Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 178 of 204
Found at i:52676690 original size:28 final size:27
Alignment explanation
Indices: 52676658--52676719 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 27
52676648 ATTTTTTAAT
*
52676658 TTATATATTAAATTATTTAA-ATTATTTC
1 TTATAT-TTAAATTATTTAAGA-GATTTC
52676686 TTATAGTTTAAATTATTTAAGAGATTTC
1 TTATA-TTTAAATTATTTAAGAGATTTC
52676714 TTATAT
1 TTATAT
52676720 GGTTTACTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 1 0.03
28 28 0.90
29 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (27 bp):
TTATATTTAAATTATTTAAGAGATTTC
Found at i:52681334 original size:12 final size:12
Alignment explanation
Indices: 52681317--52681341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52681307 TGCAAGCCCC
52681317 GTGGTTGGTGGA
1 GTGGTTGGTGGA
52681329 GTGGTTGGTGGA
1 GTGGTTGGTGGA
52681341 G
1 G
52681342 ATAGGTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.60, T:0.32
Consensus pattern (12 bp):
GTGGTTGGTGGA
Found at i:52681857 original size:43 final size:43
Alignment explanation
Indices: 52681792--52681889 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
52681782 TAGTCATATT
* ** * * * *
52681792 TTTAGTGGCGTTTGTGGTGGAAGTGCTGCTAAAGGCCATGAGC
1 TTTAGCGGCGTTCATGGAGGAAGCGCCGCTAAAGGCCATAAGC
* *
52681835 TTTAGCGGCGTTCATGGAGGAAGCGCCGCTAAAGGTCATAATC
1 TTTAGCGGCGTTCATGGAGGAAGCGCCGCTAAAGGCCATAAGC
*
52681878 TTTAGCGACGTT
1 TTTAGCGGCGTT
52681890 TGTGGAAAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTCATGGAGGAAGCGCCGCTAAAGGCCATAAGC
Found at i:52683257 original size:18 final size:19
Alignment explanation
Indices: 52683220--52683262 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
52683210 ATATATATTT
*
52683220 TTAAAAAATATATAATATA
1 TTAAAAAATATATAAAATA
52683239 -TAAAAAATACTA-AAAATA
1 TTAAAAAATA-TATAAAATA
52683257 TTAAAA
1 TTAAAA
52683263 TAAATGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAAAATATATAAAATA
Found at i:52693869 original size:21 final size:21
Alignment explanation
Indices: 52693843--52693885 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
52693833 CTCGGCGTGG
*
52693843 CCGGTTTTTTCTTTGAGGCAT
1 CCGGTTGTTTCTTTGAGGCAT
52693864 CCGGTTGTTTCTTTGAGGCAT
1 CCGGTTGTTTCTTTGAGGCAT
52693885 C
1 C
52693886 GGACTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.21, G:0.26, T:0.44
Consensus pattern (21 bp):
CCGGTTGTTTCTTTGAGGCAT
Found at i:52696907 original size:21 final size:21
Alignment explanation
Indices: 52696883--52696932 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
52696873 TTTGCCTAAG
*
52696883 ATGTGAATTGGATTAAATTGA
1 ATGTAAATTGGATTAAATTGA
*
52696904 ATGTAAATTGTATTAAATTG-
1 ATGTAAATTGGATTAAATTGA
52696924 ATGTTAAAT
1 ATG-TAAAT
52696933 CCATTCGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (21 bp):
ATGTAAATTGGATTAAATTGA
Found at i:52697523 original size:24 final size:24
Alignment explanation
Indices: 52697496--52697556 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
52697486 TAGCTCGTAT
***
52697496 GAGCTTCCCGTTAATGGCTCTCTA
1 GAGCTTCCCGTTAATGGCTCGAAA
* *
52697520 GAGCTTCTCGTTTTATGGCTCGAAA
1 GAGCTTCCCG-TTAATGGCTCGAAA
52697545 GAGCTTCCCGTT
1 GAGCTTCCCGTT
52697557 TGCATATTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.34
Consensus pattern (24 bp):
GAGCTTCCCGTTAATGGCTCGAAA
Found at i:52705105 original size:18 final size:18
Alignment explanation
Indices: 52705082--52705147 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 18
52705072 TCTTTAGAAT
52705082 TTTTTGAATTTTTTATAA
1 TTTTTGAATTTTTTATAA
***
52705100 TTTTTGAA--AAGTATAA
1 TTTTTGAATTTTTTATAA
* *
52705116 ATTTTGAAATTTTTATAAA
1 TTTTTGAATTTTTTAT-AA
52705135 TGTTTTGAATTTT
1 T-TTTTGAATTTT
52705148 AAAAATTATT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
16 12 0.34
18 11 0.31
19 2 0.06
20 10 0.29
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (18 bp):
TTTTTGAATTTTTTATAA
Found at i:52705148 original size:18 final size:17
Alignment explanation
Indices: 52705082--52705154 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 17
52705072 TCTTTAGAAT
*
52705082 TTTTTGAATTTTTTATAA
1 TTTTTGAATTTTATA-AA
***
52705100 TTTTTGAAAAGTATAAA
1 TTTTTGAATTTTATAAA
52705117 -TTTTGAAATTTTTATAAA
1 TTTTTG-AA-TTTTATAAA
*
52705135 TGTTTTGAATTTTAAAAA
1 T-TTTTGAATTTTATAAA
52705153 TT
1 TT
52705155 ATTTTGATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
16 5 0.12
17 5 0.12
18 26 0.60
19 2 0.05
20 5 0.12
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (17 bp):
TTTTTGAATTTTATAAA
Found at i:52705166 original size:19 final size:18
Alignment explanation
Indices: 52705124--52705166 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
52705114 AAATTTTGAA
* *
52705124 ATTTTTATAAATGTTTTG
1 ATTTTTAAAAATATTTTG
*
52705142 AATTTTAAAAATTATTTTG
1 ATTTTTAAAAA-TATTTTG
52705161 ATTTTT
1 ATTTTT
52705167 TTTTTGTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTTTTAAAAATATTTTG
Found at i:52708607 original size:25 final size:25
Alignment explanation
Indices: 52708573--52708623 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
52708563 CAATTTTAGC
*
52708573 AAGAAAAAGAGAAATCATAAAACAT
1 AAGAAAAAGAAAAATCATAAAACAT
52708598 AAGAAAAAGAAAAATCATAAAACAT
1 AAGAAAAAGAAAAATCATAAAACAT
52708623 A
1 A
52708624 CTTTCGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.71, C:0.08, G:0.10, T:0.12
Consensus pattern (25 bp):
AAGAAAAAGAAAAATCATAAAACAT
Found at i:52712463 original size:42 final size:42
Alignment explanation
Indices: 52712378--52712464 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
52712368 AATTGGGAAG
* * **
52712378 ATAATTCCCTTATTCTAATCAACTACTAAAACATAAGCGAAA
1 ATAATTCCCTGATTCTAATAAACTACTAAAACATAAAAGAAA
* *
52712420 ATAATTCCCTGATTCTAATAAACTACTAAAAGATAAAATAAA
1 ATAATTCCCTGATTCTAATAAACTACTAAAACATAAAAGAAA
52712462 ATA
1 ATA
52712465 TTTCTAGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (42 bp):
ATAATTCCCTGATTCTAATAAACTACTAAAACATAAAAGAAA
Found at i:52712508 original size:19 final size:18
Alignment explanation
Indices: 52712486--52712525 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
52712476 TGAATAAAAC
52712486 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
52712505 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
52712523 TTA
1 TTA
52712526 AAATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:52732918 original size:41 final size:41
Alignment explanation
Indices: 52732873--52732961 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 41
52732863 AAATATATTT
* *
52732873 ATTTTTTAAAATTTTAAAATATTTTTTACATACTTTTTT-AA
1 ATTTTTT-AAATTTTAAAATATTTTTAAAATACTTTTTTAAA
52732914 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAAA
52732955 ATTTTTT
1 ATTTTTT
52732962 TTAAATACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 29 0.64
41 16 0.36
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (41 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAAA
Found at i:52740456 original size:16 final size:16
Alignment explanation
Indices: 52740431--52740488 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
52740421 AAATATTTTT
52740431 AAATACTTTTTTAATTA
1 AAATA-TTTTTTAATTA
52740448 AAATATTTTTTAATTTA
1 AAATATTTTTTAA-TTA
*
52740465 AAAT-TATTTTAAATT-
1 AAATAT-TTTTTAATTA
52740480 AAATATTTT
1 AAATATTTT
52740489 AAATATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
15 7 0.19
16 12 0.32
17 18 0.49
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATATTTTTTAATTA
Found at i:52740501 original size:11 final size:11
Alignment explanation
Indices: 52740485--52740534 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
52740475 AAATTAAATA
52740485 TTTTAAATATT
1 TTTTAAATATT
52740496 TTTTAAATATT
1 TTTTAAATATT
*
52740507 TTTAAAATACTT
1 TTTTAAATA-TT
*
52740519 TTTTTAAT-TT
1 TTTTAAATATT
52740529 TTTTAA
1 TTTTAA
52740535 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 7 0.21
11 19 0.56
12 8 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTAAATATT
Found at i:52740503 original size:20 final size:23
Alignment explanation
Indices: 52740478--52740534 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
52740468 TTATTTTAAA
52740478 TTAAATA-TTTT-AAATA-TTTT
1 TTAAATATTTTTAAAATACTTTT
52740498 TTAAATATTTTTAAAATACTTTT
1 TTAAATATTTTTAAAATACTTTT
* *
52740521 TTTAATTTTTTTAA
1 TTAAATATTTTTAA
52740535 TTTTTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 7 0.22
21 4 0.12
22 5 0.16
23 16 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAAATATTTTTAAAATACTTTT
Found at i:52741054 original size:26 final size:26
Alignment explanation
Indices: 52741022--52741074 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
52741012 TTTTTTTGTC
*
52741022 TTTTTAAATTATTTAAAAAATTTATT
1 TTTTTAAATTATTTAAAAAATTAATT
*
52741048 TTTTTAATTTATTTAAAAAATTAATT
1 TTTTTAAATTATTTAAAAAATTAATT
52741074 T
1 T
52741075 GCAAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTTTAAATTATTTAAAAAATTAATT
Found at i:52742076 original size:2 final size:2
Alignment explanation
Indices: 52742069--52742108 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
52742059 TATATTTTGT
52742069 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
52742109 AAAGGAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52745074 original size:2 final size:2
Alignment explanation
Indices: 52745067--52745100 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
52745057 GGATCTGAGA
52745067 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
52745101 CGTTGTTTGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52748943 original size:18 final size:18
Alignment explanation
Indices: 52748885--52748943 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
52748875 TTTAAATATT
52748885 ATTTAAAAAATTATATT-A
1 ATTTAAAAAATTA-ATTAA
**
52748903 ATTATAAAACATATTTTTTAA
1 ATT-TAAAA-A-ATTAATTAA
52748924 ATTTAAAAAATTAATTAA
1 ATTTAAAAAATTAATTAA
52748942 AT
1 AT
52748944 GTTGACATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 12 0.36
19 6 0.18
20 8 0.24
21 7 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAAAAATTAATTAA
Found at i:52750736 original size:22 final size:24
Alignment explanation
Indices: 52750705--52750753 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
52750695 TGTTTTGATG
