Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 16
Found at i:1380719 original size:55 final size:55
Alignment explanation
Indices: 1380653--1380789 Score: 220
Period size: 55 Copynumber: 2.5 Consensus size: 55
1380643 ACCTCCTGGA
1380653 GGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAATCTTACATGG
1 GGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAATCTTACATGG
* * *
1380708 GGGTATCGGTACCCTCCAAGAAATCTGTTATTTCTCGGAGTCAAATCTTACATGG
1 GGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAATCTTACATGG
* * *
1380763 AGGTATCGGTACCCTCTGGGCAATCTG
1 GGGTATCGGTACCCTCCGAGCAATCTG
1380790 GTTTTTCAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 74 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (55 bp):
GGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAATCTTACATGG
Found at i:1386020 original size:20 final size:21
Alignment explanation
Indices: 1385982--1386020 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1385972 TTGTTTCTCA
* *
1385982 AAATCTTTTATTTTGACTTGC
1 AAATCTTTAATCTTGACTTGC
1386003 AAATCTTTAATCTT-ACTT
1 AAATCTTTAATCTTGACTT
1386021 TCGAGTTCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.51
Consensus pattern (21 bp):
AAATCTTTAATCTTGACTTGC
Found at i:1388144 original size:21 final size:21
Alignment explanation
Indices: 1388118--1388169 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1388108 CAAAGGAGTA
1388118 GTATCGGTACCATTGGCTATG
1 GTATCGGTACCATTGGCTATG
1388139 GTATCGGTACCATTGGCTATG
1 GTATCGGTACCATTGGCTATG
*
1388160 GTATCAGTAC
1 GTATCGGTAC
1388170 TACTATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (21 bp):
GTATCGGTACCATTGGCTATG
Found at i:1388438 original size:18 final size:18
Alignment explanation
Indices: 1388415--1388470 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
1388405 TTTGTGATAT
*
1388415 TCGAATATAATATTTAAA
1 TCGAATATAAAATTTAAA
* *
1388433 TCGAATACAAAATTTGAA
1 TCGAATATAAAATTTAAA
1388451 TCGAATATAAAATCTTAAA
1 TCGAATATAAAAT-TTAAA
1388470 T
1 T
1388471 TTCATTAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 27 0.84
19 5 0.16
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (18 bp):
TCGAATATAAAATTTAAA
Found at i:1389671 original size:5 final size:5
Alignment explanation
Indices: 1389661--1389690 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1389651 ATTGTAATAA
1389661 TATTT TATTT TATTT T-TTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT T
1389691 TTCAATTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TATTT
Found at i:1389682 original size:14 final size:14
Alignment explanation
Indices: 1389663--1389692 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1389653 TGTAATAATA
1389663 TTTTATTTTATTTT
1 TTTTATTTTATTTT
1389677 TTTTATTTTATTTT
1 TTTTATTTTATTTT
1389691 TT
1 TT
1389693 CAATTATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTATTTTATTTT
Found at i:1405746 original size:24 final size:26
Alignment explanation
Indices: 1405716--1405774 Score: 104
Period size: 24 Copynumber: 2.3 Consensus size: 26
1405706 TATTCAAGAT
1405716 TGGCAGCCACATTTGTTGAAAGTT-G
1 TGGCAGCCACATTTGTTGAAAGTTGG
1405741 -GGCAGCCACATTTGTTGAAAGTTGG
1 TGGCAGCCACATTTGTTGAAAGTTGG
1405766 TGGCAGCCA
1 TGGCAGCCA
1405775 GCGGCTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 23 0.72
25 1 0.03
26 8 0.25
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.27
Consensus pattern (26 bp):
TGGCAGCCACATTTGTTGAAAGTTGG
Found at i:1413140 original size:29 final size:29
Alignment explanation
Indices: 1413098--1413155 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1413088 CAGTGTTGGC
1413098 TGTAGGTCGCCATGCCCTCCGGGCGACCT
1 TGTAGGTCGCCATGCCCTCCGGGCGACCT
*
1413127 TGTAGGTCGTCATGCCCTCCGGGCGACCT
1 TGTAGGTCGCCATGCCCTCCGGGCGACCT
1413156 ACCCTCGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.10, C:0.36, G:0.31, T:0.22
Consensus pattern (29 bp):
TGTAGGTCGCCATGCCCTCCGGGCGACCT
Found at i:1413211 original size:10 final size:10
Alignment explanation
Indices: 1413157--1413279 Score: 66
Period size: 10 Copynumber: 11.3 Consensus size: 10
1413147 GGGCGACCTA
* *
1413157 CCCTCGGCTT
1 CCCTCGGATG
*
1413167 CCCTCGGATT
1 CCCTCGGATG
*
1413177 CCCTCGCATAG
1 CCCTCGGAT-G
*
1413188 CTCGCTCGGTTG
1 C-C-CTCGGATG
1413200 CCCTCGGATG
1 CCCTCGGATG
*
1413210 CCCTCGCATAG
1 CCCTCGGAT-G
*
1413221 CTCGTTCGGATG
1 C-C-CTCGGATG
*
1413233 GCCTCGGATG
1 CCCTCGGATG
*
1413243 CTCTCGGATAG
1 CCCTCGGAT-G
1413254 CCTCGGTCGGATG
1 CC-C--TCGGATG
*
1413267 GCCTCGGATG
1 CCCTCGGATG
1413277 CCC
1 CCC
1413280 AGCGTGTTGG
Statistics
Matches: 87, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
10 55 0.63
11 7 0.08
12 7 0.08
13 12 0.14
14 6 0.07
ACGTcount: A:0.10, C:0.37, G:0.28, T:0.24
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:1413269 original size:34 final size:33
Alignment explanation
Indices: 1413168--1413279 Score: 152
Period size: 33 Copynumber: 3.4 Consensus size: 33
1413158 CCTCGGCTTC
* * *
1413168 CCTCGGATTCCCTCGCATAGCTCGCTCGGTTGC
1 CCTCGGATGCCCTCGCATAGCTCGCTCGGATGG
*
1413201 CCTCGGATGCCCTCGCATAGCTCGTTCGGATGG
1 CCTCGGATGCCCTCGCATAGCTCGCTCGGATGG
* * *
1413234 CCTCGGATGCTCTCGGATAGCCTCGGTCGGATGG
1 CCTCGGATGCCCTCGCATAG-CTCGCTCGGATGG
1413268 CCTCGGATGCCC
1 CCTCGGATGCCC
1413280 AGCGTGTTGG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 47 0.67
34 23 0.33
ACGTcount: A:0.11, C:0.36, G:0.29, T:0.24
Consensus pattern (33 bp):
CCTCGGATGCCCTCGCATAGCTCGCTCGGATGG
Found at i:1413353 original size:29 final size:29
Alignment explanation
Indices: 1413316--1413373 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1413306 GCAATCTCTT
*
1413316 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
1413345 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
1413374 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:1420941 original size:42 final size:42
Alignment explanation
Indices: 1420887--1420975 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
1420877 GAGAGTATCA
** * * *
1420887 ATACTGGTGTTACGGTTTCGATACTACTATATTGTAGTATGG
1 ATACTGGTGTTACAATATCGATAATACTATATAGTAGTATGG
*
1420929 ATACTAGG-GTTACAATATCGATAATACTATATAGTAGTATTG
1 ATACT-GGTGTTACAATATCGATAATACTATATAGTAGTATGG
1420971 ATACT
1 ATACT
1420976 CCTTTAAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
42 38 0.95
43 2 0.05
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38
Consensus pattern (42 bp):
ATACTGGTGTTACAATATCGATAATACTATATAGTAGTATGG
Found at i:1440966 original size:17 final size:17
Alignment explanation
Indices: 1440940--1440979 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1440930 TCAATTATTT
* * *
1440940 TAATATATTTTTATTAA
1 TAATAAATTTTAAATAA
1440957 TAATAAATTTTAAATAA
1 TAATAAATTTTAAATAA
1440974 TAATAA
1 TAATAA
1440980 GTCAAAGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATAAATTTTAAATAA
Found at i:1445379 original size:37 final size:38
Alignment explanation
Indices: 1445337--1445423 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 38
1445327 CGATATAAAA
*
1445337 CACTACGGTG-TACAAGGTGGGTAAAGCTCGACCTCAG
1 CACTACGGTGATACAAGGTGAGTAAAGCTCGACCTCAG
* **
1445374 TACTACGGTGCATTATTAGGTGAGTAAAGCTCGACCTCAG
1 CACTACGGTG-A-TACAAGGTGAGTAAAGCTCGACCTCAG
*
1445414 CACTGCGGTG
1 CACTACGGTG
1445424 CAATATTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
37 9 0.22
40 32 0.78
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (38 bp):
CACTACGGTGATACAAGGTGAGTAAAGCTCGACCTCAG
Found at i:1445401 original size:40 final size:40
Alignment explanation
Indices: 1445351--1445430 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
1445341 ACGGTGTACA
* * *
1445351 AGGTGGGTAAAGCTCGACCTCAGTACTACGGTGCATTATT
1 AGGTGAGTAAAGCTCGACCTCAGCACTACGGTGCAATATT
*
1445391 AGGTGAGTAAAGCTCGACCTCAGCACTGCGGTGCAATATT
1 AGGTGAGTAAAGCTCGACCTCAGCACTACGGTGCAATATT
1445431 TGACTCCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
AGGTGAGTAAAGCTCGACCTCAGCACTACGGTGCAATATT
Found at i:1446833 original size:21 final size:21
Alignment explanation
Indices: 1446807--1446860 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1446797 TTTAAAGGGG
1446807 TAGTATCGATACTCGTTCATA
1 TAGTATCGATACTCGTTCATA
1446828 TAGTATCGATACTCGTTCATA
1 TAGTATCGATACTCGTTCATA
1446849 TAGTATCGATAC
1 TAGTATCGATAC
1446861 CAGGACATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (21 bp):
TAGTATCGATACTCGTTCATA
Found at i:1447087 original size:29 final size:30
Alignment explanation
Indices: 1447018--1447076 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1447008 CAATTTAAGG
1447018 CAAAATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
*
1447048 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1447077 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1447182 original size:21 final size:21
Alignment explanation
Indices: 1447156--1447196 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1447146 AGGGTGTCAA
1447156 AGTGCATCCATACATCCCTGC
1 AGTGCATCCATACATCCCTGC
1447177 AGTGCATCCATACATCCCTG
1 AGTGCATCCATACATCCCTG
1447197 TAGTTGTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATACATCCCTGC
Found at i:1456600 original size:13 final size:14
Alignment explanation
Indices: 1456582--1456616 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
1456572 GGTCAAAGGA
1456582 GGTCAACGGTC-AC
1 GGTCAACGGTCAAC
1456595 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
1456609 GGTCAACG
1 GGTCAACG
1456617 ATCGGGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.26, C:0.29, G:0.31, T:0.14
