Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008338.1 Hibiscus syriacus cultivar Beakdansim tig00111059_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: 2210178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 12
Found at i:401749 original size:23 final size:23
Alignment explanation
Indices: 401723--401790 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
401713 ACAAAAGCAT
** *
401723 AGAAAAAAGTGTCACAAGTGTAG
1 AGAAAAAAGTGTCACAAGAATAA
401746 AGAAAAAAGTG-CTACAAGAATAA
1 AGAAAAAAGTGTC-ACAAGAATAA
* *
401769 AGAAAAACGTGTCACAAAAATA
1 AGAAAAAAGTGTCACAAGAATA
401791 TAAATTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.56, C:0.10, G:0.19, T:0.15
Consensus pattern (23 bp):
AGAAAAAAGTGTCACAAGAATAA
Found at i:402325 original size:16 final size:16
Alignment explanation
Indices: 402304--402340 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
402294 ACAGAGCTTC
*
402304 TGAATTATTCAGCATT
1 TGAATTATTCAACATT
402320 TGAATTATTCAACATT
1 TGAATTATTCAACATT
402336 TGAAT
1 TGAAT
402341 CATTTAACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (16 bp):
TGAATTATTCAACATT
Found at i:402504 original size:2 final size:2
Alignment explanation
Indices: 402497--402529 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
402487 ATTGATCATT
402497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
402530 CCATAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:408997 original size:322 final size:316
Alignment explanation
Indices: 408411--409051 Score: 1187
Period size: 322 Copynumber: 2.0 Consensus size: 316
408401 CTAATTCTAG
408411 TACAGATTTCATTCCTGACCCACGGGGGCCATGATCGTTGTTATCGTAACATGCAGGTCCAGATA
1 TACAGATTTCATTCCTGACCCACGGGGGCCATGATCGTTGTTATCGTAACATGCAGGTCCAGATA
*
408476 TGTGCATATCTTCTTGTGTCTGCTTTCTTTCTATATCATTGTTACATACTTTAGTCACTTGTCTA
66 TGTGCATATATTCTTGTGTCTGCTTTCTTTCTATATCATTGTTACATACTTTAGTCACTTGTCTA
408541 TATATTTGATGAACTGTTGGCATGAATGTCAAATGTTGCCATGTTTCCATCATTTTTGAGGATTT
131 TATATTTGATGAACTGTTGGCATGAATGTCAAATGTTGCCATGTTTCCATCATTTTTGAGGATTT
408606 TGTATTTTGTCCGAGGCCTTAATAGATAATTCAATTCTTTTACCATGTGCAACTTACTATACCAA
196 TGTATTTTGTCCGAGGCCTTAATAGATAATTCAATTCTTTTACCATGTGCAACTTACTATACCAA
408671 GTATTTTTGTG-TGAGAAATGGTTTGAAACAGGAGCCATATGGTGTTATATTCAAAT
261 GTATTTTTGTGTTGAGAAATGGTTTGAAACAGGAGCCATATGGTGTTATA-TCAAAT
408727 TACAGATTTCATTCCTGACCCACGGGGGCCATGATCGTTGTTATCGTAACATGCAGGTCCAGATA
1 TACAGATTTCATTCCTGACCCACGGGGGCCATGATCGTTGTTATCGTAACATGCAGGTCCAGATA
408792 TGTGCATATATTCTT-TGTCTGCTTATTCTTTCTATATCATTGTTACATACTTTAGTCACTTGTC
66 TGTGCATATATTCTTGTGTCTGC-T-TTCTTTCTATATCATTGTTACATACTTTAGTCACTTGTC
408856 TATATATTTTGATGAACTGTTGGCATGAAATGTCAAATAGTTGCCATGTGTTCCATCATTTTTGA
129 TATATA-TTTGATGAACTGTTGGCATG-AATGTCAAAT-GTTGCCATGT-TTCCATCATTTTTGA
408921 GGAATTTTGTATTTTGTCCGAGGCCTTAATAGATAATTCAATTCTTTTACCATGTGCAACTTACT
190 GG-ATTTTGTATTTTGTCCGAGGCCTTAATAGATAATTCAATTCTTTTACCATGTGCAACTTACT
408986 ATACCAAGTATTTTTGTGTTGAGAAATGGTTTGAAACAGGAGCCATATGGTGTTATATCAAAT
254 ATACCAAGTATTTTTGTGTTGAGAAATGGTTTGAAACAGGAGCCATATGGTGTTATATCAAAT
409049 TAC
1 TAC
409052 GAATGGTAGG
Statistics
Matches: 316, Mismatches: 1, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
315 7 0.02
316 80 0.25
317 45 0.14
318 20 0.06
319 10 0.03
320 10 0.03
321 17 0.05
322 89 0.28
323 38 0.12
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (316 bp):
TACAGATTTCATTCCTGACCCACGGGGGCCATGATCGTTGTTATCGTAACATGCAGGTCCAGATA
TGTGCATATATTCTTGTGTCTGCTTTCTTTCTATATCATTGTTACATACTTTAGTCACTTGTCTA
TATATTTGATGAACTGTTGGCATGAATGTCAAATGTTGCCATGTTTCCATCATTTTTGAGGATTT
TGTATTTTGTCCGAGGCCTTAATAGATAATTCAATTCTTTTACCATGTGCAACTTACTATACCAA
GTATTTTTGTGTTGAGAAATGGTTTGAAACAGGAGCCATATGGTGTTATATCAAAT
Found at i:413616 original size:30 final size:31
Alignment explanation
Indices: 413582--413654 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
413572 AAGTTAAAAA
413582 ATTAAATTTTGATCACTTATGTTATC-GTTT
1 ATTAAATTTTGATCACTTATGTTATCAGTTT
* * *
413612 ATTAAACTTTGATTACTTATGTTATCATTTT
1 ATTAAATTTTGATCACTTATGTTATCAGTTT
413643 ATT-AATTTTGAT
1 ATTAAATTTTGAT
413655 ACATGACACG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 32 0.84
31 6 0.16
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (31 bp):
ATTAAATTTTGATCACTTATGTTATCAGTTT
Found at i:415537 original size:45 final size:46
Alignment explanation
Indices: 415450--415537 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
415440 CAAAATAGCA
* * *
415450 TGAGTGCATCGATGCATGACTTTGTGCATCGATGCATCAAATGTAC
1 TGAGTGCATCGATGCATGACTATATGCATCGATGCATAAAATGTAC
*
415496 TGAGTGCATCGATGCATG-GTATATGCATCGATGCATAAAATG
1 TGAGTGCATCGATGCATGACTATATGCATCGATGCATAAAATG
415538 CATTTGATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (46 bp):
TGAGTGCATCGATGCATGACTATATGCATCGATGCATAAAATGTAC
Found at i:415620 original size:44 final size:45
Alignment explanation
Indices: 415519--415620 Score: 179
Period size: 45 Copynumber: 2.3 Consensus size: 45
415509 GCATGGTATA
415519 TGCATCGATGCATAAAATGCATTTGATGTTCAATTTATTCATTGG
1 TGCATCGATGCATAAAATGCATTTGATGTTCAATTTATTCATTGG
*
415564 TGCATCGATGCATAAAATGCATTTGATGTTTAATTTA-TCATTGG
1 TGCATCGATGCATAAAATGCATTTGATGTTCAATTTATTCATTGG
*
415608 TGCATCAATGCAT
1 TGCATCGATGCAT
415621 GGATTGGTGC
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
44 19 0.35
45 36 0.65
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (45 bp):
TGCATCGATGCATAAAATGCATTTGATGTTCAATTTATTCATTGG
Found at i:418238 original size:44 final size:44
Alignment explanation
Indices: 418145--418242 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
418135 ATGGCCTGTA
** *
418145 CATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATAGTG
1 CATCGATGCACATTCAAGGAATGCATCGATGCACCTTCATAGTG
* *
418189 TATCGATGCACATTCAAAGGAATGCATCGATGCA-CTGTTA-AGTG
1 CATCGATGCACATTC-AAGGAATGCATCGATGCACCT-TCATAGTG
418233 CATCGATGCA
1 CATCGATGCA
418243 TGAAGTACAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 29 0.63
45 17 0.37
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (44 bp):
CATCGATGCACATTCAAGGAATGCATCGATGCACCTTCATAGTG
Found at i:434432 original size:20 final size:20
Alignment explanation
Indices: 434404--434742 Score: 158
Period size: 20 Copynumber: 16.1 Consensus size: 20
434394 ATAAGTAAAA
434404 ATATATAAACTATATA-TATT
1 ATATATAAACTATATAGT-TT
*
434424 ATGTATAAACTATATAGTTT
1 ATATATAAACTATATAGTTT
*
434444 ATTAATATAAACTATATAGTGT
1 A-T-ATATAAACTATATAGTTT
434466 ATATATAAACTATATAGTTT
1 ATATATAAACTATATAGTTT
* * * *
434486 ATATTTATATTAT-TA-TAT
1 ATATATAAACTATATAGTTT
434504 ACTATATAAACTATATAGTTT
1 A-TATATAAACTATATAGTTT
*
434525 ATTAATATAAATTATATAG-TT
1 A-T-ATATAAACTATATAGTTT
* *
434546 AGTATATAAATTATATATGAATT
1 A-TATATAAACTATATA-G-TTT
* **
434569 ATATTTAAA-TATATACAACTT
1 ATATATAAACTATAT--AGTTT
* * *
434590 ATATTTATA-TAT-TA-TGT
1 ATATATAAACTATATAGTTT
* *
434607 ATAATTATAAATTATATA-TACT
1 AT-A-TATAAACTATATAGT-TT
* * *
434629 ATGTATAAATTATATTGTTT
1 ATATATAAACTATATAGTTT
434649 ATTAATATAAACTATAAATTA-TATAT
1 A-T-ATATAAACTAT--A-TAGT-T-T
*
434675 ACTATGTATAAATTATATAGTTT
1 A-TA--TATAAACTATATAGTTT
* *
434698 ATATATAAAGTATATAAGTAT
1 ATATATAAACTATAT-AGTTT
*
434719 ATAATATAAAGTATATAGTTT
1 AT-ATATAAACTATATAGTTT
434740 ATA
1 ATA
434743 AAACCCTAAA
Statistics
Matches: 254, Mismatches: 35, Indels: 60
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.01
18 5 0.02
19 15 0.06
20 91 0.36
21 47 0.19
22 65 0.26
23 6 0.02
24 5 0.02
25 5 0.02
26 3 0.01
27 9 0.04
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (20 bp):
ATATATAAACTATATAGTTT
Found at i:434562 original size:11 final size:11
Alignment explanation
Indices: 434506--434643 Score: 53
Period size: 11 Copynumber: 13.3 Consensus size: 11
434496 TATTATATAC
*
434506 TATATAAACTA
1 TATATAAATTA
**
434517 TATAGTTTATTA
1 TATA-TAAATTA
434529 -ATATAAA-T-
1 TATATAAATTA
*
434537 TATAT-AGTTA
1 TATATAAATTA
434547 GTATATAAATTA
1 -TATATAAATTA
*
434559 TATATGAATTA
1 TATATAAATTA
*
434570 TATTTAAA-TA
1 TATATAAATTA
* *
434580 TATACAACTTA
1 TATATAAATTA
* *
434591 TATTTATA-TA
1 TATATAAATTA
** *
434601 T-TATGTATAA
1 TATATAAATTA
434611 T-TATAAATTA
1 TATATAAATTA
*
434621 TATAT--ACTA
1 TATATAAATTA
*
434630 TGTATAAATTA
1 TATATAAATTA
434641 TAT
1 TAT
434644 TGTTTATTAA
Statistics
Matches: 89, Mismatches: 27, Indels: 22
0.64 0.20 0.16
Matches are distributed among these distances:
8 1 0.01
9 17 0.19
10 21 0.24
11 42 0.47
12 8 0.09
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (11 bp):
TATATAAATTA
Found at i:434583 original size:21 final size:22
Alignment explanation
Indices: 434552--434605 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
434542 AGTTAGTATA
434552 TAAATTATATATGAA-TTATATT
1 TAAA-TATATATGAACTTATATT
*
434574 TAAATATATA-CAACTTATATT
1 TAAATATATATGAACTTATATT
*
434595 TATATAT-TATG
1 TAAATATATATG
