Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009628.1 Hibiscus syriacus cultivar Beakdansim tig00117021_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: 2284295
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1316673 original size:27 final size:27
Alignment explanation
Indices: 1316619--1316717 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 27
1316609 TGATGATGAC
* * * *
1316619 GAAGATGATGATGAAGATGACGAAGAT
1 GAAGACGATGATGACGACGACGACGAT
* * * *
1316646 GATGACGAAGATGACGACGATGAGGAT
1 GAAGACGATGATGACGACGACGACGAT
* *
1316673 GAAGACGATGATGACAACGACGACGAC
1 GAAGACGATGATGACGACGACGACGAT
1316700 GAAGACGATGATGACGAC
1 GAAGACGATGATGACGAC
1316718 TAAGACGAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (27 bp):
GAAGACGATGATGACGACGACGACGAT
Found at i:1318950 original size:31 final size:31
Alignment explanation
Indices: 1318913--1318975 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1318903 GCCATTCAAC
1318913 TTATTTAGTTATTTTCACTCAGTACGACCTT
1 TTATTTAGTTATTTTCACTCAGTACGACCTT
*
1318944 TTATTTAGTTATTTTCACTCAGTATGACCTT
1 TTATTTAGTTATTTTCACTCAGTACGACCTT
1318975 T
1 T
1318976 AAATTAAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.51
Consensus pattern (31 bp):
TTATTTAGTTATTTTCACTCAGTACGACCTT
Found at i:1319407 original size:22 final size:22
Alignment explanation
Indices: 1319355--1319407 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1319345 TCAAGAGTTA
** *
1319355 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTACATGATATAATTC
*
1319377 CAAGG-GTTACATGATATAATTT
1 C-AGGAGTTACATGATATAATTC
1319399 CAGGAGTTA
1 CAGGAGTTA
1319408 TAACAGCTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 19 0.76
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (22 bp):
CAGGAGTTACATGATATAATTC
Found at i:1320069 original size:27 final size:27
Alignment explanation
Indices: 1320011--1320071 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
1320001 TCGAGGGCTT
* * *
1320011 CATTAATT-TTTTTAAGAAAAATGAGA
1 CATTATTTATTTTTAAGAAAAATAAAA
*
1320037 C-CTATTTATTTTTAAGAAAAATAAAA
1 CATTATTTATTTTTAAGAAAAATAAAA
1320063 CATTATTTA
1 CATTATTTA
1320072 AATTTCAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 4 0.14
26 18 0.64
27 6 0.21
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (27 bp):
CATTATTTATTTTTAAGAAAAATAAAA
Found at i:1321336 original size:12 final size:12
Alignment explanation
Indices: 1321319--1321343 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1321309 TTATGCATTG
1321319 AGACATCAAATT
1 AGACATCAAATT
1321331 AGACATCAAATT
1 AGACATCAAATT
1321343 A
1 A
1321344 ACCTAGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
AGACATCAAATT
Found at i:1321643 original size:31 final size:31
Alignment explanation
Indices: 1321605--1321668 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1321595 CTTACAAACT
1321605 CATATTCATAAATCTCAACCACTTGTGCCAA
1 CATATTCATAAATCTCAACCACTTGTGCCAA
*
1321636 CATATTCATGAATCTCAACCACTTGTGCCAA
1 CATATTCATAAATCTCAACCACTTGTGCCAA
1321667 CA
1 CA
1321669 GTCATTGGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.30, G:0.08, T:0.28
Consensus pattern (31 bp):
CATATTCATAAATCTCAACCACTTGTGCCAA
Found at i:1322227 original size:23 final size:23
Alignment explanation
Indices: 1322200--1322253 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1322190 AAAATAAAAA
* *
1322200 AAACGTGGCACAAAGATAGAGAT
1 AAACGTGCCACAAAGACAGAGAT
1322223 AAACGTGCCACAAAGACAGAGAT
1 AAACGTGCCACAAAGACAGAGAT
1322246 AAACGTGC
1 AAACGTGC
1322254 AACACATGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (23 bp):
AAACGTGCCACAAAGACAGAGAT
Found at i:1329210 original size:25 final size:25
Alignment explanation
Indices: 1329182--1329234 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1329172 ACTAATAAAG
1329182 ATAAGATCTAATATAATAAATTATT
1 ATAAGATCTAATATAATAAATTATT
* * *
1329207 ATAATATTTATTATAATAAATTATT
1 ATAAGATCTAATATAATAAATTATT
1329232 ATA
1 ATA
1329235 CAATCGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
ATAAGATCTAATATAATAAATTATT
Found at i:1329219 original size:12 final size:13
Alignment explanation
Indices: 1329193--1329234 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
1329183 TAAGATCTAA
1329193 TATAATAAATTAT
1 TATAATAAATTAT
*
1329206 TATAAT-ATTTAT
1 TATAATAAATTAT
1329218 TATAATAAATTAT
1 TATAATAAATTAT
1329231 TATA
1 TATA
1329235 CAATCGTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATAATAAATTAT
Found at i:1329343 original size:12 final size:11
Alignment explanation
Indices: 1329311--1329345 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1329301 AAAATTATTT
1329311 TTTTATAATTA
1 TTTTATAATTA
*
1329322 TTTAATAATTA
1 TTTTATAATTA
1329333 CTTTTATAATTA
1 -TTTTATAATTA
1329345 T
1 T
1329346 AATATTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTATAATTA
Found at i:1345455 original size:19 final size:19
Alignment explanation
Indices: 1345431--1345479 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1345421 GGTGATTTGT
1345431 GTATCGATGCATGAGTAGG
1 GTATCGATGCATGAGTAGG
1345450 GTATCGATGCATGAGTAGG
1 GTATCGATGCATGAGTAGG
*
1345469 GCATCGATGCA
1 GTATCGATGCA
1345480 CATATTAAAG
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:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (19 bp):
GTATCGATGCATGAGTAGG
Found at i:1347018 original size:23 final size:23
Alignment explanation
Indices: 1346950--1347010 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1346940 ATATTTTATA
1346950 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1346973 CGGCACTTCAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1346996 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1347011 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1357291 original size:12 final size:13
Alignment explanation
Indices: 1357246--1357291 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
1357236 ATATAAATAG
*
1357246 TTAATTAAATCAA
1 TTAATTAAATTAA
1357259 TTAATTAAATTAA
1 TTAATTAAATTAA
*
1357272 TTGA-TAAATTAA
1 TTAATTAAATTAA
1357284 TT-ATTAAA
1 TTAATTAAA
1357292 ATTATCTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 1 0.03
12 14 0.47
13 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (13 bp):
TTAATTAAATTAA
Found at i:1361110 original size:20 final size:19
Alignment explanation
Indices: 1361063--1361111 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1361053 GTGTATATAT
*
1361063 TTATTTATTTTTATTTTCA
1 TTATATATTTTTATTTTCA
*
1361082 TTATTTATTTTATATTTT-A
1 TTATATATTTT-TATTTTCA
1361101 TGTATATATTT
1 T-TATATATTT
1361112 AATTATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTATATATTTTTATTTTCA
Found at i:1361237 original size:17 final size:17
Alignment explanation
Indices: 1361215--1361247 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1361205 TTTTTGTCTT
1361215 TATTATT-TATATATATA
1 TATTATTGTAT-TATATA
1361232 TATTATTGTATTATAT
1 TATTATTGTATTATAT
1361248 TACATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTATTGTATTATATA
Found at i:1368132 original size:13 final size:13
Alignment explanation
Indices: 1368114--1368141 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1368104 ACAAACGCAT
1368114 GATTTTATGTTGG
1 GATTTTATGTTGG
1368127 GATTTTATGTTGG
1 GATTTTATGTTGG
1368140 GA
1 GA
1368142 GGGCGAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (13 bp):
GATTTTATGTTGG
Found at i:1381668 original size:34 final size:34
Alignment explanation
Indices: 1381625--1381703 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
1381615 CTCTTCACAA
1381625 GTAAAACTATATGAAGGTAGCACGTTGAGGAAAT
1 GTAAAACTATATGAAGGTAGCACGTTGAGGAAAT
*
1381659 GTAAAACTATATGAAGGTTGCACGTTGAGGAAAT
1 GTAAAACTATATGAAGGTAGCACGTTGAGGAAAT
* *
1381693 GCAAAAATATA
1 GTAAAACTATA
1381704 AGGGTTTTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (34 bp):
GTAAAACTATATGAAGGTAGCACGTTGAGGAAAT
Found at i:1384181 original size:20 final size:20
Alignment explanation
Indices: 1384153--1384205 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1384143 GATTTTCCAG
* *
1384153 AATCACAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
1384173 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
1384193 AATCGCAACGCGA
1 AATCGCAACGCGA
1384206 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:1384256 original size:61 final size:61
Alignment explanation
Indices: 1384214--1384364 Score: 196
Period size: 61 Copynumber: 2.5 Consensus size: 61
1384204 GATTCTGACT
1384214 ATCGCAAAGAGTATCCGTAAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAAAGAGTATCCGT-AAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
* * * * * *
1384276 ATCGCAACGCGTGTCCGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT-AA
1 ATCGCAAAGAGTATCCGTAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
* * * *
1384336 ATCGTAATGCGTATCCGTAAATCTCAACG
1 ATCGCAAAGAGTATCCGTAAATCACAACG
1384365 ACAATACGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 27 0.34
61 37 0.47
62 15 0.19
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (61 bp):
ATCGCAAAGAGTATCCGTAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
