Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005876.1 Hibiscus syriacus cultivar Beakdansim tig00013808_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: 777889
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:203355 original size:16 final size:15
Alignment explanation
Indices: 203333--203371 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
203323 GAAATCATTG
203333 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
203349 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
203364 AAAAATTA
1 AAAAATTA
203372 GAGATAGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:203614 original size:21 final size:20
Alignment explanation
Indices: 203588--203659 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
203578 CAAAATTTGC
*
203588 GTTGCGAATTTGAAATTCAGG
1 GTTGCGAATTTGAAATTC-GA
*
203609 GTTGCGAATTTGGAAACT-GA
1 GTTGCGAATTT-GAAATTCGA
* * *
203629 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGA
203649 GTTGCGAATTT
1 GTTGCGAATTT
203660 ATTGGTCATT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 4 0.10
20 22 0.52
21 11 0.26
22 5 0.12
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:209144 original size:81 final size:81
Alignment explanation
Indices: 209018--209181 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
209008 ATAAGATTAC
209018 TTGAATGCAAATTTTACCAAATTATCCTTGTGATATATATAATTTTAAAGATATTAAACTGTAAT
1 TTGAATGCAAATTTTACCAAATTATCCTTGTGATATATATAATTTTAAAGATATTAAACTGTAAT
209083 GTTAAATTATAAATAT
66 GTTAAATTATAAATAT
209099 TTGAATGCAAATTTTACCAAATTATCCTTGTGATATATATAATTTTAAAGATATTAAACTGTAAT
1 TTGAATGCAAATTTTACCAAATTATCCTTGTGATATATATAATTTTAAAGATATTAAACTGTAAT
209164 GTTAAATTATAAATAT
66 GTTAAATTATAAATAT
209180 TT
1 TT
209182 TTAAATAATT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (81 bp):
TTGAATGCAAATTTTACCAAATTATCCTTGTGATATATATAATTTTAAAGATATTAAACTGTAAT
GTTAAATTATAAATAT
Found at i:216251 original size:83 final size:82
Alignment explanation
Indices: 215906--216270 Score: 251
Period size: 83 Copynumber: 4.4 Consensus size: 82
215896 CAAAATGGTA
* ** * * ** *
215906 ACTTTAGCGACGTTTTTATGCAAATGTCGCAATAAGGTCCATCTATAGTGGCGTTTTTTCAATAA
1 ACTTTAGCGACGTTTTTATACAAATACCGTAATAAGGTTCATCTATAGT-GATTTTTTTCAACAA
* *
215971 ACGCCGCAATCGAGTACT
65 ACGCCGCAATAGAGTAGT
* * * ** * * *
215989 AC-TTAGCGGCGTTTGTATAAAAATACCACAATAAGGTTCATTTATAGTGAAATATTTT-AACAA
1 ACTTTAGCGACGTTTTTATACAAATACCGTAATAAGGTTCATCTATAGTG-ATTTTTTTCAACAA
* * *
216052 ACACCGCAACAGAGTGGT
65 ACGCCGCAATAGAGTAGT
* * ** * *
216070 ACTTTAGCG--GTATTTTTTATAAATGTCGTAATAGGGTTCATTTATAGTG-TCGTTTTTTCAAC
1 ACTTTAGCGACGT-TTTTATACAAATACCGTAATAAGGTTCATCTATAGTGAT--TTTTTTCAAC
* * *
216132 AAATGCCGTAATATAGT-GTT
63 AAACGCCGCAATAGAGTAG-T
* * * * *
216152 ACTTTAACGGCTTTTTTATACAAATACCATAATAGGGTTCATCTATAGTG-TTTTTTCTCCAACA
1 ACTTTAGCGACGTTTTTATACAAATACCGTAATAAGGTTCATCTATAGTGATTTTTT-T-CAACA
* *
216216 AACGTCGCAATAGTGTAGT
64 AACGCCGCAATAGAGTAGT
*
216235 ACTTTAGCGACGTTTTTCA-ACAAACACCGTAATAAG
1 ACTTTAGCGACGTTTTT-ATACAAATACCGTAATAAG
216271 AAAATGTATT
Statistics
Matches: 217, Mismatches: 52, Indels: 26
0.74 0.18 0.09
Matches are distributed among these distances:
80 2 0.01
81 60 0.28
82 73 0.34
83 79 0.36
84 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (82 bp):
ACTTTAGCGACGTTTTTATACAAATACCGTAATAAGGTTCATCTATAGTGATTTTTTTCAACAAA
CGCCGCAATAGAGTAGT
Found at i:217999 original size:195 final size:199
Alignment explanation
Indices: 217651--218045 Score: 753
Period size: 195 Copynumber: 2.0 Consensus size: 199
217641 ATTGTATCTC
217651 CACCTTTGAAACAAAGTGTTTTGTTTGTAGTACCCCGCATATATCTGAGGATCCATTTGACAGCT
1 CACCTTTGAAACAAAGTGTTTTGTTTGTAGTACCCCGCATATATCTGAGGATCCATTTGA-AGCT
217716 TCCCAGTGTACCTTGACTGGATTATTCATGTACCTGCTAACAACTCCCACTGCATGAGTAATATC
65 TCCCAGTGTACCTTGACTGGATTATTCATGTACCTGCTAACAACTCCCACTGCATGAGTAATATC
217781 TGGTCTGGTAAAAACCATGGCATACATCAGACTTCCAATTGTTGAGGCATACGACACCTTCACCA
130 TGGTCTGGTAAAAACCATGGCATACATCAGACTTCCAATTGTTGAGGCATACGACACCTTCACCA
217846 TATGT
195 TATGT
217851 CACCTTTG-AAC-AAGTGTTTTGTTTGTAGTACCCCGCATATATCTGAGGATCCATTTG-A-CTT
1 CACCTTTGAAACAAAGTGTTTTGTTTGTAGTACCCCGCATATATCTGAGGATCCATTTGAAGCTT
217912 CCCAGTGTACCTTGACTGGATTATTCATGTACCTGCTAACAACTCCCACTGCATGAGTAATATCT
66 CCCAGTGTACCTTGACTGGATTATTCATGTACCTGCTAACAACTCCCACTGCATGAGTAATATCT
217977 GGTCTGGTAAAAACCATGGCATACATCAGACTTCCAATTGTTGAGGCATACGACACCTTCACCAT
131 GGTCTGGTAAAAACCATGGCATACATCAGACTTCCAATTGTTGAGGCATACGACACCTTCACCAT
218042 ATGT
196 ATGT
218046 GCACGTTCTT
Statistics
Matches: 195, Mismatches: 0, Indels: 5
0.98 0.00 0.03
Matches are distributed among these distances:
195 137 0.70
196 1 0.01
198 46 0.24
199 3 0.02
200 8 0.04
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (199 bp):
CACCTTTGAAACAAAGTGTTTTGTTTGTAGTACCCCGCATATATCTGAGGATCCATTTGAAGCTT
CCCAGTGTACCTTGACTGGATTATTCATGTACCTGCTAACAACTCCCACTGCATGAGTAATATCT
GGTCTGGTAAAAACCATGGCATACATCAGACTTCCAATTGTTGAGGCATACGACACCTTCACCAT
ATGT
Found at i:219529 original size:31 final size:30
Alignment explanation
Indices: 219441--219534 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 30
219431 GAACCTCAAC
* * *
219441 AACTGTCCATAGGTCCCAAAAAACCTAGGTA
1 AACTGTCCATATGTCTC-AAAAACATAGGTA
* * *
219472 AATTGTCCATATG-CTTCTTATAACATAGGTA
1 AACTGTCCATATGTC-TC-AAAAACATAGGTA
*
219503 TACTGTCCATATGTCTCAAAAGACATAGGTA
1 AACTGTCCATATGTCTCAAAA-ACATAGGTA
219534 A
1 A
219535 TTTTGTTCAT
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
30 3 0.06
31 44 0.92
32 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (30 bp):
AACTGTCCATATGTCTCAAAAACATAGGTA
Found at i:219730 original size:16 final size:16
Alignment explanation
Indices: 219709--219739 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
219699 ATAACTTGTA
*
219709 TCACATATATACATAT
1 TCACATATACACATAT
219725 TCACATATACACATA
1 TCACATATACACATA
219740 GATACATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (16 bp):
TCACATATACACATAT
Found at i:219764 original size:23 final size:21
Alignment explanation
Indices: 219732--219773 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
219722 TATTCACATA
219732 TACACATAGATACATTGTTCACT
1 TACACATAGA-ACATT-TTCACT
*
219755 TACACGTAGAACATTTTCA
1 TACACATAGAACATTTTCA
219774 TATGATTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 5 0.28
23 9 0.50
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (21 bp):
TACACATAGAACATTTTCACT
Found at i:223876 original size:24 final size:23
Alignment explanation
Indices: 223832--223876 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
223822 ATCATATACT
* *
223832 CATATATTCATTCATTTAAGCCA
1 CATATATTCATTCAATCAAGCCA
*
223855 CATATGATTCATTTAATCAAGC
1 CATAT-ATTCATTCAATCAAGC
223877 AATATACACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (23 bp):
CATATATTCATTCAATCAAGCCA
Found at i:225588 original size:24 final size:24
Alignment explanation
Indices: 225556--225612 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
225546 TCTATAGTGT
225556 ATCGATGCATCCCTTAACATGTGC
1 ATCGATGCATCCCTTAACATGTGC
*
225580 ATCGATGCATCCCTTAACATGTGT
1 ATCGATGCATCCCTTAACATGTGC
225604 ATCGATGCA
1 ATCGATGCA
225613 CTACCCATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (24 bp):
ATCGATGCATCCCTTAACATGTGC
Found at i:225670 original size:64 final size:64
Alignment explanation
Indices: 225600--225760 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
225590 CCCTTAACAT
225600 GTGTATCGATGCACTACC-CATGCATCGATACA-TAAAT-CACCTTCGATGTTT-CAATCTTAAG
1 GTGTATCGATGCACT-CCTCATGCATCGATACACTAAATGCA--TTCGATGTTTCCAATCTTAA-
225661 GGG
62 GGG
* * * * *
225664 GTGTATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAAGGG
1 GTGTATCGATGCACTCCTCATGCATCGATACACTAAATGCATTCGATGTTTCCAATCTTAAGGG
* * *
225728 GTGCATCGATGCACTTCCT-GTGCATCGGTACAC
1 GTGTATCGATGCAC-TCCTCATGCATCGATACAC
225761 ACTGAATAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 2 0.02
64 64 0.77
65 15 0.18
66 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (64 bp):
GTGTATCGATGCACTCCTCATGCATCGATACACTAAATGCATTCGATGTTTCCAATCTTAAGGG
Found at i:238290 original size:29 final size:30
Alignment explanation
Indices: 238238--238327 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 30
238228 AATAAATATG
* * *
238238 CTCTCAACCCATAAACAT-TCACAACAATC
1 CTCTCAACCCGTAAAAATCACACAACAATC
* *
238267 CTCTCAACCCG-AAAAATCATACAACAAAC
1 CTCTCAACCCGTAAAAATCACACAACAATC
* * * *
238296 CTTTTAACCCGTAAATATCACACGACAATC
1 CTCTCAACCCGTAAAAATCACACAACAATC
238326 CT
1 CT
238328 TTTATCTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 5 0.10
29 27 0.56
30 16 0.33
ACGTcount: A:0.41, C:0.34, G:0.03, T:0.21
Consensus pattern (30 bp):
CTCTCAACCCGTAAAAATCACACAACAATC
Found at i:238330 original size:30 final size:29
Alignment explanation
Indices: 238257--238331 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 29
238247 CATAAACATT
* *
238257 CACAACAATCCTCTCAACCCGAAAAATCA
1 CACAACAATCCTTTTAACCCGAAAAATCA
* * *
238286 TACAACAAACCTTTTAACCCGTAAATATCA
1 CACAACAATCCTTTTAACCCG-AAAAATCA
*
238316 CACGACAATCCTTTTA
1 CACAACAATCCTTTTA
238332 TCTTTTATTC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.41, C:0.32, G:0.04, T:0.23
Consensus pattern (29 bp):
CACAACAATCCTTTTAACCCGAAAAATCA
Found at i:248220 original size:2 final size:2
Alignment explanation
