Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009458.1 Hibiscus syriacus cultivar Beakdansim tig00113719_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: 1407308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:602576 original size:18 final size:18
Alignment explanation
Indices: 602545--602579 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
602535 ACAATGCTTT
*
602545 CTTCTTCAAGCAAGACAG
1 CTTCTGCAAGCAAGACAG
*
602563 CTTCTGCAATCAAGACA
1 CTTCTGCAAGCAAGACA
602580 AAACAAATTG
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:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (18 bp):
CTTCTGCAAGCAAGACAG
Found at i:603733 original size:18 final size:18
Alignment explanation
Indices: 603710--603753 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
603700 GTCGAGCATA
*
603710 GATATTCTGTCAAAAATT
1 GATATTCCGTCAAAAATT
*
603728 GATATTCCGTCGAAAATT
1 GATATTCCGTCAAAAATT
*
603746 GATTTTCC
1 GATATTCC
603754 AACTGATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (18 bp):
GATATTCCGTCAAAAATT
Found at i:605168 original size:2 final size:2
Alignment explanation
Indices: 605161--605188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
605151 TTCCTTTTTC
605161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
605189 CTTTTGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:606317 original size:14 final size:14
Alignment explanation
Indices: 606298--606327 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
606288 AGTCGCTCAT
606298 TATCGGACCTAACA
1 TATCGGACCTAACA
606312 TATCGGACCTAACA
1 TATCGGACCTAACA
606326 TA
1 TA
606328 GCAACGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (14 bp):
TATCGGACCTAACA
Found at i:612228 original size:16 final size:16
Alignment explanation
Indices: 612204--612237 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
612194 TATTGCCGAC
*
612204 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
612220 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
612236 CG
1 CG
612238 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:614733 original size:12 final size:10
Alignment explanation
Indices: 614691--614732 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
614681 TTTTATCACA
614691 TCAAATTCTC
1 TCAAATTCTC
614701 TCAAATTCTC
1 TCAAATTCTC
614711 T-AAATTTCTC
1 TCAAA-TTCTC
*
614721 TCAAATACTC
1 TCAAATTCTC
614731 TC
1 TC
614733 TTTTTAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.10
10 23 0.79
11 3 0.10
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:615050 original size:111 final size:111
Alignment explanation
Indices: 614856--615077 Score: 372
Period size: 111 Copynumber: 2.0 Consensus size: 111
614846 TAGAAATCAT
*
614856 ATATCTCTACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
* * *
614921 TATTTAGTTGATTTATTTAATGAATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGAATGATTATTAGATAAAGAATTAA
* *
614967 ATATCTCGACATTTTGTTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
* *
615032 TAATTAGTTGATTCATTTAATGCATGATTATTATATAAAGAATTAA
66 TAATTAGTTGATTCATTTAATGAATGATTATTAGATAAAGAATTAA
615078 TTTTTGTAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGAATGATTATTAGATAAAGAATTAA
Found at i:616990 original size:12 final size:12
Alignment explanation
Indices: 616973--616998 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
616963 ACCTGCTCAG
616973 GACGACGACGAT
1 GACGACGACGAT
616985 GACGACGACGAT
1 GACGACGACGAT
616997 GA
1 GA
616999 TGGTGACAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.35, T:0.08
Consensus pattern (12 bp):
GACGACGACGAT
Found at i:623616 original size:48 final size:47
Alignment explanation
Indices: 623515--623611 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 47
623505 TACTGGAGGT
** * *
623515 AATTTTTTATTTTTTCTCACCTGTTTACTTGTTACATCATTTAGTAAC
1 AATTTTTTATAATTTCTCACCTGTTTACTGGATACATCATTTAG-AAC
*
623563 AATTTTTTATAATTTCTCACCTGTTTAGTTCTGGATACTTCATTTAGAA
1 AATTTTTTATAATTTCTCACCTGTTTA---CTGGATACATCATTTAGAA
623612 ATTTTCAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 25 0.61
50 2 0.05
51 14 0.34
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (47 bp):
AATTTTTTATAATTTCTCACCTGTTTACTGGATACATCATTTAGAAC
Found at i:629063 original size:10 final size:10
Alignment explanation
Indices: 629048--629074 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
629038 CAAGCCACCT
629048 CACTTCCCTG
1 CACTTCCCTG
629058 CACTTCCCTG
1 CACTTCCCTG
629068 CACTTCC
1 CACTTCC
629075 AACCGTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.52, G:0.07, T:0.30
Consensus pattern (10 bp):
CACTTCCCTG
Found at i:629766 original size:26 final size:26
Alignment explanation
Indices: 629737--629789 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
629727 AGTAAGCAAT
629737 AGGTAAACTGGTATCTGCCAAGCGCC
1 AGGTAAACTGGTATCTGCCAAGCGCC
*
629763 AGGTAAACTGGTATCTGCCAAGTGCC
1 AGGTAAACTGGTATCTGCCAAGCGCC
629789 A
1 A
629790 ATGGTCAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (26 bp):
AGGTAAACTGGTATCTGCCAAGCGCC
Found at i:634755 original size:2 final size:2
Alignment explanation
Indices: 634748--634812 Score: 75
Period size: 2 Copynumber: 33.5 Consensus size: 2
634738 TTCTTGTACC
*
634748 TA TA TA TA TA TG TA TA TA TA T- TA TA TA TGA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
634789 TA T- TA TA TA TGA -A TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA T
634813 GTGTGTGTGA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
1 4 0.07
2 49 0.89
3 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:634781 original size:23 final size:23
Alignment explanation
Indices: 634748--634812 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
634738 TTCTTGTACC
*
634748 TATATAT--ATATGTATATATAT
1 TATATATGAATATATATATATAT
634769 TATATATGAATATATATATATAT
1 TATATATGAATATATATATATAT
634792 TATATATGAATATATATATAT
1 TATATATGAATATATATATAT
634813 GTGTGTGTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 7 0.17
23 34 0.83
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
TATATATGAATATATATATATAT
Found at i:639292 original size:14 final size:14
Alignment explanation
Indices: 639273--639306 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
639263 AAACATAAAC
639273 GAATGACCAAAAAT
1 GAATGACCAAAAAT
639287 GAATGACCAAAAAT
1 GAATGACCAAAAAT
639301 GAATGA
1 GAATGA
639307 ATAAAAACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.18, T:0.15
Consensus pattern (14 bp):
GAATGACCAAAAAT
Found at i:639312 original size:14 final size:14
Alignment explanation
Indices: 639273--639313 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
639263 AAACATAAAC
*
639273 GAATGACCAAAAAT
1 GAATGAACAAAAAT
*
639287 GAATGACCAAAAAT
1 GAATGAACAAAAAT
*
639301 GAATGAATAAAAA
1 GAATGAACAAAAA
639314 CGAACGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (14 bp):
GAATGAACAAAAAT
Found at i:640308 original size:2 final size:2
Alignment explanation
Indices: 640301--640335 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
640291 ATTCCCATCC
640301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
640336 TGTAAATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:642879 original size:55 final size:55
Alignment explanation
Indices: 642798--642906 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
642788 TCCGGATCAT
* * *
642798 ATACTGTAGAGGTAAGAGTTACCCTCCCAACCCAGTTTACTCCATTAACAATCGG
