Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009573.1 Hibiscus syriacus cultivar Beakdansim tig00116938_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: 1247605
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:435908 original size:2 final size:2
Alignment explanation
Indices: 435903--436036 Score: 193
Period size: 2 Copynumber: 67.0 Consensus size: 2
435893 TTTTATAGTT
* *
435903 TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA CA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
*
435947 TA -A TA TA TA TA TA TA TA TA TA TA GT- TA TA TA -A TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
435987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
436029 TA TA TA TA
1 TA TA TA TA
436037 GTTGTTTTAA
Statistics
Matches: 120, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
1 3 0.03
2 113 0.94
3 4 0.03
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:435908 original size:9 final size:9
Alignment explanation
Indices: 435885--436036 Score: 52
Period size: 10 Copynumber: 15.7 Consensus size: 9
435875 GTTTATAAAC
435885 TATATAATT
1 TATATAATT
* *
435894 TTTATAGTT
1 TATATAATT
*
435903 TATATATATA
1 TATATA-ATT
*
435913 TATATATATA
1 TATATA-ATT
*
435923 TATATAGTT
1 TATATAATT
* *
435932 TACATATATAG
1 TATATA-AT-T
*
435943 TATATAATA
1 TATATAATT
*
435952 TATATATATA
1 TATATA-ATT
*
435962 TATATATAGT
1 TATATA-ATT
*
435972 TATATAATA
1 TATATAATT
* *
435981 TAAATATATA
1 TATATA-ATT
*
435991 TATATATATA
1 TATATA-ATT
*
436001 TATATATATA
1 TATATA-ATT
*
436011 TATATATATA
1 TATATA-ATT
*
436021 TATATATATA
1 TATATA-ATT
436031 TATATA
1 TATATA
436037 GTTGTTTTAA
Statistics
Matches: 120, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
9 30 0.25
10 85 0.71
11 5 0.04
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (9 bp):
TATATAATT
Found at i:436743 original size:216 final size:216
Alignment explanation
Indices: 436118--436811 Score: 1164
Period size: 216 Copynumber: 3.2 Consensus size: 216
436108 TCCCTTTGTA
* * *
436118 TTGTTTAATTTACTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTT
*
436183 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTACTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* * *
436248 TAAATGGGTATAATTTAGTAC-TTTTTGTAGTAATTTTAACCTCACAATTTAAAGTTATTTCGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
436312 TTGATCCCTCATCAATGTGTG
196 TTGATCCCTCATCAATGTGTG
436333 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTT
* * *
436398 ATTTGCATATGAAATTGA-CC---CTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* *
436459 TAAATGGGTATAATTTAGTAATTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTTGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
*
436524 TTGATTCCTCATCAATGTGTG
196 TTGATCCCTCATCAATGTGTG
*
436545 TTGTTTAATTTATTTAAATTTTTATTTTTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTT
436610 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* *
436675 TAAATGGTTATAATTTAGTACTTTTTTGTATTAATTTCAATCTCACAATTTAAAATTATTTCGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
436740 TTGATCCCTCATCAATGTGTG
196 TTGATCCCTCATCAATGTGTG
* * * * *
436761 TTGTTTAATTTATTTAAATGTTTATTTTTAATTCCATTTTTGTTCAATTTA
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTA
436812 ATTCTTAAAT
Statistics
Matches: 448, Mismatches: 26, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
211 59 0.13
212 139 0.31
213 2 0.00
214 2 0.00
215 78 0.17
216 168 0.38
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (216 bp):
TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTT
ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
TTGATCCCTCATCAATGTGTG
Found at i:443323 original size:17 final size:18
Alignment explanation
Indices: 443303--443338 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
443293 ATTATAATCC
*
443303 ATAAATTTATAAA-ATAT
1 ATAAAATTATAAAGATAT
443320 ATAAAATTATAAAGATAT
1 ATAAAATTATAAAGATAT
443338 A
1 A
443339 CATATAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAATTATAAAGATAT
Found at i:444745 original size:25 final size:26
Alignment explanation
Indices: 444717--444771 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
444707 AAATATGTTC
*
444717 AAATCAACTTGACT-CAAATTTTATA
1 AAATCAACTTGACTAAAAATTTTATA
* *
444742 AAATCGACTTGACTAAAAATTTTTTA
1 AAATCAACTTGACTAAAAATTTTATA
444768 AAAT
1 AAAT
444772 AAAGTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (26 bp):
AAATCAACTTGACTAAAAATTTTATA
Found at i:447493 original size:20 final size:20
Alignment explanation
Indices: 447468--447507 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
447458 AATTAATTAT
447468 TTTCCTTTTATTTCTTATTC
1 TTTCCTTTTATTTCTTATTC
*
447488 TTTCCTTTTATTTTTTATTC
1 TTTCCTTTTATTTCTTATTC
447508 AATATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCCTTTTATTTCTTATTC
Found at i:459337 original size:16 final size:16
Alignment explanation
Indices: 459316--459346 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
459306 ATAAATAAAT
459316 GAACATAAACGAACAC
1 GAACATAAACGAACAC
459332 GAACATAAACGAACA
1 GAACATAAACGAACA
459347 AAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:459427 original size:10 final size:10
Alignment explanation
Indices: 459412--459486 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
459402 CATTTAATAA
459412 ATAAACGAAC
1 ATAAACGAAC
459422 ATAAACGAAC
1 ATAAACGAAC
459432 ----ACGAAC
1 ATAAACGAAC
459438 ATAAACGAAC
1 ATAAACGAAC
** *
459448 ACGAAC-ATAA
1 ATAAACGA-AC
459458 ATGAACACGAAC
1 AT-AA-ACGAAC
459470 ATAAACGAAC
1 ATAAACGAAC
459480 ATAAACG
1 ATAAACG
459487 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:459437 original size:16 final size:16
Alignment explanation
Indices: 459416--459480 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
459406 TAATAAATAA
459416 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
459432 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
459448 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
459464 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
459480 A
1 A
459481 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:460210 original size:14 final size:14
Alignment explanation
Indices: 460193--460225 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
460183 GAATGAACAT
460193 AAACGAACATAACC
1 AAACGAACATAACC
460207 AAACGAACATAACC
1 AAACGAACATAACC
*
460221 GAACG
1 AAACG
460226 TTCACGAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:469995 original size:23 final size:23
Alignment explanation
Indices: 469961--470017 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
469951 AATTGTTAAT
469961 ATAACA-ATTTTAAAATTTATATA
1 ATAACACA-TTTAAAATTTATATA
*
469984 ATAACACATTT--AATTTTTATA
1 ATAACACATTTAAAATTTATATA
* *
470005 TTTACACATTTAA
1 ATAACACATTTAA
470018 TCAATTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 18 0.64
23 9 0.32
24 1 0.04
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAACACATTTAAAATTTATATA
Found at i:470004 original size:21 final size:21
Alignment explanation
Indices: 469974--470018 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
469964 ACAATTTTAA
469974 AATTTATATAATAACACATTT
1 AATTTATATAATAACACATTT
* * *
469995 AATTTTTATATTTACACATTT
1 AATTTATATAATAACACATTT
470016 AAT
1 AAT
470019 CAATTTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTTATATAATAACACATTT
Found at i:481962 original size:48 final size:42
Alignment explanation
Indices: 481857--481976 Score: 152
Period size: 42 Copynumber: 2.9 Consensus size: 42
481847 GATTGATAAA
*
481857 TCTAAAACCGAGGGTGAGTGTGCTGATGGTGAGGCTAAAAAG
1 TCTAAAACCGAGGGTGAGGGTGCTGATGGTGAGGCTAAAAAG
* *
481899 TCTAAAACCGAGGGTGAGGGTGCTGATGGTGAGGCTGAGAAG
1 TCTAAAACCGAGGGTGAGGGTGCTGATGGTGAGGCTAAAAAG
* ** * *
481941 TCTAACAA-TGAACGTGAGGGTGCTAAGGGTGAGGCT
1 TCTAA-AACCGAGGGTGAGGGTGCTGATGGTGAGGCT
481977 GACAGTGAGA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 67 0.97
43 2 0.03
ACGTcount: A:0.28, C:0.12, G:0.38, T:0.21
Consensus pattern (42 bp):
TCTAAAACCGAGGGTGAGGGTGCTGATGGTGAGGCTAAAAAG
Found at i:486828 original size:21 final size:21
Alignment explanation
Indices: 486796--486835 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
486786 AACTACCAAG
486796 TATAGAGGGTATCAGTACTCC
1 TATAGAGGGTATCAGTACTCC
*
486817 TATAG-GGAGTATCGGTACT
1 TATAGAGG-GTATCAGTACT
486836 ACCTTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
TATAGAGGGTATCAGTACTCC
Found at i:489372 original size:24 final size:23
Alignment explanation
Indices: 489334--489385 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
489324 AAGAATGTGC
489334 CACAAGAGCAAAGAAGAAACATGT
1 CACAAGAGCAAAGAA-AAACATGT
** * *
489358 CACAAGAGCGGAGAAAAGCTTGT
1 CACAAGAGCAAAGAAAAACATGT
489381 CACAA
1 CACAA
489386 TGATACAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.48, C:0.19, G:0.23, T:0.10
Consensus pattern (23 bp):
CACAAGAGCAAAGAAAAACATGT
Found at i:493474 original size:26 final size:26
Alignment explanation
Indices: 493445--493499 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
493435 TAGTGTTAAG
493445 TTATGTCTTATA-TAATTTATTTACAT
1 TTATGTCTTATAGT-ATTTATTTACAT
493471 TTATGTCTTATAGTATTTATTTACAT
1 TTATGTCTTATAGTATTTATTTACAT
493497 TTA
1 TTA
493500 GTAAGCTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 27 0.96
27 1 0.04
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.58
Consensus pattern (26 bp):
TTATGTCTTATAGTATTTATTTACAT
Found at i:502765 original size:60 final size:60
Alignment explanation
