Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002501.1 Hibiscus syriacus cultivar Beakdansim tig00005096_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: 167908
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:425 original size:39 final size:39
Alignment explanation
Indices: 371--449 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
361 GGAGAAGGGA
371 AATCTGGAAAATATGAAACCTGCGCACGGGGAGGAGCTT
1 AATCTGGAAAATATGAAACCTGCGCACGGGGAGGAGCTT
410 AATCTGGAAAATATGAAACCTGCGCACGGGGAGGAGCTT
1 AATCTGGAAAATATGAAACCTGCGCACGGGGAGGAGCTT
449 A
1 A
450 TAATTCATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (39 bp):
AATCTGGAAAATATGAAACCTGCGCACGGGGAGGAGCTT
Found at i:5659 original size:16 final size:15
Alignment explanation
Indices: 5631--5661 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5621 CGGTCGAGTG
5631 ATTAATTTATTATAA
1 ATTAATTTATTATAA
5646 ATTAATTATATTATAA
1 ATTAATT-TATTATAA
5662 TATCAATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTAATTTATTATAA
Found at i:6220 original size:90 final size:90
Alignment explanation
Indices: 6068--6258 Score: 323
Period size: 90 Copynumber: 2.1 Consensus size: 90
6058 AAGATGCTAT
*
6068 CGGTTTTGTTATTATTTTTTAACAAAACTAATAAAAAATTATCAAAAACATTATTATTTCTATCG
1 CGGTTTTGTTATTATTTTTTAACAAAACTAATAAAAAATTATCAAAAACATTATTATTTCTATCA
*
6133 TTTTT-TTATTA-TTGGACACTTTTC
66 TTTTTGTTATTATTTGG-CACTTTAC
6157 CGGTTTTGTTATTATTTTTTTAACAAAACTAATAAAAAATTATCAAAAACATTATTATTTCTATC
1 CGGTTTTGTTATTA-TTTTTTAACAAAACTAATAAAAAATTATCAAAAACATTATTATTTCTATC
6222 ATTTTTGTTATTATTTGGCACTTTAC
65 ATTTTTGTTATTATTTGGCACTTTAC
*
6248 CGATTTTGTTA
1 CGGTTTTGTTA
6259 ATATATCCGA
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
89 14 0.15
90 55 0.57
91 23 0.24
92 4 0.04
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (90 bp):
CGGTTTTGTTATTATTTTTTAACAAAACTAATAAAAAATTATCAAAAACATTATTATTTCTATCA
TTTTTGTTATTATTTGGCACTTTAC
Found at i:6365 original size:21 final size:21
Alignment explanation
Indices: 6340--6383 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
6330 AAAAATATTA
*
6340 AAAAACATTAATATTTTAAAT
1 AAAAACAATAATATTTTAAAT
*
6361 AAAAATAATAATATTTTAAAT
1 AAAAACAATAATATTTTAAAT
6382 AA
1 AA
6384 TTTTTTACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAACAATAATATTTTAAAT
Found at i:11161 original size:10 final size:10
Alignment explanation
Indices: 11146--11170 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11136 CTGCAAAATG
11146 TAATAAATAA
1 TAATAAATAA
11156 TAATAAATAA
1 TAATAAATAA
11166 TAATA
1 TAATA
11171 TTTTTTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TAATAAATAA
Found at i:11630 original size:3 final size:3
Alignment explanation
Indices: 11624--11674 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
11614 CATTAAAGAA
11624 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11672 AAT
1 AAT
11675 CAAAGCTTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12154 original size:22 final size:22
Alignment explanation
Indices: 12120--12161 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12110 AAGTTTAGTA
12120 TTTAAATTATTATTATTTTATT
1 TTTAAATTATTATTATTTTATT
*
12142 TTTAATATT-TTATTTTTTTA
1 TTTAA-ATTATTATTATTTTA
12162 AAAAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTAAATTATTATTATTTTATT
Found at i:29217 original size:87 final size:87
Alignment explanation
Indices: 29071--29301 Score: 349
Period size: 87 Copynumber: 2.7 Consensus size: 87
29061 AAATATGTCA
* * ** *
29071 ATATAAGCACTACCTAATATATTATTGTACTTGATAATATTTCCGACTAAATGCTTATTTTATTA
1 ATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCATATTTTATTA
* *
29136 TATAAGCGATGTC-TATTACATT
66 TATAAACGAT-ACATATTACATT
*
29158 ATATAAGCTCTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCATATTTTATTA
1 ATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCATATTTTATTA
*
29223 TATAAACGCTACATATTACATT
66 TATAAACGATACATATTACATT
*
29245 ATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATG-ATAT
1 ATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCATAT
29302 AACATAATCG
Statistics
Matches: 133, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
86 5 0.04
87 128 0.96
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCATATTTTATTA
TATAAACGATACATATTACATT
Found at i:29269 original size:23 final size:23
Alignment explanation
Indices: 29219--29263 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29209 TGCATATTTT
*
29219 ATTATATAAACGCTACATATTAC
1 ATTATATAAACGCTACATAATAC
* *
29242 ATTATATAAGCGCTACCTAATA
1 ATTATATAAACGCTACATAATA
29264 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAACGCTACATAATAC
Found at i:32466 original size:6 final size:6
Alignment explanation
Indices: 32455--32487 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
32445 TCATACTCAC
32455 ATGTTT ATGTTT ATGTTT ATGTTT ATGTTT ATG
1 ATGTTT ATGTTT ATGTTT ATGTTT ATGTTT ATG
32488 AAACTCGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (6 bp):
ATGTTT
Found at i:44205 original size:21 final size:21
Alignment explanation
Indices: 44157--44207 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
44147 GCCTTCACTA
* *
44157 CCGCCATCCGTCGCTAGCCTT
1 CCGCCGTCCGTCGCTAGCCGT
* *
44178 CCACCGTCCGTCGCTAGTCGT
1 CCGCCGTCCGTCGCTAGCCGT
44199 CCGCCGTCC
1 CCGCCGTCC
44208 TCCGACCACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.08, C:0.49, G:0.22, T:0.22
Consensus pattern (21 bp):
CCGCCGTCCGTCGCTAGCCGT
Found at i:56140 original size:150 final size:150
Alignment explanation
Indices: 55859--56157 Score: 440
Period size: 150 Copynumber: 2.0 Consensus size: 150
55849 TTCCTCACCG
* * * *
55859 TCATCATTCTTATCATTCCTGTCTTTCTTCCCCTCGGATTTATCCTTGAAAAGTTTCCGGAAAAA
1 TCATCATTCATATAATTCCCGTCTTTCTTCCCCTCAGATTTATCCTTGAAAAGTTTCCGGAAAAA
* *
55924 CCCCTCCTTTTGATCGTATTCACCTGATTTTGAAGCTTTTTCTGCAGAGTTAACCATATGTACAT
66 CCCCTCCTTTTCATCATATTCACCTGATTTTGAAGCTTTTTCTGCAGAGTTAACCATATGTACAT
* *
55989 CATCACTTCTTTCATTTACA
131 CATCAATTCTATCATTTACA
**
56009 TCATCATTCATATAATTCCCGTCTTTCTTTTCCTCAGATTTATCCTTGAAAAGTTTCCGGAAGAA
1 TCATCATTCATATAATTCCCGTCTTTCTTCCCCTCAGATTTATCCTTGAAAAGTTTCCGGAA-AA
* ** *
56074 A-CCCTCCTTTTCATCATCTTCACCTGATTTTGAAGCTTTTTCTGCAGAGTTCGCCAT-TCGTGC
