Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1554
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: 40670
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:715 original size:2 final size:2
Alignment explanation
Indices: 708--739 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
698 GCTTTCTTTA
708 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
740 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20498 original size:250 final size:241
Alignment explanation
Indices: 20066--20623 Score: 882
Period size: 250 Copynumber: 2.3 Consensus size: 241
20056 CCCAAACATG
* *
20066 CTACTGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
* *
20131 TTGAAGCGTTTTTATACTATTTGCTCAACTCGAAATTAATTTTTCCAAGACCTACTGTAGCAAAA
66 TTGAAGCATTTTTATACTATTTACTCAACTCGAAATTAATTTTTCCAAGACCTACTGTAGCAAAA
*
20196 CCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTT
131 CCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTT
* *
20261 ATACTATTTGCTTAGAAACGTCAACCCAAAATTATTTTTGCATGAC
196 ATACTATTTGCTCAGAAACGTCAACCCAAAATTATTTTTGCAGGAC
*
20307 CTACTGTAGCAAAAGTGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
* *
20372 TTGAAGCATTTTTATACTATTTACTCAAAAACGTCAACTCGAAATTATTTTTTCCAGGACCTACT
66 TTGAAGCATTTTTATACTA-TT--T-----AC-TCAACTCGAAATTAATTTTTCCAAGACCTACT
* *
20437 GTAGCAAAAGCGCGTCCACGAGGGTGCAATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAA
122 GTAGCAAAACCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAA
* *
20502 GCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTGCAGGAC
187 GCGTTTTTTATACTATTTGCTCAGAAACGTCAACCCAAAATTATTTTTGCAGGAC
* * *
20557 CTACTGTAGCAAAAGCGCGTACACATGGGCGCGACTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
20622 TT
66 TT
20624 TGATTTTATT
Statistics
Matches: 290, Mismatches: 18, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
241 80 0.28
242 2 0.01
244 1 0.00
249 1 0.00
250 206 0.71
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (241 bp):
CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCATTTTTATACTATTTACTCAACTCGAAATTAATTTTTCCAAGACCTACTGTAGCAAAA
CCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTT
ATACTATTTGCTCAGAAACGTCAACCCAAAATTATTTTTGCAGGAC
Found at i:20636 original size:125 final size:125
Alignment explanation
Indices: 20155--20623 Score: 708
Period size: 125 Copynumber: 3.7 Consensus size: 125
20145 TACTATTTGC
* * *
20155 TCAACTCGAAATTAATTTTTCCAAGACCTACTGTAGCAAAACCGCGTCCACGAGGGCGCGATTTC
1 TCAACTCGAAATT-ATTTTTCCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
*
20220 ACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTTAGAAACG
65 ACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
* * * * * *
20281 TCAACCCAAAATTATTTTTGCATGACCTACTGTAGCAAAAGTGCGTACACGTGGGCGCGATTTCA
1 TCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTCA
* * * *
20346 CAAATTCTTCTGATAAAGCATCCTGCTTGAAGC-ATTTTTATACTATTTACTCAAAAACG
66 CAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
* * *
20405 TCAACTCGAAATTATTTTTTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGGTGCAATTTC
1 TCAACTCGAAATTA-TTTTTCCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
20470 ACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
65 ACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
* *
20531 TCAACTCGAAATTATTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACAC-ATGGGCGCGACTTC
1 TCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCGTACACGA-GGGCGCGATTTC
* *
20595 AGAAATTCTTCTGATAAAGCATCCTGCTT
65 ACAAATTCTTCTCATAAAGCATCCTGCTT
20624 TGATTTTATT
Statistics
Matches: 307, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
124 35 0.11
125 224 0.73
126 48 0.16
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (125 bp):
TCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTCA
CAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
Found at i:31329 original size:20 final size:21
