Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015305.1 Kokia drynarioides strain JFW-HI SEQ_130350, 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: 751316
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 443 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:391257 original size:60 final size:61
Alignment explanation
Indices: 391189--391359 Score: 233
Period size: 60 Copynumber: 2.8 Consensus size: 61
391179 GGTCAAATTT
* *
391189 GAATTTTTGGAAACTTCAAGGGTTAAATTGGAATTTTT-GAAAAATTTAGGGGCCAAA-TCA
1 GAATTTTTGGAAAGTTCAAGGGTTAAATTTGAATTTTTAG-AAAATTTAGGGGCCAAATTCA
* * * *
391249 GAATTTTTGGAAAGTTCAAAGGTCAAATTTGAATTTTTAGAAAATTTAGGGGTCAAATTTA
1 GAATTTTTGGAAAGTTCAAGGGTTAAATTTGAATTTTTAGAAAATTTAGGGGCCAAATTCA
*
391310 -AATTTTTGGAAAGTT-TAGTGGTTAAATTTGAATTTTTAGAAAATTTAGGG
1 GAATTTTTGGAAAGTTCAAG-GGTTAAATTTGAATTTTTAGAAAATTTAGGG
391360 TTAAATTTGA
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
59 1 0.01
60 95 0.96
61 3 0.03
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (61 bp):
GAATTTTTGGAAAGTTCAAGGGTTAAATTTGAATTTTTAGAAAATTTAGGGGCCAAATTCA
Found at i:391314 original size:90 final size:89
Alignment explanation
Indices: 391179--391419 Score: 259
Period size: 90 Copynumber: 2.7 Consensus size: 89
391169 ATTAAAACCT
* * * * * **
391179 GGTCAAATTTGAATTTTTGGAAACTTCAAGGGTTAAATTGGAATTTTTGAAAAATTTAGGGGCCA
1 GGTCAAATTTGAATTTTTAGAAAATTTAGGGGTCAAATTTAAATTTTTGAAAAATTTAGGGGCCA
* *
391244 AATCAGAATTTTTGGAAAGTTCAAA
66 AATCAGAATTTTTAGAAAATT-AAA
* * * **
391269 GGTCAAATTTGAATTTTTAGAAAATTTAGGGGTCAAATTTAAATTTTTGGAAAGTTTAGTGGTTA
1 GGTCAAATTTGAATTTTTAGAAAATTTAGGGGTCAAATTTAAATTTTTGAAAAATTTAGGGGCCA
** * *
391334 AATTTGAATTTTTAGAAAATTTAG
66 AATCAGAATTTTTAGAAAATTAAA
* * *
391358 GGTTAAATTTGAATTTTTA-AAAAGTGTAGGGGTCAAATTTAAATTTTTGGAAAAATTAAGGG
1 GGTCAAATTTGAATTTTTAGAAAA-TTTAGGGGTCAAATTTAAATTTTT-GAAAAATTTAGGG
391420 CTTCACGGGC
Statistics
Matches: 125, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
88 4 0.03
89 42 0.34
90 79 0.63
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (89 bp):
GGTCAAATTTGAATTTTTAGAAAATTTAGGGGTCAAATTTAAATTTTTGAAAAATTTAGGGGCCA
AATCAGAATTTTTAGAAAATTAAA
Found at i:391414 original size:60 final size:59
Alignment explanation
Indices: 391269--391411 Score: 196
Period size: 59 Copynumber: 2.4 Consensus size: 59
391259 AAAGTTCAAA
** * *
391269 GGTCAAATTTGAATTTTTAGAAAATTTAGGGGTCAAATTTAAATTTTTGGAAAGTTTAGT
1 GGTCAAATTTGAATTTTTAGAAAATTTA-GGGTCAAATTTAAATTTTTAAAAAGTGTAGG
* * *
391329 GGTTAAATTTGAATTTTTAGAAAATTTAGGGTTAAATTTGAATTTTTAAAAAGTGTAGG
1 GGTCAAATTTGAATTTTTAGAAAATTTAGGGTCAAATTTAAATTTTTAAAAAGTGTAGG
* *
391388 GGTCAAATTTAAATTTTTGGAAAA
1 GGTCAAATTTGAATTTTTAGAAAA
391412 ATTAAGGGCT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 46 0.63
60 27 0.37
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (59 bp):
GGTCAAATTTGAATTTTTAGAAAATTTAGGGTCAAATTTAAATTTTTAAAAAGTGTAGG
Found at i:392666 original size:29 final size:29
Alignment explanation
Indices: 392576--392649 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
392566 AAATTAAAAA
392576 TTTTGGAAAATTTGAGATTAAAATCGAAC
1 TTTTGGAAAATTTGAGATTAAAATCGAAC
392605 TTTTGGAAAATTTGAGATTAAAATCGAAC
1 TTTTGGAAAATTTGAGATTAAAATCGAAC
392634 TTTTGGAAAATTTGAG
1 TTTTGGAAAATTTGAG
392650 GTCGAAAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.36
Consensus pattern (29 bp):
TTTTGGAAAATTTGAGATTAAAATCGAAC
Found at i:392694 original size:29 final size:28
Alignment explanation
Indices: 392654--392929 Score: 220
Period size: 30 Copynumber: 9.4 Consensus size: 28
392644 TTTGAGGTCG
* * *
392654 AAAATGTGATTTTTGGAAATTTAGGGGT
1 AAAATGTAATTTTAGGAAATTTAGGGTT
* * *
392682 AAAATGGTAATTTTTGG--ATGTTCGGGGT
1 AAAAT-GTAATTTTAGGAAAT-TTAGGGTT
* *
392710 AAAATGTTAATTTTAGAGAAGTTTAGTGTT
1 AAAATG-TAATTTTAG-GAAATTTAGGGTT
*
392740 AAAATGTGATTTTAGAGAAATTTAGGGGTT
1 AAAATGTAATTTTAG-GAAATTTA-GGGTT
*
392770 AAAATGTAATTTT-GGAAAAAATTAAGGGTT
1 AAAATGTAATTTTAGG---AAATTTAGGGTT
* *
392800 AAAATGTAATTTTAGAAAAATTTAGGGGTC
1 AAAATGTAATTTTAG-GAAATTTA-GGGTT
*
392830 AAAATGTAA-TTTAGGAAAAGTTAAGGGTT
1 AAAATGTAATTTTAGG-AAA-TTTAGGGTT
*
392859 AAAATGTAATTAT-GGAAAAGTTTATGGGTT
1 AAAATGTAATTTTAGG-AAA-TTTA-GGGTT
392889 AAAATGTAATTTTAGGAAAGTTTAAGGGTT
1 AAAATGTAATTTTAGGAAA-TTT-AGGGTT
*
392919 AAAATGAAATT
1 AAAATGTAATT
392930 ATGAAAAATT
Statistics
Matches: 207, Mismatches: 22, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
27 3 0.01
28 26 0.13
29 65 0.31
30 102 0.49
31 11 0.05
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTAGGAAATTTAGGGTT
Found at i:392745 original size:30 final size:29
Alignment explanation
Indices: 392709--392985 Score: 265
Period size: 30 Copynumber: 9.3 Consensus size: 29
392699 ATGTTCGGGG
* *
392709 TAAAATGTTAATTTTAGAGAAGTTTAGTGT
1 TAAAATG-TAATTTTAGAAAAGTTTAGGGT
*
392739 TAAAATGTGATTTTAGAGAAA-TTTAGGGGT
1 TAAAATGTAATTTTAGA-AAAGTTTA-GGGT
* * *
392769 TAAAATGTAATTTTGGAAAAAATTAAGGGT
1 TAAAATGTAATTTTAG-AAAAGTTTAGGGT
*
392799 TAAAATGTAATTTTAGAAAAATTTAGGGGT
1 TAAAATGTAATTTTAGAAAAGTTTA-GGGT
* *
392829 CAAAATGTAA-TTTAGGAAAAGTTAAGGGT
1 TAAAATGTAATTTTA-GAAAAGTTTAGGGT
* *
392858 TAAAATGTAATTATGGAAAAGTTTATGGGT
1 TAAAATGTAATTTTAGAAAAGTTTA-GGGT
*
392888 TAAAATGTAATTTTAGGAAAGTTTAAGGGT
1 TAAAATGTAATTTTAGAAAAGTTT-AGGGT
* * *
392918 TAAAATGAAATTAT-GAAAAATTTTAGGGGT
1 TAAAATGTAATTTTAG-AAAAGTTTA-GGGT
* *
392948 CAAAATATAATTTTA-AAAAGTTTGAGGGT
1 TAAAATGTAATTTTAGAAAAGTTT-AGGGT
*
392977 AAAAATGTA
1 TAAAATGTA
392986 TTACTAACGT
Statistics
Matches: 205, Mismatches: 29, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
29 67 0.33
30 133 0.65
31 5 0.02
ACGTcount: A:0.43, C:0.01, G:0.21, T:0.35
Consensus pattern (29 bp):
TAAAATGTAATTTTAGAAAAGTTTAGGGT
Found at i:392962 original size:60 final size:60
Alignment explanation
Indices: 392705--392985 Score: 308
Period size: 60 Copynumber: 4.7 Consensus size: 60
392695 TTGGATGTTC
* * * *
392705 GGGGT-AAAATGTTAATTTTA-GAGAAGTTT-AGTGTTAAAATGTGATTTTAGAGAAATTTA
1 GGGGTCAAAATG-TAATTTTAGGA-AAGTTTAAGGGTTAAAATGTAATTATAGAAAAATTTA
* ** *
392764 GGGGTTAAAATGTAATTTT-GGAAAAAATTAAGGGTTAAAATGTAATTTTAGAAAAATTTA
1 GGGGTCAAAATGTAATTTTAGG-AAAGTTTAAGGGTTAAAATGTAATTATAGAAAAATTTA
* *
392824 GGGGTCAAAATGTAA-TTTAGGAAAAG-TTAAGGGTTAAAATGTAATTATGGAAAAGTTTA
1 GGGGTCAAAATGTAATTTTAGG-AAAGTTTAAGGGTTAAAATGTAATTATAGAAAAATTTA
* * *
392883 TGGGTTAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGAAATTAT-GAAAAATTTTA
1 GGGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGTAATTATAGAAAAA-TTTA
* * * *
392943 GGGGTCAAAATATAATTTTA-AAAAGTTTGAGGGTAAAAATGTA
1 GGGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGTA
392986 TTACTAACGT
Statistics
Matches: 193, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
59 91 0.47
60 102 0.53
ACGTcount: A:0.42, C:0.01, G:0.22, T:0.35
Consensus pattern (60 bp):
GGGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGTAATTATAGAAAAATTTA
Found at i:392967 original size:89 final size:87
Alignment explanation
Indices: 392670--392985 Score: 282
Period size: 89 Copynumber: 3.6 Consensus size: 87
392660 TGATTTTTGG
*** * * *
392670 AAATTTAGGGG-TAAAATGGTAATTTTTGGATG-TTCGGGGTAAAATGTTAATTTTA-GAGAAGT
1 AAATTTAGGGGTTAAAAT-GTAATTTTAAAAAGTTTAGGGTTAAAATG-TAATTTTAGGA-AAGT
* * *
392732 TT-AGTGTTAAAATGTGATTTTAGAG
63 TTAAGGGTTAAAATGT-AATTTAGAA
* * * *
392757 AAATTTAGGGGTTAAAATGTAATTTTGGAAAAAATTAAGGGTTAAAATGTAATTTTAGAAAAATT
1 AAATTTAGGGGTTAAAATGTAATTTT--AAAAAGTTTAGGGTTAAAATGTAATTTTAGGAAAGTT
* * *
392822 TAGGGGTCAAAATGTAATTTAGGA
64 TAAGGGTTAAAATGTAATTTAGAA
* * **
392846 AAAGTTAAGGGTTAAAATGTAATTATGGAAAAGTTTATGGGTTAAAATGTAATTTTAGGAAAGTT
1 AAATTTAGGGGTTAAAATGTAATT-TTAAAAAGTTTA-GGGTTAAAATGTAATTTTAGGAAAGTT
*
392911 TAAGGGTTAAAATG-AAATTATGAA
64 TAAGGGTTAAAATGTAATTTA-GAA
* * *
392935 AAATTTTAGGGGTCAAAATATAATTTTAAAAAGTTTGAGGGTAAAAATGTA
1 AAA-TTTAGGGGTTAAAATGTAATTTTAAAAAGTTT-AGGGTTAAAATGTA
392986 TTACTAACGT
Statistics
Matches: 183, Mismatches: 35, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
87 19 0.10
88 18 0.10
89 105 0.57
90 41 0.22
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.35
Consensus pattern (87 bp):
AAATTTAGGGGTTAAAATGTAATTTTAAAAAGTTTAGGGTTAAAATGTAATTTTAGGAAAGTTTA
AGGGTTAAAATGTAATTTAGAA
Found at i:395615 original size:29 final size:29
Alignment explanation
Indices: 395449--395946 Score: 256
Period size: 30 Copynumber: 17.0 Consensus size: 29
395439 TTTCGAGGAA
* *
395449 TTTGGGGTCAAAATTGAAATTTTTGGAAAA-
1 TTTGAGGTCAAAA-TGTAA-TTTTGGAAAAG
*
395479 TTTG-GGATTAAAATCG-AACTTTTGGAAAAG
1 TTTGAGG-TCAAAAT-GTAA-TTTTGGAAAAG
* *
395509 -TTAAGGTCGAAAATGTGATTTTTGG-AAA-
1 TTTGAGGTC-AAAATGT-AATTTTGGAAAAG
* *
395537 TTTGGGGGT-AAAATGATAATTTTTGG--ATG
1 TTT-GAGGTCAAAATG-TAA-TTTTGGAAAAG
* * *
395566 TTCGAGG-CAAAACGATAATTTTGGAGAAG
1 TTTGAGGTCAAAATG-TAATTTTGGAAAAG
* * *
395595 TTTGAGGTCAAAATGTGATTTTAGAGAAG
1 TTTGAGGTCAAAATGTAATTTTGGAAAAG
** *
395624 TTT-AGGGATCAAAACATAATTTTGGAGAAG
1 TTTGA-GG-TCAAAATGTAATTTTGGAAAAG
** *
395654 TTT-AGGGATCAAAACATAATTTTGGAAAAA
1 TTTGA-GG-TCAAAATGTAATTTTGGAAAAG
* * *
395684 TAT-AGGGCTTAAAATGTAATTTAGGAAAAG
1 TTTGA-GG-TCAAAATGTAATTTTGGAAAAG
* * **
395714 -TTAAGGTTAAAATGTAATAATGGAAAAG
1 TTTGAGGTCAAAATGTAATTTTGGAAAAG
* * * *
395742 TTTAGGGGTTAACATGTAATTTTTGAAAAG
1 TTT-GAGGTCAAAATGTAATTTTGGAAAAG
* * *
395772 TTTAAGGT-TAAATGTAATTATGGAAAAG
1 TTTGAGGTCAAAATGTAATTTTGGAAAAG
* *
395800 TTTAAGTTCAAAATGTAATTTTGGAAAAG
1 TTTGAGGTCAAAATGTAATTTTGGAAAAG
* * * *
395829 TTTGGGGTTAAAATGAAATTATGG-AAAG
1 TTTGAGGTCAAAATGTAATTTTGGAAAAG
* * *
395857 TTT-ACGGGTTAAAATGTAATTTTAGAAAAA
1 TTTGA--GGTCAAAATGTAATTTTGGAAAAG
*
395887 TTTAGAGGGTCAAAATTTAATTTTGGAAAAG
1 TTT-GA-GGTCAAAATGTAATTTTGGAAAAG
* * *
395918 TTTAAGGGTTAAAATATAATTTTGGAAAA
1 TTTGA-GGTCAAAATGTAATTTTGGAAAA
395947 TTTTAGGGTT
Statistics
Matches: 374, Mismatches: 67, Indels: 54
0.76 0.14 0.11
Matches are distributed among these distances:
27 6 0.02
28 70 0.19
29 118 0.32
30 154 0.41
31 25 0.07
32 1 0.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (29 bp):
TTTGAGGTCAAAATGTAATTTTGGAAAAG
Found at i:395759 original size:58 final size:58
Alignment explanation
Indices: 395581--395961 Score: 302
Period size: 58 Copynumber: 6.5 Consensus size: 58
395571 GGCAAAACGA
* * * * * * * * * **
395581 TAATTTTGGAGAAGTTTGAGGTCAAAATGTGATTTTAGAGAAGTTTAGGGATCAAAACA
1 TAATTTTGGAAAAG-TTAAGGTTAAAATGTAATTATGGAAAAGTTTAGGGGTTAAAATG
* * * ** * * * *
395640 TAATTTTGGAGAAGTTTAGGGATCAAAACATAATTTTGGAAAAATATAGGGCTTAAAATG
1 TAATTTTGGAAAAG-TTAAGG-TTAAAATGTAATTATGGAAAAGTTTAGGGGTTAAAATG
* * *
395700 TAATTTAGGAAAAGTTAAGGTTAAAATGTAATAATGGAAAAGTTTAGGGGTTAACATG
1 TAATTTTGGAAAAGTTAAGGTTAAAATGTAATTATGGAAAAGTTTAGGGGTTAAAATG
* *
395758 TAATTTTTGAAAAGTTTAAGGTT-AAATGTAATTATGGAAAAGTTTA--AGTTCAAAATG
1 TAATTTTGGAAAAG-TTAAGGTTAAAATGTAATTATGGAAAAGTTTAGGGGTT-AAAATG
** * *
395815 TAATTTTGGAAAAGTTTGGGGTTAAAATGAAATTATGG-AAAGTTTACGGGTTAAAATG
1 TAATTTTGGAAAAG-TTAAGGTTAAAATGTAATTATGGAAAAGTTTAGGGGTTAAAATG
* * * * * * *
395873 TAATTTTAGAAAAATTTAGAGGGTCAAAATTTAATTTTGGAAAAGTTTAAGGGTTAAAATA
1 TAATTTT-GGAAAAGTTA-A-GGTTAAAATGTAATTATGGAAAAGTTTAGGGGTTAAAATG
* *
395934 TAATTTTGGAAAATTTTAGGGTTAAAAT
1 TAATTTTGGAAAA-GTTAAGGTTAAAAT
