
Period size: 96 Copynumber: 4.6 Consensus size: 96
5327 ACACTTTCAC
5337 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
5402 CATCGGCCATTAGGCCTTATCACATATATAT
66 CATCGGCCATTAGGCCTTATCACATATATAT
* * *
5433 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATTACATATATACACTTTCACATTCATCA
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
5498 CATCGGCCATTAGGCCTTATCACATATATAT
66 CATCGGCCATTAGGCCTTATCACATATATAT
*
5529 ACACTTTCACATTCATCACATCGGCCGTTAGGCCTTATCACATATATACACTTTCACATTCATCA
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
* *
5594 CATCGGCTATTAGGCCTTATTAC--ATATAT
66 CATCGGCCATTAGGCCTTATCACATATATAT
5623 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCAT
5688 CACATCGGCCATTAGGCCTTATCACATATATAT
64 CACATCGGCCATTAGGCCTTATCACATATATAT
*
5721 ACACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATACACTTTCACATT
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
5781 TATTCAAATA
Statistics
Matches: 331, Mismatches: 13, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
94 46 0.14
96 239 0.72
98 46 0.14
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (96 bp):
ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
CATCGGCCATTAGGCCTTATCACATATATAT
Found at i:10895 original size:38 final size:40
Alignment explanation
Indices: 10804--10895 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
10794 TGGTACCTTT
* *
10804 TGGTGTGTAGGG-TTGGATGAGTTGATTATATCCCCATACT
1 TGGTGTGTAGGGTTTGGATGAGTCGATTATATCCCCA-ACA
* *
10844 TGGTGTGTAGGGTTTGG-TGGGTCGATTCTATCCCC-ACA
1 TGGTGTGTAGGGTTTGGATGAGTCGATTATATCCCCAACA
*
10882 TGGTGTGTTGGGTT
1 TGGTGTGTAGGGTT
10896 GGTCGAAGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 15 0.33
40 27 0.59
41 4 0.09
ACGTcount: A:0.14, C:0.13, G:0.35, T:0.38
Consensus pattern (40 bp):
TGGTGTGTAGGGTTTGGATGAGTCGATTATATCCCCAACA
Found at i:21724 original size:40 final size:39
Alignment explanation
Indices: 21680--21774 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 39
21670 ACGGTACCTT
* * *
21680 TTGGTCTGTAGGGTTGGATGGGTTGATTATATCCGCATA
1 TTGGTGTGTAGGGTTGGATGGGTCGATTATATCCCCATA
* *
21719 CTTGGTGTGTAGGGTTGGGTGGGTCGATTCTATCCCCATA
1 -TTGGTGTGTAGGGTTGGATGGGTCGATTATATCCCCATA
*
21759 -TGGTGTGTTGGGTTGG
1 TTGGTGTGTAGGGTTGG
21775 TCGGAGATGG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
38 15 0.31
40 34 0.69
ACGTcount: A:0.13, C:0.12, G:0.38, T:0.38
Consensus pattern (39 bp):
TTGGTGTGTAGGGTTGGATGGGTCGATTATATCCCCATA
Found at i:25609 original size:29 final size:29
Alignment explanation
Indices: 25567--25625 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
25557 ATGCTGAATG
25567 TTAGAAATTAATGGTAGAAAATAAAAGGT
1 TTAGAAATTAATGGTAGAAAATAAAAGGT
* *
25596 TTAGAAATTTATGGTAGAAAATAAGAGGT
1 TTAGAAATTAATGGTAGAAAATAAAAGGT
25625 T
1 T
25626 GTTGATAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (29 bp):
TTAGAAATTAATGGTAGAAAATAAAAGGT
Found at i:27234 original size:16 final size:17
Alignment explanation
Indices: 27202--27234 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27192 GTTATACGAA
27202 CTTACTTAGCATTTTATG
1 CTTACTTAG-ATTTTATG
27220 CTTACTTAG-TTTTAT
1 CTTACTTAGATTTTAT
27235 TTCTATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (17 bp):
CTTACTTAGATTTTATG
Found at i:28546 original size:43 final size:43
Alignment explanation
Indices: 28457--28551 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
28447 TGTGATTACA
* * * *
28457 TGTAAAACCATGTCTGGGACATTGGCATTGTACTGAGATTATG
1 TGTAAGACCATGTCTAGGACATTGGCATCGTAATGAGATTATG
*
28500 TGTAAGACCATGTCTAGGACATTGGCATCGTTAAT-CGATT-TCG
1 TGTAAGACCATGTCTAGGACATTGGCATCG-TAATGAGATTAT-G
28543 TGTAAGACC
1 TGTAAGACC
28552 CTATCTGGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 1 0.02
43 41 0.91
44 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATTGGCATCGTAATGAGATTATG
Found at i:28600 original size:22 final size:22
Alignment explanation
Indices: 28572--28617 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
28562 TATCGCATTG
28572 TGATAACATATAAGACCATATC
1 TGATAACATATAAGACCATATC
28594 TGATAACATATAAGACCATATC
1 TGATAACATATAAGACCATATC
28616 TG
1 TG
28618 GGATATCGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (22 bp):
TGATAACATATAAGACCATATC
Found at i:29987 original size:18 final size:18
Alignment explanation
Indices: 29964--29999 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29954 CCTTCAATGT
29964 AAAAAGATAGATATATTG
1 AAAAAGATAGATATATTG
29982 AAAAAGATAGATATATTG
1 AAAAAGATAGATATATTG
30000 TCACATCCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.28
Consensus pattern (18 bp):
AAAAAGATAGATATATTG
Found at i:31983 original size:27 final size:27
Alignment explanation
Indices: 31953--32054 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
31943 GTTCTGTTAA
* *
31953 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* *
31980 GTGGCTATGCCACAAACATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
*
32007 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
32034 GTGGCTCTACCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
32055 ATAACTGAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 7 0.11
