Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009000.1 Hibiscus syriacus cultivar Beakdansim tig00112382_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: 1742898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1249016 original size:16 final size:15
Alignment explanation
Indices: 1248997--1249036 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
1248987 TTATAATGTG
1248997 AAAATATTATTATTA
1 AAAATATTATTATTA
*
1249012 TAAAATATAATTATTA
1 -AAAATATTATTATTA
1249028 AATAATATT
1 AA-AATATT
1249037 TAATTTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATATTATTATTA
Found at i:1251743 original size:21 final size:21
Alignment explanation
Indices: 1251719--1251763 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1251709 ACTTAAAGCA
*
1251719 TTTAGTTCCTAAACTATCAAT
1 TTTAGTGCCTAAACTATCAAT
* *
1251740 TTTAGTGCCTAAACTTTTAAT
1 TTTAGTGCCTAAACTATCAAT
1251761 TTT
1 TTT
1251764 TTTCTTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAGTGCCTAAACTATCAAT
Found at i:1253925 original size:18 final size:20
Alignment explanation
Indices: 1253881--1253926 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
1253871 AGTATTTACT
*
1253881 AAAAACTAAATTATACATTA
1 AAAAATTAAATTATACATTA
**
1253901 ATTAATTAAATTA-A-ATTA
1 AAAAATTAAATTATACATTA
1253919 AAAAATTA
1 AAAAATTA
1253927 TATATTTATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTAAATTATACATTA
Found at i:1254069 original size:23 final size:19
Alignment explanation
Indices: 1254029--1254074 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1254019 GGATGCAAAC
1254029 AAAAATATCTATTCAAGAA
1 AAAAATATCTATTCAAGAA
1254048 AAAAATATCTATTCAAGAA
1 AAAAATATCTATTCAAGAA
*
1254067 AGAAATAT
1 AAAAATAT
1254075 ACAAGCTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAAATATCTATTCAAGAA
Found at i:1255948 original size:2 final size:2
Alignment explanation
Indices: 1255941--1255974 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1255931 AAAAATTTCT
1255941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1255975 ACCCTTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1268138 original size:4 final size:4
Alignment explanation
Indices: 1268129--1268283 Score: 229
Period size: 4 Copynumber: 38.8 Consensus size: 4
1268119 ACAAGCGATC
* * * * * *
1268129 AGAT AGAT AGAT AGAT AGAT AGAC ATAT AGAC AGAT AGAC AGAC AGAC
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
* * *
1268177 AGAC AGAT AGAT AGAC AGAT AGAT AGAC AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1268225 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1268273 AGAT AGAT AGA
1 AGAT AGAT AGA
1268284 CAGACAGACA
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 139 1.00
ACGTcount: A:0.50, C:0.05, G:0.25, T:0.20
Consensus pattern (4 bp):
AGAT
Found at i:1268296 original size:12 final size:12
Alignment explanation
Indices: 1268128--1268311 Score: 197
Period size: 12 Copynumber: 15.0 Consensus size: 12
1268118 CACAAGCGAT
1268128 CAGATAGATAGA
1 CAGATAGATAGA
*
1268140 TAGATAGATAGA
1 CAGATAGATAGA
*
1268152 CATATAGACAGATAGA
1 C----AGATAGATAGA
* *
1268168 CAGACAGACAGA
1 CAGATAGATAGA
1268180 CAGATAGATAGA
1 CAGATAGATAGA
1268192 CAGATAGATAGA
1 CAGATAGATAGA
1268204 CAGATAGATAGA
1 CAGATAGATAGA
*
1268216 TAGATAGATAGA
1 CAGATAGATAGA
*
1268228 TAGATAGATAGA
1 CAGATAGATAGA
*
1268240 TAGATAGATAGA
1 CAGATAGATAGA
*
1268252 TAGATAGATAGA
1 CAGATAGATAGA
*
1268264 TAGATAGATAGA
1 CAGATAGATAGA
* *
1268276 TAGATAGACAGA
1 CAGATAGATAGA
* * *
1268288 CAGACAGACAGG
1 CAGATAGATAGA
*
1268300 CAGACAGATAGA
1 CAGATAGATAGA
1268312 AATAAAAATG
Statistics
Matches: 155, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
12 144 0.93
16 11 0.07
ACGTcount: A:0.49, C:0.08, G:0.25, T:0.17
Consensus pattern (12 bp):
CAGATAGATAGA
Found at i:1270125 original size:16 final size:16
Alignment explanation
Indices: 1270104--1270136 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1270094 TATCTCAAAT
1270104 TTAAATACTATGAAAA
1 TTAAATACTATGAAAA
*
1270120 TTAAATATTATGAAAA
1 TTAAATACTATGAAAA
1270136 T
1 T
1270137 GGTTTAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (16 bp):
TTAAATACTATGAAAA
Found at i:1270400 original size:60 final size:60
Alignment explanation
Indices: 1270287--1270400 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
1270277 ACTATGGCTA
* *
1270287 TTGCTTTATCAAATCCTTCGACTATTAAAAGTTACAAAATGATCCTCTAACTATAGAATT
1 TTGCTTTATCAAATCCCTCGACTATTAAAAGTTACAAAATGATCATCTAACTATAGAATT
* * *
1270347 TTGCTTTATTAAATCCCTC-ACCTATTAAAAGTTACAAAATGGTCATCTGACTAT
1 TTGCTTTATCAAATCCCTCGA-CTATTAAAAGTTACAAAATGATCATCTAACTAT
1270401 TCATTATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (60 bp):
TTGCTTTATCAAATCCCTCGACTATTAAAAGTTACAAAATGATCATCTAACTATAGAATT
Found at i:1273437 original size:2 final size:2
Alignment explanation
Indices: 1273426--1273462 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1273416 TATACTTGTG
1273426 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1273463 AATGCACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1273531 original size:24 final size:24
Alignment explanation
Indices: 1273495--1273560 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
1273485 TATGCATATG
* *
1273495 TATA-ATATATATGTGTGTGTATT
1 TATATATACATATGTATGTGTATT
1273518 TATATATACATATGTATGTGTATT
1 TATATATACATATGTATGTGTATT
1273542 TATATATACATATGTATGT
1 TATATATACATATGTATGT
1273561 TTGTGTGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 4 0.10
24 36 0.90
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (24 bp):
TATATATACATATGTATGTGTATT
Found at i:1273598 original size:20 final size:20
Alignment explanation
Indices: 1273551--1273615 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
1273541 TTATATATAC
* *
1273551 ATATGTATGTT-TGTGTGAT
1 ATATGTATATTATGTGTTAT
* *
1273570 ACATATATATTATGTGTTAT
1 ATATGTATATTATGTGTTAT
*
1273590 ATATGTATATGA-GTGTATAT
1 ATATGTATATTATGTGT-TAT
1273610 ATATGT
1 ATATGT
1273616 TACACTTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.32
20 25 0.68
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (20 bp):
ATATGTATATTATGTGTTAT
Found at i:1274504 original size:16 final size:16
Alignment explanation
Indices: 1274485--1274516 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1274475 TTGTAACTTA
*
1274485 TAAGTCAGGTAAATAT
1 TAAGTCAAGTAAATAT
1274501 TAAGTCAAGTAAATAT
1 TAAGTCAAGTAAATAT
1274517 CATATCAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (16 bp):
TAAGTCAAGTAAATAT
Found at i:1274587 original size:16 final size:16
Alignment explanation
Indices: 1274568--1274601 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1274558 TCAATTACAG
1274568 GTCAGATTCATAACAA
1 GTCAGATTCATAACAA
* *
1274584 GTCAGGTTGATAACAA
1 GTCAGATTCATAACAA
1274600 GT
1 GT
1274602 TAGGTAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (16 bp):
GTCAGATTCATAACAA
Found at i:1287160 original size:13 final size:13
Alignment explanation
Indices: 1287130--1287160 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1287120 GATTTTCTTG
1287130 GAAAATCAATTTT
1 GAAAATCAATTTT
1287143 G-AAATCAATTTT
1 GAAAATCAATTTT
1287155 GAAAAT
1 GAAAAT
1287161 GTGAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (13 bp):
GAAAATCAATTTT
Found at i:1299466 original size:23 final size:23
Alignment explanation
Indices: 1299440--1299507 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1299430 CATCTTATAT
* *
1299440 GGCACTTCGGTGCATTTTTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1299463 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
1299486 GGTACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1299508 AGCTGTGGTG
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:0.21, G:0.26, T:0.35
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1300540 original size:20 final size:21
Alignment explanation
Indices: 1300501--1300540 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1300491 GAAGCTTTAA
* *
1300501 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
1300522 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
1300541 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:1312077 original size:22 final size:21
Alignment explanation
Indices: 1312051--1312130 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 21
1312041 TTGGTGTATA
1312051 GGGAATCGATACCCCCTTGAAG
1 GGGAA-CGATACCCCCTTGAAG
*
1312073 GGGAACTGATTCCCCCTTTGAAG
1 GGGAAC-GATACCCCC-TTGAAG
* *
1312096 GGGAACCAGT-TCCCCTT--AG
1 GGGAACGA-TACCCCCTTGAAG
1312115 GGGAATCGATACCCCC
1 GGGAA-CGATACCCCC
1312131 CACGGGTTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 8 0.17
20 6 0.12
21 3 0.06
22 18 0.38
23 13 0.27
ACGTcount: A:0.24, C:0.30, G:0.26, T:0.20
Consensus pattern (21 bp):
GGGAACGATACCCCCTTGAAG
Found at i:1312108 original size:23 final size:22
Alignment explanation
Indices: 1312062--1312110 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1312052 GGAATCGATA
*
1312062 CCCCCTTGAAGGGGAACTGATT
1 CCCCCTTGAAGGGGAACAGATT
1312084 CCCCCTTTGAAGGGGAACCAG-TT
1 CCCCC-TTGAAGGGGAA-CAGATT
1312107 CCCC
1 CCCC
1312111 TTAGGGGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
23 17 0.71
24 2 0.08
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.20
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACAGATT
Found at i:1314426 original size:15 final size:15
Alignment explanation
Indices: 1314406--1314436 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1314396 GTTAAAGTGT
1314406 TTTAAAGGGGAGAAG
1 TTTAAAGGGGAGAAG
1314421 TTTAAAGGGGAGAAG
1 TTTAAAGGGGAGAAG
1314436 T
1 T
1314437 GTTAGAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.23
Consensus pattern (15 bp):
TTTAAAGGGGAGAAG
Found at i:1316798 original size:23 final size:24
Alignment explanation
Indices: 1316772--1316818 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1316762 AAAAAATGTT
1316772 ATATTTTTAAT-AATAATTTCAGC
1 ATATTTTTAATAAATAATTTCAGC
*
1316795 ATATTTTTAATAAATATTTTCAGC
1 ATATTTTTAATAAATAATTTCAGC
1316819 TACACCTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTTTTAATAAATAATTTCAGC
Found at i:1317221 original size:50 final size:50
Alignment explanation
Indices: 1317146--1317245 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1317136 CATTCAGCTT
1317146 ATCTAATTTGAATCTCTTGTATTTTGCCCCTTGAACTCGTTTCTGTATCA
1 ATCTAATTTGAATCTCTTGTATTTTGCCCCTTGAACTCGTTTCTGTATCA
1317196 ATCTAATTTGAATCTCTTGTATTTTGCCCCTTGAACTCGTTTCTGTATCA
1 ATCTAATTTGAATCTCTTGTATTTTGCCCCTTGAACTCGTTTCTGTATCA
1317246 CTTTGATACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (50 bp):
ATCTAATTTGAATCTCTTGTATTTTGCCCCTTGAACTCGTTTCTGTATCA
Found at i:1322769 original size:116 final size:120
Alignment explanation
Indices: 1322560--1322789 Score: 326
Period size: 116 Copynumber: 1.9 Consensus size: 120
1322550 TTCGTAAAGT
* ** ** *
1322560 TTGTTTTGGTTAACTGATCCTGTTAATTAGATTGGCATTGGTATGGGTAAGCCTAAACCTATTGG
1 TTGTTTTGGTAAACTGATCCAATTAATTAGATTGGCATCAGTATGGGTAACCCTAAACCTA-TGG
*
