Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005236.1 Hibiscus syriacus cultivar Beakdansim tig00011850_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: 53837
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1535 original size:66 final size:63
Alignment explanation
Indices: 1391--1617 Score: 276
Period size: 65 Copynumber: 3.5 Consensus size: 63
1381 TTTCTACTCA
*
1391 AAACAAATTTTGTATCTCTTGAGACAATTTCTCTTGAAACAAAATCTTTGATTATGTTTCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAATCTTTGA-TATGTTTCCTTG
1455 AAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACCAAAATCTTTGTATATGTTTCCCT
1 AAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAA-CAAAATCTTTG-ATATGTTT-CCT
1520 TG
62 TG
* * * * *
1522 AAACAAAGTTTGTCTCCCTTGAGA-AGTTTCTCTTGAAACACCAATCTTTGACATCGTTTTCCTT
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACA-AAATCTTTGATAT-G-TTTCCTT
1586 G
63 G
* * * * *
1587 AAACGAACTTCGTCTCGCTTGAGACAGTTTC
1 AAACAAATTTTGTCTCTCTTGAGACAATTTC
1618 CCTCGAATAA
Statistics
Matches: 145, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
64 9 0.06
65 81 0.56
66 45 0.31
67 10 0.07
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (63 bp):
AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAATCTTTGATATGTTTCCTTG
Found at i:1750 original size:39 final size:39
Alignment explanation
Indices: 1664--1748 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 39
1654 TTAAAACCAT
* * * *
1664 AAGATTTTATCTCGCTTGAGATTATTTCACTCGAAATAG
1 AAGATTTTATCTCACTTGAGATTAGTTCACTCGAAACAA
*
1703 AAGATTTTATCTCACTTGAGA-TAGTTCGCTCGAAACAA
1 AAGATTTTATCTCACTTGAGATTAGTTCACTCGAAACAA
1741 AAGATTTT
1 AAGATTTT
1749 TAGAAACTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 21 0.51
39 20 0.49
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCACTTGAGATTAGTTCACTCGAAACAA
Found at i:1939 original size:52 final size:53
Alignment explanation
Indices: 1750--1939 Score: 206
Period size: 52 Copynumber: 3.6 Consensus size: 53
1740 AAAGATTTTT
* * * *
1750 AGAAACTAAGCTTGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTAA
* * * *
1803 AGAAGCTAAGCCTAATTTT-AGTGTTTTCTTAATGTTTTCAAATGAATTTTAA
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTAA
* * * * * **
1855 AGAAATTAAGCCTAATTTTTA-AGGATTCTTGATGTTTTC-AATGATTTTTTT
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTAA
* *
1906 AGAAACTAAGCCTGATTTTCAGGGGTTCCTTGAT
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGAT
1940 AATGATTTTC
Statistics
Matches: 112, Mismatches: 23, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 27 0.24
52 68 0.61
53 17 0.15
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (53 bp):
AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTAA
Found at i:2383 original size:144 final size:144
Alignment explanation
Indices: 2123--2638 Score: 703
Period size: 144 Copynumber: 3.6 Consensus size: 144
2113 AGCAAAATGA
* ** * * *
2123 TAAGTCCTTCTGGCCATCCATAAGATATTCGAGCATGATGTTTTCAACATTTCCTTTGCTTGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
* **
2188 CACAACACTTCGAATTAGCAACACCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAC
66 CACAACACTTCGAATCAGCAATGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAC
2253 ACTTCGAATCAGCT
131 ACTTCGAATCAGCT
* * * * *
2267 TAAGTCCTTCGGGCCATCCATATGACCTTCGGGCAAGAAGTTTTCAATATTTCCTTTTCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
* * * *
2332 CACAACACTTTGAATCAGCAATGCCCCACTAGATGGGTTAACATTTCCTATTGATCGATTCACAC
66 CACAACACTTCGAATCAGCAATGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAC
*
2397 ACTTCGAAACAGCT
131 ACTTCGAATCAGCT
* ** * * *
2411 TAAGTCCTTCGTGCCATCCATAAGACCTTCGGGCAGGGCGTTTTCAATATTTTCTTTACTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
* * * * *
2476 CACAACACTTCGAATTAGTAATGCCCCACCATAGGGGTTAATATTTCCTATTGCTCAATTCACAC
66 CACAACACTTCGAATCAGCAATGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAC
*
2541 ACTTCAAATCAGCT
131 ACTTCGAATCAGCT
* *
2555 TAAGT-CTATTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTAGAT
1 TAAGTCCT-TCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGAT
*
2619 TCATAA-ACTTCGAATCAGCA
65 TCACAACACTTCGAATCAGCA
2639 TAAGTCCTTC
Statistics
Matches: 324, Mismatches: 47, Indels: 3
0.87 0.13 0.01
Matches are distributed among these distances:
143 14 0.04
144 310 0.96
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (144 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
CACAACACTTCGAATCAGCAATGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAC
ACTTCGAATCAGCT
Found at i:2664 original size:20 final size:20
Alignment explanation
Indices: 2639--2710 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
2629 CGAATCAGCA
2639 TAAGTCCTTCGAGCCATCAG
1 TAAGTCCTTCGAGCCATCAG
* *
2659 TAAGTCTTTCGAG--ATGAG
1 TAAGTCCTTCGAGCCATCAG
* *
2677 TAAGTTCTTCGGGCCATCAG
1 TAAGTCCTTCGAGCCATCAG
*
2697 TAAGTCTTTCGAGC
1 TAAGTCCTTCGAGC
2711 ATGATTCTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 14 0.34
20 27 0.66
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (20 bp):
TAAGTCCTTCGAGCCATCAG
Found at i:2681 original size:38 final size:39
Alignment explanation
Indices: 2639--2714 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
2629 CGAATCAGCA
2639 TAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAG-ATGAG
1 TAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGAG
* *
2677 TAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
1 TAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGA
2715 TTCTTAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 31 0.89
39 4 0.11
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (39 bp):
TAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGAG
Found at i:3974 original size:98 final size:99
Alignment explanation
Indices: 3860--4053 Score: 300
Period size: 98 Copynumber: 2.0 Consensus size: 99
3850 ATTCACGGCA
* * *
3860 TTTCGAATCAGTGACGCCTCTCTTGAGCAATAAATATTTCAAATGGAGAGTTCATAATGAGAAGA
1 TTTCGAATCAGTGACGCCTCGCTTGAGCAATAAACACTTCAAATGGAGAGTTCATAATGAGAAGA
3925 ACTCATCCGAAAAA-AAGAAGAAGTTCATACGAT
66 ACTCATCCGAAAAAGAAGAAGAAGTTCATACGAT
* ** *
3958 TTTCGATTCAGTGACGCCTCGCTTGAGGGATTAACACTTCAAATGGAGAGTTCATAATGAGAAGA
1 TTTCGAATCAGTGACGCCTCGCTTGAGCAATAAACACTTCAAATGGAGAGTTCATAATGAGAAGA
*
4023 ACTCATCCGAAAAAGGGAGAAGAAGTTCATA
66 ACTCATCCGAAAAA-GAAGAAGAAGTTCATA
4054 ATGAGAAAAG
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 72 0.84
100 14 0.16
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (99 bp):
TTTCGAATCAGTGACGCCTCGCTTGAGCAATAAACACTTCAAATGGAGAGTTCATAATGAGAAGA
ACTCATCCGAAAAAGAAGAAGAAGTTCATACGAT
Found at i:4265 original size:132 final size:134
Alignment explanation
Indices: 3982--4342 Score: 424
Period size: 132 Copynumber: 2.7 Consensus size: 134
3972 CGCCTCGCTT
* * *
3982 GAGGGATTAACACTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAA
1 GAGGGATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAACACATCCG-AAGA-GGAGAAGAA
* * * * * * ** *
4047 GTTCATAATGAGAAAAGCTTATTCAACTTATCGCTCGATTCACGACATTTCGAATCAGTGATACC
64 GTTCATAATGAGAAGAGCTTGTTCAACCTATCGCTCGATTCACAACACTTCAAATCAGCAACACC
* *
4112 TCGCTT
129 TCACTC
* * *
4118 GAGGGATTAACATTTCAAATAGAGAGTTCATAATGAGAATAACACATCCGACGAGG-G-AGAAGT
1 GAGGGATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAACACATCCGAAGAGGAGAAGAAGT
* * *
4181 TCATAATGAGAAGAGTTTGTTCAACCTATC-ATCTGATTTACAACACTTCAAATCAGCAACACCT
66 TCATAATGAGAAGAGCTTGTTCAACCTATCGCTC-GATTCACAACACTTCAAATCAGCAACACCT
4245 CACTC
130 CACTC
* * * *
4250 GAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAA-ATCATCCTATGAAGGAGAAGAA
1 GAGGGATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAACA-CATCCGAAG-AGGAGAAGAA
*
4314 GTTCATAATGAGAAGAACTTGTTCAACCT
64 GTTCATAATGAGAAGAGCTTGTTCAACCT
4343 CTCTTGTTTC
Statistics
Matches: 192, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
131 3 0.02
132 103 0.54
133 4 0.02
134 3 0.02
135 33 0.17
136 46 0.24
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (134 bp):
GAGGGATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAACACATCCGAAGAGGAGAAGAAGT
TCATAATGAGAAGAGCTTGTTCAACCTATCGCTCGATTCACAACACTTCAAATCAGCAACACCTC
ACTC
Found at i:10652 original size:21 final size:21
Alignment explanation
Indices: 10628--10673 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
10618 ACCCTATGGT
* *
10628 GGTGGCATCTGAACCGGTTGC
1 GGTGCCATCTGAAACGGTTGC
10649 GGTGCCATCTGAAACGGTTGC
1 GGTGCCATCTGAAACGGTTGC
10670 GGTG
1 GGTG
10674 TATCCATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.39, T:0.24
Consensus pattern (21 bp):
GGTGCCATCTGAAACGGTTGC
Found at i:13197 original size:2 final size:2
Alignment explanation
Indices: 13192--13253 Score: 70
Period size: 2 Copynumber: 30.0 Consensus size: 2
13182 AAACACACTC
* * * *
13192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT GAT CAA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT -AT AT
13236 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