Indices: 502697--502832 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 60
502687 TTTGGATGAA
* * **
502697 TTTGGGGATGAAATTGGAA-GATTCAAAAGTTTGGGGATC-AATTTAGAATGAGAGTCATAG
1 TTTGGGGATGAAATTAGAATG-TTCAAAACTTTAAGG-TCTAATTTAGAATGAGAGTCATAG
* *
502757 TTTGGGGATGGAATTAGAATGTTTAAAACTTTAAGGTCTAATTTAGAATGAGAGTCATAG
1 TTTGGGGATGAAATTAGAATGTTCAAAACTTTAAGGTCTAATTTAGAATGAGAGTCATAG
* *
502817 TTTAGGGATAAAATTA
1 TTTGGGGATGAAATTA
502833 AAAATATTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 2 0.03
60 62 0.95
61 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (60 bp):
TTTGGGGATGAAATTAGAATGTTCAAAACTTTAAGGTCTAATTTAGAATGAGAGTCATAG
Found at i:502999 original size:15 final size:15
Alignment explanation
Indices: 502971--503003 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
502961 TGACAGATGC
502971 ATACCTTGTGACATCA
1 ATACCTTGTGACAT-A
502987 ATACCTT-TGACATA
1 ATACCTTGTGACATA
503001 ATA
1 ATA
503004 TTGACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (15 bp):
ATACCTTGTGACATA
Found at i:506613 original size:13 final size:13
Alignment explanation
Indices: 506595--506633 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
506585 AATAATAATA
506595 AAAATTAAACA-TT
1 AAAATTAAA-ATTT
506608 AAAATTAAAATTT
1 AAAATTAAAATTT
506621 AAAATTAATAATT
1 AAAATTAA-AATT
506634 AGATAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 1 0.04
13 19 0.79
14 4 0.17
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:506614 original size:6 final size:6
Alignment explanation
Indices: 506595--506634 Score: 53
Period size: 7 Copynumber: 6.2 Consensus size: 6
506585 AATAATAATA
506595 AAAATT AAACATT AAAATT AAAATTT AAAATT AATAATT A
1 AAAATT AAA-ATT AAAATT AAAA-TT AAAATT AA-AATT A
506635 GATAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 14 0.45
7 17 0.55
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (6 bp):
AAAATT
Found at i:506642 original size:3 final size:3
Alignment explanation
Indices: 506626--506664 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
506616 AATTTAAAAT
*
506626 TAA TAA TTAGA TAA TAA TAA TAA TAA TAA CAA TAA TAA T
1 TAA TAA -TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA T
506665 TAAATTATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 27 0.84
4 4 0.12
5 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:507195 original size:132 final size:132
Alignment explanation
Indices: 506842--507348 Score: 493
Period size: 132 Copynumber: 3.8 Consensus size: 132
506832 AGAGATTTTT
* * * * * *
506842 GAAGATCGAATCT-G-AAAAGGGGTCTGCTCCGCTGC-TCTTCAAGGTATATCATATCTGGAAAT
1 GAAGATCAAATCTGGAAAAAAGGATCTGCTCCGCTGCTTCTTCAGGGTAGATCAGATCTGGAAAT
** * * * * * * *
506904 ACTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATTGAGGCAGACTTGTTCCACTACTACTTA
66 GTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGAC-TATTCCACTGCTTCTTC
506969 AGG
130 AGG
* * * ** * ** *
506972 GAAGATCAAATATGGAAAAAGGGGATTTGCTCCATTGTTTCTTCAGGGTAGATCAGATCCAGAAT
1 GAAGATCAAATCTGGAAAAA-AGGATCTGCTCCGCTGCTTCTTCAGGGTAGATCAGATCTGGAAA
* * * *
507037 TGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAGGAAGACGTATTTCACTGCTTCTT
65 TGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGAC-TATTCCACTGCTTCTT
507102 CAGG
129 CAGG
* *
507106 GAAGATCAAATCT-GAAAAAAGAATCTGCTTCGCTGCTTCTTCAGGGTAGATCAGATCTGGAAAT
1 GAAGATCAAATCTGGAAAAAAGGATCTGCTCCGCTGCTTCTTCAGGGTAGATCAGATCTGGAAAT
* * * *
507170 GTTGATTCATTCCACTATTATTCAGGGAATATTGAATCGAGGCATACTAGTTCCACTGCATCTTC
66 GTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTA-TTCCACTGCTTCTTC
*
507235 ATG
130 AGG
* * * * * *
507238 AAAGATCAAATCTGGAAAAAGAAAGGGGATATGATCTGCTGCTTCTTCAGGGTAAATTAGAT-TC
1 GAAGATCAAATCTGG--AAA-AAA--GGATCTGCTCCGCTGCTTCTTCAGGGTAGATCAGATCT-
* * *
507302 GGAAACGTTTATTTATTCCACTATTCTTCAGGGAAGATTGAATCGAG
60 GGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAG
507349 TTCGATTTGC
Statistics
Matches: 309, Mismatches: 56, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
130 11 0.04
131 3 0.01
132 109 0.35
133 19 0.06
134 89 0.29
135 3 0.01
136 3 0.01
137 1 0.00
138 71 0.23
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (132 bp):
GAAGATCAAATCTGGAAAAAAGGATCTGCTCCGCTGCTTCTTCAGGGTAGATCAGATCTGGAAAT
GTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTATTCCACTGCTTCTTCA
GG
Found at i:520840 original size:23 final size:23
Alignment explanation
Indices: 520809--520869 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
520799 GCTGTATAAA
520809 TGCAACGAAGTGCCACGAAGAAT
1 TGCAACGAAGTGCCACGAAGAAT
* * *
520832 TGCACCGAAGTGCCGCGTAGAAT
1 TGCAACGAAGTGCCACGAAGAAT
*
520855 TGCATCGAAGTGCCA
1 TGCAACGAAGTGCCA
520870 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.28, T:0.16
Consensus pattern (23 bp):
TGCAACGAAGTGCCACGAAGAAT
Found at i:522479 original size:24 final size:20
Alignment explanation
Indices: 522426--522483 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
522416 TTCCCCTTGA
*
522426 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
522446 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
522469 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
522484 CTATCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:525630 original size:21 final size:21
Alignment explanation
Indices: 525606--525645 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
525596 ATGGTTCAAA
525606 AAAACCGGTTTGACAGGTTTT
1 AAAACCGGTTTGACAGGTTTT
* * *
525627 AAAACTGTTTTGACCGGTT
1 AAAACCGGTTTGACAGGTT
525646 CTGACCTGAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (21 bp):
AAAACCGGTTTGACAGGTTTT
Found at i:528236 original size:24 final size:24
Alignment explanation
Indices: 528209--528255 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
528199 TGATTTCTTA
* *
528209 TCTGGATTCTGTTTTGATATATGT
1 TCTGAATTCCGTTTTGATATATGT
*
528233 TCTGAATTCCGTTTTGATTTATG
1 TCTGAATTCCGTTTTGATATATG
528256 ATATCTCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.53
Consensus pattern (24 bp):
TCTGAATTCCGTTTTGATATATGT
Found at i:529332 original size:23 final size:23
Alignment explanation
Indices: 529306--529354 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
529296 TGACTAAAAT
* *
529306 AAAA-TAATATAAAAGTAACATGC
1 AAAATTAAAATAAAACTAA-ATGC
529329 AAAATTAAAATAAAACTAAATGC
1 AAAATTAAAATAAAACTAAATGC
529352 AAA
1 AAA
529355 TATGACTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.20
Consensus pattern (23 bp):
AAAATTAAAATAAAACTAAATGC
Found at i:530623 original size:16 final size:16
Alignment explanation
Indices: 530602--530644 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
530592 AATGCACATA
530602 AAACGTGAATTAGGAT
1 AAACGTGAATTAGGAT
*
530618 AAACGTGAATTAGGCT
1 AAACGTGAATTAGGAT
530634 AAACGTGAATT
1 AAACGTGAATT
530645 GTCTTTCGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (16 bp):
AAACGTGAATTAGGAT
Found at i:531908 original size:13 final size:13
Alignment explanation
Indices: 531883--531909 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
531873 AAATTAAAGA
531883 TTAAAATTATAAT
1 TTAAAATTATAAT
531896 TTAAAATTATAAT
1 TTAAAATTATAAT
531909 T
1 T
531910 ATATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAAATTATAAT
Found at i:536496 original size:30 final size:32
Alignment explanation
Indices: 536433--536504 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
536423 TTATAGTTAG
* *
536433 ATTTAAAAATTAAATTGATATTTTATTTAAAA
1 ATTTAAAAATTAAATTAATATTTTATCTAAAA
*
536465 ATTTAAAAATTATATTAAT-TTTTATCT-AAA
1 ATTTAAAAATTAAATTAATATTTTATCTAAAA
*
536495 ATTCAAAAAT
1 ATTTAAAAAT
536505 GAAAATATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 12 0.33
31 7 0.19
32 17 0.47
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (32 bp):
ATTTAAAAATTAAATTAATATTTTATCTAAAA
Found at i:541952 original size:11 final size:11
Alignment explanation
Indices: 541936--541979 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
541926 AAATATCAAG
541936 AGCTCGATTGA
1 AGCTCGATTGA
* *
541947 AGCTCGAGACTCA
1 AGCTC--GATTGA
541960 AGCTCGATTGA
1 AGCTCGATTGA
541971 AGCTCGATT
1 AGCTCGATT
541980 TTGAGCTCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 18 0.67
13 9 0.33
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:543425 original size:35 final size:35
Alignment explanation
Indices: 543379--543501 Score: 162
Period size: 35 Copynumber: 3.5 Consensus size: 35
543369 CAGATCAAGA
* *
543379 GTTTAGGGTTTAGAGTTTATGACTTA-GATTTTAGG
1 GTTTAGGGTTTAGAGTTTATGATTTATG-GTTTAGG
*
543414 GTTTAGGGTTTAGGGTTTATGATTTATGGTTTAGG
1 GTTTAGGGTTTAGAGTTTATGATTTATGGTTTAGG
* *
543449 GTTTAGGGTTTATGA-TTTATGGTTTATGGTTTAGA
1 GTTTAGGGTTTA-GAGTTTATGATTTATGGTTTAGG
543484 GTTTAGGGTTTA-AGTTTA
1 GTTTAGGGTTTAGAGTTTA
543502 AGGTTTAAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
33 1 0.01
34 4 0.05
35 72 0.91
36 2 0.03
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (35 bp):
GTTTAGGGTTTAGAGTTTATGATTTATGGTTTAGG
Found at i:543487 original size:28 final size:28
Alignment explanation
Indices: 543408--543514 Score: 128
Period size: 28 Copynumber: 3.9 Consensus size: 28
543398 TGACTTAGAT
* *
543408 TTTAGGGTTTAGGGTTTAGGGTTTATGA
1 TTTATGGTTTAGGGTTTAGAGTTTATGA
*
543436 TTTATGGTTTAGGGTTTAGGGTTTATGA
1 TTTATGGTTTAGGGTTTAGAGTTTATGA
* * *
543464 TTTATGGTTTATGGTTTAGAGTTTAGGG
1 TTTATGGTTTAGGGTTTAGAGTTTATGA
* *
543492 TTTA-AGTTTAAGGTTTA-AGTTTA
1 TTTATGGTTTAGGGTTTAGAGTTTA
543515 GGCGGTAATC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
26 6 0.08
27 11 0.15
