Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007950.1 Hibiscus syriacus cultivar Beakdansim tig00110372_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: 1941792
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:858832 original size:31 final size:31
Alignment explanation
Indices: 858761--858852 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 31
858751 AGTCGAGGGT
*
858761 TTACCTATGTTCTATGGAACATATGGACAGAA
1 TTACCTATG-TCTATCGAACATATGGACAGAA
* * *
858793 TTACCTATGTCTTTCGAGACATATGGATAGTA
1 TTACCTATGTCTATCGA-ACATATGGACAGAA
**
858825 -TACCTATGTTCTAAGGAACATATGGACA
1 TTACCTATG-TCTATCGAACATATGGACA
858853 TTTTACCTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
31 24 0.48
32 26 0.52
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (31 bp):
TTACCTATGTCTATCGAACATATGGACAGAA
Found at i:860878 original size:22 final size:22
Alignment explanation
Indices: 860843--860895 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
860833 TCAAAAGGGA
860843 AGATGTC-AATCTAAAGAATGT
1 AGATGTCGAATCTAAAGAATGT
860864 AGATGTCGAATCTAAAGAATGT
1 AGATGTCGAATCTAAAGAATGT
860886 AGATGTCGAA
1 AGATGTCGAA
860896 CTATGTAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (22 bp):
AGATGTCGAATCTAAAGAATGT
Found at i:865362 original size:21 final size:21
Alignment explanation
Indices: 865336--865380 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
865326 GATTTCTGGG
* *
865336 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
865357 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
865378 CAA
1 CAA
865381 ACGTCTTGAG
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:865809 original size:26 final size:26
Alignment explanation
Indices: 865762--865811 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
865752 ATGCTTTTGA
*
865762 ATGTAATGTTATGAGAAGTATGTGCT
1 ATGTAATGTTATGAGAACTATGTGCT
*
865788 ATGTAATGTATAT-ATAACTATGTG
1 ATGTAATGT-TATGAGAACTATGTG
865812 AAACTCACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (26 bp):
ATGTAATGTTATGAGAACTATGTGCT
Found at i:866205 original size:31 final size:31
Alignment explanation
Indices: 866167--866322 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
866157 AGGGTCGAGG
*
866167 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
866198 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
866229 GATTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
866260 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
866291 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
866322 G
1 G
866323 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:866321 original size:62 final size:62
Alignment explanation
Indices: 866169--866322 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
866159 GGTCGAGGGT
*
866169 TTACCTATGTTCTTCTGG-ACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
866231 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
866293 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
866323 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 2 0.02
62 83 0.97
63 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:867232 original size:22 final size:22
Alignment explanation
Indices: 867181--867234 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
867171 TCAAAAGGGA
*
867181 AGATGTCAAATCTAAAGAATGT
1 AGATGTCGAATCTAAAGAATGT
867203 AGATGTCGAATCTAAAGAATGT
1 AGATGTCGAATCTAAAGAATGT
867225 AGATGTCGAA
1 AGATGTCGAA
867235 CTATGTAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (22 bp):
AGATGTCGAATCTAAAGAATGT
Found at i:870057 original size:21 final size:21
Alignment explanation
Indices: 870033--870073 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
870023 GTGTCATGCT
*
870033 TGCATTATATGT-TATGTGATG
1 TGCATT-TATGTCTATATGATG
870054 TGCATTTATGTCTATATGAT
1 TGCATTTATGTCTATATGAT
870074 AATGATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (21 bp):
TGCATTTATGTCTATATGATG
Found at i:870920 original size:23 final size:23
Alignment explanation
Indices: 870888--870961 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
870878 TTTTATATGT
* *
870888 CACTTTGGTGCAATTCTACGGGG
1 CACTTCGGTGCAATTCTACGCGG
870911 CACTTCGGTGCAATTCTACGCGG
1 CACTTCGGTGCAATTCTACGCGG
* * **
870934 CACTTCGATGCAACTCTACATGG
1 CACTTCGGTGCAATTCTACGCGG
870957 CACTT
1 CACTT
870962 TGGTACATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.28
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGG
Found at i:875738 original size:27 final size:27
Alignment explanation
Indices: 875643--875722 Score: 160
Period size: 27 Copynumber: 3.0 Consensus size: 27
875633 GGTTCCAGAG
875643 AACTATTCACGATAGTGAAATAGTGGT
1 AACTATTCACGATAGTGAAATAGTGGT
875670 AACTATTCACGATAGTGAAATAGTGGT
1 AACTATTCACGATAGTGAAATAGTGGT
875697 AACTATTCACGATAGTGAAATAGTGG
1 AACTATTCACGATAGTGAAATAGTGG
875723 GAGCTATCCG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (27 bp):
AACTATTCACGATAGTGAAATAGTGGT
Found at i:886245 original size:16 final size:16
Alignment explanation
Indices: 886221--886254 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
886211 TATCGCCGAC
*
886221 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
886237 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
886253 CG
1 CG
886255 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:888874 original size:31 final size:31
Alignment explanation
Indices: 888836--888916 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
888826 TTAGTTCTTA
888836 TGGTTGATTGGATTCAAGTTATATGTTATTC
1 TGGTTGATTGGATTCAAGTTATATGTTATTC
888867 TGGTTGATTGGATTCAAGTTATATGTTATTC
1 TGGTTGATTGGATTCAAGTTATATGTTATTC
*
888898 TGGTTG-TTGGTCTTCAAGT
1 TGGTTGATTGG-ATTCAAGT
888917 CTATCTTGGT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 4 0.08
31 44 0.92
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.48
Consensus pattern (31 bp):
TGGTTGATTGGATTCAAGTTATATGTTATTC
Found at i:897584 original size:26 final size:26
Alignment explanation
Indices: 897522--897587 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
897512 ATTTTTTTGT
*
897522 TTTATTTATTTTAAATTAACCCCTGA
1 TTTATTTATTTTAAATTAACCACTGA
* * *
897548 TTTGCTTTATTTTAATTTAATCACTGA
1 TTT-ATTTATTTTAAATTAACCACTGA
*
897575 TTTATATATTTTA
1 TTTATTTATTTTA
897588 TGTTTCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 11 0.33
27 22 0.67
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.56
Consensus pattern (26 bp):
TTTATTTATTTTAAATTAACCACTGA
Found at i:898557 original size:16 final size:16
Alignment explanation
Indices: 898522--898558 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
898512 CACACACCAA
898522 TTTTTGTCTTAAATTT
1 TTTTTGTCTTAAATTT
898538 TTTTT-TCTTAAATTT
1 TTTTTGTCTTAAATTT
898553 GTTTTT
1 -TTTTT
898559 AAAAGACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (16 bp):
TTTTTGTCTTAAATTT
Found at i:905611 original size:2 final size:2
Alignment explanation
Indices: 905604--905643 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
905594 AGTAAAGGTA
905604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
905644 GAACCAAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:913289 original size:220 final size:221
Alignment explanation
Indices: 912850--913290 Score: 850
Period size: 220 Copynumber: 2.0 Consensus size: 221
912840 GGAAGCTATA
912850 TATTTATATATGATTTTTTATTCTTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTTA
1 TATTTATATATGATTTTTTATTCTTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTTA
912915 TCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAATAAAATAAAATCTAAGATCCTAATGG
66 TCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAATAAAATAAAATCTAAGATCCTAATGG
*
912980 AAGAGGGAAAAATCGTATCTGTTAGCAATGAAAATTTTAAATTTTAGGAACGAAATTAATAATAG
131 AAGAGGGAAAAATCGTATCTGTTAGCAATGAAAATTTTAAATTTTAGGAAAGAAATTAATAATAG
913045 ATGGGTATAACCAACAACTAGTTAGT
196 ATGGGTATAACCAACAACTAGTTAGT
913071 TATTTATATATGATTTTTTATTCTTTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTT
1 TATTTATATATGATTTTTTATTC-TTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTT
913136 ATCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAA-AAAATAAAATCTAAGATCCTAATG
65 ATCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAATAAAATAAAATCTAAGATCCTAATG
913200 GAAGAGGG-AAAATCGTATCTGTTAGCAATGAAAATTTTAAATTTTAGGAAAGAAATTAATAATA
130 GAAGAGGGAAAAATCGTATCTGTTAGCAATGAAAATTTTAAATTTTAGGAAAGAAATTAATAATA
913264 GATGGGTATAACCAACAACTAGTTAGT
195 GATGGGTATAACCAACAACTAGTTAGT
913291 CTAGTAGGAT
Statistics
Matches: 218, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
220 82 0.38
221 55 0.25
222 81 0.37
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (221 bp):
TATTTATATATGATTTTTTATTCTTTTAATTATTTAATTAAGTCAAAGTAAAATTAAGGCCCTTA
TCAAGATCTAAGATCGTTTTCATCAATAAATAAATAAAATAAAATAAAATCTAAGATCCTAATGG
AAGAGGGAAAAATCGTATCTGTTAGCAATGAAAATTTTAAATTTTAGGAAAGAAATTAATAATAG
ATGGGTATAACCAACAACTAGTTAGT
Found at i:915507 original size:18 final size:18
Alignment explanation
Indices: 915486--915534 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
915476 ATTATCAGTA
*
915486 GTCCTTCAGGACATAGTG
1 GTCCTTCGGGACATAGTG
915504 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
915522 GTCCTTCGGGACA
1 GTCCTTCGGGACA
915535 AATATTCAGT
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:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:920761 original size:10 final size:10
