Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008806.1 Hibiscus syriacus cultivar Beakdansim tig00111959_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: 454619
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:358591 original size:25 final size:24
Alignment explanation
Indices: 358563--358643 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
358553 ACTACTTAGT
358563 AGTTATCCTTATCTAACTTTCTAAG
1 AGTTAT-CTTATCTAACTTTCTAAG
* * *
358588 AGTTAAT-TTAAACTAAAC-TACTTAG
1 AGTT-ATCTT-ATCT-AACTTTCTAAG
358613 TAGTTATCTTTATCTAACTTTCTAAG
1 -AGTTATC-TTATCTAACTTTCTAAG
358639 AGTTA
1 AGTTA
358644 GTGTTATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 2 0.05
25 22 0.51
26 17 0.40
27 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (24 bp):
AGTTATCTTATCTAACTTTCTAAG
Found at i:358615 original size:51 final size:51
Alignment explanation
Indices: 358539--358680 Score: 203
Period size: 51 Copynumber: 2.8 Consensus size: 51
358529 GAACAAGTAT
358539 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
*
358590 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* * * * * * *
358641 TTAGTGTTATATTAAAGTACTAATTAATTATCCTTATCTA
1 TTAAT-TTAAACTAAACTACTTAGTAGTTATCCTTATCTA
358681 TTGCATAACC
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 54 0.67
52 27 0.33
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (51 bp):
TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
Found at i:361568 original size:3 final size:3
Alignment explanation
Indices: 361562--361600 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
361552 CCATGATCAT
* * *
361562 CAC CAC CAC CAC CAT CAC CAT CAT CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
361601 TTCATGTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.59, G:0.00, T:0.08
Consensus pattern (3 bp):
CAC
Found at i:361573 original size:21 final size:21
Alignment explanation
Indices: 361547--361596 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
361537 CCTTCATTAT
* *
361547 CACCACCATGATCATCACCAC
1 CACCACCATCACCATCACCAC
*
361568 CACCACCATCACCATCATCAC
1 CACCACCATCACCATCACCAC
361589 CACCACCA
1 CACCACCA
361597 CCACTTCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.52, G:0.02, T:0.12
Consensus pattern (21 bp):
CACCACCATCACCATCACCAC
Found at i:361577 original size:15 final size:15
Alignment explanation
Indices: 361545--361600 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
361535 TACCTTCATT
** *
361545 ATCACCACCATGATC
1 ATCACCACCACCACC
361560 ATCACCACCACCACC
1 ATCACCACCACCACC
* *
361575 ATCACCATCATCACC
1 ATCACCACCACCACC
*
361590 ACCACCACCAC
1 ATCACCACCAC
361601 TTCATGTTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.34, C:0.52, G:0.02, T:0.12
Consensus pattern (15 bp):
ATCACCACCACCACC
Found at i:361580 original size:9 final size:9
Alignment explanation
Indices: 361557--361600 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
361547 CACCACCATG
*
361557 ATCATCACC
1 ATCACCACC
*
361566 ACCACCACC
1 ATCACCACC
*
361575 ATCACCATC
1 ATCACCACC
361584 ATCACCACC
1 ATCACCACC
*
361593 ACCACCAC
1 ATCACCAC
361601 TTCATGTTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.34, C:0.55, G:0.00, T:0.11
Consensus pattern (9 bp):
ATCACCACC
Found at i:363940 original size:16 final size:16
Alignment explanation
Indices: 363906--363940 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
363896 CCTAATCTTA
*
363906 TTCTTTCCTCTAATTC
1 TTCTTTCCTCTAATGC
*
363922 TTCTTTCCTCTTATGC
1 TTCTTTCCTCTAATGC
363938 TTC
1 TTC
363941 AAAGCTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.31, G:0.03, T:0.57
Consensus pattern (16 bp):
TTCTTTCCTCTAATGC
Found at i:364792 original size:75 final size:74
Alignment explanation
Indices: 364664--365533 Score: 1060
Period size: 75 Copynumber: 11.8 Consensus size: 74
364654 CAGTAACGAT
* * *
364664 TAATAATGTAAACGGT-TAAAAAAATAGGTGCTACCTATTACATTAAACTACCTACCAGTTTTTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC-GTTTTTT
*
364728 TGAAGGTTAC
65 TGAAGGTTGC
* * *
364738 TAATAATGTAAACGGTAAAAAAAAATAGGCGTTACCTATTATATTAAAACACCTACCAGTTTTTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC-GTTTTTT
* * *
364803 TAAAGATTAC
65 TGAAGGTTGC
* * *
364813 TAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAACTAACTACCGTTTTTTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGTTTTTTT
364878 -AAGGTTGC
66 GAAGGTTGC
* *
364886 TAATAATGTAAACGGT-AAAAAAAATAGGCGCTACCTATTATATTAAAATACCTACCGATTTATT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCG-TTTTTT
* * *
364950 TAAAGATTAC
65 TGAAGGTTGC
* * * * * *
364960 TAATAATATAAATGGTAAAATAAAATAGGCGCTACCTATTACATTAAACTGCCTATCGGTTTTTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTA-CCGTTTTTT
365025 T-AAGGTTGC
65 TGAAGGTTGC
* * *
365034 TAATAATGTAAACGGTAAAAAAAAGTAGGCGTTACCTATTACATTAAAATACCTA-CGGTTTTTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGTTTTTTT
365098 GAAGGTTGC
66 GAAGGTTGC
* * * **
365107 TAATAATGTAAACGGT-AAAAAAAATAAGCGCTACCTATTACATTAAAATACTTAACAATTTTTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGTTTTTTT
365171 GAAGGTTGC
66 GAAGGTTGC
* * * * *
365180 TAATAATGTAAACGGTAAAAAAAAATAGGTGCTACCTATTATATTAAACTACATATCGATTTTTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCG-TTTTTT
*
365245 TTAAGGTTGC
65 TGAAGGTTGC
* * *
365255 TAATAATGTAAATGGT--TAAAAAA-AGGCGCTACCTATTACATTAAAATACCTACCTGTTTGTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC-GTTTTTT
* ** *
365317 TAAATATTGT
65 TGAAGGTTGC
* * ** *
365327 TAATAATGTAAACGATAAAATAAAATAGGTACTACCTATTACATTAAAATATCTACCGGTGTTTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC-GT-TTTT
