Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 16
Found at i:1576478 original size:105 final size:105
Alignment explanation
Indices: 1576292--1576816 Score: 749
Period size: 105 Copynumber: 4.9 Consensus size: 105
1576282 AGGTTTTACC
1576292 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1576357 ACGAAGGGACCACTGGTTGTCAACAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTTAATTT
*
1576397 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1576462 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTTAATTT
1576502 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1576567 ACGAAGGGACCACTGGTTGTCAA-TAA-A---C--AATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTTAATTT
1576600 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1576665 ACGAAGGGACCGGTGGTTGTCAATAAACAACTTCCCAATTTCAAAGCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-A-TT-TC---TT-------AATTT
* * * * *
1576718 CAGAGCCAATTTCAACTTCACAACGAAAGAAATTGGGCCCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1576783 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTC
1576817 CCAATTCCAA
Statistics
Matches: 384, Mismatches: 16, Indels: 29
0.90 0.04 0.07
Matches are distributed among these distances:
98 91 0.24
99 2 0.01
100 1 0.00
101 1 0.00
103 1 0.00
104 2 0.01
105 188 0.49
106 1 0.00
116 1 0.00
117 2 0.01
118 94 0.24
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTTAATTT
Found at i:1576573 original size:43 final size:43
Alignment explanation
Indices: 1576512--1576671 Score: 131
Period size: 43 Copynumber: 3.4 Consensus size: 43
1576502 CAGAGCCAAT
1576512 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * ** * * *
1576555 TTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCAGAGCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---C---G-CAAG
1576610 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
1576653 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
1576672 GACCGGTGGT
Statistics
Matches: 88, Mismatches: 17, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
43 37 0.42
44 4 0.05
45 4 0.05
46 2 0.02
47 1 0.01
48 5 0.06
50 5 0.06
51 1 0.01
52 2 0.02
53 4 0.05
54 4 0.05
55 19 0.22
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:1576716 original size:12 final size:12
Alignment explanation
Indices: 1576699--1576732 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1576689 AAACAACTTC
1576699 CCAATTTCAAAG
1 CCAATTTCAAAG
*
1576711 CCAATTTCAGAG
1 CCAATTTCAAAG
1576723 CCAATTTCAA
1 CCAATTTCAA
1576733 CTTCACAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.26
Consensus pattern (12 bp):
CCAATTTCAAAG
Found at i:1576802 original size:118 final size:118
Alignment explanation
Indices: 1576594--1576822 Score: 395
Period size: 118 Copynumber: 1.9 Consensus size: 118
1576584 TGTCAATAAA
* * * *
1576594 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAAGAAATTGGACCCCAGACAACACAAGTTCAAC
*
1576659 TTCACGACGAAGGGACCGGTGGTTGTCAATAAACAACTTCCCAATTTCAAAGC
66 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAAAGC
*
1576712 CAATTTCAGAGCCAATTTCAACTTCACAACGAAAGAAATTGGGCCCCAGACAACACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAAGAAATTGGACCCCAGACAACACAAGTTCAAC
*
1576777 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATT
66 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATT
1576823 CCAACTTCAC
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 104 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (118 bp):
CAATTTCAGAGCCAATTTCAACTTCACAACGAAAGAAATTGGACCCCAGACAACACAAGTTCAAC
TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAAAGC
Found at i:1578482 original size:8 final size:8
Alignment explanation
Indices: 1578449--1578491 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
1578439 TTATTTTACT
1578449 TATATGT-
1 TATATGTA
1578456 TATAT-TA
1 TATATGTA
*
1578463 TGTATGTA
1 TATATGTA
*
1578471 TATATATA
1 TATATGTA
1578479 TATATGTA
1 TATATGTA
1578487 TATAT
1 TATAT
1578492 TTTGTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 1 0.03
7 9 0.30
8 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:1578803 original size:43 final size:47
Alignment explanation
Indices: 1578755--1578842 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 47
1578745 TTTATTTCAC
*
1578755 TTTTATTATG-C-T-TTAT-TTATTTATTTATTCTTTCCTTTTTTCG
1 TTTTATTATGTCTTATTATCTTATTTATTTATTCTTTCATTTTTTCG
* * *
1578798 TTTTATTGTGTCTTATTTTCTTATTTCTTTATTCTTTCATTTTTT
1 TTTTATTATGTCTTATTATCTTATTTATTTATTCTTTCATTTTTT
1578843 ACCTTATCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 9 0.24
44 1 0.03
45 1 0.03
46 3 0.08
47 23 0.62
ACGTcount: A:0.12, C:0.11, G:0.05, T:0.72
Consensus pattern (47 bp):
TTTTATTATGTCTTATTATCTTATTTATTTATTCTTTCATTTTTTCG
Found at i:1580299 original size:3 final size:3
Alignment explanation
Indices: 1580293--1580317 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1580283 TCTTGATTGA
1580293 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1580318 TATTTTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1580582 original size:344 final size:347
Alignment explanation
Indices: 1579955--1580615 Score: 960
Period size: 344 Copynumber: 1.9 Consensus size: 347
1579945 TTCTGATTGA
* *
1579955 TATTATTTATTTATTTATTTATTTTGGTTGCCCTCCCGGTTTCAAGGCTTCATATTGATTAATTT
1 TATTATTTATTTATTTATTTATTTTGGTTGCCCTCCCGGTTTCAAGGCTTCACATTGACTAATTT
* * * * * *
1580020 GGACTAACTTGCCTCGCACACCTAGTTTTGGTGGGTGAGTCTCTCAGTAGGAATTTTATGCATAC
66 GGACTAACTCGCCTCGCACACATAGTTTTGGTGAGTGAATCTCTCAGTAAGAATTTTATACATAC
* * * ** *
1580085 ACAATAACTCGAACTCGAGATCTTGTTTATTGCTTGAACCAACATTGTTAGTAATTTGATTGATA
131 ACAAGAACTCGAACTCGAGACCATGTTTACCGCTTGAACCAACACTGTTAGTAATTTGATTGATA
*
1580150 TTATTATTAGCTTAACATTTAAGATATCGTGTTTAAATATTTTTATTATAATTAAGGGTAAAGTA
196 TTATTATTAGCTTAACATTTAAGATATCATGTTTAAATATTTTTATTATAATTAAGGGTAAAGTA
* *
1580215 TATAAAATGGTCCCAAGTTATAGGGTGTTGCTTTGTTGAGTTCATCGACTATTAAAATTAATTAT
261 TATAAAATGGTCCCAAGTTATAGGGTGTTGCTTTGATGAGTTCATCAACTATTAAAATTAATTAT
1580280 TAATCTTGATTGATATTATTAT
326 TAATCTTGATTGATATTATTAT
* * *
1580302 TATTA-TTA-TTA-TTATTTATTTTGGTTTCCCTCCCGG-TTCTAAGGCTTCGCCTTGACTAATT
1 TATTATTTATTTATTTATTTATTTTGGTTGCCCTCCCGGTTTC-AAGGCTTCACATTGACTAATT
* * *
1580363 TGGACTAA-TCCGCCTTGCACACATGGTTTTGGTGAGTGAATCTC-CGAGTAA-AGATTTTCTAC
65 TGGACTAACT-CGCCTCGCACACATAGTTTTGGTGAGTGAATCTCTC-AGTAAGA-ATTTTATAC
** ** *
1580425 ATACACAAGGGCTCGAACTCGAGACCATGTTTACCGCTTGAATTAACCCTGTTAGTAATTTGATT
127 ATACACAAGAACTCGAACTCGAGACCATGTTTACCGCTTGAACCAACACTGTTAGTAATTTGATT
1580490 GATATTATTATTAGCTTAACATTTAAGATATCATGTTTAAATATTTTTATTATAATTAAGGGTAA
192 GATATTATTATTAGCTTAACATTTAAGATATCATGTTTAAATATTTTTATTATAATTAAGGGTAA
*
1580555 AGTATATAAAATGGTCCTC-AGTTATAGGGTGTTGCTTTGATGCGTTCATCAACTATTAAAA
257 AGTATATAAAATGGTCC-CAAGTTATAGGGTGTTGCTTTGATGAGTTCATCAACTATTAAAA
1580616 GTTACAAAAT
Statistics
Matches: 280, Mismatches: 29, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
343 6 0.02
344 262 0.94
345 4 0.01
346 3 0.01
347 5 0.02
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.41
Consensus pattern (347 bp):
TATTATTTATTTATTTATTTATTTTGGTTGCCCTCCCGGTTTCAAGGCTTCACATTGACTAATTT
GGACTAACTCGCCTCGCACACATAGTTTTGGTGAGTGAATCTCTCAGTAAGAATTTTATACATAC
ACAAGAACTCGAACTCGAGACCATGTTTACCGCTTGAACCAACACTGTTAGTAATTTGATTGATA
TTATTATTAGCTTAACATTTAAGATATCATGTTTAAATATTTTTATTATAATTAAGGGTAAAGTA
TATAAAATGGTCCCAAGTTATAGGGTGTTGCTTTGATGAGTTCATCAACTATTAAAATTAATTAT
TAATCTTGATTGATATTATTAT
Found at i:1583629 original size:11 final size:11
Alignment explanation
Indices: 1583615--1583666 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1583605 TTAAATAAAA
*
1583615 AAATTATAATT
1 AAATTAAAATT
1583626 AAATTAAAATT
1 AAATTAAAATT
**
1583637 CTATTAAAATT
1 AAATTAAAATT
1583648 ATAATTAAATGATT
1 A-AATTAAA--ATT
1583662 AAATT
1 AAATT
1583667 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
11 19 0.58
12 6 0.18
13 4 0.12
14 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:1584510 original size:60 final size:60
Alignment explanation
Indices: 1584429--1584563 Score: 243
Period size: 60 Copynumber: 2.2 Consensus size: 60
1584419 GTAACGTTTG
* *
1584429 TAATGTTAGGCACTTGAATGGACCAAAAAATACTATAGGCACCTATTCGGAAAAAATGGTA
1 TAAT-TTAAGCACTTGAATGGACCAAAAAATACTATAGGCACCTATTCGGAAAAAATAGTA
1584490 TAATTTAAGCACTTGAATGGACCAAAAAATACTATAGGCACCTATTCGGAAAAAATAGTA
1 TAATTTAAGCACTTGAATGGACCAAAAAATACTATAGGCACCTATTCGGAAAAAATAGTA
1584550 TAATTTAAGCACTT
1 TAATTTAAGCACTT
1584564 ATTTGGGCAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
60 68 0.94
61 4 0.06
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (60 bp):
TAATTTAAGCACTTGAATGGACCAAAAAATACTATAGGCACCTATTCGGAAAAAATAGTA
Found at i:1584651 original size:18 final size:18
Alignment explanation
Indices: 1584628--1584662 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1584618 AATTATAAAG
*
1584628 ATTTATTTAAAATTAATC
1 ATTTATTGAAAATTAATC
*
1584646 ATTTATTGAAATTTAAT
1 ATTTATTGAAAATTAAT
1584663 TATAATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTATTGAAAATTAATC
Found at i:1584711 original size:27 final size:28
Alignment explanation
Indices: 1584655--1584715 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1584645 CATTTATTGA
* * *
1584655 AATTTAATTATAATTTTAATAGAATTAT
1 AATTAAATAATAATTTTAATAGAATAAT
1584683 AATTAAATAATAATTTTTAA-A-AATAAT
1 AATTAAATAATAA-TTTTAATAGAATAAT
1584710 AATTAA
1 AATTAA
1584716 TTTAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 11 0.38
