Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000287.1 Hibiscus syriacus cultivar Beakdansim tig00000529_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: 111629
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4174 original size:22 final size:21
Alignment explanation
Indices: 4132--4171 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4122 GAGTTTATTT
4132 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
4153 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4172 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:6201 original size:45 final size:46
Alignment explanation
Indices: 6113--6203 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
6103 TTGAAAAAGC
* *
6113 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
6159 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
6204 TTCGATGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:8126 original size:27 final size:28
Alignment explanation
Indices: 8063--8127 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
8053 ATTCCTATAA
8063 ATTTCAATTTAGTCCCTAATTCTAATTT
1 ATTTCAATTTAGTCCCTAATTCTAATTT
* * * *
8091 ATTGCAATTTAGTTCCT-ATTTTATTTT
1 ATTTCAATTTAGTCCCTAATTCTAATTT
8118 ATTTCAATTT
1 ATTTCAATTT
8128 TGTCTTTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.55
Consensus pattern (28 bp):
ATTTCAATTTAGTCCCTAATTCTAATTT
Found at i:10660 original size:20 final size:20
Alignment explanation
Indices: 10631--10669 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10621 CTCTCATTTT
* *
10631 TGCATCTTTGCATTTGCATG
1 TGCATATTTGCATTAGCATG
10651 TGCATATTTGCATTAGCAT
1 TGCATATTTGCATTAGCAT
10670 ATATATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (20 bp):
TGCATATTTGCATTAGCATG
Found at i:12099 original size:22 final size:21
Alignment explanation
Indices: 12024--12117 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 21
12014 GAAGATTATC
12024 AAAAAGAAGAA-AAAAGA-AA
1 AAAAAGAAGAAGAAAAGACAA
12043 CACAAAA-AAGAGAGAAAAGA-AA
1 -A-AAAAGAAGA-AGAAAAGACAA
*
12065 ATAAAGCAA-AAGAAAAGCACAA
1 AAAAAG-AAGAAGAAAAG-ACAA
12087 AAAAAGAAGAAGATGAAAGA-AA
1 AAAAAGAAGAAGA--AAAGACAA
12109 AAGAAAGAA
1 AA-AAAGAA
12118 AGAAAAAGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
20 15 0.25
21 10 0.16
22 25 0.41
23 7 0.11
24 4 0.07
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAGAAGAAGAAAAGACAA
Found at i:12120 original size:14 final size:14
Alignment explanation
Indices: 12101--12127 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12091 AGAAGAAGAT
12101 GAAAGAAAAAGAAA
1 GAAAGAAAAAGAAA
12115 GAAAGAAAAAGAA
1 GAAAGAAAAAGAA
12128 GACGAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAGAAA
Found at i:12129 original size:13 final size:13
Alignment explanation
Indices: 12089--12129 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
12079 AAGCACAAAA
* *
12089 AAAGAAGAAGATG
1 AAAGAAAAAGAAG
12102 AAAGAAAAAGAAAG
1 AAAGAAAAAG-AAG
12116 AAAGAAAAAGAAG
1 AAAGAAAAAGAAG
12129 A
1 A
12130 CGAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAGAAG
Found at i:14283 original size:112 final size:111
Alignment explanation
Indices: 14087--14345 Score: 342
Period size: 112 Copynumber: 2.3 Consensus size: 111
14077 ATGAATTTTT
* *
14087 AAGAAGCTAAGCCTAATTTTTAGGAGTTTCTTGATGTTTTCAAATGAGTTTTTTAGAAACTACGC
1 AAGAAGCTAAGCCTATTTTTTAGG-GTTTCTTGATGTTTTCAAATGAGTTTTTTAGAAACTAAGC
* * * **
14152 ATGATTTTTAGGGGTTTCTTGATTATGATTTCTAAAGAATTTTTTGA
65 ATGATTTTTAGGGGTTTCTTGATGATGACTTCCAAAGAATTTTTAAA
*
14199 AAGAAGCTAAGCTTATTTTTTAAGGGTTTCTTGATGTTTTCAAATGA-TTTTTTAAAGAAACTAA
1 AAGAAGCTAAGCCTATTTTTT-AGGGTTTCTTGATGTTTTCAAATGAGTTTTTT--AGAAACTAA
* * * *
14263 GCCTGATTTTTAGGGG-TTCTTGATGATTACTTCCAATGGATTTTTAAA
63 GCATGATTTTTAGGGGTTTCTTGATGATGACTTCCAAAGAATTTTTAAA
* *
14311 AAGAAGTTAAGCCTATTTTTTGGGGTTTCTTGATG
1 AAGAAGCTAAGCCTATTTTTTAGGGTTTCTTGATG
14346 ATAACTGTAA
Statistics
Matches: 129, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
111 19 0.15
112 84 0.65
113 26 0.20
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (111 bp):
AAGAAGCTAAGCCTATTTTTTAGGGTTTCTTGATGTTTTCAAATGAGTTTTTTAGAAACTAAGCA
TGATTTTTAGGGGTTTCTTGATGATGACTTCCAAAGAATTTTTAAA
Found at i:14322 original size:58 final size:57
Alignment explanation
Indices: 14064--14347 Score: 236
Period size: 53 Copynumber: 5.1 Consensus size: 57
14054 CCCAAGCGAT
* * *
14064 ATGATGTATTCAAATGAATTTTT--AAGAAGCTAAGCCTAATTTTTAGGAGTTTCTTG
1 ATGAT-TATTCAAATGGATTTTTAAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTG
* * * *
14120 ATG-TT-TTCAAAT-GAGTTTTT--TAGAAACTACGCATGATTTTTAGGGGTTTCTTG
1 ATGATTATTCAAATGGA-TTTTTAAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTG
* * * * * *
14173 ATTATGATTTCTAAA-GAATTTTTTGAAAGAAGCTAAG-CTTATTTTTTAAGGGTTTCTTG
1 ATGATTA-TTC-AAATGGA-TTTTTAAAAGAAGCTAAGCCTGA-TTTTTAGGGGTTTCTTG