52750705 TTGTTCTTGATTTGT-T-CTGGAAA
1 TTGTTCTTGA-TTGTCTGCTGGAAA
52750728 TTGTT-TTGATTGTCTGCTGGAAA
1 TTGTTCTTGATTGTCTGCTGGAAA
52750751 TTG
1 TTG
52750754 AATTTGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.17
22 5 0.21
23 15 0.62
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.51
Consensus pattern (24 bp):
TTGTTCTTGATTGTCTGCTGGAAA
Found at i:52758504 original size:24 final size:25
Alignment explanation
Indices: 52758476--52758523 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
52758466 TTATGAAATT
52758476 TAAT-ATTAATTA-TTAAATTATATG
1 TAATAATT-ATTATTTAAATTATATG
52758500 TAATAATTATTATTTTAAATTATA
1 TAATAATTATTA-TTTAAATTATA
52758524 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATAATTATTATTTAAATTATATG
Found at i:52758677 original size:66 final size:63
Alignment explanation
Indices: 52758602--52758824 Score: 195
Period size: 66 Copynumber: 3.6 Consensus size: 63
52758592 AAATATATTT
52758602 AATATTAATTATTTCAAATTTTCATTTATAGTATTATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATTATATATTATGATTTGAGTAAATTCATATAA
52758667 G
63 G
* * * **
52758668 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATTATATATTATGATTTGAGTAAATTCATATAAG
* *
52758722 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATTATATATTATGATTTGAGTAAATTCATATA
52758786 AG
62 AG
*
52758788 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT
1 AATATTAATTATTTA-AATTTTATTTAAGTATTATATATT
52758825 TTAATTATAA
Statistics
Matches: 125, Mismatches: 15, Indels: 39
0.70 0.08 0.22
Matches are distributed among these distances:
53 5 0.04
54 13 0.10
55 5 0.04
56 4 0.03
57 3 0.02
58 1 0.01
59 10 0.08
60 8 0.06
61 20 0.16
62 1 0.01
63 4 0.03
64 7 0.06
65 7 0.06
66 32 0.26
67 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTAAGTATTATATATTATGATTTGAGTAAATTCATATAAG
Found at i:52758702 original size:120 final size:120
Alignment explanation
Indices: 52758564--52758853 Score: 478
Period size: 120 Copynumber: 2.4 Consensus size: 120
52758554 AATTATTTTA
* * *
52758564 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
* *
52758626 TTTATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
52758684 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
52758749 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
52758804 AATTTTATTAAATTATATATTTTAATTATAATATATTTAGTAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
52758854 CTTTAAATAT
Statistics
Matches: 161, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
119 6 0.04
120 153 0.95
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:52758724 original size:15 final size:15
Alignment explanation
Indices: 52758689--52758740 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
52758679 TTAAGAATTT
*
52758689 TATTAAATTAT-ATA
1 TATTTAATTATAATA
52758703 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
52758717 TATTTAATAATAAT-
1 TATTTAATTATAATA
52758731 TATGTTAATT
1 TAT-TTAATT
52758741 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:52758809 original size:61 final size:61
Alignment explanation
Indices: 52758626--52758824 Score: 189
Period size: 61 Copynumber: 3.3 Consensus size: 61
52758616 CAAATTTTCA
52758626 TTTATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
1 TTTATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
* * * * * * * *
52758687 TTTATTA-AATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TA
1 TTTA-TAGTATTATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAA
52758745 T
61 T
* *
52758746 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
1 TTTATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
*
52758807 TTTATTA-AATTATATATT
1 TTTA-TAGTATTATATATT
52758825 TTAATTATAA
Statistics
Matches: 104, Mismatches: 21, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 7 0.07
59 18 0.17
60 16 0.15
61 32 0.31
62 9 0.09
63 11 0.11
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
TTTATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
Found at i:52758948 original size:151 final size:154
Alignment explanation
Indices: 52758793--52759103 Score: 529
Period size: 151 Copynumber: 2.0 Consensus size: 154
52758783 ATAAGAATAT
* *
52758793 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAGTAATAATTATCTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATCTTT
*
52758858 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAAT-AAT-
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAAATA
*
52758921 A-ATTTACCAAAACAAATTTCTGC
131 ACATTTACCAAAACAAATTTATGC
*
52758944 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATCTTT
52759009 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAAAAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAAT--AAA
52759074 TAATCATTTACCAAAACAAATTTATGC
129 TAA-CATTTACCAAAACAAATTTATGC
52759101 TAA
1 TAA
52759104 AGGTATTCTA
Statistics
Matches: 149, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
151 121 0.81
154 3 0.02
155 1 0.01
157 24 0.16
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (154 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATCTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAAATA
ACATTTACCAAAACAAATTTATGC
Found at i:52758984 original size:18 final size:17
Alignment explanation
Indices: 52758956--52758990 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52758946 ATTATTAAGA
*
52758956 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52758973 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52758991 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52759024 original size:75 final size:75
Alignment explanation
Indices: 52758794--52759026 Score: 190
Period size: 75 Copynumber: 3.1 Consensus size: 75
52758784 TAAGAATATT
* *
52758794 AATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAGTAATAATTATCTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATCTTTA
52758859 AATATGATTA
66 AATATGATTA
* ** * * * ** * * *
52758869 AATTATTTATTATTGATATT-AATAATCTTATTAAAATTTAAATA-A--CAATAATAATT-TACC
1 AATTATTAAGAATT-TTATTAAATTAT-ATATTTTAATTAAAATATATTTAATAATAATTAT-CT
** * * *
52758929 AAAACAAAT-TTCTGCT
63 TTAA-ATATGAT-T--A
*
52758945 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATCTTTA
52759010 AATATGATTA
66 AATATGATTA
52759020 AATTATT
1 AATTATT
52759027 TATTATTGAT
Statistics
Matches: 110, Mismatches: 35, Indels: 26
0.64 0.20 0.15
Matches are distributed among these distances:
72 1 0.01
73 13 0.12
74 4 0.04
75 41 0.37
76 33 0.30
77 4 0.04
78 13 0.12
79 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATCTTTA
AATATGATTA
Found at i:52759243 original size:16 final size:16
Alignment explanation
Indices: 52759222--52759267 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
52759212 AGTTGATTTG
52759222 CTATTACACCTCTATT
1 CTATTACACCTCTATT
*
52759238 CTATTACACCTTTATT
1 CTATTACACCTCTATT
*
52759254 CCATTACACCTCTA
1 CTATTACACCTCTA
52759268 ATCCAATACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (16 bp):
CTATTACACCTCTATT
Found at i:52759272 original size:16 final size:16
Alignment explanation
Indices: 52759224--52759277 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
52759214 TTGATTTGCT
*
52759224 ATTACACCTCTATTCT
1 ATTACACCTCTATTCC
*
52759240 ATTACACCTTTATTCC
1 ATTACACCTCTATTCC
*
52759256 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
52759272 AATACA
1 ATTACA
52759278 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:52760046 original size:27 final size:27
Alignment explanation
Indices: 52760012--52760076 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
52760002 AAATAAAAAA
52760012 TACCAAAATATTATATATATTTTTATT
1 TACCAAAATATTATATATATTTTTATT
*
52760039 TACCAAAATATTATATATTTTTTTATT
1 TACCAAAATATTATATATATTTTTATT
52760066 TACCAAAATAT
1 TACCAAAATAT
52760077 ACCAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (27 bp):
TACCAAAATATTATATATATTTTTATT
Found at i:52760144 original size:27 final size:27
Alignment explanation
Indices: 52760102--52760164 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
52760092 CAGGACTGAA
52760102 TGGCGGCACCAATGGTGCCATTCTCAT
1 TGGCGGCACCAATGGTGCCATTCTCAT
* *
52760129 TGGCAGCACCAGTGGTGCCATTCTCAT
1 TGGCGGCACCAATGGTGCCATTCTCAT
52760156 TGGCGGCAC
1 TGGCGGCAC
52760165 AGGACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (27 bp):
TGGCGGCACCAATGGTGCCATTCTCAT
Found at i:52761782 original size:27 final size:27
Alignment explanation
Indices: 52761752--52761810 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
52761742 AGTCCTATGT
52761752 CGCCAATAAGAATAGCACCACTGGTGC
1 CGCCAATAAGAATAGCACCACTGGTGC
* * *
52761779 CGCCAATGAGAATGGCACCATTGGTGC
1 CGCCAATAAGAATAGCACCACTGGTGC
52761806 CGCCA
1 CGCCA
52761811 TTGTTAGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15
Consensus pattern (27 bp):
CGCCAATAAGAATAGCACCACTGGTGC
Found at i:52763327 original size:18 final size:18
Alignment explanation
Indices: 52763285--52763319 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
52763275 TAATAGCAAT
52763285 TTTGGGCCAATTGATGGC
1 TTTGGGCCAATTGATGGC
52763303 TTTGGGCCGAA-TGATGG
1 TTTGGGCC-AATTGATGG
52763320 TATTGGGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.17, C:0.14, G:0.37, T:0.31
Consensus pattern (18 bp):
TTTGGGCCAATTGATGGC
Found at i:52764107 original size:15 final size:15
Alignment explanation
Indices: 52764087--52764117 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52764077 ATTCAAATTC
52764087 AATAAAATTGCTATG
1 AATAAAATTGCTATG
*
52764102 AATAAAGTTGCTATG
1 AATAAAATTGCTATG
52764117 A
1 A
52764118 GTGATGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.32
Consensus pattern (15 bp):
AATAAAATTGCTATG
Found at i:52779173 original size:22 final size:22
Alignment explanation
Indices: 52779128--52779182 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
52779118 GTTGATGGTT
*
52779128 ATTTAGTTTCAATTATGTATTTG
1 ATTTAGTTTAAATTA-GTATTTG
52779151 ATTTATGTTTAAATTA-TATTTG
1 ATTTA-GTTTAAATTAGTATTTG
*
52779173 AATTAAGTTT
1 -ATTTAGTTT
52779183 GAACAATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 10 0.36
23 9 0.32
24 9 0.32
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (22 bp):
ATTTAGTTTAAATTAGTATTTG
Found at i:52782134 original size:41 final size:41
Alignment explanation
