Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008560.1 Hibiscus syriacus cultivar Beakdansim tig00111467_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: 753118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:581011 original size:27 final size:28
Alignment explanation
Indices: 580964--581017 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
580954 GATACTATAA
* *
580964 GTCATTTTACACTTTATGGGC-ATTTTG
1 GTCATTTTACACTTCAAGGGCAATTTTG
580991 GTCATTTTACACTTCAAGGGCAATTTT
1 GTCATTTTACACTTCAAGGGCAATTTT
581018 ATAATTGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
GTCATTTTACACTTCAAGGGCAATTTTG
Found at i:584084 original size:66 final size:66
Alignment explanation
Indices: 583978--584101 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
583968 TAGGTCCATA
* * *
583978 AGGAATTACCAGTCGGTGATGAACTTATACAATGAATTACCAACAGCGACTGAACCTGACATAGA
1 AGGAATTACCAGACGATGATGAACCTATACAATGAATTACCAACAGCGACTGAACCTGACATAGA
584043 T
66 T
* *
584044 AGGAATTACCAGACGATGTTGAACCTATACAA-GAACTTACCAGCAGCGACTGAACCTG
1 AGGAATTACCAGACGATGATGAACCTATACAATGAA-TTACCAACAGCGACTGAACCTG
584102 CCTAAGTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
65 3 0.06
66 49 0.94
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (66 bp):
AGGAATTACCAGACGATGATGAACCTATACAATGAATTACCAACAGCGACTGAACCTGACATAGA
T
Found at i:586102 original size:2 final size:2
Alignment explanation
Indices: 586095--586129 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
586085 AAGTACTGCC
586095 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
586130 GGGTTAAAAA
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:587293 original size:60 final size:60
Alignment explanation
Indices: 587184--587307 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 60
587174 TAAAAAGTTC
* * * ** * *
587184 AATTGGAATGTTTAAAACTTTGGAGATTAATTTAGAATGAGAATTATAGTTTAG-GGATGA
1 AATTGGAATGATCAAAACTTTGGAGATCAAAGTAAAATGAGAATAATAG-TTAGAGGATGA
* *
587244 AATTGGAATGATCAAAAGTTTGGAGATCAAAGTAAAAT-ATGAATAATAGTTCGAGGATGA
1 AATTGGAATGATCAAAACTTTGGAGATCAAAGTAAAATGA-GAATAATAGTTAGAGGATGA
587304 AATT
1 AATT
587308 AAAATATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 4 0.08
60 49 0.92
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (60 bp):
AATTGGAATGATCAAAACTTTGGAGATCAAAGTAAAATGAGAATAATAGTTAGAGGATGA
Found at i:587828 original size:48 final size:48
Alignment explanation
Indices: 587666--587828 Score: 147
Period size: 46 Copynumber: 3.5 Consensus size: 48
587656 TAAAACACCT
* * * *
587666 TAACATACCACCCTTACTGTCGCGCATCAAT-T-TATCATCATGTCCC
1 TAACATACCATCCTTACCGTCGCACACCAATATATATCATCATGTCCC
* * * *
587712 TATCACACCATCCTTACC-TC-CACACACAA-ATATATTATAATGTCCC
1 TAACATACCATCCTTACCGTCGCACAC-CAATATATATCATCATGTCCC
* * ** * *
587758 TATCATATCATCCTTATTGTCGCACACCAATATATATCATCGTGTCTC
1 TAACATACCATCCTTACCGTCGCACACCAATATATATCATCATGTCCC
*
587806 TAACATACGATCCTTACCGTCGC
1 TAACATACCATCCTTACCGTCGC
587829 TATCAAGTAG
Statistics
Matches: 90, Mismatches: 21, Indels: 10
0.74 0.17 0.08
Matches are distributed among these distances:
44 3 0.03
45 6 0.07
46 40 0.44
47 5 0.06
48 36 0.40
ACGTcount: A:0.29, C:0.33, G:0.07, T:0.31
Consensus pattern (48 bp):
TAACATACCATCCTTACCGTCGCACACCAATATATATCATCATGTCCC
Found at i:588336 original size:2 final size:2
Alignment explanation
Indices: 588331--588365 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
588321 TTGTGGTGTG
588331 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
588366 CTCGGTGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:588354 original size:15 final size:15
Alignment explanation
Indices: 588334--588363 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
588324 TGGTGTGTAT
588334 ATATATATATATATA
1 ATATATATATATATA
588349 ATATATATATATATA
1 ATATATATATATATA
588364 TACTCGGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:588354 original size:17 final size:17
Alignment explanation
Indices: 588332--588365 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
588322 TGTGGTGTGT
588332 ATATATATATATATATA
1 ATATATATATATATATA
588349 ATATATATATATATATA
1 ATATATATATATATATA
588366 CTCGGTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:592829 original size:65 final size:65
Alignment explanation
Indices: 592756--592898 Score: 182
Period size: 65 Copynumber: 2.2 Consensus size: 65
592746 AATTAAATTG
*
592756 AACATCGAATGCATTCCATGCATCAATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATT
1 AACATCGAATGCATTCCATGCATCAATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TT
592819 AA
64 AA
** * * * * *
592821 AACATCGAATGCATTTTATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTTGA
1 AACATCGAATGCATTCCATGCATCAATGCACCAACCATGCACCGATGCACTCAGGATATTTTTAA
592886 AACATCGAATGCA
1 AACATCGAATGCA
592899 CTTGATGAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
65 63 0.93
66 5 0.07
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTCCATGCATCAATGCACCAACCATGCACCGATGCACTCAGGATATTTTTAA
Found at i:592911 original size:65 final size:63
Alignment explanation
Indices: 592715--592912 Score: 172
Period size: 65 Copynumber: 3.0 Consensus size: 63
592705 TTTTCAGAGT
* *
592715 GATGCACCAATCCATGCATCGATGCAC-CAT-GAATTAAATTG-AACATCGAATGCATTCCATGC
1 GATGCACCAA-CCATGCATCGATGCACTC-TGGTATT--TTTGAAACATCGAATGCATT-CATGC
592777 ATC
61 ATC
* * ** * *
592780 AATGCA-CATACCATGCACCGATGCACTGAGG-ATTTTATTAAAACATCGAATGCATTTTATGCA
1 GATGCACCA-ACCATGCATCGATGCACTCTGGTA-TTT-TTGAAACATCGAATGCA-TTCATGCA
592843 TC
62 TC
* *
592845 GATGCACCAACCATGCATCGATGCACTCTGGCTATTTTTGAAACATCGAATGCACTTGATGAATC
1 GATGCACCAACCATGCATCGATGCACTCTGG-TATTTTTGAAACATCGAATGCA-TTCATGCATC
592910 GAT
1 GAT
592913 TCACTCTTAG
Statistics
Matches: 108, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
64 20 0.19
65 80 0.74
66 7 0.06
67 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (63 bp):
GATGCACCAACCATGCATCGATGCACTCTGGTATTTTTGAAACATCGAATGCATTCATGCATC
Found at i:598158 original size:24 final size:24
Alignment explanation
Indices: 598131--598211 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
598121 TTTGTGCTTA
598131 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
598155 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
598177 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
598199 GTGCATCGATGCA
1 GTGCATCGATGCA
598212 CATGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:598201 original size:44 final size:44
Alignment explanation
Indices: 598132--598234 Score: 138
Period size: 44 Copynumber: 2.3 Consensus size: 44
598122 TTGTGCTTAG
* * *
598132 TGCATCGATGCATCCCTTTGAATGTGCATCGATTCATCATGTTGA
1 TGCATCGATGCATCCCTTTGAATGTGCATCGATGCA-CATGGTCA
*
598177 TGCACCGATGCA-CGCC-TTGAATGTGCATCGATGCACATGGTCA
1 TGCATCGATGCATC-CCTTTGAATGTGCATCGATGCACATGGTCA
598220 TGCATCGATGCATCC
1 TGCATCGATGCATCC
598235 GTCGGGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 18 0.35
44 20 0.39
45 13 0.25
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (44 bp):
TGCATCGATGCATCCCTTTGAATGTGCATCGATGCACATGGTCA
Found at i:600331 original size:2 final size:2
Alignment explanation
Indices: 600324--600366 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
600314 CAACTTAAGC
600324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
600366 T
1 T
600367 TAATCAATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:600982 original size:84 final size:83
Alignment explanation
Indices: 600893--601052 Score: 225
Period size: 84 Copynumber: 1.9 Consensus size: 83
600883 GAATGCATTT
*
600893 CATGCATCGATGCA-CATACCATGCACCGATGCACTAAGG-ATTTTATAAAAACATCGAATGCAT
1 CATGCATCGATGCATCAT-CCATGCACCGATGCACTAAGGCATTTT-T-AAAACATCGAATGCAC
600956 TTGATGCATCGATGCACCAGC
63 TTGATGCATCGATGCACCAGC
* ** *
600977 CATGCATCGATGCATCATCCATGCATCGATGCACTCTGGCTATTTTTGAAACATCGAATGCACTT
1 CATGCATCGATGCATCATCCATGCACCGATGCACTAAGGC-ATTTTTAAAACATCGAATGCACTT
601042 GATGCATCGAT
65 GATGCATCGAT
601053 ACACTCTTAG
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
84 59 0.87
85 4 0.06
86 5 0.07
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (83 bp):
CATGCATCGATGCATCATCCATGCACCGATGCACTAAGGCATTTTTAAAACATCGAATGCACTTG
ATGCATCGATGCACCAGC
Found at i:600983 original size:19 final size:19
Alignment explanation
Indices: 600959--601010 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
600949 AATGCATTTG
600959 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
* *
600978 ATGCATCGATGCATCATCC
1 ATGCATCGATGCACCAGCC
600997 ATGCATCGATGCAC
1 ATGCATCGATGCAC
601011 TCTGGCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACCAGCC
Found at i:603670 original size:62 final size:62
Alignment explanation
Indices: 603179--603672 Score: 652
Period size: 62 Copynumber: 8.0 Consensus size: 62
603169 TCTTGTGTCC
* * * *
603179 TAGAATCAATCCTTGACTTTCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACT-CCCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* *
603240 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * * * * *
603302 TAGAGTCAATCCTTGA-TTTCTCGTGAAGAGAAGTCAAAATTTATTATTTGTGACTCCCTAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * * * * * ** *
603363 TAGAGTCAATCTTTAACTTCCTCTTAAAGAGAAGTCAACCTTTATTATTTTTGACTCTTCAA
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* *
603425 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCTCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * * * *
603487 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTTAATATTTGTTATTTTTGACTCCTCAA
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * *
603549 TAGAGTCAATCTTTGACTCCCTCGTGAAGAAAAGTCAACATTTGTTATTCCTGACTCCCCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * *
603611 TAGAGTCAAAT-TTTAACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCCCAG
1 TAGAGTC-AATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
603673 AGGAATTAAT
Statistics
Matches: 382, Mismatches: 48, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
61 107 0.28
62 272 0.71
63 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (62 bp):
TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
Found at i:603911 original size:36 final size:36
Alignment explanation
Indices: 603852--604563 Score: 1019
Period size: 36 Copynumber: 19.8 Consensus size: 36
603842 TATTTCAAAT
* * * *
603852 TTAGCCTCAACGGAATAGCAGTGAAGCAAAGTAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
*
603888 TTAGCCTCCACAGAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
603924 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* *
