Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002475.1 Hibiscus syriacus cultivar Beakdansim tig00005057_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: 48540
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1420 original size:2 final size:2
Alignment explanation
Indices: 1413--1441 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1403 CGTTCTTCAA
1413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1442 ATTGCGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4810 original size:29 final size:28
Alignment explanation
Indices: 4726--4810 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 28
4716 CTAAAAATTT
* *
4726 AAACGAACATGTACACCTTAAAAACAA-AC
1 AAACAAACATGAACA-CTTAAAAA-AACAC
* **
4755 AAACAAACATGAACATTTAAACGAACAC
1 AAACAAACATGAACACTTAAAAAAACAC
* *
4783 GAATCAAACATTAACACTTAAAAAAACA
1 -AAACAAACATGAACACTTAAAAAAACA
4811 ATCAAACTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
27 2 0.05
28 7 0.16
29 35 0.80
ACGTcount: A:0.58, C:0.21, G:0.06, T:0.15
Consensus pattern (28 bp):
AAACAAACATGAACACTTAAAAAAACAC
Found at i:5306 original size:16 final size:16
Alignment explanation
Indices: 5265--5306 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
5255 TATAAGTTTA
*
5265 TAAATTATAA-ATTAT
1 TAAAATATAATATTAT
*
5280 TAAAATTTAATATTAT
1 TAAAATATAATATTAT
*
5296 TATAATATAAT
1 TAAAATATAAT
5307 TTTAATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATAATATTAT
Found at i:6241 original size:21 final size:22
Alignment explanation
Indices: 6216--6273 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
6206 GGTGAAATGG
6216 TATTATAATAATAATAA-TAAT
1 TATTATAATAATAATAAGTAAT
* * *
6237 TATTATTATTATAAAAATGTAAT
1 TATTATAATAATAATAA-GTAAT
6260 TATT-TAA-AATAATA
1 TATTATAATAATAATA
6274 TTTAATTTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 19 0.66
22 2 0.07
23 8 0.28
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTATAATAATAATAAGTAAT
Found at i:7051 original size:16 final size:16
Alignment explanation
Indices: 7030--7068 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
7020 GGTATTACCC
7030 GACCTGTTATGAACCT
1 GACCTGTTATGAACCT
7046 GACCTGTTATGAACCT
1 GACCTGTTATGAACCT
7062 GACCTGT
1 GACCTGT
7069 AACTAACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (16 bp):
GACCTGTTATGAACCT
Found at i:7899 original size:23 final size:23
Alignment explanation
Indices: 7873--7923 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
7863 CAGCAAACAA
*
7873 CAACAGGCAGCATTGAATCAATT
1 CAACAAGCAGCATTGAATCAATT
*** *
7896 CAACAAGCATTGTTGCATCAATT
1 CAACAAGCAGCATTGAATCAATT
7919 CAACA
1 CAACA
7924 TTTTTGCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (23 bp):
CAACAAGCAGCATTGAATCAATT
Found at i:10728 original size:46 final size:46
Alignment explanation
Indices: 10678--11005 Score: 315
Period size: 46 Copynumber: 7.0 Consensus size: 46
10668 GAGACAGAAG
* * *
10678 AAGATGAAGAGTCTCAGTTATATTTAGGGTTAGAGAATATGAACAA
1 AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAACAA
*
10724 AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATAAACAAA
1 AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAAC-AA
* * *
10771 AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAAAAAAGATGAACAT
1 AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAACAA
* * * * *
10817 AAGATAAAGA-TC-CTTGATTAGATTTAGGGTTAAAGAAAATAAACAG
1 AAGATAAAGAGTCTC-AG-TTAGATTTAGGGTTAGAGAAGATGAACAA
* * * *
10863 AAGAATAAGAAGAGTCTC-GATTAGATTCAAGGTTATAGAAGAT-AAAAA
1 AAG-AT-A-AAGAGTCTCAG-TTAGATTTAGGGTTAGAGAAGATGAACAA
* *
10911 GAAGAAAAAGAGTCTTAGTTAGATTTAGGGTTAGAGAAGATGAACAAAA
1 -AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAAC--AA
** * * *
10960 AAGAGGAAGAGTCTC-GATTAGATTTGGGGTTAGAAAATATGAACAA