13254 GATCAAATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
2 52 0.96
3 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13237 original size:26 final size:26
Alignment explanation
Indices: 13208--13264 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
13198 ATATATATAT
* * *
13208 ATATATATATATATGTGTGTGATCAA
1 ATATATATATATATATATATGATCAA
13234 ATATATATATATATATATATGATCAA
1 ATATATATATATATATATATGATCAA
13260 ATATA
1 ATATA
13265 GATTTTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (26 bp):
ATATATATATATATATATATGATCAA
Found at i:16675 original size:5 final size:5
Alignment explanation
Indices: 16667--16699 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
16657 TTAATTGATC
16667 GATTT GATTT GATTT GATTT GATTT GATTT GAT
1 GATTT GATTT GATTT GATTT GATTT GATTT GAT
16700 CTTAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (5 bp):
GATTT
Found at i:18382 original size:12 final size:12
Alignment explanation
Indices: 18270--18384 Score: 85
Period size: 12 Copynumber: 9.4 Consensus size: 12
18260 CTTCAAACAG
18270 ATTTT-ATATTTA
1 ATTTTAATA-TTA
18282 ATTTT-ATATT-
1 ATTTTAATATTA
* *
18292 ATATTTGATTTTA
1 AT-TTTAATATTA
18305 ATTTTAATATTA
1 ATTTTAATATTA
*
18317 ATTTT-TTAATTA
1 ATTTTAAT-ATTA
* *
18329 AATTAAATATTA
1 ATTTTAATATTA
18341 ATTTTTAATATTA
1 A-TTTTAATATTA
* *
18354 TATTATAGATATGA
1 -ATTTTA-ATATTA
18368 ATTTTAATATTA
1 ATTTTAATATTA
18380 ATTTT
1 ATTTT
18385 TTAAATAAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
10 2 0.02
11 6 0.07
12 47 0.57
13 21 0.26
14 6 0.07
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
ATTTTAATATTA
Found at i:18421 original size:64 final size:63
Alignment explanation
Indices: 18279--18438 Score: 238
Period size: 63 Copynumber: 2.6 Consensus size: 63
18269 GATTTTATAT
* * *
18279 TTAA-TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAATTAAATTAAATA
1 TTAATTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATAAAATA
*
18338 TTAATTTTTAATATTATATTATAGATATGAATTTTAATATTAATTTTTTAAATAAATAAAATA
1 TTAATTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATAAAATA
18401 TTAATTTTTTAATATTATATTATAGATATTTAATTTTA
1 TTAA-TTTTTAATATTATATTATAGATA-TTAATTTTA
18439 TATCATATAA
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
59 4 0.04
60 4 0.04
61 10 0.11
62 1 0.01
63 40 0.44
64 23 0.26
65 8 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (63 bp):
TTAATTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATAAAATA
Found at i:18493 original size:20 final size:19
Alignment explanation
Indices: 18433--18494 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
18423 TAGATATTTA
*
18433 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
18452 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
18470 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
18490 ATTTT
1 ATTTT
18495 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:18989 original size:31 final size:31
Alignment explanation
Indices: 18954--19013 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
18944 TAGTTGTATG
* *
18954 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
*
18985 AATTATTTAAATCTCATTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
19014 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:19945 original size:45 final size:44
Alignment explanation
Indices: 19883--20000 Score: 141
Period size: 45 Copynumber: 2.7 Consensus size: 44
19873 AAAAATGCTA
*
19883 CAAAAGGTTAGGTCATTTAGTAGCGTTTTTTGGAACAACCGACG
1 CAAAAGGTTAGGTCATTTAGTAGCGTTTTTTGGAACAAACGACG
* * * * *
19927 CAAAAAGGTTATGTCATTTTGTGGCG-TTTTGGGAACAAACGTCG
1 C-AAAAGGTTAGGTCATTTAGTAGCGTTTTTTGGAACAAACGACG
* *
19971 CAAAAGG-TAGGTAATTTAGTAGCATTTTTT
1 CAAAAGGTTAGGTCATTTAGTAGCGTTTTTT
20001 AAAGTAAAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
42 12 0.20
43 10 0.17
44 17 0.28
45 21 0.35
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.33
Consensus pattern (44 bp):
CAAAAGGTTAGGTCATTTAGTAGCGTTTTTTGGAACAAACGACG
Found at i:20011 original size:44 final size:42
Alignment explanation
Indices: 19963--20053 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 42
19953 TTTTGGGAAC
*
19963 AAACGTCGCAAAAGGTAGGTAATTTAGTAGCATTTTTTAAAGTA
1 AAACGTCGCAAAAAGTAGGTAATTTAGTAGCA-TTTTT-AAGTA
*
20007 AAACGTCGCAAAAAGTAGGTAATTTAGTGGCATTTTTAAGTA
1 AAACGTCGCAAAAAGTAGGTAATTTAGTAGCATTTTTAAGTA
20049 AAACG
1 AAACG
20054 CCACAATTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 10 0.22
