Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008522.1 Hibiscus syriacus cultivar Beakdansim tig00111390_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: 1416293
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:263274 original size:28 final size:28
Alignment explanation
Indices: 263252--263316 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
263242 TATTTTTTAT
*
263252 TATTATT-ATGATTATTATTATTTATTAA
1 TATTATTAAT-ATCATTATTATTTATTAA
*
263280 TATTATTAATATCATTATTATATTAATAA
1 TATTATTAATATCATTATTAT-TTATTAA
263309 TATTATTA
1 TATTATTA
263317 TTTATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
TATTATTAATATCATTATTATTTATTAA
Found at i:263305 original size:17 final size:17
Alignment explanation
Indices: 263283--263317 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
263273 TTATTAATAT
263283 TATTAAT-ATCATTATTA
1 TATTAATAAT-ATTATTA
263300 TATTAATAATATTATTA
1 TATTAATAATATTATTA
263317 T
1 T
263318 TTATTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTAATAATATTATTA
Found at i:270370 original size:2 final size:2
Alignment explanation
Indices: 270363--270400 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
270353 GTACAAAACA
270363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
270401 TACATCTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:277629 original size:60 final size:60
Alignment explanation
Indices: 277478--277650 Score: 165
Period size: 60 Copynumber: 2.9 Consensus size: 60
277468 TTGAAGATGC
** * * * * *
277478 AATTAGAA-GATTCAAATACTTGAGGACCAAATTAGAATGAGAGTCATGGTTTGGGGATGA
1 AATTAGAATG-TTCAAATGTTTGAAGACTAATTTAGAATGAGAGTCATAGTTTGGGAATGA
*
277538 AATTAGAATGTTCAAATGTTTGAAGACTAATTTAGAATGAGAATCATAGTTTGGGAATGA
1 AATTAGAATGTTCAAATGTTTGAAGACTAATTTAGAATGAGAGTCATAGTTTGGGAATGA
* * ** *
277598 AATTGGATTGTTTTGAA-GTTT-AAGGATTAATTT-GAAATGAGAGTCATAGTTTG
1 AATTAGAATG-TTCAAATGTTTGAA-GACTAATTTAG-AATGAGAGTCATAGTTTG
277651 AGTAGATATG
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
59 3 0.03
60 87 0.92
61 5 0.05
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (60 bp):
AATTAGAATGTTCAAATGTTTGAAGACTAATTTAGAATGAGAGTCATAGTTTGGGAATGA
Found at i:277919 original size:20 final size:19
Alignment explanation
Indices: 277859--277919 Score: 52
Period size: 23 Copynumber: 2.9 Consensus size: 19
277849 TATGATATAT
*
277859 TTTTTAATT-ATTTTAGTA
1 TTTTTAATTAATTTTATTA
277877 GTTTTTAAATTATTATTTATATTA
1 -TTTTT-AATTA--ATTT-TATTA
277901 TTATTTAATTAATTTTATT
1 TT-TTTAATTAATTTTATT
277920 CAAAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
19 5 0.14
20 8 0.23
21 4 0.11
23 11 0.31
24 7 0.20
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTTAATTAATTTTATTA
Found at i:278260 original size:14 final size:16
Alignment explanation
Indices: 278228--278269 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
278218 GAGCTTCCAT
*
278228 ATTTTGTTTTAATTTA
1 ATTTTGTTTTAATTCA
278244 ATTTT-TTTT-ATTCA
1 ATTTTGTTTTAATTCA
*
278258 ATTTGGTTTTAA
1 ATTTTGTTTTAA
278270 AAGATTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 8 0.36
15 8 0.36
16 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (16 bp):
ATTTTGTTTTAATTCA
Found at i:282675 original size:59 final size:59
Alignment explanation
Indices: 282516--282703 Score: 216
Period size: 60 Copynumber: 3.2 Consensus size: 59
282506 TGCTTCATAT
* * * * * *
282516 ATCCTCAAACTATGATCCTCATTTTATATTGGTCACTAAACTTTTGAATATTCCAATTTC
1 ATCCTCAAACTATGATACTCATTCTAAATTAGTCACCAAACTTTTGAACATT-CAATTTC
* * *
282576 ATCCTCAAACTATGATACTCATTCTAAATTTGTCATCAAACTTTTGAACATTAAATTTC
1 ATCCTCAAACTATGATACTCATTCTAAATTAGTCACCAAACTTTTGAACATTCAATTTC
* * * * *
282635 ATCCTCAAACTATGACT-CTCATTCTAAATTAGCCCCCAAACTTTTAAATCTTTCAATTTT
1 ATCCTCAAACTATGA-TACTCATTCTAAATTAGTCACCAAACTTTTGAA-CATTCAATTTC
282695 ATCCTCAAA
1 ATCCTCAAA
282704 TTCATCCAAA
Statistics
Matches: 110, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
59 47 0.43
60 63 0.57
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (59 bp):
ATCCTCAAACTATGATACTCATTCTAAATTAGTCACCAAACTTTTGAACATTCAATTTC
Found at i:293781 original size:24 final size:23
Alignment explanation
Indices: 293731--293790 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
293721 AAATTCAATG
*
293731 CCCCTTTTGTTGAAAAAACTGCT
1 CCCCCTTTGTTGAAAAAACTGCT
293754 CCCCCTTTGTTGAAAAAACTAAGC-
1 CCCCCTTTGTTGAAAAAACT--GCT
*
293778 CCCCCATTGTTGA
1 CCCCCTTTGTTGA
293791 CTTTTCCTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 19 0.58
24 12 0.36
25 2 0.06
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (23 bp):
CCCCCTTTGTTGAAAAAACTGCT
Found at i:297072 original size:15 final size:16
Alignment explanation
Indices: 297042--297074 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
297032 AAAATCTTTC
*
297042 TTTCCCGTTCTTGATT
1 TTTCCCGTTCTGGATT
297058 TTTCCC-TTCTGGATT
1 TTTCCCGTTCTGGATT
297073 TT
1 TT
297075 GATCTTCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.06, C:0.24, G:0.12, T:0.58
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:298333 original size:24 final size:23
Alignment explanation
Indices: 298289--298343 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
298279 GGGGCACCGA
298289 ATTGTTGAAAAAACTGCTCCCCC
1 ATTGTTGAAAAAACTGCTCCCCC
*
298312 TTTGTTGAAAAAACTAAG-TCCCCC
1 ATTGTTGAAAAAACT--GCTCCCCC
298336 ATTGTTGA
1 ATTGTTGA
298344 CTTTTCCTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 14 0.50
24 13 0.46
25 1 0.04
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (23 bp):
ATTGTTGAAAAAACTGCTCCCCC
Found at i:302114 original size:31 final size:31
Alignment explanation
Indices: 302079--302140 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
302069 CTCCAGTTAG
*
302079 TTACTCAGG-CTGAGCAGCACTTACCGAATCA
1 TTACTC-GGACTGAGCAACACTTACCGAATCA
* *
302110 TTACTCGGACTGAGCAATACTTACTGAATCA
1 TTACTCGGACTGAGCAACACTTACCGAATCA
302141 GAGCAGTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (31 bp):
TTACTCGGACTGAGCAACACTTACCGAATCA
Found at i:305190 original size:131 final size:131
Alignment explanation
Indices: 305044--305347 Score: 423
Period size: 131 Copynumber: 2.3 Consensus size: 131
305034 CTTTAAAGCG
* *
305044 TGAGAGGTCATTTATTCTCGATTGGAAATAATTCGATATTATCGTTTTCTCTCGAATCAAAATTG
1 TGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAAAATTG
** * * *
305109 ATTTTTAAGATGAAATGGT-GATATCTCTTCATTTCGATT-AGAGCAATAAATGACTCCTTTAAG
66 AAATTTAAGACGAAATAGTAG-TATCTCTTCATTTCGATTGA-AACAATAAATGACTCCTTTAAG
**
305172 GTA
129 ACA
* * *
305175 TGAGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTCGAATCGATATTG
1 TGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAAAATTG
* * **
305240 AAATTTAAGACGAAATAGTAGTATCTCTTCATTTCGATTGAAATAATAAATGATTGTTTTAAGAC
66 AAATTTAAGACGAAATAGTAGTATCTCTTCATTTCGATTGAAACAATAAATGACTCCTTTAAGAC
305305 A
131 A
*
305306 TGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
1 TGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
305348 TATTTTTTCT
Statistics
Matches: 153, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
131 151 0.99
132 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (131 bp):
TGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAAAATTG
AAATTTAAGACGAAATAGTAGTATCTCTTCATTTCGATTGAAACAATAAATGACTCCTTTAAGAC
A
Found at i:314109 original size:20 final size:20
Alignment explanation
Indices: 314084--314135 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
314074 TAGTATGGTA
314084 GTATCGATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
314104 GTATCGATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
314124 GTATCGATACCA
1 GTATCGATACCA
314136 GGCAGCATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (20 bp):
GTATCGATACCATGGTAAGG
Found at i:314109 original size:114 final size:115
Alignment explanation
Indices: 313990--314215 Score: 310
Period size: 114 Copynumber: 2.0 Consensus size: 115
313980 CGATGAGGTA
* * *
313990 GTATCGATACCATGGTATGGGTATCGATACCAAGAAACATCGAATCTAAAATTGGTATCGATACC
1 GTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAACCTAAAATGGGTATCGATACC
* *** * * * *
314055 AGAA-GGGGTATTGGTACCATAGTATGGTAGTATCGATACCATGGTAAGG
66 AAAAGGGGGTATCAATACCATAGTATAGAAGTATCGAAACCAGGGTAAGG
* * * *
314104 GTATCGATACCATGGTAAGGGTATCGATACCAGGCAGCATCGAACCTAAAATGGGTATTGATACC
1 GTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAACCTAAAATGGGTATCGATACC
314169 AAAAGGGGGTATCAATACCATAGTATAGAAGTATCGAAACCAGGGTA
66 AAAAGGGGGTATCAATACCATAGTATAGAAGTATCGAAACCAGGGTA
314216 GTAGTATCGA
Statistics
Matches: 96, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
114 61 0.64
115 35 0.36
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (115 bp):
GTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAACCTAAAATGGGTATCGATACC
AAAAGGGGGTATCAATACCATAGTATAGAAGTATCGAAACCAGGGTAAGG
Found at i:314643 original size:20 final size:20
Alignment explanation
Indices: 314620--314692 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 20
314610 ATGCATAAAC
314620 GGATGCATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
* *
314640 GGATGCCATAACTAAAAATGCATGAAC
1 GGATG-CAT---T---AAGGCATGAAA
*
314667 GGATGTATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
314687 GGATGC
1 GGATGC
314693 CATAATTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
20 19 0.47
21 3 0.08
23 1 0.03
24 1 0.03
26 2 0.05
27 14 0.35
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (20 bp):
GGATGCATTAAGGCATGAAA
