Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 24
Found at i:4033036 original size:30 final size:30
Alignment explanation
Indices: 4032990--4033061 Score: 126
Period size: 30 Copynumber: 2.3 Consensus size: 30
4032980 TCCCCCTTAC
4032990 TTTAACACTTCTTCAATTTATTATGTAAAACA
1 TTTAACAC--CTTCAATTTATTATGTAAAACA
4033022 TTTAACACCTTCAATTTATTATGTAAAACA
1 TTTAACACCTTCAATTTATTATGTAAAACA
4033052 TTTAACACCT
1 TTTAACACCT
4033062 ATTCTTCTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 32 0.80
32 8 0.20
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTAACACCTTCAATTTATTATGTAAAACA
Found at i:4035324 original size:19 final size:20
Alignment explanation
Indices: 4035254--4035337 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 20
4035244 AACAGAACCC
* *
4035254 CAAGGGGGTATCGATTCCCCT
1 CAAGGGGGAATCGGTT-CCCT
**
4035275 GTAGGGGGAATCGGTTCCCCTT
1 CAAGGGGGAATCGGTT-CCC-T
4035297 CAAAGGGGGAATCGGTTCCCT
1 C-AAGGGGGAATCGGTTCCCT
* *
4035318 C-AGGGGGGATCGATTCCCT
1 CAAGGGGGAATCGGTTCCCT
4035337 C
1 C
4035338 TGCACCAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
19 17 0.32
21 18 0.34
22 4 0.08
23 14 0.26
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (20 bp):
CAAGGGGGAATCGGTTCCCT
Found at i:4039169 original size:22 final size:21
Alignment explanation
Indices: 4039127--4039166 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4039117 GAGTTTGTTT
*
4039127 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
4039148 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4039167 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:4041239 original size:77 final size:77
Alignment explanation
Indices: 4041039--4041278 Score: 375
Period size: 77 Copynumber: 3.2 Consensus size: 77
4041029 GTTGTACAAG
* * * * *
4041039 GGGGGAATCGGTACC-CC-CTGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
**
4041100 C-AAACTGTTTA
66 CAAAACCATTTA
4041111 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
4041175 CAAAACCATTTA
66 CAAAACCATTTA
4041187 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
4041252 CAAAACCATTTA
66 CAAAACCATTTA
4041264 GGGGGAATCGGTTCC
1 GGGGGAATCGGTTCC
4041279 CTCTGAGCAA
Statistics
Matches: 155, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
72 14 0.09
73 8 0.05
74 33 0.21
75 1 0.01
76 29 0.19
77 70 0.45
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.23
Consensus pattern (77 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
CAAAACCATTTA
Found at i:4070486 original size:12 final size:12
Alignment explanation
Indices: 4070469--4070493 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4070459 AGAGCTACAG
4070469 AGAAATGAAAAA
1 AGAAATGAAAAA
4070481 AGAAATGAAAAA
1 AGAAATGAAAAA
4070493 A
1 A
4070494 AAGACAAACA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AGAAATGAAAAA
Found at i:4072273 original size:47 final size:48
Alignment explanation
Indices: 4072176--4072274 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 48
4072166 GTTTAATATC
* * *
4072176 TAATTTTTATTTCATTTTAATATTTCATTGTTAAAAACTTTAGGTATT
1 TAATTTTTATTTCATTTTAATATCTCATTGTTAAAAACTTAACGTATT
* * *
4072224 TAATTTTTATTTCATTTTAGTA-CTCATTGTTGAAAACTTAACGTGTT
1 TAATTTTTATTTCATTTTAATATCTCATTGTTAAAAACTTAACGTATT
4072271 TAAT
1 TAAT
4072275 ACTTAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
47 24 0.53
48 21 0.47
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (48 bp):
TAATTTTTATTTCATTTTAATATCTCATTGTTAAAAACTTAACGTATT
Found at i:4077003 original size:15 final size:15
Alignment explanation
Indices: 4076983--4077092 Score: 54
Period size: 15 Copynumber: 7.7 Consensus size: 15
4076973 TATTTTAAAA
4076983 AATAATTTATTATTT
1 AATAATTTATTATTT
4076998 AATAA-TT-TTATTT
1 AATAATTTATTATTT
* * ***
4077011 AATTATTTA-AAAGA
1 AATAATTTATTATTT
*
4077025 ATATAATTTATTACTT
1 A-ATAATTTATTATTT
*
4077041 AATAATTTAATA-TT
1 AATAATTTATTATTT
* * **
4077055 AA-CA-TCATTA-AA
1 AATAATTTATTATTT
*
4077067 AATAAATTATTATTT
1 AATAATTTATTATTT
4077082 AATAATTTATT
1 AATAATTTATT
4077093 TTAATTACTT
Statistics
Matches: 67, Mismatches: 21, Indels: 14
0.66 0.21 0.14
Matches are distributed among these distances:
12 6 0.09
13 12 0.18
14 15 0.22
15 32 0.48
16 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (15 bp):
AATAATTTATTATTT
Found at i:4077018 original size:41 final size:41
Alignment explanation
Indices: 4076973--4077099 Score: 134
Period size: 41 Copynumber: 3.0 Consensus size: 41
4076963 AATATTAACA
4076973 TATTTTAAAAAATAATTTATTATTTAATAATTTTATTTAAT
1 TATTTTAAAAAATAATTTATTATTTAATAATTTTATTTAAT
* * *
4077014 TATTTAAAAGAATATAATTTATTACTTAATAATTTAATATTAA-
1 TATTTTAAA-AA-ATAATTTATTATTTAATAATTTTAT-TTAAT
* * *
4077057 CATCATT-AAAAATAAATTATTATTTAATAA-TTTATTTTAAT
1 TAT-TTTAAAAAATAATTTATTATTTAATAATTTTA-TTTAAT
4077098 TA
1 TA
4077100 CTTATATCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
40 7 0.10
41 27 0.39
42 4 0.06
43 27 0.39
44 5 0.07
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (41 bp):
TATTTTAAAAAATAATTTATTATTTAATAATTTTATTTAAT
Found at i:4077031 original size:43 final size:42
Alignment explanation
Indices: 4076977--4077099 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 42
4076967 TTAACATATT
4076977 TTAAAAA-ATAATTTATTATTTAATAATTTTATTTAATTAT-
1 TTAAAAATATAATTTATTATTTAATAATTTTATTTAATTATA
* * *
4077017 TTAAAAGAATATAATTTATTACTTAATAATTTAATATTAA-CATCA
1 TT-AAA-AATATAATTTATTATTTAATAATTTTAT-TTAATTAT-A
4077062 TTAAAAATA-AA-TTATTATTTAATAA-TTTATTTTAATTA
1 TTAAAAATATAATTTATTATTTAATAATTTTA-TTTAATTA
4077100 CTTATATCTT
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
40 9 0.13
41 18 0.26
42 4 0.06
43 29 0.42
44 7 0.10
45 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (42 bp):
TTAAAAATATAATTTATTATTTAATAATTTTATTTAATTATA
Found at i:4079900 original size:20 final size:20
Alignment explanation
Indices: 4079866--4079936 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
4079856 CCAAGGGTAT
*
4079866 AGATTCCCCCTCAGGGCGTAC
1 AGATTCCCCC-CAGGGAGTAC
* *
4079887 AGATTCCCCCCAGGGGGAAC
1 AGATTCCCCCCAGGGAGTAC
4079907 AGATTCCCCCCAGGGAGTATC
1 AGATTCCCCCCAGGGAGTA-C
4079928 -GATTCCCCC
1 AGATTCCCCC
4079937 TGTCTAAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
20 34 0.76
21 11 0.24
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (20 bp):
AGATTCCCCCCAGGGAGTAC
Found at i:4088583 original size:43 final size:43
Alignment explanation
Indices: 4088522--4088607 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
4088512 CTTATTCTGT
*
4088522 TTTATTTTGTGTTAAGATATATTATGTGATATATTTTTTTGAG
1 TTTATTCTGTGTTAAGATATATTATGTGATATATTTTTTTGAG
*
4088565 TTTATTCTGTGTTAAGATATATTATGTGATGTATTTTTTTGAG
1 TTTATTCTGTGTTAAGATATATTATGTGATATATTTTTTTGAG
4088608 CAATGACAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.24, C:0.01, G:0.17, T:0.57
Consensus pattern (43 bp):
TTTATTCTGTGTTAAGATATATTATGTGATATATTTTTTTGAG
Found at i:4089410 original size:14 final size:14
Alignment explanation
Indices: 4089375--4089412 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
4089365 TTATTAATAA
*
4089375 TTTAATTTATAATT
1 TTTAATTTTTAATT
4089389 TTTAATTTTTAATT
1 TTTAATTTTTAATT
4089403 TATT-ATTTTT
1 T-TTAATTTTT
4089413 TCGAATTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTAATTTTTAATT
Found at i:4094498 original size:17 final size:18
Alignment explanation
Indices: 4094468--4094503 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
4094458 ATGTATATAA
4094468 TTTATTTAAGTATTTTAC
1 TTTATTTAAGTATTTTAC
4094486 TTTATTTAA-TATTTTAC
1 TTTATTTAAGTATTTTAC
4094503 T
1 T
4094504 AATATAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTATTTAAGTATTTTAC
Found at i:4094703 original size:111 final size:111
Alignment explanation
Indices: 4094562--4094846 Score: 500
Period size: 111 Copynumber: 2.6 Consensus size: 111
4094552 TGTAAATCAT
* * * *
4094562 ATATCTCTACACTTTGTTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
4094627 -TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TTA-TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
4094673 ATATCTCAACATTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
4094738 TTATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TTATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
4094784 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGT
1 ATATCTCAACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGT
4094847 TGATTTATTT
Statistics
Matches: 166, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
111 164 0.99
112 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (111 bp):
ATATCTCAACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TTATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:4096413 original size:18 final size:18
Alignment explanation
Indices: 4096390--4096428 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
4096380 CCAATAGCCA
4096390 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
4096408 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
4096426 CCG
1 CCG
4096429 TCATCGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:4100693 original size:51 final size:51
Alignment explanation
Indices: 4100630--4100743 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
4100620 AGCACGGAGT
* * * * * *
4100630 AGGGGGCACGCTATACCCCACGTGTAACCCAGTCAGCGTATAGCGCGGTAC
1 AGGGGGCGCGCTATACCCCACATGGAACCAAATCAGCATATAGCGCGGTAC
* ** *
4100681 AGGGGGCGCGCTATACTCCACATGGCGCCAAATCAGCATATAGCGCGGTTC
1 AGGGGGCGCGCTATACCCCACATGGAACCAAATCAGCATATAGCGCGGTAC
4100732 AGGGGGCGCGCT
1 AGGGGGCGCGCT
4100744 TTACTGCTAC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.22, C:0.30, G:0.32, T:0.16
Consensus pattern (51 bp):
AGGGGGCGCGCTATACCCCACATGGAACCAAATCAGCATATAGCGCGGTAC
Found at i:4102885 original size:22 final size:22
Alignment explanation
Indices: 4102860--4102903 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4102850 ATTATGACTA
4102860 TTTTT-TATGATTTGAATTTTGG
1 TTTTTATATGATTT-AATTTTGG
*
4102882 TTTTTATTTGATTTAATTTTGG
1 TTTTTATATGATTTAATTTTGG
4102904 AGTCGTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (22 bp):
TTTTTATATGATTTAATTTTGG
Found at i:4103970 original size:16 final size:16
Alignment explanation
Indices: 4103934--4103995 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
4103924 AAATGGTAAG
4103934 AAAT-AAATAAAT-AA
1 AAATAAAATAAATAAA
* *
4103948 AATTAAAATGAATAAA
1 AAATAAAATAAATAAA
*
4103964 AAATAAATTAAATAAA
1 AAATAAAATAAATAAA
* *
4103980 AGATAAGATAAATAAA
1 AAATAAAATAAATAAA
4103996 GCAAAGATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 3 0.08
15 7 0.18
16 28 0.74
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAATAAATAAA
Found at i:4103995 original size:20 final size:21
Alignment explanation
Indices: 4103966--4104005 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4103956 TGAATAAAAA
*
4103966 ATAAATTAAATAAAAGATAAG
1 ATAAATTAAAGAAAAGATAAG
*
4103987 ATAAA-TAAAGCAAAGATAA
1 ATAAATTAAAGAAAAGATAA
4104006 AATAGTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.20
Consensus pattern (21 bp):
ATAAATTAAAGAAAAGATAAG
Found at i:4104075 original size:13 final size:13
Alignment explanation
Indices: 4104057--4104081 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4104047 AGAAAAATAT
4104057 ATATAAATAAAAC
1 ATATAAATAAAAC
4104070 ATATAAATAAAA
1 ATATAAATAAAA
4104082 TAATAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
ATATAAATAAAAC
Found at i:4104079 original size:17 final size:16
Alignment explanation
Indices: 4103936--4104142 Score: 63
Period size: 15 Copynumber: 12.7 Consensus size: 16
4103926 ATGGTAAGAA
*
4103936 ATAAATAAATAAAATT
1 ATAAATAAATAAAAAT
*
4103952 A-AAATGAATAAAAA-
1 ATAAATAAATAAAAAT
4103966 ATAAATTAAATAAAAGAT
1 ATAAA-TAAATAAAA-AT
* *
4103984 A-AGATAAATAAAGCAAAG
1 ATAAATAAAT-AA--AAAT
*
4104002 ATAAAATAGTAAGT-GAAAT
1 AT-AAATA--AA-TAAAAAT
* *
4104021 AAAAATATATAAAAAT
1 ATAAATAAATAAAAAT
* * *
4104037 AAAAAAAAGAAGAAAAAT
1 -ATAAATA-AATAAAAAT
*
4104055 ATATATAAATAAAACAT
1 ATAAATAAATAAAA-AT
*
4104072 ATAAAT-AA-AATAAT
1 ATAAATAAATAAAAAT
*
4104086 AATAAA-AAGTAAAAAT
1 -ATAAATAAATAAAAAT
* * * *
4104102 -TATATATATATATAT
1 ATAAATAAATAAAAAT
*
4104117 AT-AATAAATAAAAAC
1 ATAAATAAATAAAAAT
*
4104132 ATAAAAAAATA
1 ATAAATAAATA
4104143 GTAAATATGT
Statistics
Matches: 136, Mismatches: 33, Indels: 44
0.64 0.15 0.21
Matches are distributed among these distances:
14 6 0.04
15 40 0.29
16 40 0.29
17 22 0.16
18 15 0.11
19 6 0.04
20 4 0.03
22 2 0.01
23 1 0.01
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (16 bp):
ATAAATAAATAAAAAT
Found at i:4104119 original size:88 final size:87
Alignment explanation
Indices: 4104025--4104217 Score: 207
Period size: 88 Copynumber: 2.2 Consensus size: 87
4104015 TGAAATAAAA
* *
4104025 ATATATAAAAATAAAAA-A-AAGAAGAAA-AATATATATAAATAAAACATATAAATAAAATA-AT
1 ATATATAAAAATAAAAACATAA-AA-AAATAATAAATATAAATAAAA-AT-T-AATAAAACATAT
4104086 AATAAAAAGTAAAA-ATTATATATATAT
61 AATAAAAAGTAAAATA-TATATATATAT
* ** *
4104113 ATATATAATAAATAAAAACATAAAAAAATAGTAAATATGTATATAAATTAATAAAACATATAATA
1 ATATATAA-AAATAAAAACATAAAAAAATAATAAATATAAATAAAAATTAATAAAACATATAATA
*
4104178 AAAAGTAACATATATATATATAT
65 AAAAGTAAAATATATATATATAT
* *
4104201 ATCTAAAAAAATAAAAA
1 ATATATAAAAATAAAAA
4104218 TATATATTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
87 17 0.19
88 41 0.46
89 15 0.17
90 15 0.17
91 2 0.02
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (87 bp):
ATATATAAAAATAAAAACATAAAAAAATAATAAATATAAATAAAAATTAATAAAACATATAATAA
AAAGTAAAATATATATATATAT
Found at i:4104125 original size:48 final size:46
Alignment explanation
Indices: 4104032--4104216 Score: 131
Period size: 48 Copynumber: 4.1 Consensus size: 46
4104022 AAAATATATA
* * * **
4104032 AAAATAA-AAAAAAGAAG-AAAAATATATATAAATAAAACATATAAAT
1 AAAATAATAATAAA-AAGTAAAAATATATATATATATATTA-ATAAAT
4104078 AAAATAATAATAAAAAGTAAAAATTATATATATATATATATAATAAAT
1 AAAATAATAATAAAAAGTAAAAA-TATATATATATATAT-TAATAAAT
* *
4104126 AAAA-ACATAA-AAAAA-TAGTAAATATGTATATA-A-ATTAAT-AA-
1 AAAATA-ATAATAAAAAGTA-AAAATATATATATATATATTAATAAAT
* * *
4104167 AACAT-ATAATAAAAAGT-AACATATATATATATATATCTAAAAAAAT
1 AAAATAATAATAAAAAGTAAAAATATATATATATATAT-T-AATAAAT
4104213 AAAA
1 AAAA
4104217 ATATATATTA
Statistics
Matches: 111, Mismatches: 13, Indels: 30
0.72 0.08 0.19
Matches are distributed among these distances:
40 15 0.14
41 9 0.08
42 5 0.05
43 5 0.05
44 4 0.04
45 3 0.03
46 24 0.22
47 19 0.17
48 26 0.23
49 1 0.01
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (46 bp):
AAAATAATAATAAAAAGTAAAAATATATATATATATATTAATAAAT
Found at i:4104140 original size:40 final size:39
Alignment explanation
Indices: 4104061--4104223 Score: 113
Period size: 40 Copynumber: 4.2 Consensus size: 39
4104051 AAATATATAT
* * *
4104061 AAATA-AAACATATAAATAAAAT-AATAATAAAAAGT-AAA
1 AAATATAAATATATATATATAATAAATAA-AAAAA-TAAAA
* * *
4104099 AATTATATATATATATATATAATAAATAAAAACATAAAA
1 AAATATAAATATATATATATAATAAATAAAAAAATAAAA
* * *
4104138 AAATAGTAAATATGTATATA-AATTAATAAAACATATAATAA
1 AAATA-TAAATATATATATATAATAAATAAAA-AAATAA-AA
* **
4104179 AAAGTA-ACATATATATATAT-ATATCTAAAAAAATAAAA
1 AAA-TATAAATATATATATATAATAAATAAAAAAATAAAA
*
4104217 ATATATA
1 AAATATA
4104224 TTAAAGTAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
37 2 0.02
38 10 0.10
39 39 0.40
40 40 0.41
41 5 0.05
42 2 0.02
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.29
Consensus pattern (39 bp):
AAATATAAATATATATATATAATAAATAAAAAAATAAAA
Found at i:4104808 original size:37 final size:37
Alignment explanation
Indices: 4104756--4104865 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
4104746 GCTTGTGGAG
*
4104756 CCTATTTTTAGGAGTTTGAATCATAGTAAAACT-TGAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT-AT
*
4104793 CTTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
*
4104830 CCTATTTTTAGGAGTTTGAATCCTACTAAAACTCTA
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
4104866 ACGTTTGTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 67 0.99
38 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
Found at i:4105543 original size:36 final size:35
Alignment explanation
Indices: 4105471--4105588 Score: 204
Period size: 36 Copynumber: 3.4 Consensus size: 35
4105461 AAGATCTTGG
*
4105471 GTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
4105506 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGG-TTTTTTTTGT
4105542 GTTTCAAGAGAAACAATTTCAAAGG-TTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
4105576 G-TTCAAGAGAAAC
1 GTTTCAAGAGAAAC
4105589 TGTCTCAAGG
Statistics
Matches: 81, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
33 12 0.15
34 10 0.12
35 24 0.30
36 35 0.43
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (35 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
Found at i:4105680 original size:67 final size:70
Alignment explanation
Indices: 4105541--4105691 Score: 184
Period size: 67 Copynumber: 2.2 Consensus size: 70
4105531 TTTTTTTTTG
* ** * * *
4105541 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGTTCAAGAGAAACTGTCTCAAGGGTGGCAA
1 TGTTTCAAGAGAAACAATTTCAAAGGTATTGGTGTGTTCAAGAGAAACTGTCTCAAGAGAGACAA
*
4105606 AATTT
66 AACTT
*
4105611 TGTTTCAAGAGAAAC-ATATTCAAA-G-ATTGGTGT-TTCAAGAGAAACTGTCTCAAGAGAGATA
