Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008236.1 Hibiscus syriacus cultivar Beakdansim tig00110882_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: 1100419
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:474814 original size:39 final size:39
Alignment explanation
Indices: 474765--474840 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
474755 TAAAGAATAT
* *
474765 TTTTGTCTCGCTTGAGATGGTTTCCCTCGAAAAAAAAGA
1 TTTTATCTCGCTTGAGATAGTTTCCCTCGAAAAAAAAGA
* *
474804 TTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTATCTCGCTTGAGATAGTTTCCCTCGAAAAAAAA
474841 TTATGTCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (39 bp):
TTTTATCTCGCTTGAGATAGTTTCCCTCGAAAAAAAAGA
Found at i:474863 original size:37 final size:38
Alignment explanation
Indices: 474768--474874 Score: 126
Period size: 37 Copynumber: 2.8 Consensus size: 38
474758 AGAATATTTT
* * * *
474768 TGTCTCGCTTGAGATGGTTTCCCTCGAAAAAAAAGATTT
1 TGTCTCGCTTGAGATAGTTTCCCTTG-AAACAAAGATTA
*
474807 TATCTCGCTTGAGATAGTTTCCCTTGAAACAAA-ATTA
1 TGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAGATTA
* * *
474844 TGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TGTCTCGCTTGAGATAGTTTCCCTTGAAACA
474875 TAAAAAATTG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 30 0.51
38 6 0.10
39 23 0.39
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (38 bp):
TGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAGATTA
Found at i:475013 original size:36 final size:36
Alignment explanation
Indices: 474973--475044 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
474963 ATTTGAAATG
* *
474973 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
*
475009 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
475045 TAAACTGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
Found at i:475162 original size:129 final size:130
Alignment explanation
Indices: 475011--475306 Score: 436
Period size: 129 Copynumber: 2.3 Consensus size: 130
475001 TTGAAACAAA
* *
475011 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTGTGAAAATAGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTATGAAAACAGTTTCCCTTGAAAC-A
* *
475076 AAATCTTTGAATATGTTTTACATTAAACAAATTTCATCTCCCTTGAGACAGTTTC-TTTTG-GAA
65 AAATATTTGAATATGTTTTACATTAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTTGAAAA
475139 G
130 G
* *
475140 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTATGAAGACAGTTTCCCTTGAAACAT
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTATGAAAACAGTTTCCCTTGAAACAA
* **
475205 AATATTTGAATATGTTTTACATTAAACTAATTTTGTCTCCCTTGAGACAGTTTCTTTTTGAAACA
66 AATATTTGAATATGTTTTACATTAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTTG--A-A
475270 AAG
128 AAG
*
475273 TTTTGTCTCCTTTGAG-CATGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACA-GTTTCTCTTGAAACA
475307 CCAAACCTTT
Statistics
Matches: 151, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
128 51 0.34
129 65 0.43
132 2 0.01
133 33 0.22
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (130 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTATGAAAACAGTTTCCCTTGAAACAA
AATATTTGAATATGTTTTACATTAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTTGAAAAG
Found at i:475288 original size:38 final size:37
Alignment explanation
Indices: 475235--475306 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
475225 ATTAAACTAA
*
475235 TTTTGTCTCCCTTGAGACA-GTTTCTTTTTGAAACAAAG
1 TTTTGTCTCCCTTGAG-CATGTTTC-TCTTGAAACAAAG
*
475273 TTTTGTCTCCTTTGAGCATGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGCATGTTTCTCTTGAAACA
475307 CCAAACCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 11 0.35
38 20 0.65
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.44
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGCATGTTTCTCTTGAAACAAAG
Found at i:476854 original size:38 final size:38
Alignment explanation
Indices: 476780--476859 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 38
476770 TTTTACTAAA
* *
476780 TATTATTTATCTATATTTATCTGTTTGATTTATTTTAT
1 TATTATTTATCTATATTAATCTGTTTCATTTATTTTAT
*
476818 TATTA-TTAT-TATATTAATTCTTTTTCATTTATTTTTAT
1 TATTATTTATCTATATTAA-TCTGTTTCATTTA-TTTTAT
476856 TATT
1 TATT
476860 TTCCCCTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 7 0.19
37 15 0.41
38 15 0.41
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (38 bp):
TATTATTTATCTATATTAATCTGTTTCATTTATTTTAT
Found at i:477443 original size:98 final size:98
Alignment explanation
Indices: 477274--477466 Score: 287
Period size: 98 Copynumber: 2.0 Consensus size: 98
477264 ATATATAAAG
* * *
477274 ATATCTATTAGAAGGAGCTCCATCATTATTCTGAAGGTGAAGATAGAACCCTCCATCATTGGTTA
1 ATATCAATTAGAAGGAGCTCAATCATTAATCTGAAGGTGAAGATAGAACCCTCCATCATTGGTTA
*
477339 AGTGATATATTTTCTGTTAAACAATATGTGTGT
66 AGTGATAAATTTTCTGTTAAACAATATGTGTGT
* * * *
477372 ATATCAATTAGAATGAGCTCAATGATTAATCTGAATGTGAAGATTGAACCCTCCATCATTGGTTA
1 ATATCAATTAGAAGGAGCTCAATCATTAATCTGAAGGTGAAGATAGAACCCTCCATCATTGGTTA
* * *
477437 AGTGATAAATTTTCTTTTAAATAATGTGTG
66 AGTGATAAATTTTCTGTTAAACAATATGTG
477467 CGCGTGTGTG
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 84 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (98 bp):
ATATCAATTAGAAGGAGCTCAATCATTAATCTGAAGGTGAAGATAGAACCCTCCATCATTGGTTA
AGTGATAAATTTTCTGTTAAACAATATGTGTGT
Found at i:477516 original size:10 final size:10
Alignment explanation
Indices: 477484--477522 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
477474 GTGTGTGCAT
*
477484 GTGTGTGTGA
1 GTGTGTGTGG
* *
477494 GTGCGTATGG
1 GTGTGTGTGG
477504 GTGTGTGTGG
1 GTGTGTGTGG
477514 GTGTGTGTG
1 GTGTGTGTG
477523 CATGTGGGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.05, C:0.03, G:0.54, T:0.38
Consensus pattern (10 bp):
GTGTGTGTGG
Found at i:478187 original size:2 final size:2
Alignment explanation
Indices: 478180--478310 Score: 118
Period size: 2 Copynumber: 70.0 Consensus size: 2
478170 TCGAGCTGGG
* * * *
478180 TA TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
478220 TA TA TA TT TT TA -A TT TA -A TT TA -A T- TT TA T- TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
478255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
478297 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
478311 ATTATTTTTA
Statistics
Matches: 105, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
1 9 0.09
2 96 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:478416 original size:35 final size:35
Alignment explanation
Indices: 478377--478448 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 35
478367 CCCGCCCCTG
*
478377 TCCCCGTTTAGCATAAACA-ATTTTCCCCGTCCCCA
1 TCCCCGTTTAACATAAA-AGATTTTCCCCGTCCCCA
*
478412 TCCCCGTTTAACATAAAAGGTTTTTCCCCGTCCCCA
1 TCCCCGTTTAACATAAAA-GATTTTCCCCGTCCCCA
478448 T
1 T
478449 TTAATTCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 1 0.03
35 16 0.48
36 16 0.48
ACGTcount: A:0.22, C:0.38, G:0.10, T:0.31
Consensus pattern (35 bp):
TCCCCGTTTAACATAAAAGATTTTCCCCGTCCCCA
Found at i:481662 original size:2 final size:2
Alignment explanation
Indices: 481655--481679 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
481645 TATTATCGCT
481655 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 T
481680 TTAAGGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:486133 original size:27 final size:27
Alignment explanation
Indices: 486102--486169 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
486092 TCTATTTACA
486102 AAATCACATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
*
486129 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
486156 AAAT--CATCTCTATA
1 AAATCACATCTCTATA
486170 ATTCCTACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 9 0.23
27 30 0.77
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (27 bp):
AAATCACATCTCTATAGGAATGGTAAC
Found at i:486205 original size:12 final size:12
Alignment explanation
Indices: 486188--486212 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
486178 ACTCCCCCTC
486188 AAGCTGGAGAAT
1 AAGCTGGAGAAT
486200 AAGCTGGAGAAT
1 AAGCTGGAGAAT
486212 A
1 A
486213 TACATTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.32, T:0.16
Consensus pattern (12 bp):
AAGCTGGAGAAT
Found at i:489802 original size:27 final size:27
Alignment explanation
Indices: 489769--489836 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
489759 TCTATTTACA
489769 AAATCATATCTCTATAGAAATGGTAAC
1 AAATCATATCTCTATAGAAATGGTAAC
*
489796 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGAAATGGTAAC
489823 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
489837 ATTCCTACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 9 0.22
27 31 0.77
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGAAATGGTAAC
Found at i:495063 original size:32 final size:31
Alignment explanation
Indices: 494982--495076 Score: 111
Period size: 31 Copynumber: 3.0 Consensus size: 31
494972 CTTAATATAC
* *
494982 AGCTAGAAAAAAGCGGTATC-GATTTTGTTATT
1 AGCTA-AAAAATGCGGTACCAG-TTTTGTTATT
*
495014 GGCTAAAAAATGCGGTACCAGTTTTGTTATT
1 AGCTAAAAAATGCGGTACCAGTTTTGTTATT
* *
495045 AGCTAAAAAATTGTGGTACCTGTTTTGTTATT
1 AGCTAAAAAA-TGCGGTACCAGTTTTGTTATT
495077 GTTGTGTATA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
31 31 0.56
32 24 0.44
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (31 bp):
