Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009602.1 Hibiscus syriacus cultivar Beakdansim tig00116982_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1420948
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:453690 original size:11 final size:11
Alignment explanation
Indices: 453674--453698 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
453664 TAATATATAG
453674 TTTTGAAAACA
1 TTTTGAAAACA
453685 TTTTGAAAACA
1 TTTTGAAAACA
453696 TTT
1 TTT
453699 ATATGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:453806 original size:11 final size:11
Alignment explanation
Indices: 453790--453814 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
453780 TAATATATAG
453790 TTTTGAAAACA
1 TTTTGAAAACA
453801 TTTTGAAAACA
1 TTTTGAAAACA
453812 TTT
1 TTT
453815 ATATGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:453940 original size:115 final size:113
Alignment explanation
Indices: 453500--453973 Score: 509
Period size: 116 Copynumber: 4.1 Consensus size: 113
453490 GCAAACGATC
* * *
453500 TTTGAAAATACGTATATAATATATAGTTTTTAAAACATTTTT---AA-CTATATAATATATAGTT
1 TTTGAAAATA--TATATAATATATAATTTTGAAAACATTTTTGAAAATTTATATAATATATAG--
* * * * *
453561 TTTTAAAAAACGTTTT-AAAAAATATAGATA-ATATATAGTTTTT-AAAATCATT
62 TTTT-GAAAACATTTTGAAAACATGT--ATAGATATATAGTTTTTAAAAAACATT
*
453613 TTTG-AAATCTTATATAATATATAATTTTGAAAACATTTTTGAAAATTTATATAATATATAGTTT
1 TTTGAAAAT-ATATATAATATATAATTTTGAAAACATTTTTGAAAATTTATATAATATATAGTTT
* *
453677 TGAAAACATTTTGAAAACATTTATATGTTATATAGTTTTTTAAAAAAACATT
65 TGAAAACATTTTGAAAACATGTATA-GATATATAG-TTTTT-AAAAAACATT
453729 TTTGAAAATATATATAATATATAATTTTGAAAACATTTTTGAAAATTTATATAATATATAGTTTT
1 TTTGAAAATATATATAATATATAATTTTGAAAACATTTTTGAAAATTTATATAATATATAGTTTT
* *
453794 GAAAACATTTTGAAAACATTTATATGTTATATAGATTTTTAAAAAACATT
66 GAAAACATTTTGAAAACATGTATA-GATATATAG-TTTTTAAAAAACATT
* * ** *
453844 TTTGAAAATATATATAATATATAATTTTTAAAACATTTTTAAAAATGCATATATTATATAGTTTT
1 TTTGAAAATATATATAATATATAATTTTGAAAACATTTTTGAAAATTTATATAATATATAG--TT
* * * *
453909 TTG-AAACGTTTTTGAAAATACGTATA-ATATATAGTTTTTAAAAAATATT
64 TTGAAAAC-ATTTTGAAAACATGTATAGATATATAGTTTTTAAAAAACATT
* *
453958 TTGGAAATTTATATAT
1 TTTGAAA-ATATATAT
453974 TATGAGCTTT
Statistics
Matches: 320, Mismatches: 25, Indels: 30
0.85 0.07 0.08
Matches are distributed among these distances:
111 31 0.10
112 13 0.04
113 22 0.07
114 27 0.08
115 94 0.29
116 110 0.34
117 23 0.07
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (113 bp):
TTTGAAAATATATATAATATATAATTTTGAAAACATTTTTGAAAATTTATATAATATATAGTTTT
GAAAACATTTTGAAAACATGTATAGATATATAGTTTTTAAAAAACATT
Found at i:454001 original size:3 final size:3
Alignment explanation
Indices: 453993--454033 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
453983 TTGAACATTT
453993 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
454034 TCTAATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:456470 original size:3 final size:3
Alignment explanation
Indices: 456462--456512 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
456452 TCGTTTTTAA
** *
456462 TAT TAT TAT CGT TA- TAT TAT TAT TGT T-T ATAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
456506 TAT TAT T
1 TAT TAT T
456513 GTTTTTTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 3 0.08
3 36 0.90
4 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:456493 original size:15 final size:15
Alignment explanation
Indices: 456461--456516 Score: 66
Period size: 14 Copynumber: 4.0 Consensus size: 15
456451 CTCGTTTTTA
*
456461 ATATTATTATCG-TT
1 ATATTATTATTGTTT
456475 ATATTATTATTGTTT
1 ATATTATTATTGTTT
*
456490 ATATTATTA-T-TAT
1 ATATTATTATTGTTT
456503 -TATTATTATTGTTT
1 ATATTATTATTGTTT
456517 TTTTACAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
14 14 0.39
15 11 0.31
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (15 bp):
ATATTATTATTGTTT
Found at i:458651 original size:131 final size:131
Alignment explanation
Indices: 458411--458777 Score: 506
Period size: 131 Copynumber: 2.8 Consensus size: 131
458401 TCGATATTGT
* * * * *
458411 GAATAGTAATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTCTAAGGCATGAGAGATCAT
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
* * * * *
458476 TTCTTCTCGATTGGAAATAATTCGATATTATCATTCTCTA-TCGAATTAATATTGATTTTTAAGA
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTC-ACTCGAATCAATATTGAATTTTAAGA
*
458540 TA
130 CA
* *
458542 GAATAGTGATATCTCTTCATTTCTATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
* *
458607 TTATTCTCGATTGGAAATCATTAGATAATATCATTTTCACTCGAATCAATATTGAATTTTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAGAC
458672 A
131 A
* * *
458673 GAATAGTGGTATCTCTTCATTTCGATTAGAGTAATAAATGATTGCTTTAAGGTATGAGAGGT-AT
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
* ** *
458737 TTATTCTTGATTATAAATAATTAGATATTATC-GTTTCACTC
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTC
458778 TTAAAATTAT
Statistics
Matches: 209, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
129 8 0.04
130 30 0.14
131 171 0.82
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (131 bp):
GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAGAC
A
Found at i:466514 original size:401 final size:400
Alignment explanation
Indices: 465780--467002 Score: 1481
Period size: 394 Copynumber: 3.1 Consensus size: 400
465770 TAATCTTTAG
* *
465780 TGAAG-ACTAGTGGAATGAATCAACG-CCCCAGATCTAATTTTCCCTCAAGAAGAAGCAGAACAA
1 TGAAGAAC-AGTGGAATGAATCAACGTCCCCAAATCTAATTTTCCCTCAAGAAAAAGCAGAACAA
* * * *
465843 ATCCCTCTCTTTCAAGATTTGATATTCCCCTGAATAACAGTAGAACAAGTCTGCCTCTATTCAAT
65 ATCCCTCTCTTTCAATATTTGATATT-CCCTGAGTAACAGTGGAACAAGTC-GCCTCGATTCAAT
* *
465908 TTTCCCTGAAGAATAGTGGAATGAATCAATGTCCCT-ATATCTGATTTTCCCTCAAGAAGAAGTA
128 ATTCCCTGAAGAATAGTGGAATGAATCAATG-CCCTCAAATCTGATTTTCCCTCAAGAAGAAG-A
* * *
465972 TAATAGAT-C-CCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAG-TCGAACTC
191 TAA-ACATACTCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTTTG-ACTC
* * * *
466034 GATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCCTCTAGA
254 GATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
* *
466099 AGAAGCAGAACATATCCCTCTATTTCAAGATTTGGTATTCCCTGAGTAACAGTGGAATAAGTCTG
319 AGAAGCA-AACATATCCCTCTATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
* * *
466164 TCTTGATTTAATCTTCCC
383 CCTCGATTCAATCTTCCC
* * * *
466182 TGAAGAACACTGGAATGAATCAACGTCCTCAAATCTGA-TTTCCCTCAAGAAAAAGCAGAACATA
1 TGAAGAACAGTGGAATGAATCAACGTCCCCAAATCTAATTTTCCCTCAAGAAAAAGCAGAACAAA
* * * * *
466246 TCCCTCTCTTTCAATATTTGATATTCTCTGAGTAATAGTGGAACAAGTCGAACTAGATTCAGTAT
66 TCCCTCTCTTTCAATATTTGATATTCCCTGAGTAACAGTGGAACAAGTCG-CCTCGATTCAATAT
* * * * *
466311 TCTCTAAAGAACACTGGAATGAATCAATGCCCTCAAATATGATTTTCCCTCAAGAAGAAGATAAA
130 TCCCTGAAGAATAGTGGAATGAATCAATGCCCTCAAATCTGATTTTCCCTCAAGAAGAAGATAAA
* * * * * *
466376 CATACTCTTCTCTTTCAAAATTTGATATTCCATGAGTAATAGTGGAACACGTTTGCCTCGATTCA
195 CATACTCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTTTGACTCGATTCA
* * ** *
466441 ATCTTCCCTGAAGAATAGTGAAATGAATCAATGTCTTCAGAGCTGATTTTCCCTCAAGAAGAAGC
260 ATCTTCCCTGAAGAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGC
*
466506 GAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGA
325 -AAACATATCCCTCTATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGA
*
466571 TTCAATATTCCC
389 TTCAATCTTCCC
* * * * * * *
466583 TGGAGAACAGTAGAATGAATCAACATCCCCATATCTAATTTTTCATCAAGAAAAAGTAGAA-AAA
1 TGAAGAACAGTGGAATGAATCAACGTCCCCAAATCTAATTTTCCCTCAAGAAAAAGCAGAACAAA
* * * * *
466647 T--C-C-ATATC--T-TTTGATATTCCCAGAGTAACAGTGGAACAAGTTTGCCTCGATTCAATCT
66 TCCCTCTCTTTCAATATTTGATATTCCCTGAGTAACAGTGGAACAAG-TCGCCTCGATTCAATAT
* * * * * ***
466705 TCCCTGAAGAATAGTGGAATGAATCAACGTCCGCAGATCTGATTCTT-CCTCAAGAAAAAGCGGA
130 TCCCTGAAGAATAGTGGAATGAATCAATGCCCTCAAATCTGATT-TTCCCTCAAGAAGAAGATAA
* * * *
466769 ACATA-TCCCTCTCTTTCAAGATTTGGTATTCCCTGAGTAACGGTAGAACAAGTCTGACTCGATT
194 ACATACT-CCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTTTGACTCGATT
* * * * *
466833 CAATCTTCCGTGGAGAATAGTGGAATGAATCAACGTCCCCATATCTGATTTTCCCTCAAAAATAA
258 CAATCTTCCCTGAAGAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAA
* *
466898 GTCAAACATATCCCTCTGTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTCCCTC
323 G-CAAACATATCCCTCTATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTC
*
466963 AATTCAATCTTCCC
387 GATTCAATCTTCCC
*
466977 TAAAGAACAGTGGAATGAATCAACGT
1 TGAAGAACAGTGGAATGAATCAACGT
467003 TTCTCGATCT
Statistics
Matches: 699, Mismatches: 109, Indels: 34
0.83 0.13 0.04
Matches are distributed among these distances:
393 1 0.00
394 288 0.41
395 6 0.01
397 3 0.00
398 1 0.00
399 4 0.01
400 10 0.01
401 284 0.41
402 91 0.13
403 11 0.02
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (400 bp):
TGAAGAACAGTGGAATGAATCAACGTCCCCAAATCTAATTTTCCCTCAAGAAAAAGCAGAACAAA
TCCCTCTCTTTCAATATTTGATATTCCCTGAGTAACAGTGGAACAAGTCGCCTCGATTCAATATT
CCCTGAAGAATAGTGGAATGAATCAATGCCCTCAAATCTGATTTTCCCTCAAGAAGAAGATAAAC
ATACTCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTTTGACTCGATTCAA
TCTTCCCTGAAGAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGCA
AACATATCCCTCTATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATT
CAATCTTCCC
Found at i:467015 original size:134 final size:134
Alignment explanation
Indices: 465780--467002 Score: 1431
Period size: 134 Copynumber: 9.2 Consensus size: 134
465770 TAATCTTTAG
* *
465780 TGAAG-ACTAGTGGAATGAATCAACG-CCCCAGATCTAATTTTCCCTCAAGAAGAAGCAGAACAA
1 TGAAGAAC-AGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGCAGAACAT
* * *
465843 ATCCCTCTCTTTCAAGATTTGATATTCCCCTGAATAACAGTAGAACAAGTCTGCCTCTATTCAAT
65 ATCCCTCTCTTTCAAGATTTGATATT-CCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAAT
*
465908 TTTCCC
129 CTTCCC
* * * * * * * *
465914 TGAAGAATAGTGGAATGAATCAATGTCCCTATATCTGATTTTCCCTCAAGAAGAAGTATAATAGA
1 TGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGCAGAACATA
* *
465979 TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAGTC-GAACTCGATTCAATC
66 TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG-CCTCGATTCAATC
466043 TTCCC
130 TTCCC
* * *
466048 TAAAGAACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCCTCTAGAAGAAGCAGAACATA
1 TGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGCAGAACATA
* * * * * *
466113 TCCCTCTATTTCAAGATTTGGTATTCCCTGAGTAACAGTGGAATAAGTCTGTCTTGATTTAATCT
66 TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCT
466178 TCCC
131 TCCC
* * * *
466182 TGAAGAACACTGGAATGAATCAACGTCCTCAAATCTGA-TTTCCCTCAAGAAAAAGCAGAACATA
1 TGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGCAGAACATA
* * * * * * *
466246 TCCCTCTCTTTCAATATTTGATATTCTCTGAGTAATAGTGGAACAAGTC-GAACTAGATTCAGTA
66 TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG-CCTCGATTCAATC