Indices: 248213--248242 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
248203 TTCCAATAGA
248213 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
248243 GGATCTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251960 original size:52 final size:53
Alignment explanation
Indices: 251851--251996 Score: 188
Period size: 53 Copynumber: 2.8 Consensus size: 53
251841 TTCATACTAC
* * * * *
251851 AAAAAAAGTGTAGCATTTAATACATAATTTACACCAATGTAAGTGAATAAAAT-
1 AAAAAAAGTGTAACATTTAACACAT-ACTTACACCGATGTAAATGAATAAAATA
* *
251904 -AAAAAAGTGCAACATTTAACACATACTTGCACCGATGTAAATGAATAAAATA
1 AAAAAAAGTGTAACATTTAACACATACTTACACCGATGTAAATGAATAAAATA
* *
251956 AAAAAAAGTGTAACACTTAACACATACTTACATCGATGTAA
1 AAAAAAAGTGTAACATTTAACACATACTTACACCGATGTAA
251997 GTATATATTG
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 23 0.29
52 21 0.26
53 36 0.45
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (53 bp):
AAAAAAAGTGTAACATTTAACACATACTTACACCGATGTAAATGAATAAAATA
Found at i:252318 original size:4 final size:4
Alignment explanation
Indices: 252309--252349 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
252299 AAATAAGTAA
*
252309 AAAT AAAT AAAT GGAA- AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
252350 TTAATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 2 0.06
4 29 0.88
5 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:252438 original size:18 final size:18
Alignment explanation
Indices: 252389--252442 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
252379 AAAATAGAAA
*
252389 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
252410 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
252429 AATA-TAATATAAAA
1 AATAGTAATATAAAA
252443 AAAACCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:252443 original size:18 final size:19
Alignment explanation
Indices: 252393--252443 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
252383 TAGAAAAATA
*
252393 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
252413 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
252432 ATAATATAAAAA
1 ATAATATAAAAA
252444 AAACCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:252690 original size:23 final size:23
Alignment explanation
Indices: 252643--252706 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
252633 AAAAAAAAGT
*
252643 ATATATATATAAAATAATAATAA
1 ATATATATATAAAATAATAACAA
252666 ATATAGTAT-TAAAA-AATAACCAA
1 ATATA-TATATAAAATAATAA-CAA
* *
252689 ATAAATATAAATAAATAA
1 ATATATATATA-AAATAA
252707 AAAATCAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 8 0.24
23 17 0.52
24 6 0.18
25 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (23 bp):
ATATATATATAAAATAATAACAA
Found at i:253213 original size:37 final size:36
Alignment explanation
Indices: 253172--253275 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 36
253162 GTGCTTATGG
* * *
253172 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAAAACTCT
* *
253209 ATCCTATTTTAAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTT-AGGAGTTTGAATCCTAGTAAAACTCT
*
253246 ATCATATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTA
253276 TGACGAAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 3 0.05
37 51 0.88
38 4 0.07
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:254184 original size:26 final size:26
Alignment explanation
Indices: 254155--254206 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
254145 TTGAGAGATA
* *
254155 GTTAAACTCAAAGTTGTATATGTTAC
1 GTTAAAATCAAAATTGTATATGTTAC
254181 GTTAAAATCAAAATTGTATATGTTAC
1 GTTAAAATCAAAATTGTATATGTTAC
254207 TCATAGTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (26 bp):
GTTAAAATCAAAATTGTATATGTTAC
Found at i:263883 original size:29 final size:29
Alignment explanation
Indices: 263844--264052 Score: 251
Period size: 29 Copynumber: 7.2 Consensus size: 29
263834 ATCGGGTGAC
* *
263844 ATTTTGAGAATTAATTCGAAATAGGTGCT
1 ATTTTGGGAATTAATTCGAAAAAGGTGCT
*
263873 ATTTTGGGAATTAATTCGAAAATGGTGCT
1 ATTTTGGGAATTAATTCGAAAAAGGTGCT
*
263902 ATTTTGGGAATTAATTCGAAAATGGTGCT
1 ATTTTGGGAATTAATTCGAAAAAGGTGCT
**
263931 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAAAAGGTGCT
* *
263960 ATTTTGGGAATTTAATTC-AAAAATGTACT
1 ATTTTGGGAA-TTAATTCGAAAAAGGTGCT
* * *
263989 ATATTGGGAATTTAATTC-AAAAATGTGTT
1 ATTTTGGGAA-TTAATTCGAAAAAGGTGCT
* * *
264018 ATTTTAGGAATTTAATTCAAAAAAGGTGTT
1 ATTTTGGGAA-TTAATTCGAAAAAGGTGCT
264048 ATTTT
1 ATTTT
264053 AGTAATTATT
Statistics
Matches: 163, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
29 141 0.87
30 22 0.13
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (29 bp):
ATTTTGGGAATTAATTCGAAAAAGGTGCT
Found at i:263996 original size:87 final size:87
Alignment explanation
Indices: 263844--264052 Score: 278
Period size: 87 Copynumber: 2.4 Consensus size: 87
263834 ATCGGGTGAC
* * * *
263844 ATTTTGAGAATTAATTCGAAATAGGTGCTATTTTGGGAATTAATTCGAAAATGGTGCTATTTTGG
1 ATTTTGGGAATTAATTCGAAATAGGTGCTATTTTGGGAATTAATTCAAAAATGGTACTATATTGG
*
263909 GAA-TTAATTCGAAAATGGTGCT
66 GAATTTAATTCAAAAAT-GTGCT
*
263931 ATTTTGGGAATTAATTCGAAATGGGTGCTATTTTGGGAATTTAATTCAAAAAT-GTACTATATTG
1 ATTTTGGGAATTAATTCGAAATAGGTGCTATTTTGGGAA-TTAATTCAAAAATGGTACTATATTG
*
263995 GGAATTTAATTCAAAAATGTGTT
65 GGAATTTAATTCAAAAATGTGCT
* * * *
264018 ATTTTAGGAATTTAATTCAAAAAAGGTGTTATTTT
1 ATTTTGGGAA-TTAATTCGAAATAGGTGCTATTTT
264053 AGTAATTATT
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
87 63 0.59
88 44 0.41
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (87 bp):
ATTTTGGGAATTAATTCGAAATAGGTGCTATTTTGGGAATTAATTCAAAAATGGTACTATATTGG
GAATTTAATTCAAAAATGTGCT
Found at i:269519 original size:30 final size:30
Alignment explanation
Indices: 269483--269549 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
269473 TTGGCCAAAT
*
269483 TCAAAGTCAACGGTCAACGAGTTAACTTGG
1 TCAAAGTCAACGGTCAACGAGTTAACTCGG
* * *
269513 TCAAAGTCAATGGTCAACGGGTTGACTCGG
1 TCAAAGTCAACGGTCAACGAGTTAACTCGG
269543 TCAAAGT
1 TCAAAGT
269550 TAATGAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (30 bp):
TCAAAGTCAACGGTCAACGAGTTAACTCGG
Found at i:273124 original size:3 final size:3
Alignment explanation
Indices: 273096--273154 Score: 59
Period size: 3 Copynumber: 19.0 Consensus size: 3
273086 TTTGGGTCTG
*
273096 TAA T-A TAA TAA -AA TTAA TAA CAAA TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA
273142 TAA TAAA TAA TAA
1 TAA T-AA TAA TAA
273155 AAAACCAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
2 4 0.08
3 34 0.71
4 10 0.21
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:273128 original size:13 final size:12
Alignment explanation
Indices: 273100--273158 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 12
273090 GGTCTGTAAT
*
273100 ATAATAAAATTA
1 ATAATAAAAATA
*
273112 ATAACAAATAATA
1 ATAATAAA-AATA
273125 ATAATAATAAATA
1 ATAATAA-AAATA
273138 ATAATAATAAATA
1 ATAATAA-AAATA
273151 ATAA-AAAA
1 ATAATAAAA
273159 CCAAATGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
11 2 0.05
12 9 0.21
13 30 0.71
14 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAATAAAAATA
Found at i:273154 original size:16 final size:16
Alignment explanation
Indices: 273096--273147 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
273086 TTTGGGTCTG
273096 TAATATAATAA-AATTAA
1 TAATA-AATAATAA-TAA
*
273113 TAACAAATAATAATAA
1 TAATAAATAATAATAA
273129 TAATAAATAATAATAA
1 TAATAAATAATAATAA
273145 TAA
1 TAA
273148 ATAATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 26 0.81
17 6 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATAAATAATAATAA
Found at i:273834 original size:113 final size:112
Alignment explanation
Indices: 273489--274260 Score: 993
Period size: 113 Copynumber: 6.8 Consensus size: 112
273479 ATAGAGTTAT
*
273489 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCTTCAGATAAGTTCTTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC--CTTCTTCAGATAAGTTCTTC
* * *
273554 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
64 TCATTATGAACTTAC-CTGGAAATGCTGATCCATCGAGTGATGAATT-AAA
* * *
273605 -CAAAAAGTTAAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACAAGTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---AAGTTCTT
* * * *
273665 CTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
63 CTCATTATGAACT-TACCTGGAAATGCTGATCCATCGAGTGATGAA-TTAAA
*
273717 -CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* * * **
273781 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTTAC-CTGGAAATGCTGATCCATCGAGTGATGAATTAAA
* * * *
273829 GCAAAAGGTTGAACAAGCTCTTTTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* * * * *
273894 ATTATGAACTTTCTCTGGAAATGATTATCCATAGAATGATGAATTCAAA
66 ATTATGAACTTAC-CTGGAAATGCTGATCCATCGAGTGATGAATT-AAA
*
273943 -CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCT
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCT
* *
274006 CATTATGAACTTGACCTGGCAATGCTGATCCATCGGGTGATGAATTAAA
65 CATTATGAACTT-ACCTGGAAATGCTGATCCATCGAGTGATGAATTAAA
* * *
274055 GTAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* *
274120 ATTATGAACTTGACCTGGCAATGCTGATCCATCGGGTGATGAATTAAA
66 ATTATGAACTT-ACCTGGAAATGCTGATCCATCGAGTGATGAATTAAA
* * * *
274168 GTAAAAGGTTGAACAAGTTCTTCTTATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
*
274233 ATTATGAACTATACCTGGTAATGCTGAT