603960 GTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATG
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* *
603996 TTAGCCTCCACGTAAGAGTGGTGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* *
604032 TTAGCTTCCACAGAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* *
604068 TTAGCCTCCACAGCAGAGTAGTGAAGCAAA-TCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGT-CATC
*
604104 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATG
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
*
604140 TTAGCCTCCACGTAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
*
604176 TTAGCCTCCACAGAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
*
604212 TTAGCCTCCACAGCAA-AGTAGTGAAGCAAA-TCCATC
1 TTAGCCTCCAC-GGAAGAGTAGTGAAGCAAAGT-CATC
604248 TTAGCCTCCACGGAAGAGTAGTGAAGCAAA-TCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGT-CATC
*
604284 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
604320 TTAGCCTTCC-CGGAAGAGTAGTGAAG-AAAGGTCATC
1 TTAGCC-TCCACGGAAGAGTAGTGAAGCAAA-GTCATC
*
604356 TTAGCCTCCACGAAAGAGTAGTGAAGCAAAG-CAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTC-ATC
*
604392 TTAGCCTCAACGGAAGAGTA-TGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
604427 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* * *
604463 TTAGCCTCCACAGAAGAGTACTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* * *
604499 TTAGCCTCCAC-GAAAAATAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* * **
604534 ATAGCCTTCACAAAAAGAGTAGTGAAGCAA
1 TTAGCCTCCAC-GGAAGAGTAGTGAAGCAA
604564 GAACAGATCA
Statistics
Matches: 616, Mismatches: 45, Indels: 29
0.89 0.07 0.04
Matches are distributed among these distances:
35 74 0.12
36 519 0.84
37 23 0.04
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.19
Consensus pattern (36 bp):
TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
Found at i:604747 original size:3 final size:3
Alignment explanation
Indices: 604729--604768 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
604719 TTTTGTCCCG
*
604729 TAT TTT TAT ATAT TAT TAT TAT TAT ATAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT TA
604769 CAAATAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:604753 original size:16 final size:16
Alignment explanation
Indices: 604729--604768 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
604719 TTTTGTCCCG
*
604729 TATTTTTATATATTAT
1 TATTATTATATATTAT
604745 TATTATTATATATTAT
1 TATTATTATATATTAT
604761 TATTATTA
1 TATTATTA
604769 CAAATAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTATATATTAT
Found at i:609776 original size:18 final size:19
Alignment explanation
Indices: 609755--609801 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
609745 AAATAAATCC
*
609755 AATAATAAAA-CAAAATAA
1 AATAATAAAATCAAAAGAA
*
609773 AATAATAAAATCAAAGGAA
1 AATAATAAAATCAAAAGAA
609792 AA-AATAAAAT
1 AATAATAAAAT
609802 AATAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (19 bp):
AATAATAAAATCAAAAGAA
Found at i:619812 original size:29 final size:30
Alignment explanation
Indices: 619775--619832 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
619765 GATTTAATGA
* * *
619775 GTGATCAAATTATAAA-TTTGTAAAGTTTG
1 GTGACCAAAATATAAACTTTGAAAAGTTTG
619804 GTGACCAAAATATAAACTTTGAAAAGTTT
1 GTGACCAAAATATAAACTTTGAAAAGTTT
619833 AGGGACTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (30 bp):
GTGACCAAAATATAAACTTTGAAAAGTTTG
Found at i:622844 original size:40 final size:40
Alignment explanation
Indices: 622800--622961 Score: 297
Period size: 40 Copynumber: 4.0 Consensus size: 40
622790 ACCGTAGTGC
622800 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
622840 TACACATAAGGCCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
622880 TACACATAAGGTCGTACCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
622920 TACACATAAGGTCGTGTCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
622960 TA
1 TA
622962 TAAACCTGCA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:629178 original size:40 final size:40
Alignment explanation
Indices: 629134--629215 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
629124 ACCGTAGTGC
629134 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
629174 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
629214 TA
1 TA
629216 TAAACCTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:631591 original size:6 final size:6
Alignment explanation
Indices: 631580--631638 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
631570 AATGTATTAC
* * * *
631580 ATGATA ATGATA TTGATG TTGATA ATGATA ATGATA GA-GATC ATGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA -ATGATA ATGATA
*
631628 ATGATA TTGAT
1 ATGATA ATGAT
631639 GTTGATTATG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 1 0.02
6 42 0.95
7 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (6 bp):
ATGATA
Found at i:631598 original size:24 final size:24
Alignment explanation
Indices: 631571--631640 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
631561 GATGAGTGAA
631571 ATGTATTACATGATAATGATATTG
1 ATGTATTACATGATAATGATATTG
631595 ATGT-TGATA-ATGATAATGATA--G
1 ATGTAT--TACATGATAATGATATTG
631617 A-G-A-T-CATGATAATGATATTG
1 ATGTATTACATGATAATGATATTG
631637 ATGT
1 ATGT
631641 TGATTATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 18
0.68 0.00 0.32
Matches are distributed among these distances:
18 13 0.34
20 2 0.05
21 2 0.05
22 2 0.05
23 1 0.03
24 16 0.42
25 2 0.05
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.39
Consensus pattern (24 bp):
ATGTATTACATGATAATGATATTG
Found at i:631602 original size:18 final size:18
Alignment explanation
Indices: 631581--631650 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 18
631571 ATGTATTACA
631581 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
*
631599 TGATAATGATAATGATAGAGAT
1 TGATAATGATATTGAT---G-T
631621 CATGATAATGATATTGATGT
1 --TGATAATGATATTGATGT
*
631641 TGATTATGAT
1 TGATAATGAT
631651 GACATATGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 24 0.56
20 1 0.02
21 2 0.05
22 1 0.02
24 15 0.35
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.40
Consensus pattern (18 bp):
TGATAATGATATTGATGT
Found at i:631649 original size:24 final size:24
Alignment explanation
Indices: 631580--631650 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
631570 AATGTATTAC
631580 ATGATAATGATATTGATGTTGATA
1 ATGATAATGATATTGATGTTGATA
*
631604 ATGATAATGATA--GA----GATC
1 ATGATAATGATATTGATGTTGATA
*
631622 ATGATAATGATATTGATGTTGATT
1 ATGATAATGATATTGATGTTGATA
631646 ATGAT
1 ATGAT
631651 GACATATGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
18 15 0.38
20 2 0.05
22 2 0.05
24 20 0.51
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.39
Consensus pattern (24 bp):
ATGATAATGATATTGATGTTGATA
Found at i:636271 original size:774 final size:774
Alignment explanation
Indices: 634767--636318 Score: 2959
Period size: 772 Copynumber: 2.0 Consensus size: 774
634757 ACTGAGTTGA
634767 TAAGGAAAGATGTATCATTTGTTTGGACTCTTGAATGTCAAGAAAGTTTGAAACGTTGAAGAAAT
1 TAAGGAAAGATGTATCATTTGTTTGGACTCTTGAATGTCAAGAAAGTTTGAAACGTTGAAGAAAT
634832 TTTGACAGAAGCTCCAGTATTGGTTTAACCTGAATCTGGCAAGAACTATATGGTTTATAGCGACG
66 TTTGACAGAAGCTCCAGTATTGGTTTAACCTGAATCTGGCAAGAACTATATGGTTTATAGCGACG
634897 CGTCTCATAAGGATTTGGGATGTGTGTTGATGTAAGAGGGCAAGGTGGTGGCTTATTCTTTGAGA
131 CGTCTCATAAGGATTTGGGATGTGTGTTGATGTAAGAGGGCAAGGTGGTGGCTTATTCTTTGAGA
634962 CAATTGAAACCTCATGAAAAGAAATATCCAATATACGATCTAGAGTTGGCTGCAGTAGTGTTTGC
196 CAATTGAAACCTCATGAAAAGAAATATCCAATATACGATCTAGAGTTGGCTGCAGTAGTGTTTGC
635027 CTTGAAGATTTGGCGTCACTACTTATATGGTGAACGTTGCTATTTATATACCGATCATAAGAGCT
261 CTTGAAGATTTGGCGTCACTACTTATATGGTGAACGTTGCTATTTATATACCGATCATAAGAGCT
635092 TGAAGTATTTGATGAATCAGAAAGAGTTGAACTTAAGACAAAGGATATGGGTAAAATTTCTAAAA
326 TGAAG-ATTTGATGAATCAGAAAGAGTTGAACTTAAGACAAAGGATATGGGTAAAATTTCTAAAA
*
635157 GACTATGATGTGATAATTGATTTCCACCCTGGAAAAACAAACGTGGTGGCTGATGCTTTAAGTCA
390 GACTATGATGTGATAATTGATTTCCACCCTGGAAAAACAAACGTGGTAGCTGATGCTTTAAGTCA
635222 AAAAAACATTTGCAGTTTTACGAGCTTTAGATGCAAAATTGTCATTGAAGGGAGATGGAGCTCTA
455 AAAAAACATTTGCAGTTTTACGAGCTTTAGATGCAAAATTGTCATTGAAGGGAGATGGAGCTCTA
635287 TATGCAGAATTAAAGATTAGGTCCATGTTTTTGGATCAAAACAAAGAGTTGCAGGGCAAAGATGA
520 TATGCAGAATTAAAGATTAGGTCCATGTTTTTGGATCAAAACAAAGAGTTGCAGGGCAAAGATGA
635352 AAAGTGTTTGAAGAAAATGGAGCAAGTAAATAGTAAAGAAAGTAAAGATTTTAAGGTTAAGCCAT
585 AAAGTGTTTGAAGAAAATGGAGCAAGTAAATAGTAAAGAAAGTAAAGATTTTAAGGTTAAGCCAT
*
635417 ATGGAAATTCGTATTGTAAAGGGAGACTTATGATTCCTGAGGATGAGGAATTGAAAATTATTTGT
650 ATGGAAATTCGTATTGTAAAGGGAGACTTATGATTCCTGAGGATGAGGAATTGAAAAGTATTTGT
*
635482 TAATGGAAGCCATTGTAGTCCGATGACTATG-CTAGGTGGGAACAAGACGTATGTAGATC
715 TAATGGAAGCCATTGTAGTCCGATGACTATGACTAGGTGGGAACAAGACGTATATAGATC
635541 TAAGGAAAGATGTATCATTTGTTTGGACTCTTGAATGTCAAG-AAGTTTTGAAACGTTGAAGAAA
1 TAAGGAAAGATGTATCATTTGTTTGGACTCTTGAATGTCAAGAAAG-TTTGAAACGTTGAAG-AA
635605 ATTTTGACAGAAGCTCCAGTATTGG-TTAACCTGAATCTGGCAAGAACTATATGGTTTATAGCGA
64 ATTTTGACAGAAGCTCCAGTATTGGTTTAACCTGAATCTGGCAAGAACTATATGGTTTATAGCGA
635669 CGCGTCTCATAAGGATTTGGGATGTGTGTTGATGTAAGAGGGCAAGGTGGTGGCTTATTCTTTGA
129 CGCGTCTCATAAGGATTTGGGATGTGTGTTGATGTAAGAGGGCAAGGTGGTGGCTTATTCTTTGA
*
635734 GACAATTGAAACCTCATGAAAAGAACTATCCAATATACGATCTAGAGTTGGCTGCAGTAGTGTTT
194 GACAATTGAAACCTCATGAAAAGAAATATCCAATATACGATCTAGAGTTGGCTGCAGTAGTGTTT
635799 GCCTTGAAGATTTGGCGTCACTACTTATATGGTGAACGTTGCTATTTATATACCGATCATAAGAG
259 GCCTTGAAGATTTGGCGTCACTACTTATATGGTGAACGTTGCTATTTATATACCGATCATAAGAG
*
635864 CTTGAAG-TTTGATGAATCAGAAATAGTTGAACTTAAGACAAAGGATATGGGTAAAATTTCTAAA
324 CTTGAAGATTTGATGAATCAGAAAGAGTTGAACTTAAGACAAAGGATATGGGTAAAATTTCTAAA
635928 AGACTATGATGTGATAATTGATTTCCACCCTGGAAAAACAAACGTGGTAGCTGATGCTTTAAGTC
389 AGACTATGATGTGATAATTGATTTCCACCCTGGAAAAACAAACGTGGTAGCTGATGCTTTAAGTC
635993 AAAAAAACATTTGCAGTTTTACGAGCTTTAGATGCAAAATTGTCATTGAAGGGAGATGGAGCTCT
454 AAAAAAACATTTGCAGTTTTACGAGCTTTAGATGCAAAATTGTCATTGAAGGGAGATGGAGCTCT
636058 ATATGCAGAATTAAAGATTAGGTCCATGTTTTTGGATCAAAACAAAGAGTTGCAGGGCAAAGATG
519 ATATGCAGAATTAAAGATTAGGTCCATGTTTTTGGATCAAAACAAAGAGTTGCAGGGCAAAGATG
636123 AAAAGTGTTTGAAGAAAATGGAGCAAGTAAATAGTAAAGAAAGTAAAGATTTTAAGGTTAAGCCA
584 AAAAGTGTTTGAAGAAAATGGAGCAAGTAAATAGTAAAGAAAGTAAAGATTTTAAGGTTAAGCCA
*
636188 TATGGAAATTCGTATTGTAAATGGAGACTTATGATTCCTGAGGATGAGGAATTGAAAAAGTATTT
649 TATGGAAATTCGTATTGTAAAGGGAGACTTATGATTCCTGAGGATGAGGAATTG-AAAAGTATTT
636253 GTTAATGGAAGCCCATTGTAGTCCGATGACTATGCATCTAGGTGGGAACAAGACGTATATAGATC
