Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008418.1 Hibiscus syriacus cultivar Beakdansim tig00111198_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: 855397
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:471970 original size:2 final size:2
Alignment explanation
Indices: 471963--471988 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
471953 AAATAAATAA
471963 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
471989 TAAGTAGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:473442 original size:3 final size:3
Alignment explanation
Indices: 473434--473479 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
473424 ACAATTTATT
473434 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
473480 GTGAAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:473464 original size:23 final size:23
Alignment explanation
Indices: 473434--473479 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
473424 ACAATTTATT
*
473434 TAATAATAATAATAATATAATAA
1 TAATAATAATAATAATAAAATAA
473457 TAATAATAATAATAATAAAATAA
1 TAATAATAATAATAATAAAATAA
473480 GTGAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TAATAATAATAATAATAAAATAA
Found at i:473974 original size:140 final size:136
Alignment explanation
Indices: 473617--473974 Score: 423
Period size: 140 Copynumber: 2.6 Consensus size: 136
473607 TGGAAATATT
* * *
473617 GAACAAATTCTTCTTATTATGAACTT-TTCTTCCTTTTCAAATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAACT-
* * * ** * *
473681 CTTCTGAAAATATCGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATTTGATGAATTAAGG
65 CTTCTGAAAATATTGATCCTCAAAAGAGGTGTCGTTAATTCAACTCCATAGGTGACGAATCAAGG
*
473746 CAAGGTT
130 CAAGGTC
* * *
473753 GAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAAC-T
* * * * *
473818 CCTCTGAAAATGTTGATCCCTCGAATGAGGT-TCTTTTCTAATTCAACTCCATAGGTGACGAATC
65 CTTCTGAAAATATTGAT-CCTCAAAAGAGGTGTC--GT-TAATTCAACTCCATAGGTGACGAATC
**
473882 AAGTTAAGGTC
126 AAGGCAAGGTC
*
473893 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCATATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAACTC
* *
473958 TATCTGGAAATTTTGAT
66 T-TCTGAAAATATTGAT
473975 GTTGATCTAT
Statistics
Matches: 188, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
136 23 0.12
137 49 0.26
138 12 0.06
139 3 0.02
140 101 0.54
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (136 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAACTC
TTCTGAAAATATTGATCCTCAAAAGAGGTGTCGTTAATTCAACTCCATAGGTGACGAATCAAGGC
AAGGTC
Found at i:474021 original size:123 final size:123
Alignment explanation
Indices: 473887--474220 Score: 560
Period size: 123 Copynumber: 2.7 Consensus size: 123
473877 GAATCAAGTT
* *
473887 AAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCATATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
*
473952 GAACTCTATCTGGAAATTTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGAAA
66 GAACTCTATCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGAAA
* *
474010 AAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
* * *
474075 GAACTCTCTCTGGAAATGTTGGTGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
66 GAACTCTATCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGAAA
* *
474133 AAGGTTGCACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
* *
474198 GAACTCTACCTGGCAATGTTGAT
66 GAACTCTATCTGGAAATGTTGAT
474221 CCATCGAGTG
Statistics
Matches: 196, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 196 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
GAACTCTATCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGAAA
Found at i:475148 original size:11 final size:11
Alignment explanation
Indices: 475126--475160 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
475116 TCCTTTTTTA
475126 TTTTA-TTT-T
1 TTTTATTTTCT
475135 TTTTATTTTCT
1 TTTTATTTTCT
475146 TTTTATTTTCT
1 TTTTATTTTCT
475157 TTTT
1 TTTT
475161 TTATTCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.21
10 3 0.12
11 16 0.67
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTATTTTCT
Found at i:475162 original size:14 final size:14
Alignment explanation
Indices: 475119--475162 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
475109 TTGACCCTCC
*
475119 TTTTTTATTTTATT
1 TTTTTTATTTTCTT
475133 TTTTTTATTTTC--
1 TTTTTTATTTTCTT
475145 -TTTTTATTTTCTT
1 TTTTTTATTTTCTT
475158 TTTTT
1 TTTTT
475163 ATTCAAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 11 0.42
14 15 0.58
ACGTcount: A:0.09, C:0.05, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTATTTTCTT
Found at i:478704 original size:13 final size:13
Alignment explanation
Indices: 478686--478718 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
478676 AAAGAATGAA
478686 AAATAATAAATGT
1 AAATAATAAATGT
478699 AAATAATAAATGT
1 AAATAATAAATGT
478712 AAATAAT
1 AAATAAT
478719 GTAAAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (13 bp):
AAATAATAAATGT
Found at i:482465 original size:14 final size:16
Alignment explanation
Indices: 482448--482479 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
482438 ATTATTTTTT
482448 TGAAT-TTTA-CTTAA
1 TGAATGTTTATCTTAA
482462 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
482478 TG
1 TG
482480 TGAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 4 0.25
16 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:482532 original size:15 final size:15
Alignment explanation
Indices: 482508--482539 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
482498 ATACATATAT
482508 AAAATAAATGTATGC
1 AAAATAAATGTATGC
*
482523 AAAATGAATGTATGC
1 AAAATAAATGTATGC
482538 AA
1 AA
482540 GAGGTATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
AAAATAAATGTATGC
Found at i:486740 original size:22 final size:21
Alignment explanation
Indices: 486694--486741 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
486684 CCTTAAAATT
* * *
486694 ATTAAATATATCACATTATAG
1 ATTAAAAATATAAAATTATAG
486715 -TTAAAAATATAAAATTATAGG
1 ATTAAAAATATAAAATTATA-G
486736 ATTAAA
1 ATTAAA
486742 TTAAAAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 16 0.73
21 1 0.05
22 5 0.23
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (21 bp):
ATTAAAAATATAAAATTATAG
Found at i:487679 original size:235 final size:234
Alignment explanation
Indices: 487268--487736 Score: 893
Period size: 235 Copynumber: 2.0 Consensus size: 234
487258 GGAAACCAAT
* *
487268 CACCGACCGATAGTCGTATACAGCCGTCGGTAGCCACCCTCGGCCATCATGAACGGTGGCCGAAA
1 CACCGACCGACAATCGTATACAGCCGTCGGTAGCCACCCTCGGCCATCATGAACGGTGGCCGAAA
*
487333 TTCCCAAATTACCCTAAAATATAGATCCTGACATCCCAAGGTCGAATCTAGCCGTTGTTTCCCTT
66 TTCCCAAATTACCCTAAAATATAGAACCTGACATCCCAAGGTCGAATCTAGCCGTTGTTTCCCTT
487398 AAAAAGCTCCTAATCGGAGTAGATCTATAATTATACCTTCGTATTTCGATTGCTTCGGAGACGCG
131 AAAAAGCTCCTAATCGGAGTAGATCTATAATTATACCTTCGTATTTCGATTGCTTCGGAGACGCG
*
487463 TGGCGGTGCGTGGAGTCTCTAGTCACCGTGCAGTCTTCAA
196 TGGCGGTGCGTGGAGTCTCTAGTCA-CGTGCAGTCCTCAA
487503 CACCGACCGACAATCGTATACAGCCGTCGGTAGCCACCCTCGGCCATCATGAACGGTGGCCGAAA
1 CACCGACCGACAATCGTATACAGCCGTCGGTAGCCACCCTCGGCCATCATGAACGGTGGCCGAAA
487568 TTCCCAAATTACCCTAAAATATAGAACCTGACATCCCAAGGTCGAATCTAGCCGTTGTTTCCCTT
66 TTCCCAAATTACCCTAAAATATAGAACCTGACATCCCAAGGTCGAATCTAGCCGTTGTTTCCCTT
487633 AAAAAGCTCCTAATCGGAGTAGATCTATAATTATACCTTCGTATTTCGATTGCTTCGGAGACGCG
131 AAAAAGCTCCTAATCGGAGTAGATCTATAATTATACCTTCGTATTTCGATTGCTTCGGAGACGCG
487698 TGGCGGTGCGTGGAGTCTCTAGTCACGTGCAGTCCTCAA
196 TGGCGGTGCGTGGAGTCTCTAGTCACGTGCAGTCCTCAA
487737 TAAGTTTATC
Statistics
Matches: 230, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
234 13 0.06
235 217 0.94
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (234 bp):
CACCGACCGACAATCGTATACAGCCGTCGGTAGCCACCCTCGGCCATCATGAACGGTGGCCGAAA
TTCCCAAATTACCCTAAAATATAGAACCTGACATCCCAAGGTCGAATCTAGCCGTTGTTTCCCTT
AAAAAGCTCCTAATCGGAGTAGATCTATAATTATACCTTCGTATTTCGATTGCTTCGGAGACGCG
TGGCGGTGCGTGGAGTCTCTAGTCACGTGCAGTCCTCAA
Found at i:488291 original size:20 final size:20
Alignment explanation
Indices: 488249--488291 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
488239 TTGGGCATGC
* ** *
488249 AATAGTAATAATAATTTATT
1 AATAATAATAATAATAAAAT
488269 AATAATAATAATAATAAAAT
1 AATAATAATAATAATAAAAT
488289 AAT
1 AAT
488292 GAAAAAAATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AATAATAATAATAATAAAAT
Found at i:488415 original size:21 final size:21
Alignment explanation
Indices: 488390--488429 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
488380 TAATGCATAC
488390 ATTATAAATA-AGTATATAATT
1 ATTATAAATATA-TATATAATT
*
488411 ATTATATATATATATATAA
1 ATTATAAATATATATATAA
488430 AGTATGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTATAAATATATATATAATT
Found at i:488686 original size:30 final size:29
Alignment explanation
Indices: 488622--488686 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
488612 TTTATAATAT
*
488622 CATACATACATATACATTAATTAATTATA
1 CATACATACATATACATTAATGAATTATA
* * *
488651 AATACATACAT-TAATCATTAATGAATTTTG
1 CATACATACATAT-A-CATTAATGAATTATA
488681 CATACA
1 CATACA
488687 ATATACATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.03
29 11 0.38
30 17 0.59
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (29 bp):
CATACATACATATACATTAATGAATTATA
Found at i:495641 original size:30 final size:29
Alignment explanation
Indices: 495607--495699 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 29
495597 TTTATTTTAT
* *
495607 TTTGGGGACTAAATTAAAATTTTGGTGAAA
1 TTTGGGGA-TAAAATAAAATTTTGGTAAAA
495637 TTTGGGGATCAAAATAAAATTTTGGTAAAA
1 TTTGGGGAT-AAAATAAAATTTTGGTAAAA
* * *
495667 TTTGGGGATTAAAATGAAATTTTGATTAAA
1 TTTGGGGA-TAAAATAAAATTTTGGTAAAA
495697 TTT
1 TTT
495700 AGATCCAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.02
30 54 0.96
31 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTGGGGATAAAATAAAATTTTGGTAAAA
Found at i:497586 original size:64 final size:63
Alignment explanation
Indices: 497514--497651 Score: 161
Period size: 64 Copynumber: 2.2 Consensus size: 63
497504 TTCAATGTGT
* * * *
497514 ATCGATGCACTCTTTAAAAAAGAAAACATCGAATGCAATTAGTGCATCGATGCATAAGG-AGTGC
1 ATCGATGCACCCCTT-AAAAAGAAAACATCAAAGGCAATTAGTGCATCGATGCAT-AGGTAGTGC
* ** * *
497578 ATCGATGCACCCCCTTAAAATGAAAACATCAAAGGTGATTGGTGTATCGATGCATAGGTAGTGC
1 ATCGATGCA-CCCCTTAAAAAGAAAACATCAAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
497642 ATCGATGCAC
1 ATCGATGCAC
497652 ATGTTAAAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
63 4 0.06
64 55 0.87
65 4 0.06
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (63 bp):
ATCGATGCACCCCTTAAAAAGAAAACATCAAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
Found at i:498922 original size:21 final size:18
Alignment explanation
Indices: 498902--498975 Score: 78
Period size: 18 Copynumber: 3.9 Consensus size: 18
498892 AGGGATTATC
498902 AGTGGTCCTTTGGGACATAT
1 AGTGGTCCTTTGGGAC--AT
* *
498922 CAGTGGTCATTCGGGACAT
1 -AGTGGTCCTTTGGGACAT
*
498941 AGTGGT-CTTTCGAGACAT
1 AGTGGTCCTTT-GGGACAT
498959 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTTGGGACA
498976 AATATTCAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
17 2 0.04
18 23 0.51
19 6 0.13
21 14 0.31
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTTGGGACAT
Found at i:509627 original size:21 final size:21
Alignment explanation
Indices: 509603--509662 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
509593 GTCGAGGGAT
