Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1404
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: 38995
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Found at i:4161 original size:29 final size:28
Alignment explanation
Indices: 4122--4197 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 28
4112 CACTTTGTGC
*
4122 TATTCTAGTGTGTTTTGGATGGATCATAT
1 TATTCTAGTGTGTTTGGGA-GGATCATAT
*
4151 TATTCTGGTGTGTTTGGGAGGAT--TA-
1 TATTCTAGTGTGTTTGGGAGGATCATAT
**
4176 TATGATAGTGTGTTT-GGAGGAT
1 TATTCTAGTGTGTTTGGGAGGAT
4198 TATACTGGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
24 7 0.17
25 12 0.29
26 2 0.05
28 4 0.10
29 17 0.40
ACGTcount: A:0.20, C:0.04, G:0.32, T:0.45
Consensus pattern (28 bp):
TATTCTAGTGTGTTTGGGAGGATCATAT
Found at i:4210 original size:24 final size:23
Alignment explanation
Indices: 4149--4215 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
4139 GATGGATCAT
* *
4149 ATTATTCTGGTGTGTTTGGGAGG
1 ATTATACTGGTGTGTTTTGGAGG
*
4172 ATTATA-TGATAGTGTGTTTGGAGG
1 ATTATACTGGT-GTGT-TTTGGAGG
4196 ATTATACTGGTGTGTTTTGG
1 ATTATACTGGTGTGTTTTGG
4216 TTGGACATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
22 3 0.08
23 14 0.38
24 17 0.46
25 3 0.08
ACGTcount: A:0.18, C:0.03, G:0.34, T:0.45
Consensus pattern (23 bp):
ATTATACTGGTGTGTTTTGGAGG
Found at i:5315 original size:19 final size:18
Alignment explanation
Indices: 5276--5327 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
5266 CACGTTCTCC
*
5276 TTTTGTTATT-TCTTTCT
1 TTTTGTTATTATTTTTCT
5293 TTTTGTTATTATTTTTCCT
1 TTTTGTTATTATTTTT-CT
* *
5312 TTTTATTTTTATTTTT
1 TTTTGTTATTATTTTT
5328 ATTTATTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 10 0.33
18 4 0.13
19 16 0.53
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTGTTATTATTTTTCT
Found at i:5348 original size:16 final size:15
Alignment explanation
Indices: 5275--5350 Score: 64
Period size: 16 Copynumber: 4.7 Consensus size: 15
5265 CCACGTTCTC
*
5275 CTTTTGTTATTTCTTT
1 CTTTT-TTATTTTTTT
5291 CTTTTTGTTATTATTTTT
1 C-TTTT-TTATT-TTTTT
*
5309 CCTTTTTATTTTTATT
1 CTTTTTTATTTTT-TT
5325 -TTTATTTATTTCTTTT
1 CTTT-TTTATTT-TTTT
5341 CTTTTTTATT
1 CTTTTTTATT
5351 CTCAACTCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
15 5 0.10
16 23 0.45
17 18 0.35
18 5 0.10
ACGTcount: A:0.11, C:0.09, G:0.03, T:0.78
Consensus pattern (15 bp):
CTTTTTTATTTTTTT
Found at i:5478 original size:19 final size:19
Alignment explanation
Indices: 5454--5494 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
5444 TTCCTTCTCC
5454 TCTACTTCTACGATTCAAA
1 TCTACTTCTACGATTCAAA
5473 TCTACTTCTACGATTCAAA
1 TCTACTTCTACGATTCAAA
5492 TCT
1 TCT
5495 CTTATAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (19 bp):
TCTACTTCTACGATTCAAA
Found at i:11717 original size:15 final size:15
Alignment explanation
Indices: 11697--11748 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
11687 ACTACAAAAC
11697 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
11712 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
11731 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
11746 ATT
1 ATT
11749 AACATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:11812 original size:16 final size:16
Alignment explanation
Indices: 11781--11817 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
11771 ATGCTAATAA
11781 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
11797 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
11813 TATTA
1 TATTA
11818 AAATAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:19900 original size:17 final size:17
Alignment explanation
Indices: 19864--19908 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
19854 GCCCACAAAT
*
19864 TTCCTTTTTTGTCATTCC
1 TTCCTTTCTT-TCATTCC
*
19882 TTCCTTTCTTTCTTTCC
1 TTCCTTTCTTTCATTCC
19899 TTCC-TTCTTT
1 TTCCTTTCTTT
19909 TCCACGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.24
17 10 0.40
18 9 0.36
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.64
Consensus pattern (17 bp):
