Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008342.1 Hibiscus syriacus cultivar Beakdansim tig00111069_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: 1228932
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:536796 original size:42 final size:42
Alignment explanation
Indices: 536703--536796 Score: 95
Period size: 42 Copynumber: 2.2 Consensus size: 42
536693 CACCTCCTAT
*
536703 CGTTCAAGAGGCCTCTCTCATCATCGAAGAGGTCCCTCTCAC
1 CGTTCAAGAGGCCCCTCTCATCATCGAAGAGGTCCCTCTCAC
* * * *
536745 CATTTAAGAGGCCCCTGTCATCGTTC-AAGAGGTCCCGT-T-AGC
1 CGTTCAAGAGGCCCCTCTCATC-ATCGAAGAGGTCCC-TCTCA-C
536787 CGTTCAAGAG
1 CGTTCAAGAG
536797 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.02
42 38 0.90
43 3 0.07
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCATCATCGAAGAGGTCCCTCTCAC
Found at i:538453 original size:20 final size:20
Alignment explanation
Indices: 538411--538455 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
538401 TAAAGTTAAA
* * * *
538411 TTCGAGTTGCGATTTTGATT
1 TTCGCGTTGCGAATTTAACT
538431 TTCGCGTTGCGAATTTAACT
1 TTCGCGTTGCGAATTTAACT
538451 TTCGC
1 TTCGC
538456 AATAAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTAACT
Found at i:538723 original size:18 final size:18
Alignment explanation
Indices: 538700--538735 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
538690 AAGCCGGTTG
*
538700 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
538718 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
538736 CCTTTTTCTT
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:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:542009 original size:20 final size:21
Alignment explanation
Indices: 541986--542036 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
541976 TAAATGCGTG
541986 GTTGCGAATTCGAAAATC-GA
1 GTTGCGAATTCGAAAATCAGA
* * * *
542006 GTTGCAAATTTGAAATTCAGT
1 GTTGCGAATTCGAAAATCAGA
542027 GTTGCGAATT
1 GTTGCGAATT
542037 TGACTTATGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (21 bp):
GTTGCGAATTCGAAAATCAGA
Found at i:542050 original size:20 final size:20
Alignment explanation
Indices: 542025--542078 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
542015 TTGAAATTCA
542025 GTGTTGCGAATTTGACTTAT
1 GTGTTGCGAATTTGACTTAT
*
542045 GTGTTGCGAATTTGACTTTT
1 GTGTTGCGAATTTGACTTAT
*
542065 GCGTTGCGAATTTG
1 GTGTTGCGAATTTG
542079 GAAACTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.44
Consensus pattern (20 bp):
GTGTTGCGAATTTGACTTAT
Found at i:543929 original size:2 final size:2
Alignment explanation
Indices: 543922--543955 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
543912 TTTCATGATA
543922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
543956 TTAACATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:551195 original size:2 final size:2
Alignment explanation
Indices: 551184--551226 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
551174 CCACCGTGAC
551184 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
551225 TA
1 TA
551227 AAGCTAAGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:553967 original size:28 final size:28
Alignment explanation
Indices: 553931--554001 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
553921 TATTAAAATA
*
553931 ATTTT-AAATAATTTAATAAGTTTATTT
1 ATTTTAAAATAATTTAATAAGGTTATTT
553958 ATTTTAAAATAATTTAATAAGGTTATTT
1 ATTTTAAAATAATTTAATAAGGTTATTT
553986 ATTTTAAAATAATTTA
1 ATTTTAAAATAATTTA
554002 TGTTAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 5 0.12
28 37 0.88
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (28 bp):
ATTTTAAAATAATTTAATAAGGTTATTT
Found at i:554045 original size:45 final size:45
Alignment explanation
Indices: 553954--554115 Score: 195
Period size: 45 Copynumber: 3.5 Consensus size: 45
553944 TAATAAGTTT
** *
553954 ATTTATTTTAAAATAATTTA--ATAAGGTTATTTATTTTAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATA
*
553997 ATTTATGTTAAAATAATTTATTATAAAATAATTTATTTTAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATA
*
554042 ATTTATTTTAAAATAAATTATTATAAAATATAGATTGATTTATTTTAAAATA
1 ATTTATTTTAAAATAATTTATTAT-AAA-AT--A---ATTTATTTTAAAATA
554094 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
554116 GTATGGATTG
Statistics
Matches: 103, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
43 19 0.18
45 42 0.41
46 3 0.03
47 2 0.02
49 1 0.01
51 12 0.12
52 24 0.23
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (45 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATA
Found at i:554108 original size:14 final size:15
Alignment explanation
Indices: 553954--554114 Score: 166
Period size: 15 Copynumber: 10.5 Consensus size: 15
553944 TAATAAGTTT
553954 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* ** *
553969 ATTTA--ATAAGGTT
1 ATTTATTTTAAAATA
553982 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
553997 ATTTATGTTAAAATA
1 ATTTATTTTAAAATA
*
554012 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
554027 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
554042 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
554057 AATTATTATAAAATATAGA
1 ATTTATT-TTAAA-AT--A
554076 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
554094 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
554108 ATTTATT
1 ATTTATT
554115 AGTATGGATT
Statistics
Matches: 121, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
13 9 0.07
14 12 0.10
15 80 0.66
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:554132 original size:32 final size:32
Alignment explanation
Indices: 554094--554529 Score: 374
Period size: 32 Copynumber: 15.4 Consensus size: 32
554084 TTTTAAAATA
554094 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
554126 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
554148 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
554180 ATTTATTTT--A-AA---A-TA-TA--GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
554202 ATATATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
554234 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
554266 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
554288 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
554320 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
554342 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
554374 ATTTA--TT--AT--TGTAGTT-GTATAGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
554400 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
554432 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
554454 ATTTATTTTAAATAATTTATTAGCATGTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
554486 ATTTATTTTAAATAATTTATTTGTATGTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
554518 ATTTATTTTAAA
1 ATTTATTTTAAA
554530 ATATAGATTG
Statistics
Matches: 332, Mismatches: 14, Indels: 116
0.72 0.03 0.25
Matches are distributed among these distances:
22 68 0.20
23 16 0.05
24 3 0.01
25 8 0.02
26 30 0.09
27 2 0.01
28 17 0.05
29 8 0.02
30 7 0.02
31 18 0.05
32 155 0.47
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:554133 original size:22 final size:22
Alignment explanation
Indices: 554117--554159 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
554107 AATTTATTAG
554117 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
554139 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
554160 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:554159 original size:54 final size:54
Alignment explanation
Indices: 554094--554673 Score: 271
Period size: 54 Copynumber: 10.4 Consensus size: 54
554084 TTTTAAAATA
554094 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
554148 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * **
554202 ATATATTTTAAATAATTTATTAGTATAGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * *
554257 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATA---ATTT
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * *
554306 A-TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTTA-TTTTAAATAATTTA--TT--AGTATGGATTGATTTATTTT-AA-AA--TA-T-GGATTG
* * * **
554370 ATTGA-TTT--ATTATTGTAGTT-GTATAGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATT-TA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * *
554423 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGCATGTATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTG
* * *
554486 ATTTATTTTAAATAATTTATTTGTATGTATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * * *
554540 ATTTATTATT--GT-AGTGA-TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATT-TTAAATAATTTATTA-GTATGGATTGA-TTT--AT--TTTA-AAATATGGATTG
*
554598 ATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
554652 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
554674 TTGTAGTTGT
Statistics
Matches: 400, Mismatches: 73, Indels: 106
0.69 0.13 0.18
Matches are distributed among these distances:
47 1 0.00
48 1 0.00
49 9 0.02
50 3 0.01