1 TGTTTCAAGAGAAACAAT-TTCAAAGGTATTGGTGTGTTCAAGAGAAACTGTCTCAAGAGAGACA
4105672 AAACTT
65 AAACTT
*
4105678 TGTTTCAAGGGAAA
1 TGTTTCAAGAGAAA
4105692 TTGTCTCAAG
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
67 42 0.59
68 5 0.07
69 3 0.04
70 21 0.30
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (70 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTATTGGTGTGTTCAAGAGAAACTGTCTCAAGAGAGACAA
AACTT
Found at i:4105697 original size:37 final size:37
Alignment explanation
Indices: 4105641--4105967 Score: 367
Period size: 37 Copynumber: 9.1 Consensus size: 37
4105631 CAAAGATTGG
* *
4105641 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
*
4105678 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
*
4105714 TGTTTC-AGGAGAAACTGTCTCAAGAGAGACAGAACTT
1 TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAACTT
* * ** * *
4105751 AGTTCCAAAAGAAACTGTCACAAGGGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
* * *
4105787 TGTTTCAAGGAAAACAGAT-TC-A-A-AG-----ATTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAACTT
*
4105816 TGTTTCAAGGGAAACTGTCTCAAAAGAGAC-AAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
* * *
4105851 TTTTTCCAAGTGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTT-CAAGGGAAACTGTCTCAAGAGAGACAAAACTT
4105889 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
*
4105926 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
4105963 TGTTT
1 TGTTT
4105968 TGAATAAATT
Statistics
Matches: 244, Mismatches: 30, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.01
29 19 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
35 10 0.04
36 67 0.27
37 133 0.55
38 7 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:4105731 original size:73 final size:73
Alignment explanation
Indices: 4105641--4105967 Score: 372
Period size: 73 Copynumber: 4.6 Consensus size: 73
4105631 CAAAGATTGG
* *
4105641 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAGAG
1 TGTTTCAGGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
4105706 ACAAAATT
66 ACAAAATT
* * * * ** * *
4105714 TGTTTCAGGAGAAACTGTCTCAAGAGAGACAGAACTTAGTTCCAAAAGAAACTGTCACAAGGGAG
1 TGTTTCAGGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
4105779 ACAAAATT
66 ACAAAATT
* *
4105787 TGTTTCAAGGA-AAACAGAT-TC-A-A-AGAT-----TTTGTTTCAAGGGAAACTGTCTCAAAAG
1 TGTTTC-AGGAGAAACTG-TCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
4105842 AGAC-AAATT
64 AGACAAAATT
* * *
4105851 TTTTTCCAAGTGAAACTGTCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TGTTT-CAGGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
4105916 GACAAAACTT
65 GACAAAA-TT
* *
4105926 TGTTTCAAGG-GAAACTATCTCAAGAGAGACAAAACTTTGTTT
1 TGTTTC-AGGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTT
4105968 TGAATAAATT
Statistics
Matches: 210, Mismatches: 28, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
64 12 0.06
65 33 0.16
66 1 0.00
67 1 0.00
68 4 0.02
70 3 0.01
71 1 0.00
72 1 0.00
73 107 0.51
74 39 0.19
75 8 0.04
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (73 bp):
TGTTTCAGGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
ACAAAATT
Found at i:4105836 original size:138 final size:139
Alignment explanation
Indices: 4105676--4105940 Score: 381
Period size: 138 Copynumber: 1.9 Consensus size: 139
4105666 GAGATAAAAC
* * *
4105676 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTT-CAGGAGAAACTGTCTCAAGAG
1 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGAC-AAATTTGTTTCCAAGAGAAACTGTCTCAAGAG
* *
4105740 AGACAGAACTTAGTTCCAAAAGAAACTGTCACAAGGGAGACAAAA-TTTGTTTCAAGGAAAACAG
65 AGACAAAACTTAGTTCCAAAAGAAACTGTCACAAGAGAGACAAAACTTTGTTTCAAGGAAAACAG
4105804 ATTCAAAGAT
130 ATTCAAAGAT
* *
4105814 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAATTTTTTTCCAAGTGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAATTTGTTTCCAAGAGAAACTGTCTCAAGAGA
* * * ** * *
4105879 GATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC
66 GACAAAACTTAGTTCCAAAAGAAACTGTCACAAGAGAGACAAAACTTTGTTTCAAGGAAAAC
4105941 TATCTCAAGA
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
137 9 0.08
138 86 0.77
139 16 0.14
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (139 bp):
TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAATTTGTTTCCAAGAGAAACTGTCTCAAGAGA
GACAAAACTTAGTTCCAAAAGAAACTGTCACAAGAGAGACAAAACTTTGTTTCAAGGAAAACAGA
TTCAAAGAT
Found at i:4105893 original size:175 final size:177
Alignment explanation
Indices: 4105583--4105967 Score: 512
Period size: 175 Copynumber: 2.2 Consensus size: 177
4105573 TGTGTTCAAG
* * * *
4105583 AGAAACTGTCTCAAGGGTGGCAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCA
1 AGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAGAGAAACAGATTCAAAGATTGGTGTTTCA
* *
4105648 AGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAAT
66 AGAGAAACTGTCTCAAAAGAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
*
4105713 TTGTTTC-AGGAGAAACTGTCTCAAGAGAGACAGAACTTAGTTCCAAA
131 TTGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
* *
4105760 AGAAACTGTCACAAGGGAGACAAAA-TTTGTTTCAAG-GAAAACAGATTCAAAGATT-TTGTTTC
1 AGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAGAG-AAACAGATTCAAAGATTGGTGTTTC
* * * * *
4105822 AAGGGAAACTGTCTCAAAAGAGA-CAAA-TTTTTTTCCAAGTGAAACTGTCTCAAGAGAGATAAA
65 AAGAGAAACTGTCTCAAAAGAGATAAAACTTTGTTT-CAAGGGAAACTGTCTCAAGAGAGACAAA
* * *
4105885 ACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAG
129 A-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
* * *
4105935 GGAAACTATCTCAAGAGAGACAAAACTTTGTTT
1 AGAAACTGTCTCAAGGGAGACAAAACTTTGTTT
4105968 TGAATAAATT
Statistics
Matches: 183, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
173 6 0.03
174 29 0.16
175 89 0.49
176 37 0.20
177 22 0.12
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (177 bp):
AGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAGAGAAACAGATTCAAAGATTGGTGTTTCA
AGAGAAACTGTCTCAAAAGAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:4105897 original size:22 final size:21
Alignment explanation
Indices: 4105871--4105934 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
4105861 TGAAACTGTC
4105871 TCAAGAGAGATAAAACTTTGTT
1 TCAAGAGAGA-AAAACTTTGTT
*
4105893 TCAAG-G-G--AAAC--TGTC
1 TCAAGAGAGAAAAACTTTGTT
4105908 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGA-AAAACTTTGTT
4105930 TCAAG
1 TCAAG
4105935 GGAAACTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 8 0.24
16 1 0.03
17 5 0.15
20 5 0.15
21 1 0.03
22 13 0.39
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (21 bp):
TCAAGAGAGAAAAACTTTGTT
Found at i:4106610 original size:32 final size:30
Alignment explanation
Indices: 4106574--4106641 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
4106564 GGTCTGATAG
* *
4106574 TGAATCCCCAAAGATGCCCCAATATTCGATGT
1 TGAATCCCCAAA-AT-ACCCAACATTCGATGT
* *
4106606 TGAATCTCCAAAATACCCAACATTTGATGT
1 TGAATCCCCAAAATACCCAACATTCGATGT
4106636 TGAATC
1 TGAATC
4106642 TTAAAGATCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 19 0.59
31 2 0.06
32 11 0.34
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (30 bp):
TGAATCCCCAAAATACCCAACATTCGATGT
Found at i:4107041 original size:32 final size:32
Alignment explanation
Indices: 4106996--4107084 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
4106986 GGTCTGATTA
* *
4106996 GTTGAATCCCCAAAGATGCCCCAATATTCGAT
1 GTTGAATCTCCAAAGATACCCCAATATTCGAT
* * *
4107028 GTTGAATCTCCAAAAATACCCCAACATTTGAT
1 GTTGAATCTCCAAAGATACCCCAATATTCGAT
** *
4107060 GTTGAATCTTAAAAGATCCCCCAAT
1 GTTGAATCTCCAAAGATACCCCAAT
4107085 GTTCCTCATT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (32 bp):
GTTGAATCTCCAAAGATACCCCAATATTCGAT
Found at i:4108180 original size:19 final size:19
Alignment explanation
Indices: 4108121--4108182 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 19
4108111 TCACTTTTCC
4108121 TTTGTTTTTGTTTCTCTTTTT
1 TTTG-TTTT-TTTCTCTTTTT
* *
4108142 TATT-TTCTCTTTGCTTTTTTT
1 T-TTGTT-T-TTTTCTCTTTTT
4108163 TTTGTTTTTTTCTCTTTTT
1 TTTGTTTTTTTCTCTTTTT
4108182 T
1 T
4108183 CTTTTTGTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
19 11 0.33
20 5 0.15
21 14 0.42
22 3 0.09
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.81
Consensus pattern (19 bp):
TTTGTTTTTTTCTCTTTTT
Found at i:4109731 original size:20 final size:20
Alignment explanation
Indices: 4109706--4109748 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4109696 TCTAAAGGCC
4109706 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
4109726 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
4109746 CAT
1 CAT
4109749 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:4117111 original size:21 final size:21
