Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008524.1 Hibiscus syriacus cultivar Beakdansim tig00111393_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: 760704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:336904 original size:24 final size:23
Alignment explanation
Indices: 336846--336947 Score: 123
Period size: 23 Copynumber: 4.3 Consensus size: 23
336836 CACCACAGCT
*
336846 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
336869 CATATAATTGCACCGGAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
336892 TATAATAATTGCACCGGAGTGCCA
1 CAT-ATAATTGCACCGGAGTGCCA
* * * *
336916 CGTAGAATTGTACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
336939 TATAATAAT
1 CAT-ATAAT
336948 GTCCATAAGG
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 42 0.63
24 25 0.37
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:336913 original size:47 final size:47
Alignment explanation
Indices: 336849--336947 Score: 153
Period size: 47 Copynumber: 2.1 Consensus size: 47
336839 CACAGCTCAT
*
336849 ATAATTGCACCGAAGTGCCACATATAATTGCACCGGAGTGCCATATA
1 ATAATTGCACCGAAGTGCCACATAGAATTGCACCGGAGTGCCATATA
* * * *
336896 ATAATTGCACCGGAGTGCCACGTAGAATTGTACCGTAGTGCCATATA
1 ATAATTGCACCGAAGTGCCACATAGAATTGCACCGGAGTGCCATATA
336943 ATAAT
1 ATAAT
336948 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.25
Consensus pattern (47 bp):
ATAATTGCACCGAAGTGCCACATAGAATTGCACCGGAGTGCCATATA
Found at i:337125 original size:103 final size:103
Alignment explanation
Indices: 336954--337171 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
336944 TAATGTCCAT
* * *
336954 AAGGACCACGTATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
337019 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
*
337057 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
337122 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
337160 AAGGACCACATA
1 AAGGACCACATA
337172 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:342052 original size:24 final size:24
Alignment explanation
Indices: 342017--342064 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
342007 CGTTCAGTTA
*
342017 TGTTCGGCTATGTTTGTTTATGTT
1 TGTTCGGCTATGTTCGTTTATGTT
*
342041 TGTTCGGTTATGTTCGTTTATGTT
1 TGTTCGGCTATGTTCGTTTATGTT
342065 CATTCATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.08, C:0.08, G:0.25, T:0.58
Consensus pattern (24 bp):
TGTTCGGCTATGTTCGTTTATGTT
Found at i:342075 original size:24 final size:24
Alignment explanation
Indices: 342025--342078 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
342015 TATGTTCGGC
* ** *
342025 TATGTTTGTTTATGTTTGTTCGGT
1 TATGTTCGTTTATGTTCATTCAGT
*
342049 TATGTTCGTTTATGTTCATTCATT
1 TATGTTCGTTTATGTTCATTCAGT
342073 TATGTT
1 TATGTT
342079 TAACTCAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.13, C:0.07, G:0.19, T:0.61
Consensus pattern (24 bp):
TATGTTCGTTTATGTTCATTCAGT
Found at i:342562 original size:24 final size:24
Alignment explanation
Indices: 342535--342582 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
342525 CAGAAAACAA
342535 AACAAAGGTTTCTATGCAATTTCT
1 AACAAAGGTTTCTATGCAATTTCT
342559 AACAAAGGTTTCTATGCAATTTCT
1 AACAAAGGTTTCTATGCAATTTCT
342583 GAAAAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (24 bp):
AACAAAGGTTTCTATGCAATTTCT
Found at i:343199 original size:16 final size:16
Alignment explanation
Indices: 343178--343244 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 16
343168 GTCTCCAACG
*
343178 TTTATGTCCGTGTTCA
1 TTTATGTTCGTGTTCA
*
343194 TTTATGTT-GTTGTTCG
1 TTTATGTTCG-TGTTCA
**
343210 TTTATGTTCGTGTTTG
1 TTTATGTTCGTGTTCA
343226 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
343240 TTTAT
1 TTTAT
343245 TAAATGAACG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.11
15 3 0.07
16 36 0.80
17 1 0.02
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:343327 original size:16 final size:16
Alignment explanation
Indices: 343306--343336 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
343296 AAAAATAATT
343306 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
343322 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
343337 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:352720 original size:29 final size:28
Alignment explanation
Indices: 352688--352751 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
352678 CTTATAGTTC
* *
352688 TTTAATATTT-TATTATATTTAGTATTTTA
1 TTTAATATTTAAATT-T-TTTAATATTTTA
352717 TTTAACTATTTAAATTTTTTAATATTTTA
1 TTTAA-TATTTAAATTTTTTAATATTTTA
352746 TTTAAT
1 TTTAAT
352752 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 21 0.68
30 6 0.19
31 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTAATATTTAAATTTTTTAATATTTTA
Found at i:354819 original size:22 final size:22
Alignment explanation
Indices: 354787--354833 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
354777 ACAATAACAT
354787 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
*
354809 TTTTACTCATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
354831 TTT
1 TTT
354834 AAATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (22 bp):
TTTTACACATAAACGTAAATAA
Found at i:355847 original size:2 final size:2
Alignment explanation
Indices: 355840--355867 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
355830 AAGGACGGCA
355840 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
355868 TAATGAATGA
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:359998 original size:15 final size:15
Alignment explanation
Indices: 359980--360110 Score: 185
Period size: 15 Copynumber: 8.9 Consensus size: 15
359970 ATAAGGTTAT
*
359980 TTATTTTAAAATAAT
1 TTATTTTAAAATAAA
359995 TTATTTTAAAAT-AA
1 TTATTTTAAAATAAA
*
360009 TT-TTTTAAAATAAT
1 TTATTTTAAAATAAA
* *
360023 TTATTATAAAATAAT
1 TTATTTTAAAATAAA
360038 TTATTTTAAAATAAA
1 TTATTTTAAAATAAA
*
360053 TTATTATAAAATAAA
1 TTATTTTAAAATAAA
*
360068 TTATTATAAAATAAA
1 TTATTTTAAAATAAA
360083 TTATTTTAAAATAAA
1 TTATTTTAAAATAAA
*
360098 TTATTATAAAATA
1 TTATTTTAAAATA
360111 TAGATTGATT
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
13 9 0.08
14 6 0.06
15 91 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATTTTAAAATAAA
Found at i:360078 original size:45 final size:45
Alignment explanation
Indices: 359980--360110 Score: 212
Period size: 45 Copynumber: 3.0 Consensus size: 45
359970 ATAAGGTTAT
* * *
359980 TTATTTTAAAATAATTTATTTTAAAAT-AATT-TTTTAAAATAAT
1 TTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATAAA
360023 TTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATAAA
1 TTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATAAA
*
360068 TTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAATA
1 TTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATA
360111 TAGATTGATT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
43 26 0.32
44 4 0.05
45 52 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (45 bp):
TTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATAAA
Found at i:360150 original size:32 final size:28
Alignment explanation
Indices: 360113--360505 Score: 163
Period size: 32 Copynumber: 14.6 Consensus size: 28
360103 ATAAAATATA
360113 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAA-AA--TATTAGTAT
360144 GAATTGATTTATTTT-AAAATA-T-G--T
1 G-ATTGATTTATTTTAAAAATATTAGTAT
**
360168 -ATTGATTTATTTTAAGTACTTTATTAGTAT
1 GATTGATTTATTTTAA--A-AATATTAGTAT
360198 GAATTGATTTATTTT--AAA-ATTAGTAT
1 G-ATTGATTTATTTTAAAAATATTAGTAT
360224 GTATTGATTTATTTT-AAAATA-T-G---
1 G-ATTGATTTATTTTAAAAATATTAGTAT
*
360247 GATTGATTGATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAA-AA--TATTAGTAT
360278 GGATTGATTTATTTT--AAA-A-TA-T-T
1 -GATTGATTTATTTTAAAAATATTAGTAT
* *
360301 GATTGATTGATTTTAAATAATTTATAAGTAT
1 GATTGATTTATTTTAAA-AA--TATTAGTAT
360332 GGATTGATTTATTTT-AAAATA-T-G---
1 -GATTGATTTATTTTAAAAATATTAGTAT
*
360355 GATTGATTTATTTTAAATAATTTATTTGTAT
1 GATTGATTTATTTTAAA-AA--TATTAGTAT
360386 GGATTGATTTATTTT-AAAATA-T-G---
1 -GATTGATTTATTTTAAAAATATTAGTAT
*
360409 GATTGATTTATTATT----GTAGTT-GTAT
1 GATTGATTTATT-TTAAAAATA-TTAGTAT
360434 GAATTGATTTATTTTAAATAATTTATTAGTAT
1 G-ATTGATTTATTTTAAA-AA--TATTAGTAT
360466 GGATTGATTTATTTT-AAAATA-T-G---
1 -GATTGATTTATTTTAAAAATATTAGTAT
360489 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
360506 TAATTTTTAT
Statistics
Matches: 289, Mismatches: 13, Indels: 128
0.67 0.03 0.30
Matches are distributed among these distances:
20 2 0.01
22 80 0.28
23 11 0.04
24 7 0.02
25 8 0.03
26 45 0.16
27 10 0.03
28 14 0.05
29 3 0.01
30 11 0.04
31 12 0.04
32 85 0.29
33 1 0.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (28 bp):
GATTGATTTATTTTAAAAATATTAGTAT
Found at i:360163 original size:54 final size:55
Alignment explanation
Indices: 360098--360241 Score: 220
Period size: 54 Copynumber: 2.6 Consensus size: 55
360088 TTAAAATAAA
*
360098 TTATTATAAAATATAG-ATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAAATATAGTATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
* *
360152 TTATTTTAAAATAT-GTATTGATTTATTTTAAGTACTTTATTAGTATGAATTGAT
1 TTATTTTAAAATATAGTATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
360206 TTATTTTAAAATTAGTATGTATTGATTTATTTTAAA
1 TTATTTTAAAA-TA-TA-GTATTGATTTATTTTAAA
360242 ATATGGATTG
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
53 1 0.01
54 60 0.74
55 2 0.02
56 1 0.01
58 17 0.21
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.53
Consensus pattern (55 bp):
TTATTTTAAAATATAGTATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
Found at i:360232 original size:80 final size:80
Alignment explanation
Indices: 360136--360504 Score: 342
Period size: 80 Copynumber: 4.6 Consensus size: 80
360126 TAAATAATTT
* *
360136 ATTAGTATGAATTGATTTATTTTAAAATATGTATTGATTTATTTTAAGTACTTTATTAGTATGAA
1 ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAGTA-TTTATTAGTATGAA
360201 TTGATTTATTTT-AAA
65 TTGATTTATTTTAAAA
* * * *
360216 ATTAGTATGTATTGATTTATTTTAAAATATGGATTGATTGATTTTAAATAATTTATTAGTATGGA
1 ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAGT-ATTTATTAGTATGAA
360281 TTGATTTATTTTAAAA
65 TTGATTTATTTTAAAA
* *
