Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 18 of 290
Found at i:5723658 original size:27 final size:27
Alignment explanation
Indices: 5723626--5723681 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5723616 ATAGTGAGAC
5723626 AGGCCTGAATACTAAAACTGAAGATGA
1 AGGCCTGAATACTAAAACTGAAGATGA
5723653 AGGCCTGAATACTAAAACTGAAGATGA
1 AGGCCTGAATACTAAAACTGAAGATGA
5723680 AG
1 AG
5723682 TTTGCGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18
Consensus pattern (27 bp):
AGGCCTGAATACTAAAACTGAAGATGA
Found at i:5727223 original size:13 final size:13
Alignment explanation
Indices: 5727205--5727230 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5727195 CCAAAACCCA
5727205 CATGCTTGTGTGG
1 CATGCTTGTGTGG
5727218 CATGCTTGTGTGG
1 CATGCTTGTGTGG
5727231 GCCCACACGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.38, T:0.38
Consensus pattern (13 bp):
CATGCTTGTGTGG
Found at i:5729754 original size:19 final size:20
Alignment explanation
Indices: 5729712--5729766 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5729702 TGGGCCTTAA
5729712 CCCATATCAATACAGTTGGG
1 CCCATATCAATACAGTTGGG
*
5729732 CCCATTTCAATACAGTT-GG
1 CCCATATCAATACAGTTGGG
* *
5729751 CCCATAACAAAACAGT
1 CCCATATCAATACAGT
5729767 CTTATATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (20 bp):
CCCATATCAATACAGTTGGG
Found at i:5734138 original size:19 final size:20
Alignment explanation
Indices: 5734076--5734139 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
5734066 TGGGCCTTAA
* *
5734076 CCCATATCAACACAGTTGGG
1 CCCATTTCAATACAGTTGGG
5734096 CCCATTTCAATACAGTTGGG
1 CCCATTTCAATACAGTTGGG
5734116 CCCATTTCAATACAGTT-GG
1 CCCATTTCAATACAGTTGGG
5734135 CCCAT
1 CCCAT
5734140 AACAAAATAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
19 7 0.17
20 35 0.83
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (20 bp):
CCCATTTCAATACAGTTGGG
Found at i:5736613 original size:3 final size:3
Alignment explanation
Indices: 5736605--5736647 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
5736595 CTAAACTAAC
*
5736605 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5736648 AAAGATCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5754160 original size:25 final size:26
Alignment explanation
Indices: 5754126--5754178 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
5754116 ATTTAGCCAA
5754126 AAAAGGACAAAATATACAAAAAAATT
1 AAAAGGACAAAATATACAAAAAAATT
*
5754152 AAAA-GACAAAATTTACAAAAAAATT
1 AAAAGGACAAAATATACAAAAAAATT
5754177 AA
1 AA
5754179 CTCAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.70, C:0.08, G:0.06, T:0.17
Consensus pattern (26 bp):
AAAAGGACAAAATATACAAAAAAATT
Found at i:5758652 original size:24 final size:24
Alignment explanation
Indices: 5758609--5758655 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5758599 CTGTCAGGAG
**
5758609 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
*
5758633 AGGATTTAGGAGCAGGTAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
5758656 GGAAATCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.40, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:5760112 original size:27 final size:28
Alignment explanation
Indices: 5760072--5760149 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
5760062 AGGAAGCGTC
*
5760072 CTGGTGGCTATGCCACAATTATCTTATT
1 CTGGTGGCTCTGCCACAATTATCTTATT
5760100 -TGGTGGCTCTGCCACATATT-TC-TATT
1 CTGGTGGCTCTGCCACA-ATTATCTTATT
*
5760126 CTGGTGGCTCTGCCACGATTATCT
1 CTGGTGGCTCTGCCACAATTATCT
5760150 GTATCTCGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 7 0.16
27 34 0.77
28 3 0.07
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACAATTATCTTATT
Found at i:5766489 original size:24 final size:24
Alignment explanation
Indices: 5766446--5766492 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5766436 CTGTCAGGAG
**
5766446 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
*
5766470 AGGATTTAGGAGCAGGTAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
5766493 GGAAATCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.40, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:5767951 original size:27 final size:27
Alignment explanation
Indices: 5767911--5768023 Score: 124
Period size: 27 Copynumber: 4.2 Consensus size: 27
5767901 AGGAAGTGTC
*
5767911 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
5767938 CTGGTGGCTCTGCCACATATT-TCT-ATT
1 CTGGTGGCTCTGCCACA-ATTATCTGA-T
*
5767965 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * * *
5767993 CTGGTGACTCTGTCAC-ATTAGCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
5768019 CTGGT
1 CTGGT
5768024 AGCCATGCTG
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
26 10 0.13
27 46 0.61
28 18 0.24
29 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:5768021 original size:54 final size:54
Alignment explanation
Indices: 5767911--5768023 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
5767901 AGGAAGTGTC
* **
5767911 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTATT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATAGCTATT
* * * *
5767965 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TAGCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATAGCTATT
5768019 CTGGT
1 CTGGT
5768024 AGCCATGCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATAGCTATT
Found at i:5770666 original size:27 final size:27
Alignment explanation
Indices: 5770636--5770892 Score: 120
Period size: 27 Copynumber: 9.6 Consensus size: 27
5770626 TCTAGGGTAG
* * *
5770636 AATTACTAAAATACCCTTGGTTTA-CAA
1 AATTACCAAAATACCC-TCGATTAGCAA
*
5770663 AATTACCAAAATATCCTCGATTAGCAA
1 AATTACCAAAATACCCTCGATTAGCAA
* **
5770690 AATTACCAAAATACCC-CTGATTTGTGA
1 AATTACCAAAATACCCTC-GATTAGCAA
* * ** * *
5770717 AATTACCGACATACCCTTAACCT-G-TA
1 AATTACCAAAATACCCTCGA-TTAGCAA
* *
5770743 AATTACCAAAATATCCTCGATTAGTAA
1 AATTACCAAAATACCCTCGATTAGCAA
5770770 AATTACCAAAATACCC-CTGATTTA-CAA
1 AATTACCAAAATACCCTC-GA-TTAGCAA
* * * *
5770797 AATTA-CAGAGATACCCTTGACCT-GTAA
1 AATTACCA-AAATACCCTCGA-TTAGCAA
** * *
5770824 AATTACTGAAATACCCTCGATTTGTAA
1 AATTACCAAAATACCCTCGATTAGCAA
* * * * *
5770851 AATTATCGAAATACCC-CCATTTGGAA
1 AATTACCAAAATACCCTCGATTAGCAA
5770877 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
5770893 ATGACTTTCA
Statistics
Matches: 178, Mismatches: 38, Indels: 29
0.73 0.16 0.12
Matches are distributed among these distances:
25 2 0.01
26 48 0.27
27 124 0.70
28 4 0.02
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCTCGATTAGCAA
Found at i:5770765 original size:80 final size:80
Alignment explanation
Indices: 5770661--5770892 Score: 297
Period size: 80 Copynumber: 2.9 Consensus size: 80
5770651 CTTGGTTTAC
* *
5770661 AAAATTACCAAAATATCCTCGATTAGCAAAATTACCAAAATACCCCTGATTTGTGAAATTACCGA
1 AAAATTACCAAAATATCCTCGATTAGTAAAATTACCAAAATACCCCTGATTTG-GAAATTACAGA
*
5770726 CATACCCTTAACCTGT
65 AATACCCTTAACCTGT
**
5770742 -AAATTACCAAAATATCCTCGATTAGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGA
1 AAAATTACCAAAATATCCTCGATTAGTAAAATTACCAAAATACCCCTGATTT-GGAAATTACAGA
* *
5770806 GATACCCTTGACCTGT
65 AATACCCTTAACCTGT
** * * * * *
5770822 AAAATTACTGAAATACCCTCGATTTGTAAAATTATCGAAATACCCC-CATTTGGAAAATTACAGA
1 AAAATTACCAAAATATCCTCGATTAGTAAAATTACCAAAATACCCCTGATTTGG-AAATTACAGA
5770886 AATACCC
65 AATACCC
5770893 ATGACTTTCA
Statistics
Matches: 132, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
80 93 0.70
81 39 0.30
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (80 bp):
AAAATTACCAAAATATCCTCGATTAGTAAAATTACCAAAATACCCCTGATTTGGAAATTACAGAA
ATACCCTTAACCTGT
Found at i:5770850 original size:107 final size:106
Alignment explanation
Indices: 5770661--5770975 Score: 262
Period size: 107 Copynumber: 2.9 Consensus size: 106
5770651 CTTGGTTTAC
* * *
5770661 AAAATTACCAAAATA-TCCTCGA-TTAGCAAAATTACCA-AAATACCCCTGATTTGTGAAATTAC
1 AAAATTACCAAAATACCCCT-GATTTA-CAAAATTA-CAGAAATACCCTTGATTTGTAAAATTAC
* * * ** * * *
5770723 CGACATACCCTTAACCTGTAAATTACCAAAATATCCTCGATTAGT
63 TGAAATACCCTTGATTTGTAAATTACCAAAATA-CCCCCATTAGG
* **
5770768 AAAATTACCAAAATACCCCTGATTTACAAAATTACAGAGATACCCTTGACCTGTAAAATTACTGA
1 AAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGATTTGTAAAATTACTGA
* * * *
5770833 AATACCCTCGATTTGTAAAATTATCGAAATACCCCCATTTGG
66 AATACCCTTGATTTGT-AAATTACCAAAATACCCCCATTAGG
* * * * * *
5770875 AAAATTA-CAGAAATACCCATGACTTTCAAAAAATTATAGAAATACCATTGGTTTGCAAAATTA-
1 AAAATTACCA-AAATACCCCTGA-TTT-ACAAAATTACAGAAATACCCTTGATTTGTAAAATTAC
* * *
5770938 TCGAAATACCCTTGGTTTGTAGATTTACCAAAACACCC
63 T-GAAATACCCTTGATTTGTA-AATTACCAAAATACCC
5770976 TTGTAGGGTG
Statistics
Matches: 166, Mismatches: 33, Indels: 16
0.77 0.15 0.07
Matches are distributed among these distances:
106 4 0.02
107 83 0.50
108 23 0.14
109 56 0.34
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (106 bp):
AAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGATTTGTAAAATTACTGA
AATACCCTTGATTTGTAAATTACCAAAATACCCCCATTAGG
Found at i:5770943 original size:27 final size:27
Alignment explanation
Indices: 5770904--5770956 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5770894 TGACTTTCAA
5770904 AAAATTATAGAAATACCATTGGTTTGC
1 AAAATTATAGAAATACCATTGGTTTGC
* *
5770931 AAAATTATCGAAATACCCTTGGTTTG
1 AAAATTATAGAAATACCATTGGTTTG
5770957 TAGATTTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTGC
Found at i:5771459 original size:22 final size:22
Alignment explanation
Indices: 5771399--5771461 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
5771389 GCCAATTATT
* *
5771399 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
5771421 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