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:1456603 original size:7 final size:7
Alignment explanation
Indices: 1456582--1456616 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
1456572 GGTCAAAGGA
1456582 GGTCAAC
1 GGTCAAC
1456589 GGTC-AC
1 GGTCAAC
1456595 GGTCAAC
1 GGTCAAC
1456602 GGTCAAC
1 GGTCAAC
1456609 GGTCAAC
1 GGTCAAC
1456616 G
1 G
1456617 ATCGGGTCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.26, C:0.29, G:0.31, T:0.14
Consensus pattern (7 bp):
GGTCAAC
Found at i:1456631 original size:17 final size:17
Alignment explanation
Indices: 1456609--1456647 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1456599 AACGGTCAAC
1456609 GGTCAACGATCGGGTCG
1 GGTCAACGATCGGGTCG
*
1456626 GGTCAACGGTCGGGTCG
1 GGTCAACGATCGGGTCG
1456643 GGTCA
1 GGTCA
1456648 GGTCAGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.23, G:0.44, T:0.18
Consensus pattern (17 bp):
GGTCAACGATCGGGTCG
Found at i:1459163 original size:29 final size:30
Alignment explanation
Indices: 1459094--1459152 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1459084 CAATTTAAGG
1459094 CAAAATGA-TTTTGGACTTGAATTGAATTTA
1 CAAAAT-ATTTTTGGACTTGAATTGAATTTA
1459124 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATATTTTTGGACTTGAATTGAATTTA
1459153 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (30 bp):
CAAAATATTTTTGGACTTGAATTGAATTTA
Found at i:1459258 original size:21 final size:20
Alignment explanation
Indices: 1459232--1459329 Score: 99
Period size: 21 Copynumber: 4.7 Consensus size: 20
1459222 AGGGTGTCAA
1459232 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCAT-CCTGC
1459253 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCAT-CCTGC
*
1459274 AGTGTATCCATGCA-CCTGCAC
1 AGTGCATCCATGCATCCTG--C
* * *
1459295 TAATGCATCGATGCATCATGC
1 -AGTGCATCCATGCATCCTGC
*
1459316 AATGCATCCATGCA
1 AGTGCATCCATGCA
1459330 CTCAAACATC
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 36 0.54
22 11 0.16
23 3 0.04
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (20 bp):
AGTGCATCCATGCATCCTGC
Found at i:1459321 original size:20 final size:18
Alignment explanation
Indices: 1459296--1459404 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
1459286 CACCTGCACT
1459296 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATC-T-C
*
1459316 AATGCATCCATGCA-CTC
1 AATGCATCGATGCATCTC
* *
1459333 AA-ACATCGAATGCA-CTT
1 AATGCATCG-ATGCATCTC
* *
1459350 ATTGCATCGATGCACCCTAC
1 AATGCATCGATGCA-TCT-C
*
1459370 CATGCATCGATGCATCCTGC
1 AATGCATCGATGCAT-CT-C
* *
1459390 CATGCATCCATGCAT
1 AATGCATCGATGCAT
1459405 TAAGGCTGCA
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
16 4 0.06
17 16 0.23
18 6 0.08
19 3 0.04
20 42 0.59
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (18 bp):
AATGCATCGATGCATCTC
Found at i:1464477 original size:31 final size:30
Alignment explanation
Indices: 1464442--1464578 Score: 114
Period size: 31 Copynumber: 4.4 Consensus size: 30
1464432 CTAATGTGAC
* * * *
1464442 TCTTGTGTAGGCTCTACGGCCCTGGGATTTT
1 TCTTGGGTAGGC-CTGCGGCCCTGAGATCTT
* * *
1464473 TCTTGGGTAGGCCTTGTGGCCCTAAGATCAT
1 TCTTGGGTAGGCC-TGCGGCCCTGAGATCTT
*
1464504 TCTTGGGTAGGCCCTGCAGCCCTGAGATCTT
1 TCTTGGGTAGG-CCTGCGGCCCTGAGATCTT
* * * *
1464535 TCTTGTGTAGGCC-CCGTTGCCCAGAGAACTT
1 TCTTGGGTAGGCCTGCG--GCCCTGAGATCTT
1464566 TCTTGGGTAGGCC
1 TCTTGGGTAGGCC
1464579 CATAGGCCCC
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
29 1 0.01
30 3 0.04
31 79 0.93
32 2 0.02
ACGTcount: A:0.13, C:0.26, G:0.29, T:0.32
Consensus pattern (30 bp):
TCTTGGGTAGGCCTGCGGCCCTGAGATCTT
Found at i:1464539 original size:62 final size:62
Alignment explanation
Indices: 1464442--1464579 Score: 152
Period size: 62 Copynumber: 2.2 Consensus size: 62
1464432 CTAATGTGAC
* * * * * ** *
1464442 TCTTGTGTAGGCTCTACGGCCCTGGGATTTTTCTTGGGTAGGCCTTGTGGCCCTA-AGATCAT
1 TCTTGGGTAGGCCCTACAGCCCTGAGATCTTTCTTGGGTAGGCCCCGTGGCCC-AGAGAACAT
* * * *
1464504 TCTTGGGTAGGCCCTGCAGCCCTGAGATCTTTCTTGTGTAGGCCCCGTTGCCCAGAGAACTT
1 TCTTGGGTAGGCCCTACAGCCCTGAGATCTTTCTTGGGTAGGCCCCGTGGCCCAGAGAACAT
1464566 TCTTGGGTAGGCCC
1 TCTTGGGTAGGCCC
1464580 ATAGGCCCCA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
61 1 0.02
62 62 0.98
ACGTcount: A:0.13, C:0.26, G:0.29, T:0.32
Consensus pattern (62 bp):
TCTTGGGTAGGCCCTACAGCCCTGAGATCTTTCTTGGGTAGGCCCCGTGGCCCAGAGAACAT
Found at i:1464579 original size:31 final size:31
Alignment explanation
Indices: 1464471--1464579 Score: 121
Period size: 31 Copynumber: 3.5 Consensus size: 31
1464461 CCCTGGGATT
* *
1464471 TTTCTTGGGTAGGCCTTGTGGCCCTA-AGATC
1 TTTCTTGGGTAGGCCCTGTAGCCC-AGAGATC
* * *
1464502 ATTCTTGGGTAGGCCCTGCAGCCCTGAGATC
1 TTTCTTGGGTAGGCCCTGTAGCCCAGAGATC
* * * *
1464533 TTTCTTGTGTAGGCCCCGTTGCCCAGAGAAC
1 TTTCTTGGGTAGGCCCTGTAGCCCAGAGATC
1464564 TTTCTTGGGTAGGCCC
1 TTTCTTGGGTAGGCCC
1464580 ATAGGCCCCA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.14, C:0.27, G:0.28, T:0.31
Consensus pattern (31 bp):
TTTCTTGGGTAGGCCCTGTAGCCCAGAGATC
Found at i:1468174 original size:31 final size:31
Alignment explanation
Indices: 1468133--1468277 Score: 177
Period size: 31 Copynumber: 4.7 Consensus size: 31
1468123 AGCAACCCCA
* *
1468133 AGATCATTCTTGGGTAGGCCCTGCGACCCTG
1 AGATCTTTCTTGGGTAGGCCCTGCGGCCCTG
* * * *
1468164 GGATTTTTCTTGGGTAGGCCTTGTGGCCCTG
1 AGATCTTTCTTGGGTAGGCCCTGCGGCCCTG
*
1468195 AGATCATTCTTGGGTAGGCCCTGCGGCCCTG
1 AGATCTTTCTTGGGTAGGCCCTGCGGCCCTG
*
1468226 AGATCTTTCTTGGGTAGG-CCT-CGTAGCCTTG
1 AGATCTTTCTTGGGTAGGCCCTGCG--GCCCTG
*
1468257 AGAACTTTCTTGGGTAGGCCC
1 AGATCTTTCTTGGGTAGGCCC
1468278 ATAGGCCCCA
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
29 2 0.02
30 3 0.03
31 90 0.93
32 2 0.02
ACGTcount: A:0.13, C:0.25, G:0.31, T:0.31
Consensus pattern (31 bp):
AGATCTTTCTTGGGTAGGCCCTGCGGCCCTG
Found at i:1468206 original size:62 final size:62
Alignment explanation
Indices: 1468133--1468277 Score: 218
Period size: 62 Copynumber: 2.3 Consensus size: 62
1468123 AGCAACCCCA
* * * *
1468133 AGATCATTCTTGGGTAGGCCCTGCGACCCTGGGATTTTTCTTGGGTAGGCCTTGTGGCCCTG
1 AGATCATTCTTGGGTAGGCCCTGCGACCCTGAGATCTTTCTTGGGTAGGCCTCGTAGCCCTG
* *
1468195 AGATCATTCTTGGGTAGGCCCTGCGGCCCTGAGATCTTTCTTGGGTAGGCCTCGTAGCCTTG
1 AGATCATTCTTGGGTAGGCCCTGCGACCCTGAGATCTTTCTTGGGTAGGCCTCGTAGCCCTG
* *
1468257 AGAACTTTCTTGGGTAGGCCC
1 AGATCATTCTTGGGTAGGCCC
1468278 ATAGGCCCCA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 75 1.00
ACGTcount: A:0.13, C:0.25, G:0.31, T:0.31
Consensus pattern (62 bp):
AGATCATTCTTGGGTAGGCCCTGCGACCCTGAGATCTTTCTTGGGTAGGCCTCGTAGCCCTG
Found at i:1473854 original size:12 final size:12
Alignment explanation
Indices: 1473819--1473854 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1473809 TGTGGGAAGC
*
1473819 AGAGAGAGAAAG
1 AGAGAGAGATAG
*
1473831 AGAGAGACATAG
1 AGAGAGAGATAG
1473843 AGAGAGAGATAG
1 AGAGAGAGATAG
1473855 GAAGGACCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.39, T:0.06
Consensus pattern (12 bp):
AGAGAGAGATAG
Found at i:1479522 original size:21 final size:21
Alignment explanation
Indices: 1479496--1479543 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1479486 GTAAATAAGA
1479496 CGAGATAGATCGTGAGCTACT
1 CGAGATAGATCGTGAGCTACT
1479517 CGAGATAGATCGTGAGCTACT
1 CGAGATAGATCGTGAGCTACT
1479538 CGAGAT
1 CGAGAT
1479544 TGACTCAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (21 bp):
CGAGATAGATCGTGAGCTACT
Found at i:1480156 original size:31 final size:33
Alignment explanation
Indices: 1480102--1480176 Score: 104
Period size: 31 Copynumber: 2.4 Consensus size: 33
1480092 GAGTGAGTTT
*
1480102 AATAAT-TTTAAATTTATAAATTTTTCGAGTTA
1 AATAATATTTAAATTTATAAATTTTTCGAATTA
1480134 AATCAA-ATTTAAA-TT-TAAATTTTTCGAATTA
1 AAT-AATATTTAAATTTATAAATTTTTCGAATTA
1480165 AATAATATTTAA
1 AATAATATTTAA
1480177 CAATACTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 2 0.05
31 24 0.62
32 5 0.13
33 8 0.21
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (33 bp):
AATAATATTTAAATTTATAAATTTTTCGAATTA
Found at i:1487783 original size:35 final size:35
Alignment explanation
Indices: 1487737--1487807 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1487727 AAAAAAACGA
1487737 TGGTTTATGTACGGCGTGGAGAGAGACGTTTTAAG
1 TGGTTTATGTACGGCGTGGAGAGAGACGTTTTAAG
1487772 TGGTTTATGTACGGCGTGGAGAGAGACGTTTTAAG
1 TGGTTTATGTACGGCGTGGAGAGAGACGTTTTAAG
1487807 T
1 T
1487808 TTGTTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.37, T:0.32
Consensus pattern (35 bp):
TGGTTTATGTACGGCGTGGAGAGAGACGTTTTAAG
Found at i:1493638 original size:3 final size:3
Alignment explanation
Indices: 1493612--1493710 Score: 148
Period size: 3 Copynumber: 33.0 Consensus size: 3
1493602 TTTTGCCCAT
* *
1493612 TTA TTT TTA TTTA TGA TT- TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1493656 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1493702 TTA TTA TTA
1 TTA TTA TTA
1493711 AATAAATATT
Statistics
Matches: 88, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.05
3 78 0.89
4 6 0.07
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1503060 original size:1 final size:1
Alignment explanation
Indices: 1503045--1503337 Score: 199
Period size: 1 Copynumber: 293.0 Consensus size: 1
1503035 ATTCATCAGG
* * * * ** * * * *
1503045 AAAAGAAAAAGAAAAAAGAAAAAAGAAAAAAGGAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
1503110 AAAAAAGAAAAAGAAAAAAAAAAAGAAAAAGAGAAAAAAAAAAAAAGAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * * * *
1503175 AAAAAAAGAGAAAAGAAAAAGAAAAGAGAAAAAGAAAAAGAAAAGAGAAGAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
1503240 AGAAAAAAAAAGAAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAGAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
1503305 AGAAAATAAAAAAAGAAAATAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1503338 GAAATTGAAT
Statistics
Matches: 208, Mismatches: 84, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 208 1.00
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (1 bp):
A
Found at i:1503062 original size:7 final size:7
Alignment explanation
Indices: 1503045--1503337 Score: 357
Period size: 7 Copynumber: 43.3 Consensus size: 7
1503035 ATTCATCAGG
1503045 AAAAG-A
1 AAAAGAA
1503051 AAAAGAA
1 AAAAGAA
1503058 AAAAGAA
1 AAAAGAA
1503065 AAAAGAA
1 AAAAGAA
*
1503072 AAAAGGA
1 AAAAGAA
1503079 AAAAGAA
1 AAAAGAA
1503086 AAAAGAA
1 AAAAGAA
1503093 AAAAGAA
1 AAAAGAA
1503100 AAAAG-A
1 AAAAGAA
1503106 AAAA-AA
1 AAAAGAA
1503112 AAAAG-A
1 AAAAGAA
1503118 AAAAG-A
1 AAAAGAA
1503124 AAAA-AA
1 AAAAGAA
1503130 AAAAGAA
1 AAAAGAA
1503137 AAAGAGAA
1 AAA-AGAA
*
1503145 AAAAAAA
1 AAAAGAA
1503152 AAAAGAA
1 AAAAGAA
1503159 AAAA-AA
1 AAAAGAA
1503165 AAAAGAA
1 AAAAGAA
1503172 AAAA-AA
1 AAAAGAA
*
1503178 AAAAGAG
1 AAAAGAA
1503185 AAAAG-A
1 AAAAGAA
1503191 AAAAGAA
1 AAAAGAA
*
1503198 AAGAG-A
1 AAAAGAA
1503204 AAAAG-A
1 AAAAGAA
1503210 AAAAGAA
1 AAAAGAA
*
1503217 AAGAGAAGA
1 AAAAG-A-A
1503226 AAAAGAA
1 AAAAGAA
1503233 AAAA-AA
1 AAAAGAA
*
1503239 AAGAAAAA
1 AA-AAGAA
1503247 AAAAGAAA
1 AAAAG-AA
1503255 AAAAGAA
1 AAAAGAA
1503262 AAAAGAA
1 AAAAGAA
1503269 AAAAGAA
1 AAAAGAA
1503276 AAAAGAA
1 AAAAGAA
1503283 AAAAG-A
1 AAAAGAA
1503289 AAAAGAA
1 AAAAGAA
1503296 AAAAG-A
1 AAAAGAA
1503302 AAAAGAA
1 AAAAGAA
*
1503309 AATA-AA
1 AAAAGAA
1503315 AAAAGAA
1 AAAAGAA
1503322 AATAA-AA
1 AA-AAGAA
1503329 AAAAGAA
1 AAAAGAA
1503336 AA
1 AA
1503338 GAAATTGAAT
Statistics
Matches: 254, Mismatches: 13, Indels: 39
0.83 0.04 0.13
Matches are distributed among these distances:
6 82 0.32
7 145 0.57
8 22 0.09
9 5 0.02
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (7 bp):
AAAAGAA
Found at i:1503069 original size:14 final size:14
Alignment explanation
Indices: 1503045--1503337 Score: 357
Period size: 13 Copynumber: 21.6 Consensus size: 14
1503035 ATTCATCAGG
1503045 AAAAG-AAAAAGAA
1 AAAAGAAAAAAGAA
1503058 AAAAGAAAAAAGAA
1 AAAAGAAAAAAGAA
*
1503072 AAAAGGAAAAAGAA
1 AAAAGAAAAAAGAA
1503086 AAAAGAAAAAAGAA
1 AAAAGAAAAAAGAA
1503100 AAAAG-AAAAA-AA
1 AAAAGAAAAAAGAA
1503112 AAAAG-AAAAAG-A
1 AAAAGAAAAAAGAA
1503124 AAAA-AAAAAAGAA
1 AAAAGAAAAAAGAA
*
1503137 AAAGAGAAAAAAAAA
1 AAA-AGAAAAAAGAA
1503152 AAAAGAAAAAA-AA
1 AAAAGAAAAAAGAA
1503165 AAAAGAAAAAA-AA
1 AAAAGAAAAAAGAA
*
1503178 AAAAGAGAAAAG-A
1 AAAAGAAAAAAGAA
*
1503191 AAAAGAAAAGAG-A
1 AAAAGAAAAAAGAA
1503204 AAAAG-AAAAAGAA
1 AAAAGAAAAAAGAA
*
1503217 AAGAGAAGAAAAAGAA
1 AAAAG-A-AAAAAGAA
*
1503233 AAAA-AAAAGAAAAA
1 AAAAGAAAA-AAGAA
1503247 AAAAGAAAAAAAGAA
1 AAAAG-AAAAAAGAA
1503262 AAAAGAAAAAAGAA
1 AAAAGAAAAAAGAA
1503276 AAAAGAAAAAAG-A
1 AAAAGAAAAAAGAA
1503289 AAAAGAAAAAAG-A
1 AAAAGAAAAAAGAA
*
1503302 AAAAGAAAATA-AA
1 AAAAGAAAAAAGAA
1503315 AAAAGAAAATAA-AA
1 AAAAGAAAA-AAGAA
1503329 AAAAGAAAA
1 AAAAGAAAA
1503338 GAAATTGAAT
Statistics
Matches: 251, Mismatches: 13, Indels: 31
0.85 0.04 0.11
Matches are distributed among these distances:
12 28 0.11
13 98 0.39
14 90 0.36
15 20 0.08
16 15 0.06
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:1504545 original size:70 final size:70
Alignment explanation
Indices: 1504413--1504546 Score: 184
Period size: 70 Copynumber: 1.9 Consensus size: 70
1504403 AGGGGCATGT
* *
1504413 TGAAAGCCCATTTTAACTAAAAATGATCCATGTGGGGCATATTGAAAGCTCGCAGAAGTATGAAA
1 TGAAAGCCCATTTTAACTAAAAATGATCCATGTGGGGCATATTCAAAGCTCGCACAAGTATGAAA
1504478 CATTC
66 CATTC
* *
1504483 TGAAGGCCCATTTTAGAC-AGAAATGATCCATGTGGGGCAT-TTCAAAGGCTCGCATCAA-TATG
1 TGAAAGCCCATTTTA-ACTAAAAATGATCCATGTGGGGCATATTCAAA-GCTCGCA-CAAGTATG
1504545 AA
63 AA
1504547 TATTTGAGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
69 5 0.09
70 48 0.84
71 4 0.07
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (70 bp):
TGAAAGCCCATTTTAACTAAAAATGATCCATGTGGGGCATATTCAAAGCTCGCACAAGTATGAAA
CATTC
Found at i:1505068 original size:3 final size:3
Alignment explanation
Indices: 1505042--1505138 Score: 151
Period size: 3 Copynumber: 32.0 Consensus size: 3
1505032 TTTTACCCAT
* *
1505042 TTA TTT TTA TTTA TGA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1505087 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1505133 TTA TTA
1 TTA TTA
1505139 AATAAATATT
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
2 2 0.02
3 79 0.91
4 6 0.07
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1506257 original size:11 final size:11
Alignment explanation
Indices: 1506241--1506265 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1506231 AAATTAGTAC
1506241 TTTAATTATTA
1 TTTAATTATTA
1506252 TTTAATTATTA
1 TTTAATTATTA
1506263 TTT
1 TTT
1506266 TAGTCATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:1506278 original size:2 final size:2
Alignment explanation
Indices: 1506271--1506324 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1506261 TATTTTAGTC
1506271 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
1506313 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1506325 GAAAGATTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1506526 original size:16 final size:16
Alignment explanation
Indices: 1506505--1506540 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1506495 GTTGTTTTAG
1506505 TTTTATTCAAATTATT
1 TTTTATTCAAATTATT
**
1506521 TTTTATTCTTATTATT
1 TTTTATTCAAATTATT
1506537 TTTT
1 TTTT
1506541 TAATATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTCAAATTATT
Found at i:1506686 original size:151 final size:150
Alignment explanation
Indices: 1506409--1506686 Score: 316
Period size: 151 Copynumber: 1.8 Consensus size: 150
1506399 AAGAAAAGGT
* * *
1506409 TGTCTTAAATTAACTAGAGGTCTTATTCTGATATTTTTAAATAAATAAATATCTTACTTATAAAA
1 TGTCTTAAAATAACTAGAGATCTTATTCTGATATTTCTAAATAAATAAATATCTTACTTATAAAA
* * * ***
1506474 ACAAATATATATATATATATAGTTGTTTTAGTTTTATTCAAATTATTTTTTATTCTTATTATTTT
66 ACAAATATATATATATATATA-TTATTTTAGTTTTAATCAAATTATTTTCTATTAGAATTATTTT
1506539 TTTAATATCAAAGAAATGAGC
130 TTTAATATCAAAGAAATGAGC
*
1506560 TGTCTTAAAATAACTAGATATCATT-TTCTGATATTTCTAAATAAATAAATA-CTCTACTTATAA
1 TGTCTTAAAATAACTAGAGATC-TTATTCTGATATTTCTAAATAAATAAATATCT-TACTTATAA
* * **
1506623 AACCCTAAGTATATATATATATACT-TTAATTTTA-TTTTAAT-ATTTTAATTTTCT-TTAGAAT
64 AA-AC-AAATATATATATATATA-TATT-ATTTTAGTTTTAATCAAATT-ATTTTCTATTAGAAT
1506684 TAT
124 TAT
1506687 GCGATTGAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
150 2 0.02
151 65 0.61
152 17 0.16
153 21 0.20
154 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (150 bp):
TGTCTTAAAATAACTAGAGATCTTATTCTGATATTTCTAAATAAATAAATATCTTACTTATAAAA
ACAAATATATATATATATATATTATTTTAGTTTTAATCAAATTATTTTCTATTAGAATTATTTTT
TTAATATCAAAGAAATGAGC
Found at i:1511124 original size:28 final size:29
Alignment explanation
Indices: 1511093--1511156 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1511083 GTGATTATAC
*
1511093 ATGAGATTATA-TCCCGTCTTGATTTTGT
1 ATGAGATTATATTCCCATCTTGATTTTGT
* *
1511121 ATGAGATTATATTCTCATCTTGTTTTTGT
1 ATGAGATTATATTCCCATCTTGATTTTGT
*
1511150 TTGAGAT
1 ATGAGAT
1511157 CTTCTTTGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (29 bp):
ATGAGATTATATTCCCATCTTGATTTTGT
Found at i:1512778 original size:13 final size:13
Alignment explanation
Indices: 1512762--1512786 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1512752 CCCTTTTATT
1512762 TATTATTGAGATA
1 TATTATTGAGATA
1512775 TATTATTGAGAT
1 TATTATTGAGAT
1512787 CGTTTGATAA
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:0.16, T:0.48
Consensus pattern (13 bp):
TATTATTGAGATA
Found at i:1521522 original size:34 final size:34
Alignment explanation
Indices: 1521476--1521542 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1521466 CCTTTACAAC
* *
1521476 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTTA
1 TCCCTAGCTTTTCAAGGGCTAAACTAGAACCTTA
*
1521510 TCCCTAGCTTTTCAAGGGCTCAACTAGAACCTT
1 TCCCTAGCTTTTCAAGGGCTAAACTAGAACCTT
1521543 TCCTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTCAAGGGCTAAACTAGAACCTTA
Found at i:1521984 original size:20 final size:20
Alignment explanation
Indices: 1521959--1522026 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1521949 TACTGTTCAT
* *
1521959 TACTATTCACACAGTATCGG
1 TACTATTCACACAATATCAG
*
1521979 TACTATTCATACAATATCAG
1 TACTATTCACACAATATCAG
*
1521999 TACTA-TCTATACAATA-CAG
1 TACTATTC-ACACAATATCAG
*
1522018 TATTATTCA
1 TACTATTCA
1522027 TAAAAACATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 10 0.24
20 32 0.76
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (20 bp):
TACTATTCACACAATATCAG
Found at i:1525167 original size:35 final size:36
Alignment explanation
Indices: 1525116--1525186 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
1525106 GATAAGTTAT
* * *
1525116 TCAAGGAGTATCGATACCTTAGAGG-CAGTATCGATA
1 TCAAGGAGTACCGATACCATA-AGGTAAGTATCGATA
1525152 TCAAGG-GTACCGATACCATAAGGTAAGTATCGATA
1 TCAAGGAGTACCGATACCATAAGGTAAGTATCGATA
1525187 CCATTTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 3 0.10
35 22 0.71
36 6 0.19
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (36 bp):
TCAAGGAGTACCGATACCATAAGGTAAGTATCGATA
Found at i:1526257 original size:30 final size:30
Alignment explanation
Indices: 1526223--1526289 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
