Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008014.1 Hibiscus syriacus cultivar Beakdansim tig00110480_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: 624021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:467782 original size:32 final size:30
Alignment explanation
Indices: 467683--467791 Score: 114
Period size: 30 Copynumber: 3.6 Consensus size: 30
467673 AATATCACCG
** * *
467683 TTTTATAAATAATTAACAGAATGTCA-TCTT
1 TTTTA-AAATAATTCCCAAAATGTCATTTTT
*
467713 TTATAAAA-AATTCCCAAAATGTCATTTTT
1 TTTTAAAATAATTCCCAAAATGTCATTTTT
*
467742 TTTTAAAATAATTCTCAAAATGTCACTTTTT
1 TTTTAAAATAATTCCCAAAATGTCA-TTTTT
*
467773 TTTTCAAAATAATTTCCAA
1 TTTT-AAAATAATTCCCAA
467792 GATATCACTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
28 13 0.20
29 13 0.20
30 19 0.29
31 9 0.14
32 12 0.18
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.44
Consensus pattern (30 bp):
TTTTAAAATAATTCCCAAAATGTCATTTTT
Found at i:467800 original size:32 final size:31
Alignment explanation
Indices: 467711--467800 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 31
467701 GAATGTCATC
* * *
467711 TTTTATAAAA-AATTCCCAAAATGTCA-TTT
1 TTTTTTAAAATAATTCTCAAAATATCACTTT
*
467740 TTTTTTAAAATAATTCTCAAAATGTCACTTT
1 TTTTTTAAAATAATTCTCAAAATATCACTTT
*
467771 TTTTTTCAAAATAATT-TCCAAGATATCACT
1 TTTTTT-AAAATAATTCT-CAAAATATCACT
467801 GGGTCGGGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
29 9 0.17
30 15 0.28
31 10 0.19
32 19 0.36
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTTTTAAAATAATTCTCAAAATATCACTTT
Found at i:472045 original size:26 final size:26
Alignment explanation
Indices: 472015--472068 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
472005 TGCAAAAATC
472015 GAAAGAGTTGAATCTGCACGTAAACT
1 GAAAGAGTTGAATCTGCACGTAAACT
*
472041 GAAAGAGTTGATTCTGCACGTAAACT
1 GAAAGAGTTGAATCTGCACGTAAACT
472067 GA
1 GA
472069 GCTGTTTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAGTTGAATCTGCACGTAAACT
Found at i:475250 original size:57 final size:57
Alignment explanation
Indices: 475085--475254 Score: 190
Period size: 57 Copynumber: 3.0 Consensus size: 57
475075 ATTTCTTTGT
* ** *
475085 TTTGCAATGGATT-AA-GCTCTTCCTCCTTATCCACTTCATCTTTTATTGCTT--CTTCG
1 TTTGCAATGGATTCAATGC-CTT-CT-CATATCCACTTCATCTTTTATCACTTGAATTCG
*
475141 TTTTGCAATGGATTCAATGCC-TCTTCATTATCCACTTCATCGTTTATCACTTGAATTC-
1 -TTTGCAATGGATTCAATGCCTTC-TCA-TATCCACTTCATCTTTTATCACTTGAATTCG
475199 TTTGCAATGGATTCAATGCCTTCTCGATATCCACTTCATCTTTTATCACTTGAATT
1 TTTGCAATGGATTCAATGCCTTCTC-ATATCCACTTCATCTTTTATCACTTGAATT
475255 TCTTCGATTT
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
56 2 0.02
57 86 0.87
58 6 0.06
59 5 0.05
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.44
Consensus pattern (57 bp):
TTTGCAATGGATTCAATGCCTTCTCATATCCACTTCATCTTTTATCACTTGAATTCG
Found at i:476117 original size:23 final size:23
Alignment explanation
Indices: 476091--476138 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
476081 ATAAAGTACA
*
476091 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
476114 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
476137 AT
1 AT
476139 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:476544 original size:23 final size:23
Alignment explanation
Indices: 476518--476590 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
476508 ACACTTTACA
*
476518 ATATAACCACTACCTATTACATT
1 ATATAACGACTACCTATTACATT
476541 ATATAAACGA-TACCTATTACATT
1 ATAT-AACGACTACCTATTACATT
* * *
476564 ATATAAGGGCTACCTATTACATC
1 ATATAACGACTACCTATTACATT
476587 ATAT
1 ATAT
476591 GTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.07
23 37 0.84
24 4 0.09
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAACGACTACCTATTACATT
Found at i:476561 original size:44 final size:45
Alignment explanation
Indices: 476495--476590 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 45
476485 ATGGACACTT
* *
476495 TTATAAAAAGGATACACTTTACA-ATATAACCACTACCTATTACA
1 TTATATAAACGATACACTTTACATATATAACCACTACCTATTACA
***
476539 TTATATAAACGATAC-CTATTACATTATATAAGGGCTACCTATTACA
1 TTATATAAACGATACACT-TTACA-TATATAACCACTACCTATTACA
*
476585 TCATAT
1 TTATAT
476591 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
43 2 0.05
44 18 0.42
46 23 0.53
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (45 bp):
TTATATAAACGATACACTTTACATATATAACCACTACCTATTACA
Found at i:477048 original size:39 final size:39
Alignment explanation
Indices: 476994--477080 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
476984 TCAAGTTGTA
*
476994 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
477033 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
477072 GATTTTGAT
1 GATTTTGAT
477081 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:477363 original size:18 final size:18
Alignment explanation
Indices: 477340--477376 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
477330 CGAAATATAT
477340 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
477358 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
477376 A
1 A
477377 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:477705 original size:25 final size:25
Alignment explanation
Indices: 477671--477721 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
477661 TTTTTCCAAA
*
477671 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
477696 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
477721 T
1 T
477722 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:477981 original size:21 final size:22
Alignment explanation
Indices: 477956--478007 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
477946 ACACTTTACA
*
477956 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
477979 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
478002 ATATAA
1 ATATAA
478008 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:477992 original size:23 final size:23
Alignment explanation
Indices: 477966--478028 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
477956 ATATAACCAC
477966 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
477989 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
478012 TACCTATTACATCATAT
1 TACCTATTACATTATAT
478029 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:479516 original size:3 final size:3
Alignment explanation
Indices: 479508--479594 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
479498 ACTTGTTTGG
* * * **
479508 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
479556 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
479595 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:479531 original size:18 final size:18
Alignment explanation
Indices: 479508--479609 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
479498 ACTTGTTTGG
479508 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
479526 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
479544 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
479562 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
479580 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
479598 AGCTTCATCTTC
1 ATCATCATCTTC
479610 TGCGACCGCT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:479575 original size:42 final size:42
Alignment explanation
Indices: 479516--479606 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
479506 GGATCATCAT
*
479516 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
479558 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
479600 CTTCATC
1 CTTCATC
479607 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:481493 original size:19 final size:19
Alignment explanation
Indices: 481447--481495 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
481437 TTATATTCAC
*
481447 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
481466 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
481485 ATACAAAATTA
1 ATACAAAATTA
481496 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:483322 original size:33 final size:33
Alignment explanation
Indices: 483285--483350 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
483275 CATCTTAATA
*
483285 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
483318 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
483351 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:483424 original size:21 final size:22
Alignment explanation
Indices: 483400--483448 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
483390 AGTGTATCTT
*
483400 CGACTCT-CTCAAGTTTCTCTA
1 CGACTCTGATCAAGTTTCTCTA
*
483421 CGACT-TGATCAAGTTTCTCTT