Found at i:314668 original size:47 final size:47
Alignment explanation
Indices: 314599--314985 Score: 639
Period size: 47 Copynumber: 8.2 Consensus size: 47
314589 AAACTGAATA
* *
314599 CATAACTAAAAATGCATAAACGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* *
314646 CATAACTAAAAATGCATGAACGGATGTATTAAGGCATGAAAGGATGC
1 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* **
314693 CATAATTGAAAATGCATGAACAAATGCATTAAGGCATGAAAGGATGC
1 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * *
314740 CATAACTGAAAATGTATGAACGGATGCATTAAGGCATAAAATGATGC
1 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
*
314787 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
314834 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* **
314881 CATACCTGAAAATGCATGAACAAATGCATTAAGGCATGAAAGGATGC
1 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
314928 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
*
314975 CATAAGTGAAA
1 CATAACTGAAA
314986 TTAACAAATA
Statistics
Matches: 315, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 315 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (47 bp):
CATAACTGAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
Found at i:314812 original size:27 final size:25
Alignment explanation
Indices: 314795--314954 Score: 89
Period size: 27 Copynumber: 6.8 Consensus size: 25
314785 GCCATAACTA
314795 AAAATGCATGAACGGATG-CAT--T
1 AAAATGCATGAACGGATGCCATACT
* *
314817 --AAGGCATGAAAGGATGCCATAACT
1 AAAATGCATGAACGGATGCCAT-ACT
314841 GAAAATGCATGAACGGATG-CAT--T
1 -AAAATGCATGAACGGATGCCATACT
* *
314864 --AAGGCATGAAAGGATGCCATACCT
1 AAAATGCATGAACGGATGCCATA-CT
**
314888 GAAAATGCATGAACAAATG-CAT--T
1 -AAAATGCATGAACGGATGCCATACT
* *
314911 --AAGGCATGAAAGGATGCCATAACT
1 AAAATGCATGAACGGATGCCAT-ACT
314935 GAAAATGCATGAACGGATGC
1 -AAAATGCATGAACGGATGC
314955 ATTAAGGCAT
Statistics
Matches: 101, Mismatches: 16, Indels: 37
0.66 0.10 0.24
Matches are distributed among these distances:
20 40 0.40
21 9 0.09
23 2 0.02
24 3 0.03
26 6 0.06
27 41 0.41
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (25 bp):
AAAATGCATGAACGGATGCCATACT
Found at i:314980 original size:20 final size:20
Alignment explanation
Indices: 314800--314974 Score: 82
Period size: 20 Copynumber: 7.7 Consensus size: 20
314790 AACTAAAAAT
*
314800 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
314820 GCATGAAAGGATGCCATAACTGAAAAT
1 GCATGAAAGGATG-CAT---T---AAG
*
314847 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
314867 GCATGAAAGGATGCCATACCTGAAAAT
1 GCATGAAAGGATG-CAT---T---AAG
*
314894 GCATGAACA-AATGCATTAAG
1 GCATGAA-AGGATGCATTAAG
*
314914 GCATGAAAGGATGCCATAACTGAAAAT
1 GCATGAAAGGATG-CAT---T---AAG
*
314941 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
314961 GCATGAAAGGATGC
1 GCATGAAAGGATGC
314975 CATAAGTGAA
Statistics
Matches: 119, Mismatches: 13, Indels: 46
0.67 0.07 0.26
Matches are distributed among these distances:
19 1 0.01
20 53 0.45
21 9 0.08
23 3 0.03
24 3 0.03
26 9 0.08
27 40 0.34
28 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:315505 original size:29 final size:29
Alignment explanation
Indices: 315438--315498 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
315428 TATGCCAGTT
*
315438 AGATGAACGGTTAAACACTATTGAGTAAA
1 AGATGAATGGTTAAACACTATTGAGTAAA
* *
315467 AGATGAATGGTTAAACACTGTTGTGTAAA
1 AGATGAATGGTTAAACACTATTGAGTAAA
315496 AGA
1 AGA
315499 ATAATGGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.26
Consensus pattern (29 bp):
AGATGAATGGTTAAACACTATTGAGTAAA
Found at i:315644 original size:2 final size:2
Alignment explanation
Indices: 315637--315701 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
315627 TGAAGGGATA
315637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
315679 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
315702 ATGTACCATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:316887 original size:134 final size:130
Alignment explanation
Indices: 316729--317133 Score: 454
Period size: 134 Copynumber: 3.1 Consensus size: 130
316719 AAGAACAGCT
* * * *
316729 GAACATATCCTTTTTTTAGATTTGATATTCCCTGAGTAATAATGGAACAAGTATGCCTCGATTCA
1 GAACATATCCCTTTTTTAGATTTGATCTTCCCTGAGTAACAATGGAACAAGTCTGCCTCGATTCA
*
316794 ATCTTCCCTGAAGAATAATGGAATGAATCAACATTTCCAGATCTGATTTTACCTCAAGAAGAAAT
66 ATCTTCCCTGAAGAA-AATGGAATGAATCAACATTTCCAGATCTGATTTTACCTCAAGAAGAAAC
316859 A
130 A
* *
316860 GAACATATCCCTTTCTTTCAAGATTTGATCTTCCTTGAGTAACAATGGAACAAGTCTGCCTTGAT
1 GAACATATCCCTTT-TTT--AGATTTGATCTTCCCTGAGTAACAATGGAACAAGTCTGCCTCGAT
* * * * * * * * *
316925 TCAATCTTCCCTGAGGAACAGTGGAATAAATCAACTTTTCTAGATCTGA-TATCCCTTAAGAAGT
63 TCAATCTTCCCTGAAGAA-AATGGAATGAATCAACATTTCCAGATCTGATTTTACCTCAAGAAGA
* *
316989 AGCG
127 AACA
* * * * *
316993 GAAAAAATCTCTCTTTTTTAGATTTGATCTTACCTAAGAAACAATGGAACAAGTCTGCCTCGATT
1 GAACATATC-C-CTTTTTTAGATTTGATCTTCCCTGAGTAACAATGGAACAAGTCTGCCTCGATT
* * * * *
317058 GAATCTTCCCTGAAGAAAAGTGAAATGAATCAACATTTCCATATCTGATTTT-CTCTCATGAAGC
64 CAATCTTCCCTGAAGAAAA-TGGAATGAATCAACATTTCCAGATCTGATTTTAC-CTCAAGAAGA
*
317122 AGCA
127 AACA
317126 GAACATAT
1 GAACATAT
317134 ATCTCTCTTT
Statistics
Matches: 225, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
131 14 0.06
132 83 0.37
133 37 0.16
134 87 0.39
135 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (130 bp):
GAACATATCCCTTTTTTAGATTTGATCTTCCCTGAGTAACAATGGAACAAGTCTGCCTCGATTCA
ATCTTCCCTGAAGAAAATGGAATGAATCAACATTTCCAGATCTGATTTTACCTCAAGAAGAAACA
Found at i:317064 original size:132 final size:129
Alignment explanation
Indices: 316735--317106 Score: 431
Period size: 132 Copynumber: 2.8 Consensus size: 129
316725 AGCTGAACAT
* * * *
316735 ATCCTTTTTTTAGATTTGATATTCCCTGAGTAATAATGGAACAAGTATGCCTCGATTCAATCTTC
1 ATCCCTTTTTTAGATTTGATCTT-CCTGAGTAACAATGGAACAAGTCTGCCTCGATTCAATCTTC
* * *
316800 CCTGAAGAATAA-TGGAATGAATCAACATTTCCAGATCTGATTTTACCTCAAGAAGAAATAGAAC
65 CCTGAAGAA-AAGTGGAATGAATCAACATTTCCAGATCTGA-TATACCTCAAGAAGAAACAGAAA
*
316864 AT
128 AA
*
316866 ATCCCTTTCTTTCAAGATTTGATCTTCCTTGAGTAACAATGGAACAAGTCTGCCTTGATTCAATC
1 ATCCCTTT-TTT--AGATTTGATCTTCC-TGAGTAACAATGGAACAAGTCTGCCTCGATTCAATC
* * * * * * * * * *
316931 TTCCCTGAGGAACAGTGGAATAAATCAACTTTTCTAGATCTGATATCCCTTAAGAAGTAGCGGAA
62 TTCCCTGAAGAAAAGTGGAATGAATCAACATTTCCAGATCTGATATACCTCAAGAAGAAACAGAA
316996 AAA
127 AAA
* * *
316999 ATCTCTCTTTTTTAGATTTGATCTTACCTAAGAAACAATGGAACAAGTCTGCCTCGATTGAATCT
1 ATC-C-CTTTTTTAGATTTGATCTT-CCTGAGTAACAATGGAACAAGTCTGCCTCGATTCAATCT
* *
317064 TCCCTGAAGAAAAGTGAAATGAATCAACATTTCCATATCTGAT
63 TCCCTGAAGAAAAGTGGAATGAATCAACATTTCCAGATCTGAT
317107 TTTCTCTCAT
Statistics
Matches: 203, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
131 7 0.03
132 84 0.41
133 24 0.12
134 84 0.41
135 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (129 bp):
ATCCCTTTTTTAGATTTGATCTTCCTGAGTAACAATGGAACAAGTCTGCCTCGATTCAATCTTCC
CTGAAGAAAAGTGGAATGAATCAACATTTCCAGATCTGATATACCTCAAGAAGAAACAGAAAAA
Found at i:317519 original size:134 final size:134
Alignment explanation
Indices: 317188--317989 Score: 759
Period size: 134 Copynumber: 6.0 Consensus size: 134
317178 ATCATCCTTT
* * * * * * * *
317188 CCAGATCTGATTTTGCCTCAAGAAGCAGCAGAACATATCCCTCTTTTTCAAGATTTAACCTTCCC
1 CCAGATATGATTTTCCCTCAAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATCTTCCC
* * * * * * * ** *
317253 TAAGTAACAATGGAATAAGTCTGCCTCGATTCAATCTTTCCTTAAGAACAATATAATGAATCAAT
66 TGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAAC
* *
317318 GT-G
131 ATCC
* * * * * *
317321 CCAGATATGATTTTCCCACAAGAAGAAACAGAACATATCCCTCTCTTTCAAGATTTTATTTTCCC
1 CCAGATATGATTTTCCCTCAAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATCTTCCC
** * * * *
317386 TGAGTAACAGTGGAATGAGTCCGTCTCAATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAAC
66 TGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAAC
317451 ATCC
131 ATCC
* * * *
317455 CCAAATATAATTTTCCCTCAAGAAGAAGTGGAACAGATTCCTCTCTTTCAAGATTTGATCTTCCC
1 CCAGATATGATTTTCCCTCAAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATCTTCCC
** * * *
317520 TGAGTAACAGTTAAACAAGTATGACTCGATTCAATCTTCACTGAAGAATAGTGGAATGAATCAAC
66 TGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAAC
317585 ATCC
131 ATCC
* * * * ** * * * *
317589 CCATATCTAATTTTCCCTCAAGAAGTA-CCAAATCAGATCTCTATCTTTCAATATTTGATCTTTC
1 CCAGATATGATTTTCCCTCAAGAAGAAGCGGAA-CAGATCCCTCTCTTTCAAGATTTGATCTTCC
* * * *
317653 CAGAGTAACAGTGGAACAAGTATGCCTCGATTCAATCTTCCCTGAAAAATAGTAGAATGAATCAA
65 CTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAA
**
317718 CATTT
130 CATCC
*
317723 CCAGATCA-GATTTTCCTTCAAGAAGAAGCGGAAC-GTATCCCTCTCTTTCAA-ATACTTGATCT
1 CCAGAT-ATGATTTTCCCTCAAGAAGAAGCGGAACAG-ATCCCTCTCTTTCAAGAT--TTGATCT
* * * * * *
317785 TCCCTAAGTAACATTGGAACAAGTCTGCCTCAATTCAATCTTCCATGAAAAATAGTGGAATTAAT
62 TCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAAT
* **
317850 CAATATTT
127 CAACATCC
* * * * * * * * * *
317858 CCATATATGATTTTCCCTTAAGAAGCAGCGAAACAAATCCCTCTTTTTTCCATATTTGATATTCT
1 CCAGATATGATTTTCCCTCAAGAAGAAGCGGAACAGATCCCTC-TCTTTCAAGATTTGATCTTCC
* * * * * * *
317923 CTGAGGAACAATGGAATAAATTTACCCCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAA
65 CTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAA
317988 CA
130 CA
317990 GTGGAGCATA
Statistics
Matches: 553, Mismatches: 105, Indels: 20
0.82 0.15 0.03
Matches are distributed among these distances:
133 115 0.21
134 261 0.47
135 169 0.31
136 6 0.01
137 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (134 bp):
CCAGATATGATTTTCCCTCAAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATCTTCCC
TGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAAC
ATCC
Found at i:318139 original size:3 final size:3
Alignment explanation
Indices: 318131--318168 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
318121 GTCCCATTTT
318131 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
318169 TTAGGCTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:321282 original size:2 final size:2
Alignment explanation
Indices: 321275--321311 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
321265 ACCGTTCACA
321275 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
321312 GAAAATGTAA
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:322094 original size:3 final size:3
Alignment explanation
Indices: 322088--322121 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
322078 TTTCGTCCCG
322088 TTA TTA TTAA GTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TT
322122 TAAGATTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 25 0.86
4 2 0.07
5 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:323524 original size:69 final size:69
Alignment explanation
Indices: 323442--323577 Score: 236
Period size: 69 Copynumber: 2.0 Consensus size: 69
323432 AGTGACCCAC
* *
323442 GTTGGTTGTGGTGTCTTATATATATTTTATGTAGGTTTACTTTACCTTTATATTTTATATTAAAA
1 GTTGGTTGTGGTGTCTTATATATATTTTATGTAGGATTACTTTACCTTTATATTATATATTAAAA
323507 GTGT
66 GTGT
* *
323511 GTTGGTTGTGGTGTTTTATATATATTTTATGTATGATTACTTTACCTTTATATTATATATTAAAA
1 GTTGGTTGTGGTGTCTTATATATATTTTATGTAGGATTACTTTACCTTTATATTATATATTAAAA
323576 GT
66 GT
323578 ATGGTAATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (69 bp):
GTTGGTTGTGGTGTCTTATATATATTTTATGTAGGATTACTTTACCTTTATATTATATATTAAAA
GTGT
Found at i:323805 original size:2 final size:2
Alignment explanation
Indices: 323740--323797 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
323730 TTTATTATCC
323740 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
323781 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
323798 GCATATATGC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:323883 original size:10 final size:9
Alignment explanation
Indices: 323864--323954 Score: 65
Period size: 8 Copynumber: 11.0 Consensus size: 9
323854 TTAATTTACG
323864 TATATA-TA
1 TATATATTA
323872 TATA-ATTA
1 TATATATTA
323880 TATATATTA
1 TATATATTA
* *
323889 TTTTTATTA
1 TATATATTA
*
323898 -A-ACATTA
1 TATATATTA
* *
323905 -ATCTATGA
1 TATATATTA
323913 -ATATA-TA
1 TATATATTA
323920 TATATA-TA
1 TATATATTA
323928 TATATA-TA
1 TATATATTA
323936 TATATATATA
1 TATATAT-TA
323946 TATATATTA
1 TATATATTA
323955 GTTAGTTGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
7 7 0.10
8 38 0.57
9 13 0.19
10 9 0.13
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (9 bp):
TATATATTA
Found at i:323920 original size:2 final size:2
Alignment explanation
Indices: 323913--323952 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
323903 TAATCTATGA
323913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
323953 TAGTTAGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:324117 original size:80 final size:79
Alignment explanation
Indices: 324021--324223 Score: 291
Period size: 80 Copynumber: 2.5 Consensus size: 79
324011 AGTAGTTTTT
* *
324021 TTTTAATTATAATATATATAGAATCATTATAATATTTGTTTGTCCACTTGTTTCCTTAATTTAAG
1 TTTTAATTATAATATATAT-GAATCATTATAATATTTGTTTCTCCACTTATTTCCTTAATTTAAG
* *
324086 CTATAGTGGTTTAGC
65 CAATAGAGGTTTAGC
324101 TTTTAATTATAATATATATGAAATCATTATAATATTTGTTTCTCCACTTATTTCCTTAATTTAAG
1 TTTTAATTATAATATATATG-AATCATTATAATATTTGTTTCTCCACTTATTTCCTTAATTTAAG
*
324166 CAATAGAGGTTTAGT
65 CAATAGAGGTTTAGC
* *
324181 TTTTTATTGATTATAATATATGGAATCATTATAATATTT-TTTC
1 TTTTAATT-ATAAT-ATATAT-GAATCATTATAATATTTGTTTC
324224 ACTTTCCCTA
Statistics
Matches: 112, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
79 1 0.01
80 80 0.71
81 8 0.07
82 22 0.20
83 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (79 bp):
TTTTAATTATAATATATATGAATCATTATAATATTTGTTTCTCCACTTATTTCCTTAATTTAAGC
AATAGAGGTTTAGC
Found at i:332244 original size:2 final size:2
Alignment explanation
Indices: 332237--332267 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
332227 CATGTATTTG
332237 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 T
332268 CCTTTTGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:337134 original size:111 final size:111
Alignment explanation
Indices: 336940--337391 Score: 688
Period size: 111 Copynumber: 4.1 Consensus size: 111
336930 GATCGATCCC
* * * *
336940 GATTCGATGGATCAACTTTCTCAAATCTGATATTCCCTCAGAAGAAGCATAACAAATCCCTCTCT
1 GATTCAATGGATCAACTTTCTCAGATCTGATATTCCCTCAGAAGAAGCAGAACAGATCCCTCTCT
*
337005 TTCAAGATTTGATATTCCCTGAGTGACAGCGGAATAAATCTACCCT
66 TTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAATCTACCCT
* * * *
337051 GATTCAATGGATCAACTTTCTCAGATCTGATATTCCCACAGAAAAAGCGGAACAGATCCCTATCT
1 GATTCAATGGATCAACTTTCTCAGATCTGATATTCCCTCAGAAGAAGCAGAACAGATCCCTCTCT
*
337116 TTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAATCTACCCT
66 TTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAATCTACCCT
* * * * *
337162 GATTCAATGGATCAACTTTCCCAGATCTAATATTCCCTCAGAAGAAGCGGAATAGATCCCTCTTT
1 GATTCAATGGATCAACTTTCTCAGATCTGATATTCCCTCAGAAGAAGCAGAACAGATCCCTCTCT
*
337227 TTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCT
66 TTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAATCTACCCT
*
337273 GATTCAATAGATCAACTTTCTCAGATCTGATATTCCCTCAGAAGAAGCAGAACAGATCCCTCTCT
1 GATTCAATGGATCAACTTTCTCAGATCTGATATTCCCTCAGAAGAAGCAGAACAGATCCCTCTCT
** * *** *
337338 TTCAAGATTTGATATTCTATGAGTGATAATAGAACAAGTCTACCCT
66 TTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAATCTACCCT
337384 GATTCAAT
1 GATTCAAT
337392 CTTCCTTGAA
Statistics
Matches: 310, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 310 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (111 bp):
GATTCAATGGATCAACTTTCTCAGATCTGATATTCCCTCAGAAGAAGCAGAACAGATCCCTCTCT
TTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAATCTACCCT
Found at i:337601 original size:3 final size:3
Alignment explanation
Indices: 337593--337633 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
337583 TTTTCGTCCC
337593 ATT ATT ATT AAGTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
337634 TAAGATTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 32 0.89
4 2 0.06
5 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:339026 original size:69 final size:69
Alignment explanation
Indices: 338951--339086 Score: 247
Period size: 69 Copynumber: 2.0 Consensus size: 69
338941 AGTGACCCAC
*
338951 GTTGGTTGTGGTGTCTTATATATATTTTATGTAT-ATTTACTTTACCTTTATATTTTATATTAAA
1 GTTGGTTGTGGTGTCTTATATATATTTTATGTATGA-TTACTTTACCTTTATATTATATATTAAA
339015 AGTGT
65 AGTGT
339020 GTTGGTTGTGGTGTCTTATATATATTTTATGTATGATTACTTTACCTTTATATTATATATTAAAA
1 GTTGGTTGTGGTGTCTTATATATATTTTATGTATGATTACTTTACCTTTATATTATATATTAAAA
339085 GT
66 GT
339087 ATGGTAATTC
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 64 0.98
70 1 0.02
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.54
Consensus pattern (69 bp):
GTTGGTTGTGGTGTCTTATATATATTTTATGTATGATTACTTTACCTTTATATTATATATTAAAA
GTGT
Found at i:339278 original size:2 final size:2
Alignment explanation
Indices: 339225--339270 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
339215 TTTATTATCC
339225 AT AT -T AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
339265 AT -T AT A
1 AT AT AT A
339271 GCATATATGC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339355 original size:13 final size:13
Alignment explanation
Indices: 339337--339363 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
339327 TTAATTTACG
339337 TATATATATTATT
1 TATATATATTATT
339350 TATATATATTATT
1 TATATATATTATT
339363 T
1 T
339364 TTATTAAACA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATATATTATT
Found at i:339573 original size:80 final size:79
Alignment explanation
Indices: 339477--339675 Score: 274
Period size: 80 Copynumber: 2.5 Consensus size: 79
339467 AGTTTGTTTT
* * *
339477 TTTTAATTATAATATATATAGAATCATTATAATATTTGTTTGTCCACTTGTTTCTTTAATTTAAG
1 TTTTAATTATAATATATAT-GAATCATTATAATATTTGTTTCTCCACTTATTTCCTTAATTTAAG
*
339542 CTATA-ATGGTTTAGC
65 CAATAGA-GGTTTAGC
339557 TTTTAATTATAATATATATGAAATCATTATAATATTTGTTTCTCCACTTATTTCCTTAATTTAAG
1 TTTTAATTATAATATATATG-AATCATTATAATATTTGTTTCTCCACTTATTTCCTTAATTTAAG
*
339622 CAATAGAGGTTTAGT
65 CAATAGAGGTTTAGC
* *
339637 TTTTTATTGATTATAATATATGGAATCATTATAATATTT
1 TTTTAATT-ATAAT-ATATAT-GAATCATTATAATATTT
339676 TTCCACTTTC
Statistics
Matches: 107, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
79 1 0.01
80 78 0.73
81 5 0.05
82 22 0.21
83 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (79 bp):
TTTTAATTATAATATATATGAATCATTATAATATTTGTTTCTCCACTTATTTCCTTAATTTAAGC
AATAGAGGTTTAGC
Found at i:343162 original size:23 final size:23
Alignment explanation
Indices: 343126--343215 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
343116 TCGTGAACAT
* *
343126 GTTCGTAAATATGTTCATTTAAA
1 GTTCGTGAACATGTTCATTTAAA
* ** *
343149 GTTTGTGAACATGTTCGCTTATAT
1 GTTCGTGAACATGTTCATTTA-AA
* *
343173 GTTCGTGAACAAGTTTATTTAACA
1 GTTCGTGAACATGTTCATTTAA-A
*
343197 -TTCGTGAACATGTGCATTT
1 GTTCGTGAACATGTTCATTT
343216 GCAAGATAAA
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
