Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006489.1 Hibiscus syriacus cultivar Beakdansim tig00015782_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: 102961
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:7838 original size:21 final size:21
Alignment explanation
Indices: 7812--7860 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
7802 ACAACATAGT
7812 CAAGGGATCGGTATGAATGGG
1 CAAGGGATCGGTATGAATGGG
*
7833 CAAGGGATCGGTATGGATGGG
1 CAAGGGATCGGTATGAATGGG
*
7854 CATGGGA
1 CAAGGGA
7861 CTCGAACCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.45, T:0.18
Consensus pattern (21 bp):
CAAGGGATCGGTATGAATGGG
Found at i:8189 original size:27 final size:27
Alignment explanation
Indices: 8123--8189 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
8113 GTTTGGTCGG
*
8123 TTTCGGGTCA-GGTGGAGGATGTAAAAT
1 TTTCGGGT-AGGGTGGAGGAAGTAAAAT
* * * *
8150 TTTCTGTTGGGGTGGGGGAAGTAAAAT
1 TTTCGGGTAGGGTGGAGGAAGTAAAAT
8177 TTTCGGGTAGGGT
1 TTTCGGGTAGGGT
8190 CGGGTTGACC
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.21, C:0.06, G:0.40, T:0.33
Consensus pattern (27 bp):
TTTCGGGTAGGGTGGAGGAAGTAAAAT
Found at i:15068 original size:19 final size:18
Alignment explanation
Indices: 15038--15073 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
15028 AAAATAAATA
15038 ATAAAATTAAAATCATTT
1 ATAAAATTAAAATCATTT
15056 ATAAAATTTAAAATCATT
1 ATAAAA-TTAAAATCATT
15074 AAAAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAATTAAAATCATTT
Found at i:15079 original size:18 final size:18
Alignment explanation
Indices: 15025--15079 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
15015 ATATATATAT
* *
15025 TTTAAAATAAATAATAAAA
1 TTTAAAATCATTAA-AAAA
*
15044 -TTAAAATCATTTATAAAA
1 TTTAAAATCA-TTAAAAAA
15062 TTTAAAATCATTAAAAAA
1 TTTAAAATCATTAAAAAA
15080 GTTTGGCCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAATCATTAAAAAA
Found at i:15214 original size:9 final size:9
Alignment explanation
Indices: 15200--15224 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
15190 GTTTTGATTA
15200 TTAAAATTT
1 TTAAAATTT
15209 TTAAAATTT
1 TTAAAATTT
15218 TTAAAAT
1 TTAAAAT
15225 AATAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTAAAATTT
Found at i:16391 original size:31 final size:31
Alignment explanation
Indices: 16356--16428 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
16346 GTTAACATGT
16356 AGTGACCACT-TCTTAAATAAATAAAAATAAA
1 AGTGACCA-TATCTTAAATAAATAAAAATAAA
* * *
16387 AGTGATCATATCTTAATTAAATAAAAATGAA
1 AGTGACCATATCTTAAATAAATAAAAATAAA
* *
16418 TGTGAACATAT
1 AGTGACCATAT
16429 AAATTTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (31 bp):
AGTGACCATATCTTAAATAAATAAAAATAAA
Found at i:23057 original size:7 final size:7
Alignment explanation
Indices: 23045--23070 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23035 TTGTTTTTAA
23045 AATTTCG
1 AATTTCG
23052 AATTTCG
1 AATTTCG
23059 AATTTCG
1 AATTTCG
23066 AATTT
1 AATTT
23071 AGGGTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (7 bp):
AATTTCG
Found at i:23964 original size:3 final size:3
Alignment explanation
Indices: 23956--24029 Score: 114
Period size: 3 Copynumber: 24.7 Consensus size: 3
23946 CCAACATATG
* *
23956 ATA ATA ATA ATA ATA ATA ATA AT- ATT ATT ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24003 ATA TATA ATA ATA ATA ATA ATA ATA AT
1 ATA -ATA ATA ATA ATA ATA ATA ATA AT
24030 GATGATGATG
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
2 2 0.03
3 63 0.93
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:27284 original size:98 final size:97
Alignment explanation
Indices: 27067--27328 Score: 341
Period size: 98 Copynumber: 2.7 Consensus size: 97
27057 ATAATGTCTT
* * * * *
27067 CTCGACCTTAAAACATATGCATGGATCCTCTTAACCCCG-TCTTTTTCCATCATATATAAAATGT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTT-CATTATGTATAAAATGT
* *
27131 ATTTTGCATTCCGTCTAGATACTAGTATAACTTCTA
65 ATTTAGCATTCCGTATAGATACTAG---AACTTCTA
* *
27167 CTCGACCTTAAAAGATATGCGTGGATTCTCTTAGCCCTGTTCTTTTTCATTTTATGTATAAAATG
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCA--TTATGTATAAAATG
*
27232 TATTTAGCATTCTGTATAGATA-TACG-ACTTCTA
64 TATTTAGCATTCCGTATAGATACTA-GAACTTCTA
*
27265 GTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTATGTATAAAATGT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTATGTATAAAATGT
27329 CTTTTTCTAT
Statistics
Matches: 145, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
