Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 24
Found at i:1442502 original size:20 final size:21
Alignment explanation
Indices: 1442471--1442509 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1442461 CAGAGATTTT
*
1442471 TCCCCAAACAGCTGGAAATCA
1 TCCCCAAACAGCTAGAAATCA
1442492 TCCCC-AACAGCTAGAAAT
1 TCCCCAAACAGCTAGAAAT
1442510 GACTACATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.33, G:0.13, T:0.15
Consensus pattern (21 bp):
TCCCCAAACAGCTAGAAATCA
Found at i:1446666 original size:21 final size:21
Alignment explanation
Indices: 1446642--1446691 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1446632 AATCAAGTTT
1446642 TTTTATTTCACAAAAATCCTC
1 TTTTATTTCACAAAAATCCTC
1446663 TTTTATTTCACAAAAATCCTC
1 TTTTATTTCACAAAAATCCTC
*
1446684 TTGTATTT
1 TTTTATTT
1446692 TCTTCCTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTTATTTCACAAAAATCCTC
Found at i:1451625 original size:21 final size:21
Alignment explanation
Indices: 1451601--1451648 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1451591 ATGGAAGGCC
1451601 GGGAGAGGC-CAACGGATGA-GA
1 GGGAG-GGCTCAACGGA-GAGGA
*
1451622 GGGAGTGCTCAACGGAGAGGA
1 GGGAGGGCTCAACGGAGAGGA
1451643 GGGAGG
1 GGGAGG
1451649 AAAGCGGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.29, C:0.12, G:0.52, T:0.06
Consensus pattern (21 bp):
GGGAGGGCTCAACGGAGAGGA
Found at i:1451945 original size:23 final size:23
Alignment explanation
Indices: 1451917--1451976 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1451907 ATCAAGCACA
* * * *
1451917 ATAATATATTAGGTATCGTTTTT
1 ATAATATAATAGGTAGCGCTTAT
1451940 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1451963 ATAATAAAATAGGT
1 ATAATATAATAGGT
1451977 TAATTACTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:1452039 original size:23 final size:23
Alignment explanation
Indices: 1452004--1452063 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1451994 ATAAAGCATA
* *
1452004 ATAATATATTAGGTATCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
*
1452027 ATAATGTAATAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
*
1452050 ATAATAAAATAGGT
1 ATAATATAATAGGT
1452064 TAATTACTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:1452047 original size:87 final size:87
Alignment explanation
Indices: 1451900--1452204 Score: 450
Period size: 87 Copynumber: 3.5 Consensus size: 87
1451890 ATTTAGTTAA
* * * * *
1451900 AAATATTATCAAGCACAATAATATATTAGGTATCGTTTTTATAATATAATAGGTAGCGCTTATAT
1 AAATATTATTAAGCACAATAACATATTAGGTATCGCTTATATAATGTAATAGGTAGCGCTTATAT
1451965 AATAAAATAGGTTAATTACTGG
66 AATAAAATAGGTTAATTACTGG
* * * *
1451987 AAATATTATAAAGCATAATAATATATTAGGTATCGCTTATATAATGTAATAGGTAACGCTTATAT
1 AAATATTATTAAGCACAATAACATATTAGGTATCGCTTATATAATGTAATAGGTAGCGCTTATAT
*
1452052 AATAAAATAGGTTAATTACTAG
66 AATAAAATAGGTTAATTACTGG
* * *
1452074 AAATATTATTAAGCAAAATAACATATTAGGTA-CAACTTATATAATGTAATAGGTAGCGTTTATA
1 AAATATTATTAAGCACAATAACATATTAGGTATC-GCTTATATAATGTAATAGGTAGCGCTTATA
1452138 TAATAAAATAGGTTAATTACTGG
65 TAATAAAATAGGTTAATTACTGG
* * *
1452161 AAACATTATTAATCACAATAACATATTAGGTAACGCTTATATAA
1 AAATATTATTAAGCACAATAACATATTAGGTATCGCTTATATAA
1452205 CGTGTTGAAA
Statistics
Matches: 198, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
86 1 0.01
87 196 0.99
88 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (87 bp):
AAATATTATTAAGCACAATAACATATTAGGTATCGCTTATATAATGTAATAGGTAGCGCTTATAT
AATAAAATAGGTTAATTACTGG
Found at i:1452487 original size:19 final size:20
Alignment explanation
Indices: 1452447--1452488 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1452437 AATCATATTG
*
1452447 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGATACAGATTCCC
*
1452467 CCCAGGGGATACCGATTCCC
1 CCCAGGGGATACAGATTCCC
1452487 CC
1 CC
1452489 TGTCTAACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.40, G:0.26, T:0.14
Consensus pattern (20 bp):
CCCAGGGGATACAGATTCCC
Found at i:1455215 original size:19 final size:20
Alignment explanation
Indices: 1455175--1455216 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1455165 AATCATATTG
1455175 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
1455195 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
1455215 CC
1 CC
1455217 TGTCTAACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:1457949 original size:19 final size:20
Alignment explanation
Indices: 1457909--1457950 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1457899 AATCAGATTG
1457909 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
1457929 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
1457949 CC
1 CC
1457951 TGTCTAACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:1460658 original size:23 final size:23
Alignment explanation
Indices: 1460627--1460672 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1460617 AAGCAGATTG
*
1460627 CCCAGGGGGTACAGATTCCCCCC
1 CCCAAGGGGTACAGATTCCCCCC
*
1460650 CCCAAGGGGTACAGATTCTCCCC
1 CCCAAGGGGTACAGATTCCCCCC
1460673 TAGGGGGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.41, G:0.24, T:0.15
Consensus pattern (23 bp):
CCCAAGGGGTACAGATTCCCCCC
Found at i:1460677 original size:20 final size:20
Alignment explanation
Indices: 1460630--1460693 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
1460620 CAGATTGCCC
*
1460630 AGGGGGTACAGATTCCCCCCCCC
1 AGGGGGTACAGATT---CCCCCT
*
1460653 AAGGGGTACAGATTCTCCCCT
1 AGGGGGTACAGATTC-CCCCT
*
1460674 AGGGGGTACCGATTCCCCCT
1 AGGGGGTACAGATTCCCCCT
1460694 GTCTAACGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.17
21 17 0.47
23 13 0.36
ACGTcount: A:0.19, C:0.36, G:0.27, T:0.19
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCT
Found at i:1461803 original size:23 final size:23
Alignment explanation
Indices: 1461707--1461797 Score: 146
Period size: 23 Copynumber: 4.0 Consensus size: 23
1461697 AATCTATTTT
*
1461707 ATTATATAAGCGCTACTTATTAC
1 ATTATATAAGCGCTACCTATTAC
* *
1461730 ATTATATAAGCGTTACATATTAC
1 ATTATATAAGCGCTACCTATTAC
1461753 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
*
1461776 ATTATATAAGCGGTACCTATTA
1 ATTATATAAGCGCTACCTATTA
1461798 TGTTATTGTG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTATTAC
Found at i:1462027 original size:23 final size:23
Alignment explanation
Indices: 1461984--1462027 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1461974 TATGTTGAAA
*
1461984 GTATAGATACTTTTTATAAAAAT
1 GTATAGATACTTTTTAGAAAAAT
*
1462007 GTATCGATACTTTGTT-GAAAA
1 GTATAGATACTTT-TTAGAAAA
1462028 TTATGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (23 bp):
GTATAGATACTTTTTAGAAAAAT
Found at i:1463025 original size:3 final size:3
Alignment explanation
Indices: 1463019--1463047 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1463009 CATCATCATC
1463019 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1463048 ATGACTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1469100 original size:30 final size:30
Alignment explanation
Indices: 1469064--1469125 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1469054 TGTGAATGTC
1469064 GCGGATGTTATGAAATGTGTTGCGATTGTT
1 GCGGATGTTATGAAATGTGTTGCGATTGTT
1469094 GCGGATGTTATGAAATGTGTTGCGATTGTT
1 GCGGATGTTATGAAATGTGTTGCGATTGTT
1469124 GC
1 GC
1469126 AGGCGTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.08, G:0.34, T:0.39
Consensus pattern (30 bp):
GCGGATGTTATGAAATGTGTTGCGATTGTT
Found at i:1469710 original size:2 final size:2
Alignment explanation
Indices: 1469703--1469728 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1469693 CGAAAATGAC
1469703 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
1469729 CAACACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1471971 original size:21 final size:21
Alignment explanation
Indices: 1471819--1471991 Score: 121
Period size: 21 Copynumber: 8.0 Consensus size: 21
1471809 TTCTACGCGA
* * *
1471819 TCCTTCGAGACATAAATGTGA
1 TCCTTCGGGACATATATGTGG
* * *
1471840 TCCTTTGGAACATATATGGGG
1 TCCTTCGGGACATATATGTGG
* *
1471861 TCCTTTGGGACATATATTTGG
1 TCCTTCGGGACATATATGTGG
* *
1471882 TCCTTTGGAACATATATGTGG
1 TCCTTCGGGACATATATGTGG
* * * * *
1471903 TCCTACGAGATAATTCTATGTGA
1 TCCTTCGGGA-CA-TATATGTGG
* * *
1471926 TCCTTTGGGACATTTCTATGCGG
1 TCCTTCGGGACA--TATATGTGG
*
1471949 TCATTCGGGACATATATGTGG
1 TCCTTCGGGACATATATGTGG
*
1471970 TCCTTCGGGACATTCTATGTGG
1 TCCTTCGGGACA-TATATGTGG
1471992 CACTTCGATG
Statistics
Matches: 118, Mismatches: 30, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
21 76 0.64
22 10 0.08
23 32 0.27
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (21 bp):
TCCTTCGGGACATATATGTGG
Found at i:1472014 original size:23 final size:23
Alignment explanation
Indices: 1471982--1472029 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1471972 CTTCGGGACA
*
1471982 TTCTATGTGGCACTTCGATGCAT
1 TTCTACGTGGCACTTCGATGCAT
* *
1472005 TTCTACGTGGCACTTTGGTGCAT
1 TTCTACGTGGCACTTCGATGCAT
