Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001481.1 Hibiscus syriacus cultivar Beakdansim tig00002877_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: 67811
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:700 original size:19 final size:20
Alignment explanation
Indices: 646--689 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
636 GAAAGAATAT
646 AGGGAAATT-GAAAATTTAG
1 AGGGAAATTAGAAAATTTAG
665 AGGGAAATTAG-AAATTTAG
1 AGGGAAATTAGAAAATTTAG
684 AGGGAA
1 AGGGAA
690 TAGAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.23
Consensus pattern (20 bp):
AGGGAAATTAGAAAATTTAG
Found at i:932 original size:17 final size:15
Alignment explanation
Indices: 910--943 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
900 TGTATGTATG
910 TATGTATATAAACTATA
1 TATGTATA-AAA-TATA
927 TATGTATAAAATATA
1 TATGTATAAAATATA
942 TA
1 TA
944 AAATATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (15 bp):
TATGTATAAAATATA
Found at i:941 original size:24 final size:25
Alignment explanation
Indices: 914--966 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
904 TGTATGTATG
*
914 TATATAAACTATATA-TGTATAAAA
1 TATATAAAATATATAGTGTATAAAA
* *
938 TATATAAAATATATAGTTTATAAAT
1 TATATAAAATATATAGTGTATAAAA
963 TATA
1 TATA
967 ATTTATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
TATATAAAATATATAGTGTATAAAA
Found at i:1200 original size:20 final size:20
Alignment explanation
Indices: 1177--1235 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1167 TATTGTACAT
*
1177 GTATGTATAAACCATGTATA
1 GTATGTATAAACCATATATA
*
1197 GTATGTATAAACTATATATA
1 GTATGTATAAACCATATATA
1217 -TATGTAT-AACCTATATATA
1 GTATGTATAAACC-ATATATA
1236 TATATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.09
19 14 0.40
20 18 0.51
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (20 bp):
GTATGTATAAACCATATATA
Found at i:1235 original size:23 final size:23
Alignment explanation
Indices: 1211--1256 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1201 GTATAAACTA
* *
1211 TATATATATGTATAACCTATATA
1 TATATATATATATAAACTATATA
1234 TATATATATATATAAACTATATA
1 TATATATATATATAAACTATATA
1257 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (23 bp):
TATATATATATATAAACTATATA
Found at i:1256 original size:19 final size:19
Alignment explanation
Indices: 1178--1243 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
1168 ATTGTACATG
* *
1178 TATGTATAAACCATGTATA
1 TATGTATAAACTATATATA
1197 GTATGTATAAACTATATATA
1 -TATGTATAAACTATATATA
*
1217 TATGTATAACCTATATATA
1 TATGTATAAACTATATATA
*
1236 TATATATA
1 TATGTATA
1244 TATAAACTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 25 0.60
20 17 0.40
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (19 bp):
TATGTATAAACTATATATA
Found at i:1345 original size:7 final size:7
Alignment explanation
Indices: 1331--1395 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
1321 TAGTTTATAG
1331 AAACCCT
1 AAACCCT
*
1338 AAATCCT
1 AAACCCT
**
1345 AAACTTT
1 AAACCCT
*
1352 AAACCAT
1 AAACCCT
***
1359 AAATAGT
1 AAACCCT
1366 AAACCCT
1 AAACCCT
1373 AAACCCT
1 AAACCCT
1380 AAACCCT
1 AAACCCT
1387 AAACCCT
1 AAACCCT
1394 AA
1 AA
1396 TATAAATAGA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:1355 original size:21 final size:21
Alignment explanation
Indices: 1331--1395 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1321 TAGTTTATAG
**
1331 AAACCCTAAATCCTAAACTTT
1 AAACCCTAAATCCTAAACCCT
* **
1352 AAACCATAAATAGTAAACCCT
1 AAACCCTAAATCCTAAACCCT
*
1373 AAACCCTAAACCCTAAACCCT
1 AAACCCTAAATCCTAAACCCT
1394 AA
1 AA
1396 TATAAATAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.20
Consensus pattern (21 bp):
AAACCCTAAATCCTAAACCCT
Found at i:2385 original size:24 final size:24
Alignment explanation
Indices: 2270--2388 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
2260 AAACATAATT
*
2270 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
2294 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* * *
2318 CAAGTCAAGTATCAGATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
2342 CATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
2366 CATGTCAAGTATCATATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
2389 TCAAATAGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:2404 original size:48 final size:48
Alignment explanation
Indices: 2270--2406 Score: 145
Period size: 48 Copynumber: 2.9 Consensus size: 48
2260 AAACATAATT
* *
2270 CATGTCAAGTATCATATCAAAATCCAGGT--CAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAAAATCCAAGTAGCAA--ATCAGATCAGAATC
* * * *
2318 CAAGTCAAGTATCAGATCAAAATCCATGTCAG-ATATCAGATCAGAATC
1 CATGTCAAGTATCATATCAAAATCCAAGT-AGCAAATCAGATCAGAATC
* * *
2366 CATGTCAAGTATCATATCAGAATTCAAATAGCAAATCAGAT
1 CATGTCAAGTATCATATCAAAATCCAAGTAGCAAATCAGAT
2407 AAAATATTCA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
47 2 0.03
48 70 0.96
50 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.26
Consensus pattern (48 bp):
CATGTCAAGTATCATATCAAAATCCAAGTAGCAAATCAGATCAGAATC
Found at i:2404 original size:72 final size:70
Alignment explanation
Indices: 2270--2411 Score: 180
Period size: 72 Copynumber: 2.0 Consensus size: 70
2260 AAACATAATT
* *
2270 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGAT
1 CATGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAATCAAG-ATCAGAT
2335 CAAAATC
65 -AAAATC
* * *
2342 CATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCATATCAGAATTCAAATAGCAA-ATCAG
1 CATGTCAAG-TATCAGATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAAT--CAAGATCAG
2405 ATAAAAT
63 ATAAAAT
2412 ATTCATGTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
71 7 0.11
72 52 0.84
74 3 0.05
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (70 bp):
CATGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAATCAAGATCAGATA
AAATC
Found at i:6006 original size:13 final size:13
Alignment explanation
Indices: 5980--6020 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
5970 CCATGTAATA
5980 ATATA-AAACTAT
1 ATATATAAACTAT
*
5992 ATATATAACCTAT
1 ATATATAAACTAT
6005 ATATATAAACTAT
1 ATATATAAACTAT
6018 ATA
1 ATA
6021 AAGTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATATAAACTAT
Found at i:6141 original size:21 final size:21
Alignment explanation
Indices: 6117--6159 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6107 CTGAAATTTG
6117 AACCATAAA-CATTAAACCCTA
1 AACCATAAATCA-TAAACCCTA
*
6138 AACCCTAAATCATAAACCCTA
1 AACCATAAATCATAAACCCTA
6159 A
1 A
6160 TATAAATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCATAAATCATAAACCCTA
Found at i:6541 original size:13 final size:13
Alignment explanation
Indices: 6523--6567 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
6513 CCATGTATAG
6523 TATATATAAACTA
1 TATATATAAACTA
6536 TATATAT-AACTTATA
1 TATATATAAAC---TA
6551 TATATATAAACTA
1 TATATATAAACTA
6564 TATA
1 TATA
6568 AAGTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
15 9 0.32
16 3 0.11
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:6541 original size:20 final size:21
Alignment explanation
Indices: 6492--6542 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
6482 TTAAATATTT
*
6492 TATATAATATGTATGTATAAAC
1 TATAT-ATATGTATATATAAAC
* *
6514 CATGTATA-GTATATATAAAC
1 TATATATATGTATATATAAAC
6534 TATATATAT
1 TATATATAT
6543 AACTTATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 3 0.13
22 3 0.13
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (21 bp):
TATATATATGTATATATAAAC
Found at i:6543 original size:15 final size:15
Alignment explanation
Indices: 6518--6567 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
6508 ATAAACCATG
6518 TATAGTATATATAAAC
1 TATA-TATATATAAAC
6534 --TATATATAT-AAC
1 TATATATATATAAAC
6546 TTATATATATATAAAC
1 -TATATATATATAAAC
6562 TATATA
1 TATATA
6568 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
