Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 2 of 22
Found at i:615003 original size:64 final size:64
Alignment explanation
Indices: 614917--615042 Score: 150
Period size: 64 Copynumber: 2.0 Consensus size: 64
614907 CACTCTGGAA
* * * *
614917 TTCCCAATTTCCTCCAACGGG-CCTTGTTTTGGCCCAA-TAGAATTAATATGTGGAAAGCCCAAT
1 TTCCCAATTTCCTCCAACGGGCCCCT-ATTTGGCCCAATTA-AATCAATATATGGAAAGCCCAAT
614980 C
64 C
* *
614981 TTCCC-ATTTTCTACCAACGGGCCCCTATTTGGCCCAATTAAGTCAATATATGGAAAGCCCAA
1 TTCCCAATTTCCT-CCAACGGGCCCCTATTTGGCCCAATTAAATCAATATATGGAAAGCCCAA
615043 CCTAGTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
63 6 0.11
64 42 0.79
65 5 0.09
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (64 bp):
TTCCCAATTTCCTCCAACGGGCCCCTATTTGGCCCAATTAAATCAATATATGGAAAGCCCAATC
Found at i:617297 original size:80 final size:81
Alignment explanation
Indices: 617178--617337 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 81
617168 TATTGCACCT
* * *
617178 TAACTACGAAACCAACCCTGAATTTATCACTTATATTTGTTCCTTC-AGGATGGTGACAATGCTG
1 TAACTACCAAACCAACACTGAATCTATCACTTATATTTGTTCCTTCAAGGATGGTGACAATGCTG
617242 ATATTTGATCAAGTTA
66 ATATTTGATCAAGTTA
* * *
617258 TAACTACCAAACCAACAGTGAATCTATCACTTATTTTTGTTCCTTCAAGGATGGTGAGAATGCTG
1 TAACTACCAAACCAACACTGAATCTATCACTTATATTTGTTCCTTCAAGGATGGTGACAATGCTG
617323 ATATTTGATCAAGTT
66 ATATTTGATCAAGTT
617338 TGCCAATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 41 0.56
81 32 0.44
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (81 bp):
TAACTACCAAACCAACACTGAATCTATCACTTATATTTGTTCCTTCAAGGATGGTGACAATGCTG
ATATTTGATCAAGTTA
Found at i:619401 original size:2 final size:2
Alignment explanation
Indices: 619394--619421 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
619384 TAAAATATTC
619394 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
619422 CAACAATGCA
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:622437 original size:120 final size:121
Alignment explanation
Indices: 622271--622492 Score: 324
Period size: 120 Copynumber: 1.8 Consensus size: 121
622261 ACATTTTTCC
* * *
622271 TTTTTTAATCTTTTAATTTTATTTTTATTAAAATTTTAAAATATTAATAACTTATTATTAAATTA
1 TTTTTTAATCTTTTAATTTTATTTTCATTAAAAATTTAAAACATTAATAACTTATTATTAAATTA
* *
622336 GTAGTACGATTTTT-TATTTCAATTTCTTTTTA-TTTTGCTTCTATTTGTATTTGTA
66 GTAATA-GATTTTTCCATTTCAATTTCTTTTTACTTTTGCTTCTATTTGTATTTGTA
*
622391 TTTTTTAATCTTTTAATTTTTATTTTCATTAAAAATTT-AAACATTAATAATTTATTATTAAATT
1 TTTTTTAATCTTTTAA-TTTTATTTTCATTAAAAATTTAAAACATTAATAACTTATTATTAAATT
* * *
622455 ATTAATATATTTTTCCATTTTAATTTCTTTTTACTTTT
65 AGTAATAGATTTTTCCATTTCAATTTCTTTTTACTTTT
622493 TCTTATTTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
119 6 0.07
120 61 0.68
121 23 0.26
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (121 bp):
TTTTTTAATCTTTTAATTTTATTTTCATTAAAAATTTAAAACATTAATAACTTATTATTAAATTA
GTAATAGATTTTTCCATTTCAATTTCTTTTTACTTTTGCTTCTATTTGTATTTGTA
Found at i:625542 original size:16 final size:16
Alignment explanation
Indices: 625501--625571 Score: 58
Period size: 15 Copynumber: 4.6 Consensus size: 16
625491 TAAGTTGAAC
* *
625501 TTTTGTTTTGTTA-TA
1 TTTTATTTTATTATTA
* *
625516 TTTGATGTTATTATTA
1 TTTTATTTTATTATTA
*
625532 TTTTATTTTATTATAA
1 TTTTATTTTATTATTA
* *
625548 TTAT-TTTTATAATTA
1 TTTTATTTTATTATTA
625563 -TTTATTTTA
1 TTTTATTTTA
625572 AACTTAAATA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
14 2 0.05
15 23 0.53
16 18 0.42
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTATTTTATTATTA
Found at i:678979 original size:22 final size:23
Alignment explanation
Indices: 678943--678990 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
678933 CTACAACTTC
* *
678943 ATTTTCACGGTAAATT-CTTTTT
1 ATTTTCACGGAAAATTCCCTTTT
*
678965 ATTTTCTCGGAAAATTCCCTTTT
1 ATTTTCACGGAAAATTCCCTTTT
678988 ATT
1 ATT
678991 AAAGTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (23 bp):
ATTTTCACGGAAAATTCCCTTTT
Found at i:683415 original size:27 final size:27
Alignment explanation
Indices: 683385--683437 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
683375 AATTAAATAA
683385 TATATAAATACTTGTTA-AATTGATATT
1 TATATAAA-ACTTGTTATAATTGATATT
* *
683412 TATATAAAATTTTTTATAATTGATAT
1 TATATAAAACTTGTTATAATTGATAT
683438 ATATTCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (27 bp):
TATATAAAACTTGTTATAATTGATATT
Found at i:690810 original size:17 final size:18
Alignment explanation
Indices: 690788--690821 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
690778 AATACCTCGT
690788 TGTGTTG-ATGTTTAGTC
1 TGTGTTGCATGTTTAGTC
690805 TGTGTTGCATGTTTAGT
1 TGTGTTGCATGTTTAGT
690822 TTTCTTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.12, C:0.06, G:0.29, T:0.53
Consensus pattern (18 bp):
TGTGTTGCATGTTTAGTC
Found at i:695583 original size:14 final size:14
Alignment explanation
Indices: 695564--695594 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
695554 TTCCTAAGAA
695564 TGAAGGGAAGTGCT
1 TGAAGGGAAGTGCT
695578 TGAAGGGAAGTGCT
1 TGAAGGGAAGTGCT
695592 TGA
1 TGA
695595 GATCTGATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.42, T:0.23
Consensus pattern (14 bp):
TGAAGGGAAGTGCT
Found at i:714482 original size:30 final size:29
Alignment explanation
Indices: 714447--714527 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
714437 TGTAATAAAA
714447 ATTTTTTTAACATAGTGTGTAACAATAAT
1 ATTTTTTTAACATAGTGTGTAACAATAAT
714476 ATTTTTTTAACATGAG-GTGTAACAATAAT
1 ATTTTTTTAACAT-AGTGTGTAACAATAAT
* *
714505 ATTTTTTTCAATATCGTGTGTAA
1 ATTTTTTT-AACATAGTGTGTAA
714528 GATATTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 35 0.74
30 12 0.26
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
ATTTTTTTAACATAGTGTGTAACAATAAT
Found at i:714569 original size:55 final size:55
Alignment explanation
Indices: 714479--714619 Score: 171
Period size: 55 Copynumber: 2.6 Consensus size: 55
714469 CAATAATATT
* * *
714479 TTTTTA-ACATGAGGTGTAACAATAATA-TTTTTTTCAATATCG-TGTGTAAGATA
1 TTTTTATACATGACGTGTAACAATAATATTTTTTTTCAATAT-GACGTGTAACATA
* * *
714532 TTTTTATACATGACGTATAATAATAATATTTTTTTTCAATATGACGTGTAACTTA
1 TTTTTATACATGACGTGTAACAATAATATTTTTTTTCAATATGACGTGTAACATA
* * *
714587 TTTTTATATATAACATGTAACAATAATATTTTT
1 TTTTTATACATGACGTGTAACAATAATATTTTT
714620 CTTAAACATG
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
53 6 0.08
54 19 0.26
55 49 0.66
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (55 bp):
TTTTTATACATGACGTGTAACAATAATATTTTTTTTCAATATGACGTGTAACATA
Found at i:716419 original size:16 final size:16
Alignment explanation
Indices: 716398--716433 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
716388 ATATTAATAT
716398 ATAAAT-TATTTTTTTG
1 ATAAATCTA-TTTTTTG
716414 ATAAATCTATTTTTTG
1 ATAAATCTATTTTTTG
716430 ATAA
1 ATAA
716434 TATGTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (16 bp):
ATAAATCTATTTTTTG
Found at i:722387 original size:15 final size:16
Alignment explanation
Indices: 722356--722398 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
722346 TTATTTTGTG
722356 TTAACATTATAAAAATTA
1 TTAAC-TTAT-AAAATTA
722374 -TAACTTATAAAATTA
1 TTAACTTATAAAATTA
722389 TTAA-TTATAA
1 TTAACTTATAA
722399 TATATATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAACTTATAAAATTA
Found at i:723202 original size:9 final size:9
Alignment explanation
Indices: 723186--723215 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
723176 TAATTAAGGA
723186 TAAATTAAT
1 TAAATTAAT
*
723195 TTAATTAAT
1 TAAATTAAT
723204 TAAATTAAT
1 TAAATTAAT
723213 TAA
1 TAA
723216 TAAAATTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TAAATTAAT
Found at i:723206 original size:13 final size:13
Alignment explanation
Indices: 723188--723223 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
723178 ATTAAGGATA
*
723188 AATTAATTTAATT
1 AATTAAATTAATT
723201 AATTAAATTAATT
1 AATTAAATTAATT
*
723214 AATAAAATTA
1 AATTAAATTA
723224 TGATTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTAAATTAATT
Found at i:730057 original size:336 final size:333
Alignment explanation
Indices: 729543--730590 Score: 1028
Period size: 336 Copynumber: 3.1 Consensus size: 333
729533 TATTTTGTAT
* * * *
729543 TAATATTATAAAATTATTAATTATAGTATATATACCATTGTTTATATAAATTTATAATATATAAA
1 TAAT-TTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAA
* ** * * * * * *
729608 CTTAAAGAGAGCTTTTGAGATTTGACTATGTTTGGAATTTAACTTTTTTTTTTAA-TTTCATAAA
65 CCTAAAGAGAAATTGTGA-AATAGA-TAT-TTTGAAACTT-ACTTATTTTTTTAATTTTCAT-AA
* * *
729672 ATTAAAGACAAATACATATAGTTAATTAAATTAATTATGAAACTATAATTATTAATTAACTTGTA
125 ATTAAAGACAAAT-CATATAATTAATTAAATTAATTATAAAATTATAATTATTAATTAACTTGTA
* * *
729737 ATATCTTTTAATATATATAGTTGATATATTGTGTTAATTTATAAGAAATATAATT-CTTATTATA
189 ATGTCTTTTAATATATATACTTTATATATT-TGTTAATTTATAAGAAATATAATTACTTATTATA
* *
729801 CATATACTAAAATA-TTTTA-ATATATATTTTAAATATAAGCATATTTATTTTCTATTTTATGTT
253 CATATATTAAAATACTTTTATATATATATTTTAAATATAAACATATTTATTTTCTATTTTATGTT
*
729864 AATATTAAAAAAATTA
318 AACATTAAAAAAATTA
* * *
729880 TAATTTATAAAATTATTAATTATAATATATATACTTTTATTTTTATATACTTATAATATATAAAC
1 TAATTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAAC
* *
729945 CTAAAGAAAAATTGTGAACATAGAATAGTTTTGAAACCTACTTATTTTTTTAATTTTCAGT-AAT
66 CTAAAGAGAAATTGTGAA-ATAG-ATA-TTTTGAAACTTACTTATTTTTTTAATTTTCA-TAAAT
* *
730009 TAAAGACAAACTCATATAATTAATTAAATTAATTCATAAAATTATAATTATTAATTAACATATAA
127 TAAAGACAAA-TCATATAATTAATTAAATTAATT-ATAAAATTATAATTATTAATTAACTTGTAA
* ** * *
730074 TGTCTTTAAATATATATATACTTTATATATATTAAGTTCCTTTTTAAGGAATATAATTAC-TATT
190 TGTCTTT-TA-ATATATATACTTTATATAT-TT--GTTAATTTATAAGAAATATAATTACTTATT
* ***********
730138 ATATATATATTAAAATACTTTTAGTATATATATATACTTTAAATATANNNNNNNNNNCTTTCTAT
250 ATACATATATTAAAATAC-TTT--TATATATATAT--TTTAAATATAAACATATTTATTTTCTAT