1 CGACTCTGATCAAGTTTCTCTA
483442 CGACTCT
1 CGACTCT
483449 TGATTGTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.18, C:0.31, G:0.12, T:0.39
Consensus pattern (22 bp):
CGACTCTGATCAAGTTTCTCTA
Found at i:485697 original size:17 final size:18
Alignment explanation
Indices: 485675--485717 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
485665 ATATATCCGG
485675 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
485692 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
485712 TATCAT
1 TATCAT
485718 ATTTTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:485725 original size:20 final size:19
Alignment explanation
Indices: 485680--485725 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
485670 TCCGGTATCA
485680 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
485699 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
485720 TTTTAC
1 TTTTAC
485726 TTGTTATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:485874 original size:20 final size:20
Alignment explanation
Indices: 485848--485893 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
485838 CACTTTTAAA
485848 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
485867 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
485888 TTTACC
1 TTTACC
485894 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:486391 original size:228 final size:225
Alignment explanation
Indices: 485959--486404 Score: 768
Period size: 228 Copynumber: 2.0 Consensus size: 225
485949 TTAAAACTGC
485959 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
486024 TTAATTTAATAATTTAATTTACACAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATTT
66 TTAATTTAATAATTTAATTTACACAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTT
* *
486089 AGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAGT
131 AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAGT
*
486154 ATGACACTTTTATAAAAATGATATATATTT
196 ATGACACTTTTATAAAAAGGATATATATTT
*
486184 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
486249 ATTAATTTAATAATTTCATTTACACTAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTTAATAATTTAATTTACAC--AAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
486314 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAATA
128 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATA
486378 AGTATGGACACTTTTATAAAAAGGATA
193 AGTAT-GACACTTTTATAAAAAGGATA
486405 GATAATTTAC
Statistics
Matches: 208, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
225 4 0.02
226 83 0.40
227 16 0.08
228 105 0.50
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (225 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTT
AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAGT
ATGACACTTTTATAAAAAGGATATATATTT
Found at i:490905 original size:14 final size:14
Alignment explanation
Indices: 490886--490925 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
490876 ATGGGCAAAT
*
490886 TTTGAAAAACTATG
1 TTTGAAAAACAATG
490900 TTTG-AAAACAATG
1 TTTGAAAAACAATG
*
490913 TTTGAAAATCAAT
1 TTTGAAAAACAAT
490926 ACATAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (14 bp):
TTTGAAAAACAATG
Found at i:491462 original size:22 final size:22
Alignment explanation
Indices: 491412--491468 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 22
491402 CCCTCAGGGA
*
491412 GGTATCGACACCCATTCAAAGAG
1 GGTATCGATACCCATTCAAAG-G
*
491435 GGTATCGGTACCCATTCAAAGG
1 GGTATCGATACCCATTCAAAGG
491457 GGTATCGATACC
1 GGTATCGATACC
491469 TAACGCACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (22 bp):
GGTATCGATACCCATTCAAAGG
Found at i:491865 original size:15 final size:15
Alignment explanation
Indices: 491847--491880 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
491837 ACATCTTCTT
*
491847 TAATGACATGATCTC
1 TAATGAAATGATCTC
*
491862 TAATGAAATGATGTC
1 TAATGAAATGATCTC
491877 TAAT
1 TAAT
491881 TTCAATGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (15 bp):
TAATGAAATGATCTC
Found at i:492840 original size:13 final size:13
Alignment explanation
Indices: 492822--492846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
492812 AATGAATTTT
492822 AAGATTTTCTAAA
1 AAGATTTTCTAAA
492835 AAGATTTTCTAA
1 AAGATTTTCTAA
492847 GTATATTCGA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:499123 original size:103 final size:103
Alignment explanation
Indices: 498939--499156 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
498929 GTCGAGGGTC
498939 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
499004 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
499042 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
499107 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
499145 TATGTGGTCCTT
1 TATGTGGTCCTT
499157 ATATACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:505016 original size:103 final size:103
Alignment explanation
Indices: 504791--505008 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
504781 GTCGAGGGTC
*
504791 TATGTGATCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
504856 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
504894 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
504959 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
504997 TATGTGGTCCTT
1 TATGTGGTCCTT
505009 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:505091 original size:23 final size:23
Alignment explanation
Indices: 505015--505092 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
505005 CCTTATGGAC
* *
505015 ATTATTATATGGCACTACAGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
505039 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
505062 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
505085 ATTATATG
1 ATTATATG
505093 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:506953 original size:21 final size:21
Alignment explanation
Indices: 506910--506954 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
506900 GATTTCTGGG
* * *
506910 CAAGGGGAATCGGTATCCATT
1 CAAGGGGAACCGATACCCATT
*
506931 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
506952 CAA
1 CAA
506955 ACGACAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:507557 original size:18 final size:18
Alignment explanation
Indices: 507534--507568 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
507524 CTAGGAGATT
507534 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
507552 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
507569 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:507654 original size:21 final size:22
Alignment explanation
Indices: 507625--507668 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
507615 GTTGTATGAT
507625 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
507646 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
507668 A
1 A
507669 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:507901 original size:2 final size:2
Alignment explanation
Indices: 507894--507919 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
507884 GAACATGTGA
507894 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
507920 CTAAGAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:508635 original size:149 final size:149
Alignment explanation
Indices: 508454--508757 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
508444 GAGTCGAGGG
*
508454 TCTACGTGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
508519 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
508584 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
508603 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
508668 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
508733 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
508752 TCTACG
1 TCTACG
508758 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:508780 original size:23 final size:23
Alignment explanation
Indices: 508736--508780 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
508726 ATCATTATAT
*
508736 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
508759 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
508781 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:509496 original size:20 final size:21
Alignment explanation
Indices: 509473--509552 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 21
509463 TTGGTGCAGA
509473 GGGAATCGATACCCCCATGA-
1 GGGAATCGATACCCCCATGAG
* * *
509493 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-ATG-AG
*
509516 GGGAA-CTGATCCCCCCCAT-AG
1 GGGAATC-GAT-ACCCCCATGAG
