Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008802.1 Hibiscus syriacus cultivar Beakdansim tig00111952_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: 1147353
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:3320 original size:13 final size:13
Alignment explanation
Indices: 3302--3326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3292 ACAGTCAACG
3302 GTCAACGGGTCGA
1 GTCAACGGGTCGA
3315 GTCAACGGGTCG
1 GTCAACGGGTCG
3327 GGTCGGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:8685 original size:3 final size:3
Alignment explanation
Indices: 8677--8709 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
8667 GTTGTCATAT
*
8677 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8710 GGCTAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:25512 original size:27 final size:27
Alignment explanation
Indices: 25477--25537 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
25467 TCCCTTGACG
25477 GGTGCATCGATGCACTATCTATGCATC
1 GGTGCATCGATGCACTATCTATGCATC
*
25504 GGTGCATCGATGCACTATCTATGCATT
1 GGTGCATCGATGCACTATCTATGCATC
25531 GGTGCAT
1 GGTGCAT
25538 AAATCTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (27 bp):
GGTGCATCGATGCACTATCTATGCATC
Found at i:26532 original size:17 final size:17
Alignment explanation
Indices: 26512--26551 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
26502 AACTTTACTT
26512 CATTACTTTAATTCTTC
1 CATTACTTTAATTCTTC
26529 CATTACTTTAATTCTTC
1 CATTACTTTAATTCTTC
26546 CATTAC
1 CATTAC
26552 CTTTTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (17 bp):
CATTACTTTAATTCTTC
Found at i:29971 original size:27 final size:27
Alignment explanation
Indices: 29936--30023 Score: 149
Period size: 27 Copynumber: 3.3 Consensus size: 27
29926 TCCTTTGACG
29936 GGTGCATCGATGCACTATCTATGCATC
1 GGTGCATCGATGCACTATCTATGCATC
29963 GGTGCATCGATGCACTATCTATGCATC
1 GGTGCATCGATGCACTATCTATGCATC
* * *
29990 GGTGTATCGATGCACTATCTATGGATT
1 GGTGCATCGATGCACTATCTATGCATC
30017 GGTGCAT
1 GGTGCAT
30024 AAATCTCATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (27 bp):
GGTGCATCGATGCACTATCTATGCATC
Found at i:35473 original size:16 final size:18
Alignment explanation
Indices: 35446--35488 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
35436 AATTAAATAT
*
35446 AATATTATATATAAACAA
1 AATAATATATATAAACAA
*
35464 AATAATATATATAAACAT
1 AATAATATATATAAACAA
35482 AATAATA
1 AATAATA
35489 ATACATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATATATATAAACAA
Found at i:35613 original size:19 final size:19
Alignment explanation
Indices: 35573--35613 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
35563 TGAAATGTAA
*
35573 ATATAATCTTAATATATAT
1 ATATAATCTTAATAAATAT
35592 ATATAATCTTATATAAAT-T
1 ATATAATCTTA-ATAAATAT
35611 ATA
1 ATA
35614 AAATACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAATCTTAATAAATAT
Found at i:39569 original size:2 final size:2
Alignment explanation
Indices: 39564--39608 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
39554 ATAAAAAATA
39564 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39606 AT A
1 AT A
39609 ATTATTAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40413 original size:14 final size:14
Alignment explanation
Indices: 40396--40461 Score: 91
Period size: 14 Copynumber: 4.7 Consensus size: 14
40386 GTAACCCGAA
40396 CTGAGTCAACTCGT
1 CTGAGTCAACTCGT
*
40410 CTGAGTCAACTCAT
1 CTGAGTCAACTCGT
40424 CTGAGTCAACTCGT
1 CTGAGTCAACTCGT
40438 CTGTA-TCAACTCGT
1 CTG-AGTCAACTCGT
40452 -TCGAGTCAAC
1 CT-GAGTCAAC
40462 CTGTTGACTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.04
14 44 0.94
15 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (14 bp):
CTGAGTCAACTCGT
Found at i:40484 original size:13 final size:13
Alignment explanation
Indices: 40466--40490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40456 GTCAACCTGT
40466 TGACTTTGACCGC
1 TGACTTTGACCGC
40479 TGACTTTGACCG
1 TGACTTTGACCG
40491 AAAAGTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (13 bp):
TGACTTTGACCGC
Found at i:41007 original size:38 final size:38
Alignment explanation
Indices: 40956--41034 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
40946 TTAAGCAAAT
*
40956 AACCTCAGAATCTCTAAATTCTATTTATCCTCGTTAAA
1 AACCTCAGAATCTCTAAATTCTATTTATCCTCATTAAA
40994 AACCTCAGAATCTCTAAATTCTATTTATCCTCATTAAA
1 AACCTCAGAATCTCTAAATTCTATTTATCCTCATTAAA
41032 AAC
1 AAC
41035 TTTAATTTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (38 bp):
AACCTCAGAATCTCTAAATTCTATTTATCCTCATTAAA
Found at i:48221 original size:14 final size:14
Alignment explanation
Indices: 48204--48269 Score: 105
Period size: 14 Copynumber: 4.7 Consensus size: 14
48194 GTAACTCGAA
48204 CTGAGTCAACTCGT
1 CTGAGTCAACTCGT
*
48218 CTGAGTCAACTCAT
1 CTGAGTCAACTCGT
*
48232 TTGAGTCAACTCGT
1 CTGAGTCAACTCGT
*
48246 CTGTGTCAACTCGT
1 CTGAGTCAACTCGT
48260 CTGAGTCAAC
1 CTGAGTCAAC
48270 CTGTTGACTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (14 bp):
CTGAGTCAACTCGT
Found at i:48292 original size:13 final size:13
Alignment explanation
Indices: 48274--48298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48264 GTCAACCTGT
48274 TGACTTTGACCGC
1 TGACTTTGACCGC
48287 TGACTTTGACCG
1 TGACTTTGACCG
48299 AAAAGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (13 bp):
TGACTTTGACCGC
Found at i:48816 original size:38 final size:38
Alignment explanation
Indices: 48765--48843 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
48755 TTAAGCAAAT
*
48765 AACCTCAGAATCTCTAAATTATATTTATCCTCGTTAAA
1 AACCTCAGAATCTCTAAATTATATTTATCCTCATTAAA
*
48803 AACCTCAGAATCTCTAAATTCTATTTATCCTCATTAAA
1 AACCTCAGAATCTCTAAATTATATTTATCCTCATTAAA
48841 AAC
1 AAC
48844 TTTAATATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (38 bp):
AACCTCAGAATCTCTAAATTATATTTATCCTCATTAAA
Found at i:57954 original size:77 final size:76
Alignment explanation
Indices: 57873--58083 Score: 293
Period size: 76 Copynumber: 2.8 Consensus size: 76
57863 ATTTTAAACA
*
57873 TTATATTTTATCTT-TGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATA
1 TTATATTTT-T-TTATGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGGATA
57937 TTATTTTTATATT
64 TTATTTTTATATT
*
57950 TTATATTTGTTTTATGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGGATAT
1 TTATATTT-TTTTATGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGGATAT
58014 TATTTTTATATT
65 TATTTTTATATT
* * * * * *
58026 ATATTATTTTTTTAGGTATTTTAATTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 TTA-TATTTTTTTATGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTA
58084 AGATGTTTAG
Statistics
Matches: 123, Mismatches: 7, Indels: 9
0.88 0.05 0.06
Matches are distributed among these distances:
75 1 0.01
76 87 0.71
77 34 0.28
78 1 0.01
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (76 bp):
TTATATTTTTTTATGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGGATATT
ATTTTTATATT
Found at i:63338 original size:2 final size:2
Alignment explanation
Indices: 63331--63376 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
63321 AAGACTTGAG
63331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63373 AT AT
1 AT AT
63377 TTAAGAGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66516 original size:3 final size:3
Alignment explanation
Indices: 66498--66608 Score: 96
Period size: 3 Copynumber: 35.3 Consensus size: 3
66488 TTCTTTTAAA
* * * *
66498 ATT ATT TTT AATT ATT ATT ATT ATC AAT ATT AATCT AGT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT -AT-T ATT ATT ATT ATT
** * *
66546 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AAT ATT ATAC ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T
*
66593 CTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
66609 AATAATTACA
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
3 75 0.88
4 9 0.11
5 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:68493 original size:113 final size:111
Alignment explanation
Indices: 68265--68500 Score: 291
Period size: 113 Copynumber: 2.1 Consensus size: 111
68255 TAATATATAT
*
68265 TTTTTTCAATATTAAGAAAGGGCAGTCTTAAAGCACTGGATGTCCATTTTCTAATATTTCTAAAA
1 TTTTTT-AATATTAAGAAAGGGCAGTCTTAAAGCACTGGATGTCCATTTTATAATATTTCTAAAA
* *
68330 TAAATATAAATTATATATATTAATCTATATATTAATATTTTATTATTA
65 TAAATAT-AATTATATATATCAATATATATATTAATATTTTATTATTA
* * *
68378 TTTTTTAATATTAAGAAATGGCAGTCTTAAAGCAACTGGATGTCCATTTTATGATATTT-TTAAA
1 TTTTTTAATATTAAGAAAGGGCAGTCTTAAAGC-ACTGGATGTCCATTTTATAATATTTCTAAAA
* *
68442 TAAATAT-TTTACT-TTTATCAATTATATATATTAATCTAATTTT-TTATTA