27 53 0.80
28 6 0.09
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:32207 original size:19 final size:19
Alignment explanation
Indices: 32185--32241 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
32175 TTCTAATTTT
32185 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
*
32204 TGATTCTG--A--T--T-T
1 TGATTCTGTTACCTGATAC
32216 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
32235 TGATTCT
1 TGATTCT
32242 AATTCTGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
12 8 0.28
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 15 0.52
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:32220 original size:31 final size:31
Alignment explanation
Indices: 32185--32285 Score: 148
Period size: 31 Copynumber: 3.3 Consensus size: 31
32175 TTCTAATTTT
*
32185 TGATTCTGTTACCTGATACTGATTCTGATTT
1 TGATTCTGTTACCTGATACTGATTCTGATTC
*
32216 TGATTCTGTTACCTGATACTGATTCTAATTC
1 TGATTCTGTTACCTGATACTGATTCTGATTC
* * **
32247 TGATTCTGTCACCTAATTTTGATTCTGATTC
1 TGATTCTGTTACCTGATACTGATTCTGATTC
32278 TGATTCTG
1 TGATTCTG
32286 ATTCTAATTC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (31 bp):
TGATTCTGTTACCTGATACTGATTCTGATTC
Found at i:32314 original size:6 final size:6
Alignment explanation
Indices: 32197--32296 Score: 78
Period size: 6 Copynumber: 16.3 Consensus size: 6
32187 ATTCTGTTAC
* * * *
32197 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTAATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * * *
32246 CTGATT CTG-TCAC CTAATT TTGATT CTGATT CTGATT CTGATT CTAATT
1 CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGATT CTGATT
32295 CT
1 CT
32297 AATAATGTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
5 3 0.04
6 64 0.86
7 5 0.07
8 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (6 bp):
CTGATT
Found at i:33113 original size:49 final size:49
Alignment explanation
Indices: 33055--33184 Score: 206
Period size: 49 Copynumber: 2.7 Consensus size: 49
33045 TATGGAGGAA
* *
33055 GTATCTGGCAATAAATCTACATTTTCTGGTGGCATGTCCACATTATTCT
1 GTATGTGGCAATAAATCTGCATTTTCTGGTGGCATGTCCACATTATTCT
* *
33104 GTATGTGGCAATAAATTTGCATTTTCTGGTAGCATGTCCACATTATTCT
1 GTATGTGGCAATAAATCTGCATTTTCTGGTGGCATGTCCACATTATTCT
* *
33153 GTATGTGGCAATAAATCTGCAATATCTGGTGG
1 GTATGTGGCAATAAATCTGCATTTTCTGGTGG
33185 TTCAACACAC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 73 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (49 bp):
GTATGTGGCAATAAATCTGCATTTTCTGGTGGCATGTCCACATTATTCT
Found at i:33898 original size:33 final size:33
Alignment explanation
Indices: 33856--33921 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
33846 CTTGTTGCAT
*
33856 TGTTTTAATTTAATTACGATGTATTCTCTAAAA
1 TGTTTTAATTTAATTACGATGTATTCCCTAAAA
33889 TGTTTTAATTTAATTACGATGTATTCCCTAAAA
1 TGTTTTAATTTAATTACGATGTATTCCCTAAAA
33922 CACTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (33 bp):
TGTTTTAATTTAATTACGATGTATTCCCTAAAA
Found at i:39655 original size:47 final size:47
Alignment explanation
Indices: 39588--40272 Score: 1199
Period size: 47 Copynumber: 14.6 Consensus size: 47
39578 TATTTGAATA
* * *
39588 AATGTGAAAGTTTATATATGTGATAAGGCCTAATAGCCGATGTGGTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39635 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39682 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGGTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39729 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGGTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39776 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39823 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGGTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39870 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
39917 AATGTGATAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGGTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39964 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40011 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
40058 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGGTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40105 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
40152 AATGTGAAAATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
40199 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40246 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
40273 TCCCGAAGGG
Statistics
Matches: 615, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 615 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40172 original size:25 final size:25
Alignment explanation
Indices: 40144--40222 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
40134 CTAATGGCCG
40144 ATGTGATGAATGTGAAAATGTATAT
1 ATGTGATGAATGTGAAAATGTATAT
** ***
40169 ATGTGAT-AA-G-GCCGAATGGCCA-
1 ATGTGATGAATGTG-AAAATGTATAT
*
40191 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAATGTATAT
40216 ATGTGAT
1 ATGTGAT
40223 AGGGCCGAGT
Statistics
Matches: 38, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 7 0.18
25 15 0.39
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAATGTATAT
Done.