395962 ATGATTTTTG
Statistics
Matches: 263, Mismatches: 48, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
56 3 0.01
57 33 0.13
58 91 0.35
59 48 0.18
60 59 0.22
61 29 0.11
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (58 bp):
TAATTTTGGAAAAGTTAAGGTTAAAATGTAATTATGGAAAAGTTTAGGGGTTAAAATG
Found at i:395968 original size:29 final size:29
Alignment explanation
Indices: 395581--395980 Score: 353
Period size: 30 Copynumber: 13.6 Consensus size: 29
395571 GGCAAAACGA
* *
395581 TAATTTTGGAGAAGTTT-GAGGTCAAAATG
1 TAATTTTGGAAAAGTTTAG-GGTTAAAATG
* * * * **
395610 TGATTTTAGAGAAGTTTAGGGATCAAAACA
1 TAATTTTGGAAAAGTTTAGGG-TTAAAATG
* * **
395640 TAATTTTGGAGAAGTTTAGGGATCAAAACA
1 TAATTTTGGAAAAGTTTAGGG-TTAAAATG
* *
395670 TAATTTTGGAAAAATATAGGGCTTAAAATG
1 TAATTTTGGAAAAGTTTAGGG-TTAAAATG
* *
395700 TAATTTAGGAAAAG-TTAAGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGTTAAAATG
** *
395728 TAATAATGGAAAAGTTTAGGGGTTAACATG
1 TAATTTTGGAAAAGTTTA-GGGTTAAAATG
* *
395758 TAATTTTTGAAAAGTTTAAGGTT-AAATG
1 TAATTTTGGAAAAGTTTAGGGTTAAAATG
* *
395786 TAATTATGGAAAAGTTTA-AGTTCAAAATG
1 TAATTTTGGAAAAGTTTAGGGTT-AAAATG
*
395815 TAATTTTGGAAAAGTTTGGGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGTTAAAATG
* *
395844 AAATTATGG-AAAGTTTACGGGTTAAAATG
1 TAATTTTGGAAAAGTTTA-GGGTTAAAATG
* * * *
395873 TAATTTTAGAAAAATTTAGAGGGTCAAAATT
1 TAATTTTGGAAAAGTTT--AGGGTTAAAATG
*
395904 TAATTTTGGAAAAGTTTAAGGGTTAAAATA
1 TAATTTTGGAAAAGTTT-AGGGTTAAAATG
* *
395934 TAATTTTGGAAAATTTTAGGGTTAAAATA
1 TAATTTTGGAAAAGTTTAGGGTTAAAATG
*
395963 TGATTTTTGG-AAAGTTTA
1 T-AATTTTGGAAAAGTTTA
395981 AGGACCTTTT
Statistics
Matches: 309, Mismatches: 50, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
27 3 0.01
28 46 0.15
29 99 0.32
30 136 0.44
31 24 0.08
32 1 0.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (29 bp):
TAATTTTGGAAAAGTTTAGGGTTAAAATG
Found at i:396806 original size:6 final size:6
Alignment explanation
Indices: 396795--396848 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
396785 TAAAAGAGTT
* * *
396795 TTTTTC TTTTTC TTTTTC TATTTC TTTTCTC TTTTTAC -ATTTG TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT-TC TTTTT-C TTTTTC TTTTTC
396844 TTTTT
1 TTTTT
396849 AGGTTATACC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 32 0.82
7 7 0.18
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:396829 original size:19 final size:18
Alignment explanation
Indices: 396797--396849 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
396787 AAAGAGTTTT
396797 TTTCTTTTTCTTTTT-CTA
1 TTTCTTTTTCTTTTTAC-A
396815 TTTCTTTTCTCTTTTTACA
1 TTTCTTTT-TCTTTTTACA
*
396834 TTTGTTTTTCTTTTTA
1 TTTCTTTTTCTTTTTA
396850 GGTTATACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 16 0.50
19 15 0.47
20 1 0.03
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTACA
Found at i:397367 original size:31 final size:28
Alignment explanation
Indices: 397332--397400 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 28
397322 AGAGCAAATA
397332 TTCGAATGCT-TAGTGTTGTATTTAGTATTGC
1 TTCGAATGCTGTA-T-TTGT-TTT-GTATTGC
397363 TTCGAATGCTGGTATTTGTTTTGTATTGC
1 TTCGAATGCT-GTATTTGTTTTGTATTGC
*
397392 TTTGAATGC
1 TTCGAATGC
397401 ACTGTTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 15 0.43
30 3 0.09
31 14 0.40
32 1 0.03
33 2 0.06
ACGTcount: A:0.17, C:0.10, G:0.23, T:0.49
Consensus pattern (28 bp):
TTCGAATGCTGTATTTGTTTTGTATTGC
Found at i:397826 original size:17 final size:17
Alignment explanation
Indices: 397808--397880 Score: 110
Period size: 17 Copynumber: 4.2 Consensus size: 17
397798 AACATTTTTT
397808 AAATAAATTTAAATTTTA
1 AAATAAATTTAAA-TTTA
*
397826 AAATAAATTTAAACTTA
1 AAATAAATTTAAATTTA
* *
397843 AAACAAATTTAAAGTTA
1 AAATAAATTTAAATTTA
397860 AAATAAATTTAAATTTA
1 AAATAAATTTAAATTTA
397877 AAAT
1 AAAT
397881 TGGGTTTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 37 0.74
18 13 0.26
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (17 bp):
AAATAAATTTAAATTTA
Found at i:397827 original size:7 final size:6
Alignment explanation
Indices: 397811--397878 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
397801 ATTTTTTAAA
* * * * *
397811 TAAATT TAAATTT TAAA-A TAAATT TAAACT TAAA-A CAAATT TAAAGT
1 TAAATT TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
397858 TAAA-A TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAA
397879 ATTGGGTTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
5 11 0.23
6 31 0.65
7 6 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (6 bp):
TAAATT
Found at i:404498 original size:79 final size:80
Alignment explanation
Indices: 404358--404533 Score: 185
Period size: 79 Copynumber: 2.2 Consensus size: 80
404348 TATTCCTATT
* ** * * * * * *
404358 GTTCAATAAAATTTATTCGATTTTCTATTTCCAAACAGAAATTATTTGAACAATTTTTGTTTCGG
1 GTTCAATAGAATTTATTAAAGTTTCTATTTCCAAACAAAAATTAATTAAACAATTTCTGTTTCAG
* **
404423 GA-TTTAATCTTGTC
66 GATTTTAATCCTACC
* *
404437 GTTCAATAGAATTTATTAAAGTTTCTGTTTCCAAACAAAAATTAAATTAAATAA-TTCTGTTTCA
1 GTTCAATAGAATTTATTAAAGTTTCTATTTCCAAACAAAAATT-AATTAAACAATTTCTGTTTCA
*
404501 GGATTTTATTCCTACC
65 GGATTTTAATCCTACC
*
404517 GTTCAACAGAATTTATT
1 GTTCAATAGAATTTATT
404534 TGATTTTTGT
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
79 48 0.61
80 31 0.39
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (80 bp):
GTTCAATAGAATTTATTAAAGTTTCTATTTCCAAACAAAAATTAATTAAACAATTTCTGTTTCAG
GATTTTAATCCTACC
Found at i:404833 original size:15 final size:15
Alignment explanation
Indices: 404813--404841 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
404803 AAAATCTATC
404813 TTTTTTTTTT-CTTT
1 TTTTTTTTTTGCTTT
404827 TTTTTTTTTTGCTTT
1 TTTTTTTTTTGCTTT
404842 CGAATCAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTTGCTTT
Found at i:409564 original size:36 final size:36
Alignment explanation
Indices: 409514--409588 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
409504 AACTAAATAT
* *
409514 TAATATTATTCCTAAACCATCAATTAAACACAAAAC
1 TAATATTATCCCTAAACCATAAATTAAACACAAAAC
409550 TAATATTATCCCTAAACCATAAATTAAACACAAAAC
1 TAATATTATCCCTAAACCATAAATTAAACACAAAAC
409586 TAA
1 TAA
409589 CTAAAATAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (36 bp):
TAATATTATCCCTAAACCATAAATTAAACACAAAAC
Found at i:411469 original size:105 final size:105
Alignment explanation
Indices: 411287--411497 Score: 413
Period size: 105 Copynumber: 2.0 Consensus size: 105
411277 GACTCTTGAA
411287 CAATTTTTTGTCCCAACAACCGATGCTCAATCAACTCAGTCCAACCAATAGAAGTGCGACACTTG
1 CAATTTTTTGTCCCAACAACCGATGCTCAATCAACTCAGTCCAACCAATAGAAGTGCGACACTTG
*
411352 CACCCATACAAAGCCTCATACGGAGCCATCTTAATACTGG
66 CACCCATACAAAGCCTCATACGGAGACATCTTAATACTGG
411392 CAATTTTTTGTCCCAACAACCGATGCTCAATCAACTCAGTCCAACCAATAGAAGTGCGACACTTG
1 CAATTTTTTGTCCCAACAACCGATGCTCAATCAACTCAGTCCAACCAATAGAAGTGCGACACTTG
411457 CACCCATACAAAGCCTCATACGGAGACATCTTAATACTGG
66 CACCCATACAAAGCCTCATACGGAGACATCTTAATACTGG
411497 C
1 C
411498 CAGATAACTG
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (105 bp):
CAATTTTTTGTCCCAACAACCGATGCTCAATCAACTCAGTCCAACCAATAGAAGTGCGACACTTG
CACCCATACAAAGCCTCATACGGAGACATCTTAATACTGG
Found at i:413560 original size:17 final size:17
Alignment explanation
Indices: 413517--413566 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
413507 TAGCAATAAT
*
413517 TTTTTTTCTTCTTT-TCT
1 TTTTTTTCTT-TTTCTCA
413534 TTTCTCTTTCTTTTTCTCA
1 TTT-T-TTTCTTTTTCTCA
413553 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
413567 AAGTGACTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 13 0.45
18 5 0.17
19 11 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTCTTTTTCTCA
Found at i:414680 original size:15 final size:15
Alignment explanation
Indices: 414645--414685 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
414635 CTTTCATTTC
414645 ATTC-TCTT-CTTCT
1 ATTCTTCTTCCTTCT
414658 -TT-TTCTTCCTTCT
1 ATTCTTCTTCCTTCT
414671 ATTCTTCTTCCTTCT
1 ATTCTTCTTCCTTCT
414686 CTTTTTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.25
13 5 0.21
14 2 0.08
15 11 0.46
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTCTTCTTCCTTCT
Found at i:426298 original size:36 final size:36
Alignment explanation
Indices: 426251--426326 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
426241 ACCACTCTAA
* * *
426251 ATCGGCCTAACCTAGAAGTTGAACCCGATGCAGCTG
1 ATCGGCCTAACCTAAAAGCTAAACCCGATGCAGCTG
* *
426287 ATCGGCCTAACCTAAAAGCTAAACTCGATGCAGTTG
1 ATCGGCCTAACCTAAAAGCTAAACCCGATGCAGCTG
426323 ATCG
1 ATCG
426327 ACCTGTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.21
Consensus pattern (36 bp):
ATCGGCCTAACCTAAAAGCTAAACCCGATGCAGCTG
Found at i:428753 original size:17 final size:18
Alignment explanation
Indices: 428733--428772 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
428723 ACTACAATGC
*
428733 AAATGTACTAACAAATA-
1 AAATGTAATAACAAATAG
*
428750 AAATGTAATGACAAATAG
1 AAATGTAATAACAAATAG
428768 AAATG
1 AAATG
428773 CAATGACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.23
Consensus pattern (18 bp):
AAATGTAATAACAAATAG
Found at i:428777 original size:18 final size:17
Alignment explanation
Indices: 428743--428786 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
428733 AAATGTACTA
*
428743 ACAAATAAAATGTAATG
1 ACAAATAAAATGCAATG
428760 ACAAATAGAAATGCAATG
1 ACAAATA-AAATGCAATG
*
428778 ACAACTAAA
1 ACAAATAAA
428787 TGCTATGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.18
Consensus pattern (17 bp):
ACAAATAAAATGCAATG
Found at i:429215 original size:24 final size:24
Alignment explanation
Indices: 429187--429236 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
429177 TGTCGGGGCA
429187 TCTTCCTTC-TCTTCATCCTTCTCT
1 TCTT-CTTCTTCTTCATCCTTCTCT
* *
429211 TCTTCTTCTTTTTCTTCCTTCTCT
1 TCTTCTTCTTCTTCATCCTTCTCT
429235 TC
1 TC
429237 CTCATTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (24 bp):
TCTTCTTCTTCTTCATCCTTCTCT
Found at i:433142 original size:41 final size:41
Alignment explanation
Indices: 433061--433225 Score: 122
Period size: 41 Copynumber: 3.9 Consensus size: 41
433051 ATTTTTGTGC
* * *
433061 TGTTTTTTTATTGTTTTGGTTGTTATTTTTTGTTGGTTTTT
1 TGTTTTTTTACTGTTTTGGTTGTTATTTTATGTTGCTTTTT
433102 TGTTTTTTTACTGTTTTGGTTGTTATTTTCATGTT-CTTTTT
1 TGTTTTTTTACTGTTTTGGTTGTTATTTT-ATGTTGCTTTTT
* * * *
433143 ACTGTTATTTTTGTTGCTATTTTTGTTGTT-TTTAATGTTG-TTTGCTGT
1 --TG---TTTTT-TTACTGTTTTGGTTGTTATTTTATGTTGCTTT--T-T
* *
433191 TATTTTTGCTACTGTTTTGGTTGTTATTTT-TGTTG
1 TGTTTTT-TTACTGTTTTGGTTGTTATTTTATGTTG
433226 TTTGGATGTT
Statistics
Matches: 99, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
41 33 0.33
42 4 0.04
43 26 0.26
44 3 0.03
45 8 0.08
46 9 0.09
47 15 0.15
48 1 0.01
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (41 bp):
TGTTTTTTTACTGTTTTGGTTGTTATTTTATGTTGCTTTTT
Found at i:433218 original size:67 final size:64
Alignment explanation
Indices: 433072--433225 Score: 170
Period size: 65 Copynumber: 2.4 Consensus size: 64
433062 GTTTTTTTAT
* * * *
433072 TGTTTTGGTTGTTATTTTTTGTTGGTTTTTTGTTTTTTTACTGTTTTGGTTGTTATTTTCATGTT
1 TGTTTTGGTTGTTA-TTTTTGTTGCTTTTTTGTTTTTTTAATGTTTTGGCTGTTATTTT-ATGTA
433137 C
64 C
** *
433138 T-TTTT-ACTGTTATTTTTGTTGCTATTTTTGTTGTTTTTAATGTTGTTTGCTGTTATTTT-TGC
