Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004096.1 Hibiscus syriacus cultivar Beakdansim tig00008957_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: 961865
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:418698 original size:24 final size:24
Alignment explanation
Indices: 418671--418736 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
418661 TTTTTGTCCC
*
418671 TTTTTCTTTTTAATTTTTG-TTCT
1 TTTTTTTTTTTAATTTTTGTTTCT
* **
418694 TTTTTTGTTCTTCTTTTTTGTTTCT
1 TTTTTT-TTTTTAATTTTTGTTTCT
* *
418719 TTTCTTTTTTTGATTTTT
1 TTTTTTTTTTTAATTTTT
418737 CCCTTTTTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
23 5 0.15
24 19 0.58
25 9 0.27
ACGTcount: A:0.05, C:0.09, G:0.06, T:0.80
Consensus pattern (24 bp):
TTTTTTTTTTTAATTTTTGTTTCT
Found at i:418709 original size:30 final size:30
Alignment explanation
Indices: 418674--418730 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
418664 TTGTCCCTTT
418674 TTCTTTTTAATTT-TTGTTCTTTTTTTGTTC
1 TTCTTTTTAATTTCTT-TTCTTTTTTTGTTC
**
418704 TTCTTTTTTGTTTCTTTTCTTTTTTTG
1 TTCTTTTTAATTTCTTTTCTTTTTTTG
418731 ATTTTTCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.04, C:0.11, G:0.07, T:0.79
Consensus pattern (30 bp):
TTCTTTTTAATTTCTTTTCTTTTTTTGTTC
Found at i:418712 original size:16 final size:15
Alignment explanation
Indices: 418672--418729 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 15
418662 TTTTGTCCCT
418672 TTTTCTTTTTAATTTT-
1 TTTTCTTTTT--TTTTC
*
418688 TGTTCTTTTTTTGTTC
1 TTTTCTTTTTTT-TTC
418704 --TTCTTTTTTGTTTC
1 TTTTCTTTTTT-TTTC
418718 TTTTCTTTTTTT
1 TTTTCTTTTTTT
418730 GATTTTTCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
14 14 0.39
15 4 0.11
16 18 0.50
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTTTTTC
Found at i:426794 original size:19 final size:19
Alignment explanation
Indices: 426761--426797 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
426751 TGCAGATGAT
426761 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
426780 GGAAA-AAAATAAAA-AGA
1 GGAAATAAAATAAAAGAGA
426797 G
1 G
426798 TTAGTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:428111 original size:13 final size:13
Alignment explanation
Indices: 428095--428148 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 13
428085 CATAATGAAA
*
428095 ATAAATAAATAGT
1 ATAAATAAATAAT
428108 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
428122 A-AAATAAA-AA-
1 ATAAATAAATAAT
*
428132 ATATATAAA-AAT
1 ATAAATAAATAAT
428144 ATAAA
1 ATAAA
428149 AATGTATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 1 0.03
11 10 0.29
12 7 0.20
13 10 0.29
14 7 0.20
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:428142 original size:17 final size:16
Alignment explanation
Indices: 428114--428151 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
428104 TAGTATAAAT
428114 AAAATAATAAAATA-A
1 AAAATAATAAAATATA
428129 AAAATATATAAAAATATA
1 AAAATA-AT-AAAATATA
428147 AAAAT
1 AAAAT
428152 GTATGTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 2 0.10
17 6 0.30
18 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAATAAAATATA
Found at i:428282 original size:2 final size:2
Alignment explanation
Indices: 428275--428301 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
428265 TGAAGTAAGA
428275 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
428302 CGTTAGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:428364 original size:2 final size:2
Alignment explanation
Indices: 428359--428385 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
428349 TAAAAAAATA
428359 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
428386 ATAATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:428462 original size:8 final size:9
Alignment explanation
Indices: 428451--428510 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 9
428441 AATAAATAAA
428451 ATATAAT-T
1 ATATAATAT
428459 ATAT-ATAT
1 ATATAATAT
428467 ATAT-ATAT
1 ATATAATAT
428475 ATAT-ATAT
1 ATATAATAT
428483 ATATATATAT
1 ATATA-ATAT
*
428493 TTATACATAT
1 ATATA-ATAT
*
428503 AAATAATA
1 ATATAATA
428511 AGGGTTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
7 2 0.04
8 25 0.56
9 3 0.07
10 15 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATAATAT
Found at i:428465 original size:2 final size:2
Alignment explanation
Indices: 428458--428503 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
428448 AAAATATAAT
* *
428458 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
428500 TA TA
1 TA TA
428504 AATAATAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:430003 original size:17 final size:15
Alignment explanation
Indices: 429981--430020 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
429971 TGGGGTTATG
429981 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
429997 CTTAAATATTATAATA
1 -TTAAATATTATAAAA
430013 TTAAATAT
1 TTAAATAT
430021 GCATGTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:430179 original size:22 final size:22
Alignment explanation
Indices: 430140--430181 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
430130 TTTAAAAAGA
*
430140 ATAAATTCTACTATTTATAAAT
1 ATAAATTCGACTATTTATAAAT
430162 ATAAATTCGACT-TGTTATAA
1 ATAAATTCGACTAT-TTATAA
430182 GTTCAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (22 bp):
ATAAATTCGACTATTTATAAAT
Found at i:430180 original size:16 final size:16
Alignment explanation
Indices: 430161--430203 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
430151 TATTTATAAA
430161 TATAAATTCGACT-TGT
1 TATAAATTCGACTAT-T
* *
430177 TATAAGTTCAACTATT
1 TATAAATTCGACTATT
430193 TATAAATTCGA
1 TATAAATTCGA
430204 TTTAAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (16 bp):
TATAAATTCGACTATT
Found at i:430219 original size:20 final size:19
Alignment explanation
Indices: 430190--430230 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
430180 AAGTTCAACT
430190 ATTTATAAATTCGATTTAA
1 ATTTATAAATTCGATTTAA
*
430209 ATTTAATAAATTCTATTTAA
1 ATTT-ATAAATTCGATTTAA
430229 AT
1 AT
430231 ATTTAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTATAAATTCGATTTAA
Found at i:430244 original size:11 final size:11
Alignment explanation
Indices: 430230--430280 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
430220 TCTATTTAAA
*
430230 TATTTAATCAT
1 TATTAAATCAT
*
430241 TATTAAATAAT
1 TATTAAATCAT
430252 TATTAGTAATCAT
1 TATTA--AATCAT
*
430265 TATTAAATTAT
1 TATTAAATCAT
430276 TATTA
1 TATTA
430281 GTAATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 24 0.71
13 10 0.29
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (11 bp):
TATTAAATCAT
Found at i:430261 original size:24 final size:24
Alignment explanation
Indices: 430234--430325 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
430224 TTTAAATATT
430234 TAATCATTATTAAATAATTATTAG
1 TAATCATTATTAAATAATTATTAG
*
430258 TAATCATTATTAAATTATTATTAG
1 TAATCATTATTAAATAATTATTAG
* * *
430282 TAATTATTA-TAATTTAATTATTAC
1 TAATCATTATTAA-ATAATTATTAG
* * *
430306 TAATTATTACTAAATCATTA
1 TAATCATTATTAAATAATTA
430326 ATATCAAATC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.05
24 53 0.90
25 3 0.05
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.49
Consensus pattern (24 bp):
TAATCATTATTAAATAATTATTAG
Found at i:430273 original size:21 final size:22
Alignment explanation
Indices: 430234--430295 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
430224 TTTAAATATT
430234 TAATCATTATTAAATAATTATTAG
1 TAATCATTATT--ATAATTATTAG
*
430258 TAATCATTATTA-AATTATTAT
1 TAATCATTATTATAATTATTAG
* *
430279 TAGTAATTATTATAATT
1 TAATCATTATTATAATT