12 3 0.10
13 7 0.23
14 2 0.07
15 15 0.50
16 3 0.10
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:6689 original size:13 final size:14
Alignment explanation
Indices: 6642--6705 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
6632 TAGTTTATAG
**
6642 AAACCCTAAACTTT
1 AAACCCTAAACACT
**
6656 AAACTATAAACACT
1 AAACCCTAAACACT
6670 AAACCCTAAAC-CT
1 AAACCCTAAACACT
*
6683 AAGCCCTAAATCAC-
1 AAACCCTAAA-CACT
6697 AAACCCTAA
1 AAACCCTAA
6706 TGTAAATGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 11 0.28
14 28 0.70
15 1 0.03
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (14 bp):
AAACCCTAAACACT
Found at i:6804 original size:546 final size:545
Alignment explanation
Indices: 5696--7387 Score: 2549
Period size: 546 Copynumber: 3.1 Consensus size: 545
5686 CGGGTGTTAC
* *
5696 AAATGGACTAGCACTAATGCAAATGGACTTATTTTTTGG-TTTATTATT--TTATTCATAACAAC
1 AAATGGACTAGCACTAATGCAAATAGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAAC
* * * *
5758 AAATAAATGGGT-TAATAT-AATTAACCTAACATGCAACTAAAATACTAATTATGCAAATAAAAT
66 AAAT-AATGGATATTATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAAT
*
5821 TAATATGACATGTACTACTATTTATGAACC--ATAATATGCAATGTGACAAACTAATTATTTAAC
130 TAATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAAC
5884 ACCTAATTAATCATGTTTTATATAATTTACATTTAAATTATTTTTTAAAATTTATTAAATAATTT
195 ACCTAATTAATCATGTTTTATATAA-TTACATTTAAATTATTTTTT-AAATTTATTAAATAATTT
*
5949 TATATAATATGTATGTATAAACCATGTA-A-TA-ATATAAAACTATATATATAAC--CTATATAT
258 TATATAATATGTATGTATAAACCATGTATAGTATATAT-AAACTATATATATAACTTATATATAT
* *
6009 ATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTACACATAAACTATATAAAGT
322 ATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTACGCATAAACTATATAAAAT
* * * * *
6074 AATAAAGTATATAGCTTATAGAAACCCTAAACCCTGAAA-TTTGAACCATAAACATTAAACCCTA
387 AATAAAGTATATAGTTTATAGAAACCCTAAA-CTTTAAACTTTAAACCATAAACACTAAA-CCT-
* *
6138 AACCCTAAATCATAAACCCTAATATAAATGGACTATCAGTAATGCCTATATATTTGTAATAAAAG
449 AACCCTAAATCA-AAACCCTAAT-TAAATGGACTAGCACTAATG-CTATATA-TTGTAATAAAAG
* *
6203 AGTGAGCTTATGTATTGGGCCTATGTAAATTAATGT
510 AGTGGGCTTATGTATTGGGCCTATGTAAACTAATGT
* * *
6239 AAATGGACTAGCTCTAATGCAAATGGGCTTATTTTTGGGTTTTATTATTACTTATTCATAACAAC
1 AAATGGACTAGCACTAATGCAAATAGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAAC
6304 AAATAATGGATATTATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAA-T
66 AAATAATGGATATTATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATT
* *
6368 AATATGACATGTACTATTATTTATGAACCATATAATATGTAATGTGACATACTAATTATTTAACA
131 AATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACA
6433 CCTAATTAATCATGTTTTATATAATTACATTTAAATTA-TTTTTAAA-TTATTAAAT-ATTTTAT
196 CCTAATTAATCATGTTTTATATAATTACATTTAAATTATTTTTTAAATTTATTAAATAATTTTAT
6495 ATAATATGTATGTATAAACCATGTATAGTATATATAAACTATATATATAACTTATATATATATAA
261 ATAATATGTATGTATAAACCATGTATAGTATATATAAACTATATATATAACTTATATATATATAA
6560 ACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTACGCATAAACTATATAAAATAATA
326 ACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTACGCATAAACTATATAAAATAATA
* * *
6625 AAGTTTATAGTTTATAGAAACCCTAAACTTTAAACTATAAA-CACTAAACCCTAAACCTAAGCCC
391 AAGTATATAGTTTATAGAAACCCTAAACTTTAAACTTTAAACCA-TAAACACTAAACCTAA-CCC
6689 TAAATCACAAACCCTAATGTAAATGGACTAGCACTAATGCATATATATCTGTAATAAAAGAGTGG
454 TAAATCA-AAACCCTAAT-TAAATGGACTAGCACTAATGC-TATATAT-TGTAATAAAAGAGTGG
6754 GCTTATGTATTGGGCCTATGTAAACTAATGT
515 GCTTATGTATTGGGCCTATGTAAACTAATGT
* *
6785 AAATGGACTAGCACTAATGCAAATAGACTTATTTTTGGGTTGTATTATTACTTATTCATAATAAC
1 AAATGGACTAGCACTAATGCAAATAGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAAC
* *
6850 AAAACAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGA
66 -AAA-TAAT-GGATATT-ATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGA
* *
6915 AATTAATATGACATGTACTACTATTTATGAACCATATAATATGCACTATGACATACTAATTATTT
127 AATTAATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTT
* * *
6980 AACACCTAATTAATCATGTTTTACATCATTTACATTTAAATTATTTTTTAAATTTCTTAAATAAT
192 AACACCTAATTAATCATGTTTTATAT-AATTACATTTAAATTATTTTTTAAATTTATTAAATAAT
7045 TTTAT-TAATATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATAACCTATATA
256 TTTATATAATATGTATGTATAAACCATGTATAGTATATATAAAC--TATATATATAA-CT-TATA
* * *
7109 TATATATAAACAATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATCAACTATA-
317 TATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTACGCATAAACTATAT
*
7173 AAAAGTAATAAAGTATATAGTTTATAGAAA-CCTAAA-TCCTAAACTTTAAACCATAAACACTAA
382 AAAA-TAATAAAGTATATAGTTTATAGAAACCCTAAACT-TTAAACTTTAAACCATAAACACTAA
*
7236 ACCTTAA--ATAAA--AAAACCCTAATTAAATGGACTAGCACTAATGC-ATATATTGTATATAAA
445 ACC-TAACCCTAAATCAAAACCCTAATTAAATGGACTAGCACTAATGCTATATATTGTA-ATAAA
7296 AGAGTGGGCTTATGTATTGGGCCTATGTAAACT-ATGT
508 AGAGTGGGCTTATGTATTGGGCCTATGTAAACTAATGT
7333 AAATGGACTAGCACTAATGCAAATAGACTTATTTTTGGGTTTTATTATTACTTAT
1 AAATGGACTAGCACTAATGCAAATAGACTTATTTTTGGGTTTTATTATTACTTAT
7388 GTCGACACTA
Statistics
Matches: 1064, Mismatches: 50, Indels: 65
0.90 0.04 0.06
Matches are distributed among these distances:
543 68 0.06
544 19 0.02
545 31 0.03
546 219 0.21
547 172 0.16
548 121 0.11
549 50 0.05
550 49 0.05
551 104 0.10
552 25 0.02
553 9 0.01
554 46 0.04
555 11 0.01
556 12 0.01
557 34 0.03
558 94 0.09
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (545 bp):
AAATGGACTAGCACTAATGCAAATAGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAAC
AAATAATGGATATTATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATT
AATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACA
CCTAATTAATCATGTTTTATATAATTACATTTAAATTATTTTTTAAATTTATTAAATAATTTTAT
ATAATATGTATGTATAAACCATGTATAGTATATATAAACTATATATATAACTTATATATATATAA
ACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTACGCATAAACTATATAAAATAATA
AAGTATATAGTTTATAGAAACCCTAAACTTTAAACTTTAAACCATAAACACTAAACCTAACCCTA
AATCAAAACCCTAATTAAATGGACTAGCACTAATGCTATATATTGTAATAAAAGAGTGGGCTTAT
GTATTGGGCCTATGTAAACTAATGT
Found at i:7099 original size:17 final size:16
Alignment explanation
Indices: 7072--7125 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
7062 ATAAACCATG
7072 TATAGTATATATAAAC-
1 TATA-TATATATAAACA
*
7088 TATATATATATAACCTA
1 TATATATATATAAAC-A
7105 TATATATATATAAACA
1 TATATATATATAAACA
7121 -ATATA
1 TATATA
7126 AAGTAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 15 0.44
16 5 0.15
17 14 0.41
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (16 bp):
TATATATATATAAACA
Found at i:7125 original size:13 final size:15
Alignment explanation
Indices: 7072--7114 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
7062 ATAAACCATG
7072 TATAGTATATATAAAC
1 TATA-TATATATAAAC
*
7088 TATATATATATAACC
1 TATATATATATAAAC
7103 TATATATATATA
1 TATATATATATA
7115 TAAACAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:8527 original size:23 final size:21
Alignment explanation
Indices: 8487--8528 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
8477 ATTTCAATTA
*
8487 TTAATTATTATTATTATAAGG
1 TTAATTATTATTAGTATAAGG
8508 TTAATTATAATATTAGTATAA
1 TTAATTAT--TATTAGTATAA
8529 TTATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TTAATTATTATTAGTATAAGG
Found at i:9394 original size:32 final size:31
Alignment explanation
Indices: 9358--9431 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 31
9348 TCATGTCATT
9358 AACAAGTCGGATCATTTACAGGTCAGGTTAAA
1 AACAAGTCGGATCA-TTACAGGTCAGGTTAAA
* *
9390 AACAAGTCAGGTTCATTACAGGTCAGGTTGAA
1 AACAAGTC-GGATCATTACAGGTCAGGTTAAA
*
9422 AACAGGTCGG
1 AACAAGTCGG
9432 GTAATACCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 2 0.05
32 31 0.82
33 5 0.13
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (31 bp):
AACAAGTCGGATCATTACAGGTCAGGTTAAA
Found at i:9426 original size:16 final size:16
Alignment explanation
Indices: 9375--9429 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
