Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3627
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: 26809
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2458 original size:41 final size:40
Alignment explanation
Indices: 2369--2464 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 40
2359 TATTGGATAT
*** *
2369 AACAAAAAAATCAAAAAAAATCGAAAAAAAAATTTGATTG
1 AACAAAAAAATCAAAAAAAATCGAAAAAAAAAAAAGAGTG
*
2409 AAAAAAAAAATTCAAAAAAAATCGAAAAAGAAAAAAAGAAGTG
1 AACAAAAAAA-TCAAAAAAAATCGAAAAA-AAAAAAAG-AGTG
2452 -ACAAAAAAATCAA
1 AACAAAAAAATCAA
2465 GTTAAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
40 9 0.19
41 22 0.47
42 13 0.28
43 3 0.06
ACGTcount: A:0.72, C:0.07, G:0.08, T:0.12
Consensus pattern (40 bp):
AACAAAAAAATCAAAAAAAATCGAAAAAAAAAAAAGAGTG
Found at i:3508 original size:7 final size:6
Alignment explanation
Indices: 3483--3591 Score: 62
Period size: 6 Copynumber: 17.7 Consensus size: 6
3473 AAAGAAATTG
* * *
3483 AAAGAA ACA-AA AAAGAA AACGAA AAAGAA AAAGAA ATCA-AA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
* ** * * *
3530 AAAGAA ATCA-AA AAAGTG AGAGAAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAG-AA AAAGAA AAAG-A-A AAAGAA AA-AGAA
3582 AAAGAA AAAG
1 AAAGAA AAAG
3592 CGAAAAAAAA
Statistics
Matches: 76, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
5 6 0.08
6 54 0.71
7 12 0.16
8 4 0.05
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:3515 original size:18 final size:18
Alignment explanation
Indices: 3492--3591 Score: 74
Period size: 18 Copynumber: 5.3 Consensus size: 18
3482 GAAAGAAACA
3492 AAAAAGAAAACGAAAAAG
1 AAAAAGAAAACGAAAAAG
* *
3510 AAAAAGAAATCAAAAAAG
1 AAAAAGAAAACGAAAAAG
* *
3528 AAAAAGAAATCAAAAAAG
1 AAAAAGAAAACGAAAAAG
** * * *
3546 TGAGAGAAAAAAGAAAATG
1 AAAAAG-AAAACGAAAAAG
*
3565 AAGAAAAGAAAATTGAAAAAG
1 -A-AAAAGAAAA-CGAAAAAG
3586 AAAAAG
1 AAAAAG
3592 CGAAAAAAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 7
0.75 0.16 0.08
Matches are distributed among these distances:
18 37 0.58
19 13 0.20
20 5 0.08
21 9 0.14
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAACGAAAAAG
Found at i:3571 original size:14 final size:13
Alignment explanation
Indices: 3553--3608 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
3543 AAGTGAGAGA
3553 AAAAAGAAAA-TG
1 AAAAAGAAAATTG
3565 AAGAAAAGAAAATTG
1 -A-AAAAGAAAATTG
**
3580 AAAAAGAAAAAGCG
1 AAAAAG-AAAATTG
3594 AAAAA-AAAATTG
1 AAAAAGAAAATTG
3606 AAA
1 AAA
3609 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
12 8 0.22
13 6 0.17
14 20 0.56
15 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATTG
Found at i:3583 original size:27 final size:26
Alignment explanation
Indices: 3553--3608 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
3543 AAGTGAGAGA
* *
3553 AAAAAGAAAATGAAGAAAAGAAAATTG
1 AAAAAGAAAAAG-AGAAAAAAAAATTG
*
3580 AAAAAGAAAAAGCGAAAAAAAAATTG
1 AAAAAGAAAAAGAGAAAAAAAAATTG
3606 AAA
1 AAA
3609 GAGAGCTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (26 bp):
AAAAAGAAAAAGAGAAAAAAAAATTG
Found at i:3656 original size:33 final size:32
Alignment explanation
Indices: 3605--3666 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
3595 AAAAAAAATT
3605 GAAAGAGAGCTTGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGCTTGAAAAGAAA-CAAGTGAAAAA
* *
3638 GAAAGAGAG-TCTGTAAAGAAACGAGTGAA
1 GAAAGAGAGCT-TGAAAAGAAACAAGTGAA
3667 GTGAGATCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.53, C:0.06, G:0.27, T:0.13
Consensus pattern (32 bp):
GAAAGAGAGCTTGAAAAGAAACAAGTGAAAAA
Found at i:5705 original size:29 final size:30
Alignment explanation
Indices: 5673--5730 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
5663 TTAAGACTTT
* * *
5673 ATTAATTTGTCTAATTTA-ATTTATGTTTA
1 ATTAATGTGTCTAAATTATATTAATGTTTA
*
5702 ATTAGTGTGTCTAAATTATATTAATGTTT
1 ATTAATGTGTCTAAATTATATTAATGTTT
5731 GTTCAGCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (30 bp):
ATTAATGTGTCTAAATTATATTAATGTTTA
Found at i:8731 original size:22 final size:21
Alignment explanation
Indices: 8700--8752 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
8690 ACCTCTTTGA
8700 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCGTACC-AAT
* *
8723 ACCATACCATTTTGTACCAAT
1 ACCATACCAATTCGTACCAAT
*
8744 TCCATACCA
1 ACCATACCA
8753 TTTTGAACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
22 12 0.44
23 4 0.15
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.28
Consensus pattern (21 bp):
ACCATACCAATTCGTACCAAT
Found at i:8750 original size:21 final size:21
Alignment explanation
Indices: 8705--8767 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
8695 TTTGAACCAT
* * *
8705 TACCAATTCGTACCAAATACCA