1472028 TT
1 TT
1472030 TATACGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (23 bp):
TTCTACGTGGCACTTCGATGCAT
Found at i:1474811 original size:21 final size:20
Alignment explanation
Indices: 1474785--1474883 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
1474775 AGGGTGTCAA
1474785 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
1474806 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
1474827 AGTGCATCCATGCA-CCTGAAC
1 AGTGCATCCATGCACCCTG--C
* *
1474848 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
*
1474869 AGAGCATCCATGCAC
1 AGTGCATCCATGCAC
1474884 TCAAACACCA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 36 0.52
22 13 0.19
23 3 0.04
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.20
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:1474967 original size:20 final size:20
Alignment explanation
Indices: 1474904--1474977 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
1474894 AATGCAATTA
1474904 GTGCATCGATGCATCCTT-TT
1 GTGCATCGATGCAT-CTTGTT
* **
1474924 GTCCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC-TTGTT
1474945 GTGCATCGATGCATCTTGTT
1 GTGCATCGATGCATCTTGTT
*
1474965 GTGCATCCATGCA
1 GTGCATCGATGCA
1474978 CGAAGGCTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 28 0.62
21 16 0.36
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (20 bp):
GTGCATCGATGCATCTTGTT
Found at i:1478329 original size:120 final size:122
Alignment explanation
Indices: 1478018--1478366 Score: 431
Period size: 123 Copynumber: 2.9 Consensus size: 122
1478008 AGGATAAACT
* * * *
1478018 GGAAATGTTATTATTTTTTTAACATTTCCGATAAAACGCTACCTAAATCATTATTTTTCTATTGA
1 GGAAATGTTATTATTTTTTTAACATTTCAG-TAAAGCGCTACCTAAATCATTATTTTTCTACTGG
* *
1478083 AAATGTTAATATTGGGCACTACCTAAAACATTATTTTTTTTACTAAAAATACGCTACTA
65 AAATGTTAATATTGGGCGCTACCTAAAACATTA-TTTTTCTACTAAAAATACGCTACTA
* *
1478142 GG-AATTTTATTATTTTTTTAACATTTTC-GATAAAGCGCTACCTAAATCATTATTTTTCTACTA
1 GGAAATGTTATTATTTTTTTAACA-TTTCAG-TAAAGCGCTACCTAAATCATTATTTTTCTACTG
* * ** * *
1478205 GAAATGTTAATATTGAGCGCTACCTAAAATATTA-TTTTCTACTGGAAATGCGCTAC-C
64 GAAATGTTAATATTGGGCGCTACCTAAAACATTATTTTTCTACTAAAAATACGCTACTA
** * *
1478262 GGAAATGTTATTA-TTTTTTAACATTTCAAGTAAAGTTCTACCTAAAACATTATTTTTCTACCGG
1 GGAAATGTTATTATTTTTTTAACATTTC-AGTAAAGCGCTACCTAAATCATTATTTTTCTACTGG
* *
1478326 AAATATTAATA-TGGGCGCTACCTCAAACATTATTTTTCTAC
65 AAATGTTAATATTGGGCGCTACCTAAAACATTATTTTTCTAC
1478367 CAGAATTTTT
Statistics
Matches: 197, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
119 22 0.11
120 59 0.30
121 28 0.14
123 82 0.42
124 6 0.03
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (122 bp):
GGAAATGTTATTATTTTTTTAACATTTCAGTAAAGCGCTACCTAAATCATTATTTTTCTACTGGA
AATGTTAATATTGGGCGCTACCTAAAACATTATTTTTCTACTAAAAATACGCTACTA
Found at i:1478687 original size:26 final size:26
Alignment explanation
Indices: 1478651--1478700 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1478641 AAAAAATAAT
1478651 AATGTTTTAGGTAATTTTTTATCGAA
1 AATGTTTTAGGTAATTTTTTATCGAA
1478677 AATGTTTTAGGTAATTTTTTATCG
1 AATGTTTTAGGTAATTTTTTATCG
1478701 GAAACGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.52
Consensus pattern (26 bp):
AATGTTTTAGGTAATTTTTTATCGAA
Found at i:1478712 original size:68 final size:70
Alignment explanation
Indices: 1478612--1478740 Score: 199
Period size: 68 Copynumber: 1.9 Consensus size: 70
1478602 AATAATAATA
* *
1478612 TTTTAGGTAATATTTTTACCGAAAATATTAAAAAATAATAATGTTTTAGGTAATT-TTTTATCGA
1 TTTTAGGTAATATTTTTACCGAAAACATTAAAAAATAATAATGTTTTAAGTAATTGTTTTATCGA
1478676 AAATG
66 AAATG
* * *
1478681 TTTTAGGTAAT-TTTTTATCGGAAACGTTAAAAAATAATAATGTTTTAAGTAATTGTTTTA
1 TTTTAGGTAATATTTTTACCGAAAACATTAAAAAATAATAATGTTTTAAGTAATTGTTTTA
1478741 GCGTCTATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 38 0.70
69 16 0.30
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (70 bp):
TTTTAGGTAATATTTTTACCGAAAACATTAAAAAATAATAATGTTTTAAGTAATTGTTTTATCGA
AAATG
Found at i:1479720 original size:10 final size:10
Alignment explanation
Indices: 1479686--1479724 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1479676 GATTGAAACC
1479686 AAAAAA-AAT
1 AAAAAATAAT
1479695 AAAAAATAAT
1 AAAAAATAAT
*
1479705 GGAAAAATAAT
1 -AAAAAATAAT
1479716 AAAAAATAA
1 AAAAAATAA
1479725 AAATATAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 6 0.23
10 11 0.42
11 9 0.35
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:1480784 original size:2 final size:2
Alignment explanation
Indices: 1480777--1480812 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1480767 ATTCTTTTAG
1480777 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
1480813 CCTAAATTGA
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):
TA
Found at i:1481695 original size:2 final size:2
Alignment explanation
Indices: 1481680--1481732 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
1481670 AGGATTCAAT
1481680 TA TA -A TA T- 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
1481720 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1481733 TGTAGTTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1489745 original size:12 final size:12
Alignment explanation
Indices: 1489728--1489752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1489718 CTCAAACAGA
1489728 GAGAATGAACGT
1 GAGAATGAACGT
1489740 GAGAATGAACGT
1 GAGAATGAACGT
1489752 G
1 G
1489753 TTGCATGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:1489814 original size:29 final size:29
Alignment explanation
Indices: 1489781--1489836 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1489771 TCCCAACACA
*
1489781 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
1489810 TAGGTCGCCATGCACTCCGGGTGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
1489837 ACCCTCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:1489895 original size:23 final size:23
Alignment explanation
Indices: 1489855--1489913 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
1489845 TCGGCTTCCT
* * *
1489855 TCGGATTCCCCCGCATAGCTCGC
1 TCGGATGCCCTCGTATAGCTCGC
* *
1489878 TCGGTTGCCCTCGTATAGCTCGT
1 TCGGATGCCCTCGTATAGCTCGC
*
1489901 TCGGATGGCCTCG
1 TCGGATGCCCTCG
1489914 GATGCTCTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.10, C:0.36, G:0.27, T:0.27
Consensus pattern (23 bp):
TCGGATGCCCTCGTATAGCTCGC
Found at i:1490028 original size:29 final size:29
Alignment explanation
Indices: 1489991--1490048 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1489981 GCAATCTCTT
*
1489991 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
1490020 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
1490049 CGGCCAACAG
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:1498977 original size:22 final size:23
Alignment explanation
Indices: 1498942--1498987 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1498932 TTATAATATA
1498942 TATTATTAAGTATTT-TTATTAT
1 TATTATTAAGTATTTATTATTAT
** *
1498964 TATTATTACTTATTTATTTTTAT
1 TATTATTAAGTATTTATTATTAT
1498987 T
1 T
1498988 TTTTATTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTATTAAGTATTTATTATTAT
Found at i:1498993 original size:17 final size:17
Alignment explanation
Indices: 1498954--1498995 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1498944 TTATTAAGTA
1498954 TTTTTA-TTATTATTAT
1 TTTTTATTTATTATTAT
** *
1498970 TACTTATTTATTTTTAT
1 TTTTTATTTATTATTAT
1498987 TTTTTATTT
1 TTTTTATTT
1498996 CAGGTCAAGG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTTATTATTAT
Found at i:1499714 original size:20 final size:20
Alignment explanation
Indices: 1499652--1499720 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1499642 AAATTGTTTT
*
1499652 TGAATAGTAT-TATACTGTA
1 TGAATAGTATCGATACTGTA
* *
1499671 TGAATAGTACCGATACTATA
1 TGAATAGTATCGATACTGTA
*
1499691 TGAATAGTATCGATACTGTG
1 TGAATAGTATCGATACTGTA
*
1499711 TGAACAGTAT
1 TGAATAGTAT
1499721 TGAATAGTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 9 0.21
20 33 0.79
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (20 bp):
TGAATAGTATCGATACTGTA
Found at i:1502455 original size:20 final size:20
Alignment explanation
Indices: 1502430--1502498 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1502420 CAATTTTTTT
*
1502430 TGAATAGTACTAATATTGTA
1 TGAATAGTACTGATATTGTA
*
1502450 TGAATAGTACTGATACTGTA
1 TGAATAGTACTGATATTGTA
* * * *
1502470 TGAATAATACCGATATTTTG
1 TGAATAGTACTGATATTGTA
1502490 TGAATAGTA
1 TGAATAGTA
1502499 ATGAACAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (20 bp):
TGAATAGTACTGATATTGTA
Found at i:1502569 original size:20 final size:20
Alignment explanation
Indices: 1502544--1502599 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1502534 AAATGGGTAC
*
1502544 CGATACTGCTATAGTAGTAT
1 CGATACTGCTACAGTAGTAT
*
1502564 CGATACTGTTACAGTAGTAT
1 CGATACTGCTACAGTAGTAT
1502584 CGATACTGCTACAGTA
1 CGATACTGCTACAGTA