51 1 0.00
52 13 0.03
53 12 0.03
54 206 0.51
55 23 0.06
56 9 0.02
57 12 0.03
58 34 0.09
59 9 0.02
60 14 0.04
61 8 0.02
62 7 0.02
63 13 0.03
64 23 0.06
65 2 0.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:554196 original size:22 final size:22
Alignment explanation
Indices: 554171--554213 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
554161 AATTTATTAG
*
554171 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATATATTTTAAAA
554193 TATAGATTGATATATTTTAAA
1 TATAGATTGATATATTTTAAA
554214 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
TATAGATTGATATATTTTAAAA
Found at i:554253 original size:140 final size:140
Alignment explanation
Indices: 554094--554380 Score: 531
Period size: 140 Copynumber: 2.0 Consensus size: 140
554084 TTTTAAAATA
554094 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
554159 ATAATTTATTAGTAT-AGATTGATTTATTTTAAAATATAGATTGATATATTTTAAATAATTTATT
66 ATAATTTATTAGTATGA-ATTGATTTATTTTAAAATATAGATTGATATATTTTAAATAATTTATT
554223 AGTATAGATTG
130 AGTATAGATTG
554234 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* *
554299 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
66 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATATATTTTAAATAATTTATTA
*
554364 GTATGGATTG
131 GTATAGATTG
554374 ATTTATT
1 ATTTATT
554381 ATTGTAGTTG
Statistics
Matches: 143, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
140 142 0.99
141 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (140 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATATATTTTAAATAATTTATTA
GTATAGATTG
Found at i:554282 original size:22 final size:22
Alignment explanation
Indices: 554257--554299 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
554247 AATTTATTAG
554257 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
554279 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
554300 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:554336 original size:22 final size:22
Alignment explanation
Indices: 554311--554353 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
554301 AATTTATTAG
554311 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
554333 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
554354 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:554427 original size:166 final size:165
Alignment explanation
Indices: 554144--554609 Score: 582
Period size: 166 Copynumber: 2.8 Consensus size: 165
554134 TAAAATATGG
** * ** *
554144 ATTGATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAAATATAGATTGATATAT
1 ATTGATTTATTTTAAATAATGGATTTGTAT-GTATTGAAATAATTTAAAATATAGATTGAT-T-T
* * *
554208 TTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
63 ATT--AT--TGTAGT-GTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
*
554273 TTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
123 TTAAAATATGGATTGATTTATTTTAAATAATTTATTAGCATGA
* * * * *
554316 ATTGATTTATTTTAAA-ATATGGA-TTG-ATTTATTTTAAATAATTTATTAGTATGGATTGATTT
1 ATTGATTTATTTTAAATA-ATGGATTTGTATGTA-TTGAAATAATTTA-AAATATAGATTGATTT
554378 ATTATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
63 ATTATTGTAG-TGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
*
554443 AATATGGATTGATTTATTTTAAATAATTTATTAGCATGT
127 AATATGGATTGATTTATTTTAAATAATTTATTAGCATGA
** ** *
554482 ATTGATTTATTTTAAATAATTTATTTGTATGTATTGATTTATTTTAAAATATAGATTGATTTATT
1 ATTGATTTATTTTAAATAATGGATTTGTATGTATTGAAATAATTTAAAATATAGATTGATTTATT
554547 ATTGTAGTG-ATATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
66 ATTGTAGTGTATA-G-ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
554610 TAATTTATTA
Statistics
Matches: 258, Mismatches: 26, Indels: 26
0.83 0.08 0.08
Matches are distributed among these distances:
164 3 0.01
165 3 0.01
166 183 0.71
167 14 0.05
168 6 0.02
170 6 0.02
171 13 0.05
172 30 0.12
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (165 bp):
ATTGATTTATTTTAAATAATGGATTTGTATGTATTGAAATAATTTAAAATATAGATTGATTTATT
ATTGTAGTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
TGGATTGATTTATTTTAAATAATTTATTAGCATGA
Found at i:554448 original size:22 final size:22
Alignment explanation
Indices: 554423--554465 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
554413 AATTTATTAG
554423 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
554445 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
554466 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:554603 original size:32 final size:32
Alignment explanation
Indices: 554557--554641 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
554547 ATTGTAGTGA
*
554557 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
554589 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
554621 TATTGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
554642 ATATGGATTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:554641 original size:112 final size:110
Alignment explanation
Indices: 554139--554658 Score: 478
Period size: 112 Copynumber: 4.6 Consensus size: 110
554129 TATTTTAAAA
* *
554139 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAG-ATTGA
1 TATGGATTGATTTATTTTAAATAATGTATT-GTATTGATTGATTTATTTTAAAATATAGAATTGA
* *
554203 TATATT-TTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTAG
65 TTTATTATT---TAA---A--A-TATGGATTGATTTATTTTAAATAATTTATTAG
* * * ** * * *
554257 TATGGATTGATTTATTTTAAA-ATATGGATTG-ATTTATTTTAAATAATTTATTAGTAT-GAATT
1 TATGGATTGATTTATTTTAAATA-ATGTATTGTATTGA-TTGATTTATTTTA-AAATATAGAATT
554319 GATTTA-T-TTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
63 GATTTATTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
554365 TATGGATTGATTTA--TT--AT--TGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATGTA-TTGTATTGATTGATTTATTTT-AA-AA--TA-TAGA
* *
554424 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
60 ATTGATTTA-TTA-TTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* * *
554477 CATGTATTGATTTATTTTAAATAATTTATTTGTA-TGTATTGATTTATTTTAAAATATAG-ATTG
1 TATGGATTGATTTATTTTAAATAATGTA-TTGTATTG-ATTGATTTATTTTAAAATATAGAATTG
** *
554540 ATTTATTATTGTAGTGATATGAATTGATTTATTTTAAATAATTTATTAG
64 ATTTATTATT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
554589 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATAT-GGATTGA
1 TATGGATTGATTTATTTTAAATAATGTATT-GTATTGATTGATTTATTTTAAAATATAGAATTGA
554653 TTTATT
65 TTTATT
554659 TTAAATAATT
Statistics
Matches: 337, Mismatches: 36, Indels: 64
0.77 0.08 0.15
Matches are distributed among these distances:
102 3 0.01
103 11 0.03
104 6 0.02
106 4 0.01
107 1 0.00
108 53 0.16
109 1 0.00
110 3 0.01
111 9 0.03
112 150 0.45
113 5 0.01
114 7 0.02
116 7 0.02
117 18 0.05
118 59 0.18
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (110 bp):
TATGGATTGATTTATTTTAAATAATGTATTGTATTGATTGATTTATTTTAAAATATAGAATTGAT
TTATTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:554723 original size:31 final size:31
Alignment explanation
Indices: 554688--554746 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
554678 AGTTGTATAG
* *
554688 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
554719 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
554747 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:555584 original size:15 final size:16
Alignment explanation
Indices: 555546--555586 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
555536 ACAGAGTCTC
*
555546 TGAATCATTTAGCATT
1 TGAATCATTCAGCATT
*
555562 TGAATCATTCAGCGTT
1 TGAATCATTCAGCATT
555578 T-AATCATTC
1 TGAATCATTC
555587 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:562133 original size:13 final size:13
Alignment explanation
Indices: 562115--562210 Score: 67
Period size: 13 Copynumber: 7.4 Consensus size: 13
562105 AAAATTATAT
562115 TATAATAAATAAA
1 TATAATAAATAAA
562128 TATAAT-AAT-AA
1 TATAATAAATAAA
562139 TAATAAGT-AAT-AA
1 T-ATAA-TAAATAAA
* *
562152 TATTAATTATTAAA
1 TA-TAATAAATAAA
*
562166 TATAATAAATAAT
1 TATAATAAATAAA
*
562179 TAAAATATAAT-AA
1 TATAATA-AATAAA
*
562192 TATAATAATTAAAA
1 TATAATAAAT-AAA
562206 TATAA
1 TATAA
562211 AATTTATAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
11 3 0.04
12 11 0.16
13 39 0.58
14 14 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (13 bp):
TATAATAAATAAA
Found at i:562135 original size:3 final size:3
Alignment explanation
Indices: 562116--562200 Score: 56
Period size: 3 Copynumber: 28.7 Consensus size: 3
562106 AAATTATATT
* * *
562116 ATA ATAA ATA A-A TATA ATA ATA ATA ATA AGTA ATA ATA TTA ATT ATT
1 ATA AT-A ATA ATA -ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
562163 A-A AT- ATA ATAA ATA ATTA A-A AT- ATA ATA AT- ATA ATA AT
1 ATA ATA ATA AT-A ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT
562201 TAAAATATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
2 10 0.15
3 44 0.66
4 13 0.19
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:562135 original size:16 final size:16
Alignment explanation
Indices: 562111--562522 Score: 89