509537 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
509553 TGGGGTACTG
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
20 19 0.40
21 12 0.25
22 3 0.06
23 9 0.19
24 5 0.10
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAATCGATACCCCCATGAG
Found at i:509551 original size:21 final size:21
Alignment explanation
Indices: 509473--509552 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
509463 TTGGTGCAGA
509473 GGGAATCGATA-CCCCCAT-G
1 GGGAATCGATACCCCCCATAG
* * **
509492 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAATCGATACCCCCCAT--AG
*
509516 GGGAA-CTGATCCCCCCCATAG
1 GGGAATC-GATACCCCCCATAG
509537 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
509553 TGGGGTACTG
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
20 9 0.20
21 20 0.43
22 2 0.04
23 14 0.30
24 1 0.02
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAATCGATACCCCCCATAG
Found at i:511241 original size:18 final size:17
Alignment explanation
Indices: 511203--511237 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
511193 AACAAACGCA
511203 TCAAATGCCTCCATATT
1 TCAAATGCCTCCATATT
511220 TCAAATGCCTCCATATT
1 TCAAATGCCTCCATATT
511237 T
1 T
511238 TCAATCCTTT
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:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (17 bp):
TCAAATGCCTCCATATT
Found at i:514235 original size:20 final size:22
Alignment explanation
Indices: 514190--514247 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
514180 TCATGGGTAG
514190 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
514214 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
514234 TGCATCGATGCACT
1 TGCATCGATGCACT
514248 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:520319 original size:34 final size:30
Alignment explanation
Indices: 520281--520350 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 30
520271 TTTGATATAA
520281 CAATTTAAGGCAAAATGGTTTTTGGACTTGAATT
1 CAATTTAA--CAAAAT-GTTTTTGGACTT-AATT
520315 CAATTT-ACAAAATGTTTTTGGACTTAATT
1 CAATTTAACAAAATGTTTTTGGACTTAATT
*
520344 GAATTTA
1 CAATTTA
520351 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 9 0.26
30 12 0.35
31 6 0.18
33 1 0.03
34 6 0.18
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (30 bp):
CAATTTAACAAAATGTTTTTGGACTTAATT
Found at i:520361 original size:29 final size:30
Alignment explanation
Indices: 520291--520350 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
520281 CAATTTAAGG
520291 CAAAATGGTTTTTGGACTTGAATTCAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTCAATTTA
*
520322 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTCAATTTA
520351 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTCAATTTA
Found at i:520742 original size:20 final size:21
Alignment explanation
Indices: 520713--520786 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 21
520703 GCAACCTTCG
*
520713 TGCATGGATGCACA-ACAAGA
1 TGCATCGATGCACAGACAAGA
* **
520733 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAGACAAGA
* *
520754 TGCATCGATGAACAGA-AGGA
1 TGCATCGATGCACAGACAAGA
*
520774 TGCATTGATGCAC
1 TGCATCGATGCAC
520787 TAATTGCATT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 26 0.60
21 17 0.40
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (21 bp):
TGCATCGATGCACAGACAAGA
Found at i:520832 original size:20 final size:21
Alignment explanation
Indices: 520807--520860 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
520797 CGGTGTTTGA
520807 GTGCATGGATGCACT-G-CATG
1 GTGCATGGATGCACTAGACA-G
*
520827 GTGCATCGATGCACTAGTACAG
1 GTGCATGGATGCACTAG-ACAG
520849 GTGCATGGATGC
1 GTGCATGGATGC
520861 GCGGATGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 1 0.03
22 12 0.41
23 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTAGACAG
Found at i:521004 original size:29 final size:31
Alignment explanation
Indices: 520972--521030 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 31
520962 AAACTTTGAA
520972 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
521001 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
521031 TCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:522323 original size:19 final size:20
Alignment explanation
Indices: 522280--522327 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
522270 TCTAAATCCT
*
522280 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
522300 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
522319 TTTTCAAAA
1 TTTTCAAAA
522328 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:534551 original size:21 final size:20
Alignment explanation
Indices: 534465--534663 Score: 114
Period size: 21 Copynumber: 9.8 Consensus size: 20
534455 AAATGACCAA
**
534465 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
534484 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
534504 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
534524 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
534545 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
534566 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
534586 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* **
534607 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
534627 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
534648 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
534664 ACACATAAAT
Statistics
Matches: 134, Mismatches: 39, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
19 16 0.12
20 56 0.42
21 62 0.46
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:534613 original size:20 final size:20
Alignment explanation
Indices: 534465--534682 Score: 113
Period size: 20 Copynumber: 10.8 Consensus size: 20
534455 AAATGACCAA
534465 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAATAT
* **
534484 AAAAATCGCAACGCG-ATCCC
1 CAAAATCGCAACGCGAAT-AT
* ** * *
534504 CAGAATCGCAAATC-AGTTT
1 CAAAATCGCAACGCGAATAT
* *
534523 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGAAT-AT
* *
534545 GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGAATA-T
* ** * *
534565 ACAAATTCGCATTGCGATTTT
1 -CAAAATCGCAACGCGAATAT
534586 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* ** * *
534607 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGAATAT
534627 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* *
534648 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
534667 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
534683 TATCCGTAAA
Statistics
Matches: 146, Mismatches: 42, Indels: 21
0.70 0.20 0.10
Matches are distributed among these distances:
18 1 0.01
19 15 0.10
20 69 0.47
21 58 0.40
22 3 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:534625 original size:41 final size:41
Alignment explanation
Indices: 534546--534657 Score: 174
Period size: 41 Copynumber: 2.7 Consensus size: 41
534536 GCGATTCTTG
*
534546 AAAATCGCAATGCG-ATA-GTACAAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATG-A-AAA-TCGCATTGCGATTTTCC
534588 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
534629 AAAATCGCAACGCGAATATGAAAATCGCA
1 AAAATCGCAACGCGAATATGAAAATCGCA
534658 ACGCGAACAC
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
41 46 0.69
42 16 0.24
43 4 0.06
44 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
Found at i:534692 original size:20 final size:20
Alignment explanation
Indices: 534630--534823 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
534620 CGATTTTCCA
* ** *
534630 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
534650 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
534670 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
534690 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
534710 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
534730 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
534750 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
534770 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
534790 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
534811 AAATCGCAACGCG
1 AAATCGCAACGCG
534824 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:534722 original size:60 final size:60
Alignment explanation
Indices: 534630--534823 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
534620 CGATTTTCCA
* ** * *
534630 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
534690 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
534750 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
534811 AAATCGCAACGCG
1 AAATCGCAACGCG
534824 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:535345 original size:21 final size:20
