Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010573.1 Kokia drynarioides strain JFW-HI SEQ_125496, whole genome shotgun sequence
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: 690509
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 15 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:545482 original size:21 final size:20
Alignment explanation
Indices: 545432--545481 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
545422 ATAAAATTTT
545432 TGGAAGTTTTAGGGTCAAAAA
1 TGGAA-TTTTAGGGTCAAAAA
*
545453 TGGGATTTTAAGGGT-AAAAA
1 TGGAATTTT-AGGGTCAAAAA
545473 TGGAATTTT
1 TGGAATTTT
545482 TGGAAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (20 bp):
TGGAATTTTAGGGTCAAAAA
Found at i:545488 original size:50 final size:50
Alignment explanation
Indices: 545413--545511 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
545403 TGGAAGTTCG
545413 AGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTA
1 AGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTA
** *
545463 AGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTT
1 AGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTT
545512 GGGAAGTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.34
Consensus pattern (50 bp):
AGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTA
Found at i:545568 original size:88 final size:89
Alignment explanation
Indices: 545459--545667 Score: 278
Period size: 88 Copynumber: 2.3 Consensus size: 89
545449 AAAATGGGAT
** * * *
545459 TTTAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTGGGAAGTTTTGG
1 TTTAAGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTGGGAAGTTTCGA
545524 GGTT-AAAAT-GAGATTTTGGGAAG
66 GGTTAAAAATAG-GATTTTGGGAAG
* *
545547 TTTAAGGGTAAAAATAAAATTTTTAGAAGTTTTAGGGTTAAAAATGGGATTTTGGGAAGTTTCGA
1 TTTAAGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTGGGAAGTTTCGA
*
545612 GGTTAAAAATAGGATTTTTGGAAG
66 GGTTAAAAATAGGATTTTGGGAAG
*** *
545636 TTCGGGGGTAAAAACAAAATTTTTGGACAGTT
1 TTTAAGGGTAAAAATAAAATTTTTGGA-AGTT
545668 CAGGGACCTT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
88 62 0.59
89 38 0.36
90 5 0.05
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (89 bp):
TTTAAGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTGGGAAGTTTCGA
GGTTAAAAATAGGATTTTGGGAAG
Found at i:545647 original size:29 final size:29
Alignment explanation
Indices: 545459--545672 Score: 162
Period size: 30 Copynumber: 7.2 Consensus size: 29
545449 AAAATGGGAT
*
545459 TTTAAGGGTAAAAAT-GGAATTTTTGGAAG
1 TTTAGGGGTAAAAATAGG-ATTTTTGGAAG
* * *
545488 TTTTGGGGTCAAAAATGGGATTTTGGGAAG
1 TTTAGGGGT-AAAAATAGGATTTTTGGAAG
* * *
545518 TTTTGGGGTTAAAAT-GAGATTTTGGGAAG
1 TTTAGGGGTAAAAATAG-GATTTTTGGAAG
* ** *
545547 TTTAAGGGTAAAAATAAAATTTTTAGAAG
1 TTTAGGGGTAAAAATAGGATTTTTGGAAG
* * *
545576 TTTTAGGGTTAAAAATGGGATTTTGGGAAG
1 -TTTAGGGGTAAAAATAGGATTTTTGGAAG
* *
545606 TTTCGAGGTTAAAAATAGGATTTTTGGAAG
1 TTTAG-GGGTAAAAATAGGATTTTTGGAAG
** * **
545636 TTCGGGGGTAAAAACAAAATTTTTGGACAG
1 TTTAGGGGTAAAAATAGGATTTTTGGA-AG
*
545666 TTCAGGG
1 TTTAGGG
545673 ACCTTCATGG
Statistics
Matches: 150, Mismatches: 28, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
28 1 0.01
29 67 0.45
30 80 0.53
31 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
TTTAGGGGTAAAAATAGGATTTTTGGAAG
Found at i:545648 original size:59 final size:58
Alignment explanation
Indices: 545459--545649 Score: 193
Period size: 59 Copynumber: 3.2 Consensus size: 58
545449 AAAATGGGAT
* * * * * * *
545459 TTTAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTGGGAAG
1 TTTAGGGGTAAAAATGGGATTTTGGGAAG-TTTGAGGTTAAAAATAGGATTTTTGGAAG
* * * * * ** *
545518 TTTTGGGGTTAAAATGAGATTTTGGGAAGTTTAAGGGTAAAAATAAAATTTTTAGAAG
1 TTTAGGGGTAAAAATGGGATTTTGGGAAGTTTGAGGTTAAAAATAGGATTTTTGGAAG
*
545576 TTTTAGGGTTAAAAATGGGATTTTGGGAAGTTTCGAGGTTAAAAATAGGATTTTTGGAAG
1 -TTTAGGGGTAAAAATGGGATTTTGGGAAGTTT-GAGGTTAAAAATAGGATTTTTGGAAG
**
545636 TTCGGGGGTAAAAA
1 TTTAGGGGTAAAAA
545650 CAAAATTTTT
Statistics
Matches: 103, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
58 20 0.19
59 62 0.60
60 21 0.20
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.35
Consensus pattern (58 bp):
TTTAGGGGTAAAAATGGGATTTTGGGAAGTTTGAGGTTAAAAATAGGATTTTTGGAAG
Found at i:547333 original size:18 final size:18
Alignment explanation
Indices: 547310--547395 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 18
547300 TTTTTTAATT
547310 AATTAAATTTTAAA-TTCA
1 AATTAAATTTTAAACTT-A
547328 AATT-AATTTTAAACTTA
1 AATTAAATTTTAAACTTA
*
547345 ATTTAAA-TTTAAACTTAA
1 AATTAAATTTTAAACTT-A
** *
547363 AAGAAAAGTTTAAACTTTA
1 AATTAAATTTTAAAC-TTA
*
547382 AACTAAA-TTTAAAC
1 AATTAAATTTTAAAC
547396 CCAAAATGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
17 22 0.39
18 20 0.35
19 13 0.23
20 2 0.04
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (18 bp):
AATTAAATTTTAAACTTA
Found at i:548420 original size:2 final size:2
Alignment explanation
Indices: 548413--548440 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
548403 TTATGGAAGA
548413 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
548441 TTATGGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:549007 original size:21 final size:19
Alignment explanation
Indices: 548973--549011 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
548963 TTTTATTTTA
548973 ATATTAAATAAATATAATT
1 ATATTAAATAAATATAATT
548992 ATATTAATATTAAATATAAT
1 ATATTAA-A-TAAATATAAT
549012 AAAAATACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTAAATAAATATAATT
Found at i:550403 original size:24 final size:24
Alignment explanation
Indices: 550369--550417 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
550359 ATTATGATAC
*
550369 TGTTTTTATTGTT-ATTTTTGTTGT
1 TGTTTTGATTGTTGA-TTTTGTTGT
550393 TGTTTTGATTGTTGATTTTGTTGT
1 TGTTTTGATTGTTGATTTTGTTGT
550417 T
1 T
550418 TGAGTGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.08, C:0.00, G:0.20, T:0.71
Consensus pattern (24 bp):
TGTTTTGATTGTTGATTTTGTTGT
Found at i:553989 original size:26 final size:27
Alignment explanation
Indices: 553957--554021 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
553947 TGCCCAGTCA
*
553957 ATAGGCGGCACC-AAAATGCCTATCCC
1 ATAGGCGGCACCAAAAACGCCTATCCC
* * * *
553983 ATTGGCGACACCAAAAACGTCTATCCT
1 ATAGGCGGCACCAAAAACGCCTATCCC
554010 ATAGGCGGCACC
1 ATAGGCGGCACC
554022 CATGTTACAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.17
Consensus pattern (27 bp):
ATAGGCGGCACCAAAAACGCCTATCCC
Found at i:554264 original size:27 final size:27
Alignment explanation
Indices: 554211--554264 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
554201 GTTGTTGTTG
* *
554211 TTTTTAATTTATTTTAAAATTATTTTA
1 TTTTTAATTTATTATAAAATTAGTTTA
*
554238 TTTTTAA-TTATTATAAAGTTTAGTTTA
1 TTTTTAATTTATTATAAA-ATTAGTTTA
554265 ATACTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (27 bp):
TTTTTAATTTATTATAAAATTAGTTTA
Found at i:554337 original size:15 final size:17
Alignment explanation
Indices: 554317--554354 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
554307 TAAAGGAAAT
554317 TTTATTGA-AA-TTTTA
1 TTTATTGAGAATTTTTA
554332 TTTATTGAGAATTTTTA
1 TTTATTGAGAATTTTTA
554349 TTTATT
1 TTTATT
554355 TTTTAACAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.38
16 2 0.10
17 11 0.52
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (17 bp):
TTTATTGAGAATTTTTA
Found at i:568069 original size:13 final size:14
Alignment explanation
Indices: 568019--568071 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
568009 CTAAAAAAAT
*
568019 AAATCA-TTTTCTAA
1 AAATCATTTTTC-GA
568033 AAATCATTTTTCGA
1 AAATCATTTTTCGA
*
568047 AAATCTTTTTTCGA
1 AAATCATTTTTCGA
568061 AAATC-TTTTTC
1 AAATCATTTTTC
568072 ATCGAAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 6 0.17
14 25 0.69
15 5 0.14
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (14 bp):
AAATCATTTTTCGA
Found at i:568078 original size:16 final size:14
Alignment explanation
Indices: 568032--568070 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
568022 TCATTTTCTA
*
568032 AAAATCATTTTTCG
1 AAAATCTTTTTTCG
568046 AAAATCTTTTTTCG
1 AAAATCTTTTTTCG
568060 AAAATCTTTTT
1 AAAATCTTTTT
568071 CATCGAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (14 bp):
AAAATCTTTTTTCG
Found at i:568693 original size:17 final size:17
Alignment explanation
Indices: 568673--568744 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
568663 AATAAGTTTG
568673 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* * * *
568690 AATTCATTTTGAGTTTG
1 AATTTATTTTAAATTTA
*
568707 AATTTACTTTAAATTTA
1 AATTTATTTTAAATTTA
*
568724 AATTTATTTTAAATTAA
1 AATTTATTTTAAATTTA
568741 AATT
1 AATT
568745 AATTAAAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:568706 original size:34 final size:34
Alignment explanation
Indices: 568667--568733 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
568657 TTTTAAAATA
*
568667 AGTTTGAATTTATTTTAAATTTAAATTCATTTTG
1 AGTTTGAATTTACTTTAAATTTAAATTCATTTTG
*
568701 AGTTTGAATTTACTTTAAATTTAAATTTATTTT
1 AGTTTGAATTTACTTTAAATTTAAATTCATTTT
568734 AAATTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (34 bp):
AGTTTGAATTTACTTTAAATTTAAATTCATTTTG
Found at i:570648 original size:59 final size:60
Alignment explanation
Indices: 570565--570984 Score: 303
Period size: 59 Copynumber: 7.2 Consensus size: 60
