Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008097.1 Hibiscus syriacus cultivar Beakdansim tig00110621_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: 3094402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 6 of 12
Found at i:1379980 original size:14 final size:14
Alignment explanation
Indices: 1379961--1380013 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
1379951 CGTTCGTGAA
1379961 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1379975 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1379989 CG-T---TTATGTT
1 CGTTCGGTTATGTT
1379999 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1380013 C
1 C
1380014 ATTTATGTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.08, C:0.15, G:0.26, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1380007 original size:24 final size:24
Alignment explanation
Indices: 1379962--1380021 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
1379952 GTTCGTGAAC
*
1379962 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
1379986 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
*
1380010 GTTCATTTATGT
1 GTTCGTTTATGT
1380022 CCATTCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.10, C:0.12, G:0.25, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:1380033 original size:24 final size:24
Alignment explanation
Indices: 1379981--1380036 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1379971 TGTTCGTTCG
* * * *
1379981 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCATTTATGTCCATTCA
1380005 GTTATGTTCATTTATGTCCATTCA
1 GTTATGTTCATTTATGTCCATTCA
*
1380029 TTTATGTT
1 GTTATGTT
1380037 TAACCTAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.55
Consensus pattern (24 bp):
GTTATGTTCATTTATGTCCATTCA
Found at i:1381119 original size:10 final size:10
Alignment explanation
Indices: 1381104--1381178 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
1381094 GGGTCTCCAA
1381104 CGTTTATGTT
1 CGTTTATGTT
1381114 CGTTTATGTT
1 CGTTTATGTT
1381124 CG----TGTT
1 CGTTTATGTT
*
1381130 CATTTATGTT
1 CGTTTATGTT
1381140 CGTGTT-TGTTT
1 CGT-TTATG-TT
* **
1381151 ATGTTCGTGTT
1 -CGTTTATGTT
1381162 CGTTTATGTT
1 CGTTTATGTT
1381172 CGTTTAT
1 CGTTTAT
1381179 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1381135 original size:16 final size:16
Alignment explanation
Indices: 1381110--1381174 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1381100 CCAACGTTTA
1381110 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1381126 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1381142 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1381158 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1381174 T
1 T
1381175 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1381265 original size:16 final size:16
Alignment explanation
Indices: 1381244--1381274 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1381234 AAAAATATTT
1381244 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1381260 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
1381275 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1388041 original size:2 final size:2
Alignment explanation
Indices: 1388034--1388065 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1388024 GCTTTTAATG
1388034 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
1388066 TAAAAATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1389275 original size:23 final size:23
Alignment explanation
Indices: 1389248--1389318 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
1389238 TTAAACAAAT
* * *
1389248 ATGTTCTCAAATGTTGAATGAAC
1 ATGTTCGCAAACGTTAAATGAAC
1389271 ATGTTCGCAAACGTTAAATGAAC
1 ATGTTCGCAAACGTTAAATGAAC
* *
1389294 ATGTTCGCAAACGCTAAACGAAC
1 ATGTTCGCAAACGTTAAATGAAC
1389317 AT
1 AT
1389319 AAACACCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (23 bp):
ATGTTCGCAAACGTTAAATGAAC
Found at i:1393178 original size:45 final size:44
Alignment explanation
Indices: 1393109--1393201 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 44
1393099 ATTCATATTA
* *
1393109 TTAAACTTTTAAGTCTTTAATTATAGTATTAAATTTTAATATAT
1 TTAAACTTTTAAGTCTTTAATTATAATATTAAATTTTAATAAAT
* *
1393153 TTAAACTTTTAATTTCTTTAATTATAATATTAAATTTTGATAAAT
1 TTAAACTTTTAA-GTCTTTAATTATAATATTAAATTTTAATAAAT
1393198 TTAA
1 TTAA
1393202 CGAGTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 12 0.27
45 32 0.73
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (44 bp):
TTAAACTTTTAAGTCTTTAATTATAATATTAAATTTTAATAAAT
Found at i:1395700 original size:3 final size:3
Alignment explanation
Indices: 1395692--1395721 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1395682 CTATAATTAG
1395692 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1395722 GTATTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1400064 original size:23 final size:24
Alignment explanation
Indices: 1400014--1400057 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1400004 ATAAATTTCA
1400014 ATTTACATTTAAAATTTTATTTGT
1 ATTTACATTTAAAATTTTATTTGT
*
1400038 ATTTA-ATTTATAA-TTTATTT
1 ATTTACATTTAAAATTTTATTT
1400058 TTTATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTTACATTTAAAATTTTATTTGT
Found at i:1402526 original size:20 final size:20
Alignment explanation
Indices: 1402498--1402544 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1402488 ACGAAATAAG
* * *
1402498 TTACTAGTGTGAATAAAATA
1 TTACCAGTGGGAATAAAAGA
1402518 TTACCAGTGGGAATAAAAGA
1 TTACCAGTGGGAATAAAAGA
1402538 TTACCAG
1 TTACCAG
1402545 GGAATAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (20 bp):
TTACCAGTGGGAATAAAAGA
Found at i:1402549 original size:18 final size:19
Alignment explanation
Indices: 1402508--1402550 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1402498 TTACTAGTGT
*
1402508 GAATAAAATATTACCAGTGG
1 GAATAAAAGATTACCAG-GG
1402528 GAATAAAAGATTACCA-GG
1 GAATAAAAGATTACCAGGG
1402546 GAATA
1 GAATA
1402551 GAATTACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (19 bp):
GAATAAAAGATTACCAGGG
Found at i:1402771 original size:36 final size:36
Alignment explanation
Indices: 1402700--1402772 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
1402690 GTTTGAAAAT
* * *
1402700 ATTTATGTATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
1402736 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
1402772 A
1 A
1402773 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:1405312 original size:18 final size:19
Alignment explanation
Indices: 1405277--1405313 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1405267 AACGGAATGT
1405277 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1405297 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1405314 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1409171 original size:6 final size:6
Alignment explanation
Indices: 1409156--1409193 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1409146 TTTTAGTGAA
1409156 CATG-C CATGCC CATGCC CATGCC CATGCC CATGCC CAT
1 CATGCC CATGCC CATGCC CATGCC CATGCC CATGCC CAT
1409194 ACCTTAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.18, C:0.47, G:0.16, T:0.18
Consensus pattern (6 bp):
CATGCC
Found at i:1409612 original size:4 final size:4
Alignment explanation
Indices: 1409603--1409633 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1409593 CCTTGAAAGG
1409603 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1409634 ACAACTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1419023 original size:25 final size:25
Alignment explanation
Indices: 1418989--1419038 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1418979 ATTTGAACTC
1418989 GAAACCTTACTTAACGATATTAAGT
1 GAAACCTTACTTAACGATATTAAGT
1419014 GAAACCTTACTTAACGATATTAAGT
1 GAAACCTTACTTAACGATATTAAGT
1419039 TACTTACCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (25 bp):
GAAACCTTACTTAACGATATTAAGT
Found at i:1423933 original size:87 final size:84
Alignment explanation