713 GTTAATGGAAG-CCATTGTAGTCCGATGACTATG-A-CTAGGTGGGAACAAGACGTATATAGATC
636318 T
1 T
636319 TAAGAGTCAG
Statistics
Matches: 765, Mismatches: 6, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
772 368 0.48
773 23 0.03
774 319 0.42
775 27 0.04
777 28 0.04
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (774 bp):
TAAGGAAAGATGTATCATTTGTTTGGACTCTTGAATGTCAAGAAAGTTTGAAACGTTGAAGAAAT
TTTGACAGAAGCTCCAGTATTGGTTTAACCTGAATCTGGCAAGAACTATATGGTTTATAGCGACG
CGTCTCATAAGGATTTGGGATGTGTGTTGATGTAAGAGGGCAAGGTGGTGGCTTATTCTTTGAGA
CAATTGAAACCTCATGAAAAGAAATATCCAATATACGATCTAGAGTTGGCTGCAGTAGTGTTTGC
CTTGAAGATTTGGCGTCACTACTTATATGGTGAACGTTGCTATTTATATACCGATCATAAGAGCT
TGAAGATTTGATGAATCAGAAAGAGTTGAACTTAAGACAAAGGATATGGGTAAAATTTCTAAAAG
ACTATGATGTGATAATTGATTTCCACCCTGGAAAAACAAACGTGGTAGCTGATGCTTTAAGTCAA
AAAAACATTTGCAGTTTTACGAGCTTTAGATGCAAAATTGTCATTGAAGGGAGATGGAGCTCTAT
ATGCAGAATTAAAGATTAGGTCCATGTTTTTGGATCAAAACAAAGAGTTGCAGGGCAAAGATGAA
AAGTGTTTGAAGAAAATGGAGCAAGTAAATAGTAAAGAAAGTAAAGATTTTAAGGTTAAGCCATA
TGGAAATTCGTATTGTAAAGGGAGACTTATGATTCCTGAGGATGAGGAATTGAAAAGTATTTGTT
AATGGAAGCCATTGTAGTCCGATGACTATGACTAGGTGGGAACAAGACGTATATAGATC
Found at i:638375 original size:11 final size:11
Alignment explanation
Indices: 638359--638385 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
638349 ATTGAGTGAG
638359 AAAATTATGGA
1 AAAATTATGGA
638370 AAAATTATGGA
1 AAAATTATGGA
638381 AAAAT
1 AAAAT
638386 CATATAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (11 bp):
AAAATTATGGA
Found at i:639415 original size:33 final size:33
Alignment explanation
Indices: 639372--639453 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
639362 GGGTTATATG
*
639372 ACAAGAATGTTATACAAGGATCTATGAGATCAT
1 ACAAGAATGTTATACAAGGATCTACGAGATCAT
* * *
639405 TCAAGAATGTTACACAATGATCTACGAGATCAT
1 ACAAGAATGTTATACAAGGATCTACGAGATCAT
639438 ACAAGAATG--ATACAAG
1 ACAAGAATGTTATACAAG
639454 TGATGTGAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 5 0.12
33 37 0.88
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (33 bp):
ACAAGAATGTTATACAAGGATCTACGAGATCAT
Found at i:639669 original size:21 final size:21
Alignment explanation
Indices: 639643--639684 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
639633 CTTAAGGAGT
639643 AGTCCTCCAGGACATACAAGA
1 AGTCCTCCAGGACATACAAGA
* *
639664 AGTCCTTCGGGACATACAAGA
1 AGTCCTCCAGGACATACAAGA
639685 GTATAGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (21 bp):
AGTCCTCCAGGACATACAAGA
Found at i:639757 original size:21 final size:21
Alignment explanation
Indices: 639696--639773 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
639686 TATAGAGTTC
*
639696 TATGTGGTCCTTTGGGATATA
1 TATGTGGTCCTTTGGGACATA
** *
639717 TATGTAATCCTTTGGAACATA
1 TATGTGGTCCTTTGGGACATA
* *
639738 TATGTGGTTCTTCGGGACATA
1 TATGTGGTCCTTTGGGACATA
*
639759 TATTTGGTCCTTTGG
1 TATGTGGTCCTTTGG
639774 AATACATATA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.42
Consensus pattern (21 bp):
TATGTGGTCCTTTGGGACATA
Found at i:639760 original size:42 final size:44
Alignment explanation
Indices: 639696--639785 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 44
639686 TATAGAGTTC
* *
639696 TATGTGGTCCTTTGGGATATATATGTAATCCTTTGG-A-ACATA
1 TATGTGGTCCTTCGGGACATATATGTAATCCTTTGGAATACATA
* * **
639738 TATGTGGTTCTTCGGGACATATATTTGGTCCTTTGGAATACATA
1 TATGTGGTCCTTCGGGACATATATGTAATCCTTTGGAATACATA
639782 TATG
1 TATG
639786 ATTTTTAAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
42 30 0.75
43 1 0.03
44 9 0.22
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (44 bp):
TATGTGGTCCTTCGGGACATATATGTAATCCTTTGGAATACATA
Found at i:639812 original size:156 final size:156
Alignment explanation
Indices: 639540--639831 Score: 415
Period size: 156 Copynumber: 1.9 Consensus size: 156
639530 TCAAGGGTTT
639540 TATGTGGTCCTTCGGGATATATATGTAATCCTTTGGAACATACATGCGATTCTTCAGGACACATA
1 TATGTGGTCCTTCGGGATATATATGTAATCCTTTGGAACATACATGCGATTCTTCAGGACACATA
* * * *
639605 TTTGGTTATTTGGAATATATATGTGATTCTTAAGGAGTAGTCCTCCAGGACATACAAGA-AGTCC
66 TTTGGTCATTTGGAATACATATATGATTCTTAAGGAGTAGACCTCCAGGACATACAAGAGA-TCC
639669 TTCGGGACATACAAGAGTATAGAGTTC
130 TTCGGGACATACAAGAGTATAGAGTTC
* * * * * *
639696 TATGTGGTCCTTTGGGATATATATGTAATCCTTTGGAACATATATGTGGTTCTTCGGGACATATA
1 TATGTGGTCCTTCGGGATATATATGTAATCCTTTGGAACATACATGCGATTCTTCAGGACACATA
* * * * * * *
639761 TTTGGTCCTTTGGAATACATATATGATTTTTAAGGAGTGGACCTTCGGGACATATACGAGATCCT
66 TTTGGTCATTTGGAATACATATATGATTCTTAAGGAGTAGACCTCCAGGACATACAAGAGATCCT
639826 TCGGGA
131 TCGGGA
639832 TAATTTTACA
Statistics
Matches: 118, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
156 117 0.99
157 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (156 bp):
TATGTGGTCCTTCGGGATATATATGTAATCCTTTGGAACATACATGCGATTCTTCAGGACACATA
TTTGGTCATTTGGAATACATATATGATTCTTAAGGAGTAGACCTCCAGGACATACAAGAGATCCT
TCGGGACATACAAGAGTATAGAGTTC
Found at i:642216 original size:19 final size:15
Alignment explanation
Indices: 642179--642237 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
642169 TTTAATAAGG
642179 TTATTTATTATAAAA
1 TTATTTATTATAAAA
642194 TTATTTATTATAAAA
1 TTATTTATTATAAAA
* *
642209 TAACTTATTATAAAA
1 TTATTTATTATAAAA
*
642224 TAATTTATTATAAA
1 TTATTTATTATAAA
642238 TATGGATTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATTTATTATAAAA
Found at i:642302 original size:32 final size:31
Alignment explanation
Indices: 642261--642412 Score: 142
Period size: 32 Copynumber: 5.4 Consensus size: 31
642251 ATTTAAAATA
642261 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAG-ATGGATTG
642293 ATTTATTTT-AA-AA--TA-T-GA---ATTG
1 ATTTATTTTAAATAATTTATTAGATGGATTG
*
642315 ATTTATTTTAAATAATTTATTAGCATGGATTA
1 ATTTATTTTAAATAATTTATTAG-ATGGATTG
642347 ATTTATTTT-AA-AA--TA-T-GA---ATTG
1 ATTTATTTTAAATAATTTATTAGATGGATTG
642369 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAG-ATGGATTG
642401 ATTTATTTTAAA
1 ATTTATTTTAAA
642413 ATATGAATTG
Statistics
Matches: 98, Mismatches: 2, Indels: 40
0.70 0.01 0.29
Matches are distributed among these distances:
22 25 0.26
23 4 0.04
24 4 0.04
25 2 0.02
26 6 0.06
27 4 0.04
28 6 0.06
29 2 0.02
30 4 0.04
31 4 0.04
32 37 0.38
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.52
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTAGATGGATTG
Found at i:642309 original size:22 final size:22
Alignment explanation
Indices: 642284--642326 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
642274 AATTTATTAG
*
642284 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
642306 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
642327 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:642327 original size:54 final size:54
Alignment explanation
Indices: 642261--642853 Score: 616
Period size: 54 Copynumber: 11.1 Consensus size: 54
642251 ATTTAAAATA
*
642261 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * *
642315 ATTTATTTTAAATAATTTATTAGCATGGATTAATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
642369 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * **
642423 AGTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * *
642472 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAAATATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
642525 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
642579 ATTTA---T-GAT--TGTAGTT-GTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
**
642627 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAACA-ATTTATT-
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA-ATATGGATTG
* ** * * * * * ***
642680 AGTATAGATTGATTTATTT-TAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 A-TTTATTTTAAATAATTTAT-TAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
642739 ATTTATTTTAAATAATCTT-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAAT-TTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
642793 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
642847 ATTTATT
1 ATTTATT
642854 ATTGTAGTTG
Statistics
Matches: 448, Mismatches: 59, Indels: 64
0.78 0.10 0.11
Matches are distributed among these distances:
47 4 0.01
48 66 0.15
49 5 0.01
50 6 0.01
51 3 0.01
52 7 0.02
53 17 0.04
54 289 0.65
55 11 0.02
56 4 0.01
57 3 0.01
58 29 0.06
59 4 0.01
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:642457 original size:156 final size:156
Alignment explanation
Indices: 642283--642853 Score: 634
Period size: 156 Copynumber: 3.6 Consensus size: 156
642273 TAATTTATTA
* * *
642283 GTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGCATGGATTAA
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
*
642348 TTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
66 TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
* *
642413 ATATGAATTGAGTTATTATTGTAGTT
131 ATATGGATTGATTTATTATTGTAGTT
** ** * ** * * *
642439 GTATGGATTGATTTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGAT
1 GTATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGAT
*
642501 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT
63 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
*
642566 AAAATATGGATTGATTTATGATTGTAGTT
128 AAAATATGGATTGATTTATTATTGTAGTT
642595 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
** * ** * * * * *
642660 TTTATTTTAAACA-ATTTATT-AGTATAGATTGATTTATTT-TAAAATATGGATTGATTTATTAT
66 TTTATTTTAAA-ATATGGATTGA-TTTATTTTAAATAATTTAT-TAGTATGGATTGATTTA-T-T
*** * *
642722 TGTAGTTGTATGGATTGATTTATT-TTAAATAATCTTTT
126 T-TA-AAATATGGATTGATTTATTATT--GT-A---GTT
642760 AGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 -GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
*
642825 ATTTATTTTAAATTATGGATTGATTTATT
65 ATTTATTTTAAAATATGGATTGATTTATT
642854 ATTGTAGTTG
Statistics
Matches: 343, Mismatches: 50, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
154 3 0.01
155 16 0.05
156 195 0.57
157 16 0.05
158 5 0.01
159 4 0.01
160 15 0.04
161 1 0.00
162 1 0.00
165 2 0.01
166 84 0.24
167 1 0.00
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.51
Consensus pattern (156 bp):
GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
ATATGGATTGATTTATTATTGTAGTT
Found at i:642460 original size:80 final size:79
Alignment explanation
Indices: 642360--642616 Score: 403
Period size: 80 Copynumber: 3.3 Consensus size: 79
642350 TATTTTAAAA
* *
642360 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA-
642425 TTATTATTGTAGTTG
65 TTATTATTGTAGTTG
642440 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA-
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* ***