* *
14232 ATG-TT-TTCAAAT-GATTTTTTAAAGAAACTAAGCCTGATTTTTAGGGG-TTCTTG
1 ATGATTATTCAAATGGATTTTTAAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTG
* * *
14285 ATGATTACTTCCAATGGATTTTTAAAAAGAAGTTAAGCCT-ATTTTTTGGGGTTTCTTG
1 ATGATTA-TTCAAATGGATTTTT-AAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTG
14343 ATGAT
1 ATGAT
14348 AACTGTAAAT
Statistics
Matches: 182, Mismatches: 29, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
52 1 0.01
53 50 0.27
54 29 0.16
55 8 0.04
56 15 0.08
57 26 0.14
58 27 0.15
59 26 0.14
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.44
Consensus pattern (57 bp):
ATGATTATTCAAATGGATTTTTAAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTG
Found at i:14516 original size:41 final size:42
Alignment explanation
Indices: 14430--14521 Score: 96
Period size: 41 Copynumber: 2.2 Consensus size: 42
14420 GAGCCATTAG
* ** * ** *
14430 TAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTTATCTA
1 TAAGTCTTTCGAGCAAGATGTACAAATACTTCGGGCCATCCA
*
14472 TAAGTCTTTCGAGCAAGATG-ACAAGTACTTCGGGCCATCCA
1 TAAGTCTTTCGAGCAAGATGTACAAATACTTCGGGCCATCCA
*
14513 TAAGACTTT
1 TAAGTCTTT
14522 TGGGTAGGAT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 22 0.54
42 19 0.46
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGTACAAATACTTCGGGCCATCCA
Found at i:14716 original size:42 final size:41
Alignment explanation
Indices: 14657--14756 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
14647 GAGTAAGTCC
* * *
14657 TTCGGGCCAT-TAGTAAGTCTTTCGAGCATGATGTTTAAATCA
1 TTCGGGCCATCTA-TAAGTCTTTCGAACAAGATG-ATAAATCA
* *
14699 TTCGGGTCATCTATAAGTCTTTCGAACAAGATGATAAGTCA
1 TTCGGGCCATCTATAAGTCTTTCGAACAAGATGATAAATCA
*
14740 TTCGGGCCATCCATAAG
1 TTCGGGCCATCTATAAG
14757 ACCTTTAGGC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 21 0.42
42 27 0.54
43 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (41 bp):
TTCGGGCCATCTATAAGTCTTTCGAACAAGATGATAAATCA
Found at i:14731 original size:240 final size:239
Alignment explanation
Indices: 14406--15327 Score: 1215
Period size: 240 Copynumber: 3.9 Consensus size: 239
14396 GGTTTATTTA
* * *
14406 TGAGTAAGTCCCTT-GAGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTTATC
1 TGAGTAAGT-CCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAATCATTCGGGTCATC
* * * ** *
14470 TATAAGTCTTTCGAGCAAGATGACAAGTACTTCGGGCCATCCATAAGACTTTTGGGTAGGATGTT
65 TATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAGGATGTT
* * * *
14535 TTCGCATGATTTTAAAAAATGAGAAAGTGATTTCAAAAGTTACTCATTTAAATCTTTGCTGAAAA
130 TTCACATGATTTTCAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTT-CTGAAAA
* *
14600 TTGATTTTTCTTCAAAAGTAGAAAAGTGATTTCCAAAGTTTCTTAC
194 TTGATTTTTCTTGAAAAGTAGAAAAGCGATTTCCAAAGTTTCTTAC
14646 TGAGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAATCATTCGGGTCATCT
1 TGAGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAATCATTCGGGTCATCT
* * *
14711 ATAAGTCTTTCGAACAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTTAGGCAGGATGTTT
66 ATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAGGATGTTT
*
14776 TCACATGATTTTCAAAAATGAGAAAGTGATTTCTAAAGTTTCTCATTTAAATCTTTTCTGAAAAT
131 TCACATGATTTTCAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATC-TTTCTGAAAAT
*
14841 TGTTTTTTCTTGAAAAGTA-AGAAAGCGATTTCCAAAGTTTCTTAC
195 TGATTTTTCTTGAAAAGTAGA-AAAGCGATTTCCAAAGTTTCTTAC
* * * * * * *
14886 TAAGTAAGACATTCGGGCCATCAATAAGTTTTTCAAGCATGATGTTTAAATCATTCGGGTCATCT
1 TGAGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAATCATTCGGGTCATCT
* * * * * *
14951 ATAAGTCTTTCGATCAAGGTGATAAGTCCTTCAGGCCATCCATTAGACCTTCAGGCACGATATTT
66 ATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAGGATGTTT
* *
15016 TCACATGATTTTCTAAAATGAGAAAGTGTTTTCCAAAGTTTCTCATTT--A--------AAAATT
131 TCACATGATTTTCAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTCTGAAAATT
* *
15071 GATTTTTCTTGAAAGGTAAGAAAA-CAATTTCCAAAGTTTCTTAC
196 GATTTTTCTTGAAAAGT-AGAAAAGCGATTTCCAAAGTTTCTTAC
* * *
15115 TGAGTAAGCCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAATCTTTCAGGTCATCT
1 TGAGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAATCATTCGGGTCATCT
* * * *
15180 ATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCATAAAACCTTCGGGCAAGATGTTT
66 ATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAGGATGTTT
* * * * * * *
15245 TCACTTAATTTTTGAAAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAAATCTTTCCTAAAAA
131 TCACATGA-TTTTCAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTT-CTGAAAA
*
15310 CTGATTTTTC-TGAAAAGT
194 TTGATTTTTCTTGAAAAGT
15328 TTATCATTTA
Statistics
Matches: 599, Mismatches: 66, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
229 158 0.26
230 38 0.06
231 1 0.00
232 1 0.00
238 1 0.00
239 5 0.01
240 379 0.63
241 16 0.03
