Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_89.0, 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: 4184555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 83639 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:4011720 original size:18 final size:18
Alignment explanation
Indices: 4011681--4011714 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4011671 ACATTGAAAA
*
4011681 ATATAATCAGTTAATTAC
1 ATATAATCAGTAAATTAC
4011699 ATATAATCA-TAAATTA
1 ATATAATCAGTAAATTA
4011715 TTATATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (18 bp):
ATATAATCAGTAAATTAC
Found at i:4017453 original size:11 final size:11
Alignment explanation
Indices: 4017437--4017468 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4017427 ACTTACGATG
4017437 ATGAATCATTT
1 ATGAATCATTT
4017448 ATGAATCATTT
1 ATGAATCATTT
*
4017459 ATTAATCATT
1 ATGAATCATT
4017469 CATTTACCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
ATGAATCATTT
Found at i:4026248 original size:13 final size:13
Alignment explanation
Indices: 4026230--4026265 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
4026220 CTTATTGAGG
4026230 GAAGAAAAAAAGA
1 GAAGAAAAAAAGA
*
4026243 GAAGAAAGAAAGA
1 GAAGAAAAAAAGA
*
4026256 AAAGAAAAAA
1 GAAGAAAAAA
4026266 GTGGCTAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAGA
Found at i:4026841 original size:15 final size:17
Alignment explanation
Indices: 4026823--4026855 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4026813 AGTATAATTA
4026823 ATAA-TTTTATAA-GTT
1 ATAATTTTTATAATGTT
4026838 ATAATTTTTATAATGTT
1 ATAATTTTTATAATGTT
4026855 A
1 A
4026856 ACACAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATAATTTTTATAATGTT
Found at i:4027228 original size:16 final size:15
Alignment explanation
Indices: 4027194--4027231 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4027184 GGTATATACA
4027194 TTATAATTAATAATT
1 TTATAATTAATAATT
4027209 TTATAAGTT-ATAATTT
1 TTATAA-TTAATAA-TT
4027225 TTATAAT
1 TTATAAT
4027232 ATTAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAATTAATAATT
Found at i:4027423 original size:366 final size:361
Alignment explanation
Indices: 4026446--4028193 Score: 2168
Period size: 366 Copynumber: 4.8 Consensus size: 361
4026436 AAAGTGTGCA
* * *
4026446 TATATATATTATAATTAAAAATTTTATAAGTTATAATTTTTATATTGTTAACACAAAATAAAAAG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAGAAAG
* * * *
4026511 TAAATATATTTGTATTTAAAGTATATATATATATATATA-TGAAAAGTATTTTAGTGTATATATA
66 TAAATATATTTATATTTAAAGTATATATATATACACACACT-AAAAGTATTTTAGT-TATATATA
* * * * *
4026575 TAATAATAATTATATTCCTTATAAATGAATGCC-ATATATATAAAGTAAATAAATTAAAAGACAT
129 TAATAGTAAGTATATTCTTTATAAATGAA-CCCAATATATATAAAGTAAATATATTAAAAGACAT
* * * *
4026639 TACAAGGTAATTAATAATGATAGTTTCATAAATTAA-TTATTTAATTATATGGGTTTGTACTTAA
193 TACAAGGTAATTAATAATCATAGTTTCATAAATTAATTTAATTAATTATATGGATTTGTCCTTAA
* * *
4026703 TTACATAAAATTAAAAAAAAAAGCCAAGTTTCAAAACTATTCTAATCTCATAACTTCTTCTTA-A
258 TTACATAAAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAATCTCATAACTTCTTTTTAGA
* * *
4026767 TAATTAAGTTTATATATTAAAAGTTTATACAAACAAATG
323 TAATTAAGTTTACATATTATAAGTTTATACAAACAAAGG
* *
4026806 CATATATAGTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAGAAAG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAGAAAG
* *
4026871 TAAATAT-GTTATATTTAAAGTGTGTGTGTGTGTGTGTGTATATATATATATATACACACATTAA
66 TAAATATATTTATATTTAAA------------------G----TATATATATATACACACACTAA
4026935 TAA-TATTTTAG-TATATATATAATAGTAAGTATATTCTTTATAAATG-ACCCAATATATATAAA
109 -AAGTATTTTAGTTATATATATAATAGTAAGTATATTCTTTATAAATGAACCCAATATATATAAA
* *
4026997 GTAAATATATTAAAAGACATTACAGGGTAATTAATAATCATAGTTTCATTAATTAATTTAATTAA
173 GTAAATATATTAAAAGACATTACAAGGTAATTAATAATCATAGTTTCATAAATTAATTTAATTAA
* *
4027062 TTATATAGATTTGTCCTTAATTACATAAAATTAAAAAAAATAGCTAATTTTCAAAACTATTCTAA
238 TTATATGGATTTGTCCTTAATTACATAAAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAA
4027127 TCTCATAACTTCTTTTTAGATAATTAAGTTTACATATTATAAGTTTATACAAACAAAGG
303 TCTCATAACTTCTTTTTAGATAATTAAGTTTACATATTATAAGTTTATACAAACAAAGG
* *
4027186 TATATACATTATAATTAATAATTTTATAAGTTATAATTTTTATAATATTAACACAAAATAGAAAG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAGAAAG
*
4027251 TAAATATATTTTTATTTAAATTGTATATATATATACGCACACACTAAAAGTATTTTAGTATATAT
66 TAAATATATTTATATTTAAA--GTATATATATATA--CACACACTAAAAGTATTTTAGT-TATAT
*
4027316 ATATAATAGTAAGTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGAT
126 ATATAATAGTAAGTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGAC
* * *
4027381 ATTACAAGATAATTAATAATCATAGTTTCATGAATTAATTTAATTAATTATATGGATTTGTCTTT
191 ATTACAAGGTAATTAATAATCATAGTTTCATAAATTAATTTAATTAATTATATGGATTTGTCCTT
4027446 AATTACATAAAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAATCTCATAACTTCTTTTTA
256 AATTACATAAAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAATCTCATAACTTCTTTTTA
*
4027511 GATAATTAAGTTTACATATTATAAGTTTATACAAACTAAGG
321 GATAATTAAGTTTACATATTATAAGTTTATACAAACAAAGG