509603 TATCAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGGGACA
509624 TATCAGTGGTCCTTCGGGAC-
1 TATCAGTGGTCCTTCGGGACA
*
509644 -AT-AGTGGTCCTTCAGGACA
1 TATCAGTGGTCCTTCGGGACA
509663 AATATTCAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 15 0.41
19 2 0.05
21 20 0.54
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
TATCAGTGGTCCTTCGGGACA
Found at i:511712 original size:2 final size:2
Alignment explanation
Indices: 511705--511730 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
511695 AAAAACATTA
511705 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
511731 TAGCCATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:513790 original size:111 final size:111
Alignment explanation
Indices: 513596--514018 Score: 566
Period size: 111 Copynumber: 3.8 Consensus size: 111
513586 ATTAAATCGA
* ** * * * ** *
513596 GGTAGACTTCTTCCATTGTCACTTATGGAATATCAAATCTTGAAAGAGAGGGATCTATTTTGTTT
1 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTT
* * *
513661 CTTCTAAGGGAATATCAGATATGGGAAAA-TTGATCTATTGAA-CTGG
66 CTTCTAAGGGAATATCAGATCT-GGAAAAGTTGATCTGTTGAATC-AG
* * *
513707 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGATTTGTTTCGCTT
1 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTT
* *
513772 CTTCTAAGGGAATATCAGATCTGGAAAAGTTGATCCGTTAAATCAG
66 CTTCTAAGGGAATATCAGATCTGGAAAAGTTGATCTGTTGAATCAG
*
513818 GGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTT
1 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTT
513883 CTTCTAAGGGAATATCAGATCTGGAAAAGTTGAT-TCGTTGAATCAG
66 CTTCTAAGGGAATATCAGATCTGGAAAAGTTGATCT-GTTGAATCAG
* * * * *
513929 AGTAAACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGATATGTTCCACTT
1 GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTT
*
513994 CTT-TGAAAGGAATATCAGATCTGGA
66 CTTCT-AAGGGAATATCAGATCTGGA
514019 TCAATTAATC
Statistics
Matches: 280, Mismatches: 28, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
110 7 0.03
111 272 0.97
112 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (111 bp):
GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTT
CTTCTAAGGGAATATCAGATCTGGAAAAGTTGATCTGTTGAATCAG
Found at i:515357 original size:17 final size:18
Alignment explanation
Indices: 515325--515358 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
515315 TTAGACCATC
515325 TGCTTCAAGATTTTGGAA
1 TGCTTCAAGATTTTGGAA
*
515343 TGCTTCATG-TTTTGGA
1 TGCTTCAAGATTTTGGA
515359 TTTCTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.44
Consensus pattern (18 bp):
TGCTTCAAGATTTTGGAA
Found at i:521508 original size:2 final size:2
Alignment explanation
Indices: 521501--521527 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
521491 TGGGGATCCC
521501 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
521528 CTATTATAAC
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:525783 original size:4 final size:4
Alignment explanation
Indices: 525774--525805 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
525764 TATATCATTC
*
525774 TATT TATT TATT TATT TATT TATT TTTT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
525806 ATTAGCGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TATT
Found at i:526284 original size:3 final size:3
Alignment explanation
Indices: 526276--526311 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
526266 ATTTATTTAT
526276 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
526312 ATGTGTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:538636 original size:87 final size:87
Alignment explanation
Indices: 538438--538642 Score: 227
Period size: 87 Copynumber: 2.4 Consensus size: 87
538428 GTACATGCAT
* * * * *
538438 AAGGATGAGCTTT-TGCTCTTAATGGAA-TTATAGCCCAGGTTTTGGGTGGTCCTATTGAGAAGG
1 AAGGATGAGCTTTACGCTCTTAAT-GAATTTATAGCCCAGGATTTGAGTGGTCATAGTGAGAAGG
*
538501 ACTTGATAAATTCACCGACGTGA
65 ACTTGATAAATTCACCAACGTGA
* * *
538524 AAGGATGAGCTTTACACTCTCAATGAATTTATAGCTCAGGATTTGAGTGGTCATAGTGAGAAGGA
1 AAGGATGAGCTTTACGCTCTTAATGAATTTATAGCCCAGGATTTGAGTGGTCATAGTGAGAAGGA
* * *
538589 CTTGATGAATTCACTAACTTGA
66 CTTGATAAATTCACCAACGTGA
* * * *
538611 GATGTTGAG-TCTTACGCTCTTAATGAGTTTAT
1 AAGGATGAGCT-TTACGCTCTTAATGAATTTAT
538643 GTCCTAATAT
Statistics
Matches: 98, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
86 17 0.17
87 81 0.83
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (87 bp):
AAGGATGAGCTTTACGCTCTTAATGAATTTATAGCCCAGGATTTGAGTGGTCATAGTGAGAAGGA
CTTGATAAATTCACCAACGTGA
Found at i:539259 original size:20 final size:20
Alignment explanation
Indices: 539231--539279 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
539221 TTTTATAGAC
539231 CAATT-TCTTCTTTTCTCTA
1 CAATTCTCTTCTTTTCTCTA
539250 CAATTCTCTTCTTTTCTCTA
1 CAATTCTCTTCTTTTCTCTA
539270 CAATTCTCTT
1 CAATTCTCTT
539280 ATACTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (20 bp):
CAATTCTCTTCTTTTCTCTA
Found at i:544028 original size:15 final size:15
Alignment explanation
Indices: 543985--544031 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
543975 TTAAAGGTAT
543985 AAAATTAAAATATAA
1 AAAATTAAAATATAA
* *
544000 ATAA--AAACTATAA
1 AAAATTAAAATATAA
*
544013 AAAATTAAATTATAA
1 AAAATTAAAATATAA
544028 AAAA
1 AAAA
544032 ACTTCAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTAAAATATAA
Found at i:544512 original size:61 final size:60
Alignment explanation
Indices: 544447--544584 Score: 150
Period size: 61 Copynumber: 2.3 Consensus size: 60
544437 ACTATGATCC
* * ** * **
544447 TCATTTTAAATGGGTCCTTAAACTTTTGAGTATTTTAATTTCATCCCCAAAACTATGACAT
1 TCATTCTAAATGAGTCCTTAAACTTTTGAAAAATCAAATTTCAT-CCCAAAACTATGACAT
* * **
544508 TCATTCTAAATTAGTCCTTAAATTTTTGAAAAATCAAATTTCATCCCAAAACTATGACCC
1 TCATTCTAAATGAGTCCTTAAACTTTTGAAAAATCAAATTTCATCCCAAAACTATGACAT
* *
544568 CCATTCTAAATTAGTCC
1 TCATTCTAAATGAGTCC
544585 CTATATTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
60 30 0.46
61 35 0.54
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (60 bp):
TCATTCTAAATGAGTCCTTAAACTTTTGAAAAATCAAATTTCATCCCAAAACTATGACAT
Found at i:544848 original size:59 final size:57
Alignment explanation
Indices: 544750--544932 Score: 172
Period size: 60 Copynumber: 3.1 Consensus size: 57
544740 ATAGTTTATT
** *
544750 ATGAAATTGAAATGTTCAAGAAGTTTGGGGACTGATTTAGAATAAAGGTCATAGTATGAGG
1 ATGAAATTGAAATGTTCAA-AAGTTTAAGGACTAATTTAGAATAAA-GTCATA-T-TGAGG
* *
544811 ATGAAA-TGAAATGTTCAAAAGTTTAAGGACTAATTTAGAATGATAGTCGATATTTAGAG
1 ATGAAATTGAAATGTTCAAAAGTTTAAGGACTAATTTAGAAT-AAAGTC-ATATTGAG-G
* * * *
544870 ATGAAATTTG-AATGTTTAAAAGTCTAAGGACTAGTTTAGAATAAAAGTCGTAATTTGAGG
1 ATGAAA-TTGAAATGTTCAAAAGTTTAAGGACTAATTTAGAAT-AAAGTCAT-A-TTGAGG
544930 ATG
1 ATG
544933 TGATGGAATT
Statistics
Matches: 103, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
58 3 0.03
59 32 0.31
60 56 0.54
61 12 0.12
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (57 bp):
ATGAAATTGAAATGTTCAAAAGTTTAAGGACTAATTTAGAATAAAGTCATATTGAGG
Found at i:554522 original size:44 final size:45
Alignment explanation
Indices: 554473--554564 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 45
554463 AATAAATGAT
554473 ATAAACTATGATGCCATGAGGAATCTTGAGACTCATG-ATGTACG
1 ATAAACTATGATGCCATGAGGAATCTTGAGACTCATGTATGTACG
554517 ATAAACTATGATGCCATGAGGAATCTTGAGACTCATGTATGTACG
1 ATAAACTATGATGCCATGAGGAATCTTGAGACTCATGTATGTACG
554562 ATA
1 ATA
554565 TATGTGCAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 37 0.79
45 10 0.21
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (45 bp):
ATAAACTATGATGCCATGAGGAATCTTGAGACTCATGTATGTACG
Found at i:561668 original size:14 final size:15
Alignment explanation
Indices: 561636--561665 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
561626 AAAGAAAATA
*
561636 TGACTAATTTAATTT
1 TGACTAATTCAATTT
561651 TGACTAATTCAATTT
1 TGACTAATTCAATTT
561666 GACCGGTGAC
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:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (15 bp):
TGACTAATTCAATTT
Found at i:561911 original size:3 final size:3
Alignment explanation
Indices: 561903--561948 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
561893 TCTGGGTTAA
561903 TAT TAT TAT TATT TAT TAT TAT TAT TAT TA- TAT TAT T-T ATAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
561948 T
1 T
561949 TTTTAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 3 0.08
3 32 0.82
4 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:561989 original size:16 final size:17
Alignment explanation
Indices: 561955--562001 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
561945 TATTTTTTAA
*
561955 AAAAAATAGAAAAA-TAC
1 AAAAAATA-AAAAAGGAC
*
561972 AAAAGA-AAAAAAGGAC
1 AAAAAATAAAAAAGGAC
561988 AAAAAATAAAAAAG
1 AAAAAATAAAAAAG
562002 TTACCCTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 5 0.20
16 8 0.32
17 12 0.48
ACGTcount: A:0.79, C:0.04, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAAATAAAAAAGGAC
Found at i:563867 original size:26 final size:26
Alignment explanation
Indices: 563831--564332 Score: 214
Period size: 20 Copynumber: 22.1 Consensus size: 26
563821 ATGCCTTAAT
*
563831 GCATCCTTTCATACATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
563857 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
* *
563877 GCATCTTTTCATGAATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* ** *
563903 ACATATTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
563923 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
563949 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
* *
563969 GTATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
563989 GCATCATTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* *
564015 ACATCCTTTGCATGC--CTTA--T-T-
1 GCATCCTTT-CATGCATTTTAGTTATG
*
564036 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
564056 GCATCCTTTCATGC--CTTA---A-G
1 GCATCCTTTCATGCATTTTAGTTATG
*
564076 GCATCCTTTTATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
564102 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
564122 GCATCATTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
564148 GCATCCTGTCATGCA--TTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
564168 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
564194 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
* *
564214 GCATCATTTCATGCA-TTTAATTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* * *
564239 GCATCTTTTCAAGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
564259 GCATCCTTTCATGTATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* *
564285 ACATCCTTTCATG--TCTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
564305 GTATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
564331 GC
1 GC
564333 TTCGTTTTAG
Statistics
Matches: 373, Mismatches: 47, Indels: 112
0.70 0.09 0.21
Matches are distributed among these distances:
20 158 0.42
21 27 0.07
22 26 0.07
23 1 0.00
24 27 0.07
25 30 0.08
26 99 0.27
27 5 0.01
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAGTTATG
Found at i:563927 original size:66 final size:64
Alignment explanation
Indices: 563807--564318 Score: 277
Period size: 66 Copynumber: 7.6 Consensus size: 64
563797 TAATTTCATT
* *
563807 TATGACATCC-TTTCATGCCTTA-ATGCATCCTTTCATACATTTTAGTTATGGCATCCTTTCATG
1 TATG-CATCCTTTTCATGCCTTATATGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATG
563870 C-CTTA
59 CACTTA
** **
563875 -ATGCAT-CTTTTCATGAATTTTAGTTATGACATATTTTCATGCCTTAATGCATCCTTTCATGCA
