Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009631.1 Hibiscus syriacus cultivar Beakdansim tig00117027_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: 652059
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:358490 original size:92 final size:91
Alignment explanation
Indices: 358333--358522 Score: 353
Period size: 92 Copynumber: 2.1 Consensus size: 91
358323 ACTGAAAGTA
358333 TCGATACTAGCCCAAGAGTATCGATACTCCTGCAAAATTTTTCATACTTTCTACAAGTATCGATA
1 TCGATACTAGCCCAAGAGTATCGATACTCCTGCAAAATTTTTCATACTTTCTACAAGTATCGATA
358398 CTTTTAAACATTCTGGACTGCATAGTT
66 CTTTTAAACATTCTGGACTGCATA-TT
*
358425 TCGATACTAGCCCAAGAGTATCGATACTCCTGCAAAATTTTTCATATTTTCTACAAGTATCGATA
1 TCGATACTAGCCCAAGAGTATCGATACTCCTGCAAAATTTTTCATACTTTCTACAAGTATCGATA
358490 CTTTTAAACATTCTGGACTGCATATT
66 CTTTTAAACATTCTGGACTGCATATT
*
358516 TCTATAC
1 TCGATAC
358523 ATTTTACATC
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
91 8 0.08
92 88 0.92
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (91 bp):
TCGATACTAGCCCAAGAGTATCGATACTCCTGCAAAATTTTTCATACTTTCTACAAGTATCGATA
CTTTTAAACATTCTGGACTGCATATT
Found at i:359348 original size:25 final size:25
Alignment explanation
Indices: 359313--359386 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
359303 TTAAATATAG
*
359313 TAAATAATATTATTTATTATAAAAC
1 TAAATATTATTATTTATTATAAAAC
*
359338 TAAATATTATTATTT-TTA-AAATAT
1 TAAATATTATTATTTATTATAAA-AC
*
359362 TAAA-ATAATTTATTTATTATTAAAA
1 TAAATATTA-TTATTTATTA-TAAAA
359387 TCTTATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
23 6 0.15
24 14 0.34
25 17 0.41
26 1 0.02
27 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATATTATTATTTATTATAAAAC
Found at i:359544 original size:23 final size:22
Alignment explanation
Indices: 359496--359563 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 22
359486 GTGTTATATT
**
359496 ATATTTTAAAATATTAATTAGT
1 ATATTTTAAAATATTAATTAAA
* *
359518 ATATTTTAAATATGTTTATTAAA
1 ATATTTTAAA-ATATTAATTAAA
* *
359541 ATATTATTAGATTATTATATTAA
1 ATATT-TTAAAATATTA-ATTAA
359564 TATTAAATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 10 0.29
23 16 0.46
24 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
ATATTTTAAAATATTAATTAAA
Found at i:359670 original size:29 final size:27
Alignment explanation
Indices: 359638--359728 Score: 89
Period size: 26 Copynumber: 3.4 Consensus size: 27
359628 TAATTTACTA
359638 TATATTATTAAAATAAAAATATAATATCT
1 TATATTATTAAAAT-AAAATATAATAT-T
* * * *
359667 TATATTATTATAATATAATTTATTATT
1 TATATTATTAAAATAAAATATAATATT
*
359694 T-TATTA-TAAAATTAAAATATAA-AAT
1 TATATTATTAAAA-TAAAATATAATATT
359719 TATATTATTA
1 TATATTATTA
359729 GAAAATTAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
25 7 0.14
26 17 0.34
27 4 0.08
28 9 0.18
29 13 0.26
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
TATATTATTAAAATAAAATATAATATT
Found at i:359685 original size:23 final size:23
Alignment explanation
Indices: 359655--359702 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
359645 TTAAAATAAA
*
359655 AATATAATATCTTATATTATTAT
1 AATATAATATATTATATTATTAT
* *
359678 AATATAATTTATTATTTTATTAT
1 AATATAATATATTATATTATTAT
359701 AA
1 AA
359703 AATTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:366706 original size:73 final size:76
Alignment explanation
Indices: 366549--366741 Score: 234
Period size: 73 Copynumber: 2.5 Consensus size: 76
366539 GGTAATTTGG
*
366549 CTGAATCCCGATATTATTGATGTATGTTTATGTCGGT-TAGACTGTCAAATCTTGATACATTGAT
1 CTGAATCCCGATATTATTGATGTATGTTTATGTCGGTGCA-ACTGT---ATCTTGATACATTGAT
366613 AGTCCAGGGAGATGT
62 AGTCCAGGGAGATGT
*
366628 CTGAATCCCGATATTATTGATGTATGTTTATGGCGGTGCAACTGT-TC-T-ATACATTGAT-GTT
1 CTGAATCCCGATATTATTGATGTATGTTTATGTCGGTGCAACTGTATCTTGATACATTGATAG-T
* *
366689 CCTGTGAGATGT
65 CCAGGGAGATGT
* * * *
366701 TTGAATCCGGATATCATTGATGTATGTTTATGTCGGCGCAA
1 CTGAATCCCGATATTATTGATGTATGTTTATGTCGGTGCAA
366742 GTATCGAATC
Statistics
Matches: 103, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
72 1 0.01
73 57 0.55
74 1 0.01
75 2 0.02
79 41 0.40
80 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (76 bp):
CTGAATCCCGATATTATTGATGTATGTTTATGTCGGTGCAACTGTATCTTGATACATTGATAGTC
CAGGGAGATGT
Found at i:366785 original size:79 final size:77
Alignment explanation
Indices: 366549--366788 Score: 233
Period size: 79 Copynumber: 3.1 Consensus size: 77
366539 GGTAATTTGG
** * * *
366549 CTGAATCCCGATATTATTGATGTATGTTTATGTCGGTTAGACTGTCAAATCTTGATACATTGATA
1 CTGAATCCCGATATTATTGATGTATGTTTATGTCGGGCA-A-TATCGAATCTCGATACATTGAT-
**
366614 G-TCCAGGGAGATGT
63 GTTCCATTGAGATGT
* * *
366628 CTGAATCCCGATATTATTGATGTATGTTTATGGCGGTGCAA-CT-G--T-TCTATACATTGATGT
1 CTGAATCCCGATATTATTGATGTATGTTTATGTCGG-GCAATATCGAATCTCGATACATTGATGT
366688 TCC-TGTGAGATGT
65 TCCAT-TGAGATGT
* * * *
366701 TTGAATCCGGATATCATTGATGTATGTTTATGTCGGCGCAAGTATCGAATCTCGGTACATTGATG
1 CTGAATCCCGATATTATTGATGTATGTTTATGTCGG-GCAA-TATCGAATCTCGATACATTGATG
*
366766 TTCCATTGAGATAT
64 TTCCATTGAGATGT
366780 CTGAATCCC
1 CTGAATCCC
366789 AGATCTTAAT
Statistics
Matches: 131, Mismatches: 20, Indels: 20
0.77 0.12 0.12
Matches are distributed among these distances:
72 1 0.01
73 57 0.44
74 1 0.01
75 1 0.01
76 1 0.01
77 1 0.01
78 1 0.01
79 66 0.50
80 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (77 bp):
CTGAATCCCGATATTATTGATGTATGTTTATGTCGGGCAATATCGAATCTCGATACATTGATGTT
CCATTGAGATGT
Found at i:376500 original size:45 final size:48
Alignment explanation
Indices: 376436--376529 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 48
376426 ATTTAAATAA
376436 TTATTTTTAAAAATCAACTCATGAGT-A-TAACA-TAGTACCATTCAG
1 TTATTTTTAAAAATCAACTCATGAGTAACTAACACTAGTACCATTCAG
376481 TTATTTTTAAAAATCAACTCATGAGTAACTAACACTAGTACCATTCAG
1 TTATTTTTAAAAATCAACTCATGAGTAACTAACACTAGTACCATTCAG
376529 T
1 T
376530 CGTCCGAGCC
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
45 26 0.57
46 1 0.02
47 5 0.11
48 14 0.30
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (48 bp):
TTATTTTTAAAAATCAACTCATGAGTAACTAACACTAGTACCATTCAG
Found at i:377354 original size:54 final size:57
Alignment explanation
Indices: 377268--377385 Score: 152
Period size: 55 Copynumber: 2.1 Consensus size: 57
377258 GTTATCGAAC
* * *
377268 ATTAAACGAACGTTAAATTAACATGTTGACATACGTCAAAT-GAACATTTTTGTGAAT
1 ATTAAACGAACG-TAAATTAACATGTTGACATACGTCAAATAAAACATATTCGTGAAT
* * *
377325 ATTAAACGAACG-AAA-TAACATGTTTACATACTTTAAATAAAACATATTCGTGAAT
1 ATTAAACGAACGTAAATTAACATGTTGACATACGTCAAATAAAACATATTCGTGAAT
377380 ATTAAA
1 ATTAAA
377386 TGAGCATGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
54 20 0.37
55 22 0.41
57 12 0.22
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (57 bp):
ATTAAACGAACGTAAATTAACATGTTGACATACGTCAAATAAAACATATTCGTGAAT
Found at i:384864 original size:118 final size:115
Alignment explanation
Indices: 384645--384877 Score: 423
Period size: 118 Copynumber: 2.0 Consensus size: 115
384635 TCATTTTTAA
384645 ATATTCAAGAAAAAGGGATCGTGTTATTCGTTCAAAATCACAACCGTCTTTCCTGTTTTGATGTG
1 ATATTCAAGAAAAAGGGATCGTGTTATTCGTTCAAAATCACAACCGTCTTTCCTGTTTTGATGTG
384710 TAATGGGAAAGGCTAAACAATGCACTTTGAGTTTTGAGTATC-AACGGTT
66 TAATGGGAAAGGCTAAACAATGCACTTTGAGTTTTGAGTATCTAACGGTT
384759 ATATTCAAGAAAAAGGGATCGTGTTATTCGTTCACAAATCACAACCGTCTTTCCTTGTTTTGATG
1 ATATTCAAGAAAAAGGGATCGTGTTATTCGTTCA-AAATCACAACCGTCTTTCC-TGTTTTGATG
384824 TGTAACTTGGGAAAGGCTAAACAATGCACTTTGAGTTTTGAGTATCTAACGGTT
64 TGTAA--TGGGAAAGGCTAAACAATGCACTTTGAGTTTTGAGTATCTAACGGTT
384878 GCTTTGCTTT
Statistics
Matches: 114, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
114 34 0.30
115 19 0.17
116 15 0.13
118 39 0.34
119 7 0.06
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (115 bp):
ATATTCAAGAAAAAGGGATCGTGTTATTCGTTCAAAATCACAACCGTCTTTCCTGTTTTGATGTG
TAATGGGAAAGGCTAAACAATGCACTTTGAGTTTTGAGTATCTAACGGTT
Found at i:393123 original size:20 final size:21
Alignment explanation
Indices: 393084--393124 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
393074 CCTGGTGGAG
393084 TCCGATTTCCACCGGGAATGC
1 TCCGATTTCCACCGGGAATGC
393105 TCCGATTTCCACC-GGAATGC
1 TCCGATTTCCACCGGGAATGC
393125 CTCGGTGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.20, C:0.34, G:0.22, T:0.24
Consensus pattern (21 bp):
TCCGATTTCCACCGGGAATGC
Found at i:397776 original size:20 final size:18
Alignment explanation
Indices: 397751--397794 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
397741 TCATTTCAAT
397751 TAATAAAATACTACTATTAA
1 TAATAAAATACTAC-ATT-A
* *
397771 TAATAAATTATTACATTA
1 TAATAAAATACTACATTA
397789 TAATAA
1 TAATAA
397795 TTTTCTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 3 0.14