*
365392 TT-AAGGTTGT
64 TTGAAGGTTGC
* * * *
365402 TAATAATGTAAACGGT-AAAAAAACTAAGCGTTACCTATTACATTAAAATACCTACTGATTTTTT
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCG-TTTTTT
*
365466 TGAAAGTTGC
65 TGAAGGTTGC
* *
365476 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAACTGCCTACCG
1 TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCG
365534 GATATGTTGA
Statistics
Matches: 682, Mismatches: 97, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
72 129 0.19
73 98 0.14
74 192 0.28
75 256 0.38
76 7 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (74 bp):
TAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGTTTTTTT
GAAGGTTGC
Found at i:364952 original size:147 final size:146
Alignment explanation
Indices: 364664--365533 Score: 1082
Period size: 147 Copynumber: 5.9 Consensus size: 146
364654 CAGTAACGAT
* * *
364664 TAATAATGTAAACGGTTAAAAAAATAGGTGCTACCTATTACATTAAACTACCTACCAGTTTTTTT
1 TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC-GTTTTTTT
* * * *
364729 GAAGGTTACTAATAATGTAAACGGTAAAAAAAAATAGGCGTTACCTATTATATTAAAACACCTAC
65 -AAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTAC
* * *
364794 CAGTTTTTTTAAAGATTAC
129 C-GATTTTTTAAAGGTTGC
* *
364813 TAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAACTAACTACCGTTTTTTT
1 TAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGTTTTTTT
*
364878 AAGGTTGCTAATAATGTAAACGGT-AAAAAAAATAGGCGCTACCTATTATATTAAAATACCTACC
65 AAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC
* *
364942 GATTTATTTAAAGATTAC
130 GATTT-TTTAAAGGTTGC
* * * * *
364960 TAATAATATAAATGGTAAAATAAAATAGGCGCTACCTATTACATTAAACTGCCTATCGGTTTTTT
1 TAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTA-CCGTTTTTT
* *
365025 TAAGGTTGCTAATAATGTAAACGGTAAAAAAAAGTAGGCGTTACCTATTACATTAAAATACCTA-
64 TAAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTAC
* *
365089 CGGTTTTTTGAAGGTTGC
129 CGATTTTTTAAAGGTTGC
* * ** *
365107 TAATAATGTAAACGGTAAAAAAAATAAGCGCTACCTATTACATTAAAATACTTAACAATTTTTTG
1 TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCT-ACCGTTTTTTT
* * * * *
365172 AAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGTGCTACCTATTATATTAAACTACATATC
65 AAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC
*
365237 GATTTTTTTTAAGGTTGC
130 GA-TTTTTTAAAGGTTGC
* *
365255 TAATAATGTAAATGGT-TAAAAAA-AGGCGCTACCTATTACATTAAAATACCTACCTGTTTGTTT
1 TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC-GTTT-TTT
* ** * * * ** *
365318 AAATATTGTTAATAATGTAAACGATAAAATAAAATAGGTACTACCTATTACATTAAAATATCTAC
64 TAAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTAC
* * *
365383 CGGTGTTTTTTAAGGTTGT
129 CGAT-TTTTTAAAGGTTGC
* * * *
365402 TAATAATGTAAACGGTAAAAAAACTAAGCGTTACCTATTACATTAAAATACCTACTGATTTTTTT
1 TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCG-TTTTTTT
* * *
365467 GAAAGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAACTGCCTAC
65 -AAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTAC
365532 CG
129 CG
365534 GATATGTTGA
Statistics
Matches: 634, Mismatches: 73, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
145 2 0.00
146 127 0.20
147 223 0.35
148 99 0.16
149 149 0.24
150 34 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (146 bp):
TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGTTTTTTTA
AGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCG
ATTTTTTAAAGGTTGC
Found at i:365112 original size:221 final size:220
Alignment explanation
Indices: 364664--365533 Score: 1106
Period size: 221 Copynumber: 3.9 Consensus size: 220
364654 CAGTAACGAT
* * * *
364664 TAATAATGTAAACGGTTAAAAAAATAGGTGCTACCTATTACATTAAACTACCTACCAGTTTTTTT
1 TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC-GATTTTTT
* *
364729 GAAGGTTACTAATAATGTAAACGGTAAAAAAAAATAGGCGTTACCTATTATATTAAAAC-ACCTA
65 GAAGGTTACTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATT-AAACTACCTA
* * * *
364793 CCAGTTTTTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATT
129 TCGGTTTTTTTAAAGGTTGCTAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATT
* * *
364858 AAACTAACTACCGTTTTTTTAAGGTTGC
193 AAAATACCTACCGTTTTTTAAAGGTTGC
*
364886 TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTATATTAAAATACCTACCGATTTATTT
1 TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGATTT-TTT
* * * * * *
364951 AAAGATTACTAATAATATAAATGGTAAAATAAAATAGGCGCTACCTATTACATTAAACTGCCTAT
65 GAAGGTTACTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAACTACCTAT
*
365016 CGGTTTTTTT-AAGGTTGCTAATAATGTAAACGGTAAAAAAAAGTAGGCGTTACCTATTACATTA
130 CGGTTTTTTTAAAGGTTGCTAATAATGTAAACGGTAAAAAAAA-TAGGCGCTACCTATTACATTA
* *
365080 AAATACCTACGGTTTTTTGAAGGTTGC
194 AAATACCTACCGTTTTTTAAAGGTTGC
* * * *
365107 TAATAATGTAAACGGTAAAAAAAATAAGCGCTACCTATTACATTAAAATACTTAACAATTTTTTG
1 TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGATTTTTTG
* * * *
365172 AAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGTGCTACCTATTATATTAAACTACATATC
66 AAGGTTACTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAACTACCTATC
* * * *
365237 GATTTTTTTTAAGGTTGCTAATAATGTAAATGGT-TAAAAAA-AGGCGCTACCTATTACATTAAA
131 GGTTTTTTTAAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAA
** *
365300 ATACCTACCTGTTTGTTTAAATATTGT
196 ATACCTACC-GTTT-TTTAAAGGTTGC
* ** * *
365327 TAATAATGTAAACGATAAAATAAAATAGGTACTACCTATTACATTAAAATATCTACCGGTGTTTT
1 TAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGAT-TTTT
* ** * * * *
365392 TTAAGGTTGTTAATAATGTAAACGGT-AAAAAAACTAAGCGTTACCTATTACATTAAAATACCTA
64 TGAAGGTTACTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAACTACCTA
*
365456 -CTGATTTTTTTGAAA-GTTGCTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACA
129 TC-GGTTTTTTT-AAAGGTTGCTAATAATGTAAACGGT-AAAAAAAATAGGCGCTACCTATTACA
* *
365519 TTAAACTGCCTACCG
191 TTAAAATACCTACCG
365534 GATATGTTGA
Statistics
Matches: 566, Mismatches: 69, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
218 29 0.05
219 4 0.01
220 105 0.19
221 247 0.44
222 145 0.26
223 7 0.01
224 29 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (220 bp):
TAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGATTTTTTG
AAGGTTACTAATAATGTAAACGGTAAAAAAAAATAGGCGCTACCTATTACATTAAACTACCTATC
GGTTTTTTTAAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAA
ATACCTACCGTTTTTTAAAGGTTGC
Found at i:365570 original size:21 final size:21
Alignment explanation
Indices: 365544--365585 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
365534 GATATGTTGA
* *
365544 AAGTATCGATACTTTTTAAAT
1 AAGTATCGACACTTTTGAAAT
365565 AAGTATCGACACTTTTGAAAT
1 AAGTATCGACACTTTTGAAAT
365586 TTAAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (21 bp):
AAGTATCGACACTTTTGAAAT
Found at i:366398 original size:19 final size:18
Alignment explanation
Indices: 366377--366439 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 18
366367 TTGATTGTGA
366377 TTTTTTATTTATAATATT
1 TTTTTTATTTATAATATT
* *
366395 ATTTTTTATTTACATTAATT
1 -TTTTTTATTTATAAT-ATT
366415 TTTTTTATTT-T-ATATT
1 TTTTTTATTTATAATATT
366431 TTTTTTATT
1 TTTTTTATT
366440 ATGAATAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
16 12 0.31
17 1 0.03
19 23 0.59
20 3 0.08
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTATTTATAATATT
Found at i:366984 original size:20 final size:21
Alignment explanation
Indices: 366959--367051 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
366949 TTTTCCCAAT
*
366959 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
366979 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
367000 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
367020 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
367041 TCGCAATGCGA
1 TCGCAATGCGA
367052 TACTTACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:367004 original size:41 final size:41
Alignment explanation
Indices: 366959--367051 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
366949 TTTTCCCAAT
*
366959 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
367000 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
367041 TCGCAATGCGA
1 TCGCAATGCGA
367052 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:367064 original size:41 final size:41
Alignment explanation
Indices: 366978--367112 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
366968 GAATAAGTAA
* ** *
366978 ATCGCAATGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
367019 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
367060 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
* *
367101 TTTGCAACGCGA
1 ATCGCAACGCGA
367113 TACTGACTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 5 0.06
41 72 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:367065 original size:20 final size:20
Alignment explanation
Indices: 367040--367133 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
367030 AATTGGGAAA
*
367040 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
367060 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
367081 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
367101 TTTGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
367121 TTCGCAACGCGAT
1 ATCGCAACGCGAT
367134 TTACATAATC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 42 0.70
21 12 0.20
22 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:367349 original size:22 final size:22
Alignment explanation
Indices: 367321--367364 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
367311 CACTCTCTCA
367321 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
367343 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
367365 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:368999 original size:18 final size:18
Alignment explanation
Indices: 368978--369022 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
368968 TCCACTTCGG
* *
368978 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
368996 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
*
369014 GATCCATCA
1 GAGCCATCA
369023 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.47, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:369529 original size:20 final size:21
Alignment explanation
Indices: 369503--369560 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
369493 TTTCGCAACA
369503 CGAAATGACTATCGCAACGTG
1 CGAAATGACTATCGCAACGTG
*
369524 -GAAATGGCTATCGCAA--TG
1 CGAAATGACTATCGCAACGTG
**
369542 CGAAATGAAAATCGCAACG
1 CGAAATGACTATCGCAACG
369561 ACAAAATCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 13 0.43
20 15 0.50
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (21 bp):
CGAAATGACTATCGCAACGTG
Found at i:369568 original size:14 final size:14
Alignment explanation
Indices: 369549--369606 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
369539 ATGCGAAATG
369549 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
369563 AAAATCGTAACGCGAA
1 AAAATCGCAA--CGAC
369579 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
369595 AAAATCGCAACG
1 AAAATCGCAACG
369607 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:369587 original size:18 final size:18
Alignment explanation
Indices: 369495--369628 Score: 77
Period size: 19 Copynumber: 7.6 Consensus size: 18
369485 TAGTTTACTT
* *
369495 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGA-AA
