Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007928.1 Hibiscus syriacus cultivar Beakdansim tig00110334_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: 336612
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 1 of 2
Found at i:10451 original size:19 final size:20
Alignment explanation
Indices: 10415--10453 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10405 AATAAAGACA
*
10415 TATAAAATTAATAACTAATT
1 TATAAAAATAATAACTAATT
10435 TATAAAAATAA-AACTAATT
1 TATAAAAATAATAACTAATT
10454 ACTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAAAAATAATAACTAATT
Found at i:11775 original size:3 final size:3
Alignment explanation
Indices: 11767--11872 Score: 131
Period size: 3 Copynumber: 35.0 Consensus size: 3
11757 TTAATATATT
* *
11767 TAA TAA TAA AAA TAA TAA TAA TAA TAA TAAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * * * *
11813 AAA TAA TAA TGA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
11861 TAA TGA TAA TAA
1 TAA TAA TAA TAA
11873 AATGGATAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:11880 original size:12 final size:11
Alignment explanation
Indices: 11769--11885 Score: 54
Period size: 12 Copynumber: 10.8 Consensus size: 11
11759 AATATATTTA
11769 ATAATAAAA--
1 ATAATAAAATG
*
11778 ATAATAATAATA
1 ATAATAA-AATG
*
11790 ATAAT-AAATA
1 ATAATAAAATG
* *
11800 ATAAAAATAATA
1 ATAATAA-AATG
*
11812 AAAATAATAATG
1 ATAATAA-AATG
*
11824 ATAATAATAT-
1 ATAATAAAATG
11834 -TAAT--AATG
1 ATAATAAAATG
11842 ATAATAATAAT-
1 ATAATAA-AATG
11853 ATTAATAATAATG
1 A-TAATAA-AATG
11866 ATAATAAAATGG
1 ATAATAAAAT-G
11878 ATAA-AAAA
1 ATAATAAAA
11886 AATAGTATCT
Statistics
Matches: 88, Mismatches: 7, Indels: 24
0.74 0.06 0.20
Matches are distributed among these distances:
7 2 0.02
9 15 0.17
10 10 0.11
11 12 0.14
12 48 0.55
13 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:22757 original size:23 final size:24
Alignment explanation
Indices: 22704--22754 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
22694 CTTTATTTTC
* * *
22704 TTTTCTTCTTTTTGAGTGCTTGAA
1 TTTTCTTCTTTTGGAGTACTTCAA
22728 TTTTCTTCTTTTGGAGTACTTCAA
1 TTTTCTTCTTTTGGAGTACTTCAA
22752 TTT
1 TTT
22755 CTTTGCTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTACTTCAA
Found at i:24917 original size:2 final size:2
Alignment explanation
Indices: 24910--24939 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24900 TGAAAGTGGA
24910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24940 GTTGGTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26699 original size:21 final size:17
Alignment explanation
Indices: 26655--26697 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
26645 CTTGAGTATG
26655 AGGTGAATGTATTTTAA
1 AGGTGAATGTATTTTAA
26672 AGGTGAATGTATTTTAA
1 AGGTGAATGTATTTTAA
*
26689 AGGTTAATG
1 AGGTGAATG
26698 AACATGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (17 bp):
AGGTGAATGTATTTTAA
Found at i:27429 original size:11 final size:11
Alignment explanation
Indices: 27413--27437 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27403 TACAAAAAAA
27413 GAAGTGCAAGT
1 GAAGTGCAAGT
27424 GAAGTGCAAGT
1 GAAGTGCAAGT
27435 GAA
1 GAA
27438 AGAAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:27502 original size:24 final size:24
Alignment explanation
Indices: 27469--27519 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
27459 ATCAACAAAG
* * *
27469 AAATTGAAGCACTCTAAAAGAAGA
1 AAATTCAAGCACTCAAAAAGAAAA
27493 AAATTCAAGCACTCAAAAAGAAAA
1 AAATTCAAGCACTCAAAAAGAAAA
27517 AAA
1 AAA
27520 GAAAAGAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.14, G:0.12, T:0.14
Consensus pattern (24 bp):
AAATTCAAGCACTCAAAAAGAAAA
Found at i:31583 original size:11 final size:11
Alignment explanation
Indices: 31569--31593 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31559 TACAAAAAAA
31569 GAAGTGCAAGT
1 GAAGTGCAAGT
31580 GAAGTGCAAGT
1 GAAGTGCAAGT
31591 GAA
1 GAA
31594 AGAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:31650 original size:24 final size:24
Alignment explanation
Indices: 31617--31667 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
31607 ATCAACAAAT
* *
31617 AAATTGAAGCACTCCAAAAGAAGA
1 AAATTCAAGCACTCAAAAAGAAGA
31641 AAATTCAAGCACTCAAAAAGAAGA
1 AAATTCAAGCACTCAAAAAGAAGA
31665 AAA
1 AAA
31668 GAAAAGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.12
Consensus pattern (24 bp):
AAATTCAAGCACTCAAAAAGAAGA
Found at i:36522 original size:31 final size:31
Alignment explanation
Indices: 36486--36558 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
36476 AAAGTTTTTA
** *
36486 AAATTTGTGGTGGAATATGTGGACCCATCAC
1 AAATTTGTGACGGAATAGGTGGACCCATCAC
*
36517 AAATTTGTGACGGAATAGGTGGACCCGTCAC
1 AAATTTGTGACGGAATAGGTGGACCCATCAC
*
36548 AAATTTCTGAC
1 AAATTTGTGAC
36559 ATATTCACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (31 bp):
AAATTTGTGACGGAATAGGTGGACCCATCAC
Found at i:36576 original size:31 final size:31
Alignment explanation
Indices: 36541--36617 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
36531 ATAGGTGGAC
*
36541 CCGTCACAAATTTCTGACATATTCACATATT
1 CCGTCACAAATTTCTGACAGATTCACATATT
* *
36572 CCGTCACAAATTTCTGATAGATTCACTTATT
1 CCGTCACAAATTTCTGACAGATTCACATATT
* *
36603 TCATCACAAATTTCT
1 CCGTCACAAATTTCT
36618 TACGGGTCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (31 bp):
CCGTCACAAATTTCTGACAGATTCACATATT
Found at i:38212 original size:20 final size:20
Alignment explanation
Indices: 38189--38260 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
38179 GTTTCCAGAT
*
38189 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
38209 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
* *
38229 TCGCAATGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
38249 TCGCAACGCGAT
1 TCGCAACGCGAT
38261 CTCCAGTATC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:38854 original size:19 final size:19
Alignment explanation
Indices: 38830--38866 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
38820 TTATTTTGGA
38830 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
38849 TTTTTCACTATCGCAACA
1 TTTTTCACTATCGCAACA
38867 ACACGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:47211 original size:163 final size:163
Alignment explanation
Indices: 47003--47547 Score: 548
Period size: 163 Copynumber: 3.4 Consensus size: 163
46993 TTTTTTTAAC
* * *
47003 AAACGCCGCTATAG-GTTCATCCATAGT-GCGTTTCTC-ACAAACGCCATGACATAGTAGTACTT
1 AAACACCGCAATAGTGTTCATCCATAGTGGCGTTTCTCAACAAACGCCATGACAGAGTAGTACTT
* *** * *
47065 TAGCGGCGTTTGTATAAAAATACCGTAATAGGCTTTATCTATCGTGGTGTTTTTAACGAACACCG
66 TAGCGGCGTTTGTATAAAAATACCGTAATAGGCTTCATCTATAAAGGCGTTTTTAACAAACACCG
47130 CAACAGAGTAGTACTTTAGCGGCGTTTGTATAA
131 CAACAGAGTAGTACTTTAGCGGCGTTTGTATAA
* *
47163 AAACACTGCAATAGTGTTCATCCATAGTGGCGTTTCTCAACAAACGCCATGACAGAGTAGTCCTT
1 AAACACCGCAATAGTGTTCATCCATAGTGGCGTTTCTCAACAAACGCCATGACAGAGTAGTACTT
* ** *
47228 TAGAGGCGTTTGTATAAAAATGTCGTAATTGGCTTCATCTATAAAGGCGTTTTTAACAAACACCG
66 TAGCGGCGTTTGTATAAAAATACCGTAATAGGCTTCATCTATAAAGGCGTTTTTAACAAACACCG
*
47293 CAACAGAGTAGTACTTTAGCGGCGTTTGTGTAA
131 CAACAGAGTAGTACTTTAGCGGCGTTTGTATAA
* * * * * *
47326 AAACGCCGCAATAGTGTCCATCTATAGTGGCATTTTTTAACAAACGTCGCA--ACAGAGTAGTAC
1 AAACACCGCAATAGTGTTCATCCATAGTGGCGTTTCTCAACAAACG-C-CATGACAGAGTAGTAC
* * * ** *** ** * * *
47389 TTTAGCGGTGTTTTTATACAAACGCTACAATAGG-TTCATAC-ATAGTGGCATTTCTCAACAAAT
64 TTTAGCGGCGTTTGTATAAAAATACCGTAATAGGCTTCAT-CTATAAAGGCGTTT-TTAACAAAC
* ** * *
47452 GCCGTGACAGAGTAATACTTTAGCGGCGTTTGTATCA
127 ACCGCAACAGAGTAGTACTTTAGCGGCGTTTGTATAA
** * * * * * * *
47489 AAATGCCGTAATAGGGTTCAT-CTTAGTGACGTTTTTTCAACAAACGCCATAAAAGAGTA
1 AAACACCGCAATAGTGTTCATCCATAGTGGCG-TTTCTCAACAAACGCCATGACAGAGTA
47548 TTATTTTTTT
Statistics
Matches: 320, Mismatches: 55, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
160 11 0.03
161 15 0.05
162 30 0.09
163 261 0.82
164 1 0.00
165 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (163 bp):
AAACACCGCAATAGTGTTCATCCATAGTGGCGTTTCTCAACAAACGCCATGACAGAGTAGTACTT
TAGCGGCGTTTGTATAAAAATACCGTAATAGGCTTCATCTATAAAGGCGTTTTTAACAAACACCG
CAACAGAGTAGTACTTTAGCGGCGTTTGTATAA
Found at i:47318 original size:81 final size:80
Alignment explanation
Indices: 47013--47536 Score: 478
Period size: 81 Copynumber: 6.5 Consensus size: 80
47003 AAACGCCGCT
* * * *** *
47013 ATAGGTTCATCCATAGT-GCGTTTCTCACAAACGCCATGACATAGTAGTACTTTAGCGGCGTTTG
1 ATAGGTTCATCTATAGTGGCGTTTTTAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTG
*
47077 TATAAAAATACCGTA
66 TATAAAAATGCCGTA
* * * * *
47092 ATAGGCTTTATCTATCGTGGTGTTTTTAACGAACACCGCAACAGAGTAGTACTTTAGCGGCGTTT
1 ATAGG-TTCATCTATAGTGGCGTTTTTAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTT
** * *
47157 GTATAAAAACACTGCA
65 GTATAAAAATGCCGTA
* * *** * *
47173 ATAGTGTTCATCCATAGTGGCGTTTCTCAACAAACGCCATGACAGAGTAGTCCTTTAGAGGCGTT
1 ATAG-GTTCATCTATAGTGGCGTTT-TTAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTT
*
47238 TGTATAAAAATGTCGTA
64 TGTATAAAAATGCCGTA
* ** *
47255 ATTGGCTTCATCTATAAAGGCGTTTTTAACAAACACCGCAACAGAGTAGTACTTTAGCGGCGTTT
1 ATAGG-TTCATCTATAGTGGCGTTTTTAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTT
* * *
47320 GTGTAAAAACGCCGCA
65 GTATAAAAATGCCGTA
* * * *
47336 ATAGTGTCCATCTATAGTGGCATTTTTTAACAAACGTCGCAACAGAGTAGTACTTTAGCGGTGTT
1 ATAG-GTTCATCTATAGTGGC-GTTTTTAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTT
* * * ***
47401 TTTATACAAACGCTACA
64 TGTATAAAAATGCCGTA
* * * ** *
47418 ATAGGTTCATAC-ATAGTGGCATTTCTCAACAAATGCCGTGACAGAGTAATACTTTAGCGGCGTT
1 ATAGGTTCAT-CTATAGTGGCGTTT-TTAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTT
*
47482 TGTATCAAAATGCCGTA
64 TGTATAAAAATGCCGTA
*
47499 ATAGGGTTCATCT-TAGTGACGTTTTTTCAACAAACGCC
1 ATA-GGTTCATCTATAGTGGCG-TTTTT-AACAAACGCC
47537 ATAAAAGAGT
Statistics
Matches: 352, Mismatches: 80, Indels: 23
0.77 0.18 0.05
Matches are distributed among these distances:
79 5 0.01
80 12 0.03
81 196 0.56
82 139 0.39
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (80 bp):
ATAGGTTCATCTATAGTGGCGTTTTTAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTG
TATAAAAATGCCGTA
Found at i:47403 original size:41 final size:41
Alignment explanation
Indices: 47273--47413 Score: 130
Period size: 41 Copynumber: 3.5 Consensus size: 41
47263 CATCTATAAA
*
47273 GGCG-TTTTTAACAAACACCGCAACAGAGTAGTACTTTAGC
1 GGCGTTTTTTAACAAACGCCGCAACAGAGTAGTACTTTAGC
* * * * *
47313 GGCGTTTGTGTAA-AAACGCCGCAATAGTGTCCA-T-CTATAGT
1 GGCGTTT-TTTAACAAACGCCGCAACAGAGT--AGTACTTTAGC
* *
47354 GGCATTTTTTAACAAACGTCGCAACAGAGTAGTACTTTAGC
1 GGCGTTTTTTAACAAACGCCGCAACAGAGTAGTACTTTAGC
*
47395 GGTG-TTTTTATACAAACGC
1 GGCGTTTTTTA-ACAAACGC
47414 TACAATAGGT
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
39 1 0.01
40 15 0.19
41 55 0.71
42 5 0.06
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (41 bp):
GGCGTTTTTTAACAAACGCCGCAACAGAGTAGTACTTTAGC
Found at i:47484 original size:244 final size:244
Alignment explanation
Indices: 47055--47511 Score: 632
Period size: 244 Copynumber: 1.9 Consensus size: 244
47045 GCCATGACAT
* * ** *
47055 AGTAGTACTTTAGCGGCGTTTGTATAAAAATACCGTAATAGGCTTTATCTATCGTGGTGTTTTTA
1 AGTAGTACTTTAGCGGCGTTTGTATAAAAACACCGCAATAGGCTCCATCTATAGTGGTGTTTTTA
* * *
47120 ACGAACACCGCAACAGAGTAGTACTTTAGCGGCGTTTGTATAAAAACACTGCAATAGTGTTCATC
66 ACAAACACCGCAACAGAGTAGTACTTTAGCGGCGTTTGTATAAAAACACTACAATAGTGTTCATA
* * *
47185 CATAGTGGCGTTTCTCAACAAACGCCATGACAGAGTAGTCCTTTAGAGGCGTTTGTATAAAAATG
131 CATAGTGGCATTTCTCAACAAACGCCATGACAGAGTAATACTTTAGAGGCGTTTGTATAAAAATG
* *