20 12 0.55
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATAAAATACTACATTA
Found at i:405966 original size:14 final size:14
Alignment explanation
Indices: 405944--405990 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
405934 TGCAAAGGAA
*
405944 AATTAATATAGTTT
1 AATTTATATAGTTT
405958 AATTTATATA----
1 AATTTATATAGTTT
405968 AA-TTATATAGTTT
1 AATTTATATAGTTT
405981 AATTTATATA
1 AATTTATATA
405991 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:405977 original size:23 final size:24
Alignment explanation
Indices: 405943--405992 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
405933 ATGCAAAGGA
405943 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
405967 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
405990 AAA
1 AAA
405993 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:406506 original size:19 final size:20
Alignment explanation
Indices: 406466--406510 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
406456 AATTTTTCTA
*
406466 TTCCATCTAAATTTTCCAAT
1 TTCCATCTAAATTCTCCAAT
*
406486 TTCCCTCTAAATTCT-CAAT
1 TTCCATCTAAATTCTCCAAT
406505 TTCCAT
1 TTCCAT
406511 ATATTCTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (20 bp):
TTCCATCTAAATTCTCCAAT
Found at i:408769 original size:26 final size:24
Alignment explanation
Indices: 408707--408769 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
408697 CATTTTAATC
408707 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
408731 AAAATATAT-TTATTAACAT-TTT
1 AAAATATATATTATTAAAATATTT
408753 CAATAATATAATATTAT
1 -AA-AATAT-ATATTAT
408770 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 3 0.09
23 11 0.33
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:408772 original size:32 final size:31
Alignment explanation
Indices: 408735--408804 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
408725 ATATTTAAAA
* *
408735 TATATTTATTAACATTTTCAATAATATAAT-AT
1 TATATTT-TTAACATTAT-AATAAAATAATAAT
*
408767 TATATTTTTAATATTATAATAAAATAATCAAT
1 TATATTTTTAACATTATAATAAAATAAT-AAT
408799 TATATT
1 TATATT
408805 ATAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 10 0.30
31 8 0.24
32 15 0.45
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (31 bp):
TATATTTTTAACATTATAATAAAATAATAAT
Found at i:408806 original size:23 final size:23
Alignment explanation
Indices: 408777--408830 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
408767 TATATTTTTA
408777 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAA-CATATT
* *
408800 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAACATATT
408823 ATATTATA
1 ATATTATA
408831 TTATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAACATATT
Found at i:408844 original size:28 final size:28
Alignment explanation
Indices: 408756--408849 Score: 72
Period size: 28 Copynumber: 3.4 Consensus size: 28
408746 ACATTTTCAA
* *
408756 TAATATAATATTATATT-T-TTAATATTA
1 TAATAAAATATTATATTATATT-ATATTT
* *
408783 TAATAAAATAATCA-ATTATATTATA--A
1 TAATAAAAT-ATTATATTATATTATATTT
408809 TAATATAAGATATTATATTATATTATATTT
1 TAATA-AA-ATATTATATTATATTATATTT
*
408839 TAATAATATAT
1 TAATAAAATAT
408850 AATAAATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
26 6 0.11
27 16 0.30
28 24 0.44
29 3 0.06
30 5 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
TAATAAAATATTATATTATATTATATTT
Found at i:408940 original size:27 final size:28
Alignment explanation
Indices: 408894--408947 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
408884 ATTTCATAGA
408894 AATAATATTATTAAATTA-TTAATAATG
1 AATAATATTATTAAATTATTTAATAATG
*
408921 AATAATATTATT-TATATATTTAATAAT
1 AATAATATTATTAAAT-TATTTAATAAT
408948 AATCTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 2 0.08
27 14 0.58
28 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
AATAATATTATTAAATTATTTAATAATG
Found at i:409293 original size:14 final size:14
Alignment explanation
Indices: 409262--409293 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
409252 ACAACATCGT
*
409262 AAAACATTTTTCAG
1 AAAACATTTTTCAA
409276 AAAACATTTTTCAA
1 AAAACATTTTTCAA
409290 AAAA
1 AAAA
409294 TATAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (14 bp):
AAAACATTTTTCAA
Found at i:424815 original size:23 final size:24
Alignment explanation
Indices: 424776--424831 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
424766 ATAATAAGTG
*
424776 AATTTCTAAAAT-TTAAAAAA-TAA
1 AATTT-TAAAATATAAAAAAATTAA
424799 AATATTTAAAATATAAAAAAATTAA
1 AAT-TTTAAAATATAAAAAAATTAA
424824 AATTTTAA
1 AATTTTAA
424832 GAGAACGACT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 9 0.31
24 14 0.48
25 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AATTTTAAAATATAAAAAAATTAA
Found at i:424823 original size:16 final size:16
Alignment explanation
Indices: 424783--424826 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
424773 GTGAATTTCT
*
424783 AAAATTTAAAAAATAA
1 AAAATTTAAAATATAA
*
424799 AATATTTAAAATATAA
1 AAAATTTAAAATATAA
*
424815 AAAAATTAAAAT
1 AAAATTTAAAAT
424827 TTTAAGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTTAAAATATAA
Found at i:451558 original size:18 final size:18
Alignment explanation
Indices: 451535--451579 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
451525 AACATTCCCG
*
451535 GTAATCTTATTCCCGCCT
1 GTAATCTTATTCCCGCCA
* *
451553 GTAATCATATTCTCGCCA
1 GTAATCTTATTCCCGCCA
451571 GTAATCTTA
1 GTAATCTTA
451580 CATTAACCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (18 bp):
GTAATCTTATTCCCGCCA
Found at i:463713 original size:147 final size:147
Alignment explanation
Indices: 463447--463741 Score: 558
Period size: 147 Copynumber: 2.0 Consensus size: 147
463437 TTGGATTCGG
463447 ATTCAGGACGTTGAAAGCATAAAATATGACTTTCGGAAATTTGGAATTTCGGTCAAAATCAAAGT
1 ATTCAGGACGTTGAAAGCATAAAATATGACTTTCGGAAATTTGGAATTTCGGTCAAAATCAAAGT
463512 CAACGGGTTTGACTGACAATTTCGAGGCATTCGGGTTCTAATTTCGAAAAACGGACAGCAGAATC
66 CAACGGGTTTGACTGACAATTTCGAGGCATTCGGGTTCTAATTTCGAAAAACGGACAGCAGAATC
463577 -GATTTGGAACGTCGAA
131 GGATTTGGAACGTCGAA
463593 ATTCAGGACGTTGAAAGCATAAAATATGACTTTTCGGAAATTTGGAATTTTCGGTC-AAATCAAA
1 ATTCAGGACGTTGAAAGCATAAAATATGAC-TTTCGGAAATTTGGAA-TTTCGGTCAAAATCAAA
463657 GTCAACGGGTTTGACTGACAATTTCGAGGCATTCGGGTTCTAATTTCGAAAAACGGACAGCAGAA
64 GTCAACGGGTTTGACTGACAATTTCGAGGCATTCGGGTTCTAATTTCGAAAAACGGACAGCAGAA
463722 TCGGATTTGGAACGTCGAA
129 TCGGATTTGGAACGTCGAA
463741 A
1 A
463742 AATTGTCAGG
Statistics
Matches: 146, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
146 30 0.21
147 91 0.62
148 25 0.17
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (147 bp):
ATTCAGGACGTTGAAAGCATAAAATATGACTTTCGGAAATTTGGAATTTCGGTCAAAATCAAAGT
CAACGGGTTTGACTGACAATTTCGAGGCATTCGGGTTCTAATTTCGAAAAACGGACAGCAGAATC
GGATTTGGAACGTCGAA
Found at i:463857 original size:5 final size:5
Alignment explanation
Indices: 463847--463946 Score: 65
Period size: 5 Copynumber: 17.0 Consensus size: 5
463837 CAACGGTCAA
463847 CGGGT CGGGT CAACGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT CAACGGGT
1 CGGGT CGGGT C---GGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT ---CGGGT
463901 CGGGT CGGGT CAACGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT
1 CGGGT CGGGT ---CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT
463947 TGTGACCGGT
Statistics
Matches: 80, Mismatches: 0, Indels: 30
0.73 0.00 0.27
Matches are distributed among these distances:
5 55 0.69
8 25 0.31
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (5 bp):
CGGGT
Found at i:463859 original size:13 final size:11
Alignment explanation
Indices: 463847--463946 Score: 57
Period size: 13 Copynumber: 8.5 Consensus size: 11
463837 CAACGGTCAA
463847 CGGGTCGGGTC
1 CGGGTCGGGTC
463858 AACGGGTCGGGT-
1 --CGGGTCGGGTC
463870 CGGGTCAACGGGT-
1 CGGGT---CGGGTC
463883 CGGGTCGGGTC
1 CGGGTCGGGTC
463894 AACGGGTCGGGT-
1 --CGGGTCGGGTC
463906 CGGGTCAACGGGT-
1 CGGGT---CGGGTC
463919 CGGGTCGGGTC
1 CGGGTCGGGTC
463930 AACGGGTCGGGT-
1 --CGGGTCGGGTC
463942 CGGGT
1 CGGGT
463947 TGTGACCGGT
Statistics
Matches: 75, Mismatches: 0, Indels: 27
0.74 0.00 0.26
Matches are distributed among these distances:
10 25 0.33
13 50 0.67
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (11 bp):
CGGGTCGGGTC
Found at i:463870 original size:18 final size:18
Alignment explanation
Indices: 463847--463946 Score: 200
Period size: 18 Copynumber: 5.6 Consensus size: 18
463837 CAACGGTCAA
463847 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
463865 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
463883 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