*
466310 TTCTC
130 TTCCC
* * * * * *
466315 TAAAGAACACTGGAATGAATCAATG-CCCTCAAATATGATTTTCCCTCAAGAAGAAG-ATAAACA
1 TGAAGAACAGTGGAATGAATCAACGTCCC-CAGATCTGATTTTCCCTCAAGAAGAAGCA-GAACA
* * * * * *
466378 TA-CTCTTCTCTTTCAAAATTTGATATTCCATGAGTAATAGTGGAACACGTTTGCCTCGATTCAA
64 TATC-CCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAA
466442 TCTTCCC
128 TCTTCCC
* * * ** *
466449 TGAAGAATAGTGAAATGAATCAATGTCTTCAGAGCTGATTTTCCCTCAAGAAGAAGC-GAAACAT
1 TGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGCAG-AACAT
*
466513 ATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATA
65 ATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATC
466578 TTCCC
130 TTCCC
* * * * * * * * * *
466583 TGGAGAACAGTAGAATGAATCAACATCCCCATATCTAATTTTTCATCAAGAAAAAGTAGAA-AAA
1 TGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGCAGAACATA
* * * *
466647 TCCATATC--T-----TTTGATATTCCCAGAGTAACAGTGGAACAAGTTTGCCTCGATTCAATCT
66 TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCT
466705 TCCC
131 TCCC
* * * *
466709 TGAAGAATAGTGGAATGAATCAACGTCCGCAGATCTGATTCTT-CCTCAAGAAAAAGCGGAACAT
1 TGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATT-TTCCCTCAAGAAGAAGCAGAACAT
* * * *
466773 ATCCCTCTCTTTCAAGATTTGGTATTCCCTGAGTAACGGTAGAACAAGTCTGACTCGATTCAATC
65 ATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATC
*
466838 TTCCG
130 TTCCC
* * * * *
466843 TGGAGAATAGTGGAATGAATCAACGTCCCCATATCTGATTTTCCCTCAAAAATAAGTCA-AACAT
1 TGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAG-CAGAACAT
* * *
466907 ATCCCTCTGTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTCCCTCAATTCAATC
65 ATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATC
466972 TTCCC
130 TTCCC
*
466977 TAAAGAACAGTGGAATGAATCAACGT
1 TGAAGAACAGTGGAATGAATCAACGT
467003 TTCTCGATCT
Statistics
Matches: 919, Mismatches: 144, Indels: 52
0.82 0.13 0.05
Matches are distributed among these distances:
126 98 0.11
127 10 0.01
129 1 0.00
131 1 0.00
132 3 0.00
133 123 0.13
134 619 0.67
135 64 0.07
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (134 bp):
TGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGCAGAACATA
TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCT
TCCC
Found at i:467182 original size:3 final size:3
Alignment explanation
Indices: 467174--467212 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
467164 TCGTTTTTAA
*
467174 TAT TAT TAT CAT TA- TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
467213 GCTTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:469596 original size:130 final size:131
Alignment explanation
Indices: 469342--469655 Score: 402
Period size: 130 Copynumber: 2.4 Consensus size: 131
469332 ATGTCTACTC
* *
469342 TAAGGCATGAGAGGTCATTTATTATCGATTGGAAATAATTCA-ATATTATCATTCTCTCTCGAAT
1 TAAGGTATGAGAGGTCATTTATTATCGATTGGAAATAATT-AGATATTATCATTCTCACTCGAAT
* * * * ** *
469406 TAATTTTGATTTTTAAGATAGAATAGTGATATCTCTTCATTTCTATTGGAGCAATAAATGATTGC
65 TAATATTGAATTTTAAGACAGAATAGTGATATCTCTTCATTTCGATCAGAGCAATAAATGAATGC
469471 TT
130 TT
* * * *
469473 TAAGGTATGAGAGGTTATTTATTTTCGATTGGAAATCATTAGATATTATCGTT-TCACTCGAATC
1 TAAGGTATGAGAGGTCATTTATTATCGATTGGAAATAATTAGATATTATCATTCTCACTCGAAT-
* *
469537 T-ATATTGAATTTTAAGACAGAATAGTGATATCT-TATCATTTCGATCATAGTAATAAATGAATG
65 TAATATTGAATTTTAAGACAGAATAGTGATATCTCT-TCATTTCGATCAGAGCAATAAATGAATG
469600 CTT
129 CTT
** * *
469603 TAAGGTATGAGAAATCATTTATTCTCGATTAGAAATAATTAGATATTATCATT
1 TAAGGTATGAGAGGTCATTTATTATCGATTGGAAATAATTAGATATTATCATT
469656 TTCAATCTTA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
129 1 0.01
130 110 0.70
131 47 0.30
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.40
Consensus pattern (131 bp):
TAAGGTATGAGAGGTCATTTATTATCGATTGGAAATAATTAGATATTATCATTCTCACTCGAATT
AATATTGAATTTTAAGACAGAATAGTGATATCTCTTCATTTCGATCAGAGCAATAAATGAATGCT
T
Found at i:472433 original size:21 final size:22
Alignment explanation
Indices: 472407--472447 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
472397 CCAAGACAGG
472407 GAGTATCAATACT-TCTTTAAT
1 GAGTATCAATACTATCTTTAAT
472428 GAGTATCAATACTATCTTTA
1 GAGTATCAATACTATCTTTA
472448 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
GAGTATCAATACTATCTTTAAT
Found at i:473862 original size:194 final size:194
Alignment explanation
Indices: 473533--473921 Score: 724
Period size: 194 Copynumber: 2.0 Consensus size: 194
473523 CTTTTCAACA
473533 TACATGAGATGAAAAACATAAAATTAATTTAAAATCAAAACTTATGCATGCTTAAAACTAAATGA
1 TACATGAGATGAAAAACATAAAATTAATTTAAAATCAAAACTTATGCATGCTTAAAACTAAATGA
*
473598 GCAACCAATTATGCAAGATAATTAAAATAAGCTTAAAGGTTACCCATTCTTTTTCAAGTGTGGCT
66 GCAACCAATTATGCAAGATAATTAAAATAAGCTTAAAGGTTACCCATTCCTTTTCAAGTGTGGCT
* *
473663 AGAGCATTTAAACATCTTCACTTTCATCACCATTGCTCTCACACACCTACGAGAGACATTCATT
131 AGAGCATTTAAACATCTTCACTTTCATCACCATTGCTCCCACACACCTACAAGAGACATTCATT
473727 TACATGAGATGAAAAACATAAAATTAATTTAAAATCAAAACTTATGCATGCTTAAAACTAAATGA
1 TACATGAGATGAAAAACATAAAATTAATTTAAAATCAAAACTTATGCATGCTTAAAACTAAATGA
**
473792 GCAACCAATTATGCAAGATAATTAAAATAAGCTTAAAGGTTGTCCATTCCTTTTCAAGTGTGGCT
66 GCAACCAATTATGCAAGATAATTAAAATAAGCTTAAAGGTTACCCATTCCTTTTCAAGTGTGGCT
*
473857 AGAGCATTTGAACATCTTCACTTTCATCACCATTGCTCCCACACACCTACAAGAGACATTCATT
131 AGAGCATTTAAACATCTTCACTTTCATCACCATTGCTCCCACACACCTACAAGAGACATTCATT
473921 T
1 T
473922 TAATTTTGGT
Statistics
Matches: 189, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
194 189 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (194 bp):
TACATGAGATGAAAAACATAAAATTAATTTAAAATCAAAACTTATGCATGCTTAAAACTAAATGA
GCAACCAATTATGCAAGATAATTAAAATAAGCTTAAAGGTTACCCATTCCTTTTCAAGTGTGGCT
AGAGCATTTAAACATCTTCACTTTCATCACCATTGCTCCCACACACCTACAAGAGACATTCATT
Found at i:474226 original size:15 final size:15
Alignment explanation
Indices: 474208--474238 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
474198 AAATTTCATT
474208 TTTTTCTTTTCAAAA
1 TTTTTCTTTTCAAAA
474223 TTTTTCTTTTCAAAA
1 TTTTTCTTTTCAAAA
474238 T
1 T
474239 CCAATTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTCTTTTCAAAA
Found at i:478641 original size:77 final size:76
Alignment explanation
Indices: 478475--479147 Score: 653
Period size: 77 Copynumber: 8.8 Consensus size: 76
478465 CCTAAAAATA
* * *
478475 TCATGGTTCACTAAGAAACA-GGTTGCGATATGTAATGTTAATA-TTTTATTAATAAAAT-AGGT
1 TCATGGTTCACTAAGAAATATGG-TACGATCTG-AATGTTAATATTTTTATTAATAAAATGA-GT
*
478537 TGCGTCCAAGAATG
63 TGCGCCCAAGAATG
* * * *
478551 TTATGGTTCACTAAGAAATAAGGTACGATTTAGAATGTTAATATTTTTATTAATAAAATGGGTTG
1 TCATGGTTCACTAAGAAATATGGTACGATCT-GAATGTTAATATTTTTATTAATAAAATGAGTTG
*
478616 CGCCCATGAATG
65 CGCCCAAGAATG
* * * * * ** * *
478628 GCCTAGTTTACTAATAAATATGTTGTAATATC-AAATGCTAATATTTTTATTAATAAAATGAGTT
1 TCATGGTTCACTAAGAAATATG--GTACGATCTGAATGTTAATATTTTTATTAATAAAATGAGTT
**
478692 GCATCCAA-AAGTG
64 GCGCCCAAGAA-TG
* *
478705 TCATGGTTCACTAAGAAATA-GGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAATAAGTT
1 TCATGGTTCACTAAGAAATATGG-TACGATCT-GAATGTTAATATTTTTATTAATAAAATGAGTT
*
478769 TCGCCCAAGAATG
64 GCGCCCAAGAATG
* * * *
478782 TCATGATTCACTAATAAATATGTTGTA--ATCT-AATGTTCATATTTATATTAATAAAATGAGTT
1 TCATGGTTCACTAAGAAATATG--GTACGATCTGAATGTTAATATTTTTATTAATAAAATGAGTT
**
478844 GCGCTTAAGAATG
64 GCGCCCAAGAATG
* * * *
478857 TCATGATTCACTAAGAAATATGTTGCGATCTGGAATGTTAATATTTTTATTAATAAAATGAGTTT
1 TCATGGTTCACTAAGAAATATGGTACGATCT-GAATGTTAATATTTTTATTAATAAAATGAGTTG
478922 CGCCCAAGAATG
65 CGCCCAAGAATG
* * * ** *
478934 CCATGGTTCACTAATAAATATGTTGTGATCTTGAATGTTAATATTTTTATTAATAAAACGAGTTG
1 TCATGGTTCACTAAGAAATATGGTACGATC-TGAATGTTAATATTTTTATTAATAAAATGAGTTG
* *
478999 TGCTCAAGAATG
65 CGCCCAAGAATG
* * * * * * *
479011 TCATGATTCACTAAGAAATGTGTTGCGATCTGGAATGTTAATATTTTTATTAATAATATAAGTTT
1 TCATGGTTCACTAAGAAATATGGTACGATCT-GAATGTTAATATTTTTATTAATAAAATGAGTTG
*
479076 CTCCCAAGAATG
65 CGCCCAAGAATG
* * * * * *
479088 TCATGGTTCACTAAGAAATAAGTTAGGATATGAAATTTTAATAATTTTATTAATAAAATG
1 TCATGGTTCACTAAGAAATATGGTACGATCTG-AATGTTAATATTTTTATTAATAAAATG
479148 GGTCACACAC
Statistics
Matches: 492, Mismatches: 84, Indels: 41
0.80 0.14 0.07
Matches are distributed among these distances:
73 1 0.00
74 1 0.00
75 67 0.14
76 39 0.08
77 373 0.76
78 4 0.01
79 6 0.01
80 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37
Consensus pattern (76 bp):
TCATGGTTCACTAAGAAATATGGTACGATCTGAATGTTAATATTTTTATTAATAAAATGAGTTGC
GCCCAAGAATG
Found at i:479074 original size:306 final size:305
Alignment explanation
Indices: 478475--479146 Score: 854
Period size: 306 Copynumber: 2.2 Consensus size: 305
478465 CCTAAAAATA
* * * * *
478475 TCATGGTTCACTAAGAAACAGGTTGCGATATGTAATGTTAATATTTTATTAATAAAATAGGTTGC
1 TCATGATTCACTAAGAAATATGTTG-TA-ATCTAATGTTAATATTTTATTAATAAAATAGGTTGC
* * *
478540 GTCCAAGAATGTTATGGTTCACTAAGAAATAAGGTACGATTTAGAATGTTAATATTTTTATTAAT
64 GTCCAAGAATGTCATGATTCACTAAGAAATAAGGTACGATCTAGAATGTTAATATTTTTATTAAT
* * *
478605 AAAATGGGTTGCGCCCATGAATGGCCTAGTTTACTAATAAATATGTTGTAATATCAAATGCTAAT
129 AAAATGAGTTGCGCCCAAGAATGGCCTAGTTCACTAATAAATATGTTGTAATATCAAATGCTAAT
* *
478670 ATTTTTATTAATAAAATGAGTTGCATCCAAAAGTGTCATGGTTCACTAAGAAATAGGTTGCGATC
194 ATTTTTATTAATAAAACGAGTTGCATCCAAAAGTGTCATGATTCACTAAGAAATAGGTTGCGATC
478735 TAGAATGTTAATATTTTTATTAATAAAATAAGTTTCGCCCAAGAATG
259 TAGAATGTTAATATTTTTATTAATAAAATAAGTTTCGCCCAAGAATG
* *
478782 TCATGATTCACTAATAAATATGTTGTAATCTAATGTTCATATTTATATTAATAAAAT-GAGTTGC
1 TCATGATTCACTAAGAAATATGTTGTAATCTAATGTTAATATTT-TATTAATAAAATAG-GTTGC
* * * * *
478846 G-CTTAAGAATGTCATGATTCACTAAGAAATATGTTGCGATCTGGAATGTTAATATTTTTATTAA
64 GTC-CAAGAATGTCATGATTCACTAAGAAATAAGGTACGATCTAGAATGTTAATATTTTTATTAA
* * * * ** *
478910 TAAAATGAGTTTCGCCCAAGAAT-GCCATGGTTCACTAATAAATATGTTGTGATCTTGAATGTTA
128 TAAAATGAGTTGCGCCCAAGAATGGCC-TAGTTCACTAATAAATATGTTGTAATATCAAATGCTA
478974 ATATTTTTATTAATAAAACGAGTTG--TGCTCAAGAA-TGTCATGATTCACTAAGAAAT-GTGTT
192 ATATTTTTATTAATAAAACGAGTTGCAT-C-CAA-AAGTGTCATGATTCACTAAGAAATAG-GTT
* * *
479035 GCGATCTGGAATGTTAATATTTTTATTAATAATATAAGTTTCTCCCAAGAATG
253 GCGATCTAGAATGTTAATATTTTTATTAATAAAATAAGTTTCGCCCAAGAATG
* * * ** *
479088 TCATGGTTCACTAAGAAATAAGTTAGGATATGAAATTTTAATAATTTTATTAATAAAAT
1 TCATGATTCACTAAGAAATATGTT-GTA-ATCTAATGTTAAT-ATTTTATTAATAAAAT
479147 GGGTCACACA
Statistics
Matches: 316, Mismatches: 38, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
304 1 0.00
305 22 0.07
306 243 0.77
307 25 0.08
308 21 0.07
309 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37
Consensus pattern (305 bp):
TCATGATTCACTAAGAAATATGTTGTAATCTAATGTTAATATTTTATTAATAAAATAGGTTGCGT
CCAAGAATGTCATGATTCACTAAGAAATAAGGTACGATCTAGAATGTTAATATTTTTATTAATAA
AATGAGTTGCGCCCAAGAATGGCCTAGTTCACTAATAAATATGTTGTAATATCAAATGCTAATAT
TTTTATTAATAAAACGAGTTGCATCCAAAAGTGTCATGATTCACTAAGAAATAGGTTGCGATCTA
GAATGTTAATATTTTTATTAATAAAATAAGTTTCGCCCAAGAATG
Found at i:479199 original size:154 final size:152