65 ACCCCTCCTTTTCATCATATTCACCTGATTTTGAAGCTTTTTCTGCAGAGTTAACCATAT-GTAC
56137 ATCATCAATTCTATCATTTAC
129 ATCATCAATTCTATCATTTAC
56158 CTCTTTCTTA
Statistics
Matches: 133, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
149 1 0.01
150 129 0.97
151 3 0.02
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (150 bp):
TCATCATTCATATAATTCCCGTCTTTCTTCCCCTCAGATTTATCCTTGAAAAGTTTCCGGAAAAA
CCCCTCCTTTTCATCATATTCACCTGATTTTGAAGCTTTTTCTGCAGAGTTAACCATATGTACAT
CATCAATTCTATCATTTACA
Found at i:58920 original size:64 final size:63
Alignment explanation
Indices: 58848--58968 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 63
58838 CAAATAAATG
* * *
58848 AACATCGAATGTCATTAGTGTATCGATGCATAAGG-AGTGCATCGATGCACCCGCTTAAAATACA
1 AACATCGAATGGCATTAGTGTACCGATGCA-AAGGTAGTGCATCGATACACCCG-TTAAAATACA
* * * *
58912 AACATCGAATGGGATTTGTGTACCGATGCACAGGTAGTGCATTGATACACCCGTTAA
1 AACATCGAATGGCATTAGTGTACCGATGCAAAGGTAGTGCATCGATACACCCGTTAA
58969 GGAATGCATC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 7 0.14
64 42 0.86
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (63 bp):
AACATCGAATGGCATTAGTGTACCGATGCAAAGGTAGTGCATCGATACACCCGTTAAAATACA
Found at i:59543 original size:21 final size:21
Alignment explanation
Indices: 59519--59575 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
59509 GAGGGATTAA
59519 CAGTGGTCATTCGGGACATAT
1 CAGTGGTCATTCGGGACATAT
*
59540 CAGTGGTCCTTCGGG--ATAT
1 CAGTGGTCATTCGGGACATAT
59559 -AGTGGTCATTCGGGACA
1 CAGTGGTCATTCGGGACA
59576 AATATTCAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 13 0.41
19 4 0.12
20 1 0.03
21 14 0.44
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (21 bp):
CAGTGGTCATTCGGGACATAT
Found at i:59564 original size:18 final size:19
Alignment explanation
Indices: 59519--59573 Score: 76
Period size: 18 Copynumber: 2.8 Consensus size: 19
59509 GAGGGATTAA
59519 CAGTGGTCATTCGGGACATAT
1 CAGTGGTCATTCGGG--ATAT
*
59540 CAGTGGTCCTTCGGGATAT
1 CAGTGGTCATTCGGGATAT
59559 -AGTGGTCATTCGGGA
1 CAGTGGTCATTCGGGA
59574 CAAATATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 14 0.44
19 4 0.12
21 14 0.44
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (19 bp):
CAGTGGTCATTCGGGATAT
Found at i:63614 original size:12 final size:12
Alignment explanation
Indices: 63597--63659 Score: 83
Period size: 12 Copynumber: 5.3 Consensus size: 12
63587 AAACCTGCTA
*
63597 AGCTCATAATCG
1 AGCTCAAAATCG
63609 AGCTCAAAATCG
1 AGCTCAAAATCG
63621 AGCTCAAAATCG
1 AGCTCAAAATCG
**
63633 AGCT-TGAATCG
1 AGCTCAAAATCG
*
63644 AGCTCAAAATCT
1 AGCTCAAAATCG
63656 AGCT
1 AGCT
63660 TCAATCGAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
11 9 0.20
12 35 0.80
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (12 bp):
AGCTCAAAATCG
Found at i:63646 original size:23 final size:23
Alignment explanation
Indices: 63597--63668 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
63587 AAACCTGCTA
* *
63597 AGCTCATAATCGAGCTCAAAATCG
1 AGCTCAAAATCGAGCT-TAAATCG
*
63621 AGCTCAAAATCGAGCTTGAATCG
1 AGCTCAAAATCGAGCTTAAATCG
* *
63644 AGCTCAAAATCTAGCTTCAATCG
1 AGCTCAAAATCGAGCTTAAATCG
63667 AG
1 AG
63669 TTTGAGTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 28 0.65
24 15 0.35
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (23 bp):
AGCTCAAAATCGAGCTTAAATCG
Found at i:68684 original size:64 final size:64
Alignment explanation
Indices: 68584--68713 Score: 154
Period size: 64 Copynumber: 2.0 Consensus size: 64
68574 ATGCACTCTC
* * * *
68584 AAATAAATGAACATCGAATGTCATTAGTGCATCGATGCATAAGGAGTGCATCGATGCACCCGCTT
1 AAATAAA-GAACATCGAATGGCATTAGTGCACCGATGCACAAGGAGTGCATCGATACACCCG-TT
68649 A
64 A
* * * * *
68650 AAATAAA-AACATCGAATGGGATTTGTGTACCGATGCACATGTAGTGCATCGATACACCCGTTA
1 AAATAAAGAACATCGAATGGCATTAGTGCACCGATGCACAAGGAGTGCATCGATACACCCGTTA
68713 A
1 A
68714 GGAATGCATC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
63 4 0.07
64 44 0.80
66 7 0.13
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (64 bp):
AAATAAAGAACATCGAATGGCATTAGTGCACCGATGCACAAGGAGTGCATCGATACACCCGTTA
Found at i:69325 original size:18 final size:18
Alignment explanation
Indices: 69272--69326 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
69262 AGGGATTAGC
*
69272 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
*
69290 ATCGTGGTCCTTCAGGACAT
1 A--GTGGTCCTTCGGGACAT
*
69310 AGTGGTCTTTCGGGACA
1 AGTGGTCCTTCGGGACA
69327 AATATTCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 15 0.48
20 16 0.52
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:72886 original size:36 final size:36
Alignment explanation
Indices: 72812--72886 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
72802 TTTTTATATT
*
72812 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
*
72848 TTTAATTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
72884 TTT
1 TTT
72887 GTAATTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 17 0.49
36 18 0.51
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:80543 original size:18 final size:18
Alignment explanation
Indices: 80508--80543 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
80498 CAATGCAATT
**
80508 TCTTTGCTAGTTTTAGCC
1 TCTTTGCTAGTTGCAGCC
80526 TCTTTGCTAGTTGCAGCC
1 TCTTTGCTAGTTGCAGCC
80544 ATACCTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.44
Consensus pattern (18 bp):
TCTTTGCTAGTTGCAGCC
Found at i:84858 original size:15 final size:16
Alignment explanation
Indices: 84830--84861 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
84820 AAAATCTTTC
84830 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
84846 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
84861 T
1 T
84862 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:99356 original size:22 final size:23
Alignment explanation
Indices: 99321--99368 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
99311 ACTTAATTTT
99321 TTTAACTAATTTATAA-TTATACA
1 TTTAACTAATTTATAATTTA-ACA
*
99344 TTTAA-TACTTTATAATTTAACA
1 TTTAACTAATTTATAATTTAACA
99366 TTT
1 TTT
99369 TATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAACTAATTTATAATTTAACA
Found at i:99363 original size:15 final size:15
Alignment explanation