463901 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
463919 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
463937 CGGGTCGGGT
1 CGGGTCGGGT
463947 TGTGACCGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 82 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:468340 original size:5 final size:5
Alignment explanation
Indices: 468332--468405 Score: 67
Period size: 5 Copynumber: 13.0 Consensus size: 5
468322 GTCGGGTCAA
468332 CGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT
468383 CGGGT CAACGGGT CGGGT CGGGT
1 CGGGT ---CGGGT CGGGT CGGGT
468406 TGTGACCGTC
Statistics
Matches: 60, Mismatches: 0, Indels: 18
0.77 0.00 0.23
Matches are distributed among these distances:
5 45 0.75
8 15 0.25
ACGTcount: A:0.08, C:0.22, G:0.53, T:0.18
Consensus pattern (5 bp):
CGGGT
Found at i:468379 original size:23 final size:23
Alignment explanation
Indices: 468350--468405 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
468340 GTCGGGTCAA
468350 CGGGTCGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCGGGTCAACGGGT
468373 CGGGTCGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCGGGTCAACGGGT
468396 CGGGTCGGGT
1 CGGGTCGGGT
468406 TGTGACCGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.07, C:0.21, G:0.54, T:0.18
Consensus pattern (23 bp):
CGGGTCGGGTCGGGTCAACGGGT
Found at i:468405 original size:18 final size:18
Alignment explanation
Indices: 468321--468383 Score: 126
Period size: 18 Copynumber: 3.5 Consensus size: 18
468311 AACGGTCAAC
468321 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
468339 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
468357 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
468375 GGTCGGGTC
1 GGTCGGGTC
468384 GGGTCAACGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:470547 original size:24 final size:24
Alignment explanation
Indices: 470520--470626 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
470510 AAACGGAGAT
*
470520 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
470544 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
470568 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
470592 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
470616 ATCAGAAATCA
1 ATCAGAAATCA
470627 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:470626 original size:48 final size:48
Alignment explanation
Indices: 470520--470628 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
470510 AAACGGAGAT
* * * *
470520 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
470568 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
470616 ATCAGAAATCAGA
1 ATCAGAAATCAGA
470629 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:473100 original size:7 final size:7
Alignment explanation
Indices: 473088--473119 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
473078 TGGTCAACTC
473088 CGGTCAA
1 CGGTCAA
473095 CGGTCAA
1 CGGTCAA
473102 CGGGTCAA
1 C-GGTCAA
473110 CGGTCAA
1 CGGTCAA
473117 CGG
1 CGG
473120 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:473109 original size:15 final size:15
Alignment explanation
Indices: 473089--473135 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
473079 GGTCAACTCC
473089 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
473104 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
473119 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
473132 GGTC
1 GGTC
473136 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:473140 original size:18 final size:18
Alignment explanation
Indices: 473117--473203 Score: 129
Period size: 18 Copynumber: 4.6 Consensus size: 18
473107 CAACGGTCAA
473117 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
473135 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCAA-----CGGGT
473158 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
473176 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
473194 CGGGTCGGGT
1 CGGGTCGGGT
473204 TGTGACCGGT
Statistics
Matches: 64, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
18 46 0.72
23 18 0.28
ACGTcount: A:0.09, C:0.22, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:473153 original size:8 final size:8
Alignment explanation
Indices: 473089--473135 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
473079 GGTCAACTCC
473089 GGTCAAC-
1 GGTCAACG
473096 GGTCAACG
1 GGTCAACG
473104 GGTCAAC-
1 GGTCAACG
473111 GGTCAACG
1 GGTCAACG
473119 GGT---CG
1 GGTCAACG
473124 GGTCAACG
1 GGTCAACG
473132 GGTC
1 GGTC
473136 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:473168 original size:41 final size:41
Alignment explanation
Indices: 473117--473203 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
473107 CAACGGTCAA
473117 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAACGGGTCGGGT
473158 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAACGGGTCGGGT
473199 CGGGT
1 CGGGT
473204 TGTGACCGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.52, T:0.17
Consensus pattern (41 bp):
CGGGTCGGGTCAACGGGTCGGGTCGGGTCAACGGGTCGGGT
Found at i:473199 original size:13 final size:13
Alignment explanation
Indices: 473096--473181 Score: 79
Period size: 13 Copynumber: 6.3 Consensus size: 13
473086 TCCGGTCAAC
*
473096 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
473111 GGTCAACGGGTCG
1 GGTCAACGGGTCG
473124 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
473142 GGTCAACGGGTCG
1 GGTCAACGGGTCG
473155 GGT---CGGGTCG
1 GGTCAACGGGTCG
473165 GGTCAACGGGTCG
1 GGTCAACGGGTCG
473178 GGTC
1 GGTC
473182 GGGTCAACGG
Statistics
Matches: 62, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
10 10 0.16
13 27 0.44
15 12 0.19
18 13 0.21
ACGTcount: A:0.14, C:0.23, G:0.47, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:473199 original size:23 final size:23
Alignment explanation
Indices: 473130--473186 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
473120 GTCGGGTCAA
473130 CGGGTCGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCGGGTCAACGGGT
473153 CGGGTCGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCGGGTCAACGGGT
473176 CGGGTCGGGTC
1 CGGGTCGGGTC
473187 AACGGGTCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.07, C:0.23, G:0.53, T:0.18
Consensus pattern (23 bp):
CGGGTCGGGTCGGGTCAACGGGT
Found at i:475790 original size:2 final size:2
Alignment explanation
Indices: 475783--475815 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
475773 ATCATTGATT
475783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
475816 TATTTTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:478177 original size:21 final size:19
Alignment explanation
Indices: 478149--478311 Score: 128
Period size: 21 Copynumber: 7.9 Consensus size: 19
478139 ATTTTCTAAA
478149 TTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCCAAG
* *
478168 TTCGCGTTGCGATTTATTCCAAA
1 TT--CGTTGCGA--TAGTCCAAG
*
478191 TTCGTTACGATAGTCCAAG
1 TTCGTTGCGATAGTCCAAG
*
478210 TTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCCAAG
*
478229 TTCGCGTTGCGATTTATTCCAAG
1 TT--CGTTGCGA--TAGTCCAAG
*
478252 TTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCCAAG
* *
478271 TTCGCGTTGCGATTTATTCCAAA
1 TT--CGTTGCGA--TAGTCCAAG
* *
478294 TTCATTACGATAGTCCAA
1 TTCGTTGCGATAGTCCAA
478312 AATCGCAACG
Statistics
Matches: 115, Mismatches: 17, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
19 44 0.38
21 45 0.39
23 26 0.23
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (19 bp):
TTCGTTGCGATAGTCCAAG
Found at i:478218 original size:61 final size:61
Alignment explanation
Indices: 478149--478283 Score: 216
Period size: 61 Copynumber: 2.2 Consensus size: 61
478139 ATTTTCTAAA
478149 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTACGATAGTCCAAG
1 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTACGATAGTCCAAG
* * * *
478210 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTACGATAGTCCAAG
478271 TTCGCGTTGCGAT
1 TT--CGTTGCGAT
478284 TTATTCCAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 59 0.87
63 9 0.13
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (61 bp):
TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTACGATAGTCCAAG
Found at i:478250 original size:42 final size:42
Alignment explanation
Indices: 478204--478308 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
478194 GTTACGATAG
478204 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
478246 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * *
478288 TCCAAATTCATTACGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
