Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3125
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: 63237
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:717 original size:1 final size:1
Alignment explanation
Indices: 713--803 Score: 83
Period size: 1 Copynumber: 91.0 Consensus size: 1
703 TAATATTAAT
* * * * * * *
713 AAAAAAAAAAAAAAAAATAAAAAAAAAAATAACAAAAATAGAAAAAAAAAAAAAAAAAAAATAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ***
778 AGAAAAAAAAAATTTAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
804 TTTTCAAGGT
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.88, C:0.01, G:0.03, T:0.08
Consensus pattern (1 bp):
A
Found at i:789 original size:39 final size:39
Alignment explanation
Indices: 710--803 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 39
700 TTTTAATATT
710 AATAAAAAAAAAAAAAAAAATAAAAAAAAAAATAACAAA
1 AATAAAAAAAAAAAAAAAAATAAAAAAAAAAATAACAAA
*
749 AATAGAAAAAAAAAAAAAAAA-AAAATAAGAGAAA-AA-AAA
1 AATA-AAAAAAAAAAAAAAAATAAAA-AA-AAAAATAACAAA
**
788 AATTTAAAAAAAAAAA
1 AATAAAAAAAAAAAAA
804 TTTTCAAGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
38 11 0.22
39 14 0.29
40 20 0.41
41 4 0.08
ACGTcount: A:0.87, C:0.01, G:0.03, T:0.09
Consensus pattern (39 bp):
AATAAAAAAAAAAAAAAAAATAAAAAAAAAAATAACAAA
Found at i:796 original size:26 final size:23
Alignment explanation
Indices: 713--799 Score: 92
Period size: 24 Copynumber: 3.8 Consensus size: 23
703 TAATATTAAT
713 AAAAAAAAAA-AAAAAAAT---A
1 AAAAAAAAAATAAAAAAATAGAA
732 AAAAAAAAAATAACAAAAATAGAA
1 AAAAAAAAAATAA-AAAAATAGAA
*
756 AAAAAAAAAAAAAAAAAATAAGAGA
1 AAAAAAAAAATAAAAAAAT-AGA-A
*
781 AAAAAAAAATTTAAAAAAA
1 AAAAAAAAA-ATAAAAAAA
800 AAAATTTTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.18
20 2 0.04
21 6 0.11
23 6 0.11
24 16 0.28
25 10 0.18
26 7 0.12
ACGTcount: A:0.87, C:0.01, G:0.03, T:0.08
Consensus pattern (23 bp):
AAAAAAAAAATAAAAAAATAGAA
Found at i:805 original size:14 final size:14
Alignment explanation
Indices: 780--806 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
770 AAAATAAGAG
780 AAAAAAAAAATTTA
1 AAAAAAAAAATTTA
794 AAAAAAAAAATTT
1 AAAAAAAAAATTT
807 TCAAGGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAAAAAAATTTA
Found at i:9859 original size:27 final size:26
Alignment explanation
Indices: 9829--9914 Score: 77
Period size: 29 Copynumber: 3.1 Consensus size: 26
9819 GTGTTGGTGT
9829 TATTTTTTAGATTTTAAAATATTTATA
1 TATTTTTTA-ATTTTAAAATATTTATA
9856 TATTTTATTTAATATTTAATAA-ATTTATA
1 TA-TTT-TTTAAT-TTTAA-AATATTTATA
* *
9885 TAGTTTTTAATTTATTAAGAT-TTTATA
1 TATTTTTTAA-TT-TTAAAATATTTATA
9912 TAT
1 TAT
9915 AAGTATCTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
27 17 0.35
28 12 0.24
29 18 0.37
30 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (26 bp):
TATTTTTTAATTTTAAAATATTTATA
Found at i:9882 original size:20 final size:20
Alignment explanation
Indices: 9846--9883 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9836 TAGATTTTAA
*
9846 AATATTTATATATTTTATTT
1 AATATTTATATAATTTATTT
9866 AATATTTA-ATAAATTTAT
1 AATATTTATAT-AATTTAT
9884 ATAGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTTATATAATTTATTT
Found at i:10784 original size:14 final size:13
Alignment explanation
Indices: 10765--10795 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
10755 AGTTTGAAGT
10765 AAAAAAAATTATTA
1 AAAAAAAATT-TTA
10779 AAAAAAAATTTTA
1 AAAAAAAATTTTA
10792 AAAA
1 AAAA
10796 TTTTATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAAAATTTTA
Found at i:11451 original size:10 final size:11
Alignment explanation
Indices: 11435--11471 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
11425 AAAGAGTTTT
11435 TATTTTTTAAA
1 TATTTTTTAAA
11446 -A-TTTTTAAA
1 TATTTTTTAAA
11455 TATATTTTTAAA
1 TAT-TTTTTAAA
11467 TATTT
1 TATTT
11472 ATGTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.35
10 2 0.09
11 2 0.09
12 11 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTTTAAA
Found at i:17319 original size:11 final size:11
Alignment explanation
