Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008570.1 Hibiscus syriacus cultivar Beakdansim tig00111495_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: 912507
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 5 of 5
Found at i:695446 original size:14 final size:14
Alignment explanation
Indices: 695427--695455 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
695417 GCATTATAAG
695427 ACTATGCCATCATA
1 ACTATGCCATCATA
695441 ACTATGCCATCATA
1 ACTATGCCATCATA
695455 A
1 A
695456 TTCATGTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (14 bp):
ACTATGCCATCATA
Found at i:697173 original size:32 final size:32
Alignment explanation
Indices: 697132--697195 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
697122 CAATACTTCC
697132 CTGTTCCTCCAGCTCGACATAATCCACCACCT
1 CTGTTCCTCCAGCTCGACATAATCCACCACCT
*
697164 CTGTTCCTCCAGCTCGACATATTCCACCACCT
1 CTGTTCCTCCAGCTCGACATAATCCACCACCT
697196 TCAATAAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.44, G:0.09, T:0.27
Consensus pattern (32 bp):
CTGTTCCTCCAGCTCGACATAATCCACCACCT
Found at i:700786 original size:39 final size:39
Alignment explanation
Indices: 700743--700825 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 39
700733 CTCATGATTT
*
700743 TATCAAA-ACAATGATAAACAATATCATACATAATAGTCA
1 TATCAAAGAC-ATGATAAAAAATATCATACATAATAGTCA
* *
700782 TATCAAAGGCATGATAAAAAATATCATGCATAATAGTCA
1 TATCAAAGACATGATAAAAAATATCATACATAATAGTCA
700821 TATCA
1 TATCA
700826 TATTCTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 39 0.98
40 1 0.03
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (39 bp):
TATCAAAGACATGATAAAAAATATCATACATAATAGTCA
Found at i:700894 original size:12 final size:12
Alignment explanation
Indices: 700855--700915 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
700845 ACAATACAAA
700855 ACTTTCATATCTC
1 ACTTTCATAT-TC
* *
700868 ATTTTTCATCTTTC
1 A-CTTTCAT-ATTC
700882 ACTTTCATATTC
1 ACTTTCATATTC
*
700894 ACTTTCAAATTTC
1 ACTTTCATA-TTC
*
700907 ATTTTCATA
1 ACTTTCATA
700916 ATATATACTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
12 11 0.29
13 17 0.45
14 9 0.24
15 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (12 bp):
ACTTTCATATTC
Found at i:701325 original size:12 final size:12
Alignment explanation
Indices: 701308--701343 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
701298 TAAATAGTAA
701308 TGAACAGTACCG
1 TGAACAGTACCG
* *
701320 TGAACAATACCA
1 TGAACAGTACCG
701332 TGAACAGTACCG
1 TGAACAGTACCG
701344 ATTCTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:701997 original size:32 final size:32
Alignment explanation
Indices: 701922--702051 Score: 203
Period size: 32 Copynumber: 4.1 Consensus size: 32
701912 GCTCGTATAA
*
701922 TAAT-CTGTCCATATGTCCC-GAAGAACATAGG
1 TAATACTGTCCATATGTCCCAAAAG-ACATAGG
*
701953 TAA-ACTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
701984 TAATACTGTCCATATGTCCCAAAAGACATAGG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
*
702016 TAATACTATCCATATGTCCCAAAAGACATAGG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
702048 TAAT
1 TAAT
702052 CCCTCGACTC
Statistics
Matches: 93, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
31 28 0.30
32 65 0.70
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (32 bp):
TAATACTGTCCATATGTCCCAAAAGACATAGG
Found at i:705329 original size:20 final size:21
Alignment explanation
Indices: 705304--705351 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
705294 AAAAATAGTC
*
705304 AAATTCCA-CATTCTAACACT
1 AAATTCCATCACTCTAACACT
*
705324 AAATT-CATCACTCTAACATT
1 AAATTCCATCACTCTAACACT
*
705344 AATTTCCA
1 AAATTCCA
705352 GCATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATTCCATCACTCTAACACT
Found at i:714027 original size:13 final size:13
Alignment explanation
Indices: 714009--714034 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
713999 GTTGTTATAT
714009 TTTTTTATAAATA
1 TTTTTTATAAATA
714022 TTTTTTATAAATA
1 TTTTTTATAAATA
714035 ATATTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTATAAATA
Found at i:714044 original size:17 final size:17
Alignment explanation
Indices: 714018--714089 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
714008 TTTTTTTATA
714018 AATATT-TTTTATAAAT
1 AATATTATTTTATAAAT
*
714034 AATATTATTTTTTATAA-
1 AATATTATTTTATA-AAT
* *
714051 AATAATATTTATATAATT
1 AATATTATTT-TATAAAT
*
714069 ATTATT-TTTT-TAAAT
1 AATATTATTTTATAAAT
714084 -ATATTA
1 AATATTA
714090 ATTATTTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
14 4 0.09
15 4 0.09
16 7 0.16
17 19 0.44
18 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTATTTTATAAAT
Found at i:714044 original size:19 final size:20
Alignment explanation
Indices: 714020--714059 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
714010 TTTTTATAAA
714020 TATTTTTTAT-AAATAATAT
1 TATTTTTTATAAAATAATAT
714039 TATTTTTTATAAAATAATAT
1 TATTTTTTATAAAATAATAT
714059 T
1 T
714060 TATATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTTTATAAAATAATAT
Found at i:714050 original size:32 final size:31
Alignment explanation
Indices: 714009--714103 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 31
713999 GTTGTTATAT
*
714009 TTTTTTATAAATATTTTTTATA-AATAATATTA
1 TTTTTTATAAATATTATTTATATAAT--TATTA
*
714041 TTTTTTATAAAATAATATTTATATAATTATTA
1 TTTTTTAT-AAATATTATTTATATAATTATTA
* *
714073 TTTTTT-TAAATA-TATTAAT-TATTTATTA
1 TTTTTTATAAATATTATTTATATAATTATTA
714101 TTT
1 TTT
714104 GTGCTAATTA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
28 11 0.19
29 6 0.11
30 5 0.09
31 1 0.02
32 19 0.33
33 12 0.21
34 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTTTATAAATATTATTTATATAATTATTA
Found at i:714218 original size:28 final size:27
Alignment explanation
Indices: 714187--714245 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
714177 CTCAAGACAT
714187 TTTAGTGAT-ATGGTAATATTTTTTTTAA
1 TTTA-TGATAATGGTAATA-TTTTTTTAA
* * *
714215 TTTATGTTAATGTTTATATTTTTTTAA
1 TTTATGATAATGGTAATATTTTTTTAA
714242 TTTA
1 TTTA
714246 AATTTATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (27 bp):
TTTATGATAATGGTAATATTTTTTTAA
Found at i:715518 original size:24 final size:24
Alignment explanation
Indices: 715473--715522 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
715463 ATAAAGAACC
*
715473 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
715497 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
715521 AA
1 AA
715523 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:718824 original size:26 final size:25
Alignment explanation
Indices: 718788--718863 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 25
718778 ATGAATGAAG
718788 GAAAGAGAAAAAGTAAAAGTAAAAAT
1 GAAAGAGAAAAAG-AAAAGTAAAAAT
*
718814 GAAAGAGAAAAA-AAAATTAATAAA-
1 GAAAGAGAAAAAGAAAAGTAA-AAAT
718838 GAAAGAG-AAAAGAAAAAGTTAAAAAT
1 GAAAGAGAAAAAG-AAAAG-TAAAAAT