570555 GAACTTTCTA
** * *
570565 AAAAATTA-CA-TTTACCCTTAAACTTTTC-GAAAATTACCATTTTTCCCTTGAACTTCC
1 AAAAATTACCATTTTACCCTCGAACTTTTCTAAAAATTACCATTTTTCCCTCGAACTTCC
* * * * * *
570622 AAAAATTATCATTTTGCCCTCGAAC--TTCCAAAAATTACCATTTTACACT-AAACTTCC
1 AAAAATTACCATTTTACCCTCGAACTTTTCTAAAAATTACCATTTTTCCCTCGAACTTCC
* * * *
570679 AAAAATTACCA-TTTACCCT-TAA-ATTTCTAAAAATT-CCATTTTTGACCTCAAACTTTCC
1 AAAAATTACCATTTTACCCTCGAACTTTTCTAAAAATTACCATTTTT-CCCTCGAAC-TTCC
* * * * *
570737 -AAATTTACCATTTTACCCT--AAATTTCCAAAAAATT-TCATTTTTGACCC-CGAACTTTCC
1 AAAAATTACCATTTTACCCTCGAACTTTTCTAAAAATTACCATTTTT--CCCTCGAAC-TTCC
* * ** *
570795 AAAAATTACCATTTTACCCTCAAACATCAC-AAAAATTA-CATTTTTGCTCC-CGAGCTTCC
1 AAAAATTACCATTTTACCCTCGAACTTTTCTAAAAATTACCATTTTT-C-CCTCGAACTTCC
* * * *
570854 AAAAATTACCATTTTACCATCGAAC-TTTCTAAAAATTACCA-TTTTACCTTGAATTTCC
1 AAAAATTACCATTTTACCCTCGAACTTTTCTAAAAATTACCATTTTTCCCTCGAACTTCC
* * *
570912 AAAAATT-CCATTTTTTACCC-CGAA-TTTTCTAAAAATTACCATTTTACCCTCGATCATCC
1 AAAAATTACCA--TTTTACCCTCGAACTTTTCTAAAAATTACCATTTTTCCCTCGAACTTCC
*
570971 AAAAATCA-CATTTT
1 AAAAATTACCATTTT
570985 TGGCTCCGTT
Statistics
Matches: 294, Mismatches: 45, Indels: 48
0.76 0.12 0.12
Matches are distributed among these distances:
55 9 0.03
56 19 0.06
57 52 0.18
58 92 0.31
59 96 0.33
60 22 0.07
61 4 0.01
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.36
Consensus pattern (60 bp):
AAAAATTACCATTTTACCCTCGAACTTTTCTAAAAATTACCATTTTTCCCTCGAACTTCC
Found at i:570748 original size:30 final size:30
Alignment explanation
Indices: 570647--570809 Score: 93
Period size: 28 Copynumber: 5.6 Consensus size: 30
570637 GCCCTCGAAC
* *
570647 TTCCAAAAATTACCA-TTTT-ACACTAAAC-
1 TTCCAAAATTTACCATTTTTGAC-CCAAACT
*
570675 TTCCAAAAATTACCA--TTT-ACCCTTAAA-T
1 TTCCAAAATTTACCATTTTTGACCC--AAACT
* *
570703 TTCTAAAAATT-CCATTTTTGACCTCAAACT
1 TTCCAAAATTTACCATTTTTGACC-CAAACT
570733 TTCC-AAATTTACCA-TTTT-ACCCTAAA-T
1 TTCCAAAATTTACCATTTTTGACCC-AAACT
*
570760 TTCCAAAAAATTT--CATTTTTGACCCCGAACT
1 TTCC--AAAATTTACCATTTTTGA-CCCAAACT
*
570791 TTCCAAAAATTACCATTTT
1 TTCCAAAATTTACCATTTT
570810 ACCCTCAAAC
Statistics
Matches: 110, Mismatches: 6, Indels: 35
0.73 0.04 0.23
Matches are distributed among these distances:
26 1 0.01
27 14 0.13
28 36 0.33
29 25 0.23
30 19 0.17
31 15 0.14
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
TTCCAAAATTTACCATTTTTGACCCAAACT
Found at i:570974 original size:29 final size:29
Alignment explanation
Indices: 570524--570984 Score: 308
Period size: 29 Copynumber: 15.8 Consensus size: 29
570514 GAAGGTCCTT
* *
570524 GAACTGTCCAAAAATCA-TATTTTGACCCTC
1 GAACT-TCCAAAAATTACCATTTT-ACCCTC
* *
570554 TGAACTTTCTAAAAAATTA-CA-TTTACCCTT
1 -GAAC-TTC-CAAAAATTACCATTTTACCCTC
* * * * *
570584 AAACTTTTCGAAAATTACCATTTTTCCCTT
1 GAAC-TTCCAAAAATTACCATTTTACCCTC
* *
570614 GAACTTCCAAAAATTATCATTTTGCCCTC
1 GAACTTCCAAAAATTACCATTTTACCCTC
*
570643 GAACTTCCAAAAATTACCATTTTACACT-
1 GAACTTCCAAAAATTACCATTTTACCCTC
* *
570671 AAACTTCCAAAAATTACCA-TTTACCCTT
1 GAACTTCCAAAAATTACCATTTTACCCTC
* * *
570699 AAATTTCTAAAAATT-CCATTTTTGA-CCTC
1 GAACTTCCAAAAATTACCA-TTTT-ACCCTC
* *
570728 AAACTTTCC-AAATTTACCATTTTACCCT-
1 GAAC-TTCCAAAAATTACCATTTTACCCTC
* * *
570756 AAATTTCCAAAAAATT-TCATTTTTGACCC-C
1 GAACTTCC-AAAAATTACCA-TTTT-ACCCTC
570786 GAACTTTCCAAAAATTACCATTTTACCCTC
1 GAAC-TTCCAAAAATTACCATTTTACCCTC
* * *
570816 AAACATCACAAAAATTA-CATTTTTGCTCC-C
1 GAACTTC-CAAAAATTACCA-TTTTAC-CCTC
* *
570846 GAGCTTCCAAAAATTACCATTTTACCATC
1 GAACTTCCAAAAATTACCATTTTACCCTC
* *
570875 GAACTTTCTAAAAATTACCATTTTA-CCTT
1 GAAC-TTCCAAAAATTACCATTTTACCCTC
*
570904 GAATTTCCAAAAATT-CCATTTTTTACCC-C
1 GAACTTCCAAAAATTACCA--TTTTACCCTC
* *
570933 GAATTTTCTAAAAATTACCATTTTACCCTC
1 GAA-CTTCCAAAAATTACCATTTTACCCTC
* * *
570963 GATCATCCAAAAATCA-CATTTT
1 GAACTTCCAAAAATTACCATTTT
570985 TGGCTCCGTT
Statistics
Matches: 346, Mismatches: 53, Indels: 65
0.75 0.11 0.14
Matches are distributed among these distances:
27 17 0.05
28 61 0.18
29 139 0.40
30 100 0.29
31 20 0.06
32 9 0.03
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
GAACTTCCAAAAATTACCATTTTACCCTC
Found at i:576148 original size:17 final size:17
Alignment explanation
Indices: 576126--576198 Score: 69
Period size: 18 Copynumber: 4.2 Consensus size: 17
576116 GGATTCAATG
*
576126 AAAAAACAAGGAAAGAAA
1 AAAAAAGAA-GAAAGAAA
576144 AAAAAAGAAGAAAG-AA
1 AAAAAAGAAGAAAGAAA
*
576160 AAAGAAGAA-AAAGCAAA
1 AAAAAAGAAGAAAG-AAA
*
576177 ATAAAAAAAAGAAAGAGAA
1 A-AAAAAGAAGAAAGA-AA
576196 AAA
1 AAA
576199 GAGAGGTCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
15 4 0.09
16 10 0.22
17 8 0.17
18 17 0.37
19 7 0.15
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.01
Consensus pattern (17 bp):
AAAAAAGAAGAAAGAAA
Found at i:576154 original size:13 final size:13
Alignment explanation
Indices: 576138--576198 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
576128 AAAACAAGGA
576138 AAGAAAAAAAAAG
1 AAGAAAAAAAAAG
*
576151 AAGAAAGAAAAAG
1 AAGAAAAAAAAAG
*
576164 AAGAAAAAGCAAAAT
1 AAGAAAAA--AAAAG
576179 AA-AAAAAAGAAAG
1 AAGAAAAAA-AAAG
576192 -AGAAAAA
1 AAGAAAAA
576199 GAGAGGTCGA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.05
13 27 0.68
14 5 0.12
15 6 0.15
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (13 bp):
AAGAAAAAAAAAG
Found at i:576170 original size:21 final size:21
Alignment explanation
Indices: 576136--576200 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
576126 AAAAAACAAG
*
576136 GAAAGAAAA-AAAAAGAAGAAA
1 GAAAAAAAAGAAAAAGAA-AAA
* *
576157 GAAAAAGAAGAAAAAGCAAAA
1 GAAAAAAAAGAAAAAGAAAAA
* *
576178 TAAAAAAAAGAAAGAGAAAAA
1 GAAAAAAAAGAAAAAGAAAAA
576199 GA
1 GA
576201 GAGGTCGAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 28 0.80
22 7 0.20
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
GAAAAAAAAGAAAAAGAAAAA
Found at i:577289 original size:99 final size:99
Alignment explanation
Indices: 577113--577411 Score: 438
Period size: 99 Copynumber: 3.0 Consensus size: 99
577103 AGCTGAGAAA
* *
577113 ACCATGAAGATTTTAAGGGAAAGGTTGAGGCCGC-ATGGCGAACCTAGTACCTTAGAAGATATGA
1 ACCATGAAGATTTTAAGGGAAAGGTTGAGGCCGCAATGGCGAACATGGTACCTTAGAAGATATGA
* * *
577177 AGGGAAAGGTTGAGGCCGGAATGGTGAACCCTGT
66 AGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGT
* **
577211 ACCATGAAGATTTTAAGGGAAAGGTTGAGGCCGCAATGGCGAACATGGTATCTTAGTGGATATGA
1 ACCATGAAGATTTTAAGGGAAAGGTTGAGGCCGCAATGGCGAACATGGTACCTTAGAAGATATGA
577276 AGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGT
66 AGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGT
* * * * ** *
577310 ACCATGAAGAATTTAAGGAAAAGGTTGAGGTCGCAACGGTAAACTTGGTACCTTAGAAGATATGA
1 ACCATGAAGATTTTAAGGGAAAGGTTGAGGCCGCAATGGCGAACATGGTACCTTAGAAGATATGA
* *
577375 AGGGAAAGGTTGAGGCTGCAATGGCGAACTCGGT
66 AGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGT
577409 ACC
1 ACC
577412 TTAGAAAACA
Statistics
Matches: 180, Mismatches: 20, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
98 34 0.19
99 146 0.81
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.20
Consensus pattern (99 bp):
ACCATGAAGATTTTAAGGGAAAGGTTGAGGCCGCAATGGCGAACATGGTACCTTAGAAGATATGA
AGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGT
Found at i:577292 original size:50 final size:50
Alignment explanation
Indices: 577118--577417 Score: 333
Period size: 49 Copynumber: 6.1 Consensus size: 50
577108 AGAAAACCAT
* * *
577118 GAAGATTTTAAGGGAAAGGTTGAGGCCGC-ATGGCGAACCTAGTACCTTA
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCTGGTACCTTA
* * *
577167 GAAGATATGAAGGGAAAGGTTGAGGCCGGAATGGTGAACCCT-GTACCAT-
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAA-CCTGGTACCTTA
* * * *
577216 GAAGATTTTAAGGGAAAGGTTGAGGCCGCAATGGCGAACATGGTATCTTA
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCTGGTACCTTA
** * *
577266 GTGGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCAT-
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCTGGTACCTTA
* * * * ** *
577315 GAAGA-ATTTAAGGAAAAGGTTGAGGTCGCAACGGTAAACTTGGTACCTTA
1 GAAGATA-TGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCTGGTACCTTA
*
577365 GAAGATATGAAGGGAAAGGTTGAGGCTGCAATGGCGAA-CTCGGTACCTTA
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCT-GGTACCTTA
577415 GAA
1 GAA
577418 AACAAGATGA
Statistics
Matches: 204, Mismatches: 39, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
48 3 0.01
49 102 0.50
50 95 0.47
51 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (50 bp):
GAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCTGGTACCTTA
Found at i:577653 original size:41 final size:41
Alignment explanation
Indices: 577571--577666 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 41
577561 TACATCATCA
* * *
577571 TTCAGTCTTTTACCCCTAATCAAGAATGATAGATTGAAGAT
1 TTCAGTCTTTTACCCCTAATCAAGAAGGATAAATAGAAGAT
* *
577612 TTCAGTCTTTTACCCTTAATCAAGAAGGGTAAAATAG-AGAT
1 TTCAGTCTTTTACCCCTAATCAAGAAGGAT-AAATAGAAGAT
577653 TTC-GATCTTTTACC
1 TTCAG-TCTTTTACC
577667 TCGAGCCCGG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.02
41 43 0.90
42 4 0.08
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (41 bp):
TTCAGTCTTTTACCCCTAATCAAGAAGGATAAATAGAAGAT
Found at i:577720 original size:39 final size:38
Alignment explanation
Indices: 577657--577768 Score: 111
Period size: 39 Copynumber: 2.9 Consensus size: 38
577647 AGAGATTTCG
* *
577657 ATCTTTTACCTCGAGCCCGGGGCAGATCACCATCAGTCA