Alignment explanation
Indices: 478475--479222 Score: 769
Period size: 154 Copynumber: 4.9 Consensus size: 152
478465 CCTAAAAATA
* * * * *
478475 TCATGGTTCACTAAGAAACAGGTTGCGATATGTAATGTTAAT-ATTTTATTAATAAAAT-AGGTT
1 TCATGGTTCACTAATAAATATGTTGTGATATGAAATGTTAATAATTTTATTAATAAAATGA-GTT
* * * * * *
478538 GCGTCCAAGAATGTTATGGTTCACTAAGAAATAAGGTACGATTTAGAATGTTAATATTTTTATTA
65 GC-ACCAAGAATGTCAT-GTTCACTAAGAAATAAGTTGCGATCTGGAATGTTAATATTTTTATTA
** * *
478603 ATAAAATGGGTTGCGCCCATGAATG
128 ATAAAATAAGTTTCGCCCAAGAATG
* * * * * * * *
478628 GCCTAGTTTACTAATAAATATGTTGTAATATCAAATGCTAATATTTTTATTAATAAAATGAGTTG
1 TCATGGTTCACTAATAAATATGTTGTGATATGAAATGTTAATAATTTTATTAATAAAATGAGTTG
* *
478693 CATCCAA-AAGTGTCATGGTTCACTAAGAAATAGGTTGCGATCTAGAATGTTAATATTTTTATTA
66 CA-CCAAGAA-TGTCAT-GTTCACTAAGAAATAAGTTGCGATCTGGAATGTTAATATTTTTATTA
478757 ATAAAATAAGTTTCGCCCAAGAATG
128 ATAAAATAAGTTTCGCCCAAGAATG
* ** *
478782 TCATGATTCACTAATAAATATGTTGT-A-ATCTAATGTTCAT-ATTTATATTAATAAAATGAGTT
1 TCATGGTTCACTAATAAATATGTTGTGATATGAAATGTTAATAATTT-TATTAATAAAATGAGTT
* * *
478844 GCGCTTAAGAATGTCATGATTCACTAAGAAATATGTTGCGATCTGGAATGTTAATATTTTTATTA
65 GCAC-CAAGAATGTCATG-TTCACTAAGAAATAAGTTGCGATCTGGAATGTTAATATTTTTATTA
*
478909 ATAAAATGAGTTTCGCCCAAGAATG
128 ATAAAATAAGTTTCGCCCAAGAATG
* * * *
478934 CCATGGTTCACTAATAAATATGTTGTGATCTTG-AATGTTAATATTTTTATTAATAAAACGAGTT
1 TCATGGTTCACTAATAAATATGTTGTGAT-ATGAAATGTTAATAATTTTATTAATAAAATGAGTT
** **
478998 GTGCTCAAGAATGTCATGATTCACTAAGAAATGTGTTGCGATCTGGAATGTTAATATTTTTATTA
65 GCAC-CAAGAATGTCATG-TTCACTAAGAAATAAGTTGCGATCTGGAATGTTAATATTTTTATTA
* *
479063 ATAATATAAGTTTCTCCCAAGAATG
128 ATAAAATAAGTTTCGCCCAAGAATG
* * * * *
479088 TCATGGTTCACTAAGAAATAAGTTAG-GATATGAAATTTTAATAATTTTATTAATAAAATGGGTC
1 TCATGGTTCACTAATAAATATGTT-GTGATATGAAATGTTAATAATTTTATTAATAAAATGAGTT
* * * * * * *
479152 ACACACAA-AATGTTATAGTGCACTAAAAAAGCAAGTTACGATTTGGAATGTTAAT-TTTTCTAT
65 GCAC-CAAGAATGTCAT-GTTCACTAAGAAA-TAAGTTGCGATCTGGAATGTTAATATTTT-TAT
*
479215 TATTAAAA
126 TAATAAAA
479223 ATGTGAAAGT
Statistics
Matches: 505, Mismatches: 73, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
151 5 0.01
152 129 0.26
153 59 0.12
154 306 0.61
155 6 0.01
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (152 bp):
TCATGGTTCACTAATAAATATGTTGTGATATGAAATGTTAATAATTTTATTAATAAAATGAGTTG
CACCAAGAATGTCATGTTCACTAAGAAATAAGTTGCGATCTGGAATGTTAATATTTTTATTAATA
AAATAAGTTTCGCCCAAGAATG
Found at i:479256 original size:20 final size:20
Alignment explanation
Indices: 479227--479282 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
479217 TTAAAAATGT
479227 GAAAGTATGGATACTTTTTC
1 GAAAGTATGGATACTTTTTC
*
479247 GAATGTATGGATAC-TTTTC
1 GAAAGTATGGATACTTTTTC
*
479266 GAAAGTATAGATACTTT
1 GAAAGTATGGATACTTT
479283 AGAATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (20 bp):
GAAAGTATGGATACTTTTTC
Found at i:479466 original size:65 final size:65
Alignment explanation
Indices: 479338--479471 Score: 148
Period size: 65 Copynumber: 2.0 Consensus size: 65
479328 ATGTTTTTCC
* * * *
479338 AAAAGTATCGATGCTTTTAAATTCGAAAGTTAAAATATCTTTTTTTTTCATTTTTTTAAAAATTT
1 AAAAGTATCGATACTTTTAAATTAGAAAGTTAAAATATCTTTTTTTTT-ATTTGTTTAAAAATTC
479403 G
65 G
* * *
479404 AAAA-TATCGATACTTTTAAATTATAACGTTAAAATATCATTTTCTATTTT-TTTGTTT-CAAAT
1 AAAAGTATCGATACTTTTAAATTAGAAAGTTAAAATATC-TTTT-T-TTTTATTTGTTTAAAAAT
479466 TCG
63 TCG
479469 AAA
1 AAA
479472 GCATCAATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
65 39 0.67
66 14 0.24
67 1 0.02
68 4 0.07
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (65 bp):
AAAAGTATCGATACTTTTAAATTAGAAAGTTAAAATATCTTTTTTTTTATTTGTTTAAAAATTCG
Found at i:479576 original size:19 final size:20
Alignment explanation
Indices: 479552--479595 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
479542 TTTAAATTTG
479552 AGTATGAATACTTTTCG-AA
1 AGTATGAATACTTTTCGAAA
* * *
479571 AGTATGGATATTTTTGGAAA
1 AGTATGAATACTTTTCGAAA
479591 AGTAT
1 AGTAT
479596 CTATATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
AGTATGAATACTTTTCGAAA
Found at i:479968 original size:100 final size:101
Alignment explanation
Indices: 479696--480103 Score: 506
Period size: 100 Copynumber: 4.1 Consensus size: 101
479686 AATAATGTTG
* * * *
479696 TAGGTAACACCTTTTTTTTAATGTAAACTGTTTAAGTTATAAGTATGAAATTGTTTATATGATGC
1 TAGGTAACACC-TTTTTTTAATGTCAACAGTTTAAGTTATAAGTATGAAACTGTTTATATTATGC
* * * * * *
479761 AAAAGTAAGATAAAACATGTTTCTCACGATAACGTAG
65 AAAAGTAAGACAAAACATGTTGCTTATGATAACATAC
* * *
479798 TAGGTAACA-CATTTTTT-ATGTCAGTC-GTTTAAGTTATAAGTATGAAACTATTTATATTATGC
1 TAGGTAACACCTTTTTTTAATGTCA-ACAGTTTAAGTTATAAGTATGAAACTGTTTATATTATGC
* *
479860 AAAAGTAAGACAAAACATGTTGATTATGATAACGTAC
65 AAAAGTAAGACAAAACATGTTGCTTATGATAACATAC
* * *
479897 TAGGTAACA-CTTTTTTTAATGTCAACAGTTTAAATTATAAGGATGAAACTGTTAATATTATGCA
1 TAGGTAACACCTTTTTTTAATGTCAACAGTTTAAGTTATAAGTATGAAACTGTTTATATTATGCA
479961 AAAGTAAGACAAAACATGTTGCTTATGATAACATAC
66 AAAGTAAGACAAAACATGTTGCTTATGATAACATAC
* * *
479997 TAGGTAACACCTTTTTTAAAATGTTAATCA-TTTAAGTTATAAGTATGAAACCGTTTATATTATG
1 TAGGTAACACCTTTTTT-TAATGTCAA-CAGTTTAAGTTATAAGTATGAAACTGTTTATATTATG
* * *
480061 -TAAAGTAAGACAAAACATGTT-TTTCATGATAACATAA
64 CAAAAGTAAGACAAAACATGTTGCTT-ATGATAACATAC
480098 TAGGTA
1 TAGGTA
480104 GTGTCTTTTT
Statistics
Matches: 270, Mismatches: 29, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
99 86 0.32
100 91 0.34
101 45 0.17
102 46 0.17
103 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (101 bp):
TAGGTAACACCTTTTTTTAATGTCAACAGTTTAAGTTATAAGTATGAAACTGTTTATATTATGCA
AAAGTAAGACAAAACATGTTGCTTATGATAACATAC
Found at i:480774 original size:77 final size:77
Alignment explanation
Indices: 480533--480774 Score: 200
Period size: 77 Copynumber: 3.1 Consensus size: 77
480523 CCATTTTTTT
* * * * * * * * *
480533 ACGTAACCTATTTTATTAATAAAAATATTAATATAACATACCATAACCTATTTTTTAATGAATCA
1 ACGTAACCTATTTTATTAATAAAAATATTAACATCATATATCACAACATATTTCTTAGTGAACCA
* *
480598 TTACATTCTTTA-
66 TAACATT-ATTAG
* * * * *
480610 TCGCAACCTATTTTATTAA-AAAAATATTAACATTACAGTACATATCACAACTTACATTCATAGT
1 ACGTAACCTATTTTATTAATAAAAATATTAACA-T-CA-T--ATATCACAACATA-TTTCTTAGT
* * *
480674 GAACCATAATATTCTTGG
60 GAACCATAACATTATTAG
* * *
480692 GCGTAACCTATTTTATTAATAAAAATATTAACATCATATATCGCAACATGTTTCTTAGTGAACCA
1 ACGTAACCTATTTTATTAATAAAAATATTAACATCATATATCACAACATATTTCTTAGTGAACCA
*
480757 TGACATTATTAG
66 TAACATTATTAG
480769 ACGTAA
1 ACGTAA
480775 TTGTATTTCT
Statistics
Matches: 128, Mismatches: 29, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
76 12 0.09
77 44 0.34
78 11 0.09
80 1 0.01
81 14 0.11
82 33 0.26
83 13 0.10
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (77 bp):
ACGTAACCTATTTTATTAATAAAAATATTAACATCATATATCACAACATATTTCTTAGTGAACCA
TAACATTATTAG
Found at i:481056 original size:2 final size:2
Alignment explanation
Indices: 481049--481113 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
481039 TCCTATTTCT
481049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
481091 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
481114 TCATAACATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:481943 original size:77 final size:77
Alignment explanation
Indices: 481857--482321 Score: 584
Period size: 77 Copynumber: 6.1 Consensus size: 77
481847 ATATATCTGA
* * * *
481857 AAAAT-GGTTGCGCCTAA-AGATGTCATGGTTCCCTAAGAAATAGGTTGAGATATGGAATGTTAA
1 AAAATGGGTTGCGCCCAAGA-ATGTCATGGTTCACTAAGAAATAGGTTGTGATATAGAATGTTAA
481920 TATTTTTATTAAT
65 TATTTTTATTAAT
* * *
481933 AAAATGGGTTGCGTCCAAGAATGTCATGGTTCACTAAGAAATAAGTTGTGATATAGAATATTAAT
1 AAAATGGGTTGCGCCCAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATAGAATGTTAAT
*
481998 ATTTTTATTGAT
66 ATTTTTATTAAT
* *
482010 AAAATGGGTTGCGCCCAAGAATGTTATGGTTCACTAAGAAATAGGTTGTGATCTAGAATGTTAAT
1 AAAATGGGTTGCGCCCAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATAGAATGTTAAT
482075 ATTTTTATTAAT
66 ATTTTTATTAAT
* * ** * *
482087 AAAATGGGTTGTGCCCAAGAATGTCATGGATCACTAAGAAATAGGTTGCAATCTGGAATGTTAAT
1 AAAATGGGTTGCGCCCAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATAGAATGTTAAT
*
482152 ATTTTATTTTAA-
66 ATTTT-TATTAAT
*** * * *
482164 AAAATGGGCTT-TAACCAA-ATATGTTATGGTTCATTAAGAAATAGGTTGTGATCTAGAATGTTA
1 AAAATGGG-TTGCGCCCAAGA-ATGTCATGGTTCACTAAGAAATAGGTTGTGATATAGAATGTTA
482227 ATATTTTTATTAAT
64 ATATTTTTATTAAT
* * * *
482241 AAAATAGGTTGCGCCCAAGAATGTTATGGTTCACTAAGAAAGTAAGTTGCGATAT-GCAATGTTA
1 AAAATGGGTTGCGCCCAAGAATGTCATGGTTCACTAAGAAA-TAGGTTGTGATATAG-AATGTTA
482305 ATATTTTTATT-AT
64 ATATTTTTATTAAT
482318 AAAA
1 AAAA
482322 AATTCAGAAG
Statistics
Matches: 341, Mismatches: 38, Indels: 19
0.86 0.10 0.05
Matches are distributed among these distances:
76 13 0.04
77 291 0.85
78 37 0.11
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (77 bp):
AAAATGGGTTGCGCCCAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATAGAATGTTAAT
ATTTTTATTAAT
Found at i:481955 original size:40 final size:40
Alignment explanation
Indices: 481911--482110 Score: 121
Period size: 40 Copynumber: 5.2 Consensus size: 40
481901 TTGAGATATG
*
481911 GAATGTTAATATTTTTATTAATAAAATGGGTTGCGTCCAA
1 GAATGTTAATATTTTTATTAATAAAATGGGTTGTGTCCAA
* ** * * * **
481951 GAATG-TCAT-GGTTCACTAA-GAAATAAGTTGTGAT--ATA
1 GAATGTTAATATTTTTATTAATAAAATGGGTTGTG-TCCA-A
* * * *
481988 GAATATTAATATTTTTATTGATAAAATGGGTTGCGCCCAA
1 GAATGTTAATATTTTTATTAATAAAATGGGTTGTGTCCAA
** * * * * *
482028 GAATGTT-AT-GGTTCACTAA-GAAATAGGTTGTGAT-CTA
1 GAATGTTAATATTTTTATTAATAAAATGGGTTGTG-TCCAA
*
482065 GAATGTTAATATTTTTATTAATAAAATGGGTTGTGCCCAA
1 GAATGTTAATATTTTTATTAATAAAATGGGTTGTGTCCAA
482105 GAATGT
1 GAATGT
482111 CATGGATCAC
Statistics
Matches: 108, Mismatches: 40, Indels: 24
0.63 0.23 0.14
Matches are distributed among these distances:
36 1 0.01
37 33 0.31
38 17 0.16
39 16 0.15
40 40 0.37
41 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (40 bp):
GAATGTTAATATTTTTATTAATAAAATGGGTTGTGTCCAA
Found at i:482057 original size:37 final size:37
Alignment explanation
Indices: 482011--482135 Score: 97
Period size: 37 Copynumber: 3.3 Consensus size: 37
482001 TTTATTGATA
*
482011 AAATGGGTTGCGCCCAAGAATGTTATGGTTCACTAAG
1 AAATAGGTTGCGCCCAAGAATGTTATGGTTCACTAAG
* ** * ** * * *
482048 AAATAGGTTGTGATCTAGAATGTTAATATTTTTATTAATA
1 AAATAGGTTGCGCCCAAGAATGTT-AT-GGTTCACTAA-G
* * * *
482088 AAATGGGTTGTGCCCAAGAATGTCATGGATCACTAAG
1 AAATAGGTTGCGCCCAAGAATGTTATGGTTCACTAAG
482125 AAATAGGTTGC
1 AAATAGGTTGC
482136 AATCTGGAAT
Statistics
Matches: 62, Mismatches: 23, Indels: 6
0.68 0.25 0.07
Matches are distributed among these distances:
37 28 0.45
38 7 0.11
39 8 0.13
40 19 0.31
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (37 bp):
AAATAGGTTGCGCCCAAGAATGTTATGGTTCACTAAG
Found at i:482245 original size:231 final size:231
Alignment explanation
Indices: 481876--482321 Score: 643