1 AAGATAAAGAGTCTCAG-TTAGATTTAGGGTTAGAGAAGATGAACAA
11006 TACTCTGTTA
Statistics
Matches: 237, Mismatches: 31, Indels: 28
0.80 0.10 0.09
Matches are distributed among these distances:
44 1 0.00
45 3 0.01
46 109 0.46
47 50 0.21
48 41 0.17
49 30 0.13
50 2 0.01
51 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (46 bp):
AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAACAA
Found at i:10799 original size:93 final size:93
Alignment explanation
Indices: 10678--11005 Score: 335
Period size: 93 Copynumber: 3.5 Consensus size: 93
10668 GAGACAGAAG
* * * *
10678 AAGATGAAGAGTCTC-AGTTATATTTAGGGTTAGAGAATATGAACAAAAGATAAAGAGTCTCAGT
1 AAGATAAAGAGTCTCGA-TTAGATTTAGGGTTAGAAAAGATGAACAAAAGATAAAGAGTCTCAGT
10742 TAGATTTAGGGTTAGAGAAGATAAACAAA
65 TAGATTTAGGGTTAGAGAAGATAAACAAA
* * *
10771 AAGATAAAGAGTCTC-AGTTAGATTTAGGGTTAAAAAAGATGAACATAAGATAAAGA-TC-CTTG
1 AAGATAAAGAGTCTCGA-TTAGATTTAGGGTTAGAAAAGATGAACAAAAGATAAAGAGTCTC-AG
* * *
10833 ATTAGATTTAGGGTTAAAGAAAATAAAC-AG
64 -TTAGATTTAGGGTTAGAGAAGATAAACAAA
* * * * * * *
10863 AAGAATAAGAAGAGTCTCGATTAGATTCAAGGTTATAGAAGAT-AAAAAGAAGAAAAAGAGTCTT
1 AAG-AT-A-AAGAGTCTCGATTAGATTTAGGGTTAGAAAAGATGAACAA-AAGATAAAGAGTCTC
*
10927 AGTTAGATTTAGGGTTAGAGAAGATGAACAAAA
62 AGTTAGATTTAGGGTTAGAGAAGATAAAC-AAA
** * *
10960 AAGAGGAAGAGTCTCGATTAGATTTGGGGTTAGAAAATATGAACAA
1 AAGATAAAGAGTCTCGATTAGATTTAGGGTTAGAAAAGATGAACAA
11006 TACTCTGTTA
Statistics
Matches: 191, Mismatches: 32, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
91 1 0.01
92 7 0.04
93 77 0.40
94 32 0.17
95 65 0.34
96 5 0.03
97 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (93 bp):
AAGATAAAGAGTCTCGATTAGATTTAGGGTTAGAAAAGATGAACAAAAGATAAAGAGTCTCAGTT
AGATTTAGGGTTAGAGAAGATAAACAAA
Found at i:10921 original size:95 final size:93
Alignment explanation
Indices: 10724--10983 Score: 294
Period size: 95 Copynumber: 2.8 Consensus size: 93
10714 ATATGAACAA
* *
10724 AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATAAACAAAAAGATA-AAGAGTCTC-A
1 AAGAAAAAGAGTCTTAGTTAGATTTAGGGTTAGAGAAGATAAACAAAAAGA-AGAAGAGTCTCGA
* * * * *
10787 GTTAGATTTAGGGTTAAAAAAGATGAACAT
65 -TTAGATTCAAGGTTAAAAAAGATAAAAAG
* * * *
10817 AAGATAAAGA-TCCTT-GATTAGATTTAGGGTTAAAGAAAATAAACAGAAGAATAAGAAGAGTCT
1 AAGAAAAAGAGT-CTTAG-TTAGATTTAGGGTTAGAGAAGATAAACA-AA-AAGAAGAAGAGTCT
* *
10880 CGATTAGATTCAAGGTTATAGAAGATAAAAAG
62 CGATTAGATTCAAGGTTAAAAAAGATAAAAAG
* *
10912 AAGAAAAAGAGTCTTAGTTAGATTTAGGGTTAGAGAAGATGAACAAAAAAGAGGAAGAGTCTCGA
1 AAGAAAAAGAGTCTTAGTTAGATTTAGGGTTAGAGAAGATAAAC-AAAAAGAAGAAGAGTCTCGA
10977 TTAGATT
65 TTAGATT
10984 TGGGGTTAGA
Statistics
Matches: 141, Mismatches: 17, Indels: 17
0.81 0.10 0.10
Matches are distributed among these distances:
92 2 0.01
93 38 0.27
94 25 0.18
95 72 0.51
96 4 0.03
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.24
Consensus pattern (93 bp):
AAGAAAAAGAGTCTTAGTTAGATTTAGGGTTAGAGAAGATAAACAAAAAGAAGAAGAGTCTCGAT
TAGATTCAAGGTTAAAAAAGATAAAAAG
Found at i:11431 original size:93 final size:93
Alignment explanation
Indices: 11235--11483 Score: 251
Period size: 93 Copynumber: 2.7 Consensus size: 93
11225 ACAAGTTGGG
* * * * *
11235 TATTGGGTTTTT-GTGTTTGTAAAGATTGAATGAGGATTTTGGGGATGAACAAGGGTTGAGTTTT
1 TATT-GGTTTTTGGTGTTTGTAAAGATCGAATGAGGGTTTT-GGGATAAACAAGAGTTGAATTTT
* * *
11299 GTGTGTTGTATTGAAAATAAATTGGTTTGA
64 GAGTGTTGTATCGAAAATAAAATGGTTTGA
* *
11329 TATTGGTTTTTGGTGTTTGTGAAGATCGAATGAGGGTTTTGGGATAAACACGAGTTGAATTTTAG
1 TATTGGTTTTTGGTGTTTGTAAAGATCGAATGAGGGTTTTGGGATAAACAAGAGTTGAATTTT--
11394 GAGT-TTG-ATCGAAAA-AAACAT-GTTTGA
64 GAGTGTTGTATCGAAAATAAA-ATGGTTTGA
* * * *
11421 TATT-GTGTTTTGGTGTTTGTAAAGGTCAAATAAGGGTTTTGGGGATACACATAG-GTTGAATTT
1 TATTGGT-TTTTGGTGTTTGTAAAGATCGAATGAGGGTTTT-GGGATAAACA-AGAGTTGAATTT
