Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008526.1 Hibiscus syriacus cultivar Beakdansim tig00111398_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: 3043201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:380018 original size:23 final size:23
Alignment explanation
Indices: 379983--380030 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
379973 ATCAAGTACA
*
379983 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
380006 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
380029 AT
1 AT
380031 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:380775 original size:182 final size:182
Alignment explanation
Indices: 380462--380918 Score: 725
Period size: 182 Copynumber: 2.5 Consensus size: 182
380452 ACTTTTTTAC
* *
380462 TACCGATTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
* * *
380527 TACATTATTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
* * * *
380592 TGTCGATATTTATAGTAAAGTATCGACACTTTCAACATATCCGGTAGCTCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
*
380644 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATAGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
* *
380709 TATATTTTTATAAAATATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
*
380774 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
** ** * *
380826 TACTTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCG
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCA-TATTTTTACATGTTATATTGTTATGGATCG
*
380891 ATACAATTTTATAAAGTATCGACACTTT
65 ATACATTTTTATAAAGTATCGACACTTT
380919 CAATATATCC
Statistics
Matches: 251, Mismatches: 23, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
182 199 0.79
183 52 0.21
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
Found at i:381029 original size:112 final size:112
Alignment explanation
Indices: 380788--381591 Score: 1320
Period size: 112 Copynumber: 7.1 Consensus size: 112
380778 GATACTTATA
* * * *
380788 ATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
380853 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACAATTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
380901 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
380966 TTTGTCATTTTTTTACCTGTTATATTGTTATGGAACGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
381013 ATAAAGTATCGACACTTTCAATATATCCGGTAGTGTTTTACCTGTTTTGTCATTTATAGAGCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
381078 TTTGTCATTTTTTTACCTGTTATATTGTTATTGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
381125 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
381190 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
381237 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
381302 TTTGTCATTTTTTTTTACTTGTTATATTGTTATGGATCGATACATTTTTT
66 TTTGTCA--TTTTTTTACCTGTTATATTGTTATGGATCGATACA-TTTTT
* * *
381352 ATAAAGTATAGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
381417 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
381465 ATAAAGTATCGACATTTTCAATATATTCGGTAGCGCTTTACCTCTTTTGTCATTTATAGAACGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
** *
381530 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATTAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
381577 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
381592 AAACCGACAA
Statistics
Matches: 653, Mismatches: 35, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
112 371 0.57
113 138 0.21
114 69 0.11
115 75 0.11
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:385008 original size:17 final size:18
Alignment explanation
Indices: 384986--385022 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
384976 ATATATATAT
*
384986 ATATATAAT-TTTTTAAA
1 ATATATAATAATTTTAAA
385003 ATATATAATAATTTTAAA
1 ATATATAATAATTTTAAA
385021 AT
1 AT
385023 TTTCAGCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATATAATAATTTTAAA
Found at i:385009 original size:2 final size:2
Alignment explanation
Indices: 384958--384992 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
384948 ATTTTCAATA
384958 AT AT AT AT 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 AT AT AT AT A
384993 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:388600 original size:28 final size:29
Alignment explanation
Indices: 388546--388600 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
388536 TTGAATCGTC
* *
388546 CAACTATAAAAAATTATAAAATGATTAGT
1 CAACTATAAAAAATAATAAAATAATTAGT
*
388575 CAACT-TAAAAAATAATAAATTAATTA
1 CAACTATAAAAAATAATAAAATAATTA
388601 TCTTTCAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (29 bp):
CAACTATAAAAAATAATAAAATAATTAGT
Found at i:394910 original size:15 final size:15
Alignment explanation
Indices: 394890--394921 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
394880 ATTCCGATAA
*
394890 AACCGAATCGAATCG
1 AACCGAATCAAATCG
394905 AACCGAATCAAATCG
1 AACCGAATCAAATCG
394920 AA
1 AA
394922 TTAACTATAA
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:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (15 bp):
AACCGAATCAAATCG
Found at i:395807 original size:33 final size:33
Alignment explanation
Indices: 395770--395836 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
395760 ATTAAGATTT
395770 TTCATTTGTTCATCGTTGAAAA-TAGTCTTTCTA
1 TTCATTTGTTCATCGTTGAAAATTA-TCTTTCTA
395803 TTCATTTGTTCATCGTTGAAAATTATCTTTCTA
1 TTCATTTGTTCATCGTTGAAAATTATCTTTCTA
395836 T
1 T
395837 GAGTCTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (33 bp):
TTCATTTGTTCATCGTTGAAAATTATCTTTCTA
Found at i:397692 original size:34 final size:35
Alignment explanation
Indices: 397651--397720 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
397641 GTTAAAAAAT
*
397651 ATATTAATATACTAAATTAAAAGCA-GGCCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGCCCATAA
397685 ATATTAATAAACTAAATTAAAAGCAGGGCCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGCCCATAA
397720 A
1 A
397721 CTTATTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 24 0.71
35 10 0.29
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.24
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAAAAGCAGGGCCCATAA
Found at i:403337 original size:61 final size:59
Alignment explanation
Indices: 403272--403445 Score: 188
Period size: 60 Copynumber: 2.9 Consensus size: 59
403262 ATGATACTGG
* *
403272 AATATTTAGAAAGTTTGGGGACCAATTTAGAATTGAGGTCATAGTTTGAGGATGGAATTAA
1 AATATTTA-AAAGTTTGGGGACCAATTTA-AAATGAGGTCATAGTTTGAGGATAGAATTAA
* * * * * *
403333 AATATTCAAACGTTTGAGGACTAATTTAAAATGATAGTCATAGTTT-AGGGATAGAATTGA
1 AATATTTAAAAGTTTGGGGACCAATTTAAAATGA-GGTCATAGTTTGA-GGATAGAATTAA
* * * *
403393 AATATTTAAAAGTTTAGAGACCAACTTAAAATGAGAGTCATACTTTGAGGATA
1 AATATTTAAAAGTTTGGGGACCAATTTAAAATGAG-GTCATAGTTTGAGGATA
403446 TGTAGTGTAA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
59 6 0.07
60 78 0.85
61 8 0.09
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (59 bp):
AATATTTAAAAGTTTGGGGACCAATTTAAAATGAGGTCATAGTTTGAGGATAGAATTAA
Found at i:405089 original size:29 final size:29
Alignment explanation
Indices: 405055--405113 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
405045 CCTAAATTAA
405055 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
405084 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
405113 T
1 T
405114 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:409769 original size:29 final size:29
Alignment explanation
Indices: 409735--409793 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
409725 CCTAAATTAA
409735 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
409764 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
409793 T
1 T
409794 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:421354 original size:229 final size:227
Alignment explanation
Indices: 420944--421392 Score: 790
Period size: 229 Copynumber: 2.0 Consensus size: 227
420934 GTAAATTATC
* * *
420944 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
421009 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
421074 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
421139 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
421172 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
421237 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
421302 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
421367 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
