Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008092.1 Hibiscus syriacus cultivar Beakdansim tig00110607_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: 2324158
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1647485 original size:71 final size:73
Alignment explanation
Indices: 1647369--1647510 Score: 270
Period size: 71 Copynumber: 2.0 Consensus size: 73
1647359 CTAATTGATC
1647369 ACAAGTAAGCAGGCTGATAGAGATGTACTAATTAAGGTTTTCAAAACGATTT-GGG-GATCACCT
1 ACAAGTAAGCAGGCTGATAGAGATGTACTAATTAAGGTTTTCAAAACGATTTGGGGAGATCACCT
1647432 CTTGTTTG
66 CTTGTTTG
1647440 ACAAGTAAGCAGGCTGATAGAGATGTACTAATTAAGGTTTTCAAAACGATTTGGGGAGATCACCT
1 ACAAGTAAGCAGGCTGATAGAGATGTACTAATTAAGGTTTTCAAAACGATTTGGGGAGATCACCT
1647505 CTTGTT
66 CTTGTT
1647511 GGAGGCCTCT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 52 0.75
72 3 0.04
73 14 0.20
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (73 bp):
ACAAGTAAGCAGGCTGATAGAGATGTACTAATTAAGGTTTTCAAAACGATTTGGGGAGATCACCT
CTTGTTTG
Found at i:1649089 original size:19 final size:18
Alignment explanation
Indices: 1649049--1649097 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1649039 TTTATATCTC
* *
1649049 TTCTTCTTATTCTCTTCAT
1 TTCTTCTTTTTTTC-TCAT
1649068 TTCTTCTTTTTTTCTCAT
1 TTCTTCTTTTTTTCTCAT
*
1649086 TT-TCCTTTTTTT
1 TTCTTCTTTTTTT
1649098 TTTCTGCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 9 0.33
18 6 0.22
19 12 0.44
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (18 bp):
TTCTTCTTTTTTTCTCAT
Found at i:1653605 original size:81 final size:82
Alignment explanation
Indices: 1653504--1653667 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 82
1653494 ATCCACCGAC
1653504 ACCATACTTTGTCTACCTTTTTCTTAAGGAATTTGTATTCTCCGCTCATTACTTTACCAAAGAAA
1 ACCATACTTTGTCTACCTTTTTCTTAAGGAATTTGTATTCTCCGCTCATTACTTTACCAAAGAAA
1653569 ATG-AAAAAAAAATTTA
66 ATGAAAAAAAAAATTTA
1653585 ACCATACTTTGTCTACCTTTTTCTTAAGGAATTTGTATTCTCCGCTCATTACTTTACCAAAGAAA
1 ACCATACTTTGTCTACCTTTTTCTTAAGGAATTTGTATTCTCCGCTCATTACTTTACCAAAGAAA
1653650 ATGAAAAAAAAAATTTA
66 ATGAAAAAAAAAATTTA
1653667 A
1 A
1653668 AGAACGGAAG
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 68 0.83
82 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (82 bp):
ACCATACTTTGTCTACCTTTTTCTTAAGGAATTTGTATTCTCCGCTCATTACTTTACCAAAGAAA
ATGAAAAAAAAAATTTA
Found at i:1655610 original size:12 final size:12
Alignment explanation
Indices: 1655593--1655619 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1655583 ACACATAGGA
1655593 TTAGCTCTCGTC
1 TTAGCTCTCGTC
1655605 TTAGCTCTCGTC
1 TTAGCTCTCGTC
1655617 TTA
1 TTA
1655620 AAAAGTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.30, G:0.15, T:0.44
Consensus pattern (12 bp):
TTAGCTCTCGTC
Found at i:1664921 original size:18 final size:18
Alignment explanation
Indices: 1664895--1664929 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1664885 TCACAATGAA
1664895 ATGTCTCGAAGGACCACT
1 ATGTCTCGAAGGACCACT
*
1664913 ATGTTTCGAAGGACCAC
1 ATGTCTCGAAGGACCAC
1664930 GTAGAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (18 bp):
ATGTCTCGAAGGACCACT
Found at i:1665481 original size:20 final size:20
Alignment explanation
Indices: 1665456--1665494 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1665446 TTTTCAATGG
1665456 CATGCACCGATACACCAATC
1 CATGCACCGATACACCAATC
* *
1665476 CATGCATCGATACATCAAT
1 CATGCACCGATACACCAAT
1665495 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (20 bp):
CATGCACCGATACACCAATC
Found at i:1665546 original size:19 final size:20
Alignment explanation
Indices: 1665522--1665574 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1665512 AATGCATTTT
*
1665522 ATGCATCGATGCAC-ATACC
1 ATGCATCGATGCACAAGACC
* * *
1665541 ATGCATCGTTTCACAAGACT
1 ATGCATCGATGCACAAGACC
1665561 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1665575 TCAGGCTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (20 bp):
ATGCATCGATGCACAAGACC
Found at i:1679557 original size:23 final size:22
Alignment explanation
Indices: 1679527--1679570 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1679517 ATTTTTTGGT
1679527 AAAAAATT-CATTAATATTTTAC
1 AAAAAATTACATTAAT-TTTTAC
*
1679549 AAAATAATTACTTTAATTTTTA
1 AAAA-AATTACATTAATTTTTA
1679571 TTTTTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAAATTACATTAATTTTTAC
Found at i:1681520 original size:10 final size:11
Alignment explanation
Indices: 1681477--1681522 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
1681467 TAAAACGTGG
1681477 GAAATAATATA
1 GAAATAATATA
*
1681488 GAAAGAA-A-A
1 GAAATAATATA
*
1681497 GGAATAATATA
1 GAAATAATATA
1681508 GAAATAA-ATA
1 GAAATAATATA
1681518 GAAAT
1 GAAAT
1681523 TTAAATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
9 6 0.21
10 10 0.34
11 13 0.45
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (11 bp):
GAAATAATATA
Found at i:1683283 original size:22 final size:22
Alignment explanation
Indices: 1683255--1683299 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1683245 AATCCAATTA
**
1683255 CTTTATTCTGGTTTACTAAGTC
1 CTTTATTCTGGTCCACTAAGTC
1683277 CTTTATTCTGGTCCACTAAGTC
1 CTTTATTCTGGTCCACTAAGTC
1683299 C
1 C
1683300 GTTACTTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.44
Consensus pattern (22 bp):
CTTTATTCTGGTCCACTAAGTC
Found at i:1686717 original size:36 final size:36
Alignment explanation
Indices: 1686646--1686718 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
1686636 GTTGAAAAAT
*
1686646 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
*
1686682 ATTTATATAATTTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATT-AAAATCATAAA
1686718 A
1 A
1686719 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:1687772 original size:9 final size:9
Alignment explanation
Indices: 1687760--1687811 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
1687750 TAATATTTTG
1687760 TATTTAATT
1 TATTTAATT
*
1687769 TATTTAA-G
1 TATTTAATT
1687777 TATTTAATT
1 TATTTAATT
1687786 TATTTAA--
1 TATTTAATT
*
1687793 TATTTTATT
1 TATTTAATT
*
1687802 TAATTAATT
1 TATTTAATT
1687811 T
1 T
1687812 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:1687781 original size:17 final size:17
Alignment explanation
Indices: 1687759--1687808 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1687749 TTAATATTTT
1687759 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1687776 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
1687793 -TATTTTATTTAATTAA
1 GTATTTAATTTATTTAA
1687809 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1692997 original size:221 final size:221
Alignment explanation
Indices: 1692614--1693056 Score: 886
Period size: 221 Copynumber: 2.0 Consensus size: 221
1692604 AAGCTAGCAG
1692614 TCAAATGCCTCCCCCTGGAGCTTGAAGTCATCGTGTCAAATGGAAACTGCACAGATTGTTGCATC
1 TCAAATGCCTCCCCCTGGAGCTTGAAGTCATCGTGTCAAATGGAAACTGCACAGATTGTTGCATC
1692679 GATGGCATCTCCATATTAAGGTCAAAGGGATTTGCAGATGAATGCCTTCCCCTTGAATTGGACGT
66 GATGGCATCTCCATATTAAGGTCAAAGGGATTTGCAGATGAATGCCTTCCCCTTGAATTGGACGT
1692744 GATGTTGCCATACGGATTGTTCGTCGACTCACCTCGATACATATCGTAAGGAGTTGCGGATGAAT
131 GATGTTGCCATACGGATTGTTCGTCGACTCACCTCGATACATATCGTAAGGAGTTGCGGATGAAT
1692809 GTCCCCCCATTATGGCATTAAAATCA
196 GTCCCCCCATTATGGCATTAAAATCA
1692835 TCAAATGCCTCCCCCTGGAGCTTGAAGTCATCGTGTCAAATGGAAACTGCACAGATTGTTGCATC
1 TCAAATGCCTCCCCCTGGAGCTTGAAGTCATCGTGTCAAATGGAAACTGCACAGATTGTTGCATC
1692900 GATGGCATCTCCATATTAAGGTCAAAGGGATTTGCAGATGAATGCCTTCCCCTTGAATTGGACGT
66 GATGGCATCTCCATATTAAGGTCAAAGGGATTTGCAGATGAATGCCTTCCCCTTGAATTGGACGT
1692965 GATGTTGCCATACGGATTGTTCGTCGACTCACCTCGATACATATCGTAAGGAGTTGCGGATGAAT
131 GATGTTGCCATACGGATTGTTCGTCGACTCACCTCGATACATATCGTAAGGAGTTGCGGATGAAT
1693030 GTCCCCCCATTATGGCATTAAAATCA
196 GTCCCCCCATTATGGCATTAAAATCA
1693056 T
1 T
1693057 TACACATTAC
Statistics
Matches: 222, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 222 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (221 bp):
TCAAATGCCTCCCCCTGGAGCTTGAAGTCATCGTGTCAAATGGAAACTGCACAGATTGTTGCATC
GATGGCATCTCCATATTAAGGTCAAAGGGATTTGCAGATGAATGCCTTCCCCTTGAATTGGACGT
GATGTTGCCATACGGATTGTTCGTCGACTCACCTCGATACATATCGTAAGGAGTTGCGGATGAAT
GTCCCCCCATTATGGCATTAAAATCA
Found at i:1706711 original size:16 final size:16
Alignment explanation
Indices: 1706692--1706744 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1706682 AAATTTAAAA
*
1706692 AATTCAAAATATATTT
1 AATTTAAAATATATTT
*
1706708 AATTTATAATCATA-TT
1 AATTTAAAAT-ATATTT
*
1706724 ATTTTAAAATATATTT
1 AATTTAAAATATATTT
1706740 -ATTTA
1 AATTTA
1706745 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 7 0.23
16 20 0.67
17 3 0.10
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAAAATATATTT
Found at i:1706737 original size:15 final size:16
Alignment explanation
Indices: 1706697--1706743 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1706687 TAAAAAATTC
*
1706697 AAAATATATTTAATTT
1 AAAATATATTTATTTT
*
1706713 ATAATCATA-TTATTTT
1 AAAAT-ATATTTATTTT
1706729 AAAATATATTTATTT
1 AAAATATATTTATTT
1706744 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATATTTATTTT
Found at i:1706890 original size:2 final size:2
Alignment explanation
Indices: 1706883--1706910 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1706873 AATTTAAACA
1706883 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
1706911 TACATGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1708724 original size:3 final size:3
Alignment explanation
Indices: 1708716--1708768 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
1708706 TATTTATTTC
1708716 ATA ATA ATA ATA AT- ATA AT- ATA ATA ATA ATA ATA A-A CA-A ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA
1708759 ATA ATA ATA A
1 ATA ATA ATA A
1708769 ATAAAACAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.13
3 37 0.82
4 2 0.04