TTCCTTTCTTTCATTCC
Found at i:19943 original size:17 final size:17
Alignment explanation
Indices: 19921--19992 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
19911 CACGTTCTCC
19921 TTTTGTTATTTCTTTCT
1 TTTTGTTATTTCTTTCT
*
19938 TTTTGTTATTATTTTTCCT
1 TTTTGTTATT-TCTTT-CT
* *
19957 TTTTATT-TTTATTT-T
1 TTTTGTTATTTCTTTCT
*
19972 TATT-TTATTTCTTTTCT
1 TTTTGTTATTTC-TTTCT
19989 TTTT
1 TTTT
19993 TATTCTCAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 2 0.05
15 7 0.16
16 3 0.07
17 18 0.41
18 6 0.14
19 8 0.18
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTGTTATTTCTTTCT
Found at i:19960 original size:19 final size:18
Alignment explanation
Indices: 19921--19977 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 18
19911 CACGTTCTCC
*
19921 TTTTGTTATT-TCTTTCT
1 TTTTGTTATTATTTTTCT
19938 TTTTGTTATTATTTTTCCT
1 TTTTGTTATTATTTTT-CT
* * *
19957 TTTTATTTTTATTTTTAT
1 TTTTGTTATTATTTTTCT
19975 TTT
1 TTT
19978 ATTTCTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.29
18 8 0.24
19 16 0.47
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTGTTATTATTTTTCT
Found at i:26351 original size:15 final size:15
Alignment explanation
Indices: 26331--26382 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
26321 ACTACAAAAC
26331 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
26346 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
26365 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
26380 ATT
1 ATT
26383 AACATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:26446 original size:16 final size:16
Alignment explanation
Indices: 26415--26451 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
26405 ATGCTAATAA
26415 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
26431 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
26447 TATTA
1 TATTA
26452 AAATAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:37489 original size:23 final size:23
Alignment explanation
Indices: 37463--37530 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 23
37453 GATGGATCAT
37463 ATTATTCTGGTGTGTTTGGGAGG
1 ATTATTCTGGTGTGTTTGGGAGG
*
37486 ATTATATGATACTGGTGTGTTTTGGAGG
1 A-T-TAT--T-CTGGTGTGTTTGGGAGG
*
37514 ATTATACTGGTGTGTTT
1 ATTATTCTGGTGTGTTT
37531 TGGTTGGACA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 12 0.32
24 1 0.03
25 3 0.08
26 3 0.08
27 2 0.05
28 17 0.45
ACGTcount: A:0.18, C:0.04, G:0.32, T:0.46
Consensus pattern (23 bp):
ATTATTCTGGTGTGTTTGGGAGG
Found at i:37492 original size:28 final size:28
Alignment explanation
Indices: 37436--37519 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
37426 CACTTTGTGC
* *
37436 TATTCTAGTGTGTTTTGGATGGATCATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
37465 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
37493 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
37520 CTGGTGTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 32 0.65
29 17 0.35
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:38584 original size:18 final size:18
Alignment explanation
Indices: 38541--38588 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
38531 AGCCACAAAT
38541 TTCCTTTT-TTGTCATTCC
1 TTCCTTTTCTT-TCATTCC
*
38559 TTCC-TTTCTTTCTTTCC
1 TTCCTTTTCTTTCATTCC
38576 TTCCTTTTCTTTC
1 TTCCTTTTCTTTC
38589 CACGTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (18 bp):
TTCCTTTTCTTTCATTCC
Found at i:38615 original size:17 final size:16
Alignment explanation
Indices: 38593--38671 Score: 79
Period size: 17 Copynumber: 4.7 Consensus size: 16
38583 TCTTTCCACG
38593 TCTTTTGTTATTTCTTT
1 TCTTTT-TTATTTCTTT
*
38610 TCTTTTGTTATTATTTTT
1 TCTTTT-TTATT-TCTTT
*
38628 TCCTTTTTATTT-TTAT
1 TCTTTTTTATTTCTT-T
*
38644 TTTTATTTTATTTCTTT
1 TCTT-TTTTATTTCTTT
38661 TCTTTTTTATT
1 TCTTTTTTATT
38672 CTCAACTCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
15 2 0.04
16 11 0.21
17 29 0.55
18 11 0.21
ACGTcount: A:0.10, C:0.09, G:0.03, T:0.78
Consensus pattern (16 bp):
TCTTTTTTATTTCTTT
Done.