421393 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 40 0.19
229 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:421481 original size:20 final size:20
Alignment explanation
Indices: 421458--421507 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
421448 CGATATACCA
421458 GGTAAAATTATGATAAAACC
1 GGTAAAATTATGATAAAACC
*
421478 GGTAACAA-AATGATAAAACC
1 GGTAA-AATTATGATAAAACC
421498 GGTAAAATTA
1 GGTAAAATTA
421508 AAAGTGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (20 bp):
GGTAAAATTATGATAAAACC
Found at i:421648 original size:20 final size:19
Alignment explanation
Indices: 421625--421671 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
421615 CGATATAACA
*
421625 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
421645 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
421665 GGTAAAA
1 GGTAAAA
421672 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:424033 original size:32 final size:33
Alignment explanation
Indices: 423979--424043 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
423969 AAATAGATGG
*
423979 AGTGGTGAAAGAAGTAGAGGTG-TGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
424011 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
424044 TATTAAGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 19 0.68
33 9 0.32
ACGTcount: A:0.29, C:0.02, G:0.46, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:425877 original size:19 final size:19
Alignment explanation
Indices: 425833--425871 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
425823 AATGTCGAGT
425833 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
425852 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
425871 T
1 T
425872 TTTTTTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:426465 original size:198 final size:198
Alignment explanation
Indices: 425957--426974 Score: 1812
Period size: 198 Copynumber: 5.1 Consensus size: 198
425947 TTAAGGGTCA
*
425957 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
426022 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
426086 AATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
426150 ATG
196 ATG
* *** *
426153 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
426217 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
426282 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
426347 TAATG
194 TAATG
426352 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
426417 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
426482 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
426547 ATG
196 ATG
* *** *
426550 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
426615 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
426680 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
426745 TAATG
194 TAATG
*
426750 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
426814 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
426878 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
426943 ATG
196 ATG
*
426946 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
426975 CTAATTTAAA
Statistics
Matches: 785, Mismatches: 30, Indels: 14
0.95 0.04 0.02
Matches are distributed among these distances:
195 18 0.02
196 198 0.25
197 28 0.04
198 214 0.27
199 168 0.21
200 159 0.20
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:426703 original size:398 final size:397
Alignment explanation
Indices: 425957--426974 Score: 1954
Period size: 398 Copynumber: 2.6 Consensus size: 397
425947 TTAAGGGTCA
*
425957 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
426022 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
426086 AATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
426150 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGAATGAATTAAAAACAAGGTGCA
196 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGAATGAATTAAAAACAAGGTGCA
426215 CCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
261 CCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
426280 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
326 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
426345 AATAATG
391 AATAATG
426352 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
426417 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
426482 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
426547 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGC
196 ATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGC
426612 ACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
260 ACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
*
426677 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
325 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
426742 AAATAATG
390 AAATAATG
*
426750 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
426814 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
426878 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
*
426943 ATGTGTCGACACTAATATATTTTGTGTCGATA
196 ATGTGTCGACACTAATATAGTTTGTGTCGATA
426975 CTAATTTAAA
Statistics
Matches: 615, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
395 113 0.18
396 162 0.26
397 142 0.23
398 198 0.32
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (397 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGAATGAATTAAAAACAAGGTGCA
CCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
AATAATG
Found at i:428456 original size:18 final size:18
Alignment explanation
Indices: 428433--428494 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
428423 ATCGGTCGCA
* * *
428433 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
428451 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
428469 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
428487 GAAGATGA
1 GAAGATGA
428495 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:428457 original size:6 final size:6
Alignment explanation
Indices: 428433--428494 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
428423 ATCGGTCGCA
* * * * * *
428433 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
428481 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
428495 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:428468 original size:3 final size:3
Alignment explanation
Indices: 428448--428498 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
428438 TGAAGCTGAC
* * * *
428448 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
428496 GAT
1 GAT
428499 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:428495 original size:12 final size:12
Alignment explanation
Indices: 428436--428498 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
428426 GGTCGCAGAA
* *
428436 GATGAAGCTGAC
1 GATGAAGATGAT
*
428448 GATGAAGATGAC
1 GATGAAGATGAT
*
428460 GATGATGATGAT
1 GATGAAGATGAT
*
428472 GATGACGATGAT
1 GATGAAGATGAT
428484 GATGAAGATGAT
1 GATGAAGATGAT
428496 GAT
1 GAT
428499 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:430425 original size:182 final size:184
Alignment explanation
Indices: 429862--430900 Score: 1914
Period size: 183 Copynumber: 5.7 Consensus size: 184
429852 CTTTCAACAT
**
429862 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
429926 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
429991 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
430045 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTC-TATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
430108 GGTCTACAACCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTG
66 GG--T-----CTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTG
430172 GAAGAAAAATGTGTCGATACAATTTAAAAAAGTGTCGACA-TTTACACATCGGAACCCATA
124 GAAGAAAAATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
430232 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
430297 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
430362 AATGTGTCGATACAATTT-AAAAAGTGTCGACATTTTACACATCGGAA-CCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
430414 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
430479 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
430544 AATGTGTCGATACAATTTAAAAAAGTGTCGACA-TTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
430597 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
430662 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
430727 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
