Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000880.1 Hibiscus syriacus cultivar Beakdansim tig00001713_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: 1459553
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:308819 original size:60 final size:61
Alignment explanation
Indices: 308693--308840 Score: 167
Period size: 60 Copynumber: 2.4 Consensus size: 61
308683 GAGGTGGCAC
* * * **
308693 AAAGGTGCATCCTCGGGGACGCGCTTTACCTGGGTTTATGCTGAGTCGGATGCCACGCGGG
1 AAAGGCGCATCCTCGGGGACGCACTTTACCTGGGTTTATGCTGAGTCAGATGCCACAAGGG
* *
308754 AAAGGCGCATCCTTGGGGACGCACTTT-CAC-GGGATTT-TGCTGAGTCAGATGCCATAAGGG
1 AAAGGCGCATCCTCGGGGACGCACTTTAC-CTGGG-TTTATGCTGAGTCAGATGCCACAAGGG
* * *
308814 TAAGGCACATCCCCGGGGACGCACTTT
1 AAAGGCGCATCCTCGGGGACGCACTTT
308841 TCATTAATTG
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
60 46 0.62
61 28 0.38
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.22
Consensus pattern (61 bp):
AAAGGCGCATCCTCGGGGACGCACTTTACCTGGGTTTATGCTGAGTCAGATGCCACAAGGG
Found at i:308983 original size:24 final size:24
Alignment explanation
Indices: 308956--309001 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
308946 TTATTAATTG
308956 TTATATTTTATATTAATATAATCA
1 TTATATTTTATATTAATATAATCA
308980 TTATATTTTATATTAATATAAT
1 TTATATTTTATATTAATATAAT
309002 TATATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATATTTTATATTAATATAATCA
Found at i:309015 original size:32 final size:32
Alignment explanation
Indices: 308947--309031 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 32
308937 AAATCATTTT
*
308947 TATTA-ATTGTTATATT-TTAT-ATTAATATAA
1 TATTATATT-TTATATTAATATAATTAATATAA
308977 TCATTATATTTTATATTAATATAATT-ATATAAA
1 T-ATTATATTTTATATTAATATAATTAATAT-AA
*
309010 TATTAT-TTTT-TATTAAAATAAT
1 TATTATATTTTATATTAATATAAT
309032 ATTTATATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
30 12 0.25
31 15 0.31
32 15 0.31
33 6 0.12
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (32 bp):
TATTATATTTTATATTAATATAATTAATATAA
Found at i:309024 original size:30 final size:32
Alignment explanation
Indices: 308983--309055 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
308973 ATAATCATTA
*
308983 TATTTTATATT-AAT-ATAATTATATAAATAT
1 TATTTTTTATTAAATAATAATTATATAAATAT
* *
309013 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTTTATT-AAATAATAATTATATAAATAT
309046 TATTTATTTA
1 TATTT-TTTA
309056 AATTTATTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 10 0.28
32 3 0.08
33 19 0.53
34 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTTTTTATTAAATAATAATTATATAAATAT
Found at i:309047 original size:33 final size:30
Alignment explanation
Indices: 308964--309078 Score: 94
Period size: 32 Copynumber: 3.7 Consensus size: 30
308954 TGTTATATTT
* *
308964 TATATTAATATAATCATTATATTTTATATTAA
1 TATATTTATATAATTATTAT-TTTT-TATTAA
* *
308996 TATAATTATATAAATATTATTTTTTATTAAAA
1 TATATTTATATAATTATTATTTTTTATT--AA
309028 TAATATTTATATAATTATTATTTATTTA--AA
1 T-ATATTTATATAATTATTATTT-TTTATTAA
*
309058 TTTA-TTACT-TAATTATTATTT
1 TATATTTA-TATAATTATTATTT
309079 GTGCTAATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
28 15 0.21
29 3 0.04
30 7 0.10
31 4 0.06
32 19 0.27
33 19 0.27
34 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
TATATTTATATAATTATTATTTTTTATTAA
Found at i:309225 original size:24 final size:25
Alignment explanation
Indices: 309175--309231 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
309165 AGTGATATGG
*
309175 TAATATTT-TTTTTATAATTAATGT
1 TAATATTTATTATTATAATTAATGT
**
309199 TAATATTTATTATTATTTTTAAT-T
1 TAATATTTATTATTATAATTAATGT
309223 TAA-ATTTAT
1 TAATATTTAT
309232 CATGAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.21
24 12 0.41
25 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TAATATTTATTATTATAATTAATGT
Found at i:310891 original size:21 final size:21
Alignment explanation
Indices: 310867--310927 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
310857 TATCTCGTAG
* *
310867 GGTTACATTCCTAGCCCGCTA
1 GGTTACATGCCTAGCCCGCCA
**
310888 GGTTTTATGCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
310909 GGTTACATGCCTAGCCCGC
1 GGTTACATGCCTAGCCCGC
310928 AGGGTTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.16, C:0.34, G:0.23, T:0.26
Consensus pattern (21 bp):
GGTTACATGCCTAGCCCGCCA
Found at i:311482 original size:34 final size:34
Alignment explanation
Indices: 311443--311511 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
311433 ATGTTTTTAT
311443 AATACAAATTATAGTATTCAAAAATTAAAATTAA
1 AATACAAATTATAGTATTCAAAAATTAAAATTAA
* *
311477 AATACAAATTATAGTATTCAAAATTTAACATTAA
1 AATACAAATTATAGTATTCAAAAATTAAAATTAA
311511 A
1 A
311512 TTCAACTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (34 bp):
AATACAAATTATAGTATTCAAAAATTAAAATTAA
Found at i:311616 original size:14 final size:14
Alignment explanation
Indices: 311597--311627 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
311587 TTTTATCCTT
311597 AACATATACATTAA
1 AACATATACATTAA
311611 AACATATACATTAA
1 AACATATACATTAA
311625 AAC
1 AAC
311628 CCACGTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:313423 original size:22 final size:22
Alignment explanation
Indices: 313398--313441 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
313388 GTAAAATGAT
313398 TAATT-ATATTTATTTAATATAA
1 TAATTAATA-TTATTTAATATAA
*
313420 TAATTAATATTATTTATTATAA
1 TAATTAATATTATTTAATATAA
313442 AAATATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTAATATTATTTAATATAA
Found at i:313456 original size:22 final size:22
Alignment explanation
Indices: 313407--313452 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
313397 TTAATTATAT
*
313407 TTATTTAATATAATAATTAATA
1 TTATTTAATATAATAAATAATA
* *
313429 TTATTTATTATAA-AAATATTA
1 TTATTTAATATAATAAATAATA
313450 TTA
1 TTA
313453 ATTTTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTTAATATAATAAATAATA
Found at i:313463 original size:17 final size:18
Alignment explanation
Indices: 313425--313467 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
313415 TATAATAATT
*
313425 AATATTATTTATTATAAA
1 AATATTATTAATTATAAA
*
313443 AATATTATTAATT-TTAA
1 AATATTATTAATTATAAA
313460 AATATTAT
1 AATATTAT
313468 AATAATTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATTATTAATTATAAA
Found at i:313991 original size:19 final size:18
Alignment explanation
Indices: 313958--313993 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
313948 AACACTTTAC
*
313958 ATAATATATTAATAATTT
1 ATAATATAATAATAATTT
313976 ATAATAATAATAATAATT
1 ATAAT-ATAATAATAATT
313994 AAATCTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATATAATAATAATTT
Found at i:317092 original size:16 final size:16
Alignment explanation
Indices: 317071--317106 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
317061 TAACTCTCCC
317071 ACATATCATTGATAGT
1 ACATATCATTGATAGT
*
317087 ACATATTATTGATAGT
1 ACATATCATTGATAGT
317103 ACAT
1 ACAT
317107 TTTACTCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (16 bp):
ACATATCATTGATAGT
Found at i:323293 original size:101 final size:102
Alignment explanation
Indices: 323113--323341 Score: 259
Period size: 101 Copynumber: 2.3 Consensus size: 102
323103 TCTGATGTTT
* * ** *
323113 AGGTCGAACAAGTTCGCAGATGAATGCATTCCCCTTAAACTTGAAGGCATCGTGTCATATGCGTT
1 AGGTCGAACAAGTTGGCAGATGAATGCACTCCCCTTAAACTTGAAGGCATAATATCATATGCGTT
*
323178 TTGAATTAACTGTTGTGTCAAAGGCATCTCCATATTG
66 TTGAATCAACTGTTGTGTCAAAGGCATCTCCATATTG
* *
323215 AGGTCGAAGAAGTTGGCAAATGAATGC-CTCCCC-TAGAACTTGAAGGCATAATATCATATG-GT
1 AGGTCGAACAAGTTGGCAGATGAATGCACTCCCCTTA-AACTTGAAGGCATAATATCATATGCGT
* * * *
323277 TATTGAA-CAGATTGTTGTGTCGAATGCATCTCCATATTT
65 T-TTGAATCA-ACTGTTGTGTCAAAGGCATCTCCATATTG
* * * *
323316 ATGTCAAATAAATTGGCAGATGAATG
1 AGGTCGAACAAGTTGGCAGATGAATG
323342 TCTTCCCATT
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
100 6 0.06
101 77 0.72
102 24 0.22
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (102 bp):
AGGTCGAACAAGTTGGCAGATGAATGCACTCCCCTTAAACTTGAAGGCATAATATCATATGCGTT
TTGAATCAACTGTTGTGTCAAAGGCATCTCCATATTG
Found at i:324507 original size:15 final size:15
Alignment explanation
Indices: 324483--324524 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
324473 CAAAGTAGTA
*
324483 GCATCAGTACCAGGG
1 GCATCGGTACCAGGG
324498 GCATCGGTACCAGGG
1 GCATCGGTACCAGGG
* *
324513 GTATCGATACCA
1 GCATCGGTACCA
324525 ATGTTTAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.31, T:0.17
Consensus pattern (15 bp):
GCATCGGTACCAGGG
Found at i:325218 original size:14 final size:14
Alignment explanation
Indices: 325199--325233 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
325189 TTATATGAAC
325199 ATGTGATATAAGCT
1 ATGTGATATAAGCT
325213 ATGTGATATAAGCT
1 ATGTGATATAAGCT
325227 ATGTGAT
1 ATGTGAT
325234 GGGGTTGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (14 bp):
ATGTGATATAAGCT
Found at i:325396 original size:23 final size:23
Alignment explanation
Indices: 325378--325458 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
325368 GGTTCTATGC
* *
325378 GGTCCTTCGGGATAATTCTACGT
1 GGTCATTCGGGACAATTCTACGT
*
325401 GGTCATTCGGGACATTTCTACGT
1 GGTCATTCGGGACAATTCTACGT
* * *
325424 GGTCCTTCGGGACAATACTATGT
1 GGTCATTCGGGACAATTCTACGT
