Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1388
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: 51295
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:68 original size:11 final size:12
Alignment explanation
Indices: 48--106 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 12
38 AAATACGAAT
48 ATAATATAAAAA
1 ATAATATAAAAA
*
60 ATAAT-TAAAAG
1 ATAATATAAAAA
71 ATAATATTAAATTAA
1 ATAATA-TAAA--AA
86 TATAATAT--AAA
1 -ATAATATAAAAA
97 ATAATATAAA
1 ATAATATAAA
107 TATGATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
10 7 0.18
11 12 0.32
12 6 0.16
13 5 0.13
15 2 0.05
16 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:101 original size:15 final size:16
Alignment explanation
Indices: 71--127 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 16
61 TAATTAAAAG
*
71 ATAATATTAAATTAAT
1 ATAATATTAAAATAAT
87 ATAATA-TAAAATAAT
1 ATAATATTAAAATAAT
*
102 ATAAATATGATAAAAAAAT
1 AT-AATAT--TAAAATAAT
121 -TAATATT
1 ATAATATT
128 TAATATTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 11 0.31
16 10 0.29
17 5 0.14
18 1 0.03
19 8 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAATATTAAAATAAT
Found at i:108 original size:21 final size:19
Alignment explanation
Indices: 45--133 Score: 58
Period size: 21 Copynumber: 4.5 Consensus size: 19
35 TTTAAATACG
45 AATATAATATAAAAAA-TA
1 AATATAATATAAAAAATTA
* * *
63 ATTAAAAGATAATATTAAATT-
1 AATATAATATAA-A--AAATTA
84 AATATAATATAAAATAATATA
1 AATATAATATAAAA-AAT-TA
*
105 AATATGATA-AAAAAATTA
1 AATATAATATAAAAAATTA
*
123 ATATTTAATAT
1 A-ATATAATAT
134 TATGTAATAC
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
18 13 0.25
19 13 0.25
20 6 0.11
21 20 0.38
22 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AATATAATATAAAAAATTA
Found at i:817 original size:13 final size:13
Alignment explanation
Indices: 799--831 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
789 CATTGATCAC
*
799 AAAATAATTAAAT
1 AAAATAAATAAAT
812 AAAATAAATAAAT
1 AAAATAAATAAAT
825 -AAATAAA
1 AAAATAAA
832 CTTTTTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:979 original size:2 final size:2
Alignment explanation
Indices: 972--1007 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
962 TCTTACATAC
*
972 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1008 CATCTCTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2206 original size:21 final size:19
Alignment explanation
Indices: 2180--2235 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 19
2170 ACCATTACCA
2180 AAATAAAAAATTTATTTAT
1 AAATAAAAAATTTATTTAT
*
2199 GGAAATAAAATA-TTATTT-T
1 --AAATAAAAAATTTATTTAT
*
2218 AAA-AAATAATTTATTTAT
1 AAATAAAAAATTTATTTAT
2236 TTATTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
16 4 0.13
17 9 0.30
18 1 0.03
19 1 0.03
20 6 0.20
21 9 0.30
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
AAATAAAAAATTTATTTAT
Found at i:2719 original size:18 final size:19
Alignment explanation
Indices: 2678--2723 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
2668 ATTATGCATC
* *
2678 TAAATAATTTACAATTATA
1 TAAATAATTTACAAATAAA
2697 T-AATAATTT-CAAATAAA
1 TAAATAATTTACAAATAAA
2714 TAAAT-ATTTA
1 TAAATAATTTA
2724 ATTTATACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 11 0.48
18 11 0.48
19 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATAATTTACAAATAAA
Found at i:3612 original size:19 final size:20
Alignment explanation
Indices: 3584--3624 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3574 TATATTTAAA
*
3584 TATATCA-TTTCATAGTTAT