* * *
730203 TTTGTGTTAACATTACAAAAAGTA
310 TTTATGTTAACATTAAAAAAATTA
* * * **
730227 TAACTTATAAAATTATTAATTACAATATATATACCTTTATTTATATACACTTATAATATATAAGT
1 TAATTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAAC
* * *
730292 CTAAAGGGAAGTTGT---A-AG--A-TTTGAAACTTAGTTATTTTTTTTAATTTT-ATAAATTAA
66 CTAAAGAGAAATTGTGAAATAGATATTTTGAAACTTACTTA-TTTTTTTAATTTTCATAAATTAA
* * *
730349 GGATAAATTTATATAATTAATTAAATTAATTAATAAAATTATAATTATT-ATTAACTTGTAATGT
130 AGACAAA-TCATATAATTAATTAAATTAATT-ATAAAATTATAATTATTAATTAACTTGTAATGT
* *
730413 ATTTTAATATATATACTTTATATACATTATGTTTATTTATAAGAAATATAATTACTATTTTATAT
193 CTTTTAATATATATACTTTATAT--ATT-TGTTAATTTATAAGAAATATAATTAC----TTAT-T
* * *
730478 ATACTAAAATATTAAAATACTTTTAGTATATATACACTTTAAAAATAAACATATTTATTTTCTAT
250 ATAC--ATATATTAAAATACTTTTA-TATATAT--ATTTTAAATATAAACATATTTATTTTCTAT
* *
730543 TTTTTGTTAACATTATAAAAATTA
310 TTTATGTTAACATTAAAAAAATTA
730567 TAATTTATAAAATTATTAATTATA
1 TAATTTATAAAATTATTAATTATA
730591 TTTGAGATAT
Statistics
Matches: 582, Mismatches: 93, Indels: 69
0.78 0.12 0.09
Matches are distributed among these distances:
334 38 0.07
335 50 0.09
336 135 0.23
337 72 0.12
338 31 0.05
339 7 0.01
340 108 0.19
341 4 0.01
342 19 0.03
343 1 0.00
344 2 0.00
345 8 0.01
347 107 0.18
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (333 bp):
TAATTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAAC
CTAAAGAGAAATTGTGAAATAGATATTTTGAAACTTACTTATTTTTTTAATTTTCATAAATTAAA
GACAAATCATATAATTAATTAAATTAATTATAAAATTATAATTATTAATTAACTTGTAATGTCTT
TTAATATATATACTTTATATATTTGTTAATTTATAAGAAATATAATTACTTATTATACATATATT
AAAATACTTTTATATATATATTTTAAATATAAACATATTTATTTTCTATTTTATGTTAACATTAA
AAAAATTA
Found at i:730256 original size:347 final size:324
Alignment explanation
Indices: 729649--730488 Score: 827
Period size: 347 Copynumber: 2.5 Consensus size: 324
729639 TTGGAATTTA
* * *
729649 ACTT-TTTTTTTTAATTTCATAAAATTAAAGACAAA-TACATATAGTTAATTAAATTAATT-ATG
1 ACTTATTTTTTTTAATTTTAT-AAATTAAAGACAAACT-CATATAATTAATTAAATTAATTAATA
* * * * * * * * ** *
729711 AAACTATAATTATTAATTAACTTGTAATATCTTTTAATATATATAGTTGATAT--ATTGTGTTAA
64 AAATTATAATTATT-ATTAACATATAATGTATTTAAATATATATACTTTATATACATTAAGTTCA
* * * * *
729774 TTTATAAGAAATATAATT-CTTATTATACATATACTAAAATA-TTTTAATATATAT-TTTAAATA
128 TTTATAAGAAATATAATTAC-TATTATATATATACTAAAATACTTTTAGTATATATATAT-ACTT
* * * *
729836 TAAGCATATTTATTTTCTATTTTATGTTAATATTAAAAAAATTATAATTTATAAAATTATTAATT
191 TAA--ATA--TACTTTCTATTTTATGTTAACATTAAAAAAAGTATAACTTATAAAATTATTAATT
* * * *
729901 ATAATATATATACTTTTATTTTTATATACTTATAATATATAAACCTAAAGAAAAATTGTGAACAT
252 ACAATATATATACCTTTATTTATATACACTTATAATATATAAACCTAAAGAAAAATTGT----A-
729966 AGAATAGTTTTGAAACCT
312 AG---A--TTTGAAACCT
*
729984 ACTTA-TTTTTTTAATTTTCAGT-AATTAAAGACAAACTCATATAATTAATTAAATTAATTCATA
1 ACTTATTTTTTTTAATTTT-A-TAAATTAAAGACAAACTCATATAATTAATTAAATTAATTAATA
* *
730047 AAATTATAATTATTAATTAACATATAATGTCTTTAAATATATATATACTTTATATATATTAAGTT
64 AAATTATAATTATT-ATTAACATATAATGTATTT-AA-ATATATATACTTTATATACATTAAGTT
* * * *
730112 CCTTTTTAAGGAATATAATTACTATTATATATATATTAAAATACTTTTAGTATATATATATACTT
126 CATTTATAAGAAATATAATTACTATTATATATATACTAAAATACTTTTAGTATATATATATACTT
* *
730177 TAAATATANNNNNNNNNNCTTTCTATTTTGTGTTAACATTACAAAAAGTATAACTTATAAAATTA
191 TAAATATA----------CTTTCTATTTTATGTTAACATTAAAAAAAGTATAACTTATAAAATTA
** ** *
730242 TTAATTACAATATATATACCTTTATTTATATACACTTATAATATATAAGTCTAAAGGGAAGTTGT
246 TTAATTACAATATATATACCTTTATTTATATACACTTATAATATATAAACCTAAAGAAAAATTGT
*
730307 AAGATTTGAAACTT
311 AAGATTTGAAACCT
* * * * *
730321 AGTTATTTTTTTTAATTTTATAAATTAAGGATAAATTTATATAATTAATTAAATTAATTAATAAA
1 ACTTATTTTTTTTAATTTTATAAATTAAAGACAAACTCATATAATTAATTAAATTAATTAATAAA
* * * * *
730386 ATTATAATTATTATTAACTTGTAATGTATTTTAATATATATACTTTATATACATTATGTTTATTT
66 ATTATAATTATTATTAACATATAATGTATTTAAATATATATACTTTATATACATTAAGTTCATTT
*
730451 ATAAGAAATATAATTACTATTTTATATATACTAAAATA
131 ATAAGAAATATAATTACTATTATATATATACTAAAATA
730489 TTAAAATACT
Statistics
Matches: 425, Mismatches: 56, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
334 62 0.15
335 51 0.12
336 51 0.12
337 68 0.16
338 28 0.07
339 4 0.01
340 41 0.10
341 18 0.04
342 4 0.01
343 1 0.00
347 97 0.23
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.45
Consensus pattern (324 bp):
ACTTATTTTTTTTAATTTTATAAATTAAAGACAAACTCATATAATTAATTAAATTAATTAATAAA
ATTATAATTATTATTAACATATAATGTATTTAAATATATATACTTTATATACATTAAGTTCATTT
ATAAGAAATATAATTACTATTATATATATACTAAAATACTTTTAGTATATATATATACTTTAAAT
ATACTTTCTATTTTATGTTAACATTAAAAAAAGTATAACTTATAAAATTATTAATTACAATATAT
ATACCTTTATTTATATACACTTATAATATATAAACCTAAAGAAAAATTGTAAGATTTGAAACCT
Found at i:730580 original size:15 final size:17
Alignment explanation
Indices: 730555--730587 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
730545 TTTGTTAACA
730555 TTATAAAAATTA-TAAT
1 TTATAAAAATTATTAAT
730571 TTAT-AAAATTATTAAT
1 TTATAAAAATTATTAAT
730587 T
1 T
730588 ATATTTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATAAAAATTATTAAT
Found at i:737688 original size:31 final size:31
Alignment explanation
Indices: 737631--737689 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
737621 TTATATTTTT
* *
737631 ATTTTAAATTACATAAAATTGTTTATATATC
1 ATTTTAAATCACATAAAATTGATTATATATC
*
737662 ATTTTATATCACAT-AAATATGATTATAT
1 ATTTTAAATCACATAAAAT-TGATTATAT
737690 GATTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTTTAAATCACATAAAATTGATTATATATC
Found at i:737739 original size:21 final size:22
Alignment explanation
Indices: 737714--737754 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
737704 CGAGAATATA
737714 AAATGATAAATAA-TATTTAAT
1 AAATGATAAATAATTATTTAAT
*
737735 AAATGATAATTAATTATTTA
1 AAATGATAAATAATTATTTA
737755 TTTATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATGATAAATAATTATTTAAT
Found at i:737772 original size:17 final size:17
Alignment explanation
Indices: 737750--737783 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
737740 ATAATTAATT
737750 ATTTATTT-ATTATAAAA
1 ATTTATTTGA-TATAAAA
737767 ATTTATTTGATATAAAA
1 ATTTATTTGATATAAAA
737784 TAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTATTTGATATAAAA
Found at i:746751 original size:24 final size:24
Alignment explanation
Indices: 746715--746769 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
746705 TTTAATAAAT
746715 AATTATTTAAAAAT-TGATTTATTCAA
1 AATT-TTTAAAAATAT-ATTT-TTCAA
746741 AATTTTTAAAAATATATTTTTCAA
1 AATTTTTAAAAATATATTTTTCAA
746765 AATTT
1 AATTT
746770 AATTAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.36
25 13 0.46
26 5 0.18
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
AATTTTTAAAAATATATTTTTCAA
Found at i:747817 original size:2 final size:2
Alignment explanation
Indices: 747812--747845 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
747802 CTCCCACTCA
747812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
747846 GTGTGTGTGT
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):
AT
Found at i:748564 original size:24 final size:24
Alignment explanation
Indices: 748534--748580 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
748524 TCCAATTAGA
748534 TCGATTAATTCAACTTATAATTAC
1 TCGATTAATTCAACTTATAATTAC
*
748558 TCGATTAATTCAACTTGTAATTA
1 TCGATTAATTCAACTTATAATTA
748581 TATTAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (24 bp):
TCGATTAATTCAACTTATAATTAC
Found at i:766060 original size:7 final size:7
Alignment explanation
Indices: 766048--766079 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
766038 AAAACTACTG
766048 GATGACA
1 GATGACA
766055 GATGACA
1 GATGACA
766062 GATGACA
1 GATGACA
766069 GATGACA
1 GATGACA
766076 GATG
1 GATG
766080 GCTTCAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (7 bp):
GATGACA
Found at i:770224 original size:22 final size:22
Alignment explanation
Indices: 770196--770246 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
770186 GGAACATTGA
770196 TTCAACTAATAATAATGATAAT
1 TTCAACTAATAATAATGATAAT
* *
770218 TTCAACTAATATTAATGATGAT
1 TTCAACTAATAATAATGATAAT
770240 TTCAACT
1 TTCAACT
770247 GTAATTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (22 bp):
TTCAACTAATAATAATGATAAT
Found at i:782362 original size:11 final size:12
Alignment explanation
Indices: 782338--782370 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
782328 TAAATTTTAA
782338 TTTTATACATATT
1 TTTTATA-ATATT
782351 TTTTATAA-ATT
1 TTTTATAATATT
782362 TTTTATAAT
1 TTTTATAAT
782371 TAATATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 1 0.05
13 7 0.37
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTATAATATT
Found at i:782826 original size:26 final size:26
Alignment explanation
Indices: 782796--782859 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
782786 TATGTCACCA
* *
782796 ATTTATATTTTTAATTTAAAAAATA-T
1 ATTTATATTATTAA-ATAAAAAATACT
782822 ATTTATATCTATTAAATAAAAAATACTT
1 ATTTATAT-TATTAAATAAAAAATAC-T
782850 ATTTATATTA
1 ATTTATATTA
782860 ATATAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 17 0.52
27 7 0.21
28 9 0.27
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTATATTATTAAATAAAAAATACT
Found at i:782851 original size:24 final size:26
Alignment explanation
Indices: 782814--782867 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
782804 TTTTAATTTA
* *
782814 AAAAATATATTTATATCTATTAA-AT
1 AAAAATATACTTATATATATTAATAT
*
782839 AAAAA-ATACTTATTTATATTAATAT
1 AAAAATATACTTATATATATTAATAT
782864 AAAA
1 AAAA
782868 TTTATAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAAATATACTTATATATATTAATAT
Found at i:793116 original size:11 final size:13
Alignment explanation
Indices: 793086--793118 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
793076 TTTTTATTTA
793086 CCTTTTTCACCCT
