Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1257
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: 106541
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:425 original size:35 final size:37
Alignment explanation
Indices: 380--474 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 37
370 TTTATTTAAG
*
380 TTCGGGTCATTTCGAATTAATATTCGATCATT-TGGA
1 TTCGGGTCATTTCGAATTAAGATTCGATCATTATGGA
* **
416 TTC-GGTCA-TTCGGATTTGGATTCGATCATTATGGA
1 TTCGGGTCATTTCGAATTAAGATTCGATCATTATGGA
* * *
451 TTCGGGTAATTTCGGATTCAGATT
1 TTCGGGTCATTTCGAATTAAGATT
475 GTTAACTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
34 18 0.37
35 12 0.24
36 7 0.14
37 12 0.24
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.41
Consensus pattern (37 bp):
TTCGGGTCATTTCGAATTAAGATTCGATCATTATGGA
Found at i:5161 original size:2 final size:2
Alignment explanation
Indices: 5154--5189 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5144 TTGCTTCTAC
5154 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
5190 GTGGTATTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6758 original size:2 final size:2
Alignment explanation
Indices: 6751--6784 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6741 ACCCTTATTG
6751 CT 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 CT
6785 TTTTGAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8973 original size:19 final size:19
Alignment explanation
Indices: 8949--8988 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8939 TTTACTAGTC
8949 ATTGTGCTACATGAGTTTT
1 ATTGTGCTACATGAGTTTT
8968 ATTGTGCTACATGAGTTTT
1 ATTGTGCTACATGAGTTTT
8987 AT
1 AT
8989 GTGATTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (19 bp):
ATTGTGCTACATGAGTTTT
Found at i:11202 original size:6 final size:6
Alignment explanation
Indices: 11191--11223 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
11181 GTAGAGGTGT
11191 TACATA TACATA TACATA TACATA TACATA TAC
1 TACATA TACATA TACATA TACATA TACATA TAC
11224 GTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (6 bp):
TACATA
Found at i:14454 original size:2 final size:2
Alignment explanation
Indices: 14442--14471 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
14432 CTTAATTTGC
14442 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14472 GTTTGTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16716 original size:29 final size:30
Alignment explanation
Indices: 16662--16721 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
16652 AGTAAAAGAG
16662 ATATTTTAATTTATATATTATTAAAT-TTA
1 ATATTTTAATTTATATATTATTAAATATTA
* * *
16691 ATATTTTAGTTTTTA-ATTTTTAAAATATTA
1 ATATTTTAATTTATATATTATT-AAATATTA
16721 A
1 A
16722 CAAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 17 0.65
30 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
ATATTTTAATTTATATATTATTAAATATTA
Found at i:22544 original size:2 final size:2
Alignment explanation
Indices: 22539--22563 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22529 ATATATATAT
22539 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
22564 ACAAATTAGA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22742 original size:18 final size:18
Alignment explanation
Indices: 22721--22779 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
22711 TGTAATATTT
22721 TAATTAATATAATTATCA
1 TAATTAATATAATTATCA
* *
22739 TAATTGATTGTAA-TATCA
1 TAATT-AATATAATTATCA
*
22757 TTTATT-ATATCAATTATCA
1 -TAATTAATAT-AATTATCA
22776 TAAT
1 TAAT
22780 AAACATAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
17 2 0.06
18 15 0.48
19 14 0.45
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (18 bp):
TAATTAATATAATTATCA
Found at i:22772 original size:37 final size:36
Alignment explanation
Indices: 22709--22779 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 36
22699 TTATTTTATA
22709 ATTGTAATATTTTAATTAATATAATTATCATAATTG
1 ATTGTAATATTTTAATTAATATAATTATCATAATTG
22745 ATTGTAATATCATTT-ATT-ATATCAATTATCATAAT
1 ATTGTAATAT--TTTAATTAATAT-AATTATCATAAT
22780 AAACATAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
36 14 0.44
37 15 0.47
38 3 0.09
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (36 bp):
ATTGTAATATTTTAATTAATATAATTATCATAATTG
Found at i:23423 original size:24 final size:25
Alignment explanation
Indices: 23395--23447 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
23385 TCGATTATCA
23395 ATTTTT-AATTTCA-TACCTA-ATTT
1 ATTTTTCAA-TTCAGTACCTACATTT
*
23418 TTTTTTCAATTCAGTACCTACATTT
1 ATTTTTCAATTCAGTACCTACATTT
23443 ATTTT
1 ATTTT
23448 GTCATGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 9 0.36
24 8 0.32
25 8 0.32
ACGTcount: A:0.26, C:0.15, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTTCAATTCAGTACCTACATTT
Found at i:25199 original size:23 final size:24
Alignment explanation
Indices: 25159--25208 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
25149 AAATAATATA
*
25159 AAAAATTAAAATATAATACA-ACAT
1 AAAAACTAAAATATAATA-AGACAT
*
25183 AAAAACTAACATA-AATAAGACAT
1 AAAAACTAAAATATAATAAGACAT
25206 AAA
1 AAA
25209 TATATGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.04
23 11 0.48
24 11 0.48
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.20
Consensus pattern (24 bp):
AAAAACTAAAATATAATAAGACAT
Found at i:26301 original size:24 final size:23
Alignment explanation
Indices: 26274--26321 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
26264 TAAAGAGTAA
26274 AATAATATAAATATTA-AAAAAATT
1 AATAAT-TAAA-ATTATAAAAAATT
26298 AATAATTAAAATTATAAAAAATT
1 AATAATTAAAATTATAAAAAATT
26321 A
1 A
26322 TATATCAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.17
23 13 0.57
24 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAATTAAAATTATAAAAAATT
Found at i:26334 original size:23 final size:23
Alignment explanation
Indices: 26286--26335 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
26276 TAATATAAAT
*
26286 ATTA-AAAAAATTAATAATTAAA
1 ATTATAAAAAATTAATAATCAAA
*
26308 ATTATAAAAAATT-ATATATCAAG
1 ATTATAAAAAATTAATA-ATCAAA
26331 ATTAT
1 ATTAT
26336 CTCTCAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATTATAAAAAATTAATAATCAAA
Found at i:26543 original size:46 final size:47
Alignment explanation
Indices: 26488--26627 Score: 164
Period size: 46 Copynumber: 3.0 Consensus size: 47
26478 TTAGTATAAA
**
26488 TAATA-AAAAATAATATTTTAATAATTATTGTGA-TATTTTAAAT-TT
1 TAATATAAAAATAATATTTTAATAATTATAAT-ATTATTTTAAATATT
*
26533 TAATATAAAAATAATATTTTAATAATAAATAATATTATTTTAAATATT