1502600 AAATAAAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (20 bp):
CGATACTGCTACAGTAGTAT
Found at i:1508101 original size:2 final size:2
Alignment explanation
Indices: 1508094--1508124 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1508084 AATTGATTAA
1508094 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
1508125 GCTTAAGCTG
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:1510336 original size:23 final size:23
Alignment explanation
Indices: 1510262--1510342 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
1510252 GTATGACTAT
1510262 GTGCATCGATGCACATTC-AAGG
1 GTGCATCGATGCACATTCAAAGG
* * *
1510284 AGTGCATTGGTG--CA-TCAACATG
1 -GTGCATCGATGCACATTCAA-AGG
* *
1510306 ATGAATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTCAAAGG
1510329 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1510343 TAACCACAGA
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
20 2 0.05
21 10 0.23
22 2 0.05
23 25 0.58
24 4 0.09
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAAGG
Found at i:1516177 original size:45 final size:45
Alignment explanation
Indices: 1516113--1516219 Score: 205
Period size: 45 Copynumber: 2.4 Consensus size: 45
1516103 CGGTGCATTA
*
1516113 AGAGTGCATCGATGCATCAAGTGCATTCGATATTTCGAAATAGCC
1 AGAGTGCATCGATGCATCAAGTGCATTCGATATTTCAAAATAGCC
1516158 AGAGTGCATCGATGCATCAAGTGCATTCGATATTTCAAAATAGCC
1 AGAGTGCATCGATGCATCAAGTGCATTCGATATTTCAAAATAGCC
1516203 AGAGTGCATCGATGCAT
1 AGAGTGCATCGATGCAT
1516220 GGCTGGTGCA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (45 bp):
AGAGTGCATCGATGCATCAAGTGCATTCGATATTTCAAAATAGCC
Found at i:1516294 original size:65 final size:65
Alignment explanation
Indices: 1516160--1516320 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
1516150 AAATAGCCAG
* *
1516160 AGTGCATCGATGCATCAAGTGCATTCGAT-ATTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGATTTCAAAATAGCCACAGTGCATCGATGCATGGCT
* * * * *
1516224 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGATTTCA-AAATAGCCACAGTGCATCGATGCATGGC
1516287 T
65 T
*
1516288 AAGTGCATCGATGCATGAAATGCATTCGATGAT
1 -AGTGCATCGATGCATCAAATGCATTCGATGAT
1516321 CAATTTAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 28 0.33
65 53 0.63
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGATTTCAAAATAGCCACAGTGCATCGATGCATGGCT
Found at i:1520164 original size:6 final size:6
Alignment explanation
Indices: 1520145--1520175 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1520135 CAATCCCGAT
*
1520145 AACCCG AACTCG AACCCG AACCCG AACCCG A
1 AACCCG AACCCG AACCCG AACCCG AACCCG A
1520176 CCTGATCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.45, G:0.16, T:0.03
Consensus pattern (6 bp):
AACCCG
Found at i:1520630 original size:35 final size:33
Alignment explanation
Indices: 1520568--1520675 Score: 171
Period size: 35 Copynumber: 3.2 Consensus size: 33
1520558 GGGTTTGTAT
*
1520568 TATATAATTAAAATAAAAAATAAAAAATATTATA
1 TATATAATTAATATAAAAAAT-AAAAATATTATA
*
1520602 TATATCATTAATATAAAAAAATATAAAATATTATA
1 TATATAATTAATAT-AAAAAATA-AAAATATTATA
1520637 TATATAATTAATATAAAAAATAAAAATATTATA
1 TATATAATTAATATAAAAAATAAAAATATTATA
1520670 TATATA
1 TATATA
1520676 TATAATCGGG
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
33 17 0.25
34 21 0.30
35 31 0.45
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (33 bp):
TATATAATTAATATAAAAAATAAAAATATTATA
Found at i:1521098 original size:11 final size:11
Alignment explanation
Indices: 1521082--1521144 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
1521072 AAAATTATAT
1521082 TATTAAAAATA
1 TATTAAAAATA
1521093 TATTAAAAATA
1 TATTAAAAATA
* * ***
1521104 CACTATTGATA
1 TATTAAAAATA
1521115 -ATTATAAAAT-
1 TATTA-AAAATA
1521125 T-TTAAAAATA
1 TATTAAAAATA
1521135 TATTAAAAAT
1 TATTAAAAAT
1521145 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:1521673 original size:7 final size:7
Alignment explanation
Indices: 1521663--1521746 Score: 78
Period size: 7 Copynumber: 12.0 Consensus size: 7
1521653 CCATAAATAA
1521663 TAAACCC
1 TAAACCC
**
1521670 TAAACTA
1 TAAACCC
**
1521677 TAAACAT
1 TAAACCC
*
1521684 TAAACCA
1 TAAACCC
1521691 TAAACCC
1 TAAACCC
1521698 TAAACCC
1 TAAACCC
1521705 TAAACCC
1 TAAACCC
**
1521712 TAAACTA
1 TAAACCC
*
1521719 TAAATCC
1 TAAACCC
**
1521726 TAAACTA
1 TAAACCC
1521733 TAAACCC
1 TAAACCC
1521740 TAAACCC
1 TAAACCC
1521747 AATTATGTGA
Statistics
Matches: 60, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:1521679 original size:14 final size:14
Alignment explanation
Indices: 1521649--1521744 Score: 113
Period size: 14 Copynumber: 6.9 Consensus size: 14
1521639 ACAATGAACC
*
1521649 TAAACCATAAA-TAA
1 TAAACCCTAAACT-A
1521663 TAAACCCTAAACTA
1 TAAACCCTAAACTA
** *
1521677 TAAACATTAAACCA
1 TAAACCCTAAACTA
**
1521691 TAAACCCTAAACCC
1 TAAACCCTAAACTA
1521705 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
1521719 TAAATCCTAAACTA
1 TAAACCCTAAACTA
1521733 TAAACCCTAAAC
1 TAAACCCTAAAC
1521745 CCAATTATGT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
14 69 0.99
15 1 0.01
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:1521727 original size:21 final size:21
Alignment explanation
Indices: 1521647--1521730 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
1521637 TTACAATGAA
**
1521647 CCTAAACCATAAATAATAAAC
1 CCTAAACCATAAATCCTAAAC
* *
1521668 CCTAAACTATAAA-CATTAAAC
1 CCTAAACCATAAATC-CTAAAC
* * *
1521689 CATAAACCCTAAACCCTAAAC
1 CCTAAACCATAAATCCTAAAC
*
1521710 CCTAAACTATAAATCCTAAAC
1 CCTAAACCATAAATCCTAAAC
1521731 TATAAACCCT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 49 0.98
22 1 0.02
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (21 bp):
CCTAAACCATAAATCCTAAAC
Found at i:1524931 original size:31 final size:30
Alignment explanation
Indices: 1524896--1524953 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
1524886 GTTCGAGCCT
* *
1524896 TTTCGAGTTCTAGTCGAGTTTCAATAATATA
1 TTTCGAGTTCGAGTCGAGCTTC-ATAATATA
*
1524927 TTTCGAGTTCGAGTTGAGCTTCATAAT
1 TTTCGAGTTCGAGTCGAGCTTCATAAT
1524954 TTTTAGCTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (30 bp):
TTTCGAGTTCGAGTCGAGCTTCATAATATA
Found at i:1527396 original size:40 final size:40
Alignment explanation
Indices: 1527339--1527417 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
1527329 AAAGACATTT
1527339 ATATAAACTTCCAACAAAGTTGAAGTGATGATCTCTCTTC
1 ATATAAACTTCCAACAAAGTTGAAGTGATGATCTCTCTTC
*
1527379 ATATAAACTTCCTACAAAGTTGAAGTGATGATCTCTCTT
1 ATATAAACTTCCAACAAAGTTGAAGTGATGATCTCTCTT
1527418 TTTTCTCTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (40 bp):
ATATAAACTTCCAACAAAGTTGAAGTGATGATCTCTCTTC
Found at i:1527580 original size:14 final size:15
Alignment explanation
Indices: 1527561--1527592 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1527551 TATTTTGGTA
1527561 TTTC-TTCATTCAAT
1 TTTCTTTCATTCAAT
1527575 TTTCTTTCATTCAAT
1 TTTCTTTCATTCAAT
1527590 TTT
1 TTT
1527593 AACTTCCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTCTTTCATTCAAT
Found at i:1529866 original size:23 final size:23
Alignment explanation
Indices: 1529836--1529889 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1529826 ACATTATAAA
1529836 GAAGAGAAGAGAAAATAAGAAAG
1 GAAGAGAAGAGAAAATAAGAAAG
*
1529859 GAAGAGAAGAGAAAATAAGAGAG
1 GAAGAGAAGAGAAAATAAGAAAG
1529882 GAAGAGAA
1 GAAGAGAA
1529890 AAATACTCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (23 bp):
GAAGAGAAGAGAAAATAAGAAAG
Found at i:1534737 original size:95 final size:95
Alignment explanation
Indices: 1534574--1534767 Score: 309
Period size: 95 Copynumber: 2.0 Consensus size: 95
1534564 ATAATATTGT
* *
1534574 ATATACAATCAAGCTTGAGCTGTCCCTCTAAGGCAACTGGTTAAACGCCCCGTCTTCATGGATAA
1 ATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAACTGGTTAAACGCCCCGTCTTCATGGATAA
*
1534639 GATTCACCTAGCCTGATAAAGGTGATTATA
66 GATTCACCTAGCCCGATAAAGGTGATTATA
* * *
1534669 ATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAG-CTTTATGGATA
1 ATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAACTGGTTAAACGCCCC-GTCTTCATGGATA
*
1534733 AGATTCAGCTAGCCCGATAAAGGTGATTATA
65 AGATTCACCTAGCCCGATAAAGGTGATTATA
1534764 ATAT
1 ATAT
1534768 TGAGTTGTCC
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 90 0.99
96 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (95 bp):
ATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAACTGGTTAAACGCCCCGTCTTCATGGATAA
GATTCACCTAGCCCGATAAAGGTGATTATA
Found at i:1535420 original size:65 final size:66
Alignment explanation
Indices: 1535310--1535465 Score: 210
Period size: 65 Copynumber: 2.4 Consensus size: 66
1535300 CACCCATTTT
* *
1535310 GAATGCATTTTGTGTACCGATGCAC-GAGCCATGCATCGATTCACTCTTGAAT-ATTTTGAAACA
1 GAATGCATTTTGTGTACCGATGCACAGAGCCATGCATCGATGCACTCTAGAATCA-TTTGAAACA
1535373 TC
65 TC
* **
1535375 GAATACATTTTGTGTACCGATGCACAGA-CCATGCATCGATGCACTCTAGGCTCATTTGAAACAT
1 GAATGCATTTTGTGTACCGATGCACAGAGCCATGCATCGATGCACTCTAGAATCATTTGAAACAT
