Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold937
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: 14352
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:73 original size:24 final size:25
Alignment explanation
Indices: 14--83 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 25
4 CCCTTTGTGA
* *
14 TTTGTCAAAAATATGGTGGTTATTTTG
1 TTTGTC-AAAA-ATGGTGGCTATGTTG
41 TTTGT-AAAAATGGTGGCT-TGTTG
1 TTTGTCAAAAATGGTGGCTATGTTG
*
64 TTTGTCAAAATTGGTGGCTA
1 TTTGTCAAAAATGGTGGCTA
84 ATTTTTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 9 0.24
24 20 0.53
25 4 0.11
27 5 0.13
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (25 bp):
TTTGTCAAAAATGGTGGCTATGTTG
Found at i:1485 original size:23 final size:25
Alignment explanation
Indices: 1451--1496 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1441 AATAAAAATT
1451 AGCCATCAA-TTTTGACAAACAACA
1 AGCCATCAATTTTTGACAAACAACA
1475 AGCCA-CAATTTTTGACAAACAA
1 AGCCATCAATTTTTGACAAACAA
1497 AAAAATGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.22
Consensus pattern (25 bp):
AGCCATCAATTTTTGACAAACAACA
Found at i:1545 original size:27 final size:27
Alignment explanation
Indices: 1506--1583 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
1496 AAAAAATGAT
*
1506 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTGTTGACAAATACAAAGTAA
1533 CCACCATTGTTGACAAATACAAAGTAA
1 CCACCATTGTTGACAAATACAAAGTAA
*
1560 CCACCATTGTTGACAAACACAAAG
1 CCACCATTGTTGACAAATACAAAG
1584 GGTGGCTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.22
Consensus pattern (27 bp):
CCACCATTGTTGACAAATACAAAGTAA
Found at i:5626 original size:8 final size:8
Alignment explanation
Indices: 5613--5637 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5603 CTACTATTAT
5613 AAAATATA
1 AAAATATA
5621 AAAATATA
1 AAAATATA
5629 AAAATATA
1 AAAATATA
5637 A
1 A
5638 TATAAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:6401 original size:13 final size:14
Alignment explanation
Indices: 6383--6411 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6373 TATTTAAAAT
6383 ATTTT-ATATATAA
1 ATTTTAATATATAA
6396 ATTTTAATATATAA
1 ATTTTAATATATAA
6410 AT
1 AT
6412 AATTTATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTTAATATATAA
Found at i:6794 original size:24 final size:24
Alignment explanation
Indices: 6762--6840 Score: 97
Period size: 24 Copynumber: 3.2 Consensus size: 24
6752 ATTATATGAT
6762 AAATATGATATTAAAAATTAATTA
1 AAATATGATATTAAAAATTAATTA
* *
6786 AAATGTGATTTAATTAAAAAATAA-TA
1 AAATATGA--T-ATTAAAAATTAATTA
6812 TAAATATGATATTAAAAATTAATTA
1 -AAATATGATATTAAAAATTAATTA
6837 AAAT
1 AAAT
6841 GTGACTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 22 0.48
25 3 0.07
26 3 0.07
27 18 0.39
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (24 bp):
AAATATGATATTAAAAATTAATTA
Found at i:6810 original size:27 final size:26
Alignment explanation
Indices: 6771--6857 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 26
6761 TAAATATGAT
*
6771 ATTAAAAATTAATTAAAATGTGATTTA
1 ATTAAAAAATAATTAAAATGTGA-TTA
*
6798 ATTAAAAAATAA-TATAAATATGA-T-
1 ATTAAAAAATAATTA-AAATGTGATTA
*
6822 ATTAAAAATTAATTAAAATGTGACTTA
1 ATTAAAAAATAATTAAAATGTGA-TTA
6849 ATTAAAAAA
1 ATTAAAAAA
6858 ATATATAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
24 18 0.36
25 3 0.06
26 3 0.06
27 26 0.52
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (26 bp):
ATTAAAAAATAATTAAAATGTGATTA
Found at i:6822 original size:51 final size:51
Alignment explanation
Indices: 6755--6869 Score: 196
Period size: 51 Copynumber: 2.2 Consensus size: 51
6745 TTGTAAAATT
*
6755 ATATGATAAATATGATATTAAAAATTAATTAAAATGTGATTTAATT-AAAAA
1 ATAT-ATAAATATGATATTAAAAATTAATTAAAATGTGACTTAATTAAAAAA
