Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003204.1 Hibiscus syriacus cultivar Beakdansim tig00006743_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: 68185
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:489 original size:49 final size:49
Alignment explanation
Indices: 436--573 Score: 204
Period size: 49 Copynumber: 2.8 Consensus size: 49
426 GGTGCTAAAA
* *
436 TAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATGAAAGT
* ** *
485 TAAATGCATAACAGTGCATTTCTCCATAAAATGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATGAAAGT
* *
534 TAAATGCAGAACGGTGCATTTCGACATAAATGGTGCCACT
1 TAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACT
574 CATTGTATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 78 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (49 bp):
TAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATGAAAGT
Found at i:5259 original size:22 final size:21
Alignment explanation
Indices: 5217--5256 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5207 GAGTTTATTT
*
5217 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5238 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5257 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:7307 original size:46 final size:45
Alignment explanation
Indices: 7238--7335 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
7228 CGATGTTTTG
* *
7238 AAAATGC-CTGAGTGCATCAATGCATGGTCTTGTGCATCGATGCAT
1 AAAATGCACTGAGTGCATCAATGCATGGT-ATGTGCATCAATGCAT
* *
7283 CAAATGCACTGAGTGCATCGATGCATGGTATGTGCATCAATGCAT
1 AAAATGCACTGAGTGCATCAATGCATGGTATGTGCATCAATGCAT
7328 AAAATGCA
1 AAAATGCA
7336 TTCGATGTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 27 0.57
46 20 0.43
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (45 bp):
AAAATGCACTGAGTGCATCAATGCATGGTATGTGCATCAATGCAT
Found at i:17224 original size:17 final size:17
Alignment explanation
Indices: 17202--17240 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
17192 TACAAGGCAG
*
17202 CAACAGGGAACAACATC
1 CAACAGGCAACAACATC
*
17219 CAACAGGCAGCAACATC
1 CAACAGGCAACAACATC
17236 CAACA
1 CAACA
17241 TTTCTGCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.33, G:0.15, T:0.05
Consensus pattern (17 bp):
CAACAGGCAACAACATC
Found at i:20106 original size:53 final size:52
Alignment explanation
Indices: 19986--20157 Score: 168
Period size: 53 Copynumber: 3.3 Consensus size: 52
19976 TGTGACAGTA
* * * *
19986 AGGGTTAGGG-TTAGAGAAGATGAACAGAGACAAAAGATGAAGAGGCTTGATT
1 AGGGTTTGGGATTAGAGAAGATGAACAGAGAC-AAAGATGAAAAGGCTAGGTT
* * * *
20038 TGAGTTTGGGGTTAGAGAATATGAACAGAGACAGAAGATGAAAAGGCTAGGTT
1 AGGGTTTGGGATTAGAGAAGATGAACAGAGACA-AAGATGAAAAGGCTAGGTT
* ** * * * *
20091 AGGGTATGGGATTAGAGGGGATGAACTGAGATAAAG-TGAATAGGCTCGGTT
1 AGGGTTTGGGATTAGAGAAGATGAACAGAGACAAAGATGAAAAGGCTAGGTT
*
20142 AGGGTTTGGGTTTAGA
1 AGGGTTTGGGATTAGA
20158 TTTGGGTTTA
Statistics
Matches: 98, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 27 0.28
52 11 0.11
53 60 0.61
ACGTcount: A:0.35, C:0.05, G:0.37, T:0.23
Consensus pattern (52 bp):
AGGGTTTGGGATTAGAGAAGATGAACAGAGACAAAGATGAAAAGGCTAGGTT
Found at i:20166 original size:18 final size:18
Alignment explanation
Indices: 20143--20326 Score: 75
Period size: 18 Copynumber: 10.6 Consensus size: 18
20133 GGCTCGGTTA
20143 GGGTTTGGGTTTAGATTT
1 GGGTTTGGGTTTAGATTT
* *
20161 GGGTTT-AGTTCCAG-TTCT
1 GGGTTTGGGTT-TAGATT-T
* * *
20179 -AGTTTGGGTTTGGGTTT
1 GGGTTTGGGTTTAGATTT
* * * *
20196 GGGATCGGGTTTGGGTTT
1 GGGTTTGGGTTTAGATTT
* *
20214 GGGTTTGGGTTTGGGA-TC
1 GGGTTTGGGTTT-AGATTT
20232 GGGTTT-GG----GA-TT
1 GGGTTTGGGTTTAGATTT
* *
20244 GGGTTTGGGTTTGGTTTT
1 GGGTTTGGGTTTAGATTT
* *
20262 GGGTCTGGG-TTCGAGTTT
1 GGGTTTGGGTTTAGA-TTT
* *
20280 GGGTTTGGGTTTAGGTTC
1 GGGTTTGGGTTTAGATTT
* *
20298 GGTTTTGGGTTTAGGTTT
1 GGGTTTGGGTTTAGATTT
*
20316 GGGTTAGGGTT
1 GGGTTTGGGTT
20327 AGTGTTATAG
Statistics
Matches: 126, Mismatches: 26, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
12 9 0.07
13 2 0.02
17 17 0.13
18 93 0.74
19 5 0.04
ACGTcount: A:0.07, C:0.04, G:0.43, T:0.46
Consensus pattern (18 bp):
GGGTTTGGGTTTAGATTT
Found at i:20189 original size:6 final size:6
Alignment explanation
Indices: 20180--20326 Score: 168
Period size: 6 Copynumber: 24.5 Consensus size: 6
20170 TCCAGTTCTA
* *
20180 GTTTGG GTTTGG GTTTGG GATCGG GTTTGG GTTTGG GTTTGG GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * * * *
20228 GATCGG GTTTGG GATTGG GTTTGG GTTTGG TTTTGG GTCTGG GTTCGA
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * *
20276 GTTTGG GTTTGG GTTTAG GTTCGG TTTTGG GTTTAG GTTTGG GTTAGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
20324 GTT
1 GTT
20327 AGTGTTATAG
Statistics
Matches: 114, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 114 1.00