718864 TTAAGAGGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
23 4 0.09
24 14 0.33
25 10 0.23
26 15 0.35
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (25 bp):
GAAAGAGAAAAAGAAAAGTAAAAAT
Found at i:718829 original size:30 final size:28
Alignment explanation
Indices: 718757--718829 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 28
718747 GGCTATGGAG
**
718757 AGAGAATAAAAAAAGAAAAAGATGAATGA
1 AGAGAA-AAAAAAAGAAAAAGAAAAATGA
*
718786 AG-GAAAGAGAAAAAGTAAAAGTAAAAATGAA
1 AGAGAAA-A-AAAAAGAAAAAG-AAAAATG-A
718817 AGAGAAAAAAAAA
1 AGAGAAAAAAAAA
718830 TTAATAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
27 1 0.03
28 4 0.11
29 13 0.36
30 10 0.28
31 4 0.11
32 4 0.11
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (28 bp):
AGAGAAAAAAAAAGAAAAAGAAAAATGA
Found at i:718870 original size:26 final size:26
Alignment explanation
Indices: 718788--718863 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 26
718778 ATGAATGAAG
*
718788 GAAAGAGAAAAAGTAAAAG-TAAAAAT
1 GAAAGAG-AAAAGAAAAAGTTAAAAAT
718814 GAAAGAGAAAA-AAAAA-TTAATAAA-
1 GAAAGAGAAAAGAAAAAGTTAA-AAAT
718838 GAAAGAGAAAAGAAAAAGTTAAAAAT
1 GAAAGAGAAAAGAAAAAGTTAAAAAT
718864 TTAAGAGGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
24 18 0.41
25 15 0.34
26 11 0.25
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (26 bp):
GAAAGAGAAAAGAAAAAGTTAAAAAT
Found at i:720937 original size:23 final size:23
Alignment explanation
Indices: 720911--720955 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
720901 CACCACAGCT
*
720911 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
720934 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
720956 ATATAATGAT
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:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:721193 original size:149 final size:149
Alignment explanation
Indices: 720923--721237 Score: 596
Period size: 149 Copynumber: 2.1 Consensus size: 149
720913 TATAATTGCA
*
720923 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
720987 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACTTGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
721052 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
721072 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
721137 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
721202 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
721221 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
721238 CCCTCGACTC
Statistics
Matches: 163, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 162 0.99
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:722140 original size:18 final size:18
Alignment explanation
Indices: 722119--722153 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
722109 TCCCATCTAG
722119 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
722137 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
722154 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:722758 original size:21 final size:21
Alignment explanation
Indices: 722734--722778 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
722724 TGTTGTTCGT
* *
722734 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
722755 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
722776 TTG
1 TTG
722779 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:726311 original size:149 final size:149
Alignment explanation
Indices: 726041--726355 Score: 596
Period size: 149 Copynumber: 2.1 Consensus size: 149
726031 TATAGTTGCA
726041 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
726105 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATAATATATGTGTCTTTCCAGACTTCACACATGTT
726170 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
*
726190 CCGAAGGACCGCGTAGAATTGCACTGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
726255 TCCTTAAGAATCATATACATATGCTAGGGATAATATATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATAATATATGTGTCTTTCCAGACTTCACACATGTTC
726320 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
726339 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
726356 CCCTCGACTC
Statistics
Matches: 163, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 162 0.99
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATAATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:727262 original size:18 final size:18
Alignment explanation
Indices: 727241--727275 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
727231 TCCCATCTAG
727241 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
727259 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
727276 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:727878 original size:21 final size:21
Alignment explanation
Indices: 727854--727898 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
727844 TGTTGTTCGT
* *
727854 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
727875 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
727896 TTG
1 TTG
727899 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:734091 original size:24 final size:24
Alignment explanation
Indices: 734046--734095 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
734036 ATAAAGAACC
*
734046 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
734070 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
734094 AA
1 AA
734096 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:735511 original size:17 final size:17
Alignment explanation
Indices: 735489--735524 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
735479 GCTTGATATA
735489 ATTAGAA-TATTATATTT
1 ATTAGAATTA-TATATTT
735506 ATTAGAATTATATATTT
1 ATTAGAATTATATATTT
735523 AT
1 AT
735525 GTTTCAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTAGAATTATATATTT
Found at i:736134 original size:42 final size:41
Alignment explanation
Indices: 736082--736173 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
736072 GATGCCACAG
* *
736082 GGGTACATGCCCAGTCCACCAGTTCAGATGCCATTTCCGCAA
1 GGGTACATGCCAAGTCCACCAGTTCAGATGCCATCTCCGC-A
* * *
736124 GGGTATATGCCAAGTCCACCAGTTCATATGTCATCTCCGCA
1 GGGTACATGCCAAGTCCACCAGTTCAGATGCCATCTCCGCA
736165 GGGTTACAT
1 GGG-TACAT
736174 TCCTAGCTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 4 0.09
42 39 0.91
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (41 bp):
GGGTACATGCCAAGTCCACCAGTTCAGATGCCATCTCCGCA
Found at i:736152 original size:21 final size:21
Alignment explanation
Indices: 736088--736153 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
736078 ACAGGGGTAC
* *
736088 ATGCCCAGTCCACCAGTTCAG
1 ATGCCAAGTCCACCAGTTCAT
** * * *
736109 ATGCCATTTCCGCAAGGGT-AT
1 ATGCCAAGTCCACCA-GTTCAT
736130 ATGCCAAGTCCACCAGTTCAT
1 ATGCCAAGTCCACCAGTTCAT
736151 ATG
1 ATG
736154 TCATCTCCGC
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (21 bp):