Period size: 16 Copynumber: 24.6 Consensus size: 16
562101 TCCAAAAATT
*
562111 ATATTATAATAAATAA
1 ATATAATAATAAATAA
562127 ATATAATAATAATAATAA
1 ATATAATAAT-A-AATAA
* *
562145 GTAATAATATTAATTATTAA
1 AT-ATAATAATAA--A-TAA
*
562165 ATATAATAAATAATTAAA
1 ATATAAT-AATAAAT-AA
562183 ATATAATAATATAATAA
1 ATATAATAATA-AATAA
* * *
562200 TTAAAAT-ATAAA-AT
1 ATATAATAATAAATAA
*
562214 TTATAA-AA-AAATAA
1 ATATAATAATAAATAA
* ***
562228 TTATAATATATTTTGTAAA
1 ATATAATA-A-TAAAT-AA
*
562247 ATTTGAAATAATAAA-AA
1 ATAT--AATAATAAATAA
*
562264 TTATATTATAATAAATAA
1 --ATATAATAATAAATAA
*
562282 ATAAAATAAT-AAT-A
1 ATATAATAATAAATAA
*
562296 ATAATTAATAAT-ATTAA
1 AT-A-TAATAATAAATAA
*
562313 ATATAATAAATAATTAAA
1 ATATAAT-AATAAAT-AA
* *
562331 ATGTAATAATATATAA
1 ATATAATAATAAATAA
*
562347 ATATAGTAATTAAAATATA
1 ATATAATAA-T-AAATA-A
* *
562366 TATTTTATAA-AAATAA
1 -ATATAATAATAAATAA
* ***
562382 TTATAATATATTTTGTAAA
1 ATATAATA-A-TAAAT-AA
* *
562401 ATTTGAAATAATGAAA-AC
1 ATAT--AATAAT-AAATAA
* *
562419 TTATTATAATAAATAA
1 ATATAATAATAAATAA
562435 ATATAATAAT-AAT--
1 ATATAATAATAAATAA
*
562448 A-ATAATAAT-AATTA
1 ATATAATAATAAATAA
* * *
562462 ATCATATTAATTATTAA
1 AT-ATAATAATAAATAA
*
562479 ATATAATAAATAATTAAA
1 ATATAAT-AATAAAT-AA
*
562497 ATATAATAATATATAA
1 ATATAATAATAAATAA
*
562513 ATATAGTAAT
1 ATATAATAAT
562523 TAAAATAGAT
Statistics
Matches: 289, Mismatches: 61, Indels: 92
0.65 0.14 0.21
Matches are distributed among these distances:
12 11 0.04
13 4 0.01
14 18 0.06
15 22 0.08
16 80 0.28
17 57 0.20
18 46 0.16
19 27 0.09
20 16 0.06
21 8 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
ATATAATAATAAATAA
Found at i:562286 original size:25 final size:23
Alignment explanation
Indices: 562252--562349 Score: 85
Period size: 22 Copynumber: 4.2 Consensus size: 23
562242 GTAAAATTTG
562252 AAAT-AATAAAAATTATATTATAAT
1 AAATAAAT-AAAATTA-ATTATAAT
*
562276 AAATAAATAAAA-TAATAATAAT
1 AAATAAATAAAATTAATTATAAT
* * *
562298 -AATTAATAATATTAAATATAAT
1 AAATAAATAAAATTAATTATAAT
* *
562320 AAATAATTAAAATGTAATAATATAT
1 AAATAAATAAAAT-TAATTATA-AT
562345 AAATA
1 AAATA
562350 TAGTAATTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
21 9 0.15
22 15 0.25
23 11 0.19
24 14 0.24
25 10 0.17
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (23 bp):
AAATAAATAAAATTAATTATAAT
Found at i:562290 original size:155 final size:154
Alignment explanation
Indices: 562104--562509 Score: 595
Period size: 155 Copynumber: 2.6 Consensus size: 154
562094 TTTATAATCC
* *
562104 AAAAATTATATTATAATAAATAAATATAATAATAATAATAAGTAATAATATTAATTATTAAATAT
1 AAAAATTATATTATAATAAATAAATAAAATAATAATAATAATTAATAATATTAATTATTAAATAT
562169 AATAAATAATTAAAATATAATAATATAATAATTAAAATATAAAATTTATAAAAAAATAATTATAA
66 AATAAATAATTAAAATATAATAATATAATAATTAAAATAT-AAATTT-TAAAAAAATAATTATAA
562234 TATATTTTGTAAAATTTGAAATAAT-
129 TATATTTTGTAAAATTTGAAATAATG
* *
562259 AAAAATTATATTATAATAAATAAATAAAATAATAATAATAATTAATAATATTAAATA-TAATAAA
1 AAAAATTATATTATAATAAATAAATAAAATAATAATAATAATTAATAATATTAATTATTAA-ATA
* * * *
562323 TAATTAA-AATGTAATAATAT-ATAAATATAGTAATTAAAATATATATTTTATAAAAATAATTAT
65 TAATAAATAAT-TAA-AATATAAT-AATATAATAATTAAAATATAAATTTTAAAAAAATAATTAT
562386 AATATATTTTGTAAAATTTGAAATAATG
127 AATATATTTTGTAAAATTTGAAATAATG
* * *
562414 AAAACTTATTATAATAAATAAATATAATAATAATAATAATAATAATTAATCATATTAATTATTAA
1 AAAAATTA-TATTAT-AATAAATA-AATAA-AATAATAATAATAATTAATAATATTAATTATTAA
562479 ATATAATAAATAATTAAAATATAATAATATA
62 ATATAATAAATAATTAAAATATAATAATATA
562510 TAAATATAGT
Statistics
Matches: 225, Mismatches: 14, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
154 47 0.21
155 79 0.35
156 28 0.12
157 8 0.04
158 16 0.07
159 41 0.18
160 6 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (154 bp):
AAAAATTATATTATAATAAATAAATAAAATAATAATAATAATTAATAATATTAATTATTAAATAT
AATAAATAATTAAAATATAATAATATAATAATTAAAATATAAATTTTAAAAAAATAATTATAATA
TATTTTGTAAAATTTGAAATAATG
Found at i:562430 original size:3 final size:3
Alignment explanation
Indices: 562424--562512 Score: 53
Period size: 3 Copynumber: 29.3 Consensus size: 3
562414 AAAACTTATT
* *
562424 ATA ATAA ATA A-A TATA ATA ATA ATA ATA ATA ATA ATTA ATC ATA TTA
1 ATA AT-A ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* *
562471 ATT ATT A-A AT- ATA ATAA ATA ATTA A-A AT- ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA AT-A ATA A-TA ATA ATA ATA ATA ATA -ATA A
562513 ATATAGTAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
2 8 0.12
3 45 0.65
4 16 0.23
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:562495 original size:166 final size:161
Alignment explanation
Indices: 562104--562578 Score: 619
Period size: 166 Copynumber: 3.0 Consensus size: 161
562094 TTTATAATCC
*
562104 AAAAATTA-TATTAT-AATAAATAAAT-ATAATAATAATAATAAGTAATAATATTAATTATTAAA
1 AAAAATTATTATAATAAATAAATAAATAATAATAATAATAATAA-TAAT-ATATTAATTATTAAA
* *
562166 TATAATAAATAATTAAAA-T-ATAATA-AT--ATA-A-TAATTAAAATATAAAATTTATAAAAAA
64 TATAATAAATAATTAAAATTAATAATATATAAATATAGTAATTAAAATAT-ATATTT-TATAAAA
562224 ATAATTATAATATATTTTGTAAAATTTGAAATAAT
127 ATAATTATAATATATTTTGTAAAATTTGAAATAAT
*
562259 AAAAATTA-TATTAT-AATAAATAAATAA-AATAATAATAATAAT--TA-A-TAA-TATTAAATA
1 AAAAATTATTATAATAAATAAATAAATAATAATAATAATAATAATAATATATTAATTATTAAATA
562316 TAATAAATAATTAAAATGTAATAATATATAAATATAGTAATTAAAATATATATTTTATAAAAATA
66 TAATAAATAATTAAAAT-TAATAATATATAAATATAGTAATTAAAATATATATTTTATAAAAATA
562381 ATTATAATATATTTTGTAAAATTTGAAATAAT
130 ATTATAATATATTTTGTAAAATTTGAAATAAT
*
562413 GAAAACTTATTATAATAAATAAATATAATAATAATAATAATAATAATTAATCATATTAATTATTA
1 -AAAAATTATTATAATAAATAAATA-AATAATAATAATAATAATAA-TAAT-ATATTAATTATTA
*
562478 AATATAATAAATAATTAAAATATAATAATATATAAATATAGTAATTAAAATAGATATTTTATAAA
62 AATATAATAAATAATTAAAAT-TAATAATATATAAATATAGTAATTAAAATATATATTTTAT---
* *
562543 AAAAATAATTATAGTATATTTTG-AAATTTTTGAAAT
123 AAAAATAATTATAATATATTTTGTAAA-ATTTGAAAT
562579 TTGAATTAAA
Statistics
Matches: 287, Mismatches: 8, Indels: 36
0.87 0.02 0.11
Matches are distributed among these distances:
148 25 0.09
149 3 0.01
150 2 0.01
151 7 0.02
152 3 0.01
154 45 0.16
155 52 0.18
156 18 0.06
157 8 0.03
158 5 0.02
159 14 0.05
160 1 0.00
162 1 0.00
163 1 0.00
164 1 0.00
165 3 0.01
166 65 0.23
168 3 0.01
169 30 0.10
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (161 bp):
AAAAATTATTATAATAAATAAATAAATAATAATAATAATAATAATAATATATTAATTATTAAATA
TAATAAATAATTAAAATTAATAATATATAAATATAGTAATTAAAATATATATTTTATAAAAATAA
TTATAATATATTTTGTAAAATTTGAAATAAT
Found at i:562551 original size:29 final size:30
Alignment explanation
Indices: 562433--562553 Score: 84
Period size: 30 Copynumber: 4.0 Consensus size: 30
562423 TATAATAAAT
* *
562433 AAATATAATAATA-ATAATAATAATAATTA
1 AAATATAATAATATATAAAAAAAATAATTA
* * * * *
562462 ATCATATTAATTATTAAATATAATAAATAATTA
1 A-AATA-TAA-TAATATATAAAAAAAATAATTA
* * *
562495 AAATATAATAATATATAAATATAGTAATTA
1 AAATATAATAATATATAAAAAAAATAATTA
* * *
562525 AAATA-GATATTTTATAAAAAAAATAATTA
1 AAATATAATAATATATAAAAAAAATAATTA
562554 TAGTATATTT
Statistics
Matches: 68, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
29 19 0.28
30 23 0.34
31 6 0.09
32 7 0.10
33 13 0.19
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (30 bp):
AAATATAATAATATATAAAAAAAATAATTA
Found at i:565047 original size:19 final size:18
Alignment explanation
Indices: 565015--565059 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
565005 CTACCGATAT
565015 TTATCGAACAATTTTTAA
1 TTATCGAACAATTTTTAA
* *
565033 TTATGCGAACTATTTTTCA
1 TTAT-CGAACAATTTTTAA
565052 TTAGTCGA
1 TTA-TCGA
565060 TTCATCTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 18 0.78
20 1 0.04
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (18 bp):
TTATCGAACAATTTTTAA
Found at i:565755 original size:13 final size:13
Alignment explanation
Indices: 565737--565762 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
565727 CGGGTAACAA
565737 CTCAACTAAAATG
1 CTCAACTAAAATG
565750 CTCAACTAAAATG
1 CTCAACTAAAATG
565763 TCGAGGACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
CTCAACTAAAATG
Found at i:570496 original size:17 final size:17
Alignment explanation
Indices: 570474--570520 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
570464 GAATCTAAGA
570474 AGGAATTAGAATCTGTC
1 AGGAATTAGAATCTGTC
570491 AGGAATTAGAATCTGTC
1 AGGAATTAGAATCTGTC
570508 AGGAATTAGAATC
1 AGGAATTAGAATC
570521 AAATTCCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (17 bp):
AGGAATTAGAATCTGTC
Found at i:572324 original size:35 final size:35
Alignment explanation
Indices: 572252--572365 Score: 140
Period size: 35 Copynumber: 3.2 Consensus size: 35
572242 AAAACATTCC
* * *
572252 TCAATTTCATTATATATATCCC-AAATTTCAAAGTAAT
1 TCAATTTCATTCTA-A-A-CCCTAAATTCCAAAATAAT
572289 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
* * *
572324 TCAATTACATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
572359 TCAATTT
1 TCAATTT
572366 AAGGAGAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 3 0.04
35 52 0.75