5771443 CTGATTATAGCTGTGTGCC
1 CTGATTATGGCTCTGTGCC
5771462 GAACGTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:5776557 original size:68 final size:66
Alignment explanation
Indices: 5776485--5776651 Score: 169
Period size: 67 Copynumber: 2.5 Consensus size: 66
5776475 CATCATGTGT
* * *
5776485 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCACGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCACGCGTGATACTAGTGAAGGACACCA
5776548 TGTAG
62 TGTAG
** * * *
5776553 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCTAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCACGCGTGATACTA-GTGAAGGACACCATGT
5776618 AG
65 AG
* * *
5776620 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTC
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTC
5776652 ACATGGGTGG
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
64 24 0.28
65 3 0.04
66 13 0.15
67 32 0.38
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCACGCGTGATACTAGTGAAGGACACCATGTA
G
Found at i:5785576 original size:11 final size:11
Alignment explanation
Indices: 5785560--5785590 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5785550 ATTGAGCTTA
5785560 TTACTCATACG
1 TTACTCATACG
5785571 TTACTCATACG
1 TTACTCATACG
*
5785582 TTACACATA
1 TTACTCATA
5785591 ATTTCATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (11 bp):
TTACTCATACG
Found at i:5791433 original size:46 final size:46
Alignment explanation
Indices: 5791381--5791686 Score: 354
Period size: 46 Copynumber: 6.7 Consensus size: 46
5791371 GTGCTCTCTA
* *
5791381 ATATGAAATATGTAAGACCATGGTCGAAAGATACCATGGCAACCTG
1 ATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATG
* * *
5791427 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACCTG
1 ATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATG
* *
5791473 ATATG-AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTG
1 ATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATG
*
5791518 ATATGAAATGA-ATAAGACCATGGTTGAAAGATACCATGGCAACATG
1 ATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAACATG
*** * * * *
5791564 ACGGGAAATGA-ATAAGACCATGGTTGAAAGATACTATGGCAGCGTG
1 ATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAACATG
* *
5791610 ACATGAAATGA-ATAAGACCATGGTTGAAAGATACCATGGCAACATG
1 ATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAACATG
* *
5791656 ACA-GAAA-ATGAGTAAGACCATAGTTGAAAGA
1 ATATGAAATAT--GTAAGACCATGGTTGAAAGA
5791687 CACTATAGCA
Statistics
Matches: 234, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.00
45 47 0.20
46 186 0.79
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
ATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATG
Found at i:5791618 original size:92 final size:92
Alignment explanation
Indices: 5791392--5791686 Score: 430
Period size: 92 Copynumber: 3.2 Consensus size: 92
5791382 TATGAAATAT
* **
5791392 GTAAGACCATGGTCGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAG
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAG
* * * * *
5791457 ATACCATGACAACCTGATATG-AATGT
66 ATACCATGGCAACATGACAGGAAATGA
*
5791483 GTAAGACCATGGTTGAAAGATACCATGGCAACTTGATATGAAATGAATAAGACCATGGTTGAAAG
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAG
*
5791548 ATACCATGGCAACATGACGGGAAATGA
66 ATACCATGGCAACATGACAGGAAATGA
* * * * *
5791575 ATAAGACCATGGTTGAAAGATACTATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAG
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAG
*
5791640 ATACCATGGCAACATGACAGAAAATGA
66 ATACCATGGCAACATGACAGGAAATGA
*
5791667 GTAAGACCATAGTTGAAAGA
1 GTAAGACCATGGTTGAAAGA
5791687 CACTATAGCA
Statistics
Matches: 184, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
91 77 0.42
92 107 0.58
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (92 bp):
GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAG
ATACCATGGCAACATGACAGGAAATGA
Found at i:5797637 original size:40 final size:40
Alignment explanation
Indices: 5797584--5797808 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
5797574 CAATGTCACG
* * * *
5797584 CACACTAAGTGCCATACATAGCCGAAGTTATCTCAAATCA
1 CACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCA
* *
5797624 CACACTAAGTGCCATATATAGCCAAAGCTATGTCGAATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCA
* * * * *
5797664 CACACTAAGTGCTAGAAATAGCTGAAGCTATGTCAAATCA
1 CACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCA
*
5797704 CACACTAAGTGCCATATATAGTCGAAGCTATGTCGAATCA
1 CACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCA
* * *
5797744 TACACTAAGTGCCATATATAGCCGAAACTATGTCGAATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCA
* * *
5797784 CACACTAAATGCCACAAATAGCCGA
1 CACACTAAGTGCCATATATAGCCGA
5797809 TTTTTTGTCG
Statistics
Matches: 158, Mismatches: 27, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 158 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.22
Consensus pattern (40 bp):
CACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCA
Found at i:5797803 original size:120 final size:120
Alignment explanation
Indices: 5797584--5797805 Score: 347
Period size: 120 Copynumber: 1.9 Consensus size: 120
5797574 CAATGTCACG
*
5797584 CACACTAAGTGCCATACATAGCCGAAGTTATCTCAAATCACACACTAAGTGCCATATATAGCCAA
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCACACACTAAGTGCCATATATAGCCAA
* * *
5797649 AGCTATGTCGAATCGCACACTAAGTGCTAGAAATAGCTGAAGCTATGTCAAATCA
66 AGCTATGTCGAATCGCACACTAAATGCCACAAATAGCTGAAGCTATGTCAAATCA
* * * * *
5797704 CACACTAAGTGCCATATATAGTCGAAGCTATGTCGAATCATACACTAAGTGCCATATATAGCCGA
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCACACACTAAGTGCCATATATAGCC-A
5797769 AA-CTATGTCGAATCGCACACTAAATGCCACAAATAGC
65 AAGCTATGTCGAATCGCACACTAAATGCCACAAATAGC
5797806 CGATTTTTTG
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
120 89 0.97
121 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (120 bp):
CACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCACACACTAAGTGCCATATATAGCCAA
AGCTATGTCGAATCGCACACTAAATGCCACAAATAGCTGAAGCTATGTCAAATCA
Found at i:5799160 original size:40 final size:38
Alignment explanation
Indices: 5799116--5799215 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 38
5799106 TGAATATAAT
* *
5799116 AATTATAATTACCATAATTATAATAATGTTTGA-CCAAAAA
1 AATTATAATTACAATAATTATAATAATATTTGATCC---AA
* * *
5799156 AATTACAATTACAATAATTATAATAATATTTTATCCTA
1 AATTATAATTACAATAATTATAATAATATTTGATCCAA
5799194 AATTATAATTACAATAATTATA
1 AATTATAATTACAATAATTATA
5799216 CAAGGATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 22 0.42
40 29 0.55
41 2 0.04
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTTGATCCAA
Found at i:5807857 original size:19 final size:18
Alignment explanation
Indices: 5807802--5807857 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
5807792 TATTTTATGC
* *
5807802 AAAAGAAAGGAAACAAAT
1 AAAAGAAAGAAAACAAAG
*
5807820 AAAAGAAAGAATAAAAAAG
1 AAAAGAAAGAA-AACAAAG
*
5807839 AAAAGTAATGAAAACAAAG
1 AAAAG-AAAGAAAACAAAG
5807858 CTTGTATTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 10 0.32
19 16 0.52
20 5 0.16
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (18 bp):
AAAAGAAAGAAAACAAAG
Found at i:5809614 original size:40 final size:40
Alignment explanation
Indices: 5809547--5810031 Score: 579
Period size: 40 Copynumber: 12.2 Consensus size: 40
5809537 GGACTAAGAT
*
5809547 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC
* * * *
5809587 CCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTATGAT-
1 CCGAAGGCATTTGTGCGAGTTG-CTATATCCGGGCTAAG-TC
* *
5809627 CCGAAGGCATTTGTGCGAGTTGCTATATCTGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC
* * * *
5809667 CCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGAC
1 CCGAAGGCATTTGTGCGAGTTG-CTATATCCGGGCTAAGTC
* *
5809707 TCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC
* * * *
5809747 CCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGAC
1 CCGAAGGCATTTGTGCGAGTTG-CTATATCCGGGCTAAGTC
* *
5809787 TCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC
* * * *
5809827 CCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGAC
1 CCGAAGGCATTTGTGCGAGTTG-CTATATCCGGGCTAAGTC
* *
5809867 TCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC
* * *
5809907 CCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTG-CTATATCCGGGCTAAGTC
*
5809947 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGAC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC
* * *
5809987 CCGAGGGCATTTGTGCGAGTTGTTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC
5810026 CCGAAG
1 CCGAAG
5810032 ATACTTGGGT
Statistics
Matches: 376, Mismatches: 57, Indels: 25
0.82 0.12 0.05
Matches are distributed among these distances:
39 23 0.06
40 342 0.91
41 11 0.03
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC
Found at i:5809677 original size:80 final size:80
Alignment explanation
Indices: 5809535--5810022 Score: 831
Period size: 80 Copynumber: 6.1 Consensus size: 80
5809525 CGGATGATAA
*
5809535 CCGGACTAAGA-TCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTT
1 CCGGGCTAAGACT-CGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTT
5809599 ATGCTAGTGATTATAT
65 ATGCTAGTGATTATAT
* *
5809615 CCGGGCTATGA-TCCGAAGGCATTTGTGCGAGTTGCTATATCTGGGCTATGTCCCGAAGGCATTT
1 CCGGGCTAAGACT-CGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTT
5809679 ATGCTAGTGATTATAT
65 ATGCTAGTGATTATAT
5809695 CCGGGCTAAGACTCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACTCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
5809760 TGCTAGTGATTATAT
66 TGCTAGTGATTATAT
5809775 CCGGGCTAAGACTCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACTCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