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1709242 original size:112 final size:111
Alignment explanation
Indices: 1709113--1709747 Score: 922
Period size: 112 Copynumber: 5.7 Consensus size: 111
1709103 AGAATTATGC
*
1709113 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAAATGAGTTCTTCTCAT
* *
1709178 TATGAACTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCG
64 TATGAACTCTCTCTAACAAGTTGATCCATCGAATGATGAATTCAAGCG
*
1709226 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-ACTTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAAATGAGTTCTTCTCATT
* * *
1709290 ATGAACTCGAC-CTAACAATGCTGATTCATCGAATGATGAATTCAAGCG
65 ATGAACTC-TCTCTAACAA-GTTGATCCATCGAATGATGAATTCAAGCG
*
1709338 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAAATGAGTTCTTCTCATT
* * *
1709403 ATGAACTCT-TCCGGAA-ATGTTGATCCATCGAATGATGAATTCAAGTG
65 ATGAACTCTCT-C-TAACAAGTTGATCCATCGAATGATGAATTCAAGCG
* *
1709450 AAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAAATGAGTTCTTCTCATT
* **
1709515 ATGAACTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTTGAGCG
65 ATGAACTCTCTCTAACAAGTTGATCCATCGAATGATGAATTCAAGCG
*
1709562 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-ACTTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAAATGAGTTCTTCTCATT
* *
1709626 ATGAACTCGAC-CTAACAATGCTGATCCATCGAATGATGAATTCAAGCG
65 ATGAACTC-TCTCTAACAA-GTTGATCCATCGAATGATGAATTCAAGCG
* *
1709674 AAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAAATGAATTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAAATGAGTTCTTCTCATT
1709739 ATGAACTCT
65 ATGAACTCT
1709748 TCCGGAAATG
Statistics
Matches: 474, Mismatches: 34, Indels: 29
0.88 0.06 0.05
Matches are distributed among these distances:
110 2 0.00
111 78 0.16
112 315 0.66
113 77 0.16
114 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (111 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAAATGAGTTCTTCTCATTA
TGAACTCTCTCTAACAAGTTGATCCATCGAATGATGAATTCAAGCG
Found at i:1709734 original size:336 final size:336
Alignment explanation
Indices: 1709119--1709775 Score: 1260
Period size: 336 Copynumber: 2.0 Consensus size: 336
1709109 ATGCAAAAGA
1709119 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
1709184 CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCA
66 CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCA
1709249 TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTAACAATGCTGA
131 TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTAACAATGCTGA
*
1709314 TTCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
196 TCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
* *
1709379 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATT
261 TTCTTCAAATGAATTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATT
1709444 CAAGTGAAAAT
326 CAAGTGAAAAT
1709455 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
1709520 CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTTGAGCGAAAAGTTGAACAAGTTCTTCTCA
66 CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCA
1709585 TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTAACAATGCTGA
131 TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTAACAATGCTGA
*
1709650 TCCATCGAATGATGAATTCAAGCGAAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
196 TCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
*
1709715 TTCTTCAAATGAATTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATTGAATGATG
261 TTCTTCAAATGAATTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATCGAATGATG
1709776 GATTTGAATC
Statistics
Matches: 315, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
336 315 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (336 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCA
TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTAACAATGCTGA
TCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
TTCTTCAAATGAATTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATT
CAAGTGAAAAT
Found at i:1710209 original size:22 final size:22
Alignment explanation
Indices: 1710184--1710257 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
1710174 AATAAAGCTT
* *
1710184 TCATATTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
1710206 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1710228 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1710250 TCATCTTT
1 TCATCTTT
1710258 AAAGAGTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1712863 original size:83 final size:83
Alignment explanation
Indices: 1712724--1713219 Score: 838
Period size: 83 Copynumber: 6.0 Consensus size: 83
1712714 TCTACTATGA
1712724 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
1712788 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
* *
1712807 GCAAATTCATCTTCTAAATTCAATGATTAGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
*
1712871 TTTCCAGAAGATGCTA-TG
65 CTTCCAGAAGATGCTATTG
*
1712889 AGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
1 -GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
1712954 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
*
1712973 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1713038 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* *
1713056 GCAAATTCATCTTCTAAATTAAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
*
1713121 TTCCAAAAGATGCTA-TG
66 TTCCAGAAGATGCTATTG
*
1713138 AGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
1 -GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
*
1713203 CTTCCAGAATATGCTAT
65 CTTCCAGAAGATGCTAT
1713220 GGAGCATATT
Statistics
Matches: 392, Mismatches: 16, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
82 4 0.01
83 384 0.98
84 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:1716939 original size:12 final size:12
Alignment explanation
Indices: 1716922--1716946 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1716912 GGGGGTTCTG
1716922 AATGCTCATTTC
1 AATGCTCATTTC
1716934 AATGCTCATTTC
1 AATGCTCATTTC
1716946 A
1 A
1716947 GCTATAACTG
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:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (12 bp):
AATGCTCATTTC
Found at i:1719148 original size:68 final size:67
Alignment explanation
Indices: 1719034--1719183 Score: 214
Period size: 68 Copynumber: 2.2 Consensus size: 67
1719024 ACCCATTCAA
* *
1719034 GGGAACCGATA-CCCCTCAATGAAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCAGG
1 GGGAACCGATACCCCCTCAATGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAGG
1719098 GG
66 GG
* * *
1719100 GGGAACCGATACCCCCTC-ATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGAACCGATACCCCCTCAAT-G-AAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1719164 GGGG
64 GGGG
*
1719168 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
1719184 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
66 13 0.17
67 7 0.09
68 55 0.73
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (67 bp):
GGGAACCGATACCCCCTCAATGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAGG
GG
Found at i:1719519 original size:29 final size:29
Alignment explanation
Indices: 1719485--1719554 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
1719475 CATATTATGA
**
1719485 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
1719514 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
1719543 TACATGACATGA
1 TACATGACATGA
1719555 TATGCAGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:1719610 original size:30 final size:31
Alignment explanation
Indices: 1719570--1719628 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1719560 AGAAAAGTTC
*
1719570 TATGCACTATGTGATAAAGGTATGTAAATGA
1 TATGCACTATGTGATAAAGGTATGGAAATGA
*
1719601 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAGGTATGGAAAT
1719629 ACTATGTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAGGTATGGAAATGA
Found at i:1719894 original size:43 final size:44
Alignment explanation
Indices: 1719844--1719931 Score: 169
Period size: 43 Copynumber: 2.0 Consensus size: 44
1719834 TTATGGACAT
1719844 AATTCTACGGGCACTTCGGTGC-ATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGCAATTCTACGGGCACTTCGGTGC
1719887 AATTCTACGGGCACTTCGGTGCAATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGCAATTCTACGGGCACTTCGGTGC
1719931 A
1 A
1719932 TTTATACGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 22 0.50
44 22 0.50
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (44 bp):
AATTCTACGGGCACTTCGGTGCAATTCTACGGGCACTTCGGTGC
Found at i:1719939 original size:22 final size:22
Alignment explanation
Indices: 1719844--1719931 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
1719834 TTATGGACAT
1719844 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1719866 -ATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1719887 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1719909 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1719931 A
1 A
1719932 TTTATACGAG
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
21 21 0.32
22 44 0.68
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1725993 original size:21 final size:21
Alignment explanation
Indices: 1725951--1725993 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1725941 TTTCTGGGTT
* * *
1725951 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1725972 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1725993 A
1 A
1725994 TGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1726059 original size:68 final size:69
Alignment explanation
Indices: 1725973--1726120 Score: 219
Period size: 69 Copynumber: 2.2 Consensus size: 69
1725963 ACCCATTCAA
* *
1725973 GGGGAACCGATACCCCCTCAAT-G-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCC
1 GGGGAACCGATACCCCCTC-ATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
*
1726036 AGGGG