430781 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
430846 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
430901 CCATTTAAAA
Statistics
Matches: 836, Mismatches: 5, Indels: 29
0.96 0.01 0.03
Matches are distributed among these distances:
182 233 0.28
183 285 0.34
184 139 0.17
187 40 0.05
188 106 0.13
189 33 0.04
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:430638 original size:365 final size:367
Alignment explanation
Indices: 429862--430900 Score: 1928
Period size: 365 Copynumber: 2.8 Consensus size: 367
429852 CTTTCAACAT
**
429862 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
429926 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
429991 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
430056 ATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTC-TATGCGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGG--T-----C
430119 TACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATG
254 TACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATG
430183 TGTCGATACAATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
319 TGTCGATACAATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
430232 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
430297 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
430362 AATGTGTCGATACAATTT-AAAAAGTGTCGACATTTTACACATCGGAA-CCATAATTATAATGTA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
430425 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACC
430490 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
261 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
430555 ACAATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
326 ACAATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
430597 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
430662 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
430727 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
* *
430792 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACC
430857 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
261 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
430901 CCATTTAAAA
Statistics
Matches: 658, Mismatches: 5, Indels: 15
0.97 0.01 0.02
Matches are distributed among these distances:
364 19 0.03
365 243 0.37
366 29 0.04
367 123 0.19
369 25 0.04
370 98 0.15
371 121 0.18
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (367 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
ACAATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:433477 original size:23 final size:22
Alignment explanation
Indices: 433451--433512 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
433441 AATAGGTAAC
*
433451 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTA-CCCTT
* *
433474 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTACCCTT
433496 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
433513 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.37
Consensus pattern (22 bp):
ATATAATGTAATAGGTACCCTT
Found at i:433500 original size:22 final size:22
Alignment explanation
Indices: 433451--433522 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
433441 AATAGGTAAC
* * *
433451 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTA-TCGTT
433474 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTATCGTT
*
433496 ATATAATGTAATAGGTAATGGTT
1 ATATAATGTAATAGGT-ATCGTT
433519 ATAT
1 ATAT
433523 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 19 0.43
23 25 0.57
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (22 bp):
ATATAATGTAATAGGTATCGTT
Found at i:433902 original size:23 final size:23
Alignment explanation
Indices: 433876--433938 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
433866 AATAGGTAAC
*
433876 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
433899 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
433922 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
433939 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:433946 original size:23 final size:23
Alignment explanation
Indices: 433876--433948 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
433866 AATAGGTAAC
* * **
433876 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
433899 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
433922 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
433945 ATAT
1 ATAT
433949 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:437311 original size:24 final size:24
Alignment explanation
Indices: 437274--437326 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
437264 TTTTATATTT
* * *
437274 GTTTACGCTCGTTCGTTTGTGTTC
1 GTTTACGCTAGTTCATTTGCGTTC
*
437298 GTTTACGTTAGTTCATTTGCGTTC
1 GTTTACGCTAGTTCATTTGCGTTC
437322 GTTTA
1 GTTTA
437327 TCATTTTAAC
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:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (24 bp):
GTTTACGCTAGTTCATTTGCGTTC
Found at i:440337 original size:24 final size:23
Alignment explanation
Indices: 440293--440343 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
440283 ATTTTACCGC
* *
440293 CTAAAATTTTATAAGTACGTCATT
1 CTAAAATTTTAAAAATACGTC-TT
*
440317 CTAAAATTTTAAAAATCCGTCTT
1 CTAAAATTTTAAAAATACGTCTT
440340 CTAA
1 CTAA
440344 CCTAAAATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (23 bp):
CTAAAATTTTAAAAATACGTCTT
Found at i:440994 original size:32 final size:30
Alignment explanation
Indices: 440936--440995 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 30
440926 ATTTAAATTA
*
440936 TTAATATTTATAATAATATAATATTATATT
1 TTAATATTTATAATAATACAATATTATATT
440966 TTAATATTATATAAATAAT-CAATAATTATA
1 TTAATATT-TAT-AATAATACAAT-ATTATA
440996 ATAATATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 8 0.31
31 6 0.23
32 12 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAATATTTATAATAATACAATATTATATT
Found at i:440995 original size:48 final size:50
Alignment explanation
Indices: 440920--441015 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 50
440910 TTTTCATCAA
* * * *
440920 AATATTATTTAAATTATTAATATTTATAATAATAT-A-ATATTATATTTT
1 AATATTATATAAATAATCAATAATTATAATAATATAAGATATTATATTTT
440968 AATATTATATAAATAATCAATAATTATAATAATATAAGATATTATATT
1 AATATTATATAAATAATCAATAATTATAATAATATAAGATATTATATT
441016 GTTATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 31 0.74
49 1 0.02
50 10 0.24
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (50 bp):
AATATTATATAAATAATCAATAATTATAATAATATAAGATATTATATTTT
Found at i:441028 original size:45 final size:43
Alignment explanation
Indices: 440924--441029 Score: 104
Period size: 48 Copynumber: 2.3 Consensus size: 43
440914 CATCAAAATA
* * * * *
440924 TTATTTAAATTATTAATATTTATAATAATATAATATTATATTT
1 TTATTTTAATAATCAATAATTATAATAATATAATATTATATTG
440967 TAATATTATATAAATAATCAATAATTATAATAATATAAGATATTATATTG
1 T--TATT-T-T-AATAATCAATAATTATAATAATAT-A-ATATTATATTG
441017 TTATTTTAATAAT
1 TTATTTTAATAAT
441030 ATATAATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
43 1 0.02
45 10 0.20
46 2 0.04
47 1 0.02
48 25 0.49
49 1 0.02
50 11 0.22
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (43 bp):
TTATTTTAATAATCAATAATTATAATAATATAATATTATATTG
Found at i:441058 original size:28 final size:28
Alignment explanation
Indices: 441026--441108 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 28
441016 GTTATTTTAA
*
441026 TAATATATAATAAAAAAATTTATATATT
1 TAATATATAATAAAAATATTTATATATT
* *
441054 TAATA-ATGAATAATATTATTTATAT-TT
1 TAATATAT-AATAAAAATATTTATATATT
* * *
441081 AAATATTTAATAAATATATTTAATATAT
1 TAATATATAATAAAAATATTT-ATATAT
441109 ACTAATTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
27 18 0.42
28 24 0.56
29 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
TAATATATAATAAAAATATTTATATATT
Found at i:441093 original size:27 final size:26
Alignment explanation
Indices: 441048--441102 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
441038 AAAAAATTTA
441048 TATATTTAATAATGAAT-AATATTATT
1 TATATTTAATAATGAATAAATA-TATT
* *
441074 TATATTTAAATATTTAATAAATATATT
1 TATATTT-AATAATGAATAAATATATT
441101 TA
1 TA
441103 ATATATACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 14 0.56
28 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TATATTTAATAATGAATAAATATATT
Found at i:441131 original size:23 final size:22
Alignment explanation
