Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold598
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: 47513
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:388 original size:21 final size:21
Alignment explanation
Indices: 350--389 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
340 CCACGTCTTT
*
350 TTCATTTGTTTCTTTTTCTAA
1 TTCATTTGTCTCTTTTTCTAA
371 TTCATTT-TCTCTTCTTTCT
1 TTCATTTGTCTCTT-TTTCT
390 TCGATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.68
Consensus pattern (21 bp):
TTCATTTGTCTCTTTTTCTAA
Found at i:9036 original size:12 final size:12
Alignment explanation
Indices: 9019--9045 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9009 AAAGATCCGT
9019 AAAAAAAATTCA
1 AAAAAAAATTCA
9031 AAAAAAAATTCA
1 AAAAAAAATTCA
9043 AAA
1 AAA
9046 TTTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:10033 original size:18 final size:18
Alignment explanation
Indices: 9977--10036 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
9967 AGTGCGAGCG
9977 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
9998 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
10016 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
10034 AGA
1 AGA
10037 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:12269 original size:34 final size:33
Alignment explanation
Indices: 12205--12270 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
12195 TTAAAGATGT
* *
12205 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
12238 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
12271 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:13385 original size:12 final size:12
Alignment explanation
Indices: 13368--13396 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
13358 AAAGATCTGT
13368 AAAAAAAATTCA
1 AAAAAAAATTCA
13380 AAAAAAAATTCA
1 AAAAAAAATTCA
13392 AAAAA
1 AAAAA
13397 TTTTTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:16363 original size:18 final size:18
Alignment explanation
Indices: 16307--16366 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
16297 AGTGCGAGCG
16307 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
16328 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
16346 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
16364 AGA
1 AGA
16367 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:18606 original size:34 final size:33
Alignment explanation
Indices: 18542--18607 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
18532 TTAAAGATGT
* *
18542 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
18575 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
18608 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:20837 original size:24 final size:25
Alignment explanation
Indices: 20810--20863 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
20800 ATGAGTGATA
*
20810 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
20834 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
20858 AAAAAA
1 AAAAAA
20864 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:39195 original size:18 final size:18
Alignment explanation
Indices: 39174--39208 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39164 AGAAAAGAAA
39174 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
39192 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
39209 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:41584 original size:12 final size:12
Alignment explanation
Indices: 41569--41625 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
41559 CAAAAAAATC
41569 AAAAAAATTCAA
1 AAAAAAATTCAA
*
41581 AAAAAAATTGATTGA
1 AAAAAAATTCA---A
41596 AAAAAAATTCAA
1 AAAAAAATTCAA
* *
41608 AAAAAAAGTGAA
1 AAAAAAATTCAA
41620 AAAAAA
1 AAAAAA
41626 TCGAGCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 27 0.71
15 11 0.29
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.16
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:41625 original size:27 final size:27
Alignment explanation
Indices: 41569--41625 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
41559 CAAAAAAATC
* ***