434606 TATAATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
TAAATATATATGAACTTATATT
Found at i:434665 original size:49 final size:47
Alignment explanation
Indices: 434612--434721 Score: 166
Period size: 49 Copynumber: 2.3 Consensus size: 47
434602 TATGTATAAT
*
434612 TATAAATTATATATACTATGTATAAATTATATTGTTTATTAATATAAAC
1 TATAAATTATATATACTATGTATAAATTATATAGTTTA-T-ATATAAAC
*
434661 TATAAATTATATATACTATGTATAAATTATATAGTTTATATATAAAG
1 TATAAATTATATATACTATGTATAAATTATATAGTTTATATATAAAC
*
434708 TATATAAGTATATA
1 TATA-AATTATATA
434722 ATATAAAGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 11 0.19
48 9 0.16
49 37 0.65
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (47 bp):
TATAAATTATATATACTATGTATAAATTATATAGTTTATATATAAAC
Found at i:434713 original size:22 final size:21
Alignment explanation
Indices: 434681--434742 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
434671 ATATACTATG
434681 TATAAA-TTATATAGTTTATA
1 TATAAAGTTATATAGTTTATA
*
434701 TATAAAG-TATATAAGTATATAA
1 TATAAAGTTATAT-AGTTTAT-A
434723 TATAAAG-TATATAGTTTATA
1 TATAAAGTTATATAGTTTATA
434743 AAACCCTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 12 0.32
21 12 0.32
22 13 0.35
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (21 bp):
TATAAAGTTATATAGTTTATA
Found at i:434943 original size:35 final size:36
Alignment explanation
Indices: 434872--434945 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 36
434862 ACAATAGTTA
* **
434872 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTATAGTACATGTATA-ATACAAACT
* *
434909 ATATATGTAACTTATAGTACATGTAT-GTACAAACT
1 ATATATGTAACCTATAGTACATGTATAATACAAACT
434944 AT
1 AT
434946 GTATAGTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 8 0.25
37 24 0.75
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACATGTATAATACAAACT
Found at i:434954 original size:20 final size:20
Alignment explanation
Indices: 434931--434974 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
434921 TATAGTACAT
* *
434931 GTATGTACAAACTATGTATA
1 GTATATACAAACTATATATA
*
434951 GTATATATAAACTATATATA
1 GTATATACAAACTATATATA
434971 -TATA
1 GTATA
434975 ACTTACATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (20 bp):
GTATATACAAACTATATATA
Found at i:434970 original size:13 final size:13
Alignment explanation
Indices: 434952--434996 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
434942 CTATGTATAG
434952 TATATATAAACTA
1 TATATATAAACTA
434965 TATATATATAACTTA
1 TATATATA-AAC-TA
* *
434980 CATATATAAACCA
1 TATATATAAACTA
434993 TATA
1 TATA
434997 AAGTACATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 12 0.44
14 6 0.22
15 9 0.33
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:435033 original size:7 final size:7
Alignment explanation
Indices: 435023--435054 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
435013 TAGTTTATAG
435023 AAACCCT
1 AAACCCT
435030 AAACCCT
1 AAACCCT
435037 AAACCCT
1 AAACCCT
435044 AAACCCT
1 AAACCCT
435051 AAAC
1 AAAC
435055 ATTAAACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.41, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:435060 original size:14 final size:14
Alignment explanation
Indices: 435023--435061 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
435013 TAGTTTATAG
*
435023 AAACCCTAAACCCT
1 AAACACTAAACCCT
*
435037 AAACCCTAAACCCT
1 AAACACTAAACCCT
*
435051 AAACATTAAAC
1 AAACACTAAAC
435062 ATAGACCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACACTAAACCCT
Found at i:435193 original size:13 final size:13
Alignment explanation
Indices: 435175--435208 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
435165 CTATGTATAT
435175 TATATATAAACTA
1 TATATATAAACTA
*
435188 TATATATAACCTA
1 TATATATAAACTA
435201 TAGTATAT
1 TA-TATAT
435209 GTATATACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:435202 original size:20 final size:20
Alignment explanation
Indices: 435159--435202 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
435149 TACATGTATG
* * *
435159 TATAAACTATGTATATTATA
1 TATAAACTATATATATAACA
*
435179 TATAAACTATATATATAACC
1 TATAAACTATATATATAACA
435199 TATA
1 TATA
435203 GTATATGTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (20 bp):
TATAAACTATATATATAACA
Found at i:435213 original size:22 final size:22
Alignment explanation
Indices: 435188--435244 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
435178 ATATAAACTA
*
435188 TATATATAACCTATAGTATATG
1 TATATATAAACTATAGTATATG
* * *
435210 TATATACAATCTAT-TTATATG
1 TATATATAAACTATAGTATATG
435231 T-TATATAAACTATA
1 TATATATAAACTATA
435245 TATGTAACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 10 0.34
21 7 0.24
22 12 0.41
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATATAAACTATAGTATATG
Found at i:435243 original size:20 final size:20
Alignment explanation
Indices: 435190--435244 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
435180 ATAAACTATA
*
435190 TATATAACCTATAGTATATG
1 TATATAAACTATAGTATATG
*
435210 TATATACAATCTAT-TTATATG
1 TATATA-AA-CTATAGTATATG
435231 TTATATAAACTATA
1 -TATATAAACTATA
435245 TATGTAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 10 0.34
21 9 0.31
22 10 0.34
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (20 bp):
TATATAAACTATAGTATATG
Found at i:435258 original size:55 final size:55
Alignment explanation
Indices: 435126--435259 Score: 180
Period size: 55 Copynumber: 2.4 Consensus size: 55
435116 TGTATACATG
* * * *
435126 TAAACTATATATGTAACTTATAATACATGTATGTATAAACTATGTATATTATATA
1 TAAACTATATATGTAACCTATAGTACATGTATATACAAACTATGTATATTATATA
* * * *
435181 TAAACTATATATATAACCTATAGTATATGTATATACAATCTATTTATATGT-TATA
1 TAAACTATATATGTAACCTATAGTACATGTATATACAAACTATGTATAT-TATATA
435236 TAAACTATATATGTAACCTATAGT
1 TAAACTATATATGTAACCTATAGT
435260 TTATAGACAA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 68 0.99
56 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.42
Consensus pattern (55 bp):
TAAACTATATATGTAACCTATAGTACATGTATATACAAACTATGTATATTATATA
Found at i:435343 original size:21 final size:21
Alignment explanation
Indices: 435290--435344 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
435280 TAGTGTACTA
* *
435290 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
* *
435311 CATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
435332 TATAGTTTATAAT
1 TATAGTTTATAAT
435345 AATGTAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:435493 original size:21 final size:21
Alignment explanation
Indices: 435447--435493 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
435437 TAATTATTAA
*
435447 TTATAGTTTATAAACTATACT
1 TTATAATTTATAAACTATACT
* *
435468 ATATAATTTAT-AACATATAGT
1 TTATAATTTATAAAC-TATACT
435489 TTATA
1 TTATA
435494 TTAATATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (21 bp):
TTATAATTTATAAACTATACT
Found at i:435550 original size:129 final size:130
Alignment explanation
Indices: 435318--435565 Score: 297
Period size: 129 Copynumber: 1.9 Consensus size: 130
435308 ACCCATAGTA
* * * * *
435318 TATAATTTATAAACTATAGTTTATAATAATGTAATATATAGTTTATATTAATGTTAATTATCTTA
1 TATAATTTATAAACTATACTATATAATAATATAACATATAGTTTATATTAATATTAATTATCTTA
* * ** * *
435383 TATATAATTTATATTAATATAATAAATAGTTTATAAACTATAATGTATTAATATTAATTATTAAT
66 GACATAATTTATATTAATATAATAAATAAATTATAAACTAGAATATATTAATATTAATTATTAAT
* *
435448 TATAGTTTATAAACTATACTATATAAT-TTATAACATATAGTTTATATTAATATTAATT-T-TAT
1 TATAATTTATAAACTATACTATATAATAATATAACATATAGTTTATATTAATATTAATTATCT-T
* * *
435510 AGACCATATTTTATATTAATATTAAT-TATAAATTATAAACTAGATTATATTAATAT
65 AGA-CATAATTTATATTAATA-TAATAAATAAATTATAAACTAGAATATATTAATAT
435566 AAGTTAATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
127 1 0.01
128 4 0.04
129 66 0.67
130 28 0.28
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (130 bp):
TATAATTTATAAACTATACTATATAATAATATAACATATAGTTTATATTAATATTAATTATCTTA
GACATAATTTATATTAATATAATAAATAAATTATAAACTAGAATATATTAATATTAATTATTAAT
Found at i:435582 original size:22 final size:20
Alignment explanation
Indices: 435556--435629 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 20
435546 AAACTAGATT
435556 ATATTAATATAAGTTAATATTA
1 ATATTAATATAA-TT-ATATTA
*
435578 ATATTAATATTTAATTATTTTA
1 ATATTAATA--TAATTATATTA
*
435600 ATATTAATTATAAATA-ATT-
1 ATATTAA-TATAATTATATTA
435619 -TATTAATATAA
1 ATATTAATATAA
435630 ATTTTATAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
17 5 0.11
18 6 0.13
20 2 0.04
21 5 0.11
22 21 0.46
23 4 0.09
24 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (20 bp):
ATATTAATATAATTATATTA
Found at i:435600 original size:16 final size:15
Alignment explanation
Indices: 435569--435610 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
435559 TTAATATAAG
435569 TTAATATTAA-TA--
1 TTAATATTAATTATT
435581 TTAATATTTAATTATT
1 TTAATA-TTAATTATT
435597 TTAATATTAATTAT
1 TTAATATTAATTAT