ATGCCAAGTCCACCAGTTCAT
Found at i:743645 original size:14 final size:15
Alignment explanation
Indices: 743628--743657 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
743618 TTCTAAATAT
743628 TTTA-ATAAAAATTA
1 TTTATATAAAAATTA
743642 TTTATATAAAAATTA
1 TTTATATAAAAATTA
743657 T
1 T
743658 ATCTGTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTATATAAAAATTA
Found at i:746595 original size:2 final size:2
Alignment explanation
Indices: 746588--746616 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
746578 AATATGAATA
746588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
746617 AGAAAATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:757304 original size:41 final size:41
Alignment explanation
Indices: 757163--757322 Score: 121
Period size: 41 Copynumber: 3.9 Consensus size: 41
757153 AAATGGTAAA
* *
757163 TTTAGCGGCATTTTTATAAAAACGCCGCAATATG-GTTAAT-C
1 TTTAGCGGCATTTTTATACAAACGCCGCAATA-GAG-TAGTAC
* * * ** * * *
757204 TATAGTGGCGTTTGGAGTACAAACGCCACAACAGAGAAGTA-
1 TTTAGCGGCATTTTTA-TACAAACGCCGCAATAGAGTAGTAC
* * * *
757245 TTGTAGCAGCGTTGTTATACAAATGCCGCAATAGAGTAGTAC
1 TT-TAGCGGCATTTTTATACAAACGCCGCAATAGAGTAGTAC
*
757287 TTTAGCGGCATTTTTATACAAACACCGCAAT-GAGTA
1 TTTAGCGGCATTTTTATACAAACGCCGCAATAGAGTA
757323 AAATGTATTT
Statistics
Matches: 89, Mismatches: 25, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
40 5 0.06
41 59 0.66
42 25 0.28
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCATTTTTATACAAACGCCGCAATAGAGTAGTAC
Found at i:757493 original size:41 final size:41
Alignment explanation
Indices: 757430--757528 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
757420 AAATGCCGTA
*
757430 AAAGACTCAG-ACTTTAGCGGCGTTTGTATACAAACACCACT
1 AAAGACTC-GTACTTTAGCGGCGTTTGTATAAAAACACCACT
* * * * * *
757471 ATAGACTCGTATTTTAGTGGCGTTTTTATAAAAACGCCGCT
1 AAAGACTCGTACTTTAGCGGCGTTTGTATAAAAACACCACT
757512 AAAGACTCGTACTTTAG
1 AAAGACTCGTACTTTAG
757529 GAAACACATC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
40 1 0.02
41 47 0.98
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (41 bp):
AAAGACTCGTACTTTAGCGGCGTTTGTATAAAAACACCACT
Found at i:759746 original size:22 final size:22
Alignment explanation
Indices: 759721--760130 Score: 578
Period size: 22 Copynumber: 18.8 Consensus size: 22
759711 CTATTTTAAA
759721 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
759743 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
759765 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
759787 ATTTATTTTAAAATATGGA--A
1 ATTTATTTTAAAATATGGATTG
*
759807 ATTTATTTTAAAATATGGA--A
1 ATTTATTTTAAAATATGGATTG
**
759827 ATTTTATTTTAAAATATTAATTG
1 A-TTTATTTTAAAATATGGATTG
759850 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
759872 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
759894 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
*
759916 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
759938 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
759960 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
759982 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
760004 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
760026 ATTTATTTT-AAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
760047 ATTTATTTTTAAAATATGAAAAA
1 ATTTA-TTTTAAAATATGGATTG
*
760070 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
760092 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
760114 ATTTATTTTAAAATATG
1 ATTTATTTTAAAATATG
760131 AATTTTATTA
Statistics
Matches: 351, Mismatches: 32, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
20 22 0.06
21 30 0.09
22 286 0.81
23 13 0.04
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:760212 original size:31 final size:31
Alignment explanation
Indices: 760155--760213 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
760145 AGTTGTATGG
*
760155 ATTATTTAAATTCCAGTATTATAAAACTAAA
1 ATTATTTAAATTCCAGTATTACAAAACTAAA
* *
760186 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTCCAGTATTACAAAACT
760214 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATTCCAGTATTACAAAACTAAA
Found at i:772314 original size:32 final size:31
Alignment explanation
Indices: 772262--772324 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
772252 CCTTAATATT
* *
772262 TTCTTCTTATTTTTTACTTTTTATCTCTCATA
1 TTCTTCATATTCTTTACTTTTTATCTC-CATA
* *
772294 TTCTTCATATTCTTTCCTTTTTTTCTCCATA
1 TTCTTCATATTCTTTACTTTTTATCTCCATA
772325 GCCGAATCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.63
Consensus pattern (31 bp):
TTCTTCATATTCTTTACTTTTTATCTCCATA
Found at i:773823 original size:11 final size:11
Alignment explanation
Indices: 773807--773838 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
773797 ATTGCATGGA
773807 ATTTAGTTTAT
1 ATTTAGTTTAT
773818 ATTTAGTTTAT
1 ATTTAGTTTAT
773829 ATTTAGTTTA
1 ATTTAGTTTA
773839 GTTCTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (11 bp):
ATTTAGTTTAT
Found at i:806152 original size:21 final size:21
Alignment explanation
Indices: 806124--806189 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
806114 AGCCGAAGCT
806124 GAAGCGAGAGAAGTAGAGAGA
1 GAAGCGAGAGAAGTAGAGAGA
* *
806145 GTAGCGAGAGAAGTACAGAGA
1 GAAGCGAGAGAAGTAGAGAGA
* * *
806166 GAAGTGATAGAAGCAGAGAGA
1 GAAGCGAGAGAAGTAGAGAGA
806187 GAA
1 GAA
806190 ACATCTTTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.47, C:0.06, G:0.39, T:0.08
Consensus pattern (21 bp):
GAAGCGAGAGAAGTAGAGAGA
Found at i:806802 original size:44 final size:44
Alignment explanation
Indices: 806752--806848 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
806742 CAAACCTGTT
* *
806752 GCGGCG-TTT-GTATACTAAAACGCCGCTATATAACCTGACCTTTA
1 GCGGCGTTTTAGTATAC--AAACACCGCTACATAACCTGACCTTTA
* * *
806796 GTGGCGTTTTAGTATACAAACACCGCTACATAACTTGACTTTTA
1 GCGGCGTTTTAGTATACAAACACCGCTACATAACCTGACCTTTA
806840 GCGGCGTTT
1 GCGGCGTTT
806849 CATAGTAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 36 0.80
45 3 0.07
46 6 0.13
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (44 bp):
GCGGCGTTTTAGTATACAAACACCGCTACATAACCTGACCTTTA
Found at i:808752 original size:17 final size:16
Alignment explanation
Indices: 808725--808756 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
808715 GATATCATCA
808725 ACATAAACAAGAATAT
1 ACATAAACAAGAATAT
808741 ACATATAACAAGAATA
1 ACATA-AACAAGAATA
808757 GCTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (16 bp):
ACATAAACAAGAATAT
Found at i:809132 original size:11 final size:11
Alignment explanation
Indices: 809116--809143 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
809106 TTCATTCACT
809116 TAACAGCCTAC
1 TAACAGCCTAC
809127 TAACAGCCTAC
1 TAACAGCCTAC
809138 TAACAG
1 TAACAG
809144 TCTAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.18
Consensus pattern (11 bp):
TAACAGCCTAC
Found at i:828137 original size:25 final size:25