642504 T-TTATTTTA-AAA
66 TATTATTGTAGTTG
*
642516 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA-
*
642581 TTATGATTGTAGTTG
65 TTATTATTGTAGTTG
642596 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
642617 ATATGGATTG
Statistics
Matches: 161, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
76 63 0.39
77 7 0.04
78 2 0.01
79 6 0.04
80 83 0.52
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (79 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TATTATTGTAGTTG
Found at i:642480 original size:32 final size:32
Alignment explanation
Indices: 642439--642702 Score: 171
Period size: 32 Copynumber: 8.7 Consensus size: 32
642429 TATTGTAGTT
642439 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
642471 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
642494 -TATGGATTGATTTATTTTAAAA---------
1 GTATGGATTGATTTATTTTAAATAATTTATTA
642516 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
642547 GTATAGATTGATTTATTTTAAAATATGGATTGATT-
1 GTATGGATTGATTTATTTT-AAATA---ATTTATTA
* * * * *
642582 -TAT-GATTGTAGTTGTATGGATTGATTTATTT-TAAA
1 GTATGGATTG-A-TT-TAT--TTTAAATAATTTAT-TA
*
642617 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
642649 GTATGGATTGATTTATTTTAAACAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
642681 GTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
642703 ATATGGATTG
Statistics
Matches: 186, Mismatches: 18, Indels: 56
0.72 0.07 0.22
Matches are distributed among these distances:
22 35 0.19
23 4 0.02
25 1 0.01
28 3 0.02
31 3 0.02
32 92 0.49
33 12 0.06
34 10 0.05
35 4 0.02
36 13 0.07
37 7 0.04
38 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:642497 original size:22 final size:22
Alignment explanation
Indices: 642472--642638 Score: 154
Period size: 22 Copynumber: 7.0 Consensus size: 22
642462 AATTTATTAG
642472 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
642494 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
642516 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
642540 TTTATTAGTATAGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
***
642570 TATGGATTGATTTATGATTGTAGTTG
1 TATGGATTGATTTAT--TT-TA-AAA
642596 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
642618 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
642639 TAATTTATTA
Statistics
Matches: 119, Mismatches: 12, Indels: 28
0.75 0.08 0.18
Matches are distributed among these distances:
22 61 0.51
23 4 0.03
24 5 0.04
25 3 0.03
26 25 0.21
27 3 0.03
28 10 0.08
29 2 0.02
30 2 0.02
31 2 0.02
32 2 0.02
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:642654 original size:80 final size:78
Alignment explanation
Indices: 642275--642894 Score: 325
Period size: 80 Copynumber: 7.8 Consensus size: 78
642265 ATTTTAAATA
* *
642275 ATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGCA
1 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTA
*
642340 TGGATTAATTTAT
66 TGGATTGATTTAT
* * * ** ** * ** * *
642353 -TTTA-AAATATGAATTGATTTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AA
1 ATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTA
* * *
642413 ATATGAATTGAGTTATT
63 GTATGGATTGATTTA-T
** ** * ** *
642430 ATTGTAGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-
1 ATT-TA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTAT
* *
642491 AAATATGGATTGATTTAT
61 TAGTATGGATTGATTTAT
* * * * * * *
642509 -TTTA-AAATATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATAGATTGATTTATTTTA
1 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTA-AATAATTTA--TT-
*
642567 AAATATGGATTGATTTAT
62 -AGTATGGATTGATTTAT
642585 GATTGTAGTT-GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1 -ATT-TA-TTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
642649 GTATGGATTGATTTATTTT
63 GTATGGATTGATTTA---T
* * *
642668 AAACAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATT--GTAGTTGT
1 -----ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT-TTAAATAATT-T
* * *
642731 A-T-GGATTGATTTATTTTAAAT
59 ATTAGTATGGATTGA-TTT--AT
642752 AATCTT-TTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1 -AT-TTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
642816 TATGGATTGATTTAT
64 TATGGATTGATTTAT
* * ***
642831 -TTTA-AATTATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATT
1 ATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATT
642894 A
62 A
642895 TTTTAGTTGT
Statistics
Matches: 434, Mismatches: 59, Indels: 96
0.74 0.10 0.16
Matches are distributed among these distances:
69 1 0.00
70 3 0.01
71 6 0.01
72 3 0.01
75 5 0.01
76 90 0.21
77 19 0.04
78 11 0.03
79 11 0.03
80 175 0.40
81 15 0.03
82 10 0.02
83 1 0.00
84 20 0.05
85 16 0.04
86 42 0.10
87 6 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (78 bp):
ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTA
TGGATTGATTTAT
Found at i:642676 original size:134 final size:132
Alignment explanation
Indices: 642261--642884 Score: 647
Period size: 134 Copynumber: 4.7 Consensus size: 132
642251 ATTTAAAATA
* *
642261 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTA---T-A
* * * *
642326 ATAATTTA-TTAGCATGGATTAATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATT
62 AT--TGTAGTT-GTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TTTAAATAATTTA-T
642390 AGTATGGATTG
122 AGTATGGATTG
** * ** *
642401 ATTTATTTTAAA-ATATGAATTGAGT-T--ATT-ATTGTAGTTGTATGGAT-T-GATTTATTTTA
1 ATTTATTTTAAATA-ATTTATT-AGTATAGATTGATT-TA-TTTTA-AAATATGGATTGA-TTT-
642459 AATAATT-TA-TTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTT---TAA---A-
59 -ATAATTGTAGTT-GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAAATAATTTAT
642515 A-TATGGATTG
122 AGTATGGATTG
*
642525 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATAATTG
642590 TAGTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGG
66 TAGTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TTTAAATAATTTA-TAGTATGG
642655 ATTG
129 ATTG
* *
642659 ATTTATTTTAAACAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATAATTG
*** ** * ** * * *
642724 TAGTTGTATGGATTGATTTATTTT-AAATAATCTTTTAGTATGGATTGATTTATTTTAAAATATG
66 TAGTTGTATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATTTAAATAATTTATAGTATG
642788 GATTG
128 GATTG
* * *
642793 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATTATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATAATTG
642858 TAGTTGTATGGATTGATTTATTTTAAA
66 TAGTTGTATGGATTGATTTATTTTAAA
642885 TAATTTATTA
Statistics
Matches: 420, Mismatches: 33, Indels: 67
0.81 0.06 0.13
Matches are distributed among these distances:
123 8 0.02
124 68 0.16
125 15 0.04
126 10 0.02
127 4 0.01
128 3 0.01
130 3 0.01
131 1 0.00
133 8 0.02
134 235 0.56
135 13 0.03
136 3 0.01
137 6 0.01
138 10 0.02
139 9 0.02
140 20 0.05
141 4 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (132 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATAATTG
TAGTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAAATAATTTATAGTATGGAT
TG
Found at i:642788 original size:22 final size:22
Alignment explanation
Indices: 642762--642804 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
642752 AATCTTTTAG
642762 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
642784 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
642805 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:642830 original size:18 final size:18
Alignment explanation
Indices: 642807--642854 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
642797 ATTTTAAATA
642807 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
*
642825 ATTTATTTTAAATTATGGATTG
1 ATTTA--TT--AGTATGGATTG
642847 ATTTATTA
1 ATTTATTA
642855 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:642841 original size:22 final size:23
Alignment explanation
Indices: 642815--642885 Score: 90
Period size: 22 Copynumber: 3.0 Consensus size: 23
642805 TAATTTATTA
642815 GTATGGATTGATTTATTTTAAAT
1 GTATGGATTGATTTATTTTAAAT
**
642838 -TATGGATTGATTTATTATTGTAGTT
1 GTATGGATTGATTTA-T-TT-TAAAT
642863 GTATGGATTGATTTATTTTAAAT
1 GTATGGATTGATTTATTTTAAAT
642886 AATTTATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 14 0.35
23 4 0.10
24 4 0.10
25 4 0.10
26 14 0.35
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (23 bp):
GTATGGATTGATTTATTTTAAAT
Found at i:642944 original size:31 final size:31
Alignment explanation
Indices: 642909--642967 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
642899 AGTTGTATGG
* *
642909 ATTATTTAAATT-TCAGTATTGTAAAACTAAA
1 ATTATTT-AATTCTCAATATTGCAAAACTAAA
642940 ATTATTTAATTCTCAATATTGCAAAACT
1 ATTATTTAATTCTCAATATTGCAAAACT
642968 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAATTCTCAATATTGCAAAACTAAA
Found at i:653843 original size:13 final size:13
Alignment explanation
Indices: 653825--653851 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
653815 ACATTCACGT
653825 AGTGAAGGACATA
1 AGTGAAGGACATA
653838 AGTGAAGGACATA
1 AGTGAAGGACATA
653851 A
1 A
653852 TAATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.30, T:0.15
Consensus pattern (13 bp):
AGTGAAGGACATA
Found at i:654191 original size:103 final size:104
Alignment explanation
Indices: 654048--654243 Score: 333
Period size: 103 Copynumber: 1.9 Consensus size: 104
654038 AATATATATA
**
654048 AAACTTAAAGATAGATGTAATAAATCAAAGAAAATTCAAATTTTAGAATGAGTACAATATTCTCA
1 AAACTTAAAGATAGACATAATAAATCAAAGAAAATTCAAATTTTAGAATGAGTACAATATTCTCA
654113 ATTGGAAGCA-TGGGCAGAATTTCACGAGAGTCAAGGCTC
66 ATTGGAAGCAGT-GGCAGAATTTCACGAGAGTCAAGGCTC
*
654152 AAACTTAAAGATAGACATAATCAAT-AAAGAAAATTCAAATTTTAGAATGAGTACAATATTCTCA
1 AAACTTAAAGATAGACATAATAAATCAAAGAAAATTCAAATTTTAGAATGAGTACAATATTCTCA
*
654216 ATTGGAAGCAGTGGTAGAATTTCACGAG
66 ATTGGAAGCAGTGGCAGAATTTCACGAG
654244 CGCTAAGATG
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
103 64 0.74
104 23 0.26
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (104 bp):
AAACTTAAAGATAGACATAATAAATCAAAGAAAATTCAAATTTTAGAATGAGTACAATATTCTCA
ATTGGAAGCAGTGGCAGAATTTCACGAGAGTCAAGGCTC
Found at i:659985 original size:2 final size:2
Alignment explanation
Indices: 659978--660005 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
659968 ATCACATAAG
659978 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
660006 CTTCATATTA
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:662252 original size:15 final size:15
Alignment explanation
Indices: 662234--662289 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
662224 TAACCGGTTT
662234 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
