Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1343
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: 19661
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Found at i:318 original size:2 final size:2
Alignment explanation
Indices: 311--348 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
301 CTTTCATTTC
311 AT AT AT AT 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 AT AT AT AT
349 TACGATACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2761 original size:17 final size:18
Alignment explanation
Indices: 2741--2774 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2731 TTAAATATTT
2741 TAAA-AAAAATTTAATAG
1 TAAATAAAAATTTAATAG
*
2758 TAAATAAAATTTTAATA
1 TAAATAAAAATTTAATA
2775 TATTAAGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAATAAAAATTTAATAG
Found at i:2929 original size:11 final size:11
Alignment explanation
Indices: 2914--2943 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2904 TAAAAAAATT
2914 ATTTTTTAATA
1 ATTTTTTAATA
*
2925 TTTTTTTAATA
1 ATTTTTTAATA
2936 ATTTTTTA
1 ATTTTTTA
2944 TCGATTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:5663 original size:28 final size:30
Alignment explanation
Indices: 5624--5692 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
5614 ATTTGTAGAT
5624 AAAAACT--AAGATG-AAAT-AAGAAGAAA
1 AAAAACTAAAAGATGAAAATGAAGAAGAAA
*
5650 AAAAA-TATAAAGATGAAAATGAAGAGGAAA
1 AAAAACTA-AAAGATGAAAATGAAGAAGAAA
5680 AAAAACTAAAAGA
1 AAAAACTAAAAGA
5693 AAGAATAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
28 6 0.17
29 4 0.11
30 18 0.50
31 2 0.06
ACGTcount: A:0.70, C:0.03, G:0.16, T:0.12
Consensus pattern (30 bp):
AAAAACTAAAAGATGAAAATGAAGAAGAAA
Found at i:5694 original size:27 final size:26
Alignment explanation
Indices: 5624--5707 Score: 64
Period size: 27 Copynumber: 3.0 Consensus size: 26
5614 ATTTGTAGAT
*
5624 AAAAACTAAGATG-AAATAAGAAGAAA
1 AAAAACTAA-AAGAAAATAAGAAGAAA
* *
5650 AAAAATATAAAGATGAAAATGAAGAGGAAA
1 AAAAA-CTAAA-A-GAAAAT-AAGAAGAAA
5680 AAAAACTAAAAGAAAGA-ATAGAAGAAA
1 AAAAACTAAAAGAAA-ATA-AGAAGAAA
5707 A
1 A
5708 CTACCTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
26 7 0.15
27 15 0.33
28 3 0.07
29 8 0.17
30 13 0.28
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (26 bp):
AAAAACTAAAAGAAAATAAGAAGAAA
Found at i:5704 original size:30 final size:29
Alignment explanation
Indices: 5637--5705 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 29
5627 AACTAAGATG
5637 AAAT-AAGAAGAAAAAAAATATAAAGATGA
1 AAATGAAGAAGAAAAAAAATATAAAGA-GA
*
5666 AAATGAAGAGGAAAAAAAACTA-AAAGA-A
1 AAATGAAGAAGAAAAAAAA-TATAAAGAGA
5694 AGAATAGAAGAA
1 A-AAT-GAAGAA
5706 AACTACCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.06
29 7 0.21
30 23 0.68
31 2 0.06
ACGTcount: A:0.71, C:0.01, G:0.17, T:0.10
Consensus pattern (29 bp):
AAATGAAGAAGAAAAAAAATATAAAGAGA
Found at i:7509 original size:2 final size:2
Alignment explanation
Indices: 7502--7533 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7492 CTTCCATTTC
7502 AT 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 AT
7534 TACGTCACAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8477 original size:14 final size:14
Alignment explanation
Indices: 8460--8490 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8450 TATATATATG
8460 TATGTATGTATGCA
1 TATGTATGTATGCA
*
8474 TATGTATGTATGTA
1 TATGTATGTATGCA
8488 TAT
1 TAT
8491 ACAGGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.48
Consensus pattern (14 bp):
TATGTATGTATGCA
Found at i:11651 original size:2 final size:2
Alignment explanation
Indices: 11644--11668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11634 TTCTTCCAAG
11644 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
11669 ACTTTCTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13697 original size:14 final size:14
Alignment explanation
Indices: 13678--13711 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
13668 AAACCAGCCA
13678 AATTAATTTTAA-TT
1 AATTAA-TTTAATTT
13692 AATTAATTTAATTT
1 AATTAATTTAATTT
13706 AATTAA
1 AATTAA
13712 GTATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTAATTTAATTT
Found at i:13899 original size:21 final size:21
Alignment explanation
Indices: 13875--13915 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13865 AATTAAAAAA
13875 ATATTATAT-ATTAATATTTAT
1 ATATTATATAATTAA-ATTTAT
*
13896 ATATTTTATAATTAAATTTA
1 ATATTATATAATTAAATTTA
13916 ATTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTATATAATTAAATTTAT
Found at i:14337 original size:28 final size:28
Alignment explanation
Indices: 14305--14361 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