* *
4027552 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTGTAATATTAACACAAAATAGAAAG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAGAAAG
* * * * *
4027617 TAAATATATTTTTATTTAAA-T-TATATATATGCAAAAATTAAAAGTATTTTAG-TATATATATA
66 TAAATATATTTATATTTAAAGTATATATATATACACACACTAAAAGTATTTTAGTTATATATATA
4027679 ATAGTAAGTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAG-CATTAC
131 ATAGTAAGTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGACATTAC
* * * * *
4027743 AAGGTAATTAATAATCACAGTTTCATGAATTAATTTAATTAATTATACGAATTTATCCTTAATTA
196 AAGGTAATTAATAATCATAGTTTCATAAATTAATTTAATTAATTATATGGATTTGTCCTTAATTA
* * * * * * * *
4027808 CATTAAATT--AAAAAATAACTAGGTTTCAAAACTATTCTAATTTCACAACTTCTCTTAAGGT--
261 CATAAAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAATCTCATAACTTCTTTTTAGATAA
*
4027869 TT--G--T--ATATTATAAGTTTATATAAACAAAGG
326 TTAAGTTTACATATTATAAGTTTATACAAACAAAGG
* * * *
4027899 TGTATATATTATAATTAATAATTTTACAAGTTATAATTTTTGTAATGTTAACATAAAATCA-AAA
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAAT-AGAAA
* *
4027963 GTAAATATATTTATATTTAAAG-A-ATATATAT------ACTAAAAGTA--TTAG-TATATACAC
65 GTAAATATATTTATATTTAAAGTATATATATATACACACACTAAAAGTATTTTAGTTATATATAT
* ** * * * *
4028017 AATA-TAGTAGTTATATT-TCTTATAAATGAACCCCATATATGGAATGTATATATATTAAAAAAT
130 AATAGTA--AG-TATATTCT-TTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGAC
* * * * ** *
4028080 ATTACAAGTTAATTAATAATCATAGATTCATAAAGTAATTTAATTTACCATATGGATTTGTCTTT
191 ATTACAAGGTAATTAATAATCATAGTTTCATAAATTAATTTAATTAATTATATGGATTTGTCCTT
* *
4028145 AATTACAAAAAATT-AAAAAAATAG-TTAGATTTCAAAACTATTCTAATCT
256 AATTACATAAAATTAAAAAAAATAGCTAAG-TTTCAAAACTATTCTAATCT
4028194 TAAAGACTCT
Statistics
Matches: 1243, Mismatches: 101, Indels: 105
0.86 0.07 0.07
Matches are distributed among these distances:
338 2 0.00
339 15 0.01
340 3 0.00
341 51 0.04
342 67 0.05
343 27 0.02
347 110 0.09
348 1 0.00
349 1 0.00
351 1 0.00
353 2 0.00
355 45 0.04
357 72 0.06
358 68 0.05
359 10 0.01
360 85 0.07
361 12 0.01
362 11 0.01
363 18 0.01
365 37 0.03
366 280 0.23
377 3 0.00
378 64 0.05
379 115 0.09
380 105 0.08
381 35 0.03
382 3 0.00
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (361 bp):
TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAGAAAG
TAAATATATTTATATTTAAAGTATATATATATACACACACTAAAAGTATTTTAGTTATATATATA
ATAGTAAGTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGACATTAC
AAGGTAATTAATAATCATAGTTTCATAAATTAATTTAATTAATTATATGGATTTGTCCTTAATTA
CATAAAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAATCTCATAACTTCTTTTTAGATAA
TTAAGTTTACATATTATAAGTTTATACAAACAAAGG
Found at i:4027776 original size:723 final size:716
Alignment explanation
Indices: 4026446--4028193 Score: 2253
Period size: 723 Copynumber: 2.4 Consensus size: 716
4026436 AAAGTGTGCA
* *
4026446 TATATATATTATAATTAAAAATTTTATAAGTTATAATTTTTATATTGTTAACACAAAATAAAAAG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAAT-AAAAG
* *
4026511 TAAATATATTTGTATTTAAAGTATATATATATATATATA-TGAAAAGTATTTTAGTGTATATATA
65 TAAATATATTTATATTTAAAGTATATATATATA-A-A-ACT-AAAAGTATTTTAGTATATATATA
* * * * * *
4026575 TAATAATAATTATATTCCTTATAAATGAATGCCATATATATAAAGTAAATAAATTAAAAGACATT
126 TAATAGTAAGTATATTCTTTATAAATGAA-CCCATATATATAAAGTAAATATATTAAAAGATATT
* * * *
4026640 ACAAGGTAATTAATAATGATAGTTTCATAAATTAA-TTATTTAATTATATGGGTTTGTAC-TTAA
190 ACAAGATAATTAATAATCATAGTTTCATAAATTAATTTAATTAATTATATGGATTTGT-CTTTAA
* *
4026703 TTACATAAAATTAAAAAAAAAAGCCAAGTTTCAAAACTATTCTAATCTCATAACTTCTTCTTAAT
254 TTACATAAAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAATCTCATAACTTCTTCTTAAT
* *
4026768 AATTAAGTTTATATATTAAAAGTTTATACAAACAAATGCATATATAGTATAATTAATAATTTTAT
319 AATTAAGTTTACATATTAAAAGTTTATACAAACAAAGGCATATATAGTATAATTAATAATTTTAT
*
4026833 AAGTTATAATTTTTATAATGTTAACACAAAATAGAAAGTAAATATGTTATATTTAAAGTGTGTGT
384 AAGTTATAATTTTTATAATATTAACACAAAATAGAAAGT-AATA---TATA-TT-AA----GTGT
* * * *
4026898 GTGTGTGTGTGTATATATATATATATACACACATTAATAATATTTTAGTATATATATAATAGTAA
439 GTGTGTATGTGTAAATATATATATATACAAAAATTAATAATATTTTAGTATATATATAATAGTAA
*
4026963 GTATATTCTTTATAAATGACCCAATATATATAAAGTAAATATATTAAAAGACATTACAGGGTAAT
504 GTATATTCTTTATAAATGACCCAATATATATAAAGTAAATATATTAAAAGACATTACAAGGTAAT
* * *
4027028 TAATAATCATAGTTTCATTAATTAATTTAATTAATTATATAG-ATTTGTCCTTAATTACATAAAA
569 TAATAATCACAGTTTCATGAATTAATTTAATTAATTATA-AGAATTTATCCTTAATTACATAAAA
* * * * *
4027092 TTAAAAAAAATAGCTAATTTTCAAAACTATTCTAATCTCATAACTTCTTTTTAGATAATTAAGTT
633 TT--AAAAAATAACTAAGTTTCAAAACTATTCTAATCTCACAACTTCTCTTAAGAT--TT--G--
4027157 TACATATTATAAGTTTATACAAACAAAGG
690 T--ATATTATAAGTTTATACAAACAAAGG
* *
4027186 TATATACATTATAATTAATAATTTTATAAGTTATAATTTTTATAATATTAACACAAAATAGAAAG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATA-AAAG
*
4027251 TAAATATATTTTTATTTAAATTGTATATATATATACGCACACACTAAAAGTATTTTAGTATATAT
65 TAAATATATTTATATTTAAA--GTATATATATATA---A-A-ACTAAAAGTATTTTAGTATATAT
4027316 ATATAATAGTAAGTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGAT
123 ATATAATAGTAAGTATATTCTTTATAAATGAACCC-ATATATATAAAGTAAATATATTAAAAGAT
*
4027381 ATTACAAGATAATTAATAATCATAGTTTCATGAATTAATTTAATTAATTATATGGATTTGTCTTT
187 ATTACAAGATAATTAATAATCATAGTTTCATAAATTAATTTAATTAATTATATGGATTTGTCTTT
*
4027446 AATTACATAAAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAATCTCATAACTTCTTTTTA
252 AATTACATAAAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAATCTCATAACTTCTTCTTA
* * * *
4027511 GATAATTAAGTTTACATATTATAAGTTTATACAAACTAAGGTATATATATTATAATTAATAATTT
317 -ATAATTAAGTTTACATATTAAAAGTTTATACAAACAAAGGCATATATAGTATAATTAATAATTT
*
4027576 TATAAGTTATAATTTTTGTAATATTAACACAAAATAGAAAGT-A-A-ATA-T-A-T-T-T-T-TA
381 TATAAGTTATAATTTTTATAATATTAACACAAAATAGAAAGTAATATATATTAAGTGTGTGTGTA
*
4027631 T-T-TAAAT-TATATATATGCAAAAATTAA-AAGTATTTTAGTATATATATAATAGTAAGTATAT
446 TGTGTAAATATATATATATACAAAAATTAATAA-TATTTTAGTATATATATAATAGTAAGTATAT
4027692 TCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAG-CATTACAAGGTAATTAATA
510 TCTTTATAAATG-ACCCAATATATATAAAGTAAATATATTAAAAGACATTACAAGGTAATTAATA
* *
4027756 ATCACAGTTTCATGAATTAATTTAATTAATTATACGAATTTATCCTTAATTACATTAAATTAAAA
574 ATCACAGTTTCATGAATTAATTTAATTAATTATAAGAATTTATCCTTAATTACATAAAATTAAAA
* * *
4027821 AATAACTAGGTTTCAAAACTATTCTAATTTCACAACTTCTCTTAAGGTTTGTATATTATAAGTTT
639 AATAACTAAGTTTCAAAACTATTCTAATCTCACAACTTCTCTTAAGATTTGTATATTATAAGTTT
*
4027886 ATATAAACAAAGG
704 ATACAAACAAAGG
* * * *
4027899 TGTATATATTATAATTAATAATTTTACAAGTTATAATTTTTGTAATGTTAACATAAAATCAAAAG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAAT-AAAAG
* *
4027964 TAAATATATTTATATTTAAAG-A-ATATATAT---ACTAAAAGTA--TTAGTATATACACA-ATA
65 TAAATATATTTATATTTAAAGTATATATATATAAAACTAAAAGTATTTTAGTATATATATATA-A
** * * *
4028021 TAGT-AGTTATATT-TCTTATAAATGAACCCCATATATGGAATGTATATATATTAAAAAATATTA
129 TAGTAAG-TATATTCT-TTATAAATGAA-CCCATATATATAAAGTAAATATATTAAAAGATATTA
* * * * **
4028084 CAAGTTAATTAATAATCATAGATTCATAAAGTAATTTAATTTACCATATGGATTTGTCTTTAATT
191 CAAGATAATTAATAATCATAGTTTCATAAATTAATTTAATTAATTATATGGATTTGTCTTTAATT
* *
4028149 ACAAAAAATT-AAAAAAATAG-TTAGATTTCAAAACTATTCTAATCT
256 ACATAAAATTAAAAAAAATAGCTAAG-TTTCAAAACTATTCTAATCT
4028194 TAAAGACTCT
Statistics
Matches: 915, Mismatches: 74, Indels: 80
0.86 0.07 0.07
Matches are distributed among these distances:
697 3 0.00
698 34 0.04
699 129 0.14
700 3 0.00
701 10 0.01
709 8 0.01
710 1 0.00
711 1 0.00
713 101 0.11
714 1 0.00
715 1 0.00
717 1 0.00
719 2 0.00
721 44 0.05
722 3 0.00
723 132 0.14
724 36 0.04
725 1 0.00
726 2 0.00
727 1 0.00
728 1 0.00
729 1 0.00
730 1 0.00
735 1 0.00
737 1 0.00
739 4 0.00
740 78 0.09
742 13 0.01
743 3 0.00
744 115 0.13
745 85 0.09
746 98 0.11
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (716 bp):
TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAAAAGT
AAATATATTTATATTTAAAGTATATATATATAAAACTAAAAGTATTTTAGTATATATATATAATA
GTAAGTATATTCTTTATAAATGAACCCATATATATAAAGTAAATATATTAAAAGATATTACAAGA
TAATTAATAATCATAGTTTCATAAATTAATTTAATTAATTATATGGATTTGTCTTTAATTACATA
AAATTAAAAAAAATAGCTAAGTTTCAAAACTATTCTAATCTCATAACTTCTTCTTAATAATTAAG
TTTACATATTAAAAGTTTATACAAACAAAGGCATATATAGTATAATTAATAATTTTATAAGTTAT
AATTTTTATAATATTAACACAAAATAGAAAGTAATATATATTAAGTGTGTGTGTATGTGTAAATA
TATATATATACAAAAATTAATAATATTTTAGTATATATATAATAGTAAGTATATTCTTTATAAAT
GACCCAATATATATAAAGTAAATATATTAAAAGACATTACAAGGTAATTAATAATCACAGTTTCA
TGAATTAATTTAATTAATTATAAGAATTTATCCTTAATTACATAAAATTAAAAAATAACTAAGTT
TCAAAACTATTCTAATCTCACAACTTCTCTTAAGATTTGTATATTATAAGTTTATACAAACAAAG
G
Found at i:4028215 original size:2 final size:2
Alignment explanation
Indices: 4028210--4028239 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4028200 CTCTCTGTAC
4028210 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4028240 AGTTATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4033355 original size:22 final size:23
Alignment explanation
Indices: 4033316--4033368 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
4033306 TCAAATTGAT
* *
4033316 TGAATTAAATATGCTTT-GAAAA
1 TGAATGAAAGATGCTTTGGAAAA
* *
4033338 TGAATGAAAGATGTTTTGGAATA
1 TGAATGAAAGATGCTTTGGAAAA
4033361 TGAA-GAAA
1 TGAATGAAA
4033369 ATCCTCAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.32
Consensus pattern (23 bp):
TGAATGAAAGATGCTTTGGAAAA
Found at i:4033473 original size:21 final size:21
Alignment explanation
Indices: 4033432--4033473 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4033422 TAAAATTGAT
*
4033432 TGAACATACTTTGAAAGTTAA
1 TGAACATACTTTGAAACTTAA
*
4033453 TGAACATGCTCTTG-AACTTAA
1 TGAACATACT-TTGAAACTTAA
4033474 AGAAATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
TGAACATACTTTGAAACTTAA
Found at i:4049303 original size:9 final size:9
Alignment explanation
Indices: 4049277--4049312 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
4049267 TTGCAATTTC
4049277 TCCTTTCCT
1 TCCTTTCCT
4049286 TCTCTTTCCT
1 TC-CTTTCCT
4049296 TCCTTTCCT
1 TCCTTTCCT
*
4049305 TTCTTTCC
1 TCCTTTCC
4049313 CTTCACAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (9 bp):