Indices: 441074--441132 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
441064 TAATATTATT
*
441074 TATATTTAAATAT-TTAATAAA
1 TATATTTAAATATACTAATAAA
*
441095 TATATTTAATATATACTAATTAA
1 TATATTTAA-ATATACTAATAAA
*
441118 TATTTTTTAAATATA
1 TA-TATTTAAATATA
441133 ATATAACACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 9 0.28
22 4 0.12
23 13 0.41
24 6 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTTAAATATACTAATAAA
Found at i:441495 original size:30 final size:30
Alignment explanation
Indices: 441459--441517 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
441449 TTTAAATTCC
441459 AGTAATTCAAATTCCAGTAATTCATTTTCT
1 AGTAATTCAAATTCCAGTAATTCATTTTCT
441489 AGTAATTCAAATTCCAGTAATTCATTTTC
1 AGTAATTCAAATTCCAGTAATTCATTTTC
441518 CTAATTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (30 bp):
AGTAATTCAAATTCCAGTAATTCATTTTCT
Found at i:441518 original size:15 final size:15
Alignment explanation
Indices: 441447--441512 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
441437 CATTTTCTAG
*
441447 AATTTAAATTCCAGT
1 AATTCAAATTCCAGT
441462 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
** *
441477 AATTCATTTTCTAGT
1 AATTCAAATTCCAGT
441492 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
441507 AATTCA
1 AATTCA
441513 TTTTCCTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:441887 original size:23 final size:23
Alignment explanation
Indices: 441857--441900 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
441847 AAGGGTACTC
441857 TGTTT-AAATTTTGAAGAAAAAAT
1 TGTTTAAAATTTTGAA-AAAAAAT
*
441880 TGTTTAAAATTTTTAAAAAAA
1 TGTTTAAAATTTTGAAAAAAA
441901 TCTATTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (23 bp):
TGTTTAAAATTTTGAAAAAAAAT
Found at i:445267 original size:16 final size:16
Alignment explanation
Indices: 445246--445303 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
445236 ATTAAAATAA
**
445246 ACGAACATAAACGCGC
1 ACGAACATAAACGAAC
445262 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
445278 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
445294 ACGAACATAA
1 ACGAACATAA
445304 CGTTGGAGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.53, C:0.24, G:0.14, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:446391 original size:15 final size:14
Alignment explanation
Indices: 446371--446427 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
446361 AATGAACATA
446371 AACGAACATAAACCG
1 AACGAACAT-AACCG
446386 AACGAACATAA---
1 AACGAACATAACCG
446397 AACGAACATAACCG
1 AACGAACATAACCG
*
446411 AACGAAAATAAACCG
1 AACGAACAT-AACCG
446426 AA
1 AA
446428 ACGTTCACGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
11 11 0.30
14 10 0.27
15 16 0.43
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:446396 original size:25 final size:25
Alignment explanation
Indices: 446351--446423 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
446341 AGATTGGGTT
* *
446351 AACATAAA-TGAATGAACATAAACG
1 AACATAAACCGAACGAACATAAACG
446375 AACATAAACCGAACGAACATAAAACG
1 AACATAAACCGAACGAACAT-AAACG
*
446401 AACAT-AACCGAACGAAAATAAAC
1 AACATAAACCGAACGAACATAAAC
446424 CGAAACGTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
24 12 0.27
25 22 0.50
26 10 0.23
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.11
Consensus pattern (25 bp):
AACATAAACCGAACGAACATAAACG
Found at i:447007 original size:2 final size:2
Alignment explanation
Indices: 447000--447032 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
446990 AATTTTCTTT
447000 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
447033 TTTTGTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:450085 original size:36 final size:35
Alignment explanation
Indices: 450007--450108 Score: 160
Period size: 36 Copynumber: 3.0 Consensus size: 35
449997 GTCCCTGTTG
450007 TTTATGGATTTAA-TTCTACTATAATTTAAAC---
1 TTTATGGATTTAATTTCTACTATAATTTAAACATT
450038 TTTATGGATTTAATTTCTACTATAATTTAAAACATT
1 TTTATGGATTTAATTTCTACTATAATTT-AAACATT
450074 TTTATGGATTTAATTTCTACTAT-ATTTAAACATT
1 TTTATGGATTTAATTTCTACTATAATTTAAACATT
450108 T
1 T
450109 CTATCTATGT
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
31 13 0.20
32 14 0.21
33 4 0.06
34 8 0.12
35 4 0.06
36 23 0.35
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (35 bp):
TTTATGGATTTAATTTCTACTATAATTTAAACATT
Found at i:453626 original size:35 final size:36
Alignment explanation
Indices: 453553--453626 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
453543 TTTTTATATT
*
453553 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
*
453589 TTTAATTTT-TAAAGAAAA-TATAT-AATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
453624 TTT
1 TTT
453627 GTAATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 7 0.21
35 14 0.41
36 13 0.38
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:453802 original size:20 final size:20
Alignment explanation
Indices: 453766--453803 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
453756 ATCCTATTCC
**
453766 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
453786 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
453804 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:470025 original size:18 final size:18
Alignment explanation
Indices: 470004--470038 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
469994 ACTATATATA
*
470004 AAAATGAAACTTAAACTT
1 AAAATAAAACTTAAACTT
470022 AAAATAAAACTTAAACT
1 AAAATAAAACTTAAACT
470039 AAACGTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAATAAAACTTAAACTT
Found at i:473346 original size:2 final size:2
Alignment explanation
Indices: 473327--473494 Score: 66
Period size: 2 Copynumber: 90.5 Consensus size: 2
473317 TAATAACATG
* * *
473327 AT AT A- AT AA AT A- AT AT AT AT AT A- AT AG AGT AT A- AT AT ACC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T
* * * *
473367 AT AT A- AT AT ACC AT AT TT AT A- AT AT AA AT AT A- AC ACT A- AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
473407 AT AT AT -T TT AT A- AT AT AT AT -T AT A- AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
473443 AT AT ACT AT AT AT AG AT AT AT A- AT AT AT A- AT AT A- AT AT AC
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
473483 AA AT AT AT -T AT A
1 AT AT AT AT AT AT A
473495 CTATCCCAGA
Statistics
Matches: 124, Mismatches: 19, Indels: 46
0.66 0.10 0.24
Matches are distributed among these distances:
1 18 0.15
2 100 0.81
3 6 0.05
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:473375 original size:5 final size:5
Alignment explanation
Indices: 473332--473481 Score: 82
Period size: 5 Copynumber: 29.6 Consensus size: 5
473322 ACATGATATA
* *
473332 ATAA- ATAAT ATATAT ATAAT AGAGT ATAAT ATACCAT ATAAT ATACCAT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATA--AT ATAAT ATA--AT
* * ** *
473381 AT-TT ATAAT ATAAAT ATAAC ACTAAT AT-AT ATTTT ATAAT AT-AT ATTAT
1 ATAAT ATAAT AT-AAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
473430 A-ATAT ATAAT ATAAT ATACT AT-AT ATAGAT AT-AT A-ATAT ATAAT
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATA-AT ATAAT
473474 ATAAT ATA
1 ATAAT ATA
473482 CAAATATATT
Statistics
Matches: 114, Mismatches: 14, Indels: 35
0.70 0.09 0.21
Matches are distributed among these distances:
4 21 0.18
5 64 0.56
6 20 0.18
7 9 0.08
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:473424 original size:12 final size:12
Alignment explanation
Indices: 473407--473481 Score: 84
Period size: 12 Copynumber: 6.4 Consensus size: 12
473397 TAACACTAAT
*
473407 ATATATTTTATA
1 ATATATATTATA
473419 ATATATATTATA
1 ATATATATTATA
*
473431 ATATATAATATA
1 ATATATATTATA
473443 ATATACTA-TAT-
1 ATATA-TATTATA
*
473454 ATAGATA-TATA
1 ATATATATTATA
*
473465 ATATATAATATA
1 ATATATATTATA
473477 ATATA
1 ATATA
473482 CAAATATATT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
10 5 0.09
11 10 0.18
12 39 0.70
13 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (12 bp):
ATATATATTATA
Found at i:473425 original size:7 final size:7
Alignment explanation
Indices: 473403--473476 Score: 77
Period size: 7 Copynumber: 11.0 Consensus size: 7
473393 AATATAACAC
473403 TAATATA
1 TAATATA
* *
473410 TATTTTA
1 TAATATA
473417 TAATATA
1 TAATATA
473424 T-AT-TA
1 TAATATA
473429 TAATATA
1 TAATATA
473436 T-A-ATA
1 TAATATA
473441 TAATATA
1 TAATATA
473448 CT-ATATA
1 -TAATATA
473455 TAGATATA
1 TA-ATATA
473463 TAATATA
1 TAATATA
473470 TAATATA