435611 AAATAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 2 0.08
15 8 0.31
16 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATATTAATTATT
Found at i:435617 original size:16 final size:15
Alignment explanation
Indices: 435556--435631 Score: 50
Period size: 16 Copynumber: 4.9 Consensus size: 15
435546 AAACTAGATT
*
435556 ATATTAATATAAGTTA
1 ATATTAATATAA-ATA
*
435572 ATATTAATATTAAT-
1 ATATTAATATAAATA
**
435586 AT-TTAAT-TATTTTA
1 ATATTAATATA-AATA
435600 ATATTAATTATAAATA
1 ATATTAA-TATAAATA
435616 ATTTATTAATATAAAT
1 A--TATTAATATAAAT
435632 TTTATAGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
12 1 0.02
13 6 0.13
14 4 0.09
15 5 0.11
16 15 0.33
17 9 0.20
18 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
ATATTAATATAAATA
Found at i:440190 original size:19 final size:19
Alignment explanation
Indices: 440166--440205 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
440156 TTTATAATAC
*
440166 AAGAATTATAAATAATATA
1 AAGAATTAGAAATAATATA
* *
440185 AAGAATTGGAATTAATATA
1 AAGAATTAGAAATAATATA
440204 AA
1 AA
440206 AGTCAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (19 bp):
AAGAATTAGAAATAATATA
Found at i:447027 original size:31 final size:31
Alignment explanation
Indices: 446974--447163 Score: 148
Period size: 31 Copynumber: 5.8 Consensus size: 31
446964 ATTTAATAGA
446974 GATAATGGTGTAGTGACCATTTTGTTACAAATC
1 GATAAT-GT-TAGTGACCATTTTGTTACAAATC
* *
447007 GATAATGTCAGTGGCCATTTTGTTACATGTTACAAATC
1 GATAATGTTAGTGACCA---T-TT---TGTTACAAATC
* *
447045 GATAATGTTAGTGGCCATTTTGTTACAAATT
1 GATAATGTTAGTGACCATTTTGTTACAAATC
* * *
447076 GATAACGTTAGTGACTATTTTGTTACAAATA
1 GATAATGTTAGTGACCATTTTGTTACAAATC
* * **
447107 GAT-ATCGATAGTGACAATTTTCCTACAAATC
1 GATAAT-GTTAGTGACCATTTTGTTACAAATC
** * *
447138 GATAACATAAGTGACCATTTTATTAC
1 GATAATGTTAGTGACCATTTTGTTAC
447164 TTTTGAAACT
Statistics
Matches: 127, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
30 1 0.01
31 84 0.66
32 3 0.02
33 6 0.05
34 3 0.02
35 3 0.02
38 27 0.21
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (31 bp):
GATAATGTTAGTGACCATTTTGTTACAAATC
Found at i:447047 original size:38 final size:38
Alignment explanation
Indices: 446996--447071 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
446986 GTGACCATTT
446996 TGTTACAAATCGATAATGTCAGTGGCCATTTTGTTACA
1 TGTTACAAATCGATAATGTCAGTGGCCATTTTGTTACA
*
447034 TGTTACAAATCGATAATGTTAGTGGCCATTTTGTTACA
1 TGTTACAAATCGATAATGTCAGTGGCCATTTTGTTACA
447072 AATTGATAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (38 bp):
TGTTACAAATCGATAATGTCAGTGGCCATTTTGTTACA
Found at i:448461 original size:27 final size:30
Alignment explanation
Indices: 448428--448484 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
448418 TTGAATTAAA
448428 AAATTAT-AA-AGTTATA-ATTTTAAAAAT
1 AAATTATGAATAGTTATACATTTTAAAAAT
**
448455 AAATTATGAATTTTTATACATTTTAAAAAT
1 AAATTATGAATAGTTATACATTTTAAAAAT
448485 CATTTTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.28
28 2 0.08
29 5 0.20
30 11 0.44
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTATGAATAGTTATACATTTTAAAAAT
Found at i:448979 original size:31 final size:32
Alignment explanation
Indices: 448920--449005 Score: 122
Period size: 31 Copynumber: 2.7 Consensus size: 32
448910 GTTCAAATCG
* * *
448920 AAAATCAATCGATCTGGTATTGACCCGACCC-
1 AAAATCAACCGATCTGATATTGAACCGACCCA
448951 AAAATCTAACCGATCTGATATT-AACCGACCCA
1 AAAATC-AACCGATCTGATATTGAACCGACCCA
448983 AAAATCAACCGATCTGATATTGA
1 AAAATCAACCGATCTGATATTGA
449006 TTTGAACCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
31 29 0.59
32 20 0.41
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (32 bp):
AAAATCAACCGATCTGATATTGAACCGACCCA
Found at i:451477 original size:192 final size:192
Alignment explanation
Indices: 451128--451497 Score: 548
Period size: 192 Copynumber: 1.9 Consensus size: 192
451118 GTGTCTCTGG
451128 AAAATAACATCTCCCTTGAGATTATCTTTCTCAAGATACAAACATTGAAAATATCTCCCTTGATA
1 AAAATAACATCTCCCTTGAGATTATCTTTCTCAAGATACAAACATTGAAAATA-CTCCCTTGATA
* * * * *
451193 AATATTATTTTCTGCCTCGCTTGAGACAACATCAAATTTCAAAGTAAAAGATGTAATCGAACGAA
65 AATATCATTTTCAGCCTCACTTGAGACAACATCAAATTTCAAAGCAAAAGATGTAATCGAACAAA
* * *
451258 AATTGTTTTCTTTGCCCTTTCCGTGTCTTCAGACCAATGGGTAAAGAGATTGTCTTTCTCGAA
130 AATTGTTGTCTTTGCCCTTTCCGTGTCTTCACACCAATGGATAAAGAGATTGTCTTTCTCGAA
* * * *
451321 AAAATACCATCTCCCTTGATATTATCTTTCTCAAGATATAAATATTGAAAATA-TCCCTAAT-AT
1 AAAATAACATCTCCCTTGAGATTATCTTTCTCAAGATACAAACATTGAAAATACTCCCT--TGAT
*
451384 AAATATCATTTTCAGCCTCACTTGAGACAACATCAAATTTCAAAGCAAAAGTTGTAATCGAACAA
64 AAATATCATTTTCAGCCTCACTTGAGACAACATCAAATTTCAAAGCAAAAGATGTAATCGAACAA
* *
451449 AAATTGTTGTCTTTG-TCTTATTCGTGTCTTCACACCAATGGATAAAGAG
129 AAATTGTTGTCTTTGCCCTT-TCCGTGTCTTCACACCAATGGATAAAGAG
451498 GTGCAGCTGT
Statistics
Matches: 159, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
191 8 0.05
192 101 0.64
193 50 0.31
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (192 bp):
AAAATAACATCTCCCTTGAGATTATCTTTCTCAAGATACAAACATTGAAAATACTCCCTTGATAA
ATATCATTTTCAGCCTCACTTGAGACAACATCAAATTTCAAAGCAAAAGATGTAATCGAACAAAA
ATTGTTGTCTTTGCCCTTTCCGTGTCTTCACACCAATGGATAAAGAGATTGTCTTTCTCGAA
Found at i:457337 original size:20 final size:20
Alignment explanation
Indices: 457300--457340 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
457290 TTATTTTATT
*
457300 ACATTTTTAACAATTAAAAA
1 ACATTTTTAACAACTAAAAA
457320 ACATATTTTAAC-ACTAAAAA
1 ACAT-TTTTAACAACTAAAAA
457340 A
1 A
457341 TCCCTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (20 bp):
ACATTTTTAACAACTAAAAA
Found at i:462857 original size:20 final size:20
Alignment explanation
Indices: 462828--462873 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
462818 TAATTTTCAA
*
462828 ACATTATGCACCTAAATTTG
1 ACATTGTGCACCTAAATTTG
*
462848 ACATTGTGCACCTAATTTTG
1 ACATTGTGCACCTAAATTTG
462868 ACATTG
1 ACATTG
462874 CAATATTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (20 bp):
ACATTGTGCACCTAAATTTG
Found at i:468606 original size:21 final size:21
Alignment explanation
Indices: 468571--468619 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
468561 TAATTTTCAA
* *
468571 ACATTATTGCACCTAATTTTG
1 ACATTGTTACACCTAATTTTG
*
468592 ATATTGTTACACCTAATTTTG
1 ACATTGTTACACCTAATTTTG
468613 ACATTGT
1 ACATTGT
468620 AATATTAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (21 bp):
ACATTGTTACACCTAATTTTG
Found at i:470326 original size:24 final size:24
Alignment explanation
Indices: 470253--470312 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
470243 ACCAAATCCA
470253 TTCGGTGCATTTAATTTTTCCACT
1 TTCGGTGCATTTAATTTTTCCACT
470277 TTCGGTGCATTTAATTTTTCCACT
1 TTCGGTGCATTTAATTTTTCCACT
470301 TTCGGTGCATTT
1 TTCGGTGCATTT
470313 GTTTTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (24 bp):
TTCGGTGCATTTAATTTTTCCACT
Found at i:476726 original size:14 final size:14
Alignment explanation
Indices: 476673--476720 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
476663 CACATGCATT
*
476673 CTCTCTCTCTCTCC
1 CTCTCCCTCTCTCC
* *
476687 CTCCCCCCCCCTCTCC
1 CT--CTCCCTCTCTCC
476703 CTCTCCCTCTCTCC
1 CTCTCCCTCTCTCC
476717 CTCT
1 CTCT
476721 TTCTCTTATC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 16 0.59
16 11 0.41
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (14 bp):
CTCTCCCTCTCTCC
Found at i:479383 original size:21 final size:22
Alignment explanation
Indices: 479358--479407 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
479348 AATTTGACCG
* *
479358 TAAATATTAATTTTTAATTT-T
1 TAAATATTAAATATTAATTTAT
479379 TAAATATTAAATATTAATTTAT
1 TAAATATTAAATATTAATTTAT
479401 TAAATAT
1 TAAATAT
479408 AAAACTTACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAAATATTAAATATTAATTTAT
Found at i:479403 original size:15 final size:15
Alignment explanation
Indices: 479358--479407 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 15
479348 AATTTGACCG
479358 TAAATATTAATTT-T
1 TAAATATTAATTTAT
* * *
479372 TAATTTTTAA-ATAT
1 TAAATATTAATTTAT
479386 TAAATATTAATTTAT
1 TAAATATTAATTTAT
479401 TAAATAT
1 TAAATAT
479408 AAAACTTACG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 1 0.04
14 17 0.61
15 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAAATATTAATTTAT
Found at i:481191 original size:2 final size:2
Alignment explanation
Indices: 481184--481213 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
481174 ACTGAGCACC
481184 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
481214 TTCCCCTTCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:482848 original size:21 final size:21
Alignment explanation
Indices: 482821--482879 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
482811 GTCCGAGTTA
* *
482821 CCCGCGACGGCTGCAATAGCG
1 CCCGCGACGGCAGCAATAACG
* *
482842 TCCGCGATGGCAGCAATAACG
1 CCCGCGACGGCAGCAATAACG
*
482863 CCCGCGACGGCCGCAAT
1 CCCGCGACGGCAGCAAT