Indices: 17303--17327 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17293 TAAATGCGAA
17303 AAAAAAAAAAG
1 AAAAAAAAAAG
17314 AAAAAAAAAAG
1 AAAAAAAAAAG
17325 AAA
1 AAA
17328 GGAAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:26823 original size:201 final size:201
Alignment explanation
Indices: 26478--26879 Score: 795
Period size: 201 Copynumber: 2.0 Consensus size: 201
26468 ATTCAGGCAC
26478 ATCTGCAGGTTTTAAATCTCTCAAAGATATTTCATTTTGTTTTCTCAAATACTTAACAACGTAAT
1 ATCTGCAGGTTTTAAATCTCTCAAAGATATTTCATTTTGTTTTCTCAAATACTTAACAACGTAAT
26543 TGCAAGTTGCAACATTTTATCGAACTTGAATTTTTTTTCATTTTTTTTTCTTCTCGGATTTCTGG
66 TGCAAGTTGCAACATTTTATCGAACTTGAATTTTTTTTCATTTTTTTTTCTTCTCGGATTTCTGG
26608 TTAGAGAGTCAGAAGTAGAACTTAATTCCTACAGTTTAATGATATCTAACATTCAATCTACCCAA
131 TTAGAGAGTCAGAAGTAGAACTTAATTCCTACAGTTTAATGATATCTAACATTCAATCTACCCAA
26673 TAGTGA
196 TAGTGA
26679 ATCTGCAGGTTTTAAATCTCTCAAAGATATTTCATTTTGTTTTCTCAAATACTTAACAACGTAAT
1 ATCTGCAGGTTTTAAATCTCTCAAAGATATTTCATTTTGTTTTCTCAAATACTTAACAACGTAAT
26744 TGCAAGTTGCAACATTTTATCGAACTTGAATTTTTTTTCATTTTTTTTTCTTCTCGGATTTCTGG
66 TGCAAGTTGCAACATTTTATCGAACTTGAATTTTTTTTCATTTTTTTTTCTTCTCGGATTTCTGG
*
26809 TTAGAGAGTCAGAAGTAGAACTTAATTCCTACAGTTTAATGATATCTAACATTCAATCTATCCAA
131 TTAGAGAGTCAGAAGTAGAACTTAATTCCTACAGTTTAATGATATCTAACATTCAATCTACCCAA
26874 TAGTGA
196 TAGTGA
26880 GTCTACATTT
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 200 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (201 bp):
ATCTGCAGGTTTTAAATCTCTCAAAGATATTTCATTTTGTTTTCTCAAATACTTAACAACGTAAT
TGCAAGTTGCAACATTTTATCGAACTTGAATTTTTTTTCATTTTTTTTTCTTCTCGGATTTCTGG
TTAGAGAGTCAGAAGTAGAACTTAATTCCTACAGTTTAATGATATCTAACATTCAATCTACCCAA
TAGTGA
Found at i:38852 original size:30 final size:30
Alignment explanation
Indices: 38810--38866 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
38800 TTAATAGTTT
38810 TTTATAAAAATTAAATCAAATCAAAATTTAA
1 TTTATAAAAATTAAAT-AAATCAAAATTTAA
* *
38841 TTTAT-AAAATTACATAAATTAAAATT
1 TTTATAAAAATTAAATAAATCAAAATT
38867 CATGCATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.42
30 9 0.38
31 5 0.21
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (30 bp):
TTTATAAAAATTAAATAAATCAAAATTTAA
Found at i:39904 original size:31 final size:31
Alignment explanation
Indices: 39858--39942 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
39848 TTTAAATGTC
*
39858 TATAATTGAAA-TAAAATTAAAATTTTATGTA
1 TATAATT-AAACTAAAATTAAAATTTTATATA
* * * *
39889 TATATTTAAACTAAAATCAAAGTATTATATA
1 TATAATTAAACTAAAATTAAAATTTTATATA
*
39920 TATAATTACAC-AAAATTAAAATT
1 TATAATTAAACTAAAATTAAAATT
39943 CATATATCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
30 12 0.28
31 31 0.72
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (31 bp):
TATAATTAAACTAAAATTAAAATTTTATATA
Found at i:40859 original size:18 final size:17
Alignment explanation
Indices: 40813--40864 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
40803 ATTATTTTAA
40813 ATTTAAAATCATTAAAATT
1 ATTTAAAA--ATTAAAATT
40832 ATTTAAAAATATAAAATT
1 ATTTAAAAAT-TAAAATT
**
40850 ATTTTTAAATTAAAA
1 ATTTAAAAATTAAAA
40865 AATAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 7 0.23
18 15 0.50
19 8 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAAAATTAAAATT
Found at i:41863 original size:3 final size:3
Alignment explanation
Indices: 41855--41909 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
41845 TGTTTATTTA
*
41855 TAT TAT TAT TACT GTAT TAT TAT TAG T-T TAT TAT TA- TAT TAT ATAT
1 TAT TAT TAT TA-T -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
41901 TAT TAT TAT
1 TAT TAT TAT
41910 ACTTACTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 3 0.07
3 35 0.78
4 5 0.11
5 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:41874 original size:14 final size:14
Alignment explanation
Indices: 41855--41891 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
41845 TGTTTATTTA
41855 TATTATTATTACTG
1 TATTATTATTACTG
* *
41869 TATTATTATTAGTT
1 TATTATTATTACTG
41883 TATTATTAT
1 TATTATTAT
41892 ATTATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (14 bp):