1 TAATATA
473477 ATATACAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
5 7 0.12
6 7 0.12
7 34 0.61
8 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (7 bp):
TAATATA
Found at i:475143 original size:18 final size:18
Alignment explanation
Indices: 475120--475155 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
475110 ATTTCAATAA
475120 ATAATAAAAGATTTTTAT
1 ATAATAAAAGATTTTTAT
* *
475138 ATAATAAATGGTTTTTAT
1 ATAATAAAAGATTTTTAT
475156 TCATAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
ATAATAAAAGATTTTTAT
Found at i:478295 original size:62 final size:62
Alignment explanation
Indices: 478217--478340 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
478207 ATATTTTTCA
478217 TTGAAGAGTACAATTAATAATGATCATATGCTTATCACGTTGATTGATAACATAACATGTTG
1 TTGAAGAGTACAATTAATAATGATCATATGCTTATCACGTTGATTGATAACATAACATGTTG
478279 TTGAAGAGTACAATTAATAATGATCATATGCTTATCACGTTGATTGATAACATAACATGTTG
1 TTGAAGAGTACAATTAATAATGATCATATGCTTATCACGTTGATTGATAACATAACATGTTG
478341 AATTATGGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (62 bp):
TTGAAGAGTACAATTAATAATGATCATATGCTTATCACGTTGATTGATAACATAACATGTTG
Found at i:484875 original size:21 final size:20
Alignment explanation
Indices: 484849--484912 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
484839 CATATTATAT
*
484849 ATCGTGAATCGCCACATCATC
1 ATCGTGAATC-CCACATCAAC
*
484870 ATCGTGAATCACCACTTCAAC
1 ATCGTGAATC-CCACATCAAC
*
484891 ATCGTGAATCACACATCAAC
1 ATCGTGAATCCCACATCAAC
484911 AT
1 AT
484913 TGTAATGATC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
20 10 0.26
21 28 0.74
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.23
Consensus pattern (20 bp):
ATCGTGAATCCCACATCAAC
Found at i:494027 original size:23 final size:23
Alignment explanation
Indices: 494001--494045 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
493991 GCCATTCGAG
494001 CGAGCTATGCGAGAGCATCCGAC
1 CGAGCTATGCGAGAGCATCCGAC
*
494024 CGAGCTATGCGAGGGCATCCGA
1 CGAGCTATGCGAGAGCATCCGA
494046 GGGCAAGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.33, T:0.13
Consensus pattern (23 bp):
CGAGCTATGCGAGAGCATCCGAC
Found at i:495208 original size:38 final size:35
Alignment explanation
Indices: 495166--495249 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 35
495156 ACCCTTTCAT
*
495166 TAAATCTTTTTATATTTTCAATTTTATAAAAAAATATA
1 TAAAT-TTTTTA-A-TTTAAATTTTATAAAAAAATATA
* *
495204 TAAATTTTATTAATTTAAATTTTTTTAAAAAATATA
1 TAAATTTT-TTAATTTAAATTTTATAAAAAAATATA
*
495240 TAAATATTTT
1 TAAATTTTTT
495250 CTAACTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 2 0.05
36 27 0.66
37 4 0.10
38 8 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (35 bp):
TAAATTTTTTAATTTAAATTTTATAAAAAAATATA
Found at i:504150 original size:21 final size:21
Alignment explanation
Indices: 504124--504168 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
504114 GATTTCTGGG
* *
504124 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
504145 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
504166 CAA
1 CAA
504169 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:505474 original size:18 final size:17
Alignment explanation
Indices: 505447--505483 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
505437 CTTAAGGAAT
505447 GATATGTGGTCATTCGG
1 GATATGTGGTCATTCGG
*
505464 GATATTGTGGTCCTTCGG
1 GATA-TGTGGTCATTCGG
505482 GA
1 GA
505484 CATATATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.16, C:0.14, G:0.35, T:0.35
Consensus pattern (17 bp):
GATATGTGGTCATTCGG
Found at i:505562 original size:121 final size:121
Alignment explanation
Indices: 505348--505578 Score: 426
Period size: 121 Copynumber: 1.9 Consensus size: 121
505338 CGAGGGTCTA
505348 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* *
505413 GATCCTTGGCATATGTATATGATTCTTAAGGAATGATATGTGGTCATTCGGGATAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCATTCGGGATAT
*
505469 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
505534 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTC
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
505579 CTTATGGACA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 106 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCATTCGGGATAT
Found at i:505680 original size:23 final size:23
Alignment explanation
Indices: 505592--505672 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
505582 ATGGACATTA
*
505592 TTATATGGCACTACGGTGCAATT
1 TTATGTGGCACTACGGTGCAATT
* * *
505615 CTACGCGGCACTACGGTGCAATT
1 TTATGTGGCACTACGGTGCAATT
**
505638 TTATGTGGCACTTTGGTGCAATT
1 TTATGTGGCACTACGGTGCAATT
505661 TTATGTGGCACT
1 TTATGTGGCACT
505673 TTGGTGCATT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (23 bp):
TTATGTGGCACTACGGTGCAATT
Found at i:505688 original size:23 final size:23
Alignment explanation
Indices: 505592--505688 Score: 106
Period size: 23 Copynumber: 4.2 Consensus size: 23
505582 ATGGACATTA
* **
505592 TTATATGGCACTACGGTGCAATT
1 TTATGTGGCACTTTGGTGCAATT
* * * **
505615 CTACGCGGCACTACGGTGCAATT
1 TTATGTGGCACTTTGGTGCAATT
505638 TTATGTGGCACTTTGGTGCAATT
1 TTATGTGGCACTTTGGTGCAATT
505661 TTATGTGGCACTTTGGTGC-ATT
1 TTATGTGGCACTTTGGTGCAATT
505683 TATATG
1 T-TATG
505689 AGCTGTGGTG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 4 0.06
23 60 0.94
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (23 bp):
TTATGTGGCACTTTGGTGCAATT
Found at i:515241 original size:21 final size:21
Alignment explanation
Indices: 515182--515242 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
515172 AACTTTGAAA
* *
515182 AAATGATTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGAT
515203 AAAT-G-TTTC----TTTGA-
1 AAATGGTTTTCAAAGTTTGAT
515217 AAATGGTTTTCAAAGTTTGAT
1 AAATGGTTTTCAAAGTTTGAT
515238 AAATG
1 AAATG
515243 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 4 0.13
15 5 0.16
16 4 0.13
19 4 0.13
20 5 0.16
21 9 0.29
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGAT
Found at i:515288 original size:36 final size:36
Alignment explanation
Indices: 515174--515295 Score: 167
Period size: 35 Copynumber: 3.4 Consensus size: 36
515164 TGGTAACCAA
515174 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
515211 CTTTG-AAAATGGTTTTCAAAGTTTGATAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
515246 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
515283 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
515296 AATGGGATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 35 0.46
36 14 0.18
37 27 0.36
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:515724 original size:16 final size:16
Alignment explanation
Indices: 515703--515735 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
515693 TACTATTCAT
*
515703 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
515719 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
515735 G
1 G
515736 GTCGACGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:519832 original size:21 final size:20
Alignment explanation
Indices: 519808--519871 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
519798 AACTTTGAAA
519808 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
519829 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
519843 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
519864 AAATGTTT
1 AAATGTTT
519872 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:519846 original size:35 final size:36
Alignment explanation
Indices: 519800--519921 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
519790 TGGTAACCAA
519800 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
519837 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
519872 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
519909 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
519922 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:521416 original size:40 final size:40
Alignment explanation
Indices: 521341--521418 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
521331 AAATTAATCC
* *
521341 TCAAACTTTTGAACATTTCAATTTCACCCATAAACTATGA
1 TCAAACTTTTGAACATTCCAATTTCACCCACAAACTATGA
* *
521381 TCAAACTTTTTGAATATTCCAATTTCA-TCACAAACTAT
1 TCAAAC-TTTTGAACATTCCAATTTCACCCACAAACTAT
521419 ATGTATATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 15 0.45
41 18 0.55
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (40 bp):
TCAAACTTTTGAACATTCCAATTTCACCCACAAACTATGA