11484 GGGTTTATTG
Statistics
Matches: 132, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
91 2 0.02
92 42 0.32
93 52 0.39
94 33 0.25
95 3 0.02
ACGTcount: A:0.27, C:0.04, G:0.29, T:0.40
Consensus pattern (93 bp):
TATTGGTTTTTGGTGTTTGTAAAGATCGAATGAGGGTTTTGGGATAAACAAGAGTTGAATTTTGA
GTGTTGTATCGAAAATAAAATGGTTTGA
Found at i:11820 original size:2 final size:2
Alignment explanation
Indices: 11813--12196 Score: 62
Period size: 2 Copynumber: 190.0 Consensus size: 2
11803 TCAATTAATA
* * *
11813 AT AT AT AT AT AT AT AT AT AT AC AC AT GA- AT AT AT -T CAT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT -AT AT AT
* * *
11855 AT AGT AT -T CAT AT GT AT A- AT AT AT ACT TT GA- AT TT AT AT AT
1 AT A-T AT AT -AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT AT AT
* * *
11896 AA ACT AT AT A- AT TT AT AT AGT AT AT A- AT -T AT AT AGT TT A-
1 AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT
* * * *
11935 ACT AT AA AA AT -T AT AT AGT AT AT AA ACT AT AT AT AGT TT A- ACT
1 A-T AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT A-T AT AT A-T
* * *
11978 AT AT -T AT AT AA ACT AT AT AGT AT AT AA AT -T AT AT AGT TT AT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT
* *
12019 AT AT AGT -T CAT AT AA AT -T AT AGT AT AT AGT TT AT AT A- AT AT
1 AT AT A-T AT -AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* * * *
12060 AT AT AT A- AT TT A- ACT AT AT AGT GT AT AA AT -T AT AT AGT TT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT
* * *
12100 AT AT AT AGT TT AT AT AA ACT AT A- AT AT AT AGT AT AT AA AT -T
1 AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* * *
12141 AT AT AGT TT AT AT AT AGT TT AT AC AT AT -T AT AT -T AT -T AT AT
1 AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
12182 A- AT TT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT
12197 TAATAAATTA
Statistics
Matches: 272, Mismatches: 56, Indels: 108
0.62 0.13 0.25
Matches are distributed among these distances:
1 25 0.09
2 213 0.78
3 34 0.12
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12021 original size:11 final size:11
Alignment explanation
Indices: 12007--12163 Score: 95
Period size: 11 Copynumber: 13.2 Consensus size: 11
11997 GTATATAAAT
12007 TATATAGTTTA
1 TATATAGTTTA
*
12018 TATATAGTTCA
1 TATATAGTTTA
*
12029 TATA-AATTATA
1 TATATAGTT-TA
12040 GTATATAGTTTA
1 -TATATAGTTTA
*
12052 TATA-A-TATA
1 TATATAGTTTA
*
12061 TATATAATTTAA
1 TATATAGTTT-A
12073 CTATATAGTGTATAAA
1 -TATATAGT-T-T--A
12089 TTATATAGTTTA
1 -TATATAGTTTA
12101 TATATAGTTTA
1 TATATAGTTTA
* * *
12112 TATAAACTATAA
1 TATATAGT-TTA
12124 TATATAGTATATAAA
1 TATATAGT-T-T--A
12139 TTATATAGTTTA
1 -TATATAGTTTA
12151 TATATAGTTTA
1 TATATAGTTTA
12162 TA
1 TA
12164 CATATTATAT
Statistics
Matches: 117, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
9 7 0.06
10 5 0.04
11 51 0.44
12 19 0.16
13 10 0.09
14 3 0.03
15 4 0.03
16 18 0.15
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:12075 original size:83 final size:79
Alignment explanation
Indices: 11988--12173 Score: 250
Period size: 83 Copynumber: 2.3 Consensus size: 79
11978 ATATTATATA
* *
11988 AACTATATAGTATATAAATTATATAGTTTATATATAGTTCATATAAATTATAGTATATAGTTTAT
1 AACTATATAGTATATAAATTATATAGTTTATATATAGTTCATATAAACTATAATATATAG--TAT
12053 ATAATATATATATAATTT
64 ATAA-AT-TATATAATTT
* *
12071 AACTATATAGTGTATAAATTATATAGTTTATATATAGTTTATATAAACTATAATATATAGTATAT
1 AACTATATAGTATATAAATTATATAGTTTATATATAGTTCATATAAACTATAATATATAGTATAT
*
12136 AAATTATATAGTTT
66 AAATTATATAATTT
*
12150 -A-TATATAGTTTATACATATTATAT
1 AACTATATAGTATATA-A-ATTATAT
12174 TATTATATAA
Statistics
Matches: 95, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
77 12 0.13
78 2 0.02
