Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 17
Found at i:1259763 original size:21 final size:20
Alignment explanation
Indices: 1259738--1259801 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1259728 AACTTTGGAA
1259738 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
1259759 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
1259773 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
1259794 AAATGTTT
1 AAATGTTT
1259802 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:1259819 original size:36 final size:36
Alignment explanation
Indices: 1259730--1259848 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
1259720 TGGCAACCAA
*
1259730 CTTTGGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTT-GAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1259767 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
1259802 CTTTGAAAAATGGTTTTCCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGGTTTT-CAAAGTTTGGTAAATGTTT
*
1259839 -GTTGAAAAAT
1 CTTTGAAAAAT
1259849 TGTAATGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 34 0.44
36 21 0.27
37 22 0.29
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1264422 original size:35 final size:36
Alignment explanation
Indices: 1264346--1264422 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 36
1264336 ACCAACTTTG
*
1264346 GAAAAATGATTTATAAAGTTTGGTAAATGTTTCTTT
1 GAAAAATGATTTATAAAGTTTGGTAAATGTTTCGTT
* *
1264382 G-AAAATGGTTT-TCAAAGTTTGGTAGATGTTT-GTT
1 GAAAAATGATTTAT-AAAGTTTGGTAAATGTTTCGTT
1264416 GAAAAAT
1 GAAAAAT
1264423 TGTAATGGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 4 0.11
35 31 0.86
36 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.42
Consensus pattern (36 bp):
GAAAAATGATTTATAAAGTTTGGTAAATGTTTCGTT
Found at i:1266286 original size:23 final size:22
Alignment explanation
Indices: 1266260--1266316 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
1266250 GGTCCTCTAA
1266260 TTTTATTTTATTTTATCATTAT
1 TTTTATTTTATTTTATCATTAT
* *
1266282 TTTT-TTCTTCATATTATTATTAT
1 TTTTATT-TT-ATTTTATCATTAT
*
1266305 TATTATTTTATT
1 TTTTATTTTATT
1266317 GCTTAGACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 2 0.07
22 8 0.29
23 16 0.57
24 2 0.07
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTATTTTATTTTATCATTAT
Found at i:1266373 original size:15 final size:15
Alignment explanation
Indices: 1266353--1266397 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1266343 TCTTTACCGT
1266353 TTTTATTATTCTTTA
1 TTTTATTATTCTTTA
*
1266368 TTTTATTATTATTT-
1 TTTTATTATTCTTTA
1266382 TTTCT-TT-TTCTTTA
1 TTT-TATTATTCTTTA
1266396 TT
1 TT
1266398 ATTTTATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 5 0.19
14 7 0.27
15 14 0.54
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATTATTCTTTA
Found at i:1266392 original size:28 final size:28
Alignment explanation
Indices: 1266352--1266412 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1266342 TTCTTTACCG
*
1266352 TTTTTATTATTCTTTATT-TTATTATTAT
1 TTTTTATTATTCTTTATTATT-TTATCAT
* *
1266380 TTTTTCTTTTTCTTTATTATTTTATCAT
1 TTTTTATTATTCTTTATTATTTTATCAT
1266408 TTTTT
1 TTTTT
1266413 GAATATCGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTTATTATTCTTTATTATTTTATCAT
Found at i:1266410 original size:20 final size:20
Alignment explanation
Indices: 1266373--1266410 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1266363 CTTTATTTTA
* *
1266373 TTATTATTTTTTCTTTTTCT
1 TTATTATTTTATCATTTTCT
1266393 TTATTATTTTATCATTTT
1 TTATTATTTTATCATTTT
1266411 TTGAATATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (20 bp):
TTATTATTTTATCATTTTCT
Found at i:1266474 original size:18 final size:18
Alignment explanation
Indices: 1266451--1266485 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1266441 ACCTAACATC
*
1266451 TTTTTATTTATTTATTTA
1 TTTTTATTTACTTATTTA
1266469 TTTTTATTTACTTATTT
1 TTTTTATTTACTTATTT
1266486 CCTCTAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTATTTACTTATTTA
Found at i:1269272 original size:23 final size:24
Alignment explanation
Indices: 1269245--1269299 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
1269235 TGGTCCTCTA
* *
1269245 ATTTTATTTTATTTTATCATTATT
1 ATTTTATTTCATATTATCATTATT
*
1269269 -TTTT-TCTTCATATTATTATTATT
1 ATTTTAT-TTCATATTATCATTATT
1269292 ATTTTATT
1 ATTTTATT
1269300 GCTTATACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
22 1 0.04
23 18 0.72
24 5 0.20
25 1 0.04
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTTTATTTCATATTATCATTATT
Found at i:1270072 original size:31 final size:31
Alignment explanation
Indices: 1270037--1270108 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
1270027 CCGTTAAATA
*
1270037 TATCATTGAATTTTAATATATATATCGATTT
1 TATCATTAAATTTTAATATATATATCGATTT
* * * * *
1270068 TATCATTAAATTTTTATTTTTGTATTGATTT
1 TATCATTAAATTTTAATATATATATCGATTT
1270099 TATCATTAAA
1 TATCATTAAA
1270109 CCTCAAATCG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (31 bp):
TATCATTAAATTTTAATATATATATCGATTT
Found at i:1274283 original size:30 final size:30
Alignment explanation
Indices: 1274247--1274321 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
1274237 TGCACATGCA
1274247 TATACATATGCATATATGAATACCTGTATG
1 TATACATATGCATATATGAATACCTGTATG
1274277 TATACATATGCATATATGAATACCTGTATG
1 TATACATATGCATATATGAATACCTGTATG
*
1274307 TATACACATGCATAT
1 TATACATATGCATAT
1274322 TCATTTTCGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (30 bp):
TATACATATGCATATATGAATACCTGTATG
Found at i:1277962 original size:2 final size:2
Alignment explanation
Indices: 1277955--1277981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1277945 ATTTACTAAT
1277955 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1277982 GAGCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1286227 original size:7 final size:7
Alignment explanation
Indices: 1286197--1286286 Score: 81
Period size: 7 Copynumber: 12.9 Consensus size: 7
1286187 TGTCCTCCGG
1286197 CCGCCGT
1 CCGCCGT
* *
1286204 CTGTCGT
1 CCGCCGT
* *
1286211 CCGACAT
1 CCGCCGT
1286218 CCGCCGT
1 CCGCCGT
1286225 CCGCCGT
1 CCGCCGT
*
1286232 CTGCCGT
1 CCGCCGT
* *
1286239 CCGACAT
1 CCGCCGT
1286246 CCGCCGT
1 CCGCCGT
*
1286253 TCGCCGT
1 CCGCCGT
*
1286260 CTGCCGT
1 CCGCCGT
* *
1286267 CCGACAT
1 CCGCCGT
1286274 CCGCCGT
1 CCGCCGT
1286281 CCGCCG
1 CCGCCG
1286287 CCACTTTCCG
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.07, C:0.49, G:0.26, T:0.19
Consensus pattern (7 bp):
CCGCCGT
Found at i:1286228 original size:28 final size:28
Alignment explanation
Indices: 1286197--1286286 Score: 162
Period size: 28 Copynumber: 3.2 Consensus size: 28
1286187 TGTCCTCCGG
*
1286197 CCGCCGTCTGTCGTCCGACATCCGCCGT
1 CCGCCGTCTGCCGTCCGACATCCGCCGT
1286225 CCGCCGTCTGCCGTCCGACATCCGCCGT
1 CCGCCGTCTGCCGTCCGACATCCGCCGT
*
1286253 TCGCCGTCTGCCGTCCGACATCCGCCGT
1 CCGCCGTCTGCCGTCCGACATCCGCCGT
1286281 CCGCCG
1 CCGCCG
1286287 CCACTTTCCG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.07, C:0.49, G:0.26, T:0.19
Consensus pattern (28 bp):
CCGCCGTCTGCCGTCCGACATCCGCCGT
Found at i:1292604 original size:23 final size:23
Alignment explanation
Indices: 1292578--1292638 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
1292568 ATATTTGATC
*
1292578 TATTAATCGATTAATTCGAATCT
1 TATTAATCGATTAATTCAAATCT
1292601 TATTAATCGATTAATTCAAATCT
1 TATTAATCGATTAATTCAAATCT
1292624 TATTAATCGATTAAT
1 TATTAATCGATTAAT
1292639 CTAAACAGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (23 bp):
TATTAATCGATTAATTCAAATCT
Found at i:1295421 original size:24 final size:25
Alignment explanation
Indices: 1295387--1295436 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
1295377 CATGTAGGTA
*
1295387 GTTCTAGCGGTCACTGTACGGACAG
1 GTTCTAGCGGTCACTGTACAGACAG
1295412 GTTCT-GCGGTCACTGTACAGACAG
1 GTTCTAGCGGTCACTGTACAGACAG
1295436 G
1 G
1295437 CTTAGAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (25 bp):
GTTCTAGCGGTCACTGTACAGACAG
Found at i:1302745 original size:23 final size:23
Alignment explanation
Indices: 1302719--1302763 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1302709 GTTTTATATT
1302719 ATCAAAATGATTAAA-ATTAAAAC
1 ATCAAAATG-TTAAATATTAAAAC
1302742 ATCAAAATGTTAAATATTAAAA
1 ATCAAAATGTTAAATATTAAAA
1302764 AAAATAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (23 bp):
ATCAAAATGTTAAATATTAAAAC
Found at i:1304809 original size:11 final size:11
Alignment explanation
Indices: 1304793--1304818 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1304783 AATTATATAA
1304793 TATATATTATT
1 TATATATTATT
1304804 TATATATTATT
1 TATATATTATT
1304815 TATA
1 TATA
1304819 AATTTCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATATTATT
Found at i:1307726 original size:21 final size:20
Alignment explanation
Indices: 1307702--1307769 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
1307692 AGGAGTGTCA
1307702 ATACGCATACAATAGGTATCG
1 ATAC-CATACAATAGGTATCG
* *
1307723 ATACCATA-AGTAACGTATCG
1 ATACCATACAAT-AGGTATCG
* * *
1307743 ATAATCATACAATGGGTATCA
1 AT-ACCATACAATAGGTATCG
1307764 ATACCA
1 ATACCA
1307770 ATTTCACTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
19 2 0.06
20 16 0.44
21 16 0.44
22 2 0.06
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (20 bp):
ATACCATACAATAGGTATCG
Found at i:1317676 original size:23 final size:22
Alignment explanation
Indices: 1317644--1317701 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
1317634 CAACGGTACA
1317644 ATTTTT-TTTTATGATTTTTTT
1 ATTTTTATTTTATGATTTTTTT