360297 TATT-G-ATTGATTGATTTTAAATAATTTATAAGTATGGATTGATTTATTTT-A--A---A--A-
1 -ATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTTAAGTATTTATTAG
*
360351 TATGGATTGATTTATTTTAAATA
59 TATGAATTGATTTATTTTAAA-A
*
360374 ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATT--GTA---GTT-GTA
1 A-TTA---GTATGGATTGATTTATTTTAAAATATGGATTGATTTATT-TTAAGTATTTATTAGTA
360433 TGAATTGATTTATTTTAAATAA
61 TGAATTGATTTATTTT-AA-AA
360455 TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ---ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
360505 ATAATTTTTA
Statistics
Matches: 247, Mismatches: 13, Indels: 57
0.78 0.04 0.18
Matches are distributed among these distances:
76 40 0.16
77 10 0.04
78 1 0.00
79 5 0.02
80 133 0.54
81 15 0.06
82 13 0.05
83 5 0.02
84 1 0.00
85 5 0.02
86 19 0.08
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (80 bp):
ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAGTATTTATTAGTATGAAT
TGATTTATTTTAAAA
Found at i:360246 original size:22 final size:24
Alignment explanation
Indices: 360138--360507 Score: 109
Period size: 22 Copynumber: 14.1 Consensus size: 24
360128 AATAATTTAT
360138 TAGTATGAATTGATTTATTTTAAA
1 TAGTATGAATTGATTTATTTTAAA
*
360162 -A-TATGTATTGATTTATTTTAAGTACTTTA
1 TAGTATGAATTGATTTATTTT-A--A----A
360191 TTAGTATGAATTGATTTATTTTAAAA
1 -TAGTATGAATTGATTTATTTT-AAA
*
360217 TTAGTATGTATTGATTTATTTTAAA
1 -TAGTATGAATTGATTTATTTTAAA
* *
360242 -A-TATGGATTGATTGATTTTAAATAATTTA
1 TAGTATGAATTGATTTA-TTT---TAA---A
*
360271 TTAGTATGGATTGATTTATTTTAAA
1 -TAGTATGAATTGATTTATTTTAAA
*
360296 -A-TATTG-ATTGATTGATTTTAAATAATTTA
1 TAGTA-TGAATTGATTTA-TTT---TAA---A
*
360325 TAAGTATGGATTGATTTATTTTAAA
1 T-AGTATGAATTGATTTATTTTAAA
*
360350 -A-TATGGATTGATTTATTTTAAATAA
1 TAGTATGAATTGATTTATTTT--A-AA
*
360375 TTTATTTGTATGGATTGATTTATTTTAAA
1 --TA---GTATGAATTGATTTATTTTAAA
* * *
360404 -A-TATGGATTGATTTATTATTGTAG
1 TAGTATGAATTGATTTATT-TT-AAA
*
360428 TTGTATGAATTGATTTATTTTAAATAATTTA
1 TAGTATGAATTGATTTA-TTT---TAA---A
*
360459 TTAGTATGGATTGATTTATTTTAAA
1 -TAGTATGAATTGATTTATTTTAAA
*
360484 -A-TATGGATTGATTTATTTTAAA
1 TAGTATGAATTGATTTATTTTAAA
360506 TA
1 TA
360508 ATTTTTATAA
Statistics
Matches: 275, Mismatches: 16, Indels: 111
0.68 0.04 0.28
Matches are distributed among these distances:
22 94 0.34
23 17 0.06
24 2 0.01
25 9 0.03
26 43 0.16
27 2 0.01
28 11 0.04
29 6 0.02
30 2 0.01
31 14 0.05
32 75 0.27
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (24 bp):
TAGTATGAATTGATTTATTTTAAA
Found at i:360319 original size:188 final size:188
Alignment explanation
Indices: 360098--360511 Score: 611
Period size: 188 Copynumber: 2.2 Consensus size: 188
360088 TTAAAATAAA
* *
360098 TTATTATAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATAAGTATGAATTGATTTATTTTAAAA
* * * *
360163 TATGTATTGATTTATTTTAAGTACTTTATTAGTATGAATTGATTTATTTTAAAATTAGTATGTAT
66 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AAA--A-TATGGAT
*
360228 TGATTTA-T-TT-TA-AAATATGGATTGATTGATTTTAAATAATTTATTAGTATGGATTGAT
127 TGATTTATTATTGTAGAAATATGAATTGATTGATTTTAAATAATTTATTAGTATGGATTGAT
* * *
360286 TTATTTTAAAATATTGATTGATTGATTTTAAATAATTTATAAGTATGGATTGATTTATTTTAAAA
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATAAGTATGAATTGATTTATTTTAAAA
* *
360351 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
66 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
*** *
360416 TTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
131 TTATTATTGTAGAAATATGAATTGATTGATTTTAAATAATTTATTAGTATGGATTGAT
*
360474 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTT
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTT
360512 TTATAATTGC
Statistics
Matches: 204, Mismatches: 18, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
184 13 0.06
185 2 0.01
186 2 0.01
187 5 0.02
188 182 0.89
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (188 bp):
TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATAAGTATGAATTGATTTATTTTAAAA
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGAAATATGAATTGATTGATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:360420 original size:54 final size:54
Alignment explanation
Indices: 360216--360416 Score: 357
Period size: 54 Copynumber: 3.7 Consensus size: 54
360206 TTATTTTAAA
*
360216 ATTAGTATGTATTGATTTATTTTAAAATATGGATTGATTGATTTTAAATAATTT
1 ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTGATTTTAAATAATTT
*
360270 ATTAGTATGGATTGATTTATTTTAAAATATTGATTGATTGATTTTAAATAATTT
1 ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTGATTTTAAATAATTT
* *
360324 ATAAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTT
1 ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTGATTTTAAATAATTT
*
360378 ATTTGTATGGATTGATTTATTTTAAAATATGGATTGATT
1 ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
360417 TATTATTGTA
Statistics
Matches: 140, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 140 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (54 bp):
ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTGATTTTAAATAATTT
Found at i:360506 original size:134 final size:131
Alignment explanation
Indices: 360122--360511 Score: 439
Period size: 134 Copynumber: 2.9 Consensus size: 131
360112 AGATTGATTT
* * * * * *
360122 ATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGT-ATTGATTTATTTTAAGTA
1 ATTTGAAATAATTTATAAATATGGATTGATTTATTTTAAAATATATGATTGATTTATTTTAAATA
* * * **
360186 CTTTATTAGTATGAATTGATTTATTTTAAAATTAGTATGTATTGATTTATTTTAAA-ATATGGAT
66 ATTTATTAGTATGGATTGATTTATTTT-AAA--A-TATGGATTGATTTATTTTAAATA-ATTTAT
*
360250 TGATTG
126 TGATGG
* * * *
360256 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-TGATTGATTGATTTTAAATA
1 ATTTGAAATAATTTATAAATATGGATTGATTTATTTTAAAATATATGATTGATTTATTTTAAATA
*
360320 ATTTATAAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTTGTA
66 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTG-A
360385 TGG
129 TGG
** * * ** *
360388 A-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAA
1 ATTTGAAATAATTTATAAATATGGATTGATTTATT-TT-AAAATATATG-ATTGATTTATTTTAA
360451 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTT
63 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTT
360512 TTATAATTGC
Statistics
Matches: 226, Mismatches: 22, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
130 40 0.18
131 16 0.07
132 7 0.03
133 6 0.03
134 157 0.69
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (131 bp):
ATTTGAAATAATTTATAAATATGGATTGATTTATTTTAAAATATATGATTGATTTATTTTAAATA
ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTGATG
G
Found at i:360982 original size:29 final size:29
Alignment explanation
Indices: 360890--360984 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
360880 TTTTTTAATA
* * *
360890 TTCTAATTTCATCCTTAAACTATAACTCT
1 TTCTAATTACATCCTTAAACTATGACACT
*
360919 CATTCTAAATTA-ATCCTTAAACT-TG-CGAACA
1 --TTCT-AATTACATCCTTAAACTATGAC--ACT
*
360950 TTCTAATTACATCCCTAAACTATGACACT
1 TTCTAATTACATCCTTAAACTATGACACT
360979 TTCTAA
1 TTCTAA
360985 ATTGGTCACA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
28 5 0.10
29 23 0.44
30 3 0.06
31 17 0.33
32 4 0.08
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
TTCTAATTACATCCTTAAACTATGACACT
Found at i:377260 original size:36 final size:36
Alignment explanation
Indices: 377189--377261 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
377179 GTTAGAAAAT
* *
377189 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
377225 ATTTATATATATTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAT-TTTCTTTA-AAAATTGAAAATCATAAA
377261 A
1 A
377262 AAATTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 20 0.61
37 13 0.39
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:378408 original size:59 final size:58
Alignment explanation
Indices: 378286--378413 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 58
378276 TAGAACAAAG
* * *
378286 GTCATAGTCTGAGAATGAAATTGAAATATTCAAAAGTTTGAGGACTAATTTAAAATAATA
1 GTCATAGT-TTAGAATGAAATTGAAATATT-AAAAGTTTGAGGACCAATTTAAAATAAGA
378346 GTCATAGTTTAGATATGAAATTGAAATA-TATAAAGTTT-AGAGACCAATTTAAAATAAGA
1 GTCATAGTTTAGA-ATGAAATTGAAATATTA-AAAGTTTGAG-GACCAATTTAAAATAAGA
378405 GTCAT-GTTT
1 GTCATAGTTT
378414 TAAAGACATG
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
58 7 0.11
59 33 0.53
60 22 0.35
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (58 bp):
GTCATAGTTTAGAATGAAATTGAAATATTAAAAGTTTGAGGACCAATTTAAAATAAGA
Found at i:378526 original size:23 final size:24
Alignment explanation
Indices: 378500--378547 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
378490 TAAATTATAC
*
378500 TTAAAAATTT-AGGATATAAAATT
1 TTAAAAATTTAAAGATATAAAATT
378523 TTAAAAATTTAAAAGATATAAAATT
1 TTAAAAATTT-AAAGATATAAAATT
378548 AGATTACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.45
25 12 0.55
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
TTAAAAATTTAAAGATATAAAATT
Found at i:381700 original size:19 final size:19
Alignment explanation
Indices: 381668--381706 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
381658 TGTATGCTTT
* *
381668 ACAACTACATAAAAGCAAA
1 ACAACCACAGAAAAGCAAA
*
381687 ACAACCACAGAAAATCAAA
1 ACAACCACAGAAAAGCAAA
381706 A
1 A
381707 ACAAAAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.23, G:0.05, T:0.08
Consensus pattern (19 bp):
ACAACCACAGAAAAGCAAA
Found at i:396103 original size:13 final size:14
Alignment explanation
Indices: 396065--396104 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
396055 GTGAAATTCT
*
396065 AAATATTTAAATAA
1 AAATATTTATATAA
396079 AAATTATTTATATAA
1 AAA-TATTTATATAA
396094 AAAT-TTTATAT
1 AAATATTTATAT
396105 GTTGATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 7 0.29
14 4 0.17
15 13 0.54
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATATTTATATAA
Found at i:397184 original size:17 final size:17
Alignment explanation
Indices: 397162--397194 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
397152 AATGATCAGG
*
397162 TGAATCATTTGTCATTA
1 TGAATCAATTGTCATTA
397179 TGAATCAATTGTCATT
1 TGAATCAATTGTCATT
397195 CTTTTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TGAATCAATTGTCATTA
Found at i:398523 original size:19 final size:19
Alignment explanation