Found at i:523086 original size:17 final size:19
Alignment explanation
Indices: 523049--523092 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
523039 TTATGTGATG
523049 AAAAAATAATATTATTGTA
1 AAAAAATAATATTATTGTA
*
523068 AAAAAATTA-ATTATT-TA
1 AAAAAATAATATTATTGTA
*
523085 AAACAATA
1 AAAAAATA
523093 TTTAACTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 6 0.27
19 8 0.36
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAAATAATATTATTGTA
Found at i:523186 original size:5 final size:5
Alignment explanation
Indices: 523176--523204 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
523166 TGTTTTTCTC
523176 ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
523205 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:527069 original size:2 final size:2
Alignment explanation
Indices: 527062--527093 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
527052 AAATAGCTCA
527062 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
527094 GCATGGTTGG
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:529499 original size:3 final size:3
Alignment explanation
Indices: 529491--529516 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
529481 GTCTTTTGGG
529491 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
529517 TAAACCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:535125 original size:23 final size:24
Alignment explanation
Indices: 535099--535144 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
535089 TAAATTATTT
535099 TAATATTTTGAAAAT-AATAATAC
1 TAATATTTTGAAAATAAATAATAC
* * *
535122 TAATTTTTTTATAATAAATAATA
1 TAATATTTTGAAAATAAATAATA
535145 TTATTTATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TAATATTTTGAAAATAAATAATAC
Found at i:541135 original size:3 final size:3
Alignment explanation
Indices: 541129--541166 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
541119 TAATATTTAT
541129 TAA TAA TAA -AA TAA TAA TAA TAA TAA T-A TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
541167 AAAAATGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 26 0.81
4 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:542696 original size:16 final size:17
Alignment explanation
Indices: 542675--542709 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
542665 TTTAATTTAT
*
542675 TAATAAAAATTAA-ATA
1 TAATAAAAAATAATATA
542691 TAATAAAAAATAATATA
1 TAATAAAAAATAATATA
542708 TA
1 TA
542710 TATTTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATAAAAAATAATATA
Found at i:542744 original size:18 final size:17
Alignment explanation
Indices: 542700--542748 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
542690 ATAATAAAAA
* *
542700 ATAATATATATATTTTT
1 ATAATATTTAAATTTTT
*
542717 CTAA-ATTTAAATTATTT
1 ATAATATTTAAATT-TTT
542734 ATAATATTTAAATTT
1 ATAATATTTAAATTT
542749 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 9 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAATATTTAAATTTTT
Found at i:547687 original size:22 final size:20
Alignment explanation
Indices: 547638--547679 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
547628 ATCACCAACC
* *
547638 TTTGTTTTGTGGATCTAAGA
1 TTTGTTTTGTAGATATAAGA
547658 TTTGTTTTGTAGATATAAGA
1 TTTGTTTTGTAGATATAAGA
547678 TT
1 TT
547680 CTTGTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.21, T:0.52
Consensus pattern (20 bp):
TTTGTTTTGTAGATATAAGA
Found at i:550740 original size:17 final size:17
Alignment explanation
Indices: 550718--550797 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
550708 AAAATTTAAA
550718 AATTTAAAAATATATTT
1 AATTTAAAAATATATTT
* *
550735 AATTT-ATAATCCTA-TT
1 AATTTAAAAAT-ATATTT
* *
550751 ATTTTCAAAATTATATTT
1 AATTT-AAAAATATATTT
*
550769 -ATTTAAAATATTTATTT
1 AATTTAAAA-ATATATTT
550786 -ATTTAAAAATAT
1 AATTTAAAAATAT
550798 CAGAAAAGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
16 17 0.35
17 26 0.54
18 5 0.10
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTAAAAATATATTT
Found at i:550795 original size:34 final size:33
Alignment explanation
Indices: 550719--550795 Score: 77
Period size: 34 Copynumber: 2.3 Consensus size: 33
550709 AAATTTAAAA
*
550719 ATTTAAAAA-TATATTTAATTTATAATCCTATT
1 ATTTAAAAATTATATTTAATTTAAAATCCTATT
* **
550751 ATTTTCAAAATTATATTT-ATTTAAAATATTTATTT
1 A-TTTAAAAATTATATTTAATTTAAAAT-CCTA-TT
550786 ATTTAAAAAT
1 ATTTAAAAAT
550796 ATCAGAAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
32 1 0.03
33 15 0.42
34 17 0.47
35 3 0.08
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (33 bp):
ATTTAAAAATTATATTTAATTTAAAATCCTATT
Found at i:550992 original size:18 final size:19
Alignment explanation
Indices: 550971--551008 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
550961 TATTATAAGT
*
550971 ATATTTAT-GAATATAAAA
1 ATATTTATACAATATAAAA
550989 ATATTTATACAATATAAAA
1 ATATTTATACAATATAAAA
551008 A
1 A
551009 ATAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (19 bp):
ATATTTATACAATATAAAA
Found at i:551919 original size:19 final size:18
Alignment explanation
Indices: 551869--551919 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
551859 CTAGTTTGTT
551869 TTTTTTTCTTTCTCTGTC
1 TTTTTTTCTTTCTCTGTC
* *
551887 TTTTTCTCCGTTCTCTGTC
1 TTTTT-TTCTTTCTCTGTC
551906 TCTTTTTTCTTTCT
1 T-TTTTTTCTTTCT
551920 TTCGCAGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 5 0.19
19 18 0.67
20 4 0.15
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTTTTCTTTCTCTGTC
Found at i:552329 original size:3 final size:3
Alignment explanation
Indices: 552321--552421 Score: 166
Period size: 3 Copynumber: 33.7 Consensus size: 3
552311 TTAATATATT
*
552321 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
552369 TAA TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
552417 AAA TA
1 TAA TA
552422 TTAGTATCTT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:554618 original size:31 final size:31
Alignment explanation
Indices: 554580--554657 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
554570 GGATAGGATT
554580 TGAGGTTAAGGATGTGATAAATGAGTATTAA
1 TGAGGTTAAGGATGTGATAAATGAGTATTAA
554611 TGAGGTTAAGGATGTGATAAATGAGTATTAA
1 TGAGGTTAAGGATGTGATAAATGAGTATTAA
*
554642 TG-GGTTTAAGCATGTG
1 TGAGG-TTAAGGATGTG
554658 TATGTGAGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 2 0.04
31 43 0.96
ACGTcount: A:0.35, C:0.01, G:0.31, T:0.33
Consensus pattern (31 bp):
TGAGGTTAAGGATGTGATAAATGAGTATTAA
Found at i:555605 original size:32 final size:33
Alignment explanation
Indices: 555564--555654 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 33
555554 AAGAGTCGAG
555564 GATTACCTATGTCTTTCGGGACATATGAAC-AT
1 GATTACCTATGTCTTTCGGGACATATGAACAAT
* * * *
555596 GATTACCTATATCCTTCAGGACATATGGACAAT
1 GATTACCTATGTCTTTCGGGACATATGAACAAT
* *
555629 G-TTATCTATGT-TCTTCGGAACATATG
1 GATTACCTATGTCT-TTCGGGACATATG
555655 GATAGGTCTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
32 45 0.94
33 3 0.06
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (33 bp):
GATTACCTATGTCTTTCGGGACATATGAACAAT
Found at i:563757 original size:18 final size:18
Alignment explanation
Indices: 563734--563774 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
563724 ATAAATGTTG
563734 TTTTAATTATTATTAATA
1 TTTTAATTATTATTAATA
*
563752 TTTTAATTATTATTAATT
1 TTTTAATTATTATTAATA
563770 TTTTA
1 TTTTA
563775 CTGCTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAATTATTATTAATA
Found at i:567651 original size:15 final size:15
Alignment explanation
Indices: 567631--567662 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
567621 TATAAAATTT
*
567631 TAAAAATAAAATAAA
1 TAAAAATAAAACAAA
567646 TAAAAATAAAACAAA
1 TAAAAATAAAACAAA
567661 TA
1 TA
567663 TAGATTTTAG
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:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:569396 original size:12 final size:12
Alignment explanation
Indices: 569379--569403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
569369 TTTAGATAAA
569379 AAATAATTTTTT
1 AAATAATTTTTT
569391 AAATAATTTTTT
1 AAATAATTTTTT
569403 A
1 A
569404 TCAAAAATAA
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:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATAATTTTTT
Found at i:570214 original size:30 final size:30
Alignment explanation
Indices: 570178--570235 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
570168 TTTTATTAAA
570178 TTTTAAAATATTGTAAATTTAATCATTTAG
