Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2755
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: 48735
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Found at i:1514 original size:14 final size:14
Alignment explanation
Indices: 1495--1527 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1485 CTTATTATCT
*
1495 TATTATTTAATTTA
1 TATTATCTAATTTA
1509 TATTATCTAATTTA
1 TATTATCTAATTTA
1523 TATTA
1 TATTA
1528 GAATATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATCTAATTTA
Found at i:1570 original size:24 final size:20
Alignment explanation
Indices: 1519--1558 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1509 TATTATCTAA
1519 TTTATATTAGAATATTCATT
1 TTTATATTAGAATATTCATT
1539 TTTATATTAGAATATTCATT
1 TTTATATTAGAATATTCATT
1559 CTATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTATATTAGAATATTCATT
Found at i:1595 original size:25 final size:25
Alignment explanation
Indices: 1587--1680 Score: 58
Period size: 23 Copynumber: 3.9 Consensus size: 25
1577 TTCTATTCTA
*
1587 TATTCTATTATAT-TAATA-TATTC
1 TATTCTATTATATATTATATTATTC
*
1610 TATTCTATTA-AT-TCTAT-TAATTC
1 TATTCTATTATATAT-TATATTATTC
* *
1633 TATTATATTAATATATTCTATTCTATT-
1 TATTCTATT-ATATATTATA-T-TATTC
*
1660 AATTCTATTATATA-TATATTA
1 TATTCTATTATATATTATATTA
1681 ATATATATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
22 3 0.05
23 26 0.47
24 2 0.04
25 7 0.13
26 6 0.11
27 8 0.15
28 3 0.05
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTCTATTATATATTATATTATTC
Found at i:1597 original size:32 final size:32
Alignment explanation
Indices: 1551--1679 Score: 104
Period size: 32 Copynumber: 3.8 Consensus size: 32
1541 TATATTAGAA
* **
1551 TATTCATTCTATTATATATTCTATTATTCTATTC
1 TATTAATTCTATTATAT-TAATA-TATTCTATTC
1585 TA-T-ATTCTATTATATTAATATATTCTATTCTATTAATTC
1 TATTAATTCTATTATATT-A-ATA---TATTCTA-T---TC
1624 TATTAATTCTATTATATTAATATATTCTATTC
1 TATTAATTCTATTATATTAATATATTCTATTC
1656 TATTAATTCTATTATA-T-ATATATT
1 TATTAATTCTATTATATTAATATATT
1680 AATATATATA
Statistics
Matches: 82, Mismatches: 3, Indels: 24
0.75 0.03 0.22
Matches are distributed among these distances:
30 7 0.09
31 2 0.02
32 30 0.37
33 3 0.04
34 2 0.02
35 8 0.10
36 8 0.10
39 7 0.09
40 2 0.02
41 13 0.16
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTAATTCTATTATATTAATATATTCTATTC
Found at i:1617 original size:23 final size:23
Alignment explanation
Indices: 1587--1660 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
1577 TTCTATTCTA
1587 TATTCTATTATATTAATATATTC
1 TATTCTATTATATTAATATATTC
*
1610 TATTCTATTA-A-T--TCTATT-
1 TATTCTATTATATTAATATATTC
*
1628 AATTCTATTATATTAATATATTC
1 TATTCTATTATATTAATATATTC
1651 TATTCTATTA
1 TATTCTATTA
1661 ATTCTATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.21
19 6 0.14
20 1 0.02
21 1 0.02
22 6 0.14
23 19 0.45
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTCTATTATATTAATATATTC
Found at i:1625 original size:9 final size:9
Alignment explanation
Indices: 1611--1669 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
1601 AATATATTCT
1611 ATTCTATTA
1 ATTCTATTA
1620 ATTCTATTA
1 ATTCTATTA
1629 ATTCTATT-
1 ATTCTATTA
1637 A---TATTA
1 ATTCTATTA
* *
1643 A-TATATTCT
1 ATTCTATT-A
1652 ATTCTATTA
1 ATTCTATTA
1661 ATTCTATTA
1 ATTCTATTA
1670 TATATATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
5 4 0.10
6 1 0.02
8 5 0.12
9 27 0.64
10 5 0.12
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTCTATTA
Found at i:1640 original size:41 final size:41
Alignment explanation
Indices: 1567--1696 Score: 178
Period size: 41 Copynumber: 3.2 Consensus size: 41
1557 TTCTATTATA
1567 TATTCTATT-ATTCTATTCTATATTCTATTATATTAATATATTC
1 TATTCTATTAATTCTA-T-TA-ATTCTATTATATTAATATATTC
1610 TATTCTATTAATTCTATTAATTCTATTATATTAATATATTC
1 TATTCTATTAATTCTATTAATTCTATTATATTAATATATTC
* *
1651 TATTCTATTAATTCTATT-A-TATA-TATATTAATATATATA
1 TATTCTATTAATTCTATTAATTCTATTATATTAATATAT-TC
1690 TATTCTA
1 TATTCTA
1697 ATTTAACTAA
Statistics
Matches: 83, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
38 13 0.16
39 11 0.13
40 1 0.01
41 40 0.48
42 2 0.02
43 10 0.12
44 6 0.07
