Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 33
Found at i:454832 original size:146 final size:149
Alignment explanation
Indices: 454556--454894 Score: 392
Period size: 146 Copynumber: 2.3 Consensus size: 149
454546 TTTTGAAAAT
* *
454556 ATATGATATATAGTTTTTAAAAATATTTTTG--AAA-ATATATATTATATCGTTTTGAAAACTTT
1 ATAT-ATATATAG-TTTTGAAAATATTTTTGAAAAACATATATATTATATAGTTTTGAAAACTTT
* * *
454618 TAAAAATATATATATATATAATATAATTTTTAAAAAAAGTTTTGAAAAACATATATATTATATGG
64 TAAAAATATATACATATATAATATAAGTTTTAAAAAAAGTTTTGAAAAACATATATATTATATAG
*
454683 TTTTGAAAATTAGTTTTTAAA
129 TTTTAAAAATTAGTTTTTAAA
* *
454704 A-ATCTATATAGTTTTGAAAACATTTTTGAAAAACATATATATTATATAGTTTTGAAAA-TTAGT
1 ATATATATATAGTTTTGAAAATATTTTTGAAAAACATATATATTATATAGTTTTGAAAACTT--T
*** * *
454767 TTTTAA-ATATACATAT-T-ATAT-AGTTTTAAAAATTAGCTTTT-AAAAATATATATATTATAT
64 TAAAAATATATACATATATAATATAAGTTTTAAAAA-AAG-TTTTGAAAAACATATATATTATAT
454827 AGTTTTAAAAATTAGTTTTTAAA
127 AGTTTTAAAAATTAGTTTTTAAA
*
454850 ATATATATTATATGGTTTTGAAAATTATTTTTTAAAAACATATAT
1 ATATATA-TATA--GTTTTGAAAA-TATTTTTGAAAAACATATAT
454895 TGTGTAATTT
Statistics
Matches: 163, Mismatches: 16, Indels: 21
0.81 0.08 0.10
Matches are distributed among these distances:
145 25 0.15
146 53 0.33
147 16 0.10
148 37 0.23
149 4 0.02
150 10 0.06
151 18 0.11
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (149 bp):
ATATATATATAGTTTTGAAAATATTTTTGAAAAACATATATATTATATAGTTTTGAAAACTTTTA
AAAATATATACATATATAATATAAGTTTTAAAAAAAGTTTTGAAAAACATATATATTATATAGTT
TTAAAAATTAGTTTTTAAA
Found at i:454923 original size:4 final size:4
Alignment explanation
Indices: 454914--454977 Score: 92
Period size: 4 Copynumber: 15.5 Consensus size: 4
454904 TTAAAAAATG
*
454914 TTAT TTAT TTAT TTAT TTAT TTAT TTAT CTAT TTATT TTATT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTA-T TTAT TTAT
*
454964 TTAT TTAT CTAT TT
1 TTAT TTAT TTAT TT
454978 TCTTTCTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
4 46 0.84
5 9 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:456373 original size:2 final size:2
Alignment explanation
Indices: 456368--456400 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
456358 TCTGTTTTTC
*
456368 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
456401 TTATTCTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:458729 original size:54 final size:54
Alignment explanation
Indices: 458665--458827 Score: 292
Period size: 54 Copynumber: 3.0 Consensus size: 54
458655 TGGCTACCGA
458665 GGCCGTGGGCGTGGAGGATACAATGGACCCCATTTCGACAGGCAGCAAGATGAT
1 GGCCGTGGGCGTGGAGGATACAATGGACCCCATTTCGACAGGCAGCAAGATGAT
*
458719 GGCCGTGGGCGTGGAGGATACAATGGACCGCAGTTT-GACAGGCAGCAAGATGAT
1 GGCCGTGGGCGTGGAGGATACAATGGACCCCA-TTTCGACAGGCAGCAAGATGAT
*
458773 GGCCGTGGGCGTGGAGGATACAATGGACCCCAGTTCGACAGGCAGCAAGATGAT
1 GGCCGTGGGCGTGGAGGATACAATGGACCCCATTTCGACAGGCAGCAAGATGAT
458827 G
1 G
458828 TCTACAACTA
Statistics
Matches: 104, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
53 2 0.02
54 99 0.95
55 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.37, T:0.16
Consensus pattern (54 bp):
GGCCGTGGGCGTGGAGGATACAATGGACCCCATTTCGACAGGCAGCAAGATGAT
Found at i:465225 original size:38 final size:38
Alignment explanation
Indices: 465174--465250 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
465164 GTAAATGTCG
*
465174 TACACCTTATACTTCTCCCGAAATAAGAAAATCCAAAA
1 TACACCTTATACTTCTCACGAAATAAGAAAATCCAAAA
465212 TACACCTTATACTTCTCACGAAATAAGAAAATCCAAAA
1 TACACCTTATACTTCTCACGAAATAAGAAAATCCAAAA
465250 T
1 T
465251 TTAAACTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (38 bp):
TACACCTTATACTTCTCACGAAATAAGAAAATCCAAAA
Found at i:471236 original size:13 final size:13
Alignment explanation
Indices: 471218--471272 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
471208 TACGTCATAA
*
471218 ATTTATGACGCGT
1 ATTTATGACGCGC
* *
471231 ATTTATGACACAC
1 ATTTATGACGCGC
*
471244 ATTTATGGCGCGC
1 ATTTATGACGCGC
*
471257 ATTTATGACGCTC
1 ATTTATGACGCGC
471270 ATT
1 ATT
471273 GTGCGTCATT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:471358 original size:85 final size:84
Alignment explanation
Indices: 471254--471409 Score: 235
Period size: 85 Copynumber: 1.8 Consensus size: 84
471244 ATTTATGGCG
*
471254 CGCATTTATGACGCTCATTGTGCGTCATTGAAG-CCCCAGTCATAAATGAAGACGACACACATTT
1 CGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCA-TCATAAATGAAGACGACACACA-TT
471318 GTGTGTCATAAATTTATAACA
64 GTGTGTCATAAATTTATAACA
* * *
471339 CGCATTTATGAC-TTACATTGCGTGTCATTGAAGCCCCCATCATAAATGAAGATGACACACATTG
1 CGCATTTATGACGCT-CATTGCGCGTCATTGAAGCCCCCATCATAAATGAAGACGACACACATTG
471403 TGTGTCA
65 TGTGTCA
471410 AAGAGTATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
84 11 0.17
85 49 0.75
86 5 0.08
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (84 bp):
CGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCATCATAAATGAAGACGACACACATTGT
GTGTCATAAATTTATAACA
Found at i:475345 original size:19 final size:18
Alignment explanation
Indices: 475321--475366 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
475311 AATGTGCTGC
475321 AAAATGAACATACATTAGA-
1 AAAATGAACAT-CATTA-AT
475340 AAAATGAAACATCATTAAT
1 AAAATG-AACATCATTAAT
475359 AAAATGAA
1 AAAATGAA
475367 TGAACATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.12
19 17 0.68
20 5 0.20
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.22
Consensus pattern (18 bp):
AAAATGAACATCATTAAT
Found at i:477482 original size:22 final size:22
Alignment explanation
Indices: 477457--477507 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
477447 ATGCATGGTG
477457 TGAACATGAATGCCTTAATGAC
1 TGAACATGAATGCCTTAATGAC
*
477479 TGAACATGAATGCCTTAATGAG
1 TGAACATGAATGCCTTAATGAC
477501 TGAACAT
1 TGAACAT
477508 TCATGGATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (22 bp):
TGAACATGAATGCCTTAATGAC
Found at i:481830 original size:29 final size:30
Alignment explanation
Indices: 481798--481864 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
481788 ATTATTTTAA
*
481798 ATATTTTAAACTATT-AA-ATCTTATAAAAT
1 ATATTTTAAAATATTGAAGAT-TTATAAAAT
* *
481827 ATATATTTAAAATTTTGAAGATTTTTAAAAT
1 ATAT-TTTAAAATATTGAAGATTTATAAAAT
481858 ATATTTT
1 ATATTTT
481865 TTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.12
30 12 0.38
31 14 0.44
32 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (30 bp):
ATATTTTAAAATATTGAAGATTTATAAAAT
Found at i:484105 original size:3 final size:3
Alignment explanation
Indices: 484097--484336 Score: 480
Period size: 3 Copynumber: 80.0 Consensus size: 3
484087 AGCTCTTTTC
484097 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
484145 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
484193 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
484241 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
484289 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
484337 CATTTTGTTA
Statistics
Matches: 237, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 237 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:485245 original size:23 final size:24
Alignment explanation
Indices: 485201--485245 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
485191 TACTTAAATT
*
485201 TAATATAAATATAGTTTATTTTTG
1 TAATATAAAAATAGTTTATTTTTG
*
485225 TAATCTAAAAATA-TTTATTTT
1 TAATATAAAAATAGTTTATTTT
485246 CAATTATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATATAAAAATAGTTTATTTTTG
Found at i:485404 original size:35 final size:35
Alignment explanation
Indices: 485363--485448 Score: 163
Period size: 35 Copynumber: 2.5 Consensus size: 35
485353 AAAATATTAT
*
485363 ATTTATATTTAAAAATCTAGTTAATTGATAATAAA
1 ATTTATAATTAAAAATCTAGTTAATTGATAATAAA
485398 ATTTATAATTAAAAATCTAGTTAATTGATAATAAA
1 ATTTATAATTAAAAATCTAGTTAATTGATAATAAA
485433 ATTTATAATTAAAAAT
1 ATTTATAATTAAAAAT
485449 TTATAAAACT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (35 bp):
ATTTATAATTAAAAATCTAGTTAATTGATAATAAA
Found at i:486440 original size:26 final size:26
Alignment explanation
Indices: 486386--486445 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
486376 TGTATAAATA
**
486386 TTATTTATATTATGTCTTGACGGATT
1 TTATTTATATTATGTCCAGACGGATT
*
486412 TTATTTATATTATGTCCAGA-GTATCT
1 TTATTTATATTATGTCCAGACGGAT-T
486438 TTATTTAT
1 TTATTTAT
486446 TATTTATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (26 bp):
TTATTTATATTATGTCCAGACGGATT
Found at i:488550 original size:21 final size:20
Alignment explanation
Indices: 488526--488566 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
488516 GAAAATAAAC
488526 TTATGAATAAAAAAAAATATT
1 TTATGAA-AAAAAAAAATATT
* *
488547 TTATTAAAAAAATAAATATT
1 TTATGAAAAAAAAAAATATT
488567 AAAATTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TTATGAAAAAAAAAAATATT
Found at i:489410 original size:14 final size:14
Alignment explanation
Indices: 489391--489431 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
489381 TTAAATTATT
489391 AATTATTTTATTTA
1 AATTATTTTATTTA
489405 AATTATTTT-TATTA
1 AATTATTTTAT-TTA
*
489419 AATGA-TTTATTTA
1 AATTATTTTATTTA
489432 TTGATTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
AATTATTTTATTTA
Found at i:489416 original size:15 final size:14
Alignment explanation
Indices: 489386--489426 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
489376 TAACTTTAAA
489386 TTATT-AATTA-TT
1 TTATTAAATTATTT
489398 TTATTTAAATTATTT
1 TTA-TTAAATTATTT
*
489413 TTATTAAATGATTT
1 TTATTAAATTATTT
489427 ATTTATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 3 0.12
13 2 0.08
14 15 0.60
15 5 0.20
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TTATTAAATTATTT
Found at i:491054 original size:21 final size:21
Alignment explanation