* **
369514 TCGCAACGTGGAAATGGCTA
1 TCGCAACG-CGAAAT-GAAA
*
369534 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATG-AAA
*
369553 TCGCAA--CGACA--AAA
1 TCGCAACGCGAAATGAAA
*
369567 TCGTAACGCGAAATGAAA
1 TCGCAACGCGAAATGAAA
*
369585 TCGCAA--CGACA--AAA
1 TCGCAACGCGAAATGAAA
369599 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATG-AAA
*
369618 TCGCAATGCGA
1 TCGCAACGCGA
369629 TTGTGTTTCG
Statistics
Matches: 89, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
14 17 0.19
16 12 0.13
17 4 0.04
18 9 0.10
19 32 0.36
20 14 0.16
21 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (18 bp):
TCGCAACGCGAAATGAAA
Found at i:369591 original size:32 final size:33
Alignment explanation
Indices: 369533--369623 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
369523 GGAAATGGCT
*
369533 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
369566 ATCGTAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
369598 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
369624 TGCGATTGTG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:369645 original size:18 final size:16
Alignment explanation
Indices: 369624--369682 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 16
369614 AAAATCGCAA
369624 TGCGATTGTGTTTCGCGT
1 TGCGATT-T-TTTCGCGT
*
369642 TGCGATTTTGT--CGT
1 TGCGATTTTTTCGCGT
369656 TGCGATTTCATTTCGCGT
1 TGCGATTT--TTTCGCGT
369674 TGCGATTTT
1 TGCGATTTT
369683 GTCGTTGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 11 0.31
16 5 0.14
17 1 0.03
18 18 0.51
ACGTcount: A:0.08, C:0.17, G:0.27, T:0.47
Consensus pattern (16 bp):
TGCGATTTTTTCGCGT
Found at i:369658 original size:14 final size:14
Alignment explanation
Indices: 369639--369696 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
369629 TTGTGTTTCG
369639 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
369653 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
369669 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
369685 CGTTGTGATTTT
1 CGTTGCGATTTT
369697 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:369670 original size:32 final size:33
Alignment explanation
Indices: 369634--369712 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
369624 TGCGATTGTG
369634 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
369666 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
369699 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
369713 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:369731 original size:20 final size:19
Alignment explanation
Indices: 369697--369751 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
369687 TTGTGATTTT
*
369697 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
369716 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
369736 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
369752 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:371766 original size:19 final size:19
Alignment explanation
Indices: 371742--371914 Score: 258
Period size: 19 Copynumber: 9.6 Consensus size: 19
371732 AAAACAGACT
* *
371742 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
371761 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
371780 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
371799 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
371818 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
371837 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
371851 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
371870 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
371889 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
371903 ATCGCAATGCGA
1 ATCGCAATGCGA
371915 TTTTCATTTC
Statistics
Matches: 144, Mismatches: 2, Indels: 18
0.88 0.01 0.11
Matches are distributed among these distances:
14 22 0.15
15 2 0.01
16 4 0.03
17 4 0.03
18 1 0.01
19 111 0.77
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:371873 original size:52 final size:52
Alignment explanation
Indices: 371742--371914 Score: 283
Period size: 52 Copynumber: 3.2 Consensus size: 52
371732 AAAACAGACT
* *
371742 ATCGCAACGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
371799 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAA
371851 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAA
371903 ATCGCAATGCGA
1 ATCGCAATGCGA
371915 TTTTCATTTC
Statistics
Matches: 114, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
52 68 0.60
53 1 0.01
55 2 0.02
57 43 0.38
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:371990 original size:20 final size:20
Alignment explanation
Indices: 371933--371990 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
371923 TCACATTGCG
* *
371933 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
371953 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
371973 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
371991 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:373078 original size:24 final size:24
Alignment explanation
Indices: 373051--373104 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
373041 GTATTCGAAA
* *
373051 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
373075 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
373099 TTTGAT
1 TTTGAT
373105 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:375631 original size:33 final size:33
Alignment explanation
Indices: 375589--375715 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
375579 GGAAATTACT
375589 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
375622 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