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (41 bp):
TATTCTATTAATTCTATTAATTCTATTATATTAATATATTC
Found at i:6297 original size:14 final size:14
Alignment explanation
Indices: 6261--6310 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
6251 ACTCGCTTAG
6261 ATATACTTAGTATTTA
1 ATATACTTAGTA--TA
6277 TATATACTTAGTATA
1 -ATATACTTAGTATA
* *
6292 ATATACTAATTATA
1 ATATACTTAGTATA
6306 ATATA
1 ATATA
6311 ATCATTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 17 0.55
15 2 0.06
17 12 0.39
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (14 bp):
ATATACTTAGTATA
Found at i:10911 original size:11 final size:11
Alignment explanation
Indices: 10897--10933 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
10887 AGGATAATAT
10897 AATAAGTATAA
1 AATAAGTATAA
10908 AATAAGTAT-A
1 AATAAGTATAA
10918 AATAAGTATAA
1 AATAAGTATAA
*
10929 TATAA
1 AATAA
10934 TAAGGAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (11 bp):
AATAAGTATAA
Found at i:10921 original size:21 final size:19
Alignment explanation
Indices: 10869--10935 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
10859 AGATTTACTT
* *
10869 ATAATAGAATAAGTAATAAGG
1 ATAATATAATAAGT-ATAA-A
10890 ATAATATAATAAGTATAAA
1 ATAATATAATAAGTATAAA
*
10909 ATAAGTATAAATAAGTATAAT
1 ATAA-TAT-AATAAGTATAAA
10930 ATAATA
1 ATAATA
10936 AGGAATGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.10
20 9 0.22
21 28 0.68
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (19 bp):
ATAATATAATAAGTATAAA
Found at i:15483 original size:21 final size:21
Alignment explanation
Indices: 15443--15481 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
15433 AAATCATGGA
15443 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
15464 TAAATCCAAGCGA-TCTTT
1 TAAATCCAAGCGACTCTTT
15482 TCGTAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:15847 original size:9 final size:8
Alignment explanation
Indices: 15832--15874 Score: 54
Period size: 7 Copynumber: 5.4 Consensus size: 8
15822 GTGTCGTAAG
15832 AAAGAAAT
1 AAAGAAAT
15840 ATAAGAAA-
1 A-AAGAAAT
15848 AAAGAAAT
1 AAAGAAAT
15856 ATAAGAAA-
1 A-AAGAAAT
15864 AAAGAAAT
1 AAAGAAAT
15872 AAA
1 AAA
15875 TAAAAGAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 12 0.39
8 7 0.23
9 12 0.39
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAGAAAT
Found at i:15853 original size:16 final size:16
Alignment explanation
Indices: 15832--15872 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
15822 GTGTCGTAAG
15832 AAAGAAATATAAGAAA
1 AAAGAAATATAAGAAA
15848 AAAGAAATATAAGAAA
1 AAAGAAATATAAGAAA
15864 AAAGAAATA
1 AAAGAAATA
15873 AATAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAGAAATATAAGAAA
Found at i:15854 original size:20 final size:19
Alignment explanation
Indices: 15829--15882 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 19
15819 GTCGTGTCGT
15829 AAGAAAGAAATATAAG--A
1 AAGAAAGAAATATAAGAAA
15846 AA-AAAGAAATATAAGAAAA
1 AAGAAAGAAATATAAG-AAA
* *
15865 AAGAAATAAATAAAAGAA
1 AAGAAAGAAATATAAGAA
15883 TCGAATACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 13 0.42
17 2 0.06
19 5 0.16
20 11 0.35
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (19 bp):
AAGAAAGAAATATAAGAAA
Found at i:19275 original size:22 final size:22
Alignment explanation
Indices: 19244--19288 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
19234 TCTTATTTAT
*
19244 ATTTATAATTTTTAAATAAAAA
1 ATTTAGAATTTTTAAATAAAAA
19266 ATTTAGAATTTTTAAATAAAAA
1 ATTTAGAATTTTTAAATAAAAA
19288 A
1 A
19289 AAAATTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTTAGAATTTTTAAATAAAAA
Found at i:30527 original size:19 final size:19
Alignment explanation
Indices: 30503--30553 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 19
30493 ATTTAACCTT
30503 ATAGAATTTCCTTATAGAA
1 ATAGAATTTCCTTATAGAA
30522 ATAGAA-----TT-TAGAA
1 ATAGAATTTCCTTATAGAA
30535 ATAGAATTTCCTTATAGAA
1 ATAGAATTTCCTTATAGAA
30554 TTTAGAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
18 2 0.08
19 11 0.42
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (19 bp):
ATAGAATTTCCTTATAGAA
Found at i:32227 original size:14 final size:14
Alignment explanation