1 TAATATAAAAATAATATTTTAATAAT-TATAATATTATTTTAAATATT
* *
26581 TAATATGAATATAATATTTTAA-AATTA-AATATTATTATTAGAATATT
1 TAATATAAAAATAATATTTTAATAATTATAATATTATT-TTA-AATATT
26628 ACTATTTAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
45 14 0.17
46 25 0.30
47 22 0.27
48 22 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (47 bp):
TAATATAAAAATAATATTTTAATAATTATAATATTATTTTAAATATT
Found at i:26554 original size:26 final size:26
Alignment explanation
Indices: 26520--26612 Score: 88
Period size: 26 Copynumber: 3.7 Consensus size: 26
26510 AATTATTGTG
26520 ATATTTTAAATTTTAATATAAAAATA
1 ATATTTTAAATTTTAATATAAAAATA
*
26546 ATATTTT-AA---TAATA-AATAATA
1 ATATTTTAAATTTTAATATAAAAATA
* * *
26567 TTATTTTAAATATTTAATATGAATATA
1 ATATTTTAAAT-TTTAATATAAAAATA
* *
26594 ATATTTTAAAATTAAATAT
1 ATATTTTAAATTTTAATAT
26613 TATTATTAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
21 12 0.23
22 7 0.13
25 2 0.04
26 19 0.36
27 13 0.25
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
ATATTTTAAATTTTAATATAAAAATA
Found at i:26564 original size:18 final size:19
Alignment explanation
Indices: 26529--26575 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
26519 GATATTTTAA
26529 ATTTTAATATAAAAATAAT
1 ATTTTAATATAAAAATAAT
*
26548 ATTTTAATAATAAATAATATT
1 ATTTTAAT-ATAAA-AATAAT
26569 ATTTTAA
1 ATTTTAA
26576 ATATTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 8 0.32
20 5 0.20
21 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTAATATAAAAATAAT
Found at i:26580 original size:30 final size:27
Alignment explanation
Indices: 26545--26612 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
26535 ATATAAAAAT
*
26545 AATATTTTAATAATAAATAATATTATTTTA
1 AATA-TTTAAT-ATAAAT-ATAATATTTTA
*
26575 AATATTTAATATGAATATAATATTTTA
1 AATATTTAATATAAATATAATATTTTA
*
26602 AA-ATTAAATAT
1 AATATTTAATAT
26613 TATTATTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.23
27 12 0.34
28 5 0.14
29 6 0.17
30 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
AATATTTAATATAAATATAATATTTTA
Found at i:26602 original size:48 final size:47
Alignment explanation
Indices: 26488--26619 Score: 148
Period size: 48 Copynumber: 2.8 Consensus size: 47
26478 TTAGTATAAA
**
26488 TAATA-AAAAATAATATTTTAATAATT--ATTGTGA-TATTTTAAATTT
1 TAATATAAAAATAATATTTTAA-AATTAAATAAT-ATTATTTTAAATTT
26533 TAATATAAAAATAATATTTTAATAA-TAAATAATATTATTTTAAATATT
1 TAATATAAAAATAATATTTTAA-AATTAAATAATATTATTTTAAAT-TT
* * *
26581 TAATATGAATATAATATTTTAAAATTAAATATTATTATT
1 TAATATAAAAATAATATTTTAAAATTAAATAATATTATT
26620 AGAATATTAC
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
45 6 0.08
46 20 0.26
47 15 0.20
48 35 0.46
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (47 bp):
TAATATAAAAATAATATTTTAAAATTAAATAATATTATTTTAAATTT
Found at i:26650 original size:14 final size:14
Alignment explanation
Indices: 26607--26661 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
26597 TTTTAAAATT
*
26607 AAATATTATTATTA
1 AAATATTAATATTA
* *
26621 GAATATTACTATTTA
1 AAATATTAATA-TTA
26636 AAATATTAATATTA
1 AAATATTAATATTA
26650 AAA-ATTAATATT
1 AAATATTAATATT
26662 TTAATAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 9 0.25
14 15 0.42
15 12 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (14 bp):
AAATATTAATATTA
Found at i:26657 original size:21 final size:21
Alignment explanation
Indices: 26633--26672 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
26623 ATATTACTAT
*
26633 TTAAAATATTAATATTAAAAA
1 TTAAAATATTAATAATAAAAA
* *
26654 TTAATATTTTAATAATAAA
1 TTAAAATATTAATAATAAA
26673 TAGTTTTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATATTAATAATAAAAA
Found at i:26665 original size:29 final size:29
Alignment explanation
Indices: 26607--26662 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
26597 TTTTAAAATT
* * *
26607 AAATATTATTATTAGAATATTACTATTTA
1 AAATATTAATATTAGAAAATTAATATTTA
26636 AAATATTAATATTA-AAAATTAATATTT
1 AAATATTAATATTAGAAAATTAATATTT
26663 TAATAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
AAATATTAATATTAGAAAATTAATATTTA
Found at i:33052 original size:70 final size:69
Alignment explanation
Indices: 32919--33051 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 69
32909 ATTTTTTAAA
** *
32919 TTAATTAAATTTAAAAAATTTAATAAATAATAATGTATTAATTATTATTTTTTAATAAAAAAATA
1 TTAATTAAATTTAAAAAATTTAATAAATAATAAAATATTAATTATTATTTTTAAATAAAAAAATA
32984 ATAT
66 ATAT
* *
32988 TTAATTAAATTTTTAAAAATTTATATTAATAAATTAAAATATTAATTA-T-TTTTTAAATAAAAA
1 TTAATTAAA-TTTAAAAAATTTA-ATAAAT-AA-TAAAATATTAATTATTATTTTTAAATAAAAA
33051 A
62 A
33052 TTAAATTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
69 9 0.16
70 12 0.22
71 19 0.35
72 3 0.05
73 12 0.22
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (69 bp):
TTAATTAAATTTAAAAAATTTAATAAATAATAAAATATTAATTATTATTTTTAAATAAAAAAATA
ATAT
Found at i:33101 original size:113 final size:107
Alignment explanation
Indices: 32954--33246 Score: 318
Period size: 113 Copynumber: 2.7 Consensus size: 107
32944 AATAATAATG
*
32954 TATTAATTATTATTTTTTAAT-AAA-AAAATAATATTTAATTAAATTTTTAAAAATTTATATTAA
1 TATT-ATTATTA-TTTTTAATAAAATAAAAT-ATATTTAATTAAATTTTTAAAAATTTACATTAA
*
33017 TAAATTAAAATATTAA-TTAT-TTTTTAAATAAAAAATTAAATTAAAAGGATT
63 CAAATTAAAATATTAATTTATGTTTTT--AT-AAAAA-T--A--AAAAGGATT
*
33068 TATTATTATTATTTTTAATAAAATTAAAAATATTATTTAATT-AA-GTTTAAAAA-TTACATTAA
1 TATTATTATTATTTTTAATAAAA-T-AAAATA-TATTTAATTAAATTTTTAAAAATTTACATTAA
*
33130 CAAATTAAAATATTAATTTTATGTTTTTATAAAAATAAAAAGTATT
63 CAAATTAAAATATTAA-TTTATGTTTTTATAAAAATAAAAAGGATT
*
33176 TATTATTA-T-TTTTTAATAAAATAAAAATGATATTTAATTAAATTTTAAAAAATTT-CATTAAC
1 TATTATTATTATTTTTAATAAAAT-AAAAT-ATATTTAATTAAATTTTTAAAAATTTACATTAAC
33238 AAATTAAAA
64 AAATTAAAA
33247 ATAACATTTA
Statistics
Matches: 161, Mismatches: 6, Indels: 31
0.81 0.03 0.16
Matches are distributed among these distances:
105 16 0.10
106 15 0.09
107 24 0.15
108 18 0.11
110 1 0.01
112 9 0.06
113 38 0.24
114 14 0.09
115 7 0.04
116 19 0.12
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (107 bp):
TATTATTATTATTTTTAATAAAATAAAATATATTTAATTAAATTTTTAAAAATTTACATTAACAA
ATTAAAATATTAATTTATGTTTTTATAAAAATAAAAAGGATT
Found at i:33189 original size:32 final size:32
Alignment explanation
Indices: 33131--33211 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 32
33121 TTACATTAAC
* *
33131 AAATTAAAA-TATTAATTTTATGTTTTT-ATAA
1 AAATAAAAAGTATTTATTTTATGTTTTTAAT-A
33162 AAATAAAAAGTATTTATTATTAT-TTTTTAATA
1 AAATAAAAAGTATTTATT-TTATGTTTTTAATA
33194 AAATAAAAATGATATTTA
1 AAATAAAAA-G-TATTTA