Indices: 99337--99379 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
99327 TAATTTATAA
99337 TTATACATTTAATACT
1 TTATA-ATTTAATACT
* *
99353 TTATAATTTAACATT
1 TTATAATTTAATACT
*
99368 TTATAAATTAAT
1 TTATAATTTAAT
99380 TTAATTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATAATTTAATACT
Found at i:99834 original size:23 final size:25
Alignment explanation
Indices: 99787--99838 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
99777 TAAAGTATAT
* *
99787 TATATTTTTATGTAAACATTGAATA
1 TATATTTTTATGTAAACAATAAATA
99812 TATATTTTT-TGTAAA-AATAAATA
1 TATATTTTTATGTAAACAATAAATA
99835 TATA
1 TATA
99839 AAGTATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 6 0.24
25 9 0.36
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (25 bp):
TATATTTTTATGTAAACAATAAATA
Found at i:99837 original size:25 final size:26
Alignment explanation
Indices: 99777--99838 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
99767 TTTATATATT
*
99777 TAAAGTATATTATATTTTTATGTAAACA
1 TAAA-TATA-TATATTTTTATGTAAAAA
**
99805 TTGA-ATATATATTTTT-TGTAAAAA
1 TAAATATATATATTTTTATGTAAAAA
99829 TAAATATATA
1 TAAATATATA
99839 AAGTATTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
24 9 0.32
25 14 0.50
26 3 0.11
28 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (26 bp):
TAAATATATATATTTTTATGTAAAAA
Found at i:101970 original size:78 final size:78
Alignment explanation
Indices: 101841--101990 Score: 207
Period size: 78 Copynumber: 1.9 Consensus size: 78
101831 ATTGGCATCA
** * *
101841 ACCTTCTTATGAACCTTCATCCCTAGCAGGAACTTCAACTGATTGGAACCATCAAC-CCAGGCCG
1 ACCTTCTTATGAACCTTCATCCCTAGCAGGAACTTCAACTGATACGAACCATC-ACTCCAGACAG
101905 CAAGCCCCGTTTAC
65 CAAGCCCCGTTTAC
*
101919 ACCTTCTTATGCACCTTCATCCCTAGCAGGAACTTCAA-TGGA-ACGACACCATCACTCCAGACA
1 ACCTTCTTATGAACCTTCATCCCTAGCAGGAACTTCAACT-GATACGA-ACCATCACTCCAGACA
101982 GCAAGCCCC
64 GCAAGCCCC
101991 ATCTATACCT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
77 5 0.08
78 59 0.92
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (78 bp):
ACCTTCTTATGAACCTTCATCCCTAGCAGGAACTTCAACTGATACGAACCATCACTCCAGACAGC
AAGCCCCGTTTAC
Found at i:110608 original size:22 final size:22
Alignment explanation
Indices: 110578--110628 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
110568 CGGGATATAT
110578 ACAATATACAGAGGT-TATTCGGG
1 ACAA-ATACAGAGGTCT-TTCGGG
*
110601 ACAAATACATAGGTCTTTCGGG
1 ACAAATACAGAGGTCTTTCGGG
110623 ACAAAT
1 ACAAAT
110629 TTCACATGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (22 bp):
ACAAATACAGAGGTCTTTCGGG
Found at i:114506 original size:20 final size:20
Alignment explanation
Indices: 114481--114528 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
114471 TTTATATGTG
114481 TGCATAAGTACATGTTAGTA
1 TGCATAAGTACATGTTAGTA
*
114501 TGCATAAGTACATGTTAGTG
1 TGCATAAGTACATGTTAGTA
114521 TG-ATAAGT
1 TGCATAAGT
114529 TATGTAGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.35
Consensus pattern (20 bp):
TGCATAAGTACATGTTAGTA
Found at i:114933 original size:22 final size:22
Alignment explanation
Indices: 114908--114950 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
114898 ACATCGTAGC
*
114908 ACTGTTAACGGTACTATTCATT
1 ACTGGTAACGGTACTATTCATT
*
114930 ACTGGTCACGGTACTATTCAT
1 ACTGGTAACGGTACTATTCAT
114951 ATCGTATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (22 bp):
ACTGGTAACGGTACTATTCATT
Found at i:115670 original size:22 final size:22
Alignment explanation
Indices: 115639--115684 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
115629 CATATACAAT
115639 ATACAAAGGTCCTTCGGGAAAA
1 ATACAAAGGTCCTTCGGGAAAA
* *
115661 ATACATAGGTCCTTCGGGACAA
1 ATACAAAGGTCCTTCGGGAAAA
115683 AT
1 AT
115685 TTCACATGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (22 bp):
ATACAAAGGTCCTTCGGGAAAA
Found at i:118552 original size:85 final size:86
Alignment explanation
Indices: 118445--118604 Score: 268
Period size: 85 Copynumber: 1.9 Consensus size: 86
118435 TGAGTATGAT
* * *
118445 TTTGAAAAAAAATTAAACTTTAGAAACTAAAATAAGTCAAAATTGATAGTTTAAATACTAAACTA
1 TTTGAAAAAAAATAAAACTTTAGAAACTAAAATAAGTCAAAATTAATAGTTTAAATACTAAACGA
118510 GTAGTTTACCTTTGGGTATGG
66 GTAGTTTACCTTTGGGTATGG
* *
118531 TTTG-AAAAAAATAAAAGTTTAGATACTAAAATAAGTCAAAATTAATAGTTTAAATACTAAACGA
1 TTTGAAAAAAAATAAAACTTTAGAAACTAAAATAAGTCAAAATTAATAGTTTAAATACTAAACGA
118595 GTAGTTTACC
66 GTAGTTTACC
118605 AAAAAAAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 65 0.94
86 4 0.06
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (86 bp):
TTTGAAAAAAAATAAAACTTTAGAAACTAAAATAAGTCAAAATTAATAGTTTAAATACTAAACGA
GTAGTTTACCTTTGGGTATGG
Found at i:127142 original size:20 final size:21
Alignment explanation
Indices: 127117--127206 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 21
127107 TTTTCCCAAT
*
127117 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
127137 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* **
127158 TCGCAATGCG-A-TACTGACTA
1 TCGCAATGCGAATTA-AGAAAA
*
127178 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCGA-ATTAAGAAAA
127199 TCGCAATG
1 TCGCAATG
127207 AGATACTTAC
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
19 1 0.02
20 25 0.47
21 24 0.45
22 1 0.02
23 2 0.04
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:127181 original size:41 final size:41
Alignment explanation
Indices: 127154--127231 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
127144 GCGAATTGGG
* *
127154 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAATGAGATACTGACTATCGCAACGCGATAATAA
* *
127195 AAAATCGCAATGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAATGAGATACTGACTATCGCAACGCGATA
127232 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGCGATAATAA
Found at i:127224 original size:20 final size:20
Alignment explanation
Indices: 127199--127251 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
127189 TAATAAAAAA
* *
127199 TCGCAATGAGATACTTACTT
1 TCGCAACGAGATACTGACTT
*
127219 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
*
127239 TCGCAACGCGATA
1 TCGCAACGAGATA
127252 ATACATAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:127467 original size:22 final size:22
Alignment explanation
Indices: 127439--127482 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