Alignment explanation
Indices: 920746--920820 Score: 70
Period size: 10 Copynumber: 7.7 Consensus size: 10
920736 CATTTAATAA
920746 ATAAACGAAC
1 ATAAACGAAC
920756 ATAAACGAAC
1 ATAAACGAAC
920766 ----ACGAAC
1 ATAAACGAAC
920772 ATAAACGAAC
1 ATAAACGAAC
* *
920782 ACAAAC-ATAA
1 ATAAACGA-AC
920792 ATGAACACGAAC
1 AT-AA-ACGAAC
920804 ATAAACGAAC
1 ATAAACGAAC
920814 ATAAACG
1 ATAAACG
920821 TTGGAGACCC
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
6 6 0.11
9 1 0.02
10 36 0.68
11 4 0.08
12 5 0.09
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:920771 original size:16 final size:16
Alignment explanation
Indices: 920750--920814 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
920740 TAATAAATAA
920750 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
920766 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
920782 ACAAACATAAATGAAC
1 ACGAACATAAACGAAC
920798 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
920814 A
1 A
920815 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:924949 original size:24 final size:24
Alignment explanation
Indices: 924914--924968 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
924904 TATTATGTTA
*
924914 AACATAAATGAACGCACATAAACG
1 AACATAAATGAACACACATAAACG
* *
924938 AACATAATTGAACACATATAAACG
1 AACATAAATGAACACACATAAACG
924962 AACATAA
1 AACATAA
924969 CCGAATGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.16
Consensus pattern (24 bp):
AACATAAATGAACACACATAAACG
Found at i:930752 original size:18 final size:18
Alignment explanation
Indices: 930729--930799 Score: 133
Period size: 18 Copynumber: 3.9 Consensus size: 18
930719 AGGGATTATC
*
930729 AGTGGTCCTTCGGGACGT
1 AGTGGTCCTTCGGGACAT
930747 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
930765 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
930783 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
930800 AATATTCAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.15, C:0.23, G:0.35, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:939448 original size:18 final size:18
Alignment explanation
Indices: 939425--939475 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
939415 AGGGATTATC
939425 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
939443 AGTGGTCCTTCAGCACAT
1 AGTGGTCCTTCGGGACAT
939461 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
939476 TAAATATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:942188 original size:32 final size:32
Alignment explanation
Indices: 942132--942207 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
942122 CCAATATTGT
* *
942132 ATTCAAATAATGCACAGTAGAGTTAGCATGAC
1 ATTCAAATAATGCACAGCAAAGTTAGCATGAC
* *
942164 ATTCAAATAATGCACCA-CAAAGTTAGTATTAC
1 ATTCAAATAATGCA-CAGCAAAGTTAGCATGAC
*
942196 ATTCAGATAATG
1 ATTCAAATAATG
942208 TACATGAGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (32 bp):
ATTCAAATAATGCACAGCAAAGTTAGCATGAC
Found at i:947478 original size:31 final size:31
Alignment explanation
Indices: 947443--947546 Score: 123
Period size: 31 Copynumber: 3.5 Consensus size: 31
947433 TTAAAAAACA
947443 TAAGATATGA-TCACTTTCTTTTCATTTTAAT
1 TAAGAT-TGAGTCACTTTCTTTTCATTTTAAT
*
947474 TAAGATTTAGTCA----C-TTTCATTTTAAT
1 TAAGATTGAGTCACTTTCTTTTCATTTTAAT
*
947500 TAAGATTTAGTCACTTTCTTTTCATTTTAAT
1 TAAGATTGAGTCACTTTCTTTTCATTTTAAT
947531 TAAGATATG-GTCACTT
1 TAAGAT-TGAGTCACTT
947547 AAGTTAACAG
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
26 25 0.39
27 1 0.02
30 3 0.05
31 34 0.53
32 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (31 bp):
TAAGATTGAGTCACTTTCTTTTCATTTTAAT
Found at i:947497 original size:26 final size:26
Alignment explanation
Indices: 947462--947521 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
947452 ATCACTTTCT
947462 TTTCATTTTAATTAAGATTTAGTCAC
1 TTTCATTTTAATTAAGATTTAGTCAC
947488 TTTCATTTTAATTAAGATTTAGTCAC
1 TTTCATTTTAATTAAGATTTAGTCAC
947514 TTTC-TTTT
1 TTTCATTTT
947522 CATTTTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.12
26 30 0.88
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.55
Consensus pattern (26 bp):
TTTCATTTTAATTAAGATTTAGTCAC
Found at i:949620 original size:31 final size:31
Alignment explanation
Indices: 949577--949650 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
949567 TCTCATTTTC
*
949577 AAGTGACCAAAACGTAATAAAATGATAACGT
1 AAGTGACTAAAACGTAATAAAATGATAACGT
* * **
949608 AAGTGACTAAAACTTGATAAAATGATAATTT
1 AAGTGACTAAAACGTAATAAAATGATAACGT
949639 AAGTGACTAAAA
1 AAGTGACTAAAA
949651 ATGTACAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.24
Consensus pattern (31 bp):
AAGTGACTAAAACGTAATAAAATGATAACGT
Found at i:950081 original size:25 final size:24
Alignment explanation
Indices: 950048--950111 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
950038 AAACTATTGT
*
950048 ATAATTTTATAATTAAAATAAAAC
1 ATAATTTTATAATAAAAATAAAAC
* *
950072 ATATATTTTACAAGAAAAATAAAAC
1 ATA-ATTTTATAATAAAAATAAAAC
*
950097 ATAATTCTATAATAA
1 ATAATTTTATAATAA
950112 TTCTATAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 12 0.36
25 21 0.64
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (24 bp):
ATAATTTTATAATAAAAATAAAAC
Found at i:950113 original size:11 final size:11
Alignment explanation
Indices: 950097--950122 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
950087 AAAATAAAAC
950097 ATAATTCTATA
1 ATAATTCTATA
950108 ATAATTCTATA
1 ATAATTCTATA
950119 ATAA
1 ATAA
950123 AAATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAATTCTATA
Found at i:950129 original size:17 final size:17
Alignment explanation
Indices: 950107--950157 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
950097 ATAATTCTAT
950107 AATAATTCTATAATAAA
1 AATAATTCTATAATAAA
*
950124 AATAATT-T-TACA-AGA
1 AATAATTCTATA-ATAAA
950139 AATAATTCTATAATAAA
1 AATAATTCTATAATAAA
950156 AA
1 AA
950158 AAACATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 13 0.46
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (17 bp):
AATAATTCTATAATAAA
Found at i:950363 original size:128 final size:126
Alignment explanation
Indices: 950135--950366 Score: 371
Period size: 128 Copynumber: 1.8 Consensus size: 126
950125 ATAATTTTAC
* *
950135 AAGAAATAATTCTATAATAAAAAAAACATAAATTTTACGAGAAAAATGTATTTCCAACTCTCAAC
1 AAGAAATAATTCTATAATAAAAAAAACATAAATTTTACAAGAAAAATGTATTTCCAACTCCCAAC
950200 TCTATTTATGTTTGTTCTTTTCAAGGATGAGAACTAGATCGAGCAACCAAATGGTACAACA
66 TCTATTTATGTTTGTTCTTTTCAAGGATGAGAACTAGATCGAGCAACCAAATGGTACAACA
*
950261 AAGAAATAATTCTATAATAAAAATAAAACATAAATTTTATAAGAAAAATGTATTTCCAACTCCCA
1 AAGAAATAATTCTATAAT-AAAA-AAAACATAAATTTTACAAGAAAAATGTATTTCCAACTCCCA
950326 ACTCTATTTGA-GTTTGTT-TTCTTCAAGGATGCA-AACTAGAT
64 ACTCTATTT-ATGTTTGTTCTT-TTCAAGGATG-AGAACTAGAT
950367 TCGAACGCGA
Statistics
Matches: 98, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
126 18 0.18
127 6 0.06
128 72 0.73
129 2 0.02
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (126 bp):
AAGAAATAATTCTATAATAAAAAAAACATAAATTTTACAAGAAAAATGTATTTCCAACTCCCAAC
TCTATTTATGTTTGTTCTTTTCAAGGATGAGAACTAGATCGAGCAACCAAATGGTACAACA
Found at i:951314 original size:17 final size:16
Alignment explanation
Indices: 951289--951343 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
951279 AGAGGTAATT
*
951289 TTTATTTATTTATTTA
1 TTTAATTATTTATTTA
*
951305 CTTTAATTATATATTTA
1 -TTTAATTATTTATTTA
*
951322 TTTTAAATAATTTATTTA
1 -TTT-AATTATTTATTTA
951340 TTTA
1 TTTA
951344 TGTAATAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 1 0.03
17 20 0.62
18 11 0.34
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAATTATTTATTTA
Found at i:951355 original size:34 final size:34
Alignment explanation
Indices: 951296--951376 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
951286 ATTTTTATTT
*
951296 ATTTATTTACTTTAATTATATATTTATTTTA-AATA
1 ATTTATTTA-TTTAATTATATATTTA-ATTAGAATA
951331 ATTTATTTATTT-ATGTA-ATAATTTAATTAGAATA
1 ATTTATTTATTTAAT-TATAT-ATTTAATTAGAATA
951365 ATTTATTTATTT
1 ATTTATTTATTT
951377 GTTTCGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
33 7 0.17
34 26 0.62
35 9 0.21
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.59
Consensus pattern (34 bp):
ATTTATTTATTTAATTATATATTTAATTAGAATA
Found at i:953592 original size:17 final size:17
Alignment explanation
Indices: 953567--953631 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
953557 TATAATGTTA
953567 TTGTTTAAATTATTAAT
1 TTGTTTAAATTATTAAT
* *
953584 TTTTTTAAATTGTTAAT
1 TTGTTTAAATTATTAAT
*
953601 TAAGTTTAAATTATTAAT
1 T-TGTTTAAATTATTAAT
*
953619 TTGTTTAATTTAT
1 TTGTTTAAATTAT
953632 CATTGGATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 26 0.65
18 14 0.35
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
TTGTTTAAATTATTAAT
Found at i:956055 original size:2 final size:2
Alignment explanation
Indices: 956048--956085 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
956038 TCCTAACCCA
956048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
956086 TGGATTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:956550 original size:63 final size:64
Alignment explanation
Indices: 956449--956577 Score: 226
Period size: 63 Copynumber: 2.0 Consensus size: 64
956439 GAAATTTCTC
*
956449 TGTTGATTTTTTTTGGTAAATGTCTTCTTTGTTGATTATATATTCAATGTGTGGTTTTTGA-TA
1 TGTTGATTTTTTTTGGTAAATGTCTTCTTTGTTGATTATATATTCAATGTGTGGATTTTGACTA
956512 TGTTGATTGTTTTTTGGTAAATGTCTTCTTT-TTGATTATATATTCAATGTGTGGATTTTGACTA
