Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000880.1 Hibiscus syriacus cultivar Beakdansim tig00001713_pilon, 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: 1459553
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:460901 original size:41 final size:41
Alignment explanation
Indices: 460850--460959 Score: 145
Period size: 41 Copynumber: 2.7 Consensus size: 41
460840 TAATATCTTA
* *
460850 AAATAGTTAAAATAATATATTTATAAT-TTTTATTATATTTT
1 AAATAATTAAAATAATATATTTATAATAATTT-TTATATTTT
460891 AAATAATTAAAATAATATATTTATAATAATTTTTATATTTT
1 AAATAATTAAAATAATATATTTATAATAATTTTTATATTTT
* * *
460932 TACTAATT-AAAGAATATATTT-TAATAAT
1 AAATAATTAAAATAATATATTTATAATAAT
460960 ATAAAAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
39 7 0.11
40 12 0.19
41 41 0.65
42 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (41 bp):
AAATAATTAAAATAATATATTTATAATAATTTTTATATTTT
Found at i:460918 original size:23 final size:23
Alignment explanation
Indices: 460842--460921 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 23
460832 AAATATATTA
* *
460842 ATATCTTAAAATAGTTAAAATAAT
1 ATAT-TTATAATAATTAAAATAAT
** *
460866 ATATTTATAAT--TT-TTATTAT
1 ATATTTATAATAATTAAAATAAT
460886 AT-TTTA-AATAATTAAAATAAT
1 ATATTTATAATAATTAAAATAAT
460907 ATATTTATAATAATT
1 ATATTTATAATAATT
460922 TTTATATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
18 3 0.07
19 4 0.09
20 8 0.18
21 8 0.18
22 4 0.09
23 13 0.30
24 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
ATATTTATAATAATTAAAATAAT
Found at i:460953 original size:21 final size:22
Alignment explanation
Indices: 460924--460968 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
460914 TAATAATTTT
*
460924 TATATTTTTACTAAT-TAAAGAA
1 TATATTTTTAATAATATAAA-AA
460946 TATA-TTTTAATAATATAAAAA
1 TATATTTTTAATAATATAAAAA
460967 TA
1 TA
460969 AAATTTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATTTTTAATAATATAAAAA
Found at i:460964 original size:22 final size:21
Alignment explanation
Indices: 460883--460994 Score: 63
Period size: 23 Copynumber: 5.3 Consensus size: 21
460873 TAATTTTTAT
*
460883 TATATTTTAAATAATTAAAATAA
1 TATATTTTTAATAATT-AAA-AA
* **
460906 TATATTTATAATAATT---TT
1 TATATTTTTAATAATTAAAAA
*
460924 TATATTTTTACTAATTAAAGAA
1 TATATTTTTAATAATTAAA-AA
460946 TATA-TTTTAATAATATAAAAA
1 TATATTTTTAATAAT-TAAAAA
* **
460967 TAAAATTTTCTAA-AATTTTAAA
1 T-ATATTTT-TAATAATTAAAAA
460989 TATATT
1 TATATT
460995 ATATATACAA
Statistics
Matches: 68, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
18 14 0.21
21 16 0.24
22 15 0.22
23 20 0.29
24 3 0.04
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (21 bp):
TATATTTTTAATAATTAAAAA
Found at i:471043 original size:63 final size:63
Alignment explanation
Indices: 470959--471081 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 63
470949 TAATAATATC
* * *
470959 TTTTAATTTGAAATATTCAAAA-TATATAAACTCAT-TTTACTATTCAAACTTAAATATATATTA
1 TTTTAATTTAAAATATCCAAAACTATAT-AA-TCATCTTTAATATTCAAACTTAAATATATATTA
* *
471022 TTTTAATTTAAAATATCCAAAACTATATAATTATCTTTAATATTCAAAGTTAAATATATA
1 TTTTAATTTAAAATATCCAAAACTATATAATCATCTTTAATATTCAAACTTAAATATATA
471082 ATAAATACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
62 3 0.06
63 45 0.85
64 5 0.09
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (63 bp):
TTTTAATTTAAAATATCCAAAACTATATAATCATCTTTAATATTCAAACTTAAATATATATTA
Found at i:475111 original size:23 final size:23
Alignment explanation
Indices: 475044--475130 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
475034 TCATATAAAT
*
475044 TTGCACCGTAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
475067 TTTTGTC-CCGAAG-GACCGCGTAGAA
1 --TTG-CACCGAAGTG-CCACGTAGAA
*
475092 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
475115 TTACACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
475131 TATAATATGT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
22 1 0.02
23 30 0.59
24 2 0.04
25 17 0.33
26 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:481060 original size:23 final size:23
Alignment explanation
Indices: 481034--481079 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
481024 CGAAGGACCG
*
481034 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* *
481057 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
481080 TATAATATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:485695 original size:21 final size:21
Alignment explanation
Indices: 485630--485695 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
485620 CCAAAATGTC
485630 AAATATATATAAATTTTCATT-
1 AAATATATATAAATTTT-ATTA
*
485651 AAATATATAT-AATTTAATTAA
1 AAATATATATAAATTTTATT-A
* *
485672 AAATATGTATAAATTTTGTTA
1 AAATATATATAAATTTTATTA
485693 AAA
1 AAA
485696 CATTATATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 3 0.08
20 5 0.13
21 23 0.61
22 7 0.18
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (21 bp):
AAATATATATAAATTTTATTA
Found at i:487504 original size:13 final size:13
Alignment explanation
Indices: 487488--487512 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
487478 AAGATTAGTA
487488 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
487501 AAAAAGAAAAAA
1 AAAAAGAAAAAA
487513 TCCCCCGCCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:487765 original size:6 final size:6
Alignment explanation
Indices: 487754--487780 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
487744 TGTCTTCATA
487754 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
487781 CTCTGCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:504137 original size:18 final size:18
Alignment explanation
Indices: 504117--504153 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
504107 GGTTTTTTTT
504117 AAATATTAATATTTTAATA
1 AAATA-TAATATTTTAATA
504136 AAATATAATATTTTAATA
1 AAATATAATATTTTAATA
504154 TTAAAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATATAATATTTTAATA
Found at i:508286 original size:40 final size:39
Alignment explanation
Indices: 508240--508319 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 39
508230 CGCACTAGTC
*
508240 TATATGTGCCAATGATTTGTATATTTTTTTTTTCATTCTT
1 TATATGTGCCAATGATTTGTATA-TATTTTTTTCATTCTT
508280 TATATGTGCCAATGATTTGTATATATTTTTTTCATTCTT
1 TATATGTGCCAATGATTTGTATATATTTTTTTCATTCTT
508319 T
1 T
508320 CTATAAAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 16 0.41
40 23 0.59
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (39 bp):
TATATGTGCCAATGATTTGTATATATTTTTTTCATTCTT
Found at i:512510 original size:35 final size:35
Alignment explanation
Indices: 512464--512531 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
512454 GACATCTTAT
512464 AGACGGTCACTAGTAAAACCACGTGTTTGCACATA
1 AGACGGTCACTAGTAAAACCACGTGTTTGCACATA
512499 AGACGGTCACTAGTAAAACCACGTGTTTGCACA
1 AGACGGTCACTAGTAAAACCACGTGTTTGCACA
512532 CGTGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (35 bp):
AGACGGTCACTAGTAAAACCACGTGTTTGCACATA
Found at i:512820 original size:14 final size:14
Alignment explanation
Indices: 512801--512828 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
512791 AATTCAACCA
512801 TTCCCCTTCTCCTT
1 TTCCCCTTCTCCTT
512815 TTCCCCTTCTCCTT
1 TTCCCCTTCTCCTT
512829 CCACAACAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (14 bp):
TTCCCCTTCTCCTT
Found at i:513030 original size:24 final size:24
Alignment explanation
Indices: 513002--513055 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
512992 CCGATCGTTG
*
513002 TAAATCAC-AACTCCATTGCAAAGT
1 TAAATCACTAAATCCATTGCAAA-T
*
513026 TAAAT-ACTAAATCCTTTGCAAAT
1 TAAATCACTAAATCCATTGCAAAT
513049 TCAAATC
1 T-AAATC
513056 TTTGCACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.30
Consensus pattern (24 bp):
TAAATCACTAAATCCATTGCAAAT
Found at i:514225 original size:17 final size:17
Alignment explanation
Indices: 514203--514236 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
514193 ATTTTAAGAT
514203 TTTTTC-AATCTTCAAAA
1 TTTTTCAAATCTT-AAAA
514220 TTTTTCAAATCTTAAAA
1 TTTTTCAAATCTTAAAA
514237 CCTTTAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTTCAAATCTTAAAA
Found at i:514666 original size:14 final size:14
Alignment explanation
Indices: 514647--514673 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
514637 ATTTTCCTAG
514647 CTAAATTCATTCTC
1 CTAAATTCATTCTC
514661 CTAAATTCATTCT
1 CTAAATTCATTCT
514674 ATTTTCATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (14 bp):
CTAAATTCATTCTC
Found at i:527882 original size:23 final size:23
Alignment explanation
Indices: 527816--527880 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
527806 ACCCCCATAA
527816 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAT
527839 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAT
*
527862 GGGAACCAATTCCCTCCTT
1 GGGAACCGATTCCC-CCTT
527881 GAGGGAATCG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 36 0.90
24 4 0.10
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAT
Found at i:530177 original size:21 final size:21
Alignment explanation
Indices: 530153--530210 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
530143 TATGCTCGGA
*
530153 GGGAACCGATTCCCCCCTAGG
1 GGGAACCGATTCCCCCCCAGG
530174 GGGAACCGATTCCCCCCCAGG
1 GGGAACCGATTCCCCCCCAGG
*
530195 GGGTACCGATTCCCCC
1 GGGAACCGATTCCCCC
530211 TGTTCAACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.41, G:0.28, T:0.14
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCCAGG
Found at i:535402 original size:22 final size:22
Alignment explanation
Indices: 535376--535458 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 22
535366 TTAGTGCAGA
535376 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * * *
535398 GGGAACCAATTTCCCCTTTGAAG
1 GGGAATCGA-TACCCCCTTGAAG
* * *
535421 GGGAATCGAT-TCCCCATGTAG
1 GGGAATCGATACCCCCTTGAAG
535442 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
535459 GAGGGTTCTG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 17 0.36
22 12 0.26
23 18 0.38
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:536973 original size:18 final size:18