1 TATATCATTTTCATACTTAT
*
3603 TATATTATTTTCATACTTAT
1 TATATCATTTTCATACTTAT
3623 TA
1 TA
3625 AACATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TATATCATTTTCATACTTAT
Found at i:3634 original size:21 final size:20
Alignment explanation
Indices: 3591--3634 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3581 AAATATATCA
* * *
3591 TTTCATAGTTATTATATTAT
1 TTTCATACTTATTAAAATAT
3611 TTTCATACTTATTAAACATAT
1 TTTCATACTTATTAAA-ATAT
3632 TTT
1 TTT
3635 ATTTGTGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTCATACTTATTAAAATAT
Found at i:4765 original size:26 final size:27
Alignment explanation
Indices: 4736--4810 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 27
4726 TTTATTTTTA
4736 TATATAAATAATTAATATATTAAA-AT
1 TATATAAATAATTAATATATTAAATAT
* *
4762 TATATAAATATTTAATATTTTAAATAT
1 TATATAAATAATTAATATATTAAATAT
*
4789 TAT-TAAAT-ATAAAATATATTAA
1 TATATAAATAAT-TAATATATTAA
4811 TACACGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 1 0.02
26 36 0.86
27 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TATATAAATAATTAATATATTAAATAT
Found at i:6001 original size:21 final size:20
Alignment explanation
Indices: 5963--6015 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
5953 ACTTGGTTGA
* *
5963 TAAACATTTATAAATATTAAT
1 TAAA-ATTTTTAATTATTAAT
*
5984 TAAAATTATTTAATTATTATT
1 TAAAATT-TTTAATTATTAAT
*
6005 TTAAATTTTTA
1 TAAAATTTTTA
6016 TTTAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAATTTTTAATTATTAAT
Found at i:6007 original size:12 final size:11
Alignment explanation
Indices: 5988--6035 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
5978 ATTAATTAAA
5988 ATTATTTAATT
1 ATTATTTAATT
5999 ATTATTTTAAATT
1 ATTA-TTT-AATT
*
6012 TTTATTTAATAT
1 ATTATTTAAT-T
*
6024 ATTATTTTATT
1 ATTATTTAATT
6035 A
1 A
6036 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 9 0.29
12 15 0.48
13 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTATTTAATT
Found at i:6085 original size:27 final size:27
Alignment explanation
Indices: 6032--6086 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
6022 ATATTATTTT
*
6032 ATTAAATTTTTTAAAAATAATTTATTA
1 ATTAAATTTTTTAAAAATAATTCATTA
*
6059 ATTAAATTTTTTACAAA-AATTACATTA
1 ATTAAATTTTTTAAAAATAATT-CATTA
6086 A
1 A
6087 ACAATGACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTAAATTTTTTAAAAATAATTCATTA
Found at i:6600 original size:16 final size:17
Alignment explanation
Indices: 6559--6602 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
6549 TTTAAAATAT
*
6559 TAAATATTTA-TTTATG
1 TAAATATTTATTTTATA
*
6575 TTAATATTTATTTTATA
1 TAAATATTTATTTTATA
6592 TAAAT-TTTATT
1 TAAATATTTATT
6603 ATATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TAAATATTTATTTTATA
Found at i:6622 original size:20 final size:20
Alignment explanation
Indices: 6562--6622 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
6552 AAAATATTAA
*
6562 ATATTTATTTATGTTAATATT
1 ATATTTATTTATATT-ATATT
* * *
6583 -TATTTTATATAAATTTTATT
1 ATA-TTTATTTATATTATATT
6603 ATATTTATTTATATTATATT
1 ATATTTATTTATATTATATT
6623 TTTATATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATATTTATTTATATTATATT
Found at i:6623 original size:25 final size:25
Alignment explanation
Indices: 6578--6690 Score: 79
Period size: 25 Copynumber: 4.3 Consensus size: 25
6568 ATTTATGTTA
6578 ATATTTATTT-TATATAAATTTTATT
1 ATATTTATTTATAT-TAAATTTTATT
*
6603 ATATTTATTTATATTATA-TTT-TT
1 ATATTTATTTATATTAAATTTTATT
* *
6626 ATATTTTACTTAAAATTAAATTTTAATT
1 ATA-TTTA-TTTATATTAAATTTT-ATT
* *
6654 ATTTTTTTATTTATATTATATAATTATATT