1 CCTTTTTCACCCT
793099 CCTTTTTC-CCCT
1 CCTTTTTCACCCT
793111 -CTTTTTCA
1 CCTTTTTCA
793119 TCTTTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.37
12 4 0.21
13 8 0.42
ACGTcount: A:0.06, C:0.42, G:0.00, T:0.52
Consensus pattern (13 bp):
CCTTTTTCACCCT
Found at i:796820 original size:45 final size:45
Alignment explanation
Indices: 796757--796931 Score: 217
Period size: 45 Copynumber: 3.9 Consensus size: 45
796747 TTAATAAAAT
* * * *** * * *
796757 TACACGTTATGTACAAAAATATGTTACACGTTATGGTTAGGTTGT
1 TACACATTATGTACAAAAACATGATACACACCATAGTTAAGTTGA
* *
796802 TACACTTTATATACAAAAACATG-TGACACACCATAGTTAAGTTGA
1 TACACATTATGTACAAAAACATGAT-ACACACCATAGTTAAGTTGA
796847 TACACATTATGTACAAAAACATGATACACACCATAGTTAAGTTGA
1 TACACATTATGTACAAAAACATGATACACACCATAGTTAAGTTGA
* *
796892 TACACATTATGTACAAAAATATGATACACACTATAGTTAA
1 TACACATTATGTACAAAAACATGATACACACCATAGTTAA
796932 ATTGTTATAC
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
44 1 0.01
45 113 0.98
46 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (45 bp):
TACACATTATGTACAAAAACATGATACACACCATAGTTAAGTTGA
Found at i:796921 original size:24 final size:24
Alignment explanation
Indices: 796844--796921 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
796834 ATAGTTAAGT
*
796844 TGATACACATTATGTACAAAAACA
1 TGATACACATTATGTACAAAAATA
** * *
796868 TGATACACACCATAGT---TAAGT-
1 TGATACACATTAT-GTACAAAAATA
796889 TGATACACATTATGTACAAAAATA
1 TGATACACATTATGTACAAAAATA
796913 TGATACACA
1 TGATACACA
796922 CTATAGTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
20 2 0.05
21 11 0.28
22 2 0.05
23 3 0.08
24 20 0.50
25 2 0.05
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (24 bp):
TGATACACATTATGTACAAAAATA
Found at i:796955 original size:45 final size:45
Alignment explanation
Indices: 796816--796955 Score: 147
Period size: 45 Copynumber: 3.1 Consensus size: 45
796806 CTTTATATAC
* * * *
796816 AAAAACATG-TGACACACCATAGTTAAGTTGATACACATTATGTAC
1 AAAAACATGAT-ACACACCATAGTTAAATTGATACACATCATGCAA
* * * *
796861 AAAAACATGATACACACCATAGTTAAGTTGATACACATTATGTAC
1 AAAAACATGATACACACCATAGTTAAATTGATACACATCATGCAA
* * * * *
796906 AAAAATATGATACACACTATAGTTAAATTGTTATACGTCATGCAA
1 AAAAACATGATACACACCATAGTTAAATTGATACACATCATGCAA
796951 AAAAA
1 AAAAA
796956 AATATTGTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 84 0.99
46 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (45 bp):
AAAAACATGATACACACCATAGTTAAATTGATACACATCATGCAA
Found at i:796955 original size:90 final size:90
Alignment explanation
Indices: 796792--796955 Score: 195
Period size: 90 Copynumber: 1.8 Consensus size: 90
796782 ACACGTTATG
* * * * *
796792 GTTAGGTTGTTACACTTTATATACAAAAACATGTGACACACCATAGTTAAGTTGATACACATTAT
1 GTTAAGTTGATACACATTATATACAAAAACATGTGACACACCATAGTTAAATTGATACACATCAT
* *
796857 GTACAAAAACATGATACACACCATA
66 GCAAAAAAACATGATACACACCATA
* * * * * *
796882 GTTAAGTTGATACACATTATGTACAAAAATATGAT-ACACACTATAGTTAAATTGTTATACGTCA
1 GTTAAGTTGATACACATTATATACAAAAACATG-TGACACACCATAGTTAAATTGATACACATCA
796946 TGCAAAAAAA
65 TGCAAAAAAA
796956 AATATTGTTA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
90 59 0.98
91 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (90 bp):
GTTAAGTTGATACACATTATATACAAAAACATGTGACACACCATAGTTAAATTGATACACATCAT
GCAAAAAAACATGATACACACCATA
Found at i:797652 original size:10 final size:10
Alignment explanation
Indices: 797637--797667 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
797627 TTTATCAAGT
797637 TATAATTAAA
1 TATAATTAAA
797647 TATAATTAAA
1 TATAATTAAA
*
797657 AATAATTAAA
1 TATAATTAAA
797667 T
1 T
797668 TTATTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TATAATTAAA
Found at i:805080 original size:30 final size:30
Alignment explanation
Indices: 805046--805138 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
805036 TCCAATTAGC
*
805046 CTTTTCAAAATCGATTTCACTTTTTTTTTT
1 CTTTTCAAAATCGATTTCTCTTTTTTTTTT
* * *
805076 CTTTTCCAAAA-CCAGTTTCTCTTTCTGTTTT
1 CTTTT-CAAAATCGA-TTTCTCTTTTTTTTTT
* * *
805107 GTTTTGAAAATCGATGTCTCTTTTTCTTTTT
1 CTTTTCAAAATCGATTTCTCTTTTT-TTTTT
805138 C
1 C
805139 ATTGCGTATA
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
30 20 0.42
31 28 0.58
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (30 bp):
CTTTTCAAAATCGATTTCTCTTTTTTTTTT
Found at i:806790 original size:22 final size:22
Alignment explanation
Indices: 806731--806791 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 22
806721 AATTAAATAA
806731 ATTTTATATTTAATAATTAATTATT
1 ATTTTATA--TAAT-ATTAATTATT
* *
806756 A-TTTATTAAAATATTATTTATT
1 ATTTTA-TATAATATTAATTATT
806778 ATTTTATATAATAT
1 ATTTTATATAATAT
806792 GAGATTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 17 0.55
23 7 0.23
24 4 0.13
25 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTATATAATATTAATTATT
Found at i:811448 original size:138 final size:138
Alignment explanation
Indices: 811195--811468 Score: 395
Period size: 138 Copynumber: 2.0 Consensus size: 138
811185 CCTCATCGAA
* * *
811195 GGCAATTTTCTTGAGTTTTCTAAAGATATGTTTCATATTAGTTAACAAAGAGATTCTGACTAAAT
1 GGCAATTTTCTTGAGTTTTCTAAAGATATGGTTCATATTAGTTAACAAAGACATTCTAACTAAAT
* *
811260 CTGATCAAGAAAGCCTGTCACTTGATGGATACAAGACAACCACGGCAGATGAACAGATTTTCAAG
66 CTGATCAAGAAAGCCTATCACTTGATGGATACAAGACAACCACGGCAGATGAAAAGATTTTCAAG
811325 TAGAAGGG
131 TAGAAGGG
* * ** * *
811333 GGCACTTTTCTTGGGTTTTCTCCAGATATGGTTCATATTAGTTAGCACAGACATTCTAACTAAAT
1 GGCAATTTTCTTGAGTTTTCTAAAGATATGGTTCATATTAGTTAACAAAGACATTCTAACTAAAT
* ** * *
811398 CTGATCAAGAGAGCCTATTGCTTGATGGATCCAAGACAACCATGGCAGATGAAAAGATTTTCAAG
66 CTGATCAAGAAAGCCTATCACTTGATGGATACAAGACAACCACGGCAGATGAAAAGATTTTCAAG
*
811463 TGGAAG
131 TAGAAG
811469 TGTTCATGAG
Statistics
Matches: 119, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 119 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (138 bp):
GGCAATTTTCTTGAGTTTTCTAAAGATATGGTTCATATTAGTTAACAAAGACATTCTAACTAAAT
CTGATCAAGAAAGCCTATCACTTGATGGATACAAGACAACCACGGCAGATGAAAAGATTTTCAAG
TAGAAGGG
Found at i:820029 original size:100 final size:100
Alignment explanation
Indices: 819856--820042 Score: 277
Period size: 100 Copynumber: 1.9 Consensus size: 100
819846 ACCATTAAAA
* * * * *
819856 GCTCCAAAAAATTTAGAGACTACTGCCCTTGAACATTCCAGCTTGCTTGGCATAACAGAGGAATG
1 GCTCCAAAAAATTTACAGACAACTGCCCTTGAACATTCCAGCTTCCATGGCAAAACAGAGGAATG
819921 TGGTAAGGACTCCATATAAACATTGAGAAAGGGAT
66 TGGTAAGGACTCCATATAAACATTGAGAAAGGGAT
* ** *
819956 GCTCCAACAAAA-TTACAGACAATTGCCCTTGAACATTCTGGCTTCCATGGCAAAACAGAGGAGT
1 GCTCCAA-AAAATTTACAGACAACTGCCCTTGAACATTCCAGCTTCCATGGCAAAACAGAGGAAT
820020 GTGGTAAGGACTCCATATAAACA
65 GTGGTAAGGACTCCATATAAACA
820043 AATACCATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 73 0.95
101 4 0.05
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (100 bp):
GCTCCAAAAAATTTACAGACAACTGCCCTTGAACATTCCAGCTTCCATGGCAAAACAGAGGAATG
TGGTAAGGACTCCATATAAACATTGAGAAAGGGAT
Found at i:825076 original size:3 final size:3
Alignment explanation
Indices: 825068--825092 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
825058 TGTTTGCTTT
825068 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
825093 GAAACTGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:831392 original size:19 final size:19
Alignment explanation
Indices: 831362--831413 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
831352 GGAAGTTTGA
* *
831362 CGTGAGTGGATACGGTAAT
1 CGTGAGTAGATACGGAAAT
831381 AC-TGAGTAGATACGGAAAT
1 -CGTGAGTAGATACGGAAAT
831400 CGTGAGTAGATACG
1 CGTGAGTAGATACG
831414 TTAAACGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 1 0.03
19 27 0.93
20 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.23
Consensus pattern (19 bp):
CGTGAGTAGATACGGAAAT
Found at i:831405 original size:38 final size:38
Alignment explanation
Indices: 831362--831497 Score: 109
Period size: 38 Copynumber: 3.5 Consensus size: 38
831352 GGAAGTTTGA
*
831362 CGTGAGTGGATACGGTAATACTGAGTAGATACGGAAAT
1 CGTGAGTAGATACGGTAATACTGAGTAGATACGGAAAT
*
831400 CGTGAGTAGATACGTTAA-AC-GA-TCA-ATTAACGGTCAAAAT
1 CGTGAGTAGATACGGTAATACTGAGT-AGA-T-ACGG---AAAT
* ** *
831440 AACGTGAGTGGATACGGTAATGGTGAGTAGATACCGAAAT
1 --CGTGAGTAGATACGGTAATACTGAGTAGATACGGAAAT
*
831480 CGGGAGTAGATACGGTAA
1 CGTGAGTAGATACGGTAA
831498 ACGATCAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
35 2 0.03
36 4 0.05
37 6 0.08
38 32 0.42
40 8 0.10
42 16 0.21
43 3 0.04
44 4 0.05
45 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (38 bp):
CGTGAGTAGATACGGTAATACTGAGTAGATACGGAAAT
Found at i:831467 original size:19 final size:20
Alignment explanation
Indices: 831443--831497 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
831433 TCAAAATAAC
*
831443 GTGAGTGGATACGGTAAT-G
1 GTGAGTAGATACGGTAATCG
* *
831462 GTGAGTAGATACCGAAATCG
1 GTGAGTAGATACGGTAATCG
831482 G-GAGTAGATACGGTAA
1 GTGAGTAGATACGGTAA
831498 ACGATCAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 28 0.93
20 2 0.07
ACGTcount: A:0.33, C:0.09, G:0.36, T:0.22
Consensus pattern (20 bp):
GTGAGTAGATACGGTAATCG
Found at i:831479 original size:80 final size:80
Alignment explanation
Indices: 831361--831553 Score: 323
Period size: 80 Copynumber: 2.4 Consensus size: 80
831351 CGGAAGTTTG
* * * *
831361 ACGTGAGTGGATACGGTAATACTGAGTAGATACGGAAATCGTGAGTAGATACGTTAAACGATCAA
1 ACGTGAGTGGATACGGTAATAGTGAGTAGATACCGAAATCGGGAGTAGATACGGTAAACGATCAA
831426 TTAACGGTCAAAATA
66 TTAACGGTCAAAATA
*
831441 ACGTGAGTGGATACGGTAATGGTGAGTAGATACCGAAATCGGGAGTAGATACGGTAAACGATCAA
1 ACGTGAGTGGATACGGTAATAGTGAGTAGATACCGAAATCGGGAGTAGATACGGTAAACGATCAA
*
831506 TTAACTGTCAAAATA
66 TTAACGGTCAAAATA
*
831521 ACGTGAGTGGATACGGTAATCGTGAGTAGATAC
1 ACGTGAGTGGATACGGTAATAGTGAGTAGATAC
831554 GGTGAACGGT