*
1317665 AGTTTTTATTTTATTTTATTTTTTT
1 A-TTTTTATTTTA--TGATTTTTTT
1317690 A-TTTTATTTTAT
1 ATTTTTATTTTAT
1317702 TTTCTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
21 2 0.06
22 5 0.16
23 15 0.47
25 10 0.31
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.79
Consensus pattern (22 bp):
ATTTTTATTTTATGATTTTTTT
Found at i:1317678 original size:5 final size:5
Alignment explanation
Indices: 1317668--1317709 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
1317658 TTTTTTTAGT
*
1317668 TTTTA TTTTA TTTTA -TTT- TTTTA TTTTA TTTTA TTTTC TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1317710 TAATTTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
4 6 0.18
5 28 0.82
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:1317681 original size:18 final size:19
Alignment explanation
Indices: 1317660--1317699 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1317650 TTTTATGATT
1317660 TTTTTA-GTTTTTATTTTA
1 TTTTTATGTTTTTATTTTA
*
1317678 -TTTTATTTTTTTATTTTA
1 TTTTTATGTTTTTATTTTA
1317696 TTTT
1 TTTT
1317700 ATTTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 5 0.26
18 11 0.58
19 3 0.16
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTATGTTTTTATTTTA
Found at i:1317689 original size:13 final size:13
Alignment explanation
Indices: 1317644--1317699 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
1317634 CAACGGTACA
*
1317644 ATTTTTTT-TTATG
1 ATTTTTTTATT-TT
*
1317657 ATTTTTTTAGTTT
1 ATTTTTTTATTTT
*
1317670 -TTATTTTATTTT
1 ATTTTTTTATTTT
1317682 ATTTTTTTATTTT
1 ATTTTTTTATTTT
1317695 ATTTT
1 ATTTT
1317700 ATTTTCTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 10 0.28
13 25 0.69
14 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
ATTTTTTTATTTT
Found at i:1317700 original size:18 final size:18
Alignment explanation
Indices: 1317667--1317704 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1317657 ATTTTTTTAG
1317667 TTTTTATTTTATTTTATT
1 TTTTTATTTTATTTTATT
1317685 TTTTTATTTTATTTTATT
1 TTTTTATTTTATTTTATT
1317703 TT
1 TT
1317705 CTTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTATTTTATTTTATT
Found at i:1317702 original size:23 final size:24
Alignment explanation
Indices: 1317657--1317710 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
1317647 TTTTTTTATG
1317657 ATTTTTTTAGTTTTTATTTTATTTT
1 ATTTTTTTAG-TTTTATTTTATTTT
1317682 ATTTTTTTA-TTTTATTTTATTTT
1 ATTTTTTTAGTTTTATTTTATTTT
*
1317705 CTTTTT
1 ATTTTT
1317711 AATTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 19 0.68
25 9 0.32
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (24 bp):
ATTTTTTTAGTTTTATTTTATTTT
Found at i:1317715 original size:17 final size:16
Alignment explanation
Indices: 1317673--1317740 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 16
1317663 TTAGTTTTTA
*
1317673 TTTTATTTTATTTTTTT
1 TTTTATTTTA-TTTTCT
1317690 ATTTTATTTTATTTTCT
1 -TTTTATTTTATTTTCT
*
1317707 TTTTAATTTTCTTTTCT
1 TTTT-ATTTTATTTTCT
**
1317724 TTGTTACATTATTTTCT
1 TT-TTATTTTATTTTCT
1317741 CTTATTCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
16 4 0.09
17 27 0.63
18 12 0.28
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.76
Consensus pattern (16 bp):
TTTTATTTTATTTTCT
Found at i:1317913 original size:26 final size:26
Alignment explanation
Indices: 1317884--1317937 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1317874 TAATTTTTTG
1317884 AAACATA-AAAACTAC-AACAAACATAA
1 AAACATAGAAAA-TACTAACAAAC-TAA
*
1317910 AAACATAGAAAATACTAATAAACTAA
1 AAACATAGAAAATACTAACAAACTAA
1317936 AA
1 AA
1317938 CAACATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.69, C:0.15, G:0.02, T:0.15
Consensus pattern (26 bp):
AAACATAGAAAATACTAACAAACTAA
Found at i:1326554 original size:30 final size:30
Alignment explanation
Indices: 1326474--1326556 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 30
1326464 ATAAGGAATG
*
1326474 ATATGAACATGTGATATGTGAACATAAGAGA
1 ATATG-ACATGAGATATGTGAACATAAGAGA
* * * * *
1326505 TTAAGTGATATGAGCTATGTGACCATATGAGA
1 AT-A-TGACATGAGATATGTGAACATAAGAGA
1326537 ATATGACATGAGATATGTGA
1 ATATGACATGAGATATGTGA
1326557 TATGTGAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 15 0.37
31 2 0.05
32 22 0.54
33 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (30 bp):
ATATGACATGAGATATGTGAACATAAGAGA
Found at i:1327018 original size:28 final size:28
Alignment explanation
Indices: 1326986--1327047 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
1326976 TAAGAATGAA
1326986 GATAAGGATATATGCTTTTGTATGATAT
1 GATAAGGATATATGCTTTTGTATGATAT
1327014 GATAAGGATATATGCTTTTGTATGATAT
1 GATAAGGATATATGCTTTTGTATGATAT
*
1327042 AATAAG
1 GATAAG
1327048 TATAATTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.40
Consensus pattern (28 bp):
GATAAGGATATATGCTTTTGTATGATAT
Found at i:1327404 original size:29 final size:29
Alignment explanation
Indices: 1327372--1327433 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1327362 TAAAATTTGA
1327372 ATTTTCCTCTATTTTATATAAGAAAAATG
1 ATTTTCCTCTATTTTATATAAGAAAAATG
1327401 ATTTTCCTCTATTTTATATAAGAAAAATG
1 ATTTTCCTCTATTTTATATAAGAAAAATG
1327430 ATTT
1 ATTT
1327434 GAAAAATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (29 bp):
ATTTTCCTCTATTTTATATAAGAAAAATG
Found at i:1329012 original size:17 final size:17
Alignment explanation
Indices: 1328990--1329030 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1328980 TATAATAAAC
1328990 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
1329007 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
*
1329024 ATATGAT
1 TTATGAT
1329031 TACTCTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:1329058 original size:51 final size:52
Alignment explanation
Indices: 1329000--1329097 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 52
1328990 TTATGATAAT
* *
1329000 TAAATTATTATGATAATTAAATTAATATGATTAC-TCTTTGAAATTTTATCA
1 TAAATTATTATGATAATCAAATTAATATAATTACTTCTTTGAAATTTTATCA
*
1329051 TAAATTATTATGATAATCAAATTAATATAATTACTTTTTTGAAATTT
1 TAAATTATTATGATAATCAAATTAATATAATTACTTCTTTGAAATTT
1329098 AATTTTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
51 32 0.74
52 11 0.26
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (52 bp):
TAAATTATTATGATAATCAAATTAATATAATTACTTCTTTGAAATTTTATCA
Found at i:1329939 original size:20 final size:20
Alignment explanation
Indices: 1329914--1329958 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1329904 AACCCGTACA
*
1329914 AATATCAAGT-AGAAGCAATC
1 AATATCAA-TCAGAAGCAAAC
1329934 AATATCAATCAGAAGCAAAC
1 AATATCAATCAGAAGCAAAC
1329954 AATAT
1 AATAT
1329959 AAAACAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.20
Consensus pattern (20 bp):
AATATCAATCAGAAGCAAAC
Found at i:1329969 original size:20 final size:20
Alignment explanation
Indices: 1329926--1329971 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1329916 TATCAAGTAG
* * * *
1329926 AAGCAATCAATATCAATCAG
1 AAGCAAACAATATAAAACAA
1329946 AAGCAAACAATATAAAACAA
1 AAGCAAACAATATAAAACAA
1329966 AAGCAA
1 AAGCAA
1329972 GCATAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.61, C:0.17, G:0.09, T:0.13
Consensus pattern (20 bp):
AAGCAAACAATATAAAACAA
Found at i:1330552 original size:45 final size:45
Alignment explanation
Indices: 1330488--1330577 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1330478 GAGAAAGTAC
1330488 CGGATATGAAATACTTTGATTTTTCCAATAATCCAAAATATCAAA
1 CGGATATGAAATACTTTGATTTTTCCAATAATCCAAAATATCAAA
1330533 CGGATATGAAATACTTTGATTTTTCCAATAATCCAAAATATCAAA
1 CGGATATGAAATACTTTGATTTTTCCAATAATCCAAAATATCAAA
1330578 TTCAGTTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (45 bp):
CGGATATGAAATACTTTGATTTTTCCAATAATCCAAAATATCAAA
Found at i:1332403 original size:31 final size:31
Alignment explanation
Indices: 1332362--1332817 Score: 581
Period size: 31 Copynumber: 14.7 Consensus size: 31
1332352 ACATGGTTAG
** * *
1332362 TTTACATCAACAGTAATAAATCAGTACATAA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
1332393 TTAACATCAACATCAATAAACCAGTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
1332424 TTTACATCAACAATAATAAACCAGTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
1332455 TTTACATCAACAATAATAAACCAGTACATAA
1 TTTACATCAACAACAATAAACCAGTACATCA
* * * *
1332486 TTAACATCAACAGCAATAAACCAATACATAA
1 TTTACATCAACAACAATAAACCAGTACATCA
* ** * *
1332517 TTAACATCAACAGTAATAAACCAATAAATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
1332548 TGTACATCAACAGCAATAAACCAGTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
1332579 TTTACATAAACAACAATAAACCAGTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
** * *
1332610 TTTACATCAACAGTAATAAACCAGTATATAA
1 TTTACATCAACAACAATAAACCAGTACATCA
* * * *
1332641 TTAACATCGACAACAATAAACCAATACATAA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
1332672 TTAACATCAACAACAATAAACCAATACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
1332703 TTTACATCAACAACAATAAATCAGTACATAA
1 TTTACATCAACAACAATAAACCAGTACATCA
1332734 TTTACATCAACAACAATAAACCAGTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
1332765 TTTACATCAACAGCAATAAACCAATACAT-A
1 TTTACATCAACAACAATAAACCAGTACATCA
*
1332795 TTTACATCAACAGCAATAAACCA
1 TTTACATCAACAACAATAAACCA
1332818 TTATATATAT
Statistics
Matches: 380, Mismatches: 45, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 0.06
31 356 0.94
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.23
Consensus pattern (31 bp):
TTTACATCAACAACAATAAACCAGTACATCA
Found at i:1332577 original size:22 final size:22
Alignment explanation