65 AAGGG
* * *
1726041 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1726106 AGGG
66 AGGG
1726110 GGGGAACCGAT
1 GGGGAACCGAT
1726121 TGCCCCATGA
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
67 2 0.03
68 20 0.28
69 50 0.69
ACGTcount: A:0.28, C:0.25, G:0.29, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
AGGG
Found at i:1726464 original size:29 final size:29
Alignment explanation
Indices: 1726430--1726501 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1726420 CATATTATGA
**
1726430 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
1726459 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
1726488 TACATGACATGAAT
1 TACATGACATGAAT
1726502 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:1726579 original size:29 final size:32
Alignment explanation
Indices: 1726515--1726579 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 32
1726505 CAGAAAAGTT
*
1726515 CTATGCACTATGTGATAAAGGTATGTAAATGA
1 CTATGCACTATGTGATAAAGGTATGGAAATGA
*
1726547 -TATGC-CTATGTG-TTAAGGTATGGAAAT-A
1 CTATGCACTATGTGATAAAGGTATGGAAATGA
1726575 CTATG
1 CTATG
1726580 TCTACGCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 1 0.03
29 17 0.57
30 7 0.23
31 5 0.17
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (32 bp):
CTATGCACTATGTGATAAAGGTATGGAAATGA
Found at i:1726889 original size:22 final size:22
Alignment explanation
Indices: 1726793--1726881 Score: 178
Period size: 22 Copynumber: 4.0 Consensus size: 22
1726783 TTATGGACAT
1726793 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1726815 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1726837 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1726859 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1726881 A
1 A
1726882 TTTATACGAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1727899 original size:14 final size:14
Alignment explanation
Indices: 1727865--1727918 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
1727855 TTGTGCAATA
* *
1727865 CAAATGCAAAGATG
1 CAAATGTAAATATG
1727879 CCAAATGTAAATATG
1 -CAAATGTAAATATG
1727894 CAAATGTAAA-ATTG
1 CAAATGTAAATA-TG
*
1727908 TAAATGTAAAT
1 CAAATGTAAAT
1727919 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.03
14 21 0.62
15 12 0.35
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:1730036 original size:16 final size:16
Alignment explanation
Indices: 1730017--1730069 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1730007 AAATTTAAAA
*
1730017 AATTCAAAATATATTT
1 AATTTAAAATATATTT
*
1730033 AATTTATAATCATA-TT
1 AATTTAAAAT-ATATTT
*
1730049 ATTTTAAAATATATTT
1 AATTTAAAATATATTT
1730065 -ATTTA
1 AATTTA
1730070 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 7 0.23
16 20 0.67
17 3 0.10
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAAAATATATTT
Found at i:1730062 original size:15 final size:16
Alignment explanation
Indices: 1730022--1730068 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1730012 TAAAAAATTC
*
1730022 AAAATATATTTAATTT
1 AAAATATATTTATTTT
*
1730038 ATAATCATA-TTATTTT
1 AAAAT-ATATTTATTTT
1730054 AAAATATATTTATTT
1 AAAATATATTTATTT
1730069 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATATTTATTTT
Found at i:1730219 original size:2 final size:2
Alignment explanation
Indices: 1730212--1730241 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1730202 ATTTAAACAA
1730212 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
1730242 TTACATGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1732083 original size:3 final size:3
Alignment explanation
Indices: 1732075--1732125 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
1732065 TATTTATTTC
* *
1732075 ATA ATA ATA AT- ATA AT- ATA ATA ATA ATA ATA A-A ACA A-A TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1732119 ATA ATA A
1 ATA ATA A
1732126 ATAAAACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 7 0.17
3 35 0.83
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1732099 original size:19 final size:17
Alignment explanation
Indices: 1732075--1732130 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 17
1732065 TATTTATTTC
1732075 ATAATAATAATATAATATA
1 ATAATAATAATA-AATA-A
*
1732094 ATAATAATAATAAAACAA
1 ATAATAATAAT-AAATAA
1732112 ATTAATAATAATAAATAA
1 A-TAATAATAATAAATAA
1732130 A
1 A
1732131 ACAAATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 8 0.24
19 24 0.73
20 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:1732103 original size:22 final size:22
Alignment explanation
Indices: 1732092--1732136 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
1732082 TAATATAATA
1732092 TAATAATAATAATAAAACAAAT
1 TAATAATAATAATAAAACAAAT
1732114 TAATAATAATAAATAAAACAAAT
1 TAATAATAAT-AATAAAACAAAT
1732137 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
TAATAATAATAATAAAACAAAT
Found at i:1734028 original size:24 final size:23
Alignment explanation
Indices: 1733967--1734032 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
1733957 TTTGTTTTTT
* *
1733967 TTATAGAAATTATA-TGA-AATAA
1 TTATAAAAATTATATTTATAAT-A
*
1733989 TTATAAAACTTATATTTATAATA
1 TTATAAAAATTATATTTATAATA
*
1734012 TTATAAAAATATTTATTTATA
1 TTATAAAAAT-TATATTTATA
1734033 TTTTAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 12 0.33
23 12 0.33
24 12 0.33
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
TTATAAAAATTATATTTATAATA
Found at i:1734071 original size:19 final size:18
Alignment explanation
Indices: 1734049--1734107 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
1734039 AATACAATTA
1734049 ATTATTTATTTGAAATAAT
1 ATTATTTATTT-AAATAAT
1734068 ATTA-TT-TTTAAAT--T
1 ATTATTTATTTAAATAAT
1734082 ATCTATTTAATTTTAAATAAT
1 AT-TATTT-A-TTTAAATAAT
1734103 ATTAT
1 ATTAT
1734108 ACGGAACCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
14 3 0.09
15 2 0.06
16 6 0.18
17 3 0.09
18 2 0.06
19 11 0.33
20 3 0.09
21 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTATTTATTTAAATAAT
Found at i:1734268 original size:34 final size:37
Alignment explanation
Indices: 1734228--1734305 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 37
1734218 ATTTAAAAAA
*
1734228 ATAAATAAACATTTTAAAAT-ATTT-TTAT-AATATT
1 ATAAATAAACATTTTAAAATAATTTAATATAAATATT
* * *
1734262 ATAAATAAACTTTTTAGAATAATTTAATATAAATTTT
1 ATAAATAAACATTTTAAAATAATTTAATATAAATATT
1734299 ATAAATA
1 ATAAATA
1734306 CATAAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 18 0.49
35 4 0.11
36 3 0.08
37 12 0.32
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (37 bp):
ATAAATAAACATTTTAAAATAATTTAATATAAATATT
Found at i:1734275 original size:22 final size:23
Alignment explanation
Indices: 1734248--1734302 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
1734238 ATTTTAAAAT
1734248 ATTTTTATAAT-ATTATAA-ATAA
1 ATTTTTATAATAATT-TAATATAA
*
1734270 ACTTTTTAGAATAATTTAATATAA
1 A-TTTTTATAATAATTTAATATAA
1734294 A-TTTTATAA
1 ATTTTTATAA
1734303 ATACATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 8 0.29
23 12 0.43
24 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTTTATAATAATTTAATATAA
Found at i:1734667 original size:18 final size:18
Alignment explanation
Indices: 1734644--1734685 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1734634 CATGTCACAT
*
1734644 TTAATTTGTTAAATAAAA
1 TTAATTGGTTAAATAAAA
1734662 TTAATTGGTTAAATAAAA
1 TTAATTGGTTAAATAAAA
1734680 TTAATT
1 TTAATT
1734686 AAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (18 bp):
TTAATTGGTTAAATAAAA
Found at i:1739339 original size:22 final size:23
Alignment explanation
Indices: 1739297--1739339 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
1739287 ATAATCTGGT
*
1739297 TTTTATATAAAACTAATCTAAAA
1 TTTTATATAAAACAAATCTAAAA
1739320 TTTTAT-TAAAA-AAATACTAA
1 TTTTATATAAAACAAAT-CTAA
1739340 GCAAAATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 9 0.50
23 6 0.33
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTTATATAAAACAAATCTAAAA
Found at i:1745043 original size:54 final size:56
Alignment explanation
Indices: 1744921--1745046 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 56
1744911 CTTGGGTCCG
* * * * **
1744921 AGACATTGGTGCAAGCGTCCGACAAGGAGGTTCAAGATAGAGTATCGGTCTTTCCA
1 AGACATTGGTGCAAGTGTCCGACAAGGAGGTTCAAGACAAAGTATCGGGCTTGACA
* * * *
1744977 TGACATTGGTGCAAGTGTCCGATATGGA-GTT-AAGACAAAGTATTGGGCTTGACA
1 AGACATTGGTGCAAGTGTCCGACAAGGAGGTTCAAGACAAAGTATCGGGCTTGACA
1745031 AGACATTGGTGCAAGT
1 AGACATTGGTGCAAGT
1745047 ATTCTACATG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 32 0.54
55 3 0.05
56 24 0.41
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (56 bp):
AGACATTGGTGCAAGTGTCCGACAAGGAGGTTCAAGACAAAGTATCGGGCTTGACA
Found at i:1745760 original size:35 final size:35
Alignment explanation
Indices: 1745714--1745789 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
1745704 AAAACAGTCC
* *
1745714 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
1745749 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1745784 TCAATT
1 TCAATT
1745790 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1746337 original size:128 final size:124
Alignment explanation
Indices: 1746174--1746429 Score: 395
Period size: 128 Copynumber: 2.0 Consensus size: 124
1746164 TTCAGTCTTT
* **
1746174 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGG
1 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGG
* *
1746239 ATCTGACATGTGTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
66 ATCTAACATGTGTTAACACATGATCATGACA--TGTCATTGGTGACACATGTCACCACCTA
* *
1746300 ATTATTTATATGCTATCAATTTGGTTCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
1 ATTATTTATAT--AATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
* *
1746365 GGATCTAACATGTGTTAACACATGATCATGATATGTTATTGGTGACACATGTCACCACCTA
64 GGATCTAACATGTGTTAACACATGATCATGACATGTCATTGGTGACACATGTCACCACCTA