Alignment explanation
Indices: 536938--536978 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
536928 ATAACAACAC
**
536938 GAGGAACAAGTTCCACCA
1 GAGGAACAAGCACCACCA
*
536956 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACCACCA
536974 GAGGA
1 GAGGA
536979 TCAAATGCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.29, T:0.05
Consensus pattern (18 bp):
GAGGAACAAGCACCACCA
Found at i:537335 original size:21 final size:22
Alignment explanation
Indices: 537288--537336 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
537278 TGAATGACTT
* *
537288 TGGATTGTTTTAACTTTGATTGT
1 TGGA-TGTTTGAACTTTGATTGA
*
537311 TGGATGTTTGAA-TTTGTTTGA
1 TGGATGTTTGAACTTTGATTGA
537332 TGGAT
1 TGGAT
537337 TATGGATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 12 0.52
22 7 0.30
23 4 0.17
ACGTcount: A:0.18, C:0.02, G:0.27, T:0.53
Consensus pattern (22 bp):
TGGATGTTTGAACTTTGATTGA
Found at i:548663 original size:93 final size:93
Alignment explanation
Indices: 548504--548689 Score: 354
Period size: 93 Copynumber: 2.0 Consensus size: 93
548494 AAGTGAACTA
*
548504 CCTTACTTAAATGAATCAGCATACACATTTATTCATGTGTAATTTATTTATGTTCAATAATGAAC
1 CCTTACTTAAATGAATCAGCATACACATTTATTCATGTGTAATTTATTTATGTGCAATAATGAAC
548569 TGCCATGCATTATTAAACATGCAAATTT
66 TGCCATGCATTATTAAACATGCAAATTT
*
548597 CCTTACTTAAATGAATCAGCATACACATTTCTTCATGTGTAATTTATTTATGTGCAATAATGAAC
1 CCTTACTTAAATGAATCAGCATACACATTTATTCATGTGTAATTTATTTATGTGCAATAATGAAC
548662 TGCCATGCATTATTAAACATGCAAATTT
66 TGCCATGCATTATTAAACATGCAAATTT
548690 ATTAATGCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (93 bp):
CCTTACTTAAATGAATCAGCATACACATTTATTCATGTGTAATTTATTTATGTGCAATAATGAAC
TGCCATGCATTATTAAACATGCAAATTT
Found at i:549435 original size:43 final size:42
Alignment explanation
Indices: 549388--549496 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
549378 TCGCTCTCTA
** * * *
549388 TAGAGGATCCCATGTAGAAACAAGAAGGGGACTATGCCCTCCG
1 TAGAGGATCCCATACAGAAAC-AGAACGAGACTATGCCATCCG
* * *
549431 TAGAGGATCCCATACAGAAACAGGACGAGATTATGCCATCTG
1 TAGAGGATCCCATACAGAAACAGAACGAGACTATGCCATCCG
* *
549473 TAGAGGATCCC-TGCAAAAACAGAA
1 TAGAGGATCCCATACAGAAACAGAA
549497 TATATCAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 10 0.18
42 26 0.47
43 19 0.35
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.17
Consensus pattern (42 bp):
TAGAGGATCCCATACAGAAACAGAACGAGACTATGCCATCCG
Found at i:549479 original size:42 final size:43
Alignment explanation
Indices: 549388--549483 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
549378 TCGCTCTCTA
** * * *
549388 TAGAGGATCCCATGTAGAAACAAGAAGGGGACTATGCCCTCCG
1 TAGAGGATCCCATACAGAAACAAGAACGAGACTATGCCATCCG
* * *
549431 TAGAGGATCCCATACAGAAAC-AGGACGAGATTATGCCATCTG
1 TAGAGGATCCCATACAGAAACAAGAACGAGACTATGCCATCCG
549473 TAGAGGATCCC
1 TAGAGGATCCC
549484 TGCAAAAACA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 26 0.58
43 19 0.42
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (43 bp):
TAGAGGATCCCATACAGAAACAAGAACGAGACTATGCCATCCG
Found at i:550747 original size:13 final size:13
Alignment explanation
Indices: 550729--550753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
550719 TTCCCTTAAG
550729 AAAATTTTACCTT
1 AAAATTTTACCTT
550742 AAAATTTTACCT
1 AAAATTTTACCT
550754 AACAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTTTACCTT
Found at i:552598 original size:56 final size:56
Alignment explanation
Indices: 552456--552824 Score: 586
Period size: 55 Copynumber: 6.7 Consensus size: 56
552446 TAAGTGTGCA
552456 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
552512 -AAACTTAAGAAATTCATACTAAGTCGATGAATTTCCGTATGGGCAATATATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
552567 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
*
552623 AAAACTTAAGAAATTCATACTAAGTGGATTAATTTCCGTATGGGCACTA-ATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
*
552678 AAAACTTAAGAAATTCATACTATGTGGATGAATTTCCGTATGGGCACTA-ATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* ** *
552733 AAAACTTAAGAAATTCATACTGAGTGGATGAATTTATGTATGGGCACTTTATGT-T
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
552788 CAAAAC-TAGGAAATTCATAGTAAGTGTATAAATTTCC
1 -AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCC
552825 ATATTGGTAG
Statistics
Matches: 291, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
55 181 0.62
56 110 0.38
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (56 bp):
AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:552676 original size:111 final size:111
Alignment explanation
Indices: 552456--552824 Score: 575
Period size: 111 Copynumber: 3.3 Consensus size: 111
552446 TAAGTGTGCA
552456 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT-AAACTTAA
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAACTTAA
* *
552520 GAAATTCATACTAAGTCGATGAATTTCCGTATGGGCAATATATGTGT
66 GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTA-ATGTGT
552567 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAACTTAA
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAACTTAA
*
552632 GAAATTCATACTAAGTGGATTAATTTCCGTATGGGCACTAATGTGT
66 GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTAATGTGT
*
552678 AAAACTTAAGAAATTCATACTATGTGGATGAATTTCCGTATGGGCACTA-ATGTGTAAAACTTAA
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAACTTAA
* ** *
552742 GAAATTCATACTGAGTGGATGAATTTATGTATGGGCACTTTATGT-T
66 GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCAC-TAATGTGT
* * * *
552788 CAAAAC-TAGGAAATTCATAGTAAGTGTATAAATTTCC
1 -AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCC
552825 ATATTGGTAG
Statistics
Matches: 241, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
110 76 0.32
111 120 0.50
112 45 0.19
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (111 bp):
AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAACTTAA
GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTAATGTGT
Found at i:557316 original size:30 final size:30
Alignment explanation
Indices: 557282--557349 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
557272 CAAGAGTGTG
*
557282 AGAGTGAAGGAAA-AATTCAAAAATAACATA
1 AGAGTGAA-GAAAGAATTCAAAAAGAACATA
* *
557312 AGAGTGAAGAAAGAGTTCAAAAAGAACATT
1 AGAGTGAAGAAAGAATTCAAAAAGAACATA
*
557342 AGTGTGAA
1 AGAGTGAA
557350 AAGAATGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 4 0.12
30 29 0.88
ACGTcount: A:0.54, C:0.06, G:0.22, T:0.18
Consensus pattern (30 bp):
AGAGTGAAGAAAGAATTCAAAAAGAACATA
Found at i:559346 original size:22 final size:22
Alignment explanation
Indices: 559297--559375 Score: 126
Period size: 22 Copynumber: 3.7 Consensus size: 22
559287 TTCTGGGCAA
*
559297 GGGGAATCGGTACCCATTCAA-
1 GGGGAATCGATACCCATTCAAT
559318 -GGGAATCGATACCCATTCAAT
1 GGGGAATCGATACCCATTCAAT
*
559339 GGGGAATCGGTACCCATTCAAT
1 GGGGAATCGATACCCATTCAAT
559361 GGGGAATCGATACCC
1 GGGGAATCGATACCC
559376 CCCCTCAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 19 0.36
22 34 0.64
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGGAATCGATACCCATTCAAT
Found at i:559456 original size:23 final size:22
Alignment explanation
Indices: 559412--559456 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
559402 AATCTCATAG
*
559412 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
559434 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
559457 AAATTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:560865 original size:103 final size:103
Alignment explanation
Indices: 560686--560898 Score: 354
Period size: 103 Copynumber: 2.1 Consensus size: 103
560676 GGGTCTACGC
*
560686 GGTCCTTCGGAACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGAACATATATGCATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACTTGAT
* *
560751 CATTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CACTAGCATATGTATATGATTCTTAAGGAATGATATGT
* * *
560789 GGTCCTTCGGGACATATATGCATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGAACATATATGCATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACTTGAT
* *
560854 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CACTAGCATATGTATATGATTCTTAAGGAATGATATGT
560892 GGTCCTT
1 GGTCCTT
560899 ATGGACGTTA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGAACATATATGCATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACTTGAT
CACTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:560941 original size:23 final size:23
Alignment explanation
Indices: 560915--560982 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
560905 GTTATTATAT
*
560915 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
* *
560938 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
560961 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
560983 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:567965 original size:21 final size:21
Alignment explanation
Indices: 567931--567983 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
567921 CACAGTCATG
567931 AGATATTAATGGATCACGATCT
1 AGATATT-ATGGATCACGATCT
567953 AGATATTATGGATCACGATCT
1 AGATATTATGGATCACGATCT
567974 AGATATTATG
1 AGATATTATG
567984 ATTTACGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 24 0.77
22 7 0.23
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (21 bp):
AGATATTATGGATCACGATCT
Found at i:570159 original size:14 final size:14
Alignment explanation
Indices: 570126--570176 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
570116 TCCATTCACC
*
570126 GAGTCAACTCGATCT
1 GAGTCAACTC-ATAT
* *
570141 GAGTCAAATCATTT
1 GAGTCAACTCATAT
*
570155 GAGTCAACTCGTAT
1 GAGTCAACTCATAT
570169 GAGTCAAC
1 GAGTCAAC
570177 CCATTGACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
14 22 0.71
15 9 0.29
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (14 bp):
GAGTCAACTCATAT
Found at i:570181 original size:28 final size:29
Alignment explanation
Indices: 570126--570181 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
570116 TCCATTCACC
* *
570126 GAGTCAACTCGATCTGAGTCAAATCATTT
1 GAGTCAACTCGATATGAGTCAAACCATTT
*