23 33 0.66
24 17 0.34
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (23 bp):
GTTCGTGAACATGTTCATTTAAA
Found at i:344106 original size:18 final size:19
Alignment explanation
Indices: 344083--344121 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
344073 TTGACAAGAG
344083 AATATTTTA-TAATTTTTA
1 AATATTTTAGTAATTTTTA
*
344101 AATATTTTAGTACTTTTTA
1 AATATTTTAGTAATTTTTA
344120 AA
1 AA
344122 AAAATCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
AATATTTTAGTAATTTTTA
Found at i:344163 original size:18 final size:18
Alignment explanation
Indices: 344138--344188 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
344128 TTAATGTTGT
344138 TAATTTTATTTATTTC-AA
1 TAATTTTATTT-TTTCTAA
*
344156 TTATTTTATATTTTTCTAA
1 TAATTTTAT-TTTTTCTAA
344175 TAATTTCTATTTTT
1 TAATTT-TATTTTT
344189 ACTAGCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 12 0.43
19 13 0.46
20 3 0.11
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATTTTATTTTTTCTAA
Found at i:345012 original size:24 final size:24
Alignment explanation
Indices: 344980--345049 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
344970 TCGTTGAAAG
344980 ACTGAAAACCCATTCGCCTTCATC
1 ACTGAAAACCCATTCGCCTTCATC
*
345004 ACTGAAAACCCATTCGCCTTTATC
1 ACTGAAAACCCATTCGCCTTCATC
* * *
345028 GCAGAAAACCTATTCGCCTTCA
1 ACTGAAAACCCATTCGCCTTCA
345050 ACCTCCTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.30, C:0.34, G:0.10, T:0.26
Consensus pattern (24 bp):
ACTGAAAACCCATTCGCCTTCATC
Found at i:345581 original size:10 final size:10
Alignment explanation
Indices: 345566--345592 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
345556 ATATGTTAGG
345566 GAGTTTATAT
1 GAGTTTATAT
345576 GAGTTTATAT
1 GAGTTTATAT
345586 GAGTTTA
1 GAGTTTA
345593 GTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (10 bp):
GAGTTTATAT
Found at i:345612 original size:28 final size:27
Alignment explanation
Indices: 345525--345612 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 27
345515 TATATGAGAA
345525 TATATGAGTTTAGCGGGTTTACTGTTAG
1 TATATGAGTTTAG-GGGTTTACTGTTAG
* *
345553 TATAT-A-TGTTAGGGAGTTTA-TATGAG
1 TATATGAGT-TTAGGG-GTTTACTGTTAG
345579 TTTATATGAGTTTAGTGGGTTTACTGTTAG
1 --TATATGAGTTTAG-GGGTTTACTGTTAG
345609 TATA
1 TATA
345613 AATGGTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
26 7 0.15
27 10 0.21
28 14 0.29
29 10 0.21
30 7 0.15
ACGTcount: A:0.25, C:0.03, G:0.26, T:0.45
Consensus pattern (27 bp):
TATATGAGTTTAGGGGTTTACTGTTAG
Found at i:345960 original size:22 final size:22
Alignment explanation
Indices: 345932--345982 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
345922 TGAATTTCAG
**
345932 TATGTTGACTTTTGCAT-GAATA
1 TATGTTGACCATTG-ATAGAATA
345954 TATGTTGACCATTGATAGAATA
1 TATGTTGACCATTGATAGAATA
345976 TATGTTG
1 TATGTTG
345983 TGATAGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (22 bp):
TATGTTGACCATTGATAGAATA
Found at i:346712 original size:15 final size:15
Alignment explanation
Indices: 346694--346883 Score: 100
Period size: 15 Copynumber: 12.7 Consensus size: 15
346684 CAGAACCAGT
*
346694 TGAACCAGAAATTAG
1 TGAACCAGAAATTAA
*
346709 TGAACCCGAAATTAA
1 TGAACCAGAAATTAA
** *
346724 TGAACCAG-AACCAGC
1 TGAACCAGAAATTA-A
* **
346739 CGAGTCAGAAATTAA
1 TGAACCAGAAATTAA
* *
346754 TGAACCAG-AACTAGT
1 TGAACCAGAAATTA-A
* *
346769 TGAGCTAGAAATTAA
1 TGAACCAGAAATTAA
* ** *
346784 TAAACCAG-AACCAGC
1 TGAACCAGAAATTA-A
*
346799 TGAGCCAGAAATTAA
1 TGAACCAGAAATTAA
*
346814 TGAACCTGAAATTAA
1 TGAACCAGAAATTAA
** *
346829 TGAACCAG-AACCAGC
1 TGAACCAGAAATTA-A
*
346844 TGAGCCAGAAATTAA
1 TGAACCAGAAATTAA
* *
346859 TGAACCTGAAATTGA
1 TGAACCAGAAATTAA
346874 TGAACCAGAA
1 TGAACCAGAA
346884 CCTGTTGAGG
Statistics
Matches: 121, Mismatches: 46, Indels: 16
0.66 0.25 0.09
Matches are distributed among these distances:
14 13 0.11
15 95 0.79
16 13 0.11
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (15 bp):
TGAACCAGAAATTAA
Found at i:346728 original size:30 final size:31
Alignment explanation
Indices: 346694--346838 Score: 120
Period size: 30 Copynumber: 4.8 Consensus size: 31
346684 CAGAACCAGT
* *
346694 TGAACCAGAAATTAG-TGAACCCGAAATTAA
1 TGAACCAGAAACTAGCTGAACCAGAAATTAA
* * **
346724 TGAACCAG-AACCAGCCGAGTCAGAAATTAA
1 TGAACCAGAAACTAGCTGAACCAGAAATTAA
* * *
346754 TGAACCAG-AACTAGTTGAGCTAGAAATTAA
1 TGAACCAGAAACTAGCTGAACCAGAAATTAA
* * *
346784 TAAACCAG-AACCAGCTGAGCCAGAAATTAA
1 TGAACCAGAAACTAGCTGAACCAGAAATTAA
* * *
346814 TGAACCTGAAATTA-ATGAACCAGAA
1 TGAACCAGAAACTAGCTGAACCAGAA
346839 CCAGCTGAGC
Statistics
Matches: 92, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
29 4 0.04
30 85 0.92
31 3 0.03
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.18
Consensus pattern (31 bp):
TGAACCAGAAACTAGCTGAACCAGAAATTAA
Found at i:346748 original size:45 final size:45
Alignment explanation
Indices: 346661--346885 Score: 180
Period size: 45 Copynumber: 4.7 Consensus size: 45
346651 GGTCTGAACA
* * ** *
346661 TAATGAACCTGAAATTGATGAAGCAGAACCAGTTGAACCAGAAAT
1 TAATGAACCTGAAATTAATGAACCAGAACCAGCCGAGCCAGAAAT
* * *
346706 TAGTGAACCCGAAATTAATGAACCAGAACCAGCCGAGTCAGAAAT
1 TAATGAACCTGAAATTAATGAACCAGAACCAGCCGAGCCAGAAAT
* * ** *
346751 TAATGAACCAGAACTAGTTGAGCTAGAAATTAATAAACCAGAACCAGCTGAGCCAGAAAT
1 TAATGAACCTGAA--A-TT-A-AT-G-AA-CCA-GAACCAG---C--C-GAGCCAGAAAT
*
346811 TAATGAACCTGAAATTAATGAACCAGAACCAGCTGAGCCAGAAAT
1 TAATGAACCTGAAATTAATGAACCAGAACCAGCCGAGCCAGAAAT
*
346856 TAATGAACCTGAAATTGATGAACCAGAACC
1 TAATGAACCTGAAATTAATGAACCAGAACC
346886 TGTTGAGGTG
Statistics
Matches: 143, Mismatches: 22, Indels: 30
0.73 0.11 0.15
Matches are distributed among these distances:
45 88 0.62
47 1 0.01
48 3 0.02
49 1 0.01
50 1 0.01
51 7 0.05
52 3 0.02
53 3 0.02
54 7 0.05
55 1 0.01
56 1 0.01
57 3 0.02
58 1 0.01
59 1 0.01
60 22 0.15
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (45 bp):
TAATGAACCTGAAATTAATGAACCAGAACCAGCCGAGCCAGAAAT
Found at i:346748 original size:60 final size:59
Alignment explanation
Indices: 346694--346819 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 59
346684 CAGAACCAGT
* * * * *
346694 TGAACCAGAAATTAG-TGAACCCGAAATTAATGAACCAGAACCAGCCGAGTCAGAAATTAA
1 TGAACCAG-AACTAGTTGAACCAGAAATTAATAAACCAGAACCAGCCGAGCCAGAAAGT-A
* * * *
346754 TGAACCAGAACTAGTTGAGCTAGAAATTAATAAACCAGAACCAGCTGAGCCAGAAATTAA
1 TGAACCAGAACTAGTTGAACCAGAAATTAATAAACCAGAACCAGCCGAGCCAGAAAGT-A
346814 TGAACC
1 TGAACC
346820 TGAAATTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 5 0.09
60 53 0.91
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.17
Consensus pattern (59 bp):
TGAACCAGAACTAGTTGAACCAGAAATTAATAAACCAGAACCAGCCGAGCCAGAAAGTA
Found at i:348789 original size:13 final size:13
Alignment explanation
Indices: 348773--348843 Score: 90
Period size: 13 Copynumber: 5.5 Consensus size: 13
348763 ATTCTTCATG
348773 CATATTGTTATTA
1 CATATTGTTATTA
*
348786 CATATTGTTACTA
1 CATATTGTTATTA
* *
348799 CATAATGTTATTG
1 CATATTGTTATTA
*
348812 CATATTGTTCA-TG
1 CATATTGTT-ATTA
348825 CATATTGTTATTA
1 CATATTGTTATTA
348838 CATATT
1 CATATT
348844 CTTCATGCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
12 1 0.02
13 48 0.96
14 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (13 bp):
CATATTGTTATTA
Found at i:348802 original size:26 final size:26
Alignment explanation
Indices: 348758--348906 Score: 114
Period size: 26 Copynumber: 5.9 Consensus size: 26
348748 AACTTGCTAA
* *
348758 TACATATTCTTCATGCATATTGTTAT
1 TACATATTGTTCATACATATTGTTAT
*
348784 TACATATTGTT-ACTACATAATGTTAT
1 TACATATTGTTCA-TACATATTGTTAT
* *
348810 TGCATATTGTTCATGCATATTGTTAT
1 TACATATTGTTCATACATATTGTTAT
* * * *
348836 TACATATTCTTCATGCATTTTGTAAT
1 TACATATTGTTCATACATATTGTTAT
* * *
348862 TGCATAATTG-----A-ATACTGATAT
1 TACAT-ATTGTTCATACATATTGTTAT
*
348883 TACATATTGTTCATGCATATTGTT
1 TACATATTGTTCATACATATTGTT
348907 GTTGGCCCAT
Statistics
Matches: 93, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
20 4 0.04
21 10 0.11
25 1 0.01
26 74 0.80
27 4 0.04
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.48
Consensus pattern (26 bp):
TACATATTGTTCATACATATTGTTAT
Found at i:348802 original size:39 final size:39
Alignment explanation
Indices: 348758--348867 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 39
348748 AACTTGCTAA
*
348758 TACATATTCTTCATGCATATTGTTATTACATATTGTTAC
1 TACATATTCTTCATGCATATTGTTATTGCATATTGTTAC
* * *
348797 TACATAATGTT-ATTGCATATTGTTCA-TGCATATTGTTAT
1 TACATATTCTTCA-TGCATATTGTT-ATTGCATATTGTTAC
* *
348836 TACATATTCTTCATGCATTTTGTAATTGCATA
1 TACATATTCTTCATGCATATTGTTATTGCATA
348868 ATTGAATACT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
38 2 0.03
39 55 0.93
40 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (39 bp):
TACATATTCTTCATGCATATTGTTATTGCATATTGTTAC
Found at i:350110 original size:26 final size:26
Alignment explanation
Indices: 350074--350126 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
350064 GTTACATACA
350074 TTGCATCTTCAATTCTAACACAAGTC
1 TTGCATCTTCAATTCTAACACAAGTC
350100 TTGCATCTTCAATTCTAACACAAGTC
1 TTGCATCTTCAATTCTAACACAAGTC
350126 T
1 T
350127 ATTAAACGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (26 bp):
TTGCATCTTCAATTCTAACACAAGTC
Found at i:350564 original size:23 final size:23
Alignment explanation
Indices: 350538--350583 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
350528 ATGTTTTAAT
350538 TGACGTGGCGT-GTTGCATGTCCA
1 TGACGTGGCGTAG-TGCATGTCCA
*
350561 TGACGTGGTGTAGTGCATGTCCA
1 TGACGTGGCGTAGTGCATGTCCA