1 TGTTGATT-TTTTTTGGTAAATGTCTTCTTTGTTGATTATATATTCAATGTGTGGATTTTGACTA
956576 TG
1 TG
956578 AGATATATAT
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
63 37 0.59
64 26 0.41
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.56
Consensus pattern (64 bp):
TGTTGATTTTTTTTGGTAAATGTCTTCTTTGTTGATTATATATTCAATGTGTGGATTTTGACTA
Found at i:956725 original size:106 final size:104
Alignment explanation
Indices: 956591--956801 Score: 350
Period size: 104 Copynumber: 2.0 Consensus size: 104
956581 TATATATATA
* * *
956591 TATTGAGTTGCCTACGTTGTTGAGTTATATCAAAGAAACTTCTCTGTTGATTTTTTTTTTGGGTA
1 TATTGAGTTGCCTACGTTGTTGAGTTATATAAAAGAAACTTATCTGTTGA--TTTTTTTGGGGTA
* * *
956656 AATTATCTTCTCCGTTGATTATATGCTCAATGTGTGGTTTT
64 AACTATCTTCTACGTTGATTATATACTCAATGTGTGGTTTT
956697 TATTGAGTTGCCTACGTTGTTGAGTTATATAAAAGAAACTTATCTGTTGATTTTTTTGGGGTAAA
1 TATTGAGTTGCCTACGTTGTTGAGTTATATAAAAGAAACTTATCTGTTGATTTTTTTGGGGTAAA
956762 CTATCTTCTACGTTGATTATATACTCAATGTGTGGTTTT
66 CTATCTTCTACGTTGATTATATACTCAATGTGTGGTTTT
956801 T
1 T
956802 GAATATGAGA
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
104 51 0.52
106 48 0.48
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (104 bp):
TATTGAGTTGCCTACGTTGTTGAGTTATATAAAAGAAACTTATCTGTTGATTTTTTTGGGGTAAA
CTATCTTCTACGTTGATTATATACTCAATGTGTGGTTTT
Found at i:957317 original size:21 final size:21
Alignment explanation
Indices: 957286--957339 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
957276 TTATTAAAAG
*
957286 ATTTT-AAAAATAAAAATATT
1 ATTTTAAAAAATAAAAACATT
* *
957306 TTTTTAAAAAATAAATACATT
1 ATTTTAAAAAATAAAAACATT
*
957327 ATTTAAAAAAATA
1 ATTTTAAAAAATA
957340 CCCCACCACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTTAAAAAATAAAAACATT
Found at i:959648 original size:2 final size:2
Alignment explanation
Indices: 959591--959633 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
959581 CAAAACTGCA
959591 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
959633 A
1 A
959634 CACACACACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:961881 original size:19 final size:20
Alignment explanation
Indices: 961857--961896 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
961847 TTTAATTATC
961857 TTAAATTAGCAAAAAA-AAT
1 TTAAATTAGCAAAAAATAAT
961876 TTAAATTAGCAAAAAATAAT
1 TTAAATTAGCAAAAAATAAT
961896 T
1 T
961897 AGAGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (20 bp):
TTAAATTAGCAAAAAATAAT
Found at i:961919 original size:14 final size:14
Alignment explanation
Indices: 961870--961919 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
961860 AATTAGCAAA
961870 AAAAATTTAAATTAG
1 AAAAATTT-AATTAG
*
961885 CAAAAA-ATAATTAG
1 -AAAAATTTAATTAG
961899 AGAAAATTTAATTAG
1 A-AAAATTTAATTAG
961914 AAAAAT
1 AAAAAT
961920 AGAATAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 1 0.03
14 15 0.50
15 9 0.30
16 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (14 bp):
AAAAATTTAATTAG
Found at i:985991 original size:42 final size:42
Alignment explanation
Indices: 985944--986065 Score: 183
Period size: 42 Copynumber: 2.8 Consensus size: 42
985934 CATTTATATA
*
985944 TATTATGAAAATATATTATTTAATTATTAAAAATATAA-AAAT
1 TATTAT-AAAATATATTATTTAATTATTTAAAATATAATAAAT
985986 TATTATAAAATATATTTATTTAATTATTTAAAATATAATAAAT
1 TATTATAAAATATA-TTATTTAATTATTTAAAATATAATAAAT
*
986029 AATTATAAAATATATTATTTTAATTATTTTAAAATAT
1 TATTATAAAATATATTA-TTTAATTA-TTTAAAATAT
986066 TCATATATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
41 8 0.11
42 31 0.42
43 25 0.34
44 10 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.48
Consensus pattern (42 bp):
TATTATAAAATATATTATTTAATTATTTAAAATATAATAAAT
Found at i:986636 original size:26 final size:23
Alignment explanation
Indices: 986588--986631 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
986578 ATTTAAAAGC
986588 TAAAAAATTATTATTTATTTTTA
1 TAAAAAATTATTATTTATTTTTA
986611 TAAAAAATTATTATTTATTTT
1 TAAAAAATTATTATTTATTTT
986632 CTTTAACTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TAAAAAATTATTATTTATTTTTA
Found at i:993412 original size:21 final size:21
Alignment explanation
Indices: 993386--993425 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
993376 AGTACCATTG
993386 AGTCCATCAAGAAAAGTACGA
1 AGTCCATCAAGAAAAGTACGA
993407 AGTCCATCAAGAAAAGTAC
1 AGTCCATCAAGAAAAGTAC
993426 AGAGTCCTTA
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:0.47, C:0.20, G:0.17, T:0.15
Consensus pattern (21 bp):
AGTCCATCAAGAAAAGTACGA
Found at i:993431 original size:21 final size:20
Alignment explanation
Indices: 993385--993432 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 20
993375 AAGTACCATT
993385 GAGTCCATCAAGAAAAGTAC
1 GAGTCCATCAAGAAAAGTAC
993405 GAAGTCCATCAAGAAAAGTAC
1 G-AGTCCATCAAGAAAAGTAC
993426 AGAGTCC
1 -GAGTCC
993433 TTAGTCGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.15
Consensus pattern (20 bp):
GAGTCCATCAAGAAAAGTAC
Found at i:1000211 original size:7 final size:7
Alignment explanation
Indices: 1000193--1000256 Score: 60
Period size: 7 Copynumber: 9.1 Consensus size: 7
1000183 TCCTAAGTCG
1000193 AAAGAAA
1 AAAGAAA
*
1000200 AAA-AAG
1 AAAGAAA
1000206 AAA-AAA
1 AAAGAAA
1000212 AAAGAAA
1 AAAGAAA
*
1000219 AAGAGAAG
1 AA-AGAAA
*
1000227 AAATAACA
1 AAAGAA-A
1000235 AAAGAAA
1 AAAGAAA
*
1000242 AAAGAGA
1 AAAGAAA
1000249 AAAGAAA
1 AAAGAAA
1000256 A
1 A
1000257 TAAGGTGGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
6 10 0.22
7 25 0.54
8 11 0.24
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:1000228 original size:30 final size:31
Alignment explanation
Indices: 1000194--1000253 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 31
1000184 CCTAAGTCGA
*
1000194 AAGAAA-AAAAAGAAAAAAAA-AGAAAAAGAG
1 AAGAAATAAAAAAAAAAAAAAGAG-AAAAGAG
* *
1000224 AAGAAATAACAAAAGAAAAAAGAGAAAAGA
1 AAGAAATAAAAAAAAAAAAAAGAGAAAAGA
1000254 AAATAAGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
30 6 0.24
31 17 0.68
32 2 0.08
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (31 bp):
AAGAAATAAAAAAAAAAAAAAGAGAAAAGAG
Found at i:1000243 original size:24 final size:21
Alignment explanation
Indices: 1000193--1000256 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 21
1000183 TCCTAAGTCG
1000193 AAAGAAAAA-A-AAGAAAAAA
1 AAAGAAAAAGAGAAGAAAAAA
1000212 AAAGAAAAAGAGAAGAAATAACA
1 AAAGAAAAAGAGAAGAAA-AA-A
*
1000235 AAAGAAAAA-AG-AGAAAAGA
1 AAAGAAAAAGAGAAGAAAAAA
1000254 AAA
1 AAA
1000257 TAAGGTGGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 11 0.28
22 4 0.10
23 10 0.25
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAGAGAAGAAAAAA
Found at i:1000253 original size:26 final size:23
Alignment explanation
Indices: 1000201--1000256 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
1000191 CGAAAGAAAA
1000201 AAAAGAAAAAAAAAGAAAAAGAG
1 AAAAGAAAAAAAAAGAAAAAGAG
1000224 --AAGAAATAACAAAAGAAAAAAGAG
1 AAAAGAAA-AA-AAAAG-AAAAAGAG
1000248 AAAAGAAAA
1 AAAAGAAAA
1000257 TAAGGTGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
21 6 0.21
22 2 0.07
23 5 0.18
24 8 0.29
25 1 0.04
26 6 0.21
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAGAAAAAAAAAGAAAAAGAG
Found at i:1001564 original size:102 final size:102
Alignment explanation
Indices: 1001378--1001565 Score: 268
Period size: 102 Copynumber: 1.8 Consensus size: 102
1001368 ATTTCAGAGC
* *
1001378 CAATTTTAACTTCACAACGAAGAATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAACGAAGAATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
* * *
1001443 GGGCGGCTGATTGTCAACAAACAGTTTTATTCGGAGT
66 GAGCGACTGACTGTCAACAAACAGTTTTATTCGGAGT
* * * * * *
1001480 CAATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAGCATAAGCTTAACTTCACAGCGAAG
1 CAATTTCAACTTCACAACGAAGAATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
*
1001545 GAGCGACTGACTGTTAACAAA
66 GAGCGACTGACTGTCAACAAA
1001566 TAATTTCCCA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 74 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (102 bp):
CAATTTCAACTTCACAACGAAGAATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
GAGCGACTGACTGTCAACAAACAGTTTTATTCGGAGT
Found at i:1003507 original size:28 final size:27
Alignment explanation
Indices: 1003442--1003512 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 27
1003432 ATTATTATTA
*
1003442 TTTATTCATT-TTTTTTATAAATCTTAT
1 TTTATTTATTCTTTTTTAT-AATCTTAT
1003469 TTTCATGTTATTCTTTTTTAT-ATCTGATAT
1 TTT-AT-TTATTCTTTTTTATAATCT--TAT
*
1003499 TTTATTTATACTTT
1 TTTATTTATTCTTT
1003513 ATCATGTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 3 0.08
28 14 0.38
29 6 0.16
30 14 0.38
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.66
Consensus pattern (27 bp):
TTTATTTATTCTTTTTTATAATCTTAT
Found at i:1003693 original size:2 final size:2
Alignment explanation
Indices: 1003686--1003731 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1003676 ACTTTATCAT
1003686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1003727 TA TA T
1 TA TA T
1003732 TTATTTATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1003793 original size:15 final size:16
Alignment explanation
Indices: 1003770--1003820 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
1003760 TATCTATTAA
*
1003770 TTCTCTTTTT-TTTAT
1 TTCTATTTTTATTTAT
1003785 TTCTATTTTTATTTACT
1 TTCTATTTTTATTTA-T
* *
1003802 TGTATATATTTATTTAT
1 T-TCTATTTTTATTTAT
1003819 TT
1 TT