36 1 0.01
37 13 0.19
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
Found at i:573438 original size:35 final size:33
Alignment explanation
Indices: 573389--573501 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 33
573379 AAAAAAGACA
*
573389 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTT-GAATTTGGG-TTTAGAAT
*
573424 GTAATTGAATTATTTTGAAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTG-AATTT-GGGTTTAGAAT
* *
573459 AAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTA-TTTTGAATTTG-GGTTTAGAAT
573494 GAAATTGA
1 GAAATTGA
573502 GAATTGTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
34 2 0.03
35 59 0.87
36 7 0.10
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.42
Consensus pattern (33 bp):
GAAATTGAATTATTTTGAATTTGGGTTTAGAAT
Found at i:587235 original size:31 final size:33
Alignment explanation
Indices: 587174--587236 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
587164 TAAAAATAAA
*
587174 GAATAAATTTGAAATTTAGAGTGATTAAATTAG
1 GAATAAATTTGAAATTTAGAGTAATTAAATTAG
587207 GAAT-AATTTGAAATTTA-AGTAATTAAATTA
1 GAATAAATTTGAAATTTAGAGTAATTAAATTA
587237 AAAATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 12 0.41
32 13 0.45
33 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (33 bp):
GAATAAATTTGAAATTTAGAGTAATTAAATTAG
Found at i:588387 original size:2 final size:2
Alignment explanation
Indices: 588380--588410 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
588370 TTTTCTTTAA
588380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
588411 GTTTTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:591382 original size:11 final size:11
Alignment explanation
Indices: 591356--591388 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
591346 CATGCATGTA
591356 TGTATGTATG-
1 TGTATGTATGC
591366 TGTATGTATGC
1 TGTATGTATGC
*
591377 TGTATGCATGC
1 TGTATGTATGC
591388 T
1 T
591389 TTCAAAGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.18, C:0.09, G:0.27, T:0.45
Consensus pattern (11 bp):
TGTATGTATGC
Found at i:596261 original size:53 final size:49
Alignment explanation
Indices: 596182--596311 Score: 156
Period size: 53 Copynumber: 2.6 Consensus size: 49
596172 ATAATTTACC
* *
596182 AAAAAATGTATTATCGATTTTGTTATTAT-CGATAATTCTACTTAACGTTTATA
1 AAAAAATGTATTATCGATTTTGTTATTATCCG-T--TCCTACTTAAC-CTTA-A
596235 AAAAAATGTATTATCGATTTTGTTATT-TCCGTTCCTACTTAACCTTAA
1 AAAAAATGTATTATCGATTTTGTTATTATCCGTTCCTACTTAACCTTAA
* * *
596283 TAATAGTGTATTATCGATTTTGTTATTAT
1 AAAAAATGTATTATCGATTTTGTTATTAT
596312 ATATAACGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
48 25 0.36
49 4 0.06
50 10 0.14
52 2 0.03
53 29 0.41
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (49 bp):
AAAAAATGTATTATCGATTTTGTTATTATCCGTTCCTACTTAACCTTAA
Found at i:598789 original size:13 final size:13
Alignment explanation
Indices: 598771--598807 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
598761 ACATTATCTA
598771 TATTTTATTT-TAT
1 TATTTTATTTCT-T
598784 TATTTTATTTCTT
1 TATTTTATTTCTT
598797 TATTTT-TTTCT
1 TATTTTATTTCT
598808 ATTGTCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.22
13 17 0.74
14 1 0.04
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTATTTCTT
Found at i:598888 original size:2 final size:2
Alignment explanation
Indices: 598881--598913 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
598871 CTGAAAGCAA
598881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
598914 GAGTTGCGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:604456 original size:5 final size:5
Alignment explanation
Indices: 604442--604481 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
604432 ATTTGATTTA
604442 ATAAT AATAAT ATAAT ATAAT A-AAT ATAAT AT-AT ATAAT A
1 ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
604482 AGTATATATC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.25
5 19 0.59
6 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:604467 original size:14 final size:14
Alignment explanation
Indices: 604440--604479 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
604430 GCATTTGATT
604440 TAATAATAAT-AATA
1 TAAT-ATAATAAATA
604454 TAATATAATAAATA
1 TAATATAATAAATA
604468 TAATATATATAA
1 TAATATA-ATAA
604480 TAAGTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.21
14 15 0.62
15 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATATAATAAATA
Found at i:604481 original size:14 final size:14
Alignment explanation
Indices: 604448--604490 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
604438 TTTAATAATA
604448 ATAATATAATATA-
1 ATAATATAATATAT
604461 ATAAATATAATATAT
1 AT-AATATAATATAT
*
604476 ATAATA-AGTATAT
1 ATAATATAATATAT
604489 AT
1 AT
604491 CCGAATCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 10 0.37
14 15 0.56
15 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
ATAATATAATATAT
Found at i:604489 original size:11 final size:10
Alignment explanation
Indices: 604440--604489 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
604430 GCATTTGATT
604440 TAATAATA-A
1 TAATAATATA
604449 TAAT-ATAATA
1 TAATAAT-ATA
604459 TAATAA-ATA
1 TAATAATATA
604468 TAAT-ATATA
1 TAATAATATA
604477 TAATAAGTATA
1 TAATAA-TATA
604488 TA
1 TA
604490 TCCGAATCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 19 0.54
10 6 0.17
11 7 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
TAATAATATA
Found at i:604489 original size:13 final size:12
Alignment explanation
Indices: 604442--604490 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
604432 ATTTGATTTA
604442 ATAATAATA-AT
1 ATAATAATATAT
604453 ATAAT-ATA-AT
1 ATAATAATATAT
*
604463 AAATATAATATAT
1 ATA-ATAATATAT
604476 ATAATAAGTATAT
1 ATAATAA-TATAT
604489 AT
1 AT
604491 CCGAATCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.22
11 7 0.22
12 7 0.22
13 11 0.34
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:610938 original size:60 final size:61
Alignment explanation
Indices: 610844--610961 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 61
610834 AATATGTATA
* * * * *
610844 CATTTTGTTAACTTTTAATAGTGGAGGGACTCAACAAAGTAACATCCTATAATCGGGGGAC
1 CATTTTGTTAACTTTTAATAGTCGAAGGACTCAACAAAATAAAATCATATAATCGGGGGAC
* *
610905 CATTTTG-TAACTTTTAATAGTCGAAGGATTCAACAAAATAAAATTATATAATCGGGG
1 CATTTTGTTAACTTTTAATAGTCGAAGGACTCAACAAAATAAAATCATATAATCGGGG
610962 ATTATTTGTG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 43 0.86
61 7 0.14
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (61 bp):
CATTTTGTTAACTTTTAATAGTCGAAGGACTCAACAAAATAAAATCATATAATCGGGGGAC
Found at i:611214 original size:18 final size:19
Alignment explanation
Indices: 611193--611231 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
611183 ATAAAAAATC
611193 ATTTTTAA-ATCAAATCAA
1 ATTTTTAACATCAAATCAA
*
611211 ATTTTTAACATCGAATCAA
1 ATTTTTAACATCAAATCAA
611230 AT
1 AT
611232 AAAAAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (19 bp):
ATTTTTAACATCAAATCAA
Found at i:611461 original size:24 final size:25
Alignment explanation
Indices: 611430--611491 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
611420 AAATACAATA
611430 AATAATATTATTTATTAACAA-A-AT
1 AATAATATTATTTATTAA-AATATAT
611454 AATAATATTATTT-TTAAAATATTAT
1 AATAATATTATTTATTAAAATA-TAT
611479 AATAAT-TTATTTA
1 AATAATATTATTTA
611492 ATTTTATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.06
23 5 0.15
24 19 0.56
25 8 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
AATAATATTATTTATTAAAATATAT
Found at i:611523 original size:14 final size:14
Alignment explanation
Indices: 611506--611655 Score: 55
Period size: 14 Copynumber: 10.9 Consensus size: 14
611496 TATTTATGTC
611506 AATATTATTATTAA
1 AATATTATTATTAA
*
611520 AATATTA-TATCTAC
1 AATATTATTAT-TAA
* * *
611534 AATTTTATAAATAAA
1 AATATTAT-TATTAA
** *
611549 AATATTAAGATTAT
1 AATATTATTATTAA
*
611563 TATATT-TTATTAA
1 AATATTATTATTAA
* *
611576 AATATAAATT-TTAT
1 AATAT-TATTATTAA
611590 AA-ATT-TTATT-A
1 AATATTATTATTAA
* *
611601 ATTACTTATTA-CAA
1 AATA-TTATTATTAA
*
611615 TAATAATATTATTAA
1 -AATATTATTATTAA
** *
611630 AATATTAAAATTAT
1 AATATTATTATTAA
611644 AATATTA-TATTA
1 AATATTATTATTA
611656 TAAGGAATAA
Statistics
Matches: 95, Mismatches: 29, Indels: 25
0.64 0.19 0.17
Matches are distributed among these distances:
11 3 0.03
12 3 0.03
13 19 0.20
14 54 0.57
15 14 0.15
16 2 0.02
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:611724 original size:22 final size:24
Alignment explanation
Indices: 611682--611725 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
611672 AATATTCAAC
*
611682 AATTCAATAATATAATTTTAATGA
1 AATTCAATAATATAATATTAATGA
611706 AATTC-ATAA-ATAATATTAAT
1 AATTCAATAATATAATATTAAT
611726 TCTATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (24 bp):
AATTCAATAATATAATATTAATGA
Found at i:611768 original size:31 final size:30
Alignment explanation
Indices: 611733--611797 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
611723 AATTCTATTA