570155 GAGTCAACTCG-TATGAGTCAACCCATT
1 GAGTCAACTCGATATGAGTCAAACCATT
570182 GACTTTGACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (29 bp):
GAGTCAACTCGATATGAGTCAAACCATTT
Found at i:570202 original size:14 final size:14
Alignment explanation
Indices: 570175--570213 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
570165 GTATGAGTCA
*
570175 ACCCATTGACTTTG
1 ACCCGTTGACTTTG
* *
570189 ACCTGTTGATTTTG
1 ACCCGTTGACTTTG
570203 ACCCGTTGACT
1 ACCCGTTGACT
570214 GTTAACTTTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (14 bp):
ACCCGTTGACTTTG
Found at i:570216 original size:21 final size:22
Alignment explanation
Indices: 570186--570226 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
570176 CCCATTGACT
* *
570186 TTGACCTGTTGATTTTGACCCG
1 TTGACCTGTTAACTTTGACCCG
570208 TTGA-CTGTTAACTTTGACC
1 TTGACCTGTTAACTTTGACC
570227 AAAAGTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (22 bp):
TTGACCTGTTAACTTTGACCCG
Found at i:573132 original size:11 final size:11
Alignment explanation
Indices: 573116--573142 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
573106 AAACATAAAT
573116 AATTATACTAA
1 AATTATACTAA
573127 AATTATACTAA
1 AATTATACTAA
573138 AATTA
1 AATTA
573143 GTTATACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTATACTAA
Found at i:573848 original size:17 final size:17
Alignment explanation
Indices: 573823--573855 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
573813 TCTGTTGCTT
573823 GATCCCTAGTGCAAAGA
1 GATCCCTAGTGCAAAGA
*
573840 GATCTCTAGTGCAAAG
1 GATCCCTAGTGCAAAG
573856 TCTTTGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (17 bp):
GATCCCTAGTGCAAAGA
Found at i:575985 original size:18 final size:18
Alignment explanation
Indices: 575960--576008 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
575950 GTCGAGATTA
*
575960 AGGTTTAGGGTTT-GGTT
1 AGGTTTAGGGTTTAGGTC
*
575977 TGAGTTTAGGGTTTAGGTC
1 AG-GTTTAGGGTTTAGGTC
575996 AGGTTTAGGGTTT
1 AGGTTTAGGGTTT
576009 TTTAGATCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 22 0.81
19 4 0.15
ACGTcount: A:0.14, C:0.02, G:0.39, T:0.45
Consensus pattern (18 bp):
AGGTTTAGGGTTTAGGTC
Found at i:576483 original size:17 final size:17
Alignment explanation
Indices: 576461--576508 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
576451 GTTTCAGATT
576461 CAGATTCCAATTCCTGA
1 CAGATTCCAATTCCTGA
576478 CAGATTCCAATTCCTGA
1 CAGATTCCAATTCCTGA
576495 CAGATTCCAATTCC
1 CAGATTCCAATTCC
576509 CTCAGAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.29
Consensus pattern (17 bp):
CAGATTCCAATTCCTGA
Found at i:580214 original size:26 final size:27
Alignment explanation
Indices: 580162--580225 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
580152 AGAACAAAAA
580162 TTGATTTGACTTGATAAATTAATCTTT
1 TTGATTTGACTTGATAAATTAATCTTT
** *
580189 TTGATTTGTTTTGAT-AATTGATCTTT
1 TTGATTTGACTTGATAAATTAATCTTT
580215 TTGATTTGACT
1 TTGATTTGACT
580226 CAATTTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.56
Consensus pattern (27 bp):
TTGATTTGACTTGATAAATTAATCTTT
Found at i:585887 original size:28 final size:28
Alignment explanation
Indices: 585841--585909 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
585831 GTCTTTTTTC
*
585841 TTTTTCTTT-TTTTCCAAATAACTTCTAT
1 TTTTTCTTTCTTTTCCAAAT-ACTGCTAT
* *
585869 TTTTTCTTTCTTTT-GAAATACTGCTGT
1 TTTTTCTTTCTTTTCCAAATACTGCTAT
585896 TCTTTT-TTTCTTTT
1 T-TTTTCTTTCTTTT
585910 TTTTTTTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 15 0.42
28 17 0.47
29 4 0.11
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTTTCTTTCTTTTCCAAATACTGCTAT
Found at i:595292 original size:310 final size:306
Alignment explanation
Indices: 594743--595358 Score: 1155
Period size: 310 Copynumber: 2.0 Consensus size: 306
594733 AAGCTTCAAT
594743 CTTTATCAAATTTCAATTTCCAGCAATCTATATTACACAAAGTTTTCCAATTCCTAGAACATTCG
1 CTTTATCAAATTTCAATTTCCAGCAATCTATATTACACAAAGTTTTCCAATTCCTAGAACATTCG
594808 GATCTTTGTGATTTAGTCACATGTAAACCTTAAGCTTTTCGGTTATCACCCTTTACCAAATCAAT
66 GATCTTTGTGATTTAGTCACATGTAAACCTTAAGCTTTTCGGTTATCACCCTTTACCAAATCAAT
594873 ATACAATTTGTTTAAATCCTACAAATTTTTGGTCATGCATGTTCATTACATCATGATCTATGTTA
131 ATACAATTTGTTTAAATCCTACAAATTTTTGGTCATGCATGTTCATTACATCATGATCTATGTTA
594938 ATGTTTAATACCATACACTATAATAATAGATAAATATAGCCTAAACAAAATTTGAGAATCATTCA
196 ATGTTTAATACCATACACTATAATAATAGATAAATATAGCCTAAACAAAATTTGAGAATCATTCA
595003 AATTGATCCTTATCAAATTTAGAATAGAAGAAGAAAAGAAGCTTACA
261 AATTGATCCTTATCAAATTTAGAATAGAAGAAG-AAAGAAGCTTACA
*
595050 CTTTATCAAATTTCAATTTCCAGCAAATCTATATTACACAAAGTTTTCCAATTTAGTCTAGAACA
1 CTTTATCAAATTTCAATTTCCAGC-AATCTATATTACACAAAGTTTTCCAA-TT--CCTAGAACA
595115 TTCGGATCTTTGTGATTTAGTCACATGT-AACCTTAAGCTTTTCGGTTATCACCCTTTACCAAAT
62 TTCGGATCTTTGTGATTTAGTCACATGTAAACCTTAAGCTTTTCGGTTATCACCCTTTACCAAAT
595179 CAATATACAATTTGTTTAAATCCTACAAA-TTTTGGTCATGCATGTTCATTACATCATGATCTAT
127 CAATATACAATTTGTTTAAATCCTACAAATTTTTGGTCATGCATGTTCATTACATCATGATCTAT
595243 GTTAATGTTTAATACCATACACTATTAATAATAGATAAATATAGCCTAAACAAAATTTGAGAATC
192 GTTAATGTTTAATACCATACACTA-TAATAATAGATAAATATAGCCTAAACAAAATTTGAGAATC
595308 ATTCAAATTGATCCTTATCAAATTTAGAATAGAAGAAGAAAGAAGCTTACA
256 ATTCAAATTGATCCTTATCAAATTTAGAATAGAAGAAGAAAGAAGCTTACA
595359 TGGATACTAG
Statistics
Matches: 303, Mismatches: 1, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
307 24 0.08
308 26 0.09
309 74 0.24
310 143 0.47
311 36 0.12
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (306 bp):
CTTTATCAAATTTCAATTTCCAGCAATCTATATTACACAAAGTTTTCCAATTCCTAGAACATTCG
GATCTTTGTGATTTAGTCACATGTAAACCTTAAGCTTTTCGGTTATCACCCTTTACCAAATCAAT
ATACAATTTGTTTAAATCCTACAAATTTTTGGTCATGCATGTTCATTACATCATGATCTATGTTA
ATGTTTAATACCATACACTATAATAATAGATAAATATAGCCTAAACAAAATTTGAGAATCATTCA
AATTGATCCTTATCAAATTTAGAATAGAAGAAGAAAGAAGCTTACA
Found at i:596955 original size:20 final size:20
Alignment explanation
Indices: 596930--596968 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
596920 ATAGGTTAGG
*
596930 GTATCGATACTAGATGAATA
1 GTATCGATAATAGATGAATA
*
596950 GTATCGATAATGGATGAAT
1 GTATCGATAATAGATGAAT
596969 TTGATGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (20 bp):
GTATCGATAATAGATGAATA
Found at i:604955 original size:2 final size:2
Alignment explanation
Indices: 604950--604983 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
604940 ATATAAACCA
604950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
604984 GCTAACATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:611770 original size:60 final size:61
Alignment explanation
Indices: 611687--611849 Score: 146
Period size: 60 Copynumber: 2.7 Consensus size: 61
611677 AGTTTACCCT
* * *
611687 ATTCTAAATTAAT-CTCTAAAC-TTTGAA-TTGTTCTAATTTCATTCAT-AAACTATGA-CTATC
1 ATTCTAAATTAGTCCTCTAAACTTTTGAACAT-TTC-AATTTCATGC-TCAAACTATGATCT-TC
*
611747 ATTCTAAATTAGTCCTC-AGACTTTTGAACATTTCAATTTCATGCTCAAACTATGATCTTC
1 ATTCTAAATTAGTCCTCTAAACTTTTGAACATTTCAATTTCATGCTCAAACTATGATCTTC
* *
611807 ATTTTAAATTAGTCGC-C-AAACTTTTTAAACATTGT-AATTTCAT
1 ATTCTAAATTAGTC-CTCTAAAC-TTTTGAACATT-TCAATTTCAT
611850 TCCAAAATGT
Statistics
Matches: 88, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
59 1 0.01
60 52 0.59
61 33 0.38
62 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (61 bp):
ATTCTAAATTAGTCCTCTAAACTTTTGAACATTTCAATTTCATGCTCAAACTATGATCTTC
Found at i:618167 original size:7 final size:7
Alignment explanation
Indices: 618157--618187 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
618147 AGAAAAAAGA
618157 AAATGGG
1 AAATGGG
618164 AAATGGG
1 AAATGGG
*
618171 AAAAGGG
1 AAATGGG
618178 AAATGGG
1 AAATGGG
618185 AAA
1 AAA
618188 AGAAAAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.39, T:0.10
Consensus pattern (7 bp):
AAATGGG
Found at i:618178 original size:14 final size:14
Alignment explanation
Indices: 618155--618189 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
618145 AAAGAAAAAA
618155 GAAAATGGGAAATGG
1 GAAAA-GGGAAATGG
618170 GAAAAGGGAAATGG
1 GAAAAGGGAAATGG
618184 GAAAAG
1 GAAAAG
618190 AAAAAGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.40, T:0.09
Consensus pattern (14 bp):
GAAAAGGGAAATGG
Found at i:623372 original size:18 final size:17
Alignment explanation
Indices: 623343--623380 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
623333 GTTTGACCAA
623343 TTTGACAATTTGAAAAG
1 TTTGACAATTTGAAAAG
*
623360 TTTGACTAATTTGAGAAG
1 TTTGAC-AATTTGAAAAG
623378 TTT
1 TTT
623381 TATATGCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (17 bp):
TTTGACAATTTGAAAAG
Found at i:623455 original size:18 final size:18
Alignment explanation
Indices: 623432--623468 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
623422 ATTTGGTTGT
*
623432 TCGTTACCCATGTCATGC
1 TCGTTACCCACGTCATGC
623450 TCGTTACCCACGTCATGC
1 TCGTTACCCACGTCATGC
623468 T
1 T
623469 TCTATGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.35, G:0.16, T:0.32
Consensus pattern (18 bp):
TCGTTACCCACGTCATGC
Found at i:624522 original size:94 final size:94
Alignment explanation
Indices: 624361--624548 Score: 333
Period size: 94 Copynumber: 2.0 Consensus size: 94
624351 ATATGCGTGC
* *
624361 GTGTGGAGTTCCACATGTTTTTGTATAACAACTTTTATTACTATTTTATTATGACTATTTATGAT
1 GTGTGGAGTTCCACATATTTTTGTATAAAAACTTTTATTACTATTTTATTATGACTATTTATGAT
*
624426 TTTTTTTCTTATATGAAATATTTTTATGT
66 TTTTTTTCTTATATGAAATATTTTAATGT
624455 GTGTGGAGTTCCACATATTTTTGTA-AAAATACTTTTATTACTATTTTATTATGACTATTTATGA
1 GTGTGGAGTTCCACATATTTTTGTATAAAA-ACTTTTATTACTATTTTATTATGACTATTTATGA
624519 TTTTTTTTCTTATATGAAATATTTTAATGT
65 TTTTTTTTCTTATATGAAATATTTTAATGT
624549 TTTAAAATAT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 3 0.03
94 87 0.97
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (94 bp):
GTGTGGAGTTCCACATATTTTTGTATAAAAACTTTTATTACTATTTTATTATGACTATTTATGAT
TTTTTTTCTTATATGAAATATTTTAATGT
Found at i:624948 original size:2 final size:2
Alignment explanation
Indices: 624941--624991 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
624931 CCTACCTTAC
624941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