Found at i:1384259 original size:41 final size:40
Alignment explanation
Indices: 1384214--1384408 Score: 176
Period size: 41 Copynumber: 4.8 Consensus size: 40
1384204 GATTCTGACT
* * * *
1384214 ATCGCAAAGAGTATCCGTAAAATCACAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGT-AAATCGCAACGCGAATACGTAA
** * ** *
1384255 ATCGCAACGACAATACGTAAAATCGCAACGCGTGTCCGTAA
1 ATCGCAACGAGTATCCGT-AAATCGCAACGCGAATACGTAA
* * *
1384296 ATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAAATCGCAACGCGAATACGTAA
* * * *
1384336 ATCGTAATGCGTATCCGTAAATCTCAACGAC-AATACGTAAA
1 ATCGCAACGAGTATCCGTAAATCGCAACG-CGAATACGT-AA
* *
1384377 ATTGCAACGTGTATCCGTAAATCGCAACGCGA
1 ATCGCAACGAGTATCCGTAAATCGCAACGCGA
1384409 TTTTTAAAGC
Statistics
Matches: 126, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
40 51 0.40
41 75 0.60
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAGTATCCGTAAATCGCAACGCGAATACGTAA
Found at i:1384262 original size:20 final size:20
Alignment explanation
Indices: 1384214--1384407 Score: 176
Period size: 20 Copynumber: 9.6 Consensus size: 20
1384204 GATTCTGACT
* *
1384214 ATCGCAAAGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
1384235 ATCACAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
1384255 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
1384276 ATCGCAACGCGTGTCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
1384296 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1384316 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* *
1384336 ATCGTAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1384356 ATCTCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
* *
1384377 ATTGCAACGTGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
1384397 ATCGCAACGCG
1 ATCGCAACGCG
1384408 ATTTTTAAAG
Statistics
Matches: 135, Mismatches: 32, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
20 89 0.66
21 46 0.34
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:1385059 original size:33 final size:35
Alignment explanation
Indices: 1385017--1385116 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 35
1385007 CAAAATCGCA
1385017 TTGCGATTTTCATTTCGCGTTGCGATTC-TCT-CG
1 TTGCGATTTTCATTTCGCGTTGCGATTCATCTGCG
* *
1385050 TTGCGATTTTCATTTCGCATTGCGATAGTCATTTGAGCG
1 TTGCGATTTTCATTTCGCGTTGCGAT--TCATCT--GCG
*
1385089 TTGCGATTTTCATTCTCTCGTTGCGATT
1 TTGCGATTTTCATT-TCGCGTTGCGATT
1385117 TTTATTTCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
33 25 0.45
35 2 0.04
36 2 0.04
38 1 0.02
39 16 0.29
40 10 0.18
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (35 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCATCTGCG
Found at i:1385101 original size:20 final size:19
Alignment explanation
Indices: 1385017--1385123 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 19
1385007 CAAAATCGCA
*
1385017 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTAGCG
*
1385036 TTGCGA--TTC-TCT--CG
1 TTGCGATTTTCATTTAGCG
* *
1385050 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTAGCG
**
1385069 TTGCGATAGTCATTTGAGCG
1 TTGCGATTTTCATTT-AGCG
**
1385089 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TAGCG
*
1385109 TTGCGATTTTTATTT
1 TTGCGATTTTCATTT
1385124 CAACCAAAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
14 8 0.12
16 5 0.07
17 5 0.07
19 21 0.30
20 29 0.42
21 1 0.01
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTAGCG
Found at i:1386955 original size:94 final size:94
Alignment explanation
Indices: 1386813--1387181 Score: 530
Period size: 94 Copynumber: 4.1 Consensus size: 94
1386803 TAGATTGCTT
* * *
1386813 AGTAAATTTATCCGGTTGCTGCCAATACTGCTAAACTGTCTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1386878 ATTTGTCTTTTATTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTATTTTGTCTTTTGGTTGAA
*
1386907 AGTAAATTTATTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1386972 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTATTTTGTCTTTTGGTTGAA
* * *
1387001 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATTTATTCTTTAACACTGTGAAG-T--T
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1387063 A---G----TA-TTTGTCTTTTGGTTGAA
66 ATTTGTCTTTATTTTGTCTTTTGGTTGAA
* * *
1387084 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1387149 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTATTTTGTCTTTTGGTTGAA
1387177 AGTAA
1 AGTAA
1387182 TGCAATCCAT
Statistics
Matches: 248, Mismatches: 15, Indels: 25
0.86 0.05 0.09
Matches are distributed among these distances:
83 73 0.29
84 2 0.01
86 2 0.01
88 1 0.00
89 1 0.00
91 2 0.01
93 27 0.11
94 140 0.56
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTATTTTGTCTTTTGGTTGAA
Found at i:1387128 original size:83 final size:83
Alignment explanation
Indices: 1386984--1387158 Score: 314
Period size: 83 Copynumber: 2.1 Consensus size: 83
1386974 TTGTCTTTGT
*
1386984 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATTTATTCTTT
1 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTT
*
1387049 AACACTGTGAAGTTAGTA
66 AACACTCTGAAGTTAGTA
*
1387067 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTT
*
1387132 AATACTCTGAAGTTAGTA
66 AACACTCTGAAGTTAGTA
1387150 TTTGTCTTT
1 TTTGTCTTT
1387159 GTTTTGTCTT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 88 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (83 bp):
TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTT
AACACTCTGAAGTTAGTA
Found at i:1387215 original size:19 final size:17
Alignment explanation
Indices: 1387191--1387249 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 17
1387181 ATGCAATCCA
1387191 TGCGATTTTCATTTCGTAT
1 TGCGATTTTCATTTCG--T
*
1387210 TGCGA--TTC-TCTCGT
1 TGCGATTTTCATTTCGT
1387224 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTT--CGT
1387243 TGCGATT
1 TGCGATT
1387250 CTCTCATTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 5 0.15
19 15 0.45
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (17 bp):
TGCGATTTTCATTTCGT
Found at i:1387228 original size:14 final size:14
Alignment explanation
Indices: 1387209--1387297 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
1387199 TCATTTCGTA
1387209 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1387223 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
*
1387242 TTGCGATTCTCTCA
1 TTGCGATTCTCTCG
*
1387256 TTGCGAATTTCATTTCGCG
1 TTGCG-A-TTC---TCTCG
*
1387275 TTGCGATTATCTCG
1 TTGCGATTCTCTCG
1387289 TTGCGATTC
1 TTGCGATTC
1387298 ATTTCGCGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
14 26 0.46
15 1 0.02
16 6 0.11
17 5 0.09
18 1 0.02
19 18 0.32
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1387233 original size:33 final size:33
Alignment explanation
Indices: 1387191--1387312 Score: 185
Period size: 33 Copynumber: 3.8 Consensus size: 33
1387181 ATGCAATCCA
**
1387191 TGCGATTTTCATTTCGTATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1387224 TGCGATTTTCATTTCGCGTTGCGATTCTCTCAT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
* *
1387257 TGCGAATTTCATTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1387290 TGCGA--TTCATTTCGCGTTGCGAT
1 TGCGATTTTCATTTCGCGTTGCGAT
1387313 AGTCATTTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 18 0.22
33 65 0.78
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1387280 original size:19 final size:17
Alignment explanation
Indices: 1387221--1387312 Score: 79
Period size: 14 Copynumber: 5.5 Consensus size: 17
1387211 GCGATTCTCT
1387221 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTCATTTCG
*
1387240 CGTTGCGATTC---TCT
1 CGTTGCGATTCATTTCG
*
1387254 CATTGCGAATTTCATTTCG
1 CGTTGCG-A-TTCATTTCG
*
1387273 CGTTGCGATT-A--TCT
1 CGTTGCGATTCATTTCG
1387287 CGTTGCGATTCATTTCG
1 CGTTGCGATTCATTTCG
1387304 CGTTGCGAT
1 CGTTGCGAT
1387313 AGTCATTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 16 0.27
18 1 0.02
19 16 0.27
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (17 bp):
CGTTGCGATTCATTTCG
Found at i:1387813 original size:42 final size:42
Alignment explanation
Indices: 1387737--1387825 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1387727 GACTCGCCTG
* * *
1387737 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
1387779 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
1387821 TCATC
1 TCATC
1387826 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:1389355 original size:19 final size:19
Alignment explanation
Indices: 1389333--1389391 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
1389323 AAAAATGACT
1389333 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1389352 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1389366 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1389385 ACCGCAA
1 ATCGCAA
1389392 CGACAAAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 15 0.50
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1389379 original size:33 final size:33
Alignment explanation
Indices: 1389337--1389422 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
1389327 ATGACTATCG
* *