127429 CACTCTCTCA
127439 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
127461 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
127483 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:127772 original size:20 final size:20
Alignment explanation
Indices: 127747--127784 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
127737 CGATTCTCTC
127747 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
127767 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
127785 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:129123 original size:18 final size:18
Alignment explanation
Indices: 129102--129147 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
129092 CTCCACTTCG
*
129102 AGAGCCATCACCTCGCCC
1 AGAGCCATCACCTCACCC
*
129120 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
129138 AGAGCCATCA
1 AGAGCCATCA
129148 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.13
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:129654 original size:20 final size:20
Alignment explanation
Indices: 129629--129681 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
129619 TAGTTTACTT
*
129629 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
129649 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
129669 TCGCAACGCGAAA
1 TCGCAACGCGAAA
129682 CGAAAATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:129690 original size:19 final size:19
Alignment explanation
Indices: 129648--129754 Score: 74
Period size: 14 Copynumber: 6.2 Consensus size: 19
129638 GAAAATGACT
* **
129648 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAACGAAA
129668 ATCGCAACGCGAAACGAAA
1 ATCGCAACGCGAAACGAAA
129687 ATCGCAA--CG--AC-AAA
1 ATCGCAACGCGAAACGAAA
* *
129701 ATCGCAATGCGAAATG-AA
1 ATCGCAACGCGAAACGAAA
129719 ATCGCAA--CG--AC-AAA
1 ATCGCAACGCGAAACGAAA
*
129733 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAACGAAA
129752 ATC
1 ATC
129755 CCAATGCGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
14 20 0.29
15 2 0.03
16 6 0.09
17 2 0.03
18 11 0.16
19 19 0.27
20 10 0.14
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAACGAAA
Found at i:129726 original size:32 final size:32
Alignment explanation
Indices: 129668--129751 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
129658 GGAAATGACT
*
129668 ATCGCAACGCGAAACGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
*
129701 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
129733 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
129752 ATCCCAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 34 0.71
33 14 0.29
ACGTcount: A:0.48, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:129794 original size:14 final size:14
Alignment explanation
Indices: 129775--129832 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
129765 TTGTGTTTCG
129775 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
129789 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
129805 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
129821 CGTTGCGATTTT
1 CGTTGCGATTTT
129833 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:129809 original size:32 final size:33
Alignment explanation
Indices: 129770--129848 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
129760 GCGATTTGTG
129770 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
129802 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
129835 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
129849 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:129847 original size:19 final size:19
Alignment explanation
Indices: 129789--129906 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
129779 GCGATTTTGT
129789 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
129807 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
129821 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
129840 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
129860 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
129879 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
129899 TGTTGCGA
1 CGTTGCGA
129907 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:131770 original size:14 final size:14
Alignment explanation
Indices: 131750--131827 Score: 95
Period size: 14 Copynumber: 5.6 Consensus size: 14
131740 GATTGTTTAA
131750 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
131764 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
**
131778 TTGATTTGTTTAA-
1 TTGATTTGTAAAAG
131791 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
131805 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
131819 TTGATTTGT
1 TTGATTTGT
131828 TTAATTGATG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
13 11 0.21
14 41 0.79
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:131782 original size:28 final size:28
Alignment explanation
Indices: 131750--131827 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
131740 GATTGTTTAA
* *
131750 TTGATTTGTAAAAGATGATTTGTAAATG
1 TTGATTTGTAAAAGTTGATTTGTAAAAG
**
131778 TTGATTTGTTTAA-TTGATTTGTAAAAG
1 TTGATTTGTAAAAGTTGATTTGTAAAAG
* *
131805 ATGATTTGTAAATGTTGATTTGT
1 TTGATTTGTAAAAGTTGATTTGT
131828 TTAATTGATG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (28 bp):
TTGATTTGTAAAAGTTGATTTGTAAAAG
Found at i:131790 original size:41 final size:41
Alignment explanation
Indices: 131738--131841 Score: 192
Period size: 41 Copynumber: 2.6 Consensus size: 41
131728 TTATTATTTT
131738 TTGA-TTGTTTAATTGATTTGTAAAAGATGATTTGTAAATG
1 TTGATTTGTTTAATTGATTTGTAAAAGATGATTTGTAAATG
131778 TTGATTTGTTTAATTGATTTGTAAAAGATGATTTGTAAATG
1 TTGATTTGTTTAATTGATTTGTAAAAGATGATTTGTAAATG
*
131819 TTGATTTGTTTAATTGATGTGTA
1 TTGATTTGTTTAATTGATTTGTA
131842 CATAATTTAT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
40 4 0.06
41 58 0.94
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (41 bp):
TTGATTTGTTTAATTGATTTGTAAAAGATGATTTGTAAATG
Found at i:131836 original size:27 final size:27
Alignment explanation
Indices: 131738--131841 Score: 74
Period size: 27 Copynumber: 3.9 Consensus size: 27
131728 TTATTATTTT
*
131738 TTGA-TTGTTTAA-TTGATTTGTAAAAG
1 TTGATTTGTTAAAGTTGATTTGT-AAAG