Alignment explanation
Indices: 535319--535426 Score: 95
Period size: 21 Copynumber: 5.7 Consensus size: 20
535309 TTTGCAGAAG
535319 AATCGCAACGAGATAAATGAA
1 AATCGCAACGAGA-AAATGAA
* *
535340 AATCGCAACGAGAGAATGAC
1 AATCGCAACGAGAAAATGAA
**
535360 TGTCGCAACGAGAGAAATGAA
1 AATCGCAACGAGA-AAATGAA
*
535381 AAGCGCAACGAG---A-G--
1 AATCGCAACGAGAAAATGAA
*
535395 AATCGCAACGCG-AAATGAA
1 AATCGCAACGAGAAAATGAA
535414 AATCGCAACGAGA
1 AATCGCAACGAGA
535427 GAATCGCAAC
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.16
20 16 0.24
21 27 0.40
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
AATCGCAACGAGAAAATGAA
Found at i:535378 original size:41 final size:37
Alignment explanation
Indices: 535320--535437 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 37
535310 TTGCAGAAGA
*
535320 ATCGCAACGAGATAAATGAAAATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
*
535357 GACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAGAG-A-
1 -A---TCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
*
535396 ATCGCAAC--GCGAAATGAAAATCGCAACGAGAG-A-
1 ATCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
535429 ATCGCAACG
1 ATCGCAACG
535438 CGAAACCAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
33 31 0.43
35 7 0.10
38 2 0.03
40 1 0.01
41 31 0.43
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (37 bp):
ATCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
Found at i:535403 original size:14 final size:14
Alignment explanation
Indices: 535384--535437 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
535374 AAATGAAAAG
535384 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
535398 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
535417 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
535431 CGCAACG
1 CGCAACG
535438 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:535449 original size:33 final size:33
Alignment explanation
Indices: 535379--535453 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
535369 GAGAGAAATG
* **
535379 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
535412 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
535445 AAAATCGCA
1 AAAATCGCA
535454 TTGCGATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:535501 original size:33 final size:33
Alignment explanation
Indices: 535454--535567 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
535444 CAAAATCGCA
* *
535454 TTGCGA-TTTCATTTCGCGTTACGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
535486 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
535519 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
535552 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
535568 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 6 0.08
33 69 0.92
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:535508 original size:19 final size:18
Alignment explanation
Indices: 535449--535545 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
535439 GAAACCAAAA
*
535449 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
* *
535467 TCGCGTTACGA-TTC-TG
1 TCGCGTTGCGATTTCATT
535483 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
535500 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
* *
535514 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATT
535533 TCGCGTTGCGATT
1 TCGCGTTGCGATT
535546 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 17 0.27
15 1 0.02
16 7 0.11
17 8 0.13
18 9 0.15
19 20 0.32
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:535522 original size:14 final size:14
Alignment explanation
Indices: 535503--535559 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
535493 TTTCATTTCG
535503 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
535517 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
535534 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
535550 CGTTGCGATT
1 CGTTGCGATT
535560 TTCATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 5 0.13
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:537848 original size:182 final size:183
Alignment explanation
Indices: 537258--538179 Score: 1707
Period size: 182 Copynumber: 5.0 Consensus size: 183
537248 TAGATTGCTT
* *
537258 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
537323 TTTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-
537387 GTGTATTCTTTAACACTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
537441 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
537504 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-
537568 GTGTATTCTTTAACACTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
537622 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
537687 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACG
537751 TGTATTCTTTAACACTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
537804 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
537869 -TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-
537933 GTGTATTCTTTAACACTG-AATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
537986 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
538051 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-
538116 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTC-TTTGGTTGAA
130 GTGTATTCTTTAACAC--TGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
538171 AGTAAATTT
1 AGTAAATTT
538180 ATCCATTCAA
Statistics
Matches: 727, Mismatches: 2, Indels: 18
0.97 0.00 0.02
Matches are distributed among these distances:
181 222 0.31
182 238 0.33
183 190 0.26
184 32 0.04
185 21 0.03
186 24 0.03
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (183 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACG
TGTATTCTTTAACACTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:538263 original size:19 final size:19
Alignment explanation
Indices: 538223--538351 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
538213 TAGTTTACTT
* *
538223 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
538243 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
538262 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
538281 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
538295 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
538314 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
538328 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
538347 TCGCA
1 TCGCA
538352 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:538302 original size:33 final size:32
Alignment explanation
Indices: 538259--538351 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
538249 CGCGAAACCA
**
538259 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
538291 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
538324 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
538352 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:538349 original size:52 final size:52
Alignment explanation
Indices: 538223--538351 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
538213 TAGTTTACTT
**
538223 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
538275 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
538328 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
538352 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:538369 original size:19 final size:19
Alignment explanation
Indices: 538347--538481 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
538337 GAAACCAAAA
*
538347 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
538366 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
538382 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
538399 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
538415 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
538432 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
538451 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
538471 TCGTGTTGCGA
1 TCGCGTTGCGA
538482 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:538388 original size:14 final size:14
Alignment explanation
Indices: 538369--538425 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
538359 TTTCATTTCG
538369 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
538383 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
538400 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
538416 CGTTGCGATT
1 CGTTGCGATT
538426 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:538394 original size:33 final size:33
Alignment explanation