Indices: 1423777--1423944 Score: 223
Period size: 84 Copynumber: 2.0 Consensus size: 84
1423767 TAATCTCAAT
* * *
1423777 CATTTGACAATAAACGCTCAATCACCCTTGCAGTCGCTGACGCTCAAACCTGTGACCTCTAAAAT
1 CATTTGACAATAAACACTCAATCACCCTTGCAGT--CTGACCCTCAAACCTATGACCTCTAAAAT
1423842 CAACAACATTTCATTTAACAAC
64 -AACAACATTTCATTTAACAAC
* * *
1423864 CATTTGACAATAAATACTCAATCACCCTTGCAGT-TGACCCTTGACACC-ATGACCTCTAGAAAT
1 CATTTGACAATAAACACTCAATCACCCTTGCAGTCTGACCC-TCAAACCTATGACCTCTA-AAAT
1423927 AACAACATTTCATTTAAC
64 AACAACATTTCATTTAAC
1423945 TACTAGGTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
84 32 0.44
85 9 0.12
87 32 0.44
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.27
Consensus pattern (84 bp):
CATTTGACAATAAACACTCAATCACCCTTGCAGTCTGACCCTCAAACCTATGACCTCTAAAATAA
CAACATTTCATTTAACAAC
Found at i:1426732 original size:2 final size:2
Alignment explanation
Indices: 1426725--1426773 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1426715 TAGACAGATA
1426725 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1426767 AG AG AG A
1 AG AG AG A
1426774 CCCAACACAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1430362 original size:25 final size:24
Alignment explanation
Indices: 1430318--1430365 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1430308 GGATTTTTAG
*
1430318 AATTTTTTTTACTTTGATTATTAA
1 AATTTTTTTTACTTTAATTATTAA
1430342 AATTTGTTTTTA-TTATAATTATTA
1 AATTT-TTTTTACTT-TAATTATTA
1430366 TTAATTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (24 bp):
AATTTTTTTTACTTTAATTATTAA
Found at i:1434500 original size:17 final size:17
Alignment explanation
Indices: 1434480--1434513 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1434470 TTCGTTTTCA
*
1434480 TTTTTGGATAAAATATC
1 TTTTAGGATAAAATATC
*
1434497 TTTTAGGGTAAAATATC
1 TTTTAGGATAAAATATC
1434514 CAAATAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (17 bp):
TTTTAGGATAAAATATC
Found at i:1444111 original size:92 final size:94
Alignment explanation
Indices: 1443954--1444141 Score: 362
Period size: 92 Copynumber: 2.0 Consensus size: 94
1443944 CGACCGTGAT
1443954 GAAGCGTGCGTGTGATTGTACGAATGGGACCGGAACTGATTTTACACACAAAACCAACACCTTAT
1 GAAGCGTGCGTGTGATTGTACGAATGGGACCGGAACTGATTTTACACACAAAACCAACACCTTAT
1444019 GGAACGCAGGC-GG-TTGTGACAAAATGG
66 GGAACGCAGGCAGGTTTGTGACAAAATGG
1444046 GAAGCGTGCGTGTGATTGTACGAATGGGACCGGAACTGATTTTACACACAAAACCAACACCTTAT
1 GAAGCGTGCGTGTGATTGTACGAATGGGACCGGAACTGATTTTACACACAAAACCAACACCTTAT
1444111 GGAACGCAGGCAGGTTTGTGACAAAATGG
66 GGAACGCAGGCAGGTTTGTGACAAAATGG
1444140 GA
1 GA
1444142 GAAGATTGCA
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
92 76 0.81
93 2 0.02
94 16 0.17
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (94 bp):
GAAGCGTGCGTGTGATTGTACGAATGGGACCGGAACTGATTTTACACACAAAACCAACACCTTAT
GGAACGCAGGCAGGTTTGTGACAAAATGG
Found at i:1447294 original size:14 final size:14
Alignment explanation
Indices: 1447271--1447304 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1447261 TATGACATGA
*
1447271 AAGGATTATAGGAT
1 AAGGAATATAGGAT
1447285 AAGGAATATAGGAT
1 AAGGAATATAGGAT
1447299 AAGGAA
1 AAGGAA
1447305 CATGGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (14 bp):
AAGGAATATAGGAT
Found at i:1448855 original size:51 final size:53
Alignment explanation
Indices: 1448790--1448893 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
1448780 CTGGCAAATG
1448790 CTGTAGCACTGGGGTCAAAAG-CCC-CGCTGCTGTTGCTCCTGCAAAGCACGA
1 CTGTAGCACTGGGGTCAAAAGCCCCTCGCTGCTGTTGCTCCTGCAAAGCACGA
1448841 CTGTAGCACTGGGGTCAAAAGCCCCTCGCTGCTGTTGCTCCTGCAAAGCACGA
1 CTGTAGCACTGGGGTCAAAAGCCCCTCGCTGCTGTTGCTCCTGCAAAGCACGA
1448894 TTCATTTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 21 0.41
52 3 0.06
53 27 0.53
ACGTcount: A:0.21, C:0.32, G:0.27, T:0.20
Consensus pattern (53 bp):
CTGTAGCACTGGGGTCAAAAGCCCCTCGCTGCTGTTGCTCCTGCAAAGCACGA
Found at i:1449571 original size:30 final size:30
Alignment explanation
Indices: 1449518--1449599 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
1449508 CCAGCAGCAA
*
1449518 CTGCTGCCGCTGAAGCT-CAACTGCTGCTG
1 CTGCCGCCGCTGAAGCTCCAACTGCTGCTG
1449547 CTGCCGCCGCTGAAGCTCCAACTGCTGCTG
1 CTGCCGCCGCTGAAGCTCCAACTGCTGCTG
*
1449577 CTGCCGTCGCTGAAGCTCCAACT
1 CTGCCGCCGCTGAAGCTCCAACT
1449600 TCCGCTGTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.22
Consensus pattern (30 bp):
CTGCCGCCGCTGAAGCTCCAACTGCTGCTG
Found at i:1449582 original size:27 final size:27
Alignment explanation
Indices: 1449518--1449663 Score: 141
Period size: 27 Copynumber: 5.2 Consensus size: 27
1449508 CCAGCAGCAA
1449518 CTGCTGCCGCTGAAGCT-CAACTGCTGCTG
1 CTGCTGCCGCTGAAGCTCCAACTGC--C-G
* *
1449547 CTGCCGCCGCTGAAGCTCCAACTGCTG
1 CTGCTGCCGCTGAAGCTCCAACTGCCG
*
1449574 CTGCTGCCGTCGCTGAAGCTCCAACTTCCG
1 CTGCTG-C--CGCTGAAGCTCCAACTGCCG
* ** *
1449604 CTGTTGTTGCTGAAGTTCCAACTGCCG
1 CTGCTGCCGCTGAAGCTCCAACTGCCG
** *
1449631 CTGCTGTTGCTGAAGTTCCAACTGCCG
1 CTGCTGCCGCTGAAGCTCCAACTGCCG
1449658 CTGCTG
1 CTGCTG
1449664 TTCAAATTGA
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
27 55 0.54
28 1 0.01
29 16 0.16
30 30 0.29
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (27 bp):
CTGCTGCCGCTGAAGCTCCAACTGCCG
Found at i:1453373 original size:7 final size:7
Alignment explanation
Indices: 1453322--1453373 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
1453312 TTTAAAATGG
1453322 ATTACATT
1 ATTA-ATT
1453330 ATTAATT
1 ATTAATT
*
1453337 ATAAATT
1 ATTAATT
1453344 -TTAAATT
1 ATT-AATT
1453351 ATTAATT
1 ATTAATT
*
1453358 GATTTATT
1 -ATTAATT
1453366 ATTAATT
1 ATTAATT
1453373 A
1 A
1453374 AAGTATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
6 1 0.03
7 24 0.65
8 12 0.32
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (7 bp):
ATTAATT
Found at i:1463468 original size:25 final size:25
Alignment explanation
Indices: 1463434--1463495 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
1463424 AACAACCAGT
1463434 ATTTACTTTGAATTTTTTTTAATAG
1 ATTTACTTTGAATTTTTTTTAATAG
1463459 ATTTACTTTGAATTTTTTTTAATAG
1 ATTTACTTTGAATTTTTTTTAATAG
1463484 ATTTACTTTGAA
1 ATTTACTTTGAA
1463496 ATTAAAACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (25 bp):
ATTTACTTTGAATTTTTTTTAATAG
Found at i:1470350 original size:22 final size:22
Alignment explanation
Indices: 1470320--1470391 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
1470310 TTCCATTTCG
1470320 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
1470342 CGTTACGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
1470361 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1470383 CGTTGCGAT
1 CGTTGCGAT
1470392 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 9 0.24
20 5 0.14
21 5 0.14
22 18 0.49
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1470365 original size:41 final size:41
Alignment explanation
Indices: 1470320--1470413 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1470310 TTCCATTTCG
1470320 CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
*
1470361 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
*
1470402 CGTTGTGATAGT
1 CGTTGCGATAGT
1470414 TTAAAAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
Found at i:1470369 original size:19 final size:19
Alignment explanation
Indices: 1470341--1470406 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
1470331 TCTACAGTTG
*
1470341 TCGTTACGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
1470360 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1470381 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
1470401 TCGTTG
1 TCGTTG
1470407 TGATAGTTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 15 0.43
20 5 0.14
21 5 0.14
22 10 0.29
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1470524 original size:12 final size:12
Alignment explanation
Indices: 1470491--1470524 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1470481 GACACGTATT
*
1470491 ACCACGACCACG
1 ACCACGACCCCG
1470503 ACCACGACCCCG