Alignment explanation
Indices: 828095--828166 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
828085 CATAACAGAA
*
828095 AATTTTCTTCA-TAAAGAATGTCGTT
1 AATTTTCTT-ATTAGAGAATGTCGTT
828120 AATTTTCTTATTAGAGAATGTCGTT
1 AATTTTCTTATTAGAGAATGTCGTT
**
828145 AACCTTCTTATTAGAGAATGTC
1 AATTTTCTTATTAGAGAATGTC
828167 TTAGCATTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 1 0.02
25 42 0.98
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (25 bp):
AATTTTCTTATTAGAGAATGTCGTT
Found at i:828510 original size:11 final size:11
Alignment explanation
Indices: 828482--828513 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
828472 TTCATACACT
*
828482 TAACAGCCTAC
1 TAACAGTCTAC
828493 TAACAGTCTAC
1 TAACAGTCTAC
828504 TAACAGTCTA
1 TAACAGTCTA
828514 ATACCTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.25
Consensus pattern (11 bp):
TAACAGTCTAC
Found at i:829278 original size:12 final size:12
Alignment explanation
Indices: 829261--829285 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
829251 AATAGCTCCT
829261 ATGATGATGAAA
1 ATGATGATGAAA
829273 ATGATGATGAAA
1 ATGATGATGAAA
829285 A
1 A
829286 GGAGAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
ATGATGATGAAA
Found at i:832956 original size:28 final size:31
Alignment explanation
Indices: 832882--833003 Score: 108
Period size: 32 Copynumber: 4.0 Consensus size: 31
832872 AACTAATTAA
* * *
832882 ATATATTTTATTTTTATTTTAA-TATGAAAAAT
1 ATATATTTTATTCTTATCTTAACT-T-CAAAAT
* *
832914 ATATATTTTAATCTTATCTTCAC-T-AAAA-
1 ATATATTTTATTCTTATCTTAACTTCAAAAT
* *
832942 ATATATCTTATTCTTATTTTAACTTCAAAAT
1 ATATATTTTATTCTTATCTTAACTTCAAAAT
* *
832973 ATATATTTTATACTTATCTTTAACTTTAAAA
1 ATATATTTTATTCTTATC-TTAACTTCAAAA
833004 AAATGTTCTT
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
28 19 0.26
29 5 0.07
30 4 0.05
31 16 0.22
32 29 0.40
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.52
Consensus pattern (31 bp):
ATATATTTTATTCTTATCTTAACTTCAAAAT
Found at i:832991 original size:59 final size:60
Alignment explanation
Indices: 832880--832992 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
832870 TTAACTAATT
* *
832880 AAATATATTTTATTTTTATTTTAATATGAAAAATATATATTTTAATCTTATCTTCACTAA
1 AAATATATCTTATTCTTATTTTAATATGAAAAATATATATTTTAATCTTATCTTCACTAA
*
832940 AAATATATCTTATTCTTATTTTAACT-T-CAAAATATATATTTT-ATACTTATCTT
1 AAATATATCTTATTCTTATTTTAA-TATGAAAAATATATATTTTAAT-CTTATCTT
832993 TAACTTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 2 0.04
59 22 0.46
60 23 0.48
61 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (60 bp):
AAATATATCTTATTCTTATTTTAATATGAAAAATATATATTTTAATCTTATCTTCACTAA
Found at i:839626 original size:65 final size:65
Alignment explanation
Indices: 839545--839674 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
839535 ATGTTTAAGA
*
839545 TTGTTTAATTTAGTCATTAACCGTTGATAATGATTATGATATGATCCTAAACTATGCTAAATTAT
1 TTGTTTAATTTAGTCATTAACAGTTGATAATGATTATGATATGATCCTAAACTATGCTAAATTAT
***
839610 TTGTTTAATTTAGTCATTGGTAGTTGATAATGATTATGATATGATCCTAAACTATGCTAAATTAT
1 TTGTTTAATTTAGTCATTAACAGTTGATAATGATTATGATATGATCCTAAACTATGCTAAATTAT
839675 GTAATTAGTC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (65 bp):
TTGTTTAATTTAGTCATTAACAGTTGATAATGATTATGATATGATCCTAAACTATGCTAAATTAT
Found at i:842529 original size:39 final size:39
Alignment explanation
Indices: 842467--842623 Score: 224
Period size: 39 Copynumber: 4.0 Consensus size: 39
842457 CTTGTAAACC
* * *
842467 CAGTAAGGGCTTACCCTGTGCACAAAGCAGAGGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
** * *
842506 CAGTAAGGTTTTATCCTGAGCACAAAGTCGAGGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
* * *
842545 CAGTAAGGACTTACCCTTAGTACAAAGCCGAGGAGCCTA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
842584 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
842623 C
1 C
842624 GAAAAGCGGT
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 102 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.17
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
Found at i:843471 original size:19 final size:19
Alignment explanation
Indices: 843431--843473 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
843421 CTGAGTCGGA
*
843431 TCGGG-TCGGGCAAGTGGG
1 TCGGGTTCGGGCAAGTAGG
*
843449 TCGGGTTCGGGCAAGTAGT
1 TCGGGTTCGGGCAAGTAGG
843468 TCGGGT
1 TCGGGT
843474 CAATGAGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.12, C:0.16, G:0.49, T:0.23
Consensus pattern (19 bp):
TCGGGTTCGGGCAAGTAGG
Found at i:851523 original size:20 final size:20
Alignment explanation
Indices: 851498--851548 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
851488 AAACTAAGAT
*
851498 AGTATCGATATTGACTTACC
1 AGTATCGATACTGACTTACC
* **
851518 AGTATCAATACTGACTTAGG
1 AGTATCGATACTGACTTACC
851538 AGTATCGATAC
1 AGTATCGATAC
851549 CCCCATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTGACTTACC
Found at i:853156 original size:20 final size:20
Alignment explanation
Indices: 853131--853198 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
853121 CCTCTCAGTG
853131 TCAATACTGACCCAGAAGTA
1 TCAATACTGACCCAGAAGTA
* * *** *
853151 TCAATATTGATCCTCTAGTG
1 TCAATACTGACCCAGAAGTA
*
853171 TCAATATTGACCCAGAAGTA
1 TCAATACTGACCCAGAAGTA
853191 TCAATACT
1 TCAATACT
853199 CCACTTTTGA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.29
Consensus pattern (20 bp):
TCAATACTGACCCAGAAGTA
Found at i:853182 original size:40 final size:41
Alignment explanation
Indices: 853107--853196 Score: 155
Period size: 40 Copynumber: 2.2 Consensus size: 41
853097 CAGGGTAGTG
*
853107 GTATCGATATTGATCCTCTCAGTGTCAATACTGACCCAGAA
1 GTATCAATATTGATCCTCTCAGTGTCAATACTGACCCAGAA
*
853148 GTATCAATATTGATCCTCT-AGTGTCAATATTGACCCAGAA
1 GTATCAATATTGATCCTCTCAGTGTCAATACTGACCCAGAA
853188 GTATCAATA
1 GTATCAATA
853197 CTCCACTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 29 0.62
41 18 0.38
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (41 bp):
GTATCAATATTGATCCTCTCAGTGTCAATACTGACCCAGAA
Found at i:856107 original size:2 final size:2
Alignment explanation
Indices: 856100--856128 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
856090 AGCTTTCTTT
856100 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 T
856129 GTTTGTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:858632 original size:27 final size:27
Alignment explanation
Indices: 858594--858672 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
858584 TTCTTTCTGG
858594 TTTTTAGGATAATTTCACGAGAATACA
1 TTTTTAGGATAATTTCACGAGAATACA
*
858621 TTTTTAGGATAATTT--C-----T-GA
1 TTTTTAGGATAATTTCACGAGAATACA
858640 TTTTTAGGATAATTTCACGAGAATACA
1 TTTTTAGGATAATTTCACGAGAATACA
858667 TTTTTA
1 TTTTTA
858673 ACATACAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
19 16 0.38
20 1 0.02
21 1 0.02
25 1 0.02
26 1 0.02
27 22 0.52
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (27 bp):
