Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006710.1 Hibiscus syriacus cultivar Beakdansim tig00016725_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: 2941931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:512157 original size:95 final size:94
Alignment explanation
Indices: 512035--512254 Score: 233
Period size: 95 Copynumber: 2.3 Consensus size: 94
512025 GATGAGGTAA
* * ** *
512035 TATCGATACCATGGTAAGGGTATCGATACTAGGTAACATCAAACCTAATTTTGGTATTGATACCG
1 TATCGATACCATGGT-AGGGTATCGATACTAAGCAACATCAAACCTAATTTTGGTATCAATACCA
* * * * *
512100 GAAGGGGGTATTGGTACCCTAGAATAGTAG
65 AAAGGGGGTATCGATACCATAGAAGAGTAG
* * ** * *
512130 TATCGATATCATGGTGAGGGTATCGATACAAAGCCTCATCGAAGCTAATTTTGGTATCAATACCA
1 TATCGATACCATGGT-AGGGTATCGATACTAAGCAACATCAAACCTAATTTTGGTATCAATACCA
* *
512195 AAAGGGGGTATCGATACCATAGTAGGGTAG
65 AAAGGGGGTATCGATACCATAGAAGAGTAG
* *
512225 TATCGATAGCATGGTATGTGTATCGATACT
1 TATCGATACCATGGTA-GGGTATCGATACT
512255 GAAGGGCCAT
Statistics
Matches: 102, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
94 1 0.01
95 101 0.99
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (94 bp):
TATCGATACCATGGTAGGGTATCGATACTAAGCAACATCAAACCTAATTTTGGTATCAATACCAA
AAGGGGGTATCGATACCATAGAAGAGTAG
Found at i:512230 original size:22 final size:20
Alignment explanation
Indices: 512202--512253 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
512192 CCAAAAGGGG
512202 GTATCGATACCATAGTAGGGT
1 GTATCGATACCATAGTA-GGT
* * *
512223 AGTATCGATAGCATGGTATGT
1 -GTATCGATACCATAGTAGGT
512244 GTATCGATAC
1 GTATCGATAC
512254 TGAAGGGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 9 0.35
21 2 0.08
22 15 0.58
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (20 bp):
GTATCGATACCATAGTAGGT
Found at i:512636 original size:59 final size:59
Alignment explanation
Indices: 512571--513146 Score: 877
Period size: 59 Copynumber: 9.8 Consensus size: 59
512561 ATGGCACTAA
* *
512571 GTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* *
512630 ATGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGTACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * * *
512689 GTGTGCTAAAATGGTAAAGAAATCATACAAAGTGTATGAATTTCCAAATAGGACACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
*
512748 GTGTGCTAAAATGGTAAGGAAATCATGCTAAGTGTATGAATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
*
512807 GTGTGCTAAAATGGTAAGGAAAGCATACTAAGTGT-TAGAATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTAT-GAATTTCCAGATAGGGCACTTC
* * * * *
512866 ATGTGTTAAAATAGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGTACTCC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* *
512925 GTGTGCTAAAATGGTAAAGAAATCATACTATGTGTATGAATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * * *
512984 GTATGCTAAAATGGTAAGGAAATAATACTAAGTGTATGACTTTCCAGATAGGGCACTTT
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * **
513043 ATGTGATAAAATGGTAAAAAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* *
513102 GTGTGCTAAAATGATAAGGAAATCATACTAA-TAGTGTGAATTTCC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGT-GTATGAATTTCC
513147 TTTTGAATTT
Statistics
Matches: 464, Mismatches: 50, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
58 2 0.00
59 461 0.99
60 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (59 bp):
GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
Found at i:525956 original size:21 final size:21
Alignment explanation
Indices: 525902--525957 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
525892 AAATGTCTGC
*
525902 AAATCTTATTATAGTTAGTAAT
1 AAATATTATTATAGTTAG-AAT
*
525924 AAATA-AATTTATAGTGTA-AAT
1 AAATATTA-TTATAGT-TAGAAT
525945 AAATATTATTATA
1 AAATATTATTATA
525958 TTAAATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 14 0.50
22 12 0.43
23 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (21 bp):
AAATATTATTATAGTTAGAAT
Found at i:525993 original size:23 final size:24
Alignment explanation
Indices: 525949--525994 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
525939 GTAAATAAAT
*
525949 ATTATTATATTAAATTATATTTTA
1 ATTATTATATTAAATTAGATTTTA
*
525973 ATTATTA-ATTAAATTGGATTTT
1 ATTATTATATTAAATTAGATTTT
525995 TAAATTAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTATTATATTAAATTAGATTTTA
Found at i:527309 original size:15 final size:16
Alignment explanation
Indices: 527274--527307 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
527264 ATATTATACG
527274 TATA-TTTTAAAATAA
1 TATAGTTTTAAAATAA
527289 TATAGTTTTAAAATTAA
1 TATAGTTTTAAAA-TAA
527306 TA
1 TA
527308 GTAAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TATAGTTTTAAAATAA
Found at i:532658 original size:15 final size:15
Alignment explanation
Indices: 532635--532668 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
532625 AATTCAAATA
532635 TTTGAGAGTTATCAT
1 TTTGAGAGTTATCAT
*
532650 TTTGGGAGTTATCAT
1 TTTGAGAGTTATCAT
532665 TTTG
1 TTTG
532669 TTATTTAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.50
Consensus pattern (15 bp):
TTTGAGAGTTATCAT
Found at i:535886 original size:11 final size:11
Alignment explanation
Indices: 535870--535920 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
535860 GAGACAACCC
535870 ATTTTTATTTT
1 ATTTTTATTTT
*
535881 ATTTTTTTGTTT
1 ATTTTTAT-TTT
535893 AATTTTTA-TTT
1 -ATTTTTATTTT
*
535904 ATTTTTATTAT
1 ATTTTTATTTT
535915 ATTTTT
1 ATTTTT
535921 TTAAATTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 7 0.21
11 18 0.53
12 3 0.09
13 6 0.18
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:536895 original size:25 final size:25
Alignment explanation
Indices: 536864--536922 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
536854 TACACCAGAA
536864 TTTTGGCTAGTGACCAAAATGTAAT
1 TTTTGGCTAGTGACCAAAATGTAAT
*
536889 TTTTGGCTAGTTACCAAAATGTAAT
1 TTTTGGCTAGTGACCAAAATGTAAT
536914 TTTTGGCTA
1 TTTTGGCTA
536923 AAGTGTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (25 bp):
TTTTGGCTAGTGACCAAAATGTAAT
Found at i:542626 original size:12 final size:12
Alignment explanation
Indices: 542597--542626 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
542587 GAAACTCTAG
542597 TAAAAAGATTCT
1 TAAAAAGATTCT
542609 TGAAAAAGATTCT
1 T-AAAAAGATTCT
542622 TAAAA
1 TAAAA
542627 CTCTAGGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (12 bp):
TAAAAAGATTCT
Found at i:544956 original size:36 final size:37
Alignment explanation
Indices: 544887--544956 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
544877 AAGTTTTCTT
*
544887 AAAAACAAAATTTGTTTCGCTTGAGACATATTTCGCA
1 AAAAACAAAATTTGTTTCGCTTGAGACAAATTTCGCA
544924 AAAAAC-AAATTTCGTCTT-GCTTGAGA-AAATTTC
1 AAAAACAAAATTT-GT-TTCGCTTGAGACAAATTTC
544957 TTTCAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
36 12 0.40
37 16 0.53
38 2 0.07
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (37 bp):
AAAAACAAAATTTGTTTCGCTTGAGACAAATTTCGCA
Found at i:545636 original size:134 final size:129
Alignment explanation
Indices: 545310--545640 Score: 340
Period size: 130 Copynumber: 2.5 Consensus size: 129
545300 TGGCATGATG
* * * * * * *
545310 TCCTCATCACATAGGAACTGTTTCATCCCCCGACCAGACCTCCTTATCACGTAGGAGCTGTGTCA
1 TCCTCATCACGTAAGAACCGTGTCATCCACTGACCAGACCTCCTCATCACGTAGGAGC-GTGTCA
* * * * * * **
545375 TCCCTAGATAACCAGTCGTCCTCATCATGTAGGAACAGTGTTATCATCCCTAAAGATGGCCTCTT
65 CCCCTAGATAACCAGTCGTCCTCATCATATAGAAACAGTGCTATCATCCATAAAGATGGCATCCA
* * *
545440 TCCTCATCACGTAAGACCCGTGTTATCCACTGACTAGACCTCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAAGAACCGTGTCATCCACTGACCAGACCTCCTCATCACGTAGGAG-CGTGTCA
* *
545505 CCCCTAGATAACCAGTCGTCCTCATCGTATAGAAACCA-TGCTATCACCCTCCATAAAGATGTCA
65 CCCCTAGATAACCAGTCGTCCTCATCATATAGAAA-CAGTGCTATCA---TCCATAAAGATGGCA
545569 TGCCA
126 T-CCA
* * * * * * *
545574 TCTTCATCGCGTAGGAACCGTGTCGTCCACTGACCAGATCTCTTCTTCACGTAGGAGTCGTGTCA
1 TCCTCATCACGTAAGAACCGTGTCATCCACTGACCAGACCTCCTCATCACGTAGGAG-CGTGTCA
545639 CC
65 CC
545641 TTTAGATGAT
Statistics
Matches: 164, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
130 91 0.55
131 3 0.02
133 13 0.08
134 57 0.35
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (129 bp):
TCCTCATCACGTAAGAACCGTGTCATCCACTGACCAGACCTCCTCATCACGTAGGAGCGTGTCAC
CCCTAGATAACCAGTCGTCCTCATCATATAGAAACAGTGCTATCATCCATAAAGATGGCATCCA
Found at i:547477 original size:30 final size:30
Alignment explanation
Indices: 547401--547483 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
547391 CGTTTAGCCC
* * * *
547401 TTTAAGTTTC-AATTTTAGCTATTTTATTCT
1 TTTAAGTTTCTATTTTTA-CTATTGTAATCA
547431 TTTAAGTTTCTATTTTTACTATTGTAATCA
1 TTTAAGTTTCTATTTTTACTATTGTAATCA
* *
547461 TTTAAGTTTCTGTTTTTCCTATT
1 TTTAAGTTTCTATTTTTACTATT
547484 TTGGTCCTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 40 0.87
31 6 0.13
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (30 bp):
TTTAAGTTTCTATTTTTACTATTGTAATCA
Found at i:547495 original size:29 final size:29
Alignment explanation
Indices: 547462--547521 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
547452 TTGTAATCAT
*** *
547462 TTAAGTTTCTGTTTTTCCTATTTTGGTCC
1 TTAAGTTTCTGTAAATCATATTTTGGTCC
*
547491 TTAAGTTTTTGTAAATCATATTTTGGTCC
1 TTAAGTTTCTGTAAATCATATTTTGGTCC
547520 TT
1 TT
547522 TAAATTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (29 bp):
TTAAGTTTCTGTAAATCATATTTTGGTCC
Found at i:569725 original size:13 final size:14
Alignment explanation
Indices: 569705--569734 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
569695 CAAATCAGCC
*
569705 AACAAAATGGTTAA
1 AACAAATTGGTTAA
569719 AACAAATTGGTTAA
1 AACAAATTGGTTAA
569733 AA
1 AA
569735 AAAGAATATG
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:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (14 bp):
AACAAATTGGTTAA
Found at i:569964 original size:12 final size:12
Alignment explanation
Indices: 569947--569971 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
569937 CACTAAAATA
569947 ATTTTCACTTTG
1 ATTTTCACTTTG
569959 ATTTTCACTTTG
1 ATTTTCACTTTG
569971 A
1 A
569972 CCATTACCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (12 bp):
ATTTTCACTTTG
Found at i:569982 original size:6 final size:6
Alignment explanation
Indices: 569971--570000 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
569961 TTTCACTTTG
569971 ACCATT ACCATT ACCATT ACCATT ACCATT
1 ACCATT ACCATT ACCATT ACCATT ACCATT
570001 TGTTGGCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
ACCATT
Found at i:573716 original size:32 final size:33
Alignment explanation
Indices: 573637--573729 Score: 100
Period size: 32 Copynumber: 2.8 Consensus size: 33
573627 ATATTTACAT
* * *
573637 AATATGGAGTAATCAA-CAAACAAATCATCGAAA
1 AATATCGAGAAATCAACCAAA-AACTCATCGAAA
573670 AATATCGAGAAATCAACCAAAAACTCATC-AAA
1 AATATCGAGAAATCAACCAAAAACTCATCGAAA
* * * *
573702 AATCTTGAGCAATCAACCAACAACTCAT
1 AATATCGAGAAATCAACCAAAAACTCAT
573730 TAGTATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 27 0.52
33 21 0.40
34 4 0.08
ACGTcount: A:0.52, C:0.22, G:0.09, T:0.18
Consensus pattern (33 bp):
AATATCGAGAAATCAACCAAAAACTCATCGAAA
Found at i:575949 original size:8 final size:8
Alignment explanation
Indices: 575933--575966 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
575923 TACGGATAAG
575933 TAATTAAA
1 TAATTAAA
*
575941 TAGTTAAA
1 TAATTAAA
575949 TAATTAAA
1 TAATTAAA
575957 TAATTAAA
1 TAATTAAA
575965 TA
1 TA
575967 TATAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:589050 original size:8 final size:8
Alignment explanation
Indices: 589006--589057 Score: 70
Period size: 8 Copynumber: 6.5 Consensus size: 8
588996 AAAATGAGTG
589006 AAAATGAA
1 AAAATGAA
*
589014 AAAATAAA
1 AAAATGAA
*
589022 AAAATAAA
1 AAAATGAA
589030 AAAAT-AA
1 AAAATGAA
589037 AAAATGAA
1 AAAATGAA
589045 AAAATGGAA
1 AAAAT-GAA
589054 AAAA
1 AAAA
589058 AGAAGGGTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
7 7 0.17
8 27 0.66
9 7 0.17
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:589056 original size:16 final size:15
Alignment explanation