611733 ATAATTTATTATATATTTCTAA-AATAAAAAT
1 ATAA-TTATTATATATTT-TAATAATAAAAAT
611764 ATAA-TATTATATATTTTAATAATAAAAAT
1 ATAATTATTATATATTTTAATAATAAAAAT
611793 ATAAT
1 ATAAT
611798 AATAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
28 3 0.09
29 25 0.78
31 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
ATAATTATTATATATTTTAATAATAAAAAT
Found at i:615460 original size:4 final size:4
Alignment explanation
Indices: 615446--615485 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
615436 AGTATCTATA
*
615446 TATG T-TG TATG TATG TA-- TATA TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
615486 AGATCTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
2 2 0.06
3 3 0.09
4 27 0.84
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:615474 original size:18 final size:18
Alignment explanation
Indices: 615437--615486 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
615427 ATTAGTACAA
* *
615437 GTATCTATATATGTTGTAT
1 GTATGTATATAT-ATGTAT
615456 GTATGTATATATATGTAT
1 GTATGTATATATATGTAT
*
615474 GTATGTATGTATA
1 GTATGTATATATA
615487 GATCTGAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.50
Consensus pattern (18 bp):
GTATGTATATATATGTAT
Found at i:619970 original size:18 final size:19
Alignment explanation
Indices: 619937--619972 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
619927 ACTCTTCATA
619937 TCTTCTCATATTTCTTTAT
1 TCTTCTCATATTTCTTTAT
*
619956 TCTTCT-ATCTTTCTTTA
1 TCTTCTCATATTTCTTTA
619973 AGTAATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTTCTCATATTTCTTTAT
Found at i:620508 original size:20 final size:20
Alignment explanation
Indices: 620483--620527 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
620473 AGCATGTTTG
620483 GGGATCTCACTAAGATCTTA
1 GGGATCTCACTAAGATCTTA
*
620503 GGGATCTCACTAAGATCTTT
1 GGGATCTCACTAAGATCTTA
620523 GGGAT
1 GGGAT
620528 TGAATTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (20 bp):
GGGATCTCACTAAGATCTTA
Found at i:627082 original size:21 final size:21
Alignment explanation
Indices: 627058--627104 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
627048 AATGAAAGAA
627058 AAAAAAACAGCAGTTCGAAAG
1 AAAAAAACAGCAGTTCGAAAG
** **
627079 AAAAAAAGGGTTGTTCGAAAG
1 AAAAAAACAGCAGTTCGAAAG
627100 AAAAA
1 AAAAA
627105 GAGAGAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.21, T:0.13
Consensus pattern (21 bp):
AAAAAAACAGCAGTTCGAAAG
Found at i:632273 original size:33 final size:33
Alignment explanation
Indices: 632236--632299 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
632226 TTTCCCCGTA
*
632236 TTTCCCCCTTTCTCCTCATCAGTTTCTAATTTG
1 TTTCCCCCTTTCTCCTCATCAGTTTCCAATTTG
* *
632269 TTTCCCCTTTTCTGCTCATCAGTTTCCAATT
1 TTTCCCCCTTTCTCCTCATCAGTTTCCAATT
632300 CTGCCTCCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.12, C:0.33, G:0.06, T:0.48
Consensus pattern (33 bp):
TTTCCCCCTTTCTCCTCATCAGTTTCCAATTTG
Found at i:634795 original size:34 final size:32
Alignment explanation
Indices: 634733--634802 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
634723 ACCTTACAAC
* * *
634733 TCCCTAGTTTTTCCGGGTTAAACTAGAACCTT
1 TCCCTAGTTTTTACGGGCTAAACTAGAACATT
*
634765 TCCCTAGCTTTTATACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTT-TACGGGCTAAACTAGAACATT
634799 TCCC
1 TCCC
634803 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGCTAAACTAGAACATT
Found at i:635110 original size:21 final size:21
Alignment explanation
Indices: 635084--635126 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
635074 CCCAGAATGG
*
635084 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
635105 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
635126 A
1 A
635127 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:635190 original size:21 final size:21
Alignment explanation
Indices: 635164--635204 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
635154 GTTGAACAGG
635164 GGGGGAATCGGTACCCCCTGT
1 GGGGGAATCGGTACCCCCTGT
635185 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
635205 GACATTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.29, G:0.39, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGT
Found at i:635438 original size:29 final size:31
Alignment explanation
Indices: 635406--635465 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
635396 AAACTTTGAA
635406 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
635435 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
635466 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:635668 original size:21 final size:20
Alignment explanation
Indices: 635624--635670 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
635614 AAGCTCCCCC
635624 TTTTTCATTAAGAAATTGAA
1 TTTTTCATTAAGAAATTGAA
*
635644 TTTTTTATTAAGAAATTGAA
1 TTTTTCATTAAGAAATTGAA
635664 TTTTTCA
1 TTTTTCA
635671 AACCAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (20 bp):
TTTTTCATTAAGAAATTGAA
Found at i:636786 original size:19 final size:20
Alignment explanation
Indices: 636743--636790 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
636733 TCTAAATCCT
*
636743 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
636763 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
636782 TTTTCAAAA
1 TTTTCAAAA
636791 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:637663 original size:32 final size:34
Alignment explanation
Indices: 637627--637696 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
637617 ACCTTACAAC
* * *
637627 TCCCTAG-TTTT-TCCGGGTTAAACTAGAACTTT
1 TCCCTAGCTTTTATACGGGCTAAACTAGAACCTT
*
637659 TCCCTAGCTTTTATACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTATACGGGCTAAACTAGAACCTT
637693 TCCC
1 TCCC
637697 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (34 bp):
TCCCTAGCTTTTATACGGGCTAAACTAGAACCTT
Found at i:638004 original size:21 final size:21
Alignment explanation
Indices: 637978--638020 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
637968 CCCAGAATGG
*
637978 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
637999 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
638020 A
1 A
638021 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:638082 original size:21 final size:21
Alignment explanation
Indices: 638056--638099 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
638046 CTGTTGAACA
638056 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
638077 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
638098 GG
1 GG
638100 ACATTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:638174 original size:15 final size:15
Alignment explanation
Indices: 638154--638183 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
638144 TACCCCCTGG
638154 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
638169 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
638184 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:638204 original size:36 final size:35
Alignment explanation
Indices: 638134--638204 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
638124 AACCTGCAGG
* *
638134 GGGGAATCTGTACCCCCTGGGGGGTATCTGTACCC
1 GGGGAATCTGTACCCCCTGGGGGGAATCTATACCC
*
638169 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGAATCTGTACCCCCT-GGGGGGAATCTATACCC
638205 CCTGGGCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.15, C:0.28, G:0.34, T:0.23
Consensus pattern (35 bp):
GGGGAATCTGTACCCCCTGGGGGGAATCTATACCC
Found at i:638368 original size:34 final size:29
Alignment explanation
Indices: 638300--638359 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
638290 AAACTTTGAA
*
638300 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
638329 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
638360 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:641380 original size:33 final size:33
Alignment explanation
Indices: 641333--641398 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
641323 AATTTCCCCG
*
641333 TGTTTCCCCCTTTCTCCTCATCAGTTTCTAATT
1 TGTTTCCCCCTTTCTCCTCATCAGTTTCCAATT
* *
641366 TGTTTCCCCTTTTCTGCTCATCAGTTTCCAATT
1 TGTTTCCCCCTTTCTCCTCATCAGTTTCCAATT
641399 CTGCTTCCTG
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:0.12, C:0.32, G:0.08, T:0.48
Consensus pattern (33 bp):
TGTTTCCCCCTTTCTCCTCATCAGTTTCCAATT
Found at i:644879 original size:79 final size:80
Alignment explanation
Indices: 644787--644965 Score: 297
Period size: 81 Copynumber: 2.2 Consensus size: 80
644777 GAACGCACCC
*
644787 GTATATCTCGTATACATGAGTGCTCTGT-GTTGTTCCAAGTTAATCTAATTCAGATACGAGTGTT
1 GTATATCTTGTATACATGAGTGCTCTGTGGTTGTTCCAAGTTAATCTAATTCAGATACGAGTGTT
*
644851 GAATACATGCAAATA
66 GAATACATGCAAACA
**
644866 GTATATCTTGTATACATGAGTGCTCTGTGGGTTGTTCTGAGTTAATCTAATTCAGATACGAGTGT
1 GTATATCTTGTATACATGAGTGCTCTGT-GGTTGTTCCAAGTTAATCTAATTCAGATACGAGTGT
*
644931 TGAATACATGCACACA
65 TGAATACATGCAAACA
644947 GTATATCTTGTATACATGA
1 GTATATCTTGTATACATGA
644966 TCGCTCTCTG
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