325447 GGTCATTCGGGA
1 GGTCATTCGGGA
325459 TATTTATATG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (23 bp):
GGTCATTCGGGACAATTCTACGT
Found at i:325428 original size:46 final size:46
Alignment explanation
Indices: 325378--325472 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 46
325368 GGTTCTATGC
* * *
325378 GGTCCTTCGGGATAATTCTACGTGGTCATTCGGGACATTTCTACGT
1 GGTCCTTCGGGACAATACTACGTGGTCATTCGGGACATTTATACGT
* * *
325424 GGTCCTTCGGGACAATACTATGTGGTCATTCGGGATATTTATATGT
1 GGTCCTTCGGGACAATACTACGTGGTCATTCGGGACATTTATACGT
325470 GGT
1 GGT
325473 ATTTCAGTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (46 bp):
GGTCCTTCGGGACAATACTACGTGGTCATTCGGGACATTTATACGT
Found at i:325468 original size:23 final size:23
Alignment explanation
Indices: 325399--325472 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
325389 ATAATTCTAC
* *
325399 GTGGTCATTCGGGACATTTCTAC
1 GTGGTCATTCGGGACATTTATAT
* *
325422 GTGGTCCTTCGGGACA-ATACTAT
1 GTGGTCATTCGGGACATTTA-TAT
*
325445 GTGGTCATTCGGGATATTTATAT
1 GTGGTCATTCGGGACATTTATAT
325468 GTGGT
1 GTGGT
325473 ATTTCAGTGA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.02
23 39 0.93
24 2 0.05
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.36
Consensus pattern (23 bp):
GTGGTCATTCGGGACATTTATAT
Found at i:325492 original size:24 final size:24
Alignment explanation
Indices: 325460--325511 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
325450 CATTCGGGAT
* *
325460 ATTTATATGTGGTATTTCAGTGAA
1 ATTTATATGCGGTACTTCAGTGAA
* * *
325484 ATTTCTATGCGGTACTTCGGTGTA
1 ATTTATATGCGGTACTTCAGTGAA
325508 ATTT
1 ATTT
325512 GTACGAGCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (24 bp):
ATTTATATGCGGTACTTCAGTGAA
Found at i:331970 original size:167 final size:167
Alignment explanation
Indices: 331482--331998 Score: 729
Period size: 169 Copynumber: 3.1 Consensus size: 167
331472 AAAAGAAGAA
* * *
331482 ATGATCTTGGCAGTCGGGGAATTATTCCCGTCAACCCAATTTATGTTTGATGGGATGAGATACTA
1 ATGATGTTGGCAGTCGGGGAACTATTCCCGTCAACCCAATTTATGTTTGATGGGATGAGACACTA
* * * *
331547 TGACATGGCAGAGCTTCTTTGAGAAAAGGAAAAGCGCTTCCCTGGAACGAGCCTTTCTTTTTGTC
66 TGACATGACAGAGATTCTTTGAGAAAAGGAAAA--ACTTCCTTGGAACGAGCCTTTCTTTTTGTC
* *
331612 AAATTTTACCTGCATGCCTCACTAAATTATGTTGAAGTT
129 AGATTTTATCTGCATGCCTCACTAAATTATGTTGAAGTT
* *
331651 ATGATGTTGGTAGTCGGGGAACTATTCCCTTCAACCCAATTTATGTTTGATGGGATGAGACACTA
1 ATGATGTTGGCAGTCGGGGAACTATTCCCGTCAACCCAATTTATGTTTGATGGGATGAGACACTA
* * ** *
331716 TGACTTGACAGAGATTCTTTGAGAAAAAGAAAAGTTTCCCTTGGAACGAGCCTTCCTTTTTGTCA
66 TGACATGACAGAGATTCTTTGAGAAAAGGAAAAACTT-CCTTGGAACGAGCCTTTCTTTTTGTCA
331781 GA-TTTATCTGCATGCCTCACTAAATTATGTT-AAGTT
130 GATTTTATCTGCATGCCTCACTAAATTATGTTGAAGTT
*
331817 ATGATGTTGGCAGTCGGGGAACTATTCTCGTCAACCCAA-TTATGTTT-ATGGGATGAGACACTA
1 ATGATGTTGGCAGTCGGGGAACTATTCCCGTCAACCCAATTTATGTTTGATGGGATGAGACACTA
* * * * * *
331880 TGACATGCCAAAGATTCTCTGAGAAAAGGAAAAACTATCTCTTAGAATGAGTCTTTTCTTTTTGT
66 TGACATGACAGAGATTCTTTGAGAAAAGGAAAAACT-TC-CTTGGAACGAG-CCTTTCTTTTTGT
331945 CAGATTTTATCTGCATGCCTCACTAAA-TATGTTGAAGTT
128 CAGATTTTATCTGCATGCCTCACTAAATTATGTTGAAGTT
*
331984 ATGATGTTGACAGTC
1 ATGATGTTGGCAGTC
331999 ATGAACTATA
Statistics
Matches: 313, Mismatches: 29, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
164 46 0.15
165 18 0.06
166 62 0.20
167 72 0.23
168 26 0.08
169 89 0.28
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (167 bp):
ATGATGTTGGCAGTCGGGGAACTATTCCCGTCAACCCAATTTATGTTTGATGGGATGAGACACTA
TGACATGACAGAGATTCTTTGAGAAAAGGAAAAACTTCCTTGGAACGAGCCTTTCTTTTTGTCAG
ATTTTATCTGCATGCCTCACTAAATTATGTTGAAGTT
Found at i:333727 original size:2 final size:2
Alignment explanation
Indices: 333720--333770 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
333710 GCTAAAACAA
*
333720 AT AT AT AT AT -T CT -T 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
333760 AT AT AT AT AT A
1 AT AT AT AT AT A
333771 ATCTTATCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:334913 original size:208 final size:208
Alignment explanation
Indices: 334545--334960 Score: 672
Period size: 208 Copynumber: 2.0 Consensus size: 208
334535 TTTTTCACTG
* * *
334545 AAGTTTCAAAAGTAACAAATTGGTCACTAATGTTATCGATTTATAACAAATCAGTCACTCACCGT
1 AAGTTTCAAAAGTAACAAATTGGTCACTAACGTTATCAATTTATAACAAATCAGTCACTCACCAT
*
334610 TAATAGTTGTTACTGCAATAACGGAATGCTGACATGGCACGTTAAACCAGCTGACTCGATATGTT
66 TAATAGTCGTTACTGCAATAACGGAATGCTGACATGGCACGTTAAACCAGCTGACTCGATATGTT
*
334675 TGACTCTTCTCCTTCTTCTTCTTATGTTGGGCATGTTCTTTGATGCAACCTTATACTTGGAACAA
131 TGACACTTCTCCTTCTTCTTCTTATGTTGGGCATGTTCTTTGATGCAACCTTATACTTGGAACAA
334740 CGCTTCTACGGTC
196 CGCTTCTACGGTC
* * *
334753 AAGTTTTAAAAGTAACAAATTGGTCACTAACGTTATTAATTTATAACAAATCAGTCACTCATCAT
1 AAGTTTCAAAAGTAACAAATTGGTCACTAACGTTATCAATTTATAACAAATCAGTCACTCACCAT
* * *
334818 TAATAGTCGTTACTGCAATAATGGAATGCTGACATGGCACGTTAAACTAGTTGACTC-AGTATGT
66 TAATAGTCGTTACTGCAATAACGGAATGCTGACATGGCACGTTAAACCAGCTGACTCGA-TATGT
** * * *
334882 TTGACACTTCTTGTTCTTCTTCTTTTGTTGGGCATGTTGTTTGCTGCAACCTTATACTTGGAACA
130 TTGACACTTCTCCTTCTTCTTCTTATGTTGGGCATGTTCTTTGATGCAACCTTATACTTGGAACA
334947 ACGCTTCTACGGTC
195 ACGCTTCTACGGTC
334961 GATGTTTTCT
Statistics
Matches: 191, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
207 1 0.01
208 190 0.99
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (208 bp):
AAGTTTCAAAAGTAACAAATTGGTCACTAACGTTATCAATTTATAACAAATCAGTCACTCACCAT
TAATAGTCGTTACTGCAATAACGGAATGCTGACATGGCACGTTAAACCAGCTGACTCGATATGTT
TGACACTTCTCCTTCTTCTTCTTATGTTGGGCATGTTCTTTGATGCAACCTTATACTTGGAACAA
CGCTTCTACGGTC
Found at i:336588 original size:14 final size:14
Alignment explanation
Indices: 336564--336629 Score: 123
Period size: 14 Copynumber: 4.6 Consensus size: 14
336554 AAAGCTACTC
336564 CAGATGCATGTGTTG
1 CAGA-GCATGTGTTG
336579 CAGAGCATGTGTTG
1 CAGAGCATGTGTTG
336593 CAGAGCATGTGTTG
1 CAGAGCATGTGTTG
336607 CAGAGCATGTGTTG
1 CAGAGCATGTGTTG
336621 CAGAGCATG
1 CAGAGCATG
336630 ATGCACATGA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
14 47 0.92
15 4 0.08
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.27
Consensus pattern (14 bp):
CAGAGCATGTGTTG
Found at i:341486 original size:20 final size:20
Alignment explanation
Indices: 341461--341512 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
341451 GCGAAATAAA
341461 AATCGCAACGC-GATCTCCAG
1 AATCGCAACGCAGATC-CCAG
** *
341481 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGCAGATCCCAG
341501 AATCGCAACGCA
1 AATCGCAACGCA
341513 ATTATGAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.35, C:0.33, G:0.17, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCAGATCCCAG
Found at i:341576 original size:21 final size:21
Alignment explanation
Indices: 341461--341576 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
341451 GCGAAATAAA
*
341461 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
341481 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* * **
341501 AATCGCAACGCAATTATGAAG
1 AATCGCAACGCGATTTTCCAG
* ** *
341522 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
* **
341542 AATTAGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
341564 AATCGCAACGCGA
1 AATCGCAACGCGA
341577 GTATGAAAAT
Statistics
Matches: 67, Mismatches: 25, Indels: 7
0.68 0.25 0.07
Matches are distributed among these distances:
19 1 0.01
20 25 0.37
21 39 0.58
22 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:341589 original size:20 final size:20
Alignment explanation
Indices: 341564--341656 Score: 75
Period size: 20 Copynumber: 4.6 Consensus size: 20
341554 GATTTTCCAG
341564 AATCGCAACGCGAGTATGAA
1 AATCGCAACGCGAGTATGAA
**
341584 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAGTATGA-A
* * *
341604 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAGTATGAA
*
341624 TATCGCAA--CGAGTATCCGTAA
1 AATCGCAACGCGAGTAT--G-AA
341645 AATCGCAACGCG
1 AATCGCAACGCG
341657 TATCCGTAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
18 5 0.09
19 1 0.02
20 38 0.69
21 9 0.16
23 2 0.04
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGAGTATGAA
Found at i:341656 original size:41 final size:41
Alignment explanation
Indices: 341625--341715 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
341615 GATTCTGACT
** *
341625 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
*
341666 ATCGCAACGACAATACGTAAAATCGCAACGCATATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
341707 ATCGCAACG
1 ATCGCAACG
341716 CGTTTTTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:341669 original size:20 final size:21
Alignment explanation
Indices: 341625--341718 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
341615 GATTCTGACT
*
341625 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGTAAA
341646 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
* *
341666 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGTAAA
*
341687 ATCGCAACGCATATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
341707 ATCGCAACGCGT
1 ATCGCAACGCGT
341719 TTTTTAAAGC
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
20 30 0.47
21 34 0.53
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGTATCCGTAAA
Found at i:342298 original size:20 final size:19
Alignment explanation