65 TAAATATAATTA-TATATATCAA-TATATATATTAA--T-ATTTTATTATTA
*
68491 TTTTTAAATA
1 TTTTTTAATA
68501 AATATTTTAT
Statistics
Matches: 108, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
110 9 0.08
111 12 0.11
112 37 0.34
113 45 0.42
114 5 0.05
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (111 bp):
TTTTTTAATATTAAGAAAGGGCAGTCTTAAAGCACTGGATGTCCATTTTATAATATTTCTAAAAT
AAATATAATTATATATATCAATATATATATTAATATTTTATTATTA
Found at i:68496 original size:112 final size:110
Alignment explanation
Indices: 68262--68497 Score: 284
Period size: 112 Copynumber: 2.1 Consensus size: 110
68252 ATTTAATATA
*
68262 TATT-TTTTTCAATATTAAGAAAGGGCAGTCTTAAAGCACTGGATGTCCATTTTCTAATATTTCT
1 TATTATTTTT-AATATTAAGAAAGGGCAGTCTTAAAGCACTGGATGTCCATTTTATAATATTTCT
* *
68326 AAAATAAATATAAATTATATATATTAATCTATATATTAATATTTTAT
65 AAAATAAATAT-AATTATATATATCAATATATATATTAATATTTTAT
* *
68373 TATTATTTTTTAATATTAAGAAATGGCAGTCTTAAAGCAACTGGATGTCCATTTTATGATATTT-
1 TATTA-TTTTTAATATTAAGAAAGGGCAGTCTTAAAGC-ACTGGATGTCCATTTTATAATATTTC
* * *
68437 TTAAATAAATAT-TTTACT-TTTATCAATTATATATATTAATCTAATTTT-T
64 TAAAATAAATATAATTA-TATATATCAA-TATATATATTAA--T-ATTTTAT
68486 TATTATTTTTAA
1 TATTATTTTTAA
68498 ATAAATATTT
Statistics
Matches: 109, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
110 9 0.08
111 16 0.15
112 44 0.40
113 35 0.32
114 5 0.05
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (110 bp):
TATTATTTTTAATATTAAGAAAGGGCAGTCTTAAAGCACTGGATGTCCATTTTATAATATTTCTA
AAATAAATATAATTATATATATCAATATATATATTAATATTTTAT
Found at i:69821 original size:10 final size:10
Alignment explanation
Indices: 69806--69834 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
69796 CTAACTATTC
69806 TATTTTTTCT
1 TATTTTTTCT
69816 TATTTTTTCT
1 TATTTTTTCT
69826 TATTTTTTC
1 TATTTTTTC
69835 ATGCATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (10 bp):
TATTTTTTCT
Found at i:70713 original size:8 final size:7
Alignment explanation
Indices: 70689--70730 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
70679 TTTTCATACA
70689 TGCA-TT
1 TGCATTT
70695 TGCATTT
1 TGCATTT
70702 TGCATCTT
1 TGCAT-TT
70710 TGCATTT
1 TGCATTT
* *
70717 TTCATTG
1 TGCATTT
70724 TGCATTT
1 TGCATTT
70731 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:70713 original size:15 final size:14
Alignment explanation
Indices: 70689--70730 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
70679 TTTTCATACA
70689 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
70702 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
70717 TTCATTGTGCATTT
1 TGCATTTTGCATTT
70731 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:70806 original size:12 final size:12
Alignment explanation
Indices: 70789--70842 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
70779 ACATTCACAT
70789 ATTTACATTTGC
1 ATTTACATTTGC
70801 ATTTACATTTGC
1 ATTTACATTTGC
* *
70813 ATTTTTACGTTTGT
1 A--TTTACATTTGC
*
70827 ATTTACATTTTC
1 ATTTACATTTGC
70839 ATTT
1 ATTT
70843 TTTACATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 25 0.71
14 10 0.29
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.57
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:70819 original size:26 final size:27
Alignment explanation
Indices: 70790--70849 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
70780 CATTCACATA
70790 TTTACATTTGCATTTACATTTGCA-TT
1 TTTACATTTGCATTTACATTTGCATTT
* * *
70816 TTTACGTTTGTATTTACATTTTCATTT
1 TTTACATTTGCATTTACATTTGCATTT
70843 TTTACAT
1 TTTACAT
70850 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:77360 original size:22 final size:22
Alignment explanation
Indices: 77334--77388 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
77324 ATCTACACTC
77334 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
77356 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
77378 TTCAAAGATGA
1 TTCAAAGATGA
77389 ATGCTTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:78188 original size:76 final size:76
Alignment explanation
Indices: 78062--78851 Score: 1409
Period size: 76 Copynumber: 10.4 Consensus size: 76
78052 CTATTTCCCA
78062 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
78127 AGCCTTAGGGT
66 AGCCTTAGGGT
78138 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
78203 AGCCTTAGGGT
66 AGCCTTAGGGT
*
78214 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
78279 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * *
78290 CATCTGTAATTCCTACAATGCATGATGTTTCCAAAAAACCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
78355 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
78366 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
78431 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
78442 CATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
78507 AACCTTAGGGT
66 AGCCTTAGGGT
*
78518 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
78583 AACCTTAGGGT
66 AGCCTTAGGGT
*
78594 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
78659 AGCCTTAGGGT
66 AGCCTTAGGGT
*
78670 CATCTGTAAGGCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
78735 AGCCTTAGGGT
66 AGCCTTAGGGT
*
78746 CATCTGTAAGGCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
78811 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
78822 CATCTGTAAGCCCTTCAGTGAATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
78852 TTAAGACCTC
Statistics
Matches: 689, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 689 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:79026 original size:3 final size:3
Alignment explanation
Indices: 79008--79114 Score: 83
Period size: 3 Copynumber: 35.3 Consensus size: 3
78998 TTCTTTTAAA
* * * * *
79008 ATT ATT TTT AATT ATT ATT ATT ATC AAT ATT AAT A-T AGT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * *
79053 ATT A-T ATT ATT AAA ATT ATT ATT ATT ATT AAT ATT ATAC ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T
*
79099 CTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
79115 AATAATTACA
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
2 4 0.05
3 71 0.88
4 6 0.07
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:79049 original size:26 final size:23
Alignment explanation
Indices: 79020--79088 Score: 84
Period size: 23 Copynumber: 2.8 Consensus size: 23
79010 TATTTTTAAT
79020 TATTATTATTATCAATATTAATATAG
1 TATTATTATTAT-AATATTAA-A-AG
* *
79046 TATTATTATTATATTATTAAAAT
1 TATTATTATTATAATATTAAAAG
79069 TATTATTATTATTAATATTA
1 TATTATTATTA-TAATATTA
79089 TACATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
23 12 0.31
24 8 0.21
25 7 0.18
26 12 0.31
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (23 bp):
TATTATTATTATAATATTAAAAG
Found at i:80877 original size:11 final size:11
Alignment explanation
Indices: 80861--80897 Score: 53
Period size: 9 Copynumber: 3.6 Consensus size: 11
80851 AATCTATATA
80861 TTTTAATTATT
1 TTTTAATTATT
80872 TTTTAA-TATT
1 TTTTAATTATT
80882 TTTT--TTATT
1 TTTTAATTATT
80891 TTTTAAT
1 TTTTAAT
80898 ATTAAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.35
10 8 0.35
11 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTAATTATT
Found at i:80879 original size:123 final size:123
Alignment explanation
Indices: 80738--80959 Score: 329
Period size: 124 Copynumber: 1.8 Consensus size: 123
80728 TATAAATAAC
*
80738 TTTTAATCATATTTTAATA-TATATTTATTTTTCAATATTAATAAAGGGCAGTCTTAAAGCAACT
1 TTTTAATCATATTTTAATATTATATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAGCAACT
80802 GGATGACAATTTTCTGATATTTCTAAAATAAATATAAATTATATATATTAATCTATATA
66 GGATGACAATTTTCTGATATTT-TAAAATAAATATAAATTATATATATTAATCTATATA
* * * * * * *
80861 TTTTAATTATTTTTTAATATTTTTTTTATTTTTTAATATTAAGAAATGGTAGTCTTAAAGCAACT
1 TTTTAATCATATTTTAATATTATATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAGCAACT
* * *
80926 GGATGTCTATTTTCTGATATTTTTAAATAAATAT
66 GGATGACAATTTTCTGATATTTTAAAATAAATAT
80960 TTTACTTTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
123 28 0.32
124 59 0.68
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (123 bp):
TTTTAATCATATTTTAATATTATATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAGCAACT
GGATGACAATTTTCTGATATTTTAAAATAAATATAAATTATATATATTAATCTATATA
Found at i:80882 original size:19 final size:19
Alignment explanation
Indices: 80858--80900 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
80848 ATTAATCTAT
80858 ATATTTTAATTATTTTTTA
1 ATATTTTAATTATTTTTTA
**
80877 ATATTTTTTTTATTTTTTA
1 ATATTTTAATTATTTTTTA
80896 ATATT
1 ATATT
80901 AAGAAATGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATATTTTAATTATTTTTTA
Found at i:80900 original size:10 final size:10
Alignment explanation
Indices: 80856--80900 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
80846 ATATTAATCT
*
80856 ATATATTTTA
1 ATATTTTTTA
80866 ATTATTTTTTA
1 A-TATTTTTTA
80877 ATATTTTTT-
1 ATATTTTTTA
*
80886 TTATTTTTTA
1 ATATTTTTTA
80896 ATATT
1 ATATT
80901 AAGAAATGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.27
10 13 0.43
11 9 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATATTTTTTA
Found at i:89790 original size:237 final size:245
Alignment explanation
Indices: 89425--89907 Score: 867
Period size: 241 Copynumber: 2.0 Consensus size: 245
89415 TTAGTTTTTC
89425 TTTTTAACAGTGGCAGCTGGAGTGGGGTCCAAAAGCGTGGGGTGGCGGAGATGGTCTTAATTGGA
1 TTTTTAACAGTGGCAGCTGGAGTGGGGTCCAAAAGCGTGGGGTGGCGGAGATGG--TTAATTGGA
89490 CATTCGTGGTCGCCACAAATAGTGGGATTTTGGGGGCTCCGAGACCGACATTATTTTTTAAATTA
64 CATTCGTGGTCGCCACAAATAGTGGGATTTTGGGGGCTCCGAGACCGACATTATTTTTTAAATTA
89555 TTTACTTA-T-TTA-TATTATT-TTATTATTGTTACCGGCTTTTGTCATAAAATTA-TTTAAAGT
129 TTTACTTATTATTATTATTATTATTATTATTGTTACCGGCTTTTGTCATAAAATTATTTTAAAGT
89615 CATTTCC-AAAATAAATTAAAGTGC-TTATTATGCAAAATCATTATCACATCT
194 CATTTCCAAAAAT-AATTAAAGTGCTTTATTATGCAAAATCATTATCACATCT
89666 TTTTTAACAGTGGCAGCTGGAGTGGGGTCCAAAAGCGTGGGGTGGCGGAGATGG-TAATTGGACA
1 TTTTTAACAGTGGCAGCTGGAGTGGGGTCCAAAAGCGTGGGGTGGCGGAGATGGTTAATTGGACA
89730 TTCGTGGTCGCCAC-AATAGTGGGATTTTGGGGGCTCCGAGACCGACATTATTTTTTAAATTATT
66 TTCGTGGTCGCCACAAATAGTGGGATTTTGGGGGCTCCGAGACCGACATTATTTTTTAAATTATT
89794 TACTTATTATTATTATTATTATTATTATTGTTACCGGCTTTTGTCATAAAATTATTTTTAAAGTC
131 TACTTATTATTATTATTATTATTATTATTGTTACCGGCTTTTGTCATAAAATTA-TTTTAAAGTC
89859 ATTTCCAAAAATAATTAAAGTGCTTTATTATGCAAAATCATTATCACAT
195 ATTTCCAAAAATAATTAAAGTGCTTTATTATGCAAAATCATTATCACAT
89908 TTTCTTTGAG
Statistics
Matches: 234, Mismatches: 0, Indels: 13
0.95 0.00 0.05
Matches are distributed among these distances:
237 56 0.24
238 25 0.11
239 3 0.01
240 7 0.03
241 87 0.37
243 26 0.11
244 30 0.13
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (245 bp):
TTTTTAACAGTGGCAGCTGGAGTGGGGTCCAAAAGCGTGGGGTGGCGGAGATGGTTAATTGGACA
TTCGTGGTCGCCACAAATAGTGGGATTTTGGGGGCTCCGAGACCGACATTATTTTTTAAATTATT
TACTTATTATTATTATTATTATTATTATTGTTACCGGCTTTTGTCATAAAATTATTTTAAAGTCA
TTTCCAAAAATAATTAAAGTGCTTTATTATGCAAAATCATTATCACATCT
Found at i:89805 original size:3 final size:3
Alignment explanation
Indices: 89797--89822 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
89787 AATTATTTAC
89797 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
89823 GTTACCGGCT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:94028 original size:11 final size:11
Alignment explanation
Indices: 93973--94035 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
93963 TTATTATAGA
93973 ATTTTTAATAT
1 ATTTTTAATAT
*
93984 ATATTTAA-A-
1 ATTTTTAATAT
93993 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
94004 ATCAATAATGT
1 ATTTTTAATAT
94015 ATTTTTAATAT
1 ATTTTTAATAT
94026 ATTTTTAATA
1 ATTTTTAATA
94036 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 4 0.10
10 8 0.21
11 27 0.69
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:100895 original size:26 final size:28
Alignment explanation
Indices: 100843--100907 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
100833 TAATATACTG
100843 ATTTATATGCATTTATCATTTACTTTTTTT
1 ATTTATATGCATTTATCA-TTA-TTTTTTT
*
100873 ATTTATATGCTTTTATCA-T-TTTTTTT
1 ATTTATATGCATTTATCATTATTTTTTT
100899 ATTTTATAT
1 A-TTTATAT
100908 TGTAATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 8 0.24
27 7 0.21
28 1 0.03
30 17 0.52
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.66
Consensus pattern (28 bp):
ATTTATATGCATTTATCATTATTTTTTT
Found at i:102336 original size:31 final size:32
Alignment explanation
Indices: 102301--102361 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
102291 GAAAAATTCA
* *
102301 GGGACC-ATTTTGAAATTTTTAAAAAGTTGGG
1 GGGACCAATTTAGAAATTTTGAAAAAGTTGGG
* *
102332 GGGACCAATTTAGCAATTTTGGAAAAGTTG
1 GGGACCAATTTAGAAATTTTGAAAAAGTTG
102362 TGAATGGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (32 bp):
GGGACCAATTTAGAAATTTTGAAAAAGTTGGG
Found at i:103470 original size:30 final size:31
Alignment explanation
Indices: 103436--103495 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
103426 GAAAAATTTA
* * *
103436 GGGACC-ATTTTGTAATTTTTAAAAAGTTGG
1 GGGACCAATTTAGCAATTTTGAAAAAGTTGG
*
103466 GGGACCAATTTAGCAATTTTGGAAAAGTTG
1 GGGACCAATTTAGCAATTTTGAAAAAGTTG
103496 TGAATGGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (31 bp):
GGGACCAATTTAGCAATTTTGAAAAAGTTGG
Found at i:105494 original size:40 final size:40
Alignment explanation
Indices: 105445--105526 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
105435 TGTATGTTTA
*
105445 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATATG
105485 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATATG
105525 TA
1 TA
105527 GCACTACGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATATG
Found at i:105725 original size:45 final size:45
Alignment explanation
Indices: 105631--105806 Score: 282
Period size: 45 Copynumber: 3.9 Consensus size: 45
105621 GTAACCATGC
*
105631 AAATAAGCTTACGAGCTTATGGAAT-AATGACAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGACAAGTATATTGGTA
*
105675 AAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGACAAGTATATTGGTA
* **
105720 AAATAAGCTTACGAGCTTATGGGATAAATGATAAGTATATTAATA
1 AAATAAGCTTACGAGCTTATGGGATAAATGACAAGTATATTGGTA
**
105765 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTG
1 AAATAAGCTTACGAGCTTATGGGATAAATGACAAGTATATTG
105807 ATAAGAAATT
Statistics
Matches: 123, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
44 24 0.20
45 99 0.80
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGACAAGTATATTGGTA
Found at i:105748 original size:25 final size:25
Alignment explanation
Indices: 105675--105748 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
105665 TATATTGGTA
105675 AAATAAGCTTACGAGCTTATGGGAT
1 AAATAAGCTTACGAGCTTATGGGAT
* *
105700 AAAT-GGC--A--AG-TATATTGG-T
1 AAATAAGCTTACGAGCT-TATGGGAT
105719 AAAATAAGCTTACGAGCTTATGGGAT
1 -AAATAAGCTTACGAGCTTATGGGAT
105745 AAAT
1 AAAT
105749 GATAAGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 2 0.06
22 1 0.03
23 1 0.03
24 2 0.06
25 15 0.42
26 2 0.06
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.28
Consensus pattern (25 bp):
AAATAAGCTTACGAGCTTATGGGAT
Found at i:107923 original size:92 final size:90
Alignment explanation
Indices: 107719--108015 Score: 341
Period size: 91 Copynumber: 3.2 Consensus size: 90
107709 TGAACCATCA
* * *
107719 AAAATTTGTGAAGGGTCCACATGTTCCGTCACAAAATTTAGAGTTTTGTTTATTTA--TGCTCAT
1 AAAATTTGTG-AGGGTCCACATGTTTCGTCACAAAATTTAGAGTTTT-TTTAATTACCCGCTCAT
** * *
107782 TACCTCCAATTTACCTCCATTGAAACAT
64 TTTCTTCAATTTCCCT-CATTGAAACAT
*
107810 AAAATTTGTGGAGGGTACACATGTTTCGTCACAAAATTTAGAGTTTTTTTAATTACCCGCTCATT
1 AAAATTTGT-GAGGGTCCACATGTTTCGTCACAAAATTTAGAGTTTTTTTAATTACCCGCTCATT
107875 TTCTTCAATTTCCCTCTATTGAAACAT
65 TTCTTCAATTTCCCTC-ATTGAAACAT
* * * * * *
107902 GAAATTTGTGACGAGTCCACATG-TTCTTCACAAAATTTAGAGTTTTTTTAGTTACCCGTTTA-T
1 AAAATTTGTGA-GGGTCCACATGTTTCGTCACAAAATTTAGAGTTTTTTTAATTACCCGCTCATT
*
107965 TTCTTCCAATTTCTCTACATTGAAACAT
65 TTCTT-CAATTTCCCT-CATTGAAACAT
*
107993 AAAATTTGTGATGGGTTCACATG
1 AAAATTTGTGA-GGGTCCACATG
108016 CACAAAATTT
Statistics
Matches: 179, Mismatches: 20, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
90 13 0.07
91 119 0.66
92 47 0.26
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (90 bp):
AAAATTTGTGAGGGTCCACATGTTTCGTCACAAAATTTAGAGTTTTTTTAATTACCCGCTCATTT
TCTTCAATTTCCCTCATTGAAACAT
Found at i:109024 original size:33 final size:33
Alignment explanation
Indices: 108987--109064 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
108977 TATTTAGTTA
108987 AATAAAAATTTAGATTCATAATATTTTGGAGGG
1 AATAAAAATTTAGATTCATAATATTTTGGAGGG
*
109020 AATAAAAATTTGGATTCATAATATTTTGGAGGG
1 AATAAAAATTTAGATTCATAATATTTTGGAGGG
**
109053 AATGGAAATTTA
1 AATAAAAATTTA
109065 AATTTCTGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (33 bp):
AATAAAAATTTAGATTCATAATATTTTGGAGGG
Found at i:116520 original size:26 final size:26
Alignment explanation
Indices: 116484--116537 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
116474 GCTAAGTGGA
**
116484 TATGGTGGGCATGACCTTATGTGTAT
1 TATGGTGGGCACAACCTTATGTGTAT
116510 TATGGTGGGCACAACCTTATGTGTAT
1 TATGGTGGGCACAACCTTATGTGTAT
116536 TA
1 TA