Indices: 1332489--1332578 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 22
1332479 TACATAATTA
*
1332489 ACATCAACAGCAATAAACCAAT
1 ACATCAACAGCAATAAACCAGT
* * *
1332511 ACAT-AATTAAC-ATCAA-CAGT
1 ACATCAA-CAGCAATAAACCAGT
* *
1332531 A-AT-AA-ACCAATAAATCATGT
1 ACATCAACAGCAATAAACCA-GT
1332551 ACATCAACAGCAATAAACCAGT
1 ACATCAACAGCAATAAACCAGT
1332573 ACATCA
1 ACATCA
1332579 TTTACATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
17 2 0.04
18 4 0.08
19 6 0.11
20 7 0.13
21 8 0.15
22 16 0.30
23 10 0.19
ACGTcount: A:0.52, C:0.23, G:0.06, T:0.19
Consensus pattern (22 bp):
ACATCAACAGCAATAAACCAGT
Found at i:1332826 original size:2 final size:2
Alignment explanation
Indices: 1332819--1332893 Score: 68
Period size: 2 Copynumber: 38.5 Consensus size: 2
1332809 AATAAACCAT
*
1332819 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA -A TA -A CA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
* * *
1332858 AA CA GTA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1332894 CAAACATATA
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
1 4 0.06
2 57 0.90
3 2 0.03
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1333133 original size:7 final size:7
Alignment explanation
Indices: 1333121--1333171 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
1333111 GAATAGCTTA
1333121 GGTTTAG
1 GGTTTAG
1333128 GGTTTAG
1 GGTTTAG
1333135 GGTTTAG
1 GGTTTAG
*
1333142 GATTTAG
1 GGTTTAG
*
1333149 GGTTTGG
1 GGTTTAG
1333156 GGTTTAG
1 GGTTTAG
1333163 GGTTT-G
1 GGTTTAG
1333169 GGT
1 GGT
1333172 CTATGCTAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
6 4 0.10
7 36 0.90
ACGTcount: A:0.12, C:0.00, G:0.45, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:1333601 original size:112 final size:103
Alignment explanation
Indices: 1333453--1333716 Score: 329
Period size: 102 Copynumber: 2.5 Consensus size: 103
1333443 CACGATATGG
1333453 TTTGTGTTTAGGTGTTTTTGAAGATCAAAGGAGGGTTTTGGGGAAGAACTGGATGAACAAATAAA
1 TTTGTGTTTAGGTGTTTTTGAAGATCAAA-GAGGGTTTTGGGGAAGAAC---AT----AAATAAA
*
1333518 GAACACGGAAGAATATTTGGGTGTTTGAT-AGAAAAAATATGAAAATA
58 GAACACAGAAGAA-ATTTGGGTGTTTGATGA-AAAAAATATGAAAATA
* *
1333565 TTTGTGTTTAGGTGTTTGTGAAGATCAAAGAAGGGTTTTGGGGAAG-A-ATAAATGAAGAACACA
1 TTTGTGTTTAGGTGTTTTTGAAGATCAAAG-AGGGTTTTGGGGAAGAACATAAATAAAGAACACA
*
1333628 GAAGAAATTTGGGTGTTTGATGAAAAAAATATGAAAATG
65 GAAGAAATTTGGGTGTTTGATGAAAAAAATATGAAAATA
* *
1333667 TTT-TGGTTTAGGTGTTTTTGAAGATCAAATGAGGCTTTTGGGGATGAACA
1 TTTGT-GTTTAGGTGTTTTTGAAGATCAAA-GAGGGTTTTGGGGAAGAACA
1333717 AGTGAAGAAC
Statistics
Matches: 139, Mismatches: 7, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
101 1 0.01
102 69 0.50
103 21 0.15
104 1 0.01
107 2 0.01
111 2 0.01
112 43 0.31
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.31
Consensus pattern (103 bp):
TTTGTGTTTAGGTGTTTTTGAAGATCAAAGAGGGTTTTGGGGAAGAACATAAATAAAGAACACAG
AAGAAATTTGGGTGTTTGATGAAAAAAATATGAAAATA
Found at i:1334246 original size:52 final size:47
Alignment explanation
Indices: 1334152--1334314 Score: 165
Period size: 45 Copynumber: 3.4 Consensus size: 47
1334142 TGAATTTTTC
1334152 AATATATAGTTTATATATGCTATA-TAATTTATATATAGTAATGAACTATAT
1 AATATATAGTTTATATA--CTATACT-A--TATATATAGTAATGAACTATAT
*
1334203 AATATATAGTTTGTATACCATATACTATAGGTTATATAGTAATGAACTATAT
1 AATATATAGTTTATATA-C-TATACTATA---TATATAGTAATGAACTATAT
* * *
1334255 -A-ATATAGTTTATATACTATAGTTTATATATACTAATGAACTATAT
1 AATATATAGTTTATATACTATACTATATATATAGTAATGAACTATAT
1334300 -A-ATATAGTTTATATA
1 AATATATAGTTTATATA
1334315 TACTAATCAA
Statistics
Matches: 101, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
45 34 0.34
48 7 0.07
49 3 0.03
50 14 0.14
51 22 0.22
52 21 0.21
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.44
Consensus pattern (47 bp):
AATATATAGTTTATATACTATACTATATATATAGTAATGAACTATAT
Found at i:1334336 original size:45 final size:45
Alignment explanation
Indices: 1334235--1334336 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
1334225 TACTATAGGT
* * **
1334235 TATATAGTAATGAACTATATAATATAGTTTATATACTATAGTTTA
1 TATATACTAATGAACTATATAATATAGTTTATATACTATAATAAA
1334280 TATATACTAATGAACTATATAATATAGTTTATATA-TACTAATCAAA
1 TATATACTAATGAACTATATAATATAGTTTATATACTA-TAAT-AAA
1334326 TATATA-TAATG
1 TATATACTAATG
1334337 TTAGTTTATA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 2 0.04
45 42 0.82
46 7 0.14
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (45 bp):
TATATACTAATGAACTATATAATATAGTTTATATACTATAATAAA
Found at i:1334366 original size:2 final size:2
Alignment explanation
Indices: 1334361--1334579 Score: 59
Period size: 2 Copynumber: 107.0 Consensus size: 2
1334351 CCCTATAGTT
*
1334361 TA TA TA TA TA TA GTT TA TA TA TA CTA -A TA TA TA TA TA -A T- TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
1334402 TA TG T- TA TA TA GTT TA TA TA TA -A TA TA GTA TA AA T- TA T- TT
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
1334442 TA TA TA GTA TA TA AA TA TCA -A CTA TA -A TA TA TA GTT TA TT TGG
1 TA TA TA -TA TA TA TA TA T-A TA -TA TA TA TA TA TA -TA TA TA T-A
* *
1334485 T- TT TA TA TA TA GT- TCA TA TGA AA T- TA TA CTA TA TA GTA TA TA
1 TA TA TA TA TA TA -TA T-A TA T-A TA TA TA TA -TA TA TA -TA TA TA
* * *
1334527 TA GTT TA TA TA TA TA -A TA TA TA GTA TA TA AA TA TA AA CTA TA
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
1334569 GTA TA TA TA TA
1 -TA TA TA TA TA
1334580 GGTCATATGT
Statistics
Matches: 163, Mismatches: 23, Indels: 62
0.66 0.09 0.25
Matches are distributed among these distances:
1 13 0.08
2 125 0.77
3 25 0.15
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1334410 original size:31 final size:31
Alignment explanation
Indices: 1334264--1334447 Score: 144
Period size: 31 Copynumber: 5.6 Consensus size: 31
1334254 TAATATAGTT
* *
1334264 TATATACTATAGTTTATATATACTAATGAA-C
1 TATATAATATAGTTTATATATACTAAT-AATA
1334295 TATATAATATAGTTTATATATACTAATCAAATA
1 TATATAATATAGTTTATATATACTAAT--AATA
* * *
1334328 TATATAATGTTAGTTTATATATACCCT-ATAGTT
1 TATATAAT-ATAGTTTATATATA--CTAATAATA
1334361 TATATATATATAGTTTATATATACTAAT-ATA
1 TATATA-ATATAGTTTATATATACTAATAATA
*
1334392 TATATAATTATATGTTATATAGTTTA-TATATAATA
1 TATATAA-TATA-GTT-TATA-TATACTA-ATAATA
*
1334427 TAGTATAA-ATTATTTTATATA
1 TA-TATAATA-TAGTTTATATA
1334448 GTATATAAAT
Statistics
Matches: 126, Mismatches: 12, Indels: 29
0.75 0.07 0.17
Matches are distributed among these distances:
30 1 0.01
31 39 0.31
32 8 0.06
33 39 0.31
34 23 0.18
35 9 0.07
36 7 0.06
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (31 bp):
TATATAATATAGTTTATATATACTAATAATA
Found at i:1334415 original size:40 final size:37
Alignment explanation
Indices: 1334367--1334459 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 37
1334357 AGTTTATATA
1334367 TATATAGTTTATATATACTAATATA-TATATAATTATATGT
1 TATATAGTTTATATATA-TAATATAGTATA-AATTAT-T-T
1334407 TATATAG-TT-TATATATAATATAGTATAAATTATTT
1 TATATAGTTTATATATATAATATAGTATAAATTATTT
* *
1334442 TATATAGTATATAAATAT
1 TATATAGTTTATATATAT
1334460 CAACTATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
35 8 0.17
36 2 0.04
37 19 0.40
38 10 0.21
39 2 0.04
40 7 0.15
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.49
Consensus pattern (37 bp):
TATATAGTTTATATATATAATATAGTATAAATTATTT
Found at i:1334420 original size:16 final size:16
Alignment explanation
Indices: 1334250--1334430 Score: 102
Period size: 16 Copynumber: 11.8 Consensus size: 16
1334240 AGTAATGAAC
1334250 TATATAATATAG-TT-
1 TATATAATATAGTTTA
*
1334264 TATATACTATAGTTTA
1 TATATAATATAGTTTA
* **
1334280 TATATACTA-A-TGAA
1 TATATAATATAGTTTA
1334294 CTATATAATATAGTTTA
1 -TATATAATATAGTTTA
* **
1334311 TATATACTAATCA-AATA
1 TATATAAT-AT-AGTTTA
*
1334328 TATATAATGTTAGTTTA
1 TATATAAT-ATAGTTTA
*
1334345 TATATACCCTATAGTTTA
1 TATATA--ATATAGTTTA
1334363 TATAT-ATATAGTTTA
1 TATATAATATAGTTTA
*
1334378 TATATACTA-A---TA
1 TATATAATATAGTTTA
1334390 TATAT-ATA-A--TTA
1 TATATAATATAGTTTA
* *
1334402 TATGTTATATAGTTTA
1 TATATAATATAGTTTA
1334418 TATATAATATAGT
1 TATATAATATAGT
1334431 ATAAATTATT
Statistics
Matches: 129, Mismatches: 22, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
11 3 0.02
12 13 0.10
13 3 0.02
14 14 0.11
15 26 0.20
16 34 0.26
17 22 0.17
18 13 0.10
19 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (16 bp):
TATATAATATAGTTTA
Found at i:1334445 original size:42 final size:39
Alignment explanation
Indices: 1334354--1334454 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 39
1334344 ATATATACCC
* * *
1334354 TATAGTTTATATATATATAGTTTATATATACTAATATATA
1 TATA-TTTATATGTATATAGTTTATATATAATAATATAAA
*
1334394 TATAATTATATGTTATATAGTTTATATATAATATAGTATAAA
1 TATATTTATATG-TATATAGTTTATATATAATA-A-TATAAA
1334436 T-TATTTTATATAGTATATA
1 TATA-TTTATAT-GTATATA
1334455 AATATCAACT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
39 6 0.12
40 23 0.45
41 3 0.06
42 18 0.35
43 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (39 bp):
TATATTTATATGTATATAGTTTATATATAATAATATAAA
Found at i:1334528 original size:9 final size:9
Alignment explanation
Indices: 1334514--1334577 Score: 51
Period size: 9 Copynumber: 6.7 Consensus size: 9
1334504 GAAATTATAC
1334514 TATATAGTA
1 TATATAGTA
1334523 TATATAGTTTA
1 TATATAG--TA
1334534 TATATA-TAA
1 TATATAGT-A
1334543 TATATAGTA
1 TATATAGTA
1334552 TATAAATA-TA
1 TAT--ATAGTA
*
1334562 AACTATAGTA
1 TA-TATAGTA
1334572 TATATA
1 TATATA
1334578 TAGGTCATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
8 1 0.02
9 25 0.56
10 7 0.16
11 12 0.27