1389337 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
* *
1389370 CAATGCGAAATGAAAACCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
* * *
1389403 CAACGCGAAATTAAATTCGC
1 CAATGCGAAATGAAAATCGC
1389423 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:1389440 original size:19 final size:19
Alignment explanation
Indices: 1389418--1389522 Score: 112
Period size: 19 Copynumber: 5.7 Consensus size: 19
1389408 CGAAATTAAA
1389418 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1389437 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1389452 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1389470 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
1389489 TTCCGCGTTGCGATTTTCAT
1 TT-CGCGTTGCGATTTTCAT
*
1389509 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
1389523 CTCTCGTTGC
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
14 9 0.13
16 3 0.04
17 3 0.04
19 38 0.55
20 16 0.23
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1389464 original size:33 final size:33
Alignment explanation
Indices: 1389422--1389535 Score: 156
Period size: 33 Copynumber: 3.3 Consensus size: 33
1389412 ATTAAATTCG
*
1389422 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1389455 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
1389494 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1389527 CGTTGCGAT
1 CGTTGCGAT
1389536 AGTAATTTCC
Statistics
Matches: 72, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
33 37 0.51
34 1 0.01
35 2 0.03
37 2 0.03
38 1 0.01
39 29 0.40
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1389501 original size:20 final size:19
Alignment explanation
Indices: 1389418--1389562 Score: 85
Period size: 19 Copynumber: 8.1 Consensus size: 19
1389408 CGAAATTAAA
**
1389418 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTCAT
*
1389437 TTCGCTTTGCGAT--TC--
1 TTCGCGTTGCGATAGTCAT
* **
1389452 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTCAT
*
1389470 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATAGTCAT
**
1389489 TTCCGCGTTGCGATTTTCAT
1 TT-CGCGTTGCGATAGTCAT
*
1389509 TTCGCATTGCGAT--TC--
1 TTCGCGTTGCGATAGTCAT
* *
1389524 -TCTCGTTGCGATAGTAAT
1 TTCGCGTTGCGATAGTCAT
*
1389542 TTCCGCGTTGCGATAGACAT
1 TT-CGCGTTGCGATAGTCAT
1389562 T
1 T
1389563 AAGATGATTG
Statistics
Matches: 97, Mismatches: 17, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
14 20 0.21
16 3 0.03
17 4 0.04
19 39 0.40
20 31 0.32
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTCAT
Found at i:1389506 original size:72 final size:73
Alignment explanation
Indices: 1389420--1389562 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 73
1389410 AAATTAAATT
* ** *
1389420 CGCGTTGCGATTTTCATTTCGCTTTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATA
1 CGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCGATA
*
1389484 GTCATTTC
66 GACATTTC
*
1389492 CGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCGTTGCGATA
1 CGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCGATA
1389557 GACATT
66 GACATT
1389563 AAGATGATTG
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
72 48 0.75
73 16 0.25
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (73 bp):
CGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCGATA
GACATTTC
Found at i:1389601 original size:20 final size:20
Alignment explanation
Indices: 1389455--1389601 Score: 80
Period size: 20 Copynumber: 7.7 Consensus size: 20
1389445 GCGATTCTCT
**
1389455 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
1389474 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
**
1389494 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
1389513 CATTGCGAT--TC---T-CT
1 CGTTGCGATAGTCATTTCCG
*
1389527 CGTTGCGATAGTAATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
1389547 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
1389566 ATGATTGCGA-ATGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
1389588 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1389602 AATGAATGCC
Statistics
Matches: 97, Mismatches: 19, Indels: 23
0.70 0.14 0.17
Matches are distributed among these distances:
14 10 0.10
16 1 0.01
17 2 0.02
19 28 0.29
20 41 0.42
21 12 0.12
22 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1392110 original size:24 final size:24
Alignment explanation
Indices: 1392072--1392125 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1392062 CTGAAAAATC
1392072 ATCAAAATCCAAGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
* *
1392096 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
1392120 ATCAAA
1 ATCAAA
1392126 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCAAGTATTGACCAAG
Found at i:1393018 original size:20 final size:19
Alignment explanation
Indices: 1392987--1393031 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
1392977 CATAATCTCG
1392987 TTGCGATTACGTATTCGCA
1 TTGCGATTACGTATTCGCA
*
1393006 TTGCGATTTACGTATTCGTA
1 TTGCGA-TTACGTATTCGCA
1393026 TTGCGA
1 TTGCGA
1393032 ATTAGGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (19 bp):
TTGCGATTACGTATTCGCA
Found at i:1393054 original size:21 final size:21
Alignment explanation
Indices: 1393028--1393073 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1393018 TATTCGTATT
1393028 GCGAATTAGGAAAATCACAAC
1 GCGAATTAGGAAAATCACAAC
* * * *
1393049 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCACAAC
1393070 GCGA
1 GCGA
1393074 TAGTAAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCACAAC
Found at i:1410938 original size:44 final size:44
Alignment explanation
Indices: 1410838--1410918 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
1410828 TCGGGATGGG
1410838 TATATA-T-ATTTAAATTAAATATATAAATATTATATATATATA
1 TATATATTAATTTAAATTAAATATATAAATATTATATATATATA
* *
1410880 TATATATTAATTTAAATTAAATTTATTAATA-TATATATA
1 TATATATTAATTTAAATTAAATATATAAATATTATATATA
1410919 ATAATAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
42 6 0.17
43 9 0.26
44 20 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (44 bp):
TATATATTAATTTAAATTAAATATATAAATATTATATATATATA
Found at i:1410960 original size:12 final size:12
Alignment explanation
Indices: 1410943--1410968 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1410933 TTTTAATATT
1410943 TATCGGGCCGGG
1 TATCGGGCCGGG
1410955 TATCGGGCCGGG
1 TATCGGGCCGGG
1410967 TA
1 TA
1410969 ATCAGGGCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.19
Consensus pattern (12 bp):
TATCGGGCCGGG
Found at i:1412443 original size:19 final size:18
Alignment explanation
Indices: 1412412--1412460 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1412402 ACCTAATTTA
*
1412412 TTGATTATTGACTTTGATTG
1 TTGATT-TTGACTTT-ATTC
1412432 TTGATTTTGACTTTATTC
1 TTGATTTTGACTTTATTC
1412450 TATGATTTTGA
1 T-TGATTTTGA
1412461 TCTATTGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 17 0.63
20 6 0.22
ACGTcount: A:0.20, C:0.06, G:0.16, T:0.57
Consensus pattern (18 bp):
TTGATTTTGACTTTATTC
Found at i:1414799 original size:19 final size:19
Alignment explanation
Indices: 1414775--1414816 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1414765 TAAATAACTT
*
1414775 ATAAATGTTAGTATTATTA
1 ATAAATGTTAATATTATTA
1414794 ATAAATGTTAATATTATTA
1 ATAAATGTTAATATTATTA
1414813 ATAA
1 ATAA
1414817 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (19 bp):
ATAAATGTTAATATTATTA
Found at i:1415943 original size:3 final size:3
Alignment explanation
Indices: 1415935--1415970 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1415925 TCAAGAAACA
* *
1415935 AAT AAT AAT AAT AAT AAT ATT AAA AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1415971 CTACATTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1418604 original size:109 final size:109
Alignment explanation
Indices: 1418404--1418625 Score: 363
Period size: 109 Copynumber: 2.0 Consensus size: 109
1418394 CATTTTCAAA
*
1418404 GTTTATTTGCTTAAGAAATGTGATTGCCTAGGGATCTCTTTTATAGCATACTTCCCTTTTGTTCT
1 GTTTATTTGCTTAAGAAATGTGATTGCCTAGGGATCTCTTTTATAGCATACTTCCCTTTTGCTCT
* * *
1418469 TAATCTTTTGCCTTCATATTGAATGCTGCAACCATGATCTTCTT
66 TAATCTTTTGCCTTAATATCGAATGCTGCAACCATGAGCTTCTT
* * * *
1418513 GTTTATTTGTTTAAGAAATGTGATTTCCTAGGGATCTCTTTTATCGCATAGTTCCCTTTTGCTCT
1 GTTTATTTGCTTAAGAAATGTGATTGCCTAGGGATCTCTTTTATAGCATACTTCCCTTTTGCTCT
*
1418578 TAATCTTTTGCCTTAATATCGGATGCTGCAACCATGAGCTTCTT
66 TAATCTTTTGCCTTAATATCGAATGCTGCAACCATGAGCTTCTT
1418622 GTTT
1 GTTT
1418626 GCTTGATCAT
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (109 bp):
GTTTATTTGCTTAAGAAATGTGATTGCCTAGGGATCTCTTTTATAGCATACTTCCCTTTTGCTCT
TAATCTTTTGCCTTAATATCGAATGCTGCAACCATGAGCTTCTT
Found at i:1436350 original size:21 final size:21
Alignment explanation
Indices: 1436326--1436368 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1436316 TGGATTAAAC
1436326 ATTATAACAACATTTACGATA
1 ATTATAACAACATTTACGATA
** *
1436347 ATTATATTAATATTTACGATA
1 ATTATAACAACATTTACGATA
1436368 A
1 A
1436369 CAATATTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTATAACAACATTTACGATA
Found at i:1443505 original size:55 final size:55