Indices: 342273--342344 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
342263 TTCTAAACTT
*
342273 AAAATCACAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
342293 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
342313 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
342334 AAAATCGCAAC
1 AAAATCGCAAC
342345 GAGAGAATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:342334 original size:21 final size:21
Alignment explanation
Indices: 342288--342351 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
342278 CACAACATGA
342288 AAATGAAAATCGCAAC-ACGA-
1 AAATGAAAATCGCAACGA-GAG
**
342308 AAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
342329 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
342350 AA
1 AA
342352 TCGCAACGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAG
Found at i:342355 original size:14 final size:14
Alignment explanation
Indices: 342333--342397 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
342323 CGAGAGAAAT
342333 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
342347 GAGAATCGCAACGCTAAA
1 GAAAATCGCAACG----A
342365 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
342380 GATAATCGCAACGC
1 GAAAATCGCAACGA
342394 GAAA
1 GAAA
342398 CCAAAATTGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 27 0.66
15 1 0.02
18 1 0.02
19 12 0.29
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:342370 original size:33 final size:33
Alignment explanation
Indices: 342329--342393 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
342319 GCAACGAGAG
342329 AAATGAAAATCGCAACGAGAGAATCGCAACGCT
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCT
*
342362 AAATGAAAATCGCAACGAGATAATCGCAACGC
1 AAATGAAAATCGCAACGAGAGAATCGCAACGC
342394 GAAACCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCT
Found at i:342404 original size:33 final size:33
Alignment explanation
Indices: 342334--342404 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
342324 GAGAGAAATG
* **
342334 AAAATCGCAACGAGAGAATCGCAACGCTAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
*
342367 AAAATCGCAACGAGATAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
342400 AAAAT
1 AAAAT
342405 TGCATTGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:342481 original size:20 final size:19
Alignment explanation
Indices: 342418--342474 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 19
342408 ATTGCGATTT
342418 TCATTTCGCGTTGCGATAG
1 TCATTTCGCGTTGCGATAG
342437 TCATTTCCGCGTTGCGATAG
1 TCATTT-CGCGTTGCGATAG
*
342457 TCATTCTCTCGTTGCGAT
1 TCATT-TCGCGTTGCGAT
342475 TTTCATTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.23, T:0.39
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:344283 original size:94 final size:94
Alignment explanation
Indices: 344122--344499 Score: 602
Period size: 94 Copynumber: 4.1 Consensus size: 94
344112 TAGATTGCTT
* * * * * *
344122 AGTAAATTTATTCCGTTACTGCCAATACTGCTAAACTGTTTATTCTTTAACAATGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
344187 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
344216 AGTAAATTTATTCGGCTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
344281 ATTTGTCTTTG--TTGTGTTTAGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
344308 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
344373 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
344402 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
344467 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
344495 AGTAA
1 AGTAA
344500 TGCAATCCAT
Statistics
Matches: 266, Mismatches: 15, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
91 12 0.05
92 75 0.28
93 10 0.04
94 169 0.64
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:344436 original size:186 final size:186
Alignment explanation
Indices: 344122--344479 Score: 601
Period size: 186 Copynumber: 1.9 Consensus size: 186
344112 TAGATTGCTT
*
344122 AGTAAATTTATTCCGTTACTGCCAATACTGCTAAACTGTTTATTCTTTAACAATGTAAAGTTAGT
1 AGTAAATTTATTCCGTTACTGCCAATACTGCTAAACTGTGTATTCTTTAACAATGTAAAGTTAGT
344187 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGCTGCTGCCAATTCTGCTAAAC
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGCTGCTGCCAATTCTGCTAAAC
*
344252 TGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTGTGTTTAGGTTGAA
131 TGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTGTGTTTAGGTTGAA
* * * * * *
344308 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCCGTTACTGCCAATACTGCTAAACTGTGTATTCTTTAACAATGTAAAGTTAGT
* *
344373 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTCGGCTGCTGCCAATTCTGCTAAA
*
344437 CTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTT
130 CTGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTT
344480 TTGTCTTTTG
Statistics
Matches: 160, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
185 20 0.12
186 140 0.88
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCCGTTACTGCCAATACTGCTAAACTGTGTATTCTTTAACAATGTAAAGTTAGT
ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGCTGCTGCCAATTCTGCTAAAC
TGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTGTGTTTAGGTTGAA
Found at i:344603 original size:19 final size:18
Alignment explanation
Indices: 344579--344698 Score: 96
Period size: 19 Copynumber: 6.9 Consensus size: 18
344569 ACAACGTGAA
344579 AAATGAATATCGCAACGCG
1 AAATGAA-ATCGCAACGCG
344598 AAATG-AATCGCAACGCG
1 AAATGAAATCGCAACGCG
*
344615 AAATGAAAATCGTAA--CG
1 AAATG-AAATCGCAACGCG
*
344632 AGA-G-AATCGCAACGCG
1 AAATGAAATCGCAACGCG
344648 AAATGAAAATCGCAA--CG
1 AAATG-AAATCGCAACGCG
*
344665 ACA--AAATCGCAACGCG
1 AAATGAAATCGCAACGCG
**
344681 AAACCAAAATCGCAACGC
1 AAA-TGAAATCGCAACGC
344699 TAAACTATAA
Statistics
Matches: 83, Mismatches: 6, Indels: 24
0.73 0.05 0.21
Matches are distributed among these distances:
14 16 0.19
16 9 0.11
17 25 0.30
18 1 0.01
19 32 0.39
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (18 bp):
AAATGAAATCGCAACGCG
Found at i:344641 original size:33 final size:33
Alignment explanation
Indices: 344579--344697 Score: 148
Period size: 33 Copynumber: 3.5 Consensus size: 33
344569 ACAACGTGAA
* *
344579 AAATGAATATCGCAACGCGAAATGAATCGCAACGCG
1 AAATGAAAATCGCAA--CGACA-GAATCGCAACGCG
* *
344615 AAATGAAAATCGTAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGACAGAATCGCAACGCG
*
344648 AAATGAAAATCGCAACGACAAAATCGCAACGCG
1 AAATGAAAATCGCAACGACAGAATCGCAACGCG
**
344681 AAACCAAAATCGCAACG
1 AAATGAAAATCGCAACG
344698 CTAAACTATA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
33 58 0.77
34 4 0.05
36 13 0.17
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
AAATGAAAATCGCAACGACAGAATCGCAACGCG
Found at i:344799 original size:19 final size:19
Alignment explanation
Indices: 344709--344791 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
344699 TAAACTATAA
344709 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
344728 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
344742 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
344761 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
344780 TCGCGTTGCGAT
1 TCGCGTTGCGAT
344792 AGTCATTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 9 0.16
16 3 0.05
17 3 0.05
19 40 0.73
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:345292 original size:21 final size:21
Alignment explanation
Indices: 345268--345334 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
345258 TAATTCCTCG
345268 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
345289 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
345310 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
345331 AGAG
1 AGAG
345335 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:346840 original size:19 final size:19
Alignment explanation
Indices: 346824--346889 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
346814 AAAAATGACT
346824 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
346843 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
346857 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
346876 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
346890 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:346941 original size:33 final size:33
Alignment explanation
Indices: 346899--347046 Score: 161
Period size: 33 Copynumber: 4.3 Consensus size: 33
346889 ACTAAATTCG
*
346899 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
346932 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTT
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC--TCT
* * * *
346969 CGCATTGCGATATTCATATTCGCGTTGCGATTTTCA
1 CG--TTGCGATTTTCAT-TTCGCATTGCGATTCTCT
*
347005 CGTCGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
347038 CATTGCGAT
1 CGTTGCGAT
347047 AGTAATTTCC
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
33 49 0.52
34 11 0.12
35 2 0.02
36 3 0.03
37 4 0.04
38 1 0.01
39 12 0.13
40 12 0.13
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:347004 original size:20 final size:19
Alignment explanation
Indices: 346895--347033 Score: 109
Period size: 20 Copynumber: 7.7 Consensus size: 19
346885 CGAAACTAAA
346895 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