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 106 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.23
Consensus pattern (80 bp):
ACGTGAGTGGATACGGTAATAGTGAGTAGATACCGAAATCGGGAGTAGATACGGTAAACGATCAA
TTAACGGTCAAAATA
Found at i:838721 original size:31 final size:29
Alignment explanation
Indices: 838683--838791 Score: 106
Period size: 29 Copynumber: 3.9 Consensus size: 29
838673 ATAATATTAT
838683 AATTAAAATAAATATATAATATAAGAATAAA
1 AATTAAAATAAATATATAATATAA-AA-AAA
*
838714 AATTAAAATAAA-ATA-AA-AT-ATAAAA
1 AATTAAAATAAATATATAATATAAAAAAA
** *
838739 AATT--AATATTTATATAATATAATAAACA
1 AATTAAAATAAATATATAATATAA-AAAAA
838767 AATTAAAAT-AATATATAATATAAAA
1 AATTAAAATAAATATATAATATAAAA
838792 TATATTAAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
23 4 0.06
24 3 0.05
25 9 0.14
26 3 0.05
27 2 0.03
28 11 0.17
29 14 0.22
30 6 0.09
31 12 0.19
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (29 bp):
AATTAAAATAAATATATAATATAAAAAAA
Found at i:838736 original size:24 final size:24
Alignment explanation
Indices: 838680--839127 Score: 82
Period size: 27 Copynumber: 17.4 Consensus size: 24
838670 TTTATAATAT
*
838680 TATAAT-T-AAAA-TAAATATATAA
1 TATAATATAAAAATTAAA-ATAAAA
*
838702 TATAAGAATAAAAATTAAAATAAAA
1 TATAA-TATAAAAATTAAAATAAAA
* *
838727 TAAAATATAAAAAATTAATATTTATATAA
1 TATAATAT-AAAAATTAA-A---ATAAAA
*
838756 TATAATA-AACAAATTAAAATAATA
1 TATAATATAA-AAATTAAAATAAAA
* *
838780 TATAATAT-AAAA-T-ATATTAAA
1 TATAATATAAAAATTAAAATAAAA
* * *
838801 GA-AATGAAAAAAATATAAAATTATAA
1 TATAAT-ATAAAAAT-TAAAA-TAAAA
*
838827 TAATAA-ATAAAAA-TAAAAT-ATA
1 T-ATAATATAAAAATTAAAATAAAA
* * * **
838849 TGACATTAAAAATATATTTAAAATATGA
1 T-ATAATATAAA-A-A-TTAAAATAAAA
* *
838877 TATTATATAAAAA-TATAATATAAA
1 TATAATATAAAAATTAAAATA-AAA
*
838901 TATAATATATTAAAAAATAAAATATAAA
1 TAT-A-ATA-TAAAAATTAAAATA-AAA
* *
838929 -ATATTATAATATAATAAAAATAAAA
1 TATAATATAA-A-AATTAAAATAAAA
* ** *
838954 TATATGACATTAAAAATATTTAA-GAAA
1 TATA--ATA-TAAAAAT-TAAAATAAAA
*
838981 TGATATTATATAAAATTAATAATATAAA
1 T-ATAATATA-AAAATTAA-AATA-AAA
*
839009 TATAAATATATAAAAATAAAATATAAA
1 TAT-AATATA-AAAATTAAAATA-AAA
* *
839036 -ATATTTAATAATAATTAAAAATAAAA
1 TATA-AT-ATAAAAATT-AAAATAAAA
**
839062 TATATGATATTAAAAA-TATATTTAAAA
1 TATA--ATA-TAAAAATTA-AAATAAAA
839089 TGATATTATATAAAAATTAATAATAAAAAA
1 T-ATA--ATATAAAAATTAA-AAT--AAAA
839119 TATAATATA
1 TATAATATA
839128 TTAAACTTAT
Statistics
Matches: 309, Mismatches: 62, Indels: 105
0.65 0.13 0.22
Matches are distributed among these distances:
20 3 0.01
21 7 0.02
22 14 0.05
23 14 0.05
24 29 0.09
25 36 0.12
26 49 0.16
27 74 0.24
28 61 0.20
29 17 0.06
30 5 0.02
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (24 bp):
TATAATATAAAAATTAAAATAAAA
Found at i:838762 original size:29 final size:29
Alignment explanation
Indices: 838683--838789 Score: 116
Period size: 28 Copynumber: 3.8 Consensus size: 29
838673 ATAATATTAT
*
838683 AATTAAAATAAATATATAATATAAGAATAAA
1 AATTAAAAT-AATATATAATATAATAA-AAA
*
838714 AATTAAAATAA-A-ATAAAAT-AT-AAAA
1 AATTAAAATAATATATAATATAATAAAAA
* * *
838739 AATTAATAT-TTATATAATATAATAAACA
1 AATTAAAATAATATATAATATAATAAAAA
838767 AATTAAAATAATATATAATATAA
1 AATTAAAATAATATATAATATAA
838790 AATATATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
25 12 0.19
26 7 0.11
27 3 0.05
28 17 0.27
29 13 0.21
30 2 0.03
31 9 0.14
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (29 bp):
AATTAAAATAATATATAATATAATAAAAA
Found at i:838794 original size:36 final size:37
Alignment explanation
Indices: 838735--838837 Score: 104
Period size: 36 Copynumber: 2.8 Consensus size: 37
838725 AATAAAATAT
* * *
838735 AAAAAAT-TAATATTTATATAATATAATAAACAAATTA
1 AAAAAATATAA-AATTATAAAATATAATAAACAAATGA
* * * *
838772 AAATAATATATAA-TATAAAATATATTAAAGAAATGA
1 AAAAAATATAAAATTATAAAATATAATAAACAAATGA
838808 AAAAAATATAAAATTATAATAATA-AATAAA
1 AAAAAATATAAAATTATAA-AATATAATAAA
838838 AATAAAATAT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
36 30 0.57
37 17 0.32
38 6 0.11
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (37 bp):
AAAAAATATAAAATTATAAAATATAATAAACAAATGA
Found at i:838857 original size:58 final size:53
Alignment explanation
Indices: 838809--839077 Score: 200
Period size: 53 Copynumber: 5.0 Consensus size: 53
838799 AAGAAATGAA
838809 AAAAATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATAT
1 AAAAATATAAAATTAT-ATAATAAATAAAAATAAAATATATGACATTAAAAA-AT
* * * *
838864 ATTTAAAATATGATATTATATAA-AAAT-ATAATATAAATATAAT-ATATTAAAAAAT
1 A---AAAATATAAAATTATATAATAAATAAAAATA-AAATAT-ATGACATTAAAAAAT
838919 -AAAATATAAAA-TATTATAATATAATAAAAATAAAATATATGACATTAAAAATATTT
1 AAAAATATAAAATTA-TATAATA-AATAAAAATAAAATATATGACATTAAAAA-A--T
* * * * *
838975 AAGAA-ATGATATTATATAA-AATTAATAATATAAATATA--A-ATATATAAAAAT
1 AAAAATATAAAATTATATAATAAATAAAAATA-AAATATATGACAT-TA-AAAAAT
* * *
839026 -AAAATATAAAATATTTAATAATAATTAAAAATAAAATATATGATATTAAAAA
1 AAAAATATAAAAT-TAT-ATAATAAATAAAAATAAAATATATGACATTAAAAA
839078 TATATTTAAA
Statistics
Matches: 171, Mismatches: 18, Indels: 51
0.71 0.08 0.21
Matches are distributed among these distances:
50 5 0.03
51 20 0.12
52 7 0.04
53 33 0.19
54 32 0.19
55 19 0.11
56 31 0.18
57 11 0.06
58 13 0.08
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (53 bp):
AAAAATATAAAATTATATAATAAATAAAAATAAAATATATGACATTAAAAAAT
Found at i:838891 original size:29 final size:28
Alignment explanation
Indices: 838771--839132 Score: 139
Period size: 29 Copynumber: 13.1 Consensus size: 28
838761 TAAACAAATT
* *
838771 AAAATA-ATATATAATATAAAATATATTA
1 AAAATATATATAAAATATAATATATA-TA
* *
838799 AAGAA-ATGA-AAAAAATATAAAATTATAATA
1 AA-AATAT-ATATAAAATATAATA-TAT-ATA
* * *
838829 ATAAATAAAAATAAAATAT-ATGACAT-TA
1 A-AAATATATATAAAATATAAT-ATATATA
* *
838857 AAAATATATTTAAAATATGATATTATATA
1 AAAATATATATAAAATATAATA-TATATA
838886 AAAATATA-ATATAAATATAATATAT-TAA
1 AAAATATATATA-AAATATAATATATAT-A
* *
838914 AAAATAAAATATAAAATATTATA-ATATA
1 AAAAT-ATATATAAAATATAATATATATA
* *
838942 ATAA-A-A-ATAAAATAT-ATGACAT-TA
1 AAAATATATATAAAATATAAT-ATATATA
*
838966 AAAATAT-T-TAAGAA-ATGATATTATATA
1 AAAATATATATAA-AATATAATA-TATATA
*
838993 AAATTA-ATAATATAAATATAA-ATATATA
1 AAAATATAT-ATA-AAATATAATATATATA
*
839021 AAAATAAAATATAAAATAT--T-TA-ATA
1 AAAAT-ATATATAAAATATAATATATATA
* * *
839046 ATAATTAAAAATAAAATAT-ATGATAT-TA
1 A-AAATATATATAAAATATAAT-ATATATA
*
839074 AAAATATATTTAAAATGAT-AT-TATATA
1 AAAATATATATAAAAT-ATAATATATATA
*
839101 AAAATTAATAATAAAAAATATAATATAT-TA
1 AAAA-T-AT-ATATAAAATATAATATATATA
839131 AA
1 AA
839133 CTTATATTTT
Statistics
Matches: 260, Mismatches: 28, Indels: 90
0.69 0.07 0.24
Matches are distributed among these distances:
23 2 0.01
24 15 0.06
25 26 0.10
26 16 0.06
27 41 0.16
28 53 0.20
29 57 0.22
30 35 0.13
31 15 0.06
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAATATATATAAAATATAATATATATA
Found at i:838896 original size:5 final size:5
Alignment explanation
Indices: 838870--838944 Score: 52
Period size: 5 Copynumber: 15.8 Consensus size: 5
838860 ATATATTTAA
* * *
838870 AATAT GATAT TATAT AA-A- AATAT AATAT AAATAT AATAT -AT-T AA-AA
1 AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT
* * *
838916 AATAA AATAT AAAAT ATTAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATA
838945 AAAATAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
3 3 0.05
4 7 0.13
5 40 0.73
6 5 0.09
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:838925 original size:22 final size:25
Alignment explanation
Indices: 838888--838958 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 25
838878 ATTATATAAA
838888 AATATAATATAAATATAATATATTA-
1 AATATAATA-AAATATAATATATTAT
*
838913 AA-A-AATAAAATATAAAATATTAT
1 AATATAATAAAATATAATATATTAT
*
838936 AATATAATAAAAATAAAATATAT
1 AATATAAT-AAAATATAATATAT
838959 GACATTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 14 0.36
23 6 0.15
24 2 0.05
25 5 0.13
26 12 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
AATATAATAAAATATAATATATTAT
Found at i:838953 original size:109 final size:110
Alignment explanation
Indices: 838771--839132 Score: 501
Period size: 108 Copynumber: 3.3 Consensus size: 110
838761 TAAACAAATT
* *
838771 AAAATAAT-ATATAATATAAAATATATTAAAGAAATGAAAAAAATATAAA-ATTATAATAATAAA
1 AAAATAATAATATAA-ATATAATATATTAAA-AAAT--AAAATATA-AAATATTATAATAAT-AA
838834 TAAAAATAAAATATATGACATTAAAAATATATTTAAAATATGATATTATATA
60 TAAAAATAAAATATATGACATTAAAAATATATTTAAAA-ATGATATTATATA
838886 AAAAT-ATAATATAAATATAATATATTAAAAAATAAAATATAAAATATTATAAT-ATAATAAAAA
1 AAAATAATAATATAAATATAATATATTAAAAAATAAAATATAAAATATTATAATAATAATAAAAA
838949 TAAAATATATGACATT-AAAA-ATATTTAAGAAATGATATTATATA
66 TAAAATATATGACATTAAAAATATATTTAA-AAATGATATTATATA
*
838993 AAATTAATAATATAAATATAA-ATA-TATAAAAATAAAATATAAAATATT-TAATAATAATTAAA
1 AAAATAATAATATAAATATAATATATTA-AAAAATAAAATATAAAATATTATAATAATAA-TAAA
*
839055 AATAAAATATATGATATTAAAAATATATTT-AAAATGATATTATATA
64 AATAAAATATATGACATTAAAAATATATTTAAAAATGATATTATATA
*
839101 AAAATTAATAATAAAAAATATAATATATTAAA
1 AAAA-TAATAAT-ATAAATATAATATATTAAA
839133 CTTATATTTT
Statistics
Matches: 228, Mismatches: 6, Indels: 30
0.86 0.02 0.11
Matches are distributed among these distances:
106 6 0.03
107 53 0.23
108 60 0.26
109 36 0.16
110 20 0.09
111 20 0.09
112 2 0.01
113 4 0.02
114 16 0.07
115 11 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (110 bp):
AAAATAATAATATAAATATAATATATTAAAAAATAAAATATAAAATATTATAATAATAATAAAAA
TAAAATATATGACATTAAAAATATATTTAAAAATGATATTATATA
Found at i:839012 original size:22 final size:20
Alignment explanation
Indices: 838987--839049 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 20
838977 GAAATGATAT
838987 TATATAAAATTAATAATATAAA
1 TATA-AAAATTAATAATA-AAA
* *
839009 TATAAATATATAAAAATAAAA
1 TATAAAAAT-TAATAATAAAA
839030 TATAAAATATTTAATAATAA