1 ATACTGCAGAGGTAAGAGTTACCCTCCCAACACAGTTTACTCAATTAACAATCGG
* *
642853 ATACTGCAGAGGTAAGAGTTACCCTCCCAACATAGTTTACTCAATTTACAATCG
1 ATACTGCAGAGGTAAGAGTTACCCTCCCAACACAGTTTACTCAATTAACAATCG
642907 TCAGGATTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (55 bp):
ATACTGCAGAGGTAAGAGTTACCCTCCCAACACAGTTTACTCAATTAACAATCGG
Found at i:645553 original size:14 final size:14
Alignment explanation
Indices: 645534--645572 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
645524 TAGGCTGAAT
645534 ATAAATGAACGAAC
1 ATAAATGAACGAAC
* *
645548 ATAAATGAACAAAT
1 ATAAATGAACGAAC
*
645562 ATAAACGAACG
1 ATAAATGAACG
645573 GATTATCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:658718 original size:82 final size:82
Alignment explanation
Indices: 658529--659300 Score: 1043
Period size: 82 Copynumber: 9.4 Consensus size: 82
658519 TAGGCGAAAT
* * * *
658529 AATAATGGTGCATTATCATGTTCTGCAACTTTTCAAAGGTCATTCAATGCACAATTTAAACAA-T
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
*
658593 TTTCAGAAAACGTGTGA
66 TTTCAGAAAACGGGTGA
* *
658610 AATAGTAGTGCATTATCATCTTCTGCAACTTTCCA-ATGGTCATTCAATGCATAATTTAAACAAC
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGA-GGTCATTCAATGCATAATTTAAACAAC
*
658674 TTTTCAGGCAAA-GGGTGA
65 TTTTCA-GAAAACGGGTGA
* *
658692 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTTAATGCATAATTTAAACAATT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
*
658757 TTTCAGAAAACAGGTGA
66 TTTCAGAAAACGGGTGA
* * *
658774 AATAGTGGTGCATTATCATCTTCTGCAACTTTTTAAAGGTCA-TCTAATTCATAATTTAAACAAC
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTC-AATGCATAATTTAAACAAC
*
658838 TTTTCAGAAAACAGGTGA
65 TTTTCAGAAAACGGGTGA
* * * * *
658856 AATAATAGTGTATTCTCATTTTCTGCAACTTTTTCAGAGGTCATTCAATGCATAATTTTAAA-AA
1 AATAGTGGTGCATTATCATCTTCTGCAAC-TTTTCAGAGGTCATTCAATGCATAA-TTTAAACAA
* * *
658920 CTTTTCAAAAAATGGGTTA
64 CTTTTCAGAAAACGGGTGA
* * ** * * *
658939 AATAGTGGTGCATTATCATCTTTTGCAACTTTTCAGAGGTTATTCAATGTGTGATTTAAATAATT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
* *
659004 TTTCAGACAACGAGTGA
66 TTTCAGAAAACGGGTGA
659021 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
*
659086 TTTCAAAAAACGGGTGA
66 TTTCAGAAAACGGGTGA
* * * *
659103 ATTAGTGATGCATTATCATCTTCTACAATTTTTCAGAGGTCATTCAATGCATAATTTAAACAA-T
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
*
659167 TTTCAGAAAACGTGTGA
66 TTTCAGAAAACGGGTGA
* * * * * *
659184 AATAATGATGCATTATCATTTTCTGCCACTTTTTAGAGGTCATTCAATGCATAATTTAAACAATT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
* *
659249 TTTTAGAAAATGGGTGA
66 TTTCAGAAAACGGGTGA
659266 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCA
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCA
659301 CCGACGTATC
Statistics
Matches: 603, Mismatches: 77, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.00
81 139 0.23
82 391 0.65
83 64 0.11
84 8 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (82 bp):
AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
TTTCAGAAAACGGGTGA
Found at i:668542 original size:43 final size:44
Alignment explanation
Indices: 668451--668579 Score: 167
Period size: 43 Copynumber: 3.0 Consensus size: 44
668441 AACAACTCCA
*
668451 AGTCTCCGAGGGTAAAACCGTAAAGATA-GACGGACACCACAAGG
1 AGTCTCTGAGGGTAAAACCGTAAAGATACG-CGGACACCACAAGG
668495 AGTCTCTGAGGGTAAAACCGTAAA-ATACGCGGACACCACAAGG
1 AGTCTCTGAGGGTAAAACCGTAAAGATACGCGGACACCACAAGG
* * **
668538 AG--TCTGAGAGTAAAACCGAAAAAGATACGTAGACACCACAAG
1 AGTCTCTGAGGGTAAAACCG-TAAAGATACGCGGACACCACAAG
668580 ATTAAAATAT
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
41 15 0.19
42 3 0.04
43 35 0.45
44 24 0.31
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (44 bp):
AGTCTCTGAGGGTAAAACCGTAAAGATACGCGGACACCACAAGG
Found at i:675074 original size:11 final size:11
Alignment explanation
Indices: 675054--675083 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
675044 CTTTAACCCA
*
675054 CAAATGTACTC
1 CAAATATACTC
675065 CAAATATACTC
1 CAAATATACTC
675076 CAAATATA
1 CAAATATA
675084 TAAATCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (11 bp):
CAAATATACTC
Found at i:675763 original size:5 final size:5
Alignment explanation
Indices: 675753--675777 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
675743 CACACATGCT
675753 GAATC GAATC GAATC GAATC GAATC
1 GAATC GAATC GAATC GAATC GAATC
675778 CATTGAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
GAATC
Found at i:679234 original size:15 final size:15
Alignment explanation
Indices: 679214--679242 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
679204 AGGGCCCACG
679214 GTTGATTGCTTCAGT
1 GTTGATTGCTTCAGT
679229 GTTGATTGCTTCAG
1 GTTGATTGCTTCAG
679243 CCCATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (15 bp):
GTTGATTGCTTCAGT
Found at i:681176 original size:10 final size:10
Alignment explanation
Indices: 681161--681191 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
681151 CACTATTCAC
681161 ATGAATAGTA
1 ATGAATAGTA
681171 ATGAATAGTA
1 ATGAATAGTA
681181 ATGAATAGTA
1 ATGAATAGTA
681191 A
1 A
681192 CCTCGCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (10 bp):
ATGAATAGTA
Found at i:682452 original size:30 final size:27
Alignment explanation
Indices: 682396--682452 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 27
682386 TATTAGGACA
682396 ATTATAAAAACTAATAAATTTAATAAT
1 ATTATAAAAACTAATAAATTTAATAAT
* *
682423 ATTATGAAAATCTAATGATAATTTTATAAT
1 ATTAT-AAAAACTAAT-A-AATTTAATAAT
682453 TATTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 9 0.36
29 1 0.04
30 10 0.40
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (27 bp):
ATTATAAAAACTAATAAATTTAATAAT
Found at i:686840 original size:40 final size:40
Alignment explanation
Indices: 686795--686876 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
686785 ATATATTTAA
**
686795 ATAATTTTAAATCCTAAATTTTA-AGCTTTAAACAAAATAT
1 ATAATTTTAAATCCTAAACCTTACA-CTTTAAACAAAATAT
*
686835 ATAATTTTAAATCCTAAACCTTACACTTTAAATAAAATAT
1 ATAATTTTAAATCCTAAACCTTACACTTTAAACAAAATAT
686875 AT
1 AT
686877 GATATCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 37 0.97
41 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (40 bp):
ATAATTTTAAATCCTAAACCTTACACTTTAAACAAAATAT
Found at i:692704 original size:64 final size:62
Alignment explanation
Indices: 692636--692864 Score: 244
Period size: 64 Copynumber: 3.6 Consensus size: 62
692626 TGTTTGAATG
* * *
692636 TGCATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAAAAGAAGAACATCGAATGCCTTTGA
1 TGCATCGATGCATAGGTAGTGCATCGATGCA-TCTTTTAAAAGAA-AACATCGAATGCATTTAA
* * * * *
692700 TGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCAATCAA
1 TGCATCGATGCATAGGTAGTGCATCGATGCAT-CTTTTAAAAGAA-AACATCGAATGCATTTAA
* * *
692764 TGCATCGATGCATAAGG-AGTCCATCGATGCATCTCATTAATAAGGAAACATCGAATGCATTTAA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCT-TTTAA-AAGAAAACATCGAATGCATTTAA
* * * *
692828 TGCACCGATGTACAAGTAGTGCATCGATGCATACTTT
1 TGCATCGATGCATAGGTAGTGCATCGATGCAT-CTTT
692865 CATTAAAAGA
Statistics
Matches: 136, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
63 5 0.04
64 124 0.91
65 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (62 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCTTTTAAAAGAAAACATCGAATGCATTTAA
Found at i:693328 original size:15 final size:16
Alignment explanation
Indices: 693308--693337 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
693298 GATCTACGTG