662249 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
662266 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
662281 CGATTTTAA
1 CGGTTTTAA
662290 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:662262 original size:17 final size:17
Alignment explanation
Indices: 662237--662287 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
662227 CCGGTTTCGG
662237 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
662254 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
662269 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
662286 TT
1 TT
662288 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:662706 original size:13 final size:13
Alignment explanation
Indices: 662685--662739 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
662675 AAGTTCAATA
*
662685 AATTCAAATACTT
1 AATTGAAATACTT
662698 AATTGAAATACTT
1 AATTGAAATACTT
* *
662711 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
662725 AATTGAAATACTT
1 AATTGAAATACTT
662738 AA
1 AA
662740 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:662770 original size:33 final size:33
Alignment explanation
Indices: 662725--662819 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
662715 AACTCAACAT
* * *
662725 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
662758 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
662791 AATTCAAATACTTAAAAAC-TCCAAGTTCG
1 AATTCAAATACTTAAAAACTTCCAAGTTCG
662820 TAGTGATCCC
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 10 0.17
33 49 0.83
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:663155 original size:12 final size:12
Alignment explanation
Indices: 663138--663183 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
663128 TTCGGATAAA
663138 AACCGGTTTTTT
1 AACCGGTTTTTT
663150 AACCGGTTTTTTT
1 AACCGG-TTTTTT
663163 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
663177 ATCCGGT
1 AACCGGT
663184 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:663168 original size:15 final size:14
Alignment explanation
Indices: 663137--663176 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
663127 TTTCGGATAA
663137 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
663150 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
663163 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
663177 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:667694 original size:19 final size:20
Alignment explanation
Indices: 667670--667714 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
667660 AAATGTCTTT
667670 AAAAAAT-AATTTTAAGGA-A
1 AAAAAATCAATTTTAA-GACA
*
667689 AAAAAATCATTTTTAAGACA
1 AAAAAATCAATTTTAAGACA
667709 AAAAAA
1 AAAAAA
667715 CTAGTCTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAAAATCAATTTTAAGACA
Found at i:668013 original size:5 final size:5
Alignment explanation
Indices: 667999--668034 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
667989 TTTCATAACG
* *
667999 ATAAA ATAAA CTAAA ATGAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
668035 GTGAAATAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:668024 original size:20 final size:21
Alignment explanation
Indices: 667999--668042 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
667989 TTTCATAACG
*
667999 ATAAAATAAACTAAAA-TGAA
1 ATAAAATAAAATAAAAGTGAA
668019 ATAAAATAAAATAAAAGTGAA
1 ATAAAATAAAATAAAAGTGAA
668040 ATA
1 ATA
668043 GATGATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (21 bp):
ATAAAATAAAATAAAAGTGAA
Found at i:668921 original size:32 final size:32
Alignment explanation
Indices: 668880--668944 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
668870 GTAAAATATT
668880 ACTACATCATTTCAATTGTCATAACCTGTCAA
1 ACTACATCATTTCAATTGTCATAACCTGTCAA
668912 ACTACATCATTTCAATTGTCATAACCTGTCAA
1 ACTACATCATTTCAATTGTCATAACCTGTCAA
668944 A
1 A
668945 GAGATACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (32 bp):
ACTACATCATTTCAATTGTCATAACCTGTCAA
Found at i:669707 original size:3 final size:3
Alignment explanation
Indices: 669699--669748 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
669689 GTAATAAGAT
*
669699 TAA TAA TAA TAA TAA TAA T-A TAGA TAA TAA -AA TAT TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
669742 TTAA TAA
1 -TAA TAA
669749 CGTTTTTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 28 0.70
4 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:670541 original size:91 final size:91
Alignment explanation
Indices: 670386--670558 Score: 276
Period size: 91 Copynumber: 1.9 Consensus size: 91
670376 AAGTGTTGAA
* * * *
670386 TTGAACAAGTTCTTCTCATTATGAATTTCTTCTCTCTTGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTATTCTCATTATGAACTTCTTCTCTCTCGTTAGATGAGTTCTTCTCATTATGAAC
670451 TCTCCACTAGAAATGTTAATGTAAGG
66 TCTCCACTAGAAATGTTAATGTAAGG
670477 TTGAACAAGTTATTCTCATTATGAACTTCTTCT-TCCTCGTTAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTATTCTCATTATGAACTTCTTCTCT-CTCGTTAGATGAGTTCTTCTCATTATGAA
* *
670541 CTCTTCACTGGAAATGTT
65 CTCTCCACTAGAAATGTT
670559 GATCCACCTC
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
90 1 0.01
91 74 0.99
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (91 bp):
TTGAACAAGTTATTCTCATTATGAACTTCTTCTCTCTCGTTAGATGAGTTCTTCTCATTATGAAC
TCTCCACTAGAAATGTTAATGTAAGG
Found at i:670685 original size:117 final size:117
Alignment explanation
Indices: 670473--671007 Score: 503
Period size: 117 Copynumber: 4.8 Consensus size: 117
670463 ATGTTAATGT
* * *
670473 AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTCGTTAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
* * *
670538 GAACTCTTCACTGGAAATGTTGATCCACCTCATTCTGTGATAGAATCGAACC
66 GAACTCTTCACTGAAAATGTCGATCCACCTCATTCTGTGATAGAATCAAACC
*
670590 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
* * * * *
670655 GAACTTTTCACTGAAAATGTCGATCTACCTCTTTCTTTGATGGAATCAAACC
66 GAACTCTTCACTGAAAATGTCGATCCACCTCATTCTGTGATAGAATCAAACC
*
670707 AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
* * * * * * * * * **
670772 GAACTCTT--CTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGACT-TGA--
66 GAACTCTTCACTGAAAATGTCGATCCACCTCATTCTGTGATAGAATCAAACC
* * *
670819 AA-G--GAACAAGTTTTTCTCGTTATGAA-TT-TTC-TCCT--TTAGGACGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATT-GGATGAGTTCTTCTCATTA
* * * * * * * ***
670876 TGAACTCTT--CTGGAAATATTGGTTCACCTCCTTCTTTGAT-GAATTTGA--
65 TGAACTCTTCACTGAAAATGTCGATCCACCTCATTCTGTGATAGAATCAAACC
*
670924 AA-G--GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGACGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATT-GGATGAGTTCTTCTCATTA
*
670981 TGAACTCTTCA-TTAGAAATGTCGATCC
65 TGAACTCTTCACTGA-AAATGTCGATCC
671008 CTCAAGCGAG
Statistics
Matches: 369, Mismatches: 43, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
104 5 0.01
105 120 0.33
106 5 0.01
107 11 0.03
108 2 0.01
109 21 0.06
111 1 0.00
112 2 0.01
114 1 0.00
115 26 0.07
117 175 0.47
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (117 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
GAACTCTTCACTGAAAATGTCGATCCACCTCATTCTGTGATAGAATCAAACC
Found at i:670899 original size:105 final size:105
Alignment explanation
Indices: 670713--670990 Score: 414
Period size: 105 Copynumber: 2.6 Consensus size: 105
670703 AACCAAGGTT
*
670713 GAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCATT-GGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAA-TT-TTC-TCCT--TTAGGACGAGTTCTTCTCATTATGAACT
* * *
670777 CTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGACTTGAAAG
61 CTTCTGGAAATATTGGTTCACCTCCTTCTGCGATGAACTTGAAAG
* *
670822 GAACAAGTTTTTCTCGTTATGAATTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGTTCTTCTCATTATGAATTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
** *
670887 GGAAATATTGGTTCACCTCCTTCTTTGATGAATTTGAAAG
66 GGAAATATTGGTTCACCTCCTTCTGCGATGAACTTGAAAG
*
670927 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTC
1 GAACAAGTTCTTCTCATTATGAATTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTC
670991 ATTAGAAATG
Statistics
Matches: 156, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
104 2 0.01
105 124 0.79
106 4 0.03
107 3 0.02
108 2 0.01
109 21 0.13
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.41
Consensus pattern (105 bp):
GAACAAGTTCTTCTCATTATGAATTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
GGAAATATTGGTTCACCTCCTTCTGCGATGAACTTGAAAG
Found at i:671140 original size:96 final size:96
Alignment explanation
Indices: 670970--671178 Score: 355
Period size: 96 Copynumber: 2.2 Consensus size: 96
670960 TAGGACGAGT
*
670970 TCTTCTCATTATGAACTCTTCATTAGAAATGTCGATCCCTCAAGCGAGGTGTCACTGATTCAAAA
1 TCTTCTCATTATGAACTCTTCATTAGAAATGTCGATCCCTCAAGCGAGGTGTCACTAATTCAAAA
*
671035 TGTCGTGAATCGAGGGATAAGTCAAACAAGC
66 TGTCATGAATCGAGGGATAAGTCAAACAAGC
*
671066 TCTTCTCATTATGAACTCTTCATTAGAAATGTCGATCCCTCAAGCGAGGTGTCACTAATTCGAAA
1 TCTTCTCATTATGAACTCTTCATTAGAAATGTCGATCCCTCAAGCGAGGTGTCACTAATTCAAAA
* * * *
671131 TGTTATGAATCGAGTGATAGGTCGAACAAGC
66 TGTCATGAATCGAGGGATAAGTCAAACAAGC
671162 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
671179 TGTTCTCCCT
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 106 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (96 bp):
TCTTCTCATTATGAACTCTTCATTAGAAATGTCGATCCCTCAAGCGAGGTGTCACTAATTCAAAA
TGTCATGAATCGAGGGATAAGTCAAACAAGC
Found at i:671598 original size:73 final size:73
Alignment explanation
Indices: 671494--671724 Score: 329
Period size: 73 Copynumber: 3.2 Consensus size: 73
671484 AGAGAAGCAC
* * *
671494 TCTCAAGTGGGATAAATTTTG-TTCTGAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAA
1 TCTCAAGTGAGATAAATTTTGTTTC-AAAGGAAAACTGTCTCAAGCAAGACGAAGTAGGTTTTAA
671558 GAAAAACCA
65 GAAAAACCA
*
671567 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCCAGACGAAGTAGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
671632 AAAAACCA
66 AAAAACCA
** * * ** * *
671640 TCTCAAGTGAGATTCATTTTGTTTCAAGGGAAAGCTGTCTCAAGTGAGACGAACTTGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
671705 AAAAACCA
66 AAAAACCA
*
671713 TCTCAAGGGAGA
1 TCTCAAGTGAGA
671725 CAAAACTTTA
Statistics
Matches: 144, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
73 141 0.98
74 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (73 bp):
TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
AAAAACCA
Found at i:671608 original size:37 final size:37
Alignment explanation
Indices: 671567--671688 Score: 102
Period size: 37 Copynumber: 3.3 Consensus size: 37
