Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1909
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: 27925
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:29 original size:13 final size:13
Alignment explanation
Indices: 11--35 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1 TAAAGATCAG
11 TGTATCGATACAA
1 TGTATCGATACAA
24 TGTATCGATACA
1 TGTATCGATACA
36 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:914 original size:50 final size:50
Alignment explanation
Indices: 835--994 Score: 198
Period size: 50 Copynumber: 3.2 Consensus size: 50
825 GACAGGTGGT
* * * *
835 CGTAATTGTTTATTATTATTCACCTACCTTTGACAATCGAGAGAGATGGA
1 CGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGATGGA
* * * *
885 CGTAATTGTTGACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTAGC
1 CGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGATGGA
* *
935 CGTAATTGTTGACTATTCTTCACCAACCTTTGATAAT--AGAGAAATGTGA
1 CGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGATG-GA
984 CCGTAATTGTT
1 -CGTAATTGTT
995 AACTCTAAGT
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 6 0.06
49 1 0.01
50 87 0.93
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (50 bp):
CGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGATGGA
Found at i:5393 original size:50 final size:50
Alignment explanation
Indices: 5330--5504 Score: 271
Period size: 50 Copynumber: 3.5 Consensus size: 50
5320 GCAAAGCAAT
* *
5330 TTGATTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGTCGTAATTA
1 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGTCGTAATTG
* * *
5380 TTGACTATTCTTCACCAACCTTTGATAATCGAGAGAAGTGATCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGTCGTAATTG
5430 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGG-CTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGTC-GTAATTG
* *
5480 TTAACTATTCTTCATCAACCTTTGA
1 TTGACTATTCTTCACCAACCTTTGA
5505 CAAAAGAGAA
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 113 0.99
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGTCGTAATTG
Found at i:5525 original size:50 final size:49
Alignment explanation
Indices: 5330--5533 Score: 223
Period size: 50 Copynumber: 4.1 Consensus size: 49
5320 GCAAAGCAAT
* * * * *
5330 TTGATTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTG-GTCGTAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGA-AAGTGACT-GTAATTG
*
5380 TTGACTATTCTTCACCAACCTTTGATAATCGAGAGAAGTGA-TCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGA-AAGTGACT-GTAATTG
* * *
5430 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGCTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGA-AAGTGACTGTAATTG
* * **
5480 TTAACTATTCTTCATCAACCTTTGACAAAAGAGAAATGTGACTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAAA-GTGACTGTAATTG
5530 TTGA
1 TTGA
5534 TTTTAAGCAT
Statistics
Matches: 136, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
49 1 0.01
50 134 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (49 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAAAGTGACTGTAATTG
Found at i:5527 original size:100 final size:100
Alignment explanation
Indices: 5330--5533 Score: 297
Period size: 100 Copynumber: 2.0 Consensus size: 100
5320 GCAAAGCAAT
* *
5330 TTGATTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGTCGTAATTATTGACTATTCTTCAC
1 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGTCGTAATTATTAACTATTCTTCAC
* **
5395 CAACCTTTGATAATCGAGAGAAGTGATCGTAATTG
66 CAACCTTTGACAAAAGAGAGAAGTGATCGTAATTG
*
5430 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGG-CTGTAATTGTTAACTATTCTTCA