1 TATGCATCCTTTTCATG--CCTTA--TATG-CATCCTTTCATGCCTTAATGCATCCTTTCATGCA
*
563938 TTTTA
61 -CTTA
* * *
563943 GTTATGGCATCC-TTTCATGCCTTA-ATGTATCCTTTCATGCCTTAATGCATCATTTCATGCATT
1 --TAT-GCATCCTTTTCATGCCTTATATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA-C
564006 TTA
62 TTA
*
564009 GTTATGACATCCTTTGCATGCCTTAT-TGCATCCTTTCATGCCTTAATGCATCCTTTCATGC-CT
1 --TATG-CATCCTTTTCATGCCTTATATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCACT
564072 TA
63 TA
* * *
564074 -AGGCATCCTTTT-ATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCA
1 TATGCATCCTTTTCATGC--CTTA--TAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
*
564137 TTTTA
61 -CTTA
* * *
564142 GTTATGGCATCC-TGTCATGCATTA-ATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCA
1 --TAT-GCATCCTTTTCATGCCTTATATGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCA
564205 TGC-CTTA
57 TGCACTTA
* * * * *
564212 -ATGCAT-CATTTCATGCATTTAATTATGGCATCTTTTCAAGCCTTAATGCATCCTTTCATGTAT
1 TATGCATCCTTTTCATGC-CTT-A-TAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCA-
*
564275 TTTA
61 CTTA
* *
564279 GTTATGACATCC-TTTCATGTCTTA-ATGTATCCTTTCATGC
1 --TATG-CATCCTTTTCATGCCTTATATGCATCCTTTCATGC
564319 ATTTTAGTTA
Statistics
Matches: 355, Mismatches: 40, Indels: 100
0.72 0.08 0.20
Matches are distributed among these distances:
60 4 0.01
61 8 0.02
62 5 0.01
64 1 0.00
65 20 0.06
66 140 0.39
67 63 0.18
68 13 0.04
69 4 0.01
70 19 0.05
71 32 0.09
72 45 0.13
73 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (64 bp):
TATGCATCCTTTTCATGCCTTATATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCACTTA
Found at i:563981 original size:46 final size:46
Alignment explanation
Indices: 563806--563982 Score: 282
Period size: 46 Copynumber: 3.8 Consensus size: 46
563796 TTAATTTCAT
*
563806 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATACATTTTAG
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
* * *
563852 TTATGGCATCCTTTCATGCCTTAATGCATCTTTTCATGAATTTTAG
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
**
563898 TTATGACATATTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
* *
563944 TTATGGCATCCTTTCATGCCTTAATGTATCCTTTCATGC
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
563983 CTTAATGCAT
Statistics
Matches: 118, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (46 bp):
TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
Found at i:564020 original size:92 final size:87
Alignment explanation
Indices: 563949--564318 Score: 451
Period size: 91 Copynumber: 4.2 Consensus size: 87
563939 TTTAGTTATG
* *
563949 GCATCCTTTCATGCCTTAATGTATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
564014 GACATCCTTTGCATGCCTTAT-T
66 GACATCCTTT-CATGCCTTATAT
* *
564036 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCCTTAAGGCATCCTTTTATGCATTTTAGTTAT
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
*
564101 GGCATCCTTTCATGCCTTA-AT
66 GACATCCTTTCATGCCTTATAT
* * * *
564122 GCATCATTTCATGCATTTTAGTTATGGCATCCTGTCATGCATTAATGCATCCTTTCATGCATTTT
1 GCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
*
564187 AGTTATGGCATCCTTTCATGCCTTA-AT
60 AGTTATGACATCCTTTCATGCCTTATAT
* * * * *
564214 GCATCATTTCATGCATTTAATTATGGCATCTTTTCAAGCCTTAATGCATCCTTTCATGTATTTTA
1 GCATCCTTTCATGC-CTT-A--AT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
*
564279 GTTATGACATCCTTTCATGTCTTA-AT
61 GTTATGACATCCTTTCATGCCTTATAT
*
564305 GTATCCTTTCATGC
1 GCATCCTTTCATGC
564319 ATTTTAGTTA
Statistics
Matches: 254, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
86 23 0.09
87 70 0.28
88 3 0.01
91 81 0.32
92 77 0.30
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.43
Consensus pattern (87 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTAT
GACATCCTTTCATGCCTTATAT
Found at i:564021 original size:46 final size:46
Alignment explanation
Indices: 563971--564332 Score: 513
Period size: 46 Copynumber: 8.0 Consensus size: 46
563961 GCCTTAATGT
* *
563971 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGAC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGC
* *
564017 ATCCTTTGCATGCCTTATTGCATCCTTTCATGC--CTTA---AT-GC
1 ATCCTTT-CATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGC
* *
564058 ATCCTTTCATGCCTTAAGGCATCCTTTTATGCATTTTAGTTATGGC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGC
*
564104 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGC
* *
564150 ATCCTGTCATGCATTAATGCATCCTTTCATGCATTTTAGTTATGGC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGC
* *
564196 ATCCTTTCATGCCTTAATGCATCATTTCATGCA-TTTAATTATGGC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGC
* * * *
564241 ATCTTTTCAAGCCTTAATGCATCCTTTCATGTATTTTAGTTATGAC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGC
* *
564287 ATCCTTTCATGTCTTAATGTATCCTTTCATGCATTTTAGTTATGGC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGC
564333 TTCGTTTTAG
Statistics
Matches: 278, Mismatches: 30, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
40 22 0.08
41 8 0.03
42 5 0.02
45 45 0.16
46 175 0.63
47 23 0.08
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (46 bp):
ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGC
Found at i:564280 original size:137 final size:137
Alignment explanation
Indices: 563971--564332 Score: 522
Period size: 137 Copynumber: 2.7 Consensus size: 137
563961 GCCTTAATGT
*
563971 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATCCTTTGCATGCCTTATT
1 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATCCTTT-CATG-CTTAAT
* * *
564036 GCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGCCTTAAGGCATCCTTTTATGCATTTT
64 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAGGCATCATTTCATGCATTTT
*
564095 AGTTATGGC
129 AATTATGGC
* *
564104 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCCTGTCATGCATTAATG
1 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATCCTTTCATGC-TTAATG
*
564169 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCA-TTTA
65 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAGGCATCATTTCATGCATTTTA
564233 ATTATGGC
130 ATTATGGC
* * * *
564241 ATCTTTTCAAGCCTTAATGCATCCTTTCATGTATTTTAGTTATGACATCCTTTCATGTCTTAATG
1 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATCCTTTCATG-CTTAATG
*
564306 TATCCTTTCATGCATTTTAGTTATGGC
65 CATCCTTTCATGCATTTTAGTTATGGC
564333 TTCGTTTTAG
Statistics
Matches: 206, Mismatches: 15, Indels: 12
0.88 0.06 0.05
Matches are distributed among these distances:
131 1 0.00
132 22 0.11
133 51 0.25
134 3 0.01
137 96 0.47
138 33 0.16
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (137 bp):
ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATCCTTTCATGCTTAATGC
ATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAGGCATCATTTCATGCATTTTAA
TTATGGC
Found at i:566410 original size:13 final size:13
Alignment explanation
Indices: 566392--566424 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
566382 TAAGATTTTC
*
566392 TTTGAAAATCATT
1 TTTGAAAATCAAT
566405 TTTG-AAATCAAT
1 TTTGAAAATCAAT
566417 TTTGAAAA
1 TTTGAAAA
566425 ATTACTCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:568177 original size:13 final size:13
Alignment explanation
Indices: 568159--568197 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
568149 AATTGGCAAA
* *
568159 TTTGAAAACTATT
1 TTTGAAAACAATG
568172 TTTGAAAACAATG
1 TTTGAAAACAATG
568185 TTTGAAAATCAAT
1 TTTGAAAA-CAAT
568198 ATTTAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:568742 original size:21 final size:21
Alignment explanation
Indices: 568676--568742 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
568666 CGGTACATTG
*
568676 CATAGTGTATCGATGCATATT
1 CATAATGTATCGATGCATATT
* * * * **
568697 CAAGGAATGCATCGGTGTACCTT
1 C-A-TAATGTATCGATGCATATT
568720 CATAATGTATCGATGCATATT
1 CATAATGTATCGATGCATATT
568741 CA
1 CA
568743 ATGAATGCAT
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
21 16 0.52
22 2 0.06
23 13 0.42
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (21 bp):
CATAATGTATCGATGCATATT
Found at i:568754 original size:23 final size:23
Alignment explanation
Indices: 568684--568754 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
568674 TGCATAGTGT
*
568684 ATCGATGCATATTCAAGGAATGC
1 ATCGATGCATATTCAATGAATGC
* * ** *
568707 ATCGGTGTACCTTC-AT-AATGT
1 ATCGATGCATATTCAATGAATGC
568728 ATCGATGCATATTCAATGAATGC
1 ATCGATGCATATTCAATGAATGC
568751 ATCG
1 ATCG
568755 TACACTTTTA
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
21 14 0.40
22 3 0.09
23 18 0.51
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (23 bp):
ATCGATGCATATTCAATGAATGC
Found at i:580557 original size:26 final size:26
Alignment explanation
Indices: 580528--581138 Score: 474
Period size: 26 Copynumber: 26.1 Consensus size: 26
580518 AAACCCTAAT
* * *
580528 GCATCCTTTCTTGTATTTTTGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
580554 GCATACTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* *
580580 GAATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
580600 GCATCCTTTCATGCATTTTAGTTATA
1 GCATCCTTTCATGCATTTTAGTTATG
* *
580626 GCATCATTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
580646 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* * *
580672 GCATCCTTTCCTGC--CTTA---A-A
1 GCATCCTTTCATGCATTTTAGTTATG
* *
580692 ACATCATTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* * *
580718 ACATGCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
580738 GCATCCCTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* *
580764 GCATCCTTTCATTC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
580784 GCATCATTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
580810 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
580836 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
580862 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
580882 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
580908 GAATCCTTTCATGC---TTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
580927 GCATCATTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
580953 GCATCCTTTCATGAATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
580979 GCATCCTTTCAAGC--TTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
580999 GCATCATTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* *
581025 GCATTCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
581045 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
581071 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
581091 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
581111 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
581137 GC
1 GC
581139 TTCATTTTAG
Statistics
Matches: 471, Mismatches: 53, Indels: 122
0.73 0.08 0.19
Matches are distributed among these distances:
19 12 0.03
20 135 0.29
21 17 0.04
22 31 0.07
23 3 0.01
24 28 0.06
25 19 0.04
26 226 0.48
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.44
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAGTTATG
Found at i:580596 original size:118 final size:118
Alignment explanation
Indices: 580468--580681 Score: 329
Period size: 118 Copynumber: 1.8 Consensus size: 118
580458 CATGACATCA
* *
580468 TTTCATGCCTTAATGCATCCATTCATACATTTTAGTTATGGCATCTTTTCAAACCCTAATGCATC
1 TTTCATGCCTTAATGCATCCATTCATACATTTTAGTTATAGCATCATTTCAAACCCTAATGCATC
* * *
580533 CTTTCTTGTATTTTTGTTATGGCATACTTTCATGCATTTTAGTTATGGAATCC