482880 CACGGTAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.37, G:0.31, T:0.10
Consensus pattern (21 bp):
CCCGCGACGGCAGCAATAACG
Found at i:484885 original size:18 final size:18
Alignment explanation
Indices: 484862--484898 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
484852 ACAAGAAATC
484862 TCTCCTTAAGTAAGGGTT
1 TCTCCTTAAGTAAGGGTT
* *
484880 TCTCCTTATGTTAGGGTT
1 TCTCCTTAAGTAAGGGTT
484898 T
1 T
484899 ATTTTAGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (18 bp):
TCTCCTTAAGTAAGGGTT
Found at i:490313 original size:27 final size:28
Alignment explanation
Indices: 490282--490359 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 28
490272 TAAGATGTAT
*
490282 TTTATTATATTTAATATTTTTTT-TTAA
1 TTTATTATATTTAATATTTTTTTAATAA
*
490309 TTTATTTAACTATTTAA-ATTTTTTTAATAT
1 TTTA-TT-A-TATTTAATATTTTTTTAATAA
*
490339 TTTATT-TAATTAAT-TTTTTTT
1 TTTATTATATTTAATATTTTTTT
490360 GCAGATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
26 13 0.30
27 4 0.09
28 2 0.05
29 11 0.26
30 13 0.30
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTATTATATTTAATATTTTTTTAATAA
Found at i:490314 original size:22 final size:23
Alignment explanation
Indices: 490281--490323 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
490271 TTAAGATGTA
490281 TTTTATTATATTTAA-TATTTTT
1 TTTTATTATATTTAACTATTTTT
490303 TTTTAATT-TATTTAACTATTT
1 TTTT-ATTATATTTAACTATTT
490324 AAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTATTATATTTAACTATTTTT
Found at i:490324 original size:30 final size:30
Alignment explanation
Indices: 490289--490347 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
490279 TATTTTATTA
*
490289 TATTTAATATTTTTTT-TTAATTTATTTAAC
1 TATTTAA-ATTTTTTTAATAATTTATTTAAC
*
490319 TATTTAAATTTTTTTAATATTTTATTTAA
1 TATTTAAATTTTTTTAATAATTTATTTAA
490348 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (30 bp):
TATTTAAATTTTTTTAATAATTTATTTAAC
Found at i:490339 original size:17 final size:18
Alignment explanation
Indices: 490307--490340 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
490297 ATTTTTTTTT
490307 AATTTATTTAACTATTTA
1 AATTTATTTAACTATTTA
*
490325 AATTTTTTTAA-TATTT
1 AATTTATTTAACTATTT
490341 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTATTTAACTATTTA
Found at i:490342 original size:18 final size:19
Alignment explanation
Indices: 490302--490342 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
490292 TTAATATTTT
*
490302 TTTTTAATTTATTTAACTA
1 TTTTAAATTTATTTAACTA
*
490321 -TTTAAATTTTTTTAA-TA
1 TTTTAAATTTATTTAACTA
490338 TTTTA
1 TTTTA
490343 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAAATTTATTTAACTA
Found at i:492062 original size:33 final size:33
Alignment explanation
Indices: 492025--492142 Score: 164
Period size: 33 Copynumber: 3.6 Consensus size: 33
492015 TTACCTGATG
*
492025 CCGCCGCCGCCACCATCACCTGGTTTTATGACC
1 CCGCCGCCGCCACCGTCACCTGGTTTTATGACC
*
492058 CCGCCGCCACCACCGTCACCTGGTTTTATGACC
1 CCGCCGCCGCCACCGTCACCTGGTTTTATGACC
* ** *
492091 TCGCTACCGCCACCGTCACCTAGTTTTATGACC
1 CCGCCGCCGCCACCGTCACCTGGTTTTATGACC
* *
492124 CCGCCGCCGCTATCGTCAC
1 CCGCCGCCGCCACCGTCAC
492143 AGATTTTTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.15, C:0.45, G:0.18, T:0.22
Consensus pattern (33 bp):
CCGCCGCCGCCACCGTCACCTGGTTTTATGACC
Found at i:500256 original size:29 final size:30
Alignment explanation
Indices: 500209--500290 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
500199 CTCGAAGGAC
* *
500209 CTATCCAGAGGCCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
* *
500238 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
* * *
500268 CTGTCCATAGGTCCCAAAGAACC
1 CTATCCAGAGGTCACAAAGAACC
500291 TAGGTAAACT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 17 0.39
30 27 0.61
ACGTcount: A:0.34, C:0.32, G:0.20, T:0.15
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGGCAA
Found at i:500280 original size:30 final size:31
Alignment explanation
Indices: 500236--500330 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 31
500226 AGACCCCGGT
* * * * *
500236 AACTATCCAGAGGTCATAAAGAACCTCGG-C
1 AACTGTCCATAGGTCACAAAGAACCTAGGTA
*
500266 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATAGGTCACAAAGAACCTAGGTA
* * *
500297 AACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATAGGTCAC-AAAGAACCTAGGTA
500328 AAC
1 AAC
500331 CCTTAACTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
30 24 0.44
31 26 0.48
32 4 0.07
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (31 bp):
AACTGTCCATAGGTCACAAAGAACCTAGGTA
Found at i:500304 original size:31 final size:32
Alignment explanation
Indices: 500253--500330 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 32
500243 CAGAGGTCAT
* *
500253 AAAGAACCTCGG-CAACTGTCCATAGGTC-CC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCTCC
* *
500283 AAAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAAGAACCTAGGTAAACTGTCCATAGGTCTCC
*
500315 AAAG-ACATAGGTAAAC
1 AAAGAACCTAGGTAAAC
500331 CCTTAACTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 11 0.27
31 25 0.61
32 5 0.12
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (32 bp):
AAAGAACCTAGGTAAACTGTCCATAGGTCTCC
Found at i:508251 original size:13 final size:13
Alignment explanation
Indices: 508233--508272 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
508223 GAGAAAAGTT
508233 AAAATAAAGA-AAA
1 AAAATAAA-ATAAA
508246 AAAATAAAATAAA
1 AAAATAAAATAAA
*
508259 GAAATAAAATAAA
1 AAAATAAAATAAA
508272 A
1 A
508273 TAAAAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 1 0.04
13 23 0.96
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:508253 original size:18 final size:18
Alignment explanation
Indices: 508232--508276 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
508222 AGAGAAAAGT
508232 TAAAATAAAGAAAAAAAA
1 TAAAATAAAGAAAAAAAA
*
508250 TAAAATAAAGAAATAAAA
1 TAAAATAAAGAAAAAAAA
508268 TAAAATAAA
1 TAAAATAAA
508277 AATGAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (18 bp):
TAAAATAAAGAAAAAAAA
Found at i:508402 original size:22 final size:22
Alignment explanation
Indices: 508374--508435 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
508364 TGTGGATCCC
*
508374 CTACAAAATTAATTAAAATTAT
1 CTACAAAATAAATTAAAATTAT
508396 CTACAAAATAAATTAAAATTAT
1 CTACAAAATAAATTAAAATTAT
*
508418 CTACAAAATAAAATAAAA
1 CTACAAAATAAATTAAAA
508436 ATAAAGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (22 bp):
CTACAAAATAAATTAAAATTAT
Found at i:514312 original size:25 final size:25
Alignment explanation
Indices: 514278--514332 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
514268 TTGATTTAAG
*
514278 GATTCTAAAACTTATCTCTCAAGAA
1 GATTTTAAAACTTATCTCTCAAGAA
*
514303 GATTTTAAAACTTATCTCTCAAGCA
1 GATTTTAAAACTTATCTCTCAAGAA
514328 GATTT
1 GATTT
514333 AATCTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (25 bp):
GATTTTAAAACTTATCTCTCAAGAA
Found at i:516880 original size:307 final size:307
Alignment explanation
Indices: 516326--516939 Score: 1210
Period size: 307 Copynumber: 2.0 Consensus size: 307
516316 CCAGGACTTG
516326 GATATCTTTTCGATGAGGACATTATCTTAGAGTACTTCACACAATTGCATTCCTTCAGCAAGGAT
1 GATATCTTTTCGATGAGGACATTATCTTAGAGTACTTCACACAATTGCATTCCTTCAGCAAGGAT
516391 GTCGGCCACCAGATTCTCGTAGTCATGGACTTTATCCATTATGGGCTTATCATTCTTCATTTGGA
66 GTCGGCCACCAGATTCTCGTAGTCATGGACTTTATCCATTATGGGCTTATCATTCTTCATTTGGA
516456 ATTTGAGCCATTCTCCAACAACATATTTCTTTATCCCCGCATCGTCAGCACTGTAGTTCTTCTCC
131 ATTTGAGCCATTCTCCAACAACATATTTCTTTATCCCCGCATCGTCAGCACTGTAGTTCTTCTCC
*
516521 AGAGTGTCCCAGATCACCTTAGTACTTATTTCCTAAGGAACATGTCAGACAATTTATTAGACATG
196 AGAGTGACCCAGATCACCTTAGTACTTATTTCCTAAGGAACATGTCAGACAATTTATTAGACATG
516586 TGGCTGAAAAGATGTCCTCACACTGTCTTATTGTCCTTCTCGTATTT
261 TGGCTGAAAAGATGTCCTCACACTGTCTTATTGTCCTTCTCGTATTT
516633 GATATCTTTTCGATGAGGACATTATCTTAGAGTACTTCACACAATTGCATTCCTTCAGCAAGGAT
1 GATATCTTTTCGATGAGGACATTATCTTAGAGTACTTCACACAATTGCATTCCTTCAGCAAGGAT
516698 GTCGGCCACCAGATTCTCGTAGTCATGGACTTTATCCATTATGGGCTTATCATTCTTCATTTGGA
66 GTCGGCCACCAGATTCTCGTAGTCATGGACTTTATCCATTATGGGCTTATCATTCTTCATTTGGA
516763 ATTTGAGCCATTCTCCAACAACATATTTCTTTATCCCCGCATCGTCAGCACTGTAGTTCTTCTCC
131 ATTTGAGCCATTCTCCAACAACATATTTCTTTATCCCCGCATCGTCAGCACTGTAGTTCTTCTCC
*
516828 AGAGTGACCCAGATCACCTTGGTACTTATTTCCTAAGGAACATGTCAGACAATTTATTAGACATG
196 AGAGTGACCCAGATCACCTTAGTACTTATTTCCTAAGGAACATGTCAGACAATTTATTAGACATG
516893 TGGCTGAAAAGATGTCCTCACACTGTCTTATTGTCCTTCTCGTATTT
261 TGGCTGAAAAGATGTCCTCACACTGTCTTATTGTCCTTCTCGTATTT
516940 CTTGGTAGTA
Statistics
Matches: 305, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
307 305 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (307 bp):
GATATCTTTTCGATGAGGACATTATCTTAGAGTACTTCACACAATTGCATTCCTTCAGCAAGGAT
GTCGGCCACCAGATTCTCGTAGTCATGGACTTTATCCATTATGGGCTTATCATTCTTCATTTGGA
ATTTGAGCCATTCTCCAACAACATATTTCTTTATCCCCGCATCGTCAGCACTGTAGTTCTTCTCC