1746426 ATTA
1 ATTA
1746430 GAAGAAAATT
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
126 42 0.35
128 77 0.65
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (124 bp):
ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGG
ATCTAACATGTGTTAACACATGATCATGACATGTCATTGGTGACACATGTCACCACCTA
Found at i:1746783 original size:28 final size:27
Alignment explanation
Indices: 1746752--1746814 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1746742 AATTGATACA
*
1746752 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1746780 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1746808 ATATTTT
1 ATATTTT
1746815 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1746912 original size:16 final size:18
Alignment explanation
Indices: 1746891--1746924 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1746881 ATTTCTTATT
1746891 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1746907 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1746925 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1754948 original size:28 final size:28
Alignment explanation
Indices: 1754895--1755105 Score: 194
Period size: 29 Copynumber: 7.4 Consensus size: 28
1754885 ACCCGACCCA
1754895 GTGACATTTT-GGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTT-AAAAAG
* *
1754923 GTGATATTTTGGGAATTATTTTAAAAAT
1 GTGACATTTTGGGAATTATTTTAAAAAG
*
1754951 GTAACATTTTGGGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTT-AAAAAG
* * *
1754980 GTGATATTTTGGAAATT-TTTTAAACCCA-
1 GTGACATTTTGGGAATTATTTTAAA--AAG
* * *
1755008 GTGACATTCTGGTAATTATTTTTAAAATG
1 GTGACATTTTGGGAATTA-TTTTAAAAAG
* *
1755037 ATGACATTTTGGGAATTATTTGTAAAATG
1 GTGACATTTTGGGAATTATTT-TAAAAAG
* **
1755066 GTGATATTTTGATAATTATTTTTAATAAAG
1 GTGACATTTTGGGAATTA-TTTTAA-AAAG
*
1755096 GTGATATTTT
1 GTGACATTTT
1755106 TGTAATTTTC
Statistics
Matches: 151, Mismatches: 22, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
27 3 0.02
28 55 0.36
29 70 0.46
30 23 0.15
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (28 bp):
GTGACATTTTGGGAATTATTTTAAAAAG
Found at i:1754985 original size:57 final size:57
Alignment explanation
Indices: 1754895--1755105 Score: 232
Period size: 57 Copynumber: 3.7 Consensus size: 57
1754885 ACCCGACCCA
1754895 GTGACATTTT-GGAATTATTTTGAAAAAGGTGATATTTTGGGAATTATTTTAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAGGTGATATTTTGGGAATTATTTTAAAAAT
* * *
1754951 GTAACATTTTGGGAATTATTTTGAAAAAGGTGATATTTTGGAAATT-TTTTAAACCCA-
1 GTGACATTTTGGGAATTATTTTGAAAAAGGTGATATTTTGGGAATTATTTTAAA--AAT
* * * * * *
1755008 GTGACATTCTGGTAATTATTTTTAAAATGATGACATTTTGGGAATTATTTGT-AAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAGGTGATATTTTGGGAATTATTT-TAAAAAT
* ** *
1755065 GGTGATATTTTGATAATTATTTTTAATAAAGGTGATATTTT
1 -GTGACATTTTGGGAATTATTTTGAA-AAAGGTGATATTTT
1755106 TGTAATTTTC
Statistics
Matches: 129, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
56 17 0.13
57 72 0.56
58 28 0.22
59 12 0.09
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (57 bp):
GTGACATTTTGGGAATTATTTTGAAAAAGGTGATATTTTGGGAATTATTTTAAAAAT
Found at i:1759508 original size:28 final size:28
Alignment explanation
Indices: 1759468--1759523 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1759458 TGTGAGCTTT
1759468 GGCTTCAAGAAGTGTCATTTTTGGGGCA
1 GGCTTCAAGAAGTGTCATTTTTGGGGCA
* *
1759496 GGCTTCAAGAAGTGTCGTTTTTTGGGCA
1 GGCTTCAAGAAGTGTCATTTTTGGGGCA
1759524 TATTATTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (28 bp):
GGCTTCAAGAAGTGTCATTTTTGGGGCA
Found at i:1762500 original size:29 final size:29
Alignment explanation
Indices: 1762458--1762642 Score: 162
Period size: 29 Copynumber: 6.4 Consensus size: 29
1762448 GACCCGACCC
1762458 AGTGATATTTTGGGAATTATTTTGAAAAA
1 AGTGATATTTTGGGAATTATTTTGAAAAA
*
1762487 AGTGACATTTTGGGAATTATTTTGAAAAA
1 AGTGATATTTTGGGAATTATTTTGAAAAA
* * * *
1762516 AATGACATTTT-GG-ATTTTTTTTAAAAA
1 AGTGATATTTTGGGAATTATTTTGAAAAA
* * * * *
1762543 CAATGACATTCTGGTAATTATTTT-TAAAA
1 -AGTGATATTTTGGGAATTATTTTGAAAAA
* *
1762572 TGATGATATTTTGGGAATTA-TTTGTAAAAT
1 AG-TGATATTTTGGGAATTATTTTG-AAAAA
* * *
1762602 GGTGATATTTTGGTAATTATTTTTAATAAA
1 AGTGATATTTTGGGAATTATTTTGAA-AAA
*
1762632 GGTGATATTTT
1 AGTGATATTTT
1762643 TGTAATTTTC
Statistics
Matches: 129, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
27 12 0.09
28 15 0.12
29 75 0.58
30 27 0.21
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (29 bp):
AGTGATATTTTGGGAATTATTTTGAAAAA
Found at i:1764405 original size:21 final size:21
Alignment explanation
Indices: 1764379--1764431 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1764369 GTTTCCAGAT
1764379 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
1764400 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
1764421 TCGCAATGCGA
1 TCGCAACGCGA
1764432 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:1764451 original size:19 final size:19
Alignment explanation
Indices: 1764427--1764493 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
1764417 ACTATCGCAA
1764427 TGCGATTTTCCAAATTCGT
1 TGCGATTTTCCAAATTCGT
** *
1764446 TGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATT--CGT
1764467 TGCGATTTATTCCAAATTCGT
1 TGCGA-TT-TTCCAAATTCGT
1764488 TGCGAT
1 TGCGAT
1764494 AGTCGAAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
19 13 0.34
20 1 0.03
21 16 0.42
22 1 0.03
23 7 0.18
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
TGCGATTTTCCAAATTCGT
Found at i:1764469 original size:21 final size:21
Alignment explanation
Indices: 1764443--1764521 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
1764433 TTTCCAAATT
1764443 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1764464 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
1764485 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
1764506 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
1764522 AATCGCAACG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.17
21 31 0.65
23 9 0.19
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:1764484 original size:42 final size:41
Alignment explanation
Indices: 1764427--1764514 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 41
1764417 ACTATCGCAA
1764427 TGCGA-TTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
*
1764467 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1764509 TGCGAT
1 TGCGAT
1764515 AGTCCAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.11
41 2 0.04
42 38 0.84
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:1765414 original size:21 final size:21
Alignment explanation
Indices: 1765388--1765541 Score: 90
Period size: 21 Copynumber: 7.4 Consensus size: 21
1765378 ATTTTGGACT
1765388 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
1765409 ATCGCAACGCAAACTTCGACT--
1 ATCGCAACG--AATTTGGAATAA
* * *
1765430 ATCGCGACGAACTTGGACT--
1 ATCGCAACGAATTTGGAATAA
* *
1765449 ATCGCAATGAATTTGTAATAA
1 ATCGCAACGAATTTGGAATAA
* *
1765470 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
* *
1765491 ATCGCAACAAATTTGGAGTAA
1 ATCGCAACGAATTTGGAATAA
1765512 ATCGCAACGCGAATTTGG-A-AA
1 ATCGCAA--CGAATTTGGAATAA
1765533 ATCGCAACG
1 ATCGCAACG
1765542 CGAACTTCGA
Statistics
Matches: 104, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
19 34 0.33
21 47 0.45
23 23 0.22
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:1765476 original size:61 final size:60
Alignment explanation
Indices: 1765381--1765606 Score: 251
Period size: 61 Copynumber: 3.6 Consensus size: 60
1765371 CGTTGCGATT
* *
1765381 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCGCGACGAAC
1 TTGGACTATCGCAACGAATTT-GAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
* * * *
1765442 TTGGACTATCGCAATGAATTTGTAATAAATCGCAACGCGAACTTGGACTATCGCAACAAAT
1 TTGGACTATCGCAACGAATTTG-AATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
* *
1765503 TTGGAGTAAATCGCAACGCGAATTTGGA-AAATCGCAACGCGAACTTCGACTATCGCAACGCGAA
1 TTGGACT--ATCGCAA--CGAATTTGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAA
1765567 C
60 C
* *
1765568 TTGGACTATCGCAATGCGAATATG--TAAATCGCAATGCGA
1 TTGGACTATCGCAA--CGAATTTGAATAAATCGCAACGCGA
1765607 TAGTCGAAGT
Statistics
Matches: 141, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
60 1 0.01
61 59 0.42
62 13 0.09
63 51 0.36
64 1 0.01
65 16 0.11
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (60 bp):
TTGGACTATCGCAACGAATTTGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
Found at i:1765484 original size:42 final size:41
Alignment explanation
Indices: 1765437--1765606 Score: 159
Period size: 42 Copynumber: 4.1 Consensus size: 41
1765427 ACTATCGCGA
*
1765437 CGAACTTGGACTATCGCAATGAATTTGTAATAAATCGCAACG
1 CGAACTTGGACTATCGCAACGAATTTG-AATAAATCGCAACG
* *
1765479 CGAACTTGGACTATCGCAACAAATTTGGAGTAAATCGCAACG
1 CGAACTTGGACTATCGCAACGAATTT-GAATAAATCGCAACG
* ** * *
1765521 CGAATTTGGAAAATCGCAACGCGAACTTCGACT--ATCGCAACG
1 CGAACTTGGACTATCGCAA--CGAA-TTTGAATAAATCGCAACG
* *
1765563 CGAACTTGGACTATCGCAATGCGAATATG--TAAATCGCAATG
1 CGAACTTGGACTATCGCAA--CGAATTTGAATAAATCGCAACG
1765604 CGA
1 CGA
1765607 TAGTCGAAGT
Statistics
Matches: 106, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
39 1 0.01
41 13 0.12
42 83 0.78
43 1 0.01
44 6 0.06
45 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (41 bp):
CGAACTTGGACTATCGCAACGAATTTGAATAAATCGCAACG
Found at i:1765542 original size:21 final size:21
Alignment explanation
Indices: 1765468--1765587 Score: 109
Period size: 21 Copynumber: 5.7 Consensus size: 21
1765458 AATTTGTAAT
1765468 AAATCGCAACGCGAACTTGGA
1 AAATCGCAACGCGAACTTGGA
** * *
1765489 CTATCGCAA--CAAATTTGGA
1 AAATCGCAACGCGAACTTGGA
*
1765508 GTAAATCGCAACGCGAATTTGGA
1 --AAATCGCAACGCGAACTTGGA
*
1765531 AAATCGCAACGCGAACTTCGA
1 AAATCGCAACGCGAACTTGGA
**
1765552 CTATCGCAACGCGAACTTGGA
1 AAATCGCAACGCGAACTTGGA