TTTTTAGGATAATTTCACGAGAATACA
Found at i:859988 original size:3 final size:3
Alignment explanation
Indices: 859973--860055 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
859963 TAATTTTGGA
*
859973 TCG TCG TCA TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
*
860021 TCG TCG TCG TCG TCG TCG TCG TCA TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
860056 ATCATCATCA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.02, C:0.34, G:0.30, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:861257 original size:26 final size:25
Alignment explanation
Indices: 861228--861299 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 25
861218 TTAAATTCAT
861228 AATATTTTATATATATTAACTTAAAA
1 AATATTTT-TATATATTAACTTAAAA
* **
861254 AATATTTTT-TATGTTAACTTATTA
1 AATATTTTTATATATTAACTTAAAA
861278 AATATATTTTAT-TATTAACTTA
1 AATAT-TTTTATATATTAACTTA
861300 TTTTAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 17 0.43
25 14 0.35
26 9 0.22
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (25 bp):
AATATTTTTATATATTAACTTAAAA
Found at i:861278 original size:27 final size:26
Alignment explanation
Indices: 861251--861317 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
861241 TATTAACTTA
861251 AAAAATATTTT-TTATGTTAACTTA-TT
1 AAAAATATTTTATTA--TTAACTTATTT
*
861277 AAATATATTTTATTATTAACTTATTTT
1 AAAAATATTTTATTATTAACTTA-TTT
861304 AAAAATATTTTATT
1 AAAAATATTTTATT
861318 TTTTATTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 8 0.22
26 10 0.28
27 18 0.50
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (26 bp):
AAAAATATTTTATTATTAACTTATTT
Found at i:861303 original size:16 final size:17
Alignment explanation
Indices: 861272--861304 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
861262 TTATGTTAAC
861272 TTATTAAATATATTTTA
1 TTATTAAATATATTTTA
*
861289 TTATTAACT-TATTTTA
1 TTATTAAATATATTTTA
861305 AAAATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTAAATATATTTTA
Found at i:861515 original size:31 final size:31
Alignment explanation
Indices: 861466--861526 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
861456 CCACATCTTA
*
861466 ATTAAATAAAAATGAAAGT-GATCATATATTG
1 ATTAAATAAAAATAAAAGTAGA-CATATATTG
861497 ATTAAAT-AAAATCAAAAGTAGACATATATT
1 ATTAAATAAAAAT-AAAAGTAGACATATATT
861527 ATGTTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 5 0.19
31 20 0.74
32 2 0.07
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (31 bp):
ATTAAATAAAAATAAAAGTAGACATATATTG
Found at i:862772 original size:6 final size:6
Alignment explanation
Indices: 862761--862787 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
862751 TTATTTGCAA
862761 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
862788 ACGTTCGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:862910 original size:38 final size:40
Alignment explanation
Indices: 862866--862959 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 40
862856 AACAAATGAT
862866 AAATAAATATTAAAT-AAATG-AAAGGGAAAAA-GAA-AAAA
1 AAATAAA-A-TAAATAAAATGAAAAGGGAAAAATGAAGAAAA
862904 AAATAAAATAAATCAAAATGAAAAAAGGGAAAAATGAAGAAAA
1 AAATAAAATAAAT-AAAATG--AAAAGGGAAAAATGAAGAAAA
862947 AAATAAAAATAAA
1 AAAT-AAAATAAA
862960 AATAGATCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
36 5 0.10
37 1 0.02
38 12 0.25
41 11 0.23
42 3 0.06
43 8 0.17
44 8 0.17
ACGTcount: A:0.73, C:0.01, G:0.12, T:0.14
Consensus pattern (40 bp):
AAATAAAATAAATAAAATGAAAAGGGAAAAATGAAGAAAA
Found at i:863052 original size:1 final size:1
Alignment explanation
Indices: 863037--863106 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
863027 GAAATTAAGT
* * * * * * * * * *
863037 AAAAAATAAATAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAAATAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
863102 AAAAA
1 AAAAA
863107 TAGAATAAAA
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (1 bp):
A
Found at i:863058 original size:7 final size:7
Alignment explanation
Indices: 863044--863135 Score: 102
Period size: 7 Copynumber: 13.3 Consensus size: 7
863034 AGTAAAAAAT
863044 AAAT-AA
1 AAATAAA
863050 AAATAAA
1 AAATAAA
863057 AAATAAA
1 AAATAAA
863064 AAATAAA
1 AAATAAA
863071 AAATAAA
1 AAATAAA
863078 AAATAAA
1 AAATAAA
863085 AAAT-AA
1 AAATAAA
*
863091 AAA-AAT
1 AAATAAA
863097 AAATAAA
1 AAATAAA
863104 AAATAGAA
1 AAATA-AA
*
863112 TAAA-ATA
1 -AAATAAA
*
863119 GAATAAA
1 AAATAAA
863126 AATATAAA
1 AA-ATAAA
863134 AA
1 AA
863136 GGTTTAAATT
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
6 15 0.21
7 45 0.62
8 10 0.14
9 3 0.04
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:868244 original size:124 final size:125
Alignment explanation
Indices: 868010--868258 Score: 482
Period size: 124 Copynumber: 2.0 Consensus size: 125
868000 GGGTAAAATA
868010 TTGTTGAGAGTATAAAGGAGTCAAAAAATAGATGTGAAGAAAGAATTTGCAAACAATTGTAATCA
1 TTGTTGAGAGTATAAAGGAGTCAAAAAATAGATGTGAAGAAAGAATTTGCAAACAATTGTAATCA
868075 AAATACCAGATTGAGTAAAATTCAAAGTTAAGGAATTAAATAGAGAGAGAAAAAGAGTAT
66 AAATACCAGATTGAGTAAAATTCAAAGTTAAGGAATTAAATAGAGAGAGAAAAAGAGTAT
*
868135 TTGTTGAGAGTATAAAGGAGTCAAAAAATTGATGTGAAGAAAGAATTTGCAAACAATT-TAATCA
1 TTGTTGAGAGTATAAAGGAGTCAAAAAATAGATGTGAAGAAAGAATTTGCAAACAATTGTAATCA
868199 AAATACCAGATTGAGTAAAATTCAAAGTTAAGGAATTAAATAGAGAGAGAAAAAGAGTAT
66 AAATACCAGATTGAGTAAAATTCAAAGTTAAGGAATTAAATAGAGAGAGAAAAAGAGTAT
868259 ATTTTTAATA
Statistics
Matches: 123, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
124 66 0.54
125 57 0.46
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.24
Consensus pattern (125 bp):
TTGTTGAGAGTATAAAGGAGTCAAAAAATAGATGTGAAGAAAGAATTTGCAAACAATTGTAATCA
AAATACCAGATTGAGTAAAATTCAAAGTTAAGGAATTAAATAGAGAGAGAAAAAGAGTAT
Found at i:868521 original size:27 final size:27
Alignment explanation
Indices: 868453--868522 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
868443 TTGAATGCAC
**
868453 ATATGTACTCCATAATGGTTTAGGAGT
1 ATATGTACTCCACGATGGTTTAGGAGT
868480 ATATGTACTCCACGATGGTTTAGGAGT
1 ATATGTACTCCACGATGGTTTAGGAGT
*
868507 ATATGTACTCAACGAT
1 ATATGTACTCCACGAT
868523 TGACTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (27 bp):
ATATGTACTCCACGATGGTTTAGGAGT
Found at i:875154 original size:20 final size:21
Alignment explanation
Indices: 875108--875168 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
875098 TTCCCCTGTG
875108 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
875131 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
875151 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
875169 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:881661 original size:18 final size:18
Alignment explanation
Indices: 881638--881672 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
881628 AGCAAAAGAC
*
881638 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
881656 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