430296 TAATTATTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 18 0.53
22 5 0.15
24 11 0.32
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (22 bp):
TAATCATTATTATAATTATTAG
Found at i:430299 original size:14 final size:15
Alignment explanation
Indices: 430282--430310 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
430272 TTATTATTAG
430282 TAATTATTA-TAATT
1 TAATTATTACTAATT
430296 TAATTATTACTAATT
1 TAATTATTACTAATT
430311 ATTACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATTACTAATT
Found at i:430355 original size:21 final size:22
Alignment explanation
Indices: 430316--430360 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
430306 TAATTATTAC
*
430316 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATAAT
430338 TAAAT-ATTAATAAT-AAATAAT
1 TAAATCATTAAT-ATCAAATAAT
430359 TA
1 TA
430361 TTAATAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATCATTAATATCAAATAAT
Found at i:440131 original size:2 final size:2
Alignment explanation
Indices: 440124--440177 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
440114 CTAAATAATA
440124 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
440166 AT AT AT AT AT AT
1 AT AT AT AT AT AT
440178 TCGTGTCCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:444502 original size:37 final size:37
Alignment explanation
Indices: 444430--444622 Score: 146
Period size: 37 Copynumber: 5.1 Consensus size: 37
444420 TGAAAATACG
* *
444430 TATATAATATATGGTTTTTAAAACACTTTTAAAAAACTA
1 TATATAATATAT-ATTTTTAAAACA-TTTTTAAAAACTA
* *
444469 TATATTATATATATTTTCAAAACATTTTT-AAAA--A
1 TATATAATATATATTTTTAAAACATTTTTAAAAACTA
* * *
444503 TATATAATATGTAATTTTTGAAAAAATATTTTGAAAAC-A
1 TATATAATATAT-ATTTTT-AAAACAT-TTTTAAAAACTA
* * * *
444542 TA-A-AACATATAATTTTTAGAGCATTTTTGAAAACTTA
1 TATATAATATAT-ATTTTTAAAACATTTTTAAAAAC-TA
*
444579 TATATAATATATAATTTTTTAAAACATTTTTTAAAAATTA
1 TATATAATATAT-A-TTTTTAAAACA-TTTTTAAAAACTA
444619 TATA
1 TATA
444623 ATTTTTAAAA
Statistics
Matches: 125, Mismatches: 18, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
34 11 0.09
35 15 0.12
36 14 0.11
37 23 0.18
38 16 0.13
39 22 0.18
40 15 0.12
41 9 0.07
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATAATATATATTTTTAAAACATTTTTAAAAACTA
Found at i:444596 original size:39 final size:38
Alignment explanation
Indices: 444430--444624 Score: 172
Period size: 38 Copynumber: 5.2 Consensus size: 38
444420 TGAAAATACG
** **
444430 TATATAATATATGGTTTTTAAAACACTTTTAAAAAACTA
1 TATATAATATATAATTTTTAAAACA-TTTTTGAAAACTA
* *
444469 TATATTATATAT-ATTTTCAAAACATTTTT-AAAA--A
1 TATATAATATATAATTTTTAAAACATTTTTGAAAACTA
* *
444503 TATATAATATGTAATTTTTGAAAAAATATTTTGAAAAC-A
1 TATATAATATATAATTTTT-AAAACAT-TTTTGAAAACTA
* * *
444542 TA-A-AACATATAATTTTTAGAGCATTTTTGAAAACTTA
1 TATATAATATATAATTTTTAAAACATTTTTGAAAAC-TA
* *
444579 TATATAATATATAATTTTTTAAAACATTTTTTAAAAAT-
1 TATATAATATATAA-TTTTTAAAACATTTTTGAAAACTA
444617 TATATAAT
1 TATATAAT
444625 TTTTAAAAGA
Statistics
Matches: 128, Mismatches: 18, Indels: 21
0.77 0.11 0.13
Matches are distributed among these distances:
34 11 0.09
35 15 0.12
36 14 0.11
37 23 0.18
38 24 0.19
39 23 0.18
40 18 0.14
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATAATATATAATTTTTAAAACATTTTTGAAAACTA
Found at i:444647 original size:32 final size:31
Alignment explanation
Indices: 444586--444686 Score: 125
Period size: 32 Copynumber: 3.2 Consensus size: 31
444576 TTATATATAA
*
444586 TATATAATTTTTTAAAACATTTTTTAAAAAT
1 TATATAATTTTTAAAAACATTTTTTAAAAAT
444617 TATATAATTTTTAAAAGAACA-TTTTTAAAAAT
1 TATATAATTTTT-AAA-AACATTTTTTAAAAAT
* *
444649 TAT-TAGTTTTTTGAAAAACATTTTTTAAAACT
1 TATATA-ATTTTT-AAAAACATTTTTTAAAAAT
444681 TATATA
1 TATATA
444687 TAGTATATAG
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
31 18 0.30
32 37 0.61
33 6 0.10
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (31 bp):
TATATAATTTTTAAAAACATTTTTTAAAAAT
Found at i:444756 original size:13 final size:13
Alignment explanation
Indices: 444738--444763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
444728 ATATTATATA
444738 GTTTTTATTTATT
1 GTTTTTATTTATT
444751 GTTTTTATTTATT
1 GTTTTTATTTATT
444764 ATTATTCACC
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:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTTATTTATT
Found at i:448196 original size:19 final size:19
Alignment explanation
Indices: 448162--448206 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
448152 ATTTAGACAT
448162 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
448180 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
448199 TTTGCATT
1 TTTGCATT
448207 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:451508 original size:165 final size:165
Alignment explanation
Indices: 451266--452355 Score: 1663
Period size: 165 Copynumber: 6.6 Consensus size: 165
451256 ACCTGCCACC
* * *
451266 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTACAGAATAGCTTAAGTCGA
1 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
*
451330 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACA
65 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
* * *
451395 GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
130 GCATAACTTAAGTCTAGAAGGGTTATCTGTAACCAA
451431 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* * *
451496 AAAGGCTATCTGCCAAAGACCCCCAAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
66 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
* *
451561 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-A
131 CATAACTTAAGTCTAGAAGGGTTATCTG-TAACCAA
*
451596 AAGACCTTTGAGTTCGACTACGCTCAGCGCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAGACCTTTGAGTTCGACTACGCTCAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
* *
451660 GAAGGGCTATCTGCCAAAGACCCCCAAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTGCA
65 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
* *
451725 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-A
130 GCATAACTTAAGTCTAGAAGGGTTATCTG-TAACCAA
* * * *
451761 AAGACCTTTGAGCTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGAATAACTTAAGTCAA
1 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
*
451825 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGCA
65 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
* * * * *
451890 GCACAACTTAAGTCTACAAGGGTTGTTTGCCAA-CAA
130 GCATAACTTAAGTCTAGAAGGGTTATCTG-TAACCAA
* *
451926 AAGACCTTTGAGTTTGACTACGATCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
*
451991 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAG
66 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
* * *
452056 CATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
131 CATAACTTAAGTCTAGAAGGGTTATCTGTAACCAA
* *
452091 AGGACCTTTGAGTTCAACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* *
452156 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGTAG
66 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
* *
452221 CACAACTTAAGTCTAGAAGGGTTGTCTGCTAA-CAA
131 CATAACTTAAGTCTAGAAGGGTTATCTG-TAACCAA
** *
452256 AAGACCTTTGAGTTCGACTACATTCAGCTCAACGGCACAACATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* **
452321 AAGGGCTATCTGCTAAAGACCTTCGAGTTCGATTA
66 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
452356 TATTCAACTT
Statistics
Matches: 852, Mismatches: 65, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
164 8 0.01
165 836 0.98
166 8 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (165 bp):
AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
CATAACTTAAGTCTAGAAGGGTTATCTGTAACCAA