Indices: 589006--589049 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
588996 AAAATGAGTG
589006 AAAATGAAAAAATAAA
1 AAAATGAAAAAAT-AA
*
589022 AAAATAAAAAAATAA
1 AAAATGAAAAAATAA
589037 AAAATGAAAAAAT
1 AAAATGAAAAAAT
589050 GGAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (15 bp):
AAAATGAAAAAATAA
Found at i:590245 original size:54 final size:54
Alignment explanation
Indices: 589997--590451 Score: 335
Period size: 54 Copynumber: 8.4 Consensus size: 54
589987 TTGAAGATTG
* * * * *
589997 TTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGATGAAGAT-
1 TTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTGAAGAAGATA
* * * * * * * * ** *
590050 TGT-G-GGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATCGTCGAAGATCG
1 T-TCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTGAAGAAGAT-A
* * * * ** *
590105 TTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTG
1 TTCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTGAAGAAGA-TA
* * * **
590160 TTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATA
1 TTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTGAAGAAGATA
* * *
590214 TTCGAGTTCTATTCTCCCT-ATAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATA
1 TTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCAGACCCGATTGAAGAAGATA
* *
590268 TTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGC-GAACCCGTTTGAAGAAG-TA
1 TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAG-ACCCGATTGAAGAAGATA
* *
590321 TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGC-GAACC-AGTTAGCAGAAGAT-
1 TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACCCGA-TT-GAAGAAGATA
* * *
590374 TCTTGAGTTCTATACTCCCTGAA-ACAATAGGGAGCAGACCCG-TTAGCAGAAGATTA
1 T-TCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCAGACCCGATT-GAAGAAGA-TA
590430 TTCGAGTTCTATACTCCCTGAA
1 TTCGAGTTCTATACTCCCTGAA
590452 ACAATAGGGA
Statistics
Matches: 349, Mismatches: 31, Indels: 42
0.83 0.07 0.10
Matches are distributed among these distances:
52 6 0.02
53 86 0.25
54 133 0.38
55 121 0.35
56 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (54 bp):
TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTGAAGAAGATA
Found at i:590274 original size:163 final size:163
Alignment explanation
Indices: 589987--590451 Score: 366
Period size: 163 Copynumber: 2.9 Consensus size: 163
589977 CCAACAATTA
*
589987 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGATGAAGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTG
* * * * * ** *
590052 TGGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATCGTCGAAGATCGTTCGAG-TCTTA
66 TGGGTCTTATACTCCCTGAAGAAAGAGGGAGCAAACACAATCGAAGAAGATCATTCGAGTTC-TA
* *
590116 TACTCTCTGAAGAAATAGGGGGCAGACGCGATTG
130 TACTCCCTGAAGAAAGAGGGGGCAGACGCGATTG
* *
590150 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATAT
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGAT-T
* * * ** *
590215 -TCGAGT-TCTATTCTCCCT-ATAGAAAGAGGGAGCAAACCCGTTTGAAGAAGAT-ATTCGAGTT
65 GT-GGGTCT-TATACTCCCTGA-AGAAAGAGGGAGCAAACACAATCGAAGAAGATCATTCGAGTT
* * *
590276 CTATTCTCCCTGAAGAAAGAGGGAGC-GAACCCG--T-
127 CTATACTCCCTGAAGAAAGAGGGGGCAG-ACGCGATTG
* * * * *
590310 TTGAAGAAGTATTCGAGT-TCTATACTCCCTGAAGAAAGAGGGAGC-GA-ACCAGTTAGCA-GAA
1 TTGAAG-ATTGTTCGAGTCTC-ATACTCTCTGAAGAAATAGGGAGCAGACA-CAATT-G-ATGAA
* * * * * ** * * *
590371 GATTCTTGAGT-TCTATACTCCCTGAA-ACAATAGGGAGCAGACCCGTTAGCAGAAGATTATTCG
61 GATT-GTGGGTCT-TATACTCCCTGAAGA-AAGAGGGAGCAAACACAATCGAAGAAGATCATTCG
590434 AGTTCTATACTCCCTGAA
123 AGTTCTATACTCCCTGAA
590452 ACAATAGGGA
Statistics
Matches: 251, Mismatches: 35, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
159 1 0.00
160 15 0.06
161 80 0.32
162 25 0.10
163 94 0.37
164 36 0.14
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (163 bp):
TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTG
TGGGTCTTATACTCCCTGAAGAAAGAGGGAGCAAACACAATCGAAGAAGATCATTCGAGTTCTAT
ACTCCCTGAAGAAAGAGGGGGCAGACGCGATTG
Found at i:590346 original size:107 final size:107
Alignment explanation
Indices: 590105--590471 Score: 361
Period size: 107 Copynumber: 3.4 Consensus size: 107
590095 TCGAAGATCG
* * * * * * **
590105 TTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGAG-TC
1 TTCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGA-T-TTCGAGTTC
* * * **
590168 TCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATA
63 T-ATACTCCCTGAAGAAATAGGGAGCAGACCCGTTTGAAGAAGATA
*
590214 TTCGAGTTCTATTCTCCCT-ATAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATATTCGAGTTCT
1 TTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCAAACCCGTTTGAAGAAGAT-TTCGAGTTCT
* *
590278 ATTCTCCCTGAAGAAAGAGGGAGC-GAACCCGTTTGAAGAAG-TA
64 ATACTCCCTGAAGAAATAGGGAGCAG-ACCCGTTTGAAGAAGATA
* * * * *
590321 TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCAGTTAGCAGAAGATTCTTGAGTTCTA
1 TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATT-TCGAGTTCTA
* *
590386 TACTCCCTGAA-ACAATAGGGAGCAGACCCGTTAGCAGAAGATTA
65 TACTCCCTGAAGA-AATAGGGAGCAGACCCGTTTGAAGAAGA-TA
* *
590430 TTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGT
1 TTCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCAAACCCGT
590472 CCCCAGAAGA
Statistics
Matches: 218, Mismatches: 29, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
106 2 0.01
107 90 0.41
108 43 0.20
109 81 0.37
110 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (107 bp):
TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATTTCGAGTTCTAT
ACTCCCTGAAGAAATAGGGAGCAGACCCGTTTGAAGAAGATA
Found at i:590462 original size:55 final size:54
Alignment explanation
Indices: 589989--590506 Score: 354
Period size: 55 Copynumber: 9.6 Consensus size: 54
589979 AACAATTATT
* * **
589989 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTG-A
1 GAAGATTATTCGAGTTCT-ATACTCCCTGAAGAAATAGGGAGCAGAC-CCGTTGCA
* * * * * ** *
590043 TGAAGATT-GT-G-GGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATCGTC-
1 -GAAGATTATTCGAGTTC-TATACTCCCTGAAGAAATAGGGAGCAGAC-CCGTTG-CA
** * * * **
590097 GAAGATCGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTATTCGAGTTC-TATACTCCCTGAAGAAATAGGGAGCAGACCCG-TTGCA
* * * **
590152 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 GAAGATTATTCGAGTTCT-ATACTCCCTGAAGAAATAGGGAGCAGACCCG-TTGCA
* * * *
590207 GAAGA-TATTCGAGTTCTATTCTCCCT-ATAGAAAGAGGGAGCAAACCCGTTTGAA
1 GAAGATTATTCGAGTTCTATACTCCCTGA-AGAAATAGGGAGCAGACCCG-TTGCA
* * *
590261 GAAGA-TATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGC-GAACCCGTTTGAA
1 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAATAGGGAGCAG-ACCCG-TTGCA
* *
590315 GAAG--TATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGC-GAACCAGTTAGCA
1 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAATAGGGAGCAG-ACCCGTT-GCA
*
590368 GAAGATTCTT-GAGTTCTATACTCCCTGAA-ACAATAGGGAGCAGACCCGTTAGCA
1 GAAGATTATTCGAGTTCTATACTCCCTGAAGA-AATAGGGAGCAGACCCGTT-GCA
**
590422 GAAGATTATTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGC-GAACCCGTCCCCA
1 GAAGATTATTCGAGTTCTATACTCCCTGAAGA-AATAGGGAGCAG-ACCCGT-TGCA
* * **
590477 GAAGATTCTTCAAGTTCTATGTTCCCTGAA
1 GAAGATTATTCGAGTTCTATACTCCCTGAA
590507 ACGATAGGGA
Statistics
Matches: 402, Mismatches: 39, Indels: 44
0.83 0.08 0.09
Matches are distributed among these distances:
52 3 0.01
53 89 0.22
54 140 0.35
55 169 0.42
56 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (54 bp):
GAAGATTATTCGAGTTCTATACTCCCTGAAGAAATAGGGAGCAGACCCGTTGCA
Found at i:590507 original size:55 final size:55
Alignment explanation
Indices: 590214--590525 Score: 327
Period size: 54 Copynumber: 5.7 Consensus size: 55
590204 GTTGAAGATA
* * * * * *
590214 TTCGAGTTCTATTCTCCCT-ATAGA-AAGAGGGAGCAAACCCGTTTGAAGAAGA-TA
1 TTCGAGTTCTATACTCCCTGA-A-ACAATAGGGAGCGAACCCGTTAGCAGAAGATTC
* * * * *
590268 TTCGAGTTCTATTCTCCCTGAAGA-AAGAGGGAGCGAACCCGTTTGAAGAAG--TA
1 TTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGTTAGCAGAAGATTC
* *
590321 TTCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCGAACCAGTTAGCAGAAGATTC
1 TTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGTTAGCAGAAGATTC
*
590376 TT-GAGTTCTATACTCCCTGAAACAATAGGGAGC-AGACCCGTTAGCAGAAGATTA
1 TTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGA-ACCCGTTAGCAGAAGATTC
***
590430 TTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCGTCCCCAGAAGATTC
1 TTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCGTTAGCAGAAGATTC
* ** *
590485 TTCAAGTTCTATGTTCCCTGAAACGATAGGGAGCGAACCCG
1 TTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCG
590526 ATTTTGAAGA
Statistics
Matches: 234, Mismatches: 17, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
53 51 0.22
54 95 0.41
55 87 0.37
56 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (55 bp):
TTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCGTTAGCAGAAGATTC
Found at i:590813 original size:8 final size:8
Alignment explanation
Indices: 590797--590830 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
590787 TACGGATAAG
590797 TAATTAAA
1 TAATTAAA
*
590805 TAGTTAAA
1 TAATTAAA
590813 TAATTAAA
1 TAATTAAA
590821 TAATTAAA
1 TAATTAAA
590829 TA
1 TA
590831 TATAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:600144 original size:19 final size:19
Alignment explanation
Indices: 600116--600163 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
600106 AGTGAGTTGT
600116 TGATCGTTAACCCAGTCGC
1 TGATCGTTAACCCAGTCGC
* *
600135 TGATCATTAACCCAGTCGT
1 TGATCGTTAACCCAGTCGC
600154 TGATCGTTAA
1 TGATCGTTAA
600164 TTGGTCGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (19 bp):
TGATCGTTAACCCAGTCGC
Found at i:601594 original size:76 final size:75
Alignment explanation
Indices: 601498--601706 Score: 328
Period size: 76 Copynumber: 2.7 Consensus size: 75
601488 ATTTTAAATA
* * * *
601498 TTATATTTTATCTTTATTTTAGGTAGTTTAGATTAAATATGTTTTAGTATTTTAATTAATTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGTTTTA
*
601563 GGATATTATTT
65 GGATATCATTT
*
601574 TTATATTTTACCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGTTTTA
601639 GGATATCATTT
65 GGATATCATTT
*
601650 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATT
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATT
601707 TATATTTAAG
Statistics
Matches: 123, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
75 5 0.04
76 118 0.96
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGTTTTAG
GATATCATTT
Found at i:606762 original size:21 final size:21
Alignment explanation
Indices: 606738--606777 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
606728 GCGTAGAATT
606738 TGTCCCAAAGGACTACATAGA
1 TGTCCCAAAGGACTACATAGA
**
606759 TGTCCCAAATTACTACATA
1 TGTCCCAAAGGACTACATA
606778 TAATTCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (21 bp):
TGTCCCAAAGGACTACATAGA
Found at i:607628 original size:24 final size:20
Alignment explanation
Indices: 607573--607610 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
607563 TTCCCCTTGA
*
607573 AGTGTATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
607593 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
607611 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:611636 original size:9 final size:9
Alignment explanation
Indices: 611618--611716 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
611608 GGTCGGGTCG
*
611618 GGTCAGACC
1 GGTCAAACC
611627 GGTCAAACC
1 GGTCAAACC
*
611636 GGTTCAGACC
1 GG-TCAAACC
611646 GGTCAAACC
1 GGTCAAACC
*
611655 GGTTCGAACC
1 GG-TCAAACC
*
611665 GGTTGAAACC
1 GG-TCAAACC
*
611675 GGTTAAACC
1 GGTCAAACC
611684 GGTCAGAACC
1 GGTCA-AACC
*
611694 GGTTGAAAACC
1 GG-T-CAAACC
*
611705 GGTTAAACC
1 GGTCAAACC
611714 GGT
1 GGT
611717 TTCCAGCAGC
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
9 36 0.48
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:611642 original size:19 final size:19
Alignment explanation
Indices: 611620--611717 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
611610 TCGGGTCGGG
611620 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