AGCTAAAAAATGCGGTACCAGTTTTGTTATT
Found at i:495418 original size:23 final size:22
Alignment explanation
Indices: 495388--495445 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
495378 TTATATCTAT
*
495388 AATT-TTATAAATAAAAAATTAT
1 AATTATTATAAATAAAAAA-TAA
* **
495410 GATTATTATATTTTAAAAAATAA
1 AATTATTATA-AATAAAAAATAA
495433 AATTATTATAAAT
1 AATTATTATAAAT
495446 TATATTTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
22 4 0.15
23 16 0.59
24 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTATTATAAATAAAAAATAA
Found at i:495423 original size:30 final size:30
Alignment explanation
Indices: 495389--495452 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
495379 TATATCTATA
*
495389 ATTTTATAAATAA-AAAATTATGAT-TATTAT
1 ATTTTA-AAA-AATAAAATTATGATAAATTAT
*
495419 ATTTTAAAAAATAAAATTATTATAAATTAT
1 ATTTTAAAAAATAAAATTATGATAAATTAT
495449 ATTT
1 ATTT
495453 ATTATAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 13 0.43
30 15 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
ATTTTAAAAAATAAAATTATGATAAATTAT
Found at i:496027 original size:198 final size:199
Alignment explanation
Indices: 495550--496039 Score: 607
Period size: 201 Copynumber: 2.5 Consensus size: 199
495540 CGCATATGTT
* *
495550 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATATCGG
1 ACATCGAAACCGATAATTATCATGTAATAGGTAAATTTACAATGTTACCGGTATAAATATATCGG
* *
495615 TTTTATGAGATAATATGTCAACATAATGTATCGAAACAAATTTAAAAAGTGTCGATACATTTTGT
66 TTTTATGAGAAAATAGGTCAACATAATGTATCG-AACAAATTTAAAAAGTGTCGATACATTTTGT
* *
495680 CCAAAATGAATGCCAAACGAGGTGCAAGCATAAAGTGTCGATATATTTATTAAAAGTATCGATCC
130 CCAAAATGAATACCAAACGAGGTGCAAGCATAAAGTGTCGATACATTTA-TAAAAGTATCGATCC
495745 TAAAAA
194 TAAAAA
* * *
495751 ACATCGAAACCGATAATTA-CAATGTAATAAGTAAATTTACAATG-TACCGGGTAGAAATATACC
1 ACATCGAAACCGATAATTATC-ATGTAATAGGTAAATTTACAATGTTACC-GGTATAAATATATC
* ** ***
495814 GGTTTTATGAGAAAATAGGTCTACATAATGTATCG-ACATGTTTTAAGTTTGTGTCGATAC-TTT
64 GGTTTTATGAGAAAATAGGTCAACATAATGTATCGAACA-AATTTAA-AAAGTGTCGATACATTT
* * * * * *
495877 TTTTCAGAATGAATACCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA-AAATTGTATCGA
127 TGTCCAAAATGAATACCAAACGAGGTGCAAGCATAAAGTGTCGATACATTTATAAA-AGTATCGA
*
495941 TCC-CAAAA
191 TCCTAAAAA
* * * *
495949 ATATCGAAACCAATAATTATCATGTAATAGGTAAATTTGCAATGTTACCGGTATAATTATATCGG
1 ACATCGAAACCGATAATTATCATGTAATAGGTAAATTTACAATGTTACCGGTATAAATATATCGG
* *
496014 -TTTAGTTAGAAAATAGGTCAATATAA
66 TTTTA-TGAGAAAATAGGTCAACATAA
496040 ACGCTATCTA
Statistics
Matches: 249, Mismatches: 32, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
197 4 0.02
198 76 0.31
199 18 0.07
200 56 0.22
201 95 0.38
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (199 bp):
ACATCGAAACCGATAATTATCATGTAATAGGTAAATTTACAATGTTACCGGTATAAATATATCGG
TTTTATGAGAAAATAGGTCAACATAATGTATCGAACAAATTTAAAAAGTGTCGATACATTTTGTC
CAAAATGAATACCAAACGAGGTGCAAGCATAAAGTGTCGATACATTTATAAAAGTATCGATCCTA
AAAA
Found at i:496138 original size:87 final size:87
Alignment explanation
Indices: 496034--496195 Score: 270
Period size: 87 Copynumber: 1.9 Consensus size: 87
496024 AAATAGGTCA
*
496034 ATATAAACGCTATCTATTACATTATATAAGCGCTACATAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCGCTACATAATATGTTATTGTACTTGATAATATTT
496099 CCGATTAAATACTTATTTTATT
66 CCGATTAAATACTTATTTTATT
* * * *
496121 ATATAAGCGCTACCTATTACATTATATAGGCGCTACCTAATATGTTATTGTATTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCGCTACATAATATGTTATTGTACTTGATAATATTT
*
496186 CCGGTTAAAT
66 CCGATTAAAT
496196 GATATAACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTATATAAGCGCTACATAATATGTTATTGTACTTGATAATATTT
CCGATTAAATACTTATTTTATT
Found at i:496168 original size:23 final size:23
Alignment explanation
Indices: 496118--496162 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
496108 TACTTATTTT
*
496118 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
496141 ATTATATAGGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
496163 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:503153 original size:20 final size:19
Alignment explanation
Indices: 503115--503153 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
503105 ACTTAATCAC
*
503115 ATAAGATTTATTTACTAAA
1 ATAAGATTTACTTACTAAA
*
503134 ATAAGTATTTACTTATTAAA
1 ATAAG-ATTTACTTACTAAA
503154 TAAATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (19 bp):
ATAAGATTTACTTACTAAA
Found at i:505492 original size:22 final size:23
Alignment explanation
Indices: 505466--505518 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
505456 GATCGAAATT
505466 ACTGTAGCAAGGGTATCGATA-C
1 ACTGTAGCAAGGGTATCGATACC
505488 ACTGTAGC-AGGGTATCGATACC
1 ACTGTAGCAAGGGTATCGATACC
*
505510 CCTGTAGCA
1 ACTGTAGCA
505519 TTCTGGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
ACTGTAGCAAGGGTATCGATACC
Found at i:506151 original size:4 final size:4
Alignment explanation
Indices: 506142--506172 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
506132 TAAGTGGATC
506142 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTA
1 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTA
506173 TATACATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CTAA
Found at i:509825 original size:2 final size:2
Alignment explanation
Indices: 509818--509845 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
509808 ACTTGTAATA
509818 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
509846 TAAGTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:510079 original size:144 final size:147
Alignment explanation
Indices: 509818--510099 Score: 410
Period size: 144 Copynumber: 1.9 Consensus size: 147
509808 ACTTGTAATA
* * * *
509818 ATATATATATATATATATATATATATATTAAGTTTGTATAATTAATCATCAGTCACATATCTAAA
1 ATATATATATATATATAAATATATATATTAAGTTTGTATAACTAATCATCAGACACAGATCTAAA
* *
509883 AATAATTTTGAGGGTGAATATATATTTATTAATCACATAAAATTTTTGTATG-AATAAAAATAAA
66 AATAATTTTGAGGGTGAATATATATTTACTAATCACATAAAATTTTTATATGAAATAAAAATAAA
509947 TAAAATTTCAGGTAGTT
131 TAAAATTTCAGGTAGTT
*
509964 ATATATATATATATATAAACT-TATA-ATTAAG-TTGTATAACTAGTCATCAGACACAGATCTAA
1 ATATATATATATATATAAA-TATATATATTAAGTTTGTATAACTAATCATCAGACACAGATCTAA
* * * ** *
510026 AATTAGTTTTGAGGGTGAGTATATATTTACTAATCACATAATTTTTTTATATGAAATAAATATAA
65 AAATAATTTTGAGGGTGAATATATATTTACTAATCACATAAAATTTTTATATGAAATAAAAATAA
510091 ATAAAATTT
130 ATAAAATTT
510100 TAGATAGATT
Statistics
Matches: 121, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
144 73 0.60
145 25 0.21
146 22 0.18
147 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.40
Consensus pattern (147 bp):
ATATATATATATATATAAATATATATATTAAGTTTGTATAACTAATCATCAGACACAGATCTAAA
AATAATTTTGAGGGTGAATATATATTTACTAATCACATAAAATTTTTATATGAAATAAAAATAAA
TAAAATTTCAGGTAGTT
Found at i:517759 original size:22 final size:21
Alignment explanation
Indices: 517734--517789 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
517724 TTTTTAGATT
*
517734 TTTAAATGTTGATAATAAATTA
1 TTTAAAT-TTGAAAATAAATTA
*
517756 TTTAAATTTTAAAATAAATT-
1 TTTAAATTTGAAAATAAATTA
*
517776 TATAAATTT-AAAAT
1 TTTAAATTTGAAAAT
517790 TAAAATTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 8 0.26
21 11 0.35
22 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
TTTAAATTTGAAAATAAATTA
Found at i:517783 original size:20 final size:20
Alignment explanation
Indices: 517747--517789 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
517737 AAATGTTGAT
*
517747 AATAAATTATTTAAATTTTAA
1 AATAAATTATATAAA-TTTAA
517768 AATAAATT-TATAAATTTAA
1 AATAAATTATATAAATTTAA
517787 AAT
1 AAT
517790 TAAAATTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATAAATTATATAAATTTAA
Found at i:517793 original size:20 final size:21
Alignment explanation
Indices: 517758--517798 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
517748 ATAAATTATT
517758 TAAATTTTAAAAT-AAATTTA
1 TAAATTTTAAAATAAAATTTA
517778 TAAA-TTTAAAATTAAAATTTA
1 TAAATTTTAAAA-TAAAATTTA
517799 CAATTAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATTTTAAAATAAAATTTA
Found at i:521235 original size:9 final size:9
Alignment explanation
Indices: 521221--521245 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
521211 TTGAAATATG
521221 TATTTAACA
1 TATTTAACA
521230 TATTTAACA
1 TATTTAACA
521239 TATTTAA
1 TATTTAA
521246 TAATTTCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (9 bp):
TATTTAACA
Found at i:522524 original size:2 final size:2
Alignment explanation
Indices: 522517--522554 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
522507 AGATTATGAA
522517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
522555 GTGTGTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:524230 original size:23 final size:22
Alignment explanation
Indices: 524180--524231 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
524170 AATCTCACGT
*
524180 AATTTAATTTAAAGTATTACAA
1 AATTAAATTTAAAGTATTACAA
** *
524202 CTTTAAATTTTAAGTCATTACAA
1 AATTAAATTTAAAGT-ATTACAA
524225 AATTAAA
1 AATTAAA
524232 AACTGCAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTAAATTTAAAGTATTACAA
Found at i:531198 original size:20 final size:20
Alignment explanation
Indices: 531173--531218 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
531163 TTTTGAGTTG
*
531173 TAGTATTAATATTGTTCTTA
1 TAGTATTAATATTGATCTTA
*