478309 CAAAATCGCA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:479178 original size:21 final size:21
Alignment explanation
Indices: 479154--479245 Score: 116
Period size: 21 Copynumber: 4.4 Consensus size: 21
479144 CACCAATAGT
479154 TCGCAACGAATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAA
* *
479175 TCGCAACGCGAACTTGGACT--A
1 TCGCAA--CGAATTTGGAATAAA
*
479196 TCGCAACGAATTTGTAATAAA
1 TCGCAACGAATTTGGAATAAA
*
479217 TCGCAACAAATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAA
479238 TCGCAACG
1 TCGCAACG
479246 CGAACTTCGA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.15
21 40 0.68
23 10 0.17
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (21 bp):
TCGCAACGAATTTGGAATAAA
Found at i:488811 original size:15 final size:15
Alignment explanation
Indices: 488793--488848 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
488783 TAACCGGTTT
488793 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
488808 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
488825 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
488840 CGATTTTAA
1 CGGTTTTAA
488849 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:488821 original size:17 final size:17
Alignment explanation
Indices: 488796--488846 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
488786 CCGGTTTCGG
488796 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
488813 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
488828 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
488845 TT
1 TT
488847 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:489265 original size:13 final size:13
Alignment explanation
Indices: 489244--489298 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
489234 AAGTTCGATA
*
489244 AATTCAAATACTT
1 AATTGAAATACTT
489257 AATTGAAATACTT
1 AATTGAAATACTT
* *
489270 AATT-AATTCAACAT
1 AATTGAAAT--ACTT
489284 AATTGAAATACTT
1 AATTGAAATACTT
489297 AA
1 AA
489299 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:489380 original size:32 final size:33
Alignment explanation
Indices: 489284--489382 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
489274 AATTCAACAT
* * *
489284 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
489317 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
489350 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
489382 A
1 A
489383 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:489401 original size:21 final size:21
Alignment explanation
Indices: 489377--489416 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
489367 ACTTCAAGTT
489377 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
489398 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
489417 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:491732 original size:11 final size:12
Alignment explanation
Indices: 491711--491756 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
491701 TCCGGATAAA
491711 AACCGGTTTTTT
1 AACCGGTTTTTT
491723 AACCGGTTTTTTT
1 AACCGG-TTTTTT
491736 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
491750 ATCCGGT
1 AACCGGT
491757 AAAAAAATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:491741 original size:15 final size:14
Alignment explanation
Indices: 491710--491749 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
491700 TTCCGGATAA
491710 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
491723 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
491736 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
491750 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:495553 original size:16 final size:16
Alignment explanation
Indices: 495532--495564 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
495522 TACTATTCAT
*
495532 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
495548 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
495564 G
1 G
495565 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:504250 original size:20 final size:20
Alignment explanation
Indices: 504220--504388 Score: 117
Period size: 20 Copynumber: 8.3 Consensus size: 20
504210 GTTTCCAGAT
*
504220 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
504240 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
** *
504260 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
504283 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
504303 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
*
504323 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
504343 TTGCAACGAGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
504363 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
504383 TCGCAA
1 TCGCAA
504389 CACTGAATTT
Statistics
Matches: 117, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.03
20 90 0.77
21 11 0.09
22 9 0.08
23 3 0.03
24 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:504292 original size:22 final size:22
Alignment explanation
Indices: 504235--504293 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
504225 ACGCGATTCT
504235 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
504257 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
504278 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
504294 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:504389 original size:20 final size:20
Alignment explanation
Indices: 504302--504389 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
504292 GAATATGTAA
* *
504302 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
504322 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
504342 ATTGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
504362 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
504382 GTCGCAAC
1 ATCGCAAC
504390 ACTGAATTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:505246 original size:24 final size:24
Alignment explanation
Indices: 505214--505267 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
505204 GTATTCAAAA
505214 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
505238 TTTGATCTTGGTTAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
505262 TTTGAT
1 TTTGAT
505268 GATGTTTCAG
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:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:505459 original size:12 final size:12
Alignment explanation
Indices: 505442--505466 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
505432 ATATAATCCT
505442 GAAGAAGAAAAA
1 GAAGAAGAAAAA
505454 GAAGAAGAAAAA
1 GAAGAAGAAAAA
505466 G
1 G
505467 TTCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:507511 original size:18 final size:19
Alignment explanation
Indices: 507461--507503 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
507451 AATCATCTTT
507461 TCCTCTACCAAAATATGGA
1 TCCTCTACCAAAATATGGA
507480 TCCTCTACCAAAATATGGA
1 TCCTCTACCAAAATATGGA
507499 TCCTC
1 TCCTC
507504 ATCAAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.30, G:0.09, T:0.28
Consensus pattern (19 bp):
TCCTCTACCAAAATATGGA
Found at i:507565 original size:18 final size:18
Alignment explanation
Indices: 507542--507581 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
507532 AGAAAAAGGC
*
507542 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
*
507560 AATCAAAATCCCAATCAC
1 AATCAAAATCCCAATCAA
507578 AATC
1 AATC
507582 GGCTTCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.28, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:507893 original size:140 final size:140
Alignment explanation
Indices: 507636--507906 Score: 515
Period size: 140 Copynumber: 1.9 Consensus size: 140
507626 AAACGTTGTA
507636 TTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
507701 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
507766 TATGTGTATT
131 TATGTGTATT
*
507776 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
507841 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
507906 T
131 T
507907 GCAACGCGAA
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (140 bp):
TTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
TATGTGTATT
Found at i:507901 original size:20 final size:20
Alignment explanation
Indices: 507876--508114 Score: 145
Period size: 20 Copynumber: 12.8 Consensus size: 20
507866 TTACACATTC
* *
507876 ATTTGAATATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
507896 ATTTGACTATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
507916 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
507935 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