5809840 TGCTAGTGATTATAT
66 TGCTAGTGATTATAT
5809855 CCGGGCTAAGACTCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACTCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
5809920 TGCTAGTGATTATAT
66 TGCTAGTGATTATAT
* * * * * *
5809935 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAGGGCATTTG
1 CCGGGCTAAGACTCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
*
5810000 TGCGAGTTG-TTATAT
66 TGCTAG-TGATTATAT
5810015 CC-GGCTAA
1 CCGGGCTAA
5810023 ATCCCGAAGA
Statistics
Matches: 394, Mismatches: 12, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
79 6 0.02
80 385 0.98
81 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (80 bp):
CCGGGCTAAGACTCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
TGCTAGTGATTATAT
Found at i:5816100 original size:26 final size:26
Alignment explanation
Indices: 5816071--5816128 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 26
5816061 TTTGCCATGT
5816071 TTACTGTTATTAGCAGCTTTGTTGCA
1 TTACTGTTATTAGCAGCTTTGTTGCA
*
5816097 TTAC---TATTAGCAGCTTTGTTGCT
1 TTACTGTTATTAGCAGCTTTGTTGCA
5816120 TTACTGTTA
1 TTACTGTTA
5816129 GCAGCTTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 22 0.79
26 6 0.21
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (26 bp):
TTACTGTTATTAGCAGCTTTGTTGCA
Found at i:5816105 original size:23 final size:23
Alignment explanation
Indices: 5816078--5816136 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
5816068 TGTTTACTGT
5816078 TATTAGCAGCTTTGTTGCATTAC
1 TATTAGCAGCTTTGTTGCATTAC
*
5816101 TATTAGCAGCTTTGTTGCTTTAC
1 TATTAGCAGCTTTGTTGCATTAC
*
5816124 TGTTAGCAGCTTT
1 TATTAGCAGCTTT
5816137 ACTGCGATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (23 bp):
TATTAGCAGCTTTGTTGCATTAC
Found at i:5819804 original size:29 final size:29
Alignment explanation
Indices: 5819762--5819819 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5819752 AAAAGAAATA
5819762 AGGTACGATGAGAATGTGTATAGATTATC
1 AGGTACGATGAGAATGTGTATAGATTATC
5819791 AGGTACGATGAGAATGTGTATAGATTATC
1 AGGTACGATGAGAATGTGTATAGATTATC
5819820 GTCAGTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (29 bp):
AGGTACGATGAGAATGTGTATAGATTATC
Found at i:5835586 original size:26 final size:26
Alignment explanation
Indices: 5835557--5835630 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
5835547 AACACACCAG
*
5835557 TATCGCAGCATAGTTGCCAGTAATAA
1 TATCGCAGCAAAGTTGCCAGTAATAA
*
5835583 TATCGCAGCAAAGTTGCCAGTAATAG
1 TATCGCAGCAAAGTTGCCAGTAATAA
* * * *
5835609 TAACGCAACAAAGCTACCAGTA
1 TATCGCAGCAAAGTTGCCAGTA
5835631 TCAGTATATG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (26 bp):
TATCGCAGCAAAGTTGCCAGTAATAA
Found at i:5835698 original size:40 final size:40
Alignment explanation
Indices: 5835639--5835770 Score: 219
Period size: 40 Copynumber: 3.3 Consensus size: 40
5835629 TATCAGTATA
*
5835639 TGGCACAAAGCCATGAGTAGTGGCACAAAGCCATCAATAG
1 TGGCACAAAGCCATCAGTAGTGGCACAAAGCCATCAATAG
* * *
5835679 TGGTACAAAGCTATCAGTAGTGGCACAAAGCCATAAATAG
1 TGGCACAAAGCCATCAGTAGTGGCACAAAGCCATCAATAG
*
5835719 CGGCACAAAGCCATCAGTAGTGGCACAAAGCCATCAATAG
1 TGGCACAAAGCCATCAGTAGTGGCACAAAGCCATCAATAG
5835759 TGGCACAAAGCC
1 TGGCACAAAGCC
5835771 TTAAATATCA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (40 bp):
TGGCACAAAGCCATCAGTAGTGGCACAAAGCCATCAATAG
Found at i:5835724 original size:60 final size:60
Alignment explanation
Indices: 5835629--5835777 Score: 208
Period size: 60 Copynumber: 2.5 Consensus size: 60
5835619 AAGCTACCAG
* * * * *
5835629 TATCAGTATATGGCACAAAGCCATGAGTAGTGGCACAAAGCCATCAATAGTGGTACAAAGC
1 TATCAGTA-GTGGCACAAAGCCATAAATAGCGGCACAAAGCCATCAATAGTGGCACAAAGC
*
5835690 TATCAGTAGTGGCACAAAGCCATAAATAGCGGCACAAAGCCATCAGTAGTGGCACAAAGC
1 TATCAGTAGTGGCACAAAGCCATAAATAGCGGCACAAAGCCATCAATAGTGGCACAAAGC
* * *
5835750 CATCAATAGTGGCACAAAGCCTTAAATA
1 TATCAGTAGTGGCACAAAGCCATAAATA
5835778 TCATAACAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
60 71 0.90
61 8 0.10
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (60 bp):
TATCAGTAGTGGCACAAAGCCATAAATAGCGGCACAAAGCCATCAATAGTGGCACAAAGC
Found at i:5835777 original size:20 final size:20
Alignment explanation
Indices: 5835639--5835770 Score: 192
Period size: 20 Copynumber: 6.6 Consensus size: 20
5835629 TATCAGTATA
* *
5835639 TGGCACAAAGCCATGAGTAG
1 TGGCACAAAGCCATCAATAG
5835659 TGGCACAAAGCCATCAATAG
1 TGGCACAAAGCCATCAATAG
* * *
5835679 TGGTACAAAGCTATCAGTAG
1 TGGCACAAAGCCATCAATAG
*
5835699 TGGCACAAAGCCATAAATAG
1 TGGCACAAAGCCATCAATAG
* *
5835719 CGGCACAAAGCCATCAGTAG
1 TGGCACAAAGCCATCAATAG
5835739 TGGCACAAAGCCATCAATAG
1 TGGCACAAAGCCATCAATAG
5835759 TGGCACAAAGCC
1 TGGCACAAAGCC
5835771 TTAAATATCA
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 98 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (20 bp):
TGGCACAAAGCCATCAATAG
Found at i:5839720 original size:34 final size:34
Alignment explanation
Indices: 5839628--5839720 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 34
5839618 GTGAATACAT
* *
5839628 TCTGGGCCTAAGCCTATATCAGTAACAGTAGCAG
1 TCTGGGCCTTAGCCTATTTCAGTAACAGTAGCAG
* * *
5839662 TCTAGGCCTTAGCCCATTTTAGTAACAGTA-CAAG
1 TCTGGGCCTTAGCCTATTTCAGTAACAGTAGC-AG
* *
5839696 TCTGGGCTTTAGCCTGTTTCAGTAA
1 TCTGGGCCTTAGCCTATTTCAGTAA
5839721 TAATAATCAG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
33 1 0.02
34 47 0.98
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (34 bp):
TCTGGGCCTTAGCCTATTTCAGTAACAGTAGCAG
Found at i:5840174 original size:27 final size:27
Alignment explanation
Indices: 5840143--5840273 Score: 156
Period size: 27 Copynumber: 4.9 Consensus size: 27
5840133 AGGTATTGTA
*
5840143 GTCATTTTACCCTATAAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * *
5840170 ATCATTCTACCATTTG-GAGGTATTTCG
1 GTCATTTTACCCTATGAG-GGTATTTCG
*
5840197 GTCATTTTATCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
5840224 GTCCTTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
5840251 GTCATTTTATCCTATGAGGGTAT
1 GTCATTTTACCCTATGAGGGTAT
5840274 AAGTCGTTAT
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 1 0.01
27 82 0.98
28 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:5840201 original size:54 final size:54
Alignment explanation
Indices: 5840143--5840273 Score: 199
Period size: 54 Copynumber: 2.4 Consensus size: 54
5840133 AGGTATTGTA
* * *
5840143 GTCATTTTACCCTATAAGGGTATTTCGATCATTCTACCATTTGGAGGTATTTCG
1 GTCATTTTATCCTATGAGGGTATTTCGATCATTCTACCATATGGAGGTATTTCG
* * * *
5840197 GTCATTTTATCCTATGAGGGTATTTCGGTCCTTCTACCCTATGGGGGTATTTCG
1 GTCATTTTATCCTATGAGGGTATTTCGATCATTCTACCATATGGAGGTATTTCG
5840251 GTCATTTTATCCTATGAGGGTAT
1 GTCATTTTATCCTATGAGGGTAT
5840274 AAGTCGTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (54 bp):
GTCATTTTATCCTATGAGGGTATTTCGATCATTCTACCATATGGAGGTATTTCG
Found at i:5840317 original size:27 final size:27
Alignment explanation
Indices: 5840251--5840379 Score: 116
Period size: 27 Copynumber: 4.7 Consensus size: 27
5840241 GGGTATTTCG
* * *
5840251 GTCATTTTATC-CTATGAGGGTATAAGTC
1 GTCATTTTATCAC-ATAAGGGCA-AAATC
* * *
5840279 GTTATTTTATCATATAAGGGCAAAATT
1 GTCATTTTATCACATAAGGGCAAAATC
5840306 GTCATTTTATCACATAAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* * * *
5840333 GTTATTTTATGACATAAAGGTAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* * *
5840360 GTAATTATATCACATGAGGG
1 GTCATTTTATCACATAAGGG
5840380 TTCAGGTATG
Statistics
Matches: 82, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
27 65 0.79
28 17 0.21
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (27 bp):
GTCATTTTATCACATAAGGGCAAAATC
Found at i:5840341 original size:54 final size:55
Alignment explanation
Indices: 5840251--5840379 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 55
5840241 GGGTATTTCG
* * * * *
5840251 GTCATTTTATC-CTATGAGGGTATAAGTCGTTATTTTATCATATAAGGGCAAAATT
1 GTCATTTTATCAC-ATGAGGGCATAAATCGTTATTTTATCACATAAAGGCAAAATC
* * *
5840306 GTCATTTTATCACATAAGGGCA-AAATCGTTATTTTATGACATAAAGGTAAAATC
1 GTCATTTTATCACATGAGGGCATAAATCGTTATTTTATCACATAAAGGCAAAATC
* *
5840360 GTAATTATATCACATGAGGG
1 GTCATTTTATCACATGAGGG
5840380 TTCAGGTATG
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
54 43 0.69
55 18 0.29
56 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (55 bp):
GTCATTTTATCACATGAGGGCATAAATCGTTATTTTATCACATAAAGGCAAAATC
Found at i:5840509 original size:18 final size:18
Alignment explanation
Indices: 5840483--5840523 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5840473 CCATAATGTG
5840483 GCCCATATGGGCCCAC-AA
1 GCCCATAT-GGCCCACGAA
*
5840501 GCCCGTATGGCCCACGAA
1 GCCCATATGGCCCACGAA
5840519 GCCCA
1 GCCCA
5840524 AAAATGGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.24, C:0.41, G:0.24, T:0.10
Consensus pattern (18 bp):
GCCCATATGGCCCACGAA
Found at i:5845554 original size:42 final size:43
Alignment explanation
Indices: 5845446--5845617 Score: 124
Period size: 43 Copynumber: 4.0 Consensus size: 43
5845436 AGCTCGTACA
* ***
5845446 ATGCCGAC-GTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACAAAATCAAATATCG
* *
5845489 ATGCCACTATCCCAGACAGGGTCTTACACAAAATCAAATA-CG
1 ATGCCACTGTCCCAGACATGGTCTTACACAAAATCAAATATCG
* * **
5845531 ATGTCGA-TGTCCCAAACATGGTCTTACACATAAATC--ATGAGTTA
1 ATG-CCACTGTCCCAGACATGGTCTTACACA-AAATCAAAT-A-TCG
* *
5845575 ATGCCAAC-GTCCGAGACATGGTCTTACACGAAAA-CACATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACAC-AAAATCAAATATCG
5845618 GATCCTATTT
Statistics
Matches: 101, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
41 2 0.02
42 28 0.28
43 41 0.41
44 27 0.27
45 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACACAAAATCAAATATCG
Found at i:5845566 original size:43 final size:44
Alignment explanation
Indices: 5845446--5845567 Score: 128
Period size: 43 Copynumber: 2.8 Consensus size: 44
5845436 AGCTCGTACA
* **
5845446 ATGCCGAC-GTCCCAGACGTGGTCTTACATGT-AATCAAATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACATAAATCAAATATCG
* *
5845489 ATGCCACTATCCCAGACAGGGTCTTACACA-AAATCAAATA-CG
1 ATGCCACTGTCCCAGACATGGTCTTACACATAAATCAAATATCG
* *
5845531 ATGTCGA-TGTCCCAAACATGGTCTTACACATAAATCA
1 ATG-CCACTGTCCCAGACATGGTCTTACACATAAATCA
5845568 TGAGTTAATG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
42 27 0.41
43 39 0.59
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (44 bp):
ATGCCACTGTCCCAGACATGGTCTTACACATAAATCAAATATCG
Found at i:5849674 original size:15 final size:14
Alignment explanation
Indices: 5849632--5849671 Score: 55
Period size: 13 Copynumber: 2.8 Consensus size: 14
5849622 ACTTATTGCC
5849632 TATTTTTTACATTATA
1 TATTTTTT--ATTATA
5849648 TA-TTTTTATTATA
1 TATTTTTTATTATA
5849661 TATTTTTTATT
1 TATTTTTTATT
5849672 TATTAACCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.35
14 8 0.35
15 5 0.22
16 2 0.09
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTTTTATTATA
Found at i:5855727 original size:27 final size:27
Alignment explanation
Indices: 5855697--5855822 Score: 139
Period size: 27 Copynumber: 4.6 Consensus size: 27
5855687 AAATTGTACA
5855697 GCACTAAGTGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATTCGACTATGTT
* * *
5855724 GCACTAAGTGTGCGAAATGGA-TATGAT
1 GCACTAAGTGTGCG-ATTCGACTATGTT
* **
5855751 GCACTAAGTGTGCGAATT-GACCATGCG
1 GCACTAAGTGTGCG-ATTCGACTATGTT
* *
5855778 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGATTC-GACTATGTT
5855806 GCACTAAGTGTGCGATT
1 GCACTAAGTGTGCGATT
5855823 TGATTGTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
26 4 0.05
27 53 0.64
28 26 0.31
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTCGACTATGTT
Found at i:5857044 original size:58 final size:59
Alignment explanation
Indices: 5856954--5857068 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 59
5856944 GAACTTTGAC
5856954 TAATAAACTGTACTAATTGGCCCAACCAAAAATTCTAG-AAAAAATACATAGATGGGCT
1 TAATAAACTGTACTAATTGGCCCAACCAAAAATTCTAGAAAAAAATACATAGATGGGCT
5857012 TAATAAACTGTACTAATTGGCCCAACCAAAAATTCTAGAAAAAAATACATAGATGGG
1 TAATAAACTGTACTAATTGGCCCAACCAAAAATTCTAGAAAAAAATACATAGATGGG
5857069 AACATGAGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 38 0.68
59 18 0.32
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (59 bp):
TAATAAACTGTACTAATTGGCCCAACCAAAAATTCTAGAAAAAAATACATAGATGGGCT
Found at i:5859391 original size:44 final size:44
Alignment explanation
Indices: 5859328--5859414 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
5859318 AAGGAGTTGA
5859328 AAGCTCAGTTGCAAGAATTGACGGATAGAGGCTTCGCTCGACCG
1 AAGCTCAGTTGCAAGAATTGACGGATAGAGGCTTCGCTCGACCG
* *
5859372 AAGCTCAGTTGCAAGAATTGACGGATAGAGGTTTTGCTCGACC
1 AAGCTCAGTTGCAAGAATTGACGGATAGAGGCTTCGCTCGACC
5859415 AAGTTTCTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (44 bp):
AAGCTCAGTTGCAAGAATTGACGGATAGAGGCTTCGCTCGACCG
Found at i:5860421 original size:52 final size:53
Alignment explanation
Indices: 5860343--5860453 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
5860333 CGAACTAGCC
*
5860343 GCCAT-TGTGTTTGCATTGAAAATATGGCGACATTATTTGTTTGGTGAGAAGT
1 GCCATGTGTGTTTGCATTGAAAATATGGCGACATTATCTGTTTGGTGAGAAGT
5860395 GCCATGTG-GTTTGCATTGAAAATATGGCGACATTATCTGTTTGGTGAGAAGT
1 GCCATGTGTGTTTGCATTGAAAATATGGCGACATTATCTGTTTGGTGAGAAGT
5860447 GCCATGT
1 GCCATGT
5860454 ATTTTCGGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 55 0.96
53 2 0.04
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (53 bp):
GCCATGTGTGTTTGCATTGAAAATATGGCGACATTATCTGTTTGGTGAGAAGT
Found at i:5862680 original size:27 final size:27
Alignment explanation
Indices: 5862649--5862826 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5862639 TAAATTGTAC
5862649 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
5862676 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5862702 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
5862730 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
5862758 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5862785 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5862812 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5862827 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:5862763 original size:82 final size:81
Alignment explanation
Indices: 5862650--5862805 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5862640 AAATTGTACA
* *
5862650 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
5862714 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
5862731 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
5862796 TGCGAGTTGA
65 TGCGAATTGA
5862806 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:5862817 original size:82 final size:81
Alignment explanation
Indices: 5862646--5862826 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
5862636 GATTAAATTG
* *
5862646 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
5862711 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
5862727 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
5862791 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
5862809 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
5862827 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:5868029 original size:20 final size:20
Alignment explanation
Indices: 5868006--5868044 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5867996 TACTAGCTAG
*
5868006 TCTTTAATTAATGTGTTTAA
1 TCTTTAATTAATATGTTTAA
5868026 TCTTTAATTAATATGTTTA
1 TCTTTAATTAATATGTTTA
5868045 GTTTTGCTTA
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:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (20 bp):
TCTTTAATTAATATGTTTAA
Found at i:5870433 original size:9 final size:10
Alignment explanation
Indices: 5870426--5870482 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 10
5870416 ACGAGAAAAC
5870426 AAAGAAAAGA
1 AAAGAAAAGA
5870436 AAAGAAAAAGA
1 AAAG-AAAAGA
*
5870447 AAA-AGAAGA
1 AAAGAAAAGA
5870456 AAATGAAAATGA
1 AAA-GAAAA-GA
*
5870468 AAAAAAAAGA
1 AAAGAAAAGA
5870478 AAAGA
1 AAAGA
5870483 GAGGCAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 8 0.21
10 10 0.26
11 16 0.41
12 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:5870436 original size:5 final size:5
Alignment explanation
Indices: 5870426--5870482 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
5870416 ACGAGAAAAC
* *
5870426 AAAGA AAAGA AAAGAA AAAGA AAA-A GAAGA AAATGA AAATGA AAAAA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAA-GA AAA-GA AAAGA
5870473 AAAGA AAAGA
1 AAAGA AAAGA
5870483 GAGGCAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 3 0.07
5 26 0.58
6 16 0.36
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:5870455 original size:25 final size:27
Alignment explanation
Indices: 5870419--5870475 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
5870409 TCTTGTAACG
5870419 AGAAAACAAAGAAAA-GAAAA-GAAAA
1 AGAAAACAAAGAAAATGAAAATGAAAA
5870444 AGAAAA-AGAAGAAAATGAAAATGAAAA
1 AGAAAACA-AAGAAAATGAAAATGAAAA
5870471 A-AAAA
1 AGAAAA
5870476 GAAAAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 1 0.03
25 13 0.45
26 9 0.31
27 6 0.21
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (27 bp):
AGAAAACAAAGAAAATGAAAATGAAAA
Found at i:5870573 original size:12 final size:12
Alignment explanation
Indices: 5870551--5870575 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5870541 TTTGAAAAAC
5870551 AAAAAGAAAATG
1 AAAAAGAAAATG
5870563 AAAAAGAAAATG
1 AAAAAGAAAATG
5870575 A
1 A
5870576 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:5870582 original size:18 final size:18
Alignment explanation
Indices: 5870542--5870595 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
5870532 GAAAAAGCCT
* *
5870542 TTGAAAAACAAAAAGAAA
1 TTGAAAAAGAAAATGAAA
* *
5870560 ATGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAATGAAA
*
5870578 TTGAAAAAGAGAATGAAA
1 TTGAAAAAGAAAATGAAA
5870596 AAGAGTTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.13
Consensus pattern (18 bp):
TTGAAAAAGAAAATGAAA
Found at i:5875172 original size:9 final size:10
Alignment explanation
Indices: 5875165--5875221 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 10
5875155 ACGAGAAAAC
5875165 AAAGAAAAGA
1 AAAGAAAAGA
5875175 AAAGAAAAAGA
1 AAAG-AAAAGA
*
5875186 AAA-AGAAGA
1 AAAGAAAAGA
5875195 AAATGAAAATGA
1 AAA-GAAAA-GA
*
5875207 AAAAAAAAGA
1 AAAGAAAAGA
5875217 AAAGA
1 AAAGA
5875222 GAGGCAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 8 0.21
10 10 0.26
11 16 0.41
12 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:5875175 original size:5 final size:5
Alignment explanation
Indices: 5875165--5875221 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
5875155 ACGAGAAAAC
* *
5875165 AAAGA AAAGA AAAGAA AAAGA AAA-A GAAGA AAATGA AAATGA AAAAA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAA-GA AAA-GA AAAGA
5875212 AAAGA AAAGA
1 AAAGA AAAGA
5875222 GAGGCAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 3 0.07
5 26 0.58
6 16 0.36
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:5875194 original size:25 final size:27
Alignment explanation
Indices: 5875158--5875214 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
5875148 TCTTGTAACG
5875158 AGAAAACAAAGAAAA-GAAAA-GAAAA
1 AGAAAACAAAGAAAATGAAAATGAAAA
5875183 AGAAAA-AGAAGAAAATGAAAATGAAAA
1 AGAAAACA-AAGAAAATGAAAATGAAAA
5875210 A-AAAA
1 AGAAAA