624983 AT AT AT AT A
1 AT AT AT AT A
624992 GAATTTATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:626186 original size:83 final size:83
Alignment explanation
Indices: 625933--626245 Score: 325
Period size: 83 Copynumber: 3.8 Consensus size: 83
625923 CACGACATAT
* *
625933 TAGTACTTTAGCGGCGTTTGTATAAAAA-TGCCGCAATATGGTTCAT-TGATAGTGGCATTTTTT
1 TAGTACTTTAGCGGTGTTTGTATAAAAATTG-CGCAATAGGGTTCATCT-ATAGTGGCATTTTTT
*
625996 CAATAAACGCCGCAACAGAG
64 CAACAAACGCCGCAACAGAG
* * * *** * * *
626016 TAGTGCTTTAGTGGTGTTT-TAATAGAAACACCGCAATA-GGTTCATCCATAGTCGCATTTCTT-
1 TAGTACTTTAGCGGTGTTTGT-ATAAAAATTGCGCAATAGGGTTCATCTATAGTGGCATTTTTTC
***
626078 AACAAACGCCATGACAGAG
65 AACAAACGCCGCAACAGAG
* *
626097 TAGTACTCTAGCGGTGTTTGTATAAAAATTGCGTAATAGGGTTCATCTATAGTGGCATTTTTTCA
1 TAGTACTTTAGCGGTGTTTGTATAAAAATTGCGCAATAGGGTTCATCTATAGTGGCATTTTTTCA
*
626162 ACAAACGCCGCAACAAAG
66 ACAAACGCCGCAACAGAG
* * * * *
626180 TAGTACTTTAGCGGTGTTTTTATACAAACGTT--ACAATAGGGTTCATCTTTAGTGGCCTTTTTT
1 TAGTACTTTAGCGGTGTTTGTATA-AAA-ATTGCGCAATAGGGTTCATCTATAGTGGCATTTTTT
626243 CAA
64 CAA
626246 GAAAACACCA
Statistics
Matches: 187, Mismatches: 35, Indels: 16
0.79 0.15 0.07
Matches are distributed among these distances:
81 43 0.23
82 43 0.23
83 96 0.51
84 3 0.02
85 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (83 bp):
TAGTACTTTAGCGGTGTTTGTATAAAAATTGCGCAATAGGGTTCATCTATAGTGGCATTTTTTCA
ACAAACGCCGCAACAGAG
Found at i:630399 original size:21 final size:21
Alignment explanation
Indices: 630383--630442 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
630373 TCCGAGAGAG
*
630383 GAGTCTCTTGATCCGAGACTA
1 GAGTCTCTCGATCCGAGACTA
630404 GAGTCTCTCGATCCGAGACTA
1 GAGTCTCTCGATCCGAGACTA
630425 GAGTCTCTCGATCCGAGA
1 GAGTCTCTCGATCCGAGA
630443 TCATGGTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (21 bp):
GAGTCTCTCGATCCGAGACTA
Found at i:642240 original size:23 final size:22
Alignment explanation
Indices: 642214--642258 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
642204 ATTAAAAATA
*
642214 ATTTATTATTTAAGAATTTAATT
1 ATTTATTACTTAAGAA-TTAATT
*
642237 ATTTATTACTTAATAATTAATT
1 ATTTATTACTTAAGAATTAATT
642259 TTAATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTATTACTTAAGAATTAATT
Found at i:645067 original size:18 final size:20
Alignment explanation
Indices: 645044--645083 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
645034 AGTTGTGAAA
*
645044 TTTGGT-TTTGCAA-AGAGT
1 TTTGGTATTTGAAACAGAGT
645062 TTTGGTATTTGAAACAGAGT
1 TTTGGTATTTGAAACAGAGT
645082 TT
1 TT
645084 GTACTCGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 6 0.32
20 7 0.37
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (20 bp):
TTTGGTATTTGAAACAGAGT
Found at i:645439 original size:22 final size:22
Alignment explanation
Indices: 645409--645460 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
645399 TGTTTTTCTA
* *
645409 CTTTCGAATAGAAAAATAATAG
1 CTTTTGAATAGAAAAATAACAG
*
645431 CTTTTGAATAGGAAAATAACAG
1 CTTTTGAATAGAAAAATAACAG
645453 CTTTTGAA
1 CTTTTGAA
645461 AACGTGAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (22 bp):
CTTTTGAATAGAAAAATAACAG
Found at i:652703 original size:42 final size:41
Alignment explanation
Indices: 652610--652703 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 41
652600 AACAATACCT
* * *
652610 GCGTTTGTACAAAAAATGCCGCTATATACCAGACCTTTTGC
1 GCGTTTGTATAAAAAACGCCGCTATATACCACACCTTTTGC
* *
652651 GCAGTTTGTATAAAAAACGCCGTTATATATCACACCTTTTGC
1 GC-GTTTGTATAAAAAACGCCGCTATATACCACACCTTTTGC
652693 GACGTTTGTAT
1 G-CGTTTGTAT
652704 CTGAAAAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 2 0.04
42 43 0.93
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (41 bp):
GCGTTTGTATAAAAAACGCCGCTATATACCACACCTTTTGC
Found at i:661879 original size:185 final size:187
Alignment explanation
Indices: 661546--661882 Score: 462
Period size: 185 Copynumber: 1.8 Consensus size: 187
661536 GCCATTGTAG
* * * * * * * *
661546 TATGGTTATGCTCTCTGTTTATTCTTTTTGTGTTTTATGTTTTATTGCTATTGTTTTGGTGTATA
1 TATGATTATGCTATCTGTTTATTCTCTTTGTGTGTTATGTTTTATTGCAATTGCTTTAGAGTATA
* * *
661611 TATAAGCTAAAATTCATTGAAAGTAGACAATTACATATGGAAAATTTGGATTTTCTTCATAAAAT
66 TATAAGATAAAATTCATTGAAAGTAGACAATTACATATGAAAAATTTAGATTTTCTTCATAAAAT
661676 ACAGATACTAAAATCCTTGTTTCGAGTATCTATAAGCTAAAACTTAGAGAAAAAAAC
131 ACAGATACTAAAATCCTTGTTTCGAGTATCTATAAGCTAAAACTTAGAGAAAAAAAC
* *
661733 TATGATTATGCTATTTG-TTATTCTCTTTGTGTGTTGTGTTTTATTGCAATTGCTTTAGAGTATA
1 TATGATTATGCTATCTGTTTATTCTCTTTGTGTGTTATGTTTTATTGCAATTGCTTTAGAGTATA
* * * * ** *
661797 TATAAGATAAACTTGATTG-ACGTAGAGAATTTTATATGAAAAATTTAGATTTTCTTCATTAAAT
66 TATAAGATAAAATTCATTGAAAGTAGACAATTACATATGAAAAATTTAGATTTTCTTCATAAAAT
**
661861 ACAGATACTATGATCCTTGTTT
131 ACAGATACTAAAATCCTTGTTT
661883 TGATATTTTG
Statistics
Matches: 128, Mismatches: 22, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
185 58 0.45
186 56 0.44
187 14 0.11
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (187 bp):
TATGATTATGCTATCTGTTTATTCTCTTTGTGTGTTATGTTTTATTGCAATTGCTTTAGAGTATA
TATAAGATAAAATTCATTGAAAGTAGACAATTACATATGAAAAATTTAGATTTTCTTCATAAAAT
ACAGATACTAAAATCCTTGTTTCGAGTATCTATAAGCTAAAACTTAGAGAAAAAAAC
Found at i:689343 original size:18 final size:19
Alignment explanation
Indices: 689325--689418 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 19
689315 AATGACCAAC
*
689325 AAAATCGCAATGCGAAACA
1 AAAATCGCAACGCGAAACA
***
689344 AAAATCGCAACGCGATTTA
1 AAAATCGCAACGCGAAACA
* *
689363 GAAAATCGCAATGTTGAAA-A
1 -AAAATCGCAACG-CGAAACA
*
689383 GAAAATCGCAACG-GTCAAAAA
1 -AAAATCGCAACGCG--AAACA
689404 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
689419 TCTTCCAAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
18 1 0.02
19 16 0.27
20 39 0.65
21 4 0.07
ACGTcount: A:0.49, C:0.19, G:0.18, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:689369 original size:20 final size:20
Alignment explanation
Indices: 689344--689522 Score: 116
Period size: 20 Copynumber: 8.8 Consensus size: 20
689334 ATGCGAAACA
*
689344 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
689364 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
* *
689384 AAAATCGCAACG-G-TCAAAAA
1 AAAATCGCAACGCGAT--TAAG
***
689404 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
689425 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
* *
689446 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
*
689466 AAAATCGCAACGCGATTCCAG
1 AAAATCGCAACGCGATT-AAG
* * *
689487 -GAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTAAG
689506 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
689523 CCAAGAATCG
Statistics
Matches: 124, Mismatches: 24, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 97 0.78
21 9 0.07
22 14 0.11
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:689482 original size:40 final size:40
Alignment explanation
Indices: 689428--689535 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
689418 ATCTTCCAAG
* *
689428 AATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
* *
689468 AATCGCAACGCGATTCCAGGAATCGCAATGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
689508 AATCGCAACGCGATTCCAAGAATCGCAA
1 AATCGCAACGCGATTCCAAGAATCGCAA
689536 AACGGCAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
Found at i:689512 original size:60 final size:61
Alignment explanation
Indices: 689404--689522 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 61
689394 CGGTCAAAAA
689404 AAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGA-CTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAG
* *
689466 AAAATCGCAACGCGA-TTCCAGGAATCGCAATGCGATTGAGAA-AATCGCAACGCGATT
1 AAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCA-AAGAATCGCAACGCGATT
689523 CCAAGAATCG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
60 37 0.69
61 2 0.04
62 15 0.28
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.18
Consensus pattern (61 bp):
AAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAG
Found at i:689531 original size:20 final size:20
Alignment explanation
Indices: 689406--689535 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
689396 GTCAAAAAAA
689406 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
689428 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
689448 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
*
689468 AATCGCAACGCGATTCCAGG
1 AATCGCAACGCGATTCCAAG
* * *
689488 AATCGCAATGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
689508 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
689528 AATCGCAA
1 AATCGCAA
689536 AACGGCAAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.02
20 73 0.82
21 2 0.02
22 12 0.13
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:689657 original size:6 final size:6
Alignment explanation
Indices: 689646--689718 Score: 146
Period size: 6 Copynumber: 12.2 Consensus size: 6
689636 GACACGTATT
689646 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
689694 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
689719 GACGGCGGCG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:699950 original size:23 final size:23
Alignment explanation
Indices: 699921--699964 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
699911 GCAAGCACTC
699921 AAAAGAAGAAAACAAAAAGAAGA
1 AAAAGAAGAAAACAAAAAGAAGA
* * *
699944 AAAAGAATAGAACAACAAGAA
1 AAAAGAAGAAAACAAAAAGAA
699965 AAGTTGAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAGAAGAAAACAAAAAGAAGA
Found at i:699989 original size:27 final size:27
Alignment explanation
Indices: 699954--700016 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
699944 AAAAGAATAG
699954 AACAACAAGAAAAGTTGAAAGCACACA
1 AACAACAAGAAAAGTTGAAAGCACACA
699981 AACAACAAGAAAAGTTGAAAGCACACA
1 AACAACAAGAAAAGTTGAAAGCACACA
700008 AACAACAAG
1 AACAACAAG
700017 TCTCATCACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.60, C:0.19, G:0.14, T:0.06
Consensus pattern (27 bp):
AACAACAAGAAAAGTTGAAAGCACACA
Found at i:702819 original size:10 final size:10
Alignment explanation
