Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002633.1 Hibiscus syriacus cultivar Beakdansim tig00005367_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: 111620
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:1301 original size:20 final size:21
Alignment explanation
Indices: 1255--1309 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1245 ATTTATATCA
*
1255 AAGATAAAAATAAAAATAGAAC
1 AAGAT-AAAATAAAAATACAAC
* *
1277 GAGAT-AAATAAAAATACAAT
1 AAGATAAAATAAAAATACAAC
1297 AAGATAAAATAAA
1 AAGATAAAATAAA
1310 GCAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 17 0.61
21 7 0.25
22 4 0.14
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (21 bp):
AAGATAAAATAAAAATACAAC
Found at i:1847 original size:16 final size:16
Alignment explanation
Indices: 1811--1846 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1801 GGGACTGAAA
*
1811 TAAAATGCAACAAAAT
1 TAAAAGGCAACAAAAT
1827 TAAAAGGCAA-AAAAT
1 TAAAAGGCAACAAAAT
1842 TAAAA
1 TAAAA
1847 ATGTTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.17
Consensus pattern (16 bp):
TAAAAGGCAACAAAAT
Found at i:2124 original size:32 final size:32
Alignment explanation
Indices: 2044--2152 Score: 103
Period size: 32 Copynumber: 3.3 Consensus size: 32
2034 GTGTTAGTAA
* *
2044 GTTAGTAATAACAATAAAAAAATAAAAAGTTAGTAT
1 GTTAGTAAGAACAAT---AAAATAAAAA-TTAGAAT
2080 GTTAGTAAGAACAA-ATAAATAAAAATTAGAAT
1 GTTAGTAAGAACAATA-AAATAAAAATTAGAAT
** * *
2112 GTTAGTTCGAACAATAAAATAAAAGTAAGAAT
1 GTTAGTAAGAACAATAAAATAAAAATTAGAAT
*
2144 GCTAGTAAG
1 GTTAGTAAG
2153 TTAGTGATTA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
32 39 0.63
33 10 0.16
36 13 0.21
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.26
Consensus pattern (32 bp):
GTTAGTAAGAACAATAAAATAAAAATTAGAAT
Found at i:6296 original size:43 final size:44
Alignment explanation
Indices: 6222--6304 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
6212 CTTTCTAGAA
* *
6222 GATATGGGCCCTCAAAAATGCCTCGAAATTTATCATTTCTCTAT
1 GATATGGGCCCTAAAAAATGCCTCCAAATTTATCATTTCTCTAT
*
6266 GATATGGG-CCTAAAAAATGCC-CCACCATTTATCATTTCT
1 GATATGGGCCCTAAAAAATGCCTCCA-AATTTATCATTTCT
6305 GGGTTCAGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 2 0.06
43 25 0.71
44 8 0.23
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (44 bp):
GATATGGGCCCTAAAAAATGCCTCCAAATTTATCATTTCTCTAT
Found at i:6706 original size:16 final size:16
Alignment explanation
Indices: 6685--6717 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6675 AACATTTATG
6685 TTTCAGTTCTATGAAA
1 TTTCAGTTCTATGAAA
6701 TTTCAGTTCTATGAAA
1 TTTCAGTTCTATGAAA
6717 T
1 T
6718 CTTCCGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (16 bp):
TTTCAGTTCTATGAAA
Found at i:6929 original size:2 final size:2
Alignment explanation
Indices: 6922--6980 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
6912 CTTATTGTAC
6922 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6963 AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT A
6981 ATTGCCTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11910 original size:6 final size:6
Alignment explanation
Indices: 11901--11979 Score: 51
Period size: 6 Copynumber: 12.8 Consensus size: 6
11891 TATTTATATC
11901 AAAAAT AAAAAT -AAAAT AAAAAT AGCACAAGAT -AAAAT -AAAAT -AAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT A--A-AA-AT AAAAAT AAAAAT AAAAAT
*
11949 AAAAAGAT AAAAAT AAAGCA- AAAAAT AAAAA
1 -AAAA-AT AAAAAT AAA-AAT AAAAAT AAAAA
11980 GAAGACTATC
Statistics
Matches: 61, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
5 18 0.30
6 27 0.44
7 9 0.15
8 3 0.05
9 2 0.03
10 2 0.03
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:11979 original size:18 final size:18
Alignment explanation
Indices: 11901--11979 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
11891 TATTTATATC
*
11901 AAAAATAAAA-ATAAAAT
1 AAAAATAAAACAAAAAAT
**
11918 AAAAATAGCACAAGATAAA-
1 AAAAATAAAACAA-A-AAAT
*
11937 ATAAAATAAAATAAAAAGAT
1 A-AAAATAAAACAAAAA-AT
*