1 ACCACGACCCCG
*
1470515 ACCCCGACCC
1 ACCACGACCC
1470525 GAGACGAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.59, G:0.15, T:0.00
Consensus pattern (12 bp):
ACCACGACCCCG
Found at i:1471042 original size:6 final size:6
Alignment explanation
Indices: 1471031--1471081 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
1471021 TCTCGTCTCG
1471031 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1471079 GGT
1 GGT
1471082 AATGGTAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1471253 original size:20 final size:20
Alignment explanation
Indices: 1471228--1471341 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
1471218 ACTGTAGACT
1471228 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1471248 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1471268 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
1471289 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1471309 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1471329 ATCGCAACGCGAA
1 ATCGCAACGCGAA
1471342 TTTGCGATAG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 68 0.82
21 15 0.18
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1471292 original size:61 final size:61
Alignment explanation
Indices: 1471225--1471340 Score: 232
Period size: 61 Copynumber: 1.9 Consensus size: 61
1471215 ACAACTGTAG
1471225 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1471286 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGA
1471341 ATTTGCGATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.14
Consensus pattern (61 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1471348 original size:28 final size:28
Alignment explanation
Indices: 1471317--1471371 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1471307 AAATCGCAAC
1471317 GCGA-AATGGAAAATCGCAACGCGAATTT
1 GCGATAATGG-AAATCGCAACGCGAATTT
* * *
1471345 GCGATAGTGGAGATCGCAATGCGAATT
1 GCGATAATGGAAATCGCAACGCGAATT
1471372 AGAGATCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (28 bp):
GCGATAATGGAAATCGCAACGCGAATTT
Found at i:1471863 original size:2 final size:2
Alignment explanation
Indices: 1471856--1471886 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1471846 CAATGCTTTA
1471856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1471887 GACAATGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1477769 original size:16 final size:16
Alignment explanation
Indices: 1477748--1477779 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1477738 ACATGATCCG
1477748 AAAATTTTGAATCTTT
1 AAAATTTTGAATCTTT
1477764 AAAATTTTGAATCTTT
1 AAAATTTTGAATCTTT
1477780 GTCAAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
AAAATTTTGAATCTTT
Found at i:1479692 original size:22 final size:21
Alignment explanation
Indices: 1479650--1479689 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1479640 TGAGTTATTT
*
1479650 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1479671 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1479690 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1497149 original size:11 final size:11
Alignment explanation
Indices: 1497133--1497174 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
1497123 AAATGCCATG
1497133 TAATACAAAAA
1 TAATACAAAAA
1497144 TAATACAAAAA
1 TAATACAAAAA
1497155 TAATACAAAAA
1 TAATACAAAAA
*
1497166 TAATTCAAA
1 TAATACAAA
1497175 GTAATCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (11 bp):
TAATACAAAAA
Found at i:1505682 original size:2 final size:2
Alignment explanation
Indices: 1505677--1505708 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1505667 TCTCACGTGA
1505677 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1505709 TTTCAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1506009 original size:13 final size:14
Alignment explanation
Indices: 1505982--1506008 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1505972 TGATTCATCA
1505982 AAATTTAATTTTTT
1 AAATTTAATTTTTT
1505996 AAATTTAATTTTT
1 AAATTTAATTTTT
1506009 ATATAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AAATTTAATTTTTT
Found at i:1508869 original size:58 final size:58
Alignment explanation
Indices: 1508778--1508961 Score: 226
Period size: 58 Copynumber: 3.2 Consensus size: 58
1508768 TGAATCGAAT
* * ** * * * *
1508778 GAACACAAATAAGCGTGCGTTCATGTTCGTTCGTTTAATTTTAACAAAAAAAAATTAAC
1 GAACACAAATGAGAGTATGTTCATGTTCGTTCGTTTAACTTTAAC-CAAATAAATGAAC
* * * *
1508837 GAACAC-GATGAGAGTATGTTCATGTTCGTTCGTTTTACTTTAACCGAATAAATGAAT
1 GAACACAAATGAGAGTATGTTCATGTTCGTTCGTTTAACTTTAACCAAATAAATGAAC
* *
1508894 GAACACAAATGAGGGTATGTTCATGTTTGTTCGTTTAACTTTAACCAAATAAATGAAC
1 GAACACAAATGAGAGTATGTTCATGTTCGTTCGTTTAACTTTAACCAAATAAATGAAC
1508952 GAACACAAAT
1 GAACACAAAT
1508962 AACTAAATGA
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
57 14 0.13
58 86 0.81
59 6 0.06
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (58 bp):
GAACACAAATGAGAGTATGTTCATGTTCGTTCGTTTAACTTTAACCAAATAAATGAAC
Found at i:1510699 original size:2 final size:2
Alignment explanation
Indices: 1510694--1510734 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1510684 AAAACACACA
* *
1510694 CT CT CT CT CT CT CT CT CT CG CT CT CT CT CT CT CG CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1510735 CAAATTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.05, T:0.44
Consensus pattern (2 bp):
CT
Found at i:1510717 original size:14 final size:14
Alignment explanation
Indices: 1510694--1510734 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
1510684 AAAACACACA
*
1510694 CTCTCTCTCTCTCT
1 CTCTCGCTCTCTCT
1510708 CTCTCGCTCTCTCT
1 CTCTCGCTCTCTCT
1510722 CTCTCGCTCTCTC
1 CTCTCGCTCTCTC
1510735 CAAATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.00, C:0.51, G:0.05, T:0.44
Consensus pattern (14 bp):
CTCTCGCTCTCTCT
Found at i:1514732 original size:22 final size:22
Alignment explanation
Indices: 1514704--1514746 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1514694 ATACATTTAT
1514704 TCGTTAG-TTTTACCGAATTGGC
1 TCGTTAGCTTTT-CCGAATTGGC
*
1514726 TCGTTAGCTTTTCTGAATTGG
1 TCGTTAGCTTTTCCGAATTGG
1514747 ATAGTTGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (22 bp):
TCGTTAGCTTTTCCGAATTGGC
Found at i:1519848 original size:15 final size:16
Alignment explanation
Indices: 1519828--1519866 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1519818 TTTACTTCAG
*
1519828 ATGATT-AAGCGCTGA
1 ATGATTCAAACGCTGA
*
1519843 ATGATTCAAATGCTGA
1 ATGATTCAAACGCTGA
1519859 ATGATTCA
1 ATGATTCA
1519867 GAGGCTCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (16 bp):
ATGATTCAAACGCTGA
Found at i:1537598 original size:21 final size:21
Alignment explanation
Indices: 1537564--1537611 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1537554 AGTGTTATTT
* * *
1537564 AAAATATTATTTTTTTTACCG
1 AAAATGTTAATTTTGTTACCG
*
1537585 AAAATGTTAATTTTGTTACCT
1 AAAATGTTAATTTTGTTACCG
1537606 AAAATG
1 AAAATG
1537612 AATATTTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (21 bp):
AAAATGTTAATTTTGTTACCG
Found at i:1538255 original size:25 final size:24
Alignment explanation
Indices: 1538219--1538266 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1538209 TATCTTTCTT
1538219 AATTTTAAATTTAAATATTTAATA
1 AATTTTAAATTTAAATATTTAATA
* *
1538243 AATTATTATATTTTAATATTTAAT
1 AATT-TTAAATTTAAATATTTAAT
1538267 CTTACTTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTTTAAATTTAAATATTTAATA
Found at i:1541367 original size:18 final size:18
Alignment explanation
Indices: 1541344--1541379 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1541334 TTAAGAAAAT
1541344 TCGCATACAATCAACTTC
1 TCGCATACAATCAACTTC
1541362 TCGCATACAATCAACTTC
1 TCGCATACAATCAACTTC
1541380 ACAGAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.28
Consensus pattern (18 bp):
TCGCATACAATCAACTTC
Found at i:1542266 original size:20 final size:20
Alignment explanation