Indices: 491030--491095 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
491020 AACAATTCTC
491030 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAATCCT
* **
491051 TTCATGAAAAGGTTAAGCCCTT
1 TTCATGAAAAGATTAAATCC-T
*
491073 TTCATCAAAAGGA-TAAATCCT
1 TTCATGAAAA-GATTAAATCCT
491094 TT
1 TT
491096 AATTGAAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
21 20 0.56
22 15 0.42
23 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (21 bp):
TTCATGAAAAGATTAAATCCT
Found at i:491094 original size:22 final size:22
Alignment explanation
Indices: 491030--491095 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
491020 AACAATTCTC
491030 TTCATGAAAA-GATTAAATCC-T
1 TTCATGAAAAGGA-TAAATCCTT
* **
491051 TTCATGAAAAGGTTAAGCCCTT
1 TTCATGAAAAGGATAAATCCTT
*
491073 TTCATCAAAAGGATAAATCCTT
1 TTCATGAAAAGGATAAATCCTT
491095 T
1 T
491096 AATTGAAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.42
22 21 0.58
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
TTCATGAAAAGGATAAATCCTT
Found at i:492500 original size:16 final size:15
Alignment explanation
Indices: 492479--492541 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
492469 TTAAACATAC
492479 AAATATAGAAAAAATT
1 AAATATA-AAAAAATT
*
492495 AAATATAAAAAATTT
1 AAATATAAAAAAATT
*
492510 AAA-AT--TAAAATT
1 AAATATAAAAAAATT
492522 AAATTATTAAAAAAATT
1 AAA-TA-TAAAAAAATT
492539 AAA
1 AAA
492542 AAATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
12 8 0.21
14 3 0.08
15 11 0.29
16 7 0.18
17 9 0.24
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
AAATATAAAAAAATT
Found at i:492506 original size:14 final size:14
Alignment explanation
Indices: 492487--492541 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
492477 ACAAATATAG
492487 AAAAAATTAAATAT
1 AAAAAATTAAATAT
492501 AAAAAATTTAAA-AT
1 AAAAAA-TTAAATAT
*
492515 -TAAAATTAAATTATT
1 AAAAAATTAAA-TA-T
492530 AAAAAAATTAAA
1 -AAAAAATTAAA
492542 AAATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
12 5 0.15
13 4 0.12
14 9 0.27
15 6 0.18
17 9 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAAATTAAATAT
Found at i:492521 original size:27 final size:29
Alignment explanation
Indices: 492489--492542 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
492479 AAATATAGAA
*
492489 AAAATTAAA-TA-TAAAAAATTTAAAATT
1 AAAATTAAATTATTAAAAAAATTAAAATT
492516 AAAATTAAATTATTAAAAAAATTAAAA
1 AAAATTAAATTATTAAAAAAATTAAAA
492543 AATATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.38
28 2 0.08
29 13 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
AAAATTAAATTATTAAAAAAATTAAAATT
Found at i:492652 original size:21 final size:22
Alignment explanation
Indices: 492608--492655 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
492598 TTAGAGAATT
* * *
492608 TTTTCTCTCTGAACATGGTTGA
1 TTTTCTCTCTGAACAAGATCGA
492630 TTTT-TCTCTGAACAAGATCGA
1 TTTTCTCTCTGAACAAGATCGA
492651 TTTTC
1 TTTTC
492656 CTTGGTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.46
Consensus pattern (22 bp):
TTTTCTCTCTGAACAAGATCGA
Found at i:496466 original size:18 final size:18
Alignment explanation
Indices: 496443--496484 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
496433 GTAATCAAAG
496443 TTCACCTCGATATTTTCA
1 TTCACCTCGATATTTTCA
496461 TTCACCTCGATATTTTCA
1 TTCACCTCGATATTTTCA
496479 TTCACC
1 TTCACC
496485 CCGCCTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.31, G:0.05, T:0.43
Consensus pattern (18 bp):
TTCACCTCGATATTTTCA
Found at i:498362 original size:94 final size:94
Alignment explanation
Indices: 498238--498425 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
498228 ACTCAGATGG
498238 AGCATGCAGAGCAACTTCGGGACTGGCCACAGTAGGGGGCTTATCAGATATGAGAACAACCAATG
1 AGCATGCAGAGCAACTTCGGGACTGGCCACAGTAGGGGGCTTATCAGATATGAGAACAACCAATG
498303 GATTCAGGGGTTCATGTACAACATCGGCA
66 GATTCAGGGGTTCATGTACAACATCGGCA
498332 AGCATGCAGAGCAACTTCGGGACTGGCCACAGTAGGGGGCTTATCAGATATGAGAACAACCAATG
1 AGCATGCAGAGCAACTTCGGGACTGGCCACAGTAGGGGGCTTATCAGATATGAGAACAACCAATG
498397 GATTCAGGGGTTCATGTACAACATCGGCA
66 GATTCAGGGGTTCATGTACAACATCGGCA
498426 GAACTACAAG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (94 bp):
AGCATGCAGAGCAACTTCGGGACTGGCCACAGTAGGGGGCTTATCAGATATGAGAACAACCAATG
GATTCAGGGGTTCATGTACAACATCGGCA
Found at i:501910 original size:23 final size:23
Alignment explanation
Indices: 501884--501928 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
501874 CACCACAGCT
*
501884 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
501907 CGTAGAATTGTACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
501929 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:502195 original size:141 final size:146
Alignment explanation
Indices: 501896--502203 Score: 475
Period size: 150 Copynumber: 2.1 Consensus size: 146
501886 TATAAATGCA
*
501896 CCGAAGTG-CCGCGTAGAATTGTACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
501960 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAG-A--ATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTT-ACACATGT
* *
502025 TCCACAGAATATATATATATC
126 TCCAAAGAATATACATATATC
*
502046 CCGAAGGACCGCGTAGTATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
502111 TCCTTAAG-A-AT-CATATACTAGGGATCAAGTATGTGTCTTT-CAAGACTT-CACATGTTCCAA
66 TCCTTAAGAATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTACACATGTTCCAA
*
502171 AGAATATACATATGTC
131 AGAATATACATATATC
*
502187 CCGAAGGACCACGTAGA
1 CCGAAGGACCGCGTAGA
502204 CCCTCTACCC
Statistics
Matches: 150, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
141 40 0.27
143 8 0.05
144 29 0.19
145 2 0.01
146 1 0.01
149 1 0.01
150 69 0.46
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (146 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTACACATGTTCCAA
AGAATATACATATATC
Found at i:504526 original size:149 final size:150
Alignment explanation
Indices: 504348--504654 Score: 544
Period size: 150 Copynumber: 2.1 Consensus size: 150
504338 GGTAGAGGGT
* * *
504348 CTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGATACAT
1 CTACGCGGTCCTTCGGGACATATATATATTCTATGGAACATGTGTGAAGTCTTGGAAAGACACAT
504412 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
504477 TATGGCACTACGGTACAATA
131 TATGGCACTACGGTACAATA
* *
504497 CTACGTGGTCCTTCGGGATATATATATATTCTATGGAACATGTGTGAAGTCTTGGAAAGACACAT
1 CTACGCGGTCCTTCGGGACATATATATATTCTATGGAACATGTGTGAAGTCTTGGAAAGACACAT
504562 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
* *
504627 TATGGCACTACGGTGCAATT
131 TATGGCACTACGGTACAATA
504647 CTACGCGG
1 CTACGCGG
504655 CACTTTGGTG
Statistics
Matches: 149, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
149 49 0.33
150 100 0.67
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (150 bp):
CTACGCGGTCCTTCGGGACATATATATATTCTATGGAACATGTGTGAAGTCTTGGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTACAATA
Found at i:505437 original size:2 final size:2
Alignment explanation
Indices: 505430--505463 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
505420 AAGACAATTT
505430 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
505464 AAGCCTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:505914 original size:41 final size:41
Alignment explanation
Indices: 505860--506207 Score: 615
Period size: 41 Copynumber: 8.4 Consensus size: 41
505850 ATTCGCGTTG
* * *
505860 CATTTCGCATTGCGATAGTTGGAAATTGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
505901 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTT--G--CGATTTTC
*
505946 CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
505987 CATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
506028 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
506069 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
506110 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
506151 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
506192 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
506208 TTTCCATTTC
Statistics
Matches: 296, Mismatches: 7, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
41 255 0.86
43 2 0.01
45 39 0.13
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:505958 original size:24 final size:24
Alignment explanation
Indices: 505893--505961 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 24
505883 AATTGCGTTG
505893 CGATTTTCCATTTCGCGTTGCGAT
1 CGATTTTCCATTTCGCGTTGCGAT
* ** **
505917 --A-GTTGAAAATCGCGTTGCGAT
1 CGATTTTCCATTTCGCGTTGCGAT
505938 CGATTTTCCATTTCGCGTTGCGAT
1 CGATTTTCCATTTCGCGTTGCGAT
505962 AGTTGAAAAT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 15 0.47
22 1 0.03
23 1 0.03
24 15 0.47
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (24 bp):
CGATTTTCCATTTCGCGTTGCGAT
Found at i:506241 original size:41 final size:40
Alignment explanation
Indices: 506196--506316 Score: 149
Period size: 41 Copynumber: 3.0 Consensus size: 40
506186 ATTTTCCATT
506196 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT-AAAA
* * *
506237 TCGCGTTGCGATTTTTCATTTCGCATTGCGATAGTCTACAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TAAAA
*
506278 T-GTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTTAAAA
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTTAAAA
506317 AAAAGATTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
39 4 0.06
40 12 0.17
41 50 0.71
42 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (40 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTAAAA
Found at i:506288 original size:21 final size:19
Alignment explanation
Indices: 506262--506311 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
506252 TCATTTCGCA
*
506262 TTGCGATAGTCTACAATGTCG
1 TTGCGATAGTCCA-AAT-TCG