11957 AAAAATAAAGCAAAAAAT
1 AAAAATAAAACAAAAAAT
11975 AAAAA
1 AAAAA
11980 GAAGACTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
17 8 0.17
18 10 0.21
19 17 0.35
20 13 0.27
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAAATAAAACAAAAAAT
Found at i:12747 original size:34 final size:33
Alignment explanation
Indices: 12695--12764 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
12685 TTAGTTTGTG
** *
12695 CAATAAAATAAAGTGTTAGTAAGTTAGTAATAA
1 CAATAAAATAAAAAGTTAGTAAGTTAGTAAGAA
*
12728 CAATAAAAATAAAAAGTTAGTATGTTAGTAAGAA
1 CAAT-AAAATAAAAAGTTAGTAAGTTAGTAAGAA
12762 CAA
1 CAA
12765 ATAATGTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 4 0.12
34 28 0.88
ACGTcount: A:0.54, C:0.04, G:0.14, T:0.27
Consensus pattern (33 bp):
CAATAAAATAAAAAGTTAGTAAGTTAGTAAGAA
Found at i:12773 original size:19 final size:19
Alignment explanation
Indices: 12749--12787 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12739 AAAAGTTAGT
12749 ATGTTAGTAAGAACAAATA
1 ATGTTAGTAAGAACAAATA
*
12768 ATGTTAGTAGGAACAAATA
1 ATGTTAGTAAGAACAAATA
12787 A
1 A
12788 ATAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (19 bp):
ATGTTAGTAAGAACAAATA
Found at i:12803 original size:32 final size:32
Alignment explanation
Indices: 12767--12840 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
12757 AAGAACAAAT
* *
12767 AATGTTAGTAGGAACAA-ATAAATAAAATTTAG
1 AATGTTAGTACGAACAATA-AAATAAAAGTTAG
* *
12799 AATGTTATTTCGAACAATAAAATAAAAGTTAG
1 AATGTTAGTACGAACAATAAAATAAAAGTTAG
12831 AATGTTAGTA
1 AATGTTAGTA
12841 AGTTAGTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 34 0.97
33 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (32 bp):
AATGTTAGTACGAACAATAAAATAAAAGTTAG
Found at i:19690 original size:20 final size:19
Alignment explanation
Indices: 19622--19687 Score: 105
Period size: 19 Copynumber: 3.4 Consensus size: 19
19612 AAACCCCAAA
*
19622 TTCCTTTTCGATCTCAAAT
1 TTCCTTTTCGATCTCGAAT
*
19641 TTCCTTTTTTGATCTCGAAT
1 TTCC-TTTTCGATCTCGAAT
19661 TTCCTTTTCGATCTCGAAT
1 TTCCTTTTCGATCTCGAAT
19680 TTCCTTTT
1 TTCCTTTT
19688 TCGCTCATCT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 26 0.60
20 17 0.40
ACGTcount: A:0.15, C:0.24, G:0.08, T:0.53
Consensus pattern (19 bp):
TTCCTTTTCGATCTCGAAT
Found at i:22154 original size:26 final size:26
Alignment explanation
Indices: 22125--22176 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
22115 CCCTTCCAGG
22125 GAATCCTATCTCTAAAAGTGAGAATA
1 GAATCCTATCTCTAAAAGTGAGAATA
22151 GAATCCTATCTCTAAAAGTGAGAATA
1 GAATCCTATCTCTAAAAGTGAGAATA
22177 TATATATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (26 bp):
GAATCCTATCTCTAAAAGTGAGAATA
Found at i:24576 original size:21 final size:21
Alignment explanation
Indices: 24550--24609 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
24540 GCAAAACCTG
*
24550 CTGAAAATCCTATAGCCACTA
1 CTGAAAATCCTACAGCCACTA
* *
24571 CTGAAAATCCTACAACCACTG
1 CTGAAAATCCTACAGCCACTA
*
24592 CTGAAATTCCTACAGCCA
1 CTGAAAATCCTACAGCCA
24610 TTGTAATTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (21 bp):
CTGAAAATCCTACAGCCACTA
Found at i:27693 original size:2 final size:2
Alignment explanation
Indices: 27686--27725 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
27676 ATTCTAATCC
27686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27726 GCTCTCATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33221 original size:32 final size:32
Alignment explanation
Indices: 33185--33250 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
33175 CCCACTTATT
33185 TCTCTTCTACATCCTCATGAAGACAGAGAATA
1 TCTCTTCTACATCCTCATGAAGACAGAGAATA
33217 TCTCTTCTACATCCTCATGAAGACAGAGAATA
1 TCTCTTCTACATCCTCATGAAGACAGAGAATA
33249 TC
1 TC
33251 GACATTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (32 bp):
TCTCTTCTACATCCTCATGAAGACAGAGAATA
Found at i:34001 original size:37 final size:37
Alignment explanation
Indices: 33958--34061 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
33948 ATTTTCGTCT
*