507950 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
507970 ATATGACTATCGCAACAC-A
1 ATTTGACTATCGCAACGCGA
* *
507989 A----A-AATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * * *
508004 ATTTGATTATTGCAATGGGT
1 ATTTGACTATCGCAACGCGA
* *
508024 ATTTGACTATCGTAACGAGA
1 ATTTGACTATCGCAACGCGA
*
508044 A----A--AACGCAACGCGA
1 ATTTGACTATCGCAACGCGA
508058 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
508078 ACTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
508098 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
508115 AGAAAATCGC
Statistics
Matches: 167, Mismatches: 34, Indels: 36
0.70 0.14 0.15
Matches are distributed among these distances:
14 27 0.16
15 6 0.04
16 1 0.01
18 1 0.01
19 6 0.04
20 126 0.75
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:507971 original size:54 final size:53
Alignment explanation
Indices: 507884--508093 Score: 249
Period size: 54 Copynumber: 3.9 Consensus size: 53
507874 TCATTTGAAT
* * *
507884 ATCGCAACGCAAATTTGACTATTGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAAC-CAAAA
* *
507938 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACACAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAAC-CAAAA
* * * * * * * *
507992 ATTGCAACGCGAATTTGATTATTGCAATGGGTATTTGACTATCGTAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACCA-AAA
* * *
508046 AACGCAACGCGAATTTGACTATCGCAACGCGAACTTGATTATCGCAAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAAC
508094 GGGTATTTGA
Statistics
Matches: 129, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
53 1 0.01
54 128 0.99
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (53 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACCAAAA
Found at i:508076 original size:74 final size:74
Alignment explanation
Indices: 507995--508154 Score: 239
Period size: 74 Copynumber: 2.2 Consensus size: 74
507985 CACAAAAATT
* * * *
507995 GCAACGCGAATTTGATTATTGCAATGGGTATTTGACTATCGTAACGAGAAAAACGCAACGCGAAT
1 GCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAAACGCAAAGCGAAT
*
508060 TTGACTATC
66 TAGACTATC
* * *
508069 GCAACGCGAACTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCGTAT
1 GCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAAACGCAAAGCGAAT
508134 TAGACTATC
66 TAGACTATC
*
508143 ACAACGCGAATT
1 GCAACGCGAATT
508155 GACTTTCGCG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (74 bp):
GCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAAACGCAAAGCGAAT
TAGACTATC
Found at i:508089 original size:108 final size:108
Alignment explanation
Indices: 507887--508093 Score: 283
Period size: 108 Copynumber: 1.9 Consensus size: 108
507877 TTTGAATATC
* *
507887 GCAACGCAAATTTGACTATTGCAACGCGAATTTGATTATCGCAACTCAAAAATCGCAACGCGAAT
1 GCAACGCAAATTTGACTATTGCAACGCGAATTTGACTATCGCAACTCAAAAAACGCAACGCGAAT
507952 TTGACTATCGCAACACGAATATGACTATCGCAACACAAAAATT
66 TTGACTATCGCAACACGAATATGACTATCGCAACACAAAAATT
* * * * * * *
507995 GCAACGCGAATTTGATTATTGCAATGGGTATTTGACTATCGTAAC-GAGAAAAACGCAACGCGAA
1 GCAACGCAAATTTGACTATTGCAACGCGAATTTGACTATCGCAACTCA-AAAAACGCAACGCGAA
* *
508059 TTTGACTATCGCAACGCGAACT-TGATTATCGCAAC
65 TTTGACTATCGCAACACGAA-TATGACTATCGCAAC
508094 GGGTATTTGA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 1 0.01
108 84 0.98
109 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (108 bp):
GCAACGCAAATTTGACTATTGCAACGCGAATTTGACTATCGCAACTCAAAAAACGCAACGCGAAT
TTGACTATCGCAACACGAATATGACTATCGCAACACAAAAATT
Found at i:508103 original size:40 final size:39
Alignment explanation
Indices: 507995--508156 Score: 128
Period size: 34 Copynumber: 4.4 Consensus size: 39
507985 CACAAAAATT
* *
507995 GCAACGCGAATTTGATTATTGCAATGGGTATTTGACTATC
1 GCAACGCGAA-TTGATTATCGCAACGGGTATTTGACTATC
* * * * *
508035 GTAACGAGAA---A--AACGCAACGCGAATTTGACTATC
1 GCAACGCGAATTGATTATCGCAACGGGTATTTGACTATC
508069 GCAACGCGAACTTGATTATCGCAACGGGTATTTGACTATC
1 GCAACGCGAA-TTGATTATCGCAACGGGTATTTGACTATC
* * * *
508109 GCAACGAGAA---A--ATCGCAAAGCGTATTAGACTATC
1 GCAACGCGAATTGATTATCGCAACGGGTATTTGACTATC
*
508143 ACAACGCGAATTGA
1 GCAACGCGAATTGA
508157 CTTTCGCGTT
Statistics
Matches: 95, Mismatches: 18, Indels: 21
0.71 0.13 0.16
Matches are distributed among these distances:
34 54 0.57
36 2 0.02
37 1 0.01
38 1 0.01
40 37 0.39
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (39 bp):
GCAACGCGAATTGATTATCGCAACGGGTATTTGACTATC
Found at i:508175 original size:14 final size:14
Alignment explanation
Indices: 508158--508188 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
508148 GCGAATTGAC
*
508158 TTTCGCGTTGCGAT
1 TTTCGCATTGCGAT
508172 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
508186 TTT
1 TTT
508189 GAGTTTAGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (14 bp):
TTTCGCATTGCGAT
Found at i:508363 original size:14 final size:14
Alignment explanation
Indices: 508303--508364 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
508293 CACAAATAAG
*
508303 AATTATTTACACATC
1 AATT-TTTACAAATC
**
508318 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
508333 AACTTTTACAAATC
1 AATTTTTACAAATC
*
508347 AATTTTTATAAATC
1 AATTTTTACAAATC
508361 AATT
1 AATT
508365 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:510411 original size:20 final size:20
Alignment explanation
Indices: 510386--510432 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
510376 CGATTCTTTT
510386 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
510406 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
510426 GTTGCGA
1 GTTGCGA
510433 ACGCGAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:510522 original size:20 final size:20
Alignment explanation
Indices: 510497--510540 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
510487 GCGATTTTTT
510497 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
510517 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
510537 CGTT
1 CGTT
510541 ACGAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:510530 original size:112 final size:111
Alignment explanation
Indices: 510334--510545 Score: 381
Period size: 112 Copynumber: 1.9 Consensus size: 111
510324 CAAATTTGAC
510334 TATCGCAACGAGAGAATCGCAATGCGATTTTCATTCGCATTGCGATTCTTTTGTTGCGATAGTCA
1 TATCGCAACGAGAGAATCGCAATGCGATTTTCATTCGCATTGCGATTCTTTTGTTGCGATAGTCA
*
510399 AATTCGCGTTGCGATAGTCATTTTCGCGTTGCGAACGCGAATGTGT
66 AATTCGCGTTGCGATAGTCATTTTCGCGTTACGAACGCGAATGTGT
*
510445 TATCGCAACGAGATAATCGCAATGCGATTTTCATTTCGCATTGCGATT-TTTTCGTTGCGATAGT
1 TATCGCAACGAGAGAATCGCAATGCGATTTTCA-TTCGCATTGCGATTCTTTT-GTTGCGATAGT
510509 CAAATTCGCGTTGCGATAGTCATTTTCGCGTTACGAA
64 CAAATTCGCGTTGCGATAGTCATTTTCGCGTTACGAA
510546 AGTAAACTAT
Statistics
Matches: 97, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
111 36 0.37
112 61 0.63
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (111 bp):
TATCGCAACGAGAGAATCGCAATGCGATTTTCATTCGCATTGCGATTCTTTTGTTGCGATAGTCA
AATTCGCGTTGCGATAGTCATTTTCGCGTTACGAACGCGAATGTGT
Found at i:510715 original size:18 final size:18
Alignment explanation
Indices: 510692--510741 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
510682 TTTACTAAGC
510692 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
510710 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
510728 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
510742 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:512519 original size:20 final size:20
Alignment explanation
Indices: 512473--512513 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
512463 TCTGAAACTT
512473 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
512493 AAAATCGCAATACGAAAATG
1 AAAATCGCAACACGAAAATG
512513 A
1 A
512514 CTATCGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.17, G:0.15, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:513075 original size:20 final size:20
Alignment explanation
Indices: 513050--513265 Score: 202
Period size: 20 Copynumber: 10.7 Consensus size: 20
513040 GCGCTTTGAA
513050 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
513070 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* * *
513090 AATCTCGTTGTGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
513110 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
513130 AATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
513150 AATCGCACTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* *
513170 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* *
513190 ATTCGCATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGTC--AG
** * *
513212 AATCGCAACGCGA-ATTTGCAA
1 AATCGCATTGCGATA-GT-CAG
*