Indices: 1542225--1542266 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1542215 TAATTTTATT
* *
1542225 TTTATTTTTCTCTTAAATTA
1 TTTATTTTTCTCTAAAAATA
1542245 TTTA-TTTTCTTCTAAAAATA
1 TTTATTTTTC-TCTAAAAATA
1542265 TT
1 TT
1542267 ATATACTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTTTTCTCTAAAAATA
Found at i:1554882 original size:45 final size:46
Alignment explanation
Indices: 1554833--1554931 Score: 128
Period size: 45 Copynumber: 2.1 Consensus size: 46
1554823 TGTTATCCAC
* *
1554833 AAAAAGAAATCCTAACCTCATCATATCTAATTCGCATGC-TTATTCA
1 AAAAATAAA-CCTAACCGCATCATATCTAATTCGCATGCATTATTCA
* *
1554879 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGA
1 AAAAATAAACCTAACCGCATCATATCTAATTCGCATGCA-TTATTC-A
1554927 AAAAA
1 AAAAA
1554932 AACGAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 26 0.57
46 8 0.17
47 6 0.13
48 6 0.13
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.28
Consensus pattern (46 bp):
AAAAATAAACCTAACCGCATCATATCTAATTCGCATGCATTATTCA
Found at i:1557760 original size:63 final size:63
Alignment explanation
Indices: 1557690--1557815 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
1557680 GTTAGTTTAT
1557690 ATACCTTACTCGGTCTCGTTTTTACTCGCATCGGAGGTACCTTAGGTCAGTTAGTTGGGTGCC
1 ATACCTTACTCGGTCTCGTTTTTACTCGCATCGGAGGTACCTTAGGTCAGTTAGTTGGGTGCC
1557753 ATACCTTACTCGGTCTCGTTTTTACTCGCATCGGAGGTACCTTAGGTCAGTTAGTTGGGTGCC
1 ATACCTTACTCGGTCTCGTTTTTACTCGCATCGGAGGTACCTTAGGTCAGTTAGTTGGGTGCC
1557816 GGCGAGTAGC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (63 bp):
ATACCTTACTCGGTCTCGTTTTTACTCGCATCGGAGGTACCTTAGGTCAGTTAGTTGGGTGCC
Found at i:1565386 original size:26 final size:26
Alignment explanation
Indices: 1565350--1565403 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1565340 AGTCAATTAC
1565350 ATAGTTTATAAGAGGAAAATGTAGCA
1 ATAGTTTATAAGAGGAAAATGTAGCA
*
1565376 ATAGTTTATAAGTGGAAAATGTAGCA
1 ATAGTTTATAAGAGGAAAATGTAGCA
1565402 AT
1 AT
1565404 GCTCTTTGAG
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:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (26 bp):
ATAGTTTATAAGAGGAAAATGTAGCA
Found at i:1567638 original size:29 final size:30
Alignment explanation
Indices: 1567598--1567654 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
1567588 CTCACCCCGT
*
1567598 AAACATTCACACAAAAATCCTCTCAACCGA
1 AAACATTCACACAAAAATCATCTCAACCGA
*
1567628 AAACA-TCACACAACAATCATCTCAACC
1 AAACATTCACACAAAAATCATCTCAACC
1567655 CGTAAATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.47, C:0.35, G:0.02, T:0.16
Consensus pattern (30 bp):
AAACATTCACACAAAAATCATCTCAACCGA
Found at i:1571633 original size:31 final size:31
Alignment explanation
Indices: 1571598--1571794 Score: 175
Period size: 31 Copynumber: 6.3 Consensus size: 31
1571588 GTTTTTCGGG
* *
1571598 ACATATTGACAGTATACATATGTTCTACGGA
1 ACATATGGACAATATACATATGTTCTACGGA
* * * *
1571629 ACATATGGACAAAATTACCTATG-TCTTTCGGG
1 ACATATGGACAATA-TACATATGTTC-TACGGA
* * *
1571661 ACATATGGTCAATATACCTATGTTCTACGAA
1 ACATATGGACAATATACATATGTTCTACGGA
* * * *
1571692 ACATATAGAC-ATAATTACCTATG-TCTTTCGGG
1 ACATATGGACAAT-A-TACATATGTTC-TACGGA
* *
1571724 ACATATGGACAGTATACATATGTTCTAAGGA
1 ACATATGGACAATATACATATGTTCTACGGA
*
1571755 ACATATGGACAATATACATATGTTCTAAGGA
1 ACATATGGACAATATACATATGTTCTACGGA
*
1571786 ACGTATGGA
1 ACATATGGA
1571795 TAGTTTACCT
Statistics
Matches: 134, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
30 2 0.01
31 83 0.62
32 48 0.36
33 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (31 bp):
ACATATGGACAATATACATATGTTCTACGGA
Found at i:1571658 original size:63 final size:63
Alignment explanation
Indices: 1571578--1571766 Score: 297
Period size: 63 Copynumber: 3.0 Consensus size: 63
1571568 AGAGTCGAAG
* *
1571578 AATTACCTATGTTTTTCGGGACATATTGACAGTATACATATGTTCTACGGAACATATGGACAA
1 AATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTACGGAACATATGGACAA
* * * * * *
1571641 AATTACCTATGTCTTTCGGGACATATGGTCAATATACCTATGTTCTACGAAACATATAGACAT
1 AATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTACGGAACATATGGACAA
*
1571704 AATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTAAGGAACATATGGACAA
1 AATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTACGGAACATATGGACAA
1571767 TATACATATG
Statistics
Matches: 111, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 111 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (63 bp):
AATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTACGGAACATATGGACAA
Found at i:1571665 original size:32 final size:31
Alignment explanation
Indices: 1571578--1571734 Score: 138
Period size: 32 Copynumber: 5.0 Consensus size: 31
1571568 AGAGTCGAAG
* *
1571578 AATTACCTATGTTTTTCGGGACATATTGACAG
1 AATTACCTATG-TTTTCGGGACATATGGACAA
* * * *
1571610 TA-TACATATGTTCTACGGAACATATGGACAA
1 AATTACCTATGTT-TTCGGGACATATGGACAA
*
1571641 AATTACCTATGTCTTTCGGGACATATGGTCAA
1 AATTACCTATGT-TTTCGGGACATATGGACAA
* * ** * *
1571673 TA-TACCTATGTTCTACGAAACATATAGACAT
1 AATTACCTATGTT-TTCGGGACATATGGACAA
1571704 AATTACCTATGTCTTTCGGGACATATGGACA
1 AATTACCTATGT-TTTCGGGACATATGGACA
1571735 GTATACATAT
Statistics
Matches: 96, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
30 3 0.03
31 44 0.46
32 47 0.49
33 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (31 bp):
AATTACCTATGTTTTCGGGACATATGGACAA
Found at i:1572584 original size:14 final size:14
Alignment explanation
Indices: 1572565--1572592 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1572555 TTCACTGTTC
1572565 ACGGTATTGTTCAT
1 ACGGTATTGTTCAT
1572579 ACGGTATTGTTCAT
1 ACGGTATTGTTCAT
1572593 TGTTCATACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
ACGGTATTGTTCAT
Found at i:1574438 original size:29 final size:31
Alignment explanation
Indices: 1574404--1574468 Score: 116
Period size: 29 Copynumber: 2.2 Consensus size: 31
1574394 ACTGTAAAAA
1574404 AAATAATTAAATAAAATACTAA-AAAAT-TT
1 AAATAATTAAATAAAATACTAACAAAATATT
1574433 AAATAATTAAATAAAATACTAACAAAATATT
1 AAATAATTAAATAAAATACTAACAAAATATT
1574464 AAATA
1 AAATA
1574469 GAATAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 22 0.65
30 5 0.15
31 7 0.21
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (31 bp):
AAATAATTAAATAAAATACTAACAAAATATT
Found at i:1575517 original size:23 final size:24
Alignment explanation
Indices: 1575475--1575519 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1575465 TTATGACTTT
1575475 TAATATTTTAAAAATTAAAAAAAA
1 TAATATTTTAAAAATTAAAAAAAA
*
1575499 TAATATTTT-ATAATTAAAAAA
1 TAATATTTTAAAAATTAAAAAA
1575520 TTATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TAATATTTTAAAAATTAAAAAAAA
Found at i:1583555 original size:13 final size:13
Alignment explanation
Indices: 1583537--1583563 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1583527 ACAAGGAAAC
1583537 AATTTTTTTTTCT
1 AATTTTTTTTTCT
1583550 AATTTTTTTTTCT
1 AATTTTTTTTTCT
1583563 A
1 A
1583564 TTGCGAAAGG
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:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (13 bp):
AATTTTTTTTTCT
Found at i:1586257 original size:20 final size:21
Alignment explanation
Indices: 1586232--1586284 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1586222 GACCAACAAA
1586232 TTCGCAACGCGAAC-TCCAAT
1 TTCGCAACGCGAACTTCCAAT
*
1586252 TTCGCAACTC--ACTTTCCAAT
1 TTCGCAACGCGAAC-TTCCAAT
1586272 TTCGCAACGCGAA
1 TTCGCAACGCGAA
1586285 TATGTAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.07
20 24 0.89
22 1 0.04
ACGTcount: A:0.28, C:0.34, G:0.13, T:0.25
Consensus pattern (21 bp):
TTCGCAACGCGAACTTCCAAT
Found at i:1586334 original size:21 final size:20
Alignment explanation
Indices: 1586273--1586340 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1586263 CTTTCCAATT
1586273 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
** * * **
1586293 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATATGTAAA
*
1586313 TTCGCAACGCGAATCTGTAAA
1 -TCGCAACGCGAATATGTAAA
1586334 TCGCAAC
1 TCGCAAC
1586341 ACAGAAGTCA