33958 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
33995 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * * *
34032 TACTAAGATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
34062 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:34456 original size:18 final size:17
Alignment explanation
Indices: 34417--34459 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
34407 ATTATATGGA
34417 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
34433 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
34451 TATTATTAT
1 TATTATTAT
34460 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:34509 original size:12 final size:12
Alignment explanation
Indices: 34416--34549 Score: 61
Period size: 12 Copynumber: 11.1 Consensus size: 12
34406 TATTATATGG
34416 ATATTTTATTCAT
1 ATATTTTATT-AT
*
34429 TTATTTTTATTAT
1 ATA-TTTTATTAT
*
34442 -TCATGTTATTAT
1 AT-ATTTTATTAT
*
34454 -TATTATATGTAT
1 ATATTTTAT-TAT
* *
34466 ATATATATATTAA
1 ATAT-TTTATTAT
34479 ATTATTTTCATT-T
1 A-TATTTT-ATTAT
34492 AT-TTTT-TTACT
1 ATATTTTATTA-T
34503 ATATTTTATTAT
1 ATATTTTATTAT
*
34515 ATA-TATA-TAT
1 ATATTTTATTAT
34525 ATATTTCT-TTA-
1 ATATTT-TATTAT
34536 ATATTTTACTTAT
1 ATATTTTA-TTAT
34549 A
1 A
34550 AGTCTAATAT
Statistics
Matches: 95, Mismatches: 9, Indels: 34
0.69 0.07 0.25
Matches are distributed among these distances:
9 2 0.02
10 7 0.07
11 22 0.23
12 28 0.29
13 18 0.19
14 18 0.19
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:39753 original size:182 final size:183
Alignment explanation
Indices: 39229--39764 Score: 950
Period size: 183 Copynumber: 2.9 Consensus size: 183
39219 ATTAAATCCG
39229 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
39294 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGATTGCTCTACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
39359 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
**
39412 TAAAATTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
39477 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
39542 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
39595 TAAAGCTGAGCTATTCCACTAAGGTAATTGGTTATAGAGG-AACTCGAAAGCCCTAGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
39659 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* *
39723 TTTGTCAGGTCAAAGACTTTGTAATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
39765 TAAACCTGAT
Statistics
Matches: 339, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
181 1 0.00
182 122 0.36
183 216 0.64
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:40939 original size:36 final size:34
Alignment explanation
Indices: 40899--41012 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 34
40889 CACTCAAATT
40899 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
40935 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
40971 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
41007 CGTTTT
1 TGTTTT
41013 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 49 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:40975 original size:72 final size:75
Alignment explanation
Indices: 40883--41066 Score: 220
Period size: 72 Copynumber: 2.5 Consensus size: 75
40873 ATGCAGATGA
* * * *
40883 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
40945 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
40955 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
41020 AAGAAGGCAT
66 AAGAAGGCAT
** *
41030 TTCATTTCACTCAAGGCTGTTTTT-TT-AAAGAAGATTT
1 TT-ATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTT
41067 TATCTTGCTT
Statistics
Matches: 98, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
71 1 0.01
72 50 0.51
73 11 0.11
74 11 0.11
75 6 0.06
76 19 0.19
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:41117 original size:39 final size:39
Alignment explanation
Indices: 41074--41194 Score: 133
Period size: 39 Copynumber: 3.2 Consensus size: 39
41064 TTTTATCTTG
41074 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * * ** * *