693308 AATACATGT-ATATGT
1 AATACATGTGATATGT
693323 AATACATGTGATATG
1 AATACATGTGATATG
693338 ATATGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (16 bp):
AATACATGTGATATGT
Found at i:696672 original size:21 final size:21
Alignment explanation
Indices: 696625--696674 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
696615 CCGCCATGTT
*
696625 ATCAACCACCGTGGACTACCAC
1 ATCAA-CACCGTGGACGACCAC
*
696647 GTCAACACCGTGGATCGA-CAC
1 ATCAACACCGTGGA-CGACCAC
696668 ATCAACA
1 ATCAACA
696675 TAGTGAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.34, C:0.36, G:0.16, T:0.14
Consensus pattern (21 bp):
ATCAACACCGTGGACGACCAC
Found at i:702625 original size:21 final size:21
Alignment explanation
Indices: 702592--702643 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
702582 ACGAGCCACA
702592 ATATAATAATTTTAAAAAAATT
1 ATATAA-AATTTTAAAAAAATT
702614 ATATAAAATTTTAAAAAAATT
1 ATATAAAATTTTAAAAAAATT
702635 ATATTAAAA
1 ATA-TAAAA
702644 AAAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAAATTTTAAAAAAATT
Found at i:704965 original size:21 final size:21
Alignment explanation
Indices: 704939--704988 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
704929 GGACCGGCGA
704939 AAGAGCCGGAGAAGAAGAAAG
1 AAGAGCCGGAGAAGAAGAAAG
704960 AAGAGCCGGAGAAGAAGAAAG
1 AAGAGCCGGAGAAGAAGAAAG
704981 AAGAGCCG
1 AAGAGCCG
704989 AAAAAGGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.50, C:0.12, G:0.38, T:0.00
Consensus pattern (21 bp):
AAGAGCCGGAGAAGAAGAAAG
Found at i:705759 original size:21 final size:21
Alignment explanation
Indices: 705735--705781 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
705725 AATATGTAAA
705735 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
705756 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
705777 TCGCA
1 TCGCA
705782 ACGTGATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:705797 original size:20 final size:20
Alignment explanation
Indices: 705772--705846 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
705762 TGCGATTTTC
*
705772 CAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGCGATAGT
* * *
705792 CAAATTCTCAATGCGAAAGT
1 CAAATTCGCAACGCGATAGT
*
705812 CAAATTCGCAACGCGATAAT
1 CAAATTCGCAACGCGATAGT
*
705832 CAAATTTGCAACGCG
1 CAAATTCGCAACGCG
705847 GATTTAATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:706628 original size:12 final size:12
Alignment explanation
Indices: 706607--706640 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
706597 ACCACATTTT
*
706607 CAATACCAAACA
1 CAATATCAAACA
706619 CAATATCAAACA
1 CAATATCAAACA
*
706631 CAATCTCAAA
1 CAATATCAAA
706641 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:706793 original size:24 final size:24
Alignment explanation
Indices: 706766--706819 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
706756 GTATTCGAAA
706766 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
706790 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
706814 TTTGAT
1 TTTGAT
706820 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:709081 original size:18 final size:18
Alignment explanation
Indices: 709058--709093 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
709048 AAGCAAAAGG
*
709058 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
709076 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
709094 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:709437 original size:20 final size:20
Alignment explanation
Indices: 709412--709473 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
709402 CGCGAAATAA
709412 GCGTAGCGAATTTGACTATC
1 GCGTAGCGAATTTGACTATC
*
709432 GCGTAGCGAATTTGACTTTC
1 GCGTAGCGAATTTGACTATC
*
709452 GCGTTGCGAATTTGACTATC
1 GCGTAGCGAATTTGACTATC
709472 GC
1 GC
709474 AACGCTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (20 bp):
GCGTAGCGAATTTGACTATC
Found at i:709507 original size:20 final size:20
Alignment explanation
Indices: 709482--709523 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
709472 GCAACGCTTA
*
709482 TTTCGCGTTGTAAATTTACC
1 TTTCGCGTTGCAAATTTACC
*
709502 TTTCGCGTTGCGAATTTACC
1 TTTCGCGTTGCAAATTTACC
709522 TT
1 TT
709524 CAATAGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTACC
Found at i:709612 original size:25 final size:25
Alignment explanation
Indices: 709584--709633 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
709574 AAATCAATTA
*
709584 AACATTGTTGTGGGTAAATTATTTG
1 AACATTGTTATGGGTAAATTATTTG
*
709609 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTAAATTATTTG
709634 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTAAATTATTTG
Found at i:710041 original size:18 final size:18
Alignment explanation
Indices: 710020--710056 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
710010 GTAATTGGAG
710020 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
710038 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
710056 T
1 T
710057 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:710063 original size:24 final size:24
Alignment explanation
Indices: 710012--710064 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
710002 TTTCATATGT
* * *
710012 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
710036 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
710060 AATTT
1 AATTT
710065 CGGCTTCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:710402 original size:39 final size:39
Alignment explanation
Indices: 710359--710445 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
710349 TCCGATGCTC
710359 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
710398 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
710437 ATCAAAATC
1 ATCAAAATC
710446 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:710716 original size:20 final size:20
Alignment explanation
Indices: 710682--710719 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
710672 GCAACGCTTA
**
710682 TTTTGCGTTGTGAATTTGAC
1 TTTTGCGTTACGAATTTGAC
710702 TTTTGCGTTACGAATTTG
1 TTTTGCGTTACGAATTTG
710720 TATCTTCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.11, G:0.24, T:0.50
Consensus pattern (20 bp):
TTTTGCGTTACGAATTTGAC
Found at i:712030 original size:21 final size:21
Alignment explanation
Indices: 711988--712030 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
711978 TTTCTGGGTT
* * *
711988 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
712009 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
712030 A
1 A
712031 CGAATATGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:712127 original size:66 final size:67
Alignment explanation
Indices: 711988--712159 Score: 258
Period size: 66 Copynumber: 2.6 Consensus size: 67
711978 TTTCTGGGTT
* * *
711988 AGGGGAATCGGTACCCATTCAA-GGGGAACCGATACCCCCTCAACGAATATGGATTTCCAGAATG
1 AGGGGAATCGATACCC--CCAAGGGGGAACCGATACCCCCTCAACGAATATGGAATTCCAGAATG
712052 CTAG
64 CTAG
712056 AGGGGAATCGATACCCCCAAGGGGGAACCGATACCCCCTCAACGAATAT-GAATTCCAGAATGCT
1 AGGGGAATCGATACCCCCAAGGGGGAACCGATACCCCCTCAACGAATATGGAATTCCAGAATGCT
712120 AG
66 AG
* * *
712122 TGGGGAATCGATACCCCCAGGGGGGAACCGATTCCCCC
1 AGGGGAATCGATACCCCCAAGGGGGAACCGATACCCCC
712160 ATGAGAAAAA
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
66 54 0.56
67 28 0.29
68 15 0.15
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (67 bp):
AGGGGAATCGATACCCCCAAGGGGGAACCGATACCCCCTCAACGAATATGGAATTCCAGAATGCT
AG