66 CTTTCATGCATTTTAGTTATGGCATACTTTCATGCATTTTAGTTATGGAATCC
* * ** *
580586 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATAGCATCATTTCATGCCTTAATGCATC
1 TTTCATGCCTTAATGCATCCATTCATACATTTTAGTTATAGCATCATTTCAAACCCTAATGCATC
*
580651 CTTTCATGCATTTTAGTTATGGCATCCTTTC
66 CTTTCATGCATTTTAGTTATGGCATACTTTC
580682 CTGCCTTAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 85 1.00
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (118 bp):
TTTCATGCCTTAATGCATCCATTCATACATTTTAGTTATAGCATCATTTCAAACCCTAATGCATC
CTTTCATGCATTTTAGTTATGGCATACTTTCATGCATTTTAGTTATGGAATCC
Found at i:580606 original size:72 final size:71
Alignment explanation
Indices: 580482--581136 Score: 452
Period size: 72 Copynumber: 9.4 Consensus size: 71
580472 ATGCCTTAAT
* * * ** * * *
580482 GCATCCATTCATACATTTTAGTTATGGCATCTTTTCAAACCCTAATGCATCCTTTCTTGTATTTT
1 GCATCCTTTCATGCATTTTAGTTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
*
580547 TGTTATG
65 AGTTATG
* *
580554 GCATACTTTCATGCATTTTAGTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 GCATCCTTTCATGCATTTTAGTTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
*
580619 AGTTATA
65 AGTTATG
* * * *
580626 GCATCATTTCATGC--CTTA---ATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCCTGC
1 GCATCCTTTCATGCATTTTAGTTATGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGC
* *
580686 --CTTA---A-A
60 ATTTTAGTTATG
* * * *
580692 ACATCATTTCATGCATTTTAGTTATGACATGCTTTCATGCCTTAATGCATCCCTTCATGCATTTT
1 GCATCCTTTCATGCATTTTAGTTATG-CATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
580757 AGTTATG
65 AGTTATG
* * * *
580764 GCATCCTTTCATTC--CTTA---ATGCATCATTTCATGCATTTTAGTTATGGCATCCTTTCATGC
1 GCATCCTTTCATGCATTTTAGTTATGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGC
580824 ATTTTAGTTATG
60 ATTTTAGTTATG
580836 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 GCATCCTTTCATGCATTTTAGTTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
580901 AGTTATG
65 AGTTATG
* * * *
580908 GAATCCTTTCATGC---TTA---ATGCATCATTTCATGCATTTTAGTTATGGCATCCTTTCATGA
1 GCATCCTTTCATGCATTTTAGTTATGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGC
580967 ATTTTAGTTATG
60 ATTTTAGTTATG
* * * *
580979 GCATCCTTTCAAGC--TTTA---ATGCATCATTTCATGCATTTTAGTTATGGCATTCTTTCATGC
1 GCATCCTTTCATGCATTTTAGTTATGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGC
*
581039 --CTTA---AT-
60 ATTTTAGTTATG
*
581045 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC--CTT
1 GCATCCTTTCATGCATTTTAGTTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
581108 A---AT-
65 AGTTATG
581111 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
581137 GCTTCATTTT
Statistics
Matches: 488, Mismatches: 52, Indels: 93
0.77 0.08 0.15
Matches are distributed among these distances:
65 14 0.03
66 109 0.22
67 15 0.03
68 16 0.03
69 3 0.01
70 20 0.04
71 47 0.10
72 241 0.49
73 2 0.00
74 3 0.01
76 3 0.01
77 2 0.00
78 13 0.03
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (71 bp):
GCATCCTTTCATGCATTTTAGTTATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
GTTATG
Found at i:580940 original size:45 final size:46
Alignment explanation
Indices: 580554--580965 Score: 619
Period size: 46 Copynumber: 8.8 Consensus size: 46
580544 TTTTGTTATG
* *
580554 GCATACTTTCATGCATTTTAGTTATGGAATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
580600 GCATCCTTTCATGCATTTTAGTTATAGCATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
580646 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCCTGCCTTAAA
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* * * *
580692 ACATCATTTCATGCATTTTAGTTATGACATGCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
580738 GCATCCCTTCATGCATTTTAGTTATGGCATCCTTTCATTCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
580784 GCATCATTTCATGCATTTTAGTTATGGCATCCTTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGC--CTTA---AT
580835 GGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
*
580882 GCATCCTTTCATGCATTTTAGTTATGGAATCCTTTCATG-CTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
*
580927 GCATCATTTCATGCATTTTAGTTATGGCATCCTTTCATG
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATG
580966 AATTTTAGTT
Statistics
Matches: 331, Mismatches: 29, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
45 43 0.13
46 239 0.72
47 2 0.01
48 3 0.01
50 3 0.01
51 2 0.01
52 39 0.12
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
Found at i:581020 original size:46 final size:46
Alignment explanation
Indices: 580953--581104 Score: 259
Period size: 46 Copynumber: 3.3 Consensus size: 46
580943 TTTAGTTATG
* * *
580953 GCATCCTTTCATGAATTTTAGTTATGGCATCCTTTCAAGCTTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
580999 GCATCATTTCATGCATTTTAGTTATGGCATTCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
581045 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
581091 GCATCCTTTCATGC
1 GCATCCTTTCATGC
581105 CTTAATGCAT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.43
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
Found at i:582048 original size:188 final size:188
Alignment explanation
Indices: 581731--582109 Score: 713
Period size: 188 Copynumber: 2.0 Consensus size: 188
581721 AGTATCGATA
* *
581731 CCACTTGCATCGGTATCGATATTGTTCGTCATATCTCTACCTATTTACAACTATAGTATTGGTAT
1 CCACTTGCATCGGTATCGATATTGTTCGTCACATCTCTACCTATTTACAACTATAGTATCGGTAT
581796 TGTTCTATCAGTACAGATACCCTTACCCATATTTGCCATTTTCAGCCCGATGTTTACTAAATTTC
66 TGTTCTATCAGTACAGATACCCTTACCCATATTTGCCATTTTCAGCCCGATGTTTACTAAATTTC
581861 CCCCTCTAATCTCTTAATTTTACATCCAACAATTCTATTAAACTTTTATTTACTTAAC
131 CCCCTCTAATCTCTTAATTTTACATCCAACAATTCTATTAAACTTTTATTTACTTAAC
* *
581919 CCACTTGCATCGGTATCGATATTGTTCGTCACATTTCTACCTATTTACACCTATAGTATCGGTAT
1 CCACTTGCATCGGTATCGATATTGTTCGTCACATCTCTACCTATTTACAACTATAGTATCGGTAT
581984 TGTTCTATCAGTACAGATACCCTTACCCATATTTGCCATTTTCAGCCCGATGTTTACTAAATTTC
66 TGTTCTATCAGTACAGATACCCTTACCCATATTTGCCATTTTCAGCCCGATGTTTACTAAATTTC
*
582049 CCCCTCTAATCTCTTAATTTTACCTCCAACAATTCTATTAAACTTTTATTTACTTAAC
131 CCCCTCTAATCTCTTAATTTTACATCCAACAATTCTATTAAACTTTTATTTACTTAAC
582107 CCA
1 CCA
582110 ACTAACTTTA
Statistics
Matches: 186, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
188 186 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (188 bp):
CCACTTGCATCGGTATCGATATTGTTCGTCACATCTCTACCTATTTACAACTATAGTATCGGTAT
TGTTCTATCAGTACAGATACCCTTACCCATATTTGCCATTTTCAGCCCGATGTTTACTAAATTTC
CCCCTCTAATCTCTTAATTTTACATCCAACAATTCTATTAAACTTTTATTTACTTAAC
Found at i:583251 original size:14 final size:15
Alignment explanation
Indices: 583235--583284 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
583225 GTATTTTATT
* *
583235 TTTATGGCCTTTA-T
1 TTTATGTCCTTTACA
* *
583249 TTTTTGTCATTTACA
1 TTTATGTCCTTTACA
583264 TTTATGTCCTTTA-A
1 TTTATGTCCTTTACA
583278 TTTATGT
1 TTTATGT
583285 TATTTATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.60
Consensus pattern (15 bp):
TTTATGTCCTTTACA
Found at i:583261 original size:29 final size:29
Alignment explanation
Indices: 583229--583294 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
583219 TTTTCAGTAT
* * *
583229 TTTATTTTTATGGCCTTTATTTTTTGTCA
1 TTTATATTTATGGCCTTTAATTTATGTCA
* * *
583258 TTTACATTTATGTCCTTTAATTTATGTTA
1 TTTATATTTATGGCCTTTAATTTATGTCA
583287 TTTATATT
1 TTTATATT
583295 CTTTCCCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.09, G:0.08, T:0.64
Consensus pattern (29 bp):
TTTATATTTATGGCCTTTAATTTATGTCA
Found at i:583290 original size:14 final size:15
Alignment explanation
Indices: 583253--583290 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
583243 CTTTATTTTT
583253 TGTCATTTACATTTA
1 TGTCATTTACATTTA
*
583268 TGTCCTTTA-ATTTA
1 TGTCATTTACATTTA
*
583282 TGTTATTTA
1 TGTCATTTA
583291 TATTCTTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.58
Consensus pattern (15 bp):
TGTCATTTACATTTA
Found at i:584060 original size:45 final size:45
Alignment explanation
Indices: 583727--584208 Score: 435
Period size: 45 Copynumber: 11.0 Consensus size: 45
583717 GTCTGATAAC
583727 ACAATACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATGA
1 ACAATACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT-A
* * * ***
583773 A-AACAC-CAATATATTGAC-TCATCTTCGTAAGAAAGTCAAGAATA
1 ACAATACTGAA-AGATTGACTTC-TCTTCACGAGAAAGTCAAGAATA
* * * * * *
583817 AC-ATCACTAAAAGGTTAACCTCTCCTCCCGAGAAAGTCAAG-AT-
1 ACAAT-ACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATA
* *
583860 -CAACACTGAAAGATTGAC-TCTTTTTCACGAG-AAGTCAAGAATA
1 ACAATACTGAAAGATTGACTTC-TCTTCACGAGAAAGTCAAGAATA
* *
583903 AC-AT--TGAAAGATTGACTCCTCTTCACGATG-GAGTCAAGAATA
1 ACAATACTGAAAGATTGACTTCTCTTCACGA-GAAAGTCAAGAATA
* * *
583945 AC-AT--TGAAAGATTGAATTCTCTTCATGAAAAAGTCAAGAATA
1 ACAATACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATA
* *
583987 ACATTACTGAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATG
1 ACAATACTG-AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATA
* *
584033 ACAATACTAAAAGATTGACTTCTCTTCACAAGAAAGTCAAGAATA
1 ACAATACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATA
* * * **
584078 AC-AT--TGAAAGATTGACTCCTCTTCATGAGGAAGTCAAGAACG
1 ACAATACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATA
* * * *
584120 ACAATACTAAAAGATTGATTTCTCTTCATGAGAAAGACAAGAATA
1 ACAATACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATA
* * ** *
584165 ACATTATTGAAAGATTGTTTTCTCTTCACGAGAAAGTCATGAAT
1 ACAATACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT
584209 GACTTTCTTG
Statistics
Matches: 354, Mismatches: 61, Indels: 43
0.77 0.13 0.09
Matches are distributed among these distances:
41 30 0.08
42 105 0.30
43 5 0.01
44 12 0.03
45 158 0.45
46 44 0.12
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.26
Consensus pattern (45 bp):
ACAATACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATA
Found at i:584126 original size:87 final size:87
Alignment explanation
Indices: 583734--584211 Score: 413
Period size: 87 Copynumber: 5.5 Consensus size: 87
583724 AACACAATAC
* * * * * * *
583734 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATGAAAACACCAATATATTGAC-TCATCTT
1 TGAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATGACAATACTAAAAGATTGACTTC-TCTT
**
583798 CGTAAGAAAGTCAAGAATAACAT
65 CACAAGAAAGTCAAGAATAACAT
* * * * * * * *
583821 CACTAAAAGGTTAAC-CTCTCCTCCCGAGAAAGTCAAG-AT--CAACACTGAAAGATTGAC-TCT
1 ---TGAAAGATTGACTC-CTCTTCACGAGGAAGTCAAGAATGACAATACTAAAAGATTGACTTC-
* *
583881 TTTTCACGAG-AAGTCAAGAATAACAT
61 TCTTCACAAGAAAGTCAAGAATAACAT
* * *
583907 TGAAAGATTGACTCCTCTTCACGATGG-AGTCAAGAATAAC-AT--TGAAAGATTGAATTCTCTT
1 TGAAAGATTGACTCCTCTTCACGA-GGAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTT
*
583968 CATGAA-AAAGTCAAGAATAACATT
65 CA-CAAGAAAGTCAAGAATAACA-T
* *
583992 ACTGAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATGACAATACTAAAAGATTGACTTCTC
1 --TG-AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATGACAATACTAAAAGATTGACTTCTC
584057 TTCACAAGAAAGTCAAGAATAACAT
63 TTCACAAGAAAGTCAAGAATAACAT
* * *
584082 TGAAAGATTGACTCCTCTTCATGAGGAAGTCAAGAACGACAATACTAAAAGATTGATTTCTCTTC
1 TGAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTTC
** *
584147 ATGAGAAAGACAAGAATAACATTAT
66 ACAAGAAAGTCAAGAATAAC---AT
** * * *
584172 TGAAAGATTGTTTTCTCTTCACGAGAAAGTCATGAATGAC
1 TGAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATGAC
584212 TTTCTTGCAT
Statistics