33212 ATTAAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 8 0.19
32 22 0.51
33 7 0.16
34 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (32 bp):
AAATAAAAAGTATTTATTTTATGTTTTTAATA
Found at i:33222 original size:32 final size:30
Alignment explanation
Indices: 33154--33228 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
33144 AATTTTATGT
**
33154 TTTTATAAAAATAAAAAGTATTTATTATTATT
1 TTTTA-AAAAATAAAAAGTATTTA-TATTAAA
33186 TTTTAATAAAATAAAAATGATATTTA-ATTAAA
1 TTTTAA-AAAATAAAAA-G-TATTTATATTAAA
33218 TTTTAAAAAAT
1 TTTTAAAAAAT
33229 TTCATTAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 6 0.16
32 25 0.66
33 1 0.03
34 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTTAAAAAATAAAAAGTATTTATATTAAA
Found at i:33257 original size:21 final size:19
Alignment explanation
Indices: 33233--33275 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
33223 AAAAATTTCA
33233 TTAACAAATTAAAAATAACAT
1 TTAACAAATTAAAAA-AA-AT
**
33254 TTAAGGAATTAAAAAAAAT
1 TTAACAAATTAAAAAAAAT
33273 TTA
1 TTA
33276 TCATTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
TTAACAAATTAAAAAAAAT
Found at i:33745 original size:106 final size:107
Alignment explanation
Indices: 33565--33778 Score: 319
Period size: 107 Copynumber: 2.0 Consensus size: 107
33555 TTTTTTATTT
*
33565 TAAAAATATAATAATTAATATTTTAATTTGTTAATGTAAATTTTTAAACTTAATTAAATATTATT
1 TAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTTAAACTTAATTAAATATTATT
* * *
33630 TTTTATTTATT-AAAAATTATAATAAAACATCTTTTTATTTTTA
66 TTTAATTTATTAAAAAATAATAATAAAACA--GTTTTATTTTTA
*
33673 TAAAAACATAATAA-TAATATTTTAATTTGTTAATGT-AATTTTTAAACTTAATTATATA-TATT
1 TAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTTAAACTTAATTAAATATTATT
*
33735 TTTAATTTTATTAAAAAATAATAATAAACCAGTTTTATTTTTA
66 TTTAA-TTTATTAAAAAATAATAATAAAACAGTTTTATTTTTA
33778 T
1 T
33779 TTAAATTTTT
Statistics
Matches: 98, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
105 20 0.20
106 27 0.28
107 38 0.39
108 13 0.13
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.50
Consensus pattern (107 bp):
TAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTTAAACTTAATTAAATATTATT
TTTAATTTATTAAAAAATAATAATAAAACAGTTTTATTTTTA
Found at i:34563 original size:91 final size:92
Alignment explanation
Indices: 34357--34704 Score: 546
Period size: 91 Copynumber: 3.8 Consensus size: 92
34347 TAATGTATAA
* * * *
34357 ATTGTAAATGTCAGACTG-TAAGAAATAGACTAATGCATGATTTATATTTGAGAATCAGATTCTT
1 ATTGTAAATGTCAGACTGCAAAG-ATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTT
34421 TTTTATAGAAAAAAAGAAAAGTTGATTG
65 TTTTATAGAAAAAAAGAAAAGTTGATTG
* *
34449 ATTGTAAATATCAGACTGTAAAGATTAGACTAATGCATGAATTATATCTGAGAATCA-ATTCTTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTT
34513 TTTATAGAAAAAAAGAAAAGTTGATTG
66 TTTATAGAAAAAAAGAAAAGTTGATTG
* * * *
34540 ATTGTAAATGTAAAACTGCAAAGATTAGACTAATGCATTAATTATATCTAAGAATCAGATT-TTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTT
34604 TTTAT-GAAAAAAAAGAAAAGTTGATTG
66 TTTATAG-AAAAAAAGAAAAGTTGATTG
34631 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTA-ATCTGAGAATCA-ATTCTTT
1 ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTT
34694 TTTATAGAAAA
66 TTTATAGAAAA
34705 GAACTTTTTG
Statistics
Matches: 236, Mismatches: 15, Indels: 12
0.90 0.06 0.05
Matches are distributed among these distances:
89 3 0.01
90 24 0.10
91 155 0.66
92 51 0.22
93 3 0.01
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.34
Consensus pattern (92 bp):
ATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTT
TTTATAGAAAAAAAGAAAAGTTGATTG
Found at i:35868 original size:11 final size:12
Alignment explanation
Indices: 35845--35880 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
35835 AAATTTGTGT
35845 AATTTATAAATA
1 AATTTATAAATA
35857 AATTTA-AAAT-
1 AATTTATAAATA
35867 AATTTATAAATA
1 AATTTATAAATA
35879 AA
1 AA
35881 AAGTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.27
11 8 0.36
12 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTTATAAATA
Found at i:36144 original size:46 final size:44
Alignment explanation
Indices: 36093--36222 Score: 115
Period size: 43 Copynumber: 2.9 Consensus size: 44
36083 CAATTATAAA
*
36093 AATAATACATGTAAAATATTAATTAATTTTAATAAAAATAAATTT
1 AATAATACATGTAAAATATTAATTAATTTTAATAAAAATAAA-AT
* ** * * *
36138 GTATAATTTATAGATAAATTA-AAAATAA-TTT-ATAAATAA-AAAAT
1 -AATAATACAT-G-TAAAATATTAATTAATTTTAATAAA-AATAAAAT
*
36182 AATAATACATGTACAATATTAATTAATTTTAATAAAAATAA
1 AATAATACATGTAAAATATTAATTAATTTTAATAAAAATAA
36223 TACATGTACA
Statistics
Matches: 63, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
41 5 0.08
42 6 0.10
43 12 0.19
44 8 0.13
45 8 0.13
46 12 0.19
47 6 0.10
48 6 0.10
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (44 bp):
AATAATACATGTAAAATATTAATTAATTTTAATAAAAATAAAAT
Found at i:36201 original size:297 final size:295
Alignment explanation
Indices: 35642--36297 Score: 1001
Period size: 296 Copynumber: 2.2 Consensus size: 295
35632 AAGTTGAGGA
* * *
35642 AAATTTTTTCTTTGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCGTTATCGAAAAATGA
1 AAATTTTTTCTTGGTCATTTTACAGATAAAG-AAAGCTCGTATTTAAGTCGTTACCGAAAAATAA
* * * * **
35707 AATGTGTGCGTCTGTAAATCCGAAATAAATCGTTATAAAAAAACTAATTTATTGTTGGCTAACAT
65 AATATGTACGTCTGTAAATCCAAAATAAATCATTATAAAAAAACTAAAATATTGTTGGCTAACAT
*
35772 AAATTTAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAAAAAAATAA
130 AAATTTAAGTTCTATCAATTATAAAAATAATACATGTAAAATATTAATTAATTTTAAAAAAATAA
* * * *
35837 ATTTGTGTAATTTATAAATAAATTTAAAATAATTTATAAATAAAAAGTAATAATTCATGTACAAT
195 ATTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAATAATAATACATGTACAAT
* *
35902 ATTAATCAATTTTAATAAAAATAATACTTGTATAAT
260 ATTAATCAATTTTAATAAAAATAATACATGTACAAT
35938 AAATTTTTT-TTGGTCATTTTACAGATAAAGGAAAGCTCGTATTTAAGTCGTTACCGAAAAATAA
1 AAATTTTTTCTTGGTCATTTTACAGATAAA-GAAAGCTCGTATTTAAGTCGTTACCGAAAAATAA
* * * * * *
36002 AATATGTACGTCTGTAAATTCAAAATAAGTCATTATTGAAAAAAGTAAAATATTTTTGGTTAACA
65 AATATGTACGTCTGTAAATCCAAAATAAATCATTA-TAAAAAAACTAAAATATTGTTGGCTAACA
36067 TAAATTTAAGTTCTATCAATTATAAAAATAATACATGTAAAATATTAATTAATTTTAATAAAAAT
129 TAAATTTAAGTTCTATCAATTATAAAAATAATACATGTAAAATATTAATTAATTTTAA-AAAAAT
*
36132 AAATTTGTATAATTTATAGATAAATTAAAAATAATTTATAAATAAAAAATAATAATACATGTACA
193 AAATTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAATAATAATACATGTACA
*
36197 ATATTAATTAATTTTAATAAAAATAATACATGTACAAT
258 ATATTAATCAATTTTAATAAAAATAATACATGTACAAT
* * * **
36235 ACATTTTTTCTTGGTCATTTTACAGATAAA-AAAACTTGTATTTAAGTCGTTACAAAAAAATAA
