Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005653.1 Hibiscus syriacus cultivar Beakdansim tig00013216_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: 47806
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:103 original size:55 final size:55
Alignment explanation
Indices: 4--284 Score: 420
Period size: 55 Copynumber: 5.1 Consensus size: 55
1 AAT
* * * *
4 AATCTTGTCTGCTCTCTA-TTCGTTCAGAGAGTATGAGACACGAACAATCTTCAAC
1 AATCGTGTCTGCCCCCTATTTC-TTCAGAGAGTATGAGACTCGAACAATCTTCAAC
* *
59 AATCGTGTCCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAAC
* * * *
114 GATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAAC
1 AATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAAC
* *
169 AATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATGAGACTCGAACAATCTTCAAC
1 AATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAAC
* *
224 AATCGTGTCTTCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAAC
1 AATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAAC
279 AATCGT
1 AATCGT
285 TGGGAATCCT
Statistics
Matches: 207, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
55 204 0.99
56 3 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (55 bp):
AATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAAC
Found at i:1294 original size:7 final size:8
Alignment explanation
Indices: 1275--1300 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1265 GAACCCTCAT
1275 TTTTTTCA
1 TTTTTTCA
1283 TTTTTTCA
1 TTTTTTCA
1291 TTTTTTCA
1 TTTTTTCA
1299 TT
1 TT
1301 CATTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1328 original size:20 final size:20
Alignment explanation
Indices: 1279--1315 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1269 CCTCATTTTT
1279 TTCATTTTTTCATTTTTTCA
1 TTCATTTTTTCATTTTTTCA
1299 TTCATTTTTT-ATTTTTT
1 TTCATTTTTTCATTTTTT
1316 TATTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (20 bp):
TTCATTTTTTCATTTTTTCA
Found at i:3126 original size:30 final size:30
Alignment explanation
Indices: 3067--3155 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
3057 CCCGAAGGAC
* * *
3067 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3096 CTATCAAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3126 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3156 ACTGTCCATA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 17 0.32
30 36 0.68
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3191 original size:31 final size:31
Alignment explanation
Indices: 3151--3251 Score: 132
Period size: 31 Copynumber: 3.2 Consensus size: 31
3141 AAAGATCCTC
*
3151 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
3182 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
3213 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
3245 GGTAAAC
1 GGTAAAC
3252 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.56
32 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:4027 original size:2 final size:2
Alignment explanation
Indices: 4020--4051 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4010 TATACAATTC
4020 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
4052 CTAACTCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4554 original size:21 final size:21
Alignment explanation
Indices: 4524--4568 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4514 ATTCTGTCGT
* *
4524 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
4545 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
4566 TTG
1 TTG
4569 CCCAGAAATC