531193 TAGTATTGATATTGATCTTA
1 TAGTATTAATATTGATCTTA
531213 TAGTAT
1 TAGTAT
531219 CGATACTATT
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:0.30, C:0.04, G:0.13, T:0.52
Consensus pattern (20 bp):
TAGTATTAATATTGATCTTA
Found at i:531223 original size:20 final size:20
Alignment explanation
Indices: 531181--531223 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
531171 TGTAGTATTA
* *
531181 ATATTGTTCTTATAGTATTG
1 ATATTGATCTTATAGTATCG
531201 ATATTGATCTTATAGTATCG
1 ATATTGATCTTATAGTATCG
531221 ATA
1 ATA
531224 CTATTCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (20 bp):
ATATTGATCTTATAGTATCG
Found at i:531231 original size:20 final size:20
Alignment explanation
Indices: 531187--531311 Score: 83
Period size: 20 Copynumber: 6.0 Consensus size: 20
531177 ATTAATATTG
* *
531187 TTCTTATAGTATTGATATTGA
1 TTCTTATAGTATCGATACT-A
531208 -TCTTATAGTATCGATACTA
1 TTCTTATAGTATCGATACTA
*
531227 TTCTTTATAGCATCGATACTA
1 TTC-TTATAGTATCGATACTA
* * *
531248 TTTTTTTGTAGTATCGATACTGT
1 --TTCTTATAGTATCGATACT-A
* * * *
531271 TTTTTGTAGTATC-ATTATTG
1 TTCTTATAGTATCGA-TACTA
*
531291 TTCTTGTAGTATCGATACTA
1 TTCTTATAGTATCGATACTA
531311 T
1 T
531312 ATACCATAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.01
20 35 0.41
21 33 0.39
22 14 0.16
23 2 0.02
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (20 bp):
TTCTTATAGTATCGATACTA
Found at i:531236 original size:21 final size:21
Alignment explanation
Indices: 531213--531311 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
531203 ATTGATCTTA
*
531213 TAGTATCGATACTATTCTTTA
1 TAGTATCGATACTATTCTTTG
* *
531234 TAGCATCGATACTATTTTTTTG
1 TAGTATCGATACTA-TTCTTTG
* *
531256 TAGTATCGATACTGTTTTTTG
1 TAGTATCGATACTATTCTTTG
* *
531277 TAGTATC-ATTATTGTTC-TTG
1 TAGTATCGA-TACTATTCTTTG
531297 TAGTATCGATACTAT
1 TAGTATCGATACTAT
531312 ATACCATAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 15 0.23
21 34 0.52
22 17 0.26
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.49
Consensus pattern (21 bp):
TAGTATCGATACTATTCTTTG
Found at i:531261 original size:43 final size:41
Alignment explanation
Indices: 531202--531311 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 41
531192 ATAGTATTGA
* *
531202 TATTGATCTTATAGTATCGATACTATTCTTTATAGCATCGAT
1 TATTGTTCTTGTAGTATCGATACTATTCTTTATAGCATC-AT
* * * * *
531244 ACTATT-TTTTTGTAGTATCGATACTGTTTTTTGTAGTATCAT
1 --TATTGTTCTTGTAGTATCGATACTATTCTTTATAGCATCAT
531286 TATTGTTCTTGTAGTATCGATACTAT
1 TATTGTTCTTGTAGTATCGATACTAT
531312 ATACCATAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
40 4 0.07
41 19 0.34
42 2 0.04
43 27 0.48
44 4 0.07
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.50
Consensus pattern (41 bp):
TATTGTTCTTGTAGTATCGATACTATTCTTTATAGCATCAT
Found at i:537199 original size:19 final size:19
Alignment explanation
Indices: 537175--537221 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
537165 TTGGACTCTC
537175 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
537194 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
537213 AGTGCATCG
1 AGTGCATCG
537222 ATTCATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:537283 original size:20 final size:20
Alignment explanation
Indices: 537255--537312 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
537245 TGAAAAATTA
*
537255 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGGTGCATGG
*
537275 ATTGATGCATCGGTGCATGG
1 ATTGGTGCATCGGTGCATGG
537295 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGGTGCAT
537313 CACCTTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (20 bp):
ATTGGTGCATCGGTGCATGG
Found at i:537638 original size:13 final size:13
Alignment explanation
Indices: 537611--537651 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
537601 TAAGATTTTC
*
537611 TTTGAAAA-TAAG
1 TTTGAAAACCAAG
537623 TTTGAAAACCAAG
1 TTTGAAAACCAAG
537636 TTTGAAAACCAAG
1 TTTGAAAACCAAG
537649 TTT
1 TTT
537652 TAAGTTACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.32
Consensus pattern (13 bp):
TTTGAAAACCAAG
Found at i:545926 original size:26 final size:26
Alignment explanation
Indices: 545895--545944 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
545885 GCATGGTCTT
*
545895 GTGCATCGATGCATCAAATGCATTGA
1 GTGCATCGATGCATAAAATGCATTGA
545921 GTGCATCGATGCATAAAATGCATT
1 GTGCATCGATGCATAAAATGCATT
545945 TGATGTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (26 bp):
GTGCATCGATGCATAAAATGCATTGA
Found at i:549444 original size:38 final size:38
Alignment explanation
Indices: 549363--549445 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
549353 AAATAAATAA
* *
549363 AATAAACGAGTTTGTTGACGAACATAAATGAACGACTC
1 AATAAACGAGATTGTTCACGAACATAAATGAACGACTC
* * * * *
549401 GATAAATGAGATTGTTCATGAACATAAATGAGCGAGTC
1 AATAAACGAGATTGTTCACGAACATAAATGAACGACTC
549439 AATAAAC
1 AATAAAC
549446 AAACTTGTTC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.24
Consensus pattern (38 bp):
AATAAACGAGATTGTTCACGAACATAAATGAACGACTC
Found at i:555305 original size:22 final size:22
Alignment explanation
Indices: 555248--555305 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
555238 GATCCTTTAA
* *
555248 TCAATGATGTTTTGTTGAGTTTT
1 TCAAT-ATTTTTTGTTGAGTTTC
* *
555271 TCGATATTATTTGTTGAG-TTC
1 TCAATATTTTTTGTTGAGTTTC
555292 TCAATATATTTTTG
1 TCAATAT-TTTTTG
555306 AAAGAGTGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 8 0.29
22 16 0.57
23 4 0.14
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (22 bp):
TCAATATTTTTTGTTGAGTTTC
Found at i:557156 original size:38 final size:38
Alignment explanation
Indices: 557113--557190 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
557103 CTCAAACAAA
557113 TGCTACAGGACAAAAATCGACTTGTGATCAGATTGCAT
1 TGCTACAGGACAAAAATCGACTTGTGATCAGATTGCAT
557151 TGCTACAGGACAAAAATCGACTTGTGATCAGATTGCAT
1 TGCTACAGGACAAAAATCGACTTGTGATCAGATTGCAT
557189 TG
1 TG
557191 TCATGTCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (38 bp):
TGCTACAGGACAAAAATCGACTTGTGATCAGATTGCAT
Found at i:559883 original size:70 final size:70
Alignment explanation
Indices: 559766--559905 Score: 228
Period size: 70 Copynumber: 2.0 Consensus size: 70
559756 AAAATAAAGT
* * *
559766 GACGACCAATTAGTGAGAGTTAGACAATGAAAATATTGACTGGTGATGATTTATTTGACGATAAC
1 GACGACCAATTAGTGAGAGTTAGACAATGAAAAGATTGACTGGTGATGACTGATTTGACGATAAC
559831 ATATA
66 ATATA
*
559836 GACGACCAATTAGTGAGAGTCT-GACAATGAAAAGATTGACTGTTGATGACTGATTTGACGATAA
1 GACGACCAATTAGTGAGAGT-TAGACAATGAAAAGATTGACTGGTGATGACTGATTTGACGATAA
559900 CATATA
65 CATATA
559906 AAATTTAATG
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
70 64 0.98
71 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (70 bp):
GACGACCAATTAGTGAGAGTTAGACAATGAAAAGATTGACTGGTGATGACTGATTTGACGATAAC
ATATA
Found at i:562016 original size:2 final size:2
Alignment explanation
Indices: 562011--562052 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
562001 ATATAAAAAT
562011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
562053 ACAACACTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:562773 original size:2 final size:2
Alignment explanation
Indices: 562766--562797 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
562756 AATATTCTTA
562766 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
562798 TAAATGATAC
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:565717 original size:29 final size:29
Alignment explanation
Indices: 565684--565741 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
565674 TATACAGTGG
*
565684 TCTTGGAGGTCGCCATGCAATCCAGGCGA
1 TCTTGGAGGACGCCATGCAATCCAGGCGA
*
565713 TCTTGTAGGACGCCATGCAATCCAGGCGA
1 TCTTGGAGGACGCCATGCAATCCAGGCGA
565742 CATACGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.21
Consensus pattern (29 bp):
TCTTGGAGGACGCCATGCAATCCAGGCGA
Found at i:565792 original size:35 final size:35
Alignment explanation
Indices: 565752--565826 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
565742 CATACGGGAA
565752 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
565787 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
565822 CATAC
1 CATAC
565827 TCCCCATGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.27, C:0.35, G:0.19, T:0.20
Consensus pattern (35 bp):
CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
Found at i:565829 original size:22 final size:22
Alignment explanation
Indices: 565804--565848 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
565794 GCCAATGGTT
565804 CTCCCCATGCATACGAGCCATA
1 CTCCCCATGCATACGAGCCATA
565826 CTCCCCATGCATACGAGCCATA
1 CTCCCCATGCATACGAGCCATA
565848 C
1 C
565849 GAGCCAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.13, T:0.18
Consensus pattern (22 bp):
CTCCCCATGCATACGAGCCATA
Found at i:565841 original size:57 final size:57
Alignment explanation
Indices: 565769--565883 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
565759 GCCAATGGTT
565769 CTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
1 CTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
565826 CTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
1 CTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
565883 C
1 C
565884 GAGCGTTCTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.19
Consensus pattern (57 bp):
CTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