Alignment explanation
Indices: 4117087--4117127 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4117077 ACGTTTTCAC
*
4117087 CTTTCACTTTCTATCTTTTTA
1 CTTTCACTTTCTATCATTTTA
* *
4117108 CTTTTACTTTTTATCATTTT
1 CTTTCACTTTCTATCATTTT
4117128 CTTCTCCCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.66
Consensus pattern (21 bp):
CTTTCACTTTCTATCATTTTA
Found at i:4119687 original size:20 final size:20
Alignment explanation
Indices: 4119662--4119704 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4119652 TCTAAAGGCC
4119662 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
4119682 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
4119702 CAT
1 CAT
4119705 GTAGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:4121211 original size:21 final size:20
Alignment explanation
Indices: 4121186--4121232 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
4121176 TTTGCCACAT
4121186 CATTTTCA-ATTACCATCATTC
1 CATTTTCACATTACC-T-ATTC
* *
4121207 CATTTCCACATTAGCTATTC
1 CATTTTCACATTACCTATTC
4121227 CATTTT
1 CATTTT
4121233 GCCACAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.41
21 8 0.36
22 5 0.23
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.45
Consensus pattern (20 bp):
CATTTTCACATTACCTATTC
Found at i:4128932 original size:22 final size:22
Alignment explanation
Indices: 4128906--4128986 Score: 94
Period size: 23 Copynumber: 3.7 Consensus size: 22
4128896 ATAGGGCAGA
*
4128906 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
4128928 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
4128951 GGGAACCAATTCCCCCTT--AG
1 GGGAACCGATACCCCCTTGAAG
*
4128971 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
4128987 CTGGGGTTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.29
22 16 0.31
23 21 0.40
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.19
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:4132484 original size:25 final size:24
Alignment explanation
Indices: 4132450--4132527 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 24
4132440 AATAAAGAAA
*
4132450 ATAAAGAAAAAGAAGAAAAATATAT
1 ATAAATAAAAAGAA-AAAAATATAT
4132475 ATAAATAAAACA-AATAAATAATA-AT
1 ATAAATAAAA-AGAA-AAA-AATATAT
*
4132500 A-ATAATAAAAAGTAAAAATATATAT
1 ATA-AATAAAAAG-AAAAAAATATAT
4132525 ATA
1 ATA
4132528 TATATAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
24 5 0.12
25 30 0.70
26 8 0.19
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (24 bp):
ATAAATAAAAAGAAAAAAATATAT
Found at i:4132537 original size:33 final size:34
Alignment explanation
Indices: 4132489--4132577 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 34
4132479 ATAAAACAAA
*
4132489 TAAATA-ATAATAATAATAAAAA-GTAAAAATATA-
1 TAAATATAT-ATAATAATAAAAACATAAAAA-ATAG
*
4132522 TATATATATATAATAAATAAAAACATAAAAAATAG
1 TAAATATATATAAT-AATAAAAACATAAAAAATAG
*
4132557 TAAATATATATAA-ATTAAAAA
1 TAAATATATATAATAATAAAAA
4132578 AATGGATAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
33 17 0.35
34 13 0.27
35 18 0.38
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (34 bp):
TAAATATATATAATAATAAAAACATAAAAAATAG
Found at i:4132564 original size:35 final size:33
Alignment explanation
Indices: 4132488--4132578 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 33
4132478 AATAAAACAA
*
4132488 ATAAATA-ATAATAATAATAAAAAGTAAAAATAT
1 ATAAATATAT-ATAATAATAAAAAATAAAAATAT
*
4132521 ATATATATATATAATAAATAAAAACATAAAAA-AT
1 ATAAATATATATAAT-AATAAAAA-ATAAAAATAT
*
4132555 AGTAAATATATATAA-ATTAAAAAA
1 A-TAAATATATATAATAATAAAAAA
4132579 ATGGATAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
32 1 0.02
33 18 0.36
34 13 0.26
35 18 0.36
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (33 bp):
ATAAATATATATAATAATAAAAAATAAAAATAT
Found at i:4132589 original size:91 final size:94
Alignment explanation
Indices: 4132424--4132598 Score: 225
Period size: 93 Copynumber: 1.9 Consensus size: 94
4132414 AAAATAATAT
4132424 ATATATATATATATAAAATAAAGAAAATAAAGAAAAAGAAGAAAAATATATATAAATAAAACAAA
1 ATATATATATATATAAAATAAAGAAAATAAAGAAAAAGAAGAAAAATATATATAAATAAAACAAA
*
4132489 TAAATAAT-AATAATAATAAAAAGTAAAA
66 TAAATAATAAAAAATAATAAAAAGTAAAA
* * * * *
4132517 ATATATATATATATATAATAAATAAAA-ACATAAAAA-ATAG-TAAATATATATAAATTAAAA-A
1 ATATATATATATATAAAATAAAGAAAATAAAGAAAAAGA-AGAAAAATATATATAAA-TAAAACA
**
4132578 AATGGATAATAAAAAATAATA
64 AATAAATAATAAAAAATAATA
4132599 TATATATATA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
91 23 0.32
92 23 0.32
93 25 0.35
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.26
Consensus pattern (94 bp):
ATATATATATATATAAAATAAAGAAAATAAAGAAAAAGAAGAAAAATATATATAAATAAAACAAA
TAAATAATAAAAAATAATAAAAAGTAAAA
Found at i:4133229 original size:37 final size:37
Alignment explanation
Indices: 4133179--4133249 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
4133169 TTGTGGAGTC
*
4133179 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATACTAAAACTCTATCA
*
4133216 TATTTTTAGGAGTTTGAATCCTACTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATACTAAAACTCTA
4133250 ACGTTTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATACTAAAACTCTATCA
Found at i:4133388 original size:6 final size:6
Alignment explanation
Indices: 4133377--4133405 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4133367 AAATTATTAA
4133377 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
4133406 GAAGTATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:4133828 original size:18 final size:18
Alignment explanation
Indices: 4133796--4133833 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
4133786 AATAAGGTAC
*
4133796 AAATGTGTAAAAC-AACA
1 AAATGTATAAAACAAACA
4133813 AAATGTATACAAACAAACA
1 AAATGTATA-AAACAAACA
4133832 AA
1 AA
4133834 GGAAGGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 4 0.22
19 6 0.33
ACGTcount: A:0.63, C:0.13, G:0.08, T:0.16
Consensus pattern (18 bp):
AAATGTATAAAACAAACA
Found at i:4135692 original size:20 final size:20
Alignment explanation
Indices: 4135662--4135720 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
4135652 CACTGAATAT
*
4135662 TTGTCCTGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
4135682 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
4135701 -TGTCCCGAAAGACCACTGA
1 TTGTCCCGAAGGACCACTGA
4135720 T
1 T
4135721 AATGGGCATG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 14 0.45
19 2 0.06
20 15 0.48
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:4135715 original size:18 final size:20
Alignment explanation
Indices: 4135662--4135720 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 20
4135652 CACTGAATAT
* *
4135662 TTGTCCTGAAGGACCACTGA
1 TTGTCCCGAAAGACCACTGA
*
4135682 TTGTTCCG-AAGAACCACT-A
1 TTGTCCCGAAAG-ACCACTGA
4135701 -TGTCCCGAAAGACCACTGA
1 TTGTCCCGAAAGACCACTGA
4135720 T
1 T
4135721 AATGGGCATG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 12 0.39
19 7 0.23
20 12 0.39
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (20 bp):
TTGTCCCGAAAGACCACTGA
Found at i:4137839 original size:3 final size:3
Alignment explanation
Indices: 4137831--4137866 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
4137821 GGGAAGAGAG
4137831 GAA GAA GAA GAA GAAA GAA GAA GAA GGAA GAA GAA G
1 GAA GAA GAA GAA G-AA GAA GAA GAA -GAA GAA GAA G
4137867 TTCTGGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4137850 original size:13 final size:13
Alignment explanation
Indices: 4137832--4137866 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
4137822 GGAAGAGAGG
4137832 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
*
4137845 AAGAAGAAGAAGG
1 AAGAAGAAGAAGA
4137858 AAGAAGAAG
1 AAGAAGAAG
4137867 TTCTGGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:4137866 original size:10 final size:10
Alignment explanation
Indices: 4137831--4137866 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
4137821 GGGAAGAGAG
4137831 GAAGAA-GAA
1 GAAGAAGGAA
*
4137840 GAAGAAAGAA
1 GAAGAAGGAA
4137850 GAAGAAGGAA
1 GAAGAAGGAA
4137860 GAAGAAG
1 GAAGAAG
4137867 TTCTGGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 6 0.24
10 19 0.76
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (10 bp):
GAAGAAGGAA
Found at i:4140861 original size:8 final size:8
Alignment explanation
Indices: 4140769--4140859 Score: 145
Period size: 8 Copynumber: 11.9 Consensus size: 8
4140759 GTAACAAATA
4140769 CATACATG
1 CATACATG
4140777 CATACATG
1 CATACATG
4140785 CATACATG
1 CATACATG
4140793 CATACATG
1 CATACATG
4140801 CATACATG
1 CATACATG
4140809 CATACATG
1 CATACATG
4140817 CATACATG
1 CATACATG
4140825 CAT--A--
1 CATACATG