79 16 0.17
80 2 0.02
81 7 0.07
83 56 0.59
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (79 bp):
AACTATATAGTATATAAATTATATAGTTTATATATAGTTCATATAAACTATAATATATAGTATAT
AAATTATATAATTT
Found at i:12146 original size:50 final size:51
Alignment explanation
Indices: 12041--12172 Score: 182
Period size: 50 Copynumber: 2.6 Consensus size: 51
12031 TAAATTATAG
* * *
12041 TATATAGTTTATATA-A-TATATATATAATTTAACTATATAGTGTATAAAT
1 TATATAGTTTATATATAGTTTATATATAATATAACTATATAGTATATAAAT
12090 TATATAGTTTATATATAGTTTATATA-AACTATAA-TATATAGTATATAAAT
1 TATATAGTTTATATATAGTTTATATATAA-TATAACTATATAGTATATAAAT
* *
12140 TATATAGTTTATATATAGTTTATACATATTATA
1 TATATAGTTTATATATAGTTTATATATAATATA
12173 TTATTATATA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
49 15 0.20
50 47 0.64
51 12 0.16
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (51 bp):
TATATAGTTTATATATAGTTTATATATAATATAACTATATAGTATATAAAT
Found at i:13731 original size:64 final size:64
Alignment explanation
Indices: 13552--13712 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
13542 GAATAAATTG
* *
13552 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATACACTCATGGTTTTATGAA
1 AACATCAAATGCATTTTATGCATCGATGCACATA-CATGCATCGATGCACTCATGGTTTTATGAA
* *
13617 AACATCAAATGCATTTAATGCATCGATGCACAAGACATGCATCGATGCACTCA-GGCTATTT-TG
1 AACATCAAATGCATTTTATGCATCGATGCAC-ATACATGCATCGATGCACTCATGG-T-TTTATG
13680 -A
63 AA
13681 AACATCAAATGCATTTTATGCATCGATGCACA
1 AACATCAAATGCATTTTATGCATCGATGCACA
13713 CTTAGTGCAC
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
63 1 0.01
64 33 0.38
65 49 0.56
66 5 0.06
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (64 bp):
AACATCAAATGCATTTTATGCATCGATGCACATACATGCATCGATGCACTCATGGTTTTATGAA
Found at i:22317 original size:64 final size:65
Alignment explanation
Indices: 22161--22321 Score: 238
Period size: 65 Copynumber: 2.5 Consensus size: 65
22151 GAATAAATTG
* * *
22161 AACATCGAATGCATTTTATGCATCGATACACATACCATACATCGATGCACTCAGGGTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACATAACATACATCGATGCACTCAGGCTTTTATGAA
* *
22226 AACATCGAATGCATTTGATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-TG
1 AACATCGAATGCATTTTATGCATCGATGCACATA-ACATACATCGATGCACTCAGGCT-TTTATG
22289 -A
64 AA
22290 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTTATGCATCGATGCACA
22322 CTTAGTGCAC
Statistics
Matches: 88, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 33 0.38
65 52 0.59
66 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACATAACATACATCGATGCACTCAGGCTTTTATGAA
Found at i:22336 original size:64 final size:66
Alignment explanation
Indices: 22161--22339 Score: 235
Period size: 65 Copynumber: 2.8 Consensus size: 66
22151 GAATAAATTG
* *
22161 AACATCGAATGCATTTTATGCATCGAT--ACACATACCATACATCGATGCACTCAGGGTTTTATG
1 AACATCGAATGCATTTTATGCATCGATGCACACATA-CATGCATCGATGCACTCAGGCTTTTATG
22224 AA
65 AA
* *
22226 AACATCGAATGCATTTGATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-TG
1 AACATCGAATGCATTTTATGCATCGATGCACACATACATGCATCGATGCACTCAGGCT-TTTATG
22289 -A
65 AA
* * *
22290 AACATCGAATGCATTTTATGCATCGATGCACACTTA-GTGCACCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCACACATACATGCATCGATGCAC
22340 CTTGTGTATG
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
64 44 0.44
65 49 0.49
66 5 0.05
67 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (66 bp):
AACATCGAATGCATTTTATGCATCGATGCACACATACATGCATCGATGCACTCAGGCTTTTATGA
A
Found at i:24323 original size:25 final size:23
Alignment explanation
Indices: 24279--24328 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
24269 CGGGACATAC
*
24279 AGTGATCATTCGGGATATTTCAT
1 AGTGATCATTCGGGAAATTTCAT
*
24302 AGTGGTCATTCGGGACAAATTTCAT
1 AGTGATCATTCGGG--AAATTTCAT