5875215 GAAAAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 1 0.03
25 13 0.45
26 9 0.31
27 6 0.21
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (27 bp):
AGAAAACAAAGAAAATGAAAATGAAAA
Found at i:5875312 original size:12 final size:12
Alignment explanation
Indices: 5875290--5875314 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5875280 TTTGAAAAAC
5875290 AAAAAGAAAATG
1 AAAAAGAAAATG
5875302 AAAAAGAAAATG
1 AAAAAGAAAATG
5875314 A
1 A
5875315 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:5875321 original size:18 final size:18
Alignment explanation
Indices: 5875281--5875334 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
5875271 GAAAAAGCCT
* *
5875281 TTGAAAAACAAAAAGAAA
1 TTGAAAAAGAAAATGAAA
* *
5875299 ATGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAATGAAA
*
5875317 TTGAAAAAGAGAATGAAA
1 TTGAAAAAGAAAATGAAA
5875335 AAGAGTTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.13
Consensus pattern (18 bp):
TTGAAAAAGAAAATGAAA
Found at i:5875346 original size:30 final size:30
Alignment explanation
Indices: 5875290--5875371 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
5875280 TTTGAAAAAC
**
5875290 AAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
* ***
5875320 AAAAAGAGAATGAAAAAGAGTTTGAGAGAG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
** *
5875350 AAAAAGAATGTGAACAAGAAAA
1 AAAAAGAAAATGAAAAAGAAAA
5875372 AAGAGTGGAA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.63, C:0.01, G:0.23, T:0.12
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGAGAG
Found at i:5885511 original size:20 final size:20
Alignment explanation
Indices: 5885486--5885524 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5885476 TATAAATTAA
*
5885486 AATGAGATAGAATCGAGCTC
1 AATGAGATAGAAGCGAGCTC
*
5885506 AATGAGTTAGAAGCGAGCT
1 AATGAGATAGAAGCGAGCT
5885525 AGATAAGCTA
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:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (20 bp):
AATGAGATAGAAGCGAGCTC
Found at i:5886293 original size:40 final size:38
Alignment explanation
Indices: 5886182--5886274 Score: 150
Period size: 38 Copynumber: 2.4 Consensus size: 38
5886172 TATTTTAGTT
* *
5886182 TGTGTCTTTAATTATGTCTTAGTATGAACATCATTAATA
1 TGTGT-TTTAATTATGTCTTAGTTTGAACATCATGAATA
5886221 TGTGTTTTAATTATGTCTTAGTTTGAACATCATGAATA
1 TGTGTTTTAATTATGTCTTAGTTTGAACATCATGAATA
*
5886259 TGTGTTTTTATTATGT
1 TGTGTTTTAATTATGT
5886275 GTCTTAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 46 0.90
39 5 0.10
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.51
Consensus pattern (38 bp):
TGTGTTTTAATTATGTCTTAGTTTGAACATCATGAATA
Found at i:5887950 original size:29 final size:27
Alignment explanation
Indices: 5887932--5888001 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
5887922 ATATTAAGTC
5887932 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
5887959 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
5887987 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
5888002 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:5887995 original size:28 final size:28
Alignment explanation
Indices: 5887932--5888029 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
5887922 ATATTAAGTC
*
5887932 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
5887959 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
5887987 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
5888016 CGCACACTTAGTGC
1 CGCACACTTAGTGC
5888030 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:5894215 original size:6 final size:6
Alignment explanation
Indices: 5894206--5894289 Score: 73
Period size: 6 Copynumber: 13.7 Consensus size: 6
5894196 ATCAAAATGG
* * * *
5894206 GAATCA GAATCA GAATCA AAATTA G-GTGACA GAATCA GAATCA GTATCA
1 GAATCA GAATCA GAATCA GAATCA GAAT--CA GAATCA GAATCA GAATCA
*
5894255 GGTAA-CA GAATCA GAATCA GAATCA GAATAA GAAT
1 -G-AATCA GAATCA GAATCA GAATCA GAATCA GAAT
5894290 TAGGTGACAA
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
5 3 0.05
6 53 0.84
7 5 0.08
8 2 0.03
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (6 bp):
GAATCA
Found at i:5894244 original size:25 final size:25
Alignment explanation
Indices: 5894193--5894280 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 25
5894183 TATTAGAACT
*
5894193 AGAATCAAAAT--GGGAATCAGAATC
1 AGAATCAAAATCAGGTAA-CAGAATC
* *
5894217 AGAATCAAAATTAGGTGACAGAATC
1 AGAATCAAAATCAGGTAACAGAATC
**
5894242 AGAATCAGTATCAGGTAACAGAATC
1 AGAATCAAAATCAGGTAACAGAATC
*
5894267 AGAATCAGAATCAG
1 AGAATCAAAATCAG
5894281 AATAAGAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
24 11 0.20
25 41 0.75
26 3 0.05
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (25 bp):
AGAATCAAAATCAGGTAACAGAATC
Found at i:5894244 original size:31 final size:31
Alignment explanation
Indices: 5894206--5894311 Score: 103
Period size: 31 Copynumber: 3.4 Consensus size: 31
5894196 ATCAAAATGG
5894206 GAATCAGAATCAGAATCAAAATTAGGTGACA
1 GAATCAGAATCAGAATCAAAATTAGGTGACA
* * * *
5894237 GAATCAGAATCAGTATCAGGTAA-CA-G-AATCA
1 GAATCAGAATCAGAATCA--AAATTAGGTGA-CA
5894268 GAATCAGAATCAGAAT-AAGAATTAGGTGACA
1 GAATCAGAATCAGAATCAA-AATTAGGTGACA
*
5894299 AAATCAGAATCAG
1 GAATCAGAATCAG
5894312 TGTCAAGTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
29 2 0.03
30 3 0.05
31 50 0.85
32 2 0.03
33 2 0.03
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.19
Consensus pattern (31 bp):
GAATCAGAATCAGAATCAAAATTAGGTGACA
Found at i:5894276 original size:37 final size:37
Alignment explanation
Indices: 5894235--5894311 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
5894225 AATTAGGTGA
* * *
5894235 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAAT
1 CAGAATCAGAATAAGAATCAGGTAACAAAATCAGAAT
* *
5894272 CAGAATCAGAATAAGAATTAGGTGACAAAATCAGAAT
1 CAGAATCAGAATAAGAATCAGGTAACAAAATCAGAAT
5894309 CAG
1 CAG
5894312 TGTCAAGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.18
Consensus pattern (37 bp):
CAGAATCAGAATAAGAATCAGGTAACAAAATCAGAAT
Found at i:5894280 original size:62 final size:62
Alignment explanation
Indices: 5894206--5894339 Score: 216
Period size: 62 Copynumber: 2.2 Consensus size: 62
5894196 ATCAAAATGG
* *
5894206 GAATCAGAATCAGAATCAA-AATTAGGTGACAGAATCAGAATCAGTATCAGGTAACAGAATCA
1 GAATCAGAATCAGAAT-AAGAATTAGGTGACAAAATCAGAATCAGTATCAAGTAACAGAATCA
*
5894268 GAATCAGAATCAGAATAAGAATTAGGTGACAAAATCAGAATCAGTGTCAAGTAACAGAATCA
1 GAATCAGAATCAGAATAAGAATTAGGTGACAAAATCAGAATCAGTATCAAGTAACAGAATCA
*
5894330 AAATCAGAAT
1 GAATCAGAAT
5894340 GTGAATGCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 2 0.03
62 65 0.97
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (62 bp):
GAATCAGAATCAGAATAAGAATTAGGTGACAAAATCAGAATCAGTATCAAGTAACAGAATCA
Found at i:5894494 original size:27 final size:26
Alignment explanation
Indices: 5894446--5894547 Score: 114
Period size: 27 Copynumber: 3.8 Consensus size: 26
5894436 TCTCAGTTAT
* * *
5894446 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAAAGCCACCAGA-A
5894473 CAGATATTGTGGCAAAGCCACCAGAA
1 CAGATATTGTGGCAAAGCCACCAGAA
* *
5894499 CAAATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAAAGCCACCAG-AA
* *
5894527 CAGATAATGTGGCAAATCCAC
1 CAGATATTGTGGCAAAGCCAC
5894548 TTAACAGAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 6 0.09
27 51 0.80
28 7 0.11
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGGCAAAGCCACCAGAA
Found at i:5895181 original size:27 final size:27
Alignment explanation
Indices: 5895115--5895201 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
5895105 GGGAAAAATG
* * * *
5895115 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
5895142 GTAATTCTACCCTACATGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
5895169 GTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
5895196 ATAATT
1 GTAATT
5895202 TTGTAAATCG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:5895216 original size:27 final size:27
Alignment explanation
Indices: 5895186--5895289 Score: 93
Period size: 27 Copynumber: 3.9 Consensus size: 27
5895176 TACCCTATAG
*
5895186 GGGTATTTCAATAATTTTGTAAATCGA
1 GGGTATTTCAGTAATTTTGTAAATCGA
*** *
5895213 GGGTAAAACAGTAATTTTGTAAATCGG
1 GGGTATTTCAGTAATTTTGTAAATCGA
* ** *
5895240 GGGTACTTT-GGTAATTTTACAAGTCGA
1 GGGTA-TTTCAGTAATTTTGTAAATCGA
* *
5895267 GGGTATTTCATTAATTTGGTAAA
1 GGGTATTTCAGTAATTTTGTAAA
5895290 CTAAAGTATT
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
26 3 0.05
27 53 0.95
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.38
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTGTAAATCGA
Found at i:5900759 original size:32 final size:31
Alignment explanation
Indices: 5900723--5900785 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 31
5900713 CTGTACGACC
5900723 TCACCCCCATACCGATGAGGTGTATATAACG
1 TCACCCCCATACCGATGAGGTGTATATAACG
*
5900754 NTCACCCCCTTACCGATGAGGTGTATATAACG
1 -TCACCCCCATACCGATGAGGTGTATATAACG
5900786 GAAATTGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (31 bp):
TCACCCCCATACCGATGAGGTGTATATAACG
Found at i:5902733 original size:68 final size:66
Alignment explanation
Indices: 5902661--5902832 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
5902651 CATCATGTGT
* * * *
5902661 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
5902724 TGTAG
62 TGTAG
** * *
5902729 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
5902794 AG
65 AG
* * * *
5902796 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
5902833 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:5902766 original size:64 final size:64
Alignment explanation
Indices: 5902685--5902868 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