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:1586357 original size:20 final size:20
Alignment explanation
Indices: 1586334--1586380 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1586324 AATCTGTAAA
*
1586334 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
1586354 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
1586374 TCGCAAC
1 TCGCAAC
1586381 GCGAACTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.28, G:0.13, T:0.15
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:1586420 original size:20 final size:20
Alignment explanation
Indices: 1586397--1586482 Score: 154
Period size: 20 Copynumber: 4.2 Consensus size: 20
1586387 TCCAATTTCA
1586397 CAACGTGAATAGTAAAATCG
1 CAACGTGAATAGTAAAATCG
1586417 CAACGTGAATAGTAAAATCG
1 CAACGTGAATAGTAAAATCG
*
1586437 CAACGTGAATAGTAAAAATCA
1 CAACGTGAATAGT-AAAATCG
1586458 CAACGTGAATAGTAAAATCG
1 CAACGTGAATAGTAAAATCG
1586478 CAACG
1 CAACG
1586483 AATCTATATG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
20 44 0.70
21 19 0.30
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (20 bp):
CAACGTGAATAGTAAAATCG
Found at i:1586467 original size:41 final size:40
Alignment explanation
Indices: 1586397--1586482 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 40
1586387 TCCAATTTCA
*
1586397 CAACGTGAATAGTAAAATCGCAACGTGAATAGTAAAATCG
1 CAACGTGAATAGTAAAATCACAACGTGAATAGTAAAATCG
1586437 CAACGTGAATAGTAAAAATCACAACGTGAATAGTAAAATCG
1 CAACGTGAATAGT-AAAATCACAACGTGAATAGTAAAATCG
1586478 CAACG
1 CAACG
1586483 AATCTATATG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 13 0.30
41 31 0.70
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (40 bp):
CAACGTGAATAGTAAAATCACAACGTGAATAGTAAAATCG
Found at i:1586873 original size:20 final size:20
Alignment explanation
Indices: 1586845--1586901 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
1586835 GATTTTCTAA
*
1586845 ATTCGCGTTGCGATTTTACT
1 ATTCACGTTGCGATTTTACT
* *
1586865 ATTCACGTTACGCTTTTTACT
1 ATTCACGTTGCG-ATTTTACT
1586886 ATTCACGTTGCGATTT
1 ATTCACGTTGCGATTT
1586902 GGAAACTGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.46
Consensus pattern (20 bp):
ATTCACGTTGCGATTTTACT
Found at i:1587360 original size:17 final size:17
Alignment explanation
Indices: 1587330--1587362 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1587320 TCATTCTTTA
1587330 AAATATATTATAATTTT
1 AAATATATTATAATTTT
1587347 AAATGATATT-TAATTT
1 AAAT-ATATTATAATTT
1587363 ATTAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
AAATATATTATAATTTT
Found at i:1587706 original size:24 final size:23
Alignment explanation
Indices: 1587657--1587706 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
1587647 AAACAAAGTG
*
1587657 ATTAAATATTATATTTAATCTTT
1 ATTAAACATTATATTTAATCTTT
1587680 ATTAAACATTAATGATTT-ATCTTT
1 ATTAAACATT-AT-ATTTAATCTTT
1587704 ATT
1 ATT
1587707 TTAATCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 11 0.46
25 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTAAACATTATATTTAATCTTT
Found at i:1594328 original size:31 final size:32
Alignment explanation
Indices: 1594293--1594358 Score: 125
Period size: 31 Copynumber: 2.1 Consensus size: 32
1594283 TACTCGCCAA
1594293 AAGAGCTTTATCCATAAC-TTCATCGCAAAAT
1 AAGAGCTTTATCCATAACTTTCATCGCAAAAT
1594324 AAGAGCTTTATCCATAACTTTCATCGCAAAAT
1 AAGAGCTTTATCCATAACTTTCATCGCAAAAT
1594356 AAG
1 AAG
1594359 TGTTGGTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 18 0.53
32 16 0.47
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (32 bp):
AAGAGCTTTATCCATAACTTTCATCGCAAAAT
Found at i:1595027 original size:149 final size:149
Alignment explanation
Indices: 1594757--1595122 Score: 367
Period size: 149 Copynumber: 2.4 Consensus size: 149
1594747 AAGCTCAGCC
* * * *
1594757 TTTTCATATTCCAATGAACCAATTGAATTAGAACTCTTGTGATCATCAATGAGATGTTTGAAGGA
1 TTTTCAGATTCCAATGAACCAATGGAATTAGAACTCTTATGATCATAAATGAGATGTTTGAAGGA
* * * * * * *
1594822 AGATTTGCTTCCCGCTCTCGGAATTTTTCCCACCGGTTCTGATTTCACCTTGCTCAAATCATAAT
66 AGATTTGCTTCCCACTCTCGAAATCTTCCCCACCGATTCGGATTTCACCTTACTCAAATCATAAT
1594887 AGTGTTCACCAGCCACTTT
131 AGTGTTCACCAGCCACTTT
* * * *
1594906 TTTTCAGATTGCAATGAACCAATGGAATTGGAACTCTTATGATCATAAATGGGTTGTTTGAAGGA
1 TTTTCAGATTCCAATGAACCAATGGAATTAGAACTCTTATGATCATAAATGAGATGTTTGAAGGA
* * * * **
1594971 AGATTTGTTTCCCATTGTCGAAATCTTCCCCACTGATTCGGATTT-ATCCTTACTCAAATGGTAA
66 AGATTTGCTTCCCACTCTCGAAATCTTCCCCACCGATTCGGATTTCA-CCTTACTCAAATCATAA
* * * *
1595035 TAATGTACACCATG-CACCGTC
130 TAGTGTTCACCA-GCCA-CTTT
* * * * * ** * * * *
1595056 GTTCCATATTCCGATGAAGCAATGGAACCAGAACTCTCACGATCATCAACGAGATGTTTGAAGGA
1 TTTTCAGATTCCAATGAACCAATGGAATTAGAACTCTTATGATCATAAATGAGATGTTTGAAGGA
1595121 AG
66 AG
1595123 GTTCGTTTGC
Statistics
Matches: 174, Mismatches: 40, Indels: 5
0.79 0.18 0.02
Matches are distributed among these distances:
148 1 0.01
149 118 0.68
150 55 0.32
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (149 bp):
TTTTCAGATTCCAATGAACCAATGGAATTAGAACTCTTATGATCATAAATGAGATGTTTGAAGGA
AGATTTGCTTCCCACTCTCGAAATCTTCCCCACCGATTCGGATTTCACCTTACTCAAATCATAAT
AGTGTTCACCAGCCACTTT
Found at i:1598764 original size:29 final size:29
Alignment explanation
Indices: 1598694--1598767 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
1598684 AATTGCTCAG
* * * *
1598694 GCCTCACTCCTTTGATATTTATACTTAGG
1 GCCTCACTCTTTTAATATTTATAATTAGA
* *
1598723 GCCACATTCTTTTAATATTTATAATTAGA
1 GCCTCACTCTTTTAATATTTATAATTAGA
*
1598752 GCCTCACTGTTTTAAT
1 GCCTCACTCTTTTAAT
1598768 CTTACATGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (29 bp):
GCCTCACTCTTTTAATATTTATAATTAGA
Found at i:1611194 original size:14 final size:13
Alignment explanation
Indices: 1611162--1611195 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1611152 AAAATTAAAA
1611162 ATTAATAATTTTT
1 ATTAATAATTTTT
*
1611175 AATAATAATTTTTT
1 ATTAATAA-TTTTT
1611189 ATTAATA
1 ATTAATA
1611196 TAAATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTAATAATTTTT
Found at i:1614411 original size:30 final size:30
Alignment explanation
Indices: 1614341--1614413 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1614331 GGTTTTTCGG
*
1614341 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTATGGATAGTTACCGAGGATCTTTAT
*
1614371 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTATGGATAGTTACCGAGGATCTTTAT
*
1614401 GACCTTTGGATAG
1 GACCTATGGATAG
1614414 GTACTTCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTATGGATAGTTACCGAGGATCTTTAT
Found at i:1616731 original size:2 final size:2
Alignment explanation
Indices: 1616724--1616751 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1616714 AATTTATTTA
1616724 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
1616752 CAAAGTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1622466 original size:19 final size:19
Alignment explanation
Indices: 1622442--1622479 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1622432 AGGATCAGCA
*
1622442 GCAATGCCGACCTTTTGCC
1 GCAATGCCCACCTTTTGCC
1622461 GCAATGCCCACCTTTTGCC
1 GCAATGCCCACCTTTTGCC
1622480 TCTTGGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.39, G:0.18, T:0.26
Consensus pattern (19 bp):
GCAATGCCCACCTTTTGCC
Found at i:1627761 original size:2 final size:2
Alignment explanation
Indices: 1627754--1627789 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1627744 GAAATGACAA
1627754 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
1627790 TAATTTACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1627946 original size:15 final size:15
Alignment explanation
Indices: 1627907--1627946 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1627897 CGTACCTTTA
* *
1627907 AATGATTTAATGTTG
1 AATGATTCAGTGTTG
1627922 AATGATTCAGTGTTG
1 AATGATTCAGTGTTG
*
1627937 ATTGATTCAG
1 AATGATTCAG
1627947 CACAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (15 bp):
AATGATTCAGTGTTG
Found at i:1628034 original size:15 final size:15
Alignment explanation