1535439 C
66 C
* * *
1535440 GAATGTAATTAGTGTACCGATGCACA
1 GAATGCATTTTGTGTACCGATGCACA
1535466 CCTAGTGTAC
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 77 0.96
66 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (66 bp):
GAATGCATTTTGTGTACCGATGCACAGAGCCATGCATCGATGCACTCTAGAATCATTTGAAACAT
C
Found at i:1545991 original size:85 final size:85
Alignment explanation
Indices: 1545890--1546390 Score: 587
Period size: 85 Copynumber: 5.9 Consensus size: 85
1545880 AACTATTGGA
* ** * *
1545890 AGCATAGCTCAAGGCGAAAAGGACTATCTGTCAACCAAGACCTTCGAGTTTGATTACATTCAGCT
1 AGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCT
*
1545955 CAAAGGTATATCAAATTTAC
66 CAAAGGCATATCAAATTTAC
* * * * *
1545975 AGCATAACTCAAGGCGAGAAA-GGTTATTTGTCAATAAAGACCTTCGAATTCGATTACATTAAGT
1 AGCATAACTCAAGGCGA-AAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
**
1546039 TCAAAGGCACGTCAAATTTAC
65 TCAAAGGCATATCAAATTTAC
** * * * * *
1546060 AGCATAGTTCAAGGCGAGAATGGATATTTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
1 AGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCT
* *
1546125 CAAAGGAACATCAAATTTAC
66 CAAAGGCATATCAAATTTAC
* * * * *
1546145 ATCATAATTTAAGACGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCT
1 AGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCT
* *
1546210 CAAAGGCATATCCAATTTAT
66 CAAAGGCATATCAAATTTAC
* * * * *
1546230 AACATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACATTCGAGTTCGATTACAATCAGCT
1 AGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCT
*
1546295 AAAAGGCATATCAAATTTAC
66 CAAAGGCATATCAAATTTAC
* * * * *
1546315 AGTATAACTCAAGGCGAGAAGGGTTATTTGTC-A-ATA-ACTTTCGAGTTCGATTACATTCAGCT
1 AGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCT
* *
1546377 CAAAAGCCTATCAA
66 CAAAGGCATATCAA
1546391 CCACATGGTA
Statistics
Matches: 358, Mismatches: 56, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
82 35 0.10
83 2 0.01
84 3 0.01
85 315 0.88
86 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (85 bp):
AGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCT
CAAAGGCATATCAAATTTAC
Found at i:1546963 original size:3 final size:3
Alignment explanation
Indices: 1546955--1546979 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1546945 ATAATACATA
1546955 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1546980 TCTTTTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1546967 original size:25 final size:26
Alignment explanation
Indices: 1546924--1546972 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1546914 ACATACTTAT
*
1546924 TACATATTTTATTTATATT-TTATAA
1 TACATATATTATTTATATTATTATAA
1546949 TACATATATTA-TTATTATTATTAT
1 TACATATATTATTTA-TATTATTAT
1546973 TATTATTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (26 bp):
TACATATATTATTTATATTATTATAA
Found at i:1548604 original size:7 final size:7
Alignment explanation
Indices: 1548587--1548652 Score: 64
Period size: 7 Copynumber: 9.1 Consensus size: 7
1548577 GTCTAGATTT
1548587 TTTTATTA
1 TTTT-TTA
1548595 TTTTTTA
1 TTTTTTA
1548602 -TTTTTA
1 TTTTTTA
1548608 TGTTTTT-
1 T-TTTTTA
* *
1548615 TCCTTTGA
1 T-TTTTTA
1548623 TTTATTTA
1 TTT-TTTA
1548631 TTTTTTA
1 TTTTTTA
1548638 TTTTTTA
1 TTTTTTA
1548645 TTTTTTA
1 TTTTTTA
1548652 T
1 T
1548653 CTAATATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
6 6 0.12
7 27 0.55
8 16 0.33
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:1549676 original size:23 final size:23
Alignment explanation
Indices: 1549629--1549676 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1549619 AATAACATAT
**
1549629 TAGGTACCGCTTATATAATGTAA
1 TAGGTACCGCTTATATAATAAAA
*
1549652 TAGGTAGCGCTTATATAATAAAA
1 TAGGTACCGCTTATATAATAAAA
1549675 TA
1 TA
1549677 TGTTAATTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (23 bp):
TAGGTACCGCTTATATAATAAAA
Found at i:1549733 original size:23 final size:23
Alignment explanation
Indices: 1549707--1549763 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
1549697 ATCAAGCACA
* * *
1549707 ATAATATATTAGGTACCGCTTAT
1 ATAATATAATAGATACCACTTAT
* *
1549730 ATAATGTAATAGATATCACTTAT
1 ATAATATAATAGATACCACTTAT
*
1549753 ATAATAAAATA
1 ATAATATAATA
1549764 TGTTAATTAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGATACCACTTAT
Found at i:1549765 original size:87 final size:87
Alignment explanation
Indices: 1549619--1549850 Score: 392
Period size: 87 Copynumber: 2.7 Consensus size: 87
1549609 TACCAAGTAA
1549619 AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATATGTTAAT
1 AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATATGTTAAT
* * *
1549684 TGCTGGAACCATTATCAAGCAC
66 TACTGGAAACATTATCAAACAC
* * * *
1549706 AATAATATATTAGGTACCGCTTATATAATGTAATAGATATCACTTATATAATAAAATATGTTAAT
1 AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATATGTTAAT
1549771 TACTGGAAACATTATCAAACAC
66 TACTGGAAACATTATCAAACAC
*
1549793 AATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATA
1 AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATA
1549851 GGTAGCGCTT
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 133 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (87 bp):
AATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATATGTTAAT
TACTGGAAACATTATCAAACAC
Found at i:1549820 original size:23 final size:23
Alignment explanation
Indices: 1549794--1549876 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
1549784 ATCAAACACA
* *
1549794 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1549817 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1549840 ATAATAAAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1549863 ATAATAAAATAGGT
1 ATAATATAATAGGT
1549877 TAATTACTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:1549926 original size:87 final size:87
Alignment explanation
Indices: 1549826--1550058 Score: 385
Period size: 87 Copynumber: 2.7 Consensus size: 87
1549816 TATAATGTAA
** *
1549826 TAGGTAGCGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAAC
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTGGAAAC
1549891 ATTATCAAGCACAATAACATAT
66 ATTATCAAGCACAATAACATAT
* * * *
1549913 TAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAATTACTGGAAAT
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTGGAAAC
1549978 ATTATCAAGCACAATAACATAT
66 ATTATCAAGCACAATAACATAT
* *
1550000 TAGGTAGCGCTTATATAACGTAATAGGTAGCTCTTATATAATAAAATAGGTTAATTACT
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACT
1550059 TAATTTGTTA
Statistics
Matches: 134, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 134 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (87 bp):
TAGGTAGCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTGGAAAC
ATTATCAAGCACAATAACATAT
Found at i:1549930 original size:23 final size:23
Alignment explanation
Indices: 1549904--1549963 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1549894 ATCAAGCACA
* *
1549904 ATAACATATTAGGTACCACTTAT
1 ATAACATAATAGGTAACACTTAT
**
1549927 ATAATGTAATAGGTAACACTTAT
1 ATAACATAATAGGTAACACTTAT
* *
1549950 ATAATAAAATAGGT
1 ATAACATAATAGGT
1549964 TAATTACTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACACTTAT
Found at i:1549962 original size:110 final size:110
Alignment explanation
Indices: 1549707--1549963 Score: 388
Period size: 110 Copynumber: 2.3 Consensus size: 110
1549697 ATCAAGCACA
* * * ** * * *
1549707 ATAATATATTAGGTACCGCTTATATAATGTAATAGATATCACTTATATAATAAAATATGTTAATT
1 ATAATGTAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATT
* *
1549772 ACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTAT
66 ACTGGAAACATTATCAAACACAATAACATATTAGGTACCACTTAT
* *
1549817 ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
1 ATAATGTAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATT
*
1549882 ACTGGAAACATTATCAAGCACAATAACATATTAGGTACCACTTAT
66 ACTGGAAACATTATCAAACACAATAACATATTAGGTACCACTTAT
*
1549927 ATAATGTAATAGGTAACACTTATATAATAAAATAGGT
1 ATAATGTAATAGGTAACGCTTATATAATAAAATAGGT
1549964 TAATTACTGG
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 133 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (110 bp):
ATAATGTAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATT
ACTGGAAACATTATCAAACACAATAACATATTAGGTACCACTTAT
Found at i:1549971 original size:197 final size:197
Alignment explanation
Indices: 1549620--1550050 Score: 709
Period size: 197 Copynumber: 2.2 Consensus size: 197
1549610 ACCAAGTAAA
* * * ** *
1549620 ATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATATGTTAATT
1 ATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
* * * * *
1549685 GCTGGAACCATTATCAAGCACAATAATATATTAGGTACCGCTTATATAATGTAATAGATATCACT
66 ACTGGAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGATAACACT
*
1549750 TATATAATAAAATATGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTT
131 TATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTT
1549815 AT
196 AT
*