47250 TCGTAATTGGCTTCATCTATAAAGGCGTTTTTAACAAACACCGCAACAG
196 CCGTAATAGGCTTCATCTATAAAGGCGTTTTTAACAAACACCGCAACAG
* *
47299 AGTAGTACTTTAGCGGCGTTTGTGTAAAAACGCCGCAATAGTG-TCCATCTATAGTGGCAT-TTT
1 AGTAGTACTTTAGCGGCGTTTGTATAAAAACACCGCAATAG-GCTCCATCTATAGTGG--TGTTT
** * * * *
47362 TTAACAAACGTCGCAACAGAGTAGTACTTTAGCGGTGTTTTTATACAAACGCTACAATAG-GTTC
63 TTAACAAACACCGCAACAGAGTAGTACTTTAGCGGCGTTTGTATAAAAACACTACAATAGTGTTC
* * * *
47426 ATACATAGTGGCATTTCTCAACAAATGCCGTGACAGAGTAATACTTTAGCGGCGTTTGTATCAAA
128 ATACATAGTGGCATTTCTCAACAAACGCCATGACAGAGTAATACTTTAGAGGCGTTTGTATAAAA
*
47491 ATGCCGTAATAGGGTTCATCT
193 ATGCCGTAATAGGCTTCATCT
47512 TAGTGACGTT
Statistics
Matches: 184, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
244 127 0.69
245 56 0.30
246 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (244 bp):
AGTAGTACTTTAGCGGCGTTTGTATAAAAACACCGCAATAGGCTCCATCTATAGTGGTGTTTTTA
ACAAACACCGCAACAGAGTAGTACTTTAGCGGCGTTTGTATAAAAACACTACAATAGTGTTCATA
CATAGTGGCATTTCTCAACAAACGCCATGACAGAGTAATACTTTAGAGGCGTTTGTATAAAAATG
CCGTAATAGGCTTCATCTATAAAGGCGTTTTTAACAAACACCGCAACAG
Found at i:51901 original size:43 final size:43
Alignment explanation
Indices: 51816--51971 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 43
51806 AAGATAATTA
* * * * *
51816 GCGGCGTTTTTGTTAAAAACGCCGTTATAGA-TTATGAGCTTTT
1 GCGGCGTTTTTATTAAAAACGCCGCTATTGAGCT-TGACCTTTT
*
51859 GCGGCGTTTTTATTAAAAATGCCGCTATTGAGCTTGACCTTTT
1 GCGGCGTTTTTATTAAAAACGCCGCTATTGAGCTTGACCTTTT
* * * **
51902 GCGGTGTATTTATTATAAACGCCGCTATTGATGCTT-ATTTTTT
1 GCGGCGTTTTTATTAAAAACGCCGCTATTGA-GCTTGACCTTTT
* *
51945 GCGG-TTTTTTCTTAAAAACGCCGCTAT
1 GCGGCGTTTTTATTAAAAACGCCGCTAT
51972 AGAGTTGGAT
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
42 19 0.20
43 71 0.75
44 5 0.05
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.41
Consensus pattern (43 bp):
GCGGCGTTTTTATTAAAAACGCCGCTATTGAGCTTGACCTTTT
Found at i:56517 original size:2 final size:2
Alignment explanation
Indices: 56494--56541 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
56484 TTAGTATTAT
* *
56494 TA TA TA -A TA TA AA TA TA AA 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
*
56535 TT TA TA T
1 TA TA TA T
56542 TTCCTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:60183 original size:25 final size:27
Alignment explanation
Indices: 60154--60204 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
60144 ACATTGCATA
60154 TTTTTCATTTTATA-TTT-CATGTTTG
1 TTTTTCATTTTATATTTTCCATGTTTG
* *
60179 TTTTTTATTTTGTATTTTCCATGTTT
1 TTTTTCATTTTATATTTTCCATGTTT
60205 TTACATTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 3 0.14
27 7 0.32
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.71
Consensus pattern (27 bp):
TTTTTCATTTTATATTTTCCATGTTTG
Found at i:64053 original size:65 final size:63
Alignment explanation
Indices: 63976--64155 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 63
63966 GAATTAATTG
*
63976 AACATCGAATGCATTTCATGCATCGATGCACATACTATGCACCGATGCACT-GAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCAC-TACTATGCACCGATGCACTCGA-GATATTT-T-
64039 AA
62 AA
* * * *
64041 AACATCGAATGCATTTGATGCATCGATGCACTAGCCATGCATCGATGCACTCTAGCTATTTTAA
1 AACATCGAATGCATTTGATGCATCGATGCACTA-CTATGCACCGATGCACTCGAGATATTTTAA
* * *
64105 ATCATTGAATGCACTTGATGCATCGATGCACT-CTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTAC-TA-TGCACCGATGCACT
64156 AAGGGTACAA
Statistics
Matches: 100, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 46 0.46
65 48 0.48
66 4 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTACTATGCACCGATGCACTCGAGATATTTTAA
Found at i:64135 original size:17 final size:19
Alignment explanation
Indices: 64113--64155 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
64103 AAATCATTGA
*
64113 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
64130 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
64149 ATGCACT
1 ATGCACT
64156 AAGGGTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:72148 original size:2 final size:2
Alignment explanation
Indices: 72141--72179 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
72131 CTTAGCAGCT
*
72141 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72180 TTAATCAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:72792 original size:65 final size:63
Alignment explanation
Indices: 72701--72860 Score: 169
Period size: 65 Copynumber: 2.5 Consensus size: 63
72691 AATTAAATTG
* * * *
72701 AACATCGAATGCATTTCAAGTATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-T-A
72765 A
63 A
* * * * **
72766 AACATTGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGTCTATTTTAA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTAA
* *
72830 ATCATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
72861 TCTTAGTGCA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.36
65 45 0.56
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTAA
Found at i:72875 original size:19 final size:19
Alignment explanation
Indices: 72848--72899 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
72838 ATGCACTTGA
*
72848 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
*
72867 TGCACCGATGCACTCTTGG
1 TGCACCGATGCACTCTTAG
72886 TGCACCGATGCACT
1 TGCACCGATGCACT
72900 AAGGGTCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.19, C:0.31, G:0.23, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:77361 original size:83 final size:83
Alignment explanation
Indices: 77210--77363 Score: 195
Period size: 83 Copynumber: 1.9 Consensus size: 83
77200 GCTTAAGATG
* ** * * *
77210 AAAACCTGAAAGGGCGTCTTAAGTTGAAAAAAGAAGAAAAAGGAAAAAACAAAAAACAAAAAAGA
1 AAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAGAAAAACGAAAAAACAAAAAACAAAAAAGA
77275 GAAAAAACGTTTAGGGTA
66 GAAAAAACGTTTAGGGTA
* * *
77293 AAAACCCGAAAGGGCACCCTAAATTGAAAAAAG-AGAAAAACGAGAAAAAGAACAAAAGAAAGAA
1 AAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAGAAAAACGA-AAAAACAA-AAAACAAAAAA
77357 -AGAAAAA
64 GAGAAAAA
77364 GAAAAAGAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
82 9 0.15
83 42 0.70
84 9 0.15
ACGTcount: A:0.62, C:0.10, G:0.19, T:0.08
Consensus pattern (83 bp):
AAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAGAAAAACGAAAAAACAAAAAACAAAAAAGA
GAAAAAACGTTTAGGGTA
Found at i:77374 original size:8 final size:8
Alignment explanation
Indices: 77320--77375 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
77310 CCTAAATTGA
77320 AAAAAGAG
1 AAAAAGAG
77328 AAAAACGAG
1 AAAAA-GAG
77337 AAAAAGA-
1 AAAAAGAG
77344 ACAAAAGA-
1 A-AAAAGAG
*
77352 AAGAA-AG
1 AAAAAGAG
77359 -AAAA-AG
1 AAAAAGAG
77365 AAAAAGAG
1 AAAAAGAG
77373 AAA
1 AAA
77376 TAAGGTGGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
6 6 0.15
7 8 0.20
8 19 0.46
9 8 0.20
ACGTcount: A:0.77, C:0.04, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:78685 original size:109 final size:107
Alignment explanation
Indices: 78485--78741 Score: 306
Period size: 109 Copynumber: 2.4 Consensus size: 107
78475 GGGCTTCCAA
* * * **
78485 TTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTA
1 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTAAAGACAACACAAGCTCAACTTA
* * *
78550 ACGACAACGGGGTGACTGATTGTCAACAAACAACTTTTCAATTT
66 ACGACAACGGGGAGACTGATTGTCAACAAACAA-TTTCCAA-GT
*
78594 TATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTAAAGA-AACACAAGCTCAACTT
1 T-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTAAAGACAACACAAGCTCAACTT
* * *
78658 CACGACGAA-GGGGCAG-CTGATTGTCAACAAATAATTTCCCAGT
65 AACGAC-AACGGGG-AGACTGATTGTCAACAAACAATTTCCAAGT
* * *
78701 TCT-AGAGCCAATTTCAACTTCACGACGGAGGATATTAGACT
1 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACT
78742 CGGAGCAATA
Statistics
Matches: 129, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
105 35 0.27
106 1 0.01
107 2 0.02
108 5 0.04
109 43 0.33
110 43 0.33
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (107 bp):
TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTAAAGACAACACAAGCTCAACTTA
ACGACAACGGGGAGACTGATTGTCAACAAACAATTTCCAAGT
Found at i:80944 original size:32 final size:32
Alignment explanation
Indices: 80883--80944 Score: 74
Period size: 32 Copynumber: 1.9 Consensus size: 32
80873 TTGTTGCCTT
* *
80883 TATTATTATTATTTATATATTTTCTTTATTAC
1 TATTATTATTATTTATATAATTTCATTATTAC
80915 TATTATTA-TATGTTATATAAATTT-ATTATT
1 TATTATTATTAT-TTATAT-AATTTCATTATT
80945 TTGTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 3 0.12
32 19 0.73
33 4 0.15
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (32 bp):
TATTATTATTATTTATATAATTTCATTATTAC
Found at i:84006 original size:20 final size:20
Alignment explanation
Indices: 83969--84008 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
83959 CAATCAGAAC
*
83969 AAAAAGAAAAAAGAGAAAAT
1 AAAAAAAAAAAAGAGAAAAT
83989 AAAAAAAAACAAAG-GAAAAT
1 AAAAAAAAA-AAAGAGAAAAT
84009 TGAAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAAAGAGAAAAT
Found at i:84191 original size:69 final size:69
Alignment explanation
Indices: 84080--84217 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
84070 GATTCAAACT
*
84080 ATGAGATTGATCAAGCACAATCATTTTTGAATCACTGAATCACTTCACTCGAAGATCATAGAGAA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGAA
84145 TCAA
66 TCAA
* *
84149 ATGAGATTGATCAAGGACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGAA
84214 TCAA
66 TCAA
84218 TAGAGAGACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGAA
TCAA
Found at i:85178 original size:32 final size:31
Alignment explanation
Indices: 85142--85261 Score: 141
Period size: 32 Copynumber: 3.7 Consensus size: 31
85132 GGAACAATGA
85142 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTG-AGATTCAACATCAAATGTTG
* * *
85174 GGGCATTTTTTTAGATTTAACATCAAATGTTG
1 GGGCA-TCTTTGAGATTCAACATCAAATGTTG
* * *
85206 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCA-TCTTTGAGATTCAACATCAAATGTTG
*
85238 GGGCATCTTTGGGAATTCAACATC
1 GGGCATCTTTGAG-ATTCAACATC
85262 CTAATGCAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
31 6 0.08
32 67 0.87
33 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATGTTG
Found at i:85958 original size:106 final size:106
Alignment explanation
Indices: 85837--86157 Score: 430
Period size: 106 Copynumber: 3.0 Consensus size: 106
85827 ATATGGTGCC
*
85837 ACTCGAGACAACACAAGTTCAACTCCATAATGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
1 ACTCGAGACAACACAAGTTCAACTTCATAATGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
**
85902 AATTTCAGAGCCAATTTCAACTTCACAGCGAATAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
85943 ACTCGAGACAACACAAGTTCAACTTCATAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCATAATGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
*
86008 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * ** * * * * * *
86049 ACTCGAGACAGCATAAGCCCAAATTCACAGTGAAGGG--GGCTGGCTGTCAACAAACAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCATAATGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
* * * * * *
86112 AGTTCCAGAGACAATTTTAACTTCACGGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
86153 ACTCG
1 ACTCG
86158 GAACGATACA
Statistics
Matches: 190, Mismatches: 25, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
104 61 0.32
106 129 0.68
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCATAATGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:86505 original size:37 final size:36
Alignment explanation
Indices: 86429--86513 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 36
86419 AACATAAACA
* * *