5902675 AGACATTATG
* * *
5902685 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
5902749 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
5902814 AA
63 AA
* * *
5902816 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
5902869 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:5916337 original size:24 final size:24
Alignment explanation
Indices: 5916310--5916413 Score: 69
Period size: 23 Copynumber: 4.5 Consensus size: 24
5916300 CAGCTCGTAA
5916310 GAGCTTACTATTTTCAACTCAT-T
1 GAGCTTACTATTTTCAACTCATAT
* * *
5916333 GGAGCTTACCA-TTTCAGCTCGTAT
1 -GAGCTTACTATTTTCAACTCATAT
*
5916357 GAGCTTACTA--TTCAGCTCGATA-
1 GAGCTTACTATTTTCAACTC-ATAT
** *
5916379 GAGCTTAC-CGTTTCAGCTCA-AT
1 GAGCTTACTATTTTCAACTCATAT
5916401 AGAGCTTACTATT
1 -GAGCTTACTATT
5916414 CACCAGCTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
21 1 0.02
22 17 0.26
23 36 0.55
24 11 0.17
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (24 bp):
GAGCTTACTATTTTCAACTCATAT
Found at i:5916360 original size:23 final size:23
Alignment explanation
Indices: 5916275--5916397 Score: 99
Period size: 23 Copynumber: 5.2 Consensus size: 23
5916265 GACTCACCAT
* *
5916275 AGCTCGTATAAGGTTACCGATATATC
1 AGCTCGTATGAGCTTACC-AT-T-TC
* *
5916301 AGCTCGTAAGAGCTTACTATTTTC
1 AGCTCGTATGAGCTTACCA-TTTC
* *
5916325 AACTCAT-TGGAGCTTACCATTTC
1 AGCTCGTAT-GAGCTTACCATTTC
*
5916348 AGCTCGTATGAGCTTACTA-TTC
1 AGCTCGTATGAGCTTACCATTTC
*
5916370 AGCTCG-ATAGAGCTTACCGTTTC
1 AGCTCGTAT-GAGCTTACCATTTC
5916393 AGCTC
1 AGCTC
5916398 AATAGAGCTT
Statistics
Matches: 79, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.03
22 17 0.22
23 26 0.33
24 17 0.22
25 2 0.03
26 15 0.19
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (23 bp):
AGCTCGTATGAGCTTACCATTTC
Found at i:5916402 original size:23 final size:21
Alignment explanation
Indices: 5916334--5916409 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 21
5916324 CAACTCATTG
*
5916334 GAGCTTACCATTTCAGCTCGTA
1 GAGCTTACC-TTTCAGCTCATA
5916356 TGAGCTTA-CTATTCAGCTCGATA
1 -GAGCTTACCT-TTCAGCTC-ATA
5916379 GAGCTTACCGTTTCAGCTCAATA
1 GAGCTTACC-TTTCAGCTC-ATA
5916402 GAGCTTAC
1 GAGCTTAC
5916410 TATTCACCAG
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.02
22 16 0.34
23 29 0.62
24 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
GAGCTTACCTTTCAGCTCATA
Found at i:5923935 original size:32 final size:32
Alignment explanation
Indices: 5923894--5923955 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
5923884 TCCAAGAGAG
** *
5923894 TATAACATCAGTGCAAGTTTTAATGTATCTGA
1 TATAACATCAACGCAAGTTTTAACGTATCTGA
5923926 TATAACATCAACGCAAGTTTTAACGTATCT
1 TATAACATCAACGCAAGTTTTAACGTATCT
5923956 AATTTATCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TATAACATCAACGCAAGTTTTAACGTATCTGA
Found at i:5924372 original size:38 final size:39
Alignment explanation
Indices: 5924330--5924405 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 39
5924320 TTTAGTTTGT
* *
5924330 GTCTTTAATTATTTCCTAG-TTAAACATCATTAATATGA
1 GTCTTTAATTATGTCATAGTTTAAACATCATTAATATGA
*
5924368 GTCTTTAATTATGTCATAGTTTGAACATCATTAATATG
1 GTCTTTAATTATGTCATAGTTTAAACATCATTAATATG
5924406 TGTTCTGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 17 0.50
39 17 0.50
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (39 bp):
GTCTTTAATTATGTCATAGTTTAAACATCATTAATATGA
Found at i:5924756 original size:28 final size:28
Alignment explanation
Indices: 5924724--5924811 Score: 108
Period size: 28 Copynumber: 3.1 Consensus size: 28
5924714 TACATGCATG
*
5924724 CATATGGCCCACTAGG-CCCAATCTCATT
1 CATATGGCCCA-TAGGCCCCAATCACATT
*
5924752 CATATGGCCCATCGGCCCCAATCACATT
1 CATATGGCCCATAGGCCCCAATCACATT
* *
5924780 CATATGGCCCATCA-GCCCTAATCACATC
1 CATATGGCCCAT-AGGCCCCAATCACATT
5924808 CATA
1 CATA
5924812 GTCATGCAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
27 3 0.06
28 50 0.94
ACGTcount: A:0.27, C:0.38, G:0.12, T:0.23
Consensus pattern (28 bp):
CATATGGCCCATAGGCCCCAATCACATT
Found at i:5957752 original size:10 final size:10
Alignment explanation
Indices: 5957739--5957770 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
5957729 AAATAAGTTT
5957739 AATTTATATC
1 AATTTATATC
5957749 AATTTATATC
1 AATTTATATC
5957759 AATTTATATC
1 AATTTATATC
5957769 AA
1 AA
5957771 GAAAAGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (10 bp):
AATTTATATC
Found at i:5974983 original size:42 final size:43
Alignment explanation
Indices: 5974866--5974996 Score: 156
Period size: 42 Copynumber: 3.0 Consensus size: 43
5974856 CAATATGTGT
* * *
5974866 TTTCGTGTAAGACCATGTCTGGAACGTTGGCATCGATATTGAGA
1 TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATT-TGA
* * **
5974910 TTACGTGTAATACCATGTCTCAGACATTGGCATC-ATATTTGA
1 TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGA
* * *
5974952 TTTCGTGTAAGACCCTGTTTGGGACAATGGCATCGATATTTGA
1 TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGA
5974995 TT
1 TT
5974997 ACATGTGTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
42 29 0.40
43 15 0.21
44 28 0.39
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (43 bp):
TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGA
Found at i:5981110 original size:42 final size:42
Alignment explanation
Indices: 5981058--5981209 Score: 180
Period size: 42 Copynumber: 3.6 Consensus size: 42
5981048 CTAAGACTAT
* *
5981058 GTGTAAGACCATATCTGGGATATGGCATCTATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCAATAAGAGACTTC
*
5981100 GTGTAAGACCATATCTGGGATATGGCATCAATAAAAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCAATAAGAGACTTC
* * * * * * *
5981142 GTGTAAGACCATAGCTAGGCTATTAGCATCGATACGAGA-TCCC
1 GTGTAAGACCATATCTGGGATA-TGGCATCAATAAGAGACT-TC
*
5981185 ATGTAAGACCATATCTGGGATATGG
1 GTGTAAGACCATATCTGGGATATGG
5981210 AATTGGTATG
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 61 0.66
43 31 0.34
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCAATAAGAGACTTC
Found at i:5989394 original size:21 final size:21
Alignment explanation
Indices: 5989370--5989412 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5989360 TTCAATCTTG
*
5989370 TCAAGCTTTTGGATTTGTTCT
1 TCAAGCTTTTGGATTTCTTCT
* *
5989391 TCAATCTTTTTGATTTCTTCT
1 TCAAGCTTTTGGATTTCTTCT
5989412 T
1 T
5989413 GTGATGATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.58
Consensus pattern (21 bp):
TCAAGCTTTTGGATTTCTTCT
Found at i:5990866 original size:48 final size:48
Alignment explanation
Indices: 5990795--5990972 Score: 248
Period size: 48 Copynumber: 3.7 Consensus size: 48
5990785 ATGTCATTAA
* * *
5990795 GAGCTTCATTAATTTGGCTTCAGGCCATGAAATTAGTACTTCGGGTGT
1 GAGCTTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGGGTGT
* *
5990843 GAGCTTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTTGGATGT
1 GAGCTTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGGGTGT
** * * *
5990891 GAGCTTCATTGATTTGGCTTTGGGCCATGATATTGGCACTTCAGGTGC
1 GAGCTTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGGGTGT
* *
5990939 GAGTTTCATTGATTTGGCTTCGGGCCATGATATT
1 GAGCTTCATTGATTTGGCTTCAGGCCATGATATT
5990973 GGTATCTAGG
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 116 1.00
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (48 bp):
GAGCTTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGGGTGT
Found at i:6003565 original size:40 final size:39
Alignment explanation
Indices: 6003511--6003628 Score: 182
Period size: 40 Copynumber: 2.9 Consensus size: 39
6003501 CGGATGTAAC
* *
6003511 AACCAGCACAAATGCCTTCGGAACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGG-ACTTAACCCGGTTATAAT
6003551 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTC-GGACTTAACCCGGTTATAAT
*
6003591 AACCCGCACGAATGCCTTCAGGACTTAACCCAGTTATA
1 AACCCGCACGAATGCCTTC-GGACTTAACCCGGTTATA
6003629 TTTTTTTTCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 71 0.97
41 2 0.03
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (39 bp):
AACCCGCACGAATGCCTTCGGACTTAACCCGGTTATAAT
Found at i:6017670 original size:46 final size:46
Alignment explanation
Indices: 6017603--6017694 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
6017593 TCGATTTCCC
6017603 GTTGAACTCATCAGAATAATAACAGATACACAATTGCCTGCACATT
1 GTTGAACTCATCAGAATAATAACAGATACACAATTGCCTGCACATT
*
6017649 GTTGAACTCATCGGAATAATAACAGATACACAATTGCCTGCACATT
1 GTTGAACTCATCAGAATAATAACAGATACACAATTGCCTGCACATT
6017695 TTCTCAGTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (46 bp):
GTTGAACTCATCAGAATAATAACAGATACACAATTGCCTGCACATT
Found at i:6017851 original size:49 final size:49
Alignment explanation
Indices: 6017728--6018596 Score: 1605
Period size: 49 Copynumber: 17.7 Consensus size: 49
6017718 GAAGCTATCT
* * * * *
6017728 GGTACGCATAGTAGCCTGCACTTAGTACTACACACT-TGATCGAAGTTATCA
1 GGTACACATAGTAGCCTGCACTTAGTACTACACA-TGCGA-CCAA-TTACCC
*
6017779 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6017828 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6017877 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6017926 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6017975 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018024 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018073 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018122 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018171 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018220 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018269 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018318 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018367 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018416 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