1526213 GGACTGGCAA
*
1526223 TGAACC-AGCTGAAAACCGGTAAAACCGGAC
1 TGAACCGA-CTGAAAACCGGCAAAACCGGAC
**
1526253 TGAACCGACTGAAAACCGGCAAAACCGGTT
1 TGAACCGACTGAAAACCGGCAAAACCGGAC
1526283 TGAACCG
1 TGAACCG
1526290 CCGGTTCACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.37, C:0.27, G:0.24, T:0.12
Consensus pattern (30 bp):
TGAACCGACTGAAAACCGGCAAAACCGGAC
Found at i:1530637 original size:33 final size:34
Alignment explanation
Indices: 1530599--1530677 Score: 103
Period size: 33 Copynumber: 2.4 Consensus size: 34
1530589 GTAAATTAAG
1530599 ATAAAATATATATTTT-AAAAATTTAAAATAA-TT
1 ATAAAATATAT-TTTTGAAAAATTTAAAATAAGTT
* *
1530632 ATAAAATATATTTTTGAAAAGTTTAAATTAAGTT
1 ATAAAATATATTTTTGAAAAATTTAAAATAAGTT
1530666 -T-AAATATATTTT
1 ATAAAATATATTTT
1530678 ATTTGATTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 15 0.36
33 25 0.60
34 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (34 bp):
ATAAAATATATTTTTGAAAAATTTAAAATAAGTT
Found at i:1530675 original size:32 final size:31
Alignment explanation
Indices: 1530590--1530677 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 31
1530580 AATAATATAG
* *
1530590 TAAATTAAGATAAAATATATATTTTAAAAATT
1 TAAATTAAGTTTAAATATAT-TTTTAAAAATT
* *
1530622 TAAAATAA-TTATAAAATATATTTTTGAAAAGTT
1 TAAATTAAGTT-T-AAATATATTTTT-AAAAATT
1530655 TAAATTAAGTTTAAATATATTTT
1 TAAATTAAGTTTAAATATATTTT
1530678 ATTTGATTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
31 1 0.02
32 22 0.47
33 22 0.47
34 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (31 bp):
TAAATTAAGTTTAAATATATTTTTAAAAATT
Found at i:1531869 original size:23 final size:23
Alignment explanation
Indices: 1531826--1531869 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1531816 ACATATTAGG
**
1531826 TAGCGCTTATATAATGTAATAGA
1 TAGCGCTTATATAATAAAATAGA
1531849 TAGCGCTTATATAATAAAATA
1 TAGCGCTTATATAATAAAATA
1531870 AGTATTTAAC
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:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (23 bp):
TAGCGCTTATATAATAAAATAGA
Found at i:1531946 original size:87 final size:87
Alignment explanation
Indices: 1531786--1531947 Score: 288
Period size: 87 Copynumber: 1.9 Consensus size: 87
1531776 ATGTTATATC
1531786 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
1 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
*
1531851 GCGCTTATATAATAAAATAAGT
66 GCACTTATATAATAAAATAAGT
* *
1531873 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
*
1531938 GCATTTATAT
66 GCACTTATAT
1531948 TGACCTATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
GCACTTATATAATAAAATAAGT
Found at i:1532406 original size:200 final size:198
Alignment explanation
Indices: 1531942--1532641 Score: 766
Period size: 200 Copynumber: 3.5 Consensus size: 198
1531932 TAGGTAGCAT
* ** * * *
1531942 TTATATTGACCTATTTTCGAAGT-AAACCGATATATTTATACCGGTAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTTTCTCA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* * * * * **
1532006 TTATATTATTATTATCAGTTACGATGTTTTTTAGATCGATACAATTT-TAAATGTATCGACACTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTGAGATCGATACTTTTTATAAATGTATCGACACTT
** * *
1532070 TATGCTTGCACCTGGTTGGGCATTCATATTTCATTCTGGAAAAAAGTATCGACACAAACTAACAA
130 TATGCTTGCACCT-GTT-----TTGGTA-TTCATTCTGGACAAAAGTATCGACACAAATTAACAA
*
1532135 CGTGCCGATACA
188 -GTGTCGATACA
* * * *
1532147 TTAT-TTAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTGAAAATTTACCTA
1 TTATGTT-GACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* * ** *
1532211 TTACATTATACTTATGGGTTTCGATGTTTCCGAGATCGATATTTTTTATAAATGTATCGACACTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTGAGATCGATACTTTTTATAAATGTATCGACACTT
* * * *
1532276 TATGATTGCACCCT-TTTTGGTATTCATTATGGACCAAAAGTATCGGCACAAATTTAGCAAGTGT
130 TATGCTTGCA-CCTGTTTTGGTATTCATTCTGGA-CAAAAGTATCGACACAAA-TTAACAAGTGT
1532340 CGATAC-
192 CGATACA
* *
1532346 TTGATGTTGACCTATTTTATCATAAAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTA
1 TT-ATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* * *
1532411 ATACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTGAGATCGATACTTTTTATAAATGTATCGACACTT
* * *
1532476 TATGCGTGCACCTCG-TTTGTGCATTCATCCTGGACAATAAGTATCGACACAAATTACACAAGTG
130 TATGCTTGCACCT-GTTTTG-GTATTCATTCTGGACAA-AAGTATCGACACAAATTA-ACAAGTG
1532540 TCGATACA
191 TCGATACA
* * * * * *
1532548 TTATGTTGACATGTTTTCTAAT-TAACCAGTATATTTATACCGGTTACATTGTTAATTTACCTAT
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
* *
1532612 TACATTATAATTATTGGTTTTGATGTTTTT
66 TACATTATAATTATCGGTTTCGATGTTTTT
1532642 TTGGGTCGAT
Statistics
Matches: 420, Mismatches: 61, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
199 15 0.04
200 222 0.53
201 61 0.15
202 2 0.00
204 3 0.01
205 88 0.21
206 26 0.06
207 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (198 bp):
TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATGTTTTTGAGATCGATACTTTTTATAAATGTATCGACACTTT
ATGCTTGCACCTGTTTTGGTATTCATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGAT
ACA
Found at i:1535299 original size:29 final size:30
Alignment explanation
Indices: 1535230--1535288 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1535220 AATTTAAGGA
1535230 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
*
1535261 AAAATATTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
1535289 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:1535396 original size:21 final size:21
Alignment explanation
Indices: 1535370--1535445 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
1535360 GGTGTCAAAG
1535370 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAA
* *
1535391 TGCATCCATGCATCCCTACAG
1 TGCATCCATGCATCCCTGCAA
1535412 TGCATCCATGCA--CCTGTACTAA
1 TGCATCCATGCATCCCTG--C-AA
1535434 TGCATCCATGCA
1 TGCATCCATGCA
1535446 CTCAAATATC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 3 0.06
21 32 0.67
22 13 0.27
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAA
Found at i:1538295 original size:29 final size:29
Alignment explanation
Indices: 1538259--1538326 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1538249 CATTTTACAC
* *
1538259 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
* *
1538288 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
*
1538317 GAATAGCACC
1 AAATAGCACC
1538327 AAAACCAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:1545750 original size:29 final size:29
Alignment explanation
Indices: 1545712--1545779 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1545702 CATTTTACAC
* * *
1545712 AAATATCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
* *
1545741 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
1545770 AAATAGCACC
1 AAATAGCACC
1545780 AAAACCAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:1545790 original size:29 final size:29
Alignment explanation
Indices: 1545732--1545808 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
1545722 CTTTTTAAAA
* *** *
1545732 TAATTACCAAAATAGCACCCATTTCGAAT
1 TAATTACCAAAATAGCACCAAAACCAAAT
1545761 TAATTACCAAAATAGCACCAAAACCAAAT
1 TAATTACCAAAATAGCACCAAAACCAAAT
* *
1545790 TATTTACCAGAATAGCACC
1 TAATTACCAAAATAGCACC
1545809 GGTCAACGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.45, C:0.25, G:0.06, T:0.23
Consensus pattern (29 bp):
TAATTACCAAAATAGCACCAAAACCAAAT
Found at i:1545846 original size:18 final size:17
Alignment explanation
Indices: 1545816--1545850 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1545806 ACCGGTCAAC
1545816 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1545833 GGTCAACGGGTCGGGTCG
1 GGTCAAC-GGTCGGGTCG
1545851 TGACCGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1546780 original size:19 final size:20
Alignment explanation
Indices: 1546756--1546803 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1546746 AATGATTTTC
*
1546756 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1546775 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1546795 TTTTGAAAA
1 TTTTGAAAA
1546804 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1548147 original size:29 final size:30
Alignment explanation
Indices: 1548078--1548136 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1548068 AATTTAAGGC
1548078 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
1548109 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
1548137 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:1548242 original size:21 final size:21
Alignment explanation
Indices: 1548216--1548268 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1548206 AGGGTGTCAA
1548216 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
* *
1548237 AGTGCATCCCTGCATCCTTGC
1 AGTGCATCCATGCATCCCTGC
1548258 AGTGCATCCAT
1 AGTGCATCCAT
1548269 ACACATGCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:1548244 original size:13 final size:13
Alignment explanation
Indices: 1548226--1548250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1548216 AGTGCATCCA
1548226 TGCATCCCTGCAG
1 TGCATCCCTGCAG
1548239 TGCATCCCTGCA
1 TGCATCCCTGCA
1548251 TCCTTGCAGT
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:0.40, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCCTGCAG
Found at i:1548891 original size:14 final size:14
Alignment explanation
Indices: 1548872--1548905 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1548862 CTCTCATAAA
1548872 ACCGGTATATTTAT
1 ACCGGTATATTTAT
1548886 ACCGGTATATTTAT
1 ACCGGTATATTTAT
1548900 ACCGGT
1 ACCGGT