Matches: 319, Mismatches: 48, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
83 40 0.13
84 22 0.07
85 2 0.01
86 17 0.05
87 99 0.31
88 35 0.11
89 4 0.01
90 65 0.20
91 35 0.11
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (87 bp):
TGAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTTC
ACAAGAAAGTCAAGAATAACAT
Found at i:585114 original size:3 final size:3
Alignment explanation
Indices: 585106--585140 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
585096 AGGTTAATAA
*
585106 ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
585141 AGATTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:587777 original size:45 final size:45
Alignment explanation
Indices: 587674--588344 Score: 594
Period size: 45 Copynumber: 15.3 Consensus size: 45
587664 GAAGCTTCAA
* * * *
587674 CTTGACTTCCTCATGAAGAGGAGTCAATCTTTCAATA-T-T-ATT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
*
587716 CTTGACTTTCTCGTGAAAAGAAGTCAATCTTTCAGTATTGTCATT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * * *
587761 CCTGACTTTCTTGTGAAGAGAAGTCAATCTTTCAATAATGTTATT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * *
587806 CTTGACTTTCTCGTGAATAGAATTCAATCTTTTAGTATTGTCGTT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * * *
587851 CTTGACTTCCTCATGAAGAGTAGTCAATATTTCAG---TGTTATT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
587893 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * *
587938 CCTGACTTTCTCATGAAGAGAAGTCAATCTTTCAGTAATGTTATT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* *
587983 CTTGACTTTCTTGTGAAGAGAAGTCAATCTTTCA--ATTTTC-TT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
** * * *
588025 CTTGACTCCCTCGTGAAGAGGAGTCAATCGTTCA--A-TGTTATT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
*
588067 CTTGAC-TTCTCGTAAAGA-AGAGTCAATCTTTCAGTATTG--A-T
1 CTTGACTTTCTCGTGAAGAGA-AGTCAATCTTTCAGTATTGTCATT
* * * * * * * *
588108 CTTAACTTTCTCGGGAAGAGAAAT-TACCTTTTAGTGA-CGTTATT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGT-ATTGTCATT
* ** * * * *
588152 CTTGACTTTCTTGCAAAGAGGAGTCAATATATT-GGTGTTGTCATT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCT-TTCAGTATTGTCATT
*
588197 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTGTTGTC-TT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * * * * *
588241 CCTTGACTTTCTCATGAAGA-AGATTCCATCTTTTAGTGTTATCCTT
1 -CTTGACTTTCTCGTGAAGAGA-AGTCAATCTTTCAGTATTGTCATT
* * * * *
588287 CTTGACTTTCTCGTGAAGAGGAGTCCATCTTTTAGTGTTGTCCTTT
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGT-CATT
*
588333 TTTGACTTTCTC
1 CTTGACTTTCTC
588345 ACGAAGAAGA
Statistics
Matches: 509, Mismatches: 94, Indels: 48
0.78 0.14 0.07
Matches are distributed among these distances:
41 38 0.07
42 122 0.24
43 7 0.01
44 27 0.05
45 297 0.58
46 18 0.04
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (45 bp):
CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATT
Found at i:587911 original size:132 final size:132
Alignment explanation
Indices: 587674--588318 Score: 573
Period size: 132 Copynumber: 4.9 Consensus size: 132
587664 GAAGCTTCAA
* * * * * *
587674 CTTGACTTCCTCATGAAGAGGAGTCAATCTTTCAATA-T-T-ATTCTTGACTTTCTCGTGAAAAG
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCGTTCTTGACTTTCTCGTGAAGAG
* * * * *
587736 AAGTCAATCTTTCAGTATTGTCATTCCTGACTTTCTTGTGAAGAGAAGTCAATCTTTCAATAATG
66 AAGTCAATCTTTCAG---TGTTATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTAATG
*
587801 TTATT
128 TCATT
* * * * *
587806 CTTGACTTTCTCGTGAATAGAATTCAATCTTTTAGTATTGTCGTTCTTGACTTCCTCATGAAGAG
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCGTTCTTGACTTTCTCGTGAAGAG
* * * *
587871 TAGTCAATATTTCAGTGTTATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCA
66 AAGTCAATCTTTCAGTGTTATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTAATGTCA
587936 TT
131 TT
* * * ** *
587938 CCTGACTTTCTCATGAAGAGAAGTCAATCTTTCAGTAATGTTATTCTTGACTTTCTTGTGAAGAG
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCGTTCTTGACTTTCTCGTGAAGAG
* * * ** * *
588003 AAGTCAATCTTTCAATTTTCTTCTTGACTCCCTCGTGAAGAGGAGTCAATCGTTC---AATGTTA
66 AAGTCAATCTTTCAGTGTTATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTAATGTCA
588065 TT
131 TT
* * * *
588067 CTTGAC-TTCTCGTAAAGA-AGAGTCAATCTTTCAGTA-T-T-GATCTTAACTTTCTCGGGAAGA
1 CTTGACTTTCTCGTGAAGAGA-AGTCAATCTTTCAGTATTGTCGTTCTTGACTTTCTCGTGAAGA
* * * * * ** * * **
588127 GAAAT-TACCTTTTAGTGACGTTATTCTTGACTTTCTTGCAAAGAGGAGTCAATATATT-GGTGT
65 GAAGTCAATCTTTCAGT---GTTATTCTTGACTTTCTCGTGAAGAGGAGTCAATCT-TTCAGTAA
588190 TGTCATT
126 TGTCATT
* *
588197 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTGTTGTC-TTCCTTGACTTTCTCATGAAGA
1 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCGTT-CTTGACTTTCTCGTGAAGA
* * * *
588261 -AGATTCCATCTTTTAGTGTTATCCTTCTTGACTTTCTCGTGAAGAGGAGTCCATCTTT
65 GA-AGTCAATCTTTCAGTGTTA---TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTT
588319 TAGTGTTGTC
Statistics
Matches: 411, Mismatches: 80, Indels: 42
0.77 0.15 0.08
Matches are distributed among these distances:
124 7 0.02
125 21 0.05
126 1 0.00
127 29 0.07
128 28 0.07
129 12 0.03
130 12 0.03
131 26 0.06
132 182 0.44
133 4 0.01
134 21 0.05
135 68 0.17
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (132 bp):
CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCGTTCTTGACTTTCTCGTGAAGAG
AAGTCAATCTTTCAGTGTTATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTAATGTCA
TT
Found at i:588402 original size:91 final size:90
Alignment explanation
Indices: 588192--588413 Score: 223
Period size: 91 Copynumber: 2.5 Consensus size: 90
588182 ATTGGTGTTG
* * * * *
588192 TCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTGTTGTCTTCCTTGACTTTCTCATG
1 TCATTCTTAACTCTCTCGGGAAGAGGAGTCAATCTTTCAGTGTTGTCTTCCTTGACTTTCTCACG
* * * *
588257 AAGAAGATTCCATCTTTTAGTGTTA
66 AAGAAGAGTCAACCTTTTAGTGGTA
* * * * * * **
588282 TCCTTCTTGACTTTCTCGTGAAGAGGAGTCCATCTTTTAGTGTTGTCCTTTTTTGACTTTCTCAC
1 TCATTCTTAACTCTCTCGGGAAGAGGAGTCAATCTTTCAGTGTTGT-CTTCCTTGACTTTCTCAC
*
588347 GAAGAAGAGTCAACCTTTTAGTGGTG
65 GAAGAAGAGTCAACCTTTTAGTGGTA
* *
588373 TTATTCTTAACTCTCTCGCGGAA-ATGAGTCAA-CTTTTCAGT
1 TCATTCTTAACTCTCTCG-GGAAGAGGAGTCAATC-TTTCAGT
588414 AGTACCCTTC
Statistics
Matches: 109, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
90 43 0.39
91 63 0.58
92 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (90 bp):
TCATTCTTAACTCTCTCGGGAAGAGGAGTCAATCTTTCAGTGTTGTCTTCCTTGACTTTCTCACG
AAGAAGAGTCAACCTTTTAGTGGTA
Found at i:589239 original size:130 final size:130
Alignment explanation
Indices: 589092--589444 Score: 457
Period size: 130 Copynumber: 2.7 Consensus size: 130
589082 GTGGAGAAGA
* *
589092 TTCTTCTTCTTTCATATTTTGTCTTCCTAAAGAGCAGTGAAGCAAATCGACTTTGATTCAACTTT
1 TTCTTCTTCTTTCATATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGACTTTGATTCAAC-TT
* *
589157 CCCTGAAGAGAACTGAAGTGGATCAAAATTTGTCAAGATCTGATTACCCAAAAAGTGGGGT-GAT
65 CCCTGAAGAGAACTGAAGTGAATCAAAATTTGTCAAGATCTGATTACCCAAAAAATGGGGTGGAT
589221 T
130 T
* *
589222 TTCTTCTTCTTTCATATTTGGTCTTCCTGAAGCGCAGTGAAGCAAATCGACTTCGATTCAACCTT
1 TTCTTCTTCTTTCATATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGACTTTGATTCAA-CTT
* * *
589287 CCCTGAAAAGTAGTGAAGTGAATCAAAATTTGTCAAGATCTGATTACCCAAAAAATGGGGTGGAT
65 CCCTGAAGAGAACTGAAGTGAATCAAAATTTGTCAAGATCTGATTACCCAAAAAATGGGGTGGAT
589352 T
130 T
* * * *
589353 TTAC--C-TCTATT-AGATTTGGTTCTTCCTGAATAGCAGTGAAGCAAGTCGAGTTTGATTCAAG
1 TT-CTTCTTCT-TTCATATTTGG-TCTTCCTGAAGAGCAGTGAAGCAAATCGACTTTGATTCAA-
* * *
589414 CGTCCCTGAAGAGCAA-GGAAATGAATCAAAA
62 CTTCCCTGAAGAG-AACTGAAGTGAATCAAAA
589445 AAAATTTAGA
Statistics
Matches: 196, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
129 10 0.05
130 177 0.90
131 8 0.04
132 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (130 bp):
TTCTTCTTCTTTCATATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGACTTTGATTCAACTTC
CCTGAAGAGAACTGAAGTGAATCAAAATTTGTCAAGATCTGATTACCCAAAAAATGGGGTGGATT
Found at i:589953 original size:3 final size:3
Alignment explanation
Indices: 589947--589975 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
589937 TTATTATTAT
589947 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
589976 AATAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:593654 original size:29 final size:30
Alignment explanation
Indices: 593591--593656 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
593581 TATTCCAATG
**
593591 TTTTAATTTTCAGTATTTTATTTTTATGCC
1 TTTTAATTTTCAGTATTTTACATTTATGCC
* *
593621 CTTTAATTTTC-G-ATATTTACATTTCTGCC
1 TTTTAATTTTCAGTAT-TTTACATTTATGCC
593650 TTTTAAT
1 TTTTAAT
593657 ATTCCGGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.07
29 18 0.60
30 10 0.33
ACGTcount: A:0.21, C:0.14, G:0.06, T:0.59
Consensus pattern (30 bp):
TTTTAATTTTCAGTATTTTACATTTATGCC
Found at i:594123 original size:17 final size:18
Alignment explanation
Indices: 594098--594138 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
594088 TTAATCACTC
* *
594098 TAAACTATTTAAA-AAAA
1 TAAATTATTGAAACAAAA
594115 TAAATTATTGAAACAAAA
1 TAAATTATTGAAACAAAA
594133 TAAATT
1 TAAATT
594139 GATGTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (18 bp):
TAAATTATTGAAACAAAA
Found at i:599921 original size:21 final size:21
Alignment explanation
Indices: 599878--599930 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
599868 ATTCTGACTA
599878 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * **
599899 TCGCGTTGCGATTTTCCTTAT
1 TCGCATTGCGATTTCCCAAAT
*
599920 TCGCAATGCGA
1 TCGCATTGCGA
599931 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:599945 original size:20 final size:20
Alignment explanation
Indices: 599920--600045 Score: 218
Period size: 20 Copynumber: 6.3 Consensus size: 20
599910 TTTTCCTTAT
599920 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
599940 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
599960 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
599980 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
600000 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
600020 TCGCAATGCGAAT-CTATAAA
1 TCGCAATGCGAATAC-GTAAA
600040 TCGCAA
1 TCGCAA
600046 CGAGATTCTG
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
19 1 0.01
20 101 0.99
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:600953 original size:24 final size:24
Alignment explanation
Indices: 600893--600960 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
600883 GTGAGTACTA
* *
600893 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
* *
600917 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
*
600941 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGGAATTTGAT
600961 GATTTTTCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (24 bp):
GTCAATACTCGGAATTTGATCTTG
Found at i:603418 original size:20 final size:20
Alignment explanation
Indices: 603393--603479 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
603383 CAACGCGGAA
603393 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* *
603413 ATCGCAACACGGAAATGAAT
1 ATCGCAACGCGGAAATGACT
* *
603433 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
603453 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
603473 ATAGCAA
1 ATCGCAA
603480 TGAGAGAATC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 54 0.95
21 3 0.05
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:603452 original size:40 final size:40