9365 CGGATCATTT
9375 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* * **
9391 ACAAGTCAGGTTCATT
1 ACAGGTCAGGTTAAAA
*
9407 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
9423 ACAGGTC
1 ACAGGTC
9430 GGGTAATACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:9564 original size:22 final size:22
Alignment explanation
Indices: 9539--9583 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
9529 TTGGGTTCAA
*
9539 GTCGTTCTCAGTTCGGATGCAG
1 GTCGTTCTCAGGTCGGATGCAG
9561 GTCGTTCTCAGGTCGGATGCAG
1 GTCGTTCTCAGGTCGGATGCAG
9583 G
1 G
9584 CCGGGTTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.22, G:0.36, T:0.29
Consensus pattern (22 bp):
GTCGTTCTCAGGTCGGATGCAG
Found at i:9963 original size:23 final size:23
Alignment explanation
Indices: 9916--9964 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
9906 AATAACATAT
** **
9916 TAGGTAGTGCTTATATAATGCAA
1 TAGGTAGCACTTATATAATAAAA
9939 TAGGTAGCACTTATATAATAAAA
1 TAGGTAGCACTTATATAATAAAA
9962 TAG
1 TAG
9965 ACATTTAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
TAGGTAGCACTTATATAATAAAA
Found at i:10018 original size:23 final size:23
Alignment explanation
Indices: 9992--10048 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
9982 TTATCAAGCA
9992 ATAACATATTAGGTAGCACTTAT
1 ATAACATATTAGGTAGCACTTAT
** * *
10015 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATATTAGGTAGCACTTAT
*
10038 ATTAACCTATT
1 A-TAACATATT
10049 TTCTAACTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (23 bp):
ATAACATATTAGGTAGCACTTAT
Found at i:10026 original size:85 final size:86
Alignment explanation
Indices: 9879--10039 Score: 261
Period size: 85 Copynumber: 1.9 Consensus size: 86
9869 TATGTTATAT
**
9879 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGTGCTTATATAATGCAATAGGT
1 CATTTAACCGAAAATATTATCAAG-ACAATAACATATTAGGTAGCACTTATATAATGCAATAGGT
9944 AGCACTTATATAATAAAATAGA
65 AGCACTTATATAATAAAATAGA
* *
9966 CATTTAACCGGAAATATTATCAAG-CAATAACATATTAGGTAGCACTTATATAATGTAATAGGTA
1 CATTTAACCGAAAATATTATCAAGACAATAACATATTAGGTAGCACTTATATAATGCAATAGGTA
*
10030 GCGCTTATAT
66 GCACTTATAT
10040 TAACCTATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
85 46 0.67
87 23 0.33
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (86 bp):
CATTTAACCGAAAATATTATCAAGACAATAACATATTAGGTAGCACTTATATAATGCAATAGGTA
GCACTTATATAATAAAATAGA
Found at i:10493 original size:200 final size:196
Alignment explanation
Indices: 10046--10754 Score: 759
Period size: 198 Copynumber: 3.6 Consensus size: 196
10036 ATATTAACCT
* * * *** * *
10046 ATTTTCTAACTAAATCGGTTTATTTATACTGGTAATATTGCAAATTTACCTATTACATTATAATT
1 ATTTTATAATTAAATCGGTATATTTATACCAATTACATTGCAAATTTACCTATTACATTATAATT
* * **
10111 ATCGGTTTTGATGTTTTTGGGATCGATATAATTTTAAATGTATCGACACTTTATTTGTGTACCTC
66 ATCGGTTTCGATGTTTTTGGGATCGATA-CATTTTAAATGTATCGACACTTTATGCGTGTACCTC
*
10176 ATTGGGCATTCATTCTGGA-AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTG
130 ATTGGGCATTCATTCTGGACAATAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTG
10240 AC
195 AC
* * * * * *
10242 ATATTCTCTCA-TAAAACTGGTATATTTATACCAGTTACATTGCAAATTTACCTACTATATTATA
1 AT-TT-TATAATTAAATC-GGTATATTTATACCAATTACATTGCAAATTTACCTATTACATTATA
* * * * *
10306 ATTATTGATTTTGATGTTTTTGGGATCAATACAATTTTAAATGTATCGACACTTTATGCGTATAC
63 ATTATCGGTTTCGATGTTTTTGGGATCGATAC-ATTTTAAATGTATCGACACTTTATGCGTGTAC
* * * *
10371 CCCATTTGGGGATTGATTCTAGACAATAAGTATCGACACAAATTTAAAAAGTGTCGATACATTAT
127 CTCA-TTGGGCATTCATTCTGGACAATAAGTATCGACACAAATTTAAAAAGTGTCGATACATTAT
10436 GTTGATC
191 GTTGA-C
* * *
10443 ACTTTTATAATTAAATCGTTATATTTATATCAATTACATTGTAAATTTACCTATTACATTATAAT
1 A-TTTTATAATTAAATCGGTATATTTATACCAATTACATTGCAAATTTACCTATTACATTATAAT
* * *
10508 TATCGGTTTCGATGTTTTTGGGATCGAT--TTTTTATAAGTATATCGACACTTTATGCGTGCACC
65 TATCGGTTTCGATGTTTTTGGGATCGATACATTTTA-AA-TGTATCGACACTTTATGCGTGTACC
* * * * * *
10571 TCGGTTGGGCATTCATTCTGGACACAT-AGTATTGACGCAAA-TTACATAATTTTCGATACATTA
128 TC-ATTGGGCATTCATTCTGGACA-ATAAGTATCGACACAAATTTA-AAAAGTGTCGATACATTA
10634 TGTTGAC
190 TGTTGAC
* * * * ***
10641 TTTTTTGTAATT-AAT-GGTATATTTATACCGATTATATTATTAATTTACCTATTACATTATAAT
1 -ATTTTATAATTAAATCGGTATATTTATACCAATTACATTGCAAATTTACCTATTACATTATAAT
* * * *
10704 TATTGGTTTCGATGTCTTTGGGGTCGATACTTTTATAAAATGTATCGACAC
65 TATCGGTTTCGATGTTTTTGGGATCGATACATTT-T-AAATGTATCGACAC
10755 ATATGTTTAC
Statistics
Matches: 434, Mismatches: 60, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
196 69 0.16
197 15 0.03
198 132 0.30
199 91 0.21
200 117 0.27
201 9 0.02
202 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (196 bp):
ATTTTATAATTAAATCGGTATATTTATACCAATTACATTGCAAATTTACCTATTACATTATAATT
ATCGGTTTCGATGTTTTTGGGATCGATACATTTTAAATGTATCGACACTTTATGCGTGTACCTCA
TTGGGCATTCATTCTGGACAATAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGA
C
Found at i:10694 original size:20 final size:19
Alignment explanation
Indices: 10666--10704 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
10656 GGTATATTTA
*
10666 TACCGATTATATTATTAATT
1 TACCGATTACATTA-TAATT
*
10686 TACCTATTACATTATAATT
1 TACCGATTACATTATAATT
10705 ATTGGTTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (19 bp):
TACCGATTACATTATAATT
Found at i:14820 original size:21 final size:21
Alignment explanation
Indices: 14794--14833 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14784 AAACACTTAT
14794 TTTAAAAAATATCGATACAAA
1 TTTAAAAAATATCGATACAAA
* *
14815 TTTAAAAAGTGTCGATACA
1 TTTAAAAAATATCGATACA
14834 TTATGTACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTAAAAAATATCGATACAAA
Found at i:15151 original size:178 final size:179
Alignment explanation
Indices: 14818--15186 Score: 492
Period size: 177 Copynumber: 2.1 Consensus size: 179
14808 ATACAAATTT
* * * *
14818 AAAAAGTGTCGATACATTATGTACACTTATTTTCTCATAAAACCGGTAAATTTATACCGGTTACA
1 AAAAAGTATCGATACATTATGTACACCTATTTTCTAATAAAACCGATAAATTTATACCGGTTACA
** *
14883 TTATTAATTTACCTATTACATTGTAATTATCAGTTTCGATGTTTTTGGGAGCGATACATTTTAAA
66 TTAGAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGAGCGATACATTTTAAA
* *
14948 ATATATCGACACTTTATGTGTGCACC-CCCTTTGCCATTCATTCTGGAC
131 ATATATCGACACTTTATGCGTGCACCTCCCTTGGCCATTCATTCTGGAC
* * * * *
14996 AAAAAGTATCGATACATTATGTAGACCTATTTTCTAAT-TAACCGATATATTTTTATCGGTTACA
1 AAAAAGTATCGATACATTATGTACACCTATTTTCTAATAAAACCGATAAATTTATACCGGTTACA
* * * *
15060 TTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGCTAC-TTTTAAT
66 TTAGAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGAGCGATACATTTT-A-
* ** *
15124 AAATGTATCGACACTTTATGCGTGCACCTCGGTTGGGCATTCATTCTGGAC
129 AAATATATCGACACTTTATGCGTGCACCTCCCTTGGCCATTCATTCTGGAC
*
15175 AACAAGTATCGA
1 AAAAAGTATCGA
15187 CACAATTTAA
Statistics
Matches: 165, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
176 4 0.02
177 72 0.44
178 60 0.36
179 29 0.18
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (179 bp):
AAAAAGTATCGATACATTATGTACACCTATTTTCTAATAAAACCGATAAATTTATACCGGTTACA
TTAGAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGAGCGATACATTTTAAA
ATATATCGACACTTTATGCGTGCACCTCCCTTGGCCATTCATTCTGGAC
Found at i:15476 original size:196 final size:196
Alignment explanation
Indices: 14996--15734 Score: 1027
Period size: 196 Copynumber: 3.7 Consensus size: 196
14986 CATTCTGGAC
* * * *
14996 AAAAAGTATCGATACATTATGTAGACCTATTTTCTAATTAACCGATATATTTTTATCGGTTACAT
1 AAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAACCGGTATATTTCTATCGGTTACAT
* *
15061 TGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGCTACTTTTAATAA
66 TGGAAATTTACCTATTACATTATAATTATCTGTTTCGATATTTTTGGGATCGATACTTTTAATAA
15126 ATGTATCGACACTTTATGCGTGCACCTCGGTTGGGCATTCATTCTGGACAACAAGTATCGACACA
131 ATGTATCGACACTTTATGCGTGCACC-C-GTTGGGCATTCATTCTGGACAA-AAGTATCGACACA
*
15191 ATTT
193 AATT
* ** * * *
15195 AAAAAGTGCCGATACATTATGTTTACCTATTCTCTAATTAAACCGGTATATATCTACCGGTTACA