* *
131764 ATGATTTG-TAAATGTTGATTTGTTTAA-
1 TTGATTTGTTAAA-GTTGATTTG-TAAAG
* *
131791 TTGATTTGTAAAAGATGATTTGTAAATG
1 TTGATTTGTTAAAGTTGATTTGTAAA-G
* *
131819 TTGATTTGTTTAA-TTGATGTGTA
1 TTGATTTGTTAAAGTTGATTTGTA
131842 CATAATTTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
26 9 0.15
27 26 0.43
28 24 0.40
29 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (27 bp):
TTGATTTGTTAAAGTTGATTTGTAAAG
Found at i:131953 original size:14 final size:14
Alignment explanation
Indices: 131934--131987 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
131924 CGAAATGGTT
131934 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
131948 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
131967 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
131981 ATCGCAA
1 ATCGCAA
131988 TACGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:131960 original size:33 final size:33
Alignment explanation
Indices: 131915--131988 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
131905 AAAACAGGCT
* ***
131915 ATCGCAACGCGAAATGGTTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
131948 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
131981 ATCGCAAT
1 ATCGCAAT
131989 ACGATTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:131980 original size:19 final size:19
Alignment explanation
Indices: 131944--131980 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
131934 ATCGCAACGA
* *
131944 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
131963 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
131981 ATCGCAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:132036 original size:20 final size:20
Alignment explanation
Indices: 132011--132106 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
132001 TCGCATTGCG
* *
132011 ATTTTCTCGTTGCGATAATC
1 ATTTTCGCGTTGCGATAACC
*
132031 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAACC
132051 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
132071 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAACC
*
132091 ATTTTCGCATTGCGAT
1 ATTTTCGCGTTGCGAT
132107 TTTCTCGTTG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:132056 original size:40 final size:40
Alignment explanation
Indices: 132011--132106 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
132001 TCGCATTGCG
* *
132011 ATTTTCTCGTTGCGATAATCATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAACCATTTTCGCGTTGCGATAGCC
132051 ATTTTCGCGTTGCGATAACCATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAACCATTTTCGCGTTGCGATAGCC
*
132091 ATTTTCGCATTGCGAT
1 ATTTTCGCGTTGCGAT
132107 TTTCTCGTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.39
Consensus pattern (40 bp):
ATTTTCGCGTTGCGATAACCATTTTCGCGTTGCGATAGCC
Found at i:132116 original size:34 final size:35
Alignment explanation
Indices: 132031--132121 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 35
132021 TGCGATAATC
*
132031 ATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAA
1 ATTTTCGCGTTGCGATAGCCATTTTCGCATTGCG---A
132069 CCATTTTCGCGTTGCGATAGCCATTTTCGCATTGCG-
1 --ATTTTCGCGTTGCGATAGCCATTTTCGCATTGCGA
*
132105 ATTTTCTCGTTGCGATA
1 ATTTTCGCGTTGCGATA
132122 ACCTTTTGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
34 16 0.33
40 33 0.67
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.38
Consensus pattern (35 bp):
ATTTTCGCGTTGCGATAGCCATTTTCGCATTGCGA
Found at i:133078 original size:24 final size:24
Alignment explanation
Indices: 133051--133104 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
133041 GTATTCGAAA
* *
133051 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
133075 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
133099 TTTGAT
1 TTTGAT
133105 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:135607 original size:19 final size:19
Alignment explanation
Indices: 135585--135714 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
135575 GGAAATTACT
*
135585 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
135604 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
135618 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
135637 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
135651 TTCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
**
135669 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
135683 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
135702 ATCGCAACGCGAA
1 ATCGCAATGCGAA
135715 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 13, Indels: 32
0.65 0.10 0.25
Matches are distributed among these distances:
13 1 0.01
14 27 0.33
15 2 0.02
16 8 0.10
17 4 0.05
18 10 0.12
19 30 0.37
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:135632 original size:33 final size:33
Alignment explanation
Indices: 135585--135710 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
135575 GGAAATTACT
*
135585 ATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
135618 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
135650 TTTCGCAATGCGAAATG-AAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
135683 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
135711 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
32 27 0.33
33 55 0.67
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:135695 original size:65 final size:66
Alignment explanation
Indices: 135590--135717 Score: 231
Period size: 65 Copynumber: 2.0 Consensus size: 66
135580 TTACTATCGT
*
135590 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
135655 C
66 C
*
135656 AATGCGAAATG-AAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
135718 AATTTCGCGT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 49 0.82
66 11 0.18
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
C
Found at i:135740 original size:18 final size:19
Alignment explanation
Indices: 135714--135753 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
135704 CGCAACGCGA
135714 ATTTAA-TTTCGCGTTGAG
1 ATTTAATTTTCGCGTTGAG
* *
135732 ATTTCATTTTCGCGTTGCG
1 ATTTAATTTTCGCGTTGAG
135751 ATT
1 ATT
135754 CTCTCGTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.47
Consensus pattern (19 bp):
ATTTAATTTTCGCGTTGAG