375654 TTTCACAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
375688 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
375716 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:375699 original size:66 final size:66
Alignment explanation
Indices: 375593--375722 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 66
375583 ATTACTATCG
*
375593 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTC
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
375658 A
66 A
*
375659 CAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
375723 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (66 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
A
Found at i:375737 original size:19 final size:20
Alignment explanation
Indices: 375715--375757 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
375705 AAATCGCAAC
375715 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
375734 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
375754 GCGA
1 GCGA
375758 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:375742 original size:14 final size:14
Alignment explanation
Indices: 375743--375776 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
375733 TGCGATTTTC
375743 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
375757 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
375771 ATTTTC
1 ATTTTC
375777 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:375917 original size:14 final size:14
Alignment explanation
Indices: 375898--375934 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
375888 CATCAATTAA
375898 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
375912 ACAAATCACCTTTT
1 ACAAATCAACTTTT
375926 ACAAATCAA
1 ACAAATCAA
375935 TTAAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:377356 original size:21 final size:21
Alignment explanation
Indices: 377290--377356 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
377280 GTGAATCGGG
*
377290 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
377310 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
377332 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
377353 CTCT
1 CTCT
377357 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:377375 original size:42 final size:41
Alignment explanation
Indices: 377290--377412 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
377280 GTGAATCGGG
* * * *
377290 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
*
377332 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
377374 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAATGGTGGGAGGGGACTCTCGA-GGATGATAGG
377413 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:379494 original size:33 final size:33
Alignment explanation
Indices: 379437--379535 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
379427 ACGAGATAAT
*
379437 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
379471 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
379504 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
379536 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:379529 original size:19 final size:19
Alignment explanation
Indices: 379412--379577 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
379402 TCTTTTGGTT
* *
379412 GAAATAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
379431 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
379451 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
379469 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
379485 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
379503 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
379518 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
379538 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
379557 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
379576 GA
1 GA
379578 TTTTGGTTTC
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.36
20 44 0.37
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:379589 original size:19 final size:19
Alignment explanation
Indices: 379573--379636 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
379563 AAAATCGCAA
*
379573 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
379592 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
379611 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
379630 TGCGATT
1 TGCGATT
379637 ATCTCGTAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:380283 original size:20 final size:20
Alignment explanation
Indices: 380190--380283 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
380180 CGCTATGTAA
* *
380190 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
380210 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
380230 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
380251 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
380271 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
380284 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:380301 original size:21 final size:21
Alignment explanation
Indices: 380272--380364 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
380262 ATAGTAAGTA
380272 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
380293 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
380313 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
380334 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
380354 TCGCATTGCGA
1 TCGCATTGCGA
380365 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:380302 original size:41 final size:41
Alignment explanation