96 15 0.10
98 53 0.37
100 36 0.25
101 9 0.06
102 32 0.22
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (97 bp):
CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTATGTATAAAATGTA
TTTAGCATTCCGTATAGATACTAGAACTTCTA
Found at i:28167 original size:28 final size:29
Alignment explanation
Indices: 28127--28185 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
28117 GGTTTATTAC
28127 GATCCTGTTAAAGA-GGAAGGGGAAGGAG
1 GATCCTGTTAAAGAGGGAAGGGGAAGGAG
*
28155 GATCCTGTTAAAGAGGGGAGGGGAAGGAG
1 GATCCTGTTAAAGAGGGAAGGGGAAGGAG
28184 GA
1 GA
28186 GGGAATATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.34, C:0.07, G:0.46, T:0.14
Consensus pattern (29 bp):
GATCCTGTTAAAGAGGGAAGGGGAAGGAG
Found at i:32443 original size:2 final size:2
Alignment explanation
Indices: 32438--32465 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32428 ACACACACAC
32438 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
32466 GTAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34999 original size:16 final size:16
Alignment explanation
Indices: 34978--35009 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
34968 TGTCACGTCC
34978 ATATTTTAAAAAAAAT
1 ATATTTTAAAAAAAAT
34994 ATATTTTAAAAAAAAT
1 ATATTTTAAAAAAAAT
35010 CTAGATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATTTTAAAAAAAAT
Found at i:39497 original size:59 final size:59
Alignment explanation
Indices: 39402--39519 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
39392 AACACTCGTC
* * *
39402 GGCCTGACATTACTTATCTTATCAAATCTTTCATTAACTTATACGGATTGTTCTAATTT
1 GGCCTGACATTACTTATCTTATCAAAGCTTTAATTAACTTACACGGATTGTTCTAATTT
* *
39461 GGCCTGCCATTGCTTATCTTATCAAAGCTTTAATTAACTTACACGGATTGTTCTAATTT
1 GGCCTGACATTACTTATCTTATCAAAGCTTTAATTAACTTACACGGATTGTTCTAATTT
39520 AAGTATAGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (59 bp):
GGCCTGACATTACTTATCTTATCAAAGCTTTAATTAACTTACACGGATTGTTCTAATTT
Found at i:42624 original size:21 final size:22
Alignment explanation
Indices: 42598--42644 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
42588 ATGGCGCGTC
42598 TTTTTCTACT-TTTATGACACA
1 TTTTTCTACTCTTTATGACACA
** *
42619 TTTTTCTTGTCTTTATGACATA
1 TTTTTCTACTCTTTATGACACA
42641 TTTT
1 TTTT
42645 CAATCGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.19, C:0.15, G:0.06, T:0.60
Consensus pattern (22 bp):
TTTTTCTACTCTTTATGACACA
Found at i:47270 original size:22 final size:22
Alignment explanation
Indices: 47227--47267 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
47217 CAATCTATTT
47227 TTTTTATTAAATATTTTTAATA
1 TTTTTATTAAATATTTTTAATA
*
47249 TTTTTATTTAAT-TTTTTAA
1 TTTTTATTAAATATTTTTAA
47268 ATAATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTAAATATTTTTAATA
Found at i:48130 original size:16 final size:18
Alignment explanation
Indices: 48106--48138 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48096 TATTGAATAA
48106 AAATAATATT-ATTTTAC
1 AAATAATATTAATTTTAC
48123 AAAT-ATATTAATTTTA
1 AAATAATATTAATTTTA
48139 AGTAAGATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATAATATTAATTTTAC
Found at i:51757 original size:42 final size:42
Alignment explanation
Indices: 51710--51800 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
51700 TCCAAAATCT
* * *
51710 CGTGTTTGTTTCATGTAATTAGTTTT-TCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTAGTTTTCT-GAAAAATGTTTTAC
*
51752 CGTGTTTGTTTCACGTAATTCGTTTTCTGAAAAATGTTTTAC
1 CGTGTTTGTTTCACGTAATTAGTTTTCTGAAAAATGTTTTAC
*
51794 AGTGTTT
1 CGTGTTT
51801 AGTTGGAGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 42 0.98
43 1 0.02
ACGTcount: A:0.20, C:0.12, G:0.19, T:0.49
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTAGTTTTCTGAAAAATGTTTTAC
Found at i:52064 original size:22 final size:22
Alignment explanation
Indices: 52039--52181 Score: 90
Period size: 25 Copynumber: 6.0 Consensus size: 22
52029 TTTATTAGTA
*
52039 TTTATAATAATATATATAATAT
1 TTTATAATAATAAATATAATAT
52061 TTTAATATTATAATAAATAATCAATTAT
1 TTT-ATA--ATAATAAAT-AT-AA-TAT
* * *
52089 ATTATAATAATAAAGATTATAT
1 TTTATAATAATAAATATAATAT
**
52111 TTTATTTTAATAAATATAATATT
1 TTTATAATAATAAATATAATA-T
*
52134 TTTATTTAATAAT-AATAATATTAT
1 TTTA--TAATAATAAAT-ATAATAT
*
52158 TTATATATTAATATTAATATAATA
1 TT-TATAATAATA--AATATAATA
52182 ATCTAATATT
Statistics
Matches: 93, Mismatches: 14, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
22 22 0.24
23 15 0.16
24 8 0.09
25 33 0.35
26 5 0.05