14295 ACAGAGAGTG
*
14305 TAATTAGTTTATTTAATTTTTTAAAATT
1 TAATTAATTTATTTAATTTTTTAAAATT
14333 TAATTAATTTATTTAATTTTTTAAAATT
1 TAATTAATTTATTTAATTTTTTAAAATT
14361 T
1 T
14362 TATAATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TAATTAATTTATTTAATTTTTTAAAATT
Found at i:14823 original size:2 final size:2
Alignment explanation
Indices: 14816--14846 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14806 TCATGAGAAT
14816 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14847 GTCTACAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15992 original size:42 final size:42
Alignment explanation
Indices: 15932--16025 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
15922 TTTTTTGAAC
* *
15932 TAAATTTTTTTAA-TATTTTTAAACTAAA-AA-ATTTAATTTAAT
1 TAAATTTATATAATTATTTTTAAA--AAATAATATTTAA-TTAAT
*
15974 T-AATTTATATAATTATTTTTAAAAAATAATATTTAATTATT
1 TAAATTTATATAATTATTTTTAAAAAATAATATTTAATTAAT
16015 TAAATTTATAT
1 TAAATTTATAT
16026 TTATATTCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
40 3 0.07
41 16 0.36
42 26 0.58
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (42 bp):
TAAATTTATATAATTATTTTTAAAAAATAATATTTAATTAAT
Found at i:16821 original size:10 final size:11
Alignment explanation
Indices: 16806--16835 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
16796 TAAAATGTTC
16806 AATTAAGATA-
1 AATTAAGATAT
16816 AATTAAGATAT
1 AATTAAGATAT
16827 AATTAAGAT
1 AATTAAGAT
16836 TCATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (11 bp):
AATTAAGATAT
Found at i:18596 original size:5 final size:6
Alignment explanation
Indices: 18579--18616 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
18569 AAGATTTGAG
* *
18579 TATTTT TATTTT TATTTT TATTTC TCTTTT T-TTTT TAT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TAT
18617 CGAAACTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:19526 original size:113 final size:115
Alignment explanation
Indices: 19354--19590 Score: 349
Period size: 113 Copynumber: 2.1 Consensus size: 115
19344 ATTTATTTTA
* * *
19354 TTATATCATCATTGAATTTAAAATATTTTCTATTTATATAAAATTTGATCAATTAATAATTTATA
1 TTATATCATCATTGAATTTAAAATATTTTATATTTATATAAAATTTAATCAATTAATAATTCATA
*
19419 TTATATAAATTTAAAATATATATTTGTATCATATTT-TATTATT-T-TATAT
66 TTATAT--ATTTAAAACATATATTTGTATCATATTTATATTATTATATATAT
* *
19468 TTATATCATTATTGTATTTAAAATA-TTTATATTTATATAAAATTTAAT-ATATTAATAATTCAT
1 TTATATCATCATTGAATTTAAAATATTTTATATTTATATAAAATTTAATCA-ATTAATAATTCAT
19531 ATTATATATTTAAAACATATATTTGTATCATATTTATATTATTATATATAT
65 ATTATATATTTAAAACATATATTTGTATCATATTTATATTATTATATATAT
*
19582 ATATATCAT
1 TTATATCAT
19591 ATTAAAATAA
Statistics
Matches: 112, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
111 27 0.24
112 8 0.07
113 41 0.37
114 36 0.32
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (115 bp):
TTATATCATCATTGAATTTAAAATATTTTATATTTATATAAAATTTAATCAATTAATAATTCATA
TTATATATTTAAAACATATATTTGTATCATATTTATATTATTATATATAT
Found at i:19603 original size:29 final size:29
Alignment explanation
Indices: 19547--19606 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
19537 TATTTAAAAC
* * * * *
19547 ATATATTTGTATCATATTTATATTATTAT
1 ATATATATATATCATATTAAAATAATTAT
19576 ATATATATATATCATATTAAAATAATTAT
1 ATATATATATATCATATTAAAATAATTAT
19605 AT
1 AT
19607 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (29 bp):
ATATATATATATCATATTAAAATAATTAT
Found at i:19607 original size:113 final size:112
Alignment explanation
Indices: 19333--19609 Score: 312
Period size: 113 Copynumber: 2.4 Consensus size: 112
19323 TCATGTATTT
* * ** *
19333 ATATTTTATT-TATTTATTTTATTATATCATCATTGAATTTAAAATATTTTCTATTTATATAAAA
1 ATATTTTATTAT-TTTA-TATA-TATATCATTATTGAAAATAAAATA-TTTATATTTATATAAAA
* * *
19397 TTTGATCAATTAATAATTTATATTATATAAATTTAAAATATATATTTGTATC
62 TTTAATCAATTAATAATTCATATTATAT-AATTTAAAACATATATTTGTATC
* * **
19449 ATATTTTATTATTTTATATTTATATCATTATTGTATTTAAAATATTTATATTTATATAAAATTTA
1 ATATTTTATTATTTTATATATATATCATTATTGAAAATAAAATATTTATATTTATATAAAATTTA
19514 AT-ATATTAATAATTCATATTATAT-ATTTAAAACATATATTTGTATC
66 ATCA-ATTAATAATTCATATTATATAATTTAAAACATATATTTGTATC
*
19560 ATATTTATATTATTATATATATATATATCA-TATT-AAAATAATTATATTTA
1 ATATTT-TATTATT-T-TATATATATATCATTATTGAAAATAA-AATATTTA
19610 AAATTATCGA
Statistics
Matches: 142, Mismatches: 13, Indels: 15
0.84 0.08 0.09
Matches are distributed among these distances:
111 27 0.19
112 12 0.08
113 52 0.37
114 34 0.24
115 2 0.01
116 14 0.10
117 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (112 bp):
ATATTTTATTATTTTATATATATATCATTATTGAAAATAAAATATTTATATTTATATAAAATTTA
ATCAATTAATAATTCATATTATATAATTTAAAACATATATTTGTATC
Done.