4140829 CATACATG
1 CATACATG
4140837 CATACATG
1 CATACATG
*
4140845 CATACATA
1 CATACATG
4140853 CATACAT
1 CATACAT
4140860 ACGTGTATGT
Statistics
Matches: 78, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
4 3 0.04
6 2 0.03
8 73 0.94
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (8 bp):
CATACATG
Found at i:4141230 original size:20 final size:20
Alignment explanation
Indices: 4141201--4141261 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
4141191 CACTGAATAT
*
4141201 TTGTCTCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* * *
4141221 TTGTTCCGAAGAACCACTGT
1 TTGTCCCGAAGGACCACTGA
*
4141241 TTGTCCCGAATGACCACTGA
1 TTGTCCCGAAGGACCACTGA
4141261 T
1 T
4141262 AATCCCTCGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:4141487 original size:13 final size:13
Alignment explanation
Indices: 4141469--4141502 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
4141459 TATTACTTAT
4141469 ATTCACATTACCA
1 ATTCACATTACCA
4141482 ATTCACATTACCA
1 ATTCACATTACCA
4141495 ATTCACAT
1 ATTCACAT
4141503 AAGCTCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTCACATTACCA
Found at i:4142243 original size:32 final size:34
Alignment explanation
Indices: 4142207--4142276 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
4142197 CCTTACAAAC
*
4142207 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACATT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACATT
* *
4142239 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACATT
4142273 TCCC
1 TCCC
4142277 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACATT
Found at i:4146781 original size:14 final size:14
Alignment explanation
Indices: 4146762--4146797 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4146752 ATTGTTTAAT
4146762 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
4146776 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
4146790 TGATTTGT
1 TGATTTGT
4146798 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4146929 original size:19 final size:19
Alignment explanation
Indices: 4146907--4146962 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
4146897 AATGACTATT
4146907 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
4146926 GCAA--CG--A-GAGAATC
1 GCAATGCGAAATGAAAATC
* *
4146940 ACAATGCGAAATTAAAATC
1 GCAATGCGAAATGAAAATC
4146959 GCAA
1 GCAA
4146963 CGACAAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 10
0.64 0.12 0.24
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 12 0.44
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATC
Found at i:4146950 original size:33 final size:33
Alignment explanation
Indices: 4146908--4146983 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
4146898 ATGACTATTG
* *
4146908 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
* *
4146941 CAATGCGAAATTAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
4146974 CAACGCGAAA
1 CAATGCGAAA
4146984 CTAAATTCGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:4147035 original size:33 final size:33
Alignment explanation
Indices: 4146993--4147086 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
4146983 ACTAAATTCG
4146993 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
* *
4147026 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
* * *
4147059 CGTTGTGATTTTTATTTTGCATTGCGAT
1 CGTTGCGATTTTAATTTCGCATTGCGAT
4147087 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
Found at i:4147119 original size:34 final size:34
Alignment explanation
Indices: 4147080--4147173 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
4147070 TTATTTTGCA
* *
4147080 TTGCGATAGTCATTTCCGCGTTACGATTTTCACG
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTCACG
** * *
4147114 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTCACG
*
4147147 TTGCGATAGTAATTTCCGCGTTGCGAT
1 TTGCGATAGTCATTTCCGCGTTGCGAT
4147174 AGACATTAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
33 26 0.53
34 23 0.47
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.40
Consensus pattern (34 bp):
TTGCGATAGTCATTTCCGCGTTGCGATTCTCACG
Found at i:4147122 original size:53 final size:52
Alignment explanation
Indices: 4147028--4147139 Score: 134
Period size: 53 Copynumber: 2.1 Consensus size: 52
4147018 GATTCCCTCG
** * * * * *
4147028 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTTATTTTGCA
1 TTGCGATAGTCATTTCGCATTACGATTCTCACGTTGCGATTTTCATTTCGCA
* *
4147080 TTGCGATAGTCATTTCCGCGTTACGATTTTCACGTTGCGATTTTCATTTCGCA
1 TTGCGATAGTCATTT-CGCATTACGATTCTCACGTTGCGATTTTCATTTCGCA
4147133 TTGCGAT
1 TTGCGAT
4147140 TCTCTCGTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
52 13 0.26
53 37 0.74
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (52 bp):
TTGCGATAGTCATTTCGCATTACGATTCTCACGTTGCGATTTTCATTTCGCA
Found at i:4147219 original size:20 final size:20
Alignment explanation
Indices: 4147146--4147219 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
4147136 CGATTCTCTC
* * *
4147146 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTACGT
* *
4147166 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTACG-T
*
4147186 GATTGCGA-ACGTCATTTTCGT
1 G-TTGCGATA-GTCATTTACGT
4147207 GTTGCGATAGTCA
1 GTTGCGATAGTCA
4147220 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCATTTACGT
Found at i:4149726 original size:24 final size:24
Alignment explanation
Indices: 4149689--4149742 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4149679 CTGAAAAATC
4149689 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
4149713 ATCAAAGTCTGAGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
4149737 ATCAAA
1 ATCAAA
4149743 TTTCGAATAC
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:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4150690 original size:20 final size:20
Alignment explanation
Indices: 4150598--4150784 Score: 138
Period size: 20 Copynumber: 9.6 Consensus size: 20
4150588 ATAGTCAGAA
4150598 TCTCGTTGCGATTTACAG-AT
1 TCTCGTTGCGATTTAC-GTAT
* *
4150618 TCGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGTAT
* * * * *
4150638 TCGCATTGTGATTTATGGAT
1 TCTCGTTGCGATTTACGTAT
* * * *
4150658 ACGCATTGTGATTTACGTAT
1 TCTCGTTGCGATTTACGTAT
*
4150678 TCTCGTTGCGATTTCCG-A-
1 TCTCGTTGCGATTTACGTAT
4150696 ----GTTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGTAT
*
4150712 TCTCGTTGCGATTTACGGAT
1 TCTCGTTGCGATTTACGTAT
* *
4150732 ACGT-GTTGCAATTTTACGTAT
1 TC-TCGTTGCGA-TTTACGTAT
*
4150753 TCTCGTTGCGATTTACGGAT
1 TCTCGTTGCGATTTACGTAT
*
4150773 ACTCGTTGCGAT
1 TCTCGTTGCGAT
4150785 AGTCAGAATC
Statistics
Matches: 135, Mismatches: 22, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
14 12 0.09
15 1 0.01
19 2 0.01
20 104 0.77
21 16 0.12
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
TCTCGTTGCGATTTACGTAT
Found at i:4150691 original size:40 final size:40
Alignment explanation
Indices: 4150598--4150784 Score: 206
Period size: 40 Copynumber: 4.8 Consensus size: 40
4150588 ATAGTCAGAA
* *
4150598 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
* * * * *
4150638 TCGCATTGTGATTTATGGATACGCATTGTGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
*
4150678 TCTCGTTGCGATTT-CCG--A-G--TTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
** *
4150712 TCTCGTTGCGATTTACGGATACGTGTTGCAATTTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGTAT
* *
4150753 TCTCGTTGCGATTTACGGATACTCGTTGCGAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGAT
4150785 AGTCAGAATC
Statistics
Matches: 122, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
34 28 0.23
35 2 0.02
36 1 0.01
37 2 0.02
38 1 0.01
39 1 0.01
40 50 0.41
41 37 0.30
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (40 bp):
TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
Found at i:4150710 original size:34 final size:36
Alignment explanation
Indices: 4150667--4150768 Score: 127
Period size: 34 Copynumber: 2.8 Consensus size: 36
4150657 TACGCATTGT
4150667 GATTTACGTATTCTCGTTGCGATTT-C-CGAGTTGC
1 GATTTACGTATTCTCGTTGCGATTTACACGAGTTGC
*
4150701 GATTTACGTATTCTCGTTGCGATTTACGGATACGTGTTGC
1 GATTTACGTATTCTCGTTGCGATTTAC----ACGAGTTGC
*
4150741 AATTTTACGTATTCTCGTTGCGATTTAC
1 GA-TTTACGTATTCTCGTTGCGATTTAC
4150769 GGATACTCGT
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
34 25 0.42
35 1 0.02
40 8 0.14
41 25 0.42
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.42
Consensus pattern (36 bp):
GATTTACGTATTCTCGTTGCGATTTACACGAGTTGC
Found at i:4150725 original size:74 final size:75
Alignment explanation
Indices: 4150623--4150766 Score: 209
Period size: 74 Copynumber: 1.9 Consensus size: 75
4150613 CAGATTCGCA
* * **