41113 CTTGA-AAACATTTCCCTTG-AA-A-TTAATTTTTTCTCT
1 CTTGAGATA-GTTTCCCTCGAAACAGAAAATTTTGTCTCC
*
41149 CATGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
41188 CTTGAGA
1 CTTGAGA
41195 CAATTTCTCT
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
36 22 0.36
37 5 0.08
38 5 0.08
39 29 0.48
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (39 bp):
CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:41210 original size:39 final size:39
Alignment explanation
Indices: 41074--41211 Score: 131
Period size: 39 Copynumber: 3.6 Consensus size: 39
41064 TTTTATCTTG
*
41074 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAATTTCCCTCGAAACAGAAAATTTTGTCTCC
* * ** * *
41113 CTTGA-AAACATTTCCCTTG-AA-A-TTAATTTTTTCTCT
1 CTTGAGATA-ATTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
41149 CATGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAATTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
41188 CTTGAGACAATTTCTCTTGAAACA
1 CTTGAGATAATTTCCCTCGAAACA
41212 TAAACATTGA
Statistics
Matches: 74, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
36 22 0.30
37 5 0.07
38 5 0.07
39 42 0.57
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (39 bp):
CTTGAGATAATTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:41279 original size:102 final size:102
Alignment explanation
Indices: 41114--41429 Score: 494
Period size: 102 Copynumber: 3.1 Consensus size: 102
41104 TTTGTCTCCC
*
41114 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCATGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAA-TAATTTTTT-TCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
*
41179 TTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACA
64 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
41218 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTT
1 TTGAAAACATTTCCCTTGAAATAATTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTT
41283 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
41320 TTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAAT-AATTTT-TTTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
41382 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
64 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
41421 TTGAAAACA
1 TTGAAAACA
41430 ATTTAACGAA
Statistics
Matches: 200, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
101 48 0.24
102 92 0.46
103 14 0.07
104 46 0.23
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (102 bp):
TTGAAAACATTTCCCTTGAAATAATTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTT
TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:41376 original size:36 final size:36
Alignment explanation
Indices: 41329--41404 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
41319 ATTGAAAACA
* * *
41329 TTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAG
* *
41365 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAG
41401 TTTC
1 TTTC
41405 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAG
Found at i:41804 original size:105 final size:105
Alignment explanation
Indices: 41573--42234 Score: 931
Period size: 105 Copynumber: 6.3 Consensus size: 105
41563 AACATCCGCG
* * * * * *
41573 ATTTCAACTCCACAACGGAGGATATCGTGACACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TG-GACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
41638 GGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
*
41682 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTAAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
41747 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
41787 ATTTCAAATTCACAACGAAGGATATTGGATTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
41852 ACTGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
41892 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
41957 ACCGTTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
41997 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