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (239 bp):
TGAGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAATCATTCGGGTCATCT
ATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAGGATGTTT
TCACATGATTTTCAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTCTGAAAATT
GATTTTTCTTGAAAAGTAGAAAAGCGATTTCCAAAGTTTCTTAC
Found at i:15910 original size:23 final size:23
Alignment explanation
Indices: 15875--15922 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
15865 AAAAACCTGA
*
15875 CCTATTTATAAAATAAAACCAAAC
1 CCTATTTACAAAAT-AAACCAAAC
*
15899 CCTA-TTACAAAATAAACCAGAC
1 CCTATTTACAAAATAAACCAAAC
15921 CC
1 CC
15923 GAATTGAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 8 0.36
24 4 0.18
ACGTcount: A:0.50, C:0.27, G:0.02, T:0.21
Consensus pattern (23 bp):
CCTATTTACAAAATAAACCAAAC
Found at i:15922 original size:22 final size:24
Alignment explanation
Indices: 15866--15922 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
15856 AGAAAAAAGA
* *
15866 AAAACCTGA-CCTATTTATAAAAT
1 AAAACCAGACCCTATTTACAAAAT
*
15889 AAAACCAAACCCTA-TTACAAAAT
1 AAAACCAGACCCTATTTACAAAAT
15912 -AAACCAGACCC
1 AAAACCAGACCC
15923 GAATTGAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 10 0.34
23 15 0.52
24 4 0.14
ACGTcount: A:0.51, C:0.26, G:0.04, T:0.19
Consensus pattern (24 bp):
AAAACCAGACCCTATTTACAAAAT
Found at i:21330 original size:30 final size:30
Alignment explanation
Indices: 21290--21352 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
21280 GAACCGGCGG
* * *
21290 TTCACACCGGTTTTATCGGTTTTCAGCCGA
1 TTCACACCGGTTTTACCGGTTCTCAACCGA
* *
21320 TTCACCCCGGTTTTGCCGGTTCTCAACCGA
1 TTCACACCGGTTTTACCGGTTCTCAACCGA
21350 TTC
1 TTC
21353 TGTGCTCATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.14, C:0.32, G:0.19, T:0.35
Consensus pattern (30 bp):
TTCACACCGGTTTTACCGGTTCTCAACCGA
Found at i:22337 original size:77 final size:79
Alignment explanation
Indices: 22226--22378 Score: 195
Period size: 77 Copynumber: 2.0 Consensus size: 79
22216 TTCGAATTAA
* * *
22226 TTAAACTCTTATTTAATTAATTCAAATTATATATCTATT-AAAGACTTATAATCTGAATTACACT
1 TTAAACTCTTATTTAATTAATTCAAATTAAATATCCATTAAAAGACTTATAATCAGAATTACACT
22290 C-TTTAATGTTCAT
66 CTTTTAATGTTCAT
* * * * * *
22303 TTAAAC-CTTTATTTAGTTATTTCGAATTAAATATCCATTAAAAGAGTTGTAATCAGAATTACAT
1 TTAAACTC-TTATTTAATTAATTCAAATTAAATATCCATTAAAAGACTTATAATCAGAATTACAC
22367 TCTTTTAATGTT
65 TCTTTTAATGTT
22379 TACTTACTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
76 1 0.02
77 32 0.50
78 22 0.34
79 9 0.14
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (79 bp):
TTAAACTCTTATTTAATTAATTCAAATTAAATATCCATTAAAAGACTTATAATCAGAATTACACT
CTTTTAATGTTCAT
Found at i:37843 original size:23 final size:24
Alignment explanation
Indices: 37799--37844 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
37789 TATTTAATTT
37799 TTAAAAAAGTAAAAAATTATTTATA
1 TTAAAAAAGTAAAAAA-TATTTATA
37824 TTAAAAATA-TAAAAAA-ATTTA
1 TTAAAAA-AGTAAAAAATATTTA
37845 CTACGATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.25
25 14 0.70
26 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
TTAAAAAAGTAAAAAATATTTATA
Found at i:44181 original size:21 final size:21
Alignment explanation
Indices: 44157--44199 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
44147 AAACTGATTT
44157 TCACGTACAAAGTATTGATAC
1 TCACGTACAAAGTATTGATAC
44178 TCACGTACAAAGTATTGATAC
1 TCACGTACAAAGTATTGATAC
44199 T
1 T
44200 ATTCTTATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (21 bp):
TCACGTACAAAGTATTGATAC
Found at i:44476 original size:21 final size:21
Alignment explanation
Indices: 44452--44509 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
44442 TTACAAAGGT
*
44452 AGTATCGATACTCC-CTGTAGG
1 AGTACCGATAC-CCTCTGTAGG
*
44473 AGTACCGATACCCTCTGTTGG
1 AGTACCGATACCCTCTGTAGG
44494 AGTACCGATACCCTCT
1 AGTACCGATACCCTCT
44510 ATTCTGGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.06
21 32 0.94
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (21 bp):
AGTACCGATACCCTCTGTAGG
Found at i:47105 original size:25 final size:25
Alignment explanation
Indices: 47071--47122 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
47061 GCCCTACATA
47071 TGACTTTAGACATCATCTAGTCCTG
1 TGACTTTAGACATCATCTAGTCCTG
47096 TGACTTTAGACATCATCTAGTCCTG
1 TGACTTTAGACATCATCTAGTCCTG
47121 TG
1 TG
47123 TGGCAAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (25 bp):
TGACTTTAGACATCATCTAGTCCTG
Found at i:60987 original size:122 final size:121
Alignment explanation
Indices: 60800--61025 Score: 271
Period size: 122 Copynumber: 1.9 Consensus size: 121
60790 TATAAATAAG
* * * * *
60800 ATATTTATTTATTTAGAAATATCAGAAAAGAGCTTCTACGTGTTTTAAGACAGCTCTTTTTTTAA
1 ATATTTATTTATTTAAAAATATCAAAAAAGAGCTACTACGTGTTTTAAGACAGCTCCTTTCTTAA
60865 TA-TAAAAAATAAATAAATATTAAAAAAATAGATTTATATATAATTTATAAAAGTAAA