Alignment explanation
Indices: 1443417--1443735 Score: 262
Period size: 55 Copynumber: 5.8 Consensus size: 55
1443407 ATGAGGGATT
* * ***
1443417 TGCTCCCTCTTTCTTTCAG-GAAGTATAGAACTCGAATAATCTTTTGTAATCGGGTC
1 TGCTCCCTATTTC-TTCAGAG-AGTATAGAACTCGAACAATCTTCAATAATCGGGTC
* * ** *
1443473 TGCTCTCTATTACTTCAGAGAGTAT-GAGACTCGAACAATCTTCAATAATCATGTA
1 TGCTCCCTATTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAATCGGGTC
* *
1443528 TGCTCCCTATTTCTTTAGAGAGTATA-AGACTCGAACAATCTTCAATAAACGGGT-
1 TGCTCCCTATTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAATCGGGTC
* * * **
1443582 TCGCTCCATCTTTCTTTCAG-GAAGTATAGAACTCGAATAATCTTCTGTAATCGGGTC
1 T-GCTCCCTATTTC-TTCAGAG-AGTATAGAACTCGAACAATCTTCAATAATCGGGTC
* * **
1443639 TGCTCCCTATTTCTTCAGAGAGTATGGAACTCGAAC-ATCTTC-TTCTTACGGGT-
1 TGCTCCCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAT-CGGGTC
* * *
1443692 TCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAAC-ATCTTCA
1 T-GCTCCCTATTTCTTC-AGAGAGTATAGAACTCGAACAATCTTCA
1443736 TCTTACAAGT
Statistics
Matches: 218, Mismatches: 32, Indels: 27
0.79 0.12 0.10
Matches are distributed among these distances:
53 5 0.02
54 50 0.23
55 107 0.49
56 54 0.25
57 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (55 bp):
TGCTCCCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAATCGGGTC
Found at i:1443616 original size:111 final size:106
Alignment explanation
Indices: 1443492--1444058 Score: 618
Period size: 108 Copynumber: 5.2 Consensus size: 106
1443482 TTACTTCAGA
*
1443492 GAGTAT-GAGACTCGAACAATCTTCAATAATCATGTATGCTCCCTATTTCTTTAGAGAGTATA-A
1 GAGTATGGA-ACTCGAAC-ATCTTC-ATAATCAAGT-TGCTCCCTATTTCTTTAGAGAGTATAGA
* ** * *
1443555 GACTCGAACAATCTTCAAT-AAACGGGTTCGCTCCATCTTTCTTTCAGG
62 -ACTCGAAC-ATCTTC-TTCTTACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * * ** * *
1443603 AAGTATAGAACTCGAATAATCTTCTGTAATCGGGTCTGCTCCCTATTTCTTCAGAGAGTATGGAA
1 GAGTATGGAACTCGAA-CATCTTC-ATAATCAAGT-TGCTCCCTATTTCTTTAGAGAGTATAGAA
1443668 CTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
63 CTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
** * * * *
1443712 GAGTATGGAACTCGAACATCTTCATCTTACAAGTTCGCTCCCTCTTTCTCTAGGGAGTATTGAAC
1 GAGTATGGAACTCGAACATCTTCATAAT-CAAGTT-GCTCCCTATTTCTTTAGAGAGTATAGAAC
1443777 TCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
64 TCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* ** * * * * *
1443820 GAGTATGGAACTCGAACATCTTCTTCTTACAGGTTCTCTCCCTCTTTCTCTAGAGAGTATGGAAC
1 GAGTATGGAACTCGAACATCTTCATAAT-CAAGTT-GCTCCCTATTTCTTTAGAGAGTATAGAAC
1443885 TCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
64 TCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * ** ** * * * *
1443928 GAGTATGAAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
1 GAGTATGGAACTCGAACATCTTCATAAT-CAAGTT-GCTCCCTATTTCTTTAGAGAGTATAGAAC
1443993 TCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
64 TCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1444036 GAGTATGGAACTCGAACATCTTC
1 GAGTATGGAACTCGAACATCTTC
1444059 TTCTGCTTTA
Statistics
Matches: 413, Mismatches: 37, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
107 3 0.01
108 305 0.74
109 18 0.04
110 27 0.07
111 57 0.14
112 3 0.01
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (106 bp):
GAGTATGGAACTCGAACATCTTCATAATCAAGTTGCTCCCTATTTCTTTAGAGAGTATAGAACTC
GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:1443700 original size:54 final size:54
Alignment explanation
Indices: 1443576--1444062 Score: 755
Period size: 54 Copynumber: 9.0 Consensus size: 54
1443566 TCTTCAATAA
* * * * * * *
1443576 ACGGGTTCGCTCCATCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTC-TGTA
1 ACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAA-CATCTTCTTCTT
* *
1443631 ATCGGG-TCTGCTCCCTATTTCT-TCAGAGAGTATGGAACTCGAACATCTTCTTCTT
1 A-CGGGTTC-GCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACATCTTCTTCTT
*
1443686 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCATCTT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
** *
1443740 ACAAGTTCGCTCCCTCTTTCTCTAGGGAGTATTGAACTCGAACATCTTCTTCTT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
1443794 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
* * *
1443848 ACAGGTTCTCTCCCTCTTTCTCTAGAGAGTATGGAACTCGAACATCTTCTTCTT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
*
1443902 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATCTTCTTCTT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
1443956 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
1444010 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCT
1444063 GCTTTACTAC
Statistics
Matches: 401, Mismatches: 26, Indels: 11
0.92 0.06 0.03
Matches are distributed among these distances:
54 359 0.90
55 27 0.07
56 15 0.04
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.35
Consensus pattern (54 bp):
ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
Found at i:1444135 original size:37 final size:37
Alignment explanation
Indices: 1444062--1444141 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
1444052 CATCTTCTTC
* * * *
1444062 TGCTTTACTACTTTCTTGTGAAGACTTTTAGATGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTTAAGATGATT
*
1444099 TGCTTCACTACTCTCTCGTGAAGAC-TTAAGTTTGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTTAAG-ATGATT
1444136 TGCTTC
1 TGCTTC
1444142 TAAGGTCGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 4 0.11
37 33 0.89
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (37 bp):
TGCTTCACTACTCTCTCGTGAAGACTTTAAGATGATT
Found at i:1444490 original size:37 final size:37
Alignment explanation
Indices: 1444439--1444562 Score: 169
Period size: 37 Copynumber: 3.4 Consensus size: 37
1444429 TTGCTCCAAC
* * * *
1444439 ACTCTTTCGAGAAGGCTTAAAAAGGATATGCTTCACT
1 ACTCTTTGGTGAAGGCTTAAAATGGATTTGCTTCACT
* *
1444476 ACTCTTCGGTGAAGGCTTAAGATGG-TTTGCTTCACT
1 ACTCTTTGGTGAAGGCTTAAAATGGATTTGCTTCACT
* *
1444512 ACTCTTTGGTGAAAGCTCAAAATGGATTTGCTTCACT
1 ACTCTTTGGTGAAGGCTTAAAATGGATTTGCTTCACT
1444549 ACTCTTTGGTGAAG
1 ACTCTTTGGTGAAG
1444563 ACTTGACTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
36 31 0.41
37 44 0.59
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (37 bp):
ACTCTTTGGTGAAGGCTTAAAATGGATTTGCTTCACT
Found at i:1444546 original size:73 final size:73
Alignment explanation
Indices: 1444423--1444562 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
1444413 CTGATAGTCT
* *
1444423 GATGGTTTGCTCCAACACTCTTTCGAGAAGGCTTAAAAAGGATATGCTTCACTACTCTTCGGTGA
1 GATGGTTTGCTCCAACACTCTTTCGAGAAAGCTCAAAAAGGATATGCTTCACTACTCTTCGGTGA
1444488 AGGCTTAA
66 AGGCTTAA
* * * * * *
1444496 GATGGTTTGCTTC-ACTACTCTTTGGTGAAAGCTCAAAATGGATTTGCTTCACTACTCTTTGGTG
1 GATGGTTTGCTCCAAC-ACTCTTTCGAGAAAGCTCAAAAAGGATATGCTTCACTACTCTTCGGTG
1444560 AAG
65 AAG
1444563 ACTTGACTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 2 0.03
73 56 0.97
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (73 bp):
GATGGTTTGCTCCAACACTCTTTCGAGAAAGCTCAAAAAGGATATGCTTCACTACTCTTCGGTGA
AGGCTTAA
Found at i:1449475 original size:72 final size:72
Alignment explanation
Indices: 1449384--1449534 Score: 275
Period size: 72 Copynumber: 2.1 Consensus size: 72
1449374 CCCCTAACAG
*
1449384 GTTCTTGATCAGTTGCTATCATCATATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1449449 TTCATCT
66 TTCATCT
*
1449456 GTTCTTGATCATTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1449521 TTCATCT
66 TTCATCT
*
1449528 TTTCTTG
1 GTTCTTG
1449535 TGTAATAGGG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (72 bp):
GTTCTTGATCAGTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATCT
Found at i:1450645 original size:47 final size:47
Alignment explanation
Indices: 1450582--1450680 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 47
1450572 TGTTATTTGC
* *
1450582 AAAAAAAATCCTAACCGCATGATATCTAATTCGCATGC-TTGTTCGA
1 AAAAAAAAACCTAACCGCATGATATCTAATTCGCATGCATTATTCGA
* *
1450628 AAAAAATAAACCTAACCGCATGATATTTAGTTCGCATGCATTTATTCGA
1 AAAAAA-AAACCTAACCGCATGATATCTAATTCGCATGCA-TTATTCGA
1450677 AAAA
1 AAAA
1450681 CGAAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
46 6 0.13
47 29 0.63
49 11 0.24
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (47 bp):
AAAAAAAAACCTAACCGCATGATATCTAATTCGCATGCATTATTCGA
Found at i:1454621 original size:3 final size:3
Alignment explanation
Indices: 1454615--1454654 Score: 62
Period size: 3 Copynumber: 12.7 Consensus size: 3
1454605 ATATTTATAT
1454615 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA T-TA TT
1454655 CCAGGCTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1455173 original size:32 final size:33
Alignment explanation
Indices: 1455104--1455173 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
1455094 AAAAAAAGAG
*
1455104 ACAGAGAGCAACGAAGGCAGTAACCAACAGACC
1 ACAGAGAGCAACGAAGGCAGTAACCAACAGACA
1455137 ACAGAGAGCAACGAA-G-AG-ATACCGAACAGACA
1 ACAGAGAGCAACGAAGGCAGTA-ACC-AACAGACA
1455169 ACAGA
1 ACAGA
1455174 AAACAGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 1 0.03
31 5 0.15
32 13 0.38
33 15 0.44