Indices: 538352--538444 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
538342 CAAAATCGCA
*
538352 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
538385 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
538418 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
538445 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:539413 original size:14 final size:14
Alignment explanation
Indices: 539394--539429 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
539384 ATTGTTTAAT
539394 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
539408 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
539422 TGATTTGT
1 TGATTTGT
539430 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:539552 original size:19 final size:18
Alignment explanation
Indices: 539536--539632 Score: 121
Period size: 19 Copynumber: 5.4 Consensus size: 18
539526 AAAAATGACT
539536 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
539555 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
539573 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
539587 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
539606 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
539626 ATCGCAA
1 ATCGCAA
539633 CGAGAGAACC
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
14 8 0.11
15 1 0.01
16 8 0.11
17 1 0.01
18 9 0.13
19 27 0.39
20 16 0.23
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:539612 original size:51 final size:53
Alignment explanation
Indices: 539536--539650 Score: 207
Period size: 51 Copynumber: 2.2 Consensus size: 53
539526 AAAAATGACT
539536 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
539587 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
539640 ACCGCAATGCG
1 ATCGCAATGCG
539651 TTTATAATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 29 0.48
52 6 0.10
53 26 0.43
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:539694 original size:33 final size:33
Alignment explanation
Indices: 539657--539809 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
539647 TGCGTTTATA
539657 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
539690 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
539730 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
539761 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
539794 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
539810 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:539703 original size:19 final size:19
Alignment explanation
Indices: 539679--539894 Score: 247
Period size: 19 Copynumber: 12.4 Consensus size: 19
539669 GATTCTCTCG
539679 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
539698 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
539717 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
539731 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
539750 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
539769 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
539783 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
539802 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
539821 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
539835 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
539854 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
539868 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
539887 TTGCGATT
1 TTGCGATT
539895 GTAATTTTCG
Statistics
Matches: 169, Mismatches: 8, Indels: 40
0.78 0.04 0.18
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 23 0.14
19 94 0.56
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:539735 original size:52 final size:52
Alignment explanation
Indices: 539657--539866 Score: 411
Period size: 52 Copynumber: 4.0 Consensus size: 52
539647 TGCGTTTATA
539657 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
539709 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
539761 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
539813 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
539865 AT
1 AT
539867 GTTGGGATTT
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 156 1.00
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:539839 original size:33 final size:33
Alignment explanation
Indices: 539698--539894 Score: 195
Period size: 33 Copynumber: 5.8 Consensus size: 33
539688 TCATTTCGCA
*
539698 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
539731 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
539767 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
539802 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
539835 TTGCGATTTTCATTTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
* *
539868 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
539895 GTAATTTTCG
Statistics
Matches: 137, Mismatches: 15, Indels: 24
0.78 0.09 0.14
Matches are distributed among these distances:
31 9 0.07
32 5 0.04
33 91 0.66
34 1 0.01
35 5 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.07
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:542391 original size:24 final size:24
Alignment explanation
Indices: 542357--542403 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
542347 CTGAAACATC
542357 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
542381 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
542404 GACCAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:543107 original size:20 final size:20
Alignment explanation
Indices: 543079--543328 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
543069 AAATTTCAGT
* *
543079 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
543099 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
543119 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
543139 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
543159 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
543179 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
543199 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
543219 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
543239 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
543259 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
543279 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
543299 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
543319 GTTGCGATTT
1 GTTGCGATTT
543329 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:543345 original size:21 final size:21
Alignment explanation
Indices: 543315--543397 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
543305 ATTTTCATAT
*
543315 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
543336 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
543357 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
543378 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
543398 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:543388 original size:42 final size:43
Alignment explanation
Indices: 543295--543393 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
543285 ATTTATGTGT
* *
543295 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
543336 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
543378 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
543394 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:552095 original size:8 final size:8
Alignment explanation
Indices: 552082--552114 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
552072 CTCATTTTCA
552082 GAGAATTT
1 GAGAATTT
552090 GAGAATTT
1 GAGAATTT
*
552098 -AGAGTTT
1 GAGAATTT
552105 GAGAATTT
1 GAGAATTT
552113 GA
1 GA
552115 AAGCTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (8 bp):
GAGAATTT
Found at i:552431 original size:128 final size:128
Alignment explanation
Indices: 552210--552801 Score: 1040
Period size: 128 Copynumber: 4.6 Consensus size: 128
552200 GTGCGTTCCT
* *
552210 GGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTTCCCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
* *
552275 CCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGTGGACTTGAAGGCACGTTCAC
66 CCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCACGTTCTC
*
552338 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAGTCATGT
1 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
*
552403 CCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCTC
66 CCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCACGTTCTC
* *
552466 GGGGACGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATATCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