6018465 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
* *
6018514 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCT
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
* * *
6018563 AGTACACGTAGTAGCCTACACTTAGTACTACACA
1 GGTACACATAGTAGCCTGCACTTAGTACTACACA
6018597 CGTGACCTCA
Statistics
Matches: 807, Mismatches: 10, Indels: 4
0.98 0.01 0.00
Matches are distributed among these distances:
49 767 0.95
50 4 0.00
51 36 0.04
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (49 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTACCC
Found at i:6019284 original size:30 final size:30
Alignment explanation
Indices: 6019250--6019309 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
6019240 CTTTAATACG
6019250 AACTTTGGAAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGAAAAATTACAC-TTTTGCCCCTA
* * *
6019280 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
6019310 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:6021386 original size:15 final size:15
Alignment explanation
Indices: 6021355--6021393 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6021345 AACAGAGAAG
6021355 CCAAGAATAAAGAAAT
1 CCAAG-ATAAAGAAAT
*
6021371 CCAAGATAAAGGAAT
1 CCAAGATAAAGAAAT
*
6021386 CCATGATA
1 CCAAGATA
6021394 CGAGAATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:6021804 original size:51 final size:51
Alignment explanation
Indices: 6021728--6021829 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
6021718 GATCGGGGAA
6021728 CATTTCCTTATTTCGAACATTATTCCTTTAACTATTTCTACCATCCCAAAT
1 CATTTCCTTATTTCGAACATTATTCCTTTAACTATTTCTACCATCCCAAAT
6021779 CATTTCCTTATTTCGAACATTATTCCTTTAACTATTTCTACCATCCCAAAT
1 CATTTCCTTATTTCGAACATTATTCCTTTAACTATTTCTACCATCCCAAAT
6021830 TCCATAATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.43
Consensus pattern (51 bp):
CATTTCCTTATTTCGAACATTATTCCTTTAACTATTTCTACCATCCCAAAT
Found at i:6021816 original size:24 final size:24
Alignment explanation
Indices: 6021736--6021816 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
6021726 AACATTTCCT
6021736 TATTTCGAACATTATTCCTTTAAC
1 TATTTCGAACATTATTCCTTTAAC
* * * * * *
6021760 TATTTCTACCATCCCAAATCATTT-CC
1 TATTTCGAACAT---TATTCCTTTAAC
6021786 TTATTTCGAACATTATTCCTTTAAC
1 -TATTTCGAACATTATTCCTTTAAC
6021811 TATTTC
1 TATTTC
6021817 TACCATCCCA
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
24 22 0.55
25 1 0.03
26 1 0.03
27 16 0.40
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.46
Consensus pattern (24 bp):
TATTTCGAACATTATTCCTTTAAC
Found at i:6023134 original size:39 final size:39
Alignment explanation
Indices: 6023080--6023157 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
6023070 GATTTATAAG
6023080 TTAGAATCATTAGCTCACTAAAGACAAATATATTTGGCC
1 TTAGAATCATTAGCTCACTAAAGACAAATATATTTGGCC
6023119 TTAGAATCATTAGCTCACTAAAGACAAATATATTTGGCC
1 TTAGAATCATTAGCTCACTAAAGACAAATATATTTGGCC
6023158 AAATAATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (39 bp):
TTAGAATCATTAGCTCACTAAAGACAAATATATTTGGCC
Found at i:6024267 original size:51 final size:50
Alignment explanation
Indices: 6024201--6024451 Score: 310
Period size: 51 Copynumber: 5.0 Consensus size: 50
6024191 CACTTGTAGC
* * *
6024201 CGAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
1 CGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA
* *
6024251 TCGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA
1 -CGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA
* * *
6024302 CCAA-TTACCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA
1 CGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA
* * *
6024351 TCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA
1 -CGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA
* * * * *
6024402 CCAA-TTATCTA-GTACACGTAGTAACCTACACTTTGTACTACACACGTGA
1 CGAAGTTATC-AGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA
6024451 C
1 C
6024452 CTCACAATAG
Statistics
Matches: 173, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
49 78 0.45
50 10 0.06
51 85 0.49
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
CGAAGTTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA
Found at i:6024385 original size:100 final size:100
Alignment explanation
Indices: 6024212--6024450 Score: 397
Period size: 100 Copynumber: 2.4 Consensus size: 100
6024202 GAAGCTATCT
*
6024212 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACACATAGTAG
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACACATAGTAG
6024277 CCTGCACTTAGTACTACACATGCGACCAATTACCC
66 CCTGCACTTAGTACTACACATGCGACCAATTACCC
*
6024312 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAG
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACACATAGTAG
* *
6024377 CCTGCACTTAGTACTACACATGCGACCAATTATCT
66 CCTGCACTTAGTACTACACATGCGACCAATTACCC
* * * * *
6024412 AGTACACGTAGTAACCTACACTTTGTACTACACACGTGA
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA
6024451 CCTCACAATA
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 130 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (100 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACACATAGTAG
CCTGCACTTAGTACTACACATGCGACCAATTACCC
Found at i:6026092 original size:16 final size:16
Alignment explanation
Indices: 6026073--6026103 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6026063 CTTCTTCACT
6026073 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
6026089 TACTTACTTACTTAA
1 TACTCACTTACTTAA
6026104 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:6026109 original size:20 final size:20
Alignment explanation
Indices: 6026070--6026109 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6026060 AAACTTCTTC
* *
6026070 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
6026090 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
6026110 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:6026519 original size:55 final size:54
Alignment explanation
Indices: 6026295--6026548 Score: 226
Period size: 55 Copynumber: 4.8 Consensus size: 54
6026285 ACATGGGTAC
* * * *
6026295 CTTACC-ATTGCCATGACTTGTCATGGTCTTACGTGGTATCCTT---TT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAA
* * *
6026344 CTTACC-ATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAA
* * * ** *
6026398 -TCACCAA-TGCCATGCCTTGGCATGTTCTTAC-TGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCC-T-TAGAAA
* *
6026451 CTT-CTCAA-TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAA
1 CTTAC-CAATTGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAA
*
6026504 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGATATCCTT
6026549 AAACCCTAAT
Statistics
Matches: 167, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
49 39 0.23
51 2 0.01
52 11 0.07
53 34 0.20
54 39 0.23
55 40 0.24
56 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAA
Found at i:6028069 original size:30 final size:30
Alignment explanation
Indices: 6028035--6028098 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 30
6028025 CTTTAAGAGA
6028035 TTAAAAATCACTC-CTCTTAAGTTTTTAAAT
1 TTAAAAATCACTCACTCTTAAGTTTTT-AAT
6028065 TTAAAAATCACTCACTCTTAAGTTTTTAAT
1 TTAAAAATCACTCACTCTTAAGTTTTTAAT
6028095 TTAA
1 TTAA
6028099 GATTTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.44
Consensus pattern (30 bp):
TTAAAAATCACTCACTCTTAAGTTTTTAAT
Found at i:6029217 original size:20 final size:20
Alignment explanation
Indices: 6029192--6029237 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
6029182 GTGAGTTACT
*
6029192 CTTTTAGATTTAGTTTTAGA
1 CTTTTACATTTAGTTTTAGA
*
6029212 CTTTTACTTTTAGTTTTAGA
1 CTTTTACATTTAGTTTTAGA
*
6029232 TTTTTA
1 CTTTTA
6029238 TTTTTATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.61
Consensus pattern (20 bp):
CTTTTACATTTAGTTTTAGA
Found at i:6029242 original size:20 final size:20
Alignment explanation
Indices: 6029200--6029243 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
6029190 CTCTTTTAGA
6029200 TTTAGTTTTAGACTTTTACT
1 TTTAGTTTTAGACTTTTACT
* *
6029220 TTTAGTTTTAGATTTTTATT
1 TTTAGTTTTAGACTTTTACT
6029240 TTTA
1 TTTA
6029244 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.05, G:0.09, T:0.66
Consensus pattern (20 bp):
TTTAGTTTTAGACTTTTACT
Found at i:6032617 original size:15 final size:15
Alignment explanation
Indices: 6032597--6032627 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6032587 AAATATGAAA
6032597 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
6032612 GATATGTTTTGTATT
1 GATATGTTTTGGATT
6032627 G
1 G
6032628 GAATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:6036598 original size:39 final size:40
Alignment explanation
Indices: 6036538--6036637 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
6036528 ACCCAAGTAT
* * * *
6036538 CTTCGGGAT-TTAGCCTGATATAGCCACTCGCA-CAAGGC
1 CTTCGGGATCTTAGCCGGATATAGCCACTAGCATAAAAGC
*
6036576 CTTC-GGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGATCTTAG-CCGGATATAGCCACTAGCATAAAAGC
6036616 CTTCGGGA-CTTAGCCCGGATAT
1 CTTCGGGATCTTAG-CCGGATAT
6036638 CATTCGAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
37 4 0.08
38 8 0.15
39 16 0.31
40 21 0.40
41 3 0.06
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGATCTTAGCCGGATATAGCCACTAGCATAAAAGC
Found at i:6044808 original size:39 final size:40
Alignment explanation
Indices: 6044748--6044847 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
6044738 ACCCAAGTAT
* * * *
6044748 CTTCGGGAT-TTAGCCAGATATAGCCACTCGCA-CAAGGC
1 CTTCGGGATCTTAGCCGGATATAGCCACTAGCATAAAAGC
*
6044786 CTTC-GGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGATCTTAG-CCGGATATAGCCACTAGCATAAAAGC
