Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3634
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: 40769
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:6062 original size:29 final size:29
Alignment explanation
Indices: 5999--6066 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
5989 TAATCAACCA
5999 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
6028 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
6057 CGCACACTTA
1 CGCACACTTA
6067 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:6207 original size:29 final size:30
Alignment explanation
Indices: 6168--6246 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
6158 CTTAATAATC
6168 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
6198 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
6227 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
6247 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:9423 original size:79 final size:81
Alignment explanation
Indices: 9287--9471 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
9277 TTGAATGATG
* *
9287 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
9351 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
9366 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
9428 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
9446 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
9472 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:9485 original size:40 final size:40
Alignment explanation
Indices: 9288--9471 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
9278 TGAATGATGT
* * * *
9288 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
9328 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
9368 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
9406 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
9447 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
9472 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:9493 original size:79 final size:79
Alignment explanation
Indices: 9340--9494 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
9330 GGACTAAGAT
* * **
9340 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
9405 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
9419 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
9482 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
9495 ATTCTGAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.59
80 25 0.38
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:13433 original size:17 final size:17
Alignment explanation
Indices: 13411--13446 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
13401 AGTAATTAAT
*
13411 AAGTTATAATATACTAA
1 AAGTTATAATATAATAA
13428 AAGTTATAATATAATAA
1 AAGTTATAATATAATAA
13445 AA
1 AA
13447 CATACAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (17 bp):
AAGTTATAATATAATAA
Found at i:15459 original size:20 final size:20
Alignment explanation
Indices: 15414--15460 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
15404 ATAAGCTCGG
*
15414 TTGAGCTCAAACGAGCTGAA
1 TTGAGCTCAAACGAACTGAA
** *
15434 ACGAGCTCAAATGAACTGAA
1 TTGAGCTCAAACGAACTGAA
15454 TTGAGCT
1 TTGAGCT
15461 GGACGAAGCT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.21
Consensus pattern (20 bp):
TTGAGCTCAAACGAACTGAA
Found at i:17195 original size:17 final size:16
Alignment explanation
Indices: 17173--17218 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
17163 TTTTTCAATT
17173 TTCTTTTTCTTCTCACA
1 TTCTTTTTCTTCTC-CA
*
17190 TTCTTTTTCACTCTCCA
1 TTCTTTTTC-TTCTCCA
17207 TCTCTTTTTCTT
1 T-TCTTTTTCTT
17219 TTTCCTTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCTTTTTCTTCTCCA
Found at i:17218 original size:6 final size:6
Alignment explanation
Indices: 17209--17284 Score: 71
Period size: 6 Copynumber: 12.2 Consensus size: 6
17199 ACTCTCCATC
* * ** **
17209 TCTTTT TCTTTT TCCTTC TCTTTT TCTTTT TCACTT TCTTTT TCAATT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
17257 TCATTTT TCTTTT TCTTATT CTCTTTT T
1 TC-TTTT TCTTTT TCTT-TT -TCTTTT T
17285 GCACTTTTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
6 43 0.78
7 8 0.15
8 4 0.07
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (6 bp):
TCTTTT
Found at i:17228 original size:18 final size:19
Alignment explanation
Indices: 17159--17273 Score: 87
Period size: 18 Copynumber: 6.3 Consensus size: 19
17149 TCAGACTCAA
* *
17159 TTTCTTTTTCAATTTTCTT
1 TTTCTTTTTCACTTCTCTT
* *
17178 TTTC-TTCTCACAT-TCTT