1 ATCTCTTACCTCGAG-CCTGGGCAGATCACCATCAGTCA
** * *
577696 ATCTCTTACCTCGAGCCTGAGGCAGAT-TGCAGTCATTCG
1 ATCTCTTACCTCGAGCCTG-GGCAGATCACCA-TCAGTCA
577735 ATCTCTTACGC-CGAGCCTCGGGCAGATCACCATC
1 ATCTCTTAC-CTCGAGCCT-GGGCAGATCACCATC
577769 GACCTATCTC
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
38 5 0.08
39 51 0.85
40 4 0.07
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.24
Consensus pattern (38 bp):
ATCTCTTACCTCGAGCCTGGGCAGATCACCATCAGTCA
Found at i:577798 original size:78 final size:78
Alignment explanation
Indices: 577653--577802 Score: 182
Period size: 78 Copynumber: 1.9 Consensus size: 78
577643 AAATAGAGAT
* * * *
577653 TTCGATCTTTTACCTCGAGCCCGGGGCAGATCACCATCAGTCAATCTCTTACCTCGAGCCTGAGG
1 TTCGATCTCTTACCTCGAGCCCGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCATGAGG
577718 CAGATTGCAGTCA
66 CAGATTGCAGTCA
*
577731 TTCGATCTCTTACGC-CGAGCCTC-GGGCAGATCACCATC-GACCTATCTCTTACCCCGAG-ATA
1 TTCGATCTCTTAC-CTCGAGCC-CGGGGCAGATCACCATCAG-CCAATCTCTTACCCCGAGCAT-
*
577792 GGGGCAGATTG
62 GAGGCAGATTG
577803 TAACCACCCG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
77 2 0.03
78 58 0.94
79 2 0.03
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (78 bp):
TTCGATCTCTTACCTCGAGCCCGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCATGAGG
CAGATTGCAGTCA
Found at i:577861 original size:39 final size:38
Alignment explanation
Indices: 577735--577878 Score: 94
Period size: 39 Copynumber: 3.7 Consensus size: 38
577725 CAGTCATTCG
* * * * *
577735 ATCTCTTACGCCGAGCC-TCGGGCAGATCACCATCGACCT
1 ATCTCTTACCCCGA-CCATAGGGCAGATCA-CAACCACCA
* *** *
577774 ATCTCTTACCCCGA-GATAGGGGCAGATTGTAACCACCCG
1 ATCTCTTACCCCGACCATA-GGGCAGATCACAACCA-CCA
* *
577813 ATCTTTTACCCCGACCATAGGGCAGATCACAGCCATCCA
1 ATCTCTTACCCCGACCATAGGGCAGATCACAACCA-CCA
* * *
577852 ATCTCTTACCTCGACCATGGGGTAGAT
1 ATCTCTTACCCCGACCATAGGGCAGAT
577879 TACGATTATC
Statistics
Matches: 80, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
38 4 0.05
39 73 0.91
40 3 0.04
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.22
Consensus pattern (38 bp):
ATCTCTTACCCCGACCATAGGGCAGATCACAACCACCA
Found at i:578678 original size:209 final size:210
Alignment explanation
Indices: 577905--579537 Score: 2001
Period size: 209 Copynumber: 7.8 Consensus size: 210
577895 AAAGAGACGA
* * * * * *
577905 TCATCTTCCTAATGAGATATTGAGAAGCAAACCAAATCAATGAAACCAAGGCTCGATGTGAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* * * *
577970 AACTTCGAACCCTAACTTCCTGATGAGGTACTGAGAAGCAGGTTGAAGCAATAAAGTGGTTACCT
66 AACTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCT
* * * * * ** *
578035 TCCTTATGAGATACAAAGAAGTAAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGCAGATTA
131 TCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
* * *
578100 AAATAAATGAGGCGG
196 AAACAAGTGATGCGG
* * ***
578115 TCATCTTTCTGATGAGATACTGAGAAGTAGACCAAATCGATGAAACCAAGGCTCGGTGTGAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
** * * * *
578180 AACTTCGAACCTTAGCTTTCTAATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCAGTTATCT
66 AACTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCT
* * * * * ** *
578245 TCCTGATGAGATACAGAGAAGTAAACCAAATCTGTCTACCTAATGAGATACAGAGAAGCAGATTA
131 TCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
* * *
578310 AAATAAATGAGGCGG
196 AAACAAGTGATGCGG
* * * * * *
578325 TCATCTTTCTGATGAGATATTGAGAAGCAGACCAAATCGATGAAACCAAGGCTCTATGTGAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* *
578390 AACTTCGAACCCCAGCTTCTTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTACCT
66 AACTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCT
* * * * *
578455 TCTTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTAATGAAACACAGAGAAGTGGATCA
131 TCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
*
578520 AAACAAGTGATGCGA
196 AAACAAGTGATGCGG
* * * *
578535 TCATCTTCCTGATGAGATACTAATAAGTAAACCCAATCAATGAAACC-AGGCTCAAAGTGAGC-A
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
** * **
578598 AATCTTTAAACCCCAGCTTCCTGATGAGGTATTGAGAAGCAGGTCGAAGCAATAAAATGGTTACC
66 AA-CTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACC
* * *
578663 TTCCTGATAAGATACAGAGAAGTGAACCAGATCCCTCTTCCTGATGAGACACAGAGAAGTGGATC
130 TTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGGATC
578728 AAAACAAGTGATGCGG
195 AAAACAAGTGATGCGG
* * *
578744 TCATCTTCTTGATGAGATACTAAGAAGTAAACCAAATCAATGAAACC-AGGCTCAAAGTGAGC-A
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* * * *
578807 AATCTTCGAACCCCAGCTTCTTGATAAGGTAC-CAAAAGCAGGTCGAAGCAATAAAGCGGTTACC
66 AA-CTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACC
* * *
578871 TTCCTGATGAGATACAGAGAAGTGAACCAGATCCAG-CTTCCTGATGAGACACATAGAAGTGAAT
130 TTCCTGATGAGATACAGAGAAGTGAACCAAATCC-GTCTTCCTGATGAGACACAGAGAAGTGGAT
*
578935 AAAAACAAGTGATGCGG
194 CAAAACAAGTGATGCGG
*
578952 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATTAATGAAACC-AGGCTCAAAGTGAGC-A
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* * * *
579015 AATCTTCGAACCTCAGCTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAGCAGTTACC
66 AA-CTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACC
* * * * *
579080 TTCTTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCCTGACGAGACACAGAGAAGTAGATC
130 TTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGGATC
579145 AAAACAAGTGATGCGG
195 AAAACAAGTGATGCGG
*
579161 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC-AGACTCAAAGTGAGC-A
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* * * *
579224 AATCTTCGAACCTCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAGCGATTACC
66 AA-CTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACC
* * * * * ** * * *
579289 TTCCTGATAATATACAGAAAAGTGGACCAAATCCGTCTTCCTGGTGAGTTATAGAGAAGCGGATG
130 TTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGGATC
** *
579354 AAAACAAACGATGCGA
195 AAAACAAGTGATGCGG
* * * ** *
579370 TCATCTTCCTAATGAGATATTGAGAAGTAGACCAAATCAATGAAACCAAAGCTTGATGTGAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* * * * * * * * *
579435 AACTTCGAACCCTAGCTTCCTGATGAGATACTGAAAAGCAAGTTGATGCAAT-AAGATGGTCATC
66 AACTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAG-CGGTTACC
* **
579499 TTCCTGACGAGATGTAGAGAAGTGAACCAAATCCGTCTT
130 TTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTT
579538 TCTAGTAAAA
Statistics
Matches: 1266, Mismatches: 150, Indels: 14
0.89 0.10 0.01
Matches are distributed among these distances:
208 194 0.15
209 565 0.45
210 504 0.40
211 3 0.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (210 bp):
TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
AACTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCT
TCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
AAACAAGTGATGCGG
Found at i:578996 original size:417 final size:420
Alignment explanation
Indices: 577905--579537 Score: 1994
Period size: 417 Copynumber: 3.9 Consensus size: 420
577895 AAAGAGACGA
* * * *
577905 TCATCTTCCTAATGAGATATTGAGAAGCAAACCAAATCAATGAAACCAAGGCTCGATGTGAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGCAAACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* * * *
577970 AACTTCGAACCCTAACTTCCTGATGAGGTACTGAGAAGCAGGTTGAAGCAATAAAGTGGTTACCT
66 AACTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCT
* * * * * * *
578035 TCCTTATGAGATACAAAGAAGTAAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGCAGATTA
131 TCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAG-TGAATA
* * * *
578100 AAATA-AA-TGAGGCGGTCATCTTTCTGATGAGATACTGAGAAGTAGACCAAATCGATGAAACCA
195 AAA-ACAAGTGATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
*** ** * * *
578163 AGGCTCGGTGTGAGCGAAACTTCGAACCTTAGCTTTCTAATGAGGTACTGAGAAGCAGGTCGAAG
259 AGGCTCAAAGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* * * * * *
578228 CAATAAAGCAGTTATCTTCCTGATGAGATACAGAGAAGTAAACCAAATCTGTCTACCTAATGAGA
324 CAATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGA
* * * * * *
578293 TACAGAGAAGCAGATTAAAATAAATGAGGCGG
389 CACAGAGAAGTAGATCAAAACAAGTGATGCGG
* * * * * *
578325 TCATCTTTCTGATGAGATATTGAGAAGCAGACCAAATCGATGAAACCAAGGCTCTATGTGAGCGA
1 TCATCTTCCTGATGAGATACTGAGAAGCAAACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* *
578390 AACTTCGAACCCCAGCTTCTTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTACCT
66 AACTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCT
* * * * * * *
578455 TCTTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTAATGAAACACAGAGAAGTGGATCA
131 TCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGAATAA
* * * *
578520 AAACAAGTGATGCGATCATCTTCCTGATGAGATACTAATAAGTAAACCCAATCAATGAAACC-AG
196 AAACAAGTGATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAG
** * *
578584 GCTCAAAGTGAGC-AAATCTTTAAACCCCAGCTTCCTGATGAGGTATTGAGAAGCAGGTCGAAGC
261 GCTCAAAGTGAGCGAAA-CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
** * * *
578648 AATAAAATGGTTACCTTCCTGATAAGATACAGAGAAGTGAACCAGATCCCTCTTCCTGATGAGAC
325 AATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGAC
*
578713 ACAGAGAAGTGGATCAAAACAAGTGATGCGG
390 ACAGAGAAGTAGATCAAAACAAGTGATGCGG
* * *
578744 TCATCTTCTTGATGAGATACTAAGAAGTAAACCAAATCAATGAAACC-AGGCTCAAAGTGAGC-A
1 TCATCTTCCTGATGAGATACTGAGAAGCAAACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* * * *
578807 AATCTTCGAACCCCAGCTTCTTGATAAGGTAC-CAAAAGCAGGTCGAAGCAATAAAGCGGTTACC
