Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1762
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: 27525
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:6796 original size:48 final size:48
Alignment explanation
Indices: 6718--6814 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
6708 TCTTCAAGTT
* *
6718 GATTGATTTACCTGATTATTTACAACCCGTATTAACTTTCGCTTTGTC
1 GATTGATTTACCTGATTATTCACAAACCGTATTAACTTTCGCTTTGTC
6766 GATTGATTTACCTGATTATTCACAAACCGTATTAACTTTCGCTTTGTC
1 GATTGATTTACCTGATTATTCACAAACCGTATTAACTTTCGCTTTGTC
6814 G
1 G
6815 GCAAATCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (48 bp):
GATTGATTTACCTGATTATTCACAAACCGTATTAACTTTCGCTTTGTC
Found at i:15540 original size:2 final size:2
Alignment explanation
Indices: 15533--15573 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
15523 CAATACGTAC
*
15533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15574 AATACCTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:17471 original size:2 final size:2
Alignment explanation
Indices: 17464--17488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17454 GAATTTCCCC
17464 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17489 ACACATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18358 original size:21 final size:20
Alignment explanation
Indices: 18334--18378 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
18324 AAAATATTTT
*
18334 TTTAAATTATAAAAATAAAAA
1 TTTAAATGATAAAAA-AAAAA
* *
18355 TTTAAATGATTAAAAAATAA
1 TTTAAATGATAAAAAAAAAA
18375 TTTA
1 TTTA
18379 CTTGAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAAATGATAAAAAAAAAA
Found at i:19185 original size:10 final size:11
Alignment explanation
Indices: 19160--19204 Score: 58
Period size: 10 Copynumber: 4.1 Consensus size: 11
19150 AATTTTATTT
19160 ATTTAAATTATA
1 ATTTAAA-TATA
19172 ATTTAAAT-TA
1 ATTTAAATATA
19182 ATTT-AATATA
1 ATTTAAATATA
19192 ATTTAAATTATA
1 ATTTAAA-TATA
19204 A
1 A
19205 AATATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.10
10 12 0.40
11 3 0.10
12 12 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTAAATATA
Found at i:19193 original size:41 final size:43
Alignment explanation
Indices: 19083--19195 Score: 112
Period size: 41 Copynumber: 2.7 Consensus size: 43
19073 TAAACTCTAT
* * *
19083 TTTATTATTTAAAATAATATTAAAAT-ATATTTTTATATTAATA
1 TTTATAATTTAAATTAAT-TTAAAATAATTTTTTTATATTAATA
*
19126 TTTATAA-TTAAATTTAA-ATAAAATAATTTTATTTAT-TTAA-A
1 TTTATAATTTAAA-TTAATTTAAAATAATTTT-TTTATATTAATA
*
19167 -TTATAATTTAAATTAATTTAATATAATTT
1 TTTATAATTTAAATTAATTTAAAATAATTT
19196 AAATTATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
40 10 0.17
41 22 0.37
42 13 0.22
43 14 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (43 bp):
TTTATAATTTAAATTAATTTAAAATAATTTTTTTATATTAATA
Found at i:19263 original size:16 final size:16
Alignment explanation
Indices: 19242--19273 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19232 AATGGCTGCC
*
19242 TGGCTCATACAGTCTT
1 TGGCTCATAAAGTCTT
19258 TGGCTCATAAAGTCTT
1 TGGCTCATAAAGTCTT
19274 GGTATGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (16 bp):
TGGCTCATAAAGTCTT
Found at i:19632 original size:5 final size:5
Alignment explanation
Indices: 19613--19740 Score: 52
Period size: 5 Copynumber: 25.2 Consensus size: 5
19603 AAAATAATTA
* * *
19613 AATAT AATAT AATAT AATAT ATTAT -TTA- AACT-T TATAT AATAT AATTAAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AA-T-AT
* * * * * *
19663 AATAT ATTAA AAAAT -ATAT AAATAT AAAAT ATTTAA AATAT AATTAT
1 AATAT AATAT AATAT AATAT -AATAT AATAT A-ATAT AATAT AA-TAT
*
19710 AATAT -A-AT AATAT AATAAA AATAT AAATAT A
1 AATAT AATAT AATAT AAT-AT AATAT -AATAT A
19741 TCTCGAATTC
Statistics
Matches: 91, Mismatches: 18, Indels: 28
0.66 0.13 0.20
Matches are distributed among these distances:
3 2 0.02
4 9 0.10
5 54 0.59
6 22 0.24
7 4 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:19701 original size:16 final size:15
Alignment explanation
Indices: 19585--19741 Score: 69
Period size: 15 Copynumber: 10.3 Consensus size: 15
19575 TAAATATGAT
19585 TATATAAATATAAAA
1 TATATAAATATAAAA
* *
19600 TA-AAAAATAATTAAA
1 TATATAAAT-ATAAAA
19615 TATAATATAATAT--AA
1 TAT-ATA-AATATAAAA
* * *
19630 TATAT-TATTTAAAC
1 TATATAAATATAAAA
*
19644 TTTATATAATATAATTAA
1 TATATA-AATATAA--AA
* *
19662 TA-ATATATTAAAAAA
1 TATATA-AATATAAAA
19677 TATATAAATATAAAA
1 TATATAAATATAAAA
* *
19692 TATTTAAA-ATATAA
1 TATATAAATATAAAA
19706 T-TAT-AATATAATAA
1 TATATAAATATAA-AA
*
19720 TATAATAAAAATATAAA
1 TAT-ATAAATATA-AAA
19737 TATAT
1 TATAT
19742 CTCGAATTCA
Statistics
Matches: 105, Mismatches: 20, Indels: 33
0.66 0.13 0.21
Matches are distributed among these distances:
12 5 0.05
13 5 0.05