881673 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:881868 original size:20 final size:20
Alignment explanation
Indices: 881843--882028 Score: 215
Period size: 20 Copynumber: 9.7 Consensus size: 20
881833 TTACACATTC
*
881843 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
881863 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
881883 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
881903 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
*
881923 ATTTGACTATCGTAACGC-A
1 ATTTGACTATCGCAACGCGA
* * *
881942 A----A-AATCGCAATGCAA
1 ATTTGACTATCGCAACGCGA
* *
881957 ATTTGAATATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
881977 ATTTAATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
881997 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
882017 A-TTGACTTTCGC
1 ATTTGACTATCGC
882029 GTTGCGATTT
Statistics
Matches: 142, Mismatches: 18, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
14 8 0.06
15 3 0.02
19 13 0.09
20 118 0.83
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:881970 original size:74 final size:74
Alignment explanation
Indices: 881871--882014 Score: 207
Period size: 74 Copynumber: 1.9 Consensus size: 74
881861 GAATTTGACT
* * * *
881871 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTTGACTATCGT
1 ATCGCAACGCAAATTTGAATATCGCAACGCGAATTTAACTATCACAACGCGAATTTGACTATCGC
881936 AACGCAAAA
66 AACGCAAAA
* * * * *
881945 ATCGCAATGCAAATTTGAATATCGCAACGTGAATTTAATTATCGCAACGGGAATTTGACTATCGC
1 ATCGCAACGCAAATTTGAATATCGCAACGCGAATTTAACTATCACAACGCGAATTTGACTATCGC
882010 AACGC
66 AACGC
882015 GAATTGACTT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCAAATTTGAATATCGCAACGCGAATTTAACTATCACAACGCGAATTTGACTATCGC
AACGCAAAA
Found at i:881988 original size:54 final size:54
Alignment explanation
Indices: 881843--881993 Score: 149
Period size: 54 Copynumber: 2.7 Consensus size: 54
881833 TTACACATTC
* * * *
881843 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
1 ATTTGAATATCACAACGCGAATTTAACTATCGCAACGC-AA----A-AATCGCAACGCAA
* * * *
881903 ATTTGACTATCACAACGCGAATTTGACTATCGTAACGCAAAAATCGCAATGCAA
1 ATTTGAATATCACAACGCGAATTTAACTATCGCAACGCAAAAATCGCAACGCAA
* * *
881957 ATTTGAATATCGCAACGTGAATTTAATTATCGCAACG
1 ATTTGAATATCACAACGCGAATTTAACTATCGCAACG
881994 GGAATTTGAC
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
54 41 0.52
55 1 0.01
59 2 0.03
60 35 0.44
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (54 bp):
ATTTGAATATCACAACGCGAATTTAACTATCGCAACGCAAAAATCGCAACGCAA
Found at i:882013 original size:94 final size:93
Alignment explanation
Indices: 881851--882023 Score: 265
Period size: 94 Copynumber: 1.8 Consensus size: 93
881841 TCATTTGAAT
* * *
881851 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCAC
1 ATCGCAACGCAAATTTGAATATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCAC
881916 AACGCGAATTTGACTATCGTAACGCAAAA
66 AACGCGAA-TTGACTATCGTAACGCAAAA
* * * * *
881945 ATCGCAATGCAAATTTGAATATCGCAACGTGAATTTAATTATCGCAACGGGAATTTGACTATCGC
1 ATCGCAACGCAAATTTGAATATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCAC
882010 AACGCGAATTGACT
66 AACGCGAATTGACT
882024 TTCGCGTTGC
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 6 0.08
94 65 0.92
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (93 bp):
ATCGCAACGCAAATTTGAATATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCAC
AACGCGAATTGACTATCGTAACGCAAAA
Found at i:882047 original size:20 final size:21
Alignment explanation
Indices: 882018--882075 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
882008 GCAACGCGAA
882018 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
882038 TTG-GCTTTCGCATTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
882058 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
882076 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.43
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:882214 original size:14 final size:14
Alignment explanation
Indices: 882195--882231 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
882185 CATCAATTAA
882195 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
882209 ACAAATAAACTTTT
1 ACAAATCAACTTTT
882223 ACAAATCAA
1 ACAAATCAA
882232 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:883680 original size:21 final size:20
Alignment explanation
Indices: 883614--883683 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
883604 GTGAATCGGG
*
883614 CTCTTGAATGGTGGGAGGGA
1 CTCTTGAACGGTGGGAGGGA
* * ** *
883634 CCTCTTCAACGATGACAAGGGC
1 -CTCTTGAACGGTG-GGAGGGA
883656 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGA-GGGA
883677 CTCTTGA
1 CTCTTGA
883684 GGGATGATAG
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 1 0.03
21 31 0.86
22 4 0.11
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGA
Found at i:883732 original size:42 final size:41
Alignment explanation
Indices: 883614--883734 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 41
883604 GTGAATCGGG
*
883614 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAAGGGC
1 CTCTTGAATGGTGGGAGGG-CCTCTTGAACGATGACAAGGGC
* * ** * *
883656 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGGTGGGA-GGGCCTCTTGAACGATGACAAGGGC
* * *
883698 CTCTTGAATGATAGGAGAGGCCTCTTGAATGATGACA
1 CTCTTGAATGGTGGGAG-GGCCTCTTGAACGATGACA
883735 GGTGAGTCGG
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 1 0.02
42 59 0.94
43 3 0.05
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGCCTCTTGAACGATGACAAGGGC
Found at i:884236 original size:20 final size:20
Alignment explanation
Indices: 884211--884249 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
884201 GAATAGTTTC
884211 TGAAACTTAAAATCGCAACA
1 TGAAACTTAAAATCGCAACA
884231 TGAAACTTAAAATCGCAAC
1 TGAAACTTAAAATCGCAAC
884250 GCGAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (20 bp):
TGAAACTTAAAATCGCAACA
Found at i:884255 original size:20 final size:20
Alignment explanation
Indices: 884212--884255 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
884202 AATAGTTTCT
*
884212 GAAACTTAAAATCGCAACAT
1 GAAACTTAAAATCGCAACAC
*
884232 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
884252 GAAA
1 GAAA
884256 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:884265 original size:20 final size:20
Alignment explanation
Indices: 884242--884289 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
884232 GAAACTTAAA
884242 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
884262 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
884282 ATCGCAAC
1 ATCGCAAC
884290 AAGATAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:884327 original size:19 final size:20
Alignment explanation
Indices: 884295--884333 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
884285 GCAACAAGAT
*
884295 AATCGCAATACGAAA-TAAA
1 AATCGCAACACGAAACTAAA
*
884314 AATCGCAACGCGAAACTAAA