671557 AGAAAAACCA
671567 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
** ** * ** * * **
671604 TCTCAAGCCAGACGAAGTAGGTTT-TAAGAAAAACCA
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
** * *
671640 TCTCAAGTGAGATTCATTTTGTTTCAAGGGAAAGCTG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
671677 TCTCAAGTGAGA
1 TCTCAAGTGAGA
671689 CGAACTTGGT
Statistics
Matches: 59, Mismatches: 25, Indels: 2
0.69 0.29 0.02
Matches are distributed among these distances:
36 24 0.41
37 35 0.59
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (37 bp):
TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
Found at i:671725 original size:36 final size:36
Alignment explanation
Indices: 671531--671725 Score: 138
Period size: 36 Copynumber: 5.4 Consensus size: 36
671521 AGGAAAATTG
** *
671531 TCTCAAGCAAGACGAAGTAGGTTTTAAGAAAAACCA
1 TCTCAAGTGAGACGAAGTTGGTTTTAAGAAAAACCA
** * * * * **
671567 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
1 TCTCAAGTGAGACGAAGTTGGTTT-TAAGAAAAACCA
** *
671604 TCTCAAGCCAGACGAAGTAGGTTTTAAGAAAAACCA
1 TCTCAAGTGAGACGAAGTTGGTTTTAAGAAAAACCA
*** * * * * * **
671640 TCTCAAGTGAGATTCATTTTGTTTCAAGGGAAAGCTG
1 TCTCAAGTGAGACGAAGTTGGTTTTAA-GAAAAACCA
*
671677 TCTCAAGTGAGACGAACTTGGTTTTAAGAAAAACCA
1 TCTCAAGTGAGACGAAGTTGGTTTTAAGAAAAACCA
*
671713 TCTCAAGGGAGAC
1 TCTCAAGTGAGAC
671726 AAAACTTTAT
Statistics
Matches: 111, Mismatches: 46, Indels: 4
0.69 0.29 0.02
Matches are distributed among these distances:
36 60 0.54
37 51 0.46
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (36 bp):
TCTCAAGTGAGACGAAGTTGGTTTTAAGAAAAACCA
Found at i:671766 original size:28 final size:29
Alignment explanation
Indices: 671726--671783 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
671716 CAAGGGAGAC
*
671726 AAAACTTTATTTCAAGAGAAACTGTATCA
1 AAAACTTTATTTCAAGAGAAACTATATCA
*
671755 AAAAC-TTGTTTCAAGAGAAACTATATCA
1 AAAACTTTATTTCAAGAGAAACTATATCA
671783 A
1 A
671784 GGGAGACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (29 bp):
AAAACTTTATTTCAAGAGAAACTATATCA
Found at i:671801 original size:36 final size:36
Alignment explanation
Indices: 671755--671823 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
671745 AACTGTATCA
671755 AAAACTTGTTTCAA-GAGAAACTATATCAAGGGAGAC
1 AAAACTTGTTTCAATG-GAAACTATATCAAGGGAGAC
* * *
671791 AAAATTTGTTTCAATGGAAACTGTCTCAAGGGA
1 AAAACTTGTTTCAATGGAAACTATATCAAGGGA
671824 AACTATCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 28 0.97
37 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
AAAACTTGTTTCAATGGAAACTATATCAAGGGAGAC
Found at i:671841 original size:51 final size:51
Alignment explanation
Indices: 671755--671874 Score: 152
Period size: 51 Copynumber: 2.3 Consensus size: 51
671745 AACTGTATCA
* *
671755 AAAACTTGTTTCAAGAGAAACTATATCAAGGGAGACAAAATTTGTTTCAATGG
1 AAAAC-TGTCTCAAGAGAAACTATATCAAGAGAGACAAAATTTGTTTCAA-GG
* * * *
671808 -AAACTGTCTCAAGGGAAACTATCTCATGAGAGACAAAATTTGTTTTAAGG
1 AAAACTGTCTCAAGAGAAACTATATCAAGAGAGACAAAATTTGTTTCAAGG
*
671858 AAAACTATCTCAAGAGA
1 AAAACTGTCTCAAGAGA
671875 GACAAAATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 2 0.03
51 52 0.90
52 4 0.07
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (51 bp):
AAAACTGTCTCAAGAGAAACTATATCAAGAGAGACAAAATTTGTTTCAAGG
Found at i:671867 original size:36 final size:36
Alignment explanation
Indices: 671816--671954 Score: 206
Period size: 36 Copynumber: 3.9 Consensus size: 36
671806 GGAAACTGTC
*
671816 TCAAGGGAAACTATCTCATGAGAGACAAAATTTGTT
1 TCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTT
* *
671852 TTAAGGAAAACTATCTCAAGAGAGACAAAATTTGTT
1 TCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTT
* **
671888 TCGAGGGAAACTGCCTCAAGAGAGACAAAATTTGTT
1 TCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTT
* *
671924 TCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TCAAGGGAAACTATCTCAAGAGAGACAAAAT
671955 CTTATGTTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 90 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (36 bp):
TCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTT
Found at i:671989 original size:40 final size:40
Alignment explanation
Indices: 671945--672142 Score: 283
Period size: 40 Copynumber: 5.0 Consensus size: 40
671935 TATCTCAAGC
* *
671945 GAGATAAAATCTTATGTTTCAATGAAAAACAATCTTGAGC
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGT
* * *
671985 GAGATAAAATCTTCTGTTTCAAGGAAAAATAATATTGAGT
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGT
*
672025 GAGATAAAATCTTCAT-TTTCAAGGAAAAATAATCTTGAGT
1 GAGATAAAATCTT-ATGTTTCAAGGAAAAACAATCTTGAGT
* *
672065 GAGATAAAATCTTATGTTTCAA-GAAAACCCAATCTTGAAT
1 GAGATAAAATCTTATGTTTCAAGGAAAA-ACAATCTTGAGT
*
672105 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGA
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGA
672143 TCGCATTGTT
Statistics
Matches: 142, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 7 0.05
40 129 0.91
41 6 0.04
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGT
Found at i:673815 original size:127 final size:126
Alignment explanation
Indices: 673588--673820 Score: 313
Period size: 127 Copynumber: 1.8 Consensus size: 126
673578 AGTAGAATCA
* * *
673588 AGAGGGAGTCTACCTACCAAGGAGATGATCCAGACATTTGTCTGCTGAGGTAACATGTTGGACTC
1 AGAGAGAGTCTACCTACCAAGGAGACGATCCAGACATTTGTCTGCTGAGGTAACAAGTTGGACTC
* * * * *
673653 GAGACAATTCAACGCTGAAGCCAATAGTTGAAGATCACGAATAAGAGATGAAGTAGGAGCT
66 AAGACAATTCAACGCCGAAACCAACAGTGGAAGATCACGAATAAGAGATGAAGTAGGAGCT
* * * * * **
673714 AGAGAGAGTCTATCTACCAAGTAGACGATCCAGGCATTTTTCCTGTTGAGGTAGTAAGTTGGACT
1 AGAGAGAGTCTACCTACCAAGGAGACGATCCAGACATTTGT-CTGCTGAGGTAACAAGTTGGACT
*
673779 CAAGACAATTCGACGCCGAAACCAACAGTGGAAGATCACGAA
65 CAAGACAATTCAACGCCGAAACCAACAGTGGAAGATCACGAA
673821 CCAGCTCGAA
Statistics
Matches: 90, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
126 35 0.39
127 55 0.61
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (126 bp):
AGAGAGAGTCTACCTACCAAGGAGACGATCCAGACATTTGTCTGCTGAGGTAACAAGTTGGACTC
AAGACAATTCAACGCCGAAACCAACAGTGGAAGATCACGAATAAGAGATGAAGTAGGAGCT
Found at i:675257 original size:6 final size:6
Alignment explanation
Indices: 675236--675287 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
675226 AAGGAAAAAC
* * * * *
675236 AAAGAAA AAAGTA AAAGAA AAAGCA AAAGAA AAAGCA AAAGCA AAGGAA
1 AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
675285 AAA
1 AAA
675288 AGACAAGAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
6 33 0.89
7 4 0.11
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:675263 original size:18 final size:18
Alignment explanation
Indices: 675197--675287 Score: 69
Period size: 18 Copynumber: 4.8 Consensus size: 18
675187 ATATTAAATC
675197 AAAGCAAAGAGAAAAAG--
1 AAAGCAAA-AGAAAAAGAA
*
675214 AAAGCTAAAAGAAAGGAAAAA
1 AAAGC-AAAAGAAA--AAGAA
* *
675235 CAAAGAAAAAAGTAAAAGAA
1 -AAAG-CAAAAGAAAAAGAA
*
675255 AAAGCAAAAGAAAAAGCA
1 AAAGCAAAAGAAAAAGAA
*
675273 AAAGCAAAGGAAAAA
1 AAAGCAAAAGAAAAA
675288 AGACAAGAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
17 10 0.17
18 28 0.47
19 6 0.10
20 4 0.07
22 11 0.19
ACGTcount: A:0.73, C:0.07, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAGCAAAAGAAAAAGAA
Found at i:675270 original size:24 final size:22
Alignment explanation
Indices: 675197--675269 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
675187 ATATTAAATC
* **
675197 AAAGCAAAGAGAAAAAGAAAGCTA
1 AAAG-AAA-AGAAAAACAAAGAAA
*
675221 AAAGAAAGGAAAAACAAAGAAA
1 AAAGAAAAGAAAAACAAAGAAA
675243 AAAGTAAAAGAAAAAGCAAAAGAAA
1 AAAG-AAAAGAAAAA-C-AAAGAAA
675268 AA
1 AA
675270 GCAAAAGCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 15 0.37
23 12 0.29
24 5 0.12
25 9 0.22
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (22 bp):
AAAGAAAAGAAAAACAAAGAAA
Found at i:675281 original size:5 final size:6
Alignment explanation
Indices: 675242--675280 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
675232 AAACAAAGAA
* * *
675242 AAAAGT AAAAGA AAAAGC AAAAGA AAAAGC AAAAGC AAA
1 AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAA
675281 GGAAAAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAGC
Found at i:675287 original size:12 final size:12
Alignment explanation
Indices: 675197--675274 Score: 72
Period size: 12 Copynumber: 6.7 Consensus size: 12
675187 ATATTAAATC
675197 AAAGCAAAGAGAA
1 AAAGCAAAG-GAA
**
675210 AAAG-AAAGCTA
1 AAAGCAAAGGAA
675221 AAAG-AAAGGAA
1 AAAGCAAAGGAA
*
675232 AAA-CAAAGAAA
1 AAAGCAAAGGAA
* *
675243 AAAGTAAAAGAA
1 AAAGCAAAGGAA
*
675255 AAAGCAAAAGAA
1 AAAGCAAAGGAA
675267 AAAGCAAA
1 AAAGCAAA
675275 AGCAAAGGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
11 22 0.41
12 28 0.52
13 4 0.07
ACGTcount: A:0.73, C:0.06, G:0.18, T:0.03
Consensus pattern (12 bp):
AAAGCAAAGGAA
Found at i:675622 original size:39 final size:39
Alignment explanation
Indices: 675570--675860 Score: 426
Period size: 39 Copynumber: 7.5 Consensus size: 39
675560 CGTACATTAA
* *
675570 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAGCAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
*
675609 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
* * *
675648 AAGATTTTGTCTCACTTGAGATAGTTTCCCTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
*
675687 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
* * ** *
675726 AAGATTTTATGTCACTTGAGATAGTTTCCCTCGAAGTAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
*
675765 AAGATTTTACCTCGCTTGAGATAGTTTCCCTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
*
675804 AAGATTTTATCTCGCTTGAGATTGTTTCCCTCGAAAC--
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
*
675841 AA-ATTTTGTCTCGCTTGAGA
1 AAGATTTTATCTCGCTTGAGA
675861 AAGTCTCATT
Statistics
Matches: 229, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
36 17 0.07
37 2 0.01
39 210 0.92
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
Found at i:675699 original size:78 final size:77
Alignment explanation
Indices: 675570--675898 Score: 425
Period size: 78 Copynumber: 4.3 Consensus size: 77
675560 CGTACATTAA
* *
675570 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAGCAAAAGATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAAC-AAAGATTTTATCTCGCTTGAGATAGTT
*
675635 TCCCTCGAAACAT
65 TCCCTCGAAACAG
* *
675648 AAGATTTTGTCTCACTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAACA-AAGATTTTATCTCGCTTGAGATAGTT
*
675713 TCCCTTGAAACAG
65 TCCCTCGAAACAG
* ** *
675726 AAGATTTTATGTCACTTGAGATAGTTTCCCTCGAAGTATAAGATTTTACCTCGCTTGAGATAGTT