28 12 0.41
29 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTAAATAATAATTTTAATAGAATAAT
Found at i:1587500 original size:17 final size:17
Alignment explanation
Indices: 1587468--1587500 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1587458 GTTGATAAAC
1587468 ATTAATATTATCTATTA
1 ATTAATATTATCTATTA
1587485 ATTAACTATTAT-TATT
1 ATTAA-TATTATCTATT
1587501 TTTTAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTAATATTATCTATTA
Found at i:1592697 original size:24 final size:24
Alignment explanation
Indices: 1592670--1592798 Score: 150
Period size: 24 Copynumber: 5.4 Consensus size: 24
1592660 GTTTTATCTA
* *
1592670 ATTTCTTATTTGAATTCTATTATG
1 ATTTCTGATCTGAATTCTATTATG
*
1592694 ATTTCTGATCTGAATTCTGTTATG
1 ATTTCTGATCTGAATTCTATTATG
*
1592718 ATTTCTGATCTGAATTCTATTCTG
1 ATTTCTGATCTGAATTCTATTATG
* * *
1592742 ATTTCTTATATGGATTCTATTATG
1 ATTTCTGATCTGAATTCTATTATG
* * * * *
1592766 ATATATGATCTGAATTTTGTTTTG
1 ATTTCTGATCTGAATTCTATTATG
1592790 ATTTCTGAT
1 ATTTCTGAT
1592799 ATCTACGTTT
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 86 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.53
Consensus pattern (24 bp):
ATTTCTGATCTGAATTCTATTATG
Found at i:1594201 original size:90 final size:90
Alignment explanation
Indices: 1594044--1594221 Score: 270
Period size: 90 Copynumber: 2.0 Consensus size: 90
1594034 CCTAACACAC
* *
1594044 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATATAT
1 CCTTTTATATCCAAGTTACCCAAATCATATTAGGATTTTCATTATTTCAAATTAATTAAATATAT
* * *
1594109 ATTTGATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
1594134 CCTTTTATGTCCAAGTTACCCAAATCATATTATGGATTTT-ATTATTTCAAATTAATTAAATCA-
1 CCTTTTATATCCAAGTTACCCAAATCATATTA-GGATTTTCATTATTTCAAATTAATTAAAT-AT
1594197 ATATTTAATTAATTGAAATTAAATA
64 ATATTTAATTAATTGAAATTAAATA
1594222 TTCAGGATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
90 73 0.91
91 7 0.09
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATATCCAAGTTACCCAAATCATATTAGGATTTTCATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:1594208 original size:20 final size:20
Alignment explanation
Indices: 1594183--1594252 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 20
1594173 TATTATTTCA
1594183 AATTAATTAAATCAATATTT
1 AATTAATTAAATCAATATTT
* *
1594203 AATTAATTGAAATTAAATATTC
1 AATTAATT-AAA-TCAATATTT
*
1594225 AGGATT-ATTAAAACATATATTT
1 A--ATTAATTAAATCA-ATATTT
1594247 AATTAA
1 AATTAA
1594253 CTCCAAGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
20 11 0.28
21 5 0.13
22 17 0.44
23 3 0.08
24 3 0.08
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (20 bp):
AATTAATTAAATCAATATTT
Found at i:1600999 original size:90 final size:89
Alignment explanation
Indices: 1600854--1601016 Score: 256
Period size: 90 Copynumber: 1.8 Consensus size: 89
1600844 TTTTATATCC
* *
1600854 AAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATAAAATCTATATTTAATTAATT
1 AAGTTACCCAAATCATATTAGGGTTTTCATTATTTCAAATTAATAAAATCAATATTTAATTAATT
*
1600919 AGAATTTAATAATCCTTTTATGTTT
66 -GAAATTAATAATCCTTTTATGTTT
* *
1600944 AAGTTACCCAAATCATATTAGGGATTTT-ATTATTTTAAATTAATTAAATCAATATTTAATTAAT
1 AAGTTACCCAAATCATATTAGGG-TTTTCATTATTTCAAATTAATAAAATCAATATTTAATTAAT
1601008 TGAAATTAA
65 TGAAATTAA
1601017 ATATTCAGGA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
89 7 0.10
90 56 0.84
91 4 0.06
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (89 bp):
AAGTTACCCAAATCATATTAGGGTTTTCATTATTTCAAATTAATAAAATCAATATTTAATTAATT
GAAATTAATAATCCTTTTATGTTT
Found at i:1601006 original size:20 final size:20
Alignment explanation
Indices: 1600981--1601050 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 20
1600971 TATTATTTTA
1600981 AATTAATTAAATCAATATTT
1 AATTAATTAAATCAATATTT
* *
1601001 AATTAATTGAAATTAAATATTC
1 AATTAATT-AAA-TCAATATTT
*
1601023 AGGATT-ATTAAAACATATATTT
1 A--ATTAATTAAATCA-ATATTT
1601045 AATTAA
1 AATTAA
1601051 CTCCACATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
20 11 0.28
21 5 0.13
22 17 0.44
23 3 0.08
24 3 0.08
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (20 bp):
AATTAATTAAATCAATATTT
Found at i:1604285 original size:37 final size:37
Alignment explanation
Indices: 1604226--1604404 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 37
1604216 ACCAAATATA
*
1604226 TTTTCAAAAACTATATAATATATATATTTTCAAAAATG
1 TTTT-AAAAACTATATATTATATATATTTTCAAAAATG
*
1604264 TTTTAAAAACTATATATTATATTTATTTTC-AAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAAATG
* * *
1604300 TTTTAAAAACTATATAATATATAAATGTTTTTCAAACATG
1 TTTTAAAAACTATAT-AT-TATATAT-ATTTTCAAAAATG
* *
1604340 TTTTCAAAACTATATATTATATATATGTTTATTAAAAATG
1 TTTTAAAAACTATATATTATATATA--TTT-TCAAAAATG
* **
1604380 TTTT-CAAACTATATACAATATATAT
1 TTTTAAAAACTATATATTATATATAT
1604405 ATATATATAT
Statistics
Matches: 120, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
36 21 0.17
37 27 0.22
38 15 0.12
39 27 0.22
40 30 0.25
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAAATG
Found at i:1607397 original size:17 final size:18
Alignment explanation
Indices: 1607375--1607414 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1607365 TAAACGTAAG
1607375 ATTTAA-AATTTAAATTA
1 ATTTAATAATTTAAATTA
*
1607392 ATTTAATATTTTAAATTA
1 ATTTAATAATTTAAATTA
1607410 ATTTA
1 ATTTA
1607415 GATACATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAATAATTTAAATTA
Found at i:1607695 original size:21 final size:22
Alignment explanation
Indices: 1607649--1607700 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 22
1607639 AACTTGTTTC
*
1607649 TATTTTAAATCATACATTAACTA
1 TATTTTAAA-CATACATTAACAA
1607672 TATTTTAAA-ATACATATAA-AA
1 TATTTTAAACATACAT-TAACAA
1607693 TATATTTA
1 TAT-TTTA
1607701 TCTATAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 10 0.38
22 7 0.27
23 9 0.35
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTTTAAACATACATTAACAA
Found at i:1607696 original size:23 final size:22
Alignment explanation
Indices: 1607649--1607699 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
1607639 AACTTGTTTC
*
1607649 TATTTTAAATCATACATTAACTA
1 TATTTTAAA-CATACATTAAATA
1607672 TATTTTAAA-ATACATATAAAATA
1 TATTTTAAACATACAT-T-AAATA
1607695 TATTT
1 TATTT
1607700 ATCTATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 6 0.24
22 1 0.04
23 18 0.72
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTTTAAACATACATTAAATA
Found at i:1608402 original size:21 final size:21
Alignment explanation
Indices: 1608361--1608403 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1608351 TTTAAAAAAA
* *
1608361 TATTAAAAATATTATTATATT
1 TATTAAAAACATAATTATATT
1608382 TATTAAAAAACATAATT-TATT
1 TATT-AAAAACATAATTATATT
1608403 T
1 T
1608404 TAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTAAAAACATAATTATATT
Found at i:1612011 original size:11 final size:11
Alignment explanation
Indices: 1611995--1612033 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1611985 TTGCAATTTC
*
1611995 TTTATCTTTTT
1 TTTATCTTATT
1612006 TTTATCTTATT
1 TTTATCTTATT
*
1612017 TTAATCTTATT
1 TTTATCTTATT
1612028 TCTTAT
1 T-TTAT
1612034 TTTGTTTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 21 0.88
12 3 0.12
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:1626300 original size:14 final size:14
Alignment explanation
Indices: 1626278--1626362 Score: 64
Period size: 14 Copynumber: 5.9 Consensus size: 14
1626268 AAAATAATAT
1626278 ATAAGCTATGTGAC
1 ATAAGCTATGTGAC
* * *
1626292 ATAATCTATGTAAT
1 ATAAGCTATGTGAC
1626306 ATAAGCTATGTGAC
1 ATAAGCTATGTGAC
***
1626320 ATGTTCTATGTGAC
1 ATAAGCTATGTGAC
* *
1626334 -TGATTGTCTATGTGAT
1 AT-A-AG-CTATGTGAC
1626350 ATAAGCTATGTGA
1 ATAAGCTATGTGA
1626363 AATGGTATAA
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
13 1 0.02
14 41 0.76
15 2 0.04
16 9 0.17
17 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (14 bp):
ATAAGCTATGTGAC
Found at i:1626310 original size:28 final size:28
Alignment explanation
Indices: 1626276--1626330 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1626266 TGAAAATAAT
1626276 ATATAAGCTATGTGACATAATCTATGTA
1 ATATAAGCTATGTGACATAATCTATGTA
**
1626304 ATATAAGCTATGTGACATGTTCTATGT
1 ATATAAGCTATGTGACATAATCTATGT
1626331 GACTGATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (28 bp):
ATATAAGCTATGTGACATAATCTATGTA
Found at i:1626501 original size:23 final size:23
Alignment explanation
Indices: 1626439--1626501 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1626429 GAGTTGATGG
1626439 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
* * ** * *
1626462 ATCTAAGTAGTCATTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAA
1626485 TTCTACGCGGTCCTTCG
1 TTCTACGCGGTCCTTCG
1626502 TGTTGGGATT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:1626786 original size:34 final size:34
Alignment explanation
Indices: 1626743--1626807 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1626733 TTTACAACTT
*
1626743 CCTAGTTTTTTAAGGGCTAAACTAGAACCTTATC
1 CCTAGTTTTTCAAGGGCTAAACTAGAACCTTATC
* *
1626777 CCTAGTTTTTCAAGGGCTCATCTAGAACCTT
1 CCTAGTTTTTCAAGGGCTAAACTAGAACCTT
1626808 TCCTTTTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (34 bp):
CCTAGTTTTTCAAGGGCTAAACTAGAACCTTATC
Found at i:1627281 original size:20 final size:20
Alignment explanation
Indices: 1627232--1627284 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1627222 TATTGTTCAT
*
1627232 TACTATTCACACAGTATCGG
1 TACTATTCATACAGTATCGG
* * *
1627252 TGCTATTCATATAGTATTGG