Indices: 52782054--52782135 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
52782044 CTTTTTTGAA
* *
52782054 ATTAAATATTTTAGTCACTCTCTCGTTATTTGCCGTTAGAT
1 ATTAAATATTTTAGCCACTCTCTCGTTATTTGCCATTAGAT
52782095 ATTAAATATTTTAGCCACTCTC-CTGTTAGTTT-CCATTAGAT
1 ATTAAATATTTTAGCCACTCTCTC-GTTA-TTTGCCATTAGAT
52782136 GAGTGTCGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 1 0.03
41 33 0.89
42 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (41 bp):
ATTAAATATTTTAGCCACTCTCTCGTTATTTGCCATTAGAT
Found at i:52783738 original size:13 final size:13
Alignment explanation
Indices: 52783720--52783756 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
52783710 TTGAATGTTT
52783720 ATTAAAATATGTA
1 ATTAAAATATGTA
52783733 ATTAAAATATGTA
1 ATTAAAATATGTA
52783746 ATTAAAA-ATGT
1 ATTAAAATATGT
52783757 TTCCATGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
ATTAAAATATGTA
Found at i:52784409 original size:27 final size:27
Alignment explanation
Indices: 52784379--52784834 Score: 475
Period size: 27 Copynumber: 16.6 Consensus size: 27
52784369 ATTTGGTTAA
52784379 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
52784406 TTACATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATAAC
*
52784433 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
*
52784460 TTGCATAACTTACGTAAATTAAGTTAATTAAATAAC
1 TTACATAACTTAC----A-T-A---AATTAAATAAC
*
52784496 TTACATAAATTA-AGTAAATTAAATAAC
1 TTACATAACTTACA-TAAATTAAATAAC
* *
52784523 TTACATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATAAC
*
52784550 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* * *
52784577 TTGCATAACTTACGTAAATTAAGTTAA-
1 TTACATAACTTACATAAATTAA-ATAAC
* * *
52784604 TTAAATAACTTACATAAATTAAGTAAA
1 TTACATAACTTACATAAATTAAATAAC
* * *
52784631 TTAAATATCTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* *
52784658 TTGCATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
*
52784685 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* *
52784712 TTACATAACTTACATAAATTAAGTAAA
1 TTACATAACTTACATAAATTAAATAAC
* * * *
52784739 TTAAATAACTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
* * *
52784766 TTACATAACTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
* * * * * *
52784793 TTAAATATCTTACATTACTTATATAGC
1 TTACATAACTTACATAAATTAAATAAC
*
52784820 TTACATTACTTACAT
1 TTACATAACTTACAT
52784835 GGGGCATACA
Statistics
Matches: 368, Mismatches: 49, Indels: 24
0.83 0.11 0.05
Matches are distributed among these distances:
26 3 0.01
27 336 0.91
28 3 0.01
30 1 0.00
31 3 0.01
32 1 0.00
33 1 0.00
36 20 0.05
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.37
Consensus pattern (27 bp):
TTACATAACTTACATAAATTAAATAAC
Found at i:52784521 original size:117 final size:117
Alignment explanation
Indices: 52784379--52784813 Score: 644
Period size: 117 Copynumber: 3.8 Consensus size: 117
52784369 ATTTGGTTAA
*
52784379 TTACATAACTTACA-TAAATTAAATAACTTACATAACTTACATAAATTAAGTAATTTACATAACT
1 TTACATAAATTA-AGTAAATTAAATAACTTACATAACTTACATAAATTAAGTAATTTACATAACT
*
52784443 TACATAAATTAAATATCTTGCATAACTTACGTAAATTAAGTTAATTAAATAAC
65 TACATAAATTAAATATCTTACATAACTTACGTAAATTAAGTTAATTAAATAAC
52784496 TTACATAAATTAAGTAAATTAAATAACTTACATAACTTACATAAATTAAGTAATTTACATAACTT
1 TTACATAAATTAAGTAAATTAAATAACTTACATAACTTACATAAATTAAGTAATTTACATAACTT
*
52784561 ACATAAATTAAATATCTTGCATAACTTACGTAAATTAAGTTAATTAAATAAC
66 ACATAAATTAAATATCTTACATAACTTACGTAAATTAAGTTAATTAAATAAC
* *
52784613 TTACATAAATTAAGTAAATT--A-AA--T--AT--CTTACATAAATTAAAT-ATCTTGCATAACT
1 TTACATAAATTAAGTAAATTAAATAACTTACATAACTTACATAAATTAAGTAAT-TTACATAACT
* * * *
52784668 TACATAAATTAAATATCTTACATAACTTACATAAATTAA-ATATCTTACATAAC
65 TACATAAATTAAATATCTTACATAACTTACGTAAATTAAGTTA-ATTAAATAAC
*
52784721 TTACATAAATTAAGTAAATTAAATAACTTACATAACTTACATAAATTACA-TAACTTACATAACT
1 TTACATAAATTAAGTAAATTAAATAACTTACATAACTTACATAAATTA-AGTAATTTACATAACT
*
52784785 TACATAAATTAAATATCTTACATTACTTA
65 TACATAAATTAAATATCTTACATAACTTA
52784814 TATAGCTTAC
Statistics
Matches: 293, Mismatches: 11, Indels: 28
0.88 0.03 0.08
Matches are distributed among these distances:
107 4 0.01
108 89 0.30
110 3 0.01
111 2 0.01
112 1 0.00
113 1 0.00
114 2 0.01
115 3 0.01
116 1 0.00
117 185 0.63
118 2 0.01
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (117 bp):
TTACATAAATTAAGTAAATTAAATAACTTACATAACTTACATAAATTAAGTAATTTACATAACTT
ACATAAATTAAATATCTTACATAACTTACGTAAATTAAGTTAATTAAATAAC
Found at i:52784822 original size:18 final size:18
Alignment explanation
Indices: 52784379--52784879 Score: 344
Period size: 18 Copynumber: 27.9 Consensus size: 18
52784369 ATTTGGTTAA
*
52784379 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
*
52784397 TTAAATAACTTACATAAC
1 TTACATAACTTACATAAC
* *
52784415 TTACATAAATTA-AGTAAT
1 TTACATAACTTACA-TAAC
*
52784433 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
* * *
52784451 TTAAATATCTTGCATAAC
1 TTACATAACTTACATAAC
* *
52784469 TTACGTAAATTA-AGTTAA-
1 TTACATAACTTACA--TAAC
* *
52784487 TTAAATAACTTACATAAA
1 TTACATAACTTACATAAC
* *
52784505 TTA-AGTAAATTAAATAAC
1 TTACA-TAACTTACATAAC
*
52784523 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
*
52784541 TTA-AGTAATTTACATAAC
1 TTACA-TAACTTACATAAC
* * *
52784559 TTACATAAATTAAATATC
1 TTACATAACTTACATAAC
* * *
52784577 TTGCATAACTTACGTAAA
1 TTACATAACTTACATAAC
*
52784595 TTA-AGTTAA-TTAAATAAC
1 TTACA--TAACTTACATAAC
* *
52784613 TTACATAAATTA-AGTAAA
1 TTACATAACTTACA-TAAC
* * *
52784631 TTAAATATCTTACATAAA
1 TTACATAACTTACATAAC
* * *
52784649 TTAAATATCTTGCATAAC
1 TTACATAACTTACATAAC
* * *
52784667 TTACATAAATTAAATATC
1 TTACATAACTTACATAAC
*
52784685 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
* *
52784703 TTAAATATCTTACATAAC
1 TTACATAACTTACATAAC
* *
52784721 TTACATAAATTA-AGTAAA
1 TTACATAACTTACA-TAAC
*
52784739 TTAAATAACTTACATAAC
1 TTACATAACTTACATAAC
*
52784757 TTACATAAATTACATAAC
1 TTACATAACTTACATAAC
*
52784775 TTACATAACTTACATAAA
1 TTACATAACTTACATAAC
* * *
52784793 TTAAATATCTTACATTAC
1 TTACATAACTTACATAAC
* * *
52784811 TTATATAGCTTACATTAC
1 TTACATAACTTACATAAC
** *
52784829 TTACATGGGGCATACATAA-
1 TTACAT--AACTTACATAAC
*
52784848 -TACATAA--TACAGAAC
1 TTACATAACTTACATAAC
52784863 TTACATAACTTACATAA
1 TTACATAACTTACATAA
52784880 TACATAAAAA
Statistics
Matches: 375, Mismatches: 84, Indels: 48
0.74 0.17 0.09
Matches are distributed among these distances:
14 6 0.02
16 7 0.02
17 13 0.03
18 328 0.87
19 13 0.03
20 8 0.02
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.36
Consensus pattern (18 bp):
TTACATAACTTACATAAC
Found at i:52792254 original size:21 final size:21
Alignment explanation
Indices: 52792230--52792298 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
52792220 CAGCAACTTA
* *
52792230 AAGCAGAGGCGACAGCGAGGG
1 AAGCAGAGGCCACAGCGAGAG
* * *
52792251 AAGCAGAGACTACAGCAAGAG
1 AAGCAGAGGCCACAGCGAGAG
*
52792272 AAGCAGATGCCACAGCGAGAG
1 AAGCAGAGGCCACAGCGAGAG
52792293 AAGCAG
1 AAGCAG
52792299 CGAGAGAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.36, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCCACAGCGAGAG
Found at i:52792301 original size:12 final size:12
Alignment explanation
Indices: 52792284--52792322 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
52792274 GCAGATGCCA
52792284 CAGCGAGAGAAG
1 CAGCGAGAGAAG
52792296 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
52792308 TAGCGAGAGAAG
1 CAGCGAGAGAAG
52792320 CAG
1 CAG
52792323 AGGTTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.41, T:0.03
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:52792844 original size:43 final size:41
Alignment explanation
Indices: 52792741--52792988 Score: 247
Period size: 42 Copynumber: 5.9 Consensus size: 41
52792731 GTTTGTGAAA
**
52792741 TAAGCGCCGCTAAAGAACACT-ACTTTTAGCGGCGTTTTTGAA
1 TAAGCGCCGCTAAAGAACA-TGACTTTTAGCGGCGTTTTT-TC
* * * *
52792783 GAAGCGCCGCTATAGAACATTACTTTTAGAGGCGTTTTCTTC
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTT-TTC
*
52792825 GAAAGCGCCGCTAAAGAACATGAGC-TTTAGCGGCGTTTATTT-
1 -TAAGCGCCGCTAAAGAACATGA-CTTTTAGCGGCGTTT-TTTC
* *
52792867 TAAGCGCCGCTAAAGAACATGA-TCTTTAGGGGCTTTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGC--GTTTTTTC
*
52792910 TAAGCGCCGCTAAAGAACATGA-TCTTTAGGGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCG-TTTTTTC
*
52792952 TAAGCGCCGCTAAAGAACATGAGC-CTTAGCGGCGTTT
1 TAAGCGCCGCTAAAGAACATGA-CTTTTAGCGGCGTTT
52792989 CTTTATGTAA
Statistics
Matches: 178, Mismatches: 15, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
41 33 0.19
42 73 0.41
43 70 0.39
44 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (41 bp):
TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTC
Found at i:52801393 original size:18 final size:18
Alignment explanation
Indices: 52801347--52801393 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
52801337 GCTTGCTTAA
*
52801347 TATTTGATTTA-TTATTT
1 TATTTTATTTATTTATTT
*
52801364 TATTTTAGTTATTTATTT
1 TATTTTATTTATTTATTT
52801382 TAATTTT-TTTAT
1 T-ATTTTATTTAT
52801394 CTGACTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 11 0.44
19 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TATTTTATTTATTTATTT
Found at i:52801789 original size:16 final size:16
Alignment explanation
Indices: 52801744--52801791 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
52801734 AAAGTTATCA
52801744 AAAAAAGTACAAAAAAAT
1 AAAAAA-TA-AAAAAAAT
* **
52801762 AAAACACGAAAAAAAT
1 AAAAAATAAAAAAAAT
52801778 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
52801792 TATTATGTGG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 19 0.79
18 5 0.21
ACGTcount: A:0.81, C:0.06, G:0.04, T:0.08
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:52807144 original size:2 final size:2
Alignment explanation
Indices: 52807137--52807196 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
52807127 TGTAATGATG
* *
52807137 TA TA TA TA TG TA TA TG 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 TA TA TA TA TA TA TA TA
*
52807179 TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
52807197 CGTACATGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:52849068 original size:87 final size:86
Alignment explanation
Indices: 52848936--52849104 Score: 259
Period size: 87 Copynumber: 2.0 Consensus size: 86
52848926 TGGGTTTTGG
*