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (9 bp):
TATATAGTA
Found at i:1334539 original size:20 final size:19
Alignment explanation
Indices: 1334509--1334579 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 19
1334499 CATATGAAAT
1334509 TATACTATATAGTATATATAG
1 TATA-TATATA-TATATATAG
*
1334530 TTTATATATATAATATATAG
1 TATATATATAT-ATATATAG
* *
1334550 TATATAAATATAAACTATAG
1 TATATATATATATA-TATAG
1334570 TATATATATA
1 TATATATATA
1334580 GGTCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (19 bp):
TATATATATATATATATAG
Found at i:1334568 original size:29 final size:29
Alignment explanation
Indices: 1334500--1334580 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 29
1334490 TATATAGTTC
*
1334500 ATATGAAAT-TATACTATATAGTATATATA
1 ATAT-AAATATATAATATATAGTATATATA
* * *
1334529 GTTTATATATATAATATATAGTATATA-A
1 ATATAAATATATAATATATAGTATATATA
1334557 ATATAAACTATAGTATATATATAG
1 ATATAAA-TATA-TA-ATATATAG
1334581 GTCATATGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
28 8 0.20
29 23 0.56
30 2 0.05
31 8 0.20
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.42
Consensus pattern (29 bp):
ATATAAATATATAATATATAGTATATATA
Found at i:1334597 original size:18 final size:18
Alignment explanation
Indices: 1334576--1334645 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
1334566 ATAGTATATA
1334576 TATAGGTCATATGTAAAC
1 TATAGGTCATATGTAAAC
* * * *
1334594 TATATAGT-TTATATATA-
1 TATA-GGTCATATGTAAAC
*
1334611 TATAGTTCATATGTAAAC
1 TATAGGTCATATGTAAAC
* *
1334629 TATAGTTCATATTTAAA
1 TATAGGTCATATGTAAA
1334646 TATCAACTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
16 1 0.03
17 10 0.26
18 26 0.67
19 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (18 bp):
TATAGGTCATATGTAAAC
Found at i:1334621 original size:35 final size:35
Alignment explanation
Indices: 1334523--1334632 Score: 118
Period size: 35 Copynumber: 3.1 Consensus size: 35
1334513 CTATATAGTA
*
1334523 TATATAGTTTATATATATAATA-TAT-AGTATATAAA-
1 TATATAGTTTATATATAT-ATAGT-TCA-TATGTAAAC
* * * *
1334558 TATAAACTATAGTATATATATAGGTCATATGTAAAC
1 TATATAGTTTA-TATATATATAGTTCATATGTAAAC
1334594 TATATAGTTTATATATATATAGTTCATATGTAAAC
1 TATATAGTTTATATATATATAGTTCATATGTAAAC
1334629 TATA
1 TATA
1334633 GTTCATATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
35 46 0.74
36 16 0.26
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (35 bp):
TATATAGTTTATATATATATAGTTCATATGTAAAC
Found at i:1334633 original size:33 final size:34
Alignment explanation
Indices: 1334570--1334640 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 34
1334560 TAAACTATAG
*
1334570 TATATATATAGGTCATATGTAAACTATATAGTTTA
1 TATATATATAGGTCATATGTAAAC-ATATAGTTCA
*
1334605 TATATATATAGTTCATATGTAAAC-TATAGTTCA
1 TATATATATAGGTCATATGTAAACATATAGTTCA
1334638 TAT
1 TAT
1334641 TTAAATATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 11 0.32
35 23 0.68
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (34 bp):
TATATATATAGGTCATATGTAAACATATAGTTCA
Found at i:1334690 original size:17 final size:18
Alignment explanation
Indices: 1334596--1334691 Score: 58
Period size: 18 Copynumber: 5.2 Consensus size: 18
1334586 ATGTAAACTA
1334596 TATAGTTTATATAT--A-
1 TATAGTTTATATATAAAC
* *
1334611 TATAGTTCATATGTAAAC
1 TATAGTTTATATATAAAC
*
1334629 TATAGTTCATATTTAAATATCAAC
1 TATAGTT--TA--T--ATATAAAC
*
1334653 TATAGTTTATATGTAAAC
1 TATAGTTTATATATAAAC
1334671 TATAG-TTAGTATAT-AAC
1 TATAGTTTA-TATATAAAC
1334688 TATA
1 TATA
1334692 TATGTAAACT
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
15 12 0.19
17 11 0.17
18 22 0.35
20 2 0.03
22 3 0.05
24 13 0.21
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (18 bp):
TATAGTTTATATATAAAC
Found at i:1334714 original size:30 final size:30
Alignment explanation
Indices: 1334660--1334716 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1334650 AACTATAGTT
*
1334660 TATATGTAAACTATAGTTAGTATATAACTA
1 TATATGTAAACTATAGTCAGTATATAACTA
1334690 TATATGTAAACTATAGCTCA-TATATAA
1 TATATGTAAACTATAG-TCAGTATATAA
1334717 ATATCAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39
Consensus pattern (30 bp):
TATATGTAAACTATAGTCAGTATATAACTA
Found at i:1334758 original size:11 final size:11
Alignment explanation
Indices: 1334727--1334776 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1334717 ATATCAACTT
1334727 TAGTATATATA
1 TAGTATATATA
1334738 TAGTTCATATATA
1 TAG-T-ATATATA
*
1334751 TAGTATATAAA
1 TAGTATATATA
*
1334762 TA-TAAAT-TA
1 TAGTATATATA
1334771 TAGTAT
1 TAGTAT
1334777 GTAGTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
9 3 0.09
10 6 0.19
11 11 0.34
12 2 0.06
13 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (11 bp):
TAGTATATATA
Found at i:1334866 original size:21 final size:21
Alignment explanation
Indices: 1334840--1334898 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1334830 ACCCTAAATC
*
1334840 ATATATACTATATATATATGT
1 ATATATACTATATATATATAT
*
1334861 ATATATAACTATATAGTTTATAT
1 ATATAT-ACTATATA-TATATAT
*
1334884 A-ATAAACTATATATA
1 ATATATACTATATATA
1334899 CAATATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 14 0.44
22 11 0.34
23 6 0.19
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (21 bp):
ATATATACTATATATATATAT
Found at i:1334949 original size:18 final size:20
Alignment explanation
Indices: 1334936--1335083 Score: 63
Period size: 19 Copynumber: 7.8 Consensus size: 20
1334926 AAAATAATTG
1334936 TATA-ATTTATAATAATTCA
1 TATATATTTATAATAATTCA
*
1334955 TATATATTTAT-ATAA-AC-
1 TATATATTTATAATAATTCA
* **
1334972 TATATAGTTTATATTAATAAA
1 TATATA-TTTATAATAATTCA
*
1334993 CTATATATTTAT-ACAA-T-A
1 -TATATATTTATAATAATTCA
* * *
1335011 TATAT-TATATAATTATACA
1 TATATATTTATAATAATTCA
*
1335030 TA-ATA--TA-AATAAATT-G
1 TATATATTTATAAT-AATTCA
1335046 TATA-ATTTATATATAATTCA
1 TATATATTTATA-ATAATTCA
1335066 TATATAATTTATATATAA
1 TATAT-ATTTATA-ATAA
1335084 ACTATGTAGG
Statistics
Matches: 96, Mismatches: 14, Indels: 35
0.66 0.10 0.24
Matches are distributed among these distances:
16 10 0.10
17 18 0.19
18 11 0.11
19 19 0.20
20 15 0.16
21 5 0.05
22 18 0.19
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (20 bp):
TATATATTTATAATAATTCA
Found at i:1334967 original size:103 final size:109
Alignment explanation
Indices: 1334851--1335102 Score: 358
Period size: 110 Copynumber: 2.3 Consensus size: 109
1334841 TATATACTAT
*
1334851 ATATATATGTATATATAACTATATAGTTTATATAATAAAC-TATA-TATACAATAT-TA-T-TAT
1 ATATATATTTATATATAACTATATAGTTTATATAATAAACATATATTATACAATATATATTATAT
1334911 AATTATACATAATATAAA-ATAATTGTATAATTTATA-ATAATTC
66 AATTATACATAATATAAATA-AATTGTATAATTTATATATAATTC
1334954 ATATATATTTATATA-AACTATATAGTTTATATTAATAAACTATATATTTATACAATATATATTA
1 ATATATATTTATATATAACTATATAGTTTATA-TAATAAAC-ATATA-TTATACAATATATATTA
1335018 TATAATTATACATAATATAAATAAATTGTATAATTTATATATAATTC
63 TATAATTATACATAATATAAATAAATTGTATAATTTATATATAATTC
*
1335065 ATATATAATTTATATATAAACTATGTAGGTTCTATATA
1 ATATAT-ATTTATATAT-AACTATATA-GTT-TATATA
1335103 GTTCAATAGT
Statistics
Matches: 132, Mismatches: 2, Indels: 18
0.87 0.01 0.12
Matches are distributed among these distances:
102 16 0.12
103 22 0.17
105 4 0.03
107 10 0.08
108 2 0.02
109 1 0.01
110 37 0.28
111 14 0.11
112 9 0.07
114 8 0.06
115 5 0.04
116 4 0.03
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (109 bp):
ATATATATTTATATATAACTATATAGTTTATATAATAAACATATATTATACAATATATATTATAT
AATTATACATAATATAAATAAATTGTATAATTTATATATAATTC
Found at i:1334993 original size:22 final size:23
Alignment explanation
Indices: 1334957--1335005 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
1334947 ATAATTCATA
1334957 TATATTTATATAAACTATATAGTT
1 TATATTTATATAAACTATATA-TT
1334981 TATA-TTA-ATAAACTATATATT
1 TATATTTATATAAACTATATATT
1335002 TATA
1 TATA
1335006 CAATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 6 0.24
22 12 0.48
23 3 0.12
24 4 0.16
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
TATATTTATATAAACTATATATT
Found at i:1335057 original size:22 final size:22
Alignment explanation
Indices: 1335032--1335083 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1335022 ATTATACATA
*
1335032 ATATA-AATAAATTGTATAATTT
1 ATATATAATAAA-TATATAATTT
**
1335054 ATATATAATTCATATATAATTT
1 ATATATAATAAATATATAATTT
1335076 ATATATAA
1 ATATATAA
1335084 ACTATGTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATATAATAAATATATAATTT
Found at i:1335062 original size:11 final size:11
Alignment explanation
Indices: 1335046--1335083 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
1335036 AAATAAATTG
1335046 TATAATTTATA
1 TATAATTTATA
*
1335057 TATAATTCATA
1 TATAATTTATA
1335068 TATAATTTATA
1 TATAATTTATA
1335079 TATAA
1 TATAA
1335084 ACTATGTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:1335158 original size:2 final size:2
Alignment explanation
Indices: 1335151--1335250 Score: 80
Period size: 2 Copynumber: 49.5 Consensus size: 2
1335141 TAATACATGG
* * * *
1335151 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA AA CTA TA TA -A TT TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
1335193 TA TA TA TA -A TA CA TA TA CTT TA TA TA TA AA CTA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
1335236 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1335251 TAGTTGTTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
1 3 0.04
2 70 0.91
3 4 0.05
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1335160 original size:20 final size:20
Alignment explanation
Indices: 1335128--1335178 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1335118 TATAAACTAT