79 27 0.29
81 66 0.71
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (80 bp):
GTATATCTTGTATACATGAGTGCTCTGTGGTTGTTCCAAGTTAATCTAATTCAGATACGAGTGTT
GAATACATGCAAACA
Found at i:650235 original size:13 final size:13
Alignment explanation
Indices: 650217--650262 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
650207 TTTTACTTCA
*
650217 AATATTATATATT
1 AATATTATAAATT
650230 AATATTATGAAATT
1 AATATTAT-AAATT
* *
650244 AGTATTATAGATT
1 AATATTATAAATT
650257 AATATT
1 AATATT
650263 TTACTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
AATATTATAAATT
Found at i:650877 original size:14 final size:15
Alignment explanation
Indices: 650848--650880 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
650838 ACTAAATCAT
650848 AAGAAAATTAAATAA
1 AAGAAAATTAAATAA
*
650863 AAGAAGATT-AATAA
1 AAGAAAATTAAATAA
650877 AAGA
1 AAGA
650881 GAGAGACGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (15 bp):
AAGAAAATTAAATAA
Found at i:673212 original size:2 final size:2
Alignment explanation
Indices: 673205--673250 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
673195 ATAAACAATG
*
673205 CT CT CT CT C- CT TT CT CT C- CT CT CT CT CT CAT CT CT CT C- CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT
673245 CT CT CT
1 CT CT CT
673251 TGTAAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:673222 original size:9 final size:9
Alignment explanation
Indices: 673205--673250 Score: 65
Period size: 9 Copynumber: 4.9 Consensus size: 9
673195 ATAAACAATG
673205 CTCTCTCTC
1 CTCTCTCTC
*
673214 CTTTCTCTC
1 CTCTCTCTC
673223 CTCTCTCTC
1 CTCTCTCTC
673232 TCATCTCTCTC
1 -C-TCTCTCTC
673243 CTCTCTCT
1 CTCTCTCT
673251 TGTAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 23 0.70
10 2 0.06
11 8 0.24
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (9 bp):
CTCTCTCTC
Found at i:673230 original size:20 final size:20
Alignment explanation
Indices: 673205--673250 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
673195 ATAAACAATG
* *
673205 CTCTCTCTCCTTTCTCTCCT
1 CTCTCTCTCATCTCTCTCCT
673225 CTCTCTCTCATCTCTCTCCT
1 CTCTCTCTCATCTCTCTCCT
673245 CTCTCT
1 CTCTCT
673251 TGTAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (20 bp):
CTCTCTCTCATCTCTCTCCT
Found at i:675991 original size:9 final size:9
Alignment explanation
Indices: 675977--676006 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
675967 AAAAATCTAG
675977 ATAATATAA
1 ATAATATAA
675986 ATAATATAA
1 ATAATATAA
675995 ATAATA-AA
1 ATAATATAA
676003 ATAA
1 ATAA
676007 AAATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAATATAA
Found at i:676026 original size:20 final size:21
Alignment explanation
Indices: 675977--676015 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
675967 AAAAATCTAG
675977 ATAATATAAATAATATAAATA
1 ATAATATAAATAATATAAATA
*
675998 ATAAAATAAA-AATATAAA
1 ATAATATAAATAATATAAA
676016 ATATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAATATAAATAATATAAATA
Found at i:678082 original size:26 final size:27
Alignment explanation
Indices: 678042--678095 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
678032 ATGATCGCTT
678042 AAATTTGATATGAATCAAAATTAACTC
1 AAATTTGATATGAATCAAAATTAACTC
* * *
678069 AAATTTTA-ATGAATCGATATTAACTC
1 AAATTTGATATGAATCAAAATTAACTC
678095 A
1 A
678096 TAGTTAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.35
Consensus pattern (27 bp):
AAATTTGATATGAATCAAAATTAACTC
Found at i:686661 original size:2 final size:2
Alignment explanation
Indices: 686654--686723 Score: 77
Period size: 2 Copynumber: 35.0 Consensus size: 2
686644 TTATCTATTA
* * * *
686654 AG AG AG AG AG AG TG AG AG AG GG GG AG AG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
686696 AG GG AG GG AG AG GG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
686724 GACTTATGAT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.40, C:0.00, G:0.59, T:0.01
Consensus pattern (2 bp):
AG
Found at i:686693 original size:28 final size:28
Alignment explanation
Indices: 686654--686721 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
686644 TTATCTATTA
* *
686654 AGAGAGAGAGAGTGAGAGAGGGGGAGAG
1 AGAGAGAGAGAGGGAGAGAGGGAGAGAG
* *
686682 AGAGAGAGAGAGGGAGGGAGGGAGAGGG
1 AGAGAGAGAGAGGGAGAGAGGGAGAGAG
686710 AGAGAGAGAGAG
1 AGAGAGAGAGAG
686722 AGGACTTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.40, C:0.00, G:0.59, T:0.01
Consensus pattern (28 bp):
AGAGAGAGAGAGGGAGAGAGGGAGAGAG
Found at i:688430 original size:16 final size:18
Alignment explanation
Indices: 688409--688446 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
688399 AAGTAATAAA
688409 TAAAATATAT-AT-ATTT
1 TAAAATATATAATAATTT
688425 TAAAATATATAATAATTT
1 TAAAATATATAATAATTT
688443 TAAA
1 TAAA
688447 TTTTCAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 2 0.10
18 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATATATAATAATTT
Found at i:692286 original size:19 final size:19
Alignment explanation
Indices: 692262--692299 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
692252 TCCATTTTCT
*
692262 CTTGTATACAGTGTATGGA
1 CTTGTATACAATGTATGGA
692281 CTTGTATACAATGTATGGA
1 CTTGTATACAATGTATGGA
692300 TCCTTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (19 bp):
CTTGTATACAATGTATGGA
Found at i:694042 original size:31 final size:31
Alignment explanation
Indices: 694007--694070 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
693997 TGATGATCAC
*
694007 ATCTTAATTGAATAAAAACAAAAGTGACCAT
1 ATCTTAATTAAATAAAAACAAAAGTGACCAT
*
694038 ATCTTAATTAAATAAAAACGAAAGTGACCAT
1 ATCTTAATTAAATAAAAACAAAAGTGACCAT
694069 AT
1 AT
694071 ACTATGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGACCAT
Found at i:705628 original size:19 final size:19
Alignment explanation
Indices: 705604--705663 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
705594 TATGAATTTG
* *
705604 AAGCTATGAATCTGACAGT
1 AAGCTATGAATCTGAAAAT
*
705623 AAGCTATGAGTCTGAAAAT
1 AAGCTATGAATCTGAAAAT
* *
705642 AAGTTATGAATCTAAAAAT
1 AAGCTATGAATCTGAAAAT
705661 AAG
1 AAG
705664 TTCTGATTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (19 bp):
AAGCTATGAATCTGAAAAT
Found at i:705664 original size:19 final size:19
Alignment explanation
Indices: 705608--705681 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 19
705598 AATTTGAAGC
* * * *
705608 TATGAATCTGACAGTAAGC
1 TATGAATCTAAAAATAAGT
* *
705627 TATGAGTCTGAAAATAAGT
1 TATGAATCTAAAAATAAGT
705646 TATGAATCTAAAAATAAGT
1 TATGAATCTAAAAATAAGT
* * *
705665 TCTGATTCGAAAAATAA
1 TATGAATCTAAAAATAA
705682 ATTCTGAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (19 bp):
TATGAATCTAAAAATAAGT
Found at i:709347 original size:29 final size:30
Alignment explanation
Indices: 709292--709353 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
709282 CAAATTTTGG
* * *
709292 TTAGTGACCAAAATATAAATTTTG-AAAGT
1 TTAGTGACCAAAATAAAAAGTTGGAAAAGT
*
709321 TTAGTGACCAAAGTAAAAAGTTGGAAAAGT
1 TTAGTGACCAAAATAAAAAGTTGGAAAAGT
709351 TTA
1 TTA
709354 AGGATCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (30 bp):
TTAGTGACCAAAATAAAAAGTTGGAAAAGT
Found at i:712849 original size:166 final size:166
Alignment explanation
Indices: 712428--712926 Score: 991
Period size: 166 Copynumber: 3.0 Consensus size: 166
712418 TTTCCACGTT
712428 GAATTGTTTGGGAATTGTGTCTAGGGTAGGGTCTTTATAACTCCATGTTCCATTTTCGGTCACTA
1 GAATTGTTTGGGAATTGTGTCTAGGGTAGGGTCTTTATAACTCCATGTTCCATTTTCGGTCACTA
712493 ATCCATGTGAGTTTGTGGGGTATTCTTCAAACATAAAGAATCCAAATCCTTGAACGTAAGCTCCT
66 ATCCATGTGAGTTTGTGGGGTATTCTTCAAACATAAAGAATCCAAATCCTTGAACGTAAGCTCCT
712558 TCGATCTGCAAAACATA-TTGTTTCCTATGTTAATC
131 TCGATCTGCAAAACATATTTGTTTCCTATGTTAATC
712593 GAATTGTTTGGGAATTGTGTCTAGGGTAGGGTCTTTATAACTCCATGTTCCATTTTCGGTCACTA
1 GAATTGTTTGGGAATTGTGTCTAGGGTAGGGTCTTTATAACTCCATGTTCCATTTTCGGTCACTA
712658 ATCCATGTGAGTTTGTGGGGTATTCTTCAAACATAAAGAATCCAAATCCTTGAACGTAAGCTCCT
66 ATCCATGTGAGTTTGTGGGGTATTCTTCAAACATAAAGAATCCAAATCCTTGAACGTAAGCTCCT
712723 TCGATCTGCAAAACATATTTGTTTCCTATGTTAATC
131 TCGATCTGCAAAACATATTTGTTTCCTATGTTAATC
712759 GAATTGTTTGGGAATTGTGTCTAGGGTAGGGTCTTTATAACTCCATGTTCCATTTTCGGTCACTA
1 GAATTGTTTGGGAATTGTGTCTAGGGTAGGGTCTTTATAACTCCATGTTCCATTTTCGGTCACTA
712824 ATCCATGTGAGTTTGTGGGGTATTCTTCAAACATAAAGAATCCAAATCCTTGAACGTAAGCTCCT
66 ATCCATGTGAGTTTGTGGGGTATTCTTCAAACATAAAGAATCCAAATCCTTGAACGTAAGCTCCT
712889 TCGATCTGCAAAACATATTTGTTTCCTATGTTAATC
131 TCGATCTGCAAAACATATTTGTTTCCTATGTTAATC
712925 GA
1 GA
712927 CTTGGACGAG
Statistics
Matches: 333, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
165 147 0.44
166 186 0.56
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (166 bp):
GAATTGTTTGGGAATTGTGTCTAGGGTAGGGTCTTTATAACTCCATGTTCCATTTTCGGTCACTA
ATCCATGTGAGTTTGTGGGGTATTCTTCAAACATAAAGAATCCAAATCCTTGAACGTAAGCTCCT
TCGATCTGCAAAACATATTTGTTTCCTATGTTAATC
Found at i:714214 original size:23 final size:23
Alignment explanation
Indices: 714188--714241 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
714178 TTAATTCTAT