42062 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGAGTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * *
42097 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
42162 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * *
42203 ATTTCAATTTCACGACGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
42235 GGAACAATGC
Statistics
Matches: 506, Mismatches: 40, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
100 82 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 303 0.60
106 81 0.16
107 4 0.01
109 23 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:42830 original size:37 final size:37
Alignment explanation
Indices: 42778--42881 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
42768 ATTTTCGTCT
*
42778 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
42815 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * * *
42852 TACTAAGATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
42882 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:43276 original size:18 final size:17
Alignment explanation
Indices: 43237--43279 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
43227 ATTATATGGA
43237 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
43253 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
43271 TATTATTAT
1 TATTATTAT
43280 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:43313 original size:55 final size:55
Alignment explanation
Indices: 43249--43355 Score: 132
Period size: 55 Copynumber: 1.9 Consensus size: 55
43239 TTTTATTCAT
43249 TTATTTTTA-TTATTCATGTTA-T-TATTATTA-TATGTATATATATATATATATTAAA
1 TTATTTTTATTTATT-ATGTTACTATATT-TTATTAT-TAT-TATATATATATATTAAA
* *
43304 TTATTTTTATTTATTTTTTTACTATATTTTATTATTATTATATATATATATT
1 TTATTTTTATTTATTATGTTACTATATTTTATTATTATTATATATATATATT
43356 TCTTTAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
55 27 0.59
56 12 0.26
57 7 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (55 bp):
TTATTTTTATTTATTATGTTACTATATTTTATTATTATTATATATATATATTAAA
Found at i:46228 original size:6 final size:6
Alignment explanation
Indices: 46163--46241 Score: 95
Period size: 6 Copynumber: 13.2 Consensus size: 6
46153 TCTACAAAAA
* * * * *
46163 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAT TATTAT TATTAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
**
46211 TATTAT TATTAT TATTAT TAACAT TATTAT T
1 TATTAT TATTAT TATTAT TATTAT TATTAT T
46242 TTACAACTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (6 bp):
TATTAT
Found at i:52202 original size:2 final size:2
Alignment explanation
Indices: 52195--52227 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
52185 TACCCAACAA
52195 AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52228 CAATAAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:53605 original size:34 final size:34
Alignment explanation
Indices: 53561--53627 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
53551 TGATGGTGTT
53561 TTTCTAAAAACAAATTTTGTCTCACTTGAGACAA
1 TTTCTAAAAACAAATTTTGTCTCACTTGAGACAA
* **
53595 TTTCTCAAAACAAATTTTGTCTTGCTTGAGACA
1 TTTCTAAAAACAAATTTTGTCTCACTTGAGACA
53628 TTTTTCCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (34 bp):
TTTCTAAAAACAAATTTTGTCTCACTTGAGACAA
Found at i:54058 original size:69 final size:71
Alignment explanation
Indices: 53976--54206 Score: 228
Period size: 69 Copynumber: 3.3 Consensus size: 71
53966 AATTTATAAT
* *
53976 CTTTGAG-TCTGTTTCTCTTGAAACAAAAT-TT-TGTCTCCTCGAGA-CATTTCTTATGAAACAA
1 CTTTGAGAT-TGTTTCTCTTGAAACAAAATCTTAT-TCTCCTCGAAACCATTTCTCATGAAACAA
54037 CAACCAAA
64 CAACCAAA
* * * *
54045 CTTTGAGATTGTTTAC-CTTGAAAC-AAATCTTATTTTCCTTGAAACCGTTTCTCATGAAACAAT
1 CTTTGAGATTGTTT-CTCTTGAAACAAAATCTTATTCTCCTCGAAACCATTTCTCATGAAACAAC
54108 AACCAAA
65 AACCAAA
* * ** * *
54115 CTTTGAGATTGTTTCTCTTGAAAC-AAATC-TATTTTCCTTGAGGCCGTTTCTCATTAAACAACA
1 CTTTGAGATTGTTTCTCTTGAAACAAAATCTTATTCTCCTCGAAACCATTTCTCATGAAACAACA
* *
54178 ATC-AT
66 ACCAAA
* *
54183 CTTTGAGATCGTTTCCCTTGAAAC