Indices: 32178--32230 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
32168 TTTTTTTTTT
32178 TAATATTTCATTTTAA
1 TAATATTT-A-TTTAA
* *
32194 TAATAATAATTTAA
1 TAATATTTATTTAA
32208 TAATATTTATTTAA
1 TAATATTTATTTAA
32222 TAATATTTA
1 TAATATTTA
32231 ATATAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 26 0.79
15 1 0.03
16 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTTATTTAA
Found at i:32860 original size:14 final size:14
Alignment explanation
Indices: 32843--32873 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
32833 GATGGATATA
32843 TATCGTATAATTCT
1 TATCGTATAATTCT
32857 TATCGTATAATTCT
1 TATCGTATAATTCT
32871 TAT
1 TAT
32874 ATATATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:37114 original size:20 final size:21
Alignment explanation
Indices: 37048--37116 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
37038 TCACTTCGTT
37048 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
37069 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
37090 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
37111 -CTTTTT
1 TCTTTTT
37117 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:39515 original size:18 final size:18
Alignment explanation
Indices: 39482--39571 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
39472 AAGGTTTTCT
39482 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
39497 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
39515 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
* * *
39533 TATTGATGCTAGTGAAGC
1 TATTGATGATAGTGACGA
39551 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
39569 TAT
1 TAT
39572 CGATCGTGAC
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.17
16 1 0.02
18 54 0.82
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:40306 original size:130 final size:130
Alignment explanation
Indices: 40073--40330 Score: 516
Period size: 130 Copynumber: 2.0 Consensus size: 130
40063 CGATTAGTAT
40073 TACACAGAAGAAATCAATTATAGACACTAATACAATTAGATCTGCTCTTCATAGACAAACTTGGG
1 TACACAGAAGAAATCAATTATAGACACTAATACAATTAGATCTGCTCTTCATAGACAAACTTGGG
40138 ATTTGCGATCCCAGGTAAGATCGGTTCAGGATCATGGGATCCTTTTCTATCAGATAGGAAGGGGA
66 ATTTGCGATCCCAGGTAAGATCGGTTCAGGATCATGGGATCCTTTTCTATCAGATAGGAAGGGGA
40203 TACACAGAAGAAATCAATTATAGACACTAATACAATTAGATCTGCTCTTCATAGACAAACTTGGG
1 TACACAGAAGAAATCAATTATAGACACTAATACAATTAGATCTGCTCTTCATAGACAAACTTGGG
40268 ATTTGCGATCCCAGGTAAGATCGGTTCAGGATCATGGGATCCTTTTCTATCAGATAGGAAGGG
66 ATTTGCGATCCCAGGTAAGATCGGTTCAGGATCATGGGATCCTTTTCTATCAGATAGGAAGGG
40331 CTGTTGTACA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (130 bp):
TACACAGAAGAAATCAATTATAGACACTAATACAATTAGATCTGCTCTTCATAGACAAACTTGGG
ATTTGCGATCCCAGGTAAGATCGGTTCAGGATCATGGGATCCTTTTCTATCAGATAGGAAGGGGA
Found at i:42696 original size:22 final size:22
Alignment explanation
Indices: 42667--42712 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
42657 GAGGATGTCT
42667 TATATATATTAAGATTATATTAAA
1 TATATATA-T-AGATTATATTAAA
*
42691 TATATATATAGATTCTATTAAA
1 TATATATATAGATTATATTAAA
42713 AAGATGGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 1 0.05
24 8 0.38
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATATATAGATTATATTAAA
Found at i:47578 original size:17 final size:18
Alignment explanation
Indices: 47554--47599 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
47544 GCCCGCCCTT
47554 CCACCCCCCCCTCC-C-C
1 CCACCCCCCCCTCCACAC
47570 CCGACCCCCCCC-CCACAC
1 CC-ACCCCCCCCTCCACAC
47588 CCACCCCCCCCT
1 CCACCCCCCCCT
47600 GGATACCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.15
17 19 0.73
18 3 0.12
ACGTcount: A:0.11, C:0.83, G:0.02, T:0.04
Consensus pattern (18 bp):
CCACCCCCCCCTCCACAC
Found at i:47765 original size:1 final size:1
Alignment explanation
Indices: 47759--47830 Score: 108
Period size: 1 Copynumber: 72.0 Consensus size: 1
47749 CGCTCCACCT
** * *
47759 CCCCCCCCCCCCTACCCCCCCCCCCCACCCCCCCCCCCCGCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
47824 CCCCCCC
1 CCCCCCC
47831 ACCCGCTCGC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.03, C:0.94, G:0.01, T:0.01
Consensus pattern (1 bp):
C
Done.