116538 GAACTTCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (26 bp):
TATGGTGGGCACAACCTTATGTGTAT
Found at i:122760 original size:22 final size:22
Alignment explanation
Indices: 122720--122762 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
122710 ACTGATCGTT
* **
122720 ATATATGATGTTTTTCATGAAC
1 ATATATGATATTTAACATGAAC
122742 ATATATGATATTTAACATGAA
1 ATATATGATATTTAACATGAA
122763 TGATATTTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
ATATATGATATTTAACATGAAC
Found at i:123010 original size:26 final size:26
Alignment explanation
Indices: 122974--123027 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
122964 ACTAAGTGCA
*
122974 TATGGTGGGCACTACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
*
123000 TATGGTGGGCACGATCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
123026 TA
1 TA
123028 GCACTTCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTATGTGTAT
Found at i:132843 original size:21 final size:22
Alignment explanation
Indices: 132817--132860 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
132807 GTGAACAGTG
*
132817 AGGGTATCGGTA-CACTGTAGC
1 AGGGTATCCGTACCACTGTAGC
*
132838 AGGGTATCCGTACCCCTGTAGC
1 AGGGTATCCGTACCACTGTAGC
132860 A
1 A
132861 TTCTGGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (22 bp):
AGGGTATCCGTACCACTGTAGC
Found at i:133342 original size:45 final size:45
Alignment explanation
Indices: 133287--133482 Score: 315
Period size: 45 Copynumber: 4.4 Consensus size: 45
133277 TTATCCTTTG
* *
133287 AGCTCATAAGCTTATTTTATCAATATACTTACCATTTATTCCATA
1 AGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATA
133332 AGCTCGTAAGCTTATTTTACCAATATACTTACC-TCTTATTCCATA
1 AGCTCGTAAGCTTATTTTACCAATATACTTACCAT-TTATTCCATA
*
133377 AGCTCATAAGCTTATTTTACCAATATACTTACCATTTATTCCATA
1 AGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATA
* *
133422 AGCTCGTAAGCTTATTTTACAAATATACTTGCCA-TTATTCCATA
1 AGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATA
*
133466 AGCTTGTAAGCTTATTT
1 AGCTCGTAAGCTTATTT
133483 GCATGCATAC
Statistics
Matches: 142, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
44 27 0.19
45 114 0.80
46 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
AGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATA
Found at i:136521 original size:2 final size:2
Alignment explanation
Indices: 136516--136553 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
136506 AACAAGTGAA
136516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
136554 TTAATCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:136607 original size:17 final size:18
Alignment explanation
Indices: 136587--136631 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
136577 TCTCTTTCCC
136587 TTTCTCT-TTTCT-TTTCT
1 TTTCTCTGTTTCTATTT-T
136604 TTTCT-TGTTTCTATTTT
1 TTTCTCTGTTTCTATTTT
*
136621 TTTCTCCGTTT
1 TTTCTCTGTTT
136632 TTGTTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 16 0.67
18 7 0.29
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTCTCTGTTTCTATTTT
Found at i:136635 original size:24 final size:23
Alignment explanation
Indices: 136608--136672 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
136598 TTTTCTTTTC
136608 TTGTTTCTATTTTTTTCTCCGTTT
1 TTGTTTCTATTTTTTTCTCC-TTT
* *
136632 TTGTTTTCT-TTTTATTCTTTCTTT
1 TTG-TTTCTATTTTTTTC-TCCTTT
*
136656 TT-TTTCCATTTTTTTCT
1 TTGTTTCTATTTTTTTCT
136673 ATTATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 5 0.15
23 7 0.21
24 15 0.44
25 7 0.21
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (23 bp):
TTGTTTCTATTTTTTTCTCCTTT
Found at i:139001 original size:21 final size:22
Alignment explanation
Indices: 138968--139010 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
138958 GTGAACAGTG
*
138968 AGGGTATCGGTACAC-TGTAGC
1 AGGGTATCAGTACACTTGTAGC
* *
138989 AGGGTGTCAGTACCCTTGTAGC
1 AGGGTATCAGTACACTTGTAGC
139011 CTGGAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (22 bp):
AGGGTATCAGTACACTTGTAGC
Found at i:139518 original size:45 final size:45
Alignment explanation
Indices: 139449--139662 Score: 315
Period size: 45 Copynumber: 4.8 Consensus size: 45
139439 TATAAAACTT
* * *
139449 CTTATCATTTA-TCCTATGAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
*
139494 CTTACCATTTATTCCATAAGCTCGTAAACTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
139539 CTTACCTTTTATTCCATAAGCTCATACGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
139584 CTTACCATTTATTCCACAAGCTTGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
139629 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
139663 GCTTGCTTAC
Statistics
Matches: 152, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
44 25 0.16
45 124 0.82
46 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:140505 original size:23 final size:23
Alignment explanation
Indices: 140478--140530 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
140468 GATAAGACCA
140478 ATTCACCCTTAATGAATCTTCCT
1 ATTCACCCTTAATGAATCTTCCT
140501 ATTCACCCTTAATGAATCTTCCT
1 ATTCACCCTTAATGAATCTTCCT
140524 ATTCACC
1 ATTCACC
140531 ATAAAACCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.32, G:0.04, T:0.38
Consensus pattern (23 bp):
ATTCACCCTTAATGAATCTTCCT
Found at i:146461 original size:431 final size:431
Alignment explanation
Indices: 145613--146464 Score: 1449
Period size: 430 Copynumber: 2.0 Consensus size: 431
145603 GAGAAAGCAG
*
145613 TCATGGGCATTGAGGGTAGTAATAGAGCCAGGAATGGAGAACTAAGAATAGGTTGATTCTCATCA
1 TCATGGGCATTGAGGGTAGTAATAGAGCCAGGAATGGAGAACCAAGAATAGGTTGATTCTCATCA
* * *
145678 TCCCATCCAATGTTTTCTAGACCTAGATGGTTGGTAATTATTTTGGTGTCTAGCATAAAGGTCTT
66 TCCCAACCAATATTTTCTAGACCTAGATGGTTGGTAATTATTTCGGTGTCTAGCATAAAGGTCTT
*
145743 TCCCATAAGATAAGACTCTATAACAATAACAATGTTAATAGGTTCATCAACAATAGAATGAGTGT
131 TCCCATAAGATAAGACTCTATAACAATAACAATGTTAATAGGTTCATCAACAATAGAACGAGTGT
145808 TGTAAAAAAATTCGAGTTAAAGTGGGAAAATATTGTGGCTTAAAAACTACTAACCCGTAATTTGT
196 TGTAAAAAAATTCGAGTTAAAGTGGGAAAATATTGTGGCTTAAAAACTACTAACCCGTAATTTGT
* * * *
145873 GGCATTATAGATACTATTTTAATGAGCGTACCGATACACATTATCAATCGTATCGGTATATGCTA
261 GGCATTATAGATACTATTTTAATGAGCGTACCGATACACATTATCAATCATATCGGTACAAGCGA
*
145938 GCTTGATACTTAAAAATACCCTCTTATACGATTTTGACCCAAATTTTATCAAACCTTAGCCCTAA
326 GCTTGATACTTAAAAATACACTCTTATACGATTTTGACCCAAATTTTATCAAACCTTAGCCCTAA
146003 GAACATAATTTTCTCTAAAAACCATCCATTTATCCATCCAT
391 GAACATAATTTTCTCTAAAAACCATCCATTTATCCATCCAT
*
146044 TCATGGGCATTGAGGGTAGTAATAGAGCCGAGG-GTGGAGAACCAAGAATAGGTTGATTCTCATC
1 TCATGGGCATTGAGGGTAGTAATAGAGCC-AGGAATGGAGAACCAAGAATAGGTTGATTCTCATC
146108 ATCCCAACCAATATTTTCTAGACCTAGATGGTTGGTAATTATTTCGGTGTCTAGCATAAAGGTCT
65 ATCCCAACCAATATTTTCTAGACCTAGATGGTTGGTAATTATTTCGGTGTCTAGCATAAAGGTCT
* *
146173 TTCCCATAAGATAAGACTCTATGACAATAACAATGTTAATATGTTCATCAACAATAGAACGAGTG
130 TTCCCATAAGATAAGACTCTATAACAATAACAATGTTAATAGGTTCATCAACAATAGAACGAGTG
* ** * *
146238 TTG-GAAAATTTTTGAGTTAAAGTGGGCAAATATTGTGGCTTAAAAACTACTAACCCGTAATTTG
195 TTGTAAAAAAATTCGAGTTAAAGTGGGAAAATATTGTGGCTTAAAAACTACTAACCCGTAATTTG
146302 TGGCATTATAGATACTATTTTAATGAGCGTACCGATACACATTATCAATCATATCGGTACAAGCG
260 TGGCATTATAGATACTATTTTAATGAGCGTACCGATACACATTATCAATCATATCGGTACAAGCG
* * * * *
146367 AGGTTGATACTTACAAATATATTCTTAT-CTGATTTTGACCCAAATTTTATCAAACCTTAGCCGT
325 AGCTTGATACTTAAAAATACACTCTTATAC-GATTTTGACCCAAATTTTATCAAACCTTAGCCCT
146431 AAGAACATAATTTTCTCTAAAAATCCATCCATTT
389 AAGAACATAATTTTCTCTAAAAA-CCATCCATTT
146465 TTCACTCTAT
Statistics
Matches: 395, Mismatches: 23, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
429 1 0.00
430 196 0.50
431 195 0.49
432 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (431 bp):
TCATGGGCATTGAGGGTAGTAATAGAGCCAGGAATGGAGAACCAAGAATAGGTTGATTCTCATCA
TCCCAACCAATATTTTCTAGACCTAGATGGTTGGTAATTATTTCGGTGTCTAGCATAAAGGTCTT
TCCCATAAGATAAGACTCTATAACAATAACAATGTTAATAGGTTCATCAACAATAGAACGAGTGT
TGTAAAAAAATTCGAGTTAAAGTGGGAAAATATTGTGGCTTAAAAACTACTAACCCGTAATTTGT
GGCATTATAGATACTATTTTAATGAGCGTACCGATACACATTATCAATCATATCGGTACAAGCGA
GCTTGATACTTAAAAATACACTCTTATACGATTTTGACCCAAATTTTATCAAACCTTAGCCCTAA
GAACATAATTTTCTCTAAAAACCATCCATTTATCCATCCAT
Found at i:147181 original size:19 final size:19
Alignment explanation
Indices: 147157--147195 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
147147 GTTTCTATAT
147157 ATTTCATTTC-ATCTTCTTC
1 ATTTCATTTCTAT-TTCTTC
147176 ATTTCATTTCTATTTCTTC
1 ATTTCATTTCTATTTCTTC
147195 A
1 A
147196 ATTTTCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.18, C:0.23, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTCATTTCTATTTCTTC
Found at i:152559 original size:20 final size:20
Alignment explanation
Indices: 152530--152572 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
152520 ATTCCATCAC
*
152530 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATACTCCTAA
* *
152550 ATGCATCTATATATTCCTAA
1 ATGCAACTATATACTCCTAA
152570 ATG
1 ATG
152573 GGCTTTTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATACTCCTAA
Found at i:153444 original size:13 final size:13
Alignment explanation
Indices: 153426--153452 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
153416 AATGTCATGG
153426 CATATTCATTATA
1 CATATTCATTATA
153439 CATATTCATTATA
1 CATATTCATTATA
153452 C
1 C
153453 TAATACTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (13 bp):
CATATTCATTATA
Found at i:162920 original size:20 final size:20
Alignment explanation
Indices: 162891--162933 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
162881 ATTCCACCAC
*
162891 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
162911 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
162931 ATG
1 ATG
162934 GGCTCTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:164156 original size:17 final size:16
Alignment explanation
Indices: 164130--164161 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
164120 TTAAAAAATT
164130 CTATTGTATCGATACA
1 CTATTGTATCGATACA
164146 CTATGTGTATCGATAC
1 CTAT-TGTATCGATAC
164162 TATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (16 bp):
CTATTGTATCGATACA
Found at i:169122 original size:2 final size:2
Alignment explanation
Indices: 169115--169166 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
169105 AATCTAAATA
*
169115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
169157 AT AT AT AT AT
1 AT AT AT AT AT
169167 TAAAGTGGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:169821 original size:60 final size:60
Alignment explanation
Indices: 169757--169872 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
169747 AATGCTCATT
* * * * * *
169757 CGACTATAGGGTGTCACTTTGTTAAATCCTTCGACTATTAAAATTTATAAAATGATTCCC
1 CGACTATAGGATATCACTTTGTTAAATCCCTCAACTATTAAAAGTTACAAAATGATTCCC
** * *
169817 CGACTATAGGATATTTCTTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAATGAT
1 CGACTATAGGATATCACTTTGTTAAATCCCTCAACTATTAAAAGTTACAAAATGAT
169873 CACTCGAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (60 bp):
CGACTATAGGATATCACTTTGTTAAATCCCTCAACTATTAAAAGTTACAAAATGATTCCC
Found at i:175751 original size:28 final size:28
Alignment explanation
Indices: 175698--175756 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
175688 GCTTTTTTGG
175698 TTAAATGACACTAACAATTTCTTTTGTT
1 TTAAATGACACTAACAATTTCTTTTGTT
175726 TTAAATGACACTAACAATTTCTTTTGTT
1 TTAAATGACACTAACAATTTCTTTTGTT
175754 TTA
1 TTA
175757 TCTTATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (28 bp):
TTAAATGACACTAACAATTTCTTTTGTT
Found at i:177521 original size:23 final size:23
Alignment explanation
Indices: 177502--177607 Score: 104
Period size: 23 Copynumber: 4.6 Consensus size: 23
177492 TAATTGTTCT
*
177502 GAAGGACCATATAGGTTTGTCCC
1 GAAGGACCACATAGGTTTGTCCC
* *
177525 GAAGGACCACATCGGTTTGTCAC
1 GAAGGACCACATAGGTTTGTCCC
* * *
177548 AAAGGACCACATCGGTTTGTTCC
1 GAAGGACCACATAGGTTTGTCCC
* * **
177571 GATGAACCACATAAATTTGTCCC
1 GAAGGACCACATAGGTTTGTCCC
* *
177594 GGATGACCACATAG
1 GAAGGACCACATAG
177608 AACCCTCGAC
Statistics
Matches: 65, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (23 bp):
GAAGGACCACATAGGTTTGTCCC
Found at i:183260 original size:13 final size:14
Alignment explanation
Indices: 183232--183264 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
183222 ATAACTTTGA
*
183232 AATTTAGTCATTTT
1 AATTTTGTCATTTT
183246 AATTTTGTC-TTTT
1 AATTTTGTCATTTT
183259 AATTTT
1 AATTTT
183265 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (14 bp):
AATTTTGTCATTTT
Found at i:183494 original size:22 final size:21
Alignment explanation
Indices: 183430--183504 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 21
183420 ATTATGGTTG
* *
183430 TTAATT-TTAATATTTTCTATT
1 TTAATTATTAATA-TTTATATA
*
183451 TTAATCATTAATTATTACTATATGA
1 TTAATTATTAA-TATT--TATAT-A
*
183476 TTAATTATTAATATTTATATC
1 TTAATTATTAATATTTATATA
183497 TTATATTA
1 TTA-ATTA
183505 GGATTATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
21 8 0.19
22 15 0.35
23 2 0.05
24 8 0.19
25 10 0.23
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.57
Consensus pattern (21 bp):
TTAATTATTAATATTTATATA
Found at i:196255 original size:13 final size:14
Alignment explanation
Indices: 196227--196259 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
196217 ATAACTTTGC
*
196227 AATTTAGTCATTTT
1 AATTTTGTCATTTT
196241 AATTTTGTC-TTTT
1 AATTTTGTCATTTT
196254 AATTTT
1 AATTTT
196260 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (14 bp):
AATTTTGTCATTTT
Found at i:196550 original size:22 final size:22
Alignment explanation
Indices: 196504--196558 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
196494 ATTAGGATTA
*
196504 TTAATTTATATAATTTGATAAT
1 TTAATTTATATAATTTAATAAT
*
196526 TTAATTTATATAATTCTAAT-GT
1 TTAATTTATATAATT-TAATAAT
196548 TTAATATTATA
1 TTAAT-TTATA
196559 ATAGGATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
TTAATTTATATAATTTAATAAT
Found at i:198099 original size:21 final size:22
Alignment explanation
Indices: 198075--198127 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
198065 CACCGAAGTG
*
198075 CCACATA-ATTGTCTCGAATAA
1 CCACATAGATTGTCCCGAATAA
* *
198096 CCACATAGGTTTGTCCCGAATGA
1 CCACATA-GATTGTCCCGAATAA
198119 CCACATAGA
1 CCACATAGA
198128 ACCCTCAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.27
22 1 0.04
23 18 0.69
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (22 bp):
CCACATAGATTGTCCCGAATAA
Found at i:198115 original size:23 final size:23
Alignment explanation
Indices: 198083--198126 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
198073 TGCCACATAA
*
198083 TTGTCTCGAATAACCACATAGGT
1 TTGTCCCGAATAACCACATAGGT
*
198106 TTGTCCCGAATGACCACATAG
1 TTGTCCCGAATAACCACATAG
198127 AACCCTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (23 bp):
TTGTCCCGAATAACCACATAGGT
Found at i:203360 original size:11 final size:10
Alignment explanation
Indices: 203299--203373 Score: 60
Period size: 11 Copynumber: 6.8 Consensus size: 10
203289 AGATAAAGAG
203299 AAAGAAAAAA
1 AAAGAAAAAA
203309 AGAAGAGAGAAAA
1 A-AAGA-A-AAAA
* *
203322 CAACAAAAAGA
1 AAAGAAAAA-A
203333 AAAGAAAAATA
1 AAAGAAAAA-A
*
203344 AGAGAAAATAA
1 AAAGAAAA-AA
203355 AAAGAAAAAA
1 AAAGAAAAAA
203365 AAAGGAAAA
1 AAA-GAAAA
203374 GGAAAAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
10 9 0.17
11 34 0.65
12 5 0.10
13 4 0.08
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:205895 original size:257 final size:257
Alignment explanation
Indices: 205376--206170 Score: 1067
Period size: 257 Copynumber: 3.1 Consensus size: 257
205366 AGTTGTTTTG
* * * *
205376 AAAAATGAG-AAAGCAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTTGAAA
1 AAAAATGAGAAAAACAATTTTCAAAGTTTCTCATTTAATATTTTTAGAAAATGAAATATTTGAAA
* * *
205440 AGT-AGAAAGTGATTTCCAAAGTTTATTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCTTCG
66 AGTAAGAAAATGATTTCCAAAGTTTCTTACCCAG-AAACTATTTCCAAAATCGGTAAGTCCTTCG
* * ** *
205504 AGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTATGTTCA-AT-T--G---TTCGAGC
130 GGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATATGTCAGTCTTTCGAGC
* * * *
205562 AACATGTTAAGTCCTTCGGGCCATCTATAGGACCTTCAGGCAGGATGTTTTCACATGATTTTCG
195 AAGATGTTAAGTCCTTC-GGCCATCTATAAGACCTTCAGGCATGATGTTTTCACATGATTTTCT
** *
205626 AAAAGGGAGAAAAATAATTTTCAAAGTTTCTCATTTAATATTTTTAGAAAATGAAATATTTGAAA
1 AAAAATGAGAAAAACAATTTTCAAAGTTTCTCATTTAATATTTTTAGAAAATGAAATATTTGAAA
* * * *
205691 AGTAAGAAAACGATTTCTAAAGTTTCTTACCCAG-CACTATTTCCAAAATCGGTAAGTCATTCGG
66 AGTAAGAAAATGATTTCCAAAGTTTCTTACCCAGAAACTATTTCCAAAATCGGTAAGTCCTTCGG
* ** *
205755 GCCATCAGTAAGCCTTTCAAGCATGATGATTAAATCCTTCGGGTCATATGTCAGTCTTTCGACCA
131 GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATATGTCAGTCTTTCGAGCA
* * *
205820 AGATGTTAAGTCCTTCGAGCTATCTATAAGAACTTCAGGCATAATGTTTTCACATGATTTTCT
196 AGATGTTAAGTCCTTCG-GCCATCTATAAGACCTTCAGGCATGATGTTTTCACATGATTTTCT
* * * *
205883 AAAAATGAGAAAAGA-ATTTTTCAAAGTTTCTCATTTAATATTTTTAGAAAATAAAATCTTCGAA
1 AAAAATGAGAAAA-ACAATTTTCAAAGTTTCTCATTTAATATTTTTAGAAAATGAAATATTTGAA
* * * *
205947 AAGTAA-AAAATAATTTCCAAAGTTTCTTACTCAGTAAACTATTCCCAAAATCAGTAAGTCCTTC
65 AAGTAAGAAAATGATTTCCAAAGTTTCTTACCCAG-AAACTATTTCCAAAATCGGTAAGTCCTTC