ACGTcount: A:0.05, C:0.03, G:0.46, T:0.46
Consensus pattern (6 bp):
GTTTGG
Found at i:20319 original size:30 final size:30
Alignment explanation
Indices: 20146--20320 Score: 122
Period size: 30 Copynumber: 5.7 Consensus size: 30
20136 TCGGTTAGGG
* * *
20146 TTTGGGTTTAGATTTGGGTTTA-GTTCCAGT
1 TTTGGGTTTGGGTTTGGGTTTAGGTT-CGGT
* * * * *
20176 TCT-AGTTTGGGTTTGGGTTTGGGATCGGG
1 TTTGGGTTTGGGTTTGGGTTTAGGTTCGGT
* * *
20205 TTTGGGTTTGGGTTTGGGTTTGGGATCGGG
1 TTTGGGTTTGGGTTTGGGTTTAGGTTCGGT
* *
20235 TTTGGGATTGGGTTTGGGTTT-GGTTTTGGGT
1 TTTGGGTTTGGGTTTGGGTTTAGG--TTCGGT
*
20266 CTGGGTTCGAGTTTGGGTTTGGGTTTAGGTTCGGT
1 -T---TT-GGGTTTGGGTTTGGGTTTAGGTTCGGT
*
20301 TTTGGGTTTAGGTTTGGGTT
1 TTTGGGTTTGGGTTTGGGTT
20321 AGGGTTAGTG
Statistics
Matches: 116, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
29 20 0.17
30 64 0.55
31 5 0.04
32 1 0.01
34 1 0.01
35 7 0.06
36 16 0.14
37 2 0.02
ACGTcount: A:0.06, C:0.05, G:0.42, T:0.47
Consensus pattern (30 bp):
TTTGGGTTTGGGTTTGGGTTTAGGTTCGGT
Found at i:20771 original size:61 final size:61
Alignment explanation
Indices: 20696--20829 Score: 207
Period size: 61 Copynumber: 2.2 Consensus size: 61
20686 TAGTTGTAAG
*
20696 TTTGTTCAATTTAGTAC-AAATTTAATGATACAATGTATTAATTTAATCTTCATATTTAAAA
1 TTTGTTCAATTTAGT-CTAAATTTAATGATACAATGTATTAATTTAAACTTCATATTTAAAA
* * * *
20757 TTTGTTCAATTTAGTCTAAATTTAATGTTGCAATTTATTAGTTTAAACTTCATATTTAAAA
1 TTTGTTCAATTTAGTCTAAATTTAATGATACAATGTATTAATTTAAACTTCATATTTAAAA
20818 TTTGTTCAATTT
1 TTTGTTCAATTT
20830 GATCCTTATA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
60 1 0.01
61 66 0.99
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.49
Consensus pattern (61 bp):
TTTGTTCAATTTAGTCTAAATTTAATGATACAATGTATTAATTTAAACTTCATATTTAAAA
Found at i:20920 original size:2 final size:2
Alignment explanation
Indices: 20915--21012 Score: 55
Period size: 2 Copynumber: 49.0 Consensus size: 2
20905 ACTAATGAAC
* *
20915 TA TA TA -A TA TA TA GTC TA TA TA TA CTA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * *
20957 CTA -A TA AA CTA TA TA -A TA TA TA GTT TA TA AA TA T- TA T- TA
1 -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
20996 TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
21013 GTTCATATGT
Statistics
Matches: 74, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
1 6 0.08
2 60 0.81
3 8 0.11
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:20945 original size:51 final size:51
Alignment explanation
Indices: 20889--20985 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 51
20879 AATAAATTAA
*
20889 TATATAGGTTATATATACTAATGAACTATATAATATATAGTCTATATATAC
1 TATATAGGTTATATATACTAATAAACTATATAATATATAGTCTATATATAC
* *
20940 TATATAGTTTATATATACTAATAAACTATATAATATATAGTTTATA
1 TATATAGGTTATATATACTAATAAACTATATAATATATAGTCTATA
20986 AATATTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (51 bp):
TATATAGGTTATATATACTAATAAACTATATAATATATAGTCTATATATAC
Found at i:20970 original size:33 final size:33
Alignment explanation
Indices: 20931--21069 Score: 104
Period size: 33 Copynumber: 4.0 Consensus size: 33
20921 ATATATAGTC
20931 TATATATACTATATAGTTTATATATACTA-ATAA
1 TATATATA-TATATAGTTTATATATACTATATAA
* *
20964 -ACTATATAATATATAGTTTATAAATATTATTATAA
1 TA-TATAT-ATATATAGTTTATATATACTA-TATAA
* * *
20999 TATATATATATATAGTTCATATGTAAACTATACATTA
1 TATATATATATATAGTT--TATATATACTAT--ATAA
* *
21036 TATATAAACTATATA-TGTAGTATATACTATATAA
1 TATATATA-TATATAGTTTA-TATATACTATATAA
21070 ATAGTTCATT
Statistics
Matches: 83, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
32 1 0.01
33 23 0.28
34 14 0.17
35 12 0.14
36 16 0.19
37 11 0.13
38 6 0.07
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (33 bp):
TATATATATATATAGTTTATATATACTATATAA
Found at i:21068 original size:9 final size:9
Alignment explanation
Indices: 20898--21068 Score: 64
Period size: 9 Copynumber: 19.7 Consensus size: 9
20888 ATATATAGGT
20898 TATATATAC
1 TATATATAC
20907 TA-ATGA-AC
1 TATAT-ATAC
20915 TATATA-A-
1 TATATATAC
20922 TATATAGT-C
1 TATATA-TAC
20931 TATATATAC
1 TATATATAC
*
20940 TATATAGT-T
1 TATATA-TAC
20949 TATATATAC
1 TATATATAC
*
20958 TA-ATAAAC
1 TATATATAC
20966 TATATA-A-
1 TATATATAC
*
20973 TATATAGT-T
1 TATATA-TAC
* *
20982 TATAAATAT
1 TATATATAC
*
20991 TAT-TATAA
1 TATATATAC
20999 TATATATA-
1 TATATATAC
*
21007 TATATAGTTC
1 TATATA-TAC
* *
21017 ATATGTAAAC
1 -TATATATAC
*
21027 TATACATTA-
1 TATATA-TAC
*
21036 TATATAAAC
1 TATATATAC
*
21045 TATATAT-G
1 TATATATAC
21053 TAGTATATAC
1 TA-TATATAC
21063 TATATA
1 TATATA
21069 AATAGTTCAT
Statistics
Matches: 123, Mismatches: 18, Indels: 42
0.67 0.10 0.23
Matches are distributed among these distances:
7 12 0.10
8 34 0.28
9 67 0.54
10 5 0.04
11 5 0.04
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (9 bp):
TATATATAC
Found at i:21151 original size:14 final size:15