1 TACCATTTTGTACC-AATTCCA
8727 TACCATTTTGTACCAATTCCA
1 TACCATTTTGTACCAATTCCA
*
8748 TACCATTTTGAACCAATTCC
1 TACCATTTTGTACCAATTCC
8768 GAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTTGTACCAATTCCA
Found at i:9468 original size:41 final size:41
Alignment explanation
Indices: 9423--9505 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
9413 TGTAAGAACT
** * * *
9423 AAGACACATAATTGGAGTGTAGTATTTAAGACGCACATTTA
1 AAGACACATAATTAAAGTGCAATATTTAAGACACACATTTA
*
9464 AAGACTCATAATTAAAGTGCAATATTTAAGACACACATTTA
1 AAGACACATAATTAAAGTGCAATATTTAAGACACACATTTA
9505 A
1 A
9506 TATGTCTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (41 bp):
AAGACACATAATTAAAGTGCAATATTTAAGACACACATTTA
Found at i:9663 original size:27 final size:27
Alignment explanation
Indices: 9625--9677 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
9615 AGCACATTGC
*
9625 ATGGGATGCATGG-TTCGCATGAAATGT
1 ATGGGATGCATGGAAT-GCATGAAATGT
*
9652 ATGGGTTGCATGGAATGCATGAAATG
1 ATGGGATGCATGGAATGCATGAAATG
9678 CATGTCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.28
Consensus pattern (27 bp):
ATGGGATGCATGGAATGCATGAAATGT
Found at i:9690 original size:27 final size:27
Alignment explanation
Indices: 9641--9693 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
9631 TGCATGGTTC
* *
9641 GCATGAAATGTATGGGTTGCATGGAAT
1 GCATGAAATGCATGGCTTGCATGGAAT
* *
9668 GCATGAAATGCATGTCTTTCATGGAA
1 GCATGAAATGCATGGCTTGCATGGAA
9694 CACATGGAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.30
Consensus pattern (27 bp):
GCATGAAATGCATGGCTTGCATGGAAT
Found at i:10628 original size:29 final size:30
Alignment explanation
Indices: 10548--10634 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 30
10538 AAAGTCATGC
*
10548 ATTATGTAACTTTCATGTTAGTTAAGTTTGC
1 ATTATGTAACTTTCATGTTAGTTAA-TTTGA
* * * *
10579 ATCAT-TAA-ATTAAT-TCAAGTTAATTT-A
1 ATTATGTAACTTTCATGT-TAGTTAATTTGA
10606 ATTATGTAACTTTCATGTTAGTTAATTTG
1 ATTATGTAACTTTCATGTTAGTTAATTTG
10635 CATTTCAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 11
0.68 0.15 0.18
Matches are distributed among these distances:
27 4 0.10
28 7 0.17
29 23 0.55
30 4 0.10
31 4 0.10
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.48
Consensus pattern (30 bp):
ATTATGTAACTTTCATGTTAGTTAATTTGA
Found at i:11956 original size:22 final size:22
Alignment explanation
Indices: 11928--11969 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
11918 TAGTAGTTTC
11928 TCAAAAAAAATCAAAAAAAAAT
1 TCAAAAAAAATCAAAAAAAAAT
*
11950 TCAAAAAAATTCAAAAAAAA
1 TCAAAAAAAATCAAAAAAAA
11970 TTGGTTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (22 bp):
TCAAAAAAAATCAAAAAAAAAT
Found at i:11970 original size:11 final size:11
Alignment explanation
Indices: 11928--11971 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
11918 TAGTAGTTTC
11928 TCAAAAAAAA-
1 TCAAAAAAAAT
11938 TCAAAAAAAAAT
1 TC-AAAAAAAAT
11950 TC-AAAAAAAT
1 TCAAAAAAAAT
11960 TCAAAAAAAAT
1 TCAAAAAAAAT
11971 T
1 T
11972 GGTTTCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 12 0.39
11 17 0.55
12 2 0.06
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TCAAAAAAAAT
Found at i:12031 original size:15 final size:16
Alignment explanation
Indices: 12008--12049 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
11998 GATATCAAGT
12008 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
12024 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
12040 TGAAAAAAAA
1 TGAAAAAAAA
12050 GAAGAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.17
Consensus pattern (16 bp):
TGAAAAAAAAAATTCG
Found at i:25495 original size:88 final size:83
Alignment explanation
Indices: 25297--25524 Score: 269
Period size: 88 Copynumber: 2.7 Consensus size: 83
25287 TTTGGAAACA
* * * *
25297 AAATAAATTGTTATTAAACAGCGGGAGTAAATCCCGAAATAGATTTTATTTAATTCTATTCTAAT
1 AAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAATAGATTTTATTTAATT-TATTCTAAT
25362 TTGGAAACAAAATAAAATC
65 TTGGAAACAAAATAAAATC
*
25381 AAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAATAGATTTGATTTAATTTAATTTCTCA
1 AAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAATAGATTTTATTTAATTT-A-TTCT-A
* * *
25446 TTTTTTGACAACAAAATCAAATC
63 -ATTTGGA-AACAAAATAAAATC
* * ***
25469 AAA-CAAATCTTTATTAAACGGTGGGAATAAAAAACGAAATAGATTTTATTTAATTT
1 AAATAAAATC-TTATTAAACGGCGGGAATAAATCCCGAAATAGATTTTATTTAATTT
25525 CTCATTTTTG
Statistics
Matches: 124, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
83 1 0.01
84 51 0.41
85 4 0.03
86 1 0.01
87 10 0.08
88 57 0.46
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (83 bp):
AAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAATAGATTTTATTTAATTTATTCTAATT
TGGAAACAAAATAAAATC
Done.