1 AAATTTTTTCTTGGTCATTTTACAGATAAAGAAAGCTCGTATTTAAGTCGTTACCGAAAAATAA
36298 TACATGTAAA
Statistics
Matches: 327, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
295 79 0.24
296 119 0.36
297 109 0.33
298 20 0.06
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (295 bp):
AAATTTTTTCTTGGTCATTTTACAGATAAAGAAAGCTCGTATTTAAGTCGTTACCGAAAAATAAA
ATATGTACGTCTGTAAATCCAAAATAAATCATTATAAAAAAACTAAAATATTGTTGGCTAACATA
AATTTAAGTTCTATCAATTATAAAAATAATACATGTAAAATATTAATTAATTTTAAAAAAATAAA
TTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAATAATAATACATGTACAATA
TTAATCAATTTTAATAAAAATAATACATGTACAAT
Found at i:36364 original size:22 final size:22
Alignment explanation
Indices: 36322--36364 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
36312 AATTTAATAA
* *
36322 AAATAAATTAAATTAATTTTAT
1 AAATAAATAAAATTAACTTTAT
36344 AAATAAA-AAAATTATACTTTA
1 AAATAAATAAAATTA-ACTTTA
36365 AAAAAGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATAAATAAAATTAACTTTAT
Found at i:36533 original size:9 final size:9
Alignment explanation
Indices: 36519--36556 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
36509 TTAATATATT
36519 ATTTATTAA
1 ATTTATTAA
36528 ATTTATTAA
1 ATTTATTAA
36537 ATTTAATTAA
1 ATTT-ATTAA
*
36547 TTTTATTAA
1 ATTTATTAA
36556 A
1 A
36557 AGATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTTATTAA
Found at i:36551 original size:19 final size:18
Alignment explanation
Indices: 36519--36556 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
36509 TTAATATATT
36519 ATTTATTAAATTTATTAA
1 ATTTATTAAATTTATTAA
*
36537 ATTTAATTAATTTTATTAA
1 ATTT-ATTAAATTTATTAA
36556 A
1 A
36557 AGATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTATTAAATTTATTAA
Found at i:38163 original size:2 final size:2
Alignment explanation
Indices: 38156--38184 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38146 TTATTTGTTT
38156 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 T
38185 CAAGCAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44471 original size:58 final size:59
Alignment explanation
Indices: 44391--45007 Score: 266
Period size: 59 Copynumber: 10.6 Consensus size: 59
44381 GACTTAGGTT
* * *
44391 TTTCATGTCA-TTTCATTTCATTTAGGTCATTTTCCTTGACTTAGAGACTTTGATAC-AA
1 TTTCATGT-ATTTTGATATCATTTAGGTCATTTTCCATGACTTAGAGACTTTGATACAAA
* * * *
44449 TATCATGCATTTTGATATCATTTAAGTCATTTTCCATGA-TGTA-AGAACTTTCG-TGCAAA
1 TTTCATGTATTTTGATATCATTTAGGTCATTTTCCATGACT-TAGAG-ACTTT-GATACAAA
* * * * * * * * *
44508 TTTTATATAGTTTT-ATGTCATTTAGATCATTTTTCATGACTTAGGGACTTTAATGCAAT
1 TTTCATGTA-TTTTGATATCATTTAGGTCATTTTCCATGACTTAGAGACTTTGATACAAA
* * * *
44567 TTTACA--TATTTTGATGTCATTTACGTCATTTTTCATGATTTAGAGACTTTGATACAAA
1 TTT-CATGTATTTTGATATCATTTAGGTCATTTTCCATGACTTAGAGACTTTGATACAAA
* * * * * * * * *
44625 TTTCATGTATGTTGAGATTATTTAGGCCATTTTCAATCACTTAGGGAC--TAATTACGTAA
1 TTTCATGTATTTTGATATCATTTAGGTCATTTTCCATGACTTAGAGACTTTGA-TAC-AAA
* *** * * * *
44684 TTTCATGTATATTGGGGTCATTTAGGTTATTTTTCATGA-TCTAGA-ACTTTAATGC-AA
1 TTTCATGTATTTTGATATCATTTAGGTCATTTTCCATGACT-TAGAGACTTTGATACAAA
* * *** * * * **
44741 TTTCATATATGTTAGGGGTCATTTAGGTCATTTTCTATGA-TCTAGGGACTTTCACGCAAA
1 TTTCATGTAT-TTTGATATCATTTAGGTCATTTTCCATGACT-TAGAGACTTTGATACAAA
* * * * * * * *
44801 TTTCATGTATTTTAATGTCACTTAAGTCATTTTTCATGACCT-GAGACTTTAATGC-AA
1 TTTCATGTATTTTGATATCATTTAGGTCATTTTCCATGACTTAGAGACTTTGATACAAA
* ** * * ** * * **
44858 TTTTATACATTTTGATGTCATTTAGGTTATTTTTTTATGATCTAAG-GACTTTGGT-GTAA
1 TTTCATGTATTTTGATATCATTTAGGTCA-TTTTCCATGA-CTTAGAGACTTTGATACAAA
* * * * * * * **
44917 TTTCATTTATTTTGATGTCATTTAGGTTATTTTCCATAATTTTGAGACTTTCAT-GTAA
1 TTTCATGTATTTTGATATCATTTAGGTCATTTTCCATGACTTAGAGACTTTGATACAAA
* * *
44975 TTTCATGAATTTTAGAGAT-ATTTAAGTCATTTT
1 TTTCATGTATTTT-GATATCATTTAGGTCATTTT
45008 ACATTATTTA
Statistics
Matches: 429, Mismatches: 102, Indels: 56
0.73 0.17 0.10
Matches are distributed among these distances:
57 49 0.11
58 178 0.41
59 180 0.42
60 22 0.05
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (59 bp):
TTTCATGTATTTTGATATCATTTAGGTCATTTTCCATGACTTAGAGACTTTGATACAAA
Found at i:44616 original size:117 final size:115
Alignment explanation
Indices: 44408--44988 Score: 360
Period size: 117 Copynumber: 5.0 Consensus size: 115
44398 TCATTTCATT
* * * * * *
44408 TCATTTAGGTCATTTTCCTTGACTTAGAGACTTTGATACAA-TAT-CATGCATTTTGATATCATT
1 TCATTTAGGTCATTTTTCATGACTTAGGGACTTTGATGCAATTTTACAT--ATTTTGATGTCATT
* * ** *
44471 TAAGTCATTTTCCATGATGTA-AGAACTTTCGTGCAAATTTTATATAGTTTTATG
64 TAAGTCATTTTTCATGATCTAGAG-ACTTTAATGC-AATTTCATATA-TTTTATG
* *
44525 TCATTTAGATCATTTTTCATGACTTAGGGACTTTAATGCAATTTTACATATTTTGATGTCATTTA
1 TCATTTAGGTCATTTTTCATGACTTAGGGACTTTGATGCAATTTTACATATTTTGATGTCATTTA
* * * * * *
44590 CGTCATTTTTCATGATTTAGAGACTTTGATACAAATTTCATGTATGTTGA-G
66 AGTCATTTTTCATGATCTAGAGACTTTAATGC-AATTTCATATAT-TTTATG
* * * * * * ** * **
44641 ATTATTTAGGCCA-TTTTCAATCACTTAGGGACTAATT-ACGTAATTTCATGTATATTGGGGTCA
1 -TCATTTAGGTCATTTTTC-ATGACTTAGGGACT--TTGATGCAATTTTACATATTTTGATGTCA
* * * *
44704 TTTAGGTTATTTTTCATGATCTAGA-ACTTTAATGCAATTTCATATATGTTAGGGG
62 TTTAAGTCATTTTTCATGATCTAGAGACTTTAATGCAATTTCATATATTTTA--TG
* * * *
44759 TCATTTAGGTCA-TTTTCTATGA-TCTAGGGACTTTCACGCAAATTT-CATGTATTTTAATGTCA
1 TCATTTAGGTCATTTTTC-ATGACT-TAGGGACTTTGATGCAATTTTACA--TATTTTGATGTCA
* * * *
44821 CTTAAGTCATTTTTCATGACCT-GAGACTTTAATGCAATTTTATACATTTTGATG
62 TTTAAGTCATTTTTCATGATCTAGAGACTTTAATGCAATTTCATATATTTT-ATG
* * * * * * **
44875 TCATTTAGGTTATTTTTTTATGA-TCTAAGGACTTTGGTGTAATTTCATTTATTTTGATGTCATT
1 TCATTTAGGTCA-TTTTTCATGACT-TAGGGACTTTGATGCAATTTTACATATTTTGATGTCATT
* * * * * * * *
44939 TAGGTTATTTTCCATAATTTTGAGACTTTCATGTAATTTCATGA-ATTTTA
64 TAAGTCATTTTTCATGATCTAGAGACTTTAATGCAATTTCAT-ATATTTTA
44989 GAGATATTTA
Statistics
Matches: 362, Mismatches: 80, Indels: 45
0.74 0.16 0.09
Matches are distributed among these distances:
115 4 0.01
116 68 0.19
117 234 0.65
118 51 0.14
119 5 0.01
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (115 bp):
TCATTTAGGTCATTTTTCATGACTTAGGGACTTTGATGCAATTTTACATATTTTGATGTCATTTA
AGTCATTTTTCATGATCTAGAGACTTTAATGCAATTTCATATATTTTATG
Found at i:44929 original size:59 final size:58
Alignment explanation
Indices: 44408--44949 Score: 305
Period size: 59 Copynumber: 9.3 Consensus size: 58
44398 TCATTTCATT
* * * * * * * ** *
44408 TCATTTAGGTCATTTTCCTTGA-CTTAGAGACTTTGATACAATATCATGCATTTTGATA
1 TCATTTAGGTTATTTTTCATGATCTAAG-GACTTTAATGCAATTTCATATATTTTGATG
* * * * * ** *