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:14223 original size:16 final size:16
Alignment explanation
Indices: 14202--14239 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
14192 AACCTTATTC
14202 ACATGATATCTACCCA
1 ACATGATATCTACCCA
14218 ACATGATATCTACCCA
1 ACATGATATCTACCCA
14234 ATCATG
1 A-CATG
14240 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:15086 original size:54 final size:53
Alignment explanation
Indices: 15025--15635 Score: 643
Period size: 54 Copynumber: 11.5 Consensus size: 53
15015 CCACCTGTTT
*
15025 GAAGAAGATGTTCGAGTTTCATACTCTCTAGAGAAAGAGGGAGCGAACCCGTAA
1 GAAGAAGATGTTCGAGTTCCATACTC-CTAGAGAAAGAGGGAGCGAACCCGTAA
* * *
15079 GAAGAAGATGTTTGAGTTCTATACTCCT-GAAGAAAGAGGGAGTGAACCCGT--
1 GAAGAAGATGTTCGAGTTCCATACTCCTAG-AGAAAGAGGGAGCGAACCCGTAA
** * ** **
15130 -TTGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAATGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTCCATACTCC-TAGAGAAAGAGGGAGCGAACCCGTAA
* * * *
15183 GAAG-ATATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGAGAACCCGTAA
1 GAAGAAGATGTTCGAGTTCCATACTCC-TAGAGAAAGAGGGAGCGAACCCGTAA
* * * * **
15236 TAAGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCTGTTT
1 GAAGAAGATGTTCGAGTTCCATACTCC-TAGAGAAAGAGGGAGCGAACCCGTAA
* * * *
15290 GAAG-ATATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGAGAACCCGTAA
1 GAAGAAGATGTTCGAGTTCCATACTCC-TAGAGAAAGAGGGAGCGAACCCGTAA
* *
15343 TAAGAAGA-GTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAA
1 GAAGAAGATG-TTCGAGTTCCATACT-CCTAGAGAAAGAGGGAGCGAACCCGTAA
* * * **
15397 GAAGAAGATTTTCGAGTTCTATACTTCCTAGAGAAAGAGGGAGCGAACCTGTTT
1 GAAGAAGATGTTCGAGTTCCATAC-TCCTAGAGAAAGAGGGAGCGAACCCGTAA
*
15451 GAAGAAGATGTTCGAGTTCCATACTCTCTAGAGAAAGAGGGAGCGAACCTGTAA
1 GAAGAAGATGTTCGAGTTCCATACTC-CTAGAGAAAGAGGGAGCGAACCCGTAA
* *
15505 GAAGAAGATGTTTGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCGT--
1 GAAGAAGATGTTCGAGTTCCATACT-CCTAG-AGAAAGAGGGAGCGAACCCGTAA
** * * **
15557 -TTGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTCCATACTCC-TAGAGAAAGAGGGAGCGAACCCGTAA
*
15610 GAAG-ATATGTTCGAGTTCCATACTCC
1 GAAGAAGATGTTCGAGTTCCATACTCC
15636 CCAGCAGAGT
Statistics
Matches: 479, Mismatches: 58, Indels: 41
0.83 0.10 0.07
Matches are distributed among these distances:
50 24 0.05
51 60 0.13
52 1 0.00
53 141 0.29
54 249 0.52
55 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (53 bp):
GAAGAAGATGTTCGAGTTCCATACTCCTAGAGAAAGAGGGAGCGAACCCGTAA
Found at i:15271 original size:107 final size:105
Alignment explanation
Indices: 15026--15635 Score: 705
Period size: 107 Copynumber: 5.8 Consensus size: 105
15016 CACCTGTTTG
* * *
15026 AAGAAGATGTTCGAGTTTCATACT-CTCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGT
1 AAGAAGATGTTCGAGTTCCATACTCCT-TAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATGT
* * * *
15090 TTGAGTTCTATACTCCTGAAGAAAGAGGGAGTGAACCCGTT
65 TCGAGTTCCATACTCCTAAAGAAAGAGGGAGAGAACCCGTT
* * ** *
15131 -TGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTGAAG-ATATGTT
1 AAGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATGTT
*
15194 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGAGAACCCGTAAT
66 CGAGTTCCATACTCC-TAAAGAAAGAGGGAGAGAACCCGT--T
* ** *
15237 AAGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCTGTTTGAAG-ATATGTT
1 AAGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATGTT
*
15301 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGAGAACCCGTAAT
66 CGAGTTCCATACTCC-TAAAGAAAGAGGGAGAGAACCCGT--T
* * * * *
15344 AAGAAGA-GTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATTT
1 AAGAAGATG-TTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATGT
* * * *
15408 TCGAGTTCTATACTTCCTAGAGAAAGAGGGAGCGAACCTGTTT
65 TCGAGTTCCATAC-TCCTAAAGAAAGAGGGAGAGAACCCG-TT
* * *
15451 GAAGAAGATGTTCGAGTTCCATACT-CTCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATG
1 -AAGAAGATGTTCGAGTTCCATACTCCT-TAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATG
* * * *
15515 TTTGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
64 TTCGAGTTCCATACT-CCTAAAGAAAGAGGGAGAGAACCCGTT
* ** *
15558 -TGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-ATATGTT
1 AAGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATGTT
15621 CGAGTTCCATACTCC
66 CGAGTTCCATACTCC
15636 CCAGCAGAGT
Statistics
Matches: 448, Mismatches: 43, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
103 21 0.05
104 84 0.19
105 49 0.11
106 4 0.01
107 158 0.35
108 127 0.28
109 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (105 bp):
AAGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATGTT
CGAGTTCCATACTCCTAAAGAAAGAGGGAGAGAACCCGTT
Found at i:20868 original size:22 final size:22
Alignment explanation
Indices: 20842--20884 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20832 CATCATATAT
20842 TTATAACATAAATTATAAAATA
1 TTATAACATAAATTATAAAATA
***
20864 TTATATTTTAAATTATAAAAT
1 TTATAACATAAATTATAAAAT
20885 GTATTTATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATAACATAAATTATAAAATA
Found at i:30686 original size:16 final size:17
Alignment explanation
Indices: 30655--30687 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30645 TTCCCTGCAC
30655 TCACCTGGAAACCAAAT
1 TCACCTGGAAACCAAAT
*
30672 TCACC-GGAAAGCAAAT
1 TCACCTGGAAACCAAAT
30688 CAACCCAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (17 bp):
TCACCTGGAAACCAAAT
Found at i:39611 original size:43 final size:43
Alignment explanation
Indices: 39534--39801 Score: 257
Period size: 43 Copynumber: 6.2 Consensus size: 43
39524 AATGCTGCAA
* ** ** *
39534 TAGGTGTTGATATTTAGCGGCGTTTGGCAGACAAACGCCGCAA
1 TAGGTGTTGATGTTTAGCGGCGTTTTTCCCACAAACGCCGCAG
* * ** * *
39577 TAAGTGTTGATGTTTAGCGGCATTTTTTTCACAAATGTCGCAG
1 TAGGTGTTGATGTTTAGCGGCGTTTTTCCCACAAACGCCGCAG
* * *
39620 TAGGTGTTGATGTTTTGCGGCGTTTTTCCCGCTAACGCCGCAG
1 TAGGTGTTGATGTTTAGCGGCGTTTTTCCCACAAACGCCGCAG
* * * * *
39663 TAGGTGTTGATTTTTAGCGACGTTTTTCCCACAAACTCTGTAG
1 TAGGTGTTGATGTTTAGCGGCGTTTTTCCCACAAACGCCGCAG
* * *
39706 TAGGTATTGATGTTTAGCGGCGTTTTTCCCACAAACGTCGTAG
1 TAGGTGTTGATGTTTAGCGGCGTTTTTCCCACAAACGCCGCAG
* * * ** * * *
39749 TAGATGTTGATATTTAGCGGTGTTTTTATCGCAAACGCCACAA
1 TAGGTGTTGATGTTTAGCGGCGTTTTTCCCACAAACGCCGCAG
39792 TAGGTGTTGA
1 TAGGTGTTGA
39802 GATTTCGTAG
Statistics
Matches: 179, Mismatches: 46, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 179 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (43 bp):
TAGGTGTTGATGTTTAGCGGCGTTTTTCCCACAAACGCCGCAG
Found at i:39826 original size:43 final size:42
Alignment explanation
Indices: 39768--39848 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
39758 ATATTTAGCG
39768 GTGTTTTTATCGCAAACGCCACAATAGGTGTTGAGATTTCGTA
1 GTGTTTTTATCGCAAACGCCACAATAGG-GTTGAGATTTCGTA
* ** *
39811 GTGTTTTTAGT-GCAAATGCCGTAATAGGGTTGATATTT
1 GTGTTTTTA-TCGCAAACGCCACAATAGGGTTGAGATTT
39849 TGCGACTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 9 0.27
43 23 0.70
44 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (42 bp):
GTGTTTTTATCGCAAACGCCACAATAGGGTTGAGATTTCGTA
Found at i:44022 original size:41 final size:41
Alignment explanation
Indices: 43887--44121 Score: 236