AGAGTGACCCAGATCACCTTAGTACTTATTTCCTAAGGAACATGTCAGACAATTTATTAGACATG
TGGCTGAAAAGATGTCCTCACACTGTCTTATTGTCCTTCTCGTATTT
Found at i:530288 original size:16 final size:17
Alignment explanation
Indices: 530267--530309 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
530257 ATGTAAAATT
530267 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
530283 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
530300 AAATATTTAA
1 AAATATTTAA
530310 TCAATAAGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:530811 original size:25 final size:25
Alignment explanation
Indices: 530782--530839 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
530772 CAGAATTAAT
530782 AATTTAAAATAAATTAAATATATAA
1 AATTTAAAATAAATTAAATATATAA
530807 AATTTAAAATAAATTAAATATATAA
1 AATTTAAAATAAATTAAATATATAA
530832 AATTTAAA
1 AATTTAAA
530840 TCCAATCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATTTAAAATAAATTAAATATATAA
Found at i:533770 original size:13 final size:13
Alignment explanation
Indices: 533753--533783 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
533743 AAATTGTTTT
533753 CAAAAACTAAAAA
1 CAAAAACTAAAAA
*
533766 TAAAAACTAAAAA
1 CAAAAACTAAAAA
533779 CAAAA
1 CAAAA
533784 CATACTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (13 bp):
CAAAAACTAAAAA
Found at i:534381 original size:20 final size:20
Alignment explanation
Indices: 534352--534395 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
534342 TCCAAATTCG
534352 CAACGAGAATATGTAAATCA
1 CAACGAGAATATGTAAATCA
* * *
534372 CAACGCGAATTTGTAAATCG
1 CAACGAGAATATGTAAATCA
534392 CAAC
1 CAAC
534396 ACATAAGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
CAACGAGAATATGTAAATCA
Found at i:541296 original size:23 final size:20
Alignment explanation
Indices: 541245--541304 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
541235 TTTTGGTGCA
*
541245 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
541264 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
541285 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
541305 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:541331 original size:20 final size:21
Alignment explanation
Indices: 541287--541326 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
541277 CCCCCTTTGA
*
541287 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
541308 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
541327 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:546110 original size:42 final size:42
Alignment explanation
Indices: 546020--546118 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
546010 ACCCCCACTT
* * *
546020 CGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTCTACACCTCCACAA
* *
546062 CTAGAGCCATCACCTGATCGAGCCGATTAC-ACACCTCCATAA
1 CGAGAGCCATCACCTGATCGAGCCGATT-CTACACCTCCACAA
546104 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
546119 ATTCCATCAC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 49 0.98
43 1 0.02
ACGTcount: A:0.28, C:0.36, G:0.18, T:0.17
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTCTACACCTCCACAA
Found at i:546718 original size:21 final size:21
Alignment explanation
Indices: 546691--546745 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
546681 ATTCACCTGT
546691 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
546712 TATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
546733 CACCGTTCAAGAG
1 CATCGTTCAAGAG
546746 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:548146 original size:16 final size:16
Alignment explanation
Indices: 548121--548156 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
548111 TGTAAATAAG
*
548121 AATTGTTTTTTTGTTT
1 AATTGATTTTTTGTTT
548137 AATTGATTTTTTGTTT
1 AATTGATTTTTTGTTT
548153 AATT
1 AATT
548157 TCAATCTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.69
Consensus pattern (16 bp):
AATTGATTTTTTGTTT
Found at i:548279 original size:20 final size:20
Alignment explanation
Indices: 548254--548302 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
548244 TTTGCGTTGC
*
548254 GATTTTTGCGTTACGAATTT
1 GATTTTCGCGTTACGAATTT
*
548274 GATTTTCGCGTTGCGAATTT
1 GATTTTCGCGTTACGAATTT
*
548294 GACTTTCGC
1 GATTTTCGC
548303 AACAATCGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.45
Consensus pattern (20 bp):
GATTTTCGCGTTACGAATTT
Found at i:550836 original size:24 final size:24
Alignment explanation
Indices: 550785--550836 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
550775 ATATGAGTAT
** *
550785 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
550809 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
550833 TGAC
1 TGAC
550837 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:551568 original size:16 final size:15
Alignment explanation
Indices: 551546--551584 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
551536 GAAATCATTG
551546 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
551562 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
551577 AAAAATTA
1 AAAAATTA
551585 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:551778 original size:20 final size:20
Alignment explanation
Indices: 551720--551798 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
551710 CCCAAAACAT
*
551720 TTGTGTTGCGAAAA-CAAAA
1 TTGTGTTGCGAAAAGGAAAA
**
551739 TTCGTGTTGCGATTTA-GAAAA
1 TT-GTGTTGCGA-AAAGGAAAA
*
551760 TCT-TGTTGCGAAAAGGAAAC
1 T-TGTGTTGCGAAAAGGAAAA
551780 TTGTGTTGCGAAAAGGAAA
1 TTGTGTTGCGAAAAGGAAA
551799 TTCACGTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 4 0.08
20 38 0.78
21 6 0.12
22 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (20 bp):
TTGTGTTGCGAAAAGGAAAA
Found at i:551807 original size:20 final size:20
Alignment explanation
Indices: 551764--551811 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
551754 AGAAAATCTT
**
551764 GTTGCGAAAAGGAAACTTGT
1 GTTGCGAAAAGGAAACTTAC
551784 GTTGCGAAAAGGAAA-TTCAC
1 GTTGCGAAAAGGAAACTT-AC
551804 GTTGCGAA
1 GTTGCGAA
551812 TTTAGAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGCGAAAAGGAAACTTAC
Found at i:551890 original size:21 final size:20
Alignment explanation
Indices: 551803--551892 Score: 92
Period size: 20 Copynumber: 4.4 Consensus size: 20
551793 AGGAAATTCA
*
551803 CGTTGCGAATTTAGAAATCG
1 CGTTGCGAATTTGGAAATCG
*
551823 AGTTGCGAATTT-GAAACTCCG
1 CGTTGCGAATTTGGAAA-T-CG
* *
551844 TGTTGCAAATTTGGAAATCG
1 CGTTGCGAATTTGGAAATCG
* *
551864 CATTGCGAATTTGGAAAATTG
1 CGTTGCGAATTTGG-AAATCG
551885 CGTTGCGA
1 CGTTGCGA
551893 GAAAGAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
19 4 0.07
20 25 0.43
21 25 0.43
22 4 0.07
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (20 bp):
CGTTGCGAATTTGGAAATCG
Found at i:551890 original size:41 final size:41
Alignment explanation
Indices: 551803--551890 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 41
551793 AGGAAATTCA
* *
551803 CGTTGCGAATTTAGAAATCGAGTTGCGAATTTGAAACTCCG
1 CGTTGCAAATTTAGAAATCGAGTTGCGAATTTGAAAATCCG
* * *
551844 TGTTGCAAATTTGGAAATCGCA-TTGCGAATTTGGAAAAT-TG
1 CGTTGCAAATTTAGAAATCG-AGTTGCGAATTT-GAAAATCCG
551885 CGTTGC
1 CGTTGC
551891 GAGAAAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
41 33 0.85
42 6 0.15
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (41 bp):
CGTTGCAAATTTAGAAATCGAGTTGCGAATTTGAAAATCCG
Found at i:551909 original size:102 final size:101
Alignment explanation
Indices: 551774--551977 Score: 263
Period size: 102 Copynumber: 2.0 Consensus size: 101
551764 GTTGCGAAAA
* * *
551774 GGAAACTTGTGTTGCGAAAAGGAAATTCACGTTGCGAATT-TAGAAA-TCGAGTTGCGAATTT-G
1 GGAAAATTGCGTTGCGAAAAGGAAATTCACGTTGCG-ATTACAGAAACT-GAGTTGCGAATTTGG
*
551836 AAACTCCGTGTTGCAAATTTGGAAATCGCATTGCGAATTT
64 AAACT--GTGTTGCAAAATTGGAAATCGCATTGCGAATTT
*
551876 GGAAAATTGCGTTGCGAGAAA-GAAATTCGCGTTGCGATTACAGAAACTGAGTTGCGAATTTGGA
1 GGAAAATTGCGTTGCGA-AAAGGAAATTCACGTTGCGATTACAGAAACTGAGTTGCGAATTTGGA
** *
551940 AACTGTGTTGCAAAATTGGAGTTCGCGTTGCGAATTT
65 AACTGTGTTGCAAAATTGGAAATCGCATTGCGAATTT
551977 G
1 G
551978 TTGGTCATTT
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
101 33 0.37
102 47 0.52
103 10 0.11
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (101 bp):
GGAAAATTGCGTTGCGAAAAGGAAATTCACGTTGCGATTACAGAAACTGAGTTGCGAATTTGGAA
ACTGTGTTGCAAAATTGGAAATCGCATTGCGAATTT
Found at i:551958 original size:20 final size:20
Alignment explanation
Indices: 551918--551959 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
551908 TGCGATTACA
* *
551918 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCAAAATTG
*
551938 GAAACTGTGTTGCAAAATTG
1 GAAACTGAGTTGCAAAATTG
551958 GA
1 GA
551960 GTTCGCGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTGCAAAATTG
Found at i:552592 original size:17 final size:17
Alignment explanation
Indices: 552525--552593 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 17