Found at i:135908 original size:14 final size:14
Alignment explanation
Indices: 135889--135925 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
135879 CATCAATTAA
135889 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
135903 ACAAATCACCTTTT
1 ACAAATCAACTTTT
135917 ACAAATCAA
1 ACAAATCAA
135926 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:137294 original size:42 final size:42
Alignment explanation
Indices: 137248--137331 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
137238 CGATGACAGT
* * *
137248 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
137290 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
137332 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:139402 original size:33 final size:33
Alignment explanation
Indices: 139345--139443 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
139335 AACGAGATAT
*
139345 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
139379 GAGAATCGCAACGTGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
139412 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
139444 GCGAAATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:139484 original size:19 final size:19
Alignment explanation
Indices: 139321--139484 Score: 116
Period size: 19 Copynumber: 9.1 Consensus size: 19
139311 GTCTTTGGTT
* *
139321 GAAATGAAAATAGCAACGA
1 GAAATGAAAATCGCAACGC
* *
139340 GATATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
139359 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
139377 G--A-GAGAATCGCAACGT
1 GAAATGAAAATCGCAACGC
** *
139393 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
139411 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
139426 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
139446 GAAAT-AAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
139464 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
139483 GA
1 GA
139485 TTTTGGTTTC
Statistics
Matches: 114, Mismatches: 18, Indels: 26
0.72 0.11 0.16
Matches are distributed among these distances:
14 19 0.17
15 3 0.03
16 1 0.01
17 1 0.01
18 11 0.10
19 58 0.51
20 21 0.18
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:139513 original size:19 final size:19
Alignment explanation
Indices: 139480--139560 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
139470 AAAATCGCAA
**
139480 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
139499 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
139518 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
139532 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
139552 TGCGATTTT
1 TGCGATTTT
139561 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:140161 original size:20 final size:20
Alignment explanation
Indices: 140076--140169 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
140066 CGCTATGTAA
* *
140076 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGATAGTCAGT
*
140096 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
140116 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGT
*
140137 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
140157 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
140170 TTACTTATTC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:140517 original size:20 final size:20
Alignment explanation
Indices: 140494--140541 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
140484 TTATATTAAT
140494 ATTAAAAATTT-AGAGATAAA
1 ATTAAAAATTTAAGAG-TAAA
140514 ATTATAAAATTTAAGATGTAAA
1 ATTA-AAAATTTAAGA-GTAAA
140536 ATTAAA
1 ATTAAA
140542 TTATCAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.16
21 9 0.36
22 11 0.44
23 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
ATTAAAAATTTAAGAGTAAA
Found at i:140535 original size:22 final size:20
Alignment explanation
Indices: 140494--140541 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
140484 TTATATTAAT
140494 ATTAAAAATTTAGAGATAAA
1 ATTAAAAATTTAGAGATAAA
140514 ATTATAAAATTTA-AGATGTAAA
1 ATTA-AAAATTTAGAGA--TAAA
140536 ATTAAA
1 ATTAAA
140542 TTATCAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.28
21 10 0.40
22 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
ATTAAAAATTTAGAGATAAA
Found at i:141315 original size:21 final size:20
Alignment explanation
Indices: 141234--141315 Score: 53
Period size: 21 Copynumber: 4.0 Consensus size: 20
141224 CGCAAATCAG
141234 TTTCCAGATTCGCAACGCGAT
1 TTTCCA-ATTCGCAACGCGAT
141255 TCTTACC-A-TCGCATA-GCGAT
1 T-TT-CCAATTCGCA-ACGCGAT
* ***
141275 TTCCCAAATTCGCGTTGCGAT
1 TTTCC-AATTCGCAACGCGAT
141296 TTTCCTAATTCGCAACGCGA
1 TTTCC-AATTCGCAACGCGA
141316 ATACGTAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 12 0.26
21 27 0.59
22 2 0.04
23 2 0.04
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.30
Consensus pattern (20 bp):
TTTCCAATTCGCAACGCGAT
Found at i:141950 original size:21 final size:21
Alignment explanation
Indices: 141890--141968 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
141880 TTCTAAACTT
141890 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
141910 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
** *
141930 ACTATCGCGACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
141951 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
141969 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 29 0.58
21 21 0.42
ACGTcount: A:0.51, C:0.18, G:0.20, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:141972 original size:14 final size:14
Alignment explanation
Indices: 141953--142009 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
141943 GAGAAATGAA
141953 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
141967 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
141986 AATCGCAACGAGAG
1 AATCGCAACGAGAG
142000 AATCGCAACG
1 AATCGCAACG
142010 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:141982 original size:33 final size:33
Alignment explanation
Indices: 141945--142025 Score: 162
Period size: 33 Copynumber: 2.5 Consensus size: 33
141935 CGCGACGAGA
141945 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
141978 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
142011 GAAATGAAAATCGCA