86429 TTTCCCTTCAAATGAATTTTATCTCGATTGAGATAG
1 TTTCCCTTGAAATAAATTTTATCTCCATTGAGATAG
* *
86465 TTTCCCTTGAAATAAACTTTTGTCTCCCTTGAGACT-G
1 TTTCCCTTGAAATAAA-TTTTATCTCCATTGAGA-TAG
*
86502 TTTCTCTTGAAA
1 TTTCCCTTGAAA
86514 CATAAACATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 14 0.34
37 26 0.63
38 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTATCTCCATTGAGATAG
Found at i:86634 original size:101 final size:101
Alignment explanation
Indices: 86424--86817 Score: 443
Period size: 100 Copynumber: 3.9 Consensus size: 101
86414 CTTGAAACAT
* * ** *
86424 AAACATTTCCCTTCAAATGAATTTTATCTCGATTGAGATAGTTTCCCTTGAAATAAACTTTTGTC
1 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA-AAAATTTTGTC
*
86489 TCCCTTGAGACTGTTTCTCTTGAAACATAAACATTGA
65 TCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
*
86526 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAAAAATTTTGGCT
1 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAAAAATTTTGTCT
*
86591 CCCTTAAGACAGTTTCTCTTGAAACATAAACATTGA
66 CCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
* * * * *
86627 AAACATTTCCCTTGAAAT-AAATTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCT
1 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAAAAATTTTGTCT
* * *
86691 CTCTTGAGACAGTTTCCCTTGAAACA-AAATATTTGA
66 CCCTTGAGACAGTTTCTCTTGAAACATAAACA-TTGA
* * *** ** * * * ** * *
86727 ATA-TTTTTTTTTGAAACAAATTTAGTCTCCCTTGAGACAGTTTCTTTTGAAACGAAGTTTTGTC
1 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA-AAAATTTTGTC
** *
86791 TTTCTTGAGGCAGTTTCTCTTGAAACA
65 TCCCTTGAGACAGTTTCTCTTGAAACA
86818 AATTTCGTCT
Statistics
Matches: 254, Mismatches: 35, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
99 13 0.05
100 98 0.39
101 94 0.37
102 49 0.19
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (101 bp):
AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAAAAATTTTGTCT
CCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
Found at i:86699 original size:36 final size:35
Alignment explanation
Indices: 86531--86855 Score: 196
Period size: 36 Copynumber: 9.5 Consensus size: 35
86521 ATTGAAAACA
* * * *
86531 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAA-CAAATTTATCTCTCTTGAGACAG
* * *
86567 TTTCCCTTGAAAAAAATTT-TGGCTCCCTTAAGACAG
1 TTTCCCTTGAAACAAATTTAT--CTCTCTTGAGACAG
* * *
86603 TTTCTCTTGAAACATAA---A---C-ATTGAAAACA-
1 TTTCCCTTGAAACA-AATTTATCTCTCTTG-AGACAG
* **
86632 TTTCCCTTGAAATAAATTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTATCTCTCTTGAGACAG
86667 TTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTATCTCTCTTGAGACAG
* * *
86703 TTTCCCTTGAAACAAA---A--TAT-TTGA-ATAT
1 TTTCCCTTGAAACAAATTTATCTCTCTTGAGACAG
*** *
86731 TTTTTTTTGAAACAAATTTAGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTA-TCTCTCTTGAGACAG
** * * * *
86767 TTTCTTTTGAAACGAAGTTTTGTCTTTCTTGAGGCAG
1 TTTCCCTTGAAAC-AA-ATTTATCTCTCTTGAGACAG
* *
86804 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTT-ATCTCTCTTGAGACAG
86840 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
86856 ATCTTTGAAT
Statistics
Matches: 225, Mismatches: 39, Indels: 50
0.72 0.12 0.16
Matches are distributed among these distances:
28 17 0.08
29 18 0.08
30 7 0.03
31 1 0.00
32 1 0.00
34 7 0.03
35 30 0.13
36 113 0.50
37 28 0.12
38 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (35 bp):
TTTCCCTTGAAACAAATTTATCTCTCTTGAGACAG
Found at i:86805 original size:37 final size:36
Alignment explanation
Indices: 86737--86918 Score: 157
Period size: 36 Copynumber: 5.2 Consensus size: 36
86727 ATATTTTTTT
* *
86737 TTGAAACAAATTTAGTCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTAGTCTCTCTTGAGACAGTTTCTC
* * * *
86773 TTGAAACGAAGTTTTGTCTTTCTTGAGGCAGTTTCTC
1 TTGAAAC-AAATTTAGTCTCTCTTGAGACAGTTTCTC
* *
86810 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCC
1 TTGAAACAAATTTAGTCTCTCTTGAGACAGTTTCTC
*
86846 TTGAAACAAA---A---TCT-TTGA-ATTTA-TTTCTC
1 TTGAAACAAATTTAGTCTCTCTTGAGA--CAGTTTCTC
* * * *
86875 CTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTC
1 TTGAAACAAATTTAGTCTCTCTTGAGACAGTTTCTC
86911 TTGAAACA
1 TTGAAACA
86919 CAAAATCTTC
Statistics
Matches: 113, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.01
29 17 0.15
30 4 0.04
35 3 0.03
36 57 0.50
37 31 0.27
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAAACAAATTTAGTCTCTCTTGAGACAGTTTCTC
Found at i:86821 original size:137 final size:138
Alignment explanation
Indices: 86651--86917 Score: 412
Period size: 137 Copynumber: 1.9 Consensus size: 138
86641 AAATAAATTC
*
86651 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAAC
** * *
86716 AAAATATTTGAATATT-TTT-TTTTGAAACAAATTTAGTCTCCCTTGAGACAGTTTCTTTTGAAA
66 AAAATATTTGAAT-TTATTTCTCCTAAAACAAATTTAGTCTCCCTTGAGACAGTTTCTCTTGAAA
86779 CGAAGTTTT
130 CGAAGTTTT
* * * *
86788 GTCTTTCTTGAGGCAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAAC
* *
86853 AAAATCTTTGAATTTATTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
66 AAAATATTTGAATTTATTTCTCCTAAAACAAATTTAGTCTCCCTTGAGACAGTTTCTCTTGAAAC
86918 ACAAAATCTT
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
136 2 0.02
137 75 0.64
138 40 0.34
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATTTATTTCTCCTAAAACAAATTTAGTCTCCCTTGAGACAGTTTCTCTTGAAAC
GAAGTTTT
Found at i:86908 original size:65 final size:67
Alignment explanation
Indices: 86804--86970 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 67
86794 CTTGAGGCAG
* * * * **
86804 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATT
1 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATT
86867 TA
66 TA
*
86869 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATT
86934 TA
66 TA
* * *
86936 TTTC-CCTTAAAATAATATTTTATTTCCCTTGAGAC
1 TTTCTCC-TAAAACAA-ATTTTGTCTCCCTTGAGAC
86971 CATTTTTCAT
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 40 0.45
66 4 0.05
67 27 0.31
68 17 0.19
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (67 bp):
TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATT
TA
Found at i:87901 original size:110 final size:108
Alignment explanation
Indices: 87703--87960 Score: 297
Period size: 110 Copynumber: 2.4 Consensus size: 108
87693 GCTTCCCAAT
* *
87703 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAAATTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* * * * *
87768 TAATGAAGGGGCGACTGATTGTCAATAAACAACTTT-TCAGTTTC
66 CAACGAAGGGGCGACTGACTGTCAACAAACAA-TTTCCCAG-TTC
* * * * *
87812 ATTCAGAGTCAATTTCAACTTCATAGTGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTC
1 -TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTC
* * * *
87877 ACAGCGAAGGGGTGGCTGGCTGTCAACAAACAATTTCCCAGTTC
65 ACAACGAAGGGGCGACTGACTGTCAACAAACAATTTCCCAGTTC
* * *
87921 --CAGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTC
87961 GGAACAGTAC
Statistics
Matches: 125, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
106 34 0.27
109 6 0.05
110 85 0.68
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (108 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
CAACGAAGGGGCGACTGACTGTCAACAAACAATTTCCCAGTTC
Found at i:88311 original size:85 final size:81
Alignment explanation
Indices: 88141--88313 Score: 222
Period size: 82 Copynumber: 2.1 Consensus size: 81
88131 ATCCAACTCA
* * * *
88141 AAGAAGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAGACACATAATTTA
1 AAGAAGGTTATCTATCAACAAAGACCTTCGAGTTCGACTACATTCAACTCCAGAAACATAATTTA
88206 CAGCATAACTCAAGGC
66 CAGCATAACTCAAGGC
* * *
88222 AAGAAGTGTTATCTATCATCAAAGACCTTCGAGTTCGATTACATTCAACTCAGAGGTAAATCA-A
1 AAGAAG-GTTATCTATCAACAAAGACCTTCGAGTTCGACTACATTCAACTC-CA-G-AAA-CATA
*
88286 ATTTACAGCATAGCTCAAGGC
61 ATTTACAGCATAACTCAAGGC
88307 AAGAAGG
1 AAGAAGG
88314 GCTATCTGCC
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
81 6 0.08
82 39 0.49
83 1 0.01
84 2 0.03
85 29 0.37
86 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (81 bp):
AAGAAGGTTATCTATCAACAAAGACCTTCGAGTTCGACTACATTCAACTCCAGAAACATAATTTA
CAGCATAACTCAAGGC
Found at i:89434 original size:14 final size:14
Alignment explanation
Indices: 89415--89454 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
89405 CTCTTTTTTT
89415 TTATTTATATTATA
1 TTATTTATATTATA
*
89429 TTATTTTTATTATA
1 TTATTTATATTATA
89443 TATATCTTATAT
1 T-TAT-TTATAT
89455 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:89436 original size:25 final size:25
Alignment explanation
Indices: 89374--89454 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 25
89364 ATATTTTTTA
* *
89374 ATTATATTTTTTTTATTTATTTACTAT
1 ATTATTTTTTTTTTATTTA--TATTAT
*
89401 ATTCCTCTTTTTTTTTATTTATATTAT
1 ATT-AT-TTTTTTTTTATTTATATTAT
* * * *
89428 ATTATTTTTATTATATATATCTTAT
1 ATTATTTTTTTTTTATTTATATTAT
89453 AT
1 AT
89455 CATTATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
25 18 0.41
26 1 0.02
27 11 0.25
28 1 0.02
29 13 0.30
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (25 bp):
ATTATTTTTTTTTTATTTATATTAT
Found at i:89554 original size:39 final size:35
Alignment explanation
Indices: 89511--89612 Score: 91
Period size: 39 Copynumber: 2.9 Consensus size: 35
89501 ATCTACTATG
**
89511 TATATATTTTTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATTTACTTTCTT-ATATTATATTTT-T--GTTTT
* *
89550 TATATATATACTTTCTTATATTCTATTTTTGTTTT
1 TATATATTTACTTTCTTATATTATATTTTTGTTTT
* * *
89585 TATTTATTTA-TAT-ATATATTATATTTTT
1 TATATATTTACTTTCTTATATTATATTTTT
89613 ACGTTATTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
33 13 0.24
34 2 0.04
35 13 0.24
37 1 0.02
38 11 0.20
39 14 0.26
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (35 bp):
TATATATTTACTTTCTTATATTATATTTTTGTTTT
Found at i:89868 original size:16 final size:18
Alignment explanation
Indices: 89833--89871 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
89823 TTTTTTAACA
*
89833 TTTTATTCATTTTTTTAT
1 TTTTATTCATTTTATTAT
89851 TTTTATT-A-TTTATTAT
1 TTTTATTCATTTTATTAT
89867 TTTTA
1 TTTTA
89872 CGTGTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 1 0.05
18 7 0.35
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATTCATTTTATTAT
Found at i:91473 original size:17 final size:17
Alignment explanation
Indices: 91453--91485 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
91443 TTTAGGGAAG
91453 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
91470 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
91486 TTAAATCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:95155 original size:94 final size:94
Alignment explanation
Indices: 94994--95188 Score: 291
Period size: 94 Copynumber: 2.1 Consensus size: 94
94984 TGATTCAATC
* * * *
94994 AGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCGAATCTAAATTTATTATTGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAACCTAAATTTAGTATCGATAC
* * *
95059 CGGAAGGGGTATCGATACCATAGTATTGT
66 CGGAAGGGGTATCGATACCATAATATAGA
* * *
95088 AGTATCGATATCATGGTAAGGGTATCGATACCAAGAAACATTGAACCTAAATTTGGTATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAACCTAAATTTAGTATCGATAC
*
95153 CGGAAGGGGTATCGGTACCATAATATAGA
66 CGGAAGGGGTATCGATACCATAATATAGA
95182 AGTATCG
1 AGTATCG
95189 GTACTAGGGT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (94 bp):
AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAACCTAAATTTAGTATCGATAC
CGGAAGGGGTATCGATACCATAATATAGA
Found at i:95606 original size:59 final size:59
Alignment explanation
Indices: 95538--95956 Score: 622
Period size: 59 Copynumber: 7.1 Consensus size: 59
95528 ATGGCACTAA
* *
95538 GTGTGCTAAAATGTTAAGAAATCCATACTAAGTGTATGAATTTCTGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* ** * *