6806 ATAATATAAATATGATATTAAAAATTAATTAAAATGTGACTTAATTAAAAAA
1 AT-ATATAAATATGATATTAAAAATTAATTAAAATGTGACTTAATTAAAAAA
6858 ATATATAAATAT
1 ATATATAAATAT
6870 ATAAATGTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
51 52 0.85
52 9 0.15
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.37
Consensus pattern (51 bp):
ATATATAAATATGATATTAAAAATTAATTAAAATGTGACTTAATTAAAAAA
Found at i:6867 original size:27 final size:26
Alignment explanation
Indices: 6786--6867 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
6776 AAATTAATTA
6786 AAATGTGATTTAATT-AAAAAATAATAT
1 AAATGTGA-TTAATTAAAAAAAT-ATAT
*
6813 AAATATGA-T-ATTAAAAATTAAT-TA-
1 AAATGTGATTAATTAAAAA--AATATAT
6837 AAATGTGACTTAATTAAAAAAATATAT
1 AAATGTGA-TTAATTAAAAAAATATAT
6864 AAAT
1 AAAT
6868 ATATAAATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
24 10 0.22
25 10 0.22
26 3 0.07
27 22 0.49
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.35
Consensus pattern (26 bp):
AAATGTGATTAATTAAAAAAATATAT
Found at i:6917 original size:32 final size:33
Alignment explanation
Indices: 6860--6935 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 33
6850 TTAAAAAAAT
*
6860 ATATAAATATATAAATGTATTAAAATTTATATA
1 ATATAAATATATAAATGTATCAAAATTTATATA
*
6893 ATATAAATA-ATTAATGTATCAAAATTTATATA
1 ATATAAATATATAAATGTATCAAAATTTATATA
*
6925 A-ATAGATATAT
1 ATATAAATATAT
6936 GAAACAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.15
32 24 0.62
33 9 0.23
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (33 bp):
ATATAAATATATAAATGTATCAAAATTTATATA
Found at i:7344 original size:31 final size:30
Alignment explanation
Indices: 7302--7373 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
7292 TTCTAAAAAC
* *
7302 TATCAAATTTAT-AAGTAATTTTGTTTAATAT
1 TATCAAATTTATGAA-TAATTATATTTAAT-T
*
7333 TATTAAATTTATGAATAATTATATTTAATT
1 TATCAAATTTATGAATAATTATATTTAATT
7363 TATCAAATTTA
1 TATCAAATTTA
7374 CGATTAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 11 0.31
31 23 0.64
32 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (30 bp):
TATCAAATTTATGAATAATTATATTTAATT
Found at i:7390 original size:31 final size:30
Alignment explanation
Indices: 7302--7394 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 30
7292 TTCTAAAAAC
* * *
7302 TATCAAATTTA-TAAGTAATTTTGTTTAATAT
1 TATCAAATTTACGAA-TAATTATATTTAAT-T
* *
7333 TATTAAATTTATGAATAATTATATTTAATT
1 TATCAAATTTACGAATAATTATATTTAATT
*
7363 TATCAAATTTACGATTAA-TATTAATTTAATT
1 TATCAAATTTACGAATAATTA-T-ATTTAATT
7394 T
1 T
7395 TTTTAGAAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
29 2 0.04
30 17 0.33
31 31 0.60
32 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (30 bp):
TATCAAATTTACGAATAATTATATTTAATT
Found at i:7414 original size:2 final size:2
Alignment explanation
Indices: 7409--7457 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
7399 AGAAACGTGT
7409 TA TA TA TA TA 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 TA TA TA TA TA
7451 TA TA TA T
1 TA TA TA T
7458 GCACTTCCAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9050 original size:15 final size:15
Alignment explanation
Indices: 9030--9059 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9020 TGATATAATT
*
9030 ATATAATATAAAAAA
1 ATATAAAATAAAAAA
9045 ATATAAAATAAAAAA
1 ATATAAAATAAAAAA
9060 TAATACGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATATAAAATAAAAAA
Found at i:9184 original size:13 final size:13
Alignment explanation
Indices: 9130--9195 Score: 57
Period size: 13 Copynumber: 5.0 Consensus size: 13
9120 GTATCAAATT
*
9130 TATATAAATAAAA
1 TATATAAATATAA
*
9143 TATA-AAATATTA
1 TATATAAATATAA
9155 T-TATAAAATATAAAA
1 TATAT-AAATAT--AA
9170 TATATAAATATAA