350584 ACCTCGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.15, C:0.20, G:0.35, T:0.30
Consensus pattern (23 bp):
TGACGTGGCGTAGTGCATGTCCA
Found at i:357325 original size:25 final size:25
Alignment explanation
Indices: 357296--357360 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
357286 AATTTAAAAT
357296 ATTTTAAAAATTAATAAATAATATG
1 ATTTTAAAAATTAATAAATAATATG
*
357321 ATTTTAAAAATTAATAAATAATATT
1 ATTTTAAAAATTAATAAATAATATG
357346 ATTTTAAAAATTAAT
1 ATTTTAAAAATTAAT
357361 TAGAATACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTTTAAAAATTAATAAATAATATG
Found at i:357392 original size:20 final size:22
Alignment explanation
Indices: 357364--357403 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
357354 AATTAATTAG
357364 AATACTTGAAAATAT-TTTTCT
1 AATACTTGAAAATATATTTTCT
357385 AATA-TTGAAAATATATTTT
1 AATACTTGAAAATATATTTT
357404 TTAGAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (22 bp):
AATACTTGAAAATATATTTTCT
Found at i:358173 original size:23 final size:24
Alignment explanation
Indices: 358121--358177 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
358111 GTTTACAAAT
* *
358121 ATGTTCGTTTATATGTTCGTGAAC
1 ATGTTCATTTATACGTTCGTGAAC
* *
358145 AAGTTCATTTA-ACGTTTGTGAAC
1 ATGTTCATTTATACGTTCGTGAAC
358168 ATGTTCATTT
1 ATGTTCATTT
358178 GTAAGCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.46
Consensus pattern (24 bp):
ATGTTCATTTATACGTTCGTGAAC
Found at i:359548 original size:185 final size:185
Alignment explanation
Indices: 359223--359612 Score: 651
Period size: 185 Copynumber: 2.1 Consensus size: 185
359213 TTTTCTAATT
* *
359223 TATATAA-AAATTAAATATTTTTTAATTAAAAAAACAGTTTCAAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTCAAATTAATTTAAATAATATATAA
* *
359287 TTATGAAATATAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATATAAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
* ** *
359352 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAACCCATATGTTA
131 AGGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGACTGAACCCATATGTTA
359407 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTT-ACAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTTTAATT-AAAAAAACAGTTTCA-AATTAATTTAAATAATATAT
359471 AATTATAAAATA-AAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
64 AATTATAAAATATAAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
*
359535 ATAGGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGACTGAGCCCATATGTTA
129 ATAGGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGACTGAACCCATATGTTA
*
359592 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
359613 AATTTCGGTT
Statistics
Matches: 193, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
184 7 0.04
185 142 0.74
186 44 0.23
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTCAAATTAATTTAAATAATATATAA
TTATAAAATATAAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
AGGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGACTGAACCCATATGTTA
Found at i:360274 original size:84 final size:86
Alignment explanation
Indices: 360150--360367 Score: 273
Period size: 84 Copynumber: 2.6 Consensus size: 86
360140 GCTTTTACTG
* * * *
360150 TAATTTATAAAAGTTTTGGGCCATTTTTGTAATTT-TAAAAGTTTTGGGCCATTATTGTAATTTG
1 TAATTTATAAAA-TTTTGGGCCATTATTGTAATTTATAAAAGTTTTGGGCAACTATTGTAATTTA
* * *
360214 TAAAAGTTTTGGTCCATTATT-
65 TAAAAGTTTTGGGCAACTATTA
* *
360235 TAATTTGTAAAATTTTGAG-CATTATTGTAATTTATAAAAGTTTTGGGCAACTATTGTAATTTAT
1 TAATTTATAAAATTTTGGGCCATTATTGTAATTTATAAAAGTTTTGGGCAACTATTGTAATTTAT
360299 AAAAGTTTTGGGCAACTATTA
66 AAAAGTTTTGGGCAACTATTA
** * *
360320 TAATTTATAAAAATTTTGGGTAATTATTATAATTTAT-AAACTTTTGGG
1 TAATTTAT-AAAATTTTGGGCCATTATTGTAATTTATAAAAGTTTTGGG
360368 TATTATCGAC
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
83 13 0.11
84 50 0.43
85 18 0.16
86 20 0.17
87 14 0.12
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (86 bp):
TAATTTATAAAATTTTGGGCCATTATTGTAATTTATAAAAGTTTTGGGCAACTATTGTAATTTAT
AAAAGTTTTGGGCAACTATTA
Found at i:360369 original size:28 final size:29
Alignment explanation
Indices: 360148--360367 Score: 270
Period size: 29 Copynumber: 7.8 Consensus size: 29
360138 AGGCTTTTAC
*
360148 TGTAATTTATAAAAGTTTTGGGCCATTTT
1 TGTAATTTATAAAAGTTTTGGGCCATTAT
360177 TGTAATTT-TAAAAGTTTTGGGCCATTAT
1 TGTAATTTATAAAAGTTTTGGGCCATTAT
* *
360205 TGTAATTTGTAAAAGTTTTGGTCCATTAT
1 TGTAATTTATAAAAGTTTTGGGCCATTAT
* *
360234 T-TAATTTGTAAAA-TTTTGAG-CATTAT
1 TGTAATTTATAAAAGTTTTGGGCCATTAT
* *
360260 TGTAATTTATAAAAGTTTTGGGCAACTAT
1 TGTAATTTATAAAAGTTTTGGGCCATTAT
* *
360289 TGTAATTTATAAAAGTTTTGGGCAACTAT
1 TGTAATTTATAAAAGTTTTGGGCCATTAT
* * **
360318 TATAATTTATAAAAATTTTGGGTAATTAT
1 TGTAATTTATAAAAGTTTTGGGCCATTAT
* *
360347 TATAATTTAT-AAACTTTTGGG
1 TGTAATTTATAAAAGTTTTGGG
360368 TATTATCGAC
Statistics
Matches: 174, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
26 7 0.04
27 16 0.09
28 55 0.32
29 96 0.55
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (29 bp):
TGTAATTTATAAAAGTTTTGGGCCATTAT
Found at i:363147 original size:27 final size:27
Alignment explanation
Indices: 363117--363174 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
363107 AAATGAATAA
363117 GACTAGCATATTTATAGATTTTGAAGG
1 GACTAGCATATTTATAGATTTTGAAGG
363144 GACTAGCATATTTATAGATTTTGAAGG
1 GACTAGCATATTTATAGATTTTGAAGG
363171 GACT
1 GACT
363175 TGGCCGAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (27 bp):
GACTAGCATATTTATAGATTTTGAAGG
Found at i:366303 original size:16 final size:16
Alignment explanation
Indices: 366278--366317 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
366268 ATTAACGTAT
*
366278 AAGTGTTATTCTCTCA
1 AAGTGCTATTCTCTCA
366294 AAGTGCTATTCTCTCA
1 AAGTGCTATTCTCTCA
366310 AAGTGCTA
1 AAGTGCTA
366318 ATAATAGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (16 bp):
AAGTGCTATTCTCTCA
Found at i:368168 original size:3 final size:3
Alignment explanation
Indices: 368160--368189 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
368150 TTTTGTATTT
368160 TTG TTG TTG TTG TTG TTG TTG TATG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG T-TG TTG TT
368190 TCTTCCACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.03, C:0.00, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:370161 original size:22 final size:22
Alignment explanation
Indices: 370136--370187 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
370126 CTTGCTGTTC
370136 ATATTGTCTAGTTCTTCTTTCA
1 ATATTGTCTAGTTCTTCTTTCA
370158 ATATTGTCTAGTTCTTCTTTCA
1 ATATTGTCTAGTTCTTCTTTCA
370180 ATATTGTC
1 ATATTGTC
370188 CTTGACTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (22 bp):
ATATTGTCTAGTTCTTCTTTCA
Found at i:376573 original size:22 final size:21
Alignment explanation
Indices: 376541--376582 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
376531 CCTTCTCCAT
376541 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
376562 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
376583 TTCTGCATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:376595 original size:24 final size:22
Alignment explanation
Indices: 376546--376595 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
376536 TCCATTTCAT
*
376546 CATCAACACCATCAACTTCATC
1 CATCAACACCATCAACTGCATC
*
376568 CATCAAGACCATCAATTCTGCATC
1 CATCAACACCATCAA--CTGCATC
376592 CATC
1 CATC
376596 TCTATCCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.58
24 10 0.42
ACGTcount: A:0.34, C:0.38, G:0.04, T:0.24
Consensus pattern (22 bp):
CATCAACACCATCAACTGCATC
Found at i:376936 original size:29 final size:27
Alignment explanation
Indices: 376891--376955 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
376881 AAAAAGAAAG
*
376891 AAAAGAGAAAAAGAAGAAAAAATTTCAAA
1 AAAAGA-AAAAAAAAG-AAAAATTTCAAA
* *
376920 AAAAGAAAAGAAAAAGAAGAATTTCAGA
1 AAAAGAAAA-AAAAAGAAAAATTTCAAA
376948 AAAAGAAA
1 AAAAGAAA
376956 GCAAATCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 21 0.66
29 11 0.34
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.09
Consensus pattern (27 bp):
AAAAGAAAAAAAAAGAAAAATTTCAAA
Found at i:376943 original size:28 final size:26
Alignment explanation
Indices: 376899--376955 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
376889 AGAAAAGAGA
*
376899 AAAAGAAGAAAAAATTTCAAAAAAAG
1 AAAAGAAAAAAAAATTTCAAAAAAAG
*
376925 AAAAGAAAAAGAAGAATTTCAGAAAAAG
1 AAAAGAAAAA-AA-AATTTCAAAAAAAG
376953 AAA
1 AAA
376956 GCAAATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 9 0.33
27 2 0.07
28 16 0.59
ACGTcount: A:0.72, C:0.04, G:0.14, T:0.11
Consensus pattern (26 bp):
AAAAGAAAAAAAAATTTCAAAAAAAG
Found at i:379813 original size:20 final size:20
Alignment explanation
Indices: 379788--379830 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
379778 TCTAAGAGCC
* *
379788 CATTTAGGATCATTTAGATG
1 CATTTAGGAGCATATAGATG
*
379808 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
379828 CAT
1 CAT
379831 GAGGTAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:387861 original size:10 final size:10
Alignment explanation
Indices: 387846--387870 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
387836 CCCTTTCTAA
387846 AAAAAGAAAG
1 AAAAAGAAAG
387856 AAAAAGAAAG
1 AAAAAGAAAG
387866 AAAAA
1 AAAAA
387871 AAACAACGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:388536 original size:27 final size:27
Alignment explanation
Indices: 388498--388550 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