95597 GTGTTCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTCGGTACCTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* **
95656 GTGTGCTAAAATGTTAAGAAATTTATACTAAGTGTATGAATTTTTGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
*
95715 GTCTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* ***
95774 GTCTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTTTTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * **
95833 GTATGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTACATATAGGTAACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * *
95892 GAGTGCTAAAATGTTAAGAAATTCATACTACGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
95951 GTGTGC
1 GTGTGC
95957 AAATCAGGGA
Statistics
Matches: 322, Mismatches: 38, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 322 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
Found at i:105613 original size:3 final size:3
Alignment explanation
Indices: 105605--105663 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
105595 ATATTACCAC
105605 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
*
105650 TTT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
105664 CAGTATCCAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:105929 original size:13 final size:13
Alignment explanation
Indices: 105889--105948 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
105879 ATTGTGATTC
* *
105889 AAAGTAAAAGCAA
1 AAAGCAAAAGTAA
105902 AAGAG-AAAAG-AA
1 AA-AGCAAAAGTAA
105914 AAAGCAAAATGTAA
1 AAAGCAAAA-GTAA
*
105928 AAAGTAAAAGTAA
1 AAAGCAAAAGTAA
105941 AAAG-AAAA
1 AAAGCAAAA
105949 AACACAATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
11 2 0.05
12 12 0.29
13 16 0.38
14 12 0.29
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (13 bp):
AAAGCAAAAGTAA
Found at i:105949 original size:13 final size:13
Alignment explanation
Indices: 105900--105949 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
105890 AAGTAAAAGC
105900 AAAAGAGAAAAG-A
1 AAAAGA-AAAAGTA
*
105913 AAAAGCAAAATGTA
1 AAAAG-AAAAAGTA
*
105927 AAAAGTAAAAGTA
1 AAAAGAAAAAGTA
105940 AAAAGAAAAA
1 AAAAGAAAAA
105950 ACACAATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 24 0.77
14 7 0.23
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.08
Consensus pattern (13 bp):
AAAAGAAAAAGTA
Found at i:105950 original size:7 final size:6
Alignment explanation
Indices: 105889--105949 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
105879 ATTGTGATTC
* * * *
105889 AAAGTA AAAGCA AAAGAGA AAAGAA AAAGCAA AATGTAA AAAGTA AAAGTAA
1 AAAGAA AAAGAA AAAGA-A AAAGAA AAAG-AA AAAG-AA AAAGAA AAAG-AA
105941 AAAGAA AAA
1 AAAGAA AAA
105950 ACACAATGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
6 24 0.53
7 21 0.47
ACGTcount: A:0.72, C:0.03, G:0.16, T:0.08
Consensus pattern (6 bp):
AAAGAA
Found at i:108183 original size:20 final size:20
Alignment explanation
Indices: 108144--108205 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
108134 GGCAGATTGT
*
108144 CCAGAGGGAACTGATT-CCCC
1 CCAG-GGGATCTGATTCCCCC
108164 CCAGGGGATCTGATTCCCCC
1 CCAGGGGATCTGATTCCCCC
* *
108184 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGAT-CTGATTCCCCC
108205 C
1 C
108206 TTAATGGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.27
20 16 0.43
21 11 0.30
ACGTcount: A:0.18, C:0.40, G:0.26, T:0.16
Consensus pattern (20 bp):
CCAGGGGATCTGATTCCCCC
Found at i:110149 original size:21 final size:21
Alignment explanation
Indices: 110123--110164 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
110113 TTTTTTATTT
* *
110123 ATGAATATTGAATAGTGAACA
1 ATGAATATTAAACAGTGAACA
110144 ATGAATATTAAACAGTGAACA
1 ATGAATATTAAACAGTGAACA
110165 GTGGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (21 bp):
ATGAATATTAAACAGTGAACA
Found at i:111012 original size:24 final size:24
Alignment explanation
Indices: 110980--111025 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
110970 TCTTCCAGAT
110980 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
111004 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
111026 CATACCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:118786 original size:21 final size:21
Alignment explanation
Indices: 118762--118803 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
118752 GGCAGATTGT
*
118762 CCAGAGGGAACCGATTCCCCC
1 CCAGAGGGAACCGATTACCCC
* *
118783 CCAGGGGGTACCGATTACCCC
1 CCAGAGGGAACCGATTACCCC
118804 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.40, G:0.26, T:0.12
Consensus pattern (21 bp):
CCAGAGGGAACCGATTACCCC
Found at i:119535 original size:19 final size:19
Alignment explanation
Indices: 119511--119553 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
119501 TTTAATTACT
119511 AATTCACCCCCTCTTGGCC
1 AATTCACCCCCTCTTGGCC
119530 AATTCACCCCCTCTTGGCC
1 AATTCACCCCCTCTTGGCC
119549 AATTC
1 AATTC
119554 CATCGATCGA
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:0.19, C:0.44, G:0.09, T:0.28
Consensus pattern (19 bp):
AATTCACCCCCTCTTGGCC
Found at i:121112 original size:5 final size:5
Alignment explanation
Indices: 121097--121186 Score: 92
Period size: 5 Copynumber: 16.6 Consensus size: 5
121087 TACTTGAAGT
*
121097 AAAGAA AAAGA AAAGA AAAGA AAAGAA AAAGAA CAAAGA ACAGA AAAGA
1 AAAG-A AAAGA AAAGA AAAGA AAAG-A AAAG-A -AAAGA AAAGA AAAGA
121146 AAAGAA AAAGAA AAAGAA AAAGA AAAGA AAA-A AGAAGA AAA
1 AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA A-AAGA AAA
121187 AAGGGAAAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 11
0.86 0.02 0.12
Matches are distributed among these distances:
4 2 0.03
5 40 0.52
6 31 0.40
7 4 0.05
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:121134 original size:28 final size:27
Alignment explanation
Indices: 121097--121187 Score: 139
Period size: 28 Copynumber: 3.3 Consensus size: 27
121087 TACTTGAAGT
121097 AAAGAAAAAGAAAAGAAAAGAAAAGAA
1 AAAGAAAAAGAAAAGAAAAGAAAAGAA
*
121124 AAAGAACAAAGAACAGAAAAGAAAAGAA
1 AAAGAA-AAAGAAAAGAAAAGAAAAGAA
121152 AAAGAAAAAGAAAAAGAAAAGAAAA-AA
1 AAAGAAAAAG-AAAAGAAAAGAAAAGAA
*
121179 GAAGAAAAA
1 AAAGAAAAA
121188 AGGGAAAAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
27 20 0.34
28 39 0.66
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (27 bp):
AAAGAAAAAGAAAAGAAAAGAAAAGAA
Found at i:121187 original size:33 final size:35
Alignment explanation
Indices: 121098--121215 Score: 138
Period size: 33 Copynumber: 3.4 Consensus size: 35
121088 ACTTGAAGTA
121098 AAGAAAAAGAAAAGAAAAG-AAAAGAAAAAGAACA
1 AAGAAAAAGAAAAGAAAAGAAAAAGAAAAAGAACA
*
121132 AAG-AACAGAAAAGAAAAGAAAAAGAAAAAGAA-A
1 AAGAAAAAGAAAAGAAAAGAAAAAGAAAAAGAACA
*
121165 AAG-AAAAGAAAA-AAGAAGAAAAAAGGGAAAAAGAATA
1 AAGAAAAAGAAAAGAA-AAG-AAAAA--GAAAAAGAACA
121202 AAGAATAAAGAAAA
1 AAGAA-AAAGAAAA
121216 AAATATATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
32 2 0.03
33 29 0.39
34 21 0.28
36 9 0.12
37 4 0.05
38 1 0.01
39 8 0.11
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (35 bp):
AAGAAAAAGAAAAGAAAAGAAAAAGAAAAAGAACA
Found at i:121212 original size:32 final size:29
Alignment explanation
Indices: 121100--121218 Score: 91
Period size: 30 Copynumber: 3.9 Consensus size: 29
121090 TTGAAGTAAA
*
121100 GAAAAAGAAAAG--AAAAGAAAAGAAAA-A
1 GAAAAAGAAAAGAAAAAAGAAAA-AAAAGG
* **
121127 GAACAAAGAACAGAAAAGAAAAGAAAAAGAAAAA
1 GAA-AAAGAA-A-AGAA-AAAAGAAAAA-AAAGG
121161 GAAAAAGAAAAGAAAAAAGAAGAAAAAAGG
1 GAAAAAGAAAAGAAAAAAGAA-AAAAAAGG
*
121191 GAAAAAGAATAAAGAATAAAGAAAAAAA
1 GAAAAAG-A-AAAGAAAAAAGAAAAAAA
121219 TATATAAAGC
Statistics
Matches: 76, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
27 3 0.04
28 6 0.08
29 1 0.01
30 18 0.24
31 12 0.16
32 14 0.18
33 18 0.24
34 4 0.05
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (29 bp):
GAAAAAGAAAAGAAAAAAGAAAAAAAAGG
Found at i:122496 original size:42 final size:42
Alignment explanation
Indices: 122437--122832 Score: 287
Period size: 42 Copynumber: 9.0 Consensus size: 42
122427 TCTCTCTTTT
* *
122437 CCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGT-TTGC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTT-C
* * * *
122479 CCAAGATCTGATATTCCCTGAGTGACAGTAGAATAAATCACTCC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGT--CTTC
* * *
122523 CTTTCAATATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTC
1 C---CAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTTC
* * * *
122568 CCCAGATCTGATATTCCTTGAGTGACAGTGGAATAGATCCTCTTTC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACA-A--GTC-TTC
* * * * *
122614 TCAATATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTTC
* * *
122656 ACGAGATCTGATATTTCCTGAGTGACAGTGGAAC-AGATCACTCTC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAG-T--CT-TC
* * * *
122701 TTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAGTCTGC
1 --CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTTC
* *
122745 CCCAGATCTGATATTCTCTGAGTGACAGTGGAATAGATCCATATGT-TTC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGG---A-A--CA-A-GTCTTC
* *
122794 CC-AGATCTGATATTCCCTGAGTGATAGAGGAACAAGTCT
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCT
122833 ACCCTGATTC
Statistics
Matches: 277, Mismatches: 51, Indels: 53
0.73 0.13 0.14
Matches are distributed among these distances:
40 2 0.01
41 4 0.01
42 120 0.43
43 3 0.01
44 6 0.02
45 13 0.05
46 32 0.12
47 61 0.22
48 29 0.10
49 5 0.02
50 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (42 bp):
CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTTC
Found at i:122547 original size:89 final size:89
Alignment explanation
Indices: 122442--122832 Score: 527
Period size: 89 Copynumber: 4.4 Consensus size: 89
122432 CTTTTCCAAG
* *
122442 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTTTGCCCAAGATCTGATATTCCCTGAGTGACAG
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
* *
122507 TAGAATAAATCACTCCCTTTCAAT
66 TGGAATAGATCACTCCCTTTCAAT
* *
122531 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTCCCCAGATCTGATATTCCTTGAGTGACAG
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
*
122596 TGGAATAGATC-CT-CTTTCTCAAT
66 TGGAATAGATCACTCCCTT-TCAAT
* * *
122619 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACGAGATCTGATATTTCCTGAGTGACAG
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
* * *
122684 TGGAACAGATCACTCTCTTTCAAG
66 TGGAATAGATCACTCCCTTTCAAT
* *
122708 ATTTGATATTCCCTGAGTGACAGAGGAACAAGTCTGCCCCAGATCTGATATTCTCTGAGTGACAG
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
*** * *
122773 TGGAATAGATC-CATATGTTTCCCAG
66 TGGAATAGATCAC-TCCCTTT-CAAT
* * *
122798 ATCTGATATTCCCTGAGTGATAGAGGAACAAGTCT
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT
122833 ACCCTGATTC
Statistics
Matches: 270, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
87 3 0.01
88 78 0.29
89 151 0.56
90 38 0.14
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (89 bp):
ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
TGGAATAGATCACTCCCTTTCAAT
Found at i:122738 original size:177 final size:178
Alignment explanation
Indices: 122434--122832 Score: 590
Period size: 177 Copynumber: 2.2 Consensus size: 178
122424 ATATCTCTCT
* *
122434 TTTC-CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTTTGCCCAAGATCTGATATTCCCT
1 TTTCTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACAAGATCTGATATTCCCT
* * *
122498 GAGTGACAGTAGAATAAATCACTCCCTTTCAATATTTGATATTCCCTGAGTGACAGCGGAACAAG
66 GAGTGACAGTAGAACAAATCACTCCCTTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAG
* *
122563 TCTTCCCCAGATCTGATATTC-CTTGAGTGACAGTGGAATAGATCC-TC
131 TCTGCCCCAGATCTGATATTCTC-TGAGTGACAGTGGAATAGATCCATA
* * *
122610 TTTCTCAATATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACGAGATCTGATATTTCCT
1 TTTCTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACAAGATCTGATATTCCCT
* * *
122675 GAGTGACAGTGGAACAGATCACTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAG
66 GAGTGACAGTAGAACAAATCACTCCCTTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAG
122740 TCTGCCCCAGATCTGATATTCTCTGAGTGACAGTGGAATAGATCCATA
131 TCTGCCCCAGATCTGATATTCTCTGAGTGACAGTGGAATAGATCCATA
* * * *
122788 TGTT-TCCCAGATCTGATATTCCCTGAGTGATAGAGGAACAAGTCT
1 T-TTCT-CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT
122833 ACCCTGATTC
Statistics
Matches: 200, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
176 4 0.02
177 156 0.78
178 4 0.02
179 36 0.18
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (178 bp):
TTTCTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACAAGATCTGATATTCCCT
GAGTGACAGTAGAACAAATCACTCCCTTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAG
TCTGCCCCAGATCTGATATTCTCTGAGTGACAGTGGAATAGATCCATA
Found at i:122940 original size:111 final size:111
Alignment explanation
Indices: 122801--123050 Score: 367
Period size: 111 Copynumber: 2.3 Consensus size: 111
122791 TTCCCAGATC
* * *
122801 TGATATTCCCTGAGTGATAGA-GGAACAAGTCTACCCTGATTCAATTGATCAACACCCCCAGATC
1 TGATATTCCCTGAGTGACA-ACGGAACAAGTCTACCCCGATTCAATGGATCAACACCCCCAGATC
**
122865 TGATATCCCCTTAGAAGAAGCGGAACATATCACCCTCTTCCAATATT
65 TGATATCCCCTTAGAAGAAGCAAAACATATCACCCTCTTCCAATATT
* *
122912 TGATATTCCCTGAGTGACAACGTAACAAGTCTACCCCGATTCAATGGATCAACTCCCCCAGATCT
1 TGATATTCCCTGAGTGACAACGGAACAAGTCTACCCCGATTCAATGGATCAACACCCCCAGATCT
* * * * *
122977 TATATTCCCTTAGAAGAATCAAAACATATCACTCTCTTTCAATATT
66 GATATCCCCTTAGAAGAAGCAAAACATATCACCCTCTTCCAATATT
*
123023 TGATATTCCCTGAGTGACAGCGGAACAA
1 TGATATTCCCTGAGTGACAACGGAACAA
123051 TTTTTCCCCA
Statistics
Matches: 124, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
110 1 0.01
111 123 0.99
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (111 bp):
TGATATTCCCTGAGTGACAACGGAACAAGTCTACCCCGATTCAATGGATCAACACCCCCAGATCT
GATATCCCCTTAGAAGAAGCAAAACATATCACCCTCTTCCAATATT
Found at i:123245 original size:3 final size:3
Alignment explanation
Indices: 123237--123329 Score: 143
Period size: 3 Copynumber: 30.7 Consensus size: 3
123227 ATATTACCAC
123237 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
123285 TAT TAT TAT TAT TAT T-T TAT TAT TAACT TTT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-A-T TAT TAT TAT TAT TAT TA
123330 CAAGATCCAA
Statistics
Matches: 84, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.02
3 79 0.94
4 1 0.01
5 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:126159 original size:19 final size:19
Alignment explanation
Indices: 126135--126171 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
126125 GATCGCAATT
126135 TCTCAATGGTTAAAGTACA
1 TCTCAATGGTTAAAGTACA
126154 TCTCAATGGTTAAAGTAC
1 TCTCAATGGTTAAAGTAC
126172 TTATTGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
TCTCAATGGTTAAAGTACA
Found at i:130359 original size:17 final size:18
Alignment explanation
Indices: 130337--130378 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
130327 CTTTAGATTA
*
130337 TTTATTTAATTATTTTC-
1 TTTATTTAATTATTATCT
*
130354 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
130372 TTTATTT
1 TTTATTT
130379 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:133469 original size:64 final size:65
Alignment explanation
Indices: 133381--133536 Score: 210
Period size: 65 Copynumber: 2.4 Consensus size: 65
133371 TTAAGACTTA
* * *
133381 GTGCATCGGTACACTAATTACATTCGATGTTTC-AAAGA-GCAAGGAGTGCATCGATGCATGG-T
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGATGCAA-GAGTGCATCGATGCATGGCT
133443 CT
65 -T
* * *
133445 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGTTGCATGGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGATGCAAGAGTGCATCGATGCATGGCTT
*
133510 GTGCATCGATACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
133537 AATGAGTGTG
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
64 30 0.37
65 48 0.59
66 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGATGCAAGAGTGCATCGATGCATGGCTT
Found at i:139730 original size:79 final size:79
Alignment explanation
Indices: 139599--139758 Score: 302
Period size: 79 Copynumber: 2.0 Consensus size: 79
139589 TGTTCATCAT
*
139599 AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATACTAATTTAAAACCAAAAACTCAT
1 AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATAATAATTTAAAACCAAAAACTCAT
139664 GCATGTATAGACTA
66 GCATGTATAGACTA
*
139678 AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATAATCATTTAAAACCAAAAACTCAT
1 AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATAATAATTTAAAACCAAAAACTCAT
139743 GCATGTATAGACTA
66 GCATGTATAGACTA
139757 AA
1 AA
139759 TGAGCAACCA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (79 bp):
AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATAATAATTTAAAACCAAAAACTCAT
GCATGTATAGACTA
Found at i:140344 original size:117 final size:117
Alignment explanation
Indices: 140124--140345 Score: 277
Period size: 117 Copynumber: 1.9 Consensus size: 117
140114 CTTTCAAATC
* * *
140124 GAAATTTTATTTTTCAATACTTTTAAATTTCATTTTTGAAAACTCTAAATCCTTCTTCAATATTT
1 GAAAATTTATTTTTCAATACTTTTAAATTTCATTTTTGAAAACTCTAAATCCTTCTTCAACATCT
* * *
140189 CTTTTTTATTTTCAAAATCCATTTTAGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * ** * *
140241 GAAAATTTATTTTTCAA-AGTTTTCAGATTTCATTTTTGAAAGTTCTAACTCCTTTTTCAACATC
1 GAAAATTTATTTTTCAATACTTTT-AAATTTCATTTTTGAAAACTCTAAATCCTTCTTCAACATC
* * *
140305 TCATTTTGATTTTCCAAGTCTATTTTAGCTTTC-AAAAGAAG
65 TCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
140346 ATAATTTTTA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
116 5 0.06
117 79 0.90
118 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.49
Consensus pattern (117 bp):
GAAAATTTATTTTTCAATACTTTTAAATTTCATTTTTGAAAACTCTAAATCCTTCTTCAACATCT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:141794 original size:65 final size:64
Alignment explanation
Indices: 141665--141817 Score: 200
Period size: 65 Copynumber: 2.4 Consensus size: 64
141655 ACTAGGGGTC
* * * * *
141665 CATCGGTACACTAATTACATTTGATGTTTCAAAGAGCCAAGAGTGCATCGATGCATGGTCTGTG
1 CATCGGTACACAAAATGCATTCGATGTTTCAAAGAGCCAAGAGTACATCGATGCATGGTCTGTG
* **
141729 CATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTACATCGATGCATGG-CTTGT
1 CATCGGTACACAAAATGCATTCGATGTTTC-AAAGAGCCAAGAGTACATCGATGCATGGTC-TGT
141793 G
64 G
*
141794 CATCAGTACACAAAATGCATTCGA
1 CATCGGTACACAAAATGCATTCGA
141818 AATGGGCGTG
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 27 0.35
65 51 0.65
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (64 bp):
CATCGGTACACAAAATGCATTCGATGTTTCAAAGAGCCAAGAGTACATCGATGCATGGTCTGTG
Found at i:146773 original size:42 final size:40
Alignment explanation
Indices: 146725--146944 Score: 119
Period size: 42 Copynumber: 5.2 Consensus size: 40
146715 GAGGAATATA
*
146725 CCACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCAT
1 CCACTTGG-TTTCCCGTGAAGGGGAGTCATCCGAAGATCAT
** *
146766 CTCACTTGG-TTCAAACC-TGCTAAGGGGAACCA-CCTGAGGAAT-AT
1 C-CACTTGGTTTC---CCGTG--AAGGGGAGTCATCC-GAAG-ATCAT
* *
146810 ACCACTTGGCTTTCCCGTGAAGGGCAGTCATCCAAAGATCAT
1 -CCACTTGG-TTTCCCGTGAAGGGGAGTCATCCGAAGATCAT
* ** **
146852 CTCACTTGGTTCAGACCCACGAAGGGGAACCA-CCTGAAGAAT-AT
1 C-CACTTGGTT---TCCCGTGAAGGGGAGTCATCC-GAAG-ATCAT
146896 ACCACTTGGATTTCCCGTGAAGGGGAGTCATCCGAAGATCAT
1 -CCACTTGG-TTTCCCGTGAAGGGGAGTCATCCGAAGATCAT
146938 CACACTT
1 C-CACTT
146945 TGTTCAGACC
Statistics
Matches: 133, Mismatches: 21, Indels: 49
0.66 0.10 0.24
Matches are distributed among these distances:
40 3 0.02
41 9 0.07
42 52 0.39
43 12 0.09
44 46 0.35
45 8 0.06
46 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCACTTGGTTTCCCGTGAAGGGGAGTCATCCGAAGATCAT
Found at i:146785 original size:86 final size:86
Alignment explanation
Indices: 146641--147442 Score: 1133
Period size: 86 Copynumber: 9.3 Consensus size: 86
146631 ACAAACATCT
* * * * * * *
146641 CACTTGGGTTTCCCGTGAA-AGGAGTCCTCCAAAGATCATCTTACTTGGTTTAGACCTGCTAACG
1 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGG
146705 GGAACCACTTGAGGAATATAC
66 GGAACCACTTGAGGAATATAC
* *
146726 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAAACCTGCTAAGG
1 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGG
*
146791 GGAACCACCTGAGGAATATAC
66 GGAACCACTTGAGGAATATAC
* * *
146812 CACTTGGCTTTCCCGTGAAGGGCAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCACGAAGG
1 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGG
* *
146877 GGAACCACCTGAAGAATATAC
66 GGAACCACTTGAGGAATATAC
* * * *
146898 CACTTGGATTTCCCGTGAAGGGGAGTCATCCGAAGATCATCACACTTTGTTCAGACCCGCTAAGG
1 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGG
*
146963 GGAACCATTTGAGGAATATAC
66 GGAACCACTTGAGGAATATAC
* * ** *
146984 CACTTGGATTTCCCGTGAAGGGGAATCATCCAAATCTCATCTCACTTGGTTCAAACCCGCTAAGG
1 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGG
147049 GGAACCACTTGAGGAATATAC
66 GGAACCACTTGAGGAATATAC
** * *
147070 CACTTGGCTTTCCCGTGAATAGGAGTCATCCAAATATAATCTCACTTGGTTCAGACCCGCTAAGG
1 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGG
*
147135 GGAACCACATGAGGAATATAC
66 GGAACCACTTGAGGAATATAC
* * *
147156 CACTTGGCTTTCCCGTG-AGGAGGAGTCATCCAAAGATCCTCTCACTTGGTTCAGACCTGATAAG
1 CACTTGGCTTTCCCGTGAAGG-GGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAG
*
147220 GGGAACCACATGAGGAATATAC
65 GGGAACCACTTGAGGAATATAC
* * * * *
147242 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCGAAGACCATATCACTTGATTCAGACCCGCAAAGG
1 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGG
147307 GGAACCACTTGAGGAATATAC
66 GGAACCACTTGAGGAATATAC
* * * * * *
147328 CACTTTGCTTTCCCGTGAAGGGGAGTCATCTAAAAAACATCTCACTTGGTTCA-ACCCCACGAAG
1 CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGA-CCCGCTAAG
*
147392 GGGAACCACCTGAGGAATATAC
65 GGGAACCACTTGAGGAATATAC
* *
147414 CACTTGGCTTTCCCATGAAGGGGAATCAT
1 CACTTGGCTTTCCCGTGAAGGGGAGTCAT
147443 TTAAAGAATT
Statistics
Matches: 644, Mismatches: 69, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
85 20 0.03
86 621 0.96
87 3 0.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (86 bp):
CACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGG
GGAACCACTTGAGGAATATAC
Found at i:147074 original size:44 final size:42
Alignment explanation
Indices: 146940--147162 Score: 106
Period size: 44 Copynumber: 5.2 Consensus size: 42
146930 AAGATCATCA
*
146940 CACTTTGTTCAGACCCGCTAAGGGGAACCATTTGAGGAATATAC
1 CACTTGGTTCA-ACCCGCTAAGGGGAACCA-TTGAGGAATATAC
* * ** *
146984 CACTTGGATT--TCCCG-TGAAGGGGAATCATCCA--AATCTCATC
1 CACTTGG-TTCAACCCGCT-AAGGGGAACCATTGAGGAATAT-A-C
147025 TCACTTGGTTCAAACCCGCTAAGGGGAACCACTTGAGGAATATAC
1 -CACTTGGTTC-AACCCGCTAAGGGGAACCA-TTGAGGAATATAC
* ** ** **
147070 CACTTGGCTT--TCCCG-TGAATAGGAGTCATCCA--AATATAATC
1 CACTTGG-TTCAACCCGCT-AAGGGGAACCATTGAGGAATAT-A-C
*
147111 TCACTTGGTTCAGACCCGCTAAGGGGAACCACATGAGGAATATAC
1 -CACTTGGTTCA-ACCCGCTAAGGGGAACCA-TTGAGGAATATAC
147156 CACTTGG
1 CACTTGG
147163 CTTTCCCGTG
Statistics
Matches: 129, Mismatches: 26, Indels: 48
0.64 0.13 0.24
Matches are distributed among these distances:
39 9 0.07
40 2 0.02
41 12 0.09
42 39 0.30
44 45 0.35
45 11 0.09
46 2 0.02
47 9 0.07
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (42 bp):