27 5 0.05
28 5 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (22 bp):
TTTATAATAATAAATATAATAT
Found at i:52079 original size:20 final size:21
Alignment explanation
Indices: 52014--52076 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
52004 TAATTAATAA
* *
52014 AATATTTAAAAT-ATATTTATT
1 AATATTTATAATAATATATA-T
*
52035 AGTATTTATAATAATATATAT
1 AATATTTATAATAATATATAT
*
52056 AATATTT-TAATATTATA-AT
1 AATATTTATAATAATATATAT
52075 AA
1 AA
52077 ATAATCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 9 0.25
21 17 0.47
22 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATATTTATAATAATATATAT
Found at i:52150 original size:19 final size:20
Alignment explanation
Indices: 52126--52173 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
52116 TTTAATAAAT
*
52126 ATAATATTTTTATTTA-ATA
1 ATAATATTATTATTTATATA
*
52145 ATAATAATATTATTTATATA
1 ATAATATTATTATTTATATA
*
52165 TTAATATTA
1 ATAATATTA
52174 ATATAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAATATTATTATTTATATA
Found at i:52197 original size:50 final size:52
Alignment explanation
Indices: 52042--52198 Score: 143
Period size: 50 Copynumber: 3.1 Consensus size: 52
52032 ATTAGTATTT
*
52042 ATAATAATA-TATATAATATTTTAATATT-ATAATAAATAATC-AATTATATTATA
1 ATAATAATATTATATTATATTTTAATATTAAT-AT-AATAATCTAA-TAT-TTATA
* * **
52095 ATAATAAAGATTATATTTTATTTTAATA--AATATAAT-AT-TTTTATTTAATA
1 ATAAT-AATATTATATTATATTTTAATATTAATATAATAATCTAATATTT-ATA
*
52145 ATAATAATATTAT-TTATATATTAATATTAATATAATAATCTAATATTT-TA
1 ATAATAATATTATATTATATTTTAATATTAATATAATAATCTAATATTTATA
52195 ATAA
1 ATAA
52199 AGATATTTAA
Statistics
Matches: 85, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
48 11 0.13
49 9 0.11
50 25 0.29
51 4 0.05
52 9 0.11
53 7 0.08
54 5 0.06
55 15 0.18
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (52 bp):
ATAATAATATTATATTATATTTTAATATTAATATAATAATCTAATATTTATA
Found at i:52219 original size:23 final size:23
Alignment explanation
Indices: 52193--52237 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
52183 TCTAATATTT
52193 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
52216 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
52238 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:55840 original size:14 final size:14
Alignment explanation
Indices: 55823--55866 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
55813 AATAAAATTA
55823 AATAATTAAATAAT
1 AATAATTAAATAAT
55837 AATAA-TAAATAAAT
1 AATAATTAAAT-AAT
55851 AATAATATAATATAAT
1 AATAAT-TAA-ATAAT
55867 GTTTTTGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.19
14 13 0.50
16 6 0.23
17 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATAATTAAATAAT
Found at i:55865 original size:17 final size:18
Alignment explanation
Indices: 55823--55865 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
55813 AATAAAATTA
55823 AATAAT-TAAATAATAAT
1 AATAATATAAATAATAAT
55840 AATAA-ATAAATAATAAT
1 AATAATATAAATAATAAT
55857 -ATAATATAA
1 AATAATATAA
55866 TGTTTTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATATAAATAATAAT
Found at i:56273 original size:84 final size:83
Alignment explanation
Indices: 56167--56417 Score: 219
Period size: 84 Copynumber: 3.1 Consensus size: 83
56157 GTTTGCCTCT
* ** *
56167 GAGCTGAGTGTAATTGAACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAATCAAACTCGAAGGTCTT-GGTTGGCAGATAGCCCTTCTCGACTTAAGATATG
56232 CTTCAAATGATGTGCCTTG
65 CTTCAAATGATGTGCCTTG
* ** * * * * * *
56251 GAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGG-TCACAGATAACCCTTGTAGCCTTGAGTTATG
1 GAGCTGAGCGTAATCAAACTCGAAGGTC-TTGGTTGGCAGATAGCCCTTCTCGACTTAAGATATG
* * *
56315 CTGT-AAATGATATACCCTCG
65 CT-TCAAATGATGT-GCCTTG
* * * **
56335 AAGCTGAGTGTAATCGAACTCGGGGGTC-T--TTGGCAGATAGCCCTTCTCGACTTAAGATATGC
1 GAGCTGAGCGTAATCAAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGATATGC
*
56397 TGCAAATGATGTG-CTT-
66 TTCAAATGATGTGCCTTG
56413 GAGCT
1 GAGCT
56418 TAGTCGAACT
Statistics
Matches: 128, Mismatches: 34, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
78 4 0.03
79 2 0.02
81 33 0.26
82 1 0.01
83 33 0.26
84 53 0.41
85 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (83 bp):
GAGCTGAGCGTAATCAAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGATATGC
TTCAAATGATGTGCCTTG
Found at i:56809 original size:106 final size:106
Alignment explanation
Indices: 56624--57475 Score: 1386
Period size: 106 Copynumber: 8.0 Consensus size: 106