346914 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
346929 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
346947 TTCGCATTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCA-T
* *
346967 TTCGCATTGCGATATTCAT
1 TTCGCGTTGCGATTTTCAT
346986 ATTCGCGTTGCGATTTTCA-
1 -TTCGCGTTGCGATTTTCAT
*
347005 ----CGTCGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
347020 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
347034 CTCTCATTGC
Statistics
Matches: 95, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
14 22 0.23
16 3 0.03
17 3 0.03
19 33 0.35
20 34 0.36
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:347013 original size:73 final size:72
Alignment explanation
Indices: 346895--347032 Score: 213
Period size: 73 Copynumber: 1.9 Consensus size: 72
346885 CGAAACTAAA
* * * * *
346895 TTCGCGTTGCGATTTTCATTTCGCTTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TTCGCATTGCGATATTCATTTCGCGTTGCGATTCTCACGTCGCGATTTTCATTTCGCATTGCGAT
346960 AGTCATT
66 AGTCATT
*
346967 TTCGCATTGCGATATTCATATTCGCGTTGCGATTTTCACGTCGCGATTTTCATTTCGCATTGCGA
1 TTCGCATTGCGATATTCAT-TTCGCGTTGCGATTCTCACGTCGCGATTTTCATTTCGCATTGCGA
347032 T
65 T
347033 TCTCTCATTG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
72 17 0.29
73 42 0.71
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (72 bp):
TTCGCATTGCGATATTCATTTCGCGTTGCGATTCTCACGTCGCGATTTTCATTTCGCATTGCGAT
AGTCATT
Found at i:347112 original size:20 final size:20
Alignment explanation
Indices: 347040--347112 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
347030 GATTCTCTCA
* *
347040 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* **
347060 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
347080 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
347101 TTGCGATAGTCA
1 TTGCGATAGTCA
347113 AATGAATGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:349607 original size:24 final size:24
Alignment explanation
Indices: 349573--349626 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
349563 CTGAAAAATC
349573 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
349597 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
349621 ATCAAA
1 ATCAAA
349627 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:350511 original size:20 final size:20
Alignment explanation
Indices: 350488--350543 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
350478 CAGAATCTCG
*
350488 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
350508 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
350528 TTGCGATTTACGTAAT
1 TTGCGATTTACGTAAT
350544 GCGATTACGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:350578 original size:21 final size:21
Alignment explanation
Indices: 350541--350609 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
350531 CGATTTACGT
* *
350541 AATGCG-ATTACGTAAATCGC
1 AATGCGAATTAGGAAAATCGC
* *
350561 ATTGCGAATTAGGAAAATCGT
1 AATGCGAATTAGGAAAATCGC
* * *
350582 AACGCGAATTTGGGAAATCGC
1 AATGCGAATTAGGAAAATCGC
350603 AATGCGA
1 AATGCGA
350610 TAGTCAGAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 5 0.13
21 33 0.87
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (21 bp):
AATGCGAATTAGGAAAATCGC
Found at i:350704 original size:20 final size:20
Alignment explanation
Indices: 350660--350892 Score: 249
Period size: 20 Copynumber: 11.6 Consensus size: 20
350650 TACCGGAGAT
*
350660 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
350679 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
350699 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
350719 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
350740 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
350760 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
** *
350780 CGCGTTGCGATTTACATATT
1 CGCGTTGCGATTTACGGATA
*
350800 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
350820 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
350840 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
350861 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
350882 CTCGTTGCGAT
1 CGCGTTGCGAT
350893 AGTCAGAATC
Statistics
Matches: 179, Mismatches: 26, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
18 1 0.01
19 16 0.09
20 109 0.61
21 53 0.30
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:350914 original size:41 final size:41
Alignment explanation
Indices: 350681--350892 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
350671 TTATCGATCG
*
350681 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
350722 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
350762 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACATATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
350802 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
350843 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
350884 CGTTGCGAT
1 CGTTGCGAT
350893 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 75 0.47
41 84 0.53
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:350924 original size:20 final size:20
Alignment explanation
Indices: 350901--350953 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
350891 ATAGTCAGAA
*
350901 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
350921 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
350941 TCGCGTTGCGATT
1 TCGCGTTGCGATT
350954 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:350928 original size:81 final size:81
Alignment explanation
Indices: 350660--350953 Score: 332
Period size: 81 Copynumber: 3.6 Consensus size: 81
350650 TACCGGAGAT
* * * *
350660 CGCGTTGCGAATTAT-CGATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCG
350724 TTGCGATTTACGGATA
66 TTGCGATTTACGGATA
* * *
350740 CGCATTGCGA-TT-TACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACATATTCT
1 CGCGTTGCGATTTATACG--TTCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
350802 CGTTGCGATTTACGGATA
64 CGTTGCGATTTACGGATA
* * * *
350820 CGCGTTGCGATTT-TACGTATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGCGTTGCGATTTATACGT-TCG-CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
* *
350884 CGTTGCGATAGT-CAGA-A
64 CGTTGCGAT-TTACGGATA
* * * *
350901 TCGCGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 -CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACAGATACGCGTTGCGATT
350954 CTGGAAAATC
Statistics
Matches: 183, Mismatches: 21, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
78 1 0.01
79 5 0.03
80 47 0.26
81 89 0.49
82 36 0.20
83 5 0.03
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (81 bp):
CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCG
TTGCGATTTACGGATA
Found at i:350945 original size:40 final size:40
Alignment explanation
Indices: 350660--350953 Score: 262
Period size: 40 Copynumber: 7.3 Consensus size: 40
350650 TACCGGAGAT
* *
350660 CGCGTTGCGAATTAT-CGATCGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACGGATA
*
350699 CGCGTTGCGATTT-TACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATACGT-TCG-CGTTGCGATTTACGGATA
* * *
350740 CGCATTGCGA-TT-TACGTATTCTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTATACG--TTCGCGTTGCGATTTACGGATA
* ** *
350780 CGCGTTGCGATTTACATATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACGGATA
*
350820 CGCGTTGCGATTT-TACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATACGT-TCG-CGTTGCGATTTACGGATA
* * * *
350861 CGCGTTGCGATTT-TACGGATACTCGTTGCGATAGT-CAGA-A
1 CGCGTTGCGATTTATAC-G-TTCGCGTTGCGAT-TTACGGATA
* * ** *
350901 TCGCGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATT
1 -CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACGGATA
350942 CGCGTTGCGATT
1 CGCGTTGCGATT
350954 CTGGAAAATC
Statistics
Matches: 211, Mismatches: 28, Indels: 31
0.78 0.10 0.11
Matches are distributed among these distances:
38 1 0.00
39 17 0.08
40 96 0.45
41 90 0.43
42 6 0.03
43 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CGCGTTGCGATTTATACGTTCGCGTTGCGATTTACGGATA
Found at i:351052 original size:20 final size:20
Alignment explanation
Indices: 351002--351056 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
350992 GATTCTTCAT
351002 AATCGCGTTGCGATTCTAGG
1 AATCGCGTTGCGATTCTAGG
**
351022 AA-CTGATTTGCGATTCT-GG
1 AATC-GCGTTGCGATTCTAGG
351041 AGATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
351057 TTTATTTCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 4 0.14
20 23 0.82
21 1 0.04
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTAGG
Found at i:353225 original size:20 final size:19
Alignment explanation
Indices: 353187--353237 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
353177 TTCCCAAAAG
* *
353187 GTTTCGATACTTTTCAAGA
1 GTTTCGAAACTTCTCAAGA
353206 GTTTCGAAACTATCTCAAGA
1 GTTTCGAAACT-TCTCAAGA
*
353226 GTTTCAAAACTT
1 GTTTCGAAACTT
353238 TCCCTAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (19 bp):
GTTTCGAAACTTCTCAAGA
Found at i:355999 original size:21 final size:21
Alignment explanation
Indices: 355973--356027 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
355963 ACTCTATGGT
*
355973 GGTGACATCTGAACGAGTTGA
1 GGTGACATCTGAACCAGTTGA
355994 GGTGACATCTGAACCAGTTGA
1 GGTGACATCTGAACCAGTTGA
*
356015 GGTGGCATCTGAA