1 GAAATGAAAATCGCA
142026 TTTGCGATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:142113 original size:40 final size:39
Alignment explanation
Indices: 142051--142155 Score: 156
Period size: 40 Copynumber: 2.6 Consensus size: 39
142041 TCGCATTGCG
*
142051 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCAATTTTC
* **
142090 ATTTCTCTCGTCGCGATAGTCATTTCCGCGTTGCAATTTTC
1 A-TTCTCTCGTTGCGATTTTCATTT-CGCGTTGCAATTTTC
142131 ATTCTCTCGTTGCGATTTTCATTTC
1 ATTCTCTCGTTGCGATTTTCATTTC
142156 AACCAAAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.04
40 40 0.70
41 15 0.26
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (39 bp):
ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCAATTTTC
Found at i:142141 original size:20 final size:20
Alignment explanation
Indices: 142051--142153 Score: 120
Period size: 20 Copynumber: 5.2 Consensus size: 20
142041 TCGCATTGCG
142051 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
142071 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* **
142090 ATTTCTCTCGTCGCGATAGTC
1 A-TTCTCTCGTTGCGATTTTC
* *
142111 ATT-TCCGCGTTGCAATTTTC
1 ATTCT-CTCGTTGCGATTTTC
142131 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
142151 ATT
1 ATT
142154 TCAACCAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
19 17 0.25
20 36 0.54
21 14 0.21
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:144039 original size:94 final size:93
Alignment explanation
Indices: 143848--144223 Score: 607
Period size: 94 Copynumber: 4.1 Consensus size: 93
143838 TCGATTGCTT
* *
143848 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
143909 ATTTGTCTTTTGTTTTGTATTTTGGTTGA
66 ATTTGTC-TTTGTTTTATCTTTTGGTTGA
143938 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
144003 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTATCTTTTGGTTG-A
*
144032 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
144097 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTATCTTTTGGTTG-A
* * * *
144126 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
144191 ATTTGTCTTTGTTTTATCTTTTGGTTGA
66 ATTTGTCTTTGTTTTATCTTTTGGTTGA
144219 AGTAA
1 AGTAA
144224 TGCAATCCAT
Statistics
Matches: 271, Mismatches: 10, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
90 35 0.13
92 3 0.01
93 26 0.10
94 207 0.76
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTATCTTTTGGTTGA
Found at i:144415 original size:33 final size:33
Alignment explanation
Indices: 144365--144464 Score: 112
Period size: 39 Copynumber: 2.8 Consensus size: 33
144355 ACTATAACCG
*
144365 CGTTGCG-TTTTTAATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTT-ATTTCGCGTTGCGATTCTCT
144398 CGTTGCGATTTTTATTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTTATTTCGCGTTGCG------ATTCTCT
*
144437 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTTATTTCGCGTTGCGAT
144465 AGTCATTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
33 21 0.36
34 5 0.09
39 32 0.55
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTTATTTCGCGTTGCGATTCTCT
Found at i:144442 original size:20 final size:19
Alignment explanation
Indices: 144398--144488 Score: 110
Period size: 19 Copynumber: 4.6 Consensus size: 19
144388 GCGATTCTCT
*
144398 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTCATTTCG
*
144417 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
144437 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
** *
144456 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCG
144477 CGTTGCGATTTT
1 CGTTGCGATTTT
144489 AAGTTCCAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 29 0.48
20 18 0.30
21 14 0.23
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:144445 original size:39 final size:39
Alignment explanation
Indices: 144391--144488 Score: 142
Period size: 39 Copynumber: 2.5 Consensus size: 39
144381 TCGCATTGCG
* **
144391 ATTCTCTCGTTGCGATTTTTATTTCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
144430 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
* *
144469 ATTTTTCACGTTGCGATTTT
1 A-TTCTCTCGTTGCGATTTT
144489 AAGTTCCAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 37 0.70
40 16 0.30
ACGTcount: A:0.12, C:0.20, G:0.18, T:0.49
Consensus pattern (39 bp):
ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
Found at i:146381 original size:14 final size:14
Alignment explanation
Indices: 146362--146397 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
146352 ATTATTTAAT
146362 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
146376 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
146390 TGATTTGT
1 TGATTTGT
146398 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:146563 original size:19 final size:19
Alignment explanation
Indices: 146504--146564 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
146494 AAAAATGACT
*
146504 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
146523 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
146537 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
146556 ATCGCAACG
1 ATCGCAACG
146565 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:146594 original size:33 final size:33
Alignment explanation
Indices: 146504--146583 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
146494 AAAAATGACT
* * *
146504 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
146537 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
146570 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
146584 CTAAATTCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:146611 original size:19 final size:18
Alignment explanation
Indices: 146589--146739 Score: 101
Period size: 19 Copynumber: 8.7 Consensus size: 18
146579 CGAAACTAAA
146589 TTCGCATTGCGATTTTCAT
1 TTCGC-TTGCGATTTTCAT
*
146608 TTCGCTTTGCGA--TTC-C
1 TTCGC-TTGCGATTTTCAT
*
146624 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
146641 TTCGCTTTGCGA--TTC-T
1 TTCGC-TTGCGATTTTCAT
*
146657 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
*
146674 TTCGCATTGCGATTCTC--
1 TTCGC-TTGCGATTTTCAT
146691 TT-G-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
**
146707 TTCGCATTGCGATAGTCAT
1 TTCGC-TTGCGATTTTCAT