1 CTTTGAGATTGTTTCTCTTGAAAC
54207 GAATTAAATC
Statistics
Matches: 142, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
68 27 0.19
69 63 0.44
70 52 0.37
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (71 bp):
CTTTGAGATTGTTTCTCTTGAAACAAAATCTTATTCTCCTCGAAACCATTTCTCATGAAACAACA
ACCAAA
Found at i:54116 original size:70 final size:68
Alignment explanation
Indices: 54022--54206 Score: 255
Period size: 70 Copynumber: 2.7 Consensus size: 68
54012 CCTCGAGACA
*
54022 TTTCTTATGAAACAACAACCAAACTTTGAGATTGTTTACCTTGAAACAAATCTTATTTTCCTTGA
1 TTTCTCATGAAACAACAACCAAACTTTGAGATTGTTT-CCTTGAAACAAATC-TATTTTCCTTGA
54087 AACCG
64 AACCG
* *
54092 TTTCTCATGAAACAATAACCAAACTTTGAGATTGTTTCTCTTGAAACAAATCTATTTTCCTTGAG
1 TTTCTCATGAAACAACAACCAAACTTTGAGATTGTTTC-CTTGAAACAAATCTATTTTCCTTGAA
*
54157 GCCG
65 ACCG
* * * *
54161 TTTCTCATTAAACAACAATC-ATCTTTGAGATCGTTTCCCTTGAAAC
1 TTTCTCATGAAACAACAACCAAACTTTGAGATTGTTT-CCTTGAAAC
54207 GAATTAAATC
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
68 22 0.21
69 34 0.33
70 48 0.46
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (68 bp):
TTTCTCATGAAACAACAACCAAACTTTGAGATTGTTTCCTTGAAACAAATCTATTTTCCTTGAAA
CCG
Found at i:54218 original size:33 final size:33
Alignment explanation
Indices: 54181--54252 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
54171 AACAACAATC
*
54181 ATCTTTGAGATCGTTTCCCTTGAAACGAATTAA
1 ATCTTTGAGAACGTTTCCCTTGAAACGAATTAA
*
54214 ATCTTTGAGAACGTTTCTCTTGAAACGAATTAA
1 ATCTTTGAGAACGTTTCCCTTGAAACGAATTAA
54247 ATCTTT
1 ATCTTT
54253 AAGCCTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (33 bp):
ATCTTTGAGAACGTTTCCCTTGAAACGAATTAA
Found at i:54263 original size:33 final size:33
Alignment explanation
Indices: 54181--54271 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
54171 AACAACAATC
* * *
54181 ATCTTTGAGATCGTTTCCCTTGAAACGAATTAA
1 ATCTTTAAGAACGTTTCTCTTGAAACGAATTAA
*
54214 ATCTTTGAGAACGTTTCTCTTGAAACGAATTAA
1 ATCTTTAAGAACGTTTCTCTTGAAACGAATTAA
*
54247 ATCTTTAAG-CCTGTTTCTCTTGAAA
1 ATCTTTAAGAAC-GTTTCTCTTGAAA
54272 GAAAACCATC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 1 0.02
33 52 0.98
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (33 bp):
ATCTTTAAGAACGTTTCTCTTGAAACGAATTAA
Found at i:54979 original size:3 final size:3
Alignment explanation
Indices: 54971--55013 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
54961 TCTACAAAAA
54971 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
55014 TTACAACTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:55866 original size:14 final size:16
Alignment explanation
Indices: 55837--55867 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55827 CCCATAGTGG
55837 GAGAGTTTTCTCTCTC
1 GAGAGTTTTCTCTCTC
55853 GAGAGTTTTCTCTCT
1 GAGAGTTTTCTCTCT
55868 GTGAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (16 bp):
GAGAGTTTTCTCTCTC
Found at i:60783 original size:16 final size:16
Alignment explanation
Indices: 60751--60784 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
60741 TCTTATAAAA
* *
60751 TTGTTTTCTTTCGTTT
1 TTGTTTTCTTCCCTTT
60767 TTGTTTTCTTCCCTTT
1 TTGTTTTCTTCCCTTT
60783 TT
1 TT
60785 TATTTATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.09, T:0.74
Consensus pattern (16 bp):
TTGTTTTCTTCCCTTT
Found at i:63294 original size:23 final size:23
Alignment explanation
Indices: 63268--63312 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
63258 CACCACAGCT
*
63268 CGTATAATTGCACCGAAGTGCCC
1 CGTAGAATTGCACCGAAGTGCCC
*
63291 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
63313 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCC
Found at i:64364 original size:18 final size:18
Alignment explanation
Indices: 64343--64377 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
64333 TCCCATCTAG
64343 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
64361 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
64378 AATATCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:64985 original size:21 final size:21