* *
206011 GGGTCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATTTGTCAGTCTTTCGAG
129 GGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATATGTCAGTCTTTCGAG
*
206076 CAAGATGTTAAGTCCTTCGGCCATCTATAAGACCTTCGGGCATGATGTTTTCACATGATTTT-T
194 CAAGATGTTAAGTCCTTCGGCCATCTATAAGACCTTCAGGCATGATGTTTTCACATGATTTTCT
*
206139 GAAAAATGAGAAAAACAATTTTTAAAGTTTCT
1 -AAAAATGAGAAAAACAATTTTCAAAGTTTCT
206171 TACTTAGTAA
Statistics
Matches: 474, Mismatches: 56, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
250 72 0.15
251 55 0.12
252 27 0.06
254 1 0.00
256 27 0.06
257 189 0.40
258 103 0.22
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (257 bp):
AAAAATGAGAAAAACAATTTTCAAAGTTTCTCATTTAATATTTTTAGAAAATGAAATATTTGAAA
AGTAAGAAAATGATTTCCAAAGTTTCTTACCCAGAAACTATTTCCAAAATCGGTAAGTCCTTCGG
GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATATGTCAGTCTTTCGAGCA
AGATGTTAAGTCCTTCGGCCATCTATAAGACCTTCAGGCATGATGTTTTCACATGATTTTCT
Found at i:206053 original size:42 final size:41
Alignment explanation
Indices: 206005--206095 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 41
205995 AATCAGTAAG
* *
206005 TCCTTCGGGTCATCAGTAAGTCTTTTGAGCATGATGATTAAA
1 TCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATG-TTAAA
** * *
206047 TCCTTCGGGTCATTTGTCAGTCTTTCGAGCAAGATGTTAAG
1 TCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGTTAAA
206088 TCCTTCGG
1 TCCTTCGG
206096 CCATCTATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 12 0.28
42 31 0.72
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
TCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGTTAAA
Found at i:221765 original size:53 final size:54
Alignment explanation
Indices: 221642--221769 Score: 168
Period size: 53 Copynumber: 2.4 Consensus size: 54
221632 GATGGATTTG
* *
221642 GCACCTCTGTGCTGCAATCGAGAAACTGGCACCTCTGTACTTAAAAATTATTGA
1 GCACCTCTGTGCTGCAATCGAGAAACTGGCACCTCTATACTTAAAAATTACTGA
* * * * * *
221696 GTACCTCTATGTTGCAATCGATAAACTGGCA-CTTTATGCTTAAAAATTACTGA
1 GCACCTCTGTGCTGCAATCGAGAAACTGGCACCTCTATACTTAAAAATTACTGA
*
221749 GCACCTATGTGCTGCAATCGA
1 GCACCTCTGTGCTGCAATCGA
221770 ATATTTGACA
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 35 0.56
54 27 0.44
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (54 bp):
GCACCTCTGTGCTGCAATCGAGAAACTGGCACCTCTATACTTAAAAATTACTGA
Found at i:227322 original size:19 final size:20
Alignment explanation
Indices: 227298--227338 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
227288 GCACATGACA
*
227298 ACCTCC-TTGCTTGCATATG
1 ACCTCCTTTGATTGCATATG
*
227317 ACCTCCTTTGATTGCTTATG
1 ACCTCCTTTGATTGCATATG
227337 AC
1 AC
227339 TTCCCACGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.17, C:0.29, G:0.15, T:0.39
Consensus pattern (20 bp):
ACCTCCTTTGATTGCATATG
Found at i:235045 original size:19 final size:19
Alignment explanation
Indices: 235023--235065 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
235013 TTATCAATCT
*
235023 TTATATATTTTAAA-AATTA
1 TTAT-TATTATAAATAATTA
235042 TTATTATTATAAATAATTA
1 TTATTATTATAAATAATTA
235061 TTATT
1 TTATT
235066 CATCTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTATTATAAATAATTA
Found at i:235055 original size:16 final size:16
Alignment explanation
Indices: 235023--235065 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
235013 TTATCAATCT
235023 TTATATATT-TTAAAAA
1 TTAT-TATTATTAAAAA
*
235039 TTATTATTATTATAAA
1 TTATTATTATTAAAAA
*
235055 TAATTATTATT
1 TTATTATTATT
235066 CATCTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTATTATTAAAAA
Found at i:235561 original size:13 final size:13
Alignment explanation
Indices: 235543--235567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
235533 CAAAATGCCT
235543 AATATTTTTTTAA
1 AATATTTTTTTAA
235556 AATATTTTTTTA
1 AATATTTTTTTA
235568 TTTAAATCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATATTTTTTTAA
Found at i:249825 original size:40 final size:39
Alignment explanation
Indices: 249765--249840 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
249755 TGAATTTAAT
* *
249765 ATTAATAAAATATTTTAATATCATTTTAATCAAAATATTG
1 ATTAATAAAATATTTAAATATCATTATAAT-AAAATATTG
* *
249805 ATTATTAAAATATTTAAATATTATTATAATAAAATA
1 ATTAATAAAATATTTAAATATCATTATAATAAAATA
249841 ATCAATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 6 0.19
40 26 0.81
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (39 bp):
ATTAATAAAATATTTAAATATCATTATAATAAAATATTG
Found at i:249849 original size:40 final size:40
Alignment explanation
Indices: 249765--249849 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
249755 TGAATTTAAT
* * * **
249765 ATTAATAAAATATTTTAATATCATTTTAATCAAAATATTG
1 ATTATTAAAATATTTAAATATCATTATAATCAAAATATCA
*
249805 ATTATTAAAATATTTAAATATTATTATAAT-AAAATAATCA
1 ATTATTAAAATATTTAAATATCATTATAATCAAAAT-ATCA
249845 ATTAT
1 ATTAT
249850 ATTATAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 5 0.13
40 33 0.87
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (40 bp):
ATTATTAAAATATTTAAATATCATTATAATCAAAATATCA
Found at i:250033 original size:23 final size:23
Alignment explanation
Indices: 250007--250051 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
249997 AATAGTATTT
250007 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
250030 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
250052 ATATAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:250157 original size:89 final size:86
Alignment explanation
Indices: 250020--250186 Score: 205
Period size: 89 Copynumber: 1.9 Consensus size: 86
250010 TAAAGATATT
* * * *
250020 TAAAATATACTAATTAATATTTTTAAAATATAATATAACAATATTACTTTAATAAATAATTAATA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAACAATAATACTTTAAT-AATAAATAA-A
250085 TAATTTATAATATTTTTATTTCAA
64 TAATTT-TAATATTTTTATTTCAA
*
250109 TAAAATATACCAATATTAATATTTTT-TAATAAAATTATAA-AA-AATACTTTAATAATAAATAA
1 TAAAATATA-CAA-ATTAATATTTTTAAAATAAAA-TATAACAATAATACTTTAATAATAAATAA
*
250171 ATTATTTTAATATTTT
63 ATAATTTTAATATTTT
250187 AAAAATAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
86 9 0.13
87 6 0.09
88 8 0.12
89 19 0.28
90 10 0.14
91 17 0.25
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAACAATAATACTTTAATAATAAATAAATA
ATTTTAATATTTTTATTTCAA
Found at i:252756 original size:20 final size:20
Alignment explanation
Indices: 252731--252865 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
252721 AATTGGGAAA
252731 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
252751 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
252771 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
252792 ATTGCAATGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
252812 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
252832 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
252852 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
252866 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:252775 original size:61 final size:61
Alignment explanation
Indices: 252728--252861 Score: 187
Period size: 61 Copynumber: 2.2 Consensus size: 61
252718 GCAAATTGGG
* * * *
252728 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
252789 AAAATTGCAATGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
252850 ATAATCGCAATG
1 AAAATCGCAATG
252862 CGATTTTCAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:253061 original size:22 final size:22
Alignment explanation
Indices: 253033--253076 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
253023 CACTCTCTCA
253033 CCCATCTCCGACAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
* *
253055 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
253077 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:253391 original size:20 final size:20
Alignment explanation
Indices: 253337--253385 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
253327 GCGATTCTCT
**
253337 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
253357 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
253377 TGTTGCGAT
1 CGTTGCGAT
253386 TTTCATATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:253586 original size:25 final size:24
Alignment explanation
Indices: 253532--253586 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
253522 TGTTTATTAT
* *
253532 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
253556 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
253582 TGTTT
1 TGTTT
253587 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:254716 original size:18 final size:18