Alignment explanation
Indices: 21132--21165 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21122 TACTTTGAAT
*
21132 TTATAT-AGTATAAA
1 TTATATAAGTAAAAA
21146 TTATATAAGTAAAAA
1 TTATATAAGTAAAAA
21161 TTATA
1 TTATA
21166 ATATATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
TTATATAAGTAAAAA
Found at i:21165 original size:27 final size:27
Alignment explanation
Indices: 21135--21259 Score: 153
Period size: 27 Copynumber: 4.7 Consensus size: 27
21125 TTTGAATTTA
* * * ** *
21135 TATAGTATAAATTATATAAGTAAAAAT
1 TATAGTATATAGTATATAAATATCAAC
*
21162 TATAATATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
21189 TATAGTATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
*
21216 TATAGTATATAGTATATAAATATCAAT
1 TATAGTATATAGTATATAAATATCAAC
* *
21243 TACAGTTTATA-TATATA
1 TATAGTATATAGTATATA
21260 GTTTAGATAT
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 6 0.07
27 81 0.93
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATCAAC
Found at i:21389 original size:44 final size:44
Alignment explanation
Indices: 21294--21396 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 44
21284 TCAACTAAAG
* * *
21294 TAAATAGTTTATATATATATTGTTCATATGTAAACTATATAGTA
1 TAAATAGTTTATATATAAATTGTACATATGTAAACTACATAGTA
* *
21338 TATATAGTTTATATATAAAGTT-TACATATGTAGTA-TACACTA-TA
1 TAAATAGTTTATATATAAA-TTGTACATATGTA-AACTACA-TAGTA
21382 TAAATAGTTTATATA
1 TAAATAGTTTATATA
21397 GTTCATACGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
44 45 0.90
45 5 0.10
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.45
Consensus pattern (44 bp):
TAAATAGTTTATATATAAATTGTACATATGTAAACTACATAGTA
Found at i:21767 original size:2 final size:2
Alignment explanation
Indices: 21762--22104 Score: 139
Period size: 2 Copynumber: 171.5 Consensus size: 2
21752 CATATAGTTC
* * * *
21762 AT AT AT AA ACT AT AT AGT TT AT AT AT GGT AT AT AT AG AT -T AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT -AT AT AT AT AT AT AT AT
* * *
21804 AC AT A- AT AT AT AT AT AGT TT AT AT AT A- AC AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
21843 AT AA AT AT AA ACT AT AT AGT TT TT AT AT AT A- AT AT AT AT ACT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * * * *
21885 TT AT AT AT AA AGT AT AT AGT TT AT A- AT A- AT AT AGT TT AT AC
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT
* * *
21926 AT A- AT AC AT AT A- AT AT AT A- AT A- AT AT AA AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * *
21965 AA AGT TT AT AT AT AGT AT AT A- AT AT AT ACT TT AT AT AT AC ACT
1 AT A-T AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T
* * * *
22008 AT AT A- AT TT AT AT -T A- AT AA ACT AT AT AGT TT AT AC AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
22048 AT AT AT AGT -T CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22091 AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A
22105 ATTGTTTCAA
Statistics
Matches: 252, Mismatches: 51, Indels: 76
0.66 0.13 0.20
Matches are distributed among these distances:
1 19 0.08
2 214 0.85
3 19 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:21918 original size:15 final size:16
Alignment explanation
Indices: 21898--21931 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
21888 TATATAAAGT
21898 ATATAGTTTATA-ATA
1 ATATAGTTTATACATA
21913 ATATAGTTTATACATA
1 ATATAGTTTATACATA
21929 ATA
1 ATA
21932 CATATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
ATATAGTTTATACATA
Found at i:22003 original size:20 final size:20
Alignment explanation
Indices: 21734--22106 Score: 176
Period size: 20 Copynumber: 17.9 Consensus size: 20
21724 AAATAACTTG
*
21734 TATAGTTTATATATA-ATTCA
1 TATAGTTTATATATATAAT-A
*
21754 TATAGTTCATATATA-AACTA
1 TATAGTTTATATATATAA-TA
*
21774 TATAGTTTATATATGGT-ATA
1 TATAGTTTATATAT-ATAATA
* *
21794 TATAGATTATACATAATATATA
1 TATAGTTTATATAT-ATA-ATA
21816 TATAGTTTATATATA-ACATA
1 TATAGTTTATATATATA-ATA
* * *
21836 TAATAATATAAATATA-AACTA
1 T-ATAGTTTATATATATAA-TA
*
21857 TATAGTTTTTATATATAATATA
1 TATAGTTTATATATAT-A-ATA
*
21879 TATACTTTATATATA-AAGTA
1 TATAGTTTATATATATAA-TA
* *
21899 TATAGTTTATAATAATATAGTT
1 TATAGTTTAT-AT-ATATAATA
** * *
21921 TATACATAATACATATAATA
1 TATAGTTTATATATATAATA
* * *
21941 TATAATAATATAAATATAAACTA
1 TATAGT-TTATATATAT-AA-TA
*
21964 TAAAGTTTATATATAGTATATAATA
1 TATAG--T-T-TATA-TATATAATA
* * *
21989 TATACTTTATATATACACTA
1 TATAGTTTATATATATAATA
*
22009 TATAATTTATAT-TAATAAACTA
1 TATAGTTTATATAT-AT-AA-TA
*
22031 TATAGTTTATACATA-ATATA
1 TATAGTTTATATATATA-ATA
*
22051 TATAGTTCATATATAT-ATA
1 TATAGTTTATATATATAATA
*
22070 TATA-TATATATATAT-ATA
1 TATAGTTTATATATATAATA
*
22088 TATA-TATATATATTATAAT
1 TATAGTTTATATA-TATAAT
22107 TGTTTCAAAT
Statistics
Matches: 273, Mismatches: 51, Indels: 58
0.71 0.13 0.15
Matches are distributed among these distances:
18 24 0.09
19 12 0.04
20 119 0.44
21 34 0.12
22 58 0.21
23 9 0.03
25 7 0.03
26 6 0.02
27 4 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAGTTTATATATATAATA
Found at i:23219 original size:53 final size:52
Alignment explanation
Indices: 23099--23270 Score: 168
Period size: 53 Copynumber: 3.3 Consensus size: 52
23089 TGTGACAGTA
* * * *
23099 AGGGTTAGGG-TTAGAGAAGATGAACAGAGACAAAAGATGAAGAGGCTTGATT
1 AGGGTTTGGGATTAGAGAAGATGAACAGAGAC-AAAGATGAAAAGGCTAGGTT
* * * *
23151 TGAGTTTGGGGTTAGAGAATATGAACAGAGACAGAAGATGAAAAGGCTAGGTT
1 AGGGTTTGGGATTAGAGAAGATGAACAGAGACA-AAGATGAAAAGGCTAGGTT
* ** * * * *
23204 AGGGTATGGGATTAGAGGGGATGAACTGAGATAAAG-TGAATAGGCTCGGTT
1 AGGGTTTGGGATTAGAGAAGATGAACAGAGACAAAGATGAAAAGGCTAGGTT
*
23255 AGGGTTTGGGTTTAGA
1 AGGGTTTGGGATTAGA
23271 TTTGGGTTTA
Statistics
Matches: 98, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 27 0.28
52 11 0.11
53 60 0.61
ACGTcount: A:0.35, C:0.05, G:0.37, T:0.23
Consensus pattern (52 bp):
AGGGTTTGGGATTAGAGAAGATGAACAGAGACAAAGATGAAAAGGCTAGGTT
Found at i:23279 original size:18 final size:18
Alignment explanation
Indices: 23256--23439 Score: 75
Period size: 18 Copynumber: 10.6 Consensus size: 18
23246 GGCTCGGTTA
23256 GGGTTTGGGTTTAGATTT
1 GGGTTTGGGTTTAGATTT
* *
23274 GGGTTT-AGTTCCAG-TTCT
1 GGGTTTGGGTT-TAGATT-T
* * *
23292 -AGTTTGGGTTTGGGTTT
1 GGGTTTGGGTTTAGATTT
* * * *
23309 GGGATCGGGTTTGGGTTT
1 GGGTTTGGGTTTAGATTT
* *
23327 GGGTTTGGGTTTGGGA-TC
1 GGGTTTGGGTTT-AGATTT
23345 GGGTTT-GG----GA-TT
1 GGGTTTGGGTTTAGATTT
* *
23357 GGGTTTGGGTTTGGTTTT
1 GGGTTTGGGTTTAGATTT
* *
23375 GGGTCTGGG-TTCGAGTTT
1 GGGTTTGGGTTTAGA-TTT
* *
23393 GGGTTTGGGTTTAGGTTC
1 GGGTTTGGGTTTAGATTT
* *
23411 GGTTTTGGGTTTAGGTTT
1 GGGTTTGGGTTTAGATTT
*
23429 GGGTTAGGGTT
1 GGGTTTGGGTT
23440 AGTGTTATAG
Statistics
Matches: 126, Mismatches: 26, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
12 9 0.07
13 2 0.02
17 17 0.13
18 93 0.74
19 5 0.04
ACGTcount: A:0.07, C:0.04, G:0.43, T:0.46
Consensus pattern (18 bp):
GGGTTTGGGTTTAGATTT
Found at i:23302 original size:6 final size:6
Alignment explanation
Indices: 23293--23439 Score: 168
Period size: 6 Copynumber: 24.5 Consensus size: 6
23283 TCCAGTTCTA
* *
23293 GTTTGG GTTTGG GTTTGG GATCGG GTTTGG GTTTGG GTTTGG GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * * * *
23341 GATCGG GTTTGG GATTGG GTTTGG GTTTGG TTTTGG GTCTGG GTTCGA
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * *
23389 GTTTGG GTTTGG GTTTAG GTTCGG TTTTGG GTTTAG GTTTGG GTTAGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
23437 GTT
1 GTT
23440 AGTGTTATAG
Statistics
Matches: 114, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 114 1.00
ACGTcount: A:0.05, C:0.03, G:0.46, T:0.46
Consensus pattern (6 bp):
GTTTGG
Found at i:23432 original size:30 final size:30
Alignment explanation
Indices: 23259--23433 Score: 122
Period size: 30 Copynumber: 5.7 Consensus size: 30
23249 TCGGTTAGGG
* * *
23259 TTTGGGTTTAGATTTGGGTTTA-GTTCCAGT
1 TTTGGGTTTGGGTTTGGGTTTAGGTT-CGGT
* * * * *
23289 TCT-AGTTTGGGTTTGGGTTTGGGATCGGG
1 TTTGGGTTTGGGTTTGGGTTTAGGTTCGGT
* * *
23318 TTTGGGTTTGGGTTTGGGTTTGGGATCGGG
1 TTTGGGTTTGGGTTTGGGTTTAGGTTCGGT
* *
23348 TTTGGGATTGGGTTTGGGTTT-GGTTTTGGGT
1 TTTGGGTTTGGGTTTGGGTTTAGG--TTCGGT
*
23379 CTGGGTTCGAGTTTGGGTTTGGGTTTAGGTTCGGT
1 -T---TT-GGGTTTGGGTTTGGGTTTAGGTTCGGT
*
23414 TTTGGGTTTAGGTTTGGGTT
1 TTTGGGTTTGGGTTTGGGTT
23434 AGGGTTAGTG
Statistics
Matches: 116, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
29 20 0.17
30 64 0.55
31 5 0.04
32 1 0.01
34 1 0.01
35 7 0.06
36 16 0.14
37 2 0.02
ACGTcount: A:0.06, C:0.05, G:0.42, T:0.47
Consensus pattern (30 bp):
TTTGGGTTTGGGTTTGGGTTTAGGTTCGGT
Found at i:23884 original size:61 final size:61
Alignment explanation
Indices: 23809--23942 Score: 207
Period size: 61 Copynumber: 2.2 Consensus size: 61
23799 TAGTTGTAAG
*
23809 TTTGTTCAATTTAGTAC-AAATTTAATGATACAATGTATTAATTTAATCTTCATATTTAAAA
1 TTTGTTCAATTTAGT-CTAAATTTAATGATACAATGTATTAATTTAAACTTCATATTTAAAA
* * * *
23870 TTTGTTCAATTTAGTCTAAATTTAATGTTGCAATTTATTAGTTTAAACTTCATATTTAAAA
1 TTTGTTCAATTTAGTCTAAATTTAATGATACAATGTATTAATTTAAACTTCATATTTAAAA
23931 TTTGTTCAATTT
1 TTTGTTCAATTT
23943 GATCCTTATA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
60 1 0.01
61 66 0.99
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.49
Consensus pattern (61 bp):
TTTGTTCAATTTAGTCTAAATTTAATGATACAATGTATTAATTTAAACTTCATATTTAAAA
Found at i:24033 original size:2 final size:2
Alignment explanation
Indices: 24028--24121 Score: 63
Period size: 2 Copynumber: 47.0 Consensus size: 2
24018 ACTAATGAAC
* *
24028 TA TA TA -A TA TA TA GTC TA TA TA TA TA TA TA GTT TA TA TA CTA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA -TA
* * *