Alignment explanation
Indices: 64961--65005 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
64951 TCTTGTTCGT
* *
64961 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
64982 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
65003 TTG
1 TTG
65006 CCCAGAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:68091 original size:23 final size:23
Alignment explanation
Indices: 68065--68109 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
68055 CACCACAGCT
*
68065 CGTATAATTGCACCGAAGTGCCC
1 CGTAGAATTGCACCGAAGTGCCC
*
68088 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
68110 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCC
Found at i:69170 original size:18 final size:18
Alignment explanation
Indices: 69149--69183 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
69139 TCCCATCTAG
69149 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
69167 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
69184 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:69803 original size:21 final size:21
Alignment explanation
Indices: 69764--69808 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
69754 TCTTGTTCGT
* *
69764 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
69785 TTGAATGGGTACCGATTCCTC
1 TTGAAGGGGTACCGATTCCCC
69806 TTG
1 TTG
69809 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:76657 original size:87 final size:87
Alignment explanation
Indices: 76511--76700 Score: 317
Period size: 87 Copynumber: 2.2 Consensus size: 87
76501 CGAGATCGAC
*
76511 TCAACTTCACGATGAAGGAGTCATCAGCAACCTAGCTCAACTCAACAACGAGGAACTATTTTTCA
1 TCAACTTCACGATGAAGGAGTCATCAGCAACCTAGCTCAACTCAACAACAAGGAACTATTTTTCA
76576 ACCAAGGTCTTCAAGTCAAATT
66 ACCAAGGTCTTCAAGTCAAATT
* * * * *
76598 TCAACTTCATGATGAAGGATTCATCCGTAACCTAGCTCAACTCAACAGCAAGGAACTATTTTTCA
1 TCAACTTCACGATGAAGGAGTCATCAGCAACCTAGCTCAACTCAACAACAAGGAACTATTTTTCA
76663 ACCAAGGTCTTCAAGTCAAATT
66 ACCAAGGTCTTCAAGTCAAATT
*
76685 TTAACTTCACGATGAA
1 TCAACTTCACGATGAA
76701 AGATATTAGA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 95 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.26
Consensus pattern (87 bp):
TCAACTTCACGATGAAGGAGTCATCAGCAACCTAGCTCAACTCAACAACAAGGAACTATTTTTCA
ACCAAGGTCTTCAAGTCAAATT
Found at i:77573 original size:5 final size:5
Alignment explanation
Indices: 77554--77615 Score: 51
Period size: 5 Copynumber: 13.0 Consensus size: 5
77544 GAGACTTTTA
* * * *
77554 ATTAT ATAAT A-TAT ATTAT AGT-T ATTAT ATTAT ATTAC ATTAT -TTCTT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT-AT
77602 ATTAT ATTAT -TTAT
1 ATTAT ATTAT ATTAT
77616 TAAAAATTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
4 12 0.27
5 31 0.69
6 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:80828 original size:23 final size:23
Alignment explanation
Indices: 80797--80841 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
80787 TTTATTTAAT
*
80797 TTTTTATTTAGTAT-TAGTTTATA
1 TTTTAATTT-GTATATAGTTTATA
*
80820 TTTTAATTTGTATATTGTTTAT
1 TTTTAATTTGTATATAGTTTAT
80842 TTAATTAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (23 bp):
TTTTAATTTGTATATAGTTTATA
Found at i:92018 original size:14 final size:14
Alignment explanation
Indices: 91953--92020 Score: 66
Period size: 14 Copynumber: 4.7 Consensus size: 14
91943 GGTCCAGTCA
*
91953 CCGAGTCAACTTGAT
1 CCGAGTCAACTCG-T
* *
91968 CTGAGTTAACTCGT
1 CCGAGTCAACTCGT
91982 CCGAGAT-AACTCAGT
1 CCGAG-TCAACTC-GT
*
91997 CTGAGTCAACTCGT
1 CCGAGTCAACTCGT
92011 CCGAGTCAAC
1 CCGAGTCAAC
92021 CCGCTGAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
14 22 0.50
15 22 0.50
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (14 bp):
CCGAGTCAACTCGT
Found at i:92193 original size:18 final size:18
Alignment explanation
Indices: 92172--92217 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
92162 TTCAATATAT
*
92172 TTTCTCAAT-TAAGTTTAG
1 TTTCT-AATGTAAATTTAG
*
92190 TTTCTAATGTAAATTTAT
1 TTTCTAATGTAAATTTAG
92208 TTTCT-ATGTA