41569 AAAAAAATTCAAAAAAAAATTGATTGA
1 AAAAAAATTCAAAAAAAAAGTGAAAAA
41596 AAAAAAATTCAAAAAAAAAGTGAAAAA
1 AAAAAAATTCAAAAAAAAAGTGAAAAA
41623 AAA
1 AAA
41626 TCGAGCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.16
Consensus pattern (27 bp):
AAAAAAATTCAAAAAAAAAGTGAAAAA
Found at i:41660 original size:12 final size:12
Alignment explanation
Indices: 41632--41660 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41622 AAAATCGAGC
41632 AAAAA-AAAGAA
1 AAAAAGAAAGAA
41643 AAAAAGAAAGAA
1 AAAAAGAAAGAA
41655 AAAAAG
1 AAAAAG
41661 GTGACAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAGAA
Found at i:41670 original size:33 final size:32
Alignment explanation
Indices: 41608--41696 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 32
41598 AAAAATTCAA
*
41608 AAAAAAAG-TGAAAAAAAA-TCGAGCAAAAAAAAG
1 AAAAAAAGAAGAAAAAAAAGT-GA-C-AAAAAAAG
* **
41641 AAAAAAAGAAAGAAAAAAAGGTGACAAAAATCG
1 AAAAAAAG-AAGAAAAAAAAGTGACAAAAAAAG
41674 AAAAAAAGAAGAAAAAAAAGTGA
1 AAAAAAAGAAGAAAAAAAAGTGA
41697 AAAGTCTTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
32 14 0.29
33 22 0.46
34 1 0.02
35 10 0.21
36 1 0.02
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (32 bp):
AAAAAAAGAAGAAAAAAAAGTGACAAAAAAAG
Found at i:42699 original size:12 final size:12
Alignment explanation
Indices: 42678--42838 Score: 50
Period size: 12 Copynumber: 13.7 Consensus size: 12
42668 AGAAAAGGAG
*
42678 AAAGAGATTGAA
1 AAAGAAATTGAA
42690 AAAGAAATTG--
1 AAAGAAATTGAA
**
42700 AAAGAAA-ACAA
1 AAAGAAATTGAA
*
42711 AAAGAAAATGAA
1 AAAGAAATTGAA
**
42723 AAAGAAAAAGAA
1 AAAGAAATTGAA
** *
42735 ATTGCAAA-AG-A
1 AAAG-AAATTGAA
*
42746 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
42758 AAAGTGAGAGAA
1 AAAGAAATTGAA
42770 AAAGAAA-TGAAGA
1 AAAGAAATTG-A-A
42783 AAAGAAAATTG-A
1 AAAG-AAATTGAA
**
42795 AAAGAAAAGCGAA
1 AAAG-AAATTGAA
42808 AAAGAAATTGAA
1 AAAGAAATTGAA
* **
42820 AGAGAGCTTG-A
1 AAAGAAATTGAA
42831 AAAGAAAT
1 AAAGAAAT
42839 CAAGTGAAAA
Statistics
Matches: 110, Mismatches: 28, Indels: 23
0.68 0.17 0.14
Matches are distributed among these distances:
10 10 0.09
11 18 0.16
12 64 0.58
13 13 0.12
14 3 0.03
15 2 0.02
ACGTcount: A:0.66, C:0.03, G:0.20, T:0.11
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:42723 original size:6 final size:6
Alignment explanation
Indices: 42700--42814 Score: 58
Period size: 6 Copynumber: 19.2 Consensus size: 6
42690 AAAGAAATTG
* * ** *
42700 AAAG-A AAACAA AAAGAA AATGAA AAAGAA AAAGAA ATTGCA AAAG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * *
42746 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA ATGAAG-A AAAGAA AATTG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A--AAGAA AAAGAA AA-AGAA
*
42795 AAAGAA AAGCGAA AAAGAA A
1 AAAGAA AA-AGAA AAAGAA A
42815 TTGAAAGAGA
Statistics
Matches: 79, Mismatches: 23, Indels: 15
0.68 0.20 0.13
Matches are distributed among these distances:
5 12 0.15
6 56 0.71
7 8 0.10
8 3 0.04
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:42730 original size:17 final size:17
Alignment explanation
Indices: 42710--42803 Score: 75
Period size: 18 Copynumber: 5.3 Consensus size: 17
42700 AAAGAAAACA
42710 AAAAGAAAATGAAAAAG
1 AAAAGAAAATGAAAAAG
* *
42727 AAAAAGAAATTGCAAAAG
1 -AAAAGAAAATGAAAAAG
42745 AAAAG-AAATCGAAAAAG
1 AAAAGAAAAT-GAAAAAG
* * *
42762 TGAGAGAAAAAGAAATGAAG
1 -AAAAGAAAATGAAA--AAG
42782 AAAAGAAAATTG-AAAAG
1 AAAAGAAAA-TGAAAAAG
42799 AAAAG
1 AAAAG
42804 CGAAAAAGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
16 3 0.05
17 19 0.32
18 22 0.37
19 12 0.20
20 4 0.07
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (17 bp):
AAAAGAAAATGAAAAAG
Found at i:45903 original size:17 final size:18
Alignment explanation
Indices: 45864--45912 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
45854 TTGACTGATA
*
45864 TATAAAATTAAACTAAAC
1 TATAAAAATAAACTAAAC
45882 TATAAAAATAAA-TAAA-
1 TATAAAAATAAACTAAAC
45898 TAATAAAAATAAACT
1 T-ATAAAAATAAACT
45913 TTACAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 1 0.04
17 15 0.54
18 12 0.43
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (18 bp):
TATAAAAATAAACTAAAC
Done.