**
506283 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAATTCG
506302 TTGCGATAGT
1 TTGCGATAGT
506312 TAAAAAAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 11 0.46
20 3 0.12
21 10 0.42
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:506396 original size:6 final size:6
Alignment explanation
Indices: 506388--506438 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
506378 GACACGTACT
*
506388 ACCACT ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
506436 ACC
1 ACC
506439 CGAGACAGAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.33, C:0.51, G:0.14, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:506943 original size:6 final size:6
Alignment explanation
Indices: 506932--506975 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
506922 TCGTCTCGTC
506932 TCGTGG TCGTGG TCGTGG TC---G TCGTGG TCGTGG TCGTGG TCGTG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTG
506976 ATAATACGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
6 32 0.91
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:506957 original size:15 final size:15
Alignment explanation
Indices: 506937--506968 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
506927 TCGTCTCGTG
506937 GTCGTGGTCGTGGTC
1 GTCGTGGTCGTGGTC
506952 GTCGTGGTCGTGGTC
1 GTCGTGGTCGTGGTC
506967 GT
1 GT
506969 GGTCGTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.34
Consensus pattern (15 bp):
GTCGTGGTCGTGGTC
Found at i:506957 original size:21 final size:21
Alignment explanation
Indices: 506932--506974 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
506922 TCGTCTCGTC
506932 TCGTGGTCGTGGTCGTGGTCG
1 TCGTGGTCGTGGTCGTGGTCG
506953 TCGTGGTCGTGGTCGTGGTCG
1 TCGTGGTCGTGGTCGTGGTCG
506974 T
1 T
506975 GATAATACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.35
Consensus pattern (21 bp):
TCGTGGTCGTGGTCGTGGTCG
Found at i:507183 original size:6 final size:6
Alignment explanation
Indices: 507172--507218 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
507162 TCGTCTCGTC
507172 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTG
507219 ATAATACGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:507365 original size:41 final size:40
Alignment explanation
Indices: 507320--507551 Score: 153
Period size: 41 Copynumber: 5.8 Consensus size: 40
507310 ACTGTAGACT
*
507320 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGATTTT-AACTATCGCAACGCGAATTGGAAA
507361 ATCGCAACGCGA--TT---T-TCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGATTTTAACTATCGCAACGCGAA-TTGGAAA
* * *
507394 ATCGCAACGACAACTGTAGACTATCGCAA--CGAATTTGGAAA
1 ATCGCAACG-CGATTTTA-ACTATCGCAACGCGAA-TTGGAAA
* * * *
507435 ATCACAACGACAATTGTAGACTATCGCAACGCGAACTGGAAA
1 ATCGCAACG-CGATTTTA-ACTATCGCAACGCGAATTGGAAA
* ** * * ** *
507477 ATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCAACT
1 ATCGCAACGCG-ATTTTAACTATCGCAACGCGAATTGGAA-A
507518 ATCGCAACGCGATTTTCAACTATCGCAACGCGAA
1 ATCGCAACGCGATTTT-AACTATCGCAACGCGAA
507552 ATGCAACGCG
Statistics
Matches: 155, Mismatches: 21, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
32 4 0.03
33 15 0.10
34 8 0.05
35 1 0.01
36 1 0.01
39 2 0.01
40 18 0.12
41 72 0.46
42 30 0.19
43 4 0.03
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGATTTTAACTATCGCAACGCGAATTGGAAA
Found at i:507400 original size:19 final size:19
Alignment explanation
Indices: 507376--507444 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
507366 AACGCGATTT
507376 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
507395 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
507417 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
*
507436 TCACAACGA
1 TCGCAACGA
507445 CAATTGTAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 21 0.55
20 2 0.05
21 2 0.05
22 13 0.34
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:507422 original size:22 final size:21
Alignment explanation
Indices: 507394--507465 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
507384 AATTTGGAAA
507394 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAA-TGTAGACT
* * **
507416 ATCGCAACG--AATTTGGAAA
1 ATCGCAACGACAATGTAGACT
*
507435 ATCACAACGACAATTGTAGACT
1 ATCGCAACGACAA-TGTAGACT
507457 ATCGCAACG
1 ATCGCAACG
507466 CGAACTGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 2 0.05
22 21 0.57
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCGCAACGACAATGTAGACT
Found at i:507482 original size:20 final size:20
Alignment explanation
Indices: 507457--507508 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
507447 ATTGTAGACT
*
507457 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
507477 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
507497 ATCGCAACGCGA
1 ATCGCAACGCGA
507509 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:507523 original size:21 final size:21
Alignment explanation
Indices: 507497--507550 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
507487 GAAATGGAAA
507497 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
507518 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
507539 ATCGCAACGCGA
1 ATCGCAACGCGA
507551 AATGCAACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:507558 original size:21 final size:21
Alignment explanation
Indices: 507454--507558 Score: 97
Period size: 21 Copynumber: 5.1 Consensus size: 21
507444 ACAATTGTAG
* *
507454 ACTATCGCAACGCGAACTGGA
1 ACTATCGCAACGCGAAATGCA
* *
507475 A-AATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
507495 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
** *
507515 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
507536 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
507557 AC
1 AC
507559 GCGAATTTAC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 34 0.47
21 39 0.53
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:508373 original size:23 final size:23
Alignment explanation
Indices: 508346--508412 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
508336 TGCCAAATAT
*
508346 TTGTCCCGAAGGATCACATAGGA
1 TTGTCCCGAAGGACCACATAGGA
508369 TTGTCCCGAAGGACCACATAGGA
1 TTGTCCCGAAGGACCACATAGGA
508392 TTGTCCCGAAGGACCACATAG
1 TTGTCCCGAAGGACCACATAG
508413 ATCCCTCGAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGGA
Found at i:514561 original size:39 final size:39
Alignment explanation
Indices: 514515--514617 Score: 143
Period size: 39 Copynumber: 2.6 Consensus size: 39
514505 TCCTTAAACC
*
514515 ACCAACTTATACTCCTCCGCCCAAAGCACCACCCAAGCA
1 ACCAACTTATACTCCTCCACCCAAAGCACCACCCAAGCA
* * * * *
514554 ACTAACTTATGCTCCTTCACCCAAAGCACCACCCATGCC
1 ACCAACTTATACTCCTCCACCCAAAGCACCACCCAAGCA
*
514593 ACCAACTTATCCTCCTCCACCCAAA
1 ACCAACTTATACTCCTCCACCCAAA
514618 CAGTTCAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.31, C:0.46, G:0.06, T:0.17
Consensus pattern (39 bp):
ACCAACTTATACTCCTCCACCCAAAGCACCACCCAAGCA
Found at i:522568 original size:20 final size:20
Alignment explanation
Indices: 522543--522611 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
522533 TTTTCCCAAT
522543 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
522563 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
*
522584 TCGTAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
522604 TCGCAATG
1 TCGCAATG
522612 TGATACTGAC
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:522626 original size:20 final size:20
Alignment explanation
Indices: 522603--522717 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
522593 GAATAAGTAA
* *
522603 ATCGCAATGTGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
522623 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
522644 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
522664 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
522684 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
522704 TTCGCAACGCGATA
1 ATCGCAACGCGATA
522718 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:522646 original size:41 final size:41
Alignment explanation
Indices: 522601--522731 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
522591 GCGAATAAGT
* * * *
522601 AAATCGCAATGTGATACTGACTATCGCAATGCGATAATACA
1 AAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACA
* *
522642 AAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC-
1 AAATCGCAACGAGATACTGACTTTCGCAACGCGATAAT-ACA
** * *
522683 -TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACA
1 AAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACA
*
522723 TAATCGCAA
1 AAATCGCAA
522732 TGCGATTTTC
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.42
41 38 0.52
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
AAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACA
Found at i:523182 original size:20 final size:20
Alignment explanation
Indices: 523133--523196 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
523123 GCGATTTTAG
*
523133 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
* *
523153 ATTCACGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
523173 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
523193 TTTC
1 TTTC
523197 AGAAACTATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:524350 original size:66 final size:66
Alignment explanation
Indices: 524244--524375 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
524234 GAGGAAACAG
524244 ACCTTGCAATGGGAAGATTTACTACGGTATACGACAATAAATAATGTAAGTTATCATAAATACTA
1 ACCTTGCAATGGGAAGATTTACTACGGTATACGACAATAAATAATGTAAGTTATCATAAATACTA
524309 C
66 C
524310 ACCTTGCAATGGGAAGATTTACTACGGTATACGACAATAAATAATGTAAGTTATCATAAATACTA
1 ACCTTGCAATGGGAAGATTTACTACGGTATACGACAATAAATAATGTAAGTTATCATAAATACTA
524375 C
66 C