552531 CCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCACGTTCTC
66 CCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCACGTTCTC
* * *
552594 GGGGGCGCGCCTTCCATTATTTTTTCAGAGAATATGTTATCATTACCCTATTATATCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
* * *
552659 CCCTCGGGGACACTATTGATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCC
66 CCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCACGTTCTC
*
552722 GGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
*
552787 CCCTCGAGGACACTA
66 CCCTCGGGGACACTA
552802 GATGGATTGT
Statistics
Matches: 443, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 443 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (128 bp):
GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
CCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCACGTTCTC
Found at i:553156 original size:34 final size:34
Alignment explanation
Indices: 553118--553225 Score: 153
Period size: 34 Copynumber: 3.1 Consensus size: 34
553108 TAAGTTAAAA
* *
553118 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
553152 TTTAATTTTAAATTTCGAATAATATTATTTTTTAT
1 TTTAATTTTAAATTTCGAATAATA-TAATTTATAT
* *
553187 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
553221 TTTAA
1 TTTAA
553226 AAACATTTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
34 34 0.52
35 31 0.48
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:553180 original size:28 final size:28
Alignment explanation
Indices: 553149--553226 Score: 68
Period size: 35 Copynumber: 2.5 Consensus size: 28
553139 CTATAATTTA
553149 TATTTTAATTTTAAATTTCGAATAATAT
1 TATTTTAATTTTAAATTTCGAATAATAT
553177 TATTTTTTATTTTTATTTTAAATTTCGAATAATAT
1 TA--TTTTA-----ATTTTAAATTTCGAATAATAT
*
553212 AATTTGT-ATTTTAAA
1 TATTT-TAATTTTAAA
553227 AACATTTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 16
0.71 0.02 0.28
Matches are distributed among these distances:
28 10 0.24
30 5 0.12
33 3 0.07
34 1 0.02
35 22 0.54
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.58
Consensus pattern (28 bp):
TATTTTAATTTTAAATTTCGAATAATAT
Found at i:553776 original size:21 final size:20
Alignment explanation
Indices: 553749--553860 Score: 143
Period size: 21 Copynumber: 5.3 Consensus size: 20
553739 GGTATAAAAC
*
553749 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
*
553769 CCTGGCGGGCTAGGAATATAA
1 CCT-GCGGGCTAGGAATGTAA
*
553790 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
553811 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
553832 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
553853 CCCTGCGG
1 -CCTGCGG
553861 AGATGGCATA
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
20 6 0.07
21 70 0.85
22 6 0.07
ACGTcount: A:0.21, C:0.26, G:0.35, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:553809 original size:42 final size:42
Alignment explanation
Indices: 553746--553854 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
553736 TATGGTATAA
* *
553746 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATAT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATAT
*
553788 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATAT
553830 AACCCTGCGGGCTCGGAATGTAACC
1 AACCCTGCGGGCTCGGAATGTAACC
553855 CTGCGGAGAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.18
Consensus pattern (42 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATAT
Found at i:553890 original size:21 final size:21
Alignment explanation
Indices: 553864--553911 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
553854 CCTGCGGAGA
*
553864 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
553885 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
553906 GGGCAT
1 TGGCAT
553912 GTACCCCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.25
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:555658 original size:19 final size:19
Alignment explanation
Indices: 555634--555692 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
555624 TTAATAATTC
*
555634 TAAATAAATAATAATTATA
1 TAAATAAATAATATTTATA
*
555653 TAAAT--ATTAT-TTTA-A
1 TAAATAAATAATATTTATA
*
555668 TAAAAAAATAATATTTATA
1 TAAATAAATAATATTTATA
555687 TAAATA
1 TAAATA
555693 TATTAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
15 5 0.16
16 3 0.10
17 8 0.26
18 4 0.13
19 11 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATAAATAATATTTATA
Found at i:555706 original size:15 final size:15
Alignment explanation
Indices: 555672--555709 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
555662 TTTTAATAAA
*
555672 AAAATAATATTTATAT
1 AAAAT-ATATTAATAT
555688 -AAATATATTAATAT
1 AAAATATATTAATAT
555702 AAAATATA
1 AAAATATA
555710 ATAACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATATTAATAT
Found at i:555719 original size:36 final size:33
Alignment explanation
Indices: 555634--555740 Score: 103
Period size: 34 Copynumber: 3.2 Consensus size: 33
555624 TTAATAATTC
* * *
555634 TAAATAAATAATAATTATATAAATATTATT-TTAA
1 TAAAAAAATAATATTTATATAAATA-TATTAAT-A
555668 TAAAAAAATAATATTTATATAAATATATTAATA
1 TAAAAAAATAATATTTATATAAATATATTAATA
* *
555701 TAAAATATAATAACTATTTA-A-AAAAATATTAACA
1 TAAAA-A-AATAA-TATTTATATAAATATATTAATA
555735 TAAAAA
1 TAAAAA
555741 TAAATTTCTT
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
33 11 0.17
34 41 0.64
35 6 0.09
36 6 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (33 bp):
TAAAAAAATAATATTTATATAAATATATTAATA
Found at i:564668 original size:16 final size:16
Alignment explanation
Indices: 564636--564683 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
564626 ATTCAAGTCA
* *
564636 TTTTATGTTCAGTTTG
1 TTTTATGTTCGGATTG
564652 TTTTATGTTCGGATTG
1 TTTTATGTTCGGATTG
* *
564668 TTTCAAGTTCGGATTG
1 TTTTATGTTCGGATTG
564684 CTTCAAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (16 bp):
TTTTATGTTCGGATTG
Found at i:564688 original size:16 final size:16
Alignment explanation
Indices: 564658--564694 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
564648 TTTGTTTTAT
*
564658 GTTCGGATTGTTTCAA
1 GTTCGGATTGCTTCAA
564674 GTTCGGATTGCTTCAA
1 GTTCGGATTGCTTCAA
564690 GTTCG
1 GTTCG
564695 AATCATGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (16 bp):
GTTCGGATTGCTTCAA
Found at i:571043 original size:18 final size:19
Alignment explanation
Indices: 570995--571043 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
570985 CCGTTTGCTC
* *
570995 ATTGCATGTTTGTGCTTGT
1 ATTGCATGTTTTTGCTTAT
* *
571014 AATGCTTGTTTTTG-TTAT
1 ATTGCATGTTTTTGCTTAT
571032 ATTGCATGTTTT
1 ATTGCATGTTTT
571044 ACTCGTATGA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.14, C:0.08, G:0.20, T:0.57
Consensus pattern (19 bp):
ATTGCATGTTTTTGCTTAT
Found at i:575200 original size:265 final size:265
Alignment explanation
Indices: 574690--575200 Score: 961
Period size: 266 Copynumber: 1.9 Consensus size: 265
574680 TATATTAAAA
* *
574690 ATTTTGAGGGAGCACAATTAAATAATTAATAGAAAATACAAATAAAAATTTAAAATAAAACATTT
1 ATTTTGAGGGAGCACAATTAAATAATTAATAGAAAATACAAAGAAAAATCTAAAATAAAACATTT
*
574755 CATAATTTATTAATCAATTTAGAACAAAAATTATAATTTAAAATATTGTTTATAATTATATTATG
66 CATAATTTATTAATCAATTTAGAACAAAAATTATAATTTAAAATATTGTGTATAATTATATTATG
574820 TTTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATATA
131 TTTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATATA
*
574885 TAAACTTATTTTTATTTTTATTTATTTATTTGTTTGTCTTCTCAATTTCCTTAAAAATTTAGAGT
196 TAAACTTATTTTTATTTTTATTTATTTATTTGGTTGTCTTCTCAATTTCCTTAAAAATTTAGAGT
574950 TATAT
261 TATAT
*
574955 ATTTTAGAGGGTGCACAATTAAATAATTAATAGAAAATACAAAGAAAAATCTAAAATAAAACATT
1 ATTTT-GAGGGAGCACAATTAAATAATTAATAGAAAATACAAAGAAAAATCTAAAATAAAACATT
575020 TCATAATTTATTAATCAATTTAGAACAAAAATTATAATTTAAAATATTGTGTATAATTATATTAT
65 TCATAATTTATTAATCAATTTAGAACAAAAATTATAATTTAAAATATTGTGTATAATTATATTAT
575085 G-TTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATAT
130 GTTTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATAT
575149 ATAAACTTATTTTTATTTTTATTTATTTATTTGGTTGTCTTCTCAATTTCCT
195 ATAAACTTATTTTTATTTTTATTTATTTATTTGGTTGTCTTCTCAATTTCCT
575201 AGGATTTTTT
Statistics
Matches: 240, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
265 119 0.50
266 121 0.50
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (265 bp):
ATTTTGAGGGAGCACAATTAAATAATTAATAGAAAATACAAAGAAAAATCTAAAATAAAACATTT
CATAATTTATTAATCAATTTAGAACAAAAATTATAATTTAAAATATTGTGTATAATTATATTATG
TTTTTAAGTAAATAAATAAAAATTATTATTTAAAAATCAAAACACAATATTTATAAATTTATATA
TAAACTTATTTTTATTTTTATTTATTTATTTGGTTGTCTTCTCAATTTCCTTAAAAATTTAGAGT
TATAT