28 55 0.76
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.50
Consensus pattern (28 bp):
TTTATGGTTTAGGGTTTAGAGTTTATGA
Found at i:543510 original size:7 final size:7
Alignment explanation
Indices: 543379--543508 Score: 109
Period size: 7 Copynumber: 18.7 Consensus size: 7
543369 CAGATCAAGA
543379 GTTTAGG
1 GTTTAGG
*
543386 GTTTAGA
1 GTTTAGG
*
543393 GTTTATG
1 GTTTAGG
** *
543400 ACTTAGA
1 GTTTAGG
*
543407 TTTTAGG
1 GTTTAGG
543414 GTTTAGG
1 GTTTAGG
543421 GTTTAGG
1 GTTTAGG
*
543428 GTTTATG
1 GTTTAGG
* *
543435 ATTTATG
1 GTTTAGG
543442 GTTTAGG
1 GTTTAGG
543449 GTTTAGG
1 GTTTAGG
*
543456 GTTTATG
1 GTTTAGG
* *
543463 ATTTATG
1 GTTTAGG
*
543470 GTTTATG
1 GTTTAGG
*
543477 GTTTAGA
1 GTTTAGG
543484 GTTTAGG
1 GTTTAGG
*
543491 GTTTA-A
1 GTTTAGG
*
543497 GTTTAAG
1 GTTTAGG
543504 GTTTA
1 GTTTA
543509 AGTTTAGGCG
Statistics
Matches: 99, Mismatches: 23, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
6 5 0.05
7 94 0.95
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:544975 original size:16 final size:16
Alignment explanation
Indices: 544956--544989 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
544946 CAATATACGA
544956 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
544972 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
544988 AT
1 AT
544990 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:545063 original size:16 final size:18
Alignment explanation
Indices: 545031--545064 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
545021 TATTAATGTA
545031 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
545049 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
545065 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:545740 original size:130 final size:130
Alignment explanation
Indices: 545536--545783 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
545526 AATTTTCTTC
* *
545536 TAATTAGGTGATGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGATGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** * *
545601 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTATGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
545666 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGATGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
545731 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
545784 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGATGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:546229 original size:35 final size:35
Alignment explanation
Indices: 546179--546254 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
546169 AATTGAATTT
* *
546179 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
546214 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
546249 AATTGA
1 AATTGA
546255 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:548630 original size:16 final size:16
Alignment explanation
Indices: 548605--548656 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
548595 ACATTAATGA
*
548605 TAAAAATATTTTTAAT
1 TAAAAATATTTATAAT
*
548621 TAAAATTATTTATAAT
1 TAAAAATATTTATAAT
548637 TAAATAATA---ATAAT
1 TAAA-AATATTTATAAT
548651 TAAAAA
1 TAAAAA
548657 AAAGTGCGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 2 0.06
14 9 0.28
16 18 0.56
17 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAAATATTTATAAT
Found at i:549549 original size:16 final size:16
Alignment explanation
Indices: 549528--549561 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
549518 AAAATATATA
*
549528 ATAAATTTTAATTATT
1 ATAAATTTCAATTATT
549544 ATAAATTTCAATTATT
1 ATAAATTTCAATTATT
549560 AT
1 AT
549562 GGTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAAATTTCAATTATT
Found at i:550579 original size:17 final size:19
Alignment explanation
Indices: 550538--550585 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
550528 CTTTGCCTAA
*
550538 GGTATCGATATTACATGTAG
1 GGTATCGATACTACA-GTAG
550558 GGTATCGATACTACA-T-G
1 GGTATCGATACTACAGTAG
550575 GGTATCGATAC
1 GGTATCGATAC
550586 CCATTCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 12 0.44
18 1 0.04
20 14 0.52
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (19 bp):
GGTATCGATACTACAGTAG
Found at i:554867 original size:20 final size:21
Alignment explanation
Indices: 554832--554898 Score: 84
Period size: 21 Copynumber: 3.1 Consensus size: 21
554822 GATTTAAAAT
554832 AATACTAAATTTAATATTTTAA
1 AATA-TAAATTTAATATTTTAA
*
554854 AATA-AAATTCAATATTTATAA
1 AATATAAATTTAATATTT-TAA
554875 AA-ATAAATTTAATATTTTTAA
1 AATATAAATTTAATA-TTTTAA
554896 AAT
1 AAT
554899 GAATTTGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 13 0.33
21 19 0.49
22 7 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATAAATTTAATATTTTAA
Found at i:554911 original size:20 final size:20
Alignment explanation
Indices: 554837--554904 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
554827 AAAATAATAC
554837 TAAATTTAATA-TTTTAAAA
1 TAAATTTAATATTTTTAAAA
* *
554856 TAAAATTCAATATTTATAAAAA
1 T-AAATTTAATATTT-TTAAAA
554878 TAAATTTAATATTTTTAAAA
1 TAAATTTAATATTTTTAAAA
*
554898 TGAATTT
1 TAAATTT
554905 GAAATTTGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 20 0.49
21 14 0.34
22 6 0.15
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (20 bp):
TAAATTTAATATTTTTAAAA
Found at i:560466 original size:29 final size:29
Alignment explanation
Indices: 560381--560466 Score: 109
Period size: 29 Copynumber: 3.0 Consensus size: 29
560371 CCCAACTCAT
* ****
560381 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
560410 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
560439 AGGTCGCCATGCACGCCCGGCGACCAAG
1 AGGTCGCCATGCACTCCCGGCGACCAAG
560467 CTTTTAACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.20, C:0.40, G:0.29, T:0.12
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAAGG
Found at i:562543 original size:13 final size:13
Alignment explanation
Indices: 562525--562550 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
562515 ACATCACCAT
562525 AAGATAATAACAC
1 AAGATAATAACAC
562538 AAGATAATAACAC
1 AAGATAATAACAC
562551 GTTGTCATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (13 bp):
AAGATAATAACAC
Found at i:567741 original size:45 final size:45
Alignment explanation
Indices: 567623--567850 Score: 305
Period size: 45 Copynumber: 5.0 Consensus size: 45
567613 TGTTACCAAA
* * *
567623 ATAAATGAAAATGCATAACGGCGCATTATCGACATAAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGTC
** **
567668 ATACATAAAAAAATGCATAGTGGTGCATTATCGGCATAAAAGGTGTC
1 ATA-A-ATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGTC
* *
567715 ATAAATGAAAATGCATAACGGTGCATTATTGGCATAAAATGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGTC
* * *
567760 ATAAAGGGAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGTC
*
567805 ACT-AATGAAAATGCATAACGGTGCATTATTGGCATAAAAGGTGTC
1 A-TAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGTC
567850 A
1 A
567851 CTCATGGTAT
Statistics
Matches: 158, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
45 118 0.75
46 3 0.02
47 37 0.23
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (45 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGTC
Found at i:568272 original size:34 final size:30
Alignment explanation
Indices: 568234--568302 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
568224 TTGATATAAC
568234 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
568268 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
568297 AATTTA
1 AATTTA
568303 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:568313 original size:29 final size:30
Alignment explanation
Indices: 568243--568302 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
568233 CAATTTAAGG
568243 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
568274 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
568303 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:568506 original size:20 final size:20
Alignment explanation
Indices: 568481--568534 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
568471 ATGCAATTAG
* * *
568481 TGCATCGATGCATCTTTCTA
1 TGCATCGATGCATCCTGCCA
568501 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCATCCTGCCA
*
568521 TGCATCCATGCATC
1 TGCATCGATGCATC
568535 AAGGCTGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCCA
Found at i:568682 original size:20 final size:22
Alignment explanation
Indices: 568644--568683 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
568634 TTTGAGTAGA
568644 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
568666 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
568684 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:568937 original size:34 final size:32
Alignment explanation
Indices: 568898--568967 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
568888 TTTTGTAAAG
* * *
568898 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
568932 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
568964 GGGA
1 GGGA
568968 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:571638 original size:34 final size:30
Alignment explanation
Indices: 571600--571668 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
571590 TTGATATAAC
571600 AATTTAAGGCAAAATAGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
571634 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
571663 AATTTA
1 AATTTA
571669 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:571650 original size:30 final size:30