66 AA-CTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACC
* *
578871 TTCCTGATGAGATACAGAGAAGTGAACCAGATCCAG-CTTCCTGATGAGACACATAGAAGTGAAT
130 TTCCTGATGAGATACAGAGAAGTGAACCAAATCC-GTCTTCCTGATGAGACACAGAGAAGTGAAT
* *
578935 AAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATTAATGAAACC-
194 AAAAACAAGTGATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
* *
578999 AGGCTCAAAGTGAGC-AAATCTTCGAACCTCAGCTTCCTGATGAGATACAGAGAAGCAGGTCGAA
259 AGGCTCAAAGTGAGCGAAA-CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
* * * * *
579063 GCAATAAAGCAGTTACCTTCTTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCCTGACGAG
323 GCAATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAG
579128 ACACAGAGAAGTAGATCAAAACAAGTGATGCGG
388 ACACAGAGAAGTAGATCAAAACAAGTGATGCGG
* * *
579161 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC-AGACTCAAAGTGAGC-A
1 TCATCTTCCTGATGAGATACTGAGAAGCAAACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
* * * *
579224 AATCTTCGAACCTCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAGCGATTACC
66 AA-CTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACC
* * * * * ** * * * *
579289 TTCCTGATAATATACAGAAAAGTGGACCAAATCCGTCTTCCTGGTGAGTTATAGAGAAGCGGATG
130 TTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGAATA
** * *
579354 AAAACAAACGATGCGATCATCTTCCTAATGAGATATTGAGAAGTAGACCAAATCAATGAAACCAA
195 AAAACAAGTGATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAA
* ** * * * * * *
579419 AGCTTGATGTGAGCGAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAAAAGCAAGTTGATGC
260 GGCTCAAAGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* ** * * * **
579484 AATAAGATGGTCATCTTCCTGACGAGATGTAGAGAAGTGAACCAAATCCGTCTT
325 AATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTT
579538 TCTAGTAAAA
Statistics
Matches: 1050, Mismatches: 154, Indels: 19
0.86 0.13 0.02
Matches are distributed among these distances:
417 380 0.36
418 181 0.17
419 270 0.26
420 219 0.21
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (420 bp):
TCATCTTCCTGATGAGATACTGAGAAGCAAACCAAATCAATGAAACCAAGGCTCAAAGTGAGCGA
AACTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCT
TCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAGAAGTGAATAA
AAACAAGTGATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAG
GCTCAAAGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGACA
CAGAGAAGTAGATCAAAACAAGTGATGCGG
Found at i:579973 original size:17 final size:17
Alignment explanation
Indices: 579953--580024 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
579943 AACAAGTTTG
579953 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* * * *
579970 AATTCATTTTGAGTTTG
1 AATTTATTTTAAATTTA
*
579987 AATTTACTTTAAATTTA
1 AATTTATTTTAAATTTA
*
580004 AATTTATTTTAAATTAA
1 AATTTATTTTAAATTTA
580021 AATT
1 AATT
580025 AATTAAATCA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:579986 original size:34 final size:34
Alignment explanation
Indices: 579947--580013 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
579937 TTTTAAAACA
*
579947 AGTTTGAATTTATTTTAAATTTAAATTCATTTTG
1 AGTTTGAATTTACTTTAAATTTAAATTCATTTTG
*
579981 AGTTTGAATTTACTTTAAATTTAAATTTATTTT
1 AGTTTGAATTTACTTTAAATTTAAATTCATTTT
580014 AAATTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (34 bp):
AGTTTGAATTTACTTTAAATTTAAATTCATTTTG
Found at i:581844 original size:30 final size:30
Alignment explanation
Indices: 581808--581867 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
581798 CAGAAATCAT
*
581808 ATTTTGAACCTTAAACTTTCTAAAAATTAC
1 ATTTTGAACCTCAAACTTTCTAAAAATTAC
* *
581838 ATTTTGACCCTCATACTTTCTAAAAATTAC
1 ATTTTGAACCTCAAACTTTCTAAAAATTAC
581868 CATTCTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (30 bp):
ATTTTGAACCTCAAACTTTCTAAAAATTAC
Found at i:581878 original size:30 final size:30
Alignment explanation
Indices: 581822--581879 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
581812 TGAACCTTAA
*
581822 ACTTTCTAAAAATTACATTTTGACCCTCAT
1 ACTTTCTAAAAATTACATTCTGACCCTCAT
581852 ACTTTCTAAAAATTACCATTCT-ACCCTC
1 ACTTTCTAAAAATTA-CATTCTGACCCTC
581880 GAACTTCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.38
Consensus pattern (30 bp):
ACTTTCTAAAAATTACATTCTGACCCTCAT
Found at i:581893 original size:30 final size:29
Alignment explanation
Indices: 581829--582229 Score: 238
Period size: 30 Copynumber: 13.7 Consensus size: 29
581819 TAAACTTTCT
*
581829 AAAAATTA-CATTTTGACCCTC-ATACTTTCT
1 AAAAATTACCATTTT-ACCCTCGA-AC-TTCC
*
581859 AAAAATTACCATTCTACCCTCGAACTTCAC
1 AAAAATTACCATTTTACCCTCGAACTTC-C
* * *
581889 AAAAATTA-AATTTTTGCCCCCGAACTTCC
1 AAAAATTACCA-TTTTACCCTCGAACTTCC
*
581918 AAAAATTACCATTTTATCCCT-AAACTTCC
1 AAAAATTACCATTTTA-CCCTCGAACTTCC
* *
581947 AAAAATTACCATTTT-CCCTTGAATTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCC
* * **
581975 AAAAATT-TCATTTTTGA-CCTTGAACTTTTT
1 AAAAATTACCA-TTTT-ACCCTCGAAC-TTCC
* * *
582005 GAAATTTACCATTTTA-CCTCGAATTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCC
* * *
582033 AAAAAATT-TCATTATTGACCC-CAAACTTTCG
1 -AAAAATTACCATT-TT-ACCCTCGAAC-TTCC
* *
582064 AAAAATTACCATTTTTCCCCCGAACTTCAC
1 AAAAATTACCATTTTACCCTCGAACTTC-C
* * * * *
582094 AAAAATTA-CATTTTTGCTCTTGAGCTTTC
1 AAAAATTACCA-TTTTACCCTCGAACTTCC
* * *
582123 GAAAATTACCATTTTACCC-CTAAACTTGC
1 AAAAATTACCATTTTACCCTC-GAACTTCC
* *
582152 AAAAATTACCATTTT--CCTTGAATTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCC
* **
582179 AAAAATTTCGTTTTTGACCCT-GAACTTTCC
1 AAAAATTACCATTTT-ACCCTCGAAC-TTCC
582209 AAAAATTACCATTTTACCCTC
1 AAAAATTACCATTTTACCCTC
582230 AGGCATCCAA
Statistics
Matches: 284, Mismatches: 58, Indels: 58
0.71 0.14 0.14
Matches are distributed among these distances:
27 25 0.09
28 23 0.08
29 109 0.38
30 110 0.39
31 17 0.06
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCGAACTTCC
Found at i:581932 original size:29 final size:29
Alignment explanation
Indices: 581829--582228 Score: 205
Period size: 29 Copynumber: 13.7 Consensus size: 29
581819 TAAACTTTCT
* *
581829 AAAAATTA-CATTTTGACCC-TCATACTTTCT
1 AAAAATTACCATTTTG-CCCTTGA-AC-TTCC
* * *
581859 AAAAATTACCATTCTACCCTCGAACTTCAC
1 AAAAATTACCATTTTGCCCTTGAACTTC-C
* **
581889 AAAAATTA-AATTTTTGCCCCCGAACTTCC
1 AAAAATTACCA-TTTTGCCCTTGAACTTCC
* *
581918 AAAAATTACCATTTTATCCC-TAAACTTCC
1 AAAAATTACCATTTT-GCCCTTGAACTTCC
*
581947 AAAAATTACCATTTT-CCCTTGAATTTCC
1 AAAAATTACCATTTTGCCCTTGAACTTCC
* * **
581975 AAAAATT-TCATTTTTGACCTTGAACTTTTT
1 AAAAATTACCA-TTTTGCCCTTGAAC-TTCC
* * * * *
582005 GAAATTTACCATTTT-ACCTCGAATTTCC
1 AAAAATTACCATTTTGCCCTTGAACTTCC
* ** *
582033 AAAAAATT-TCATTATTGACCC-CAAACTTTCG
1 -AAAAATTACCATT-TTG-CCCTTGAAC-TTCC
* **
582064 AAAAATTACCATTTTTCCCCCGAACTTCAC
1 AAAAATTACCATTTTGCCCTTGAACTTC-C
* * *
582094 AAAAATTA-CATTTTTGCTCTTGAGCTTTC
1 AAAAATTACCA-TTTTGCCCTTGAACTTCC
* * * * *
582123 GAAAATTACCATTTTACCCCTAAACTTGC
1 AAAAATTACCATTTTGCCCTTGAACTTCC
*
582152 AAAAATTACCATTTT--CCTTGAATTTCC
1 AAAAATTACCATTTTGCCCTTGAACTTCC
* **
582179 AAAAATTTCGTTTTTGACCC-TGAACTTTCC
1 AAAAATTACCATTTTG-CCCTTGAAC-TTCC
*
582209 AAAAATTACCATTTTACCCT
1 AAAAATTACCATTTTGCCCT
582229 CAGGCATCCA
Statistics
Matches: 280, Mismatches: 64, Indels: 52
0.71 0.16 0.13
Matches are distributed among these distances:
27 25 0.09
28 24 0.09
29 109 0.39
30 105 0.38
31 17 0.06
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAAATTACCATTTTGCCCTTGAACTTCC
Found at i:581961 original size:59 final size:57
Alignment explanation
Indices: 581859--582228 Score: 204
Period size: 59 Copynumber: 6.4 Consensus size: 57
581849 CATACTTTCT
* *
581859 AAAAATTACCATTCTA-CCCTCGAACTTCACAAAAATTA-AATTTTTGCCCCCGAACTTCC
1 AAAAATTACCATTTTATCCCT-GAACTTC-CAAAAATTACCA-TTTT-CCCCCGAACTTCC
* ** *
581918 AAAAATTACCATTTTATCCCTAAACTTCCAAAAATTACCATTTTCCCTTGAATTTCC
1 AAAAATTACCATTTTATCCCTGAACTTCCAAAAATTACCATTTTCCCCCGAACTTCC
* * *** * * * *
581975 AAAAATT-TCATTTT-TGACCTTGAACTTTTTGAAATTTACCATTTTACCTCGAATTTCC
1 AAAAATTACCATTTTAT--CCCTGAAC-TTCCAAAAATTACCATTTTCCCCCGAACTTCC
* ** *
582033 AAAAAATT-TCATTATTGA-CCCCAAACTTTCGAAAAATTACCATTTTTCCCCCGAACTTCAC
1 -AAAAATTACCATT-TT-ATCCCTGAAC-TTCCAAAAATTACCA-TTTTCCCCCGAACTTC-C
* * * * ** *
582094 AAAAATTA-CATTTT-TGCTCTTGAGCTTTCGAAAATTACCATTTTACCCCTAAACTTGC
1 AAAAATTACCATTTTAT-C-CCTGAACTTCCAAAAATTACCATTTT-CCCCCGAACTTCC
* * * ** * *
582152 AAAAATTACCA-TTT-TCCTTGAATTTCCAAAAATTTCGTTTTTGACCCTGAACTTTCC
1 AAAAATTACCATTTTATCCCTGAACTTCCAAAAATTACCATTTT-CCCCCGAAC-TTCC
582209 AAAAATTACCATTTTA-CCCT
1 AAAAATTACCATTTTATCCCT
582229 CAGGCATCCA
Statistics
Matches: 244, Mismatches: 47, Indels: 41
0.73 0.14 0.12
Matches are distributed among these distances:
55 1 0.00
56 32 0.13
57 38 0.16
58 62 0.25
59 77 0.32
60 33 0.14
61 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.36
Consensus pattern (57 bp):
AAAAATTACCATTTTATCCCTGAACTTCCAAAAATTACCATTTTCCCCCGAACTTCC
Found at i:582242 original size:205 final size:204
Alignment explanation
Indices: 581829--582226 Score: 575
Period size: 205 Copynumber: 2.0 Consensus size: 204
581819 TAAACTTTCT
* * *
581829 AAAAATTACATTTTGACCCTCATACTTTCTAAAAATTACCATTCTACCCTCGAACTTCACAAAAA
1 AAAAATTACATTTTGACCCTCAAACTTTCGAAAAATTACCATTCTACCCCCGAACTTCACAAAAA
*
581894 TTAAATTTTTGCCCCCGAACTTCCAAAAATTACCATTTTATCCCTAAACTTCCAAAAATTACCAT
66 TTAAATTTTTGCCCCCGAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTACCAT
* *** *