1322625 TTCACCTAAAAATCCAAATCAAATTCAAAGCAAATTTGATAAAAACTAGAACTAGA
65 TTCACCTAAAAATCCAAATCAAATTCAAAGCAAATCTGATAAAAACTAGAACTAGA
1322681 TTGTTTTGGTAAACTGAT-CAATTAATTA-ATTTGGCATCAGTATGGGTAACCCTAAA-C-A-GG
1 TTGTTTTGGTAAACTGATCCAATTAATTAGA-TTGGCATCAGTATGGGTAACCCTAAACCTATGG
* *
1322741 TTCACCTAAACATGCAAATCAAATTCAAAGCAAATCTGATAAAAACTAG
65 TTCACCTAAAAATCCAAATCAAATTCAAAGCAAATCTGATAAAAACTAG
1322790 GAGTACAGCT
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
116 48 0.48
118 1 0.01
119 2 0.02
120 31 0.31
121 17 0.17
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (120 bp):
TTGTTTTGGTAAACTGATCCAATTAATTAGATTGGCATCAGTATGGGTAACCCTAAACCTATGGT
TCACCTAAAAATCCAAATCAAATTCAAAGCAAATCTGATAAAAACTAGAACTAGA
Found at i:1327972 original size:2 final size:2
Alignment explanation
Indices: 1327965--1327996 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1327955 TCTGCCCTAC
1327965 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1327997 GTTTCTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1329204 original size:179 final size:178
Alignment explanation
Indices: 1328874--1329230 Score: 644
Period size: 179 Copynumber: 2.0 Consensus size: 178
1328864 CGCATCTTAG
*
1328874 GTGTAATTACACAACTACCCGACTTCAATACCTCCAAACCTCCCTATAAATACCTCCATCTTCAA
1 GTGTAATTACACAACTACCCGACTTCAATACCTCCAAACCTCCCTATAAATACCTCCATCCTCAA
* *
1328939 TTACTTTCATCACACCAATTCTCTCAACTTCTCTCAAATACTCTTATAATCTCTTCTAAGGTATA
66 TTACTTTCATCACACAAATTCTCTCAACTTCTCTCAAATACTCTTATAATATCTTCTAAGGTATA
1329004 TTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
131 TTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
* *
1329052 GTGTAATTACACAACTACCCGACTTCAATACC-CTTAAACCTCCCTATAAATACCTTCATCCTCA
1 GTGTAATTACACAACTACCCGACTTCAATACCTC-CAAACCTCCCTATAAATACCTCCATCCTCA
1329116 ATTACTTTCATCACATCAAATTCTCTCAACTTCTCTCAAATACTCTTATAATATCTTCTAAGGTA
65 ATTACTTTCATCACA-CAAATTCTCTCAACTTCTCTCAAATACTCTTATAATATCTTCTAAGGTA
1329181 TATTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
129 TATTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
1329231 TTTATTTAAT
Statistics
Matches: 172, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
177 1 0.01
178 74 0.43
179 97 0.56
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (178 bp):
GTGTAATTACACAACTACCCGACTTCAATACCTCCAAACCTCCCTATAAATACCTCCATCCTCAA
TTACTTTCATCACACAAATTCTCTCAACTTCTCTCAAATACTCTTATAATATCTTCTAAGGTATA
TTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
Found at i:1329219 original size:9 final size:9
Alignment explanation
Indices: 1329207--1329258 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
1329197 TAATATTTTG
1329207 TATTTAATT
1 TATTTAATT
*
1329216 TATTTAA-G
1 TATTTAATT
1329224 TATTTAATT
1 TATTTAATT
1329233 TATTTAA--
1 TATTTAATT
* *
1329240 TATTTTACT
1 TATTTAATT
1329249 TATTTAATT
1 TATTTAATT
1329258 T
1 T
1329259 TTTTCAGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:1329228 original size:17 final size:17
Alignment explanation
Indices: 1329206--1329255 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1329196 TTAATATTTT
1329206 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1329223 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
1329240 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
1329256 TTTTTTTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1329251 original size:16 final size:16
Alignment explanation
Indices: 1329215--1329260 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1329205 TGTATTTAAT
* *
1329215 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
1329232 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
1329248 TTATTTAAT-TTTT
1 TTATTTAATATTTT
1329261 TTCAGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:1334991 original size:55 final size:55
Alignment explanation
Indices: 1334928--1335048 Score: 179
Period size: 55 Copynumber: 2.2 Consensus size: 55
1334918 AATGACGTCT
* * * **
1334928 GATGAATGAAGAAATTTGAACCTGATTAAAGAACGATTCATAAAGATGGACATCC
1 GATGAATGAAGAAATCTGAAACTGATTAAAGAACGATCCATAAAGAAAGACATCC
* *
1334983 GATGAATGAAGAAATCTGAAACTGATTGAAGATCGATCCATAAAGAAAGACATCC
1 GATGAATGAAGAAATCTGAAACTGATTAAAGAACGATCCATAAAGAAAGACATCC
1335038 GATGAATGAAG
1 GATGAATGAAG
1335049 TTTGAAGTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (55 bp):
GATGAATGAAGAAATCTGAAACTGATTAAAGAACGATCCATAAAGAAAGACATCC
Found at i:1335412 original size:6 final size:6
Alignment explanation
Indices: 1335401--1335437 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
1335391 ATTAACACCT
1335401 TTTGCA TTTGCA TTTAGCA TTTGCA TTTGCA -TTGCA T
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA T
1335438 GTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
7 6 0.21
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:1335422 original size:13 final size:12
Alignment explanation
Indices: 1335401--1335437 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
1335391 ATTAACACCT
1335401 TTTGCATTTGCA
1 TTTGCATTTGCA
1335413 TTTAGCATTTGCA
1 TTT-GCATTTGCA
1335426 TTTGCA-TTGCA
1 TTTGCATTTGCA
1335437 T
1 T
1335438 GTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 6 0.25
13 12 0.50
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:1338905 original size:125 final size:125
Alignment explanation
Indices: 1338683--1338944 Score: 366
Period size: 125 Copynumber: 2.1 Consensus size: 125
1338673 AAGTTGTGAT
* * *
1338683 ATGTTCGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAAACCAATGAGGTATGAA
1 ATGTTGGGGCACGACTGAACCCACATCATATTGAGATGACAAGATTCAAACCAATGAGGCATGAA
* * *
1338748 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGACA
66 GAATGAGCCTTACAATCTGAGATGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACA
* * *
1338808 ATGTTGGGGCACGACTGAACCCACATCATATTGAGATGATAAGATTTAGACCAA-GAAGGCATTG
1 ATGTTGGGGCACGACTGAACCCACATCATATTGAGATGACAAGATTCAAACCAATG-AGGCA-TG
* * *
1338872 -AGAGTGAGCCTTACAATCTGAGATGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
64 AAGAATGAGCCTTACAATCTGAGATGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACA
* *
1338933 ATATTGCGGCAC
1 ATGTTGGGGCAC
1338945 TAGTGAAGGC
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
124 1 0.01
125 118 0.98
126 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (125 bp):
ATGTTGGGGCACGACTGAACCCACATCATATTGAGATGACAAGATTCAAACCAATGAGGCATGAA
GAATGAGCCTTACAATCTGAGATGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACA
Found at i:1340701 original size:55 final size:54
Alignment explanation
Indices: 1340596--1340702 Score: 160
Period size: 55 Copynumber: 2.0 Consensus size: 54
1340586 AATGAAGATG
* * **
1340596 TTCGAGTTCTATACTCCCTAAAAAAGAGGGAGTAAACCCGTTTGCGGAAGATTA
1 TTCGAATTCTATACTCCCTAAAAAAGAGGGAGCAAACCCGTTTGAAGAAGATTA
*
1340650 TTCGAATTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAT
1 TTCGAATTCTATACTCCCTAAA-AAAGAGGGAGCAAACCCGTTTGAAGAAGAT
1340703 GTTCGAGTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 21 0.45
55 26 0.55
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (54 bp):
TTCGAATTCTATACTCCCTAAAAAAGAGGGAGCAAACCCGTTTGAAGAAGATTA
Found at i:1340708 original size:54 final size:53
Alignment explanation
Indices: 1340589--1340708 Score: 168
Period size: 54 Copynumber: 2.2 Consensus size: 53
1340579 TGAAGCAAAT
* * **
1340589 GAAGATGTTCGAGTTCTATACTCCCTAAAAAAGAGGGAGTAAACCCGTTTGCG
1 GAAGATGTTCGAATTCTATACTCCCTAAAAAAGAGGGAGCAAACCCGTTTGAA
* *
1340642 GAAGATTATTCGAATTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
1 GAAGA-TGTTCGAATTCTATACTCCCTAAA-AAAGAGGGAGCAAACCCGTTTGAA
1340697 GAAGATGTTCGA
1 GAAGATGTTCGA
1340709 GTCTTATACT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
53 5 0.09
54 28 0.48
55 25 0.43
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (53 bp):
GAAGATGTTCGAATTCTATACTCCCTAAAAAAGAGGGAGCAAACCCGTTTGAA
Found at i:1340769 original size:55 final size:55
Alignment explanation
Indices: 1340697--1341340 Score: 893
Period size: 55 Copynumber: 11.8 Consensus size: 55
1340687 CCCGTTTGAA
* *
1340697 GAAGA-TGTTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
*
1340751 GAAGATTGTTCGAGTCTTATACTCGCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
** * *
1340806 GAAGATTGTTCGAGTCTTATACTCTCTGAAACAATAGAGAGCATACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
*
1340861 GAATATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * *
1340916 GAAGATTGTTCGAGTCTTATACTCTCTGAAAGAATAGAGAGCATACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* *
1340971 GAATATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAACAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * *
1341026 GAAAATTGTTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * * * * *
1341081 GAAGGTTGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGCAAACCCGTTTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * * *
1341136 GAAGA-TGTTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCATACACAATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
*
1341190 GAAGGTTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * * * * *
1341245 GAAGATTATTCTAGTCATATACTTTCTGAAGTG-ATAGGGAGCAGACACGGTTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAG-GAATAGGGAGCAGACACGATTGTT
* * * * *
1341300 AAAGA-TGTTCGAGT-TCTATACTCCCTAAAGAAAGAGGGAGC
1 GAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGC
1341341 GAACCCATAA
Statistics
Matches: 522, Mismatches: 63, Indels: 10
0.88 0.11 0.02
Matches are distributed among these distances:
54 76 0.15
55 445 0.85
56 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
Found at i:1341513 original size:54 final size:54
Alignment explanation
Indices: 1341304--1341531 Score: 332
Period size: 54 Copynumber: 4.2 Consensus size: 54
1341294 GTTGATAAAG
*
1341304 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATAAGAAGAAT
1 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
* * * *
1341358 GTGTTCTAGTTTTATACTCCCTATAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
1 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
* * * *
1341412 CTGTTCGAGTTCTATACTCCATAAAGAAAGAGGGAGCGAACCTGTAAGAAGAAA
1 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
* *
1341466 ATGTTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGCAA-AAG
1 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG-AAGAAT
1341520 ATTGTTCGAGTT
1 A-TGTTCGAGTT
1341532 TCTACTCTCT
Statistics
Matches: 154, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
54 143 0.93
55 11 0.07
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (54 bp):
ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
Found at i:1341759 original size:14 final size:14
Alignment explanation
Indices: 1341740--1341768 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1341730 TTTGTCCGGG
1341740 ATATTATTATTATT
1 ATATTATTATTATT
1341754 ATATTATTATTATT
1 ATATTATTATTATT
1341768 A
1 A
1341769 ATAATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTATTATTATT
Found at i:1345423 original size:3 final size:3
Alignment explanation