1548906 TACATTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (14 bp):
ACCGGTATATTTAT
Found at i:1549408 original size:201 final size:201
Alignment explanation
Indices: 1548890--1549408 Score: 763
Period size: 201 Copynumber: 2.6 Consensus size: 201
1548880 ATTTATACCG
*
1548890 GTATATTTATACCGGTTACATTGTAAATTTACCAATTACATTATAATTATGGGTTTCGATGTTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * *
1548955 TGAGATCGATACATTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTTT
66 TGGGATCGACACATTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCT
* * * * * * *
1549020 GGACCAAAAGTATCGACACAAAATTAAAAAAGTGTCGCTCCAGGTTATAGACCTATTCTCTCATA
131 GGACAAAAAGTATCAACACAAAATTAAAAAAGTATCGATACAGATTATAGACATATTCTCTCATA
*
1549085 AAACTG
196 AAACTA
*
1549091 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGTGTTTCGATGTTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
*
1549156 TGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCT
66 TGGGATCGACACATTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCT
* * * *
1549221 GGACAAAAATTATCAACACAATATT-AAGAAGTATCGATACATATTATAGACATATTCTCTCATA
131 GGACAAAAAGTATCAACACAAAATTAAAAAAGTATCGATACAGATTATAGACATATTCTCTCATA
1549285 AAACTA
196 AAACTA
* * * ** * *
1549291 GTATATGTGTACCGGTTATATTACAAAATTACCTATTATATTATAATTATGGGTTTCGATGTTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* *
1549356 TGGGATCGACAC-TTTTAATAAATGTATCGACACTTTATGCGTGCAACCCTTTT
66 TGGGATCGACACATTTTGA-AAATGTATCGACACTTTATGCGTTC-ACCCTTTT
1549409 GGATCGACAC
Statistics
Matches: 288, Mismatches: 28, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
199 5 0.02
200 130 0.45
201 153 0.53
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (201 bp):
GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
TGGGATCGACACATTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCT
GGACAAAAAGTATCAACACAAAATTAAAAAAGTATCGATACAGATTATAGACATATTCTCTCATA
AAACTA
Found at i:1549524 original size:251 final size:250
Alignment explanation
Indices: 1549153--1549605 Score: 669
Period size: 251 Copynumber: 1.8 Consensus size: 250
1549143 GTTTCGATGT
* *
1549153 TTTTGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCAT
1 TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCAT
* * * *
1549218 TCTGGACAAAAATTATCAACACAATATTAAGAAGTATCGATACATATTATAGACATATTCTCTCA
66 TCTGGAAAAAAAGTATCAACACAATACTAAGAAGTATCGATAAATATTATAGACATATT-T-TCA
* * * *
1549283 TAAAACTAGTATATGTGTACCGGTTATATT-ACAAAATTACCTATTATATTATAATTATGGGTTT
129 TAAAACCAGTATATGTATACCGGTTATATTGA-AAAATTACCCATTACATTATAATTATGGGTTT
1549347 CGATGTTTTTGGGATCGACACTTTTAATAAATGTATCGACACTTTATGCGTGCAACCC
193 CGATGTTTTTGGGATCGACACTTTTAATAAATGTATCGACACTTTATGCGTGCAACCC
* * *
1549405 TTTT-GGATCGACACTCTATGAAAATGTATCGACGCTTTGTAG-GTTCACCCTTTTTGGTATCCA
1 TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTAT-GCGTTCACCCTTTTTGGCATCCA
* * * * *
1549468 TTCTGGAAAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATGTTGTAGACATATTTTCAT
65 TTCTGGAAAAAAAGTATCAACACAATACTAAGAAGTATCGATAAATATTATAGACATATTTTCAT
* *
1549533 AAAACCGGTATATTTATACCGGTTATATTGAAAAATTACCCATTACATTATAATTATGGGTTTCG
130 AAAACCAGTATATGTATACCGGTTATATTGAAAAATTACCCATTACATTATAATTATGGGTTTCG
1549598 ATGTTTTT
195 ATGTTTTT
1549606 TGGGTCGTTA
Statistics
Matches: 179, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
249 69 0.39
250 2 0.01
251 103 0.58
252 5 0.03
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (250 bp):
TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCAT
TCTGGAAAAAAAGTATCAACACAATACTAAGAAGTATCGATAAATATTATAGACATATTTTCATA
AAACCAGTATATGTATACCGGTTATATTGAAAAATTACCCATTACATTATAATTATGGGTTTCGA
TGTTTTTGGGATCGACACTTTTAATAAATGTATCGACACTTTATGCGTGCAACCC
Found at i:1553139 original size:200 final size:200
Alignment explanation
Indices: 1552437--1553153 Score: 1161
Period size: 201 Copynumber: 3.6 Consensus size: 200
1552427 TATTTAAATT
* *
1552437 AGTATCGACACAAAATTAAAAACGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* * * * * * *
1552502 ATATTTATACTGGTTACATTGAAAATTTACTTATTACATTATATTTAT-GGATGCATATGTTTCT
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTC-GATGTTTTT
* *
1552566 GGGATCGATACTTTTT-ATAAATGTATCGACACTTTATG-GTTGCACCCTTTTTGGCATTCATTC
130 GGGATCGACACTTTTTGA-AAATGTATCGACACTTTATGCGTT-CA-CCTTTTTGGCATCCATTC
1552629 TGGACCAAA
192 TGGACCAAA
* *
1552638 AGTATCGAAACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
1552703 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* *
1552768 GGATCGACACGTTTTGAAAATGTATCGACACTTTATGCGTTCACCATTTTTGGAATCCATTCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACC-TTTTTGGCATCCATTCTGG
*
1552833 ACTAAA
195 ACCAAA
*
1552839 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* *
1552904 ATATTTATACCGGTTACATTGTAAATTTGCCTATTACATTATAATTATGGGTTTCGATGTTTTTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
1552969 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCTTTTTGGCATCCATTCTGGA
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCTTTTTGGCATCCATTCTGGA
1553034 CCAAA
196 CCAAA
* *
1553039 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTACTCTCTCATAAAACCGAT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
1553104 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGG
1553154 ATGCATATGT
Statistics
Matches: 484, Mismatches: 28, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
200 134 0.28
201 342 0.71
202 8 0.02
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (200 bp):
AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCTTTTTGGCATCCATTCTGGA
CCAAA
Found at i:1553463 original size:19 final size:19
Alignment explanation
Indices: 1553439--1553487 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1553429 TTACATTCAC
1553439 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
1553458 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
*
1553477 ATAAAAAATTA
1 ATACAAAATTA
1553488 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:1555313 original size:33 final size:33
Alignment explanation
Indices: 1555276--1555341 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1555266 CATCTTAAGA
* *
1555276 TCACCCCTTAACACTTCAAATTCTTTCACCACT
1 TCACCCCTCAACACCTCAAATTCTTTCACCACT
* *
1555309 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAAATTCTTTCACCACT
1555342 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAAATTCTTTCACCACT
Found at i:1555400 original size:21 final size:21
Alignment explanation
Indices: 1555375--1555440 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1555365 CCCCTTATGC
* *
1555375 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1555396 CTCTCAAGTTTCTCTTTGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1555417 CTCTCAAGTTTCTCTTCAACT
1 CTCTCAAGTTTCTCTTCGACT
1555438 CTC
1 CTC
1555441 GATTGTCTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.17, C:0.32, G:0.09, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1555863 original size:22 final size:24
Alignment explanation
Indices: 1555835--1555890 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1555825 AACCTGCATT
1555835 TATAATAA-AAT-TTATAATTTTA
1 TATAATAACAATATTATAATTTTA
* *
1555857 TATAATAACTATATTATCATTTTA
1 TATAATAACAATATTATAATTTTA
*
1555881 TATAAAAACA
1 TATAATAACA
1555891 CAAAAGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 8 0.29
23 2 0.07
24 18 0.64
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (24 bp):
TATAATAACAATATTATAATTTTA
Found at i:1557730 original size:20 final size:19
Alignment explanation
Indices: 1557685--1557730 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1557675 CCGATAGCGC
*
1557685 TTTACCGGTTTTATCATTT
1 TTTACCGATTTTATCATTT
*
1557704 TGATACCGATTTTATCATATT
1 T-TTACCGATTTTATCAT-TT
1557725 TTTACC
1 TTTACC
1557731 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (19 bp):
TTTACCGATTTTATCATTT
Found at i:1557975 original size:182 final size:182
Alignment explanation
Indices: 1557651--1558126 Score: 634
Period size: 182 Copynumber: 2.6 Consensus size: 182
1557641 CGTACTTATG
* * *
1557651 AAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAATTT
1557716 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACACTTTAT
* *
1557781 AGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATAC-TTATATT
131 AGACGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGCCGAT-CTTTATATT
* * * *
1557833 AAAGTACCGACACTTTAAATATATCCGGTAGCTCTTTACCGGTTTTATTATTTCGATACCAATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAATTT
* * *
1557898 TTTCATATTTTTACTTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACACTTTAT
* * *
1557963 AGGCGTTAAAACTGATTCTCTTTTAAATTCACAAAGTGCCGGTCTTTATATT
131 AGACGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGCCGATCTTTATATT
* * * * * * **
1558015 AAAGTATCGACACATTCAATATATCCGGTAAG-GATTTACCGATATTGTCTTTTCG-TGACCGGT
1 AAAGTATCGACACTTTCAATATATCCGGT-AGCGCTTTACCGGTTTTATCATTTCGAT-ACCAAT
* * * * * *
1558078 TTTATTGATATTTTGACATGTTATATTGATATGGATCGATACATTTTTA
64 TTTA-TCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTA
1558127 ATTTGGATCG
Statistics
Matches: 256, Mismatches: 34, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
181 2 0.01
182 214 0.84
183 40 0.16
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAATTT
TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACACTTTAT
AGACGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGCCGATCTTTATATT
Found at i:1564219 original size:23 final size:23
Alignment explanation
Indices: 1564186--1564233 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1564176 ACACTTGACG