Alignment explanation
Indices: 254690--254724 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
254680 CTTCGGGAGC
* *
254690 TATCCCCTCGCCCAGAGT
1 TATCACCTCACCCAGAGT
254708 TATCACCTCACCCAGAG
1 TATCACCTCACCCAGAG
254725 CCATCATCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.43, G:0.14, T:0.20
Consensus pattern (18 bp):
TATCACCTCACCCAGAGT
Found at i:255266 original size:19 final size:20
Alignment explanation
Indices: 255212--255278 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
255202 TAGTTTACTT
* *
255212 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
255232 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
255252 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
255271 TCGCAACG
1 TCGCAACG
255279 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:255286 original size:14 final size:14
Alignment explanation
Indices: 255267--255324 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
255257 ATGCGAAATG
255267 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
255281 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
255297 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
255313 AAAATCGCAACG
1 AAAATCGCAACG
255325 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:255309 original size:32 final size:33
Alignment explanation
Indices: 255251--255341 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
255241 GGAAATGGCT
255251 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
255284 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
255316 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
255342 TTTTCGCATT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:255367 original size:14 final size:14
Alignment explanation
Indices: 255350--255406 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
255340 AATTTTCGCA
255350 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
255364 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
*
255381 CATTGCGATTTTGTCA
1 --TTGCGATTTTGTCG
255397 TTGCGATTTT
1 TTGCGATTTT
255407 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
15 3 0.09
16 3 0.09
17 4 0.11
18 3 0.09
19 6 0.17
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:255385 original size:33 final size:33
Alignment explanation
Indices: 255343--255422 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
255333 AAATCGCAAT
*
255343 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
255376 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
255409 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
255423 AGCCATTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
Found at i:255388 original size:19 final size:19
Alignment explanation
Indices: 255364--255465 Score: 79
Period size: 20 Copynumber: 5.5 Consensus size: 19
255354 GATTTTGTCG
255364 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
255383 TTGCGA-TTT--TGT--CA
1 TTGCGATTTTCATTTCGCA
255397 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** *
255416 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
** *
255436 TTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
255456 TTGCGATTTT
1 TTGCGATTTT
255466 AAGTTTCGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
14 8 0.12
15 3 0.04
16 2 0.03
17 2 0.03
18 3 0.04
19 20 0.30
20 26 0.39
21 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:255924 original size:41 final size:41
Alignment explanation
Indices: 255828--255915 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
255818 GACTCACCTG
* * *
255828 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
* *
255870 TCCTCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
255911 TCATC
1 TCATC
255916 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:257351 original size:14 final size:14
Alignment explanation
Indices: 257332--257367 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
257322 ATTGTTTAAT
257332 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
257346 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
257360 TGATTTGT
1 TGATTTGT
257368 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:257526 original size:19 final size:19
Alignment explanation
Indices: 257504--257552 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
257494 ATCGCAACGA
257504 GAAAATCGCAATGCAAAAT
1 GAAAATCGCAATGCAAAAT
*
257523 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCAAAAT
*
257542 GAAAATTGCAA
1 GAAAATCGCAA
257553 CGAGAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCAAAAT
Found at i:257559 original size:19 final size:19
Alignment explanation
Indices: 257504--257559 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
257494 ATCGCAACGA
*
257504 GAAAATCGCAATGCA-AAAT
1 GAAAATCGCAACG-AGAAAT
* *
257523 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
*
257542 GAAAATTGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
257560 ATCGCAATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.52, C:0.14, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:257683 original size:20 final size:20
Alignment explanation
Indices: 257598--257685 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 20
257588 CAATTTTCTA
* *
257598 GTTGCAATAGCCATTTTCGC
1 GTTGCGATAGACATTTTCGC
*** *
257618 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGACATTTTCGC
*
257638 ATTGCGATAGACATTTTCGC
1 GTTGCGATAGACATTTTCGC
* *
257658 GTTGCGATAGCCATTTTTGC
1 GTTGCGATAGACATTTTCGC
257678 GTTGCGAT
1 GTTGCGAT
257686 TTCCCCGTTG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
19 3 0.06
20 47 0.89
21 3 0.06
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGACATTTTCGC
Found at i:257924 original size:20 final size:20
Alignment explanation
Indices: 257899--257948 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
257889 TTGAAGATGA
257899 TTGCGATTTTCACAATCTCG
1 TTGCGATTTTCACAATCTCG
*** *
257919 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCACAATCTCG
257939 TTGCGATTTT
1 TTGCGATTTT
257949 GTATTATCTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCACAATCTCG
Found at i:258817 original size:24 final size:24
Alignment explanation
Indices: 258790--258843 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
258780 GTATTCGAAA
*
258790 TTTGATCTTGGTCAATA-TCCGGAC
1 TTTGATATTGGTCAATACT-CGGAC
*
258814 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCGGAC
258838 TTTGAT
1 TTTGAT
258844 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Found at i:259033 original size:12 final size:12
Alignment explanation
Indices: 259016--259040 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
259006 ATATAATCCT
259016 GAAGAAGAAAAA
1 GAAGAAGAAAAA
259028 GAAGAAGAAAAA
1 GAAGAAGAAAAA
259040 G
1 G
259041 TCCCCAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:261325 original size:39 final size:36
Alignment explanation
Indices: 261282--261429 Score: 136
Period size: 33 Copynumber: 4.3 Consensus size: 36
261272 CTTAATGTCT
*
261282 ATCGCAACGCGGAAATTACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAA-GA--ATCGCAATGCGAAATGAAA
*
261321 ATCGCAA--C-GAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
* ** *
261354 ATCGCAACGC--TAA-TTTTGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
*
261387 ATCGCAACGAGG---GAATCGCAATGC-AAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
261419 ATCGCAACGCG
1 ATCGCAACGCG
261430 AATTTAATTT
Statistics
Matches: 92, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
32 18 0.20
33 60 0.65
34 1 0.01
35 2 0.02
36 3 0.03
37 1 0.01
39 7 0.08
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.16
Consensus pattern (36 bp):
ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
Found at i:261344 original size:33 final size:33
Alignment explanation
Indices: 261302--261427 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
261292 GGAAATTACT
261302 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
261335 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
261367 TTTTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
261401 ATCGCAATGC-AAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
261428 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
32 18 0.22
33 63 0.77
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:261459 original size:14 final size:14
Alignment explanation
Indices: 261442--261498 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
261432 TTTAATTTCG
261442 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