1 AAAAAGTGTCGATACATTATGTAGACCTATTTTCTAA-TAAACCGGTATATTTCTATCGGTTACA
* * *
15260 TTGGAAATTTACCTATTACATTATAATTATTTGTTTTGATGTTTTTGGGATCGATACTTTTAATA
65 TTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATATTTTTGGGATCGATACTTTTAATA
* * *
15325 AATGTATCGACACTTTATG-TTGCA-CCGTTGGGTAATCATTCTGGACAAAACGTATCGACACAA
130 AATGTATCGACACTTTATGCGTGCACCCGTTGGGCATTCATTCTGGACAAAA-GTATCGACACAA
15388 ATT
194 ATT
* * * *
15391 AAAAAGTGTCGATACATTATGTAGACCTGTTTTCTTATAAAACCGGTAAATTTATATCGGTTACA
1 AAAAAGTGTCGATACATTATGTAGACCTATTTTCTAAT-AAACCGGTATATTTCTATCGGTTACA
* * *
15456 TT-GATAATTTACCTATTACATTGTAATTATCGGATTCGATATTTTTGGGATCGATA-TTTTAAT
65 TTGGA-AATTTACCTATTACATTATAATTATCTGTTTCGATATTTTTGGGATCGATACTTTTAAT
* * * *
15519 AAATGTATCGACACTTTGTGCGTACACCCCGTTTGACATTCATTCTGGACAAAAAGTATCGACAC
129 AAATGTATCGACACTTTATGCGTGCA-CCCGTTGGGCATTCATTCTGGAC-AAAAGTATCGACAC
15584 AAATTT
192 AAA-TT
* * **
15590 AAAAAGTGTTGATACATTATGTAGACCTATTTTCTAATTAACCGGTATATTTCTATCATTTACAT
1 AAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAACCGGTATATTTCTATCGGTTACAT
* * *
15655 TGGAAATTTACCTATTACATTATAATTATATGTTTCGATATTTTTGGGATCGATTCTTATAATAA
66 TGGAAATTTACCTATTACATTATAATTATCTGTTTCGATATTTTTGGGATCGATACTTTTAATAA
15720 ATGTATCGACACTTT
131 ATGTATCGACACTTT
15735 TGTTTACCTA
Statistics
Matches: 475, Mismatches: 54, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
195 31 0.07
196 137 0.29
197 1 0.00
198 101 0.21
199 102 0.21
200 103 0.22
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (196 bp):
AAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAACCGGTATATTTCTATCGGTTACAT
TGGAAATTTACCTATTACATTATAATTATCTGTTTCGATATTTTTGGGATCGATACTTTTAATAA
ATGTATCGACACTTTATGCGTGCACCCGTTGGGCATTCATTCTGGACAAAAGTATCGACACAAAT
T
Found at i:15725 original size:394 final size:394
Alignment explanation
Indices: 14996--15738 Score: 1134
Period size: 394 Copynumber: 1.9 Consensus size: 394
14986 CATTCTGGAC
* * *
14996 AAAAAGTATCGATACATTATGTAGACCTATTTTCTAATTAACCGATATATTTTTATCGGTTACAT
1 AAAAAGTATCGATACATTATGTAGACCTATTTTCTAATAAACCGATAAATTTATATCGGTTACAT
* * * *
15061 TGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGCTACTTTTAATAA
66 TGGAAATTTACCTATTACATTATAATTATCGGATTCGATATTTTTGGGATCGATACTTTTAATAA
* * * *
15126 ATGTATCGACACTTTATGCGTGCACCTCGGTTGGGCATTCATTCTGGACAACAAGTATCGACACA
131 ATGTATCGACACTTTATGCGTACACCTCCGTTGGACATTCATTCTGGACAAAAAGTATCGACACA
** *
15191 ATTTAAAAAGTGCCGATACATTATGTTTACCTATTCTCTAATTAAACCGGTATATATCTACCGGT
196 ATTTAAAAAGTGCCGATACATTATGTAGACCTATTCTCTAATTAAACCGGTATATATCTACCAGT
* * * *
15256 TACATTGGAAATTTACCTATTACATTATAATTATTTGTTTTGATGTTTTTGGGATCGATACTTTT
261 TACATTGGAAATTTACCTATTACATTATAATTATATGTTTCGATATTTTTGGGATCGATACTTAT
15321 AATAAATGTATCGACACTTTATGTTGCACCGTTGGGTAATCATTCTGGACAAAACGTATCGACAC
326 AATAAATGTATCGACACTTT-TGTTGCACCGTTGGGTAATCATTCTGGACAAAACGTATCGACAC
15386 AAATT
390 AAATT
* * * *
15391 AAAAAGTGTCGATACATTATGTAGACCTGTTTTCTTATAAAACCGGTAAATTTATATCGGTTACA
1 AAAAAGTATCGATACATTATGTAGACCTATTTTCTAAT-AAACCGATAAATTTATATCGGTTACA
*
15456 TT-GATAATTTACCTATTACATTGTAATTATCGGATTCGATATTTTTGGGATCGATA-TTTTAAT
65 TTGGA-AATTTACCTATTACATTATAATTATCGGATTCGATATTTTTGGGATCGATACTTTTAAT
* *
15519 AAATGTATCGACACTTTGTGCGTACACC-CCGTTTGACATTCATTCTGGACAAAAAGTATCGACA
129 AAATGTATCGACACTTTATGCGTACACCTCCGTTGGACATTCATTCTGGACAAAAAGTATCGACA
** * * *
15583 CAAATTTAAAAAGTGTTGATACATTATGTAGACCTATTTTCTAATT-AACCGGTATATTTCTATC
194 C-AATTTAAAAAGTGCCGATACATTATGTAGACCTATTCTCTAATTAAACCGGTATATATCTACC
* *
15647 ATTTACATTGGAAATTTACCTATTACATTATAATTATATGTTTCGATATTTTTGGGATCGATTCT
258 AGTTACATTGGAAATTTACCTATTACATTATAATTATATGTTTCGATATTTTTGGGATCGATACT
15712 TATAATAAATGTATCGACACTTTTGTT
323 TATAATAAATGTATCGACACTTTTGTT
15739 TACCTAATCT
Statistics
Matches: 313, Mismatches: 32, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
393 4 0.01
394 130 0.42
395 109 0.35
396 70 0.22
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (394 bp):
AAAAAGTATCGATACATTATGTAGACCTATTTTCTAATAAACCGATAAATTTATATCGGTTACAT
TGGAAATTTACCTATTACATTATAATTATCGGATTCGATATTTTTGGGATCGATACTTTTAATAA
ATGTATCGACACTTTATGCGTACACCTCCGTTGGACATTCATTCTGGACAAAAAGTATCGACACA
ATTTAAAAAGTGCCGATACATTATGTAGACCTATTCTCTAATTAAACCGGTATATATCTACCAGT
TACATTGGAAATTTACCTATTACATTATAATTATATGTTTCGATATTTTTGGGATCGATACTTAT
AATAAATGTATCGACACTTTTGTTGCACCGTTGGGTAATCATTCTGGACAAAACGTATCGACACA
AATT
Found at i:15862 original size:15 final size:15
Alignment explanation
Indices: 15842--15871 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15832 CGACACTTTG
15842 TTGGAAACTTTATGT
1 TTGGAAACTTTATGT
15857 TTGGAAACTTTATGT
1 TTGGAAACTTTATGT
15872 GTCGATACAT
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:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
TTGGAAACTTTATGT
Found at i:20448 original size:200 final size:200
Alignment explanation
Indices: 20163--21326 Score: 1577
Period size: 200 Copynumber: 5.8 Consensus size: 200
20153 CGTAATTTAA
* * * * * * *
20163 AAAAAGTATCGATACCAA-TTTATAAAGTGTCGAAACATTATGT-TGACCTATTTTCTAATTAAA
1 AAAATGTATCGACACAAATTTTA-AAAGTGTCGATACATTATGTAT-ACCTATTCTCTCATAAAA
** ** * * *
20226 CATGTATATTTATACCGGTTATATTGAAAAATTACCTATTACATTATAATTATTGGTTTCGATGT
64 CCGGTATATTTCCACCGGTTACATTGCAAAATTACCTATTACATTATAATTATCGGTTTCGATGT
* * * ** *
20291 TTTTGGGGTTGATACTTTTTATAAATATATCGACACTTTATCCGTGCACCTAGTTTGACATTCAT
129 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTAGTTTGGCATTCAT
20356 TCTGGAC
194 TCTGGAC
*
20363 AAAATGTATCGACACAAATTTTAAAAGTGTCGATACATTATGTATACATATTCTCTCATAAAACC
1 AAAATGTATCGACACAAATTTTAAAAGTGTCGATACATTATGTATACCTATTCTCTCATAAAACC
* * **
20428 GGTATATTTCCACCGGTTATATTGTAAAATTACCTATTACATTATAATTATTTGTTTCGATGTTT
66 GGTATATTTCCACCGGTTACATTGCAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * *
20493 TTGGGATCGAGACTTTTTATAAATGTATCGAAACTTTATGTGTGTACCTAGTTTGGCATTCATTC
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTAGTTTGGCATTCATTC
20558 TGGAC
196 TGGAC
* *
20563 AAAATGTATCGAAACAAATTTTAAAAGTATCGATACATTATGTATACCTATTCTCTCATAAAACC
1 AAAATGTATCGACACAAATTTTAAAAGTGTCGATACATTATGTATACCTATTCTCTCATAAAACC
* * * * *
20628 GGTATATTTCTAACAGTTACATTGCAAATTTACCTATTACATTGA-AATTATCAGTTTCGATGTT
66 GGTATATTTCCACCGGTTACATTGCAAAATTACCTATTACATT-ATAATTATCGGTTTCGATGTT
* * * *
20692 TTTAGGATCGATATTTTTTATAAATGTATCGAAACTTTATGCGTGCACCTAGTTTGGGCATTCAT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTAGTTT-GGCATTCAT
20757 TCTGGAC
194 TCTGGAC
* * **
20764 AAAATGTATCGACACAAATTTTGAAAGTGTAGATACATTATGTATACCTATTCTCTCATAAAAAA
1 AAAATGTATCGACACAAATTTTAAAAGTGTCGATACATTATGTATACCTATTCTCTCATAAAACC
* * * * *
20829 GGTACATTTCCACCGGTTACATTG-AAAATTTAACTATTAAATTGTAATTATCGGTTTCGATATT
66 GGTATATTTCCACCGGTTACATTGCAAAA-TTACCTATTACATTATAATTATCGGTTTCGATGTT
* * *
20893 TTTGGGATCGATACCTTTAATAAATGTATCGACACTTTATGTGTGTACCTCA-TTTGGCATTCAT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCT-AGTTTGGCATTCAT
20957 TCTGGAC
194 TCTGGAC
* *
20964 AAAATGTATCAACACAAATTTTAAAAGTGTCGATACATTATGTATACATATTCTCTCATAAAACC
1 AAAATGTATCGACACAAATTTTAAAAGTGTCGATACATTATGTATACCTATTCTCTCATAAAACC
* * * *
21029 GATATATTTTCACC-TTTACATTGCAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 GGTATATTTCCACCGGTTACATTGCAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * **
21093 TTGGGATCAAGACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTCTTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTAGTTT-GGCATTCATT
21158 CTGGAC
195 CTGGAC
* ** * * *
21164 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTATCTCATAAAACC
1 AAAATGTATCGACACAAATTTTAAAAGTGTCGATACATTATGTATACCTATTCTCTCATAAAACC
** * *
21229 GGTATATTTATACCGGTTACATTGCAAAATTACCTATTACATTATAATTATGGGTTTTGAT-TTT
66 GGTATATTTCCACCGGTTACATTGCAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTT
21293 TTGGGATCGATACTTTTTATAAATGTATCGACAC
131 TTGGGATCGATACTTTTTATAAATGTATCGACAC