611639 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
611658 TC-GAACCGGTTGAAACCGGT
1 TCAG-ACCGG-TCAAACCGGT
*
611678 T-AAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
611697 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
611717 T
1 T
611718 TCCAGCAGCC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 18 0.26
21 9 0.13
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:611648 original size:10 final size:10
Alignment explanation
Indices: 611624--611717 Score: 99
Period size: 10 Copynumber: 9.7 Consensus size: 10
611614 GTCGGGTCAG
611624 ACCGG-TCAA
1 ACCGGTTCAA
*
611633 ACCGGTTCAG
1 ACCGGTTCAA
611643 ACCGG-TCAA
1 ACCGGTTCAA
*
611652 ACCGGTTCGA
1 ACCGGTTCAA
*
611662 ACCGGTTGAA
1 ACCGGTTCAA
611672 ACCGGTT-AA
1 ACCGGTTCAA
611681 ACCGG-TCAGA
1 ACCGGTTCA-A
*
611691 ACCGGTTGAAA
1 ACCGGTT-CAA
611702 ACCGGTT-AA
1 ACCGGTTCAA
611711 ACCGGTT
1 ACCGGTT
611718 TCCAGCAGCC
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
8 1 0.01
9 30 0.41
10 32 0.44
11 9 0.12
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:611675 original size:29 final size:28
Alignment explanation
Indices: 611624--611716 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 28
611614 GTCGGGTCAG
* * *
611624 ACCGGTCAAACCGGTTCAGACCGGTCAA
1 ACCGGTCAAACCGGTTGAAACCGGTTAA
*
611652 ACCGGTTCGAACCGGTTGAAACCGGTTAA
1 ACCGG-TCAAACCGGTTGAAACCGGTTAA
611681 ACCGGTCAGAACCGGTTGAAAACCGGTTAA
1 ACCGGTCA-AACCGGTTG-AAACCGGTTAA
611711 ACCGGT
1 ACCGGT
611717 TTCCAGCAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 7 0.12
29 33 0.58
30 17 0.30
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTGAAACCGGTTAA
Found at i:618956 original size:19 final size:19
Alignment explanation
Indices: 618934--618971 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
618924 AACGGTCGGG
618934 TCGGGTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
*
618953 TCGGTTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
618972 CCGGTTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (19 bp):
TCGGGTCAGACCGGTCAAA
Found at i:618957 original size:9 final size:9
Alignment explanation
Indices: 618937--619034 Score: 79
Period size: 9 Copynumber: 10.3 Consensus size: 9
618927 GGTCGGGTCG
*
618937 GGTCAGACC
1 GGTCAAACC
*
618946 GGTCAAATC
1 GGTCAAACC
*
618955 GGTTCAGACC
1 GG-TCAAACC
618965 GGTCAAACC
1 GGTCAAACC
*
618974 GGTTCGAACC
1 GG-TCAAACC
*
618984 GGTTGAAACC
1 GG-TCAAACC
618994 GGTCAAACC
1 GGTCAAACC
619003 GGTCAGAACC
1 GGTCA-AACC
* *
619013 GATTGAAACC
1 G-GTCAAACC
*
619023 GGTTAAACC
1 GGTCAAACC
619032 GGT
1 GGT
619035 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
9 37 0.51
10 33 0.46
11 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:618976 original size:19 final size:19
Alignment explanation
Indices: 618939--619035 Score: 90
Period size: 19 Copynumber: 5.1 Consensus size: 19
618929 TCGGGTCGGG
*
618939 TCAGACCGGTCAAATCGGT
1 TCAGACCGGTCAAACCGGT
618958 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
618977 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
* *
618996 TCAAACCGGTCAGAACCGAT
1 TCAGACCGGTCA-AACCGGT
* * *
619016 TGAAACCGGTTAAACCGGT
1 TCAGACCGGTCAAACCGGT
619035 T
1 T
619036 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
18 3 0.05
19 44 0.68
20 18 0.28
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.19
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:618996 original size:29 final size:30
Alignment explanation
Indices: 618962--619035 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 30
618952 ATCGGTTCAG
*
618962 ACCGGTCAAACCGGTTC-GAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAGAACCGATTGAA
618991 ACCGGTCAAACCGG-TCAGAACCGATTGAA
1 ACCGGTCAAACCGGTTCAGAACCGATTGAA
*
619020 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
619036 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.05
29 38 0.93
30 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.18
Consensus pattern (30 bp):
ACCGGTCAAACCGGTTCAGAACCGATTGAA
Found at i:619035 original size:9 final size:9
Alignment explanation
Indices: 618943--619035 Score: 69
Period size: 10 Copynumber: 9.8 Consensus size: 9
618933 GTCGGGTCAG
*
618943 ACCGGTCAA
1 ACCGGTTAA
* *
618952 ATCGGTTCAG
1 ACCGGTT-AA
*
618962 ACCGGTCAA
1 ACCGGTTAA
*
618971 ACCGGTTCGA
1 ACCGGTT-AA
618981 ACCGGTTGAA
1 ACCGGTT-AA
*
618991 ACCGGTCAA
1 ACCGGTTAA
*
619000 ACCGGTCAGA
1 ACCGGTTA-A
*
619010 ACCGATTGAA
1 ACCGGTT-AA
619020 ACCGGTTAA
1 ACCGGTTAA
619029 ACCGGTT
1 ACCGGTT
619036 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
9 31 0.47
10 34 0.52
11 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:620906 original size:24 final size:20
Alignment explanation
Indices: 620851--620888 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
620841 TTCCCCTTTA
620851 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
620871 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
620889 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:621050 original size:65 final size:65
Alignment explanation
Indices: 620915--621059 Score: 161
Period size: 65 Copynumber: 2.2 Consensus size: 65
620905 TGTACTACCC
* * * **
620915 ATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTTAAAGGGATGATTCGATGCACTCCTT
1 ATGCATCGATACACCAATTACATTCGATGTTTTCATTTTTAAAGAGATGATTCGATGCACTCAAT
* * *
620980 ATGCATCGATGCACCAATTGCATTCGATG-TTTCTTTTTTAAAGAG-TGCA-TCGATGCACATTC
1 ATGCATCGATACACCAATTACATTCGATGTTTTCATTTTTAAAGAGATG-ATTCGATGCAC--TC
621042 AAT
63 AAT
*
621045 GTGCATCGATACACC
1 ATGCATCGATACACC
621060 TTACCCAGAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
63 11 0.16
64 15 0.22
65 41 0.61
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (65 bp):
ATGCATCGATACACCAATTACATTCGATGTTTTCATTTTTAAAGAGATGATTCGATGCACTCAAT
Found at i:621827 original size:17 final size:17
Alignment explanation
Indices: 621802--621835 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
621792 CTTTATCCCA
*
621802 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
621819 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
621836 TCATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:621907 original size:8 final size:8
Alignment explanation
Indices: 621889--621953 Score: 59
Period size: 8 Copynumber: 8.8 Consensus size: 8
621879 TCTTTATTAC
621889 TATTA-TT
1 TATTATTT
621896 TATTATTT
1 TATTATTT
621904 TATTATTT
1 TATTATTT
621912 TATTATTT
1 TATTATTT
**
621920 T-TCCTTT
1 TATTATTT
621927 T-TTA-TT
1 TATTATTT
* *
621933 TATAATTA
1 TATTATTT
621941 T-TTATTT
1 TATTATTT
621948 TATTAT
1 TATTAT
621954 ACCTTTTCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
6 3 0.07
7 18 0.39
8 25 0.54
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (8 bp):
TATTATTT
Found at i:624795 original size:123 final size:130
Alignment explanation
Indices: 624544--624800 Score: 357
Period size: 135 Copynumber: 2.0 Consensus size: 130
624534 ATCAAATACA
*
624544 TTTAAAAGTGATATTTATAAGAATTTATTAAGCGAATTTAGTAAAAAAAATACATTATTTTTTCT
1 TTTAAAAGTGATATTTATAAGAATTTATTAAGCGAATTTAGTAAAAAAAATA-ATTATTCTTTCT
* * * *
624609 AGAAATTTTAAGTTGGAACACTTATATCAATTGTTTAAACAGAAAAAGTACAAAAAGTAAACTTT
65 AGAAATTTTAAGTTCG-A-AC-TATA-CAATAGATTAAACAGAAAAAATACAAAAAGTAAACTTT
624674 ATTTC
126 ATTTC
*
624679 TTTAAAAGTGATATTTATAAGAATTTATTAAGTGAATTTAGT-AAAAAAAT-ATTATTCTTT-TA
1 TTTAAAAGTGATATTTATAAGAATTTATTAAGCGAATTTAGTAAAAAAAATAATTATTCTTTCTA
*
624741 -AGATTTTAAGTTCG-A-TATA-AATAGATTAAACAGAAAAAATACAAAAAGTAAACTTTATTT
66 GAAATTTTAAGTTCGAACTATACAATAGATTAAACAGAAAAAATACAAAAAGTAAACTTTATTT
624801 TTTTTAACAT
Statistics
Matches: 115, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
123 38 0.33
125 4 0.03
127 1 0.01
130 12 0.10
131 2 0.02
132 9 0.08
134 8 0.07
135 41 0.36
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (130 bp):
TTTAAAAGTGATATTTATAAGAATTTATTAAGCGAATTTAGTAAAAAAAATAATTATTCTTTCTA
GAAATTTTAAGTTCGAACTATACAATAGATTAAACAGAAAAAATACAAAAAGTAAACTTTATTTC
Found at i:633918 original size:6 final size:6
Alignment explanation
Indices: 633907--633979 Score: 58
Period size: 6 Copynumber: 11.2 Consensus size: 6
633897 AAAATCAAAG
*
633907 AAAAAT AAAAAT AAATAA- AAAAATTT GAAAAT AAAAAT AAAAAT AAAAAAT
1 AAAAAT AAAAAT AAA-AAT AAAAA--T AAAAAT AAAAAT AAAAAT -AAAAAT
*
633958 GAACAAACG AAAAAT AAAAAT A
1 -AA-AAA-T AAAAAT AAAAAT A
633980 TTAATGGGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
5 2 0.04
6 31 0.56
7 13 0.24
8 9 0.16
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:633926 original size:28 final size:28
Alignment explanation
Indices: 633894--633979 Score: 77
Period size: 32 Copynumber: 2.9 Consensus size: 28
633884 ACGGCATACC
633894 TAAAAAATCAAAGAAAAATAAAAATAAA
1 TAAAAAATCAAAGAAAAATAAAAATAAA
* *
633922 TAAAAAAATTTGAAAATAAAAATAAAAATAAA
1 T-AAAAAA--T-CAAAGAAAAATAAAAATAAA
*
633954 -AAATGAA-CAAACGAAAAATAAAAATA
1 TAAA-AAATCAAA-GAAAAATAAAAATA
633980 TTAATGGGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
27 3 0.06
28 14 0.30
29 6 0.13
30 3 0.06
31 3 0.06
32 18 0.38
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (28 bp):
TAAAAAATCAAAGAAAAATAAAAATAAA
Found at i:636857 original size:14 final size:13
Alignment explanation
Indices: 636847--636880 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
636837 AGGTAAAAAG
636847 ATAAGAATAAAATA
1 ATAA-AATAAAATA
636861 ATAAAAT-AAATA
1 ATAAAATAAAATA
636873 ATAAAATA
1 ATAAAATA
636881 TTTATAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.63
13 3 0.16
14 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
ATAAAATAAAATA
Found at i:637395 original size:18 final size:18
Alignment explanation
Indices: 637368--637402 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
637358 TAACGCCGAC
* *
637368 TTTTGGTTTTGTAAATCA
1 TTTTGATTTTGAAAATCA
637386 TTTTGATTTTGAAAATC
1 TTTTGATTTTGAAAATC
637403 GGTTTGATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (18 bp):
TTTTGATTTTGAAAATCA
Found at i:638468 original size:21 final size:21
Alignment explanation
Indices: 638442--638482 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
638432 TGCACCAGTA
638442 AACATGTTAGTTACAAGAAAT
1 AACATGTTAGTTACAAGAAAT
638463 AACATGTTAGTTACAAGAAA
1 AACATGTTAGTTACAAGAAA
638483 CAAGCGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (21 bp):
AACATGTTAGTTACAAGAAAT
Found at i:640940 original size:3 final size:3
Alignment explanation
Indices: 640919--641070 Score: 265
Period size: 3 Copynumber: 51.3 Consensus size: 3
640909 ACCTCCATTT
640919 TTA TT- TTA TTA TT- TGTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
640963 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
641011 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
641059 -TA ATA TTA TTA T
1 TTA TTA TTA TTA T
641071 AAATACATAA
Statistics
Matches: 144, Mismatches: 1, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
2 5 0.03
3 138 0.96
4 1 0.01
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:641866 original size:137 final size:137
Alignment explanation
Indices: 641382--641866 Score: 623
Period size: 137 Copynumber: 3.5 Consensus size: 137
641372 TCAGTGGATG
* * *
641382 ACATTGTTCCTTCGTGATGAGGACATCTGGATATCTAAGGATGACTCGGCTCCTACATGATGAAG
1 ACATGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGACTCGACTCCTACATGATGAAG
* * * * * * *
641447 AGTTCTGGCCGGTGGATGATATTGTTCTTTCGTGATGAGGACATTTGGCCATCTTTAAAAATAAT
66 AGTTCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGGACATTTGGACATCTTTGAAGATATT
641512 TGAGATA
131 TGAGATA
** * * *
641519 ACATGGTTCCTTCACGATGAGGACATTTGGTTATCTAAGGATGACTCGACTCCTACATGATGAGG
1 ACATGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGACTCGACTCCTACATGATGAAG
* * * ** *
641584 AGTTATGGACTGTGGATGACATTGTTCCTTTTTGATGAGGACATCTT--ACCTTCTTTGAAGATA
66 AGTTCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGGACAT-TTGGA-CATCTTTGAAGATA
641647 TTTGAGATA
129 TTTGAGATA
** * * * * *
641656 ACACAGTTCCTTCGTGATAAGGATATCTCGCTATCTAAGGATGACTCGACTCCTACGTGATAAAG