146726 TTCCGCGTTGCGAT
1 TT-CGC-TTGCGAT
146740 AGACATTAAG
Statistics
Matches: 104, Mismatches: 12, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
14 22 0.21
16 16 0.15
17 16 0.15
19 40 0.38
20 10 0.10
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (18 bp):
TTCGCTTGCGATTTTCAT
Found at i:146637 original size:33 final size:33
Alignment explanation
Indices: 146595--146719 Score: 214
Period size: 33 Copynumber: 3.8 Consensus size: 33
146585 TAAATTCGCA
* *
146595 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
146628 TTGCGATTTTCATTTCGCTTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
146661 TTGCGATTTTCATTTCGCATTGCGATTCTCTTG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
146694 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
146720 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:146666 original size:14 final size:14
Alignment explanation
Indices: 146614--146701 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
146604 TCATTTCGCT
*
146614 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
146628 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
146645 CTTTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
146661 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
146678 CATTGCGATTCTCTTG
1 --TTGCGATTCTCTCG
146694 TTGCGATT
1 TTGCGATT
146702 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 13 0.22
17 13 0.22
19 12 0.21
ACGTcount: A:0.10, C:0.24, G:0.19, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:146738 original size:20 final size:20
Alignment explanation
Indices: 146693--146785 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 20
146683 CGATTCTCTT
**
146693 GTTGCGATTTTCATTT-CGC
1 GTTGCGATAGTCATTTCCGC
*
146712 ATTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTCCGC
* ** *
146732 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-C
*
146752 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGC
146773 GTTGCGATAGTCA
1 GTTGCGATAGTCA
146786 AATGAATGCC
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
19 16 0.28
20 26 0.46
21 12 0.21
22 3 0.05
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGC
Found at i:149526 original size:20 final size:20
Alignment explanation
Indices: 149502--149659 Score: 113
Period size: 21 Copynumber: 7.5 Consensus size: 20
149492 CAGAATCTCG
149502 TTGCGATTTACTAAATCGCA
1 TTGCGATTTACTAAATCGCA
*
149522 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTAC-TAAATCGCA
* * **
149542 ATGCGAATTAGGAAAATCGCA
1 TTGCGATTTA-CTAAATCGCA
* *
149563 ATGCGATTGTGAATACGTAATCGCA
1 TTGCGATT-T-ACTA---AATCGCA
* *
149588 TTGCGATTTTCCTAATTCGCA
1 TTGCGA-TTTACTAAATCGCA
149609 TTGCGATTTACGT-AATCGCA
1 TTGCGATTTAC-TAAATCGCA
* *
149629 TTGCGATTTTCCTAATTCGCA
1 TTGCGA-TTTACTAAATCGCA
149650 TTGCGATTTA
1 TTGCGATTTA
149660 GGAAAATCGC
Statistics
Matches: 111, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.04
20 40 0.36
21 47 0.42
22 2 0.02
23 1 0.01
24 2 0.02
25 13 0.12
26 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (20 bp):
TTGCGATTTACTAAATCGCA
Found at i:149607 original size:21 final size:21
Alignment explanation
Indices: 149583--149658 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
149573 GAATACGTAA
149583 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
149604 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
149624 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
149645 TCGCATTGCGATTT
1 TCGCATTGCGATTT
149659 AGGAAAATCG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.36
21 32 0.64
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:149633 original size:41 final size:41
Alignment explanation
Indices: 149576--149659 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
149566 CGATTGTGAA
149576 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
149617 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
149658 TA
1 TA
149660 GGAAAATCGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (41 bp):
TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
Found at i:151057 original size:12 final size:12
Alignment explanation
Indices: 151040--151064 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
151030 TATAATAATT
151040 TAAAATTTTTAG
1 TAAAATTTTTAG
151052 TAAAATTTTTAG
1 TAAAATTTTTAG
151064 T
1 T
151065 GGACGACTAC
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TAAAATTTTTAG
Found at i:151130 original size:17 final size:17
Alignment explanation
Indices: 151108--151143 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
151098 TACTATTAAC
151108 TTTGATTTAAATTGATG
1 TTTGATTTAAATTGATG
151125 TTTGATTTAAATTGATG
1 TTTGATTTAAATTGATG
151142 TT
1 TT
151144 AGCGTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (17 bp):
TTTGATTTAAATTGATG
Found at i:151434 original size:2 final size:2
Alignment explanation
Indices: 151427--151460 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
151417 CTCAACATAC
151427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
151461 TTTTGAAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:158191 original size:15 final size:16
Alignment explanation
Indices: 158171--158206 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
158161 AAAAATTAAG
158171 AAATT-ATAAAATGGA
1 AAATTAATAAAATGGA
*
158186 AAATTAATAAAATGTA
1 AAATTAATAAAATGGA
158202 AAATT
1 AAATT
158207 TTATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (16 bp):
AAATTAATAAAATGGA
Found at i:158203 original size:23 final size:23
Alignment explanation
Indices: 158162--158205 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
158152 TTTCTTTAAA
*
158162 AAAATTAAGAAATTATAAAATGG
1 AAAATTAAGAAAATATAAAATGG
* *
158185 AAAATTAATAAAATGTAAAAT
1 AAAATTAAGAAAATATAAAAT
158206 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (23 bp):
AAAATTAAGAAAATATAAAATGG
Found at i:165248 original size:14 final size:15
Alignment explanation
Indices: 165229--165259 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
165219 TCTCCTATAT
165229 ATTTAATTTAA-TCA
1 ATTTAATTTAATTCA
165243 ATTTAATTTAATTCA
1 ATTTAATTTAATTCA
165258 AT
1 AT
165260 GACTTCAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTAATTTAATTCA
Done.