56614 TATTGTTCTA
* * * *
56624 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACT-AGGAAATTGTTTGTTGACA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTGTTGACA
56687 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
56730 AGTCCAATATCCTTCGTTGTGAATTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
56795 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
56836 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
56901 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
56942 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTGTTTTTTTTGACA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG--TTTGTTGACA
* *
57007 ACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
57050 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
57115 CAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
57156 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
57221 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
57262 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
57327 CAGCGGTCCCTTCGTCGCGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
57368 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATCGAGAA-ATGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
57432 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
57473 AGT
1 AGT
57476 GGCACGATAT
Statistics
Matches: 705, Mismatches: 37, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
105 54 0.08
106 548 0.78
107 2 0.00
108 101 0.14
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:57488 original size:426 final size:425
Alignment explanation
Indices: 56624--57506 Score: 1430
Period size: 426 Copynumber: 2.1 Consensus size: 425
56614 TATTGTTCTA
* * *
56624 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTAGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTATTTATTGACAAC
* *
56689 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
*
56754 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
56819 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
196 GAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
* * *
56884 AATTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAA
261 AATTGTTTGTTGACAACCAGCGGTCCCTTCATCGCGAAGTTGAACATGCGTTGTCTGGAGTCCAA
* * * ** *
56949 TATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTGTTTTTTTTGACAACCAGCG
326 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATCGAGAGAATG-TTTTGTTGACAACCAGCG
*
57014 GTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTTG
390 GTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTCG
* * * *
57050 AGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 AGTCCAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTATTTATTGACAA
*
57114 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
*
57179 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
130 GTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
57244 TGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG
195 TGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG
* *
57309 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGCGAAGTTGAACATGCGTTGTCTGGAGTCCA
260 AAATTGTTTGTTGACAACCAGCGGTCCCTTCATCGCGAAGTTGAACATGCGTTGTCTGGAGTCCA
57374 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATCGAGA-AATG-TTTGTTGACAACCAGCG
325 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATCGAGAGAATGTTTTGTTGACAACCAGCG
* *
57437 GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCG
390 GTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTCG
* *
57473 AGTGGCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT--C-CAATATCCTCCGTCGTGAAGTTGAAAT
57507 CGCGGATGGC
Statistics
Matches: 421, Mismatches: 31, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
423 52 0.12
425 4 0.01
426 364 0.86
427 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (425 bp):
AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTATTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
TTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
AATTGTTTGTTGACAACCAGCGGTCCCTTCATCGCGAAGTTGAACATGCGTTGTCTGGAGTCCAA
TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATCGAGAGAATGTTTTGTTGACAACCAGCGG
TCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTCG
Found at i:60225 original size:16 final size:15
Alignment explanation
Indices: 60188--60226 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
60178 GTGAATGATA