552515 GAGCGGAGCT
* *
552525 ATCGTCTGACCCAAGCC
1 ATCGTCCGAACCAAGCC
* * * *
552542 ATTGTCAGAATCGAGCC
1 ATCGTCCGAACCAAGCC
* **
552559 ATCGTCCGAGCTGAGCC
1 ATCGTCCGAACCAAGCC
552576 ATCGTCCGAACCAAGCC
1 ATCGTCCGAACCAAGCC
552593 A
1 A
552594 CTGTTTGAGC
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.26, C:0.35, G:0.22, T:0.17
Consensus pattern (17 bp):
ATCGTCCGAACCAAGCC
Found at i:558045 original size:15 final size:15
Alignment explanation
Indices: 558025--558060 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
558015 TAAGCAGTAT
558025 CAGTGACGTTGAGGA
1 CAGTGACGTTGAGGA
558040 CAGTGACGTTGAGGA
1 CAGTGACGTTGAGGA
558055 CAGTGA
1 CAGTGA
558061 AGATGACGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.14, G:0.39, T:0.19
Consensus pattern (15 bp):
CAGTGACGTTGAGGA
Found at i:559040 original size:119 final size:120
Alignment explanation
Indices: 558888--559129 Score: 351
Period size: 123 Copynumber: 2.0 Consensus size: 120
558878 TCATTTGTTT
* * *
558888 CATATTGAACCGAATATACAATTTTTT-AAAAAAATTATAGTTTCAAGTGAATTTTTATTGAAAA
1 CATATTAAACCGAATAGACAATTTTTTAAAAAAAATTATAGTTTCAAGTGAAATTTTATTGAAAA
* *
558952 ATCGATAAATAGAACCGTTAAAAAAACTGAACCGAACCAAAAAAATCGGTTTCAC
66 ATAGATAAATAGAACCGTTAAAAAAAATGAACCGAACCAAAAAAATCGGTTTCAC
* *
559007 CATATTAAACCGAATAGATAATTTTTTTTAAAAAAAAATTATAGTTTCAAGTGAAATTTTGTTGA
1 CATATTAAACCGAATAGACAA--TTTTTT-AAAAAAAATTATAGTTTCAAGTGAAATTTTATTGA
* * **
559072 AAAATAGATAAATCGAATCGTTAAAAAAAATGAACCGAACTGAAAAAATCGGTTTCAC
63 AAAATAGATAAATAGAACCGTTAAAAAAAATGAACCGAACCAAAAAAATCGGTTTCAC
559130 ATAATTTGGT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
119 18 0.17
121 6 0.06
123 84 0.78
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (120 bp):
CATATTAAACCGAATAGACAATTTTTTAAAAAAAATTATAGTTTCAAGTGAAATTTTATTGAAAA
ATAGATAAATAGAACCGTTAAAAAAAATGAACCGAACCAAAAAAATCGGTTTCAC
Found at i:560836 original size:15 final size:16
Alignment explanation
Indices: 560816--560848 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
560806 ATGGTTATGT
*
560816 TAGCTC-ATTCATTCA
1 TAGCTCAATTCATGCA
560831 TAGCTCAATTCATGCA
1 TAGCTCAATTCATGCA
560847 TA
1 TA
560849 AACATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (16 bp):
TAGCTCAATTCATGCA
Found at i:568690 original size:18 final size:18
Alignment explanation
Indices: 568667--568701 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
568657 AGGGATTATC
568667 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
568685 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
568702 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:569295 original size:21 final size:21
Alignment explanation
Indices: 569271--569312 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
569261 TGTAGCAGTA
*
569271 CTGTAGCAGGGTATCGGTACC
1 CTGTAGCAGGGTATCGATACC
*
569292 CTGTAGCATGGTATCGATACC
1 CTGTAGCAGGGTATCGATACC
569313 ATGGCAGCAA
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:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (21 bp):
CTGTAGCAGGGTATCGATACC
Found at i:574568 original size:14 final size:14
Alignment explanation
Indices: 574545--574574 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
574535 TTTATCTCTA
574545 ACTTTCCTTATCAT
1 ACTTTCCTTATCAT
*
574559 ACTTTTCTTATCAT
1 ACTTTCCTTATCAT
574573 AC
1 AC
574575 ATGAACTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (14 bp):
ACTTTCCTTATCAT
Found at i:580648 original size:2 final size:2
Alignment explanation
Indices: 580643--580677 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
580633 AAATATAGAA
580643 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
580678 TCTAGCTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:583301 original size:42 final size:41
Alignment explanation
Indices: 583255--583402 Score: 153
Period size: 41 Copynumber: 3.6 Consensus size: 41
583245 TAAACAATAA
*
583255 CGGCGTTTATAGTAAAAACGCCGCAATATAGTAG-ACATTTAG
1 CGGCGTTTATAGTAAAAACGCCGCAATATAGT-GTA-ATATAG
583297 CGGCGTTT-TAGCTAAAAACGCCGCAATATAGTGTAATATAG
1 CGGCGTTTATAG-TAAAAACGCCGCAATATAGTGTAATATAG
* * * * * *
583338 CGACGTTTATTGTATAAACGCCGCAA-AAACATGTGATATAG
1 CGGCGTTTATAGTAAAAACGCCGCAATATA-GTGTAATATAG
*
583379 TGGCGTTT-T-GTAAAAACGCCGCAA
1 CGGCGTTTATAGTAAAAACGCCGCAA
583403 AATGTTAAAT
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
39 14 0.15
40 3 0.03
41 44 0.48
42 31 0.34
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (41 bp):
CGGCGTTTATAGTAAAAACGCCGCAATATAGTGTAATATAG
Found at i:584492 original size:57 final size:57
Alignment explanation
Indices: 584425--584555 Score: 244
Period size: 57 Copynumber: 2.3 Consensus size: 57
584415 GTGAAGACTG
* *
584425 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTTTTAAGTGGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
584482 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
584539 TTTATGCATAAGTACTT
1 TTTATGCATAAGTACTT
584556 CTGTTTTAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 72 1.00
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (57 bp):
TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
Found at i:584918 original size:43 final size:43
Alignment explanation
Indices: 584818--584929 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
584808 ATATTTATAT
*
584818 TTTAGTGGCGTTT-GTATGAAAACGCCGCTACGTCCTTTCCTAC
1 TTTAGTGGCGTTTCGTATGAAAACGCCGCTACATCC-TTCCTAC
* * *
584861 TTTAGTGGCG-TTCGTATGAAAACGCCGTTATATCC-TCGTAC
1 TTTAGTGGCGTTTCGTATGAAAACGCCGCTACATCCTTCCTAC
584902 TTTAGTGGCGTTTTCGTA-G-AAACGCCGC
1 TTTAGTGGCG-TTTCGTATGAAAACGCCGC
584930 AAAGTATTAG
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
41 23 0.38
42 3 0.05
43 35 0.57
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (43 bp):
TTTAGTGGCGTTTCGTATGAAAACGCCGCTACATCCTTCCTAC
Found at i:585903 original size:46 final size:46
Alignment explanation
Indices: 585833--585923 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
585823 CTAAGGTACT
*
585833 TACTTGCCTTCGTTCCTCTTTCTTGTTTGACCATGTAGTTATTTCG
1 TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTCG
585879 TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTC
1 TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTC
585924 AGAATCGCTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.11, C:0.24, G:0.15, T:0.49
Consensus pattern (46 bp):
TACTTGCCTTCGTTCCTCTGTCTTGTTTGACCATGTAGTTATTTCG
Found at i:587702 original size:21 final size:21
Alignment explanation
Indices: 587684--587739 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
587674 ATGAAGCAAG
587684 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
587705 GGAAGCAGCCAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
587726 GGAAACAGAGAGAG
1 GGAAGCAGAGAGAG
587740 AAATAGTGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.41, T:0.00
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:587772 original size:21 final size:21
Alignment explanation
Indices: 587747--587809 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
587737 GAGAAATAGT
*
587747 GGCAGCACAAAGAGAGGCAGC
1 GGCAGCACAAAGAGAGGCAAC
*
587768 TGCAGCACAAAGAGAGGCAAC
1 GGCAGCACAAAGAGAGGCAAC
* *
587789 GGCAACACAAAGAGAAGCAAC
1 GGCAGCACAAAGAGAGGCAAC
587810 ATATCAGCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.44, C:0.24, G:0.30, T:0.02
Consensus pattern (21 bp):
GGCAGCACAAAGAGAGGCAAC
Found at i:588217 original size:42 final size:44
Alignment explanation
Indices: 588171--588307 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 44
588161 CCGATCTTTA
* * *
588171 GCGGCGTTTGTA-TTAAAGACGCCGCCAAATC-AAACACATATT
1 GCGGCGTTTGTAGCTAAAAACGCCGCCAAACCTAAACACATATT
* * * *
588213 GCGGCGTTT-AAGCTAAAAACGCCGCGAAACCTTAACACTTATT
1 GCGGCGTTTGTAGCTAAAAACGCCGCCAAACCTAAACACATATT
* * * * * * *
588256 GCGGCGTTTGT-GATAAAAACGCCACTAAACATCAACACCTACT
1 GCGGCGTTTGTAGCTAAAAACGCCGCCAAACCTAAACACATATT
588299 GCGGCGTTT
1 GCGGCGTTT
588308 CTGAGAAAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
41 1 0.01
42 24 0.31
43 52 0.68
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (44 bp):
GCGGCGTTTGTAGCTAAAAACGCCGCCAAACCTAAACACATATT
Found at i:588317 original size:43 final size:43
Alignment explanation
Indices: 588227--588350 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 43
588217 CGTTTAAGCT
* * * * * * *
588227 AAAAACGCCGCGAAACCTTAACACTTATTGCGGCGTTTGTGAT
1 AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTTCTGAG
*
588270 AAAAACGCCACTAAACATCAACACCTACTGCGGCGTTTCTGAG
1 AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTTCTGAG
* * *
588313 AAAAACGCTGCTACAA-ATCGACACCTACTGTGGCGTTT
1 AAAAACGCCGCTA-AACATCAACACCTACTGCGGCGTTT
588351 GTCTTCCAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 66 0.97
44 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTTCTGAG
Found at i:588391 original size:43 final size:43