1335128 ATAGTAT-TATAGTTAATAC
1 ATAGTATATATAGTTAATAC
* *
1335147 ATGGTATATATAGTTTATAC
1 ATAGTATATATAGTTAATAC
*
1335167 ATAATATATATA
1 ATAGTATATATA
1335179 AACTATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (20 bp):
ATAGTATATATAGTTAATAC
Found at i:1336456 original size:215 final size:214
Alignment explanation
Indices: 1335335--1336454 Score: 1688
Period size: 210 Copynumber: 5.2 Consensus size: 214
1335325 ATCCCTTTTC
* *
1335335 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCGTCCACATT
1 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATT
* * * *
1335400 TTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTATTAATTGGCCCATAACTT
66 TTATTTGCATCTGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAACTT
* * *
1335465 TTTAAATGAGTATAATTTAGTA-TATTTTTTTATTAATTTCAACCTCAAAATTTAAAATTATTTC
131 TTTAAATG-GTATAATTTAGTACT-TTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTC
1335529 GATTTGATCC-CTT---T-TG
194 GATTTGATCCTCTTCAATGTG
* * * * * *
1335545 TGTTGTTTAGTTTATTTAATTTTTTATTTGTACTTTTATAGTTATTCAATTTAGTCCTCCAAATT
1 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATT
* * * * *
1335610 TTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAAATTAGCCCATAACTT
66 TTATTTGCATCTGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAACTT
* *
1335675 TTTAAATGAGTATAATTTAGTACTTTTTTTGTATTAATTTCAACATCACAATTTAAATTTATTTT
131 TTTAAATG-GTATAATTTAGTAC-TTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTC
*
1335740 GATTTGATCCCTCATCAATGTG
194 GATTTGAT-CCTCTTCAATGTG
* *
1335762 TGTTGTTTAATTAATTTAAATTTTTATTTATAATTTCATATTTGTTCAATTTAGTCCTCCAAATT
1 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATT
1335827 TTATTTGCATCTGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAACTT
66 TTATTTGCATCTGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAACTT
1335892 TTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCG
131 TTTAAAT-GGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCG
* *
1335957 ATTTCATCC-CTT---T-TA
195 ATTTGATCCTCTTCAATGTG
* * * *
1335972 TGTTGTTTAATTTATTTGAATTTTTATTTTTTATTTCATATTTGTTCAATTTAGTCCTCCAAGTT
1 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATT
*
1336037 TTATTTGCATCTGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAAATT
66 TTATTTGCATCTGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAACTT
** * *
1336102 TTTAAATGGATATTCTTTAG-ATTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCG
131 TTTAAATGG-TATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCG
* *
1336166 ATTTCATCCCTCATCAATGTG
195 ATTTGAT-CCTCTTCAATGTG
*
1336187 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAATCCTCCAAATT
1 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATT
* *
1336252 TTATTTGCATCTGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCCTAAATT
66 TTATTTGCATCTGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAACTT
* *
1336317 TTTAAATGGTATACTTTAGTACTTTTTTGTATTAATTTCAACTTCACAATTTAAAATTATTTCGA
131 TTTAAATGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGA
1336382 TTTGATCCTTCTTCAATGTG
196 TTTGATCC-TCTTCAATGTG
1336402 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1336455 ATTCTTAAAT
Statistics
Matches: 834, Mismatches: 58, Indels: 31
0.90 0.06 0.03
Matches are distributed among these distances:
209 51 0.06
210 283 0.34
211 46 0.06
212 3 0.00
213 2 0.00
214 14 0.02
215 247 0.30
216 47 0.06
217 140 0.17
218 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (214 bp):
TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATT
TTATTTGCATCTGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAACTT
TTTAAATGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGA
TTTGATCCTCTTCAATGTG
Found at i:1338966 original size:29 final size:29
Alignment explanation
Indices: 1338923--1339032 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
1338913 TTTCATATGT
1338923 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
1338951 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
1338980 TCATGTAGCTCATGACATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1339009 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1339033 ATATCACATA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 7 0.09
29 64 0.84
30 5 0.07
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1339436 original size:64 final size:63
Alignment explanation
Indices: 1339367--1339523 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
1339357 TAATGAAGGT
* **
1339367 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
1339430 G
63 G
* * * *
1339431 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
**
1339494 AGTGCATCGATGCACTACCAGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
1339524 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 3 0.04
64 65 0.84
65 9 0.12
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:1345861 original size:29 final size:29
Alignment explanation
Indices: 1345818--1345927 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
1345808 TTTCATATGT
1345818 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
1345846 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1345875 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1345904 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1345928 ATATCACATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1346461 original size:19 final size:19
Alignment explanation
Indices: 1346437--1346475 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1346427 ATTTTAAAAG
1346437 AGTGCATCGATGCACTACC
1 AGTGCATCGATGCACTACC
1346456 AGTGCATCGATGCACTACC
1 AGTGCATCGATGCACTACC
1346475 A
1 A
1346476 AACACTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCACTACC
Found at i:1351807 original size:34 final size:34
Alignment explanation
Indices: 1351767--1351832 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1351757 TTTTAAGGAA
* * *
1351767 GAGTTAGAGAGTTTTTGAGAATTTAAGGGCTTAG
1 GAGTTAGAGAATTTATGAGAATTTAAGAGCTTAG
*
1351801 GAGTTAGATAATTTATGAGAATTTAAGAGCTT
1 GAGTTAGAGAATTTATGAGAATTTAAGAGCTT
1351833 TTTGGGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.36
Consensus pattern (34 bp):
GAGTTAGAGAATTTATGAGAATTTAAGAGCTTAG
Found at i:1360885 original size:201 final size:202
Alignment explanation
Indices: 1360540--1360943 Score: 792
Period size: 201 Copynumber: 2.0 Consensus size: 202
1360530 ATCTATACTG
1360540 GTTCCATTCCTCTTCGATCTTGAGCCGGCTGGATTTCTACTCGCCTTGGTCCTTCTTTAACCCAG
1 GTTCCATTCCTCTTCGATCTTGAGCCGGCTGGATTTCTACTCGCCTTGGTCCTTCTTTAACCCAG
1360605 AATCGCTCCTCTTCTCCATATTCTCTATTGGTGGCTAACAAATGAGCAGCGATATTTCCAGATCT
66 AATCGCTCCTCTTCTCCATATTCTCTATTGGTGGCTAACAAATGAGCAGCGATATTTCCAGATCT
1360670 GAAGATGAAATTGAACGTGCAAGATGAAAAAAGGTCAGATTTTCTTCTTA-TCCTATATCCATGT
131 GAAGATGAAATTGAACGTGCAAGATGAAAAAAGGTCAGATTTTCTTCTTAGTCCTATATCCATGT
1360734 GCTAATC
196 GCTAATC
1360741 GTTCCATTCCTCTTCGATCTTGAGCCGGCTGGATTTCTACTCGCCTTGGTCCTTCTTTAACCCAG
1 GTTCCATTCCTCTTCGATCTTGAGCCGGCTGGATTTCTACTCGCCTTGGTCCTTCTTTAACCCAG
1360806 AATCGCTCCTCTTCTCCATATTCTCTATTGGTGGCTAACAAATGAGCAGCGATATTTCCAGATCT
66 AATCGCTCCTCTTCTCCATATTCTCTATTGGTGGCTAACAAATGAGCAGCGATATTTCCAGATCT
1360871 GAAGATGAAATTGAACGTGCAAGATGAAAAAAGGTCAGATTTTCTTCTTATGTCCTATATCCATG
131 GAAGATGAAATTGAACGTGCAAGATGAAAAAAGGTCAGATTTTCTTCTTA-GTCCTATATCCATG
1360936 TGCTAATC
195 TGCTAATC
1360944 TCGAAAAGAT
Statistics
Matches: 201, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
201 180 0.90
203 21 0.10
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (202 bp):
GTTCCATTCCTCTTCGATCTTGAGCCGGCTGGATTTCTACTCGCCTTGGTCCTTCTTTAACCCAG
AATCGCTCCTCTTCTCCATATTCTCTATTGGTGGCTAACAAATGAGCAGCGATATTTCCAGATCT
GAAGATGAAATTGAACGTGCAAGATGAAAAAAGGTCAGATTTTCTTCTTAGTCCTATATCCATGT
GCTAATC
Found at i:1362381 original size:19 final size:20
Alignment explanation
Indices: 1362340--1362382 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1362330 TGCTTTAGTA
*
1362340 TTTTTAGTAAATATTTTAGG
1 TTTTTAGTAAATATTTTACG
* *
1362360 TTTTTAGT-AATTTTTTTCG
1 TTTTTAGTAAATATTTTACG
1362379 TTTT
1 TTTT
1362383 AGGGTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.21, C:0.02, G:0.12, T:0.65
Consensus pattern (20 bp):
TTTTTAGTAAATATTTTACG
Found at i:1362395 original size:72 final size:73
Alignment explanation
Indices: 1362317--1362470 Score: 292
Period size: 72 Copynumber: 2.1 Consensus size: 73
1362307 TTTTTATATA
1362317 TAATTTTTAATAGTGCTTTAGTATTTTTAGTAAATATTTTAGGTTTTTAGTAATTTTTTTCGTTT
1 TAATTTTTAATAGTGCTTTAGTATTTTTAGTAAATATTTTAGGTTTTTAGTAATTTTTTTCGTTT
1362382 TAGGG-TT
66 TAGGGTTT
1362389 TAATTTTTAATAGTGCTTTAGTATTTTTAGTAAATATTTTAGGTTTTTAGTAATTTTTTTCGTTT
1 TAATTTTTAATAGTGCTTTAGTATTTTTAGTAAATATTTTAGGTTTTTAGTAATTTTTTTCGTTT
1362454 TAGGGTTT
66 TAGGGTTT
1362462 TAATATTTT
1 TAAT-TTTT
1362471 TTTCTAAATA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
72 70 0.88
73 6 0.08
74 4 0.05
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (73 bp):
TAATTTTTAATAGTGCTTTAGTATTTTTAGTAAATATTTTAGGTTTTTAGTAATTTTTTTCGTTT
TAGGGTTT
Found at i:1362453 original size:19 final size:20
Alignment explanation
Indices: 1362412--1362454 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1362402 TGCTTTAGTA
*
1362412 TTTTTAGTAAATATTTTAGG
1 TTTTTAGTAAATATTTTACG
* *
1362432 TTTTTAGT-AATTTTTTTCG
1 TTTTTAGTAAATATTTTACG
1362451 TTTT
1 TTTT
1362455 AGGGTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.21, C:0.02, G:0.12, T:0.65
Consensus pattern (20 bp):
TTTTTAGTAAATATTTTACG