** *
1765573 CTATCGCAATGCGAA
1 AAATCGCAACGCGAA
1765588 TATGTAAATC
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
19 8 0.10
21 65 0.79
23 9 0.11
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (21 bp):
AAATCGCAACGCGAACTTGGA
Found at i:1765628 original size:21 final size:21
Alignment explanation
Indices: 1765602--1765648 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1765592 TAAATCGCAA
1765602 TGCGATAGTCGAAGTTCACGT
1 TGCGATAGTCGAAGTTCACGT
*
1765623 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCACGT
1765644 TGCGA
1 TGCGA
1765649 ATCTGGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCACGT
Found at i:1769968 original size:23 final size:24
Alignment explanation
Indices: 1769936--1769999 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
1769926 ATTCTTATTG
1769936 AATTAATCGAAACTTATAAA-TTA
1 AATTAATCGAAACTTATAAATTTA
* *
1769959 AATTAGTCGATACTTATAAATTTTA
1 AATTAATCGAAACTTATAAA-TTTA
*
1769984 AATTAATCAAAACTTA
1 AATTAATCGAAACTTA
1770000 CAATGTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 18 0.53
25 16 0.47
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (24 bp):
AATTAATCGAAACTTATAAATTTA
Found at i:1770368 original size:16 final size:15
Alignment explanation
Indices: 1770343--1770400 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
1770333 GTTTTAGTAA
*
1770343 TTTATTTTTAATACTT
1 TTTATATTTAATA-TT
*
1770359 TTTATATTTAATTTT
1 TTTATATTTAATATT
* *
1770374 TTTAATGATTGAATAAT
1 TTT-AT-ATTTAATATT
1770391 TTTATATTTA
1 TTTATATTTA
1770401 GATTTTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 9 0.26
16 15 0.44
17 10 0.29
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTATATTTAATATT
Found at i:1781851 original size:19 final size:19
Alignment explanation
Indices: 1781827--1781863 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1781817 ATGACCAATA
*
1781827 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1781846 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1781864 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1781938 original size:21 final size:21
Alignment explanation
Indices: 1781909--1782026 Score: 96
Period size: 21 Copynumber: 5.7 Consensus size: 21
1781899 ATTTTGACTA
* *
1781909 TCGCATTGCGATTTTTCAAAT
1 TCGCGTTGCGATTTTCCAAAT
*
1781930 TCTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
**
1781951 TCGCGTTGCGATTTTAGAAA-
1 TCGCGTTGCGATTTTCCAAAT
** * * **
1781971 TCGCAATGCGAATATGTAAA-
1 TCGCGTTGCGATTTTCCAAAT
** *
1781991 TCGCAATGCGATTCTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
1782012 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1782027 AGAAATCACA
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
20 30 0.39
21 47 0.61
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:1781980 original size:20 final size:19
Alignment explanation
Indices: 1781957--1782104 Score: 107
Period size: 20 Copynumber: 7.4 Consensus size: 19
1781947 AAATTCGCGT
*
1781957 TGCGATTTTAGAAATCGCAA
1 TGCGATTAT-GAAATCGCAA
*
1781977 TGCGAATATGTAAATCGCAA
1 TGCGATTATG-AAATCGCAA
* * **
1781997 TGCGATTCTCCAAATTCGCGT
1 TGCGATTAT-GAAA-TCGCAA
* *
1782018 TGCGATTTTAGAAATCACAA
1 TGCGATTAT-GAAATCGCAA
*
1782038 TGCGAATATGTAAATCGCAA
1 TGCGATTATG-AAATCGCAA
* *
1782058 TGCGATTCTGACTATCGCAA
1 TGCGATTATGA-AATCGCAA
*
1782078 TGCGAATATGTAAATCGCAA
1 TGCGATTATG-AAATCGCAA
*
1782098 CGCGATT
1 TGCGATT
1782105 CTGACTATCG
Statistics
Matches: 98, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
19 3 0.03
20 79 0.81
21 16 0.16
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (19 bp):
TGCGATTATGAAATCGCAA
Found at i:1782016 original size:61 final size:61
Alignment explanation
Indices: 1781936--1782066 Score: 244
Period size: 61 Copynumber: 2.1 Consensus size: 61
1781926 AAATTCTCGT
* *
1781936 TGCGATTTTCCAAATTCGCGTTGCGATTTTAGAAATCGCAATGCGAATATGTAAATCGCAA
1 TGCGATTCTCCAAATTCGCGTTGCGATTTTAGAAATCACAATGCGAATATGTAAATCGCAA
1781997 TGCGATTCTCCAAATTCGCGTTGCGATTTTAGAAATCACAATGCGAATATGTAAATCGCAA
1 TGCGATTCTCCAAATTCGCGTTGCGATTTTAGAAATCACAATGCGAATATGTAAATCGCAA
1782058 TGCGATTCT
1 TGCGATTCT
1782067 GACTATCGCA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (61 bp):
TGCGATTCTCCAAATTCGCGTTGCGATTTTAGAAATCACAATGCGAATATGTAAATCGCAA
Found at i:1782079 original size:40 final size:40
Alignment explanation
Indices: 1782035--1782156 Score: 183
Period size: 40 Copynumber: 3.0 Consensus size: 40
1782025 TTAGAAATCA
*
1782035 CAATGCGAATATGTAAATCGCAATGCGATTCTGACTATCG
1 CAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCG
1782075 CAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCG
1 CAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCG
* * *
1782115 CAACGCGCTAATACGT-AATCGTAACGCGATTCTGACTATCG
1 CAATGCG--AATATGTAAATCGCAACGCGATTCTGACTATCG
1782156 C
1 C
1782157 GTTGCGATAA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
40 45 0.59
41 25 0.33
42 6 0.08
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (40 bp):
CAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCG
Found at i:1782114 original size:20 final size:20
Alignment explanation
Indices: 1782051--1782156 Score: 90
Period size: 20 Copynumber: 5.2 Consensus size: 20
1782041 GAATATGTAA
*
1782051 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * * *
1782071 ATCGCAATGCGAATATGTA-A
1 ATCGCAACGCGATTCTG-ACT
1782091 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
1782111 ATCGCAACGCGCTAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
*
1782131 AATCGTAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
1782152 ATCGC
1 ATCGC
1782157 GTTGCGATAA
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.05
20 47 0.71
21 14 0.21
22 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1782168 original size:41 final size:41
Alignment explanation
Indices: 1782035--1782179 Score: 172
Period size: 40 Copynumber: 3.6 Consensus size: 41
1782025 TTAGAAATCA
* *
1782035 CAATGCG-AATATGTAAATCGCAATGCGATTCTGACTATCG
1 CAATGCGTAATACGTAAATCGCAACGCGATTCTGACTATCG
*
1782075 CAATGCG-AATATGTAAATCGCAACGCGATTCTGACTATCG
1 CAATGCGTAATACGTAAATCGCAACGCGATTCTGACTATCG
* *
1782115 CAACGCGCTAATACGT-AATCGTAACGCGATTCTGACTATCG
1 CAATGCG-TAATACGTAAATCGCAACGCGATTCTGACTATCG
** *
1782156 CGTTGCGATAATAC-AAAATCGCAA
1 CAATGCG-TAATACGTAAATCGCAA
1782180 TACGATTTTC
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
40 45 0.49
41 41 0.45
42 6 0.07
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (41 bp):
CAATGCGTAATACGTAAATCGCAACGCGATTCTGACTATCG
Found at i:1782186 original size:41 final size:40
Alignment explanation
Indices: 1782049--1782179 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 40
1782039 GCGAATATGT
* **
1782049 AAATCGCAATGCGATTCTGACTATCGCAATGCG-AATATGT
1 AAATCGCAACGCGATTCTGACTATCGCAATGCGTAATA-CA
* *
1782089 AAATCGCAACGCGATTCTGACTATCGCAACGCGCTAATACG
1 AAATCGCAACGCGATTCTGACTATCGCAATGCG-TAATACA
* * **
1782130 TAATCGTAACGCGATTCTGACTATCGCGTTGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAATGCG-TAATACA
1782171 AAATCGCAA
1 AAATCGCAA
1782180 TACGATTTTC
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 31 0.41
41 41 0.54
42 4 0.05
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (40 bp):
AAATCGCAACGCGATTCTGACTATCGCAATGCGTAATACA
Found at i:1782357 original size:22 final size:22
Alignment explanation
Indices: 1782330--1782402 Score: 128
Period size: 22 Copynumber: 3.3 Consensus size: 22
1782320 CTACGGCGAC
*
1782330 ATCCGTCCCCATCTCCGATGAA
1 ATCCGTCCCCATCTCCGACGAA
*
1782352 ATCCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATCTCCGACGAA
1782374 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1782396 ATCCGTC
1 ATCCGTC
1782403 TATCTCCATC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1782832 original size:20 final size:20
Alignment explanation
Indices: 1782809--1782855 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1782799 TAGTTTCGCA
1782809 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
**
1782829 TTGCGATTTTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
1782849 TTGCGAT
1 TTGCGAT
1782856 TTTAAGTTTT
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:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:1782856 original size:20 final size:20
Alignment explanation
Indices: 1782818--1782858 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1782808 ATTGCGATAG
1782818 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
1782838 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
1782858 T
1 T
1782859 AAGTTTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:1784793 original size:20 final size:20
Alignment explanation
Indices: 1784770--1784836 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
1784760 GAAACTTAAA
1784770 ATCGCAAAGCGAAAATGACT
1 ATCGCAAAGCGAAAATGACT
* *
1784790 ATCGCAACGCGGAAATGACT
1 ATCGCAAAGCGAAAATGACT
* **
1784810 ATCGCAATGCGAATTTGACT
1 ATCGCAAAGCGAAAATGACT
1784830 ATCGCAA
1 ATCGCAA
1784837 CGGGATAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAAAGCGAAAATGACT
Found at i:1784853 original size:34 final size:37
Alignment explanation
Indices: 1784769--1784874 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 37
1784759 CGAAACTTAA
*
1784769 AATCGCAAAGCGAAAATGACTATCGCAACGCGGAAATG
1 AATCGCAATGCGAAAATGACTATCGCAACGCGG-AATG
**
1784807 ACTATCGCAATGCGAATTTGACTATCGCAACG-GG-AT-
1 A--ATCGCAATGCGAAAATGACTATCGCAACGCGGAATG
**
1784843 AATCGCAATGCGAAAATGAAAATCGCAACGCG
1 AATCGCAATGCGAAAATGACTATCGCAACGCG
1784875 AAAAATTTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
34 25 0.43
35 1 0.02
36 1 0.02
37 2 0.03
38 1 0.02
39 2 0.03
40 26 0.45
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.17
Consensus pattern (37 bp):
AATCGCAATGCGAAAATGACTATCGCAACGCGGAATG
Found at i:1784962 original size:20 final size:20