Indices: 1345415--1345440 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1345405 ACCTACTCAA
1345415 GAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GA
1345441 TGATGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:1350229 original size:23 final size:23
Alignment explanation
Indices: 1350203--1350250 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1350193 ATAAAGTACA
*
1350203 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1350226 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1350249 AT
1 AT
1350251 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1350760 original size:23 final size:23
Alignment explanation
Indices: 1350725--1350797 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1350715 ATACTTTACA
* *
1350725 ATATAAGCACTACATATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1350748 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
1350771 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
1350794 ATAT
1 ATAT
1350798 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1351191 original size:23 final size:23
Alignment explanation
Indices: 1351161--1351233 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1351151 ATACTTTACA
*
1351161 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1351184 ATATAAACGCTATCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
1351207 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1351230 ATAT
1 ATAT
1351234 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1351450 original size:436 final size:435
Alignment explanation
Indices: 1350624--1351493 Score: 1598
Period size: 436 Copynumber: 2.0 Consensus size: 435
1350614 ATATAATTAC
* * *
1350624 TAAATTGATATCTTAAACTCACTCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAATAAG
1 TAAATTAATATCTTAAACTCAATCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAG
*
1350689 TATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAGCACTACATATTACATTATATAA
66 TATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAACACTACATATTACATTATATAA
*
1350754 ACGCTACCTATTACATTATATAAGTGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
131 ACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
*
1350819 TGTTCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTT
196 TGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTT
* *
1350884 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACATAAAAAATT
261 TTTAATAGTGTTTCATGTTTTCCACCAACAATATTAATTTAATAATTTCATTTACACAAAAAATT
1350949 ATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAG
326 ATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAG
1351014 ATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAT
391 ATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAT
*
1351059 TAAATTAATATCTTAAAACTCAATCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAA
1 TAAATTAATATCTT-AAACTCAATCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAA
* *
1351124 GTATGGACACTTTTATAAAAATGATATATACTTTACAATATAAACACTACCTATTACATTATATA
65 GTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAACACTACATATTACATTATATA
*
1351189 AACGCTATCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAA
130 AACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAA
1351254 GTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATT
195 GTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTTTCAATT
*
1351319 TTTTTAATAGTGTTTCATG-TTTCCACCAACAATATTAATTTAATAATTTCATTTGCACAAAAAA
259 TTTTTAATAGTGTTTCATGTTTTCCACCAACAATATTAATTTAATAATTTCATTTACACAAAAAA
1351383 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAA
324 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAA
1351448 AGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTA
389 AGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTA
1351494 ATAATAATAT
Statistics
Matches: 420, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
435 13 0.03
436 356 0.85
437 51 0.12
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.42
Consensus pattern (435 bp):
TAAATTAATATCTTAAACTCAATCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAG
TATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAACACTACATATTACATTATATAA
ACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
TGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTT
TTTAATAGTGTTTCATGTTTTCCACCAACAATATTAATTTAATAATTTCATTTACACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAG
ATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAT
Found at i:1354331 original size:183 final size:183
Alignment explanation
Indices: 1354023--1354966 Score: 1726
Period size: 183 Copynumber: 5.2 Consensus size: 183
1354013 ACTCCTATTG
*
1354023 TAAAGTACCAACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1354088 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
*
1354153 AATGTCGACACTTTTTGACAAAGTATCGACACATTTTTCTTCCAATCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
1354206 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1354271 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
1354336 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
* *
1354389 TAAAGTACCAACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTG
1 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
* *
1354454 GTATATTTATATCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
*
1354519 AATGTCGACACTTTTTGACAAGGTATCGATACATTTTTCTTCCAATCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
*
1354572 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAATCG
1 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
* *
1354637 GTATATTTATACCGGTTATATTACAAAATTATCTATTGCATTATAATTCTAGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
* *
1354702 AATGTTGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATTTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
1354755 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
*
1354820 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
* * * *
1354885 AATTTCGACACTTTTTAACAATGTATCGACACATTTTTCTTCCATTCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
*
1354938 TAAAGTACAGACACAATATTAAAAAGTGT
1 TAAAGTACCGACACAATATTAAAAAGTGT
1354967 GAAAACTTTG
Statistics
Matches: 733, Mismatches: 28, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 733 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
Found at i:1355990 original size:3 final size:3
Alignment explanation
Indices: 1355982--1356086 Score: 102
Period size: 3 Copynumber: 35.0 Consensus size: 3
1355972 ACTTGTTTGG
* * * * *
1355982 ATC ATC ATC ATC ATC ATC ATC GTC GTC ATC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * *
1356030 ATC GTC AGC TTC ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC GTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
1356078 ATC TTC ATC
1 ATC ATC ATC
1356087 GTCAGCTTCA
Statistics
Matches: 80, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:1355999 original size:12 final size:12
Alignment explanation
Indices: 1355982--1356090 Score: 119
Period size: 12 Copynumber: 9.1 Consensus size: 12
1355972 ACTTGTTTGG
*
1355982 ATCATCATCATC
1 ATCATCATCGTC
1355994 ATCATCATCGTC
1 ATCATCATCGTC
* *
1356006 GTCATCATCTTC
1 ATCATCATCGTC
* *
1356018 ATCGTCATCTTC
1 ATCATCATCGTC
* * *
1356030 ATCGTCAGCTTC
1 ATCATCATCGTC
*
1356042 ATCATCATCATC
1 ATCATCATCGTC
1356054 ATCATCATCGTC
1 ATCATCATCGTC
*
1356066 ATCTTCATCGTC
1 ATCATCATCGTC
*
1356078 ATCTTCATCGTC
1 ATCATCATCGTC
1356090 A
1 A
1356091 GCTTCATCTT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 86 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (12 bp):
ATCATCATCGTC
Found at i:1356101 original size:6 final size:6
Alignment explanation
Indices: 1355986--1356103 Score: 101
Period size: 6 Copynumber: 19.7 Consensus size: 6
1355976 GTTTGGATCA
* * * * * * *
1355986 TCATCA TCATCA TCATCG TCGTCA TCATCT TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * * *
1356034 TCAGCT TCATCA TCATCA TCATCA TCATCG TCATCT TCATCG TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* *
1356082 TCATCG TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCAT
1356104 TGACCGCTTG
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 92 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:1358094 original size:200 final size:200
Alignment explanation
Indices: 1357597--1358361 Score: 1298
Period size: 200 Copynumber: 3.8 Consensus size: 200
1357587 AATATTAAAC
* * * *
1357597 AGTGTCGATACA-TATTATATACCAATTCTCTCATAAAACCGGTATACTTGTACCGGTTATATTG
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* * *
1357661 AAAAATTACCTATTACATTATACTTATGGGTTTTGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
** *
1357726 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTACGGTTACACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
*
1357791 TAAAAAA
195 T-ACAAA
*
1357798 AGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1357863 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
1357928 GATCGACACTTTACGGTTACACCCTGTTTGCCATTCATTCTGGACCTAAAATATCGACACAAACT
131 GATCGACACTTTACGGTTACACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1357993 ACAAA
196 ACAAA
*
1357998 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGG
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1358063 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * *
1358128 GATCGACACTTTACGGTTGCACCCTGTTTACCATTCAATCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTACGGTTACACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1358193 ACAAA
196 ACAAA
*
1358198 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* * *
1358263 AAAATTACATATTACATTATACTTTTGGTTTTCTATGTTTTTGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
1358328 GATCGACACTTTATGGTTACACCTTGTTTGCCAT
131 GATCGACACTTTACGGTTACACCCTGTTTGCCAT
1358362 ATTGTAAATT
Statistics
Matches: 535, Mismatches: 28, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
200 353 0.66
201 178 0.33
202 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTACGGTTACACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:1358502 original size:19 final size:19
Alignment explanation
Indices: 1358474--1358521 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1358464 TTATATTCAC
1358474 ATAC-AAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1358492 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1358511 ATACAAAATTA
1 ATACAAAATTA
1358522 GCCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1360413 original size:21 final size:21
Alignment explanation
Indices: 1360388--1360452 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1360378 CCCCTTATGC
* *
1360388 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1360409 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
1360430 ATATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1360451 CT
1 CT
1360453 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1362842 original size:19 final size:18
Alignment explanation
Indices: 1362800--1362842 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1362790 TACCGTAACG