1 TGTTTTGGTTGTTATTTTTGTTGCT-TTTTTGTT-TTTTTAATGTT-TTGGCTGTTATTTTATG-
433200 TAC
62 TAC
433203 TGTTTTGGTTGTTATTTTTGTTG
1 TGTTTTGGTTGTTATTTTTGTTG
433226 TTTGGATGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
63 10 0.14
64 15 0.21
65 17 0.23
66 17 0.23
67 14 0.19
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (64 bp):
TGTTTTGGTTGTTATTTTTGTTGCTTTTTTGTTTTTTTAATGTTTTGGCTGTTATTTTATGTAC
Found at i:433250 original size:43 final size:43
Alignment explanation
Indices: 433063--433251 Score: 135
Period size: 43 Copynumber: 4.4 Consensus size: 43
433053 TTTTGTGCTG
*
433063 TTTTTTTAT-TGTTTTGGTTGTTATTTTTTGTTGGTTT--T-TTG
1 TTTTTTTATCTGTTTTGGTTGTTA-TTTTTGTT-GTTTGATGTTA
* *
433104 TTTTTTTA-CTGTTTTGGTTGTTATTTTCATGTTCTTTTTACTGTTA
1 TTTTTTTATCTGTTTTGGTTGTTATTTT--TGTT-GTTTGA-TGTTA
* * * * *
433150 TTTTTGTT-GCTATTTTTGTTGTT-TTTAATGTTGTTTGCTGTTA
1 TTTTT-TTATCTGTTTTGGTTGTTATTT-TTGTTGTTTGATGTTA
*
433193 TTTTTGCTA-CTGTTTTGGTTGTTATTTTTGTTGTTTGGATGTT-
1 TTTTT-TTATCTGTTTTGGTTGTTATTTTTGTTGTTT-GATGTTA
*
433236 TTTTTTTATGTGTTTT
1 TTTTTTTATCTGTTTT
433252 TACTATTGTT
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
40 4 0.03
41 22 0.19
42 9 0.08
43 43 0.36
44 11 0.09
45 5 0.04
46 10 0.08
47 14 0.12
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (43 bp):
TTTTTTTATCTGTTTTGGTTGTTATTTTTGTTGTTTGATGTTA
Found at i:439009 original size:29 final size:29
Alignment explanation
Indices: 438976--439044 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
438966 AACTATCTTA
438976 GTATTATTTAA-GTATAAATATTTTTTAAT
1 GTATT-TTTAATGTATAAATATTTTTTAAT
*
439005 GTATTTTTAATTTATAAATATTTTTTAAT
1 GTATTTTTAATGTATAAATATTTTTTAAT
*
439034 ATATTTTTAAT
1 GTATTTTTAAT
439045 TTGTTGAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 5 0.14
29 32 0.86
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.59
Consensus pattern (29 bp):
GTATTTTTAATGTATAAATATTTTTTAAT
Found at i:439045 original size:29 final size:29
Alignment explanation
Indices: 438988--439046 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
438978 ATTATTTAAG
*
438988 TATAAATATTTTTTAATGTATTTTTAATT
1 TATAAATATTTTTTAATATATTTTTAATT
439017 TATAAATATTTTTTAATATATTTTTAATT
1 TATAAATATTTTTTAATATATTTTTAATT
439046 T
1 T
439047 GTTGAGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
TATAAATATTTTTTAATATATTTTTAATT
Found at i:439374 original size:21 final size:21
Alignment explanation
Indices: 439333--439374 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
439323 TGAAAATTTA
**
439333 TTTATTTAAAATAAATCATAT
1 TTTATTTAAAATAAAAAATAT
439354 TTTATTTAAAA-ACAAAAATAT
1 TTTATTTAAAATA-AAAAATAT
439375 ATCATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTATTTAAAATAAAAAATAT
Found at i:440994 original size:16 final size:16
Alignment explanation
Indices: 440969--441001 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
440959 AGCGGTTAAT
440969 TGCCTCAGAAATAAGG
1 TGCCTCAGAAATAAGG
*
440985 TGCCTTAGAAATAAGG
1 TGCCTCAGAAATAAGG
441001 T
1 T
441002 TAGACATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (16 bp):
TGCCTCAGAAATAAGG
Found at i:446092 original size:31 final size:30
Alignment explanation
Indices: 446038--446111 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
446028 TAAATTTAGA
446038 AAAATTATTAAAATTTGTAAAAAACGTATTT
1 AAAATTATTAAAATTTGTAAAAAA-GTATTT
*
446069 AAAATTATTAAAAGGTTT-T-AAAAATTATTT
1 AAAATTATTAAAA--TTTGTAAAAAAGTATTT
* *
446099 AATATTATAAAAA
1 AAAATTATTAAAA
446112 AGTTGAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 16 0.42
31 18 0.47
32 1 0.03
33 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.39
Consensus pattern (30 bp):
AAAATTATTAAAATTTGTAAAAAAGTATTT
Found at i:450120 original size:106 final size:106
Alignment explanation
Indices: 449935--450267 Score: 648
Period size: 106 Copynumber: 3.1 Consensus size: 106
449925 ATGCATGATC
*
449935 ATATGGTACAGATATATTTCCTAATTTTAAATCTTTTTATAGCACCAAAAACAAAGCTTAGGCCT
1 ATATGGTACAGATATATTTCCTAATTTTAAATCTTTTTATAGCACCAAAAACCAAGCTTAGGCCT
450000 AATGCTAAACTTGATCAGCCATGTGGGAAGAAGACTAATAA
66 AATGCTAAACTTGATCAGCCATGTGGGAAGAAGACTAATAA
*
450041 ATATGGCACAGATATATTTCCTAATTTTAAATCTTTTTATAGCACCAAAAACCAAGCTTAGGCCT
1 ATATGGTACAGATATATTTCCTAATTTTAAATCTTTTTATAGCACCAAAAACCAAGCTTAGGCCT
450106 AATGCTAAACTTGATCAGCCATGTGGGAAGAAGACTAATAA
66 AATGCTAAACTTGATCAGCCATGTGGGAAGAAGACTAATAA
450147 ATATGGTACAGATATATTTCCTAATTTTAAATCTTTTTATAGCACCAAAAACCAAGCTTAGGCCT
1 ATATGGTACAGATATATTTCCTAATTTTAAATCTTTTTATAGCACCAAAAACCAAGCTTAGGCCT
450212 AATGCTAAACTTGATCAGCCATGTGGGAAGAAGACTAATAA
66 AATGCTAAACTTGATCAGCCATGTGGGAAGAAGACTAATAA
450253 ATATGGTACAGATAT
1 ATATGGTACAGATAT
450268 TTATGCATGA
Statistics
Matches: 224, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 224 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (106 bp):
ATATGGTACAGATATATTTCCTAATTTTAAATCTTTTTATAGCACCAAAAACCAAGCTTAGGCCT
AATGCTAAACTTGATCAGCCATGTGGGAAGAAGACTAATAA
Found at i:457104 original size:3 final size:3
Alignment explanation
Indices: 457098--457122 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
457088 AAACAAAATA
457098 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
457123 TGGTGTAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:457239 original size:2 final size:2
Alignment explanation
Indices: 457223--457266 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
457213 GTGATTCATC
* * *
457223 CT CT CT TT CT TT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
457265 CT
1 CT
457267 TAACACTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (2 bp):
CT
Found at i:457244 original size:16 final size:16
Alignment explanation
Indices: 457223--457264 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
457213 GTGATTCATC
*
457223 CTCTCTTTCTTTCTCT
1 CTCTCTCTCTTTCTCT
457239 CTCTCTCTCTTTCTCT
1 CTCTCTCTCTTTCTCT
457255 CTCTCTCTCT
1 CTCTCTCTCT
457265 CTTAACACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (16 bp):
CTCTCTCTCTTTCTCT
Found at i:460593 original size:3 final size:3
Alignment explanation
Indices: 460585--460649 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
460575 ATTCAATCAA
* * *
460585 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGAT CAA AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
460631 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
460650 TAAAGAAAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 54 0.96
4 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:467161 original size:3 final size:3
Alignment explanation
Indices: 467153--467177 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
467143 AATGATAAGA
467153 TGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC T
467178 TGACTTAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.32, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:467722 original size:46 final size:43
Alignment explanation
Indices: 467671--467755 Score: 100
Period size: 46 Copynumber: 1.9 Consensus size: 43
467661 TGAATACTTA
*
467671 AAAATTT-TATAACAAATATTCAAAAAAAATTCTATAAAAAATGTTT
1 AAAATTTGTAAAACAAA-ATTC-AAAAAAATT-T-TAAAAAATGTTT
* *
467717 AAAATTTGTAAAAGAAAATTCTAAAAAATTTTAAAAAAT
1 AAAATTTGTAAAACAAAATTCAAAAAAATTTTAAAAAAT
467756 TAAAAAGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
43 8 0.23
44 1 0.03
45 8 0.23
46 11 0.31
47 7 0.20
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.33
Consensus pattern (43 bp):
AAAATTTGTAAAACAAAATTCAAAAAAATTTTAAAAAATGTTT
Found at i:468187 original size:17 final size:17
Alignment explanation
Indices: 468161--468193 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
468151 GTAGTTATAT
468161 TTAAATAATATTTATAAG
1 TTAAATAATA-TTATAAG
468179 TTAAA-AATATTATAA
1 TTAAATAATATTATAA
468194 CAGTGAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAAATAATATTATAAG
Found at i:484830 original size:30 final size:30
Alignment explanation
Indices: 484786--485103 Score: 305
Period size: 29 Copynumber: 10.7 Consensus size: 30
484776 CATCCGGGGG
* *
484786 AAAATGGTAATTTTTGAAAGTTTCAAGGTCA
1 AAAATGG-AATTTTTGGAAGTTTCGAGGTCA
*
484817 AAAATGGAATTTTTGGAAG-TTCGAGGGCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
* * *
484846 AAAATGGCATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
* * *
484876 AAAATTGAATTTTTGGAAGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
484905 AAAATGGAA-TTTTGGAAGTTTC-AGGTTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGG-TCA
*
484934 AAAATGGAATTTTTGGAAG-TTCGAGGGCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
* * * * * *
484963 AAAATGTAATCTTCGAATAGTTTTGAGGTTA
1 AAAATGGAATTTTTGGA-AGTTTCGAGGTCA
*
484994 AAAATGGAATTTTTGGAAG-TTCGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTC-GAGGTCA
* * *
485023 AAAATGAAATTTTTGGAAGTTTTGAGGT-T
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
485052 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
* * *
485081 AAAAAGTAATTTTCGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
485104 AAAGACCTCC
Statistics
Matches: 238, Mismatches: 37, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
27 2 0.01
28 17 0.07
29 123 0.52
30 67 0.28
31 29 0.12
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTCA
Found at i:484946 original size:58 final size:58
Alignment explanation
Indices: 484643--485103 Score: 353
Period size: 58 Copynumber: 7.9 Consensus size: 58
484633 TACCCAGAGG
** *
484643 AAAATGGTAA-TTTTGGATTTTCGAGGGT-AACATGGTAATTTTGGGAAAG-TTCAGGGTT-A
1 AAAATGG-AATTTTTGGAAGTTCGAGGGTAAAAATGG-AATTTT-GG-AAGTTTCA-GGTTCA
* * * *
484702 AAAATGAAAATTTTAGACA-TTCGAGGGT-AAAAGGGTAATTTT-GAGAGTTTCAAGG-TC-
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGG-AATTTTGGA-AGTTTC-AGGTTCA
* * *
484759 AAAAT-GAAGTTTTTGGACA-TCCG-GGG-GAAAATGGTAATTTTTGAAAGTTTCAAGG-TCA
1 AAAATGGAA-TTTTTGGA-AGTTCGAGGGTAAAAATGG-AA-TTTTGGAAGTTTC-AGGTTCA
* * ** *
484817 AAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGGCATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGG-AATTTTGGAAGTTTCAGGTTCA
* * *
484876 AAAATTGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTGGAAGTTTCAGGTTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTGGAAGTTTCAGGTTCA
* * * * *
484934 AAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGTAATCTTCGAATAGTTTTGAGGTT-A
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAAT-TTTGGA-AG-TTTCAGGTTCA
* * *
484994 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTGGAAGTTTTGAGGTT--
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAA-TTTTGGAAG-TTTCAGGTTCA
* *
485052 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAAGTAATTTTCGGATAGTTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT-GGA-AGTTT
485104 AAAGACCTCC
Statistics
Matches: 338, Mismatches: 42, Indels: 45
0.80 0.10 0.11
Matches are distributed among these distances:
56 15 0.04
57 41 0.12
58 119 0.35
59 104 0.31
60 50 0.15
61 9 0.03
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTGGAAGTTTCAGGTTCA
Found at i:485034 original size:118 final size:119
Alignment explanation
Indices: 484754--485103 Score: 441
Period size: 118 Copynumber: 3.0 Consensus size: 119
484744 GAGAGTTTCA
* * *
484754 AGGTC-AAAAT-GAAGTTTTTGGACA-TCCGGGGG--AAAATGGTAATTTTTGAAAGTTTCAAGG