Alignment explanation
Indices: 571609--571668 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
571599 CAATTTAAGG
571609 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTTTTTGGACTT-AATTGAATTTA
571640 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATAGTTTTTGGACTTAATTGAATTTA
571669 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATAGTTTTTGGACTTAATTGAATTTA
Found at i:571775 original size:21 final size:21
Alignment explanation
Indices: 571749--571804 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
571739 AGGGTGTCAA
*
571749 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCATCCCTGC
571770 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
571791 AGTGCATCCATGCA
1 AGTGCATCCATGCA
571805 CCTGCACTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:571906 original size:40 final size:40
Alignment explanation
Indices: 571860--571954 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
571850 AATGCAATTA
* *
571860 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCCTGCC
571900 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCCTGCC
1 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCCTGCC
* *
571940 ATGCATCCATGCATC
1 GTGCATCGATGCATC
571955 AAGGCTGCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.17, C:0.32, G:0.20, T:0.32
Consensus pattern (40 bp):
GTGCATCGATGCATCCTTCTGTGCATCGATGCATCCTGCC
Found at i:571954 original size:20 final size:20
Alignment explanation
Indices: 571860--571936 Score: 154
Period size: 20 Copynumber: 3.9 Consensus size: 20
571850 AATGCAATTA
571860 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
571880 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
571900 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
571920 GTGCATCGATGCATCCT
1 GTGCATCGATGCATCCT
571937 GCCATGCATC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.16, C:0.30, G:0.21, T:0.34
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:573702 original size:2 final size:2
Alignment explanation
Indices: 573695--573731 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
573685 AACAAAATGC
573695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
573732 CTATCATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:579396 original size:18 final size:18
Alignment explanation
Indices: 579356--579401 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
579346 ATATACTATC
* *
579356 ATTATCATCATCAACATT
1 ATTATCATTACCAACATT
* *
579374 CTTATCATTACCAATATT
1 ATTATCATTACCAACATT
579392 ATTATCATTA
1 ATTATCATTA
579402 ATCCTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTATCATTACCAACATT
Found at i:579670 original size:23 final size:22
Alignment explanation
Indices: 579613--579672 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 22
579603 TGAGTGCCAT
579613 ATAGAATGTCCCGAAGAACCAC
1 ATAGAATGTCCCGAAGAACCAC
*
579635 ATA-TATGTCCCGAATG-ACCAC
1 ATAGAATGTCCCGAA-GAACCAC
579656 ATAGAATTGTCCCGAAG
1 ATAGAA-TGTCCCGAAG
579673 GAGCGCGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 18 0.55
22 6 0.18
23 9 0.27
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATAGAATGTCCCGAAGAACCAC
Found at i:580510 original size:18 final size:20
Alignment explanation
Indices: 580487--580525 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
580477 TAGAATTCTG
580487 ATTTAAA-A-TGGTATCGAT
1 ATTTAAACATTGGTATCGAT
580505 ATTTAAACATTGGTATCGAT
1 ATTTAAACATTGGTATCGAT
580525 A
1 A
580526 CCCCTAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (20 bp):
ATTTAAACATTGGTATCGAT
Found at i:581717 original size:19 final size:19
Alignment explanation
Indices: 581693--581762 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
581683 TGCAAAAATG
581693 GTATCGATACCATAGTAGA
1 GTATCGATACCATAGTAGA
* *
581712 GTATCGGTACCATAGTATAATA
1 GTATCGATACCATAG--T-AGA
*
581734 GTATCGATACCATGGTAG-
1 GTATCGATACCATAGTAGA
581752 GCTATCGATAC
1 G-TATCGATAC
581763 TATGGAGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.02
19 24 0.57
20 1 0.02
21 1 0.02
22 15 0.36
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (19 bp):
GTATCGATACCATAGTAGA
Found at i:582322 original size:79 final size:79
Alignment explanation
Indices: 582138--582474 Score: 469
Period size: 79 Copynumber: 4.3 Consensus size: 79
582128 AGTTTTAGAG
* * * *
582138 TAATGCATATGGGTGCATTATTGGCATAAAATGATGTCATAGTTCAAATGCATATGGGTGCATTT
1 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTAAAATGCATATGGGTGCA-TT
* *
582203 TTCTGCATAAAAGAA
65 ATCGGCATAAAAGAA
** * * *
582218 TAATGCATATGGACGCATTATTGGCATGAAAGGATGCCACAGTTAAAATGCATATGGGTGCATTA
1 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTAAAATGCATATGGGTGCATTA
*
582283 TCGGCTTAAAAGAA
66 TCGGCATAAAAGAA
** *
582297 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATA-CCGAAATGCATATGGATGCATTA
1 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTAAAATGCATATGGGTGCATTA
582361 TCGGCATAAAAGAA
66 TCGGCATAAAAGAA
* ***
582375 TAATGTATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTAAAACATATATGGGTGCATTA
1 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTAAAATGCATATGGGTGCATTA
* *
582440 TTGGCTTAAAAGAA
66 TCGGCATAAAAGAA
582454 TAATGCATATGGGTGCATTAT
1 TAATGCATATGGGTGCATTAT
582475 CAGCATAAAA
Statistics
Matches: 227, Mismatches: 29, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
78 72 0.32
79 100 0.44
80 55 0.24
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (79 bp):
TAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTAAAATGCATATGGGTGCATTA
TCGGCATAAAAGAA
Found at i:582348 original size:44 final size:42
Alignment explanation
Indices: 582298--582444 Score: 132
Period size: 44 Copynumber: 3.6 Consensus size: 42
582288 TTAAAAGAAT
582298 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATACCGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATA-C-A
* * *
582342 AATGCATATGGATGCATTATCGGCAT-AAA--A-G--A-A-T
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATACA
*
582376 AATGTATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATA-C-A
*
582420 AA-ACATATATGGGTGCATTATTGGC
1 AATGC--ATATGGGTGCATTATTGGC
582445 TTAAAAGAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
34 23 0.28
35 3 0.04
37 2 0.02
38 2 0.02
40 2 0.02
41 2 0.02
43 3 0.04
44 26 0.32
45 19 0.23
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (42 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATACA
Found at i:582392 original size:34 final size:34
Alignment explanation
Indices: 582342--582514 Score: 157
Period size: 34 Copynumber: 4.8 Consensus size: 34
582332 GTCATACCGA
* * *
582342 AATGCATATGGATGCATTATCGGCATAAAAGAAT
1 AATGTATATGGGTGCATTATTGGCATAAAAGAAT
582376 AATGTATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCT
1 AATGTATATGGGTGCATTATTGGCAT-AAA--A-G--A-A--T
** *
582419 AAAACATATATGGGTGCATTATTGGCTTAAAAGAAT
1 --AATGTATATGGGTGCATTATTGGCATAAAAGAAT
* **
582455 AATGCATATGGGTGCATTATCAGCATAAAAGAAT
1 AATGTATATGGGTGCATTATTGGCATAAAAGAAT
*
582489 AATGTATATGGGTTCATTATTGGCAT
1 AATGTATATGGGTGCATTATTGGCAT
582515 GAAATGATGC
Statistics
Matches: 112, Mismatches: 16, Indels: 22
0.75 0.11 0.15
Matches are distributed among these distances:
34 73 0.65
35 3 0.03
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 3 0.03
45 23 0.21
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (34 bp):
AATGTATATGGGTGCATTATTGGCATAAAAGAAT
Found at i:582430 original size:157 final size:158
Alignment explanation
Indices: 582138--582485 Score: 502
Period size: 157 Copynumber: 2.2 Consensus size: 158
582128 AGTTTTAGAG
* * *
582138 TAATGCATATGGGTGCATTATTGGCATAAAATGATGTCATAGTTCAAATGCATATGGGTGCATTT
1 TAATGCATATGGGTGCATTATTGGCATAAAAGGATGTCATAG-CCAAATGCATATGGATGCATTT
* * * **
582203 TTCTGCATAAAAGAATAATGCATATGGACGCATTATTGGCATGAAAGGATGCCACAGTTAAAATG
65 ATCGGCATAAAAGAATAATGCATATGGACGCATTATTGGCATGAAAGGATGCCACAGCTAAAACA
582268 CATATGGGTGCATTATCGGCTTAAAAGAA
130 CATATGGGTGCATTATCGGCTTAAAAGAA
*
582297 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATA-CCGAAATGCATATGGATGCA-TT
1 TAATGCATATGGGTGCATTATTGGCATAAAAGGATGTCATAGCC-AAATGCATATGGATGCATTT
* ** * *
582360 ATCGGCATAAAAGAATAATGTATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTAAAACA
65 ATCGGCATAAAAGAATAATGCATATGGACGCATTATTGGCATGAAAGGATGCCACAGCTAAAACA
* *
582425 TATATGGGTGCATTATTGGCTTAAAAGAA
130 CATATGGGTGCATTATCGGCTTAAAAGAA
**
582454 TAATGCATATGGGTGCATTATCAGCATAAAAG
1 TAATGCATATGGGTGCATTATTGGCATAAAAG
582486 AATAATGTAT
Statistics
Matches: 169, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
157 114 0.67
158 16 0.09
159 39 0.23
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (158 bp):
TAATGCATATGGGTGCATTATTGGCATAAAAGGATGTCATAGCCAAATGCATATGGATGCATTTA
TCGGCATAAAAGAATAATGCATATGGACGCATTATTGGCATGAAAGGATGCCACAGCTAAAACAC
ATATGGGTGCATTATCGGCTTAAAAGAA
Found at i:582584 original size:20 final size:20
Alignment explanation
Indices: 582510--582631 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
582500 GTTCATTATT
*
582510 GGCATGAAATGATGCATTAA
1 GGCATGAAAGGATGCATTAA
*
582530 GGCAGGAAAGGATGCCATAAATAAAA
1 GGCATGAAAGGATG-CAT---T--AA
* * *
582556 TGTATGAAATGATGCATTAA
1 GGCATGAAAGGATGCATTAA
*
582576 GGCATGAAAAGATGTCATAAATAAAA
1 GGCATGAAAGGATG-CAT---T--AA
*
582602 TGCATGAAAGGATGCATTAA
1 GGCATGAAAGGATGCATTAA
582622 GGCATGAAAG
1 GGCATGAAAG
582632 AAAATGTATG
Statistics
Matches: 78, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
20 36 0.46
21 6 0.08
22 2 0.03
24 2 0.03
25 6 0.08
26 26 0.33
