Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold996
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: 29615
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:647 original size:21 final size:20
Alignment explanation
Indices: 602--648 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
592 GTTAGGAATA
*
602 AAGAAATAAACGAAATTAGCC
1 AAGAAATAAAAGAAA-TAGCC
623 AAGAAATTAAAAGAAA-AGCC
1 AAGAAA-TAAAAGAAATAGCC
643 TAAGAA
1 -AAGAA
649 CCCTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 8 0.35
ACGTcount: A:0.62, C:0.11, G:0.15, T:0.13
Consensus pattern (20 bp):
AAGAAATAAAAGAAATAGCC
Found at i:5238 original size:21 final size:22
Alignment explanation
Indices: 5196--5238 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5186 TTTTGAACCA
5196 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
5218 TTACCATTTCGTACC-AATCCC
1 TTACCATTTCGTACCAAATCCC
5239 AAATACCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.26, C:0.37, G:0.05, T:0.33
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:6486 original size:23 final size:22
Alignment explanation
Indices: 6435--6486 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
6425 CCTCGTCTTT
*
6435 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
6457 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
6480 TTCTTTT
1 TTCTTTT
6487 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:11250 original size:11 final size:10
Alignment explanation
Indices: 11225--11285 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
11215 ACCAATAAAA
11225 TAAA-TGAGC
1 TAAATTGAGC
*
11234 TGAATTGTAGC
1 TAAATTG-AGC
11245 TAAATTGAGC
1 TAAATTGAGC
**
11255 TCGATTGAGC
1 TAAATTGAGC
11265 TGAAA-TGAGC
1 T-AAATTGAGC
*
11275 TCAATTGAGC
1 TAAATTGAGC
11285 T
1 T
11286 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:11286 original size:20 final size:20
Alignment explanation
Indices: 11226--11286 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
11216 CCAATAAAAT
*
11226 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
11246 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
11267 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
11287 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:13372 original size:18 final size:18
Alignment explanation
Indices: 13351--13385 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13341 TTTTTCTTTT
13351 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
13369 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
13386 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:13382 original size:6 final size:6
Alignment explanation
Indices: 13373--13477 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
13363 TCAATCTCAA
* * * ** **
13373 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
13425 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
13471 TTTCTT T
1 TTTCTT T
13478 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:13490 original size:6 final size:6
Alignment explanation
Indices: 13424--13477 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
13414 ACTATTTTGA
* ** * *
13424 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
13471 TTTCTT T
1 TTTCTT T
13478 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:16854 original size:22 final size:22
Alignment explanation
Indices: 16824--16867 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16814 TTTGGTATTT
16824 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
16846 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
16868 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:21083 original size:17 final size:17
Alignment explanation
Indices: 21058--21111 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
21048 TCTCTTTTCA
*
21058 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
21075 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
21092 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
21109 TTC
1 TTC
21112 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:23668 original size:22 final size:22
Alignment explanation
Indices: 23638--23681 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
23628 TTTGGTATTT
23638 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
23660 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
23682 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Done.