ACGTcount: A:0.49, C:0.24, G:0.24, T:0.03
Consensus pattern (33 bp):
ACAGAGAGCAACGAAGGCAGTAACCAACAGACA
Found at i:1455546 original size:7 final size:7
Alignment explanation
Indices: 1455536--1455560 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1455526 AGAGAGAAGA
1455536 GAGAAAT
1 GAGAAAT
1455543 GAGAAAT
1 GAGAAAT
1455550 GAGAAAT
1 GAGAAAT
1455557 GAGA
1 GAGA
1455561 TGCTGGCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.32, T:0.12
Consensus pattern (7 bp):
GAGAAAT
Found at i:1456022 original size:23 final size:22
Alignment explanation
Indices: 1455974--1456033 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
1455964 CAATTTTATT
* *
1455974 TTATTGTTATATATTTAAATTAA
1 TTATTATTAT-TATTTAAATCAA
*
1455997 TTATTATTATTATTTTAATCATA
1 TTATTATTATTATTTAAATCA-A
*
1456020 TTAATA-TATTATTT
1 TTATTATTATTATTT
1456034 GATTAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTATTATTATTTAAATCAA
Found at i:1456335 original size:140 final size:140
Alignment explanation
Indices: 1456065--1456327 Score: 327
Period size: 140 Copynumber: 1.9 Consensus size: 140
1456055 TATAACAATG
* * * * *
1456065 TTTATTTATTTTTTAATATCAAAGAAAAGGGCAGTCTTAAAGCAACTAGATGTCTGTTTTCTGAT
1 TTTATTTATTTTTTAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCTCTTTTATGAT
* * * * *** *
1456130 ATTTTTAAATAAATAAATATTTTACTTTTATAAATTGTATATATTAATCTATTTTTTTAGATAAA
66 ATTTCTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAAAATTATAGATAAA
1456195 TGTTTTAATA
131 TGTTTTAATA
* * *
1456205 TTTATTTATTTTTTAATATCAAAGGAAAGAGCTGTCTTAAAACACCTAGAAG-CTCTTTTATGAT
1 TTTATTTATTTTTTAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCTCTTTTATGAT
*
1456269 ATTTCTAAATAAATAAATATCTTA-TTTATATAAATTAATAAAT-TTACT-TAAAATTATAG
66 ATTTCTAAATAAATAAATATCTTACTTT-TATAAATT-ATAAATATTAATCTAAAATTATAG
1456328 TAATAAATTT
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
138 10 0.10
139 44 0.42
140 50 0.48
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (140 bp):
TTTATTTATTTTTTAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCTCTTTTATGAT
ATTTCTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAAAATTATAGATAAA
TGTTTTAATA
Found at i:1458501 original size:14 final size:14
Alignment explanation
Indices: 1458463--1458516 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
1458453 ATTTTAAATA
*
1458463 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
1458477 TTTTACATTTGCAT
1 ATTTACATTTGCAT
1458491 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
1458506 CTTTGCATTTG
1 ATTTACATTTG
1458517 TAATTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:1462093 original size:3 final size:3
Alignment explanation
Indices: 1462085--1462143 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
1462075 ATATTTATAT
* *
1462085 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA ATA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1462134 TTA TATA TTA
1 TTA T-TA TTA
1462144 CAGACACAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1463480 original size:22 final size:21
Alignment explanation
Indices: 1463450--1463503 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1463440 TATTTTATTG
1463450 TTATATATTTAAATTAATAATAA
1 TTAT-TATTTAAA-TAATAATAA
* * *
1463473 TTATTATTTTAATCATATTAA
1 TTATTATTTAAATAATAATAA
1463494 TATATTATTT
1 T-TATTATTT
1463504 GATTAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 15 0.56
23 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTATTTAAATAATAATAA
Found at i:1464148 original size:29 final size:29
Alignment explanation
Indices: 1464107--1464165 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1464097 CCGTCAAGTA
*
1464107 AAAAATTCGTATCCGGACGAAAACCGATT
1 AAAAATTCGTATCCGAACGAAAACCGATT
1464136 AAAAATTCGTATCCGAACGAAAACCGATT
1 AAAAATTCGTATCCGAACGAAAACCGATT
1464165 A
1 A
1464166 CGACACGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.20
Consensus pattern (29 bp):
AAAAATTCGTATCCGAACGAAAACCGATT
Found at i:1466297 original size:32 final size:32
Alignment explanation
Indices: 1466261--1466326 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
1466251 CTTTAGGAGT
* *
1466261 AAGACCCGATTGGTAGGAAACGTCTTAATTGA
1 AAGACCCGAATGGTAGGAAACGTCTTAACTGA
*
1466293 AAGACTCGAATGGTAGGAAACGTCTTAACTGA
1 AAGACCCGAATGGTAGGAAACGTCTTAACTGA
1466325 AA
1 AA
1466327 ATCGTTGACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (32 bp):
AAGACCCGAATGGTAGGAAACGTCTTAACTGA
Found at i:1466592 original size:8 final size:8
Alignment explanation
Indices: 1466579--1466662 Score: 52
Period size: 8 Copynumber: 10.8 Consensus size: 8
1466569 ATTTTTATAA
1466579 TTTATTAT
1 TTTATTAT
1466587 TTTATTCA-
1 TTTATT-AT
*
1466595 -TTAATATT
1 TTTATTA-T
1466603 TTTATTAT
1 TTTATTAT
* * *
1466611 TTAAGTAA
1 TTTATTAT
*
1466619 TTAATTAT
1 TTTATTAT
1466627 TTTATTAT
1 TTTATTAT
1466635 TATT-TTAT
1 T-TTATTAT
*
1466643 TTTAGTA-
1 TTTATTAT
1466650 TTTATT-T
1 TTTATTAT
1466657 TTTATT
1 TTTATT
1466663 TGATTATTTA
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
6 1 0.02
7 17 0.29
8 33 0.56
9 8 0.14
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (8 bp):
TTTATTAT
Found at i:1466606 original size:24 final size:26
Alignment explanation
Indices: 1466579--1466662 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 26
1466569 ATTTTTATAA
*
1466579 TTTATTATTTTATTCATTAA-TA-TT
1 TTTATTATTTTATTAATTAATTATTT
* *
1466603 TTTATTATTTAAGTAATTAATTATTT
1 TTTATTATTTTATTAATTAATTATTT
* * *
1466629 TATTATTATTTTATTTTAGTATTTATTT
1 T-TTATTATTTTA-TTAATTAATTATTT
1466657 TTTATT
1 TTTATT
1466663 TGATTATTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 17 0.35
25 2 0.04
26 3 0.06
27 15 0.31
28 11 0.23
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTATTATTTTATTAATTAATTATTT
Found at i:1466614 original size:16 final size:16
Alignment explanation
Indices: 1466568--1466614 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1466558 AAGGTATAAC
* *
1466568 TATTTTTATAATTTAT
1 TATTTTTATTATTTAA
1466584 TA-TTTTATTCA-TTAA
1 TATTTTTATT-ATTTAA
1466599 TATTTTTATTATTTAA
1 TATTTTTATTATTTAA
1466615 GTAATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTTTATTATTTAA
Found at i:1466669 original size:32 final size:32
Alignment explanation
Indices: 1466607--1466671 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
1466597 AATATTTTTA
1466607 TTATTTAAGTAATTAATTATTTTATTATTATT
1 TTATTTAAGTAATTAATTATTTTATTATTATT
* *
1466639 TTATTTTAGT-ATTTATT-TTTTATTTGATTATT
1 TTATTTAAGTAATTAATTATTTTA-TT-ATTATT
1466671 T
1 T
1466672 AATTGTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 8 0.28
32 16 0.55
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (32 bp):
TTATTTAAGTAATTAATTATTTTATTATTATT
Found at i:1466670 original size:19 final size:20
Alignment explanation
Indices: 1466631--1466672 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1466621 AATTATTTTA
*
1466631 TTATTATTTTATTTTAGTAT
1 TTATTATTTTATTTGAGTAT
*
1466651 TTATT-TTTTATTTGATTAT
1 TTATTATTTTATTTGAGTAT
1466670 TTA
1 TTA
1466673 ATTGTAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
TTATTATTTTATTTGAGTAT
Found at i:1466672 original size:12 final size:12
Alignment explanation
Indices: 1466583--1466672 Score: 51
Period size: 12 Copynumber: 7.2 Consensus size: 12
1466573 TTATAATTTA
1466583 TTATTTTATTCAT
1 TTATTTTATT-AT
1466596 TAATATTTTTATTAT
1 T--TA-TTTTATTAT
** * *
1466611 TTAAGTAATTAA
1 TTATTTTATTAT
1466623 TTATTTTATTA-
1 TTATTTTATTAT
1466634 TTATTTTA-T-T
1 TTATTTTATTAT
*
1466644 TTAGTATTTATTTT
1 TTA-T-TTTATTAT
*
1466658 TTATTTGATTAT
1 TTATTTTATTAT
1466670 TTA
1 TTA
1466673 ATTGTAAACT
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
10 4 0.07
11 9 0.15
12 26 0.43
13 5 0.08
14 4 0.07
15 5 0.08
16 7 0.12
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (12 bp):
TTATTTTATTAT
Found at i:1467664 original size:2 final size:2
Alignment explanation
Indices: 1467657--1467708 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1467647 ATAGAATGAC
1467657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1467699 AT AT AT AT AT
1 AT AT AT AT AT
1467709 TAAATAGGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1469664 original size:103 final size:103
Alignment explanation
Indices: 1469479--1469804 Score: 571
Period size: 103 Copynumber: 3.2 Consensus size: 103
1469469 GTAGAGGGTC
* * *
1469479 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1469544 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* * * *
1469582 TATATAGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTATGTTGAGACATATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1469647 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
1469685 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
1469750 TTGATCTTTGGCATATGTATATAATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1469788 TATGTGGTCCTTAGGGA
1 TATGTGGTCCTTCGGGA
1469805 CAACTTTATA
Statistics
Matches: 210, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1469842 original size:23 final size:23
Alignment explanation