Found at i:1362462 original size:26 final size:25
Alignment explanation
Indices: 1362425--1362474 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1362415 TTAGTAAATA
* *
1362425 TTTTAGGTTTTTAGTAATTTTTTTCG
1 TTTTAGGGTTTTAAT-ATTTTTTTCG
1362451 TTTTAGGGTTTTAATATTTTTTTC
1 TTTTAGGGTTTTAATATTTTTTTC
1362475 TAAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.16, C:0.04, G:0.14, T:0.66
Consensus pattern (25 bp):
TTTTAGGGTTTTAATATTTTTTTCG
Found at i:1362527 original size:26 final size:24
Alignment explanation
Indices: 1362475--1362528 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
1362465 TATTTTTTTC
**
1362475 TAAATATTTTTATATTTTAAATTT
1 TAAATATTTTTATATTTTAAAAAT
*
1362499 TAAATTATTTTTATTCTTTTAAAAAT
1 TAAA-TATTTTTA-TATTTTAAAAAT
1362525 TAAA
1 TAAA
1362529 CAAGTACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 8 0.32
26 13 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TAAATATTTTTATATTTTAAAAAT
Found at i:1362763 original size:28 final size:26
Alignment explanation
Indices: 1362699--1362763 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
1362689 TGACCAACAA
* *
1362699 AATT-GCAATGCGATCTCTAATTCGC
1 AATTCGCATTGCGATCTCCAATTCGC
*
1362724 AATTCGCATTGCGATCTCCACTATCGC
1 AATTCGCATTGCGATCTCCAAT-TCGC
*
1362751 AAATTCGCGTTGC
1 -AATTCGCATTGC
1362764 ATTTCGCGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 4 0.12
26 14 0.42
27 4 0.12
28 11 0.33
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (26 bp):
AATTCGCATTGCGATCTCCAATTCGC
Found at i:1362796 original size:21 final size:19
Alignment explanation
Indices: 1362770--1362821 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
1362760 TTGCATTTCG
*
1362770 CGTTGCGATAGTCTACAATGT
1 CGTTGCGATAGTCCA-AAT-T
**
1362791 CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAATT
1362810 CGTTGCGATAGT
1 CGTTGCGATAGT
1362822 TAAAAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 11 0.42
20 3 0.12
21 12 0.46
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:1362910 original size:6 final size:6
Alignment explanation
Indices: 1362899--1362931 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1362889 GACACGTATT
1362899 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1362932 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1363550 original size:19 final size:18
Alignment explanation
Indices: 1363526--1363573 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
1363516 TTTTTTAACT
*
1363526 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAA-ATGGAAA
1363545 ATCGCAACGCGAAATGGAAA
1 ATCGCAA--CGAAATGGAAA
1363565 ATCGCAACG
1 ATCGCAACG
1363574 CGATTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 7 0.27
20 13 0.50
21 4 0.15
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.15
Consensus pattern (18 bp):
ATCGCAACGAAATGGAAA
Found at i:1363564 original size:20 final size:20
Alignment explanation
Indices: 1363539--1363576 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1363529 GCAACGAATT
1363539 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
1363559 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
1363577 TTTTTCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.11
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:1364972 original size:46 final size:43
Alignment explanation
Indices: 1364922--1365016 Score: 109
Period size: 46 Copynumber: 2.1 Consensus size: 43
1364912 TAAATGTTAG
* * *
1364922 TAATATGAATATTTGGTAATGAAACCATATTTAGTATGTGTATATA
1 TAATATGAATATTCGGTAATGAAACCATAATTA-TA--TATATATA
* * *
1364968 TAATATGATTGTTCGGTAATGAAATCATAATTATATATATATA
1 TAATATGAATATTCGGTAATGAAACCATAATTATATATATATA
1365011 TAATAT
1 TAATAT
1365017 ATAAAAGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
43 13 0.30
45 2 0.05
46 28 0.65
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (43 bp):
TAATATGAATATTCGGTAATGAAACCATAATTATATATATATA
Found at i:1365205 original size:18 final size:17
Alignment explanation
Indices: 1365161--1365214 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
1365151 ATAATATGTT
*
1365161 TTTTTAAGTAATTTTTTA
1 TTTTTAA-TAATTTTATA
*
1365179 TTTTATAATTATTTTATA
1 TTTT-TAATAATTTTATA
*
1365197 CTTTTTAATAATTCTATA
1 -TTTTTAATAATTTTATA
1365215 GTATTGTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 23 0.77
19 7 0.23
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTTAATAATTTTATA
Found at i:1365292 original size:23 final size:24
Alignment explanation
Indices: 1365250--1365304 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
1365240 TTAAATGATT
* *
1365250 TATTTTTA-ATTTTAG-TTTTAAA
1 TATTTTTATATTCTAGATTTAAAA
1365272 TATTTTTATATTCTAGATTTAAAA
1 TATTTTTATATTCTAGATTTAAAA
1365296 TATTTTTAT
1 TATTTTTAT
1365305 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.28
23 6 0.21
24 15 0.52
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (24 bp):
TATTTTTATATTCTAGATTTAAAA
Found at i:1368072 original size:154 final size:154
Alignment explanation
Indices: 1367792--1368100 Score: 519
Period size: 154 Copynumber: 2.0 Consensus size: 154
1367782 AATTTGGTAA
*
1367792 TGGTGCCATTTGTTGTTTGCTTATGAATCACGCTCGTATGGTTTGAAGGCGGTGCTTTAAAGTGT
1 TGGTGCCATTTGTTGTTTGCTTATGAATCACGCTCGTATGGCTTGAAGGCGGTGCTTTAAAGTGT
* * * * *
1367857 TGATTAGGGTTGTAAATGAGATGAGACAGATCGCGAGTTACTCGAGATCAATTCGATCAAGGTTA
66 TGATTAGGGTTGTAAATGAAACGAGACAGATCGCGAGCTACTCGAGATCAACTCGATCAAGGCTA
1367922 GATAAATACTCGGATCGAATGGAC
131 GATAAATACTCGGATCGAATGGAC
* *
1367946 TGGTGCCATTTGTTGTTTGCTTATGAATCACGCTTGTATGGCTTGAAGGTGGTGCTTTAAAGTGT
1 TGGTGCCATTTGTTGTTTGCTTATGAATCACGCTCGTATGGCTTGAAGGCGGTGCTTTAAAGTGT
* * *
1368011 TGATTAGGGTTGTAAATGAAACGAGATAGATCGCGAGCTACTCGAGATCGACTCGATCAAGGCTC
66 TGATTAGGGTTGTAAATGAAACGAGACAGATCGCGAGCTACTCGAGATCAACTCGATCAAGGCTA
1368076 GATAAATACTCGGATCGAATGGAC
131 GATAAATACTCGGATCGAATGGAC
1368100 T
1 T
1368101 TGACTCGAGC
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 144 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (154 bp):
TGGTGCCATTTGTTGTTTGCTTATGAATCACGCTCGTATGGCTTGAAGGCGGTGCTTTAAAGTGT
TGATTAGGGTTGTAAATGAAACGAGACAGATCGCGAGCTACTCGAGATCAACTCGATCAAGGCTA
GATAAATACTCGGATCGAATGGAC
Found at i:1368320 original size:7 final size:7
Alignment explanation
Indices: 1368308--1368411 Score: 81
Period size: 7 Copynumber: 15.3 Consensus size: 7
1368298 AATTATGTGA
1368308 TAGGGTT
1 TAGGGTT
1368315 TAGGGTT
1 TAGGGTT
1368322 TA--GTAT
1 TAGGGT-T
*
1368328 TAGAGTT
1 TAGGGTT
1368335 TAGGG-T
1 TAGGGTT
1368341 TAGGGTT
1 TAGGGTT
*
1368348 TAAGG-T
1 TAGGGTT
***
1368354 TAAAATT
1 TAGGGTT
* *
1368361 AAGGGGT
1 TAGGGTT
***
1368368 TATATTT
1 TAGGGTT
1368375 TAGGGTT
1 TAGGGTT
1368382 TAGGGTT
1 TAGGGTT
1368389 TAGGGTT
1 TAGGGTT
1368396 TAGGGTT
1 TAGGGTT
1368403 TAGGGTT
1 TAGGGTT
1368410 TA
1 TA
1368412 AGTTATACAC
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
5 2 0.03
6 13 0.17
7 58 0.77
8 2 0.03
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (7 bp):
TAGGGTT
Found at i:1368730 original size:17 final size:17
Alignment explanation
Indices: 1368701--1368733 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1368691 AATTAAAATT
1368701 ACAAGACACAATTGAAA
1 ACAAGACACAATTGAAA
1368718 ACAAG-CACAAATTGAA
1 ACAAGACAC-AATTGAA
1368734 GGAACACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (17 bp):
ACAAGACACAATTGAAA
Found at i:1369210 original size:17 final size:16
Alignment explanation
Indices: 1369188--1369221 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1369178 AAGCCATCTC
1369188 TTTGGATTAATGATGTG
1 TTTGGATTAATGA-GTG
1369205 TTTGGATTAATGAGTG
1 TTTGGATTAATGAGTG
1369221 T
1 T
1369222 CAAAAGGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (16 bp):
TTTGGATTAATGAGTG
Found at i:1371397 original size:43 final size:43
Alignment explanation
Indices: 1371341--1371589 Score: 362
Period size: 43 Copynumber: 5.8 Consensus size: 43
1371331 AGGTCTTATA
* *
1371341 CTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAGA-CCTGGGGGAACTGTAAGGCTTACC
*
1371384 CTTGCACACAGCAAA-AGAACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAG-ACCTGGGGGAACTGTAAGGCTTACC
*
1371426 CTTGCACACATCAAAG-GAACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAG-ACCTGGGGGAACTGTAAGGCTTACC
* *
1371469 CTTGCACACAGCAAAGGGACCTGGGGGAACTATAAGGCTTACC
1 CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACC
*
1371512 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACC
* *
1371555 CTTGCACACAACAAAGGGACCTGGGGGAACTGTAA
1 CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAA
1371590 CGGTAATTAA
Statistics
Matches: 195, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
42 40 0.21
43 153 0.78
44 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.27, T:0.17
Consensus pattern (43 bp):
CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACC
Found at i:1377283 original size:27 final size:26
Alignment explanation
Indices: 1377237--1377300 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
1377227 AAGAGAGTAG
1377237 TATTTATATTTTAATAAAATATTT-A
1 TATTTATATTTTAATAAAATATTTGA
* *
1377262 TATTTATATATTTTATCGAAATATTTGA
1 TATTTATAT-TTTAAT-AAAATATTTGA
*
1377290 TA-TGATATTTT
1 TATTTATATTTT
1377301 TTTATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 9 0.27
26 8 0.24
27 13 0.39
28 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (26 bp):
TATTTATATTTTAATAAAATATTTGA
Found at i:1382148 original size:17 final size:17
Alignment explanation
Indices: 1382098--1382149 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