1 AGGTCAAAAATGGAA-TTTTTGGA-AGTTCGGGGGTAAAAAT-GAAATTTTTGGAAGTTTC-AGG
** *
484814 -TCAAAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGGCATTTTTGGA-AGTTTTG
62 TTCAAAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTCGGATAGTTTTG
* * * *
484870 GGGTCAAAAATTGAATTTTTGGAAGTTTGGGGGTAAAAATGGAA-TTTTGGAAGTTTCAGGTTCA
1 AGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTGGAAGTTTCAGGTTCA
* *
484934 AAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGTAATCTTCGAATAGTTTTG
66 AAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTCGGATAGTTTTG
* *
484988 AGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTGGAAGTTTTGAGGTT-
1 AGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTGGAAG-TTTCAGGTTC
* *
485052 -AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAAGTAATTTTCGGATAGTTT
65 AAAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTCGGATAGTTT
485104 AAAGACCTCC
Statistics
Matches: 205, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
116 8 0.04
117 75 0.37
118 100 0.49
119 14 0.07
120 8 0.04
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (119 bp):
AGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTGGAAGTTTCAGGTTCA
AAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTCGGATAGTTTTG
Found at i:486557 original size:6 final size:6
Alignment explanation
Indices: 486546--486625 Score: 60
Period size: 6 Copynumber: 14.0 Consensus size: 6
486536 TAATGAGACT
* * * **
486546 TTTAAA TTTAAA -ATAAT TTTAAT TTTAAA AGTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
486593 --CAAA TTTAAA TTTAAA -ACAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
486626 ATAAATTAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
4 3 0.05
5 6 0.11
6 47 0.84
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:486565 original size:17 final size:17
Alignment explanation
Indices: 486546--486653 Score: 130
Period size: 17 Copynumber: 6.4 Consensus size: 17
486536 TAATGAGACT
*
486546 TTTAAATTTAAAATAAT
1 TTTAAATTTAAAATAAA
*
486563 TTTAATTTTAAAAGTAAA
1 TTTAAATTTAAAA-TAAA
*
486581 TTTAAATTT-AAACAAA
1 TTTAAATTTAAAATAAA
*
486597 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
486614 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
486631 -TTAAATATTATAGTAAA
1 TTTAAAT-TTAAAATAAA
486648 TTTAAA
1 TTTAAA
486654 AAGGAATTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
16 18 0.22
17 46 0.57
18 16 0.20
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:487324 original size:209 final size:209
Alignment explanation
Indices: 486958--487350 Score: 637
Period size: 209 Copynumber: 1.9 Consensus size: 209
486948 GGTGTTATTG
* * * *
486958 TTGATTTGGTTTACTTCTCAGTATCTCATCAGGAATATGACCACCTCTTTCGTTTCAATCCGCTT
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCACCACTTTCGTTTCAATCCGCTT
* * *
487023 CTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTTAGTATCTCATCAAGAAGCTAATCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
* * *
487088 TTTATTGCTTTGACCTGCTTATCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTTACTT
131 TTTATTGCTTCGACCTACTTATCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTACTT
487153 TGAGCCTGACTTCA
196 TGAGCCTGACTTCA
*
487167 TTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACTGCATCAC-TT-GTTTCAATCCGC
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGAC--CACCACTTTCGTTTCAATCCGC
487230 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACC
64 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACC
* *
487295 ATTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCTAAGA
129 ATTTTATTGCTTCGACCTACTTATCAGTATCTCATCAGGAAGCTGGGGTTCGAAGA
487351 ATCGTTCACA
Statistics
Matches: 169, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
209 163 0.96
210 2 0.01
211 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (209 bp):
TTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCACCACTTTCGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
TTTATTGCTTCGACCTACTTATCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTACTT
TGAGCCTGACTTCA
Found at i:487599 original size:115 final size:114
Alignment explanation
Indices: 487265--487581 Score: 357
Period size: 116 Copynumber: 2.7 Consensus size: 114
487255 AATTTGGTCC
* * * *
487265 ACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCAGTATCTCAT
* * * * * *
487330 CAGGAAGCTGGGGTTCTAAGAATCGTTCACATCGGGCCCTAAGTTGGTAT
66 CAGGAAGCT-GGGTTCGAAGAATTGATCACATCGAGCCTTAACTTGGTAT
* * * * **** ** * *
487380 TCTTCTCTGTATCTTATCAGGAAGATGACTGCCTTACTTGTTTC-AATTCGCTTCTCTGTATCTT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTA-TTGTTTCGACCT-GCTTCTCAGTATCTC
* *
487444 ATCAGGAAGCTGGGATTCGAAGACTTGATCACATCGAGCCTTGACTTGGTAT
64 ATCAGGAAGCTGGG-TTCGAAGAATTGATCACATCGAGCCTTAACTTGGTAT
*
487496 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCAGTATCTCAT
487561 CAGGAAGCTAGGGTTCGAAGA
66 CAGGAAGCT-GGGTTCGAAGA
487582 TTTGCTCGCT
Statistics
Matches: 160, Mismatches: 37, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
115 69 0.43
116 91 0.57
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (114 bp):
ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTGGGTTCGAAGAATTGATCACATCGAGCCTTAACTTGGTAT
Found at i:494569 original size:59 final size:59
Alignment explanation
Indices: 494448--494733 Score: 187
Period size: 59 Copynumber: 4.9 Consensus size: 59
494438 TTTCGGGGTT
* ** * * * *
494448 AAAAATGGAATTTTAAGACATTCAGGGGTAAAAG--GGTAA-TTTTGAGAGTTTTGAGGTT
1 AAAAATAGAATTTTTGGACATTC-GGGGGAAAAGATGG-AATTTTTGAAAGTTTTAAGGTC
* * *
494506 AAAAATAGAGTTTTTGGACATTCGGGGGAAAAGTTGTAATTTTTGAAAGTTTTAAGGTC
1 AAAAATAGAATTTTTGGACATTCGGGGGAAAAGATGGAATTTTTGAAAGTTTTAAGGTC
* * * ** * * *
494565 AAAAATGGAAATTTTAGAGGTTTGGAGGTAAAA-ATGGAATTTTTGGAAG-TTTAGAGGTC
1 AAAAATAGAATTTTTGGACATTCGG-GGGAAAAGATGGAATTTTTGAAAGTTTTA-AGGTC
* * * * *
494624 AAAAATGGAATTTTTGGA-AGTT--TGGGAATATAAATGGAATTTTTGGAAGTTTCAAGGTC
1 AAAAATAGAATTTTTGGACA-TTCGGGGGAA-A-AGATGGAATTTTTGAAAGTTTTAAGGTC
* * *
494683 AAAAATAGAATTTTTGGA-AGTTCGAGGGTAAAA-ATAGAATTTTTGGAAGTT
1 AAAAATAGAATTTTTGGACA-TTCG-GGGGAAAAGATGGAATTTTTGAAAGTT
494734 CGAGGGAAAA
Statistics
Matches: 185, Mismatches: 30, Indels: 25
0.77 0.12 0.10
Matches are distributed among these distances:
56 4 0.02
57 10 0.05
58 26 0.14
59 130 0.70
60 10 0.05
61 1 0.01
62 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAAATAGAATTTTTGGACATTCGGGGGAAAAGATGGAATTTTTGAAAGTTTTAAGGTC
Found at i:494599 original size:29 final size:30
Alignment explanation
Indices: 494543--494821 Score: 236
Period size: 29 Copynumber: 9.5 Consensus size: 30
494533 GAAAAGTTGT
* **
494543 AATTTTTGAAAGTTTTAAGGTCAAAAATGG
1 AATTTTTGGAAGTTTGGAGGTCAAAAATGG
* * *
494573 AAATTTTAGAGGTTTGGAGGT-AAAAATGG
1 AATTTTTGGAAGTTTGGAGGTCAAAAATGG
*
494602 AATTTTTGGAAGTTTAGAGGTCAAAAATGG
1 AATTTTTGGAAGTTTGGAGGTCAAAAATGG
* *
494632 AATTTTTGGAAGTTTGG-GAAT-ATAAATGG
1 AATTTTTGGAAGTTTGGAG-GTCAAAAATGG
** *
494661 AATTTTTGGAAGTTTCAAGGTCAAAAATAG
1 AATTTTTGGAAGTTTGGAGGTCAAAAATGG
* *
494691 AATTTTTGGAAG-TTCGAGGGT-AAAAATAG
1 AATTTTTGGAAGTTTGGA-GGTCAAAAATGG
* * *
494720 AATTTTTGGAAG-TTCGAGG-GAAAATATGT
1 AATTTTTGGAAGTTTGGAGGTCAAAA-ATGG
* * * * *
494749 AATTTTCGAATAGTTTCGAGATTAAAAATGG
1 AATTTTTGGA-AGTTTGGAGGTCAAAAATGG
494780 AATTTTTGGAAGTTT-GAGG-CTAAAAATGG
1 AATTTTTGGAAGTTTGGAGGTC-AAAAATGG
*
494809 -ATTTTTTGAAGTT
1 AATTTTTGGAAGTT
494822 CAAGGGTTAA
Statistics
Matches: 207, Mismatches: 31, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
28 18 0.09
29 99 0.48
30 69 0.33
31 17 0.08
32 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAGTTTGGAGGTCAAAAATGG
Found at i:494638 original size:89 final size:85
Alignment explanation
Indices: 494543--494818 Score: 243
Period size: 89 Copynumber: 3.1 Consensus size: 85
494533 GAAAAGTTGT
* *
494543 AATTTTTGAAAGTTTTAAGGTCAAAAATGGAAATTTTAGAGGTTTGGAGGTAAAAATGGAATTTT
1 AATTTTTGAAAG-TTT-AGGT-AAAAATGGAAATTTTAGAAGTTTCGAGGTAAAAATGGAATTTT
494608 TGGAAGTTTAGAGGTCAAAAATGG
63 TGGAAGTTT-GAGGTCAAAAATGG
* * * * * * *
494632 AATTTTTGGAAGTTTGGGAATATAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATAGAATTTT
1 AATTTTTGAAAGTTTAGG--TAAAAATGGAAATTTTAGAAGTTTCGAGGT-AAAAATGGAATTTT
* *
494697 TGGAAGTTCGAGGGT-AAAAATAG
63 TGGAAGTTTGA-GGTCAAAAATGG
* * * * * *
494720 AATTTTTGGAAGTTCGAGGGAAAATAT-GTAATTTTCGAATAGTTTCGAGATTAAAAATGGAATT
1 AATTTTTGAAAGTT-TAGGTAAAA-ATGGAAATTTTAG-A-AGTTTCGAG-GTAAAAATGGAATT
494784 TTTGGAAGTTTGAGG-CTAAAAATGG
61 TTTGGAAGTTTGAGGTC-AAAAATGG
*
494809 ATTTTTTGAA
1 AATTTTTGAA
494819 GTTCAAGGGT
Statistics
Matches: 151, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
87 12 0.08
88 54 0.36
89 84 0.56
90 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (85 bp):
AATTTTTGAAAGTTTAGGTAAAAATGGAAATTTTAGAAGTTTCGAGGTAAAAATGGAATTTTTGG
AAGTTTGAGGTCAAAAATGG
Found at i:495655 original size:67 final size:66
Alignment explanation
Indices: 495575--495708 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 66
495565 CTAGATTTGG
495575 ATTTAATCCAGATCTAAAATAAGTTTTTAATCTTTCTCTTTTTTCCTTTAAAACCCCTCTGTTTC
1 ATTTAATCCAGATCTAAAATAAGTTTTTAATCTTTCTCTTTTTTCCTTTAAAACCCCTCTGTTTC
495640 A
66 A
495641 ATTTAAATCCAGATCTAAAATAAGTTTTTAATCTTTCTCTTTTTTCCTTTAAAACCCCTCTGTTT
1 ATTT-AATCCAGATCTAAAATAAGTTTTTAATCTTTCTCTTTTTTCCTTTAAAACCCCTCTGTTT
495706 CA
65 CA
495708 A
1 A
495709 AACCCAAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 4 0.06
67 63 0.94
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.46
Consensus pattern (66 bp):
ATTTAATCCAGATCTAAAATAAGTTTTTAATCTTTCTCTTTTTTCCTTTAAAACCCCTCTGTTTC
A
Found at i:496054 original size:3 final size:3
Alignment explanation
Indices: 496041--496106 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
496031 TCTTTATTTT
** *
496041 TTA TT- TTA TTA TTA ACA TTA TTA ATA TTA -TA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
496085 CTA TTA TTA TTAA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA
496107 ATAGTCTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.82
4 5 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:496802 original size:17 final size:17
Alignment explanation
Indices: 496781--496889 Score: 112
Period size: 17 Copynumber: 6.4 Consensus size: 17
496771 AATGAGATTT
* *
496781 TTTAATTTTAAAATAAT
1 TTTAAATTTAAAATAAA
*
496798 TTTAATTTTAAAAGTAAA
1 TTTAAATTTAAAA-TAAA
* **
496816 TTTAAACTTAATTTAAA
1 TTTAAATTTAAAATAAA
* *
496833 TTTAAATTTAAATTAAG
1 TTTAAATTTAAAATAAA
496850 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
496867 -TTAAATCTTATAATAAA
1 TTTAAAT-TTAAAATAAA
496884 TTTAAA
1 TTTAAA
496890 AAAGAATTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
16 6 0.08
17 55 0.71
18 17 0.22
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:496821 original size:6 final size:6
Alignment explanation
Indices: 496798--496889 Score: 70
Period size: 6 Copynumber: 16.0 Consensus size: 6
496788 TTAAAATAAT
* ** *
496798 TTTAAT TTTAAA AGTAAA TTTAAA CTT-AA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
496845 -TTAAG TTTAAA TTTAAA -ATAAA -TTAAA TCTTATAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTA-AA TTTAAA TTTAAA
496890 AAAGAATTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
4 2 0.03
5 18 0.26
6 43 0.63