Indices: 380211--380345 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
380201 AAAGTCAGTA
* * * ** *
380211 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
380251 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
380293 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
380334 TCGCGTTGCGAT
1 TCGCGTTGCGAT
380346 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:380346 original size:41 final size:41
Alignment explanation
Indices: 380272--380364 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
380262 ATAGTAAGTA
380272 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
380313 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
380354 TCGCATTGCGA
1 TCGCATTGCGA
380365 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:386157 original size:45 final size:45
Alignment explanation
Indices: 385881--386158 Score: 306
Period size: 45 Copynumber: 6.2 Consensus size: 45
385871 CATTTTTACT
* * * * * *
385881 TATAACATACATTTATGTTAATAATGCACCCATATGCATTTCAA-
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
** * * * * *
385925 TCATAATATATTTTTATGTTGATAATGCACCTATATGCATTTCAAC
1 T-ATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * *
385971 AATATCATACTTTTTTGTTGATAATGTACTCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* * *
386016 TATAGTATACTTTACTATTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* *
386061 TATTGCATACTTTTCAGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * *
386106 TGTAGCATACTTTTCTGTTGAGAATGTACCCATATACATTCCAAT
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
386151 TATAGCAT
1 TATAGCAT
386159 CAGTTCATGC
Statistics
Matches: 199, Mismatches: 33, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
44 1 0.01
45 198 0.99
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (45 bp):
TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
Found at i:386191 original size:90 final size:90
Alignment explanation
Indices: 385993--386191 Score: 238
Period size: 90 Copynumber: 2.2 Consensus size: 90
385983 TTTTGTTGAT
* * *
385993 AATGTACTCATATACATTTCAACTATAGTATACTTTACTATTGATAATGTACCCATATACATTTC
1 AATGTACTCATATACATTTCAACTATAGCATACTTTACTATTGAGAATGTACCCATATACATTCC
* ** * *
386058 AACTATTGCATACTTTTCAGTTGAT
66 AACTATAGCATACAGTTCAGCTGAA
* * * *
386083 AATGTACCCATATACATTTCAACTGTAGCATACTTTTCTGTTGAGAATGTACCCATATACATTCC
1 AATGTACTCATATACATTTCAACTATAGCATACTTTACTATTGAGAATGTACCCATATACATTCC
*
386148 AATTATAGCAT-CAGTTCATGCTGAA
66 AACTATAGCATACAGTTCA-GCTGAA
* * *
386173 AATGCACTCGTATGCATTT
1 AATGTACTCATATACATTT
386192 TAATTTTTCA
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 5 0.05
90 86 0.95
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (90 bp):
AATGTACTCATATACATTTCAACTATAGCATACTTTACTATTGAGAATGTACCCATATACATTCC
AACTATAGCATACAGTTCAGCTGAA
Found at i:386869 original size:20 final size:23
Alignment explanation
Indices: 386817--386873 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
386807 ATCCTTAACC
**
386817 TGGTATCGATACCCCCTATGTTA
1 TGGTATCGATACCCCCTATGCCA
*
386840 TGGTACCGATACCCCCT-T-CCA
1 TGGTATCGATACCCCCTATGCCA
386861 -GGTATCGATACCC
1 TGGTATCGATACCC
386874 ATTGAATACT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
22 1 0.03
23 16 0.53
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (23 bp):
TGGTATCGATACCCCCTATGCCA
Found at i:392962 original size:45 final size:43
Alignment explanation
Indices: 392902--393160 Score: 184
Period size: 45 Copynumber: 5.8 Consensus size: 43
392892 ATAACATACA
* * * *
392902 TTTAGGTTAATAATGCACCTATATGCATTTCAATCATAATATATT
1 TTTATGTTGATAATGCACCCATATACATTTCAA-CATAATATA-T
*
392947 TTTATGTTGATAATGCACCCATATGCATTTCAACAGTAGGATA-AT
1 TTTATGTTGATAATGCACCCATATACATTTCAACA-TA--ATATAT
* * * * * *
392992 TTTCTGTTGATAATGTATCCATATACATTTAAACTACAATATAC
1 TTTATGTTGATAATGCACCCATATACATTTCAAC-ATAATATAT
* *
393036 TTTACTGTTGATAATGTACCCATATACATTTCAAC-TATTGCATACT
1 TTTA-TGTTGATAATGCACCCATATACATTTCAACATAAT--ATA-T
* * *
393082 TTTCA-GTTGATAATGTACCCATATACATTTCAACTGTAGCATACA-
1 TTT-ATGTTGATAATGCACCCATATACATTTCAAC-ATA--ATATAT
* * * *
393127 TTTCTGTTGAGAATGTACCCATATACATTCCAAC
1 TTTATGTTGATAATGCACCCATATACATTTCAAC
393161 TATAGCTTCA
Statistics
Matches: 178, Mismatches: 21, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
43 5 0.03
44 6 0.03
45 153 0.86
46 5 0.03
47 8 0.04
49 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (43 bp):
TTTATGTTGATAATGCACCCATATACATTTCAACATAATATAT
Found at i:393161 original size:45 final size:45
Alignment explanation
Indices: 392951--393201 Score: 258
Period size: 45 Copynumber: 5.6 Consensus size: 45
392941 TATATTTTTA
* * *
392951 TGTTGATAATGCACCCATATGCATTTCAAC-AGTAGGATA-ATTTTC
1 TGTTGATAATGTACCCATATACATTTCAACTA-TAGCATACA-TTTC
* * * **
392996 TGTTGATAATGTATCCATATACATTTAAACTACAATATAC-TTTAC
1 TGTTGATAATGTACCCATATACATTTCAACTATAGCATACATTT-C
* *
393041 TGTTGATAATGTACCCATATACATTTCAACTATTGCATACTTTTC
1 TGTTGATAATGTACCCATATACATTTCAACTATAGCATACATTTC
* *
393086 AGTTGATAATGTACCCATATACATTTCAACTGTAGCATACATTTC
1 TGTTGATAATGTACCCATATACATTTCAACTATAGCATACATTTC
* * * *
393131 TGTTGAGAATGTACCCATATACATTCCAACTATAGC-TTCAGTTC
1 TGTTGATAATGTACCCATATACATTTCAACTATAGCATACATTTC
* * * *
393175 ATGCTGATAATGCACCCGTATGCATTT
1 -TGTTGATAATGTACCCATATACATTT
393202 TAATTTTTCA
Statistics
Matches: 172, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
44 9 0.05
45 159 0.92
46 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (45 bp):
TGTTGATAATGTACCCATATACATTTCAACTATAGCATACATTTC
Found at i:393183 original size:135 final size:135
Alignment explanation
Indices: 392952--393201 Score: 308
Period size: 135 Copynumber: 1.9 Consensus size: 135