24327 AG
1 AG
24329 CCCCTAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
25 10 0.43
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (23 bp):
AGTGATCATTCGGGAAATTTCAT
Found at i:31528 original size:17 final size:17
Alignment explanation
Indices: 31508--31540 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31498 ATATTTATTT
31508 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
31525 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
31541 TGTGATCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:31638 original size:17 final size:16
Alignment explanation
Indices: 31613--31648 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
31603 TTAAATATTA
31613 TTTTAAATAATAATAT
1 TTTTAAATAATAATAT
31629 TTTTACAATAATAATAT
1 TTTTA-AATAATAATAT
31646 TTT
1 TTT
31649 CACCTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAATAATAATAT
Found at i:32564 original size:24 final size:24
Alignment explanation
Indices: 32533--32594 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
32523 ACAACCGTCT
32533 TCTCTTCCTCTTTCTTCTTCTGGC
1 TCTCTTCCTCTTTCTTCTTCTGGC
32557 TCTCTTCCTCTTTCTTCTTCTGGC
1 TCTCTTCCTCTTTCTTCTTCTGGC
*
32581 ACTCTTCCTCTTTC
1 TCTCTTCCTCTTTC
32595 AATCCATTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.02, C:0.39, G:0.06, T:0.53
Consensus pattern (24 bp):
TCTCTTCCTCTTTCTTCTTCTGGC
Found at i:33613 original size:20 final size:20
Alignment explanation
Indices: 33573--33614 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
33563 TTTATTTTAA
*
33573 TTCTATTCAATTTAGTCGTG
1 TTCTATTCAATTTAATCGTG
*
33593 TTCTATTCAATTTAATTGTG
1 TTCTATTCAATTTAATCGTG
33613 TT
1 TT
33615 GATGCTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (20 bp):
TTCTATTCAATTTAATCGTG
Found at i:37589 original size:20 final size:20
Alignment explanation
Indices: 37566--37603 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
37556 TACCATGGAC
37566 AAAATTATAAGATTTTTAAT
1 AAAATTATAAGATTTTTAAT
*
37586 AAAATTATAAGTTTTTTA
1 AAAATTATAAGATTTTTA
37604 GCTTATGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAATTATAAGATTTTTAAT
Found at i:38298 original size:2 final size:2
Alignment explanation
Indices: 38291--38319 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38281 AGAAGCATGC
38291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38320 GCAAAATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39161 original size:17 final size:17
Alignment explanation
Indices: 39139--39177 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
39129 TGAATCAAAT
39139 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
39156 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
39173 -AATTA
1 TAATTA
39178 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:39235 original size:18 final size:18
Alignment explanation
Indices: 39209--39284 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 18
39199 TAAAAAATAT
39209 TAAAATATTT-TATATTAA
1 TAAAATATTTATA-ATTAA
*
39227 TAAAGTATTTATAATTAATA
1 TAAAATATTTATAATT-A-A
*
39247 TTAAAATAATTATATATT-A
1 -TAAAATATTTATA-ATTAA
*
39266 TAATATA-TTATAATTAA
1 TAAAATATTTATAATTAA
39283 TA
1 TA
39285 TTAATTTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
16 3 0.06
17 8 0.17
18 18 0.38
19 4 0.08
20 1 0.02
21 11 0.23
22 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (18 bp):
TAAAATATTTATAATTAA
Found at i:39265 original size:16 final size:16
Alignment explanation
Indices: 39237--39282 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
39227 TAAAGTATTT
39237 ATAATTA-ATATTAAA
1 ATAATTATATATTAAA
*
39252 ATAATTATATATTATA
1 ATAATTATATATTAAA
39268 ATATATTATA-ATTAA
1 ATA-ATTATATATTAA
39283 TATTAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 14 0.52