60188 AAAAAAATGAAAAAG
1 AAAAAAATGAAAAAG
*
60203 AACAAAAATGAAAGGAG
1 AA-AAAAATGAAA-AAG
60220 AAAAAAA
1 AAAAAAA
60227 GTTAGTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 15 0.71
17 4 0.19
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (15 bp):
AAAAAAATGAAAAAG
Found at i:63731 original size:13 final size:12
Alignment explanation
Indices: 63707--63756 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
63697 GGCCTGTAAA
63707 AAAATAAA-AAT
1 AAAATAAATAAT
63718 AAAATTAAATAAT
1 AAAA-TAAATAAT
63731 AATAATAAATAA-
1 AA-AATAAATAAT
*
63743 ATAATAATATAAT
1 AAAATAA-ATAAT
63756 A
1 A
63757 TAATGTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 9 0.27
12 9 0.27
13 13 0.39
14 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:63747 original size:14 final size:14
Alignment explanation
Indices: 63714--63756 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
63704 AAAAAAATAA
63714 AAATAA-AATTAAAT
1 AAATAATAA-TAAAT
63728 -AATAATAATAAAT
1 AAATAATAATAAAT
63741 AAATAATAATATAAT
1 AAATAATAATA-AAT
63756 A
1 A
63757 TAATGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 10 0.38
14 12 0.46
15 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAATAATAAAT
Found at i:63759 original size:17 final size:17
Alignment explanation
Indices: 63708--63759 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
63698 GCCTGTAAAA
* *
63708 AAATAAAAATAAAAT-T
1 AAATAATAATATAATAT
63724 AAATAATAATAATAA-AT
1 AAATAATAAT-ATAATAT
63741 AAATAATAATATAATAT
1 AAATAATAATATAATAT
63758 AA
1 AA
63760 TGTTTTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAATAATATAATAT
Found at i:65633 original size:32 final size:32
Alignment explanation
Indices: 65596--65680 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
65586 ACCCGAATCC
* * *
65596 GACTTGTTATTGATCTAA-TATGATATTTACCT
1 GACTTGATATTGACCTAACT-TGACATTTACCT
* *
65628 GACTTGACATTTACCTAACTTGACATTTACCT
1 GACTTGATATTGACCTAACTTGACATTTACCT
* *
65660 GACTTGATATTTACCTGACTT
1 GACTTGATATTGACCTAACTT
65681 ATGTATCATC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 44 0.98
33 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (32 bp):
GACTTGATATTGACCTAACTTGACATTTACCT
Found at i:65639 original size:16 final size:16
Alignment explanation
Indices: 65620--65680 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
65610 CTAATATGAT
65620 ATTTACCTGACTTGAC
1 ATTTACCTGACTTGAC
*
65636 ATTTACCTAACTTGAC
1 ATTTACCTGACTTGAC
*
65652 ATTTACCTGACTTGAT
1 ATTTACCTGACTTGAC
65668 ATTTACCTGACTT
1 ATTTACCTGACTT
65681 ATGTATCATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (16 bp):
ATTTACCTGACTTGAC
Found at i:65777 original size:21 final size:21
Alignment explanation
Indices: 65753--65795 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
65743 AATCATACTA
*
65753 ATTAATAAATATATTTAATAT
1 ATTAATAAATATAATTAATAT
* *
65774 ATTAATTATTATAATTAATAT
1 ATTAATAAATATAATTAATAT
65795 A
1 A
65796 CTTTATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATAAATATAATTAATAT
Found at i:65816 original size:22 final size:21
Alignment explanation
Indices: 65791--65978 Score: 108
Period size: 22 Copynumber: 8.7 Consensus size: 21
65781 ATTATAATTA
*
65791 ATATACTTTATAATTAATACTT
1 ATATA-TTTATACTTAATACTT
65813 ATAT-TTATATACTTTAATACTT
1 ATATATT-TATAC-TTAATACTT
65835 -TATATTTAATACTT-ATA-TT
1 ATATATTT-ATACTTAATACTT
*
65854 ATATAGTTTAATACTTTATA-TT
1 ATATA-TTT-ATACTTAATACTT
65876 ATATACTTTAGTACTTATATACTT
1 ATATA-TTTA-TACTTA-ATACTT
*
65900 -TATATTTAATACTT-ATATTT
1 ATATATTT-ATACTTAATACTT
65920 ATATACTTTAATAC-TAATA-TT
1 ATATA-TTT-ATACTTAATACTT
* * *
65941 CAAACACTTTATTACTTTATA-TT
1 -ATATA-TTTA-TACTTAATACTT
65964 ATATATTTTATACTT
1 ATATA-TTTATACTT
65979 TATATATAAA
Statistics
Matches: 139, Mismatches: 10, Indels: 35
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.01
20 14 0.10
21 34 0.24
22 73 0.53
23 14 0.10
24 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (21 bp):
ATATATTTATACTTAATACTT
Found at i:65834 original size:36 final size:36
Alignment explanation
Indices: 65793--65934 Score: 174
Period size: 36 Copynumber: 4.1 Consensus size: 36
65783 TATAATTAAT
65793 ATACTTTATAATTAATACTTATATTTATATACTTTA
1 ATACTTTATAATTAATACTTATATTTATATACTTTA
* *
65829 ATACTTTATATTTAATACTTATA-TTATATAGTTTA
1 ATACTTTATAATTAATACTTATATTTATATACTTTA
* *
65864 ATACTTTAT-ATT-ATA--TA-CTTTA-GTAC-TTA
1 ATACTTTATAATTAATACTTATATTTATATACTTTA
*
65893 TATACTTTATATTTAATACTTATATTTATATACTTTA