1382088 GGTTGGCTAC
*
1382098 AATAAAATAATAATGTT
1 AATAAAATAATAATATT
**
1382115 TTTAAAAATATATAATATT
1 AAT-AAAATA-ATAATATT
1382134 AATAAAATAATAATAT
1 AATAAAATAATAATAT
1382150 ATCAACTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 8 0.29
18 12 0.43
19 8 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AATAAAATAATAATATT
Found at i:1385055 original size:19 final size:20
Alignment explanation
Indices: 1385027--1385067 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1385017 TATTTAATTT
**
1385027 AATATAATTATGTTAAAATA
1 AATATAATTAAATTAAAATA
1385047 AATAT-ATTAAATTAAAATA
1 AATATAATTAAATTAAAATA
1385066 AA
1 AA
1385068 CTTAAACCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AATATAATTAAATTAAAATA
Found at i:1389185 original size:20 final size:20
Alignment explanation
Indices: 1389145--1389185 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1389135 TTTGATCATG
*
1389145 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
1389165 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
1389185 A
1 A
1389186 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:1395976 original size:20 final size:20
Alignment explanation
Indices: 1395936--1395976 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1395926 TTTGATCATG
*
1395936 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
1395956 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
1395976 A
1 A
1395977 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:1396845 original size:18 final size:18
Alignment explanation
Indices: 1396822--1396856 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1396812 TTCATTTAGG
1396822 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
1396840 GGGGAATCGATACCCCC
1 GGGGAATCGATACCCCC
1396857 TGAACATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.29, T:0.11
Consensus pattern (18 bp):
GGGGAATCGATACCCCCA
Found at i:1407360 original size:34 final size:34
Alignment explanation
Indices: 1407322--1407393 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
1407312 TAGTTTATTG
*
1407322 ATTATGAAATATTGTTTTATTAAGTTTTTTTATC
1 ATTATAAAATATTGTTTTATTAAGTTTTTTTATC
1407356 ATTATAAAATATTGTTTTATTAAGTTTTTTTATC
1 ATTATAAAATATTGTTTTATTAAGTTTTTTTATC
1407390 ATTA
1 ATTA
1407394 AAAGTTATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (34 bp):
ATTATAAAATATTGTTTTATTAAGTTTTTTTATC
Found at i:1408955 original size:10 final size:10
Alignment explanation
Indices: 1408940--1408964 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1408930 TATTTAAGGT
1408940 ATATTTTATA
1 ATATTTTATA
1408950 ATATTTTATA
1 ATATTTTATA
1408960 ATATT
1 ATATT
1408965 ATGTATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATTTTATA
Found at i:1409006 original size:17 final size:18
Alignment explanation
Indices: 1408970--1409010 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1408960 ATATTATGTA
*
1408970 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
1408988 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
1409005 TTTACT
1 TTTACT
1409011 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:1421759 original size:23 final size:23
Alignment explanation
Indices: 1421729--1421812 Score: 150
Period size: 23 Copynumber: 3.7 Consensus size: 23
1421719 CTCATATAAA
1421729 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1421752 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1421775 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1421798 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1421813 TACAATAATG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1424699 original size:2 final size:2
Alignment explanation
Indices: 1424692--1424720 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1424682 ACTCTGACTT
1424692 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1424721 CATACACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1426353 original size:23 final size:23
Alignment explanation
Indices: 1426296--1426356 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1426286 CTCATATAAA
* *
1426296 TGCACTGAAGTACCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1426319 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1426342 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1426357 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1427412 original size:21 final size:21
Alignment explanation
Indices: 1427386--1427442 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1427376 TTCAACCTTG
* *
1427386 ATGCATCGGTGCATTACGAAT
1 ATGCATCGATGCACTACGAAT
*
1427407 ATGCATCGATGCACTATGAAT
1 ATGCATCGATGCACTACGAAT
1427428 ATGCATCGATGCACT
1 ATGCATCGATGCACT
1427443 CTTCCCAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (21 bp):
ATGCATCGATGCACTACGAAT
Found at i:1434140 original size:181 final size:180
Alignment explanation
Indices: 1433654--1434332 Score: 886
Period size: 181 Copynumber: 3.7 Consensus size: 180
1433644 TTGTCGGTTT
* *
1433654 GTGTCGATACTTTATAAAAATGTATCGATCCAT-ATCAATATAATAGGTAAAAATATGACAAAAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAAT-GATATAACAGGTAAAAATATGACAAAAT
* * *
1433718 CGGTTTCGAAAAGACAAAACCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTTTAA
65 CGGTCTCAAAAAGACAAAA-CAGTAAAGCGCTACCGAATATATTGAAAGTGTCGATAC--TTTAA
* ** * *
1433783 GTTTGTGTCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGTGCCTATAAA
127 ATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAA
* * *
1433837 GTGTCGATACTTTATAAAAATGTATCGATCTATAACGATATAACAGGTAAAAATATGAAAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAATC
* * * * * *
1433902 GATCTCGAAATGACAAAACCGATAAAGCGCTACTGGATATATTGAAAGTGTCGATACTTTAACAT
66 GGTCTCAAAAAGACAAAACAG-TAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAA-AT
* * ** * *
1433967 GAGTATCGACACTTTG-GTAATTTAAAAGAAAAATATTTTTAGCGCTTATAAA
129 AAGTATCGACACTTTGTG-AATTTAAAAGAGAAGCAATTTTAGCGCCTATAAA
* * * * *
1434019 ATGTCGTTACTTTATAAAAATGTATTGATCCATAATGATACAACAGGT-AAAATATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAATC
1434083 GGTCTCAAAAAGACAAAACTAGTAAAGCGCTACC-AGATATATTGAAAGTGTCGATACTTTAATA
66 GGTCTCAAAAAGACAAAAC-AGTAAAGCGCTACCGA-ATATATTGAAAGTGTCGATACTTTAA-A
*
1434147 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAA
128 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAA
*
1434200 GTGTTGATACTTTATAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAATC
* *
1434265 GGTCT-AGAAATGACAAAA-ACGATAAAGAGCTACCGAATATATTGAAAGTGTCGATACTTT-AA
66 GGTCTCA-AAAAGACAAAACA-G-TAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAAA
1434327 TAAGTA
128 TAAGTA
1434333 CGCGTAATAA
Statistics
Matches: 434, Mismatches: 50, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
180 8 0.02
181 165 0.38
182 153 0.35
183 107 0.25
184 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (180 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAATC
GGTCTCAAAAAGACAAAACAGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAAATAA
GTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAA
Found at i:1436711 original size:21 final size:21
Alignment explanation
Indices: 1436685--1436728 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1436675 AAGACAATCA
*
1436685 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAAAGACACTTGAG
1436706 AGAGTCGAAAAGACACTTGAG
1 AGAGTCGAAAAGACACTTGAG
1436727 AG
1 AG
1436729 GCACAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.32, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAAAGACACTTGAG
Found at i:1437035 original size:18 final size:18
Alignment explanation
Indices: 1437012--1437050 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1437002 AAAAAAATAT
*
1437012 GAAGAAGAAAAGATGGAG
1 GAAGAAAAAAAGATGGAG
1437030 GAAGAAAAAAAGATGGAG
1 GAAGAAAAAAAGATGGAG
1437048 GAA
1 GAA
1437051 ATGGGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.36, T:0.05
Consensus pattern (18 bp):
GAAGAAAAAAAGATGGAG
Found at i:1438354 original size:19 final size:19
Alignment explanation
Indices: 1438330--1438378 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1438320 AATGTAGGGT
1438330 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1438349 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1438368 TAATTTTGTAT
1 TAATTTTGTAT
1438379 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1439199 original size:201 final size:199
Alignment explanation
Indices: 1438730--1439407 Score: 986
Period size: 201 Copynumber: 3.4 Consensus size: 199
1438720 GTAAGCAGAT
* * *
1438730 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACACATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* *
1438795 GGTAATTTTGTAATATAACCGGTATAAATATACCT-ATTTTATGTGAGAATAGGTCTACATAATG
66 GGTAATTTTGTAATGTAACCGGTATAAATATA-CTGGTTTTATGTGAGAATAGGTCTACATAATG
* * * *
1438859 TATCTACACTTTTTAATTTGGTGTC-AATACATTTTGTCCAGAATGAATGCCCAAAATGGTGAAA
130 TATCGACACTTTTTAATTT-GTGTCGAA-ACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCAC
1438923 GCATAAA
193 GCATAAA
* * *
1438930 GTGTCTATACATTTATAAAAAGTATCAATCCCAGAAACATCAAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* ** * * * *
1438995 GGTAAATTTACAATGTAACTGGTATAATTATACTGGTTTTATGAGAGAATAGATCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACTGGTTTTATGTGAGAATAGGTCTACATAATGT
** *
1439060 ATCGACACTTGTGGAATTTGTGTCGAAACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACG
131 ATCGACACTT-TTTAATTTGTGTCGAAACTTTTTGTCCAGAATGAATGCCCAAAA-TGGTGCACG
1439125 CATAAA