1 TATAAAA-A-TTAATAATAA
839050 TTAAAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 13 0.38
22 20 0.59
23 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATAAAAATTAATAATAAAA
Found at i:839021 original size:8 final size:7
Alignment explanation
Indices: 838988--839065 Score: 69
Period size: 6 Copynumber: 11.7 Consensus size: 7
838978 AAATGATATT
838988 ATATAAA
1 ATATAAA
838995 AT-TAATA
1 ATATAA-A
839002 ATAT-AA
1 ATATAAA
839008 ATATAAA
1 ATATAAA
839015 TATATAAA
1 -ATATAAA
839023 A-ATAAA
1 ATATAAA
839029 ATATAAA
1 ATATAAA
**
839036 ATATTTA
1 ATATAAA
*
839043 ATA-ATA
1 ATATAAA
839049 AT-TAAA
1 ATATAAA
839055 A-ATAAA
1 ATATAAA
839061 ATATA
1 ATATA
839066 TGATATTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
6 26 0.44
7 25 0.42
8 8 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATATAAA
Found at i:839072 original size:32 final size:32
Alignment explanation
Indices: 839012--839089 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
839002 ATATAAATAT
839012 AAATATA-TAAAAATAAAATATAAAATATTTAA
1 AAATATATTAAAAATAAAATATAAAATA-TTAA
* **
839044 TAATA-ATTAAAAATAAAATATATGATATTAA
1 AAATATATTAAAAATAAAATATAAAATATTAA
*
839075 AAATATATTTAAAAT
1 AAATATATTAAAAAT
839090 GATATTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 9 0.23
32 30 0.77
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (32 bp):
AAATATATTAAAAATAAAATATAAAATATTAA
Found at i:839088 original size:12 final size:15
Alignment explanation
Indices: 839057--839105 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
839047 TAATTAAAAA
839057 TAAAATATATGATAT
1 TAAAATATATGATAT
839072 TAAAA-ATAT-AT-T
1 TAAAATATATGATAT
*
839084 TAAAATGATATTATAT
1 TAAAAT-ATATGATAT
*
839100 AAAAAT
1 TAAAAT
839106 TAATAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 6 0.21
13 2 0.07
14 8 0.28
15 7 0.24
16 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (15 bp):
TAAAATATATGATAT
Found at i:839305 original size:15 final size:15
Alignment explanation
Indices: 839285--839338 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
839275 TTTTCCCTGT
*
839285 AATCACATTGCTTGC
1 AATCACATTACTTGC
839300 AATCACATTACTTGC
1 AATCACATTACTTGC
* *
839315 AATCACATTACCTGT
1 AATCACATTACTTGC
839330 AATCACATT
1 AATCACATT
839339 GCATTGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:842783 original size:21 final size:19
Alignment explanation
Indices: 842746--842784 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
842736 CAACCTTTGC
*
842746 TTGTCTTTTCTTTCTTTTA
1 TTGTCTTTTCTTACTTTTA
842765 TTGTCATTTATCTTACTTTT
1 TTGTC-TTT-TCTTACTTTT
842785 TCGAGTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.69
Consensus pattern (19 bp):
TTGTCTTTTCTTACTTTTA
Found at i:845454 original size:21 final size:22
Alignment explanation
Indices: 845417--845460 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
845407 GAGAAATGTG
*
845417 TTGAATTTATCATC-TTTTCAA
1 TTGAATTTATCAACTTTTTCAA
845438 TTGAATTT-TCAAACTTTTTCAA
1 TTGAATTTATC-AACTTTTTCAA
845460 T
1 T
845461 CTACAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 10 0.50
22 8 0.40
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.52
Consensus pattern (22 bp):
TTGAATTTATCAACTTTTTCAA
Found at i:848129 original size:17 final size:17
Alignment explanation
Indices: 848109--848142 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
848099 TAAAAAATAA
848109 TTTTA-AATAAAATAAAT
1 TTTTATAAT-AAATAAAT
848126 TTTTATAATAAATAAAT
1 TTTTATAATAAATAAAT
848143 AATTAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTATAATAAATAAAT
Found at i:848137 original size:18 final size:16
Alignment explanation
Indices: 848098--848142 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
848088 AACCCGTTTG
848098 TTAAA-AAAT-AA-TT
1 TTAAATAAATAAATTT
848111 TTAAATAAAATAAATTT
1 TTAAAT-AAATAAATTT
848128 TTATAATAAATAAAT
1 TTA-AATAAATAAAT
848143 AATTAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.19
15 4 0.15
16 2 0.07
17 13 0.48
18 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATAAATAAATTT
Found at i:848322 original size:18 final size:18
Alignment explanation
Indices: 848301--848356 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
848291 TCTAAATTAA
848301 TAATAATTAATTAATTTT
1 TAATAATTAATTAATTTT
* *
848319 TAATTATTTATTTAATTTT
1 TAA-TAATTAATTAATTTT
* *
848338 AAATAA-AAATATAATTTT
1 TAATAATTAAT-TAATTTT
848356 T
1 T
848357 TAAATGATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 2 0.07
18 12 0.41
19 15 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATAATTAATTAATTTT
Found at i:861266 original size:19 final size:19
Alignment explanation
Indices: 861230--861266 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
861220 ATGATGTTTA
* *
861230 ATCATGAAAGAACGTATTT
1 ATCATGAAAAAACATATTT
861249 ATCATGAAAAAACATATT
1 ATCATGAAAAAACATATT
861267 AAAAATAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (19 bp):
ATCATGAAAAAACATATTT
Found at i:862021 original size:2 final size:2
Alignment explanation
Indices: 862014--862043 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
862004 AGCTAGAAAA
862014 AT AT AT AT AT AT AT AT AT AT AT AGT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
862044 GGATCACGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:867150 original size:2 final size:2
Alignment explanation
Indices: 867143--867171 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
867133 GTTTTAAGTT
867143 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
867172 TTAAAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:871381 original size:98 final size:98
Alignment explanation
Indices: 871257--871614 Score: 470
Period size: 98 Copynumber: 3.7 Consensus size: 98
871247 TTTTCAAAGT
* * * * * *
871257 TTTCAACGTAAATTTAAATTTGCACGTACGATATGAAAAGTATATTAATAATCTATCATAACTTA
1 TTTCAACGTGAACTTAAATTTTCACGTACAATATGAAAAGTACATTAAAAATCTATCATAACTTA
*
871322 TGATATAGACATCATTTTTTGGTTTTATTCAAA
66 TGATATAGACATTATTTTTTGGTTTTATTCAAA
* * * *
871355 TTTCAACATGAACTTAAATTTTCACGTACGATATGAAAAGTATATTAATAATCTATCATAACTTA
1 TTTCAACGTGAACTTAAATTTTCACGTACAATATGAAAAGTACATTAAAAATCTATCATAACTTA
* *
871420 TGATATAGACATTATTTTTTGTTTTTATTCAGA
66 TGATATAGACATTATTTTTTGGTTTTATTCAAA
* *
871453 TTTCAACGTGAACTTAAATTTTCACGTACAATGTGAAAAGTACATTAAAAATCTATCACAACTTA
1 TTTCAACGTGAACTTAAATTTTCACGTACAATATGAAAAGTACATTAAAAATCTATCATAACTTA
* * *
871518 TGATAT-GAACATTA-TTTTTGGTATTATTTAAT
66 TGATATAG-ACATTATTTTTTGGTTTTATTCAAA
* * * * *
871550 TTTCAACGT-ACACTTAAATTTACGCGTACAACATGAAGAGTACATTAAAAATTTATCATAACTT
1 TTTCAACGTGA-ACTTAAATTTTCACGTACAATATGAAAAGTACATTAAAAATCTATCATAACTT
871614 A
65 A
871615 CTATATGAGC
Statistics
Matches: 233, Mismatches: 25, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
96 1 0.00
97 70 0.30
98 162 0.70
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (98 bp):
TTTCAACGTGAACTTAAATTTTCACGTACAATATGAAAAGTACATTAAAAATCTATCATAACTTA
TGATATAGACATTATTTTTTGGTTTTATTCAAA
Found at i:883523 original size:3 final size:3
Alignment explanation
Indices: 883515--883550 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
883505 TCCCCTCTCC
883515 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
883551 ACAACAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:887995 original size:6 final size:7
Alignment explanation
Indices: 887979--888003 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
887969 TACACTATAC
887979 AAAATTA
1 AAAATTA
887986 AAAATTA
1 AAAATTA
887993 AAAATTA
1 AAAATTA
888000 AAAA
1 AAAA
888004 GAATCTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:889629 original size:71 final size:71
Alignment explanation
Indices: 889548--889684 Score: 265
Period size: 71 Copynumber: 1.9 Consensus size: 71
889538 TGCATACCCG
*
889548 TTTAAGAAAAAAAGATGAAATAGCTGATTTCGAATGATATGGTTAGAGAATATTGGAATAGAAAT
1 TTTAAGAAAAAAAGATGAAATAGCTGATTTCAAATGATATGGTTAGAGAATATTGGAATAGAAAT
889613 GGTTCA
66 GGTTCA
889619 TTTAAGAAAAAAAGATGAAATAGCTGATTTCAAATGATATGGTTAGAGAATATTGGAATAGAAAT
1 TTTAAGAAAAAAAGATGAAATAGCTGATTTCAAATGATATGGTTAGAGAATATTGGAATAGAAAT
889684 G
66 G
889685 TTATAGTGGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (71 bp):
TTTAAGAAAAAAAGATGAAATAGCTGATTTCAAATGATATGGTTAGAGAATATTGGAATAGAAAT
GGTTCA
Found at i:894844 original size:2 final size:2
Alignment explanation
Indices: 894837--894875 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
894827 ATTGTTTCAA
894837 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 A
894876 ACTTAATCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:897844 original size:23 final size:24
Alignment explanation
Indices: 897800--897844 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
897790 AGGAAACGAG
* *
897800 TTGGAATTAAGGATTTTTCCTTTT
1 TTGGAATGAAAGATTTTTCCTTTT
897824 TTGGAATGAAAGA-TTTTCCTT
1 TTGGAATGAAAGATTTTTCCTT
897845 GTTAAAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.49
Consensus pattern (24 bp):
TTGGAATGAAAGATTTTTCCTTTT
Found at i:900461 original size:27 final size:28
Alignment explanation
Indices: 900424--900476 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
900414 AGAAGGAGAC
* *
900424 GGAGAGAAAGGCGGGGGAGGTGGAGGGT
1 GGAGAGAAAGGCGAGGGAGATGGAGGGT
*
900452 GGAGAG-AAGGTGAGGGAGATGGAGG
1 GGAGAGAAAGGCGAGGGAGATGGAGG
900477 TACACGTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.28, C:0.02, G:0.62, T:0.08
Consensus pattern (28 bp):
GGAGAGAAAGGCGAGGGAGATGGAGGGT
Found at i:909312 original size:213 final size:213
Alignment explanation
Indices: 908945--909806 Score: 1370
Period size: 213 Copynumber: 4.0 Consensus size: 213
908935 ATGTCATTTC
* * *
908945 TGAAAATT-ACGAAATGTTTAAGCATATATAAATTCTTCTAAGGTATCCAAAACAGAGAAAGAAC