66 ATTATGAACT-TACCTGGAAATGCTGAT
274261 GACCCGAAGG
Statistics
Matches: 588, Mismatches: 51, Indels: 37
0.87 0.08 0.05
Matches are distributed among these distances:
109 11 0.02
112 128 0.22
113 364 0.62
114 41 0.07
115 33 0.06
116 11 0.02
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
ATTATGAACTTACCTGGAAATGCTGATCCATCGAGTGATGAATTAAA
Found at i:274025 original size:339 final size:336
Alignment explanation
Indices: 273489--274242 Score: 1115
Period size: 339 Copynumber: 2.2 Consensus size: 336
273479 ATAGAGTTAT
* *
273489 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCTTCAGATAAGTTCTTC
1 GCAAAAGGTTGAACAAGCTCTTTTCATTATGAACTTCTTCTTC-T-TTCTTCAGATGAGTTCTTC
* *
273554 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTAAACA
64 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATAGAATGATGAATTCAAACAAAAAGTTAAACA
273619 AATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACAAGTTCTTCTCATTATGAACTCTACCT
129 AATTCTTCTCATTATGAATTTCTTCTTCTTCAGAT-A-AAGTTCTTCTCATTATGAACTCTACCT
*
273684 GGCAATGTTGATCCATCAAATGATGAATTTAAA-CAAAAGGTTGAACAAGCTCTTCTCATTATGA
192 GGCAATGCTGATCCATCAAATGATGAA-TTAAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGA
*
273748 ACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTT-TCTCTGGAAAAGCTGATCCA
256 ACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTGAC-CTGGAAAAGCTGATCCA
* **
273812 TCGAGTGATGGATTTGA
320 TCGAGTGATGAATTAAA
273829 GCAAAAGGTTGAACAAGCTCTTTTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTTTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
* *
273894 ATTATGAACTTTCTCTGGAAATGATT-ATCCATAGAATGATGAATTCAAACAAAAAAGTTGAACA
66 ATTATGAACTTTCTCTGGAAAAG-TTGATCCATAGAATGATGAATTCAAAC-AAAAAGTTAAACA
*
273958 AGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT-AAGTTCTTCTCATTATGAACT-TGAC
129 AATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATAAAGTTCTTCTCATTATGAACTCT-AC
*** * * *
274021 CTGGCAATGCTGATCCATCGGGTGATGAATTAAAGTAAAAGGTTGAACAAGTTCTTCTTATTATG
190 CTGGCAATGCTGATCCATCAAATGATGAATTAAAGCAAAAGGTTGAACAAGCTCTTCTCATTATG
* * *
274086 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGACCTGGCAATGCTGATCCA
255 AACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTGACCTGGAAAAGCTGATCCA
*
274151 TCGGGTGATGAATTAAA
320 TCGAGTGATGAATTAAA
* * * *
274168 GTAAAAGGTTGAACAAGTTCTTCTT-ATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAGCTCTT-TTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCT
274232 CATTATGAACT
65 CATTATGAACT
274243 ATACCTGGTA
Statistics
Matches: 379, Mismatches: 26, Indels: 19
0.89 0.06 0.04
Matches are distributed among these distances:
338 70 0.18
339 247 0.65
340 45 0.12
341 1 0.00
342 16 0.04
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (336 bp):
GCAAAAGGTTGAACAAGCTCTTTTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGTTGATCCATAGAATGATGAATTCAAACAAAAAGTTAAACAAA
TTCTTCTCATTATGAATTTCTTCTTCTTCAGATAAAGTTCTTCTCATTATGAACTCTACCTGGCA
ATGCTGATCCATCAAATGATGAATTAAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTGACCTGGAAAAGCTGATCCATCGAGT
GATGAATTAAA
Found at i:274384 original size:76 final size:76
Alignment explanation
Indices: 274258--274413 Score: 258
Period size: 76 Copynumber: 2.1 Consensus size: 76
274248 TGGTAATGCT
* *
274258 GATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTA
1 GATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTA
*
274323 TAGGACTTACA
66 CAGGACTTACA
* * *
274334 GATGACCCTAAGGCTTTGAAAACATCAAAAATCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTA
274399 CAGGACTTACA
66 CAGGACTTACA
274410 GATG
1 GATG
274414 TGGGAAATAG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
GATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTA
CAGGACTTACA
Found at i:275172 original size:22 final size:22
Alignment explanation
Indices: 275093--275170 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
275083 AATAAAGCTT
275093 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
275115 TCATCTTTTAAAAAGAGAATATA
1 TCATC-TTTGAAAAGAGAATCTA
* *
275138 TCATCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAAAGAGAATCTA
275160 TCATCTTTGAA
1 TCATCTTTGAA
275171 GAATGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 29 0.59
23 20 0.41
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:277888 original size:114 final size:114
Alignment explanation
Indices: 277688--277907 Score: 352
Period size: 114 Copynumber: 1.9 Consensus size: 114
277678 GATCGTGCAG
* * *
277688 TTCATCTTTTAATTCCAATAATTAGTTATGGGGTTTCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATAATTAGTTATGGGGTTTCTACCAAACCAGATCAGATAACTCAAAGA
277753 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * * * *
277802 TTCATCTTTCAAATCTAATGATTGGTTTTGGGG-TTCATACCAAATCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATAATTAGTTATGGGGTTTC-TACCAAACCAGATCAGATAACTCAAAG
277866 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
65 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
277908 CGAGAACGTG
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 3 0.03
114 94 0.97
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATAATTAGTTATGGGGTTTCTACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:286330 original size:18 final size:17
Alignment explanation
Indices: 286307--286340 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
286297 TTTGGTCTCA
286307 GTTGCTGTTGATGTGTTT
1 GTTGCTGTTG-TGTGTTT
286325 GTTGCTGTTGTGTGTT
1 GTTGCTGTTGTGTGTT
286341 CGTCTCTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.03, C:0.06, G:0.35, T:0.56
Consensus pattern (17 bp):
GTTGCTGTTGTGTGTTT
Found at i:286862 original size:3 final size:3
Alignment explanation
Indices: 286842--286891 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
286832 TTTGGGCCTG
*
286842 TAA T-A TAA TAA -AA TTAA TAA TAT TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
286887 TAA TA
1 TAA TA
286892 GAAAACCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 4 0.10
3 32 0.78
4 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:287428 original size:23 final size:23
Alignment explanation
Indices: 287385--287428 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
287375 AGCATCAGTT
*
287385 TTTTTTTTTCATTAGAGCATCGG
1 TTTTTTTTTCATTAGACCATCGG
287408 TTTTTTTTT-ATATAGACCATC
1 TTTTTTTTTCAT-TAGACCATC
287429 ATAACATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (23 bp):
TTTTTTTTTCATTAGACCATCGG
Found at i:293319 original size:16 final size:16
Alignment explanation
Indices: 293298--293328 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
293288 AAATTTATAT
293298 ATTTAATATAATTTTG
1 ATTTAATATAATTTTG
*
293314 ATTTAATATTATTTT
1 ATTTAATATAATTTT
293329 AATTCATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTAATATAATTTTG
Found at i:295195 original size:23 final size:23
Alignment explanation
Indices: 295165--295237 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
295155 ATACTTTACA
*
295165 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
295188 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
295211 ATATAAACGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
295234 ATAT
1 ATAT
295238 TTTTACCTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:295690 original size:23 final size:23
Alignment explanation
Indices: 295655--295727 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
295645 ATACTTTACA
*
295655 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
295678 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
295701 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
295724 ATAT
1 ATAT
295728 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:295958 original size:490 final size:489
Alignment explanation
Indices: 294764--296345 Score: 2852
Period size: 490 Copynumber: 3.2 Consensus size: 489
294754 TTATAATATG
* *
294764 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCAATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
294829 TTC--TATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
294892 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
*
294957 TTAACCAAAGATAATAATAAATATGTAATAAATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
295022 TA-TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCA
260 TACT-GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCA
* *
295086 CTCAAAAGATAACCTTAAATTAATGTTTTTC-CAGTGAAAAAAGTATGGACATTTTTATAAAAAG
324 CTCAAAAGATAACCTTAAATTAATG-TTTTCAAAGTGAAAAAAGTATGGACACTTTTATAAAAAG
*
295150 GATAGATACTTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
388 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
*
295215 AAACGCTACCTATTACATCATATTTTTACCTATTATA
453 AAGCGCTACCTATTACATCATATTTTTACCTATTATA
*
295252 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCAATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
295317 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
295382 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
295447 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATTATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
295512 ACTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ACTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* * *