21327 ATACCTATTC
Statistics
Matches: 855, Mismatches: 98, Indels: 22
0.88 0.10 0.02
Matches are distributed among these distances:
199 86 0.10
200 548 0.64
201 220 0.26
202 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (200 bp):
AAAATGTATCGACACAAATTTTAAAAGTGTCGATACATTATGTATACCTATTCTCTCATAAAACC
GGTATATTTCCACCGGTTACATTGCAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTT
TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTAGTTTGGCATTCATTC
TGGAC
Found at i:21793 original size:19 final size:19
Alignment explanation
Indices: 21769--21817 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
21759 TTACATTCAC
21769 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
*
21788 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
21807 ATACAAAATTA
1 ATACAAAATTA
21818 ACCCTACATT
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:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:22159 original size:18 final size:18
Alignment explanation
Indices: 22136--22174 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
22126 TCCTCCTCAT
*
22136 TTCCTCCATCTTTTCTTC
1 TTCCTCCATATTTTCTTC
22154 TTCCTCCATATTTTCTTC
1 TTCCTCCATATTTTCTTC
22172 TTC
1 TTC
22175 ATATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATATTTTCTTC
Found at i:22844 original size:22 final size:23
Alignment explanation
Indices: 22816--22872 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 23
22806 AACCTGCATT
*
22816 TATAATAAAAT-TTATCATTTTA
1 TATAATAAAATACTATCATTTTA
22838 TATAATAAATATACTATCATTTTA
1 TATAATAAA-ATACTATCATTTTA
*
22862 TATAAAAAAAT
1 TATAATAAAAT
22873 GTTCTTCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 9 0.29
23 4 0.13
24 18 0.58
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAATAAAATACTATCATTTTA
Found at i:25229 original size:182 final size:182
Alignment explanation
Indices: 24731--25384 Score: 971
Period size: 182 Copynumber: 3.6 Consensus size: 182
24721 TACGCGTACT
* * *
24731 TATTAAAGTATCAACACTTTCAACATATCCGGTAGCGCTTTACTGATTTTGTCATTTCAAGTCCG
1 TATTAAAGTATCAACACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATTTCGAGACCG
* *
24796 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACT
24861 TTATAGGCGCTATTATTGCTTCTC--TT---TTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTATTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * * *
24908 TATTAATGTATCGACACTTTCAACATATCCGGTAGCGCTTTACTGGTTTTGTCGTTTCGAGACCA
1 TATTAAAGTATCAACACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATTTCGAGACCG
* *
24973 G-TTTGTCATATTTTTACCTGTTTTATTATTATGGATCGATACATTTTTATAAAGTATCGACACC
66 GTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
25037 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATATTTA
131 TTATAGGCGCTATTATTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * * *
25089 TATTAATGTATTAACACTTTCAACATATCCGGTAGTGTTTTACCGATTTTTTCGTTTCGAGACCG
1 TATTAAAGTATCAACACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATTTCGAGACCG
* *
25154 GTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAATATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACT
* **
25219 TTATAGGCGCTATTATTGCTTGTCTTTTAAATTCCAAAAGTACCGATACTTA
131 TTATAGGCGCTATTATTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
25271 TATTAAAGTATCGACACTTTCAACATATCTGGTAGCGCTTTACCG-GTTTGATCATTTCGAAACC
1 TATTAAAGTATCAACACTTTCAACATATCCGGTAGCGCTTTACCGATTTTG-TCATTTCGAGACC
*
25335 GGTTTTGTCATATTTTTACCTGTTATATTATTATAGATCGATACATTTTT
65 GGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTT
25385 TATTTGTATC
Statistics
Matches: 428, Mismatches: 42, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
176 83 0.19
177 58 0.14
178 2 0.00
181 81 0.19
182 204 0.48
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
TATTAAAGTATCAACACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATTTCGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTATTATTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:25458 original size:11 final size:11
Alignment explanation
Indices: 25442--25468 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
25432 TTTTTTTAAT
25442 ATTTCTTCATG
1 ATTTCTTCATG
25453 ATTTCTTCATG
1 ATTTCTTCATG
25464 ATTTC
1 ATTTC
25469 CACCTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.56
Consensus pattern (11 bp):
ATTTCTTCATG
Found at i:28572 original size:21 final size:21
Alignment explanation
Indices: 28528--28592 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
28518 ATTAATTTAG
* **
28528 AAACCCTAAATCTTAAACTTT
1 AAACCATAAATCTTAAACCCT
*
28549 AAACCATAAATATTAAACCCT
1 AAACCATAAATCTTAAACCCT
* * *
28570 AAACTATGAACCTTAAACCCT
1 AAACCATAAATCTTAAACCCT
28591 AA
1 AA
28593 TGTAAACGGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.26
Consensus pattern (21 bp):
AAACCATAAATCTTAAACCCT
Found at i:28983 original size:13 final size:13
Alignment explanation
Indices: 28965--29010 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
28955 ACCATGTATA
28965 ATATATATAAACT
1 ATATATATAAACT
28978 ATATATATATAACCT
1 ATATATATA-AA-CT
*
28993 ATATATATAAACG
1 ATATATATAAACT
29006 ATATA
1 ATATA
29011 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 15 0.50
14 4 0.13
15 11 0.37
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:28984 original size:20 final size:19
Alignment explanation
Indices: 28950--28988 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
28940 AATATGTATG
*
28950 TATAAACCATGTATAATATA
1 TATAAACCATATAT-ATATA
*
28970 TATAAACTATATATATATA
1 TATAAACCATATATATATA
28989 ACCTATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (19 bp):
TATAAACCATATATATATA
Found at i:28985 original size:15 final size:15
Alignment explanation
Indices: 28965--29001 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
28955 ACCATGTATA
28965 ATATATATAAACTAT
1 ATATATATAAACTAT
*
28980 ATATATATAACCTAT
1 ATATATATAAACTAT
28995 ATATATA
1 ATATATA
29002 AACGATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATATATAAACTAT
Found at i:29010 original size:15 final size:14
Alignment explanation
Indices: 28965--29010 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
28955 ACCATGTATA
28965 ATATATATAAAC-T
1 ATATATATAAACAT
*
28978 ATATATATATAACCT
1 ATATATATA-AACAT
28993 ATATATATAAACGAT
1 ATATATATAAAC-AT
29008 ATA
1 ATA
29011 AAGTAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 9 0.31
14 6 0.21
15 14 0.48
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (14 bp):
ATATATATAAACAT
Found at i:29095 original size:7 final size:7
Alignment explanation
Indices: 29085--29156 Score: 72
Period size: 7 Copynumber: 10.3 Consensus size: 7
29075 TAGTTTATAG
*
29085 AAACCTT
1 AAACCCT
29092 AAACCCT
1 AAACCCT
**
29099 AAACATT
1 AAACCCT
29106 AAACCCT
1 AAACCCT
29113 AAACCCT
1 AAACCCT
**
29120 AAACATT
1 AAACCCT
*
29127 AAATCCT
1 AAACCCT
*
29134 AAACCAT
1 AAACCCT
*
29141 AAACCAT
1 AAACCCT
29148 AAACCCT
1 AAACCCT
29155 AA
1 AA
29157 TATAAATAGA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:29115 original size:21 final size:21
Alignment explanation
Indices: 29085--29156 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
29075 TAGTTTATAG
*
29085 AAACCTTAAACCCTAAACATT
1 AAACCCTAAACCCTAAACATT
29106 AAACCCTAAACCCTAAACATT
1 AAACCCTAAACCCTAAACATT
* *
29127 AAATCCTAAACCATAAACCA-T
1 AAACCCTAAACCCTAAA-CATT
29148 AAACCCTAA
1 AAACCCTAA
29157 TATAAATAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 44 0.96
22 2 0.04
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (21 bp):
AAACCCTAAACCCTAAACATT
Found at i:29548 original size:13 final size:13
Alignment explanation
Indices: 29530--29576 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 13
29520 CCATGTATAG
29530 TATATATAAACTA
1 TATATATAAACTA
29543 TATATATATAACCTATA
1 TATATATA-AA-C--TA
29560 TATATATAAACTA
1 TATATATAAACTA