Alignment explanation
Indices: 1784939--1785011 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1784929 TATATTCAAA
1784939 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
* *
1784959 TTCGTGTTGTGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
*
1784979 TTCGCATTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
**
1784999 TTCATGTTGCGAT
1 TTCGCGTTGCGAT
1785012 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCATT
Found at i:1785553 original size:21 final size:21
Alignment explanation
Indices: 1785458--1785565 Score: 101
Period size: 21 Copynumber: 5.1 Consensus size: 21
1785448 GCCCGACTCA
1785458 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1785479 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
1785500 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1785521 CCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* * *
1785542 TCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
1785563 CCT
1 CCT
1785566 CCCACCATTA
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.26
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:1785566 original size:42 final size:42
Alignment explanation
Indices: 1785458--1785571 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 42
1785448 GCCCGACTCA
*
1785458 CCTGTCATCGTTCAAGAGG--CCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGTCCCTCT-C-ACCGTTCAAGAGGCC
* **
1785500 CCTATCATCCCTCAAGA-GTCCCCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGT-CCCTCTCACCGTTCAAGAGGCC
* * *
1785542 TCTGTCATCGTTGAAGAGGTCCCTCCCACC
1 CCTGTCATCGTTCAAGAGGTCCCTCTCACC
1785572 ATTATAGAGC
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.02
42 49 0.84
43 3 0.05
44 5 0.09
ACGTcount: A:0.19, C:0.38, G:0.18, T:0.25
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGTCCCTCTCACCGTTCAAGAGGCC
Found at i:1787079 original size:20 final size:20
Alignment explanation
Indices: 1787051--1787106 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1787041 GCGATTTTCT
*
1787051 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
* *
1787071 CGTTACGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
1787091 CGTTGTGATAGTCAAA
1 CGTTGCGATAGTCAAA
1787107 ATCGCAATGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:1787128 original size:20 final size:20
Alignment explanation
Indices: 1787103--1787141 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1787093 TTGTGATAGT
*
1787103 CAAAATCGCAATGCGAAAGC
1 CAAAATCGCAACGCGAAAGC
1787123 CAAAATCGCAACGCGAAAG
1 CAAAATCGCAACGCGAAAG
1787142 TCAATTCGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.26, G:0.21, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACGCGAAAGC
Found at i:1787212 original size:20 final size:20
Alignment explanation
Indices: 1787187--1787467 Score: 230
Period size: 20 Copynumber: 14.7 Consensus size: 20
1787177 ATTTTCTCGG
*
1787187 TGCGATAGTCAAATTCCCGT
1 TGCGATAGTCAAATTCGCGT
* *
1787207 TGCGATAATCAAATTCACGT
1 TGCGATAGTCAAATTCGCGT
* * **
1787227 TGCGATAGTCAAAATCACAA
1 TGCGATAGTCAAATTCGCGT
* * **
1787247 TGCGAAAGCCAAAATT-GCAA
1 TGCGATAGTC-AAATTCGCGT
*
1787267 TGCGAAAGTC-AATTCGCGT
1 TGCGATAGTCAAATTCGCGT
* * *
1787286 TGCGATGGTCTAATTCGCTT
1 TGCGATAGTCAAATTCGCGT
*
1787306 TGCGAT--T----TTCTCGT
1 TGCGATAGTCAAATTCGCGT
* *
1787320 TGCGATAATCAAATTCACGT
1 TGCGATAGTCAAATTCGCGT
*
1787340 TGCGATAGTCAAATTCGTGT
1 TGCGATAGTCAAATTCGCGT
*
1787360 TGCGATAGTGAAATTCGCGT
1 TGCGATAGTCAAATTCGCGT
*
1787380 TGCGAT--T----TTTGCGT
1 TGCGATAGTCAAATTCGCGT
* *
1787394 TACGATAGTCAAATTTGCGT
1 TGCGATAGTCAAATTCGCGT
1787414 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGT
*
1787434 TGCGATAGTCAAATTCGCAT
1 TGCGATAGTCAAATTCGCGT
*
1787454 TGCGATATTCAAAT
1 TGCGATAGTCAAAT
1787468 GAATATGTAA
Statistics
Matches: 216, Mismatches: 30, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
14 22 0.10
16 2 0.01
18 6 0.03
19 10 0.05
20 172 0.80
21 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (20 bp):
TGCGATAGTCAAATTCGCGT
Found at i:1787374 original size:40 final size:40
Alignment explanation
Indices: 1787051--1787467 Score: 255
Period size: 40 Copynumber: 10.9 Consensus size: 40
1787041 GCGATTTTCT
* * * *
1787051 CGTTGCGATAGTCAAATTCCCGTTACGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* * ** * * *
1787091 CGTTGTGATAGTCAAAATCGCAATGCGAAAGCCAAAATCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
*** * * * *
1787131 CAACGCGAAAGTC-AATTCGCGTTGCGATGGTCTAATACG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* * * * *
1787170 CTTTGC-A-A-T---TTTCTCGGTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* * * *
1787204 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
** * * ** *
1787244 CAATGCGAAAGCCAAAATT-GCAATGCGAAAGTC-AATTCG
1 CGTTGCGATAGTC-AAATTCGCGTTGCGATAGTCAAATTCG
* * * *
1787283 CGTTGCGATGGTCTAATTCGCTTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* *
1787317 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* * *
1787357 TGTTGCGATAGTGAAATTCGCGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* *
1787391 CGTTACGATAGTCAAATTTGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* *
1787431 CGTTGCGATAGTCAAATTCGCATTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
1787468 GAATATGTAA
Statistics
Matches: 275, Mismatches: 82, Indels: 40
0.69 0.21 0.10
Matches are distributed among these distances:
34 78 0.28
35 1 0.00
36 4 0.01
37 3 0.01
38 6 0.02
39 39 0.14
40 139 0.51
41 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
Found at i:1787375 original size:74 final size:74
Alignment explanation
Indices: 1787267--1787459 Score: 264
Period size: 74 Copynumber: 2.6 Consensus size: 74
1787257 AAAATTGCAA
* * * * *
1787267 TGCGAAAGTC-AATTCGCGTTGCGATGGTCTAATTCGCTTTGCGATTTTCT-CGTTGCGATAATC
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTT-TGCGTTACGATAATC
1787330 AAATTCACGT
65 AAATTCACGT
* * * *
1787340 TGCGATAGTCAAATTCGTGTTGCGATAGTGAAATTCGCGTTGCGATTTTTGCGTTACGATAGTCA
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTGCGTTACGATAATCA
**
1787405 AATTTGCGT
66 AATTCACGT
1787414 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGAT
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGAT
1787460 ATTCAAATGA
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
73 10 0.10
74 95 0.90
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (74 bp):
TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTGCGTTACGATAATCA
AATTCACGT
Found at i:1787384 original size:133 final size:133
Alignment explanation
Indices: 1787017--1787377 Score: 569
Period size: 133 Copynumber: 2.7 Consensus size: 133
1787007 AGGCAAAAGA
* * *
1787017 CGTTGCAATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTACGATAA
1 CGTTGCGATGGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAA
*
1787082 TCAAATTCACGTTGTGATAGTCAAAATCGCAATGCGAAAGCCAAAATCGCAACGCGAAAGTCAAT
66 TCAAATTCACGTTGCGATAGTCAAAATCGCAATGCGAAAGCCAAAATCGCAACGCGAAAGTCAAT
1787147 TCG
131 TCG
* *
1787150 CGTTGCGATGGTCTAATACGCTTTGCAATTTTCTCGGTGCGATAGTCAAATTCCCGTTGCGATAA
1 CGTTGCGATGGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAA
* * *
1787215 TCAAATTCACGTTGCGATAGTCAAAATCACAATGCGAAAGCCAAAATTGCAATGCGAAAGTCAAT
66 TCAAATTCACGTTGCGATAGTCAAAATCGCAATGCGAAAGCCAAAATCGCAACGCGAAAGTCAAT
1787280 TCG
131 TCG
* * * *
1787283 CGTTGCGATGGTCTAATTCGCTTTGCGATTTTCTCGTTGCGATAATCAAATTCACGTTGCGATAG
1 CGTTGCGATGGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAA
** * *
1787348 TCAAATTCGTGTTGCGATAGTGAAATTCGC
66 TCAAATTCACGTTGCGATAGTCAAAATCGC
1787378 GTTGCGATTT
Statistics
Matches: 208, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
133 208 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (133 bp):
CGTTGCGATGGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAA
TCAAATTCACGTTGCGATAGTCAAAATCGCAATGCGAAAGCCAAAATCGCAACGCGAAAGTCAAT
TCG
Found at i:1787400 original size:54 final size:54
Alignment explanation
Indices: 1787337--1787439 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
1787327 ATCAAATTCA
* * *
1787337 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTGAAATTCGCGTTGCGATTTTTG
1 CGTTACGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
*
1787391 CGTTACGATAGTCAAATTTGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTACGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1787440 AGTCAAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (54 bp):
CGTTACGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:1787690 original size:140 final size:140
Alignment explanation
Indices: 1787438--1787720 Score: 476
Period size: 140 Copynumber: 2.0 Consensus size: 140
1787428 TCGCGTTGCG
* *
1787438 ATAGTCAAATTCGCATTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCATTGCGATATTAAAATGAATATGTAACAAGTGATAACAACTGAACAGATCA
* * * *
1787503 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGATCAAAATCAAGGTACTAATAAATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
1787568 AATACACATA
131 AATACACATA
* * *
1787578 ATAGTCAAATTCGCGTTGCGATATTAAAATGAATGTGTAACAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCATTGCGATATTAAAATGAATATGTAACAAGTGATAACAACTGAACAGATCA
*
1787643 TAGCAATGATCAAAATCAAGGTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGATCAAAATCAAGGTACTAATAAATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
1787708 AATACACATA
131 AATACACATA
1787718 ATA
1 ATA
1787721 AAACGTTTGC
Statistics
Matches: 133, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
140 133 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (140 bp):
ATAGTCAAATTCGCATTGCGATATTAAAATGAATATGTAACAAGTGATAACAACTGAACAGATCA
TAGCAATGATCAAAATCAAGGTACTAATAAATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1790119 original size:24 final size:24
Alignment explanation