24070 -A TA AA CTA TA TA TA TA GTT TA TA AA TA T- TA T- TA TA -A TA TA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
24110 TA TA TA TA TA TA
1 TA TA TA TA TA TA
24122 GTTCATATGT
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
1 5 0.07
2 61 0.85
3 6 0.08
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:24082 original size:26 final size:25
Alignment explanation
Indices: 23975--24092 Score: 84
Period size: 28 Copynumber: 4.6 Consensus size: 25
23965 CTTTCAATTA
*
23975 ATATATATGTTTATAT-TAATAAATT
1 ATATATA-GTTTATATCTAATAAACT
*
24000 AATATATAGGTTATATATACTAATGAACT
1 -ATATATA-GTT-TATAT-CTAATAAACT
* *
24029 ATATA-A-TATATAGTCT-ATATA-T
1 ATATATAGTTTATA-TCTAATAAACT
24051 ATATATAGTTTATATACTAATAAACTAT
1 ATATATAGTTTATAT-CTAATAAAC--T
24079 ATATATAGTTTATA
1 ATATATAGTTTATA
24093 AATATTATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
22 6 0.08
23 5 0.07
24 13 0.18
25 6 0.08
26 10 0.14
27 6 0.08
28 20 0.27
29 7 0.10
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (25 bp):
ATATATAGTTTATATCTAATAAACT
Found at i:24112 original size:32 final size:28
Alignment explanation
Indices: 24045--24117 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
24035 TATATAGTCT
24045 ATATATATATATAGTTTATATACTAATA
1 ATATATATATATAGTTTATATACTAATA
*
24073 A-ACTATATATATAGTTTATAAATATTATTATA
1 ATA-TATATATATAGTTTAT--ATACTA--ATA
24105 ATATATATATATA
1 ATATATATATATA
24118 TATAGTTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 1 0.03
28 17 0.45
30 5 0.13
32 14 0.37
33 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (28 bp):
ATATATATATATAGTTTATATACTAATA
Found at i:24115 original size:30 final size:27
Alignment explanation
Indices: 23975--24049 Score: 50
Period size: 33 Copynumber: 2.7 Consensus size: 27
23965 CTTTCAATTA
23975 ATATATAT-GTTTATAT--TAATAAAT
1 ATATATATAGTTTATATACTAATAAAT
23999 -TAATATATAGGTTATATATACTAATGAACTAT
1 AT-ATATATA-GTT-TATATACTAAT-AA--AT
*
24031 ATAATATATAGTCTATATA
1 AT-ATATATAGTTTATATA
24050 TATATATAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
23 1 0.03
24 6 0.15
26 3 0.08
27 5 0.12
29 4 0.10
30 2 0.05
31 6 0.15
32 4 0.10
33 9 0.22
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (27 bp):
ATATATATAGTTTATATACTAATAAAT
Found at i:24129 original size:17 final size:16
Alignment explanation
Indices: 24001--24129 Score: 67
Period size: 17 Copynumber: 7.9 Consensus size: 16
23991 TAATAAATTA
24001 ATATATAGGTTATATAT
1 ATATATA-GTTATATAT
**
24018 ACTA-ATGAACTATATA-
1 A-TATAT-AGTTATATAT
24034 ATATATAGTCTATATAT
1 ATATATAGT-TATATAT
24051 ATATATAGTT-TATAT
1 ATATATAGTTATATAT
24066 ACTA-ATA---A-ACTAT
1 A-TATATAGTTATA-TAT
*
24079 ATATATAGTTTATAAAT
1 ATATATAG-TTATATAT
*
24096 ATTATTATAATATATATAT
1 A-TA-TATAGT-TATATAT
24115 ATATATAGTTCATAT
1 ATATATAGTT-ATAT
24130 GTAAACTATA
Statistics
Matches: 86, Mismatches: 8, Indels: 36
0.66 0.06 0.28
Matches are distributed among these distances:
12 3 0.03
13 7 0.08
15 12 0.14
16 13 0.15
17 31 0.36
18 9 0.10
19 11 0.13
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (16 bp):
ATATATAGTTATATAT
Found at i:24135 original size:60 final size:61
Alignment explanation
Indices: 24034--24187 Score: 145
Period size: 60 Copynumber: 2.5 Consensus size: 61
24024 GAACTATATA
* * * * *
24034 ATATATAGTCTATATATATATATAGTTTATATACTAATAAACTATATATATAGTTTATAAA-TAT
1 ATATATAATATATATATATATATAG-TT-CATACTAATAAACTATACAT-TA-TATATAAACTAT
*
24098 -TATTATAATATATATATATATATAGTTCATA-T-GTAAACTATACATTATATATAAACTAT
1 ATA-TATAATATATATATATATATAGTTCATACTAATAAACTATACATTATATATAAACTAT
* * *
24157 ATATGTAGTATATACTATATAAATAGTTCAT
1 ATATATAATATATA-TATATATATAGTTCAT
24188 TAATTAAGGT
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
58 7 0.09
59 14 0.18
60 28 0.36
61 1 0.01
62 3 0.04
63 4 0.05
64 20 0.26
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (61 bp):
ATATATAATATATATATATATATAGTTCATACTAATAAACTATACATTATATATAAACTAT
Found at i:24260 original size:14 final size:15
Alignment explanation
Indices: 24241--24274 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
24231 TACTTTGAAT
*
24241 TTATAT-AGTATAAA
1 TTATATAAGTAAAAA
24255 TTATATAAGTAAAAA
1 TTATATAAGTAAAAA
24270 TTATA
1 TTATA
24275 ATATATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
TTATATAAGTAAAAA
Found at i:24274 original size:27 final size:27
Alignment explanation
Indices: 24244--24368 Score: 153
Period size: 27 Copynumber: 4.7 Consensus size: 27
24234 TTTGAATTTA
* * * ** *
24244 TATAGTATAAATTATATAAGTAAAAAT
1 TATAGTATATAGTATATAAATATCAAC
*
24271 TATAATATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
24298 TATAGTATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
*
24325 TATAGTATATAGTATATAAATATCAAT
1 TATAGTATATAGTATATAAATATCAAC
* *
24352 TACAGTTTATA-TATATA
1 TATAGTATATAGTATATA
24369 GTTTAGATAT