TCCTTTCCT
Found at i:4049316 original size:19 final size:19
Alignment explanation
Indices: 4049277--4049312 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4049267 TTGCAATTTC
4049277 TCCTTTCCTTCTCTTTCCT
1 TCCTTTCCTTCTCTTTCCT
4049296 TCCTTTCCTT-TCTTTCC
1 TCCTTTCCTTCTCTTTCC
4049313 CTTCACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (19 bp):
TCCTTTCCTTCTCTTTCCT
Found at i:4064183 original size:16 final size:16
Alignment explanation
Indices: 4064144--4064187 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
4064134 CATTCAAGTA
*
4064144 TTATTTCTTATTTTTCTT
1 TTATTT-TT-TTTTTATT
4064162 TCTATTTTTTTTTTATT
1 T-TATTTTTTTTTTATT
4064179 TTATTTTTT
1 TTATTTTTT
4064188 ATCTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 8 0.33
18 3 0.12
19 5 0.21
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (16 bp):
TTATTTTTTTTTTATT
Found at i:4064194 original size:23 final size:23
Alignment explanation
Indices: 4064151--4064196 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4064141 GTATTATTTC
*
4064151 TTATTTTTCTTTCTATTTTTTTT
1 TTATTTTTCTTTCTATCTTTTTT
*
4064174 TTATTTTAT-TTTTTATCTTTTTT
1 TTATTTT-TCTTTCTATCTTTTTT
4064197 GTTTGGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.83
Consensus pattern (23 bp):
TTATTTTTCTTTCTATCTTTTTT
Found at i:4068197 original size:7 final size:7
Alignment explanation
Indices: 4068180--4068226 Score: 51
Period size: 7 Copynumber: 6.3 Consensus size: 7
4068170 TTATAAAACA
4068180 TTAATATT
1 TTAA-ATT
4068188 TTAAATT
1 TTAAATT
4068195 TTAAATT
1 TTAAATT
4068202 TTAAAATT
1 TT-AAATT
4068210 ATTAATATT
1 -TTAA-ATT
4068219 TT-AATT
1 TTAAATT
4068225 TT
1 TT
4068227 TTATTCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 5 0.14
7 13 0.36
8 13 0.36
9 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTAAATT
Found at i:4068223 original size:8 final size:8
Alignment explanation
Indices: 4068180--4068229 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
4068170 TTATAAAACA
4068180 TTAATATT
1 TTAATATT
4068188 TTAA-ATT
1 TTAATATT
4068195 TTAA-ATT
1 TTAATATT
*
4068202 TTAAAATT
1 TTAATATT
4068210 ATTAATATT
1 -TTAATATT
*
4068219 TTAATTTT
1 TTAATATT
4068227 TTA
1 TTA
4068230 TTCAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
7 14 0.37
8 17 0.45
9 7 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTAATATT
Found at i:4068557 original size:20 final size:19
Alignment explanation
Indices: 4068529--4068603 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 19
4068519 ATTTTTTATC
4068529 ATAATAATATTCAAATTATAA
1 ATAA-AATATT-AAATTATAA
*
4068550 ATAAAATATTAATATTTTAAA
1 ATAAAATATTAA-ATTAT-AA
*
4068571 ATATTAATGATTAAATTATAA
1 ATA-AAAT-ATTAAATTATAA
4068592 ATAAAATATTAA
1 ATAAAATATTAA
4068604 CATTTAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
19 7 0.15
20 13 0.28
21 14 0.30
22 7 0.15
23 5 0.11
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (19 bp):
ATAAAATATTAAATTATAA
Found at i:4068587 original size:42 final size:41
Alignment explanation
Indices: 4068533--4068631 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 41
4068523 TTTATCATAA
*
4068533 TAATATTCAAATTATAAATAAAATATTAATATTTTAA-AATAT
1 TAATATT-AAATTATAAATAAAATATTAACA-TTTAAGAATAT
*
4068575 TAATGATTAAATTATAAATAAAATATTAACATTTAAGAATTT
1 TAAT-ATTAAATTATAAATAAAATATTAACATTTAAGAATAT
4068617 TAATATTTAAATTAT
1 TAATA-TTAAATTAT
4068632 TAATTACTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
41 6 0.12
42 43 0.83
43 3 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (41 bp):
TAATATTAAATTATAAATAAAATATTAACATTTAAGAATAT
Found at i:4080075 original size:15 final size:15
Alignment explanation
Indices: 4080055--4080118 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
4080045 TTTTCTTTAG
4080055 GTTTATATATTATAA
1 GTTTATATATTATAA
**
4080070 GTTTATATAAGCA-AA
1 GTTTATAT-ATTATAA
4080085 GTTATATATATTAT-A
1 GTT-TATATATTATAA
* *
4080100 GTTAATAATTTTATAA
1 GTTTAT-ATATTATAA
4080116 GTT
1 GTT
4080119 ATAATTTTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 2 0.05
15 25 0.66
16 11 0.29
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (15 bp):
GTTTATATATTATAA
Found at i:4080122 original size:15 final size:15
Alignment explanation
Indices: 4080083--4080126 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4080073 TATATAAGCA
*
4080083 AAGTTATATATATTAT
1 AAGTTATA-ATTTTAT
4080099 -AGTTAATAATTTTAT
1 AAGTT-ATAATTTTAT
4080114 AAGTTATAATTTT
1 AAGTTATAATTTT
4080127 GTAATGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
AAGTTATAATTTTAT
Found at i:4080152 original size:359 final size:341
Alignment explanation
Indices: 4079397--4080518 Score: 1141
Period size: 359 Copynumber: 3.2 Consensus size: 341
4079387 TATCTCAAAC
* * * * * *
4079397 ATAATTAATAAATTTATTAGCTATAACTTTTGTAATATTAACAC--AATAAAAAGAAAATATATT
1 ATAATTAATAATTTTATAAGTTATAA-TTTTGTAATGTTAACACAAAATAAAAAGTAAATATGTT
* * *