Found at i:565871 original size:35 final size:35
Alignment explanation
Indices: 565826--566020 Score: 189
Period size: 35 Copynumber: 5.8 Consensus size: 35
565816 ACGAGCCATA
565826 CTCCCCATGCATACGAGCCATACGAGCCAATGGTT
1 CTCCCCATGCATACGAGCCATACGAGCCAATGGTT
565861 CTCCCCATGCATACGAGCCATACGAG-C----GTT
1 CTCCCCATGCATACGAGCCATACGAGCCAATGGTT
* * * * *
565891 CTCCCCATGC-GAGGTGGCCAAACG-G-----GGTGA
1 CTCCCCATGCATACG-AGCCATACGAGCCAATGGT-T
* **
565921 CATACGGAGTGACATACGAGCCATACGAGCCAATGGTT
1 C-TCCCCA-TG-CATACGAGCCATACGAGCCAATGGTT
565959 CTCCCCATGCATACGAGCCATACGAGCCAATGGTT
1 CTCCCCATGCATACGAGCCATACGAGCCAATGGTT
565994 CTCCCCATGCATACGAGCCATACGAGC
1 CTCCCCATGCATACGAGCCATACGAGC
566021 GTTCTCCCCA
Statistics
Matches: 131, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
29 5 0.04
30 21 0.16
31 3 0.02
32 2 0.02
33 8 0.06
34 4 0.03
35 79 0.60
36 2 0.02
37 3 0.02
38 1 0.01
39 3 0.02
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.18
Consensus pattern (35 bp):
CTCCCCATGCATACGAGCCATACGAGCCAATGGTT
Found at i:566036 original size:26 final size:26
Alignment explanation
Indices: 566007--566062 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
565997 CCCATGCATA
566007 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
566033 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
566059 CGAG
1 CGAG
566063 GTGGCCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.20, C:0.38, G:0.25, T:0.18
Consensus pattern (26 bp):
CGAGCCATACGAGCGTTCTCCCCATG
Found at i:566135 original size:29 final size:29
Alignment explanation
Indices: 566085--566164 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
566075 TGGAATAGAG
* *
566085 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
566114 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
566143 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
566165 CCATTCCCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:566245 original size:13 final size:13
Alignment explanation
Indices: 566227--566258 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
566217 AGTCCCGGCG
*
566227 CCATTCCCATCGT
1 CCATTCCCATCAT
566240 CCATTCCCATCAT
1 CCATTCCCATCAT
566253 CCATTC
1 CCATTC
566259 ACATGCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.47, G:0.03, T:0.31
Consensus pattern (13 bp):
CCATTCCCATCAT
Found at i:566440 original size:25 final size:25
Alignment explanation
Indices: 566412--566463 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
566402 TGTACAATTA
*
566412 TTGGTGAAATAATTAAGGCAGTCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
*
566437 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
566462 TT
1 TT
566464 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (25 bp):
TTGGTGAAATAATTAAGGCAGCCGG
Found at i:566534 original size:4 final size:4
Alignment explanation
Indices: 566525--566586 Score: 56
Period size: 4 Copynumber: 15.5 Consensus size: 4
566515 ATTGCAGCCG
** **
566525 AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGGG AGAA AGGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA A-GAA AGAA
566575 AG-A AG-A AGAA AG
1 AGAA AGAA AGAA AG
566587 GGAGATAAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
3 6 0.13
4 33 0.70
5 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:566550 original size:21 final size:21
Alignment explanation
Indices: 566526--566578 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
566516 TTGCAGCCGA
566526 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
566547 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
566568 GAAAGAAAGAA
1 GAAAGAAAGAA
566579 GAAGAAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:566820 original size:46 final size:46
Alignment explanation
Indices: 566781--566869 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
566771 TTATATAGTT
566781 AAAAA-TAATTAATTAGTTTGTATT-GTT-AATAGTTAGTTATATA
1 AAAAATTAATTAATTAGTTTGTATTAGTTAAATAGTTAGTTATATA
* *
566824 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTAATTAATTAGTTTGTATTAGTTAAATAGTT-AGTTATAT
566870 TGTTTGTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 5 0.12
44 17 0.43
45 3 0.08
46 7 0.17
47 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (46 bp):
AAAAATTAATTAATTAGTTTGTATTAGTTAAATAGTTAGTTATATA
Found at i:566845 original size:44 final size:43
Alignment explanation
Indices: 566740--566869 Score: 128
Period size: 44 Copynumber: 3.0 Consensus size: 43
566730 TACATAAATT
*
566740 AAAAATTATTTAATTAGTATATGTTTG---ATAGTTA--TATAGTT
1 AAAAATTATTTAATTAGT-T-TGTTTGTTAATAGTTAGTTATA-TA
*
566781 AAAAA-TAATTAATTAGTTTGTATTGTTAATAGTTAGTTATATA
1 AAAAATTATTTAATTAGTTTGT-TTGTTAATAGTTAGTTATATA
566824 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TT-GTT-AATAGTT-AGTTATAT
566870 TGTTTGTTGA
Statistics
Matches: 75, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
38 3 0.04
39 4 0.05
40 11 0.15
41 5 0.07
42 7 0.09
43 6 0.08
44 21 0.28
45 3 0.04
46 7 0.09
47 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (43 bp):
AAAAATTATTTAATTAGTTTGTTTGTTAATAGTTAGTTATATA
Found at i:569278 original size:24 final size:22
Alignment explanation
Indices: 569239--569305 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 22
569229 AAATCATTAC
569239 TAGTATC-AATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
569260 TAGTAATCAACTATTTTAAATCA-T
1 TAGT-ATCAAATA-ATTAAAT-ATT
569284 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
569306 AACAATAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
21 5 0.14
22 10 0.27
23 10 0.27
24 11 0.30
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:569498 original size:26 final size:26
Alignment explanation
Indices: 569460--569875 Score: 316
Period size: 26 Copynumber: 16.7 Consensus size: 26
569450 TAACTAAATA
* *
569460 ATTATTATAAAATCATGATTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
569486 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * *
569511 ATCA-AATC-ATTAAATATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
569532 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
569558 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
569584 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
** *
569610 ATTATTATCAAATCATTGCTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * **
569635 ATCA-AATC-ATTAAAAATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
569656 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
569682 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
569708 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
569734 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * *
569759 ATCA-AATC-ATTAAATATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
569780 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
*
569806 ATTATTA-CTTAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
569832 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
569858 ATTATTATCAAATCATTA
1 ATTATTATCAAATCATTA
569876 CTAAATCATC
Statistics
Matches: 306, Mismatches: 60, Indels: 48
0.74 0.14 0.12
Matches are distributed among these distances:
21 12 0.04
22 6 0.02
23 39 0.13
24 18 0.06
25 18 0.06
26 210 0.69
27 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (26 bp):
ATTATTATCAAATCATTATTATAATG
Found at i:569609 original size:124 final size:124
Alignment explanation
Indices: 569460--569933 Score: 894
Period size: 124 Copynumber: 3.8 Consensus size: 124
569450 TAACTAAATA
* * *
569460 ATTATTATAAAATCATGATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
569525 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
*
569584 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTGCTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
*
569649 AATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
569708 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
*
569773 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTTAATCATTATTATAATG
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
569832 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
569897 TATTTAAATCATTATTAAATCATTTTTATAATGATTA
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTA
569934 ATAAATACAT
Statistics
Matches: 342, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 342 1.00
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (124 bp):
ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
Found at i:569820 original size:150 final size:145
Alignment explanation
Indices: 569535--569878 Score: 403
Period size: 150 Copynumber: 2.3 Consensus size: 145
569525 TATTTAAATC
* *
569535 ATTATTAAATCATTTTTATAATGATTATTA-CTAAATCATTATTATAATGATTATTATCAAATCA
1 ATTA-TAAATCATTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAATCA
* * *
569599 TTACTATAATGATTATTATCAAATCATTGCTAAATCATCAAATCATTAAAAATTTAAATCATTAT
64 TTACTATAATCATAATCATCAAATCATT-CTAAATCAT---ATCATTAAAAATTTAAATCATTAT
*
569664 TAAATCATTTTTATAATGATT
125 TAAATCATTATTATAATGATT
569685 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTA-TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
* * *
569750 TACTA-AATCATCAAATCATTAAAT-ATT-TAAATCAT-T-ATTAAATCATTTTTATAATGATTA
65 TACTATAATCAT--AATCATCAAATCATTCTAAATCATATCATTAAA--A-ATTTA-AATCATTA