Period size: 231 Copynumber: 1.9 Consensus size: 231
481866 GCGCCTAAAG
* *
481876 ATGTCATGGTTCCCTAAGAAATAGGTTGAGATATGGAATGTTAATATTTTTATTAATAAAATGGG
1 ATGTCATGGATCACTAAGAAATAGGTTGAGATATGGAATGTTAATATTTTTATTAATAAAATGGG
**
481941 TTGCGTCCAAGAATGTCATGGTTCACTAAGAAATAAGTTGTGATATAGAATATTAATATTTTTAT
66 TTGCAACCAAGAATGTCATGGTTCACTAAGAAATAAGTTGTGATATAGAATATTAATATTTTTAT
* * * * *
482006 TGATAAAATGGGTTGCGCCCAAGAATGTTATGGTTCACTAAGAAA-TAGGTTGTGATCTAG-AAT
131 TAATAAAATAGGTTGCGCCCAAGAATGTTATGGTTCACTAAGAAAGTAAGTTGCGATAT-GCAAT
482069 GTTAATATTTTTATTAATAAAATGGGTTGTGCCCAAGA
195 GTTAATATTTTTATT-ATAAAATGGGTTGTGCCCAAGA
* *
482107 ATGTCATGGATCACTAAGAAATAGGTTGCA-ATCTGGAATGTTAATATTTTATTTTAA-AAAATG
1 ATGTCATGGATCACTAAGAAATAGGTTG-AGATATGGAATGTTAATATTTT-TATTAATAAAATG
* * * * * *
482170 GGCTT-TAACCAA-ATATGTTATGGTTCATTAAGAAATAGGTTGTGATCTAGAATGTTAATATTT
64 GG-TTGCAACCAAGA-ATGTCATGGTTCACTAAGAAATAAGTTGTGATATAGAATATTAATATTT
482233 TTATTAATAAAATAGGTTGCGCCCAAGAATGTTATGGTTCACTAAGAAAGTAAGTTGCGATATGC
127 TTATTAATAAAATAGGTTGCGCCCAAGAATGTTATGGTTCACTAAGAAAGTAAGTTGCGATATGC
482298 AATGTTAATATTTTTATTATAAAA
192 AATGTTAATATTTTTATTATAAAA
482322 AATTCAGAAG
Statistics
Matches: 192, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
230 1 0.01
231 155 0.81
232 36 0.19
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (231 bp):
ATGTCATGGATCACTAAGAAATAGGTTGAGATATGGAATGTTAATATTTTTATTAATAAAATGGG
TTGCAACCAAGAATGTCATGGTTCACTAAGAAATAAGTTGTGATATAGAATATTAATATTTTTAT
TAATAAAATAGGTTGCGCCCAAGAATGTTATGGTTCACTAAGAAAGTAAGTTGCGATATGCAATG
TTAATATTTTTATTATAAAATGGGTTGTGCCCAAGA
Found at i:482933 original size:101 final size:102
Alignment explanation
Indices: 482565--482996 Score: 479
Period size: 101 Copynumber: 4.3 Consensus size: 102
482555 GTTAAGCTCG
* * * * *
482565 TGATAACGTAGTAGGTAGCTCC-TTTTTCAATGTCAATC-ATTTAAGTTATAAGTAAGAAATCGT
1 TGATAACGTACTAGGTAGCGCCTTTTTTTAATGTCAATCGA-TTAAGTTATAAGTATGAAACCGT
* * * * *
482628 TTATATGATGCAAAAGTAAGACAAACCAAGTTTC-CTA
65 TTATATTATGCAAAAGTAAGACAAAACATGTTGCTCAA
* * * * * *
482665 TGATAACGTAATAAGTATCG-CTTTTTTT-ATGTCAATC-ATTTAACTTATAAGTATGACACCAT
1 TGATAACGTACTAGGTAGCGCCTTTTTTTAATGTCAATCGA-TTAAGTTATAAGTATGAAACCGT
*
482727 TTATATTATGAAAAAGTAAGACAAAACATGTTGCTCAA
65 TTATATTATGCAAAAGTAAGACAAAACATGTTGCTCAA
* * * * *
482765 TGATAACGTACTAGGTAGTGCCTTTTCTTAATGTCAATCGTTTAATTTGTAAGTATGAAACCGTT
1 TGATAACGTACTAGGTAGCGCCTTTTTTTAATGTCAATCGATTAAGTTATAAGTATGAAACCGTT
*
482830 TATATTATGCAAAAGTAAGATAAAACATGTTGCTC-A
66 TATATTATGCAAAAGTAAGACAAAACATGTTGCTCAA
* * * * * *
482866 TGATAATGTACTAGGTAGGGCCTTTTTTTAATGTC-ATCTGATTAAGTTATAAGCATGCAATCTT
1 TGATAACGTACTAGGTAGCGCCTTTTTTTAATGTCAATC-GATTAAGTTATAAGTATGAAACCGT
482930 TTATATTATGCAAAAGTAAGACAAAACATGTTGCTC-A
65 TTATATTATGCAAAAGTAAGACAAAACATGTTGCTCAA
* *
482967 TGATAACATGA-TAGGTAGCGCATTTTTTTA
1 TGATAACGT-ACTAGGTAGCGCCTTTTTTTA
482997 TGCAAAAGTG
Statistics
Matches: 282, Mismatches: 43, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
99 59 0.21
100 42 0.15
101 118 0.42
102 63 0.22
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (102 bp):
TGATAACGTACTAGGTAGCGCCTTTTTTTAATGTCAATCGATTAAGTTATAAGTATGAAACCGTT
TATATTATGCAAAAGTAAGACAAAACATGTTGCTCAA
Found at i:483303 original size:74 final size:73
Alignment explanation
Indices: 483225--483394 Score: 184
Period size: 73 Copynumber: 2.3 Consensus size: 73
483215 GAACCATATA
* * *
483225 ACATATGTATCGATATTTTAACTAT-CAATCATATTCATCAACTTGTTCAATATCTAAAAGTATC
1 ACATAAGTATCGATATTTCAAAT-TCCAATCATA-TCATCAACTTGTTCAATATCTAAAAGTATC
*
483289 GATCATAATC
64 GATAATAATC
* * * * * *
483299 ACATAAGTATCGATATTTCAAATTCCGATCTTATCTTCAACTTTTTTAATATTTAAAAGTATCGA
1 ACATAAGTATCGATATTTCAAATTCCAATCATATCATCAACTTGTTCAATATCTAAAAGTATCGA
483364 TAATAAT-
66 TAATAATC
* *
483371 ATATTAAGTATTGATATTT-AAATT
1 ACA-TAAGTATCGATATTTCAAATT
483395 TTTGAACTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
72 7 0.09
73 49 0.60
74 26 0.32
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (73 bp):
ACATAAGTATCGATATTTCAAATTCCAATCATATCATCAACTTGTTCAATATCTAAAAGTATCGA
TAATAATC
Found at i:483563 original size:82 final size:82
Alignment explanation
Indices: 483413--483689 Score: 406
Period size: 82 Copynumber: 3.4 Consensus size: 82
483403 ATTTTTTGTG
*
483413 CAACCTATTTTATTAATAAAAATATTAACA-T--A--ACATATCACAACATATTTCTTAGTGAAC
1 CAACCTATTTTATTAATAAAAATATTAACATTACATTACATATCACAACATATTTCTCAGTGAAC
* **
483473 CATGACATTCTTGGGTG
66 CATAACATTCTTGGGCA
* *
483490 CAACCTATTTTATT-ATAAAAATATTAGCATTACATTACATATCACAACATATTTTCTCAATGAA
1 CAACCTATTTTATTAATAAAAATATTAACATTACATTACATATCACAACATA-TTTCTCAGTGAA
483554 CCATAACATTCTTGGGCA
65 CCATAACATTCTTGGGCA
*
483572 CAACCTATTTTATTAA-AAAAATATTAACATTACATTACATATCACAACCTACTTTCTCAGTGAA
1 CAACCTATTTTATTAATAAAAATATTAACATTACATTACATATCACAACATA-TTTCTCAGTGAA
483636 CCATAACATTCTTGGGCA
65 CCATAACATTCTTGGGCA
* *
483654 CAAGCTATTTTATTAAGAAAAATATTAACATTACAT
1 CAACCTATTTTATTAATAAAAATATTAACATTACAT
483690 ATTGGAACTT
Statistics
Matches: 181, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
76 14 0.08
77 15 0.08
79 1 0.01
81 15 0.08
82 116 0.64
83 20 0.11
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (82 bp):
CAACCTATTTTATTAATAAAAATATTAACATTACATTACATATCACAACATATTTCTCAGTGAAC
CATAACATTCTTGGGCA
Found at i:483622 original size:44 final size:44
Alignment explanation
Indices: 483490--483622 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 44
483480 TTCTTGGGTG
* *
483490 CAACCTATTTTATTATAAAAATATTAGCATTACATTACATATCA
1 CAACCTATTTTATTAAAAAAATATTAACATTACATTACATATCA
* * * ** ** ***
483534 CAACATATTTTCTCAATGAACCA-TAACATT-C-TT---GGGCA
1 CAACCTATTTTATTAAAAAAATATTAACATTACATTACATATCA
483572 CAACCTATTTTATTAAAAAAATATTAACATTACATTACATATCA
1 CAACCTATTTTATTAAAAAAATATTAACATTACATTACATATCA
483616 CAACCTA
1 CAACCTA
483623 CTTTCTCAGT
Statistics
Matches: 61, Mismatches: 22, Indels: 12
0.64 0.23 0.13
Matches are distributed among these distances:
38 18 0.30
39 7 0.11
40 1 0.02
41 4 0.07
42 1 0.02
43 6 0.10
44 24 0.39
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.35
Consensus pattern (44 bp):
CAACCTATTTTATTAAAAAAATATTAACATTACATTACATATCA
Found at i:483935 original size:9 final size:9
Alignment explanation
Indices: 483911--483952 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
483901 AGGAGATTTA
*
483911 AAATTAATG
1 AAATAAATG
483920 AAAATAAATG
1 -AAATAAATG
483930 AAATAAAT-
1 AAATAAATG
483938 AAATAAATG
1 AAATAAATG
483947 AAATAA
1 AAATAA
483953 TGAGAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 8 0.27
9 14 0.47
10 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (9 bp):
AAATAAATG
Found at i:483963 original size:11 final size:11
Alignment explanation
Indices: 483947--483974 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
483937 TAAATAAATG
483947 AAATAATGAGA
1 AAATAATGAGA
483958 AAATAATGAGA
1 AAATAATGAGA
483969 AAATAA
1 AAATAA
483975 GTAAAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (11 bp):
AAATAATGAGA
Found at i:484549 original size:13 final size:13
Alignment explanation
Indices: 484531--484563 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
484521 AGCAACATGA
*
484531 AAAGAAAATAATG
1 AAAGAAAATAAAG
484544 AAAGAAAATAAAG
1 AAAGAAAATAAAG
484557 AAAGAAA
1 AAAGAAA
484564 TATGAGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:485447 original size:17 final size:19
Alignment explanation
Indices: 485403--485453 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
485393 AGCGCTTATT
* **
485403 TTTCCTCTCATTTTTTTATT
1 TTTCCTTTC-TTTTTTTAAA
485423 TTTCCTTT-TTTTTTTAAA
1 TTTCCTTTCTTTTTTTAAA
485441 TTT-CTTTCTTTTT
1 TTTCCTTTCTTTTT
485454 GCTCTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 16 0.59
20 7 0.26
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTCCTTTCTTTTTTTAAA
Found at i:499605 original size:15 final size:15
Alignment explanation
Indices: 499585--499634 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
499575 TCACATTAAA
499585 ATTTTATTTATATCT
1 ATTTTATTTATATCT
499600 ATTTTATTTA-A---
1 ATTTTATTTATATCT
*
499611 A-TTTATTTGTATCT
1 ATTTTATTTATATCT
499625 ATTTTATTTA
1 ATTTTATTTA
499635 AAATTTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
10 7 0.25
11 2 0.07
14 2 0.07
15 17 0.61
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (15 bp):
ATTTTATTTATATCT
Found at i:499612 original size:26 final size:27
Alignment explanation
Indices: 499580--499648 Score: 106
Period size: 25 Copynumber: 2.6 Consensus size: 27
499570 GTTACTCACA
499580 TTAAAATTTTATTTATATCTATTTTAT
1 TTAAAATTTTATTTATATCTATTTTAT
*
499607 TT-AAA-TTTATTTGTATCTATTTTAT
1 TTAAAATTTTATTTATATCTATTTTAT
499632 TTAAAATTTTATGTTAT
1 TTAAAATTTTAT-TTAT
499649 TGATAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 21 0.57
26 6 0.16
27 7 0.19
28 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (27 bp):
TTAAAATTTTATTTATATCTATTTTAT
Found at i:506326 original size:23 final size:23
Alignment explanation
Indices: 506300--506363 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
506290 CAGCTTGTAT
506300 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
506323 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
506346 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
506364 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:506552 original size:103 final size:103
Alignment explanation
Indices: 506379--506593 Score: 394
Period size: 103 Copynumber: 2.1 Consensus size: 103
506369 TAATGTCCAT
* *
506379 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
506444 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
506482 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
506547 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
506585 AAGGACCAC
1 AAGGACCAC
506594 GTAGACCCTC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:507957 original size:22 final size:21
Alignment explanation
Indices: 507932--507991 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
507922 TTTGCTTGAG
*
507932 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
507954 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
507974 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
507992 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:509248 original size:20 final size:21
Alignment explanation
Indices: 509197--509253 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
509187 CAATTTAATG
* *
509197 GTATCGATACTAAGCCTTGTA
1 GTATCGATACTAACCCTCGTA
*
509218 GTATTGATACTAACCCTCG-A
1 GTATCGATACTAACCCTCGTA
* *
509238 GTATCGGTACTCACCC
1 GTATCGATACTAACCC
509254 ATGGTATCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (21 bp):
GTATCGATACTAACCCTCGTA
Found at i:510412 original size:21 final size:21
Alignment explanation