295577 CAAAAGATAACCTTAAATTAATGTTATCAAAGTGAAAAAAGTATGAACACTTTTATAAAAAAAGA
326 CAAAAGATAACCTTAAATTAATGTTTTCAAAGTGAAAAAAGTATGGACACTTTTAT-AAAAAGGA
*
295642 TAAATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
295707 GCGCTACCTATTACATCATATTTTTACCTATTATA
455 GCGCTACCTATTACATCATATTTTTACCTATTATA
*
295742 TTGAAAGTGTTC-ATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTG-TCAATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* *
295806 TTCAATTTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
295871 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
*
295936 TTAACCAAAGATAATAATAAATATGTAATATACATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* *
296001 TACCGTAACGTAAAAAATAAATCATTAGACGCTTATAATTACTAAATTAATATCTTAAAACTCAC
260 TACTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
*
296066 TCAAAAGATAACCTTAAATTAATGTTTTCCAAAGTGAGAAAAGTATGGACACTTTTATAAAAAGG
325 TCAAAAGATAACCTTAAATTAATGTTTT-CAAAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
296131 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
389 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
*
296196 AGCGTTACCTATTACATCATATTTTTACCTATTATA
454 AGCGCTACCTATTACATCATATTTTTACCTATTATA
*
296232 TTGAAAGTGTCAATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATATAATTTATGTT
1 TTGAAAGTGTCAATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
296297 TTAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTA
296346 TTGAAAGTGT
Statistics
Matches: 1056, Mismatches: 30, Indels: 15
0.96 0.03 0.01
Matches are distributed among these distances:
487 50 0.05
488 19 0.02
489 344 0.33
490 614 0.58
491 29 0.03
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (489 bp):
TTGAAAGTGTCAATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
ACTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAGATAACCTTAAATTAATGTTTTCAAAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
CGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:296180 original size:23 final size:23
Alignment explanation
Indices: 296145--296217 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
296135 ATACTTTACA
*
296145 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
296168 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
296191 ATATAAGCGTTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
296214 ATAT
1 ATAT
296218 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:296430 original size:114 final size:114
Alignment explanation
Indices: 296230--296459 Score: 433
Period size: 114 Copynumber: 2.0 Consensus size: 114
296220 TTACCTATTA
296230 TATTGAAAGTGTCAATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATATAATTTATG
1 TATTGAAAGTGTCAATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATATAATTTATG
*
296295 TTTTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATT
66 TTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATT
* *
296344 TATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATG
1 TATTGAAAGTGTCAATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATATAATTTATG
296409 TTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATT
66 TTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATT
296458 TA
1 TA
296460 ATAATTTCCA
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (114 bp):
TATTGAAAGTGTCAATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATATAATTTATG
TTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATT
Found at i:296698 original size:25 final size:25
Alignment explanation
Indices: 296670--296734 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
296660 ACTCAAAATA
*
296670 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATATAGTTAT
296695 TGTACATACCTAAATATATAGTTAT
1 TGTACATACCTAAATATATAGTTAT
*
296720 TATACATACCTAAAT
1 TGTACATACCTAAAT
296735 TTAATGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (25 bp):
TGTACATACCTAAATATATAGTTAT
Found at i:296748 original size:25 final size:25
Alignment explanation
Indices: 296672--296748 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 25
296662 TCAAAATATG
* * * *
296672 TACATACCTAAATATGTAGTTATTG
1 TACATACCTAAATATATAGATAATA
* *
296697 TACATACCTAAATATATAGTTATTA
1 TACATACCTAAATATATAGATAATA
*
296722 TACATACCTAAATTTA-ATGATAATA
1 TACATACCTAAATATATA-GATAATA
296747 TA
1 TA
296749 TACTTATAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 1 0.02
25 45 0.98
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (25 bp):
TACATACCTAAATATATAGATAATA
Found at i:299518 original size:183 final size:183
Alignment explanation
Indices: 299210--300511 Score: 2415
Period size: 183 Copynumber: 7.1 Consensus size: 183
299200 TTAAAATTAG
*
299210 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
299275 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTTTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
299340 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTATGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
299393 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
299458 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
299523 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
*
299576 CGACACAATATTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
299641 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
299706 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTATAGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
299759 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
299824 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
299889 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
*
299942 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
300007 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
300072 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTTTAGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
* *
300125 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCTCATAAAACCGATATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
300190 ATACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
300255 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
* *
300308 CGACACAATGTTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* *
300373 ATACCGGTTATATTACAAAATTATCTATTACGTTATAATTCTAGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
300438 CACTTTTTGATAAGGTATCGACACATTTTTCTTCCATTCTAGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
*
300491 CAACACAATATTAAAAAGTGT
1 CGACACAATATTAAAAAGTGT
300512 GAAAACTTTG
Statistics
Matches: 1088, Mismatches: 31, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 1088 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
Found at i:301751 original size:12 final size:12
Alignment explanation
Indices: 301736--301787 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
301726 ATCATCATTA
*
301736 TCATCGTCATCG
1 TCATCTTCATCG
301748 TCATCTTCATCG
1 TCATCTTCATCG
301760 TCATCTTCATCG
1 TCATCTTCATCG
* *
301772 TCAGCTTCATCT
1 TCATCTTCATCG
301784 TCAT
1 TCAT
301788 TGACCGCTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.17, C:0.33, G:0.10, T:0.40
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:301751 original size:18 final size:18
Alignment explanation
Indices: 301724--301770 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
301714 ATTTGGATCA
301724 TCATCATCAT-TATCATCG
1 TCATCATCATCT-TCATCG
*
301742 TCATCGTCATCTTCATCG
1 TCATCATCATCTTCATCG
*
301760 TCATCTTCATC
1 TCATCATCATC
301771 GTCAGCTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.21, C:0.32, G:0.06, T:0.40
Consensus pattern (18 bp):
TCATCATCATCTTCATCG
Found at i:301787 original size:6 final size:6
Alignment explanation
Indices: 301736--301774 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
301726 ATCATCATTA
* *
301736 TCATCG TCATCG TCATCT TCATCG TCATCT TCATCG TCA
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCA
301775 GCTTCATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.18, C:0.33, G:0.10, T:0.38
Consensus pattern (6 bp):
TCATCG
Found at i:303794 original size:200 final size:200
Alignment explanation
Indices: 303285--304247 Score: 1714
Period size: 200 Copynumber: 4.8 Consensus size: 200
303275 AACATTAAAC
* * * *
303285 AGTGTCGATACA-TATTATATACCAATTCTCTCATAAAACCGGTATACTTGTACCGGTTATATTG
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* *
303349 AAAAATTACATATTACATTATACTTATGGGTTTCGATGTTTATGGGATAGACACTTTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
* *
303414 GGATCGAAACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
303479 TA-AAA
195 TACAAA
303484 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
303549 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
303614 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
303679 ACAAA
196 ACAAA
* *
303684 AGTGTCGACACATTATTTAGACCTATTCTCTTATAAAACCGGTATACTTGTACCAGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
303749 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * *
303814 GATTGACACTTTATAGTTGCACCCTATTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
303879 ACAAA
196 ACAAA
*
303884 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAAATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
303949 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