43 5 0.11
44 30 0.67
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (42 bp):
AAACGTCGCAAAAAGTAGGTAATTTAGTAGCATTTTTAAGTA
Found at i:20924 original size:185 final size:185
Alignment explanation
Indices: 20607--20996 Score: 669
Period size: 185 Copynumber: 2.1 Consensus size: 185
20597 AACCGAAATT
* *
20607 AAATTTTAAATATATTATATATAACATATGGGCTTAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
* *
20672 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAATTATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATATTATATAAAATTT
20737 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTATTTTGAATT-AA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTT-TTTTGAATTAAA
*
20792 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCGAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
*
20857 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAA-ATTTATATAAAATT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATA-TTATATAAAATT
20921 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTAAA
* *
20977 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
20997 AATTCGAAAT
Statistics
Matches: 195, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
184 18 0.09
185 177 0.91
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTAAA
Found at i:23289 original size:42 final size:41
Alignment explanation
Indices: 23127--23403 Score: 142
Period size: 42 Copynumber: 6.6 Consensus size: 41
23117 CAAGATGACG
* ** * * *
23127 TTTTAATAACAAATGCCACTAAAATACGACTCAATTGTGAC
1 TTTTAATAACAAACGCCACTAAGGTACGAATCTATTGTGGC
* * ** ** *
23168 ATTTTAATAACAAACTCCACTAACGTGTGCTTCTACTGTGATG-
1 -TTTTAATAACAAACGCCACTAAGGTACGAATCTATTGTG--GC
* * ** * ** * *
23211 TTTCAACAACAAACGCCACTAACATGCGCCTATATTGCGGC
1 TTTTAATAACAAACGCCACTAAGGTACGAATCTATTGTGGC
*
23252 ATTTTAATAATAAACGCCACTAAGGTACGAATCTATTGTGGC
1 -TTTTAATAACAAACGCCACTAAGGTACGAATCTATTGTGGC
* * * **
23294 GTTTTAGTAACAAGCGCCACTAAGGTTCGCCTCTATTGTGGTC
1 -TTTTAATAACAAACGCCACTAAGGTACGAATCTATTGTGG-C
* * * ** * * *
23337 TTTTTATAACAGATGCCACTAAGGTACGGCTCTGTAGTGTC
1 TTTTAATAACAAACGCCACTAAGGTACGAATCTATTGTGGC
* *
23378 ATTTTAGTGACAAACGCCACTAAGGT
1 -TTTTAATAACAAACGCCACTAAGGT
23404 TCTCCTCTAT
Statistics
Matches: 177, Mismatches: 52, Indels: 12
0.73 0.22 0.05
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 174 0.98
43 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (41 bp):
TTTTAATAACAAACGCCACTAAGGTACGAATCTATTGTGGC
Found at i:23306 original size:84 final size:84
Alignment explanation
Indices: 23218--23400 Score: 197
Period size: 84 Copynumber: 2.2 Consensus size: 84
23208 ATGTTTCAAC
*
23218 AACAAACGCCACTAACATGCGCCTATATTGCGG-CATTTTAATAATAAACGCCACTAAGGTACGA
1 AACAAACGCCACTAACATGCGCCTATATTGCGGTC-TTTTAATAACAAACGCCACTAAGGTACGA
* *
23282 ATCTATTGTGGCGTTTTAGT
65 ATCTATAGTGGCATTTTAGT
* ** * * * * * * **
23302 AACAAGCGCCACTAAGGTTCGCCTCTATTGTGGTCTTTTTATAACAGATGCCACTAAGGTACGGC
1 AACAAACGCCACTAACATGCGCCTATATTGCGGTCTTTTAATAACAAACGCCACTAAGGTACGAA
* *
23367 TCTGTAGTGTCATTTTAGT
66 TCTATAGTGGCATTTTAGT
*
23386 GACAAACGCCACTAA
1 AACAAACGCCACTAA
23401 GGTTCTCCTC
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
84 79 0.99
85 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (84 bp):
AACAAACGCCACTAACATGCGCCTATATTGCGGTCTTTTAATAACAAACGCCACTAAGGTACGAA
TCTATAGTGGCATTTTAGT
Found at i:30453 original size:20 final size:19
Alignment explanation
Indices: 30426--30487 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 19
30416 CATTTTGGTG
30426 CAGAGGGAATCGATCCCCC
1 CAGAGGGAATCGATCCCCC
*
30445 CATGAGGGAACCGATTCCCCC
1 CA-GAGGGAATCGA-TCCCCC
*
30466 CACAGGGGAATCGATACCCCC
1 CAGA-GGGAATCGAT-CCCCC
30487 C
1 C
30488 TGGGGTTCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.06
20 12 0.33
21 22 0.61
ACGTcount: A:0.26, C:0.39, G:0.24, T:0.11
Consensus pattern (19 bp):
CAGAGGGAATCGATCCCCC
Found at i:30465 original size:21 final size:20
Alignment explanation
Indices: 30428--30467 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
30418 TTTTGGTGCA
*
30428 GAGGGAATCGATCCCCCCAT
1 GAGGGAACCGATCCCCCCAT
30448 GAGGGAACCGATTCCCCCCA
1 GAGGGAACCGA-TCCCCCCA
30468 CAGGGGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCAT
Found at i:35284 original size:30 final size:30
Alignment explanation
Indices: 35250--35308 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
35240 TAATACGTGG
* * *
35250 GAGGTGGAGGTGATTTGTAGACGTATGGAC