1549817 ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
1 ATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
*
1549882 ACTGGAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAACACT
66 ACTGGAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGATAACACT
* *
1549947 TATATAATAAAATAGGTTAATTACTGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTT
131 TATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTT
1550012 AT
196 AT
*
1550014 ATAACGTAATAGGTAGCTCTTATATAATAAAATAGGT
1 ATAACGTAATAGGTAGCGCTTATATAATAAAATAGGT
1550051 TAATTACTTA
Statistics
Matches: 216, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
197 216 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (197 bp):
ATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
ACTGGAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGATAACACT
TATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTT
AT
Found at i:1550026 original size:23 final size:23
Alignment explanation
Indices: 1549991--1550050 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1549981 ATCAAGCACA
*
1549991 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
1550014 ATAACGTAATAGGTAGCTCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
1550037 ATAATAAAATAGGT
1 ATAACATAATAGGT
1550051 TAATTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1550224 original size:18 final size:19
Alignment explanation
Indices: 1550201--1550244 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1550191 ACTTAACTTG
1550201 TACGTTAT-AAAAAAAAGC
1 TACGTTATAAAAAAAAAGC
1550219 TACGTTATAAAAAAAAAGC
1 TACGTTATAAAAAAAAAGC
1550238 TACGTTA
1 TACGTTA
1550245 ATTGATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (19 bp):
TACGTTATAAAAAAAAAGC
Found at i:1550623 original size:24 final size:23
Alignment explanation
Indices: 1550594--1550649 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
1550584 TTACCAAGGA
1550594 TAACAATAAAATAATATTATTTAT
1 TAACAATAAAATAATATTATTT-T
1550618 TAACAA-AATAATAATATTATTTT
1 TAACAATAA-AATAATATTATTTT
1550641 TAA-AATAAA
1 TAACAATAAA
1550650 CATTACAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.10
23 8 0.27
24 19 0.63
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
TAACAATAAAATAATATTATTTT
Found at i:1551033 original size:196 final size:196
Alignment explanation
Indices: 1550656--1551283 Score: 921
Period size: 196 Copynumber: 3.2 Consensus size: 196
1550646 TAAACATTAC
* *
1550656 AAATTTATC-TATTACATTATAATTATCGGTTTCGATGTTTTTGGGATTGATACAATTT--TAAA
1 AAATTTA-CATATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAA
* * *
1550718 TGTATTGACACTTTATGTGTGCACCTCGTTGCATTCATTCTGGAAAAAAATATCAACACAAACTT
64 TGTATCGACACTTTATGTGTGCACCTTGTTGCATTCATTCTGG-AAAAAATATCGACACAAACTT
* *
1550783 AAAATGTGTCGATACATTATGTAGAGCTATTTTCTCATAAAACCGGTATATTTATACTGAGTACA
128 AAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACCGAGTACA
1550848 TTGT
193 TTGT
*
1550852 AAATTTACATATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
1 AAATTTACATATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
*
1550917 TATCGACACTTTATGTGTGCAACTTGTTGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAA
66 TATCGACACTTTATGTGTGCACCTTGTTGCATTCATTCTGGAAAAAA-TATCGACACAAACTTAA
1550982 AATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA-CGGTATATTTATACCGAGTACATT
130 AATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACCGAGTACATT
1551046 GT
195 GT
*
1551048 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
1 AAATTTACATATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
* * * ***
1551113 TATCGACACTTTATGTGTATC-CCGTT-TGGCATTCATTCTAGACAAAATATATCGACAC-TTTT
66 TATCGACACTTTATGTGT-GCACC-TTGTTGCATTCATTCTGGA-AAAA-ATATCGACACAAACT
* * * *
1551175 TAAATTTTTGTCGATACATTATGTTGACCTATTTTCTCATAAAATCGGTATATTTATACCG-GTT
127 TAAA-ATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACCGAG-T
*
1551239 ATATTGT
190 ACATTGT
1551246 AAATTTACATATTACATTATAATTATCGGTTTCGATGT
1 AAATTTACATATTACATTATAATTATCGGTTTCGATGT
1551284 AACATATGTG
Statistics
Matches: 398, Mismatches: 23, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
195 4 0.01
196 181 0.45
197 152 0.38
198 61 0.15
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (196 bp):
AAATTTACATATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
TATCGACACTTTATGTGTGCACCTTGTTGCATTCATTCTGGAAAAAATATCGACACAAACTTAAA
ATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACCGAGTACATTG
T
Found at i:1551456 original size:28 final size:27
Alignment explanation
Indices: 1551399--1551463 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
1551389 ATAATTTATA
*
1551399 ATAATTTATT-TTAATAAAATATAATC
1 ATAATTTTTTATTAATAAAATATAATC
*
1551425 ATAATTTTTTATTTATAAAATTATAGAT-
1 ATAATTTTTTATTAATAAAA-TATA-ATC
*
1551453 ATAATATTTTA
1 ATAATTTTTTA
1551464 ATAGTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 9 0.27
27 8 0.24
28 14 0.42
29 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
ATAATTTTTTATTAATAAAATATAATC
Found at i:1552490 original size:21 final size:21
Alignment explanation
Indices: 1552466--1552506 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1552456 TAAATAACCC
*
1552466 AATAATAACATTTTCGATAAA
1 AATAATAACATTTTAGATAAA
*
1552487 AATAATAATATTTTAGATAA
1 AATAATAACATTTTAGATAA
1552507 TTTTTACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
AATAATAACATTTTAGATAAA
Found at i:1553440 original size:73 final size:73
Alignment explanation
Indices: 1553363--1553602 Score: 257
Period size: 73 Copynumber: 3.3 Consensus size: 73
1553353 TTTAATATAA
1553363 AATTATTAAATTTATTTTTATTTTAGATCTTATTTTAACTACATTTTTAAATATATATAATATGT
1 AATTATTAAATTTATTTTTATTTTAGATCTTATTTTAACTACATTTTTAAATATATATAATATGT
1553428 ATTTAATT
66 ATTTAATT
* *
1553436 AATTATTAATAAGTTTACTTTTTACTTTTTA-A--TTATTTT-A-TATC-TTATTAAAAATAT-T
1 AATTATT-A-AA-TTTA-TTTTTA--TTTTAGATCTTATTTTAACTA-CATTTTTAAATATATAT
*
1553494 AA-ATTTAATTTAATAT
59 AATATGT-ATTTAAT-T
* * *
1553510 AAACATATTAAATTTACTTTTATTTTAGATCTTATTTTAACTACATTTTTTAATATATATAATAT
1 -AA-TTATTAAATTTATTTTTATTTTAGATCTTATTTTAACTACATTTTTAAATATATATAATAT
1553575 GTATTTAATT
64 GTATTTAATT
1553585 AATTATT-AA-TTATTTTTA
1 AATTATTAAATTTATTTTTA
1553603 AATATATAAA
Statistics
Matches: 137, Mismatches: 11, Indels: 40
0.73 0.06 0.21
Matches are distributed among these distances:
70 5 0.04
71 9 0.07
72 10 0.07
73 32 0.23
74 21 0.15
75 20 0.15
76 25 0.18
77 9 0.07
78 1 0.01
79 5 0.04
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (73 bp):
AATTATTAAATTTATTTTTATTTTAGATCTTATTTTAACTACATTTTTAAATATATATAATATGT
ATTTAATT
Found at i:1553982 original size:27 final size:27
Alignment explanation
Indices: 1553952--1554026 Score: 141
Period size: 27 Copynumber: 2.8 Consensus size: 27
1553942 ATTTAAAATA
1553952 AAAATAAATTTAATATATTTATATTTT
1 AAAATAAATTTAATATATTTATATTTT
1553979 AAAATAAATTTAATATATTTATATTTT
1 AAAATAAATTTAATATATTTATATTTT
*
1554006 AAATTAAATTTAATATATTTA
1 AAAATAAATTTAATATATTTA
1554027 ATTACTTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AAAATAAATTTAATATATTTATATTTT
Found at i:1553985 original size:33 final size:31
Alignment explanation
Indices: 1553942--1554026 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 31
1553932 TTAAAATAAG
1553942 ATTTAAAATAAAAATAAATTTAATATATTTAT
1 ATTT-AAATAAAAATAAATTTAATATATTTAT
1553974 ATTT---T-AAAATAAATTTAATATATTTAT
1 ATTTAAATAAAAATAAATTTAATATATTTAT
*
1554001 ATTT---T-AAATTAAATTTAATATATTTA
1 ATTTAAATAAAAATAAATTTAATATATTTA
1554027 ATTACTTAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
27 47 0.90
28 1 0.02
32 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTTAAATAAAAATAAATTTAATATATTTAT
Found at i:1554043 original size:27 final size:25
Alignment explanation
Indices: 1553954--1554044 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 25
1553944 TTAAAATAAA
1553954 AATAAATTTAATATATTTATATTTT
1 AATAAATTTAATATATTTATATTTT
1553979 AAAATAAATTTAATATATTTATATTTT
1 --AATAAATTTAATATATTTATATTTT
1554006 AAATTAAATTTAATATATTTA-ATTACTT
1 -AA-TAAATTTAATATATTTATATT--TT
1554034 AATAATATTTA
1 AATAA-ATTTA
1554045 TTTTGAATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.15
27 49 0.82
28 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
AATAAATTTAATATATTTATATTTT
Found at i:1554224 original size:20 final size:20
Alignment explanation
Indices: 1554199--1554245 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1554189 CAATTTTCTT
*
1554199 TCATCATATGGTCTCACGTG
1 TCATCATATGGTCTCACATG
1554219 TCATCATATGGTCTCACATG
1 TCATCATATGGTCTCACATG
*
1554239 TTATCAT
1 TCATCAT
1554246 CTAATTGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (20 bp):
TCATCATATGGTCTCACATG
Found at i:1558226 original size:26 final size:26
Alignment explanation
Indices: 1558197--1558253 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1558187 CCGAACCTGA
1558197 CGGGTTTTGACCCGATCAGATTCGAT
1 CGGGTTTTGACCCGATCAGATTCGAT