1 -ATACTTTATAATTAATACTTATATTTATATACTTTA
65930 ATACT
1 ATACT
65935 AATATTCAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 18
0.77 0.08 0.16
Matches are distributed among these distances:
29 3 0.03
30 11 0.12
31 7 0.08
32 3 0.03
33 3 0.03
34 4 0.05
35 24 0.27
36 30 0.34
37 3 0.03
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (36 bp):
ATACTTTATAATTAATACTTATATTTATATACTTTA
Found at i:65840 original size:73 final size:73
Alignment explanation
Indices: 65762--65901 Score: 180
Period size: 73 Copynumber: 1.9 Consensus size: 73
65752 AATTAATAAA
*
65762 TATATTTAATATATTA-ATTATTATAATTAATATACTTTATAATTA-ATAC-TTA-TATTTATAT
1 TATATTTAATA-ATTATATTA-TATAATTAA-ATACTTTAT-ATTATATACTTTAGTACTTATAT
65823 ACTTTAATACTT
62 ACTTTAATACTT
* * *
65835 TATATTTAATACTTATATTATATAGTTTAATACTTTATATTATATACTTTAGTACTTATATACTT
1 TATATTTAATAATTATATTATATAATTAAATACTTTATATTATATACTTTAGTACTTATATACTT
65900 TA
66 TA
65902 TATTTAATAC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
70 4 0.07
71 13 0.22
72 13 0.22
73 29 0.49
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (73 bp):
TATATTTAATAATTATATTATATAATTAAATACTTTATATTATATACTTTAGTACTTATATACTT
TAATACTT
Found at i:65914 original size:65 final size:64
Alignment explanation
Indices: 65822--65986 Score: 203
Period size: 65 Copynumber: 2.6 Consensus size: 64
65812 TATATTTATA
* * * *
65822 TACTTTAATACTTTATATTTAATACTTATATTATATAGTTTAATACTTTATATT-ATATACTTTA
1 TACTTT-ATACTTTATATTTAATACTTATATTATATACTTTAATAC-TAATATTCAAACACTTTA
65886 G
64 G
65887 TACTTATATACTTTATATTTAATACTTATATTTATATACTTTAATACTAATATTCAAACACTTTA
1 TACTT-TATACTTTATATTTAATACTTATA-TTATATACTTTAATACTAATATTCAAACACTTTA
*
65952 T
64 G
*
65953 TACTTTATA-TTATATATTTTATACTT-TA-TATATA
1 TACTTTATACTT-TATATTTAATACTTATATTATATA
65987 AAGTATCAAA
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
62 6 0.07
64 4 0.04
65 51 0.57
66 29 0.32
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.53
Consensus pattern (64 bp):
TACTTTATACTTTATATTTAATACTTATATTATATACTTTAATACTAATATTCAAACACTTTAG
Found at i:65975 original size:14 final size:15
Alignment explanation
Indices: 65811--65985 Score: 66
Period size: 14 Copynumber: 11.9 Consensus size: 15
65801 TAATTAATAC
*
65811 TTATATTTATATACTT
1 TTATACTTATATA-TT
*
65827 TAATACTT-TATATT
1 TTATACTTATATATT
*
65841 TAATAC-T-TATATT
1 TTATACTTATATATT
* * *
65854 ATATAGTT-TAATACT
1 TTATACTTAT-ATATT
*
65869 TTATA-TTATATACT
1 TTATACTTATATATT
*
65883 TTAGTACTTATATACT
1 TTA-TACTTATATATT
* *
65899 TTATATTTA-ATA-C
1 TTATACTTATATATT
*
65912 TTATATTTATATACTT
1 TTATACTTATATA-TT
*
65928 TAATAC-TA-ATATT
1 TTATACTTATATATT
** * *
65941 CAAACACTT-TATTACT
1 -TTATACTTATA-TATT
65957 TTATA-TTATATATT
1 TTATACTTATATATT
65971 TTATACTTTATATAT
1 TTATAC-TTATATAT
65986 AAAGTATCAA
Statistics
Matches: 125, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
13 21 0.17
14 43 0.34
15 28 0.22
16 33 0.26
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (15 bp):
TTATACTTATATATT
Found at i:67623 original size:4 final size:4
Alignment explanation
Indices: 67614--67882 Score: 520
Period size: 4 Copynumber: 67.0 Consensus size: 4
67604 ATGCATGTAT
67614 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
67662 CATA CATA CATA TATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67710 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67758 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67806 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67854 CATA CATA CATA CATA CATA CATA TCATA
1 CATA CATA CATA CATA CATA CATA -CATA
67883 AAATCAAATT
Statistics
Matches: 262, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
4 258 0.98
5 4 0.02
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:67986 original size:17 final size:16
Alignment explanation
Indices: 67951--67990 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
67941 ATTAATACAC
67951 ACAT-TATGCATATAT
1 ACATATATGCATATAT
*
67966 ACATATATGCATGTAAT
1 ACATATATGCATAT-AT
67983 ACATATAT
1 ACATATAT
67991 TAGGGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 8 0.36
17 10 0.45
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (16 bp):
ACATATATGCATATAT
Found at i:68019 original size:21 final size:20
Alignment explanation
Indices: 67994--68052 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
67984 CATATATTAG
*
67994 GGTTTATGGTATAGAGTTTA
1 GGTTTATGGTTTAGAGTTTA
*