1 AAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAACA-AAGATTTTATCTCGCTTGAGATAGTT
675791 TCCCTCGAAACAG
65 TCCCTCGAAACAG
* * * * *
675804 AAGATTTTATCTCGCTTGAGATTGTTTCCCTCGAAAC-AA-ATTTTGTCTCGCTTGAGAAAGTCT
1 AAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAACAAAGATTTTATCTCGCTTGAGATAGTTT
* **
675867 -CATTTAATACAG
66 CCCTCGAA-ACAG
675879 AAGA--TTATCTCACTTGAGAT
1 AAGATTTTATCTCACTTGAGAT
675899 TGATTTTCTT
Statistics
Matches: 222, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
73 15 0.07
74 4 0.02
75 28 0.13
76 2 0.01
77 1 0.00
78 172 0.77
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (77 bp):
AAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAACAAAGATTTTATCTCGCTTGAGATAGTTT
CCCTCGAAACAG
Found at i:676077 original size:39 final size:38
Alignment explanation
Indices: 676034--676205 Score: 200
Period size: 39 Copynumber: 4.4 Consensus size: 38
676024 ATTGTTTTTA
* *
676034 AAACATAAGATTTTATCTCGCTTGAGATAATTTACCTCG
1 AAACAGAAGATTTTATCTCGCTTGAGATAGTTT-CCTCG
*
676073 AAACAGAATATTTTATCTCGCTTGAGATAGTTTCCCTCG
1 AAACAGAAGATTTTATCTCGCTTGAGATAGTTT-CCTCG
* **
676112 AAACATAAGATTTTATCTCTATTGAGATAGTCTTCCTCG
1 AAACAGAAGATTTTATCTCGCTTGAGATAGT-TTCCTCG
* * * * *
676151 AAATAGAATATTTTATGTCGTTTGAGATAGTTTTGCTCG
1 AAACAGAAGATTTTATCTCGCTTGAGATAG-TTTCCTCG
*
676190 AAACAAAAGATTTTAT
1 AAACAGAAGATTTTAT
676206 AAGAAACTAA
Statistics
Matches: 113, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 110 0.97
40 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (38 bp):
AAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCTCG
Found at i:676163 original size:78 final size:78
Alignment explanation
Indices: 676034--676205 Score: 247
Period size: 78 Copynumber: 2.2 Consensus size: 78
676024 ATTGTTTTTA
*
676034 AAACATAAGATTTTATCTCGCTTGAGATAATTTACCTCGAAACAGAATATTTTATCTCGCTTGAG
1 AAACATAAGATTTTATCTCGATTGAGATAATTTACCTCGAAACAGAATATTTTATCTCGCTTGAG
676099 ATAGTTTCCCTCG
66 ATAGTTTCCCTCG
* * * * *
676112 AAACATAAGATTTTATCTCTATTGAGATAGTCTT-CCTCGAAATAGAATATTTTATGTCGTTTGA
1 AAACATAAGATTTTATCTCGATTGAGATAAT-TTACCTCGAAACAGAATATTTTATCTCGCTTGA
**
676176 GATAGTTTTGCTCG
65 GATAGTTTCCCTCG
*
676190 AAACAAAAGATTTTAT
1 AAACATAAGATTTTAT
676206 AAGAAACTAA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
78 82 0.98
79 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (78 bp):
AAACATAAGATTTTATCTCGATTGAGATAATTTACCTCGAAACAGAATATTTTATCTCGCTTGAG
ATAGTTTCCCTCG
Found at i:676297 original size:42 final size:41
Alignment explanation
Indices: 676250--676349 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
676240 GAGTAAGTCA
* *
676250 TTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAA-ATCC
1 TTCGGGCCATCAATAAGTCTTTCGAGCAAGATG-ATAAGA-CC
* *
676292 TTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGACC
1 TTCGGGCCATCAATAAGTCTTTCGAGCAAGATGATAAGACC
* *
676333 TTCAGGCCATCCATAAG
1 TTCGGGCCATCAATAAG
676350 ACCTTCGGGC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 19 0.38
42 31 0.62
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (41 bp):
TTCGGGCCATCAATAAGTCTTTCGAGCAAGATGATAAGACC
Found at i:682389 original size:20 final size:20
Alignment explanation
Indices: 682364--682403 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
682354 ATGCCTGCAC
682364 TTTAAAATAATATTTACTGT
1 TTTAAAATAATATTTACTGT
682384 TTTAAAATAATATTTACTGT
1 TTTAAAATAATATTTACTGT
682404 CATATATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTAAAATAATATTTACTGT
Found at i:683608 original size:12 final size:12
Alignment explanation
Indices: 683579--683616 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
683569 AATTACTAAA
683579 ATATTTAA-AAT
1 ATATTTAATAAT
*
683590 ATATTTATTAAT
1 ATATTTAATAAT
*
683602 ATTTTTAATAAT
1 ATATTTAATAAT
683614 ATA
1 ATA
683617 ATATTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:683625 original size:22 final size:23
Alignment explanation
Indices: 683582--683641 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
683572 TACTAAAATA
*
683582 TTTAA-AATATATTTATTAATATT
1 TTTAATAATATA-ATATTAATATT
683605 TTTAATAATATAATATT-ATATT
1 TTTAATAATATAATATTAATATT
*
683627 TTTAATATTATAATA
1 TTTAATAATATAATA
683642 AAATAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 19 0.56
23 9 0.26
24 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAATAATATAATATTAATATT
Found at i:683668 original size:49 final size:49
Alignment explanation
Indices: 683609--683709 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 49
683599 AATATTTTTA
*
683609 ATAATATAATAT-TATATTTTTAATATTATAATAAA-ATAATTAA-TTATAT
1 ATAATATAATATAT-TATTTTT--TATTATAATAAATATAATAAATTTATAT
*
683658 ATAATATAATATATTATTTTTTATTTTAATAAATATAATAAATTTATAT
1 ATAATATAATATATTATTTTTTATTATAATAAATATAATAAATTTATAT
683707 ATA
1 ATA
683710 TTTAATAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
47 11 0.23
48 7 0.15
49 28 0.60
50 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (49 bp):
ATAATATAATATATTATTTTTTATTATAATAAATATAATAAATTTATAT
Found at i:683673 original size:19 final size:18
Alignment explanation
Indices: 683631--683674 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
683621 TATATTTTTA
683631 ATATTATAATAAAATAAT
1 ATATTATAATAAAATAAT
*
683649 -TAATTATATATAATATAAT
1 AT-ATTATA-ATAAAATAAT
683668 ATATTAT
1 ATATTAT
683675 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 1 0.05
18 6 0.27
19 14 0.64
20 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATTATAATAAAATAAT
Found at i:683727 original size:19 final size:19
Alignment explanation
Indices: 683705--683772 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
683695 ATAAATTTAT
*
683705 ATATATTTAATAATGAATA
1 ATATATTTAATAATTAATA
683724 ATATTATTT-AT-ATTAATA
1 ATA-TATTTAATAATTAATA
* *
683742 TTA-ATATAATAATCTAATA
1 ATATATTTAATAAT-TAATA
683761 ATAT-TTTAATAA
1 ATATATTTAATAA
683773 AGATATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.08
17 2 0.05
18 10 0.26
19 19 0.49
20 5 0.13
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (19 bp):
ATATATTTAATAATTAATA
Found at i:683740 original size:53 final size:48
Alignment explanation
Indices: 683609--683753 Score: 132
Period size: 49 Copynumber: 2.9 Consensus size: 48
683599 AATATTTTTA
* *
683609 ATAATATAATATTATATT-TTTAATATTATAATAAA-ATAATTAATTATAT
1 ATAATATAATATAATATTATTT-ATA-T-TAATAAATATAATAAATTATAT
* * *
683658 ATAATATAATATATTATTTTTTATTTTAATAAATATAATAAATTTATAT
1 ATAATATAATATAATATTATTTATATTAATAAATATAATAAA-TTATAT
*
683707 ATATTTAATAATGAATAATATTATTTATATTAATATTAATATAATAA
1 ATA-AT-ATAAT--ATAATATTATTTATATTAATA--AATATAATAA
683754 TCTAATAATA
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
47 7 0.09
48 8 0.10
49 27 0.34
50 4 0.05
51 5 0.06
53 18 0.23
55 10 0.13
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (48 bp):
ATAATATAATATAATATTATTTATATTAATAAATATAATAAATTATAT
Found at i:683793 original size:23 final size:23
Alignment explanation
Indices: 683767--683811 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
683757 AATAATATTT
683767 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* *
683790 TAATTAATATATTTAAAATATA
1 TAATAAAGATATTTAAAATATA
683812 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:683943 original size:20 final size:20
Alignment explanation
Indices: 683907--683946 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
683897 TAATAAAATT
683907 ATAAAAAATAATATTTAATA
1 ATAAAAAATAATATTTAATA
*
683927 ATAAATAAATTAT-TTTAATA
1 ATAAA-AAATAATATTTAATA
683947 TTTTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAATAATATTTAATA
Found at i:684148 original size:14 final size:14
Alignment explanation
Indices: 684115--684155 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
684105 AAATATAATT
*
684115 CATTTTACGGAAAA
1 CATTTTTCGGAAAA
684129 CATTTTTCGGAAAA
1 CATTTTTCGGAAAA
* *
684143 CTTTTTTCAGAAA
1 CATTTTTCGGAAA
684156 TGTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (14 bp):
CATTTTTCGGAAAA
Found at i:684178 original size:14 final size:14
Alignment explanation
Indices: 684159--684203 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
684149 TCAGAAATGT
684159 AATTCATTTTCCAG
1 AATTCATTTTCCAG
**
684173 AATTCAAATTCCAG
1 AATTCATTTTCCAG
*
684187 TAATTCATTTTCTAG
1 -AATTCATTTTCCAG
684202 AA
1 AA
684204 AACCAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (14 bp):
AATTCATTTTCCAG
Found at i:684393 original size:20 final size:20
Alignment explanation
Indices: 684370--684439 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
684360 GAACTCTAAT
684370 TTCGCAACAGAGTTTCCAAA
1 TTCGCAACAGAGTTTCCAAA
* * *
684390 TTCGCAACCCGAATTTCCCAGA
1 TTCGCAA-CAGAGTTT-CCAAA
** **
684412 TTCGCAACTCAGTTTTGAAA
1 TTCGCAACAGAGTTTCCAAA
684432 TTCGCAAC
1 TTCGCAAC
684440 TCGAATTTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 17 0.44
21 11 0.28
22 11 0.28
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (20 bp):
TTCGCAACAGAGTTTCCAAA
Found at i:685067 original size:20 final size:20
Alignment explanation
Indices: 685044--685082 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
685034 TTTGAAACTT
*
685044 AAATTCGCAACACGAAAATG
1 AAATTCACAACACGAAAATG
685064 AAATTCACAACACGAAAAT
1 AAATTCACAACACGAAAAT
685083 CGCAACGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.15
Consensus pattern (20 bp):
AAATTCACAACACGAAAATG
Found at i:685114 original size:20 final size:20
Alignment explanation
Indices: 685089--685163 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
685079 AAATCGCAAC
*
685089 GCGATTTTAGTTTTTGCGTT
1 GCGATTTTAGTTTTCGCGTT
*
685109 GCGATTTT-GACTTTCGCGTT
1 GCGATTTTAG-TTTTCGCGTT
* * *
685129 GCGAATTTAATTTTCGTGTT
1 GCGATTTTAGTTTTCGCGTT
*
685149 GCGAATTTAAGTTTT
1 GCG-ATTTTAGTTTT
685164 AAAAACTACT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 34 0.79
21 8 0.19
ACGTcount: A:0.16, C:0.12, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTAGTTTTCGCGTT
Found at i:686714 original size:42 final size:42
Alignment explanation
Indices: 686655--686754 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
686645 TACCCCCACT
* *
686655 TCGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACA
1 TCGAGAGCCATCACCTGATCGAGCCGATTATACACCTCGACA
* *
686697 TCGAGAGCCATTACCTGATCGAGCTGATTATACACCTCGACA
1 TCGAGAGCCATCACCTGATCGAGCCGATTATACACCTCGACA
* *
686739 CCTAGAGCCATCACCT
1 TCGAGAGCCATCACCT
686755 ATTCCATCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (42 bp):
TCGAGAGCCATCACCTGATCGAGCCGATTATACACCTCGACA
Found at i:686912 original size:21 final size:21
Alignment explanation