52848936 TCAAGTTGCAATTATCCTAGTAAACAATTTGCAAGCTTCTCTTTTTCCCTAATTGGAGTTTATAT
1 TCAAGTTGCAATTATCCAAGTAAACAATTTGCAAGCTTCTCTTTTTCCCTAATTGGAGTTTATAT
*
52849001 TGTTTAGAGATTTGGATGAGTGA
66 TATTT--AGATTTGGATGAGTGA
* * * *
52849024 TCAAGTTGCAATTATCCAAGTACAGAA-TTGCAAGTTTCTCTTTTTCCCTATTTGGAGTTTATAT
1 TCAAGTTGCAATTATCCAAGTAAACAATTTGCAAGCTTCTCTTTTTCCCTAATTGGAGTTTATAT
52849088 TATTTAGATTTGGATGA
66 TATTTAGATTTGGATGA
52849105 TTGGGGGATT
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
85 12 0.16
87 39 0.52
88 24 0.32
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (86 bp):
TCAAGTTGCAATTATCCAAGTAAACAATTTGCAAGCTTCTCTTTTTCCCTAATTGGAGTTTATAT
TATTTAGATTTGGATGAGTGA
Found at i:52859753 original size:31 final size:31
Alignment explanation
Indices: 52859718--52859788 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
52859708 GAATATAGGA
* *
52859718 TGCCGAATTTGATTTATGTATGATTATACAT
1 TGCCGAATTTGATTCATGAATGATTATACAT
* * *
52859749 TGCCGAACTTGATTCGTGAATGGTTATACAT
1 TGCCGAATTTGATTCATGAATGATTATACAT
52859780 TGCCGAATT
1 TGCCGAATT
52859789 GTTGGGTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (31 bp):
TGCCGAATTTGATTCATGAATGATTATACAT
Found at i:52859780 original size:184 final size:185
Alignment explanation
Indices: 52859471--52859827 Score: 504
Period size: 184 Copynumber: 1.9 Consensus size: 185
52859461 GTTTTATACC
* * * * *
52859471 TTGCTGAAATTAAATTGTACATGGTTATATATTTTCGATATTGAATTGTTTATGTATATATGATG
1 TTGCTGAAATTAAATTATACATGGTTATATATTGTCAATATTGAATTGTTTATGAATATAGGATG
* * * *
52859536 CCGAATTGGATTTGTATTTGATTATACATTATCAAACTTGATTCGTGTATGGCTATACATTGCCA
66 CCGAATTGGATTTATATATGATTATACATTACCAAACTTGATTCGTGAATGGCTATACATTGCCA
* **
52859601 AATTGTTTGGTATATGGATA-TAAGTTGCTGAATT-GATTCGTACAGGGTTGTACA
131 AATTGTTGGGTATATCAATATTAA-TTGCTGAATTGGATTCGTACAGGGTTGTACA
52859655 TTGCTGAAATT-AATTCATACATGGTTATATATTGTCAATATTGAATTGTTTATGAATATAGGAT
1 TTGCTGAAATTAAATT-ATACATGGTTATATATTGTCAATATTGAATTGTTTATGAATATAGGAT
* * * * *
52859719 GCCGAATTTGATTTATGTATGATTATACATTGCCGAACTTGATTCGTGAATGGTTATACATTGCC
65 GCCGAATTGGATTTATATATGATTATACATTACCAAACTTGATTCGTGAATGGCTATACATTGCC
* *
52859784 GAATTGTTGGGTATATCAATATTCATTGCTGAATTGGATTCGTA
130 AAATTGTTGGGTATATCAATATTAATTGCTGAATTGGATTCGTA
52859828 TATGAATATA
Statistics
Matches: 151, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
183 4 0.03
184 137 0.91
185 10 0.07
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (185 bp):
TTGCTGAAATTAAATTATACATGGTTATATATTGTCAATATTGAATTGTTTATGAATATAGGATG
CCGAATTGGATTTATATATGATTATACATTACCAAACTTGATTCGTGAATGGCTATACATTGCCA
AATTGTTGGGTATATCAATATTAATTGCTGAATTGGATTCGTACAGGGTTGTACA
Found at i:52860689 original size:15 final size:15
Alignment explanation
Indices: 52860662--52860703 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52860652 AAATGTTGGC
52860662 AAAAAAAAA--AATG
1 AAAAAAAAATGAATG
52860675 AAAAAAAAATGAATG
1 AAAAAAAAATGAATG
**
52860690 AAACGAAAATGAAT
1 AAAAAAAAATGAAT
52860704 TGACTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 9 0.36
15 16 0.64
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAAAAAATGAATG
Found at i:52862425 original size:2 final size:2
Alignment explanation
Indices: 52862418--52862450 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52862408 GTTCTTTTTA
52862418 AT AT AT AT 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 AT A
52862451 ATTTGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52867689 original size:111 final size:110
Alignment explanation
Indices: 52867523--52867955 Score: 429
Period size: 124 Copynumber: 3.7 Consensus size: 110
52867513 AAAAAAGAAG
* * * *
52867523 GATATTTAGCCATTTGGTTGAA-CGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCTCTCG
1 GATATTTGGCTATTCGGTT-AAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCG
* *
52867587 AATTTTCCAAACGCAAAACATTGCCTTATTTCGAAAATTTTTAAAAT
65 AATTTCCCAAACGCAAAACATTGCCTTATTT-AAAAATTTTTAAAAT
* ***
52867634 GATGTTTGGCTATTCGGTTAAATAAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGA
1 GATATTTGGCTATTCGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGA
*
52867699 ATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTATTTTTAAATTTTTTTTTAAAG
66 ATTTCCCAAACGCAAAACATTGCCTTA-TTTAAAA--ATTTTT--A---------AAAT
** * *
52867758 GATATTAAGCCATTTGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGA
1 GATATTTGGCTATTCGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGA
*
52867823 ATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTATTTTAAAATTTTTT
66 ATTTCCCAAACGCAAAACATTGCCTTA-TTTAAAAAT-TTTTAAAA-----T
** * *
52867875 AAAGGATATTAAGCCATTTGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTC
1 ----GATATTTGGCTATTCGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTC
52867940 TCGAATTT-CCAAACGC
62 TCGAATTTCCCAAACGC
52867956 TAAGTATTGC
Statistics
Matches: 277, Mismatches: 20, Indels: 41
0.82 0.06 0.12
Matches are distributed among these distances:
110 2 0.01
111 84 0.30
112 6 0.02
113 6 0.02
115 1 0.00
120 8 0.03
121 70 0.25
122 1 0.00
123 4 0.01
124 95 0.34
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (110 bp):
GATATTTGGCTATTCGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGA
ATTTCCCAAACGCAAAACATTGCCTTATTTAAAAATTTTTAAAAT
Found at i:52867844 original size:124 final size:121
Alignment explanation
Indices: 52867658--52867955 Score: 553
Period size: 121 Copynumber: 2.4 Consensus size: 121
52867648 CGGTTAAATA
52867658 AGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAACGCAAAACATTGCC
1 AGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAACGCAAAACATTGCC
*
52867723 TTATTTTAAAATTATTTTTAAATTTTTTTTTAAAGGATATTAAGCCATTTGGTTAAGCG
66 TTATTTTAAAATTA-TTTTAAA--ATTTTTTAAAGGATATTAAGCCATTTGGTTAAGCG
52867782 AGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAACGCAAAACATTGCC
1 AGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAACGCAAAACATTGCC
52867847 TTATTTTAAAATTATTTTAAAATTTTTTAAAGGATATTAAGCCATTTGGTTAAGCG
66 TTATTTTAAAATTATTTTAAAATTTTTTAAAGGATATTAAGCCATTTGGTTAAGCG
52867903 AGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAACGC
1 AGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAACGC
52867956 TAAGTATTGC
Statistics
Matches: 173, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
120 8 0.05
121 79 0.46
123 7 0.04
124 79 0.46
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (121 bp):
AGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAACGCAAAACATTGCC
TTATTTTAAAATTATTTTAAAATTTTTTAAAGGATATTAAGCCATTTGGTTAAGCG
Found at i:52867876 original size:10 final size:11
Alignment explanation
Indices: 52867847--52867877 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
52867837 AAACATTGCC
52867847 TTATTTTAAAA
1 TTATTTTAAAA
52867858 TTATTTTAAAA
1 TTATTTTAAAA
52867869 TT-TTTTAAA
1 TTATTTTAAA
52867878 GGATATTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTATTTTAAAA
Found at i:52868436 original size:40 final size:38
Alignment explanation
Indices: 52868360--52868439 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 38
52868350 TATCATAAAA
* *
52868360 AAGTATATATATATATAAAATATAAAAAGTATATATAT
1 AAGTATATATATATATAAAATATAAAAAGAACATATAT
*
52868398 AAGTATATATATGAATCATAAAA-ATATAAAGAACATATAT
1 AAGTATATATAT--AT-ATAAAATATAAAAAGAACATATAT
52868438 AA
1 AA
52868440 AATACGTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 12 0.33
40 18 0.50
41 6 0.17
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.33
Consensus pattern (38 bp):
AAGTATATATATATATAAAATATAAAAAGAACATATAT
Found at i:52868436 original size:42 final size:38
Alignment explanation
Indices: 52868360--52868438 Score: 97
Period size: 42 Copynumber: 2.0 Consensus size: 38
52868350 TATCATAAAA
*
52868360 AAGTATATATATATATAAAATATAAAAAGTATATATAT
1 AAGTATATATATATATAAAATATAAAAAGCATATATAT
52868398 AAGTATATATATGAATCATAAAAATATAAAGAA-CATATATA
1 AAGTATATATAT--AT-AT-AAAATATAAA-AAGCATATATA
52868439 AAATACGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
38 12 0.34
40 2 0.06
41 2 0.06
42 17 0.49
43 2 0.06
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (38 bp):
AAGTATATATATATATAAAATATAAAAAGCATATATAT
Found at i:52868701 original size:3 final size:3
Alignment explanation
Indices: 52868687--52868766 Score: 99
Period size: 3 Copynumber: 26.3 Consensus size: 3
52868677 AAATACGATG
* *
52868687 ATA ATA AAA ATA ATA TTAA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
52868733 ATA ATA ATA ATA ATA CTA ATGA ACA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA A
52868767 AAATGCTACA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
2 2 0.03
3 61 0.91
4 4 0.06
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:52871022 original size:48 final size:48
Alignment explanation
Indices: 52870950--52871045 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
52870940 TTTCTTTGCT
* **
52870950 TAAAAACGCCTAAGTCAGCCTAACTTGCAATGATAAAAGATTCAACAG
1 TAAAAAAGCCTAAGTCAGCCTAACTCACAATGATAAAAGATTCAACAG
* *
52870998 TAAAAAAGCCTAAGTCAGCTTAACTCACAATGATAAAGGATTCAACAG
1 TAAAAAAGCCTAAGTCAGCCTAACTCACAATGATAAAAGATTCAACAG
52871046 AATTCCCTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.21
Consensus pattern (48 bp):
TAAAAAAGCCTAAGTCAGCCTAACTCACAATGATAAAAGATTCAACAG
Found at i:52876156 original size:48 final size:48
Alignment explanation
Indices: 52876084--52876179 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
52876074 TTTCTTTGCT
*
52876084 TAAAAACGCCTAAGTCAGCCTAACTTGCAATGATAAAAGATTCAACAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAAGATTCAACAG
* *
52876132 TAAAAACGCCTAAGTCAGCTTAACTCGCAATGATAAAGGATTCAACAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAAGATTCAACAG
52876180 AATTCCCTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.21
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAAGATTCAACAG
Found at i:52880022 original size:18 final size:18
Alignment explanation
Indices: 52879983--52880235 Score: 184
Period size: 17 Copynumber: 14.3 Consensus size: 18
52879973 CGAGATTTTT
52879983 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
52880001 -TTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * **
52880018 TTTTTAAAAATACGAGGA
1 TTTTTGAAAACACGAAAA
*
52880036 TTTTTG-AAATACGCAAAA
1 TTTTTGAAAACACG-AAAA
52880054 -TTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