304014 GATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
304079 ACAAA
196 ACAAA
* *
304084 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
304149 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACATTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
304214 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
304248 ATTGTAAATT
Statistics
Matches: 736, Mismatches: 26, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
199 184 0.25
200 552 0.75
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:304492 original size:18 final size:18
Alignment explanation
Indices: 304469--304529 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
304459 TCTCATTCAT
*
304469 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
304487 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
304506 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
304525 AATTA
1 AATTA
304530 ACTCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:304505 original size:19 final size:19
Alignment explanation
Indices: 304481--304529 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
304471 TTATATTCAC
304481 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
304500 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
304519 ATACAAAATTA
1 ATACAAAATTA
304530 ACTCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:305118 original size:4 final size:4
Alignment explanation
Indices: 305109--305149 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
305099 AATGTCCTTT
*
305109 CATA CATA CATA CATA CATA CATA TATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
305150 CAATCTCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:306086 original size:14 final size:14
Alignment explanation
Indices: 306067--306093 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
306057 TCCAAATCTG
306067 CTGCTATAACACTA
1 CTGCTATAACACTA
306081 CTGCTATAACACT
1 CTGCTATAACACT
306094 CTCCGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (14 bp):
CTGCTATAACACTA
Found at i:306398 original size:33 final size:33
Alignment explanation
Indices: 306359--306424 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
306349 CATCTTAATA
*
306359 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
306392 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
306425 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:306483 original size:21 final size:21
Alignment explanation
Indices: 306458--306522 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
306448 CCCCTTATGC
*
306458 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTATCTTCGACT
*
306479 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTATCTTCGACT
* *
306500 CTATCAAGTTTTTCTTCGACT
1 CTCTCAAGTTTATCTTCGACT
306521 CT
1 CT
306523 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTATCTTCGACT
Found at i:308778 original size:20 final size:19
Alignment explanation
Indices: 308732--308778 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
308722 TCCGGTATCA
*
308732 TTTTACCGGTTTTATCATT
1 TTTTACCGGATTTATCATT
*
308751 TTGATACCGGATTTATCATAT
1 TT-TTACCGGATTTATCAT-T
308772 TTTTACC
1 TTTTACC
308779 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTTACCGGATTTATCATT
Found at i:308940 original size:20 final size:20
Alignment explanation
Indices: 308913--308959 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
308903 TCCGGTAACG
308913 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
308932 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
308953 TTTTACC
1 TTTTACC
308960 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:309003 original size:181 final size:182
Alignment explanation
Indices: 308699--309171 Score: 689
Period size: 181 Copynumber: 2.6 Consensus size: 182
308689 CGTACTTACG
* * *
308699 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGATT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* ** *
308764 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
308829 AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
308880 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
308945 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* ** *
309010 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * **
309062 AAAGTA-CATACACTTTAAATGTATTCGGTAGCGCTTTACCGGTTTTATCATTTCCATACCGGTT
1 AAAGTATC-GACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTT
* * *
309126 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
309172 AATTTGGATC
Statistics
Matches: 262, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
181 166 0.63
182 96 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:310501 original size:25 final size:24
Alignment explanation
Indices: 310459--310506 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
310449 CACATCAGAT
310459 TTTAAAAACATTTAAAAATATATAA
1 TTTAAAAACATTTAAAAAT-TATAA
310484 TTTAAAAA-ATTTAAAAAATTATA
1 TTTAAAAACATTT-AAAAATTATA
310507 GGGACTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TTTAAAAACATTTAAAAATTATAA
Found at i:326238 original size:260 final size:260
Alignment explanation
Indices: 325739--326255 Score: 878
Period size: 260 Copynumber: 2.0 Consensus size: 260
325729 GATGAGCAAG
* *
325739 AAAAGCAGAGTCTTGGTGGCTCGATGGTCCATAAAAAGCAACAAATGTTTCCTATCAGCACGTTC
1 AAAAGCAGAGTCTTGGCGGCTCGATGGTCCATAAAAAGCAACAAATGTTTCCTATCAGCACATTC
* * *
325804 TCCTTCGAAAGAAAGCTATCTTGCTCACAAAGCAGCGATTCTAATGATAACGAGGTTATCGAGTG
66 TCCTTCGAAAGAAAGCTATCTTGCTCACAAAACAGCGATTCTAATGATAACGAGGGTACCGAGTG
*
325869 TGCTTTTATGTATTGTAGCATCTACAACCACTTCCTTCACAATTGAATACATCTCAACCGGAGAC
131 TGCTTTTATGTATTGTAACATCTACAACCACTTCCTTCACAATTGAATACATCTCAACCGGAGAC
*
325934 ATATAATGGACATTTTATTATATAGCAAATATATGATCCTACCAGCAACAGCAGGAAATATACAT
196 ATATAATGGACATTTTATTATATAGCAAATATACGATCCTACCAGCAACAGCAGGAAATATACAT
* * *
325999 AAAA-CAGAGTCTTGGCGGCTCGATGGTCCATAAAATGCAACAAATGTTTCTTATCAGCGCATTC
1 AAAAGCAGAGTCTTGGCGGCTCGATGGTCCATAAAAAGCAACAAATGTTTCCTATCAGCACATTC
* *
326063 T-CTGTCGGAAGAAAGCTATCTTGCTCGCAAAACAGCGATTCTAATGATAACGAGGGTACCGAGT
66 TCCT-TCGAAAGAAAGCTATCTTGCTCACAAAACAGCGATTCTAATGATAACGAGGGTACCGAGT
326127 GTGCTGTTTATGTATTGTAACATCTACAACCACTTCCTTCACAATTGAATACAT-TACAACCGGA
130 GTGCT-TTTATGTATTGTAACATCTACAACCACTTCCTTCACAATTGAATACATCT-CAACCGGA
326191 GACATATAATGGACATTTTATTATATAGCAAATATACGATCCTACCAGCAACAGCAGGAAATATA
193 GACATATAATGGACATTTTATTATATAGCAAATATACGATCCTACCAGCAACAGCAGGAAATATA
326256 TATATATATA
Statistics
Matches: 242, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
258 2 0.01
259 117 0.48
260 123 0.51
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (260 bp):
AAAAGCAGAGTCTTGGCGGCTCGATGGTCCATAAAAAGCAACAAATGTTTCCTATCAGCACATTC
TCCTTCGAAAGAAAGCTATCTTGCTCACAAAACAGCGATTCTAATGATAACGAGGGTACCGAGTG
TGCTTTTATGTATTGTAACATCTACAACCACTTCCTTCACAATTGAATACATCTCAACCGGAGAC
ATATAATGGACATTTTATTATATAGCAAATATACGATCCTACCAGCAACAGCAGGAAATATACAT
Found at i:326258 original size:2 final size:2
Alignment explanation
Indices: 326251--326275 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
326241 ACAGCAGGAA
326251 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
326276 GGACATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:328666 original size:16 final size:17
Alignment explanation
Indices: 328645--328679 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
328635 TACTGTTCAC
*
328645 GTGAATAGT-AAATTTT
1 GTGAATAGTGAAAATTT
328661 GTGAATAGTGAAAATTT
1 GTGAATAGTGAAAATTT
328678 GT
1 GT
328680 CGGCGATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (17 bp):
GTGAATAGTGAAAATTT
Found at i:333843 original size:18 final size:17
Alignment explanation
Indices: 333816--333849 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
333806 ACATTCCGTT
333816 AATCATTTATTTAATAA
1 AATCATTTATTTAATAA
333833 AATCTATTTATTTAATA
1 AATC-ATTTATTTAATA
333850 TATATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
AATCATTTATTTAATAA
Found at i:334691 original size:18 final size:19
Alignment explanation
Indices: 334651--334688 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
334641 TGGTTCATAA
*
334651 AATGTAAGATTATCAGTGGG
1 AATGTAAGATTACCAG-GGG
334671 AATGTAAGATTACCAGGG
1 AATGTAAGATTACCAGGG
334689 AATAGGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.26
Consensus pattern (19 bp):
AATGTAAGATTACCAGGGG
Found at i:335151 original size:37 final size:37
Alignment explanation
Indices: 335078--335152 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
335068 GTTGAAAAAT
* *
335078 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
335115 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
335152 A
1 A
335153 ATATTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:335224 original size:235 final size:235
Alignment explanation
Indices: 334761--335231 Score: 827
Period size: 235 Copynumber: 2.0 Consensus size: 235
334751 CGTGTTTGGT
334761 TAAAGGAATAAAAGATTATTGAAATGTATATTTGACCAAATTGTCCTTATTATATATTTATTTTT
1 TAAAGGAATAAAAGATTATTGAAATGTATATTTGACCAAATTGTCCTTATTATATATTTATTTTT
* *
334826 TTAACAAGTTGGAAAATATTTATATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATGTAAT
66 TTAACAAGTTGAAAAATATTTATATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATATAAT
* * *
334891 TGTTTTTACAAAATTGAAAATATAAAAGGTTTAATGAAATGGTAAAATTTTATTTTAAACTCTGA