714188 AAATTTAAAATTTAAATCAATTA
1 AAATTTAAAATTTAAATCAATTA
* * * *
714211 AAATAATACAATTTAATTCATTTA
1 AAAT-TTAAAATTTAAATCAATTA
714235 AAATTTA
1 AAATTTA
714242 TTTAAATTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTTAAAATTTAAATCAATTA
Found at i:718213 original size:8 final size:8
Alignment explanation
Indices: 718200--718240 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
718190 CTCATTTTCA
718200 GAGAATTT
1 GAGAATTT
718208 GAGAATTT
1 GAGAATTT
*
718216 -AGAGTTT
1 GAGAATTT
*
718223 GGGAATTT
1 GAGAATTT
718231 GAGAATTT
1 GAGAATTT
718239 GA
1 GA
718241 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:718539 original size:128 final size:128
Alignment explanation
Indices: 718311--719194 Score: 1707
Period size: 128 Copynumber: 6.9 Consensus size: 128
718301 TAATCGGAGT
*
718311 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTTAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
718376 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
718439 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
718504 CATTGCCCTATTATGTCACTCATATCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
718567 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
718632 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
718695 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
718760 CATTGCCCTATTATGTCACTCATGTCCCTAGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
718823 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
718888 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
718951 ACTATTGACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
719016 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
719079 ACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
719143 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
719195 AATCAGGTAA
Statistics
Matches: 746, Mismatches: 10, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
127 91 0.12
128 655 0.88
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:719672 original size:32 final size:34
Alignment explanation
Indices: 719594--719691 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 34
719584 AAATTTAATG
*
719594 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * *
719628 TTAAATTT-GAATAATATTATTT-T-TTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
719659 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
719692 AACATTTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
31 14 0.26
32 14 0.26
33 13 0.24
34 13 0.24
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:720243 original size:21 final size:20
Alignment explanation
Indices: 720215--720283 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 20
720205 GTATAAAACT
*
720215 CTGCGGGCTAGGCATGTAAC
1 CTGCGGGCTAGGAATGTAAC
720235 CTGGCGGGCTAGGAATGTAACC
1 CT-GCGGGCTAGGAATGTAA-C
*
720257 CTGCGGGCTCGGAATGTAACC
1 CTGCGGGCTAGGAATGTAA-C
720278 CTGCGG
1 CTGCGG
720284 AGATGGCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 2 0.04
21 40 0.89
22 3 0.07
ACGTcount: A:0.19, C:0.26, G:0.36, T:0.19
Consensus pattern (20 bp):
CTGCGGGCTAGGAATGTAAC
Found at i:720313 original size:21 final size:21
Alignment explanation
Indices: 720287--720334 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
720277 CCTGCGGAGA
*
720287 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
720308 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
720329 GGGCAT
1 TGGCAT
720335 GTAACCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:722092 original size:34 final size:31
Alignment explanation
Indices: 722049--722137 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
722039 TTAATAATTC
*
722049 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
722083 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
722114 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
722138 AAAATACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:722094 original size:31 final size:33
Alignment explanation
Indices: 722052--722126 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
722042 ATAATTCTAA
* * *
722052 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
722084 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
722115 ATAAAAAATAAT
1 ATAAAAAATAAT
722127 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:728203 original size:30 final size:29
Alignment explanation
Indices: 728167--728231 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
728157 AGTGAACCGG
* * *
728167 CGGTTCAAACCGGTTTTGTCGGTTTTCAGC
1 CGGTTCAAACCGGTTTT-ACCGTTTTCAAC
**
728197 CGGTTCACCCCGGTTTTACCGTTTTCAAC
1 CGGTTCAAACCGGTTTTACCGTTTTCAAC
728226 CGGTTC
1 CGGTTC
728232 TATCGGTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.12, C:0.29, G:0.23, T:0.35
Consensus pattern (29 bp):
CGGTTCAAACCGGTTTTACCGTTTTCAAC
Found at i:728230 original size:19 final size:20
Alignment explanation
Indices: 728206--728251 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
728196 CCGGTTCACC
*
728206 CCGGTTTTA-CCGTTTTCAA
1 CCGGTTCTATCCGTTTTCAA
*
728225 CCGGTTCTATCGGTTTTCAA
1 CCGGTTCTATCCGTTTTCAA
728245 CCGGTTC
1 CCGGTTC
728252 ATTGCCAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.13, C:0.28, G:0.20, T:0.39
Consensus pattern (20 bp):
CCGGTTCTATCCGTTTTCAA
Found at i:747597 original size:19 final size:19
Alignment explanation
Indices: 747556--747598 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
747546 TATGGAAAGA
* *
747556 ATTTTATACTATCATTTTC
1 ATTTTATACTATCAATATC
747575 ATTTTATACTATCAAATAT-
1 ATTTTATACTATC-AATATC
747594 ATTTT
1 ATTTT
747599 TAAAAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTATACTATCAATATC
Found at i:747915 original size:14 final size:13
Alignment explanation
Indices: 747876--747916 Score: 59
Period size: 12 Copynumber: 3.2 Consensus size: 13
747866 ATTAAAAAAT
747876 TATTTTTAAATTA
1 TATTTTTAAATTA
747889 T-TTTTTAAA-TA
1 TATTTTTAAATTA
747900 TATTTTTATAATTA
1 TATTTTTA-AATTA
747914 TAT
1 TAT
747917 ATATGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.12
12 14 0.56
13 3 0.12
14 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTTTAAATTA
Found at i:748996 original size:35 final size:35
Alignment explanation
Indices: 748949--749082 Score: 187
Period size: 35 Copynumber: 3.8 Consensus size: 35
748939 CTAAACCTTA
*
748949 AATTGAAGTATTTTAGAATTTGGGGTTTAAAATTT
1 AATTGAATTATTTTAGAATTTGGGGTTTAAAATTT
748984 AATTGAATTATTTTAGAATTTGGGGTTTAAAATTT
1 AATTGAATTATTTTAGAATTTGGGGTTTAAAATTT
* * * **
749019 AATTGAATTATTTTGGAATTTAGGGTTTATAATGA
1 AATTGAATTATTTTAGAATTTGGGGTTTAAAATTT
* * *
749054 AATTGAATTACTTTGGAAATTGGGGTTTA
1 AATTGAATTATTTTAGAATTTGGGGTTTA
749083 GAATGAAATT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 90 1.00
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.46
Consensus pattern (35 bp):
AATTGAATTATTTTAGAATTTGGGGTTTAAAATTT
Found at i:749965 original size:20 final size:20
Alignment explanation
Indices: 749942--750093 Score: 123
Period size: 20 Copynumber: 7.5 Consensus size: 20
749932 AAACTCCAAT
*
749942 TTCGCAACACAGTTTTCAAA
1 TTCGCAACGCAGTTTTCAAA
* *
749962 TTCGTAACTCAG-TTTCGGAAA
1 TTCGCAACGCAGTTTTC--AAA
749983 -TCGCAACGC-GATTTTCCAAA
1 TTCGCAACGCAG-TTTT-CAAA
* *
750003 TTCGCAATGCAATTTTCAAA
1 TTCGCAACGCAGTTTTCAAA
* *
750023 TTCGCAACGTAATTTTCCAAA
1 TTCGCAACGCAGTTTT-CAAA
* * *
750044 TTCTCAATGCAATTTTTCAAA
1 TTCGCAACGC-AGTTTTCAAA
750065 TTCGCAACGC-GATTTTCAAA
1 TTCGCAACGCAG-TTTTCAAA
750085 TTCGCAACG
1 TTCGCAACG
750094 GTAATTACTG
Statistics
Matches: 107, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
19 5 0.05
20 55 0.51
21 41 0.38
22 6 0.06
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (20 bp):
TTCGCAACGCAGTTTTCAAA
Found at i:749998 original size:21 final size:20
Alignment explanation
Indices: 749983--750093 Score: 141
Period size: 21 Copynumber: 5.4 Consensus size: 20
749973 GTTTCGGAAA
*
749983 TCGCAACGCGATTTTCCAAAT
1 TCGCAACGCAATTTT-CAAAT
*
750004 TCGCAATGCAATTTTCAAAT
1 TCGCAACGCAATTTTCAAAT
*
750024 TCGCAACGTAATTTTCCAAAT
1 TCGCAACGCAATTTT-CAAAT
* *
750045 TCTCAATGCAATTTTTCAAAT
1 TCGCAACGCAA-TTTTCAAAT
*
750066 TCGCAACGCGATTTTCAAAT
1 TCGCAACGCAATTTTCAAAT
750086 TCGCAACG
1 TCGCAACG
750094 GTAATTACTG
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
20 35 0.45
21 39 0.50
22 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (20 bp):
TCGCAACGCAATTTTCAAAT
Found at i:750028 original size:41 final size:42
Alignment explanation
Indices: 749983--750091 Score: 177
Period size: 41 Copynumber: 2.6 Consensus size: 42
749973 GTTTCGGAAA
749983 TCGCAACGCGATTTTCCAAATTCGCAATGCAA-TTTTCAAAT
1 TCGCAACGCGATTTTCCAAATTCGCAATGCAATTTTTCAAAT
** *
750024 TCGCAACGTAATTTTCCAAATTCTCAATGCAATTTTTCAAAT
1 TCGCAACGCGATTTTCCAAATTCGCAATGCAATTTTTCAAAT
750066 TCGCAACGCGATTTT-CAAATTCGCAA
1 TCGCAACGCGATTTTCCAAATTCGCAA
750092 CGGTAATTAC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 39 0.64
42 22 0.36