52880071 TTTTTG-AAATACGAACA
1 TTTTTGAAAACACGAAAA
* *
52880088 TTTTAG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
52880105 TTTTT-AAAACACGACAA
1 TTTTTGAAAACACGAAAA
52880122 TTTTTG-AAACACGAGAAAAA
1 TTTTTGAAAACAC--G-AAAA
** *** *
52880142 AGTTT-AGAAATTTGGAAA
1 TTTTTGA-AAACACGAAAA
52880160 TTTTTAGAAAACACGAAAA
1 TTTTT-GAAAACACGAAAA
* * * *
52880179 ATTTTGAAAA-ATGGAAT
1 TTTTTGAAAACACGAAAA
*
52880196 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
52880214 TTTTTGAAAACATG-AAA
1 TTTTTGAAAACACGAAAA
52880231 TTTTT
1 TTTTT
52880236 TTTGATTTTT
Statistics
Matches: 180, Mismatches: 41, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
17 99 0.55
18 58 0.32
19 13 0.07
20 7 0.04
21 3 0.02
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:52880080 original size:35 final size:34
Alignment explanation
Indices: 52879984--52880222 Score: 160
Period size: 35 Copynumber: 6.8 Consensus size: 34
52879974 GAGATTTTTT
*
52879984 TTTTGAAAACACGAAAA-TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAATTTTTG-AAATACGAAAA
* * **
52880018 TTTTTAAAAATACGAGGATTTTTGAAATACGCAAAA
1 -TTTTGAAAACACGAAAATTTTTGAAATACG-AAAA
*
52880054 TTTTGAAAACACGAAAATTTTTGAAATACGAACA
1 TTTTGAAAACACGAAAATTTTTGAAATACGAAAA
* * * *
52880088 TTTT-AGAAACATGAAAATTTTTAAAACACGACAAT
1 TTTTGA-AAACACGAAAATTTTTGAAATACGA-AAA
* * ** *
52880123 TTTTG-AAACACGAGAAAAAAGTTTAGAAATTTGGAAAT
1 TTTTGAAAACAC--G--AAAATTTTTGAAA-TACGAAAA
* * * **
52880161 TTTTAGAAAACACGAAAAATTTTGAAAAATGGAATT
1 TTTT-GAAAACACGAAAATTTTTGAAATA-CGAAAA
*
52880197 TTTTGAAAACACGAGAATTTTTGAAA
1 TTTTGAAAACACGAAAATTTTTGAAA
52880223 ACATGAAATT
Statistics
Matches: 162, Mismatches: 29, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
33 1 0.01
34 34 0.21
35 70 0.43
36 30 0.19
38 18 0.11
39 3 0.02
40 6 0.04
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (34 bp):
TTTTGAAAACACGAAAATTTTTGAAATACGAAAA
Found at i:52880364 original size:19 final size:18
Alignment explanation
Indices: 52880340--52880400 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 18
52880330 TCGTTACCTT
52880340 ATTTTTGAAAACACGAGAA
1 ATTTTTGAAAACACGAG-A
*
52880359 ATTTTTTTGAAGACACGAGA
1 A--TTTTTGAAAACACGAGA
* *
52880379 A-TTTTG-AAACCCGAGG
1 ATTTTTGAAAACACGAGA
52880395 ATTTTT
1 ATTTTT
52880401 TTTAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 8 0.23
17 9 0.26
19 1 0.03
20 2 0.06
21 15 0.43
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (18 bp):
ATTTTTGAAAACACGAGA
Found at i:52880381 original size:20 final size:21
Alignment explanation
Indices: 52880341--52880383 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
52880331 CGTTACCTTA
52880341 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGAGAAATT
*
52880362 TTTTTGAAGACACGAG-AATT
1 TTTTTGAAAACACGAGAAATT
52880382 TT
1 TT
52880384 GAAACCCGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
TTTTTGAAAACACGAGAAATT
Found at i:52880569 original size:17 final size:16
Alignment explanation
Indices: 52880547--52880584 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
52880537 TTAAAAGTAT
52880547 TTAAAATAGAATTAAAA
1 TTAAAATAGAATT-AAA
*
52880564 TTAAAATTGAATTAAA
1 TTAAAATAGAATTAAA
52880580 TTAAA
1 TTAAA
52880585 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (16 bp):
TTAAAATAGAATTAAA
Found at i:52880755 original size:16 final size:16
Alignment explanation
Indices: 52880734--52880851 Score: 102
Period size: 16 Copynumber: 7.4 Consensus size: 16
52880724 CAAATTAGAG
52880734 TCTTTTTTTCTCTTTT
1 TCTTTTTTTCTCTTTT
*
52880750 TCTTTTTTTTTCTTTT
1 TCTTTTTTTCTCTTTT
*
52880766 T-TTCTCTTTT-TTTTTT
1 TCTT-T-TTTTCTCTTTT
*
52880782 TC-TTTTTCCTTCTTTT
1 TCTTTTTTTC-TCTTTT
52880798 TC-TTTTTTCT-TTTT
1 TCTTTTTTTCTCTTTT
*
52880812 TGCTTTCTTTCTCTTTT
1 T-CTTTTTTTCTCTTTT
* *
52880829 TCTTTCTTTCTTTTTTT
1 TCTTTTTTTC-TCTTTT
52880846 TCTTTT
1 TCTTTT
52880852 CGGCCTGTTG
Statistics
Matches: 85, Mismatches: 8, Indels: 17
0.77 0.07 0.15
Matches are distributed among these distances:
14 8 0.09
15 5 0.06
16 53 0.62
17 19 0.22
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (16 bp):
TCTTTTTTTCTCTTTT
Found at i:52880805 original size:48 final size:48
Alignment explanation
Indices: 52880744--52880851 Score: 130
Period size: 48 Copynumber: 2.2 Consensus size: 48
52880734 TCTTTTTTTC
** * *
52880744 TCTTTTTCTTTTTT-TTTCTTTTTTTCTCTTTTTTTTTTTCTTT-TTCCT
1 TCTTTTTCTTTTTTCTTT-TTTGCTT-TCTTTCTCTTTTTCTTTCTTCCT
*
52880792 TCTTTTTCTTTTTTCTTTTTTGCTTTCTTTCTCTTTTTCTTTCTTTCT
1 TCTTTTTCTTTTTTCTTTTTTGCTTTCTTTCTCTTTTTCTTTCTTCCT
*
52880840 TTTTTTTCTTTT
1 TCTTTTTCTTTT
52880852 CGGCCTGTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 15 0.29
48 34 0.65
49 3 0.06
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (48 bp):
TCTTTTTCTTTTTTCTTTTTTGCTTTCTTTCTCTTTTTCTTTCTTCCT
Found at i:52881000 original size:19 final size:17
Alignment explanation
Indices: 52880967--52881012 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
52880957 TCTTTTCCCT
52880967 CTTTTTTTTGCTGTTTA
1 CTTTTTTTTGCTGTTTA
* *
52880984 TTTTTTTTTGCTTTGTTTG
1 CTTTTTTTTGC--TGTTTA
52881003 CTTTTTTTTG
1 CTTTTTTTTG
52881013 AGCTGCTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
19 14 0.58
ACGTcount: A:0.02, C:0.09, G:0.13, T:0.76
Consensus pattern (17 bp):
CTTTTTTTTGCTGTTTA
Found at i:52881068 original size:18 final size:18
Alignment explanation
Indices: 52881042--52881077 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52881032 ATTGGGCTTG
* *
52881042 CTGGGTCGGGTTGGGTCA
1 CTGGATCGGGTCGGGTCA
52881060 CTGGATCGGGTCGGGTCA
1 CTGGATCGGGTCGGGTCA
52881078 GACCCGGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.19, G:0.47, T:0.25
Consensus pattern (18 bp):
CTGGATCGGGTCGGGTCA
Found at i:52881156 original size:3 final size:3
Alignment explanation
Indices: 52881144--52881195 Score: 59
Period size: 3 Copynumber: 15.7 Consensus size: 3
52881134 TTCCTTTCCC
52881144 TCT TCTT TCT TCT TCT CTCTT TCTT TCT TCT TCT TCT TCT ATCT TCT
1 TCT TC-T TCT TCT TCT -TC-T TC-T TCT TCT TCT TCT TCT -TCT TCT
52881191 TCT TC
1 TCT TC
52881196 AAAACCGAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
3 30 0.67
4 14 0.31
5 1 0.02
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:52881159 original size:10 final size:10
Alignment explanation
Indices: 52881144--52881195 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
52881134 TTCCTTTCCC
52881144 TCTTCTTTCT
1 TCTTCTTTCT
*
52881154 TCTTCTCTC-
1 TCTTCTTTCT
52881163 T-TTCTTTCT
1 TCTTCTTTCT
52881172 TCTTC-TTCT
1 TCTTCTTTCT
52881181 TCTATC-TTCT
1 TCT-TCTTTCT
52881191 TCTTC
1 TCTTC
52881196 AAAACCGAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 6 0.16
9 11 0.30
10 20 0.54
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (10 bp):
TCTTCTTTCT
Found at i:52881188 original size:13 final size:13
Alignment explanation
Indices: 52881144--52881195 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 13
52881134 TTCCTTTCCC
52881144 TCTTCTTTCTTCT
1 TCTTCTTTCTTCT
52881157 TCTCTCTTTCTTTCT
1 TCT-TCTTTC-TTCT
52881172 TCTTC-TTCTTCT
1 TCTTCTTTCTTCT
52881184 ATCTTC-TTCTTC
1 -TCTTCTTTCTTC
52881196 AAAACCGAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.11
13 17 0.47
14 8 0.22
15 7 0.19
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (13 bp):
TCTTCTTTCTTCT
Found at i:52881587 original size:29 final size:28
Alignment explanation
Indices: 52881546--52881622 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 28
52881536 GAATTTTGAG
*
52881546 AAAATTTAGGGGTCAAAATGTAATTTCA
1 AAAAGTTAGGGGTCAAAATGTAATTTCA
52881574 AAAAGTTAGTGGGTCAAAATGTAATTTCA
1 AAAAGTTAG-GGGTCAAAATGTAATTTCA
52881603 AAAAGTTTAGGGGTCAAAAT
1 AAAAG-TTAGGGGTCAAAAT
52881623 ATATTTTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 8 0.17
29 34 0.74
30 4 0.09
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (28 bp):
AAAAGTTAGGGGTCAAAATGTAATTTCA
Found at i:52883995 original size:2 final size:2
Alignment explanation
Indices: 52883988--52884024 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
52883978 AATTTCCAAT
52883988 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52884025 AAATAATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52884099 original size:40 final size:40
Alignment explanation
Indices: 52884054--52884135 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
52884044 CAAATTTATG
* *
52884054 AAAAAACATCAATATAAAAAGATAATACACTAGAAAGATA
1 AAAAAAAATCAATACAAAAAGATAATACACTAGAAAGATA
* * *
52884094 AAAAAAAATCAATACAAAGAGATAGTACACTTGAAAGATA
1 AAAAAAAATCAATACAAAAAGATAATACACTAGAAAGATA
52884134 AA
1 AA
52884136 TGAGAGATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (40 bp):
AAAAAAAATCAATACAAAAAGATAATACACTAGAAAGATA
Found at i:52888549 original size:27 final size:27
Alignment explanation
Indices: 52888485--52888549 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
52888475 AATAATGTAA
52888485 TTATTTATATATATATGTAATTATTAT
1 TTATTTATATATATATGTAATTATTAT
*
52888512 TT-TTATCTATATATATGT-ATATATTTAT
1 TTATT-TATATATATATGTAAT-TA-TTAT
52888540 TTATTT-TATA
1 TTATTTATATA
52888550 AGTGTACATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
26 4 0.12
27 20 0.61
28 7 0.21
29 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (27 bp):
TTATTTATATATATATGTAATTATTAT
Found at i:52891410 original size:45 final size:45
Alignment explanation
Indices: 52891353--52891456 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 45
52891343 TTTTAGTCTT
*
52891353 ATTACTACTATTATATTATATCATTA-ATATA-GTATTATTATTATCG
1 ATTACTATTATTATATT-TATCATTATATATATGTA-TATTATTAT-G
* ** *
52891399 -TTATTATTATTATATTTATTTTTATATATATGTATATTTTTATG
1 ATTACTATTATTATATTTATCATTATATATATGTATATTATTATG
52891443 ATTACTATTATTAT
1 ATTACTATTATTAT
52891457 GCCATTAGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
44 7 0.14
45 39 0.80
46 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.58
Consensus pattern (45 bp):
ATTACTATTATTATATTTATCATTATATATATGTATATTATTATG
Found at i:52891423 original size:18 final size:19
Alignment explanation
Indices: 52891402--52891453 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
52891392 ATTATCGTTA
52891402 TTATTATTATATT-TATTT
1 TTATTATTATATTATATTT
52891420 TTA-TA-TATATGTATATTT
1 TTATTATTATAT-TATATTT
*
52891438 TTATGATTACTATTAT