261456 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
261475 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
261489 CGTTGCGATT
1 CGTTGCGATT
261499 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:261478 original size:33 final size:33
Alignment explanation
Indices: 261427--261516 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
261417 AAATCGCAAC
* *
261427 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
261460 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
261493 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
261517 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:261480 original size:19 final size:19
Alignment explanation
Indices: 261456--261516 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
261446 GCGATTCTCT
261456 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
261475 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
261489 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
261508 CATTGCGAT
1 CGTTGCGAT
261517 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:261639 original size:13 final size:14
Alignment explanation
Indices: 261623--261657 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
261613 CATCAATTAA
261623 ACAAATCA-CTTTT
1 ACAAATCACCTTTT
261636 ACAAATCACCTTTT
1 ACAAATCACCTTTT
261650 ACAAATCA
1 ACAAATCA
261658 ATTAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCACCTTTT
Found at i:263119 original size:42 final size:42
Alignment explanation
Indices: 263052--263131 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
263042 CGATGACAGT
* * *
263052 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
263094 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
263132 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:263533 original size:91 final size:90
Alignment explanation
Indices: 263354--263538 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
263344 ATTTCAAACT
*
263354 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
263419 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGAAGCAACCGAATAAATTTAC
263447 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
263511 GTATTGGAAGTAACCGAATAAATTTAC
64 GAATTGGAAGCAACCGAATAAATTTAC
263538 T
1 T
263539 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGAAGCAACCGAATAAATTTAC
Found at i:265303 original size:33 final size:33
Alignment explanation
Indices: 265246--265413 Score: 201
Period size: 33 Copynumber: 4.9 Consensus size: 33
265236 ACGAGATAAT
265246 GAGAATCGCAACGCGGAAATGACTATCGCAACAA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACAA
* *
265280 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACAA
* *
265313 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACAA
**
265346 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA--C--AA
* **
265383 TGAAAATCGCAACGCGAAATGAAAATCGCAA
1 -GAGAATCGCAACGCGAAATGACTATCGCAA
265414 TGCGATTTTG
Statistics
Matches: 122, Mismatches: 7, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
33 77 0.63
34 14 0.11
35 1 0.01
37 1 0.01
38 29 0.24
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACAA
Found at i:265339 original size:19 final size:18
Alignment explanation
Indices: 265221--265418 Score: 125
Period size: 19 Copynumber: 11.1 Consensus size: 18
265211 TCTTTTGGTT
*
265221 GAAATGAAAATCGCAACGA
1 GAAATG-AAATCGCAACGC
265240 GATAATGAGAATCGCAACGC
1 GA-AATGA-AATCGCAACGC
*
265260 GGAAATGACTATCGCAA--C
1 -GAAATGA-AATCGCAACGC
265278 --AA-GAGAATCGCAACGC
1 GAAATGA-AATCGCAACGC
* *
265294 GAAATGACTATCGCGA--C
1 GAAATGA-AATCGCAACGC
*
265311 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
* *
265327 GAAATGACTATCGCGA--C
1 GAAATGA-AATCGCAACGC
*
265344 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
265360 GAAATGAAAATCGCAACGC
1 GAAATG-AAATCGCAACGC
265379 GAAATGAAAATCGCAACGC
1 GAAATG-AAATCGCAACGC
*
265398 GAAATGAAAATCGCAATGC
1 GAAATG-AAATCGCAACGC
265417 GA
1 GA
265419 TTTTGGTTTC
Statistics
Matches: 142, Mismatches: 19, Indels: 36
0.72 0.10 0.18
Matches are distributed among these distances:
14 21 0.15
15 2 0.01
16 11 0.08
17 10 0.07
18 3 0.02
19 67 0.47
20 26 0.18
21 2 0.01
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.12
Consensus pattern (18 bp):
GAAATGAAATCGCAACGC
Found at i:265447 original size:19 final size:19
Alignment explanation
Indices: 265414--265480 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
265404 AAAATCGCAA
**
265414 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
265433 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
265452 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
265472 TGCGATTTT
1 TGCGATTTT
265481 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:266061 original size:20 final size:20
Alignment explanation
Indices: 266036--266089 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
266026 GATTTTGTAT
266036 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
266056 TATCGCATTGCGATAGTTAG
1 TATCGCATTGCGATAGTAAG
266076 TATCGCATTGCGAT
1 TATCGCATTGCGAT
266090 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:270696 original size:14 final size:14
Alignment explanation
Indices: 270677--270709 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
270667 TGTTGTAATT
270677 GATAATAATGACAA
1 GATAATAATGACAA
270691 GATAATAATGACAA
1 GATAATAATGACAA
270705 GATAA
1 GATAA
270710 GCATGTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.15, T:0.21
Consensus pattern (14 bp):
GATAATAATGACAA
Found at i:271891 original size:44 final size:45
Alignment explanation
Indices: 271675--271942 Score: 414
Period size: 46 Copynumber: 5.9 Consensus size: 45
271665 GATAAAATCT
*
271675 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
271720 CTTACCATTTAATACCATAAGCTCCTAAGCGTATTTTACCAATATA
1 CTTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
271766 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
271812 CTTACCATTTAATCCAATAAGCTCGTGAGCTTATTTTACCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
*
271858 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
271902 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAAT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAT
271943 TTATCATTTA
Statistics
Matches: 209, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
44 70 0.33
45 19 0.09
46 120 0.57
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:272097 original size:40 final size:40
Alignment explanation
Indices: 272023--272098 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
272013 AGTCAAATGT
* * *
272023 TGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCTAATAA
1 TGCACCGAAGTGCTGAGGTCGAGATTTACCCACCTAATAA
* *
272063 TGCACCGTAGTGCTGAGGTCGGGATTTACCCACCTA
1 TGCACCGAAGTGCTGAGGTCGAGATTTACCCACCTA
272099 GTACACCGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.25
Consensus pattern (40 bp):
TGCACCGAAGTGCTGAGGTCGAGATTTACCCACCTAATAA
Found at i:276634 original size:26 final size:26
Alignment explanation
Indices: 276597--276650 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
276587 ACTGAAGTGC
*
276597 TAATACACATAAGGTCGTGCCCACCA
1 TAATACAAATAAGGTCGTGCCCACCA
276623 TAATACAAATAAGGTCGTGCCCACCA
1 TAATACAAATAAGGTCGTGCCCACCA
276649 TA
1 TA
276651 TGCACGTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (26 bp):
TAATACAAATAAGGTCGTGCCCACCA
Found at i:279926 original size:19 final size:19
Alignment explanation
Indices: 279840--279948 Score: 87
Period size: 19 Copynumber: 5.7 Consensus size: 19
279830 ATATGCATTC
*
279840 AGCTATGAACTTGAAAGTA
1 AGCTATGAATTTGAAAGTA
* *
279859 GGCTAT-ACATTTGAAAATA
1 AGCTATGA-ATTTGAAAGTA
** *
279878 AGCTATGAATCCGAAATTA
1 AGCTATGAATTTGAAAGTA
*
279897 ACCTATGAATTTGAAAGTA
1 AGCTATGAATTTGAAAGTA
* * *
279916 AGTTATGAATTGGGAAGTA
1 AGCTATGAATTTGAAAGTA
*
279935 TG-TACTGAATTTGA
1 AGCTA-TGAATTTGA
279949 GAATGAATTC
Statistics
Matches: 69, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
18 3 0.04
19 65 0.94
20 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.31
Consensus pattern (19 bp):
AGCTATGAATTTGAAAGTA
Found at i:283480 original size:14 final size:15
Alignment explanation
Indices: 283461--283500 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
283451 TTTCTGTCTA
*
283461 TATGCAGAGATTT-T
1 TATGCAGGGATTTAT
283475 TATGCAGGGATTTAT
1 TATGCAGGGATTTAT
283490 T-TGCAGGGATT
1 TATGCAGGGATT
283501 AGTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.25, C:0.07, G:0.28, T:0.40
Consensus pattern (15 bp):
TATGCAGGGATTTAT
Done.