524376 CATATGTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (66 bp):
ACCTTGCAATGGGAAGATTTACTACGGTATACGACAATAAATAATGTAAGTTATCATAAATACTA
C
Found at i:524583 original size:18 final size:18
Alignment explanation
Indices: 524557--524601 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
524547 CTCCACTTCG
*
524557 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
524575 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
524593 GAGCCATCA
1 GAGCCATCA
524602 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:525028 original size:20 final size:21
Alignment explanation
Indices: 524988--525030 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
524978 CTAAACTGTT
524988 TTTGTTAGTATTTGTTTTTGG
1 TTTGTTAGTATTTGTTTTTGG
525009 TTTGTT-GT-TTTGTCTTTTGG
1 TTTGTTAGTATTTGT-TTTTGG
525029 TT
1 TT
525031 GAAGTAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 10 0.48
21 6 0.29
ACGTcount: A:0.05, C:0.02, G:0.23, T:0.70
Consensus pattern (21 bp):
TTTGTTAGTATTTGTTTTTGG
Found at i:525138 original size:19 final size:20
Alignment explanation
Indices: 525084--525129 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
525074 TAGTTTACTT
* *
525084 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
525104 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
525124 TCGCAA
1 TCGCAA
525130 TGTGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:525158 original size:14 final size:14
Alignment explanation
Indices: 525139--525196 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
525129 ATGTGAAATG
525139 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
525153 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
525169 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
525185 AAAATCGCAACG
1 AAAATCGCAACG
525197 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:525181 original size:32 final size:32
Alignment explanation
Indices: 525123--525213 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
525113 GGAAATGGCT
*
525123 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
525156 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
525188 ATCGCAACGCGAAATGGAAATCGCAA
1 ATCGCAATGCGAAAT-GAAATCGCAA
525214 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:525208 original size:19 final size:18
Alignment explanation
Indices: 525123--525218 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 18
525113 GGAAATGGCT
*
525123 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
525142 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
525156 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
525174 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
*
525188 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAAT-GAA
525207 ATCGCAATGCGA
1 ATCGCAATGCGA
525219 TTTGTGTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 18 0.29
16 12 0.19
17 3 0.05
18 9 0.15
19 20 0.32
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:525293 original size:20 final size:19
Alignment explanation
Indices: 525256--525310 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
525246 TTGCGATTTT
* *
525256 CATTTCGTGTTACGATAGC
1 CATTTCGCGTTGCGATAGC
*
525275 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
525295 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
525311 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:527192 original size:14 final size:14
Alignment explanation
Indices: 527173--527208 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
527163 ATTGTTTAAT
527173 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
527187 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
527201 TGATTTGT
1 TGATTTGT
527209 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:527333 original size:14 final size:14
Alignment explanation
Indices: 527314--527367 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
527304 CGAAATGGCT
527314 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
527328 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
527347 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
527361 ATCGCAA
1 ATCGCAA
527368 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:527385 original size:33 final size:33
Alignment explanation
Indices: 527295--527372 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
527285 CAAACAGACT
* ***
527295 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
527328 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
527361 ATCGCAATGCGA
1 ATCGCAATGCGA
527373 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:527416 original size:20 final size:20
Alignment explanation
Indices: 527391--527448 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
527381 TCGCATTGCG
*
527391 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
527411 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
527431 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
527449 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:528539 original size:23 final size:24
Alignment explanation
Indices: 528484--528541 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
528474 AGTCAGTATT
*
528484 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACC
*
528508 CGAACTTTGATATTGGTCAATA-C
1 CGAAATTTGATATTGGTCAATACC
*
528531 CGAATTTTGAT
1 CGAAATTTGAT
528542 GATGTTTCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACC
Found at i:531193 original size:33 final size:33
Alignment explanation
Indices: 531151--531276 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
531141 GGAAATTACT
531151 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
531184 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
531216 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
531250 ATCGCAATGCGAAATGAAAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCGCAAC
531277 ACGAATTTAA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:531258 original size:66 final size:66
Alignment explanation
Indices: 531152--531276 Score: 241
Period size: 66 Copynumber: 1.9 Consensus size: 66
531142 GAAATTACTA
531152 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
531217 T
66 T
*
531218 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAAC
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAAC
531277 ACGAATTTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.15
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
T
Found at i:531477 original size:14 final size:14
Alignment explanation
Indices: 531458--531494 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
531448 CATCAATTAA
531458 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
531472 ACAAATCACCTTTT
1 ACAAATCAACTTTT
531486 ACAAATCAA
1 ACAAATCAA
531495 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:532907 original size:21 final size:21
Alignment explanation
Indices: 532841--532907 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
532831 GTGAATCGGG
*
532841 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
532861 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
532883 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
532904 CTCT
1 CTCT
532908 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:534999 original size:20 final size:19
Alignment explanation
Indices: 534954--535108 Score: 79
Period size: 19 Copynumber: 8.8 Consensus size: 19
534944 TCTTTTGGTT
534954 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
534973 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
534994 GAAATGACTATCGCAAC--
1 GAAATGAAAATCGCAACGA
*
535011 G--AT-AGAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
535027 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
535041 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
535057 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
535074 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
535093 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
535109 TGCGATTTTT
Statistics
Matches: 106, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
14 27 0.25
15 3 0.03
16 5 0.05
17 4 0.04
18 1 0.01
19 35 0.33
20 29 0.27
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:535022 original size:14 final size:14
Alignment explanation
Indices: 535003--535039 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
534993 GGAAATGACT
*
535003 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
535017 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
535031 ATCGCAACG
1 ATCGCAACG
535040 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:535085 original size:19 final size:19
Alignment explanation
Indices: 535063--535113 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
535053 GCGACCAGAC
535063 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
535082 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
535101 AATCGCAATGCGA
1 AATCGCAACGCGA
535114 TTTTTGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:535087 original size:33 final size:33
Alignment explanation
Indices: 535016--535090 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
535006 GCAACGATAG
* * *
535016 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
535049 TATCGCGACCAGACAATCGCAACGCGAAATGAA
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
535082 AATCGCAAC
1 AATCGCAAC
535091 GCGAAATGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.27, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGACAATCGCAACGCGAAATGAA
Found at i:535145 original size:19 final size:19
Alignment explanation
Indices: 535109--535175 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
535099 AAAATCGCAA
*