7 3 0.04
8 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:496830 original size:11 final size:11
Alignment explanation
Indices: 496814--496860 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
496804 TTTAAAAGTA
*
496814 AATTTAAACTT
1 AATTTAAATTT
496825 AATTTAAATTT
1 AATTTAAATTT
496836 AAATTTAAA-TT
1 -AATTTAAATTT
496847 AAGTTTAAATTT
1 AA-TTTAAATTT
496859 AA
1 AA
496861 AATAAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 2 0.06
11 18 0.56
12 12 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:496844 original size:29 final size:29
Alignment explanation
Indices: 496781--496846 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
496771 AATGAGATTT
* *
496781 TTTAATTTTAAAATAATTTTAATTTTAAA
1 TTTAAATTTAAAATAATTTTAAATTTAAA
** *
496810 AGTAAATTTAAACTTAA-TTTAAATTTAAA
1 TTTAAATTTAAA-ATAATTTTAAATTTAAA
496839 TTTAAATT
1 TTTAAATT
496847 AAGTTTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTAAATTTAAAATAATTTTAAATTTAAA
Found at i:498730 original size:58 final size:58
Alignment explanation
Indices: 498665--498780 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
498655 ATAAACGAAC
498665 TACTCTGATTAGTAATTGCAATTTGGAGTTAGTTTCTAAGTTAATTGATTATGAATAT
1 TACTCTGATTAGTAATTGCAATTTGGAGTTAGTTTCTAAGTTAATTGATTATGAATAT
498723 TACTCTGATTAGTAATTGCAATTTGGAGTTAGTTTCTAAGTTAATTGATTATGAATAT
1 TACTCTGATTAGTAATTGCAATTTGGAGTTAGTTTCTAAGTTAATTGATTATGAATAT
498781 AGACTACAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (58 bp):
TACTCTGATTAGTAATTGCAATTTGGAGTTAGTTTCTAAGTTAATTGATTATGAATAT
Found at i:498767 original size:29 final size:29
Alignment explanation
Indices: 498677--498769 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
498667 CTCTGATTAG
498677 TAATTGCAATTTGGAGTTAGTTTCTAAGT
1 TAATTGCAATTTGGAGTTAGTTTCTAAGT
* * * ** *
498706 TAATTG--ATTATGAATATTACTCTGATTAG-
1 TAATTGCAATT-TGGA-GTTAGT-TTCTAAGT
498735 TAATTGCAATTTGGAGTTAGTTTCTAAGT
1 TAATTGCAATTTGGAGTTAGTTTCTAAGT
498764 TAATTG
1 TAATTG
498770 ATTATGAATA
Statistics
Matches: 46, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
27 3 0.07
28 7 0.15
29 26 0.57
30 7 0.15
31 3 0.07
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (29 bp):
TAATTGCAATTTGGAGTTAGTTTCTAAGT
Found at i:513526 original size:16 final size:17
Alignment explanation
Indices: 513500--513535 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
513490 ATAATAAAAA
*
513500 TAATAATTTTATTATTT
1 TAATAATTTTATAATTT
513517 TAAT-ATTTTATAATTT
1 TAATAATTTTATAATTT
513533 TAA
1 TAA
513536 AGAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATAATTTTATAATTT
Found at i:513554 original size:29 final size:30
Alignment explanation
Indices: 513517--513583 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
513507 TTTATTATTT
*
513517 TAATATTTTA-TAATTTTAAAGAATTAAATCA
1 TAAT-TTTTATTAATTTTAAAGAATAAAAT-A
*
513548 -AATTTTTATTATTTTTAAAGAATAAAATA
1 TAATTTTTATTAATTTTAAAGAATAAAATA
513577 TAATTTT
1 TAATTTT
513584 ATCTTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (30 bp):
TAATTTTTATTAATTTTAAAGAATAAAATA
Found at i:514115 original size:7 final size:7
Alignment explanation
Indices: 514103--514127 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
514093 TAATTACAAT
514103 AATGAAG
1 AATGAAG
514110 AATGAAG
1 AATGAAG
514117 AATGAAG
1 AATGAAG
514124 AATG
1 AATG
514128 GTATCCAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (7 bp):
AATGAAG
Found at i:518717 original size:18 final size:18
Alignment explanation
Indices: 518694--518737 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
518684 TTTGGCCCTT
*
518694 ATATTTGTATAGTTTTA-A
1 ATATTT-TATAATTTTATA
518712 ATA-TTTATAATTTTATA
1 ATATTTTATAATTTTATA
518729 ATATTTTAT
1 ATATTTTAT
518738 TAAGTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 6 0.26
18 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
ATATTTTATAATTTTATA
Found at i:519196 original size:18 final size:18
Alignment explanation
Indices: 519173--519221 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
519163 AATTACAATA
519173 TTAAAATA-TTTTATATTT
1 TTAAAATATTTTTATA-TT
*
519191 TTAAAATATTTTTTTATT
1 TTAAAATATTTTTATATT
519209 TTAAAATATTTTT
1 TTAAAATATTTTT
519222 GAATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 23 0.79
19 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTAAAATATTTTTATATT
Found at i:519231 original size:28 final size:29
Alignment explanation
Indices: 519185--519243 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
519175 AAAATATTTT
**
519185 ATATTTTTAAAATATTTTTTTATTTTAAA
1 ATATTTTTAAAATATTTTTAAATTTTAAA
* *
519214 ATATTTTT-GAATTTTTTTAAATTTTAAA
1 ATATTTTTAAAATATTTTTAAATTTTAAA
519242 AT
1 AT
519244 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATATTTTTAAAATATTTTTAAATTTTAAA
Found at i:519254 original size:18 final size:18
Alignment explanation
Indices: 519173--519250 Score: 70
Period size: 18 Copynumber: 4.3 Consensus size: 18
519163 AATTACAATA
*
519173 TTAAAATATTTTATATTT
1 TTAAAATATTTTATAATT
* *
519191 TTAAAATATTTTTTTATT
1 TTAAAATATTTTATAATT
519209 TTAAAATATTTT-TGAATTT
1 TTAAAATATTTTAT-AA-TT
** *
519228 TTTTAA-ATTTTAAAATT
1 TTAAAATATTTTATAATT
519245 TTAAAA
1 TTAAAA
519251 AATTATTTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
17 7 0.15
18 35 0.73
19 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (18 bp):
TTAAAATATTTTATAATT
Found at i:522367 original size:17 final size:17
Alignment explanation
Indices: 522345--522403 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
522335 GTCTTCTTCG
522345 AATCCCTAAAATATTAA
1 AATCCCTAAAATATTAA
*
522362 AATCCCT-AAATATTGA
1 AATCCCTAAAATATTAA
* ** **
522378 AACCCCCCAAATATTTT
1 AATCCCTAAAATATTAA
522395 AATCCCTAA
1 AATCCCTAA
522404 CCCAAGATCG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
16 13 0.39
17 20 0.61
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.29
Consensus pattern (17 bp):
AATCCCTAAAATATTAA
Found at i:523352 original size:33 final size:33
Alignment explanation
Indices: 523265--523357 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 33
523255 TGTTGACTGC
* * ***
523265 TGGGGAAGGAGATGATGAAGTTATAGAAGTTGA
1 TGGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
* * *
523298 T-GGAAGGGTAATG-TAGGAGGGGTAGAAGTTGA
1 TGGGGAGGGTGATGAT-GAAGGGGTAGAAGTTGA
523330 TGGGGAGGGTGATGATGAAGGGGTAGAA
1 TGGGGAGGGTGATGATGAAGGGGTAGAA
523358 TCTGATAGTG
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
31 1 0.02
32 22 0.48
33 22 0.48
34 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (33 bp):
TGGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
Found at i:523374 original size:33 final size:33
Alignment explanation
Indices: 523308--523444 Score: 127
Period size: 33 Copynumber: 4.2 Consensus size: 33
523298 TGGAAGGGTA
* * * * *
523308 ATGTAGGAGGGGTAGAAGTTGATGGGGAGGGTG
1 ATGTAGAAGGGGTAGAAGCTGATAGTGAAGGTG
*
523341 ATG-ATGAAGGGGTAGAATCTGATAGTGAAGGTG
1 ATGTA-GAAGGGGTAGAAGCTGATAGTGAAGGTG
* * *
523374 ATCTAGAAAGGGTAGAAGCTGTTGAG-GAAGGTG
1 ATGTAGAAGGGGTAGAAGCTGAT-AGTGAAGGTG
* *
523407 ATGTAGGAGGGGTTGAAGCTGAT-GTGAAGAGTG
1 ATGTAGAAGGGGTAGAAGCTGATAGTGAAG-GTG
523440 ATGTA
1 ATGTA
523445 AGAGGGTCAA
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
31 1 0.01
32 5 0.06
33 75 0.89
34 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.44, T:0.23
Consensus pattern (33 bp):
ATGTAGAAGGGGTAGAAGCTGATAGTGAAGGTG
Found at i:523408 original size:66 final size:66
Alignment explanation
Indices: 523317--523441 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 66
523307 AATGTAGGAG
* * * *
523317 GGGTAGAAGTTGATGGGGAGGGTGATG-ATGAAGGGGTAGAATCTGATAGTGAAG-GTGATCTAG
1 GGGTAGAAGCTGATGAGGAAGGTGATGTA-GAAGGGGTAGAAGCTGAT-GTGAAGAGTGATCTAG
523380 AAA
64 AAA
* * *
523383 GGGTAGAAGCTGTTGAGGAAGGTGATGTAGGAGGGGTTGAAGCTGATGTGAAGAGTGAT
1 GGGTAGAAGCTGATGAGGAAGGTGATGTAGAAGGGGTAGAAGCTGATGTGAAGAGTGAT
523442 GTAAGAGGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
65 6 0.12
66 43 0.86
67 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.44, T:0.23
Consensus pattern (66 bp):
GGGTAGAAGCTGATGAGGAAGGTGATGTAGAAGGGGTAGAAGCTGATGTGAAGAGTGATCTAGAA
A
Found at i:523450 original size:33 final size:32
Alignment explanation
Indices: 523288--523450 Score: 116
Period size: 33 Copynumber: 5.0 Consensus size: 32
523278 GATGAAGTTA
* * *
523288 TAGAAGTTGAT-GGAAGGGTAATGTAGGAGGGG
1 TAGAAGCTGATGGGAA-GGTGATGTAAGAGGGG
* * *
523320 TAGAAGTTGATGGGGAGGGTGATG-ATGAAGGGG
1 TAGAAGCTGAT-GGGAAGGTGATGTAAG-AGGGG
* * * *
523353 TAGAATCTGATAGTGAAGGTGATCT-AGAAAGGG
1 TAGAAGCTGAT-GGGAAGGTGATGTAAG-AGGGG
* *
523386 TAGAAGCTGTTGAGGAAGGTGATGTAGGAGGGG
1 TAGAAGCTGATG-GGAAGGTGATGTAAGAGGGG
* *
523419 TTGAAGCTGATGTGAAGAGTGATGTAAGAGGG
1 TAGAAGCTGATGGGAAG-GTGATGTAAGAGGG
523451 TCAACTATTA
Statistics
Matches: 103, Mismatches: 21, Indels: 13
0.75 0.15 0.09
Matches are distributed among these distances:
32 18 0.17
33 81 0.79
34 4 0.04
ACGTcount: A:0.31, C:0.02, G:0.44, T:0.23
Consensus pattern (32 bp):
TAGAAGCTGATGGGAAGGTGATGTAAGAGGGG
Found at i:523546 original size:51 final size:51
Alignment explanation
Indices: 523490--523616 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 51
523480 AAAGTTGCTA
* *
523490 CTGATGAATATGCTGCTGATTTTGTAACATTAAATGGAGAGGATAATGTTG
1 CTGATGAATATGCTGCTGATTTTGCAACATTAAATAGAGAGGATAATGTTG
* * * * *
523541 CTGATGAATATGATGCTAATTTTCCAACATTAGATAGAGTGGATAATGTTG
1 CTGATGAATATGCTGCTGATTTTGCAACATTAAATAGAGAGGATAATGTTG
*
523592 CTGATGAAGT-TACTGCTGATTTTGC
1 CTGATGAA-TATGCTGCTGATTTTGC
523617 TGATAAAAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 63 0.98
52 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (51 bp):
CTGATGAATATGCTGCTGATTTTGCAACATTAAATAGAGAGGATAATGTTG
Found at i:530777 original size:50 final size:50
Alignment explanation
Indices: 530719--530820 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
530709 AAGCTAGTTG
* *
530719 GTGATGCTCGATGTCCTCGGTGTGGTGGTGATGATGAAACAGTGGACTAT
1 GTGATGCTCGATGTCCCCGATGTGGTGGTGATGATGAAACAGTGGACTAT
530769 GTGATGCTCGATGTCCCCGATGTGGTGGTGATGATGAAACAGTGGACTAT
1 GTGATGCTCGATGTCCCCGATGTGGTGGTGATGATGAAACAGTGGACTAT
530819 GT
1 GT
530821 CATGTGTAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (50 bp):
GTGATGCTCGATGTCCCCGATGTGGTGGTGATGATGAAACAGTGGACTAT
Found at i:533261 original size:76 final size:74
Alignment explanation
Indices: 533154--533312 Score: 214
Period size: 74 Copynumber: 2.1 Consensus size: 74
533144 CAAACCCAGA
* *
533154 TATTTGGCACCATTATTATTCACCCTTTTTATTTATTTATTTTTAAAAAA-TATTTTTTTATTTG
1 TATTTGGCACCATCATTATTCACCCTTTTTATCTATTTA--TTTAAAAAATTA-TTTTTTATTTG
533218 ATGGTG-TCAATC
63 ATGGTGCT-AATC
* * * *
533230 TATTTGTCATCATCATTATTCACCTTTTTTATCTATTTATTTAAAAAATTATTTTTTATTTGGTG
1 TATTTGGCACCATCATTATTCACCCTTTTTATCTATTTATTTAAAAAATTATTTTTTATTTGATG
533295 GTGCTAATC
66 GTGCTAATC
533304 TATTTGGCA
1 TATTTGGCA
533313 GCATACTCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
74 37 0.50
75 3 0.04
76 34 0.46
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (74 bp):
TATTTGGCACCATCATTATTCACCCTTTTTATCTATTTATTTAAAAAATTATTTTTTATTTGATG
GTGCTAATC
Found at i:534398 original size:15 final size:14
Alignment explanation
Indices: 534378--534460 Score: 67