Found at i:577738 original size:19 final size:19
Alignment explanation
Indices: 577695--577740 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
577685 AGATAATCAC
*
577695 ACTTTT-TAAAATTTAAAT
1 ACTTTTATATAATTTAAAT
*
577713 -TTTTTATATAATTTAAAT
1 ACTTTTATATAATTTAAAT
577731 ACTTTTATAT
1 ACTTTTATAT
577741 TTATAGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 8 0.35
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
ACTTTTATATAATTTAAAT
Found at i:583181 original size:184 final size:183
Alignment explanation
Indices: 582715--583107 Score: 457
Period size: 184 Copynumber: 2.0 Consensus size: 183
582705 TCTCGGGATT
* * * * * *
582715 TTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATTTTTATATTATTATTAGTTTTT
1 TTAG-TTTAATTA-CCTTTTATATTAC---AT-ATATTTATA-TATCATACTATTATTAGTATTA
* * *
582780 TTTACACATTCGTATATATTTATTATTAGTATAGTATTA-TTCACTTATATGTTATATTATATAT
59 TATACA-A-TCGTATACATTTATTATTAGTATAGTATTATTTCA-TT-TATG---T-GT-TATAT
582844 ATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTACTTCTTTTATTATTTA
115 ATATATATA--TATATATGTACACATTTTGTATTTTACCCTATTTGTTACTTCTTTTATTATTTA
582909 TTTACA
178 TTTACA
* * *
582915 TTAGTTTTAATTACCTTTTATATTACATATATTTATATATTATACTATTATTAGTTTTTTATACA
1 TTAG-TTTAATTACCTTTTATATTACATATATTTATATATCATACTATTATTAGTATTATATACA
*
582980 TTCGTATACATTTATTATTAGTATAGTATTATTTCATTTATGTGTTATATATATATATATATATA
65 ATCGTATACATTTATTATTAGTATAGTATTATTTCATTTATGTGTTATATATATATATATATATA
*
583045 TGTACACATTTTGTATTTTACCCTATTTTTTACTTCTTTATTATTATTTATTTACA
130 TGTACACATTTTGTATTTTACCCTATTTGTTACTTC-TT-TTATTATTTATTTACA
583101 TTA-TTTA
1 TTAGTTTA
583108 TTTTTTTTTC
Statistics
Matches: 182, Mismatches: 8, Indels: 22
0.86 0.04 0.10
Matches are distributed among these distances:
184 45 0.25
185 2 0.01
186 33 0.18
187 1 0.01
188 1 0.01
191 4 0.02
192 31 0.17
193 4 0.02
194 25 0.14
195 9 0.05
196 2 0.01
199 12 0.07
200 13 0.07
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (183 bp):
TTAGTTTAATTACCTTTTATATTACATATATTTATATATCATACTATTATTAGTATTATATACAA
TCGTATACATTTATTATTAGTATAGTATTATTTCATTTATGTGTTATATATATATATATATATAT
GTACACATTTTGTATTTTACCCTATTTGTTACTTCTTTTATTATTTATTTACA
Found at i:583301 original size:14 final size:14
Alignment explanation
Indices: 583261--583292 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
583251 TATATATATA
583261 TATTTTC-TTATTT
1 TATTTTCATTATTT
583274 TATTTTCATTATTT
1 TATTTTCATTATTT
583288 T-TTTT
1 TATTTT
583293 ATATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTTTCATTATTT
Found at i:594838 original size:105 final size:105
Alignment explanation
Indices: 594656--595246 Score: 1146
Period size: 105 Copynumber: 5.6 Consensus size: 105
594646 AGGTTTTACC
*
594656 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
594721 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
594761 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
594826 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
594866 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
594931 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
594971 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
595036 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
595076 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
595141 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
*
595181 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
595246 A
66 A
595247 TGAGGGAGCC
Statistics
Matches: 482, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 482 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
Found at i:596815 original size:2 final size:2
Alignment explanation
Indices: 596803--596844 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
596793 ATTTATGTGT
*
596803 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
596844 T
1 T
596845 GTACACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:597104 original size:15 final size:14
Alignment explanation
Indices: 597062--597099 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
597052 TATATATATA
597062 TATTTTC-TTATTT
1 TATTTTCATTATTT
597075 TATTTTCATTATTT
1 TATTTTCATTATTT
597089 T-TTTT-ATTATT
1 TATTTTCATTATT
597100 ATTTTACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 11 0.46
14 7 0.29
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTCATTATTT
Found at i:603020 original size:25 final size:24
Alignment explanation
Indices: 602945--603045 Score: 77
Period size: 24 Copynumber: 4.2 Consensus size: 24
602935 TTTTTAATAA
*
602945 TTTATAA-ATATTT-T-TTTTTAT
1 TTTATAATATATTTATATTTATAT
**
602966 TTT-TAACCTATTTATATTTATAT
1 TTTATAATATATTTATATTTATAT
*
602989 TTTATAATATATTTATCTTT-TATT
1 TTTATAATATATTTATATTTATA-T
* *
603013 TTTAATAATATACTTTTTATATTATTT
1 TTT-ATAATATA-TTTATAT-TTATAT
603040 TTTATA
1 TTTATA
603046 CTTAATATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.05
21 8 0.13
22 1 0.02
23 11 0.17
24 17 0.27
25 8 0.13
26 8 0.13
27 6 0.10
28 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTATAATATATTTATATTTATAT
Found at i:603032 original size:46 final size:43
Alignment explanation
Indices: 602935--603035 Score: 105
Period size: 46 Copynumber: 2.2 Consensus size: 43
602925 AGTGTCTAAT
* * *
602935 TTTTTAATAATTTATAAATATTTTTTTTTATTTTTAACCTATTTA
1 TTTTT-ATATTTTATAAATATTTTCTTTTATTTTTAA-CTATATA
*
602980 TATTTATATTTTATAATATATTTATCTTTTATTTTTAA-TAATATA
1 TTTTTATATTTTATAA-ATATTT-TCTTTTATTTTTAACT-ATATA
603025 CTTTTTATATT
1 -TTTTTATATT
603036 ATTTTTTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
44 11 0.23
45 14 0.30
46 22 0.47
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (43 bp):
TTTTTATATTTTATAAATATTTTCTTTTATTTTTAACTATATA
Found at i:603035 original size:23 final size:23
Alignment explanation
Indices: 602980--603035 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
602970 AACCTATTTA
*
602980 TATTTATA-TTTTATAATATATT
1 TATTTATATTTTTATAATATACT
*
603002 TATCTTTTATTTTTAATAATATACT
1 TAT-TTATATTTTT-ATAATATACT
603027 T-TTTATATT
1 TATTTATATT
603036 ATTTTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.11
23 10 0.36
24 5 0.18
25 10 0.36
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTATATTTTTATAATATACT
Found at i:603218 original size:30 final size:30
Alignment explanation
Indices: 603184--603288 Score: 113
Period size: 30 Copynumber: 3.3 Consensus size: 30
603174 GTCATTATCC
603184 ATGTATATTGCTATATATATTATATCAACA
1 ATGTATATTGCTATATATATTATATCAACA
** *
603214 ATGTATATTATTGTAT-TATTAATATACATACGAATA
1 ATGTATATTGCTATATATATT-ATAT-CA-AC----A
603250 ATGTATATTGCTATATATATTATATCAACA
1 ATGTATATTGCTATATATATTATATCAACA
603280 ATGTATATT
1 ATGTATATT
603289 ATTATATTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
29 4 0.07
30 27 0.44
31 2 0.03
32 2 0.03
34 2 0.03
35 2 0.03
36 18 0.30
37 4 0.07
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (30 bp):
ATGTATATTGCTATATATATTATATCAACA
Found at i:603253 original size:36 final size:36
Alignment explanation
Indices: 603213--603324 Score: 139
Period size: 36 Copynumber: 3.3 Consensus size: 36
603203 TTATATCAAC
*
603213 AATGTATATTATTGTATTATTAATATACATACGAAT
1 AATGTATATTATTATATTATTAATATACATACGAAT
**
603249 AATGTATATTGCTATATATATT-ATAT-CA-AC----
1 AATGTATATTATTATAT-TATTAATATACATACGAAT
603279 AATGTATATTATTATATTATTAATATACATACGAAT
1 AATGTATATTATTATATTATTAATATACATACGAAT
603315 AATGTATATT
1 AATGTATATT
603325 GCTATGTTAG
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
29 4 0.06
30 19 0.30
31 2 0.03
32 2 0.03
34 2 0.03
35 2 0.03
36 28 0.44
37 4 0.06
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (36 bp):
AATGTATATTATTATATTATTAATATACATACGAAT
Found at i:603290 original size:66 final size:66
Alignment explanation
Indices: 603184--603329 Score: 283
Period size: 66 Copynumber: 2.2 Consensus size: 66
603174 GTCATTATCC
*
603184 ATGTATATTGCTATATATATTATATCAACAATGTATATTATTGTATTATTAATATACATACGAAT
1 ATGTATATTGCTATATATATTATATCAACAATGTATATTATTATATTATTAATATACATACGAAT
603249 A
66 A
603250 ATGTATATTGCTATATATATTATATCAACAATGTATATTATTATATTATTAATATACATACGAAT
1 ATGTATATTGCTATATATATTATATCAACAATGTATATTATTATATTATTAATATACATACGAAT
603315 A
66 A
603316 ATGTATATTGCTAT
1 ATGTATATTGCTAT
603330 GTTAGTAACG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 79 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (66 bp):
ATGTATATTGCTATATATATTATATCAACAATGTATATTATTATATTATTAATATACATACGAAT
A
Found at i:603518 original size:33 final size:34
Alignment explanation
Indices: 603475--603554 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 34
603465 CAATATATCT
*
603475 TTTATAAAAATATAAGATT-TTAGA-TACTATTAAA-