513233 AATCGCAATGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
513253 AATCGCGTTGCGA
1 AATCGCATTGCGA
513266 ATCTGGAAAC
Statistics
Matches: 165, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.01
20 133 0.81
21 17 0.10
22 13 0.08
23 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:513245 original size:43 final size:40
Alignment explanation
Indices: 513150--513258 Score: 110
Period size: 43 Copynumber: 2.6 Consensus size: 40
513140 CGATAGTCAG
* * ** *
513150 AATCGCACTGCGATAGTCATAATCGCATTGCGATTTACAT
1 AATCGCAATGCGATAGTCAAAATCGCAACGCGATTTACAA
* * *
513190 ATTCGCATTGCGATAGTCGGAAAATCGCAACGCGAATTTGCAA
1 AATCGCAATGCGATAGTC--AAAATCGCAACGCG-ATTTACAA
*
513233 AATCGCAATGCGATAGTCAGAATCGC
1 AATCGCAATGCGATAGTCAAAATCGC
513259 GTTGCGAATC
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 16 0.29
41 7 0.12
42 11 0.20
43 22 0.39
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (40 bp):
AATCGCAATGCGATAGTCAAAATCGCAACGCGATTTACAA
Found at i:515864 original size:62 final size:62
Alignment explanation
Indices: 515767--515892 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
515757 TAGATATCAC
*
515767 AAGTAATTGACCGTATAAGGTTCACATCTGAGAATTTATAGCCAAATGTATGAACCTTACAA
1 AAGTAATTGACCGTACAAGGTTCACATCTGAGAATTTATAGCCAAATGTATGAACCTTACAA
* * * **
515829 AAGTAATTGACCGTACAAGGTTCGCATCTGAGAATTTATAGCTAAATGTGTGAAGGTTACAA
1 AAGTAATTGACCGTACAAGGTTCACATCTGAGAATTTATAGCCAAATGTATGAACCTTACAA
515891 AA
1 AA
515893 TCAATTCCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (62 bp):
AAGTAATTGACCGTACAAGGTTCACATCTGAGAATTTATAGCCAAATGTATGAACCTTACAA
Found at i:524280 original size:9 final size:9
Alignment explanation
Indices: 524266--524300 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
524256 TTCTTCATCG
524266 TCGTCCTCT
1 TCGTCCTCT
524275 TCGTCCTCT
1 TCGTCCTCT
* *
524284 TCTTCCTCC
1 TCGTCCTCT
524293 TCGTCCTC
1 TCGTCCTC
524301 GTCCTCATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.49, G:0.09, T:0.43
Consensus pattern (9 bp):
TCGTCCTCT
Found at i:524361 original size:12 final size:12
Alignment explanation
Indices: 524324--524376 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
524314 TCCACTTCCT
524324 CTTCCTCTTCAA
1 CTTCCTCTTCAA
*
524336 C-TCCTCTTCTA
1 CTTCCTCTTCAA
*
524347 CTTCTTCTTCAA
1 CTTCCTCTTCAA
*
524359 CTTCCTCCTCAA
1 CTTCCTCTTCAA
524371 CTTCCT
1 CTTCCT
524377 GAAGTTGTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
11 10 0.29
12 25 0.71
ACGTcount: A:0.13, C:0.43, G:0.00, T:0.43
Consensus pattern (12 bp):
CTTCCTCTTCAA
Found at i:543478 original size:2 final size:2
Alignment explanation
Indices: 543471--543513 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
543461 TCCGTTCTAC
543471 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
543513 T
1 T
543514 GTCTTTATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:549380 original size:22 final size:22
Alignment explanation
Indices: 549353--549399 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
549343 AGTAAAATAC
*
549353 ATAATGAATAGTA-CTGTGAACA
1 ATAATGAACAGTATC-GTGAACA
549375 ATAATGAACAGTATCGTGAACA
1 ATAATGAACAGTATCGTGAACA
549397 ATA
1 ATA
549400 CCCTGCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.26
Consensus pattern (22 bp):
ATAATGAACAGTATCGTGAACA
Found at i:549486 original size:21 final size:22
Alignment explanation
Indices: 549446--549487 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
549436 TTGTCATAGG
*
549446 GGAACCGATTCCCCTACTACAA
1 GGAACCGATTACCCTACTACAA
*
549468 GGAACCGA-TACCCTGCTACA
1 GGAACCGATTACCCTACTACA
549488 GTACTTTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.31, C:0.36, G:0.17, T:0.17
Consensus pattern (22 bp):
GGAACCGATTACCCTACTACAA
Found at i:560227 original size:42 final size:42
Alignment explanation
Indices: 560140--560229 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
560130 ATGTCCCACA
**
560140 CTATATATAATTATAAAGGTCAGGCGTGGCTCCTGAACCGCG
1 CTATATATAATTATAAAGGTCAGGCGCAGCTCCTGAACCGCG
* *
560182 CTATATATAATTATAAAGGTCAGGCGCAGC-CCTTGACCCGTG
1 CTATATATAATTATAAAGGTCAGGCGCAGCTCC-TGAACCGCG
560224 CTATAT
1 CTATAT
560230 CCTACGTGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (42 bp):
CTATATATAATTATAAAGGTCAGGCGCAGCTCCTGAACCGCG
Found at i:561325 original size:36 final size:37
Alignment explanation
Indices: 561264--561346 Score: 166
Period size: 37 Copynumber: 2.2 Consensus size: 37
561254 TACAAAAACT
561264 AAAAATATTCAATTTATTTTAAAAAAACATAACGTAA
1 AAAAATATTCAATTTATTTTAAAAAAACATAACGTAA
561301 AAAAATATTCAATTTATTTTAAAAAAACATAACGTAA
1 AAAAATATTCAATTTATTTTAAAAAAACATAACGTAA
561338 AAAAATATT
1 AAAAATATT
561347 TTAATAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (37 bp):
AAAAATATTCAATTTATTTTAAAAAAACATAACGTAA
Found at i:566512 original size:34 final size:34
Alignment explanation
Indices: 566469--566626 Score: 149
Period size: 34 Copynumber: 4.6 Consensus size: 34
566459 AGATTGAGGT
* *
566469 ATATTATCACATCCTTTAACACTTGAAGTTTAAC
1 ATATTATCACATTCTTTAACACTTGAAGTTTGAC
* ** * *
566503 ATATTATCACATTCTTCAACTTTTGAAGTTGGGC
1 ATATTATCACATTCTTTAACACTTGAAGTTTGAC
*
566537 ATATTATCACATTC-TTCAC-CTTCTGAAGTTTGAC
1 ATATTATCACATTCTTTAACAC-T-TGAAGTTTGAC
* * * ** *
566571 ATATTATCACACTCTTCACCTTTTGAAGTTTGGC
1 ATATTATCACATTCTTTAACACTTGAAGTTTGAC
566605 AATATTATCACATTCTTTAACA
1 -ATATTATCACATTCTTTAACA
566627 TATGAACATC
Statistics
Matches: 97, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
33 4 0.04
34 73 0.75
35 20 0.21
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (34 bp):
ATATTATCACATTCTTTAACACTTGAAGTTTGAC
Found at i:566578 original size:68 final size:69
Alignment explanation
Indices: 566492--566621 Score: 217
Period size: 68 Copynumber: 1.9 Consensus size: 69
566482 CTTTAACACT
*
566492 TGAAGTTTAACATATTATCACATTCTTCAACTTTTGAAGTTGGGC-ATATTATCACATTCTTCAC
1 TGAAGTTTAACATATTATCACACTCTTCAACTTTTGAAGTTGGGCAATATTATCACATTCTTCAC
566556 CTTC
66 CTTC
* * *
566560 TGAAGTTTGACATATTATCACACTCTTCACCTTTTGAAGTTTGGCAATATTATCACATTCTT
1 TGAAGTTTAACATATTATCACACTCTTCAACTTTTGAAGTTGGGCAATATTATCACATTCTT
566622 TAACATATGA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
68 41 0.72
69 16 0.28
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.42
Consensus pattern (69 bp):
TGAAGTTTAACATATTATCACACTCTTCAACTTTTGAAGTTGGGCAATATTATCACATTCTTCAC
CTTC
Found at i:568927 original size:60 final size:60
Alignment explanation
Indices: 568862--569022 Score: 187
Period size: 60 Copynumber: 2.7 Consensus size: 60
568852 GATAAAAATG
* ** * * *
568862 GGGATGAAATTGGAATATTTAAAAGTTTGGGGATTAATTTAGAAAGAGGGTAATGGTTTA
1 GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAAAGAGAGTAATAGTTTA
* * * *
568922 GGGATGAAATTAGAATGTTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTT
1 GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAAAGAGAGTAATAGTTTA
* ** * *
568982 GGGATAAAATTAGAAGCTTTAAAAGTTTAAGAACCAATTTA
1 GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTA
569023 AATAAGAGTT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 86 1.00
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAAAGAGAGTAATAGTTTA
Found at i:577962 original size:17 final size:17
Alignment explanation
Indices: 577940--577975 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
577930 AATCATTTAT
577940 TTTTTTAATAGTTTAGA
1 TTTTTTAATAGTTTAGA
*
577957 TTTTTTAATGGTTTAGA
1 TTTTTTAATAGTTTAGA
577974 TT
1 TT
577976 CTTAATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (17 bp):
TTTTTTAATAGTTTAGA
Found at i:589921 original size:76 final size:76
Alignment explanation
Indices: 589831--589979 Score: 212
Period size: 76 Copynumber: 2.0 Consensus size: 76
589821 TAAACTCAAA
* *
589831 TTTAGGATAATA-TTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATATGTTTTTAGT
1 TTTAGGATAATATTTTTAAA-ATTATATCTTTATCTTTGTATTTGAGTTTAAATA-GGTTTTAGT
589894 ATTTTAATTAATT
64 ATTTTAATTAATT
* * * *
589907 TTTAGGATATTATTTTTATATTTTTATCTTTATCTTTGTATTTGAGTTTAAATAGGTTTTAGTAT
1 TTTAGGATAATATTTTTAAAATTATATCTTTATCTTTGTATTTGAGTTTAAATAGGTTTTAGTAT
589972 TTTAATTA
66 TTTAATTA
589980 GGATTTAGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
76 34 0.52
77 31 0.48
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (76 bp):
TTTAGGATAATATTTTTAAAATTATATCTTTATCTTTGTATTTGAGTTTAAATAGGTTTTAGTAT
TTTAATTAATT
Found at i:589987 original size:76 final size:77
Alignment explanation
Indices: 589858--590008 Score: 216
Period size: 76 Copynumber: 2.0 Consensus size: 77
589848 AACATTATAT
* * ** *
589858 TTTATCTTTGTATTTTAGTTTAAATATGTTTTTAGTATTTTAATTAATTTTTAGGATATTAT-TT