Found at i:712148 original size:20 final size:20
Alignment explanation
Indices: 712123--712160 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
712113 GAATGCTAGT
*
712123 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
712143 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
712161 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:712837 original size:23 final size:23
Alignment explanation
Indices: 712771--712829 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
712761 ATCATTATAT
*
712771 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
712793 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
712816 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
712830 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:716698 original size:20 final size:20
Alignment explanation
Indices: 716675--716716 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
716665 AAAAGTTTCT
* * *
716675 GAAACTTAAATTCGTAACGC
1 GAAAATTAAAATCGCAACGC
716695 GAAAATTAAAATCGCAACGC
1 GAAAATTAAAATCGCAACGC
716715 GA
1 GA
716717 TTTTAGTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAATTAAAATCGCAACGC
Found at i:717198 original size:20 final size:20
Alignment explanation
Indices: 717173--717233 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
717163 GCGTAAAAAC
717173 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
717193 ATTTGACTATCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
717213 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
717233 A
1 A
717234 ATTGGAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:717270 original size:20 final size:21
Alignment explanation
Indices: 717221--717273 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
717211 GAATTTGACT
*
717221 TTCGCGTTGCGAAATTGGAAA
1 TTCGCATTGCGAAATTGGAAA
717242 TT-G-AGTTGCGAAATTGG-AA
1 TTCGCA-TTGCGAAATTGGAAA
717261 TTCGCATTGCGAA
1 TTCGCATTGCGAA
717274 TTTATTGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 4 0.14
20 21 0.75
21 3 0.11
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGAAATTGGAAA
Found at i:719389 original size:22 final size:22
Alignment explanation
Indices: 719334--719390 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
719324 ATTTTTTAAA
*
719334 TAAGTTATTAATATTTATCTAT
1 TAAGTTATTAATATATATCTAT
**
719356 TATTTTCA-TAATATAATAT-TAT
1 TAAGTT-ATTAATAT-ATATCTAT
719378 TAAGTTATTAATA
1 TAAGTTATTAATA
719391 ATAAGTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
21 1 0.04
22 22 0.81
23 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
TAAGTTATTAATATATATCTAT
Found at i:722196 original size:21 final size:22
Alignment explanation
Indices: 722165--722205 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
722155 TCAGATACGT
*
722165 GAAGAAAAGTGAAGAGAAGAAA
1 GAAGAAAAGTGAAGAAAAGAAA
722187 GAAG-AAAGTGAAGAAAAGA
1 GAAGAAAAGTGAAGAAAAGA
722206 TGGGATGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.32, T:0.05
Consensus pattern (22 bp):
GAAGAAAAGTGAAGAAAAGAAA
Found at i:723170 original size:22 final size:22
Alignment explanation
Indices: 723115--723171 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
723105 ATTTTTTAAA
*
723115 TAAGTTATTAATATTTATCTAT
1 TAAGTTATTAATATATATCTAT
**
723137 TATTTTCA-TAATATAATAT-TAT
1 TAAGTT-ATTAATAT-ATATCTAT
723159 TAAGTTATTAATA
1 TAAGTTATTAATA
723172 ATAAGTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
21 1 0.04
22 22 0.81
23 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
TAAGTTATTAATATATATCTAT
Found at i:723734 original size:18 final size:19
Alignment explanation
Indices: 723693--723735 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
723683 TTAATTTGTT
*
723693 AAATAATCAATCAAAATTT
1 AAATAATCAATCAAAATTA
* *
723712 TAATAATTAAT-AAAATTA
1 AAATAATCAATCAAAATTA
723730 AAATAA
1 AAATAA
723736 AATTAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATCAATCAAAATTA
Found at i:724121 original size:21 final size:21
Alignment explanation
Indices: 724096--724143 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
724086 GTTGATCGAT
* *
724096 ACGGTGCTCACATGGCAATTC
1 ACGGTGCTCACATGACAATCC
* *
724117 ACGGTGCTGACGTGACAATCC
1 ACGGTGCTCACATGACAATCC
724138 ACGGTG
1 ACGGTG
724144 ATGATGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Consensus pattern (21 bp):
ACGGTGCTCACATGACAATCC
Found at i:728825 original size:39 final size:39
Alignment explanation
Indices: 728744--728828 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
728734 ACTTTATTTT
* * * *
728744 TCAATCCTATAAAATGAACCCTTCTTCAACGTGTCTCTA
1 TCAATCCTAGAAAATGAACCCTTCTTCAACGTGCCCCAA
* *
728783 TCAATGCTAGAAAATGAACCCTTCTTTAACGTGCCCCAA
1 TCAATCCTAGAAAATGAACCCTTCTTCAACGTGCCCCAA
728822 TCAATCC
1 TCAATCC
728829 CTAGTTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.29
Consensus pattern (39 bp):
TCAATCCTAGAAAATGAACCCTTCTTCAACGTGCCCCAA
Found at i:730708 original size:124 final size:125
Alignment explanation
Indices: 730455--730710 Score: 302
Period size: 125 Copynumber: 2.1 Consensus size: 125
730445 ATTAATCTTG
* * * ** * *
730455 TAAATTTTAAATTATCGTTTATTTTAATTTTTTTTTAAATTTTTATTTATTATTTTATTTTATTT
1 TAAATTTTAAATAATCATATATTTTAAGATTTTTTTAAATTTTTATTTATAATTTAATTTTATTT
* ** * * *
730520 TTAAAATTTTAAAAGGTAAAAATATATAAATAGTTATTAGATTATAAGATAACATTTTCA
66 TAAAAAAATTAAAAGGTAAAAATATACAAATAGTTATCAGATTATAAGATAACAATTTCA
*
730580 TAAATTTTAAATAATCATATATTTTAAGATTTTTTTATATTTTTTATTTATAATTTAATTTT-TT
1 TAAATTTTAAATAATCATATATTTTAAGATTTTTTTA-AATTTTTATTTATAATTTAATTTTATT
* * * * *
730644 TTAAAAAAATTATAAGGT-AAAATATACAATTAGTTCTCGGATTATAAGATAATAATTT-A
65 TTAAAAAAATTAAAAGGTAAAAATATACAAATAGTTATCAGATTATAAGATAACAATTTCA
730703 TTAAATTT
1 -TAAATTT
730711 ATCAAATATT
Statistics
Matches: 110, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
123 1 0.01
124 40 0.36
125 48 0.44
126 21 0.19
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (125 bp):
TAAATTTTAAATAATCATATATTTTAAGATTTTTTTAAATTTTTATTTATAATTTAATTTTATTT
TAAAAAAATTAAAAGGTAAAAATATACAAATAGTTATCAGATTATAAGATAACAATTTCA
Found at i:730734 original size:17 final size:16
Alignment explanation
Indices: 730701--730734 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
730691 GATAATAATT
*
730701 TATTAAATTTATCAAA
1 TATTAAATTTATAAAA
730717 TATTAAATTTTATAAAA
1 TATTAAA-TTTATAAAA
730734 T
1 T
730735 GATCATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTAAATTTATAAAA
Found at i:738768 original size:21 final size:21
Alignment explanation
Indices: 738743--738782 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
738733 AAAAAATTAC
738743 CTAAAACATTATTATTTTTAT
1 CTAAAACATTATTATTTTTAT
738764 CTAAAACATTATTATTTTT
1 CTAAAACATTATTATTTTT
738783 TAACATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
CTAAAACATTATTATTTTTAT
Found at i:739350 original size:21 final size:21
Alignment explanation
Indices: 739326--739365 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
739316 CCGAAAACTC
739326 TAACAATAAAAATAATTTCTT
1 TAACAATAAAAATAATTTCTT
* * *
739347 TAACTATTAAAATTATTTC
1 TAACAATAAAAATAATTTC
739366 GTTGGTGACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (21 bp):
TAACAATAAAAATAATTTCTT
Found at i:741978 original size:23 final size:25
Alignment explanation
Indices: 741951--741996 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
741941 AATTTAATTG
741951 AATTA-AAAAAT-CAATTAATGAGA
1 AATTATAAAAATACAATTAATGAGA
*
741974 AATTATAAAAATACCATTAATGA