4079460 TATATTTAAAGT--GTACATATACTAAAAGTATTTT--AATATATATAATAGTAATTATATTTTT
65 TATATTTAAAGTAAATACA-A-ACTAAAAATATTTTAGAATATATATAATAGTAATTATATTTCT
* * * *
4079521 TATAAATGAACCCAATGTATATAAAGTATATATATTAAAAGACATTACAAGTCAATTAATAATCA
128 TATAAATGAACACAA--TATATAAAATATATATATTAAAAGACATTACAAGTTAATTAATAATAA
* * * * * *
4079586 TAGTTTCATTAACTAATTTAATTAACTATATAAGTTTATCCTTAATTACAAGAAACT-AAAAAAA
191 TAGTTTCATGAATTAATTTAATTAACTATATGAGTTTGTCCTTAATTA-ATGAAATTAAAAAAAA
* * * * *
4079650 ATAACTAAGTTTC-TAAACTATTCTAATCTCACAACTTCCCTTTAGATTTATGTGTTCTAAGTTT
255 ATAACTAAGTTTCAT-AACTATTCTAATCTCAAAACTTCTCTTTAGGTTTATATGTTATAAGTTT
*
4079714 ATATAAACAAAGGTATATATATT
319 ATATAAACAAAGATATATATATT
* * * * * * *
4079737 GTAATTAAGAATTTAATATGTTATTATTTTTGTAGTGTTAAAACAAAATAAAAAGTAAATATGTT
1 ATAATTAATAATTTTATAAGTTA-TAATTTTGTAATGTTAACACAAAATAAAAAGTAAATATGTT
* *
4079802 TATATTTAAAGTACATACGCACACAC-ACATACACTCATATATATATATATATATATATAATAGT
65 TATATTTAAAGTAAATA--CA-A-ACTA-A-A-A---ATAT-T-T-TAGA-ATATATATAATAGT
* ** *
4079866 AATTATATTCCTTATAAATGAACTTAATACATATAAAATATATATATATTAAAAGACATCACAAG
116 AATTATATTTCTTATAAATGAACACAAT--ATAT-AAA-ATATATATATTAAAAGACATTACAAG
* * * *
4079931 TTAATTAATTATTATAGTTTCATGAATTAATTTAATTAACTGTATGAGTTTGTTCTTAATTGAAT
177 TTAATTAATAATAATAGTTTCATGAATTAATTTAATTAACTATATGAGTTTGTCCTTAATT-AAT
* * *
4079996 GAAATTAAAAAAAAATAACTACGTTTCATAACTATTCTAATCTCAGAACTTTTCTTTAGGTTTAT
241 GAAATTAAAAAAAAATAACTAAGTTTCATAACTATTCTAATCTCAAAACTTCTCTTTAGGTTTAT
* * *
4080061 ATATTATAAGTTTATATAAGCAAAGTTATATATATT
306 ATGTTATAAGTTTATATAAACAAAGATATATATATT
* * *
4080097 ATAGTTAATAATTTTATAAGTTATAATTTTGTAATGTTAACACAGAAGAAAAAGTAAATATGTTT
1 ATAATTAATAATTTTATAAGTTATAATTTTGTAATGTTAACACAAAATAAAAAGTAAATATGTTT
* *
4080162 ATATTTAAAGTAAATATAAACTAAAAATATTTTAGAATATATATAATTGTAATTATATTTCTTAT
66 ATATTTAAAGTAAATACAAACTAAAAATATTTTAGAATATATATAATAGTAATTATATTTCTTAT
* * * * * * *
4080227 AAATTAACACAATATATAGACTATACACATTGAAAGGCATTACAAGTTAATTAATAATAATAGTT
131 AAATGAACACAATATATAAAATATATATATTAAAAGACATTACAAGTTAATTAATAATAATAGTT
* * *
4080292 TCATGAATTAATTTAATTAACTATAAG-GATTTGTCCTTCATTTCATGAAATTAAAAAAAAAATA
196 TCATGAATTAATTTAATTAACTATATGAG-TTTGTCCTT-AATTAATGAAATT-AAAAAAAAATA
** * * * * * * **
4080356 GTTAGGTTCCAAAAGTATCCTAATCTCAAAAGC-TCTCTTTAAGCATATATGTTATAAGTTTATA
258 ACTAAGTTTCATAACTATTCTAATCTCAAAA-CTTCTCTTTAGGTTTATATGTTATAAGTTTATA
* * *
4080420 TAAATAATGATATATCTATT
322 TAAACAAAGATATATATATT
* *
4080440 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAAAACACAAAATAGAAAGTAAATATA
1 ATAATTAATAATTTTATAAGTTATAA-TTTTGTAATGTT--AACACAAAATAAAAAGTAAATATG
* *
4080505 TTTATGTTAAAAGT
63 TTTATATTTAAAGT
4080519 TTGTATATAT
Statistics
Matches: 647, Mismatches: 101, Indels: 62
0.80 0.12 0.08
Matches are distributed among these distances:
340 30 0.05
341 3 0.00
342 107 0.17
343 105 0.16
344 19 0.03
345 1 0.00
346 75 0.12
347 4 0.01
348 2 0.00
349 1 0.00
350 4 0.01
351 3 0.00
352 1 0.00
353 2 0.00
354 2 0.00
355 4 0.01
356 3 0.00
357 42 0.06
358 3 0.00
359 134 0.21
360 101 0.16
361 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (341 bp):
ATAATTAATAATTTTATAAGTTATAATTTTGTAATGTTAACACAAAATAAAAAGTAAATATGTTT
ATATTTAAAGTAAATACAAACTAAAAATATTTTAGAATATATATAATAGTAATTATATTTCTTAT
AAATGAACACAATATATAAAATATATATATTAAAAGACATTACAAGTTAATTAATAATAATAGTT
TCATGAATTAATTTAATTAACTATATGAGTTTGTCCTTAATTAATGAAATTAAAAAAAAATAACT
AAGTTTCATAACTATTCTAATCTCAAAACTTCTCTTTAGGTTTATATGTTATAAGTTTATATAAA
CAAAGATATATATATT
Found at i:4091369 original size:38 final size:38
Alignment explanation
Indices: 4091318--4091392 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
4091308 TGGAAGAAGT
4091318 TGATGCATATAAGACTGAACCCCAGCCCCCACCAAAGC
1 TGATGCATATAAGACTGAACCCCAGCCCCCACCAAAGC
4091356 TGATGCATATAAGACTGAACCCCAGCCCCCACCAAAG
1 TGATGCATATAAGACTGAACCCCAGCCCCCACCAAAG
4091393 GGATTGTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.35, C:0.36, G:0.16, T:0.13
Consensus pattern (38 bp):
TGATGCATATAAGACTGAACCCCAGCCCCCACCAAAGC
Found at i:4096237 original size:2 final size:2
Alignment explanation
Indices: 4096230--4096260 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4096220 GCTTTACAAA
4096230 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4096261 AATACTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4102407 original size:2 final size:2
Alignment explanation
Indices: 4102354--4102395 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4102344 CCCCCCCTTC
4102354 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4102396 TTGTTTCTCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4111017 original size:28 final size:28
Alignment explanation
Indices: 4110943--4111017 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
4110933 GTGGGTTGAG
* * *
4110943 GTATCCATCTACTTTTGATACGTTAAAA
1 GTATACATCTACTTTTGGTAAGTTAAAA
* *
4110971 GTATTCATCTA-TTTGTGGTAAGTTACAA
1 GTATACATCTACTTT-TGGTAAGTTAAAA
*
4110999 GTATACATCCACTTTTGGT
1 GTATACATCTACTTTTGGT