1 TGAAAATTGA-GAAATGTTTAAGCAAACATAAATTCTTCTAATGTATCCAAAACAGAGAAAGAAC
*
909009 AAGCTCCTAAATTAATTGTTCATCAGATTCGTCTCCTTCACGTC-AGGACCTTGTATCCAAACTC
65 AAGCTCCTAAATTAATTGTTCATCAGATTCGTCTCCTTCACGTCGA-AACCTTGTATCCAAACTC
* * * *
909073 CATAATAAAGTGTTCAGATCATTCGAACAAAATTACAAGTTCCAAACCTACTTTTTCTGTTTTCT
129 CACAATAAAATGTTCAGATCATTCGAACACAATTACAAGTTCCAAACCTACGTTTTCTGTTTTCT
* * *
909138 TTAATTTCTGCACTGATATA
194 TTAATTCCTGCAGTGATAAA
909158 TGAAAATTGAGAAATGTTTAAGCAAACATAAATTCTTCTAATGTATCCAAAACAGAGAAAGAACA
1 TGAAAATTGAGAAATGTTTAAGCAAACATAAATTCTTCTAATGTATCCAAAACAGAGAAAGAACA
* * *
909223 AGCTCCTAAATTAATTGTTCATCAGATTAGTCTCCTTCAAGTCGAAACCTTGTATCCAGACTCCA
66 AGCTCCTAAATTAATTGTTCATCAGATTCGTCTCCTTCACGTCGAAACCTTGTATCCAAACTCCA
* *
909288 CAATAAAATGGTCAGATCATTCGAACACAATTACAAGTTCTAAACCTACGTTTTCTGTTTTCTTT
131 CAATAAAATGTTCAGATCATTCGAACACAATTACAAGTTCCAAACCTACGTTTTCTGTTTTCTTT
*
909353 AATTTCTGCAGTGATAAA
196 AATTCCTGCAGTGATAAA
* *
909371 TGAAAATTGAGAAATGTTTAAGCAAACACAAATTGTTCTAATGTATCCAAAACAGAGAAAGAGA-
1 TGAAAATTGAGAAATGTTTAAGCAAACATAAATTCTTCTAATGTATCCAAAACAGAGAAAGA-AC
*
909435 AAGCCCCTAAATTAATTGTTCATCAGATTCGTCTCCTTCACGTCGAAACCTTGTATCCAAACTCC
65 AAGCTCCTAAATTAATTGTTCATCAGATTCGTCTCCTTCACGTCGAAACCTTGTATCCAAACTCC
* *
909500 ACAATAAAATGTTCAGATCATTCGAACACAATAACAAGTTCTAAACCTACGTTTTCTGTTTTCTT
130 ACAATAAAATGTTCAGATCATTCGAACACAATTACAAGTTCCAAACCTACGTTTTCTGTTTTCTT
909565 TAATTCCTGCAGTGATAAA
195 TAATTCCTGCAGTGATAAA
* *
909584 TGAAATTTGAGAAATGTTTAAGCAAACATAAATTCTTCTAATGTATACAAAACAGAGAAAGAACA
1 TGAAAATTGAGAAATGTTTAAGCAAACATAAATTCTTCTAATGTATCCAAAACAGAGAAAGAACA
* *
909649 AGCTCCTAAATTAATTGCTCATCAGATTCGTCTCCTTCGCGTCGAAACCTTGTATCCAAACTCCA
66 AGCTCCTAAATTAATTGTTCATCAGATTCGTCTCCTTCACGTCGAAACCTTGTATCCAAACTCCA
**
909714 CAATAAAATGTTCAGATCATTCGAACACAATTACAAGTTGTTTCCAAACCTATTTTTTCTGTTTT
131 CAATAAAATGTTCAGATCATTCGAACACAATTACAA---G-TTCCAAACCTACGTTTTCTG-TTT
*
909779 TCTTTAATTCCCGCAGTGATAAA
191 TCTTTAATTCCTGCAGTGATAAA
909802 TGAAA
1 TGAAA
909807 TTCAACGTTT
Statistics
Matches: 604, Mismatches: 36, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
212 1 0.00
213 552 0.91
214 3 0.00
216 1 0.00
217 17 0.03
218 30 0.05
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (213 bp):
TGAAAATTGAGAAATGTTTAAGCAAACATAAATTCTTCTAATGTATCCAAAACAGAGAAAGAACA
AGCTCCTAAATTAATTGTTCATCAGATTCGTCTCCTTCACGTCGAAACCTTGTATCCAAACTCCA
CAATAAAATGTTCAGATCATTCGAACACAATTACAAGTTCCAAACCTACGTTTTCTGTTTTCTTT
AATTCCTGCAGTGATAAA
Found at i:910558 original size:23 final size:20
Alignment explanation
Indices: 910532--910584 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 20
910522 TCCTTAATTT
910532 TTTTTTAATTTATATAATAATAA
1 TTTTTTAATTTA-ATAA-AA-AA
*
910555 TTTTTTAAATTAATAAAAAA
1 TTTTTTAATTTAATAAAAAA
*
910575 TATTTTAATT
1 TTTTTTAATT
910585 CTTTTATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.37
21 2 0.07
22 4 0.15
23 11 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTTAATTTAATAAAAAA
Found at i:910582 original size:20 final size:23
Alignment explanation
Indices: 910534--910582 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 23
910524 CTTAATTTTT
* *
910534 TTTTAATTTATATAATAATAATT
1 TTTTAAATTATATAATAATAATA
910557 TTTTAAATTA-ATAA-AA-AATA
1 TTTTAAATTATATAATAATAATA
910577 TTTTAA
1 TTTTAA
910583 TTCTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 2 0.08
22 4 0.17
23 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTAAATTATATAATAATAATA
Found at i:916436 original size:20 final size:21
Alignment explanation
Indices: 916403--916442 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
916393 CATTGTAGCA
* *
916403 ACAGATGATTCTGCTTTTGGG
1 ACAGATGATACTGCTCTTGGG
916424 ACAG-TGATACTGCTCTTGG
1 ACAGATGATACTGCTCTTGG
916443 TAGTGAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (21 bp):
ACAGATGATACTGCTCTTGGG
Found at i:917534 original size:31 final size:30
Alignment explanation
Indices: 917479--917550 Score: 108
Period size: 31 Copynumber: 2.4 Consensus size: 30
917469 ACATTCAATC
*
917479 AAATTTTCATACTTTTATTATAAATCAAAT
1 AAATTTTTATACTTTTATTATAAATCAAAT
* *
917509 AAATTTTTATACTTTTTATTTTAAATTAAAT
1 AAATTTTTATAC-TTTTATTATAAATCAAAT
917540 AAATTTTTATA
1 AAATTTTTATA
917551 ATTAATAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 11 0.29
31 27 0.71
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (30 bp):
AAATTTTTATACTTTTATTATAAATCAAAT
Found at i:933896 original size:16 final size:17
Alignment explanation
Indices: 933875--933909 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
933865 AATTTTTTTA
933875 TAAAATTAAT-AAAATT
1 TAAAATTAATAAAAATT
933891 TAAAATTAATAAAAATT
1 TAAAATTAATAAAAATT
933908 TA
1 TA
933910 TTTAGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAATTAATAAAAATT
Found at i:934936 original size:23 final size:25
Alignment explanation
Indices: 934893--934939 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
934883 TTTTTTTTTT
934893 TAATCAAATATTACTATTCTTCAAA
1 TAATCAAATATTACTATTCTTCAAA
*
934918 TAATC-AATTTTA-TATTCTTCAA
1 TAATCAAATATTACTATTCTTCAA
934940 TAGTATCGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 6 0.29
25 5 0.24
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (25 bp):
TAATCAAATATTACTATTCTTCAAA
Found at i:942727 original size:13 final size:12
Alignment explanation
Indices: 942699--942751 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
942689 GTTTATCTTT
942699 AAAATTAACAAA
1 AAAATTAACAAA
*
942711 AAAATTAAGATAA
1 AAAATTAACA-AA
* *
942724 AAAATTATC-GA
1 AAAATTAACAAA
*
942735 AAAATTAAAAAA
1 AAAATTAACAAA
942747 AAAAT
1 AAAAT
942752 ACCTTTGAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 8 0.25
12 15 0.47
13 9 0.28
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.21
Consensus pattern (12 bp):
AAAATTAACAAA
Found at i:962807 original size:15 final size:16
Alignment explanation
Indices: 962787--962828 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
962777 TTTATTTAAA
*
962787 ATTTTTAAATAAT-TT
1 ATTTTTAAAAAATATT
962802 ATTTTTAAAAAATATT
1 ATTTTTAAAAAATATT
*
962818 ATATTTAAAAA
1 ATTTTTAAAAA
962829 TAAAAATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTTAAAAAATATT
Found at i:962814 original size:18 final size:16
Alignment explanation
Indices: 962790--962828 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
962780 ATTTAAAATT
* *
962790 TTTAAATAAT-TTATT
1 TTTAAAAAATATTATA
962805 TTTAAAAAATATTATA
1 TTTAAAAAATATTATA
962821 TTTAAAAA
1 TTTAAAAA
962829 TAAAAATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAAAAATATTATA
Found at i:965449 original size:2 final size:2
Alignment explanation
Indices: 965444--965475 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
965434 TGAAAAAATA
*
965444 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
965476 TGTATTTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:965993 original size:17 final size:18
Alignment explanation
Indices: 965958--965994 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
965948 TTCTATAGAT
965958 TAATATTTGATAAATTAA
1 TAATATTTGATAAATTAA
965976 TAATA-TTGATTAAA-TAA
1 TAATATTTGA-TAAATTAA
965993 TA
1 TA
965995 TTTTTCATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
TAATATTTGATAAATTAA
Found at i:966421 original size:17 final size:18
Alignment explanation
Indices: 966370--966423 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
966360 AAATTATTAA
* *
966370 TTTATTAATTAAAATAATTT
1 TTTATAAATT-AAA-AATTG
966390 TTTATAAATTAAAAATTG
1 TTTATAAATTAAAAATTG
*
966408 TTTATAATTTAAAAAT
1 TTTATAAATTAAAAAT
966424 AACAGTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 19 0.61
19 3 0.10
20 9 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTTATAAATTAAAAATTG
Found at i:991804 original size:14 final size:13
Alignment explanation
Indices: 991800--991984 Score: 62
Period size: 14 Copynumber: 13.8 Consensus size: 13
991790 ATTATAATTA
991800 AAATAAAAATATT
1 AAATAAAAATATT
991813 AAAATAAAAATATT
1 -AAATAAAAATATT
991827 AAAATAAAATATATAT
1 -AAATAAAA-ATAT-T
*
991843 AATATAAGATAAAATT
1 AA-ATAA-A-AATATT
*
991859 AAAATAAAAAAATAT
1 -AAATAAAAATAT-T
*
991874 AAA-AAATAACATT
1 AAATAAA-AATATT
* *
991887 -TAT-ATAATA-T
1 AAATAAAAATATT
** *
991897 AGGTAAAACAAATT
1 AAATAAAA-ATATT
*
991911 AAA-ATAAATATAT
1 AAATAAAAATAT-T
991924 AATATAAAAA-A-T
1 AA-ATAAAAATATT
* *
991936 ATATAAAAA-ATA
1 AAATAAAAATATT
*
991948 AAATAAAAATATA
1 AAATAAAAATATT
* * *
991961 AAATTATAATAAT
1 AAATAAAAATATT
991974 AAATAAAAATA
1 AAATAAAAATA
991985 AAATATATGA
Statistics
Matches: 130, Mismatches: 23, Indels: 37
0.68 0.12 0.19
Matches are distributed among these distances:
10 1 0.01
11 12 0.09
12 17 0.13
13 33 0.25
14 38 0.29
15 12 0.09
16 10 0.08
17 6 0.05
18 1 0.01
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (13 bp):
AAATAAAAATATT
Found at i:991812 original size:20 final size:20
Alignment explanation
Indices: 991787--991824 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
991777 AATATTTTAT
* *
991787 AATATTATAATTAAAATAAA
1 AATATTAAAATAAAAATAAA
991807 AATATTAAAATAAAAATA
1 AATATTAAAATAAAAATA
991825 TTAAAATAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATTAAAATAAAAATAAA
Found at i:991872 original size:26 final size:26
Alignment explanation
Indices: 991826--991991 Score: 71
Period size: 25 Copynumber: 6.5 Consensus size: 26
991816 ATAAAAATAT
* *
991826 TAAAATAAAATATATATAATATAAGA
1 TAAAATAAAATATAAAAAATATAAGA
991852 TAAAATTAAAATA-AAAAAATAT-A-A
1 TAAAA-TAAAATATAAAAAATATAAGA
* * * * *
991876 -AAAATAACATTTATATAATAT-AGG
1 TAAAATAAAATATAAAAAATATAAGA
* * * *
991900 TAAAACAAATTAAAATAAATATATAATA
1 TAAAATAAAATATAA-AAA-ATATAAGA
* * *
991928 TAAAA-AATATATAAAAAATAAAATA
1 TAAAATAAAATATAAAAAATATAAGA