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.21
Consensus pattern (20 bp):
GGCATGAAAGGATGCATTAA
Found at i:582595 original size:46 final size:46
Alignment explanation
Indices: 582511--582630 Score: 195
Period size: 46 Copynumber: 2.6 Consensus size: 46
582501 TTCATTATTG
* *
582511 GCATGAAATGATGCATTAAGGCAGGAAAGGATGCCATAAATAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAAGATGCCATAAATAAAAT
* *
582557 GTATGAAATGATGCATTAAGGCATGAAAAGATGTCATAAATAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAAGATGCCATAAATAAAAT
*
582603 GCATGAAAGGATGCATTAAGGCATGAAA
1 GCATGAAATGATGCATTAAGGCATGAAA
582631 GAAAATGTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.22
Consensus pattern (46 bp):
GCATGAAATGATGCATTAAGGCATGAAAAGATGCCATAAATAAAAT
Found at i:582615 original size:26 final size:25
Alignment explanation
Indices: 582535--582618 Score: 79
Period size: 26 Copynumber: 3.5 Consensus size: 25
582525 ATTAAGGCAG
*
582535 GAAAGGATGCCATAAATAAAATGTAT
1 GAAAGGATG-CATAAATAAAATGCAT
* *
582561 GAAATGATGCAT---T--AAGGCAT
1 GAAAGGATGCATAAATAAAATGCAT
*
582581 GAAAAGATGTCATAAATAAAATGCAT
1 GAAAGGATG-CATAAATAAAATGCAT
582607 GAAAGGATGCAT
1 GAAAGGATGCAT
582619 TAAGGCATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
20 13 0.28
21 3 0.07
22 1 0.02
24 1 0.02
25 6 0.13
26 22 0.48
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (25 bp):
GAAAGGATGCATAAATAAAATGCAT
Found at i:582636 original size:34 final size:34
Alignment explanation
Indices: 582598--582665 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
582588 TGTCATAAAT
582598 AAAATGCATGAAAGGATGCATTAAGGCATGAAAG
1 AAAATGCATGAAAGGATGCATTAAGGCATGAAAG
* * * *
582632 AAAATGTATGAAATGATGTATTTAGGCATGAAAG
1 AAAATGCATGAAAGGATGCATTAAGGCATGAAAG
582666 GATACCATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.24
Consensus pattern (34 bp):
AAAATGCATGAAAGGATGCATTAAGGCATGAAAG
Found at i:587060 original size:20 final size:20
Alignment explanation
Indices: 587035--587085 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
587025 GATTCAATCG
*
587035 GTATCGATACCGAAGGG-GT
1 GTATCGATACCGAAGGGAAT
*
587054 AGTATCGATATCGAAGGGAAT
1 -GTATCGATACCGAAGGGAAT
587075 GTATCGATACC
1 GTATCGATACC
587086 ATTTCAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (20 bp):
GTATCGATACCGAAGGGAAT
Found at i:587156 original size:22 final size:19
Alignment explanation
Indices: 587110--587180 Score: 88
Period size: 19 Copynumber: 3.5 Consensus size: 19
587100 TGCAAAAATG
587110 GTATCGATACCATAGTAGA
1 GTATCGATACCATAGTAGA
*
587129 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAG--TAG-A
*
587151 GTATCGATACCATGGTAGGA
1 GTATCGATACCATAGTA-GA
587171 GTATCGATAC
1 GTATCGATAC
587181 TATGGAGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
19 14 0.31
20 13 0.29
21 4 0.09
22 14 0.31
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (19 bp):
GTATCGATACCATAGTAGA
Found at i:587175 original size:20 final size:20
Alignment explanation
Indices: 587110--587185 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
587100 TGCAAAAATG
*
587110 GTATCGATACCATAGTA-GA
1 GTATCGATACCATGGTAGGA
* * *
587129 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCAT-G-GTAGGA
587151 GTATCGATACCATGGTAGGA
1 GTATCGATACCATGGTAGGA
*
587171 GTATCGATACTATGG
1 GTATCGATACCATGG
587186 AGTTAGAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.26
20 18 0.39
21 3 0.07
22 13 0.28
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (20 bp):
GTATCGATACCATGGTAGGA
Found at i:587735 original size:79 final size:79
Alignment explanation
Indices: 587586--588417 Score: 1190
Period size: 79 Copynumber: 10.6 Consensus size: 79
587576 GAATGAATGA
* * *
587586 ATAAAAGAATAATGCATATGGGTGCATAATT-GCATGAAATGATGTCTTAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
587650 GGTGCATTATCGAC
66 GGTGCATTATCGAC
* * * *
587664 ATAAAAGAATAATACATATGGATGCATTATTGGCATAAAAGGATGTCATAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
*
587729 AGTGCATTATCGAC
66 GGTGCATTATCGAC
* * * *
587743 TTAAAAGTATAATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTAAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
*
587808 GGTGCATTATCGGC
66 GGTGCATTATCGAC
* * *
587822 ATAAAAGAATAATGCATATGGGTGCGTTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
587887 GGTGCATTATC-AGC
66 GGTGCATTATCGA-C
* * *
587901 TTAAAAGAATAATTCATATGGGTGCATTATTGTCATGAAAGGATGTCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
*
587966 GGTGCATTATCAAC
66 GGTGCATTATCGAC
* * *
587980 ATAAAAGAAAAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
* *
588045 GGTTCATTATCGGC
66 GGTGCATTATCGAC
* *
588059 ATAAAAGAATAATGCATATGGATGCATTATTGGCATGAAAGGAT-TCCATAGTTGAAATGCATAT
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGT-CATAGCTGAAATGCATAT
*
588123 GGGTGCATTATCGGC
65 GGGTGCATTATCGAC
* * * *
588138 TTAAAAGAATAATGTATATGGGTGCATTATTGGAATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
*
588203 GGTGCATTATCAAC
66 GGTGCATTATCGAC
* * *
588217 ATAAAAGAATAATG--TATGGGTGAATTATTGGTATGAAAGGATGTCATAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
588280 GGTGCATTATC-AGC
66 GGTGCATTATCGA-C
* * * *
588294 TTAAAAGAAGAATGCATATGAGTGCATTATTGGCATGAAATGATGTCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
* *
588359 GATGCATTATCAAC
66 GGTGCATTATCGAC
* * *
588373 ATAAAATAATAATGCATATGGGTGAATTATTGGCATCAAAGGATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG
588418 CATTAAGGAA
Statistics
Matches: 673, Mismatches: 72, Indels: 17
0.88 0.09 0.02
Matches are distributed among these distances:
76 1 0.00
77 69 0.10
78 28 0.04
79 573 0.85
80 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATG
GGTGCATTATCGAC
Found at i:587804 original size:45 final size:42
Alignment explanation
Indices: 587753--588368 Score: 331
Period size: 45 Copynumber: 15.5 Consensus size: 42
587743 TTAAAAGTAT
587753 AATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTAA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAGCT-A
*
587798 AATGCATATGGGTGCATTATCGGCAT-AAA-A-G-A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTA
*
587832 AATGCATATGGGTGCGTTATTGGCATGAAAGAATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAG-ATG-CATAGCT-A
** *
587877 AATGCATATGGGTGCATTATCAGC-TTAAA-A-G-A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTA
* *
587911 AATTCATATGGGTGCATTATTGTCATGAAAGGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAGCT-A
***
587956 AATGCATATGGGTGCATTATCAACAT-AAA-A-G-A-A---A
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTA
*
587990 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAGCT-A
* *
588035 AATGCATATGGGTTCATTATCGGCAT-AAA-A-G-A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTA
* * *
588069 AATGCATATGGATGCATTATTGGCATGAAAGGATTCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GA-TGCATAGCT-A
* *
588114 AATGCATATGGGTGCATTATCGGC-TTAAA-A-G-A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTA
* *
588148 AATGTATATGGGTGCATTATTGGAATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAGCT-A
***
588193 AATGCATATGGGTGCATTATCAACAT-AAA-A-G-A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTA
* * *
588227 AATG--TATGGGTGAATTATTGGTATGAAAGGATGTCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAGCT-A
** *
588270 AATGCATATGGGTGCATTATCAGC-TTAAA-A-G-A-AG---
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTA
*
588304 AATGCATATGAGTGCATTATTGGCATGAAATGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAGCT-A
*
588349 AATGCATATGGATGCATTAT
1 AATGCATATGGGTGCATTAT
588369 CAACATAAAA
Statistics
Matches: 438, Mismatches: 54, Indels: 158
0.67 0.08 0.24
Matches are distributed among these distances:
32 15 0.03
33 3 0.01
34 137 0.31
35 22 0.05
36 6 0.01
37 6 0.01
38 14 0.03
39 8 0.02
40 6 0.01
41 14 0.03
42 7 0.02
43 8 0.02
44 24 0.05
45 168 0.38
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.29
Consensus pattern (42 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTA
Found at i:587836 original size:34 final size:34
Alignment explanation
Indices: 587798--587930 Score: 122
Period size: 34 Copynumber: 3.6 Consensus size: 34
587788 ACATAGCTAA
587798 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
587832 AATGCATATGGGTGCGTTATTGGCATGAAAGAATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT--AA-AA-G--A-A--T
* *
587875 GAAATGCATATGGGTGCATTATCAGCTTAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
587911 AATTCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
587931 TGTCATGAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
34 43 0.53
36 3 0.04
37 2 0.02
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 2 0.02
43 3 0.04
45 22 0.27
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:588073 original size:34 final size:34
Alignment explanation
Indices: 588035--588099 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
588025 CCATAGTTGA
* *
588035 AATGCATATGGGTTCATTATCGGCATAAAAGAAT
1 AATGCATATGGATGCATTATCGGCATAAAAGAAT
* *
588069 AATGCATATGGATGCATTATTGGCATGAAAG
1 AATGCATATGGATGCATTATCGGCATAAAAG
588100 GATTCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (34 bp):
AATGCATATGGATGCATTATCGGCATAAAAGAAT
Found at i:588435 original size:20 final size:20
Alignment explanation
Indices: 588410--588484 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
588400 TATTGGCATC
588410 AAAGGATGCATTAAGGAATG
1 AAAGGATGCATTAAGGAATG
* *
588430 AAAGGATGCCATAAATAAAATGTATG
1 AAAGGATG-CAT---T--AAGGAATG
*
588456 AAAGGATGCATTAAGGCATG