Period size: 15 Copynumber: 5.4 Consensus size: 14
534368 AGGATCTTTA
534378 AATCAATTTAATTAG
1 AATCAATTTAATT-G
**
534393 AATCAAATCAAATTG
1 AATC-AATTTAATTG
534408 AAATCAATTTAATTAG
1 -AATCAATTTAATT-G
**
534424 AATCAAATCAAATTG
1 AATC-AATTTAATTG
534439 AAATCAATTTAATTGG
1 -AATCAATTTAATT-G
534455 AATCAA
1 AATCAA
534461 ATCAGATTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 30 0.56
16 24 0.44
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.33
Consensus pattern (14 bp):
AATCAATTTAATTG
Found at i:534412 original size:16 final size:16
Alignment explanation
Indices: 534393--534470 Score: 72
Period size: 15 Copynumber: 5.0 Consensus size: 16
534383 ATTTAATTAG
534393 AATCAAATCAAATTGA
1 AATCAAATCAAATTGA
**
534409 AATC-AATTTAATT-A
1 AATCAAATCAAATTGA
534423 GAATCAAATCAAATTGA
1 -AATCAAATCAAATTGA
** *
534440 AATC-AATTTAATTGG
1 AATCAAATCAAATTGA
*
534455 AATCAAATCAGATTGA
1 AATCAAATCAAATTGA
534471 GATATTTTGT
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
14 1 0.02
15 23 0.49
16 22 0.47
17 1 0.02
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (16 bp):
AATCAAATCAAATTGA
Found at i:534415 original size:31 final size:31
Alignment explanation
Indices: 534377--534470 Score: 170
Period size: 31 Copynumber: 3.0 Consensus size: 31
534367 AAGGATCTTT
534377 AAATCAATTTAATTAGAATCAAATCAAATTG
1 AAATCAATTTAATTAGAATCAAATCAAATTG
534408 AAATCAATTTAATTAGAATCAAATCAAATTG
1 AAATCAATTTAATTAGAATCAAATCAAATTG
* *
534439 AAATCAATTTAATTGGAATCAAATCAGATTG
1 AAATCAATTTAATTAGAATCAAATCAAATTG
534470 A
1 A
534471 GATATTTTGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.32
Consensus pattern (31 bp):
AAATCAATTTAATTAGAATCAAATCAAATTG
Found at i:535472 original size:14 final size:15
Alignment explanation
Indices: 535447--535484 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
535437 TGAAAAAATA
535447 TATAATAATTATATT
1 TATAATAATTATATT
*
535462 TATAA-AATTATATA
1 TATAATAATTATATT
*
535476 AATAATAAT
1 TATAATAAT
535485 AAAAATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAATAATTATATT
Found at i:545163 original size:28 final size:27
Alignment explanation
Indices: 545130--545227 Score: 78
Period size: 28 Copynumber: 3.6 Consensus size: 27
545120 TGATTTTTTA
545130 ATTTTTATAAATTTATATAAAATTTAAT
1 ATTTTTATAAATTT-TATAAAATTTAAT
* **
545158 ATTTTTAATATATTTTATAATTTTTACAT
1 ATTTTT-ATAAATTTTATAAAATTTA-AT
*
545187 -TTTTTAT-TATTTT-TAAGAATTCTAAT
1 ATTTTTATAAATTTTATAA-AATT-TAAT
*
545213 ACTTTT-TAAATTTTA
1 ATTTTTATAAATTTTA
545228 AATATTTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
25 3 0.05
26 11 0.20
27 13 0.23
28 20 0.36
29 9 0.16
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (27 bp):
ATTTTTATAAATTTTATAAAATTTAAT
Found at i:545166 original size:9 final size:9
Alignment explanation
Indices: 545152--545318 Score: 71
Period size: 9 Copynumber: 18.3 Consensus size: 9
545142 TTATATAAAA
545152 TTTAATATT
1 TTTAATATT
545161 TTTAATATAT
1 TTTAATAT-T
545171 TTT-ATAATT
1 TTTAAT-ATT
545180 TTTACAT-TT
1 TTTA-ATATT
*
545189 TTTATTATT
1 TTTAATATT
* *
545198 TTTAAGAAT
1 TTTAATATT
*
545207 TCTAATACTT
1 TTTAATA-TT
545217 TTTAA-ATT
1 TTTAATATT
*
545225 TTAAATATT
1 TTTAATATT
*
545234 TTAAATAATTTT
1 TT---TAATATT
545246 TTTAAT-TT
1 TTTAATATT
* *
545254 ATT-ATA-A
1 TTTAATATT
**
545261 TTTAATAAG
1 TTTAATATT
*
545270 TTTATATCAAT
1 TTTA-AT-ATT
545281 TTTAA-ATTT
1 TTTAATA-TT
*
545290 TTTAA-GTT
1 TTTAATATT
545298 TTTAATATT
1 TTTAATATT
*
545307 TCTAATATT
1 TTTAATATT
545316 TTT
1 TTT
545319 TTCAGATTTT
Statistics
Matches: 120, Mismatches: 21, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
7 4 0.03
8 22 0.18
9 65 0.54
10 14 0.12
11 8 0.07
12 7 0.06
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTAATATT
Found at i:545219 original size:37 final size:37
Alignment explanation
Indices: 545152--545235 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
545142 TTATATAAAA
* * *
545152 TTTAATATTTTTAATATATTTTATAATTTTTACATTT
1 TTTAATATTTTTAAGATATTTAATAATTTTTAAATTT
* *
545189 TTTATTATTTTTAAGA-ATTCTAATACTTTTTAAA-TT
1 TTTAATATTTTTAAGATATT-TAATAATTTTTAAATTT
*
545225 TTAAATATTTT
1 TTTAATATTTT
545236 AAATAATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
36 14 0.36
37 25 0.64
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (37 bp):
TTTAATATTTTTAAGATATTTAATAATTTTTAAATTT
Found at i:545337 original size:9 final size:9
Alignment explanation
Indices: 545114--545301 Score: 72
Period size: 9 Copynumber: 20.7 Consensus size: 9
545104 CCGGTTCAAG
*
545114 TTTTTATGA
1 TTTTTATAA
545123 TTTTT-TAA
1 TTTTTATAA
545131 TTTTTATAAA
1 TTTTTAT-AA
*
545141 TTTATATAA
1 TTTTTATAA
**
545150 AATTTA-ATA
1 TTTTTATA-A
545159 TTTTTA-ATA
1 TTTTTATA-A
545168 TATTTTATAA
1 T-TTTTATAA
* *
545178 TTTTTACAT
1 TTTTTATAA
*
545187 TTTTTATTA
1 TTTTTATAA
*
545196 TTTTTAAGAA
1 TTTTT-ATAA
* * *
545206 TTCTAATAC
1 TTTTTATAA
545215 TTTTTA-AA
1 TTTTTATAA
545223 -TTTTA-AA
1 TTTTTATAA
545230 TATTTTAAATAA
1 T-TTTT--ATAA
*
545242 TTTTTTTAA
1 TTTTTATAA
545251 TTTATTATAA
1 TTT-TTATAA
*
545261 -TTTAATAA
1 TTTTTATAA
*
545269 GTTTATATCAA
1 -TTTTTAT-AA
545280 -TTTTA-AA
1 TTTTTATAA
545287 TTTTT-TAA
1 TTTTTATAA
545295 GTTTTTA
1 -TTTTTA
545302 ATATTTCTAA
Statistics
Matches: 133, Mismatches: 27, Indels: 37
0.68 0.14 0.19
Matches are distributed among these distances:
7 9 0.07
8 20 0.15
9 64 0.48
10 29 0.22
11 8 0.06
12 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:548999 original size:19 final size:20
Alignment explanation
Indices: 548962--549002 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
548952 ATACATTAAA
* *
548962 TTAAAAAATAACTCTTAATT
1 TTAAAAAATAAATCATAATT
548982 TTAAAAAATAAAT-ATAATT
1 TTAAAAAATAAATCATAATT
549001 TT
1 TT
549003 CTAAAAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAAAATAAATCATAATT
Found at i:550900 original size:24 final size:24
Alignment explanation
Indices: 550868--550924 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
550858 CAGCAAATGA
550868 TTTTAAAATTAATTTAAAATTATT
1 TTTTAAAATTAATTTAAAATTATT
550892 TTTTAAAATTAATTTAAAATTATT
1 TTTTAAAATTAATTTAAAATTATT
550916 TTTTAAAAT
1 TTTTAAAAT
550925 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTAAAATTAATTTAAAATTATT
Found at i:550924 original size:13 final size:11
Alignment explanation
Indices: 550862--550917 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
550852 CCACATCAGC
*
550862 AAATGATTTTA
1 AAATTATTTTA
*
550873 AAATTAATTTA
1 AAATTATTTTA
550884 AAATTATTTTTTA
1 AAATTA--TTTTA
*
550897 AAATTAATTTA
1 AAATTATTTTA
550908 AAATTATTTT
1 AAATTATTTT
550918 TTAAAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
11 28 0.74
13 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:554169 original size:29 final size:31
Alignment explanation
Indices: 554125--554199 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
554115 ATTTTCGAGG
*
554125 AATTTGAGGATCAAAATTAAA-ATTTTGGAA
1 AATTTGAGGATCAAAATCAAACATTTTGGAA
* *
554155 AATTTG-GGATTAAAATCAAACTTTTTGGAA
1 AATTTGAGGATCAAAATCAAACATTTTGGAA
554185 AATTTGAGG-TCAAAA
1 AATTTGAGGATCAAAA
554200 ATGTGATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 12 0.31
30 25 0.64
31 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.33
Consensus pattern (31 bp):
AATTTGAGGATCAAAATCAAACATTTTGGAA
Found at i:554264 original size:27 final size:27
Alignment explanation
Indices: 554219--554281 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
554209 TTGGAAATTT
554219 GGGGCAAAACGATAATTTT-GTATGTTC-
1 GGGGC-AAACGATAATTTTAG-ATGTTCG
* *
554246 GGGGCAAATGATAATTTTTAGATTTTCG
1 GGGGCAAACGATAA-TTTTAGATGTTCG
554274 GGGGCAAA
1 GGGGCAAA
554282 ATCATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 8 0.26
27 14 0.45
28 9 0.29
ACGTcount: A:0.30, C:0.10, G:0.29, T:0.32
Consensus pattern (27 bp):
GGGGCAAACGATAATTTTAGATGTTCG
Found at i:554351 original size:30 final size:29
Alignment explanation
Indices: 554297--554409 Score: 120
Period size: 30 Copynumber: 3.8 Consensus size: 29
554287 AATATTAAAG
* *
554297 AAGTTTGGGGTTAAAATAG-GATTTTGGAG
1 AAGTTTGGGGTGAAAAT-GTGATTTTGGAA
*
554326 AAGTTTGGGGGTGAAAATGTAATTTTGGAA
1 AAGTTT-GGGGTGAAAATGTGATTTTGGAA
* * *
554356 AAATTTAGGATGAAAATGTGATTTTGGAA
1 AAGTTTGGGGTGAAAATGTGATTTTGGAA
* *
554385 AAGTTTAGGAGTAAAAATGTGATTT
1 AAGTTT-GGGGTGAAAATGTGATTT
554410 AGTTCGATTG
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
29 32 0.46
30 37 0.54
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.35
Consensus pattern (29 bp):
AAGTTTGGGGTGAAAATGTGATTTTGGAA
Found at i:554456 original size:30 final size:30
Alignment explanation
Indices: 554295--554524 Score: 115
Period size: 30 Copynumber: 7.9 Consensus size: 30
554285 ATAATATTAA
* *
554295 AGAAGTTTG-GGGTTAAAATAG-GATTTTGG
1 AGAAGTTTGAGGGTTAAAAT-GTAATTTTTG
* * *
554324 AGAAGTTTGGGGGTGAAAATGTAATTTTGG
1 AGAAGTTTGAGGGTTAAAATGTAATTTTTG
* * * * * *
554354 AAAAATTT-AGGATGAAAATGTGATTTTGG
1 AGAAGTTTGAGGGTTAAAATGTAATTTTTG
* * *
554383 AAAAGTTT-AGGAGTAAAAATGTGA--TTT-
1 AGAAGTTTGAGG-GTTAAAATGTAATTTTTG
* ** *
554410 ---AGTTCGATTGTCAAAATGTAATTTTTG
1 AGAAGTTTGAGGGTTAAAATGTAATTTTTG
* * *
554437 TGAAGTTTGAGGGTTAAAATATGATTTTTG
1 AGAAGTTTGAGGGTTAAAATGTAATTTTTG
* *
554467 AGAAGTTCGAGGGTCAAAATGTAATTTTT-
1 AGAAGTTTGAGGGTTAAAATGTAATTTTTG
* *
554496 ACGAGGTTT-AGGAGTTAAAATTTAATTTT
1 A-GAAGTTTGAGG-GTTAAAATGTAATTTT
554525 AAACTAAACG
Statistics
Matches: 158, Mismatches: 31, Indels: 23
0.75 0.15 0.11
Matches are distributed among these distances:
24 14 0.09
25 1 0.01
26 3 0.02
28 2 0.01
29 42 0.27
30 96 0.61
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.37
Consensus pattern (30 bp):
AGAAGTTTGAGGGTTAAAATGTAATTTTTG
Found at i:554524 original size:60 final size:60
Alignment explanation
Indices: 554410--554524 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
554400 AATGTGATTT
** ** *
554410 AGTTCGATTGTCAAAATGTAATTTTTGTGAAGTTTGAGGGTTAAAATATGATTTTTGAGA
1 AGTTCGAGGGTCAAAATGTAATTTTTACGAAGTTTGAGGGTTAAAATATAATTTTTGAGA
* *
554470 AGTTCGAGGGTCAAAATGTAATTTTTACGAGGTTT-AGGAGTTAAAATTTAATTTT
1 AGTTCGAGGGTCAAAATGTAATTTTTACGAAGTTTGAGG-GTTAAAATATAATTTT
554525 AAACTAAACG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.32, C:0.04, G:0.23, T:0.41
Consensus pattern (60 bp):
AGTTCGAGGGTCAAAATGTAATTTTTACGAAGTTTGAGGGTTAAAATATAATTTTTGAGA
Found at i:556307 original size:7 final size:7
Alignment explanation
Indices: 556295--556320 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
556285 GTATTTGGAC
556295 ATTTAAA
1 ATTTAAA
556302 ATTTAAA
1 ATTTAAA
556309 ATTTAAA
1 ATTTAAA
556316 ATTTA
1 ATTTA
556321 TTTTGGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTTAAA
Found at i:557051 original size:39 final size:38
Alignment explanation
Indices: 557008--557429 Score: 228
Period size: 39 Copynumber: 10.8 Consensus size: 38
556998 TTTTCCCCTT
*
557008 GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAA
1 GCTCGGGGTAAGAGATT-ACTGATGGTGATCTGCCCTAG
* * * *
557047 GCTCGGGATAAGAGA-T-CGGATGGCTACAATCT-ACCTCAG
1 GCTCGGGGTAAGAGATTACTGATGG-T--GATCTGCCCT-AG
* **
557086 GCTCAGGGTAAGAGA-TAGGCTGATGGTGAT-TTACCTCAG
1 GCTCGGGGTAAGAGATTA--CTGATGGTGATCTGCCCT-AG
* * *
557125 GCTCGAGGTAAGAGATTGACTGATGGTGATTTG-ACTCAG