17 6 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTATATATTAAA
Found at i:39277 original size:38 final size:39
Alignment explanation
Indices: 39204--39302 Score: 125
Period size: 38 Copynumber: 2.6 Consensus size: 39
39194 TTAATTAAAA
*
39204 AATATTAAAAT-ATTTTATATTAATAAAGTATTTATAATT
1 AATATTAAAATAATTATATATT-ATAAAGTATTTATAATT
39243 AATATTAAAATAATTATATATTAT-AA-TATATTATAATT
1 AATATTAAAATAATTATATATTATAAAGTAT-TTATAATT
**
39281 AATATTAATTTAATTA-ATATTA
1 AATATTAAAATAATTATATATTA
39303 ACTTATATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
37 9 0.16
38 24 0.44
39 13 0.24
40 9 0.16
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (39 bp):
AATATTAAAATAATTATATATTATAAAGTATTTATAATT
Found at i:39315 original size:15 final size:15
Alignment explanation
Indices: 39276--39307 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39266 TAATATATTA
*
39276 TAATTAATATTAATT
1 TAATTAATATTAACT
39291 TAATTAATATTAACT
1 TAATTAATATTAACT
39306 TA
1 TA
39308 TATAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTAATATTAACT
Found at i:39325 original size:7 final size:7
Alignment explanation
Indices: 39315--39346 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
39305 TTATATAATA
39315 TATAGTT
1 TATAGTT
39322 TATAGTT
1 TATAGTT
39329 TATAGTT
1 TATAGTT
39336 TATAGTT
1 TATAGTT
39343 TATA
1 TATA
39347 ATTTGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (7 bp):
TATAGTT
Found at i:39332 original size:21 final size:21
Alignment explanation
Indices: 39308--39355 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
39298 TATTAACTTA
*
39308 TATAATATATAGTTTATAGTT
1 TATAATATATAGTTTATAATT
* *
39329 TATAGTTTATAGTTTATAATT
1 TATAATATATAGTTTATAATT
*
39350 TGTAAT
1 TATAAT
39356 TAATATTAAT
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:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (21 bp):
TATAATATATAGTTTATAATT
Found at i:39433 original size:14 final size:14
Alignment explanation
Indices: 39416--39477 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
39406 ATGTTATAAA
39416 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
39430 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
39444 TCATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
39459 TAATATAGTATAGT
1 TTATATAGTATAGT
39473 TTATA
1 TTATA
39478 AACTATATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.62
15 8 0.22
16 3 0.08
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:39467 original size:43 final size:40
Alignment explanation
Indices: 39418--39508 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 40
39408 GTTATAAATT
* *
39418 ATATAGTATAGTTTATAAACTATAGTTCATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA-TAC-TAT-ATTAATATAA
39461 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
39501 ATTATAGT
1 A-TATAGT
39509 TAAGATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 10 0.22
41 9 0.20
42 2 0.04
43 24 0.53
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
Found at i:39506 original size:15 final size:15
Alignment explanation
Indices: 39488--39538 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
39478 AACTATATAC
39488 TATATTAATATAAAT
1 TATATTAATATAAAT
*
39503 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
39518 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
39534 TATAT
1 TATAT
39539 AGTACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:39545 original size:22 final size:22
Alignment explanation
Indices: 39520--39622 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
39510 AAGATAATTA
39520 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
39542 ACATTAATATAAAC--TATAGT
1 ACATTAATATAAACTATATAGT