1 A--TATTTATTTATA-T-TA-AATTTTATT
6684 ATATTTA
1 ATATTTA
6691 AAATTATGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
23 5 0.07
24 7 0.10
25 21 0.31
26 6 0.09
28 12 0.18
29 5 0.07
30 7 0.10
31 5 0.07
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (25 bp):
ATATTTATTTATATTAAATTTTATT
Found at i:6680 original size:17 final size:17
Alignment explanation
Indices: 6660--6697 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6650 AATTATTTTT
*
6660 TTAT-TTATATTATATAA
1 TTATATTATATT-TAAAA
6677 TTATATTATATTTAAAA
1 TTATATTATATTTAAAA
6694 TTAT
1 TTAT
6698 GAAGATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTATATTTAAAA
Found at i:7122 original size:30 final size:29
Alignment explanation
Indices: 7088--7167 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
7078 TAAAAGTTAT
7088 AGATTAAAGATTTATTTAGATATAATATAA
1 AGATTAAAGATTTATTTAGATATAATA-AA
* *
7118 AGATT-AAGAGCTTATTTTGAT-TAATAAA
1 AGATTAAAGA-TTTATTTAGATATAATAAA
7146 AG--TATAAGTATTTATTTAGATA
1 AGATTA-AAG-ATTTATTTAGATA
7168 AGTGATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
26 1 0.02
28 16 0.39
29 10 0.24
30 14 0.34
ACGTcount: A:0.45, C:0.01, G:0.12, T:0.41
Consensus pattern (29 bp):
AGATTAAAGATTTATTTAGATATAATAAA
Found at i:7352 original size:30 final size:30
Alignment explanation
Indices: 7316--7372 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
7306 AATTTGTTAG
* *
7316 GTCAATAAATCTTATATCGTAAATAACTTA
1 GTCAATAAATCTAATATCATAAATAACTTA
*
7346 GTCAATAAATCTAATGTCATAAATAAC
1 GTCAATAAATCTAATATCATAAATAAC
7373 CTACAAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (30 bp):
GTCAATAAATCTAATATCATAAATAACTTA
Found at i:8179 original size:27 final size:27
Alignment explanation
Indices: 8148--8220 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
8138 TTTATTCTAT
* **
8148 AATTTTAAAAAATTATATATTTTTATA
1 AATTTTAAAAAATTATATAATTACATA
* *
8175 AATTTTTACAAAA-TAAATAATTACATA
1 AA-TTTTAAAAAATTATATAATTACATA
8202 AATTTTAAAAAATT-TATAA
1 AATTTTAAAAAATTATATAA
8221 CCATATTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 13 0.35
27 15 0.41
28 9 0.24
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTTTAAAAAATTATATAATTACATA
Found at i:8366 original size:16 final size:16
Alignment explanation
Indices: 8345--8390 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
8335 TATCACCTAC
8345 TTTATTTTATTTTTAT
1 TTTATTTTATTTTTAT
*
8361 TTTATTTAATTTTTAT
1 TTTATTTTATTTTTAT
8377 TTTATGTTT-TTTTT
1 TTTAT-TTTATTTTT
8391 TCATATTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 25 0.93
17 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTATTTTATTTTTAT
Found at i:8597 original size:16 final size:16
Alignment explanation
Indices: 8566--8604 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
8556 AATTAATTTT
**
8566 TATTAAAAATTTTAAA
1 TATTAAAAATAATAAA
8582 TATTAAAAATAATAAA
1 TATTAAAAATAATAAA
8598 TACTTAA
1 TA-TTAA
8605 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TATTAAAAATAATAAA
Found at i:8610 original size:20 final size:19
Alignment explanation
Indices: 8585--8640 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 19
8575 TTTTAAATAT
8585 TAAAAATA-ATAAATACTTAA
1 TAAAAATATATAAAT--TTAA
8605 TAAAAAATATATAAATTTAA
1 T-AAAAATATATAAATTTAA
8625 T--AAAT-TATAAATTTAA
1 TAAAAATATATAAATTTAA
8641 ATATCATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 11 0.32
17 4 0.12
20 6 0.18
21 7 0.21
22 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAATATATAAATTTAA
Found at i:8891 original size:20 final size:20