535109 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
535128 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
535147 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
535167 TGCGATTTT
1 TGCGATTTT
535176 CATTGTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:535742 original size:20 final size:20
Alignment explanation
Indices: 535693--535806 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
535683 CACTATGTAA
* * *
535693 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
535713 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
535733 ATCTCATTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
535754 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
535774 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
535794 ATCGCATTGCGAT
1 ATCGCATTGCGAT
535807 TTTCCCAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.78
21 13 0.16
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:535791 original size:61 final size:61
Alignment explanation
Indices: 535693--535809 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
535683 CACTATGTAA
* * * *
535693 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
535754 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
535810 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:535825 original size:61 final size:61
Alignment explanation
Indices: 535693--535827 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
535683 CACTATGTAA
* * * * ** *
535693 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
535754 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
535816 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
535828 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:535917 original size:21 final size:21
Alignment explanation
Indices: 535877--535917 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
535867 ACTGTATACC
**
535877 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
535898 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
535918 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:542384 original size:20 final size:20
Alignment explanation
Indices: 542359--542493 Score: 198
Period size: 20 Copynumber: 6.7 Consensus size: 20
542349 TTTTCCTATT
542359 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
542379 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
542400 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
542420 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
542440 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
542461 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
542481 TCGCAATGCGAAT
1 TCGCAATGCGAAT
542494 CTGACTATCG
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
20 66 0.65
21 35 0.35
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:542389 original size:41 final size:40
Alignment explanation
Indices: 542359--542493 Score: 198
Period size: 41 Copynumber: 3.3 Consensus size: 40
542349 TTTTCCTATT
* *
542359 TCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCG-ATTACGTAAA
542400 TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
* * * *
542440 TCGCAATGCGAATTAGGAAAATCGCAATACGAATACGTAAA
1 TCGCAATGCGAA-TACGTAAATCGCAATGCGATTACGTAAA
542481 TCGCAATGCGAAT
1 TCGCAATGCGAAT
542494 CTGACTATCG
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
40 21 0.24
41 66 0.76
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
Found at i:542436 original size:61 final size:61
Alignment explanation
Indices: 542359--542493 Score: 252
Period size: 61 Copynumber: 2.2 Consensus size: 61
542349 TTTTCCTATT
*
542359 TCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATACGAATACGTAAA
*
542420 TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATACGAATACGTAAA
542481 TCGCAATGCGAAT
1 TCGCAATGCGAAT
542494 CTGACTATCG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (61 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATACGAATACGTAAA
Found at i:543102 original size:20 final size:20
Alignment explanation
Indices: 543044--543094 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
543034 TTCTAAACTT
* *
543044 AAAATCGCAATATGAAAATG
1 AAAATCGCAACACGAAAATG
543064 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
543084 ACTATCGCAAC
1 AAAATCGCAAC
543095 GAGAAAATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:543218 original size:20 final size:19
Alignment explanation
Indices: 543170--543243 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 19
543160 TACGATTTTA
**
543170 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATAGTC
543189 ATTTCGCGTTGCGATAGTC
1 ATTTCGCGTTGCGATAGTC
**
543208 ATTTCCGCGTTGCGATTTTC
1 ATTT-CGCGTTGCGATAGTC
*
543228 ATTCTCTCGTTGCGAT
1 ATT-TCGCGTTGCGAT
543244 TTTCATTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 21 0.44
20 26 0.54
21 1 0.02
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGTC
Found at i:543244 original size:20 final size:19
Alignment explanation
Indices: 543121--543252 Score: 148
Period size: 19 Copynumber: 7.1 Consensus size: 19
543111 GAAACCAAAA
*
543121 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
543140 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
543154 TCTCGTTACGATTTTAATT
1 TCGCGTTGCGATTTTCATT
543173 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
543192 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
543211 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
543231 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
543251 TC
1 TC
543253 AACCAAAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 9 0.10
16 2 0.02
17 3 0.03
19 46 0.49
20 33 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:545399 original size:94 final size:94
Alignment explanation
Indices: 544938--545405 Score: 729
Period size: 94 Copynumber: 5.1 Consensus size: 94
544928 TAGATTGCTT
* *
544938 AGTAAATTTATTCGGTTGCTGCCAATAT-TGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAG
1 AGTAAATTTGTTCGGTTGCTGCCAAT-TCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAG
*
544998 TATTTGTCTTT-TGTTGTCTTTTGGTTG-A
65 TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
545026 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
*
545091 ATTTGTCTTTGTTTTGTCTTTTGGTTAAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
545120 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
* *
545185 ATTTGTCTTTGTTTTATCTTTTGGTTAAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
545214 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
*
545279 ATTTGTCTTTGTTTTGTCCTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
545308 AGTAAATTTGTTCGTTTGCTGTCAATTCTGCTAAACGTGTGTATTCTTT-ATACTCTGAAGTTAG
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-TATGTATTCTTTAACACTGTGAAGTTAG
545372 TATTTGTCTTTGTTTTGTCTTTTGGTTG-A
65 TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
545401 AGTAA
1 AGTAA
545406 TGCAATCCAT
Statistics
Matches: 358, Mismatches: 14, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
87 1 0.00
88 34 0.09
90 3 0.01
91 2 0.01
92 29 0.08
93 20 0.06
94 257 0.72
95 12 0.03
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:545545 original size:19 final size:19
Alignment explanation
Indices: 545521--545578 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
545511 ATGAGAGAAT
545521 GAAAATCGCAACGCGAAAC
1 GAAAATCGCAACGCGAAAC
*
545540 GAAAATCGTAACGCGAAACC
1 GAAAATCGCAACGCGAAA-C
*
545560 AAAAATCGCAACGCGAAAC
1 GAAAATCGCAACGCGAAAC
545579 TATAATCGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.07
Consensus pattern (19 bp):
GAAAATCGCAACGCGAAAC
Found at i:545566 original size:20 final size:20
Alignment explanation
Indices: 545522--545578 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
545512 TGAGAGAATG
*
545522 AAAATCGCAACGCGAAA-CG
1 AAAATCGCAACGCGAAACCA
*
545541 AAAATCGTAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
545561 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
545579 TATAATCGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.49, C:0.26, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:545606 original size:19 final size:19
Alignment explanation
Indices: 545584--545709 Score: 136
Period size: 19 Copynumber: 6.8 Consensus size: 19
545574 GAAACTATAA
545584 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
545603 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
545617 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
545636 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
*
545655 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
**
545674 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
545695 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
545710 AAGTTCCAGA
Statistics
Matches: 89, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
14 9 0.10
16 3 0.03
17 3 0.03
19 60 0.67
21 14 0.16
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:545676 original size:38 final size:34
Alignment explanation
Indices: 545584--545685 Score: 134
Period size: 33 Copynumber: 2.9 Consensus size: 34
545574 GAAACTATAA
*
545584 TCGCGTTGCGATTTTCATTTCGCATTGCGA-TTC
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTC
*
545617 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTC
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGA-TTTC
*
545652 GTTTCGCGTTGCGATTTTCGTTTCGCGTTGCGAT
1 ---TCGCGTTGCGATTTTCATTTCGCGTTGCGAT
545686 AGTCATTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
33 28 0.47
35 3 0.05
37 1 0.02
38 28 0.47
ACGTcount: A:0.09, C:0.23, G:0.24, T:0.45
Consensus pattern (34 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTC
Found at i:546598 original size:14 final size:14
Alignment explanation
Indices: 546579--546614 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
546569 ATTGTTTAAT
546579 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
546593 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
546607 TGATTTGT
1 TGATTTGT
546615 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:546758 original size:33 final size:33
Alignment explanation
Indices: 546721--546800 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
546711 AAAAATGACT
* * *
546721 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
546754 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
546787 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
546801 CTAAATTCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:546777 original size:19 final size:19
Alignment explanation
Indices: 546721--546779 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
546711 AAAAATGACT
546721 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
546740 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
546754 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
546773 ATCGCAA
1 ATCGCAA
546780 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.55
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:546828 original size:19 final size:19
Alignment explanation
Indices: 546806--546956 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
546796 CGAAACTAAA
546806 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
546825 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
546840 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
546858 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
546873 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
546891 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
546906 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
546924 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
546943 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
546957 AGACATTAAG
Statistics
Matches: 98, Mismatches: 18, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 26 0.27
16 9 0.09
17 9 0.09
19 44 0.45
20 10 0.10
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:546852 original size:33 final size:33
Alignment explanation
Indices: 546810--546936 Score: 236
Period size: 33 Copynumber: 3.8 Consensus size: 33
546800 ACTAAATTCG
* *
546810 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
546843 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
546876 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
546909 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
546937 AGTCATTTCC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 92 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:546883 original size:14 final size:14
Alignment explanation
Indices: 546831--546918 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
546821 TCATTTCGCT
*
546831 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
546845 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
546862 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
546878 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
546895 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
546911 TTGCGATT
1 TTGCGATT
546919 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 13 0.22
19 12 0.20
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:546955 original size:20 final size:20
Alignment explanation
Indices: 546909--547002 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
546899 GCGATTCTCT
**
546909 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
546928 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
546948 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
546967 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
546989 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
547003 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:547502 original size:27 final size:27
Alignment explanation
Indices: 547464--547518 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
547454 ATTTAAAATA
547464 TATATAATATATAG-TTTTGAAAACATT
1 TATATAATATATAGTTTTTG-AAACATT
*
547491 TATATATTATATAGTTTTTGAAACATT
1 TATATAATATATAGTTTTTGAAACATT
547518 T
1 T
547519 TGAAAACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (27 bp):
TATATAATATATAGTTTTTGAAACATT
Found at i:547555 original size:37 final size:37
Alignment explanation
Indices: 547478--547938 Score: 501
Period size: 36 Copynumber: 12.8 Consensus size: 37
547468 TAATATATAG
* *
547478 TTTTGAAAACATTTATATATTATATAGTTTTTGAAACA-
1 TTTTGAAAA-A-TTATATAATATATAGTTTTTAAAACAT
* *
547516 TTTTGAAAACTGATATAATATATAGTTTTTTAAAACAT
1 TTTTGAAAAATTATATAATATATAG-TTTTTAAAACAT
*
547554 TTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
* * *
547591 TTTTG-GAAATTATATAGTGTATAG-TTTTAAAACA-
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
* *
547625 TTTTGAAAACTTATATAGTATATAGTTTTTTAAAACAT
1 TTTTGAAAAATTATATAATATATAG-TTTTTAAAACAT
* * *
547663 TTTTGAAAAAAATATATAATATATAGTTTTAAAAACAC
1 TTTTG-AAAAATTATATAATATATAGTTTTTAAAACAT
* *
547701 TTTTG-AAAATTATATAGTATATAG-TTTTAAAATAT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
547736 TTTTGAAAAATTATATAATATATAG-TTTTAAAAGCAT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAA-CAT
* *
547773 TTTTGAAAAATCATATAGTATATAG-TTTTAAAACAT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
* *
547809 TTTTGAAAAATTATATAATATATAGTTTTAAAAAATATT
1 TTTTGAAAAATTATATAATATATAGTTTT-TAAAACA-T
* *
547848 TTTTGGAAAACT-TAT-ATA-ATA-TTTTTAAAACA-
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
* *
547880 TTTTG-AAAACTATATAATATATAGTTTTGAAAAC-T
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
*
547915 TTTT--TAAA--ATATAATATATAGTTT
1 TTTTGAAAAATTATATAATATATAGTTT
547939 AAGAAATTAT
Statistics
Matches: 368, Mismatches: 38, Indels: 40
0.83 0.09 0.09
Matches are distributed among these distances:
31 6 0.02
32 24 0.07
33 3 0.01
34 16 0.04
35 55 0.15
36 101 0.27
37 75 0.20
38 60 0.16
39 28 0.08
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (37 bp):
TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
Found at i:547650 original size:109 final size:109
Alignment explanation
Indices: 547490--547973 Score: 554
Period size: 109 Copynumber: 4.5 Consensus size: 109
547480 TTGAAAACAT
* * *
547490 TTATATATTATATAGTTTTTGAAACA-TTTTGAAAACTGATATAATATATAGTTTTTTAAAACAT
1 TTATATAGTATATAG-TTTTAAAACATTTTTGAAAACTTATATAATATATAG-TTTTTAAAACAT
*
547554 TTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTTGGAAA
64 TTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTTGAAAA
* *
547600 TTATATAGTGTATAGTTTTAAAACA-TTTTGAAAACTTATATAGTATATAGTTTTTTAAAACATT
1 TTATATAGTATATAGTTTTAAAACATTTTTGAAAACTTATATAATATATAG-TTTTTAAAACATT
* *
547664 TTTGAAAAAAATATATAATATATAGTTTTAAAAACACTTTTGAAAA
65 TTTG-AAAAATTATATAATATATAGTTTTAAAAACATTTTTGAAAA
* *
547710 TTATATAGTATATAGTTTTAAAATATTTTTGAAAAATTATATAATATATAG-TTTTAAAAGCATT
1 TTATATAGTATATAGTTTTAAAACATTTTTGAAAACTTATATAATATATAGTTTTTAAAA-CATT
* *
547774 TTTGAAAAATCATATAGTATATAGTTTT-AAAACATTTTTGAAAAA
65 TTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTTG-AAAA
* *
547819 TTATATAATATATAGTTTTAAAAAATATTTTTTGGAAAAC-T-TAT-ATA-ATA-TTTTTAAAAC
1 TTATATAGTATATAGTTTT--AAAACA-TTTTT-GAAAACTTATATAATATATAGTTTTTAAAAC
* * *
547879 A-TTTTG-AAAACTATATAATATATAGTTTTGAAAAC-TTTTTTAAAA
62 ATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTTGAAAA
* * *
547924 -TATA-A-TATATAGTTTAAGAAATTATTTTTG-AAA--TATATATTATATAGTTT
1 TTATATAGTATATAGTTTTA-AAA-CATTTTTGAAAACTTATATAATATATAGTTT
547974 ATAACATGTT
Statistics
Matches: 334, Mismatches: 24, Indels: 40
0.84 0.06 0.10
Matches are distributed among these distances:
98 1 0.00
99 6 0.02
100 4 0.01
101 11 0.03
102 15 0.04
103 1 0.00
104 4 0.01
105 4 0.01
106 25 0.07
107 10 0.03
108 13 0.04
109 112 0.34
110 85 0.25
111 32 0.10
112 6 0.02
113 5 0.01
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (109 bp):
TTATATAGTATATAGTTTTAAAACATTTTTGAAAACTTATATAATATATAGTTTTTAAAACATTT
TTGAAAAATTATATAATATATAGTTTTAAAAACATTTTTGAAAA
Found at i:547990 original size:3 final size:3
Alignment explanation
Indices: 547982--548019 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
547972 TTATAACATG
*
547982 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
548020 TATTTATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:548244 original size:16 final size:15
Alignment explanation
Indices: 548223--548252 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
548213 TTCGACCGGT
548223 ATCCTGGGACTGACCC
1 ATCCTGGGA-TGACCC
548239 ATCCTGGGATGACC
1 ATCCTGGGATGACC
548253 GGTCACACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (15 bp):
ATCCTGGGATGACCC
Found at i:550557 original size:20 final size:20
Alignment explanation
Indices: 550534--550581 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
550524 CCATGCATCG
550534 ATCGATGCCTTCAAGTGTGC
1 ATCGATGCCTTCAAGTGTGC
* *
550554 ATCGATGGCTTCCAGTGTGC
1 ATCGATGCCTTCAAGTGTGC
*
550574 ATCAATGC
1 ATCGATGC
550582 ATATTCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (20 bp):
ATCGATGCCTTCAAGTGTGC
Found at i:551803 original size:26 final size:26
Alignment explanation
Indices: 551753--551808 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
551743 TTTTTGCATG
*
551753 TTTTAATTTGGCCACTGTTCCTTTTC
1 TTTTAATTTGGCCACTGTTCCTTTTA
* **
551779 TTTTGATTTGGCCACTGTTTTTTTTA
1 TTTTAATTTGGCCACTGTTCCTTTTA
551805 TTTT
1 TTTT
551809 TGCGTTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (26 bp):
TTTTAATTTGGCCACTGTTCCTTTTA