Indices: 1790068--1790119 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1790058 ATCTGAGTAT
** *
1790068 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
1790092 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
1790116 TGAC
1 TGAC
1790120 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1790979 original size:21 final size:21
Alignment explanation
Indices: 1790949--1790989 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1790939 ATCACGTTGC
1790949 GATTACGTATTATCGCATTGT
1 GATTACGTATTATCGCATTGT
*
1790970 GATTATGTATTATCGCATTG
1 GATTACGTATTATCGCATTG
1790990 CGATAGTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (21 bp):
GATTACGTATTATCGCATTGT
Found at i:1791006 original size:20 final size:20
Alignment explanation
Indices: 1790905--1791094 Score: 91
Period size: 20 Copynumber: 9.3 Consensus size: 20
1790895 AAATTCAGTG
* * *
1790905 TTGCGAAAGTCAGAATCGCG
1 TTGCGATAGTCAAAATCGCA
* * *
1790925 TTGCGATAGTCAGAATCACG
1 TTGCGATAGTCAAAATCGCA
**
1790945 TTGCGATTACGT-ATTATCGCA
1 TTGCGA-TA-GTCAAAATCGCA
* **
1790966 TTGTGATTATGT-ATTATCGCA
1 TTGCGA-TA-GTCAAAATCGCA
*
1790987 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAAAATCGCA
* * *
1791007 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAAAATCGCA
**
1791027 TTGCGATTTTCTAAAATCGCA
1 TTGCGATAGTC-AAAATCGCA
* *
1791048 TTGCGA-ATTTGGAAAATCGCA
1 TTGCGATA-GT-CAAAATCGCA
* *
1791069 ATGCGATAGTCAAAATCGCG
1 TTGCGATAGTCAAAATCGCA
1791089 TTGCGA
1 TTGCGA
1791095 ATCTGGAAAC
Statistics
Matches: 138, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.02
20 69 0.50
21 63 0.46
22 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAAAATCGCA
Found at i:1791048 original size:21 final size:20
Alignment explanation
Indices: 1790981--1791094 Score: 102
Period size: 20 Copynumber: 5.6 Consensus size: 20
1790971 ATTATGTATT
** *
1790981 ATCGCATTGCGATAGTCAGA
1 ATCGCATTGCGATTTTCAAA
* *
1791001 ATCGCATTGCGATTTACATA
1 ATCGCATTGCGATTTTCAAA
*
1791021 TTCGCATTGCGATTTTCTAAA
1 ATCGCATTGCGATTTTC-AAA
**
1791042 ATCGCATTGCGAATTTGGAAA
1 ATCGCATTGCG-ATTTTCAAA
* **
1791063 ATCGCAATGCGATAGTCAAA
1 ATCGCATTGCGATTTTCAAA
*
1791083 ATCGCGTTGCGA
1 ATCGCATTGCGA
1791095 ATCTGGAAAC
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 46 0.61
21 25 0.33
22 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (20 bp):
ATCGCATTGCGATTTTCAAA
Found at i:1791084 original size:41 final size:41
Alignment explanation
Indices: 1790981--1791103 Score: 140
Period size: 41 Copynumber: 3.0 Consensus size: 41
1790971 ATTATGTATT
* ** *
1790981 ATCGCATTGCGATAGTCAGAATCGCATTGCG-ATTTACATA
1 ATCGCATTGCGATAGTCAAAATCGCATTGCGAATTTGGAAA
* **
1791021 TTCGCATTGCGATTTTCTAAAATCGCATTGCGAATTTGGAAA
1 ATCGCATTGCGATAGTC-AAAATCGCATTGCGAATTTGGAAA
* * *
1791063 ATCGCAATGCGATAGTCAAAATCGCGTTGCGAATCTGGAAA
1 ATCGCATTGCGATAGTCAAAATCGCATTGCGAATTTGGAAA
1791104 CTGATTTGCG
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 14 0.21
41 35 0.51
42 19 0.28
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
ATCGCATTGCGATAGTCAAAATCGCATTGCGAATTTGGAAA
Found at i:1791144 original size:19 final size:19
Alignment explanation
Indices: 1791120--1791156 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1791110 TGCGATAATG
*
1791120 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
1791139 GAGATCGTATTGCGATTT
1 GAGATCGCATTGCGATTT
1791157 TATTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1791731 original size:175 final size:175
Alignment explanation
Indices: 1791440--1791794 Score: 674
Period size: 175 Copynumber: 2.0 Consensus size: 175
1791430 TTTACATAGA
1791440 AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGGAAAGTGGATTTTTA
1 AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGGAAAGTGGATTTTTA
* * *
1791505 TTTGTTCATATAGGAATTTGAAATATTAAAAGGGGTGATAGTACAATGGCAAGTTTAAATTATCA
66 TTTGTTCATATAGGAATTTGAAATATTAAAAGGGATGACAGTACAATGGCAAGTTGAAATTATCA
1791570 TGTTTCATTAAGGGTAAAATAATAGTTTCACATTAAATGAATTTT
131 TGTTTCATTAAGGGTAAAATAATAGTTTCACATTAAATGAATTTT
1791615 AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGGAAAGTGGATTTTTA
1 AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGGAAAGTGGATTTTTA
*
1791680 TTTGTTCATATTGGAATTTGAAATATTAAAAGGGATGACAGTACAATGGCAAGTTGAAATTATCA
66 TTTGTTCATATAGGAATTTGAAATATTAAAAGGGATGACAGTACAATGGCAAGTTGAAATTATCA
1791745 TGTTTCATTAAGGGTAAAATAATAGTTTCACATTAAATGAATTTT
131 TGTTTCATTAAGGGTAAAATAATAGTTTCACATTAAATGAATTTT
1791790 AAATT
1 AAATT
1791795 CATTTATATT
Statistics
Matches: 176, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
175 176 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (175 bp):
AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGGAAAGTGGATTTTTA
TTTGTTCATATAGGAATTTGAAATATTAAAAGGGATGACAGTACAATGGCAAGTTGAAATTATCA
TGTTTCATTAAGGGTAAAATAATAGTTTCACATTAAATGAATTTT
Found at i:1798686 original size:19 final size:19
Alignment explanation
Indices: 1798662--1798757 Score: 122
Period size: 19 Copynumber: 5.1 Consensus size: 19
1798652 TATGCATTTG
*
1798662 GCTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAA
* *
1798681 GCTATGAATCTGACAGTAA
1 GCTATGAATCTGAAAATAA
* * *
1798700 GCTATGAATTTGACAGTAA
1 GCTATGAATCTGAAAATAA
1798719 GCTATGAATCTGAAAATAA
1 GCTATGAATCTGAAAATAA
1798738 GCTATGAATCT-AGAAATAA
1 GCTATGAATCTGA-AAATAA
1798757 G
1 G
1798758 TTCTGATTCG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
18 1 0.01
19 68 0.99
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:1806570 original size:41 final size:41
Alignment explanation
Indices: 1806521--1806612 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
1806511 CTACAGTTGT
** *
1806521 CGTTGCGATAATTGACTATCGCAACGCGATTTTTCATTTCG
1 CGTTGCGATAATTGAAAATCGCAACGCGATTTTCCATTTCG
*
1806562 CGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCATTTCG
1 CGTTGCGATAATTGAAAATCGCAACGCGATTTTCCATTTCG
*
1806603 CGTTGTGATA
1 CGTTGCGATA
1806613 GTCTACAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (41 bp):
CGTTGCGATAATTGAAAATCGCAACGCGATTTTCCATTTCG
Found at i:1806743 original size:6 final size:6
Alignment explanation
Indices: 1806732--1806782 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
1806722 GACACGTATT
1806732 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1806780 ACC
1 ACC
1806783 CGAGACGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1807471 original size:41 final size:41
Alignment explanation
Indices: 1807426--1807521 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1807416 AACTGTAGAT
*
1807426 TATCGCAACGCGAAATGGAAAATCGTGTTGCGATTTTCAAC
1 TATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCAAC
1807467 TATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCAAC
1 TATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCAAC
1807508 TATCGCAACGCGAA
1 TATCGCAACGCGAA
1807522 TTTGCGATAG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (41 bp):
TATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCAAC
Found at i:1807479 original size:21 final size:21
Alignment explanation
Indices: 1807455--1807520 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
1807445 AAATCGTGTT
1807455 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** * ***
1807476 GCGAAATGGAA-AATCGCGTT
1 GCGATTTTCAACTATCGCAAC
1807496 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
1807517 GCGA
1 GCGA
1807521 ATTTGCGATA
Statistics
Matches: 28, Mismatches: 16, Indels: 2
0.61 0.35 0.04
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:1810806 original size:18 final size:17
Alignment explanation
Indices: 1810776--1810809 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1810766 CAAAGTCTTT
*
1810776 AAAAAATTGAAAATTTA
1 AAAAAATTCAAAATTTA
1810793 AAAAAATATCAAAATTT
1 AAAAAAT-TCAAAATTT
1810810 TAATAGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAAAATTCAAAATTTA
Found at i:1817344 original size:3 final size:3
Alignment explanation
Indices: 1817336--1817397 Score: 87
Period size: 3 Copynumber: 22.0 Consensus size: 3
1817326 GCAAAAATTG
*
1817336 TAA TAA TAA -AA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1817381 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
1817398 CGGAAAAAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 8 0.15
3 45 0.85
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1817352 original size:11 final size:11
Alignment explanation
Indices: 1817336--1817397 Score: 88
Period size: 11 Copynumber: 5.3 Consensus size: 11
1817326 GCAAAAATTG
1817336 TAATAATAAAA
1 TAATAATAAAA
1817347 TAATAATAAAA
1 TAATAATAAAA
1817358 TAATAATATAATGA
1 TAATAATA-AA--A
1817372 TAATAATAATAA
1 TAATAATAA-AA
1817384 TAATAATAAAA
1 TAATAATAAAA
1817395 TAA
1 TAA
1817398 CGGAAAAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
11 24 0.51
12 12 0.26
13 1 0.02
14 10 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:1817755 original size:90 final size:89
Alignment explanation
Indices: 1817643--1817812 Score: 279
Period size: 90 Copynumber: 1.9 Consensus size: 89
1817633 CTTTAGGAAG
* * *
1817643 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCTTGC
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATAC
1817707 ATGATGAAGAGATCTGGCCATCTAAA
64 ATGATGAAGAGATCTGGCCATCTAAA
*
1817733 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
1817798 GATGAAGAGATCTGG
66 GATGAAGAGATCTGG
1817813 TCTGGGGATG
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
88 2 0.03
89 33 0.44
90 40 0.53
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (89 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
GATGAAGAGATCTGGCCATCTAAA
Found at i:1817776 original size:46 final size:46
Alignment explanation
Indices: 1817643--1817776 Score: 123
Period size: 46 Copynumber: 3.0 Consensus size: 46
1817633 CTTTAGGAAG
*