68014 GTGTTTATGGTTTAAAGTTTA
1 G-GTTTATGGTTTAGAGTTTA
*
68035 GGATTTAGGGTTTAGAGT
1 GG-TTTATGGTTTAGAGT
68053 ATTGGGTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.46
Consensus pattern (20 bp):
GGTTTATGGTTTAGAGTTTA
Found at i:68141 original size:2 final size:2
Alignment explanation
Indices: 68136--68188 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
68126 TTATATAGTT
** *
68136 TA TA TA TA TA GG T- TA TA TA TA TA TA TA TA TA TA TA TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68176 TA TA TA TA CTA TA
1 TA TA TA TA -TA TA
68189 CATGGTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:68145 original size:13 final size:13
Alignment explanation
Indices: 68127--68183 Score: 71
Period size: 13 Copynumber: 4.3 Consensus size: 13
68117 TAATTTACTT
68127 TATATAGTTTATA
1 TATATAGTTTATA
68140 TATATAGGTTATATA
1 TATATA-GTT-TATA
*
68155 TATATA-TATATA
1 TATATAGTTTATA
*
68167 TATATAATTTATA
1 TATATAGTTTATA
68180 TATA
1 TATA
68184 CTATACATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 10 0.26
13 16 0.41
14 3 0.08
15 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:69095 original size:20 final size:20
Alignment explanation
Indices: 69034--69088 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
69024 ATAAAATCTC
* * *
69034 AATTTCCCTCCAAATTTTTC
1 AATTTCCCTCTAAATTTCTA
* *
69054 TA-TTCCTTCTAAATTTCTA
1 AATTTCCCTCTAAATTTCTA
69073 AATTTCCCTCTAAATT
1 AATTTCCCTCTAAATT
69089 CTCAAATAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTCCCTCTAAATTTCTA
Found at i:69173 original size:2 final size:2
Alignment explanation
Indices: 69166--69204 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
69156 GCTTTGAATA
69166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
69205 TAATATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:69270 original size:15 final size:15
Alignment explanation
Indices: 69166--69352 Score: 86
Period size: 15 Copynumber: 12.3 Consensus size: 15
69156 GCTTTGAATA
*
69166 ATATATATA-TATAT
1 ATATATATAGTTTAT
*
69180 ATATATATA-TATAT
1 ATATATATAGTTTAT
*
69194 ATATACTATA-TTAAT
1 ATATA-TATAGTTTAT
* *
69209 ATAAATTATGGTTTAT
1 ATATA-TATAGTTTAT
* *
69225 AAACTATATACATTTTAT
1 --A-TATATATAGTTTAT
* *
69243 AGTTTATACATAGTTTAC
1 A---TATATATAGTTTAT
*
69261 ATATATATAGTTTAG
1 ATATATATAGTTTAT
69276 ATA-A-ATAG-TT-T
1 ATATATATAGTTTAT
69287 ATATATATAGTTTAT
1 ATATATATAGTTTAT
* * *
69302 ATAAACATAATTTAT
1 ATATATATAGTTTAT
*
69317 ATATATA-A-CTTAT
1 ATATATATAGTTTAT
69330 AATAATTATATAGTTTAT
1 -AT-A-TATATAGTTTAT
69348 ATATA
1 ATATA
69353 AACTTATATT
Statistics
Matches: 132, Mismatches: 25, Indels: 31
0.70 0.13 0.16
Matches are distributed among these distances:
11 3 0.02
12 3 0.02
13 12 0.09
14 25 0.19
15 50 0.38
16 10 0.08
17 3 0.02
18 23 0.17
19 3 0.02
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (15 bp):
ATATATATAGTTTAT
Found at i:69285 original size:13 final size:13
Alignment explanation
Indices: 69247--69306 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
69237 TTTTATAGTT
*
69247 TATACATAGTTTACA
1 TATAAATAGTTT--A
*
69262 TATATATAGTTTA
1 TATAAATAGTTTA
*
69275 GATAAATAGTTTA
1 TATAAATAGTTTA
*
69288 TATATATAGTTTA
1 TATAAATAGTTTA
69301 TATAAA
1 TATAAA
69307 CATAATTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
13 28 0.72
15 11 0.28
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (13 bp):
TATAAATAGTTTA
Found at i:69290 original size:26 final size:25
Alignment explanation
Indices: 69240--69323 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 25
69230 ATATACATTT
*
69240 TATAGTTT-ATACATAGTTTACATATA
1 TATAGTTTAATAAATAGTTT--ATATA
69266 TATAGTTTAGATAAATAGTTTATATA
1 TATAGTTTA-ATAAATAGTTTATATA
*
69292 TATAGTTTATATAAACATAATTTATATA
1 TATAGTTTA-AT-AA-ATAGTTTATATA
69320 TATA
1 TATA
69324 ACTTATAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
26 24 0.47
27 2 0.04
28 25 0.49
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (25 bp):
TATAGTTTAATAAATAGTTTATATA
Found at i:69292 original size:28 final size:27
Alignment explanation
Indices: 69240--69323 Score: 84
Period size: 26 Copynumber: 3.1 Consensus size: 27
69230 ATATACATTT
* *
69240 TATAGTTT-ATACATAGTTTACATATA
1 TATAGTTTAATAAATAGTTTATATATA
69266 TATAGTTTAGATAAATAG-TT-TATATA
1 TATAGTTTA-ATAAATAGTTTATATATA
*
69292 TATAGTTTATATAAACATAATTTATATATA
1 TATAGTTTA-AT-AA-ATAGTTTATATATA
69322 TA
1 TA
69324 ACTTATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