Indices: 702800--702833 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
702790 TGACCTCAAT
*
702800 TATAGTTGAA
1 TATAGCTGAA
702810 TATAGCTGAA
1 TATAGCTGAA
*
702820 TGTAGCTGAA
1 TATAGCTGAA
702830 TATA
1 TATA
702834 CTGCTATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (10 bp):
TATAGCTGAA
Found at i:704209 original size:23 final size:23
Alignment explanation
Indices: 704183--704231 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
704173 TTTCAGATGC
* *
704183 ATTTTGAAAGTTTTTTTATAATA
1 ATTTCGAAAGTATTTTTATAATA
*
704206 ATTTCGAAAGTATTTTTATAGTA
1 ATTTCGAAAGTATTTTTATAATA
704229 ATT
1 ATT
704232 GTGATAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (23 bp):
ATTTCGAAAGTATTTTTATAATA
Found at i:705073 original size:25 final size:25
Alignment explanation
Indices: 705039--705103 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
705029 TAAAATAGTT
705039 TAATTACAATATTTTTTTGTTACAA
1 TAATTACAATATTTTTTTGTTACAA
705064 TAATTACAATATTTTTTTGTTACAA
1 TAATTACAATATTTTTTTGTTACAA
*
705089 TAATCACAATATTTT
1 TAATTACAATATTTT
705104 GATAAATCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (25 bp):
TAATTACAATATTTTTTTGTTACAA
Found at i:708964 original size:61 final size:61
Alignment explanation
Indices: 708862--708977 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
708852 TAGTGATAGT
* ** * * *
708862 ATTGTTCCTTCGTGTTGAGGAAATCTGATTATCTAAAGATAATTTGATTTTTGAAAATGGC
1 ATTGCTCCTTCGCATTGAGGAAATCTAATTACCTAAAGATAATTTGATTATTGAAAATGGC
* ** *
708923 ATTGCTCCTTCGCATTGAGGAGATCTAATTACCTTTAGATAATTTGCTTATTGAA
1 ATTGCTCCTTCGCATTGAGGAAATCTAATTACCTAAAGATAATTTGATTATTGAA
708978 GACAACATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 45 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (61 bp):
ATTGCTCCTTCGCATTGAGGAAATCTAATTACCTAAAGATAATTTGATTATTGAAAATGGC
Found at i:716363 original size:2 final size:2
Alignment explanation
Indices: 716356--716446 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
716346 TATGCATACA
716356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
716398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
716440 AT AT AT A
1 AT AT AT A
716447 AATTTACAGT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:719481 original size:2 final size:2
Alignment explanation
Indices: 719431--719471 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
719421 AATCCATCTA
719431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
719472 ACTAATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:719590 original size:2 final size:2
Alignment explanation
Indices: 719540--719572 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
719530 AAATAAATAA
719540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
719573 CTCGCATCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:726887 original size:18 final size:18
Alignment explanation
Indices: 726864--726902 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
726854 TTATGATTAG
726864 AATAAGGATTT-TGCAAAT
1 AATAAGG-TTTATGCAAAT
*
726882 AATAAGGTTTATGCAAGT
1 AATAAGGTTTATGCAAAT
726900 AAT
1 AAT
726903 GCTAACTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (18 bp):
AATAAGGTTTATGCAAAT
Found at i:730701 original size:225 final size:226
Alignment explanation
Indices: 730192--730817 Score: 765
Period size: 225 Copynumber: 2.7 Consensus size: 226
730182 TCCATTGAGC
* * ** * * *
730192 ACGATGTCCTTCTTCGTGAAGTTGAAATCGTGGGCGGCTCCTTTG-TCGTGGAGTTGAGCTTCGA
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCCTTCGCT-GTGAAGTTGAGCTTTGA
* *
730256 ATTAGATGTCCTTCGTTGTGAAGTTGAAATCCAATCTTGTAAATTGCATCACTTTTGAGTTCAAT
65 ATTGGATG----T--TTGTGAAGTTGAAATCCAATCTTGTAAATTGCATCATTTTTGAGTTCAAT
* * *
730321 ATCTTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGATTTTTTTTATTGTTATGTCACAG
124 ATCTTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAAATGA-GTTTTTCATTGTTATGTCACAG
* *
730386 ATGACTCATTCGTCGTGAAGTTGGGTTAATCTTTTGGGT
188 ATGACTCATTCATCGTGAAGTTGGGTCAATCTTTTGGGT
* * * * *
730425 ACGATATTCTTCGTCATGAAGTTGAAATCGTGAATGGCTCCTTCACTGTGAAGTTGAGCTTTGAA
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCCTTCGCTGTGAAGTTGAGCTTTGAA
* *
730490 TTGGATGTTTGTGAAGTTGAAATCCAATCTTGTAAATTGTATCATTTTTGAGTTCAATATCCTTC
66 TTGGATGTTTGTGAAGTTGAAATCCAATCTTGTAAATTGCATCATTTTTGAGTTCAATATCTTTC
* *
730555 TTTGTGAAGTTGAAATTGACTCTGAATGAAAATG-GTTTTTCATTGTTGTGTCACAGATGACTCA
131 GTTGTGAAGTTGAAATTGACTCTGAATGAAAATGAGTTTTTCATTGTTATGTCACAGATGACTCA
730619 TTCATCGTGAAGTTGGGTCAATCTTTTGGGT
196 TTCATCGTGAAGTTGGGTCAATCTTTTGGGT
* * * *
730650 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGCTGTGAAGTTAAGTTTTGAG
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCCTTCGCTGTGAAGTTGAGCTTTGAA
* * *
730715 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATTGTGTAAATTGCA--ATTTTTCGAGTCCA
66 TTGG--AT-GTT--T-GTGAAGTTGAAATCCAAT-CT-TGTAAATTGCATCATTTTT-GAGTTCA
** * *
730778 ATATCTTTCGCCGTGAAGTTGAAATTGGCTATGAATGAAA
122 ATATCTTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAA
730818 CTGGAAAGCT
Statistics
Matches: 342, Mismatches: 41, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
225 116 0.34
227 88 0.26
228 2 0.01
229 1 0.00
230 1 0.00
231 24 0.07
232 41 0.12
233 68 0.20
234 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (226 bp):
ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCCTTCGCTGTGAAGTTGAGCTTTGAA
TTGGATGTTTGTGAAGTTGAAATCCAATCTTGTAAATTGCATCATTTTTGAGTTCAATATCTTTC
GTTGTGAAGTTGAAATTGACTCTGAATGAAAATGAGTTTTTCATTGTTATGTCACAGATGACTCA
TTCATCGTGAAGTTGGGTCAATCTTTTGGGT
Found at i:730871 original size:21 final size:21
Alignment explanation
Indices: 730830--730871 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
730820 GGAAAGCTCA
*
730830 TTCGCTGTGAATTGGATATCC
1 TTCGCTGTGAATTGGAAATCC
*
730851 TTCGTTGTGAAGTT-GAAATCC
1 TTCGCTGTGAA-TTGGAAATCC
730872 AATCTAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (21 bp):
TTCGCTGTGAATTGGAAATCC
Found at i:730951 original size:34 final size:33
Alignment explanation
Indices: 730907--731024 Score: 114
Period size: 34 Copynumber: 3.5 Consensus size: 33
730897 GGTTCGATAA
*
730907 CCTTCATCGTGAAGTTGAGCTTTGAATTGGACAT
1 CCTTCGTCGTGAAGTTGAGCTTTGAATTGGA-AT
* ** * *
730941 CCTTCGTCGTGAAGTTAAAATCGTGGA-TGG-AT
1 CCTTCGTCGTGAAGTTGAGCT-TTGAATTGGAAT
* *
730973 CCTTCGTTGTGAAGTTGAGCTTTGAATTAGATAT
1 CCTTCGTCGTGAAGTTGAGCTTTGAATTGGA-AT
*
731007 CCTTCGTTGTGAAGTTGA
1 CCTTCGTCGTGAAGTTGA
731025 AATCCAATGG
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
31 3 0.04
32 21 0.31
34 40 0.60
35 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.36
Consensus pattern (33 bp):
CCTTCGTCGTGAAGTTGAGCTTTGAATTGGAAT
Found at i:731077 original size:60 final size:61
Alignment explanation
Indices: 730991--731152 Score: 229
Period size: 60 Copynumber: 2.7 Consensus size: 61
730981 GTGAAGTTGA
* * * * *
730991 GCTTTGAATTAGATATCCTTCGTTGTGAAGTTGAAATCCAATG-GTTGTTTCACCAAATTG
1 GCTTTGAGTTGGACATCCTTCGTTGTGAAGTTGAAATCCAATGTATTGTTTCACAAAATTG
* *
731051 GTTTTGAGTTGGACATCCTTCATTGTGAAGTTGAAATCCAA-GTATTGTTTCACAAAATTG
1 GCTTTGAGTTGGACATCCTTCGTTGTGAAGTTGAAATCCAATGTATTGTTTCACAAAATTG
* *
731111 GCTTTGAGTTGGATATCTTTCGTTGTGAAGTTGAAATCCAAT
1 GCTTTGAGTTGGACATCCTTCGTTGTGAAGTTGAAATCCAAT
731153 CTCGAATATT
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.01
60 88 0.99
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.39
Consensus pattern (61 bp):
GCTTTGAGTTGGACATCCTTCGTTGTGAAGTTGAAATCCAATGTATTGTTTCACAAAATTG
Found at i:731566 original size:15 final size:15
Alignment explanation
Indices: 731543--731585 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
731533 TTTGTTTTAG
*
731543 TTTCTCCACAAAATT
1 TTTCCCCACAAAATT
731558 TTTCCCCACAAAATT
1 TTTCCCCACAAAATT
*
731573 TTACCCCA-AAAAT
1 TTTCCCCACAAAAT
731586 ATAGCTTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
TTTCCCCACAAAATT
Found at i:732505 original size:2 final size:2
Alignment explanation
Indices: 732500--732542 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
732490 ATTGTGTGTG
732500 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
732542 T
1 T
732543 TTGTTGAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:743337 original size:32 final size:32
Alignment explanation
Indices: 743296--743422 Score: 196
Period size: 32 Copynumber: 4.2 Consensus size: 32
743286 GTATTTGATT
743296 AGATGAAAGGAGTGTGTTGTGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTGTGTAAGAGATTGA
743328 AGATGAAAGGAGTGTGTTGTGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTGTGTAAGAGATTGA
*
743360 AGATGAAAGGAGAGTGTTGTGTAAGAGA-TGA
1 AGATGAAAGGAGTGTGTTGTGTAAGAGATTGA
743391 A-AT-----GAGTGTGTTGTGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTGTGTAAGAGATTGA
743417 AGATGA
1 AGATGA
743423 TGTACACTGT
Statistics
Matches: 89, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
25 18 0.20
26 4 0.04
27 2 0.02
30 2 0.02
31 4 0.04
32 59 0.66
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (32 bp):
AGATGAAAGGAGTGTGTTGTGTAAGAGATTGA
Found at i:743356 original size:25 final size:25
Alignment explanation
Indices: 743328--743413 Score: 91
Period size: 25 Copynumber: 3.2 Consensus size: 25
743318 AAGAGATTGA
743328 AGATGAAAGGAGTGTGTTGTGTAAGAGATTG
1 AGATGAAAGGAGTGTGTTGTGT---A-A--G
*
743359 AAGATGAAAGGAGAGTGTTGTGTAAG
1 -AGATGAAAGGAGTGTGTTGTGTAAG
*
743385 AGATGAAATGAGTGTGTTGTGTAAG
1 AGATGAAAGGAGTGTGTTGTGTAAG
743410 AGAT
1 AGAT
743414 TGAAGATGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 27 0.53
26 1 0.02
28 1 0.02
29 1 0.02
32 21 0.41
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (25 bp):
AGATGAAAGGAGTGTGTTGTGTAAG
Found at i:744543 original size:18 final size:18
Alignment explanation
Indices: 744520--744567 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
744510 ATTCGACGTA
744520 TACATATAATATTTTTAG
1 TACATATAATATTTTTAG
744538 TACATAATTAATA-TTTTAG
1 TACAT-A-TAATATTTTTAG
*
744557 T-CATATTATAT
1 TACATATAATAT
744568 GCGCACGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.15