Found at i:453163 original size:31 final size:31
Alignment explanation
Indices: 453125--453225 Score: 116
Period size: 32 Copynumber: 3.2 Consensus size: 31
453115 TTATATATAA
453125 TATATAATTTTTTAAAACATTTTTTAAAAAT
1 TATATAATTTTTTAAAACATTTTTTAAAAAT
* *
453156 TATATAATTTTTAAAAGAACA-TTTTTAAAAAA
1 TATATAATTTTT-TAA-AACATTTTTTAAAAAT
* *
453188 TAT-TAGTTTTTTGAAAAACATTTTTTAAAACT
1 TATATAATTTTTT--AAAACATTTTTTAAAAAT
453220 TATATA
1 TATATA
453226 TAGTATATAG
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
31 23 0.40
32 29 0.50
33 6 0.10
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (31 bp):
TATATAATTTTTTAAAACATTTTTTAAAAAT
Found at i:453295 original size:13 final size:13
Alignment explanation
Indices: 453277--453302 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
453267 ATATTATATA
453277 GTTTTTATTTATT
1 GTTTTTATTTATT
453290 GTTTTTATTTATT
1 GTTTTTATTTATT
453303 ATTATTCACC
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:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTTATTTATT
Found at i:474628 original size:21 final size:21
Alignment explanation
Indices: 474590--474655 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 21
474580 AATTAACAGT
474590 AAAAAATAAGAAGTTATTCATCGA
1 AAAAAATAAG-A--TATTCATCGA
474614 AAAAAATAAGATATTCATCGA
1 AAAAAATAAGATATTCATCGA
*
474635 AAAAAATAAGATAATC-TCGA
1 AAAAAATAAGATATTCATCGA
474655 A
1 A
474656 TGTCTATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 5 0.12
21 25 0.61
23 1 0.02
24 10 0.24
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.23
Consensus pattern (21 bp):
AAAAAATAAGATATTCATCGA
Found at i:479158 original size:18 final size:17
Alignment explanation
Indices: 479135--479174 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
479125 AATTTTATGA
*
479135 AAAAATAATTTATAAAAT
1 AAAAATAAATTAT-AAAT
*
479153 AAAAATAAATTATTAAT
1 AAAAATAAATTATAAAT
479170 AAAAA
1 AAAAA
479175 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATAAATTATAAAT
Found at i:479543 original size:18 final size:19
Alignment explanation
Indices: 479520--479556 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
479510 AAACCTTAAA
479520 TTGTA-TTTTAAAAAAATC
1 TTGTATTTTTAAAAAAATC
479538 TTGTATTTTTAAAAAAATC
1 TTGTATTTTTAAAAAAATC
479557 AACACATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (19 bp):
TTGTATTTTTAAAAAAATC
Found at i:489089 original size:22 final size:23
Alignment explanation
Indices: 489061--489105 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
489051 TCAAATTCTT
489061 GGTTAAAT-TTGACTTTTCAAAA
1 GGTTAAATGTTGACTTTTCAAAA
* *
489083 GGTTAAATGTTGATTTTTTAAAA
1 GGTTAAATGTTGACTTTTCAAAA
489106 ATAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (23 bp):
GGTTAAATGTTGACTTTTCAAAA
Found at i:491890 original size:2 final size:2
Alignment explanation
Indices: 491883--491934 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
491873 CCGGGTCTTA
491883 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
491925 AT AT AT AT AT
1 AT AT AT AT AT
491935 GCATTTTCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493340 original size:20 final size:20
Alignment explanation
Indices: 493317--493355 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
493307 AAATATAAAC
*
493317 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
493337 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
493356 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:494745 original size:3 final size:3
Alignment explanation
Indices: 494737--494834 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
494727 AATATATATT
*
494737 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
494785 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
494833 TA
1 TA
494835 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:495399 original size:113 final size:113
Alignment explanation
Indices: 495153--495824 Score: 1130
Period size: 113 Copynumber: 6.0 Consensus size: 113
495143 AGAATTATGC
* * * * *
495153 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTATTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
495218 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
*
495265 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
495330 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
495378 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
495443 TATGAACTTTCTCTGGGAAAGCTGATCTCTCAAATTATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
*
495491 AAAAGGTTGAACAAATTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
495556 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
495604 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
495669 TATGAACTTTCTCTGGAAAAGCTAATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
495717 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
495782 TATGAACTTTCTCTGGAAAAGCTAATCTTTCAAATGATAGATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATT
495825 TGAATCTTTG
Statistics
Matches: 533, Mismatches: 26, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
112 67 0.13
113 466 0.87
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
Found at i:496873 original size:83 final size:83
Alignment explanation
Indices: 496668--497045 Score: 600
Period size: 83 Copynumber: 4.6 Consensus size: 83
496658 CATACCAAAC
* *
496668 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAACTCAATGCTT
496733 G-TTCTGTCCAACCAGAT
66 GATTCTGTCCAACCAGAT
*
496750 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAACTCAATGCTT
*
496815 GATTCTGTCCAATCAGAT
66 GATTCTGTCCAACCAGAT
*
496833 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAACTCAATGCTT
*
496898 GATTCTGTCCAATCAGAT
66 GATTCTGTCCAACCAGAT
* * *
496916 CAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCCCAATTCAATGCT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCCAAACTCAATGCT
* *
496980 TGATTCTG-CTAAACCAGGT
65 TGATTCTGTC-CAACCAGAT
**
496999 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCAT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
497046 TTGTTCTATT
Statistics
Matches: 276, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
82 66 0.24
83 209 0.76
84 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (83 bp):
CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAACTCAATGCTT
GATTCTGTCCAACCAGAT
Found at i:498118 original size:12 final size:11
Alignment explanation
Indices: 498088--498134 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
498078 CTTGACCCCC
*
498088 TTTCTTTTTCT
1 TTTCTTTTTTT
*
498099 TCTCTTTTTTT
1 TTTCTTTTTTT
*
498110 TTCCTTTTTTT
1 TTTCTTTTTTT
498121 TCTTCTTTTTTT
1 T-TTCTTTTTTT
498133 TT
1 TT
498135 CTTCAAGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:498119 original size:13 final size:12
Alignment explanation
Indices: 498087--498134 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
498077 CCTTGACCCC
*
498087 CTTTCTTTTTCTT
1 CTTT-TTTTTTTT
*
498100 CTCTTTTTTTTTC
1 CT-TTTTTTTTTT
*
498113 CTTTTTTTTCTT
1 CTTTTTTTTTTT
498125 CTTTTTTTTT
1 CTTTTTTTTT
498135 CTTCAAGCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 17 0.59
13 10 0.34
14 2 0.07
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:498126 original size:25 final size:25
Alignment explanation
Indices: 498086--498134 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
498076 ACCTTGACCC
498086 CCTTTCTTTTTCTTCTCTTTTTTTTT
1 CCTTTCTTTTTCTTCT-TTTTTTTTT
498112 CCTTT-TTTTTCTTCTTTTTTTTT
1 CCTTTCTTTTTCTTCTTTTTTTTT
498135 CTTCAAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.35
25 10 0.43
