Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1341
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: 18223
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Found at i:3670 original size:8 final size:8
Alignment explanation
Indices: 3657--3731 Score: 57
Period size: 8 Copynumber: 9.1 Consensus size: 8
3647 TTAATAATAA
3657 ATTTATAT
1 ATTTATAT
3665 ATTTATAT
1 ATTTATAT
*
3673 ATTTATGT
1 ATTTATAT
*
3681 CATATATAT
1 -ATTTATAT
3690 -TTTATTAT
1 ATTTA-TAT
*
3698 ATTATAATCGT
1 ATT-T-AT-AT
3709 ATTT-TAT
1 ATTTATAT
3716 ATTT-TAT
1 ATTTATAT
3723 ATTTATAT
1 ATTTATAT
3731 A
1 A
3732 AATTTTAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
7 15 0.28
8 23 0.43
9 8 0.15
10 3 0.06
11 5 0.09
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (8 bp):
ATTTATAT
Found at i:3719 original size:43 final size:47
Alignment explanation
Indices: 3664--3751 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 47
3654 TAAATTTATA
* *
3664 TATTTATATA-TTTAT-GTCATATATATTTTATTATATT-ATAATCG
1 TATTTATATATTTTATAGTCATATAAATTTTAATATATTAATAATCG
* *
3708 TATTT-TATATTTTATATTTATATAAATTTTAATATATTAATAAT
1 TATTTATATATTTTATAGTCATATAAATTTTAATATATTAATAAT
3752 TAATATTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 4 0.11
44 10 0.27
45 18 0.49
46 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (47 bp):
TATTTATATATTTTATAGTCATATAAATTTTAATATATTAATAATCG
Found at i:5840 original size:29 final size:30
Alignment explanation
Indices: 5801--5886 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
5791 TAAATATGAC
5801 ATAAAAA-AATATAATATATTTAATAATT-
1 ATAAAAATAATATAATATATTTAATAATTA
* *
5829 ATAAAAATAATATAATACTAGTTAAATATTTAA
1 ATAAAAATAATATAATA-TA-TTTAATAATT-A
*
5862 ATATAAATAA-ATAATATATTTAATA
1 ATAAAAATAATATAATATATTTAATA
5887 TATGTATTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
28 7 0.14
29 9 0.18
30 8 0.16
31 10 0.20
32 6 0.12
33 9 0.18
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
ATAAAAATAATATAATATATTTAATAATTA
Found at i:6926 original size:17 final size:18
Alignment explanation
Indices: 6889--6927 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
6879 ATTAACATAA
6889 AATT-AATTTTTTTACTT
1 AATTCAATTTTTTTACTT
6906 -ATTCAATTTTTTTA-TT
1 AATTCAATTTTTTTACTT
6922 AATTCA
1 AATTCA
6928 CTAAATCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTCAATTTTTTTACTT
Found at i:7321 original size:19 final size:19
Alignment explanation
Indices: 7291--7332 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
7281 ATTTTTATAT
7291 ATTTTATAATTAA-AAATA
1 ATTTTATAATTAATAAATA
*
7309 ATTTTATTAATTAATTAATA
1 ATTTTA-TAATTAATAAATA
7329 ATTT
1 ATTT
7333 AAACTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
20 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTATAATTAATAAATA
Found at i:7478 original size:2 final size:2
Alignment explanation
Indices: 7471--7496 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7461 AAAGACTGTT
7471 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
7497 CTATTCGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8688 original size:3 final size:3
Alignment explanation
Indices: 8680--8717 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
8670 GATGGTATAA
8680 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
8718 GCAATCATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9055 original size:32 final size:33
Alignment explanation
Indices: 9019--9083 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
9009 ACATATGATA
* *
9019 AATATTTTAAAATTTATA-AAATATAAATTATT
1 AATATATTAAAATTTATATAAATATAAAATATT
*
9051 AATATATTAAAATTTATATAAATTTAAAATATT
1 AATATATTAAAATTTATATAAATATAAAATATT
9084 TTTAATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
AATATATTAAAATTTATATAAATATAAAATATT
Found at i:9077 original size:17 final size:17
Alignment explanation
Indices: 9024--9080 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
9014 TGATAAATAT