4111018 GGGTGATCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 3 0.08
28 33 0.85
29 3 0.08
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (28 bp):
GTATACATCTACTTTTGGTAAGTTAAAA
Found at i:4111437 original size:52 final size:53
Alignment explanation
Indices: 4111296--4111441 Score: 161
Period size: 52 Copynumber: 2.7 Consensus size: 53
4111286 TACTAAATGA
* * * **
4111296 TGTCACATTCACTTCAAGGAATAGATAGATTTATAATTTTTTATTAGTAGCTTGGT
1 TGTCACATTCACTTCAAGGAAT-GA-ACATTCATAA-TTTTCATTAGTAGCTCAGT
* * *
4111352 TGTCACATTTACTTCAAGGAATGAATATTCATAATTTTCATTAGTAGCTCATT
1 TGTCACATTCACTTCAAGGAATGAACATTCATAATTTTCATTAGTAGCTCAGT
*
4111405 TGTCACA-TCACTTC-AGAGAATGGACATTCATAATTTT
1 TGTCACATTCACTTCAAG-GAATGAACATTCATAATTTT
4111442 TTATTAATAG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
51 2 0.03
52 24 0.30
53 22 0.28
54 8 0.10
55 2 0.03
56 21 0.27
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (53 bp):
TGTCACATTCACTTCAAGGAATGAACATTCATAATTTTCATTAGTAGCTCAGT
Found at i:4111970 original size:14 final size:12
Alignment explanation
Indices: 4111930--4111963 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
4111920 ACATAAATGG
4111930 ATATTCACAAAA
1 ATATTCACAAAA
4111942 ATATTCACAAAA
1 ATATTCACAAAA
4111954 ATATTCACAA
1 ATATTCACAA
4111964 CAAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (12 bp):
ATATTCACAAAA
Found at i:4112032 original size:30 final size:30
Alignment explanation
Indices: 4111966--4112039 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
4111956 ATTCACAACA
4111966 AAATAAATTTTTAT-TTTATTATAGTATTC
1 AAATAAATTTTTATATTTATTATAGTATTC
* **
4111995 AATTAAATTTTTATATTT-TTATTTTCATTC
1 AAATAAATTTTTATATTTATTATAGT-ATTC
4112025 AAATAAATTTTTATA
1 AAATAAATTTTTATA
4112040 ACTAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 18 0.46
30 21 0.54
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (30 bp):
AAATAAATTTTTATATTTATTATAGTATTC
Found at i:4119910 original size:2 final size:2
Alignment explanation
Indices: 4119903--4119936 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4119893 TAGAAAGACT
4119903 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
4119937 ATCATGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4126672 original size:33 final size:33
Alignment explanation
Indices: 4126632--4126725 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 33
4126622 TGATCAACAT
*
4126632 CAATAATGGCATTTACATCATCACCATCAACTC
1 CAATAATGGCATTTACATCATCACCACCAACTC
* *
4126665 TAGTAATGGCA-TT-CA-CATCACCACCAACTC
1 CAATAATGGCATTTACATCATCACCACCAACTC
*
4126695 CAATAATGGCATTCACATCATCACCACCAAC
1 CAATAATGGCATTTACATCATCACCACCAAC
4126726 ATTCTGCATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
30 23 0.44
31 3 0.06
32 4 0.08
33 22 0.42
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.23
Consensus pattern (33 bp):
CAATAATGGCATTTACATCATCACCACCAACTC
Found at i:4131664 original size:55 final size:54
Alignment explanation
Indices: 4131598--4131781 Score: 212
Period size: 55 Copynumber: 3.4 Consensus size: 54
4131588 AGCTATGTCA
*
4131598 AAAATTTAGTTGTTACACATCATATTGAAAAACGTAGTTGTTACATGCCATGTTG
1 AAAATTTAGTTGTTACACACCATATTGAAAAA-GTAGTTGTTACATGCCATGTTG
** * **
4131653 AAAATTTAGTTGTTACATGCCATGTTGAAAAATGTAGTTGTTACACACCATGTTG
1 AAAATTTAGTTGTTACACACCATATTGAAAAA-GTAGTTGTTACATGCCATGTTG
* * * * *
4131708 GAGATTTAGTTGTTACACACCATATTGAAAAATTCAGTTGTTATATGCCATGATG
1 AAAATTTAGTTGTTACACACCATATTGAAAAAGT-AGTTGTTACATGCCATGTTG
*
4131763 AAAA---ATTTGTTACACACCA
1 AAAATTTAGTTGTTACACACCA
4131782 CACCATAATT
Statistics
Matches: 108, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
52 14 0.13
54 1 0.01
55 93 0.86
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (54 bp):
AAAATTTAGTTGTTACACACCATATTGAAAAAGTAGTTGTTACATGCCATGTTG
Found at i:4131769 original size:28 final size:28
Alignment explanation
Indices: 4131575--4131770 Score: 184
Period size: 28 Copynumber: 7.1 Consensus size: 28
4131565 CGTATTGAAG
* * *
4131575 ATTTAGCTGTTACA-GCTATG-TCAAAA
1 ATTTAGTTGTTACATGCCATGTTGAAAA
*** *
4131601 ATTTAGTTGTTACACATCATATTGAAAA
1 ATTTAGTTGTTACATGCCATGTTGAAAA
**
4131629 ACGTAGTTGTTACATGCCATGTTG-AAA
1 ATTTAGTTGTTACATGCCATGTTGAAAA
4131656 ATTTAGTTGTTACATGCCATGTTGAAAA
1 ATTTAGTTGTTACATGCCATGTTGAAAA
* ** * *
4131684 ATGTAGTTGTTACACACCATGTTG-GAG
1 ATTTAGTTGTTACATGCCATGTTGAAAA
** *
4131711 ATTTAGTTGTTACACACCATATTGAAAA
1 ATTTAGTTGTTACATGCCATGTTGAAAA
* * *
4131739 ATTCAGTTGTTATATGCCATGATGAAAA
1 ATTTAGTTGTTACATGCCATGTTGAAAA
4131767 ATTT
1 ATTT
4131771 GTTACACACC
Statistics
Matches: 136, Mismatches: 30, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
26 13 0.10
27 50 0.37
28 73 0.54
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (28 bp):
ATTTAGTTGTTACATGCCATGTTGAAAA
Found at i:4132050 original size:16 final size:16
Alignment explanation
Indices: 4132019--4132051 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4132009 AGATGGTGAG
4132019 ACGATGGAGAAGGAAA
1 ACGATGGAGAAGGAAA