26 5 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (25 bp):
CCTTTCTTTTTCTTCTTTTTTTTTT
Found at i:498127 original size:23 final size:22
Alignment explanation
Indices: 498091--498135 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
498081 GACCCCCTTT
498091 CTTTTTCTTCTCTTTTTTTTTC
1 CTTTTTCTTCTCTTTTTTTTTC
*
498113 CTTTTTTTTCTTCTTTTTTTTTC
1 CTTTTTCTTC-TCTTTTTTTTTC
498136 TTCAAGCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
CTTTTTCTTCTCTTTTTTTTTC
Found at i:498135 original size:13 final size:13
Alignment explanation
Indices: 498087--498138 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
498077 CCTTGACCCC
*
498087 CTTTCTTTTTCTT
1 CTTTTTTTTTCTT
*
498100 CTCTTTTTTT-TT
1 CTTTTTTTTTCTT
*
498112 CCTTTTTTTTCTT
1 CTTTTTTTTTCTT
498125 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
498138 C
1 C
498139 AAGCATAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 10 0.30
13 23 0.70
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTTTTTTTCTT
Found at i:505417 original size:14 final size:15
Alignment explanation
Indices: 505398--505430 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
505388 ATTATTTTTC
505398 AAATTTTA-ATTAAT
1 AAATTTTATATTAAT
*
505412 AAATTTTATCTTAAT
1 AAATTTTATATTAAT
505427 AAAT
1 AAAT
505431 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTATATTAAT
Found at i:509554 original size:20 final size:20
Alignment explanation
Indices: 509531--509569 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
509521 AAATATAAAC
*
509531 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
509551 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
509570 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:510954 original size:3 final size:3
Alignment explanation
Indices: 510946--511025 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
510936 AATATATATT
*
510946 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
510994 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
511026 TGGATAAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:513191 original size:3 final size:3
Alignment explanation
Indices: 513185--513210 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
513175 ATATCTAAAT
513185 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
513211 GTTGTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:513671 original size:2 final size:2
Alignment explanation
Indices: 513662--513692 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
513652 AAATAAAAAA
513662 AT AT -T 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
513693 CGGTCAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:517646 original size:21 final size:21
Alignment explanation
Indices: 517604--517646 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
517594 TGACTGTTAT
* * *
517604 AATATTAATATAGTTGTCCAC
1 AATATTAACATAATGGTCCAC
*
517625 AATATTAACATAATGGTTCAC
1 AATATTAACATAATGGTCCAC
517646 A
1 A
517647 TATGAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (21 bp):
AATATTAACATAATGGTCCAC
Found at i:522131 original size:22 final size:22
Alignment explanation
Indices: 522087--522131 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
522077 TGTTTAAATT
* ***
522087 ATATATTTTTTTTTTATTTTAA
1 ATATATTTTTTGTTTAAAATAA
522109 ATATATTTTTTGTTTAAAATAA
1 ATATATTTTTTGTTTAAAATAA
522131 A
1 A
522132 GTGTTTAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATATATTTTTTGTTTAAAATAA
Found at i:524637 original size:5 final size:5
Alignment explanation
Indices: 524627--524652 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
524617 TGACTTAGAA
524627 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
524653 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:526192 original size:18 final size:18
Alignment explanation
Indices: 526165--526224 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
526155 ACCGGTCACA
*
526165 ACCCGGCCCGGCCCGTTG
1 ACCCGACCCGGCCCGTTG
* * *
526183 ACCCGACCCGACCCATTT
1 ACCCGACCCGGCCCGTTG
526201 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCCG--G-CCCGTTG
526222 ACC
1 ACC
526225 GTTGACCCGA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 24 0.75
21 8 0.25
ACGTcount: A:0.15, C:0.48, G:0.22, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGGCCCGTTG
Found at i:526228 original size:7 final size:8
Alignment explanation
Indices: 526205--526259 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
526195 CCATTTACCC
526205 GACCCGTT
1 GACCCGTT
526213 GACCCGTT
1 GACCCGTT
526221 GA-CCGTT
1 GACCCGTT
*
526228 GACCCGAT
1 GACCCGTT
526236 GACCGTCGTT
1 GACC--CGTT
526246 GACCACTGTT
1 GACC-C-GTT
526256 GACC
1 GACC
526260 AAAACTTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 7 0.17
8 18 0.45
9 1 0.03
10 14 0.35
ACGTcount: A:0.16, C:0.35, G:0.25, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:526228 original size:15 final size:15
Alignment explanation
Indices: 526208--526241 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
526198 TTTACCCGAC
*
526208 CCGTTGACCCGTTGA
1 CCGTTGACCCGATGA
526223 CCGTTGACCCGATGA
1 CCGTTGACCCGATGA
526238 CCGT
1 CCGT
526242 CGTTGACCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
CCGTTGACCCGATGA
Found at i:527551 original size:18 final size:18
Alignment explanation
Indices: 527525--527559 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
527515 TCGAAAGGAC
*
527525 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
527543 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
527560 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:533146 original size:4 final size:4
Alignment explanation
Indices: 533105--533265 Score: 50
Period size: 4 Copynumber: 39.0 Consensus size: 4
533095 ATTTTTCATA
* *
533105 TATT TACT T-TT TATT TTTCT TATTT TATT T-TAT TATT TATT TATT TATT
1 TATT TATT TATT TATT TAT-T TA-TT TATT TAT-T TATT TATT TATT TATT
* ** *
533154 TATT T-TCT T-TT TATT ATTTT TATT CCTT T-CT TATT T-TAT T-TT TATAT
1 TATT TAT-T TATT TATT -TATT TATT TATT TATT TATT TAT-T TATT TAT-T
* * ** *
533201 TAGTTT TATT TATA TATT TATTT TCATT TGTAT T-TT CCTCT TGTT TATT
1 TA--TT TATT TATT TATT TA-TT T-ATT TAT-T TATT TAT-T TATT TATT
533250 TATT TATT TATT TATT
1 TATT TATT TATT TATT
533266 ATGTATATAC
Statistics
Matches: 120, Mismatches: 18, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
3 12 0.10
4 80 0.67
5 22 0.18
6 5 0.04
7 1 0.01
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:533184 original size:60 final size:62
Alignment explanation
Indices: 533112--533234 Score: 164
Period size: 65 Copynumber: 2.0 Consensus size: 62
533102 ATATATTTAC
* *
533112 TTTTTATTTTTCTTATTTTA-TTT-TATTA-TTTATTTATTTATTTATTTTC-TTTTTATTA
1 TTTTTATTTTTCTTATTTTATTTTATATTAGTTTATTTATATATTTATTTTCATTTGTATTA
533170 TTTTTATTCCTTTCTTATTTTATTTTTATATTAGTTTTATTTATATATTTATTTTCATTTGTATT
1 TTTTTATT--TTTCTTATTTTA-TTTTATATTAG-TTTATTTATATATTTATTTTCATTTGTATT
533235 TTCCTCTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
58 8 0.15
60 12 0.22
62 3 0.05
63 5 0.09
65 20 0.36
66 7 0.13
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.74
Consensus pattern (62 bp):
TTTTTATTTTTCTTATTTTATTTTATATTAGTTTATTTATATATTTATTTTCATTTGTATTA
Found at i:533343 original size:9 final size:9
Alignment explanation
Indices: 533328--533485 Score: 64
Period size: 9 Copynumber: 17.6 Consensus size: 9
533318 TCTCGTTATC
533328 TTTATTTTGA
1 TTTATTTT-A
533338 -TTATTTTA
1 TTTATTTTA
533346 TTTATTTT-
1 TTTATTTTA
**
533354 TCTTCGTTT-
1 T-TTATTTTA
533363 TTTATTTT-
1 TTTATTTTA
533371 TCTTCATTTT-
1 T-TT-ATTTTA
* *
533381 TTTATGTTC