1 TTTATCTTTGTATTTGAGTTTAAATATGGTTTTAGTATTTTAATTAAGATTTAGAATATTATATT
*
589922 TTATATTTTTATC
66 AT-TATTTTTATC
*
589935 TTTATCTTTGTATTTGAGTTTAAATA-GGTTTTAGTATTTTAATTAGGATTTAGAATATTATATT
1 TTTATCTTTGTATTTGAGTTTAAATATGGTTTTAGTATTTTAATTAAGATTTAGAATATTATATT
589999 ATTATTTTTA
66 ATTATTTTTA
590009 GGTATTTTAG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
76 38 0.58
77 28 0.42
ACGTcount: A:0.28, C:0.02, G:0.10, T:0.60
Consensus pattern (77 bp):
TTTATCTTTGTATTTGAGTTTAAATATGGTTTTAGTATTTTAATTAAGATTTAGAATATTATATT
ATTATTTTTATC
Found at i:590671 original size:21 final size:22
Alignment explanation
Indices: 590646--590686 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
590636 CTTTAATTTG
590646 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
590667 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
590687 TATTTTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:590741 original size:16 final size:15
Alignment explanation
Indices: 590722--590758 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
590712 AACCCCTTTT
590722 ATATTTATTACTATTA
1 ATATTTATTA-TATTA
590738 ATATTTATTATATTA
1 ATATTTATTATATTA
*
590753 TTATTT
1 ATATTT
590759 TTCTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTATTATATTA
Found at i:596376 original size:22 final size:21
Alignment explanation
Indices: 596354--596397 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
596344 CATTTCATTA
*
596354 TATTTT-TGTTTTAATTTTTT
1 TATTTTCTTTTTTAATTTTTT
*
596374 TATTTTCGTTTTTTTATTTTTT
1 TATTTTC-TTTTTTAATTTTTT
596396 TA
1 TA
596398 GCGAACTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (21 bp):
TATTTTCTTTTTTAATTTTTT
Found at i:599517 original size:21 final size:21
Alignment explanation
Indices: 599493--599537 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
599483 TTTTGTTCGT
* *
599493 TTGAAGGGGTATGGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
599514 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
599535 TTG
1 TTG
599538 CCAAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:600611 original size:15 final size:15
Alignment explanation
Indices: 600591--600647 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
600581 AACCAGGTAT
600591 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
600606 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
600623 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
600638 CGGGTACCCG
1 CGGGTACCCG
600648 TAACATCCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:600627 original size:17 final size:16
Alignment explanation
Indices: 600591--600659 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
600581 AACCAGGTAT
**
600591 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
600606 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
600623 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
600638 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
600655 CGGGT
1 CGGGT
600660 CGGGACATGG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:600632 original size:32 final size:32
Alignment explanation
Indices: 600591--600659 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
600581 AACCAGGTAT
600591 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
600623 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
600655 CGGGT
1 CGGGT
600660 CGGGACATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:601806 original size:76 final size:75
Alignment explanation
Indices: 601716--601863 Score: 217
Period size: 76 Copynumber: 2.0 Consensus size: 75
601706 TAAACTCATA
*
601716 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAATTTAAATAGG-TTTTAGTA
601780 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * * *
601792 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAATTTAAATAGGTTTTGGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAATTTAAATAGGTTTTAGTATT
601857 TTAATTA
66 TTAATTA
601864 GGATTTAGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 23 0.35
76 42 0.65
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAATTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:601962 original size:64 final size:64
Alignment explanation
Indices: 601828--601962 Score: 161
Period size: 64 Copynumber: 2.1 Consensus size: 64
601818 CTTTATCTTT
* * *
601828 GTATTTTAATTTAAATAGGTTTTGGTATTTTAATTAGGATTTAGAGTATTATATTTTTTTTTAG
1 GTATTTTAATTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAGTATTATACTTGTTTTTAG
* *
601892 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTGAGATGT-TT-TAGCTTGTTTT
1 GTATTTTAATTTAAATAGGTTTT-AGTATTTTAATTAGGATTT-AGA-GTATTATA-CTTGTTTT
601954 TAG
62 TAG
601957 G-ATTTT
1 GTATTTT
601963 GAAGGCTATA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
63 5 0.08
64 40 0.65
65 15 0.24
66 2 0.03
ACGTcount: A:0.26, C:0.01, G:0.18, T:0.56
Consensus pattern (64 bp):
GTATTTTAATTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAGTATTATACTTGTTTTTAG
Found at i:602551 original size:21 final size:23
Alignment explanation
Indices: 602526--602573 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
602516 CTTTAATTTG
602526 TTTATTTAATT-AT-TTTTTTAT
1 TTTATTTAATTCATATTTTTTAT
*
602547 TTTATTTAATTCTTATTTTTTAT
1 TTTATTTAATTCATATTTTTTAT
602570 TTTA
1 TTTA
602574 ACCATAACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.46
22 1 0.04
23 12 0.50
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTATTTAATTCATATTTTTTAT
Found at i:603796 original size:18 final size:18
Alignment explanation
Indices: 603773--603810 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
603763 TCATTTACTT
*
603773 TTTTAATAGTTTATATTC
1 TTTTAATAGTTTAAATTC
*
603791 TTTTAATATTTTAAATTC
1 TTTTAATAGTTTAAATTC
603809 TT
1 TT
603811 AATCATTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTAATAGTTTAAATTC
Found at i:616664 original size:22 final size:22
Alignment explanation
Indices: 616639--616691 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
616629 CAAAACTGAT
616639 AAAAAATAACAAAA-AAATTAAA
1 AAAAAATAACAAAATAAA-TAAA
*
616661 AAAAAATAACAAAATCAATAAA
1 AAAAAATAACAAAATAAATAAA
616683 AAAATAATA
1 AAAA-AATA
616692 TTTTTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAAAATAACAAAATAAATAAA
Found at i:616674 original size:19 final size:19
Alignment explanation
Indices: 616624--616689 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
616614 AATGTCTAAC
*
616624 AATAACAAAACTGATAAAAAAT
1 AATAACAAAA-T--TAAAAAAA
* *
616646 AACAAAAAAATTAAAAAAA
1 AATAACAAAATTAAAAAAA
*
616665 AATAACAAAATCAATAAAAA
1 AATAACAAAATTAA-AAAAA
616685 AATAA
1 AATAA
616690 TATTTTTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 18 0.49
20 10 0.27
21 1 0.03
22 8 0.22
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.15
Consensus pattern (19 bp):
AATAACAAAATTAAAAAAA
Found at i:616691 original size:11 final size:11
Alignment explanation
Indices: 616639--616691 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
616629 CAAAACTGAT
*
616639 AAAAAATAACA
1 AAAAAATAATA
616650 AAAAAAT--TA
1 AAAAAATAATA
616659 AAAAAA-AATA
1 AAAAAATAATA
*
616669 ACAAAATCAATA
1 AAAAAAT-AATA
616681 AAAAAATAATA
1 AAAAAATAATA
616692 TTTTTTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
9 7 0.20
10 7 0.20
11 11 0.31
12 10 0.29
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:617465 original size:23 final size:23
Alignment explanation
Indices: 617437--617494 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
617427 AAATTAATAA
617437 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
617460 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
617483 TATA--ATGTAAAA
1 TATATTATGTAAAA
617495 ATTATAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:617537 original size:13 final size:13
Alignment explanation
Indices: 617508--617542 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
617498 ATAACTAATA
*
617508 ATATTAAAT-ATT
1 ATATTAAATAAAT
617520 ATATTAAATAAAT
1 ATATTAAATAAAT
617533 ATATTAAATA
1 ATATTAAATA
617543 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:620548 original size:8 final size:8
Alignment explanation
Indices: 620535--620575 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
620525 CTCATTTTCA
620535 GAGAATTT
1 GAGAATTT
620543 GAGAATTT
1 GAGAATTT
*
620551 -AGAGTTT
1 GAGAATTT
*
620558 GGGAATTT
1 GAGAATTT
620566 GAGAATTT
1 GAGAATTT
620574 GA
1 GA
620576 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:621078 original size:126 final size:125
Alignment explanation
Indices: 620643--621117 Score: 875
Period size: 124 Copynumber: 3.8 Consensus size: 125