1 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGTC-GTAATTATTAACTATTCTTCA
*
5494 TCAACCTTTGACAAAAGAGA-AATGTGA-CTGTAATTG
65 CCAACCTTTGACAAAAGAGAGAA-GTGATC-GTAATTG
5530 TTGA
1 TTGA
5534 TTTTAAGCAT
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
99 4 0.04
100 90 0.96
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (100 bp):
TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGTCGTAATTATTAACTATTCTTCAC
CAACCTTTGACAAAAGAGAGAAGTGATCGTAATTG
Found at i:5772 original size:19 final size:19
Alignment explanation
Indices: 5750--5787 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5740 GCATTAACAG
5750 TAAAGACCACCATTGACGA
1 TAAAGACCACCATTGACGA
5769 TAAAGACCACCATTGACGA
1 TAAAGACCACCATTGACGA
5788 ATCAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (19 bp):
TAAAGACCACCATTGACGA
Found at i:7243 original size:42 final size:44
Alignment explanation
Indices: 7177--7265 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 44
7167 ATATATAGAA
* **
7177 TCATTTATTTTTTTTATTTGATAATT-TATATAATTATATTATAT
1 TCATTTATTTTTTATATTTGATAATTGTAT-TAAAAATATTATAT
7221 TCATTTATTTTTTATA-TT-ATAATTGTATTAAAAATATTATAT
1 TCATTTATTTTTTATATTTGATAATTGTATTAAAAATATTATAT
7263 TCA
1 TCA
7266 GGATTCAGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
42 21 0.51
43 5 0.12
44 15 0.37
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (44 bp):
TCATTTATTTTTTATATTTGATAATTGTATTAAAAATATTATAT
Found at i:8164 original size:2 final size:2
Alignment explanation
Indices: 8157--8189 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
8147 CTAGGCTAAG
8157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8190 TTAATACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9509 original size:97 final size:99
Alignment explanation
Indices: 9373--9568 Score: 333
Period size: 97 Copynumber: 2.0 Consensus size: 99
9363 TCAGACCAGG
*
9373 TGTGAGTATTGGATACGGTATGTGTCCGACACGGATATAGTCAA-TTTTTTTAAAG-TTTTTTCA
1 TGTGAGTATTGGATACGGTATGTGTCCGACAAGGATATAGTCAATTTTTTTTAAAGTTTTTTTCA
* *
9436 TGTATTTGGAGGGTCATATTTTCATACTTATGTT
66 TGTATTTGGAGGGTCATATTTCCATACCTATGTT
* *
9470 TGTGAGTATTGGATATGGTATGTGTCTGACAAGGATATAGTCAATTTTTTTTAAAGTTTTTTTCA
1 TGTGAGTATTGGATACGGTATGTGTCCGACAAGGATATAGTCAATTTTTTTTAAAGTTTTTTTCA
9535 TGTATTTGGAGGGTCATATTTCCATACCTATGTT
66 TGTATTTGGAGGGTCATATTTCCATACCTATGTT
9569 CGAAAATGTG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 41 0.45
98 11 0.12
99 40 0.43
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (99 bp):
TGTGAGTATTGGATACGGTATGTGTCCGACAAGGATATAGTCAATTTTTTTTAAAGTTTTTTTCA
TGTATTTGGAGGGTCATATTTCCATACCTATGTT
Found at i:14719 original size:53 final size:53
Alignment explanation
Indices: 14660--14766 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
14650 CAAACACAAA
*
14660 TGTGAAATATAAATAGTTCTTAAAAAAATAAAAGGTTGGAATAACATATTATG
1 TGTGAAATATAAATAGTTCTTAAAAAAATAAAAGGTCGGAATAACATATTATG
* *
14713 TGTGAAATATAAATAGTTCTTAAAAGAATAAAGGGTCGGAATAACATATTATG
1 TGTGAAATATAAATAGTTCTTAAAAAAATAAAAGGTCGGAATAACATATTATG
14766 T
1 T
14767 TGCTTTTCTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.32
Consensus pattern (53 bp):
TGTGAAATATAAATAGTTCTTAAAAAAATAAAAGGTCGGAATAACATATTATG
Found at i:18450 original size:21 final size:21
Alignment explanation
Indices: 18421--18460 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18411 ATAAGATTGT
* *
18421 TACTTTAATTGTGAGATTAGA
1 TACTATAATTATGAGATTAGA
18442 TACTATAATTATGAGATTA
1 TACTATAATTATGAGATTA
18461 AGATCAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (21 bp):
TACTATAATTATGAGATTAGA