1 GCTCGGGGTAAGAGATT-ACTGATGGTGATCTGCCCT-AG
*
557164 GCTCGGGGTAAGAGATTA--GATGGCTATAATCTGCCCTAG
1 GCTCGGGGTAAGAGATTACTGATGG---TGATCTGCCCTAG
* * *
557203 GCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCCT-T
1 GCTCGGGGTAAGAGATT-ACTGATGGTGATCTG-CCCTAG
* * *
557242 GCTCGGGGTAAGAGA-T-CGGATGGCTGCAATCTACCCCAG
1 GCTCGGGGTAAGAGATTACTGATGG-TG--ATCTGCCCTAG
* * * *
557281 GCTTGGGGTAAGAGATTAGTTAATGGTGATCTGTCCC-AA
1 GCTCGGGGTAAGAGATTA-CTGATGGTGATCTG-CCCTAG
* * *
557320 GCTCGGGGTAAGAGA-T-CGGATGGCTACAATTTGCCCTAG
1 GCTCGGGGTAAGAGATTACTGATGG-T--GATCTGCCCTAG
* *
557359 GCTCGGGGTAAGAGA-T-CGGATGGCTGCAATCTGCCTTAG
1 GCTCGGGGTAAGAGATTACTGATGG-TG--ATCTGCCCTAG
* *
557398 GCTCGGAGTAAGAGATTAGTTGATGGTGATCT
1 GCTCGGGGTAAGAGATTA-CTGATGGTGATCT
557430 ACCGCATGAT
Statistics
Matches: 302, Mismatches: 45, Indels: 72
0.72 0.11 0.17
Matches are distributed among these distances:
36 21 0.07
37 4 0.01
38 14 0.05
39 224 0.74
40 13 0.04
41 6 0.02
42 20 0.07
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.26
Consensus pattern (38 bp):
GCTCGGGGTAAGAGATTACTGATGGTGATCTGCCCTAG
Found at i:557186 original size:117 final size:117
Alignment explanation
Indices: 557008--557257 Score: 333
Period size: 117 Copynumber: 2.1 Consensus size: 117
556998 TTTTCCCCTT
*
557008 GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGCTCGGGATAAGAGATCGGATGGCTA
1 GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGCTCGGGATAAGAGATCAGATGGCTA
*
557073 CAATCTA-CCTCAGGCTCAGGGTAAGAGATAGGCTGATGGTGATTTACCTCAG
66 CAATCTACCCT-AGGCTCAGGGTAAGAGATAGGCTGATGGTGATTTACCCCAG
* * * * * *
557125 GCTCGAGGTAAGAGATTGACTGATGGTGATTTG-ACTCAGGCTCGGGGTAAGAGATTAGATGGCT
1 GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCT-AAGCTCGGGATAAGAGATCAGATGGCT
* * * * * **
557189 ATAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCCTT
65 ACAATCTACCCTAGGCTCAGGGTAAGAGATAGGCTGATGGTGATTTACCCCAG
557242 GCTCGGGGTAAGAGAT
1 GCTCGGGGTAAGAGAT
557258 CGGATGGCTG
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
116 2 0.02
117 110 0.96
118 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (117 bp):
GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGCTCGGGATAAGAGATCAGATGGCTA
CAATCTACCCTAGGCTCAGGGTAAGAGATAGGCTGATGGTGATTTACCCCAG
Found at i:557205 original size:78 final size:78
Alignment explanation
Indices: 557123--557374 Score: 317
Period size: 78 Copynumber: 3.2 Consensus size: 78
557113 GATTTACCTC
* * * **
557123 AGGCTCGAGGTAAGAGATTGACTGATGGTGATTTGACTCAGGCTCGGGGTAAGAGATTAGATGGC
1 AGGCTCGGGGTAAGAGATTGACTGATGGTGATTTGACCCAAGCTCGGGGTAAGAGATCGGATGGC
*
557188 TATAATCTGCCCT
66 TACAATCTGCCCT
* * **
557201 AGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCCTTGCTCGGGGTAAGAGATCGGATGGC
1 AGGCTCGGGGTAAGAGATTGACTGATGGTGATTTGACCCAAGCTCGGGGTAAGAGATCGGATGGC
* * *
557266 TGCAATCTACCCC
66 TACAATCTGCCCT
* * * * *
557279 AGGCTTGGGGTAAGAGATT-AGTTAATGGTGATCTGTCCCAAGCTCGGGGTAAGAGATCGGATGG
1 AGGCTCGGGGTAAGAGATTGA-CTGATGGTGATTTGACCCAAGCTCGGGGTAAGAGATCGGATGG
*
557343 CTACAATTTGCCCT
65 CTACAATCTGCCCT
557357 AGGCTCGGGGTAAGAGAT
1 AGGCTCGGGGTAAGAGAT
557375 CGGATGGCTG
Statistics
Matches: 148, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
78 148 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.25
Consensus pattern (78 bp):
AGGCTCGGGGTAAGAGATTGACTGATGGTGATTTGACCCAAGCTCGGGGTAAGAGATCGGATGGC
TACAATCTGCCCT
Found at i:557282 original size:117 final size:116
Alignment explanation
Indices: 556997--557299 Score: 317
Period size: 117 Copynumber: 2.6 Consensus size: 116
556987 GATGGTTGTA
* * * * * * *
556997 ATTTTCCCCTTGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGCTCGGGATAAGAGA
1 ATTTGCCCCTGGCTCGGGGTAAGAGATT-ACGGATGGTGATCTACCCCAGGCTCGGGGTAAGAGA
** * * * *
557062 TCGGATGGCTACAATCT-ACCTCAGGCTCAGGGTAAGAGATAGGCTGATGGTG
65 TTAGATGGCTATAATCTGCCCT-AGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * * *
557114 ATTTACCTCAGGCTCGAGGTAAGAGATTGACTGATGGTGATTTGA-CTCAGGCTCGGGGTAAGAG
1 ATTTGCCCCTGGCTCGGGGTAAGAGATT-ACGGATGGTGATCT-ACCCCAGGCTCGGGGTAAGAG
557178 ATTAGATGGCTATAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
64 ATTAGATGGCTATAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* *
557231 ATTTGCCCCTTGCTCGGGGTAAGAGA-T-CGGATGGCTGCAATCTACCCCAGGCTTGGGGTAAGA
1 ATTTGCCCCTGGCTCGGGGTAAGAGATTACGGATGG-TG--ATCTACCCCAGGCTCGGGGTAAGA
557294 GATTAG
63 GATTAG
557300 TTAATGGTGA
Statistics
Matches: 154, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
114 6 0.04
115 2 0.01
116 2 0.01
117 141 0.92
118 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.26
Consensus pattern (116 bp):
ATTTGCCCCTGGCTCGGGGTAAGAGATTACGGATGGTGATCTACCCCAGGCTCGGGGTAAGAGAT
TAGATGGCTATAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
Found at i:557391 original size:78 final size:75
Alignment explanation
Indices: 557123--557413 Score: 260
Period size: 78 Copynumber: 3.7 Consensus size: 75
557113 GATTTACCTC
* * * * * **
557123 AGGCTCGAGGTAAGAGATTGACTGATGGTGATTTGACTCAGGCTCGGGGTAAGAGATTAGATGGC
1 AGGCTCGGGGTAAGAGATT--CGGATGGTGATCTG-CCCAAGCTCGGGGTAAGAGATCGGATGGC
*
557188 TATAATCTGCCCT
63 TACAATCTGCCCT
* * **
557201 AGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCCTTGCTCGGGGTAAGAGATCGGATGGC
1 AGGCTCGGGGTAAGAGATT--CGGATGGTGATCTG-CCCAAGCTCGGGGTAAGAGATCGGATGGC
* * *
557266 TGCAATCTACCCC
63 TACAATCTGCCCT
* * *
557279 AGGCTTGGGGTAAGAGATTAGTTAATGGTGATCTGTCCCAAGCTCGGGGTAAGAGATCGGATGGC
1 AGGCTCGGGGTAAGAGATTCG--GATGGTGATCTG-CCCAAGCTCGGGGTAAGAGATCGGATGGC
*
557344 TACAATTTGCCCT
63 TACAATCTGCCCT
* * *
557357 AGGCTCGGGGTAAGAGA-TCGGATGGCTGCAATCTGCCTTAGGCTCGGAGTAAGAGAT
1 AGGCTCGGGGTAAGAGATTCGGATGG-TG--ATCTGCC-CAAGCTCGGGGTAAGAGAT
557414 TAGTTGATGG
Statistics
Matches: 177, Mismatches: 30, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
75 4 0.02
76 2 0.01
77 4 0.02
78 167 0.94
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (75 bp):
AGGCTCGGGGTAAGAGATTCGGATGGTGATCTGCCCAAGCTCGGGGTAAGAGATCGGATGGCTAC
AATCTGCCCT
Found at i:557449 original size:117 final size:117
Alignment explanation
Indices: 557242--557491 Score: 313
Period size: 117 Copynumber: 2.1 Consensus size: 117
557232 TTTGCCCCTT
* *
557242 GCTCGGGGTAAGAGATCGGATGGCTGCAATCTACCCCAGGCTTGGGGTAAGAGATTAGTTAATGG
1 GCTCGGGGTAAGAGATCGGATGGCTGCAATCTACCCCAGGCTCGGAGTAAGAGATTAGTTAATGG
* * * * * * * * * *
557307 TGATCTGTCCCAAGCTCGGGGTAAGAGATCGGATGGCTACAATTTGCCCTAG
66 TGATCTGACCCAAGATCGAGATAAGAGATCGAATGACTACAATCTACCCCAA
* ** *
557359 GCTCGGGGTAAGAGATCGGATGGCTGCAATCTGCCTTAGGCTCGGAGTAAGAGATTAGTTGATGG
1 GCTCGGGGTAAGAGATCGGATGGCTGCAATCTACCCCAGGCTCGGAGTAAGAGATTAGTTAATGG
* *
557424 TGATCT-ACCGCATGATCGAGATAAGAGATCGAATGACTGCAATCTACCCCAA
66 TGATCTGACC-CAAGATCGAGATAAGAGATCGAATGACTACAATCTACCCCAA
*
557476 GCTCTGGGTAAGAGAT
1 GCTCGGGGTAAGAGAT
557492 TGATTGATGG
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
116 2 0.02
117 111 0.98
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (117 bp):
GCTCGGGGTAAGAGATCGGATGGCTGCAATCTACCCCAGGCTCGGAGTAAGAGATTAGTTAATGG
TGATCTGACCCAAGATCGAGATAAGAGATCGAATGACTACAATCTACCCCAA
Found at i:559841 original size:3 final size:3
Alignment explanation
Indices: 559833--559862 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
559823 AGTCACCCCT
559833 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
559863 AATATCATAA
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:564199 original size:21 final size:21
Alignment explanation
Indices: 564157--564199 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
564147 TTTCGTGTCA
*
564157 TACCTATATCAATAGTGATCT
1 TACCTATATCAATAGCGATCT
564178 TACCTATATCAAT-GCGAGTCT
1 TACCTATATCAATAGCGA-TCT
564199 T
1 T
564200 GATGTTCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (21 bp):
TACCTATATCAATAGCGATCT
Found at i:569900 original size:29 final size:29
Alignment explanation
Indices: 569865--569940 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
569855 TTGAAATTTT
569865 GGGCAAAATAATAATTTTTGGATGTGCAA
1 GGGCAAAATAATAATTTTTGGATGTGCAA
** * **
569894 GGGCAAAATGGTAATTTTTGGATGTTCGG
1 GGGCAAAATAATAATTTTTGGATGTGCAA
569923 GGGCAAAATAATAATTTT
1 GGGCAAAATAATAATTTT
569941 GGAGAAGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.33
Consensus pattern (29 bp):
GGGCAAAATAATAATTTTTGGATGTGCAA
Found at i:570027 original size:29 final size:30
Alignment explanation
Indices: 569994--570072 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
569984 TAAAATTGTA
* *
569994 ATTTTGGAAAATTTTAGGGGT-GAAATGTG
1 ATTTTGGAAAATTTTAGGGGTAAAAATATG
* *
570023 ATTTTGGAAAAGTTTAAGGGTAAAAATATG
1 ATTTTGGAAAATTTTAGGGGTAAAAATATG
* *
570053 ATTTTAGAAAAGTTTGAGGG
1 ATTTTGGAAAA-TTTTAGGG
570073 TCAAAATGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 19 0.47
30 16 0.40
31 5 0.12
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (30 bp):
ATTTTGGAAAATTTTAGGGGTAAAAATATG
Found at i:570087 original size:30 final size:30
Alignment explanation
Indices: 569934--570117 Score: 123
Period size: 30 Copynumber: 6.2 Consensus size: 30
569924 GGCAAAATAA
* *
569934 TAATTTTGGAGAAGTTT--GGGTCAAAATG
1 TAATTTTAGAAAAGTTTGAGGGTCAAAATG
** *
569962 GGATTTTAGAGAAGTTTG-GGGAT-AAAATTG
1 TAATTTTAGAAAAGTTTGAGGG-TCAAAA-TG
* * *
569992 TAATTTTGGAAAA-TTTTAGGGGT-GAAATG
1 TAATTTTAGAAAAGTTTGA-GGGTCAAAATG
* * * * *
570021 TGATTTTGGAAAAGTTTAAGGGTAAAAATA
1 TAATTTTAGAAAAGTTTGAGGGTCAAAATG
*
570051 TGATTTTAGAAAAGTTTGAGGGTCAAAATG
1 TAATTTTAGAAAAGTTTGAGGGTCAAAATG
* *
570081 TAATTTTTACG--AGGTTTGAGGGTCAAAATT
1 TAA-TTTTA-GAAAAGTTTGAGGGTCAAAATG
570111 TAATTTT
1 TAATTTT
570118 TAAACCAAAC
Statistics
Matches: 127, Mismatches: 20, Indels: 17
0.77 0.12 0.10
Matches are distributed among these distances:
28 14 0.11
29 32 0.25
30 72 0.57
31 8 0.06
32 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (30 bp):
TAATTTTAGAAAAGTTTGAGGGTCAAAATG
Found at i:573545 original size:21 final size:21
Alignment explanation
Indices: 573521--573560 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
573511 TTACTATTTA
573521 AATTTAGATATTTT-TTTGGAT
1 AATTTAGAT-TTTTATTTGGAT
*
573542 AATTTTGATTTTTATTTGG
1 AATTTAGATTTTTATTTGG
573561 GGTAAAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (21 bp):
AATTTAGATTTTTATTTGGAT
Found at i:573723 original size:26 final size:26
Alignment explanation
Indices: 573667--573717 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
573657 GAAAATATTC
* * *
573667 AAAAAAAATTGTTGGGGTGGGAATGA
1 AAAAAAAATTGGTGGGATGGGAAAGA
573693 AAAAAAAATTGGTGGGAT-GGAAAGA
1 AAAAAAAATTGGTGGGATGGGAAAGA
573718 GTAAAAGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (26 bp):
AAAAAAAATTGGTGGGATGGGAAAGA
Found at i:577206 original size:30 final size:29
Alignment explanation
Indices: 577172--577232 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
577162 CTTAACAAAT
*
577172 AAATGACTCTAAAATAGTAACAAAATTAAC
1 AAATGACTCTAAAATAATAA-AAAATTAAC
*
577202 AAATGCCTCTAAAATAATAAAAAATTAAC
1 AAATGACTCTAAAATAATAAAAAATTAAC
577231 AA
1 AA
577233 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (29 bp):
AAATGACTCTAAAATAATAAAAAATTAAC
Found at i:585182 original size:11 final size:12
Alignment explanation
Indices: 585154--585180 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