Alignment explanation
Indices: 8866--8960 Score: 65
Period size: 20 Copynumber: 4.8 Consensus size: 20
8856 ATTTAATTAA
*
8866 ATTATA-ATTATATTTAAAAT
1 ATTATATATT-TATATAAAAT
8886 ATTATATATTTATATAAAAT
1 ATTATATATTTATATAAAAT
*
8906 -TTA-ATTTATTA-ATAAATTAT
1 ATTATATAT-TTATATAAA--AT
**
8926 ATTATATAAGTAT-TAAAAT
1 ATTATATATTTATATAAAAT
* *
8945 ATTTTTTATTTATATA
1 ATTATATATTTATATA
8961 TTACCTTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
18 8 0.14
19 17 0.29
20 19 0.33
21 12 0.21
22 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (20 bp):
ATTATATATTTATATAAAAT
Found at i:8897 original size:37 final size:35
Alignment explanation
Indices: 8850--8927 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 35
8840 TGTGATTTAT
* *
8850 TTATTTATTTA-ATTAAATTATAATTATATTTAA-AATA
1 TTATATATTTATATAAAATT-TAATT-TA-TTAATAA-A
8887 TTATATATTTATATAAAATTTAATTTATTAATAAA
1 TTATATATTTATATAAAATTTAATTTATTAATAAA
8922 TTATAT
1 TTATAT
8928 TATATAAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
35 11 0.30
36 4 0.11
37 15 0.41
38 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
TTATATATTTATATAAAATTTAATTTATTAATAAA
Found at i:8909 original size:27 final size:28
Alignment explanation
Indices: 8877--8961 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 28
8867 TTATAATTAT
8877 ATTTAAAATATTATATATTTATATA-AA
1 ATTTAAAATATTATATATTTATATATAA
** *
8904 ATTTAATTTATTAATAAATTATATTATATAA
1 ATTTAAAATATT-ATATATT-TA-TATATAA
* * *
8935 GTATTAAAATATTTTTTATTTATATAT
1 AT-TTAAAATATTATATATTTATATAT
8962 TACCTTTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
27 10 0.23
28 6 0.14
29 7 0.16
30 6 0.14
31 7 0.16
32 8 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
ATTTAAAATATTATATATTTATATATAA
Found at i:9362 original size:21 final size:22
Alignment explanation
Indices: 9338--9379 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9328 AAAAATAAAA
*
9338 TTTTATATTATATT-ATTTTATT
1 TTTTA-ATTAAATTAATTTTATT
9360 TTTTAATTAAATTAATTTTA
1 TTTTAATTAAATTAATTTTA
9380 ATAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTAATTAAATTAATTTTATT
Found at i:9557 original size:22 final size:22
Alignment explanation
Indices: 9532--9617 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
9522 TAATTATAAT
9532 ATAATATTATAATTATTATTTA
1 ATAATATTATAATTATTATTTA
* *
9554 ATAATTTTAAAATTTATTA-TTA
1 ATAATATTATAA-TTATTATTTA
* * *
9576 TTAATATTTATAAATAATATTT-
1 ATAATA-TTATAATTATTATTTA
* *
9598 ATTATAATTATATTTATTAT
1 ATAAT-ATTATAATTATTAT
9618 ATTTACAATC
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
22 34 0.71
23 14 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATAATATTATAATTATTATTTA
Found at i:9584 original size:32 final size:30
Alignment explanation
Indices: 9536--9613 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
9526 TATAATATAA
* *
9536 TATTATAATTATTATTTAATAATTTTAAAATT
1 TATTATAATTAATATTTAATAA--ATAAAATT
* *
9568 TATTATTATTAATATTT-ATAAATAATATT
1 TATTATAATTAATATTTAATAAATAAAATT
9597 TATTATAATT-ATATTTA
1 TATTATAATTAATATTTA
9614 TTATATTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.15
29 15 0.38
31 4 0.10
32 15 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TATTATAATTAATATTTAATAAATAAAATT
Found at i:10534 original size:2 final size:2
Alignment explanation
Indices: 10527--10575 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
10517 TATCTCTACT
10527 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10569 TC TC TC T
1 TC TC TC T
10576 TCTTTCTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:11004 original size:4 final size:4