Indices: 1469816--1469883 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1469806 AACTTTATAT
*
1469816 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
1469839 GGCACTACGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
1469862 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1469884 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1476743 original size:103 final size:103
Alignment explanation
Indices: 1476564--1476891 Score: 611
Period size: 103 Copynumber: 3.2 Consensus size: 103
1476554 GTAGAGGGTC
1476564 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1476629 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
1476667 TATGTGGTCCTTTGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTTTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1476732 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1476770 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAAGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1476835 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1476873 TATGTGGTCCTTAGGGACA
1 TATGTGGTCCTTCGGGACA
1476892 ACTTTATATG
Statistics
Matches: 217, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 217 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1476935 original size:23 final size:23
Alignment explanation
Indices: 1476909--1476968 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
1476899 ATGGCACTTT
* *
1476909 GGTGTATTTCTATGCGGCACTAC
1 GGTGAATTTCTACGCGGCACTAC
* * *
1476932 GGTGAAATTCTACGTGGCACTTC
1 GGTGAATTTCTACGCGGCACTAC
* *
1476955 GGTGCATTTATACG
1 GGTGAATTTCTACG
1476969 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (23 bp):
GGTGAATTTCTACGCGGCACTAC
Found at i:1478267 original size:24 final size:24
Alignment explanation
Indices: 1478233--1478279 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1478223 GTAATGATGA
*
1478233 CGATGAGGAGGAGGAGGAGGAGGT
1 CGATGACGAGGAGGAGGAGGAGGT
*
1478257 CGATGACGAGGATGAGGAGGAGG
1 CGATGACGAGGAGGAGGAGGAGG
1478280 ATCGGTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.06, G:0.55, T:0.09
Consensus pattern (24 bp):
CGATGACGAGGAGGAGGAGGAGGT
Found at i:1479759 original size:32 final size:31
Alignment explanation
Indices: 1479691--1479810 Score: 127
Period size: 32 Copynumber: 3.9 Consensus size: 31
1479681 GAATGACCTA
* * *
1479691 TCCATATGTTCCGAAGAACATAGGTAAT-TG
1 TCCATATGTCCCAAAGGACATAGGTAATCTG
*
1479721 TCCATATGTCCCAAAGGACATAGGTTATCATG
1 TCCATATGTCCCAAAGGACATAGGTAATC-TG
* * * *
1479753 TCCATATATCCCGAAGGACATAGGTAAACTA
1 TCCATATGTCCCAAAGGACATAGGTAATCTG
*
1479784 TCCATATGTCTCGAAA-GACATAGGTAA
1 TCCATATGTC-CCAAAGGACATAGGTAA
1479811 CCCTCGACTC
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
30 24 0.32
31 21 0.28
32 30 0.40
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
TCCATATGTCCCAAAGGACATAGGTAATCTG
Found at i:1479804 original size:31 final size:31
Alignment explanation
Indices: 1479688--1479810 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
1479678 CCCGAATGAC
1479688 CTATCCATATGT-TCCG-AAGAACATAGGT-AA
1 CTATCCATATGTCT-CGAAAG-ACATAGGTAAA
* * * * *
1479718 TTGTCCATATGTC-CCAAAGGACATAGGTTAT
1 CTATCCATATGTCTCGAAA-GACATAGGTAAA
* * * *
1479749 CATGTCCATATATCCCGAAGGACATAGGTAAA
1 C-TATCCATATGTCTCGAAAGACATAGGTAAA
1479781 CTATCCATATGTCTCGAAAGACATAGGTAA
1 CTATCCATATGTCTCGAAAGACATAGGTAA
1479811 CCCTCGACTC
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
29 1 0.01
30 20 0.27
31 27 0.37
32 22 0.30
33 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
CTATCCATATGTCTCGAAAGACATAGGTAAA
Found at i:1482069 original size:32 final size:32
Alignment explanation
Indices: 1482033--1482095 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1482023 AATAAAAGTT
1482033 TATTTTAGGTGTATGTGTATGATTTTATTTAC
1 TATTTTAGGTGTATGTGTATGATTTTATTTAC
*
1482065 TATTTTAGGTGTATGTGTATGCTTTTATTTA
1 TATTTTAGGTGTATGTGTATGATTTTATTTA
1482096 TTGTTTAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.21, C:0.03, G:0.19, T:0.57
Consensus pattern (32 bp):
TATTTTAGGTGTATGTGTATGATTTTATTTAC
Found at i:1495554 original size:2 final size:2
Alignment explanation
Indices: 1495547--1495620 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
1495537 AATAGAAGTA
1495547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1495589 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1495621 GGTTATGTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1496451 original size:23 final size:23
Alignment explanation
Indices: 1496360--1496443 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
1496350 ACATTTTATA
*
1496360 TGGCACTTCAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1496383 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * * * *
1496406 CGACACTTTGATGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1496429 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1496444 TTTATACGAG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1498716 original size:35 final size:35
Alignment explanation
Indices: 1498675--1498754 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
1498665 AACACATTCA
* * * **
1498675 TCAATTACATTTTAAACCCCAAATTCTAAATTGTT
1 TCAATTACATTCTAAACACCAAATTCCAAATTACT
*
1498710 TCAATTACATTCTAAACATCAAATTCCAAATTACT
1 TCAATTACATTCTAAACACCAAATTCCAAATTACT
1498745 TCAATTACAT
1 TCAATTACAT
1498755 GCCCAACCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTACATTCTAAACACCAAATTCCAAATTACT
Found at i:1499510 original size:148 final size:149
Alignment explanation
Indices: 1499247--1499539 Score: 466
Period size: 148 Copynumber: 2.0 Consensus size: 149
1499237 AAACTATTTA
* * *
1499247 AATTAGAATCAAATAATACTATAGTATTATAAATATTTATTATTAAATTTAAACAGAAACTCAAA
1 AATTAGAATCAAATAATACTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
1499312 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAACCCGAAAAAATTTCGAGTCAACT
66 AATTCAATTCAATTCGACTTGACTTAAATTTTATAAACTCAAACCGAAAAAATTTCGAGTCAACT
1499377 A-TTTTATAAACTGAACTG
131 ATTTTTATAAACTGAACTG
* *
1499395 AATTAGAATCAGATAATA-TAATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGA
1 AATTAGAATCAAATAATACT-ATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAA
* *
1499459 AAATTCAATTCAATTCGACTTGACTT-AATTTTATAAACTTAAATCGAAAAAATTTCGAGTCAAC
65 AAATTCAATTCAATTCGACTTGACTTAAATTTTATAAACTCAAACCGAAAAAATTTCGAGTCAAC
*
1499523 TATTTTTATAAATTGAA
130 TATTTTTATAAACTGAA
1499540 TTGAGTATTT
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
147 38 0.29
148 95 0.71
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.35
Consensus pattern (149 bp):
AATTAGAATCAAATAATACTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGACTTGACTTAAATTTTATAAACTCAAACCGAAAAAATTTCGAGTCAACT
ATTTTTATAAACTGAACTG
Found at i:1499756 original size:35 final size:35
Alignment explanation
Indices: 1499717--1499796 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
1499707 GGGGTTGGGT
1499717 ATGTAATTGAAGTATTTTGTAATTTT-AGGTTTAGA
1 ATGTAATTGAAGTATTTTG-AATTTTGAGGTTTAGA
* *
1499752 ATGTAATTGAAGTATTTTGGATTTTGGGGTTTAGA
1 ATGTAATTGAAGTATTTTGAATTTTGAGGTTTAGA
*
1499787 ATATAATTGA
1 ATGTAATTGA
1499797 TGATTGTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 5 0.12
35 36 0.88
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGAATTTTGAGGTTTAGA
Found at i:1501844 original size:18 final size:19
Alignment explanation
Indices: 1501803--1501845 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1501793 CGATGGCATG
1501803 TTAATTCTAAGACTAATAT
1 TTAATTCTAAGACTAATAT
*
1501822 TTAATT-TAATACTAA-AT
1 TTAATTCTAAGACTAATAT
1501839 TATAATT
1 T-TAATT
1501846 AAAGTGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 13 0.59
19 6 0.27
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (19 bp):
TTAATTCTAAGACTAATAT
Found at i:1508205 original size:102 final size:102
Alignment explanation
Indices: 1507895--1508209 Score: 539
Period size: 99 Copynumber: 3.1 Consensus size: 102
1507885 TAATGTCCAT
* * * *
1507895 AAGGACCACATATCGTTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAG-ATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1507960 GACTTCACACATGTTCC-AAGAATACATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1507997 AAGGACCACATATCATTCCTTAAG--CATATACATATGCCAAGGATCAAGTATGTGTCTCA-CAG
1 AAGGACCACATATCATTCCTTAAGATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
1508059 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1508096 AAGGACCACATATCATTCCTTAAGATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
*
1508161 ACTTCACACATGTTCCAAAAAATACATATATGTCCCG
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1508198 AATGACCACATA
1 AAGGACCACATA
1508210 GACCCTCGAC
Statistics
Matches: 203, Mismatches: 6, Indels: 8
0.94 0.03 0.04
Matches are distributed among these distances:
98 19 0.09
99 76 0.37
101 35 0.17
102 73 0.36
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1515989 original size:21 final size:24
Alignment explanation
Indices: 1515951--1515998 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
1515941 TCAATAAATC
* *
1515951 AAATACTAGTAATTAA-TTAA-AA
1 AAATACGAGTAATAAATTTAATAA