4132035 ACGATTGGAGAA-GAAA
1 ACGA-TGGAGAAGGAAA
4132051 A
1 A
4132052 GAGGTAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.52, C:0.06, G:0.33, T:0.09
Consensus pattern (16 bp):
ACGATGGAGAAGGAAA
Found at i:4133537 original size:21 final size:21
Alignment explanation
Indices: 4133511--4133561 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
4133501 TAGTAGGGAT
4133511 TTTTGACACTTCATTGGTGTC
1 TTTTGACACTTCATTGGTGTC
4133532 TTTTGACACTTCATTGGTGTC
1 TTTTGACACTTCATTGGTGTC
4133553 TTTTGACAC
1 TTTTGACAC
4133562 CACTTGTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TTTTGACACTTCATTGGTGTC
Found at i:4142497 original size:2 final size:2
Alignment explanation
Indices: 4142492--4142532 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4142482 ACACACACAT
4142492 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4142533 TTACTTCAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4146277 original size:83 final size:83
Alignment explanation
Indices: 4146108--4146279 Score: 195
Period size: 83 Copynumber: 2.1 Consensus size: 83
4146098 AATGCACGAG
*
4146108 AAAAAAAATTATTATATACCATGTTGAAAAAAAAAATATTACACGTCATATTAAAAAAGTGTTGT
1 AAAAAAAAATATTATATACCATGTTGAAAAAAAAAATATTACACGTCATATTAAAAAAGTGTTGT
* * * *
4146173 TGTTACATGTCATTTTGA
66 TGGTACATGTAATGTTCA
*** * * * *
4146191 AAAAAAAAATATTATATGTTATGTTGAAAAAAAAATTATTTCAC-TCCATGTTGAAAAAA-TTTT
1 AAAAAAAAATATTATATACCATGTTGAAAAAAAAAATATTACACGT-CATATT-AAAAAAGTGTT
*
4146254 GTTGGTATATGTAATGTTCA
64 GTTGGTACATGTAATGTTCA
4146274 AAAAAA
1 AAAAAA
4146280 TTTTACTACA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
82 1 0.01
83 67 0.91
84 6 0.08
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (83 bp):
AAAAAAAAATATTATATACCATGTTGAAAAAAAAAATATTACACGTCATATTAAAAAAGTGTTGT
TGGTACATGTAATGTTCA
Found at i:4146296 original size:83 final size:82
Alignment explanation
Indices: 4146209--4146388 Score: 213
Period size: 83 Copynumber: 2.2 Consensus size: 82
4146199 ATATTATATG
* * *
4146209 TTATGTTGAAAAAAAAATTATTTCACTC-CATGTT-GAAAAAATTTTGTTGGTATATG-TAATGT
1 TTATGTT-AAAAAAAAATTA-TT-ACTCGCATGTTAAAAAAAATATTGTTGGTATACGCT-ATGT
*
4146271 TCAAAAAAATTTTACTACACA
62 TAAAAAAAATTTTACTACACA
*
4146292 TTATGTTAAAAAAAAATTATTACTCGTCATGTTAAAAAAAATATTGTTGTTATACGCTATGTTAA
1 TTATGTTAAAAAAAAATTATTACTCG-CATGTTAAAAAAAATATTGTTGGTATACGCTATGTTAA
* *
4146357 AAAAAATTTTATTACACG
65 AAAAAATTTTACTACACA
* *
4146375 TCATTTTAAAAAAA
1 TTATGTTAAAAAAA
4146389 TATATTGTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
80 4 0.05
81 2 0.02
82 18 0.21
83 59 0.70
84 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.38
Consensus pattern (82 bp):
TTATGTTAAAAAAAAATTATTACTCGCATGTTAAAAAAAATATTGTTGGTATACGCTATGTTAAA
AAAAATTTTACTACACA
Found at i:4146383 original size:27 final size:27
Alignment explanation
Indices: 4146267--4146388 Score: 113
Period size: 27 Copynumber: 4.4 Consensus size: 27
4146257 GGTATATGTA
* * * *
4146267 ATGTTCAAAAAAATTTTACTACACATT
1 ATGTTAAAAAAAATTTTATTACACGTC
* *
4146294 ATGTTAAAAAAAA-ATTATTACTCGTC
1 ATGTTAAAAAAAATTTTATTACACGTC
* *
4146320 ATGTTAAAAAAAATATTGTTGTTATACG-C
1 ATGTT-AAAAAAA-ATT-TTATTACACGTC
4146349 TATGTTAAAAAAAATTTTATTACACGTC
1 -ATGTTAAAAAAAATTTTATTACACGTC
*
4146377 ATTTTAAAAAAA
1 ATGTTAAAAAAA
4146389 TATATTGTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
26 13 0.17
27 38 0.50
28 5 0.07
29 8 0.11
30 12 0.16
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (27 bp):
ATGTTAAAAAAAATTTTATTACACGTC
Found at i:4146723 original size:36 final size:36
Alignment explanation
Indices: 4146672--4146746 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 36
4146662 ATTAGAGAGA
*
4146672 TGGATGGTGAGAGAGACAA-ACAATATTTAATTTGTC
1 TGGATGGTGAAAGAGA-AATACAATATTTAATTTGTC
*
4146708 TGGATGGTGAAAGAGAAATTGAGAATATTTAATTTGTC
1 TGGATGGTGAAAGAGAAA-T-ACAATATTTAATTTGTC
4146746 T
1 T
4146747 AAAATAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 2 0.06
36 15 0.44
38 17 0.50
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.33
Consensus pattern (36 bp):
TGGATGGTGAAAGAGAAATACAATATTTAATTTGTC
Found at i:4146803 original size:16 final size:16
Alignment explanation
Indices: 4146782--4146814 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4146772 TCAAGTTATG
4146782 ATAAAAGTTAGTATAA
1 ATAAAAGTTAGTATAA
4146798 ATAAAAGTTAGTATAA
1 ATAAAAGTTAGTATAA
4146814 A
1 A
4146815 CAATTAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (16 bp):
ATAAAAGTTAGTATAA
Found at i:4148099 original size:15 final size:15
Alignment explanation
Indices: 4148075--4148107 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4148065 AATACAATAC
4148075 TTTTCTTGCTTTTGAT
1 TTTTCTTGCTTTT-AT
4148091 TTTTC-TGCTTTTAT
1 TTTTCTTGCTTTTAT
4148105 TTT
1 TTT
4148108 ATTTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (15 bp):
TTTTCTTGCTTTTAT
Found at i:4149041 original size:15 final size:15
Alignment explanation