1558223 CGGGTTTTGACCCGATCAGATTCGAT
1 CGGGTTTTGACCCGATCAGATTCGAT
1558249 CGGGT
1 CGGGT
1558254 CGATTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.30
Consensus pattern (26 bp):
CGGGTTTTGACCCGATCAGATTCGAT
Found at i:1559363 original size:28 final size:26
Alignment explanation
Indices: 1559299--1559354 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1559289 TAAAAAATTA
*
1559299 AATT-TATGTAAAATATAGAGAGATTG
1 AATTCTAT-TAAAAAATAGAGAGATTG
*
1559325 AATTCTATTAAAAAATAGAGAGGTTG
1 AATTCTATTAAAAAATAGAGAGATTG
1559351 AATT
1 AATT
1559355 AATTTTTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (26 bp):
AATTCTATTAAAAAATAGAGAGATTG
Found at i:1560556 original size:16 final size:15
Alignment explanation
Indices: 1560526--1560563 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1560516 TTAAATAAAG
1560526 AAAA-TAAAATGCAT
1 AAAATTAAAATGCAT
*
1560540 AAATTTAAAAGTGCAT
1 AAAATTAAAA-TGCAT
1560556 AAAATTAA
1 AAAATTAA
1560564 GTAACGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 3 0.15
15 5 0.25
16 12 0.60
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (15 bp):
AAAATTAAAATGCAT
Found at i:1560770 original size:32 final size:32
Alignment explanation
Indices: 1560731--1560838 Score: 141
Period size: 32 Copynumber: 3.4 Consensus size: 32
1560721 CGGTTAGTAA
*
1560731 TTAGCGGTTAGAAAGGTTAACTATTAGAAAAG
1 TTAGCGGTTAGAAAGGTTAGCTATTAGAAAAG
1560763 TTAGCGGTTAGAAAGGTTAGCTATTAGAAAAG
1 TTAGCGGTTAGAAAGGTTAGCTATTAGAAAAG
* * *
1560795 TTAGCTGTTAG--TGGTTAGC-AGTTAGAAATG
1 TTAGCGGTTAGAAAGGTTAGCTA-TTAGAAAAG
*
1560825 TTAGCTGTTAGAAA
1 TTAGCGGTTAGAAA
1560839 AATTAGCGGT
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
29 1 0.01
30 26 0.38
32 41 0.60
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (32 bp):
TTAGCGGTTAGAAAGGTTAGCTATTAGAAAAG
Found at i:1560812 original size:46 final size:46
Alignment explanation
Indices: 1560762--1560858 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 46
1560752 TATTAGAAAA
* * *
1560762 GTTAGCGGTTAGAAAGGTTAGCTATTAGAAAAGTTAGCTGTTAGTG
1 GTTAGCAGTTAGAAAGGTTAGCTATTAGAAAAATTAGCGGTTAGTG
* *
1560808 GTTAGCAGTTAGAAATGTTAGCTGTTAGAAAAATTAGCGGTTAGTG
1 GTTAGCAGTTAGAAAGGTTAGCTATTAGAAAAATTAGCGGTTAGTG
1560854 GTTAG
1 GTTAG
1560859 AAGAGTCCGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (46 bp):
GTTAGCAGTTAGAAAGGTTAGCTATTAGAAAAATTAGCGGTTAGTG
Found at i:1560850 original size:16 final size:16
Alignment explanation
Indices: 1560711--1560851 Score: 110
Period size: 16 Copynumber: 9.0 Consensus size: 16
1560701 ACAAATAAAT
1560711 AAAAGGTTAGCGGTTAG
1 AAAA-GTTAGCGGTTAG
*
1560728 -TAA-TTAGCGGTTAG
1 AAAAGTTAGCGGTTAG
* * **
1560742 AAAGGTTAACTATTAG
1 AAAAGTTAGCGGTTAG
1560758 AAAAGTTAGCGGTTAG
1 AAAAGTTAGCGGTTAG
* **
1560774 AAAGGTTAGCTATTAG
1 AAAAGTTAGCGGTTAG
*
1560790 AAAAGTTAGCTGTTAG
1 AAAAGTTAGCGGTTAG
** *
1560806 --TGGTTAGCAGTTAG
1 AAAAGTTAGCGGTTAG
* *
1560820 AAATGTTAGCTGTTAG
1 AAAAGTTAGCGGTTAG
*
1560836 AAAAATTAGCGGTTAG
1 AAAAGTTAGCGGTTAG
1560852 TGGTTAGAAG
Statistics
Matches: 96, Mismatches: 24, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 73 0.76
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.30
Consensus pattern (16 bp):
AAAAGTTAGCGGTTAG
Found at i:1563473 original size:66 final size:67
Alignment explanation
Indices: 1563382--1563546 Score: 206
Period size: 67 Copynumber: 2.5 Consensus size: 67
1563372 TTTTCAAATG
* * * *
1563382 TGTGTTTCGAGAGAAAACTATCTCAAGCAAGAC-AAAATTTGTTTTGAAAGAAATAGTCTCAAAG
1 TGTGTTTCAAGAG-AAACTATCTCAAGCAAGACGAAAATTTGTTTGGAAAGAAACAATCTCAAAG
1563446 GCT
65 GCT
* * * *
1563449 TGTGTTTCAAAAGAAACTATCTCAAGCGAGACGAAACTTTGTTTGGAGAGAAACAATCTCAAAGG
1 TGTGTTTCAAGAGAAACTATCTCAAGCAAGACGAAAATTTGTTTGGAAAGAAACAATCTCAAAGG
*
1563514 TT
66 CT
* * *
1563516 TATATTTCAAGAGAAACTGTCTCAAGCAAGA
1 TGTGTTTCAAGAGAAACTATCTCAAGCAAGA
1563547 ATTTTTTTTT
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 18 0.22
67 65 0.78
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (67 bp):
TGTGTTTCAAGAGAAACTATCTCAAGCAAGACGAAAATTTGTTTGGAAAGAAACAATCTCAAAGG
CT
Found at i:1563606 original size:36 final size:37
Alignment explanation
Indices: 1563560--1563645 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
1563550 TTTTTTTAGG
* * **
1563560 AAAACAATCTCAAGTGAGAC-CAGTTTTGTTTCAAGA
1 AAAACAATCTCAAATGAGACAAAACTTTGTTTCAAGA
*
1563596 AAAACTATCTCAAATGAGACAAAACTTTGTTTCAAGA
1 AAAACAATCTCAAATGAGACAAAACTTTGTTTCAAGA
*
1563633 GAAACAATCTCAA
1 AAAACAATCTCAA
1563646 CGGTGACAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 18 0.43
37 24 0.57
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (37 bp):
AAAACAATCTCAAATGAGACAAAACTTTGTTTCAAGA
Found at i:1565525 original size:23 final size:23
Alignment explanation
Indices: 1565479--1565546 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1565469 TGCTATATAA
* * *
1565479 AATTATCCCGAAGGACCTCGTAT
1 AATTATCTCGAAGGACCACATAT
*
1565502 AATTATCTCGAATGACCACATAT
1 AATTATCTCGAAGGACCACATAT
*
1565525 -A-TCTCTCGAAGGACCACATAT
1 AATTATCTCGAAGGACCACATAT
1565546 A
1 A
1565547 TGTCCCGAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 18 0.47
22 1 0.03
23 19 0.50
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.26
Consensus pattern (23 bp):
AATTATCTCGAAGGACCACATAT
Found at i:1565533 original size:21 final size:21
Alignment explanation
Indices: 1565507--1565560 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1565497 CGTATAATTA
*
1565507 TCTCGAATGACCACATATATC
1 TCTCGAAGGACCACATATATC
*
1565528 TCTCGAAGGACCACATATATG
1 TCTCGAAGGACCACATATATC
*
1565549 TCCCGAAGGACC
1 TCTCGAAGGACC
1565561 GCGTAGAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (21 bp):
TCTCGAAGGACCACATATATC
Found at i:1572671 original size:12 final size:12
Alignment explanation
Indices: 1572656--1572686 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1572646 ATTTTCTTCC
1572656 TTTTTTTTCTCT
1 TTTTTTTTCTCT
1572668 TTTTTTTTCTCT
1 TTTTTTTTCTCT
1572680 TTTTTTT
1 TTTTTTT
1572687 ATATGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTTCTCT
Found at i:1572672 original size:10 final size:11
Alignment explanation
Indices: 1572637--1572686 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 11
1572627 TAATTTGTTC
*
1572637 TTTTTCTTCATT
1 TTTTTC-TCTTT
*
1572649 TTCTTC-CTTT
1 TTTTTCTCTTT
1572659 TTTTTCTCTTTT
1 TTTTTCTC-TTT
1572671 TTTTTCTCTTT
1 TTTTTCTCTTT
1572682 TTTTT
1 TTTTT
1572687 ATATGTCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 8 0.24
11 9 0.27
12 16 0.48
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:1576436 original size:16 final size:16
Alignment explanation
Indices: 1576410--1576451 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1576400 CGGTTAGTAA
* *
1576410 TTAGCGGTTAGAAAGG
1 TTAGCGATTAGAAAAG
*
1576426 TTAGCTATTAGAAAAG
1 TTAGCGATTAGAAAAG
1576442 TTAGCGATTA
1 TTAGCGATTA
1576452 ACTGTTAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (16 bp):
TTAGCGATTAGAAAAG
Found at i:1576865 original size:2 final size:2
Alignment explanation
Indices: 1576858--1576882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1576848 ACTAGATTTA
1576858 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 A
1576883 GGACTTTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1585958 original size:23 final size:25
Alignment explanation
Indices: 1585932--1585981 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
1585922 AATCTTATAT
1585932 GGCACTACGGTG-AAA-TTCTACGC
1 GGCACTACGGTGCAAATTTCTACGC
*
1585955 GGCACTTCGGTGCAAATTTCTACGC
1 GGCACTACGGTGCAAATTTCTACGC
1585980 GG
1 GG
1585982 TCCTTGGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.46
24 3 0.12
25 10 0.42
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (25 bp):
GGCACTACGGTGCAAATTTCTACGC
Found at i:1586019 original size:24 final size:24
Alignment explanation
Indices: 1585932--1586021 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
1585922 AATCTTATAT
*
1585932 GGCACTACGGTG-AAATTCTACGC
1 GGCACTTCGGTGCAAATTCTACGC
1585955 GGCACTTCGGTGCAAATTTCTACGC
1 GGCACTTCGGTGCAAA-TTCTACGC
* * *
1585980 GGTC-CTT-GGGGACAAATTCTATGT
1 GG-CACTTCGGTG-CAAATTCTACGC
1586004 GGCACTTCGGTGCAAATT
1 GGCACTTCGGTGCAAATT
1586022 TATACGAGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
23 12 0.21
24 23 0.41
25 20 0.36
26 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (24 bp):
GGCACTTCGGTGCAAATTCTACGC
Found at i:1586576 original size:21 final size:21
Alignment explanation
Indices: 1586550--1586600 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1586540 AGCTGAAGTT
1586550 ACTGTAGCAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
* *
1586571 ACTGTAGCAGTGCATCGGTGC
1 ACTGTAGCAGTGCATCGATAC
1586592 ACTGTAGCA
1 ACTGTAGCA
1586601 CTGTTCATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:1588014 original size:9 final size:8
Alignment explanation