1003821 TTTACGTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 9 0.30
16 5 0.17
17 4 0.13
18 12 0.40
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (16 bp):
TTCTATTTTTATTTAT
Found at i:1003930 original size:3 final size:3
Alignment explanation
Indices: 1003922--1003947 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1003912 TTCTTTGTAT
1003922 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1003948 TTAAACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1005536 original size:2 final size:2
Alignment explanation
Indices: 1005529--1005565 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1005519 ACATACATAC
1005529 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1005566 GTCACAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1006062 original size:124 final size:123
Alignment explanation
Indices: 1005874--1006131 Score: 380
Period size: 124 Copynumber: 2.1 Consensus size: 123
1005864 AAATAGAATT
* *
1005874 AATAAAC-CTTTATGTAGAAACATACCACCCATACCTAGATGAAATAGACACCACGTGGGTTTGA
1 AATAAACTCTTTATGTAGAAACAAACAACCCATACCTAGATGAAATAGACACCACGTGGGTTTGA
*
1005938 TTAACCCACCAATTTTAACACTAAAATACTAAACAATTATTATCATATTACTAACCCA
66 TTAACCAACCAATTTTAACACTAAAATACTAAACAATTATTATCATATTACTAACCCA
* *
1005996 AATAAACTCTTATATG-A-AAACAAACAACCTCATACCTATATGAAAT-GGCTACCCACGTGGGT
1 AATAAACTCTT-TATGTAGAAACAAACAACC-CATACCTAGATGAAATAGAC-A-CCACGTGGGT
* * *
1006058 TTGATTAACTAATCAATTTTAACACTAAAATATTAAACAATTATTATCATATTACTAACCCA
62 TTGATTAACCAACCAATTTTAACACTAAAATACTAAACAATTATTATCATATTACTAACCCA
1006120 AATAAACTCTTT
1 AATAAACTCTTT
1006132 TATTTTTGCT
Statistics
Matches: 123, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
122 19 0.15
123 21 0.17
124 83 0.67
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.29
Consensus pattern (123 bp):
AATAAACTCTTTATGTAGAAACAAACAACCCATACCTAGATGAAATAGACACCACGTGGGTTTGA
TTAACCAACCAATTTTAACACTAAAATACTAAACAATTATTATCATATTACTAACCCA
Found at i:1007117 original size:3 final size:3
Alignment explanation
Indices: 1007111--1007155 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
1007101 AAATTATTAT
* *
1007111 TAA TAA TAA TAC TAA TAA TAT TAA TAA TAA TAA TAA -ATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
1007156 GTATAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1007128 original size:9 final size:8
Alignment explanation
Indices: 1007113--1007163 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 8
1007103 ATTATTATTA
1007113 ATAATAAT
1 ATAATAAT
1007121 ACTAATAAT
1 A-TAATAAT
1007130 ATTAATAAT
1 A-TAATAAT
1007139 AATAATAAAT
1 -ATAAT-AAT
1007149 ATAATAAGT
1 ATAATAA-T
1007158 ATAATA
1 ATAATA
1007164 TTTTTTAAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 3 0.08
9 31 0.82
10 4 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (8 bp):
ATAATAAT
Found at i:1007573 original size:90 final size:90
Alignment explanation
Indices: 1007394--1007716 Score: 511
Period size: 90 Copynumber: 3.6 Consensus size: 90
1007384 AAGGCTTACA
* * * * *
1007394 GATGACCCGAAGGATTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTTTTAAAATCTCATTTGA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTT-AGATCTCATTTGA
*
1007459 AAACATCCTGCACTGATGGTCTTATG
65 AAACATCCTGCACTGAAGGTCTTATG
* * *
1007485 GATGGCCCGAAGGACTTAATACTCAAGAAACCCCCAAAGGCTCAGTTTCTTAGATCTCATTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
* * *
1007550 AACATCATGCACTGAAAGTCTTATA
66 AACATCCTGCACTGAAGGTCTTATG
* *
1007575 GATGGCCCGAATGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATATCATTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
1007640 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
1007665 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
1007717 ATTGTCACCA
Statistics
Matches: 211, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
90 167 0.79
91 44 0.21
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (90 bp):
GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
AACATCCTGCACTGAAGGTCTTATG
Found at i:1007831 original size:43 final size:43
Alignment explanation
Indices: 1007761--1008363 Score: 455
Period size: 43 Copynumber: 13.2 Consensus size: 43
1007751 TCCCTCAAGT
* * * *
1007761 GTTCATCAAGTTTGTCATCAAGGAACCCCTACATATCATGATG
1 GTTCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
*
1007804 GTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
1 GTTCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
* * *
1007847 GTTTCTCAAGCTTATCATCAA-AGAACCCCTACATATCACGATG
1 GTTCCTCAAGATTGTCATCAAGA-AACCCCTACATATCACGATG
* * *
1007890 GTCCTTCAAGCTTATCATCAAATTTTTCATCAAGGAACCCCTACATATCACGATG
1 G---TTC---C---TCA--AGA-TTGTCATCAAGAAACCCCTACATATCACGATG
*
1007945 GTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
1 GTTCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
* *
1007988 GTTTCTCAAGCTTGTCATCAA-AGAACCCCTACATATCACGATG
1 GTTCCTCAAGATTGTCATCAAGA-AACCCCTACATATCACGATG
*
1008031 G-TCCTTCAAGCTTATCATCCAATTTGTCATCAAGGAACCCCTACATATCACGATG
1 GTTCC-TCAAG-----------A-TTGTCATCAAGAAACCCCTACATATCACGATG
1008086 GTTCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
1 GTTCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
* * *
1008129 GTTTCTCAAGTTTGTCATCAA-AGAACCCTTACATATCACGATG
1 GTTCCTCAAGATTGTCATCAAGA-AACCCCTACATATCACGATG
* * * *
1008172 G-TCCTTTAAGTGTTCATTAAATTTTTTATCAAGGAAA-CTCTACATATCACGATG
1 GTTCC---------TCA--AGA-TTGTCATCAA-GAAACCCCTACATATCACGATG
* * * * *
1008226 GTTCCTTAAGCTTTTCATCAAGAAAACCCTATATATCACGATG
1 GTTCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
* * *
1008269 GTTTCTCAAGCTTGTCATCAA-AGAACCCCTACATATCACAATG
1 GTTCCTCAAGATTGTCATCAAGA-AACCCCTACATATCACGATG
* * * * *
1008312 GTTCTTCAAGCTTTTCTTCAAGAAACCCCTGCATATCACGATG
1 GTTCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
*
1008355 GTTTCTCAA
1 GTTCCTCAA
1008364 AATATTGTGT
Statistics
Matches: 456, Mismatches: 55, Indels: 98
0.75 0.09 0.16
Matches are distributed among these distances:
42 12 0.03
43 321 0.70
44 5 0.01
46 7 0.02
49 2 0.00
51 3 0.01
52 5 0.01
53 1 0.00
54 25 0.05
55 71 0.16
56 4 0.01
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (43 bp):
GTTCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
Found at i:1007932 original size:98 final size:95
Alignment explanation
Indices: 1007809--1008356 Score: 354
Period size: 98 Copynumber: 5.9 Consensus size: 95
1007799 TGATGGTCCC
* * *
1007809 TCAAGATTGTCATCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTATCATCAAAGAACC
1 TCAA-ATTTTCATCAAGGAACCCCTACATATCACGATGGTTCCTCAAGCTTATCATCAAAGAACC
1007874 CCTACATATCACGATGGTCCTTCAAGCTTATCA
65 CCTACATATCACGATGGT-CTTCAAGCTT-TCA
* * *
1007907 TCAAATTTTTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGATTGTCATC-AAGAAAC
1 TCAAA-TTTTCATCAAGGAACCCCTACATATCACGATGGTTCCTCAAGCTTATCATCAAAG-AAC
* *
1007971 CCCTACATATCACGATGGTTTCTCAAGC-TT-G
64 CCCTACATATCACGATGGTCT-TCAAGCTTTCA
1008002 TC--A---TCA--AA-GAACCCCTACATATCACGATGG-TCCTTCAAGCTTATCATCCAATTTGT
1 TCAAATTTTCATCAAGGAACCCCTACATATCACGATGGTTCC-TCAAGC-T-T-AT-C-A----T
1008058 CATCAAGGAACCCCTACATATCACGATGG--TTC---C--TCA
56 CA--AA-GAACCCCTACATATCACGATGGTCTTCAAGCTTTCA
* * * * * *
1008094 --AGATTGTCATCAAGAAACCCCTACATATCACGATGGTTTCTCAAGTTTGTCATCAAAGAACCC
1 TCAAATTTTCATCAAGGAACCCCTACATATCACGATGGTTCCTCAAGCTTATCATCAAAGAACCC
* *
1008157 TTACATATCACGATGGTCCTTTAAG-TGTTCA
66 CTACATATCACGATGGT-CTTCAAGCT-TTCA
* * * * * * *
1008188 TTAAATTTTTTATCAAGGAAACTCTACATATCACGATGGTTCCTTAAGCTTTTCATC-AAGAAAA
1 TCAAA-TTTTCATCAAGGAACCCCTACATATCACGATGGTTCCTCAAGCTTATCATCAAAG-AAC
* * *
1008252 CCCTATATATCACGATGGTTTCTCAAGC-TT-G
64 CCCTACATATCACGATGGTCT-TCAAGCTTTCA
* * * *
1008283 TC--A---TCA--AA-GAACCCCTACATATCACAATGGTTCTTCAAGCTTTTCTTC-AAGAAACC
1 TCAAATTTTCATCAAGGAACCCCTACATATCACGATGGTTCCTCAAGCTTATCATCAAAG-AACC
*
1008339 CCTGCATATCACGATGGT
65 CCTACATATCACGATGGT
1008357 TTCTCAAAAT
Statistics
Matches: 363, Mismatches: 45, Indels: 96
0.72 0.09 0.19
Matches are distributed among these distances:
85 2 0.01
86 105 0.29
87 7 0.02
88 1 0.00
89 11 0.03
90 1 0.00
91 2 0.01
92 2 0.01
93 3 0.01
94 4 0.01
95 11 0.03
96 11 0.03
97 74 0.20
98 126 0.35
99 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (95 bp):
TCAAATTTTCATCAAGGAACCCCTACATATCACGATGGTTCCTCAAGCTTATCATCAAAGAACCC
CTACATATCACGATGGTCTTCAAGCTTTCA
Found at i:1007933 original size:141 final size:140
Alignment explanation
Indices: 1007718--1008325 Score: 923
Period size: 141 Copynumber: 4.3 Consensus size: 140
1007708 AGTTTCTTAA
* * * * * *
1007718 TTGTCACCAAGGAACCCCTACATATCACGTTCGTCCCTCAAG-TGTTCATCAAGTTTGTCATCAA
1 TTGTCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCT-TTCATCAAATTTGTCATCAA
*
1007782 GGAACCCCTACATATCATGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
65 GGAACCCCTACATATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
1007847 GTTTCTCAAGC
130 GTTTCTCAAGC
* *
1007858 TTATCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCTTATCATCAAATTTTTCATCAA
1 TTGTCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCTT-TCATCAAATTTGTCATCAA
1007923 GGAACCCCTACATATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
65 GGAACCCCTACATATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
1007988 GTTTCTCAAGC
130 GTTTCTCAAGC
*
1007999 TTGTCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCTTATCATCCAATTTGTCATCAA
1 TTGTCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCTT-TCATCAAATTTGTCATCAA
