Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold895
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: 17770
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1366 original size:21 final size:21
Alignment explanation
Indices: 1336--1377 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1326 TTTTATCAAT
1336 ACATGATGAATTGTATAGATA
1 ACATGATGAATTGTATAGATA
* *
1357 ACATGGTGAATTGTATCGATA
1 ACATGATGAATTGTATAGATA
1378 CATTAAAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.33
Consensus pattern (21 bp):
ACATGATGAATTGTATAGATA
Found at i:1866 original size:36 final size:32
Alignment explanation
Indices: 1815--1908 Score: 113
Period size: 32 Copynumber: 2.9 Consensus size: 32
1805 AGTGATTGAA
1815 AGGG-TCTATCTTAGCCTTTGAAAAAGATAGAGAG
1 AGGGTTCTATCTTAGCCTTTG-AAAAGATAG-G-G
*
1849 AGAGGTTCTATCTTAGCCTGTGAAAAGATAGGG
1 AG-GGTTCTATCTTAGCCTTTGAAAAGATAGGG
*
1882 AGGTTTCTATCTTAGCCTTT--AAAGATA
1 AGGGTTCTATCTTAGCCTTTGAAAAGATA
1909 ATGTTGTAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
30 7 0.13
32 16 0.29
33 3 0.05
34 3 0.05
35 11 0.20
36 15 0.27
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (32 bp):
AGGGTTCTATCTTAGCCTTTGAAAAGATAGGG
Found at i:1895 original size:32 final size:36
Alignment explanation
Indices: 1819--1899 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 36
1809 ATTGAAAGGG
*
1819 TCTATCTTAGCCTTTGAAAAAGATAGAGAGAGAGGT
1 TCTATCTTAGCCTGTGAAAAAGATAGAGAGAGAGGT
*
1855 TCTATCTTAGCCTGTG-AAAAGATAG-G-GAG-GTT
1 TCTATCTTAGCCTGTGAAAAAGATAGAGAGAGAGGT
1887 TCTATCTTAGCCT
1 TCTATCTTAGCCT
1900 TTAAAGATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 15 0.35
33 3 0.07
34 1 0.02
35 9 0.21
36 15 0.35
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (36 bp):
TCTATCTTAGCCTGTGAAAAAGATAGAGAGAGAGGT
Found at i:2915 original size:21 final size:21
Alignment explanation
Indices: 2891--2931 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2881 TAATACTCTT
*
2891 GAAAAGAAAGTAAATGAGTTG
1 GAAAAGAAAATAAATGAGTTG
*
2912 GAAAAGAAAATAAGTGAGTT
1 GAAAAGAAAATAAATGAGTT
2932 ACAAAATAAA
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:0.54, C:0.00, G:0.27, T:0.20
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAGTTG
Found at i:2937 original size:21 final size:21
Alignment explanation
Indices: 2892--2942 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2882 AATACTCTTG
* **
2892 AAAAGAAAGTAAATGAGTTGG
1 AAAAGAAAATAAATGAGTTAC
*
2913 AAAAGAAAATAAGTGAGTTAC
1 AAAAGAAAATAAATGAGTTAC
*
2934 AAAATAAAA
1 AAAAGAAAA
2943 ATGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.18
Consensus pattern (21 bp):
AAAAGAAAATAAATGAGTTAC
Found at i:4933 original size:22 final size:21
Alignment explanation
Indices: 4907--4952 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4897 TCCATGAAAA
* *
4907 TTTTACTCCTTAATGCTCTATT
1 TTTTACTCATGAATGCT-TATT
*
4929 TTTTATTCATGAATGCTTATT
1 TTTTACTCATGAATGCTTATT
4950 TTT
1 TTT
4953 AATTTCCCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTTACTCATGAATGCTTATT
Found at i:5750 original size:20 final size:21
Alignment explanation
Indices: 5711--5754 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
5701 TTAAGTATAG
*
5711 ATGTTTTTCAAGCATAAAAATA
1 ATGTTTTGCAAG-ATAAAAATA
5733 ATGTTTTGCAAG-TAAAAATA
1 ATGTTTTGCAAGATAAAAATA
5753 AT
1 AT
5755 TCTTTGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (21 bp):
ATGTTTTGCAAGATAAAAATA
Found at i:6279 original size:13 final size:13
Alignment explanation
Indices: 6261--6309 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
6251 ACATTATGCT
6261 TTGTATCGATACA
1 TTGTATCGATACA
6274 TTGTATCGATACA
1 TTGTATCGATACA
6287 -TG-AT-G--A-A
1 TTGTATCGATACA
6294 TTGTATCGATACA
1 TTGTATCGATACA
6307 TTG
1 TTG
6310 CTTCAAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 1 0.03
8 3 0.10
9 2 0.07
10 2 0.07
11 2 0.07
12 3 0.10
13 17 0.57
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:6284 original size:33 final size:33
Alignment explanation
Indices: 6242--6309 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
6232 CACACCCAGA
* **
6242 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGATGAATTGTATCGATACAT
6275 TGTATCGATACATGATGAATTGTATCGATACAT
1 TGTATCGATACATGATGAATTGTATCGATACAT
6308 TG
1 TG
6310 CTTCAAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATACAT
Found at i:13780 original size:13 final size:13
Alignment explanation
Indices: 13762--13788 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13752 ACATTATGCT