44466 TCATTTAAGTCATTTTCCATGATGTAAGAACTTTCGTGCAAATTTTATATAGTTTT-ATG
1 TCATTTAGGTTATTTTTCATGATCTAAGGACTTTAATGC-AATTTCATATA-TTTTGATG
* * * * *
44525 TCATTTAGATCATTTTTCATGA-CTTAGGGACTTTAATGCAATTTTACATATTTTGATG
1 TCATTTAGGTTATTTTTCATGATC-TAAGGACTTTAATGCAATTTCATATATTTTGATG
* * * * * * *
44583 TCATTTACGTCATTTTTCATGAT-TTAGAGACTTTGATACAAATTTCATGTATGTTGA-G
1 TCATTTAGGTTATTTTTCATGATCTAAG-GACTTTAATGC-AATTTCATATATTTTGATG
* ** * * * * * * **
44641 ATTATTTAGGCCA-TTTTCAATCA-CTTAGGGACTAATT-ACGTAATTTCATGTATATTGGGG
1 -TCATTTAGGTTATTTTTC-ATGATC-TAAGGACT--TTAATGCAATTTCATATATTTTGATG
* * **
44701 TCATTTAGGTTATTTTTCATGATCT-AGAACTTTAATGCAATTTCATATATGTTAGGGG
1 TCATTTAGGTTATTTTTCATGATCTAAGGACTTTAATGCAATTTCATATAT-TTTGATG
* * * * * *
44759 TCATTTAGGTCA-TTTTCTATGATCTAGGGACTTTCACGCAAATTTCATGTATTTTAATG
1 TCATTTAGGTTATTTTTC-ATGATCTAAGGACTTTAATGC-AATTTCATATATTTTGATG
* * * * * * *
44818 TCACTTAAGTCATTTTTCATGACCTGA-GACTTTAATGCAATTTTATACATTTTGATG
1 TCATTTAGGTTATTTTTCATGATCTAAGGACTTTAATGCAATTTCATATATTTTGATG
* ** * *
44875 TCATTTAGGTTATTTTTTTATGATCTAAGGACTTTGGTGTAATTTCATTTATTTTGATG
1 TCATTTAGGTTA-TTTTTCATGATCTAAGGACTTTAATGCAATTTCATATATTTTGATG
44934 TCATTTAGGTTATTTT
1 TCATTTAGGTTATTTT
44950 CCATAATTTT
Statistics
Matches: 372, Mismatches: 87, Indels: 50
0.73 0.17 0.10
Matches are distributed among these distances:
56 2 0.01
57 48 0.13
58 127 0.34
59 163 0.44
60 30 0.08
61 2 0.01
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (58 bp):
TCATTTAGGTTATTTTTCATGATCTAAGGACTTTAATGCAATTTCATATATTTTGATG
Found at i:51135 original size:22 final size:22
Alignment explanation
Indices: 51110--51158 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
51100 GCTTTGCCTT
*
51110 TTTTTAAGCAAAAAAGAAATCA
1 TTTTCAAGCAAAAAAGAAATCA
*
51132 TTTTCGAGCAAAAAAGAAATCA
1 TTTTCAAGCAAAAAAGAAATCA
51154 TTTTC
1 TTTTC
51159 TATGATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (22 bp):
TTTTCAAGCAAAAAAGAAATCA
Found at i:51955 original size:31 final size:30
Alignment explanation
Indices: 51908--51966 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
51898 TATTATGTAA
51908 TTATATAAATTAATATATTAATA-ATTTAT
1 TTATATAAATTAATATATTAATATATTTAT
*
51937 TTATATAAATTTTAATATATTTATATATTT
1 TTATATAAA--TTAATATATTAATATATTT
51967 GAATCATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.35
31 13 0.50
32 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTATATAAATTAATATATTAATATATTTAT
Found at i:51957 original size:20 final size:18
Alignment explanation
Indices: 51929--52046 Score: 68
Period size: 19 Copynumber: 6.5 Consensus size: 18
51919 AATATATTAA
*
51929 TAATTTATTTATATAAATTT
1 TAATATATTTATAT--ATTT
51949 TAATATATTTATATATTT
1 TAATATATTTATATATTT
* *
51967 GAATCATATTTATATTTTT
1 TAAT-ATATTTATATATTT
*
51986 TAA-A-ATTATATTATAATT
1 TAATATATT-TA-TATATTT
52004 TAAT-TA-TTAT-T-TTT
1 TAATATATTTATATATTT
* * *
52018 ATATTATATTTTTATATTA
1 -TAATATATTTATATATTT
52037 TAATAATATT
1 TAAT-ATATT
52047 AAAATTCATA
Statistics
Matches: 76, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
14 2 0.03
15 4 0.05
16 6 0.08
17 8 0.11
18 20 0.26
19 23 0.30
20 13 0.17
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (18 bp):
TAATATATTTATATATTT
Found at i:52027 original size:13 final size:13
Alignment explanation
Indices: 51991--52038 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
51981 TTTTTTAAAA
*
51991 TTATATTATA-AT
1 TTATATTATATTT
52003 TTA-ATTATTATTT
1 TTATATTA-TATTT
52016 TTATATTATATTT
1 TTATATTATATTT
52029 TTATATTATA
1 TTATATTATA
52039 ATAATATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 4 0.12
12 5 0.16
13 19 0.59
14 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATATTATATTT
Found at i:52622 original size:20 final size:20
Alignment explanation
Indices: 52580--52622 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
52570 ATTTAATCTT
**
52580 TAATTTAATAAATTTAATGA
1 TAATTTAATAAATTTAAAAA
*
52600 TAATTTAATAATTTTAAAAA
1 TAATTTAATAAATTTAAAAA
52620 TAA
1 TAA
52623 ATATTATCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TAATTTAATAAATTTAAAAA
Found at i:52663 original size:13 final size:14
Alignment explanation
Indices: 52637--52672 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
52627 TATCTAAAAT
52637 TTTTAAAAATATAA
1 TTTTAAAAATATAA
52651 TTTTAAAAA-ATAA
1 TTTTAAAAATATAA
52664 TTATTAAAA
1 TT-TTAAAA
52673 TAAATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:52677 original size:16 final size:14
Alignment explanation
Indices: 52637--52683 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 14
52627 TATCTAAAAT
*
52637 TTTTAAAAATATAA
1 TTTTAAAAAAATAA
52651 TTTT-AAAAAATAA
1 TTTTAAAAAAATAA
52664 TTATTAAAATAAATATA
1 TT-TTAAAA-AAATA-A
52681 TTT
1 TTT
52684 ATTTTATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.36
14 6 0.21
15 3 0.11
16 6 0.21
17 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTTAAAAAAATAA
Found at i:53614 original size:27 final size:28
Alignment explanation
Indices: 53576--53631 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
53566 AACAATAAAC
53576 TGGCTAATCAAGTTTATCCT-AATTTTT
1 TGGCTAATCAAGTTTATCCTAAATTTTT
*
53603 TGGCTAATCAAGTTTATCGTAAATTTTT
1 TGGCTAATCAAGTTTATCCTAAATTTTT
53631 T
1 T
53632 TTTATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (28 bp):
TGGCTAATCAAGTTTATCCTAAATTTTT
Found at i:53880 original size:19 final size:20
Alignment explanation
Indices: 53833--53888 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 20
53823 ATAATTTTTT
*
53833 ATATGATTAATATTTTAATAA
1 ATATAATTAA-ATTTTAATAA
53854 ATTAATAATTAAATTTTAAT-A
1 A-T-ATAATTAAATTTTAATAA
*
53875 ATATAATTATATTT
1 ATATAATTAAATTT
53889 ATTATGCACG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 11 0.35
20 1 0.03
21 3 0.10
22 9 0.29
23 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATAATTAAATTTTAATAA
Found at i:54897 original size:16 final size:16
Alignment explanation
Indices: 54858--54897 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
54848 ATCGATATTA
*
54858 TTTTATTTTGATATAT
1 TTTTATATTGATATAT
* *
54874 ATTAATATTGATATAT
1 TTTTATATTGATATAT
54890 TTTTATAT
1 TTTTATAT
54898 ATCATTTTAG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTATATTGATATAT
Found at i:55006 original size:27 final size:27
Alignment explanation
Indices: 54976--55027 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
54966 ATAATGATAT
*
54976 ATTATATAAATATGTAAATATATTTTA
1 ATTATATAAATATATAAATATATTTTA
** *
55003 ATTATATTTATATATATATATATTT
1 ATTATATAAATATATAAATATATTT