1 GAGGTGGAGGTGACTTGTACACATATGGAC
*
35280 GAGGTGGGGGTGACTTGTACACATATGGA
1 GAGGTGGAGGTGACTTGTACACATATGGA
35309 GACGGAGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.42, T:0.25
Consensus pattern (30 bp):
GAGGTGGAGGTGACTTGTACACATATGGAC
Found at i:35338 original size:60 final size:59
Alignment explanation
Indices: 35272--35576 Score: 205
Period size: 60 Copynumber: 5.1 Consensus size: 59
35262 ATTTGTAGAC
* *
35272 GTATGGACGAGGTGGGGGTGACTTGTACACATATGGA-GACGGAGGTGGTGATTCATACTT
1 GTATGGA-GAGGTAGGGGTGACTTGTACACATATGGAGGA-GGAGGAGGTGATTCATACTT
* * * * *
35332 GTATGGAGATGGTAGAGGTGATTTGTATACATATGAAGGAGGAGGCA-GTGACTTGTATAC--
1 GTATGGAGA-GGTAGGGGTGACTTGTACACATATGGAGGAGGAGG-AGGTGA-TT-CATACTT
* *** * ** *
35392 ATAT-G-GAGGTCCTGATGA-TTCGTACTTATATGGAGGAGGAGGAGGTGATTCATATTT
1 GTATGGAGAGGTAGGGGTGACTT-GTACACATATGGAGGAGGAGGAGGTGATTCATACTT
* ** * * * *
35449 GTATGGTGGAGGTAGGAATGATTTGTACAGATATGGAGGTGGAGGTA-GTGATTCATGCTT
1 GTATGG-AGAGGTAGGGGTGACTTGTACACATATGGAGGAGGAGG-AGGTGATTCATACTT
* ** **
35509 GTATGGTAGAGGT-GGTGGTGACTTGTATACATACAGAGGAGGAGGAGGTGATTTGTACTT
1 GTATGG-AGAGGTAGG-GGTGACTTGTACACATATGGAGGAGGAGGAGGTGATTCATACTT
35569 GTATGGAG
1 GTATGGAG
35577 GAGGCGGCGA
Statistics
Matches: 189, Mismatches: 40, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
55 3 0.02
56 5 0.03
57 31 0.16
58 3 0.02
59 8 0.04
60 128 0.68
61 7 0.04
62 4 0.02
ACGTcount: A:0.26, C:0.08, G:0.37, T:0.30
Consensus pattern (59 bp):
GTATGGAGAGGTAGGGGTGACTTGTACACATATGGAGGAGGAGGAGGTGATTCATACTT
Found at i:35550 original size:90 final size:90
Alignment explanation
Indices: 35456--35670 Score: 213
Period size: 90 Copynumber: 2.4 Consensus size: 90
35446 TTTGTATGGT
* *
35456 GGAGGTAGGA-ATGATTTGTAC-AGATATGGAGGTGGAGGTAG-TGATTCATGCTTGTATGGTA-
1 GGAGG-AGGAGATGATTTGTACTAG-TATGGAGGAGGAGG-AGATGATTCATACTTGTATGG-AG
* *
35517 GAGGTGGTGGTGACTTGTATACATACAGA
62 GAGGTGGGGGTGACTTGTACACATACAGA
* * * * *
35546 GGAGGAGGAGGTGATTTGTACTTGTATGGAGGAGGCGGCGATGATTCATATTTGTATGGAGGAGG
1 GGAGGAGGAGATGATTTGTACTAGTATGGAGGAGGAGGAGATGATTCATACTTGTATGGAGGAGG
**
35611 TGGGGGTGACTTGTACACATATGGA
66 TGGGGGTGACTTGTACACATACAGA
* * * * * *
35636 GGTGGAGGTGGTAATTCGTACTTGTATGGAGGAGG
1 GGAGGAGGAGATGATTTGTACTAGTATGGAGGAGG
35671 TGGTGGTGAC
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
89 6 0.06
90 99 0.93
91 1 0.01
ACGTcount: A:0.24, C:0.07, G:0.40, T:0.29
Consensus pattern (90 bp):
GGAGGAGGAGATGATTTGTACTAGTATGGAGGAGGAGGAGATGATTCATACTTGTATGGAGGAGG
TGGGGGTGACTTGTACACATACAGA
Found at i:35727 original size:150 final size:150
Alignment explanation
Indices: 35407--35986 Score: 474
Period size: 150 Copynumber: 3.9 Consensus size: 150
35397 GAGGTCCTGA
* * * * * **
35407 TGATTCGTACTTATATGGAGGAGGAGGAGGTGATTCATATTTGTATGGTGGAGGTAGGAATGATT
1 TGATTTGTACTTGTACGGAGGAGGAGGAGGTGATTCATATTTGTATGGAGGAGGTGGGGGTGATT
* *
35472 TGTACAGATATGGAGGTGGAGGTAGTGATTCATGCTTGTATGGTA-GAGGTGGTGGTGACTTGTA
66 TGTACACATATGGAGGTGGAGGTAGTGATTCATACTTGTATGG-AGGAGGTGGTGGTGACTTGTA
* *
35536 TACATA-CAGAGGAGGAGGA-GG
130 CACATATGA-AGGAGGA-GATGG
* * * * *
35557 TGATTTGTACTTGTATGGAGGAGGCGGCGATGATTCATATTTGTATGGAGGAGGTGGGGGTGACT
1 TGATTTGTACTTGTACGGAGGAGGAGGAGGTGATTCATATTTGTATGGAGGAGGTGGGGGTGATT
* * *
35622 TGTACACATATGGAGGTGGAGGTGGTAATTCGTACTTGTATGGAGGAGGTGGTGGTGACTTGTAC
66 TGTACACATATGGAGGTGGAGGTAGTGATTCATACTTGTATGGAGGAGGTGGTGGTGACTTGTAC
*
35687 ACGTATGAAGGAGGAGATGG
131 ACATATGAAGGAGGAGATGG
* * * * *** * *
35707 TGATTTGTA-TATGTACGGAGGTGGTGGTGGTGACTT-GTATACATATGGAGGAGGAGGTGGTGA
1 TGATTTGTACT-TGTACGGAGGAGGAGGAGGTGA-TTCATATTTGTATGGAGGAGGTGGGGGTGA
*** * * *
35770 TTTGTACTTGTATGGAGGAGGATGTAGTGATTCATATTTGTAT-GAGGAAGGTGG-GAGTGACTT
64 TTTGTACACATATGGAGGTGGAGGTAGTGATTCATACTTGTATGGAGG-AGGTGGTG-GTGACTT
* * *
35833 GTACACATATGGAGGTGGAGTTGG
127 GTACACATATGAAGGAGGAGATGG
* * * * * * * * ** * * * *
35857 TGATTCGTAGTTGTATGGAAGAGGTGGTGGTGACTT-GTACTCATATAGAAGAGGAGGTGGTGAT
1 TGATTTGTACTTGTACGGAGGAGGAGGAGGTGA-TTCATATTTGTATGGAGGAGGTGGGGGTGAT
* ** * * * * * * *
35921 TTGTATATGTATGGAGGTGGTGGTGGTGACTCATAATTGTACGGAGGTGGTGGTGGTGATTTGTA
65 TTGTACACATATGGAGGTGGAGGTAGTGATTCATACTTGTATGGAGGAGGTGGTGGTGACTTGTA
35986 C
130 C
35987 TTGTATGGAG
Statistics
Matches: 358, Mismatches: 62, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
149 9 0.03
150 340 0.95
151 9 0.03
ACGTcount: A:0.23, C:0.06, G:0.39, T:0.31
Consensus pattern (150 bp):
TGATTTGTACTTGTACGGAGGAGGAGGAGGTGATTCATATTTGTATGGAGGAGGTGGGGGTGATT
