Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2140
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: 11517
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Found at i:221 original size:71 final size:71
Alignment explanation
Indices: 2--320 Score: 380
Period size: 75 Copynumber: 4.4 Consensus size: 71
1 C
* *
2 CTCTCGCAATATGAGTT-ATTTTGAAAACAG-AATTGAAAATACCTCAGCATGTGAACC-GAGGC
1 CTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGGC
*
64 TCAACTCAC
63 TCAACTCAT
* * *
73 CTCTCGCAATATAAGTTGATTTTTTTTTTG-AAACAGAAATTGAAA-TACCTCAACGTGTCTTGA
1 CTCTCGCAATATGAGTTGA------TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGA
136 GGCTCAACTCAT
60 GGCTCAACTCAT
* *
148 TTCTCGCAATATAAGTTGATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCA
1 CTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCA
213 ACTCAT
66 ACTCAT
* *
219 TTCTCGCAATATGAGTTGATTTTTTTTTAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGG
1 CTCTCGCAATATGAGTTGA----TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGG
284 CTCAACTCA-
62 CTCAACTCAT
*
293 CTCTAGCAATATGAGTTGATTTTGAAAA
1 CTCTCGCAATATGAGTTGATTTTGAAAA
321 AACAATTAAA
Statistics
Matches: 220, Mismatches: 13, Indels: 31
0.83 0.05 0.12
Matches are distributed among these distances:
69 5 0.02
70 23 0.10
71 62 0.28
72 1 0.00
74 18 0.08
75 84 0.38
77 14 0.06
78 13 0.06
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (71 bp):
CTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCA
ACTCAT
Found at i:268 original size:146 final size:145
Alignment explanation
Indices: 2--320 Score: 466
Period size: 146 Copynumber: 2.2 Consensus size: 145
1 C
2 CTCTCGCAATATGAGTT-ATTTTGAAAACAGAATTGAAAATACCTCAGCATGTGAACCGAGGCTC
1 CTCTCGCAATATGAGTTGATTTTGAAAACAGAATTGAAAATACCTCAGCA-GTGAACCGAGGCTC
*
66 AACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAACAGAAATTGAAATACCTCAACGTGT
65 AACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTAAAACAGAAATTGAAATACCTCAACGTGT
*
131 CTTGAGGCTCAACTCA
130 CCTGAGGCTCAACTCA
* * * *
147 TTTCTCGCAATATAAGTTGATTTTGAAAACAGAAATTGAAATTACCTCAGC-GTG-TCCTGAGGC
1 -CTCTCGCAATATGAGTTGATTTTGAAAACAG-AATTGAAAATACCTCAGCAGTGAACC-GAGGC
** * *
210 TCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTTTTAAAACAGAAATTGAAATTACCTCAGCG
63 TCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTAAAACAGAAATTGAAA-TACCTCAACG
274 TGTCCTGAGGCTCAACTCA
127 TGTCCTGAGGCTCAACTCA
*
293 CTCTAGCAATATGAGTTGATTTTGAAAA
1 CTCTCGCAATATGAGTTGATTTTGAAAA
321 AACAATTAAA
Statistics
Matches: 156, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
145 51 0.33
146 75 0.48
147 13 0.08
148 17 0.11
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (145 bp):
CTCTCGCAATATGAGTTGATTTTGAAAACAGAATTGAAAATACCTCAGCAGTGAACCGAGGCTCA
ACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTAAAACAGAAATTGAAATACCTCAACGTGTC
CTGAGGCTCAACTCA
Found at i:8739 original size:12 final size:12
Alignment explanation
Indices: 8719--8754 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
8709 TGGGATATGC
*
8719 AATGTATGAATG
1 AATGCATGAATG
8731 AATGCATGAATG
1 AATGCATGAATG
8743 AATGCATGAATG
1 AATGCATGAATG
8755 TCAAATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:10316 original size:16 final size:15
Alignment explanation
Indices: 10295--10342 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
10285 GATGTGAATA
10295 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
10311 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
10326 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
10342 A
1 A
10343 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:10318 original size:24 final size:24
Alignment explanation
Indices: 10291--10346 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
10281 TAATGATGTG
*
10291 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
10315 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
10339 AATAATAA
1 AATAATAA
10347 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:10325 original size:8 final size:8
Alignment explanation
Indices: 10291--10342 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
10281 TAATGATGTG
*
10291 AATAATAA
1 AATATTAA
10299 AATATATAA
1 AATAT-TAA
10308 AATA-TAA
1 AATATTAA
10315 AATATTAA
1 AATATTAA
*
10323 AATATCAA
1 AATATTAA
*
10331 AATATTAG
1 AATATTAA
10339 AATA
1 AATA
10343 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:10508 original size:20 final size:20
Alignment explanation