1 AATTATAAAAATACAATTAATGA
741997 ATCTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 6 0.30
25 9 0.45
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (25 bp):
AATTATAAAAATACAATTAATGAGA
Found at i:759297 original size:20 final size:19
Alignment explanation
Indices: 759256--759304 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
759246 TAGTCTTCTC
* *
759256 TTTCTTTAGTTTTGTTCTG
1 TTTCTTTTGTTTTGTTCAG
759275 TTTTCTTTTGTTGTT-TTCAG
1 -TTTCTTTTGTT-TTGTTCAG
759295 TTTCTTTTGT
1 TTTCTTTTGT
759305 GCCGTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 10 0.38
20 14 0.54
21 2 0.08
ACGTcount: A:0.04, C:0.10, G:0.14, T:0.71
Consensus pattern (19 bp):
TTTCTTTTGTTTTGTTCAG
Found at i:762925 original size:12 final size:12
Alignment explanation
Indices: 762908--762940 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
762898 CCCAATGACT
762908 CAATACCCGACC
1 CAATACCCGACC
*
762920 CAATACCCGGCC
1 CAATACCCGACC
762932 CAATACCCG
1 CAATACCCG
762941 TTTAAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.48, G:0.12, T:0.09
Consensus pattern (12 bp):
CAATACCCGACC
Found at i:765089 original size:34 final size:34
Alignment explanation
Indices: 765046--765113 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
765036 GCCCTACAAC
765046 ATGAAACTATGCTTCAATTTGTTC-TAAATTATCA
1 ATGAAACTATGCTTCAATTTGTTCTTAAA-TATCA
*
765080 ATGAAACTATGCTTTAATTTGTTCTTAAATATCA
1 ATGAAACTATGCTTCAATTTGTTCTTAAATATCA
765114 GTTTTAGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (34 bp):
ATGAAACTATGCTTCAATTTGTTCTTAAATATCA
Found at i:775393 original size:15 final size:16
Alignment explanation
Indices: 775375--775404 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
775365 ATGGCAGATC
775375 AAAATCCAG-ACGGGG
1 AAAATCCAGAACGGGG
775390 AAAATCCAGAACGGG
1 AAAATCCAGAACGGG
775405 AAAGAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.20, G:0.30, T:0.07
Consensus pattern (16 bp):
AAAATCCAGAACGGGG
Found at i:782088 original size:3 final size:3
Alignment explanation
Indices: 782082--782130 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
782072 ATAAAACAAC
782082 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
782130 A
1 A
782131 CATGTTAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:794496 original size:34 final size:32
Alignment explanation
Indices: 794446--794547 Score: 87
Period size: 34 Copynumber: 3.1 Consensus size: 32
794436 GAGAAATTTA
* * * *
794446 TTTTTATGTTATTATTTTTTTAAATAATTATTAT
1 TTTTTATATTAATATTTATGTAAAT-ATTA-TAT
794480 TTTTTATATTAATATTTATGTAAATATTATATT
1 TTTTTATATTAATATTTATGTAAATATTATA-T
* * * * *
794513 TTTATTAAAATAATATTTATATAATTATTTTAT
1 TTT-TTATATTAATATTTATGTAAATATTATAT
794546 TT
1 TT
794548 AGAATTATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.04
33 11 0.19
34 44 0.77
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (32 bp):
TTTTTATATTAATATTTATGTAAATATTATAT
Found at i:794516 original size:19 final size:18
Alignment explanation
Indices: 794458--794530 Score: 52
Period size: 18 Copynumber: 4.3 Consensus size: 18
794448 TTTATGTTAT
794458 TATTTTT-TTAAATAATTA
1 TATTTTTATTAAAT-ATTA
794476 T-TATTTT-TT--ATATTA
1 TAT-TTTTATTAAATATTA
*
794491 -ATATTTATGTAAATATTA
1 TATTTTTAT-TAAATATTA
*
794509 TATTTTTATTAAA-ATAA
1 TATTTTTATTAAATATTA
794526 TATTT
1 TATTT
794531 ATATAATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.07
15 6 0.13
16 3 0.07
17 9 0.20
18 17 0.38
19 7 0.16
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
TATTTTTATTAAATATTA
Found at i:794528 original size:17 final size:19
Alignment explanation
Indices: 794494--794530 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
794484 TATATTAATA
*
794494 TTTATGTAAATATTATATT
1 TTTATGTAAATATAATATT
794513 TTTAT-TAAA-ATAATATT
1 TTTATGTAAATATAATATT
794530 T
1 T
794531 ATATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTATGTAAATATAATATT
Found at i:796287 original size:21 final size:21
Alignment explanation
Indices: 796257--796304 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
796247 GCAGGGGTAC
* *
796257 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
796278 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
796299 ATGCCA
1 ATGCCA
796305 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:796334 original size:21 final size:21
Alignment explanation
Indices: 796308--796401 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
796298 TATGCCATCT
796308 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
796329 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
796350 CTGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
* *
796371 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
796392 CCGCAGGGTT
1 CCGCAGGGTT
796402 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.29, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:796983 original size:33 final size:34
Alignment explanation
Indices: 796924--797020 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
796914 AAATGTTTTT
*
796924 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
796958 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
796991 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
797021 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:797027 original size:34 final size:33
Alignment explanation
Indices: 796922--797027 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
796912 ATAAATGTTT
*
796922 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
796956 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
796988 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
797023 TTAAA
1 TTAAA
797028 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:797649 original size:128 final size:128
Alignment explanation
Indices: 797421--797921 Score: 921
Period size: 128 Copynumber: 3.9 Consensus size: 128
797411 TTACCTGATT
797421 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
797486 TGACGAAATAATAGAAGGCGCCCCCCCGAGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
797549 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATCCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
797614 TGACAAAATAATGGAAGGCGCGCCCACGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
797677 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
797742 TGACGAAATAATGGAAGGCACGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
797805 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
797870 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
797922 ACTCCGATTA
Statistics
Matches: 359, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 359 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:798005 original size:8 final size:8
Alignment explanation
Indices: 797992--798032 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
797982 TCATAATCTT
797992 TCAAATTC
1 TCAAATTC
798000 TCAAATTC
1 TCAAATTC
* *
798008 CCAAACTC
1 TCAAATTC
798016 T-AAATTC
1 TCAAATTC
798023 TCAAATTC
1 TCAAATTC
798031 TC
1 TC
798033 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:804952 original size:2 final size:2
Alignment explanation
Indices: 804945--804970 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
804935 ACTTCCAATA
804945 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
804971 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:806699 original size:27 final size:29