Found at i:551863 original size:9 final size:9
Alignment explanation
Indices: 551849--551882 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
551839 TTCCCTTTGA
551849 TTATTTATT
1 TTATTTATT
551858 TTATTTATCT
1 TTATTTAT-T
551868 ATTATTTATT
1 -TTATTTATT
551878 TTATT
1 TTATT
551883 CAGTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.57
10 2 0.09
11 8 0.35
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTATT
Found at i:557421 original size:84 final size:83
Alignment explanation
Indices: 557193--557975 Score: 668
Period size: 84 Copynumber: 9.4 Consensus size: 83
557183 AAAAGAAACT
* * *** ** * ** * *
557193 ATTTACAGCATAAATCAAGGCTAGAAGGGTTATCTACCAATAAAAGACATTATATTTCGACTCCG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCT-GTGACCAAAGACCTTCGAGTTCGACTACG
* *
557258 CTCAACTCTAAGGCACATC
65 CTCAGCTCCAAGGCACATC
* * * * *
557277 ATTTGCAGCATAGCTTAAGTCGATAAGGGTTATC--TG-CCAAAGACCTTCGAGTTCGACTACGC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGC
*
557339 TCAGCTCCAAGGCATATC
66 TCAGCTCCAAGGCACATC
* * * *
557357 ATTTACAACATAACTCAAGGCTAGAAGTGTTATCTGTGACCAAAAGACGTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACG
*
557422 CTCAGCTCCAAGGCACGTC
65 CTCAGCTCCAAGGCACATC
** * * **
557441 ATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGACTACG
*
557506 CTCAACTCCAAGGCACATC
65 CTCAGCTCCAAGGCACATC
* * * * * * * *
557525 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCTCGAGTTCGATTACAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGC
* * *
557587 TCAGCTTCGAGGGTACATC
66 TCAGC-TCCAAGGCACATC
* * * * *
557606 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCGAAAGATCTTCGAGTTCGATTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACG
* *
557671 CTCAGCTCCAAGACATATC
65 CTCAGCTCCAAGGCACATC
* * * * * * * * * *
557690 ATTTGCAACATAGA-TTAAGTCGAGAAGGGATATC--TG-CTAAAGACCCTCGAGTTTGATTACA
1 ATTTACAGCATA-ACTCAAGGCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACG
* * *
557751 CTCAACTTCGAAGACACATC
65 CTCAGC-TCCAAGGCACATC
* * * *
557771 ATTTACAACATAACTCAAGGCTAGAAGGGTTATTTGTCACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACG
* *
557836 CTCAGCTCCAAGGAATATC
65 CTCAGCTCCAAGGCACATC
* * * * * * *
557855 ATTTGCAGCATAACTTAAGTCAATAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGT-GACCAAAGACCTTCGAGTTCGACTACG
* *
557920 CTCAACTCCAAGGAACATC
65 CTCAGCTCCAAGGCACATC
* * * * *
557939 ATTTACAACATAGCTCAAGGCAAGAAGAGCTATCTGT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGT
557976 CAATAAAATT
Statistics
Matches: 559, Mismatches: 122, Indels: 36
0.78 0.17 0.05
Matches are distributed among these distances:
80 112 0.20
81 75 0.13
82 3 0.01
83 4 0.01
84 308 0.55
85 57 0.10
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (83 bp):
ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGC
TCAGCTCCAAGGCACATC
Found at i:557682 original size:165 final size:164
Alignment explanation
Indices: 557248--557977 Score: 761
Period size: 165 Copynumber: 4.4 Consensus size: 164
557238 GACATTATAT
* * * * * * * * * *
557248 TTCGACTCCGCTCAACTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGTTATCTG
1 TTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTG
* *
557313 ---CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAACATAACTCAA
66 TCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAA
* * * **
557375 GGCTAGAAGTGTTATCTGTGACCAAAAGACGTTCGAG
131 GTCGAGAAGGGTTATC--TGACC-AAAGACCCTCGAG
* * * ** * * * *
557412 TTCGACTACGCTCAGCTCCAAGGCACGTCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTG
1 TTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTG
* * * * *
557477 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTA
66 TC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTA
*
557542 AGTCGAGAAGGGCTATCTG-CCAAAGACCCTCGAG
130 AGTCGAGAAGGGTTATCTGACCAAAGACCCTCGAG
* * * * * **
557576 TTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCT
1 TTCGACTACACTCAAC-TCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCT
* * *
557641 GTCACCGAAAGATCTTCGAGTTCGATTACGCTCAGCTCCAAGACATATCATTTGCAACATAGA-T
65 GTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATA-ACT
* *
557705 TAAGTCGAGAAGGGATATCTG-CTAAAGACCCTCGAG
128 TAAGTCGAGAAGGGTTATCTGACCAAAGACCCTCGAG
* * * * *
557741 TTTGATTACACTCAACTTCGAAGACACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATTT
1 TTCGACTACACTCAAC-TCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCT
* *
557806 GTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAATATCATTTGCAGCATAACTT
65 GTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTT
* * * *
557871 AAGTCAATAAGGGTTATCTGTCAACCAAAGACCTTTGAG
129 AAGTCGAGAAGGGTTATCTG---ACCAAAGACCCTCGAG
* * * * * *
557910 TTCGACTACGCTCAACTCCAAGGAACATCATTTACAACATAGCTCAAGGCAAGAAGAGCTATCTG
1 TTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTG
557975 TCA
66 TCA
557978 ATAAAATTGT
Statistics
Matches: 482, Mismatches: 72, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
164 87 0.18
165 256 0.53
166 2 0.00
168 112 0.23
169 25 0.05
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (164 bp):
TTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTG
TCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAA
GTCGAGAAGGGTTATCTGACCAAAGACCCTCGAG
Found at i:557726 original size:249 final size:243
Alignment explanation
Indices: 557248--557951 Score: 829
Period size: 249 Copynumber: 2.8 Consensus size: 243
557238 GACATTATAT
* * *
557248 TTCGACTCCGCTCAACTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGTTATCTG
1 TTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG
* *
557313 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAACATAACTCAAGGC
66 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAATATCATTTACAGCATAACTCAAGGC
* * * *
557378 TAGAAGTGTTATCTGTGACCAAAAGACGTTCGAGTTCGACTACGCTCAGCTCCAAGGCACGTCAT
131 TAGAAGGGTTATCTGTCACC-AAAGAC-TTCGAGTTCGACTACGCTCAGCTCCAAGACACATCAT
* * * *
557443 TTGTAGCATA-ACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
194 TTGCAACATAGACTTAAGTCGAGAAGGGATATCTG----CCAAAGACCCTCGAG
*
557496 TTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
1 TTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG
* * * * * * * *
557561 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGTATAACTCAAGG
66 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGAATATCATTTACAGCATAACTCAAGG
* *
557626 CTAGAAGGGTTATCTGTCACCGAAAGATCTTCGAGTTCGATTACGCTCAGCTCCAAGACATATCA
130 CTAGAAGGGTTATCTGTCACC-AAAGA-CTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCA
*
557691 TTTGCAACATAGA-TTAAGTCGAGAAGGGATATCTGCTAAAGACCCTCGAG
193 TTTGCAACATAGACTTAAGTCGAGAAGGGATATCTGCCAAAGACCCTCGAG
* * * * * * * * * * * *
557741 TTTGATTACACTCAACTTCGAAGACACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATTT
1 TTCGACTACGCTCAAC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT
* *
557806 GTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAATATCATTTGCAGCATAACTT
65 G---CC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAATATCATTTACAGCATAACTC
* * * * *
557871 AAGTCAATAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTCGACTACGCTCAACTCCAAGGA-A
126 AAGGCTAGAAGGGTTATCTGTC-ACCAAAGA-CTTCGAGTTCGACTACGCTCAGCTCCAA-GACA
*
557935 CATCATTTACAACATAG
188 CATCATTTGCAACATAG
557952 CTCAAGGCAA
Statistics
Matches: 389, Mismatches: 57, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
245 26 0.07
246 39 0.10
248 89 0.23
249 202 0.52
250 33 0.08
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (243 bp):
TTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAATATCATTTACAGCATAACTCAAGGC
TAGAAGGGTTATCTGTCACCAAAGACTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTT
GCAACATAGACTTAAGTCGAGAAGGGATATCTGCCAAAGACCCTCGAG
Found at i:557978 original size:84 final size:83
Alignment explanation
Indices: 557248--557942 Score: 694
Period size: 84 Copynumber: 8.4 Consensus size: 83
557238 GACATTATAT
* * * * * *
557248 TTCGACTCCGCTCAACTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGTTATCTG
1 TTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
557313 ---CCAAAGACCTTCGAG
66 TCACCAAAGACCTTCGAG
* * * * * * * *
557328 TTCGACTACGCTCAGCTCCAAGGCATATCATTTACAACATAACTCAAGGCTAGAAGTGTTATCTG
1 TTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
* *
557393 TGACCAAAAGACGTTCGAG
66 TCACC-AAAGACCTTCGAG
* * *
557412 TTCGACTACGCTCAGCTCCAAGGCACGTCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTG
1 TTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
*
557477 CCAACCAAAGACCTTCGAG
66 TC-ACCAAAGACCTTCGAG
* * * *
557496 TTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
1 TTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
*
557561 ---CCAAAGACCCTCGAG
66 TCACCAAAGACCTTCGAG
* * * * * * * * * *
557576 TTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCT
1 TTCGACTACGCTCAGC-TCCAAGGAACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
*
557641 GTCACCGAAAGATCTTCGAG
65 GTCACC-AAAGACCTTCGAG
* * * *
557661 TTCGATTACGCTCAGCTCCAA-GACATATCATTTGCAACATAGA-TTAAGTCGAGAAGGGATATC
1 TTCGACTACGCTCAGCTCCAAGGA-ACATCATTTGCAGCATA-ACTTAAGTCGAGAAGGGTTATC
* *
557724 TG---CTAAAGACCCTCGAG
64 TGTCACCAAAGACCTTCGAG
* * * * * * * * * * *
557741 TTTGATTACACTCAACTTCGAA-GACACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATT
1 TTCGACTACGCTCAGC-TCCAAGGA-ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
557805 TGTCACCAAAAGACCTTCGAG
64 TGTCACC-AAAGACCTTCGAG
* * *
557826 TTCGACTACGCTCAGCTCCAAGGAATATCATTTGCAGCATAACTTAAGTCAATAAGGGTTATCTG
1 TTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
*
557891 TCAACCAAAGACCTTTGAG
66 TC-ACCAAAGACCTTCGAG
*
557910 TTCGACTACGCTCAACTCCAAGGAACATCATTT