581959 TTTCCCTTGAATTTCCAAAAATTTCATTTTTGACCTTGAACTTTTTGAAATTTACCATTTTACCT
131 TTTCCCTTGAATTTCCAAAAATTTCATTTTTGACCCTGAACTTTCCAAAAATTACCATTTTACCT
582024 CGAATTTCCA
196 CGAA-TTCCA
* * *
582034 AAAAATTTCATTATTGACCC-CAAACTTTCGAAAAATTACCATTTTTCCCCCGAACTTCACAAAA
1 AAAAATTACATT-TTGACCCTCAAACTTTCGAAAAATTACCATTCTACCCCCGAACTTCACAAAA
* * ** * * * *
582098 ATTACATTTTTGCTCTTGAGCTTTCGAAAATTACCATTTTACCCCTAAACTTGCAAAAATTACCA
65 ATTAAATTTTTGCCCCCGAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTACCA
*
582163 TTTT-CCTTGAATTTCCAAAAATTTCGTTTTTGACCCTGAACTTTCCAAAAATTACCATTTTACC
130 TTTTCCCTTGAATTTCCAAAAATTTCATTTTTGACCCTGAACTTTCCAAAAATTACCATTTTACC
582227 CTCAGGCATC
Statistics
Matches: 171, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
204 54 0.32
205 110 0.64
206 7 0.04
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (204 bp):
AAAAATTACATTTTGACCCTCAAACTTTCGAAAAATTACCATTCTACCCCCGAACTTCACAAAAA
TTAAATTTTTGCCCCCGAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTACCAT
TTTCCCTTGAATTTCCAAAAATTTCATTTTTGACCCTGAACTTTCCAAAAATTACCATTTTACCT
CGAATTCCA
Found at i:596766 original size:52 final size:52
Alignment explanation
Indices: 596688--596864 Score: 284
Period size: 52 Copynumber: 3.4 Consensus size: 52
596678 AGATCTTATA
596688 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATG
* *
596740 ACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATAAGGTTCGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATG
* *
596792 ACTATGTGTCATCGTGAGTATATGAATCCCTTT-TGGATTATGAGGTCCGATG
1 ACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTATAAGGTCCGATG
* *
596844 ACAATGTGTCATCTTGAGTAT
1 ACTATGTGTCATCGTGAGTAT
596865 TAAATAAGAA
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 111 0.96
53 5 0.04
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.36
Consensus pattern (52 bp):
ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATG
Found at i:602061 original size:26 final size:26
Alignment explanation
Indices: 602027--602080 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
602017 AAAGAAAAAG
* * *
602027 AATTTCATTGTCTTCTTCTCTCTCAA
1 AATTTCATTATCTTATTCTCTCCCAA
602053 AATTTCATTATCTTATTCTCTCCCAA
1 AATTTCATTATCTTATTCTCTCCCAA
602079 AA
1 AA
602081 CGTGAAAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (26 bp):
AATTTCATTATCTTATTCTCTCCCAA
Found at i:603866 original size:22 final size:22
Alignment explanation
Indices: 603810--603866 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
603800 TCATGCATGT
*
603810 AAAT-TTATTTA-ATCGATTTA
1 AAATATTATTTATATCGATCTA
* *
603830 ATA-ATTATATCATATCGATCTA
1 AAATATTAT-TTATATCGATCTA
603852 AAATATTATTTATAT
1 AAATATTATTTATAT
603867 TTATAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 15 0.54
23 5 0.18
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (22 bp):
AAATATTATTTATATCGATCTA
Found at i:604090 original size:22 final size:23
Alignment explanation
Indices: 604065--604125 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
604055 ATCTCTCCCT
604065 AAAAAATATATATATTTGCTTTA
1 AAAAAATATATATATTTGCTTTA
* * * *
604088 AAAAGAATATACATTTTTTCTTTC
1 AAAA-AATATATATATTTGCTTTA
*
604112 AAGAAATATATATA
1 AAAAAATATATATA
604126 CGAGAATATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (23 bp):
AAAAAATATATATATTTGCTTTA
Found at i:609593 original size:33 final size:33
Alignment explanation
Indices: 609555--609621 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
609545 CCTTATTTAA
609555 TTTCATCCAGATCTATTGTTAAATAATATTATT
1 TTTCATCCAGATCTATTGTTAAATAATATTATT
609588 TTTCATCCAGATCTATTGTTAAATAATATTATT
1 TTTCATCCAGATCTATTGTTAAATAATATTATT
609621 T
1 T
609622 ATTGAGCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (33 bp):
TTTCATCCAGATCTATTGTTAAATAATATTATT
Found at i:610226 original size:109 final size:109
Alignment explanation
Indices: 610042--610257 Score: 283
Period size: 109 Copynumber: 2.0 Consensus size: 109
610032 AAACAAAGAA
*
610042 TATTTATCAAATTTAAATAGGAAATTCAATTATTTAGGTTCAAGGAAAAATCATACCTAACACAT
1 TATTTATCAAATTTAAATAGGAAATTCAATTATTTAGGTTCAAAGAAAAATCATACCTAACACAT
* * *
610107 TAGGACACAATTTCTCTAGTTCCCTAAAATAACAA-AACATTGAG
66 TAGGACACAATTTCTCAAATTCCCAAAAATAA-AAGAACATTGAG
* * * * * *
610151 TATTTATCGATTTTGAATAGGATATTCAATTATTTAGGTTCAAAGAAAAATCATATCC-AATACG
1 TATTTATCAAATTTAAATAGGAAATTCAATTATTTAGGTTCAAAGAAAAATCATA-CCTAACACA
** *
610215 TTAGGGTACAATTTCTCAAATTCTCAAAAATAAAAGAACATTG
65 TTAGGACACAATTTCTCAAATTCCCAAAAATAAAAGAACATTG
610258 CATTGGTTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
108 2 0.02
109 88 0.96
110 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (109 bp):
TATTTATCAAATTTAAATAGGAAATTCAATTATTTAGGTTCAAAGAAAAATCATACCTAACACAT
TAGGACACAATTTCTCAAATTCCCAAAAATAAAAGAACATTGAG
Found at i:610675 original size:21 final size:21
Alignment explanation
Indices: 610634--610673 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
610624 ATGTAAATTA
*
610634 AAATTAATAAAAGAACTAAAT
1 AAATAAATAAAAGAACTAAAT
*
610655 AAATAAATAATAGAA-TAAA
1 AAATAAATAAAAGAACTAAA
610674 ATGATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
AAATAAATAAAAGAACTAAAT
Found at i:616057 original size:70 final size:67
Alignment explanation
Indices: 615942--616074 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 67
615932 ATAAACAATA
* *
615942 TAATGGTTTTGCCTTTTAACTTAATGGGTAAACATTTATCAAAATGACAGAATTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAATGACAGAATTTTACCTTTTAA
616007 CT
66 CT
* * *
616009 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAATGACATAGTTTTGCCTTT
1 TAATGGTTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAATGACAGAATTTTACCTTT
616074 T
63 T
616075 CTTATTCGGT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
67 19 0.33
68 2 0.03
70 37 0.64
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAATGACAGAATTTTACCTTTTAA
CT
Found at i:617785 original size:44 final size:46
Alignment explanation
Indices: 617695--617785 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 46
617685 AATAGAGCTT
* *
617695 AATGGAAAAGGGCTGTAATCAGTAATTCAGTTGTTTGGTTGGATGG
1 AATGGAAAAGAGCTGTAATCAGTAATTCAGTTGTTTGGTTGAATGG
* *
617741 AATGGAATAGAGCTGTAAT-AGT-ATTC-TTATGTTTGGTTGAATGG
1 AATGGAAAAGAGCTGTAATCAGTAATTCAGT-TGTTTGGTTGAATGG
617785 A
1 A
617786 TGGTGCTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 1 0.03
44 19 0.47
45 3 0.08
46 17 0.43
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (46 bp):
AATGGAAAAGAGCTGTAATCAGTAATTCAGTTGTTTGGTTGAATGG
Found at i:620746 original size:3 final size:3
Alignment explanation
Indices: 620738--620767 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
620728 AAGCAGAGAT
620738 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
620768 GAATTTTCAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:633102 original size:23 final size:25
Alignment explanation
Indices: 633048--633102 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
633038 TTATCGGTGG
*
633048 AAATTAAAAATTGTAATTTTTAAGA
1 AAATTAAAAATTATAATTTTTAAGA
*
633073 TAA-TAAAAA-TATAATTTTTAA-A
1 AAATTAAAAATTATAATTTTTAAGA
633095 AAATTAAA
1 AAATTAAA
633103 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 3 0.12
23 15 0.58
24 6 0.23
25 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
AAATTAAAAATTATAATTTTTAAGA
Found at i:633108 original size:27 final size:30
Alignment explanation
Indices: 633076--633142 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
633066 TTTAAGATAA
*
633076 TAAAAATATAATTTTTAAAA-A-ATTAAAT
1 TAAAATTATAATTTTTAAAAGAGATTAAAT
*
633104 TAAAATTTTATTATTTTTAAAAGAGATTAAAT
1 TAAAA--TTATAATTTTTAAAAGAGATTAAAT
*
633136 TAGAATT
1 TAAAATT
633143 TTACTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
28 5 0.16
30 15 0.47
31 1 0.03
32 11 0.34
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (30 bp):
TAAAATTATAATTTTTAAAAGAGATTAAAT
Found at i:633110 original size:22 final size:23
Alignment explanation
Indices: 633062--633112 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
633052 TAAAAATTGT
* *
633062 AATTTTTAAGATAATAAAAATAT
1 AATTTTTAAGAAAATAAAAATAA
* *
633085 AATTTTTAA-AAAATTAAATTAA
1 AATTTTTAAGAAAATAAAAATAA
633107 AATTTT
1 AATTTT
633113 ATTATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTTTTAAGAAAATAAAAATAA
Found at i:633143 original size:32 final size:30
Alignment explanation
Indices: 633086--633145 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 30
633076 TAAAAATATA
633086 ATTTTTAAAAAATTAAATTAAAATTTTATT
1 ATTTTTAAAAAATTAAATTAAAATTTTATT
*
633116 ATTTTTAAAAGAGATTAAATTAGAATTTTA
1 ATTTTTAAAA-A-ATTAAATTAAAATTTTA
633146 CTTTTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 10 0.37
31 1 0.04
32 16 0.59
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
ATTTTTAAAAAATTAAATTAAAATTTTATT
Found at i:633151 original size:29 final size:29
Alignment explanation
Indices: 633088--633161 Score: 71
Period size: 32 Copynumber: 2.5 Consensus size: 29
633078 AAAATATAAT
*
633088 TTTTAAAAAATTAAATTAAAATTTTATTAT
1 TTTTAAAAAATTAAATTAAAA-TTTATTAC
*
633118 TTTTAAAAGAGATTAAATTAGAA-TT-TTAC
1 TTTTAAAA-A-ATTAAATTAAAATTTATTAC
* *
633147 TTTTAATAATTTAAA
1 TTTTAAAAAATTAAA
633162 ATTTTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 5 0.13
28 1 0.03
29 10 0.26
30 10 0.26
31 1 0.03
32 11 0.29
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (29 bp):