*
1564186 TAATTGTTTGAATCTAGAAATTT
1 TAATTGCTTGAATCTAGAAATTT
1564209 TAATTGCTTGAATCTAGAAATTT
1 TAATTGCTTGAATCTAGAAATTT
1564232 TA
1 TA
1564234 GAGAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46
Consensus pattern (23 bp):
TAATTGCTTGAATCTAGAAATTT
Found at i:1567781 original size:6 final size:6
Alignment explanation
Indices: 1567772--1567797 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1567762 GCCTAAGCCT
1567772 AATCCA AATCCA AATCCA AATCCA AA
1 AATCCA AATCCA AATCCA AATCCA AA
1567798 ACCCGGCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (6 bp):
AATCCA
Found at i:1570968 original size:13 final size:14
Alignment explanation
Indices: 1570933--1570969 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1570923 ACTTTCTATA
1570933 TTAATTAT-AATCC
1 TTAATTATAAATCC
1570946 TTATATTATAAAT-C
1 TTA-ATTATAAATCC
1570960 TTAATTATAA
1 TTAATTATAA
1570970 TAATCTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 9 0.41
15 3 0.14
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATTATAAATCC
Found at i:1570974 original size:15 final size:15
Alignment explanation
Indices: 1570938--1570983 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
1570928 CTATATTAAT
1570938 TATAATCCTTATATTA
1 TATAAT-CTTATATTA
1570954 TA-AATCTTA-ATTA
1 TATAATCTTATATTA
1570967 TAATAATCTTTATATTA
1 T-ATAATC-TTATATTA
1570984 ATTTCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 7 0.27
16 5 0.19
17 4 0.15
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATCTTATATTA
Found at i:1571535 original size:10 final size:10
Alignment explanation
Indices: 1571517--1571584 Score: 54
Period size: 10 Copynumber: 6.7 Consensus size: 10
1571507 ATCATGTTTA
1571517 ATATATACTT
1 ATATATACTT
*
1571527 ATATGTACTT
1 ATATATACTT
1571537 ATATATTA-TAT
1 ATATA-TACT-T
1571548 ATATATA-TAT
1 ATATATACT-T
1571558 ATATATA-TAT
1 ATATATACT-T
1571568 ATATATA-TAT
1 ATATATACT-T
1571578 ATATATA
1 ATATATA
1571585 TATAAATTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
10 46 0.85
11 8 0.15
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (10 bp):
ATATATACTT
Found at i:1571541 original size:2 final size:2
Alignment explanation
Indices: 1571536--1571588 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1571526 TATATGTACT
1571536 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1571577 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1571589 AATTATGTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1571871 original size:2 final size:2
Alignment explanation
Indices: 1571754--1571863 Score: 211
Period size: 2 Copynumber: 55.0 Consensus size: 2
1571744 TATGTACTTT
1571754 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1571796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1571838 TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1571864 CTTATATAAA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 106 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1571945 original size:15 final size:15
Alignment explanation
Indices: 1571927--1571966 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1571917 ATGATATACT
*
1571927 TATATGTATAACATA
1 TATATATATAACATA
* *
1571942 TATACATATAATATA
1 TATATATATAACATA
1571957 TATATATATA
1 TATATATATA
1571967 TGGTTAGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATATATAACATA
Found at i:1574946 original size:39 final size:39
Alignment explanation
Indices: 1574902--1575075 Score: 215
Period size: 39 Copynumber: 4.4 Consensus size: 39
1574892 ACTTGTTTTG
*
1574902 ATTTATTTCCTTTTACAAAATAGGAAACTAAATCCAACA
1 ATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACA
* * *
1574941 ATTTATTTCCTTTTTTACAAAATAGAAAAATAAATTCAATA
1 ATTTATTTCC--TTTTACAAAATAGGAAAATAAATCCAACA
** * * * **
1574982 ATTTATTTCCTTTTACAAACCAGGAAACTAAATTCTATG
1 ATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACA
*
1575021 ATTTATTTCCTTTT-CAAAATAGGAAAATAAATCCAACT
1 ATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACA
1575059 ATTTATTTCCTTTTACA
1 ATTTATTTCCTTTTACA
1575076 TATCAGAATC
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
38 31 0.27
39 49 0.43
41 35 0.30
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (39 bp):
ATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACA
Found at i:1574998 original size:80 final size:77
Alignment explanation
Indices: 1574902--1575075 Score: 233
Period size: 80 Copynumber: 2.2 Consensus size: 77
1574892 ACTTGTTTTG
*
1574902 ATTTATTTCCTTTTACAAAATAGGAAACTAAATCCAACAATTTATTTCCTTTTTTACAAAATAGA
1 ATTTATTTCCTTTTACAAAACAGGAAACTAAATCCAACAATTTATTTCC--TTTT-CAAAATAGA
*
1574967 AAAATAAATTCAA-T
63 AAAATAAATCCAACT
* * * ** *
1574981 AATTTATTTCCTTTTACAAACCAGGAAACTAAATTCTATGATTTATTTCCTTTTCAAAATAGGAA
1 -ATTTATTTCCTTTTACAAAACAGGAAACTAAATCCAACAATTTATTTCCTTTTCAAAATAGAAA
1575046 AATAAATCCAACT
65 AATAAATCCAACT
1575059 ATTTATTTCCTTTTACA
1 ATTTATTTCCTTTTACA
1575076 TATCAGAATC
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
77 37 0.44
78 5 0.06
80 43 0.51
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (77 bp):
ATTTATTTCCTTTTACAAAACAGGAAACTAAATCCAACAATTTATTTCCTTTTCAAAATAGAAAA
ATAAATCCAACT
Found at i:1575259 original size:96 final size:96
Alignment explanation
Indices: 1575021--1575353 Score: 344
Period size: 96 Copynumber: 3.5 Consensus size: 96
1575011 AAATTCTATG
* *
1575021 ATTTATTTCCTTTTCAAAATAGGAAAATAAATCCAACT-ATTTATTTCCTTTTACATATCAGAAT
1 ATTTATTTCCTTTTCAAAATAGGAAAATAAATCCAA-TGATTTATTTTCTCTTACATATCAGAAT
1575085 CATACAAGATTCTTAGAAAAATAAATTTACAT
65 CATACAAGATTCTTAGAAAAATAAATTTACAT
* * *
1575117 ATTTATTTCCTTTGCAAAATAGAAAAATAAATCCAAAGATTTATTTTCTCTTACATAT-AGGAAT
1 ATTTATTTCCTTTTCAAAATAGGAAAATAAATCCAATGATTTATTTTCTCTTACATATCA-GAAT
* *
1575181 CATACAAGATTTTTA-AGAAAATAAATTTACCT
65 CATACAAGATTCTTAGA-AAAATAAATTTACAT
* * * * * *
1575213 ATTTATTTCCTTTTCAAAATAGGAAAATAAATTCTATGATTCA---T-T-TTACATATTATAATT
1 ATTTATTTCCTTTTCAAAATAGGAAAATAAATCCAATGATTTATTTTCTCTTACATATCAGAATC
*** * *
1575273 ATGTGAGATTCTCA-AAATAATAAATTCAACA-
66 ATACAAGATTCTTAGAAA-AATAAATT-TACAT
* * * *
1575304 ATTTATTTCCTTTCACAAAACAGGAAAATAAATCCAACGATTTATCTTCT
1 ATTTATTTCCTTT-TCAAAATAGGAAAATAAATCCAATGATTTATTTTCT
1575354 TTAAAAAATA
Statistics
Matches: 198, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
90 2 0.01
91 42 0.21
92 28 0.14
93 1 0.01
95 3 0.02
96 122 0.62
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.38
Consensus pattern (96 bp):
ATTTATTTCCTTTTCAAAATAGGAAAATAAATCCAATGATTTATTTTCTCTTACATATCAGAATC
ATACAAGATTCTTAGAAAAATAAATTTACAT
Found at i:1575371 original size:187 final size:190
Alignment explanation
Indices: 1575021--1575376 Score: 429
Period size: 187 Copynumber: 1.9 Consensus size: 190
1575011 AAATTCTATG
* *
1575021 ATTTATTTCCTTTTCAAAATAGGAAAATAAATCCAACTATTTATTTCCTTTTACATATCAGAATC
1 ATTTATTTCCTTTTCAAAATAGGAAAATAAAT-C-ACTATTGATTTCATTTTACATATCAGAATC
* * * *
1575086 ATACAAGATTCTTAGAAAAATAAATTTACATATTTATTTCCTTTGCAAAATAGAAAAATAAATCC
64 ATACAAGATTCTCAGAAAAATAAATTAACATATTTATTTCCTTTACAAAACAGAAAAATAAATCC
* * * *
1575151 AAAGATTTATTTTCTCTTACATATAGGAATCATACAAGATTTTTAAGAAAATAAATTTACCT
129 AAAGATTTATCTTCTCTTAAAAATAGAAATCATACAAGATTTTTAAGAAAATAAATTTACCT
* * * *
1575213 ATTTATTTCCTTTTCAAAATAGGAAAATAAAT-TCTA-TGA-TTCATTTTACATATTATAATTAT
1 ATTTATTTCCTTTTCAAAATAGGAAAATAAATCACTATTGATTTCATTTTACATATCAGAATCAT
*** *
1575275 GTGAGATTCTCA-AAATAATAAATTCAACA-ATTTATTTCCTTTCACAAAACAGGAAAATAAATC
66 ACAAGATTCTCAGAAA-AATAAATT-AACATATTTATTTCCTTT-ACAAAACAGAAAAATAAATC
* *
1575338 CAACGATTTATCTTCT-TTAAAAAATA-AAATCATATAAGA
128 CAAAGATTTATCTTCTCTT-AAAAATAGAAATCATACAAGA
1575377 AAATAAATTT
Statistics
Matches: 140, Mismatches: 20, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
186 3 0.02
187 61 0.44
188 41 0.29
189 3 0.02
192 32 0.23
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (190 bp):
ATTTATTTCCTTTTCAAAATAGGAAAATAAATCACTATTGATTTCATTTTACATATCAGAATCAT
ACAAGATTCTCAGAAAAATAAATTAACATATTTATTTCCTTTACAAAACAGAAAAATAAATCCAA
AGATTTATCTTCTCTTAAAAATAGAAATCATACAAGATTTTTAAGAAAATAAATTTACCT
Found at i:1575478 original size:58 final size:58
Alignment explanation
Indices: 1575407--1575602 Score: 252
Period size: 58 Copynumber: 3.4 Consensus size: 58
1575397 TTCTTTATTC
1575407 AAGATTC-CGAAGAAAATAAATTTAACAATTTATTTCCTTTAACAAAATAGAATCATTT
1 AAGATTCTC-AAGAAAATAAATTTAACAATTTATTTCCTTTAACAAAATAGAATCATTT
* * ** *
1575465 AAGATTCTCAAGAAATTAAATTTAATAATTTATTAACTTTTACAAAATAGAATCATTT
1 AAGATTCTCAAGAAAATAAATTTAACAATTTATTTCCTTTAACAAAATAGAATCATTT
* * * * **
1575523 AATATTCTCAAGAAAATAAATTTAACAATTTATTTCTTTTTGA-AGAATAGAATCATCC
1 AAGATTCTCAAGAAAATAAATTTAACAATTTATTTC-CTTTAACAAAATAGAATCATTT
*
1575581 ACGATTCTCAAGAAAATAAATT
1 AAGATTCTCAAGAAAATAAATT
1575603 CTGTTGAGTT
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
58 114 0.96
59 5 0.04
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (58 bp):
AAGATTCTCAAGAAAATAAATTTAACAATTTATTTCCTTTAACAAAATAGAATCATTT
Found at i:1578628 original size:25 final size:26
Alignment explanation
Indices: 1578600--1578651 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
1578590 CAAAACACAA
1578600 TAATTT-GAAAA-TTAACATTTTTTTT
1 TAATTTCGAAAATTTAA-ATTTTTTTT
1578625 TAATTTCGAAAATTTAAATTTTTTTT
1 TAATTTCGAAAATTTAAATTTTTTTT
1578651 T
1 T
1578652 GAAAAATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 15 0.60
27 4 0.16
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (26 bp):
TAATTTCGAAAATTTAAATTTTTTTT
Found at i:1579083 original size:20 final size:21