17 1 0.04
18 8 0.31
19 8 0.31
20 5 0.19
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (18 bp):
TACATATAATATTTTTAG
Found at i:745394 original size:22 final size:19
Alignment explanation
Indices: 745366--745407 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
745356 ATTTATGTCA
745366 TTGTGACATACTTTTTCTGCTC
1 TTGTGACAT--TTTTT-TGCTC
745388 TTGTGACATTTTTTTGCTC
1 TTGTGACATTTTTTTGCTC
745407 T
1 T
745408 CTTGACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
22 9 0.45
ACGTcount: A:0.12, C:0.19, G:0.14, T:0.55
Consensus pattern (19 bp):
TTGTGACATTTTTTTGCTC
Found at i:745405 original size:19 final size:21
Alignment explanation
Indices: 745366--745415 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 21
745356 ATTTATGTCA
745366 TTGTGACATACTTTTTCTGCTC
1 TTGTGACATA-TTTTTCTGCTC
745388 TTGTGACAT-TTTTT-TGCTC
1 TTGTGACATATTTTTCTGCTC
745407 TCT-TGACAT
1 T-TGTGACAT
745416 GTTTCTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 12 0.44
20 6 0.22
22 9 0.33
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.52
Consensus pattern (21 bp):
TTGTGACATATTTTTCTGCTC
Found at i:748912 original size:22 final size:23
Alignment explanation
Indices: 748850--748906 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
748840 AACCTAACTT
* * *
748850 AAAAATAACAATAAT-AAAAATA
1 AAAAATAAAAATAGTAAAAAAGA
748872 AAAAATAAAAATAGTAAAAAAGA
1 AAAAATAAAAATAGTAAAAAAGA
748895 ATAAAATAAAAA
1 A-AAAATAAAAA
748907 GTAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 13 0.43
23 7 0.23
24 10 0.33
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAAATAAAAATAGTAAAAAAGA
Found at i:750380 original size:111 final size:111
Alignment explanation
Indices: 750224--750523 Score: 478
Period size: 111 Copynumber: 2.7 Consensus size: 111
750214 TCACTCATGA
*
750224 AATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTAAGGGAATATCAGTTCTTGGAAA
1 AATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTAAGGGAATATCAGATCTTGGAAA
* * * *
750289 GTTGATCCATTGAATC-GGAGTAGACTTGTTCTGCTGTCACTCACAG
66 GTTGATCCATTGAATCAGG-GTAAACTTGTTCAGATGTCACTAACAG
* *
750335 AATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTAAGGGAATATCAAATCTT-GAAA
1 AATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTAAGGGAATATCAGATCTTGGAAA
**
750399 TGTTGATCCATTGAATCAGGGTAAACTTGTTCAGATGTCACTAAGGG
66 -GTTGATCCATTGAATCAGGGTAAACTTGTTCAGATGTCACTAACAG
*
750446 AATATCAAATCTTGGAAGAGAGGGATTTGTTCCGCTTCTTCTAAGGGAATATCAGATCTTGGAAA
1 AATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTAAGGGAATATCAGATCTTGGAAA
750511 GTTGATCCATTGA
66 GTTGATCCATTGA
750524 TTGGGATCGA
Statistics
Matches: 174, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
110 4 0.02
111 164 0.94
112 6 0.03
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (111 bp):
AATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTAAGGGAATATCAGATCTTGGAAA
GTTGATCCATTGAATCAGGGTAAACTTGTTCAGATGTCACTAACAG
Found at i:750889 original size:42 final size:41
Alignment explanation
Indices: 750833--750919 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 41
750823 CCCAAAGGAC
* *
750833 TTATTATCTTGCTCGAAAAGCTTACAGATGACCCGAAAGAT
1 TTATTATCATGCTCGAAAAGCTTACAGACGACCCGAAAGAT
* * *
750874 TTATGTATCATGCTCGAAAGGCTTACTGACGACCCGAAGGAT
1 TTAT-TATCATGCTCGAAAAGCTTACAGACGACCCGAAAGAT
750916 TTAT
1 TTAT
750920 AAATTTTGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 4 0.10
42 36 0.90
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (41 bp):
TTATTATCATGCTCGAAAAGCTTACAGACGACCCGAAAGAT
Found at i:751146 original size:42 final size:42
Alignment explanation
Indices: 751029--751154 Score: 130
Period size: 42 Copynumber: 3.0 Consensus size: 42
751019 CATTTGACAA
* * *
751029 ACATCCTGCCCGAAGGACTTA-TGGATGGCCCGAAGGATTTAT
1 ACATCATGCTCGAAAGACTTACT-GATGGCCCGAAGGATTTAT
** * * *
751071 -CATTTTTCTCGAAAGACTTACAGATGACCCGAAGGATTTAT
1 ACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAT
* * *
751112 ACATCATGCTCGGAAGACTTACTGATGGCTCGAAGGACTTAT
1 ACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAT
751154 A
1 A
751155 AATTTTGGAA
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 33 0.49
42 34 0.51
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
ACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAT
Found at i:751587 original size:42 final size:41
Alignment explanation
Indices: 751511--751618 Score: 153
Period size: 42 Copynumber: 2.6 Consensus size: 41
751501 GCCCAAAGGT
* * *
751511 CTTATAGATGGCCCGAACGACTTATCATCTTGCTTGAAAGA
1 CTTACAGATGGCCCGAAGGACTTATCATCATGCTTGAAAGA
* *
751552 CTTACAGATGACCCGAAGGATTTAATCATCATGCTTGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-ATCATCATGCTTGAAAGA
*
751594 CTTACTGATGGCCCGAAGGACTTAT
1 CTTACAGATGGCCCGAAGGACTTAT
751619 AAATTTTGGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 21 0.36
42 37 0.64
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCATGCTTGAAAGA
Found at i:751617 original size:233 final size:232
Alignment explanation
Indices: 750793--751928 Score: 1553
Period size: 232 Copynumber: 4.9 Consensus size: 232
750783 AATCATGCGT
* * * * *
750793 AAACATCTTGCCCGAAA-GACTTATGGATGGCCCAAAGGACTTATTATCTTGCTCGAAA-AGCTT
1 AAACATCCTGCCC-AAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGA-CTT
* * * * * *
750856 ACAGATGACCCGAAAGATTTATGTATCATGCTCGAAAGGCTTACTGACGACCCGAAGGATTTATA
64 ACAGATGACCCGAAGGATTTAT-CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA
* * * * * *
750921 AATTTTGGAAATAGTTTATTAGGTAAGAAGCCTTTCTTACTTTTCAACAATTTCAAATCTCAGAT
128 AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAAT
* *
750986 TTAAATGAGAAACCTTTCTCATATTTTAATAGACATTTGA
193 TTAAATGAGAAACCTTTCTCATATTTCAATAGACATGTGA
* * * * * *
751026 CAAACATCCTGCCCGAAGGACTTATGGATGGCCCGAAGGATTTATCATTTTTCTCGAAAGACTTA
1 -AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTTA
* *
751091 CAGATGACCCGAAGGATTTATACATCATGCTCGGAAGACTTACTGATGGCTCGAAGGACTTATAA
65 CAGATGACCCGAAGGATTTAT-CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* *
751156 ATTTTGGAAATAGTTTACTAGGTACGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAAATT
129 ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATT
* **
751221 TGAATGAGAAACCTTTCTCATATTT-AATAGACATGAAA
194 TAAATGAGAAACCTTTCTCATATTTCAATAGACATGTGA
* * *
751259 AAACATCCTGCCCAAAGCTCTTATGGATGACCCGAAGGACTTATCATCTTGCTTGAAAGAGTTAC
1 AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTTAC
* * * * * *
751324 AGATAACCGGAGGGATTTAATCATCGTGCTCGAAAGACTTATTGATGGTCCGAAGGACTTATAAA
66 AGATGACCCGAAGGATTT-ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
*
751389 TTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTT
130 TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTT
* **
751454 GAATGAGAAACCTTTCTTGTATTTCAATAGACATGTGA
195 AAATGAGAAACCTTTCTCATATTTCAATAGACATGTGA
* *
751492 AAACATCCTGCCCAAAGGTCTTATAGATGGCCCGAACGACTTATCATCTTGCTTGAAAGACTTAC
1 AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTTAC
*
751557 AGATGACCCGAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
66 AGATGACCCGAAGGATTT-ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
* * *
751622 TTTTGGAAATAGTTTACTTGGTAATAAACCTTTCTTACTTTTC-AAAATTTCAATTTTAAAATTT
130 TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTT
* *
751686 AAATGAGAAACCTTTCTCAT-TTCCAACAGACATGTGA
195 AAATGAGAAACCTTTCTCATATTTCAATAGACATGTGA
* * * *
751723 AAACATCCTGCCCAAAGGTCTTATAGATGGCCTGAAGGACTTATCATC-TGTTTCGAAAGGCTTA
1 AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTT-GAAAGACTTA
* *
751787 TAGATGACCCG-AGG------CATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATAAA
65 CAGATGACCCGAAGGATTTATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
*
751845 TTTTGGAAATAGTTTACTAGGTAACAAACCTTTCTTACTTTTC-AAAATTTCAATTTTCAAATTT
130 TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTT
*
751909 AAATGAGAAACCATTCTCAT
195 AAATGAGAAACCTTTCTCAT
751929 TTTTTCACTT
Statistics
Matches: 813, Mismatches: 84, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
223 122 0.15
230 7 0.01
231 80 0.10
232 231 0.28
233 183 0.23
234 189 0.23
235 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (232 bp):
AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTTAC
AGATGACCCGAAGGATTTATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
TTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTTA
AATGAGAAACCTTTCTCATATTTCAATAGACATGTGA
Found at i:751666 original size:465 final size:463
Alignment explanation
Indices: 750793--751928 Score: 1571
Period size: 466 Copynumber: 2.5 Consensus size: 463
750783 AATCATGCGT
* * * * *
750793 AAACATCTTGCCCGAAAGACTTATGGATGGCCCAAAGGACTTATTATCTTGCTCGAAA-AGCTTA
1 AAACATCCTGCCC-AAAGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGAGCTTA
* * * * * *
750857 CAGATGACCCGAAAGATTTATGTATCATGCTCGAAAGGCTTACTGACGACCCGAAGGATTTATAA
65 CAGATGACCCG-AGGATTTAT-CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* * * * * *
750922 ATTTTGGAAATAGTTTATTAGGTAAGAAGCCTTTCTTACTTTTCAACAATTTCAAATCTCAGATT
128 ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATT
* * * *
750987 TAAATGAGAAACCTTTCTCATATTTTAATAGACATTTGACAAACATCCTGCCCGAAGGACTTATG
193 TAAATGAGAAACCTTTCTCATATTTCAATAGACATGTGACAAACATCCTGCCCAAAGGACTTATA
* * * *
751052 GATGGCCCGAAGGATTTATCATTTTTCTCGAAAGACTTACAGATGACCCGAAGGATTTATACATC
258 GATGGCCCGAACGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTATACATC
* * *
751117 ATGCTCGGAAGACTTACTGATGGCTCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTACG
323 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAG
* * *
751182 AAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAAATTTGAATGAGAAACCTTTCTCATATT-T
388 AAACCTTTCTTACTTTTC-AAAATTTCAATTTTAAAATTTAAATGAGAAACCTTTCTCAT-TTCC
*
751246 AATAGACATGAAA
451 AACAGACATGAAA
*
751259 AAACATCCTGCCCAAAGCTCTTATGGATGACCCGAAGGACTTATCATCTTGCTTGAAAGAG-TTA
1 AAACATCCTGCCCAAAG-TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGAGCTTA
* * * * *
751323 CAGATAACCGGAGGGATTTAATCATCGTGCTCGAAAGACTTATTGATGGTCCGAAGGACTTATAA