9024 TTTAAAATTTATA-AAA
1 TTTAAAATTTATATAAA
*
9040 TAT-AAA-TTAT-TAATA
1 TTTAAAATTTATATAA-A
9055 TATTAAAATTTATATAAA
1 T-TTAAAATTTATATAAA
9073 TTTAAAAT
1 TTTAAAAT
9081 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
14 6 0.18
15 5 0.15
16 3 0.09
17 10 0.30
18 6 0.18
19 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAATTTATATAAA
Found at i:9529 original size:19 final size:19
Alignment explanation
Indices: 9484--9534 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
9474 ATTTTTATAA
* *
9484 ATTATATTTAAATATGTTAT
1 ATTATATTT-ATTATATTAT
9504 ATT-TATTTATTATATTAT
1 ATTATATTTATTATATTAT
*
9522 TTTATATTTATTA
1 ATTATATTTATTA
9535 AAAATCTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.37
19 14 0.52
20 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTATATTTATTATATTAT
Found at i:10456 original size:2 final size:2
Alignment explanation
Indices: 10449--10476 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10439 ATAAACACCT
10449 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
10477 CACATACTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11432 original size:17 final size:17
Alignment explanation
Indices: 11412--11459 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
11402 TTAAAAAATA
11412 ATTTAATTTAAATTATT
1 ATTTAATTTAAATTATT
** *
11429 ATTTAATAAAAAAT-TT
1 ATTTAATTTAAATTATT
*
11445 ATTTAAATTAAATTA
1 ATTTAATTTAAATTA
11460 AAATATATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTTAAATTATT
Found at i:11464 original size:28 final size:30
Alignment explanation
Indices: 11406--11461 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
11396 TTTTTTTTAA
* *
11406 AAAATAATTTAATTTAAATTATTATTTAAT
1 AAAATAATTTAATTTAAATTATAATTAAAT
11436 AAAA-AATTT-ATTTAAATTA-AATTAAA
1 AAAATAATTTAATTTAAATTATAATTAAA
11462 ATATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 10 0.42
29 5 0.21
30 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AAAATAATTTAATTTAAATTATAATTAAAT
Found at i:11728 original size:17 final size:18
Alignment explanation
Indices: 11697--11730 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
11687 ATATAAAAAA
11697 TATTTATTAAAATTTAAT
1 TATTTATTAAAATTTAAT
11715 TATTTATT-AAATTTAA
1 TATTTATTAAAATTTAA
11731 AAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTATTAAAATTTAAT
Found at i:12225 original size:13 final size:13
Alignment explanation
Indices: 12207--12255 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
12197 GGCTTGATAA
12207 ATTATATTTTTAT
1 ATTATATTTTTAT
*
12220 ATTATATTTATAT
1 ATTATATTTTTAT
*
12233 ATT-TATTAGTTAT
1 ATTATATT-TTTAT
12246 AATTATATTT
1 -ATTATATTT
12256 AATTTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 4 0.14
13 18 0.62
14 3 0.10
15 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
ATTATATTTTTAT
Found at i:12235 original size:21 final size:21
Alignment explanation
Indices: 12209--12253 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12199 CTTGATAAAT
*
12209 TATATTT-TTATATTATATTTA
1 TATATTTATTA-ATTATAATTA
*
12230 TATATTTATTAGTTATAATTA
1 TATATTTATTAATTATAATTA
12251 TAT
1 TAT
12254 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TATATTTATTAATTATAATTA
Found at i:12344 original size:17 final size:18
Alignment explanation
Indices: 12324--12364 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
12314 AAAATATTTA
12324 TATATTTA-TGTTAAATT
1 TATATTTATTGTTAAATT
* *
12341 TATATTAATTGTTATATT
1 TATATTTATTGTTAAATT
12359 T-TATTT
1 TATATTT
12365 TATTTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TATATTTATTGTTAAATT
Found at i:12379 original size:16 final size:16
Alignment explanation
Indices: 12355--12389 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12345 TTAATTGTTA
*
12355 TATTTTATTTTATTTT
1 TATTATATTTTATTTT
12371 TATTATATTTTATTTT
1 TATTATATTTTATTTT
12387 TAT
1 TAT
12390 ACTGTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTATATTTTATTTT
Done.