Indices: 510347--510423 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 21
510337 ATAAAATCCA
*
510347 AATTGAA-TAAAGATTTCAATT
1 AATTGAATTAAA-ATTTAAATT
* *
510368 AATAGAATT-AAA-TAAAGATCT
1 AATTGAATTAAAATTTAA-AT-T
510389 AATTGAATTAAAATTTAAATT
1 AATTGAATTAAAATTTAAATT
510410 AATTGAATTGAAAA
1 AATTGAATT-AAAA
510424 AAAAGACCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.04
20 3 0.07
21 27 0.60
22 10 0.22
23 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (21 bp):
AATTGAATTAAAATTTAAATT
Found at i:512280 original size:41 final size:41
Alignment explanation
Indices: 512235--512695 Score: 681
Period size: 41 Copynumber: 11.2 Consensus size: 41
512225 AATTGGTTTA
* * *
512235 TGAATTACTATATGCTACCATGATCAAATCAAGTTTAATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
* * *
512276 TGAATTATTGTATTCTACCATGATCGAATCAAGTTGGATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
*
512317 TGAATTAATGTATGCTACCATGATCAAATCAAGTTGAATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
* *
512358 TGAATTATTGTATGCTACCACGAT-AGAATCAAGTTCAATGG
1 TGAATTATTGTATGCTACCATGATCA-AATCAAGTTGAATGG
* *
512399 TGAATTATTGTATGTTACCATGATCAAATCAAATTGAATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
*
512440 TGAATTATTGTATGCTACCACGATCAAATCAAGTTGAATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
*
512481 TGAATTATTGTATGCTACCATGATCTAATCAAGTTGAATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
* *
512522 TGAATTAATGTATGCTACCATGATCGAATCAAGTTGAATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
* * *
512563 TGAATTATTATATGCTATCATGATCGAATCAAGTTGAATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
* * *
512604 TGAATTATTGTATGCTACCATAACCGAATCAAGTTGAATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
* * *
512645 TGAATTATTGTATGCTACCATAACCGAATCAAGTTGAATGG
1 TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
*
512686 TGAACTATTG
1 TGAATTATTG
512696 CATGTTGTCA
Statistics
Matches: 386, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
40 1 0.00
41 384 0.99
42 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (41 bp):
TGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATGG
Found at i:512718 original size:5 final size:5
Alignment explanation
Indices: 512708--512736 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
512698 TGTTGTCATG
512708 ATTGA ATTGA ATTGA ATTGA ATTGA ATTG
1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTG
512737 TGAATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (5 bp):
ATTGA
Found at i:516699 original size:20 final size:20
Alignment explanation
Indices: 516670--516708 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
516660 TTTCCACTAC
*
516670 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
516690 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
516709 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:553858 original size:24 final size:25
Alignment explanation
Indices: 553817--553863 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
553807 AACTACAAAA
553817 AAATTTAGAAGCTCGATTGAAGCCT
1 AAATTTAGAAGCTCGATTGAAGCCT
* *
553842 AAATTTCG-AGCTTGATTGAAGC
1 AAATTTAGAAGCTCGATTGAAGC
553864 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (25 bp):
AAATTTAGAAGCTCGATTGAAGCCT
Found at i:561844 original size:21 final size:21
Alignment explanation
Indices: 561818--561860 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
561808 CCAGAAATGT
*
561818 TAAAAA-AATTAATGTTTTAGA
1 TAAAAATAA-TAATATTTTAGA
561839 TAAAAATAATAATATTTTAGA
1 TAAAAATAATAATATTTTAGA
561860 T
1 T
561861 TATTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAGA
Found at i:574778 original size:41 final size:40
Alignment explanation
Indices: 574517--574920 Score: 264
Period size: 41 Copynumber: 9.9 Consensus size: 40
574507 CATTTCTAGA
* * * *
574517 ACAAACGCCGGTAAAGACTCGT-ATTATAGCGACGTTTTAAT
1 ACAAACGCCGCTAAAGACT-GTAATT-TAGTGGCGTTTTTAT
* *
574558 AAAAACGCCGCTAAAGAC--TAATTTAGTGGCGTTTTTGT
1 ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTTAT
* * * **
574596 ACAAACGCCGCTATAGTACGAGT-CTTTACCGGCGTTTTTTAT
1 ACAAACGCCGCTAAAG-AC-TGTAATTTAGTGGCG-TTTTTAT
* * * *
574638 ACAAACGCCGCTATAA-ACT-CATTCTATAGCGGCGTTTTTAC
1 ACAAACGCCGCTA-AAGACTGTAAT-T-TAGTGGCGTTTTTAT
* * * * *
574679 AGAAACGCCGCTAAATAATTTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTTAT
* * *
574719 ACAAACGCTGCGAAAGACTGTAATTTAGTGGCGTTTTTAGA
1 ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTTA-T
* * *
574760 ACAAACGCCGCTATAGACTCGTGATTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACT-GTAATTTAGTGGCGTTTTTAT
* * * * *
574801 ACAAACACCGCTATAGTACGAGT-CTTTAGCGGCGTGTTTTAT
1 ACAAACGCCGCTAAAG-AC-TGTAATTTAGTGGCGT-TTTTAT
* * *
574843 ACAAACGCCGCTAAATACTCGTACTATAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACT-GTAATTTAGTGGCGTTTTTAT
* * * * * * *
574884 ATAAATGCCTCAAAATAATGTACTTTAGTGGCGTTTT
1 ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTT
574921 AAGCATAAAC
Statistics
Matches: 289, Mismatches: 55, Indels: 39
0.75 0.14 0.10
Matches are distributed among these distances:
38 26 0.09
39 5 0.02
40 65 0.22
41 112 0.39
42 80 0.28
43 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (40 bp):
ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTTAT
Found at i:574966 original size:12 final size:12
Alignment explanation
Indices: 574949--574974 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
574939 ATACTCGTAC
574949 ATTTTAAAATTA
1 ATTTTAAAATTA
574961 ATTTTAAAATTA
1 ATTTTAAAATTA
574973 AT
1 AT
574975 ATTGACCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:578933 original size:21 final size:21
Alignment explanation
Indices: 578909--578967 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
578899 TGATTTATTA
**
578909 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
578930 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
578951 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
578968 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:579186 original size:42 final size:44
Alignment explanation
Indices: 579159--579341 Score: 239
Period size: 43 Copynumber: 4.2 Consensus size: 44
579149 ACCAGATCTT
*
579159 TTGCGGTGTTTG-TGGGAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTTGGGAAAAACGCCGCTAAATCTCAACACCTA
579202 TTGCGGCGTTTGTTGGG-AAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTTGGGAAAAACGCCGCTAAATCTCAACACCTA
* * * * *
579245 TTGTGGCGTTTGTT-GGAGAAATGCCGCCAAATATCAACACCTA
1 TTGCGGCGTTTGTTGGGAAAAACGCCGCTAAATCTCAACACCTA
* * ***
579288 TTGCGGCGTTTGTT-GGAAAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTTGGGAAAAACGCCGCTAAATCTCAACACCTA
579331 TTGCGGCGTTT
1 TTGCGGCGTTT
579342 TTTGTTACCA
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
42 2 0.02
43 118 0.95
44 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (44 bp):
TTGCGGCGTTTGTTGGGAAAAACGCCGCTAAATCTCAACACCTA
Found at i:579330 original size:86 final size:84
Alignment explanation
Indices: 579120--579341 Score: 252
Period size: 86 Copynumber: 2.6 Consensus size: 84
579110 ATATGACATT
* * * *
579120 TTGCGGCGTTT-TT--AAAAACGCCGCTATATACCAGATCTTTTGCGGTGTTTGTGGGAAAAACG
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTATATATC-GACCTATTGCGGCGTTTGTGGGAAAAACG
* *
579182 CCGCTAAATCTCAACACCTA
65 CCGCCAAATATCAACACCTA
* * * * * * * *
579202 TTGCGGCGTTTGTTGGGAAAACGCCGCTAAATCTCAACACCTATTGTGGCGTTTGTTGGAGAAAT
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTATATATC--GACCTATTGCGGCGTTTGTGGGAAAAAC
579267 GCCGCCAAATATCAACACCTA
64 GCCGCCAAATATCAACACCTA
579288 TTGCGGCGTTTGTTGGAAAAACGCCGCTATATATCGTTACCTATTGCGGCGTTT
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTATATATCG--ACCTATTGCGGCGTTT
579342 TTTGTTACCA
Statistics
Matches: 115, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
82 11 0.10
83 2 0.02
85 15 0.13
86 87 0.76
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (84 bp):
TTGCGGCGTTTGTTGGAAAAACGCCGCTATATATCGACCTATTGCGGCGTTTGTGGGAAAAACGC
CGCCAAATATCAACACCTA
Found at i:581111 original size:68 final size:69
Alignment explanation
Indices: 580970--581150 Score: 174
Period size: 68 Copynumber: 2.6 Consensus size: 69
580960 CAAGACACTC
** * *
580970 TAATCCTTCGGGGCTTCCATGCGAG--ACATCCAGAATAATTATGAATAGGTGCTCCCGTACGAA
1 TAATCCTTTAGGGCTCCCATGCGAGACACAT-C-GAATAATTATGAATAGGTGCTCCCATACGAA
* *
581033 TTAATC
64 TCAATA
* * * * *
581039 TAATCTTTTAGGG-TCCCGTGGGAGACAC-TCGAAATAATTATGACTAGGTGCTCCCATGC-AAG
1 TAATCCTTTAGGGCTCCCATGCGAGACACATCG-AATAATTATGAATAGGTGCTCCCATACGAA-
*
581101 TCACTA
64 TCAATA
*
581107 TAATCCTTTAGGGCTCCCATGCGAGACACATTGAATAATTATGA
1 TAATCCTTTAGGGCTCCCATGCGAGACACATCGAATAATTATGA
581151 TTATATCAAG
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
67 3 0.03
68 48 0.53
69 35 0.39
70 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (69 bp):
TAATCCTTTAGGGCTCCCATGCGAGACACATCGAATAATTATGAATAGGTGCTCCCATACGAATC
AATA
Found at i:588914 original size:32 final size:31
Alignment explanation
Indices: 588837--588914 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
588827 CCTAAGGTGA
* *
588837 CTCTTAGATAGGCTCTGAGGCCCCGAGAACT
1 CTCTTAGATAGGCTCTCAGGCCCCAAGAACT
* * * *
588868 TTCTTGGGTAGGCTCTCAGGGCCCAAGATACT
1 CTCTTAGATAGGCTCTCAGGCCCCAAGA-ACT
*
588900 CTCTTAGATTGGCTC
1 CTCTTAGATAGGCTC
588915 CTTATATCAA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
31 22 0.61
32 14 0.39
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (31 bp):
CTCTTAGATAGGCTCTCAGGCCCCAAGAACT
Found at i:595965 original size:14 final size:14
Alignment explanation
Indices: 595940--596001 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
595930 AATCGGTTCA
*
595940 AGTCAACCCATCTG
1 AGTCAACTCATCTG
* *
595954 ATTCAACTCATCCG
1 AGTCAACTCATCTG
* * *
595968 AGTTAACTCGTCTC
1 AGTCAACTCATCTG
595982 AGTCAACTCATCTG
1 AGTCAACTCATCTG
595996 AGTCAA
1 AGTCAA
596002 TCAGTTGACT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (14 bp):
AGTCAACTCATCTG
Found at i:597495 original size:64 final size:65
Alignment explanation
Indices: 597422--597583 Score: 154
Period size: 64 Copynumber: 2.5 Consensus size: 65
597412 ATTGTTTGAA
* ***
597422 GGTGTATCGATGCACAAGTAGTGCATCGATGCACT-CTTTTAATCTAAA-AA-CATCGAATGCAA
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAA--TAAACAATCATCGAATGCAA
597484 TT
64 TT
* * * *
597486 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAACAATCATCGAATGTATT
1 GGTGCATCGATGCACAA-GTAGTGCATCGATGCACTCCCAGTAATAAACAATCATCGAATGCAAT
597549 T
65 T
** * *
597550 TATGCACCGATGCACAGGTAGTGCATCGATGCAC
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCAC
597584 CGATAGGGAA
Statistics
Matches: 78, Mismatches: 14, Indels: 11
0.76 0.14 0.11
Matches are distributed among these distances:
62 4 0.05
63 5 0.06
64 67 0.86
65 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (65 bp):
GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAATAAACAATCATCGAATGCAATT
Found at i:598595 original size:103 final size:103
Alignment explanation
Indices: 598370--598587 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
598360 GTCGAGGGTC
598370 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
598435 TTTATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
598473 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
598538 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
598576 TATGTGGTCCTT
1 TATGTGGTCCTT
598588 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:598653 original size:23 final size:23
Alignment explanation
Indices: 598603--598671 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
598593 CATTATTATA
* ** *
598603 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATGATATG
*
598626 CGGCAC-TCTGGTGCAATGATATG
1 TGGCACTTC-GGTGCAATGATATG
*
598649 TGGCACTTCGGTGCAATTATATG
1 TGGCACTTCGGTGCAATGATATG
598672 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 34 0.92
24 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATGATATG
Found at i:604260 original size:103 final size:104
Alignment explanation
Indices: 604074--604293 Score: 379
Period size: 103 Copynumber: 2.1 Consensus size: 104
604064 GTCGAGGGTC
604074 TATGTGGTCCTTCGGGACATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACAT
1 TATGTGGTCCTTCGGGA-ATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACAT
* *
604139 ACTTGATCCTTGGAATATGTATATGATTCTTAAGGAATGA
65 ACTTGATCCCTAGAATATGTATATGATTCTTAAGGAATGA
* *
604179 TATGTGGTCCTTCGGG-ATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 TATGTGGTCCTTCGGGAATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATA
*
604243 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 CTTGATCCCTAGAATATGTATATGATTCTTAAGGAATGA
604282 TATGTGGTCCTT
1 TATGTGGTCCTT
604294 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 94 0.85
105 16 0.15
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (104 bp):
TATGTGGTCCTTCGGGAATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATA
CTTGATCCCTAGAATATGTATATGATTCTTAAGGAATGA
Found at i:604344 original size:23 final size:23
Alignment explanation
Indices: 604310--604375 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
604300 ATTATTATAT
* *
604310 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTATACGC
* *
604333 GTCAC-TCTGGTGCAATTATACGT
1 GGCACTTC-GGTGCAATTATACGC
604356 GGCACTTCGGTGCAATTATA
1 GGCACTTCGGTGCAATTATA
604376 TGAGATGTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 33 0.92
24 2 0.06
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:606929 original size:31 final size:31
Alignment explanation
Indices: 606891--606978 Score: 108
Period size: 31 Copynumber: 2.8 Consensus size: 31
606881 TAAGGCAACC
*
606891 CTTGGGTAGGCTTTGAGGCCTCAAGAACTTT
1 CTTGGGTAGGCTTTGAGGCCCCAAGAACTTT
***
606922 CTTGGGTAGGCCCCGAGGCCCCGAA-AACTTT
1 CTTGGGTAGGCTTTGAGGCCCC-AAGAACTTT
606953 CTTGGGTAGGCTCTT-AGGCCCCAAGA
1 CTTGGGTAGGCT-TTGAGGCCCCAAGA
606979 TTCTCCCTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 2 0.04
31 43 0.91
32 2 0.04
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.25
Consensus pattern (31 bp):
CTTGGGTAGGCTTTGAGGCCCCAAGAACTTT
Found at i:623427 original size:21 final size:21
Alignment explanation
Indices: 623401--623447 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
623391 CTAATATTAC
*
623401 AATGTCAAAATTATGTGCAAA
1 AATGTCAAAATTAGGTGCAAA
*
623422 AATGTCAAAATTAGGTGCAAT
1 AATGTCAAAATTAGGTGCAAA
623443 AATGT
1 AATGT
623448 TTGAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (21 bp):
AATGTCAAAATTAGGTGCAAA
Found at i:628061 original size:21 final size:21
Alignment explanation
Indices: 628036--628083 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
628026 CCTAATATTG
628036 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
628057 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
628078 TAATGT
1 CAATGT
628084 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:633566 original size:16 final size:16
Alignment explanation
Indices: 633545--633575 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
633535 TTAAAGCTCA
633545 ACTCGAACTCAAAAAG
1 ACTCGAACTCAAAAAG
633561 ACTCGAACTCAAAAA
1 ACTCGAACTCAAAAA
633576 TAAATTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13
Consensus pattern (16 bp):
ACTCGAACTCAAAAAG
Found at i:633600 original size:30 final size:30
Alignment explanation
Indices: 633565--633624 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
633555 AAAAAGACTC
633565 GAACTCAAAAATAAATTCAAAAGATCAATT
1 GAACTCAAAAATAAATTCAAAAGATCAATT
*
633595 GAACTCAAAAATAAATTCAAGAGATCAATT
1 GAACTCAAAAATAAATTCAAAAGATCAATT
633625 AAAACTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.23
Consensus pattern (30 bp):
GAACTCAAAAATAAATTCAAAAGATCAATT
Found at i:633682 original size:59 final size:60
Alignment explanation
Indices: 633597--633710 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 60
633587 GATCAATTGA
* *
633597 ACTCAAAAATAAATTCAAGAGATCAATTAAAACT-TAAGTCTCAAACTCAATTAAAGTTCG
1 ACTCAAAAATAAATTCAAGAGATCAATTAAAACTCGAAAT-TCAAACTCAATTAAAGTTCG
* * *
633657 ACTCAAAAA-AATTTCAAGAGTTCAATTAAAGCTCGAAATTCAAACTCAATTAAA
1 ACTCAAAAATAAATTCAAGAGATCAATTAAAACTCGAAATTCAAACTCAATTAAA
633711 ACTCAATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 36 0.75
60 12 0.25
ACGTcount: A:0.49, C:0.17, G:0.08, T:0.26
Consensus pattern (60 bp):
ACTCAAAAATAAATTCAAGAGATCAATTAAAACTCGAAATTCAAACTCAATTAAAGTTCG
Found at i:633712 original size:11 final size:11
Alignment explanation
Indices: 633678--633757 Score: 52
Period size: 11 Copynumber: 7.1 Consensus size: 11
633668 TTTCAAGAGT
*
633678 TCAATTAAAGC
1 TCAATTAAAAC
*
633689 TCGAAATTCAAAC
1 TC--AATTAAAAC
633702 TCAATTAAAAC
1 TCAATTAAAAC
* **
633713 TCAATTTAAGT
1 TCAATTAAAAC
* *
633724 TCAATTGAAGC
1 TCAATTAAAAC
* *
633735 TCGATTCAAAC
1 TCAATTAAAAC
*
633746 TCAATTGAAAC
1 TCAATTAAAAC
633757 T
1 T
633758 GGAGAATTTA
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
11 45 0.83
13 9 0.17
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (11 bp):
TCAATTAAAAC
Found at i:633754 original size:22 final size:22
Alignment explanation
Indices: 633678--633751 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
633668 TTTCAAGAGT
633678 TCAATTAAAGCTCGAAATTCAAAC
1 TCAATTAAAGCTCG--ATTCAAAC
* * * **
633702 TCAATTAAAACTCAATTTAAGT
1 TCAATTAAAGCTCGATTCAAAC
*
633724 TCAATTGAAGCTCGATTCAAAC
1 TCAATTAAAGCTCGATTCAAAC
633746 TCAATT
1 TCAATT
633752 GAAACTGGAG
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 27 0.69
24 12 0.31
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (22 bp):
TCAATTAAAGCTCGATTCAAAC
Found at i:635458 original size:14 final size:14
Alignment explanation
Indices: 635439--635477 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
635429 CATAATCGGA
*
635439 TTTAGGGTTTATGT
1 TTTAGGGTTTAGGT
*
635453 TTTAGGATTTAGGT
1 TTTAGGGTTTAGGT
*
635467 TTTATGGTTTA
1 TTTAGGGTTTA
635478 AAGTTTAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (14 bp):
TTTAGGGTTTAGGT
Found at i:635461 original size:21 final size:21
Alignment explanation
Indices: 635436--635477 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
635426 TCACATAATC
*
635436 GGATTTAGGGTTTATGTTTTA
1 GGATTTAGGGTTTATGGTTTA
*
635457 GGATTTAGGTTTTATGGTTTA
1 GGATTTAGGGTTTATGGTTTA
635478 AAGTTTAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (21 bp):
GGATTTAGGGTTTATGGTTTA
Found at i:635540 original size:14 final size:14
Alignment explanation
Indices: 635521--635592 Score: 74
Period size: 14 Copynumber: 5.1 Consensus size: 14
635511 ATGAGATAAG
*
635521 TATGATTTAGGGTT
1 TATGATTTATGGTT
635535 TATGATTTA-GAGTT
1 TATGATTTATG-GTT
* *
635549 TAAGGTTTATGGTT
1 TATGATTTATGGTT
* *
635563 TAAGATTTATTGTT
1 TATGATTTATGGTT
*
635577 TATGGTTTATGGTT
1 TATGATTTATGGTT
635591 TA
1 TA
635593 GGGCTCATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
13 1 0.02
14 47 0.96
15 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (14 bp):
TATGATTTATGGTT
Found at i:635543 original size:7 final size:7
Alignment explanation
Indices: 635521--635592 Score: 65
Period size: 7 Copynumber: 10.3 Consensus size: 7
635511 ATGAGATAAG
*
635521 TATGATT
1 TATGGTT
*
635528 TAGGGTT
1 TATGGTT
*
635535 TATGATT
1 TATGGTT
635542 TA-GAGTT
1 TATG-GTT
*
635549 TAAGGTT
1 TATGGTT
635556 TATGGTT
1 TATGGTT
* *
635563 TAAGATT
1 TATGGTT
*
635570 TATTGTT
1 TATGGTT
635577 TATGGTT
1 TATGGTT
635584 TATGGTT
1 TATGGTT
635591 TA
1 TA
635593 GGGCTCATTA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
6 1 0.02
7 49 0.96
8 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (7 bp):
TATGGTT
Found at i:635571 original size:21 final size:21
Alignment explanation
Indices: 635524--635585 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
635514 AGATAAGTAT
* *
635524 GATTTAGGGTTTATGATTT-A
1 GATTTAAGGTTTATGGTTTAA
635544 GAGTTTAAGGTTTATGGTTTAA
1 GA-TTTAAGGTTTATGGTTTAA
**
635566 GATTTATTGTTTATGGTTTA
1 GATTTAAGGTTTATGGTTTA
635586 TGGTTTAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 2 0.06
21 31 0.86
22 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (21 bp):
GATTTAAGGTTTATGGTTTAA
Found at i:644574 original size:2 final size:2
Alignment explanation
Indices: 644567--644603 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
644557 ACAAGCTTCA
644567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
644604 ACTTCAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:648157 original size:35 final size:35
Alignment explanation
Indices: 648111--648186 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
648101 AAAACAGTCC
* *
648111 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
648146 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
648181 TCAATT
1 TCAATT
648187 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:648737 original size:130 final size:130
Alignment explanation
Indices: 648584--648831 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
648574 ATTTTATATA
* **
648584 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
648649 TTAGCACATGATCATGACACGTGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTAGTAACACATGTCACCACCTAATTATTTATATATGCT
648714 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
648779 TTAACACATGATCATGATATATGTTATTGGTAACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTAGTAACACATGTCACCACCTAATTA
648832 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTAGTAACACATGTCACCACCTAATTATTTATATATGCT
Found at i:648862 original size:130 final size:129