TTTTAAAAAATTAAATTAAAATTTATTAC
Found at i:636451 original size:18 final size:18
Alignment explanation
Indices: 636430--636468 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
636420 TAGACTTAAA
*
636430 ATTTA-ATATATATTATTT
1 ATTTATATAT-TAATATTT
636448 ATTTATATATTAATATTT
1 ATTTATATATTAATATTT
636466 ATT
1 ATT
636469 AAAAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTATATATTAATATTT
Found at i:636797 original size:14 final size:14
Alignment explanation
Indices: 636778--636804 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
636768 AATAAATTAA
636778 TATTGGTAGATGTT
1 TATTGGTAGATGTT
636792 TATTGGTAGATGT
1 TATTGGTAGATGT
636805 ATGAAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (14 bp):
TATTGGTAGATGTT
Found at i:638402 original size:26 final size:27
Alignment explanation
Indices: 638373--638437 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 27
638363 TTTCAAACCC
638373 AAATTAATAAATA-AATTTTAAATTTA
1 AAATTAATAAATACAATTTTAAATTTA
**
638399 AAATGT--CCAATACAATTTTAAATTTA
1 AAAT-TAATAAATACAATTTTAAATTTA
*
638425 AATTTAATTAAAT
1 AAATTAA-TAAAT
638438 TTAAAAAGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
25 5 0.17
26 20 0.69
27 1 0.03
28 3 0.10
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (27 bp):
AAATTAATAAATACAATTTTAAATTTA
Found at i:640042 original size:30 final size:30
Alignment explanation
Indices: 639948--640089 Score: 115
Period size: 30 Copynumber: 4.7 Consensus size: 30
639938 AAACCTTAAG
* * *
639948 CTTTTCCAAAATTACATTTTAACTCCTAAA
1 CTTTTCCAAAATTGCATTTTGACTCCCAAA
** * * * * ** *
639978 AATTTCCAATATTACGTTTTAACGACTAAA
1 CTTTTCCAAAATTGCATTTTGACTCCCAAA
* *
640008 CTTTTCCAAAATTGCATTTTGAC-CACCGAG
1 CTTTTCCAAAATTGCATTTTGACTC-CCAAA
*
640038 CTTTTCCAAAATTGCATGTTGACTCCCAAA
1 CTTTTCCAAAATTGCATTTTGACTCCCAAA
**
640068 CTTTTCCAAAATTATATTTTGA
1 CTTTTCCAAAATTGCATTTTGA
640090 TATCTAAATT
Statistics
Matches: 88, Mismatches: 22, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
30 87 0.99
31 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (30 bp):
CTTTTCCAAAATTGCATTTTGACTCCCAAA
Found at i:648990 original size:48 final size:48
Alignment explanation
Indices: 648917--649079 Score: 179
Period size: 48 Copynumber: 3.6 Consensus size: 48
648907 CTTCAAACCA
*
648917 CATCTTCTTGATAAGATACAGAGAAGTGGATCAAAGCAATAAAGCGAC
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGAC
* **
648965 CATCTTCTTGATGAGATACAAAGAAGTGGA-C----C-A-AATCCG--
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGAC
*
649004 C-T-TTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGTC-AC
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAG-CGAC
*
649050 CATCTTCTTGATGAGATACAGAGAAATGGA
1 CATCTTCTTGATGAGATACAGAGAAGTGGA
649080 CTAAATCAGC
Statistics
Matches: 93, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
37 24 0.26
38 2 0.02
39 1 0.01
41 4 0.04
42 2 0.02
43 2 0.02
44 2 0.02
45 1 0.01
46 1 0.01
47 2 0.02
48 52 0.56
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (48 bp):
CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGAC
Found at i:649029 original size:85 final size:85
Alignment explanation
Indices: 648925--649172 Score: 322
Period size: 85 Copynumber: 2.9 Consensus size: 85
648915 CACATCTTCT
648925 TGATAAGATACAGAGAAGTGGATCAAAGCAATAAAGCGACCATCTTCTTGATGAGATACAAAGAA
1 TGATAAGATACAGAGAAGTGGATCAAAGCAATAAAGCGACCATCTTCTTGATGAGATACAAAGAA
*
648990 GTGGACCAAATCCG-CTTTCC
66 GTGGACCAAATCAGCCTTT-C
* *
649010 TGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGTC-ACCATCTTCTTGATGAGATACAGAGA
1 TGATAAGATACAGAGAAGTGGATCAAAGCAATAAAG-CGACCATCTTCTTGATGAGATACAAAGA
* *
649074 AATGGACTAAATCAGCCTTTC
65 AGTGGACCAAATCAGCCTTTC
* * * * * ** *
649095 TGATAAGATACGGAGAAGTGAATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAA-A
1 TGATAAGATACAGAGAAGTGGATCAAAGCAATAAAGCGACCATCTTCTTGATGAGATACA-AAGA
*
649159 AGTAGACCAAATCA
65 AGTGGACCAAATCA
649173 CTGAAGCGAA
Statistics
Matches: 141, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 134 0.95
86 6 0.04
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (85 bp):
TGATAAGATACAGAGAAGTGGATCAAAGCAATAAAGCGACCATCTTCTTGATGAGATACAAAGAA
GTGGACCAAATCAGCCTTTC
Found at i:649285 original size:48 final size:47
Alignment explanation
Indices: 649223--649435 Score: 169
Period size: 48 Copynumber: 4.7 Consensus size: 47
649213 CTTCCTAATA
* *
649223 AGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCTTGATG
1 AGATACAGAGAAGT-GATCAAATCAATAAAGCGGTCATCTTCTTGATG
* * *
649271 AGATACAGAAAAGTGGACCAAATC-------C-G-CCT-TTC-TGATG
1 AGATACAGAGAAGT-GATCAAATCAATAAAGCGGTCATCTTCTTGATG
* * *
649308 AGATACAGAGAAGTCGATTAAATTAATGAAGCGGTCATCTTCTTGATG
1 AGATACAGAGAAGT-GATCAAATCAATAAAGCGGTCATCTTCTTGATG
* * * *
649356 AGATATAGAGAAGTAGACCAAATCAATGAAGCGGTCATCTTCCTGATG
1 AGATACAGAGAAGT-GATCAAATCAATAAAGCGGTCATCTTCTTGATG
* * *
649404 AGATACAGAGATGTATATCAAATCAATGAAGC
1 AGATACAGAGAAGT-GATCAAATCAATAAAGC
649436 AAAGCTTAAT
Statistics
Matches: 133, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
37 24 0.18
38 3 0.02
39 2 0.02
40 1 0.01
41 1 0.01
44 1 0.01
45 1 0.01
46 2 0.02
47 3 0.02
48 95 0.71
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (47 bp):
AGATACAGAGAAGTGATCAAATCAATAAAGCGGTCATCTTCTTGATG
Found at i:649373 original size:208 final size:208
Alignment explanation
Indices: 649006--649388 Score: 592
Period size: 208 Copynumber: 1.8 Consensus size: 208
648996 CAAATCCGCT
* *
649006 TTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGTCACCATCTTCTTGATGAGATACAG
1 TTCCTAATAAGATACAGAGAAGTGGATCAAAGCAATAAAGTCACCATCTTCTTGATGAGATACAG
* *
649071 AGAAATGGACTAAATCAGCCTTTCTGATAAGATACGGAGAAGTGAATTAAATCAATGAAGCGGTC
66 AGAAATGGACCAAATCAGCCTTTCTGATAAGATACAGAGAAGTGAATTAAATCAATGAAGCGGTC
*
649136 ATCTTCCTGATGAGATACAGAAAAGTAGACCAAATCACTGAAGCGAAGCTCAATACGAATGAGAC
131 ATCTTCCTGATGAGATACAGAAAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGAC
649201 TTCAAACCCTATC
196 TTCAAACCCTATC
* **
649214 TTCCTAATAAGATACAGAGAAGTGGGTCAAAGCAATAAAG-CGGTCATCTTCTTGATGAGATACA
1 TTCCTAATAAGATACAGAGAAGTGGATCAAAGCAATAAAGTC-ACCATCTTCTTGATGAGATACA
* * *
649278 GA-AAAGTGGACCAAATCCGCCTTTCTGATGAGATACAGAGAAGTCG-ATTAAATTAATGAAGCG
65 GAGAAA-TGGACCAAATCAGCCTTTCTGATAAGATACAGAGAAGT-GAATTAAATCAATGAAGCG
* * *
649341 GTCATCTTCTTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGCG
128 GTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAATCAATGAAGCG
649389 GTCATCTTCC
Statistics
Matches: 158, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
207 4 0.03
208 153 0.97
209 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (208 bp):
TTCCTAATAAGATACAGAGAAGTGGATCAAAGCAATAAAGTCACCATCTTCTTGATGAGATACAG
AGAAATGGACCAAATCAGCCTTTCTGATAAGATACAGAGAAGTGAATTAAATCAATGAAGCGGTC
ATCTTCCTGATGAGATACAGAAAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGAC
TTCAAACCCTATC
Found at i:649375 original size:85 final size:85
Alignment explanation
Indices: 649223--649379 Score: 233
Period size: 85 Copynumber: 1.8 Consensus size: 85
649213 CTTCCTAATA
* * *
649223 AGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCTTGATGAGATACAGAAAAGTGGA
1 AGATACAGAGAAGTCGATCAAAGCAATAAAGCGGTCATCTTCTTGATGAGATACAGAAAAGTAGA
649288 CCAAATCCGCCTTTCTGATG
66 CCAAATCCGCCTTTCTGATG
* ** * * *
649308 AGATACAGAGAAGTCGATTAAATTAATGAAGCGGTCATCTTCTTGATGAGATATAGAGAAGTAGA
1 AGATACAGAGAAGTCGATCAAAGCAATAAAGCGGTCATCTTCTTGATGAGATACAGAAAAGTAGA
649373 CCAAATC
66 CCAAATC
649380 AATGAAGCGG
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 63 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (85 bp):
AGATACAGAGAAGTCGATCAAAGCAATAAAGCGGTCATCTTCTTGATGAGATACAGAAAAGTAGA
CCAAATCCGCCTTTCTGATG
Found at i:649571 original size:257 final size:255
Alignment explanation
Indices: 649119--649617 Score: 705
Period size: 257 Copynumber: 1.9 Consensus size: 255
649109 GAAGTGAATT
* *
649119 AAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAATCACTGAAGCGAAG
1 AAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAATCAATGAAGCAAAG
* * *
649184 CTCAATACGAATGAGACTTCAAACCCTATCTTCCTAATAAGATACAGAGAAGTGGGTCAAAGCAA
66 CTCAATA-GAATGAAACTTCAAACCCTATCTTCCTAATAAGATACAAAGAAGTCGGTCAAAGCAA
* * * *
649249 TAAAGCGGTCATCTTCTTGATGAGATACAGAAAAGTGGACCAAATCCGCCTTTCTGATGAGATAC
130 TAAAGCGATCATCTTCTTGAAGAGATACAGAAAAGTGGACCAAATCAGCCTTCCTGATGAGATAC
* * * *
649314 AGAGAAGTCGATTAAATTAATGAAGCGGTCATCTTCTTGATGAGATATAGAGAAGTAGACC
195 AGAGAAGTAGATTAAATCAATGAAGCGGTCATCTTCCTAATGAGATATAGAGAAGTAGACC
* * * *
649375 AAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAGATGTATATCAAATCAATGAAGCAAAG
1 AAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAATCAATGAAGCAAAG
* * *
649440 CTTAAT-GTAAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACAAAGAAGTCGGTCAAAGC
66 CTCAATAG-AA-TGAAACTTCAAACCCT-ATCTTCCTAATAAGATACAAAGAAGTCGGTCAAAGC
* * * * *
649504 AATAAAGCGATCATCTTCTTGAAGAGATACAGAGAAGTGGATCAAATTCATCC-TCCTTATTAGA
128 AATAAAGCGATCATCTTCTTGAAGAGATACAGAAAAGTGGACCAAA-TCAGCCTTCCTGATGAGA
*
649568 TACAGAGAAGTAGATTAAATCAATGAAGCGGTCGTCTTCCTAATGAGATA
192 TACAGAGAAGTAGATTAAATCAATGAAGCGGTCATCTTCCTAATGAGATA
649618 CAAAGAAGAA
Statistics
Matches: 213, Mismatches: 26, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
254 1 0.00
255 2 0.01
256 79 0.37
257 127 0.60
258 4 0.02
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (255 bp):
AAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAATCAATGAAGCAAAG
CTCAATAGAATGAAACTTCAAACCCTATCTTCCTAATAAGATACAAAGAAGTCGGTCAAAGCAAT
AAAGCGATCATCTTCTTGAAGAGATACAGAAAAGTGGACCAAATCAGCCTTCCTGATGAGATACA
GAGAAGTAGATTAAATCAATGAAGCGGTCATCTTCCTAATGAGATATAGAGAAGTAGACC
Found at i:651691 original size:30 final size:30
Alignment explanation
Indices: 651590--651805 Score: 153
Period size: 30 Copynumber: 7.3 Consensus size: 30
651580 TTAAAAATCA
* * *
651590 CATTTTGACCCTTAAAC--TTCTAAAATTA
1 CATTTTGACCCCTAAACTTTTCCAAAATTG
* * *
651618 CATTTTGA-CCCTCAAAATTGTCCAATATTAG
1 CATTTTGACCCCT-AAACTTTTCCAAAATT-G
* * *
651649 -ATTTTAATCCCTAAACTTTTCTAAAATTG
1 CATTTTGACCCCTAAACTTTTCCAAAATTG
651678 CATTTTGACCCCTAAACTTTTCCAAAATTG
1 CATTTTGACCCCTAAACTTTTCCAAAATTG
* * *
651708 CATGTTAACCCC-AAACTTTTCCAAAATTA
1 CATTTTGACCCCTAAACTTTTCCAAAATTG
* **
651737 CATTTTGATTCCC-AAA-TTTTCCCAAAATCA
1 CATTTTGA-CCCCTAAACTTTT-CCAAAATTG
* **
651767 CATTTTGATCTCC-AAAC-TTTCTCAAAATCA
1 CATTTTGA-CCCCTAAACTTTTC-CAAAATTG
651797 CATTTTGAC
1 CATTTTGAC
651806 TTCAAAATTA
Statistics
Matches: 155, Mismatches: 23, Indels: 19
0.79 0.12 0.10
Matches are distributed among these distances:
27 3 0.02
28 11 0.07
29 29 0.19
30 108 0.70
31 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTCCAAAATTG
Found at i:651793 original size:89 final size:89
Alignment explanation
Indices: 651583--651799 Score: 214
Period size: 89 Copynumber: 2.4 Consensus size: 89
651573 GTTTTATTTA
* * *
651583 AAAATCACATTTTGACCCTTAAAC-TTCT-AAAATTACATTTTGACCCTCAAAATTGTCCAATAT
1 AAAATCACATTTTGACCC-TAAACTTTCTCAAAATTACATGTTAACCCTCAAAATTGTCCAAAAT
* *
651646 TAGATTTTAATCCCTAAACTTTTCT
65 TACATTTTAATCCCTAAACTTTTCC
** * * *
651671 AAAATTGCATTTTGACCCCTAAACTTT-TCCAAAATTGCATGTTAACCC-CAAACTTTTCCAAAA
1 AAAATCACATTTTGA-CCCTAAACTTTCT-CAAAATTACATGTTAACCCTCAAAATTGTCCAAAA
*
651734 TTACATTTTGATTCCC-AAA-TTTTCCC
64 TTACATTTT-AATCCCTAAACTTTT-CC
*
651760 AAAATCACATTTTGATCTCC-AAACTTTCTCAAAATCACAT
1 AAAATCACATTTTGA-C-CCTAAACTTTCTCAAAATTACAT
651800 TTTGACTTCA
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
88 23 0.22
89 59 0.56
90 23 0.22
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (89 bp):
AAAATCACATTTTGACCCTAAACTTTCTCAAAATTACATGTTAACCCTCAAAATTGTCCAAAATT
ACATTTTAATCCCTAAACTTTTCC
Found at i:651794 original size:60 final size:58
Alignment explanation
Indices: 651583--651814 Score: 195
Period size: 60 Copynumber: 3.9 Consensus size: 58
651573 GTTTTATTTA
* *
651583 AAAATCACATTTTGA-CCCTTAAACTTCT-AAAATTACATTTTGACCCTCAAAATTGTCC
1 AAAATCACATTTTGATCCC-TAAACTTTTCAAAATTACATTTTGACCC-CAAAATTTTCC
* * * * * *
651641 AATATTAGATTTTAATCCCTAAACTTTTCTAAAATTGCATTTTGACCCCTAAACTTTTCC
1 AAAATCACATTTTGATCCCTAAACTTTTC-AAAATTACATTTTGACCCC-AAAATTTTCC
** * * * *
651701 AAAATTGCATGTT-AACCCCAAACTTTTCCAAAATTACATTTTGATTCCC-AAATTTTCCC
1 AAAATCACATTTTGATCCCTAAACTTTT-CAAAATTACATTTTGA-CCCCAAAATTTT-CC
* **
651760 AAAATCACATTTTGATCTCC-AAACTTTCTCAAAATCACATTTTGACTTCAAAATT
1 AAAATCACATTTTGATC-CCTAAACTTT-TCAAAATTACATTTTGACCCCAAAATT
651815 ATTTTCTTTT
Statistics
Matches: 138, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
58 25 0.18
59 43 0.31
60 67 0.49
61 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (58 bp):
AAAATCACATTTTGATCCCTAAACTTTTCAAAATTACATTTTGACCCCAAAATTTTCC
Found at i:653379 original size:23 final size:23
Alignment explanation
Indices: 653349--653416 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
653339 TGCATTTTAG
*
653349 TATCAAAATCAGTTTGGTAACAA
1 TATCAAAATCAGTTCGGTAACAA
* **
653372 TATCAAAAACAGTTCGGTAATTA
1 TATCAAAATCAGTTCGGTAACAA
* *
653395 TATCAAAATCAGTACTGTAACA
1 TATCAAAATCAGTTCGGTAACA
653417 GTCTTGGTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (23 bp):
TATCAAAATCAGTTCGGTAACAA
Found at i:654949 original size:82 final size:81
Alignment explanation
Indices: 654849--655020 Score: 308
Period size: 82 Copynumber: 2.1 Consensus size: 81
654839 TATTCAAATC
*
654849 ATTTTATTTCTTTATTGAATCCATCATATATCATCTGCAAATCGGTTTTTGTACTGTTTGTTTGT
1 ATTTT-TTTCTTTATTGAATCCATCATATATCATCTGCAAATCGGTTTTTGTACGGTTTGTTTGT
654914 TGAGTTTTTCTTTTCCCA
65 TGAG-TTTTCTTTTCCCA
654932 ATTTTTTTCTTTATTGAATCCATCATATATCATCTGCAAATCGGTTTTTGTACGGTTTGTTTGTT
1 ATTTTTTTCTTTATTGAATCCATCATATATCATCTGCAAATCGGTTTTTGTACGGTTTGTTTGTT
654997 GAGTTTTCTTTTCCCA
66 GAGTTTTCTTTTCCCA
*
655013 GTTTTTTT
1 ATTTTTTT
655021 TTCATGATTT
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
81 20 0.23
82 62 0.71
83 5 0.06
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.54
Consensus pattern (81 bp):
ATTTTTTTCTTTATTGAATCCATCATATATCATCTGCAAATCGGTTTTTGTACGGTTTGTTTGTT
GAGTTTTCTTTTCCCA
Found at i:655156 original size:23 final size:22
Alignment explanation
Indices: 655103--655162 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 22
655093 TCAACACCAT
655103 GAATTGTTATGGTTGTCGAATTTG
1 GAATT-TTA-GGTTGTCGAATTTG
*
655127 GAGATTTTAGGTTGTTGAATTTGG
1 GA-ATTTTAGGTTGTCGAATTT-G
*
655151 GAATTTTGGGTT
1 GAATTTTAGGTT
655163 TGGGAGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 21 0.66
24 8 0.25
25 3 0.09
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.47
Consensus pattern (22 bp):
GAATTTTAGGTTGTCGAATTTG
Found at i:655228 original size:13 final size:15
Alignment explanation
Indices: 655196--655242 Score: 62
Period size: 14 Copynumber: 3.2 Consensus size: 15
655186 TGGGTAAGAG
655196 TTTTGATTTAGGGAT
1 TTTTGATTTAGGGAT
655211 TTTTG-TTTAGGG-T
1 TTTTGATTTAGGGAT
*
655224 TTTTGATTTTGGAGAT
1 TTTTGATTTAGG-GAT
655240 TTT
1 TTT
655243 AGGTTAGTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.21
14 12 0.43
15 6 0.21
16 4 0.14
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.60
Consensus pattern (15 bp):
TTTTGATTTAGGGAT
Found at i:655845 original size:20 final size:20
Alignment explanation
Indices: 655820--655915 Score: 58
Period size: 20 Copynumber: 4.9 Consensus size: 20
655810 GATGATGATT
655820 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
* ** ***
655840 ATAATTCTATATTTAA-AAAA
1 ATAATTTTA-AAATAATTTTA
655860 ATAATTTT--AATAA-TTTA
1 ATAATTTTAAAATAATTTTA
655877 AT-ATTTTAAAAAATAATTTTA
1 ATAATTTT--AAAATAATTTTA
* *
655898 ATAAATTTAAAATCATTT
1 ATAATTTTAAAATAATTT
655916 GTTGGCATGA
Statistics
Matches: 55, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
16 5 0.09
17 6 0.11
20 30 0.55
21 10 0.18
22 4 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:655864 original size:29 final size:29
Alignment explanation
Indices: 655828--655907 Score: 126
Period size: 29 Copynumber: 2.7 Consensus size: 29
655818 TTATAATTTT
655828 AAAATAATTTTAATAATTCT-ATATTTAAA
1 AAAATAATTTTAATAATT-TAATATTTAAA
*
655857 AAAATAATTTTAATAATTTAATATTTTAA
1 AAAATAATTTTAATAATTTAATATTTAAA
655886 AAAATAATTTTAATAAATTTAA
1 AAAATAATTTTAAT-AATTTAA
655908 AATCATTTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 1 0.02
29 40 0.83
30 7 0.15
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAATAATTTTAATAATTTAATATTTAAA
Found at i:655899 original size:21 final size:21
Alignment explanation
Indices: 655868--655909 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
655858 AAATAATTTT
*
655868 AATAATTTAAT-ATTTTAAAA
1 AATAATTTAATAAATTTAAAA
655888 AATAATTTTAATAAATTTAAAA
1 AATAA-TTTAATAAATTTAAAA
655910 TCATTTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAATTTAATAAATTTAAAA
Found at i:656237 original size:19 final size:20
Alignment explanation
Indices: 656207--656284 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
656197 AAAAATACAA
656207 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTATAAATT
*
656227 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTATAAATT
* *
656246 ATTTTCAAATTTTGA-AAATT
1 ATTTT-GAATTTTTATAAATT
*
656266 ATTTTG-ATTTTTATTAATT
1 ATTTTGAATTTTTATAAATT
656285 TTTGTTAAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
18 14 0.29
19 13 0.27
20 17 0.35
21 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:658141 original size:26 final size:26
Alignment explanation
Indices: 658112--658210 Score: 153
Period size: 26 Copynumber: 3.8 Consensus size: 26
658102 CTTTTAGAAA
658112 TTTAGCTCTTATGAGCCTAGACAGAG
1 TTTAGCTCTTATGAGCCTAGACAGAG
*
658138 TTTAGCTGTTATGAGCCTAGACAGAG
1 TTTAGCTCTTATGAGCCTAGACAGAG
* *
658164 TTTAGCTCTTACGAGCCCAGACAGAG
1 TTTAGCTCTTATGAGCCTAGACAGAG
* *
658190 TTTAGATCTTATAAGCCTAGA
1 TTTAGCTCTTATGAGCCTAGA
658211 TAGAATATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (26 bp):
TTTAGCTCTTATGAGCCTAGACAGAG
Found at i:658180 original size:52 final size:52
Alignment explanation
Indices: 658112--658236 Score: 153
Period size: 52 Copynumber: 2.4 Consensus size: 52
658102 CTTTTAGAAA
* * * * *
658112 TTTAGCTCTTATGAGCCTAGACAGAGTTTAGCTGTTATGAGCCTAGACAGAG
1 TTTAGCTCTTACGAGCCCAGACAGAGTTTAGATCTTATAAGCCTAGACAGAG
* *
658164 TTTAGCTCTTACGAGCCCAGACAGAGTTTAGATCTTATAAGCCTAGATAGAA
1 TTTAGCTCTTACGAGCCCAGACAGAGTTTAGATCTTATAAGCCTAGACAGAG
* *
658216 TATCA-CTCTTACGAGACCAGA
1 T-TTAGCTCTTACGAGCCCAGA
658237 TAGAATATCG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 61 0.97
53 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (52 bp):
TTTAGCTCTTACGAGCCCAGACAGAGTTTAGATCTTATAAGCCTAGACAGAG
Found at i:658225 original size:26 final size:25
Alignment explanation
Indices: 658196--658261 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
658186 AGAGTTTAGA
*
658196 TCTTATAAGCCTAGATAGAATATCAC