194 CATAAA
* *
1439131 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAGACATCGAAACCCATAATTATAATATAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
*
1439196 GGTAATTTTGTAACGTAACCGGTATAAATATA-TCGGTTTTATGTGAGAATAGGTCTACATAATG
66 GGTAATTTTGTAATGTAACCGGTATAAATATACT-GGTTTTATGTGAGAATAGGTCTACATAATG
* *
1439260 TATCGACACTTTTTAATTT-TGAATTGATACTTTTTGTCCAGAATGAATGCCCAAAAAAATGGTG
130 TATCGACACTTTTTAATTTGTG--TCGAAACTTTTTGTCCAGAATGAATGCCC---AAAATGGTG
1439324 CACGCATAAA
190 CACGCATAAA
1439334 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
1439399 GGTAATTTT
66 GGTAATTTT
1439408 TGAGAGAATA
Statistics
Matches: 426, Mismatches: 42, Indels: 17
0.88 0.09 0.04
Matches are distributed among these distances:
199 4 0.01
200 160 0.38
201 172 0.40
203 86 0.20
204 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (199 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGTAATGTAACCGGTATAAATATACTGGTTTTATGTGAGAATAGGTCTACATAATGT
ATCGACACTTTTTAATTTGTGTCGAAACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCACGCA
TAAA
Found at i:1440325 original size:2 final size:2
Alignment explanation
Indices: 1440318--1440368 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1440308 CATGGGGAAG
1440318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1440360 TA TA TA TA T
1 TA TA TA TA T
1440369 CTCCGGATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1442023 original size:23 final size:23
Alignment explanation
Indices: 1441993--1442042 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1441983 ATACTCTAGG
1441993 TATGACACAAATTTATTCCTGCT
1 TATGACACAAATTTATTCCTGCT
1442016 TATGACACAAATTTATTCCTGCT
1 TATGACACAAATTTATTCCTGCT
1442039 TATG
1 TATG
1442043 CGAATTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (23 bp):
TATGACACAAATTTATTCCTGCT
Found at i:1442050 original size:20 final size:21
Alignment explanation
Indices: 1441999--1442050 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
1441989 TAGGTATGAC
1441999 ACAAATTTATTCCTGCTTATG
1 ACAAATTTATTCCTGCTTATG
1442020 ACACAAATTTATTCCTGCTTATG
1 --ACAAATTTATTCCTGCTTATG
*
1442043 -CGAATTTA
1 ACAAATTTA
1442051 GTTTATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.25
23 21 0.75
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (21 bp):
ACAAATTTATTCCTGCTTATG
Found at i:1442570 original size:18 final size:18
Alignment explanation
Indices: 1442549--1442585 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1442539 GTAATTGGAG
1442549 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1442567 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1442585 T
1 T
1442586 ATAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1442592 original size:24 final size:24
Alignment explanation
Indices: 1442541--1442593 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1442531 TTTCATATGT
* * *
1442541 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1442565 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1442589 AATTT
1 AATTT
1442594 TGGGTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1443175 original size:203 final size:198
Alignment explanation
Indices: 1442821--1443789 Score: 1056
Period size: 203 Copynumber: 4.9 Consensus size: 198
1442811 TAAAATTTCC
* * * * *
1442821 CATAAAGTGTCGATACATTTTTAAAAAGTATAGATCCAAAAAATATCGAAACCAAAAATTATAAT
1 CATAAAGTGTCGATAAATTATT-AAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* * ** * *
1442886 GTAATAGGTAAATTTACAATGTGACTGGTATAAATATATTGATTTTATGAGAAAATAGGTCA-GC
65 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGT-ATAC
* * * * **
1442950 ATAAAGTATCAACACCATTTAAATTTGTGTCGATACTTTTTTTGCGAGGCT-TTGTTTGCTCAAC
129 ATAATGTATCGACA-CTTTTAAATTTGTGTCGATAC-TTTTTTGCGA-GCTAATGAATGC-CAA-
*
1443014 AAGGTGCACA
189 AAGGTGCACG
* *
1443024 CATAAAGCGTCGATATAATTATTAAAAGTATCGATCCAAAAAACATCGAAATCGAAAATTATAAT
1 CATAAAGTGTCGATA-AATTATTAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
*
1443089 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATATGTATACA
65 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTATACA
* *
1443154 TAATGTATCGACACTATTTAAATTTGTGTCGATA-TATTTTGTCCA--TAATGAATGCC-AAA--
130 TAATGTATCGACACT-TTTAAATTTGTGTCGATACTTTTTTG-CGAGCTAATGAATGCCAAAAGG
*
1443213 --CACT
193 TGCACG
* * * *
1443217 CATAAAGTGACGATACA-T-TTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
1 CATAAAGTGTCGATAAATTATTAAAA--GTATCGATCCAAAAAACATCGAAACCGAAAATTATAA
* *
1443280 TGTAATACGTAAATTTACAATGTAACCGGTATAAATATACCTGTTTTATGAGAAAATAGGTATAC
64 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTATAC
* * * *
1443345 ATAATGTATCGATACTGTTTAAATTTGTGTCGATAC-ATTTTGC--CCATAATGAATGCCAAACG
129 ATAATGTATCGACACT-TTTAAATTTGTGTCGATACTTTTTTGCGAGC-TAATGAATGCCAAA-A
1443407 GAGTGCACG
191 G-GTGCACG
* * * * *
1443416 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAAACATCGGAACCCATAATTATAA
1 CATAAAGTGTCGATA-AATTATTAAAAGTATCGAT-CCAAAAAACATCGAAACCGAAAATTATAA
* ** * * * ** *
1443481 TGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCAGTTTAATTAGAAAAGCGGTCA-G
64 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGT-ATA
* * **
1443545 CATAATGTATCGACACTTGTTAAATGTGTGTCGATACTTTTTTTGCGAGGCT-TTGTTTGCTCAA
128 CATAATGTATCGACACTT-TTAAATTTGTGTCGATAC-TTTTTTGCGA-GCTAATGAATGC-CAA
* *
1443609 CGAGGTACACG
189 -AAGGTGCACG
* *
1443620 CATAAAGTGTCGATATATTTATTAAAAGTATCGATCCAAAATACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATA-AATTATTAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
1443685 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGT-TAAC
65 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTAT-AC
* *
1443749 ATAATGTATCGACACTTTTAAATTTGTGTCAATACGTTTTT
129 ATAATGTATCGACACTTTTAAATTTGTGTCGATACTTTTTT
1443790 AAATTACGCG
Statistics
Matches: 652, Mismatches: 81, Indels: 68
0.81 0.10 0.08
Matches are distributed among these distances:
190 6 0.01
191 2 0.00
192 147 0.23
193 18 0.03
197 2 0.00
198 1 0.00
199 19 0.03
200 14 0.02
201 123 0.19
202 26 0.04
203 239 0.37
204 49 0.08
205 5 0.01
206 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
CATAAAGTGTCGATAAATTATTAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAATG
TAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTATACAT
AATGTATCGACACTTTTAAATTTGTGTCGATACTTTTTTGCGAGCTAATGAATGCCAAAAGGTGC
ACG
Found at i:1445345 original size:19 final size:19
Alignment explanation
Indices: 1445318--1445359 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1445308 AATATAGGGT
*
1445318 TAATTTTGTATAAGATTTA
1 TAATGTTGTATAAGATTTA
**
1445337 TAATGTTGTATACTATTTA
1 TAATGTTGTATAAGATTTA
1445356 TAAT
1 TAAT
1445360 TTTGCATGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (19 bp):
TAATGTTGTATAAGATTTA
Found at i:1446791 original size:38 final size:38
Alignment explanation
Indices: 1446740--1446817 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
1446730 TTATTTTTAC
1446740 TGCGGTGCTGCTTTATAAGAAAAATACTTGCCTGATGA
1 TGCGGTGCTGCTTTATAAGAAAAATACTTGCCTGATGA
** ** *
1446778 TGCGGTGCTGCTTTATGGGAAATGTACTTGTCTGATGA
1 TGCGGTGCTGCTTTATAAGAAAAATACTTGCCTGATGA
1446816 TG
1 TG
1446818 TACAGGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (38 bp):
TGCGGTGCTGCTTTATAAGAAAAATACTTGCCTGATGA
Found at i:1450368 original size:28 final size:28
Alignment explanation
Indices: 1450307--1450368 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1450297 ATTAAATACC
* * *
1450307 TATTTTATTATATAAACATTACCTATTA
1 TATTATATTATATAAACACTACCTAATA
*
1450335 TATTATATTATATAAGCACTACCTAATA
1 TATTATATTATATAAACACTACCTAATA
*
1450363 TGTTAT
1 TATTAT
1450369 TGTACTTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (28 bp):
TATTATATTATATAAACACTACCTAATA
Found at i:1450440 original size:16 final size:16
Alignment explanation
Indices: 1450419--1450453 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1450409 CGATCTAAAT
*
1450419 TTTAATCAATCACTTA
1 TTTAATCAATCACATA
*
1450435 TTTAATCGATCACATA
1 TTTAATCAATCACATA
1450451 TTT
1 TTT
1450454 TTTAACCGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (16 bp):
TTTAATCAATCACATA
Found at i:1453648 original size:3 final size:3
Alignment explanation
Indices: 1453642--1453716 Score: 66
Period size: 3 Copynumber: 25.7 Consensus size: 3
1453632 ATAATATATT
* * * * * *
1453642 TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA TAA -AA AAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1453688 TAA TAAA TAA TAA T-A TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TA
1453717 TAAATAAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
2 6 0.09
3 56 0.86
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1453699 original size:20 final size:22
Alignment explanation
Indices: 1453673--1453725 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
1453663 TTATTATTAT
1453673 TATAATAAAAAAAT-ATAATAA
1 TATAATAAAAAAATAATAATAA
* *
1453694 -ATAATAATATAATAATAATAA
1 TATAATAAAAAAATAATAATAA
1453715 TATAAATAAAA
1 TAT-AATAAAA
1453726 TCGGGACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.42
21 7 0.27
22 2 0.08
23 6 0.23
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TATAATAAAAAAATAATAATAA
Found at i:1454222 original size:24 final size:23
Alignment explanation
Indices: 1454187--1454231 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1454177 TGAACAAGTT
1454187 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
1454211 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
1454232 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Done.