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (42 bp):
TCGCAACGCGATTTTCCAAATTCGCAATGCAATTTTTCAAAT
Found at i:750144 original size:57 final size:57
Alignment explanation
Indices: 750066--750244 Score: 304
Period size: 57 Copynumber: 3.1 Consensus size: 57
750056 TTTTTCAAAT
* * *
750066 TCGCAACGCGATTTTCAAATTCGCAACGGTAATTACTGATATAGGTAAACAATACTA
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTA
* *
750123 TCGCAATGCAATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTA
*
750180 TCGCAATACGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTA
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTA
750237 TCGCAATG
1 TCGCAATG
750245 TAAACAGTAC
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 113 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (57 bp):
TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTA
Found at i:750249 original size:20 final size:20
Alignment explanation
Indices: 750224--750284 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
750214 ACCGATATAG
*
750224 GTAAACAATACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
750244 GTAAACAGTACTATTGCAAT
1 GTAAACAGTACTATCGCAAT
*
750264 GTAAACAGTGCTATCGCAAT
1 GTAAACAGTACTATCGCAAT
750284 G
1 G
750285 CGATTTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:750333 original size:97 final size:97
Alignment explanation
Indices: 750167--750359 Score: 323
Period size: 97 Copynumber: 2.0 Consensus size: 97
750157 ACCGATATAG
*
750167 GTAAACAGTACTATCGCAATACGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAA
1 GTAAACAGTACTATCGCAATACGATTTTCAAATTCACAACGCTAATTACCGATATAGGTAAACAA
* *
750232 TACTATCGCAATGTAAACAGTACTATTGCAAT
66 TACTATCGCAATATAAACAGTACTATCGCAAT
* * *
750264 GTAAACAGTGCTATCGCAATGCGATTTTCAAATTCACAACGCTAATTACCGATATAGGTAAACAG
1 GTAAACAGTACTATCGCAATACGATTTTCAAATTCACAACGCTAATTACCGATATAGGTAAACAA
*
750329 TACTATCGCAATATAAACAGTATTATCGCAA
66 TACTATCGCAATATAAACAGTACTATCGCAA
750360 CGCGATTTTC
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (97 bp):
GTAAACAGTACTATCGCAATACGATTTTCAAATTCACAACGCTAATTACCGATATAGGTAAACAA
TACTATCGCAATATAAACAGTACTATCGCAAT
Found at i:750347 original size:20 final size:20
Alignment explanation
Indices: 750322--750359 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
750312 CCGATATAGG
750322 TAAACAGTACTATCGCAATA
1 TAAACAGTACTATCGCAATA
*
750342 TAAACAGTATTATCGCAA
1 TAAACAGTACTATCGCAA
750360 CGCGATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (20 bp):
TAAACAGTACTATCGCAATA
Found at i:750441 original size:20 final size:20
Alignment explanation
Indices: 750400--750509 Score: 114
Period size: 20 Copynumber: 5.5 Consensus size: 20
750390 ATATTTCTTT
**
750400 TTGCGATTTACATATTATCG
1 TTGCGATTTACATATTCGCG
*
750420 TTGTGATTTACATATTCGCG
1 TTGCGATTTACATATTCGCG
*
750440 TTGCGATTCATC-TATTCGCG
1 TTGCGATTTA-CATATTCGCG
* * * *
750460 TTGCGAATTTAGAAAATCACG
1 TTGCG-ATTTACATATTCGCG
*
750481 TTGCGATTTACCTATTCGCG
1 TTGCGATTTACATATTCGCG
750501 TTGCGATTT
1 TTGCGATTT
750510 TGGAACCTGT
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
20 57 0.79
21 15 0.21
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCG
Found at i:751051 original size:60 final size:59
Alignment explanation
Indices: 750955--751130 Score: 175
Period size: 60 Copynumber: 2.9 Consensus size: 59
750945 AGTATAACTC
* *
750955 TCATTCTAAATTAGT-CTCTAAACTTTTAAATC-TTTCAATTTTATCCCTAAACTATGA-CT
1 TCATTCTAAATTAGTCCTC-AAACTTTTGAA-CATTTCAATTTCATCCC-AAACTATGATCT
* *
751014 ATCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATCTCATCCCCGAACTATGATCT
1 -TCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTTCAT-CCCAAACTATGATCT
* *
751075 T-ATTTCT-AATCTGGTCCTCAAACATTTTGAACA-TTCTGATTTCATCCCAAACTATG
1 TCA-TTCTAAAT-TAGTCCTCAAAC-TTTTGAACATTTC-AATTTCATCCCAAACTATG
751131 GGTATATACT
Statistics
Matches: 100, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
59 5 0.05
60 72 0.72
61 23 0.23
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (59 bp):
TCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTTCATCCCAAACTATGATCT
Found at i:752488 original size:15 final size:14
Alignment explanation
Indices: 752463--752495 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
752453 AAAAAATATG
752463 TTATTGTCATTTTA
1 TTATTGTCATTTTA
752477 TTATTAGTCATTTTA
1 TTATT-GTCATTTTA
752492 TTAT
1 TTAT
752496 GACAGTGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (14 bp):
TTATTGTCATTTTA
Found at i:754115 original size:27 final size:28
Alignment explanation
Indices: 754060--754116 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
754050 ATAATTTGTA
* *
754060 TAAATATTGATATTATTTGTAATTGGAT
1 TAAATATTGATAGTATTAGTAATTGGAT
*
754088 TAAATTTTGATAGT-TTAGTAATTGGAT
1 TAAATATTGATAGTATTAGTAATTGGAT
754115 TA
1 TA
754117 TGACTATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (28 bp):
TAAATATTGATAGTATTAGTAATTGGAT
Found at i:754208 original size:15 final size:15
Alignment explanation
Indices: 754188--754218 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
754178 AAGTTTTGAT
754188 AGTCTAGGTAATTAA
1 AGTCTAGGTAATTAA
754203 AGTCTAGGTAATTAA
1 AGTCTAGGTAATTAA
754218 A
1 A
754219 TTATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
AGTCTAGGTAATTAA
Found at i:754736 original size:17 final size:17
Alignment explanation
Indices: 754714--754761 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
754704 TTTCTTAAAA
754714 ATTTTAAATTAATATAT
1 ATTTTAAATTAATATAT
* ** *
754731 ATTTTAGATTTTTTTAT
1 ATTTTAAATTAATATAT
*
754748 ATTTTTAATTAATA
1 ATTTTAAATTAATA
754762 ATTTATTTTC
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTAAATTAATATAT
Found at i:756510 original size:35 final size:35
Alignment explanation
Indices: 756431--756510 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
756421 ATGTGACATA
* *
756431 TGTCATATCATTACTTATGTACACATGATCATATG
1 TGTCATATCATCACTTATATACACATGATCATATG
* * *
756466 TCTCATATCATCACTTATATACATATGA-CATGTG
1 TGTCATATCATCACTTATATACACATGATCATATG
*
756500 TTGTCTTATCA
1 -TGTCATATCA
756511 CTTTAGATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
34 5 0.14
35 32 0.86
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (35 bp):
TGTCATATCATCACTTATATACACATGATCATATG
Found at i:757210 original size:36 final size:36
Alignment explanation
Indices: 757170--757279 Score: 97
Period size: 36 Copynumber: 3.1 Consensus size: 36
757160 CGGCAGCTCT
757170 TCTTGTGGAGGATGCAGCGGCGGCGGCGGCAACTGG
1 TCTTGTGGAGGATGCAGCGGCGGCGGCGGCAACTGG
* * ** * *
757206 TCTTG-GTCATCG-TGCAAAGG-GTGCGGCAGC-TCT--
1 TCTTGTG-GA-GGATGCAGCGGCG-GCGGCGGCAACTGG
757239 TCTTGTGGAGGATGCAGCGGCGGCGGCGGCAACTGG
1 TCTTGTGGAGGATGCAGCGGCGGCGGCGGCAACTGG
757275 TCTTG
1 TCTTG
757280 GTCATCGTGC
Statistics
Matches: 53, Mismatches: 12, Indels: 18
0.64 0.14 0.22
Matches are distributed among these distances:
32 1 0.02
33 19 0.36
34 4 0.08
35 4 0.08
36 24 0.45
37 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.42, T:0.22
Consensus pattern (36 bp):
TCTTGTGGAGGATGCAGCGGCGGCGGCGGCAACTGG
Found at i:757301 original size:36 final size:36
Alignment explanation
Indices: 757192--757301 Score: 97
Period size: 36 Copynumber: 3.1 Consensus size: 36
757182 TGCAGCGGCG
757192 GCGGCGGCAACTGGTCTTGGTCATCGTGCAAAGGGT
1 GCGGCGGCAACTGGTCTTGGTCATCGTGCAAAGGGT
* * * * **
757228 GCGGCAGC-TCT--TCTT-GTGGA-GGATGCAGCGGCG-
1 GCGGCGGCAACTGGTCTTGGT-CATCG-TGCAAAGG-GT
757261 GCGGCGGCAACTGGTCTTGGTCATCGTGCAAAGGGT
1 GCGGCGGCAACTGGTCTTGGTCATCGTGCAAAGGGT
757297 GCGGC
1 GCGGC
757302 AGCTCTTCTT
Statistics
Matches: 53, Mismatches: 12, Indels: 18
0.64 0.14 0.22
Matches are distributed among these distances:
32 3 0.06
33 18 0.34
34 3 0.06
35 3 0.06
36 23 0.43
37 3 0.06
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.21
Consensus pattern (36 bp):
GCGGCGGCAACTGGTCTTGGTCATCGTGCAAAGGGT
Found at i:757312 original size:33 final size:33
Alignment explanation
Indices: 757137--757370 Score: 97
Period size: 33 Copynumber: 6.9 Consensus size: 33
757127 GTGCAACAGG
757137 TCTTGGTCATCGTGCAAAGGGTGCGGCAGCTCT
1 TCTTGGTCATCGTGCAAAGGGTGCGGCAGCTCT
* * ** * *
757170 TCTT-GTGGA-GGATGCAGCGGCG-GCGGCGGCAACT
1 TCTTGGT-CATCG-TGCAAAGG-GTGCGGCAGC-TCT
757204 GGTCTTGGTCATCGTGCAAAGGGTGCGGCAGCTCT
1 --TCTTGGTCATCGTGCAAAGGGTGCGGCAGCTCT
* * ** * *
757239 TCTT-GTGGA-GGATGCAGCGGCG-GCGGCGGCAACT
1 TCTTGGT-CATCG-TGCAAAGG-GTGCGGCAGC-TCT
757273 GGTCTTGGTCATCGTGCAAAGGGTGCGGCAGCTCT
1 --TCTTGGTCATCGTGCAAAGGGTGCGGCAGCTCT
* * ** * * **
757308 TCTT-GTGGA-GGATGCAGTGGGGGCGGCAACTGG
1 TCTTGGT-CATCG-TGCAAAGGGTGCGGCAGCTCT
*
757341 TCTTGGTCATCCTGCAAAGGGTGCGGCAGC
1 TCTTGGTCATCGTGCAAAGGGTGCGGCAGC
757371 ATGTCGTGTG
Statistics
Matches: 140, Mismatches: 39, Indels: 44
0.63 0.17 0.20
Matches are distributed among these distances:
32 9 0.06
33 75 0.54
34 8 0.06
35 6 0.04
36 36 0.26
37 6 0.04
ACGTcount: A:0.15, C:0.23, G:0.40, T:0.23
Consensus pattern (33 bp):
TCTTGGTCATCGTGCAAAGGGTGCGGCAGCTCT
Done.