1 AAAGGATGCATTAAGGAATG
588476 AAAGGATGC
1 AAAGGATGC
588485 CAGAAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
20 23 0.51
21 3 0.07
22 1 0.02
24 1 0.02
25 3 0.07
26 14 0.31
ACGTcount: A:0.45, C:0.08, G:0.27, T:0.20
Consensus pattern (20 bp):
AAAGGATGCATTAAGGAATG
Found at i:588477 original size:46 final size:47
Alignment explanation
Indices: 588405--588531 Score: 184
Period size: 47 Copynumber: 2.7 Consensus size: 47
588395 TGAATTATTG
* * *
588405 GCATCAAAGGATGCATTAAGGAATGAAAGGATGCCA-TAAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGAAAATAAAAT
*
588451 GTATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGAAAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGAAAATAAAAT
* * *
588498 GCGTGAAATGATGCATTAAGGCATGAAATGATGC
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGC
588532 ATCAAGGCAT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
46 33 0.46
47 39 0.54
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.20
Consensus pattern (47 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGAAAATAAAAT
Found at i:588526 original size:20 final size:20
Alignment explanation
Indices: 588501--588550 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
588491 ATAAAATGCG
*
588501 TGAAATGATGCATTAAGGCA
1 TGAAATGATGCATCAAGGCA
588521 TGAAATGATGCATCAAGGCA
1 TGAAATGATGCATCAAGGCA
*
588541 TGAAAGGATG
1 TGAAATGATG
588551 TCATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.22
Consensus pattern (20 bp):
TGAAATGATGCATCAAGGCA
Found at i:588573 original size:46 final size:46
Alignment explanation
Indices: 588520--588610 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
588510 GCATTAAGGC
588520 ATGAAATGATGCATCAAGGCATGAAAGGATG-TCATAAATAAAATGT
1 ATGAAATGATGCATCAAGGCATGAAAGGATGCT-ATAAATAAAATGT
* *** *
588566 ATGAAATGATGCATTAAGTTGTGGAAGGATGCTATAAATAAAATG
1 ATGAAATGATGCATCAAGGCATGAAAGGATGCTATAAATAAAATG
588611 AAATTTAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 38 0.97
47 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (46 bp):
ATGAAATGATGCATCAAGGCATGAAAGGATGCTATAAATAAAATGT
Found at i:588594 original size:113 final size:112
Alignment explanation
Indices: 588404--588610 Score: 297
Period size: 113 Copynumber: 1.8 Consensus size: 112
588394 GTGAATTATT
*
588404 GGCATCAAAGGATGCATTAAGGAATGAAAGGATGCCATAAATAAAATGTATGAAAGGATGCATTA
1 GGCATCAAAGGATGCATCAAGGAATGAAAGGATGCCATAAATAAAATGTATGAAAGGATGCATTA
588469 AGGCATGAAAGGATGCCAGAAAATAAAATGCGTGAAATGATGCATTAA
66 AGGCATGAAAGGATGCCA-AAAATAAAATGCGTGAAATGATGCATTAA
* * * * *
588517 GGCATGAAATGATGCATCAAGGCATGAAAGGATGTCATAAATAAAATGTATGAAATGATGCATTA
1 GGCATCAAAGGATGCATCAAGGAATGAAAGGATGCCATAAATAAAATGTATGAAAGGATGCATTA
*** * * *
588582 AGTTGTGGAAGGATGCTATAAATAAAATG
66 AGGCATGAAAGGATGCCAAAAATAAAATG
588611 AAATTTAATG
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
112 10 0.12
113 72 0.88
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.23
Consensus pattern (112 bp):
GGCATCAAAGGATGCATCAAGGAATGAAAGGATGCCATAAATAAAATGTATGAAAGGATGCATTA
AGGCATGAAAGGATGCCAAAAATAAAATGCGTGAAATGATGCATTAA
Found at i:588597 original size:66 final size:67
Alignment explanation
Indices: 588453--588583 Score: 201
Period size: 67 Copynumber: 2.0 Consensus size: 67
588443 AATAAAATGT
* *
588453 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGAAAATAAAATGCGTGAAATGATGCATTAAG
1 ATGAAAGGATGCATCAAGGCATGAAAGGATGCCAGAAAATAAAATGCATGAAATGATGCATTAAG
588518 GC
66 GC
* * * *
588520 ATGAAATGATGCATCAAGGCATGAAAGGATGTCA-TAAATAAAATGTATGAAATGATGCATTAAG
1 ATGAAAGGATGCATCAAGGCATGAAAGGATGCCAGAAAATAAAATGCATGAAATGATGCATTAAG
588584 TTGTGGAAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
66 27 0.47
67 31 0.53
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.22
Consensus pattern (67 bp):
ATGAAAGGATGCATCAAGGCATGAAAGGATGCCAGAAAATAAAATGCATGAAATGATGCATTAAG
GC
Found at i:594160 original size:24 final size:24
Alignment explanation
Indices: 594128--594177 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
594118 GATTGAAATC
594128 TAGCACATAAGCAAACACTAAACA
1 TAGCACATAAGCAAACACTAAACA
594152 TAGCACATAAGCAAACACTAAACA
1 TAGCACATAAGCAAACACTAAACA
594176 TA
1 TA
594178 ATGTCAGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.24, G:0.08, T:0.14
Consensus pattern (24 bp):
TAGCACATAAGCAAACACTAAACA
Found at i:600431 original size:313 final size:311
Alignment explanation
Indices: 599811--600606 Score: 986
Period size: 312 Copynumber: 2.5 Consensus size: 311
599801 GGATATTATA
* * ** *
599811 GCATGACTTGTTAGAACTAGTCTCTTACTATCTCATGCAAATCGCCCTACCGCTGCATTGCACCA
1 GCATGACTTGTTAGAACTAGTCTATTACTATCTCATGCAAATCACCCTACTTCTACATT--A-CA
* * *
599876 CCACCACCAATAGCCACTTCAAAAAACATTATCAACGTTAATCATAAAGTAACCTCGTTGTAATA
63 CCACCACCAATAGCCACTTC-AAAAACATCATCAACGTTAATCTTAACGTAACC-CGTTGTAATA
** * * ** *
599941 CATTAAAAATTAAGTTAGTAATCAGAATGAATAATGAATTCCATGAGGCATAAGCTTATTAACAA
126 CCCTAAAAATTCAGTTAGTAATCAAAATGAATAATGAAGGCCATGAGGCAAAAGCTTATTAACAA
*
600006 AGTTGGCGGCGGCCCTTTTTACAAAACATTCCAACCATTATCAAGTGCAACATGTAAACCTTCAA
191 AGTTGGCGGCGGCCCTTTTTACAAAACACTCCAACCATTATCAAGTGCAACATGTAAACCTTCAA
*
600071 TAGTGAGAGCACATACCTCAACAACGCTCAGGTCATGCATACGACGTAAAACCTTT
256 TAGTGAGAGCACATACCTCAACAACACTCAGGTCATGCATACGACGTAAAACCTTT
* * * * * *
600127 GCATGACTTTTTAGAACTAGTCTTTTAATATCTTATGCAAATCACCTTACTTCTACATTTCACCA
1 GCATGACTTGTTAGAACTAGTCTATTACTATCTCATGCAAATCACCCTACTTCTACATTACACCA
* * * * *
600192 CCACCGATATCCACTTCAAAATCATCATCAACGTTAATCTTAACGTAACGCCATTATAATACCCT
66 CCACCAATAGCCACTTCAAAAACATCATCAACGTTAATCTTAACGTAAC-CCGTTGTAATACCCT
* *
600257 AAAAATTCAGTTAGTAATCAAAATGAATAATGAAGGCCATGATGCAAAAGCTTATTAACCAAGTT
130 AAAAATTCAGTTAGTAATCAAAATGAATAATGAAGGCCATGAGGCAAAAGCTTATTAACAAAGTT
* * *
600322 GGTGGCGTCCCTTTTTACAAAAACACTCCAACCATTATCAAGTGCAACATGTAAACCTTCAGTAG
195 GGCGGCGGCCCTTTTTAC-AAAACACTCCAACCATTATCAAGTGCAACATGTAAACCTTCAATAG
* * * *
600387 TGAGAGCA-TTCACCTCAACCACACTC-GGTTTATGCATGCGACGTAAAACCTTT
259 TGAGAGCACAT-ACCTCAACAACACTCAGG-TCATGCATACGACGTAAAACCTTT
* * * * * * * *
600440 ACATGGCTTGTTAGAACTAGTCTATTACTATGTCATACAAATCACCCTA-TTGTTCACTACAACA
1 GCATGACTTGTTAGAACTAGTCTATTACTATCTCATGCAAATCACCCTACTTCTACATTACACCA
* * * * * * *
600504 CCTCCAAAAGCCACTCCAAAAACATCATCAATGTTAACCTTAACTTAACATCGTTGTAATACCCT
66 CCACCAATAGCCACTTCAAAAACATCATCAACGTTAATCTTAACGTAAC-CCGTTGTAATACCCT
*
600569 AAAAATTCAGTTAGTAACCAGAGAATGAATAATGAAGG
130 AAAAATTCAGTTAGTAATCA-A-AATGAATAATGAAGG
600607 TTTGGTGTCA
Statistics
Matches: 410, Mismatches: 64, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
312 196 0.48
313 149 0.36
314 15 0.04
316 50 0.12
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.28
Consensus pattern (311 bp):
GCATGACTTGTTAGAACTAGTCTATTACTATCTCATGCAAATCACCCTACTTCTACATTACACCA
CCACCAATAGCCACTTCAAAAACATCATCAACGTTAATCTTAACGTAACCCGTTGTAATACCCTA
AAAATTCAGTTAGTAATCAAAATGAATAATGAAGGCCATGAGGCAAAAGCTTATTAACAAAGTTG
GCGGCGGCCCTTTTTACAAAACACTCCAACCATTATCAAGTGCAACATGTAAACCTTCAATAGTG
AGAGCACATACCTCAACAACACTCAGGTCATGCATACGACGTAAAACCTTT
Found at i:601086 original size:19 final size:19
Alignment explanation
Indices: 601062--601099 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
601052 AGATTTCAAG
601062 GGTAAAATGGACATTTTGT
1 GGTAAAATGGACATTTTGT
*
601081 GGTAAAATGTACATTTTGT
1 GGTAAAATGGACATTTTGT
601100 ATTAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (19 bp):
GGTAAAATGGACATTTTGT
Found at i:601105 original size:19 final size:19
Alignment explanation
Indices: 601063--601108 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
601053 GATTTCAAGG
*
601063 GTAAAATGGACATTTTGTG
1 GTAAAATGGACATTTTGTA
*
601082 GTAAAATGTACATTTTGTA
1 GTAAAATGGACATTTTGTA
*
601101 TTAAAATG
1 GTAAAATG
601109 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (19 bp):
GTAAAATGGACATTTTGTA
Found at i:604583 original size:21 final size:21
Alignment explanation
Indices: 604557--604692 Score: 179
Period size: 21 Copynumber: 6.5 Consensus size: 21
604547 GTTTCCAGAT
604557 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
604578 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
604599 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
604620 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
604640 TCGCAATGCGAATTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
604661 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTCGACTA
*
604682 TCGCATTGCGA
1 TCGCAATGCGA
604693 TTTACATATT
Statistics
Matches: 103, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
20 17 0.17
21 86 0.83
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:604728 original size:21 final size:21
Alignment explanation
Indices: 604677--604738 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
604667 CGCGAACTTT
604677 GACTATCGCATTGCGAT--T-
1 GACTATCGCATTGCGATAGTC
*
604695 TACATATTCGCATTGCGATAGTC
1 GAC-TA-TCGCATTGCGATAGTC
604718 GACTATCGCATTGCGATAGTC
1 GACTATCGCATTGCGATAGTC
604739 CAAGTTCGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 12 0.32
21 16 0.43
22 3 0.08
23 2 0.05
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (21 bp):
GACTATCGCATTGCGATAGTC
Found at i:604747 original size:21 final size:20
Alignment explanation
Indices: 604701--604908 Score: 141
Period size: 21 Copynumber: 9.6 Consensus size: 20
604691 GATTTACATA
*
604701 TTCGCATTGCGATAGTCGAC
1 TTCGCATTGCGATAGTCAAC
604721 TATCGCATTGCGATAGTCCAAGTTCGC
1 T-TCGCATTGCGATAGT-CAA-----C
*
604748 AAGTTCGCATTGCGATAGTCGAAG
1 ---TTCGCATTGCGATAGTC-AAC
* *