Alignment explanation
Indices: 603393--603481 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
603383 CAACGCGGAA
*
603393 ATCGCAACGCGAATATGACTATCGCAACACGGAAATGAAT
1 ATCGCAATGCGAATATGACTATCGCAACACGGAAATGAAT
* *
603433 ATCGCAATGCGGAAT-TGACTATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAATATGACTATCGCAACACGGAAATGAAT
*
603473 ATAGCAATG
1 ATCGCAATG
603482 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.19
Consensus pattern (40 bp):
ATCGCAATGCGAATATGACTATCGCAACACGGAAATGAAT
Found at i:603541 original size:34 final size:33
Alignment explanation
Indices: 603453--603548 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
603443 GGAATTGACT
* ** * *
603453 ATCGCAACGCGGAAATGACTATAGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
603487 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
603520 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
603549 CGAAATTAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.52
34 26 0.48
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:603682 original size:14 final size:14
Alignment explanation
Indices: 603663--603699 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
603653 CATCAATTAA
603663 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
603677 ACAAATCATCTTTT
1 ACAAATCAACATTT
603691 ACAAATCAA
1 ACAAATCAA
603700 TTAAACAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:605157 original size:42 final size:42
Alignment explanation
Indices: 605050--605157 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
605040 TCTAGAATGT
* * *
605050 TGGGAG-GGACCTCTTCAACGATGAAAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGAAAGGGGCCTCTTGAACGA
* * *** *
605092 TGGGAGGGGACTCTTGCGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGAAAGGGGCCTCTTGAACGA
605134 TAGGG-GAGGCCTCTTGAACGATGA
1 T-GGGAGAGGCCTCTTGAACGATGA
605158 CAGGTGAGTC
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
42 46 0.90
43 5 0.10
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGAAAGGGGCCTCTTGAACGA
Found at i:605664 original size:20 final size:20
Alignment explanation
Indices: 605641--605749 Score: 182
Period size: 20 Copynumber: 5.5 Consensus size: 20
605631 GAAACTTAAA
605641 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
605661 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
605681 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
605701 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
605721 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
605741 ATCGCAACG
1 ATCGCAACG
605750 AGAGAATCGC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:605873 original size:20 final size:19
Alignment explanation
Indices: 605770--605877 Score: 85
Period size: 20 Copynumber: 6.1 Consensus size: 19
605760 AATGCAATTT
605770 TCATTTCGCATTGCGAT--
1 TCATTTCGCATTGCGATAG
605787 TC-TTTCG--TTGCGATAG
1 TCATTTCGCATTGCGATAG
*
605803 TCAAATTCGCATTGCGATAG
1 TC-ATTTCGCATTGCGATAG
*
605823 TCATTTTTGCATTGCGAT--
1 TCA-TTTCGCATTGCGATAG
605841 TC-TCTT-G--TTGCGATAG
1 TCAT-TTCGCATTGCGATAG
605857 TCATTTGCGCATTGCGATAG
1 TCATTT-CGCATTGCGATAG
605877 T
1 T
605878 AAACTATTCT
Statistics
Matches: 73, Mismatches: 3, Indels: 27
0.71 0.03 0.26
Matches are distributed among these distances:
14 14 0.19
16 13 0.18
17 5 0.07
18 7 0.10
19 1 0.01
20 33 0.45
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:608509 original size:20 final size:20
Alignment explanation
Indices: 608486--608619 Score: 189
Period size: 20 Copynumber: 6.7 Consensus size: 20
608476 CGATAGTCAG
*
608486 ATTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
608506 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
608526 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
608546 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
608566 AATCGCATTGCGATTTTC-T
1 ATTCGCATTGCGATTTACGT
* *
608585 AAATTCGCGTTGTGATTTACGT
1 --ATTCGCATTGCGATTTACGT
608607 ATTCGCATTGCGA
1 ATTCGCATTGCGA
608620 ATTAGCAAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 84 0.84
21 14 0.14
22 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:608640 original size:21 final size:21
Alignment explanation
Indices: 608616--608682 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
608606 TATTCGCATT
*
608616 GCGAATTAGCAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
608637 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
608658 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
608679 GCGA
1 GCGA
608683 TAGTCAGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.16
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:610462 original size:30 final size:30
Alignment explanation
Indices: 610381--610462 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
610371 ATAATAATTC
* *
610381 ATTTGATCCCGCAATTATAATTAAAAGTTT
1 ATTTGATCTCGTAATTATAATTAAAAGTTT
* *
610411 ATTTGATCTCGTAGTTGTAATTAAAAGTTT
1 ATTTGATCTCGTAATTATAATTAAAAGTTT
*
610441 ATTTGATACT-GTAATTCTAATT
1 ATTTGAT-CTCGTAATTATAATT
610463 TTATTACAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 43 0.96
31 2 0.04
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (30 bp):
ATTTGATCTCGTAATTATAATTAAAAGTTT
Found at i:610956 original size:19 final size:19
Alignment explanation
Indices: 610912--611021 Score: 130
Period size: 19 Copynumber: 5.6 Consensus size: 19
610902 ACGCGTTTGC
*
610912 CAAATTCGCAACACTGAATTT
1 CAAATTCGC-A-ACTAAATTT
*
610933 CAAATTCGTAACTAAATTT
1 CAAATTCGCAACTAAATTT
*
610952 TAAATTCGCAACTAAATTT
1 CAAATTCGCAACTAAATTT
*
610971 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACTAAATTT
* *
610990 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACT-AAATTT
*
611010 CGAATTCGCAAC
1 CAAATTCGCAAC
611022 ACGAATTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
19 55 0.69
20 17 0.21
21 8 0.10
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (19 bp):
CAAATTCGCAACTAAATTT
Found at i:614310 original size:18 final size:18
Alignment explanation
Indices: 614287--614322 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
614277 AAGCAAAAGG
*
614287 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
614305 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
614323 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:614657 original size:20 final size:20
Alignment explanation
Indices: 614634--614675 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
614624 AAATCGCAAC
614634 GCAAATTTGACTTTCGCGTT
1 GCAAATTTGACTTTCGCGTT
*
614654 GCAAATTTGATTTTCGCGTT
1 GCAAATTTGACTTTCGCGTT
614674 GC
1 GC
614676 GAAAGTGTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
GCAAATTTGACTTTCGCGTT
Found at i:614762 original size:30 final size:30
Alignment explanation
Indices: 614728--614820 Score: 77
Period size: 37 Copynumber: 3.0 Consensus size: 30
614718 ACAGATTGAA
614728 TAAACAAAAAATCAACTTTTACAAATCAAT
1 TAAACAAAAAATCAACTTTTACAAATCAAT
*
614758 TAAACAAGAAAAAAAT-AATTCTTATTTACACATCAAT
1 TAAAC----AAAAAATCAA--C-T-TTTACAAATCAAT
614795 TAAAC---AAATCAACTTTTACAAATCAA
1 TAAACAAAAAATCAACTTTTACAAATCAA
614821 AGTAAAATTC
Statistics
Matches: 52, Mismatches: 2, Indels: 21
0.69 0.03 0.28
Matches are distributed among these distances:
27 11 0.21
28 1 0.02
29 1 0.02
30 9 0.17
31 2 0.04
33 2 0.04
34 7 0.13
35 1 0.02
36 1 0.02
37 17 0.33
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (30 bp):
TAAACAAAAAATCAACTTTTACAAATCAAT
Found at i:616263 original size:20 final size:21
Alignment explanation
Indices: 616208--616330 Score: 137
Period size: 21 Copynumber: 6.0 Consensus size: 21
616198 CAGTGGGAGG
*
616208 GAGGGACC-CTTGAACGATGA
1 GAGGGGCCTCTTGAACGATGA
* * *
616228 CAGGGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTGAACGATGA
616249 GAGGGGCCT-TTGAACGATGA
1 GAGGGGCCTCTTGAACGATGA
* *
616269 GAGGGACCTCTTGCACGATGA
1 GAGGGGCCTCTTGAACGATGA
616290 GA-GGGCCTCTTGAACGAT-A
1 GAGGGGCCTCTTGAACGATGA
**
616309 GGAGGCACCTCTTGAACGATGA
1 -GAGGGGCCTCTTGAACGATGA
616331 CAGGTGCATC
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.01
20 39 0.46
21 44 0.52
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.36, T:0.19
Consensus pattern (21 bp):
GAGGGGCCTCTTGAACGATGA
Found at i:616263 original size:41 final size:41
Alignment explanation
Indices: 616206--616329 Score: 135
Period size: 41 Copynumber: 3.0 Consensus size: 41
616196 AACAGTGGGA
* * * *
616206 GGGAGGGACCCTTGAACGATGACAGGGGCCTCTTGAACGGT
1 GGGAGGGGCCTTTGAACGATGACAGGGACCTCTTGAACGAT
* *
616247 GGGAGGGGCCTTTGAACGATGAGAGGGACCTCTTGCACGAT
1 GGGAGGGGCCTTTGAACGATGACAGGGACCTCTTGAACGAT
* * *
616288 GAGA-GGGCCTCTTGAACGAT-AGGAGGCACCTCTTGAACGAT
1 GGGAGGGGCCT-TTGAACGATGA-CAGGGACCTCTTGAACGAT
616329 G
1 G
616330 ACAGGTGCAT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
40 7 0.10
41 65 0.90
ACGTcount: A:0.23, C:0.21, G:0.37, T:0.19
Consensus pattern (41 bp):
GGGAGGGGCCTTTGAACGATGACAGGGACCTCTTGAACGAT
Found at i:618506 original size:20 final size:20
Alignment explanation
Indices: 618483--618521 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
618473 AATTCACATT
618483 GCGAAAATGAAAATCGCAAA
1 GCGAAAATGAAAATCGCAAA
*
618503 GCGAACATGAAAATCGCAA
1 GCGAAAATGAAAATCGCAA
618522 CGACAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.10
Consensus pattern (20 bp):
GCGAAAATGAAAATCGCAAA
Found at i:618947 original size:22 final size:22
Alignment explanation
Indices: 618921--618975 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
618911 GATGGAGATA
618921 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGTCAGAGATGGG
*
618943 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCAGAGATGGG
618965 GACGGATTTCG
1 GACGGATTTCG
618976 CCGTAGAGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCAGAGATGGG
Found at i:619118 original size:20 final size:20
Alignment explanation
Indices: 619093--619168 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
619083 ATAAACGCGC
619093 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
619113 TTTGACTTATGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
619133 TTTGACTTCTGTATTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
619153 TTTGACTTCTATGTTG
1 TTTGACTTCTGTGTTG
619169 AGATTTACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.17, C:0.13, G:0.22, T:0.47
Consensus pattern (20 bp):
TTTGACTTCTGTGTTGCGAA
Found at i:620888 original size:3 final size:3
Alignment explanation
Indices: 620882--620938 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
620872 TTCGTTGTTG
*
620882 TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
620928 TTA TTG TTA TT
1 TTA TTA TTA TT
620939 TTACAAACCC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 47 0.96
4 2 0.04
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:620991 original size:21 final size:23
Alignment explanation
Indices: 620954--621005 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
620944 AACCCAAATT
620954 AAACCCT-AACCCAAAA-CAAGA
1 AAACCCTAAACCCAAAACCAAGA
* **
620975 AAACCCTAAATCC-AAACCAATC
1 AAACCCTAAACCCAAAACCAAGA
620997 AAACCCTAA
1 AAACCCTAA
621006 TTTACCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.54, C:0.35, G:0.02, T:0.10
Consensus pattern (23 bp):
AAACCCTAAACCCAAAACCAAGA
Found at i:624206 original size:24 final size:24
Alignment explanation
Indices: 624179--624227 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