1 ACATGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGACTCGACTCCTACATGATGAAG
641721 AGTTCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGGACATTTGGACATCTTTGAAGATATT
66 AGTTCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGGACATTTGGACATCTTTGAAGATATT
641786 TGAGATA
131 TGAGATA
* * * * ** *
641793 ACATGGTTCCTTCGTGATGAGGACTTTTGGCTATCTAAGGATGATTCGGCTCCTATGTGATGAGG
1 ACATGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGACTCGACTCCTACATGATGAAG
641858 AGTTCTGGT
66 AGTTCTGGT
641867 TATTTCCGAA
Statistics
Matches: 295, Mismatches: 49, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
136 2 0.01
137 290 0.98
138 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (137 bp):
ACATGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGACTCGACTCCTACATGATGAAG
AGTTCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGGACATTTGGACATCTTTGAAGATATT
TGAGATA
Found at i:648370 original size:65 final size:65
Alignment explanation
Indices: 648274--648407 Score: 223
Period size: 65 Copynumber: 2.1 Consensus size: 65
648264 AGTACAACAC
* * *
648274 ACAAATTTATTCTTTAAATCTAAAGATACACAATTAAATCTGAAAACATTAACAAACAAGTTAGT
1 ACAAATTTATTCCTTAAATCTAAAAACACACAATTAAATCTGAAAACATTAACAAACAAGTTAGT
* *
648339 ACAAATTTATTCCTTAAATCTAAAAACACACAATTAAATCTGGAAAGATTAACAAACAAGTTAGT
1 ACAAATTTATTCCTTAAATCTAAAAACACACAATTAAATCTGAAAACATTAACAAACAAGTTAGT
648404 ACAA
1 ACAA
648408 CTATTTATAC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (65 bp):
ACAAATTTATTCCTTAAATCTAAAAACACACAATTAAATCTGAAAACATTAACAAACAAGTTAGT
Found at i:650805 original size:43 final size:43
Alignment explanation
Indices: 650757--650926 Score: 128
Period size: 43 Copynumber: 4.0 Consensus size: 43
650747 TGTATATAAA
650757 AAACGCTGCAATAGGTTCA-AGTATTTAAAGGCATTTTTCTTAC
1 AAACGCTGCAATAGGTTCATA-TATTTAAAGGCATTTTTCTTAC
* * * ** **
650800 AAACGCCGC-ATAGGTTTATATGTTTAGCGGTGTTTTTCTTAC
1 AAACGCTGCAATAGGTTCATATATTTAAAGGCATTTTTCTTAC
* * ** ** *
650842 AATCGCTGCAATAGGTTCATACATTTAGTGGTGTTTTTATTAC
1 AAACGCTGCAATAGGTTCATATATTTAAAGGCATTTTTCTTAC
* * * * * **
650885 AAATGCCGCAACAGTTTCATACATTTAGCGGCATTTTTCTTA
1 AAACGCTGCAATAGGTTCATATATTTAAAGGCATTTTTCTTA
650927 TAAATGTCAT
Statistics
Matches: 102, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
42 32 0.31
43 70 0.69
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (43 bp):
AAACGCTGCAATAGGTTCATATATTTAAAGGCATTTTTCTTAC
Found at i:650836 original size:42 final size:42
Alignment explanation
Indices: 650790--650926 Score: 148
Period size: 43 Copynumber: 3.2 Consensus size: 42
650780 TTTAAAGGCA
* **
650790 TTTTTCTTACAAACGCCGCATAGGTTTATATGTTTAGCGGTG
1 TTTTTCTTACAAACGCCGCATAGGTTCATACATTTAGCGGTG
* * *
650832 TTTTTCTTACAATCGCTGCAATAGGTTCATACATTTAGTGGTG
1 TTTTTCTTACAAACGCCGC-ATAGGTTCATACATTTAGCGGTG
* * * * **
650875 TTTTTATTACAAATGCCGCAACAGTTTCATACATTTAGCGGCA
1 TTTTTCTTACAAACGCCGC-ATAGGTTCATACATTTAGCGGTG
650918 TTTTTCTTA
1 TTTTTCTTA
650927 TAAATGTCAT
Statistics
Matches: 78, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 17 0.22
43 61 0.78
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.42
Consensus pattern (42 bp):
TTTTTCTTACAAACGCCGCATAGGTTCATACATTTAGCGGTG
Found at i:650965 original size:43 final size:43
Alignment explanation
Indices: 650790--650966 Score: 133
Period size: 43 Copynumber: 4.1 Consensus size: 43
650780 TTTAAAGGCA
* * * * ** *
650790 TTTTTCTTACAAACGCCGC-ATAGGTTTATATGTTTAGCGGTG
1 TTTTTATTACAAATGCCACAATAGGTTCATACATTTAGTGGTG
* **
650832 TTTTTCTTAC-AATCGCTGCAATAGGTTCATACATTTAGTGGTG
1 TTTTTATTACAAAT-GCCACAATAGGTTCATACATTTAGTGGTG
* * * * **
650875 TTTTTATTACAAATGCCGCAACAGTTTCATACATTTAGCGGCA
1 TTTTTATTACAAATGCCACAATAGGTTCATACATTTAGTGGTG
* * * * * *
650918 TTTTTCTTATAAATGTCATAATAGGTTAAGACATTTAGTGGTG
1 TTTTTATTACAAATGCCACAATAGGTTCATACATTTAGTGGTG
650961 TTTTTA
1 TTTTTA
650967 ACTAAAAACA
Statistics
Matches: 106, Mismatches: 26, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
41 2 0.02
42 14 0.13
43 87 0.82
44 3 0.03
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (43 bp):
TTTTTATTACAAATGCCACAATAGGTTCATACATTTAGTGGTG
Found at i:655964 original size:37 final size:35
Alignment explanation
Indices: 655893--656204 Score: 257
Period size: 37 Copynumber: 8.7 Consensus size: 35
655883 AATAATTAAA
655893 AAACATATAAATATATAGTTTTTTAAATAG-TTTTTG
1 AAACATAT-AATATATAGTTTTTTAAA-AGATTTTTG
*
655929 AAACGTATAATATATAGTTTTTCTAAAACGATTTTTG
1 AAACATATAATATATAGTTTTT-TAAAA-GATTTTTG
* *
655966 AAATCATATAGTATATAGTTTTTTAAAATATTTTTTG
1 AAA-CATATAATATATAGTTTTTTAAAAGA-TTTTTG
*
656003 AAAACGTATAATATATAGTTTTTTACAAACGA-TTTTG
1 -AAACATATAATATATAGTTTTTTA-AAA-GATTTTTG
*
656040 AAAACATATAGTATATATAGTTTTTTAAAATATTTTTTG
1 -AAACATATA--ATATATAGTTTTTTAAAAGA-TTTTTG
* *
656079 AAAACGTATAATATATAGTTTTTTAAAA-ACTGATTTG
1 -AAACATATAATATATAGTTTTTTAAAAGA-T-TTTTG
* * *
656116 AAAGCATATAATATATA-CTTTTTAAAATAATTTT-
1 AAA-CATATAATATATAGTTTTTTAAAAGATTTTTG
** *
656150 -AATGTATAATATATAG-TTTTT-AAA-ATATTTG
1 AAACATATAATATATAGTTTTTTAAAAGATTTTTG
*
656181 AAAACATAT-ATAATATATTTTTTT
1 -AAACATATAAT-ATATAGTTTTTT
656205 TGAAAACGTA
Statistics
Matches: 232, Mismatches: 23, Indels: 44
0.78 0.08 0.15
Matches are distributed among these distances:
30 4 0.02
31 3 0.01
32 18 0.08
33 12 0.05
34 5 0.02
35 18 0.08
36 27 0.12
37 89 0.38
38 26 0.11
39 30 0.13
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (35 bp):
AAACATATAATATATAGTTTTTTAAAAGATTTTTG
Found at i:656074 original size:76 final size:71
Alignment explanation
Indices: 655870--656204 Score: 373
Period size: 76 Copynumber: 4.7 Consensus size: 71
655860 TTTTGAAAAC
** ** *
655870 ATATAG-TTTTTAAAATAATTAAAAAACATATAAATATATAGTTTTTT-AAATAGTTTTTGAAAC
1 ATATAGTTTTTTAAAACGATTTGAAAACATAT-AATATATAGTTTTTTAAAATATTTTTTGAAAC
655933 GTATAAT
65 GTATAAT
* *
655940 ATATAGTTTTTCTAAAACGATTTTTGAAATCATATAGTATATAGTTTTTTAAAATATTTTTTGAA
1 ATATAGTTTTT-TAAAACGA--TTTGAAAACATATAATATATAGTTTTTTAAAATATTTTTTG-A
656005 AACGTATAAT
62 AACGTATAAT
656015 ATATAGTTTTTTACAAACGATTTTGAAAACATATAGTATATATAGTTTTTTAAAATATTTTTTGA
1 ATATAGTTTTTTA-AAACGA-TTTGAAAACATATA--ATATATAGTTTTTTAAAATATTTTTTG-
656080 AAACGTATAAT
61 AAACGTATAAT
* * *
656091 ATATAGTTTTTTAAAAACTGATTTGAAAGCATATAATATATA-CTTTTTAAAATA-ATTTT--AA
1 ATATAGTTTTTT-AAAAC-GATTTGAAAACATATAATATATAGTTTTTTAAAATATTTTTTGAAA
*
656152 TGTATAAT
64 CGTATAAT
* *
656160 ATATAG-TTTTTAAAA-TATTTGAAAACATAT-ATAATATATTTTTTT
1 ATATAGTTTTTTAAAACGATTTGAAAACATATAAT-ATATAGTTTTTT
656205 TGAAAACGTA
Statistics
Matches: 236, Mismatches: 16, Indels: 30
0.84 0.06 0.11
Matches are distributed among these distances:
64 2 0.01
65 18 0.08
66 5 0.02
67 4 0.02
68 5 0.02
69 15 0.06
70 6 0.03
71 4 0.02
72 10 0.04
73 25 0.11
74 44 0.19
75 28 0.12
76 67 0.28
77 3 0.01
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (71 bp):
ATATAGTTTTTTAAAACGATTTGAAAACATATAATATATAGTTTTTTAAAATATTTTTTGAAACG
TATAAT
Found at i:668719 original size:18 final size:18
Alignment explanation
Indices: 668696--668744 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
668686 CCTTTATATC
668696 TAGAATAGGCACAAGTCT
1 TAGAATAGGCACAAGTCT
668714 TAGAATAGGCACAAGTCT
1 TAGAATAGGCACAAGTCT
*
668732 TAGAATAGTCACA
1 TAGAATAGGCACA
668745 CTTGTATAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (18 bp):
TAGAATAGGCACAAGTCT
Found at i:673347 original size:201 final size:200
Alignment explanation
Indices: 673002--673538 Score: 616
Period size: 201 Copynumber: 2.7 Consensus size: 200
672992 ACCATTAAGT
* *
673002 GCATAGCTCAAGGCGA-AAAGGGATATCTATAAACGAAAAATTTCGAGTTCGATTTCATTCAGCT
1 GCATAGCTCAAGGCGAGAAA-GGATATCTATCAACGAAAACTTTCGAGTTCGATTTCATTCAGC-
* * * ** **
673066 TC-AAGGCGTA-TCAGTCGCATGGTAGTAGCGAGGAACTACTTTCCAGTTGAATTTTAAATTGAG
64 TCGAGGGCGTATTAAG-CGCATGGTAGAAGCGAGGAACTACTTTCTGGTTGAATTTT-AACCGAG
* * * * * *
673129 GTCTTTAAGTCAAGAAGAATACCTATGTTGACTGCAATTTAGCAACAATGAACTATA-TCATAGC
127 GTCTTTAAGTCAAGAAGAAGACCTATGTTGACTACAATTTAGCAACAAAGAACTA-ACCCACAAC
*
673193 CTAATTTACA
191 CGAATTTACA
* * * * * *
673203 GCATAGCTCAAAGCGAGAAAGGCTATCTGTCAATGAAAACTTTCGAGTTTGATTTCGTTCAGCTC
1 GCATAGCTCAAGGCGAGAAAGGATATCTATCAACGAAAACTTTCGAGTTCGATTTCATTCAGCTC
* * * *
673268 GAGGGCATATTAAGCACATGGTAGAAGCAAGGAACTACTTTCTGGTTGAATTTTGAACCAAGGTC
66 GAGGGCGTATTAAGCGCATGGTAGAAGCGAGGAACTACTTTCTGGTTGAATTTT-AACCGAGGTC
* * * *
673333 TTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTATCAACAAAGAACTAACCCCCAACCGAA
130 TTTAAGTCAAGAAGAAGACCTATGTTGACTACAATTTAGCAACAAAGAACTAACCCACAACCGAA
*
673398 TTTATA
195 TTTACA
* * * * * *
673404 GCATAACTCAAGGCCAGAAGGGTTATCTATCAACGAAAACTTTAGAGTTCGATTTCACTCAGCTC
1 GCATAGCTCAAGGCGAGAAAGGATATCTATCAACGAAAACTTTCGAGTTCGATTTCATTCAGCTC
* * *
673469 GAGGGCGTATCAA-CTGCATGGTAGCATCGAGGAACTACTTTCTGGTTGAATTTTAACCGAGGTC
66 GAGGGCGTATTAAGC-GCATGGTAGAAGCGAGGAACTACTTTCTGGTTGAATTTTAACCGAGGTC
673533 TTTAAG
130 TTTAAG
673539 CCAAAAATAA
Statistics
Matches: 281, Mismatches: 50, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
200 19 0.07
201 256 0.91
202 6 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (200 bp):
GCATAGCTCAAGGCGAGAAAGGATATCTATCAACGAAAACTTTCGAGTTCGATTTCATTCAGCTC
GAGGGCGTATTAAGCGCATGGTAGAAGCGAGGAACTACTTTCTGGTTGAATTTTAACCGAGGTCT
TTAAGTCAAGAAGAAGACCTATGTTGACTACAATTTAGCAACAAAGAACTAACCCACAACCGAAT
TTACA
Found at i:674126 original size:37 final size:36
Alignment explanation
Indices: 674074--674467 Score: 290
Period size: 37 Copynumber: 10.8 Consensus size: 36
674064 TTTTGAAAAC
* *
674074 ATATAG-TTTTT--AAAATAATTAAAAACATATAAAT
1 ATATAGTTTTTTAAAAAATATTTGAAAACATAT-AAT
* *
674108 ATATAGTTTCTTAAAAAATAGATTTTGAAAACGTATAAT
1 ATATAGTTTTTTAAAAAAT--A-TTTGAAAACATATAAT
* * * *
674147 ATATACTTTTTTATAACAGTTTTTGAAAACATATAAT
1 ATATAGTTTTTTA-AAAAATATTTGAAAACATATAAT
* *
674184 ATATAGTTTTTTAAAATACTTTTTGAAAACATATAAT
1 ATATAGTTTTTTAAAA-AATATTTGAAAACATATAAT
* * *
674221 ATATTGCTTTTTTAAAAAGATTTTTGAAAACATATAGT
1 ATATAG-TTTTTTAAAAA-ATATTTGAAAACATATAAT
* * *
674259 ATATAGTTTTTTTAAAAAA-AATTGTAAACGTATAAT
1 ATATAG-TTTTTTAAAAAATATTTGAAAACATATAAT
* *
674295 ACATAGTTTTTTAAAAACAGT-TTTGAAAACATATATT
1 ATATAGTTTTTTAAAAA-A-TATTTGAAAACATATAAT
* * *
674332 ATATAG-TTTTTAAAATATTTTTTGAAAACGTATAAT
1 ATATAGTTTTTTAAAA-AATATTTGAAAACATATAAT
* * *
674368 ATATA-TAGATTTTAAAAACTTATTTGAAAACATATAGT
1 ATATAGT--TTTTTAAAAA-ATATTTGAAAACATATAAT
* * *
674406 ATATAG-TTTTT--AAAATGATTTAAAAAAATGTGTAAT
1 ATATAGTTTTTTAAAAAAT-ATTTGAAAACA--TATAAT
*
674442 ATATAG-TTTTTAAAATAT-TTTGAAAA
1 ATATAGTTTTTTAAAAAATATTTGAAAA
674468 TGTATATAAT
Statistics
Matches: 291, Mismatches: 44, Indels: 48
0.76 0.11 0.13
Matches are distributed among these distances:
33 1 0.00
34 18 0.06
35 16 0.05
36 74 0.25
37 77 0.26
38 76 0.26
39 15 0.05
40 14 0.05
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
ATATAGTTTTTTAAAAAATATTTGAAAACATATAAT
Found at i:674421 original size:74 final size:73
Alignment explanation
Indices: 674095--674426 Score: 334
Period size: 74 Copynumber: 4.4 Consensus size: 73
674085 AAAATAATTA
** *
674095 AAAACATATAAATATATAGTTTCTTAAAAAATAGATTTTGAAAACGTATAATATATA-CTTTTTT
1 AAAACATAT-AATATATAGTTT-TT--AAAATATTTTTTGAAAACGTATAATATATATGTTTTTT
* *
674159 ATAACAGTTTTTG
62 A-AAAACTTTTTG
* *
674172 AAAACATATAATATATAGTTTTTTAAAATACTTTTTGAAAACATATAATATAT-TGCTTTTTTAA
1 AAAACATATAATATATAG-TTTTTAAAATATTTTTTGAAAACGTATAATATATATG-TTTTTTAA
*
674236 AAAGATTTTTG
64 AAA-CTTTTTG
* *** * *
674247 AAAACATATAGTATATAGTTTTTTTAAAA-A-AAATTGTAAACGTATAATACATA-GTTTTTTAA
1 AAAACATATAATATATAG--TTTTTAAAATATTTTTTGAAAACGTATAATATATATGTTTTTTAA
*
674309 AAACAGTTTTG
64 AAAC-TTTTTG
* *
674320 AAAACATATATTATATAGTTTTTAAAATATTTTTTGAAAACGTATAATATATATAG-ATTTTAAA
1 AAAACATATAATATATAGTTTTTAAAATATTTTTTGAAAACGTATAATATATAT-GTTTTTTAAA
674384 AACTTATTTG
65 AACTT-TTTG
*
674394 AAAACATATAGTATATAGTTTTTAAAATGATTT
1 AAAACATATAATATATAGTTTTTAAAAT-ATTT
674427 AAAAAAATGT
Statistics
Matches: 218, Mismatches: 24, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
71 9 0.04
72 1 0.00
73 52 0.24
74 87 0.40
75 36 0.17
76 21 0.10