1 AATCGCAACACGAAACTAAA
884334 TTCGCGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.21, G:0.13, T:0.13
Consensus pattern (20 bp):
AATCGCAACACGAAACTAAA
Found at i:886378 original size:20 final size:20
Alignment explanation
Indices: 886355--886411 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
886345 TCTGAAACTT
886355 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
886375 AAAATCGCAACACAAAAAATG
1 AAAATCGCAACAC-GAAAATG
** *
886396 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
886412 TTTGACTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.53, C:0.23, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:886438 original size:14 final size:14
Alignment explanation
Indices: 886419--886479 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 14
886409 GAATTTGACT
*
886419 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
886433 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
886452 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
886466 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
886480 CTAAAATCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 24 0.60
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.25
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:886456 original size:19 final size:18
Alignment explanation
Indices: 886432--886489 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
886422 GCAACGAGAT
886432 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAA
886451 AATCGCAA-CG--A-GAA
1 AATCGCAAGCGAAATGAA
886465 AATCGCAACGCGAAACT-AA
1 AATCGCAA-GCGAAA-TGAA
886484 AATCGC
1 AATCGC
886490 GTTGCGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.48
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (18 bp):
AATCGCAAGCGAAATGAA
Found at i:886461 original size:33 final size:33
Alignment explanation
Indices: 886419--886489 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
886409 GAATTTGACT
* *
886419 ATCGCAACGAGATAATCGCAATGCGAAA-TGAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAACT-AAA
886452 ATCGCAACGAGAAAATCGCAACGCGAAACTAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAACTAAA
886485 ATCGC
1 ATCGC
886490 GTTGCGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAACGCGAAACTAAA
Found at i:887087 original size:21 final size:21
Alignment explanation
Indices: 887054--887149 Score: 115
Period size: 21 Copynumber: 4.6 Consensus size: 21
887044 CGCTTTGAAA
* *
887054 ATCGCATTACGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* * **
887075 ATCACGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
887095 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
887116 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
887137 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
887150 AGTCAGAATC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.05
20 12 0.19
21 44 0.71
22 3 0.05
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.41
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:887104 original size:20 final size:19
Alignment explanation
Indices: 887079--887169 Score: 74
Period size: 21 Copynumber: 4.5 Consensus size: 19
887069 TGTATTATCA
887079 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGT-AGAATCG
* **
887099 CGTTGCGATTTTGTATTATCG
1 CGTTGCGA--TAGTAGAATCG
* **
887120 CGTTGCGATTTTGTATTATCG
1 CGTTGCGA--TAGTAGAATCG
887141 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGT-AGAATCG
887161 CGTTGCGAT
1 CGTTGCGAT
887170 TTACATATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.05
20 22 0.35
21 34 0.55
22 3 0.05
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTAGAATCG
Found at i:887151 original size:62 final size:62
Alignment explanation
Indices: 887054--887171 Score: 209
Period size: 62 Copynumber: 1.9 Consensus size: 62
887044 CGCTTTGAAA
887054 ATCGCATTACGATTTTGTATTATCACGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATT
1 ATCGCATTACGATTTTGTATTATCACGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATT
* * *
887116 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTT
1 ATCGCATTACGATTTTGTATTATCACGTTGCGATAGTCAGAATCGCGTTGCGATTT
887172 ACATATTCGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (62 bp):
ATCGCATTACGATTTTGTATTATCACGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATT
Found at i:887251 original size:41 final size:41
Alignment explanation
Indices: 887116--887259 Score: 101
Period size: 41 Copynumber: 3.5 Consensus size: 41
887106 ATTTTGTATT
* * ** ** *
887116 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGAATTTGGAAAATCGCAATGCGATAGTCAAA
** * * * **
887157 ATCGCGTTGCG-ATTTACATATTCGCATTGCGATTTTCTAAA
1 ATCGCGTTGCGAATTTGGAAAATCGCAATGCGATAGTC-AAA
*** *
887198 ATCGCAACGCGAATTTGGAAAATCGTAATGCGATAGTCAAA
1 ATCGCGTTGCGAATTTGGAAAATCGCAATGCGATAGTCAAA
*
887239 ATCGCGTTGCGAATCTGGAAA
1 ATCGCGTTGCGAATTTGGAAA
887260 CTGATTTGCG
Statistics
Matches: 77, Mismatches: 24, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
40 18 0.23
41 41 0.53
42 18 0.23
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (41 bp):
ATCGCGTTGCGAATTTGGAAAATCGCAATGCGATAGTCAAA
Found at i:887567 original size:24 final size:25
Alignment explanation
Indices: 887538--887585 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
887528 TATTGAATTT
*
887538 AAAAAATATATTCA-AAATTTTCAA
1 AAAAAAAATATTCACAAATTTTCAA
*
887562 AAAAAAAATATTCACTAATTTTCA
1 AAAAAAAATATTCACAAATTTTCA
887586 TAAGGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAAAAATATTCACAAATTTTCAA
Found at i:887885 original size:2 final size:2
Alignment explanation
Indices: 887880--887912 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
887870 ACACACACAC
887880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
887913 AAATTATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:888791 original size:29 final size:29
Alignment explanation
Indices: 888755--888816 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
888745 AATAATTTAG
888755 CAATCACCCCAGTCCCCGTGTAGTTTACC
1 CAATCACCCCAGTCCCCGTGTAGTTTACC
888784 CAATCACCCCAGTCCCCGTGTAGTTTACC
1 CAATCACCCCAGTCCCCGTGTAGTTTACC
888813 CAAT
1 CAAT
888817 TAATTTACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.24
Consensus pattern (29 bp):
CAATCACCCCAGTCCCCGTGTAGTTTACC
Found at i:891398 original size:5 final size:6
Alignment explanation
Indices: 891381--891416 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
891371 TCCATAGGAG
891381 ATAAAA ATAAAA ATAAAA AT-AAA ATAAAA ATGAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT-AAAA
891417 CTAGATCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.18
6 19 0.68
7 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:892084 original size:15 final size:15
Alignment explanation
Indices: 892038--892087 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