CACTTGGTTCAACCCGCTAAGGGGAACCATTGAGGAATATAC
Found at i:147265 original size:42 final size:41
Alignment explanation
Indices: 147217--147438 Score: 117
Period size: 42 Copynumber: 5.2 Consensus size: 41
147207 CAGACCTGAT
147217 AAGGGGAACCACATGAGGAATATACCACTTGGCTTTCCCGTG
1 AAGGGGAACCAC-TGAGGAATATACCACTTGGCTTTCCCGTG
** * * ** * * * **
147259 AAGGGGAGTCATCCGAAGACCATATCACTT-GATTCAGACCCGCA
1 AAGGGGAACCA-CTGAGGAATATACCACTTGGCTT---TCCCGTG
*
147303 AAGGGGAACCACTTGAGGAATATACCACTTTGCTTTCCCGTG
1 AAGGGGAACCAC-TGAGGAATATACCACTTGGCTTTCCCGTG
** * ** * * **
147345 AAGGGGAGTCATCTAAAAAACAT-CTCACTTGG-TTCAACCCCACG
1 AAGGGGAACCA-CTGAGGAATATAC-CACTTGGCTT---TCCCGTG
*
147389 AAGGGGAACCACCTGAGGAATATACCACTTGGCTTTCCCATG
1 AAGGGGAACCA-CTGAGGAATATACCACTTGGCTTTCCCGTG
147431 AAGGGGAA
1 AAGGGGAA
147439 TCATTTAAAG
Statistics
Matches: 126, Mismatches: 41, Indels: 26
0.65 0.21 0.13
Matches are distributed among these distances:
41 6 0.05
42 59 0.47
43 3 0.02
44 52 0.41
45 6 0.05
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.21
Consensus pattern (41 bp):
AAGGGGAACCACTGAGGAATATACCACTTGGCTTTCCCGTG
Found at i:148807 original size:18 final size:18
Alignment explanation
Indices: 148784--148827 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
148774 TCTTTAGATT
*
148784 TTTTATTTAATTATTTTC
1 TTTTATTTAATTATTATC
*
148802 TTTTATTTAATTCTTATC
1 TTTTATTTAATTATTATC
148820 TTTTATTT
1 TTTTATTT
148828 TAAAAATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTATTTAATTATTATC
Found at i:148903 original size:5 final size:5
Alignment explanation
Indices: 148895--148956 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
148885 ATATTTCCCT
* * *
148895 TTTTA TTTTA TTTTG TTTTA TCTTTA TTTTC TCACTT- TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA T--TTTA TTTTA TTTTA
148942 TTTTA TTTTTA TTTT
1 TTTTA -TTTTA TTTT
148957 CTCTTTTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 2 0.04
5 32 0.68
6 11 0.23
7 2 0.04
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:148913 original size:16 final size:16
Alignment explanation
Indices: 148894--148956 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 16
148884 TATATTTCCC
148894 TTTTTATTTTATTTT-
1 TTTTTATTTTATTTTA
*
148909 GTTTTATCTTTATTTTCTCA
1 TTTTTAT-TTTA-TTT-T-A
148929 CTTTTTTATTTTATTTTA
1 --TTTTTATTTTATTTTA
148947 TTTTTATTTT
1 TTTTTATTTT
148957 CTCTTTTAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
15 6 0.15
16 14 0.36
17 3 0.08
18 2 0.05
19 1 0.03
20 3 0.08
21 4 0.10
22 6 0.15
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:148972 original size:37 final size:37
Alignment explanation
Indices: 148894--148993 Score: 98
Period size: 37 Copynumber: 2.7 Consensus size: 37
148884 TATATTTCCC
* * *
148894 TTTTTATTTTATTTT-GTTTTATCTTTATTTTCTCACT
1 TTTTTATTTTATTTTATTTTTAT-TTTATTTTCTAACA
*
148931 TTTTTATTTTATTTTATTTTTATTTTCTCTTT-TAACA
1 TTTTTATTTTATTTTATTTTTATTTTAT-TTTCTAACA
* *
148968 TTTTTATATTT-TTTAATTTTTCTTTT
1 TTTTTAT-TTTATTTTATTTTTATTTT
148994 TTGAAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
37 42 0.78
38 12 0.22
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (37 bp):
TTTTTATTTTATTTTATTTTTATTTTATTTTCTAACA
Found at i:149632 original size:42 final size:39
Alignment explanation
Indices: 149585--149721 Score: 104
Period size: 42 Copynumber: 3.4 Consensus size: 39
149575 AGTTGTAAGA
149585 TTTTAAATTTATAATAAACTATTATAATTAATATGATTACTT
1 TTTTAAA-TTA-AATAAACT-TTATAATTAATATGATTACTT
* * * *
149627 TTTTAAAGTTAAAACAAACTGT-T-AGT--TATGA-TAATT
1 TTTTAAA-TT-AAATAAACTTTATAATTAATATGATTACTT
*
149663 TTTTGAAATTAAATAAACTTTGATAATTAATATGATTACTC
1 TTTT-AAATTAAATAAACTTT-ATAATTAATATGATTACTT
*
149704 TTTAAAAGTTAATATAAA
1 TTTTAAA-TTAA-ATAAA
149722 TTTTTAGTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
35 9 0.12
36 10 0.14
37 9 0.12
38 2 0.03
39 2 0.03
40 9 0.12
41 11 0.15
42 21 0.28
43 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (39 bp):
TTTTAAATTAAATAAACTTTATAATTAATATGATTACTT
Found at i:149678 original size:77 final size:77
Alignment explanation
Indices: 149597--149739 Score: 216
Period size: 77 Copynumber: 1.9 Consensus size: 77
149587 TTAAATTTAT
* *
149597 AATAAACTATT-ATAATTAATATGATTACTTTTTTAAAGTTAAAACAAACTGTTAGTTATGATAA
1 AATAAACT-TTGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAACTGTTAGTTATGATAA
149661 TTTTTTGAAATTA
65 TTTTTTGAAATTA
* * * *
149674 AATAAACTTTGATAATTAATATGATTACTCTTTAAAAGTTAATATAAATTTTTAGTTATGATAAT
1 AATAAACTTTGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAACTGTTAGTTATGATAAT
149739 T
66 T
149740 AAATTAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 2 0.03
77 57 0.97
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (77 bp):
AATAAACTTTGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAACTGTTAGTTATGATAAT
TTTTTGAAATTA
Found at i:150123 original size:39 final size:39
Alignment explanation
Indices: 150033--150134 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 39
150023 ACCAAAATTT
* * *
150033 AGAAGAGGGAAAAATTGA-TTTTTTGAAAATTTAGAAGAG
1 AGAAGA-GGAAAATTTGATTTTTTTGAAAATGTAGAAAAG
* **
150072 AAAAGAGAGAAAATTTGATTTTTTTGGGAATGTAGAAAAG
1 AGAAGAG-GAAAATTTGATTTTTTTGAAAATGTAGAAAAG
* *
150112 GGAAGAGGAAAATTTTATTTTTT
1 AGAAGAGGAAAATTTGATTTTTT
150135 CACAAAGGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.02
39 29 0.56
40 22 0.42
ACGTcount: A:0.43, C:0.00, G:0.25, T:0.32
Consensus pattern (39 bp):
AGAAGAGGAAAATTTGATTTTTTTGAAAATGTAGAAAAG
Found at i:151303 original size:20 final size:21
Alignment explanation
Indices: 151242--151292 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
151232 TTTGAATGAG
* *
151242 GGTACCAAAACTGATAGTTTA
1 GGTACTAAAACTGATAATTTA
151263 GGTACTAAAACTGATAATTTA
1 GGTACTAAAACTGATAATTTA
*
151284 TGTACTAAA
1 GGTACTAAA
151293 CATGTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (21 bp):
GGTACTAAAACTGATAATTTA
Found at i:151355 original size:5 final size:5
Alignment explanation
Indices: 151336--151391 Score: 69
Period size: 5 Copynumber: 11.0 Consensus size: 5
151326 GCTTTATGAG
* *
151336 ATTAA ATT-T ATTAA ATTAA ATTAA ATTAA ATTAA ATTAAA ATTAGG ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATT-AA ATTA-A ATTAA
151387 ATTAA
1 ATTAA
151392 TAAAATATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
4 3 0.07
5 32 0.73
6 9 0.20
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:151980 original size:2 final size:2
Alignment explanation
Indices: 151975--152000 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
151965 TTTTAACATA
151975 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
152001 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:154094 original size:12 final size:12
Alignment explanation
Indices: 154073--154106 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
154063 ACTCACTTCA
*
154073 AGCTCGATTTTG
1 AGCTCAATTTTG
154085 AGCTCAATTTTG
1 AGCTCAATTTTG
154097 AGCTCAATTT
1 AGCTCAATTT
154107 AAGCTCGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (12 bp):
AGCTCAATTTTG
Found at i:155100 original size:20 final size:20
Alignment explanation
Indices: 155075--155113 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
155065 AAATAATGTA
155075 ATAATAATATG-ATTTGTATC
1 ATAATAA-ATGCATTTGTATC
155095 ATAATAAATGCATTTGTAT
1 ATAATAAATGCATTTGTAT
155114 GATTCTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (20 bp):
ATAATAAATGCATTTGTATC
Found at i:155413 original size:14 final size:14
Alignment explanation
Indices: 155394--155440 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
155384 TAATACTCAA
155394 GGTTTATAGTTTAG
1 GGTTTATAGTTTAG
*
155408 GGTTTAGAGTTTAG
1 GGTTTATAGTTTAG
* *
155422 GGATTATA-ATTAG
1 GGTTTATAGTTTAG
155435 GGTTTA
1 GGTTTA
155441 GGGTGTATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.45
Consensus pattern (14 bp):
GGTTTATAGTTTAG
Found at i:155586 original size:11 final size:11
Alignment explanation
Indices: 155570--155626 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
155560 TATTATAGAT
155570 TTTTTAATATA
1 TTTTTAATATA
155581 TTTTTAA-A-A
1 TTTTTAATATA
155590 TTTTATAAT-TA
1 TTTT-TAATATA
** *
155601 TCATTAATGTA
1 TTTTTAATATA
155612 TTTTTAATA-A
1 TTTTTAATATA
155622 TTTTT
1 TTTTT
155627 TTATAATGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
9 5 0.14
10 14 0.38
11 18 0.49
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (11 bp):
TTTTTAATATA
Found at i:156662 original size:12 final size:12
Alignment explanation
Indices: 156645--156669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
156635 AATATAACAA
156645 AAATTAATTTTT
1 AAATTAATTTTT
156657 AAATTAATTTTT
1 AAATTAATTTTT
156669 A
1 A
156670 TTTAGGTATT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTAATTTTT
Found at i:177265 original size:20 final size:19
Alignment explanation
Indices: 177222--177274 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
177212 CAAAATAATC
177222 CAATTTCACATCATAACAT
1 CAATTTCACATCATAACAT
177241 CAATTTCAACACTCA-AACAT
1 CAATTTC-ACA-TCATAACAT
*
177261 TAATTTC-CATCATA
1 CAATTTCACATCATA
177275 TTACATAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 7 0.23
20 14 0.47
21 3 0.10
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (19 bp):
CAATTTCACATCATAACAT
Found at i:180472 original size:16 final size:16
Alignment explanation
Indices: 180451--180481 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
180441 GACTTTGACA
180451 AAAAAGTCAAATTTTC
1 AAAAAGTCAAATTTTC
*
180467 AAAAAGTCATATTTT
1 AAAAAGTCAAATTTT
180482 ATATTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
AAAAAGTCAAATTTTC
Found at i:190779 original size:21 final size:20
Alignment explanation
Indices: 190714--190770 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
190704 AAACATTTGG
*
190714 AGTTTC-AAAATTTC-TCAAG
1 AGTTTCAAAAATTTCAT-AAA
*
190733 AGTTTCAAAAATTTTATAAA
1 AGTTTCAAAAATTTCATAAA
190753 AGTTTCAAAAACTTTCAT
1 AGTTTCAAAAA-TTTCAT
190771 TGAAGTTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 6 0.19
20 20 0.62
21 6 0.19
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (20 bp):
AGTTTCAAAAATTTCATAAA
Found at i:199914 original size:46 final size:46
Alignment explanation
Indices: 199861--199951 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
199851 TGGTCTATTA
*
199861 AATGGAGGCAGTTCTACATATTGAGGTTGAAATACCA-TCACTTTTT
1 AATGGAGGCAATTCTACATATTGAGGTTGAAATA-CAGTCACTTTTT
*
199907 AATGGAGGCAATTCTACTTATTGAGGTTGAAATACAGTCACTTTT
1 AATGGAGGCAATTCTACATATTGAGGTTGAAATACAGTCACTTTT
199952 GAATTTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 2 0.05
46 40 0.95
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (46 bp):
AATGGAGGCAATTCTACATATTGAGGTTGAAATACAGTCACTTTTT
Found at i:201269 original size:18 final size:18
Alignment explanation
Indices: 201243--201287 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
201233 TATAATTATC
201243 TGATAACTGAAAATCATA
1 TGATAACTGAAAATCATA
* *
201261 TGATCACTGAAAATCATC
1 TGATAACTGAAAATCATA
201279 TGATAACTG
1 TGATAACTG
201288 TAAACATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (18 bp):
TGATAACTGAAAATCATA
Found at i:204564 original size:28 final size:28
Alignment explanation
Indices: 204530--204583 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
204520 TCTCAGACTT
204530 AACTTTCTTTTGAAGATCGAGTCTCAGA
1 AACTTTCTTTTGAAGATCGAGTCTCAGA
* *
204558 AACTTTCTTTTTATGATCGAGTCTCA
1 AACTTTCTTTTGAAGATCGAGTCTCA
204584 TAACTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (28 bp):