Indices: 1628014--1628045 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1628004 ATGTCACATT
1628014 CAGAGCTAATTCATA
1 CAGAGCTAATTCATA
*
1628029 CAGAGCTAATTTATA
1 CAGAGCTAATTCATA
1628044 CA
1 CA
1628046 TAGGCTCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (15 bp):
CAGAGCTAATTCATA
Found at i:1628074 original size:16 final size:16
Alignment explanation
Indices: 1628053--1628109 Score: 105
Period size: 16 Copynumber: 3.6 Consensus size: 16
1628043 ACATAGGCTC
1628053 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
*
1628069 TGAATCATTCAGTATT
1 TGAATCATTCAGCATT
1628085 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
1628101 TGAATCATT
1 TGAATCATT
1628110 TAACACTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:1628752 original size:16 final size:17
Alignment explanation
Indices: 1628721--1628756 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1628711 ATTAAATACA
*
1628721 AAAATTAATATAAAAAT
1 AAAATAAATATAAAAAT
1628738 AAAATAAAT-TAAAAAT
1 AAAATAAATATAAAAAT
1628754 AAA
1 AAA
1628757 TTAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATAAATATAAAAAT
Found at i:1630379 original size:96 final size:96
Alignment explanation
Indices: 1630206--1630392 Score: 284
Period size: 96 Copynumber: 1.9 Consensus size: 96
1630196 CTGTGGTTGC
* * * *
1630206 TGAGCAGGAGGCATTGGGAATTGTTGACTTGGAGTCTCCTGAGTTTGGCCAGGAGGTGGGTAGTA
1 TGAGCAGGAGGCATTGGGAATTGCTGACTTGGAGTCTCCTGAGGTTGGCCAGGAGGCGGATAGTA
1630271 AGCATCTAGTTGAGGGACAGAAGGAACTTGA
66 AGCATCTAGTTGAGGGACAGAAGGAACTTGA
* * * *
1630302 TGAGTAGGAGGCATTTGGAATTGCTGACTTGGAGTCTCCTGTGGTTGGCCAGGTGGCGGATAGTA
1 TGAGCAGGAGGCATTGGGAATTGCTGACTTGGAGTCTCCTGAGGTTGGCCAGGAGGCGGATAGTA
* *
1630367 AGCATCTCGTTGAGGGACAGATGGAA
66 AGCATCTAGTTGAGGGACAGAAGGAA
1630393 TTTGGTTCTG
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (96 bp):
TGAGCAGGAGGCATTGGGAATTGCTGACTTGGAGTCTCCTGAGGTTGGCCAGGAGGCGGATAGTA
AGCATCTAGTTGAGGGACAGAAGGAACTTGA
Found at i:1637741 original size:10 final size:10
Alignment explanation
Indices: 1637723--1637798 Score: 53
Period size: 10 Copynumber: 6.8 Consensus size: 10
1637713 ATTATATGTT
1637723 TGTTCATTTA
1 TGTTCATTTA
*
1637733 TGTTTATTTATA
1 TGTTCA-TT-TA
1637745 TTCGTTCATTTA
1 -T-GTTCATTTA
*
1637757 TGTTTATTTA
1 TGTTCATTTA
1637767 TGTTAATTCATTTA
1 TG----TTCATTTA
1637781 TGTTCATTTA
1 TGTTCATTTA
*
1637791 TTTTCATT
1 TGTTCATT
1637799 CATTTATGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
10 30 0.57
11 3 0.06
12 4 0.08
13 3 0.06
14 13 0.25
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.63
Consensus pattern (10 bp):
TGTTCATTTA
Found at i:1637753 original size:24 final size:24
Alignment explanation
Indices: 1637725--1637808 Score: 123
Period size: 24 Copynumber: 3.5 Consensus size: 24
1637715 TATATGTTTG
*
1637725 TTCATTTATGTTTATTTATATTCG
1 TTCATTTATGTTTATTTATATTCA
* *
1637749 TTCATTTATGTTTATTTATGTTAA
1 TTCATTTATGTTTATTTATATTCA
* *
1637773 TTCATTTATGTTCATTTATTTTCA
1 TTCATTTATGTTTATTTATATTCA
1637797 TTCATTTATGTT
1 TTCATTTATGTT
1637809 CGAACAGAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.63
Consensus pattern (24 bp):
TTCATTTATGTTTATTTATATTCA
Found at i:1637781 original size:14 final size:13
Alignment explanation
Indices: 1637749--1637808 Score: 51
Period size: 14 Copynumber: 4.9 Consensus size: 13
1637739 TTTATATTCG
1637749 TTCATTTATG-T-
1 TTCATTTATGTTA
1637760 TT-ATTTATGTTAA
1 TTCATTTATGTT-A
1637773 TTCATTTATG---
1 TTCATTTATGTTA
*
1637783 TTCATTTATTTTCA
1 TTCATTTATGTT-A
1637797 TTCATTTATGTT
1 TTCATTTATGTT
1637809 CGAACAGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
10 16 0.41
11 3 0.08
13 2 0.05
14 18 0.46
ACGTcount: A:0.22, C:0.08, G:0.07, T:0.63
Consensus pattern (13 bp):
TTCATTTATGTTA
Found at i:1638107 original size:20 final size:21
Alignment explanation
Indices: 1638061--1638115 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
1638051 AAGTTTATTT
*
1638061 TTTGTGTTTGTGTTATTCGTTA
1 TTTGTGTTTGT-TCATTCGTTA
* *
1638083 ATTGTGTTTGTTCATTTG-TA
1 TTTGTGTTTGTTCATTCGTTA
*
1638103 TTTGTGTATGTTC
1 TTTGTGTTTGTTC
1638116 GTTTATCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 13 0.46
21 5 0.18
22 10 0.36
ACGTcount: A:0.11, C:0.05, G:0.22, T:0.62
Consensus pattern (21 bp):
TTTGTGTTTGTTCATTCGTTA
Found at i:1638252 original size:51 final size:51
Alignment explanation
Indices: 1638188--1638303 Score: 223
Period size: 51 Copynumber: 2.3 Consensus size: 51
1638178 AAAAAAATTA
*
1638188 TTCGTTTATGTTCGTTTATTTATTAAATGAACGAACATAAAAATATTTCTG
1 TTCGTGTATGTTCGTTTATTTATTAAATGAACGAACATAAAAATATTTCTG
1638239 TTCGTGTATGTTCGTTTATTTATTAAATGAACGAACATAAAAATATTTCTG
1 TTCGTGTATGTTCGTTTATTTATTAAATGAACGAACATAAAAATATTTCTG
1638290 TTCGTGTATGTTCG
1 TTCGTGTATGTTCG
1638304 ATTCGTTTAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (51 bp):
TTCGTGTATGTTCGTTTATTTATTAAATGAACGAACATAAAAATATTTCTG
Found at i:1640467 original size:22 final size:22
Alignment explanation
Indices: 1640441--1640482 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1640431 ATTAAAATGA
1640441 AATTAAACTATTCAAAAGTTTG
1 AATTAAACTATTCAAAAGTTTG
*
1640463 AATTAAACTATTCAATAGTT
1 AATTAAACTATTCAAAAGTT
1640483 AGTTAAGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (22 bp):
AATTAAACTATTCAAAAGTTTG
Found at i:1649366 original size:17 final size:18
Alignment explanation
Indices: 1649344--1649377 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1649334 CCCTGTTATT
1649344 TGTTATTA-TTTCATAAA
1 TGTTATTACTTTCATAAA
1649361 TGTTATTACTTTCATAA
1 TGTTATTACTTTCATAA
1649378 TATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (18 bp):
TGTTATTACTTTCATAAA
Found at i:1649505 original size:11 final size:11
Alignment explanation
Indices: 1649491--1649551 Score: 74
Period size: 11 Copynumber: 5.7 Consensus size: 11
1649481 TAATCATTAA
1649491 ATTATTAAATT
1 ATTATTAAATT
1649502 ATTA-TAAATT
1 ATTATTAAATT
1649512 AATTATTAAA-T
1 -ATTATTAAATT
1649523 -TTATTAAATT
1 ATTATTAAATT
* *
1649533 ATTATAAAATA
1 ATTATTAAATT
1649544 ATTATTAA
1 ATTATTAA
1649552 TTTTCACTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
9 8 0.19
10 7 0.16
11 24 0.56
12 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:1649517 original size:14 final size:14
Alignment explanation
Indices: 1649498--1649550 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1649488 TAAATTATTA
1649498 AATTATTATAAATT
1 AATTATTATAAATT
1649512 AATTATTA-AATTTATT
1 AATTATTATAA---ATT
*
1649528 AAATTATTATAAAAT
1 -AATTATTATAAATT
1649543 AATTATTA
1 AATTATTA
1649551 ATTTTCACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 2 0.06
14 16 0.48
15 2 0.06
16 3 0.09
17 8 0.24
18 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTATTATAAATT
Found at i:1649528 original size:9 final size:8
Alignment explanation
Indices: 1649486--1649536 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
1649476 TAAAATAATC
1649486 ATTAAATT
1 ATTAAATT
1649494 ATTAAATT
1 ATTAAATT
1649502 ATTATAA--
1 ATTA-AATT
1649509 ATT-AATT
1 ATTAAATT
1649516 ATTAAATTT
1 ATTAAA-TT
1649525 ATTAAATT
1 ATTAAATT
1649533 ATTA
1 ATTA
1649537 TAAAATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
5 2 0.05
7 6 0.16
8 20 0.53
9 10 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
ATTAAATT
Found at i:1649530 original size:31 final size:30
Alignment explanation
Indices: 1649473--1649551 Score: 131
Period size: 31 Copynumber: 2.6 Consensus size: 30
1649463 ATTTTAAAAG
*
1649473 TTATAAAATAATCATTAAATTATTAAATTA
1 TTATAAAATAATTATTAAATTATTAAATTA
*
1649503 TTATAAATTAATTATTAAATTTATTAAATTA
1 TTATAAAATAATTATTAAA-TTATTAAATTA
1649534 TTATAAAATAATTATTAA
1 TTATAAAATAATTATTAA
1649552 TTTTCACTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 17 0.38
31 28 0.62
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TTATAAAATAATTATTAAATTATTAAATTA
Found at i:1649573 original size:31 final size:31
Alignment explanation
Indices: 1649477--1649574 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