* * *
991953 AAAATATAAAAT-TATAATA-ATAA-A
1 TAAA-ATAAAATATAAAAAATATAAGA
991977 TAAAAATAAAATATA
1 T-AAAATAAAATATA
991992 TGATATTAAA
Statistics
Matches: 103, Mismatches: 26, Indels: 23
0.68 0.17 0.15
Matches are distributed among these distances:
22 5 0.05
23 12 0.12
24 9 0.09
25 27 0.26
26 23 0.22
27 21 0.20
28 6 0.06
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (26 bp):
TAAAATAAAATATAAAAAATATAAGA
Found at i:992026 original size:29 final size:28
Alignment explanation
Indices: 991963--992145 Score: 112
Period size: 28 Copynumber: 6.5 Consensus size: 28
991953 AAAATATAAA
* * *
991963 ATTATAATAATAAATAAAAATAAA-ATAT
1 ATTATATTAA-AAATATATATAAATATAT
* *
991991 ATGATATTAAAAATATATTTAAATATGAT
1 ATTATATTAAAAATATATATAAATAT-AT
992020 ATTATA-TAAAAATTAATAATATAAATATA-
1 ATTATATTAAAAA-T-AT-ATATAAATATAT
* *
992049 AATATATTAAAAATA-AAATATAA-A-AT
1 ATTATATTAAAAATATATATA-AATATAT
* * *
992075 ATTATAATAATAAATAAAAATAAA-ATAT
1 ATTATATTAA-AAATATATATAAATATAT
* * *
992103 ATGATATTAAAAATATATTTAAGAAATGAT
1 ATTATATTAAAAATATATATAA-ATAT-AT
992133 ATTATA-TAAAAAT
1 ATTATATTAAAAAT
992146 TAAAATAAAA
Statistics
Matches: 124, Mismatches: 17, Indels: 27
0.74 0.10 0.16
Matches are distributed among these distances:
25 1 0.01
26 13 0.10
27 29 0.23
28 33 0.27
29 23 0.19
30 16 0.13
31 9 0.07
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
ATTATATTAAAAATATATATAAATATAT
Found at i:992047 original size:21 final size:22
Alignment explanation
Indices: 992023--992096 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
992013 ATATGATATT
992023 ATATAAAA-ATTAATAATATAA
1 ATATAAAATATTAATAATATAA
*
992044 ATATAAATATATTAAAAATA-AA
1 ATATAAA-ATATTAATAATATAA
992066 ATATAAAATATT-ATAATAATAA
1 ATATAAAATATTAATAAT-ATAA
992088 ATA-AAAATA
1 ATATAAAATA
992097 AAATATATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.09
21 19 0.40
22 15 0.32
23 9 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATAAAATATTAATAATATAA
Found at i:992048 original size:6 final size:6
Alignment explanation
Indices: 992037--992103 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
992027 AAAAATTAAT
* *
992037 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
992087 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
992104 TGATATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:992048 original size:23 final size:23
Alignment explanation
Indices: 992022--992090 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
992012 AATATGATAT
992022 TATATAAAAATTAATAATATAAA
1 TATATAAAAATTAATAATATAAA
*
992045 TATA-AATATATTAA-AA-ATAAA
1 TATATAA-AAATTAATAATATAAA
992066 -ATATAAAATATT-ATAATAATAAA
1 TATATAAAA-ATTAATAAT-ATAAA
992089 TA
1 TA
992091 AAAATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
20 5 0.14
21 12 0.32
22 4 0.11
23 15 0.41
24 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TATATAAAAATTAATAATATAAA
Found at i:992067 original size:63 final size:60
Alignment explanation
Indices: 991999--992172 Score: 174
Period size: 57 Copynumber: 3.0 Consensus size: 60
991989 ATATGATATT
991999 AAAAATATATTTAAATATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAA
1 AAAAATATATTTAAATATGATATTATATAAAAATTAA-AATATAAATATAAATATATTAAA
* *
992060 AATAAA-ATA-TAAAATAT--TA-TA-ATAATAAA-TAAAA-ATAAA-ATATATGATATT---
1 AA-AAATATATTTAAATATGATATTATATAA-AAATTAAAATATAAATATAAAT-ATATTAAA
* *
992111 AAAAATATATTTAAGAAATGATATTATATAAAAATTAAAATAAAAAATATAAATATATTAAA
1 AAAAATATATTTAA-ATATGATATTATATAAAAATTAAAAT-ATAAATATAAATATATTAAA
992173 CTTATATTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 33
0.70 0.05 0.26
Matches are distributed among these distances:
50 3 0.03
51 5 0.06
52 3 0.03
53 8 0.09
54 10 0.11
55 4 0.04
56 12 0.13
57 14 0.16
58 2 0.02
59 9 0.10
60 12 0.13
61 5 0.06
62 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (60 bp):
AAAAATATATTTAAATATGATATTATATAAAAATTAAAATATAAATATAAATATATTAAA
Found at i:992083 original size:15 final size:14
Alignment explanation
Indices: 991916--992167 Score: 52
Period size: 16 Copynumber: 17.9 Consensus size: 14
991906 AAATTAAAAT
991916 AAATATATAATATAAA
1 AAAT-TATAATAT-AA
* *
991932 AAATATATAAAAAATA
1 AAAT-TATAATATA-A
* *
991948 AAATAAAAATAT-A
1 AAATTATAATATAA
*
991961 AAATTATAATA-AT
1 AAATTATAATATAA
*
991974 AAA-TA-AAAAT-A
1 AAATTATAATATAA
*
991985 AAATATATGATATTAA
1 AAAT-TATAATA-TAA
*
992001 AAA-TAT-ATTTAA
1 AAATTATAATATAA
* *
992013 ATATGATATTATATAA
1 AAAT--TATAATATAA
992029 AAATTAATAATATAA
1 AAATT-ATAATATAA
*
992044 ATA-TA-AATATATTA
1 AAATTATAATATA--A
* *
992058 AAAATAAAATATAA
1 AAATTATAATATAA
*
992072 AATATTATAATA-AT
1 AA-ATTATAATATAA
*
992086 AAA-TA-AAAAT-A
1 AAATTATAATATAA
*
992097 AAATATATGATATTAA
1 AAAT-TATAATA-TAA
*
992113 AAA-TAT-ATTTAA
1 AAATTATAATATAA
*
992125 GAAATGATATTATATAA
1 -AAAT--TATAATATAA
992142 AAATTA-AA-ATAA
1 AAATTATAATATAA
*
992154 AAAATATAAATATA
1 AAATTAT-AATATA
992168 TTAAACTTAT
Statistics
Matches: 173, Mismatches: 31, Indels: 65
0.64 0.12 0.24
Matches are distributed among these distances:
11 12 0.07
12 27 0.16
13 27 0.16
14 25 0.14
15 32 0.18
16 45 0.26
17 5 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AAATTATAATATAA
Found at i:992109 original size:112 final size:112
Alignment explanation
Indices: 991947--992172 Score: 386
Period size: 112 Copynumber: 2.0 Consensus size: 112
991937 TATAAAAAAT
991947 AAAATAAAAATATAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTA
1 AAAATAAAAATATAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTA
* *
992012 A-ATATGATATTATATAAAAATTAATAAT-ATAAATATAAATATATTA
66 AGAAATGATATTATATAAAAATTAA-AATAAAAAATATAAATATATTA
992058 AAAAT-AAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATT
1 AAAATAAAAATAT-AAA-ATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATT
992122 TAAGAAATGATATTATATAAAAATTAAAATAAAAAATATAAATATATTA
64 TAAGAAATGATATTATATAAAAATTAAAATAAAAAATATAAATATATTA
992171 AA
1 AA
992173 CTTATATTTT
Statistics
Matches: 109, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
110 7 0.06
111 8 0.07
112 53 0.49
113 41 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (112 bp):
AAAATAAAAATATAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTA
AGAAATGATATTATATAAAAATTAAAATAAAAAATATAAATATATTA
Found at i:992339 original size:15 final size:15
Alignment explanation
Indices: 992316--992382 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
992306 GTTATTTCCC
*
992316 TGTAATCACATTGCT
1 TGTAATCACATTACT
*
992331 TGCAATCACATTACT
1 TGTAATCACATTACT
*
992346 TGTAATCACATTACC
1 TGTAATCACATTACT
*
992361 TGTAATCACATTGCAT
1 TGTAATCACATTAC-T
992377 TGTAAT
1 TGTAAT
992383 GTACCAAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
15 39 0.87
16 6 0.13
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.37
Consensus pattern (15 bp):
TGTAATCACATTACT
Found at i:993636 original size:20 final size:20
Alignment explanation
Indices: 993611--993650 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
993601 ATTTTAATTA
993611 TTCAAA-ATTTAAAATTAAAT
1 TTCAAATATTTAAAA-TAAAT
*
993631 TTCAAATTTTTAAAATAAAT
1 TTCAAATATTTAAAATAAAT
993651 CAAGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCAAATATTTAAAATAAAT
Found at i:994365 original size:21 final size:22
Alignment explanation
Indices: 994308--994358 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
994298 ACGCTATACG
* *
994308 ATATAATATAATTAATATATTT
1 ATATAATAGAATTAATATATTA
* *
994330 AT-TAAAAGAGTTAATATATTA
1 ATATAATAGAATTAATATATTA
994351 ATATAATA
1 ATATAATA
994359 ACTTAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATAATAGAATTAATATATTA
Found at i:1006156 original size:36 final size:36
Alignment explanation
Indices: 1006111--1006192 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 36
1006101 TTGATTGATT
* *
1006111 TGAGAACGTGTCAGTAGTTAACGGATTAAGTAGTTA
1 TGAGCACGTGTCAGTAATTAACGGATTAAGTAGTTA
* *
1006147 TGAGCACGTGTTAGTAATTAACGGATTAAGTAGTTC
1 TGAGCACGTGTCAGTAATTAACGGATTAAGTAGTTA
*
1006183 TGAACACGTG
1 TGAGCACGTG
1006193 AGCGTGCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (36 bp):
TGAGCACGTGTCAGTAATTAACGGATTAAGTAGTTA
Found at i:1007770 original size:31 final size:31
Alignment explanation
Indices: 1007695--1007771 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
1007685 AGAGAATATC
*
1007695 AAAGCATATATAGAATATAGAGTGAATGGTG
1 AAAGCATATATAGCATATAGAGTGAATGGTG
*
1007726 AAAGCATATATAGCATATATAGTGAATGGT-
1 AAAGCATATATAGCATATAGAGTGAATGGTG
1007756 ATAAGCATATATAGCA
1 A-AAGCATATATAGCA
1007772 AGCTTTCGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (31 bp):
AAAGCATATATAGCATATAGAGTGAATGGTG
Found at i:1012254 original size:27 final size:25
Alignment explanation
Indices: 1012193--1012254 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 25
1012183 CTATTTAAGT
1012193 TATATTTTTTATTAAATATTAAAAA
1 TATATTTTTTATTAAATATTAAAAA
* * * *
1012218 AATTAATTTTTATTTTAATATTGTAAAA
1 TA-TATTTTTTA-TTAAATATT-AAAAA
1012246 TATATTTTT
1 TATATTTTT
1012255 AAATTTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
25 1 0.04
26 8 0.29
27 14 0.50
28 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TATATTTTTTATTAAATATTAAAAA
Found at i:1019656 original size:21 final size:21
Alignment explanation
Indices: 1019630--1019670 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1019620 CCCTCCTGTG
*
1019630 GTTGAGTTTGGCTGATATTAA
1 GTTGAGTTTAGCTGATATTAA
1019651 GTTGAGTTTAGCTGATATTA
1 GTTGAGTTTAGCTGATATTA
1019671 CCATCGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.44
Consensus pattern (21 bp):
GTTGAGTTTAGCTGATATTAA
Found at i:1027477 original size:23 final size:23
Alignment explanation
Indices: 1027430--1027481 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1027420 TTAAATATAA