Indices: 398499--398540 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
398489 ATTCACAAAG
398499 ATAATTTCAACTTTAGAGT
1 ATAATTTCAACTTTAGAGT
*
398518 ATAATTTTAACTTTAGAGT
1 ATAATTTCAACTTTAGAGT
398537 ATAA
1 ATAA
398541 GATCAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (19 bp):
ATAATTTCAACTTTAGAGT
Found at i:399594 original size:2 final size:2
Alignment explanation
Indices: 399583--399619 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
399573 TTACTGGTTT
399583 TA TA -A 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
399620 AGGACATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:403798 original size:14 final size:14
Alignment explanation
Indices: 403770--403802 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
403760 GTGAGTTTTC
403770 ATTTACATTTGTTA
1 ATTTACATTTGTTA
403784 ATTTA-ATTTGATTA
1 ATTTACATTTG-TTA
403798 ATTTA
1 ATTTA
403803 TCTTAGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (14 bp):
ATTTACATTTGTTA
Found at i:414339 original size:38 final size:38
Alignment explanation
Indices: 414288--414373 Score: 163
Period size: 38 Copynumber: 2.3 Consensus size: 38
414278 AGGAATCCAA
414288 CATTTCATTCAAGGAAAAAACACATACGAGTTCAGTAC
1 CATTTCATTCAAGGAAAAAACACATACGAGTTCAGTAC
*
414326 CATTTCATTCAAGGACAAAACACATACGAGTTCAGTAC
1 CATTTCATTCAAGGAAAAAACACATACGAGTTCAGTAC
414364 CATTTCATTC
1 CATTTCATTC
414374 GTGAAAAGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (38 bp):
CATTTCATTCAAGGAAAAAACACATACGAGTTCAGTAC
Found at i:418547 original size:20 final size:20
Alignment explanation
Indices: 418517--418570 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
418507 GTCAAACCAG
* *
418517 TTCGGGTTGACTCGGTTC-A
1 TTCGAGTTGACTCGGCTCGA
*
418536 TTACGAGTTGACTCAGCTCGA
1 TT-CGAGTTGACTCGGCTCGA
418557 TTCGAGTTGACTCG
1 TTCGAGTTGACTCG
418571 AACCAGTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (20 bp):
TTCGAGTTGACTCGGCTCGA
Found at i:420931 original size:89 final size:89
Alignment explanation
Indices: 420834--421011 Score: 320
Period size: 89 Copynumber: 2.0 Consensus size: 89
420824 TATTATCCGT
* *
420834 TGGTGGTGCTAGAAGTGTAGAGGATATTTCGTTGAACCTCGTAAATTTGACGTGTTCTCTCTATC
1 TGGTGGTGCTAGAAGTGTAGACGATATTTCGTTGAACCTCGTAAATTTGACGTGTTATCTCTATC
420899 ATTTATATTATATGTTCATTATTA
66 ATTTATATTATATGTTCATTATTA
* *
420923 TGGTGGTGCTAGAGGTGTAGACGATATTTCGTTGAACCTCGTAAATTTGACGTGTTATCTCTATT
1 TGGTGGTGCTAGAAGTGTAGACGATATTTCGTTGAACCTCGTAAATTTGACGTGTTATCTCTATC
420988 ATTTATATTATATGTTCATTATTA
66 ATTTATATTATATGTTCATTATTA
421012 GACTTTTTCT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (89 bp):
TGGTGGTGCTAGAAGTGTAGACGATATTTCGTTGAACCTCGTAAATTTGACGTGTTATCTCTATC
ATTTATATTATATGTTCATTATTA
Found at i:427475 original size:11 final size:12
Alignment explanation
Indices: 427448--427472 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
427438 CATCAGGATA
427448 TTAAAAACATTT
1 TTAAAAACATTT
427460 TTAAAAACATTT
1 TTAAAAACATTT
427472 T
1 T
427473 AAACCTTAAA
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAAAACATTT
Found at i:427668 original size:17 final size:17
Alignment explanation
Indices: 427648--427680 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
427638 TTTTTTATTA
427648 AAAAATATAATTATTTT
1 AAAAATATAATTATTTT
*
427665 AAAAATATATTTATTT
1 AAAAATATAATTATTT
427681 ATTTAGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAAATATAATTATTTT
Found at i:427681 original size:16 final size:16
Alignment explanation
Indices: 427641--427681 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
427631 AAGTATGTTT
*
427641 TTTATTAAAAAATATA
1 TTTATTTAAAAATATA
*
427657 ATTATTTTAAAAATATA
1 TTTA-TTTAAAAATATA
427674 TTTATTTA
1 TTTATTTA
427682 TTTAGAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTATTTAAAAATATA
Found at i:435656 original size:2 final size:2
Alignment explanation
Indices: 435649--435674 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
435639 TAATCTTAGC
435649 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
435675 GCTTTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:443043 original size:42 final size:42
Alignment explanation
Indices: 442996--443090 Score: 190
Period size: 42 Copynumber: 2.3 Consensus size: 42
442986 TATATCAGAC
442996 TTATGTTTATTATCCTTGATATGATGACATACATGTCCATCA
1 TTATGTTTATTATCCTTGATATGATGACATACATGTCCATCA
443038 TTATGTTTATTATCCTTGATATGATGACATACATGTCCATCA
1 TTATGTTTATTATCCTTGATATGATGACATACATGTCCATCA
443080 TTATGTTTATT
1 TTATGTTTATT
443091 GATAAAGCTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (42 bp):
TTATGTTTATTATCCTTGATATGATGACATACATGTCCATCA
Found at i:446518 original size:3 final size:3
Alignment explanation
Indices: 446510--446537 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
446500 CTCCGAATCT
446510 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
446538 TTTTAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:448463 original size:29 final size:28
Alignment explanation
Indices: 448400--448476 Score: 138
Period size: 27 Copynumber: 2.8 Consensus size: 28
448390 CATAGCCCTT
448400 TAACTTTTATAAATCATAAAATATATAA
1 TAACTTTTATAAATCATAAAATATATAA
448428 TAA-TTTTATAAATCATAAAATATATAA
1 TAACTTTTATAAATCATAAAATATATAA
448455 TAACTTTTTATAAATCATAAAA
1 TAAC-TTTTATAAATCATAAAA
448477 AGGTCTGATC
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
27 27 0.57
28 3 0.06
29 17 0.36
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (28 bp):
TAACTTTTATAAATCATAAAATATATAA
Found at i:449553 original size:34 final size:34
Alignment explanation
Indices: 449515--449583 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
449505 AACACATACG
449515 AACAAATGTGCTATAAAAGTGAAGAAAAAAATCA
1 AACAAATGTGCTATAAAAGTGAAGAAAAAAATCA
449549 AACAAATGTGCTATAAAAGTGAAGAAAAAAATCA
1 AACAAATGTGCTATAAAAGTGAAGAAAAAAATCA
449583 A
1 A
449584 CACTTCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.17
Consensus pattern (34 bp):
AACAAATGTGCTATAAAAGTGAAGAAAAAAATCA
Found at i:449664 original size:16 final size:16
Alignment explanation
Indices: 449639--449670 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
449629 TATTTAGATC
*
449639 TAAATTAAAAGAAAAT
1 TAAATAAAAAGAAAAT
449655 TAAATAAAAAGAAAAT
1 TAAATAAAAAGAAAAT
449671 CTCTCTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (16 bp):
TAAATAAAAAGAAAAT
Found at i:452605 original size:137 final size:138
Alignment explanation
Indices: 452236--452584 Score: 470
Period size: 137 Copynumber: 2.5 Consensus size: 138
452226 ATTTAGATAA
* * * ** * * *
452236 ATTTTTAATTTGATCATCGCTTTTGCTCGACATTCCATTTTAATTATTTGAATCAATAAGTG-GT
1 ATTTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAATAATTGATT
* * * *
452300 TAAAATTGAATAGATTAATATTTAGAGCCTTTATTTTAGGTTTACTTTCGAACTTAGTCTTTTAA
66 TAAAATTGAATAGATTAATATTTAGAGCCTTCATTTTAGGTTTAATTTCGAAATTAATCTTTTAA
452365 TTTAGGGGG
131 TTTA-GGGG
* * *
452374 ATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCGTTTTAATTATTCGAATAAATAATTGATT
1 ATTTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAATAATTGATT
*
452439 TAAAATTGAATAGATTAATATTTAGAGCCTTCATTTTAGGTTTAATTTTGAAATTAATC-TTTAA
66 TAAAATTGAATAGATTAATATTTAGAGCCTTCATTTTAGGTTTAATTTCGAAATTAATCTTTTAA
452503 TTTA-GGG
131 TTTAGGGG
* * * * *
452510 ATTTTTTAATTTGGTCCTCACTTTTTCTTGAGGTTCCAATTTAATTATTCAAATCAACAATTGAT
1 A-TTTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAATAATTGAT
452575 TTAAAATTGA
65 TTAAAATTGA
452585 TTCATATTAT
Statistics
Matches: 187, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
136 4 0.02
137 65 0.35
138 63 0.34
139 55 0.29
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (138 bp):
ATTTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAATAATTGATT
TAAAATTGAATAGATTAATATTTAGAGCCTTCATTTTAGGTTTAATTTCGAAATTAATCTTTTAA
TTTAGGGG
Found at i:457608 original size:2 final size:2
Alignment explanation
Indices: 457601--457633 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
457591 TCACTCCATA
457601 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
457634 ATCATTAACT
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:466767 original size:37 final size:37
Alignment explanation
Indices: 466726--466812 Score: 174
Period size: 37 Copynumber: 2.4 Consensus size: 37
466716 CATGTGGCGG
466726 TAGGCATGCCAACCTTGTTACTATTATTTTGAAAATA
1 TAGGCATGCCAACCTTGTTACTATTATTTTGAAAATA
466763 TAGGCATGCCAACCTTGTTACTATTATTTTGAAAATA
1 TAGGCATGCCAACCTTGTTACTATTATTTTGAAAATA
466800 TAGGCATGCCAAC
1 TAGGCATGCCAAC
466813 TTAAGACCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (37 bp):
TAGGCATGCCAACCTTGTTACTATTATTTTGAAAATA
Found at i:469021 original size:14 final size:13
Alignment explanation
Indices: 468999--469028 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
468989 TAAATCAGAT
468999 ATAATAATATTAC
1 ATAATAATATTAC
469012 ATAATCAATATTAC
1 ATAAT-AATATTAC
469026 ATA
1 ATA
469029 TTCTGATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATAATATTAC
Found at i:472686 original size:21 final size:21
Alignment explanation
Indices: 472655--472718 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
472645 CGATTTACAT
*
472655 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* *
472676 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
472699 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
472718 A
1 A
472719 ACCGCAACGA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 8 0.22
21 19 0.53
23 9 0.25
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (21 bp):
ATTCGCGTTGCGATAGTCCAA
Found at i:473701 original size:64 final size:63
Alignment explanation
Indices: 473587--473730 Score: 211
Period size: 64 Copynumber: 2.3 Consensus size: 63
473577 TTTGGAATAA
* * *
473587 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCACAACAAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * *
473650 ATCGCAACGTGAATTTGGACTTTCACAACAAATTTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCACAACAAA-TTTGGAATAAATCGCAACGCGAACTTCGACT
473714 ATCGCAA--CGAACTTGGA
1 ATCGCAACGCGAACTTGGA
473731 ATAAATCGCA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
62 8 0.11
63 26 0.36
64 38 0.53