TGTACACATATGGAGGTGGAGGTAGTGATTCATACTTGTATGGAGGAGGTGGTGGTGACTTGTAC
ACATATGAAGGAGGAGATGG
Found at i:36144 original size:30 final size:30
Alignment explanation
Indices: 35633--36628 Score: 513
Period size: 30 Copynumber: 33.1 Consensus size: 30
35623 GTACACATAT
* * *
35633 GGAGGTGGAGGTGGTAATTCGTACTTGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * ** *
35663 GGAGGAGGTGGTGGTGACTTGTACACGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * * *
35693 GAAGGAGGAGATGGTGATTTGTA-TATGTAC
1 GGAGGTGGAGGTGGTGACTCGTACT-TGTAC
* * ** *
35723 GGAGGTGGTGGTGGTGACTTGTA-TACATAT
1 GGAGGTGGAGGTGGTGACTCGTACT-TGTAC
* * * *
35753 GGAGGAGGAGGTGGTGATTTGTACTTGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * * * *
35783 GGAGGAGGATGTAGTGATTCATATTTGTA-
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * * *** *
35812 TGAGGAAGGTGG-GAGTGACTTGTACACATAT
1 GGAGG-TGGAGGTG-GTGACTCGTACTTGTAC
* * * *
35843 GGAGGTGGAGTTGGTGATTCGTAGTTGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * * ** *
35873 GGAAGAGGTGGTGGTGACTTGTACTCATAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * * * *
35903 AGAAGAGGAGGTGGTGATTTGTA-TATGTAT
1 GGAGGTGGAGGTGGTGACTCGTACT-TGTAC
* * *
35933 GGAGGTGGTGGTGGTGACTCATAATTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * *
35963 GGAGGTGGTGGTGGTGATTTGTACTTGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * *
35993 GGAGGTGGAGGTGGTAACTCGTAATTGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * ** * * * *
36023 GGGGGAGGTGGCAGCGATTTGTTCTTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
** * * *
36053 ATAGAAT-GAGGTGGTGGCTCATACTTGTAC
1 GGAG-GTGGAGGTGGTGACTCGTACTTGTAC
* * *
36083 GGAGGT-G-GG-GGTGACTTGTATTTGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * *
36110 AGAGGTGAAGGTGGAGACTCATACTTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * *
36140 AGAGGTGAAGGTGGAGACTCATACTTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * *
36170 GGAGGTGGTGGTGGTGACTTGTACTGGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
36200 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * * * *
36230 GGAGGAGGTGGTGGCGACTTGTATTTGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * *
36260 GGAGCTGGAGGTGGGGACTCATACTTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* * *
36290 GGAGGTGGTGGTGGTGACTTGTACTTGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* *
36320 GGAGGCGGAGGTGGTTACTCGTACTTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
** * *
36350 GGAGGAAGAGGTGGTGACTTGTACTTGTAT
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
*
36380 GGAGGTGAAGGTGGTGACTCGTACTTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
** * * * *
36410 GGAGGAAGAGGTGGTGGCTTGTATTTGTATGGAG
1 GGAGGTGGAGGTGGTGACTCGTACTTG--T--AC
* * *
36444 GTAGAGGTGGAGGTGGAGACTCATACTTATAC
1 G--GAGGTGGAGGTGGTGACTCGTACTTGTAC
* * * *
36476 -GATGGTGGTGGTGGAGACTTGTACTTGTAT
1 GGA-GGTGGAGGTGGTGACTCGTACTTGTAC
* * *
36506 GGAGGTGGAGGTGGAGACTCATACTTGTAA
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
** * * *
36536 GGAGGAAGAGGCGGTGACTCATATTTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
* *** *
36566 AGA-GAAAATGGTGGTGACT-TTACTTGTAC
1 GGAGGTGGA-GGTGGTGACTCGTACTTGTAC
** *
36595 GGAGGTGGAGGTGAAGACTCATACTTGTAC
1 GGAGGTGGAGGTGGTGACTCGTACTTGTAC
36625 GGAG
1 GGAG
36629 ACGTTGGTGG
Statistics
Matches: 727, Mismatches: 216, Indels: 46
0.74 0.22 0.05
Matches are distributed among these distances:
27 18 0.02
28 2 0.00
29 33 0.05
30 642 0.88
31 9 0.01
32 2 0.00
34 3 0.00
36 18 0.02
ACGTcount: A:0.22, C:0.09, G:0.39, T:0.30
Consensus pattern (30 bp):
GGAGGTGGAGGTGGTGACTCGTACTTGTAC
Found at i:36438 original size:90 final size:90
Alignment explanation
Indices: 35480--36453 Score: 631
Period size: 90 Copynumber: 10.9 Consensus size: 90
35470 TTTGTACAGA
* * * * * * **
35480 TATGGAGGTGGAGGTAGTGATTCATGCTTGTATGGTA-GAGGTGGTGGTGACTTGTA-TACATAC
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGG-AGGAGGAGGTGGTGACTTGTACT-TGTAC
* * * *
35543 AGAGGAGGAGGAGGTGATTTGTACTTG
64 GGAGGTGGAGGTGGTGACTTGTACTTG
* * * * * * * * * * *** *
35570 TATGGAGGAGGCGGCGATGATTCATATTTGTATGGAGGAGGTGGGGGTGACTTGTACACATATGG
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACTTGTACGG
*
35635 AGGTGGAGGTGGT-AATTCGTACTTG
66 AGGTGGAGGTGGTGACTT-GTACTTG
* * * ** * * * *
35660 TATGGAGGAGGTGGTGGTGACTTGTACACGTATGAAGGAGGAGATGGTGATTTGTA-TATGTACG
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACT-TGTACG
* **