1 TTTTAAAATATTGTAAATTTAATCATTTAG
* * * *
570208 TTTTAAATTATTTTTATTTTAATCATTT
1 TTTTAAAATATTGTAAATTTAATCATTT
570236 TGATCGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (30 bp):
TTTTAAAATATTGTAAATTTAATCATTTAG
Found at i:578810 original size:93 final size:92
Alignment explanation
Indices: 578646--578818 Score: 328
Period size: 93 Copynumber: 1.9 Consensus size: 92
578636 AAGCAAATAG
578646 TCTATCAAAAGAGGAAAAACCTGAGGTGGTGAAGTAAATGATCAGATTCCAGTGGATAATAGCTC
1 TCTATCAAAAGAGGAAAAACCTGAGGTGGTGAAGTAAATGATCAGATTCCAGTGGATAATAGCTC
*
578711 AGAAGATGATAAACTGGAAGTGAATGA
66 AGAAGATGACAAACTGGAAGTGAATGA
578738 TCTATCAAAAGAGGAAAAACCTGAGGTGGTGGAAGTAAATGATCAGATTCCAGTGGATAATAGCT
1 TCTATCAAAAGAGGAAAAACCTGAGGTGGT-GAAGTAAATGATCAGATTCCAGTGGATAATAGCT
578803 CAGAAGATGACAAACT
65 CAGAAGATGACAAACT
578819 TAGCTCATTA
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 30 0.38
93 49 0.62
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.21
Consensus pattern (92 bp):
TCTATCAAAAGAGGAAAAACCTGAGGTGGTGAAGTAAATGATCAGATTCCAGTGGATAATAGCTC
AGAAGATGACAAACTGGAAGTGAATGA
Found at i:580311 original size:37 final size:37
Alignment explanation
Indices: 580268--580370 Score: 163
Period size: 37 Copynumber: 2.8 Consensus size: 37
580258 CCGAATTCTG
*
580268 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTT
580305 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTT
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTT
***
580342 T-CCCGTTTCACGTAATTCGTTTTCCGGAA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAA
580371 TGTAATTCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 25 0.40
37 37 0.60
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (37 bp):
TGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTT
Found at i:580635 original size:52 final size:51
Alignment explanation
Indices: 580543--580661 Score: 136
Period size: 52 Copynumber: 2.3 Consensus size: 51
580533 ATTTTCATCA
* * **
580543 AAATATTA-ATTATTAAAATATTTAAAATATTTATTAATATT-TATAATAAT
1 AAATATTATATTTTTAAAATATATAAAATATCAATTAATATTATATAAT-AT
*
580593 ATAATATTATATTTTTAATATATATAAAATAATCAATT-ATATTATATAATAT
1 A-AATATTATATTTTTAAAATATATAAAAT-ATCAATTAATATTATATAATAT
580645 AAGATATTATATTTTTA
1 AA-ATATTATATTTTTA
580662 TTTTAATAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
50 1 0.02
51 8 0.14
52 39 0.66
53 11 0.19
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (51 bp):
AAATATTATATTTTTAAAATATATAAAATATCAATTAATATTATATAATAT
Found at i:580643 original size:31 final size:31
Alignment explanation
Indices: 580573--580681 Score: 88
Period size: 31 Copynumber: 3.6 Consensus size: 31
580563 TTTAAAATAT
*
580573 TTATTAATATTTATAATAATATAATATTATA
1 TTATTAATATATATAATAATATAATATTATA
* *
580604 TTTTTAATATATATAA-AATAATCA-ATTATA
1 TTATTAATATATATAATAAT-ATAATATTATA
* * *
580634 TTA-T-ATA-ATATAA-GATATTATATTTTTA
1 TTATTAATATATATAATAATATAATA-TTATA
580662 TT-TTAATAATATATAATAAT
1 TTATTAAT-ATATATAATAAT
580682 TTTTTTTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
26 3 0.05
27 9 0.15
28 10 0.16
29 3 0.05
30 12 0.19
31 23 0.37
32 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
TTATTAATATATATAATAATATAATATTATA
Found at i:580675 original size:24 final size:23
Alignment explanation
Indices: 580643--580689 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
580633 ATTATATAAT
* *
580643 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
580667 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
580690 TATATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:580688 original size:28 final size:28
Alignment explanation
Indices: 580629--580731 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 28
580619 AAATAATCAA
*
580629 TTATATTATATAATATA-AGATATTATATTT
1 TTATTTTA-ATAATATATA-ATATT-TATTT
*
580659 TTATTTTAATAATATATAATAATTTTTTT
1 TTATTTTAATAATATATAAT-ATTTATTT
580688 TATATATTTAATAATGA-ATAATA-TTATTT
1 T-TAT-TTTAATAAT-ATATAATATTTATTT
* *
580717 ATATTTCAATAATAT
1 TTATTTTAATAATAT
580732 TTTAGTAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
26 1 0.02
27 8 0.13
28 3 0.05
29 20 0.32
30 15 0.24
31 14 0.23
32 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (28 bp):
TTATTTTAATAATATATAATATTTATTT
Found at i:580972 original size:20 final size:20
Alignment explanation
Indices: 580895--580963 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
580885 TTTCCAGATG
580895 TTTT-CAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
580914 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
580934 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
580954 TTTTCCAGAA
1 TTTTCCAGAA
580964 TTCAAATTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 4 0.09
20 43 0.91
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:580972 original size:40 final size:39
Alignment explanation
Indices: 580895--580972 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
580885 TTTCCAGATG
**
580895 TTTTCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTCAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
580934 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTT-CAGAAATGTAATTCATTTTCCAGAAATCAAATTC
580973 TAGTAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (39 bp):
TTTTCAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:580982 original size:15 final size:15
Alignment explanation
Indices: 580946--581027 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
580936 TTACAGAAAT
**
580946 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
580961 G-AATTCAAATTCTA
1 GTAATTCAAATTCCA
** *
580975 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
580990 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
581005 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
581020 GTAATTCA
1 GTAATTCA
581028 TTTTCTGAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
14 11 0.20
15 45 0.80
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:580996 original size:30 final size:30
Alignment explanation
Indices: 580946--581027 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
580936 TTACAGAAAT
*
580946 GTAATTCATTTTCCAG-AATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
580975 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
581005 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
581028 TTTTCTGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 15 0.32
30 32 0.68
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:581023 original size:45 final size:44
Alignment explanation
Indices: 580946--581031 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 44
580936 TTACAGAAAT
** *
580946 GTAATTCATTTTCCAGAATTCAAATTCTAGTAATTCATTTTTCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTTCA
580990 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTT
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTT
581032 CTGAAAAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 14 0.37
45 24 0.63
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTTCA
Found at i:589609 original size:16 final size:16
Alignment explanation
Indices: 589588--589621 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
589578 TTACTATTCA
*
589588 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
589604 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
589620 CG
1 CG
589622 GTCGGCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:598435 original size:22 final size:22
Alignment explanation
Indices: 598391--598436 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
598381 TTTTTAAATT
*
598391 AAAATTCATATTTTTATATAAA
1 AAAATTCATATTTTTATAAAAA
* *
598413 AAAATTCCTATTTTT-CAAAAA
1 AAAATTCATATTTTTATAAAAA
598434 AAA
1 AAA
598437 CCCAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTCATATTTTTATAAAAA
Found at i:600527 original size:13 final size:14
Alignment explanation
Indices: 600501--600529 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
600491 CCGCATTTTC
600501 TAAAATATTTTATT
1 TAAAATATTTTATT
600515 TAAAATA-TTTATT
1 TAAAATATTTTATT
600528 TA
1 TA
600530 TTTTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAAATATTTTATT
Found at i:601923 original size:21 final size:21
Alignment explanation
Indices: 601878--601924 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
601868 TATTTTAATA
* *
601878 TATAAAAATATCAAATTAAAT
1 TATAAAAATATCAAATAAAAC
601899 TATAAAAATAT-AAATAACAAC