Alignment explanation
Indices: 588344--588476 Score: 193
Period size: 43 Copynumber: 3.2 Consensus size: 43
588334 CACCTACTGT
*
588344 GGCGTTTGTCTTCCAAATGCCGCTAAATATCAACATCTATTAC
1 GGCGTTTGTCTTCCAAATGCCGCTAAATATCAACATCTATTGC
* *
588387 GGCGTTTGTCTTCCAAACGCCGCT-AA-AT-AACATCTATTGT
1 GGCGTTTGTCTTCCAAATGCCGCTAAATATCAACATCTATTGC
*
588427 GGCGTTTGTCTGT-CAAATGCCGCTAAATATCAACACCTATTGC
1 GGCGTTTGTCT-TCCAAATGCCGCTAAATATCAACATCTATTGC
588470 GGCGTTT
1 GGCGTTT
588477 TTTCTTGAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
40 31 0.39
41 5 0.06
42 4 0.05
43 40 0.50
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (43 bp):
GGCGTTTGTCTTCCAAATGCCGCTAAATATCAACATCTATTGC
Found at i:588431 original size:40 final size:40
Alignment explanation
Indices: 588341--588455 Score: 160
Period size: 40 Copynumber: 2.8 Consensus size: 40
588331 CGACACCTAC
588341 TGTGGCGTTTGTCTTCCAAATGCCGCTAAATATCAACATCTAT
1 TGTGGCGTTTGTCTTCCAAATGCCGCT-AA-AT-AACATCTAT
** *
588384 TACGGCGTTTGTCTTCCAAACGCCGCTAAATAACATCTAT
1 TGTGGCGTTTGTCTTCCAAATGCCGCTAAATAACATCTAT
588424 TGTGGCGTTTGTCTGT-CAAATGCCGCTAAATA
1 TGTGGCGTTTGTCT-TCCAAATGCCGCTAAATA
588456 TCAACACCTA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
40 36 0.55
41 3 0.05
42 2 0.03
43 24 0.37
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (40 bp):
TGTGGCGTTTGTCTTCCAAATGCCGCTAAATAACATCTAT
Found at i:589515 original size:21 final size:20
Alignment explanation
Indices: 589474--589640 Score: 146
Period size: 21 Copynumber: 8.2 Consensus size: 20
589464 GTTTCCAGAT
* * *
589474 TCGCAACGCGAACTCGACTA
1 TCGCAATGCGAATTGGACTA
589494 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTGGACTA
*
589515 TTGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTGGACTA
*
589536 TCGCAATG-GAATATGTA--A
1 TCGCAATGCGAAT-TGGACTA
* *
589554 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTGGACTA
* *
589575 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAAT-TGGACTA
*
589595 TCGCAATGCG-ATAGTGACTA
1 TCGCAATGCGAATTG-GACTA
589615 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTGGACTA
589636 TCGCA
1 TCGCA
589641 TTACGATTTA
Statistics
Matches: 119, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
18 10 0.08
19 8 0.07
20 41 0.34
21 58 0.49
22 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATTGGACTA
Found at i:589614 original size:40 final size:40
Alignment explanation
Indices: 589474--589626 Score: 172
Period size: 41 Copynumber: 3.8 Consensus size: 40
589464 GTTTCCAGAT
* * *
589474 TCGCAACGCGA-ACTCGACTATCGCAATGCGAACT-TGGACTA
1 TCGCAATGCGATAGTCGACTATCGCAATGCGAA-TATGTA--A
* * *
589515 TTGCAATGCGA-ACTTGGACTATCGCAATG-GAATATGTAA
1 TCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAA
589554 TCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGATAGTCGACTATCGCAATGCGAATATGT-AA
589595 TCGCAATGCGATAGT-GACTATCGCAATGCGAA
1 TCGCAATGCGATAGTCGACTATCGCAATGCGAA
589627 CTTGGACTAT
Statistics
Matches: 99, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
39 25 0.25
40 27 0.27
41 33 0.33
42 14 0.14
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (40 bp):
TCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
Found at i:590295 original size:6 final size:6
Alignment explanation
Indices: 590280--590319 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
590270 TAGTGTCGTT
590280 TCGT-G TCGTGG TCGTGG TCGT-G TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
590320 ACACGTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.00, C:0.17, G:0.47, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:590302 original size:17 final size:17
Alignment explanation
Indices: 590280--590318 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
590270 TAGTGTCGTT
590280 TCGTGTCGTGGTCGTGG
1 TCGTGTCGTGGTCGTGG
590297 TCGTGTCGTGGTCGTGG
1 TCGTGTCGTGGTCGTGG
590314 TCGTG
1 TCGTG
590319 GACACGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.46, T:0.36
Consensus pattern (17 bp):
TCGTGTCGTGGTCGTGG
Found at i:590304 original size:11 final size:12
Alignment explanation
Indices: 590280--590319 Score: 66
Period size: 11 Copynumber: 3.5 Consensus size: 12
590270 TAGTGTCGTT
590280 TCGT-GTCGTGG
1 TCGTGGTCGTGG
590291 TCGTGGTCGT-G
1 TCGTGGTCGTGG
590302 TCGTGGTCGTGG
1 TCGTGGTCGTGG
590314 TCGTGG
1 TCGTGG
590320 ACACGTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 15 0.56
12 12 0.44
ACGTcount: A:0.00, C:0.17, G:0.47, T:0.35
Consensus pattern (12 bp):
TCGTGGTCGTGG
Found at i:590462 original size:21 final size:21
Alignment explanation
Indices: 590407--590547 Score: 130
Period size: 21 Copynumber: 6.7 Consensus size: 21
590397 CGTTGCGATT
*
590407 TTGGACTATCGCAACG-AAAC
1 TTGGACTATCGCAACGCGAAC
*
590427 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
590450 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
590469 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
590492 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
590511 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
590534 TTAGACTATCGCAA
1 TTGGACTATCGCAA
590548 TGCAAATATG
Statistics
Matches: 98, Mismatches: 12, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
19 20 0.20
20 6 0.06
21 35 0.36
22 9 0.09
23 28 0.29
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:590486 original size:42 final size:42
Alignment explanation
Indices: 590407--590547 Score: 246
Period size: 42 Copynumber: 3.3 Consensus size: 42
590397 CGTTGCGATT
590407 TTGGACTATCGCAACGAAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACG-AACTTGGAATAAATCGCAACGCGAAC
*
590450 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
590492 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
590534 TTAGACTATCGCAA
1 TTGGACTATCGCAA
590548 TGCAAATATG
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 78 0.83
43 16 0.17
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:591755 original size:33 final size:33
Alignment explanation
Indices: 591703--591791 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 33
591693 GTTTTCTTTG
* * * * **
591703 TTTAATAAGTAATGAGTTTTTAGTGAATTTTTA
1 TTTAATAGGTAGTGGGTTTTTAGCGAATGATTA
* *
591736 TTTAATGGGTAGTGGGTTTTTAGCGTATGATTA
1 TTTAATAGGTAGTGGGTTTTTAGCGAATGATTA
* *
591769 TTTAATAGGTATTGGATTTTTAG
1 TTTAATAGGTAGTGGGTTTTTAG
591792 ATTAAGTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.27, C:0.01, G:0.22, T:0.49
Consensus pattern (33 bp):
TTTAATAGGTAGTGGGTTTTTAGCGAATGATTA
Found at i:591813 original size:3 final size:3
Alignment explanation
Indices: 591805--591852 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
591795 AAGTTTTAAT
* * *
591805 TAA TAA TAA TAA TAA TAA AAA TAT TAA TAA TAA TAA TATT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
591851 TA
1 TA
591853 TTTTTTCGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:593996 original size:21 final size:21
Alignment explanation
Indices: 593972--594013 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
593962 AAATGTTAAA
*
593972 AAATATTAATGTTTTAAGTAT
1 AAATAATAATGTTTTAAGTAT
* *
593993 AAATAATAATTTTTTAGGTAT
1 AAATAATAATGTTTTAAGTAT
594014 TTTTACTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (21 bp):
AAATAATAATGTTTTAAGTAT
Found at i:594200 original size:39 final size:39
Alignment explanation
Indices: 594136--594211 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
594126 TATTATATAT
* *
594136 ATATAATATAGTATAATTTTTGAAAATATTTTTAAAAAA
1 ATATAATATAGTATAATTTTTGAAAACATATTTAAAAAA
594175 ATATAATATA-TATAATTTTTAGAAAACATATTTAAAA
1 ATATAATATAGTATAATTTTT-GAAAACATATTTAAAA
594212 TATATAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 10 0.29
39 24 0.71
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (39 bp):
ATATAATATAGTATAATTTTTGAAAACATATTTAAAAAA
Found at i:594280 original size:33 final size:37
Alignment explanation
Indices: 594231--594317 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 37
594221 TTGAAAATGG
*
594231 TTTTCGAAATATATATAT-TATATA-GTTTGAAAA-CA
1 TTTT-GAAATATATATATCTATATATGTTTAAAAAGCA
* *
594266 TTTTG-AATATATATATCTTTATATTTTTAAAAAGCA
1 TTTTGAAATATATATATCTATATATGTTTAAAAAGCA
*
594302 TTTTGAAAAATATATA
1 TTTTGAAATATATATA
594318 AAACATTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
33 11 0.25
34 6 0.14
35 11 0.25
36 7 0.16
37 9 0.20
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTGAAATATATATATCTATATATGTTTAAAAAGCA
Found at i:594325 original size:21 final size:22
Alignment explanation
Indices: 594295--594339 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
594285 TATATTTTTA
594295 AAAAGCATTTTGAAAA-ATATAT
1 AAAAGCA-TTTGAAAACATATAT
*
594317 AAAA-CATTTGAAAACTTATAT
1 AAAAGCATTTGAAAACATATAT
594338 AA
1 AA
594340 TATATGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (22 bp):
AAAAGCATTTGAAAACATATAT