35724 GAGGTGGTGGTGGTGACTTGTA-TACA
65 GAGGTGGAGGTGGTGACTTGTACT-TG
* * * * * * * * *
35750 TATGGAGGAGGAGGTGGTGATTTGTACTTGTATGGAGGAGGATGTAGTGA-TTCATATTTGTA-T
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTT-GTACTTGTACG
* * ***
35813 GAGGAAGGTGG-GAGTGACTTGTACACA
65 GAGG-TGGAGGTG-GTGACTTGTACTTG
* * * * * * ** **
35840 TATGGAGGTGGAGTTGGTGATTCGTAGTTGTATGGAAGAGGTGGTGGTGACTTGTACTCATATAG
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACTTGTACGG
* * *
35905 AAGAGGAGGTGGTGATTTGTA-TATG
66 AGGTGGAGGTGGTGACTTGTACT-TG
* * * * * * *
35930 TATGGAGGTGGTGGTGGTGACTCATAATTGTACGGAGGTGGTGGTGGTGATTTGTACTTGTATGG
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACTTGTACGG
* * *
35995 AGGTGGAGGTGGTAACTCGTAATTG
66 AGGTGGAGGTGGTGACTTGTACTTG
* * * ** * * * * ** * * * **
36020 TATGGGGGAGGTGGCAGCGATTTGTTCTTGTACATAGAATGAGGTGGTGGCTCATACTTGTACGG
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACTTGTACGG
*
36085 AGGT-G-GG-GGTGACTTGTATTTG
66 AGGTGGAGGTGGTGACTTGTACTTG
* * * * * * * * **
36107 TATAGAGGTGAAGGTGGAGACTCATACTTGTACAGAGGTGAAGGTGGAGACTCATACTTGTACGG
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACTTGTACGG
* *
36172 AGGTGGTGGTGGTGACTTGTACTGG
66 AGGTGGAGGTGGTGACTTGTACTTG
* * * *
36197 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGTGGTGGCGACTTGTATTTGTATGG
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACTTGTACGG
* * **
36262 AGCTGGAGGTGGGGACTCATACTTG
66 AGGTGGAGGTGGTGACTTGTACTTG
* * * * * * *
36287 TACGGAGGTGGTGGTGGTGACTTGTACTTGTATGGAGGCGGAGGTGGTTACTCGTACTTGTACGG
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACTTGTACGG
**
36352 AGGAAGAGGTGGTGACTTGTACTTG
66 AGGTGGAGGTGGTGACTTGTACTTG
* * * * *
36377 TATGGAGGTGAAGGTGGTGACTCGTACTTGTACGGAGGAAGAGGTGGTGGCTTGTATTTGTATGG
1 TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACTTGTACGG
*
36442 AGGTAGAGGTGG
66 AGGTGGAGGTGG
36454 AGGTGGAGAC
Statistics
Matches: 687, Mismatches: 178, Indels: 38
0.76 0.20 0.04
Matches are distributed among these distances:
87 62 0.09
88 3 0.00
89 15 0.02
90 596 0.87
91 11 0.02
ACGTcount: A:0.21, C:0.08, G:0.40, T:0.30
Consensus pattern (90 bp):
TATGGAGGTGGAGGTGGTGACTCGTACTTGTACGGAGGAGGAGGTGGTGACTTGTACTTGTACGG
AGGTGGAGGTGGTGACTTGTACTTG
Found at i:42205 original size:43 final size:42
Alignment explanation
Indices: 42139--42474 Score: 305
Period size: 43 Copynumber: 7.9 Consensus size: 42
42129 GTTTTTTAAA
* *
42139 AAAAACGCCGCAATGGGTATTGATATTTAGCGGCGTTTGTCAC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCAC
*
42182 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCAC
* * *
42225 AAAAATGCCACAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCAC
* * * * *
42268 AAAAACACCGCAATATGTGTAGATATTTAGCGGCGTTTTTAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCAC
* * * * *
42310 ACAAATGCCGCAATAGGT-TATGATGTTTAGCGGTGTTTTTATC
1 AAAAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTTCA-C
* * * * * *
42353 TAAAACACCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCAC
* * * * * * *
42395 ACAAACGCCGCAGTAGATTTTGATGTTTTGCGGCGTTTTTCTC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCG-TTTTCAC
* * * * *
42438 ACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTT
42475 AAGGTCTGTA
Statistics
Matches: 252, Mismatches: 37, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.00
42 67 0.27
43 183 0.73
44 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (42 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCAC
Found at i:42360 original size:85 final size:83
Alignment explanation
Indices: 42145--42474 Score: 300
Period size: 85 Copynumber: 3.9 Consensus size: 83
42135 TAAAAAAAAC
* * * * *
42145 GCCGCAATGGGTATTGATATTTAGCGGCGTTTGTCACAAAAACGCCGCAATAGGTGTTGATATTT
1 GCCGCAATAGGT-TTGATGTTTAGCGGCGTTT-TTATAAAAACACCGCAATAGGTGTTGATATTT
* *
42210 AGCGGCGTTTGTCATAAAAAT
64 AGCGGCGTTT-TCACACAAAT
* * * * *
42231 GCCACAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACACCGCAATATGTGTAGATATTT
1 GCCGCAATAGGT-TTGATGTTTAGCGGCGTTT-TTATAAAAACACCGCAATAGGTGTTGATATTT
* *
42296 AGCGGCGTTTTTAGACAAAT
64 AGCGGCGTTTTCACACAAAT
* * * *
42316 GCCGCAATAGGTTATGATGTTTAGCGGTGTTTTTATCTAAAACACCGCAGTAGGTGTTGATGTTT
1 GCCGCAATAGGTT-TGATGTTTAGCGGCGTTTTTAT-AAAAACACCGCAATAGGTGTTGATATTT
* * *
42381 TGCGGCGTTTTCCCACAAAC
64 AGCGGCGTTTTCACACAAAT
* * * * * * * * *
42401 GCCGCAGTAGATTTTGATGTTTTGCGGCGTTTTTCTCACAAACGCCGCAGTAGGTATTGATGTTT
1 GCCGCAATAG-GTTTGATGTTTAGCGGCGTTTTTAT-AAAAACACCGCAATAGGTGTTGATATTT