65 CAGATGACCCGA-GGATTT-ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
*
751388 ATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATT
128 ATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATT
* ** *
751453 TGAATGAGAAACCTTTCTTGTATTTCAATAGACATGTGA-AAACATCCTGCCCAAAGGTCTTATA
193 TAAATGAGAAACCTTTCTCATATTTCAATAGACATGTGACAAACATCCTGCCCAAAGGACTTATA
*
751517 GATGGCCCGAACGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGATTTA-ATCAT
258 GATGGCCCGAACGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTATA-CAT
* *
751581 CATGCTTGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTTGGTAA
322 CATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAA
*
751646 TAAACCTTTCTTACTTTTCAAAATTTCAATTTTAAAATTTAAATGAGAAACCTTTCTCATTTCCA
387 GAAACCTTTCTTACTTTTCAAAATTTCAATTTTAAAATTTAAATGAGAAACCTTTCTCATTTCCA
**
751711 ACAGACATGTGA
452 ACAGACATGAAA
* * *
751723 AAACATCCTGCCCAAAGGTCTTATAGATGGCCTGAAGGACTTATCATC-TGTTTCGAAAG-GCTT
1 AAACATCCTGCCCAAA-GTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTT-GAAAGAGCTT
* *
751786 ATAGATGACCCGAGG------CATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATAAA
64 ACAGATGACCCGAGGATTTATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
*
751845 TTTTGGAAATAGTTTACTAGGTAACAAACCTTTCTTACTTTTC-AAAATTTCAATTTTCAAATTT
129 TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTT
*
751909 AAATGAGAAACCATTCTCAT
194 AAATGAGAAACCTTTCTCAT
751929 TTTTTCACTT
Statistics
Matches: 595, Mismatches: 66, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
455 37 0.06
456 81 0.14
463 9 0.02
464 110 0.18
465 163 0.27
466 191 0.32
467 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (463 bp):
AAACATCCTGCCCAAAGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGAGCTTAC
AGATGACCCGAGGATTTATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
TTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTTAA
ATGAGAAACCTTTCTCATATTTCAATAGACATGTGACAAACATCCTGCCCAAAGGACTTATAGAT
GGCCCGAACGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTATACATCATG
CTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAA
CCTTTCTTACTTTTCAAAATTTCAATTTTAAAATTTAAATGAGAAACCTTTCTCATTTCCAACAG
ACATGAAA
Found at i:754893 original size:42 final size:41
Alignment explanation
Indices: 754823--754924 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
754813 AGGACTTATG
* * * *
754823 GATGGCCCAAAGGACTTATCATCTTGCTCGAAA-AGCTTACA
1 GATGACCCGAAGGATTTATCATCATGCTCGAAAGA-CTTACA
*
754864 GATGACCCGAAGGATTTATGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTAT-CATCATGCTCGAAAGACTTACA
* *
754906 GACGACCAGAAGGATTTAT
1 GATGACCCGAAGGATTTAT
754925 AAATTTTGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 16 0.31
42 35 0.67
43 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (41 bp):
GATGACCCGAAGGATTTATCATCATGCTCGAAAGACTTACA
Found at i:755138 original size:42 final size:41
Alignment explanation
Indices: 755035--755143 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
755025 ATTTGAAAAA
* * ** * *
755035 CATCCTGCTCGAAGGACTTATGGATGGCCCGAAGGATTTAT
1 CATCATGCTCGAAAGACTTACAGATGACCAGAAGGATTTAT
* *
755076 CATCTTGCTCGAAATACTTACAGATGACCAGAAGGATTTAT
1 CATCATGCTCGAAAGACTTACAGATGACCAGAAGGATTTAT
*
755117 GCATCATGCTC-AGAAGACTTACTGATG
1 -CATCATGCTCGA-AAGACTTACAGATG
755144 GCTCGAAGGA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
41 35 0.62
42 21 0.38
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTACAGATGACCAGAAGGATTTAT
Found at i:755152 original size:42 final size:39
Alignment explanation
Indices: 755035--755158 Score: 115
Period size: 42 Copynumber: 3.0 Consensus size: 39
755025 ATTTGAAAAA
*
755035 CATCCTGCTCGAAGGACTTA-TGGATGGCCCGAAGGATTTAT
1 CATCATGCTCGAA-GACTTACT-GATGG-CCGAAGGATTTAT
* * * *
755076 CATCTTGCTCGAAATACTTACAGATGACCAGAAGGATTTAT
1 CATCATGCTCG-AAGACTTACTGATGGCC-GAAGGATTTAT
*
755117 GCATCATGCTCAGAAGACTTACTGATGGCTCGAAGGACTTAT
1 -CATCATGCTC-GAAGACTTACTGATGGC-CGAAGGATTTAT
755159 AAATTTTGGA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
40 2 0.03
41 30 0.44
42 34 0.50
43 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (39 bp):
CATCATGCTCGAAGACTTACTGATGGCCGAAGGATTTAT
Found at i:755591 original size:233 final size:233
Alignment explanation
Indices: 754798--755921 Score: 1533
Period size: 230 Copynumber: 4.9 Consensus size: 233
754788 AATCATGCGT
* *
754798 AAACATCCTGCCCAAAGGACTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGAAA-AGCTTA
1 AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA-CTTA
* * * *
754862 CAGATGACCCGAAGGATTT-ATGCATCATGCTCGAAAGACTTACTGACGACCAGAAGGATTTATA
65 CAGATGACCCGAAGGATTTAAT-CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA
* * * * * * *
754926 AATTTTGGAAATAGTTTACTACGTAAGAAGCCTTTCTTACTTTTCAACAATTTTAAATCTCAGAT
129 AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAAT
* * *
754991 TTAAATGAGAAACATTTCTCATATTTTAATAGACATTTGAA
194 TTAAATGAGAAACCTTTCTCATATTTCAATAGACATGTG-A
* * * * *
755032 AAACATCCTGCTCGAAGGACTTATGGATGGCCCGAAGGATTTATCATCTTGCTCGAAATACTTAC
1 AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
* *
755097 AGATGACCAGAAGGATTT-ATGCATCATGCTC-AGAAGACTTACTGATGGCTCGAAGGACTTATA
66 AGATGACCCGAAGGATTTAAT-CATCATGCTCGA-AAGACTTACTGATGGCCCGAAGGACTTATA
*
755160 AATTTTGGAAATAGTTTACTAGGTAAAAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAAT
129 AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAAT
*
755225 TTGAATGAGAAACC--TCTCATATTT-AATAGACATGTGA
194 TTAAATGAGAAACCTTTCTCATATTTCAATAGACATGTGA
* * * * *
755262 AAACATTCTGCCCAAAGGTCTTATAGATGGCCCAAAAGACTTATCATCTTGCTTGAAAGACTTAC
1 AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
* * *
755327 AGATGACCAGAAGGATTTAATCATCATGCTCGAAAGACCTACTGATGGCCCGAATGACTTATAAA
66 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
** *
755392 TTTTGGAAATTTTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAATTTT
131 TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTT
* *
755457 GAATAAGAAACCTTTCTCATATTTCAATAGACATGTGA
196 AAATGAGAAACCTTTCTCATATTTCAATAGACATGTGA
* *
755495 AAACATCCTGCCCAAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTTGAAAGACTTAC
1 AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
* *
755560 AGATGACCCGTAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATGAA
66 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
*
755625 TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTAATTTTC---AA----AATTTTCAAATTT
131 TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTT
* *
755683 AAATGAGAAACCTTTCTCAT-TTTCAACAGACTTGTGA
196 AAATGAGAAACCTTTCTCATATTTCAATAGACATGTGA
* * * * * *
755720 AAACATCCTGCCTAAAGGTCTTATGGATGG-CCGAATGACTTATCAACTTACTCGAAAGGCTTAT
1 AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
**
755784 AGATGACCC----GA---AA-CATCATGCTATAAAGACTTACTGATGGCCCGAAGGACTTATAAA
66 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
* *
755841 TTTTGGAAATAGTTTACTAGGTAAGAAACATTTCTTACTTTTC-AAATTTTCAATTTTCAAATTT
131 TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTT
755905 AAATGAGAAACCTTTCT
196 AAATGAGAAACCTTTCT
755922 AATTTTTTCA
Statistics
Matches: 806, Mismatches: 71, Indels: 38
0.88 0.08 0.04
Matches are distributed among these distances:
216 82 0.10
217 2 0.00
218 1 0.00
220 2 0.00
222 30 0.04
224 37 0.05
225 43 0.05
226 30 0.04
230 187 0.23
231 14 0.02
232 20 0.02
233 174 0.22
234 183 0.23
235 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (233 bp):
AAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
TTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTT
AAATGAGAAACCTTTCTCATATTTCAATAGACATGTGA
Found at i:755595 original size:42 final size:41
Alignment explanation
Indices: 755520--755621 Score: 141
Period size: 42 Copynumber: 2.5 Consensus size: 41
755510 AGGTCTTATG
* *
755520 GATGACCCGAAGGACTTATCATCTTGCTTGAAAGACTTACA
1 GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
* * *
755561 GATGACCCGTAGGATTTAATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACA
*
755603 GATGGCCCGAAGGACTTAT
1 GATGACCCGAAGGACTTAT
755622 GAATTTTGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 17 0.33
42 35 0.67
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
Found at i:766073 original size:48 final size:48
Alignment explanation
Indices: 766013--766139 Score: 182
Period size: 48 Copynumber: 2.6 Consensus size: 48
766003 TTAGGATGTA
* *
766013 TGATTATCAAGGTAACGCGCTCTAATCTCTGATTATTTCTTCGTCACG
1 TGATTATTAAGGTAACGCGCTCTAATCTCTAATTATTTCTTCGTCACG
* * *
766061 TGATTATTAAGGTAACGCGCTCTAATCTCTAATTTTTTTTTCGTCGCG
1 TGATTATTAAGGTAACGCGCTCTAATCTCTAATTATTTCTTCGTCACG
* * *
766109 TGATTATTAAGGTAACACGCTCCAATTTCTA
1 TGATTATTAAGGTAACGCGCTCTAATCTCTA
766140 TCAAGGGTGT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (48 bp):
TGATTATTAAGGTAACGCGCTCTAATCTCTAATTATTTCTTCGTCACG
Found at i:767782 original size:23 final size:23
Alignment explanation
Indices: 767755--767799 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
767745 AAATCGATTA
*
767755 ATTTATAAAATTTTAATAAATAT
1 ATTTATAAAATTTTAAAAAATAT
*
767778 ATTTATTAAATTTTAAAAAATA
1 ATTTATAAAATTTTAAAAAATA
767800 AAAACAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTATAAAATTTTAAAAAATAT
Found at i:768223 original size:22 final size:22
Alignment explanation
Indices: 768178--768223 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
768168 CTATATAGAT
*
768178 ACGATAAAATTTCAGGGTATGC
1 ACGATAAAATTTCAGGGTAGGC
*
768200 ACGATAAAATTTCAGGGTGGGC
1 ACGATAAAATTTCAGGGTAGGC
768222 AC
1 AC
768224 ATGCTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (22 bp):
ACGATAAAATTTCAGGGTAGGC
Found at i:768865 original size:48 final size:48
Alignment explanation
Indices: 768794--768889 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
768784 ATGCCTATAA
768794 AATATGAATATGCTTTTCAAGGTTAACACTAAGAAGGGGCCAAAAGGT
1 AATATGAATATGCTTTTCAAGGTTAACACTAAGAAGGGGCCAAAAGGT
*
768842 AATATGAATATGCTTTTCAAGGTTAACACTTAGAAGGGGCCAAAAGGT
1 AATATGAATATGCTTTTCAAGGTTAACACTAAGAAGGGGCCAAAAGGT