131 TGTTTTTACAAAATTGAAAATATAAAAGATTTAATGAAAGGGTAAAATTTTATTTTAAACCCTGA
334956 ACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAA
196 ACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAA
* * *
334996 TAAATGAATAAAAGATTATTGGAATGTATATTTGACCAAATTGTCCTTATTATATATTTGTTTTT
1 TAAAGGAATAAAAGATTATTGAAATGTATATTTGACCAAATTGTCCTTATTATATATTTATTTTT
335061 TTAACAAGTTGAAAAATATTTATATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATATAAT
66 TTAACAAGTTGAAAAATATTTATATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATATAAT
* * *
335126 TTTTTTTACAAAATTGAAAATATAAAAATATTTAATGAAAGGGTAAAATTTTATTTTAACCCCTG
131 TGTTTTTACAAAATTGAAAATAT-AAAAGATTTAATGAAAGGGTAAAATTTTATTTTAAACCCTG
335191 AACTTCATATAAAATTTTAATTATAGA-TTTTTTTTGTAAA
195 AACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAA
335231 T
1 T
335232 CAAAAATAGT
Statistics
Matches: 224, Mismatches: 11, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
235 161 0.72
236 63 0.28
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (235 bp):
TAAAGGAATAAAAGATTATTGAAATGTATATTTGACCAAATTGTCCTTATTATATATTTATTTTT
TTAACAAGTTGAAAAATATTTATATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATATAAT
TGTTTTTACAAAATTGAAAATATAAAAGATTTAATGAAAGGGTAAAATTTTATTTTAAACCCTGA
ACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAA
Found at i:335375 original size:48 final size:48
Alignment explanation
Indices: 335321--335474 Score: 113
Period size: 48 Copynumber: 3.2 Consensus size: 48
335311 AATGGAATCC
335321 ACATTCCCCCGTTTGGTTAGCCCAGAAATCATATTCTCTGGTAATCTT
1 ACATTCCCCCGTTTGGTTAGCCCAGAAATCATATTCTCTGGTAATCTT
* ** * *** * *
335369 ACATTCCCAC---TGG-TATG-GGAGAATGTGGGATTCCCATGGGAATGGAATC-C
1 ACATTCCCCCGTTTGGTTA-GCCCAGAA-ATCATATTCTC-T-GG--T--AATCTT
335419 ACATTCCCCCGTTTGGTTAGCCCAGAAATCATATTCTCTGGTAATCTT
1 ACATTCCCCCGTTTGGTTAGCCCAGAAATCATATTCTCTGGTAATCTT
335467 ACATTCCC
1 ACATTCCC
335475 ACTGGTAATA
Statistics
Matches: 74, Mismatches: 18, Indels: 28
0.62 0.15 0.23
Matches are distributed among these distances:
44 6 0.08
45 10 0.14
46 1 0.01
47 6 0.08
48 17 0.23
49 2 0.03
50 9 0.12
51 6 0.08
52 1 0.01
53 10 0.14
54 6 0.08
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (48 bp):
ACATTCCCCCGTTTGGTTAGCCCAGAAATCATATTCTCTGGTAATCTT
Found at i:335454 original size:98 final size:98
Alignment explanation
Indices: 335285--335481 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
335275 GGGCGTTTGG
335285 ATGGGAGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTAGCCCAGAAAT
1 ATGGGAGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTAGCCCAGAAAT
335350 CATATTCTCTGGTAATCTTACATTCCCACTGGT
66 CATATTCTCTGGTAATCTTACATTCCCACTGGT
335383 ATGGGAGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTAGCCCAGAAAT
1 ATGGGAGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTAGCCCAGAAAT
335448 CATATTCTCTGGTAATCTTACATTCCCACTGGT
66 CATATTCTCTGGTAATCTTACATTCCCACTGGT
335481 A
1 A
335482 ATATTACATT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (98 bp):
ATGGGAGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTAGCCCAGAAAT
CATATTCTCTGGTAATCTTACATTCCCACTGGT
Found at i:335481 original size:20 final size:20
Alignment explanation
Indices: 335456--335532 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
335446 ATCATATTCT
335456 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
* *
335476 CTGGTAATATTACATTCTCA
1 CTGGTAATCTTACATTCCCA
335496 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
335516 CTGATAATCTTACATTC
1 CTGGTAATCTTACATTC
335533 TGTGAACCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:336006 original size:2 final size:2
Alignment explanation
Indices: 335999--336041 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
335989 ACATGATTTC
*
335999 AT AT AT AT AT AT AT AT AT AT AT AT TT 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
336041 A
1 A
336042 GAGAGAGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:337430 original size:22 final size:20
Alignment explanation
Indices: 337405--337451 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
337395 GAGGTATCAG
337405 TACCATGGTATAGTAGTATCGA
1 TACCATGGTA-AG-AGTATCGA
* *
337427 TACCATGTTAAGGGTATCGA
1 TACCATGGTAAGAGTATCGA
337447 TACCA
1 TACCA
337452 GGAAACATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 2 0.09
22 9 0.39
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (20 bp):
TACCATGGTAAGAGTATCGA
Found at i:338267 original size:30 final size:30
Alignment explanation
Indices: 338231--338291 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
338221 AGTCGAGGAT
338231 TACCTATGTCCTTCGGGACATATGGACAGG
1 TACCTATGTCCTTCGGGACATATGGACAGG
*
338261 TACCTATGTCCTTCGGGACATATGGATAGG
1 TACCTATGTCCTTCGGGACATATGGACAGG
338291 T
1 T
338292 CCTTCGGGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (30 bp):
TACCTATGTCCTTCGGGACATATGGACAGG
Found at i:340060 original size:20 final size:20
Alignment explanation
Indices: 340007--340062 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
339997 GCTCTCGCCA
340007 AGTTTAATATGTTAAAATTT
1 AGTTTAATATGTTAAAATTT
** *
340027 AG-GAAAAATAGTTAAAATTT
1 AGTTTAATAT-GTTAAAATTT
340047 AGTTTAATATGTTAAA
1 AGTTTAATATGTTAAA
340063 TGTAAAATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 4 0.14
20 20 0.71
21 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.41
Consensus pattern (20 bp):
AGTTTAATATGTTAAAATTT
Found at i:345755 original size:26 final size:27
Alignment explanation
Indices: 345726--345783 Score: 109
Period size: 26 Copynumber: 2.2 Consensus size: 27
345716 AAAATGTTTA
345726 GTAGGACCTTAATGTATT-ATTATTAT
1 GTAGGACCTTAATGTATTAATTATTAT
345752 GTAGGACCTTAATGTATTAATTATTAT
1 GTAGGACCTTAATGTATTAATTATTAT
345779 GTAGG
1 GTAGG
345784 GTACGTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (27 bp):
GTAGGACCTTAATGTATTAATTATTAT
Found at i:345953 original size:22 final size:23
Alignment explanation
Indices: 345925--345970 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
345915 CAAAAATTAG
345925 AATTTCTA-GCTTTTTCATTTTC
1 AATTTCTATGCTTTTTCATTTTC
**
345947 AATTTCTATTTTTTTTCATTTTC
1 AATTTCTATGCTTTTTCATTTTC
345970 A
1 A
345971 GCTTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.20, C:0.15, G:0.02, T:0.63
Consensus pattern (23 bp):
AATTTCTATGCTTTTTCATTTTC
Found at i:346384 original size:18 final size:17
Alignment explanation
Indices: 346358--346391 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
346348 TTTAATATTT
346358 TATAATTTTATTTAAAAG
1 TATAATTTT-TTTAAAAG
*
346376 TATATTTTTTTTAAAA
1 TATAATTTTTTTAAAA
346392 AAATTACGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TATAATTTTTTTAAAAG
Found at i:346753 original size:21 final size:21
Alignment explanation
Indices: 346729--346775 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
346719 AATACGTGAA
*
346729 TCGCATTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCCAAAT
*
346750 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
346771 TCGCA
1 TCGCA
346776 ACGCAATCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:346871 original size:20 final size:20
Alignment explanation
Indices: 346820--346890 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
346810 CGAATTTAGA
* *
346820 AAATT-GCAACAAAGAAGTC
1 AAATTCGCAACACATAAGTC
346839 AAATTCGCAACACATAAGTC
1 AAATTCGCAACACATAAGTC
*
346859 AAATTCGCAACAC-TAAATTTC
1 AAATTCGCAACACAT-AA-GTC
346880 AAATTCGCAAC
1 AAATTCGCAAC
346891 TGAATTTCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 6 0.13
20 27 0.59
21 13 0.28
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACACATAAGTC
Found at i:346964 original size:39 final size:39
Alignment explanation
Indices: 346857--346967 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 39
346847 AACACATAAG
*
346857 TCAAATTCGCAACACTAAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACAC-GAATTTCAAATTCGCAACTGAATT
* *
346897 TCAAATTCGCAAC-TGAATTTCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACT-GAATT
* *
346936 TCGAATTCGCAACACGAATTT-AATTTCGCAAC
1 TCAAATTCGCAACACGAATTTCAAATTCGCAAC
346968 AGTTTTTAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
38 18 0.29
39 26 0.41
40 19 0.30
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (39 bp):
TCAAATTCGCAACACGAATTTCAAATTCGCAACTGAATT
Found at i:346968 original size:19 final size:20
Alignment explanation
Indices: 346837--346968 Score: 137
Period size: 19 Copynumber: 6.7 Consensus size: 20
346827 AACAAAGAAG
**
346837 TCAAATTCGCAACAC-ATAAG
1 TCAAATTCGCAACACGA-ATT
*
346857 TCAAATTCGCAACACTAAATT
1 TCAAATTCGCAACAC-GAATT
*
346878 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACACGAATT
*
346897 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACACGAATT
* *
346916 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACACGAATT
*
346936 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAACACGAATT
*
346956 T-AATTTCGCAACA
1 TCAAATTCGCAACA
346969 GTTTTTAGTT
Statistics
Matches: 98, Mismatches: 11, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
19 46 0.47
20 37 0.38
21 14 0.14
22 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Found at i:350217 original size:18 final size:18
Alignment explanation
Indices: 350194--350229 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