Alignment explanation
Indices: 806653--806711 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
806643 AAAAAGTTTG
806653 GGTACCTATTTTGACAT-AAAATACTTTA
1 GGTACCTATTTTGACATAAAAATACTTTA
*
806681 GGTATCTATTTTGAC-TAAAAATACTTTA
1 GGTACCTATTTTGACATAAAAATACTTTA
806709 GGT
1 GGT
806712 GCTTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (29 bp):
GGTACCTATTTTGACATAAAAATACTTTA
Found at i:807962 original size:2 final size:2
Alignment explanation
Indices: 807955--807989 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
807945 TGAACGTTAT
807955 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
807990 TAGAGATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:813621 original size:2 final size:2
Alignment explanation
Indices: 813616--813645 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
813606 GAGAGAATGG
813616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
813646 TAGGCCGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:814071 original size:16 final size:15
Alignment explanation
Indices: 814052--814081 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
814042 TATATATATA
814052 TTAAATAATATAAATT
1 TTAAATAATA-AAATT
814068 TTAAATAATAAAAT
1 TTAAATAATAAAAT
814082 ATTATTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAATAATAAAATT
Found at i:814151 original size:2 final size:2
Alignment explanation
Indices: 814144--814170 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
814134 TACTAAACCT
814144 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
814171 GAGGGGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:815679 original size:7 final size:7
Alignment explanation
Indices: 815667--815698 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
815657 CCTATAAATG
815667 ACTCCCC
1 ACTCCCC
815674 ACTCCCC
1 ACTCCCC
815681 ACTCCCC
1 ACTCCCC
815688 ACTCCCC
1 ACTCCCC
815695 ACTC
1 ACTC
815699 TTTTCCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.69, G:0.00, T:0.16
Consensus pattern (7 bp):
ACTCCCC
Found at i:820130 original size:2 final size:2
Alignment explanation
Indices: 820123--820148 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
820113 ACAAACTATC
820123 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
820149 GGACAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:828637 original size:21 final size:21
Alignment explanation
Indices: 828611--828655 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
828601 GATTTCTGGG
* *
828611 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
828632 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
828653 CAA
1 CAA
828656 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:829308 original size:23 final size:24
Alignment explanation
Indices: 829265--829311 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
829255 ATATGGCATG
*
829265 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
829289 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
829312 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:829527 original size:31 final size:31
Alignment explanation
Indices: 829489--829645 Score: 226
Period size: 31 Copynumber: 5.0 Consensus size: 31
829479 AGGGTCGAGG
829489 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
829520 GTTTACCTATGTTCTTCGGGGACATATGGACT
1 GTTTACCTATGTTCTTC-GGGACATATGGACT
* * *
829552 GATTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
829583 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
829614 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
829645 G
1 G
829646 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
31 82 0.73
32 31 0.27
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:829569 original size:63 final size:62
Alignment explanation
Indices: 829491--829645 Score: 249
Period size: 63 Copynumber: 2.5 Consensus size: 62
829481 GGTCGAGGGT
* *
829491 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTC-GGGACATATGGACTGA
*
829554 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
829616 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
829646 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
62 42 0.49
63 44 0.51
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:830534 original size:2 final size:2
Alignment explanation
Indices: 830529--830554 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
830519 TAATTTTATC
830529 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
830555 GTTTTGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:831106 original size:14 final size:14
Alignment explanation
Indices: 831087--831113 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
831077 AAGTGAAATA
831087 ATAGTTATATAATC
1 ATAGTTATATAATC
831101 ATAGTTATATAAT
1 ATAGTTATATAAT
831114 TTTGTTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
ATAGTTATATAATC
Found at i:833136 original size:21 final size:21
Alignment explanation
Indices: 833094--833136 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
833084 TTTCTGGGCT
* *
833094 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
833115 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
833136 A
1 A
833137 ACGAGTATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:834069 original size:30 final size:30
Alignment explanation
Indices: 834035--834137 Score: 197
Period size: 30 Copynumber: 3.4 Consensus size: 30
834025 GGTTCTTCGG
*
834035 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
834065 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
834095 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
834125 GACCTCTGGATAG
1 GACCTCTGGATAG
834138 GTCCTTCGGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:836885 original size:2 final size:2
Alignment explanation
Indices: 836878--836909 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
836868 TAATTAAATG
836878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
836910 GGATAAGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:837474 original size:21 final size:21
Alignment explanation
Indices: 837432--837474 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
837422 TTTCTGGGTT
* *
837432 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
837453 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
837474 A
1 A
837475 ACGAGTATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:838408 original size:30 final size:30
Alignment explanation
Indices: 838374--838476 Score: 197
Period size: 30 Copynumber: 3.4 Consensus size: 30
838364 GGTTCTTCGG
*
838374 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
838404 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
838434 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
838464 GACCTCTGGATAG
1 GACCTCTGGATAG
838477 GTCATTCGGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:839605 original size:7 final size:7
Alignment explanation
Indices: 839590--839634 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
839580 TCAATCTGGA
*
839590 GTATTCT
1 GTATACT
839597 GTATACT
1 GTATACT
839604 GTATACT
1 GTATACT
839611 GTATACT
1 GTATACT
839618 GTATACT
1 GTATACT
*
839625 GTATATT
1 GTATACT
839632 GTA
1 GTA
839635 ATCAAATTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.47
Consensus pattern (7 bp):
GTATACT
Found at i:844784 original size:2 final size:2
Alignment explanation