1 TTTATTTTA
533390 TTTATTTTA
1 TTTATTTTA
533399 TTTA-TTT-
1 TTTATTTTA
*
533406 TTTATCCTTA
1 TTTAT-TTTA
*
533416 TTTGTTTTTA
1 TTT-ATTTTA
* *
533426 TGTATTTTC
1 TTTATTTTA
*
533435 TTTATCTTAA
1 TTTAT-TTTA
*
533445 TTTCTTTT-
1 TTTATTTTA
* *
533453 TTCATTTATT
1 TTTATTT-TA
533463 TTTATTTCT-
1 TTTATTT-TA
533472 TTTATTTTA
1 TTTATTTTA
533481 TTTAT
1 TTTAT
533486 CTTCATTGCC
Statistics
Matches: 113, Mismatches: 22, Indels: 27
0.70 0.14 0.17
Matches are distributed among these distances:
7 4 0.04
8 21 0.19
9 60 0.53
10 27 0.24
11 1 0.01
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTATTTTA
Found at i:533368 original size:17 final size:17
Alignment explanation
Indices: 533346--533382 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
533336 GATTATTTTA
*
533346 TTTATTTTTCTTCGTTT
1 TTTATTTTTCTTCATTT
533363 TTTATTTTTCTTCATTT
1 TTTATTTTTCTTCATTT
533380 TTT
1 TTT
533383 TATGTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTATTTTTCTTCATTT
Found at i:533380 original size:36 final size:35
Alignment explanation
Indices: 533311--533385 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
533301 ATTCTTATTC
533311 TTATTTTTCTCGTTATCTTTATTTTGATTATTTTAT
1 TTATTTTTCTCGTTATCTTTATTTTGATTATTTT-T
**
533347 TTATTTTTCTTCGTT-T-TTTATTTTTCTTCATTTTT
1 TTATTTTTC-TCGTTATCTTTATTTTGATT-ATTTTT
533382 TTAT
1 TTAT
533386 GTTCTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 15 0.43
36 15 0.43
37 5 0.14
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.73
Consensus pattern (35 bp):
TTATTTTTCTCGTTATCTTTATTTTGATTATTTTT
Found at i:533433 original size:53 final size:54
Alignment explanation
Indices: 533338--533439 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 54
533328 TTTATTTTGA
* * *
533338 TTATTTTATTTATTTTTCTTCGTTTTTTATTTTTCTTCATTTT-TTTATGTTCT
1 TTATTTTATTTATTTTTCTTCCTTATTTATTTTTATTCATTTTCTTTATGTTCT
*
533391 TTATTTTATTTATTTTT-TATCCTTATTTGTTTTTATGT-ATTTTCTTTAT
1 TTATTTTATTTATTTTTCT-TCCTTATTTATTTTTAT-TCATTTTCTTTAT
533440 CTTAATTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
52 1 0.02
53 35 0.83
54 6 0.14
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.75
Consensus pattern (54 bp):
TTATTTTATTTATTTTTCTTCCTTATTTATTTTTATTCATTTTCTTTATGTTCT
Found at i:533452 original size:29 final size:27
Alignment explanation
Indices: 533394--533453 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 27
533384 ATGTTCTTTA
* *
533394 TTTTATTTATTTTTTATCCTTATTTGT
1 TTTTATGTATTTTTTATCCTTATTTCT
533421 TTTTATGTATTTTCTTTAT-CTTAATTTCT
1 TTTTATGTA-TTT-TTTATCCTT-ATTTCT
533450 TTTT
1 TTTT
533454 TCATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.29
28 6 0.21
29 14 0.50
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.73
Consensus pattern (27 bp):
TTTTATGTATTTTTTATCCTTATTTCT
Found at i:535274 original size:5 final size:5
Alignment explanation
Indices: 535264--535318 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
535254 AACGGTCAAC
* * *
535264 GGTCG GGTCG GGTCAAC GGTCG GGACG GGTCG GGT-T GGTCG GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
535315 GGTC
1 GGTC
535319 AGACCGGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
4 3 0.07
5 34 0.83
7 4 0.10
ACGTcount: A:0.05, C:0.20, G:0.55, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:535277 original size:17 final size:17
Alignment explanation
Indices: 535257--535294 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
535247 GGAAGTCAAC
*
535257 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGACG
535274 GGTCAACGGTCGGGACG
1 GGTCAACGGTCGGGACG
535291 GGTC
1 GGTC
535295 GGGTTGGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.47, T:0.16
Consensus pattern (17 bp):
GGTCAACGGTCGGGACG
Found at i:535305 original size:19 final size:19
Alignment explanation
Indices: 535281--535317 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
535271 TCGGGTCAAC
535281 GGTCGGGACGGGTCGGGTT
1 GGTCGGGACGGGTCGGGTT
*
535300 GGTCGGGTCGGGTCGGGT
1 GGTCGGGACGGGTCGGGT
535318 CAGACCGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.59, T:0.22
Consensus pattern (19 bp):
GGTCGGGACGGGTCGGGTT
Found at i:535343 original size:19 final size:19
Alignment explanation
Indices: 535321--535393 Score: 103
Period size: 19 Copynumber: 3.8 Consensus size: 19
535311 GTCGGGTCAG
*
535321 ACCGGTCAAAACGGTTCGA
1 ACCGGTCAAAACGGTTCAA
535340 ACCGGTCAAAACGGTTCAA
1 ACCGGTCAAAACGGTTCAA
*
535359 ACCGGTCGAAATCGG-TCAA
1 ACCGGTC-AAAACGGTTCAA
*
535378 ACCGGTCAAACCGGTT
1 ACCGGTCAAAACGGTT
535394 TCCAGCAGCG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 6 0.12
19 37 0.76
20 6 0.12
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACGGTTCAA
Found at i:535358 original size:10 final size:9
Alignment explanation
Indices: 535315--535392 Score: 84
Period size: 9 Copynumber: 8.3 Consensus size: 9
535305 GGTCGGGTCG
*
535315 GGTCAGACC
1 GGTCAAACC
*
535324 GGTCAAAAC
1 GGTCAAACC
*
535333 GGTTCGAACC
1 GG-TCAAACC
*
535343 GGTCAAAAC
1 GGTCAAACC
535352 GGTTCAAACC
1 GG-TCAAACC
*
535362 GGTCGAAATC
1 GGTC-AAACC
535372 GGTCAAACC
1 GGTCAAACC
535381 GGTCAAACC
1 GGTCAAACC
535390 GGT
1 GGT
535393 TTCCAGCAGC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
9 34 0.60
10 23 0.40
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:542566 original size:5 final size:5
Alignment explanation
Indices: 542556--542611 Score: 69
Period size: 5 Copynumber: 11.0 Consensus size: 5
542546 GGTCAACGGT
* *
542556 GGGTC GGGTC GGGTC AACGGTC GGGTC GGGTC GGGT- TGGTC GGGTC GGGTC
1 GGGTC GGGTC GGGTC --GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC
542607 GGGTC
1 GGGTC
542612 AGACTGGTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
4 3 0.07
5 37 0.84
7 4 0.09
ACGTcount: A:0.04, C:0.20, G:0.55, T:0.21
Consensus pattern (5 bp):
GGGTC
Found at i:542598 original size:14 final size:14
Alignment explanation
Indices: 542579--542605 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
542569 TCAACGGTCG
542579 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
542593 GGTCGGGTCGGGT
1 GGTCGGGTCGGGT
542606 CGGGTCAGAC
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:0.00, C:0.15, G:0.59, T:0.26
Consensus pattern (14 bp):
GGTCGGGTCGGGTT
Found at i:542598 original size:19 final size:19
Alignment explanation
Indices: 542574--542610 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
542564 TCGGGTCAAC
542574 GGTCGGGTCGGGTCGGGTT
1 GGTCGGGTCGGGTCGGGTT
542593 GGTCGGGTCGGGTCGGGT
1 GGTCGGGTCGGGTCGGGT
542611 CAGACTGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.59, T:0.24
Consensus pattern (19 bp):
GGTCGGGTCGGGTCGGGTT
Found at i:542619 original size:24 final size:24
Alignment explanation
Indices: 542574--542620 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
542564 TCGGGTCAAC
* **
542574 GGTCGGGTCGGGTCGGGTTGGTCG
1 GGTCGGGTCGGGTCAGACTGGTCG
542598 GGTCGGGTCGGGTCAGACTGGTC
1 GGTCGGGTCGGGTCAGACTGGTC
542621 AAATCGGTTC
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:0.04, C:0.19, G:0.53, T:0.23
Consensus pattern (24 bp):
GGTCGGGTCGGGTCAGACTGGTCG
Found at i:542627 original size:19 final size:19
Alignment explanation
Indices: 542605--542642 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
542595 TCGGGTCGGG
*
542605 TCGGGTCAGACTGGTCAAA
1 TCGGGTCAGACCGGTCAAA
*
542624 TCGGTTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
542643 ACGGTTCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (19 bp):
TCGGGTCAGACCGGTCAAA
Found at i:542647 original size:19 final size:19
Alignment explanation