*
1362800 TTTT-CGGTTTTATCATT
1 TTTTACGGTGTTATCATT
1362817 TTGTTACGGTGTTATCATAT
1 TT-TTACGGTGTTATCAT-T
1362837 TTTTAC
1 TTTTAC
1362843 CTGGTATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 15 0.68
20 3 0.14
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (18 bp):
TTTTACGGTGTTATCATT
Found at i:1362895 original size:175 final size:177
Alignment explanation
Indices: 1362594--1363054 Score: 567
Period size: 175 Copynumber: 2.6 Consensus size: 177
1362584 CGTACTTACG
* *
1362594 AAAGTATCGACACTTTCAA-ATATCCGGTATCATTTTACGGTTTTATCATTTTGATACCGGTTTT
1 AAAGTATCGACACTTTCAATATATCC-GTAACGTTTT-CGGTTTTATCATTTTGATACCGGTTTT
* * *
1362658 ATCATATTTTTACAT-GTATATCG-TGTGGATCG-ATATATTTTTAAAGTATCGATACATTATAG
64 ATCATATTTTTACATGGTATATCGTTTTGGATCGAACAT-TTTTTAAAGTATCGACACATTATAG
*
1362720 GCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
128 GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
1362769 AAAGTATCGACACTTTCAATATA-CCGTAACGTTTTCGGTTTTATCATTTTGTTA-CGGTGTTAT
1 AAAGTATCGACACTTTCAATATATCCGTAACGTTTTCGGTTTTATCATTTTGATACCGGTTTTAT
* *
1362832 CATATTTTTACCTGGTATATCGTTTTGGATCGAACATTTTTTAAAAGTATCGACACTTTATAGGA
66 CATATTTTTACATGGTATATCGTTTTGGATCGAACATTTTTT-AAAGTATCGACACATTATAGGA
** * *
1362897 TTTAAAACTTCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 GCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * **
1362945 AAAGTATCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATC-CGTAACG-TTT-TCGGTTTTATCATTTTGATACCGGTTT
* * * * *
1363010 TGTCATAGTTTTACTTGTTATATCATTTTGGATCGACACATTTTT
63 TATCATATTTTTACATGGTATATCGTTTTGGATCGA-ACATTTTT
1363055 AATTTGGATC
Statistics
Matches: 246, Mismatches: 28, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
172 20 0.08
173 26 0.11
174 21 0.09
175 85 0.35
176 25 0.10
177 1 0.00
178 5 0.02
179 3 0.01
180 16 0.07
181 36 0.15
182 8 0.03
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (177 bp):
AAAGTATCGACACTTTCAATATATCCGTAACGTTTTCGGTTTTATCATTTTGATACCGGTTTTAT
CATATTTTTACATGGTATATCGTTTTGGATCGAACATTTTTTAAAGTATCGACACATTATAGGAG
CTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:1363221 original size:11 final size:11
Alignment explanation
Indices: 1363205--1363229 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1363195 ATCCGTAACG
1363205 CCGTATATTAA
1 CCGTATATTAA
1363216 CCGTATATTAA
1 CCGTATATTAA
1363227 CCG
1 CCG
1363230 CCTTTCCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (11 bp):
CCGTATATTAA
Found at i:1371792 original size:11 final size:11
Alignment explanation
Indices: 1371776--1371808 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
1371766 ATCGTAAATA
1371776 TTAATATTTTT
1 TTAATATTTTT
1371787 TTAATATTTTT
1 TTAATATTTTT
1371798 TTAATATTTTT
1 TTAATATTTTT
1371809 GATAGAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTAATATTTTT
Found at i:1371987 original size:23 final size:23
Alignment explanation
Indices: 1371961--1372005 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1371951 GAAAAGGTAG
1371961 CAATTTTGAAAACACCAGAAAAT
1 CAATTTTGAAAACACCAGAAAAT
1371984 CAATTTTGAAAACACCAGAAAA
1 CAATTTTGAAAACACCAGAAAA
1372006 GCTTGCAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.18, G:0.09, T:0.20
Consensus pattern (23 bp):
CAATTTTGAAAACACCAGAAAAT
Found at i:1372133 original size:20 final size:21
Alignment explanation
Indices: 1372085--1372134 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
1372075 CACGAAATGT
*
1372085 AAGATTATCAGTGGGAATAAAA
1 AAGATTACCAGTGGGAAT-AAA
*
1372107 AAAATTACCAGTGGGAAT-AA
1 AAGATTACCAGTGGGAATAAA
1372127 AAGATTAC
1 AAGATTAC
1372135 TAGAGAATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.36
22 16 0.64
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.22
Consensus pattern (21 bp):
AAGATTACCAGTGGGAATAAA
Found at i:1374047 original size:32 final size:32
Alignment explanation
Indices: 1374010--1374089 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
1374000 TGAAAGTAGG
*
1374010 CATCTTTGGATTTAATATTGTAAACAAAACCC
1 CATCTTTGGATTCAATATTGTAAACAAAACCC
*
1374042 CATCTTTGGCTTCAATATTGTAAACAAAACCC
1 CATCTTTGGATTCAATATTGTAAACAAAACCC
*
1374074 CATCTTTGGCTTCAAT
1 CATCTTTGGATTCAAT
1374090 TATGAACAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (32 bp):
CATCTTTGGATTCAATATTGTAAACAAAACCC
Found at i:1375259 original size:10 final size:10
Alignment explanation
Indices: 1375244--1375288 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
1375234 CATTTAATAG
1375244 ATAAACGAAC
1 ATAAACGAAC
1375254 ATAAACGAAC
1 ATAAACGAAC
1375264 ATGAATGAGCGAAC
1 AT-AA--A-CGAAC
1375278 ATAAACGAAC
1 ATAAACGAAC
1375288 A
1 A
1375289 ACACAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 18 0.58
11 3 0.10
13 3 0.10
14 7 0.23
ACGTcount: A:0.56, C:0.18, G:0.16, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1375574 original size:24 final size:24
Alignment explanation
Indices: 1375541--1375606 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
1375531 GTCCTCTGTT
1375541 CGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACATAAA
* * *
1375565 TGAACGTAAATGAACGAATATAAA
1 CGAACATAAATGAACGAACATAAA
1375589 CGAACATATAATCGAACG
1 CGAACATA-AAT-GAACG
1375607 TTCACGAGCG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 27 0.77
25 3 0.09
26 5 0.14
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.17
Consensus pattern (24 bp):
CGAACATAAATGAACGAACATAAA
Found at i:1375588 original size:14 final size:14
Alignment explanation
Indices: 1375541--1375570 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1375531 GTCCTCTGTT
1375541 CGAACATAAATGAA
1 CGAACATAAATGAA
1375555 CGAACATAAATGAA
1 CGAACATAAATGAA
1375569 CG
1 CG
1375571 TAAATGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.13
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:1376906 original size:5 final size:5
Alignment explanation
Indices: 1376896--1376926 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1376886 TTTTATTATT
*
1376896 TCGGG TCGGG TCGGG TCAGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG T
1376927 TTCTAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.19, G:0.55, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1377492 original size:270 final size:254
Alignment explanation
Indices: 1376916--1377503 Score: 754
Period size: 270 Copynumber: 2.3 Consensus size: 254
1376906 TCGGGTCAGG
* *
1376916 TCGGGTCGGGTTTCTAATTCATATA-T----TCGGGTCGAGTGAAACTTTATTTTGGTCTGGTCG
1 TCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCG
* * *
1376976 GGTCGATTTTTTTAAGTGTGATATTCGGGTCAGGTCAAGTTCGGGTTTAGGGTGAAAAATACCCG
66 GGTCGATTTTTTTAAGTGTAATATTCGGGTCAGGTCAAGGTCGGGTTTAAGGTGAAAAATACCCG
* * * *
1377041 ACCCCGAAAATATATATAATTTTACCTTATATATTTAGTAATAATTACAATAATACCCCTCCATA
131 ACCCCCAAAAAATATAAAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCCATA
* * *
1377106 TATAATTTTTTTCAATTAAGTCATTGTTTTTATTGAATAAAAATAATTTTTTTATTATT
196 TATAATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAAATTTTTTATTATT
*
1377165 TCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTTG
1 TCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCG
* * * * * ** *
1377230 GGTCGGTTTTTTTTTAAATTTTAATTTTCGGGTCGGGTCGGGGTCGGGTTTAAGGTGCAAAATAC
66 GGTC-G-ATTTTTTT-AAGTGTAATATTCGGGTCAGGTCAAGGTCGGGTTTAAGGTGAAAAATAC
* *
1377295 CCGACCCGACCCAAAAAATATAAAATTTTACCTTGTATATTTAGGAATAATTATAATAATACCCC
128 CCGA-CC--CCCAAAAAATATAAAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCC
*
1377360 TCTATATATATAATTTTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAAAATTTTTTA
190 TC--CATATATAA--TTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAAT-AAATTTTTTA
1377425 TTATT
250 TTATT
* * *
1377430 TCGGGTTGGGTCAAGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAATTTTATTTTGGTCG
1 TCGGG-TCGG----GTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCA
1377495 GGTCGGGTC
61 GGTCGGGTC
1377504 TCGGATGGAG
Statistics
Matches: 290, Mismatches: 28, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
249 25 0.09
250 1 0.00
254 35 0.12
255 1 0.00
256 7 0.02
257 43 0.15
258 2 0.01
260 52 0.18
262 8 0.03
264 37 0.13
265 19 0.07
266 3 0.01
270 57 0.20
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.41
Consensus pattern (254 bp):
TCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCG
GGTCGATTTTTTTAAGTGTAATATTCGGGTCAGGTCAAGGTCGGGTTTAAGGTGAAAAATACCCG
ACCCCCAAAAAATATAAAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCCATA
TATAATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAAATTTTTTATTATT
Found at i:1377855 original size:44 final size:44
Alignment explanation
Indices: 1377791--1377911 Score: 188
Period size: 44 Copynumber: 2.8 Consensus size: 44
1377781 CATATTTGTG
1377791 AACCAAACATAATATAGAATTGGATTCCAATTCAATTTTCTGCC
1 AACCAAACATAATATAGAATTGGATTCCAATTCAATTTTCTGCC
* * *
1377835 AACCAAACAGAATATGGAATTGAATTCCAATTCAATTTTCTGCC
1 AACCAAACATAATATAGAATTGGATTCCAATTCAATTTTCTGCC
* * *
1377879 AACCAAACATAATATATAATTAGATTTCAATTC
1 AACCAAACATAATATAGAATTGGATTCCAATTC
1377912 CTGACAAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (44 bp):
AACCAAACATAATATAGAATTGGATTCCAATTCAATTTTCTGCC
Found at i:1381631 original size:26 final size:27
Alignment explanation
Indices: 1381584--1381645 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
1381574 CATATTGTAT
*
1381584 GATAAAATTTTATAGTAAATAG-ATTA
1 GATAAAATTTTATAGTAAATAGAAATA
**
1381610 GATAAAATTTT-TAGTTTCATAGTAAATA
1 GATAAAATTTTATAG-TAAATAG-AAATA
1381638 GATAAAAT
1 GATAAAAT
1381646 ACATATACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 3 0.10
26 16 0.53
28 11 0.37
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (27 bp):
GATAAAATTTTATAGTAAATAGAAATA
Found at i:1381815 original size:16 final size:17
Alignment explanation
Indices: 1381788--1381823 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1381778 GATATGAGAA
1381788 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
1381805 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
1381821 AAA
1 AAA
1381824 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:1381963 original size:13 final size:13
Alignment explanation
Indices: 1381945--1381986 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
1381935 AAATTAGAAC
1381945 AATTCATCTATGT
1 AATTCATCTATGT
1381958 AATTCATCTATGT
1 AATTCATCTATGT
1381971 AATTCATCTATGT
1 AATTCATCTATGT
1381984 AAT
1 AAT
1381987 GTATAGCGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.45
Consensus pattern (13 bp):
AATTCATCTATGT
Found at i:1385770 original size:20 final size:20
Alignment explanation
Indices: 1385725--1385774 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1385715 AAGTGCGTAT
*
1385725 TATCGATACTCTAGCTGTAA
1 TATCGATACTCTAGCGGTAA
1385745 TATCGATACTCTAG-GGTAA
1 TATCGATACTCTAGCGGTAA
*
1385764 GTTTCGATACT
1 -TATCGATACT
1385775 TTTGGAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
TATCGATACTCTAGCGGTAA
Found at i:1385836 original size:19 final size:19
Alignment explanation