350184 AAGCAAAAGG
*
350194 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
350212 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
350230 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:350535 original size:19 final size:20
Alignment explanation
Indices: 350482--350538 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
350472 GTTGCGATTG
350482 ATGCGAAAGTTAAATTCGCA
1 ATGCGAAAGTTAAATTCGCA
* *
350502 ACGCGAAAGTTAAATTTGCA
1 ATGCGAAAGTTAAATTCGCA
*
350522 ATGC-AAAGTCAAATTCG
1 ATGCGAAAGTTAAATTCG
350539 TATTGCGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (20 bp):
ATGCGAAAGTTAAATTCGCA
Found at i:350806 original size:64 final size:65
Alignment explanation
Indices: 350726--350884 Score: 257
Period size: 65 Copynumber: 2.4 Consensus size: 65
350716 TTGAATAAAC
350726 AACAAATCAACTTTTACAAATCAATTAAACAAAC-AAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAAATAATTCTTATTTACACATCAATTA
* * * *
350790 AACAAATAAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAAATAATTCTTATTTACACATCAATTA
*
350855 AACAAATCAACTTTTACGAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
350885 ATTCAATTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 32 0.37
65 51 0.59
66 4 0.05
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.30
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:353377 original size:19 final size:20
Alignment explanation
Indices: 353353--353399 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
353343 AAACTTAAAT
*
353353 TCGCAATGCGAA-ATGAAAA
1 TCGCAACGCGAACATGAAAA
353372 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAACATGAAAA
353392 TCGCAACG
1 TCGCAACG
353400 TGAAACTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAACATGAAAA
Found at i:353466 original size:20 final size:20
Alignment explanation
Indices: 353427--353466 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
353417 TGCGATTTTT
* * *
353427 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
353447 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
353467 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:353844 original size:22 final size:22
Alignment explanation
Indices: 353787--353844 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
353777 GATGGAGATA
*
353787 GACGGATTTCTTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
** *
353809 GATAGATTTTGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
353831 GACGGATGTCGTCG
1 GACGGATTTCGTCG
353845 TAGAGAGTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.41, T:0.28
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:353984 original size:21 final size:21
Alignment explanation
Indices: 353960--353999 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
353950 ATAAATGCGC
353960 TTTGACTTCTGTGTTGCGAAA
1 TTTGACTTCTGTGTTGCGAAA
353981 TTTGACTTCTGTGTTGCGA
1 TTTGACTTCTGTGTTGCGA
354000 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (21 bp):
TTTGACTTCTGTGTTGCGAAA
Found at i:354630 original size:25 final size:26
Alignment explanation
Indices: 354601--354675 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 26
354591 TTTTAAATGG
354601 AAATAAAAATATTTTTAAATTAAGTT
1 AAATAAAAATATTTTTAAATTAAGTT
* *
354627 -AATAATAAAATATATTT-AA-TAATTT
1 AAAT-A-AAAATATTTTTAAATTAAGTT
354652 AATATAAAAATATTTTTAAATTAA
1 AA-ATAAAAATATTTTTAAATTAA
354676 TATATATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
25 18 0.45
26 7 0.17
27 15 0.38
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
AAATAAAAATATTTTTAAATTAAGTT
Found at i:354682 original size:2 final size:2
Alignment explanation
Indices: 354675--354709 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
354665 TTTTAAATTA
354675 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
354710 CATAATCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:354686 original size:22 final size:23
Alignment explanation
Indices: 354629--354704 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
354619 ATTAAGTTAA
*
354629 TAATA-AAATATATTTAATAATT
1 TAATATAAATATATTTAATAAAT
* *
354651 TAATATAAAAATATTT-TTAAAT
1 TAATATAAATATATTTAATAAAT
* * *
354673 TAATATATATATATATATATATAT
1 TAATATAAATATATTTA-ATAAAT
354697 ATAATATA
1 -TAATATA
354705 TTATACATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
22 22 0.52
23 9 0.21
24 4 0.10
25 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATATAAATATATTTAATAAAT
Found at i:354714 original size:14 final size:13
Alignment explanation
Indices: 354673--354715 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
354663 ATTTTTAAAT
354673 TAATATATATATA
1 TAATATATATATA
354686 T-ATATATATATA
1 TAATATATATATA
*
354698 TAATATATTATACA
1 TAATATA-TATATA
354712 TAAT
1 TAAT
354716 CTGAGTCACG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.44
13 6 0.22
14 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATATATATATA
Found at i:354857 original size:23 final size:23
Alignment explanation
Indices: 354831--354888 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
354821 TCTACACATA
354831 AATTTTAAAAAATCAAATTATAT
1 AATTTTAAAAAATCAAATTATAT
354854 AATTTTAAAAAATCAAATTATAT
1 AATTTTAAAAAATCAAATTATAT
354877 AA-TTTAAAAAAT
1 AATTTTAAAAAAT
354889 ATTAAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 10 0.29
23 25 0.71
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTTTAAAAAATCAAATTATAT
Found at i:358755 original size:20 final size:20
Alignment explanation
Indices: 358730--358803 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
358720 TTTTCCCAAT
*
358730 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
358750 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAAGTAAA
*
358770 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAAGTAAA
358791 TCGCAACGCGAAT
1 TCGCAACGCGAAT
358804 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:358772 original size:41 final size:41
Alignment explanation
Indices: 358727--358819 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
358717 CGATTTTCCC
358727 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
358768 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
358809 AAATCGCAATG
1 AATTCGCAATG
358820 TGATACTGAC
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:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:358776 original size:21 final size:20
Alignment explanation
Indices: 358730--358817 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
358720 TTTTCCCAAT
* *
358730 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGGAAA
**
358750 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAAGGAAA
* *
358770 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAAGGAAA
**
358791 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAATAAGG-AAA
358812 TCGCAA
1 TCGCAA
358818 TGTGATACTG
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
20 29 0.54
21 25 0.46
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGGAAA
Found at i:358835 original size:41 final size:41
Alignment explanation
Indices: 358749--358883 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 41
358739 GAATAAGTAA
* * * *
358749 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAG-ATACTG-ACT
*
358790 ATCGCAACGCGAATTGGGAAAATCGCAATGTGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
* * ** * *
358831 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGAGATACTGACT
*
358872 TTCGCAACGCGA
1 ATCGCAACGCGA
358884 TACTGACTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 72 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
Found at i:358901 original size:20 final size:20
Alignment explanation
Indices: 358857--358904 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
358847 AAAAAATCGC
* * *
358857 AACGAGATACTTACTTTCGC
1 AACGCGATACTGACTTTCGA
358877 AACGCGATACTGACTTTCGA
1 AACGCGATACTGACTTTCGA
358897 AACGCGAT
1 AACGCGAT
358905 TTACTTAGCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
AACGCGATACTGACTTTCGA
Found at i:359473 original size:19 final size:19
Alignment explanation
Indices: 359430--359494 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
359420 CGAGAATGAG
* *
359430 AATCGCAACGCGAAAATGAC
1 AATCGCAACGCG-AAATAAA
*
359450 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
359469 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
359488 AATCGCA
1 AATCGCA
359495 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:359512 original size:19 final size:19
Alignment explanation
Indices: 359490--359674 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
359480 GAAACCAAAA
*
359490 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
359509 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
359528 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
359547 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
359567 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
359583 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
359600 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
359614 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
359633 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
359653 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
359673 TC
1 TC