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (63 bp):
ATCGCAACGCGAACTTGGACTATCACAACAAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:473804 original size:21 final size:21
Alignment explanation
Indices: 473559--473909 Score: 244
Period size: 21 Copynumber: 16.8 Consensus size: 21
473549 CGTTGCGATT
*
473559 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
473578 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
473601 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
473620 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * *
473643 TTCGACTATCGCAACGTGAAT
1 TTGGACTATCGCAACGCGAAC
* * * *
473664 TTGGACTTTCACAA--CAAATT
1 TTGGACTATCGCAACGCGAA-C
*
473684 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
473707 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
473726 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * *
473749 TTCGATTATCGCAA--CAAAC
1 TTGGACTATCGCAACGCGAAC
*
473768 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
473791 TTCGACTATAGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
473812 TTGGACTATCACAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
473831 TTGGAATAAATCGCAACGCAAAC
1 TTGGACT--ATCGCAACGCGAAC
*
473854 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
473873 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
473894 TTGGATTATCGCAACG
1 TTGGACTATCGCAACG
473910 AATTTGGAAA
Statistics
Matches: 259, Mismatches: 46, Indels: 52
0.73 0.13 0.15
Matches are distributed among these distances:
19 64 0.25
20 7 0.03
21 129 0.50
22 5 0.02
23 51 0.20
24 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:473952 original size:21 final size:21
Alignment explanation
Indices: 473926--473973 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
473916 GAAAATCGTA
473926 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
*
473947 TTGCGATAGTCGATGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
473968 TTGCGA
1 TTGCGA
473974 ATATGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCG
Found at i:475213 original size:18 final size:18
Alignment explanation
Indices: 475190--475264 Score: 106
Period size: 18 Copynumber: 4.4 Consensus size: 18
475180 ACCGGTCACA
475190 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
475208 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
475225 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
475239 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
475257 ACCCGACC
1 ACCCGACC
475265 GTTGACCGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.24
18 38 0.76
ACGTcount: A:0.17, C:0.51, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:475233 original size:31 final size:31
Alignment explanation
Indices: 475194--475271 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
475184 GTCACAACCC
475194 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
475225 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
475256 GACCCGA-CCGTTGACC
1 GACCCGACCCGTTGACC
475272 GTTGACCCGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 9 0.20
31 36 0.80
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:475271 original size:12 final size:13
Alignment explanation
Indices: 475212--475248 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
475202 CCGTTGACCC
475212 GACCCGACCCGTT
1 GACCCGACCCGTT
*
475225 TACCCGACCCGTT
1 GACCCGACCCGTT
475238 GACCCGACCCG
1 GACCCGACCCG
475249 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:475273 original size:7 final size:7
Alignment explanation
Indices: 475261--475294 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
475251 CCGTTGACCC
475261 GACCGTT
1 GACCGTT
475268 GACCGTT
1 GACCGTT
475275 GACCCGTT
1 GA-CCGTT
*
475283 GACCATT
1 GACCGTT
475290 GACCG
1 GACCG
475295 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:475283 original size:15 final size:15
Alignment explanation
Indices: 475263--475293 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
475253 GTTGACCCGA
*
475263 CCGTTGACCGTTGAC
1 CCGTTGACCATTGAC
475278 CCGTTGACCATTGAC
1 CCGTTGACCATTGAC
475293 C
1 C
475294 GGAGTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCATTGAC
Found at i:476609 original size:18 final size:18
Alignment explanation
Indices: 476583--476617 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
476573 TCGAAAGGAC
*
476583 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
476601 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
476618 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:480408 original size:18 final size:18
Alignment explanation
Indices: 480385--480458 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
480375 ACCGGTCACA
480385 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
480403 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
480420 ----TACCCGA-CCGTTG
1 ACCCGACCCGACCCGTTG
480433 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
480451 ACCCGACC
1 ACCCGACC
480459 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
12 5 0.10
13 6 0.12
17 6 0.12
18 31 0.65
ACGTcount: A:0.18, C:0.50, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:480433 original size:30 final size:30
Alignment explanation
Indices: 480389--480465 Score: 136
Period size: 30 Copynumber: 2.5 Consensus size: 30
480379 GTCACAACCC
480389 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGA-CCGTTGACCCGACCCGACCCGTT
*
480420 TACCCGACCGTTGACCCGACCCGACCCGTT
1 GACCCGACCGTTGACCCGACCCGACCCGTT
480450 GACCCGACCGTTGACC
1 GACCCGACCGTTGACC
480466 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 38 0.86
31 6 0.14
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (30 bp):
GACCCGACCGTTGACCCGACCCGACCCGTT
Found at i:480462 original size:12 final size:13
Alignment explanation
Indices: 480407--480442 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
480397 CCGTTGACCC
480407 GACCCGACCCGTT
1 GACCCGACCCGTT
*
480420 TACCCGA-CCGTT
1 GACCCGACCCGTT
480432 GACCCGACCCG
1 GACCCGACCCG
480443 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:480463 original size:12 final size:13
Alignment explanation
Indices: 480437--480480 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
480427 CCGTTGACCC
480437 GACCCGACCCGTT
1 GACCCGACCCGTT
480450 GACCCGA-CCGTT
1 GACCCGACCCGTT
*
480462 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
480477 GACC
1 GACC
480481 ATTGACCGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 2 0.07
15 9 0.33
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:480467 original size:7 final size:7
Alignment explanation
Indices: 480455--480488 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
480445 CCGTTGACCC
480455 GACCGTT
1 GACCGTT
480462 GACCGTT
1 GACCGTT
480469 GACCCGTT
1 GA-CCGTT
*
480477 GACCATT
1 GACCGTT
480484 GACCG
1 GACCG
480489 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:480477 original size:15 final size:15
Alignment explanation
Indices: 480457--480487 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
480447 GTTGACCCGA
*
480457 CCGTTGACCGTTGAC
1 CCGTTGACCATTGAC
480472 CCGTTGACCATTGAC
1 CCGTTGACCATTGAC
480487 C
1 C
480488 GGAGTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCATTGAC
Found at i:481797 original size:18 final size:18
Alignment explanation
Indices: 481771--481805 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
481761 TCGAAAGGAC
*
481771 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
481789 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
481806 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:484809 original size:41 final size:42
Alignment explanation
Indices: 484764--484858 Score: 174
Period size: 42 Copynumber: 2.3 Consensus size: 42
484754 TGCCATATGC
*
484764 TCCAAACCACCCTGCAATGAC-AAAAAAGATGAACAACCGAT
1 TCCAAATCACCCTGCAATGACAAAAAAAGATGAACAACCGAT
484805 TCCAAATCACCCTGCAATGACAAAAAAAGATGAACAACCGAT
1 TCCAAATCACCCTGCAATGACAAAAAAAGATGAACAACCGAT
484847 TCCAAATCACCC
1 TCCAAATCACCC
484859 CCACAACAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 20 0.38
42 32 0.62
ACGTcount: A:0.45, C:0.31, G:0.11, T:0.14
Consensus pattern (42 bp):
TCCAAATCACCCTGCAATGACAAAAAAAGATGAACAACCGAT
Found at i:488096 original size:18 final size:16
Alignment explanation
Indices: 488059--488100 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
488049 TCTTTAAAAG
488059 TTTTAAATTTTTATTA
1 TTTTAAATTTTTATTA
488075 TTTTAAATAATTTTA-TA
1 TTTTAAAT--TTTTATTA
*
488092 TTTTTAATT
1 TTTTAAATT
488101 AAAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 8 0.35
17 9 0.39
18 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAAATTTTTATTA
Found at i:488433 original size:43 final size:43
Alignment explanation
Indices: 488372--488461 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 43
488362 CATGATTCTA
* * **
488372 ACATTGTGATGATTGAAATACATACGGACTGTAGTGTTCATGT
1 ACATTCTGATGATTGAAATACATAAGGAAGGTAGTGTTCATGT
* *
488415 ACATTCTGATGATTGAAATACATAATGAAGGTAGTGTTCATTT
1 ACATTCTGATGATTGAAATACATAAGGAAGGTAGTGTTCATGT
488458 ACAT
1 ACAT
488462 GTATACTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (43 bp):
ACATTCTGATGATTGAAATACATAAGGAAGGTAGTGTTCATGT
Found at i:493434 original size:2 final size:2
Alignment explanation
Indices: 493427--493454 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
493417 CTCCAATGCC
493427 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
493455 GCAACACTAC
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):
TA
Found at i:495506 original size:52 final size:53
Alignment explanation
Indices: 495441--495547 Score: 171
Period size: 52 Copynumber: 2.0 Consensus size: 53
495431 CACAAGATGG
* *
495441 GGCACATAGAAATAGGAAATTAGCCTAGAGTTAGGGGATTACAACTAATTACAA
1 GGCACATA-AAATAGGAAATTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
*
495495 GGCACAT-AAATAGGAGATTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
1 GGCACATAAAATAGGAAATTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
495547 G
1 G
495548 AATATTATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
52 43 0.86
54 7 0.14
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.21
Consensus pattern (53 bp):
GGCACATAAAATAGGAAATTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
Found at i:506445 original size:21 final size:21
Alignment explanation
Indices: 506416--506466 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
506406 ATGTAGTAAT
506416 AAAAT-TTATAAT-TTTTTAA
1 AAAATATTATAATATTTTTAA
*
506435 AACATAATTATAATATTTTTAA
1 AAAAT-ATTATAATATTTTTAA
506457 AAAATATTAT
1 AAAATATTAT
506467 TTTTATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
21 12 0.44
22 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATATTATAATATTTTTAA
Found at i:511233 original size:95 final size:95
Alignment explanation
Indices: 511070--511258 Score: 342
Period size: 95 Copynumber: 2.0 Consensus size: 95
511060 CACTTGTCTT
*
511070 CAATTTTATCTGTACTATCTGTTGATTCACATTAGTGATAGGACTGCAAGTTATAATAACTAGAA
1 CAATTTTATCTGTACCATCTGTTGATTCACATTAGTGATAGGACTGCAAGTTATAATAACTAGAA
511135 GTATCTGCGGTTATCATGTTTGAAATGAAA
66 GTATCTGCGGTTATCATGTTTGAAATGAAA
* **
511165 CAATTTTATCTGTACCATCTGTTGCTTCACATTAGTGATAGGTTTGCAAGTTATAATAACTAGAA
1 CAATTTTATCTGTACCATCTGTTGATTCACATTAGTGATAGGACTGCAAGTTATAATAACTAGAA
511230 GTATCTGCGGTTATCATGTTTGAAATGAA
66 GTATCTGCGGTTATCATGTTTGAAATGAA
511259 TACGGAGTCA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (95 bp):
CAATTTTATCTGTACCATCTGTTGATTCACATTAGTGATAGGACTGCAAGTTATAATAACTAGAA
GTATCTGCGGTTATCATGTTTGAAATGAAA
Found at i:513683 original size:2 final size:2
Alignment explanation
Indices: 513676--513769 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
513666 ACAATATTTG
513676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
513718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
513760 AT AT AT AT AT
1 AT AT AT AT AT
513770 TTGTTAAAGT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526362 original size:17 final size:18
Alignment explanation
Indices: 526325--526372 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
526315 GTTCGCTAAG
526325 GGAATTGGAATCTGTTCA
1 GGAATTGGAATCTGTTCA
526343 GGAATTGGAATCTG-TCA
1 GGAATTGGAATCTGTTCA
*
526360 GGAATTAGAATCT
1 GGAATTGGAATCT
526373 AATTCCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.31
Consensus pattern (18 bp):
GGAATTGGAATCTGTTCA
Found at i:527209 original size:254 final size:250
Alignment explanation
Indices: 526700--527308 Score: 886
Period size: 254 Copynumber: 2.4 Consensus size: 250
526690 TTTGGTCCAC
*
526700 CCGACCCGACCCGACAAAAATAAAGTTTCACTCGACCCGACCCGAATATATGAATTAGAAACCCG
1 CCGACCCGACCCGACCAAAATAAAG-TT---TCG-CCCGACCCGAATATATGAATTAGAAACCCG
*
526765 ACCCGACCCGAAATAATAAAAAAATATTTTTATTCCAT-AAAACAATGACTTAATTGGAAAAAAA
61 ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAA
* *
526829 TATATATAGAGGGGTATTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATTTTTTGG
126 TATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTT--
526894 GTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTAAAAAAAAA
189 GTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTAAAAAAAAA
* * *
526956 CCGACCCGACCCGACCAAAATAAAGTTTCGCCCGACCCGTATATATGAATTAGAAATCCGACCCA
1 CCGACCCGACCCGACCAAAATAAAGTTTCGCCCGACCCGAATATATGAATTAGAAACCCGACCCG
*
527021 ACCCGAAATAATAAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATT-GAAAAAAATTA
66 ACCCGAAATAAT--AAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAA-TA
*
527085 TATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAATGTAAAATTATATA-TATTT-TCG
128 TATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTTGTCG
* * * * *
527148 GGTTGGGTATTTTTTACCCTATACCCGAACTCGACCCGACCCTAATATCACACT-TAAAAAAA
193 GGTCGGGTATTTTTCACCCTAAACCCG-A----ACCCGACCCGAATATCACACTAAAAAAAAA
* * *
527210 CCGACCCGACCCGACCAAAATAAAATTTCACCCGACCCGAATATATGAATTAAAAACCCGACCCG
1 CCGACCCGACCCGACCAAAATAAAGTTTCGCCCGACCCGAATATATGAATTAGAAACCCGACCCG
*
527275 ACCCGAAACAATAAAAAAATATTTTTATTCAATA
66 ACCCGAAATAATAAAAAAATATTTTTATTCAATA
527309 TATAAATAAG
Statistics
Matches: 323, Mismatches: 21, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
250 27 0.08
251 45 0.14
252 25 0.08
253 32 0.10
254 148 0.46
255 22 0.07
256 24 0.07
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (250 bp):
CCGACCCGACCCGACCAAAATAAAGTTTCGCCCGACCCGAATATATGAATTAGAAACCCGACCCG
ACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAATATAT
ATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTTGTCGGGT
CGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTAAAAAAAAA
Found at i:532518 original size:37 final size:36
Alignment explanation
Indices: 532476--532584 Score: 175
Period size: 35 Copynumber: 3.0 Consensus size: 36
532466 CATTTTTAAC
* *
532476 AAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCATTTTTCAAAG
532513 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
532548 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
532585 TTGGTTACCA
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
35 35 0.51
36 6 0.09
37 27 0.40
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:532540 original size:21 final size:21
Alignment explanation
Indices: 532516--532576 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
532506 TTCAAAGAAA
532516 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
532537 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
532551 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
532572 CATTT
1 CATTT
532577 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:532593 original size:35 final size:36
Alignment explanation
Indices: 532483--532611 Score: 142
Period size: 35 Copynumber: 3.6 Consensus size: 36
532473 AACAAACATC
* *
532483 TACCAAACTTTGAAAAAC-TATTTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCAT-TTTTTCAAAG-AACAGT
*
532520 TACCAAACTTTGAAAACCA--TTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAG-AACAGT
***
532555 TACCAAACTTTGAAAACCATTTTTTCAAAG-TTGGT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
532590 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACCATTTT
532612 AATACTTTCA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
34 14 0.17
35 44 0.52
37 26 0.31
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (36 bp):
TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
Found at i:536248 original size:37 final size:36
Alignment explanation
Indices: 536190--536302 Score: 167
Period size: 35 Copynumber: 3.2 Consensus size: 36
536180 TCTCATTATC
* * *
536190 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAATT
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
*
536226 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
536262 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
536297 ATTTTT
1 ATTTTT
536303 TTAAAGTTAG
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 34 0.49
36 16 0.23
37 20 0.29
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
Found at i:536264 original size:21 final size:21
Alignment explanation
Indices: 536240--536300 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
536230 TTCAAAGAAA
536240 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
536261 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
536275 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
536296 TATTT
1 CATTT
536301 TTTTAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:536335 original size:34 final size:34
Alignment explanation
Indices: 536243--536369 Score: 141
Period size: 34 Copynumber: 3.7 Consensus size: 34
536233 AAAGAAACAT
** *
536243 TTACCAAACTTTGAAAACCA--TTTTCAAAGAAACAT
1 TTACCAAAC-TTGAAAACCATTTTTTCAAAG--TTAG
* *
536278 TTACCAAACTTTGAAAACTATTTTTTTAAAGTTAG
1 TTACCAAAC-TTGAAAACCATTTTTTCAAAGTTAG
*
536313 TTACCAAACTTGAAAACCATTTTTTCAAAGTTGG
1 TTACCAAACTTGAAAACCATTTTTTCAAAGTTAG
*
536347 TTGCCAAACTTGAAAACCATTTT
1 TTACCAAACTTGAAAACCATTTT
536370 AATACTTTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
34 44 0.54
35 29 0.36
37 8 0.10
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (34 bp):
TTACCAAACTTGAAAACCATTTTTTCAAAGTTAG
Found at i:544112 original size:24 final size:21
Alignment explanation
Indices: 544078--544125 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 21
544068 TCTATAAAAG
*
544078 TTTTTTCTCATTTTCCTTTTTC
1 TTTTTTCTCATTTT-CTTTTCC
544100 TTTTTTCTTTCATTTTCTTTTCC
1 TTTTTTC--TCATTTTCTTTTCC
544123 TTT
1 TTT
544126 GTTCGAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 9 0.39
24 7 0.30
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTTCTCATTTTCTTTTCC
Found at i:549386 original size:27 final size:27
Alignment explanation
Indices: 549348--549400 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
549338 CCCGGCGCAA
549348 AATTGTTTTAGCGGCGTTTAAAAATAC
1 AATTGTTTTAGCGGCGTTTAAAAATAC
549375 AATTGTTTTAGCGGCGTTTAAAAATA
1 AATTGTTTTAGCGGCGTTTAAAAATA
549401 TCGTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (27 bp):
AATTGTTTTAGCGGCGTTTAAAAATAC
Found at i:550708 original size:16 final size:16
Alignment explanation
Indices: 550687--550724 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
550677 TTAAAATTTT
550687 AAATATAAT-TTAATTA
1 AAATATAATATTAA-TA
*
550703 AAATATAATATTTATA
1 AAATATAATATTAATA
550719 AAATAT
1 AAATAT
550725 TAGTTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATAATATTAATA
Found at i:553816 original size:37 final size:36
Alignment explanation
Indices: 553741--553816 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
553731 TTTTTATATT
*
553741 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
553777 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
553814 TTT
1 TTT
553817 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:559913 original size:15 final size:15
Alignment explanation
Indices: 559893--559922 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
559883 AAGGAACGGT
559893 AGGGGTAGAGGAAGA
1 AGGGGTAGAGGAAGA
*
559908 AGGGGTGGAGGAAGA
1 AGGGGTAGAGGAAGA
559923 CAAAGAGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.57, T:0.07
Consensus pattern (15 bp):
AGGGGTAGAGGAAGA
Found at i:561842 original size:39 final size:39
Alignment explanation
Indices: 561778--561868 Score: 157
Period size: 39 Copynumber: 2.4 Consensus size: 39
561768 TTAAACATTG
* *