392942 ATATTTTTAT
* * * *
392952 GTTGATAATGCACCCATATGCATTTCAACAGTAGGATAATTTTCTGTTGATAATGTATCCATATA
1 GTTGATAATGCACCCATATACATTTCAACAGTAGCATAATTTTCTGTTGAGAATGTACCCATATA
* * * *
393017 CATTTAAACTACAATATACTTTACTGTTGATAATGTACCCATATACATTTCAACTATTGCATACT
66 CATTCAAACTACAATATACTTCACTGCTGATAATGCACCCATATACATTTCAACTATTGCATACT
393082 TTTCA
131 TTTCA
* *
393087 GTTGATAATGTACCCATATACATTTCAACTGTAGCATACA-TTTCTGTTGAGAATGTACCCATAT
1 GTTGATAATGCACCCATATACATTTCAACAGTAGCATA-ATTTTCTGTTGAGAATGTACCCATAT
* * * * * *
393151 ACATTCCAACTATAGCT-TCAGTTCA-TGCTGATAATGCACCCGTATGCATTT
65 ACATTCAAACTACA-ATAT-ACTTCACTGCTGATAATGCACCCATATACATTT
393202 TAATTTTTCA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
135 90 0.94
136 6 0.06
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (135 bp):
GTTGATAATGCACCCATATACATTTCAACAGTAGCATAATTTTCTGTTGAGAATGTACCCATATA
CATTCAAACTACAATATACTTCACTGCTGATAATGCACCCATATACATTTCAACTATTGCATACT
TTTCA
Found at i:399004 original size:19 final size:19
Alignment explanation
Indices: 398980--399016 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
398970 CAATGTGAAG
*
398980 TCTAACAAAAATATTATAA
1 TCTAACAAAAATAATATAA
398999 TCTAACAAAAATAATATA
1 TCTAACAAAAATAATATA
399017 GATACCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (19 bp):
TCTAACAAAAATAATATAA
Found at i:399189 original size:36 final size:35
Alignment explanation
Indices: 399086--399192 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 35
399076 CATATTTTGT
*
399086 ATATATTAATC-TATAATA-TATATATAATATTAT-
1 ATATATT-ATCTTATAATATTATAAATAATATTATA
* *
399119 ATATAGTA-CGTT-T-ATATAATAAATAATA-TA-A
1 ATATATTATC-TTATAATATTATAAATAATATTATA
399150 ATATATTATCTTATAATATTATAAATAATATTAATA
1 ATATATTATCTTATAATATTATAAATAATATT-ATA
399186 ATATATT
1 ATATATT
399193 TTATACATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
31 15 0.25
32 13 0.22
33 21 0.36
34 1 0.02
35 1 0.02
36 8 0.14
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.46
Consensus pattern (35 bp):
ATATATTATCTTATAATATTATAAATAATATTATA
Found at i:402751 original size:28 final size:28
Alignment explanation
Indices: 402687--402754 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
402677 TTCGGCTATC
* *
402687 CTAACTTGATAATATCCAGACCGTAAAT
1 CTAACTTGGTAATATACAGACCGTAAAT
* *
402715 CCAACTTGGTAATATACATACCGTAAAT
1 CTAACTTGGTAATATACAGACCGTAAAT
402743 CTAACTTGGTAA
1 CTAACTTGGTAA
402755 ACCACCTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (28 bp):
CTAACTTGGTAATATACAGACCGTAAAT
Found at i:405463 original size:15 final size:16
Alignment explanation
Indices: 405453--405496 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
405443 TATATAAAAG
405453 TATATTATATATATATA
1 TATATTATATA-ATATA
405470 TATATTATATAATATA
1 TATATTATATAATATA
* *
405486 TGTTTTATATA
1 TATATTATATA
405497 TTAATACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TATATTATATAATATA
Found at i:405465 original size:17 final size:17
Alignment explanation
Indices: 405443--405485 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
405433 TTATACATCG
405443 TATATA-AAAGTATATTA
1 TATATATAAA-TATATTA
*
405460 TATATATATATATATTA
1 TATATATAAATATATTA
405477 TATAATATA
1 TAT-ATATA
405486 TGTTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATATAAATATATTA
Found at i:405494 original size:14 final size:15
Alignment explanation
Indices: 405460--405497 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
405450 AAGTATATTA
405460 TATATATATATATAT
1 TATATATATATATAT
*
405475 TATATA-ATATATGT
1 TATATATATATATAT
*
405489 TTTATATAT
1 TATATATAT
405498 TAATACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:413311 original size:19 final size:19
Alignment explanation
Indices: 413287--413323 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
413277 AGCAAGTTTC
413287 TCTTACCTTATGCAGAAGT
1 TCTTACCTTATGCAGAAGT
*
413306 TCTTACCTTATGGAGAAG
1 TCTTACCTTATGCAGAAG
413324 CTCACAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (19 bp):
TCTTACCTTATGCAGAAGT
Found at i:414265 original size:15 final size:15
Alignment explanation
Indices: 414235--414273 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
414225 TAAATGCTAG
*
414235 AAATTAAATAACAT-
1 AAATTAAAAAACATA
414249 AAATTAAAAATACATA
1 AAATTAAAAA-ACATA
414265 AAATTAAAA
1 AAATTAAAA
414274 GGGAGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 4 0.18
16 9 0.41
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTAAAAAACATA
Found at i:420434 original size:49 final size:49
Alignment explanation
Indices: 420362--420696 Score: 546
Period size: 49 Copynumber: 6.8 Consensus size: 49
420352 GAATACCATG
* * * * *
420362 AGTGACACCTTTTATGTCGAAATGCACCGTTCTGCGTTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
* *
420411 AGTGGCACATTTTATGCCTAAATGCGCCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
* *
420460 AGTGGCACCTTTTATGCCGAAATGCACC-ATATTGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTA-TGCATTTAACTTTCATT
420509 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
420558 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
*
420607 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGTATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
* *
420656 AGTGGCATCTTTTATGCCTAAATGCACTGTTATGCATTTAA
1 AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAA
420697 TTTAGCACCC
Statistics
Matches: 267, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
48 2 0.01
49 263 0.99
50 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATT
Found at i:426627 original size:49 final size:49
Alignment explanation
Indices: 426565--426703 Score: 174