768890 GATCATATCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (48 bp):
AATATGAATATGCTTTTCAAGGTTAACACTAAGAAGGGGCCAAAAGGT
Found at i:769088 original size:25 final size:25
Alignment explanation
Indices: 769034--769086 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
769024 TTATCTTTGT
* *
769034 CTTTGTGGCATGTTTATTTCTCTAT
1 CTTTGTGGCACGTTTATTTCTCTAA
769059 CTTTGTGGCACGTTT-TTTCTCTAA
1 CTTTGTGGCACGTTTATTTCTCTAA
769083 CTTT
1 CTTT
769087 TGGTAATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (25 bp):
CTTTGTGGCACGTTTATTTCTCTAA
Found at i:770974 original size:19 final size:19
Alignment explanation
Indices: 770932--770987 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
770922 CAAACCGGTC
* *
770932 TGACCCATTAACTTTGACC
1 TGACCCATTGACTTTGACA
*
770951 CGACCCATTGACTTTGACA
1 TGACCCATTGACTTTGACA
**
770970 TGACCTGTTGACTTTGAC
1 TGACCCATTGACTTTGAC
770988 CAAAAAGTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (19 bp):
TGACCCATTGACTTTGACA
Found at i:772977 original size:23 final size:23
Alignment explanation
Indices: 772933--772977 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
772923 TAATGGGTTG
* ** *
772933 GGTACGTGTCAGGTGAGTGGGTA
1 GGTACGAGTCAGGACAGCGGGTA
772956 GGTACGAGTCAGGACAGCGGGT
1 GGTACGAGTCAGGACAGCGGGT
772978 CTGGTTGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.13, G:0.47, T:0.20
Consensus pattern (23 bp):
GGTACGAGTCAGGACAGCGGGTA
Found at i:774941 original size:27 final size:27
Alignment explanation
Indices: 774892--774946 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
774882 AGTATACTCT
* *
774892 AAACTTGATCCCTGCTCAACTTGCTCG
1 AAACTCGATCCATGCTCAACTTGCTCG
* *
774919 AAACTCGATCCATGTTCACCTTGCTCG
1 AAACTCGATCCATGCTCAACTTGCTCG
774946 A
1 A
774947 TAATAGAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.29
Consensus pattern (27 bp):
AAACTCGATCCATGCTCAACTTGCTCG
Found at i:777778 original size:18 final size:17
Alignment explanation
Indices: 777741--777775 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
777731 CAATGCTCGA
777741 CATCCTTTGGAGCTCCC
1 CATCCTTTGGAGCTCCC
777758 CATCCTTTGGAGCTCCC
1 CATCCTTTGGAGCTCCC
777775 C
1 C
777776 CATATATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.43, G:0.17, T:0.29
Consensus pattern (17 bp):
CATCCTTTGGAGCTCCC
Found at i:783328 original size:114 final size:115
Alignment explanation
Indices: 783127--783357 Score: 455
Period size: 114 Copynumber: 2.0 Consensus size: 115
783117 ACAATCTTAA
783127 GTAAATAAATACAATGAGAAAAGAAAATTTTAACATAAAAATATGAAACATTCATTAAAGAAAAA
1 GTAAATAAATACAATGAGAAAAGAAAATTTTAACATAAAAATATGAAACATTCATTAAAGAAAAA
783192 CTTAATCATCCATAGTAAACTTAATCCAAATAGGGTTAGTTCATGGTAGG
66 CTTAATCATCCATAGTAAACTTAATCCAAATAGGGTTAGTTCATGGTAGG
783242 GTAAATAAATACAATGAG-AAAGAAAATTTTAACATAAAAATATGAAACATTCATTAAAGAAAAA
1 GTAAATAAATACAATGAGAAAAGAAAATTTTAACATAAAAATATGAAACATTCATTAAAGAAAAA
783306 CTTAATCATCCATAGTAAACTTAATCCAAATAGGGTTAGTTCATGGTAGG
66 CTTAATCATCCATAGTAAACTTAATCCAAATAGGGTTAGTTCATGGTAGG
783356 GT
1 GT
783358 GCAAATCATC
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 98 0.84
115 18 0.16
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.27
Consensus pattern (115 bp):
GTAAATAAATACAATGAGAAAAGAAAATTTTAACATAAAAATATGAAACATTCATTAAAGAAAAA
CTTAATCATCCATAGTAAACTTAATCCAAATAGGGTTAGTTCATGGTAGG
Found at i:784477 original size:21 final size:21
Alignment explanation
Indices: 784451--784500 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
784441 ATTAAAGCAC
784451 TAATACCTTACTCCCAATTTG
1 TAATACCTTACTCCCAATTTG
784472 TAATACCTTACTCCCAATTTG
1 TAATACCTTACTCCCAATTTG
784493 TAATACCT
1 TAATACCT
784501 CAATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (21 bp):
TAATACCTTACTCCCAATTTG
Found at i:787396 original size:22 final size:21
Alignment explanation
Indices: 787371--787429 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
787361 TATGTGCTTT
*
787371 GGGTAAGTCCTTATGGACTTGA
1 GGGTAAGTCCTTATGGACCT-A
* * *
787393 GGGTAACTCC-AATGGGCCTA
1 GGGTAAGTCCTTATGGACCTA
787413 GGGTAAGTCCTTATGGA
1 GGGTAAGTCCTTATGGA
787430 TGTAGTTTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 10 0.34
21 10 0.34
22 9 0.31
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (21 bp):
GGGTAAGTCCTTATGGACCTA
Found at i:799969 original size:19 final size:19
Alignment explanation
Indices: 799945--799981 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
799935 CGAATGCATT
799945 CCATGCACCGATGCACTCA
1 CCATGCACCGATGCACTCA
*
799964 CCATGCATCGATGCACTC
1 CCATGCACCGATGCACTC
799982 TGAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (19 bp):
CCATGCACCGATGCACTCA
Found at i:799999 original size:65 final size:64
Alignment explanation
Indices: 799881--800088 Score: 201
Period size: 65 Copynumber: 3.2 Consensus size: 64
799871 TATTCAAAGG
* *
799881 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTCA--CCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
799942 ATTC
61 ATTT
799946 CATGCACCGATGCACTCACCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
800011 GATGCATCGATGCACAGGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCACCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
* *
800075 TATGCATCGATGCA
1 CATGCACCGATGCA
800089 TCCTTAGTGC
Statistics
Matches: 125, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 50 0.40
65 65 0.52
66 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:800036 original size:19 final size:20
Alignment explanation
Indices: 800012--800049 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
800002 AATGCATTTG
800012 ATGCATCGATGCA-CAGGCC
1 ATGCATCGATGCACCAGGCC
800031 ATGCATCGATGCACCAGGC
1 ATGCATCGATGCACCAGGC
800050 TATTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (20 bp):
ATGCATCGATGCACCAGGCC
Found at i:800084 original size:64 final size:65
Alignment explanation
Indices: 799930--800088 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 65
799920 GAATTAATTG
* * * *
799930 AACATCGAATGCATTCCATGCACCGATGCACTCACCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACACCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
799995 AACATCGAATGCATTTGATGCATCGATGCACAGGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACACCATGCATCGATGCACTCAGAATA-TTTTCA
800058 A
65 A
*
800059 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
800089 TCCTTAGTGC
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
64 34 0.41
65 49 0.59
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACACCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:802861 original size:18 final size:18
Alignment explanation
Indices: 802815--802866 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
802805 ATTCTAAATG
*
802815 TTTACAGTTATCAAATGA
1 TTTACAGTTATCAGATGA
* * *
802833 TTTTCAATTATTAGATGA
1 TTTACAGTTATCAGATGA
802851 TTTACAGTTATCAGAT
1 TTTACAGTTATCAGAT
802867 AATTACAAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (18 bp):
TTTACAGTTATCAGATGA
Found at i:810247 original size:41 final size:41
Alignment explanation
Indices: 810202--810512 Score: 325
Period size: 41 Copynumber: 7.5 Consensus size: 41
810192 CATTTTTTTT
* * *
810202 TATAAAAACGCAACTAAAATAAGAGTCTTTAGCGGCGTTTG
1 TATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG
* *
810243 TATAAAAGCGCCACTAAAGTACGAGTCTTTAGCGGCATTTG
1 TATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG
* * * * *
810284 TATAAAAATGACAGTAAAGTATGAGTCTTTAGCGGCATTTG
1 TATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG
* ** * * * * *
810325 TATAAAAACACCACTAAAACATGAGTTTTTAGTGACATTTG
1 TATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG
** * *
810366 TATAAAAACGCCACTACTGTATGAGTCTATAGCGGCGTTTG
1 TATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG
* * * *
810407 TAAACACAAACGCCACTAAAGTACGAGTATATAACGGCGTTTG
1 TATA-A-AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG
* * * * *
810450 TATCAAAACGCCACTAAAATACGTGTCTATAGCGGCGTTTT
1 TATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG
810491 TATAAAAACGCCACTAAAGTAC
1 TATAAAAACGCCACTAAAGTAC
810513 TACTCTGTCA
Statistics
Matches: 224, Mismatches: 44, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
41 189 0.84
42 2 0.01
43 33 0.15
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (41 bp):
TATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG
Found at i:810527 original size:41 final size:41
Alignment explanation
Indices: 810414--810634 Score: 116
Period size: 41 Copynumber: 5.4 Consensus size: 41
810404 TTGTAAACAC
* * * * * * *
810414 AAACGCCACTAAAGTACGAGTATATAACGGCGTTTGTATCA
1 AAACGCCACTAAAGTACTACTCTGTCACGGCGTTTTTATAA
* * *
810455 AAACGCCACTAAAATACGT-GTCTAT-AGCGGCGTTTTTATAA
1 AAACGCCACTAAAGTAC-TACTCTGTCA-CGGCGTTTTTATAA
*
810496 AAACGCCACTAAAGTACTACTCTGTCACGGCG-TTTGATGAAA
1 AAACGCCACTAAAGTACTACTCTGTCACGGCGTTTTTAT--AA
* ** * *
810538 AAATGCCACTATGTGTGCACATA-T-TG-CA--GCGTTTGTACAA
1 AAACGCCACTA-AAGT--AC-TACTCTGTCACGGCGTTTTTATAA
* * **
810578 AAACGCCGCTAAAGTACTACTCTGTCGCAACGTTTTGTATAA
1 AAACGCCACTAAAGTACTACTCTGTCACGGCGTTTT-TATAA
*
810620 AAACGCCGCTAAAGT
1 AAACGCCACTAAAGT
810635 TACCATTTTA
Statistics
Matches: 140, Mismatches: 23, Indels: 33
0.71 0.12 0.17
Matches are distributed among these distances:
36 2 0.01
37 3 0.02
38 2 0.01
39 3 0.02
40 18 0.13
41 66 0.47
42 35 0.25
43 4 0.03
44 2 0.01
45 3 0.02
46 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (41 bp):
AAACGCCACTAAAGTACTACTCTGTCACGGCGTTTTTATAA
Found at i:814888 original size:36 final size:38
Alignment explanation
Indices: 814812--814889 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 38
814802 AACAAGTTGG
* * * *
814812 AAAATTTTTATATATTTTCTTTAAAAATTTAAATTCAT
1 AAAATTTATATATATATTCTTTAAAAATTAAAAATCAT
814850 AAAATTTATATA-ATATT-TTTACAAAATTAAAAAT-AT
1 AAAATTTATATATATATTCTTTA-AAAATTAAAAATCAT
814886 AAAA
1 AAAA
814890 AGCTTTAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
36 10 0.29
37 14 0.40
38 11 0.31
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (38 bp):
AAAATTTATATATATATTCTTTAAAAATTAAAAATCAT
Done.