14 21 0.20
15 33 0.31
16 12 0.11
17 23 0.22
18 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (15 bp):
TATATAAATATAAAA
Found at i:19710 original size:22 final size:23
Alignment explanation
Indices: 19651--19711 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
19641 AACTTTATAT
*
19651 AATATAATTAATAATATATTAAAAA
1 AATATAATT-ATAAAATATT-AAAA
* *
19676 ATATATAAATATAAAATATT-TAA
1 A-ATATAATTATAAAATATTAAAA
19699 AATATAATTATAA
1 AATATAATTATAA
19712 TATAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 11 0.35
23 3 0.10
25 10 0.32
26 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATAATTATAAAATATTAAAA
Found at i:20153 original size:16 final size:15
Alignment explanation
Indices: 20128--20163 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
20118 TGTAATCAGT
20128 TTTA-TATATTTTTA
1 TTTATTATATTTTTA
20142 TATTATTATATTTTTA
1 T-TTATTATATTTTTA
20158 TTTATT
1 TTTATT
20164 TAAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 8 0.40
16 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTATATTTTTA
Found at i:20214 original size:27 final size:28
Alignment explanation
Indices: 20184--20259 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
20174 ATATATTAAA
20184 ATTTAAATAA-ATTAAAAATATTTAATT
1 ATTTAAATAATATTAAAAATATTTAATT
* *
20211 ATTTATATAATATAAAAAAT-TTTAATT
1 ATTTAAATAATATTAAAAATATTTAATT
20238 A-TTAAATATATATTGAAAAATA
1 ATTTAAATA-ATATT-AAAAATA
20260 ATATTTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 6 0.15
27 21 0.51
28 14 0.34
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (28 bp):
ATTTAAATAATATTAAAAATATTTAATT
Found at i:20348 original size:21 final size:20
Alignment explanation
Indices: 20318--20372 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
20308 CATACACAAT
20318 AAAT-ATAATTATATTATTA
1 AAATAATAATTATATTATTA
*
20337 AATTTAATAATTA-ATTTATTA
1 AA-ATAATAATTATA-TTATTA
*
20358 AAATATTAATTATAT
1 AAATAATAATTATAT
20373 AAAAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 16 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATAATTATATTATTA
Found at i:20380 original size:40 final size:40
Alignment explanation
Indices: 20318--20394 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
20308 CATACACAAT
**
20318 AAATATAATTATATTATTAAATT-TAATAATTAATTTATTA
1 AAATATAATTATATTAAAAAATTATAA-AATTAATTTATTA
20358 AAATATTAATTATA-TAAAAAATTATAAAATTAATTTA
1 AAATA-TAATTATATTAAAAAATTATAAAATTAATTTA
20395 ACTTACACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (40 bp):
AAATATAATTATATTAAAAAATTATAAAATTAATTTATTA
Found at i:20623 original size:2 final size:2
Alignment explanation
Indices: 20616--20644 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20606 ACCCTAAAGG
20616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20645 GAACAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22324 original size:2 final size:2
Alignment explanation
Indices: 22317--22348 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22307 CATGCATGAT
22317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22349 ATTCTACGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23430 original size:12 final size:11
Alignment explanation
Indices: 23409--23462 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
23399 TAATAAAAAA
23409 ATAA-TATATT
1 ATAATTATATT
23419 ATATATTATATT
1 ATA-ATTATATT
*
23431 ATAATTTTATT
1 ATAATTATATT
*
23442 -TAAAATATATT
1 AT-AATTATATT
23453 ATAATTATAT
1 ATAATTATAT
23463 AAATTTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 22 0.61
12 10 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATAATTATATT
Found at i:23499 original size:15 final size:15
Alignment explanation
Indices: 23458--23508 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
23448 ATATTATAAT
23458 TATA-TAAA-TTTAA
1 TATATTAAATTTTAA
*
23471 TATATTATTTATTTTAA
1 TATATTA--AATTTTAA
23488 TATATTAAATTTTAA
1 TATATTAAATTTTAA
*
23503 AATATT
1 TATATT
23509 TATATCTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.13
14 2 0.06
15 12 0.39
16 1 0.03
17 12 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTAAATTTTAA
Found at i:23510 original size:41 final size:41
Alignment explanation
Indices: 23436--23527 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 41
23426 ATATTATAAT
* *
23436 TTTATTTAAAATATATTATAATTATATAAATTTAATAT-ATTA
1 TTTATTT-TAATATATTATAATTATAAAAATTT-ATATCATTA
* *
23478 TTTATTTTAATATATTA-AATTTTAAAATATTTATATCTTTA
1 TTTATTTTAATATATTATAATTATAAAA-ATTTATATCATTA
23519 TATTATTTT
1 T-TTATTTT
23528 TTATTACGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
40 12 0.28
41 17 0.40
42 14 0.33
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (41 bp):
TTTATTTTAATATATTATAATTATAAAAATTTATATCATTA
Done.