1 TATAAAAATATCAAATAA-AAC
601920 TATAA
1 TATAA
601925 TTATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (21 bp):
TATAAAAATATCAAATAAAAC
Found at i:602329 original size:5 final size:5
Alignment explanation
Indices: 602319--602349 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
602309 CAACTTTAAT
602319 AATAA AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA AATAA A
602350 TGATTTCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:618867 original size:20 final size:20
Alignment explanation
Indices: 618844--618892 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
618834 TTTAAAATTT
*
618844 AAAAATGAATTAAATTACTA
1 AAAAATAAATTAAATTACTA
618864 AAAAATAAATTAAATTACTA
1 AAAAATAAATTAAATTACTA
618884 AAAAATAAA
1 AAAAATAAA
618893 AAATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAATAAATTAAATTACTA
Found at i:627005 original size:27 final size:26
Alignment explanation
Indices: 626930--627013 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
626920 GGTTGAAAAA
* *
626930 TAGAAAACTGAGGACTTTGAGGGACTG
1 TAGAAAACTGATGAC-TTGAGGGGCTG
* * **
626957 CAGAAAACTGGTGAACCAGAGGGGCTG
1 TAGAAAACTGATG-ACTTGAGGGGCTG
*
626984 TAGAAAACTGATGAGCTTGAGGAGCTG
1 TAGAAAACTGATGA-CTTGAGGGGCTG
627011 TAG
1 TAG
627014 GTGGGTGAGC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
26 1 0.02
27 41 0.93
28 2 0.05
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (26 bp):
TAGAAAACTGATGACTTGAGGGGCTG
Found at i:628180 original size:24 final size:24
Alignment explanation
Indices: 628131--628201 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
628121 AAGCAGAACA
*
628131 AGAACAACAAAGAAGCAGTATA-CC
1 AGAACAATAAAGAAGCAGTA-AGCC
*
628155 AGAACAATGAAGAAGCAGTAAGCC
1 AGAACAATAAAGAAGCAGTAAGCC
* * *
628179 AGACCAATTAAGAAGCAATAAGC
1 AGAACAATAAAGAAGCAGTAAGC
628202 ACAAATCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.52, C:0.18, G:0.20, T:0.10
Consensus pattern (24 bp):
AGAACAATAAAGAAGCAGTAAGCC
Found at i:631790 original size:27 final size:27
Alignment explanation
Indices: 631758--631810 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
631748 CCATCACCAC
631758 TTTGAACTTAAAACTCCATAACATCAT
1 TTTGAACTTAAAACTCCATAACATCAT
* * *
631785 TTTGAACTTGAAAGTCTATAACATCA
1 TTTGAACTTAAAACTCCATAACATCA
631811 AGATCTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (27 bp):
TTTGAACTTAAAACTCCATAACATCAT
Found at i:632553 original size:6 final size:6
Alignment explanation
Indices: 632537--632569 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
632527 CTCTTCTCTT
*
632537 TTCTCC CTCTCC TTCTCC TTCTCC TTCTCC TTC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTC
632570 CCACGCCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TTCTCC
Found at i:638002 original size:2 final size:2
Alignment explanation
Indices: 637995--638022 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
637985 TTATGCTTGA
637995 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
638023 TCATCTTCTG
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:638160 original size:132 final size:134
Alignment explanation
Indices: 638013--638254 Score: 425
Period size: 132 Copynumber: 1.8 Consensus size: 134
638003 ATATATATAT
*
638013 ATATATATATTCATCTTCTGAAGGAGCTAGTTGTGTTGGAATCTTCAAGTTTTAACTCTGAATG-
1 ATATATATATTCATCTTCTGAAGGAGCTAGTTGTGTTGGAATCTTCAAGTTTCAACTCTGAATGA
* *
638077 A-TAATTTTGAATGCTCAAATGGAGATTATGTGAATCATTGATGTCGTTTTGCTATGTTTTATGC
66 ATTAATTTTGAATGCACAAATGGAGATTATATGAATCATTGATGTCGTTTTGCTATGTTTTATGC
638141 TTGA
131 TTGA
638145 ATATATATATTCATCTTCTGAAGGAGCTAGTTGTGTTGGAATCTTCAAGTTTCAACTCTGAATGA
1 ATATATATATTCATCTTCTGAAGGAGCTAGTTGTGTTGGAATCTTCAAGTTTCAACTCTGAATG-
638210 TAATTAATTTTGAATGCACAAATGGAGATTATATGAATCATTGAT
65 -AATTAATTTTGAATGCACAAATGGAGATTATATGAATCATTGAT
638255 TTCGCTGAAA
Statistics
Matches: 103, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
132 63 0.61
135 1 0.01
136 39 0.38
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (134 bp):
ATATATATATTCATCTTCTGAAGGAGCTAGTTGTGTTGGAATCTTCAAGTTTCAACTCTGAATGA
ATTAATTTTGAATGCACAAATGGAGATTATATGAATCATTGATGTCGTTTTGCTATGTTTTATGC
TTGA
Found at i:640190 original size:20 final size:21
Alignment explanation
Indices: 640148--640190 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
640138 GTTAATAATA
* **
640148 TTAACATTTATATATTATTTT
1 TTAAAATTTATATATTAGATT
640169 TTAAAATTTA-ATATTAGATT
1 TTAAAATTTATATATTAGATT
640189 TT
1 TT
640191 TCATGTACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTAAAATTTATATATTAGATT
Found at i:640190 original size:21 final size:21
Alignment explanation
Indices: 640148--640191 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
640138 GTTAATAATA
* *
640148 TTAACATTTATATATTATTTT
1 TTAAAATTTATATATTAATTT
640169 TTAAAATTTA-ATATTAGATTT
1 TTAAAATTTATATATTA-ATTT
640190 TT
1 TT
640192 CATGTACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAAAATTTATATATTAATTT
Found at i:661899 original size:18 final size:18
Alignment explanation
Indices: 661876--661910 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
661866 GTGTAATTTA
*
661876 AAATATTATTTTTATTAG
1 AAATATTAATTTTATTAG
661894 AAATATTAATTTTATTA
1 AAATATTAATTTTATTA
661911 TTTAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AAATATTAATTTTATTAG
Found at i:662075 original size:24 final size:22
Alignment explanation
Indices: 662022--662087 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 22
662012 TTAATATTTC
* *
662022 TATTATAACTTTTTTTTGAATTA
1 TATTAAAACTTTTATTT-AATTA
*
662045 TAATAAAACTTTTATTTAATCGTA
1 TATTAAAACTTTTATTTAAT--TA
*
662069 TATTAAAACTATTAATTTA
1 TATTAAAACT-TTTATTTA
662088 TACATATGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.09
23 14 0.40
24 11 0.31
25 7 0.20
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (22 bp):
TATTAAAACTTTTATTTAATTA
Found at i:662367 original size:14 final size:13
Alignment explanation
Indices: 662319--662387 Score: 52
Period size: 14 Copynumber: 5.1 Consensus size: 13
662309 ATTAGTTGAT
*
662319 TATTTTATTTATTA
1 TATTTAATTT-TTA
*
662333 TA-TAAATATTTTA
1 TATTTAAT-TTTTA
662346 TATTTAATTTTTA
1 TATTTAATTTTTA
662359 TATTTTAATTTAATT-
1 TA-TTTAATTT--TTA
*
662374 TAGTTAATTTTTA
1 TATTTAATTTTTA
662387 T
1 T
662388 GTTGTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
12 2 0.04
13 16 0.36
14 23 0.51
15 2 0.04
16 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (13 bp):
TATTTAATTTTTA
Found at i:662398 original size:27 final size:28
Alignment explanation
Indices: 662349--662410 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
662339 TATTTTATAT
*
662349 TTAATTTTTATATTTTAATTTAATTTAG
1 TTAATTTTTATATTTTAATTTAATTAAG
* *
662377 TTAATTTTTATGTTGTT-A-TTAATTAAT
1 TTAATTTTTATATT-TTAATTTAATTAAG
662404 TTAATTT
1 TTAATTT
662411 AAAGAGATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 14 0.47
28 14 0.47
29 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (28 bp):
TTAATTTTTATATTTTAATTTAATTAAG
Found at i:663047 original size:19 final size:20
Alignment explanation
Indices: 663009--663047 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
662999 ATTAGTTTTA
*
663009 TTTCATTTTAGTATCTAAAT
1 TTTCATTTTAGTATCAAAAT
*
663029 TTTCATTTT-GTTTCAAAAT
1 TTTCATTTTAGTATCAAAAT
663048 CATACATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTCATTTTAGTATCAAAAT
Found at i:663289 original size:2 final size:2
Alignment explanation
Indices: 663282--663369 Score: 71
Period size: 2 Copynumber: 47.0 Consensus size: 2
663272 TCGGGCTGAG
* * * *
663282 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
663322 TA TA TA TA TA TA TA T- TA AA T- TA AA TT TA T- TA -A 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
663360 TA TA TA TA TA
1 TA TA TA TA TA
663370 ATTATTTTTA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
1 6 0.09
2 60 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:663311 original size:17 final size:18
Alignment explanation
Indices: 663287--663346 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 18
663277 CTGAGTATAT
663287 ATATATATATTTAAATTAA
1 ATATATATA-TTAAATTAA
* *
663306 ATATATAAATATTATATATAT
1 ATATAT--ATATTAAAT-TAA
663327 ATATATATATTAAATTAA
1 ATATATATATTAAATTAA
663345 AT
1 AT
663347 TTATTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 4 0.12
19 14 0.41
20 5 0.15
21 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATATATATTAAATTAA
Done.