1515973 AAATACGA-TAATAAATTTAATAA
1 AAATACGAGTAATAAATTTAATAA
1515996 AAA
1 AAA
1515999 ATATTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 11 0.50
23 5 0.23
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATACGAGTAATAAATTTAATAA
Found at i:1521986 original size:34 final size:34
Alignment explanation
Indices: 1521947--1522020 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
1521937 TTGATAATCC
1521947 ACCCGATAACAATAACTCATCCACCCGAAAT-TCG
1 ACCCGATAACAATAACTCATCCACCCGAAATCT-G
1521981 ACCCGATAACAATAACTCATCCACCCGAAATCTG
1 ACCCGATAACAATAACTCATCCACCCGAAATCTG
1522015 ACCCGA
1 ACCCGA
1522021 CCCAACCCGC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 38 0.97
35 1 0.03
ACGTcount: A:0.38, C:0.36, G:0.09, T:0.16
Consensus pattern (34 bp):
ACCCGATAACAATAACTCATCCACCCGAAATCTG
Found at i:1523382 original size:21 final size:21
Alignment explanation
Indices: 1523356--1523430 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
1523346 GTTCTAACTA
1523356 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
1523377 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* * * **
1523398 TCGCAATGCGAATACGTAAA-
1 TCGCATTGCGATTTCCCAAAT
1523418 TCGCATTGCGATT
1 TCGCATTGCGATT
1523431 GCGATTTACG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 11 0.26
21 32 0.74
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1523457 original size:20 final size:20
Alignment explanation
Indices: 1523428--1523468 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1523418 TCGCATTGCG
*
1523428 ATTGCGATTTACGTAATCGC
1 ATTGCAATTTACGTAATCGC
1523448 ATTGCAATTTACGTAATCGC
1 ATTGCAATTTACGTAATCGC
1523468 A
1 A
1523469 ACGAGATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (20 bp):
ATTGCAATTTACGTAATCGC
Found at i:1524356 original size:24 final size:24
Alignment explanation
Indices: 1524329--1524382 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1524319 GTATTCGAAA
1524329 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1524353 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1524377 TTTGAT
1 TTTGAT
1524383 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1524588 original size:15 final size:14
Alignment explanation
Indices: 1524570--1524605 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1524560 GAAGAAGAAG
1524570 AAGAAGAAATCCCCA
1 AAGAA-AAATCCCCA
*
1524585 AAGAAAAGTCCCCA
1 AAGAAAAATCCCCA
1524599 AAGAAAA
1 AAGAAAA
1524606 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:1526916 original size:20 final size:19
Alignment explanation
Indices: 1526849--1526931 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 19
1526839 GGCATTCATT
*
1526849 TGACTATCGCAACACGAAAA
1 TGACTATCGCAATACG-AAA
**
1526869 TGACGT-TCGCAATCATCTTAA
1 TGAC-TATCGCAAT-A-CGAAA
*
1526890 TGTCTATCGCAATACGGAAA
1 TGACTATCGCAATAC-GAAA
*
1526910 TGACTATCGCAATGCGAAA
1 TGACTATCGCAATACGAAA
1526929 TGA
1 TGA
1526932 AAATCGCAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.16
20 27 0.54
21 14 0.28
22 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (19 bp):
TGACTATCGCAATACGAAA
Found at i:1526937 original size:19 final size:19
Alignment explanation
Indices: 1526895--1527045 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
1526885 CTTAATGTCT
* **
1526895 ATCGCAATACGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
1526915 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1526934 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1526948 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1526967 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1526981 ATCGCAATGCGAACTGAAA
1 ATCGCAATGCGAAATGAAA
* **
1527000 ATCGTAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
1527014 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1527033 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1527046 TTTAGTTTCG
Statistics
Matches: 98, Mismatches: 18, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 28 0.29
15 2 0.02
16 5 0.05
17 6 0.06
18 2 0.02
19 46 0.47
20 9 0.09
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1526952 original size:14 final size:14
Alignment explanation
Indices: 1526933--1526987 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1526923 GCGAAATGAA
1526933 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1526947 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1526966 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1526980 AATCGCAA
1 AATCGCAA
1526988 TGCGAACTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1526960 original size:33 final size:33
Alignment explanation
Indices: 1526915--1527041 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
1526905 GGAAATGACT
1526915 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1526948 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1526981 ATCGCAATGCGAACTGAAAATCGTAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1527014 ATCGCAATGTGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1527042 CGAATTTAGT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1527094 original size:19 final size:19
Alignment explanation
Indices: 1527070--1527108 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1527060 GCGATTTTGT
1527070 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1527089 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1527108 C
1 C
1527109 ATTACGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1527242 original size:14 final size:14
Alignment explanation
Indices: 1527223--1527259 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1527213 CATCAATTAA
1527223 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1527237 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1527251 ACAAATCAA
1 ACAAATCAA
1527260 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1529168 original size:19 final size:19
Alignment explanation
Indices: 1529128--1529237 Score: 121
Period size: 19 Copynumber: 5.6 Consensus size: 19
1529118 TCTGGAACTT
*
1529128 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
1529149 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
1529168 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
* **
1529188 ACAATCGCAACGCGAAACA
1 AAAATCGCAACGCGAAATG
1529207 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
1529226 AAAATCGTAACG
1 AAAATCGCAACG
1529238 ACAAAATCAC
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
19 46 0.62
20 17 0.23
21 11 0.15
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1529196 original size:39 final size:38
Alignment explanation
Indices: 1529128--1529237 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 38
1529118 TCTGGAACTT
* * **
1529128 AAAATCGCAACGTGAAAAATGACTATCGCAACGCGAAATG
1 AAAATCGCAAC--GAGAAATGACAATCGCAACGCGAAACA
1529168 AAAATCGCAACGAGAGAATGACAATCGCAACGCGAAACA
1 AAAATCGCAACGAGA-AATGACAATCGCAACGCGAAACA
* * *
1529207 AAAATCGCAACGCGAAATGAAAATCGTAACG
1 AAAATCGCAACGAGAAATGACAATCGCAACG
1529238 ACAAAATCAC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 17 0.27
39 34 0.55
40 11 0.18
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (38 bp):
AAAATCGCAACGAGAAATGACAATCGCAACGCGAAACA
Found at i:1529224 original size:58 final size:53
Alignment explanation
Indices: 1529152--1529274 Score: 158
Period size: 58 Copynumber: 2.2 Consensus size: 53
1529142 AAAAATGACT
*
1529152 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATGACAATCGCAACGCGAAA-CAAAA
1 ATCGCAACGCGAAATGAAAATCGCAAC--GA-AA--A-AATCACAACGCGAAACCAAAA
* *
1529210 ATCGCAACGCGAAATGAAAATCGTAACGACAAAATCACAACGCGAAACCAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAAATCACAACGCGAAACCAAAA
1529263 ATCGCAACGCGA
1 ATCGCAACGCGA
1529275 TTATATTTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
52 14 0.23
53 18 0.30
55 1 0.02
56 2 0.03
58 26 0.43
ACGTcount: A:0.48, C:0.24, G:0.19, T:0.09
Consensus pattern (53 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAAAATCACAACGCGAAACCAAAA
Found at i:1529309 original size:20 final size:20
Alignment explanation
Indices: 1529281--1529318 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1529271 GCGATTATAT
1529281 TTTCACGTTGCGATTTTTGG
1 TTTCACGTTGCGATTTTTGG
*
1529301 TTTCGCGTTGCGATTTTT
1 TTTCACGTTGCGATTTTT
1529319 TCGTTGCGAT
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:0.08, C:0.16, G:0.24, T:0.53
Consensus pattern (20 bp):
TTTCACGTTGCGATTTTTGG
Found at i:1529336 original size:20 final size:20
Alignment explanation
Indices: 1529313--1529375 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
1529303 TCGCGTTGCG
*
1529313 ATTTTTTCGTTGCGATTTTC
1 ATTTTCTCGTTGCGATTTTC
*
1529333 A-TTTCGCGTTGCGATTTTC
1 ATTTTCTCGTTGCGATTTTC
*
1529352 ATTCTCTCGTTGCGATTTTC
1 ATTTTCTCGTTGCGATTTTC
1529372 ATTT
1 ATTT
1529376 CAACCAAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.11, C:0.19, G:0.16, T:0.54
Consensus pattern (20 bp):
ATTTTCTCGTTGCGATTTTC
Found at i:1529343 original size:33 final size:34
Alignment explanation
Indices: 1529286--1529350 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