Alignment explanation
Indices: 1579030--1579091 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
1579020 TTCCCCTGTG
1579030 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
1579054 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
1579074 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
1579092 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:1585281 original size:58 final size:58
Alignment explanation
Indices: 1585186--1585396 Score: 284
Period size: 58 Copynumber: 3.7 Consensus size: 58
1585176 TGTTTTCAAC
* * * *
1585186 AAATTCAATAATTTAGTTTT-CTTACAAAGTTAAAATCATTCAAGATT-TCCAAGAAAAT
1 AAATTCAACAATCTA-TTTTCCTTACAAAGTTAGAATCATTAAAGATTCT-CAAGAAAAT
* *
1585244 AAATTCAATAATTTATTTTCCTTACAAAGTTAGAATCATTAAAGATTCTCAAGAAAAT
1 AAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTAAAGATTCTCAAGAAAAT
* * *
1585302 AAATTCAACAATCTATTTTCCTTACAAAGTTAGAATAATTTAAGATTCTCACGAAAAT
1 AAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTAAAGATTCTCAAGAAAAT
* *
1585360 AAATTTAACAATCTATTTTCCTGA-AAAGTTAGAATCA
1 AAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCA
1585397 AAGTAAGATT
Statistics
Matches: 141, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
57 16 0.11
58 124 0.88
59 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (58 bp):
AAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTAAAGATTCTCAAGAAAAT
Found at i:1585605 original size:45 final size:44
Alignment explanation
Indices: 1585556--1585703 Score: 179
Period size: 45 Copynumber: 3.3 Consensus size: 44
1585546 TTATGTCAAC
* * *
1585556 CCAATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTCACAA
1 CCAATAATCAAAAGGAAATAATCCTTTGATTTTACTTTTGACAA
* * *
1585600 TCCAATAATCGAAAGAAAATAATCCTTTGATTTTACTTTTGGCAA
1 -CCAATAATCAAAAGGAAATAATCCTTTGATTTTACTTTTGACAA
* * *
1585645 CACAATAATCAAAATGAATTAATCCTTTGATTTTACTTTTGATAA
1 C-CAATAATCAAAAGGAAATAATCCTTTGATTTTACTTTTGACAA
*
1585690 CCCAATAATAAAAA
1 -CCAATAATCAAAA
1585704 ACATTGGATT
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
44 1 0.01
45 86 0.98
46 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (44 bp):
CCAATAATCAAAAGGAAATAATCCTTTGATTTTACTTTTGACAA
Found at i:1585923 original size:14 final size:15
Alignment explanation
Indices: 1585904--1585936 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1585894 GTTATATGAT
1585904 AATAATACCAT-AAC
1 AATAATACCATGAAC
*
1585918 AATAATATCATGAAC
1 AATAATACCATGAAC
1585933 AATA
1 AATA
1585937 TCATGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATACCATGAAC
Found at i:1587381 original size:16 final size:16
Alignment explanation
Indices: 1587360--1587390 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1587350 ATATGTACAA
1587360 TATACACACACATAAG
1 TATACACACACATAAG
*
1587376 TATACACATACATAA
1 TATACACACACATAA
1587391 TACATATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.23
Consensus pattern (16 bp):
TATACACACACATAAG
Found at i:1587417 original size:2 final size:2
Alignment explanation
Indices: 1587410--1587640 Score: 241
Period size: 2 Copynumber: 118.5 Consensus size: 2
1587400 ACATACATGC
1587410 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
1587452 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
** * ** * * *
1587494 AT -T AT A- AGT AT A- AT GG GT GC AT A- AGT GT A- AT GT AC AT -T
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
1587532 AT AT AT AC AT GT AT CAT A- AT ACT AT CAT AC AT AT AT -T AT A-
1 AT AT AT AT AT AT AT -AT AT AT A-T AT -AT AT AT AT AT AT AT AT
1587572 AT AT AT AT AT AT AT AT A- 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
1587613 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1587641 GTTGTTTATA
Statistics
Matches: 195, Mismatches: 18, Indels: 32
0.80 0.07 0.13
Matches are distributed among these distances:
1 11 0.06
2 177 0.91
3 7 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1588249 original size:22 final size:21
Alignment explanation
Indices: 1588195--1588250 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
1588185 TTTTGACATG
1588195 AACTAATATTGATCCAAACTAA
1 AACTAAT-TTGATCCAAACTAA
*
1588217 AATTAATTTGATCCAAA-TACA
1 AACTAATTTGATCCAAACTA-A
1588238 AACTGAATTTGAT
1 AACT-AATTTGAT
1588251 GTCAAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 14 0.47
22 14 0.47
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (21 bp):
AACTAATTTGATCCAAACTAA
Found at i:1588466 original size:13 final size:13
Alignment explanation
Indices: 1588448--1588484 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1588438 AGCATTGAAA
1588448 AACAAATAATAAC-
1 AACAAATAA-AACT
1588461 AACAAATAAAACT
1 AACAAATAAAACT
1588474 AACAAATAAAA
1 AACAAATAAAA
1588485 ATTGTGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.14
Consensus pattern (13 bp):
AACAAATAAAACT
Found at i:1591600 original size:2 final size:2
Alignment explanation
Indices: 1591595--1591631 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1591585 TATATTAATG
1591595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1591632 TTTGTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1593499 original size:3 final size:3
Alignment explanation
Indices: 1593489--1593561 Score: 71
Period size: 3 Copynumber: 25.0 Consensus size: 3
1593479 ATTTATTATT
* * *
1593489 TAA T-A TAA TAA TAA TAT TAA TAA TAA TAG TAA TAA TAA AAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* *
1593537 TAA -AA T-A TAA TTA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1593562 AGTTGGGACA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
2 6 0.11
3 47 0.84
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1594037 original size:121 final size:116
Alignment explanation
Indices: 1593912--1594338 Score: 479
Period size: 113 Copynumber: 3.7 Consensus size: 116
1593902 AAATTAAGGC
* * *
1593912 AAGGTTGAACAAATTCTTCTCATTATGAAATTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
1593976 TGAACACTTCTGGAAATGTTGATGCTGATATATCTCATTATGTGAT-AGAGTCATGC-A
66 TGAACTCTTCTGGAAA-----ATGCTGATATATCTCATGA-GTGATGA-ATTCA-GCAA
* *
1594033 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
1594097 TGAAC-CTTCTCTGAAAAAGTTGAT-TCT-TC--GAGTGATGAATTCGAGCAA
66 TGAACTCTTCT-GGAAAATGCTGATATATCTCATGAGTGATGAATTC-AGCAA
*
1594145 AAGGTTAAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
1594210 TGAACTCTACCTGG-CAATGC---TA-ATC-CATCGAGTGATGAATTAAAGCAA
66 TGAACTCT-TCTGGAAAATGCTGATATATCTCAT-GAGTGATGAATT-CAGCAA
*
1594258 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCCTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1594323 TGAACTCTTCTGGAAA
66 TGAACTCTTCTGGAAA
1594339 TATTGATCCA
Statistics
Matches: 268, Mismatches: 23, Indels: 38
0.81 0.07 0.12
Matches are distributed among these distances:
110 3 0.01
111 10 0.04
112 46 0.17
113 120 0.45
114 5 0.02
115 4 0.01
116 6 0.02
120 5 0.02
121 66 0.25
122 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (116 bp):
AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTTCTGGAAAATGCTGATATATCTCATGAGTGATGAATTCAGCAA
Found at i:1594764 original size:20 final size:20
Alignment explanation
Indices: 1594739--1594866 Score: 177
Period size: 20 Copynumber: 6.2 Consensus size: 20
1594729 CTTCTTTGAA
1594739 AAGAGAATCTATCATCTTTG
1 AAGAGAATCTATCATCTTTG
**
1594759 AAGAGAAAATATCATCTTTG
1 AAGAGAATCTATCATCTTTG
1594779 AAGAGAGTATCTATCATCTTTG
1 AAGAGA--ATCTATCATCTTTG
*
1594801 AAGAGAATCTATCATATTTG
1 AAGAGAATCTATCATCTTTG
1594821 AAGAGAA-CATATCATCTTTG
1 AAGAGAATC-TATCATCTTTG
1594841 AAGAGAGAATCTATCATCTTTG
1 -A-AGAGAATCTATCATCTTTG
1594863 AAGA
1 AAGA
1594867 TAGAAGATAT
Statistics
Matches: 96, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.01
20 57 0.59
21 2 0.02
22 35 0.36
23 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AAGAGAATCTATCATCTTTG
Found at i:1594791 original size:42 final size:41
Alignment explanation
Indices: 1594731--1594866 Score: 177
Period size: 42 Copynumber: 3.2 Consensus size: 41
1594721 AAATCTTTCT
* *
1594731 TCTTTGAAAAGAGAATCTATCATCTTTGAAGAGAAAATATCA
1 TCTTTGAAGAGAG-ATCTATCATCTTTGAAGAGAAACTATCA
*
1594773 TCTTTGAAGAGAGTATCTATCATCTTTGAAGAGAATCTATCA
1 TCTTTGAAGAGAG-ATCTATCATCTTTGAAGAGAAACTATCA
*
1594815 TATTTGAAGAGA-A-CATATCATCTTTGAAGAGAGAATCTATCA
1 TCTTTGAAGAGAGATC-TATCATCTTTGAAGAGA-AA-CTATCA
1594857 TCTTTGAAGA
1 TCTTTGAAGA
1594867 TAGAAGATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
39 1 0.01
40 18 0.21
41 1 0.01
42 64 0.76
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (41 bp):
TCTTTGAAGAGAGATCTATCATCTTTGAAGAGAAACTATCA
Found at i:1594833 original size:62 final size:62
Alignment explanation
Indices: 1594739--1594866 Score: 229
Period size: 62 Copynumber: 2.1 Consensus size: 62
1594729 CTTCTTTGAA
* *
1594739 AAGAGAATCTATCATCTTTGAAGAGAAAATATCATCTTTGAAGAGAGTATCTATCATCTTTG
1 AAGAGAATCTATCATATTTGAAGAGAAAATATCATCTTTGAAGAGAGAATCTATCATCTTTG
*
1594801 AAGAGAATCTATCATATTTGAAGAGAACATATCATCTTTGAAGAGAGAATCTATCATCTTTG
1 AAGAGAATCTATCATATTTGAAGAGAAAATATCATCTTTGAAGAGAGAATCTATCATCTTTG
1594863 AAGA
1 AAGA
1594867 TAGAAGATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (62 bp):
AAGAGAATCTATCATATTTGAAGAGAAAATATCATCTTTGAAGAGAGAATCTATCATCTTTG
Found at i:1594865 original size:22 final size:22
Alignment explanation
Indices: 1594722--1594871 Score: 179
Period size: 22 Copynumber: 7.1 Consensus size: 22
1594712 AAATCCAATA
* * *
1594722 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
1594744 AATCTATCATCTTTGAAGAGA-
1 AATCTATCATCTTTGAAGAGAG
*