1 TCTTACAAGCC-AGATAGAATATCAC
* *
658222 TCTTACGAGACCAGATAGAATATCGC
1 TCTTACAAG-CCAGATAGAATATCAC
658248 TCTTACAAGCCAGA
1 TCTTACAAGCCAGA
658262 ATCAGAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.14
26 28 0.80
27 2 0.06
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (25 bp):
TCTTACAAGCCAGATAGAATATCAC
Found at i:658280 original size:27 final size:27
Alignment explanation
Indices: 658224--658323 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 27
658214 AATATCACTC
*
658224 TTACGAGACCAG-AT-AGAA-TATCGCTC
1 TTACGAG-CCAGAATCAGAATTA-CGCTA
* *
658250 TTACAAGCCAGAATCAGAATTATGCTA
1 TTACGAGCCAGAATCAGAATTACGCTA
* * * *
658277 TTACGAGCAAGAATTAAAATTACGCTT
1 TTACGAGCCAGAATCAGAATTACGCTA
* *
658304 TTATGAGCCAAAATCAGAAT
1 TTACGAGCCAGAATCAGAAT
658324 GTCTTCGTCT
Statistics
Matches: 57, Mismatches: 14, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
25 4 0.07
26 8 0.14
27 43 0.75
28 2 0.04
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (27 bp):
TTACGAGCCAGAATCAGAATTACGCTA
Found at i:662853 original size:41 final size:41
Alignment explanation
Indices: 662795--663091 Score: 296
Period size: 41 Copynumber: 7.2 Consensus size: 41
662785 AGTCGTAGAC
* * *
662795 CTTCCTCTTAA-ACAATCTTATGCTC-TACCGAGTCATAAGT
1 CTTCCT-TTAATATAATCTCATGCTCATACCGAGTCATGAGT
* *
662835 ATTCCTTTAAATATAATCTCATGCTCAT-CCTGAGTCACGAGT
1 CTTCCTTT-AATATAATCTCATGCTCATACC-GAGTCATGAGT
* * ** * * *
662877 CATCCTTTAATATAATCTTAACCCCATCCCGAGACATGAGT
1 CTTCCTTTAATATAATCTCATGCTCATACCGAGTCATGAGT
* *
662918 CTTCCTTTAATATAATCTCATGCTCATCCCGAGACATGAGT
1 CTTCCTTTAATATAATCTCATGCTCATACCGAGTCATGAGT
* ***
662959 CTT-CTTTGAATTTAATCTCATGCTCATTTTGAGTCATGAGT
1 CTTCCTTT-AATATAATCTCATGCTCATACCGAGTCATGAGT
* *** *
663000 CTTCCTTTAATATAATCTCATGGTCATTTTGAGTCACGAGT
1 CTTCCTTTAATATAATCTCATGCTCATACCGAGTCATGAGT
* *
663041 CTTCCTTTAATATAATCTCATGCTCATCCCGAGACATGAGT
1 CTTCCTTTAATATAATCTCATGCTCATACCGAGTCATGAGT
663082 CTTCCATTTA
1 CTTCC-TTTA
663092 TACTTAAAGT
Statistics
Matches: 217, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.01
40 11 0.05
41 178 0.82
42 26 0.12
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (41 bp):
CTTCCTTTAATATAATCTCATGCTCATACCGAGTCATGAGT
Found at i:662945 original size:82 final size:81
Alignment explanation
Indices: 662808--663091 Score: 327
Period size: 82 Copynumber: 3.5 Consensus size: 81
662798 CCTCTTAAAC
* * * * *
662808 AATCTTATGCTC-TACCGAGTCATAAGTATTCCTTTAAATATAATCTCATGCTCATCCTGAGTCA
1 AATCTCATGCTCATCCCGAGACATGAGTCTTCCTTT-AATATAATCTCATGCTCATCCTGAGTCA
662872 CGAGTCATCCTTTAATAT
65 CGAGTC-TCCTTTAATAT
* ** * * * *
662890 AATCTTAACCCCATCCCGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCCCGAGACAT
1 AATCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCAC
* *
662955 GAGTCTTCTTTGAATTT
66 GAGTCTCCTTT-AATAT
*** * * **
662972 AATCTCATGCTCATTTTGAGTCATGAGTCTTCCTTTAATATAATCTCATGGTCATTTTGAGTCAC
1 AATCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCAC
663037 GAGTCTTCCTTTAATAT
66 GAGTC-TCCTTTAATAT
663054 AATCTCATGCTCATCCCGAGACATGAGTCTTCCATTTA
1 AATCTCATGCTCATCCCGAGACATGAGTCTTCC-TTTA
663092 TACTTAAAGT
Statistics
Matches: 166, Mismatches: 32, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
81 5 0.03
82 133 0.80
83 28 0.17
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (81 bp):
AATCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCAC
GAGTCTCCTTTAATAT
Found at i:663014 original size:123 final size:123
Alignment explanation
Indices: 662795--663085 Score: 352
Period size: 123 Copynumber: 2.4 Consensus size: 123
662785 AGTCGTAGAC
* * * * * *
662795 CTTCCTCTTAA-ACAATCTTATGCTC-TACCGAGTCATAAGTATTCCTTTAAATATAATCTCATG
1 CTTCCT-TTAATATAATCTCATGCTCATCCCGAGACATGAGTCTT-CTTTAAATATAATCTCATG
* *
662858 CTCATCCTGAGTCACGAGTCATCCTTTAATATAATCTTAACCCCATCCCGAGACATGAGT
64 CTCATCCTGAGTCACGAGTCATCCTTTAATATAATCTCAACCCCATCCCGAGACACGAGT
* *
662918 CTTCCTTTAATATAATCTCATGCTCATCCCGAGACATGAGTCTTCTTTGAATTTAATCTCATGCT
1 CTTCCTTTAATATAATCTCATGCTCATCCCGAGACATGAGTCTTCTTTAAATATAATCTCATGCT
** * * **** *** *
662983 CATTTTGAGTCATGAGTCTTCCTTTAATATAATCTCATGGTCATTTTGAGTCACGAGT
66 CATCCTGAGTCACGAGTCATCCTTTAATATAATCTCAACCCCATCCCGAGACACGAGT
663041 CTTCCTTTAATATAATCTCATGCTCATCCCGAGACATGAGTCTTC
1 CTTCCTTTAATATAATCTCATGCTCATCCCGAGACATGAGTCTTC
663086 CATTTATACT
Statistics
Matches: 144, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
122 4 0.03
123 126 0.88
124 14 0.10
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (123 bp):
CTTCCTTTAATATAATCTCATGCTCATCCCGAGACATGAGTCTTCTTTAAATATAATCTCATGCT
CATCCTGAGTCACGAGTCATCCTTTAATATAATCTCAACCCCATCCCGAGACACGAGT
Found at i:665446 original size:31 final size:30
Alignment explanation
Indices: 665408--665481 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 30
665398 AATAAAATTA
665408 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTTCAAAAAAATAAT
*
665439 TTTAATAATTTTATATTTTAAAAAAATAAT
1 TTTAATAATTTTATATTTCAAAAAAATAAT
665469 TTTAATAATTTTA
1 TTTAATAATTTTA
665482 AAATCTTTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 29 0.69
31 13 0.31
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAATAATTTTATATTTCAAAAAAATAAT
Found at i:665466 original size:21 final size:23
Alignment explanation
Indices: 665442--665484 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
665432 AAATAATTTT
665442 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
665463 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
665485 TCTTTACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:666326 original size:13 final size:13
Alignment explanation
Indices: 666308--666344 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
666298 TGTTTCACTG
666308 AAAATAATTTTAA
1 AAAATAATTTTAA
*
666321 AAAATAAATTTTGA
1 AAAAT-AATTTTAA
666335 AAAATAATTT
1 AAAATAATTT
666345 ATTTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:668427 original size:4 final size:4
Alignment explanation
Indices: 668420--668445 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
668410 ATTGATTCCT
668420 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
668446 TAAGATGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:670990 original size:19 final size:19
Alignment explanation
Indices: 670966--671010 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
670956 CTATTCAACC
670966 AACATTGTT-TTTAATTATT
1 AACATTGTTATTTAATT-TT
*
670985 AACATT-TTATTTTATTTT
1 AACATTGTTATTTAATTTT
671003 AACATTGT
1 AACATTGT
671011 GAACTCGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (19 bp):
AACATTGTTATTTAATTTT
Found at i:671313 original size:14 final size:14
Alignment explanation
Indices: 671290--671327 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
671280 TGTTTCACTG
671290 AAAATGATTTTCGA
1 AAAATGATTTTCGA
* *
671304 AAAATAATTTTTGA
1 AAAATGATTTTCGA
671318 AAAATGATTT
1 AAAATGATTT
671328 ACTTTTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (14 bp):
AAAATGATTTTCGA
Found at i:672087 original size:25 final size:24
Alignment explanation
Indices: 672058--672104 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
672048 GAATAAGATG
* *
672058 CAAAATACATAAAAAAAAGTGAAGA
1 CAAAAAACACAAAAAAAA-TGAAGA
*
672083 CAAAAAACACAAAATAAATGAA
1 CAAAAAACACAAAAAAAATGAA
672105 TTCCATCTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.70, C:0.11, G:0.09, T:0.11
Consensus pattern (24 bp):
CAAAAAACACAAAAAAAATGAAGA
Found at i:679069 original size:5 final size:5
Alignment explanation
Indices: 679050--679084 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
679040 TCAAGCAAAC
*
679050 AAAAT AAAAG TAAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAA
679085 ACATAGGTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (5 bp):
AAAAG
Found at i:679538 original size:23 final size:22
Alignment explanation
Indices: 679509--679551 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
679499 TATCTCATTC
679509 TTTCTCACCTCCTTATTTCTCCT
1 TTTCTCACCTCCTT-TTTCTCCT
*
679532 TTTCTCACCTTCTTTTTCTC
1 TTTCTCACCTCCTTTTTCTC
679552 TCCACTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTCTCACCTCCTTTTTCTCCT
Found at i:687214 original size:14 final size:14
Alignment explanation
Indices: 687197--687226 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
687187 TTTAAACATT
*
687197 AAAAGATAAATCTA
1 AAAAGATAAATATA
687211 AAAAGATAAATATA
1 AAAAGATAAATATA
687225 AA
1 AA
687227 TTAAATACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAGATAAATATA
Found at i:687233 original size:11 final size:11
Alignment explanation
Indices: 687217--687249 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
687207 TCTAAAAAGA
687217 TAAATATAAAT
1 TAAATATAAAT
*
687228 TAAATACAAAT
1 TAAATATAAAT
687239 TAAATATAAAT
1 TAAATATAAAT
687250 AATAACCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:688822 original size:12 final size:12
Alignment explanation
Indices: 688805--688857 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
688795 ACATATAATG
688805 AATAAATAAAAA
1 AATAAATAAAAA
688817 AATAAAT-AAAA
1 AATAAATAAAAA
*
688828 AATAAATATAAA
1 AATAAATAAAAA
*
688840 AGTAAA-AAGAAA
1 AATAAATAA-AAA
688852 AA-AAAT
1 AATAAAT
688858 TGGGTTGCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 15 0.44
12 19 0.56
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (12 bp):
AATAAATAAAAA
Done.