4150623 TTGCGATTTACGTATTCGCATTGTGATTTATGGATACGCATTGTGA-TTTACGTATTCTCGTTGC
1 TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTGCAATTTTACGTATTCTCGTTGC
4150687 GATTTCCGAG
66 GATTTCCGAG
* * **
4150697 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGTGTTGCAATTTTACGTATTCTCGTTGC
1 TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTGCAATTTTACGTATTCTCGTTGC
4150762 GATTT
66 GATTT
4150767 ACGGATACTC
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
74 38 0.62
75 23 0.38
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (75 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTGCAATTTTACGTATTCTCGTTGC
GATTTCCGAG
Found at i:4152477 original size:34 final size:32
Alignment explanation
Indices: 4152424--4152494 Score: 106
Period size: 34 Copynumber: 2.2 Consensus size: 32
4152414 CCTTACAAAC
*
4152424 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
4152456 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
4152490 TCCCT
1 TCCCT
4152495 TTACAAAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 7 0.20
33 5 0.14
34 23 0.66
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.32
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:4154975 original size:18 final size:18
Alignment explanation
Indices: 4154952--4155007 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
4154942 GCACTTAAAA
4154952 TTTGTCCCGAATGACCAC
1 TTTGTCCCGAATGACCAC
* *
4154970 TTTGTCCTGAAGGACCAC
1 TTTGTCCCGAATGACCAC
*
4154988 TATGTCCCGAATGACCAC
1 TTTGTCCCGAATGACCAC
4155006 TT
1 TT
4155008 ATAACCCTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (18 bp):
TTTGTCCCGAATGACCAC
Found at i:4159236 original size:13 final size:13
Alignment explanation
Indices: 4159228--4159254 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4159218 AATATCGTTA
4159228 GAACTTATCTAAG
1 GAACTTATCTAAG
4159241 GAACTTATCTAAG
1 GAACTTATCTAAG
4159254 G
1 G
4159255 TCTGATCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (13 bp):
GAACTTATCTAAG
Found at i:4160266 original size:15 final size:16
Alignment explanation
Indices: 4160225--4160270 Score: 74
Period size: 17 Copynumber: 2.8 Consensus size: 16
4160215 ACTTCTTTTA
4160225 TTTAAAAATAATAATTT
1 TTTAAAAA-AATAATTT
4160242 TTTAAAAAAATAATTT
1 TTTAAAAAAATAATTT
4160258 TTTAGAAAAAATA
1 TTTA-AAAAAATA
4160271 TAAACGTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TTTAAAAAAATAATTT
Found at i:4160267 original size:19 final size:17
Alignment explanation
Indices: 4160225--4160270 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
4160215 ACTTCTTTTA
*
4160225 TTTAAAAATAATAATTT
1 TTTAAAAAAAATAATTT
4160242 TTT-AAAAAAATAATTT
1 TTTAAAAAAAATAATTT
*
4160258 TTTAGAAAAAATA
1 TTTAAAAAAAATA
4160271 TAAACGTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTAAAAAAAATAATTT
Found at i:4160273 original size:19 final size:17
Alignment explanation
Indices: 4160228--4160273 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
4160218 TCTTTTATTT
4160228 AAAAATAATAATTTTTTA
1 AAAAAT-ATAATTTTTTA
4160246 AAAAA-ATAATTTTTTAGA
1 AAAAATATAATTTTTT--A
4160264 AAAAATATAA
1 AAAAATATAA
4160274 ACGTCACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.40
18 11 0.44
19 4 0.16
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AAAAATATAATTTTTTA
Found at i:4163495 original size:4 final size:4
Alignment explanation
Indices: 4163481--4163554 Score: 58
Period size: 4 Copynumber: 17.0 Consensus size: 4
4163471 ATAATATGAC
** * *
4163481 AAAT GAAAT AAAT AAAT AAAT AAAT ATAAT ATGT CAAAT ATAAT ATGAC
1 AAAT -AAAT AAAT AAAT AAAT AAAT A-AAT AAAT -AAAT A-AAT A-AAT
4163530 AAAT AAAAT AAAT AAAT AAAT AAAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT
4163555 GGCACACATA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
4 36 0.63
5 21 0.37
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:4164172 original size:19 final size:17
Alignment explanation
Indices: 4164132--4164173 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
4164122 AAAATATGGT
*
4164132 ACAAAATGTATAATACA
1 ACAAAATGTATAAAACA
4164149 ACAAAATGTATACAAACAA
1 ACAAAATGTATA-AAAC-A
4164168 ACAAAA
1 ACAAAA
4164174 GACGTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 3 0.14
19 7 0.32
ACGTcount: A:0.64, C:0.14, G:0.05, T:0.17
Consensus pattern (17 bp):
ACAAAATGTATAAAACA
Found at i:4167159 original size:24 final size:20
Alignment explanation
Indices: 4167132--4167189 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
4167122 GCATGGGTAG
4167132 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
4167156 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
4167176 TGTATCGATGCACT
1 TGCATCGATGCACT
4167190 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:4167996 original size:18 final size:18
Alignment explanation
Indices: 4167968--4168016 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
4167958 TCTACGCCGT
4167968 CTTTCGGGACATAGTGGTC
1 CTTT-GGGACATAGTGGTC
4167987 CTTTGGGACATAGTGGTC
1 CTTTGGGACATAGTGGTC
*
4168005 CTTCGGGACATA
1 CTTTGGGACATA
4168017 TGTGCTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (18 bp):
CTTTGGGACATAGTGGTC
Found at i:4170219 original size:24 final size:24
Alignment explanation
Indices: 4170189--4170245 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
4170179 TGAAAAAAAA
*
4170189 TTGATGAAGAAGTTTTGAA-AATGAT
1 TTGATGAAGAA-TTTTAAATAATG-T
4170214 TT-ATGAAAGAATTTTAAATAATGT
1 TTGATG-AAGAATTTTAAATAATGT
4170238 TTGATGAA
1 TTGATGAA
4170246 ATTTTTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (24 bp):
TTGATGAAGAATTTTAAATAATGT
Found at i:4170223 original size:25 final size:25
Alignment explanation
Indices: 4170189--4170271 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
4170179 TGAAAAAAAA
*
4170189 TTGATG-AAGAAGTTTTGAA-AATGAT
1 TTGATGAAAGAA-TTTTAAATAATG-T
4170214 TT-ATGAAAGAATTTTAAATAATGT
1 TTGATGAAAGAATTTTAAATAATGT
***
4170238 TTGATGAAATTTTTTTGAAA-AATGT
1 TTGATGAAAGAATTTT-AAATAATGT
4170263 TTGAT-AAAG
1 TTGATGAAAG
4170272 TTATTTGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
24 15 0.31
25 31 0.63
26 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (25 bp):
TTGATGAAAGAATTTTAAATAATGT
Found at i:4170283 original size:24 final size:25
Alignment explanation
Indices: 4170202--4170285 Score: 86
Period size: 24 Copynumber: 3.4 Consensus size: 25
4170192 ATGAAGAAGT
*
4170202 TTTG-AAAATGATTT-ATGAAAG-AA
1 TTTGAAAAATG-TTTGATGAAAGTTA
* * *
4170225 TTTTAAATAATGTTTGATGAAATTTT
1 TTTGAAA-AATGTTTGATGAAAGTTA
4170251 TTTGAAAAATGTTTGAT-AAAGTTA
1 TTTGAAAAATGTTTGATGAAAGTTA
4170275 TTTGAAAAATG
1 TTTGAAAAATG
4170286 GTGCCCCTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.06
24 21 0.42
25 20 0.40
26 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (25 bp):
TTTGAAAAATGTTTGATGAAAGTTA
Found at i:4170283 original size:25 final size:26
Alignment explanation
Indices: 4170206--4170283 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 26
4170196 AGAAGTTTTG
* *
4170206 AAAATGATTT-ATGAAAG-AATTTTAA
1 AAAATG-TTTGATGAAAGTTATTTGAA
* * *
4170231 ATAATGTTTGATGAAATTTTTTTG-A
1 AAAATGTTTGATGAAAGTTATTTGAA
4170256 AAAATGTTTGAT-AAAGTTATTTGAA
1 AAAATGTTTGATGAAAGTTATTTGAA
4170281 AAA
1 AAA
4170284 TGGTGCCCCT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 12 0.29
25 27 0.64
26 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (26 bp):
AAAATGTTTGATGAAAGTTATTTGAA
Found at i:4172371 original size:17 final size:19
Alignment explanation
Indices: 4172349--4172390 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
4172339 AAAATAAGGT
*
4172349 ACAAAATGTATA-AAAC-A
1 ACAAAATGTAAACAAACAA
4172366 ACAAAATGTAAACAAACAA
1 ACAAAATGTAAACAAACAA
4172385 ACAAAA
1 ACAAAA
4172391 AAAGGGACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 4 0.18
19 7 0.32
ACGTcount: A:0.69, C:0.14, G:0.05, T:0.12
Consensus pattern (19 bp):
ACAAAATGTAAACAAACAA
Found at i:4173190 original size:22 final size:22
Alignment explanation
Indices: 4173164--4173217 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
4173154 CCCGAAGTTC
4173164 AAAACCAAACCTCATTTTTACT
1 AAAACCAAACCTCATTTTTACT
4173186 AAAACCAAACCTCATTTTTACT
1 AAAACCAAACCTCATTTTTACT
*
4173208 AAAACTAAAC
1 AAAACCAAAC
4173218 ATAAATCCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAACCAAACCTCATTTTTACT
Found at i:4173324 original size:72 final size:72
Alignment explanation
Indices: 4173228--4173371 Score: 236
Period size: 72 Copynumber: 2.0 Consensus size: 72
4173218 ATAAATCCTA
* *
4173228 GATCTAGGAAAATCATCTCTGGTTTTACCTATTTTCCGGCGATCCTTGGGTTTCCGA-AGAGATT
1 GATCCAGGAAAATCATCTCGGGTTTTACCTATTTTCCGGCGATCCTTGGGTTTCCGACA-AGATT