77 12 0.06
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (73 bp):
AAAACATATAATATATAGTTTTTAAAATATTTTTTGAAAACGTATAATATATATGTTTTTTAAAA
ACTTTTTG
Found at i:674478 original size:36 final size:34
Alignment explanation
Indices: 674074--674512 Score: 283
Period size: 36 Copynumber: 11.9 Consensus size: 34
674064 TTTTGAAAAC
* *
674074 ATATAGTTTTTAAAATA-ATTAAAAACATATAAAT
1 ATATAGTTTTTAAAATATTTTGAAAACATAT-AAT
*
674108 ATATAGTTTCTTAAAAAATAGATTTTGAAAACGTATAAT
1 ATATAGTTT-TT--AAAAT--ATTTTGAAAACATATAAT
*
674147 ATATACTTTTTTATAACAGT-TTTTGAAAACATATAAT
1 ATATA-GTTTTTA-AA-A-TATTTTGAAAACATATAAT
674184 ATATAGTTTTTTAAAATACTTTTTGAAAACATATAAT
1 ATATAG-TTTTTAAAATA--TTTTGAAAACATATAAT
* * *
674221 ATATTGCTTTTTTAAAAAGATTTTTGAAAACATATAGT
1 ATATAG--TTTTT-AAAATA-TTTTGAAAACATATAAT
* ** * *
674259 ATATAGTTTTTTTAAAAAAAATTGTAAACGTATAAT
1 ATATAG--TTTTTAAAATATTTTGAAAACATATAAT
* * *
674295 ACATAGTTTTTTAAAAACAGTTTTGAAAACATATATT
1 ATATAG-TTTTT-AAAATA-TTTTGAAAACATATAAT
*
674332 ATATAGTTTTTAAAATATTTTTTGAAAACGTATAATAT
1 ATATAGTTTTTAAAATA--TTTTGAAAACATAT-A-AT
* *
674370 ATATAGATTTTAAAA-ACTTATTTGAAAACATATAGT
1 ATATAGTTTTTAAAATA--T-TTTGAAAACATATAAT
* * *
674406 ATATAGTTTTTAAAATGA-TTTAAAAAAATGTGTAAT
1 ATATAGTTTTTAAAAT-ATTTTGAAAACA--TATAAT
*
674442 ATATAGTTTTTAAAATATTTTGAAAATGTATATAAT
1 ATATAGTTTTTAAAATATTTTGAAAA--CATATAAT
**
674478 ATAATTTTTTTTGAAAACGTATTTTGGAAAACATA
1 AT-ATAGTTTTT-AAAA--TATTTT-GAAAACATA
674513 GTATATGGTT
Statistics
Matches: 327, Mismatches: 44, Indels: 63
0.75 0.10 0.15
Matches are distributed among these distances:
34 18 0.06
35 15 0.05
36 91 0.28
37 89 0.27
38 69 0.21
39 20 0.06
40 20 0.06
41 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (34 bp):
ATATAGTTTTTAAAATATTTTGAAAACATATAAT
Found at i:674489 original size:147 final size:145
Alignment explanation
Indices: 674095--674420 Score: 390
Period size: 147 Copynumber: 2.2 Consensus size: 145
674085 AAAATAATTA
* * * * *
674095 AAAACATATAAATATATAGTTTCTTAAAAAATAGATTTTGAAAACGTATAATATATACTTTTTT-
1 AAAACATAT-AGTATATAGTTTTTTAAAAAA-A-A--TTAAAAACGTATAATACATAGTTTTTTA
*
674159 ATAACAGTTTTTGAAAACATATAATATATAGTTTTTTAAAATACTTTTTGAAAACATATAATATA
61 AAAACAG-TTTTGAAAACATATAATATATA-TTTTTTAAAATACTTTTTGAAAACATATAATATA
*
674224 TTGCTTTTTTAAAAAGATTTTTG
124 TTGC-ATTTTAAAAAGATTTTTG
**
674247 AAAACATATAGTATATAGTTTTTTTAAAAAAAATTGTAAACGTATAATACATAGTTTTTTAAAAA
1 AAAACATATAGTATATAG-TTTTTTAAAAAAAATTAAAAACGTATAATACATAGTTTTTTAAAAA
* * * *
674312 CAGTTTTGAAAACATATATTATATAGTTTTTAAAATATTTTTTGAAAACGTATAATATATATAG-
65 CAGTTTTGAAAACATATAATATATATTTTTTAAAATACTTTTTGAAAACATATAATATAT-T-GC
*
674376 ATTTTAAAAA-CTTATTTG
128 ATTTTAAAAAGATT-TTTG
674394 AAAACATATAGTATATAG-TTTTTAAAA
1 AAAACATATAGTATATAGTTTTTTAAAA
674421 TGATTTAAAA
Statistics
Matches: 157, Mismatches: 12, Indels: 17
0.84 0.06 0.09
Matches are distributed among these distances:
145 9 0.06
146 2 0.01
147 63 0.40
148 46 0.29
149 7 0.04
150 1 0.01
151 9 0.06
152 20 0.13
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (145 bp):
AAAACATATAGTATATAGTTTTTTAAAAAAAATTAAAAACGTATAATACATAGTTTTTTAAAAAC
AGTTTTGAAAACATATAATATATATTTTTTAAAATACTTTTTGAAAACATATAATATATTGCATT
TTAAAAAGATTTTTG
Found at i:674577 original size:22 final size:21
Alignment explanation
Indices: 674552--674595 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
674542 TTTAAATATA
674552 TTATTATTA-TTTCTTTTCTTTT
1 TTATT-TTATTTTCTTTT-TTTT
674574 TTATTTTATTTTCTTTTTTTT
1 TTATTTTATTTTCTTTTTTTT
674595 T
1 T
674596 CCTCGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (21 bp):
TTATTTTATTTTCTTTTTTTT
Found at i:676100 original size:12 final size:12
Alignment explanation
Indices: 676083--676114 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
676073 ATCGGGTAAT
676083 CGGGGAAAACCG
1 CGGGGAAAACCG
676095 CGGGGAAAACCG
1 CGGGGAAAACCG
676107 CGGGGAAA
1 CGGGGAAA
676115 CGGGTATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.44, T:0.00
Consensus pattern (12 bp):
CGGGGAAAACCG
Found at i:681140 original size:133 final size:132
Alignment explanation
Indices: 680897--681165 Score: 423
Period size: 133 Copynumber: 2.0 Consensus size: 132
680887 ATCAAATACA
* * * *
680897 TTTAAAAGTAATATTTATAAGAATTTATTAAGCGAGTTCAGTAAAAATATATTATTTTGTTTGGA
1 TTTAAAAGTAATATTTATAAGAATTTATTAAGCGAATTCAGTAAAAAAATATTATTTTGTCTAGA
*
680962 AATTTTAAGTTCGAACACCTATATCAATAGATTAAACAGAGAAAGTACAAAAAGTAAACTTTATT
66 AATTTTAAGTTCGAACACCTATATCAATAGATTAAACAGAAAAAGTACAAAAAGTAAACTTTATT
681027 TC
131 TC
*
681029 TTTAAAAGTGATATTTATAAGAATTTATTAAGCGAATTCAGTAAAAAAAATATTATTCTT-TCTA
1 TTTAAAAGTAATATTTATAAGAATTTATTAAGCGAATTCAGT-AAAAAAATATTATT-TTGTCTA
* * * *
681093 TAGATTTTAAGTTCGAACGCCTATATCAATAGATTAAATAGAAAAAGTACAAAAAGTAAACTTTA
64 GAAATTTTAAGTTCGAACACCTATATCAATAGATTAAACAGAAAAAGTACAAAAAGTAAACTTTA
681158 TTTC
129 TTTC
681162 TTTA
1 TTTA
681166 TACATATTAC
Statistics
Matches: 125, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
132 40 0.32
133 83 0.66
134 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (132 bp):
TTTAAAAGTAATATTTATAAGAATTTATTAAGCGAATTCAGTAAAAAAATATTATTTTGTCTAGA
AATTTTAAGTTCGAACACCTATATCAATAGATTAAACAGAAAAAGTACAAAAAGTAAACTTTATT
TC
Found at i:684531 original size:21 final size:21
Alignment explanation
Indices: 684506--684545 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
684496 TGAATACTTT
684506 CATTCACT-CATACTATTCAGA
1 CATTC-CTACATACTATTCAGA
*
684527 CATTCCTACATAGTATTCA
1 CATTCCTACATACTATTCA
684546 CTAAGAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (21 bp):
CATTCCTACATACTATTCAGA
Found at i:689469 original size:47 final size:47
Alignment explanation
Indices: 689416--689711 Score: 502
Period size: 47 Copynumber: 6.3 Consensus size: 47
689406 GGCTATTGTC
* *
689416 TACGAGCTTATGAAATTTAAATGGAAAGTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
689463 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
*
689510 TACGAGCTTATGGAATTTAAATGGCAAGTATATAGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
* *
689557 TACGAGCTTATAGAATTTAAATGGCAATTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
*
689604 TACGAGCTTATGGAATTTAAATGGCAAGTATGTTGATAAAATTAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAA-TAAGCT
* * *
689652 TACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
689699 TACGAGCTTATGG
1 TACGAGCTTATGG
689712 GATAAATGGT
Statistics
Matches: 236, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
47 192 0.81
48 44 0.19
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (47 bp):
TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
Found at i:689578 original size:27 final size:27
Alignment explanation
Indices: 689501--689578 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
689491 TATATTGATA
*
689501 AAATAAGCTTACGAGCTTATGGAATTT
1 AAATAAGCTTACGAGCTTATAGAATTT
* *
689528 AAAT-GGC--A--AG-TATATAG-A-TA
1 AAATAAGCTTACGAGCT-TATAGAATTT
689548 AAATAAGCTTACGAGCTTATAGAATTT
1 AAATAAGCTTACGAGCTTATAGAATTT
689575 AAAT
1 AAAT
689579 GGCAATTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 18
0.62 0.08 0.30
Matches are distributed among these distances:
20 5 0.14
21 4 0.11
22 6 0.16
23 1 0.03
24 1 0.03
25 7 0.19
26 4 0.11
27 9 0.24
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.31
Consensus pattern (27 bp):
AAATAAGCTTACGAGCTTATAGAATTT
Found at i:690209 original size:20 final size:21
Alignment explanation
Indices: 690181--690230 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
690171 ATCGATTCCC
* *
690181 CACTGTTCATC-GCTACTGTT
1 CACTATTCATCGGCTACTATT
*
690201 CACTATTCA-CGGGTACTATT
1 CACTATTCATCGGCTACTATT
690221 CACTATTCAT
1 CACTATTCAT
690231 TAAAAAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (21 bp):
CACTATTCATCGGCTACTATT
Found at i:692231 original size:16 final size:17
Alignment explanation
Indices: 692210--692242 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
692200 AACAAACCCC
*
692210 AAATAAATTAAA-AAAA
1 AAATAAACTAAACAAAA
692226 AAATAAACTAAACAAAA
1 AAATAAACTAAACAAAA
692243 GAAAAACCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (17 bp):
AAATAAACTAAACAAAA
Found at i:694076 original size:20 final size:19
Alignment explanation
Indices: 694039--694103 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 19
694029 AGAAGTTTCG
*
694039 AAACTTCTAGGAAATTCCC
1 AAACTTCTAGGAAGTTCCC
*
694058 AAACTTTTAGGGAAGTTCCC
1 AAACTTCTA-GGAAGTTCCC
*
694078 AAACTTCTAGGAATGTTTCC
1 AAACTTCTAGGAA-GTTCCC
694098 AAACTT
1 AAACTT
694104 TGCATTCCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (19 bp):
AAACTTCTAGGAAGTTCCC
Found at i:699747 original size:36 final size:36
Alignment explanation
Indices: 699693--699795 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
699683 GAGCTCTGCA
699693 CACAAAGATCCTGTTAGATTGATACCAAAAGTAGTC
1 CACAAAGATCCTGTTAGATTGATACCAAAAGTAGTC
* *
699729 CACCAAA-ATCCTGTTAGATTGATATCAAAAGTATTC
1 CA-CAAAGATCCTGTTAGATTGATACCAAAAGTAGTC
*
699765 CACAAAGATCCTGTTAGATTGGTACCAAAAG
1 CACAAAGATCCTGTTAGATTGATACCAAAAG
699796 CATTTTATGG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 4 0.07
36 53 0.87
37 4 0.07
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (36 bp):
CACAAAGATCCTGTTAGATTGATACCAAAAGTAGTC
Found at i:700345 original size:42 final size:43
Alignment explanation
Indices: 700261--700345 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
700251 TGGCTTTAGA
*
700261 GAAGTTAGGAGTGAAGGTTATCCCTTATATGTAAAGTTTTGTT
1 GAAGTTAGGAGTGAAGATTATCCCTTATATGTAAAGTTTTGTT
700304 GAAGTTAGGAGTGAA-ATCTATCCC-TATATGTAAAGTTTTGTT
1 GAAGTTAGGAGTGAAGAT-TATCCCTTATATGTAAAGTTTTGTT
700346 TGATGTACCG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 19 0.47
43 21 0.52
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (43 bp):
GAAGTTAGGAGTGAAGATTATCCCTTATATGTAAAGTTTTGTT
Found at i:703080 original size:72 final size:72
Alignment explanation
Indices: 702963--703106 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
702953 ATACAATAAA
702963 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAAC
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAAC
703028 CTGTTAT
66 CTGTTAT
* * * *
703035 GCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATTGCCCCGGCTTTATGGATAATATTCAGCTAGC
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAAC
*
703100 TTGTTAT
66 CTGTTAT
703107 ACTATTATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAAC
CTGTTAT
Found at i:706234 original size:54 final size:54
Alignment explanation
Indices: 706152--706367 Score: 297
Period size: 54 Copynumber: 4.0 Consensus size: 54
706142 TATTGAGAAT
* * *
706152 ATCTGGGCAGAAGCCACATGAAATGATGACTGTGTTGTCAAATGTTTTACGAAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * * * *
706206 ATCTGGGAAGAAGCTACAAGAAAGGATGAATATGTTGTCAAATGCTTTACAAAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* *
706260 ATCTGGGCAGAAGCTACAGGAAAGGATGAATGTGTTGTCAAATGATTTACGAAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* ** *
706314 ATCTGGGCAGAAGCCATAGGAAATAATGAATGTGTTGTCAAATGTTTTATGAAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
706368 CAATGATTAT
Statistics
Matches: 143, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 143 1.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (54 bp):
ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:706779 original size:20 final size:22
Alignment explanation
Indices: 706733--706790 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
706723 TACATCTACA
706733 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
706755 CTCTTCCAATATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
706777 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
706791 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:707779 original size:47 final size:46
Alignment explanation
Indices: 707457--707939 Score: 606
Period size: 45 Copynumber: 10.5 Consensus size: 46
707447 CCCACATCTG
* *
707457 TAAGACCTTCAGTGCATGATGTTTTC-AAAGCCTTCAGGTCATCCA
1 TAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGTCATCCA
* * * * **
707502 TAAGACATTCAGTGCATGATGTTTTC-AAAGCCTTTGGGTAATCTG
1 TAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGTCATCCA
*
707547 TAAGACCTTCAGTGCATGATGTTTTCAAAA-CCTTCGGGTCATCCA
1 TAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGTCATCCA
* * **
707592 TAAGACCTACAGTGCAGGATGTTTTC-AAAGCCTTAGGGTCATCTG
1 TAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGTCATCCA
* **
707637 TAAGACCTTCAGTGCAGGATATTTTC-AAAGCCTTCGGGTCATCTT
1 TAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGTCATCCA
*
707682 TAAGACCTTCAGTACAGGATGTTTTCAAAA-CCTTCGGGTCATCCA
1 TAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGTCATCCA
* **
707727 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGTCATGTA
1 TAAGACCTTCAGTGCAGGATGTTTTC-AAAAGCCTTCGGGTCATCCA
* *
707774 TAAGACCTAT-AGTGCAGGATGTCTTCTAAAAGCCTTTGGGTCATCCA
1 TAAGACCT-TCAGTGCAGGATGTTTTC-AAAAGCCTTCGGGTCATCCA
* * *
707821 TAAGACCTAT-AGTGCATGATATTTTCAAAAAGCCTTCTGGTCATCCA
1 TAAGACCT-TCAGTGCAGGATGTTTTC-AAAAGCCTTCGGGTCATCCA
*
707868 TAAGACCTACAGTGCAGGATGTTTTCAAAACGCCTTCGGGTCATCCA
1 TAAGACCTTCAGTGCAGGATGTTTTCAAAA-GCCTTCGGGTCATCCA
707915 TAAGACCTTCAGTGTCA-GATGTTTT
1 TAAGACCTTCAGTG-CAGGATGTTTT
707940 GAAATAACAA
Statistics
Matches: 384, Mismatches: 45, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
44 3 0.01
45 213 0.55
46 14 0.04
47 152 0.40
48 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (46 bp):
TAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGTCATCCA
Found at i:708081 original size:39 final size:39
Alignment explanation
Indices: 707988--708284 Score: 414
Period size: 39 Copynumber: 7.6 Consensus size: 39
707978 AAACATTTCC
* * *
707988 AAAAGGAGTTCATAATATGAAGAACTCATCTGAAAAGGAA
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGG-A
*
708028 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAGGAGGA
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* * *
708067 AAAAGGAGTTCATAATTTGAAGAACTCCTCTAAAGAGGA
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
*
708106 AAAAGGAGTTCATAATCTAAAGAACTCGTCTGAAGAGGA
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* * *
708145 AGAAGGAGTTCATAATTTGAAGAACTCATCTGAAGAGGA
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
*
708184 AGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* * *
708223 AGAAGGAGATCATAATATGAAGAACTCGTCTGAAGAGGA
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* * **
708262 AGAATGAGTTCATCGTCTGAAGA
1 AAAAGGAGTTCATAATCTGAAGA
708285 TGAAGAATGA
Statistics
Matches: 232, Mismatches: 25, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
39 198 0.85
40 34 0.15
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (39 bp):
AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
Found at i:708195 original size:117 final size:117
Alignment explanation
Indices: 707988--708723 Score: 767
Period size: 117 Copynumber: 6.5 Consensus size: 117
707978 AAACATTTCC
* * * *
707988 AAAAGGAGTTCATAATATGAAGAACTCATCTGAAAAGGAAAAAAGGAGTTCATAATCTGAAGAAC
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGG-AAGAAGGAGTTCATAATCTGAAGAAC
* * * * *
708053 TCGTCTGAGGAGGAAAAAGGAGTTCATAATTTGAAGAACTCCTCTAAAGAGGA
65 TCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* *
708106 AAAAGGAGTTCATAATCTAAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATTTGAAGAACT
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACT
*
708171 CATCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
66 CGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* * * *
708223 AGAAGGAGATCATAATATGAAGAACTCGTCTGAAGAGGAAGAATGAG----T--TC------A-T
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACT
* * * * *
708275 CGTCTGAAGATGAAGAATGAGTTCATAGTCTCAAGAACTCGTCTAAAGA-GA
66 CGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* * * *
708326 AAGAAGGAGTTCATAGTCTGAAGAAATCATATGAAGAGGAAGAAGGAGTTCATAATCTGAAGAAC
1 AA-AAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAAC
* * * * * * *
708391 TCATCTGAAGAGGAATAAGGAGTTCCTAGTCTGAATAACTTGTTTGAAGAGGA
65 TCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* * * * * * *
708444 AGAAGAAGTTCATAGTCTGAGGAACTCGTCTG--GA-GATGATGGAGTTCATAGTCTGAAGAACT
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACT
* * *
708506 CGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAACTCATATGAAGAGGA
66 CGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* * * * * *
708558 ATAAGGAGTTCATAATCTGAAAAACTCATCTGAAGAGGAAGAAGTAGTTCATAGTCTAAAGAACT
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACT
* * *
708623 CGTCTGAAGAGGAA-TA--AG---A-AAT-T----CA-TAGTCTGAAGAGGA
66 CGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
* *
708662 AAAAGGAGTTCATAATATGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTAAAGA
1 AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGA
708724 GGAAGAAGAA
Statistics
Matches: 520, Mismatches: 80, Indels: 50
0.80 0.12 0.08
Matches are distributed among these distances:
103 3 0.01
104 149 0.29
105 2 0.00
108 1 0.00
109 1 0.00
110 4 0.01
111 2 0.00
113 1 0.00
114 98 0.19
115 2 0.00
116 4 0.01
117 216 0.42
118 37 0.07
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (117 bp):
AAAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACT
CGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGA
Found at i:708226 original size:19 final size:19
Alignment explanation
Indices: 708202--708265 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
708192 TTCATAATCT
708202 GAAGAACTCGTCTGAAGAG
1 GAAGAACTCGTCTGAAGAG
*** * *
708221 GAAGAAGGAGATCAT-AATAT
1 GAAGAACTCG-TC-TGAAGAG
708241 GAAGAACTCGTCTGAAGAG
1 GAAGAACTCGTCTGAAGAG
708260 GAAGAA
1 GAAGAA
708266 TGAGTTCATC
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.56
20 12 0.38
21 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.30, T:0.16
Consensus pattern (19 bp):
GAAGAACTCGTCTGAAGAG
Found at i:708268 original size:26 final size:27
Alignment explanation
Indices: 708239--708294 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
708229 AGATCATAAT
708239 ATGAAGAAC-TCGTCTGAAGAGGAAGA
1 ATGAAGAACATCGTCTGAAGAGGAAGA
** *
708265 ATG-AGTTCATCGTCTGAAGATGAAGA
1 ATGAAGAACATCGTCTGAAGAGGAAGA
708291 ATGA
1 ATGA
708295 GTTCATAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (27 bp):
ATGAAGAACATCGTCTGAAGAGGAAGA
Found at i:708290 original size:65 final size:65
Alignment explanation
Indices: 708209--708349 Score: 192
Period size: 65 Copynumber: 2.2 Consensus size: 65
708199 TCTGAAGAAC
* * * *
708209 TCGTCTGAAGAGGAAGAAGGAGATCATAATATGAAGAACTCGTCTGAAGAGGAAGAATGAGTTCA
1 TCGTCTGAAGAGGAAGAAGGAGATCATAATATCAAGAACTCGTCTAAAGAGAAAGAAGGAGTTCA
* * * * *
708274 TCGTCTGAAGATGAAGAATGAGTTCATAGTCTCAAGAACTCGTCTAAAGAGAAAGAAGGAGTTCA
1 TCGTCTGAAGAGGAAGAAGGAGATCATAATATCAAGAACTCGTCTAAAGAGAAAGAAGGAGTTCA
*
708339 TAGTCTGAAGA
1 TCGTCTGAAGA
708350 AATCATATGA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (65 bp):
TCGTCTGAAGAGGAAGAAGGAGATCATAATATCAAGAACTCGTCTAAAGAGAAAGAAGGAGTTCA
Found at i:708295 original size:26 final size:26
Alignment explanation
Indices: 708248--708310 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
708238 TATGAAGAAC
708248 TCGTCTGAAGAGGAAGAATGAGTTCA
1 TCGTCTGAAGAGGAAGAATGAGTTCA
*
708274 TCGTCTGAAGATGAAGAATGAGTTCA
1 TCGTCTGAAGAGGAAGAATGAGTTCA
* *
708300 TAGTCTCAAGA
1 TCGTCTGAAGA
708311 ACTCGTCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (26 bp):
TCGTCTGAAGAGGAAGAATGAGTTCA
Found at i:708313 original size:143 final size:142
Alignment explanation
Indices: 708131--708752 Score: 574
Period size: 143 Copynumber: 4.3 Consensus size: 142
708121 TCTAAAGAAC
* * *
708131 TCGTCTGAAGAGGAAGAAGGAGTTCATAATTTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCA
1 TCGTCTGAAGAGGAAGAA-GAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCA
* * * *
708196 TAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGATCATAATATGAAGAACTCGTCTGAAGAGG
65 TAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGG
* *
708261 AAGAATGAGTTCA
130 AATAAGGAGTTCA
* * * *
708274 TCGTCTGAAGATGAAGAATGAGTTCATAGTCTCAAGAACTCGTCTAAAGAGAAAGAAGGAGTTCA
1 TCGTCTGAAGAGGAAGAA-GAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCA
* * *
708339 TAGTCTGAAGAAATCATATGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGG
65 TAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGG
708404 AATAAGGAGTTCCTA
130 AATAAGGAGTT-C-A
* *
708419 GTCTGAATAACTTGTTTGAAGAGGAAGAAGAAGTTCATAGTCTGAGGAACTCGTCTG--GA-GAT
1 -TC-G--T--C-----TGAAGAGGAAGAAG-AGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAA
* *
708481 GATGGAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAACTC
54 GAAGGAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
*
708546 ATATGAAGAGGAATAAGGAGTTCATAA
119 ATCTGAAGAGGAATAAGGAGTTC---A
* *
708573 TCTGAAAAACTCATCTGAAGAGGAAGAAGTAGTTCATAGTCTAAAGAACTCGTCTGAAGAGGAAT
1 TC-G---------TCTGAAGAGGAAGAAG-AGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAG
* * * *
708638 AAGAAATTCATAGTCTGAAG-A-------G--GA--AA-AAGGAGTTCATAATATGAAGAACTCG
55 AAGGAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCA
*
708690 TCTGAAGAGGAAGAAGGAGTTCA
120 TCTGAAGAGGAATAAGGAGTTCA
** *
708713 TAATCTAAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACT
1 TCGTCTGAAGAGGAAGAAG-AGTTCATAGTCTGAAGAACT
708753 TATTCAACAT
Statistics
Matches: 404, Mismatches: 49, Indels: 65
0.78 0.09 0.13
Matches are distributed among these distances:
130 34 0.08
140 2 0.00
143 167 0.41
144 3 0.01
145 1 0.00
146 4 0.01
147 1 0.00
148 1 0.00
149 1 0.00
151 1 0.00
152 1 0.00
153 124 0.31
154 3 0.01
155 4 0.01
156 54 0.13
158 1 0.00
160 2 0.00
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (142 bp):
TCGTCTGAAGAGGAAGAAGAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCAT
AGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGA
ATAAGGAGTTCA
Found at i:708317 original size:39 final size:39
Alignment explanation
Indices: 708274--708658 Score: 479
Period size: 39 Copynumber: 9.9 Consensus size: 39
708264 AATGAGTTCA
* * *
708274 TCGTCTGAAGATGAAGAATGAGTTCATAGTCTCAAGAAC
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * *
708313 TCGTCTAAAGAGAAAGAAGGAGTTCATAGTCTGAAGAAA
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * *
708352 TCATATGAAGAGGAAGAAGGAGTTCATAATCTGAAGAAC
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * * *
708391 TCATCTGAAGAGGAATAAGGAGTTCCTAGTCTGAATAAC
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * * *
708430 TTGTTTGAAGAGGAAGAAGAAGTTCATAGTCTGAGGAAC
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* *
708469 TCGTCTG--GA-GATGATGGAGTTCATAGTCTGAAGAAC
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
708505 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * * * *
708544 TCATATGAAGAGGAATAAGGAGTTCATAATCTGAAAAAC
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * *
708583 TCATCTGAAGAGGAAGAAGTAGTTCATAGTCTAAAGAAC
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * *
708622 TCGTCTGAAGAGGAATAAGAAATTCATAGTCTGAAGA
1 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGA
708659 GGAAAAAGGA
Statistics
Matches: 294, Mismatches: 49, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
36 30 0.10
37 2 0.01
38 2 0.01
39 260 0.88
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.24
Consensus pattern (39 bp):
TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
Found at i:708441 original size:182 final size:182
Alignment explanation
Indices: 708111--708723 Score: 814
Period size: 182 Copynumber: 3.3 Consensus size: 182
708101 GAGGAAAAAG
* * *
708111 GAGTTCATAATCTAAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATTTGAAGAACTCATCT
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATAT
* * * *
708176 GAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGATCATAATAT
66 GAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAGTCT
*
708241 GAAGAACTCGTCTGAAGAGGAAGAATG-AGTTCATCGTCTGAAGATGAAGAAT
131 GAAGAACTCGTCTGAAGAGGAAGAA-GAAGTTCATAGTCTGAAGATGAAGAAT
* * * * * *