Found at i:18600 original size:35 final size:35
Alignment explanation
Indices: 18561--18674 Score: 95
Period size: 35 Copynumber: 3.5 Consensus size: 35
18551 TGTGTATTTA
18561 TATATATATAATAAATAATTAAAAATTATTAAAA-
1 TATATATATAATAAATAATTAAAAATTATTAAAAT
* *
18595 T-TATATAT--TAAATAA-T--AAA--CTTGAAAT
1 TATATATATAATAAATAATTAAAAATTATTAAAAT
* * *
18622 TATATTTATAATAAATAATTAAATATATAGTAAAAT
1 TATATATATAATAAATAATTAAAAAT-TATTAAAAT
*
18658 TATAT-TATATTAAATAA
1 TATATATATAATAAATAA
18675 CAATTGATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
26 5 0.08
27 1 0.02
28 9 0.15
30 8 0.13
31 8 0.13
33 9 0.15
34 1 0.02
35 11 0.18
36 10 0.16
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (35 bp):
TATATATATAATAAATAATTAAAAATTATTAAAAT
Found at i:18641 original size:19 final size:19
Alignment explanation
Indices: 18619--18674 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
18609 ATAAACTTGA
18619 AATTATATTTATAATAAAT
1 AATTATATTTATAATAAAT
* * *
18638 AATTAAATATATAGT-AA-
1 AATTATATTTATAATAAAT
*
18655 AATTATA-TTATATTAAAT
1 AATTATATTTATAATAAAT
18673 AA
1 AA
18675 CAATTGATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 5 0.17
17 8 0.28
18 4 0.14
19 12 0.41
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTATATTTATAATAAAT
Found at i:20570 original size:26 final size:26
Alignment explanation
Indices: 20541--20621 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
20531 TCTTCAAGAC
20541 TTTATATTTACTTAAATTCTTTTGGT
1 TTTATATTTACTTAAATTCTTTTGGT
** **
20567 TTTATGATTGT-C-T--ATT-TTCAAGAC
1 TTTAT-ATT-TACTTAAATTCTT-TTGGT
20591 TTTATATTTACTTAAATTCTTTTGGT
1 TTTATATTTACTTAAATTCTTTTGGT
20617 TTTAT
1 TTTAT
20622 GATTGTCTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 16
0.62 0.13 0.25
Matches are distributed among these distances:
22 1 0.03
23 6 0.15
24 10 0.26
26 15 0.38
27 6 0.15
28 1 0.03
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (26 bp):
TTTATATTTACTTAAATTCTTTTGGT
Found at i:20591 original size:50 final size:50
Alignment explanation
Indices: 20533--20629 Score: 194
Period size: 50 Copynumber: 1.9 Consensus size: 50
20523 CCTTTTCATC
20533 TTCAAGACTTTATATTTACTTAAATTCTTTTGGTTTTATGATTGTCTATT
1 TTCAAGACTTTATATTTACTTAAATTCTTTTGGTTTTATGATTGTCTATT
20583 TTCAAGACTTTATATTTACTTAAATTCTTTTGGTTTTATGATTGTCT
1 TTCAAGACTTTATATTTACTTAAATTCTTTTGGTTTTATGATTGTCT
20630 TGGAACTCGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.56
Consensus pattern (50 bp):
TTCAAGACTTTATATTTACTTAAATTCTTTTGGTTTTATGATTGTCTATT
Found at i:21480 original size:16 final size:16
Alignment explanation
Indices: 21448--21562 Score: 124
Period size: 16 Copynumber: 7.2 Consensus size: 16
21438 GAATTCAAAC
*
21448 TGATTTGAACCCGAAA
1 TGATTCGAACCCGAAA
* *
21464 TGATTCGAATCCAAAA
1 TGATTCGAACCCGAAA
* * *
21480 TAATTCGAATCCAAAA
1 TGATTCGAACCCGAAA
21496 TGATTCGAACCCGAAA
1 TGATTCGAACCCGAAA
*
21512 TGA-CCTGAACCCGAAA
1 TGATTC-GAACCCGAAA
** *
21528 TGACCCGAATCCGAAA
1 TGATTCGAACCCGAAA
21544 TGATTCGAACCCGAAA
1 TGATTCGAACCCGAAA
21560 TGA
1 TGA
21563 CCCGAATAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
15 1 0.01
16 82 0.96
17 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (16 bp):
TGATTCGAACCCGAAA
Found at i:22921 original size:13 final size:13
Alignment explanation
Indices: 22894--22930 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
22884 ATTATAATTA
*
22894 ATTAA-AATCAAT
1 ATTAATAATAAAT
22906 ATTAATAATAAAT
1 ATTAATAATAAAT
22919 ATTAATAATAAA
1 ATTAATAATAAA
22931 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
ATTAATAATAAAT
Done.