*
42466 TGCGGCGTT
64 AGCGGCGTT
42475 AAGGTCTGTA
Statistics
Matches: 208, Mismatches: 33, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
84 4 0.02
85 134 0.64
86 70 0.34
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (83 bp):
GCCGCAATAGGTTTGATGTTTAGCGGCGTTTTTATAAAAACACCGCAATAGGTGTTGATATTTAG
CGGCGTTTTCACACAAAT
Found at i:42895 original size:21 final size:21
Alignment explanation
Indices: 42869--42937 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
42859 CTGCTAATAT
42869 GCTGCTTCTCTCTGTGCTGCC
1 GCTGCTTCTCTCTGTGCTGCC
* *
42890 GTTGCTTCTCTTTGTGCTGCC
1 GCTGCTTCTCTCTGTGCTGCC
* * *
42911 GCTGCTTCTTTCTCTGCTTCC
1 GCTGCTTCTCTCTGTGCTGCC
42932 GCTGCT
1 GCTGCT
42938 GCTTTGGCTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.00, C:0.35, G:0.22, T:0.43
Consensus pattern (21 bp):
GCTGCTTCTCTCTGTGCTGCC
Found at i:42948 original size:21 final size:21
Alignment explanation
Indices: 42904--42951 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
42894 CTTCTCTTTG
* *
42904 TGCTGCCGCTGCTTCTTTCTC
1 TGCTGCCGCTGCTGCTTTCGC
* *
42925 TGCTTCCGCTGCTGCTTTGGC
1 TGCTGCCGCTGCTGCTTTCGC
42946 TGCTGC
1 TGCTGC
42952 TCTCTCTGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.00, C:0.35, G:0.25, T:0.40
Consensus pattern (21 bp):
TGCTGCCGCTGCTGCTTTCGC
Found at i:42950 original size:42 final size:42
Alignment explanation
Indices: 42869--42951 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
42859 CTGCTAATAT
* * * *
42869 GCTGCTTCTCTCTGTGCTGCCGTTGCTTCTCTTTGTGCTGCC
1 GCTGCTTCTCTCTCTGCTGCCGCTGCTGCTCTTGGTGCTGCC
* *
42911 GCTGCTTCTTTCTCTGCTTCCGCTGCTGCT-TTGGCTGCTGC
1 GCTGCTTCTCTCTCTGCTGCCGCTGCTGCTCTTGG-TGCTGC
42952 TCTCTCTGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 3 0.09
42 31 0.91
ACGTcount: A:0.00, C:0.34, G:0.24, T:0.42
Consensus pattern (42 bp):
GCTGCTTCTCTCTCTGCTGCCGCTGCTGCTCTTGGTGCTGCC
Found at i:49588 original size:28 final size:28
Alignment explanation
Indices: 49548--49607 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
49538 TTCAGCGATG
*
49548 AAGGTTTAAGAGGATCAAAATTCGCCGT
1 AAGGTTTAAGAGGATCAAAATTCACCGT
49576 AAGGTTTAAGAGGATCAAAATTCACCGT
1 AAGGTTTAAGAGGATCAAAATTCACCGT
49604 AAGG
1 AAGG
49608 ATTTCAGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (28 bp):
AAGGTTTAAGAGGATCAAAATTCACCGT
Found at i:52201 original size:185 final size:188
Alignment explanation
Indices: 51870--52245 Score: 503
Period size: 185 Copynumber: 2.0 Consensus size: 188
51860 GTTTTGAATA
* * * *
51870 CGGCGTTTTTTGTCAAAACGCCATAAATGTATCATTAATTTACGGCGTTTGTTACTACAACGCCG
1 CGGCGTTTTTTATCAAAACGCCATAAATGTATAATTAATTTACGGCGTTTGTTACCAAAACGCCG
* * * * * *
51935 CTATATGTGCAACCTATTGCGGCGTTTTTGTCAAAACGCTGCTAAAGTACTAATTTATTGCGGCA
66 CTATATGTGCAACCTATTACGGCGATTTTATCAAAACACCGCTAAAGTACTAATTTATTACGGCA
*
52000 TTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAAT-AAATACATTTG
131 TTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAATAAAAAACATTTG
* ** *
52057 CGGCG-TTTTTATCTAAACGCCACT-AATGTATGAATT-ATTTGTGGCGTTTGTTACCAAAATGC
1 CGGCGTTTTTTATCAAAACGCCA-TAAATGTAT-AATTAATTTACGGCGTTTGTTACCAAAACGC
* *
52119 CGCTATATGTG-AACCATATTACGGC-ATTTTATCAAAACACCGCTAAAGTACTAATTTGTTATG
64 CGCTATATGTGCAACC-TATTACGGCGATTTTATCAAAACACCGCTAAAGTACTAATTTATTACG
** *
52182 GTGTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGATGTTTAAATAAAAAACATTTG
128 GCATTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAATAAAAAACATTTG
52243 CGG
1 CGG
52246 TACTAATGTA
Statistics
Matches: 165, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
185 81 0.49
186 75 0.45
187 9 0.05
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (188 bp):
CGGCGTTTTTTATCAAAACGCCATAAATGTATAATTAATTTACGGCGTTTGTTACCAAAACGCCG
CTATATGTGCAACCTATTACGGCGATTTTATCAAAACACCGCTAAAGTACTAATTTATTACGGCA
TTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAATAAAAAACATTTG
Found at i:52328 original size:41 final size:41
Alignment explanation
Indices: 52248--52332 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
52238 ATTTGCGGTA
* * * *
52248 CTAATGTACAAATCATTGCGGCGTTTGTTATCAAAACGCCG
1 CTAAAGTACAAATCATTGCGGCATTTATTATAAAAACGCCG
*
52289 CTAAAGTACTAATCTATTGCGGCATTTATTA-AAAAACGCCG
1 CTAAAGTACAAATC-ATTGCGGCATTTATTATAAAAACGCCG
52330 CTA
1 CTA
52333 TATGTCTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 24 0.63
42 14 0.37
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (41 bp):
CTAAAGTACAAATCATTGCGGCATTTATTATAAAAACGCCG
Done.