892028 GCTCTATTAG
*
892038 ATTTAAATTAA-A-A
1 ATTTAATTTAATATA
*
892051 ATTTAA-TTCATATA
1 ATTTAATTTAATATA
*
892065 TTTTAATTTAATATA
1 ATTTAATTTAATATA
892080 ATTTAATT
1 ATTTAATT
892088 ACTTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 3 0.10
13 7 0.23
14 6 0.20
15 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTAATTTAATATA
Found at i:892722 original size:16 final size:16
Alignment explanation
Indices: 892703--892744 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
892693 TAATTTGTTG
*
892703 AGAAAAAAATTATTTA
1 AGAAAAAAATTATGTA
* *
892719 AGAAAAAAATTGTGTG
1 AGAAAAAAATTATGTA
892735 AGAAAAAAAT
1 AGAAAAAAAT
892745 CCAGTTATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (16 bp):
AGAAAAAAATTATGTA
Found at i:896291 original size:12 final size:12
Alignment explanation
Indices: 896274--896299 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
896264 CTGTTCTTTT
896274 TTTTTTTTCAGG
1 TTTTTTTTCAGG
896286 TTTTTTTTCAGG
1 TTTTTTTTCAGG
896298 TT
1 TT
896300 GGGGTGGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.15, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCAGG
Found at i:896772 original size:3 final size:3
Alignment explanation
Indices: 896764--896819 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
896754 AATATATATT
896764 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
896809 TAA TAA TAA TA
1 TAA TAA TAA TA
896820 TGGGTAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:897386 original size:114 final size:113
Alignment explanation
Indices: 896954--897581 Score: 886
Period size: 114 Copynumber: 5.5 Consensus size: 113
896944 ATTGAATAAA
* * * *
896954 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCT-GAGGATGATGATCCAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGA-AAAGATAATCCAT
* * *
897017 CAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 CAATTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * * *
897067 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATAATCC
* * * *
897131 ATCAAATGATGGATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAATTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * *
897183 TTCTTCTCCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATAATCC
** *
897247 ATCAACTTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
62 ATCAA-TTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
897300 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
* *
897365 ATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-TTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
897414 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
*
897479 ATTTGATGAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 A-TTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
897528 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
897582 CTGATCTTTC
Statistics
Matches: 482, Mismatches: 25, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
113 8 0.02
114 264 0.55
116 127 0.26
117 81 0.17
118 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
ATTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:898540 original size:83 final size:83
Alignment explanation
Indices: 898331--898887 Score: 967
Period size: 83 Copynumber: 6.7 Consensus size: 83
898321 GTAGTTCTTA
*
898331 CCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
898396 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
898414 CCAAACC--ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
898477 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
898495 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
898560 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
898578 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
898643 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
898661 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
898726 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
898744 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
898809 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
898827 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTCATCTT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTT
898888 TCATTTAATG
Statistics
Matches: 449, Mismatches: 22, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
81 76 0.17
83 372 0.83
84 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:899929 original size:8 final size:8
Alignment explanation
Indices: 899916--899988 Score: 89
Period size: 8 Copynumber: 9.4 Consensus size: 8
899906 CTTGACCCCC
899916 TTTTTCTT
1 TTTTTCTT
899924 TTTTTCTT
1 TTTTTCTT
*
899932 CTTTTCTT
1 TTTTTCTT
899940 TTTTTCTT
1 TTTTTCTT
899948 TTTTTC-T
1 TTTTTCTT
*
899955 TTTCTCTT
1 TTTTTCTT
899963 TTTTT-TCT
1 TTTTTCT-T
899971 TTTTT-TT
1 TTTTTCTT
*
899978 TCTTTCTT
1 TTTTTCTT
899986 TTT
1 TTT
899989 CTTCAAGCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
7 12 0.21
8 44 0.79
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:899941 original size:21 final size:21
Alignment explanation
Indices: 899930--899992 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
899920 TCTTTTTTTC
*
899930 TTCTTTTCTTTTTTTCTTTTT
1 TTCTTTTCTTTTTTTCTTCTT
899951 TTCTTTTCTCTTTTTT-TTCTT
1 TTCTTTTCT-TTTTTTCTTCTT
*
899972 TTTTTTTCTTTCTTTTTCTTC
1 TTCTTTTC-TT-TTTTTCTTC
899993 AAGCATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 21 0.58
22 12 0.33
23 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTCTTTTCTTTTTTTCTTCTT
Found at i:899943 original size:24 final size:24
Alignment explanation
Indices: 899916--899988 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
899906 CTTGACCCCC
899916 TTTTTCTTTTTTTCTTCTTTTCTT
1 TTTTTCTTTTTTTCTTCTTTTCTT
*
899940 TTTTTCTTTTTTTCTT-TTCTCTTT
1 TTTTTCTTTTTTTCTTCTTTTC-TT
899964 TTTTTCTTTTTTT-TTC-TTTCTT
1 TTTTTCTTTTTTTCTTCTTTTCTT
899986 TTT
1 TTT
899989 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.11
23 9 0.20
24 31 0.69
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (24 bp):
TTTTTCTTTTTTTCTTCTTTTCTT
Found at i:912112 original size:13 final size:13
Alignment explanation
Indices: 912094--912120 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
912084 TGGGTTTAGT
912094 TGTTTTTTTTTTC
1 TGTTTTTTTTTTC
912107 TGTTTTTTTTTTC
1 TGTTTTTTTTTTC
912120 T
1 T
912121 CTCGGTTCTG
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:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (13 bp):
TGTTTTTTTTTTC
Found at i:912159 original size:15 final size:15
Alignment explanation
Indices: 912139--912169 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
912129 TGTCTTGTTC
912139 TTTTTTTTTTCAGGT
1 TTTTTTTTTTCAGGT
912154 TTTTTTTTTTCAGGT
1 TTTTTTTTTTCAGGT
912169 T
1 T
912170 GGGGTGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.13, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTTCAGGT
Done.