Indices: 10456--10512 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
10446 ATACTACATC
*
10456 AATATGTACATATATAAAAAA
1 AATATGTACATA-ATATAAAA
* * *
10477 AATACGT-GATAATATTAAA
1 AATATGTACATAATATAAAA
10496 AATATGTACATAATATA
1 AATATGTACATAATATA
10513 GTGTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 12 0.43
20 10 0.36
21 6 0.21
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AATATGTACATAATATAAAA
Found at i:10554 original size:22 final size:24
Alignment explanation
Indices: 10491--10555 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
10481 CGTGATAATA
*
10491 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
10516 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
10539 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
10556 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:10580 original size:30 final size:29
Alignment explanation
Indices: 10544--10610 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
10534 TATAGTTAAG
*
10544 ATATATACATAAGATAACATGTAAAAATAT
1 ATATATAAATAAGATAACAT-TAAAAATAT
* * *
10574 ATATATAAATAATATAATATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAAATAT
10603 ATA-ATAAA
1 ATATATAAA
10611 ATAGTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 5 0.15
29 11 0.33
30 17 0.52
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAAATAT
Found at i:10607 original size:21 final size:20
Alignment explanation
Indices: 10582--10629 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
10572 ATATATATAA
*
10582 ATAATATAATATTAAAGATAT
1 ATAATATAATAGTAAA-ATAT
*
10603 ATAATAAAATAGTAAAATAT
1 ATAATATAATAGTAAAATAT
10623 AT-ATATA
1 ATAATATA
10630 CGTAATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.17
20 6 0.25
21 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
ATAATATAATAGTAAAATAT
Found at i:10612 original size:29 final size:29
Alignment explanation
Indices: 10565--10622 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
10555 AGATAACATG
*
10565 TAAAAATATATATATAAATAATATAATAT
1 TAAAAATATATATATAAATAATAAAATAT
* *
10594 TAAAGATATATA-ATAAAATAGTAAAATAT
1 TAAAAATATATATAT-AAATAATAAAATAT
10623 ATATATACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
TAAAAATATATATATAAATAATAAAATAT
Found at i:10623 original size:49 final size:48
Alignment explanation
Indices: 10567--10701 Score: 138
Period size: 49 Copynumber: 2.9 Consensus size: 48
10557 ATAACATGTA
10567 AAAATATATATATAAATAATATAATATTAAAGATATATAATAAAATAGT
1 AAAATATATATAT-AATAATATAATATTAAAGATATATAATAAAATAGT
* ** * *
10616 AAAATATATATATACGTAATATAA-ATTTAAA-ATATA-CCTAATATATT
1 AAAATATATATATA-ATAATATAATA-TTAAAGATATATAATAAAATAGT
* *
10663 AAAAGA-ATATAT-ATAATATAATATT-AAGAAATATAATAA
1 AAAATATATATATAATAATATAATATTAAAGATATATAATAA
10702 TAACAAAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
43 2 0.03
44 14 0.20
45 4 0.06
46 6 0.08
47 12 0.17
48 7 0.10
49 26 0.37
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (48 bp):
AAAATATATATATAATAATATAATATTAAAGATATATAATAAAATAGT
Found at i:10695 original size:24 final size:23
Alignment explanation
Indices: 10576--10703 Score: 79
Period size: 22 Copynumber: 5.5 Consensus size: 23
10566 AAAAATATAT
*
10576 ATATAAATAATATAATATT--AA
1 ATATATATAATATAATATTAAAA
* * *
10597 AGATATATAATAAAATAGTAAAATA
1 ATATATATAATATAATA-TTAAA-A
*
10622 TATATATACGTAATATAA-ATTTAAA
1 -ATATATA--TAATATAATATTAAAA
** *
10647 ATATACCTAATAT-AT-TAAAAGA
1 ATATATATAATATAATATTAAA-A
10669 ATATATATAATATAATATTAAGAA
1 ATATATATAATATAATATTAA-AA
10693 ATATA-ATAATA
1 ATATATATAATA
10704 ACAAAAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
21 18 0.22
22 19 0.24
23 8 0.10
24 15 0.19
25 3 0.04
26 9 0.11
27 1 0.01
28 7 0.09
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATATATAATATAATATTAAAA
Found at i:11280 original size:29 final size:29
Alignment explanation
Indices: 11211--11333 Score: 205
Period size: 29 Copynumber: 4.3 Consensus size: 29
11201 GGTGGAGCAA
*
11211 TGGCTAGTGGAGTTGGTGGTGG-AAGGTG
1 TGGCTAGTGGAGTTGGTGGTGGAAAAGTG
*
11239 TGGCTAGTGGAGTTGGTGGTGGAAAAGAG
1 TGGCTAGTGGAGTTGGTGGTGGAAAAGTG
11268 TGGCTAGTGGAGTTGGTGGTGGAAAAGTG
1 TGGCTAGTGGAGTTGGTGGTGGAAAAGTG
11297 TGGCTAGTGGAGTTGGTGGTGGAAAAG-G
1 TGGCTAGTGGAGTTGGTGGTGGAAAAGTG
11325 TGGGCTAGT
1 T-GGCTAGT
11334 TGAGAAAAGT
Statistics
Matches: 90, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
28 24 0.27
29 66 0.73
ACGTcount: A:0.20, C:0.04, G:0.50, T:0.27
Consensus pattern (29 bp):
TGGCTAGTGGAGTTGGTGGTGGAAAAGTG
Done.