Indices: 542610--542649 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
542600 TCGGGTCGGG
* *
542610 TCAGACTGGTCAAATCGGT
1 TCAGACCGGTCAAAACGGT
542629 TCAGACCGGTCAAAACGGT
1 TCAGACCGGTCAAAACGGT
542648 TC
1 TC
542650 GAACTGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (19 bp):
TCAGACCGGTCAAAACGGT
Found at i:543768 original size:17 final size:17
Alignment explanation
Indices: 543746--543821 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 17
543736 ATTCAGATTT
*
543746 CAATTCCTAACATATTC
1 CAATTCCTGACATATTC
* *
543763 CAATTCCTGACAGATTT
1 CAATTCCTGACATATTC
* *
543780 CAATTACTGATA-ATTC
1 CAATTCCTGACATATTC
* * *
543796 CAATTACTTCACATATTA
1 CAATT-CCTGACATATTC
543814 CAATTCCT
1 CAATTCCT
543822 TAAAAACACT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
16 8 0.18
17 29 0.64
18 8 0.18
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (17 bp):
CAATTCCTGACATATTC
Found at i:548338 original size:22 final size:22
Alignment explanation
Indices: 548313--548355 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
548303 GGCGACATCC
548313 GTCCCCATCTCCGACGAAATCT
1 GTCCCCATCTCCGACGAAATCT
* *
548335 GTCCCTATTTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
548356 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.37, G:0.14, T:0.26
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCT
Found at i:551474 original size:30 final size:30
Alignment explanation
Indices: 551415--551503 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
551405 CCCGAAGGAC
* * *
551415 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
551444 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
551474 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
551504 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:551539 original size:31 final size:31
Alignment explanation
Indices: 551499--551599 Score: 132
Period size: 31 Copynumber: 3.2 Consensus size: 31
551489 AAAGATCCTC
*
551499 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
551530 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
551561 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
551593 GGTAAAC
1 GGTAAAC
551600 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.56
32 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:552538 original size:29 final size:29
Alignment explanation
Indices: 552484--552539 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
552474 TTTCTCTTGT
* *
552484 TATCATATAAATCATTGCCATATAACACA
1 TATCATATAAATCATTACCACATAACACA
*
552513 TATCATATAAATTCA-TACCACCTAACA
1 TATCATATAAA-TCATTACCACATAACA
552540 TGTAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (29 bp):
TATCATATAAATCATTACCACATAACACA
Found at i:552951 original size:21 final size:21
Alignment explanation
Indices: 552927--552971 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
552917 TGTTGTTCGT
* *
552927 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
552948 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
552969 TTG
1 TTG
552972 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:556331 original size:30 final size:30
Alignment explanation
Indices: 556272--556360 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
556262 CCCGAAGGAC
* * *
556272 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
556301 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
556331 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
556361 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:556396 original size:31 final size:31
Alignment explanation
Indices: 556356--556456 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
556346 AAAGATCCTC
*
556356 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
556387 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
* *
556418 GGTAAAACTGTTCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
556450 GGTAAAC
1 GGTAAAC
556457 CCTCGACTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
31 33 0.57
32 25 0.43
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:556449 original size:32 final size:32
Alignment explanation
Indices: 556359--556455 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
556349 GATCCTCGGT
*
556359 AAACTGTCCATATGTTCCTTAGAACATAGGT-
1 AAACTGTCCATATGTTCCGTAGAACATAGGTA
* *
556390 ATACTGTCCATATG-TCTCG-AAAGACATAGGTA
1 AAACTGTCCATATGTTC-CGTAGA-ACATAGGTA
*
556422 AAACTGTTCATATGTTCCGTAGAACATAGGTA
1 AAACTGTCCATATGTTCCGTAGAACATAGGTA
556454 AA
1 AA
556456 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
30 4 0.07
31 22 0.40
32 25 0.45
33 4 0.07
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (32 bp):
AAACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:557395 original size:29 final size:29
Alignment explanation
Indices: 557341--557396 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
557331 TTTCTCTTGT
* *
557341 TATCATATAAATCATTGCCATATAACACA
1 TATCATATAAATCATTACCACATAACACA
*
557370 TATCATATAAATTCA-TACCACCTAACA
1 TATCATATAAA-TCATTACCACATAACA
557397 TGTAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (29 bp):
TATCATATAAATCATTACCACATAACACA
Found at i:557808 original size:21 final size:21
Alignment explanation
Indices: 557784--557828 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
557774 TGTTGTTCGT
* *
557784 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
557805 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
557826 TTG
1 TTG
557829 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:559882 original size:14 final size:14
Alignment explanation
Indices: 559863--559901 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
559853 TTTTTTGATT
559863 AATTGATTTGTAAA
1 AATTGATTTGTAAA
559877 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
559891 AGTTGATTTGT
1 AATTGATTTGT
559902 TTACTTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:560607 original size:18 final size:18
Alignment explanation
Indices: 560584--560626 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
560574 TTGGGCTAAT
560584 ATTTATAGTGGAGCCGAA
1 ATTTATAGTGGAGCCGAA
560602 ATTTATAGTGGAGCCGAA
1 ATTTATAGTGGAGCCGAA
560620 ATTTATA
1 ATTTATA
560627 TTGAAATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (18 bp):
ATTTATAGTGGAGCCGAA
Found at i:560649 original size:18 final size:18
Alignment explanation
Indices: 560626--560662 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
560616 CGAAATTTAT
560626 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
560644 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
560662 A
1 A
560663 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:561075 original size:25 final size:25
Alignment explanation
Indices: 561047--561098 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
561037 ACATTATTTT
*
561047 TTCAAATAATGTACCCATAACAATG
1 TTCAAATAATGTACCCACAACAATG
561072 TTCAAATAATGTACCCACAACAATG
1 TTCAAATAATGTACCCACAACAATG
561097 TT
1 TT
561099 TAATTGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (25 bp):
TTCAAATAATGTACCCACAACAATG
Found at i:561209 original size:20 final size:20
Alignment explanation
Indices: 561184--561229 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
561174 CGCGAAATAA
*
561184 GCGTTGCGAATTTGTCTTTC
1 GCGTTGCGAATTTGACTTTC
561204 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
561224 GCGTTG
1 GCGTTG
561230 ATCCTAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.11, C:0.20, G:0.28, T:0.41
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:563991 original size:12 final size:12
Alignment explanation