4173292 CTCAACCC
65 CTCAACCC
* *
4173300 GATCCAGGAAAATCATCTCGGGTTTTACCTATTTTCCGGCGATCTTTGGGTTTCTGACAAGATTC
1 GATCCAGGAAAATCATCTCGGGTTTTACCTATTTTCCGGCGATCCTTGGGTTTCCGACAAGATTC
4173365 TCAACCC
66 TCAACCC
4173372 AGAAAGGTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 66 0.99
73 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (72 bp):
GATCCAGGAAAATCATCTCGGGTTTTACCTATTTTCCGGCGATCCTTGGGTTTCCGACAAGATTC
TCAACCC
Found at i:4176598 original size:20 final size:21
Alignment explanation
Indices: 4176573--4176624 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4176563 TTTTCCCAAT
*
4176573 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
4176593 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
4176614 TCGCAATGCGA
1 TCGCAATGCGA
4176625 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:4176638 original size:20 final size:19
Alignment explanation
Indices: 4176613--4176747 Score: 108
Period size: 20 Copynumber: 6.7 Consensus size: 19
4176603 AATTGGGAAA
4176613 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
4176633 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATAC-TACT
* *
4176653 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTAC--T
* *
4176674 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACT-ACT
* * *
4176694 TTCGCAACGCGATTCTAACT
1 ATCGCAATGCGATACT-ACT
* * *
4176714 TTCGCAACGCGATAATACAT
1 ATCGCAATGCGATACTAC-T
4176734 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
4176748 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.05
20 63 0.66
21 25 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:4176657 original size:61 final size:61
Alignment explanation
Indices: 4176610--4176741 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
4176600 GCGAATTGGG
* * * * *
4176610 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTAACTATCGCAACGCGATAATAC
* * *
4176671 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTAACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTAACTATCGCAACGCGATAATAC
*
4176732 ATAATCGCAA
1 AAAATCGCAA
4176742 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTAACTATCGCAACGCGATAATAC
Found at i:4176943 original size:22 final size:22
Alignment explanation
Indices: 4176915--4176958 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4176905 CACTCTCTCA
4176915 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
4176937 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
4176959 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:4177247 original size:20 final size:20
Alignment explanation
Indices: 4177222--4177259 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4177212 CGATTCTCTC
4177222 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
4177242 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
4177260 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:4177450 original size:25 final size:24
Alignment explanation
Indices: 4177396--4177450 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
4177386 TGTTTATTAT
* *
4177396 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
4177420 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
4177446 TGTTT
1 TGTTT
4177451 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:4178600 original size:18 final size:18
Alignment explanation
Indices: 4178579--4178623 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4178569 TCCACTTCGG
**
4178579 GAGCCATCACCTCGTCCA
1 GAGCCATCACCTCACCCA
*
4178597 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
4178615 GAGCCATCA
1 GAGCCATCA
4178624 TCTGATCGAC
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:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:4179096 original size:20 final size:19
Alignment explanation
Indices: 4179073--4179182 Score: 72
Period size: 19 Copynumber: 6.1 Consensus size: 19
4179063 CACAACACGA
4179073 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGC-G
* *
4179093 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAACGCG
**
4179112 AAATGAAAATCGCAA--CG
1 AAATGACTATCGCAACGCG
*
4179129 ACAA--A--ATCGCAATGCG
1 A-AATGACTATCGCAACGCG
*
4179145 AAATGA-AATCGCAACGCG
1 AAATGACTATCGCAACGCG
** *
4179163 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAACGCG
4179182 A
1 A
4179183 TTTGTGTTTC
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.09
15 2 0.03
16 4 0.05
17 4 0.05
18 18 0.24
19 25 0.33
20 16 0.21
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:4179116 original size:19 final size:20
Alignment explanation
Indices: 4179073--4179128 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
4179063 CACAACACGA
4179073 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
4179093 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
4179112 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
4179129 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:4179174 original size:19 final size:19
Alignment explanation
Indices: 4179101--4179182 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
4179091 GGAAATGGCT
4179101 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4179120 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
4179134 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
4179152 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4179171 ATCGCAATGCGA
1 ATCGCAATGCGA
4179183 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 18 0.34
19 20 0.38
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4179217 original size:14 final size:14
Alignment explanation
Indices: 4179194--4179284 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
4179184 TTGTGTTTCG
4179194 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
4179208 CGTTGGGATTTCATTT
1 CGTTGCGATTT--TGT
4179224 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
4179240 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
4179257 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
4179273 CGTTGCGATTTT
1 CGTTGCGATTTT
4179285 CATTTCGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 26 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 11 0.18
19 6 0.10
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4179258 original size:33 final size:33
Alignment explanation
Indices: 4179189--4179300 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
4179179 GCGATTTGTG
* *
4179189 TTTCGCGTTGCGATTTTGTCGTTGGGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
4179221 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
4179254 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
4179287 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
4179301 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 25 0.32
33 52 0.68
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:4179319 original size:20 final size:20
Alignment explanation
Indices: 4179285--4179340 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
4179275 TTGCGATTTT
*
4179285 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
* *
4179304 CATTTCCGTGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
*
4179324 CATTTTCGCGTTGCGAT
1 CATTTCCGCGTTGCGAT
4179341 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:4179802 original size:41 final size:41
Alignment explanation
Indices: 4179706--4179793 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
4179696 GACTCACCTG
* * *
4179706 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
* *
4179748 TCCTCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
4179789 TCATC
1 TCATC
4179794 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:4181242 original size:14 final size:13
Alignment explanation
Indices: 4181208--4181246 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
4181198 TTGATTGTTT
4181208 AATTGATTTGTAA
1 AATTGATTTGTAA
*
4181221 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
4181235 ATATTGATTTGT
1 A-ATTGATTTGT
4181247 TTAATTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 19 0.86
15 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:4181409 original size:19 final size:19
Alignment explanation
Indices: 4181383--4181428 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
4181373 ATCGCAACGA
*
4181383 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATACGAAAT
*
4181402 GTAAATCGCAATACGAAAT
1 GAAAATCGCAATACGAAAT
4181421 GAAAATCG
1 GAAAATCG
4181429 TAACGAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (19 bp):
GAAAATCGCAATACGAAAT
Found at i:4181494 original size:20 final size:20
Alignment explanation