1 TTATTATTA-TATTAT
52891454 TATGCCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
16 5 0.18
17 3 0.11
18 11 0.39
19 1 0.04
20 5 0.18
21 3 0.11
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (19 bp):
TTATTATTATATTATATTT
Found at i:52893304 original size:68 final size:64
Alignment explanation
Indices: 52893188--52893334 Score: 199
Period size: 69 Copynumber: 2.2 Consensus size: 64
52893178 ATTGCTTACC
52893188 TATAAAAACGCCGCTAAATATTTTCCTATATTTTTTAAAGTAAAATTA-TTTTTGTGGCGTTTTT
1 TATAAAAACGCCGCTAAATATTTTCCTATATTTTTTAAAGTAAAATTATTTTTTGTGGCG-TTTT
*
52893252 TATAAAAACGCCGCTAAATGTTTTGCTGCGCTAT-TTTTTTAAAGTAAAATTATTTTTTGTGGCG
1 TATAAAAACGCCGCTAAAT-ATTT--T-C-CTATATTTTTTAAAGTAAAATTATTTTTTGTGGCG
52893316 TTTT
61 TTTT
*
52893320 TATTTAAAACGCCGC
1 TA-TAAAAACGCCGC
52893335 AAAAAATTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
64 19 0.26
65 3 0.04
67 1 0.01
68 25 0.34
69 26 0.35
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (64 bp):
TATAAAAACGCCGCTAAATATTTTCCTATATTTTTTAAAGTAAAATTATTTTTTGTGGCGTTTT
Found at i:52894245 original size:28 final size:29
Alignment explanation
Indices: 52894203--52894257 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
52894193 CCGAATCTCT
* * *
52894203 AAACCCTAAATCACTAA-CTCTTAACCCC
1 AAACCCCAAACCACTAACCTCTAAACCCC
52894231 AAACCCCAAACCACTAACCTCTAAACC
1 AAACCCCAAACCACTAACCTCTAAACC
52894258 TTATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (29 bp):
AAACCCCAAACCACTAACCTCTAAACCCC
Found at i:52894337 original size:89 final size:89
Alignment explanation
Indices: 52894226--52894400 Score: 260
Period size: 89 Copynumber: 2.0 Consensus size: 89
52894216 CTAACTCTTA
* *
52894226 ACCCCAAACCCCAAACCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTA
1 ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTA
*
52894291 ATCTAAATCATAAACCCTAACCCG
66 ATCTAAACCATAAACCCTAACCCG
* * * * *
52894315 ACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAATTA
1 ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTA
* *
52894380 ATCTAAACCCTAAACTCTAAC
66 ATCTAAACCATAAACCCTAAC
52894401 TTGACACCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 76 1.00
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (89 bp):
ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTA
ATCTAAACCATAAACCCTAACCCG
Found at i:52894424 original size:89 final size:89
Alignment explanation
Indices: 52894238--52894425 Score: 250
Period size: 89 Copynumber: 2.1 Consensus size: 89
52894228 CCCAAACCCC
* * *
52894238 AAACCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATCATA
1 AAACC-CTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATA
* *
52894303 AACCCTAACCCGACCCCAAATCCCT
65 AACCCTAACCCGACACCAAATCCAT
* * * *
52894328 AACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCCTAA
1 AAACCCTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAA
* ** *
52894393 ACTCTAACTTGACACCAAATCTAT
66 ACCCTAACCCGACACCAAATCCAT
52894417 AAACCCTAA
1 AAACCCTAA
52894426 ATCTCTAACT
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 80 0.95
90 4 0.05
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.26
Consensus pattern (89 bp):
AAACCCTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAA
ACCCTAACCCGACACCAAATCCAT
Found at i:52895062 original size:41 final size:40
Alignment explanation
Indices: 52895003--52895200 Score: 236
Period size: 41 Copynumber: 4.8 Consensus size: 40
52894993 AAATGTTTTT
*
52895003 GCGGCGCTTTTTCAAAAACGCCGCTAAAG-CCTCGAGCATTA
1 GCGGCGCTTTTT-AAAAACGCCGCTAAAGATCT-GAGCATTA
**
52895044 GCGGCGCTTCTTGGAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTT-TTTAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
52895085 GTGGCGCTTCTTCAGAAACGCCGCTAAAGATCTGAGTATTA
1 GCGGCGCTT-TTTAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
52895126 GCGGCGCTTTTTTAAAAATGCCACTAAAGATTTGAGCATTA
1 GCGGCGC-TTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
52895167 GCGGCGCTTTTTTAAAAAACGCCGCTAAAGATCT
1 GCGGCGC-TTTTT-AAAAACGCCGCTAAAGATCT
52895201 TAAAGGTAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
41 112 0.83
42 23 0.17
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (40 bp):
GCGGCGCTTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:52895153 original size:82 final size:83
Alignment explanation
Indices: 52895003--52895200 Score: 265
Period size: 82 Copynumber: 2.4 Consensus size: 83
52894993 AAATGTTTTT
* * *
52895003 GCGGCGCTTTTTCAAAAACGCCGCTAAAG-CCTCGAGCATTAGCGGCGCTTCTTGGAAAACGCCG
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTCGAGCATTAGCGGCGCTTCTTGAAAAACGCCA
52895067 CTAAAGATCTGAGCATTA
66 CTAAAGATCTGAGCATTA
* * * * * * *
52895085 GTGGCGCTTCTTCAGAAACGCCGCTAAAGATCT-GAGTATTAGCGGCGCTTTTTTAAAAATGCCA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTCGAGCATTAGCGGCGCTTCTTGAAAAACGCCA
*
52895149 CTAAAGATTTGAGCATTA
66 CTAAAGATCTGAGCATTA
*
52895167 GCGGCGCTTTTTTAAAAAACGCCGCTAAAGATCT
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAGATCT
52895201 TAAAGGTAGA
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
82 74 0.75
83 25 0.25
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (83 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTCGAGCATTAGCGGCGCTTCTTGAAAAACGCCA
CTAAAGATCTGAGCATTA
Found at i:52895303 original size:39 final size:40
Alignment explanation
Indices: 52895260--52895364 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 40
52895250 CCAAAAAACA
*
52895260 CCGCTAATGCTC-ATTTTTAGTGGCGCATT-CCTAGGA-GCG
1 CCGCTAATGCTCGATTTTTAGTGGCACATTACCTA--ATGCG
* * * ** *
52895299 CCGCTAATGCTCTATCTTTAGCGGCATTTTACTTAATGCG
1 CCGCTAATGCTCGATTTTTAGTGGCACATTACCTAATGCG
52895339 CCGCTAATGCTCGATTTTTAGTGGCA
1 CCGCTAATGCTCGATTTTTAGTGGCA
52895365 TTTTTTGTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
39 13 0.24
40 38 0.70
41 3 0.06
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (40 bp):
CCGCTAATGCTCGATTTTTAGTGGCACATTACCTAATGCG
Found at i:52896635 original size:18 final size:18
Alignment explanation
Indices: 52896618--52896665 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
52896608 TTATCGTTAT
52896618 TATTATATT-TATTTTTA
1 TATTATATTATATTTTTA
52896635 TA-TATATGTATATTTTTA
1 TATTATAT-TATATTTTTA
52896653 CTATTACTATTAT
1 -TATTA-TATTAT
52896666 TATGCCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.19
17 3 0.12
18 8 0.31
19 2 0.08
20 5 0.19
21 3 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
TATTATATTATATTTTTA
Found at i:52897650 original size:106 final size:105
Alignment explanation
Indices: 52897449--52897659 Score: 273
Period size: 106 Copynumber: 2.0 Consensus size: 105
52897439 AAGGAAATTT
* * * * * *
52897449 TTTCTAAATAAGGCAATATTTTGCGTTTGGGAATTCGAGAAATCATGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAAGCAATATTTTGCATTTGGAAATTCGAGAAAACATGCCCTAACGTGCTGGGTTT
* *
52897514 TGATTTTCGTTCGACCAAATAACTAAAATATCCTTTTAAAA
66 CGATTTTCGTTCGACCAAATAACT-AAATATCCTCTTAAAA
* *
52897555 TTTCAAAATAAAGTAATATTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAATAAAGCAATATTTTGCATTTGGAAATTCGAGAAAACATGCCCTAACGTGCTGGGTTT
*
52897620 CGATTTCTCGTT-GAACCAAATAGCCT-AATATCCTCTTAAA
66 CGATTT-TCGTTCG-ACCAAATA-ACTAAATATCCTCTTAAA
52897660 TCTCAATCCA
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
106 76 0.84
107 13 0.14
108 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (105 bp):
TTTCAAAATAAAGCAATATTTTGCATTTGGAAATTCGAGAAAACATGCCCTAACGTGCTGGGTTT
CGATTTTCGTTCGACCAAATAACTAAATATCCTCTTAAAA
Found at i:52903325 original size:21 final size:21
Alignment explanation
Indices: 52903299--52903351 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
52903289 AACAGCGGTG
*
52903299 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
52903320 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
52903341 GCAGTGAGATT
1 GCGGTGAGATT
52903352 GGGAACAGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:52907518 original size:41 final size:39
Alignment explanation
Indices: 52907473--52907582 Score: 134
Period size: 37 Copynumber: 2.8 Consensus size: 39
52907463 CGACTTTGAG
*
52907473 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTTAT
1 TCGATGAGACACTGGGTGTCAATTTA-TACTTCGG-TTTAA
* *
52907514 TCGATGAGACACTGTGTGCCAATTTAT--TTCGGTTTAA
1 TCGATGAGACACTGGGTGTCAATTTATACTTCGGTTTAA
* *
52907551 CCGATGAGACACCGGGTGTCAATTTACTACTT
1 TCGATGAGACACTGGGTGTCAATTTA-TACTT
52907583 TAAATTATCC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
37 26 0.44
38 6 0.10
40 3 0.05
41 24 0.41
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTTATACTTCGGTTTAA
Found at i:52911870 original size:7 final size:7
Alignment explanation
Indices: 52911858--52911890 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
52911848 ATTTATTTTA
52911858 ATTTAAT
1 ATTTAAT
52911865 ATTTAAT
1 ATTTAAT
52911872 ATTTAAT
1 ATTTAAT
52911879 ATTTAAAT
1 ATTT-AAT
52911887 ATTT
1 ATTT
52911891 TATTTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTAAT
Found at i:52912333 original size:20 final size:21
Alignment explanation
Indices: 52912308--52912347 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
52912298 TATATATATA
52912308 TATAATTTGTTTTTA-AAAAG
1 TATAATTTGTTTTTATAAAAG
52912328 TATAATTTGTTTTTATAAAA
1 TATAATTTGTTTTTATAAAA
52912348 TTAACCTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TATAATTTGTTTTTATAAAAG
Found at i:52922388 original size:62 final size:62
Alignment explanation
Indices: 52922284--52922630 Score: 344
Period size: 62 Copynumber: 5.6 Consensus size: 62
52922274 ATAATAAATA
* * * *
52922284 AATAGATAAATAGATAAAACAAATATACATAATATTAAATTTAAGTATTTTAGAAGTAAAAGAAT
1 AATAAATAAATAGAT-AAA-AAATATA-AAAATATTAAATTTAAGTATTTGAAAAGTAAAAGAAT
* * * *
52922349 GATAAATAAATTGATAAAAAATATAAAAATATTAAATTTAAGTATTTAAAAAGTTAAAGAAT
1 AATAAATAAATAGATAAAAAATATAAAAATATTAAATTTAAGTATTTGAAAAGTAAAAGAAT
*
52922411 AATAAACAAAT--AT----AA-AT---AATATTAAATTT-AGATATTT-AAAGAGTAAAAGAAT
1 AATAAATAAATAGATAAAAAATATAAAAATATTAAATTTAAG-TATTTGAAA-AGTAAAAGAAT
* *
52922463 AATAAATAAATAGAT-AAAAATATAAAAAAAATTAGATTTAAGTATTTGAAAAGTAAAAGAATGA
1 AATAAATAAATAGATAAAAAATAT-AAAAATATTAAATTTAAGTATTTGAAAAGTAAAAG-A--A
52922527 T
62 T
* *
52922528 AAACAAATAAATAGATATAACAAATATAAATAATATTAAATTTAGGTATTTGAAAAGTAAAAGAA