1 TTTCTTTTTCACTTCTCTT
** * *
17195 TTTCACTCTC-CATCTCTT
1 TTTCTTTTTCACTTCTCTT
17213 TTTCTTTTTC-CTTCTCTT
1 TTTCTTTTTCACTTCTCTT
17231 TTTCTTTTTCACTT-TCTT
1 TTTCTTTTTCACTTCTCTT
** * *
17249 TTTCAATTTCATTTTTCTT
1 TTTCTTTTTCACTTCTCTT
17268 TTTCTT
1 TTTCTT
17274 ATTCTCTTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
17 11 0.14
18 53 0.67
19 15 0.19
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTCTTTTTCACTTCTCTT
Found at i:18218 original size:19 final size:19
Alignment explanation
Indices: 18194--18242 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
18184 TCACTTCTCT
18194 CTTTTTTTTTATACTAAAA
1 CTTTTTTTTTATACTAAAA
* *
18213 CTTTTTTTTTATATTCAAA
1 CTTTTTTTTTATACTAAAA
18232 CTTTTTTTTTA
1 CTTTTTTTTTA
18243 ATTTCGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.65
Consensus pattern (19 bp):
CTTTTTTTTTATACTAAAA
Found at i:19881 original size:10 final size:10
Alignment explanation
Indices: 19868--19903 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
19858 TAAGCTCGGT
*
19868 TGAGCTCAAA
1 TGAGCTAAAA
19878 TGAGCTAAAA
1 TGAGCTAAAA
19888 TGAGCTAAAA
1 TGAGCTAAAA
*
19898 TAAGCT
1 TGAGCT
19904 GAATTTTGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.22
Consensus pattern (10 bp):
TGAGCTAAAA
Found at i:20644 original size:56 final size:56
Alignment explanation
Indices: 20581--20714 Score: 187
Period size: 56 Copynumber: 2.4 Consensus size: 56
20571 CATGGCATCG
** ** * *
20581 ATATATGTCAGCGAGTAAGACCATGTTTTATATGTTGGTATCAATATATGACTCTA
1 ATATATGTGTGCGAGTAAGACCACATTTTATATGTTGGCATCAATATATGACTCCA
* * *
20637 ATATATGTGTGCGAGTAAGACCACATTTTATATGTTGGCATCGATATGTGACTCCG
1 ATATATGTGTGCGAGTAAGACCACATTTTATATGTTGGCATCAATATATGACTCCA
20693 ATATATGTGTGCGAGTAAGACC
1 ATATATGTGTGCGAGTAAGACC
20715 CTGTCTGGGA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 69 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (56 bp):
ATATATGTGTGCGAGTAAGACCACATTTTATATGTTGGCATCAATATATGACTCCA
Found at i:24021 original size:64 final size:63
Alignment explanation
Indices: 23941--24123 Score: 169
Period size: 66 Copynumber: 2.8 Consensus size: 63
23931 AGACATTATG
* * *
23941 ATGTAGCTAGGTCGCATGGGTGATCCTATGTGTACACCATGTAGACAAGAGATCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTG-TCCTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* *
24005 ATGTAGCTAGGTCGCATGCTGGT-TCC-AGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATG--GGTGTCCTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
24068 TAA
61 TAA
* * * *
24071 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGT-GTCCT-ATGTGTACACCATGTAG-ACAAGAGAGC
24124 CAAACTATAT
Statistics
Matches: 98, Mismatches: 11, Indels: 21
0.75 0.08 0.16
Matches are distributed among these distances:
62 1 0.01
63 23 0.23
64 22 0.22
65 17 0.17
66 34 0.35
67 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (63 bp):
ATGTAGCTAGGTCGCATGGGTGTCCTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28837 original size:46 final size:46
Alignment explanation
Indices: 28765--28865 Score: 134
Period size: 46 Copynumber: 2.2 Consensus size: 46
28755 GACAGGACAG
**
28765 GACAGAAATGAGCCATGTAAGTCCATATCAGT-TATATGG-ATTTGGA
1 GACAGAAATGAGCCATGTAAACCCATATCA-TATATATGGCA-TTGGA
* *
28811 GACAGGAATGAGCCATGTAAACCCATATTATATATATGGCATTGGA
1 GACAGAAATGAGCCATGTAAACCCATATCATATATATGGCATTGGA
28857 GACAGAAAT
1 GACAGAAAT
28866 AATTCATGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 1 0.02
46 46 0.96
47 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (46 bp):
GACAGAAATGAGCCATGTAAACCCATATCATATATATGGCATTGGA
Found at i:30844 original size:11 final size:10
Alignment explanation
Indices: 30792--30846 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 10
30782 GATGAGATTT
30792 TGATAT-ACA
1 TGATATGACA
*
30801 TGATTTGACA
1 TGATATGACA
*
30811 TGATATACACA
1 TGATAT-GACA
*
30822 TGATATG-TA
1 TGATATGACA
30831 TGATATGCACA
1 TGATATG-ACA
30842 TGATA
1 TGATA
30847 AATTCATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 13 0.36
10 8 0.22
11 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (10 bp):
TGATATGACA
Found at i:30925 original size:25 final size:25
Alignment explanation
Indices: 30893--30958 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
30883 GAGGAAGTGC
30893 AAAAGGGCTTTGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
30918 AAAAGGGCTTTGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
30943 AAAAGGGCTTTGCCCC
1 AAAAGGGCTTTGCCCC
30959 TGTAACACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Done.