1 TTCGACTACGCTCAGCTCCAAGGAACATCATTT
557943 ACAACATAGC
Statistics
Matches: 505, Mismatches: 90, Indels: 36
0.80 0.14 0.06
Matches are distributed among these distances:
80 105 0.21
81 79 0.16
83 3 0.01
84 259 0.51
85 59 0.12
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (83 bp):
TTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
TCACCAAAGACCTTCGAG
Found at i:558666 original size:27 final size:28
Alignment explanation
Indices: 558636--558693 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
558626 AAAAATATTT
*
558636 AAAATATATATATAATATATAG-TTTTG
1 AAAACATATATATAATATATAGTTTTTG
* *
558663 AAAACATTTATATATTATATAGTTTTTG
1 AAAACATATATATAATATATAGTTTTTG
558691 AAA
1 AAA
558694 CATTTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (28 bp):
AAAACATATATATAATATATAGTTTTTG
Found at i:558672 original size:65 final size:63
Alignment explanation
Indices: 558603--558724 Score: 165
Period size: 65 Copynumber: 1.9 Consensus size: 63
558593 ATTTTCGGAA
*
558603 ATTTATATATTATATAATTTTTTAAAAATATTT-AAAATATATATATAATATATAGTTTTGAAAA
1 ATTTATATATTATATAATTTTTGAAAAAT-TTTGAAAA-AT-TATATAATATATAGTTTTGAAAA
558667 C
63 C
* * * *
558668 ATTTATATATTATATAGTTTTTGAAACATTTTGAAAACTTATATAGTATATAGTTTT
1 ATTTATATATTATATAATTTTTGAAAAATTTTGAAAAATTATATAATATATAGTTTT
558725 TTTTAAAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 17 0.33
64 4 0.08
65 30 0.59
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (63 bp):
ATTTATATATTATATAATTTTTGAAAAATTTTGAAAAATTATATAATATATAGTTTTGAAAAC
Found at i:558694 original size:27 final size:27
Alignment explanation
Indices: 558644--558698 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
558634 TTAAAATATA
558644 TATATAATATATAGTTTTGAAAACATT
1 TATATAATATATAGTTTTGAAAACATT
*
558671 TATATATTATATAGTTTTTG-AAACATT
1 TATATAATATATAG-TTTTGAAAACATT
558698 T
1 T
558699 TGAAAACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (27 bp):
TATATAATATATAGTTTTGAAAACATT
Found at i:558700 original size:38 final size:37
Alignment explanation
Indices: 558658--558847 Score: 230
Period size: 36 Copynumber: 5.1 Consensus size: 37
558648 TAATATATAG
* *
558658 TTTTGAAAACATTTATATATTATATAGTTTTTGAAACA
1 TTTTGAAAACA-TTATATAGTATATAGTTTTTAAAACA
558696 TTTTGAAAAC-TTATATAGTATATAGTTTTTTTTAAAACA
1 TTTTGAAAACATTATATAGTATATAG---TTTTTAAAACA
* *
558735 TTTTTGAAAA-ATTATATAATATATAGTTTTAAAAACA
1 -TTTTGAAAACATTATATAGTATATAGTTTTTAAAACA
*
558772 TTTTTG-GAA-ATTATATAGTATATAG-TTTTAAAACA
1 -TTTTGAAAACATTATATAGTATATAGTTTTTAAAACA
558807 TTTTGAAAAC-TTATATAGTATATAGTTTTTTAAAACA
1 TTTTGAAAACATTATATAGTATATAG-TTTTTAAAACA
558844 TTTT
1 TTTT
558848 TGACACGCGT
Statistics
Matches: 135, Mismatches: 8, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
34 5 0.04
35 26 0.19
36 31 0.23
37 30 0.22
38 10 0.07
39 10 0.07
40 23 0.17
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (37 bp):
TTTTGAAAACATTATATAGTATATAGTTTTTAAAACA
Found at i:561452 original size:21 final size:21
Alignment explanation
Indices: 561410--561452 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
561400 ACTTACTTTA
* * *
561410 TTTTGTTAAATTTGTTTGACT
1 TTTTGTTAAATGTATTTCACT
*
561431 TTTTTTTAAATGTATTTCACT
1 TTTTGTTAAATGTATTTCACT
561452 T
1 T
561453 AATTTTGTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (21 bp):
TTTTGTTAAATGTATTTCACT
Found at i:561491 original size:35 final size:33
Alignment explanation
Indices: 561452--561536 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
561442 GTATTTCACT
561452 TAATTTTGTT-TATTACCATTTAATATCTGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
561487 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
561522 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
561537 TAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:565560 original size:18 final size:18
Alignment explanation
Indices: 565537--565572 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
565527 CTTTATTGCA
565537 GGACTCTTCGTCTTCAGC
1 GGACTCTTCGTCTTCAGC
565555 GGACTCTTCGTCTTCAGC
1 GGACTCTTCGTCTTCAGC
565573 TGAACTGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.33, G:0.22, T:0.33
Consensus pattern (18 bp):
GGACTCTTCGTCTTCAGC
Found at i:568718 original size:200 final size:198
Alignment explanation
Indices: 568103--568770 Score: 628
Period size: 200 Copynumber: 3.4 Consensus size: 198
568093 GTAAACTGAT
* * * * * * *
568103 TAAAAATCACGTTGAAAATGGTTTCAAAACTT-GTTTTGTGCATGAAGAA-AATGCAAAAATGAC
1 TAAAAATCACGTTCAAAATAGTTTCAAAGCTTAGTTTTCTACATGAAGAAGAA-GCTAACATGAC
* * ** * *
568166 TTGATATG-CATATTC-GAGG-GT-TTTTTGGGCAGTTAGTCTGAAACTTTCGTCATTTATAAGA
65 TTAATA-GACATGTTCAG-GGAGTATTTTCAGGAAGTTAGTATGAAA-TTTCGTCATTTATAAGA
* * * * *
568227 TTATAGATGTAGTATTG-TAACTTATTTTTCAATTGAGGTTAGTATCGACACATACGAGACATTT
127 TTAAAGATGTAATATTGAT-ACTTATATTTCAATTGAGGTTAGTATCGGCACATACGAGACATTA
*
568291 TAAGGGTTG
191 TAAGGG-GG
* * * *
568300 TAAAAATCGCGTTCAAAATAGTTCCAAAGCTTTGTTTTCTACATGAATAAGAAGCTAACATGACT
1 TAAAAATCACGTTCAAAATAGTTTCAAAGCTTAGTTTTCTACATGAAGAAGAAGCTAACATGACT
* * * *
568365 TAATA-AGTATGTTCGGGGAGTATTTTCGGGAAGTTA--AT----TTTCGTCATTTGTAAGATTA
66 TAATAGA-CATGTTCAGGGAGTATTTTCAGGAAGTTAGTATGAAATTTCGTCATTTATAAGATTA
* * * * * ** *
568423 AAGGTGTATTATTTATACTTATGTTTCAATTGAGGCTAGTATAAGCACATACGAGACATTGTAAT
130 AAGATGTAATATTGATACTTATATTTCAATTGAGGTTAGTATCGGCACATACGAGACATTATAA-
*
568488 CGGGG
194 GGGGG
* * * * * * *
568493 T-AAAATCACTTTTAAAATTGTTTCAAAGCTTGGTTTTCTACATAAAGAGGAAGCTAGCATGACT
1 TAAAAATCACGTTCAAAATAGTTTCAAAGCTTAGTTTTCTACATGAAGAAGAAGCTAACATGACT
* * *
568557 TGATAGACATGTTCAGGGAGTATTTTCATGAAGTTAGTATGAAAATTATCATCATTTATAAGATT
66 TAATAGACATGTTCAGGGAGTATTTTCAGGAAGTTAGTATG-AAATT-TCGTCATTTATAAGATT
* ** ** * *
568622 AGAGACATAATATTGATACTTATATTTCAATAAAAGTTATTATCGGCACATACGAGACATTATAA
129 AAAGATGTAATATTGATACTTATATTTCAATTGAGGTTAGTATCGGCACATACGAGACATTATAA
568687 GGGGG
194 GGGGG
* * *
568692 TAAAAATTACGTTCAAAATGGTTTCAAAGCTTAGTTTTCTACATGAAGAAGAAGCTAACATGGCT
1 TAAAAATCACGTTCAAAATAGTTTCAAAGCTTAGTTTTCTACATGAAGAAGAAGCTAACATGACT
*
568757 TAATAGGCATGTTC
66 TAATAGACATGTTC
568771 GGGGTGTCGA
Statistics
Matches: 379, Mismatches: 73, Indels: 35
0.78 0.15 0.07
Matches are distributed among these distances:
192 82 0.22
193 74 0.20
194 5 0.01
197 27 0.07
198 36 0.09
199 12 0.03
200 143 0.38
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (198 bp):
TAAAAATCACGTTCAAAATAGTTTCAAAGCTTAGTTTTCTACATGAAGAAGAAGCTAACATGACT
TAATAGACATGTTCAGGGAGTATTTTCAGGAAGTTAGTATGAAATTTCGTCATTTATAAGATTAA
AGATGTAATATTGATACTTATATTTCAATTGAGGTTAGTATCGGCACATACGAGACATTATAAGG
GGG
Found at i:572154 original size:15 final size:15
Alignment explanation
Indices: 572113--572154 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
572103 TAGATATTTT
*
572113 TGACGTGGCAGCAGC
1 TGACGTGGCAGTAGC
572128 TGACGTGGCAGTAGC
1 TGACGTGGCAGTAGC
*
572143 TGACATGGCAGT
1 TGACGTGGCAGT
572155 TAAGGTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.19
Consensus pattern (15 bp):
TGACGTGGCAGTAGC
Found at i:585379 original size:22 final size:22
Alignment explanation
Indices: 585351--585394 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
585341 AAGGTAAGTG
585351 GTCTCAAGTTAGTTATTTCTTT
1 GTCTCAAGTTAGTTATTTCTTT
585373 GTCTCAAGTTAGTTATTTCTTT
1 GTCTCAAGTTAGTTATTTCTTT
585395 CATTTTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (22 bp):
GTCTCAAGTTAGTTATTTCTTT
Found at i:585607 original size:15 final size:16
Alignment explanation
Indices: 585578--585607 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
585568 AGTTGAAATA
585578 AGAAATTCAAAGTGTT
1 AGAAATTCAAAGTGTT
585594 AGAAATTC-AAGTGT
1 AGAAATTCAAAGTGT
585608 GTATATGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (16 bp):
AGAAATTCAAAGTGTT
Found at i:588931 original size:7 final size:7
Alignment explanation
Indices: 588915--588945 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
588905 GACCCGACCC
588915 GACCGTT
1 GACCGTT
*
588922 GACTGTT
1 GACCGTT
588929 GACCGTT
1 GACCGTT
588936 GACCGTT
1 GACCGTT
588943 GAC
1 GAC
588946 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:596077 original size:9 final size:9
Alignment explanation
Indices: 596063--596187 Score: 115
Period size: 10 Copynumber: 12.8 Consensus size: 9
596053 GGCTGCTGGA
596063 AACCGGTTT
1 AACCGGTTT
596072 AACCGGTTTT
1 AACCGG-TTT
596082 CAACCGGTTT
1 -AACCGGTTT
*
596092 GACCGGTTTT
1 AACCGG-TTT
596102 CAACCGGTTT
1 -AACCGGTTT
*
596112 GACCGGTTTT
1 AACCGG-TTT
596122 CAACCGGTTCT
1 -AACCGGTT-T
*
596133 GACCGGTTT
1 AACCGGTTT
*
596142 GACCGGTTT
1 AACCGGTTT
*
596151 CAACCGGTTCG
1 -AACCGGTT-T
596162 AACCGGTTT
1 AACCGGTTT
596171 GAACCGGTTT
1 -AACCGGTTT
596181 AACCGGT
1 AACCGGT
596188 CTGAACCGGG
Statistics
Matches: 98, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
9 33 0.34
10 48 0.49
11 17 0.17
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:596088 original size:20 final size:20
Alignment explanation
Indices: 596063--596180 Score: 136
Period size: 20 Copynumber: 5.9 Consensus size: 20
596053 GGCTGCTGGA
596063 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTAACCGGTTTTC
*
596083 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTAACCGGTTTTC
*
596103 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTAACCGGTTTTC
*
596123 AACCGGTTCTGACCGG-TTT-
1 AACCGGTT-TAACCGGTTTTC
*
596142 GACCGGTTTCAACCGG--TTC
1 AACCGGTTT-AACCGGTTTTC
596161 GAACCGGTTTGAACCGGTTT
1 -AACCGGTTT-AACCGGTTT
596181 AACCGGTCTG
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.03
19 12 0.14
20 64 0.74
21 7 0.08
22 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.32
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTTC
Done.