55028 ATATGAAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
ATTATATAAATATATAAATATATTTTA
Found at i:55409 original size:3 final size:3
Alignment explanation
Indices: 55401--55430 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55391 TGTGAAGATG
55401 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55431 GTGATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:56118 original size:22 final size:20
Alignment explanation
Indices: 56080--56120 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
56070 AATATATTAT
56080 TTAAAAATAAAATAAAATAA
1 TTAAAAATAAAATAAAATAA
56100 TTAAAAATAATTAATAAAATA
1 TTAAAAATAA--AATAAAATA
56121 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TTAAAAATAAAATAAAATAA
Found at i:57438 original size:15 final size:16
Alignment explanation
Indices: 57403--57442 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
57393 CATGGAATGT
*
57403 AATGAAAGAGAGAAGA
1 AATGAAAGAGAGAAAA
57419 AATGAAAGAGA-AAAA
1 AATGAAAGAGAGAAAA
57434 AATGAAAGA
1 AATGAAAGA
57443 AAATTTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.68, C:0.00, G:0.25, T:0.07
Consensus pattern (16 bp):
AATGAAAGAGAGAAAA
Found at i:58097 original size:22 final size:22
Alignment explanation
Indices: 58052--58097 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
58042 TTTCTTGTCA
* *
58052 TATATTAATTTATCTCATATTT
1 TATATTAATTTATCTAATAATT
58074 TATA-TAATTTATCATAATAATT
1 TATATTAATTTATC-TAATAATT
58096 TA
1 TA
58098 ATTTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (22 bp):
TATATTAATTTATCTAATAATT
Found at i:58484 original size:14 final size:16
Alignment explanation
Indices: 58455--58487 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
58445 TTTTATATTA
58455 ATATTTGAATTAAAAT
1 ATATTTGAATTAAAAT
58471 ATATTT-AATT-AAAT
1 ATATTTGAATTAAAAT
58485 ATA
1 ATA
58488 ATATCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 4 0.24
16 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATTTGAATTAAAAT
Found at i:58782 original size:12 final size:12
Alignment explanation
Indices: 58764--58793 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
58754 ACATAATCCT
58764 CTCCCATTCCCA
1 CTCCCATTCCCA
*
58776 TTCCCATTCCCA
1 CTCCCATTCCCA
58788 CTCCCA
1 CTCCCA
58794 CATGGGATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.17, C:0.57, G:0.00, T:0.27
Consensus pattern (12 bp):
CTCCCATTCCCA
Found at i:59028 original size:18 final size:18
Alignment explanation
Indices: 58989--59030 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
58979 CTATGTTTAA
* *
58989 TATTAATATTAATATATG
1 TATTAATATTAATAGATC
*
59007 TATTAATATTAATAGCTC
1 TATTAATATTAATAGATC
59025 TATTAA
1 TATTAA
59031 ATGCCAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (18 bp):
TATTAATATTAATAGATC
Found at i:59442 original size:21 final size:23
Alignment explanation
Indices: 59418--59461 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
59408 ACAAGAAAAA
59418 ATAAT-TTT-AAAATTCAGATAT
1 ATAATATTTCAAAATTCAGATAT
*
59439 ATAATATTTCAAAATTTAGATAT
1 ATAATATTTCAAAATTCAGATAT
59462 TATTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (23 bp):
ATAATATTTCAAAATTCAGATAT
Found at i:68046 original size:16 final size:16
Alignment explanation
Indices: 68025--68058 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
68015 TATAAATATA
*
68025 ATTTTTCATTATAATT
1 ATTTTTCAATATAATT
*
68041 ATTTTTTAATATAATT
1 ATTTTTCAATATAATT
68057 AT
1 AT
68059 AATAGATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTCAATATAATT
Found at i:71775 original size:19 final size:19
Alignment explanation
Indices: 71751--71799 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
71741 CTTAACATAT
*
71751 TATTTTAATTTCACTTTGA
1 TATTTTAATTTCACCTTGA
71770 TATTTTAATTTCACCTTGA
1 TATTTTAATTTCACCTTGA
* *
71789 TCTTTCAATTT
1 TATTTTAATTT
71800 TTAGTTGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.57
Consensus pattern (19 bp):
TATTTTAATTTCACCTTGA
Found at i:74012 original size:26 final size:27
Alignment explanation
Indices: 73983--74041 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
73973 TTCACTTTTT
73983 TTTTATAAATA-AAATT-TTTTAATAAA
1 TTTTATAAATATAAATTATTTT-ATAAA
* *
74009 TTTTA-AAATATATATTATTTTATTAA
1 TTTTATAAATATAAATTATTTTATAAA
74035 TTTTATA
1 TTTTATA
74042 CGTAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.18
26 18 0.64
27 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTATAAATATAAATTATTTTATAAA
Found at i:74488 original size:13 final size:12
Alignment explanation
Indices: 74470--74514 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
74460 TTATTGGCGG
74470 ATTATTGAAATTT
1 ATTATT-AAATTT
*
74483 ATTATTATATTT
1 ATTATTAAATTT
74495 ATTAATTAATATTT
1 ATT-ATTAA-ATTT
74509 ATTATT
1 ATTATT
74515 GTACTTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 8 0.29
13 13 0.46
14 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
ATTATTAAATTT
Found at i:74508 original size:14 final size:13
Alignment explanation
Indices: 74479--74512 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
74469 GATTATTGAA
74479 ATTTATT-ATTAT
1 ATTTATTAATTAT
74491 ATTTATTAATTAAT
1 ATTTATTAATT-AT
74505 ATTTATTA
1 ATTTATTA
74513 TTGTACTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 3 0.15
14 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTATTAATTAT
Found at i:75068 original size:27 final size:29
Alignment explanation
Indices: 75006--75072 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 29
74996 CTGGAGCAGT
*
75006 AAAATTCAATAAAAATCAAAATTTAGTGGT
1 AAAATTCAATAAAAA-CAAAATTTAGTGGA
** *
75036 TGAATTCAATAAAAA-AACA-TTAGTGGA
1 AAAATTCAATAAAAACAAAATTTAGTGGA
75063 AAAATTCAAT
1 AAAATTCAAT
75073 TATTGATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 15 0.48
28 3 0.10
30 13 0.42
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.28
Consensus pattern (29 bp):
AAAATTCAATAAAAACAAAATTTAGTGGA
Found at i:76248 original size:22 final size:22
Alignment explanation
Indices: 76205--76248 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
76195 TTATATATTT
* ** *
76205 TTAATTAAAAATTTTAATTATA
1 TTAATAAAAAATGATAAATATA
76227 TTAATAAAAAATGATAAATATA
1 TTAATAAAAAATGATAAATATA
76249 AATATTTTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAATAAAAAATGATAAATATA
Found at i:77840 original size:13 final size:14
Alignment explanation
Indices: 77822--77851 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
77812 ATTTATTTGA
77822 TTTTT-AAAATTAT
1 TTTTTAAAAATTAT
77835 TTTTTAAAAATTAT