1 GGTGACATCTGAA
356028 ATGGTTGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (21 bp):
GGTGACATCTGAACCAGTTGA
Found at i:356034 original size:21 final size:21
Alignment explanation
Indices: 355973--356081 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
355963 ACTCTATGGT
355973 GGTGACATCTG-AACGAGTTGA
1 GGTGACATCTGAAAC-AGTTGA
*
355994 GGTGACATCTGAACCAGTTGA
1 GGTGACATCTGAAACAGTTGA
* ** *
356015 GGTGGCATCTGAAATGGTTGT
1 GGTGACATCTGAAACAGTTGA
* * *
356036 GGT-ACAATATGAAACGGTTGC
1 GGTGAC-ATCTGAAACAGTTGA
* * * *
356057 GGTGTCATTTGAAACTGTTGC
1 GGTGACATCTGAAACAGTTGA
356078 GGTG
1 GGTG
356082 TATCCATATA
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.01
21 68 0.94
22 3 0.04
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (21 bp):
GGTGACATCTGAAACAGTTGA
Found at i:358435 original size:30 final size:29
Alignment explanation
Indices: 358401--358500 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 29
358391 TTAAAGTTAC
358401 AAGGACCAAAATGAGAAAAACAACAACTTA
1 AAGGACCAAAATGAGAAAAACAA-AACTTA
*
358431 AAGGACCAAAAT-AGCAAAACCAAAACTTA
1 AAGGACCAAAATGAG-AAAAACAAAACTTA
* * *
358460 AAGAACTAAAATG-GAATAAACATAAATTTA
1 AAGGACCAAAATGAGAA-AAACA-AAACTTA
*
358490 AAGGGCCAAAA
1 AAGGACCAAAA
358501 CAGTAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.03
29 23 0.40
30 33 0.57
ACGTcount: A:0.59, C:0.15, G:0.13, T:0.13
Consensus pattern (29 bp):
AAGGACCAAAATGAGAAAAACAAAACTTA
Found at i:358585 original size:58 final size:57
Alignment explanation
Indices: 358477--358586 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 57
358467 AAAATGGAAT
* *
358477 AAACATAAATTTAAAGGGCCAAAACAGTAAAAATAGAAACTTAAGAACTAAATAACAA
1 AAACATAAATTTAAAGGG-CAAAACAGTAAAAACAGAAACTAAAGAACTAAATAACAA
* *
358535 AAACAT-AATCTTAAAGGG-ATAAACAGTAAAAACAGTAACTAAAAGGACTAAA
1 AAACATAAAT-TTAAAGGGCA-AAACAGTAAAAACAGAAACT-AAAGAACTAAA
358587 ACAGTAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
56 1 0.02
57 21 0.47
58 23 0.51
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17
Consensus pattern (57 bp):
AAACATAAATTTAAAGGGCAAAACAGTAAAAACAGAAACTAAAGAACTAAATAACAA
Found at i:359960 original size:13 final size:13
Alignment explanation
Indices: 359942--359967 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
359932 AAAATTAATT
359942 ATAATAATAATAA
1 ATAATAATAATAA
359955 ATAATAATAATAA
1 ATAATAATAATAA
359968 TAGGGAAAAG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:360404 original size:28 final size:28
Alignment explanation
Indices: 360364--360426 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
360354 AGGGATTATG
*
360364 GTTTCAAGAGAAACCA-ACTCAAAGATTT
1 GTTTCAAAAGAAA-CATACTCAAAGATTT
360392 GTTTCAAAAGAAACATACTCAAAGATTT
1 GTTTCAAAAGAAACATACTCAAAGATTT
*
360420 GTCTCAA
1 GTTTCAA
360427 GAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 2 0.06
28 30 0.94
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (28 bp):
GTTTCAAAAGAAACATACTCAAAGATTT
Found at i:360559 original size:30 final size:29
Alignment explanation
Indices: 360487--360568 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
360477 AGACAAAATT
*
360487 TGTTTCATGGGAAACG-ACTCAAAGATGA
1 TGTTTCATGGGAAACGTTCTCAAAGATGA
* * * * *
360515 CGATTAAAGGGAAACGTTCTCAAAGATTGG
1 TGTTTCATGGGAAACGTTCTCAAAGA-TGA
360545 TGTTTCATGGGAAAC-TGTCTCAAA
1 TGTTTCATGGGAAACGT-TCTCAAA
360569 TGAGACAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
28 12 0.29
29 9 0.22
30 20 0.49
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (29 bp):
TGTTTCATGGGAAACGTTCTCAAAGATGA
Found at i:360901 original size:69 final size:65
Alignment explanation
Indices: 360748--360914 Score: 162
Period size: 69 Copynumber: 2.4 Consensus size: 65
360738 AAGTGAGATG
* * *
360748 AAATTTGTTTCAAAAGAAACAATCTC-AA-ATGTTTGTTTTTCATTAGAAAATGTCTCAAGAGAG
1 AAATTTGTTTC-AAAGAAA-TA-CTCAAAGATGTTTGTTTTTCATGAGAAAAGGTCTCAAGAGAG
360811 AAA
63 AAA
*
360814 AAATTTGTTTTTAAAGAAATGACTCAAAGATGATTTGTTGTTTCATGAGAAAAGGTCTCAAG-GA
1 AAATTTG-TTTCAAAGAAAT-ACTCAAAGATG-TTTGTT-TTTCATGAGAAAAGGTCTCAAGAGA
360878 -AAA
62 GAAA
360881 TAAGATTTGTTTCAAGAGAAACATACTCAAAGAT
1 -AA-ATTTGTTTCAA-AG-AA-ATACTCAAAGAT
360915 TACAAATTTT
Statistics
Matches: 85, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
65 3 0.04
66 17 0.20
67 9 0.11
68 15 0.18
69 27 0.32
70 12 0.14
71 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (65 bp):
AAATTTGTTTCAAAGAAATACTCAAAGATGTTTGTTTTTCATGAGAAAAGGTCTCAAGAGAGAAA
Found at i:361938 original size:6 final size:6
Alignment explanation
Indices: 361505--362295 Score: 708
Period size: 6 Copynumber: 132.5 Consensus size: 6
361495 TATGTATGTA
* * * * * **
361505 TGTGTG TATGTG TGTATG TGTGTA TGTGTG TATGTG TGTATG TGTGCA
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * *
361553 TGTGTG TATGTG TGTATG TGAGAG TGTATG TGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
361601 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* *
361649 TGTGTG TGTGTA TGTGTG TATGTG TGTGTG TGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
361697 TGTGT- TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
*
361744 TGTGTG TGTGTG TGTGTG TGTGCG TG-GTG TGTGTG -GTGTG TGTG-G
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
361789 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * *
361837 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTATG TGAGAG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * **
361885 TATGTG TGTATG TGTGTA TGTGTG TATGTG TGTATG TGTGCA TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * * * * *
361933 TATGTG TGTATG TGAGAG TGTATG TGTGTA TGTGAG AGTGTA TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * *
361981 TATGTG AGAGTG TGTGTG TGCGTG TGTGTG TGTGTG TGTGCG TGTGCG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * * * *
362029 TGTGCG TGTGCG TGTGCG TGTGTG TGTGCG TGCGTG CGTGCG TGCGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * * * * * * * *
362077 CGTGCG TGCGTG CGTGCG TGCGTG CGTGCG TGCGTG CGTGCG TGCGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * * * * * * *
362125 CGTGCG TGCGTG CGTGCG TGCGTG CGTGCG TGCGTG TGAGTG TATGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * * * * * * * * ** * *
362173 AGAGTG TGAGAG TGCGTG CGCGCG TGCGCG CGTGCG TGCCTG CGTGCG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
** * * * * *
362221 CATGTG CGAGTG TGCGTG TGTGCG TGTGTG CGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
362269 TGTGTG TGTGTG TGTGTG TGTGTG TGT
1 TGTGTG TGTGTG TGTGTG TGTGTG TGT
362296 CTGTTTTTTT
Statistics
Matches: 618, Mismatches: 163, Indels: 8
0.78 0.21 0.01
Matches are distributed among these distances:
5 19 0.03
6 599 0.97
ACGTcount: A:0.05, C:0.07, G:0.47, T:0.41
Consensus pattern (6 bp):
TGTGTG
Found at i:361993 original size:14 final size:14
Alignment explanation
Indices: 361976--362014 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
361966 GAGAGTGTAT
*
361976 GTGTGTATGTGAGA
1 GTGTGTGTGTGAGA
* *
361990 GTGTGTGTGTGCGT
1 GTGTGTGTGTGAGA
362004 GTGTGTGTGTG
1 GTGTGTGTGTG
362015 TGTGTGCGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.08, C:0.03, G:0.49, T:0.41
Consensus pattern (14 bp):
GTGTGTGTGTGAGA
Found at i:362020 original size:8 final size:8
Alignment explanation
Indices: 361505--362295 Score: 708
Period size: 8 Copynumber: 99.4 Consensus size: 8
361495 TATGTATGTA
*
361505 TGTGTGTA
1 TGTGTGTG
*
361513 TGTGTGTA
1 TGTGTGTG
*
361521 TGTGTGTA
1 TGTGTGTG
*
361529 TGTGTGTA
1 TGTGTGTG
*
361537 TGTGTGTA
1 TGTGTGTG
**
361545 TGTGTGCA
1 TGTGTGTG
*
361553 TGTGTGTA
1 TGTGTGTG
*
361561 TGTGTGTA
1 TGTGTGTG
* *
361569 TGTGAGAG
1 TGTGTGTG
*
361577 TGTATGTG
1 TGTGTGTG
361585 TGTGTGTG
1 TGTGTGTG
361593 TGTGTGTG
1 TGTGTGTG
361601 TGTGTGTG
1 TGTGTGTG
361609 TGTGTGTG
1 TGTGTGTG
361617 TGTGTGTG
1 TGTGTGTG
361625 TGTGTGTG
1 TGTGTGTG
361633 TGTGTGTG
1 TGTGTGTG
361641 TGTGTGTG
1 TGTGTGTG
361649 TGTGTGTG
1 TGTGTGTG
*
361657 TGTATGTG
1 TGTGTGTG
*
361665 TGTATGTG
1 TGTGTGTG
361673 TGTGTGTG
1 TGTGTGTG
361681 TGTGTGTG
1 TGTGTGTG
361689 TGTGTGTG
1 TGTGTGTG
361697 TGTGT-TG
1 TGTGTGTG
361704 TGTGTGTG
1 TGTGTGTG
361712 TGTGTGTG
1 TGTGTGTG
361720 TGTGTGTG
1 TGTGTGTG
361728 TGTGTGTG
1 TGTGTGTG
361736 TGTGTGTG
1 TGTGTGTG
361744 TGTGTGTG
1 TGTGTGTG
361752 TGTGTGTG
1 TGTGTGTG
*
361760 TGTGTGCG
1 TGTGTGTG
361768 TG-GTGTG
1 TGTGTGTG
361775 TGTG-GTG
1 TGTGTGTG
361782 TGTGTG-G
1 TGTGTGTG
361789 TGTGTGTG
1 TGTGTGTG
361797 TGTGTGTG
1 TGTGTGTG
361805 TGTGTGTG
1 TGTGTGTG
361813 TGTGTGTG
1 TGTGTGTG
361821 TGTGTGTG
1 TGTGTGTG
361829 TGTGTGTG
1 TGTGTGTG
361837 TGTGTGTG
1 TGTGTGTG
361845 TGTGTGTG
1 TGTGTGTG
361853 TGTGTGTG
1 TGTGTGTG
361861 TGTGTGTG
1 TGTGTGTG
*
361869 TGTGTGTA
1 TGTGTGTG
* *
361877 TGTGAGAG
1 TGTGTGTG
*
361885 TATGTGTG
1 TGTGTGTG
*
361893 TATGTGTG
1 TGTGTGTG
*
361901 TATGTGTG
1 TGTGTGTG
*
361909 TATGTGTG
1 TGTGTGTG
*
361917 TATGTGTG
1 TGTGTGTG
**
361925 CATGTGTG
1 TGTGTGTG
*
361933 TATGTGTG
1 TGTGTGTG
* *
361941 TATGTGAG
1 TGTGTGTG
* *
361949 AGTGTATG
1 TGTGTGTG
*
361957 TGTGTATG
1 TGTGTGTG
* *
361965 TGAGAGTG
1 TGTGTGTG
*
361973 TATGTGTG
1 TGTGTGTG
* *
361981 TATGTGAG
1 TGTGTGTG
*
361989 AGTGTGTG
1 TGTGTGTG
*
361997 TGTGCGTG
1 TGTGTGTG
362005 TGTGTGTG