1 TACTATTCATACAGTATCGG
1627272 TACTATTCATACA
1 TACTATTCATACA
1627285 ATACAGTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
TACTATTCATACAGTATCGG
Found at i:1630062 original size:20 final size:19
Alignment explanation
Indices: 1630034--1630103 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
1630024 TACTGTTCAT
* *
1630034 TACTGTTCACACAGTATCGG
1 TACTATTCATACAGT-TCGG
*
1630054 TACTATTCATACAGTGTAGG
1 TACTATTCATACAGT-TCGG
* *
1630074 TACTATTCATACAGTGCAG
1 TACTATTCATACAGTTCGG
1630093 TACTATTCATA
1 TACTATTCATA
1630104 AAAACATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 12 0.28
20 31 0.72
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (19 bp):
TACTATTCATACAGTTCGG
Found at i:1630097 original size:19 final size:20
Alignment explanation
Indices: 1630052--1630103 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1630042 ACACAGTATC
*
1630052 GGTACTATTCATACAGTGTA
1 GGTACTATTCATACAGTGCA
1630072 GGTACTATTCATACAGTGCA
1 GGTACTATTCATACAGTGCA
1630092 -GTACTATTCATA
1 GGTACTATTCATA
1630104 AAAACATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (20 bp):
GGTACTATTCATACAGTGCA
Found at i:1630288 original size:23 final size:24
Alignment explanation
Indices: 1630236--1630289 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
1630226 CATAGTTCAA
*
1630236 CACTTCGAGACAATACTATGTGGT
1 CACTTCGGGACAATACTATGTGGT
* * *
1630260 C-TTTCGGGACATTTCTATGTGG-
1 CACTTCGGGACAATACTATGTGGT
1630282 CACTTCGG
1 CACTTCGG
1630290 TAAAATTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 1 0.04
23 22 0.92
24 1 0.04
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (24 bp):
CACTTCGGGACAATACTATGTGGT
Found at i:1630832 original size:15 final size:15
Alignment explanation
Indices: 1630812--1630840 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1630802 ATTTAAGTTG
1630812 TATGTTATTTTGTTA
1 TATGTTATTTTGTTA
1630827 TATGTTATTTTGTT
1 TATGTTATTTTGTT
1630841 GGCATGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (15 bp):
TATGTTATTTTGTTA
Found at i:1633148 original size:30 final size:32
Alignment explanation
Indices: 1633083--1633141 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
1633073 ATATCCTCTA
*
1633083 TTTGTGTCACTTATATTATCGATTTATTAACT
1 TTTGTGTCACTTACATTATCGATTTATTAACT
*
1633115 TTTG-GTCACTTACGTTATCGA-TTATTA
1 TTTGTGTCACTTACATTATCGATTTATTA
1633142 CATTTTGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 15 0.60
32 4 0.16
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (32 bp):
TTTGTGTCACTTACATTATCGATTTATTAACT
Found at i:1633402 original size:3 final size:3
Alignment explanation
Indices: 1633396--1633452 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
1633386 CGTTGTCACC
1633396 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1633444 ATT ATT ATT
1 ATT ATT ATT
1633453 TATTCATTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1633630 original size:60 final size:61
Alignment explanation
Indices: 1633537--1633675 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 61
1633527 GAAAGAGGAT
* *
1633537 TTTCATCCCTAAAACTATAACTATCATTCTAAATTAGTCCTCAAAC-TTTTGAACATT-TCAA
1 TTTCATCCC-CAAACTATAACTATCATTCTAAATTAGTCATCAAACTTTTTGAACATTCT-AA
* * * *
1633598 TTTCATCCCCAAACTATGAC-ATTCATTTTAAATTAGTCATTAACCTTTTTGAACATTCTAA
1 TTTCATCCCCAAACTATAACTA-TCATTCTAAATTAGTCATCAAACTTTTTGAACATTCTAA
1633659 TTTCAT-CCCAAACTATA
1 TTTCATCCCCAAACTATA
1633676 CGCATATACT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
59 1 0.01
60 38 0.56
61 28 0.41
62 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (61 bp):
TTTCATCCCCAAACTATAACTATCATTCTAAATTAGTCATCAAACTTTTTGAACATTCTAA
Found at i:1633985 original size:60 final size:60
Alignment explanation
Indices: 1633920--1634079 Score: 223
Period size: 60 Copynumber: 2.7 Consensus size: 60
1633910 TCATATATTT
* * * *
1633920 GGATGAAATTGGAATATTCAAAAATTTGGGGACCAATTTAGAAAGTGT-TTCATAGTTTAG
1 GGATGAAATTGGAATGTTCAAAAGTTTGAGGACCAATTTAG-AAGTATATTCATAGTTTAG
* * *
1633980 GGATGAAATTAGAATGTTCAAAAGTTTGAGGACTAATTTAGAATTATATTCATAGTTTAG
1 GGATGAAATTGGAATGTTCAAAAGTTTGAGGACCAATTTAGAAGTATATTCATAGTTTAG
* *
1634040 GGATGAAATTGAAATGTTCAAAAGTTTAAGGACCAATTTA
1 GGATGAAATTGGAATGTTCAAAAGTTTGAGGACCAATTTA
1634080 AAACGAGAGT
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 4 0.05
60 84 0.95
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (60 bp):
GGATGAAATTGGAATGTTCAAAAGTTTGAGGACCAATTTAGAAGTATATTCATAGTTTAG
Found at i:1634005 original size:29 final size:30
Alignment explanation
Indices: 1633920--1634067 Score: 94
Period size: 29 Copynumber: 5.0 Consensus size: 30
1633910 TCATATATTT
* * * *
1633920 GGATGAAATT-GGAATATTCAAAAATTTGG
1 GGATGAAATTAGAAATGTTCAAAAGTTTAG
** * *
1633949 GGACCAATTTAGAAAGTGTTTC-ATAGTTTAG
1 GGATGAAATTAGAAA-TG-TTCAAAAGTTTAG
1633980 GGATGAAATTAG-AATGTTCAAAAGTTT-G
1 GGATGAAATTAGAAATGTTCAAAAGTTTAG
* * *
1634008 AGGACT-AATTTAGAATTATATTC-ATAGTTTAG
1 -GGA-TGAAATTAGAA--ATGTTCAAAAGTTTAG
1634040 GGATGAAATT-GAAATGTTCAAAAGTTTA
1 GGATGAAATTAGAAATGTTCAAAAGTTTA
1634068 AGGACCAATT
Statistics
Matches: 89, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
28 9 0.10
29 31 0.35
30 11 0.12
31 29 0.33
32 9 0.10
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (30 bp):
GGATGAAATTAGAAATGTTCAAAAGTTTAG
Found at i:1636297 original size:2 final size:2
Alignment explanation
Indices: 1636290--1636353 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1636280 AACTCGGAAT
1636290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1636332 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
1636354 CAAAGTAGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1639016 original size:13 final size:13
Alignment explanation
Indices: 1638998--1639022 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1638988 TGTTTATCCC
1638998 ATAAAGTTAAAAG
1 ATAAAGTTAAAAG
1639011 ATAAAGTTAAAA
1 ATAAAGTTAAAA
1639023 TATTAATTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
ATAAAGTTAAAAG
Found at i:1640618 original size:23 final size:23
Alignment explanation
Indices: 1640598--1640642 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1640588 AATAATATTT
1640598 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1640621 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1640643 ATAACACTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1640783 original size:49 final size:50
Alignment explanation
Indices: 1640729--1640827 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 50
1640719 TTTTTATTAA
*
1640729 TAAAATTATAAAAATAATATTTAATAATAAATAA-ATTATTT-TAATATTT
1 TAAAATAATAAAAATAA-ATTTAATAATAAATAATATTATTTATAATATTT
* * * * *
1640778 TAAAATAATAATATTAAATTTTATGATAAATAATATTATTTATTATATTT
1 TAAAATAATAAAAATAAATTTAATAATAAATAATATTATTTATAATATTT
1640828 AATATTTGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 14 0.33
49 21 0.50
50 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (50 bp):
TAAAATAATAAAAATAAATTTAATAATAAATAATATTATTTATAATATTT
Found at i:1644078 original size:3 final size:3
Alignment explanation
Indices: 1644072--1644162 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
1644062 AGAAGAATTC
1644072 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1644120 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1644163 GTGTCTTTAA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1649488 original size:2 final size:2
Alignment explanation
Indices: 1649481--1649511 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1649471 TAATTATTTT
1649481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1649512 TTTAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1652815 original size:22 final size:23
Alignment explanation
Indices: 1652768--1652822 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
1652758 TTTCTTGGGA
1652768 TCCTCCTTCTTTTCGACTTTCTTT
1 TCCT-CTTCTTTTCGACTTTCTTT
*
1652792 TCCTCTT-TTTTCGGCTCTTC-TT
1 TCCTCTTCTTTTCGACT-TTCTTT
*
1652814 TCTTCTTCT
1 TCCTCTTCT
1652823 CCGGCTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 16 0.59
23 7 0.26
24 4 0.15
ACGTcount: A:0.02, C:0.33, G:0.05, T:0.60
Consensus pattern (23 bp):
TCCTCTTCTTTTCGACTTTCTTT
Found at i:1653983 original size:16 final size:16
Alignment explanation
Indices: 1653962--1653995 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1653952 TATTGGTATC
1653962 AATCTATTGATAAATT
1 AATCTATTGATAAATT
*
1653978 AATCTATTGATCAATT
1 AATCTATTGATAAATT
1653994 AA
1 AA
1653996 CCCTCACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (16 bp):
AATCTATTGATAAATT
Found at i:1654459 original size:5 final size:5
Alignment explanation
Indices: 1654449--1654478 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1654439 AAACTTTGTT
*
1654449 GAAGA GAAGA GAAGA GAAGA AAAGA GAAGA
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA
1654479 TTTGTGTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:1659081 original size:41 final size:41
Alignment explanation
Indices: 1658993--1659073 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
1658983 GTTTGGTCAG
*
1658993 ATCAGGCAGGCATGTTAGGTCAGGCGAGTGGGTCAGATCGA
1 ATCAGGCAGGCAGGTTAGGTCAGGCGAGTGGGTCAGATCGA
* * * *
1659034 ATCAGGCAGGCGGGTTGGGTCGGGC-AGGTGGGTCGGATCG
1 ATCAGGCAGGCAGGTTAGGTCAGGCGA-GTGGGTCAGATCG
1659074 TTTCAGGCCG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.19, C:0.17, G:0.46, T:0.19
Consensus pattern (41 bp):
ATCAGGCAGGCAGGTTAGGTCAGGCGAGTGGGTCAGATCGA
Found at i:1667371 original size:13 final size:13