*
1008064 GGAACCCCTACATATCACGATGGTTCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
65 GGAACCCCTACATATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
*
1008129 GTTTCTCAAGT
130 GTTTCTCAAGC
* * * * *
1008140 TTGTCATCAAAGAACCCTTACATATCACGATGGTCCTTTAAG-TGTTCATTAAATTTTTTATCAA
1 TTGTCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCT-TTCATCAAATTTGTCATCAA
* * * * * * * *
1008204 GGAAACTCTACATATCACGATGGTTCCTTAAGCTTTTCATCAAGAAAACCCTATATATCACGATG
65 GGAACCCCTACATATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATG
1008269 GTTTCTCAAGC
130 GTTTCTCAAGC
* *
1008280 TTGTCATCAAAGAACCCCTACATATCACAATGGTTCTTCAAGCTTT
1 TTGTCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCTTT
1008326 TCTTCAAGAA
Statistics
Matches: 432, Mismatches: 32, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
140 161 0.37
141 271 0.63
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.30
Consensus pattern (140 bp):
TTGTCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCTTTCATCAAATTTGTCATCAAG
GAACCCCTACATATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATGG
TTTCTCAAGC
Found at i:1008457 original size:40 final size:41
Alignment explanation
Indices: 1008382--1008463 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 41
1008372 GTTTCGAGCG
* *
1008382 AAACTATCTTAAGCGAGATAAAATCTTTTGTTTCAAG-GAA
1 AAACAATCTTAAGCGAGATAAAATCTTTAGTTTCAAGTGAA
1008422 AAACAATCTTGAA-CGAGATAAAATCTTCTAG-TTCAAGTGAA
1 AAACAATCTT-AAGCGAGATAAAATCTT-TAGTTTCAAGTGAA
1008463 A
1 A
1008464 TTGTCTCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
40 29 0.78
41 8 0.22
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (41 bp):
AAACAATCTTAAGCGAGATAAAATCTTTAGTTTCAAGTGAA
Found at i:1008506 original size:36 final size:36
Alignment explanation
Indices: 1008453--1008749 Score: 422
Period size: 36 Copynumber: 8.3 Consensus size: 36
1008443 AATCTTCTAG
* *
1008453 TTCAAGTGAAATTGTCTCAAGGGAGATAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGGGAGATAAAATTTGT
*
1008489 TTCAAGGGAAACCGTCTCAAGGGAGATAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGGGAGATAAAATTTGT
* *
1008525 TTTAAGGGAAACTGTCTCAAGGGAGACT-GAATTTGT
1 TTCAAGGGAAACTGTCTCAAGGGAGA-TAAAATTTGT
* * * * *
1008561 TTTAATGGAAACTATCTCAAGGGAGACAAAATTCGT
1 TTCAAGGGAAACTGTCTCAAGGGAGATAAAATTTGT
*
1008597 TTCAAGGGAAACTGTTTCAAGGGAGAT--AATTT-T
1 TTCAAGGGAAACTGTCTCAAGGGAGATAAAATTTGT
1008630 TTCAAGGGAAACTGTCTCAAGGGAGATAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGGGAGATAAAATTTGT
* *
1008666 TTCAAGGGAAACTGTCTCAAGGGAGACAAAATTCGT
1 TTCAAGGGAAACTGTCTCAAGGGAGATAAAATTTGT
*
1008702 TTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGGGAGATAAAATTTGT
*
1008738 TTCAAGGAAAAC
1 TTCAAGGGAAAC
1008750 ATACTTAAAA
Statistics
Matches: 234, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
33 27 0.12
34 4 0.02
35 5 0.02
36 197 0.84
37 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGGGAGATAAAATTTGT
Found at i:1008648 original size:141 final size:143
Alignment explanation
Indices: 1008453--1008749 Score: 454
Period size: 141 Copynumber: 2.1 Consensus size: 143
1008443 AATCTTCTAG
* *
1008453 TTCAAGTGAAATTGTCTCAAGGGAGATAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGATAA
1 TTCAAGGGAAACTGTCTCAAGGGAGAT-AAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGATAA
* ** * * *
1008518 AATTTGTTTTAAGGGAAACTGTCTCAAGGGAGACTGAATTTGTTTTAATGGAAACTATCTCAAGG
65 AATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGG
1008583 GAGACAAAATTCGT
130 GAGACAAAATTCGT
* *
1008597 TTCAAGGGAAACTGTTTCAAGGGAGAT-AATTT-TTTCAAGGGAAACTGTCTCAAGGGAGATAAA
1 TTCAAGGGAAACTGTCTCAAGGGAGATAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGATAAA
*
1008660 ATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACTGTCTCAAGGG
66 ATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGGG
*
1008725 AGACAAAATTTGT
131 AGACAAAATTCGT
*
1008738 TTCAAGGAAAAC
1 TTCAAGGGAAAC
1008750 ATACTTAAAA
Statistics
Matches: 140, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
141 111 0.79
142 5 0.04
144 24 0.17
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (143 bp):
TTCAAGGGAAACTGTCTCAAGGGAGATAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGATAAA
ATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGGG
AGACAAAATTCGT
Found at i:1008725 original size:15 final size:15
Alignment explanation
Indices: 1008595--1008653 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
1008585 GACAAAATTC
1008595 GTTTCAAGGGAAACT
1 GTTTCAAGGGAAACT
*
1008610 GTTTCAAGGGAGATAATT
1 GTTTCAA-GG-GA-AACT
*
1008628 TTTTCAAGGGAAACT
1 GTTTCAAGGGAAACT
*
1008643 GTCTCAAGGGA
1 GTTTCAAGGGA
1008654 GATAAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 19 0.53
16 4 0.11
17 4 0.11
18 9 0.25
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (15 bp):
GTTTCAAGGGAAACT
Found at i:1008744 original size:21 final size:20
Alignment explanation
Indices: 1008646--1008744 Score: 56
Period size: 21 Copynumber: 5.3 Consensus size: 20
1008636 GGAAACTGTC
1008646 TCAAGGGAGATAAAATTTGTT
1 TCAAGGGAGA-AAAATTTGTT
* *
1008667 TCAA-GG-G--AAA-CTGTC
1 TCAAGGGAGAAAAATTTGTT
*
1008682 TCAAGGGAGACAAAATTCGTT
1 TCAAGGGAGA-AAAATTTGTT
* *
1008703 TCAA-GG-G--AAA-CTGTC
1 TCAAGGGAGAAAAATTTGTT
1008718 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGA-AAAATTTGTT
1008739 TCAAGG
1 TCAAGG
1008745 AAAACATACT
Statistics
Matches: 56, Mismatches: 10, Indels: 24
0.62 0.11 0.27
Matches are distributed among these distances:
15 13 0.23
16 10 0.18
17 2 0.04
19 2 0.04
20 10 0.18
21 19 0.34
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.25
Consensus pattern (20 bp):
TCAAGGGAGAAAAATTTGTT
Found at i:1009045 original size:34 final size:34
Alignment explanation
Indices: 1009005--1009103 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 34
1008995 TCTCGGAGAA
* * *
1009005 AAATTGTCTCGAGCGAGATGGAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGAAGAAATTTGTTTTGAG
*
1009039 AAATTGTCTCAAGTGAGAAGAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGAAGAAATTTGTTTTGAG
* * *
1009073 AAATTATCTCAAGTGAGACA-AAATTTTTTTT
1 AAATTGTCTCAAGCGAGA-AGAAATTTGTTTT
1009104 TAAAGAGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 57 0.98
35 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.37
Consensus pattern (34 bp):
AAATTGTCTCAAGCGAGAAGAAATTTGTTTTGAG
Found at i:1009257 original size:33 final size:32
Alignment explanation
Indices: 1009206--1009336 Score: 172
Period size: 32 Copynumber: 4.1 Consensus size: 32
1009196 TATTGAATGA
* * *
1009206 CCCAATATTCGATATTGAATCTCCAAAGATGC
1 CCCAACATTTGATGTTGAATCTCCAAAGATGC
1009238 CCCAACATTTTGATGTTGAATCTCCAAAGATGC
1 CCCAACA-TTTGATGTTGAATCTCCAAAGATGC
* * *
1009271 CCCAACATTTGATGTTGAATTTTCAAAGATGT
1 CCCAACATTTGATGTTGAATCTCCAAAGATGC
* * *
1009303 CTCAACATTTGATGTTGAGTCTTCAAAGATGC
1 CCCAACATTTGATGTTGAATCTCCAAAGATGC
1009335 CC
1 CC
1009337 TCTATTGCTT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
32 57 0.66
33 30 0.34
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (32 bp):
CCCAACATTTGATGTTGAATCTCCAAAGATGC
Found at i:1009298 original size:65 final size:64
Alignment explanation
Indices: 1009206--1009336 Score: 172
Period size: 65 Copynumber: 2.0 Consensus size: 64
1009196 TATTGAATGA
*
1009206 CCCAATATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAAGATGC
1 CCCAACATTCGATATTGAATCTCCAAAGATGCCCCAACA-TTTGATGTTGAATCTCCAAAGATGC
* * * * * * * *
1009271 CCCAACATTTGATGTTGAATTTTCAAAGATGTCTCAACATTTGATGTTGAGTCTTCAAAGATGC
1 CCCAACATTCGATATTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGC
1009335 CC
1 CC
1009337 TCTATTGCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
64 25 0.44
65 32 0.56
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (64 bp):
CCCAACATTCGATATTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGC
Found at i:1010399 original size:27 final size:27
Alignment explanation
Indices: 1010364--1010419 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1010354 TTTCTATTTG
*
1010364 TTTCTTTTTCT-TTGCTTTAATTTCTTT
1 TTTCCTTTTCTCTTG-TTTAATTTCTTT
**
1010391 TTTCCTTTTCTCTTGTTTCTTTTCTTT
1 TTTCCTTTTCTCTTGTTTAATTTCTTT
1010418 TT
1 TT
1010420 GCTCTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTCCTTTTCTCTTGTTTAATTTCTTT
Found at i:1010409 original size:22 final size:21
Alignment explanation
Indices: 1010349--1010438 Score: 87
Period size: 22 Copynumber: 4.3 Consensus size: 21
1010339 ATTCTTGTCC
*
1010349 TTTTTTTT-CTATTTGTTTCT
1 TTTTTTTTGCTCTTTGTTTCT
* **
1010369 TTTTCTTTGCT-TTAATTTCT
1 TTTTTTTTGCTCTTTGTTTCT
*
1010389 TTTTTCCTTTTCTC-TTGTTTCT
1 TTTTT--TTTGCTCTTTGTTTCT
1010411 TTTCTTTTTGCTCTTTGTTTCT
1 TTT-TTTTTGCTCTTTGTTTCT
1010433 TTTTTT
1 TTTTTT
1010439 CTGATTGGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
20 18 0.32
21 11 0.20
22 25 0.45
23 2 0.04
ACGTcount: A:0.03, C:0.16, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTTTTTTGCTCTTTGTTTCT
Found at i:1010621 original size:2 final size:2
Alignment explanation
Indices: 1010614--1010638 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1010604 ACAACTAGGG
1010614 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 A
1010639 AACAAAGCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1015519 original size:13 final size:13
Alignment explanation
Indices: 1015503--1015532 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1015493 TTTTAGGTGT