604772 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAC
* *
604793 TTTGCATTGCGATAGTCGAC
1 TTCGCATTGCGATAGTCAAC
*
604813 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGT-CA-AC
*
604834 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAC
*
604855 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTC-AAC
*
604876 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTC-AAC
*
604897 TTCGCGTTGCGA
1 TTCGCATTGCGA
604909 ATATGGAAAC
Statistics
Matches: 157, Mismatches: 13, Indels: 35
0.77 0.06 0.17
Matches are distributed among these distances:
20 19 0.12
21 114 0.73
22 4 0.03
27 1 0.01
28 1 0.01
29 17 0.11
30 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCAAC
Found at i:604748 original size:62 final size:62
Alignment explanation
Indices: 604682--604908 Score: 141
Period size: 62 Copynumber: 3.8 Consensus size: 62
604672 ACTTTGACTA
* *
604682 TCGCATTGCGATTTACATATTCGCATTGCGATAGT-CGACTATCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCCAAGT
* * *
604744 T--C---GC-----A-A-GTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGT
* * * *
604794 TTGCATTGCGATAGT-CGACTA-TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAG
1 TCGCATTGCGAT-TTAC-A-TATTCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCCAAG
604855 T
62 T
* * *
604856 TCGCATTGCGATAGT-CGA-AGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGA
1 TCGCATTGCGAT-TTAC-ATA-TTCGCATTGCGATAGTCCAAGTTCGCATTGCGA
604909 ATATGGAAAC
Statistics
Matches: 129, Mismatches: 15, Indels: 41
0.70 0.08 0.22
Matches are distributed among these distances:
50 37 0.29
51 3 0.02
52 2 0.02
55 2 0.02
57 2 0.02
60 2 0.02
62 55 0.43
63 26 0.20
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (62 bp):
TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGT
Found at i:604806 original size:42 final size:42
Alignment explanation
Indices: 604747--604908 Score: 213
Period size: 42 Copynumber: 3.9 Consensus size: 42
604737 TCCAAGTTCG
*
604747 CAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTC
1 CAAGTTCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTC
* * * *
604789 CAAGTTTGCATTGCGATAGTCG-ACTATCGCATTGCGAT-TTA
1 CAAGTTCGCATTGCGATAGTCGAAGT-TCGCATTGCGATAGTC
*
604830 CATA-TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 CA-AGTTCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTC
* *
604872 GAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGA
1 CAAGTTCGCATTGCGATAGTCGAAGTTCGCATTGCGA
604909 ATATGGAAAC
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
41 34 0.33
42 68 0.67
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (42 bp):
CAAGTTCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTC
Found at i:606056 original size:10 final size:10
Alignment explanation
Indices: 606041--606074 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
606031 TAGGCTAAAA
606041 AATATATAAT
1 AATATATAAT
606051 AATATAT-AT
1 AATATATAAT
*
606060 AATATTTAAT
1 AATATATAAT
606070 AATAT
1 AATAT
606075 GGGTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATATATAAT
Found at i:606161 original size:23 final size:24
Alignment explanation
Indices: 606126--606170 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
606116 AAGTTTGAAA
*
606126 AAATAATTAATCG-TTAACCGATC
1 AAATAATCAATCGATTAACCGATC
*
606149 AAATAATCGATCGATTAACCGA
1 AAATAATCAATCGATTAACCGA
606171 AAAAAATTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (24 bp):
AAATAATCAATCGATTAACCGATC
Found at i:609910 original size:7 final size:8
Alignment explanation
Indices: 609894--609918 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
609884 CTTTTATATG
609894 TTTTATTT
1 TTTTATTT
609902 TTTTATTT
1 TTTTATTT
609910 TTTTATTT
1 TTTTATTT
609918 T
1 T
609919 CTTCTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:616971 original size:3 final size:3
Alignment explanation
Indices: 616963--617005 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
616953 TGGCATTTTG
*
616963 TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
617006 AATATAGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:617081 original size:53 final size:53
Alignment explanation
Indices: 616996--617209 Score: 365
Period size: 53 Copynumber: 4.0 Consensus size: 53
616986 ATTATTATTA
* * * *
616996 TTATTATTATAATATAGTTTAGTGGAGTGATTTAGTTGCATACTTTCATATAC
1 TTATGATTATTATATGGTTTAGTGGAGTGATTTTGTTGCATACTTTCATATAC
*
617049 TTATGATTATTATATGGTTTAGTGGAGTGATTTTGTTGCTTACTTTCATATAC
1 TTATGATTATTATATGGTTTAGTGGAGTGATTTTGTTGCATACTTTCATATAC
*
617102 TTATGATTATTATATGGTTTAGTGGAGTGATTTTGTTGCTTACTTTCATATAC
1 TTATGATTATTATATGGTTTAGTGGAGTGATTTTGTTGCATACTTTCATATAC
*
617155 TTATGATTATTATATGGTTTAGTGGAGTGATTTTGTTGCATACTTTCGTATAC
1 TTATGATTATTATATGGTTTAGTGGAGTGATTTTGTTGCATACTTTCATATAC
617208 TT
1 TT
617210 TCAAAATAAC
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 154 1.00
ACGTcount: A:0.24, C:0.07, G:0.18, T:0.50
Consensus pattern (53 bp):
TTATGATTATTATATGGTTTAGTGGAGTGATTTTGTTGCATACTTTCATATAC
Found at i:622370 original size:21 final size:21
Alignment explanation
Indices: 622346--622385 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
622336 TTTATTTTAT
622346 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
622367 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
622386 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:622433 original size:33 final size:33
Alignment explanation
Indices: 622380--622478 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
622370 TTTGTTTCAA
622380 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
622412 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
622445 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
622478 T
1 T
622479 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:622740 original size:21 final size:21
Alignment explanation
Indices: 622714--622770 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
622704 TGGAGCGTGG
*
622714 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
622735 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
622756 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
622771 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:622843 original size:21 final size:22
Alignment explanation
Indices: 622805--622859 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
622795 CCGTTGAATA
622805 GGGGGAATCGGTACCCCCCTAT
1 GGGGGAATCGGTACCCCCCTAT
622827 GGGGGAATCGGTA-CCCCCTAT
1 GGGGGAATCGGTACCCCCCTAT
622848 GGGGGAATCGGT
1 GGGGGAATCGGT
622860 TCCCTCCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.18, C:0.25, G:0.38, T:0.18
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCCTAT
Found at i:623010 original size:17 final size:17
Alignment explanation
Indices: 622960--623010 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
622950 CTGGAATATT
*
622960 AAAATCGGTTTTTTT--
1 AAAACCGGTTTTTTTAA
* **
622975 ATAACCGGTTTTTAAAA
1 AAAACCGGTTTTTTTAA
622992 AAAACCGGTTTTTTTAA
1 AAAACCGGTTTTTTTAA
623009 AA
1 AA
623011 CCGAAACCGG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.41
17 16 0.59
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (17 bp):
AAAACCGGTTTTTTTAA
Found at i:623012 original size:15 final size:15
Alignment explanation
Indices: 622958--623013 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
622948 ATCTGGAATA
*
622958 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
622973 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
**
622988 AAAAAAAACCGGTTTTT
1 --TTAAAACCGGTTTTT
623005 TTAAAACCG
1 TTAAAACCG
623014 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 20 0.62
17 12 0.38
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:623130 original size:15 final size:17
Alignment explanation
Indices: 623104--623135 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
623094 TCTATGAGAA
623104 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
623120 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
623136 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:623919 original size:18 final size:19
Alignment explanation
Indices: 623896--623935 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
623886 CAATACTTAC
623896 AAAATATAAATTCTT-GAT
1 AAAATATAAATTCTTGGAT
*
623914 AAAATATAAATTTTTGGAT
1 AAAATATAAATTCTTGGAT
623933 AAA
1 AAA
623936 TTAAAACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (19 bp):
AAAATATAAATTCTTGGAT
Found at i:623981 original size:2 final size:2
Alignment explanation
Indices: 623974--624000 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
623964 TAAATAAATA
623974 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
624001 CTTATATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:626555 original size:17 final size:15
Alignment explanation
Indices: 626516--626548 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
626506 GTGAAATTTT
626516 AAATATTTAAATAAA
1 AAATATTTAAATAAA
*
626531 AAATATTTATATAAA
1 AAATATTTAAATAAA
626546 AAA
1 AAA
626549 ATTATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATTTAAATAAA
Found at i:629567 original size:30 final size:30
Alignment explanation
Indices: 629531--629590 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
629521 TTCTATCCTG
*
629531 ATTTTATCTATTTCTTACGGTTCAACTAAT
1 ATTTTATCTATTTCTTACCGTTCAACTAAT
*
629561 ATTTTATCTATTTCTTACCGTTCAATTAAT
1 ATTTTATCTATTTCTTACCGTTCAACTAAT
629591 TTTATGCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.52
Consensus pattern (30 bp):