Alignment explanation
Indices: 1667353--1667377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1667343 TGAGTGACGA
1667353 TTATTATATATAG
1 TTATTATATATAG
1667366 TTATTATATATA
1 TTATTATATATA
1667378 TAATAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTATTATATATAG
Found at i:1667379 original size:17 final size:15
Alignment explanation
Indices: 1667352--1667412 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
1667342 CTGAGTGACG
1667352 ATTATTATATATAGTT
1 ATTATTATATATAG-T
*
1667368 ATTA-TATATATAAT
1 ATTATTATATATAGT
*
1667382 AATATTATAATATAAGT
1 ATTATTAT-ATAT-AGT
*
1667399 ATTATTATTTATAG
1 ATTATTATATATAG
1667413 AGCCTGAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 4 0.11
15 13 0.35
16 11 0.30
17 9 0.24
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
ATTATTATATATAGT
Found at i:1675273 original size:65 final size:64
Alignment explanation
Indices: 1675204--1675355 Score: 155
Period size: 65 Copynumber: 2.4 Consensus size: 64
1675194 ACACTAGGGG
* *
1675204 TGCATCGGTACACTAATTACATTCGATATTTCAA-AATAGCCATGAGTGCATCGATGCATGGTCT
1 TGCATCGGTACACTAAATACATTCGATATTTCAATAA-AGCCAAGAGTGCATCGATGCATGG-CT
1675268 A
64 A
* * * ** * *
1675269 TGCATCGGTATA-TAAAATGCATTCGATGTTTCAATAAATTCAAGAGTGCATCGATGTATGGCTG
1 TGCATCGGTACACT-AAATACATTCGATATTTCAATAAAGCCAAGAGTGCATCGATGCATGGCTA
* * *
1675333 TGCATCAGAACACTAAATGCATT
1 TGCATCGGTACACTAAATACATT
1675356 TGAAATAGGG
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
64 21 0.29
65 49 0.68
66 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (64 bp):
TGCATCGGTACACTAAATACATTCGATATTTCAATAAAGCCAAGAGTGCATCGATGCATGGCTA
Found at i:1675729 original size:14 final size:14
Alignment explanation
Indices: 1675710--1675736 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1675700 TACTCCCCTT
1675710 TTTGAAAATTACTA
1 TTTGAAAATTACTA
1675724 TTTGAAAATTACT
1 TTTGAAAATTACT
1675737 CCCCCTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
TTTGAAAATTACTA
Found at i:1675732 original size:33 final size:32
Alignment explanation
Indices: 1675678--1675740 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
1675668 TAAGATTTTC
*
1675678 TTTGAAAATAATTTTTGAAAATTACTCCCCTT
1 TTTGAAAATAATATTTGAAAATTACTCCCCTT
*
1675710 TTTGAAAATTACTATTTGAAAATTACTCCCC
1 TTTGAAAA-TAATATTTGAAAATTACTCCCC
1675741 CTTACTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.41
Consensus pattern (32 bp):
TTTGAAAATAATATTTGAAAATTACTCCCCTT
Found at i:1676051 original size:8 final size:8
Alignment explanation
Indices: 1676013--1676076 Score: 85
Period size: 8 Copynumber: 7.8 Consensus size: 8
1676003 ATTCAAGTTT
1676013 AAACATCC
1 AAACATCC
1676021 -AACATCC
1 AAACATCC
*
1676028 AAAACAAATTC
1 -AAAC--ATCC
1676039 AAACATCC
1 AAACATCC
1676047 AAACATCC
1 AAACATCC
1676055 AAACATCC
1 AAACATCC
1676063 AAACATCC
1 AAACATCC
1676071 AAACAT
1 AAACAT
1676077 ATCAATAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
7 7 0.14
8 33 0.66
9 3 0.06
10 4 0.08
11 3 0.06
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (8 bp):
AAACATCC
Found at i:1686439 original size:65 final size:64
Alignment explanation
Indices: 1686341--1686496 Score: 165
Period size: 65 Copynumber: 2.4 Consensus size: 64
1686331 TACACTAGGG
* * * *
1686341 GTGCATCGGTACACTAATTACATTTGATATTTCAA-AAGAACC-AGAAGTTCATCGATGCATGGT
1 GTGCATCGGTACACTAAATGCATTCGATATTTCAATAA-AACCAAG-AGTGCATCGATGCATGG-
1686404 CT
63 CT
* ** *
1686406 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAATAAATTCAAGAGTGCATCGCTGCATGGCT
1 GTGCATCGGTACACT-AAATGCATTCGATATTTCAATAAAACCAAGAGTGCATCGATGCATGGCT
* *
1686470 ATGCATCTGTACACTAAATGCATTCGA
1 GTGCATCGGTACACTAAATGCATTCGA
1686497 AATAGGGTGT
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
64 26 0.34
65 47 0.61
66 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (64 bp):
GTGCATCGGTACACTAAATGCATTCGATATTTCAATAAAACCAAGAGTGCATCGATGCATGGCT
Found at i:1687890 original size:41 final size:41
Alignment explanation
Indices: 1687822--1687899 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
1687812 GTCATTTGTA
* * *
1687822 AGTCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCTATC
1 AGTCTTTCGAGCATGATGATAAATCCTTAGGGCCATCTATC
*
1687863 AGTCTTTCGAGC-TAGATGATAAGTCCTTAGGGCCATC
1 AGTCTTTCGAGCAT-GATGATAAATCCTTAGGGCCATC
1687900 CGCCAAACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.03
41 31 0.97
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (41 bp):
AGTCTTTCGAGCATGATGATAAATCCTTAGGGCCATCTATC
Found at i:1688871 original size:21 final size:21
Alignment explanation
Indices: 1688812--1688874 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1688802 GTTACAAAGT
* *
1688812 AAGGCACACATGCCCATTTAC
1 AAGGCGCACATGCCCAATTAC
*
1688833 AAGAG-G-ACA-GCCCGATTAC
1 AAG-GCGCACATGCCCAATTAC
1688852 AAGGCGCACATGCCCAATTAC
1 AAGGCGCACATGCCCAATTAC
1688873 AA
1 AA
1688875 CCTATCCCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 12 0.35
20 6 0.18
21 14 0.41
22 1 0.03
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.14
Consensus pattern (21 bp):
AAGGCGCACATGCCCAATTAC
Found at i:1690427 original size:20 final size:20
Alignment explanation
Indices: 1690402--1690514 Score: 199
Period size: 20 Copynumber: 5.7 Consensus size: 20
1690392 TTTTCCTAAT
1690402 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1690422 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1690442 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1690462 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1690482 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1690502 TCGCAACGCGAAT
1 TCGCAATGCGAAT
1690515 CTGACTATCG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1690524 original size:20 final size:20
Alignment explanation
Indices: 1690501--1690567 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
1690491 GAATACGTAA
* *
1690501 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
1690521 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1690541 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1690561 ATCGCAA
1 ATCGCAA
1690568 TAATGAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:1692046 original size:20 final size:21
Alignment explanation
Indices: 1692021--1692107 Score: 87
Period size: 20 Copynumber: 4.3 Consensus size: 21
1692011 CAATGCGGAA
*
1692021 ATCGCAAAGC-GAATATGATT
1 ATCGCAAAGCGGAATATGACT
1692041 ATCGCAATA-CGGAA-ATGACT
1 ATCGCAA-AGCGGAATATGACT
*
1692061 ATCGCAATGCGGAAT-TGACT
1 ATCGCAAAGCGGAATATGACT
*
1692081 ATCGCAACA-CAGAA-ATGACT
1 ATCGCAA-AGCGGAATATGACT
1692101 ATCGCAA
1 ATCGCAA
1692108 CGAGAGAATC
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
20 53 0.93
21 4 0.07
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAAAGCGGAATATGACT
Found at i:1692084 original size:40 final size:40
Alignment explanation
Indices: 1692021--1692107 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
1692011 CAATGCGGAA
* * *
1692021 ATCGCAAAGCGAATATGATTATCGCAATACGGAAATGACT
1 ATCGCAAAGCGAATATGACTATCGCAACACAGAAATGACT
*
1692061 ATCGCAATGCGGAAT-TGACTATCGCAACACAGAAATGACT
1 ATCGCAAAGC-GAATATGACTATCGCAACACAGAAATGACT
1692101 ATCGCAA
1 ATCGCAA
1692108 CGAGAGAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (40 bp):
ATCGCAAAGCGAATATGACTATCGCAACACAGAAATGACT
Found at i:1692108 original size:20 final size:20
Alignment explanation
Indices: 1692035--1692108 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
1692025 CAAAGCGAAT
* *
1692035 ATGATTATCGCAATACGGAA
1 ATGACTATCGCAACACGGAA
**
1692055 ATGACTATCGCAATGCGGAA
1 ATGACTATCGCAACACGGAA
* *
1692075 TTGACTATCGCAACACAGAA
1 ATGACTATCGCAACACGGAA
1692095 ATGACTATCGCAAC
1 ATGACTATCGCAAC
1692109 GAGAGAATCG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
ATGACTATCGCAACACGGAA
Found at i:1693413 original size:42 final size:42
Alignment explanation
Indices: 1693306--1693417 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
1693296 TCTAGAATGT
* *
1693306 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTCAACGATGACAGGGGCCTCTTGAACGA
* * * ** *
1693348 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTCAACGATGACAGGGGCCTCTTGAACGA
*
1693390 TAGGG-GAGGCCTCTTTAACGATGACAGG
1 T-GGGAGAGGCCTCTTCAACGATGACAGG
1693418 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTCAACGATGACAGGGGCCTCTTGAACGA
Found at i:1693920 original size:20 final size:20
Alignment explanation
Indices: 1693897--1694005 Score: 139
Period size: 20 Copynumber: 5.5 Consensus size: 20
1693887 GAAACTTAAA
* *
1693897 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAATTGACT
* * *
1693917 ATCGCAACGCCAAAATGACT
1 ATCGCAATGCGAAATTGACT
*
1693937 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAATTGACT
*
1693957 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAATTGACT
1693977 ATCGCAATGC-AAATTTGACT
1 ATCGCAATGCGAAA-TTGACT
1693997 ATCGCAATG
1 ATCGCAATG
1694006 AGATAATCGC
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
19 2 0.02
20 80 0.98
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAAATTGACT
Found at i:1694075 original size:53 final size:53
Alignment explanation
Indices: 1694012--1694130 Score: 134
Period size: 53 Copynumber: 2.2 Consensus size: 53
1694002 AATGAGATAA
* *
1694012 TCGCAATGCGATTTTCA-TTTCGCATTGCGATTCTT-TTGTTGCGATAGTCAAAT
1 TCGCATTGCGATTGTCATTTTCGCATTGCGATT-TTGTTGTTGCGATAGTC-AAT
* * * ** *
1694065 TCGCATTGCGATAGTCATTTTTGCGTTGCGATTTTGTTGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATTTTCGCATTGCGATTTTGTTGTTGCGATAGTCAAT