359675 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:359567 original size:39 final size:38
Alignment explanation
Indices: 359490--359579 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
359480 GAAACCAAAA
* *
359490 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
359528 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
359567 TCGCGTTGCGATT
1 TCGCGTTGCGATT
359580 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:359599 original size:33 final size:33
Alignment explanation
Indices: 359562--359649 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
359552 GTTGCGATTT
* *
359562 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
359595 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
359628 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
359650 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:359651 original size:20 final size:20
Alignment explanation
Indices: 359617--359674 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
359607 GCGATTCTCT
**
359617 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
359637 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
359657 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
359675 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:361736 original size:42 final size:42
Alignment explanation
Indices: 361676--361798 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
361666 GCCCGACTCG
* * *
361676 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
361718 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
361760 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
361799 CCCGATTTAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:361756 original size:21 final size:21
Alignment explanation
Indices: 361732--361798 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
361722 TCATTCCTCG
361732 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
361753 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
361774 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
361795 AGAG
1 AGAG
361799 CCCGATTTAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:363174 original size:14 final size:14
Alignment explanation
Indices: 363155--363190 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
363145 ATTGTTTAAT
363155 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
363169 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
363183 TGATTTGT
1 TGATTTGT
363191 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:363391 original size:19 final size:19
Alignment explanation
Indices: 363369--363486 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
363359 CGAAATTAAA
363369 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
363388 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
363403 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
363421 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
363436 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
363454 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
363473 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
363487 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:363415 original size:33 final size:33
Alignment explanation
Indices: 363373--363466 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
363363 ATTAAATTCG
363373 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
363406 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
363439 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
363467 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:365778 original size:12 final size:12
Alignment explanation
Indices: 365761--365785 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
365751 TCTTCGGGGA
365761 CTTTTTCTTCTT
1 CTTTTTCTTCTT
365773 CTTTTTCTTCTT
1 CTTTTTCTTCTT
365785 C
1 C
365786 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:367283 original size:14 final size:14
Alignment explanation
Indices: 367264--367300 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
367254 CATTAATTAA
367264 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
367278 ACAAATCATCTTTT
1 ACAAATCAACATTT
367292 ACAAATCAA
1 ACAAATCAA
367301 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:367672 original size:20 final size:20
Alignment explanation
Indices: 367647--367702 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
367637 ATTCATTTTA
367647 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
367667 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
* *
367687 TTATCGCAACGCGAAA
1 CTATCGCAACGTGAAA
367703 TGATAATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGTGAAAATGG
Found at i:367711 original size:19 final size:20
Alignment explanation
Indices: 367649--367713 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
367639 TCATTTTACT
* *
367649 ATCGCAACGTGAAAATGGCT-
1 ATCGCAACGCGAAAAT-GATA
* * *
367669 ATCGCAACGTGAAAATGGTT
1 ATCGCAACGCGAAAATGATA
367689 ATCGCAACGCG-AAATGATA
1 ATCGCAACGCGAAAATGATA
367708 ATCGCA
1 ATCGCA
367714 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGATA
Found at i:367733 original size:14 final size:14
Alignment explanation
Indices: 367714--367767 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
367704 GATAATCGCA
367714 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
367728 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
367745 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
367761 TTGCGAT
1 TTGCGAT
367768 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:367751 original size:33 final size:33
Alignment explanation
Indices: 367709--367786 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
367699 GAAATGATAA
***
367709 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
367742 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
367775 TCGCGTTGCGAT
1 TCGCATTGCGAT
367787 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:367893 original size:14 final size:14
Alignment explanation
Indices: 367874--367910 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
367864 CATCAATTAA
367874 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
367888 ACAAATCATCTTTT
1 ACAAATCAACATTT
367902 ACAAATCAA
1 ACAAATCAA
367911 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:369814 original size:20 final size:19
Alignment explanation
Indices: 369780--369845 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
369770 AAACTTAAAT
369780 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGACTA
*
369799 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
369819 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
369838 TCGCAACG
1 TCGCAACG
369846 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:369853 original size:14 final size:14
Alignment explanation
Indices: 369834--369891 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
369824 ATGCGAAATG
369834 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
369848 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
369864 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
369880 AAAATCGCAACG
1 AAAATCGCAACG
369892 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:369876 original size:32 final size:33
Alignment explanation
Indices: 369818--369896 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
369808 GGAAATGGCT
*
369818 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
369851 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
369883 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
369897 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:369925 original size:19 final size:19
Alignment explanation
Indices: 369903--369966 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
369893 GAAACACAAA
369903 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
369922 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
369938 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
369955 TCGCATTGCGAT
1 TCGCATTGCGAT
369967 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 17 0.46
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:369985 original size:20 final size:19
Alignment explanation
Indices: 369951--370005 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
369941 TTGCGATTTT
*
369951 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
369970 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
369990 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
370006 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:370503 original size:18 final size:18
Alignment explanation
Indices: 370477--370521 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
370467 GTCGATCAGA
*
370477 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
370495 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
370513 TGATGGCTC
1 TGATGGCTC
370522 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:371865 original size:20 final size:20
Alignment explanation
Indices: 371840--371877 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
371830 AATAGTTTCT
371840 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
371860 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
371878 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Done.