66 TATTAAAAAATAAATAAATATT--AAAAATAGATTTATATATAATTTATAAAAGTAAA
* * *
60922 ATATTTATTTATTTAAAAATATCAAAAAATAG--ACATACAGTTGTTTTAAGTCTGC-CCTTTCT
1 ATATTTATTTATTTAAAAATATCAAAAAAGAGCTAC-TAC-G-TGTTTTAAGACAGCTCCTTTCT
* * * *
60984 TAATATTGAAAAATAAATATATATTTAAAATATATTTATATA
63 TAATATTAAAAAATAAATAAATATTAAAAATAGATTTATATA
61026 AATGAATAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
120 1 0.01
121 18 0.20
122 40 0.45
123 29 0.33
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (121 bp):
ATATTTATTTATTTAAAAATATCAAAAAAGAGCTACTACGTGTTTTAAGACAGCTCCTTTCTTAA
TATTAAAAAATAAATAAATATTAAAAATAGATTTATATATAATTTATAAAAGTAAA
Found at i:62413 original size:3 final size:3
Alignment explanation
Indices: 62399--62470 Score: 94
Period size: 3 Copynumber: 24.3 Consensus size: 3
62389 TTTTTATTTG
**
62399 TAA TAA -AA TAA TAA TAA TAA TAA TAA T-A TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
62445 TAA TAA TAA TAA TAA TCAA GAA TAA T
1 TAA TAA TAA TAA TAA T-AA TAA TAA T
62471 TTTAATGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
2 4 0.07
3 55 0.90
4 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:62751 original size:73 final size:73
Alignment explanation
Indices: 62627--63000 Score: 604
Period size: 73 Copynumber: 5.1 Consensus size: 73
62617 GAAGTCCTAT
* * ** *
62627 CATCTTGCACTGTAGGTCTTATAGATGACAGTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
62692 TTTGAAAA
66 TTTGAAAA
* *
62700 CATCATGCACTGTAAGTATTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
62765 TTTGAAAA
66 TTTGAAAA
** * * * *
62773 CATCATGCACTGTAGGTCTTACAGATGACTTTGAGGCTTTAAAATCAAAAATCTACCGAAGGTTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGG-CT
62838 TTTTGAAAA
65 TTTTGAAAA
**
62847 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCTAAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
62912 TTTGAAAA
66 TTTGAAAA
62920 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
62985 TTTGAAAA
66 TTTGAAAA
62993 CATCATGC
1 CATCATGC
63001 TTTAAAATCA
Statistics
Matches: 275, Mismatches: 25, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
73 210 0.76
74 65 0.24
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (73 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
TTTGAAAA
Found at i:62898 original size:147 final size:146
Alignment explanation
Indices: 62627--63000 Score: 613
Period size: 147 Copynumber: 2.6 Consensus size: 146
62617 GAAGTCCTAT
* * *
62627 CATCTTGCACTGTAGGTCTTATAGATGACAGTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACACTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
62692 TTTGAAAACATCATGCACTGTAAGTATTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCC
66 TTTGAAAACATCATGCACTGTAAGTATTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCC
*
62757 GAAGGCTTTTTGAAAA
131 AAAGGCTTTTTGAAAA
** * * *
62773 CATCATGCACTGTAGGTCTTACAGATGACTTTGAGGCTTTAAAATCAAAAATCTACCGAAGGTTT
1 CATCATGCACTGTAGGTCTTACAGATGACACTGAGGCTTTAAAATCAAAAAGCTCCCGAAGG-CT
* *
62838 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCC
65 TTTTGAAAACATCATGCACTGTAAGTATTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCC
*
62903 TAAAGGCTTTTTGAAAA
130 CAAAGGCTTTTTGAAAA
* *
62920 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACACTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
62985 TTTGAAAACATCATGC
66 TTTGAAAACATCATGC
63001 TTTAAAATCA
Statistics
Matches: 210, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
146 74 0.35
147 136 0.65
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (146 bp):
CATCATGCACTGTAGGTCTTACAGATGACACTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
TTTGAAAACATCATGCACTGTAAGTATTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCC
AAAGGCTTTTTGAAAA
Found at i:63005 original size:44 final size:44
Alignment explanation
Indices: 62955--63044 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
62945 TGACCCTGAG
*
62955 GCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
62999 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
63043 GC
1 GC
63045 ACTGTAGGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (44 bp):
GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
Found at i:63096 original size:117 final size:118
Alignment explanation
Indices: 62882--63118 Score: 377
Period size: 117 Copynumber: 2.0 Consensus size: 118
62872 TGACCCTGAG
* * *
62882 GCTTTAAGATCAAAAAGCTCCTAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
1 GCTTTAAAATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATA
* *
62947 ACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGG-CTTTTTGAAAACATCAT
66 ACCCTGAGGCTTTAAAATCAAAAAGCTACCGAAGGTCTTTTTGAAAACATCAT
*
62999 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATA
1 GCTTTAAAATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATA
** * *
63064 ACTTTGAGGCTTTAAAATCAAAAATCTACCGAAGGTTTTTTTGAAAACATCAT
66 ACCCTGAGGCTTTAAAATCAAAAAGCTACCGAAGGTCTTTTTGAAAACATCAT
63117 GC
1 GC
63119 ACTATAGGTC
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
117 91 0.83
118 18 0.17
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (118 bp):
GCTTTAAAATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATA
ACCCTGAGGCTTTAAAATCAAAAAGCTACCGAAGGTCTTTTTGAAAACATCAT
Found at i:63129 original size:74 final size:73
Alignment explanation
Indices: 62999--63264 Score: 424
Period size: 73 Copynumber: 3.6 Consensus size: 73
62989 AAAACATCAT
*
62999 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATA
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
**
63064 ACTTTGAG
66 ACCCTGAG
* * * *
63072 GCTTTAAAATCAAAAATCTACCGAAGGTTTTTTTGAAAACATCATGCACTATAGGTCTTACAGAT
1 GCTTTAAAATCAAAAAGCTCCCGAAGG-CTTTTTGAAAACATCATGCACTGTAGGTCTTACAGAT
63137 GACCCTGAG
65 GACCCTGAG
* * *
63146 GCTTTAAGATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTATGTCTTACAGATG
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
63211 ACCCTGAG
66 ACCCTGAG
*
63219 GCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGC
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGC
63265 TTTAAAATCA
Statistics
Matches: 177, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
73 113 0.64
74 64 0.36
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (73 bp):
GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
ACCCTGAG
Found at i:63205 original size:264 final size:264
Alignment explanation
Indices: 62735--63400 Score: 1217
Period size: 264 Copynumber: 2.5 Consensus size: 264
62725 TGACCCTGAG
*
62735 GCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
62800 ACTTTGAGGCTTTAAAATCAAAAATCTACCGAAGGTTTTTTTGAAAACATCATGCACTGTAGGTC
66 ACTTTGAGGCTTTAAAATCAAAAATCTACCGAAGGTTTTTTTGAAAACATCATGCACTGTAGGTC
62865 TTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCTAAAGGCTTTTTGAAAACATCATGCAC
131 TTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCTAAAGGCTTTTTGAAAACATCATGCAC
62930 TGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA
196 TGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA
62995 TCAT
261 TCAT
*
62999 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATA
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
*
63064 ACTTTGAGGCTTTAAAATCAAAAATCTACCGAAGGTTTTTTTGAAAACATCATGCACTATAGGTC
66 ACTTTGAGGCTTTAAAATCAAAAATCTACCGAAGGTTTTTTTGAAAACATCATGCACTGTAGGTC
*
63129 TTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCAC
131 TTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCTAAAGGCTTTTTGAAAACATCATGCAC
*
63194 TGTATGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA
196 TGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA
63259 TCAT
261 TCAT
63263 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
** * * * * *
63328 ACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAATG-CTTTTTGAAAACATCATGCACTGTAGGTC
66 ACTTTGAGGCTTTAAAATCAAAAATCTACCGAAGGTTTTTTTGAAAACATCATGCACTGTAGGTC
63392 TTACAGATG
131 TTACAGATG
63401 TTGGAAATAG
Statistics
Matches: 388, Mismatches: 14, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
263 36 0.09
264 352 0.91
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (264 bp):
GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
ACTTTGAGGCTTTAAAATCAAAAATCTACCGAAGGTTTTTTTGAAAACATCATGCACTGTAGGTC
TTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCTAAAGGCTTTTTGAAAACATCATGCAC
TGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA
TCAT
Found at i:63269 original size:44 final size:44
Alignment explanation
Indices: 63219--63308 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
63209 TGACCCTGAG
*
63219 GCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
63263 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
63307 GC
1 GC
63309 ACTGTAGGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (44 bp):
GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
Found at i:63352 original size:117 final size:117
Alignment explanation
Indices: 63146--63381 Score: 436
Period size: 117 Copynumber: 2.0 Consensus size: 117
63136 TGACCCTGAG
* * *
63146 GCTTTAAGATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTATGTCTTACAGATG
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
63211 ACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
66 ACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
63263 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
*
63328 ACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAATGCTTTTTGAAAACATCAT
66 ACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
63380 GC
1 GC
63382 ACTGTAGGTC
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (117 bp):
GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
ACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
Found at i:63354 original size:73 final size:73
Alignment explanation
Indices: 63263--63400 Score: 258
Period size: 73 Copynumber: 1.9 Consensus size: 73
63253 AAAACATCAT
63263 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
63328 ACCCTGAG
66 ACCCTGAG
* *
63336 GCTTTAAGATCAAAAAGCTCCCGAATGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
1 GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
63401 TTGGAAATAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (73 bp):
GCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
ACCCTGAG
Found at i:64059 original size:22 final size:22
Alignment explanation
Indices: 64004--64061 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
63994 AATAAAGCGC
* *
64004 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAAAATCTA
64026 TCATCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAGAGAAAATCTA
64048 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
64062 TGTAGATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAAAATCTA
Found at i:73226 original size:28 final size:27
Alignment explanation
Indices: 73184--73237 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
73174 ACATTAATAA
*
73184 AATAATATATATAAATATTATGAAAAT
1 AATAATATATATAAAAATTATGAAAAT
*
73211 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAATTATGAAAA
73238 GAAAGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AATAATATATATAAAAATTATGAAAAT
Found at i:73987 original size:116 final size:113
Alignment explanation
Indices: 73743--73990 Score: 261
Period size: 116 Copynumber: 2.1 Consensus size: 113
73733 CTATTAATAT
* * * *
73743 ATAAATAAGATATTTATTTATTTAGAAATATCAGAAAAAGGGCTTCTATGTGCTTTAAGACAGCT
1 ATAAATAA-ATATTTATTTATTTAAAAATATCAGAAAAAGGACATCCATGTGCTTTAAGACAGCT
* **
73808 CTTTTCTTAATATAAAAAAATATTAAAAAAATAGATTTATATATAATTT
65 CCTTTCTTAATATAAAAAAATATTAAAAAAATAGATTTATATATAATGA
* *
73857 ATAAAAGTAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA-GTTGCTTTAAGACT
1 AT-AAA-T-AAATATTTATTTATTTAAAAATATCAGAAAAAGGACATCCATG-TGCTTTAAGACA
** *
73921 G-TCCTTTCTTAATATTGAAAAATAAATATATATTTAAAATATATTTATATA-AATGA
62 GCTCCTTTCTTAATA-T--AAAA-AAATAT-TA-AAAAAATAGATTTATATATAATGA
73977 ATAAAT-AATATTTA
1 ATAAATAAATATTTA
73991 AAATATTAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
114 2 0.02
115 16 0.14
116 56 0.50
117 2 0.02
118 5 0.04
119 9 0.08
120 7 0.06
121 15 0.13
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (113 bp):
ATAAATAAATATTTATTTATTTAAAAATATCAGAAAAAGGACATCCATGTGCTTTAAGACAGCTC
CTTTCTTAATATAAAAAAATATTAAAAAAATAGATTTATATATAATGA
Found at i:75358 original size:3 final size:3
Alignment explanation
Indices: 75346--75446 Score: 174
Period size: 3 Copynumber: 35.0 Consensus size: 3
75336 TTTGTATTTG
75346 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
75391 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
75438 TAA TAA TAA
1 TAA TAA TAA
75447 AGAATAATTT
Statistics
Matches: 94, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
2 8 0.09
3 86 0.91
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:78869 original size:17 final size:16
Alignment explanation
Indices: 78836--78870 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
78826 GTAATCAGAA
*
78836 TTTTTATTTGGCTATT
1 TTTTTATTTGGCAATT
78852 TTTTTATTTGGACAATT
1 TTTTTATTTGG-CAATT
78869 TT
1 TT
78871 GACTTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (16 bp):
TTTTTATTTGGCAATT
Found at i:79898 original size:378 final size:371
Alignment explanation
Indices: 79173--79931 Score: 1044
Period size: 378 Copynumber: 2.0 Consensus size: 371
79163 CTACAGTCAG
* *
79173 TTTA-TATCTAGATGATAAGAAGAGTTCTACCAGTTTGTGCCGTTCAACCTAAATCTGATTTATG
1 TTTATTATGTAGATGATAAGAAGAGTTCTACCAGTTTGTGCCGTTCAACCTAAATCTGATTTATA
* *
79237 CTTGAGCATATTGAGTGGCTTGAAAATGCCTTTTTGTGCTATACTTCTTTGACTATTCATTTTCT
66 CTTGAGCATATTGAGTGGCTTGAAAATACCTTTTTATGCTATACTTCTTTGAC-ATTCATTTTCT
* * * * *
79302 TCAAAGTACCTGTATCTGAGCGGCCAACTCATGGATACGGGGATATGACCTCTAAGGGTCCTCCA
130 TAAAAGTACCCGTATCTAAGCGGCCAACACATGGATACGGGAATATGACCTCTAAGGGTCCTCCA
* *
79367 AATACATGGAAAACCTAGAAAAAACTAATCATACATGTCAGAAACATATCCTTATCTGATAGTCT
195 AATACATGGAAAACCTAGAAAAAACTAATCATACATGTCAGAAACACATCCTTATCTGATAGTCG
* * * * *
79432 CATGCGAGTCTCGGTCAAGTTGTTATGAGCATCTTCATGGACAATACATGACATGTTCCTTGTTA
260 CATGAGAGTCTCAGTAAAGTTGTTAAGAGCATCTTCAAGGACAATACATGACATGTTCCTTGTTA
* *
79497 TTTAAACAAGCTTGACTCATAAGAACTTATTATTAGGAAATACACTC
325 TTTAAACAAGCTTGACCCATAAGAACTTATTATGAGGAAATACACTC
* * *
79544 TTTATTATGTAGATGATAAGAAGTGTTTTTACCAGTTTGAT-CC-TTGCAACCTAATTCTGATTT
1 TTTATTATGTAGATGATAAGAAGAG-TTCTACCAGTTTG-TGCCGTT-CAACCTAAATCTGATTT
* *