Indices: 1385812--1385890 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 19
1385802 TTTTGCTAAT
1385812 GAAAGTATCGATACTCTTG
1 GAAAGTATCGATACTCTTG
* *
1385831 GAAAGTATAGATACTCTGAG
1 GAAAGTATCGATACTCT-TG
1385851 GTAAAGTATCGATACTCTTG
1 G-AAAGTATCGATACTCTTG
* * * *
1385871 AAAAGCATCAATACGCTTG
1 GAAAGTATCGATACTCTTG
1385890 G
1 G
1385891 CCTGAAATCC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
19 31 0.63
20 3 0.06
21 15 0.31
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (19 bp):
GAAAGTATCGATACTCTTG
Found at i:1390978 original size:19 final size:20
Alignment explanation
Indices: 1390930--1390978 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1390920 CTAGTAGTAA
*
1390930 TATCGATACTCTAGGGTAAG
1 TATCGATACTCTAGGGAAAG
* * *
1390950 TTTCGGTACTCT-TGGAAAG
1 TATCGATACTCTAGGGAAAG
1390969 TATCGATACT
1 TATCGATACT
1390979 AAAATGGATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (20 bp):
TATCGATACTCTAGGGAAAG
Found at i:1391022 original size:19 final size:20
Alignment explanation
Indices: 1390998--1391056 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
1390988 TCTGTTGCTA
*
1390998 AAAGTATAAATACTCTTGG-
1 AAAGTATCAATACTCTTGGC
1391017 AAAGTATCAATACTC-TGAGC
1 AAAGTATCAATACTCTTG-GC
1391037 TAAAGTATCAATACTCTTGG
1 -AAAGTATCAATACTCTTGG
1391057 TCTGAAATCC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 2 0.06
19 15 0.43
21 16 0.46
22 2 0.06
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAGTATCAATACTCTTGGC
Found at i:1395010 original size:32 final size:32
Alignment explanation
Indices: 1394974--1395045 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
1394964 TGGGCATTTC
*
1394974 TGAATGCAGGACTAACTCTGGTATGCATTATT
1 TGAATGCAAGACTAACTCTGGTATGCATTATT
* *
1395006 TGAATGTAAGATTAACTCTGGTATGCATTATT
1 TGAATGCAAGACTAACTCTGGTATGCATTATT
1395038 TGAATGCA
1 TGAATGCA
1395046 TTACTAGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (32 bp):
TGAATGCAAGACTAACTCTGGTATGCATTATT
Found at i:1396696 original size:81 final size:81
Alignment explanation
Indices: 1396592--1397005 Score: 629
Period size: 81 Copynumber: 5.1 Consensus size: 81
1396582 TGTTAAGCAT
* * * * *
1396592 TTAATCTTTTACTC-ACGGTCATTTAACCTTTCATCTAACTTGCAATATTGACACCTTTCTTCTA
1 TTAATCTTTTACTCAAAGG-CATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCA
1396656 AATGCACAACTAGGCAA
65 AATGCACAACTAGGCAA
*
1396673 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGTAATATTGGCACCTTTCTGCC-A
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
*
1396737 AT-CACAACTAGGAAA
66 ATGCACAACTAGGCAA
*
1396752 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACTTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
*
1396817 ATGCACAACTAGGGAA
66 ATGCACAACTAGGCAA
*
1396833 TTAATCTTTTACTCAAAGGCTTTTAGCCTTTCATCTAACTTGCAATATTGGCA-CTTTCCTGCCA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTT-CTGCCA
*
1396897 AATGCACGACTAGGCAA
65 AATGCACAACTAGGCAA
* * * *
1396914 TTAATCTTTTACTTAAAGACATTTAGCCTTTTATCTAACTTGCAATATTGGCACTTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
* *
1396979 ATGCATAGCTAGGCAA
66 ATGCACAACTAGGCAA
1396995 TTAATCTTTTA
1 TTAATCTTTTA
1397006 TTTTAAAAAA
Statistics
Matches: 306, Mismatches: 22, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
79 73 0.24
80 9 0.03
81 218 0.71
82 6 0.02
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (81 bp):
TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
ATGCACAACTAGGCAA
Found at i:1396860 original size:160 final size:162
Alignment explanation
Indices: 1396592--1397005 Score: 638
Period size: 160 Copynumber: 2.6 Consensus size: 162
1396582 TGTTAAGCAT
* * * * * *
1396592 TTAATCTTTTACTC-ACGGTCATTTAACCTTTCATCTAACTTGCAATATTGACACCTTTCTTCTA
1 TTAATCTTTTACTCAAAGG-CATTTAGCCTTTCATCTAACTTGCAATATTGGCACTTTTCTGCCA
*
1396656 AATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGTAATAT
65 AATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATAT
1396721 TGGCACCTTT-CTGCC-AAT-CACAACTAGGAAA
130 TGGCA-CTTTCCTGCCAAATGCACAACTAGGAAA
1396752 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACTTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACTTTTCTGCCAA
* *
1396817 ATGCACAACTAGGGAATTAATCTTTTACTCAAAGGCTTTTAGCCTTTCATCTAACTTGCAATATT
66 ATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATT
* *
1396882 GGCACTTTCCTGCCAAATGCACGACTAGGCAA
131 GGCACTTTCCTGCCAAATGCACAACTAGGAAA
* * *
1396914 TTAATCTTTTACTTAAAGACATTTAGCCTTTTATCTAACTTGCAATATTGGCACTTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACTTTTCTGCCAA
* *
1396979 ATGCATAGCTAGGCAATTAATCTTTTA
66 ATGCACAACTAGGCAATTAATCTTTTA
1397006 TTTTAAAAAA
Statistics
Matches: 233, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
159 4 0.02
160 126 0.54
161 6 0.03
162 97 0.42
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (162 bp):
TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACTTTTCTGCCAA
ATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATT
GGCACTTTCCTGCCAAATGCACAACTAGGAAA
Found at i:1397562 original size:95 final size:95
Alignment explanation
Indices: 1397434--1397616 Score: 276
Period size: 95 Copynumber: 1.9 Consensus size: 95
1397424 ATATTAATAC
* * * * *
1397434 TTCTATACTATGGTACCGATACTCCCTTTCAATATCGATACCATTTCGGCATTCTGGAATCCATG
1 TTCTATACTACGGTACCGATACTCCATTACAATATCGATACCATTTAGGCATTCTGGAATCAATG
*
1397499 GTATCGATACCTTTATCCTAGTACTGATAT
66 GTATCGATACCTTTATCATAGTACTGATAT
* *
1397529 TTCTATACTACGGTACCGATATTCCATTACAATATCGATACCATTTATGCATTCTGGAATCAATG
1 TTCTATACTACGGTACCGATACTCCATTACAATATCGATACCATTTAGGCATTCTGGAATCAATG
* *
1397594 GTATTGATACCTTTCTCATAGTA
66 GTATCGATACCTTTATCATAGTA
1397617 TCGATACCCC
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 78 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (95 bp):
TTCTATACTACGGTACCGATACTCCATTACAATATCGATACCATTTAGGCATTCTGGAATCAATG
GTATCGATACCTTTATCATAGTACTGATAT
Found at i:1398373 original size:64 final size:64
Alignment explanation
Indices: 1398305--1398464 Score: 252
Period size: 64 Copynumber: 2.5 Consensus size: 64
1398295 TGAATAAATT
*
1398305 AAACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGG-TT-TTATG
1 AAACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTATT-TG
*
1398368 AAAACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCGGGCTTATTTG
1 -AAACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTATTTG
* *
1398433 AAACATCGAATGCACTTCATGCATCGATGCAC
1 AAACATCGAATGCATTTTATGCATCGATGCAC
1398465 TCTTAGTGCA
Statistics
Matches: 90, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
64 84 0.93
65 4 0.04
66 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (64 bp):
AAACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTATTTG
Found at i:1398464 original size:17 final size:19
Alignment explanation
Indices: 1398436--1398484 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1398426 TTATTTGAAA
1398436 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
1398454 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
1398473 CATCGATGCACT
1 CATCGATGCACT
1398485 AAGGGTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 14 0.50
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:1398475 original size:64 final size:63
Alignment explanation
Indices: 1398305--1398484 Score: 240
Period size: 64 Copynumber: 2.8 Consensus size: 63
1398295 TGAATAAATT
1398305 AAACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGTTTTATGA
1 AAACATCGAATGCATTTTATGCATCGATGCACAT-CCATGCATCGATGCACTCAGGTTTTATGA
* *
1398369 AAACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCGGGCTTATT-TG
1 AAACATCGAATGCATTTTATGCATCGATGCACA-TCCATGCATCGATGCACTCAGG-TT-TTATG
1398433 -
63 A
* * *
1398433 AAACATCGAATGCACTTCATGCATCGATGCAC-TCTTAGTGCATCGATGCACT
1 AAACATCGAATGCATTTTATGCATCGATGCACATC-CA-TGCATCGATGCACT
1398485 AAGGGTCCAA
Statistics
Matches: 105, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 97 0.92
65 4 0.04
66 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (63 bp):
AAACATCGAATGCATTTTATGCATCGATGCACATCCATGCATCGATGCACTCAGGTTTTATGA
Found at i:1406251 original size:21 final size:22
Alignment explanation
Indices: 1406213--1406255 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1406203 TTGAATGGTT
* *
1406213 TTGGATTGTTTTATTTTGTTTG
1 TTGGATTGTTTGAATTTGTTTG
1406235 TTGGA-TGTTTGAATTTGTTTG
1 TTGGATTGTTTGAATTTGTTTG
1406256 GATTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.63
Consensus pattern (22 bp):
TTGGATTGTTTGAATTTGTTTG
Found at i:1406565 original size:15 final size:15
Alignment explanation
Indices: 1406545--1406575 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1406535 AACAAAAAGG
1406545 GGGAGAAGTGTTATA
1 GGGAGAAGTGTTATA
1406560 GGGAGAAGTGTTATA
1 GGGAGAAGTGTTATA
1406575 G
1 G
1406576 TAAGGGGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.42, T:0.26
Consensus pattern (15 bp):
GGGAGAAGTGTTATA
Found at i:1406946 original size:19 final size:19
Alignment explanation
Indices: 1406908--1406956 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
1406898 AAAAGAGTGT
1406908 ATCGATGCACCAATCCATGC
1 ATCGATGCA-CAATCCATGC
1406928 ATCGATGCAC-ATACCATGC
1 ATCGATGCACAAT-CCATGC
1406947 ATCGATGCAC
1 ATCGATGCAC
1406957 TCAGGTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.07
19 17 0.61
20 9 0.32
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (19 bp):
ATCGATGCACAATCCATGC
Found at i:1407019 original size:63 final size:64
Alignment explanation
Indices: 1406923--1407064 Score: 198
Period size: 63 Copynumber: 2.2 Consensus size: 64
1406913 TGCACCAATC
* *
1406923 CATGCATCGATGCACATACCATGCATCGATGCACTCAGG-TTTTATGAAAGCATCGAATGCATTT
1 CATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTTTATGAAA-CATCGAATGCACTT
* * *
1406987 TATGCATCGATGCACAGA-CATGCATCGATGCACTCGGGCTTTTTTGAAACATCGAATGCACTT
1 CATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTTTATGAAACATCGAATGCACTT
* *
1407050 CATACATCAATGCAC
1 CATGCATCGATGCAC
1407065 TCTTAGTGCA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
63 44 0.64
64 25 0.36
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTTTATGAAACATCGAATGCACTT
Found at i:1411829 original size:23 final size:23
Alignment explanation
Indices: 1411799--1411846 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1411789 GAACCAAAAG
1411799 AACAATTCGTACATTTTATAGAT
1 AACAATTCGTACATTTTATAGAT
*
1411822 AACAATTCGTACCTTTTATAGAT
1 AACAATTCGTACATTTTATAGAT
1411845 AA
1 AA
1411847 TGTTAGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
AACAATTCGTACATTTTATAGAT
Found at i:1412085 original size:39 final size:39
Alignment explanation
Indices: 1412025--1412107 Score: 105
Period size: 41 Copynumber: 2.1 Consensus size: 39
1412015 AAATGTTAGC
* **
1412025 TTTTTTTAATATTTTTTATTG-AACTAAAAATGTTAAAT
1 TTTTTTTAATATATTCGATTGAAACTAAAAATGTTAAAT
*
1412063 TTTTTTATAATATATTCGATTGACAACTAAAAATGTTATAT
1 TTTTTT-TAATATATTCGATTGA-AACTAAAAATGTTAAAT
1412104 TTTT
1 TTTT
1412108 ATAAAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 6 0.16
39 12 0.32
41 20 0.53