1 -AATAAATAAATAGATA-AA-AAATATAAA-AATATTAAATTTAAGTATTTGAAAAGTAAAAGAA
52922593 T
62 T
* *
52922594 AATAAATAAATAGATAAAAAA-ATAAAAGTATGAAATT
1 AATAAATAAATAGATAAAAAATATAAAAATATTAAATT
52922631 AATTGAATGA
Statistics
Matches: 240, Mismatches: 20, Indels: 48
0.78 0.06 0.16
Matches are distributed among these distances:
51 5 0.02
52 37 0.15
54 2 0.01
55 2 0.01
56 2 0.01
57 2 0.01
58 2 0.01
60 2 0.01
61 9 0.04
62 70 0.29
63 16 0.07
64 5 0.02
65 29 0.12
66 16 0.07
68 6 0.03
69 35 0.15
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.29
Consensus pattern (62 bp):
AATAAATAAATAGATAAAAAATATAAAAATATTAAATTTAAGTATTTGAAAAGTAAAAGAAT
Found at i:52922447 original size:52 final size:50
Alignment explanation
Indices: 52922362--52922485 Score: 169
Period size: 52 Copynumber: 2.4 Consensus size: 50
52922352 AAATAAATTG
*
52922362 ATAAAAAATATAAAAATATTAAATTTAAGTATTTAAAAAGTTAAAGAATA
1 ATAAAAAATATAAAAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATA
*
52922412 ATAAACAAATATAAATAATATTAAATTT-AGATATTTAAAGAGTAAAAGAATA
1 ATAAA-AAATATAAA-AATATTAAATTTAAG-TATTTAAAAAGTAAAAGAATA
52922464 ATAAATAAATAGATAAAAATAT
1 ATAAA-AAAT--ATAAAAATAT
52922486 AAAAAAAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
50 5 0.08
51 11 0.17
52 40 0.61
53 5 0.08
54 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (50 bp):
ATAAAAAATATAAAAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATA
Found at i:52922502 original size:114 final size:114
Alignment explanation
Indices: 52922300--52922536 Score: 345
Period size: 114 Copynumber: 2.1 Consensus size: 114
52922290 TAAATAGATA
* * * *
52922300 AAACAAATATACATAATATTAAATTTAAGTATTTTAGAAGTAAAAGAATGATAAATAAATTGATA
1 AAACAAATATAAATAATATTAAATTTAAGTATTTAAGAAGTAAAAGAATAATAAATAAATAGATA
* *
52922365 AAAAATATAAAAATATTAAATTTAAGTATTTAAAAAGTTAAAGAATAAT
66 AAAAATATAAAAAAATTAAATTTAAGTATTTAAAAAGTAAAAGAATAAT
52922414 AAACAAATATAAATAATATTAAATTT-AGATATTTAA-AGAGTAAAAGAATAATAAATAAATAGA
1 AAACAAATATAAATAATATTAAATTTAAG-TATTTAAGA-AGTAAAAGAATAATAAATAAATAGA
* * *
52922477 T-AAAAATATAAAAAAAATTAGATTTAAGTATTTGAAAAGTAAAAGAATGAT
64 TAAAAAATAT-AAAAAAATTAAATTTAAGTATTTAAAAAGTAAAAGAATAAT
52922528 AAACAAATA
1 AAACAAATA
52922537 AATAGATATA
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
113 11 0.10
114 100 0.90
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (114 bp):
AAACAAATATAAATAATATTAAATTTAAGTATTTAAGAAGTAAAAGAATAATAAATAAATAGATA
AAAAATATAAAAAAATTAAATTTAAGTATTTAAAAAGTAAAAGAATAAT
Found at i:52922571 original size:69 final size:68
Alignment explanation
Indices: 52922408--52922605 Score: 245
Period size: 69 Copynumber: 3.0 Consensus size: 68
52922398 AAAGTTAAAG
52922408 AATA-ATA-AACAAATATAAATAATATTAAATTT-AGATATTT-AAAGAGTAAAAG-A-AT-AAT
1 AATAGATATAACAAATATAAATAATATTAAATTTAAG-TATTTGAAA-AGTAAAAGAATATAAAT
52922466 AAATA
64 AAATA
* * * *
52922471 AATAG--ATAA-AAATATAAAAAAAATTAGATTTAAGTATTTGAAAAGTAAAAGAATGATAAACA
1 AATAGATATAACAAATATAAATAATATTAAATTTAAGTATTTGAAAAGTAAAAGAAT-ATAAATA
52922533 AATA
65 AATA
*
52922537 AATAGATATAACAAATATAAATAATATTAAATTTAGGTATTTGAAAAGTAAAAGAATAATAAATA
1 AATAGATATAACAAATATAAATAATATTAAATTTAAGTATTTGAAAAGTAAAAGAAT-ATAAATA
52922602 AATA
65 AATA
52922606 GATAAAAAAA
Statistics
Matches: 114, Mismatches: 10, Indels: 16
0.81 0.07 0.11
Matches are distributed among these distances:
62 33 0.29
63 12 0.11
65 2 0.02
66 12 0.11
68 4 0.04
69 51 0.45
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.29
Consensus pattern (68 bp):
AATAGATATAACAAATATAAATAATATTAAATTTAAGTATTTGAAAAGTAAAAGAATATAAATAA
ATA
Found at i:52923707 original size:16 final size:15
Alignment explanation
Indices: 52923679--52923726 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
52923669 TCAAATACAT
* *
52923679 ATTTATCTAATATTT
1 ATTTATTTAATATTA
52923694 ATTATATTTAATATTA
1 ATT-TATTTAATATTA
*
52923710 ATTTTTTTAATA-TA
1 ATTTATTTAATATTA
52923724 ATT
1 ATT
52923727 AGTTGGTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 5 0.17
15 11 0.38
16 13 0.45
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTTAATATTA
Found at i:52926623 original size:65 final size:69
Alignment explanation
Indices: 52926523--52926704 Score: 219
Period size: 65 Copynumber: 2.7 Consensus size: 69
52926513 AAGTATAAGT
* * * * * * * *
52926523 AATATCAAATCTAAATATTGAAAAAGGTAAAAGAATAATGAATAAATAGAT-AA-AACAAATAT-
1 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATAAATCAATAAAAAATATA
* *
52926585 ACAT
66 AAAA
* *
52926589 AATATTAAATTTAAGTATTT-TAGAAGTAAAAGAATAATAAATAAATAAATCAATAAAAAATATA
1 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATAAATCAATAAAAAATATA
52926653 AAAA
66 AAAA
*
52926657 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAACAAATA
1 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATA
52926705 TAAATAATAT
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
65 25 0.26
66 18 0.19
67 8 0.08
68 22 0.23
69 24 0.25
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.27
Consensus pattern (69 bp):
AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATAAATCAATAAAAAATATA
AAAA
Found at i:52926691 original size:69 final size:66
Alignment explanation
Indices: 52926523--52926909 Score: 237
Period size: 69 Copynumber: 6.0 Consensus size: 66
52926513 AAGTATAAGT
* * * * * * * * *
52926523 AATATCAAATCTAAATATTGAAAAAGGTAAAAGAATAATGAATAAATAGATAAAACAAATATACA
1 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATAAATAAAAAAAATATAAA
*
52926588 T
66 A
* *
52926589 AATATTAAATTTAAGTATTT-TAGAAGTAAAAGAATAATAAATAAATAAATCAATAAAAAATATA
1 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATAAAT-AA-AAAAAATAT-
52926653 AAAA
63 AAAA
* * *
52926657 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAACAAAT--AT--AAATAATAT--T
1 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATAAATAAAAAAAATATAAA
52926716 A
66 A
* * *
52926717 AAT-TTAGATATTTAAAG-A-GT--AAAAG---AATAATAAATAAATAGATAAA-A-----AATA
1 AATATTA-A-ATTT-AAGTATTTAAAAAAGTAAAAGAAT-AATAAATAAATAAATAAAAAAAATA
52926768 TAAAA
62 TAAAA
* * * * *
52926773 AA-ATTAGATTTAAGAATTT-GAAAAGTAAAAGAATGATAAACAAATAAATAGATATAACAAATA
1 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATAAATA-A-A-AA-AAATA
*
52926836 TAAAT
62 TAAAA
* *
52926841 AATATTAAATTTAGGTATTT-GAAAAGTAAAAGAATAATAAATAAATAAATAGATCAAACAAATA
1 AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATAAATA-A--AAA-AAATA
52926905 TAAAA
62 TAAAA
52926910 GGATGAAATT
Statistics
Matches: 253, Mismatches: 36, Indels: 61
0.72 0.10 0.17
Matches are distributed among these distances:
53 3 0.01
54 10 0.04
55 6 0.02
56 20 0.08
58 17 0.07
59 9 0.04
60 6 0.02
61 5 0.02
62 3 0.01
63 8 0.03
65 25 0.10
66 18 0.07
67 10 0.04
68 32 0.13
69 80 0.32
70 1 0.00
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (66 bp):
AATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAATAAATAAATAAAAAAAATATAAA
A
Found at i:52926714 original size:53 final size:52
Alignment explanation
Indices: 52926640--52926768 Score: 172
Period size: 53 Copynumber: 2.4 Consensus size: 52
52926630 TAAATAAATC
52926640 AATAAAAAATATAAAAAAATATTAAATTTA-AGTATTTAAAAAAGTAAAAGAAT
1 AATAAAAAATATAAAAAAATATTAAATTTAGA-TATTT-AAAAAGTAAAAGAAT
* *
52926693 AATAAACAAATAT-AAATAATATTAAATTTAGATATTTAAAGAGTAAAAGAAT
1 AATAAA-AAATATAAAAAAATATTAAATTTAGATATTTAAAAAGTAAAAGAAT
*
52926745 AATAAATAAATAGATAAAAAATAT
1 AATAAA-AAATATA-AAAAAATAT
52926769 AAAAAAATTA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
52 25 0.37
53 27 0.40
54 15 0.22
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (52 bp):
AATAAAAAATATAAAAAAATATTAAATTTAGATATTTAAAAAGTAAAAGAAT
Found at i:52926754 original size:22 final size:21
Alignment explanation
Indices: 52926729--52926771 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
52926719 TTTAGATATT
52926729 TAAAGAG-TAAAAGAATAATAAA
1 TAAAGAGATAAAA-AAT-ATAAA
*
52926751 TAAATAGATAAAAAATATAAA
1 TAAAGAGATAAAAAATATAAA
52926772 AAAATTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (21 bp):
TAAAGAGATAAAAAATATAAA
Found at i:52926756 original size:52 final size:53
Alignment explanation
Indices: 52926640--52926768 Score: 174
Period size: 52 Copynumber: 2.4 Consensus size: 53
52926630 TAAATAAATC
52926640 AATAAAAAATATAAAAAAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAAT
1 AATAAAAAATATAAAAAAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAAT
* *
52926693 AATAAACAAATAT-AAATAATATTAAATTT-AGATATTT-AAAGAGTAAAAGAAT
1 AATAAA-AAATATAAAAAAATATTAAATTTAAG-TATTTAAAAAAGTAAAAGAAT
*
52926745 AATAAATAAATAGATAAAAAATAT
1 AATAAA-AAATATA-AAAAAATAT
52926769 AAAAAAATTA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
52 27 0.40
53 26 0.39
54 14 0.21
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (53 bp):
AATAAAAAATATAAAAAAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAAT
Found at i:52926780 original size:22 final size:23
Alignment explanation
Indices: 52926736--52926781 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
52926726 ATTTAAAGAG
*
52926736 TAAAAGAATAATAAATAAATAGA
1 TAAAAGAATAATAAAAAAATAGA
52926759 TAAAA-AAT-ATAAAAAAATTAGA
1 TAAAAGAATAATAAAAAAA-TAGA
52926781 T
1 T
52926782 TTAAGAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (23 bp):
TAAAAGAATAATAAAAAAATAGA
Found at i:52926868 original size:183 final size:187
Alignment explanation
Indices: 52926516--52926887 Score: 497
Period size: 183 Copynumber: 2.0 Consensus size: 187
52926506 GAAAGGGAAG
* *
52926516 TATAAGTAATATCAAATCTAAATATTGAAAAAGGTAAAAGAATAATGAATAAATAGATAAAACAA
1 TATAAATAATATCAAATCTAAATATTGAAAAAGGTAAAAGAATAATAAATAAATAGATAAAACAA
* * * * * *
52926581 ATATACATAATATTAAATTTAAGTATTTTAGAAGTAAAAGAATAATAAATAAATAAATCAATAAA
66 ATATACAAAAAATTAAATTTAAGAATTTGAAAAGTAAAAGAATAATAAACAAATAAATCAATAAA
52926646 AAATATAAAAAAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAACAAA
131 AAATATAAAAAAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAACAAA
* * * * *
52926703 TATAAATAATATTAAATTTAGATATTTAAAGA-GTAAAAGAATAATAAATAAATAGAT-AAA-AA
1 TATAAATAATATCAAATCTAAATATTGAAAAAGGTAAAAGAATAATAAATAAATAGATAAAACAA
* *
52926765 ATATA-AAAAAATTAGATTTAAGAATTTGAAAAGTAAAAGAATGATAAACAAATAAAT-AGATAT
66 ATATACAAAAAATTAAATTTAAGAATTTGAAAAGTAAAAGAATAATAAACAAATAAATCA-ATA-
* * * *
52926828 AACAAATAT-AAATAATATTAAATTTAGGTATTT-GAAAAGTAAAAGAATAATAAATAAA