Indices: 4149021--4149057 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
4149011 AAAAGAGAGG
4149021 GCATTTCGGGTAATT
1 GCATTTCGGGTAATT
4149036 GCATTTCGGGTAATT
1 GCATTTCGGGTAATT
4149051 GCATTTC
1 GCATTTC
4149058 CCCTATCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (15 bp):
GCATTTCGGGTAATT
Found at i:4160506 original size:15 final size:15
Alignment explanation
Indices: 4160486--4160516 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4160476 TAACTACTCT
*
4160486 TAAAGTAATTTAAAA
1 TAAAGTAATCTAAAA
4160501 TAAAGTAATCTAAAA
1 TAAAGTAATCTAAAA
4160516 T
1 T
4160517 TTAACTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (15 bp):
TAAAGTAATCTAAAA
Found at i:4167930 original size:73 final size:72
Alignment explanation
Indices: 4167841--4168032 Score: 228
Period size: 73 Copynumber: 2.6 Consensus size: 72
4167831 TTCTCAGATA
* * * *
4167841 GTGAGCTTTTAGCTGGCTAACCATTCTTTTTAGTTGATTAAGTTTTTTTCGTCTCT-TAATAAAA
1 GTGAGCTTTTAGCTGGCTAACCATTCTTCTTAGTAGATTAAGTTTTTTT-GACT-TGCAATAAAA
4167905 TTTTTGACC
64 TTTTTGACC
* * *
4167914 -TTACGCTTTTAACTGGCTAACCATTCTTCTTAGTAGATTAAGTCTTTTTTGACTTGCAATCAAA
1 GTGA-GCTTTTAGCTGGCTAACCATTCTTCTTAGTAGATTAAGT-TTTTTTGACTTGCAATAAAA
4167978 TTTTTGACC
64 TTTTTGACC
* * *
4167987 GTGAGCTTTTAGCTGGTTGACCATACTTCTTAGTCA-ATTAAGTTTT
1 GTGAGCTTTTAGCTGGCTAACCATTCTTCTTAGT-AGATTAAGTTTT
4168033 CTCTATCTCG
Statistics
Matches: 102, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
72 6 0.06
73 87 0.85
74 9 0.09
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (72 bp):
GTGAGCTTTTAGCTGGCTAACCATTCTTCTTAGTAGATTAAGTTTTTTTGACTTGCAATAAAATT
TTTGACC
Found at i:4180175 original size:15 final size:15
Alignment explanation
Indices: 4180157--4180196 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4180147 ATAGAGATTA
4180157 AAAAAATAAATAAAT
1 AAAAAATAAATAAAT
*
4180172 AAAATAA-AAATAACT
1 AAAA-AATAAATAAAT
4180187 AAAAAATAAA
1 AAAAAATAAA
4180197 AGTTTCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAATAAATAAAT
Found at i:4180180 original size:19 final size:17
Alignment explanation
Indices: 4180158--4180197 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
4180148 TAGAGATTAA
4180158 AAAAATAAATAAATAAAAT
1 AAAAATAAAT-AA-AAAAT
*
4180177 AAAAATAACTAAAAAAT
1 AAAAATAAATAAAAAAT
4180194 AAAA
1 AAAA
4180198 GTTTCGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAATAAATAAAAAAT
Found at i:4180193 original size:22 final size:21
Alignment explanation
Indices: 4180155--4180197 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4180145 AAATAGAGAT
4180155 TAAAAAAATAAATAAATAAAA
1 TAAAAAAATAAATAAATAAAA
4180176 TAAAAATAACTAAA-AAATAAAA
1 TAAAAA-AA-TAAATAAATAAAA
4180198 GTTTCGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAAAAAATAAATAAATAAAA
Found at i:4180691 original size:21 final size:21
Alignment explanation
Indices: 4180675--4180734 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
4180665 AAATGATGGT
4180675 ATCAGTCTTTGTCATGAAGGC
1 ATCAGTCTTTGTCATGAAGGC
4180696 ATCTA-TCTTTGTCATGAAGGC
1 ATC-AGTCTTTGTCATGAAGGC
*
4180717 ATCTGTCTTTGTCATGAA
1 ATCAGTCTTTGTCATGAA
4180735 TTGCATGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (21 bp):
ATCAGTCTTTGTCATGAAGGC
Found at i:4184547 original size:250 final size:250
Alignment explanation
Indices: 4184097--4184551 Score: 657
Period size: 250 Copynumber: 1.8 Consensus size: 250
4184087 AGCCAATGGG
*
4184097 AAAACAAACAATTAAAAGCGAACGAAAAAAAATGTACAACACAAAGACTTCCCAAGAGGTCACCC
1 AAAACAAACAATTAAAAGCAAACGAAAAAAAATGTACAACACAAAGACTTCCCAAGAGGTCACCC
* *
4184162 ATCCTAGTAATACTCTCACCCAAGCACGCTTAACTATGAGGTTTTGATGGGATCCAGTGCACTAG
66 ATCCTAGTAATACTCTCACCCAAGCACGCTTAACTATGAGGTTCTGATGGGATCCAGTACACTAG
** * *
4184227 TGTAGGTATGATCGCACACATTATTTTTGGCGCTAACAATGCACATGACCCCTCCCCGCCCCTGC
131 TGTAGGTATGATCGCACACACCATTTTTGGCGCTAACAATGCACATGACCCCTCCCCACCCCTAC
4184292 CTCCTCCATTACCTAGGCCGAGCCCAACCCGATGCTCCCGACGCCCCCAGGCCCT
196 CTCCTCCATTACCTAGGCCGAGCCCAACCCGATGCTCCCGACGCCCCCAGGCCCT
* * * * * *
4184347 AAAACAAACAGTTGAAAGCAAACGGAAAAAAATGTGCAACACGAAGACTTCCCAAGGGGTCACCC
1 AAAACAAACAATTAAAAGCAAACGAAAAAAAATGTACAACACAAAGACTTCCCAAGAGGTCACCC
* * * *
4184412 ATCCTAGTACTACTCTCACCC-AGCAGCGCTTAACTGTG-GAGTTCTGATGGGATCTAGTACATT
66 ATCCTAGTAATACTCTCACCCAAGCA-CGCTTAACTATGAG-GTTCTGATGGGATCCAGTACACT
* * **
4184475 AGTGCT-GGTATGATTGCAC-CAACCATTTTTTGCGCTAACAATGCACATGACCGTTCCCCACCC
129 AGTG-TAGGTATGATCGCACAC-ACCATTTTTGGCGCTAACAATGCACATGACCCCTCCCCACCC
4184538 CTACCTCCTCCATT
192 CTACCTCCTCCATT
4184552 CTCC
Statistics
Matches: 180, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
249 6 0.03
250 173 0.96
251 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.22
Consensus pattern (250 bp):
AAAACAAACAATTAAAAGCAAACGAAAAAAAATGTACAACACAAAGACTTCCCAAGAGGTCACCC
ATCCTAGTAATACTCTCACCCAAGCACGCTTAACTATGAGGTTCTGATGGGATCCAGTACACTAG
TGTAGGTATGATCGCACACACCATTTTTGGCGCTAACAATGCACATGACCCCTCCCCACCCCTAC
CTCCTCCATTACCTAGGCCGAGCCCAACCCGATGCTCCCGACGCCCCCAGGCCCT
Done.