1 TGTGTGTG
362013 TGTGTGTG
1 TGTGTGTG
* *
362021 CGTGTGCG
1 TGTGTGTG
*
362029 TGTGCGTG
1 TGTGTGTG
*
362037 TGCGTGTG
1 TGTGTGTG
*
362045 CGTGTGTG
1 TGTGTGTG
*
362053 TGTGCGTG
1 TGTGTGTG
* *
362061 CGTGCGTG
1 TGTGTGTG
* *
362069 CGTGCGTG
1 TGTGTGTG
* *
362077 CGTGCGTG
1 TGTGTGTG
* *
362085 CGTGCGTG
1 TGTGTGTG
* *
362093 CGTGCGTG
1 TGTGTGTG
* *
362101 CGTGCGTG
1 TGTGTGTG
* *
362109 CGTGCGTG
1 TGTGTGTG
* *
362117 CGTGCGTG
1 TGTGTGTG
* *
362125 CGTGCGTG
1 TGTGTGTG
* *
362133 CGTGCGTG
1 TGTGTGTG
* *
362141 CGTGCGTG
1 TGTGTGTG
* *
362149 CGTGCGTG
1 TGTGTGTG
* *
362157 CGTGTGAG
1 TGTGTGTG
*
362165 TGTATGTG
1 TGTGTGTG
* *
362173 AGAGTGTG
1 TGTGTGTG
* * *
362181 AGAGTGCG
1 TGTGTGTG
* * *
362189 TGCGCGCG
1 TGTGTGTG
* * *
362197 TGCGCGCG
1 TGTGTGTG
* **
362205 TGCGTGCC
1 TGTGTGTG
* *
362213 TGCGTGCG
1 TGTGTGTG
** *
362221 CATGTGCG
1 TGTGTGTG
* *
362229 AGTGTGCG
1 TGTGTGTG
*
362237 TGTGTGCG
1 TGTGTGTG
*
362245 TGTGTGCG
1 TGTGTGTG
362253 TGTGTGTG
1 TGTGTGTG
362261 TGTGTGTG
1 TGTGTGTG
362269 TGTGTGTG
1 TGTGTGTG
362277 TGTGTGTG
1 TGTGTGTG
362285 TGTGTGTG
1 TGTGTGTG
362293 TGT
1 TGT
362296 CTGTTTTTTT
Statistics
Matches: 704, Mismatches: 75, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
7 27 0.04
8 677 0.96
ACGTcount: A:0.05, C:0.07, G:0.47, T:0.41
Consensus pattern (8 bp):
TGTGTGTG
Found at i:363346 original size:2 final size:2
Alignment explanation
Indices: 363335--363393 Score: 75
Period size: 2 Copynumber: 30.0 Consensus size: 2
363325 AGCTTTATTG
* * * *
363335 TA TA TA -A TA TA TA TA TA TA TA TG TG TG TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
363376 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
363394 AACGGATTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
TA
Found at i:363367 original size:18 final size:18
Alignment explanation
Indices: 363341--363392 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
363331 ATTGTATATA
363341 ATATATATATATATATGT
1 ATATATATATATATATGT
* *
363359 GTGTATATATATATATGT
1 ATATATATATATATATGT
363377 ATATATATATATATAT
1 ATATATATATATATAT
363393 AAACGGATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
ATATATATATATATATGT
Found at i:367362 original size:29 final size:29
Alignment explanation
Indices: 367330--367457 Score: 96
Period size: 29 Copynumber: 4.3 Consensus size: 29
367320 AGAAAACAGC
*
367330 AACTTAAAGGACCAAAATAGTAAAATTGA
1 AACTTAAAGGACCAAAATAGTAAAATAGA
* * *
367359 AACTTAAAGGACTAAAATGGCATAAATAGA
1 AACTTAAAGGACCAAAATAGTA-AAATAGA
* * * * *
367389 TATTTAAAGGGCCAAAATAGTAAAAACAAA
1 AACTTAAAGGACCAAAATAGT-AAAATAGA
** **
367419 AACTT-AAGGACTTAAATACCAAAAATAGA
1 AACTTAAAGGACCAAAATA-GTAAAATAGA
*
367448 ATCTTAAAGG
1 AACTTAAAGG
367458 GATAAATAAT
Statistics
Matches: 73, Mismatches: 22, Indels: 7
0.72 0.22 0.07
Matches are distributed among these distances:
29 39 0.53
30 33 0.45
31 1 0.01
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (29 bp):
AACTTAAAGGACCAAAATAGTAAAATAGA
Found at i:367428 original size:59 final size:59
Alignment explanation
Indices: 367332--367493 Score: 161
Period size: 59 Copynumber: 2.7 Consensus size: 59
367322 AAAACAGCAA
* ** ** *
367332 CTTAAAGGACCAAAATAGT-AAAATTGAAACTTAAAGGACTAAAATGGCATAAATAGATAT
1 CTTAAAGGGCCAAAATAGTAAAAACAGAAACTT-AAGGACTAAAATACCAAAAATAGA-AT
* *
367392 -TTAAAGGGCCAAAATAGTAAAAACAAAAACTTAAGGACTTAAATACCAAAAATAGAAT
1 CTTAAAGGGCCAAAATAGTAAAAACAGAAACTTAAGGACTAAAATACCAAAAATAGAAT
* * *
367450 CTTAAAGGG--ATAAATAATAAAAACAGTAACTAAAAGGACTAAAA
1 CTTAAAGGGCCA-AAATAGTAAAAACAGAAACT-TAAGGACTAAAA
367494 CAATAATTAC
Statistics
Matches: 85, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
57 1 0.01
58 19 0.22
59 55 0.65
60 10 0.12
ACGTcount: A:0.56, C:0.10, G:0.14, T:0.20
Consensus pattern (59 bp):
CTTAAAGGGCCAAAATAGTAAAAACAGAAACTTAAGGACTAAAATACCAAAAATAGAAT
Found at i:368889 original size:23 final size:24
Alignment explanation
Indices: 368859--368906 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
368849 TAGGCCTGCA
*
368859 AACAAAATAT-GAATAATTAAAAT
1 AACAAAATATAAAATAATTAAAAT
368882 AACAAAATATAAAATAATTAAAAT
1 AACAAAATATAAAATAATTAAAAT
368906 A
1 A
368907 TAAACTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (24 bp):
AACAAAATATAAAATAATTAAAAT
Found at i:368906 original size:16 final size:16
Alignment explanation
Indices: 368876--368952 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
368866 TATGAATAAT
368876 TAAAATAA-CAAAATA
1 TAAAATAATCAAAATA
*
368891 TAAAATAATTAAAATA
1 TAAAATAATCAAAATA
* *
368907 TAAACTAATACTAAA-A
1 TAAAATAAT-CAAAATA
*
368923 -AAAATATTCAAAATAA
1 TAAAATAATCAAAAT-A
368939 TTAAAATAA-CAAAA
1 -TAAAATAATCAAAA
368953 CTTAAAATTG
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.08
15 14 0.29
16 16 0.33
17 8 0.17
18 6 0.12
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAATAATCAAAATA
Found at i:371147 original size:15 final size:16
Alignment explanation
Indices: 371121--371152 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
371111 AAATAATCTT
371121 TTAATATAATTTATAA
1 TTAATATAATTTATAA
371137 TTAAT-TAATTTATAA
1 TTAATATAATTTATAA
371152 T
1 T
371153 CAAAGAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATATAATTTATAA
Found at i:381882 original size:22 final size:21
Alignment explanation
Indices: 381832--381895 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
381822 AGTCGAGGGT
* *
381832 TTCATAGGTCCTTCGAGACAA
1 TTCATAGGTCATTCGGGACAA
* * *
381853 CTCATAGGTCTTTTGGGACATA
1 TTCATAGGTCATTCGGGACA-A
381875 TTCATAGGTCATTCGGGACAA
1 TTCATAGGTCATTCGGGACAA
381896 ATTTCATATG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (21 bp):
TTCATAGGTCATTCGGGACAA
Found at i:382524 original size:21 final size:21
Alignment explanation
Indices: 382494--382534 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
382484 GATATTTTTG
382494 TGCATCGGTACACTGTAGCAA
1 TGCATCGGTACACTGTAGCAA
*
382515 TGCATTGGTACACTGTAGCA
1 TGCATCGGTACACTGTAGCA
382535 CTGTTCATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
TGCATCGGTACACTGTAGCAA
Found at i:397574 original size:38 final size:39
Alignment explanation
Indices: 397520--397603 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 39
397510 GTGTCAAGAA
* *
397520 AGTATTGAAACGTTAAAGAGAA-TTTTGACATAAGCTCC
1 AGTATTGAAACATTAAAGAGAATTTTTGACAGAAGCTCC
*
397558 AGTATTGAAACATTAAAGAGAATTTTTTACAGAAGCTCC
1 AGTATTGAAACATTAAAGAGAATTTTTGACAGAAGCTCC
397597 AGTATTG
1 AGTATTG
397604 GTTCAACCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 21 0.50
39 21 0.50
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (39 bp):
AGTATTGAAACATTAAAGAGAATTTTTGACAGAAGCTCC
Found at i:399525 original size:19 final size:19
Alignment explanation
Indices: 399501--399537 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
399491 CATCGGATGC
399501 AAGTAGTGCATCGATGCAT
1 AAGTAGTGCATCGATGCAT
**
399520 AAGTAGTTTATCGATGCA
1 AAGTAGTGCATCGATGCA
399538 CCCCCTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (19 bp):
AAGTAGTGCATCGATGCAT
Found at i:401196 original size:23 final size:23
Alignment explanation
Indices: 401106--401196 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 23
401096 GACAATATAT
* *
401106 GGCACTACGGTGCATTTCTACAC
1 GGCACTTCGGTGCATTTCTACGC
* * *
401129 GGCACTTCGGTGCAATTCTAAGT
1 GGCACTTCGGTGCATTTCTACGC
*
401152 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
401175 GGCACTTTGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
401197 AGTTGTGGTG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:402992 original size:16 final size:16
Alignment explanation
Indices: 402963--402996 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
402953 TGTTTCCAGA
402963 TTTCTCTCATTTCTTC
1 TTTCTCTCATTTCTTC
402979 TTTCT-TCATCTTCTTC
1 TTTCTCTCAT-TTCTTC
402995 TT
1 TT
402997 CTCCTAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTCTCTCATTTCTTC
Found at i:405340 original size:24 final size:24
Alignment explanation
Indices: 405313--405369 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
405303 TTTCTCACCG
*
405313 TCATTTTTCACTCACTTTTCATCT
1 TCATCTTTCACTCACTTTTCATCT
405337 TCATCTTTCACTCACTTTTCATCT
1 TCATCTTTCACTCACTTTTCATCT
405361 TCATCTTTC
1 TCATCTTTC
405370 GTTTTGATCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.53
Consensus pattern (24 bp):
TCATCTTTCACTCACTTTTCATCT
Found at i:416579 original size:2 final size:2
Alignment explanation
Indices: 416574--416622 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
416564 TGTGTGTGTG
416574 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
416616 -A TA TA TA
1 TA TA TA TA
416623 AAACATATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:418491 original size:30 final size:30
Alignment explanation
Indices: 418430--418492 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
418420 ATTTGGATCT
* *
418430 GAATTTAATCAAAAATTCACTTTGGTCCTC
1 GAATTTAATCAAAAATTCAATTTAGTCCTC
* * * *
418460 GAATTTAGTTAAAATTTCAATTTAGTTCTC
1 GAATTTAATCAAAAATTCAATTTAGTCCTC
418490 GAA
1 GAA
418493 AAAAATTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (30 bp):
GAATTTAATCAAAAATTCAATTTAGTCCTC
Found at i:419780 original size:20 final size:20
Alignment explanation
Indices: 419755--419803 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