AACTTTCTTTTGAAGATCGAGTCTCAGA
Found at i:211509 original size:22 final size:22
Alignment explanation
Indices: 211484--211525 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
211474 GGAATTAAGT
211484 GGATGATGATGGTCTTGATGGA
1 GGATGATGATGGTCTTGATGGA
* *
211506 GGATGTTGATGGTGTTGATG
1 GGATGATGATGGTCTTGATG
211526 TTGAAATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.02, G:0.43, T:0.36
Consensus pattern (22 bp):
GGATGATGATGGTCTTGATGGA
Found at i:219313 original size:18 final size:21
Alignment explanation
Indices: 219277--219315 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
219267 GTCGGAGAGA
219277 TAAGGAATGATTTATAGATAT
1 TAAGGAATGATTTATAGATAT
219298 TAAGGAA-G-TTTA-AGATAT
1 TAAGGAATGATTTATAGATAT
219316 AATTGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 1 0.06
21 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (21 bp):
TAAGGAATGATTTATAGATAT
Found at i:219747 original size:21 final size:21
Alignment explanation
Indices: 219721--219772 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
219711 CTAAAATGTA
219721 AATTTTGAAAACTTTTTGCTC
1 AATTTTGAAAACTTTTTGCTC
* *
219742 AATTTTGAAAACTTTTTTCTT
1 AATTTTGAAAACTTTTTGCTC
*
219763 GATTTTGAAA
1 AATTTTGAAA
219773 TAAGTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
AATTTTGAAAACTTTTTGCTC
Found at i:224471 original size:225 final size:225
Alignment explanation
Indices: 223720--224817 Score: 1632
Period size: 225 Copynumber: 4.9 Consensus size: 225
223710 TGTGGATAAA
* * *
223720 GGTTGA-AACAAATCAAGTAATTAAGCTG-TTATGTTATCGTTGGATTTCTAAGGCTCCATCAAC
1 GGTTGATAACAAATCAAGTAATTAA-CCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAGC
* * *
223783 TTAAACTTTGGTAACA-TTTAGGTGTTACATAATATATTGATAATACTGATAACAAATTAAGTAA
65 TTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAA
* *
223847 TTAACCTATTTTGTTATCGTCTGCTTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
130 TTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTT-AAAAGGCGCTACCTATTA
* * * *
223912 CGTTACACATG-TGCTACCTAATATGTTGATAAA
194 CGTTACATAAGCT-CTACCTAATATGTT-ATTAT
* * *
223945 GGTTGATAACAAATCAAATAATTAACCGATTACGTTATCATCGGATTTCTAAGGCTCCATCAGCT
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCT
* * *
224010 TAAACTTTGGTAACATTTTAGGTGTTACCTAATATGTTGATAACACTGATAACAAATTTAGTAAT
66 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
*
224075 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCACTACCTATTAC
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTT-AAAAGGCGCTACCTATTAC
**
224140 GTTACATAAGGACTACCTAATATGTTATTAT
195 GTTACATAAGCTCTACCTAATATGTTATTAT
* *
224171 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTAAGGCTCCATCAGCA
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCT
*
224236 TAAACTTTGGTAATATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
66 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * * **
224301 TAACCTATTTTGTTATTGTCGGATTTCTAAGACCCCATCAACTTTAAAAGGCGTTATATATTACG
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAGGCGCTACCTATTACG
*
224366 TTACATAAGCTCTACCTAATATGCTATTAT
196 TTACATAAGCTCTACCTAATATGTTATTAT
* * * *
224396 GGTTGATAACAAATCAAGTAATTAACTGATTATGTTATCGTCGAATTTCTATGGCTCCATCAGGT
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCT
*
224461 TAAACTTTGGTATCATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
66 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* ** * * * *
224526 TAACCTATTTTGTTATCTTCAAATTTCCAAGGCCCCATCATCCTTAAAAAGACGCTACCTATTAC
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCA-GCTTTAAAAGGCGCTACCTATTAC
224591 GTTACATAAGCGT-TACCTAATATGTTATTAT
195 GTTACATAAGC-TCTACCTAATATGTTATTAT
* * * * *
224622 GGTTGATAACAAATCAAGTAATTAA-CGGTTATGTTATAGTCAGATTTCTGAGGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCT
* * *
224686 TAAACTTTGGTAACATTTTAGGCGTTACTTAATATGTTGATAATATTGGTAACAAATTAAGTAAT
66 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
224751 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAGGCGCTACCTATTACG
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAGGCGCTACCTATTACG
224816 TT
196 TT
224818 CCCAGTTAAT
Statistics
Matches: 789, Mismatches: 78, Indels: 13
0.90 0.09 0.01
Matches are distributed among these distances:
224 24 0.03
225 334 0.42
226 301 0.38
227 130 0.16
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (225 bp):
GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCT
TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAGGCGCTACCTATTACG
TTACATAAGCTCTACCTAATATGTTATTAT
Found at i:224575 original size:451 final size:451
Alignment explanation
Indices: 223720--224817 Score: 1684
Period size: 451 Copynumber: 2.4 Consensus size: 451
223710 TGTGGATAAA
* * *
223720 GGTTGA-AACAAATCAAGTAATTAAGCTGTTATGTTATCGTTGGATTTCTAAGGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAA-CCGTTATGTTATAGTCGGATTTCTAAGGCTCCATCAACT
* *
223784 TAAACTTTGGTAACA-TTTAGGTGTTACATAATATATTGATAATACTGATAACAAATTAAGTAAT
65 TAAACTTTGGTAACATTTTAGGCGTTACATAATATGTTGATAATACTGATAACAAATTAAGTAAT
* *
223848 TAACCTATTTTGTTATCGTCTGCTTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTAC
130 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTT-AAAAGGCGCTACCTATTAC
* *
223913 GTTACACATGTGCTACCTAATATGTTGATAAAGGTTGATAACAAATCAAATAATTAACCGATTAC
194 GTTACACAAGTGCTACCTAATATGCTGATAAAGGTTGATAACAAATCAAATAATTAACCGATTAC
* *
223978 GTTATCATCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGTGTTACCTAAT
259 GTTATCATCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAAT
* ** *
224043 ATGTTGATAACACTGATAACAAATTTAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGC
324 ATGTTGATAACACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAAATTTCCAAGGC
* *
224108 CCCATCAGCTTTAAAAAGGCACTACCTATTACGTTACATAAG-GACTACCTAATATGTTATTAT
389 CCCATCAGCCTTAAAAAGACACTACCTATTACGTTACATAAGCG-CTACCTAATATGTTATTAT
* *
224171 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTAAGGCTCCATCAGCA
1 GGTTGATAACAAATCAAGTAATTAACCG-TTATGTTATAGTCGGATTTCTAAGGCTCCATCAACT
* *
224236 TAAACTTTGGTAATATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
65 TAAACTTTGGTAACATTTTAGGCGTTACATAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * * **
224301 TAACCTATTTTGTTATTGTCGGATTTCTAAGACCCCATCAACTTTAAAAGGCGTTATATATTACG
130 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAGGCGCTACCTATTACG
* * * * * *
224366 TTACATAAGCT-CTACCTAATATGCT-ATTATGGTTGATAACAAATCAAGTAATTAACTGATTAT
195 TTACACAAG-TGCTACCTAATATGCTGATAAAGGTTGATAACAAATCAAATAATTAACCGATTAC
* * * *
224429 GTTATCGTCGAATTTCTATGGCTCCATCAGGTTAAACTTTGGTATCATTTTAGGCGTTACCTAAT
259 GTTATCATCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAAT
* *
224494 ATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCTTCAAATTTCCAAGGC
324 ATGTTGATAACACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAAATTTCCAAGGC
* * *
224559 CCCATCATCCTTAAAAAGACGCTACCTATTACGTTACATAAGCGTTACCTAATATGTTATTAT
389 CCCATCAGCCTTAAAAAGACACTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTAT
* * *
224622 GGTTGATAACAAATCAAGTAATTAACGGTTATGTTATAGTCAGATTTCTGAGGCTCCATCAACTT
1 GGTTGATAACAAATCAAGTAATTAACCGTTATGTTATAGTCGGATTTCTAAGGCTCCATCAACTT
* * *
224687 AAACTTTGGTAACATTTTAGGCGTTACTTAATATGTTGATAATATTGGTAACAAATTAAGTAATT
66 AAACTTTGGTAACATTTTAGGCGTTACATAATATGTTGATAATACTGATAACAAATTAAGTAATT
224752 AACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAGGCGCTACCTATTACGT
131 AACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAGGCGCTACCTATTACGT
224817 T
196 T
224818 CCCAGTTAAT
Statistics
Matches: 585, Mismatches: 57, Indels: 11
0.90 0.09 0.02
Matches are distributed among these distances:
450 154 0.26
451 242 0.41
452 102 0.17
453 87 0.15
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (451 bp):
GGTTGATAACAAATCAAGTAATTAACCGTTATGTTATAGTCGGATTTCTAAGGCTCCATCAACTT
AAACTTTGGTAACATTTTAGGCGTTACATAATATGTTGATAATACTGATAACAAATTAAGTAATT
AACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAGGCGCTACCTATTACGT
TACACAAGTGCTACCTAATATGCTGATAAAGGTTGATAACAAATCAAATAATTAACCGATTACGT
TATCATCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATAT
GTTGATAACACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAAATTTCCAAGGCCC
CATCAGCCTTAAAAAGACACTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTAT
Found at i:225778 original size:55 final size:54
Alignment explanation
Indices: 225694--225890 Score: 186
Period size: 55 Copynumber: 3.6 Consensus size: 54
225684 CCACAGTCGC
* *
225694 CCATTACCATGATTTAGCACATGGATTTTTAACCCTATGAATAATATGCTCGTAT
1 CCATTAGCATCATTTAGCACATGGATTTTTAACCCTATGAA-AATATGCTCGTAT
* * * * * * *
225749 CCATTAGCATCATTTAGCATATGGGTTTTTAACTCTGTTAACGATATGCTC-TCGT
1 CCATTAGCATCATTTAGCACATGGATTTTTAACCCTATGAA-AATATGCTCGT-AT
* * * * *
225804 CCATTA-CTGTCGTAT-GCACACGGATTTTTATTCCC-ATGAAATATATGCTCGTAT
1 CCATTAGC-ATCATTTAGCACATGGATTTTTA-ACCCTATGAAA-ATATGCTCGTAT
225858 CCATTAGCATCATTTAGCACATGGATTTTTAAC
1 CCATTAGCATCATTTAGCACATGGATTTTTAAC
225891 TATAGCGGTG
Statistics
Matches: 108, Mismatches: 27, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
54 37 0.34
55 71 0.66
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (54 bp):
CCATTAGCATCATTTAGCACATGGATTTTTAACCCTATGAAAATATGCTCGTAT
Found at i:226023 original size:55 final size:55
Alignment explanation
Indices: 225846--226070 Score: 186
Period size: 55 Copynumber: 4.1 Consensus size: 55
225836 CCCATGAAAT
* * * *
225846 ATATGCTCGTATCCATTAGCATCATTTAGCACATGGATTTTTAA-CTATAGCGGTG
1 ATATGCTCGTGTCCATTAACATCATTTAGCACATGAATTTTTAATC-ATACCGGTG
* * ** * *
225901 ATATACTCGTGTTCATTCTAACATCATTTTTCACATGAA-TTTTAATCTTGCCGGTG
1 ATATGCTCGTGTCCA-T-TAACATCATTTAGCACATGAATTTTTAATCATACCGGTG
* * * * * *
225957 ATAT-ATACGTGTCTATTAATATCATTTAGCACATGAATCTTTAATCATACCAGCG
1 ATATGCT-CGTGTCCATTAACATCATTTAGCACATGAATTTTTAATCATACCGGTG
* * * * * * *
226012 ATATGCTCGTGTCCATTAATATCATCTAACACGTGAATTTTTAACCATGCCGGTA
1 ATATGCTCGTGTCCATTAACATCATTTAGCACATGAATTTTTAATCATACCGGTG
226067 ATAT
1 ATAT
226071 ATTTGTATCT
Statistics
Matches: 132, Mismatches: 32, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
54 18 0.14
55 72 0.55
56 24 0.18
57 18 0.14
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (55 bp):
ATATGCTCGTGTCCATTAACATCATTTAGCACATGAATTTTTAATCATACCGGTG
Found at i:226023 original size:111 final size:110
Alignment explanation
Indices: 225866--226091 Score: 249
Period size: 111 Copynumber: 2.0 Consensus size: 110
225856 ATCCATTAGC
* * * * * * * *
225866 ATCATTTAGCACATGGATTTTTAACTATAGCGGTGATATACTCGTGTTCATTCTAACATCATTTT
1 ATCATTTAGCACATGAATCTTTAACTATACCAGCGATATACTCGTGTCCA-T-TAACATCATCTA
* * * * *
225931 TCACATGAA-TTTTAATCTTGCCGGTGATATATACGTGTCTATTAAT
64 ACACATGAATTTTTAACCATGCCGGTAATATATACGTATCTATTAAT
* *
225977 ATCATTTAGCACATGAATCTTTAA-TCATACCAGCGATATGCTCGTGTCCATTAATATCATCTAA
1 ATCATTTAGCACATGAATCTTTAACT-ATACCAGCGATATACTCGTGTCCATTAACATCATCTAA
* **
226041 CACGTGAATTTTTAACCATGCCGGTAATATATTTGTATCTATTAAT
65 CACATGAATTTTTAACCATGCCGGTAATATATACGTATCTATTAAT
226087 ATCAT
1 ATCAT
226092 ATGACACAAA
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
109 16 0.17
110 38 0.40
111 41 0.43
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (110 bp):
ATCATTTAGCACATGAATCTTTAACTATACCAGCGATATACTCGTGTCCATTAACATCATCTAAC
ACATGAATTTTTAACCATGCCGGTAATATATACGTATCTATTAAT
Found at i:226165 original size:76 final size:78
Alignment explanation
Indices: 226034--226190 Score: 183
Period size: 76 Copynumber: 2.0 Consensus size: 78
226024 CCATTAATAT
* * * *** **