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (39 bp):
TTTTTTTAATATATTCGATTGAAACTAAAAATGTTAAAT
Found at i:1413696 original size:20 final size:20
Alignment explanation
Indices: 1413673--1413723 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1413663 CACAGTTTCC
1413673 GAATTCGCAACTCAAATTTG
1 GAATTCGCAACTCAAATTTG
1413693 GAATTCGCAACTCAAATTTG
1 GAATTCGCAACTCAAATTTG
1413713 GAATTCGCAAC
1 GAATTCGCAAC
1413724 ACAGAAGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (20 bp):
GAATTCGCAACTCAAATTTG
Found at i:1413787 original size:21 final size:21
Alignment explanation
Indices: 1413758--1413821 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
1413748 ACATAGAAAT
*
1413758 TTTCACAACTCGAATT-TCCAA
1 TTTCGCAACTCGAATTGT-CAA
1413779 TTTCGCAACTCGAATCTGTCAA
1 TTTCGCAACTCGAAT-TGTCAA
*
1413801 TTTCGCAACTC-AATTATCAA
1 TTTCGCAACTCGAATTGTCAA
1413821 T
1 T
1413822 ATAGGTAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.15
21 17 0.44
22 15 0.38
23 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (21 bp):
TTTCGCAACTCGAATTGTCAA
Found at i:1413974 original size:98 final size:98
Alignment explanation
Indices: 1413789--1413989 Score: 287
Period size: 98 Copynumber: 2.1 Consensus size: 98
1413779 TTTCGCAACT
* * * *
1413789 CGAATCTGTCAATTTCGCAACTCAATTATCAATATAGGTAAACACGGTAAAAAAAATCGGGTAAA
1 CGAATCTGCCAATTTCGCAACTCAATTACCAATATAGGTAAACACGGTAAAAAAAATCCGATAAA
* *
1413854 AAATCCAAATTCGCCCATTTGAAAACTCAGTTG
66 AAATCCAAATTCACCAATTTGAAAACTCAGTTG
* * *
1413887 CGAATCTGACCAATTTCGCAACTTAATTACCGATATAGGTAAACACGGT-AGAAAAATCCGATAA
1 CGAATCTG-CCAATTTCGCAACTCAATTACCAATATAGGTAAACACGGTAAAAAAAATCCGATAA
* *
1413951 AAAATCCAAATTCACCAATTTGAAAACTGAGTTT
65 AAAATCCAAATTCACCAATTTGAAAACTCAGTTG
1413985 CGAAT
1 CGAAT
1413990 TTGGCAAATT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
98 55 0.60
99 36 0.40
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (98 bp):
CGAATCTGCCAATTTCGCAACTCAATTACCAATATAGGTAAACACGGTAAAAAAAATCCGATAAA
AAATCCAAATTCACCAATTTGAAAACTCAGTTG
Found at i:1415674 original size:198 final size:192
Alignment explanation
Indices: 1415092--1415675 Score: 620
Period size: 198 Copynumber: 3.0 Consensus size: 192
1415082 ATTTTGATTT
*
1415092 TAAAAGTAGTGTTGTATGATAAAATATAAGGTAAATTACGTGTTTAATATATAAAT-T-A----T
1 TAAAAGTAGTGTTGTATGATAAAATATAAGGTAAATTACGTGTTTAATATCTAAATATCATTTTT
* **
1415151 CCGTTTTAGTATCTAAATTTTTAATTTTTT-AAAATCATATATAAAATTTAGTTTTTTTT-ATTT
66 CCGTTTTAGTATCTAAACTTTTAATTTTTTCAAAATCATACCT-AAATTTAGTTTTTTTTCATTT
* * * ** *
1415214 TAGTA-CT-TTGCCTTTAAAAACTATAGTTTTTGTTTTATTTTAATAATTATGTTCAAAATGTAA
130 TAGTACCTCTTG---TTAAAAACTTTAGTTTTTATTTTATTTTAGT-ATCCTGTTCAAAATTTAA
*
1415277 CA
191 CG
* *
1415279 TAAAAGTAGCGTTGTATGATAAAATATAGGGTAAATTATACGTG--TAATATCTAAACTATCAGT
1 TAAAAGTAGTGTTGTATGATAAAATATAAGGTAAA-T-TACGTGTTTAATATCTAAA-TATCA-T
* * **
1415342 TTTAACCCGTTTTAGTAACTAAACTTTTAAAATTTTCAAAATCATACCTAAAGTTTAGTTTTTGT
62 TTT--TCCGTTTTAGTATCTAAACTTTTAATTTTTTCAAAATCATACCTAAA-TTTAGTTTTT-T
* ** *
1415407 TTCATTTTAATACCTCGCCGTTAAAAACTTTAGTTTTTATTTCATTTTAGTATCC-GTTCAAAAT
123 TTCATTTTAGTACCTC-TTGTTAAAAACTTTAGTTTTTATTTTATTTTAGTATCCTGTTCAAAAT
1415471 TTAACG
187 TTAACG
* * * *
1415477 TAAAAGTAGTATTGTGTGATAAAATATATGGTAAATTACGTGTTTAGTATCTAAATTATCACTTT
1 TAAAAGTAGTGTTGTATGATAAAATATAAGGTAAATTACGTGTTTAATATCTAAA-TATCA-TTT
** *
1415542 TGGTCCGTTTTAACATCTAAACTTTCAATTTTTTTCAAAATCATACCTAAATTTAGTTTTTATTT
64 T--TCCGTTTTAGTATCTAAACTTTTAA-TTTTTTCAAAATCATACCTAAATTTAGTTTTT-TTT
*
1415607 CATTTTAGTACCTCATTGTTAAAAACTTTAATTTTTATTTTATTTTAGTA-CCTGTTCAAAATTT
125 CATTTTAGTACCTC-TTGTTAAAAACTTTAGTTTTTATTTTATTTTAGTATCCTGTTCAAAATTT
1415671 AACG
189 AACG
1415675 T
1 T
1415676 TAAATTTTAA
Statistics
Matches: 330, Mismatches: 44, Indels: 35
0.81 0.11 0.09
Matches are distributed among these distances:
187 43 0.13
188 2 0.01
189 7 0.02
190 1 0.00
196 6 0.02
197 32 0.10
198 176 0.53
199 25 0.08
200 35 0.11
201 2 0.01
203 1 0.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (192 bp):
TAAAAGTAGTGTTGTATGATAAAATATAAGGTAAATTACGTGTTTAATATCTAAATATCATTTTT
CCGTTTTAGTATCTAAACTTTTAATTTTTTCAAAATCATACCTAAATTTAGTTTTTTTTCATTTT
AGTACCTCTTGTTAAAAACTTTAGTTTTTATTTTATTTTAGTATCCTGTTCAAAATTTAACG
Found at i:1419311 original size:17 final size:17
Alignment explanation
Indices: 1419262--1419366 Score: 68
Period size: 17 Copynumber: 6.2 Consensus size: 17
1419252 AATTAAGAGT
* * *
1419262 TAGTTTGATTAATGCAT
1 TAGTTTAATTAATGAAC
* *
1419279 TAGTTTAATGATTGAAC
1 TAGTTTAATTAATGAAC
1419296 TAGTTTAATTAATGAACC
1 TAGTTTAATTAATGAA-C
* *
1419314 AACTTT-ATTAATGAAC
1 TAGTTTAATTAATGAAC
** ** * *
1419330 TAAATGCATGAATGAAG
1 TAGTTTAATTAATGAAC
*
1419347 TAGTTTATTTAATGAAC
1 TAGTTTAATTAATGAAC
1419364 TAG
1 TAG
1419367 ATGCATAAAT
Statistics
Matches: 64, Mismatches: 22, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
16 3 0.05
17 56 0.88
18 5 0.08
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:1419344 original size:34 final size:35
Alignment explanation
Indices: 1419306--1419380 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 35
1419296 TAGTTTAATT
*
1419306 AATGAACCAACTTTA-TTAATGAACTAAATGCATG
1 AATGAACCAACTTTATTTAATGAACTAAATGCATA
** * *
1419340 AATGAA-GTAGTTTATTTAATGAACTAGATGCATA
1 AATGAACCAACTTTATTTAATGAACTAAATGCATA
1419374 AATGAAC
1 AATGAAC
1419381 TACTTCCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 5 0.15
34 29 0.85
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (35 bp):
AATGAACCAACTTTATTTAATGAACTAAATGCATA
Found at i:1422821 original size:17 final size:17
Alignment explanation
Indices: 1422799--1422886 Score: 68
Period size: 17 Copynumber: 5.2 Consensus size: 17
1422789 AATTAAAAGT
* *
1422799 TAGTTTGATTAATGCAC
1 TAGTTTAATTAATGAAC
* * *
1422816 TAGTTTAATGATTGGAC
1 TAGTTTAATTAATGAAC
1422833 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
** ** * *
1422850 TAAATGCATGAATGAAG
1 TAGTTTAATTAATGAAC
*
1422867 TAGTTTATTTAATGAAC
1 TAGTTTAATTAATGAAC
1422884 TAG
1 TAG
1422887 ATGCATAAAT
Statistics
Matches: 51, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:1422871 original size:34 final size:34
Alignment explanation
Indices: 1422833--1422899 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1422823 ATGATTGGAC
*
1422833 TAGTTTAATTAATGAACTAAATGCATGAATGAAG
1 TAGTTTAATTAATGAACTAAATGCATAAATGAAG
* *
1422867 TAGTTTATTTAATGAACTAGATGCATAAATGAA
1 TAGTTTAATTAATGAACTAAATGCATAAATGAA
1422900 CTACTTCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.34
Consensus pattern (34 bp):
TAGTTTAATTAATGAACTAAATGCATAAATGAAG
Found at i:1422915 original size:34 final size:34
Alignment explanation
Indices: 1422843--1422924 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
1422833 TAGTTTAATT
* * * * * *
1422843 AATGAACTAAATGCATGAATGAAGTAGTTTATTT
1 AATGAACTAGATGCATAAATGAACTACTTCATTA
*
1422877 AATGAACTAGATGCATAAATGAACTACTTCCTTA
1 AATGAACTAGATGCATAAATGAACTACTTCATTA
1422911 AATGAACTAGATGC
1 AATGAACTAGATGC
1422925 TTATATGCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (34 bp):
AATGAACTAGATGCATAAATGAACTACTTCATTA
Found at i:1422927 original size:17 final size:17
Alignment explanation
Indices: 1422877--1422951 Score: 73
Period size: 17 Copynumber: 4.4 Consensus size: 17
1422867 TAGTTTATTT
*
1422877 AATGAACTAGATGCATA
1 AATGAACTAGATGCTTA
** *
1422894 AATGAACTACTTCCTTA
1 AATGAACTAGATGCTTA
1422911 AATGAACTAGATGCTTA
1 AATGAACTAGATGCTTA
*
1422928 TATGCAA-T-GCATGCTTA
1 AATG-AACTAG-ATGCTTA
1422945 AATGAAC
1 AATGAAC
1422952 ATCATGCTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
16 3 0.07
17 41 0.89
18 2 0.04
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (17 bp):
AATGAACTAGATGCTTA
Found at i:1422957 original size:17 final size:18
Alignment explanation
Indices: 1422877--1422960 Score: 61
Period size: 17 Copynumber: 4.9 Consensus size: 18
1422867 TAGTTTATTT
* *
1422877 AATGAAC-TAGATGCATA
1 AATGAACATACATGCTTA
* *
1422894 AATGAAC-TACTTCCTTA
1 AATGAACATACATGCTTA
*
1422911 AATGAAC-TAGATGCTTA
1 AATGAACATACATGCTTA
* * *
1422928 TATGCA-ATGCATGCTTA
1 AATGAACATACATGCTTA
1422945 AATGAACAT-CATGCTT
1 AATGAACATACATGCTT
1422961 TATTACATGC
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
17 50 0.96
18 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (18 bp):
AATGAACATACATGCTTA
Found at i:1439516 original size:22 final size:20
Alignment explanation
Indices: 1439475--1439527 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
1439465 ACTAAAGGGG
* *
1439475 AGTATCGGTACCATATTATAGA
1 AGTATCGATACCATAGTAT--A
*
1439497 AGTATCGATACCATGGTATA
1 AGTATCGATACCATAGTATA
1439517 AGTATCGATAC
1 AGTATCGATAC
1439528 TATTAAGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 12 0.43
22 16 0.57
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTATCGATACCATAGTATA
Found at i:1439526 original size:94 final size:95
Alignment explanation
Indices: 1439328--1439527 Score: 218
Period size: 94 Copynumber: 2.1 Consensus size: 95
1439318 CATGAGGAAG
* * *
1439328 GTATCGATACTATTGATTTACAGAATGTAGAAATGGTATCGATACCGTAATAGAGTATGAGTACC
1 GTATCGATACCATGGATTTACAGAATGTAGAAATGGAATCGATACCGTAATAGAGTATGAGTACC
*
1439393 ATAGTTTAGAAGTATCGATACTAAGAGATA
66 ATAGTTTAGAAGTATCGATACCAAGAGATA
*
1439423 GATACCGATACCATGGA-TT-CAGAATGTAGAAATGGAATCGATA-C-TAA-AGGGGAGTATCG-
1 G-TATCGATACCATGGATTTACAGAATGTAGAAATGGAATCGATACCGTAATA---GAGTAT-GA
*
1439482 GTACCATA-TTATAGAAGTATCGATACCATG-GTATAA
61 GTACCATAGTT-TAGAAGTATCGATACCAAGAG-AT-A
1439518 GTATCGATAC
1 GTATCGATAC
1439528 TATTAAGCCA
Statistics
Matches: 90, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
91 1 0.01
92 3 0.03
93 4 0.04
94 64 0.71
95 6 0.07
96 12 0.13
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (95 bp):
GTATCGATACCATGGATTTACAGAATGTAGAAATGGAATCGATACCGTAATAGAGTATGAGTACC
ATAGTTTAGAAGTATCGATACCAAGAGATA
Found at i:1439938 original size:54 final size:54
Alignment explanation
Indices: 1439856--1440142 Score: 391
Period size: 54 Copynumber: 5.4 Consensus size: 54
1439846 ATATTTTAGC
* *
1439856 CACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACTGTTTTGG
1 CACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTGG
* * *
1439910 CACTATGTGTGCAACCCACGGAATTCATCATAAATTGCTGAACAACAGTTTTGG
1 CACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTGG
* * * * *
1439964 TACTATGTGTGAAACCCACGAAATTCATCATAAG-TGATGAACAACCATTTTGT
1 CACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTGG
* *
1440017 CACTATATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGG
1 CACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTGG
* * * * *
1440071 CACTATGTGTGCAACCCATGAAATTCATCATATA-TTGATGAA-AACCATTTAGC
1 CACTATGTGTGCAACCCACGGAATTCATCATA-AGTTGATGAACAACCGTTTTGG
1440124 CACTATGTGTGCAACCCAC
1 CACTATGTGTGCAACCCAC
1440143 ATAAATCATA
Statistics
Matches: 204, Mismatches: 27, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
53 70 0.34
54 133 0.65
55 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (54 bp):
CACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTGG
Found at i:1440165 original size:107 final size:107
Alignment explanation
Indices: 1439856--1440189 Score: 411
Period size: 107 Copynumber: 3.1 Consensus size: 107
1439846 ATATTTTAGC
* * ** *
1439856 CACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACTGTTTTGGCACTATGTGTG
1 CACTATGTGTGCAACCCACGAAATTCATCATAA-TTGATGAACAACCATTTTGCCACTATGTGTG
* * * *
1439921 CAACCCACGGAATTCATCATAAATTGCTGAACAACAGTTTTGG
65 CAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGG
* * * * *
1439964 TACTATGTGTGAAACCCACGAAATTCATCATAAGTGATGAACAACCATTTTGTCACTATATGTGC
1 CACTATGTGTGCAACCCACGAAATTCATCATAATTGATGAACAACCATTTTGCCACTATGTGTGC
1440029 AACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGG
66 AACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGG
* *
1440071 CACTATGTGTGCAACCCATGAAATTCATCATATATTGATGAA-AACCATTTAGCCACTATGTGTG
1 CACTATGTGTGCAACCCACGAAATTCATCATA-ATTGATGAACAACCATTTTGCCACTATGTGTG
* * * * * ** *
1440135 CAACCCACATAAATCATAATATGTTTATGAATGACCGTATTGG
65 CAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGG
*
1440178 CACCA-GTGTGCA
1 CACTATGTGTGCA
1440190 TCTTAACAAA
Statistics
Matches: 196, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
106 7 0.04
107 152 0.78
108 37 0.19
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (107 bp):
CACTATGTGTGCAACCCACGAAATTCATCATAATTGATGAACAACCATTTTGCCACTATGTGTGC
AACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGG
Found at i:1446905 original size:54 final size:54
Alignment explanation
Indices: 1446827--1447091 Score: 291
Period size: 54 Copynumber: 4.9 Consensus size: 54
1446817 AGCCATTATA
* * * *
1446827 TGTGCAACGCACGAAATTCATCATAAGTTTATGAACAATCGTTTTTGCACTATG
1 TGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
* * *
1446881 TGTGCAACCGACGTAATTCATCATAA-CTGATGAACAACCGTTTTGGCACTATG
1 TGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
* * *
1446934 TGTGCAACCCATGGAATTCATCATAAGTTGACGAACAACCGTTTTGGCACTATG
1 TGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
* * * * * *
1446988 TTTGCAACCCAC-AGAATTCATCATATGTTGATGAACAATCATTTAGGCACTGTG
1 TGTGCAACCCACGA-AATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
* * * * * ** *
1447042 TTTGCAACCCACAAAATTCATAATATGTTTATGAATGACCGTATTGGCAC
1 TGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTTGGCAC
1447092 CACGTGTACA
Statistics
Matches: 179, Mismatches: 29, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
53 46 0.26
54 132 0.74
55 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (54 bp):
TGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
Found at i:1448529 original size:31 final size:30
Alignment explanation
Indices: 1448433--1448531 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
1448423 AAAAATGGTT
* * *
1448433 AAATTTTAATTTAACCCTTAACTTTTAGATA
1 AAATATTAATTTAACCCATAA-ATTTAGATA
* * *
1448464 AAATACTAGTTTAACCCAAAAATTTAGATA
1 AAATATTAATTTAACCCATAAATTTAGATA
* *
1448494 AAATATTAATATAACCCATAAATTATATATA
1 AAATATTAATTTAACCCATAAATT-TAGATA
1448525 AAATATT
1 AAATATT
1448532 TTATCTATAG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 28 0.50
31 28 0.50
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATATTAATTTAACCCATAAATTTAGATA
Found at i:1449925 original size:37 final size:37
Alignment explanation
Indices: 1449873--1450205 Score: 260
Period size: 37 Copynumber: 9.1 Consensus size: 37
1449863 CAAAATTGGT
*
1449873 TTTTGAAATATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAA-ACATATATAATATATAGTTTTTGAAAACA
* * **
1449911 TTTTAAAAACATATATAACATATAGTTTTTG-AAATT
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
* * * * * **
1449947 TTTTGAATATATATATATATATATA-TAATAT-ATATAGT
1 TTTTGAAAACATATATA-ATATATAGT-TTTTGA-AAACA
* * ** * **
1449985 TTTTGAAAACAT-TTTGAAAATATA--TAAT-ATATAGT
1 TTTTGAAAACATATAT-AATATATAGTTTTTGA-AAACA
* *
1450020 TTTTGAACACATATATAATATATAG-TTTTGAAATCA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
*
1450056 TTTCTGAAAACTTATATAATATATAGTTTTTGAAAACA
1 TTT-TGAAAACATATATAATATATAGTTTTTGAAAACA
* *
1450094 TTTTGGAAACTTATATAATATATAG-TTTTGAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
*
1450130 TTTTTGAAAAAAATATATAATATATAG-TTTTGAAAACA
1 -TTTTG-AAAACATATATAATATATAGTTTTTGAAAACA
1450168 TTTTTG-AAA-ATATATAATATATAGTTTTT-AAAACA
1 -TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
1450203 TTT
1 TTT
1450206 CACGAAACGA
Statistics
Matches: 247, Mismatches: 35, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
34 3 0.01
35 48 0.19
36 44 0.18
37 84 0.34
38 68 0.28
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
Found at i:1449958 original size:2 final size:2
Alignment explanation
Indices: 1449953--1449982 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1449943 AATTTTTTGA
1449953 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1449983 GTTTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1450015 original size:35 final size:35
Alignment explanation
Indices: 1449967--1450205 Score: 252
Period size: 38 Copynumber: 6.9 Consensus size: 35
1449957 ATATATATAT
1449967 ATATATAATATATATAGTTTTTGAAAACATTTTGAAA
1 ATATAT-A-ATATATAGTTTTTGAAAACATTTTGAAA
*
1450004 ATATATAATATATAGTTTTTG--AAC-------AC
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAA
*
1450030 ATATATAATATATAG-TTTTGAAATCATTTCTGAAA
1 ATATATAATATATAGTTTTTGAAAACATTT-TGAAA
1450065 ACTTATATAATATATAGTTTTTGAAAACATTTTGGAAA
1 A--TATATAATATATAGTTTTTGAAAACATTTT-GAAA
*
1450103 CTTATATAATATATAG-TTTTGAAAACATTTTTGAAAAAA
1 -ATATATAATATATAGTTTTTGAAAACA-TTTTG---AAA
1450142 ATATATAATATATAG-TTTTGAAAACATTTTTGAAA
1 ATATATAATATATAGTTTTTGAAAACA-TTTTGAAA
1450177 ATATATAATATATAGTTTTT-AAAACATTT
1 ATATATAATATATAGTTTTTGAAAACATTT
1450206 CACGAAACGA
Statistics
Matches: 176, Mismatches: 6, Indels: 43
0.78 0.03 0.19
Matches are distributed among these distances:
25 5 0.03
26 16 0.09
27 2 0.01
33 3 0.02
34 3 0.02
35 40 0.23
36 17 0.10
37 39 0.22
38 48 0.27
39 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTGAAAACATTTTGAAA
Found at i:1450033 original size:26 final size:24
Alignment explanation
Indices: 1449996--1450052 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 24
1449986 TTTGAAAACA
1449996 TTTTGAAAATATATAATATATAGT
1 TTTTGAAAATATATAATATATAGT
1450020 TTTTGAACACATATATAATATATAG-
1 TTTTGAA-A-ATATATAATATATAGT
1450045 TTTTGAAA
1 TTTTGAAA
1450053 TCATTTCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 8 0.26
25 8 0.26
26 15 0.48
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (24 bp):
TTTTGAAAATATATAATATATAGT
Found at i:1453052 original size:16 final size:16
Alignment explanation
Indices: 1453031--1453071 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1453021 GAATAAACAC
1453031 TGGACACACCGAGCAT
1 TGGACACACCGAGCAT
* *
1453047 TGGACATACTGAGCAT
1 TGGACACACCGAGCAT
*
1453063 TGAACACAC
1 TGGACACAC
1453072 TCGTTCAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (16 bp):
TGGACACACCGAGCAT
Found at i:1454593 original size:36 final size:36
Alignment explanation
Indices: 1454524--1454594 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1454514 ATCCTGTTCG
*
1454524 AACTTGTTTTTTGAACTTTCTCATGTATCTTTTTGT
1 AACTTGTTTTTTGAACTTTCTCATATATCTTTTTGT
* *
1454560 AACTTGTTTTTTGAACTTTCTCATATTTGTTTTTG
1 AACTTGTTTTTTGAACTTTCTCATATATCTTTTTG
1454595 CAAGGATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (36 bp):
AACTTGTTTTTTGAACTTTCTCATATATCTTTTTGT
Found at i:1455285 original size:99 final size:98
Alignment explanation
Indices: 1455093--1455291 Score: 301
Period size: 99 Copynumber: 2.0 Consensus size: 98
1455083 TTATAATATT
* * * *
1455093 ATATGTATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCAGCTTTATGGA
1 ATATCTATACAATAAAGCTTGAGTTATCCCTCTAGAGAAATTAGTTAAACGCCCAGCTTTAGGGA
**
1455158 TAAGATTCAGTTAGCCTGATAAAGGTGATTATA
66 TAAGATTCAACTAGCCTGATAAAGGTGATTATA
* *
1455191 ATATCTATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTAGTTAAGTAC-CCCGGCTTTAGG
1 ATATCTATACAATAAAGCTTGAGTTATCCCTCTAGAGAAATTAGTTAA--ACGCCCAGCTTTAGG
1455255 GATAAGATTCAACTAGCCTGATAAAGGTGATTATA
64 GATAAGATTCAACTAGCCTGATAAAGGTGATTATA
1455290 AT
1 AT
1455292 CTTGAGCGGT
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
98 44 0.48
99 45 0.49
100 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (98 bp):
ATATCTATACAATAAAGCTTGAGTTATCCCTCTAGAGAAATTAGTTAAACGCCCAGCTTTAGGGA
TAAGATTCAACTAGCCTGATAAAGGTGATTATA
Found at i:1457255 original size:43 final size:43
Alignment explanation
Indices: 1457162--1457379 Score: 303
Period size: 43 Copynumber: 5.1 Consensus size: 43
1457152 TTGGTAACAA
* * ** *
1457162 AAACGCCGCAATAGGTGTTGATATTT-GCAGTATTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* * *
1457204 AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* *
1457247 AAATGCCGCAATAGGTTTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* * *
1457290 AAATGCCGCAATAGATTTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
1457333 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1457376 AAAC
1 AAAC
1457380 ACCGTAAAAG
Statistics
Matches: 162, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 25 0.15
43 137 0.85
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
Found at i:1457413 original size:43 final size:43
Alignment explanation
Indices: 1457194--1457412 Score: 192
Period size: 43 Copynumber: 5.1 Consensus size: 43
1457184 ATTTGCAGTA
* * * * * *
1457194 TTTTTCCAACAAACGCCGCAATAAG-TGTTGATATTTAGCGGCA
1 TTTTTCCCACAAACACCGCAA-AAGATCTTGAGATATAGCGGCG
** * * * *
1457237 TTTTTCCCACAAATGCCGCAATAGGTTTTGAGATTTAGCGGCG
1 TTTTTCCCACAAACACCGCAAAAGATCTTGAGATATAGCGGCG
** * * *
1457280 TTTTTCCCACAAATGCCGCAATAGATTTTGAGATTTAGCGGCG
1 TTTTTCCCACAAACACCGCAAAAGATCTTGAGATATAGCGGCG
* * * *
1457323 TTTTTCCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCG
1 TTTTTCCCACAAACACCGCAAAAGATCTTGAGATATAGCGGCG
* *
1457366 TTTTTCCCACAAACACCGTAAAAGATC-TG-GTATATAGCGACG
1 TTTTTCCCACAAACACCGCAAAAGATCTTGAG-ATATAGCGGCG
1457408 TTTTT
1 TTTTT
1457413 TATAACAAAC
Statistics
Matches: 158, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 18 0.11
43 139 0.88
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (43 bp):
TTTTTCCCACAAACACCGCAAAAGATCTTGAGATATAGCGGCG
Found at i:1457413 original size:86 final size:86
Alignment explanation
Indices: 1457162--1457412 Score: 260
Period size: 86 Copynumber: 2.9 Consensus size: 86
1457152 TTGGTAACAA
* * * ** * *
1457162 AAACGCCGCAATAGGTGTTGATATTT-GCAGTATTTTTCCAACAAACGCCGCAATAAG-TGT-TG
1 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAA-AAGAT-TCTG
* * * *
1457224 ATATTTAGCGGCATTTTTCCCAC
64 AGATATAGCGACGTTTTTCCCAC
* * ** * *
1457247 AAATGCCGCAATAGGTTTTGAGATTTAGCGGCGTTTTTCCCACAAATGCCGCAATAGATTTTGAG
1 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATTCTGAG
* *
1457312 ATTTAGCGGCGTTTTTCCCAC
66 ATATAGCGACGTTTTTCCCAC
*
1457333 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGTAAAAGA-TCTG-G
1 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATTCTGAG
1457396 TATATAGCGACGTTTTT
66 -ATATAGCGACGTTTTT
1457413 TATAACAAAC
