Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1838
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: 10879
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Found at i:5761 original size:18 final size:18
Alignment explanation
Indices: 5740--5781 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
5730 ATTCTCTTAC
*
5740 TTATTATGCCTTCATTAA
1 TTATTATACCTTCATTAA
5758 TTATTATACCTTCATTAA
1 TTATTATACCTTCATTAA
5776 TTATTA
1 TTATTA
5782 GTAATATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATTATACCTTCATTAA
Found at i:7564 original size:19 final size:19
Alignment explanation
Indices: 7533--7578 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
7523 AACTCTAGAT
*
7533 TAGATAT-TTGCTTTCATA
1 TAGATATATTGCTTTAATA
7551 TAGATATATTGCTTTAATA
1 TAGATATATTGCTTTAATA
*
7570 TATATATAT
1 TAGATATAT
7579 ATATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.50
Consensus pattern (19 bp):
TAGATATATTGCTTTAATA
Found at i:7605 original size:2 final size:2
Alignment explanation
Indices: 7567--7596 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7557 TATTGCTTTA
7567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7597 GCATATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8889 original size:272 final size:276
Alignment explanation
Indices: 8611--9144 Score: 772
Period size: 276 Copynumber: 1.9 Consensus size: 276
8601 AAAAAAAAAA
* ***
8611 TTCAACCTTCAACCATATAAAATATTTTATAATTATAATTTTTTT-ATTAAAATCTACGTTTCTT
1 TTCAACCTTCAACCATATAAAATATTTTATAAATATAATTTTTTTGATTAAAATCTAAACTTCTT
* * **
8675 ATATTTGAGCAAATGATGCATA-A-ATTAAAGTACATATGGCATTGGCTAACTTATTTTGAATCT
66 ATATTTGAACAAATGATACATATATATTAAAGTACATATAACATTGGCTAACTTATTTTGAATCT
* * * *
8738 ATCATAATAATTTAAACACTTTTTTTTACG-A-TTTACAAAATCATATTTAATAAAAAATAAATC
131 ATCATAACAATTAAAACACTTTTTTTTACGCAGTTTACAAAAACAAATTTAAT-AAAAATAAATC
*
8801 AACTTGAGCTTAAATAATCATAAGCTCTTATTGCCACAATTCAACTGTTTTAAGTTGAAAAAGTT
195 AACTTGAGCTTAAATAATCATAAGCTCTTATTGCCACAATTCAACTATTTTAAGTTGAAAAAGTT
8866 AAACTAAAAAAAACATT
260 AAACTAAAAAAAACATT
* *
8883 TTCAACCTTTAACCATATAAAATATTTTATAAATATAATTTTTTTGATTAGAATCTAAACTTCTT
1 TTCAACCTTCAACCATATAAAATATTTTATAAATATAATTTTTTTGATTAAAATCTAAACTTCTT
* * **
8948 ATATTTGAACATATGATATATATATATTAAAGTATGTATAACATTGGCTAACTTATTTTGAATCT
66 ATATTTGAACAAATGATACATATATATTAAAGTACATATAACATTGGCTAACTTATTTTGAATCT
* * ** *
9013 ATCATAGCGATTAAAACACTTTTTTTTTTGCAGTTTACAAAAACAAATTTAATAAAAATAAATTA
131 ATCATAACAATTAAAACACTTTTTTTTACGCAGTTTACAAAAACAAATTTAATAAAAATAAATCA
* * * *
9078 ACTTGAGCTTAAATAATTATAAGCTCTTGTTGGCACAATTCAACTATTTTAAGTTGAAAAGGTTA
196 ACTTGAGCTTAAATAATCATAAGCTCTTATTGCCACAATTCAACTATTTTAAGTTGAAAAAGTTA
9143 AA
261 AA
9145 TATTTATTTG
Statistics
Matches: 229, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
272 43 0.19
273 33 0.14
274 1 0.00
275 60 0.26
276 74 0.32
277 18 0.08
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (276 bp):
TTCAACCTTCAACCATATAAAATATTTTATAAATATAATTTTTTTGATTAAAATCTAAACTTCTT
ATATTTGAACAAATGATACATATATATTAAAGTACATATAACATTGGCTAACTTATTTTGAATCT
ATCATAACAATTAAAACACTTTTTTTTACGCAGTTTACAAAAACAAATTTAATAAAAATAAATCA
ACTTGAGCTTAAATAATCATAAGCTCTTATTGCCACAATTCAACTATTTTAAGTTGAAAAAGTTA
AACTAAAAAAAACATT
Found at i:10599 original size:17 final size:15
Alignment explanation
Indices: 10574--10611 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
10564 TTATAATTAT
10574 AATTATAT-TTAAAA
1 AATTATATATTAAAA
*
10588 ATATTATATATTAATA
1 A-ATTATATATTAAAA
10604 AATTATAT
1 AATTATAT
10612 TAACTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 14 0.67
16 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTATATATTAAAA
Found at i:10628 original size:30 final size:27
Alignment explanation
Indices: 10560--10628 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 27
10550 ATTTCATCAT
10560 ATTTTTATAATTATAATTATATTTAAAA
1 ATTTTTAT-ATTATAATTATATTTAAAA
*
10588 ATATTATATATTAATAAATTATA-TTAACTAA
1 AT-TTTTATATT-AT-AATTATATTTAA--AA
10619 ATTTTTATAT
1 ATTTTTATAT
10629 ATTTATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
28 5 0.15
29 11 0.32
30 14 0.41
31 4 0.12
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTTTTATATTATAATTATATTTAAAA
Done.