624169 CGTTCGTGAA
624179 CGTTCGGTTATGTTCATTTATGTT
1 CGTTCGGTTATGTTCATTTATGTT
*
624203 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCATTTATGTT
624227 C
1 C
624228 ATCCATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.14, G:0.22, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCATTTATGTT
Found at i:624237 original size:24 final size:24
Alignment explanation
Indices: 624185--624240 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
624175 TGAACGTTCG
* * *
624185 GTTATGTTCATTTATGTTCGTTCG
1 GTTATGTTCATTTATGTTCATCCA
*
624209 GTTATGTTCGTTTATGTTCATCCA
1 GTTATGTTCATTTATGTTCATCCA
*
624233 TTTATGTT
1 GTTATGTT
624241 TAACTCAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.55
Consensus pattern (24 bp):
GTTATGTTCATTTATGTTCATCCA
Found at i:625285 original size:16 final size:16
Alignment explanation
Indices: 625263--625316 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
625253 GTTTATTTTT
625263 GTTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
* *
625279 ATTTATGTTTGTGTTC
1 GTTTATGTTCGTGTTC
625295 GTTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
625311 GTTTAT
1 GTTTAT
625317 TTATTAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.59
Consensus pattern (16 bp):
GTTTATGTTCGTGTTC
Found at i:625900 original size:2 final size:2
Alignment explanation
Indices: 625893--625924 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
625883 ATGGACTTGG
625893 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
625925 GGGTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:631102 original size:18 final size:18
Alignment explanation
Indices: 631079--631116 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
631069 GGATTGTTTT
*
631079 CACTTATTTGATCGGTTC
1 CACTTATTTGATCAGTTC
631097 CACTTATTTGATCAGTTC
1 CACTTATTTGATCAGTTC
631115 CA
1 CA
631117 TATGATCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (18 bp):
CACTTATTTGATCAGTTC
Found at i:633913 original size:20 final size:20
Alignment explanation
Indices: 633890--633949 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
633880 GCAAAGCGCA
*
633890 TTTATTTTCGCAACGCAAAT
1 TTTATTTTCGCAACACAAAT
* *
633910 TTTATTTTCGTAACACGAAT
1 TTTATTTTCGCAACACAAAT
* *
633930 ATTAATTTCGCAACACAAAT
1 TTTATTTTCGCAACACAAAT
633950 GTAAATAGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (20 bp):
TTTATTTTCGCAACACAAAT
Found at i:636114 original size:42 final size:41
Alignment explanation
Indices: 636025--636189 Score: 142
Period size: 42 Copynumber: 4.0 Consensus size: 41
636015 CTCCACTTTT
* * *
636025 TCATCGAGTCAATTCTTCAGTTCGACA-CGAGATCCATCACC
1 TCATCGAGTCGATTCTACA-CTCGACACCGAGATCCATCACC
*
636066 TCATCGAGTCGATTCTCCACTGCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTACACT-CGACACCGAGATCCATCACC
* * *
636108 TGATCGAG-CTGATTCTACACCTCGACACCGAGAGCCAT--CG
1 TCATCGAGTC-GATTCTACA-CTCGACACCGAGATCCATCACC
* * * * *
636148 TC-TCTAGCCGACTCTACACCTTGACACCAAGATCCATCACC
1 TCATCGAGTCGATTCTACA-CTCGACACCGAGATCCATCACC
636189 T
1 T
636190 ATTCCATCAC
Statistics
Matches: 103, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
39 28 0.27
40 4 0.04
41 25 0.24
42 44 0.43
43 2 0.02
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (41 bp):
TCATCGAGTCGATTCTACACTCGACACCGAGATCCATCACC
Found at i:636466 original size:21 final size:21
Alignment explanation
Indices: 636296--636475 Score: 97
Period size: 21 Copynumber: 8.8 Consensus size: 21
636286 CGGGATAAGT
636296 TAGGTGCTTTACGTGATGAGG
1 TAGGTGCTTTACGTGATGAGG
*
636317 TCA-ATGCTTTACGTGATGAGG
1 T-AGGTGCTTTACGTGATGAGG
* **
636338 TCGGTGCTTTACGTGATGACA
1 TAGGTGCTTTACGTGATGAGG
* * *
636359 T-GGTGC-AT-GGCG-TGAGG
1 TAGGTGCTTTACGTGATGAGG
* * * *
636376 TACGGT-CTTTACATGGTAAGA
1 TA-GGTGCTTTACGTGATGAGG
* * *
636397 TAGCTGTTTTACGTGATGA-C
1 TAGGTGCTTTACGTGATGAGG
* *
636417 AATGGTG-TTTACGTGGTGAGG
1 TA-GGTGCTTTACGTGATGAGG
*
636438 TAGCTGCTTTACGTGATGAGG
1 TAGGTGCTTTACGTGATGAGG
* * *
636459 TCGGTGCTCTATGTGAT
1 TAGGTGCTTTACGTGAT
636476 ATTGTTTCGT
Statistics
Matches: 115, Mismatches: 33, Indels: 22
0.68 0.19 0.13
Matches are distributed among these distances:
17 4 0.03
18 3 0.03
19 5 0.04
20 23 0.20
21 79 0.69
22 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.34
Consensus pattern (21 bp):
TAGGTGCTTTACGTGATGAGG
Found at i:636830 original size:21 final size:21
Alignment explanation
Indices: 636810--636881 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
636800 ATTCACCTCT
*
636810 CATCGTTCAAGAGACCACTCT
1 CATCGTTCAAGAGACCACTCC
* * *
636831 CATCATTCAAGAGGCCTCTCC
1 CATCGTTCAAGAGACCACTCC
*
636852 CATCGTTCAAGCA-ACCCCTCC
1 CATCGTTCAAG-AGACCACTCC
636873 CATCGTTCA
1 CATCGTTCA
636882 TGTTCCACCT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.25, C:0.39, G:0.12, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGACCACTCC
Found at i:638565 original size:20 final size:20
Alignment explanation
Indices: 638540--638578 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
638530 TATCGAGTTG
* *
638540 CGATTTTCGTGTTGCGAATA
1 CGATTTTCGCGTTACGAATA
638560 CGATTTTCGCGTTACGAAT
1 CGATTTTCGCGTTACGAAT
638579 TTGGAATTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
CGATTTTCGCGTTACGAATA
Found at i:640999 original size:28 final size:28
Alignment explanation
Indices: 640968--641024 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
640958 CTGTGGCTCT
*
640968 TTCTTCTTCTTATT-TTCTTCGGGGCTTA
1 TTCTTCTTCTTATTCTTCTTCAGGG-TTA
*
640996 TTCTTCTTCTTTTTCTTCTTCAGGGTTA
1 TTCTTCTTCTTATTCTTCTTCAGGGTTA
641024 T
1 T
641025 ATGAATTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.07, C:0.21, G:0.12, T:0.60
Consensus pattern (28 bp):
TTCTTCTTCTTATTCTTCTTCAGGGTTA
Found at i:642186 original size:20 final size:20
Alignment explanation
Indices: 642161--642248 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
642151 AAAAATTCGT
642161 GTTGCGAAAAAGAAAATCGA
1 GTTGCGAAAAAGAAAATCGA
* *
642181 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAAATCGA
* *
642201 GTTGTGAAAAAGAAAATCTA
1 GTTGCGAAAAAGAAAATCGA
* * * *
642221 GTTGCGGAAAATAAATTCGT
1 GTTGCGAAAAAGAAAATCGA
642241 GTTGCGAA
1 GTTGCGAA
642249 TTCAAATATC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.24
Consensus pattern (20 bp):
GTTGCGAAAAAGAAAATCGA
Found at i:642202 original size:40 final size:39
Alignment explanation
Indices: 642150--642289 Score: 167
Period size: 40 Copynumber: 3.5 Consensus size: 39
642140 GTAGTTTATT
642150 AAAAAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAA
1 AAAAAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAA
* *
642189 AAAGAAATTCGTGTTGTGAAAAAGAAAATCTAGTTGCGGAA
1 AAA-AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGC-GAA
* ** *
642230 AATAAATTCGTGTTGCGAATTCA-AATATCGAGTTGCGAA
1 AAAAAATTCGTGTTGCGAA-AAAGAAAATCGAGTTGCGAA
642269 ATTAAAAATT-GTGTTGCGAAA
1 A--AAAAATTCGTGTTGCGAAA
642290 TTATCAAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
39 7 0.08
40 67 0.78
41 12 0.14
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.26
Consensus pattern (39 bp):
AAAAAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAA
Found at i:642264 original size:20 final size:20
Alignment explanation
Indices: 642213--642310 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 20
642203 TGTGAAAAAG
* *
642213 AAAATCTAGTTGCGGAAAAT-
1 AAAATCGAGTTGC-GAAATTC
* *
642233 AAATTCGTGTTGCG-AATTC
1 AAAATCGAGTTGCGAAATTC
*
642252 AAATATCGAGTTGCGAAATTA
1 AAA-ATCGAGTTGCGAAATTC
* *
642273 AAAATTGTGTTGCGAAATTATC
1 AAAATCGAGTTGCGAAA-T-TC
*
642295 AAAATCGAGTTACGAA
1 AAAATCGAGTTGCGAA
642311 TTTAACTTAT
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
18 3 0.05
19 4 0.07
20 31 0.52
21 8 0.13
22 14 0.23
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (20 bp):
AAAATCGAGTTGCGAAATTC
Found at i:642332 original size:20 final size:20
Alignment explanation
Indices: 642307--642352 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
642297 AATCGAGTTA
642307 CGAATTTAACTTATGTGTTG
1 CGAATTTAACTTATGTGTTG
* *
642327 CGAATTTGACTTCTGTGTTG
1 CGAATTTAACTTATGTGTTG
642347 CGAATT
1 CGAATT
642353 CCAAATTCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (20 bp):
CGAATTTAACTTATGTGTTG
Found at i:642432 original size:21 final size:20
Alignment explanation
Indices: 642393--642433 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
642383 GTTGTGAATA
*
642393 TAAAAACTGAGTTGCAAATT
1 TAAAAACTGAGTTACAAATT
*
642413 TAAAAACTGTGTTACGAAATT
1 TAAAAACTGAGTTAC-AAATT
642434 GGAGTTAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.32
Consensus pattern (20 bp):
TAAAAACTGAGTTACAAATT
Found at i:653434 original size:2 final size:2
Alignment explanation
Indices: 653429--653457 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
653419 TTATAAACTT
653429 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 T
653458 TTTAGTTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:659163 original size:24 final size:24
Alignment explanation
Indices: 659149--659204 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
659139 TGAAATTTAT
659149 ATTGAAATTTAAACTCAAATTGAA
1 ATTGAAATTTAAACTCAAATTGAA
** * *
659173 ATTGAAATTCCAACTCCAATTAAA
1 ATTGAAATTTAAACTCAAATTGAA
*
659197 AATGAAAT
1 ATTGAAAT
659205 GAACATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.30
Consensus pattern (24 bp):
ATTGAAATTTAAACTCAAATTGAA
Found at i:659180 original size:12 final size:12
Alignment explanation
Indices: 659139--659181 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
659129 ATAGTGGAAC
*
659139 TGAAATTTATAT
1 TGAAATTTAAAT
*
659151 TGAAATTTAAAC
1 TGAAATTTAAAT
* *
659163 TCAAATTGAAAT
1 TGAAATTTAAAT
659175 TGAAATT
1 TGAAATT
659182 CCAACTCCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (12 bp):
TGAAATTTAAAT
Found at i:662144 original size:21 final size:22
Alignment explanation
Indices: 662108--662151 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
662098 AAACACCTAT
662108 AATTTAAAAAACGTATCGATAC
1 AATTTAAAAAACGTATCGATAC
662130 AATTTAAAAAA-GTATCGATAC
1 AATTTAAAAAACGTATCGATAC
662151 A
1 A
662152 TTATGTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (22 bp):
AATTTAAAAAACGTATCGATAC
Found at i:662567 original size:198 final size:200
Alignment explanation
Indices: 662114--662722 Score: 968
Period size: 198 Copynumber: 3.1 Consensus size: 200
662104 CTATAATTTA
* *
662114 AAAAACGTATCGATACAATTTAAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAAT
1 AAAAA-GTATCGATACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAAC
* *
662179 CGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTGTCGATA-
65 CGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCGGTT-TC-AAAG
*
662243 TTTTGAGGATCGATACTTATAATAAATGTATCGACATTTTATGCGTGCATCTCGTTT-G-A-T--
128 TTTTGAGGATCGATACTTATAATAAATGTATCGACACTTTATGCGTGCATCTCGTTTGGCATTCA
662303 TT-TGGAC
193 TTCTGGAC
* *
662310 AAAAAATATTGATACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACC
1 AAAAAGTATCGATACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACC
662375 GATATATTTTTACCGGTTACATTGTAAATTTACCTATTAC-TT-TAATTATCGGTTTCAAAGTTT
66 GATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCGGTTTCAAAGTTT
*
662438 TGAGGATCGATACTTATAATAAATGTAACGACACTTTATGCGTGCATCTCGTTTGGCATTCATTC
131 TGAGGATCGATACTTATAATAAATGTATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATTC
662503 TGGAC
196 TGGAC