1694118 TCGCATTGCGATT
1 TCGCATTGCGATT
1694131 CTCTCGTTGA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 30 0.55
54 25 0.45
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTGTCATTTTCGCATTGCGATTTTGTTGTTGCGATAGTCAAT
Found at i:1694093 original size:20 final size:20
Alignment explanation
Indices: 1694049--1694096 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1694039 CGATTCTTTT
1694049 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
* ** *
1694069 ATTGCGATAGTCATTTTTGC
1 GTTGCGATAGTCAAATTCGC
1694089 GTTGCGAT
1 GTTGCGAT
1694097 TTTGTTGTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:1694108 original size:34 final size:34
Alignment explanation
Indices: 1694070--1694163 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 34
1694060 CAAATTCGCA
* * * *
1694070 TTGCGATAGTCATTTTTGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
** *
1694104 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
*
1694137 TTGAGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
1694164 AGTCATTTTC
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 25 0.52
34 23 0.48
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:1694116 original size:87 final size:87
Alignment explanation
Indices: 1694018--1694183 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 87
1694008 ATAATCGCAA
* * *
1694018 TGCGATTTTCATTTCGCATTGCGATTCTTTTGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGAGATAGTCAAATTCGCATTGCGATAGTCAT
* *
1694083 TTTTGCGTTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
** *
1694105 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGAGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGAGATAGTCAAATTCGCATTGCGATAGTCAT
1694170 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
1694184 AGTAAACTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGAGATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:1694164 original size:20 final size:20
Alignment explanation
Indices: 1694135--1694186 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1694125 GCGATTCTCT
*
1694135 CGTTGAGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1694155 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1694175 CATTGCGATAGT
1 CGTTGCGATAGT
1694187 AAACTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1694335 original size:22 final size:21
Alignment explanation
Indices: 1694295--1694335 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1694285 CAGTATTGGC
*
1694295 AGCAATCGAATGAATTTACTA
1 AGCAATCGAATGAAATTACTA
*
1694316 AGCAATCTAAGTGAAATTAC
1 AGCAATCGAA-TGAAATTAC
1694336 GAGTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (21 bp):
AGCAATCGAATGAAATTACTA
Found at i:1696465 original size:22 final size:22
Alignment explanation
Indices: 1696440--1696490 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1696430 GATTTCGCCA
1696440 GAGATGGAGACTGATATCGTCG
1 GAGATGGAGACTGATATCGTCG
* * *
1696462 GAGATGGTGACTGATTTTGTCG
1 GAGATGGAGACTGATATCGTCG
1696484 GAGATGG
1 GAGATGG
1696491 GGACGGATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.39, T:0.27
Consensus pattern (22 bp):
GAGATGGAGACTGATATCGTCG
Found at i:1696725 original size:20 final size:20
Alignment explanation
Indices: 1696700--1696783 Score: 159
Period size: 20 Copynumber: 4.2 Consensus size: 20
1696690 CAGATTTGCG
*
1696700 TTGCGATTTACATATTCGCA
1 TTGCGATTTACGTATTCGCA
1696720 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1696740 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1696760 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1696780 TTGC
1 TTGC
1696784 AAATTAGGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1696809 original size:21 final size:21
Alignment explanation
Indices: 1696785--1696827 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1696775 TCGCATTGCA
1696785 AATTAGGAAAATCGCAACGCG
1 AATTAGGAAAATCGCAACGCG
* * *
1696806 AATTTGGAAAATTGCAATGCG
1 AATTAGGAAAATCGCAACGCG
1696827 A
1 A
1696828 TAGTCATAAT
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:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (21 bp):
AATTAGGAAAATCGCAACGCG
Found at i:1696865 original size:20 final size:20
Alignment explanation
Indices: 1696842--1696907 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
1696832 CATAATCGCG
1696842 TTGCGAATCTGGAAATTGAT
1 TTGCGAATCTGGAAATTGAT
* * **
1696862 TTGCG-ATACTGGAGATCGCG
1 TTGCGAAT-CTGGAAATTGAT
* *
1696882 TTGCGAATCTCGAAACTGAT
1 TTGCGAATCTGGAAATTGAT
1696902 TTGCGA
1 TTGCGA
1696908 TTCCGGAGAC
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (20 bp):
TTGCGAATCTGGAAATTGAT
Found at i:1696916 original size:40 final size:40
Alignment explanation
Indices: 1696836--1696929 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
1696826 GATAGTCATA
* * *
1696836 ATCGCGTTGCGAATCTGGAAATTGATTTGCGATACTGGAG
1 ATCGCGTTGCGAATCTCGAAACTGATTTGCGATACCGGAG
*
1696876 ATCGCGTTGCGAATCTCGAAACTGATTTGCGATTCCGGAG
1 ATCGCGTTGCGAATCTCGAAACTGATTTGCGATACCGGAG
*
1696916 ACCGCGTTGCGAAT
1 ATCGCGTTGCGAAT
1696930 TATCGATCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
ATCGCGTTGCGAATCTCGAAACTGATTTGCGATACCGGAG
Found at i:1698484 original size:485 final size:485
Alignment explanation
Indices: 1697575--1698540 Score: 1932
Period size: 485 Copynumber: 2.0 Consensus size: 485
1697565 GCATTGAATA
1697575 AATTGAGGTTTCGTAATGTTTGATTTATCTTGTAATTTAATTCGGGACGTATATTGTATTTTTAC
1 AATTGAGGTTTCGTAATGTTTGATTTATCTTGTAATTTAATTCGGGACGTATATTGTATTTTTAC
1697640 TTTATATGTTTTTTTAAAAAAAGTTTAAATTCAATGTTCGTCATTTTAAAATATTGTCAATGATC
66 TTTATATGTTTTTTTAAAAAAAGTTTAAATTCAATGTTCGTCATTTTAAAATATTGTCAATGATC
1697705 CCATATGAATAAATTCAACAAAGTATATCTAAAAAATGAGATATGAAATTCAAGAAAAAAATATA
131 CCATATGAATAAATTCAACAAAGTATATCTAAAAAATGAGATATGAAATTCAAGAAAAAAATATA
1697770 ATAGTGTCTCGTTTAATTTTATTTTCGCACGACTCAAACGATCTTCGTGGTTAAATAGATTATTG
196 ATAGTGTCTCGTTTAATTTTATTTTCGCACGACTCAAACGATCTTCGTGGTTAAATAGATTATTG
1697835 TTATATTTAGATGTCTCAAATTCGAACATGTCGTCTGTAAAAATGTTTGGATATTTATTATCAAA
261 TTATATTTAGATGTCTCAAATTCGAACATGTCGTCTGTAAAAATGTTTGGATATTTATTATCAAA
1697900 TAATTTAAAGTCTTTTAAACATATATTAACTTGTGATCACCTAGACTAATAAAAGAATTAGTATT
326 TAATTTAAAGTCTTTTAAACATATATTAACTTGTGATCACCTAGACTAATAAAAGAATTAGTATT
1697965 CACTGACCGACCAATTGTGTTTTATATTGCGAACACAATTATAAACACAAAATTTTTCGTTTACT
391 CACTGACCGACCAATTGTGTTTTATATTGCGAACACAATTATAAACACAAAATTTTTCGTTTACT
1698030 AGATAAATCGAGTATCTTTTATTGTTGACC
456 AGATAAATCGAGTATCTTTTATTGTTGACC
1698060 AATTGAGGTTTCGTAATGTTTGATTTATCTTGTAATTTAATTCGGGACGTATATTGTATTTTTAC
1 AATTGAGGTTTCGTAATGTTTGATTTATCTTGTAATTTAATTCGGGACGTATATTGTATTTTTAC
1698125 TTTATATGTTTTTTTAAAAAAAGTTTAAATTCAATGTTCGTCATTTTAAAATATTGTCAATGATC
66 TTTATATGTTTTTTTAAAAAAAGTTTAAATTCAATGTTCGTCATTTTAAAATATTGTCAATGATC
1698190 CCATATGAATAAATTCAACAAAGTATATCTAAAAAATGAGATATGAAATTCAAGAAAAAAATATA
131 CCATATGAATAAATTCAACAAAGTATATCTAAAAAATGAGATATGAAATTCAAGAAAAAAATATA
1698255 ATAGTGTCTCGTTTAATTTTATTTTCGCACGACTCAAACGATCTTCGTGGTTAAATAGATTATTG
196 ATAGTGTCTCGTTTAATTTTATTTTCGCACGACTCAAACGATCTTCGTGGTTAAATAGATTATTG
1698320 TTATATTTAGATGTCTCAAATTCGAACATGTCGTCTGTAAAAATGTTTGGATATTTATTATCAAA
261 TTATATTTAGATGTCTCAAATTCGAACATGTCGTCTGTAAAAATGTTTGGATATTTATTATCAAA
1698385 TAATTTAAAGTCTTTTAAACATATATTAACTTGTGATCACCTAGACTAATAAAAGAATTAGTATT
326 TAATTTAAAGTCTTTTAAACATATATTAACTTGTGATCACCTAGACTAATAAAAGAATTAGTATT
1698450 CACTGACCGACCAATTGTGTTTTATATTGCGAACACAATTATAAACACAAAATTTTTCGTTTACT
391 CACTGACCGACCAATTGTGTTTTATATTGCGAACACAATTATAAACACAAAATTTTTCGTTTACT
1698515 AGATAAATCGAGTATCTTTTATTGTT
456 AGATAAATCGAGTATCTTTTATTGTT
1698541 CGATACCCTA
Statistics
Matches: 481, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
485 481 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (485 bp):
AATTGAGGTTTCGTAATGTTTGATTTATCTTGTAATTTAATTCGGGACGTATATTGTATTTTTAC
TTTATATGTTTTTTTAAAAAAAGTTTAAATTCAATGTTCGTCATTTTAAAATATTGTCAATGATC
CCATATGAATAAATTCAACAAAGTATATCTAAAAAATGAGATATGAAATTCAAGAAAAAAATATA
ATAGTGTCTCGTTTAATTTTATTTTCGCACGACTCAAACGATCTTCGTGGTTAAATAGATTATTG
TTATATTTAGATGTCTCAAATTCGAACATGTCGTCTGTAAAAATGTTTGGATATTTATTATCAAA
TAATTTAAAGTCTTTTAAACATATATTAACTTGTGATCACCTAGACTAATAAAAGAATTAGTATT
CACTGACCGACCAATTGTGTTTTATATTGCGAACACAATTATAAACACAAAATTTTTCGTTTACT
AGATAAATCGAGTATCTTTTATTGTTGACC
Found at i:1701972 original size:85 final size:85
Alignment explanation
Indices: 1701829--1701997 Score: 311
Period size: 85 Copynumber: 2.0 Consensus size: 85
1701819 TTTAAGAATG
1701829 GACGTGGCAGATTCTTATTCGTCATTTTAAAATCTCAAATGGAAAGCCATGCAGCATCTAATCCA
1 GACGTGGCAGATTCTTATTCGTCATTTTAAAATCTCAAATGGAAAGCCATGCAGCATCTAATCCA
* *
1701894 CATCTTGTACGTTCTATATT
66 CATCCTGTACCTTCTATATT
1701914 GACGTGGCAGATTCTTATTCGTCATTTTAAAATCTCAAATGGAAAGCCATGCAGCATCTAATCCA
1 GACGTGGCAGATTCTTATTCGTCATTTTAAAATCTCAAATGGAAAGCCATGCAGCATCTAATCCA
*
1701979 CATCCTGTGCCTTCTATAT
66 CATCCTGTACCTTCTATAT
1701998 GCAAACTTCT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (85 bp):
GACGTGGCAGATTCTTATTCGTCATTTTAAAATCTCAAATGGAAAGCCATGCAGCATCTAATCCA
CATCCTGTACCTTCTATATT
Found at i:1713243 original size:2 final size:2
Alignment explanation
Indices: 1713236--1713281 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1713226 TACCTTAAGC
1713236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1713278 AT AT
1 AT AT
1713282 GCTTCAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1714045 original size:11 final size:11
Alignment explanation