569810 TTACTTAATCATTATTATAATGATT
124 TTA---AATCATTATTATAATGATT
*
569835 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA
1 ATTAT-AAATCATTATTATAATGATTATTATCAAATCATTACTA
569879 AATCATCAAA
Statistics
Matches: 172, Mismatches: 11, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
143 6 0.03
144 1 0.01
145 1 0.01
146 4 0.02
147 10 0.06
148 8 0.05
149 6 0.03
150 127 0.74
151 9 0.05
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (145 bp):
ATTATAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATT
ACTATAATCATAATCATCAAATCATTCTAAATCATATCATTAAAAATTTAAATCATTATTAAATC
ATTATTATAATGATT
Found at i:572806 original size:26 final size:24
Alignment explanation
Indices: 572748--572806 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
572738 CTAATAAACC
*
572748 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
572772 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
572800 TAATAAT
1 TAATAAT
572807 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:573641 original size:28 final size:28
Alignment explanation
Indices: 573601--573850 Score: 125
Period size: 28 Copynumber: 8.2 Consensus size: 28
573591 ATTTTTTATA
573601 TAATATAATATATAACTTAAACTAATAAAC
1 TAATAT-A-ATATAACTTAAACTAATAAAC
*
573631 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAATAAAC
* *
573659 TAATAATTTATACTAAC--AAACTAATTAAC
1 TAAT-A-TAATA-TAACTTAAACTAATAAAC
*
573688 TAGATATAATA-AACTAATATAATATAACTTAAAC
1 TA-ATATAATATAACT--TA-AA-CTAA--TAAAC
* * * *
573722 TAACA-AACTAATAATTTATACTAACAAAC
1 TAATATAA-T-ATAACTTAAACTAATAAAC
*
573751 TAATTAACTAGATATAAC--AAACTAATAATTTTTTATA
1 TAA-T-A-TA-ATATAACTTAAACTAATAA------A-C
573788 TAATATAATATATAACTTAAACTAATAAAC
1 TAATAT-A-ATATAACTTAAACTAATAAAC
*
573818 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAATAAAC
573846 TAATA
1 TAATA
573851 AACTAATATA
Statistics
Matches: 170, Mismatches: 20, Indels: 62
0.67 0.08 0.25
Matches are distributed among these distances:
26 3 0.02
28 53 0.31
29 23 0.14
30 27 0.16
31 11 0.06
32 10 0.06
33 7 0.04
34 9 0.05
35 12 0.07
36 2 0.01
37 13 0.08
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.33
Consensus pattern (28 bp):
TAATATAATATAACTTAAACTAATAAAC
Found at i:573673 original size:21 final size:21
Alignment explanation
Indices: 573640--573778 Score: 97
Period size: 21 Copynumber: 6.2 Consensus size: 21
573630 CTAATATAAT
573640 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
573661 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
573682 ATTAACTAGATATAA-TAAACTAATA-TAA
1 A-TAACT---TA-AACT-AAC-AA-ACT-A
573710 TATAACTTAAACTAACAAACTA
1 -ATAACTTAAACTAACAAACTA
* *
573732 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
573753 ATTAAC-TAGATA-TAACAAACTA
1 A-TAACTTA-A-ACTAACAAACTA
573775 ATAA
1 ATAA
573779 TTTTTTATAT
Statistics
Matches: 95, Mismatches: 8, Indels: 30
0.71 0.06 0.23
Matches are distributed among these distances:
21 45 0.47
22 20 0.21
23 4 0.04
24 5 0.05
25 6 0.06
26 4 0.04
27 3 0.03
28 7 0.07
29 1 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.29
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:573703 original size:71 final size:71
Alignment explanation
Indices: 573623--573777 Score: 301
Period size: 71 Copynumber: 2.2 Consensus size: 71
573613 TAACTTAAAC
573623 TAATAAACTAATATAATATAACTTAAACTAACAAACTAATAATTTATACTAACAAACTAATTAAC
1 TAATAAACTAATATAATATAACTTAAACTAACAAACTAATAATTTATACTAACAAACTAATTAAC
573688 TAGATA
66 TAGATA
573694 TAATAAACTAATATAATATAACTTAAACTAACAAACTAATAATTTATACTAACAAACTAATTAAC
1 TAATAAACTAATATAATATAACTTAAACTAACAAACTAATAATTTATACTAACAAACTAATTAAC
573759 TAGATA
66 TAGATA
*
573765 TAACAAACTAATA
1 TAATAAACTAATA
573778 ATTTTTTATA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 83 1.00
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.30
Consensus pattern (71 bp):
TAATAAACTAATATAATATAACTTAAACTAACAAACTAATAATTTATACTAACAAACTAATTAAC
TAGATA
Found at i:573818 original size:8 final size:8
Alignment explanation
Indices: 573805--573885 Score: 57
Period size: 8 Copynumber: 10.4 Consensus size: 8
573795 ATATATAACT
573805 TAAACTAA
1 TAAACTAA
573813 TAAACTAA
1 TAAACTAA
573821 T--A-TAA
1 TAAACTAA
573826 TATAACT--
1 TA-AACTAA
573833 TAAACTAA
1 TAAACTAA
*
573841 CAAACTAA
1 TAAACTAA
573849 TAAACTAA
1 TAAACTAA
573857 TATAA-TAA
1 TA-AACTAA
*
573865 TTTATACTAA
1 --TAAACTAA
*
573875 CAAACTAA
1 TAAACTAA
573883 TAA
1 TAA
573886 TTTATACTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
5 4 0.07
6 5 0.09
7 2 0.04
8 37 0.65
9 4 0.07
10 5 0.09
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (8 bp):
TAAACTAA
Found at i:573877 original size:34 final size:36
Alignment explanation
Indices: 573806--573885 Score: 128
Period size: 34 Copynumber: 2.3 Consensus size: 36
573796 TATATAACTT
573806 AAACTAATAAACTAATATAATATAACTTAAACTAAC
1 AAACTAATAAACTAATATAATATAACTTAAACTAAC
* *
573842 AAACTAATAAACTAATAT-A-ATAATTTATACTAAC
1 AAACTAATAAACTAATATAATATAACTTAAACTAAC
573876 AAACTAATAA
1 AAACTAATAA
573886 TTTATACTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 23 0.55
35 1 0.02
36 18 0.43
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (36 bp):
AAACTAATAAACTAATATAATATAACTTAAACTAAC
Found at i:573916 original size:21 final size:21
Alignment explanation
Indices: 573711--573910 Score: 121
Period size: 21 Copynumber: 9.4 Consensus size: 21
573701 CTAATATAAT
*
573711 ATAACTTAAACTAACAAACTA
1 ATAACTTATACTAACAAACTA
*
573732 ATAATTTATACTAACAAACTA
1 ATAACTTATACTAACAAACTA
*
573753 ATTAACTAGATA-TAACAAACTA
1 A-TAACT-TATACTAACAAACTA
* *
573775 ATAATTTTTTATA-TAATATAA-TA
1 ATAA---CTTATACTAACA-AACTA
* *
573798 TATAACTTAAACTAATAAACTA
1 -ATAACTTATACTAACAAACTA
*
573820 AT-A-TAATA-TAACTTAAACTA
1 ATAACTTATACTAAC--AAACTA
* *
573840 ACAAACTAATA--AACTAATA-TA
1 A-TAACTTATACTAAC-AA-ACTA
*
573861 ATAATTTATACTAACAAACTA
1 ATAACTTATACTAACAAACTA
*
573882 ATAATTTATACTAACAAACTA
1 ATAACTTATACTAACAAACTA
573903 ATAACTTA
1 ATAACTTA
573911 AGCTAAACCC
Statistics
Matches: 144, Mismatches: 17, Indels: 36
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.02
19 3 0.02
20 15 0.10
21 69 0.48
22 30 0.21
23 17 0.12
24 7 0.05
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (21 bp):
ATAACTTATACTAACAAACTA
Found at i:574250 original size:36 final size:36
Alignment explanation
Indices: 574203--574273 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
574193 GCAGGAATCT
574203 CTGAGCTATGAGCTATGATGCAACGCATGCATGCAG
1 CTGAGCTATGAGCTATGATGCAACGCATGCATGCAG
574239 CTGAGCTATGAGCTATGATGCAACGCATGCATGCA
1 CTGAGCTATGAGCTATGATGCAACGCATGCATGCA
574274 TGCAGCTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (36 bp):
CTGAGCTATGAGCTATGATGCAACGCATGCATGCAG
Found at i:574420 original size:15 final size:15
Alignment explanation
Indices: 574396--574524 Score: 107
Period size: 15 Copynumber: 8.1 Consensus size: 15
574386 CCATCCCCTC
574396 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
*
574411 CCCAATGCATTCCCA
1 CCCCATGCATTCCCA
* *
574426 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
574444 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
574459 CATCCCATG-TTGATCCCTC
1 C--CCCATGCAT--TCCC-A
574478 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
574493 CCCCATGCATCCCCTC
1 CCCCATGCATTCCC-A
574509 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
574524 C
1 C
574525 GTCCCATGTT
Statistics
Matches: 90, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
15 30 0.33
16 30 0.33
17 23 0.26
18 6 0.07
19 1 0.01
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.22
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:574531 original size:48 final size:48
Alignment explanation
Indices: 574369--574532 Score: 136
Period size: 48 Copynumber: 3.3 Consensus size: 48
574359 CCATGCACAG
* * * *
574369 TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCAATGCA
1 TTCCCACGTCCCATG---CATCCCCTACCCCATGCATTCCCCCCCCATGCA
* * *
574420 TTCCCACGTCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATG-T
1 TTCCCACGTCCCATGCATCCCCTACCCCATGCATTCCC-C-CCCCATGCA
* * * *
574469 TGATCCCTC-CCCCATGCATTCCC-ACCCCATGCATCCCCTCCCCCATGCA
1 T--TCCCACGTCCCATGCATCCCCTACCCCATGCATTCCC-CCCCCATGCA
574518 TTCCCACGTCCCATG
1 TTCCCACGTCCCATG
574533 TTGATTGCAT
Statistics
Matches: 92, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
47 5 0.05
48 35 0.38
49 16 0.17
50 17 0.18
51 19 0.21
ACGTcount: A:0.18, C:0.52, G:0.09, T:0.22
Consensus pattern (48 bp):
TTCCCACGTCCCATGCATCCCCTACCCCATGCATTCCCCCCCCATGCA
Found at i:577006 original size:17 final size:17
Alignment explanation
Indices: 576984--577017 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
576974 TTCCATCCGG
*
576984 TCTTATTATTTAATTCA
1 TCTTATCATTTAATTCA
*
577001 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
577018 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
TCTTATCATTTAATTCA
Found at i:578186 original size:14 final size:14
Alignment explanation
Indices: 578169--578235 Score: 80
Period size: 14 Copynumber: 4.4 Consensus size: 14
578159 CTAGGCGGCT
*
578169 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
578183 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
578197 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
578215 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