388488 GCTGTTCACG
388498 GGATCTCTGATCATGACCGAGAAATCC
1 GGATCTCTGATCATGACCGAGAAATCC
388525 GGATCTCTGATCATGACCGAGAAATC
1 GGATCTCTGATCATGACCGAGAAATC
388551 TGCCTGGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (27 bp):
GGATCTCTGATCATGACCGAGAAATCC
Found at i:389777 original size:18 final size:19
Alignment explanation
Indices: 389732--389783 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
389722 ATTGCACTAC
389732 CATCATTCTATTTTCGCAT
1 CATCATTCTATTTTCGCAT
389751 CAGTCATTCTATTTT-GCCA-
1 CA-TCATTCTATTTTCG-CAT
389770 CATCATTCTCATTT
1 CATCATTCT-ATTT
389784 GTATATACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.23
19 9 0.30
20 14 0.47
ACGTcount: A:0.21, C:0.27, G:0.06, T:0.46
Consensus pattern (19 bp):
CATCATTCTATTTTCGCAT
Found at i:389784 original size:18 final size:19
Alignment explanation
Indices: 389732--389784 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 19
389722 ATTGCACTAC
*
389732 CATCATTCTATTTTCGCAT
1 CATCATTCTATTTGCGCAT
389751 CAGTCATTCTATTTTGC-CA-
1 CA-TCATTCTA-TTTGCGCAT
389770 CATCATTCTCATTTG
1 CATCATTCT-ATTTG
389785 TATATACCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 11 0.37
19 5 0.17
20 10 0.33
21 4 0.13
ACGTcount: A:0.21, C:0.26, G:0.08, T:0.45
Consensus pattern (19 bp):
CATCATTCTATTTGCGCAT
Found at i:390890 original size:22 final size:21
Alignment explanation
Indices: 390853--390894 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
390843 CCATCCCCAT
390853 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
390874 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
390895 TTTTGCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:399536 original size:21 final size:20
Alignment explanation
Indices: 399512--399550 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
399502 TTTAATGTTG
*
399512 TATGATGGTAATATTTTCTGA
1 TATGATGGAAAT-TTTTCTGA
*
399533 TATGGTGGAAATTTTTCT
1 TATGATGGAAATTTTTCT
399551 TGAGGTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (20 bp):
TATGATGGAAATTTTTCTGA
Found at i:405381 original size:20 final size:20
Alignment explanation
Indices: 405348--405386 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
405338 GGTCTACGCG
*
405348 ATCCTTCGGGACATATATGT
1 ATCCTTCGGAACATATATGT
* *
405368 ATCCTTTGGAACATCTATG
1 ATCCTTCGGAACATATATG
405387 AGGTCCTTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (20 bp):
ATCCTTCGGAACATATATGT
Found at i:405502 original size:23 final size:21
Alignment explanation
Indices: 405471--405541 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 21
405461 GGACATCTTA
405471 TATGGCACTTCGGTGCATTTC
1 TATGGCACTTCGGTGCATTTC
*
405492 TATGCGACACTTCGGTGCAATTC
1 TATG-G-CACTTCGGTGCATTTC
* *
405515 TACTTGGCAATTCGGTGCATTTA
1 TA--TGGCACTTCGGTGCATTTC
405538 TATG
1 TATG
405542 AGTTGTGGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 6 0.14
22 1 0.02
23 32 0.76
24 1 0.02
25 2 0.05
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (21 bp):
TATGGCACTTCGGTGCATTTC
Found at i:409913 original size:59 final size:59
Alignment explanation
Indices: 409793--409931 Score: 176
Period size: 59 Copynumber: 2.3 Consensus size: 59
409783 AACATAATGA
* *
409793 ATAGTCGAGTGACCATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGTAACTCCCT
1 ATAGTCGGGTGACCA-TTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACTCCCT
* *
409853 ATAGTCGGGTGACCATTTGTAACTTTTAATAGTCATA-TGACTCAACAAAGCAA-TATCCT
1 ATAGTCGGGTGACCATTTGTAACTTTTAATAGTCA-AGAGACTCAACAAAGCAACT-CCCT
*
409912 ATAGTCAAGG-GACCATTTGT
1 ATAGTC-GGGTGACCATTTGT
409932 GTACTTTACC
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
58 1 0.01
59 53 0.75
60 17 0.24
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (59 bp):
ATAGTCGGGTGACCATTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACTCCCT
Found at i:413163 original size:60 final size:60
Alignment explanation
Indices: 413048--413166 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
413038 TTTCATCATA
* * * ** * **
413048 TATCCTCAAAGTATGACTCTCATTTTAAATTAGTCCCTAAACTTTTAAATGTTCCAATTT
1 TATCCCCAAAATATGACTCTAATTCAAAATTAGTCCCTAAACTTCTAAACATTCCAATTT
* *
413108 TATCCCCAAAATATGACTCTAATTCAAAATTAGTCCTTAAACTTCTGAACATTCCAATT
1 TATCCCCAAAATATGACTCTAATTCAAAATTAGTCCCTAAACTTCTAAACATTCCAATT
413167 ACATCCCAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (60 bp):
TATCCCCAAAATATGACTCTAATTCAAAATTAGTCCCTAAACTTCTAAACATTCCAATTT
Found at i:413404 original size:19 final size:19
Alignment explanation
Indices: 413380--413419 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
413370 GTTTAAGGAC
413380 TAGTTT-AGAATGAGAATTA
1 TAGTTTGAGAATGA-AATTA
*
413399 TAGTTTGGGAATGAAATTA
1 TAGTTTGAGAATGAAATTA
413418 TA
1 TA
413420 ATATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (19 bp):
TAGTTTGAGAATGAAATTA
Found at i:413452 original size:60 final size:60
Alignment explanation
Indices: 413303--413460 Score: 155
Period size: 60 Copynumber: 2.6 Consensus size: 60
413293 AAGTGGAATA
** * * * *
413303 TTCAAAAGTTCGAGGACCAA-TTTAGAAAGAGGGTCATAGTTTAGGGATAAAATTATAATT
1 TTCAAAAGTTTAAGGA-CAAGTTTAGAATGAAGATTATAGTTTAGGGATAAAATTATAATT
* *
413363 TTCAAAAGTTTAAGGACTAGTTTAGAATG-AGAATTATAGTTT-GGGAATGAAATTATAATAT
1 TTCAAAAGTTTAAGGACAAGTTTAGAATGAAG-ATTATAGTTTAGGG-ATAAAATTATAAT-T
*
413424 TT-AAAAGTTTAAGGATCAATTTTA-AATGAAGATTATA
1 TTCAAAAGTTTAAGGA-CAAGTTTAGAATGAAGATTATA
413461 ATTAGAGGAC
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
59 6 0.07
60 65 0.79
61 11 0.13
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (60 bp):
TTCAAAAGTTTAAGGACAAGTTTAGAATGAAGATTATAGTTTAGGGATAAAATTATAATT
Found at i:415450 original size:18 final size:19
Alignment explanation
Indices: 415415--415451 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
415405 CATGGAATGT
415415 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
415435 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
415452 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:422111 original size:42 final size:43
Alignment explanation
Indices: 422039--422153 Score: 160
Period size: 43 Copynumber: 2.7 Consensus size: 43
422029 TAGGAGTTTG
* * *
422039 ATTATAAAGGTAAAAAGTGGGACTGTAAAAA-TTAAGGGTCTCA
1 ATTATAAAGGTAAAAAGTGGGATTG-AAAAAGCTAAGGGCCTCA
* *
422082 ATTATAAAGGTAAAAAGTGGGATTGAAAAAGCTAGGGGCCTCG
1 ATTATAAAGGTAAAAAGTGGGATTGAAAAAGCTAAGGGCCTCA
*
422125 ATTATAAAGGTAAAAGGTGGGATTGAAAA
1 ATTATAAAGGTAAAAAGTGGGATTGAAAA
422154 TCCTTTGAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 5 0.08
43 60 0.92
ACGTcount: A:0.43, C:0.06, G:0.27, T:0.23
Consensus pattern (43 bp):
ATTATAAAGGTAAAAAGTGGGATTGAAAAAGCTAAGGGCCTCA
Found at i:424154 original size:54 final size:54
Alignment explanation
Indices: 424095--424259 Score: 312
Period size: 54 Copynumber: 3.1 Consensus size: 54
424085 TTTTTCTTAG
*
424095 AATTTTATATGTTGGTCGTTCCTTAAAGTTTAAAAATTTACCATCCTAACATAA
1 AATTTTATATGTTGGCCGTTCCTTAAAGTTTAAAAATTTACCATCCTAACATAA
424149 AATTTTATATGTTGGCCGTTCCTTAAAGTTTAAAAATTTACCATCCTAACATAA
1 AATTTTATATGTTGGCCGTTCCTTAAAGTTTAAAAATTTACCATCCTAACATAA
*
424203 AATTTTATATGTTGGCCGTTTCTTAAAGTTTAAAAATTTACCATCCTAACATAA
1 AATTTTATATGTTGGCCGTTCCTTAAAGTTTAAAAATTTACCATCCTAACATAA
424257 AAT
1 AAT
424260 CTGCATATGT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (54 bp):
AATTTTATATGTTGGCCGTTCCTTAAAGTTTAAAAATTTACCATCCTAACATAA
Found at i:425301 original size:24 final size:24
Alignment explanation
Indices: 425273--425323 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
425263 CGGTAATATA
*
425273 TTCGTTTATGTTCGTACATTTATG
1 TTCGTTTATGTTCATACATTTATG
* *
425297 TTCGTTTATGTTTATTCATTTATG
1 TTCGTTTATGTTCATACATTTATG
425321 TTC
1 TTC
425324 ATTATGTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.59
Consensus pattern (24 bp):
TTCGTTTATGTTCATACATTTATG
Found at i:425607 original size:23 final size:23
Alignment explanation
Indices: 425533--425623 Score: 94
Period size: 23 Copynumber: 3.9 Consensus size: 23
425523 TTTTCATTTA
** *
425533 TGTTCGTTTATATTCATTTATTG
1 TGTTCGTTTACGTTCGTTTATTG
*
425556 TGTTCGTTTACGTTTGTTCGT-TTG
1 TGTTCGTTTACGTTCGTT--TATTG
*
425580 TGTTCGTTAACGTTCGTTTATTG
1 TGTTCGTTTACGTTCGTTTATTG
* *
425603 TGTTCATTTATGTTCGTTTAT
1 TGTTCGTTTACGTTCGTTTAT
425624 ATCCGTTCGT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.02
23 35 0.62
24 19 0.34
25 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.58
Consensus pattern (23 bp):
TGTTCGTTTACGTTCGTTTATTG
Found at i:428189 original size:20 final size:20
Alignment explanation
Indices: 428164--428201 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
428154 TGGGTTAGAG
428164 TATCGATATTGGATGAACAT
1 TATCGATATTGGATGAACAT
428184 TATCGATATTGGATGAAC
1 TATCGATATTGGATGAAC
428202 TGGGACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
TATCGATATTGGATGAACAT
Found at i:430792 original size:19 final size:19
Alignment explanation
Indices: 430768--430838 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
430758 AATAGCCAGA
430768 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
430787 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
430806 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
430825 GTGCATCGATGCAT
1 GTGCATCGATGCAT
430839 TCGATGTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:430886 original size:19 final size:19
Alignment explanation
Indices: 430862--430914 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
430852 AAAACACTAA