585144 CAACTGCATC
585154 AAAATACTGAAA
1 AAAATACTGAAA
585166 AAAATACTGAAA
1 AAAATACTGAAA
585178 AAA
1 AAA
585181 TATTGCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAATACTGAAA
Found at i:585344 original size:27 final size:27
Alignment explanation
Indices: 585306--585367 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
585296 TCTTAAACGT
585306 ACATGACACAAAAAAAAATATTTATGC
1 ACATGACACAAAAAAAAATATTTATGC
585333 ACATGACACAAAAAAAAATATTTATGC
1 ACATGACACAAAAAAAAATATTTATGC
585360 ACATGACA
1 ACATGACA
585368 AAATGTACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.21
Consensus pattern (27 bp):
ACATGACACAAAAAAAAATATTTATGC
Found at i:585614 original size:24 final size:26
Alignment explanation
Indices: 585587--585641 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
585577 TAACCGGACT
* *
585587 ATAAAATAAATAA-AATCCAAA-ATA
1 ATAAAATAAATAAGAACCCAAATAAA
585611 ATAAAATAAATAAGAACCCAAATAAA
1 ATAAAATAAATAAGAACCCAAATAAA
585637 ATAAA
1 ATAAA
585642 TTTAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 13 0.48
25 7 0.26
26 7 0.26
ACGTcount: A:0.71, C:0.09, G:0.02, T:0.18
Consensus pattern (26 bp):
ATAAAATAAATAAGAACCCAAATAAA
Found at i:588996 original size:16 final size:15
Alignment explanation
Indices: 588971--589005 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
588961 AATGAAGATA
588971 GAATGCGATTATTATG
1 GAATGCGATTATTA-G
*
588987 GAATGTGATTATTAG
1 GAATGCGATTATTAG
589002 GAAT
1 GAAT
589006 TTGTTTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (15 bp):
GAATGCGATTATTAG
Found at i:590152 original size:90 final size:89
Alignment explanation
Indices: 589992--590157 Score: 262
Period size: 90 Copynumber: 1.9 Consensus size: 89
589982 ATTAAACTCT
* *
589992 GATTAGTCTAGATTATTTTATTATTATTTGACCTAAGAATTTAGCCTATAAATAGGCTCTTTTAC
1 GATTAGTCTAGATTATTTTATTATTATTTGACCTAAGAATTTAACATATAAATAGGCTCTTTTAC
*
590057 GACCTTACAAAATACATTTATTAGA
66 AACCTTA-AAAATACATTTATTAGA
*
590082 GATTAGTCTAGATTATTTTATTATTATTTGACTTAAGAATTTAACATATAAATAGAG-TCTTTTA
1 GATTAGTCTAGATTATTTTATTATTATTTGACCTAAGAATTTAACATATAAATAG-GCTCTTTTA
*
590146 TAACCTTAAAAA
65 CAACCTTAAAAA
590158 CACACCCATT
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
89 4 0.06
90 65 0.93
91 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (89 bp):
GATTAGTCTAGATTATTTTATTATTATTTGACCTAAGAATTTAACATATAAATAGGCTCTTTTAC
AACCTTAAAAATACATTTATTAGA
Found at i:600424 original size:3 final size:3
Alignment explanation
Indices: 600416--600457 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
600406 TGTTATCAAC
600416 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
600458 TCCTATCGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:604475 original size:19 final size:20
Alignment explanation
Indices: 604451--604502 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
604441 ATAATTTCTT
*
604451 TTAAAAAAATAAAA-AAGGG
1 TTAAAAAAATAAAAGAAGCG
604470 TTAAAAAATAGTAAAAGAAGCG
1 TTAAAAAA-A-TAAAAGAAGCG
604492 TTAAAACAAAT
1 TTAAAA-AAAT
604503 CTAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.29
20 1 0.04
21 6 0.21
22 11 0.39
23 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.13, T:0.19
Consensus pattern (20 bp):
TTAAAAAAATAAAAGAAGCG
Found at i:605370 original size:29 final size:30
Alignment explanation
Indices: 605306--605564 Score: 207
Period size: 29 Copynumber: 8.9 Consensus size: 30
605296 TGAATTTCGT
* *
605306 AAAAATTACATTTTTAACCCTCGAACTTTTC
1 AAAAATCACATTTTT-ACCCTCGAACTTCTC
* * * * *
605337 -CAAATTATATTTTAACCC-CAAACTTCTC
1 AAAAATCACATTTTTACCCTCGAACTTCTC
* **
605365 AAAAATTACATTTTTTGTCC-CGAACTTCT-
1 AAAAATCACA-TTTTTACCCTCGAACTTCTC
*
605394 AAAAATCACATTTTTACCCTCAAACTTCTC
1 AAAAATCACATTTTTACCCTCGAACTTCTC
*
605424 AAAAATCATATTTTTACCCTCGAACTTC-C
1 AAAAATCACATTTTTACCCTCGAACTTCTC
605453 AAAAATCACATTTTTA-CCTCGAACTTCTC
1 AAAAATCACATTTTTACCCTCGAACTTCTC
** *
605482 AAAAATCATTTTTTTA-CCTCGAA-TTTTCC
1 AAAAATCACATTTTTACCCTCGAACTTCT-C
* * * *
605511 CAAAATTACATTCTTA-CCTCTAAACTT-TC
1 AAAAATCACATTTTTACCCTC-GAACTTCTC
* * *
605540 CAAAATTACATTTTGA-CCTCGAACT
1 AAAAATCACATTTTTACCCTCGAACT
605565 CTCTGAAACT
Statistics
Matches: 190, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
28 33 0.17
29 101 0.53
30 54 0.28
31 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAAATCACATTTTTACCCTCGAACTTCTC
Found at i:605371 original size:59 final size:60
Alignment explanation
Indices: 605306--605553 Score: 232
Period size: 58 Copynumber: 4.2 Consensus size: 60
605296 TGAATTTCGT
* * * *
605306 AAAAATTACATTTTTAACCCTCGAACTTTTCC-AAATTATATTTTAACCCCAAACTTCTC
1 AAAAATTACATTTTTTACCCTCGAACTTTTCCAAAATCACATTTTTACCCCAAACTTCTC
** * *
605365 AAAAATTACATTTTTTGTCC-CGAACTTCT-AAAAATCACATTTTTACCCTCAAACTTCTC
1 AAAAATTACATTTTTTACCCTCGAACTTTTCCAAAATCACATTTTTACCC-CAAACTTCTC
* *
605424 AAAAA-T-CATATTTTTACCCTCGAAC--TTCCAAAAATCACATTTTTACCTCGAACTTCTC
1 AAAAATTACAT-TTTTTACCCTCGAACTTTTCC-AAAATCACATTTTTACCCCAAACTTCTC
* * *
605482 AAAAA-T-CATTTTTTTA-CCTCGAA-TTTTCCCAAAATTACATTCTTACCTCTAAACTT-TC
1 AAAAATTACA-TTTTTTACCCTCGAACTTTT-CCAAAATCACATTTTTACC-CCAAACTTCTC
*
605540 CAAAATTACATTTT
1 AAAAATTACATTTT
605554 GACCTCGAAC
Statistics
Matches: 156, Mismatches: 20, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
57 11 0.07
58 76 0.49
59 67 0.43
60 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (60 bp):
AAAAATTACATTTTTTACCCTCGAACTTTTCCAAAATCACATTTTTACCCCAAACTTCTC
Found at i:605720 original size:16 final size:14
Alignment explanation
Indices: 605671--605722 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
605661 TTATTCATGA
605671 TTCGTAT-TTTACTT
1 TTCGTATATTTA-TT
*
605685 TTCTTATATTTATT
1 TTCGTATATTTATT
605699 TTCGTATATTTATT
1 TTCGTATATTTATT
605713 CATTCGTATA
1 --TTCGTATA
605723 ATTGTTCGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 21 0.64
15 4 0.12
16 8 0.24
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (14 bp):
TTCGTATATTTATT
Found at i:617295 original size:78 final size:78
Alignment explanation
Indices: 616996--617464 Score: 346
Period size: 78 Copynumber: 6.1 Consensus size: 78
616986 CAAATTGAAG
* * * * * * *
616996 CCATTCAATTTTTTACCTCGAGCCTGGGGCAGATCACGAT-AAGCCAATCTCTTACCCCAAGCCT
1 CCATTCGATCTTTTACCCCGAGCCTAGGGCAGATCACTATCAA-CTAATCTCTTACCCCGAGCCT
* * * *
617060 CGAGTAGATTACAA
65 GGGGCAGATTGCAA
* * * * * ** * * * * *
617074 TCAATCGATCTTTTACCTCGAGCCT-GAGACATATTGC-AGCCATTCGATCTTTTACCCCGAGCC
1 CCATTCGATCTTTTACCCCGAGCCTAG-GGCAGATCACTATCAACT-AATCTCTTACCCCGAGCC
* *
617137 TAGGGCAGATTGCAC
64 TGGGGCAGATTGCAA
* * * * * *
617152 CCATTAGATCTTTTA-CCCAAGCCGAGGGCAGATCACCAT-AAATAATCTCTTACCTCGAGCCTG
1 CCATTCGATCTTTTACCCCGAGCCTAGGGCAGATCACTATCAACTAATCTCTTACCCCGAGCCTG
*
617215 GGGCAAATTGCAA
66 GGGCAGATTGCAA
** *
617228 CCATTCGATCTTTTACTTCGACCCTAGGGCAGATCACTATCAACTAATCTCTTACCCCGAGCCTG
1 CCATTCGATCTTTTACCCCGAGCCTAGGGCAGATCACTATCAACTAATCTCTTACCCCGAGCCTG
617293 GGGCAGATTGCAA
66 GGGCAGATTGCAA
* * * * * *
617306 CCATCCGATCTCTTACCCCGAGCTTGGGGCAGATC-CTTATCAGCTAATCTCTTACCCCGAGTCT
1 CCATTCGATCTTTTACCCCGAGCCTAGGGCAGATCAC-TATCAACTAATCTCTTACCCCGAGCCT
* * * *
617370 AGGGCAAATTAC-G
65 GGGGCAGATTGCAA
* * * * * *
617383 CCATTCTATCTTTTACCCCGA-TCTTGGGACAGATCA-TCATCAACCAATCTTTTACCCCGA-TC
1 CCATTCGATCTTTTACCCCGAGCCTAGGG-CAGATCACT-ATCAACTAATCTCTTACCCCGAGCC
617445 TAGGGGCAGATTGCAA
64 T-GGGGCAGATTGCAA
617461 CCAT
1 CCAT
617465 CCAATATCTT
Statistics
Matches: 303, Mismatches: 75, Indels: 26
0.75 0.19 0.06
Matches are distributed among these distances:
76 49 0.16
77 87 0.29
78 167 0.55
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (78 bp):
CCATTCGATCTTTTACCCCGAGCCTAGGGCAGATCACTATCAACTAATCTCTTACCCCGAGCCTG
GGGCAGATTGCAA
Found at i:617334 original size:39 final size:39
Alignment explanation
Indices: 617042--617339 Score: 167
Period size: 39 Copynumber: 7.7 Consensus size: 39
617032 CGATAAGCCA
* * * * * *
617042 ATCTCTTACCCCAAGCCTCGAGTAGATTACAATCAAT-CG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAA-CCATCCG
* * * * * * *
617081 ATCTTTTACCTCGAGCCTGAGACATATTGCAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATCCG
* * * **
617120 ATCTTTTACCCCGAGCCTAGGGCAGATTGCACCCATTAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATCCG
* * ***
617159 ATCTTTTA-CCCAAGCC-GAGGGCAGA-T-C-ACCATAAATA
1 ATCTCTTACCCCGAGCCTG-GGGCAGATTGCAACCAT--CCG
* * *
617196 ATCTCTTACCTCGAGCCTGGGGCAAATTGCAACCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATCCG
* ** * * ** * * * **
617235 ATCTTTTACTTCGACCCTAGGGCAGATCACTATCAACTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATCCG
617274 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATCCG
*
617313 ATCTCTTACCCCGAGCTTGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
617340 CCTTATCAGC
Statistics
Matches: 192, Mismatches: 58, Indels: 18
0.72 0.22 0.07
Matches are distributed among these distances:
35 4 0.02
36 1 0.01
37 8 0.04
38 29 0.15
39 144 0.75
40 1 0.01
41 5 0.03
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATCCG
Found at i:617356 original size:39 final size:38
Alignment explanation
Indices: 617254--617375 Score: 127
Period size: 39 Copynumber: 3.1 Consensus size: 38
617244 TTCGACCCTA
617254 GGGCAGATCACTATCAACTAATCTCTTACCCCGAGCCTG
1 GGGCAGATC-CTATCAACTAATCTCTTACCCCGAGCCTG
* * * * ** *
617293 GGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTG
1 GGGCAGA-TCCTATCAACTAATCTCTTACCCCGAGCCTG
* * *
617332 GGGCAGATCCTTATCAGCTAATCTCTTACCCCGAGTCTA
1 GGGCAGATCC-TATCAACTAATCTCTTACCCCGAGCCTG
617371 GGGCA
1 GGGCA
617376 AATTACGCCA
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
38 2 0.03
39 62 0.95
40 1 0.02
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (38 bp):
GGGCAGATCCTATCAACTAATCTCTTACCCCGAGCCTG
Found at i:617425 original size:155 final size:155
Alignment explanation
Indices: 617120--617476 Score: 386
Period size: 155 Copynumber: 2.3 Consensus size: 155
617110 CAGCCATTCG
* * ** *
617120 ATCTTTTACCCCGAGCCTAGGGCAGATTGCACCCATTAGATCTTTTA-CCCAAGCCGAGGGCAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATTGCAACCATCCGATCTCTTACCCCAAGCCGAGGGCAGA
* * * **
617184 TCACCATAAATAATCTCTTACCTCGAGCCTGGGGCAAATTGCAACCATTCGATCTTTTACTTCGA
66 TCACCATAAATAATCTCTTACCCCGAGCCTAGGGCAAATTACAACCATTCGATCTTTTACCCCGA
*
617249 CCCTAGGGCAGATCACTATCAACTA
131 CCCTAGGGCAGATCACTATCAACCA
* * *
617274 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTG-GGGCAG
1 ATCTTTTACCCCGAGCCTGGGGCAGATTGCAACCATCCGATCTCTTACCCCAAGC-CGAGGGCAG
* ** * * *
617338 ATC-CTTATCAGCTAATCTCTTACCCCGAGTCTAGGGCAAATTAC-GCCATTCTATCTTTTACCC
65 ATCAC-CAT-AAATAATCTCTTACCCCGAGCCTAGGGCAAATTACAACCATTCGATCTTTTACCC
* *
617401 CGA-TCTTGGGACAGATCA-TCATCAACCA
128 CGACCCTAGGG-CAGATCACT-ATCAACCA
* * *
617429 ATCTTTTACCCCGA-TCTAGGGGCAGATTGCAACCATCCAATATCTTAC
1 ATCTTTTACCCCGAGCCT-GGGGCAGATTGCAACCATCCGATCTCTTAC
617477 TTAAAAAAAA
Statistics
Matches: 170, Mismatches: 26, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
154 50 0.29
155 90 0.53
156 30 0.18
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (155 bp):
ATCTTTTACCCCGAGCCTGGGGCAGATTGCAACCATCCGATCTCTTACCCCAAGCCGAGGGCAGA
TCACCATAAATAATCTCTTACCCCGAGCCTAGGGCAAATTACAACCATTCGATCTTTTACCCCGA
CCCTAGGGCAGATCACTATCAACCA
Done.