1594765 AA-ATATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
*
1594786 TATCTATCATCTTTG-A-AGAG
1 AATCTATCATCTTTGAAGAGAG
*
1594806 AATCTATCATATTTG-A-AGAG
1 AATCTATCATCTTTGAAGAGAG
1594826 AA-CATATCATCTTTGAAGAGAG
1 AATC-TATCATCTTTGAAGAGAG
*
1594848 AATCTATCATCTTTGAAGATAG
1 AATCTATCATCTTTGAAGAGAG
1594870 AA
1 AA
1594872 GATATAGATA
Statistics
Matches: 112, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.01
20 51 0.46
21 5 0.04
22 54 0.48
23 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:1596292 original size:74 final size:75
Alignment explanation
Indices: 1596154--1596322 Score: 198
Period size: 74 Copynumber: 2.3 Consensus size: 75
1596144 GATATAATTC
* * *
1596154 TTTAGCATGCCCCAACATTTGCTGATACAAGCGTTCAAAATGCGTCAACATTCCTGATTCTGATT
1 TTTAACATGCCCCAACATTTGCTGATACAAACGTTCAAAATGCGTCAACATTCCTAATTCTGATT
*
1596219 GAAATGGGTT
66 GAAATGGGCT
* * * * * *
1596229 TTTAACATGCCCC-GCATTTTCTGATACAAACGTTCAAAATGTGTTAATATTCC-AATTTTTGAT
1 TTTAACATGCCCCAACATTTGCTGATACAAACGTTCAAAATGCGTCAACATTCCTAA-TTCTGAT
1596292 TGAAATGGGCT
65 TGAAATGGGCT
* * *
1596303 TTCAACATGCTCCATCATTT
1 TTTAACATGCCCCAACATTT
1596323 ACTTCTTGTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
73 1 0.01
74 61 0.77
75 17 0.22
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (75 bp):
TTTAACATGCCCCAACATTTGCTGATACAAACGTTCAAAATGCGTCAACATTCCTAATTCTGATT
GAAATGGGCT
Found at i:1599574 original size:11 final size:11
Alignment explanation
Indices: 1599558--1599594 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1599548 CTTGATTCAA
1599558 TTTTTTTCA-T
1 TTTTTTTCATT
1599568 TTTTTTTCATT
1 TTTTTTTCATT
*
1599579 TTTTTTCCATT
1 TTTTTTTCATT
1599590 TTTTT
1 TTTTT
1599595 CCTTTTTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTCATT
Found at i:1599595 original size:10 final size:10
Alignment explanation
Indices: 1599557--1599630 Score: 65
Period size: 10 Copynumber: 8.1 Consensus size: 10
1599547 TCTTGATTCA
1599557 ATTTTTTT-C
1 ATTTTTTTCC
*
1599566 ATTTTTTTTC
1 ATTTTTTTCC
1599576 ATTTTTTTTCC
1 A-TTTTTTTCC
1599587 ATTTTTTTCC
1 ATTTTTTTCC
1599597 --TTTTTTCC
1 ATTTTTTTCC
1599605 --TTTTTTCC
1 ATTTTTTTCC
1599613 ---TTTTTCC
1 ATTTTTTTCC
*
1599620 TTTTTTTTCC
1 ATTTTTTTCC
1599630 A
1 A
1599631 GATGAGTATA
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
7 7 0.12
8 16 0.28
9 8 0.14
10 18 0.31
11 9 0.16
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTTTTCC
Found at i:1599602 original size:11 final size:10
Alignment explanation
Indices: 1599553--1599594 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
1599543 CCTATCTTGA
*
1599553 TTCAATTTTT
1 TTCATTTTTT
1599563 TTCATTTTTT
1 TTCATTTTTT
1599573 TTCATTTTTT
1 TTCATTTTTT
1599583 TTCCATTTTTT
1 TT-CATTTTTT
1599594 T
1 T
1599595 CCTTTTTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (10 bp):
TTCATTTTTT
Found at i:1599603 original size:8 final size:8
Alignment explanation
Indices: 1599579--1599625 Score: 69
Period size: 8 Copynumber: 5.8 Consensus size: 8
1599569 TTTTTTCATT
1599579 TTTTTTCC
1 TTTTTTCC
1599587 ATTTTTTTCC
1 --TTTTTTCC
1599597 TTTTTTCC
1 TTTTTTCC
1599605 TTTTTTCC
1 TTTTTTCC
1599613 -TTTTTCC
1 TTTTTTCC
1599620 TTTTTT
1 TTTTTT
1599626 TTCCAGATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.19
8 21 0.58
10 8 0.22
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCC
Found at i:1599616 original size:15 final size:16
Alignment explanation
Indices: 1599579--1599625 Score: 69
Period size: 15 Copynumber: 2.9 Consensus size: 16
1599569 TTTTTTCATT
1599579 TTTTTTCCATTTTTTTCC
1 TTTTTTCC--TTTTTTCC
1599597 TTTTTTCCTTTTTTCC
1 TTTTTTCCTTTTTTCC
1599613 -TTTTTCCTTTTTT
1 TTTTTTCCTTTTTT
1599626 TTCCAGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 13 0.45
16 8 0.28
18 8 0.28
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTCCTTTTTTCC
Found at i:1602685 original size:16 final size:16
Alignment explanation
Indices: 1602664--1602694 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1602654 TTGAAATCCT
1602664 TATTTTAATGAATGAA
1 TATTTTAATGAATGAA
*
1602680 TATTTTAATGCATGA
1 TATTTTAATGAATGA
1602695 TGTAAGTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (16 bp):
TATTTTAATGAATGAA
Found at i:1602822 original size:7 final size:7
Alignment explanation
Indices: 1602805--1602873 Score: 122
Period size: 7 Copynumber: 10.0 Consensus size: 7
1602795 ATAAAAGTAT
1602805 AAATG-A
1 AAATGCA
1602811 AAATGCA
1 AAATGCA
1602818 AAATGCA
1 AAATGCA
1602825 AAATGCA
1 AAATGCA
1602832 AAATGCA
1 AAATGCA
*
1602839 TAATGCA
1 AAATGCA
1602846 AAATGCA
1 AAATGCA
1602853 AAATGCA
1 AAATGCA
1602860 AAATGCA
1 AAATGCA
1602867 AAATGCA
1 AAATGCA
1602874 TGTATGAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
6 5 0.08
7 55 0.92
ACGTcount: A:0.57, C:0.13, G:0.14, T:0.16
Consensus pattern (7 bp):
AAATGCA
Found at i:1603018 original size:43 final size:43
Alignment explanation
Indices: 1602948--1603057 Score: 166
Period size: 43 Copynumber: 2.5 Consensus size: 43
1602938 TCGTGCATCA
* * *
1602948 AACAAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTT
1 AACAAAAC-TTTATATATAGGGGACAACTTTCAGTCCTAACTTC
*
1602992 AACAAAACTTTATATATAGGGGACAACTTTCAGTCCTACCTTC
1 AACAAAACTTTATATATAGGGGACAACTTTCAGTCCTAACTTC
*
1603035 AACAAAACTTTATATATATGGGA
1 AACAAAACTTTATATATAGGGGA
1603058 TAATCTTCCC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
43 53 0.87
44 8 0.13
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (43 bp):
AACAAAACTTTATATATAGGGGACAACTTTCAGTCCTAACTTC
Found at i:1603072 original size:43 final size:43
Alignment explanation
Indices: 1602948--1603077 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 43
1602938 TCGTGCATCA
* * * *
1602948 AACAAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTT
1 AACAAAAC-TTTATATATAGGGGACAACTTTCACTCCTAACTTC
* *
1602992 AACAAAACTTTATATATAGGGGACAACTTTCAGTCCTACCTTC
1 AACAAAACTTTATATATAGGGGACAACTTTCACTCCTAACTTC
* * *
1603035 AACAAAACTTTATATATATGGGATAA-TCTTCCCTCCTAACTTC
1 AACAAAACTTTATATATAGGGGACAACT-TTCACTCCTAACTTC
1603078 TCTAAAGCCA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
42 1 0.01
43 67 0.88
44 8 0.11
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (43 bp):
AACAAAACTTTATATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:1605382 original size:15 final size:15
Alignment explanation
Indices: 1605325--1605384 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1605315 AACAATAATA
*
1605325 AAATAATATTGCAAAT
1 AAATAATATT-AAAAT
1605341 AAATAATGATTAAAAT
1 AAATAAT-ATTAAAAT
* *
1605357 AGAAGAA-ATTAAAAG
1 A-AATAATATTAAAAT
1605372 AAATAATATTAAA
1 AAATAATATTAAA
1605385 TTGCAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
14 4 0.11
15 14 0.38
16 12 0.32
17 7 0.19
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (15 bp):
AAATAATATTAAAAT
Found at i:1606321 original size:27 final size:26
Alignment explanation
Indices: 1606272--1606322 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1606262 TCTTCTGTTT
*
1606272 TTTGTTGTTGTTGTGTTGTTGGTTGC
1 TTTGTTGTTGTTCTGTTGTTGGTTGC
1606298 TTTGTTTGTTGTTTCTGTTG-TGGTT
1 TTTG-TTGTTG-TTCTGTTGTTGGTT
1606323 TGTTTCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 11 0.50
28 7 0.32
ACGTcount: A:0.00, C:0.04, G:0.31, T:0.65
Consensus pattern (26 bp):
TTTGTTGTTGTTCTGTTGTTGGTTGC
Found at i:1606811 original size:3 final size:3
Alignment explanation
Indices: 1606805--1606878 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
1606795 ATTTATTATT
* * *
1606805 TAA TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA TAA AAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
1606854 TAA -AA T-A TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1606879 AGTTGGGACA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 4 0.07
3 53 0.88
4 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1616821 original size:16 final size:16
Alignment explanation
Indices: 1616802--1616852 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1616792 CTTGTTAATG
*
1616802 ACCTGATTTGATATTT
1 ACCTGACTTGATATTT
*
1616818 ACCTGACTTGACATTT
1 ACCTGACTTGATATTT
1616834 ACCTGACTT-ATATATT
1 ACCTGACTTGATAT-TT
1616850 ACC
1 ACC
1616853 ATGGACGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 3 0.10
16 28 0.90
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (16 bp):
ACCTGACTTGATATTT
Found at i:1617113 original size:24 final size:23
Alignment explanation
Indices: 1617086--1617136 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1617076 TGATTAAATG
*
1617086 TAAATTAATATGGTTTAATTTATA
1 TAAATT-ATATAGTTTAATTTATA
* *
1617110 TAAATTTTATAGTTTAATTTATG
1 TAAATTATATAGTTTAATTTATA
1617133 TAAA
1 TAAA
1617137 GAAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (23 bp):
TAAATTATATAGTTTAATTTATA
Found at i:1617362 original size:12 final size:12
Alignment explanation
Indices: 1617341--1617373 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1617331 CAATTATAAC
1617341 ATAA-ATAAAAG
1 ATAATATAAAAG
1617352 ATAATATAAAAG
1 ATAATATAAAAG
*
1617364 ATAATTTAAA
1 ATAATATAAA
1617374 TAACATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (12 bp):
ATAATATAAAAG
Found at i:1617388 original size:12 final size:11
Alignment explanation
Indices: 1617367--1617406 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1617357 ATAAAAGATA
*
1617367 ATTTAAATAAC
1 ATTTGAATAAC
*
1617378 ATTTGATATAAA
1 ATTTGA-ATAAC
1617390 ATTTGAATAAC
1 ATTTGAATAAC
1617401 ATTTGA
1 ATTTGA
1617407 GTGAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTGAATAAC
Done.