1529276 TATATTTTCA
**
1529286 CGTTGCGATTTTTGGTTTCGCGTTGCGATTTTTT
1 CGTTGCGATTTTTCATTTCGCGTTGCGATTTTTT
1529320 CGTTGCGA-TTTTCATTTCGCGTTGCGATTTT
1 CGTTGCGATTTTTCATTTCGCGTTGCGATTTT
1529351 CATTCTCTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.08, C:0.17, G:0.25, T:0.51
Consensus pattern (34 bp):
CGTTGCGATTTTTCATTTCGCGTTGCGATTTTTT
Found at i:1529581 original size:94 final size:94
Alignment explanation
Indices: 1529470--1529755 Score: 511
Period size: 94 Copynumber: 3.1 Consensus size: 94
1529460 ATGGATTGCA
* *
1529470 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
1529534 TTAGCAGAATTGACAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1529563 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1529628 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1529657 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
1529722 TTAGAAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1529751 TTACT
1 TTACT
1529756 AAGCAATCTA
Statistics
Matches: 186, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
93 4 0.02
94 182 0.98
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1529721 original size:17 final size:17
Alignment explanation
Indices: 1529699--1529731 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1529689 ATACTAACTT
1529699 CACAGTGTTA-AAGAATA
1 CACAGT-TTAGAAGAATA
1529716 CACAGTTTAGAAGAAT
1 CACAGTTTAGAAGAAT
1529732 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
CACAGTTTAGAAGAATA
Found at i:1530999 original size:31 final size:31
Alignment explanation
Indices: 1530961--1531147 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
1530951 CCCGAAGGAC
* *
1530961 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1530992 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1531023 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
1531054 CAGTCCATATGTTCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1531085 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1531116 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1531147 C
1 C
1531148 CCTCGACTCT
Statistics
Matches: 147, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 146 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1531955 original size:21 final size:21
Alignment explanation
Indices: 1531929--1531974 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1531919 AATTCTGTCG
* *
1531929 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1531950 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1531971 CTTG
1 CTTG
1531975 CCCAGAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1534088 original size:19 final size:18
Alignment explanation
Indices: 1534004--1534180 Score: 117
Period size: 19 Copynumber: 10.1 Consensus size: 18
1533994 TTTTGGTTGA
*
1534004 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAAC--GCG
*
1534024 AATGAAAATCGCAACACG
1 AATGAAAATCGCAACGCG
**
1534042 AAAATGACTATCGCAA--CG
1 --AATGAAAATCGCAACGCG
*
1534060 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
1534076 AATTGAAAATCGCAACGCG
1 AA-TGAAAATCGCAACGCG
1534095 AATTGAAAATCGCAA--CG
1 AA-TGAAAATCGCAACGCG
*
1534112 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
*
1534128 AAATGAAAATCACAA--CG
1 -AATGAAAATCGCAACGCG
*
1534145 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
*
1534161 AAATGAAAATCGCAATGCG
1 -AATGAAAATCGCAACGCG
1534180 A
1 A
1534181 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 14, Indels: 36
0.72 0.08 0.20
Matches are distributed among these distances:
14 28 0.22
15 2 0.02
16 7 0.06
17 5 0.04
18 6 0.05
19 51 0.40
20 27 0.21
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (18 bp):
AATGAAAATCGCAACGCG
Found at i:1534115 original size:52 final size:53
Alignment explanation
Indices: 1534010--1534144 Score: 191
Period size: 52 Copynumber: 2.5 Consensus size: 53
1534000 TTGAAATGAA
* * **
1534010 AATCGCAACGAGAGAATGAAAATCGCAACACGAAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGCGAAAATGAAAATCGCAACGAGAG
* *
1534064 AATCGCAACGCGAATTGAAAATCGCAACGCG-AATTGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAAATGAAAATCGCAACGAGAG
*
1534116 AATCGCAACGCGAAATGAAAATCACAACG
1 AATCGCAACGCGAAATGAAAATCGCAACG
1534145 AGAGAATCGC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 45 0.62
53 16 0.22
54 12 0.16
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (53 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAAATGAAAATCGCAACGAGAG
Found at i:1534120 original size:33 final size:33
Alignment explanation
Indices: 1534083--1534175 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1534073 GCGAATTGAA
*
1534083 AATCGCAACGCGAATTGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
1534116 AATCGCAACGCGAAATGAAAATCACAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1534149 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1534176 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:1534121 original size:14 final size:14
Alignment explanation
Indices: 1534102--1534158 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1534092 GCGAATTGAA
1534102 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1534116 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1534135 AATCACAACGAGAG
1 AATCGCAACGAGAG
1534149 AATCGCAACG
1 AATCGCAACG
1534159 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1534806 original size:20 final size:20
Alignment explanation
Indices: 1534783--1534874 Score: 130
Period size: 20 Copynumber: 4.5 Consensus size: 20
1534773 GCTATGTAAA
*
1534783 TCGCAATGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
1534803 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
*
1534824 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
*
1534844 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
1534864 TCGCATTGCGA
1 TCGCATTGCGA
1534875 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 44 0.71
21 18 0.29
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:1534840 original size:41 final size:40
Alignment explanation
Indices: 1534783--1534874 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
1534773 GCTATGTAAA
* * *
1534783 TCGCAATGCGATTTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT-AT
* *
1534824 TCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAT
1534864 TCGCATTGCGA
1 TCGCATTGCGA
1534875 ATTAGGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 13 0.28
41 33 0.72
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAT
Found at i:1534887 original size:41 final size:41
Alignment explanation
Indices: 1534783--1534889 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
1534773 GCTATGTAAA
* * * * *
1534783 TCGCAATGCGATTTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGAATTACGAAATCGCATTGCGATTTACCTAAT
* * * *
1534824 TCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGT-AT
1 TCGCATTGCGAATTACGAAATCGCATTGCGATTTACCTAAT
*
1534864 TCGCATTGCGAATTAGGAAAATCGCA
1 TCGCATTGCGAATTACG-AAATCGCA
1534890 ACACGAATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 17 0.30
41 39 0.70
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (41 bp):
TCGCATTGCGAATTACGAAATCGCATTGCGATTTACCTAAT
Found at i:1534896 original size:21 final size:21
Alignment explanation
Indices: 1534872--1534916 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1534862 ATTCGCATTG
1534872 CGAATTAGGAAAATCGCAACA
1 CGAATTAGGAAAATCGCAACA
* *
1534893 CGAATTTGGAAAATCGCAATA
1 CGAATTAGGAAAATCGCAACA
1534914 CGA
1 CGA
1534917 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACA
Found at i:1535639 original size:22 final size:21
Alignment explanation
Indices: 1535613--1535691 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 21
1535603 TTATTGATGT
1535613 AAATTTAGATAAATATGTTTTA
1 AAATTTA-ATAAATATGTTTTA
* *
1535635 AAATTTTAATAATTATTTTTTA
1 AAA-TTTAATAAATATGTTTTA
1535657 AATATTTAA-AAAT-TGTAGTTT-
1 AA-ATTTAATAAATATGT--TTTA
*
1535678 AAGTTTAATAAATA
1 AAATTTAATAAATA
1535692 ATAATTTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 7 0.15
21 9 0.20
22 25 0.54
23 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (21 bp):
AAATTTAATAAATATGTTTTA
Found at i:1539682 original size:15 final size:14
Alignment explanation
Indices: 1539652--1539710 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
1539642 TCCTATCCTG
*
1539652 TTATTTATATATATA
1 TTATTTA-AAATATA
*
1539667 TAATGTTAAAATATA
1 TTAT-TTAAAATATA
1539682 TTATTATAAAATATA
1 TTATT-TAAAATATA
1539697 TTATTTTAAAATAT
1 TTA-TTTAAAATAT
1539711 TGATATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.03
15 32 0.84
16 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TTATTTAAAATATA
Found at i:1539711 original size:13 final size:15
Alignment explanation
Indices: 1539673--1539710 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1539663 TATATAATGT
1539673 TAAAATATATTATTA
1 TAAAATATATTATTA
*
1539688 TAAAATATATTATTT
1 TAAAATATATTATTA
1539703 TAAAATAT
1 TAAAATAT
1539711 TGATATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATATATTATTA
Done.