419745 AAGTGGGCAA
419755 TATCGATACTCTACTTGCAG
1 TATCGATACTCTACTTGCAG
419775 TATCGATACTCTACTTGCAG
1 TATCGATACTCTACTTGCAG
*
419795 TATCAATAC
1 TATCGATAC
419804 CCTTATGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACTCTACTTGCAG
Found at i:420464 original size:2 final size:2
Alignment explanation
Indices: 420457--420481 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
420447 CTCTTTGCCA
420457 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 A
420482 ACGAAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:421639 original size:21 final size:21
Alignment explanation
Indices: 421615--421658 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
421605 CCGGTAAAAA
* *
421615 TTATGAAAAATATTATTATTT
1 TTATCAAAAATATTAATATTT
*
421636 TTATCTAAAATATTAATATTT
1 TTATCAAAAATATTAATATTT
421657 TT
1 TT
421659 TAATATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTATCAAAAATATTAATATTT
Found at i:421709 original size:20 final size:21
Alignment explanation
Indices: 421684--421729 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
421674 AGTATCCATC
*
421684 AATAACAAAACTGATAAAAA-
1 AATAACAAAACTAATAAAAAT
*
421704 AATAACAAAATTAATAAAAAT
1 AATAACAAAACTAATAAAAAT
421725 AATAA
1 AATAA
421730 TATTTCCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.20
Consensus pattern (21 bp):
AATAACAAAACTAATAAAAAT
Found at i:423312 original size:180 final size:179
Alignment explanation
Indices: 423014--423361 Score: 687
Period size: 180 Copynumber: 1.9 Consensus size: 179
423004 CTTTTAAAAT
423014 TTTATTAAATGATTTATATTTTTTTCTATTAAATAATTTAATATAATAACATAAATCATATATTT
1 TTTATTAAATGATTTATATTTTTTTCTATTAAATAATTTAATATAATAACATAAATCATATATTT
423079 CTTTGCTAAAAAAATCCATATTGAATTTTTTGTCAAGTCACATTTATTTTAAACTAAATTTTATG
66 CTTTGCTAAAAAAATCCATATTGAATTTTTTGTCAAGTCACATTTATTTTAAACTAAATTTTATG
423144 AGAATTACTCCATACATTAACATGAACAATTTAATTTTAAACTAAATCA
131 AGAATTACTCCATACATTAACATGAACAATTTAATTTTAAACTAAATCA
423193 TTTATTAAATGATTTATATTTTTTTCTATTAAATAATTTAATATAATAACATAAATCATATATTT
1 TTTATTAAATGATTTATATTTTTTTCTATTAAATAATTTAATATAATAACATAAATCATATATTT
423258 CTTTGCTAAAATAAATCCATATTGAATTTTTTGTCAAGTCACATTTATTTTAAACTAAATTTTAT
66 CTTTGCTAAAA-AAATCCATATTGAATTTTTTGTCAAGTCACATTTATTTTAAACTAAATTTTAT
423323 GAGAATTACTCCATACATTAACATGAACAATTTAATTTT
130 GAGAATTACTCCATACATTAACATGAACAATTTAATTTT
423362 TAATAGTAAA
Statistics
Matches: 168, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
179 76 0.45
180 92 0.55
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (179 bp):
TTTATTAAATGATTTATATTTTTTTCTATTAAATAATTTAATATAATAACATAAATCATATATTT
CTTTGCTAAAAAAATCCATATTGAATTTTTTGTCAAGTCACATTTATTTTAAACTAAATTTTATG
AGAATTACTCCATACATTAACATGAACAATTTAATTTTAAACTAAATCA
Found at i:428890 original size:7 final size:7
Alignment explanation
Indices: 428878--428908 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
428868 TGTTATTAAA
428878 AAATCCT
1 AAATCCT
428885 AAATCCT
1 AAATCCT
*
428892 AAACCCT
1 AAATCCT
428899 AAATCCT
1 AAATCCT
428906 AAA
1 AAA
428909 CTCTTAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (7 bp):
AAATCCT
Found at i:429099 original size:7 final size:7
Alignment explanation
Indices: 429084--429162 Score: 68
Period size: 7 Copynumber: 11.3 Consensus size: 7
429074 GGGAGAATGG
429084 TTAGGGT
1 TTAGGGT
*
429091 TTAGTGT
1 TTAGGGT
429098 TTAGGGT
1 TTAGGGT
*
429105 TTAGAGT
1 TTAGGGT
***
429112 TTAATAT
1 TTAGGGT
*
429119 TTAGGGA
1 TTAGGGT
* *
429126 TTAAGCT
1 TTAGGGT
**
429133 TTATAGT
1 TTAGGGT
429140 TTAGGGT
1 TTAGGGT
429147 TTAGGGT
1 TTAGGGT
429154 TTAGGGT
1 TTAGGGT
429161 TT
1 TT
429163 GCAAAATCAA
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:429108 original size:21 final size:21
Alignment explanation
Indices: 429084--429162 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
429074 GGGAGAATGG
429084 TTAGGGTTTAGTGTTTAGGGT
1 TTAGGGTTTAGTGTTTAGGGT
* * * *
429105 TTAGAGTTTAATATTTAGGGA
1 TTAGGGTTTAGTGTTTAGGGT
* *
429126 TTAAGCTTTA-TAGTTTAGGGT
1 TTAGGGTTTAGT-GTTTAGGGT
*
429147 TTAGGGTTTAGGGTTT
1 TTAGGGTTTAGTGTTT
429163 GCAAAATCAA
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (21 bp):
TTAGGGTTTAGTGTTTAGGGT
Found at i:431211 original size:24 final size:24
Alignment explanation
Indices: 431161--431239 Score: 151
Period size: 24 Copynumber: 3.3 Consensus size: 24
431151 CTATTCTTTC
431161 GCTTCAATTGAGCTCAAA-TTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
431184 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
431208 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
431232 GCTTCAAT
1 GCTTCAAT
431240 CAAACTTCTA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 18 0.33
24 37 0.67
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:431497 original size:30 final size:30
Alignment explanation
Indices: 431463--431528 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
431453 AGTGAACCAG
* **
431463 CGGTTCAAATTGGTTTTTCCGGTTTTCAGC
1 CGGTTCAAATCGGTTTCCCCGGTTTTCAGC
**
431493 CGGTTCACCTCGGTTTCCCCGGTTTTCAGC
1 CGGTTCAAATCGGTTTCCCCGGTTTTCAGC
431523 CGGTTC
1 CGGTTC
431529 TTTAACGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.09, C:0.29, G:0.24, T:0.38
Consensus pattern (30 bp):
CGGTTCAAATCGGTTTCCCCGGTTTTCAGC
Found at i:432709 original size:21 final size:21
Alignment explanation
Indices: 432680--432732 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
432670 ATTCTGACTA
432680 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
432701 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
432722 TCGCAATGCGA
1 TCGCATTGCGA
432733 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:432747 original size:20 final size:20
Alignment explanation
Indices: 432722--432855 Score: 205
Period size: 20 Copynumber: 6.7 Consensus size: 20
432712 TTTTCCTAAT
432722 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
432742 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
432763 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
432783 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
432803 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
432823 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
432843 TCGCAACGCGAAT
1 TCGCAATGCGAAT
432856 CTGACTATCG
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
20 87 0.85
21 15 0.15
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:432865 original size:20 final size:20
Alignment explanation
Indices: 432842--432908 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
432832 GAATACGTAA
* *
432842 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
432862 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
432882 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
432902 ATCGCAA
1 ATCGCAA
432909 TACTGAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:433775 original size:24 final size:24
Alignment explanation
Indices: 433724--433777 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
433714 GTATTCGAAA
*
433724 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
433748 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
433772 TTTGAT
1 TTTGAT
433778 GATTTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:436182 original size:20 final size:20
Alignment explanation
Indices: 436157--436211 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
436147 AGACATTCAT
*
436157 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCAGAA
436177 TTGACTATCGCAACGCAGAA
1 TTGACTATCGCAACGCAGAA
*
436197 ATGACTATCGCAACG
1 TTGACTATCGCAACG
436212 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (20 bp):
TTGACTATCGCAACGCAGAA
Found at i:436271 original size:34 final size:33
Alignment explanation
Indices: 436183--436276 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
436173 GGAATTGACT
* **
436183 ATCGCAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
436217 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
436250 ATCGCAATGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
436277 TGCGAAAATG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:436274 original size:20 final size:20
Alignment explanation
Indices: 436216--436302 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
436206 GCAACGAGAG
436216 AATCGCAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
*
436235 AATCGCAA--CG--AGTG--
1 AATCGCAATGCGAAAATGAA
436249 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
436269 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
436289 AATCGCAACGCGAA
1 AATCGCAATGCGAA
436303 TTTAGTTTCG
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 8 0.14
16 5 0.08
17 2 0.03
18 3 0.05
19 8 0.14
20 33 0.56
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:436356 original size:34 final size:34
Alignment explanation
Indices: 436313--436408 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
436303 TTTAGTTTCG
436313 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
436347 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
436380 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
436409 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:436387 original size:14 final size:14
Alignment explanation