561778 ATTTGTAT-TATAGTACTATAATATTTAATTGAACATCT
1 ATTTGTATAAATAATACTATAATATTTAATTGAACATCT
561816 ATTTGTATAAATAATACTATAATATTTAATTGAACATCT
1 ATTTGTATAAATAATACTATAATATTTAATTGAACATCT
561855 ATTTGTATAAATAA
1 ATTTGTATAAATAA
561869 CCTAACTTCC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 8 0.16
39 42 0.84
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (39 bp):
ATTTGTATAAATAATACTATAATATTTAATTGAACATCT
Found at i:563797 original size:21 final size:22
Alignment explanation
Indices: 563771--563814 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
563761 TGTGTATGTA
563771 TGTATGTATGAAT-CATGTATG
1 TGTATGTATGAATGCATGTATG
*
563792 TGTATGTATGCATGCATGTATG
1 TGTATGTATGAATGCATGTATG
563814 T
1 T
563815 TTAAGGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (22 bp):
TGTATGTATGAATGCATGTATG
Found at i:569746 original size:18 final size:17
Alignment explanation
Indices: 569706--569749 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
569696 ACAAAATAAT
*
569706 AATAATAATAATTTTAC
1 AATAATAATAATATTAC
*
569723 ACATAATAATACTATTATC
1 A-ATAATAATAATATTA-C
569742 AATAATAA
1 AATAATAA
569750 AATTCTAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 20 0.87
19 2 0.09
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAATAATATTAC
Found at i:577625 original size:19 final size:20
Alignment explanation
Indices: 577588--577625 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
577578 GAAATTTTTT
* *
577588 TATTTTTAATAAAATTAGTA
1 TATTCTTAATAAAAATAGTA
577608 TATTCTTAA-AAAAATAGT
1 TATTCTTAATAAAAATAGT
577626 TTAAGGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
TATTCTTAATAAAAATAGTA
Found at i:577972 original size:15 final size:15
Alignment explanation
Indices: 577948--578020 Score: 137
Period size: 15 Copynumber: 4.9 Consensus size: 15
577938 ATAAGGTTAT
*
577948 TTATTTTAAAATAAA
1 TTATTATAAAATAAA
577963 TTATTATAAAATAAA
1 TTATTATAAAATAAA
577978 TTATTATAAAATAAA
1 TTATTATAAAATAAA
577993 TTATTATAAAATAAA
1 TTATTATAAAATAAA
578008 TTATTATAAAATA
1 TTATTATAAAATA
578021 TGGATTGATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTATTATAAAATAAA
Found at i:578040 original size:37 final size:33
Alignment explanation
Indices: 577963--578075 Score: 99
Period size: 30 Copynumber: 3.4 Consensus size: 33
577953 TTAAAATAAA
* * * *
577963 TTATTATAAAATAAATTATTA-TA-A-AATAAA
1 TTATTTTAAAATAAATTATTAGTATAGATTGAT
*
577993 TTATTATAAAATAAATTATTA-TAAAATATGGATTGAT
1 TTATTTTAAAATAAATTATTAGT---ATA--GATTGAT
*
578030 TTATTTTAAAATAATTTATTAGTATAGATTGAT
1 TTATTTTAAAATAAATTATTAGTATAGATTGAT
578063 TTATTTTAAAATA
1 TTATTTTAAAATA
578076 TAGATTGATT
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
30 22 0.31
33 21 0.30
34 1 0.01
35 3 0.04
37 22 0.31
38 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (33 bp):
TTATTTTAAAATAAATTATTAGTATAGATTGAT
Found at i:578077 original size:22 final size:22
Alignment explanation
Indices: 578052--578202 Score: 86
Period size: 22 Copynumber: 6.0 Consensus size: 22
578042 AATTTATTAG
578052 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
578074 TATAGATTGATTTATTTTAAATAA
1 TATAGATTGATTTATTTT-AA-AA
*
578098 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-TAG-ATTGA-T---TTATTTTAAAA
*
578128 TATGGATTGATTTATTTTAAATAA
1 TATAGATTGATTTATTTT-AA-AA
*
578152 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-TAG-ATTGA-T---TTATTTTAAAA
*
578182 TATGGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
578203 TAATTTATTA
Statistics
Matches: 102, Mismatches: 7, Indels: 40
0.68 0.05 0.27
Matches are distributed among these distances:
22 35 0.34
23 4 0.04
24 4 0.04
25 2 0.02
26 12 0.12
27 9 0.09
28 12 0.12
29 2 0.02
30 4 0.04
31 4 0.04
32 14 0.14
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:578116 original size:32 final size:32
Alignment explanation
Indices: 578078--578180 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 32
578068 TTAAAATATA
578078 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
578110 GATTGATTTA-TTT---TAA---A--A-TATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
578132 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
578164 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
578181 ATATGGATTG
Statistics
Matches: 61, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
22 14 0.23
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 31 0.51
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAGTATG
Found at i:578120 original size:54 final size:54
Alignment explanation
Indices: 578008--578212 Score: 374
Period size: 54 Copynumber: 3.8 Consensus size: 54
577998 ATAAAATAAA
* *
578008 TTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTAGTATAGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTAGTATGGATTGAT
*
578063 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
578117 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
578171 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
578213 TTGTAGTTGT
Statistics
Matches: 146, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
54 119 0.82
55 27 0.18
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (54 bp):
TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:578262 original size:31 final size:31
Alignment explanation
Indices: 578227--578285 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
578217 AGTTGTATGG
* *
578227 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
578258 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
578286 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:579147 original size:12 final size:12
Alignment explanation
Indices: 579130--579156 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
579120 GGGCGACCTA
579130 CGACGTGGCTTC
1 CGACGTGGCTTC
579142 CGACGTGGCTTC
1 CGACGTGGCTTC
579154 CGA
1 CGA
579157 TGAGGGTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.33, G:0.33, T:0.22
Consensus pattern (12 bp):
CGACGTGGCTTC
Found at i:579683 original size:17 final size:17
Alignment explanation
Indices: 579661--579696 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
579651 TTATTAGTTT
579661 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
579678 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
579695 GT
1 GT
579697 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (17 bp):
GTTAGTTTAGGGTTAGG
Found at i:579903 original size:30 final size:30
Alignment explanation
Indices: 579834--579939 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
579824 TTTAGTTAAT
* *
579834 TAGTTTTTTAGTAGTGAA-TTATAATTAAAAAA
1 TAGTTTATTAGT--TGAAGTTAT-ATTAAAGAA
* *
579866 TATTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
579896 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
579926 TAGTTTATTAGTTG
1 TAGTTTATTAGTTG
579940 TTTAAAGAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 53 0.79
31 4 0.06
32 10 0.15
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAGAA
Found at i:579934 original size:15 final size:16
Alignment explanation
Indices: 579881--579935 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
579871 TATTAGTTTA
579881 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
**
579897 AGTT-TATTAGTTG-A-
1 AGTTATATTA-AAGAAT
579911 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
579927 AGTT-TATTA
1 AGTTATATTA
579936 GTTGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 17 0.55
16 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:580020 original size:15 final size:16
Alignment explanation
Indices: 579992--580025 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
579982 GTTTGTTACT
579992 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
580008 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
580023 TTA
1 TTA
580026 ATTTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:582178 original size:14 final size:14
Alignment explanation
Indices: 582159--582206 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
582149 TATTTATAAT
582159 AAATCATTACTATC
1 AAATCATTACTATC
582173 AAATCATTAC--T-
1 AAATCATTACTATC
582184 AAATCATTACTATC
1 AAATCATTACTATC
582198 AAATCATTA
1 AAATCATTA
582207 AAAATTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.32
12 1 0.03
13 1 0.03
14 19 0.61
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:582189 original size:11 final size:11
Alignment explanation
Indices: 582158--582255 Score: 52
Period size: 11 Copynumber: 9.2 Consensus size: 11
582148 ATATTTATAA
582158 TAAATCATTAC
1 TAAATCATTAC
582169 TATCAAATCATTAC
1 --T-AAATCATTAC
582183 TAAATCATTAC
1 TAAATCATTAC
582194 TATCAAATCATTA-
1 --T-AAATCATTAC
*
582207 -AAA--ATTAA
1 TAAATCATTAC
*
582215 T-AATAATT--
1 TAAATCATTAC
*
582223 T-AATTATTAC
1 TAAATCATTAC
582233 T-AATCATTAC
1 TAAATCATTAC
582243 TAAATCATTAC
1 TAAATCATTAC
582254 TA
1 TA
582256 TCAAATCATT
Statistics
Matches: 72, Mismatches: 2, Indels: 24
0.73 0.02 0.24
Matches are distributed among these distances:
7 4 0.06
8 9 0.12
9 3 0.04
10 13 0.18
11 21 0.29
12 1 0.01
13 2 0.03
14 19 0.26
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATCATTAC
Found at i:582238 original size:60 final size:60
Alignment explanation
Indices: 582174--582485 Score: 561
Period size: 60 Copynumber: 5.2 Consensus size: 60
582164 ATTACTATCA
*
582174 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTAATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
582234 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
582294 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
582354 AATCATTATTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
582414 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
582474 AAATCATTACTA
1 -AATCATTACTA
582486 TCAAATCATT
Statistics
Matches: 244, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
60 233 0.95
61 11 0.05
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (60 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:582312 original size:120 final size:120
Alignment explanation
Indices: 582253--583024 Score: 916
Period size: 120 Copynumber: 7.0 Consensus size: 120
582243 TAAATCATTA
*