Indices: 563965--564003 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
563955 GAAAAGGTTG
*
563965 TGTGTTTTGAGAT
1 TGTG-TTTGATAT
563978 TGTGTTTGATAT
1 TGTGTTTGATAT
*
563990 TGTGTTTGGTAT
1 TGTGTTTGATAT
564002 TG
1 TG
564004 GAAATGTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.13, C:0.00, G:0.31, T:0.56
Consensus pattern (12 bp):
TGTGTTTGATAT
Found at i:564810 original size:20 final size:20
Alignment explanation
Indices: 564787--564833 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
564777 CATATTCGCA
564787 TTGCGAAATTAGAAATT-GGG
1 TTGCGAAATTAG-AATTCGGG
*
564807 TTGCGAAATTAGAATTCGTG
1 TTGCGAAATTAGAATTCGGG
564827 TTGCGAA
1 TTGCGAA
564834 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGAAATTAGAATTCGGG
Found at i:566018 original size:2 final size:2
Alignment explanation
Indices: 566011--566061 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
566001 AGTCGTATTC
566011 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
566053 AT AT AT AT A
1 AT AT AT AT A
566062 CTATTATTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:566515 original size:4 final size:4
Alignment explanation
Indices: 566508--566553 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
566498 CACATTTATA
* *
566508 CATG CATG CATG CATGG ACATG TATG TATG CATG CATG CATG CATG
1 CATG CATG CATG CAT-G -CATG CATG CATG CATG CATG CATG CATG
566554 AACATGAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 33 0.87
5 2 0.05
6 3 0.08
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (4 bp):
CATG
Found at i:566538 original size:18 final size:18
Alignment explanation
Indices: 566507--566553 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
566497 ACACATTTAT
566507 ACATGCATGCATGCATGG
1 ACATGCATGCATGCATGG
* *
566525 ACATGTATGTATGCAT-G
1 ACATGCATGCATGCATGG
566542 -CATGCATGCATG
1 ACATGCATGCATG
566554 AACATGAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 10 0.40
17 1 0.04
18 14 0.56
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (18 bp):
ACATGCATGCATGCATGG
Found at i:574377 original size:32 final size:32
Alignment explanation
Indices: 574334--574404 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
574324 TTTTTTAAAT
*
574334 ATTTTA-AAATTTTAATAAT-TTATAGTTTATA
1 ATTTTATAAATTTTAAT-ATCTAATAGTTTATA
* *
574365 ATTTTATAAATTTTGATATCTAATATTTTATA
1 ATTTTATAAATTTTAATATCTAATAGTTTATA
574397 ATATTTAT
1 AT-TTTAT
574405 TTATAAACCG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 8 0.24
32 21 0.62
33 5 0.15
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (32 bp):
ATTTTATAAATTTTAATATCTAATAGTTTATA
Found at i:575152 original size:24 final size:25
Alignment explanation
Indices: 575108--575154 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
575098 TTTAACCTCA
*
575108 AATTTATTTTTTAATTATAATATAT
1 AATTTATTTATTAATTATAATATAT
575133 AATTATATTTATT-ATT-TAATAT
1 AATT-TATTTATTAATTATAATAT
575155 GTTATACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 7 0.35
26 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
AATTTATTTATTAATTATAATATAT
Found at i:579309 original size:15 final size:16
Alignment explanation
Indices: 579279--579312 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
579269 TTGTTTAAAT
*
579279 TTTAATTAATATTTAA
1 TTTAAATAATATTTAA
579295 TTTAAATAA-ATTTAA
1 TTTAAATAATATTTAA
579310 TTT
1 TTT
579313 GATTTTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAATAATATTTAA
Found at i:580303 original size:32 final size:30
Alignment explanation
Indices: 580235--580304 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
580225 TTATTATCAT
*
580235 TATTTATTATTTTTTAACAATAGTTAATAA
1 TATTTATTATTTTTTAAAAATAGTTAATAA
* *
580265 TGTTTATTCATTTTTTAAAAATTAGATT-TTAA
1 TATTTATT-ATTTTTTAAAAA-TAG-TTAATAA
580297 TATTTATT
1 TATTTATT
580305 TTAAATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 7 0.21
31 11 0.33
32 13 0.39
33 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (30 bp):
TATTTATTATTTTTTAAAAATAGTTAATAA
Found at i:580706 original size:14 final size:14
Alignment explanation
Indices: 580684--580713 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
580674 TTAATTGTTG
580684 TTAAAAAATAATAA
1 TTAAAAAATAATAA
*
580698 TTAATAAATAATAA
1 TTAAAAAATAATAA
580712 TT
1 TT
580714 CATTTGATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAAATAATAA
Found at i:585426 original size:2 final size:2
Alignment explanation
Indices: 585419--585448 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
585409 AAAAATTTGA
585419 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
585449 TTGATTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:585690 original size:23 final size:23
Alignment explanation
Indices: 585641--585720 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
585631 TTTATATTTT
* * *
585641 TATTTTTATCATT-ATAATTTATT
1 TATTTTTATTATTAATAA-TAATA
* *
585664 TATTTATTATTGTTATTAAT-ATA
1 TATTT-TTATTATTAATAATAATA
*
585687 TATTTTTTATTATTAATAATAATT
1 TA-TTTTTATTATTAATAATAATA
585711 TATTTTTATT
1 TATTTTTATT
585721 TTTTATAGGC
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
23 29 0.63
24 14 0.30
25 3 0.07
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (23 bp):
TATTTTTATTATTAATAATAATA
Found at i:585696 original size:30 final size:29
Alignment explanation
Indices: 585629--585701 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
585619 TTTTGATCAG
* * *
585629 ATTTTATATTT-TTATTTTTATCATTATA
1 ATTTTTTATTTATTATTGTTATCAATATA
*
585657 ATTTATTTATTTATTATTGTTATTAATATA
1 ATTT-TTTATTTATTATTGTTATCAATATA
585687 TATTTTTTA-TTATTA
1 -ATTTTTTATTTATTA
585702 ATAATAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
28 4 0.11
29 12 0.32
30 18 0.47
31 4 0.11
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (29 bp):
ATTTTTTATTTATTATTGTTATCAATATA
Found at i:585711 original size:20 final size:20
Alignment explanation
Indices: 585670--585720 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
585660 TATTTATTTA
*
585670 TTATTGTTATTAATATATAT
1 TTATTTTTATTAATATATAT
585690 TT-TTTATTATTAATA-ATAAT
1 TTATTT-TTATTAATATAT-AT
585710 TTATTTTTATT
1 TTATTTTTATT
585721 TTTTATAGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 4 0.15
20 20 0.74
21 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTATTTTTATTAATATATAT
Found at i:586984 original size:24 final size:24
Alignment explanation
Indices: 586956--587010 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
586946 CTCTCCCTGC
* *
586956 ATTTTTACTTTTACACTTTCTTTA
1 ATTTTTACTTTTACAATTTCTTGA
*
586980 A-TTTTACTTTTACAATTTCTTGC
1 ATTTTTACTTTTACAATTTCTTGA
587003 ATTTTTAC
1 ATTTTTAC
587011 ATTTCGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.22, C:0.16, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTTTTACTTTTACAATTTCTTGA
Found at i:587116 original size:18 final size:19
Alignment explanation
Indices: 587084--587123 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
587074 TTCTTTTTGT
* *
587084 TTTTAAATTTAATTTTTTA
1 TTTTAAAATTAATTTATTA
587103 TTTTAAAATT-ATTTATTA
1 TTTTAAAATTAATTTATTA
587121 TTT
1 TTT
587124 CTTATTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTAAAATTAATTTATTA
Found at i:588834 original size:2 final size:2
Alignment explanation
Indices: 588827--588853 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
588817 ATGAGAAAGT
588827 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
588854 TCCCCCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:596313 original size:16 final size:16
Alignment explanation
Indices: 596301--596343 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