Indices: 1587999--1588075 Score: 75
Period size: 9 Copynumber: 9.0 Consensus size: 8
1587989 CTTTTATTTA
1587999 TTTTTCTT
1 TTTTTCTT
1588007 TTTCTTCTT
1 TTT-TTCTT
*
1588016 CTTTTCTT
1 TTTTTCTT
1588024 TTTTATCTT
1 TTTT-TCTT
1588033 TTTTCTCTTTT
1 TTTT-TC--TT
1588044 TTTTTCATT
1 TTTTTC-TT
*
1588053 GTTTTC-T
1 TTTTTCTT
1588060 TTTTTCTT
1 TTTTTCTT
1588068 TTTTTCTT
1 TTTTTCTT
1588076 GATCGCATCG
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
7 6 0.10
8 20 0.34
9 24 0.41
10 2 0.03
11 6 0.10
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1588049 original size:28 final size:27
Alignment explanation
Indices: 1588000--1588072 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
1587990 TTTTATTTAT
* * *
1588000 TTTTC-TTTTTCTTCTTCTTTTC-TTT
1 TTTTCTTTTTTCTTTTTTTTTTCATTG
1588025 TTTATCTTTTTTCTCTTTTTTTTTCATTG
1 TTT-TCTTTTTTCT-TTTTTTTTTCATTG
1588054 TTTTCTTTTTTCTTTTTTT
1 TTTTCTTTTTTCTTTTTTT
1588073 CTTGATCGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 3 0.07
26 2 0.05
27 13 0.32
28 18 0.44
29 5 0.12
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.81
Consensus pattern (27 bp):
TTTTCTTTTTTCTTTTTTTTTTCATTG
Found at i:1590823 original size:21 final size:20
Alignment explanation
Indices: 1590737--1590894 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1590727 AAATGACCAA
**
1590737 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1590756 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1590776 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1590796 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1590817 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1590838 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1590858 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1590879 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1590895 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1590885 original size:20 final size:20
Alignment explanation
Indices: 1590861--1591034 Score: 208
Period size: 20 Copynumber: 8.7 Consensus size: 20
1590851 CGATTTTCCA
* ** *
1590861 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1590881 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1590901 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
1590921 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
1590941 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1590961 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
1590981 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1591001 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1591022 AAATCGCAACGCG
1 AAATCGCAACGCG
1591035 ATATTTAAAG
Statistics
Matches: 132, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 112 0.85
21 17 0.13
22 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1591456 original size:33 final size:33
Alignment explanation
Indices: 1591417--1591487 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1591407 TTCACTTAGA
*
1591417 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1591450 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1591483 TTTCA
1 TTTCA
1591488 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1591624 original size:41 final size:41
Alignment explanation
Indices: 1591566--1591643 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1591556 TTGCAGAAGA
*
1591566 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
1591607 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1591644 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:1591640 original size:21 final size:21
Alignment explanation
Indices: 1591567--1591642 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1591557 TGCAGAAGAG
*
1591567 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
1591588 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
1591608 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
1591629 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1591643 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1591646 original size:14 final size:14
Alignment explanation
Indices: 1591627--1591683 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1591617 GAGAAATGAA
1591627 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1591641 AATCGCAACGCGATATGAA
1 AATCGCAA--CG--A-GAG
1591660 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1591674 AATCGCAACG
1 AATCGCAACG
1591684 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1591662 original size:33 final size:33
Alignment explanation
Indices: 1591622--1591686 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
1591612 AACGAGAGAA
1591622 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
1591655 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1591687 AACCAAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
Found at i:1591695 original size:33 final size:33
Alignment explanation
Indices: 1591625--1591699 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
1591615 GAGAGAAATG
* **
1591625 AAAATCGCAACGAGAGAATCGCAACGCGATATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1591658 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1591691 AAAATCGCA
1 AAAATCGCA
1591700 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:1591717 original size:19 final size:19
Alignment explanation
Indices: 1591695--1591759 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
1591685 GAAACCAAAA
*
1591695 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1591714 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1591728 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
1591747 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1591760 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 10 0.27
16 2 0.05
17 3 0.08
19 22 0.59
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1591736 original size:14 final size:14
Alignment explanation
Indices: 1591717--1591773 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1591707 TTTCATTTCG
1591717 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1591731 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1591750 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1591764 CGTTGCGATT
1 CGTTGCGATT
1591774 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1591746 original size:33 final size:33
Alignment explanation
Indices: 1591700--1591781 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
1591690 CAAAATCGCA
1591700 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1591733 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1591766 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1591782 AACCAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1593636 original size:93 final size:93
Alignment explanation
Indices: 1593477--1594038 Score: 1090
Period size: 93 Copynumber: 6.1 Consensus size: 93
1593467 TAGATTGCTT
*
1593477 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1593542 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1593570 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1593635 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1593663 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1593728 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1593756 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1593821 TTTGTCTTTTTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1593849 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1593914 TTTGTCTTTGTTTTGTCTTTTGTTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1593942 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1594007 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1594034 AGTAA
1 AGTAA
1594039 TGCAATCCAT
Statistics
Matches: 464, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.01
93 458 0.99
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1594126 original size:19 final size:19
Alignment explanation
Indices: 1594086--1594214 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1594076 TAGTTTACTT
* *
1594086 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
*
1594106 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1594125 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
1594144 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1594158 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1594177 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1594191 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1594210 TCGCA
1 TCGCA
1594215 TTGCGATTTC
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 12 0.14
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1594160 original size:33 final size:32
Alignment explanation
Indices: 1594122--1594214 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1594112 CGAGAAACCA