Alignment explanation
Indices: 10997--11039 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
10987 TTCAAATATA
* *
10997 TATG TATG TATG TATG TATG TATG TATG TGTG TGTG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
11040 ATGTTTGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:15059 original size:19 final size:19
Alignment explanation
Indices: 15023--15067 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
15013 AATTTATTTA
***
15023 AATTATAATATTTTAAAAT
1 AATTATAATATAAAAAAAT
15042 AATTATAATATAAAAAAAT
1 AATTATAATATAAAAAAAT
15061 AA-TATAA
1 AATTATAA
15068 ATACATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTATAATATAAAAAAAT
Found at i:36754 original size:14 final size:15
Alignment explanation
Indices: 36735--36766 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
36725 TCAATTATTT
36735 ATTTAATTTA-ATAA
1 ATTTAATTTATATAA
36749 ATTTAATTTATATAA
1 ATTTAATTTATATAA
36764 ATT
1 ATT
36767 ACATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAATTTATATAA
Found at i:36859 original size:15 final size:15
Alignment explanation
Indices: 36839--36868 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36829 TTAATTATAA
*
36839 AATATATAAATAATT
1 AATATAAAAATAATT
36854 AATATAAAAATAATT
1 AATATAAAAATAATT
36869 TATTTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATAAAAATAATT
Found at i:37185 original size:32 final size:32
Alignment explanation
Indices: 37140--37232 Score: 91
Period size: 34 Copynumber: 2.8 Consensus size: 32
37130 GAATAAGTTC
*
37140 AAAAGTTAGTATTATGATTTAAAAT-AATATTAA
1 AAAAATTA-TATTATGATTTAAAATAAAT-TTAA
* *
37173 AAAAATTATATTAAGATTTATAATTAAATTTAA
1 AAAAATTATATTATGATTTA-AAATAAATTTAA
* *
37206 ATAAAATTATTTTATTATTT-AAATAAA
1 A-AAAATTATATTATGATTTAAAATAAA
37233 AGTTTTATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
32 17 0.34
33 15 0.30
34 18 0.36
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (32 bp):
AAAAATTATATTATGATTTAAAATAAATTTAA
Found at i:37240 original size:20 final size:21
Alignment explanation
Indices: 37200--37242 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
37190 TTATAATTAA
37200 ATTTAAATAAAATTATTTTATT
1 ATTTAAATAAAA-TATTTTATT
*
37222 ATTTAAATAAAA-GTTTTATT
1 ATTTAAATAAAATATTTTATT
37242 A
1 A
37243 AATTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTAAATAAAATATTTTATT
Found at i:37271 original size:19 final size:19
Alignment explanation
Indices: 37242--37284 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
37232 AAGTTTTATT
37242 AAATTAATTTAATTATA-A
1 AAATTAATTTAATTATATA
*
37260 AAATTAAATTTAATTTTATA
1 AAATT-AATTTAATTATATA
37280 AAATT
1 AAATT
37285 TTAATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTAATTTAATTATATA
Found at i:37290 original size:21 final size:19
Alignment explanation
Indices: 37245--37292 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
37235 TTTTATTAAA
37245 TTAATTTAATTATAAAAAT
1 TTAATTTAATTATAAAAAT
* *
37264 TAAATTTAATTTTATAAAATT
1 TTAATTTAA--TTATAAAAAT
37285 TTAATTTA
1 TTAATTTA
37293 TATTGGATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
21 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATTTAATTATAAAAAT
Found at i:37505 original size:18 final size:19
Alignment explanation
Indices: 37446--37505 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 19
37436 AAAAAAAATA
*
37446 TTTAAATGTATTTAATATATG
1 TTTAAATATA-TTAA-ATATG
* *
37467 -TTAAATATATAAAAAAT-
1 TTTAAATATATTAAATATG
37484 TTTAAA-ATATTAAATATG
1 TTTAAATATATTAAATATG