1 TTTA-AAAAATATAA-ATTATTA-ATTAATATTAAAC
*
603509 TTTAAAAAATATCAATTATTAATTAATATTAAAC
1 TTTAAAAAATATAAATTATTAATTAATATTAAAC
603543 TTTAAATAAATA
1 TTTAAA-AAATA
603555 AGAATCACCC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 4 0.10
33 21 0.52
34 10 0.25
35 5 0.12
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (34 bp):
TTTAAAAAATATAAATTATTAATTAATATTAAAC
Found at i:603908 original size:26 final size:26
Alignment explanation
Indices: 603879--603928 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
603869 GACAGATGAA
* *
603879 ATTTAATTATTATATAAGTTTAAAAT
1 ATTTAATTATAATATAAATTTAAAAT
*
603905 ATTTTATTATAATATAAATTTAAA
1 ATTTAATTATAATATAAATTTAAA
603929 CAAACAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTAATTATAATATAAATTTAAAAT
Found at i:609310 original size:14 final size:14
Alignment explanation
Indices: 609291--609320 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
609281 TTTAGATTTT
*
609291 TTAAAATTACATTA
1 TTAAAAATACATTA
609305 TTAAAAATACATTA
1 TTAAAAATACATTA
609319 TT
1 TT
609321 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:609533 original size:17 final size:17
Alignment explanation
Indices: 609504--609536 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
609494 AATTAAAATT
609504 ACAAGACACAATTGAAA
1 ACAAGACACAATTGAAA
609521 ACAAG-CACAAATTGAA
1 ACAAGACAC-AATTGAA
609537 TGAACACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (17 bp):
ACAAGACACAATTGAAA
Found at i:610660 original size:11 final size:11
Alignment explanation
Indices: 610644--610719 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
610634 GAGTTTGAGT
610644 TCGAGCTTGAA
1 TCGAGCTTGAA
610655 TCGAGCTTGAA
1 TCGAGCTTGAA
* **
610666 CCGAGCTCAAA
1 TCGAGCTTGAA
* *
610677 TTCGAGTTTGAGT
1 -TCGAGCTTGA-A
**
610690 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
610702 TCGAGCTTCAA
1 TCGAGCTTGAA
610713 TCGAGCT
1 TCGAGCT
610720 CGAGTCTCGA
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
11 28 0.58
12 19 0.40
13 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:610720 original size:23 final size:23
Alignment explanation
Indices: 610653--610720 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
610643 TTCGAGCTTG
*
610653 AATCGAGCTTGAACCGAGCTCAA
1 AATCGAGCTTGAATCGAGCTCAA
* * *
610676 ATTCGAGTTTGAGTTCGAGCTCAA
1 AATCGAGCTTGA-ATCGAGCTCAA
*
610700 AATCGAGCTTCAATCGAGCTC
1 AATCGAGCTTGAATCGAGCTC
610721 GAGTCTCGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (23 bp):
AATCGAGCTTGAATCGAGCTCAA
Found at i:611459 original size:20 final size:21
Alignment explanation
Indices: 611434--611526 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
611424 TTTTCCCAAT
*
611434 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
611454 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
611475 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
611495 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
611516 TCGCAATGCGA
1 TCGCAATGCGA
611527 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:611479 original size:41 final size:41
Alignment explanation
Indices: 611434--611526 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
611424 TTTTCCCAAT
611434 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
611475 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
611516 TCGCAATGCGA
1 TCGCAATGCGA
611527 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:611539 original size:41 final size:41
Alignment explanation
Indices: 611453--611587 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
611443 GAATAAGTAA
* *
611453 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
611494 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
611535 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
611576 TTCGCAACGCGA
1 ATCGCAACGCGA
611588 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:611540 original size:20 final size:20
Alignment explanation
Indices: 611515--611629 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
611505 AATTGGGAAA
*
611515 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
611535 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
611556 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
611576 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
611596 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
611616 TTCGCAACGCGATA
1 ATCGCAACGCGATA
611630 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:611588 original size:41 final size:41
Alignment explanation
Indices: 611512--611649 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
611502 GCGAATTGGG
* * *
611512 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
611553 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
611595 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
611634 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
611650 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:611842 original size:20 final size:21
Alignment explanation
Indices: 611817--611858 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
611807 CACTCTCTCA
611817 CCCATCTCCGACG-AATCCGT
1 CCCATCTCCGACGAAATCCGT
*
611837 CCCATCTCCGGCGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
611858 C
1 C
611859 TATCTCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.19, C:0.45, G:0.17, T:0.19
Consensus pattern (21 bp):
CCCATCTCCGACGAAATCCGT
Found at i:612159 original size:20 final size:20
Alignment explanation
Indices: 612120--612178 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
612110 GCGATTCTCT
*
612120 CGTTGCGATAGTCGA-ATTCG
1 CGTTGCGATAGTC-ATTTTCG
612140 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
612160 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
612179 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:613518 original size:18 final size:18
Alignment explanation
Indices: 613492--613536 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
613482 TCCACTTCGG
*
613492 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
613510 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
613528 GAGCCATCA
1 GAGCCATCA
613537 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:614052 original size:20 final size:19
Alignment explanation
Indices: 614029--614073 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
614019 TGCAACACGA
614029 AAATGACTATCACAACGCGG
1 AAATGACTATCACAACGC-G
* * *
614049 AAATGGCTATCGCAATGCG
1 AAATGACTATCACAACGCG
614068 AAATGA
1 AAATGA
614074 AAATCGCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (19 bp):
AAATGACTATCACAACGCG
Found at i:614072 original size:19 final size:19
Alignment explanation
Indices: 614029--614087 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
614019 TGCAACACGA
* *
614029 AAATGACTATCACAACGCGG
1 AAATGACTATCGCAATGC-G
*
614049 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAATGCG
**
614068 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAATGCG
614087 A
1 A
614088 TTTGTGTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:614118 original size:14 final size:14
Alignment explanation
Indices: 614099--614156 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
614089 TTGTGTTTCG
614099 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
614113 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
614129 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
614145 CGTTGCGATTTT
1 CGTTGCGATTTT
614157 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:614133 original size:32 final size:33
Alignment explanation
Indices: 614094--614172 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
614084 GCGATTTGTG
614094 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
614126 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
614159 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
614173 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:614171 original size:19 final size:19
Alignment explanation
Indices: 614113--614230 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
614103 GCGATTTTGT
614113 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
614131 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
614145 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
614164 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
614184 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
614203 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
614223 TGTTGCGA
1 CGTTGCGA
614231 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Done.