226034 CATCTAACACGTGAATTTTTAACCATGCCGGTAATATATTTGTATCTATTAATATCATAT-G-AC
1 CATCTAACACATGAATCTTTAACCATACCAAAAATATATTCATATCTATTAATATCATATGGTAC
226097 ACAAATTTTTAAC
66 ACAAATTTTTAAC
* * *
226110 CATCTAACACATGAATCTTTAACCATACCAAAAATATATTCATGTCTATTTATATCATCTGGTAC
1 CATCTAACACATGAATCTTTAACCATACCAAAAATATATTCATATCTATTAATATCATATGGTAC
**
226175 ATGAATTTTTAAC
66 ACAAATTTTTAAC
226188 CAT
1 CAT
226191 GCCGGGGCTA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
76 49 0.74
77 1 0.02
78 16 0.24
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (78 bp):
CATCTAACACATGAATCTTTAACCATACCAAAAATATATTCATATCTATTAATATCATATGGTAC
ACAAATTTTTAAC
Found at i:226834 original size:25 final size:26
Alignment explanation
Indices: 226783--226834 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
226773 ATCAAATCAC
* * **
226783 AAGGGTATTCTGGTAATTTTCTCTAT
1 AAGGGTATTATAGTAATTTTCAATAT
226809 AAGGGTATTATAGTAA-TTTCAATAT
1 AAGGGTATTATAGTAATTTTCAATAT
226834 A
1 A
226835 TAAGGGCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (26 bp):
AAGGGTATTATAGTAATTTTCAATAT
Found at i:230952 original size:31 final size:30
Alignment explanation
Indices: 230914--231078 Score: 179
Period size: 31 Copynumber: 5.3 Consensus size: 30
230904 AATGTGATTA
*
230914 TTGGGTAGGCTCTGTTGGCCC-GAGATCATTC
1 TTGGGTAGGC-CTG-TGGCCCTGAGATCTTTC
* * * *
230945 TTGGGTAGGCCCTGCGGCCTTGGGATTTTTC
1 TTGGGTAGG-CCTGTGGCCCTGAGATCTTTC
*
230976 TTGGGTAGGCCTCGTGGCCCTGAGATCATTC
1 TTGGGTAGGCCT-GTGGCCCTGAGATCTTTC
* **
231007 TTTGGTAGGCCCTGCAGCCCTGAGATCTTTC
1 TTGGGTAGG-CCTGTGGCCCTGAGATCTTTC
*
231038 TTGGGTAGGCCTTGTGGCCCTGAGAACTTTC
1 TTGGGTAGGCC-TGTGGCCCTGAGATCTTTC
231069 TTGGGTAGGC
1 TTGGGTAGGC
231079 TCTCAGACCC
Statistics
Matches: 111, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
30 9 0.08
31 98 0.88
32 4 0.04
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.32
Consensus pattern (30 bp):
TTGGGTAGGCCTGTGGCCCTGAGATCTTTC
Found at i:231001 original size:62 final size:62
Alignment explanation
Indices: 230914--231078 Score: 226
Period size: 62 Copynumber: 2.7 Consensus size: 62
230904 AATGTGATTA
* * * *
230914 TTGGGTAGG-CTCTGTTGGCCC-GAGATCATTCTTGGGTAGGCCCTGCGGCCTTGGGATTTTTC
1 TTGGGTAGGCCTC-G-TGGCCCTGAGATCATTCTTGGGTAGGCCCTGCAGCCCTGAGATCTTTC
*
230976 TTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTTGGTAGGCCCTGCAGCCCTGAGATCTTTC
1 TTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGCCCTGCAGCCCTGAGATCTTTC
* * *
231038 TTGGGTAGGCCTTGTGGCCCTGAGAACTTTCTTGGGTAGGC
1 TTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGC
231079 TCTCAGACCC
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
61 6 0.07
62 83 0.90
63 3 0.03
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.32
Consensus pattern (62 bp):
TTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGCCCTGCAGCCCTGAGATCTTTC
Found at i:237027 original size:2 final size:2
Alignment explanation
Indices: 237020--237048 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
237010 ATTATTCAAT
237020 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 T
237049 TAAACACGTC
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:237919 original size:55 final size:55
Alignment explanation
Indices: 237625--238206 Score: 732
Period size: 55 Copynumber: 10.7 Consensus size: 55
237615 GGGTGCAAAT
* *
237625 ATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTC-T-AGGTTGCACAC
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * *
237678 ATACTGCCAA-ACAGAAATTCATAAATTCATTATGAATTTCGTGGGGTT--ACAC
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * * * * *
237730 ACAGTGCCAATTCGAAAATTCATAAACTCATTATGAATTTGGTGGGGTTGCCCCC
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
** *
237785 ATAGTGCCAATA-ATAAATTCATAAACTAATTATGAATTTCGTGGGGTTGCACA-
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* ** *
237838 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGCAGGGTCGCACAC
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * ** *
237893 ATAGTTCCAATACGGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACAG
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
** * *
237947 ATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTAGTGGGATTGCACAC
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* ** *
238002 GTAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCATGGGGTTGCACAC
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * *
238057 ATAGTGCCAATACGGAGATTCATAAACTCATTATGAATTTCATGGGGTTGCACAT
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * * **
238112 ATAGTGGCAATACGGAAATTCTTAAACTCATTATCAATTTC-TTAGGTTGCACAC
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* *
238166 ATAGTGCCAATATGGAAATTCATGAACTCATTATGAATTTC
1 ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTC
238207 TTATGAATTT
Statistics
Matches: 457, Mismatches: 64, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
52 41 0.09
53 55 0.12
54 164 0.36
55 197 0.43
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (55 bp):
ATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
Found at i:237971 original size:109 final size:110
Alignment explanation
Indices: 237625--238206 Score: 736
Period size: 109 Copynumber: 5.4 Consensus size: 110
237615 GGGTGCAAAT
*
237625 ATAGTGCCAATAC-AGAAATTCATAAACTCATTATGAATTTC-TA-GGTTGCACACATACTGCCA
1 ATAGTGCCAATACGA-AAATTCATAAACTCATTATGAATTTCGTAGGGTTGCACACATAGTGCCA
*
237687 A-ACAGAAATTCATAAATTCATTATGAATTTCGTGGGGTT--ACAC
65 ATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * * * * *
237730 ACAGTGCCAATTCGAAAATTCATAAACTCATTATGAATTTGGTGGGGTTGCCCCCATAGTGCCAA
1 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTAGGGTTGCACACATAGTGCCAA
* *
237795 TA-ATAAATTCATAAACTAATTATGAATTTCGTGGGGTTGCACA-
66 TACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * *
237838 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGCAGGGTCGCACACATAGTTCCAA
1 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTAGGGTTGCACACATAGTGCCAA
* * ** *
237903 TACGGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACAG
66 TACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * *
237947 ATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTAGT-GGGATTGCACACGTAGTGCCA
1 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTAGGG-TTGCACACATAGTGCCA
* *
238011 ATACAAAAATTCATAAACTCATTATGAATTTCATGGGGTTGCACAC
65 ATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * * * * *
238057 ATAGTGCCAATACGGAGATTCATAAACTCATTATGAATTTCATGGGGTTGCACATATAGTGGCAA
1 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTAGGGTTGCACACATAGTGCCAA
* * * **
238122 TACGGAAATTCTTAAACTCATTATCAATTTC-TTAGGTTGCACAC
66 TACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
* * *
238166 ATAGTGCCAATATGGAAATTCATGAACTCATTATGAATTTC
1 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTC
238207 TTATGAATTT
Statistics
Matches: 413, Mismatches: 53, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
105 36 0.09
106 2 0.00
107 50 0.12
108 72 0.17
109 160 0.39
110 90 0.22
111 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (110 bp):
ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTAGGGTTGCACACATAGTGCCAA
TACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACAC
Found at i:238578 original size:20 final size:20
Alignment explanation
Indices: 238553--238606 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
238543 AAACTTAATA
*
238553 GTATCGATACCCCTCCTTTG
1 GTATCGATACCCCTCCTATG
* * *
238573 GTATCGGTACTTCTCTTCTATG
1 GTATCGATAC--CCCTCCTATG
238595 GTATCGATACCC
1 GTATCGATACCC
238607 ACTTCAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 10 0.38
22 16 0.62
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.37
Consensus pattern (20 bp):
GTATCGATACCCCTCCTATG
Found at i:238707 original size:21 final size:21
Alignment explanation
Indices: 238678--238731 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
238668 CTTCTTCCTG
*
238678 ATATCGATACTACTTGCATCA
1 ATATTGATACTACTTGCATCA
238699 ATATTGATACTACTTGCATCA
1 ATATTGATACTACTTGCATCA
*
238720 GTATTGATACTA
1 ATATTGATACTA
238732 TTATTCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATTGATACTACTTGCATCA
Found at i:243670 original size:54 final size:54
Alignment explanation
Indices: 243506--243835 Score: 362
Period size: 54 Copynumber: 6.1 Consensus size: 54
243496 CGCCCAAGTA
* * * * ** * *
243506 CCAATATGGAAATTCACAAACTCATTTTGAAATCCTT-GGGTGCACATATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTATTAGGTTGCACACATAGTG
* * * * *
243559 CTAATACAGAAATTCATAAACTCATAATGAATTT-CTAGGTTTCACACATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTATTAGGTTGCACACATAGTG
* *
243612 CCAATATGGAAATTCATAAACTTATTATGAATTTATTAGGTTGCACACATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTATTAGGTTGCACACATAGTG
* * * ** *
243666 CCAATACGGAAATTAATAAACTCAATATG-ATTTCGTGGGGTTGCACGCATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTT-ATTAGGTTGCACACATAGTG
* * *
243720 CCAATACAGAAATTCATAAACTCATTAGGAATTTCTTAGGTTGCACACATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTATTAGGTTGCACACATAGTG
* * *
243774 CTAATACGGAAATTCATAAACTCATTATGAATTTCA-TGGGTTGCACATATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTT-ATTAGGTTGCACACATAGTG
*
243828 TCAATACG
1 CCAATACG
243836 ATAAATGAAA
Statistics
Matches: 229, Mismatches: 43, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
52 1 0.00
53 72 0.31
54 152 0.66
55 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (54 bp):
CCAATACGGAAATTCATAAACTCATTATGAATTTATTAGGTTGCACACATAGTG
Found at i:251204 original size:21 final size:21
Alignment explanation
Indices: 251180--251245 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
251170 ATTACTAGCT
251180 TTTCCAACTTATTCCCTAAAA
1 TTTCCAACTTATTCCCTAAAA
* * ***
251201 TTTCAAAGC-TATTACC-AGCT
1 TTTCCAA-CTTATTCCCTAAAA
251221 TTTCCAACTTATTCCCTAAAA
1 TTTCCAACTTATTCCCTAAAA
251242 TTTC
1 TTTC
251246 AAAGCTATGT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 17 0.53
22 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.39
Consensus pattern (21 bp):
TTTCCAACTTATTCCCTAAAA
Found at i:251221 original size:41 final size:41
Alignment explanation
Indices: 251166--251253 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
251156 ACTATGTTGG
*
251166 AGCTATTACTAGCTTTTCCAACTTATTCCCTAAAATTTCAA
1 AGCTATTACCAGCTTTTCCAACTTATTCCCTAAAATTTCAA
251207 AGCTATTACCAGCTTTTCCAACTTATTCCCTAAAATTTCAA
1 AGCTATTACCAGCTTTTCCAACTTATTCCCTAAAATTTCAA
251248 AGCTAT
1 AGCTAT
251254 GTGAGATTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (41 bp):
AGCTATTACCAGCTTTTCCAACTTATTCCCTAAAATTTCAA
Found at i:251233 original size:20 final size:20
Alignment explanation
Indices: 251169--251233 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
251159 ATGTTGGAGC
*
251169 TATTACTAGCTTTTCCAACT
1 TATTACCAGCTTTTCCAACT
* *** *
251189 TATTCCCTAAAATTTCAAAGC-
1 TATTACC-AGCTTTTCCAA-CT
251210 TATTACCAGCTTTTCCAACT
1 TATTACCAGCTTTTCCAACT
251230 TATT
1 TATT
251234 CCCTAAAATT
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
19 1 0.03
20 16 0.52
21 13 0.42
22 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.42
Consensus pattern (20 bp):
TATTACCAGCTTTTCCAACT
Found at i:251618 original size:6 final size:6
Alignment explanation
Indices: 251607--251635 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
251597 AAAGAACAAA
251607 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
251636 AAATAGAACA
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
Done.