29573 TATA
1 TATA
29577 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 14 0.47
14 2 0.07
15 2 0.07
16 2 0.07
17 10 0.33
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:29550 original size:15 final size:15
Alignment explanation
Indices: 29525--29576 Score: 86
Period size: 15 Copynumber: 3.4 Consensus size: 15
29515 ATAAACCATG
29525 TATAGTATATATAAAC
1 TATA-TATATATAAAC
*
29541 TATATATATATAACC
1 TATATATATATAAAC
29556 TATATATATATAAAC
1 TATATATATATAAAC
29571 TATATA
1 TATATA
29577 AAGTAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:29670 original size:14 final size:14
Alignment explanation
Indices: 29648--29692 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
29638 TAGTTTATAG
* *
29648 AAACCTTAAACTCT
1 AAACATTAAACCCT
*
29662 AAACTTTAAACCCT
1 AAACATTAAACCCT
29676 AAACATTAAACCCT
1 AAACATTAAACCCT
29690 AAA
1 AAA
29693 TCCTAAACAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACATTAAACCCT
Found at i:29685 original size:21 final size:21
Alignment explanation
Indices: 29668--29733 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
29658 CTCTAAACTT
29668 TAAACCCTAAACATTAAACCC
1 TAAACCCTAAACATTAAACCC
* *
29689 TAAATCCTAAACAGTAAACCC
1 TAAACCCTAAACATTAAACCC
* *
29710 TAAATCATAAACCA-TAAACCC
1 TAAACCCTAAA-CATTAAACCC
29731 TAA
1 TAA
29734 TATAAATAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 39 0.95
22 2 0.05
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACATTAAACCC
Found at i:29699 original size:14 final size:13
Alignment explanation
Indices: 29648--29733 Score: 55
Period size: 14 Copynumber: 6.2 Consensus size: 13
29638 TAGTTTATAG
*
29648 AAACCTTAAACTCT
1 AAACC-TAAACCCT
*
29662 AAACTTTAAACCCT
1 AAAC-CTAAACCCT
*
29676 AAACATTAAACCCT
1 AAAC-CTAAACCCT
**
29690 AAATCCTAAACAGT
1 AAA-CCTAAACCCT
* *
29704 AAACCCTAAATCAT
1 AAA-CCTAAACCCT
29718 AAACCATAAACCCT
1 AAACC-TAAACCCT
29732 AA
1 AA
29734 TATAAATAGA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
13 2 0.04
14 54 0.95
15 1 0.02
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.22
Consensus pattern (13 bp):
AAACCTAAACCCT
Found at i:29905 original size:577 final size:577
Alignment explanation
Indices: 28528--30669 Score: 3285
Period size: 564 Copynumber: 3.8 Consensus size: 577
28518 ATTAATTTAG
** * * *
28528 AAACCCTAAATC-TTAAACTTTAAACCATAAATATTAAACCCTAAA-CTATGAACCTTAAACCCT
1 AAACCCTAAA-CATTAAACCCTAAACC-TAAACATTAAACCCTAAATC-ATAAACCATAAACCCT
* ** * * * *
28591 AATGTAAACGGACTAGCACTAATGCCTATATATTTATAATAAAAGAGTGGGCTTATGTATTGGGC
63 AATATAAATAGACTAACACTAATGCCTATATATTTGTAATAAAAGAGTAGGCTTATATATTGGGC
* * *
28656 CTATGTAAACTAATGTAAATGGACTAGCAGTAATGCAAATGGACTTATTTTTGGGTTTTATTATT
128 CTATGTAAACTAATGTAAATGAACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATT
* *
28721 ACTTATTCATAACAACAAAATAAATAGGTTATTAATGTGAATTAACCTAACATGCAAATAAAATA
193 ACTTATTCATAACAACAAAATAAATGGGTTATTAATGTGAATTAACCTAACATGCAACTAAAATA
*
28786 CTAATTATGCAAATGAAATTAATATAACATGTACTACTATATATGAACCATATAATATGCAATGT
258 CTAATTATGCAAATGAAATTAATATGACATGTACTACTATATATGAACCATATAATATGCAATGT
28851 GACATACTAATTATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATTATTTTTT
323 GACATACTAATTATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATTATTTTTT
*
28916 AAAATTTATTAAATAATTTTATATAATATGTATGTATAAACCATGTATAATATATATAAACTATA
388 -AAATTTATTAAATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATAAACTATA
*
28981 TATATATAACC--TATATATATAAACGATATAAAGTAAATTACTTATATAGTTTATAGAAACACT
452 TATATATAACCTATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACT
29044 ACGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAG------AAA--C----C-TT
517 ACGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACTTAAACTCTAAACTTT
* *
29092 AAACCCTAAACATTAAACCCTAAACCCTAAACATTAAATCCTAAACCATAAACCATAAACCCTAA
1 AAACCCTAAACATTAAACCCTAAA-CCTAAACATTAAACCCTAAATCATAAACCATAAACCCTAA
* *
29157 TATAAATAGACTAACATTAATGCCTATATATTTGTAATAAAAGAGTGGGCTTATATATTGGGCCT
65 TATAAATAGACTAACACTAATGCCTATATATTTGTAATAAAAGAGTAGGCTTATATATTGGGCCT
* *
29222 ATGTAAATTAATGTAAATGAACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTTTTAC
130 ATGTAAACTAATGTAAATGAACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTAC
29287 TTATTCATAACAACAAAATAAATGGGTTATTAATGTGAATTAACCTAACATGCAACTAAAATACT
195 TTATTCATAACAACAAAATAAATGGGTTATTAATGTGAATTAACCTAACATGCAACTAAAATACT
29352 AATTATGCAAATGAAATTAATATGACATGTACTACTATATATGAACCATATAATATGCAATGTGA
260 AATTATGCAAATGAAATTAATATGACATGTACTACTATATATGAACCATATAATATGCAATGTGA
* *
29417 CATACTAGTTATTTAACACATAATTAATCATGTTTTATATAATTTACATTTAAATTATTTTTTAA
325 CATACTAATTATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATTATTTTTT-A
29482 AATTTATTAAATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATAAACTATATA
389 AATTTATTAAATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATAAACTATATA
29547 TATATAACCTATATATATATAAACTATATAAAGTAAATTAC-T-TATA-TTTATAGAAACACTAC
454 TATATAACCTATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTAC
29609 GCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACCTTAAACTCTAAACTTT
519 GCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAA-CTTAAACTCTAAACTTT
*
29669 AAACCCTAAACATTAAACCCTAAATCCTAAACAGTAAACCCTAAATCATAAACCATAAACCCTAA
1 AAACCCTAAACATTAAACCCTAAA-CCTAAACATTAAACCCTAAATCATAAACCATAAACCCTAA
*
29734 TATAAATAGACTAACACTAATGCCTATATATTTGTAATAAAAGAGTAGACTTATATATTGGGCCT
65 TATAAATAGACTAACACTAATGCCTATATATTTGTAATAAAAGAGTAGGCTTATATATTGGGCCT
* *
29799 ATGTAAATTAATGTAAATGAACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTTTTAC
130 ATGTAAACTAATGTAAATGAACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTAC
29864 TTATTCATAACAACAAAATAAATGGGTTATTAATGTGAATTAACCTAACATGCAACTAAAATACT
195 TTATTCATAACAACAAAATAAATGGGTTATTAATGTGAATTAACCTAACATGCAACTAAAATACT
*
29929 AATTATGCAAATGAAATTAATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGA
260 AATTATGCAAATGAAATTAATATGACATGTACTACTATATATGAACCATATAATATGCAATGTGA
* *
29994 CATACTAATTATTTAACACCTAATTAATCATATTTTATATATTTTACATTTAAATTATTTTTTAA
325 CATACTAATTATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATTATTTTTTAA
* * * *
30059 ATTTGTTAAATAATTTTATATAATATGTATTTATAAACCACGTATAGCATATATAAACTATATAT
390 ATTTATTAAATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATAAACTATATAT
* * *
30124 ATATAACATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTTTAGAAACATTA
455 ATATAAC--CTATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTA
30189 CGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAATCTTAAACTCTAAACTTT
518 CGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAA-CTTAAACTCTAAACTTT
* *
30250 AAACCAT-AA-A-T--A--CTAAACC----C--TAAACCTTAAATC----A-C--AAACCCTAAT
1 AAACCCTAAACATTAAACCCTAAACCTAAACATTAAACCCTAAATCATAAACCATAAACCCTAAT
* * * * *
30295 GTAAATGGACTAGCACTAATGCATATATATTTGTAATAAAAGAGT-GG-------GTT-----TA
66 ATAAATAGACTAACACTAATGCCTATATATTTGTAATAAAAGAGTAGGCTTATATATTGGGCCTA
* *
30347 TGTAAACTAATGTAAATGGACTAGCACTAATGCAAATAGACTTA-TTTTTGGATTTTATTATTAC
131 TGTAAACTAATGTAAATGAACTAGCACTAATGCAAATGGACTTATTTTTTGG-TTTTATTATTAC
*
30411 TTATTCATAACAACAAAATAAATGAGTTATTAATGTGAATTAACCTAACATGCAACTAAAATACT
195 TTATTCATAACAACAAAATAAATGGGTTATTAATGTGAATTAACCTAACATGCAACTAAAATACT
* *
30476 AATTATGCAAATGAAATTAATATGACATGTACTATTATTTATGAACCATATAATATGCAATGTGA
260 AATTATGCAAATGAAATTAATATGACATGTACTACTATATATGAACCATATAATATGCAATGTGA
*
30541 CATACTAATTATTTAACACCTAATTAATCATGTTTTATATCATTTACATTTAAATTATTTTTTAA
325 CATACTAATTATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATTATTTTTTAA
* *
30606 ACTTATTAAATAATTTTATTTAATATGTATGTATAAACCATGTATAGTATATATAAACTATATA
390 ATTTATTAAATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATAAACTATATA
30670 AAGTAAATTA
Statistics
Matches: 1485, Mismatches: 68, Indels: 67
0.92 0.04 0.04
Matches are distributed among these distances:
546 7 0.00
547 302 0.20
552 2 0.00
559 1 0.00
560 51 0.03
562 1 0.00
563 57 0.04
564 437 0.29
565 4 0.00
566 29 0.02
567 12 0.01
569 1 0.00
570 3 0.00
572 1 0.00
573 2 0.00
574 5 0.00
576 72 0.05
577 378 0.25
578 33 0.02
579 2 0.00
580 6 0.00
581 79 0.05
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (577 bp):
AAACCCTAAACATTAAACCCTAAACCTAAACATTAAACCCTAAATCATAAACCATAAACCCTAAT
ATAAATAGACTAACACTAATGCCTATATATTTGTAATAAAAGAGTAGGCTTATATATTGGGCCTA
TGTAAACTAATGTAAATGAACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTACT
TATTCATAACAACAAAATAAATGGGTTATTAATGTGAATTAACCTAACATGCAACTAAAATACTA
ATTATGCAAATGAAATTAATATGACATGTACTACTATATATGAACCATATAATATGCAATGTGAC
ATACTAATTATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATTATTTTTTAAA
TTTATTAAATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATAAACTATATATA
TATAACCTATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTACGC
ATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACTTAAACTCTAAACTTT
Found at i:30152 original size:17 final size:17
Alignment explanation
Indices: 30107--30154 Score: 73
Period size: 15 Copynumber: 2.9 Consensus size: 17
30097 CACGTATAGC
30107 ATATATAAACTATATAT
1 ATATATAAACTATATAT
*
30124 ATATA-ACA-TATATAT
1 ATATATAAACTATATAT
30139 ATATATAAACTATATA
1 ATATATAAACTATATA
30155 AAGTAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATAAACTATATAT
Found at i:30265 original size:21 final size:21
Alignment explanation
Indices: 30249--30293 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
30239 CTCTAAACTT
30249 TAAACCATAAATACTAAACCC
1 TAAACCATAAATACTAAACCC
*
30270 TAAACCTTAAATCAC-AAACCC
1 TAAACCATAAAT-ACTAAACCC
30291 TAA
1 TAA
30294 TGTAAATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAACCATAAATACTAAACCC
Found at i:30674 original size:20 final size:20
Alignment explanation
Indices: 30632--30674 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
30622 TATTTAATAT
* * *
30632 GTATGTATAAACCATGTATA
1 GTATATATAAACCATATAAA
*
30652 GTATATATAAACTATATAAA
1 GTATATATAAACCATATAAA
30672 GTA
1 GTA
30675 AATTACTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (20 bp):
GTATATATAAACCATATAAA
Found at i:30754 original size:7 final size:7
Alignment explanation
Indices: 30744--30795 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
30734 TAGTTTATAG
30744 AAACCTT
1 AAACCTT
*
30751 AAACCAT
1 AAACCTT
*
30758 AAACCCT
1 AAACCTT
*
30765 AAACTTT
1 AAACCTT
*
30772 AAACCAT
1 AAACCTT
30779 AAACAC-T
1 AAAC-CTT
30786 AAACCTT
1 AAACCTT
30793 AAA
1 AAA
30796 TAACAAACCC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
6 1 0.03
7 35 0.95
8 1 0.03
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCTT
Found at i:30759 original size:49 final size:49
Alignment explanation
Indices: 30658--30761 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
30648 TATAGTATAT
* ** **
30658 ATAAACTATATAAAGTAAATTACTTATATAGGTTATAGAAACACTATGC
1 ATAAACTATATAAAGTAAATAAAGTATATAGGTTATAGAAACACTAACC
*
30707 ATAAACTATATAAAGT-AATAAAGTATATAGTTTATAGAAAC-CTTAAACC
1 ATAAACTATATAAAGTAAATAAAGTATATAGGTTATAGAAACAC-T-AACC
30756 ATAAAC
1 ATAAAC
30762 CCTAAACTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 1 0.02
48 22 0.47
49 24 0.51
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.31
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAAAGTATATAGGTTATAGAAACACTAACC
Found at i:30773 original size:21 final size:21
Alignment explanation
Indices: 30744--30795 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
30734 TAGTTTATAG
*
30744 AAACCTTAAACCATAAACCCT
1 AAACCTTAAACCATAAACACT
*
30765 AAACTTTAAACCATAAACACT
1 AAACCTTAAACCATAAACACT
30786 AAACCTTAAA
1 AAACCTTAAA
30796 TAACAAACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACCTTAAACCATAAACACT
Found at i:31212 original size:21 final size:20
Alignment explanation
Indices: 31132--31213 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
31122 CGTAAATCCA
31132 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
* * *
31153 TAT-GACTATCGCAATGCGAT
1 TTTCCAAT-TCGCAATGCGAT
**
31173 TTTCCAATTTCGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
31194 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
31214 ATAAGTAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
19 1 0.02
20 15 0.32
21 26 0.55
22 5 0.11
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:31246 original size:20 final size:20
Alignment explanation
Indices: 31223--31284 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
31213 AATAAGTAAA
* *
31223 TCGCAATGCGATACTGACTT
1 TCGCAACGCGATATTGACTT
**
31243 TCGCAACGCGATATTTTCTT
1 TCGCAACGCGATATTGACTT
*
31263 TCGCAACACGATATTGACTT
1 TCGCAACGCGATATTGACTT
31283 TC
1 TC
31285 TCAATGAGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (20 bp):
TCGCAACGCGATATTGACTT
Found at i:31837 original size:20 final size:20
Alignment explanation
Indices: 31788--31846 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
31778 TTTATTCTCT
* **
31788 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
31808 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
31828 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
31847 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:33191 original size:18 final size:18
Alignment explanation
Indices: 33164--33212 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
33154 CTCCACTTCG
* *
33164 AGAGTCATCACCTTACCC
1 AGAGCCATCACCTCACCC
*
33182 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
33200 AGAGCCATCACCT
1 AGAGCCATCACCT
33213 GATCGATCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.41, G:0.12, T:0.18
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:33787 original size:20 final size:19
Alignment explanation
Indices: 33764--33850 Score: 67
Period size: 19 Copynumber: 4.8 Consensus size: 19
33754 CGCAACAAGA
*
33764 AAATGATTATCGCAACGCGG
1 AAATGAATATCGCAACGC-G
** *
33784 AAATGGCTATCGCAATGCG
1 AAATGAATATCGCAACGCG
*
33803 AAATGAAAATCGCAA--CG
1 AAATGAATATCGCAACGCG
*
33820 AAA--AA-ATCGCAAAGCG
1 AAATGAATATCGCAACGCG
*
33836 AAATGAAAATCGCAA
1 AAATGAATATCGCAA
33851 TACAATTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
14 7 0.12
15 2 0.04
16 5 0.09
17 5 0.09
18 2 0.04
19 20 0.36
20 15 0.27
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AAATGAATATCGCAACGCG
Found at i:33814 original size:19 final size:19
Alignment explanation
Indices: 33792--33851 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
33782 GGAAATGGCT
33792 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
33811 ATCGCAA--CG-AA--AAA
1 ATCGCAATGCGAAATGAAA
*
33825 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
33844 ATCGCAAT
1 ATCGCAAT
33852 ACAATTTGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 10 0.29
16 4 0.11
17 4 0.11
19 17 0.49
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:35324 original size:14 final size:14
Alignment explanation
Indices: 35290--35328 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
35280 TTTATTGTTT
35290 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
35304 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
35318 TGTTGATTTGT
1 AATTGATTTGT
35329 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:35449 original size:20 final size:20
Alignment explanation
Indices: 35424--35462 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35414 ATGTTGAAGG
*
35424 CAAAACAGACTGTCGCAACA
1 CAAAACAGACTATCGCAACA
*
35444 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
35463 GAGAGATTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.31, G:0.13, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:35494 original size:19 final size:19
Alignment explanation
Indices: 35470--35532 Score: 117
Period size: 19 Copynumber: 3.3 Consensus size: 19