Statistics
Matches: 142, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
84 1 0.01
85 43 0.30
86 98 0.69
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (86 bp):
AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATTCTGAG
ATATAGCGACGTTTTTCCCAC
Found at i:1457421 original size:129 final size:129
Alignment explanation
Indices: 1457158--1457429 Score: 291
Period size: 129 Copynumber: 2.1 Consensus size: 129
1457148 GCGTTTGGTA
* * * * ** *
1457158 ACAA-AAACGCCGCAATAGGTGTTGATATTT-GCAGTATTTTTCCAACAAACGCCGCAATAAGTG
1 ACAACAAACGCCGCAATAGATTTTGAGATTTAGCGGCGTTTTTCCAACAAACGCCGCAATAAGTC
* ** * * * * *
1457221 TTGATATTTAGCGGCATTTTTCCCACAAATGCCGCAATAGGTTTTGAGATTTAGCGGCGTTTTT
66 TTGAGATTTAGCGGCATTTTTCCCACAAACACCGCAATAAGATCTGAGATATAGCGACGTTTTT
* * * * *
1457285 CCCACAAATGCCGCAATAGATTTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTC
1 ACAACAAACGCCGCAATAGATTTTGAGATTTAGCGGCGTTTTTCCAACAAACGCCGCAATAAGTC
* *
1457350 TTGAGATTTAGCGGCGTTTTTCCCACAAACACCGTAA-AAGATCTG-GTATATAGCGACGTTTTT
66 TTGAGATTTAGCGGCATTTTTCCCACAAACACCGCAATAAGATCTGAG-ATATAGCGACG-TTTT
1457413 T
129 T
*
1457414 ATAACAAACGCCGCAA
1 ACAACAAACGCCGCAA
1457430 AATGTCATAT
Statistics
Matches: 115, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
127 3 0.03
128 36 0.31
129 76 0.66
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (129 bp):
ACAACAAACGCCGCAATAGATTTTGAGATTTAGCGGCGTTTTTCCAACAAACGCCGCAATAAGTC
TTGAGATTTAGCGGCATTTTTCCCACAAACACCGCAATAAGATCTGAGATATAGCGACGTTTTT
Found at i:1457602 original size:21 final size:21
Alignment explanation
Indices: 1457576--1457634 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1457566 ATTTTCCAAT
*
1457576 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
1457597 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
1457618 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
1457635 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:1461838 original size:81 final size:82
Alignment explanation
Indices: 1461719--1462003 Score: 235
Period size: 81 Copynumber: 3.5 Consensus size: 82
1461709 AATGTTGTTT
* * * * * *
1461719 TATAGTACGAGTATTTAGTGGTGTTTGTGCT-TAAAACGCCACTAAAGTACATTATTTTGAGGCA
1 TATAGTACGAGTATTTAGCGGCGTTTGT-ATAAAAAACGCCACTAAAGTACATTATTTAGAGGCG
*
1461783 TTTATAT-AAAACGCCAC
65 TTTGTATAAAAACGCCAC
* * * * *
1461800 TATAGTACCAGTATTTAGCGGTGTTTGTATAAAAAACGCCGCTAAAG-AC-TCGTACTATAGCGG
1 TATAGTACGAGTATTTAGCGGCGTTTGTATAAAAAACGCCACTAAAGTACAT--TA-TTTAGAGG
1461863 CGTTTGTATAAAAACGCCAC
63 CGTTTGTATAAAAACGCCAC
* * * * * * * * *
1461883 TA-AATCACGAGTCTATAGCGGCGTTTGT-TCTATAAACGCCAGTAAATTACAGTT-TTTCGTGG
1 TATAGT-ACGAGTATTTAGCGGCGTTTGTAT-AAAAAACGCCACTAAAGTACA-TTATTTAGAGG
1461945 CGTTTGTATAAAAACGCCAC
63 CGTTTGTATAAAAACGCCAC
* * *
1461965 TAAAGTA-AATTATTTAGCGGCGTTTGTATAAAAAACGCC
1 TATAGTACGAGTATTTAGCGGCGTTTGTATAAAAAACGCC
1462004 GGTAAAGACT
Statistics
Matches: 162, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
79 1 0.01
80 3 0.02
81 66 0.41
82 44 0.27
83 44 0.27
84 3 0.02
86 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (82 bp):
TATAGTACGAGTATTTAGCGGCGTTTGTATAAAAAACGCCACTAAAGTACATTATTTAGAGGCGT
TTGTATAAAAACGCCAC
Found at i:1462109 original size:40 final size:41
Alignment explanation
Indices: 1461751--1462111 Score: 258
Period size: 41 Copynumber: 8.9 Consensus size: 41
1461741 GTTTGTGCTT
* * * * * *
1461751 AAAACGCCACTAAAGTAC-ATTATTTTGAGGCATTTATAT-
1 AAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTATA
* * * *
1461790 AAAACGCCACTATAGTACCAGTATTTAGCGGTGTTTGTATAA
1 AAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTAT-A
* * *
1461832 AAAACGCCGCTAAAG-ACTCGTACTATAGCGGCGTTTGTATA
1 AAAACGCCACTAAAGTACTAGT-CTTTAGCGGCGTTTGTATA
* * *
1461873 AAAACGCCACTAAA-TCACGAGTCTATAGCGGCGTTTGTTCTA
1 AAAACGCCACTAAAGT-ACTAGTCTTTAGCGGCGTTTG-TATA
* * * * * *
1461915 TAAACGCCAGTAAATTAC-AGTTTTTCGTGGCGTTTGTATA
1 AAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTATA
* * *
1461955 AAAACGCCACTAAAGTA-AATTATTTAGCGGCGTTTGTATAA
1 AAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTAT-A
** * * * * *
1461996 AAAACGCCGGTAAAG-ACTCGTATTATAGCGTCATTTGTACA
1 AAAACGCCACTAAAGTACTAGTCTT-TAGCGGCGTTTGTATA
*
1462037 AAAACGCCACTAAA-T--TAGTCTTTAGCGCCGTTTGTAT-
1 AAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTATA
* * * *
1462074 AAAACGCCGCTATAGTACGAGTCTTTACCGGCGTTTGT
1 AAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGT
1462112 TCTAGAAATG
Statistics
Matches: 254, Mismatches: 52, Indels: 31
0.75 0.15 0.09
Matches are distributed among these distances:
37 12 0.05
38 13 0.05
39 22 0.09
40 67 0.26
41 78 0.31
42 61 0.24
43 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
AAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTATA
Found at i:1462478 original size:85 final size:85
Alignment explanation
Indices: 1462342--1463000 Score: 881
Period size: 85 Copynumber: 7.8 Consensus size: 85
1462332 CTATTACAAT
* * ** * * *
1462342 ATAGCTTAAGTCGAGAAAAGCTATATGTCAACAAAAACCTACGAGTTCGATTACATTCATCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1462407 GGGCATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* ** * * *
1462427 ATAACTCAAGGTAAGAAGGGATATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTTAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
*
1462492 GGGCATATCAAATTTACAGT
66 GGGCATATCAAATTTACAGC
** * *
1462512 ATAGCTCAAGAAGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTTGATTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1462577 GGGCATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* * * * * * *
1462597 ATAGCTCAAGGAGAGAAGGGTTATATGTCAGCAAAAACCTTTGAGTTCGATTACATTCAGCTTAG
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
*
1462662 GGGCATATCAAATTTACAAC
66 GGGCATATCAAATTTACAGC
* * ** *
1462682 ATAGCTCAAGACGAGAAGGGCTATTTGTCAGTAAAAACCTTCGAGTTTGATTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
*
1462747 GGGCATATCAAATTTACAGT
66 GGGCATATCAAATTTACAGC
* * * *
1462767 ATAGCTCAAGGCGAGAAGGGATATCTATTAA-TAAAACCTTCGAGTTCGATT-CTATTCAGCTCA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTAC-ATTCAGCTCA
*
1462830 AGGGCATATCAAATTTACAGT
65 AGGGCATATCAAATTTACAGC
* * * * *
1462851 ATAACTCAAGGTGAGAAGGGCTATCGGTCAACAAAATCCTTCGAGTTCGATTTCATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1462916 GGGCATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* * * *
1462936 ATAACTCAAGGCGAGAAGGGCTATCTGTTAACAAAAACCTTCGAGTTTGATTTCATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1463001 CGACAATGAG
Statistics
Matches: 506, Mismatches: 65, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
83 1 0.00
84 74 0.15
85 430 0.85
86 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (85 bp):
ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
GGGCATATCAAATTTACAGC
Found at i:1463803 original size:32 final size:33
Alignment explanation
Indices: 1463698--1463960 Score: 169
Period size: 37 Copynumber: 7.4 Consensus size: 33
1463688 TTTAAAACAT
* *
1463698 ACATA-ATATATAGTTTTGAAAACA-ATTGAAAA
1 ACATATATATATATTTTTGAAAACATTTTG-AAA
*
1463730 TATTATATAATATATAGTTTTTGAAAACATTTTG-AA
1 -A-CATAT-ATATATA-TTTTTGAAAACATTTTGAAA
*
1463766 A-ATATATATATATTTTTGGAAACA-TTTGAAA
1 ACATATATATATATTTTTGAAAACATTTTGAAA
* *
1463797 ACATATATATATAGTTTTGAAATCATTTCTGAAA
1 ACATATATATATATTTTTGAAAACATTT-TGAAA
1463831 ACTTATATAATATATAGTTTTTGAAAACATTTTGAAAAACTCAAAA
1 AC--ATAT-ATATATA-TTTTTGAAAACATTTTG---------AAA
*
1463877 ACATATATAATATATAGTTTTGAAAACATTTTTTAAA
1 ACATATAT-ATATAT--TTTTGAAAACA-TTTTGAAA
* * *
1463914 ATATATAATATATAGTTTTAAAAACATTTTTG-AA
1 ACATAT-ATATATATTTTTGAAAACA-TTTTGAAA
1463948 ACATATATATATA
1 ACATATATATATA
1463961 ATTTAAAAAA
Statistics
Matches: 188, Mismatches: 15, Indels: 54
0.73 0.06 0.21
Matches are distributed among these distances:
30 4 0.02
31 14 0.07
32 27 0.14
33 14 0.07
34 17 0.09
35 16 0.09
36 13 0.07
37 33 0.18
38 18 0.10
43 3 0.02
44 9 0.05
45 11 0.06
46 9 0.05
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (33 bp):
ACATATATATATATTTTTGAAAACATTTTGAAA
Found at i:1463883 original size:39 final size:37
Alignment explanation
Indices: 1463803--1463885 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
1463793 GAAAACATAT
* * * *
1463803 ATATATAGTTTTGAAATCATTTCTGAAAACTTATATA
1 ATATATAGTTTTGAAAACATTTCTGAAAACTCAAAAA
1463840 ATATATAGTTTTTGAAAACATTT-TGAAAAACTCAAAAA
1 ATATATAG-TTTTGAAAACATTTCTG-AAAACTCAAAAA
1463878 CATATATA
1 -ATATATA
1463886 ATATATAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 10 0.26
38 22 0.56
39 7 0.18
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (37 bp):
ATATATAGTTTTGAAAACATTTCTGAAAACTCAAAAA
Found at i:1463918 original size:33 final size:34
Alignment explanation
Indices: 1463881--1463982 Score: 125
Period size: 35 Copynumber: 3.0 Consensus size: 34
1463871 TCAAAAACAT
* *
1463881 ATATAATATATAGTTTTGAAAACATTTTTTAAAAT
1 ATATAATATATAGTTTTAAAAACATTTTTT-AAAC
*
1463916 ATATAATATATAGTTTTAAAAACATTTTTGAAAC
1 ATATAATATATAGTTTTAAAAACATTTTTTAAAC
* * *
1463950 ATAT-ATATATAATTTAAAAAAACTTTTTTTAAA
1 ATATAATATATAGTTT-TAAAAACATTTTTTAAA
1463983 ACGTTTTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
33 10 0.17
34 21 0.36
35 28 0.47
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (34 bp):
ATATAATATATAGTTTTAAAAACATTTTTTAAAC
Found at i:1463923 original size:35 final size:36
Alignment explanation
Indices: 1463875--1463960 Score: 140
Period size: 35 Copynumber: 2.4 Consensus size: 36
1463865 AAAAACTCAA
* *
1463875 AAACATATATAATATATAGTTTTGAAAACATTTTTT
1 AAACATATATAATATATAGTTTTAAAAACATTTTTG
1463911 AAA-ATATATAATATATAGTTTTAAAAACATTTTTG
1 AAACATATATAATATATAGTTTTAAAAACATTTTTG
1463946 AAACATATAT-ATATA
1 AAACATATATAATATA
1463961 ATTTAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 38 0.81
36 9 0.19
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (36 bp):
AAACATATATAATATATAGTTTTAAAAACATTTTTG
Found at i:1464050 original size:14 final size:13
Alignment explanation
Indices: 1464013--1464083 Score: 63
Period size: 13 Copynumber: 5.3 Consensus size: 13
1464003 ATTAGTATAC
*
1464013 TTTTATTATTA-T
1 TTTTATTTTTATT
* *
1464025 TATTATTATTATT
1 TTTTATTTTTATT
1464038 TCTTTATTTTTATTT
1 T-TTTATTTTTA-TT
1464053 TTTCTATTTTTATT
1 TTT-TATTTTTATT
* *
1464067 TATTATCTTTATT
1 TTTTATTTTTATT
1464080 TTTT
1 TTTT
1464084 GTAAGGGTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
12 10 0.20
13 14 0.29
14 14 0.29
15 11 0.22
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:1464050 original size:17 final size:17
Alignment explanation
Indices: 1464024--1464082 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
1464014 TTTATTATTA
*
1464024 TTATTATTATTATTTCT
1 TTATTTTTATTATTTCT
1464041 TTATTTTTATT-TTT-T
1 TTATTTTTATTATTTCT
*
1464056 CTATTTTTATTTATTATCT
1 TTATTTTTA-TTATT-TCT
1464075 TTATTTTT
1 TTATTTTT
1464083 TGTAAGGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 9 0.26
16 5 0.14
17 12 0.34
18 1 0.03
19 8 0.23
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTTTATTATTTCT
Done.