79607 ATACTTGTGCATATTGAGTGGCTTGAAAATACCTTTTTATGCTATA-TTTTTTCGAC-TTCATTT
63 ATACTTGAGCATATTGAGTGGCTTGAAAATACCTTTTTATGCTATACTTCTTT-GACATTCATTT
* * * *
79670 T-TTAAAAAGTACCCGTATCTAATAAGCTGCCGACACGTGGATATGGGAATATGACCTCTAAGGG
127 TCTT-AAAAGTACCCGTATC---TAAGCGGCCAACACATGGATACGGGAATATGACCTCTAAGGG
* * *
79734 TCCTCCAAATACATGGAAAACCTAGAAGAATCTAATCATACCCATGTCAGACACACATCCTTATC
188 TCCTCCAAATACATGGAAAACCTAGAAAAAACTAATCATA--CATGTCAGAAACACATCCTTATC
** * * *
79799 TGATAGTCGCATGATTGTTTCAATTAATAGTTGTTAAGTGCATCTTCAAGGACAATACATGACAT
251 TGATAGTCGCATGAGAGTCTC-AGTAA-AGTTGTTAAGAGCATCTTCAAGGACAATACATGACAT
79864 GTTCCTTGTTATTTAAACAAGCTTGACCCATAAGAACTTATTATGAGGAAATACACTC
314 GTTCCTTGTTATTTAAACAAGCTTGACCCATAAGAACTTATTATGAGGAAATACACTC
79922 TTTATTATGT
1 TTTATTATGT
79932 TGTTTCATTT
Statistics
Matches: 340, Mismatches: 35, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
370 2 0.01
371 25 0.07
372 25 0.07
373 75 0.22
374 74 0.22
376 37 0.11
377 2 0.01
378 100 0.29
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (371 bp):
TTTATTATGTAGATGATAAGAAGAGTTCTACCAGTTTGTGCCGTTCAACCTAAATCTGATTTATA
CTTGAGCATATTGAGTGGCTTGAAAATACCTTTTTATGCTATACTTCTTTGACATTCATTTTCTT
AAAAGTACCCGTATCTAAGCGGCCAACACATGGATACGGGAATATGACCTCTAAGGGTCCTCCAA
ATACATGGAAAACCTAGAAAAAACTAATCATACATGTCAGAAACACATCCTTATCTGATAGTCGC
ATGAGAGTCTCAGTAAAGTTGTTAAGAGCATCTTCAAGGACAATACATGACATGTTCCTTGTTAT
TTAAACAAGCTTGACCCATAAGAACTTATTATGAGGAAATACACTC
Found at i:83623 original size:25 final size:25
Alignment explanation
Indices: 83592--83647 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
83582 CCCCGCTCCA
83592 ACAGCTGTCCCTCCACGTCCCGATT
1 ACAGCTGTCCCTCCACGTCCCGATT
83617 ACAGCTGTCCCTCCACGTCCCGATT
1 ACAGCTGTCCCTCCACGTCCCGATT
83642 ACAGCT
1 ACAGCT
83648 TACAATCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.18, C:0.43, G:0.16, T:0.23
Consensus pattern (25 bp):
ACAGCTGTCCCTCCACGTCCCGATT
Found at i:89421 original size:23 final size:23
Alignment explanation
Indices: 89395--89480 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
89385 GGTTCTACGC
89395 GGTCCTTCGGGACAAATCTATAT
1 GGTCCTTCGGGACAAATCTATAT
89418 GGTCCTTCGGGACAAATCTATAT
1 GGTCCTTCGGGACAAATCTATAT
** * *
89441 GGTCCTTAAGGACAATTCTATGT
1 GGTCCTTCGGGACAAATCTATAT
* *
89464 GGTCTTTCGAGACAAAT
1 GGTCCTTCGGGACAAAT
89481 TCTACGGGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (23 bp):
GGTCCTTCGGGACAAATCTATAT
Found at i:89491 original size:24 final size:24
Alignment explanation
Indices: 89387--89510 Score: 85
Period size: 23 Copynumber: 5.3 Consensus size: 24
89377 GAGTCGAGGG
* *
89387 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGGGGTCCTTCAGGACAAA
*** *
89411 -TCTATATGGTCCTTCGGGACAAA
1 TTCTACGGGGTCCTTCAGGACAAA
*** *
89434 -TCTATATGGTCCTTAAGGAC-AA
1 TTCTACGGGGTCCTTCAGGACAAA
* * *
89456 TTCTATGTGGTCTTTC-GAGACAAA
1 TTCTACGGGGTCCTTCAG-GACAAA
*
89480 TTCTACGGGGTCCTTCAGGATAAA
1 TTCTACGGGGTCCTTCAGGACAAA
89504 TTCTACG
1 TTCTACG
89511 TGGCACTTCG
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
22 3 0.04
23 53 0.63
24 27 0.32
25 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (24 bp):
TTCTACGGGGTCCTTCAGGACAAA
Found at i:95188 original size:28 final size:28
Alignment explanation
Indices: 95157--95213 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
95147 CCGAACGCCT
95157 TGGGATATAATGATGCTGCAATAGTGGA
1 TGGGATATAATGATGCTGCAATAGTGGA
* *
95185 TGGGATATATTGATGCTGCAGTAGTGGA
1 TGGGATATAATGATGCTGCAATAGTGGA
95213 T
1 T
95214 CTATTCGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.32
Consensus pattern (28 bp):
TGGGATATAATGATGCTGCAATAGTGGA
Found at i:98764 original size:22 final size:23
Alignment explanation
Indices: 98739--98789 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
98729 TCATATGGCT
*
98739 CATATCATATTT-TCATGTATCA
1 CATATCATATTTCTCATCTATCA
* *
98761 CATAT-ATCTTTCTCTTCTATCA
1 CATATCATATTTCTCATCTATCA
98783 CATATCA
1 CATATCA
98790 CATACACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.21
22 18 0.75
23 1 0.04
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (23 bp):
CATATCATATTTCTCATCTATCA
Found at i:106504 original size:54 final size:54
Alignment explanation
Indices: 106457--107092 Score: 763
Period size: 54 Copynumber: 11.9 Consensus size: 54
106447 GTGTGAAAAC
* * *
106457 CACGAAATTCATCCTATGTGGAGGAATAACCATTTCAGCACTAAGTGTGCATTT
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
* * * * *
106511 CACGGAATTCATCCTAGGTGGATAAATAACCGTTTCGGCACTAAGTCTGCTTTT
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
* ** * *
106565 CA-TAGAATTTTTCCTATGTGGATGAATAATCGTTTCGGAACTAAGTGTGCATTT
1 CACGA-AATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
* * * *
106619 CACGGAATTCATCCTATGTTGATGAATAACCATTTCGACACTAAGTGTGCATTT
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
* * *
106673 CACGGAATTCATTCTAGGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
* * ** * **
106727 CACGAAATTCATCGTAGGTGGATGAATAACTATTTTGGCACTAAAAGTGCA-TT
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
*
106780 -------TTCATCCTATGTGGATGAATAACCGTTTCGGCATTAAGTGTGCATTT
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
*
106827 CACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
* *
106881 CACGAAATT-ATCCTATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTT
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
* * * * *
106934 CACGAAATTCATCTTAGGTGGATGAATAACTGTTTCAGCACTAAGTGTACATTT
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
* * * * * *
106988 CAAGGAATTCATCCTAGGTGGATGAATAACCATTTCGACACTAAGTGTGCATTC
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
* * * *
107042 CAC-AGAATTCATCATACGTTGATGAATAACCGTTTCGGCACTATGTGTGCA
1 CACGA-AATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCA
107093 AACCACAGAA
Statistics
Matches: 494, Mismatches: 76, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
46 36 0.07
47 2 0.00
53 53 0.11
54 403 0.82
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (54 bp):
CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT
Found at i:107037 original size:315 final size:316
Alignment explanation
Indices: 106464--107071 Score: 909
Period size: 315 Copynumber: 1.9 Consensus size: 316
106454 AACCACGAAA
106464 TTCATCCTATGTGGAGGAATAACCATTTCAGCACTAAGTGTGCATTTCACGGAATTCATCCTAGG
1 TTCATCCTATGTGGAGGAATAACCATTTCAGCACTAAGTGTGCATTTCACGGAATTCATCCTAGG
* * *
106529 TGGATAAATAACCGTTTCGGCACTAAGTCTGCTTTTCATAGAATTTTTCCTATGTGGATGAATAA
66 TGGATAAATAACCGTTTCGGCACTAAGTCTGCATTTCATAGAAATTATCCTATGTGGATGAATAA
* * * * *
106594 TCGTTTCGGAACTAAGTGTGCATTTCACGGAATTCATCCTATGTTGATGAATAACCATTTCGACA
131 CCATTTCGGAACTAAGTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACCATTTCGACA
* * * * *
106659 CTAAGTGTGCATTTCACGGAATTCATTCTAGGTGGATGAATAACCGTTTCGGCACTAAGTGTGCA
196 CTAAGTGTACATTTCAAGGAATTCATCCTAGGTGGATGAATAACCATTTCGACACTAAGTGTGCA
* * *
106724 TTTCAC-GAAATTCATCGTAGGTGGATGAATAACTATTTTGGCACTAAAAGTGCATT
261 TTCCACAG-AATTCATCATACGTGGATGAATAACTATTTTGGCACTAAAAGTGCATT
* * * * *
106780 TTCATCCTATGTGGATGAATAACCGTTTCGGCATTAAGTGTGCATTTCACGGAATTCATCCTATG
1 TTCATCCTATGTGGAGGAATAACCATTTCAGCACTAAGTGTGCATTTCACGGAATTCATCCTAGG
* * *
106845 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCA-CGAAATTATCCTATGTGGATGAATAA
66 TGGATAAATAACCGTTTCGGCACTAAGTCTGCATTTCATAGAAATTATCCTATGTGGATGAATAA
* **
106909 CCATTTC-GACACTAAGTGTGCATTTCACGAAATTCATCTTAGGTGGATGAATAACTGTTTC-AG
131 CCATTTCGGA-ACTAAGTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACCATTTCGA-
106972 CACTAAGTGTACATTTCAAGGAATTCATCCTAGGTGGATGAATAACCATTTCGACACTAAGTGTG
194 CACTAAGTGTACATTTCAAGGAATTCATCCTAGGTGGATGAATAACCATTTCGACACTAAGTGTG
*
107037 CATTCCACAGAATTCATCATACGTTGATGAATAAC
259 CATTCCACAGAATTCATCATACGTGGATGAATAAC
107072 CGTTTCGGCA
Statistics
Matches: 261, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
314 3 0.01
315 162 0.62
316 96 0.37
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (316 bp):
TTCATCCTATGTGGAGGAATAACCATTTCAGCACTAAGTGTGCATTTCACGGAATTCATCCTAGG
TGGATAAATAACCGTTTCGGCACTAAGTCTGCATTTCATAGAAATTATCCTATGTGGATGAATAA
CCATTTCGGAACTAAGTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACCATTTCGACA
CTAAGTGTACATTTCAAGGAATTCATCCTAGGTGGATGAATAACCATTTCGACACTAAGTGTGCA
TTCCACAGAATTCATCATACGTGGATGAATAACTATTTTGGCACTAAAAGTGCATT
Found at i:107136 original size:54 final size:54
Alignment explanation
Indices: 106793--107138 Score: 178
Period size: 54 Copynumber: 6.4 Consensus size: 54
106783 ATCCTATGTG
* * *** * ** * *
106793 GATGAATAACCGTTTCGGCATTAAGTGTGCATTTCACGGAATTCATCCTATGTG
1 GATGAATAACCGTATCGGCACTAAGTGTGCAAACCACAGAATTCATAATACGTT
* *** ** * *
106847 GATGAATAACCGTTTCGGCACTAAGTGTGCATTTCAC-GAAATT-ATCCTATGTG
1 GATGAATAACCGTATCGGCACTAAGTGTGCAAACCACAG-AATTCATAATACGTT
* * * *** ** * *
106900 GATGAATAACCATTTCGACACTAAGTGTGCATTTCAC-GAAATTCATCTTAGGTG
1 GATGAATAACCGTATCGGCACTAAGTGTGCAAACCACAG-AATTCATAATACGTT
* * * * *** ** * *
106954 GATGAATAACTGTTTCAGCACTAAGTGTACATTTCA-AGGAATTCATCCTAGGTG
1 GATGAATAACCGTATCGGCACTAAGTGTGCAAACCACA-GAATTCATAATACGTT
* * * ** *
107008 GATGAATAACCATTTCGACACTAAGTGTGCATTCCACAGAATTCATCATACGTT
1 GATGAATAACCGTATCGGCACTAAGTGTGCAAACCACAGAATTCATAATACGTT
* * *
107062 GATGAATAACCGTTTCGGCACTATGTGTGCAAACCACAGAATTCATAATAGGTT
1 GATGAATAACCGTATCGGCACTAAGTGTGCAAACCACAGAATTCATAATACGTT
* * *
107116 TATGAATAATCGTATGGGCACTA
1 GATGAATAACCGTATCGGCACTA
107139 CGGGTTCATT
Statistics
Matches: 256, Mismatches: 31, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
53 52 0.20
54 202 0.79
55 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (54 bp):
GATGAATAACCGTATCGGCACTAAGTGTGCAAACCACAGAATTCATAATACGTT
Done.