1 TATATAAATATAA
9183 TATA-AATATATAA
1 TATATAA-ATATAA
9196 ATAACCCAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 2 0.05
12 9 0.20
13 22 0.50
15 8 0.18
16 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATATAAATATAA
Found at i:9184 original size:20 final size:20
Alignment explanation
Indices: 9130--9199 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
9120 GTATCAAATT
9130 TATATAAATAAAATATAAAA
1 TATATAAATAAAATATAAAA
*
9150 TAT-TATTATAAAATATAAAA
1 TATATA-AATAAAATATAAAA
*
9170 TATATAAATATAATAT-AAA
1 TATATAAATAAAATATAAAA
9189 TATATAAATAA
1 TATATAAATAA
9200 CCCAATCTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
19 15 0.34
20 27 0.61
21 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATAAATAAAATATAAAA
Found at i:9628 original size:19 final size:20
Alignment explanation
Indices: 9585--9629 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
9575 CATATTAAAA
*
9585 ATATTATATATATAATTTAAT
1 ATATTATATATAT-ATTTAAC
*
9606 ATATTATATATAT-TTTCAC
1 ATATTATATATATATTTAAC
9625 ATATT
1 ATATT
9630 TATTTATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTATATATATATTTAAC
Found at i:9628 original size:21 final size:20
Alignment explanation
Indices: 9546--9618 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 20
9536 TATTAGATAT
**
9546 TATATT-TATAT-TATTTTT
1 TATATTATATATATATTTAA
* *
9564 TATGTTATA-ATCATATTAAA
1 TATATTATATAT-ATATTTAA
*
9584 AATATTATATATATAATTTAA
1 TATATTATATATAT-ATTTAA
9605 TATATTATATATAT
1 TATATTATATATAT
9619 TTTCACATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
18 7 0.17
19 2 0.05
20 13 0.31
21 20 0.48
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (20 bp):
TATATTATATATATATTTAA
Found at i:10719 original size:11 final size:11
Alignment explanation
Indices: 10703--10732 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
10693 ATAATTATTA
10703 TATATTATTTT
1 TATATTATTTT
10714 TATATTATTTT
1 TATATTATTTT
10725 TATATTAT
1 TATATTAT
10733 AATTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATATTATTTT
Found at i:10720 original size:21 final size:20
Alignment explanation
Indices: 10700--10799 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 20
10690 TTAATAATTA
*
10700 TTATATATTATTTTTATATTAT
1 TTATATATTATATTTATA-T-T
* *
10722 TTTTATATTATAATTATATT
1 TTATATATTATATTTATATT
* * *
10742 TAAAATATTATATGTATAATT
1 TTATATATTATATTTAT-ATT
* * *
10763 TAATATATTATGTATATATT
1 TTATATATTATATTTATATT
10783 TTAATATATT-TATTTAT
1 TT-ATATATTATATTTAT
10800 TAATGATTTT
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
20 22 0.35
21 25 0.40
22 15 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATATATTATATTTATATT
Found at i:11138 original size:32 final size:33
Alignment explanation
Indices: 11102--11173 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
11092 GAGTTATAAT
*
11102 TATATTTAA-AATATTATAT-ATATAAATTTTAA
1 TATATTTAATAAT-TTATATAACATAAATTTTAA
*
11134 TATA-TTAATAATTTGTATAACATAAATTTTAA
1 TATATTTAATAATTTATATAACATAAATTTTAA
*
11166 TATTTTTA
1 TATATTTA
11174 TATATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 9 0.26
32 22 0.65
33 3 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
TATATTTAATAATTTATATAACATAAATTTTAA
Found at i:11196 original size:21 final size:23
Alignment explanation
Indices: 11172--11222 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
11162 TTAATATTTT
11172 TATATATT-TTTATTATA-TATA
1 TATATATTATTTATTATATTATA
* *
11193 TATATGTTATTTTTTATATTATA
1 TATATATTATTTATTATATTATA
11216 TCATATA
1 T-ATATA
11223 ATCGTATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 7 0.29
22 8 0.33
23 5 0.21
24 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TATATATTATTTATTATATTATA
Done.