** * * *
39562 TTATAAATTATATACTATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
39584 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
39606 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
39623 TGTTTATAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
20 10 0.15
21 22 0.34
22 28 0.43
23 5 0.08
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:39578 original size:21 final size:21
Alignment explanation
Indices: 39549--39601 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
39539 AGTACATTAA
* *
39549 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
39570 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
39591 TATAAACTATA
1 TATAAACTATA
39602 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:39637 original size:21 final size:20
Alignment explanation
Indices: 39547--39638 Score: 78
Period size: 21 Copynumber: 4.3 Consensus size: 20
39537 ATAGTACATT
39547 AATATAAACTATAGTTTATA
1 AATATAAACTATAGTTTATA
* *
39567 AATTATATACTATAGGTTATA
1 AA-TATAAACTATAGTTTATA
* *
39588 AAGTATAAACTATA-TAGTACA
1 AA-TATAAACTATAGT-TTATA
*
39609 CTAATATAAACTATTGTTTATA
1 --AATATAAACTATAGTTTATA
39631 AACTATAA
1 AA-TATAA
39639 GTTACATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
20 4 0.07
21 36 0.64
22 13 0.23
23 3 0.05
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.38
Consensus pattern (20 bp):
AATATAAACTATAGTTTATA
Found at i:39671 original size:20 final size:19
Alignment explanation
Indices: 39644--39736 Score: 52
Period size: 20 Copynumber: 4.8 Consensus size: 19
39634 TATAAGTTAC
39644 ATAT-ATAGTTTATATAAA
1 ATATAATAGTTTATATAAA
*
39662 ATATAAATAGATTGTATATATAC
1 ATAT-AATAG-TT-TATATA-AA
*
39685 ATATACTATAGGTTATAT---
1 ATATA--ATAGTTTATATAAA
*
39703 ATAT-ATAGTTTATATATA
1 ATATAATAGTTTATATAAA
*
39721 GTATACATAGTTTATA
1 ATATA-ATAGTTTATA
39737 CATACATGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 22
0.69 0.05 0.26
Matches are distributed among these distances:
15 10 0.17
18 11 0.19
20 14 0.24
21 2 0.03
22 12 0.20
23 6 0.10
24 4 0.07
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (19 bp):
ATATAATAGTTTATATAAA
Found at i:39705 original size:57 final size:55
Alignment explanation
Indices: 39632--39769 Score: 177
Period size: 59 Copynumber: 2.4 Consensus size: 55
39622 TTGTTTATAA
*
39632 ACTATAAGTTACATATATAGTTTATATAAAATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTTTATATAAAATATAAATAG-TT-TATACATACATAT
* * * * * *
39689 ACTATAGGTTATATATATATAGTTTATATATAGTATACATAGTTTATACATACATGT
1 ACTATAAG-T-TACATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
39746 ACTATAAGTTACATATATAGTTTA
1 ACTATAAGTTACATATATAGTTTA
39770 CATGTATACA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
55 14 0.20
56 1 0.01
57 25 0.36
58 3 0.04
59 27 0.39
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.42
Consensus pattern (55 bp):
ACTATAAGTTACATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
Found at i:39709 original size:15 final size:16
Alignment explanation
Indices: 39685--39725 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
39675 GTATATATAC
39685 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
39701 ATATA-TATAGTTTAT
1 ATATACTATAGGTTAT
*
39716 ATATAGTATA
1 ATATACTATA
39726 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:39715 original size:59 final size:57
Alignment explanation
Indices: 39632--39764 Score: 171
Period size: 57 Copynumber: 2.3 Consensus size: 57
39622 TTGTTTATAA
*
39632 ACTATAAGTTAC--ATATATAGTTTATATAAAATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATATAGTTTATATAAAATATAAATAG-TT-TATACATACATAT
* * * * * *
39689 ACTATAGGTTATATATATATAGTTTATATATAGTATACATAGTTTATACATACATGT