620633 CTATAATCGG
620643 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
620708 CATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTAT
66 CATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
620767 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
620832 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAG--ATATCAGTACCTACTAT
65 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
620891 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGTCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGG-CGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
620956 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGTCACTAGATATATCAGTACCTATTAT
65 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
621017 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGG-CGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
621082 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
65 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
621118 ATAACTTAAA
Statistics
Matches: 340, Mismatches: 6, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
123 4 0.01
124 145 0.43
125 67 0.20
126 124 0.36
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.32
Consensus pattern (125 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
CATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:621082 original size:250 final size:248
Alignment explanation
Indices: 620643--621117 Score: 905
Period size: 250 Copynumber: 1.9 Consensus size: 248
620633 CTATAATCGG
620643 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
620708 CATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCACT
66 CATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCACT
*
620773 ATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCATTG
131 ATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTATCATTG
*
620838 CCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATCAGTACCTACTAT
196 CCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATCAGTACCTACTAT
620891 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGTCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGG-CGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
620956 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGTCACTAGATATATCAGTACCTATTATTTCA
65 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTCA
621021 CTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
129 CTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
621086 TGCCCTATTATGTCACTCATGTCCCTCGGGGA
194 TGCCCTATTATGTCACTCATGTCCCTCGGGGA
621118 ATAACTTAAA
Statistics
Matches: 222, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
248 32 0.14
249 63 0.28
250 127 0.57
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.32
Consensus pattern (248 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
CATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCACT
ATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTATCATTG
CCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATCAGTACCTACTAT
Found at i:621566 original size:33 final size:34
Alignment explanation
Indices: 621505--621604 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
621495 AAATTTAATG
*
621505 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
621539 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
621572 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
621605 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:622212 original size:21 final size:21
Alignment explanation
Indices: 622124--622217 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
622114 TATGGTATAA
*
622124 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
622145 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
622166 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
622187 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
622208 AACCCTGCGG
1 AACCCTGCGG
622218 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:622247 original size:21 final size:21
Alignment explanation
Indices: 622221--622268 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
622211 CCTGCGGAGA
*
622221 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
622242 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
622263 GGGCAT
1 TGGCAT
622269 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:624054 original size:22 final size:22
Alignment explanation
Indices: 623998--624054 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 22
623988 TCTAAATAAA
* *
623998 TAATAATTATATAATATTATTT
1 TAATAAATATATAATAATATTT
624020 TAAT-AATA-A-AATAATA-TT
1 TAATAAATATATAATAATATTT
624038 TACATAAATATATAATA
1 TA-ATAAATATATAATA
624055 TAAAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 4 0.14
19 8 0.28
20 5 0.17
21 4 0.14
22 8 0.28
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAAATATATAATAATATTT
Found at i:624092 original size:34 final size:34
Alignment explanation
Indices: 624029--624094 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
624019 TTAATAATAA
* *
624029 AATAATATTTACATAAATATATAATATAAAAAAT
1 AATAATATTTACATAAAAATATAACATAAAAAAT
624063 AATAACTATTTA-A-AAAAATACTAACATAAAAA
1 AATAA-TATTTACATAAAAATA-TAACATAAAAA
624095 TAAATTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.21
34 16 0.57
35 6 0.21
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (34 bp):
AATAATATTTACATAAAAATATAACATAAAAAAT
Found at i:625482 original size:12 final size:12
Alignment explanation
Indices: 625465--625489 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
625455 AGAAACAATG
625465 ATTATAATAATT
1 ATTATAATAATT
625477 ATTATAATAATT
1 ATTATAATAATT
625489 A
1 A
625490 CTACATCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTATAATAATT
Found at i:627715 original size:31 final size:31
Alignment explanation
Indices: 627680--627747 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
627670 TTGCAATACA
627680 GTCCCCCAACATTCAGTCCATTTGCAAAATG
1 GTCCCCCAACATTCAGTCCATTTGCAAAATG
* * *
627711 GTCCCCCAACATTTAGTCTATTTGCAATATG
1 GTCCCCCAACATTCAGTCCATTTGCAAAATG
627742 GTCCCC
1 GTCCCC
627748 GACGTAACTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.29
Consensus pattern (31 bp):
GTCCCCCAACATTCAGTCCATTTGCAAAATG
Found at i:629433 original size:31 final size:32
Alignment explanation
Indices: 629394--629472 Score: 124
Period size: 31 Copynumber: 2.5 Consensus size: 32
629384 CAGTTACGTC
629394 AGGGACCATATTGCAAACGGACTAAATGTTGG
1 AGGGACCATATTGCAAACGGACTAAATGTTGG
*
629426 -GGGACCATATTACAAACGGACTAAATGTTGG
1 AGGGACCATATTGCAAACGGACTAAATGTTGG
**
629457 AGGGACTGTATTGCAA
1 AGGGACCATATTGCAA
629473 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 30 0.71
32 12 0.29
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (32 bp):
AGGGACCATATTGCAAACGGACTAAATGTTGG
Found at i:630268 original size:37 final size:39
Alignment explanation
Indices: 630224--630302 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
630214 TTCATTAAAT
* *
630224 AATTTTAT-ATTTTCAATT-TTATAAAA-AAAATTATATA
1 AATTTTATGAATTTAAATTCTTATAAAAGAAAA-TATATA
*
630261 AATTTTATGAATTTAAATTCTTTTAAAAGAAAATATATA
1 AATTTTATGAATTTAAATTCTTATAAAAGAAAATATATA
630300 AAT
1 AAT
630303 ATTTTTCAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 8 0.22
38 8 0.22
39 16 0.44
40 4 0.11
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (39 bp):
AATTTTATGAATTTAAATTCTTATAAAAGAAAATATATA
Found at i:639515 original size:5 final size:5
Alignment explanation
Indices: 639484--639508 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
639474 GATCTCTTCA
639484 GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT
639509 TTGTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:641471 original size:30 final size:31
Alignment explanation
Indices: 641398--641471 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
641388 AGGCTGTGGT
641398 AATTAATATTTTACTTAAAATTTAAGAGTTA
1 AATTAATATTTTACTTAAAATTTAAGAGTTA
* *
641429 ATTTGATATTTTACTTAAAATTTAAG-GTTA
1 AATTAATATTTTACTTAAAATTTAAGAGTTA
*
641459 AATTAATTTTTTA
1 AATTAATATTTTA
641472 AAGTTCAGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 14 0.37
31 24 0.63
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (31 bp):
AATTAATATTTTACTTAAAATTTAAGAGTTA
Found at i:644297 original size:2 final size:2
Alignment explanation
Indices: 644290--644318 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
644280 GAAAGGCAAG
644290 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
644319 GGGGGACGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.