129 AA-AAATATAAAAAAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAACAAA
52926886 TA
1 TA
52926888 AATAGATCAA
Statistics
Matches: 163, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
182 1 0.01
183 72 0.44
184 31 0.19
185 9 0.06
186 24 0.15
187 26 0.16
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.28
Consensus pattern (187 bp):
TATAAATAATATCAAATCTAAATATTGAAAAAGGTAAAAGAATAATAAATAAATAGATAAAACAA
ATATACAAAAAATTAAATTTAAGAATTTGAAAAGTAAAAGAATAATAAACAAATAAATCAATAAA
AAATATAAAAAAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAACAAA
Found at i:52928332 original size:44 final size:44
Alignment explanation
Indices: 52928279--52928362 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
52928269 AGGTTTTGTC
* **
52928279 GCTTCAATCTGCTCCATTGCAACTTTGGGGAGATAAGATTAGTA
1 GCTTCAATCTGCTCCACTGCAACTTCCGGGAGATAAGATTAGTA
* *
52928323 GCTTTAATCTGCTCCACTGTAACTTCCGGGAGATAAGATT
1 GCTTCAATCTGCTCCACTGCAACTTCCGGGAGATAAGATT
52928363 TATAACTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (44 bp):
GCTTCAATCTGCTCCACTGCAACTTCCGGGAGATAAGATTAGTA
Found at i:52928465 original size:96 final size:96
Alignment explanation
Indices: 52928311--52928557 Score: 298
Period size: 96 Copynumber: 2.6 Consensus size: 96
52928301 CTTTGGGGAG
* * * * * *
52928311 ATAAGATTAG-TAGCTTTAATCTGCTCCACTGTAACTTCCGGGAGATAAGATTTATAACTCATAC
1 ATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTCATAC
*
52928375 CTGTAATCTGTTCCATTACAACTTCAAAGAA
66 CTGTAATCTGTTCCACTACAACTTCAAAGAA
* * * *
52928406 ATAAGATTTGCTATCTTCAATCTACTCTACTGCAACTTCAGGGAGATAAGATTTGTAACTTATAG
1 ATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTCATAC
* * **
52928471 CTTTAATCTGTTCCACTACAACTTTAGGGAA
66 CTGTAATCTGTTCCACTACAACTTCAAAGAA
* * * * * *
52928502 ATGATATTTGCTATATTCACTCTGCTCCACTGCAACTTTAGGGAGATAAAATTTGT
1 ATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT
52928558 GGCTTTAATC
Statistics
Matches: 128, Mismatches: 23, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
95 9 0.07
96 119 0.93
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (96 bp):
ATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTCATAC
CTGTAATCTGTTCCACTACAACTTCAAAGAA
Found at i:52928500 original size:51 final size:47
Alignment explanation
Indices: 52928284--52928598 Score: 191
Period size: 45 Copynumber: 6.7 Consensus size: 47
52928274 TTGTCGCTTC
* ** * *
52928284 AATCTGCTCCATTGCAACTTTGGGGAGATAAGATTAG--TA-GCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCTATACTTT
* * * *
52928328 AATCTGCTCCACTGTAACTTCCGGGAGATAAGATTTATAACTCATACCTGT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT--CT-ATA-CTTT
* * * ** * *
52928379 AATCTGTTCCATTACAACTTCAAAGAAATAAGATTTG-CTAT-CTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCTATACTTT
* *
52928424 AATCTACTCTACTGCAACTTCAGGGAGATAAGATTTGTAACTTATAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT--C-TATA-CTTT
* * * * * * *
52928475 AATCTGTTCCACTACAACTTTAGGGAAATGATATTTG-CTATA-TTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCTATACTTT
* * * **
52928520 ACTCTGCTCCACTGCAACTTTAGGGAGATAAAATTTG--T-GGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCTATACTTT
** *
52928564 AATCTATTCCACTGCAACTTCAAGGAGATAAGATT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
52928599 CGCCACGGTG
Statistics
Matches: 205, Mismatches: 52, Indels: 28
0.72 0.18 0.10
Matches are distributed among these distances:
44 63 0.31
45 64 0.31
47 6 0.03
48 5 0.02
49 4 0.02
51 63 0.31
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (47 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCTATACTTT
Found at i:52936808 original size:21 final size:21
Alignment explanation
Indices: 52936782--52936825 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
52936772 ATTCCTTAAG
52936782 TAAATTTATTGAGATCACAAA
1 TAAATTTATTGAGATCACAAA
52936803 TAAATTTATTGAGATCACAAA
1 TAAATTTATTGAGATCACAAA
52936824 TA
1 TA
52936826 TCAAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (21 bp):
TAAATTTATTGAGATCACAAA
Found at i:52937514 original size:41 final size:41
Alignment explanation
Indices: 52937313--52937516 Score: 329
Period size: 41 Copynumber: 5.0 Consensus size: 41
52937303 TTAATTTAAA
*
52937313 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
52937355 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
52937396 CAGATCACCGGCACTTAGCCTACTAGGCTTATAGCCTAATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
52937437 TAGATCACCGGCACTTAGCCTGCTAAGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
52937478 CAGATCACCGGCACTTAGCCTGCTAGGCGTTA-AGCCTGA
1 CAGATCACCGGCACTTAGCCTGCTAGGC-TTATAGCCTGA
52937517 AAACTTCAAA
Statistics
Matches: 152, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
41 145 0.95
42 7 0.05
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:52940358 original size:13 final size:13
Alignment explanation
Indices: 52940340--52940364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52940330 AAATTTAATA
52940340 TTATTTTGTGTGT
1 TTATTTTGTGTGT
52940353 TTATTTTGTGTG
1 TTATTTTGTGTG
52940365 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:52941944 original size:41 final size:41
Alignment explanation
Indices: 52941884--52942100 Score: 371
Period size: 41 Copynumber: 5.3 Consensus size: 41
52941874 GTTTGAAATT
*
52941884 GGTGATCTGAATCAGGCTATAAGCTTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
*
52941925 GGTGATCTGAATCAAGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
52941966 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
**
52942007 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTATC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* * *
52942048 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
52942089 GGTGATCTGAAT
1 GGTGATCTGAAT
52942101 ATGTTAAATT
Statistics
Matches: 165, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 165 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
Found at i:52943064 original size:20 final size:20
Alignment explanation
Indices: 52943036--52943073 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52943026 TACATATTAT
*
52943036 CACTCTTCATGATTTGACTC
1 CACTCTTCATGACTTGACTC
*
52943056 CACTGTTCATGACTTGAC
1 CACTCTTCATGACTTGAC
52943074 CCCATTATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (20 bp):
CACTCTTCATGACTTGACTC
Found at i:52943084 original size:20 final size:20
Alignment explanation
Indices: 52943036--52943085 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
52943026 TACATATTAT
* * *
52943036 CACTCTTCATGATTTGACTC
1 CACTATTCATGACTTGACCC
*
52943056 CACTGTTCATGACTTGACCC
1 CACTATTCATGACTTGACCC
*
52943076 CATTATTCAT
1 CACTATTCAT
52943086 AAGACTGACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.30, G:0.10, T:0.38
Consensus pattern (20 bp):
CACTATTCATGACTTGACCC
Found at i:52948509 original size:26 final size:25
Alignment explanation
Indices: 52948475--52948529 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
52948465 ATTTATGTTA
52948475 TTAAAA-TAT-TTA-TTATAAAATAT
1 TTAAAATTATATTATTTAT-AAATAT
*
52948498 TTAAAATTATATTATTTATATATAT
1 TTAAAATTATATTATTTATAAATAT
52948523 TTAAAAT
1 TTAAAAT
52948530 ATTAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 6 0.21
24 3 0.11
25 15 0.54
26 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAAAATTATATTATTTATAAATAT
Found at i:52948513 original size:37 final size:34
Alignment explanation
Indices: 52948455--52948537 Score: 87
Period size: 37 Copynumber: 2.4 Consensus size: 34
52948445 GAATTTAAAT
* * * *
52948455 AAATATTTATATTTATGTTATTAAAATATTTATTATA
1 AAATATTTAAAATTATATTATT--AATATATATT-TA
*
52948492 AAATATTTAAAATTATATTATTTATATATATTTA
1 AAATATTTAAAATTATATTATTAATATATATTTA
52948526 AAATA-TTAAAAT
1 AAATATTTAAAAT
52948538 ATAATTGTCG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 7 0.17
34 7 0.17
35 8 0.20
37 19 0.46
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (34 bp):
AAATATTTAAAATTATATTATTAATATATATTTA
Found at i:52949068 original size:22 final size:23
Alignment explanation
Indices: 52949030--52949076 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
52949020 CCGTAAGTTA
52949030 GAACACAATATTTTTTTATTCTT
1 GAACACAATATTTTTTTATTCTT
*
52949053 GAACACGAT-TTTTTTTATTCTT
1 GAACACAATATTTTTTTATTCTT
52949075 GA
1 GA
52949077 GATTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (23 bp):
GAACACAATATTTTTTTATTCTT
Found at i:52951186 original size:44 final size:44
Alignment explanation
Indices: 52951133--52951231 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
52951123 TCAACATTTT
* * * *
52951133 AATCCGCTCCACCGCAACTTCGGGGAGATAGGATTAATAGT-TTC
1 AATCTGCTCCACCGCAACTTCAGGCAGATAAGATTAATA-TCTTC
** * *
52951177 AATCTGCTCCATTGCAACTTCAGGCAGATAATATTAGTATCTTC
1 AATCTGCTCCACCGCAACTTCAGGCAGATAAGATTAATATCTTC
52951221 AATCTGCTCCA
1 AATCTGCTCCA
52951232 TTGTATTCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 1 0.02
44 45 0.98
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACCGCAACTTCAGGCAGATAAGATTAATATCTTC
Found at i:52951263 original size:42 final size:44
Alignment explanation
Indices: 52951174--52951264 Score: 107
Period size: 42 Copynumber: 2.1 Consensus size: 44
52951164 GATTAATAGT
* * *
52951174 TTCAATCTGCTCCATTGCAACTTCAGGCAGATAATATTAGTATC
1 TTCAATCTGCTCCATTGCAACTTCAGGCAGATAAGACTAGTAAC
* *
52951218 TTCAATCTGCTCCATTG-TA-TTCAGGGAGATAAGACCT-GTAAC
1 TTCAATCTGCTCCATTGCAACTTCAGGCAGATAAGA-CTAGTAAC
52951260 TTCAA
1 TTCAA
52951265 CCTACTCTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 22 0.54
43 2 0.05
44 17 0.41
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (44 bp):
TTCAATCTGCTCCATTGCAACTTCAGGCAGATAAGACTAGTAAC
Found at i:52951294 original size:44 final size:43
Alignment explanation
Indices: 52951240--52951331 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 43
52951230 CATTGTATTC
* *
52951240 AGGGAGATAAGACCTGTAACTTCAACCTACTCTACTGTAACTTT
1 AGGGAAATAAGACC-GTAACTTCAACCTACTCTACTGCAACTTT
** * * * *
52951284 AGGGAAATAAGGTCGTGACTTTAATCTACTGTACTGCAACTTT
1 AGGGAAATAAGACCGTAACTTCAACCTACTCTACTGCAACTTT
52951327 AGGGA
1 AGGGA
52951332 GATAGGATTC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 29 0.73
44 11 0.28
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
AGGGAAATAAGACCGTAACTTCAACCTACTCTACTGCAACTTT
Done.