596291 CGAATAAAAC
596301 TATATTTATATAAATG
1 TATATTTATATAAATG
596317 TATATTTATATAAATG
1 TATATTTATATAAATG
596333 TATATTTATAT
1 TATATTTATAT
596344 TTAGATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
TATATTTATATAAATG
Found at i:596417 original size:16 final size:18
Alignment explanation
Indices: 596385--596418 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
596375 TATTAATGTA
596385 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
596403 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
596419 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:597080 original size:130 final size:130
Alignment explanation
Indices: 596876--597123 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
596866 AATTTTCTTC
* * *
596876 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* * *
596941 CCTAGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAAGACCAAATTGATAGCATATATAAA
* * *
597006 TAATTAGGTGGTGACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
597071 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAAGACTAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAAGACCAAATTGAT
597124 TATATAATAA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAAGACCAAATTGATAGCATATATAAA
Found at i:597569 original size:35 final size:35
Alignment explanation
Indices: 597519--597594 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
597509 AATTGAATTG
* *
597519 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
597554 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
597589 AATTGA
1 AATTGA
597595 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:602443 original size:31 final size:31
Alignment explanation
Indices: 602358--602458 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 31
602348 ATTATTAACG
* *
602358 TGATATATATCACATCA-CTAAAATAATGATG
1 TGATATATATCACATCATC-AAAATGATGATA
** * * *
602389 TGATATGCATCATATCATTAAAATGATGACA
1 TGATATATATCACATCATCAAAATGATGATA
*
602420 TGATATATATCACATTATCAAAATGATGATA
1 TGATATATATCACATCATCAAAATGATGATA
*
602451 TGGTATAT
1 TGATATAT
602459 GCATCCAAAG
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (31 bp):
TGATATATATCACATCATCAAAATGATGATA
Found at i:604328 original size:20 final size:20
Alignment explanation
Indices: 604303--604341 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
604293 ATGGTTTGCC
604303 GAGTTATTAAACAACTTGAT
1 GAGTTATTAAACAACTTGAT
604323 GAGTTATTAAACAACTTGA
1 GAGTTATTAAACAACTTGA
604342 AGATCAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
GAGTTATTAAACAACTTGAT
Found at i:604827 original size:19 final size:19
Alignment explanation
Indices: 604803--604846 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
604793 TTTAAGTTTT
604803 GAAATCTATGATGGAACTG
1 GAAATCTATGATGGAACTG
604822 GAAATCTATGATGGAACTG
1 GAAATCTATGATGGAACTG
604841 GAAATC
1 GAAATC
604847 ATTCCAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (19 bp):
GAAATCTATGATGGAACTG
Found at i:618332 original size:2 final size:2
Alignment explanation
Indices: 618327--618353 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
618317 AGAAAAATGA
618327 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
618354 ATGCAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:628664 original size:3 final size:3
Alignment explanation
Indices: 628656--628684 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
628646 ATATAATGCA
628656 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
628685 AATTGCAGTA
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:629560 original size:43 final size:43
Alignment explanation
Indices: 629505--629738 Score: 229
Period size: 43 Copynumber: 5.4 Consensus size: 43
629495 TTTCAAGAAA
629505 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-GACAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGA-AGAC
* * *
629548 AAACGCCACAATAGATGTTGATATTTCGCGGCGTTTGGAAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* *
629591 AAACGCCGCAATAGATGTTGATATTTAGCGGCATTTGGAAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* * * * ***** *
629634 AAACGCCACAGTAGGTGTCGAT-TTGTAGCAGCGTTTTTCTCAG
1 AAACGCCGCAATAGGTGTTGATATT-TAGCGGCGTTTGGAAGAC
* * * ** **
629677 AAACGCCGCAGTAGGTGTTGATGTTTAGTGGCGTTTTTATCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
*
629720 AAACGCCGCAATAAGTGTT
1 AAACGCCGCAATAGGTGTT
629739 AAGGTTTCGC
Statistics
Matches: 162, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 2 0.01
43 156 0.96
44 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
Found at i:629753 original size:43 final size:42
Alignment explanation
Indices: 629659--629813 Score: 132
Period size: 43 Copynumber: 3.6 Consensus size: 42
629649 TGTCGATTTG
* * * * * *
629659 TAGCAGCGTTTTTCTCAGAAACGCCGCAGTAGGTGTTGATGTT
1 TAGCGGCGTTTTTATCACAAACGCCGCAATAAGTGTT-AGGTT
*
629702 TAGTGGCGTTTTTATCACAAACGCCGCAATAAGTGTTAAGGTT
1 TAGCGGCGTTTTTATCACAAACGCCGCAATAAGTGTT-AGGTT
* * ** * * *
629745 TCGCGGCGTTTTTAGCTTAAACGCCGCAATATGTGTTTGATT
1 TAGCGGCGTTTTTATCACAAACGCCGCAATAAGTGTTAGGTT
* *
629787 TGGCGGCGTCTTTAAT-ACAAACGCCGC
1 TAGCGGCGT-TTTTATCACAAACGCCGC
629814 TAAAGATCGG
Statistics
Matches: 90, Mismatches: 21, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
42 20 0.22
43 70 0.78
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (42 bp):
TAGCGGCGTTTTTATCACAAACGCCGCAATAAGTGTTAGGTT
Found at i:629809 original size:42 final size:44
Alignment explanation
Indices: 629718--629813 Score: 108
Period size: 42 Copynumber: 2.2 Consensus size: 44
629708 CGTTTTTATC
* * *
629718 ACAAACGCCGCAATAAGTGTTAAGGTTTCGCGGCGTTTTTAGCT
1 ACAAACGCCGCAATAAGTGTTAAGATTTCGCGGCGTCTTTAGAT
* * * *
629762 -TAAACGCCGCAATATGTGTT-TGATTTGGCGGCGTCTTTA-AT
1 ACAAACGCCGCAATAAGTGTTAAGATTTCGCGGCGTCTTTAGAT
629803 ACAAACGCCGC
1 ACAAACGCCGC
629814 TAAAGATCGG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.02
42 24 0.56
43 18 0.42
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (44 bp):
ACAAACGCCGCAATAAGTGTTAAGATTTCGCGGCGTCTTTAGAT
Found at i:630206 original size:21 final size:21
Alignment explanation
Indices: 630181--630242 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
630171 ATATGTTGCT
630181 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
* **
630202 TCTCTTTGTGCTGCCACTGTT
1 TCTCTTTGTGCTGCCGCTGCC
*
630223 TCTCTCTT-TGCTTCCGCTGC
1 TCTCT-TTGTGCTGCCGCTGC
630243 TGCTCTGGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.02, C:0.35, G:0.19, T:0.44
Consensus pattern (21 bp):
TCTCTTTGTGCTGCCGCTGCC
Found at i:630285 original size:21 final size:21
Alignment explanation
Indices: 630224--630279 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
630214 GCCACTGTTT
*
630224 CTCTCTTTGCTTCCGCTGCTG
1 CTCTCTCTGCTTCCGCTGCTG
**
630245 CTCTGGCTGCTTCCGCTGCTG
1 CTCTCTCTGCTTCCGCTGCTG
630266 CTCTCTCTGCTTCC
1 CTCTCTCTGCTTCC
630280 CTTGCTTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.00, C:0.41, G:0.20, T:0.39
Consensus pattern (21 bp):
CTCTCTCTGCTTCCGCTGCTG
Found at i:632197 original size:46 final size:46
Alignment explanation
Indices: 632130--632220 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
632120 TAGCGATTCT
*
632130 GAAATAACTACATGGTCAAACAAGACAGAGGAACGAAGGCAAGTAC
1 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTAC
632176 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTA
1 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTA
632221 AGTACCTTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.49, C:0.15, G:0.24, T:0.11
Consensus pattern (46 bp):
GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTAC
Done.