708293 GAGTTCATAGTCTCAAGAACTCGTCTAAAGAGAAAGAAGGAGTTCATAGTCTGAAGAAATCATAT
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATAT
* *
708358 GAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAATAAGGAGTTCCTAGTCT
66 GAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAGTCT
* * * * *
708423 GAATAACTTGTTTGAAGAGGAAGAAGAAGTTCATAGTCTGAGGAACTCGTCTGGAGATGAT
131 GAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCT---GAA---G-ATGAAGA--AT
* *
708484 GGAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAACTCATA
1 -GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATA
* * *
708549 TGAAGAGGAATAAGGAGTTCATAATCTGAAAAACTCATCTGAAGAGGAAGAAGTAGTTCATAGTC
65 TGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAGTC
* * * * * *
708614 TAAAGAACTCGTCTGAAGAGGAATAAGAAATTCATAGTCTGAAGAGGAAAAAG
130 TGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGATGAAGAAT
* *
708667 GAGTTCATAATATGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTAAAGA
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGA
708724 GGAAGAAGAA
Statistics
Matches: 376, Mismatches: 44, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
181 1 0.00
182 202 0.54
183 1 0.00
185 6 0.02
186 1 0.00
188 1 0.00
189 8 0.02
191 2 0.01
192 154 0.41
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.23
Consensus pattern (182 bp):
GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATAT
GAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAGTCT
GAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGATGAAGAAT
Found at i:708493 original size:36 final size:38
Alignment explanation
Indices: 708274--708723 Score: 406
Period size: 39 Copynumber: 11.9 Consensus size: 38
708264 AATGAGTTCA
* * *
708274 TCGTCTGAAGATGAAGAATGAGTTCATAGTCTCAAGAAC
1 TCGTCTG-AGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * *
708313 TCGTCTAAAGAGAAAGAAGGAGTTCATAGTCTGAAGAAA
1 TCGTCT-GAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * *
708352 TCATATGAAGAGGAAGAAGGAGTTCATAATCTGAAGAAC
1 TCGTCTG-AGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * * *
708391 TCATCTGAAGAGGAATAAGGAGTTCCTAGTCTGAATAAC
1 TCGTCTG-AGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * * *
708430 TTGTTTGAAGAGGAAGAAGAAGTTCATAGTCTGAGGAAC
1 TCGTCTG-AGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* *
708469 TCGTCTG-GA-GATGATGGAGTTCATAGTCTGAAGAAC
1 TCGTCTGAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
708505 TCGTCTGAAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
1 TCGTCTG-AGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * * * *
708544 TCATATGAAGAGGAATAAGGAGTTCATAATCTGAAAAAC
1 TCGTCTG-AGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * *
708583 TCATCTGAAGAGGAAGAAGTAGTTCATAGTCTAAAGAAC
1 TCGTCTG-AGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* * *
708622 TCGTCTGAAGAGGAATAAGAAATTCATAGTCTGAAG-A-
1 TCGTCTG-AGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* *
708659 ------G-GA--AA-AAGGAGTTCATAATATGAAGAAC
1 TCGTCTGAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
* *
708687 TCGTCTGAAGAGGAAGAAGGAGTTCATAATCTAAAGA
1 TCGTCTG-AGAGGAAGAAGGAGTTCATAGTCTGAAGA
708724 GGAAGAAGAA
Statistics
Matches: 338, Mismatches: 55, Indels: 36
0.79 0.13 0.08
Matches are distributed among these distances:
26 16 0.05
27 3 0.01
29 2 0.01
31 1 0.00
34 1 0.00
36 32 0.09
37 2 0.01
38 5 0.01
39 276 0.82
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.23
Consensus pattern (38 bp):
TCGTCTGAGAGGAAGAAGGAGTTCATAGTCTGAAGAAC
Found at i:708673 original size:26 final size:26
Alignment explanation
Indices: 708624--708684 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
708614 TAAAGAACTC
*
708624 GTCTGAAGAGGAATAAGAAATTCATA
1 GTCTGAAGAGGAAAAAGAAATTCATA
* *
708650 GTCTGAAGAGGAAAAAGGAGTTCATA
1 GTCTGAAGAGGAAAAAGAAATTCATA
* *
708676 ATATGAAGA
1 GTCTGAAGA
708685 ACTCGTCTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.26, T:0.21
Consensus pattern (26 bp):
GTCTGAAGAGGAAAAAGAAATTCATA
Found at i:708690 original size:65 final size:65
Alignment explanation
Indices: 708585--708752 Score: 237
Period size: 65 Copynumber: 2.6 Consensus size: 65
708575 TGAAAAACTC
* * *
708585 ATCTGAAGAGGAAGAAGTAGTTCATAGTCTAAAGAACTCGTCTGAAGAGGAATAAGAAATTCATA
1 ATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGAAATTCATA
* * * * * * *
708650 GTCTGAAGAGGAAAAAGGAGTTCATAATATGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATA
1 ATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGAAATTCATA
*
708715 ATCTAAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACT
1 ATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACT
708753 TATTCAACAT
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 88 1.00
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (65 bp):
ATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGAAATTCATA
Found at i:708730 original size:26 final size:26
Alignment explanation
Indices: 708694--708749 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
708684 AACTCGTCTG
*
708694 AAGAGGAAGAAGGAGTTCATAATCTA
1 AAGAGGAAGAAGAAGTTCATAATCTA
* *
708720 AAGAGGAAGAAGAAGTTCATAGTCTG
1 AAGAGGAAGAAGAAGTTCATAATCTA
708746 AAGA
1 AAGA
708750 ACTTATTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.46, C:0.07, G:0.29, T:0.18
Consensus pattern (26 bp):
AAGAGGAAGAAGAAGTTCATAATCTA
Found at i:710312 original size:2 final size:2
Alignment explanation
Indices: 710307--710335 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
710297 ACACACACAC
710307 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 A
710336 CATACATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:710497 original size:2 final size:2
Alignment explanation
Indices: 710486--710550 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
710476 ATTCTCTACT
710486 TA TA -A 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
710527 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
710551 CTTTAGTTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:710634 original size:18 final size:20
Alignment explanation
Indices: 710597--710636 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
710587 TTTTCTTAGG
710597 AAAAATTATTATATTTTATT
1 AAAAATTATTATATTTTATT
*
710617 AAAATTTATT-TA-TTTATT
1 AAAAATTATTATATTTTATT
710635 AA
1 AA
710637 TATTAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAAAATTATTATATTTTATT
Found at i:712960 original size:81 final size:81
Alignment explanation
Indices: 712863--713024 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
712853 TTAGTCCTAA
712863 CGTATAGAAAATTCGAGGACAATTTTTCTTTAAGGGGGAGAGAATTGCAACACCACTAAAATCAG
1 CGTATAGAAAATTCGAGGACAATTTTTCTTTAAGGGGGAGAGAATTGCAACACCACTAAAATCAG
712928 TTTAGTAATTTGACTT
66 TTTAGTAATTTGACTT
712944 CGTATAGAAAATTCGAGGACAATTTTTCTTTAAGGGGGAGAGAATTGCAACACCACTAAAATCAG
1 CGTATAGAAAATTCGAGGACAATTTTTCTTTAAGGGGGAGAGAATTGCAACACCACTAAAATCAG
713009 TTTAGTAATTTGACTT
66 TTTAGTAATTTGACTT
713025 TCAATAATCA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (81 bp):
CGTATAGAAAATTCGAGGACAATTTTTCTTTAAGGGGGAGAGAATTGCAACACCACTAAAATCAG
TTTAGTAATTTGACTT
Found at i:721380 original size:38 final size:38
Alignment explanation
Indices: 721324--721401 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
721314 AACCTCCATT
721324 TTAAATTCTATTTCAAGCAATAACTAGGCAAATCAATA
1 TTAAATTCTATTTCAAGCAATAACTAGGCAAATCAATA
*
721362 TTAAGTTCTATTTCAAGCAATAACTAGGCAAATCAATA
1 TTAAATTCTATTTCAAGCAATAACTAGGCAAATCAATA
721400 TT
1 TT
721402 GTATCATATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (38 bp):
TTAAATTCTATTTCAAGCAATAACTAGGCAAATCAATA
Found at i:723109 original size:20 final size:21
Alignment explanation
Indices: 723079--723119 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
723069 AAATTATTCC
723079 AATTCAACATTCTAACATCAA
1 AATTCAACATTCTAACATCAA
*
723100 AATT-AACATTCTAATATCAA
1 AATTCAACATTCTAACATCAA
723120 TTCCCGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTCAACATTCTAACATCAA
Found at i:724369 original size:29 final size:30
Alignment explanation
Indices: 724292--724369 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 30
724282 CGTAGGGAAA
* *
724292 TTACAACTCTGGTTTCTAAATTTTCACCAAGT
1 TTAC-ACTTTGGTTACTAAATTTTCA-CAAGT
* ** *
724324 TTACACTTTAGCCACTAAATTTTCA-AATT
1 TTACACTTTGGTTACTAAATTTTCACAAGT
*
724353 TTACATTTTGGTTACTA
1 TTACACTTTGGTTACTA
724370 GTCCAAAATT
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
29 16 0.44
31 16 0.44
32 4 0.11
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (30 bp):
TTACACTTTGGTTACTAAATTTTCACAAGT
Found at i:725657 original size:104 final size:104
Alignment explanation
Indices: 725474--725678 Score: 374
Period size: 104 Copynumber: 2.0 Consensus size: 104
725464 ACAAGCGATG
725474 CTTCGGTTGCCCAAATTGGTTCGAGGTTAGTTCATGTACAAGTTAATTCTTTTGAGTTTATGAAA
1 CTTCGGTTGCCCAAATTGGTTCGAGGTTAGTTCATGTACAAGTTAATTCTTTTGAGTTTATGAAA
725539 TGTGATGCAAATTGGTTAGTTATGAAATGCTTCACCATT
66 TGTGATGCAAATTGGTTAGTTATGAAATGCTTCACCATT
* * *
725578 CTTCGGTTGCCTAAATTGGTTCGAGGTTAGTTCATGTACATGTTAATTTTTTTGAGTTTATGAAA
1 CTTCGGTTGCCCAAATTGGTTCGAGGTTAGTTCATGTACAAGTTAATTCTTTTGAGTTTATGAAA
*
725643 TGTGATGCATATTGGTTAGTTATGAAATGCTTCACC
66 TGTGATGCAAATTGGTTAGTTATGAAATGCTTCACC
725679 GTGATTTGTT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 97 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (104 bp):
CTTCGGTTGCCCAAATTGGTTCGAGGTTAGTTCATGTACAAGTTAATTCTTTTGAGTTTATGAAA
TGTGATGCAAATTGGTTAGTTATGAAATGCTTCACCATT
Found at i:726292 original size:40 final size:41
Alignment explanation
Indices: 726211--726302 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 41
726201 AATGTAGAGT
*
726211 TATATAAAGTTGACCAAAATTTTCATTCAAAATTAACAAAA
1 TATATAAAGTTGACCAAAATTTCCATTCAAAATTAACAAAA
*
726252 TATATAAAGTT-ACC-ATATTTCCATTCAATAATTAACAAAA
1 TATATAAAGTTGACCAAAATTTCCATTCAA-AATTAACAAAA
*
726292 TACATAAAGTT
1 TATATAAAGTT
726303 TAACTAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 12 0.26
40 24 0.51
41 11 0.23
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (41 bp):
TATATAAAGTTGACCAAAATTTCCATTCAAAATTAACAAAA
Found at i:726453 original size:15 final size:15
Alignment explanation
Indices: 726433--726503 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
726423 GTGGTGATGT
*
726433 CTATTGTGTTGTTGC
1 CTATTGTGTTGGTGC
* **
726448 CTATTGTGCTACTGC
1 CTATTGTGTTGGTGC
*
726463 CTCTTGTGTTGGTGC
1 CTATTGTGTTGGTGC
* * *
726478 CTCTTCTGTTGGTGT
1 CTATTGTGTTGGTGC
*
726493 CTGTTGTGTTG
1 CTATTGTGTTG
726504 CTTTTTTCTG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.04, C:0.18, G:0.28, T:0.49
Consensus pattern (15 bp):
CTATTGTGTTGGTGC
Found at i:728773 original size:42 final size:42
Alignment explanation
Indices: 728706--728813 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
728696 ACTCTCACTG
* * * *
728706 TCAGCCTTACCCTTATCACCCTCACCCT-TATTGTTAGACTTC
1 TCAGCCTCACCCTCAACACCCTCACCCTCGATT-TTAGACTTC
*
728748 TCAGCCTCACCCTCAACACCTTCACCCTCGATTTTAGACTTC
1 TCAGCCTCACCCTCAACACCCTCACCCTCGATTTTAGACTTC
* * * *
728790 CCAACCTCACCCTGAGCACCCTCA
1 TCAGCCTCACCCTCAACACCCTCA
728814 GTCTCACTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 52 0.95
43 3 0.05
ACGTcount: A:0.21, C:0.44, G:0.07, T:0.28
Consensus pattern (42 bp):
TCAGCCTCACCCTCAACACCCTCACCCTCGATTTTAGACTTC
Found at i:731832 original size:20 final size:20
Alignment explanation
Indices: 731772--731834 Score: 76
Period size: 18 Copynumber: 3.2 Consensus size: 20
731762 TGAAATGTTG
731772 AGTTTCAAAACTTCTAGGAA
1 AGTTTCAAAACTTCTAGGAA
* *
731792 AG--TCCAAACTTTTAGGGAA
1 AGTTTCAAAACTTCTA-GGAA
*
731811 AGTTTCTAAACTTCTAGGAA
1 AGTTTCAAAACTTCTAGGAA
731831 AGTT
1 AGTT
731835 CCTGAACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 10 0.28
19 6 0.17
20 10 0.28
21 10 0.28
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (20 bp):
AGTTTCAAAACTTCTAGGAA
Found at i:731842 original size:20 final size:20
Alignment explanation