1 TTTCTAATGTA
92218 TATGAGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (18 bp):
TTTCTAATGTAAATTTAG
Found at i:92951 original size:27 final size:27
Alignment explanation
Indices: 92921--92976 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
92911 GGATTTATAG
92921 AAATGCCCCTAAAGTGTAAAATGA-CTA
1 AAATGCCCCTAAAGTGT-AAATGACCTA
* *
92948 AAATGCTCCTAAGGTGTAAATGACCTA
1 AAATGCCCCTAAAGTGTAAATGACCTA
92975 AA
1 AA
92977 GTATTTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (27 bp):
AAATGCCCCTAAAGTGTAAATGACCTA
Found at i:95541 original size:23 final size:24
Alignment explanation
Indices: 95511--95559 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
95501 CCTCGTAGCC
*
95511 AAGGTCAATTGATTCCA-CAGGAT
1 AAGGTCAATTGATTCCATAAGGAT
95534 AAGGTCAATTGATTCCATAAGGAT
1 AAGGTCAATTGATTCCATAAGGAT
95558 AA
1 AA
95560 TTCTGTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (24 bp):
AAGGTCAATTGATTCCATAAGGAT
Found at i:100891 original size:19 final size:20
Alignment explanation
Indices: 100842--100892 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
100832 CTCCTACTGG
100842 GAGTATCGATACTCTACCCC
1 GAGTATCGATACTCTACCCC
* * *
100862 CAGTATTGATACTCT-CCGC
1 GAGTATCGATACTCTACCCC
100881 GAGTATCGATAC
1 GAGTATCGATAC
100893 CAAAATTGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (20 bp):
GAGTATCGATACTCTACCCC
Found at i:103726 original size:29 final size:30
Alignment explanation
Indices: 103672--103736 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
103662 AATCATTTAC
103672 GATATTAAACTTTCCAAATTTATAT-AA-TG
1 GATATTAAACTTT-CAAATTTATATAAATTG
*
103701 GATATTAAACTTT-AAATTTTCTTATAAATTG
1 GATATTAAACTTTCAAA-TTT-ATATAAATTG
103732 GATAT
1 GATAT
103737 GACAAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 3 0.10
28 3 0.10
29 16 0.52
30 2 0.06
31 7 0.23
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (30 bp):
GATATTAAACTTTCAAATTTATATAAATTG
Found at i:107338 original size:22 final size:23
Alignment explanation
Indices: 107310--107364 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
107300 CAATTCAAAC
*
107310 TATTTTTTTAT-TTTTTATTAAA
1 TATTTTTTAATATTTTTATTAAA
*
107332 TA-TTTTTAATATTTTTATTTAA
1 TATTTTTTAATATTTTTATTAAA
*
107354 T-TTTTTAAATA
1 TATTTTTTAATA
107365 ATTATAACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTTTAATATTTTTATTAAA
Found at i:107346 original size:21 final size:21
Alignment explanation
Indices: 107311--107361 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
107301 AATTCAAACT
*
107311 ATTTTTTTAT-TTTTTATTAA
1 ATTTTTTAATATTTTTATTAA
*
107331 ATATTTTTAATATTTTTATTTA
1 AT-TTTTTAATATTTTTATTAA
107353 ATTTTTTAA
1 ATTTTTTAA
107362 ATAATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 14 0.52
22 11 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTTTAATATTTTTATTAA
Found at i:108630 original size:19 final size:19
Alignment explanation
Indices: 108606--108671 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
108596 ATCGAAACCA
*
108606 GTTTTTTCGGTTTGGTTCG
1 GTTTTTTCGGTTCGGTTCG
*
108625 GTTTTTT---TAACGGTTCG
1 GTTTTTTCGGT-TCGGTTCG
*
108642 GGTTTTTCGGTTCGGTTCG
1 GTTTTTTCGGTTCGGTTCG
108661 G-TTTTTCGGTT
1 GTTTTTTCGGTT
108672 TTTCAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.03
17 12 0.31
18 10 0.26
19 15 0.38
20 1 0.03
ACGTcount: A:0.03, C:0.12, G:0.30, T:0.55
Consensus pattern (19 bp):
GTTTTTTCGGTTCGGTTCG
Found at i:108663 original size:18 final size:18
Alignment explanation
Indices: 108608--108671 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
108598 CGAAACCAGT
*
108608 TTTTTCGGTTTGGTTCGG
1 TTTTTCGGTTCGGTTCGG
108626 TTTTT---TTAACGGTTCGGG
1 TTTTTCGGTT--CGGTTC-GG
108644 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
108662 TTTTTCGGTT
1 TTTTTCGGTT
108672 TTTCAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
17 5 0.13
18 24 0.62
19 6 0.15
21 2 0.05
ACGTcount: A:0.03, C:0.12, G:0.30, T:0.55
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Done.