Indices: 1713994--1714068 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
1713984 TTTAAGAATT
1713994 ATAAAATTATC
1 ATAAAATTATC
* *
1714005 ATTAAATTTATT
1 A-TAAAATTATC
*
1714017 A-AATAATTATA
1 ATAA-AATTATC
*
1714028 AAAAAATTATC
1 ATAAAATTATC
*
1714039 ATTAAATTTATC
1 A-TAAAATTATC
*
1714051 -TAAAATGATC
1 ATAAAATTATC
1714061 ATAAAATT
1 ATAAAATT
1714069 TTATCATATT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
10 10 0.20
11 20 0.41
12 19 0.39
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (11 bp):
ATAAAATTATC
Found at i:1714745 original size:15 final size:15
Alignment explanation
Indices: 1714727--1714756 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1714717 ATTCAATGTC
1714727 ATGTTTCTAACATAA
1 ATGTTTCTAACATAA
*
1714742 ATGTTTTTAACATAA
1 ATGTTTCTAACATAA
1714757 GCTCCTCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (15 bp):
ATGTTTCTAACATAA
Found at i:1717438 original size:7 final size:7
Alignment explanation
Indices: 1717426--1717456 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1717416 ATGTGGGTAT
1717426 GGGGATA
1 GGGGATA
1717433 GGGGATA
1 GGGGATA
1717440 GGGGATA
1 GGGGATA
1717447 GGGGATA
1 GGGGATA
1717454 GGG
1 GGG
1717457 TATTCGCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.61, T:0.13
Consensus pattern (7 bp):
GGGGATA
Found at i:1718890 original size:19 final size:18
Alignment explanation
Indices: 1718855--1718912 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 18
1718845 AAGATAGAGA
1718855 AAATAAGAAAAACAAATG
1 AAATAAGAAAAACAAATG
**
1718873 AAATAAAGAAAAGGAAAT-
1 AAAT-AAGAAAAACAAATG
1718891 AAA-AAGATAAAA-AAAT-
1 AAATAAGA-AAAACAAATG
1718907 AAATAA
1 AAATAA
1718913 AATAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 11 0.32
17 5 0.15
18 7 0.21
19 11 0.32
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (18 bp):
AAATAAGAAAAACAAATG
Found at i:1718906 original size:16 final size:17
Alignment explanation
Indices: 1718831--1718920 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 17
1718821 ATATTAGAAA
*
1718831 AAATGAAAATAAATAAGAT
1 AAAT-AAAATAAA-AAAAT
* * *
1718850 AGAGAAAATAAGAAAAAC
1 AAATAAAATAA-AAAAAT
* *
1718868 AAATGAAATAAAGAAAAGG
1 AAATAAAATAAA-AAAA-T
1718887 AAATAAAAAGATAAAAAAAT
1 AAAT--AAA-ATAAAAAAAT
1718907 AAATAAAATAAAAA
1 AAATAAAATAAAAA
1718921 TAAAGAAAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
17 8 0.15
18 25 0.45
19 7 0.13
20 4 0.07
21 6 0.11
22 5 0.09
ACGTcount: A:0.74, C:0.01, G:0.11, T:0.13
Consensus pattern (17 bp):
AAATAAAATAAAAAAAT
Found at i:1718921 original size:15 final size:15
Alignment explanation
Indices: 1718873--1718929 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
1718863 AAAACAAATG
*
1718873 AAATAAAGAAAAGGAA
1 AAATAAAGAAAA-TAA
*
1718889 ATAA-AAAGATAA-AA
1 A-AATAAAGAAAATAA
*
1718903 AAATAAATAAAATAA
1 AAATAAAGAAAATAA
1718918 AAATAAAGAAAA
1 AAATAAAGAAAA
1718930 GAAATTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 9 0.26
15 13 0.38
16 8 0.24
17 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAATAAAGAAAATAA
Found at i:1719127 original size:3 final size:3
Alignment explanation
Indices: 1719121--1719166 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
1719111 GACACGAAAA
*
1719121 AAT AAT AAT AGT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1719167 CTGTATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1719217 original size:11 final size:11
Alignment explanation
Indices: 1719201--1719225 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1719191 AAAAACCAAA
1719201 AATAGAAAAAT
1 AATAGAAAAAT
1719212 AATAGAAAAAT
1 AATAGAAAAAT
1719223 AAT
1 AAT
1719226 TAAATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (11 bp):
AATAGAAAAAT
Found at i:1720837 original size:14 final size:14
Alignment explanation
Indices: 1720818--1720844 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1720808 CAGTCTTCTT
1720818 CTTGGTTTAAAAAC
1 CTTGGTTTAAAAAC
1720832 CTTGGTTTAAAAA
1 CTTGGTTTAAAAA
1720845 TTCGACTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (14 bp):
CTTGGTTTAAAAAC
Found at i:1721551 original size:80 final size:80
Alignment explanation
Indices: 1720978--1722326 Score: 1552
Period size: 80 Copynumber: 16.4 Consensus size: 80
1720968 TAACATGCGC
* * * * * *
1720978 TTGAGCTGAGTGGAATCGAACTCGAAGATATTTGTTGACATATAACCCTTCTCGCCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTAT
* *
1721043 GTTGCAAATTGGATATG-CT
63 GCTGCAAA-T-GATGTGCCT
* * * * * * *
1721062 TATGAGTTGAATATAATCGAACTCAAAGGTCTTTAGTTGGCAGACAACCCTTCTTACCTTAAGCT
1 T-TGAGCTGAGTGTAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTTGCCTTGAGCT
*
1721127 ATGTTGCAAATGATGTGCCT
61 ATGCTGCAAATGATGTGCCT
* * * *
1721147 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCATTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTAT
1721212 GCTGCAAATGATGTGCCT
63 GCTGCAAATGATGTGCCT
* * * * *
1721230 TTGAGCTGAGTGCAATCGAAATCGAAGGTTTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGG-TCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTA
* * *
1721295 TACTGTAAATGATGTACCT
62 TGCTGCAAATGATGTGCCT
* * *
1721314 TTGAGCTGAGTGCAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTTTTTCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTA
*
1721379 TGCTGCAAAT-ATTGTGTCT
62 TGCTGCAAATGA-TGTGCCT
* *
1721398 TTGAGCTGAGTGTAATCGAACTCGAACGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTA
*
1721463 TGTTGCAAATGATGTGCCT
62 TGCTGCAAATGATGTGCCT
* * * *
1721482 TTGAGCTTAGTGCAATCGAACTCGAAGGTCTTTAGCAGATAACCCTTCTTGCCTTGAGCTATGTT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
*
1721547 GCAAATAATGTGCCT
66 GCAAATGATGTGCCT
* * * * * *
1721562 TTAAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCAAATATCCATTCTTACCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTA
* *
1721627 TGTTGCAAATGATGTACCT
62 TGCTGCAAATGATGTGCCT
* * *
1721646 TTGAGCTGAGTATAATCGAACTCGAAGGTCTTTGGCAGATAATCCTTCTTGCCTTGAGATATGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
1721711 GCAAATGATGTGCCT
66 GCAAATGATGTGCCT
* * * *
1721726 TTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGAAAATATCCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTA
* * *
1721791 TGTTACAAATGATGTGCTT
62 TGCTGCAAATGATGTGCCT
* *
1721810 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTTTTGCCTTAAGCTATGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
*
1721875 ACAAATGATGTGCCT
66 GCAAATGATGTGCCT
* * * ** *
1721890 TTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTATTGGAAAATAATACTTCTTGCCTTGAGATA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTA
** * *
1721955 TATTGCAAAAGATGTGTCT
62 TGCTGCAAATGATGTGCCT
*
1721974 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAATCCTTCTTGCCTTGAGCTATGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
* *
1722039 GCAAATAATGTGTCT
66 GCAAATGATGTGCCT
* * *
1722054 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGAAGA-AAGCCCTTCTTGCCTTGAGTTATGT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAA-CCCTTCTTGCCTTGAGCTATGC
1722118 TGCAAATGATGTGCCT
65 TGCAAATGATGTGCCT
* *
1722134 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTTGCCTGGAGCTATGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
* *
1722199 GTAAATAATGTGCCT
66 GCAAATGATGTGCCT
* * *
1722214 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGACAACCCTTCTCGCTTTGAGCTATGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
1722279 GCAAATGATGTGCCT
66 GCAAATGATGTGCCT
* *
1722294 TTGTGCTGAGTGTAATCAAACTCGAAGGTCTTT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT
1722327 TGTTAGAGGT
Statistics
Matches: 1095, Mismatches: 140, Indels: 64
0.84 0.11 0.05
Matches are distributed among these distances:
79 2 0.00
80 502 0.46
81 6 0.01
82 2 0.00
83 68 0.06
84 449 0.41
85 28 0.03
86 30 0.03
87 5 0.00
89 3 0.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (80 bp):
TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
GCAAATGATGTGCCT
Found at i:1721623 original size:164 final size:164
Alignment explanation
Indices: 1720978--1722326 Score: 1703
Period size: 164 Copynumber: 8.2 Consensus size: 164
1720968 TAACATGCGC
* * * * * *
1720978 TTGAGCTGAGTGGAATCGAACTCGAAGATATTTGTTGACATATAACCCTTCTCGCCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTAT
* * * * * * * * * *
1721043 GTTGCAAATTGGATATG-CTTATGAGTTGAATATAATCGAACTCAAAGGTCTTTAGTTGGCAGAC
63 GCTGCAAA-T-AATGTGCCTT-TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAAT
* *
1721107 AACCCTTCTTACCTTAAGCTATGTTGCAAATGATGTGCCT
125 AACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
* * * *
1721147 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCATTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTAT
* * * * * *
1721212 GCTGCAAATGATGTGCCTTTGAGCTGAGTGCAATCGAAATCGAAGGTTTTTTGTTGACAGATAAC
63 GCTGCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAAC
* * ** * *
1721277 CCTTCTAGCCTTGAGTTATACTGTAAATGATGTACCT
128 CCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
* * *
1721314 TTGAGCTGAGTGCAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTTTTTCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTA
* * * * *
1721379 TGCTGCAAATATTGTGTCTTTGAGCTGAGTGTAATCGAACTCGAACGTCTTTTGTTGGCAGATAG
62 TGCTGCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAA
1721444 CCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
127 CCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
* * * *