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 6 0.07
27 81 0.93
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATCAAC
Found at i:24498 original size:44 final size:44
Alignment explanation
Indices: 24403--24505 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 44
24393 TCAACTAAAG
* * *
24403 TAAATAGTTTATATATATATTGTTCATATGTAAACTATATAGTA
1 TAAATAGTTTATATATAAATTGTACATATGTAAACTACATAGTA
* *
24447 TATATAGTTTATATATAAAGTT-TACATATGTAGTA-TACACTA-TA
1 TAAATAGTTTATATATAAA-TTGTACATATGTA-AACTACA-TAGTA
24491 TAAATAGTTTATATA
1 TAAATAGTTTATATA
24506 GTTCATACGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
44 45 0.90
45 5 0.10
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.45
Consensus pattern (44 bp):
TAAATAGTTTATATATAAATTGTACATATGTAAACTACATAGTA
Found at i:24789 original size:22 final size:21
Alignment explanation
Indices: 24758--24804 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
24748 ATAATATATA
*
24758 TATATTATAAACTATATATTT
1 TATATTATAAACTATATAATT
*
24779 TATATTAATAAAGTATATAATT
1 TATATT-ATAAACTATATAATT
24801 TATA
1 TATA
24805 CATAGTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TATATTATAAACTATATAATT
Found at i:24868 original size:20 final size:20
Alignment explanation
Indices: 24843--24906 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
24833 TAATATATAA
*
24843 ATATAACTTGTATAGTTTAT
1 ATATAACTTATATAGTTTAT
*
24863 ATATAA-TTCATATAGTTCAT
1 ATATAACTT-ATATAGTTTAT
24883 ATATAAAC-TATATAGTTTAT
1 ATAT-AACTTATATAGTTTAT
24903 ATAT
1 ATAT
24907 GGTATATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.05
20 33 0.87
21 3 0.08
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (20 bp):
ATATAACTTATATAGTTTAT
Found at i:24886 original size:2 final size:2
Alignment explanation
Indices: 24881--25167 Score: 197
Period size: 2 Copynumber: 143.5 Consensus size: 2
24871 CATATAGTTC
* * * *
24881 AT AT AT AA ACT AT AT AGT TT AT AT AT GGT AT AT AT AG AT -T AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT -AT AT AT AT AT AT AT AT
* *
24923 AC AT A- AT AT AT AT AT AT AT AT AC AT AT A- AT A- AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
24963 AT AT AT AT AT AT AT AT AT AT AT AT AGT TT AT A- AT A- AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T
* * * * * *
25005 TT AT AC AT A- AT AC AT AT AT AT AT A- AT AT AT AA AC AT AA AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
25046 TT AT AT AGT AT AT A- AT AT AT ACT -T AT AT AT ACT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT
* * *
25087 -T AT AT AA ACT AT AT AGT TT AT AC AT A- AT AT AT AT AGT -T CAT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT -AT
25128 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25168 ATTGTTTCAA
Statistics
Matches: 224, Mismatches: 33, Indels: 56
0.72 0.11 0.18
Matches are distributed among these distances:
1 14 0.06
2 194 0.87
3 16 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:24916 original size:31 final size:30
Alignment explanation
Indices: 24881--25160 Score: 164
Period size: 29 Copynumber: 9.5 Consensus size: 30
24871 CATATAGTTC
24881 ATATATAAACTATATAGTTTATATATGGTATAT
1 ATATATAAACTATATAGTTTATATA---TATAT
* * *
24914 ATAGATTATAC-ATAATA-TATATATATATAT
1 ATATA-TAAACTAT-ATAGTTTATATATATAT
* *
24944 ACATATAATAATATATAG--TATATATATAT
1 ATATATAA-ACTATATAGTTTATATATATAT
*
24973 ATATATATA-TATATAGTTTATA-ATA-AT
1 ATATATAAACTATATAGTTTATATATATAT
* * **
25000 ATAGTTTATAC-ATA-A-TACATATATATAT
1 ATA-TATAAACTATATAGTTTATATATATAT
*
25028 AATATATAAAC-ATAAAGTTTATATAGTATAT
1 -ATATATAAACTATATAGTTTATATA-TATAT
* *
25059 A-ATATATACT-TATA-TATACTATATATAT
1 ATATATAAACTATATAGTTTA-TATATATAT
*
25087 -TATATAAACTATATAGTTTATACATA-AT
1 ATATATAAACTATATAGTTTATATATATAT
** *
25115 ATATATAGTTCATATATA-TATATATATATAT
1 ATATATA-AAC-TATATAGTTTATATATATAT
*
25146 ATATATATA-TATATA
1 ATATATAAACTATATA
25161 TATTATAATT
Statistics
Matches: 196, Mismatches: 27, Indels: 53
0.71 0.10 0.19
Matches are distributed among these distances:
26 4 0.02
27 16 0.08
28 46 0.23
29 56 0.29
30 32 0.16
31 22 0.11
33 13 0.07
34 7 0.04
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (30 bp):
ATATATAAACTATATAGTTTATATATATAT
Found at i:31283 original size:15 final size:15
Alignment explanation
Indices: 31263--31292 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31253 AAATTTTAAA
31263 GAGGGGATTTCTGGT
1 GAGGGGATTTCTGGT
31278 GAGGGGATTTCTGGT
1 GAGGGGATTTCTGGT
31293 AGGAACATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.47, T:0.33
Consensus pattern (15 bp):
GAGGGGATTTCTGGT
Found at i:37571 original size:16 final size:16
Alignment explanation
Indices: 37549--37589 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
37539 TTGTCATAGG
*
37549 TATTAAAGTATAGTGGA
1 TATTAAAGTATAAT-GA