**
1594122 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1594154 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1594187 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1594215 TTGCGATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1594212 original size:52 final size:52
Alignment explanation
Indices: 1594086--1594214 Score: 122
Period size: 52 Copynumber: 2.5 Consensus size: 52
1594076 TAGTTTACTT
* **
1594086 TCGCAACACGAAACTTAAAATCGCAACGAGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGAGAAACCAAAATCGCAACGCGAAA
*** * *
1594138 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGAGAAACCAAAATCGCAACG-CGAA-A
1594191 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
1594215 TTGCGATTTC
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
51 3 0.05
52 46 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGAGAAACCAAAATCGCAACGCGAAA
Found at i:1594250 original size:14 final size:14
Alignment explanation
Indices: 1594231--1594287 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1594221 TTTCATTTCG
1594231 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1594245 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1594262 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1594278 CGTTGCGATT
1 CGTTGCGATT
1594288 TTCATTTCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1594262 original size:33 final size:33
Alignment explanation
Indices: 1594215--1594306 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1594205 CAAAATCGCA
*
1594215 TTGCGA-TTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1594247 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1594280 TTGCGATTTTCATTTCGTGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1594307 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 6 0.11
33 49 0.89
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1594271 original size:19 final size:19
Alignment explanation
Indices: 1594210--1594343 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
1594200 GAAACCAAAA
*
1594210 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
1594228 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1594244 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1594261 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1594277 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
1594294 TCGTGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1594313 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1594333 TCGTGTTGCGA
1 TCGCGTTGCGA
1594344 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
18 10 0.11
19 34 0.37
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1596283 original size:14 final size:14
Alignment explanation
Indices: 1596264--1596299 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1596254 ATTGTTTAAT
1596264 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1596278 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1596292 TGATTTGT
1 TGATTTGT
1596300 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1596492 original size:20 final size:19
Alignment explanation
Indices: 1596406--1596502 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1596396 AAAAATGACT
1596406 ATCGCAATGCGAAA-GAAA
1 ATCGCAATGCGAAATGAAA
1596424 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1596443 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1596457 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1596476 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1596496 ATCGCAA
1 ATCGCAA
1596503 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 15 0.21
19 24 0.34
20 16 0.23
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1596501 original size:53 final size:51
Alignment explanation
Indices: 1596406--1596520 Score: 203
Period size: 53 Copynumber: 2.2 Consensus size: 51
1596396 AAAAATGACT
1596406 ATCGCAATGCGAAAGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1596457 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAA-GAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
1596510 ATCACAATGCG
1 ATCGCAATGCG
1596521 TTTATAATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 14 0.23
52 14 0.23
53 33 0.54
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (51 bp):
ATCGCAATGCGAAAGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1596585 original size:19 final size:19
Alignment explanation
Indices: 1596549--1596816 Score: 291
Period size: 19 Copynumber: 15.4 Consensus size: 19
1596539 GATTCTCTCG
1596549 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
1596567 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1596586 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1596600 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1596619 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1596638 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1596652 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1596671 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1596685 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1596704 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1596723 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1596742 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1596756 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1596776 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1596790 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1596809 TTGCGATT
1 TTGCGATT
1596817 GTAATTTCCG
Statistics
Matches: 213, Mismatches: 10, Indels: 53
0.77 0.04 0.19
Matches are distributed among these distances:
14 35 0.16
16 30 0.14
17 27 0.13
18 15 0.07
19 94 0.44
20 12 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1596639 original size:52 final size:52
Alignment explanation
Indices: 1596527--1596788 Score: 415
Period size: 52 Copynumber: 5.0 Consensus size: 52
1596517 TGCGTTTATA
1596527 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA-TTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1596578 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1596630 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
1596684 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1596734 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1596787 AT
1 AT
1596789 GTTGGGATTT
Statistics
Matches: 193, Mismatches: 10, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
50 9 0.05
51 39 0.20
52 114 0.59
53 22 0.11
54 9 0.05
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1596656 original size:33 final size:33
Alignment explanation
Indices: 1596527--1596816 Score: 320
Period size: 33 Copynumber: 8.5 Consensus size: 33
1596517 TGCGTTTATA
1596527 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
1596560 A-TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
1596599 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1596630 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1596663 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
1596696 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1596734 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
1596767 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
*
1596801 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
1596817 GTAATTTCCG
Statistics
Matches: 221, Mismatches: 17, Indels: 38
0.80 0.06 0.14
Matches are distributed among these distances:
31 9 0.04
32 17 0.08
33 96 0.43
34 32 0.14
35 14 0.06
36 7 0.03
37 10 0.05
38 26 0.12
39 4 0.02
40 6 0.03
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:1596669 original size:85 final size:85
Alignment explanation
Indices: 1596567--1596730 Score: 328
Period size: 85 Copynumber: 1.9 Consensus size: 85
1596557 TTCATTCGCA
1596567 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1596632 TTCGCATTGCGATTCTCTCG
66 TTCGCATTGCGATTCTCTCG
1596652 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1596717 TTCGCATTGCGATT
66 TTCGCATTGCGATT
1596731 TTCATTTCGC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (85 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
TTCGCATTGCGATTCTCTCG
Found at i:1599108 original size:12 final size:12
Alignment explanation
Indices: 1599091--1599115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1599081 TCTTCGGGGA
1599091 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1599103 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1599115 C
1 C
1599116 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1599326 original size:24 final size:23
Alignment explanation
Indices: 1599287--1599332 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1599277 CTGAAACATC
1599287 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGTGTATTGACCAAT
1599310 ATCAAAGTCCG-GATATTGACCAA
1 ATCAAA-TCCGTG-TATTGACCAA
1599333 GACCAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGTGTATTGACCAAT
Done.