1 TTTTTAAAAATTAT
77849 TTT
1 TTT
77852 AAAAGGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTAAAAATTAT
Found at i:79566 original size:34 final size:32
Alignment explanation
Indices: 79523--79594 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
79513 TTGTTTAAAG
* *
79523 TTTTAATAACTAAATTATTCTTGTTATGTAAAATA
1 TTTTAATAACT-AATT-TTCTGGTTA-CTAAAATA
79558 TTTT-ATAACTAATTTTCTGGTTACTAAAATA
1 TTTTAATAACTAATTTTCTGGTTACTAAAATA
*
79589 TATTAA
1 TTTTAA
79595 GATAATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 10 0.30
32 9 0.27
33 4 0.12
34 6 0.18
35 4 0.12
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.49
Consensus pattern (32 bp):
TTTTAATAACTAATTTTCTGGTTACTAAAATA
Found at i:80644 original size:38 final size:36
Alignment explanation
Indices: 80580--80655 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 36
80570 CTTGTCCATA
80580 TTTGAATAATTTTTTTTGAAAATTTTAAATTAAAAT
1 TTTGAATAATTTTTTTTGAAAATTTTAAATTAAAAT
* *
80616 TTTGAATGAATTTATTTTT-AAATTTTTTAAATTTAAAT
1 TTTGAAT-AATTT-TTTTTGAAA-ATTTTAAATTAAAAT
80654 TT
1 TT
80656 AAGCATAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 7 0.20
37 8 0.23
38 20 0.57
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (36 bp):
TTTGAATAATTTTTTTTGAAAATTTTAAATTAAAAT
Found at i:81122 original size:2 final size:2
Alignment explanation
Indices: 81115--81140 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
81105 ACAGCTAGTG
81115 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
81141 CACCATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:81588 original size:14 final size:14
Alignment explanation
Indices: 81569--81621 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
81559 TTTTTCGGTT
81569 TTAAATATATTTTA
1 TTAAATATATTTTA
*
81583 TTAAATGTA--TT-
1 TTAAATATATTTTA
81594 TTAAATATATTTTA
1 TTAAATATATTTTA
*
81608 TAAAATATATTTTA
1 TTAAATATATTTTA
81622 AATATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 8 0.24
12 2 0.06
13 2 0.06
14 21 0.64
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:81597 original size:11 final size:11
Alignment explanation
Indices: 81567--81635 Score: 61
Period size: 14 Copynumber: 5.9 Consensus size: 11
81557 GTTTTTTCGG
81567 TTTTAAATATA
1 TTTTAAATATA
*
81578 TTTTATTAAATGTA
1 --TT-TTAAATATA
81592 TTTTAAATATA
1 TTTTAAATATA
81603 TTTTATAAAATATA
1 -TTT-T-AAATATA
81617 TTTT-AA-ATA
1 TTTTAAATATA
81626 TTTTAAATAT
1 TTTTAAATAT
81636 TAATTTAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
9 7 0.15
10 4 0.08
11 10 0.21
12 6 0.12
13 6 0.12
14 15 0.31
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTTAAATATA
Found at i:81630 original size:23 final size:25
Alignment explanation
Indices: 81567--81626 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
81557 GTTTTTTCGG
* *
81567 TTTTAAATATATTTTATTAAATGTA
1 TTTTAAATATATTTTATAAAATATA
81592 TTTTAAATATATTTTATAAAATATA
1 TTTTAAATATATTTTATAAAATATA
81617 TTTTAAATAT
1 TTTTAAATAT
81627 TTTAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTAAATATATTTTATAAAATATA
Found at i:82200 original size:12 final size:12
Alignment explanation
Indices: 82183--82225 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
82173 ACCATTTAAA
82183 TATATTAATTTT
1 TATATTAATTTT
*
82195 TATATTAATATT
1 TATATTAATTTT
82207 TATA-T-ATTTT
1 TATATTAATTTT
82217 TATAATTAA
1 TAT-ATTAA
82226 ATTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 16 0.62
13 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:82708 original size:19 final size:18
Alignment explanation
Indices: 82686--82735 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
82676 ATCTAATAAT
82686 TTATATATTTATTTTATA
1 TTATATATTTATTTTATA
82704 GTTATATATTT-TTTTATA
1 -TTATATATTTATTTTATA
82722 TTATA-ATTATATTT
1 TTATATATT-TATTT
82736 AAAATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.10
17 6 0.21
18 10 0.34
19 10 0.34
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTATATATTTATTTTATA
Found at i:83871 original size:7 final size:7
Alignment explanation
Indices: 83838--83904 Score: 62
Period size: 7 Copynumber: 8.9 Consensus size: 7
83828 TTTATATAAT
83838 AATTTTA
1 AATTTTA
**
83845 AATGATA
1 AATTTTA
*
83852 ATATTTAA
1 A-ATTTTA
83860 TAATTTTA
1 -AATTTTA
83868 AATTTTA
1 AATTTTA
83875 AATTTTA
1 AATTTTA
83882 AATTTTA
1 AATTTTA
83889 ATATTTATA
1 A-ATTT-TA
83898 ATATTTT
1 A-ATTTT
83905 TTTATCTTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
7 28 0.56
8 13 0.26
9 9 0.18
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (7 bp):
AATTTTA
Found at i:83881 original size:23 final size:23
Alignment explanation
Indices: 83834--83904 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
83824 TTAATTTATA
**
83834 TAATAATTTTAAATGAT-AATATT
1 TAATAATTTTAAATTTTAAAT-TT
83857 TAATAATTTTAAATTTTAAATTT
1 TAATAATTTTAAATTTTAAATTT
83880 T-A-AATTTTAATATTTATAATATTT
1 TAATAATTTTAA-ATTT-TAA-ATTT
83904 T
1 T
83905 TTTATCTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 8 0.19
22 5 0.12
23 21 0.50
24 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
TAATAATTTTAAATTTTAAATTT
Found at i:83889 original size:30 final size:30
Alignment explanation
Indices: 83838--83904 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
83828 TTTATATAAT
83838 AATTTTAAATGATAATATTTAATAATTT-TA
1 AATTTTAAATGATAATATTTAAT-ATTTATA
**
83868 AATTTTAAATTTTAA-ATTTTAATATTTATA
1 AATTTTAAATGATAATA-TTTAATATTTATA
83898 ATATTTT
1 A-ATTTT
83905 TTTATCTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 5 0.16
30 22 0.69
31 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
AATTTTAAATGATAATATTTAATATTTATA
Found at i:84388 original size:2 final size:2
Alignment explanation
Indices: 84381--84448 Score: 109
Period size: 2 Copynumber: 34.0 Consensus size: 2
84371 TTTAAAACCT
* *
84381 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
84423 TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
84449 AACGTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:84848 original size:2 final size:2
Alignment explanation
Indices: 84841--84866 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
84831 TGACCGATGG
84841 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
84867 TGCTTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87093 original size:19 final size:19
Alignment explanation
Indices: 87069--87108 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
87059 CAAAAATATG
87069 CAATTTACA-AAATTATTAA
1 CAATTTA-ATAAATTATTAA
87088 CAATTTAATAAATTATTAA