37566 -ATTAAAGTATAATGA
1 TATTAAAGTATAATGA
37581 TATTAAAGT
1 TATTAAAGT
37590 GTAGATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (16 bp):
TATTAAAGTATAATGA
Found at i:40117 original size:54 final size:54
Alignment explanation
Indices: 39991--40226 Score: 319
Period size: 54 Copynumber: 4.4 Consensus size: 54
39981 TTCGTTGAGA
* * ** * * *
39991 TGCACACGTAGTGCCGATACGGTTATTCATAAACATATTATGAAATTCTGTGGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATG-AATTCCGTGGGT
* *
40046 TGCACACATAGTACCTATACGGTCGTTCATTAACATATGATGAATTCCGTGGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * *
40100 TGCACACATATTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* *
40154 TGCACACACAGTGCCTATACGATCGTTCATCAACATATGATGAATTCCGTGGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* *
40208 TTCACACATAGAGCCTATA
1 TGCACACATAGTGCCTATA
40227 ATACACATAG
Statistics
Matches: 160, Mismatches: 21, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
54 125 0.78
55 35 0.22
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
Found at i:40763 original size:95 final size:95
Alignment explanation
Indices: 40565--40768 Score: 257
Period size: 95 Copynumber: 2.1 Consensus size: 95
40555 GTACCCTTAC
* * * * *
40565 CATGGTATCGATACTTCTATACTATGGTACCAATACTCCCTTTCAGTATCGACGCCATTTCTACA
1 CATGGTATCGATACTTCTATACTATAGTACCAATACTCCATTACAGTATCGACACCATTTATACA
* *
40630 TTCTGAAATCCATGGTATCAATACCTTTCT
66 TTCTGAAATCAATGGTATCAATACCTTCCT
* * * * * *
40660 CTTAGTATCGATAC-TCATATACTATAGTACCGATACTCCATTACAGTTTCGATACCATTTATGC
1 CATGGTATCGATACTTC-TATACTATAGTACCAATACTCCATTACAGTATCGACACCATTTATAC
*
40724 ATTCTGGAATCAATGGTATCAATACCTTCCT
65 ATTCTGAAATCAATGGTATCAATACCTTCCT
*
40755 CATGGTATCAATAC
1 CATGGTATCGATAC
40769 CCACATTAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 2 0.02
95 89 0.98
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (95 bp):
CATGGTATCGATACTTCTATACTATAGTACCAATACTCCATTACAGTATCGACACCATTTATACA
TTCTGAAATCAATGGTATCAATACCTTCCT
Found at i:48767 original size:14 final size:14
Alignment explanation
Indices: 48744--48773 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
48734 TTATACCCTA
48744 TATATATTTATTAT
1 TATATATTTATTAT
*
48758 TATATTTTTATTAT
1 TATATATTTATTAT
48772 TA
1 TA
48774 ATTACAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATATATTTATTAT
Found at i:51429 original size:24 final size:24
Alignment explanation
Indices: 51401--51479 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
51391 CTTCTCAAGG
**
51401 AGTATCGATACTACTATGTGTAGT
1 AGTATCGATACTACTATGTAAAGT
* * *
51425 AGTATC-A-A-TACCAT-TCAAGG
1 AGTATCGATACTACTATGTAAAGT
51445 AGTATCGATACTACTATGTAAAGT
1 AGTATCGATACTACTATGTAAAGT
51469 AGTATCGATAC
1 AGTATCGATAC
51480 CGGTCCGGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
20 9 0.20
21 6 0.14
22 2 0.05
23 6 0.14
24 21 0.48
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (24 bp):
AGTATCGATACTACTATGTAAAGT
Found at i:51445 original size:44 final size:44
Alignment explanation
Indices: 51395--51480 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
51385 TCTATACTTC
**
51395 TCAAGGAGTATCGATACTACTATGTGTAGTAGTATCAATACCAT
1 TCAAGGAGTATCGATACTACTATGTAAAGTAGTATCAATACCAT
*
51439 TCAAGGAGTATCGATACTACTATGTAAAGTAGTATCGATACC
1 TCAAGGAGTATCGATACTACTATGTAAAGTAGTATCAATACC
51481 GGTCCGGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (44 bp):
TCAAGGAGTATCGATACTACTATGTAAAGTAGTATCAATACCAT
Found at i:51850 original size:19 final size:19
Alignment explanation
Indices: 51823--51873 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
51813 TCGAATAATT
* *
51823 AAATTGAATATGATATTTG
1 AAATCGAATATAATATTTG
51842 AAATCGAATATAATATTTG
1 AAATCGAATATAATATTTG
51861 AAATCGAATATAA
1 AAATCGAATATAA
51874 AATCTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (19 bp):
AAATCGAATATAATATTTG
Found at i:53762 original size:18 final size:20
Alignment explanation
Indices: 53728--53772 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 20
53718 AATAAGTTTG
53728 AAAAACAATATAATTAAATC
1 AAAAACAATATAATTAAATC
53748 AAAAACAA-A-AATTAAATC
1 AAAAACAATATAATTAAATC
53766 AAAAACA
1 AAAAACA
53773 TTTTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 16 0.64
19 1 0.04
20 8 0.32
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAACAATATAATTAAATC
Found at i:54285 original size:20 final size:23
Alignment explanation
Indices: 54248--54301 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 23
54238 TCATTCAAGT
*
54248 AGTATCGGTAC-TGCATGA-A-C
1 AGTATCGATACTTGCATGATAGC
*
54268 AGTATCGATACTTG-ATGATAGT
1 AGTATCGATACTTGCATGATAGC
54290 AGTATCGATACT
1 AGTATCGATACT
54302 ATGCTAGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 3 0.10
22 12 0.41
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (23 bp):