37502 TTTA
1 TTTA
37506 TTTCAAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 9 0.28
18 12 0.38
19 3 0.09
20 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TTTAAATATATTAAATATG
Found at i:42364 original size:10 final size:9
Alignment explanation
Indices: 42336--42365 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
42326 ATATTAACTT
42336 ATTTAAATA
1 ATTTAAATA
42345 ATTTAAATA
1 ATTTAAATA
42354 ATTTGAAATA
1 ATTT-AAATA
42364 AT
1 AT
42366 CACTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.65
10 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (9 bp):
ATTTAAATA
Found at i:42722 original size:22 final size:21
Alignment explanation
Indices: 42678--42722 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
42668 ATTAATTTTT
**
42678 TAATATTTCTTTTTTTATCAA
1 TAATATTTCTTTTTTTAAAAA
*
42699 TAATATTTTTATTTTTTAAAAA
1 TAATATTTCT-TTTTTTAAAAA
42721 TA
1 TA
42723 TTTAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATATTTCTTTTTTTAAAAA
Found at i:49922 original size:19 final size:20
Alignment explanation
Indices: 49898--49935 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
49888 AATATTACAA
*
49898 ATATTTTTAT-ATTAATTTT
1 ATATTTATATAATTAATTTT
49917 ATATTTATATAATTAATTT
1 ATATTTATATAATTAATTT
49936 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTATATAATTAATTTT
Found at i:49954 original size:18 final size:19
Alignment explanation
Indices: 49928--49965 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
49918 TATTTATATA
49928 ATTAATTTAAATAA-AAAT
1 ATTAATTTAAATAATAAAT
* *
49946 ATTATTTTAATTAATAAAT
1 ATTAATTTAAATAATAAAT
49965 A
1 A
49966 ATGACTCGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTAATTTAAATAATAAAT
Found at i:50097 original size:16 final size:18
Alignment explanation
Indices: 50073--50105 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50063 CTTTTTTAAA
50073 TAAATTTTATT-TTTTAT
1 TAAATTTTATTATTTTAT
50090 TAAA-TTTATTATTTTA
1 TAAATTTTATTATTTTA
50106 CATTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAAATTTTATTATTTTAT
Found at i:50982 original size:25 final size:24
Alignment explanation
Indices: 50954--51016 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
50944 AGATATTTTT
50954 ATAAATTATTTATTTATTGTAAATA
1 ATAAATTATTTATTTATT-TAAATA
* **
50979 ATAATTTAAAT-TTTATTTAAATA
1 ATAAATTATTTATTTATTTAAATA
51002 A-AATATT-TTTATTTA
1 ATAA-ATTATTTATTTA
51017 AAATTTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
22 3 0.10
23 13 0.43
24 6 0.20
25 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATAAATTATTTATTTATTTAAATA
Found at i:51016 original size:23 final size:23
Alignment explanation
Indices: 50956--51016 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
50946 ATATTTTTAT
50956 AAATTATTTATTTATTGTAAATAA
1 AAATT-TTTATTTATTGTAAATAA
* **
50980 TAATTTAAATTTTATT-TAAATAA
1 AAATTTTTA-TTTATTGTAAATAA
51003 AATATTTTTATTTA
1 AA-ATTTTTATTTA
51017 AAATTTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AAATTTTTATTTATTGTAAATAA
Found at i:51042 original size:16 final size:16
Alignment explanation
Indices: 50984--51043 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 16
50974 AAATAATAAT
50984 TTAAATTTTATTTAAA
1 TTAAATTTTATTTAAA
*
51000 TAAAATATTTTTATTTAAAA
1 T-TAA-A-TTTTATTT-AAA
*
51020 TTTAATTTTATTTAAA
1 TTAAATTTTATTTAAA
51036 TTAAATTT
1 TTAAATTT
51044 ATCGAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 11 0.31
17 10 0.28
18 2 0.06
19 9 0.25
20 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAATTTTATTTAAA
Done.