1649467 TAAAAGTTAT
* * *
1649477 AAAATAATCATTAAA-TTATTAAATTATTAT
1 AAAATAATTATTAAATTTACTAAATTATTAC
* * *
1649507 AAATTAATTATTAAATTTATTAAATTATTAT
1 AAAATAATTATTAAATTTACTAAATTATTAC
* *
1649538 AAAATAATTATTAATTTTCACT-AATTTTTAC
1 AAAATAATTATTAAATTT-ACTAAATTATTAC
1649569 AAAATA
1 AAAATA
1649575 GCCATTAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
30 13 0.22
31 44 0.75
32 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (31 bp):
AAAATAATTATTAAATTTACTAAATTATTAC
Found at i:1650440 original size:21 final size:22
Alignment explanation
Indices: 1650403--1650456 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1650393 ACCCTGAAAT
* *
1650403 AAAAAAAATTAT--TTTTATTC
1 AAAAAAAATAATGATTTAATTC
* *
1650423 AATAAAAATAATGATTTAATTG
1 AAAAAAAATAATGATTTAATTC
1650445 AAAAAAAATAAT
1 AAAAAAAATAAT
1650457 ATATAGAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAAAAAATAATGATTTAATTC
Found at i:1650953 original size:15 final size:15
Alignment explanation
Indices: 1650933--1651144 Score: 205
Period size: 15 Copynumber: 13.5 Consensus size: 15
1650923 TAATAAGGTT
1650933 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1650948 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1650963 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1650978 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1650993 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
1651008 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
1651027 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
1651045 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
1651059 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
1651077 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1651092 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* *
1651106 ATTTATTAGTATAAATTG
1 ATTTATT--T-TAAAATA
1651124 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1651138 ATTTATT
1 ATTTATT
1651145 AGTATAGATT
Statistics
Matches: 167, Mismatches: 15, Indels: 31
0.78 0.07 0.15
Matches are distributed among these distances:
14 34 0.20
15 87 0.52
16 8 0.05
17 4 0.02
18 21 0.13
19 1 0.01
20 2 0.01
21 4 0.02
22 6 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1651059 original size:14 final size:14
Alignment explanation
Indices: 1651030--1651144 Score: 113
Period size: 14 Copynumber: 7.5 Consensus size: 14
1651020 ATATGGATTG
1651030 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
1651045 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1651059 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
1651077 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
1651092 ATTTATTTTAAATA
1 ATTTATTTTAAATA
*
1651106 ATTTATTAGTATAAATTG
1 ATTTATT--T-TAAA-TA
1651124 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1651138 ATTTATT
1 ATTTATT
1651145 AGTATAGATT
Statistics
Matches: 85, Mismatches: 7, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
14 32 0.38
15 26 0.31
16 4 0.05
17 5 0.06
18 18 0.21
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1651079 original size:47 final size:48
Alignment explanation
Indices: 1650933--1651144 Score: 283
Period size: 47 Copynumber: 4.5 Consensus size: 48
1650923 TAATAAGGTT
* *
1650933 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTA-TA--AAATA
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTAGTATGAATTG
* * * *
1650978 ATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAAAT-AA-T-TTAT-TAGTATGAATTG
1651030 ATTTATTTTAAAATAATTTATTTT-AAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTAGTATGAATTG
*
1651077 ATTTATTTTAAAATAATTTATTTT-AAATAATTTATTAGTATAAATTG
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTAGTATGAATTG
1651124 ATTTATTTT-AAATAATTTATT
1 ATTTATTTTAAAATAATTTATT
1651145 AGTATAGATT
Statistics
Matches: 150, Mismatches: 10, Indels: 13
0.87 0.06 0.08
Matches are distributed among these distances:
45 28 0.19
46 14 0.09
47 65 0.43
48 8 0.05
49 2 0.01
50 4 0.03
51 4 0.03
52 25 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (48 bp):
ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTAGTATGAATTG
Found at i:1651131 original size:32 final size:32
Alignment explanation
Indices: 1651092--1651167 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
1651082 TTTTAAAATA
*
1651092 ATTTATTTTAAATAATTTATTAGTATAAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
1651124 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
1651156 ATTTATTTTAAA
1 ATTTATTTTAAA
1651168 ATATGGATTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTG
Found at i:1651159 original size:18 final size:17
Alignment explanation
Indices: 1651059--1651162 Score: 62
Period size: 18 Copynumber: 6.4 Consensus size: 17
1651049 ATTTTAAATA
1651059 ATTTATTAGTATGAATTG
1 ATTTATTAGTAT-AATTG
* * *
1651077 ATTTATT-TTA-AAATA
1 ATTTATTAGTATAATTG
* *
1651092 ATTTATT--T-TAAATA
1 ATTTATTAGTATAATTG
1651106 ATTTATTAGTATAAATTG
1 ATTTATTAGTAT-AATTG
* *
1651124 ATTTATT--T-TAAATA
1 ATTTATTAGTATAATTG
1651138 ATTTATTAGTATAGATTG
1 ATTTATTAGTATA-ATTG
1651156 ATTTATT
1 ATTTATT
1651163 TTAAAATATG
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
14 23 0.34
15 11 0.16
16 3 0.04
17 5 0.07
18 26 0.38
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (17 bp):
ATTTATTAGTATAATTG
Found at i:1651256 original size:22 final size:22
Alignment explanation
Indices: 1651227--1651420 Score: 138
Period size: 22 Copynumber: 8.0 Consensus size: 22
1651217 AATTTATTGG
1651227 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1651249 TATAGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
** *
1651273 TTTATTAATATGGATTGATTTATTTTAAAA
1 --TATGGAT-T-GATTTA-TT---TTAAAA
1651303 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1651325 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
1651349 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
1651379 TATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAAA
1651400 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1651421 TAATTTATTA
Statistics
Matches: 138, Mismatches: 13, Indels: 42
0.72 0.07 0.22
Matches are distributed among these distances:
21 21 0.15
22 45 0.33
23 4 0.03
24 4 0.03
25 4 0.03
26 20 0.14
27 4 0.03
28 20 0.14
29 4 0.03
30 4 0.03
31 4 0.03
32 4 0.03
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1651264 original size:54 final size:54
Alignment explanation
Indices: 1651197--1651915 Score: 323
Period size: 54 Copynumber: 13.5 Consensus size: 54
1651187 TGTAGTTGTG
*
1651197 TGGATTGATTTATTTTAAATAATTTATTGGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
* *
1651251 TAGATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1651305 TGGATTGATTTA-TTT---TAA---A--A-TATGGATTGATTTATTTT-AAATAA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-A
** ** * ** * * *
1651349 TTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATA
1 TGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1651402 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
* * * ** * * *
1651455 ---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTATTTTAAAATA
* * * * * *
1651510 TGGATTGATTTATTATT--GTAGTTGTA-T-GGATTGATTTATTTTAAATAATTTATTAATA
1 TGGATTGATTTATT-TTAAATAATT-TATTAGTATGGATTGA-TTT--AT--TTTA-AAATA
** ** * ** * * *
1651568 TGGATTGATTTATTTTAAA-ATATGAATT-G-ATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATA
** ** * ** * * *
1651622 TGGATTGATTTATTTTAAA-ATATGGATT-GT-TTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATA
* *
1651676 TAGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
*
1651730 TGGATTGATTTA--TT--AT--TGTAGTT-GTATGGA-TGATTTATTTTAATAAT-
1 TGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAA-AATA
* * * * * * * * ***
1651777 T-TATT-A-GTATGGATTGATTATTTTA-AAATATGGATTGATTTATTATTGTAGTTGTA
1 TGGATTGATTTAT--TTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATA
* *