Alignment explanation
Indices: 31306--31347 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
31296 CTGGCCGGAT
31306 TCCCCTTC-CCCCTCCCTCTC
1 TCCCCTTCTCCCCTCCCTCTC
* *
31326 T-CCCTTCTCTCTTCCCTCTC
1 TCCCCTTCTCCCCTCCCTCTC
31346 TC
1 TC
31348 TCTCTCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (21 bp):
TCCCCTTCTCCCCTCCCTCTC
Found at i:31361 original size:24 final size:25
Alignment explanation
Indices: 31305--31365 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 25
31295 CCTGGCCGGA
*
31305 TTCCCCTTCCCCCTCCCTCTCTCCC
1 TTCCTCTTCCCCCTCCCTCTCTCCC
* * *
31330 TTCTCTCTTCCCTCTCTCTCTCT-CT
1 TTC-CTCTTCCCCCTCCCTCTCTCCC
31355 TTCCTC-TCCCC
1 TTCCTCTTCCCC
31366 AAATGATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 4 0.13
24 3 0.10
25 7 0.23
26 16 0.53
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (25 bp):
TTCCTCTTCCCCCTCCCTCTCTCCC
Found at i:31841 original size:3 final size:3
Alignment explanation
Indices: 31813--31872 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
31803 CTTGTCATTT
* * * *
31813 TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA TGTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
31859 TATA TTT TTA TTA T
1 T-TA TTA TTA TTA T
31873 GTACGCGTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:31869 original size:23 final size:22
Alignment explanation
Indices: 31814--31875 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
31804 TTGTCATTTT
*
31814 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
31835 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
31857 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
31876 CGCGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:31882 original size:23 final size:23
Alignment explanation
Indices: 31838--31883 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31828 GTATTACTAT
**
31838 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTACGAGTATA
* *
31861 TATTTTTATTATGTACGCGTATA
1 TATTATTATTATGTACGAGTATA
31884 CATATATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (23 bp):
TATTATTATTATGTACGAGTATA
Found at i:32215 original size:20 final size:19
Alignment explanation
Indices: 32186--32277 Score: 57
Period size: 20 Copynumber: 4.7 Consensus size: 19
32176 TTTTATGTTG
32186 TATTATTATATTTTAATACTA
1 TATTA-TATATTTTAATA-TA
* *
32207 TATTATATAATATACATATA
1 TATTATATATTTTA-ATATA
* *
32227 TTTTATATATATT-ATCAT-
1 TATTATATATTTTAAT-ATA
*
32245 T-GTATATATTTTAATAT-
1 TATTATATATTTTAATATA
32262 TATTAGTTATATTTTA
1 TATTA--TATATTTTA
32278 CACTATTATA
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
17 12 0.21
18 7 0.12
19 2 0.04
20 27 0.48
21 8 0.14
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTATATATTTTAATATA
Found at i:32332 original size:28 final size:30
Alignment explanation
Indices: 32284--32344 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
32274 TTTACACTAT
* *
32284 TATATACATTTTTTCTAATAT-TATAT-TG
1 TATATACATTGTTTATAATATATATATGTG
32312 TATATACTATTGTTTAT-ATATATATATGTG
1 TATATAC-ATTGTTTATAATATATATATGTG
32342 TAT
1 TAT
32345 GTATTTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 11 0.39
29 12 0.43
30 5 0.18
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (30 bp):
TATATACATTGTTTATAATATATATATGTG
Found at i:32713 original size:36 final size:36
Alignment explanation
Indices: 32668--32768 Score: 107
Period size: 36 Copynumber: 2.8 Consensus size: 36
32658 TATACGTACT
32668 TATACATACTTAAATATATTTTTCATATTT-CATAA
1 TATACATACTTAAATATATTTTTCATATTTACATAA
* * * * * *
32703 TTTTATATACTTACATATATTATGCATATTTACATCA
1 -TATACATACTTAAATATATTTTTCATATTTACATAA
*
32740 TATACATACTTATATATATTCTTT-ATATT
1 TATACATACTTAAATATATT-TTTCATATT
32769 CTTAAAAATG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
36 47 0.90
37 5 0.10
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (36 bp):
TATACATACTTAAATATATTTTTCATATTTACATAA
Done.