35460 AACGAGAGAT
35470 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
35489 TCGCAATACGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
35508 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
35527 TCGCAA
1 TCGCAA
35533 CGAGAAAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.16
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:35539 original size:19 final size:18
Alignment explanation
Indices: 35479--35539 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 18
35469 TTCGCAATGC
*
35479 GAAATGAAAATCGCAATA
1 GAAATGAAAATCGCAAGA
*
35497 CGAAATGAAAATCGCAATGC
1 -GAAATGAAAATCGCAA-GA
35517 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAA-GA
35536 GAAA
1 GAAA
35540 ATCGCAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.52, C:0.15, G:0.20, T:0.13
Consensus pattern (18 bp):
GAAATGAAAATCGCAAGA
Found at i:35583 original size:20 final size:20
Alignment explanation
Indices: 35558--35611 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
35548 GTGATTTTCA
*
35558 TTTCGCGTTGTGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
35578 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
35598 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
35612 TTCCCCGTTG
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:0.13, C:0.20, G:0.26, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:36189 original size:20 final size:20
Alignment explanation
Indices: 36157--36332 Score: 144
Period size: 20 Copynumber: 8.7 Consensus size: 20
36147 GATTCTGTAT
*
36157 TATCTCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
* * *
36177 AATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGATAGTCAG
*
36197 TATCGCGTTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
36217 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
* **
36237 TATCACATTGCGATTTTCTA-
1 TATCGCATTGCGATAGTC-AG
* * *
36257 AATTCGCATTGCGAT--TTACT
1 TA-TCGCATTGCGATAGTCA-G
* *
36277 TATTCGCATTGCGAATTTGT-AT
1 TA-TCGCATTGCG-A-TAGTCAG
*
36299 TATCGCGTTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
36319 TATCGCATTGCGAT
1 TATCGCATTGCGAT
36333 TTTCCAAATT
Statistics
Matches: 129, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 96 0.74
21 22 0.17
22 4 0.03
23 1 0.01
24 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAG
Found at i:36287 original size:41 final size:41
Alignment explanation
Indices: 36242--36372 Score: 142
Period size: 41 Copynumber: 3.2 Consensus size: 41
36232 GTCAGTATCA
36242 CATTGCGATTTTCTAAATTCGCATTGCGATTTACTTATTCG
1 CATTGCGATTTTCTAAATTCGCATTGCGATTTACTTATTCG
* * * * * *
36283 CATTGCGAATTTGT-ATTATCGCGTTGCGA--TAGTCAGTATCG
1 CATTGCGATTTTCTAAAT-TCGCATTGCGATTTACTTA-T-TCG
*
36324 CATTGCGATTTTCCAAATTCGCATTGCGATTTACTTATTCG
1 CATTGCGATTTTCTAAATTCGCATTGCGATTTACTTATTCG
*
36365 TATTGCGA
1 CATTGCGA
36373 ATTGAGAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
39 4 0.06
40 3 0.04
41 56 0.80
42 3 0.04
43 4 0.06
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (41 bp):
CATTGCGATTTTCTAAATTCGCATTGCGATTTACTTATTCG
Found at i:36311 original size:82 final size:82
Alignment explanation
Indices: 36217--36375 Score: 282
Period size: 82 Copynumber: 1.9 Consensus size: 82
36207 CGATAGTCAG
*
36217 TATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCTAAATTCGCATTGCGATTTACTTATTC
1 TATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCCAAATTCGCATTGCGATTTACTTATTC
36282 GCATTGCGAATTTGTAT
66 GCATTGCGAATTTGTAT
* *
36299 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTTATTC
1 TATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCCAAATTCGCATTGCGATTTACTTATTC
*
36364 GTATTGCGAATT
66 GCATTGCGAATT
36376 GAGAAAATCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (82 bp):
TATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCCAAATTCGCATTGCGATTTACTTATTC
GCATTGCGAATTTGTAT
Found at i:36402 original size:21 final size:21
Alignment explanation
Indices: 36372--36425 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
36362 TCGTATTGCG
36372 AATTGAGAAAATCGCAACGCGA
1 AATTG-GAAAATCGCAACGCGA
*
36394 AATTGGAAAATCTCAACGCGA
1 AATTGGAAAATCGCAACGCGA
36415 AATTGGAAAAT
1 AATTGGAAAAT
36426 TGCATTGCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (21 bp):
AATTGGAAAATCGCAACGCGA
Found at i:38853 original size:16 final size:16
Alignment explanation
Indices: 38832--38875 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
38822 TCATTTACAG
38832 GTCAGGTTAAAAACAT
1 GTCAGGTTAAAAACAT
* **
38848 GTCAGGTTCATTACAT
1 GTCAGGTTAAAAACAT
38864 GTCAGGTTAAAA
1 GTCAGGTTAAAA
38876 CAGGTCGGGT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (16 bp):
GTCAGGTTAAAAACAT
Found at i:39355 original size:23 final size:23
Alignment explanation
Indices: 39329--39386 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
39319 ATCAAGTACA
*
39329 ATAA-CAAATTAGGTAGCACTTAT
1 ATAATCAAA-TAGGTAGAACTTAT
**
39352 ATAATGTAATAGGTAGAACTTAT
1 ATAATCAAATAGGTAGAACTTAT
*
39375 ATAATAAAATAG
1 ATAATCAAATAG
39387 ACATTTAACC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 27 0.93
24 2 0.07
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (23 bp):
ATAATCAAATAGGTAGAACTTAT
Found at i:39854 original size:65 final size:63
Alignment explanation
Indices: 39678--39858 Score: 193
Period size: 65 Copynumber: 2.8 Consensus size: 63
39668 GAATTAATTG
* *
39678 AACATCGAATGCATTCTATGCATCGATGCACTCTCCATGCATCGATGCACTCGGGTTTAAATACA
1 AACATCGAATGCATTC-ATGCATCGATGCACTCTTCATGCATCGATGCACTCGGCTTT-AATACA
* *** * **
39743 AACATCGAATGCATTTGATGCATCGATGCACAAGTCATGCATCGATGCACTCAGGCTATT-TTTG
1 AACATCGAATGCA-TTCATGCATCGATGCACTCTTCATGCATCGATGCACTC-GGCT-TTAATAC
39807 A
63 A
** *
39808 AACATCGAATGCACTTCATGCATCGATGCACTCTTTGTGCACCGATGCACT
1 AACATCGAATGCA-TTCATGCATCGATGCACTCTTCATGCATCGATGCACT
39859 AGGAGTCCAA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
65 89 0.93
66 5 0.05
67 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTCATGCATCGATGCACTCTTCATGCATCGATGCACTCGGCTTTAATACA
Found at i:44858 original size:23 final size:23
Alignment explanation
Indices: 44828--44891 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
44818 AGCTCATATA
44828 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
44851 AATTGCACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
44874 AAATGCACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
44892 TATAAGGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:46627 original size:21 final size:21
Alignment explanation
Indices: 46603--46652 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
46593 GAGGGGATAT
46603 CGATTCCCATTGAATGGGTAC
1 CGATTCCCATTGAATGGGTAC
*
46624 CGATTTCCATTGAATGGGTAC
1 CGATTCCCATTGAATGGGTAC
46645 CGATTCCC
1 CGATTCCC
46653 CTAGCCCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (21 bp):
CGATTCCCATTGAATGGGTAC
Found at i:54243 original size:14 final size:14
Alignment explanation
Indices: 54224--54255 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
54214 GATCACGTTG
54224 AATTGAATGTAATT
1 AATTGAATGTAATT
54238 AATTGAATGTAATT
1 AATTGAATGTAATT
54252 AATT
1 AATT
54256 CATCCTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (14 bp):
AATTGAATGTAATT
Found at i:66101 original size:24 final size:24
Alignment explanation
Indices: 66073--66176 Score: 118
Period size: 24 Copynumber: 4.3 Consensus size: 24
66063 GAATGTTTTA
*
66073 TCTGATTTCCGATTTGAATTATGT
1 TCTGATTTCTGATTTGAATTATGT
66097 TCTGATTTCTGATTTGAATTATGT
1 TCTGATTTCTGATTTGAATTATGT
* * * *
66121 TTTGATTTCTTATCTGAATTTTGT
1 TCTGATTTCTGATTTGAATTATGT
* * * * *
66145 TCTGATTTATGATATGGATTCTTT
1 TCTGATTTCTGATTTGAATTATGT
66169 TCTGATTT
1 TCTGATTT
66177 GAATTATGTT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.19, C:0.10, G:0.15, T:0.56
Consensus pattern (24 bp):
TCTGATTTCTGATTTGAATTATGT
Done.