Alignment explanation
Indices: 648598--648862 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
648588 ATTTGGTCCT
* ** *
648598 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
648663 TGACACGTGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTAGTAACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
648728 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
648793 TGATATATGTTATTGGTAACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTAGTAACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
648857 -A
128 CA
648858 AAATT
1 AAATT
648863 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTAGTAACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:649313 original size:16 final size:18
Alignment explanation
Indices: 649292--649325 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
649282 ATTTCTTATT
649292 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
649308 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
649326 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:650106 original size:25 final size:26
Alignment explanation
Indices: 650074--650134 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
650064 TATATATATA
650074 TATTAACTTTAAAAAATAGT-TTTTAT
1 TATTAACTTTAAAAAATA-TATTTTAT
**
650100 T-TTAAC-TTATTAAATATATTTTAT
1 TATTAACTTTAAAAAATATATTTTAT
650124 TATTAACTTTA
1 TATTAACTTTA
650135 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 1 0.03
24 15 0.50
25 10 0.33
26 4 0.13
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (26 bp):
TATTAACTTTAAAAAATATATTTTAT
Found at i:650136 original size:17 final size:16
Alignment explanation
Indices: 650095--650150 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
650085 AAAAATAGTT
650095 TTTATTTTAACTTATTAAA
1 TTTATTTT-A-TTATT-AA
*
650114 TATATTTTATTATTAA
1 TTTATTTTATTATTAA
650130 CTTTATTTTTATT-TTAA
1 -TTTA-TTTTATTATTAA
650147 TTTA
1 TTTA
650151 AAAATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 6 0.18
17 12 0.36
18 8 0.24
19 7 0.21
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTATTTTATTATTAA
Found at i:650178 original size:41 final size:41
Alignment explanation
Indices: 650086--650179 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 41
650076 TTAACTTTAA
**
650086 AAAATAGTTTTTATTTTAACTTATTAAATATATTTTATTATT
1 AAAATA-TTTTTATTTTAACTTAAAAAATATATTTTATTATT
** * *
650128 AACTTTATTTTTATTTTAATTTAAAAATATATATTTTA-TGTT
1 AA-AATATTTTTATTTTAACTTAAAAA-ATATATTTTATTATT
650170 AAAATATTTT
1 AAAATATTTT
650180 AATATTAAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 6 0.14
42 24 0.57
43 12 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (41 bp):
AAAATATTTTTATTTTAACTTAAAAAATATATTTTATTATT
Found at i:650301 original size:33 final size:33
Alignment explanation
Indices: 650254--650326 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
650244 TTAAGATAAA
* *
650254 ATATACTTTTAAAAGTTAAAATAATAATAAAAT
1 ATATATTTTTAAAAGTTAAAATAAGAATAAAAT
* *
650287 ATTTATTTTTAAAAGTTTAAATAAGAATAAAAT
1 ATATATTTTTAAAAGTTAAAATAAGAATAAAAT
650320 ATATATT
1 ATATATT
650327 CTAAAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (33 bp):
ATATATTTTTAAAAGTTAAAATAAGAATAAAAT
Found at i:650854 original size:27 final size:31
Alignment explanation
Indices: 650780--650854 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
650770 TAACCCATGA
* *
650780 TGATCACATCTTAATTAAATAAAAACGAAAG
1 TGATCATATATTAATTAAATAAAAACGAAAG
650811 TGATCATATATTAATTAAATAAAAACGAAAG
1 TGATCATATATTAATTAAATAAAAACGAAAG
650842 TGA-CTATATATTA
1 TGATC-ATATATTA
650855 TGATTTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (31 bp):
TGATCATATATTAATTAAATAAAAACGAAAG
Found at i:651143 original size:23 final size:21
Alignment explanation
Indices: 651090--651143 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
651080 TCTTCTACAT
*
651090 TTTAGTTAAATTTTTATTTGA
1 TTTAGTTGAATTTTTATTTGA
* *
651111 TTTAATTTGAATTTTTTTTATGA
1 TTT-AGTTGAATTTTTATT-TGA
651134 TATTAGTTGA
1 T-TTAGTTGA
651144 TCGTAGGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 12 0.46
23 9 0.35
24 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (21 bp):
TTTAGTTGAATTTTTATTTGA
Found at i:651984 original size:17 final size:18
Alignment explanation
Indices: 651937--651985 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
651927 TATTTTATTT
651937 TAAT-TAAAATTT-ATAA
1 TAATATAAAATTTAATAA
* *
651953 TAATATAAATTTTAATGA
1 TAATATAAAATTTAATAA
651971 TAA-ATAAAATTTAAT
1 TAATATAAAATTTAAT
651986 CATACGAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.14
17 18 0.64
18 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATATAAAATTTAATAA
Found at i:656837 original size:22 final size:22
Alignment explanation
Indices: 656812--656864 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
656802 GAATCTCTAA
656812 TGTTGAAATTTCATGAATTTGT
1 TGTTGAAATTTCATGAATTTGT
656834 TGTTGAAATTTCATGAATTTGT
1 TGTTGAAATTTCATGAATTTGT
656856 TGTTGAAAT
1 TGTTGAAAT
656865 AACGTCGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (22 bp):
TGTTGAAATTTCATGAATTTGT
Found at i:657696 original size:15 final size:15
Alignment explanation
Indices: 657678--657734 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
657668 AAGAAATAGA
657678 GGAAGAAGAGGAAGT
1 GGAAGAAGAGGAAGT
** *
657693 GGAAGTTGAGGAAGA
1 GGAAGAAGAGGAAGT
** *
657708 GGTGGAAGAGGAGGT
1 GGAAGAAGAGGAAGT
657723 GGAAGAAGAGGA
1 GGAAGAAGAGGA
657735 TGAGGATGCT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.51, T:0.09
Consensus pattern (15 bp):
GGAAGAAGAGGAAGT
Found at i:657714 original size:24 final size:24
Alignment explanation
Indices: 657676--657734 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
657666 TGAAGAAATA
* * *
657676 GAGGAAGAAGAGGAAGTGGAAGTT
1 GAGGAAGAGGAGGAAGAGGAAGTG
* *
657700 GAGGAAGAGGTGGAAGAGGAGGTG
1 GAGGAAGAGGAGGAAGAGGAAGTG
*
657724 GAAGAAGAGGA
1 GAGGAAGAGGA
657735 TGAGGATGCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.51, T:0.08
Consensus pattern (24 bp):
GAGGAAGAGGAGGAAGAGGAAGTG
Found at i:657723 original size:12 final size:12
Alignment explanation
Indices: 657703--657733 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
657693 GGAAGTTGAG
657703 GAAGAGGTGGAA
1 GAAGAGGTGGAA
*
657715 GAGGAGGTGGAA
1 GAAGAGGTGGAA
657727 GAAGAGG
1 GAAGAGG
657734 ATGAGGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.55, T:0.06
Consensus pattern (12 bp):
GAAGAGGTGGAA
Found at i:657734 original size:30 final size:30
Alignment explanation
Indices: 657682--657739 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
657672 AATAGAGGAA
**
657682 GAAGAGGAAGTGGAAGTTGAGGAAGAGGTG
1 GAAGAGGAAGTGGAAGAAGAGGAAGAGGTG
* *
657712 GAAGAGGAGGTGGAAGAAGAGGATGAGG
1 GAAGAGGAAGTGGAAGAAGAGGAAGAGG
657740 ATGCTGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.52, T:0.10
Consensus pattern (30 bp):
GAAGAGGAAGTGGAAGAAGAGGAAGAGGTG
Found at i:660592 original size:2 final size:2
Alignment explanation
Indices: 660585--660614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
660575 TATTCTTAAA
660585 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
660615 TCTATGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:664231 original size:12 final size:12
Alignment explanation
Indices: 664214--664252 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
664204 GAGTTCGAGT
*
664214 ATTTTAAATAAA
1 ATTTTAAATATA
*
664226 ATTTT-AATTTA
1 ATTTTAAATATA
664237 ATTTTAAATATA
1 ATTTTAAATATA
664249 ATTT
1 ATTT
664253 CATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTTAAATATA
Found at i:672086 original size:21 final size:22
Alignment explanation
Indices: 672060--672110 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
672050 AAGTTTTGGG
* *
672060 TTTATTTCAAAATTTCTAT-AT
1 TTTATTTCAAAATATATATAAT
*
672081 TTTATTTTTAAAATATATATAAT
1 TTTA-TTTCAAAATATATATAAT
672104 TTTATTT
1 TTTATTT
672111 TTTAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.16
22 15 0.60
23 6 0.24
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTATTTCAAAATATATATAAT
Found at i:672122 original size:2 final size:2
Alignment explanation
Indices: 672117--672143 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
672107 ATTTTTTAAT
672117 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 T
672144 TAAAATTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:672126 original size:25 final size:23
Alignment explanation
Indices: 672079--672124 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
672069 AAATTTCTAT
672079 ATTTTATTTTTAAAATATATATA
1 ATTTTATTTTTAAAATATATATA
* *
672102 ATTTTATTTTTTAATTATATATA
1 ATTTTATTTTTAAAATATATATA
672125 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTATTTTTAAAATATATATA
Found at i:672777 original size:46 final size:46
Alignment explanation
Indices: 672689--672777 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
672679 ACGCCATTCC
* **
672689 AATTTAAATATCATCTCAAACTACAGAAAAAGAATTTTAATATTTA
1 AATTTAAATATCATCTCAAACTACAGAAAAAGAAATCAAATATTTA
*
672735 AATTTAAATATCATCTCAAACTACAGAAAAATAAATCAAATAT
1 AATTTAAATATCATCTCAAACTACAGAAAAAGAAATCAAATAT
672778 AATTTAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (46 bp):
AATTTAAATATCATCTCAAACTACAGAAAAAGAAATCAAATATTTA
Found at i:676221 original size:20 final size:20
Alignment explanation
Indices: 676196--676265 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
676186 TCAGTTTTAA
*
676196 TTTGGGTTAACCTTTAAATT
1 TTTGGGTCAACCTTTAAATT
* *
676216 TTTGGGTCAACGTTTAGATT
1 TTTGGGTCAACCTTTAAATT
** ** *
676236 TTCAGGTCAATTTTTAGATT
1 TTTGGGTCAACCTTTAAATT
*
676256 TTCGGGTCAA
1 TTTGGGTCAA
676266 TTATTATCGC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (20 bp):
TTTGGGTCAACCTTTAAATT
Found at i:676266 original size:20 final size:20
Alignment explanation
Indices: 676208--676267 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
676198 TGGGTTAACC
* * **
676208 TTTAAATTTTTGGGTCAACG
1 TTTAGATTTTCGGGTCAATT
*
676228 TTTAGATTTTCAGGTCAATT
1 TTTAGATTTTCGGGTCAATT
676248 TTTAGATTTTCGGGTCAATT
1 TTTAGATTTTCGGGTCAATT
676268 ATTATCGCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.48
Consensus pattern (20 bp):
TTTAGATTTTCGGGTCAATT
Found at i:679992 original size:12 final size:12
Alignment explanation
Indices: 679969--680009 Score: 73
Period size: 12 Copynumber: 3.3 Consensus size: 12
679959 AATTTGAAAC
679969 TGTTTAGACAAAA
1 TGTTT-GACAAAA
679982 TGTTTGACAAAA
1 TGTTTGACAAAA
679994 TGTTTGACAAAA
1 TGTTTGACAAAA
680006 TGTT
1 TGTT
680010 GCAGAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (12 bp):
TGTTTGACAAAA
Found at i:683157 original size:147 final size:147
Alignment explanation
Indices: 682890--683185 Score: 592
Period size: 147 Copynumber: 2.0 Consensus size: 147