TATTATTATTACTG
Found at i:41877 original size:22 final size:22
Alignment explanation
Indices: 41827--41908 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
41817 TTTAGTTTTT
* *
41827 TTATTATATTGTTAATACTGT-
1 TTATTATATTATTATTACTGTA
41848 TTATTTATATTATTATTACTGTA
1 TTA-TTATATTATTATTACTGTA
* * *
41871 TTATTATTAGT-TTATTATTATA
1 TTATTA-TATTATTATTACTGTA
41893 TTA-TATATTATTATTA
1 TTATTATATTATTATTA
41909 TACTTACTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 3 0.06
21 11 0.22
22 31 0.61
23 6 0.12
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (22 bp):
TTATTATATTATTATTACTGTA
Found at i:41894 original size:8 final size:8
Alignment explanation
Indices: 41852--41921 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
41842 TACTGTTTAT
41852 TTATATTA
1 TTATATTA
41860 TTATTACTGTA
1 TTA-TA-T-TA
41871 TTATTATTA
1 TTA-TATTA
41880 GTT-TATTA
1 -TTATATTA
41888 TTATATTA
1 TTATATTA
41896 TATATTATTA
1 T-TA-TATTA
41906 TTATACTTA
1 TTATA-TTA
41915 CTTATAT
1 -TTATAT
41922 ATGCGTATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
7 2 0.04
8 16 0.30
9 12 0.23
10 15 0.28
11 8 0.15
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (8 bp):
TTATATTA
Found at i:41910 original size:11 final size:12
Alignment explanation
Indices: 41855--41909 Score: 60
Period size: 11 Copynumber: 4.5 Consensus size: 12
41845 TGTTTATTTA
41855 TATTATTATTACTG
1 TATTATTATTA--G
41869 TATTATTATTAG
1 TATTATTATTAG
41881 T-TTATTATTA-
1 TATTATTATTAG
*
41891 TATTATATATTAT
1 TATTAT-TATTAG
41904 TATTAT
1 TATTAT
41910 ACTTACTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 13 0.34
12 7 0.18
13 6 0.16
14 11 0.29
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (12 bp):
TATTATTATTAG
Found at i:42089 original size:25 final size:26
Alignment explanation
Indices: 42047--42097 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
42037 TTTCATAATT
*
42047 TTTATATGTTTTCCCAA-TTTTATAA
1 TTTATATGTTTTCACAATTTTTATAA
42072 TTTATATGTTTAT-ACAATTTTTATAA
1 TTTATATGTTT-TCACAATTTTTATAA
42098 CATGTACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTATATGTTTTCACAATTTTTATAA
Found at i:48325 original size:21 final size:21
Alignment explanation
Indices: 48299--48339 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48289 AGACGAGCAA
* *
48299 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
48320 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
48340 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:52740 original size:3 final size:3
Alignment explanation
Indices: 52732--52756 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52722 AAACCAGTTG
52732 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
52757 AGTTAACTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:62668 original size:23 final size:22
Alignment explanation
Indices: 62641--62710 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
62631 TTATAATCAA
62641 TTAATATTTATATTTGAAATTAT
1 TTAATATTTATATTTGAAA-TAT
* * *
62664 TTAAT-CTAATCATTTGATATAT
1 TTAATATTTAT-ATTTGAAATAT
62686 TTAATATTTGATATATT-AAATAT
1 TTAATATTT-ATAT-TTGAAATAT
62709 TT
1 TT
62711 TTCAAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
22 11 0.30
23 22 0.59
24 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (22 bp):
TTAATATTTATATTTGAAATAT
Found at i:62696 original size:16 final size:16
Alignment explanation
Indices: 62670--62710 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
62660 TTATTTAATC
62670 TAATCATTTGATATATT
1 TAAT-ATTTGATATATT
62687 TAATATTTGATATATT
1 TAATATTTGATATATT
*
62703 AAATATTT
1 TAATATTT
62711 TTCAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (16 bp):
TAATATTTGATATATT
Found at i:63068 original size:12 final size:12
Alignment explanation
Indices: 63051--63075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63041 CCCCCCCCCC
63051 AAAAAAAAGAAA
1 AAAAAAAAGAAA
63063 AAAAAAAAGAAA
1 AAAAAAAAGAAA
63075 A
1 A
63076 GAAAGAGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Done.