1817643 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCT-AA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CTAAA
* * * * * * * * **
1817689 --TGTTGACACGGCTCTTGCATGATGAAGA-GATCTGGCCATCTAAA
1 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAA
1817733 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1817777 TGGTTGACAC
Statistics
Matches: 62, Mismatches: 21, Indels: 10
0.67 0.23 0.11
Matches are distributed among these distances:
43 3 0.05
44 28 0.45
46 30 0.48
47 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (46 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAA
Found at i:1817797 original size:43 final size:44
Alignment explanation
Indices: 1817660--1817802 Score: 130
Period size: 46 Copynumber: 3.2 Consensus size: 44
1817650 ACTCGGTTCC
*
1817660 TACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTAT-CTAATGGTTGACACGGCTCA
* * * * ** * * * *
1817704 TGCATGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATCTAATGGT--TGACACGGCTCA
1817750 TACGTGATGAGGACGGCTGGTTATCT-ATGGTTGACACGGCTCA
1 TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
1817793 TACGTGATGA
1 TACGTGATGA
1817803 AGAGATCTGG
Statistics
Matches: 74, Mismatches: 20, Indels: 11
0.70 0.19 0.10
Matches are distributed among these distances:
43 24 0.32
44 18 0.24
45 4 0.05
46 27 0.36
47 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.27
Consensus pattern (44 bp):
TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
Found at i:1817813 original size:43 final size:44
Alignment explanation
Indices: 1817676--1817813 Score: 120
Period size: 43 Copynumber: 3.1 Consensus size: 44
1817666 ATGAGGACGG
* * *
1817676 CTGGTTATCCTAAT-GTTGACACGGCTCTTGCATGATGAAGAGAT
1 CTGGTTAT-CTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
** * * * * * *
1817720 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-G
1 CTGGTTATCTAATGGT--TGACACGGCTCATACGTGATGAAGA-GAT
1817766 CTGGTTATCT-ATGGTTGACACGGCTCATACGTGATGAAGAGAT
1 CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
1817809 CTGGT
1 CTGGT
1817814 CTGGGGATGA
Statistics
Matches: 71, Mismatches: 18, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
42 1 0.01
43 30 0.42
44 8 0.11
45 4 0.06
46 27 0.38
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
Found at i:1830622 original size:3 final size:3
Alignment explanation
Indices: 1830614--1830678 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
1830604 GCAAAAATTG
*
1830614 TAA TAA TAA -AA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1830659 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1830679 CGGAAAAAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 8 0.14
3 48 0.86
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1830630 original size:11 final size:11
Alignment explanation
Indices: 1830614--1830678 Score: 87
Period size: 11 Copynumber: 5.8 Consensus size: 11
1830604 GCAAAAATTG
1830614 TAATAATAAAA
1 TAATAATAAAA
1830625 TAATAATAAAA
1 TAATAATAAAA
*
1830636 TAATAATATAA
1 TAATAATAAAA
*
1830647 TGATAATAATAA
1 TAATAATAA-AA
1830659 TAATAATAATAA
1 TAATAATAA-AA
1830671 TAA-AATAA
1 TAATAATAA
1830679 CGGAAAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
11 33 0.67
12 16 0.33
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:1831603 original size:2 final size:2
Alignment explanation
Indices: 1831596--1831627 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1831586 ATAAACACCG
1831596 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1831628 TATGGTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1831956 original size:20 final size:20
Alignment explanation
Indices: 1831933--1831972 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1831923 CATTGTCCAC
1831933 CCCGACAGGAGTTTGTTCAA
1 CCCGACAGGAGTTTGTTCAA
*
1831953 CCCGACATGAGTTTGTTCAA
1 CCCGACAGGAGTTTGTTCAA
1831973 GTGATAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (20 bp):
CCCGACAGGAGTTTGTTCAA
Found at i:1833619 original size:32 final size:33
Alignment explanation
Indices: 1833574--1833640 Score: 102
Period size: 32 Copynumber: 2.0 Consensus size: 33
1833564 ATTAAGCCCT
1833574 AAACCATAAAACATTACATTAA-AGAGATAAAAAC
1 AAACCAT-AAACATTACATTAAGA-AGATAAAAAC
1833608 AAACCAT-AACATTACATTAAGAAGATAAAAAC
1 AAACCATAAACATTACATTAAGAAGATAAAAAC
1833640 A
1 A
1833641 TTACATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 24 0.75
33 1 0.03
34 7 0.22
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (33 bp):
AAACCATAAACATTACATTAAGAAGATAAAAAC
Found at i:1834468 original size:32 final size:32
Alignment explanation
Indices: 1834422--1834682 Score: 121
Period size: 32 Copynumber: 7.8 Consensus size: 32
1834412 TTTTATAATA
*
1834422 AAGTGATATATCACTGAAAAGTTTATGAAATG
1 AAGTGATATATCACTAAAAAGTTTATGAAATG
* *
1834454 AAGTTATATATCACTAAAAAGTTTATGAAGTG
1 AAGTGATATATCACTAAAAAGTTTATGAAATG
* ** * *
1834486 AAGTAAT-TAGGAACTAAAAGGTTTATGTCATTATGTATT
1 AAGTGATATA-TCACTAAAAAGTTTATG--A--A---ATG
* * * * ** *
1834525 AAATGGTTTATGAGAAAAAGACGTTTTTCTGAAATG
1 AAGTGATATATCACTAAAA-A-G-TT-TATGAAATG
*
1834561 AAGTGATATATCATTAAAAAGTTTATGAAATG
1 AAGTGATATATCACTAAAAAGTTTATGAAATG
* * ** *
1834593 AAGTTATATATCACTGAAATTTTTTTGAAATG
1 AAGTGATATATCACTAAAAAGTTTATGAAATG
* * * * *
1834625 AAGTAAT-TAGACACTGAAATGTTTTTCTGAAATG
1 AAGTGATATA-TCACTAAAAAG--TTTATGAAATG
* *
1834659 AAGTAATATATCACTGAAAAGTTT
1 AAGTGATATATCACTAAAAAGTTT
1834683 CTTTTCATAA
Statistics
Matches: 174, Mismatches: 38, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
31 4 0.02
32 101 0.58
33 2 0.01
34 28 0.16
35 3 0.02
36 16 0.09
39 11 0.06
40 2 0.01
41 2 0.01
42 2 0.01
43 3 0.02
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (32 bp):
AAGTGATATATCACTAAAAAGTTTATGAAATG
Found at i:1834565 original size:139 final size:139
Alignment explanation
Indices: 1834308--1834648 Score: 400
Period size: 139 Copynumber: 2.5 Consensus size: 139
1834298 GATATAATAC
* * * * * * * *
1834308 TGAAATGAAGTGATACATCACTGAAAAGTTTCTAAAGTGAAGTGATTGGGCACTGAAAAGTTTTT
1 TGAAATGAAGTTATATATCACTGAAAAGTTTATGAAGTGAAGTAATTAGGAACTGAAAAGTTTAT
* * *** * * *
1834373 GTGATTGTGTATTAAATGGTGCATGAGAAAAGGTTTTTTTTTTATAATAAAGTGATATATCACTG
66 GTCATTATGTATTAAATGGTGCATGAGAAAAGACGTTTTTCTGATAATAAAGTGATATATCACTA
1834438 AAAAGTTTA
131 AAAAGTTTA
*
1834447 TGAAATGAAGTTATATATCACTAAAAAGTTTATGAAGTGAAGTAATTAGGAACT-AAAAGGTTTA
1 TGAAATGAAGTTATATATCACTGAAAAGTTTATGAAGTGAAGTAATTAGGAACTGAAAA-GTTTA
** * *
1834511 TGTCATTATGTATTAAATGGTTTATGAGAAAAAGACGTTTTTCTGA-AATGAAGTGATATATCAT
65 TGTCATTATGTATTAAATGGTGCATGAG-AAAAGACGTTTTTCTGATAATAAAGTGATATATCAC
1834575 TAAAAAGTTTA
129 TAAAAAGTTTA
** * * *
1834586 TGAAATGAAGTTATATATCACTGAAATTTTTTTGAAATGAAGTAATTA-GACACTGAAATGTTT
1 TGAAATGAAGTTATATATCACTGAAAAGTTTATGAAGTGAAGTAATTAGGA-ACTGAAAAGTTT
1834649 TTCTGAAATG
Statistics
Matches: 171, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
138 6 0.04
139 150 0.88
140 15 0.09
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (139 bp):
TGAAATGAAGTTATATATCACTGAAAAGTTTATGAAGTGAAGTAATTAGGAACTGAAAAGTTTAT
GTCATTATGTATTAAATGGTGCATGAGAAAAGACGTTTTTCTGATAATAAAGTGATATATCACTA
AAAAGTTTA
Found at i:1834650 original size:34 final size:33
Alignment explanation
Indices: 1834547--1834687 Score: 137
Period size: 32 Copynumber: 4.2 Consensus size: 33
1834537 AGAAAAAGAC
* * * *
1834547 GTTTTTCTGAAATGAAGTGATATATCATTAAAAA
1 GTTTTTTTGAAATGAAGTAATATATCACT-GAAA
* *
1834581 G--TTTATGAAATGAAGTTATATATCACTGAAA
1 GTTTTTTTGAAATGAAGTAATATATCACTGAAA
*
1834612 -TTTTTTTGAAATGAAGTAAT-TAGACACTGAAA
1 GTTTTTTTGAAATGAAGTAATATA-TCACTGAAA
*
1834644 TGTTTTTCTGAAATGAAGTAATATATCACTGAAAA
1 -GTTTTTTTGAAATGAAGTAATATATCACTG-AAA
1834679 GTTTCTTTT
1 GTTT-TTTT
1834688 CATAAACTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
31 5 0.06
32 47 0.53
34 29 0.33
35 8 0.09
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (33 bp):
GTTTTTTTGAAATGAAGTAATATATCACTGAAA
Found at i:1838430 original size:108 final size:108
Alignment explanation
Indices: 1838241--1838457 Score: 425
Period size: 108 Copynumber: 2.0 Consensus size: 108
1838231 CTAGCCCTCG
1838241 TTGTGTTAGAGGAGATAGGAGCTCAGTTTCATCTCAAACACCAAGCTTAAGGTCCAATTACCATT
1 TTGTGTTAGAGGAGATAGGAGCTCAGTTTCATCTCAAACACCAAGCTTAAGGTCCAATTACCATT
1838306 ACACAGGCAGGGTTGATACTCATGCTTGTAGTAATGGCAACAA
66 ACACAGGCAGGGTTGATACTCATGCTTGTAGTAATGGCAACAA
1838349 TTGTGTTAGAGGAGATAGGAGCTCAGTTTCATCTCAAACACCAAGCTTAAGGTCCAATTACCATT
1 TTGTGTTAGAGGAGATAGGAGCTCAGTTTCATCTCAAACACCAAGCTTAAGGTCCAATTACCATT
*
1838414 ACACAGGCAGGGTTGATACTCATGCTTGTAGTAGTGGCAACAA
66 ACACAGGCAGGGTTGATACTCATGCTTGTAGTAATGGCAACAA
1838457 T
1 T
1838458 GCTGCAACTT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (108 bp):
TTGTGTTAGAGGAGATAGGAGCTCAGTTTCATCTCAAACACCAAGCTTAAGGTCCAATTACCATT
ACACAGGCAGGGTTGATACTCATGCTTGTAGTAATGGCAACAA
Found at i:1840295 original size:12 final size:13
Alignment explanation
Indices: 1840265--1840296 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1840255 TTTCGGATTA
1840265 CCAAAATAGTGAT
1 CCAAAATAGTGAT
1840278 CC-AAATA-TGAT
1 CCAAAATAGTGAT
1840289 CCAAAATA
1 CCAAAATA
1840297 ATTGAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 10 0.56
13 2 0.11
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.22
Consensus pattern (13 bp):
CCAAAATAGTGAT
Found at i:1841688 original size:24 final size:27
Alignment explanation
Indices: 1841633--1841701 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 27
1841623 ATATGTATCA
1841633 AATATTGAGGCACAAAACCATCGATCTT
1 AATATTGAGGCACAAAACCA-CGATCTT
1841661 AATATTGAGGCACAAAA-C-C-ATCTT
1 AATATTGAGGCACAAAACCACGATCTT
1841685 AATATTGAGGCACAAAA
1 AATATTGAGGCACAAAA
1841702 GATTGATTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 22 0.54
25 1 0.02
27 1 0.02
28 17 0.41
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (27 bp):
AATATTGAGGCACAAAACCACGATCTT
Done.