Period size: 49 Copynumber: 2.8 Consensus size: 49
426555 GAATACCATG
* *
426565 AGTGGTACCTTTTATGCCAAAATGCATCGTTATGCATTTAACTTT-TATT
1 AGTGGAACCTTTTATGCCTAAATGCATCGTTATGCATTTAACTTTCT-TT
* * *
426614 AGTGGAACATTTTATTCCTAAATGCACCGTTATGCATTTAACTTTCTTT
1 AGTGGAACCTTTTATGCCTAAATGCATCGTTATGCATTTAACTTTCTTT
* * *
426663 AGT-GACACCTTTTATGCCTAAATGTATTGTTATACATTTAA
1 AGTGGA-ACCTTTTATGCCTAAATGCATCGTTATGCATTTAA
426704 TTTAGCACCA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 2 0.03
49 74 0.96
50 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (49 bp):
AGTGGAACCTTTTATGCCTAAATGCATCGTTATGCATTTAACTTTCTTT
Found at i:429606 original size:108 final size:108
Alignment explanation
Indices: 429287--429606 Score: 525
Period size: 108 Copynumber: 3.0 Consensus size: 108
429277 GGTGACATTA
* * * *
429287 TTTCTTGAAAGTTTTGCCTTGGAATAAGATATTGAGATTTGGTCACAAAGGAAAGATTAGTCTAA
1 TTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAGTCTAA
* *
429352 AATTTATTAGACCCTATGAGGTGTTAGAGCGTATAGATATTGT
66 AATTTATTGGACCCTATGAGGTGTTAGAGCGTATAGATCTTGT
* *
429395 TTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAAATTTTGTCACAAAGGAAAGCTTAGTCTAA
1 TTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAGTCTAA
*
429460 AATTTATTGGACCCTATGAGGTGTTATAGCGTATAGATCTTGT
66 AATTTATTGGACCCTATGAGGTGTTAGAGCGTATAGATCTTGT
* *
429503 TTTCTTGAAAGTTACACCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAGTCTAA
1 TTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAGTCTAA
429568 AATTTTATTGGACCCTATGAGGTGTTA-AGCGTATAGATC
66 AA-TTTATTGGACCCTATGAGGTGTTAGAGCGTATAGATC
429607 CTATAGCTTA
Statistics
Matches: 198, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
108 174 0.88
109 24 0.12
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.36
Consensus pattern (108 bp):
TTTCTTGAAAGTTTCGCCTTGGAATAAGGTGTTGAGATTTGGTCACAAAGGAAAGCTTAGTCTAA
AATTTATTGGACCCTATGAGGTGTTAGAGCGTATAGATCTTGT
Found at i:431435 original size:28 final size:28
Alignment explanation
Indices: 431375--431449 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
431365 CTTAGCTGGA
* * *
431375 TATGGATGAGTGGAACAACTTCGTTAAC
1 TATGGATGAGTGGAGCAACTACGCTAAC
* *
431403 CATGGATGAGTGGAGCAACTACGCTATC
1 TATGGATGAGTGGAGCAACTACGCTAAC
*
431431 TATGGAAGAGTGG-GCAACT
1 TATGGATGAGTGGAGCAACT
431450 TGTTGTCCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 6 0.15
28 34 0.85
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (28 bp):
TATGGATGAGTGGAGCAACTACGCTAAC
Found at i:434040 original size:39 final size:39
Alignment explanation
Indices: 433997--434075 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
433987 CGTAGGCTAC
433997 CATGCTTTGGTGGCCATTCAACACTCCAACCACCATCAA
1 CATGCTTTGGTGGCCATTCAACACTCCAACCACCATCAA
* *
434036 CATGCTTTGGTGGCTATTCAACACTCCGACCACCATCAA
1 CATGCTTTGGTGGCCATTCAACACTCCAACCACCATCAA
434075 C
1 C
434076 GGTGGTCGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (39 bp):
CATGCTTTGGTGGCCATTCAACACTCCAACCACCATCAA
Found at i:435401 original size:12 final size:12
Alignment explanation
Indices: 435381--435419 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
435371 GCTCGATTGA
*
435381 AACTTAAACTCG
1 AACTCAAACTCG
435393 AACTCAAACTCG
1 AACTCAAACTCG
435405 AACTCAAACTCG
1 AACTCAAACTCG
435417 AAC
1 AAC
435420 ATAAATCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.18
Consensus pattern (12 bp):
AACTCAAACTCG
Found at i:435545 original size:13 final size:13
Alignment explanation
Indices: 435527--435553 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
435517 AAAGTGTTAA
435527 TGAATTTTAAGAT
1 TGAATTTTAAGAT
435540 TGAATTTTAAGAT
1 TGAATTTTAAGAT
435553 T
1 T
435554 TTATATTCGA
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:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TGAATTTTAAGAT
Found at i:442421 original size:12 final size:12
Alignment explanation
Indices: 442404--442440 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
442394 TCTAGTCGAT
442404 CAAACCCACCTC
1 CAAACCCACCTC
*
442416 CAAACCCACCTT
1 CAAACCCACCTC
*
442428 CAAATCCACCTC
1 CAAACCCACCTC
442440 C
1 C
442441 TATTCCACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.54, G:0.00, T:0.14
Consensus pattern (12 bp):
CAAACCCACCTC
Found at i:442448 original size:24 final size:23
Alignment explanation
Indices: 442403--442454 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
442393 TTCTAGTCGA
442403 TCAAACCCACCTCCAAACCCACC
1 TCAAACCCACCTCCAAACCCACC
* * **
442426 TTCAAATCCACCTCCTATTCCACC
1 -TCAAACCCACCTCCAAACCCACC
442450 TCAAA
1 TCAAA
442455 ATCCTATCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.19
Consensus pattern (23 bp):
TCAAACCCACCTCCAAACCCACC
Found at i:443685 original size:14 final size:13
Alignment explanation
Indices: 443640--443685 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
443630 TTTGGATGGA
*
443640 TTTTGAATATTTG
1 TTTTGGATATTTG
*
443653 GTTTGGATATTTG
1 TTTTGGATATTTG
*
443666 TTTTGGATGTTTG
1 TTTTGGATATTTG
443679 ATTTTGG
1 -TTTTGG
443686 TCTGTTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (13 bp):
TTTTGGATATTTG
Found at i:450352 original size:39 final size:38
Alignment explanation
Indices: 450270--450352 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 38
450260 AACAAGTTGG
* *
450270 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTGAAATACAT
* *
450309 -AAAATTTATATATATATTTTTTACAAAATTGAAA-ACAT
1 AAAAATTTATATAT-T-TTCTTTAAAAAATTGAAATACAT
450347 AAAAAT
1 AAAAAT
450353 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
37 10 0.27
38 7 0.19
39 20 0.54
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTGAAATACAT
Done.