578230 CGGCTC
1 CGGCTC
578236 CTCAGGCTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 31 0.66
15 2 0.04
18 2 0.04
19 12 0.26
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:578186 original size:19 final size:19
Alignment explanation
Indices: 578164--578227 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
578154 TCGATCTAGG
578164 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
578183 CGGCTC-G----GCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
578197 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
578216 CGGCTCGGCTCA
1 CGGCTCGGCTCA
578228 AACGGCTCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 13 0.33
15 1 0.03
18 1 0.03
19 24 0.62
ACGTcount: A:0.17, C:0.38, G:0.30, T:0.16
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:578189 original size:33 final size:33
Alignment explanation
Indices: 578164--578235 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
578154 TCGATCTAGG
578164 CGGCTCGGCTCAGCTCAAACGGCTCGGCTCAAA
1 CGGCTCGGCTCAGCTCAAACGGCTCGGCTCAAA
*
578197 CGGCTCGGCTCAGCTCAAGCGGCTCGGCTCAAA
1 CGGCTCGGCTCAGCTCAAACGGCTCGGCTCAAA
578230 CGGCTC
1 CGGCTC
578236 CTCAGGCTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (33 bp):
CGGCTCGGCTCAGCTCAAACGGCTCGGCTCAAA
Found at i:579014 original size:29 final size:29
Alignment explanation
Indices: 578972--579039 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
578962 GGGTGTTACA
578972 GACCTCCAAGGTCGCCCGGATGCCATGGC
1 GACCTCCAAGGTCGCCCGGATGCCATGGC
579001 GACCTCCAAGGTCGCCCGGATGCCATGGC
1 GACCTCCAAGGTCGCCCGGATGCCATGGC
579030 GACCTCCAAG
1 GACCTCCAAG
579040 ACCACTGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.38, G:0.29, T:0.13
Consensus pattern (29 bp):
GACCTCCAAGGTCGCCCGGATGCCATGGC
Found at i:579290 original size:2 final size:2
Alignment explanation
Indices: 579283--579324 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
579273 TTAACAAGTA
579283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
579325 TCTTTTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:579563 original size:15 final size:15
Alignment explanation
Indices: 579543--579572 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
579533 AAGATAATGT
579543 CACATCATCATTGAA
1 CACATCATCATTGAA
579558 CACATCATCATTGAA
1 CACATCATCATTGAA
579573 GAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
CACATCATCATTGAA
Found at i:579942 original size:37 final size:37
Alignment explanation
Indices: 579861--579961 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 37
579851 TTCGTCCTAT
* * * **
579861 TAGGATTCAAACTCCTAAAAATATGATAGAATTTTTT
1 TAGGATTTAAACTCCTAAAAATAGGATAGAATTCTAC
*
579898 TAGGATTTAAACTCCTAAAAATAGGATAGAGTTCTAC
1 TAGGATTTAAACTCCTAAAAATAGGATAGAATTCTAC
* * *
579935 TATGATTTAAACTCTTAAAGATAGGAT
1 TAGGATTTAAACTCCTAAAAATAGGAT
579962 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (37 bp):
TAGGATTTAAACTCCTAAAAATAGGATAGAATTCTAC
Found at i:580408 original size:2 final size:2
Alignment explanation
Indices: 580401--580438 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
580391 TTAATTAGTT
580401 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
580439 CATACTTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:580564 original size:24 final size:23
Alignment explanation
Indices: 580537--580644 Score: 88
Period size: 22 Copynumber: 4.9 Consensus size: 23
580527 CTTTGCATTT
580537 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTA-TA
* *
580561 TTATTTTTACTATTATATTT-TCC
1 TTATTATTACTATTATATTTAT-A
*
580584 TT-TTATT-CTACT-TATTTATA
1 TTATTATTACTATTATATTTATA
580604 TTATATATGTA-TATT-T-TTTATA
1 TTAT-TAT-TACTATTATATTTATA
*
580626 TT-TTATTATTATTATATTT
1 TTATTATTACTATTATATTT
580645 TTACTTTCTC
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
19 2 0.03
20 14 0.20
21 8 0.12
22 19 0.28
23 7 0.10
24 19 0.28
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTATTACTATTATATTTATA
Found at i:580685 original size:12 final size:11
Alignment explanation
Indices: 580663--580703 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
580653 TCTTTCTTTT
580663 TATTATTCTTG
1 TATTATTCTTG
580674 TATTATTACTTG
1 TATTATT-CTTG
* *
580686 TATTATTTTTA
1 TATTATTCTTG
580697 TATTATT
1 TATTATT
580704 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:580836 original size:11 final size:11
Alignment explanation
Indices: 580822--580856 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
580812 ATTATACATA
580822 TATTTTTCTAT
1 TATTTTTCTAT
580833 TATTTTTCTA-
1 TATTTTTCTAT
580843 TATTTTTCTAT
1 TATTTTTCTAT
580854 TAT
1 TAT
580857 CATTATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTTTCTAT
Found at i:580846 original size:10 final size:10
Alignment explanation
Indices: 580820--580853 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
580810 ATATTATACA
580820 TATATTTTTC
1 TATATTTTTC
580830 TATTATTTTTC
1 TA-TATTTTTC
580841 TATATTTTTC
1 TATATTTTTC
580851 TAT
1 TAT
580854 TATCATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (10 bp):
TATATTTTTC
Found at i:581216 original size:2 final size:2
Alignment explanation
Indices: 581209--581251 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
581199 TTATTTATTT
581209 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
581251 T
1 T
581252 TATTCGTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:581288 original size:17 final size:17
Alignment explanation
Indices: 581268--581338 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 17
581258 TACTTTGTTA
*
581268 TTATTATTTTGTTTTAT
1 TTATTATTTTATTTTAT
* *
581285 TTATTTTTTTCTTTT-T
1 TTATTATTTTATTTTAT
581301 TATATATATTTTATTTTAT
1 T-TAT-TATTTTATTTTAT
*
581320 TTTTTACTTATTATTTTAT
1 TTATTA-TT-TTATTTTAT
581339 CTTTGCTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
16 2 0.05
17 18 0.41
18 13 0.30
19 11 0.25
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (17 bp):
TTATTATTTTATTTTAT
Found at i:581317 original size:24 final size:25
Alignment explanation
Indices: 581281--581347 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 25
581271 TTATTTTGTT
*
581281 TTATTTATTTTTTTCTTTTTTA--TA
1 TTATTT-TATTTTTCTTTTTTACTTA
*
581305 TATATTTTA-TTTTATTTTTTACTTA
1 T-TATTTTATTTTTCTTTTTTACTTA
*
581330 TTATTTTATCTTTGCTTT
1 TTATTTTAT-TTTTCTTT
581348 CTTCATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 11 0.32
24 9 0.26
25 8 0.24
26 6 0.18
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (25 bp):
TTATTTTATTTTTCTTTTTTACTTA
Found at i:581337 original size:35 final size:35
Alignment explanation
Indices: 581272--581338 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
581262 TTGTTATTAT
* ** *
581272 TATTTTGTTTTATTTATTTTTTTCTTTTTTATATA
1 TATTTTATTTTATTTATTTACTTATTTTTTATATA
581307 TATTTTATTTTATTT-TTTACTTATTATTTTAT
1 TATTTTATTTTATTTATTTACTTATT-TTTTAT
581339 CTTTGCTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 7 0.26
35 20 0.74
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (35 bp):
TATTTTATTTTATTTATTTACTTATTTTTTATATA
Found at i:582518 original size:19 final size:20
Alignment explanation
Indices: 582482--582519 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
582472 ACCTTACTAA
*
582482 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
582502 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
582520 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Found at i:585941 original size:17 final size:17
Alignment explanation
Indices: 585921--585968 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
585911 AAAAAGGGCA
585921 AAAAACAAAAAAAAAAC
1 AAAAACAAAAAAAAAAC
* *
585938 AAAAAGAAGAAAAAAAAAG
1 AAAAA-CA-AAAAAAAAAC
585957 AAAGAACAAAAA
1 AAA-AACAAAAA
585969 TCAAAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 5 0.20
18 5 0.20
19 13 0.52
20 2 0.08
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAAAAAAC
Found at i:585980 original size:26 final size:24
Alignment explanation
Indices: 585919--585982 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
585909 ACAAAAAGGG
585919 CAAAAAACAAAAA-AAAAACAAAAA
1 CAAAAAA-AAAAAGAAAAACAAAAA
*
585943 GAAGAAAAAAAAAGAAAGAACAAAAA
1 CAA-AAAAAAAAAGAAA-AACAAAAA
*
585969 TCAAAAAGAAAAAG
1 -CAAAAAAAAAAAG
585983 GGACAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 7 0.21
25 7 0.21
26 17 0.52
27 2 0.06
ACGTcount: A:0.81, C:0.08, G:0.09, T:0.02
Consensus pattern (24 bp):
CAAAAAAAAAAAGAAAAACAAAAA
Found at i:586654 original size:22 final size:22
Alignment explanation
Indices: 586581--586657 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
586571 GCTACCCCAT
* *
586581 CAAACCGTTGAACATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* * *
586603 CAAACCTATGAGTACCAAATGC
1 CAAACCTTTGAGCATCAAATGC
586625 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
586647 CAAACCTTTGA
1 CAAACCTTTGA
586658 CCAAACATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:587518 original size:16 final size:17
Alignment explanation
Indices: 587493--587531 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
587483 CTTTTCTTTT
*
587493 TTTATATATTTTA-TTA
1 TTTATTTATTTTACTTA
587509 TTTATTTATTTTACTTA
1 TTTATTTATTTTACTTA
587526 -TTATTT
1 TTTATTT
587532 TATCTTTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTATTTTACTTA
Found at i:589844 original size:399 final size:399
Alignment explanation
Indices: 589255--590147 Score: 956
Period size: 399 Copynumber: 2.2 Consensus size: 399
589245 ATCTGAAATG
* * * *
589255 TTTGGTGTTGAACTTGAAGCTTCAGAGCAATTTGATGCAAGGGTCACTGGACTAGTCATGTTTCT
1 TTTGGTGTTGAACTTAAAGCTCCAGAGAAATTTGATGCAAGGGTCACAGGACTAGTCATGTTTCT
** * * * *
589320 CATTTCCAATTCATACCTCGCAACATTCAAGGGTTCTGGAGATGAGGAAATGTACTTCACAATAT
66 CATAACCAATTCATACCTCGCAACATTCAAGCGTTCTGGAGATGAAGAAAAGTACTTCACAACAT
* * *** * *
589385 CCATTTGTTGAATACCAGAGGGAACGGAGTTCCTATTGTCCACTTCTTTGACACCAGAATAATCC
131 CCATTTCTTGAACACCAGAGGGAACGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAATCC
* * * * *
589450 AAAACATTTGGTGTTGAACTTGAA-GCTTCGGAGAAACTTGATATAACAGTCACTGGTCTAGTCA
196 AAAACATTTGGTCTTGAACTT-AAGGCTTCAGAGAAACTTGAAATAACAGCCACTGGACTAGTCA
* * * * *
589514 AATTTCTCATATCCAGTTCA-CACCTCACAACTTTCATGGGTTCTGGAGATGAAGAAATGGAGTT
260 AAGTTCTCATATCCAGTTCATC-CCTCACAACATTCATGAGTTCTGGAGATGAAGAAATGCAGTA
589578 CAC-AATATCCATTTCTTTAACACCAGAGGGGACGGTGTTCATAACATCCATTTTGACACCAGAG
324 C-CTAATATCCATTTCTTTAACACCAGAGGGGACGGTGTTCATAACATCCATTTTGACACCAGAG
589642 AAATCCGAGACA
388 AAATCCGAGACA
** * *
589654 TTTGGTGTTGAACTTAAAGCTCCAGAGAAATTTGATGCACTGGTCACAGGACTGGTCGTGTTTCT
1 TTTGGTGTTGAACTTAAAGCTCCAGAGAAATTTGATGCAAGGGTCACAGGACTAGTCATGTTTCT
* * ** * * * *
589719 CATAACCAGTTCATCCCTCGTGACATTTACGCGTTTTGGAGAT-ACAGAAACAG-AGTTC-CTAA
66 CATAACCAATTCATACCTCGCAACATTCAAGCGTTCTGGAGATGA-AGAAA-AGTACTTCAC-AA
* *
589781 CATCCATTTCTTTAACACCAGAGGGAATGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAA
128 CATCCATTTCTTGAACACCAGAGGGAACGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAA
* * * **
589846 TCCGAAACATTTGGTCTTGAGCTTAAGGCTTCAGAGCAACTTGAAATAATGGCCACTGGACTAGT
193 TCCAAAACATTTGGTCTTGAACTTAAGGCTTCAGAGAAACTTGAAATAACAGCCACTGGACTAGT
** * *
589911 CATGGTTCTCATATCCAGTTCATCCCTCATAACATTCATGAGTTCTGGAGATGAGGAAATGCAGT
258 CAAAGTTCTCATATCCAGTTCATCCCTCACAACATTCATGAGTTCTGGAGATGAAGAAATGCAGT
* * * ** * * * * *
589976 ACCTAGTATCCATTTCTTTAACACTAGAGGGAATAGAGTTCCTACCATCTATTTCTTTGGCACCT
323 ACCTAATATCCATTTCTTTAACACCAGAGGGGACGGTGTTCATAACATCCA--T-TTTGACACC-
*
590041 A-A-ATAATCCGAAACA
384 AGAGA-AATCCGAGACA
* ** * * * * * *
590056 TTTGGCGTTGAACTTATTGCTTCAGAGCAACTTGATGTAGGGGTCACTGGACTAGTCATGTTTCT
1 TTTGGTGTTGAACTTAAAGCTCCAGAGAAATTTGATGCAAGGGTCACAGGACTAGTCATGTTTCT
* * * * *
590121 TATATCCAATCCATCCCTCACAACATT
66 CATAACCAATTCATACCTCGCAACATT
590148 TATGAGTTTC
Statistics
Matches: 403, Mismatches: 80, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
398 5 0.01
399 301 0.75
400 2 0.00
401 2 0.00
402 92 0.23
403 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (399 bp):
TTTGGTGTTGAACTTAAAGCTCCAGAGAAATTTGATGCAAGGGTCACAGGACTAGTCATGTTTCT
CATAACCAATTCATACCTCGCAACATTCAAGCGTTCTGGAGATGAAGAAAAGTACTTCACAACAT
CCATTTCTTGAACACCAGAGGGAACGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAATCC
AAAACATTTGGTCTTGAACTTAAGGCTTCAGAGAAACTTGAAATAACAGCCACTGGACTAGTCAA
AGTTCTCATATCCAGTTCATCCCTCACAACATTCATGAGTTCTGGAGATGAAGAAATGCAGTACC
TAATATCCATTTCTTTAACACCAGAGGGGACGGTGTTCATAACATCCATTTTGACACCAGAGAAA
TCCGAGACA
Found at i:590155 original size:201 final size:200
Alignment explanation
Indices: 589002--590151 Score: 1073
Period size: 201 Copynumber: 5.7 Consensus size: 200
588992 TTAGAGATGA
** * * * * *
589002 GGAAGTGGAGTTCCTAACATCCGCTTCTTTAACACCAGGATTATCTGAAACGTTTGGTGTTGAAC
1 GGAA-TGGAGTTCCTAACATCCATTTCTTTGACACCAGAATAATCCGAAACATTTGGTGTTGAAC
* * * * **
589067 TTAAAGCTTCAGAGCAGCTTGTTGCAACGGTCACTGGACTAGTCGTGGTTCTCATATTGAATTCA
65 TTAAAGCTTCAGAGCAACTTGATGCAACGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCA
* ** * * * *
589132 TCTCTCACAACATCAATGGGTT-TTGACGACGAGGAAATGGTGTTCCCAGTATTCC-TTTCTTTA
130 TCCCTCACAACATTTATGGGTTCTGGA-GATGAGGAAATGGAGTT-CCAATA-TCCATTTCTTTA
* *
589195 ACAACGGAG
192 ACACCAGAG
* * * * **
589204 GGCATTGG-GTTCCTAACATCCATTTCTTTCAGACCAGAATAATCTGAAATGTTTGGTGTTGAAC
1 GG-AATGGAGTTCCTAACATCCATTTCTTTGACACCAGAATAATCCGAAACATTTGGTGTTGAAC
* * * *
589268 TTGAAGCTTCAGAGCAATTTGATGCAAGGGTCACTGGACTAGTCATGTTTCTCATTTCCAATTCA
65 TTAAAGCTTCAGAGCAACTTGATGCAACGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCA
* * * * * * * * *
589333 TACCTCGCAACATTCAAGGGTTCTGGAGATGAGGAAATGTACTTCACAATATCCATTTGTTGAAT
130 TCCCTCACAACATTTATGGGTTCTGGAGATGAGGAAATGGAGTTC-CAATATCCATTTCTTTAAC
589398 ACCAGAG
194 ACCAGAG
* *** * *
589405 GGAACGGAGTTCCTATTGTCCACTTCTTTGACACCAGAATAATCCAAAACATTTGGTGTTGAACT
1 GGAATGGAGTTCCTAACATCCATTTCTTTGACACCAGAATAATCCGAAACATTTGGTGTTGAACT
* * * ** * * ** *
589470 TGAAGCTTCGGAGAAACTTGATATAACAGTCACTGGTCTAGTCAAATTTCTCATATCCAGTTCA-
66 TAAAGCTTCAGAGCAACTTGATGCAACGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCAT
*
589534 CACCTCACAAC-TTTCATGGGTTCTGGAGATGAAGAAATGGAGTTCACAATATCCATTTCTTTAA
131 C-CCTCACAACATTT-ATGGGTTCTGGAGATGAGGAAATGGAGTTC-CAATATCCATTTCTTTAA
589598 CACCAGAG
193 CACCAGAG
* * * * *
589606 GGGACGGTGTTCATAACATCCA--T-TTTGACACCAGAGA-AATCCGAGACATTTGGTGTTGAAC
1 GGAATGGAGTTCCTAACATCCATTTCTTTGACACCAGA-ATAATCCGAAACATTTGGTGTTGAAC
* * * * * * * *
589667 TTAAAGCTCCAGAGAAATTTGATGC-ACTGGTCACAGGACTGGTCGTGTTTCTCATAACCAGTTC
65 TTAAAGCTTCAGAGCAACTTGATGCAAC-GGTCACTGGACTAGTCATGTTTCTCATATCCAATTC
*** * * * * ** *
589731 ATCCCTCGTGACATTTACGCGTTTTGGAGAT-ACAGAAACAGAGTTCCTAACATCCATTTCTTTA
129 ATCCCTCACAACATTTATGGGTTCTGGAGATGA-GGAAATGGAGTTCC-AATATCCATTTCTTTA
589795 ACACCAGAG
192 ACACCAGAG
* * * *
589804 GGAATGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAATCCGAAACATTTGGTCTTGAGCT
1 GGAATGGAGTTCCTAACATCCATTTCTTTGACACCAGAATAATCCGAAACATTTGGTGTTGAACT
* *** * * * *
589869 TAAGGCTTCAGAGCAACTTGAAATAATGGCCACTGGACTAGTCATGGTTCTCATATCCAGTTCAT
66 TAAAGCTTCAGAGCAACTTGATGCAACGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCAT
* * * * * *
589934 CCCTCATAACATTCATGAGTTCTGGAGATGAGGAAATGCAGTACCTAGTATCCATTTCTTTAACA
131 CCCTCACAACATTTATGGGTTCTGGAGATGAGGAAATGGAGTTCC-AATATCCATTTCTTTAACA
*
589999 CTAGAG
195 CCAGAG
* * * * *
590005 GGAATAGAGTTCCTACCATCTATTTCTTTGGCACCTA-AATAATCCGAAACATTTGGCGTTGAAC
1 GGAATGGAGTTCCTAACATCCATTTCTTTGACACC-AGAATAATCCGAAACATTTGGTGTTGAAC
** * ** * *
590069 TTATTGCTTCAGAGCAACTTGATGTAGGGGTCACTGGACTAGTCATGTTTCTTATATCCAATCCA
65 TTAAAGCTTCAGAGCAACTTGATGCAACGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCA
590134 TCCCTCACAACATTTATG
130 TCCCTCACAACATTTATG
590152 AGTTTCCTGA
Statistics
Matches: 770, Mismatches: 158, Indels: 41
0.79 0.16 0.04
Matches are distributed among these distances:
197 4 0.01
198 153 0.20
199 6 0.01
200 11 0.01
201 584 0.76
202 11 0.01
203 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (200 bp):
GGAATGGAGTTCCTAACATCCATTTCTTTGACACCAGAATAATCCGAAACATTTGGTGTTGAACT
TAAAGCTTCAGAGCAACTTGATGCAACGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCAT
CCCTCACAACATTTATGGGTTCTGGAGATGAGGAAATGGAGTTCCAATATCCATTTCTTTAACAC
CAGAG
Found at i:590665 original size:33 final size:33
Alignment explanation
Indices: 590602--590680 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
590592 AGTTGGTCCA
* *
590602 CTTACAGGGGCATTTTCCCCAATACTTAACCAG
1 CTTACAGGGGCATTATCCCCAATACATAACCAG
* ** *
590635 CTTACAGGGGCATTATCTCTGATACATAACCTG
1 CTTACAGGGGCATTATCCCCAATACATAACCAG
* *
590668 CTTATAGGAGCAT
1 CTTACAGGGGCAT
590681 CATTACTGCT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (33 bp):
CTTACAGGGGCATTATCCCCAATACATAACCAG
Found at i:590807 original size:33 final size:33
Alignment explanation
Indices: 590770--590848 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
590760 AGCTGGTCCA
*
590770 CTTACAGGGGCATTTTCCCCAATACTTAACCAG
1 CTTACAGGGGCATTATCCCCAATACTTAACCAG
* ** *
590803 CTTACAGGGGCATTATCTCTGATACTTAACCTG
1 CTTACAGGGGCATTATCCCCAATACTTAACCAG
* *
590836 CTTATAGGAGCAT
1 CTTACAGGGGCAT
590849 CATTACTGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (33 bp):
CTTACAGGGGCATTATCCCCAATACTTAACCAG
Found at i:590861 original size:168 final size:168
Alignment explanation
Indices: 590576--591079 Score: 875
Period size: 168 Copynumber: 3.0 Consensus size: 168
590566 TTGCTAGTGA
*
590576 GGGAATATTCCCCAGCAGTTGGTCCACTTACAGGGGCATTTTCCCCAATACTTAACCAGCTTACA
1 GGGAATCTTCCCCAGCAGTTGGTCCACTTACAGGGGCATTTTCCCCAATACTTAACCAGCTTACA
*
590641 GGGGCATTATCTCTGATACATAACCTGCTTATAGGAGCATCATTACTGCTACTTGGCCTGCTTAT
66 GGGGCATTATCTCTGATACTTAACCTGCTTATAGGAGCATCATTACTGCTACTTGGCCTGCTTAT
590706 TGAAGCATCATCCCAAGTGCTTGAACTGCTCATGGAGG
131 TGAAGCATCATCCCAAGTGCTTGAACTGCTCATGGAGG
*
590744 GGGAATCTTCCCCAGCAGCTGGTCCACTTACAGGGGCATTTTCCCCAATACTTAACCAGCTTACA
1 GGGAATCTTCCCCAGCAGTTGGTCCACTTACAGGGGCATTTTCCCCAATACTTAACCAGCTTACA
590809 GGGGCATTATCTCTGATACTTAACCTGCTTATAGGAGCATCATTACTGCTACTTGGCCTGCTTAT
66 GGGGCATTATCTCTGATACTTAACCTGCTTATAGGAGCATCATTACTGCTACTTGGCCTGCTTAT
*
590874 TGAAGCATCATCCCAAGTGCTTGAACTGCTCATGAAGG
131 TGAAGCATCATCCCAAGTGCTTGAACTGCTCATGGAGG
590912 GGGAATCTTCCCCAGCAGTTGGTCCACTTACAGGGGCATTTTCCCCAATACTTAACCAGCTTACA
1 GGGAATCTTCCCCAGCAGTTGGTCCACTTACAGGGGCATTTTCCCCAATACTTAACCAGCTTACA
** * * *
590977 GGGGCACCATCTCTAACACTTAACCTGCTTATA-GAGGCATCATTACTGCTACTTGGACTGCTTA
66 GGGGCATTATCTCTGATACTTAACCTGCTTATAGGA-GCATCATTACTGCTACTTGGCCTGCTTA
* * * *
591041 TTGGAGCATCATCCCATGTGCTTGAGCTGCTCATAGAGG
130 TTGAAGCATCATCCCAAGTGCTTGAACTGCTCATGGAGG
591080 CATCATCCCT
Statistics