Indices: 844777--844806 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
844767 TAATACATTA
844777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
844807 GTGTATGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:844846 original size:65 final size:65
Alignment explanation
Indices: 844777--844911 Score: 198
Period size: 65 Copynumber: 2.1 Consensus size: 65
844767 TAATACATTA
* *
844777 ATATATATATATATATATATATATATATATGTGTATGTGTTTTTTTTATTTATGTATGTATGTTT
1 ATATATATATATATATATATATATATATATGTGTATATGTTTTTTTTATTTATGTATGTATGTAT
* * * * * *
844842 ATATATATGTGTGTTTATATATATATATGTGTGTGTATGTTTTTTTTATTTATGTATGTATGTAT
1 ATATATATATATATATATATATATATATATGTGTATATGTTTTTTTTATTTATGTATGTATGTAT
844907 ATATA
1 ATATA
844912 CATGTGTGTG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (65 bp):
ATATATATATATATATATATATATATATATGTGTATATGTTTTTTTTATTTATGTATGTATGTAT
Found at i:844856 original size:16 final size:16
Alignment explanation
Indices: 844831--844871 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
844821 TTTATTTATG
844831 TATGTATGTTTATATA
1 TATGTATGTTTATATA
*
844847 TATGTGTGTTTATATA
1 TATGTATGTTTATATA
*
844863 TATATATGT
1 TATGTATGT
844872 GTGTGTATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (16 bp):
TATGTATGTTTATATA
Found at i:844896 original size:45 final size:46
Alignment explanation
Indices: 844829--844957 Score: 134
Period size: 45 Copynumber: 2.8 Consensus size: 46
844819 TTTTTATTTA
* * *
844829 TGTATGTATGTTTATATATATGTGTGTTTATATATATATATGTGTG
1 TGTATGTATGTTTATATATATGTATGTATATATATATACATGTGTG
* * * *
844875 TGTATGT-TTTTTTTATTTATGTATGTATGTATATATACATGTGTG
1 TGTATGTATGTTTATATATATGTATGTATATATATATACATGTGTG
* * * * * *
844920 TGTGTATATATATATATATATATATATATATATATATA
1 TGTATGTATGTTTATATATATGTATGTATATATATATA
844958 TATATTATGA
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
45 36 0.55
46 30 0.45
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (46 bp):
TGTATGTATGTTTATATATATGTATGTATATATATATACATGTGTG
Found at i:844917 original size:65 final size:67
Alignment explanation
Indices: 844792--844938 Score: 235
Period size: 65 Copynumber: 2.2 Consensus size: 67
844782 TATATATATA
* * *
844792 TATATATATATATATGTGTATGTGTTTTTTTTATTTATGTATGTATGTTTATATATATGTGTGT-
1 TATATATATATATATGTGTATATGTTTTTTTTATTTATGTATGTATGTATATATACATGTGTGTG
844856 T-
66 TG
* *
844857 TATATATATATATGTGTGTGTATGTTTTTTTTATTTATGTATGTATGTATATATACATGTGTGTG
1 TATATATATATATATGTGTATATGTTTTTTTTATTTATGTATGTATGTATATATACATGTGTGTG
844922 TG
66 TG
844924 TATATATATATATAT
1 TATATATATATATAT
844939 ATATATATAT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
65 59 0.80
66 1 0.01
67 14 0.19
ACGTcount: A:0.27, C:0.01, G:0.16, T:0.57
Consensus pattern (67 bp):
TATATATATATATATGTGTATATGTTTTTTTTATTTATGTATGTATGTATATATACATGTGTGTG
TG
Found at i:844929 original size:2 final size:2
Alignment explanation
Indices: 844924--844962 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
844914 TGTGTGTGTG
844924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
844963 TATGAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:845102 original size:37 final size:36
Alignment explanation
Indices: 845029--845110 Score: 130
Period size: 36 Copynumber: 2.2 Consensus size: 36
845019 TGAAGATGTT
*
845029 TTATGAAACCTTTAATAAGAAAAATATCCAATTTTC
1 TTATGAAACCTTTAATAAGAAAAATATCCAAATTTC
845065 TTATGAAACCTTTAATAAGAAAAA-ATGCCCAAATTTC
1 TTATGAAACCTTTAATAAGAAAAATAT--CCAAATTTC
845102 TTATGAAAC
1 TTATGAAAC
845111 ATAAATTGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
35 2 0.05
36 24 0.56
37 17 0.40
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (36 bp):
TTATGAAACCTTTAATAAGAAAAATATCCAAATTTC
Found at i:846283 original size:3 final size:3
Alignment explanation
Indices: 846277--846312 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
846267 GTAAAATCAG
846277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
846313 TTTATTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:846892 original size:17 final size:17
Alignment explanation
Indices: 846870--846908 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
846860 TGAATCAAAT
846870 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
846887 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
846904 -AATTA
1 TAATTA
846909 ATAGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:847188 original size:11 final size:10
Alignment explanation
Indices: 847172--847263 Score: 57
Period size: 11 Copynumber: 8.9 Consensus size: 10
847162 TTTATAAATA
847172 TAATAATAGTT
1 TAATAATA-TT
847183 TAATAATATT
1 TAATAATATT
847193 GTAATTAAT-TT
1 -TAA-TAATATT
847204 TAATATATATTT
1 TAATA-ATA-TT
**
847216 TTGTAATATTT
1 TAATAATA-TT
847227 TAATAA-ATT
1 TAATAATATT
*
847236 TAATATTTATT
1 TAATA-ATATT
*
847247 TTATAAT-TT
1 TAATAATATT
847256 TAA-AATAT
1 TAATAATAT
847264 AAAATTATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
8 3 0.05
9 14 0.22
10 9 0.14
11 30 0.46
12 9 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (10 bp):
TAATAATATT
Found at i:847247 original size:32 final size:33
Alignment explanation
Indices: 847186--847248 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
847176 AATAGTTTAA
*
847186 TAATATTGTAATTAATTTTAATATATATTTTTG
1 TAATATTGTAATTAAATTTAATATATATTTTTG
* *
847219 TAATATTTTAA-TAAATTTAATATTTATTTT
1 TAATATTGTAATTAAATTTAATATATATTTT
847249 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (33 bp):
TAATATTGTAATTAAATTTAATATATATTTTTG
Found at i:851368 original size:38 final size:39
Alignment explanation
Indices: 851325--851398 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
851315 AATTCTTTAA
* *
851325 TTTTATATAGATTTAAGACCATTGGATAAGT-AAAAGAG
1 TTTTATATAGATTTAAAACCATTCGATAAGTGAAAAGAG
*
851363 TTTTATATAGATTTAAAATCATTCGATAAGTGAAAA
1 TTTTATATAGATTTAAAACCATTCGATAAGTGAAAA
851399 TAGGTTGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 28 0.88
39 4 0.12
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.36
Consensus pattern (39 bp):
TTTTATATAGATTTAAAACCATTCGATAAGTGAAAAGAG
Found at i:856816 original size:41 final size:41
Alignment explanation
Indices: 856763--856908 Score: 112
Period size: 41 Copynumber: 3.4 Consensus size: 41
856753 ATTTCGATTA
*
856763 TCGCATTGCGATTTACATATTCGCATTGCGATAGTTCAAGT
1 TCGCGTTGCGATTTACATATTCGCATTGCGATAGTTCAAGT
* * * * * * * *
856804 TCGCGTTACGATTTTCCAAATTCGACTATCGCAACGTGAACTTCGACT
1 TCGCGTTGCGA-TTTACATATTCG-C-ATTGCGA--T--AGTTCAAGT
* * *
856852 ATCGCATTGCGATTTATATATTCGCATTGCGATAGTCCAAGT
1 -TCGCGTTGCGATTTACATATTCGCATTGCGATAGTTCAAGT
856894 TCGCGTTGCGATTTA
1 TCGCGTTGCGATTTA
856909 TTCTAAATTC
Statistics
Matches: 76, Mismatches: 21, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
41 23 0.30
42 15 0.20
43 1 0.01
44 6 0.08
46 6 0.08
47 1 0.01
48 15 0.20
49 9 0.12
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (41 bp):
TCGCGTTGCGATTTACATATTCGCATTGCGATAGTTCAAGT
Found at i:856895 original size:90 final size:90
Alignment explanation
Indices: 856742--856907 Score: 278
Period size: 90 Copynumber: 1.8 Consensus size: 90
856732 GTTTCCAGAT
* * *
856742 TCGCAACGCGAATTTCGATTATCGCATTGCGATTTACATATTCGCATTGCGATAGTTCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
856807 CGTTACGATTTTCCAAATTCGACTA
66 CGTTACGATTTTCCAAATTCGACTA
* *
856832 TCGCAACGTGAACTTCGACTATCGCATTGCGATTTATATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
*
856897 CGTTGCGATTT
66 CGTTACGATTT