ATTTTATCTATTTCTTACCGTTCAACTAAT
Found at i:635380 original size:73 final size:74
Alignment explanation
Indices: 635259--635402 Score: 272
Period size: 73 Copynumber: 2.0 Consensus size: 74
635249 CATAATAATT
*
635259 TTTTTTTGTATACACAATGACTAAAACTCGAAATATTACTTGAGCAATATCAAATTATTTATCAC
1 TTTTTTTGTATACACAATGACTAAAACTCGAAATATTACTTGAACAATATCAAATTATTTATCAC
635324 CTGAACAAA
66 CTGAACAAA
635333 TTTTTTT-TATACACAATGACTAAAACTCGAAATATTACTTGAACAATATCAAATTATTTATCAC
1 TTTTTTTGTATACACAATGACTAAAACTCGAAATATTACTTGAACAATATCAAATTATTTATCAC
635397 CTGAAC
66 CTGAAC
635403 GAATCTTGCT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 62 0.90
74 7 0.10
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (74 bp):
TTTTTTTGTATACACAATGACTAAAACTCGAAATATTACTTGAACAATATCAAATTATTTATCAC
CTGAACAAA
Found at i:646636 original size:39 final size:39
Alignment explanation
Indices: 646582--646679 Score: 169
Period size: 39 Copynumber: 2.5 Consensus size: 39
646572 TCTATGAACA
*
646582 ACAAGTGCATTGTGCTCTTGGTATCTGATAGTATAAGGG
1 ACAAGTGCATTGTGCTCTTGGTATCTGATAGCATAAGGG
*
646621 ACAAGTGCATTGTGCTCTTGGTATCTGATAGCGTAAGGG
1 ACAAGTGCATTGTGCTCTTGGTATCTGATAGCATAAGGG
*
646660 ACAAGTGCATTCTGCTCTTG
1 ACAAGTGCATTGTGCTCTTG
646680 ATATGCCATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (39 bp):
ACAAGTGCATTGTGCTCTTGGTATCTGATAGCATAAGGG
Found at i:650790 original size:3 final size:3
Alignment explanation
Indices: 650782--650820 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
650772 TTTTTTCTTC
650782 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
650821 GTCAATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:655656 original size:20 final size:20
Alignment explanation
Indices: 655633--655682 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
655623 GAAAAATGGC
655633 TCCAACGGCTCCAAAACACT
1 TCCAACGGCTCCAAAACACT
655653 TCCAACGGCTCCAAAACACT
1 TCCAACGGCTCCAAAACACT
655673 TCCAACGGCT
1 TCCAACGGCT
655683 AGAAATGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.40, G:0.12, T:0.16
Consensus pattern (20 bp):
TCCAACGGCTCCAAAACACT
Found at i:656310 original size:27 final size:28
Alignment explanation
Indices: 656258--656324 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 28
656248 TACTAATAAT
656258 AATATATAATA-ATATGTATATATTAAA
1 AATATATAATATATATGTATATATTAAA
656285 AACTATATAATATATAT-TATAT-TTAAA
1 AA-TATATAATATATATGTATATATTAAA
656312 AATAATATAATAT
1 AAT-ATATAATAT
656325 GTTTTCAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.03
27 18 0.49
28 14 0.38
29 4 0.11
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
AATATATAATATATATGTATATATTAAA
Found at i:656415 original size:38 final size:37
Alignment explanation
Indices: 656373--656514 Score: 153
Period size: 41 Copynumber: 3.7 Consensus size: 37
656363 TCCGTTTTAA
*
656373 AAAACTATATATATATATTTTCAAAATAATATGTTTTC
1 AAAACTATAT-TATATGTTTTCAAAATAATATGTTTTC
** *
656411 AAAACTATATTATATATGTTTTCAAAA-AA-CCGTTTTAA
1 AAAACTATA-T-TATATGTTTTCAAAATAATATGTTTT-C
656449 AAAACTATATTATATGTTTTCAAATTTATAATATGTTTTTC
1 AAAACTATATTATATGTTTTCAAA---ATAATATG-TTTTC
*
656490 AAAACTATATTTTATGTTTTCAAAA
1 AAAACTATATTATATGTTTTCAAAA
656515 ACTATATATA
Statistics
Matches: 88, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
36 14 0.16
37 6 0.07
38 21 0.24
39 17 0.19
40 2 0.02
41 24 0.27
42 4 0.05
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (37 bp):
AAAACTATATTATATGTTTTCAAAATAATATGTTTTC
Found at i:656425 original size:41 final size:40
Alignment explanation
Indices: 656373--656514 Score: 135
Period size: 36 Copynumber: 3.7 Consensus size: 40
656363 TCCGTTTTAA
656373 AAAACTATATATATATA--TTTTCAAAATAATATGTTTTC
1 AAAACTATATATATATATGTTTTCAAAATAATATGTTTTC
**
656411 AAAACTATAT-TATATATGTTTTCAAAA-AA-CCGTTTT-
1 AAAACTATATATATATATGTTTTCAAAATAATATGTTTTC
*
656447 AAAA-AACTATAT-TATATGTTTTCAAATTTATAATATGTTTTTC
1 AAAACTA-TATATATATATGTTTTCAAA---ATAATATG-TTTTC
656490 AAAACTATAT-T-T-TATGTTTTCAAAA
1 AAAACTATATATATATATGTTTTCAAAA
656515 ACTATATATA
Statistics
Matches: 86, Mismatches: 6, Indels: 24
0.74 0.05 0.21
Matches are distributed among these distances:
35 1 0.01
36 21 0.24
37 12 0.14
38 13 0.15
39 10 0.12
40 2 0.02
41 13 0.15
42 6 0.07
43 7 0.08
44 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (40 bp):
AAAACTATATATATATATGTTTTCAAAATAATATGTTTTC
Found at i:656511 original size:21 final size:21
Alignment explanation
Indices: 656449--656525 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 21
656439 ACCGTTTTAA
656449 AAAACTATATTATATGTTTTC
1 AAAACTATATTATATGTTTTC
* *
656470 -AAA-TTTATAATATGTTTTTC
1 AAAACTATATTATATG-TTTTC
*
656490 AAAACTATATTTTATGTTTTC
1 AAAACTATATTATATGTTTTC
656511 AAAAACTATA-TATAT
1 -AAAACTATATTATAT
656526 TATATATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 9 0.20
20 8 0.17
21 12 0.26
22 17 0.37
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (21 bp):
AAAACTATATTATATGTTTTC
Found at i:656516 original size:76 final size:75
Alignment explanation
Indices: 656318--656516 Score: 251
Period size: 76 Copynumber: 2.6 Consensus size: 75
656308 TAAAAATAAT
* * *
656318 ATAATATGTTTTCAAAGATTATATATACTATATATGTTTTCGAAATCCGTTTTAAAAAACTATAT
1 ATAATATGTTTTCAAA-A--CTATAT--TATATATGTTTTCAAAAACCGTTTTAAAAAACTATAT
656383 ATATATATTTTCAAA
61 ATATATATTTTCAAA
656398 ATAATATGTTTTCAAAACTATATTATATATGTTTTCAAAAAACCGTTTTAAAAAACTATAT-TAT
1 ATAATATGTTTTCAAAACTATATTATATATGTTTTC-AAAAACCGTTTTAAAAAACTATATATAT
*
656462 ATGTTTTCAAA
65 ATATTTTCAAA
656473 TTTATAATATGTTTTTCAAAACTATATT-T-TATGTTTTCAAAAAC
1 ---ATAATATG-TTTTCAAAACTATATTATATATGTTTTCAAAAAC
656517 TATATATATT
Statistics
Matches: 110, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
75 26 0.24
76 28 0.25
77 14 0.13
78 9 0.08
79 17 0.15
80 16 0.15
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.45
Consensus pattern (75 bp):
ATAATATGTTTTCAAAACTATATTATATATGTTTTCAAAAACCGTTTTAAAAAACTATATATATA
TATTTTCAAA
Found at i:658376 original size:45 final size:45
Alignment explanation
Indices: 658326--658514 Score: 236
Period size: 45 Copynumber: 4.2 Consensus size: 45
658316 TGTTTTTTTG
* *
658326 TTTTTTGATTTAGAGCGCCATTTCGGGTTTTCACTATAAACACAT
1 TTTTTTGATTTAGAGCGCCCTTTCGGGTTTTCACTCTAAACACAT
* * * * *
658371 TTTTTTATATTTAGAGCGCCCTTTTGGTTTTTTACTCTAAACATAT
1 TTTTTT-GATTTAGAGCGCCCTTTCGGGTTTTCACTCTAAACACAT
* * *
658417 TTTTTTAATTTAGAGCGGCCTTTTGGGTTTTCACTCTAAACACAT
1 TTTTTTGATTTAGAGCGCCCTTTCGGGTTTTCACTCTAAACACAT
* * *
658462 TTTTTCGATTTCGAGTGCCCTTTCGGGTTTTCACTCTAAACAC-T
1 TTTTTTGATTTAGAGCGCCCTTTCGGGTTTTCACTCTAAACACAT
658506 CTTTTTTGA
1 -TTTTTTGA
658515 AAAACTTAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.01
45 84 0.68
46 38 0.31
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.47
Consensus pattern (45 bp):
TTTTTTGATTTAGAGCGCCCTTTCGGGTTTTCACTCTAAACACAT
Found at i:658445 original size:91 final size:91
Alignment explanation
Indices: 658326--658512 Score: 243
Period size: 91 Copynumber: 2.1 Consensus size: 91
658316 TGTTTTTTTG
* *
658326 TTTTTTGATTTAGAGCGCCATTTCGGGTTTTCACTATAAACACATTTTTTTATATTTAGAGCGCC
1 TTTTTTAATTTAGAGCGCCATTTCGGGTTTTCACTATAAACACA-TTTTTTAGATTTAGAGCGCC
* * *
658391 CTTTTGGTTTTTTACTCTAAACA-TAT
65 CTTTCGGGTTTTCACTCTAAACACTAT
* * * * *
658417 TTTTTTAATTTAGAGCGGCC-TTTTGGGTTTTCACTCTAAACACATTTTTTCGATTTCGAGTGCC
1 TTTTTTAATTTAGAGC-GCCATTTCGGGTTTTCACTATAAACACATTTTTTAGATTTAGAGCGCC
*
658481 CTTTCGGGTTTTCACTCTAAACACTCT
65 CTTTCGGGTTTTCACTCTAAACACTAT
658508 TTTTT
1 TTTTT
658513 GAAAAACTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
90 36 0.43
91 44 0.53
92 3 0.04
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (91 bp):
TTTTTTAATTTAGAGCGCCATTTCGGGTTTTCACTATAAACACATTTTTTAGATTTAGAGCGCCC
TTTCGGGTTTTCACTCTAAACACTAT
Found at i:662007 original size:54 final size:54
Alignment explanation
Indices: 661947--662447 Score: 752
Period size: 54 Copynumber: 9.3 Consensus size: 54
661937 TTCGTTACGA
* * * * * * *
661947 TGCACACATAGTGCCTATACGATCATTCATAAACATATTATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
*
662001 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
**
662055 TGCACACTTAGTGTTGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
* * * *
662109 TGCACTCTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTACGTGAAT
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
* * *
662163 TGTACACTTAGTGCCGAAAC-AGCTATTCATCAACATATGATGAATTCTGTGAAT
1 TGCACACTTAGTGCCGAAACGA-TTATTCATCAACATATGATGAATTCCGTGAAT
*
662217 TGGACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
* * * *
662271 TGCACACTTAGTGTCGAGATGATTATTCATCAACATATGATGAATTCTGTGAAT
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
* *
662325 TGCACACTTAGTGCCGAAACGGTTATTCATCAATATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
* *
662379 TGCACACTTAGTACCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
662433 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
662448 CCTATTTGGT
Statistics
Matches: 406, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
54 405 1.00
55 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
Found at i:662738 original size:20 final size:20
Alignment explanation
Indices: 662692--662744 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
662682 TCTGTTAACA
*
662692 ATGGTATCGATACCTTCCTC
1 ATGGTATCGATACCTCCCTC
* *
662712 ATAGTATCGATACCTCCCTT
1 ATGGTATCGATACCTCCCTC
*
662732 TTGGTATCGATAC
1 ATGGTATCGATAC
662745 TGCTTACATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGGTATCGATACCTCCCTC
Done.