* *
662508 AAAAAGTATCGATACAATTTTCAAAAGTATCGATACATTATGTTTACCTATTATCTCATTAAACC
1 AAAAAGTATCGATACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACC
* * *
662573 GATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCAGTTTCTACGTTT
66 GATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCGGTTTCAAAG-TT
*
662638 TTG-GGATCGATACTTATAATACATGTATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATT
130 TTGAGGATCGATACTTATAATAAATGTATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATT
*
662702 CTAGAC
195 CTGGAC
*
662708 AAAAAGTATTGATAC
1 AAAAAGTATCGATAC
662723 TTTATGTTTA
Statistics
Matches: 384, Mismatches: 19, Indels: 16
0.92 0.05 0.04
Matches are distributed among these distances:
191 2 0.01
192 57 0.15
193 12 0.03
194 3 0.01
195 97 0.25
196 5 0.01
197 2 0.01
198 106 0.28
199 2 0.01
200 93 0.24
201 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (200 bp):
AAAAAGTATCGATACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACC
GATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCGGTTTCAAAGTTT
TGAGGATCGATACTTATAATAAATGTATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATTC
TGGAC
Found at i:667690 original size:27 final size:27
Alignment explanation
Indices: 667659--667711 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
667649 GCTTCGTTGA
667659 TCTTTCCAACTTCAACTTCGCCATCAC
1 TCTTTCCAACTTCAACTTCGCCATCAC
*
667686 TCTTTCCAACTTCAACTTCGTCATCA
1 TCTTTCCAACTTCAACTTCGCCATCA
667712 ATCCAACTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.38, G:0.04, T:0.36
Consensus pattern (27 bp):
TCTTTCCAACTTCAACTTCGCCATCAC
Found at i:670094 original size:162 final size:163
Alignment explanation
Indices: 669896--670232 Score: 579
Period size: 162 Copynumber: 2.1 Consensus size: 163
669886 TAATAAAACT
* *
669896 GGTTTTGTGATATTTTTACCTATTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
1 GGTTTTGTCATATTTTTACCTATTATATTATTATGTATCGATACATGTTTATAAAGTATCGATAC
669961 TTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGAAT
66 TTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGAAT
*
670026 CGATACATTCAACATATCTGGTAACGT-TTTACC
131 CGATACATTCAACATATATGGTAAC-TCTTTACC
* *
670059 GGTTTTGTCATA-TTTTACCTGTTATATTATTATGTATCGATACATGTTTATAAAGTATTGATAC
1 GGTTTTGTCATATTTTTACCTATTATATTATTATGTATCGATACATGTTTATAAAGTATCGATAC
* *
670123 TTTATAGGCGCTATTATTGTTTTTCTTTTAAATTTCAAAAGTATCGATACTTATTTGAATGGAAT
66 TTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGAAT
*
670188 CGATACATTCAACATATATGGTATCTCTTTACC
131 CGATACATTCAACATATATGGTAACTCTTTACC
670221 GGTTTTGTCATA
1 GGTTTTGTCATA
670233 ATGAAACCGG
Statistics
Matches: 165, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
161 1 0.01
162 153 0.93
163 11 0.07
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (163 bp):
GGTTTTGTCATATTTTTACCTATTATATTATTATGTATCGATACATGTTTATAAAGTATCGATAC
TTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGAAT
CGATACATTCAACATATATGGTAACTCTTTACC
Found at i:670192 original size:183 final size:179
Alignment explanation
Indices: 670056--670651 Score: 788
Period size: 183 Copynumber: 3.3 Consensus size: 179
670046 GTAACGTTTT
* * *
670056 ACCGGTTTTGTCATA-TTTTACCTGTTATATTATTATGTATCGATACATGTTTATAAAGTATTGA
1 ACCGGTTTTGTAATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
* *
670120 TACTTTATAGGCGCTATTATTGTTTTTCTTTTAAATTTCAAAAGTATCGATACTTATTTGAATGG
66 TACTTTATAGGCGCTATTATT-ATTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGG
670185 AATCGATACATTCAACATATATGGTATC-TCTTTACCGGTTTTGTCATAATGAA
130 AATCGATAC-TT---CATATATGGTATCGTCTTTACCGGTTTTGTCATAATGAA
* *
670238 ACCGGTTTTGTTATATTTTTACCTGTTATATTGTTATGTATCAATACATGTTTATAAAGTATCGA
1 ACCGGTTTTGTAATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
* *
670303 TACTTTATAAGCGCTATTATTACTTTTCTTTTAAATTCCAAAAGTATCGATACATATTTGAATGG
66 TACTTTATAGGCGCTATTATTA-TTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGG
* *
670368 AATCAATACCTTCAACATATCCGGTATCG-CTTTACCGGTTTTGTCATAATGAA
130 AATCGATA-CTTC-ATATAT--GGTATCGTCTTTACCGGTTTTGTCATAATGAA
* * * *
670421 ATCGATTTTGTAATATTTTTACCTGTTATATTGTTATGTATCGGTACATGTTTATAAAGTATCAA
1 ACCGGTTTTGTAATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
*
670486 TACTTTATAGGCGCTATTACTTATTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTGAATGG
66 TACTTTATAGGCGCTATTA-TTATTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGG
* * *
670551 AATCGATACGTTCAACATATCCGGTAGCG-CTTTACCGGTTTTGTCATATTG-A
130 AATCGATAC-TTC-ATATAT--GGTATCGTCTTTACCGGTTTTGTCATAATGAA
*** * * * *
670603 ACCCAATTTCTCATATTTTTACTTGATATATTGTTATGTATCGATACAT
1 ACCGGTTTTGTAATATTTTTACCTGTTATATTGTTATGTATCGATACAT
670652 ATTAATGGTA
Statistics
Matches: 375, Mismatches: 30, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
180 1 0.00
181 5 0.01
182 57 0.15
183 308 0.82
184 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (179 bp):
ACCGGTTTTGTAATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
TACTTTATAGGCGCTATTATTATTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGA
ATCGATACTTCATATATGGTATCGTCTTTACCGGTTTTGTCATAATGAA
Found at i:671263 original size:31 final size:31
Alignment explanation
Indices: 671228--671324 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
671218 GATTTTAGTG
* * *
671228 TAACTCTTGAACTGTAGATAAAATATTAATT
1 TAACTCTTAAATTTTAGATAAAATATTAATT
* *
671259 TAACTATTAAATTTTAGATAAAATATCAATT
1 TAACTCTTAAATTTTAGATAAAATATTAATT
* * * *
671290 TGACCCTTTATATTTTAAATAAAATATTAATT
1 TAACTC-TTAAATTTTAGATAAAATATTAATT
671322 TAA
1 TAA
671325 TACATTAACC
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 29 0.55
32 24 0.45
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
TAACTCTTAAATTTTAGATAAAATATTAATT
Found at i:671741 original size:22 final size:22
Alignment explanation
Indices: 671716--671759 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
671706 AGTGCATTAG
671716 TTAGAAAATTTATATAAAATAC
1 TTAGAAAATTTATATAAAATAC
671738 TTAGAAAATTTATATAAAATAC
1 TTAGAAAATTTATATAAAATAC
671760 CAGCACTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (22 bp):
TTAGAAAATTTATATAAAATAC
Found at i:681214 original size:12 final size:13
Alignment explanation
Indices: 681188--681214 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
681178 CACGTTTAGA
681188 TTTAAAAATATTT
1 TTTAAAAATATTT
681201 TTTAAAAATATTT
1 TTTAAAAATATTT
681214 T
1 T
681215 ATTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTAAAAATATTT
Found at i:690712 original size:16 final size:18
Alignment explanation
Indices: 690693--690732 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
690683 ATATTTTGTT
690693 ATTTTAA-TAAAA-AATA
1 ATTTTAATTAAAACAATA
690709 ATTTTAATTAAAACAATA
1 ATTTTAATTAAAACAATA
*
690727 AATTTA
1 ATTTTA
690733 TGTTCTGCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 5 0.24
18 9 0.43
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTTAATTAAAACAATA
Found at i:693696 original size:19 final size:20
Alignment explanation
Indices: 693654--693700 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
693644 CTAAATCCTT
* * *
693654 TTTCAAAATTTCATTTTGGT
1 TTTCAAAATCTCATTTTAGC
693674 TTTCAAAATCT-ATTTTAGC
1 TTTCAAAATCTCATTTTAGC
693693 TTTCAAAA
1 TTTCAAAA
693701 GAAAATCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (20 bp):
TTTCAAAATCTCATTTTAGC
Found at i:695461 original size:24 final size:24
Alignment explanation
Indices: 695423--695490 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
695413 TAGGTATACA
*
695423 ATATATTTA-ATACACACACATAT
1 ATATATATATATACACACACATAT
695446 ATATATATATATACACACACATAT
1 ATATATATATATACACACACATAT
*
695470 ATATATATATACACACACACA
1 ATATATATATATACACACACA
695491 CCAAATAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
23 8 0.19
24 34 0.81
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (24 bp):
ATATATATATATACACACACATAT
Found at i:698284 original size:12 final size:12
Alignment explanation
Indices: 698237--698285 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
698227 TTTTTATTTA
698237 TTCTTTCTCTTT
1 TTCTTTCTCTTT
*
698249 CTCTTTCTCTTT
1 TTCTTTCTCTTT
* *
698261 GTCTTTAT-TTT
1 TTCTTTCTCTTT
*
698272 TTATTTCTCTTT
1 TTCTTTCTCTTT
698284 TT
1 TT
698286 TTATATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (12 bp):
TTCTTTCTCTTT
Found at i:698644 original size:42 final size:41
Alignment explanation
Indices: 698551--698651 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
698541 AAGGTCTTAT
* * *
698551 AGATGACCCAAAGGACTTATCATCTTGTTCGAAAGACTGAC
1 AGATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
* * *
698592 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGGCTTAC
1 AGATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTGAC
* *
698634 TGATGGCCCG-AGGACTTA
1 AGATGACCCGAAGGACTTA
698652 CTAATTTTGG
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
40 1 0.02
41 22 0.44
42 27 0.54
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (41 bp):
AGATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
Found at i:698963 original size:259 final size:257
Alignment explanation
Indices: 698386--699064 Score: 918
Period size: 259 Copynumber: 2.6 Consensus size: 257
698376 TGGCCCGAAA
* * * **
698386 GACTTATCAATTTTGGAAATAGTCTAATGGGTAAGAAACTTTGGTGATCACTTTCTTACTTTTCA
1 GACTTACCAATTTTGGAAATAGTCTACT-GGTAAGAAACTTTTGAAATCACTTTCTTACTTTTCA
* * * *
698451 AAGATTTCATTTTCTGAAAAATATTAAGTGAGAAACTCTGAAAACCGCTTTCTCATTTTTTTTGA
65 AAAATTTCATTTTCTG-AAAATAATAAATGAGAAACTTTGAAAACCGCTTTCTCATTTTTTTT-A
* * **
698516 AAATCATGTGAAAACATCCTACCCGAAGGTCTTATAGATGACCCAAAGGACTTATCATCTTGTTC
128 AATTCATGTGAAAACATCCTACCCGAAGGTCTTAGAGATGACCCAAAGGACTTATCATCTTACTC
* * * **
698581 GAAAGACTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGGCTTACTGATGGCCCGAG
193 GAAAGACCGACAGATGACCCGAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGCCAAAG
* * *
698646 GACTTACTAATTTTGGAAATAGTCTACTGAGTAAGAAAC-TTTGAAAATCAATTTCTTACTTTTA
1 GACTTACCAATTTTGGAAATAGTCTACTG-GTAAGAAACTTTTG-AAATCACTTTCTTACTTTTC
* ** * *
698710 AAAAATTTCATTTTCTGAAAATACTAAACAAGAAACTTTGAAAACCACTTTCTCATTTTTTTTTA
64 AAAAATTTCATTTTCTGAAAATAATAAATGAGAAACTTTGAAAACCGCTTTCTCATTTTTTTTAA
* * *
698775 ATTCATGTGAAAACATCATACCCGAAGGTCTTACGA-ATGGCCCGAAA-TACTTATCATCTTACT
129 ATTCATGTGAAAACATCCTACCCGAAGGTCTTA-GAGATGACCC-AAAGGACTTATCATCTTACT
* *
698838 CGAAAGACCGACAGATGACCCTAAGAATTTAATCATCATGCTCGAAAGATTTACTGATGGCTCAA
192 CGAAAGACCGACAGATGACCCGAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGC-CAA
698903 AG
256 AG
*
698905 GACTTACCAATTTTGGAAATAGTCTACTAGGTAAGAAACTTTTGAAATCGCTTTCTTACTTTTCA
1 GACTTACCAATTTTGGAAATAGTCTACT-GGTAAGAAACTTTTGAAATCACTTTCTTACTTTTCA
* * *
698970 AAAATTTCATTTTCTGAAAATAATAAATGGGAAACTTTGAAAATCGCTTTCTCA--TTTTTAAAA
65 AAAATTTCATTTTCTGAAAATAATAAATGAGAAACTTTGAAAACCGCTTTCTCATTTTTTTTAAA
*
699033 TTCATGTGAAAACATCCTACCCGAAGGACTTA
130 TTCATGTGAAAACATCCTACCCGAAGGTCTTA
699065 TCATCTCGCT
Statistics
Matches: 368, Mismatches: 44, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
257 37 0.10
258 107 0.29
259 153 0.42
260 71 0.19
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (257 bp):
GACTTACCAATTTTGGAAATAGTCTACTGGTAAGAAACTTTTGAAATCACTTTCTTACTTTTCAA
AAATTTCATTTTCTGAAAATAATAAATGAGAAACTTTGAAAACCGCTTTCTCATTTTTTTTAAAT
TCATGTGAAAACATCCTACCCGAAGGTCTTAGAGATGACCCAAAGGACTTATCATCTTACTCGAA
AGACCGACAGATGACCCGAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGCCAAAG
Done.