1015503 CACTGATAGGATA
1 CACTGATAGGATA
1015516 CACTGATAGGATA
1 CACTGATAGGATA
1015529 CACT
1 CACT
1015533 TTTATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (13 bp):
CACTGATAGGATA
Found at i:1016819 original size:124 final size:123
Alignment explanation
Indices: 1016597--1016824 Score: 386
Period size: 124 Copynumber: 1.8 Consensus size: 123
1016587 AAACATACCA
*
1016597 CCCATACCTAGATGAAATGGACACCACGTGGGTTTGATTAACCTACCAATTTTAACACTAAAATA
1 CCCATACCTAGATGAAATGGACACCACGTGGGTTTGATTAACCAACCAATTTTAACACTAAAATA
1016662 CTAAACAATTATTATCATATTACTAACCCAAATAAACTCTTATATGAAAACAAACAAC
66 CTAAACAATTATTATCATATTACTAACCCAAATAAACTCTTATATGAAAACAAACAAC
* *
1016720 CCCATACCTATATGAAATGG-CTACCCACGTGGGTTTGATTAACCAATCAATTTTAACACTAAAA
1 CCCATACCTAGATGAAATGGAC-A-CCACGTGGGTTTGATTAACCAACCAATTTTAACACTAAAA
* *
1016784 TATTAAACAATTATTATCATATTACTAACCTAAATAAACTC
64 TACTAAACAATTATTATCATATTACTAACCCAAATAAACTC
1016825 AATTATTATC
Statistics
Matches: 98, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
122 1 0.01
123 20 0.20
124 77 0.79
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (123 bp):
CCCATACCTAGATGAAATGGACACCACGTGGGTTTGATTAACCAACCAATTTTAACACTAAAATA
CTAAACAATTATTATCATATTACTAACCCAAATAAACTCTTATATGAAAACAAACAAC
Found at i:1016864 original size:33 final size:33
Alignment explanation
Indices: 1016791--1016857 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1016781 AAATATTAAA
*
1016791 CAATTATTATCATATTACTAACCTAAATAAACT
1 CAATTATTATCATATTACTAACCCAAATAAACT
1016824 CAATTATTATCATATTACTAACCCAAATAAACT
1 CAATTATTATCATATTACTAACCCAAATAAACT
1016857 C
1 C
1016858 TTTTATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (33 bp):
CAATTATTATCATATTACTAACCCAAATAAACT
Found at i:1017892 original size:9 final size:10
Alignment explanation
Indices: 1017855--1017895 Score: 50
Period size: 9 Copynumber: 4.1 Consensus size: 10
1017845 AATTATTATT
1017855 AATAATAATA
1 AATAATAATA
1017865 TTAATAAT-ATA
1 --AATAATAATA
1017876 AATAATAATA
1 AATAATAATA
1017886 AAT-ATAATA
1 AATAATAATA
1017895 A
1 A
1017896 TAAGTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.46
10 6 0.21
11 3 0.11
12 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AATAATAATA
Found at i:1017903 original size:12 final size:11
Alignment explanation
Indices: 1017854--1017906 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 11
1017844 AAATTATTAT
1017854 TAATAATAATA
1 TAATAATAATA
*
1017865 TTAATAATATAAA
1 -TAATAATA-ATA
1017878 TAATAATAAATA
1 TAATAAT-AATA
1017890 TAATAATAAGTA
1 TAATAATAA-TA
1017902 TAATA
1 TAATA
1017907 TTTTTTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
11 2 0.06
12 31 0.86
13 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
TAATAATAATA
Found at i:1024707 original size:39 final size:38
Alignment explanation
Indices: 1024664--1024771 Score: 148
Period size: 39 Copynumber: 2.8 Consensus size: 38
1024654 TTTAAAAAAT
1024664 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAA-AATTTAAGAAATTAAG
*
1024703 AATTTAGAATGTT-ATGGTAGAAAAATTTAAGAAATTAGG
1 AATTTAGAATGTTAAT-GT-GAAAAATTTAAGAAATTAAG
1024742 AATTTAGAATGTTAGA-GTGAAAAAATTTAA
1 AATTTAGAATGTTA-ATGTG-AAAAATTTAA
1024772 TAATTATAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
38 3 0.05
39 55 0.87
40 4 0.06
41 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (38 bp):
AATTTAGAATGTTAATGTGAAAAATTTAAGAAATTAAG
Found at i:1025375 original size:10 final size:10
Alignment explanation
Indices: 1025360--1025433 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
1025350 CATTTAATAA
1025360 ATAAACGAAC
1 ATAAACGAAC
1025370 ATAAACGAAC
1 ATAAACGAAC
1025380 ----ACGAAC
1 ATAAACGAAC
*
1025386 ATAAGCGAAC
1 ATAAACGAAC
* *
1025396 ATGAAC-ATAA
1 ATAAACGA-AC
1025406 ATGAACACGAAC
1 AT-AA-ACGAAC
*
1025418 ATAAACAAAC
1 ATAAACGAAC
1025428 ATAAAC
1 ATAAAC
1025434 ATTGGAGACC
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 33 0.67
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1025412 original size:32 final size:32
Alignment explanation
Indices: 1025366--1025435 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
1025356 ATAAATAAAC
* *
1025366 GAACATAAACGAACACGAACATAAGCGAACAT
1 GAACATAAACGAACACGAACATAAACAAACAT
*
1025398 GAACATAAATGAACACGAACATAAACAAACAT
1 GAACATAAACGAACACGAACATAAACAAACAT
*
1025430 AAACAT
1 GAACAT
1025436 TGGAGACCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.11
Consensus pattern (32 bp):
GAACATAAACGAACACGAACATAAACAAACAT
Found at i:1025435 original size:16 final size:16
Alignment explanation
Indices: 1025364--1025428 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
1025354 TAATAAATAA
1025364 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1025380 ACGAACATAAGCGAAC
1 ACGAACATAAACGAAC
* *
1025396 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
1025412 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
1025428 A
1 A
1025429 TAAACATTGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1025815 original size:24 final size:24
Alignment explanation
Indices: 1025788--1025846 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
1025778 AACATAAATA
1025788 AACGAACATAAA-AGAACATAACCG
1 AACGAACATAAACA-AACATAACCG
1025812 AACGAACATAAACAAACATAACCG
1 AACGAACATAAACAAACATAACCG
1025836 AACGAACATAA
1 AACGAACATAA
1025847 CCGAACGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 33 0.97
25 1 0.03
ACGTcount: A:0.59, C:0.22, G:0.10, T:0.08
Consensus pattern (24 bp):
AACGAACATAAACAAACATAACCG
Found at i:1025818 original size:14 final size:14
Alignment explanation
Indices: 1025801--1025853 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
1025791 GAACATAAAA
1025801 GAACATAACCGAAC
1 GAACATAACCGAAC
1025815 GAACAT-A---AAC
1 GAACATAACCGAAC
*
1025825 AAACATAACCGAAC
1 GAACATAACCGAAC
1025839 GAACATAACCGAAC
1 GAACATAACCGAAC
1025853 G
1 G
1025854 TTCACGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 23 0.70
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.08
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:1029944 original size:18 final size:18
Alignment explanation
Indices: 1029902--1029944 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1029892 GAGAAGGAGA
*
1029902 AGAAGAAAAAGAATAAGG
1 AGAAGGAAAAGAATAAGG
*
1029920 AGAAGGAAAAGAATGAGG
1 AGAAGGAAAAGAATAAGG
*
1029938 AGGAGGA
1 AGAAGGA
1029945 GGAGAAGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.37, T:0.05
Consensus pattern (18 bp):
AGAAGGAAAAGAATAAGG
Found at i:1032661 original size:32 final size:32
Alignment explanation
Indices: 1032577--1032666 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
1032567 ACGTAAACTA
*
1032577 TCCATATGTTCCTTAGAACATAGGT-ATAATG
1 TCCATATGTTCCGTAGAACATAGGTAATAATG
* * **
1032608 TCCATATGTCCCG-AAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGA-ACATAGGTAATAATG
*
1032640 TCCATATGTTCCGTAGAACATATGTAA
1 TCCATATGTTCCGTAGAACATAGGTAA
1032667 ACCCTCGACT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
30 2 0.04
31 19 0.40
32 25 0.52
33 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (32 bp):
TCCATATGTTCCGTAGAACATAGGTAATAATG
Found at i:1035412 original size:2 final size:2
Alignment explanation
Indices: 1035405--1035441 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1035395 ATTATGACTT
1035405 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1035442 CGCTTGTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1036782 original size:30 final size:31
Alignment explanation
Indices: 1036748--1036854 Score: 119
Period size: 30 Copynumber: 3.5 Consensus size: 31
1036738 CTAGGTCCGA
* *
1036748 AGAACCTAGGTAAATTGTCCA-ATGTTCCTT
1 AGAACATAGGTAAATTGTCCATATGTTCCCT
* *
1036778 AGAACATAGGTATATTGTCCATATG-TCCCG
1 AGAACATAGGTAAATTGTCCATATGTTCCCT
* * *
1036808 AAAGACATAGGTAATTCTGTCCATATGTTCCGT
1 AGA-ACATAGGTAAAT-TGTCCATATGTTCCCT
1036841 AGAACATAGGTAAA
1 AGAACATAGGTAAA
1036855 CCCTCGACTC
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
30 24 0.39
31 13 0.21
32 20 0.32
33 5 0.08
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
AGAACATAGGTAAATTGTCCATATGTTCCCT
Found at i:1036833 original size:32 final size:32
Alignment explanation
Indices: 1036744--1036853 Score: 113
Period size: 32 Copynumber: 3.5 Consensus size: 32
1036734 GTCCCTAGGT
* *
1036744 CCGAAGAACCTAGGTAA-ATTGTCCA-ATGTT
1 CCGAAGAACATAGGTAATATTGTCCATATGTC
**
1036774 CCTTAGAACATAGGT-ATATTGTCCATATGTC
1 CCGAAGAACATAGGTAATATTGTCCATATGTC
*
1036805 CCGAA-AGACATAGGTAAT-TCTGTCCATATGTT
1 CCGAAGA-ACATAGGTAATAT-TGTCCATATGTC
*
1036837 CCGTAGAACATAGGTAA
1 CCGAAGAACATAGGTAA
1036854 ACCCTCGACT
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
29 1 0.02
30 21 0.32
31 16 0.24
32 27 0.41
33 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (32 bp):
CCGAAGAACATAGGTAATATTGTCCATATGTC
Found at i:1043992 original size:20 final size:20
Alignment explanation
Indices: 1043955--1043993 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1043945 AGATTGAGTG
* * *
1043955 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
1043975 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1043994 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:1044225 original size:19 final size:20
Alignment explanation
Indices: 1044195--1044233 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1044185 TTCCCCTTTA
*
1044195 AAGGGGGAATCGGTTCCCTC