Indices: 731779--731843 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
731769 TTGAGTTTCA
731779 AAACTTCTAGGAAAG-TCC-
1 AAACTTCTAGGAAAGTTCCT
* *
731797 AAACTTTTAGGGAAAGTTTCT
1 AAACTTCTA-GGAAAGTTCCT
731818 AAACTTCTAGGAAAGTTCCT
1 AAACTTCTAGGAAAGTTCCT
*
731838 GAACTT
1 AAACTT
731844 TTCATTCCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 8 0.21
19 6 0.15
20 17 0.44
21 8 0.21
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (20 bp):
AAACTTCTAGGAAAGTTCCT
Found at i:739322 original size:29 final size:29
Alignment explanation
Indices: 739280--739338 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
739270 ATTTTCACCT
739280 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
739309 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
739338 A
1 A
739339 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:744636 original size:9 final size:9
Alignment explanation
Indices: 744622--744653 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
744612 AATATATTTA
744622 TATATCATG
1 TATATCATG
*
744631 TATATCATA
1 TATATCATG
744640 TATATCATG
1 TATATCATG
744649 TATAT
1 TATAT
744654 ATAGTGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (9 bp):
TATATCATG
Found at i:746050 original size:4 final size:4
Alignment explanation
Indices: 746041--746114 Score: 61
Period size: 4 Copynumber: 19.8 Consensus size: 4
746031 TTTAGTATCT
* *
746041 TATA TATA TATA TATA TATA TATA TATA TAGT- TATT TAT- TATT TAT-
1 TATA TATA TATA TATA TATA TATA TATA TA-TA TATA TATA TATA TATA
**
746087 TAT- TAT- TA-A TGCA TATA TATA TATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TAT
746115 TTAGTTTTCT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
3 13 0.21
4 48 0.77
5 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (4 bp):
TATA
Found at i:746052 original size:6 final size:6
Alignment explanation
Indices: 746041--746114 Score: 61
Period size: 6 Copynumber: 13.2 Consensus size: 6
746031 TTTAGTATCT
* *
746041 TATATA TATATA TATATA TATATA TATATA GT-TATT TAT-TA TTTAT-
1 TATATA TATATA TATATA TATATA TATATA -TATATA TATATA TATATA
**
746087 TAT-TA T-TA-A TGCATA TATATA TATATA T
1 TATATA TATATA TATATA TATATA TATATA T
746115 TTAGTTTTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.07
5 8 0.15
6 41 0.76
7 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
TATATA
Found at i:746056 original size:10 final size:10
Alignment explanation
Indices: 746041--746114 Score: 61
Period size: 10 Copynumber: 7.9 Consensus size: 10
746031 TTTAGTATCT
746041 TATATATATA
1 TATATATATA
746051 TATATATATA
1 TATATATATA
746061 TATATATATA
1 TATATATATA
*
746071 GT-TATTTAT-
1 -TATATATATA
*
746080 TATTTAT-TA
1 TATATATATA
746089 T-TAT-TA-A
1 TATATATATA
**
746096 TGCATATATA
1 TATATATATA
746106 TATATATAT
1 TATATATAT
746115 TTAGTTTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.06
8 6 0.12
9 6 0.12
10 34 0.68
11 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (10 bp):
TATATATATA
Found at i:750303 original size:95 final size:95
Alignment explanation
Indices: 750139--750320 Score: 276
Period size: 95 Copynumber: 1.9 Consensus size: 95
750129 ATATTATTTA
** * * *
750139 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAACTGTCCCTCTAGAGAAATTGGTTAAACGCCCCAGCTTTATGGATAAG
*
750204 ATTCAGCTAGCCTGATAAAGGTGATTATAC
66 ATTCAGCTAACCTGATAAAGGTGATTATAC
* *
750234 TATACAATAAAGCTTGAACTGTCCCTCTA-AGTAAATTGGTTAAATGCCCCAGCTTTATGGATAC
1 TATACAATAAAGCTTGAACTGTCCCTCTAGAG-AAATTGGTTAAACGCCCCAGCTTTATGGATAA
750298 GATTCAGCTAACCTGATAAAGGT
65 GATTCAGCTAACCTGATAAAGGT
750321 ATTTACATAT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 2 0.03
95 76 0.97
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTGAACTGTCCCTCTAGAGAAATTGGTTAAACGCCCCAGCTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGATTATAC
Found at i:751782 original size:17 final size:17
Alignment explanation
Indices: 751730--751783 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
751720 CTTGAGACAG
751730 TTTCTCTTAAAACAAAT
1 TTTCTCTTAAAACAAAT
* *
751747 TGTCTCTCTTGAGAC--AT
1 T-T-TCTCTTAAAACAAAT
751764 TTTCTCTTAAAACAAAT
1 TTTCTCTTAAAACAAAT
751781 TTT
1 TTT
751784 GTCTCTCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 9 0.31
16 1 0.03
17 9 0.31
18 1 0.03
19 9 0.31
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (17 bp):
TTTCTCTTAAAACAAAT
Found at i:751897 original size:37 final size:36
Alignment explanation
Indices: 751847--751966 Score: 161
Period size: 37 Copynumber: 3.3 Consensus size: 36
751837 GAAACAAAGG
751847 TTTGTCTCTCTTGAGATAGTTTCTTTTAGAACTAAAT
1 TTTGTCTCTCTTGAGA-AGTTTCTTTTAGAACTAAAT
* ** *
751884 TTTGTCTCTCTTGAGACGTTTTCTCGTAAAAC-AAAT
1 TTTGTCTCTCTTGAGAAG-TTTCTTTTAGAACTAAAT
751920 TTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAAT
1 TTTGTCTCTCTTGAGA-AGTTTCTTTTAGAACTAAAT
*
751957 TTTGCCTCTC
1 TTTGTCTCTC
751967 ATAAAAAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
36 31 0.44
37 40 0.56
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (36 bp):
TTTGTCTCTCTTGAGAAGTTTCTTTTAGAACTAAAT
Found at i:751943 original size:36 final size:36
Alignment explanation
Indices: 751701--751815 Score: 153
Period size: 34 Copynumber: 3.2 Consensus size: 36
751691 TAATTTACTA
**
751701 AAAACAAAGTTTCATCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
*
751738 AAAACAAA--TTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
751772 AAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
751808 GAAACAAA
1 AAAACAAA
751816 AACATTGAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
34 31 0.45
36 30 0.43
37 8 0.12
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:752116 original size:194 final size:194
Alignment explanation
Indices: 751782--752137 Score: 588
Period size: 194 Copynumber: 1.8 Consensus size: 194
751772 AAAACAAATT
* *
751782 TTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACATTGAATTTGTTTTCCTTGAAACAAAGG
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACATTGAATCTGTTTTCCTTGAAACAAA-G
* * *
751847 TTTGTCTCTCTTGAGATAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACGTTTTCTCGTA
65 TTCGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTA
* *
751912 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGCCTCTCATAAAAAAAA
130 AAAAAAATTTTGTCTCTCTTGAGACAATTTCTTTTAGAACTAAATTTTGCCTCTCATAAAAAAAA
* * *
751977 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAA-T
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACATTGAATCTGTTTTCCTTGAAACAAAGT
*
752041 TGCGTCTCTCTTGAGACAGTTTTTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTA
66 T-CGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTA
752106 AAAAAAATTTTGTCTCTCTTGAGACAATTTCT
130 AAAAAAATTTTGTCTCTCTTGAGACAATTTCT
752138 CTTGAAACAA
Statistics
Matches: 149, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
193 2 0.01
194 89 0.60
195 58 0.39
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (194 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACATTGAATCTGTTTTCCTTGAAACAAAGT
TCGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTAA
AAAAAATTTTGTCTCTCTTGAGACAATTTCTTTTAGAACTAAATTTTGCCTCTCATAAAAAAAA
Found at i:752129 original size:138 final size:138
Alignment explanation
Indices: 751963--752257 Score: 443
Period size: 138 Copynumber: 2.1 Consensus size: 138
751953 AAATTTTGCC
* * *
751963 TCTCATAAAAAAAA--TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTTGAATCTGTT
1 TCTCATAAAAAAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTCTGAATCTGTT
* *
752026 TTCCTTGAAACAAATTGCGTCT-CTCTTGAGACAGTTTTTTTTAGAACTAAATTTTGTCTCTCTT
66 TTCCTTGAAACAAATTGCATCTGC-CTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTT
*
752090 GAGACATTT
130 GAGACAGTT
* *
752099 TCTCGTAAAAAAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAATCTCTGAATCTGTT
1 TCTCATAAAAAAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTCTGAATCTGTT
*
752164 TTCCTTGAAACAAATTGCATCTGCCTTGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTCTTG
66 TTCCTTGAAACAAATTGCATCTGCCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTG
752229 AGACAGTT
131 AGACAGTT
* *
752237 TCCCTTAAAACAAAATCTTTG
1 TCTCATAAAA-AAAAT-TTTG
752258 AATTTGTTTT
Statistics
Matches: 143, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
136 13 0.09
138 120 0.84
139 6 0.04
140 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
TCTCATAAAAAAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTCTGAATCTGTT
TTCCTTGAAACAAATTGCATCTGCCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTG
AGACAGTT
Found at i:752165 original size:102 final size:102
Alignment explanation
Indices: 752087--752281 Score: 268
Period size: 102 Copynumber: 1.9 Consensus size: 102
752077 TTTTGTCTCT
* * *
752087 CTTGAGACATTTTCTCGT-AAAAAAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAT
1 CTTGAGACAGTTTCTCGTGAAAAAAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAAT
752151 CTCTGAATCTGTTTTCCTTGAAACAAATTGCATCTGC
66 CTCTGAATCTGTTTTCCTTGAAACAAATTGCATCTGC
** * ** *
752188 CTTGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAAT
1 CTTGAGACAGTTTCTCGTGAAAAAAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAAT
* *
752253 CTTTGAATTTGTTTTCCATT-AAACAAATT
66 CTCTGAATCTGTTTTCC-TTGAAACAAATT
752282 TCGTCTCACT
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
101 15 0.19
102 64 0.79
103 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (102 bp):
CTTGAGACAGTTTCTCGTGAAAAAAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAAT
CTCTGAATCTGTTTTCCTTGAAACAAATTGCATCTGC
Found at i:752302 original size:102 final size:102
Alignment explanation
Indices: 752110--752308 Score: 285
Period size: 102 Copynumber: 2.0 Consensus size: 102
752100 CTCGTAAAAA
* *
752110 AAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAATCTCTGAATCTGTTTTCCTTGAAAC
1 AAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAATCTCTGAATCTGTTTTCCTTGAAAC
*
752175 AAATTGCATCTGCCTTGAGACAGTTTCTTTTGGAACT
66 AAATTGCATCTGCCTCGAGACAGTTTCTTTTGGAACT
* * *
752212 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATTTGTTTTCCATT-AAA
1 AAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAATCTCTGAATCTGTTTTCC-TTGAAA
* * *
752276 CAAATTTCGTCT-CACTCGAGATAGTTTCTTTTG
65 CAAATTGCATCTGC-CTCGAGACAGTTTCTTTTG
752309 AGACAGTTTA
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 1 0.01
102 83 0.97
103 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (102 bp):
AAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAAATCTCTGAATCTGTTTTCCTTGAAAC
AAATTGCATCTGCCTCGAGACAGTTTCTTTTGGAACT
Found at i:754154 original size:6 final size:6
Alignment explanation
Indices: 754145--754274 Score: 170
Period size: 6 Copynumber: 21.7 Consensus size: 6
754135 TTATTAATGC
* * * *
754145 ATATAT ATATAT ATATAT ATATAT ATACAT ATATGT ATATAC ATATGT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
754193 ATATAT ACATAT ATGTAT ATATAT ATATAT ATATAT ATATGT ATACAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
754241 ATATGT ATATAT ATATAT ATGTAT ATATAT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
754275 TTAGTTTTCA
Statistics
Matches: 104, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 104 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (6 bp):
ATATAT
Found at i:754164 original size:14 final size:14
Alignment explanation
Indices: 754145--754274 Score: 170
Period size: 14 Copynumber: 9.3 Consensus size: 14
754135 TTATTAATGC
754145 ATATATATATATAT
1 ATATATATATATAT
*
754159 ATATATATATATAC
1 ATATATATATATAT
* *
754173 ATATATGTATATAC
1 ATATATATATATAT
* *
754187 ATATGTATATATAC
1 ATATATATATATAT
*
754201 ATATATGTATATAT
1 ATATATATATATAT
754215 ATATATATATATAT
1 ATATATATATATAT
* *
754229 ATATGTATACATAT
1 ATATATATATATAT
*
754243 ATGTATATATATAT
1 ATATATATATATAT
*
754257 ATATGTATATATAT
1 ATATATATATATAT
754271 ATAT
1 ATAT
754275 TTAGTTTTCA
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 101 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (14 bp):
ATATATATATATAT
Done.