430862 GTGCATCGATGCATAGTAT
1 GTGCATCGATGCATAGTAT
430881 GTGCATCGATGCATAGTAT
1 GTGCATCGATGCATAGTAT
*
430900 GTGCATCAATGCATA
1 GTGCATCGATGCATA
430915 AAATGCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATAGTAT
Found at i:432017 original size:23 final size:23
Alignment explanation
Indices: 431987--432035 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
431977 TGCATGGCCT
431987 TGTGCATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
* * *
432010 TGTGCATCGGTGCACCTTCATGG
1 TGTGCATCGATGCACATTCAAGG
432033 TGT
1 TGT
432036 ATTATCGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (23 bp):
TGTGCATCGATGCACATTCAAGG
Found at i:437970 original size:19 final size:19
Alignment explanation
Indices: 437946--437982 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
437936 CATAAAACTC
437946 TATGTGCATCGATGCATAG
1 TATGTGCATCGATGCATAG
437965 TATGTGCATCGATGCATA
1 TATGTGCATCGATGCATA
437983 AAATGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (19 bp):
TATGTGCATCGATGCATAG
Found at i:439711 original size:21 final size:23
Alignment explanation
Indices: 439666--439717 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
439656 ACGTATAATT
*
439666 ATAAATTAGTTAAAAATCTAAAG
1 ATAAATTAGTTAAAAATCAAAAG
*
439689 ATAAATTA-TTTAAAAT-AAAAG
1 ATAAATTAGTTAAAAATCAAAAG
*
439710 ATTAATTA
1 ATAAATTA
439718 CATCATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 11 0.42
22 7 0.27
23 8 0.31
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (23 bp):
ATAAATTAGTTAAAAATCAAAAG
Found at i:440496 original size:2 final size:2
Alignment explanation
Indices: 440489--440528 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
440479 TTAGTTATTA
440489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
440529 TTAAAATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:444214 original size:27 final size:26
Alignment explanation
Indices: 444181--444232 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
444171 TTTTACAAAA
444181 ATTCAATATAATCCCTAAATTTTTTAC
1 ATTCAATATAAT-CCTAAATTTTTTAC
* *
444208 ATTCAATATAGTCCTTAATTTTTTA
1 ATTCAATATAATCCTAAATTTTTTA
444233 ATAATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTCAATATAATCCTAAATTTTTTAC
Found at i:452180 original size:62 final size:62
Alignment explanation
Indices: 452107--452232 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
452097 AAATTAAAAC
452107 ATGTAAAAGTTTATAGACTAATTTAAATTAAAAATCATAATTTCAAAATATGTGATACAATA
1 ATGTAAAAGTTTATAGACTAATTTAAATTAAAAATCATAATTTCAAAATATGTGATACAATA
452169 ATGTAAAAGTTTATAGACTAATTTAAATTAAAAATCATAATTTCAAAATATGTGATACAATA
1 ATGTAAAAGTTTATAGACTAATTTAAATTAAAAATCATAATTTCAAAATATGTGATACAATA
452231 AT
1 AT
452233 TATTTTCTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (62 bp):
ATGTAAAAGTTTATAGACTAATTTAAATTAAAAATCATAATTTCAAAATATGTGATACAATA
Found at i:457244 original size:29 final size:30
Alignment explanation
Indices: 457211--457268 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
457201 GGACAGAGCT
*
457211 AGAAAATTTA-TTTTGGGTGTCAAATTTAA
1 AGAAAATTTACTTTTGGGTGTAAAATTTAA
457240 AGAAAATTTACTTTTGGGTGTAAAATTTA
1 AGAAAATTTACTTTTGGGTGTAAAATTTA
457269 GAAATTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.41
Consensus pattern (30 bp):
AGAAAATTTACTTTTGGGTGTAAAATTTAA
Found at i:465903 original size:19 final size:19
Alignment explanation
Indices: 465875--465914 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
465865 TTGATTCAGA
* *
465875 TCGGTTTGACTGGACTGGT
1 TCGGTCTGACTGGACCGGT
465894 TCGGTCTGACTGGACCGGT
1 TCGGTCTGACTGGACCGGT
465913 TC
1 TC
465915 CAAAAGCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.35, T:0.33
Consensus pattern (19 bp):
TCGGTCTGACTGGACCGGT
Found at i:472264 original size:16 final size:16
Alignment explanation
Indices: 472218--472267 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
472208 AATAACAAGA
* *
472218 TGATTTTTTTATTGAT
1 TGATTTGTTTATTAAT
* * *
472234 TCATGTGTTTGTTAAT
1 TGATTTGTTTATTAAT
472250 TGATTTGTTTATTAAT
1 TGATTTGTTTATTAAT
472266 TG
1 TG
472268 GCGAAAAGAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.62
Consensus pattern (16 bp):
TGATTTGTTTATTAAT
Found at i:476260 original size:2 final size:2
Alignment explanation
Indices: 476253--476288 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
476243 ACCATATACA
476253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
476289 TCTTCATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:484754 original size:43 final size:43
Alignment explanation
Indices: 484668--484983 Score: 209
Period size: 43 Copynumber: 7.4 Consensus size: 43
484658 CTATTACGAT
* * *
484668 GTTTTTTGAACAAACGCCGCAAAAGGTCGAT-ATCTATAACGGC
1 GTTTTTGGAACAAACGCCGCAAAAAGTC-ATGATCTATAGCGGC
* * *
484711 GTTTTTGGAATAAACGCCGCAAAAAGTTATGATATATAGCGGC
1 GTTTTTGGAACAAACGCCGCAAAAAGTCATGATCTATAGCGGC
* * *
484754 GTTTCTAGAAAAAAACGCCGCAAAAAGTCA-GATCTATAGCGGC
1 GTTT-TTGGAACAAACGCCGCAAAAAGTCATGATCTATAGCGGC
* * *
484797 GTTTTTGGATACAAACGTCGCAAAAGAG--AAGACCTATA-CTGGC
1 GTTTTTGGA-ACAAACGCCGCAAAA-AGTCATGATCTATAGC-GGC
* * * ** * * * * * *
484840 ATTTTTAGAATAAACGCCGTTATAGGTC-TAACCTTTTGCGGC
1 GTTTTTGGAACAAACGCCGCAAAAAGTCATGATCTATAGCGGC
* * * ** *
484882 GTTTTTAGACACAAACGCCGCAAAAGGTTA-GGCCTATAACGGC
1 GTTTTTGGA-ACAAACGCCGCAAAAAGTCATGATCTATAGCGGC
** *
484925 G-TTTTAAACACAAACGCCGCAAAAAGTCA-GACCTATAGCGGC
1 GTTTTTGGA-ACAAACGCCGCAAAAAGTCATGATCTATAGCGGC
484967 GTTTTTGGATACAAACG
1 GTTTTTGGA-ACAAACG
484984 TCGCTAATTA
Statistics
Matches: 214, Mismatches: 47, Indels: 24
0.75 0.16 0.08
Matches are distributed among these distances:
41 1 0.00
42 70 0.33
43 120 0.56
44 23 0.11
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (43 bp):
GTTTTTGGAACAAACGCCGCAAAAAGTCATGATCTATAGCGGC
Found at i:484966 original size:85 final size:85
Alignment explanation
Indices: 484676--484983 Score: 270
Period size: 85 Copynumber: 3.6 Consensus size: 85
484666 ATGTTTTTTG
* * * * * *
484676 AACAAACGCCGCAAAAGGTCGATATCTATAACGGCGTTTTTGGA-ATAAACGCCGCAAAAAGTTA
1 AACAAACGCCGCAAAAAGTCGAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTTA
* *
484740 TG-ATATATAGCGGCGTTTCTAGA
66 GGCCTATA-A-CGGCGTTT-TA-A
* * * *
484763 AAAAAACGCCGCAAAAAGTC-AGATCTATAGCGGCGTTTTTGGATACAAACGTCGCAAAAGAG-A
1 AACAAACGCCGCAAAAAGTCGAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAG-GTT
* * *
484826 AGACCTAT-ACTGGCATTTTTAG
65 AGGCCTATAAC-GGC-GTTTTAA
* ** * * * * * * *
484848 AATAAACGCCGTTATAGGTCTA-ACCTTTTGCGGCGTTTTTAGACACAAACGCCGCAAAAGGTTA
1 AACAAACGCCGCAAAAAGTCGAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTTA
484912 GGCCTATAACGGCGTTTTAA
66 GGCCTATAACGGCGTTTTAA
484932 ACACAAACGCCGCAAAAAGTC-AGACCTATAGCGGCGTTTTTGGATACAAACG
1 A-ACAAACGCCGCAAAAAGTCGAGACCTATAGCGGCGTTTTTGGATACAAACG
484984 TCGCTAATTA
Statistics
Matches: 174, Mismatches: 37, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
84 8 0.05
85 97 0.56
86 30 0.17
87 35 0.20
88 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (85 bp):
AACAAACGCCGCAAAAAGTCGAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTTA
GGCCTATAACGGCGTTTTAA
Found at i:486461 original size:80 final size:79
Alignment explanation
Indices: 486350--486513 Score: 256
Period size: 80 Copynumber: 2.1 Consensus size: 79
486340 ACGGAATCCC
* * *
486350 TGCAAGTAATATGAAGGACTAAACTTCTCAATTTACATTCAGGTCAAATTGATAACAGATATTTA
1 TGCAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGATAACAAATATTTA
*
486415 CAGACCACTGCTAAT
66 -AGACAACTGCTAAT
* *
486430 TGCAAGTAAAATGAAGGACTAAACTTCTCAATTTTCATTCAGATCAAATTTATAACAAATATTTA
1 TGCAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGATAACAAATATTTA
*
486495 AGACAACTGCTCAT
66 AGACAACTGCTAAT
486509 TGCAA
1 TGCAA
486514 CATAATCTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 17 0.22
80 60 0.78
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (79 bp):
TGCAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGATAACAAATATTTA
AGACAACTGCTAAT
Found at i:488675 original size:41 final size:41
Alignment explanation
Indices: 488630--488819 Score: 267
Period size: 41 Copynumber: 4.6 Consensus size: 41
488620 ATGTGTATAA
* * *
488630 CGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTAG
* * * *
488671 CGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTAG
*
488712 CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTAG
488753 CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTA-
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTC-TTTAG
488794 CGGCGTTTGT-TGAAAAAACGCCACTA
1 CGGCGTTTGTAT--AAAAACGCCACTA
488820 TCGATGAACC
Statistics
Matches: 135, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 118 0.87
42 16 0.12
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (41 bp):
CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTAG
Found at i:488756 original size:82 final size:82
Alignment explanation
Indices: 488629--488853 Score: 269
Period size: 82 Copynumber: 2.7 Consensus size: 82
488619 AATGTGTATA
* *
488629 ACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCAC
1 ACGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCAC
* *
488694 TAAATTACGAGTC-TTT
66 TAAAGTACGACTCTTTT
* * *
488710 AGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGTATAAAAACGCCA
1 A-CGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCA
*
488775 CTAAAGTACTACTCTTTT
65 CTAAAGTACGACTCTTTT
** * * *
488793 ACGGCGTTTGT-TGAAAAAACGCCACTATCG-ATGAAC-CTATTGCGGCGTTTTTATAAAAACG