1 AAGGGGGAATCGATTCCCTC
1044215 AAGGGGG-ATCGATTCCCTC
1 AAGGGGGAATCGATTCCCTC
1044234 TGCACCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.21
Consensus pattern (20 bp):
AAGGGGGAATCGATTCCCTC
Found at i:1050012 original size:21 final size:21
Alignment explanation
Indices: 1049987--1050040 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1049977 TGTTATACAA
1049987 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
1050008 GGGGGAATCGGTACCCCCTGT
1 GGGGGAATCGGTACCCCCTGG
1050029 GGGGGAATCGGT
1 GGGGGAATCGGT
1050041 TCCCTACGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:1052173 original size:29 final size:28
Alignment explanation
Indices: 1052141--1052199 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1052131 AATTAAAAGT
1052141 TTTAGAAATCTAGAT-AGAATTTTAAAAAA
1 TTTA-AAATCTA-ATGAGAATTTTAAAAAA
* *
1052170 TTTAAGATTTAATGAGAATTTTAAAAAA
1 TTTAAAATCTAATGAGAATTTTAAAAAA
1052198 TT
1 TT
1052200 AAAGGAGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 21 0.78
29 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (28 bp):
TTTAAAATCTAATGAGAATTTTAAAAAA
Found at i:1053629 original size:27 final size:24
Alignment explanation
Indices: 1053593--1053656 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 24
1053583 TAAATTAAAA
*
1053593 TTAAAATAAAATAT-TTATAAATTAAG
1 TTAATATAAAATATATT-T-AA-TAAG
1053619 TTAATAGTAAAATATATTTAATAAG
1 TTAATA-TAAAATATATTTAATAAG
1053644 TTAATATAAAATA
1 TTAATATAAAATA
1053657 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
24 7 0.20
25 10 0.29
26 7 0.20
27 9 0.26
28 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (24 bp):
TTAATATAAAATATATTTAATAAG
Found at i:1053664 original size:25 final size:25
Alignment explanation
Indices: 1053615--1053664 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1053605 ATTTATAAAT
* *
1053615 TAAGTTAATAGTAAAATATATTTAA
1 TAAGTTAATAGTAAAATAAAATTAA
1053640 TAAGTTAATA-TAAAATAAAAATTAA
1 TAAGTTAATAGTAAAAT-AAAATTAA
1053665 AATATATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (25 bp):
TAAGTTAATAGTAAAATAAAATTAA
Found at i:1054048 original size:31 final size:31
Alignment explanation
Indices: 1054005--1054080 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
1053995 GTTAACTCGG
*
1054005 GTGACCACATCTTAATTAAATAAAAACAAAA
1 GTGACCATATCTTAATTAAATAAAAACAAAA
*
1054036 GTGACCATATCTTAATTAAATAAAAACATAA
1 GTGACCATATCTTAATTAAATAAAAACAAAA
*
1054067 GTGATCATATCTTA
1 GTGACCATATCTTA
1054081 TATATTTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (31 bp):
GTGACCATATCTTAATTAAATAAAAACAAAA
Found at i:1055147 original size:86 final size:86
Alignment explanation
Indices: 1055002--1055258 Score: 496
Period size: 86 Copynumber: 3.0 Consensus size: 86
1054992 TTTCAGAGAA
*
1055002 AGAGACATTTGACTCTGCTAAATGTAATATAATATTAGGATTTAGGAGTTCATTACTTTTCAAAG
1 AGAGACATTTGACTCTGCTAAACGTAATATAATATTAGGATTTAGGAGTTCATTACTTTTCAAAG
1055067 TAGGAGAAAATATGTATAGAT
66 TAGGAGAAAATATGTATAGAT
1055088 AGAGACATTTGACTCTGCTAAACGTAATATAATATTAGGATTTAGGAGTTCATTACTTTTCAAAG
1 AGAGACATTTGACTCTGCTAAACGTAATATAATATTAGGATTTAGGAGTTCATTACTTTTCAAAG
1055153 TAGGAGAAAATATGTATAGAT
66 TAGGAGAAAATATGTATAGAT
1055174 AGAGACATTTGACTCTGCTAAACGTAATATAATATTAGGATTTAGGAGTTCATTACTTTTCAAAG
1 AGAGACATTTGACTCTGCTAAACGTAATATAATATTAGGATTTAGGAGTTCATTACTTTTCAAAG
*
1055239 TAGGAGAAAATATATATAGA
66 TAGGAGAAAATATGTATAGA
1055259 CCCAAGGAAG
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 169 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (86 bp):
AGAGACATTTGACTCTGCTAAACGTAATATAATATTAGGATTTAGGAGTTCATTACTTTTCAAAG
TAGGAGAAAATATGTATAGAT
Found at i:1057333 original size:22 final size:22
Alignment explanation
Indices: 1057308--1057366 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1057298 TTTTCCCAAC
*
1057308 ATTTAATTATAAATTAGTTAAA
1 ATTTAAATATAAATTAGTTAAA
*
1057330 ATTTAAATATAAATTATTTAAA
1 ATTTAAATATAAATTAGTTAAA
* *
1057352 A-TAAAATATTAATTA
1 ATTTAAATATAAATTA
1057367 CATTATTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
21 12 0.36
22 21 0.64
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTAAATATAAATTAGTTAAA
Found at i:1062704 original size:85 final size:86
Alignment explanation
Indices: 1062594--1062764 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 86
1062584 ACTGGAAAAG
1062594 AAATATCGAAGGAGAGTACCTAAAAAAATCAGTCTTTCTATTGCTTTTTCTTTTTCTTGCC-ATA
1 AAATATCGAAGGAGAGTACCTAAAAAAATCAGTCTTTCTATTGCTTTTTCTTTTTCTTGCCAATA
1062658 GTAGGATTACATTTTCTTCTC
66 GTAGGATTACATTTTCTTCTC
1062679 AAATATCGAAGGAGAGTACCTAAAAAAATCAGTCTTTCTATTGCTTTTTCTTTTTCTTGCCAATA
1 AAATATCGAAGGAGAGTACCTAAAAAAATCAGTCTTTCTATTGCTTTTTCTTTTTCTTGCCAATA
1062744 GTAGGATTACATTTTCTTCTC
66 GTAGGATTACATTTTCTTCTC
1062765 TCTTTTACAT
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 61 0.72
86 24 0.28
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.41
Consensus pattern (86 bp):
AAATATCGAAGGAGAGTACCTAAAAAAATCAGTCTTTCTATTGCTTTTTCTTTTTCTTGCCAATA
GTAGGATTACATTTTCTTCTC
Found at i:1066118 original size:30 final size:30
Alignment explanation
Indices: 1066026--1066118 Score: 73
Period size: 30 Copynumber: 3.1 Consensus size: 30
1066016 GAGCCTACAT
1066026 CAAACACATCAAGAGTCAGCCTTTCAAGAA
1 CAAACACATCAAGAGTCAGCCTTTCAAGAA
* * * *** * *
1066056 CAGACTGGC-T-AAGATTACAGGAGTTGATGAA
1 CAAAC--ACATCAAGAGT-CAGCCTTTCAAGAA
1066087 CAAACACATCAAGAGTCAGCCTTTCAAGAA
1 CAAACACATCAAGAGTCAGCCTTTCAAGAA
1066117 CA
1 CA
1066119 GACTGGCTAA
Statistics
Matches: 42, Mismatches: 16, Indels: 10
0.62 0.24 0.15
Matches are distributed among these distances:
29 1 0.02
30 21 0.50
31 19 0.45
32 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (30 bp):
CAAACACATCAAGAGTCAGCCTTTCAAGAA
Found at i:1066121 original size:61 final size:61
Alignment explanation
Indices: 1066026--1066147 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
1066016 GAGCCTACAT
1066026 CAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTACAGGAGTTGATGAA
1 CAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTACAGGAGTTGATGAA
1066087 CAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTACAGGAGTTGATGAA
1 CAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTACAGGAGTTGATGAA
1066148 AAGTGGGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (61 bp):
CAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTACAGGAGTTGATGAA
Found at i:1069022 original size:16 final size:15
Alignment explanation
Indices: 1068998--1069069 Score: 74
Period size: 15 Copynumber: 4.7 Consensus size: 15
1068988 CAAAAAGGTA
1068998 AAACAAAAAAGAAAAG
1 AAACAAAAAA-AAAAG
*
1069014 AAGCAAAAAAAAAAG
1 AAACAAAAAAAAAAG
1069029 AAACAAAAAAACAAA-
1 AAACAAAAAAA-AAAG
*
1069044 AATCAAAAAGAAAAAG
1 AAACAAAAA-AAAAAG
**
1069060 GGACAAAAAA
1 AAACAAAAAA
1069070 GCACATGCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
15 27 0.57
16 20 0.43
ACGTcount: A:0.79, C:0.08, G:0.11, T:0.01
Consensus pattern (15 bp):
AAACAAAAAAAAAAG
Found at i:1069033 original size:31 final size:32
Alignment explanation
Indices: 1068998--1069070 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
1068988 CAAAAAGGTA
1068998 AAACAAAAAAGA-AAAGAAGCAAAAA-AAAAAG
1 AAACAAAAAAGACAAA-AAGCAAAAAGAAAAAG
*
1069029 AAACAAAAAA-ACAAAAATCAAAAAGAAAAAG
1 AAACAAAAAAGACAAAAAGCAAAAAGAAAAAG
**
1069060 GGACAAAAAAG
1 AAACAAAAAAG
1069071 CACATGCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 9 0.25
31 27 0.75
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.01
Consensus pattern (32 bp):
AAACAAAAAAGACAAAAAGCAAAAAGAAAAAG
Found at i:1069701 original size:22 final size:22
Alignment explanation
Indices: 1069662--1069715 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1069652 GCTACCCCAT
*
1069662 CAAACCTTT-AGCATCAAATGC
1 CAAACCTTTGAACATCAAATGC
1069683 CAAACCTTTGAACATCAAATGC
1 CAAACCTTTGAACATCAAATGC
1069705 CAAACCTTTGA
1 CAAACCTTTGA
1069716 CCAAACACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 9 0.29
22 22 0.71
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAACATCAAATGC
Found at i:1070141 original size:18 final size:19
Alignment explanation
Indices: 1070114--1070150 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1070104 TCAACATCAA
1070114 ATATTAGGGCATT-TTTGG
1 ATATTAGGGCATTATTTGG
*
1070132 ATATTGGGGCATTATTTGG
1 ATATTAGGGCATTATTTGG
1070151 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.05, G:0.30, T:0.43
Consensus pattern (19 bp):
ATATTAGGGCATTATTTGG
Found at i:1070778 original size:106 final size:105
Alignment explanation
Indices: 1070617--1071150 Score: 752
Period size: 106 Copynumber: 5.0 Consensus size: 105
1070607 GCTATCCGCG
* * * * * *
1070617 ATTTCAACTCCAC-GACGAAGGATATCATGCCACTCGAGACAACACAAGTTCAACTTCACAACAA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
1070681 AGGGACGGCTGGTTGTCAACAAACAACTTCCTAAATTCAGAGCCA
62 AGGGAC-GCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
1070726 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAATTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1070791 ATCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCTA
66 A-CGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
1070832 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1070897 ACCGCTGGTTTTCAATAAACAACTTCCCAATTTCAGAGCCA
66 A-CGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
1070938 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1071003 ACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