Indices: 4181469--4181544 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
4181459 TCGCATTGCG
*
4181469 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
4181489 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
* *
4181510 A-TTTCAAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
4181529 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
4181545 TTCCCCGTTG
Statistics
Matches: 40, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:4181783 original size:20 final size:20
Alignment explanation
Indices: 4181758--4181807 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
4181748 TTGAAGATGA
4181758 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
4181778 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
4181798 TTGCGATTTT
1 TTGCGATTTT
4181808 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:4182714 original size:24 final size:24
Alignment explanation
Indices: 4182663--4182716 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
4182653 GTATTCGAAA
* *
4182663 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
4182687 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
4182711 TTTGAT
1 TTTGAT
4182717 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:4182908 original size:12 final size:12
Alignment explanation
Indices: 4182891--4182915 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4182881 ATATAATCCT
4182891 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4182903 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4182915 G
1 G
4182916 TCCCCGAAGA
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:4185243 original size:33 final size:33
Alignment explanation
Indices: 4185201--4185327 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
4185191 GGAAATTACT
*
4185201 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
4185234 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
4185266 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
4185300 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
4185328 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4185284 original size:66 final size:66
Alignment explanation
Indices: 4185202--4185334 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
4185192 GAAATTACTA
*
4185202 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
4185267 T
66 T
* *
4185268 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
4185333 T
66 T
4185334 T
1 T
4185335 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:4185516 original size:14 final size:14
Alignment explanation
Indices: 4185497--4185533 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4185487 CATCAATTAA
4185497 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4185511 ACAAATCACCTTTT
1 ACAAATCAACTTTT
4185525 ACAAATCAA
1 ACAAATCAA
4185534 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4187338 original size:92 final size:89
Alignment explanation
Indices: 4187229--4187410 Score: 294
Period size: 88 Copynumber: 2.0 Consensus size: 89
4187219 ATTTCAAACT
* *
4187229 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGC
4187294 AGAATTGGCAGCAACCGAATAAATTTAC
62 AGAATTGGCAGCAACCGAATAAATTTAC
*
4187322 TTCAA-CAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGTA
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGAA
4187386 TTGGCAGCAACCGAATAAATTTAC
66 TTGGCAGCAACCGAATAAATTTAC
4187410 T
1 T
4187411 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
88 42 0.49
92 39 0.45
93 5 0.06
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGAA
TTGGCAGCAACCGAATAAATTTAC
Found at i:4189201 original size:19 final size:19
Alignment explanation
Indices: 4189097--4189229 Score: 123
Period size: 20 Copynumber: 7.1 Consensus size: 19
4189087 TCTTTTGGTT
*
4189097 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
4189116 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
4189136 GAAAATGACTATCGCAACGC
1 G-AAATGAAAATCGCAACGC
** *
4189156 GCAAATGACTATCGCGA--C
1 G-AAATGAAAATCGCAACGC
*
4189174 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4189190 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
4189209 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
4189228 GA
1 GA
4189230 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
14 8 0.08
15 1 0.01
16 2 0.02
18 3 0.03
19 35 0.36
20 46 0.48
21 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:4189252 original size:19 final size:19
Alignment explanation
Indices: 4189225--4189290 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
4189215 AAAATCGCAA
**
4189225 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTTATTTCGCGT
4189243 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
4189262 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
4189282 TGCGATTTT
1 TGCGATTTT
4189291 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
18 16 0.40
19 12 0.30
20 12 0.30
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:4189282 original size:20 final size:19
Alignment explanation
Indices: 4189236--4189287 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
4189226 GCGATTTTGG
**
4189236 TTTCGCG-TGCGATTTTTA
1 TTTCGCGTTGCGATAGTTA
4189254 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
4189273 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
4189288 TTTCATTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 7 0.23
19 12 0.40
20 11 0.37
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:4189829 original size:20 final size:20
Alignment explanation
Indices: 4189804--4189857 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
4189794 GGCGCTATGT
*
4189804 AAATCGGGTTGCGAAAGTCA
1 AAATCGCGTTGCGAAAGTCA
4189824 AAATCGCGTTGCGAAAGTCA
1 AAATCGCGTTGCGAAAGTCA
** *
4189844 GTATCTCGTTGCGA
1 AAATCGCGTTGCGA
4189858 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (20 bp):
AAATCGCGTTGCGAAAGTCA
Found at i:4189918 original size:41 final size:41
Alignment explanation
Indices: 4189826--4189920 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
4189816 GAAAGTCAAA
* * * * ** *
4189826 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
4189867 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
4189909 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
4189921 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:4190010 original size:21 final size:21
Alignment explanation
Indices: 4189970--4190010 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4189960 ACTGTAGACC
**
4189970 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
4189991 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
4190011 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:4190040 original size:20 final size:20
Alignment explanation
Indices: 4190017--4190062 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
4190007 CAACGCGAAT
*
4190017 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
4190037 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
4190056 TTGCGAT
1 TTGCGAT
4190063 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:4191484 original size:20 final size:20
Alignment explanation
Indices: 4191438--4191484 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
4191428 ACTCCTATAT
* *
4191438 ATCTTAATATTTTTATTTTT
1 ATCTTAATATATTTATTTTC
*
4191458 ATATTAATA-ATTTATTTTC
1 ATCTTAATATATTTATTTTC
4191477 ACTCTTAA
1 A-TCTTAA
4191485 AATCTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.60
Consensus pattern (20 bp):
ATCTTAATATATTTATTTTC
Found at i:4196568 original size:21 final size:22
Alignment explanation
Indices: 4196534--4196575 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4196524 TTAATCACAA
4196534 ATTTATTAATTCATAA-ATACC
1 ATTTATTAATTCATAACATACC
4196555 ATTT-TTAATATCATAACATAC
1 ATTTATTAAT-TCATAACATAC
4196576 TAATGCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTATTAATTCATAACATACC
Found at i:4197472 original size:6 final size:6
Alignment explanation
Indices: 4197463--4197502 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
4197453 GTCCGTCTCG
4197463 GGTCGT GGTCGT GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
4197503 ACGTGTCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:4197486 original size:22 final size:22
Alignment explanation
Indices: 4197460--4197501 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
4197450 GCCGTCCGTC
4197460 TCGGGTCGTGGTCGTGGTCGGG
1 TCGGGTCGTGGTCGTGGTCGGG
4197482 TCGGGTCGTGGTCGTGGTCG
1 TCGGGTCGTGGTCGTGGTCG
4197502 TACGTGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.52, T:0.29
Consensus pattern (22 bp):
TCGGGTCGTGGTCGTGGTCGGG
Done.