*
1027430 AAATAATTTTATATTAATATTTT
1 AAATAATTTTATATTAATATATT
1027453 AAATATATTTTATAATTAA-A-ATT
1 AAATA-ATTTTAT-ATTAATATATT
1027476 AAATAA
1 AAATAA
1027482 AAATATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 12 0.46
24 8 0.31
25 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATAATTTTATATTAATATATT
Found at i:1036387 original size:26 final size:25
Alignment explanation
Indices: 1036358--1036416 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
1036348 TATTACATAT
**
1036358 TATTATTTTTTATTTTATTTTTTAAA
1 TATTATTTTTTA-TTTATAATTTAAA
*
1036384 TATTAATATTTTATTTATAATTTAAA
1 TATT-ATTTTTTATTTATAATTTAAA
*
1036410 TGTTATT
1 TATTATT
1036417 ATGATTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.07
26 18 0.67
27 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
TATTATTTTTTATTTATAATTTAAA
Found at i:1036428 original size:31 final size:31
Alignment explanation
Indices: 1036393--1036503 Score: 118
Period size: 31 Copynumber: 3.5 Consensus size: 31
1036383 ATATTAATAT
1036393 TTTATTTATAATTTAAATGTTATTATGATTA
1 TTTATTTATAATTTAAATGTTATTATGATTA
* * ** *
1036424 TTTATTTTTAATTT--ATTTTATTTAAAAATA
1 TTTATTTATAATTTAAATGTTA-TTATGATTA
1036454 TTAATAATTTATAATTTAAATGTTATTATGATTA
1 TT--T-ATTTATAATTTAAATGTTATTATGATTA
*
1036488 TTTATTTTTAATTTAA
1 TTTATTTATAATTTAA
1036504 TTATTTAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
29 5 0.08
30 8 0.13
31 25 0.40
32 2 0.03
33 10 0.16
34 8 0.13
35 5 0.08
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (31 bp):
TTTATTTATAATTTAAATGTTATTATGATTA
Found at i:1036433 original size:26 final size:25
Alignment explanation
Indices: 1036371--1036434 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
1036361 TATTTTTTAT
*
1036371 TTTATTTTTTAAATATTAATATTTTA
1 TTTA-TTTTTAAATATTAATATATTA
* * *
1036397 TTTATAATTTAAATGTTATTATGATTA
1 TTTAT-TTTTAAATATTAATAT-ATTA
1036424 TTTATTTTTAA
1 TTTATTTTTAA
1036435 TTTATTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 1 0.03
26 22 0.71
27 8 0.26
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTATTTTTAAATATTAATATATTA
Found at i:1036439 original size:64 final size:66
Alignment explanation
Indices: 1036356--1036559 Score: 242
Period size: 64 Copynumber: 3.0 Consensus size: 66
1036346 TTTATTACAT
*
1036356 ATTA-TTATTTTTTATTTTATTT-TTT-AAATATTAATATTTTATTTATAATTTAAATGTTATTA
1 ATTATTTA-TTTTTAATTTATTTATTTAAAATATTAATATTTTATTTATAATTTAAATGTTATTA
1036418 TG
65 TG
1036420 ATTATTTATTTTTAATTTATTTTATTTAAAAATATTAATA----ATTTATAATTTAAATGTTATT
1 ATTATTTATTTTTAATTTA-TTTATTT-AAAATATTAATATTTTATTTATAATTTAAATGTTATT
1036481 ATG
64 ATG
*
1036484 ATTATTTATTTTTAATTTAATTATTTAAAATTTAAAATATTAATATTTTATTTATAATTTTAATG
1 ATTATTTATTTTTAA--T--TTATTT---ATTTAAAATATTAATATTTTATTTATAATTTAAATG
*
1036549 TTATTGTG
59 TTATTATG
1036557 ATT
1 ATT
1036560 TAAATATTAA
Statistics
Matches: 121, Mismatches: 3, Indels: 23
0.82 0.02 0.16
Matches are distributed among these distances:
64 53 0.44
65 6 0.05
66 4 0.03
67 3 0.02
68 14 0.12
69 12 0.10
70 4 0.03
73 25 0.21
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (66 bp):
ATTATTTATTTTTAATTTATTTATTTAAAATATTAATATTTTATTTATAATTTAAATGTTATTAT
G
Found at i:1036535 original size:46 final size:47
Alignment explanation
Indices: 1036454--1036547 Score: 111
Period size: 46 Copynumber: 2.0 Consensus size: 47
1036444 TTTAAAAATA
* * *
1036454 TTAATAATTTATAATTTAAATGTTATTATGATTATTTAT-TTTTAAT
1 TTAATAATTTAAAATTTAAATATTAATATGATTATTTATATTTTAAT
* *
1036500 TTAATTATTTAAAATTTAAAATATTAATAT-TTTATTTATAATTTTAAT
1 TTAATAATTTAAAATTT-AAATATTAATATGATTATTTAT-ATTTTAAT
1036548 GTTATTGTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
46 23 0.57
47 10 0.25
48 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (47 bp):
TTAATAATTTAAAATTTAAATATTAATATGATTATTTATATTTTAAT
Found at i:1036692 original size:15 final size:16
Alignment explanation
Indices: 1036665--1036706 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
1036655 CAATTTTTAC
*
1036665 TTAATAATTTAAAAT-
1 TTAATATTTTAAAATA
*
1036680 TTTATATTTTAAAATA
1 TTAATATTTTAAAATA
1036696 TTAATATTTTA
1 TTAATATTTTA
1036707 TTTATAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATATTTTAAAATA
Found at i:1038988 original size:2 final size:2
Alignment explanation
Indices: 1038981--1039005 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1038971 TGTTCTTGAG
1038981 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 A
1039006 ATCTAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1057946 original size:12 final size:12
Alignment explanation
Indices: 1057929--1057971 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
1057919 AATTCACCGA
1057929 GCCACGTCCACG
1 GCCACGTCCACG
*
1057941 GCCACGGCCACG
1 GCCACGTCCACG
1057953 GCCACGTCCACG
1 GCCACGTCCACG
*
1057965 TCCACGT
1 GCCACGT
1057972 TGACAGCCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.16, C:0.49, G:0.26, T:0.09
Consensus pattern (12 bp):
GCCACGTCCACG
Found at i:1057952 original size:18 final size:18
Alignment explanation
Indices: 1057929--1057987 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
1057919 AATTCACCGA
1057929 GCCACGTCCACGGCCACG
1 GCCACGTCCACGGCCACG
* *
1057947 GCCACGGCCACGTCCACG
1 GCCACGTCCACGGCCACG
* ** *
1057965 TCCACGTTGACAGCCACG
1 GCCACGTCCACGGCCACG
1057983 GCCAC
1 GCCAC
1057988 CACCTGGCGG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.47, G:0.25, T:0.08
Consensus pattern (18 bp):
GCCACGTCCACGGCCACG
Found at i:1057971 original size:6 final size:6
Alignment explanation
Indices: 1057930--1057971 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
1057920 ATTCACCGAG
* * *
1057930 CCACGT CCACGG CCACGG CCACGG CCACGT CCACGT CCACGT
1 CCACGT CCACGT CCACGT CCACGT CCACGT CCACGT CCACGT
1057972 TGACAGCCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.50, G:0.24, T:0.10
Consensus pattern (6 bp):
CCACGT
Found at i:1058315 original size:101 final size:101
Alignment explanation
Indices: 1058115--1058316 Score: 309
Period size: 101 Copynumber: 2.0 Consensus size: 101
1058105 GAGTGAAAGT
* *
1058115 GGGGATGAGTATGGGGATATATACTGCAATCCAAGTGAAGAACATTGCGATGGTTCAGGAATGTT
1 GGGGATGAGTATGGGGATATATACTGCAAACAAAGTGAAGAACATTGCGATGGTTCAGGAATGTT
*
1058180 GGCTTTGCAAAGAAAAGGTAGTATATGTTCGAGAGA
66 GGCTTTACAAAGAAAAGGTAGTATATGTTCGAGAGA
* * * * *
1058216 GGGGGTGAGTATGGGGATATATATTGCAAACAAAGTGAGGAGCATTGCGATGGTTTAGGAATGTT
1 GGGGATGAGTATGGGGATATATACTGCAAACAAAGTGAAGAACATTGCGATGGTTCAGGAATGTT
*
1058281 GGCTTTAC-AAGGAAAGGTAGTATATG-TCGAGAGA
66 GGCTTTACAAAGAAAAGGTAGTATATGTTCGAGAGA
1058315 GG
1 GG
1058317 CTGTTTCTTG
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 10 0.11
100 17 0.18
101 65 0.71
ACGTcount: A:0.32, C:0.08, G:0.34, T:0.26
Consensus pattern (101 bp):
GGGGATGAGTATGGGGATATATACTGCAAACAAAGTGAAGAACATTGCGATGGTTCAGGAATGTT
GGCTTTACAAAGAAAAGGTAGTATATGTTCGAGAGA
Found at i:1067403 original size:61 final size:61
Alignment explanation
Indices: 1067304--1067431 Score: 247
Period size: 61 Copynumber: 2.1 Consensus size: 61
1067294 TTGAGCAAAA
1067304 AATTTTGGACCCAGATCGTGAACTTGAAGAAAAAATAGGCAAAAAGAAGTCCCACACCATG
1 AATTTTGGACCCAGATCGTGAACTTGAAGAAAAAATAGGCAAAAAGAAGTCCCACACCATG
*
1067365 AATTTTGGACCCAGATCGTGAACTTGAAGAAAAGATAGGCAAAAAGAAGTCCCACACCATG
1 AATTTTGGACCCAGATCGTGAACTTGAAGAAAAAATAGGCAAAAAGAAGTCCCACACCATG
1067426 AATTTT
1 AATTTT
1067432 TTTTGGACTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (61 bp):
AATTTTGGACCCAGATCGTGAACTTGAAGAAAAAATAGGCAAAAAGAAGTCCCACACCATG
Found at i:1069039 original size:81 final size:81
Alignment explanation
Indices: 1068904--1069066 Score: 272
Period size: 81 Copynumber: 2.0 Consensus size: 81
1068894 TTTTCTTTTC
* * *
1068904 GGGTGTTTATTACAATTGTTATTGTGGAGGTATAAGGTCAAGGTCAATCCAACTAGCGTACTACA
1 GGGTGTTTATTACAATTATTATTGTGGAGGTATAAGGTCAAGGTCAACCCAACTAGCCTACTACA
*
1068969 AGCCACTAAGAATGGA
66 AGCCACTAAGAACGGA
*
1068985 GGGTGTTTATTCCAATTATTATTGTGGAGGTATAAGGTCAAGGTCAACCCAACTAGCCTACTACA
1 GGGTGTTTATTACAATTATTATTGTGGAGGTATAAGGTCAAGGTCAACCCAACTAGCCTACTACA
*
1069050 AGCCATTAAGAACGGA
66 AGCCACTAAGAACGGA
1069066 G
1 G
1069067 ACCTGTTTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (81 bp):
GGGTGTTTATTACAATTATTATTGTGGAGGTATAAGGTCAAGGTCAACCCAACTAGCCTACTACA
AGCCACTAAGAACGGA
Found at i:1073718 original size:16 final size:16
Alignment explanation
Indices: 1073697--1073728 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1073687 CAAGCCGCGC
1073697 AAGAAGAGTGCTTGGG
1 AAGAAGAGTGCTTGGG
*
1073713 AAGAAGAGTGTTTGGG
1 AAGAAGAGTGCTTGGG
1073729 TGTCCTGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.44, T:0.22
Consensus pattern (16 bp):
AAGAAGAGTGCTTGGG
Found at i:1075025 original size:14 final size:13
Alignment explanation
Indices: 1075002--1075049 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1074992 TATTTCTATT
*
1075002 TAAATTTAAAATA
1 TAAATATAAAATA
1075015 CTAAATATAAAATTA
1 -TAAATATAAAA-TA
1075030 TAATATATAAAATA
1 TAA-ATATAAAATA
*
1075044 AAAATA
1 TAAATA
1075050 ATTAAATACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 3 0.10
14 17 0.57
15 10 0.33
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATATAAAATA
Found at i:1075275 original size:20 final size:18
Alignment explanation
Indices: 1075252--1075295 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1075242 AGTTACAGAG
*
1075252 AAAAGACTAAAGTAAAAATA
1 AAAAGACAAAAG-AAAAA-A
1075272 AAAAGACAAAAGAAAAAA
1 AAAAGACAAAAGAAAAAA
1075290 AAAAGA
1 AAAAGA
1075296 AGTGTGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 5 0.22
20 11 0.48
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.07
Consensus pattern (18 bp):
AAAAGACAAAAGAAAAAA
Done.