682880 CTACTCGAAC
682890 TGTTGTTAGTCGAACCACAGGAGAAAAAATTTCATTGAAATCAATACCTTCTTTTTGAGCATATC
1 TGTTGTTAGTCGAACCACAGGAGAAAAAATTTCATTGAAATCAATACCTTCTTTTTGAGCATATC
682955 CTTTGAACACCAATCTTGCACGATACCTCTCAACTTGATCGTCACCATTTCGCTTGATTTTGAAG
66 CTTTGAACACCAATCTTGCACGATACCTCTCAACTTGATCGTCACCATTTCGCTTGATTTTGAAG
683020 ACCCATTTGTTACCAAT
131 ACCCATTTGTTACCAAT
683037 TGTTGTTAGTCGAACCACAGGAGAAAAAATTTCATTGAAATCAATACCTTCTTTTTGAGCATATC
1 TGTTGTTAGTCGAACCACAGGAGAAAAAATTTCATTGAAATCAATACCTTCTTTTTGAGCATATC
683102 CTTTGAACACCAATCTTGCACGATACCTCTCAACTTGATCGTCACCATTTCGCTTGATTTTGAAG
66 CTTTGAACACCAATCTTGCACGATACCTCTCAACTTGATCGTCACCATTTCGCTTGATTTTGAAG
683167 ACCCATTTGTTACCAAT
131 ACCCATTTGTTACCAAT
683184 TG
1 TG
683186 GCTTCCTTCC
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 149 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (147 bp):
TGTTGTTAGTCGAACCACAGGAGAAAAAATTTCATTGAAATCAATACCTTCTTTTTGAGCATATC
CTTTGAACACCAATCTTGCACGATACCTCTCAACTTGATCGTCACCATTTCGCTTGATTTTGAAG
ACCCATTTGTTACCAAT
Found at i:690201 original size:21 final size:22
Alignment explanation
Indices: 690161--690208 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
690151 GGTACTGATA
690161 CCCCTCTATGGGTATCAATACT
1 CCCCTCTATGGGTATCAATACT
* *
690183 CCCCTTTAT-GGTATTAATACT
1 CCCCTCTATGGGTATCAATACT
*
690204 TCCCT
1 CCCCT
690209 GAGTATCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.21, C:0.31, G:0.10, T:0.38
Consensus pattern (22 bp):
CCCCTCTATGGGTATCAATACT
Found at i:705554 original size:23 final size:23
Alignment explanation
Indices: 705486--705546 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
705476 ACATTTTATA
*
705486 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * *
705509 CGACACTTCAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
705532 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
705547 TTTATACGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:710926 original size:26 final size:28
Alignment explanation
Indices: 710905--710963 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 28
710895 TAAGCTCGCG
*
710905 AGTTTTCGAGTCGAGTCGAGCTTCATTTCAA
1 AGTTTTCGAGTCGAGTCGAGC-TC--TGCAA
*
710936 AGTTTTCGAGTCGAGTCGAGCTCAGCAA
1 AGTTTTCGAGTCGAGTCGAGCTCTGCAA
710964 TACTCGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
30 2 0.08
31 21 0.81
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (28 bp):
AGTTTTCGAGTCGAGTCGAGCTCTGCAA
Found at i:715397 original size:25 final size:25
Alignment explanation
Indices: 715363--715412 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
715353 GATCAGGGGT
715363 ACTGAAGCATAAACATATAGTGATA
1 ACTGAAGCATAAACATATAGTGATA
*
715388 ACTGAAGCATAAACATGTAGTGATA
1 ACTGAAGCATAAACATATAGTGATA
715413 TGGTGCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (25 bp):
ACTGAAGCATAAACATATAGTGATA
Found at i:715968 original size:18 final size:18
Alignment explanation
Indices: 715922--715957 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
715912 AGGGTTCTAC
*
715922 GTGGTCCTATGGGACATA
1 GTGGTCCTACGGGACATA
715940 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
715958 TGTGTTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (18 bp):
GTGGTCCTACGGGACATA
Found at i:715971 original size:28 final size:28
Alignment explanation
Indices: 715940--716013 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
715930 ATGGGACATA
715940 GTGGTCCTACGGGACATATGTGTTCTAC
1 GTGGTCCTACGGGACATATGTGTTCTAC
*
715968 GTGGTCCTACAGGACATATGTGTTCTAC
1 GTGGTCCTACGGGACATATGTGTTCTAC
* *
715996 ATGGTCCTGCGGGACATA
1 GTGGTCCTACGGGACATA
716014 GTGGTCCTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (28 bp):
GTGGTCCTACGGGACATATGTGTTCTAC
Found at i:723163 original size:7 final size:8
Alignment explanation
Indices: 723147--723174 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
723137 AATATAATAT
723147 AATAAAAA
1 AATAAAAA
723155 AATAAAAA
1 AATAAAAA
723163 AATAAAAA
1 AATAAAAA
723171 AATA
1 AATA
723175 TAAACGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AATAAAAA
Found at i:724579 original size:34 final size:32
Alignment explanation
Indices: 724515--724641 Score: 145
Period size: 31 Copynumber: 3.9 Consensus size: 32
724505 TTTTCTAACA
*
724515 TACTAAAATTCTAAC-TTTTATTTTATTTGTTC
1 TACTAACATTCTAACTTTTTATTTTA-TTGTTC
*
724547 ATAATAACATTCTAACTTTTTATTTTTATTGTTC
1 -TACTAACATTCTAACTTTTTA-TTTTATTGTTC
724581 --CTAACATTCTAACTTTTTATTTTTATTGTTC
1 TACTAACATTCTAACTTTTTA-TTTTATTGTTC
*
724612 TCACTAAC-TTACTAACATTTTATTTTATTG
1 T-ACTAACATT-CTAACTTTTTATTTTATTG
724642 CACAAACTAA
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
31 30 0.36
33 23 0.27
34 26 0.31
35 5 0.06
ACGTcount: A:0.28, C:0.14, G:0.03, T:0.55
Consensus pattern (32 bp):
TACTAACATTCTAACTTTTTATTTTATTGTTC
Found at i:724627 original size:65 final size:63
Alignment explanation
Indices: 724517--724641 Score: 157
Period size: 65 Copynumber: 2.0 Consensus size: 63
724507 TTCTAACATA
*
724517 CTAAAATTCTAACTTTTATTTTATTTGTTCATAATAACATTCTAACTTTTTATTTTTATTGTTC
1 CTAAAATTCTAACTTTTATTTTATTTGTTCATAATAACATTCTAACATTTTA-TTTTATTGTTC
* *
724581 CTAACATTCTAACTTTTTATTTT-TATTGTTC-TCACTAAC-TTACTAACATTTTATTTTATTG
1 CTAAAATTCTAAC-TTTTATTTTAT-TTGTTCAT-AATAACATT-CTAACATTTTATTTTATTG
724642 CACAAACTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
64 24 0.44
65 30 0.56
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.55
Consensus pattern (63 bp):
CTAAAATTCTAACTTTTATTTTATTTGTTCATAATAACATTCTAACATTTTATTTTATTGTTC
Found at i:724803 original size:26 final size:25
Alignment explanation
Indices: 724758--724815 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
724748 AAACAACCCC
724758 CTAACTTTTATTTTATTTGTTCATA
1 CTAACTTTTATTTTATTTGTTCATA
*
724783 CTAACTTTTCATTTT-TATTGTTCTTA
1 CTAACTTTT-ATTTTAT-TTGTTCATA
724809 CTAACTT
1 CTAACTT
724816 ACTAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.59
Consensus pattern (25 bp):
CTAACTTTTATTTTATTTGTTCATA
Found at i:725024 original size:20 final size:20
Alignment explanation
Indices: 724999--725047 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
724989 TTTTCCAAAT
724999 TCGCAACACGAATATATAAA
1 TCGCAACACGAATATATAAA
** * *
725019 TCGCAACGTGAATTTGTAAA
1 TCGCAACACGAATATATAAA
725039 TCGCAACAC
1 TCGCAACAC
725048 AGAAATCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (20 bp):
TCGCAACACGAATATATAAA
Found at i:725062 original size:20 final size:20
Alignment explanation
Indices: 725039--725106 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
725029 AATTTGTAAA
*
725039 TCGCAACACAGAAATCAAAT
1 TCGCAACACAGAATTCAAAT
* *
725059 TCGCAACGCA-ATTTCCAAAT
1 TCGCAACACAGAATT-CAAAT
* *
725079 TTGCAACACTGAATTTCAAAT
1 TCGCAACACAGAA-TTCAAAT
725100 TCGCAAC
1 TCGCAAC
725107 TCGATTTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
19 2 0.05
20 21 0.57
21 12 0.32
22 2 0.05
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (20 bp):
TCGCAACACAGAATTCAAAT
Found at i:725063 original size:40 final size:41
Alignment explanation
Indices: 724946--725126 Score: 147
Period size: 41 Copynumber: 4.5 Consensus size: 41
724936 ATTTCGTAAA
* * ** *
724946 CAATTTCCAAATTCGCAACGC-GGATATGTAATTCACAACG
1 CAATTTCCAAATTCGCAACACAGAATATCAAATTCGCAACG
* *
724986 CGATTTTCCAAATTCGCAACAC-GAATAT-ATAAATCGCAACG
1 C-AATTTCCAAATTCGCAACACAGAATATCA-AATTCGCAACG
* **
725027 TGAATTTGTAAA-TCGCAACACAGAA-ATCAAATTCGCAACG
1 -CAATTTCCAAATTCGCAACACAGAATATCAAATTCGCAACG
* * * *
725067 CAATTTCCAAATTTGCAACACTGAATTTCAAATTCGCAACT
1 CAATTTCCAAATTCGCAACACAGAATATCAAATTCGCAACG
* **
725108 CGATTTTTAAATTCGCAAC
1 CAATTTCCAAATTCGCAAC
725127 TCGATTTTCG
Statistics
Matches: 112, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
39 8 0.07
40 33 0.29
41 71 0.63
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (41 bp):
CAATTTCCAAATTCGCAACACAGAATATCAAATTCGCAACG
Found at i:725121 original size:20 final size:20
Alignment explanation
Indices: 725053--725145 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
725043 AACACAGAAA
* *
725053 TCAAATTCGCAACGCAATTT
1 TCAAATTCGCAACTCGATTT
* * * *
725073 CCAAATTTGCAACACTGAATT
1 TCAAATTCGCAACTC-GATTT
725094 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACTCGATTT
*
725114 TTAAATTCGCAACTCGATTT
1 TCAAATTCGCAACTCGATTT
*
725134 TCGAATTCGCAA
1 TCAAATTCGCAA
725146 TACGAATTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 45 0.75
21 15 0.25
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (20 bp):
TCAAATTCGCAACTCGATTT
Found at i:725970 original size:12 final size:12
Alignment explanation
Indices: 725949--725982 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
725939 ACCACATTTC
*
725949 CAATACCAAACA
1 CAATATCAAACA
725961 CAATATCAAACA
1 CAATATCAAACA
*
725973 CAATCTCAAA
1 CAATATCAAA
725983 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:728729 original size:29 final size:29
Alignment explanation
Indices: 728672--728729 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
728662 TTGCGATTTT
* **
728672 TTGTTGCGAAAGTCAAATTCGCATTGCGA
1 TTGTTGCGAAAGTAAAATTCGCAACGCGA
728701 TTGTTGCGAAAGTAAAATTCGCAACGCGA
1 TTGTTGCGAAAGTAAAATTCGCAACGCGA
728730 ATTTGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (29 bp):
TTGTTGCGAAAGTAAAATTCGCAACGCGA
Found at i:728782 original size:20 final size:20
Alignment explanation
Indices: 728757--728798 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
728747 ATCGTAACAT
*
728757 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCGCATTGC
728777 GAATTTGACTTTCGCATTGC
1 GAATTTGACTTTCGCATTGC
728797 GA
1 GA
728799 GACTGTACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
GAATTTGACTTTCGCATTGC
Found at i:730308 original size:21 final size:21
Alignment explanation
Indices: 730279--730342 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
730269 AAACGGTGGA
* *
730279 AGGGACCTCTTGAACAATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
730300 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
730321 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
730342 A
1 A
730343 ACTGAATCAG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.20
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:730504 original size:4 final size:4
Alignment explanation
Indices: 730483--730528 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
730473 GGGCCGCTAA
* *
730483 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
730529 TGCCGAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:731559 original size:2 final size:2
Alignment explanation
Indices: 731554--731585 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
731544 AAAAAAGAAA
731554 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
731586 CAAAGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.