66 A-CGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
1071044 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC-ACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1071108 ACGCTGG-TGTCCAA-ATAAAAACTTCCCAATTTCAGAGCCA
66 ACGCTGGTTGT-CAACA-AACAACTTCCCAATTTCAGAGCCA
1071148 ATT
1 ATT
1071151 AAACGCAAGT
Statistics
Matches: 395, Mismatches: 26, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
103 4 0.01
104 34 0.09
105 17 0.04
106 314 0.79
107 3 0.01
109 22 0.06
110 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
Found at i:1071177 original size:72 final size:72
Alignment explanation
Indices: 1071081--1071223 Score: 211
Period size: 73 Copynumber: 2.0 Consensus size: 72
1071071 GACTCCAGAC
1071081 AACGCAAGTTCACTTCACGACGAA-GGGACGCTGG-TGTCCAAATAAA-AACTTCCCAATTTCAG
1 AACGCAAGTTCACTTCACGACGAAGGGGACGCTGGTTGT-C-AATAAACAACTTCCCAATTTCAG
1071143 AGCCAATTA
64 AGCCAATTA
* *
1071152 AACGCAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
1 AACGCAAGTTC-ACTTCACGACGAAGGGGACGCTGGTTGTCAATAAACAACTTCCCAATTTCAGA
*
1071217 GTCAATT
65 GCCAATT
1071224 TCAACTTTAC
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
71 11 0.17
72 19 0.29
73 32 0.49
74 3 0.05
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (72 bp):
AACGCAAGTTCACTTCACGACGAAGGGGACGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
CCAATTA
Found at i:1074459 original size:13 final size:13
Alignment explanation
Indices: 1074441--1074469 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1074431 CCTGCATATA
1074441 AATTAATAATAAT
1 AATTAATAATAAT
1074454 AATTAATAATAAT
1 AATTAATAATAAT
1074467 AAT
1 AAT
1074470 AAAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:1074928 original size:111 final size:111
Alignment explanation
Indices: 1074733--1075266 Score: 772
Period size: 111 Copynumber: 4.8 Consensus size: 111
1074723 GGGAAGATTA
* * * * * *
1074733 AATCAGGGTAGACTTGTTCAGCTGTCACTCAAGGAATATCAAATCATGAAAGAGATGGATCTGTT
1 AATCAGGGTAGACTTGTTCCGCTTTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATTTGTT
* * *
1074798 CCGCTTCCTCTGAGGGAATATTAGATCTGGTAAAGTTGATTCATTG
66 CCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTAATTG
*
1074844 AATCAGGGTAGACTTGTTCCGCTTTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATATGTT
1 AATCAGGGTAGACTTGTTCCGCTTTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATTTGTT
** * * *
1074909 CCGCTTATTCTGAGTGAATAGCAGATATGGGAAAGTTGATTAATTG
66 CCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTAATTG
*
1074955 AATCAGGGTAGACTTGTTCCG-TTGTCACTCAGAGAATATCAAATCTTGAAAGA-AAGGGATTTG
1 AATCAGGGTAGACTTGTTCCGCTT-TCACTCAGGGAATATCAAATCTTGAAAGAGAA-GGATTTG
* *
1075018 TTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAATTTGATTCATTG
64 TTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTAATTG
* *
1075066 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTT
1 AATCAGGGTAGACTTGTTCCGCTTTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATTTGTT
*
1075131 CTGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTAATTG
66 CCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTAATTG
*
1075177 AATCAGGGTAGACTTGTTCCG-TTGTCACTCAGGGAATATCAAATCTTGAAAG-GGA-GATTTGT
1 AATCAGGGTAGACTTGTTCCGCTT-TCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATTTGT
* * *
1075239 TTCACTTCTTCTGAAGGGAATATCAGAT
65 TCCGCTTCCTCTG-AGGGAATATCAGAT
1075267 AGATGGATTT
Statistics
Matches: 381, Mismatches: 36, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
109 16 0.04
110 20 0.05
111 343 0.90
112 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (111 bp):
AATCAGGGTAGACTTGTTCCGCTTTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATTTGTT
CCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTAATTG
Found at i:1075411 original size:79 final size:79
Alignment explanation
Indices: 1075267--1075434 Score: 205
Period size: 79 Copynumber: 2.1 Consensus size: 79
1075257 AATATCAGAT
* * * *** *
1075267 AGATGGATTTGCTTCACTATTCTTCTGTGAAGGCTTAAAATGGCCTGGAGGACTTAATCGACATG
1 AGATGGATTTACTTCACTATACTTCGGTGAAGGCTTAAAATGGCCCAAAGGACTTAAGCGACATG
* *
1075332 CTCGGAAGGCTTAC
66 CTCGAAAGACTTAC
* *
1075346 TGATGGATTTACTTCACTATACTTCGGTGAAGGCTTAAGATGGCCCAAAGGA-TATAAGC-ATCA
1 AGATGGATTTACTTCACTATACTTCGGTGAAGGCTTAAAATGGCCCAAAGGACT-TAAGCGA-CA
1075409 TGCTCGAAAGACTTAC
64 TGCTCGAAAGACTTAC
1075425 AGATGGATTT
1 AGATGGATTT
1075435 GATCATCATG
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
78 2 0.03
79 73 0.97
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (79 bp):
AGATGGATTTACTTCACTATACTTCGGTGAAGGCTTAAAATGGCCCAAAGGACTTAAGCGACATG
CTCGAAAGACTTAC
Found at i:1075445 original size:34 final size:34
Alignment explanation
Indices: 1075404--1075497 Score: 161
Period size: 34 Copynumber: 2.8 Consensus size: 34
1075394 AGGATATAAG
* *
1075404 CATCATGCTCGAAAGACTTACAGATGGATTTGAT
1 CATCATGCTCGGAAGACTTACTGATGGATTTGAT
1075438 CATCATGCTCGGAAGACTTACTGATGGATTTGAT
1 CATCATGCTCGGAAGACTTACTGATGGATTTGAT
*
1075472 CATCATGCTTGGAAGACTTACTGATG
1 CATCATGCTCGGAAGACTTACTGATG
1075498 ACCCGAAGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (34 bp):
CATCATGCTCGGAAGACTTACTGATGGATTTGAT
Found at i:1084401 original size:3 final size:3
Alignment explanation
Indices: 1084393--1084433 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
1084383 GTATATAAAT
1084393 TAA TAA TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1084434 TTAAAAGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1084532 original size:16 final size:16
Alignment explanation
Indices: 1084513--1084543 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1084503 TTTAAATATG
*
1084513 TAAAATTATAAAATTT
1 TAAAAATATAAAATTT
1084529 TAAAAATATAAAATT
1 TAAAAATATAAAATT
1084544 AAATCATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAAATATAAAATTT
Found at i:1089090 original size:26 final size:26
Alignment explanation
Indices: 1089048--1089097 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1089038 AAAGATATAA
* *
1089048 AAAAATAAAAATAAATAATATAATTT
1 AAAAAGAAAAATAAATAAAATAATTT
1089074 AAAAAGAAAGAAT-AATAAAATAAT
1 AAAAAGAAA-AATAAATAAAATAAT
1089098 AATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (26 bp):
AAAAAGAAAAATAAATAAAATAATTT
Found at i:1089131 original size:15 final size:15
Alignment explanation
Indices: 1089084--1089135 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1089074 AAAAAGAAAG
1089084 AATAATAAAATAAT-
1 AATAATAAAATAATA
**
1089098 AATAAATAAAA-AGGGA
1 AAT-AATAAAATA-ATA
1089114 AATAATAAAATAATA
1 AATAATAAAATAATA
1089129 AATAATA
1 AATAATA
1089136 GTAGTAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AATAATAAAATAATA
Found at i:1089196 original size:18 final size:18
Alignment explanation
Indices: 1089175--1089217 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1089165 GTTATTTTTA
* *
1089175 AAATAAAAGATAAGAGTT
1 AAATAAAAGAAAAGAATT
*
1089193 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1089211 AAATAAA
1 AAATAAA
1089218 TAATTTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1089859 original size:27 final size:28
Alignment explanation
Indices: 1089804--1089859 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1089794 GAGTATTTAG
* **
1089804 AGCCTTCAAATTCCTAAAAATAACCTAA
1 AGCCGTCAAATTCCTAAAAATAAAATAA
1089832 AGCCGTCAAATTCCT-AAAATAAAATAA
1 AGCCGTCAAATTCCTAAAAATAAAATAA
1089859 A
1 A
1089860 ATAACCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.23
Consensus pattern (28 bp):
AGCCGTCAAATTCCTAAAAATAAAATAA
Found at i:1091135 original size:17 final size:18
Alignment explanation
Indices: 1091108--1091154 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
1091098 TTTTTAAAGA
*
1091108 AAATATATAATATTTTAC
1 AAATATATAATATTATAC
*
1091126 AACT-TATAATATTATAC
1 AAATATATAATATTATAC
1091143 AAATATATAATA
1 AAATATATAATA
1091155 AGGACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:1101922 original size:21 final size:21
Alignment explanation
Indices: 1101863--1101922 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1101853 ATGAAGTTGA
1101863 AAAG-ATATATAAAATAAAAAC
1 AAAGAATA-ATAAAATAAAAAC
* * ** *
1101884 AAATAATTATAATTTAAAAAG
1 AAAGAATAATAAAATAAAAAC
1101905 AAAGAATAATAAAATAAA
1 AAAGAATAATAAAATAAA
1101923 TAATAATAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAGAATAATAAAATAAAAAC
Found at i:1101939 original size:35 final size:36
Alignment explanation
Indices: 1101879--1101965 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 36
1101869 ATATAAAATA
* * *
1101879 AAAACAAATAATTATAATTTAAAAA-GAAAGAATAAT
1 AAAATAAATAATAATAATATAAAAAGGAAA-AATAAT
*
1101915 AAAATAAATAATAATAA-ATAAAAAGGGAAAATAAT
1 AAAATAAATAATAATAATATAAAAAGGAAAAATAAT
1101950 AAAAT-AATAAATAATA
1 AAAATAAAT-AATAATA
1101966 GTAGTAAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
34 3 0.07
35 24 0.53
36 18 0.40
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (36 bp):
AAAATAAATAATAATAATATAAAAAGGAAAAATAAT
Found at i:1102039 original size:18 final size:18
Alignment explanation
Indices: 1102002--1102039 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1101992 AAAGTTTTTT
*
1102002 TTAAATAAAAGATAAGAA
1 TTAAATAAAAGAAAAGAA
*
1102020 TTAAATAAAAGAAAATAA
1 TTAAATAAAAGAAAAGAA
1102038 TT
1 TT
1102040 TAAAGAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (18 bp):
TTAAATAAAAGAAAAGAA
Done.