1651833 TGGATTGAATTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1651887 TGGATTGATTTATTTTAAATAATTTATTA
1 TGGATTGATTTATTTTAAATAATTTATTA
1651916 TTGTAGCTGT
Statistics
Matches: 523, Mismatches: 83, Indels: 118
0.72 0.11 0.16
Matches are distributed among these distances:
43 4 0.01
44 25 0.05
45 3 0.01
46 8 0.02
47 15 0.03
48 15 0.03
49 4 0.01
50 22 0.04
51 9 0.02
52 32 0.06
53 37 0.07
54 233 0.45
55 25 0.05
56 6 0.01
57 22 0.04
58 52 0.10
59 11 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
Found at i:1651438 original size:32 final size:32
Alignment explanation
Indices: 1651400--1651484 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
1651390 TTATTTTAAA
1651400 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
1651432 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
1651464 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1651485 ATATGGATTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:1651489 original size:22 final size:22
Alignment explanation
Indices: 1651464--1651523 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
1651454 AATTTATTTG
1651464 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1651486 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1651508 TATGGATTGATTTATT
1 TATGGATTGATTTATT
1651524 ATTGTAGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1651575 original size:32 final size:32
Alignment explanation
Indices: 1651534--1651726 Score: 183
Period size: 32 Copynumber: 6.7 Consensus size: 32
1651524 ATTGTAGTTG
1651534 TATGGATTGATTTATTTTAAATAATTTATTAA
1 TATGGATTGATTTATTTTAAATAATTTATTAA
1651566 TATGGATTGATTTA-TTT---T-A---A--AA
1 TATGGATTGATTTATTTTAAATAATTTATTAA
* *
1651588 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAA
1651620 TATGGATTGATTTA-TTT---T-A---A--AA
1 TATGGATTGATTTATTTTAAATAATTTATTAA
* *
1651642 TATGGATTGTTTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAA
* **
1651674 TATAGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAA
1651706 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1651727 ATATGGATTG
Statistics
Matches: 131, Mismatches: 10, Indels: 40
0.72 0.06 0.22
Matches are distributed among these distances:
22 29 0.22
23 6 0.05
24 2 0.02
26 2 0.02
27 4 0.03
28 2 0.02
30 2 0.02
31 6 0.05
32 78 0.60
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAA
Found at i:1651589 original size:22 final size:22
Alignment explanation
Indices: 1651564--1651608 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1651554 ATAATTTATT
*
1651564 AATATGGATTGATTTATTTTAA
1 AATATGAATTGATTTATTTTAA
1651586 AATATGAATTGATTTATTTTAA
1 AATATGAATTGATTTATTTTAA
1651608 A
1 A
1651609 TAATTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
AATATGAATTGATTTATTTTAA
Found at i:1651613 original size:18 final size:21
Alignment explanation
Indices: 1651357--1651422 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1651347 AATTTATTAG
*
1651357 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTT-AAA
*
1651379 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
*
1651400 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1651421 TA
1 TA
1651423 ATTTATTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 26 0.59
22 18 0.41
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (21 bp):
TATGAATTGATTTATTTTAAA
Found at i:1651645 original size:22 final size:22
Alignment explanation
Indices: 1651620--1651662 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1651610 AATTTATTAG
1651620 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1651642 TATGGATTGTTTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1651663 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1651671 original size:14 final size:14
Alignment explanation
Indices: 1651652--1651704 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1651642 TATGGATTGT
1651652 TTTATTTTAAATAA
1 TTTATTTTAAATAA
* *
1651666 TTTATTAGTATAGATTGA
1 TTTATT--T-TA-AATAA
1651684 TTTATTTTAAATAA
1 TTTATTTTAAATAA
1651698 TTTATTT
1 TTTATTT
1651705 GTATGGATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 16 0.52
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.29
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTATTTTAAATAA
Found at i:1651877 original size:18 final size:19
Alignment explanation
Indices: 1651854--1651900 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 19
1651844 ATTTTAAATA
1651854 ATTTATT-AATATGGATTG
1 ATTTATTAAATATGGATTG
1651872 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT-AAATATGGATTG
1651894 ATTTATT
1 ATTTATT
1651901 TTAAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.20
20 4 0.16
22 16 0.64
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
ATTTATTAAATATGGATTG
Found at i:1651886 original size:22 final size:22
Alignment explanation
Indices: 1651861--1651905 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1651851 ATAATTTATT
1651861 AATATGGATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAA
1651883 AATATGGATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAA
1651905 A
1 A
1651906 TAATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (22 bp):
AATATGGATTGATTTATTTTAA
Found at i:1651965 original size:31 final size:31
Alignment explanation
Indices: 1651930--1651988 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1651920 AGCTGTATGG
* *
1651930 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
1651961 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
1651989 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:1652027 original size:16 final size:16
Alignment explanation
Indices: 1652006--1652048 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1651996 GTTTAAAAAA
1652006 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
1652022 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
* *
1652038 TTAGTTCATTT
1 TCAGTTTATTT
1652049 TAACAGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:1653567 original size:23 final size:24
Alignment explanation
Indices: 1653540--1653599 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
1653530 TAAATATTGT
1653540 ATTTTAATTAAATTAT-ATTTAAG
1 ATTTTAATTAAATTATAATTTAAG
* *
1653563 ATTTTAATTAATTTATAATTTAAT
1 ATTTTAATTAAATTATAATTTAAG
1653587 ATTTT-A-TAAATTA
1 ATTTTAATTAAATTA
1653600 ATATAATGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.18
23 16 0.48
24 11 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTTAATTAAATTATAATTTAAG
Found at i:1653594 original size:15 final size:15
Alignment explanation
Indices: 1653574--1653603 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1653564 TTTTAATTAA
*
1653574 TTTATAATTTAATAT
1 TTTATAAATTAATAT
1653589 TTTATAAATTAATAT
1 TTTATAAATTAATAT
1653604 AATGATACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATAAATTAATAT
Found at i:1655442 original size:20 final size:20
Alignment explanation
Indices: 1655419--1655456 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1655409 GACTATTTTG
1655419 TAATAATTTGATAAATTTAA
1 TAATAATTTGATAAATTTAA
* *
1655439 TAATTATTTTATAAATTT
1 TAATAATTTGATAAATTT
1655457 TAAAAAAATT
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:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TAATAATTTGATAAATTTAA
Found at i:1656215 original size:15 final size:16
Alignment explanation
Indices: 1656186--1656220 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
1656176 CTCTCTTCAG
1656186 TTATTATATGTAGGCT
1 TTATTATATGTAGGCT
1656202 TTATTATA-GTAGGCT
1 TTATTATATGTAGGCT
1656217 TTAT
1 TTAT
1656221 CTAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (16 bp):
TTATTATATGTAGGCT
Found at i:1656239 original size:2 final size:2
Alignment explanation
Indices: 1656234--1656284 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1656224 GGAAAAAACA
1656234 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
1656276 AT AT AT AT A
1 AT AT AT AT A
1656285 ATTTAAAAGT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.