1721482 TTGAGCTTAGTGCAATCGAACTCGAAGGTCTTTAGCAGATAACCCTTCTTGCCTTGAGCTATGTT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
* * * *
1721547 GCAAATAATGTGCCTTTAAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCAAATATCCAT
66 GCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCT
* *
1721612 TCTTACCTTGAGCTATGTTGCAAATGATGTACCT
131 TCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
* * *
1721646 TTGAGCTGAGTATAATCGAACTCGAAGGTCTTTGGCAGATAATCCTTCTTGCCTTGAGATATGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
* * * *
1721711 GCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGAAAATATCCCT
66 GCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCT
* *
1721776 TCTTGCCTTGAGCTATGTTACAAATGATGTGCTT
131 TCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
* *
1721810 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTTTTGCCTTAAGCTATGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
* * * * * **
1721875 ACAAATGATGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTATTGGAAAATAATACT
66 GCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCT
* * * *
1721940 TCTTGCCTTGAGATATATTGCAAAAGATGTGTCT
131 TCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
*
1721974 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAATCCTTCTTGCCTTGAGCTATGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
*
1722039 GCAAATAATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGG-AAGA-AAGCC
66 GCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAA-ATAA-CC
*
1722098 CTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCT
129 CTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
* *
1722134 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTTGCCTGGAGCTATGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
* * *
1722199 GTAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGACAACCCT
66 GCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCT
* * *
1722260 TCTCGCTTTGAGCTATGCTGCAAATGATGTGCCT
131 TCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
* *
1722294 TTGTGCTGAGTGTAATCAAACTCGAAGGTCTTT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT
1722327 TGTTAGAGGT
Statistics
Matches: 1049, Mismatches: 122, Indels: 27
0.88 0.10 0.02
Matches are distributed among these distances:
159 4 0.00
160 213 0.20
161 4 0.00
164 517 0.49
165 1 0.00
167 98 0.09
168 142 0.14
169 66 0.06
170 1 0.00
171 3 0.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (164 bp):
TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCT
GCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCT
TCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
Found at i:1723353 original size:99 final size:99
Alignment explanation
Indices: 1723181--1723377 Score: 324
Period size: 99 Copynumber: 2.0 Consensus size: 99
1723171 GGACGAATCA
* *
1723181 ATATTATAATCACTTTTATCAGGCTAGCTGAATATTATCCATAAAGTTAGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTAGGGCGTTTAACCAATT
*
1723246 GCTTTAGAGGGACAACTCAAGCTTTATTGTATAG
66 GCTTTAGAGGGAAAACTCAAGCTTTATTGTATAG
* *
1723280 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTAGGGCGTTTAACCAATT
*
1723345 G-TTCTAGAGGGAAAATTCAAGCTTTATTGTATA
66 GCTT-TAGAGGGAAAACTCAAGCTTTATTGTATA
1723378 AATAATATTA
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 2 0.02
99 89 0.98
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTAGGGCGTTTAACCAATT
GCTTTAGAGGGAAAACTCAAGCTTTATTGTATAG
Found at i:1725433 original size:118 final size:118
Alignment explanation
Indices: 1725225--1725460 Score: 427
Period size: 118 Copynumber: 2.0 Consensus size: 118
1725215 CCGACATTCA
* * * *
1725225 TAGTCCTATCCAAAATGGGATCCACTAGTGGCTTCTCTCCATGGATCACAACGTTTACCATGTCC
1 TAGTCCCATCCAAAATGGGATCAACTAGTGGCTTCGCTCCATGGATCACAACATTTACCATGTCC
*
1725290 ATCAACTTAGCCATTTTTTCTCTTGATTCATTCTGAAATCTTCTTGCTTGATC
66 ATCAACTTAGCCATTTGTTCTCTTGATTCATTCTGAAATCTTCTTGCTTGATC
1725343 TAGTCCCATCCAAAATGGGATCAACTAGTGGCTTCGCTCCATGGATCACAACATTTACCATGTCC
1 TAGTCCCATCCAAAATGGGATCAACTAGTGGCTTCGCTCCATGGATCACAACATTTACCATGTCC
1725408 ATCAACTTAGCCATTTGTTCTCTTGATTCATTCTGAAATCTTCTTGCTTGATC
66 ATCAACTTAGCCATTTGTTCTCTTGATTCATTCTGAAATCTTCTTGCTTGATC
1725461 GATCATCTCC
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (118 bp):
TAGTCCCATCCAAAATGGGATCAACTAGTGGCTTCGCTCCATGGATCACAACATTTACCATGTCC
ATCAACTTAGCCATTTGTTCTCTTGATTCATTCTGAAATCTTCTTGCTTGATC
Found at i:1727481 original size:27 final size:27
Alignment explanation
Indices: 1727447--1727520 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
1727437 AACATGTTAG
*
1727447 ATAG-GAAAAAAATAAAAATAAATAAA
1 ATAGAGAAAAAAATAAAAACAAATAAA
** * *
1727473 ATAGAGAAAGTAAGAAAAACAAATGAA
1 ATAGAGAAAAAAATAAAAACAAATAAA
*
1727500 ATAAAGAAAAGGAAATAAAAA
1 ATAGAGAAAA--AAATAAAAA
1727521 GATTAAAAAG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
26 4 0.11
27 25 0.69
29 7 0.19
ACGTcount: A:0.73, C:0.01, G:0.14, T:0.12
Consensus pattern (27 bp):
ATAGAGAAAAAAATAAAAACAAATAAA
Found at i:1727716 original size:3 final size:3
Alignment explanation
Indices: 1727710--1727776 Score: 66
Period size: 3 Copynumber: 22.0 Consensus size: 3
1727700 AAACATATAG
* * *
1727710 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAGG ACAC AA- AA- AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T A-AT AAT AAT AAT AAT
1727755 AAAT AAT AAT AAT AAT AAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT
1727777 CGTATAATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 47 0.84
4 4 0.07
5 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1727894 original size:36 final size:38
Alignment explanation
Indices: 1727848--1727923 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 38
1727838 ATATATACAT
*
1727848 ATATAAAATATATAGAAAAA-A-TAATGAT-ATAAAAA
1 ATATAAAATATATAGAAAAAGAGTAATAATAATAAAAA
1727883 ATATAACAATATATAGAAAAAGAGTAATAATAATAAAAA
1 ATATAA-AATATATAGAAAAAGAGTAATAATAATAAAAA
1727922 AT
1 AT
1727924 GGAAAAATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
35 6 0.17
36 14 0.39
37 1 0.03
38 6 0.17
39 9 0.25
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (38 bp):
ATATAAAATATATAGAAAAAGAGTAATAATAATAAAAA
Found at i:1729211 original size:23 final size:23
Alignment explanation
Indices: 1729180--1729226 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1729170 GGTGTTTACA
1729180 GGTTATATTCAGGATTCATAATG
1 GGTTATATTCAGGATTCATAATG
* *
1729203 GGTTGTATTCTGGATTCATAATG
1 GGTTATATTCAGGATTCATAATG
1729226 G
1 G
1729227 ATCGATTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (23 bp):
GGTTATATTCAGGATTCATAATG
Found at i:1730082 original size:3 final size:3
Alignment explanation
Indices: 1730074--1730102 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1730064 AAAATGAATA
1730074 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1730103 AGATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1730108 original size:12 final size:11
Alignment explanation
Indices: 1730063--1730115 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 11
1730053 GACAAGAAAG
1730063 TAAAATGAATAAA
1 TAAAAT-AAT-AA
1730076 TAATAATAATAA
1 TAA-AATAATAA
1730088 TAATAATAATAA
1 TAA-AATAATAA
*
1730100 TAAAGATAAAAA
1 TAAA-ATAATAA
1730112 TAAA
1 TAAA
1730116 TAAAAAGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
11 1 0.03
12 27 0.73
13 6 0.16
14 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:1731241 original size:2 final size:2
Alignment explanation
Indices: 1731236--1731270 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1731226 TTTCAAAAAC
1731236 TA TA TA T- TA TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1731271 TAAATAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1731261 original size:22 final size:20
Alignment explanation
Indices: 1731152--1731269 Score: 82
Period size: 22 Copynumber: 5.7 Consensus size: 20
1731142 AAATGAATAA
*
1731152 AATATA-ATAAATAATATAT
1 AATATATATATATAATATAT
1731171 AATACTATACTATATAATATAT
1 AATA-TATA-TATATAATATAT
* * *
1731193 AAATATATTTTTTTAACTATAT
1 -AATATATATATATAA-TATAT
* *
1731215 AATATATATATTTTCAA-AAACT
1 AATATATATA-TAT-AATATA-T
1731237 -ATATATTATATATAATATAT
1 AATATA-TATATATAATATAT
1731257 -ATATATATATATA
1 AATATATATATATA
1731270 TTAAATAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 20
0.73 0.08 0.18
Matches are distributed among these distances:
19 12 0.15
20 10 0.12
21 25 0.31
22 27 0.34
23 6 0.08
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATATATATATAATATAT
Found at i:1733410 original size:12 final size:12
Alignment explanation
Indices: 1733393--1733417 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1733383 TAATGCTATA
1733393 ATTTAAATTTTC
1 ATTTAAATTTTC
1733405 ATTTAAATTTTC
1 ATTTAAATTTTC
1733417 A
1 A
1733418 AGATAAACTA
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTAAATTTTC
Found at i:1733563 original size:29 final size:29
Alignment explanation
Indices: 1733488--1733564 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
1733478 GTAAATTATA
*
1733488 AATTAACTCATTGAA-TTTTATTCTTTTC
1 AATTTACTCATTGAACTTTTATTCTTTTC
* * *
1733516 TATTTCACTTATTGTACTTTTAATT-TTTTC
1 AATTT-ACTCATTGAACTTTT-ATTCTTTTC
1733546 AATTTACTCATTGAACTTT
1 AATTTACTCATTGAACTTT
1733565 AACATTGTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 3 0.08
29 20 0.51
30 13 0.33
31 3 0.08
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.56
Consensus pattern (29 bp):
AATTTACTCATTGAACTTTTATTCTTTTC