AGTATCGATACTTGCATGATAGC
Found at i:54311 original size:20 final size:22
Alignment explanation
Indices: 54268--54320 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 22
54258 CTGCATGAAC
54268 AGTATCGATACTTGATGATAGT
1 AGTATCGATACTTGATGATAGT
*
54290 AGTATCGATAC-T-ATGCTAGT
1 AGTATCGATACTTGATGATAGT
*
54310 AGTATTGATAC
1 AGTATCGATAC
54321 CTAGTAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 17 0.59
21 1 0.03
22 11 0.38
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (22 bp):
AGTATCGATACTTGATGATAGT
Found at i:54334 original size:22 final size:22
Alignment explanation
Indices: 54307--54358 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
54297 ATACTATGCT
* *
54307 AGTAGTATTGATACCTAGTAAG
1 AGTAGTATTAATAACTAGTAAG
54329 AGTAGTATTAATAACTAGTAAG
1 AGTAGTATTAATAACTAGTAAG
54351 AGTAGTAT
1 AGTAGTAT
54359 CGGTACTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTAGTATTAATAACTAGTAAG
Found at i:59011 original size:19 final size:20
Alignment explanation
Indices: 58989--59042 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
58979 GACCGGTTCC
* *
58989 GACCGGTTC-GAAGCGGTTT
1 GACCGGTTCTGAACCGATTT
59008 GACCGG-TCTGAACCGATTT
1 GACCGGTTCTGAACCGATTT
*
59027 GACCGG-TCTGACCCGA
1 GACCGGTTCTGAACCGA
59043 CCCGACCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 2 0.06
19 29 0.94
ACGTcount: A:0.19, C:0.28, G:0.31, T:0.22
Consensus pattern (20 bp):
GACCGGTTCTGAACCGATTT
Found at i:59046 original size:5 final size:5
Alignment explanation
Indices: 59036--59073 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
59026 TGACCGGTCT
* *
59036 GACCC GACCC GACCC TA-CT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
59074 GTTGACCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 2 0.07
5 26 0.93
ACGTcount: A:0.21, C:0.55, G:0.18, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:59049 original size:19 final size:19
Alignment explanation
Indices: 59008--59068 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
58998 GAAGCGGTTT
* ***
59008 GACCGGTCTGAACCGATTT
1 GACCGGTCTGACCCGACCC
59027 GACCGGTCTGACCCGACCC
1 GACCGGTCTGACCCGACCC
*
59046 GACC-CTACTGACCCGACCC
1 GACCGGT-CTGACCCGACCC
59065 GACC
1 GACC
59069 CGACCGTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
18 1 0.03
19 35 0.97
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.15
Consensus pattern (19 bp):
GACCGGTCTGACCCGACCC
Found at i:59082 original size:7 final size:7
Alignment explanation
Indices: 59070--59100 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
59060 GACCCGACCC
59070 GACCGTT
1 GACCGTT
59077 GACCGTT
1 GACCGTT
59084 GACCGTT
1 GACCGTT
59091 GACCGTT
1 GACCGTT
59098 GAC
1 GAC
59101 TTCCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:59087 original size:24 final size:24
Alignment explanation
Indices: 59025--59087 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 24
59015 CTGAACCGAT
59025 TTGACCGGTCTGACCCGACCCGACCC
1 TTGACC-GT-TGACCCGACCCGACCC
* *
59051 TACTGACC--CGACCCGACCCGACCG
1 T--TGACCGTTGACCCGACCCGACCC
59075 TTGACCGTTGACC
1 TTGACCGTTGACC
59088 GTTGACCGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
22 5 0.17
24 19 0.63
26 1 0.03
28 5 0.17
ACGTcount: A:0.17, C:0.44, G:0.22, T:0.16
Consensus pattern (24 bp):
TTGACCGTTGACCCGACCCGACCC
Found at i:66261 original size:17 final size:18
Alignment explanation
Indices: 66222--66270 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
66212 TTCAACCGGT
66222 TTTGACCGGT-TCGAAGTG
1 TTTGACCGGTCT-GAAGTG
66240 TTTGACCGGTCTGAAG-G
1 TTTGACCGGTCTGAAGTG
66257 TTTGACCGGTCTGA
1 TTTGACCGGTCTGA
66271 CCCGACCCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.50
18 14 0.47
19 1 0.03
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (18 bp):
TTTGACCGGTCTGAAGTG
Found at i:66296 original size:26 final size:24
Alignment explanation
Indices: 66267--66316 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
66257 TTTGACCGGT
66267 CTGACCCGACCCGACTGACCGTTGAC
1 CTGACCCGA-CC-ACTGACCGTTGAC
*
66293 CTGACCCGACCATTGACCGTTGAC
1 CTGACCCGACCACTGACCGTTGAC
66317 GTTGACTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 2 0.09
26 9 0.39
ACGTcount: A:0.20, C:0.40, G:0.22, T:0.18
Consensus pattern (24 bp):
CTGACCCGACCACTGACCGTTGAC
Found at i:66298 original size:21 final size:23
Alignment explanation
Indices: 66259--66316 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 23
66249 TCTGAAGGTT
66259 TGACCGGTCTGACCCGACCCGA-C-
1 TGACC-GT-TGACCCGACCCGACCA
*
66282 TGACCGTTGACCTGACCCGACCA
1 TGACCGTTGACCCGACCCGACCA
66305 TTGACCGTTGAC
1 -TGACCGTTGAC
66317 GTTGACTTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 12 0.39
22 3 0.10
23 5 0.16
24 11 0.35
ACGTcount: A:0.19, C:0.38, G:0.24, T:0.19
Consensus pattern (23 bp):
TGACCGTTGACCCGACCCGACCA
Done.