Found at i:594367 original size:40 final size:36
Alignment explanation
Indices: 594316--594424 Score: 127
Period size: 40 Copynumber: 3.0 Consensus size: 36
594306 GAAAAATATA
594316 TAAAACA-TTTGAAAACTTATATAATATATGGTTTTT
1 TAAAACATTTTGAAAACTTATATAATATAT-GTTTTT
*
594352 TAAAAAATCATTTTGAAAA-TATATATAATATATGATTTT
1 T--AAAA-CATTTTGAAAACT-TATATAATATATGTTTTT
594391 TAAAACATTTT-AAAAC-TATATAATATATAGTTTT
1 TAAAACATTTTGAAAACTTATATAATATAT-GTTTT
594425 AAAAACTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
34 12 0.19
35 8 0.12
36 7 0.11
37 4 0.06
38 4 0.06
39 9 0.14
40 20 0.31
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.44
Consensus pattern (36 bp):
TAAAACATTTTGAAAACTTATATAATATATGTTTTT
Found at i:594416 original size:34 final size:34
Alignment explanation
Indices: 594316--594453 Score: 125
Period size: 34 Copynumber: 3.8 Consensus size: 34
594306 GAAAAATATA
* * *
594316 TAAAACATTTGAAAACTTATATAATATATGGTTTTT
1 TAAAACATTTTAAAA-ATATATAATATAT-GATTTT
594352 TAAAAAATCATTTTGAAAATATATATAATATATGATTTT
1 T--AAAA-CATTTT-AAAA-ATATATAATATATGATTTT
*
594391 TAAAACATTTTAAAACTATATAATATAT-AGTTTT
1 TAAAACATTTTAAAAATATATAATATATGA-TTTT
* *
594425 AAAAACTTTTTTAAAAATATATATATATA
1 TAAAAC-ATTTTAAAAATATATA-ATATA
594454 ATATATGGTT
Statistics
Matches: 87, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
33 1 0.01
34 21 0.24
35 18 0.21
36 12 0.14
37 4 0.05
38 4 0.05
39 11 0.13
40 16 0.18
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (34 bp):
TAAAACATTTTAAAAATATATAATATATGATTTT
Found at i:594483 original size:12 final size:12
Alignment explanation
Indices: 594462--594496 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
594452 TAATATATGG
594462 TTTT-AAAATAT
1 TTTTGAAAATAT
594473 TTTTGAAAATAT
1 TTTTGAAAATAT
*
594485 TTTTGGAAATAT
1 TTTTGAAAATAT
594497 ATTATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:595541 original size:20 final size:20
Alignment explanation
Indices: 595516--595568 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
595506 CAGTTTTGTT
595516 TTATTTTAATTTAGCCACTA-
1 TTATTTTAATTTAGCCAC-AG
*
595536 TTATTTTTTGATTTAGCCACAG
1 TTA--TTTTAATTTAGCCACAG
595558 TT-TTTTAATTT
1 TTATTTTAATTT
595569 TTTGCATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 8 0.29
20 3 0.11
21 1 0.04
22 16 0.57
ACGTcount: A:0.25, C:0.11, G:0.08, T:0.57
Consensus pattern (20 bp):
TTATTTTAATTTAGCCACAG
Found at i:599904 original size:99 final size:99
Alignment explanation
Indices: 599721--599919 Score: 326
Period size: 99 Copynumber: 2.0 Consensus size: 99
599711 TTATAATTTT
* * *
599721 ATATGTATACAATAAAGCTCGAGTTGTCCCTCTAGAGGAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATCTATACAATAAAGCTCGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
*
599786 ATAAGATTTAGCTAGCCTGACAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGACAAAGGTGATTATA
*
599820 ATATCTATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATCTATACAATAAAGCTCGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
* * *
599885 ATAAGATTCAGGTATCCTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGACAAAGGTGATTATA
599919 A
1 A
599920 CATTGATATG
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (99 bp):
ATATCTATACAATAAAGCTCGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
ATAAGATTCAGCTAGCCTGACAAAGGTGATTATA
Found at i:601243 original size:83 final size:84
Alignment explanation
Indices: 601098--601261 Score: 249
Period size: 83 Copynumber: 1.9 Consensus size: 84
601088 ATTTGTAGCG
* *
601098 TAGCTCAAGGCGAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1 TAGCTCAAGGAGAAAAGGGTTATCTGCCAAC--AAAACCTTCGAGTTCGATTACATTCAGCTCAA
**
601163 GGGTATATCAAATTTACATCA
64 GGACATATCAAATTTACATCA
*
601184 TAGCTCAAGGAGAAAAGGGTTATCTGTCAAC-AAACCTTCGAGTTCGATTACATTCAGCTCAAGG
1 TAGCTCAAGGAGAAAAGGGTTATCTGCCAACAAAACCTTCGAGTTCGATTACATTCAGCTCAAGG
*
601248 ACATATCAAGTTTA
66 ACATATCAAATTTA
601262 TAGTATAACT
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
83 44 0.61
86 28 0.39
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (84 bp):
TAGCTCAAGGAGAAAAGGGTTATCTGCCAACAAAACCTTCGAGTTCGATTACATTCAGCTCAAGG
ACATATCAAATTTACATCA
Found at i:601288 original size:83 final size:84
Alignment explanation
Indices: 601104--601289 Score: 241
Period size: 83 Copynumber: 2.2 Consensus size: 84
601094 AGCGTAGCTC
**
601104 AAGGCGAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGTAT
1 AAGGCGAGAAGGGTTATCTGCCAAC--AAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACAT
* *
601169 ATCAAATTTACATCATAGCTC
64 ATCAAATTTACATCATAACTA
* * *
601190 AAGGAGAAAAGGGTTATCTGTCAAC-AAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATAT
1 AAGGCGAGAAGGGTTATCTGCCAACAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATAT
* *
601254 CAAGTTTATAGT-ATAACTA
66 CAAATTTACA-TCATAACTA
*
601273 AAGGCGAGAACGGTTAT
1 AAGGCGAGAAGGGTTAT
601290 ATCAATAAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
83 64 0.74
84 1 0.01
86 22 0.25
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (84 bp):
AAGGCGAGAAGGGTTATCTGCCAACAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATAT
CAAATTTACATCATAACTA
Found at i:601724 original size:5 final size:5
Alignment explanation
Indices: 601714--601744 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
601704 TTCGTCCGGA
601714 TTTAT TTTAT TTTAT TTTAT TTTA- TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
601745 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:601933 original size:36 final size:37
Alignment explanation
Indices: 601870--602079 Score: 248
Period size: 36 Copynumber: 5.7 Consensus size: 37
601860 ATATATATAT
* ** *
601870 ATATATAATATTATATAATTTTAAAAAACATTTTGAAA
1 ATATAT-ATAATATATGGTTTTTAAAAACATTTTGAAA
*
601908 ATATATATAATATAT-GTTTTTAAAAACATTTTAAAA
1 ATATATATAATATATGGTTTTTAAAAACATTTTGAAA
*
601944 ATTTATATAATATATGGTTTTTAAAAACATTTTGAAA
1 ATATATATAATATATGGTTTTTAAAAACATTTTGAAA
* *
601981 ACT-TATATAATATATGGTTTTAAAAAAACGTTTTGAAA
1 A-TATATATAATATATGGTTTT-TAAAAACATTTTGAAA
* *
602019 ATATATATAATATAAGATTTTT-AAAACATTTTGAAA
1 ATATATATAATATATGGTTTTTAAAAACATTTTGAAA
* * *
602055 A-CTATATAATATATAGTTTTGAAAA
1 ATATATATAATATATGGTTTTTAAAA
602080 CTTTTTTAAA
Statistics
Matches: 150, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
35 15 0.10
36 49 0.33
37 48 0.32
38 38 0.25
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (37 bp):
ATATATATAATATATGGTTTTTAAAAACATTTTGAAA
Found at i:601952 original size:115 final size:114
Alignment explanation
Indices: 601744--601950 Score: 255
Period size: 115 Copynumber: 1.8 Consensus size: 114
601734 TTTATTTATT
** *
601744 TATATATATATATTATTAATATAGTATAATTTTTGAAAATATTTTTGAAAAATATAATATATAAT
1 TATATATATATATTATTAATATAGTATAATTTTAAAAAACATTTTTGAAAAATATAATATATAAT
*
601809 TTTTAGAAAACGGATTTCATAAATATATAGTTTTGAAAATGGTTTTCGAA
66 TTTTAGAAAAC-GATTTCAAAAATATATAGTTTTGAAAATGGTTTTCGAA
601859 TATATATATATA-TATATAATATTA-TATAATTTTAAAAAACA-TTTTG-AAAATATATATAATA
1 TATATATATATATTAT-TAATA-TAGTATAATTTTAAAAAACATTTTTGAAAAATATA-AT-ATA
* * *
601920 TATGTTTTTA-AAAAC-ATTTTAAAAATTTATA
62 TA-ATTTTTAGAAAACGATTTCAAAAATATATA
601951 TAATATATGG
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
113 21 0.26
114 10 0.12
115 41 0.51
116 8 0.10
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (114 bp):
TATATATATATATTATTAATATAGTATAATTTTAAAAAACATTTTTGAAAAATATAATATATAAT
TTTTAGAAAACGATTTCAAAAATATATAGTTTTGAAAATGGTTTTCGAA
Found at i:601971 original size:73 final size:73
Alignment explanation
Indices: 601868--602079 Score: 257
Period size: 73 Copynumber: 2.8 Consensus size: 73
601858 ATATATATAT
* * *
601868 ATATATATAATATTATATAATTTTAAAAAACATTTTGAAAATATATATAATATAT-GTTTTTAAA
1 ATATATATAATA-TA-A-GATTTTTAAAAACATTTTGAAAAT-TATATAATATATAGTTTTAAAA
601932 AACATTTTAAAA
62 AACATTTTAAAA
* * * *
601944 ATTTATATAATATATGGTTTTTAAAAACATTTTGAAAACTTATATAATATATGGTTTTAAAAAAA
1 ATATATATAATATAAGATTTTTAAAAACATTTTGAAAA-TTATATAATATATAGTTTT-AAAAAA
* *
602009 CGTTTTGAAA
64 CATTTTAAAA
* *
602019 ATATATATAATATAAGATTTTT-AAAACATTTTGAAAACTATATAATATATAGTTTTGAAAA
1 ATATATATAATATAAGATTTTTAAAAACATTTTGAAAATTATATAATATATAGTTTTAAAAA
602080 CTTTTTTAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
72 4 0.03
73 49 0.41
74 21 0.18
75 34 0.29
76 11 0.09
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (73 bp):
ATATATATAATATAAGATTTTTAAAAACATTTTGAAAATTATATAATATATAGTTTTAAAAAACA
TTTTAAAA
Found at i:603436 original size:6 final size:6
Alignment explanation
Indices: 603425--603465 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
603415 AAATTTAACC
* *
603425 ATTTTT ATTTTT A-TTTT -TTTAT GTTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
603466 CTATGTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
5 7 0.23
6 23 0.77
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (6 bp):
ATTTTT
Done.