Matches: 320, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
167 2 0.01
168 318 0.99
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (168 bp):
GGGAATCTTCCCCAGCAGTTGGTCCACTTACAGGGGCATTTTCCCCAATACTTAACCAGCTTACA
GGGGCATTATCTCTGATACTTAACCTGCTTATAGGAGCATCATTACTGCTACTTGGCCTGCTTAT
TGAAGCATCATCCCAAGTGCTTGAACTGCTCATGGAGG
Found at i:590862 original size:33 final size:33
Alignment explanation
Indices: 590791--590885 Score: 93
Period size: 33 Copynumber: 2.9 Consensus size: 33
590781 ATTTTCCCCA
* * * *
590791 ATACTTAACCAGCTTACAGGGGCATTATCTCTG
1 ATACTTAACCTGCTTATAGGAGCATCATCTCTG
590824 ATACTTAACCTGCTTATAGGAGCATCAT-TACTG
1 ATACTTAACCTGCTTATAGGAGCATCATCT-CTG
* ** * *
590857 CTACTTGGCCTGCTTATTGAAGCATCATC
1 ATACTTAACCTGCTTATAGGAGCATCATC
590886 CCAAGTGCTT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.02
33 50 0.98
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (33 bp):
ATACTTAACCTGCTTATAGGAGCATCATCTCTG
Found at i:591118 original size:33 final size:33
Alignment explanation
Indices: 591080--591159 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
591070 CTCATAGAGG
* * *
591080 CATCATCCCTACTACTTGTTCGGCTTAAAGGAGT
1 CATCATCCCTACTACATGTCCGACTTAAAGGA-T
*
591114 -ATCATCCCTACTACATGTCCGATTTAAAGGAT
1 CATCATCCCTACTACATGTCCGACTTAAAGGAT
*
591146 CACCATCCCTACTA
1 CATCATCCCTACTA
591160 ATCATCCTGC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
32 1 0.03
33 39 0.98
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (33 bp):
CATCATCCCTACTACATGTCCGACTTAAAGGAT
Found at i:602515 original size:23 final size:22
Alignment explanation
Indices: 602456--602531 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 22
602446 TCGTCCCCTA
*
602456 TATATATATTTTTTTATTTATT
1 TATATATCTTTTTTTATTTATT
602478 TAGTATATTCCTTTTTTTATTTATAT
1 TA-TATA-T-CTTTTTTTATTTAT-T
* *
602504 TATACTAT-TTTTTATATATATCT
1 TATA-TATCTTTTTTTATTTAT-T
602527 TATAT
1 TATAT
602532 CATTATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 3 0.07
23 20 0.44
24 1 0.02
25 16 0.36
26 5 0.11
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (22 bp):
TATATATCTTTTTTTATTTATT
Found at i:602521 original size:2 final size:2
Alignment explanation
Indices: 602516--602562 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
602506 TACTATTTTT
*
602516 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
602557 TA TA TA
1 TA TA TA
602563 GATGTATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:602681 original size:38 final size:40
Alignment explanation
Indices: 602592--602681 Score: 103
Period size: 41 Copynumber: 2.3 Consensus size: 40
602582 ATTTACTATG
* *
602592 TATATACATTTTTTCTTAATATTATATTTTATACGTTTTTA
1 TATATATATATTTTCTTAATATTATATTTTATA-GTTTTTA
* *
602633 TATATATATATTTTCTTGATATTCTATTTT-T-GTTTTTA
1 TATATATATATTTTCTTAATATTATATTTTATAGTTTTTA
* *
602671 TTTATTTATAT
1 TATATATATAT
602682 ATATATATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
38 16 0.37
40 1 0.02
41 26 0.60
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (40 bp):
TATATATATATTTTCTTAATATTATATTTTATAGTTTTTA
Found at i:602726 original size:13 final size:13
Alignment explanation
Indices: 602697--602734 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
602687 TATATATATA
*
602697 TATTA-TTTTTAC
1 TATTATTTTTTTC
602709 T-TTATTTTTTTC
1 TATTATTTTTTTC
602721 TATTATTTTTTTC
1 TATTATTTTTTTC
602734 T
1 T
602735 TAATATCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 3 0.13
12 8 0.35
13 12 0.52
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTATTTTTTTC
Found at i:602872 original size:18 final size:17
Alignment explanation
Indices: 602835--602878 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
602825 GTACATATTA
602835 TTTTTATTCATTTTTAATT
1 TTTTTA-TC-TTTTTAATT
*
602854 TCTTTTATCTTTTTTATT
1 T-TTTTATCTTTTTAATT
602872 TTTTTAT
1 TTTTTAT
602879 TCTATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 3 0.13
20 5 0.22
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTATCTTTTTAATT
Found at i:602951 original size:3 final size:3
Alignment explanation
Indices: 602937--602968 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
602927 TTTATTTTGT
*
602937 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
602969 TACGTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:603762 original size:20 final size:20
Alignment explanation
Indices: 603737--603783 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
603727 TTTTCCAAAT
603737 TCGCAACGCAAATTTGTAAA
1 TCGCAACGCAAATTTGTAAA
* *
603757 TCGCAACGCGAATTTGTATA
1 TCGCAACGCAAATTTGTAAA
603777 TCGCAAC
1 TCGCAAC
603784 ACAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
TCGCAACGCAAATTTGTAAA
Found at i:604018 original size:14 final size:15
Alignment explanation
Indices: 603999--604036 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
603989 TCCCCATCTC
603999 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
604013 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
604029 TAATTTTT
1 TAATTTTT
604037 CAATAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:604787 original size:24 final size:24
Alignment explanation
Indices: 604730--604789 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
604720 TAGTCAGTAT
604730 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
604754 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
604778 TCGAATTTTGAT
1 TCGAAATTTGAT
604790 GATGTGATGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:607077 original size:18 final size:18
Alignment explanation
Indices: 607054--607094 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
607044 AGCAAAAGGA
* *
607054 AATCAAAATTAAAATCGC
1 AATCAAAATCAAAATCCC
607072 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
607090 AATCA
1 AATCA
607095 CAACCAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.22, G:0.02, T:0.20
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:607490 original size:20 final size:20
Alignment explanation
Indices: 607465--607513 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
607455 AAACCGAAAA
*
607465 TCGCGTTGTGAATTTGACTT
1 TCGCGTTGTGAATTTAACTT
**
607485 TCGCGTTACGAATTTAACTT
1 TCGCGTTGTGAATTTAACTT
607505 TCGCGTTGT
1 TCGCGTTGT
607514 ACATTATTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
TCGCGTTGTGAATTTAACTT
Found at i:607955 original size:18 final size:18
Alignment explanation
Indices: 607934--607970 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
607924 GTAATTGGAG
607934 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
607952 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
607970 T
1 T
607971 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:607977 original size:24 final size:24
Alignment explanation
Indices: 607926--607978 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
607916 TTTCATATGT
* * *
607926 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
607950 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
607974 AATTT
1 AATTT
607979 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:608325 original size:39 final size:39
Alignment explanation
Indices: 608282--608368 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
608272 TCCGATGCTC
608282 ATCAAAATCCAAAGCTCATATAGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATAGTGCCAAGCAAAAGGAA
* *
608321 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATAGTGCCAAGCAAAAGGAA
608360 ATCAAAATC
1 ATCAAAATC
608369 TATAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATAGTGCCAAGCAAAAGGAA
Found at i:608632 original size:20 final size:20
Alignment explanation
Indices: 608607--608644 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
608597 GCAACGCTTA
608607 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
608627 TTTCGCGTTGTGAATTTG
1 TTTCGCGTTGCGAATTTG
608645 TACCTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:608785 original size:28 final size:28
Alignment explanation
Indices: 608753--608806 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
608743 ATAATTCTTA
*
608753 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
608781 TTTACAAATCAACTTCTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
608807 TTAATCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:608787 original size:14 final size:14
Alignment explanation
Indices: 608770--608806 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
608760 ATCAAATTAA
*
608770 ACAAATCAACTTTT
1 ACAAATCAACTTCT
608784 ACAAATCAACTTCT
1 ACAAATCAACTTCT
608798 ACAAATCAA
1 ACAAATCAA
608807 TTAATCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACTTCT
Found at i:610228 original size:21 final size:21
Alignment explanation
Indices: 610204--610302 Score: 87
Period size: 21 Copynumber: 4.7 Consensus size: 21
610194 TCGGGCGGGA
*
610204 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
*
610225 CCTCTTGAAC-AGTGGGAGGGG
1 CCTCTTGAACGA-TGAGAGGGG
* *
610246 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
* *
610267 CCTCTTGAACTAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
610288 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
610303 TAGATGCATC
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
20 3 0.05
21 55 0.90
22 3 0.05
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Done.