582253 CTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTACTATC
1 CTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATC
* * *
582318 AAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTATTAAATCATTA
66 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
*
582373 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATC
1 CTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATC
582438 AAATCATTAAAAATTAATAATAATTTC------A-T--T-ATTACTAAATCATTA
66 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
*
582483 CTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTACTATC
1 CTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATC
* *
582548 AAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTA
66 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
* *
582603 CTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTATTAAATCATTACTATC
1 CTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATC
*
582668 AAATCATTAAAAATTAATAATAATTTC-------GT--T-ATTACTAAATCATTA
66 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
* *
582713 CTATCAAATCATTAAAAATTAATAATAAATTCATTATTACTAATCATTACT--ATCA--A--AT-
1 CTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATC
* *
582771 ---T-ATTAAACATTAATAATAATTTC---A-T--T----ATTACT-GATCATTA
66 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
* *
582811 CTATCAAATCATTAAAAATTAATAATAATTTCA-------T--T-ATTACT-GATCATTACTATC
1 CTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATC
582865 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
66 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
*
582920 ATATCAAATCATTAAATATTAATAATAATTTC------A-T--T-ATTACT-AATCATTACTATC
1 CTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATC
* *
582974 AAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAAATC
66 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
583025 TTATAAATAC
Statistics
Matches: 591, Mismatches: 27, Indels: 79
0.85 0.04 0.11
Matches are distributed among these distances:
88 6 0.01
89 5 0.01
91 2 0.00
93 2 0.00
97 1 0.00
98 60 0.10
99 27 0.05
100 2 0.00
101 1 0.00
102 1 0.00
104 3 0.01
106 1 0.00
108 10 0.02
109 106 0.18
110 164 0.28
111 2 0.00
113 2 0.00
114 1 0.00
116 1 0.00
117 1 0.00
119 1 0.00
120 192 0.32
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (120 bp):
CTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATC
AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
Found at i:582422 original size:49 final size:49
Alignment explanation
Indices: 582356--583020 Score: 405
Period size: 60 Copynumber: 12.4 Consensus size: 49
582346 TTATTACTAA
582356 TCATTATTA--AATCATTACTATCAAATCATTAAAAATTAATAATAATT
1 TCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT
582403 TCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATT
1 TC------A-T--T-ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATT
* *
582463 TCATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATT
1 TCATTATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATT
* *
582513 TCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATT
1 TC------A-T--T-ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATT
* *
582573 TCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATT
1 TC------A-T--T-ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATT
* * *
582633 TCATTATTACTAATCATTA-T-T-AAATCATTACTATCAAATCATTAAAAATT
1 TCATTATTACTAATCATTACTATCAAATCATTA--A--AAATTAATAATAATT
* * * * * * *
582683 AATAATAATTTCGT--T-ATTACTAAATC-ATTACTATCAAATCATTAAAAATTAATAAT
1 --TCATTATTAC-TAATCATTACT--ATCAAAT-C-ATTAAA-AATTAATAA-TAAT--T
** * * * * * *
582739 AAATTCATTATTACTAATCATTACTATCAAATTATTAAACATTAATAATAATT
1 TCATT-ATTACTAATCAT-T--ACTATCAAATCATTAAAAATTAATAATAATT
*
582792 TCATTATTACTGATCATTACTATCAAATCATTAAAAATTAATAATAATT
1 TCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT
*
582841 TCATTATTACTGATCATTACTATCAAATCATTAAAAATTAATAATAATT
1 TCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT
* *
582890 TCATTATTACTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATT
1 TCATTATTACTAATCATTACT--ATCA--AATCATTAAA-AATT--A-A-TAA---TAATT
*
582950 TCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATT
1 TCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT
*
582999 TCATCATTACTAATCATTACTA
1 TCATTATTACTAATCATTACTA
583021 AATCTTATAA
Statistics
Matches: 516, Mismatches: 40, Indels: 122
0.76 0.06 0.18
Matches are distributed among these distances:
46 9 0.02
47 3 0.01
48 2 0.00
49 132 0.26
50 66 0.13
51 8 0.02
52 24 0.05
53 20 0.04
54 15 0.03
55 9 0.02
56 22 0.04
57 20 0.04
58 7 0.01
59 3 0.01
60 176 0.34
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (49 bp):
TCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT
Found at i:582523 original size:39 final size:39
Alignment explanation
Indices: 582479--582644 Score: 95
Period size: 39 Copynumber: 4.2 Consensus size: 39
582469 TTACTAAATC
*
582479 ATTACTATCAAATCATTAAATATTAATAACAATTTCATT
1 ATTACTATCAAATCATTAAATATTAATAACAATTTAATT
* * * * *
582518 ATTACTAATC--ATTACTAAATCATTACTATCAAATCATTAAAT
1 ATTACT-ATCAAATCATTAAAT-ATTAATAAC-AAT--TTAATT
* * * * * * ** * * *
582560 ATTAATAACAATTTCATT-ATTACTAATCATTACTAAATC
1 ATTACTATCAA-ATCATTAAATATTAATAACAATTTAATT
*
582599 ATTACTATCAAATCATTAAATATTAATAACAATTTCATT
1 ATTACTATCAAATCATTAAATATTAATAACAATTTAATT
582638 ATTACTA
1 ATTACTA
582645 ATCATTATTA
Statistics
Matches: 84, Mismatches: 34, Indels: 18
0.62 0.25 0.13
Matches are distributed among these distances:
38 13 0.15
39 44 0.52
40 6 0.07
41 3 0.04
42 13 0.15
43 2 0.02
44 3 0.04
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (39 bp):
ATTACTATCAAATCATTAAATATTAATAACAATTTAATT
Found at i:582532 original size:60 final size:60
Alignment explanation
Indices: 582468--582971 Score: 479
Period size: 60 Copynumber: 8.1 Consensus size: 60
582458 TAATTTCATT
582468 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
582528 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
582588 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
* * * *
582648 ATTATTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCGTTATTACTAAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT-AATC
** * * * *
582709 ATTACTATCAAATCATTAAAAAT-TAAT-AATAAATTCATT-ATTACTAA--TCATTACTA-TCA
1 ATTAC--T-AAATCATT-ACTATCAAATCATTAAA-T-ATTAATAAC-AATTTCATTATTACT-A
582768 A--
58 ATC
* * * * * *
582769 ATTATTAAA-CATTAATAAT-AATTTCATTATTACTGATCATTACTATCAAATCATTAAAAATTA
1 ATTACTAAATCATTACT-ATCAA-ATCATTA--A---AT-ATTAATAAC-AAT--TT---CATTA
* *
582832 ATAATAATTTC
52 TTACTAA--TC
* * * *
582843 ATTATTACTGATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTA--AATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
* *
582905 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
582965 ATTACTA
1 ATTACTA
582972 TCAAATCATT
Statistics
Matches: 371, Mismatches: 40, Indels: 66
0.78 0.08 0.14
Matches are distributed among these distances:
55 2 0.01
56 7 0.02
57 4 0.01
58 4 0.01
60 234 0.63
61 8 0.02
62 16 0.04
63 18 0.05
64 23 0.06
65 8 0.02
67 3 0.01
69 3 0.01
70 14 0.04
71 2 0.01
74 8 0.02
76 9 0.02
77 8 0.02
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
Found at i:582542 original size:21 final size:22
Alignment explanation
Indices: 582468--582669 Score: 79
Period size: 21 Copynumber: 10.0 Consensus size: 22
582458 TAATTTCATT
582468 ATTACTAAATCATTACT-ATCAA
1 ATTACTAAATCATTACTAATC-A
* * *
582490 ATCATTAAAT-ATTAATAA-CA
1 ATTACTAAATCATTACTAATCA
* *
582510 ATT--T-CATTATTACTAATC-
1 ATTACTAAATCATTACTAATCA
582528 ATTACTAAATCATTACT-ATCAA
1 ATTACTAAATCATTACTAATC-A
* * *
582550 ATCATTAAAT-ATTAATAA-CA
1 ATTACTAAATCATTACTAATCA
* *
582570 ATT--T-CATTATTACTAATC-
1 ATTACTAAATCATTACTAATCA
582588 ATTACTAAATCATTACT-ATCAA
1 ATTACTAAATCATTACTAATC-A
* * *
582610 ATCATTAAAT-ATTAATAA-CA
1 ATTACTAAATCATTACTAATCA
* *
582630 ATT--T-CATTATTACTAATC-
1 ATTACTAAATCATTACTAATCA
*
582648 ATTATTAAATCATTACT-ATCA
1 ATTACTAAATCATTACTAATCA
582669 A
1 A
582670 ATCATTAAAA
Statistics
Matches: 133, Mismatches: 24, Indels: 47
0.65 0.12 0.23
Matches are distributed among these distances:
17 6 0.05
18 33 0.25
19 3 0.02
20 21 0.16
21 43 0.32
22 27 0.20
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTACTAAATCATTACTAATCA
Found at i:582551 original size:230 final size:230
Alignment explanation
Indices: 582174--583024 Score: 1082
Period size: 230 Copynumber: 3.8 Consensus size: 230
582164 ATTACTATCA
*
582174 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTAATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAA-T--TAATAA--TAA-T-TT-C--ATTA
582239 TTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACT
56 TTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACT
*
582304 AAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTATTAAATC
121 AAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATC
582369 ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
186 ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
582414 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAATC
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAATC
582479 ATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTAC
66 ATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTAC
582544 TATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
131 TATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
* *
582609 AATCATTAAATATTAATAACAATTTCATTATTACT
196 AATCATTAAAAATTAATAATAATTTCATTATTACT
* *
582644 AATCATTATTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCGTTATTACTAAATC
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAATC
* * *
582709 ATTACTATCAAATCATTAAAAATTAATAATAAATTCATTATTACTAATCATTACT--ATCA--A-
66 ATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTAC
* * *
582769 -AT----T-ATTAAACATTAATAATAATTTC------A-T--T-ATTACT-GATCATTACTATCA
131 TATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
582817 AATCATTAAAAATTAATAATAATTTC------A-T
196 AATCATTAAAAATTAATAATAATTTCATTATTACT
*
582845 --T-ATTACT-GATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT-AATC
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAATC
* * * * *
582905 ATTAC--T-AAATCATT-AATATCAA-ATC-ATTAAAT-ATTAATAATAATTTCATTATTACTAA
66 ATTACTATCAAATCATTAAATATTAATAACAATT---TCATTATTACTAA--TCATTACTA--AA
* *
582963 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAAATC
124 TCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATC
583025 TTATAAATAC
Statistics
Matches: 555, Mismatches: 27, Indels: 80
0.84 0.04 0.12
Matches are distributed among these distances:
190 2 0.00
191 1 0.00
192 15 0.03
193 9 0.02
194 8 0.01
196 9 0.02
197 47 0.08
198 9 0.02
199 1 0.00
200 1 0.00
201 1 0.00
202 3 0.01
206 1 0.00
207 21 0.04
208 37 0.07
209 6 0.01
210 1 0.00
212 1 0.00
213 2 0.00
214 1 0.00
216 1 0.00
217 6 0.01
218 3 0.01
219 20 0.04
220 1 0.00
224 2 0.00
226 1 0.00
228 4 0.01
230 290 0.52
232 1 0.00
233 2 0.00
234 1 0.00
235 3 0.01
237 6 0.01
239 1 0.00
240 37 0.07
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (230 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAATC
ATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTAC
TATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
AATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:582942 original size:21 final size:22
Alignment explanation
Indices: 582910--582992 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 22
582900 TAATCATTAC
582910 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATCAT
*
582932 TAAAT-ATTAATAAT-AATTTCATTAT
1 TAAATCATTAAT-ATCAA----ATCAT
*
582957 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTAATATCAAATCAT
582981 TAAAT-ATTAATA
1 TAAATCATTAATA
582993 ATAATTTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 19
0.68 0.06 0.27
Matches are distributed among these distances:
21 14 0.29
22 10 0.21
24 6 0.12
25 6 0.12
27 5 0.10
28 7 0.15
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:582972 original size:109 final size:109
Alignment explanation
Indices: 582804--583024 Score: 397
Period size: 109 Copynumber: 2.0 Consensus size: 109
582794 ATTATTACTG
* *
582804 ATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTGATCATTACTATCAAAT
1 ATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAAT
*
582869 CATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAA
66 CATTAAAAATTAATAATAATTTCATCATTACTAATCATTACTAA
*
582913 ATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAAT
1 ATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAAT
*
582978 CATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAA
66 CATTAAAAATTAATAATAATTTCATCATTACTAATCATTACTAA
583022 ATC
1 ATC
583025 TTATAAATAC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (109 bp):
ATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAAT
CATTAAAAATTAATAATAATTTCATCATTACTAATCATTACTAA
Found at i:583094 original size:158 final size:157
Alignment explanation
Indices: 582175--583018 Score: 819
Period size: 170 Copynumber: 5.1 Consensus size: 157
582165 TTACTATCAA
* * *
582175 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTAATTATTACTAATCAT
1 ATCATTACT-AATCATTAC-ATCAAATCATTAAAAATTAATAATAATTTCATAAATACTAATCAT
* * *
582240 TACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTA
64 TACTAAATCATGAATATCAAATCATTAAATATTAATAATAATTTC------A-T--T-ATTACT-
* *
582305 AATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTA
118 AATCATTACTATCAAATCATTAAAAATTAAT---AA--T-A--ATT--TC
* * *
582355 ATCATTATTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCAT
1 ATCATTACT-AATCATTAC-ATCAAATCATTAAAAATTAATAATAATTTCATAAATACTAATCAT
* * *
582420 TACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAATCATTACT
64 TACTAAATCATGAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT-AATCATTACT
* *
582485 ATCAAATCATTAAATATTAATAACAATTTCATTATTACTA
128 ATCAAATCATTAAAAATTAAT---AA--T-A--ATT--TC
* * * *
582525 ATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCAT
1 ATCATTACT-AATCATTAC-ATCAAATCATTAAAAATTAATAATAATTTCATAAATACTAATCAT
* * *
582590 TACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTATTA
64 TACTAAATCATGAATATCAAATCATTAAATATTAATAATAATTTCATTA-T--T-A-C-----T-
582655 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTC
118 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTC
* * * * *
582695 GTTATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAAATTCATTATTACTAATCAT
1 ATCATTACT-AATCATTAC-ATCAAATCATTAAAAATTAATAATAATTTCATAAATACTAATCAT
* *
582760 TACT--ATC---AA-AT----T-ATTAAACATTAATAATAATTTCATTATTACTGATCATTACTA
64 TACTAAATCATGAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTA
582814 TCAAATCATTAAAAATTAATAATAATTTC
129 TCAAATCATTAAAAATTAATAATAATTTC
* * * *
582843 ATTATTACTGATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATT
1 ATCATTACTAATCATTAC-ATCAAATCATTAAAAATTAATAATAATTTCATAAATACTAATCATT
*
582908 ACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAT
65 ACTAAATCATGAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAT
*
582973 CAAATCATTAAATATTAATAATAATTTC
130 CAAATCATTAAAAATTAATAATAATTTC
583001 ATCATTACTAATCATTAC
1 ATCATTACTAATCATTAC
583019 TAAATCTTAT
Statistics
Matches: 615, Mismatches: 28, Indels: 64
0.87 0.04 0.09
Matches are distributed among these distances:
147 57 0.09
148 47 0.08
149 4 0.01
152 2 0.00
153 2 0.00
154 1 0.00
155 1 0.00
156 1 0.00
157 1 0.00
158 85 0.14
159 24 0.04
160 1 0.00
164 2 0.00
165 1 0.00
168 3 0.00
170 231 0.38
171 2 0.00
172 3 0.00
173 2 0.00
174 3 0.00
175 2 0.00
177 2 0.00
180 138 0.22
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (157 bp):
ATCATTACTAATCATTACATCAAATCATTAAAAATTAATAATAATTTCATAAATACTAATCATTA
CTAAATCATGAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATC
AAATCATTAAAAATTAATAATAATTTC
Found at i:585879 original size:24 final size:24
Alignment explanation
Indices: 585852--585914 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
585842 ATTTAACTTG
*
585852 ATTAATTGATTGATTACTAA-TATT
1 ATTAATT-ATTGATTAATAATTATT
*
585876 ATTAA-TAATGATTTAATAATTATT
1 ATTAATTATTGA-TTAATAATTATT
585900 ATTAATCTATTGATT
1 ATTAAT-TATTGATT
585915 TGATATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 4 0.12
23 7 0.22
24 14 0.44
25 2 0.06
26 5 0.16
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTAATTATTGATTAATAATTATT
Found at i:586225 original size:17 final size:17
Alignment explanation
Indices: 586172--586231 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
586162 AATATAAATA
*
586172 AAACAAAATATTTTTTT
1 AAACACAATATTTTTTT
* *
586189 AAAACAACACTAAATATTTTT
1 -AAAC-ACA--ATATTTTTTT
586210 AAACACAATATTTTTTT
1 AAACACAATATTTTTTT
586227 AAACA
1 AAACA
586232 AAAATTATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 13 0.38
18 4 0.12
19 5 0.15
20 4 0.12
21 8 0.24
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
AAACACAATATTTTTTT
Found at i:586752 original size:21 final size:21
Alignment explanation
Indices: 586719--586767 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
586709 AATATAATAT
586719 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
586740 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
586761 ATTAACT
1 A-TAACT
586768 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:587290 original size:13 final size:13
Alignment explanation
Indices: 587272--587298 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
587262 TGATGATGCA
587272 GACCTACCATGTC
1 GACCTACCATGTC
587285 GACCTACCATGTC
1 GACCTACCATGTC
587298 G
1 G
587299 CCGGGACTCC
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:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (13 bp):
GACCTACCATGTC
Found at i:587320 original size:29 final size:29
Alignment explanation
Indices: 587278--587356 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
587268 TGCAGACCTA
*
587278 CCATGTCGACCTACCATGTCGCCGGGACT
1 CCATGGCGACCTACCATGTCGCCGGGACT
587307 CCATGGCGACCTACCATGTCGCCGGGACT
1 CCATGGCGACCTACCATGTCGCCGGGACT
587336 CCATGGCGACCTACCATGTCG
1 CCATGGCGACCTACCATGTCG
587357 TCGGCCATGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.18, C:0.38, G:0.25, T:0.19
Consensus pattern (29 bp):
CCATGGCGACCTACCATGTCGCCGGGACT
Found at i:587372 original size:25 final size:27
Alignment explanation
Indices: 587277--587374 Score: 119
Period size: 29 Copynumber: 3.6 Consensus size: 27
587267 ATGCAGACCT
*
587277 ACCATGTCGACCTACCATGTCGCCGGG
1 ACCATGGCGACCTACCATGTCGCCGGG
587304 ACTCCATGGCGACCTACCATGTCGCCGGG
1 A--CCATGGCGACCTACCATGTCGCCGGG
*
587333 ACTCCATGGCGACCTACCATGTCGTC-GG
1 A--CCATGGCGACCTACCATGTCGCCGGG
*
587361 -CCATGGCAACCTAC
1 ACCATGGCGACCTAC
587375 GATAGAACCA
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.20
27 1 0.02
28 2 0.03
29 50 0.76
ACGTcount: A:0.19, C:0.38, G:0.24, T:0.18
Consensus pattern (27 bp):
ACCATGGCGACCTACCATGTCGCCGGG
Found at i:587637 original size:29 final size:30
Alignment explanation
Indices: 587593--587735 Score: 242
Period size: 29 Copynumber: 4.9 Consensus size: 30
587583 AAAGAATGTT
*
587593 GGACGCCGGGCATGCATGGCGACCTTAT-A
1 GGACGCCGGGCGTGCATGGCGACCTTATAA
587622 GGACGCCGGGCGTGCATGGCGACCTTAT-A
1 GGACGCCGGGCGTGCATGGCGACCTTATAA
587651 GGACGCCGGGCGTGCATGGCGACC-TATAA
1 GGACGCCGGGCGTGCATGGCGACCTTATAA
587680 GGACGCCGGGCGTGCATGGCGACC-TATAA
1 GGACGCCGGGCGTGCATGGCGACCTTATAA
587709 GGACGCCGGGCGTGCATGGCGA-CTTAT
1 GGACGCCGGGCGTGCATGGCGACCTTAT
587736 GTTGTCACTG
Statistics
Matches: 111, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
28 4 0.04
29 107 0.96
ACGTcount: A:0.19, C:0.27, G:0.38, T:0.16
Consensus pattern (30 bp):
GGACGCCGGGCGTGCATGGCGACCTTATAA
Found at i:589418 original size:2 final size:2
Alignment explanation
Indices: 589411--589436 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
589401 TATGTTAATC
589411 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
589437 CCAATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:589862 original size:9 final size:9
Alignment explanation
Indices: 589848--589876 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
589838 ACCTCGACTC
589848 TATATGATA
1 TATATGATA
589857 TATATGATA
1 TATATGATA
589866 TATAT-ATA
1 TATATGATA
589874 TAT
1 TAT
589877 CACATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (9 bp):
TATATGATA
Done.