Found at i:1743066 original size:21 final size:21
Alignment explanation
Indices: 1743033--1743072 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1743023 AGTCTAAATG
* *
1743033 TACCAAATGTTTTACTAAACA
1 TACCAAATCTTTTAATAAACA
*
1743054 TACCAATTCTTTTAATAAA
1 TACCAAATCTTTTAATAAA
1743073 ATAATAGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (21 bp):
TACCAAATCTTTTAATAAACA
Found at i:1743420 original size:18 final size:18
Alignment explanation
Indices: 1743388--1743431 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1743378 AGTGACATAT
1743388 TAAAATA-TATTATTAAC
1 TAAAATATTATTATTAAC
* *
1743405 TAAAATATTCTTATTAAG
1 TAAAATATTATTATTAAC
1743423 T-AAATATTA
1 TAAAATATTA
1743432 AATAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAAATATTATTATTAAC
Found at i:1748240 original size:17 final size:17
Alignment explanation
Indices: 1748202--1748247 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
1748192 ACTTATTGAA
*
1748202 AATAAAAAATAAAGATGT
1 AATAAAAAATAAAGA-GC
1748220 AATAAAAAATAAAG-GAC
1 AATAAAAAATAAAGAG-C
1748237 AATAAAAAATA
1 AATAAAAAATA
1748248 TCAACGATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 11 0.42
18 14 0.54
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (17 bp):
AATAAAAAATAAAGAGC
Found at i:1754381 original size:7 final size:7
Alignment explanation
Indices: 1754371--1754427 Score: 87
Period size: 7 Copynumber: 8.1 Consensus size: 7
1754361 ATTGTTTGAC
1754371 GAACGTT
1 GAACGTT
1754378 GAACGTT
1 GAACGTT
1754385 GAACGTT
1 GAACGTT
1754392 GAACGTT
1 GAACGTT
1754399 GAACGTT
1 GAACGTT
*
1754406 GAATGTT
1 GAACGTT
*
1754413 GAATGTT
1 GAACGTT
*
1754420 GAAAGTT
1 GAACGTT
1754427 G
1 G
1754428 TGTTTCTCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (7 bp):
GAACGTT
Found at i:1757664 original size:2 final size:2
Alignment explanation
Indices: 1757659--1757698 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1757649 GTGTTGTGTG
1757659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1757699 GAATATAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1760129 original size:17 final size:17
Alignment explanation
Indices: 1760107--1760198 Score: 184
Period size: 17 Copynumber: 5.4 Consensus size: 17
1760097 TCCCATTTAT
1760107 CATTTAAATTTAAAACA
1 CATTTAAATTTAAAACA
1760124 CATTTAAATTTAAAACA
1 CATTTAAATTTAAAACA
1760141 CATTTAAATTTAAAACA
1 CATTTAAATTTAAAACA
1760158 CATTTAAATTTAAAACA
1 CATTTAAATTTAAAACA
1760175 CATTTAAATTTAAAACA
1 CATTTAAATTTAAAACA
1760192 CATTTAA
1 CATTTAA
1760199 CACTTCTTCC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 75 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (17 bp):
CATTTAAATTTAAAACA
Found at i:1766401 original size:22 final size:21
Alignment explanation
Indices: 1766359--1766398 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1766349 GAGTTTATTT
*
1766359 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1766380 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1766399 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1769079 original size:19 final size:20
Alignment explanation
Indices: 1769048--1769085 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1769038 TACTTCAACT
1769048 ATCATTTTATTA-TGTTTTG
1 ATCATTTTATTATTGTTTTG
1769067 ATCA-TTTACTTATTGTTTT
1 ATCATTTTA-TTATTGTTTT
1769086 TTAAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.63
Consensus pattern (20 bp):
ATCATTTTATTATTGTTTTG
Found at i:1777505 original size:39 final size:39
Alignment explanation
Indices: 1777450--1777529 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
1777440 CTAAAGGTAA
*
1777450 GTGAATGTAAAGTTGATAGTTTCTTGTATTTTTGGTTTG
1 GTGAATGTAAAATTGATAGTTTCTTGTATTTTTGGTTTG
*
1777489 GTGAATGTAAAATTGATGGTTTCTTGTATTTTTGGTTTG
1 GTGAATGTAAAATTGATAGTTTCTTGTATTTTTGGTTTG
1777528 GT
1 GT
1777530 TTTTAGTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.51
Consensus pattern (39 bp):
GTGAATGTAAAATTGATAGTTTCTTGTATTTTTGGTTTG
Found at i:1778794 original size:24 final size:24
Alignment explanation
Indices: 1778718--1778817 Score: 107
Period size: 23 Copynumber: 4.2 Consensus size: 24
1778708 CAGTTAAGGG
* *
1778718 TTCTACGCGGTCATTCGTGACAAA
1 TTCTACGTGGTCATTCGGGACAAA
* *
1778742 -TCTATGTGGTCTTTCGGGAC-AA
1 TTCTACGTGGTCATTCGGGACAAA
1778764 TTCTACGTGGTGC-TTCGGGACAAA
1 TTCTACGTGGT-CATTCGGGACAAA
* * *
1778788 TTCTACGTGGTCCTTTGAGACAAA
1 TTCTACGTGGTCATTCGGGACAAA
1778812 TTCTAC
1 TTCTAC
1778818 ATGGCACTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
22 2 0.03
23 34 0.52
24 29 0.45
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (24 bp):
TTCTACGTGGTCATTCGGGACAAA
Found at i:1778828 original size:48 final size:46
Alignment explanation
Indices: 1778731--1778829 Score: 110
Period size: 48 Copynumber: 2.1 Consensus size: 46
1778721 TACGCGGTCA
* * * * **
1778731 TTCGTGACAAATCTATGTGGTCTTTCGGGACAATTCTACGTGGTGC
1 TTCGGGACAAATCTACGTGGTCTTTCGAGACAATTCTACATGGCAC
1778777 TTCGGGACAAATTCTACGTGGTCCTTT-GAGACAAATTCTACATGGCAC
1 TTCGGGACAAA-TCTACGTGGT-CTTTCGAGAC-AATTCTACATGGCAC
1778825 TTCGG
1 TTCGG
1778830 TGCAATTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
46 10 0.23
47 13 0.30
48 21 0.48
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.32
Consensus pattern (46 bp):
TTCGGGACAAATCTACGTGGTCTTTCGAGACAATTCTACATGGCAC
Found at i:1788246 original size:21 final size:21
Alignment explanation
Indices: 1788220--1788259 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1788210 CAGAACCCCA
*
1788220 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1788241 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1788260 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1792154 original size:22 final size:21
Alignment explanation
Indices: 1792112--1792151 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1792102 GAGTTTGTTT
*
1792112 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1792133 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1792152 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1794445 original size:24 final size:24
Alignment explanation
Indices: 1794395--1794473 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 24
1794385 TCGAGGGTTT
* *
1794395 TACGCGGTCATTC--GGGACAATTT
1 TACGTGGTCATTCGGGGGA-AATTC
1794418 TACGTGGTCATTCGGGGGAAATTC
1 TACGTGGTCATTCGGGGGAAATTC
* **
1794442 TACGAT-GTAATTCGGGAAAAATTC
1 TACG-TGGTCATTCGGGGGAAATTC
*
1794466 TACATGGT
1 TACGTGGT
1794474 ACTTCGGTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
23 13 0.28
24 28 0.61
25 5 0.11
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (24 bp):
TACGTGGTCATTCGGGGGAAATTC
Found at i:1796989 original size:34 final size:32
Alignment explanation
Indices: 1796925--1796992 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 32
1796915 CCTTACAGAC
*
1796925 TCCCTAGTTTTTCCGGGATAAACTAAAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAAAACCTT
* * *
1796957 TCCCTAGATTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAAAACCTT
1796991 TC
1 TC
1796993 TCCTTTACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 7 0.23
33 5 0.17
34 18 0.60
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAAAACCTT
Found at i:1799729 original size:48 final size:47
Alignment explanation
Indices: 1799672--1799769 Score: 112
Period size: 48 Copynumber: 2.0 Consensus size: 47
1799662 GAAAACAAAT
* *
1799672 AAAATGATAA-AAT-AAATAAACATAACAT-AAAACGAAAAAATGAATAAG
1 AAAACGATAAGAATAAAATAAA-A-AACATAAAAAAGAAAAAA--AATAAG
1799720 AAAACGATAAGAATAAAAATAAAAAACATAAAAAAGAAAAAAAATAAG
1 AAAACGATAAGAAT-AAAATAAAAAACATAAAAAAGAAAAAAAATAAG
1799768 AA
1 AA
1799770 TGAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
48 17 0.39
49 8 0.18
50 12 0.27
51 7 0.16
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.13
Consensus pattern (47 bp):
AAAACGATAAGAATAAAATAAAAAACATAAAAAAGAAAAAAAATAAG
Found at i:1799759 original size:16 final size:16
Alignment explanation
Indices: 1799734--1799787 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1799724 CGATAAGAAT
* *
1799734 AAAAATAAAAAACATA
1 AAAAAGAAAAAAAATA
1799750 AAAAAGAAAAAAAATA
1 AAAAAGAAAAAAAATA
* * *
1799766 AGAATGAAAACAAAACA
1 AAAAAGAAAA-AAAATA
1799783 AAAAA
1 AAAAA
1799788 ATATGGAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.07
Consensus pattern (16 bp):
AAAAAGAAAAAAAATA
Found at i:1802246 original size:43 final size:43
Alignment explanation
Indices: 1802182--1802300 Score: 157
Period size: 43 Copynumber: 2.8 Consensus size: 43
1802172 GAGTTTGCAT
* * * * *
1802182 GATATCCTTCGTTGTGAAGTTGAAATCGTGGATTTTTTGGCAC
1 GATATCCTCCGTCGTGGAGTTGAAATCGTGGATTTATGGGCAC
* *
1802225 GATATCCTCCGTCGTGGAGTTGAAATCATGGATTTATGGGTAC
1 GATATCCTCCGTCGTGGAGTTGAAATCGTGGATTTATGGGCAC
* *
1802268 GATATCCTCGGTCATGGAGTTGAAATCGTGGAT
1 GATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1802301 AACCCCTTCG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (43 bp):
GATATCCTCCGTCGTGGAGTTGAAATCGTGGATTTATGGGCAC
Found at i:1803241 original size:8 final size:8
Alignment explanation
Indices: 1803228--1803271 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
1803218 ATTATTTTAC
1803228 TTTTTCTT
1 TTTTTCTT
1803236 TTTTTCTT
1 TTTTTCTT
*
1803244 TTGTT-TT
1 TTTTTCTT
**
1803251 TTTTAATT
1 TTTTTCTT
1803259 TTTTTCTT
1 TTTTTCTT
1803267 TTTTT
1 TTTTT
1803272 TTTCAATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 5 0.17
8 25 0.83
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Done.