1 ACTATAAGTTACATATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
39746 ACTATAAGTTACATATATA
1 ACTATAAGTTACATATATA
39765 GTTTACATGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 38 0.58
58 2 0.03
59 25 0.38
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (57 bp):
ACTATAAGTTACATATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
Found at i:39832 original size:7 final size:7
Alignment explanation
Indices: 39820--39859 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
39810 TATGCATAAT
39820 GTTTAGG
1 GTTTAGG
*
39827 GTTTAGA
1 GTTTAGG
39834 GTTTATGG
1 GTTTA-GG
39842 G-TTAGG
1 GTTTAGG
39848 GTTTAGG
1 GTTTAGG
39855 GTTTA
1 GTTTA
39860 TATTTTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 3 0.10
7 24 0.83
8 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:39921 original size:35 final size:36
Alignment explanation
Indices: 39843--39928 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 36
39833 AGTTTATGGG
* * *
39843 TTAGGG-TTTAGGGTTTATATTTTAATGTTTATGAT
1 TTAGGGATTTAGGGTTTATAGTATAATGTTTAGGAT
* *
39878 TTA-TGATTTAGGGTTTAT-GTATATTGTTTAGGAT
1 TTAGGGATTTAGGGTTTATAGTATAATGTTTAGGAT
39912 TTAGGGATTTAGGGTTT
1 TTAGGGATTTAGGGTTT
39929 CTATAAACTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
34 16 0.37
35 27 0.63
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (36 bp):
TTAGGGATTTAGGGTTTATAGTATAATGTTTAGGAT
Found at i:40285 original size:2 final size:2
Alignment explanation
Indices: 40278--40430 Score: 122
Period size: 2 Copynumber: 77.0 Consensus size: 2
40268 GCATAGTGTT
40278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
40320 TA TA TA TA TA TA TC TA TA GA T- TA CT- TA TA T- TA GT- TA -A CA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA
* * * *
40359 TA CA TA TA TA TA CTA TA TA -A TT TA TA AA CTA TA TA TT TA TA GT-
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* *
40402 TA TA CA TA TA TA GTT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
40431 ATTAAAAGTA
Statistics
Matches: 121, Mismatches: 17, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
1 7 0.06
2 107 0.88
3 7 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:40404 original size:21 final size:21
Alignment explanation
Indices: 40380--40420 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40370 ACTATATAAT
40380 TTATAAACTATATA-TTTATAG
1 TTATAAA-TATATAGTTTATAG
*
40401 TTATACATATATAGTTTATA
1 TTATAAATATATAGTTTATA
40421 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (21 bp):
TTATAAATATATAGTTTATAG
Found at i:40867 original size:15 final size:15
Alignment explanation
Indices: 40847--40878 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40837 ATATACTTTT
40847 TATAGTTTATACATA
1 TATAGTTTATACATA
*
40862 TATAGTTTATATATA
1 TATAGTTTATACATA
40877 TA
1 TA
40879 CTTGCTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:43232 original size:2 final size:2
Alignment explanation
Indices: 43227--43297 Score: 90
Period size: 2 Copynumber: 35.5 Consensus size: 2
43217 TTATATAGTT
* * * *
43227 TA TA TA TA AA TA TA GTT TA TA TA TA AA TT TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43298 TATTTTTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
1 1 0.02
2 57 0.97
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45307 original size:20 final size:18
Alignment explanation
Indices: 45278--45324 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
45268 AATTCAAAAC
45278 TTCATTTCACTCATATTCT
1 TTCATTTCACTCATATT-T
45297 TTCATTTTCACTCATATTT
1 TTCA-TTTCACTCATATTT
*
45316 TTCCTTTCA
1 TTCATTTCA
45325 GATACTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 8 0.31
20 13 0.50
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (18 bp):
TTCATTTCACTCATATTT
Done.