13762 TTGTATCGATACA
1 TTGTATCGATACA
13775 TTGTATCGATACA
1 TTGTATCGATACA
13788 T
1 T
13789 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:13785 original size:33 final size:32
Alignment explanation
Indices: 13743--13805 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
13733 CACACCCAGA
*
13743 TGTATCGATACAT-TATGCTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
13776 TGTATCGATACATGTTCATTGTATCGATAC
1 TGTATCGATACATGTTCATTGTATCGATAC
13806 TTGGACAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.46
33 14 0.50
34 1 0.04
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:15614 original size:33 final size:33
Alignment explanation
Indices: 15574--15642 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
15564 CCGTTACAAG
*
15574 CAATGTATCAATACAATT-CATCATGTATCGATA
1 CAATGTATCAATAC-ATTGCACCATGTATCGATA
* * *
15607 CAATGTATCGATACGTTGTACCATGTATCGATA
1 CAATGTATCAATACATTGCACCATGTATCGATA
15640 CAA
1 CAA
15643 ACAGTGTAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
CAATGTATCAATACATTGCACCATGTATCGATA
Found at i:15626 original size:13 final size:13
Alignment explanation
Indices: 15596--15620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15586 ACAATTCATC
15596 ATGTATCGATACA
1 ATGTATCGATACA
15609 ATGTATCGATAC
1 ATGTATCGATAC
15621 GTTGTACCAT
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):
ATGTATCGATACA
Found at i:15695 original size:20 final size:20
Alignment explanation
Indices: 15670--15743 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
15660 CTGCCAATCT
15670 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
*
15690 CATGTATCAATACAATTGTC
1 CATGTATCGATACAATTGTC
* **
15710 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTC
*
15729 CATGTACCGATACAA
1 CATGTATCGATACAA
15744 AGCATAATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 15 0.32
20 32 0.68
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:15759 original size:20 final size:19
Alignment explanation
Indices: 15711--15762 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
15701 ACAATTGTCT
*
15711 ATGTATCGATACAATGAAC
1 ATGTATCGATACAAAGAAC
*
15730 ATGTACCGATACAAAGCATA-
1 ATGTATCGATACAAAG-A-AC
15750 ATGTATCGATACA
1 ATGTATCGATACA
15763 TCTGGGTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.50
20 13 0.46
21 1 0.04
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (19 bp):
ATGTATCGATACAAAGAAC
Found at i:16346 original size:21 final size:21
Alignment explanation
Indices: 16286--16357 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
16276 AGTTTTCGTT
*
16286 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATCAAA-AA
*
16308 TTTCT-CCCTTTAATCAAAAA
1 TTTCTCCCCCTTAATCAAAAA
*
16328 TTTCTCCCCCTTGATCAAAACA
1 TTTCTCCCCCTTAATCAAAA-A
16350 TTTCTCCC
1 TTTCTCCC
16358 GCTTTGTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.16
21 23 0.52
22 14 0.32
ACGTcount: A:0.28, C:0.32, G:0.03, T:0.38
Consensus pattern (21 bp):
TTTCTCCCCCTTAATCAAAAA
Found at i:16986 original size:21 final size:21
Alignment explanation
Indices: 16950--17021 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
16940 TTGACAAAGC
*
16950 GGGAGAAATGTTTTGATCAAGG
1 GGGAGAAAT-TTTTGATTAAGG
*
16972 GGGAGAAATTTTTGATTAA-A
1 GGGAGAAATTTTTGATTAAGG
*
16992 GGGAGAAATTCTTTAATTAAGG
1 GGGAGAAATT-TTTGATTAAGG
17014 GGGAGAAA
1 GGGAGAAA
17022 AACGAAAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.23
21 17 0.39
22 17 0.39
ACGTcount: A:0.38, C:0.03, G:0.32, T:0.28
Consensus pattern (21 bp):
GGGAGAAATTTTTGATTAAGG
Found at i:17568 original size:20 final size:19
Alignment explanation
Indices: 17545--17637 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 19
17535 CTCACCCAGA
*
17545 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
*
17565 TGTATCGGTACATGTTCAT
1 TGTATCGATACATGTTCAT
*
17584 TGTATCGATACATAG-ACAAT
1 TGTATCGATACAT-GTTC-AT
* **
17604 TGTATTGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
17624 TGTATCGATACATG
1 TGTATCGATACATG
17638 AGATTGGCAG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.25
20 46 0.73
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:17704 original size:13 final size:13
Alignment explanation
Indices: 17688--17712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17678 ATGGTACAAC
17688 GTATCGATACATT
1 GTATCGATACATT
17701 GTATCGATACAT
1 GTATCGATACAT
17713 GATGAATTGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Done.