26 24 0.50
27 4 0.08
28 10 0.21
29 2 0.04
30 8 0.17
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (27 bp):
TATAGTTTAATAAATAGTTTATATATA
Found at i:69366 original size:17 final size:16
Alignment explanation
Indices: 69344--69378 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
69334 ATTATATAGT
69344 TTATATATAAACTTATA
1 TTATATATAAA-TTATA
*
69361 TTATATATATATTATA
1 TTATATATAAATTATA
69377 TT
1 TT
69379 TTTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATATAAATTATA
Found at i:72148 original size:24 final size:25
Alignment explanation
Indices: 72117--72178 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
72107 ATATTTTATA
72117 TATATTAACTTTAAAAAATAT-TTT
1 TATATTAACTTTAAAAAATATATTT
**
72141 TATATTAAC-TTATTAAATATATTT
1 TATATTAACTTTAAAAAATATATTT
72165 TATTATTAA-TTTAA
1 TA-TATTAACTTTAA
72179 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 9 0.28
24 14 0.44
25 9 0.28
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATTAACTTTAAAAAATATATTT
Found at i:72171 original size:25 final size:25
Alignment explanation
Indices: 72106--72178 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
72096 TTAAATTCAC
72106 AATAT-TTTATATATATTAACTTTAA
1 AATATATTT-TATATATTAACTTTAA
* *
72131 AAAATATTTT-TATATTAACTTATTA
1 AATATATTTTATATATTAACTT-TAA
72156 AATATATTTTAT-TATTAA-TTTAA
1 AATATATTTTATATATTAACTTTAA
72179 TTTAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 13 0.32
25 22 0.54
26 4 0.10
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATATTTTATATATTAACTTTAA
Found at i:72189 original size:27 final size:27
Alignment explanation
Indices: 72106--72189 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 27
72096 TTAAATTCAC
72106 AATATTTTA-TA-T-ATATTAACTTTAAAA
1 AATATTTTATTATTAAT-TTAA-TTT-AAA
*
72133 AATATTTT-TATATTAACTT-A-TTAAA
1 AATATTTTAT-TATTAATTTAATTTAAA
*
72158 TATATTTTATTATTAATTTAATTTAAA
1 AATATTTTATTATTAATTTAATTTAAA
72185 AATAT
1 AATAT
72190 ATATTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
25 18 0.39
26 4 0.09
27 17 0.37
28 3 0.07
29 3 0.07
30 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATTTTATTATTAATTTAATTTAAA
Found at i:72195 original size:31 final size:30
Alignment explanation
Indices: 72157--72244 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 30
72147 AACTTATTAA
72157 ATATATTTTATTATTAATTTAATTTAAAAAT
1 ATATATTTTATT-TTAATTTAATTTAAAAAT
* **
72188 ATATATTTTATTTTTATCGAAAATTGTAAAAAT
1 ATATATTTTATTTTAAT--TTAATT-TAAAAAT
*
72221 ATATATTTTA-TTTATTTTAATTTA
1 ATATATTTTATTTTAATTTAATTTA
72245 TTAAAAGGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
29 2 0.04
30 8 0.17
31 12 0.26
32 8 0.17
33 17 0.36
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (30 bp):
ATATATTTTATTTTAATTTAATTTAAAAAT
Found at i:73275 original size:2 final size:2
Alignment explanation
Indices: 73268--73309 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
73258 TTAAAAGGTC
73268 AT 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 AT
73310 TAAATAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81568 original size:21 final size:21
Alignment explanation
Indices: 81542--81581 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
81532 CCCCCTTTGA
*
81542 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
81563 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
81582 TGAGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:88845 original size:22 final size:23
Alignment explanation
Indices: 88819--88862 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
88809 TAAAAAATTC
88819 AAAATAATA-TTTAAATTTTTAT
1 AAAATAATAGTTTAAATTTTTAT
88841 AAAATAATAGTTTTAAATTTTT
1 AAAATAATAG-TTTAAATTTTT
88863 GGGTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AAAATAATAGTTTAAATTTTTAT
Found at i:91260 original size:20 final size:19
Alignment explanation
Indices: 91232--91270 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
91222 CATGTCATAC
*
91232 ATATATTAAATTATAATTAT
1 ATATATTAAAATAT-ATTAT
*
91252 ATATTTTAAAATATATTAT
1 ATATATTAAAATATATTAT
91271 TAATGTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTAAAATATATTAT
Found at i:102362 original size:2 final size:2
Alignment explanation
Indices: 102355--102393 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
102345 TAATCACATC
102355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
102394 GCTAACAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.