Indices: 436335--436388 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
436325 CATTTTCGCA
436335 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
436349 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
436366 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
436382 TTGCGAT
1 TTGCGAT
436389 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:436526 original size:14 final size:14
Alignment explanation
Indices: 436509--436545 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
436499 GTACACATCA
436509 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
436523 ACAAATCATCTTTT
1 ACAAATCAACATTT
436537 ACAAATCAA
1 ACAAATCAA
436546 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:438486 original size:20 final size:20
Alignment explanation
Indices: 438461--438549 Score: 151
Period size: 20 Copynumber: 4.5 Consensus size: 20
438451 TGAAACTTAA
438461 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
438481 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
438501 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
438521 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
438541 ATCGCAACG
1 ATCGCAACG
438550 AGAGAATCGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:438619 original size:20 final size:20
Alignment explanation
Indices: 438594--438770 Score: 142
Period size: 20 Copynumber: 8.5 Consensus size: 20
438584 GATTCTTTTG
**
438594 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
438614 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
438634 TTGCGGTAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
438654 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
438674 TTGCGATTTTGTTGTTGCAATTTT--CA
1 TTGCGA-----TAG-T-C-ATTTTCGCA
* * * * * *
438700 TTTCGCATTGTAATTCTCTCG
1 TTGCG-ATAGTCATTTTCGCA
* *
438721 TTGTGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
438741 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
438761 TTGCGATAGT
1 TTGCGATAGT
438771 AAACTATTCT
Statistics
Matches: 127, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.03
20 100 0.79
21 5 0.04
22 3 0.02
25 2 0.02
26 6 0.05
27 2 0.02
28 5 0.04
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:438652 original size:40 final size:39
Alignment explanation
Indices: 438572--438680 Score: 138
Period size: 40 Copynumber: 2.9 Consensus size: 39
438562 TGCGATTTTC
438572 ATTTCGCATTGCGAT--TC-TTTT-G-TTGCGATAGTCA
1 ATTTCGCATTGCGATAGTCATTTTCGCTTGCGATAGTCA
* *
438606 AATTCGCATTGCGATAGTCATTTTCGCATTGCGGTAGTCA
1 ATTTCGCATTGCGATAGTCATTTTCGC-TTGCGATAGTCA
*
438646 TTTTCGCATTGCGATAGTCATTTTCGCGTTGCGAT
1 ATTTCGCATTGCGATAGTCATTTTCGC-TTGCGAT
438681 TTTGTTGTTG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
34 14 0.22
36 2 0.03
37 4 0.06
38 1 0.02
40 42 0.67
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.40
Consensus pattern (39 bp):
ATTTCGCATTGCGATAGTCATTTTCGCTTGCGATAGTCA
Found at i:440675 original size:20 final size:20
Alignment explanation
Indices: 440652--440740 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
440642 CTGAAACTTT
440652 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
440672 AAATCGCAACACAAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
440692 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** *
440712 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
440731 AAATCGCAAC
1 AAATCGCAAC
440741 GACAGAATCG
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
19 12 0.21
20 46 0.79
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.15
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:441131 original size:22 final size:22
Alignment explanation
Indices: 441069--441134 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
441059 TGACCGTGAA
*
441069 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
441091 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
441113 TGATTTCGTCAGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
441135 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:441383 original size:21 final size:21
Alignment explanation
Indices: 441359--441404 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
441349 TATTCGCATT
441359 GCGAATTAGGAAAATCGCAAA
1 GCGAATTAGGAAAATCGCAAA
* *
441380 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAA
441401 GCGA
1 GCGA
441405 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAA
Found at i:441462 original size:20 final size:20
Alignment explanation
Indices: 441439--441484 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
441429 GGAAACTGAT
441439 TTGCGATACCGGAGATCGCG
1 TTGCGATACCGGAGATCGCG
441459 TTGCGATACCGGAGATCGCG
1 TTGCGATACCGGAGATCGCG
441479 TTGCGA
1 TTGCGA
441485 ATTATCGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.22
Consensus pattern (20 bp):
TTGCGATACCGGAGATCGCG
Found at i:444436 original size:26 final size:25
Alignment explanation
Indices: 444390--444442 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
444380 AAATAAATAA
* *
444390 AATATTAAAATTAATATTTTAATCCT
1 AATATTAAAACTAATAGTTTAA-CCT
*
444416 AATATTAAAACTAATCGTTTAACCT
1 AATATTAAAACTAATAGTTTAACCT
444441 AA
1 AA
444443 AAGTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (25 bp):
AATATTAAAACTAATAGTTTAACCT
Found at i:445700 original size:31 final size:31
Alignment explanation
Indices: 445662--445721 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
445652 CATAGGTTCA
** *
445662 TGTCCATATGTCCTGAATGACATAGGTAAAC
1 TGTCCATATGTCCCAAAGGACATAGGTAAAC
445693 TGTCCATATGTCCCAAAGGACATAGGTAA
1 TGTCCATATGTCCCAAAGGACATAGGTAA
445722 CCCTCGACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
TGTCCATATGTCCCAAAGGACATAGGTAAAC
Found at i:446047 original size:19 final size:21
Alignment explanation
Indices: 445993--446050 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 21
445983 TCACAATTAT
445993 ACTAACATAGTAACATGTACTC
1 ACTAACATA-TAACATGTACTC
446015 ACTTAGATCATATAACATGTAC-C
1 AC-TA-A-CATATAACATGTACTC
446038 A-TAACATATAACA
1 ACTAACATATAACA
446051 CATACAATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 9 0.27
20 1 0.03
21 2 0.06
22 2 0.06
23 4 0.12
24 11 0.33
25 4 0.12
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (21 bp):
ACTAACATATAACATGTACTC
Found at i:446462 original size:19 final size:22
Alignment explanation
Indices: 446410--446465 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
446400 GTACTACCCT
446410 TAGGGTATCGATACCTCTATGC
1 TAGGGTATCGATACCTCTATGC
446432 TAGGGTATCGATACC-CTAT-C
1 TAGGGTATCGATACCTCTATGC
*
446452 TA-GGTACCGATACC
1 TAGGGTATCGATACC
446466 AAACTTAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 11 0.33
20 3 0.09
21 4 0.12
22 15 0.45
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (22 bp):
TAGGGTATCGATACCTCTATGC
Found at i:446519 original size:21 final size:21
Alignment explanation
Indices: 446489--446565 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
446479 AAGTTCCTCG
*
446489 GGTATTGATACCCTTCATATA
1 GGTATCGATACCCTTCATATA
**
446510 GGTATCGATACATCCACCATAT-
1 GGTATCGATAC--CCTTCATATA
** *
446532 GGTATCGATACTGTTCATACA
1 GGTATCGATACCCTTCATATA
*
446553 GATATCGATACCC
1 GGTATCGATACCC
446566 CTTTGAATGT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
20 4 0.10
21 20 0.48
22 11 0.26
23 7 0.17
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCCTTCATATA
Found at i:447141 original size:12 final size:12
Alignment explanation
Indices: 447124--447167 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
447114 AACTCTGGAA
447124 CTTTTCCTTTCC
1 CTTTTCCTTTCC
447136 CTTTTCCTTTCC
1 CTTTTCCTTTCC
*
447148 CTTTTCCCTTCC
1 CTTTTCCTTTCC
447160 CTTTTCCT
1 CTTTTCCT
447168 CATCCACGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (12 bp):
CTTTTCCTTTCC
Found at i:450426 original size:21 final size:21
Alignment explanation
Indices: 450400--450439 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
450390 TTAACTATGG
450400 AAAAGG-TATATAAATAAGTAT
1 AAAAGGATAT-TAAATAAGTAT
*
450421 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAAATAAGT
450440 TGTGTAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAAATAAGTAT
Found at i:455283 original size:21 final size:21
Alignment explanation
Indices: 455254--455307 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
455244 TTTGTTGAAT
*
455254 GTTGAGAAGATGGTGTTGTGGG
1 GTTG-GAAGATGGTGTAGTGGG
**
455276 GTTGGAAGATTTTGTAGTGGG
1 GTTGGAAGATGGTGTAGTGGG
*
455297 GTGGGAAGATG
1 GTTGGAAGATG
455308 CAGAAGGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.31
Consensus pattern (21 bp):
GTTGGAAGATGGTGTAGTGGG
Found at i:457980 original size:26 final size:26
Alignment explanation
Indices: 457940--458023 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
457930 CACATCGCTA
*
457940 ACTTTATAAACATAAACAAATCCACAT
1 ACTTT-TAACCATAAACAAATCCACAT
457967 ACTTTTAACCATAAACAAATCCACAT
1 ACTTTTAACCATAAACAAATCCACAT
*
457993 ACTTTTAACCATAAACAAATGCACAT
1 ACTTTTAACCATAAACAAATCCACAT
*
458019 TCTTT
1 ACTTT
458024 AGACAGGAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 49 0.91
27 5 0.09
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.30
Consensus pattern (26 bp):
ACTTTTAACCATAAACAAATCCACAT
Done.