1 ACGGCGTTTGTAT--AAAAACGCCACTAAAGTA-CAACTCTATAGCGGCGTTTGTATAAAAACG
488854 ATGCTAAAGT
Statistics
Matches: 125, Mismatches: 14, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
81 2 0.02
82 103 0.82
83 20 0.16
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (82 bp):
ACGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCAC
TAAAGTACGACTCTTTT
Found at i:488838 original size:123 final size:122
Alignment explanation
Indices: 488630--488853 Score: 285
Period size: 123 Copynumber: 1.8 Consensus size: 122
488620 ATGTGTATAA
* *
488630 CGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACT
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCACT
* **
488695 AAATTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTG
66 -AATGACGAACCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTG
* *
488753 CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTA-CGGCGTTTGT-TGAAAAAACGCC
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACAACTC-TATAGCGGCGTTTGTAT--AAAAACGCC
* *
488816 ACT-ATCGATGAACCTATT-GCGGCGTTTTTATAAAAACG
63 ACTAAT-GACGAACCT-TTAGCGGCGTTTGTATAAAAACG
488854 ATGCTAAAGT
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
122 3 0.03
123 68 0.78
124 16 0.18
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (122 bp):
CGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCACT
AATGACGAACCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTG
Found at i:500261 original size:9 final size:9
Alignment explanation
Indices: 500209--500264 Score: 60
Period size: 9 Copynumber: 6.0 Consensus size: 9
500199 TAAAAAGGTG
*
500209 AAAAAGGAA
1 AAAAATGAA
500218 AAAAATGAA
1 AAAAATGAA
*
500227 AAAAAAGAA
1 AAAAATGAA
500236 AAAAA-GAAAGA
1 AAAAATG--A-A
500247 AAAAATGAA
1 AAAAATGAA
500256 AAAAATGAA
1 AAAAATGAA
500265 GAGAGAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 1 0.02
9 31 0.76
10 2 0.05
11 6 0.15
12 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.05
Consensus pattern (9 bp):
AAAAATGAA
Found at i:501650 original size:91 final size:91
Alignment explanation
Indices: 501495--501753 Score: 389
Period size: 91 Copynumber: 2.9 Consensus size: 91
501485 TGGATCAATA
* * *
501495 TTTCCAAT-AATGAGTTTATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAG
1 TTTCCAATGAA-GAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAAAAGTTCATAATGAG
*
501559 AAGAACTTGTTCAACCTTGCATCAGTG
65 AAGAACTTGTTCAACCTTACATCAGTG
*
501586 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAAAAGTTCATAATGAGA
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAAAAGTTCATAATGAGA
501651 AGAACTTGTTCAACCTTACATCAGTG
66 AGAACTTGTTCAACCTTACATCAGTG
** * * *
501677 TTTTTAGTGAAGAGTTCATAATGAGAAGAACTCATTCACAAGA-G-AGAATAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCA-AAGAGGAAGAAAAAGTTCATAATGAG
501740 AAGAACTTGTTCAA
65 AAGAACTTGTTCAA
501754 TTTACCAACG
Statistics
Matches: 155, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
90 32 0.21
91 118 0.76
92 5 0.03
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (91 bp):
TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAAAAGTTCATAATGAGA
AGAACTTGTTCAACCTTACATCAGTG
Found at i:501661 original size:20 final size:20
Alignment explanation
Indices: 501598--501662 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
501588 TCCAATGGAG
501598 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
501618 CA-TCCA-AA-GAGGAAGAAAA
1 -AGTTCATAATGA-GAAGAACT
501637 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
501657 TGTTCA
1 AGTTCA
501663 ACCTTACATC
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:501751 original size:20 final size:20
Alignment explanation
Indices: 501689--501752 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
501679 TTTAGTGAAG
501689 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
501709 CA-TTCACAA-GAG-AGAA-T
1 -AGTTCATAATGAGAAGAACT
501726 AAGTTCATAATGAGAAGAACT
1 -AGTTCATAATGAGAAGAACT
*
501747 TGTTCA
1 AGTTCA
501753 ATTTACCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
17 2 0.06
18 10 0.29
19 6 0.17
20 15 0.43
21 2 0.06
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:501890 original size:3 final size:3
Alignment explanation
Indices: 501882--501973 Score: 114
Period size: 3 Copynumber: 30.7 Consensus size: 3
501872 TAAAAATATA
* * * *
501882 TAT TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TTT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
501930 TAT TAT TAT AAT AAT TAT TAT TAT TA- TATT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA
501974 ATAAAATTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.03
3 75 0.95
4 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:501930 original size:33 final size:33
Alignment explanation
Indices: 501882--501977 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
501872 TAAAAATATA
* *
501882 TATTATTATTATTATTATTATAATAATTATTAT
1 TATTATTATTTTTATTATTATAATAATAATTAT
* *
501915 TTTTATTATTTTTATTATTATTATAATAATTAT
1 TATTATTATTTTTATTATTATAATAATAATTAT
* *
501948 TATTATTATATTTATTATTATTATTAATAA
1 TATTATTATTTTTATTATTA-TAATAATAA
501978 AATTTTAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
33 47 0.87
34 7 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TATTATTATTTTTATTATTATAATAATAATTAT
Found at i:501930 original size:36 final size:36
Alignment explanation
Indices: 501882--501981 Score: 150
Period size: 36 Copynumber: 2.8 Consensus size: 36
501872 TAAAAATATA
* *
501882 TATTATTATTATTATTATTATAATAATTATTATTTT
1 TATTATTTTTATTATTATTATAATAATTATTATTAT
501918 TATTATTTTTATTATTATTATAATAATTATTATTAT
1 TATTATTTTTATTATTATTATAATAATTATTATTAT
501954 TA-TATTTATTATTATTATTAATAA-AATT
1 TATTATTT-TTATTATTATT-ATAATAATT
501982 TTAATACATA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
35 5 0.08
36 51 0.85
37 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (36 bp):
TATTATTTTTATTATTATTATAATAATTATTATTAT
Found at i:504167 original size:18 final size:18
Alignment explanation
Indices: 504139--504182 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
504129 GTTTTTCTTG
504139 TTTGA-TTGTTCATATTC
1 TTTGAGTTGTTCATATTC
*
504156 TTTGAGTTGTTCATCTTC
1 TTTGAGTTGTTCATATTC
*
504174 TATGAGTTG
1 TTTGAGTTG
504183 AGAACTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (18 bp):
TTTGAGTTGTTCATATTC
Found at i:510478 original size:15 final size:15
Alignment explanation
Indices: 510458--510494 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
510448 GTTGTTAAGG
510458 TTAGTTACCTTGAGA
1 TTAGTTACCTTGAGA
510473 TTAGTTACCTTGAGA
1 TTAGTTACCTTGAGA
510488 TTAGTTA
1 TTAGTTA
510495 GCTAGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (15 bp):
TTAGTTACCTTGAGA
Found at i:511499 original size:17 final size:17
Alignment explanation
Indices: 511464--511501 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
511454 AAATATTATT
511464 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
*
511481 TTATT-TTTATATTTTAA
1 TTATTATTTAT-TTTAAA
511498 TTAT
1 TTAT
511502 GATAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:512358 original size:65 final size:63
Alignment explanation
Indices: 512213--512366 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 63
512203 ACCCTAATTT
* * * *
512213 GAATGCATTTTATGTACCGATGCACAACCATGCATCGATGCACTCTTGTTTTTATTGAAACATC
1 GAAT-CATATTATGTACCGATGCACAACCATGCATCGATGCACTCTGGCTCTTATTGAAACATC
* *
512277 GAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCATTCCTGGCTCTT-TTGAAACAT
1 GAAT-CATATTATGTACCGATGCACA-ACCATGCATCGATGCACT-CTGGCTCTTATTGAAACAT
*
512341 T
63 C
512342 GAAT-ATAATTAGTGTACCGATGCAC
1 GAATCAT-ATTA-TGTACCGATGCAC
512367 CCCAAGTTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
63 2 0.03
64 29 0.36
65 43 0.54
66 6 0.08
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (63 bp):
GAATCATATTATGTACCGATGCACAACCATGCATCGATGCACTCTGGCTCTTATTGAAACATC
Found at i:515464 original size:19 final size:17
Alignment explanation
Indices: 515417--515464 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
515407 TTATACACTC
515417 TTTTTATTTTTTTTATA
1 TTTTTATTTTTTTTATA
*
515434 TTCTTTGTTTTTTTTTAATA
1 TT-TTT-ATTTTTTTT-ATA
*
515454 TTTTTACTTTT
1 TTTTTATTTTT
515465 AGTTTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.08
18 7 0.28
19 11 0.44
20 5 0.20
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTATTTTTTTTATA
Found at i:515528 original size:25 final size:25
Alignment explanation
Indices: 515468--515520 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
515458 TACTTTTAGT
* *
515468 TTATTATTATTATTTCGTTTGTTTA
1 TTATTATTATTATTTCATTTATTTA
515493 TTATTATTATTATTTCATTTATGTTA
1 TTATTATTATTATTTCATTTAT-TTA
515519 TT
1 TT
515521 TATTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.68
Consensus pattern (25 bp):
TTATTATTATTATTTCATTTATTTA
Found at i:515587 original size:3 final size:3
Alignment explanation
Indices: 515579--515622 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
515569 ATTTCTCCCT
**
515579 TTA TTA TTA TTA TTA TTA TCG TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
515623 GTTTTACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:518163 original size:2 final size:2
Alignment explanation
Indices: 518158--518193 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
518148 ATAATTATTA
518158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
518194 GCAATAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.