856908 ATTCTAAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (90 bp):
TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
CGTTACGATTTTCCAAATTCGACTA
Found at i:856902 original size:21 final size:20
Alignment explanation
Indices: 856878--856997 Score: 93
Period size: 21 Copynumber: 5.8 Consensus size: 20
856868 TATATTCGCA
*
856878 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTAGTCCAAATT--CG
* *
856899 TTGCGATTTATTCTAAATTCG
1 TTGCGA-TTAGTCCAAATTCG
*
856920 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTAGTCCAAATTCG
* *
856941 TTGCGA-TAGTCGAAGTTCG
1 TTGCGATTAGTCCAAATTCG
*
856960 CATTGCGATTTATTCCAAATTCG
1 --TTGCGA-TTAGTCCAAATTCG
856983 TTGCGA-TAGTCCAAA
1 TTGCGATTAGTCCAAA
856998 ATCGCAACGA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
19 18 0.22
21 46 0.56
23 18 0.22
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGCGATTAGTCCAAATTCG
Found at i:856943 original size:42 final size:42
Alignment explanation
Indices: 856897--856993 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 42
856887 TCCAAGTTCG
* *
856897 CGTTGCGATTTATTCTAAATTCG-TTGCGATTTATTCCAAATT
1 CGTTGCGA-TTAGTCGAAATTCGATTGCGATTTATTCCAAATT
*
856939 CGTTGCGA-TAGTCGAAGTTCGCATTGCGATTTATTCCAAATT
1 CGTTGCGATTAGTCGAAATTCG-ATTGCGATTTATTCCAAATT
856981 CGTTGCGA-TAGTC
1 CGTTGCGATTAGTC
856994 CAAAATCGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 10 0.20
42 40 0.80
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (42 bp):
CGTTGCGATTAGTCGAAATTCGATTGCGATTTATTCCAAATT
Found at i:857003 original size:42 final size:42
Alignment explanation
Indices: 856920--857003 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
856910 TCTAAATTCG
* **
856920 TTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCA
1 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAATCGCA
856962 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAATCGCA
1 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAATCGCA
857004 ACGACTGGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (42 bp):
TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAATCGCA
Found at i:857614 original size:6 final size:6
Alignment explanation
Indices: 857603--857633 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
857593 CCGTCTCGTC
857603 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
857634 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:857768 original size:42 final size:42
Alignment explanation
Indices: 857722--857881 Score: 257
Period size: 42 Copynumber: 3.8 Consensus size: 42
857712 TGCGATTTTG
* *
857722 GACTATCGCAACGAATTTGGAATAAATCGTAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
857764 GACTACCGCAACGAACTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
857806 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACATG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
857848 GACTATCGCAACGAATTTGGAATAAATCGCAACG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACG
857882 AATTTGGAAT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 109 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:857796 original size:21 final size:21
Alignment explanation
Indices: 857726--857902 Score: 150
Period size: 21 Copynumber: 8.4 Consensus size: 21
857716 ATTTTGGACT
*
857726 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
857747 ATCGTAATGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
857768 ACCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
857789 ATCGCAACGCGAACTTTGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
857810 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
857831 ATCGCAACGCGAACATGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
857852 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
857873 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
857894 ATCGCAACG
1 ATCGCAACG
857903 CGAACTTCGA
Statistics
Matches: 124, Mismatches: 20, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
19 28 0.23
21 68 0.55
23 28 0.23
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:857898 original size:84 final size:83
Alignment explanation
Indices: 857725--857902 Score: 243
Period size: 84 Copynumber: 2.1 Consensus size: 83
857715 GATTTTGGAC
* * *
857725 TATCGCAACGAATTTGGAATAAATCGTAATGCGAACTTCGACTACCGCAACGAACTTGGAATAAA
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACATCGACTACCGCAACGAACTTGGAATAAA
*
857790 TCGCAACGCGAACTTTGAC
66 TCGCAAC-CGAACTTTGAA
* * *
857809 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACATGGACTATCGCAACGAATTTGGAATAAA
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACATCGACTACCGCAACGAACTTGGAATAAA
857874 TCGCAA-CGAA-TTTGGAA
66 TCGCAACCGAACTTT-GAA
857891 TAAATCGCAACG
1 T--ATCGCAACG
857903 CGAACTTCGA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
81 3 0.04
82 7 0.08
84 74 0.88
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (83 bp):
TATCGCAACGAATTTGGAATAAATCGCAACGCGAACATCGACTACCGCAACGAACTTGGAATAAA
TCGCAACCGAACTTTGAA
Found at i:857918 original size:21 final size:21
Alignment explanation
Indices: 857726--857927 Score: 125
Period size: 21 Copynumber: 9.6 Consensus size: 21
857716 ATTTTGGACT
*
857726 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
* * *
857747 ATCGTAATGCGAACTTCGACT-
1 ATCGCAA-GCGAACTTGGAATA
*
857768 ACCGCAA-CGAACTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
* *
857789 ATCGCAACGCGAACTTTGACT-
1 ATCGCAA-GCGAACTTGGAATA
*
857810 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
* *
857831 ATCGCAACGCGAACATGGACT-
1 ATCGCAA-GCGAACTTGGAATA
*
857852 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
*
857873 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
* *
857894 ATCGCAACGCGAACTTCGACT-
1 ATCGCAA-GCGAACTTGGAATA
857915 ATCGCAATGCGAA
1 ATCGCAA-GCGAA
857928 TATCGCAATG
Statistics
Matches: 143, Mismatches: 24, Indels: 28
0.73 0.12 0.14
Matches are distributed among these distances:
19 28 0.20
21 78 0.55
23 37 0.26
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAAGCGAACTTGGAATA
Found at i:857933 original size:14 final size:14
Alignment explanation
Indices: 857914--857944 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
857904 GAACTTCGAC
857914 TATCGCAATGCGAA
1 TATCGCAATGCGAA
857928 TATCGCAATGCGAA
1 TATCGCAATGCGAA
857942 TAT
1 TAT
857945 GTAAATCGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (14 bp):
TATCGCAATGCGAA
Found at i:859534 original size:36 final size:36
Alignment explanation
Indices: 859487--859561 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
859477 TAGTTGCAAA
*
859487 CGGTGATGTTGGGTGACTGTAACGACAGTGTAACCT
1 CGGTGATGTTGGGTGAATGTAACGACAGTGTAACCT
859523 CGGTGATGTTGGGTGAATGTAACGACAGTGTAACCT
1 CGGTGATGTTGGGTGAATGTAACGACAGTGTAACCT
859559 CGG
1 CGG
859562 GGAAATGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.27
Consensus pattern (36 bp):
CGGTGATGTTGGGTGAATGTAACGACAGTGTAACCT
Found at i:860043 original size:31 final size:31
Alignment explanation
Indices: 860008--860081 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
859998 ACACAAATGA
*
860008 TCCCTTAACTATAGCGTAATGTTTTATTAAG
1 TCCCTCAACTATAGCGTAATGTTTTATTAAG
* * *
860039 TCCCTCAACTCTAGGGTAATGTTTTATTATG
1 TCCCTCAACTATAGCGTAATGTTTTATTAAG
* *
860070 TCCATCGACTAT
1 TCCCTCAACTAT
860082 TAAAAGTAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (31 bp):
TCCCTCAACTATAGCGTAATGTTTTATTAAG
Done.