6044826 CTTCGGGA-CTTAGCCCGGATAT
1 CTTCGGGATCTTAG-CCGGATAT
6044848 CATTCGAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
37 4 0.08
38 8 0.15
39 16 0.31
40 21 0.40
41 3 0.06
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGATCTTAGCCGGATATAGCCACTAGCATAAAAGC
Found at i:6062720 original size:52 final size:52
Alignment explanation
Indices: 6062650--6063486 Score: 1638
Period size: 52 Copynumber: 16.1 Consensus size: 52
6062640 GTTGAAGAAT
* **
6062650 TTTATGAGTATATATATATCATGACCAAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6062702 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6062754 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6062806 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6062858 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6062910 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6062962 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6063014 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6063066 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6063118 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6063170 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6063222 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6063274 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6063326 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6063378 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
*
6063430 TTTATGAGTATTTATATATCATGACAGAATGTGTATATGCTTGGGAATTAAG
1 TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
6063482 TTTAT
1 TTTAT
6063487 AATTCGATTC
Statistics
Matches: 781, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 781 1.00
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (52 bp):
TTTATGAGTATTTATATATCATGACTGAATGTGTATATGCTTGGGAATTAAG
Found at i:6063589 original size:43 final size:42
Alignment explanation
Indices: 6063541--6063758 Score: 152
Period size: 45 Copynumber: 5.0 Consensus size: 42
6063531 CCGTAGGATT
* *
6063541 TCGATATGTGCTTTCGTGTAAGACCACATCTGGGACGTTGGCA
1 TCGATATGTG-TTTCATGTAAGACCACGTCTGGGACGTTGGCA
* *
6063584 TCGATATATGTGTTTTCTTGTAAGACCACGTCTGGGACATTGGCA
1 TCG--ATATGTG-TTTCATGTAAGACCACGTCTGGGACGTTGGCA
* * * ** * * *
6063629 TTGATATATGTGGTTACGTGTAAGACCATTTCTGGGACATCGGTA
1 TCG--ATATGT-GTTTCATGTAAGACCACGTCTGGGACGTTGGCA
* * * **
6063674 TTG-TATTTGATTCATGTAAGACCTTGTCTGGGACAG-TGGCA
1 TCGATATGTGTTTCATGTAAGACCACGTCTGGGAC-GTTGGCA
* ** *
6063715 TCGATATGAGATAGCATGTAAGACCACGTCTGAGACGTTGGCA
1 TCGATATGTG-TTTCATGTAAGACCACGTCTGGGACGTTGGCA
6063758 T
1 T
6063759 TGTTTGATAT
Statistics
Matches: 139, Mismatches: 29, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
41 26 0.19
42 9 0.06
43 28 0.20
45 75 0.54
46 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (42 bp):
TCGATATGTGTTTCATGTAAGACCACGTCTGGGACGTTGGCA
Found at i:6063606 original size:45 final size:45
Alignment explanation
Indices: 6063544--6063668 Score: 169
Period size: 45 Copynumber: 2.8 Consensus size: 45
6063534 TAGGATTTCG
*
6063544 ATATGTGCTTTCGTGTAAGACCACATCTGGGACGTTGGCATCGAT
1 ATATGTGCTTTCGTGTAAGACCACATCTGGGACATTGGCATCGAT
* * * *
6063589 ATATGTGTTTTCTTGTAAGACCACGTCTGGGACATTGGCATTGAT
1 ATATGTGCTTTCGTGTAAGACCACATCTGGGACATTGGCATCGAT
* * **
6063634 ATATGTGGTTACGTGTAAGACCATTTCTGGGACAT
1 ATATGTGCTTTCGTGTAAGACCACATCTGGGACAT
6063669 CGGTATTGTA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (45 bp):
ATATGTGCTTTCGTGTAAGACCACATCTGGGACATTGGCATCGAT
Found at i:6065737 original size:43 final size:42
Alignment explanation
Indices: 6065689--6065836 Score: 122
Period size: 43 Copynumber: 3.5 Consensus size: 42
6065679 CAATGGCGAC
*
6065689 GTCCCAGACATGGTCTTACATGTAATTCAGTATCGATGCCTCT
1 GTCCCAGACATGGTCTTACATGTAATTCAG-ATCGATGCCTAT
* * * **
6065732 GTCCCAAACAGGGTCTTATATG-AAAACAGATACGATG-CTGAT
1 GTCCCAGACATGGTCTTACATGTAATTCAGAT-CGATGCCT-AT
* * * * *
6065774 -TTCCAGACATGGTCTTACACGTAAATTTCAAATCGAGGCCTGT
1 GTCCCAGACATGGTCTTACATGT-AA-TTCAGATCGATGCCTAT
*
6065817 GTCCCAGACACGGTCTTACA
1 GTCCCAGACATGGTCTTACA
6065837 CGATATCTCA
Statistics
Matches: 80, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
41 20 0.25
42 11 0.14
43 26 0.32
44 23 0.29
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACATGTAATTCAGATCGATGCCTAT
Found at i:6072960 original size:43 final size:42
Alignment explanation
Indices: 6072912--6073059 Score: 122
Period size: 43 Copynumber: 3.5 Consensus size: 42
6072902 CAATGGCGAC
*
6072912 GTCCCAGACATGGTCTTACATGTAATTCAGTATCGATGCCTCT
1 GTCCCAGACATGGTCTTACATGTAATTCAG-ATCGATGCCTAT
* * * **
6072955 GTCCCAAACAGGGTCTTATATG-AAAACAGATACGATG-CTGAT
1 GTCCCAGACATGGTCTTACATGTAATTCAGAT-CGATGCCT-AT
** * * *
6072997 GT-CCAGACATGGTCTTACACATAAATTTCAAATCGAGGCCTGT
1 GTCCCAGACATGGTCTTACATGT-AA-TTCAGATCGATGCCTAT
*
6073040 GTCCCAGACACGGTCTTACA
1 GTCCCAGACATGGTCTTACA
6073060 CGATATCTCA
Statistics
Matches: 81, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
41 18 0.22
42 13 0.16
43 28 0.35
44 22 0.27
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACATGTAATTCAGATCGATGCCTAT
Found at i:6090664 original size:33 final size:33
Alignment explanation
Indices: 6090627--6090693 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
6090617 AAGAATAAGT
*
6090627 ATCCTTTGCCATGGATTGATGACTTGTTCAATC
1 ATCCTTTGCCATGGATTGACGACTTGTTCAATC
6090660 ATCCTTTGCCATGGATTGACGACTTGTTCAATC
1 ATCCTTTGCCATGGATTGACGACTTGTTCAATC
6090693 A
1 A
6090694 GTTGAAAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (33 bp):
ATCCTTTGCCATGGATTGACGACTTGTTCAATC
Found at i:6094991 original size:22 final size:22
Alignment explanation
Indices: 6094963--6095006 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
6094953 TAGGAAAATT
6094963 CGATCAAGTGTTCATGAGATGA
1 CGATCAAGTGTTCATGAGATGA
6094985 CGATCAAGTGTTCATGAGATGA
1 CGATCAAGTGTTCATGAGATGA
6095007 AATTAGGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (22 bp):
CGATCAAGTGTTCATGAGATGA
Found at i:6095621 original size:29 final size:29
Alignment explanation
Indices: 6095588--6095690 Score: 129
Period size: 29 Copynumber: 3.6 Consensus size: 29
6095578 GTTGAGAGAT
*
6095588 TGGCACTGAGTGTGCGAGCTTGTAATACA
1 TGGCACTAAGTGTGCGAGCTTGTAATACA
* * *
6095617 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGTAATACA
*
6095646 TGGCGCTAAGTGTGCGAG-TT-TAAAGTACA
1 TGGCACTAAGTGTGCGAGCTTGT-AA-TACA
6095675 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
6095691 CGGTTGATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
28 4 0.06
29 61 0.94
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGTAATACA
Found at i:6109700 original size:29 final size:29
Alignment explanation
Indices: 6109661--6109781 Score: 172
Period size: 29 Copynumber: 4.2 Consensus size: 29
6109651 TCTTACCCAA
*
6109661 GTGCGAGCTTGAAATGCATGGCACTGAGT
1 GTGCGAGCTTGAAATGCATGGCACTAAGT
*
6109690 GTGCGAGCTTGAAATGCATGGCACTGAGT
1 GTGCGAGCTTGAAATGCATGGCACTAAGT
*
6109719 GTGCGAGCTTGAAATGCATGGCGCTAAGT
1 GTGCGAGCTTGAAATGCATGGCACTAAGT
* * *
6109748 GTGCGAG-TTTAAAGTACGTGGCACTAAGT
1 GTGCGAGCTTGAAA-TGCATGGCACTAAGT
6109777 GTGCG
1 GTGCG
6109782 CGGTTGATTA
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
28 5 0.06
29 80 0.94
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.25
Consensus pattern (29 bp):
GTGCGAGCTTGAAATGCATGGCACTAAGT
Found at i:6112362 original size:16 final size:16
Alignment explanation
Indices: 6112341--6112386 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
6112331 GGATGTTATG
6112341 GATTTGGGGATTTCAC
1 GATTTGGGGATTTCAC
* *
6112357 GATTTGGGAAATTTGAC
1 GATTTGGG-GATTTCAC
*
6112374 GAGTTGGGGATTT
1 GATTTGGGGATTT
6112387 TAGAAATTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.22, C:0.07, G:0.35, T:0.37
Consensus pattern (16 bp):
GATTTGGGGATTTCAC
Found at i:6114042 original size:20 final size:22
Alignment explanation
Indices: 6114017--6114063 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
6114007 CGTATGCTTC
*
6114017 ATTAAATACTTAATTA-TCT-A
1 ATTAAATAATTAATTACTCTCA
6114037 ATTAAATAATTAATTACTCTCA
1 ATTAAATAATTAATTACTCTCA
6114059 ATTAA
1 ATTAA
6114064 GTTATTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 15 0.62
21 3 0.12
22 6 0.25
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAATAATTAATTACTCTCA
Found at i:6119792 original size:28 final size:28
Alignment explanation
Indices: 6119750--6119807 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
6119740 AGCGTAACTG
* * *
6119750 TGAATGAGATTGGGCCTAATGGGCCATA
1 TGAATGAAATGGGGCCTAATAGGCCATA
*
6119778 TGAATGAAATGGGGCCTAGTAGGCCATA
1 TGAATGAAATGGGGCCTAATAGGCCATA
6119806 TG
1 TG
6119808 CATGTATGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (28 bp):
TGAATGAAATGGGGCCTAATAGGCCATA
Found at i:6121847 original size:21 final size:20
Alignment explanation
Indices: 6121823--6121864 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
6121813 TCATTTTCAA
6121823 TCTCAATCT-TGTTTTGCTTTC
1 TCTCAATCTCT-TTTT-CTTTC
*
6121844 TCTCACTCTCTTTTTCTTTC
1 TCTCAATCTCTTTTTCTTTC
6121864 T
1 T
6121865 TTTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 12 0.63
22 1 0.05
ACGTcount: A:0.07, C:0.29, G:0.05, T:0.60
Consensus pattern (20 bp):
TCTCAATCTCTTTTTCTTTC
Found at i:6129571 original size:37 final size:37
Alignment explanation
Indices: 6129521--6129599 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
6129511 TTATTACGAA
* * *
6129521 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
6129558 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
6129595 GTCTT
1 GTCTT
6129600 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Done.