1 CAATTTAATAAATTATTAA
87107 CA
1 CA
87109 TATCAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (19 bp):
CAATTTAATAAATTATTAA
Found at i:87176 original size:21 final size:22
Alignment explanation
Indices: 87133--87177 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
87123 TAATGTAAAC
*
87133 ATAATTATGATATGTAAAAATAT
1 ATAAATATGATA-GTAAAAATAT
*
87156 ATAAATATGATA-TAAATATAT
1 ATAAATATGATAGTAAAAATAT
87177 A
1 A
87178 GTTTGGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
ATAAATATGATAGTAAAAATAT
Found at i:87938 original size:18 final size:19
Alignment explanation
Indices: 87911--87946 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
87901 ATTATTTTTT
*
87911 ATTTTGGTTGGA-AAAGAG
1 ATTTTCGTTGGAGAAAGAG
87929 ATTTTCGTTGGAGAAAGA
1 ATTTTCGTTGGAGAAAGA
87947 TAACTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (19 bp):
ATTTTCGTTGGAGAAAGAG
Found at i:88811 original size:17 final size:17
Alignment explanation
Indices: 88743--88816 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 17
88733 GTTATAGATA
88743 AATTAATTTTTTAAATA-
1 AATTAA-TTTTTAAATAT
* * *
88760 ATTTTATATTTTAAATTT
1 AATTAAT-TTTTAAATAT
* * * *
88778 ATTTAAGTTATAGATAT
1 AATTAATTTTTAAATAT
88795 AATTAATTTTTAAATATT
1 AATTAATTTTTAAATA-T
88813 AATT
1 AATT
88817 TAAATAATTC
Statistics
Matches: 42, Mismatches: 12, Indels: 5
0.71 0.20 0.08
Matches are distributed among these distances:
16 1 0.02
17 31 0.74
18 10 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTAATTTTTAAATAT
Found at i:89982 original size:17 final size:18
Alignment explanation
Indices: 89962--89995 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
89952 ATATTAAATT
*
89962 ATTTT-TTAAATTATAAA
1 ATTTTATTAAATAATAAA
89979 ATTTTATTAAATAATAA
1 ATTTTATTAAATAATAA
89996 TTTTATATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTATTAAATAATAAA
Found at i:98303 original size:19 final size:19
Alignment explanation
Indices: 98281--98327 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
98271 ATTTTTCGGT
98281 TATAT-TATTATTATATTTA
1 TATATATATTATTA-ATTTA
*
98300 TATATATATTTTTAATTTA
1 TATATATATTATTAATTTA
98319 TATCATATA
1 TAT-ATATA
98328 AAGAATAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATATATTATTAATTTA
Found at i:100436 original size:25 final size:24
Alignment explanation
Indices: 100406--100464 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
100396 AAAATTTAAA
100406 TAAAATAATATTAAATAAATATATT
1 TAAAATAATATTAAATAAA-ATATT
* * *
100431 TTAAAT-TTAATTAATTAAAATATT
1 TAAAATAAT-ATTAAATAAAATATT
100455 TAAAATAATA
1 TAAAATAATA
100465 AAAATTAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAATAATATTAAATAAAATATT
Found at i:100735 original size:15 final size:15
Alignment explanation
Indices: 100707--100748 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
100697 CTATATATAT
* *
100707 TTTAAAATTAAAATA
1 TTTAATATTTAAATA
100722 TTTAATATTTAAATA
1 TTTAATATTTAAATA
100737 TTT-AT-TTTAAAT
1 TTTAATATTTAAAT
100749 CCTAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 7 0.28
14 2 0.08
15 16 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAATATTTAAATA
Found at i:101911 original size:17 final size:17
Alignment explanation
Indices: 101891--101941 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
101881 AAATAATAAC
101891 AATATAAAAATTTATAT
1 AATATAAAAATTTATAT
101908 AATAT--AAA-TTA-AT
1 AATATAAAAATTTATAT
101921 AATATATTAAAATTTATAT
1 AATATA--AAAATTTATAT
101940 AA
1 AA
101942 ATATTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 7 0.25
14 3 0.11
15 3 0.11
17 8 0.29
18 3 0.11
19 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATAAAAATTTATAT
Found at i:101915 original size:33 final size:33
Alignment explanation
Indices: 101878--101951 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
101868 TTTGATAAGA
101878 ATAAAATAATAACAATATAAAAATTTATAT-AAT
1 ATAAAATAATAA-AATATAAAAATTTATATAAAT
* * *
101911 ATAAATTAATAATATATTAAAATTTATATAAAT
1 ATAAAATAATAAAATATAAAAATTTATATAAAT
*
101944 ATTAAATA
1 ATAAAATA
101952 TTTTAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 15 0.43
33 20 0.57
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
ATAAAATAATAAAATATAAAAATTTATATAAAT
Found at i:101938 original size:32 final size:34
Alignment explanation
Indices: 101878--101950 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 34
101868 TTTGATAAGA
*
101878 ATAAAATAATAACAATATAAAAATTTATAT-AAT
1 ATAAATTAATAACAATATAAAAATTTATATAAAT
* *
101911 ATAAATTAATAA-TATATTAAAATTTATATAAAT
1 ATAAATTAATAACAATATAAAAATTTATATAAAT
101944 ATTAAAT
1 A-TAAAT
101951 ATTTTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 15 0.43
33 15 0.43
34 5 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
ATAAATTAATAACAATATAAAAATTTATATAAAT
Found at i:101945 original size:18 final size:18
Alignment explanation
Indices: 101891--101954 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
101881 AAATAATAAC
*
101891 AATATAAAAATTTATAT-
1 AATATTAAAATTTATATA
101908 AATA-T-AAA-TTA-ATA
1 AATATTAAAATTTATATA
101922 ATATATTAAAATTTATATA
1 A-ATATTAAAATTTATATA
101941 AATATTAAATATTT
1 AATATTAAA-ATTT
101955 TAAATATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 2 0.05
14 4 0.10
15 6 0.15
16 1 0.03
17 7 0.18
18 11 0.28
19 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATTAAAATTTATATA
Found at i:101951 original size:27 final size:31
Alignment explanation
Indices: 101892--101972 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
101882 AATAATAACA
*
101892 ATATAAAAATTTATATAATATAAATTAATAAT
1 ATATTAAAATTTATATAATAT-AATTAATAAT
101924 ATATTAAAATTTATATAA-AT-ATT-A-AAT
1 ATATTAAAATTTATATAATATAATTAATAAT
*
101951 AT-TTTAAATATTATAATAATAT
1 ATATTAAAAT-TTAT-ATAATAT
101973 GACAAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
26 6 0.14
27 9 0.20
28 5 0.11
29 5 0.11
31 2 0.05
32 17 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATTAAAATTTATATAATATAATTAATAAT
Found at i:102428 original size:42 final size:42
Alignment explanation
Indices: 102369--102455 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
102359 GACATCCAAC
102369 GGTCAAGATACTATAGATAGTGGGATATTGGAGTTACCCGTG
1 GGTCAAGATACTATAGATAGTGGGATATTGGAGTTACCCGTG
*
102411 GGTCAAGATAGTATAGATAGTGGGATATTGGAGTTACCCGTG
1 GGTCAAGATACTATAGATAGTGGGATATTGGAGTTACCCGTG
102453 GGT
1 GGT
102456 ATATTAGCCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.10, G:0.33, T:0.29
Consensus pattern (42 bp):
GGTCAAGATACTATAGATAGTGGGATATTGGAGTTACCCGTG
Done.