Indices: 686869--686918 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
686859 GTTAGTGGAG
*
686869 TTACGTGATGAGGTCAGCGCT
1 TTACGTGATGAGGTCAGCACT
* * *
686890 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGCACT
686911 TTACGTGA
1 TTACGTGA
686919 CGACAATAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGCACT
Found at i:686915 original size:42 final size:41
Alignment explanation
Indices: 686869--686968 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
686859 GTTAGTGGAG
* *
686869 TTACGTGATGAGGTCAGCGCTTTGCGTGATGAGGT-CGGTACT
1 TTACGTGATGAGGT-AGCGCATGGCGTGATGAGGTACGGT-CT
* ** *
686911 TTACGTGACGACAATAGTGCATGGCGTGATGAGGTACGGTCT
1 TTACGTGATGA-GGTAGCGCATGGCGTGATGAGGTACGGTCT
*
686953 TTACGTGGTGAGGTAG
1 TTACGTGATGAGGTAG
686969 TTGTTTTACG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
41 3 0.07
42 38 0.83
43 5 0.11
ACGTcount: A:0.20, C:0.15, G:0.36, T:0.29
Consensus pattern (41 bp):
TTACGTGATGAGGTAGCGCATGGCGTGATGAGGTACGGTCT
Found at i:687347 original size:21 final size:21
Alignment explanation
Indices: 687318--687389 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
687308 ATTCACCTGT
687318 CATCGTTCAAGAGGCCCTTCC
1 CATCGTTCAAGAGGCCCTTCC
* *
687339 CATCATTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCTTCC
*
687360 AATCGTTCAAGAGGCCCCTT-C
1 CATCGTTCAAGAGG-CCCTTCC
687381 CATCGTTCA
1 CATCGTTCA
687390 GGATCCACCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
21 40 0.91
22 4 0.09
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCTTCC
Found at i:688902 original size:20 final size:20
Alignment explanation
Indices: 688853--688906 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
688843 CTACCTTTAA
* *
688853 GAAAATCGAATTTGCAACGC
1 GAAAATCAAATTCGCAACGC
*
688873 G-AAGTCAAATTCGCAACGC
1 GAAAATCAAATTCGCAACGC
688892 GAAAATCAAATTCGC
1 GAAAATCAAATTCGC
688907 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACGC
Found at i:688977 original size:20 final size:20
Alignment explanation
Indices: 688933--688979 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
688923 TTGCGTGTCG
* * *
688933 AATTCGATTTTCGTGTTGCG
1 AATTTGATTTTCGTATTGCA
688953 AATTTGATTTTCGTATTGCA
1 AATTTGATTTTCGTATTGCA
688973 AATTTGA
1 AATTTGA
688980 GTATCGCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (20 bp):
AATTTGATTTTCGTATTGCA
Found at i:691863 original size:75 final size:75
Alignment explanation
Indices: 691713--691921 Score: 276
Period size: 75 Copynumber: 2.8 Consensus size: 75
691703 CAAAGCCAAA
* * * **
691713 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
691778 TTTGGCTCCGAG
64 TTTGGCTCCGAG
*
691790 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
691855 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
691865 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
691922 GTTCAACGGT
Statistics
Matches: 118, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 86 0.73
76 6 0.05
77 26 0.22
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:699671 original size:9 final size:8
Alignment explanation
Indices: 699649--699699 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
699639 TGTTTCAACA
699649 TTTTGGAT
1 TTTTGGAT
699657 ATTTTGGAT
1 -TTTTGGAT
699666 TGTTT-GAT
1 T-TTTGGAT
699674 TTTGTGGAT
1 TTT-TGGAT
*
699683 TGTTGGA-
1 TTTTGGAT
699690 TTTTGGAT
1 TTTTGGAT
699698 TT
1 TT
699700 ATGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:699683 original size:17 final size:17
Alignment explanation
Indices: 699651--699694 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
699641 TTTCAACATT
699651 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
699668 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
699685 TTGGATTTTG
1 TTGGATTTTG
699695 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:700466 original size:73 final size:72
Alignment explanation
Indices: 700300--700504 Score: 223
Period size: 73 Copynumber: 2.7 Consensus size: 72
700290 CAAAGCCAAA
* * * **
700300 AATTCCAGATTGCTCAGAGGGAACTGATTCCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATG
1 AATTCCAGA-TGCTCGGAGGGAACCGATT---CCCCCATAGGAGGAACCGATT--CCCCTAAACA
700365 GTTTGGCTCCGAG
60 GTTTGGCTCCGAG
* *
700378 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCTAAACAGTTTT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCTAAACAGTTTG
*
700443 GTTCCGAG
65 GCTCCGAG
* * *
700451 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCC
1 AATTCCAG-ATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCC
700505 CTGTTCAACG
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
73 60 0.54
74 6 0.05
75 21 0.19
78 24 0.21
79 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (72 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCTAAACAGTTTGG
CTCCGAG
Found at i:702265 original size:20 final size:21
Alignment explanation
Indices: 702240--702290 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
702230 AAATAAAAGC
*
702240 TGTTGCGAAATT-AAAATTCG
1 TGTTGCGAAATTCAAAAATCG
702260 TGTTGCG-AATTCGAAAAATCG
1 TGTTGCGAAATTC-AAAAATCG
*
702281 AGTTGCGAAA
1 TGTTGCGAAA
702291 AGGAAACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 7 0.27
21 13 0.50
22 2 0.08
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (21 bp):
TGTTGCGAAATTCAAAAATCG
Found at i:702359 original size:21 final size:21
Alignment explanation
Indices: 702334--702388 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
702324 CAGAAATCGA
702334 GTTGCGAATTTGAAATGCCGT
1 GTTGCGAATTTGAAATGCCGT
**
702355 GTTGCGAATTTGAAATTTCGT
1 GTTGCGAATTTGAAATGCCGT
*
702376 GTTGCGAACTTGA
1 GTTGCGAATTTGA
702389 CTTTATAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (21 bp):
GTTGCGAATTTGAAATGCCGT
Found at i:704321 original size:16 final size:16
Alignment explanation
Indices: 704297--704336 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
704287 TTTTATAAAG
* *
704297 TTAATATAAAATTATT
1 TTAAAATAAAATAATT
704313 TTAAAATAAAATAATT
1 TTAAAATAAAATAATT
*
704329 TTATAATA
1 TTAAAATA
704337 TTTATTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATAAAATAATT
Found at i:712889 original size:81 final size:81
Alignment explanation
Indices: 712749--712910 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 81
712739 AATGGACGAC
* * *
712749 TCCAGGCATCACAATGAATCAACTGCACAGACAAGCCTCGCAGAAAGAGATTTGGGTCAGAATAC
1 TCCAGGCATCACAATAAATCAACTGCACAGACAAGCCTCGCAGAAAGAGATTCGAGTCAGAATAC
712814 TACAGACGATATTGAG
66 TACAGACGATATTGAG
* *
712830 TCCAGGCATCACAATAAATCAACTGCACAGACAAGCCTCGTAGGAAGAGATTCGAGTCAGAATAC
1 TCCAGGCATCACAATAAATCAACTGCACAGACAAGCCTCGCAGAAAGAGATTCGAGTCAGAATAC
*
712895 TACAGAGGATATTGAG
66 TACAGACGATATTGAG
712911 CTGTTGGGCT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (81 bp):
TCCAGGCATCACAATAAATCAACTGCACAGACAAGCCTCGCAGAAAGAGATTCGAGTCAGAATAC
TACAGACGATATTGAG
Found at i:715096 original size:3 final size:3
Alignment explanation
Indices: 715090--715119 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
715080 AATATTATAG
715090 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
715120 ACCCAATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:722200 original size:13 final size:13
Alignment explanation
Indices: 722178--722215 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
722168 TCCTAATGGG
722178 CAAT-TTTGAAAA
1 CAATGTTTGAAAA
*
722190 CTATGTTTGAAAA
1 CAATGTTTGAAAA
722203 CAATGTTTGAAAA
1 CAATGTTTGAAAA
722216 TTAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:722772 original size:22 final size:23
Alignment explanation
Indices: 722701--722780 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
722691 CGATTCCCTT
722701 AAGGGGGAATCGGTACCTATTCA
1 AAGGGGGAATCGGTACCTATTCA
*
722724 AAGGGGGAATCAGTACCTATTCA
1 AAGGGGGAATCGGTACCTATTCA
* *
722747 AAGGGGGAATCGGTACCCATGC-
1 AAGGGGGAATCGGTACCTATTCA
*
722769 AAGGGGGTATCG
1 AAGGGGGAATCG
722781 ATTTCTAGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
22 11 0.21
23 41 0.79
ACGTcount: A:0.30, C:0.17, G:0.34, T:0.19
Consensus pattern (23 bp):
AAGGGGGAATCGGTACCTATTCA
Found at i:730785 original size:19 final size:20
Alignment explanation
Indices: 730722--730796 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 20
730712 TTGGTGCGGA
* * *
730722 GGGAATCGATCCCCCATGA-
1 GGGAACCGATTCCCCATAAG
730741 GGGAACCGATTCCCCATTGAAG
1 GGGAACCGATTCCCCA-T-AAG
*
730763 GGGAACCGATTCCCCA-CAG
1 GGGAACCGATTCCCCATAAG
* *
730782 GGGAATCGATACCCC
1 GGGAACCGATTCCCC
730797 CCTGGGGTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 29 0.62
20 1 0.02
21 1 0.02
22 16 0.34
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.15
Consensus pattern (20 bp):
GGGAACCGATTCCCCATAAG
Found at i:737408 original size:116 final size:116
Alignment explanation
Indices: 737189--737409 Score: 252
Period size: 116 Copynumber: 1.9 Consensus size: 116
737179 TTTTCAATAC
* *
737189 TTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCATTTTGATTTTGAAAATCC
1 TTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTTTGATTTTCAAAATCC
* * * **
737254 ATTTTCATTTCTAGAAGAAGTTTGTTTAATTTGAAAATTTCTTTTCAAAGT
66 ATTTTCATTTCTAAAAGAAGATTATTTAAGCTGAAAATTTCTTTTCAAAGT
* * * *
737305 TTTCAGATTTCGTTTTTGAAAGCTCTAACTCCTT-TCTCAACATTTCATTTTGATTTTCTAAATC
1 TTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACATTTCATTTTGATTTTCAAAATC
** *
737369 TGTTTT-AGCTTTC-AAAAGAAGATTATTTTAGCT-ATAAATTT
65 CATTTTCA--TTTCTAAAAGAAGATTATTTAAGCTGA-AAATTT
737410 AGAAATCAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
115 3 0.03
116 80 0.92
117 4 0.05
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (116 bp):
TTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTTTGATTTTCAAAATCC
ATTTTCATTTCTAAAAGAAGATTATTTAAGCTGAAAATTTCTTTTCAAAGT
Found at i:738821 original size:16 final size:16
Alignment explanation
Indices: 738800--738839 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
738790 GTAAGGATTG
738800 AATTTGAACTTTGAAA
1 AATTTGAACTTTGAAA
738816 AATTTGAACTTTGAAA
1 AATTTGAACTTTGAAA
*
738832 GATTTGAA
1 AATTTGAA
738840 GTAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (16 bp):
AATTTGAACTTTGAAA
Found at i:740454 original size:6 final size:6
Alignment explanation
Indices: 740443--740485 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
740433 TAGGAATAAC
740443 CACCTT CACCTT CACCTT CACCTT CACCTT CACCTT CACCTT C
1 CACCTT CACCTT CACCTT CACCTT CACCTT CACCTT CACCTT C
740486 TCTTGGCTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.16, C:0.51, G:0.00, T:0.33
Consensus pattern (6 bp):
CACCTT
Done.