Period size: 41 Copynumber: 5.6 Consensus size: 41
43877 TGAACATATT
* *
43887 GCGGCGTTTTTGAAATAAACGCCGCAAAAGTGTGGTTTATG
1 GCGGCGTTTTTGATACAAACGCCGCAAAAGTGTGGTTTATG
* * * * *
43928 GTGGCATTTTTTTATACAAACGCCGCAAAAAAATGGGGTTTATG
1 GCGGC-GTTTTTGATACAAACGCCGC--AAAAGTGTGGTTTATG
* *
43972 GCGGTGTTTTTGATACAAACGCCGCAAAAGTGCGGTTTATG
1 GCGGCGTTTTTGATACAAACGCCGCAAAAGTGTGGTTTATG
* * * * *
44013 GCTGCGTTTTTTATACAAATGCCGCAAAAAATTGTGGTTTATA
1 GCGGCGTTTTTGATACAAACGCCGC--AAAAGTGTGGTTTATG
* * * * *
44056 GCGCCGTTGTTGATACAAACGCCGTAAAAGTGTGGTCTATA
1 GCGGCGTTTTTGATACAAACGCCGCAAAAGTGTGGTTTATG
*
44097 GCGGCGTTTGTTGATAAAAACGCCG
1 GCGGCGTTT-TTGATACAAACGCCG
44122 TTAATTACCT
Statistics
Matches: 157, Mismatches: 31, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
41 60 0.38
42 30 0.19
43 50 0.32
44 17 0.11
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (41 bp):
GCGGCGTTTTTGATACAAACGCCGCAAAAGTGTGGTTTATG
Found at i:44069 original size:84 final size:84
Alignment explanation
Indices: 43903--44121 Score: 269
Period size: 84 Copynumber: 2.6 Consensus size: 84
43893 TTTTTGAAAT
*
43903 AAACGCCGCAAAAGTGTGGTTTATGG-TGGCATTTTTTTATACAAACGCCGCAAAAAAATGGGGT
1 AAACGCCGCAAAAGTGTGGTTTATGGCT-GC-GTTTTTTATACAAACGCCGCAAAAAAATGGGGT
* ** *
43967 TTATGGCGGTGTTTTTGATAC
64 TTATAGCGCCGTTGTTGATAC
* * * *
43988 AAACGCCGCAAAAGTGCGGTTTATGGCTGCGTTTTTTATACAAATGCCGCAAAAAATTGTGGTTT
1 AAACGCCGCAAAAGTGTGGTTTATGGCTGCGTTTTTTATACAAACGCCGCAAAAAAATGGGGTTT
44053 ATAGCGCCGTTGTTGATAC
66 ATAGCGCCGTTGTTGATAC
* * * * * *
44072 AAACGCCGTAAAAGTGTGGTCTATAGCGGCGTTTGTTGATAAAAACGCCG
1 AAACGCCGCAAAAGTGTGGTTTATGGCTGCGTTT-TTTATACAAACGCCG
44122 TTAATTACCT
Statistics
Matches: 115, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
84 75 0.65
85 39 0.34
86 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (84 bp):
AAACGCCGCAAAAGTGTGGTTTATGGCTGCGTTTTTTATACAAACGCCGCAAAAAAATGGGGTTT
ATAGCGCCGTTGTTGATAC
Found at i:45770 original size:82 final size:82
Alignment explanation
Indices: 45517--45867 Score: 293
Period size: 82 Copynumber: 4.3 Consensus size: 82
45507 GTGCATATTT
* * * * * * * *
45517 TTGCGGTGTTT-TTATAAAAACGCCACGATAAACAACA-TATTGCGGCGTTTGTAAG-ACAAACA
1 TTGCGGCGTTTGTTAAAAAAACGCCACTATAAATAACACTATTACGACGTTTGT--GTATAAACG
* * * *
45579 CCGTTATATTATTAATCTA
64 CCGCTAAATTACTACTCTA
* * ** * * * * * *
45598 TTGCGGTGTTTTTTGCATAAACGCCACTATAAACAATACTATTTGCGACGTTTGTTTTATAGACG
1 TTGCGGCGTTTGTTAAAAAAACGCCACTATAAATAACACTA-TTACGACGTTTG-TGTATAAACG
* *
45663 CCGCTAAATTTCTTCTCTA
64 CCGCTAAATTACTACTCTA
* * *
45682 TAGCGGCGTTTGTTAAAAAAACGCCACTATAAATAACACTATCACGACGTTTGTGTAAAAACGCC
1 TTGCGGCGTTTGTTAAAAAAACGCCACTATAAATAACACTATTACGACGTTTGTGTATAAACGCC
*
45747 GCTAAATTACCACTCTA
66 GCTAAATTACTACTCTA
*
45764 TTGCGGCGTTTGTTAAAAAAACGCCACTAT---TAACGTATCTATTACGGCGTGTT-TGCTATAA
1 TTGCGGCGTTTGTTAAAAAAACGCCACTATAAATAAC--A-CTATTACGACGT-TTGTG-TATAA
45825 ACGCCGCTAAATTACTACTCTA
61 ACGCCGCTAAATTACTACTCTA
* *
45847 TTGTGGCGTTTGTTTAAAAAA
1 TTGCGGCGTTTGTTAAAAAAA
45868 TGCCGCTAAA
Statistics
Matches: 221, Mismatches: 39, Indels: 18
0.79 0.14 0.06
Matches are distributed among these distances:
79 4 0.02
81 12 0.05
82 85 0.38
83 58 0.26
84 61 0.28
85 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (82 bp):
TTGCGGCGTTTGTTAAAAAAACGCCACTATAAATAACACTATTACGACGTTTGTGTATAAACGCC
GCTAAATTACTACTCTA
Found at i:45774 original size:41 final size:41
Alignment explanation
Indices: 45660--45877 Score: 162
Period size: 41 Copynumber: 5.3 Consensus size: 41
45650 TGTTTTATAG
* * *
45660 ACGCCGCTAAATTTCTTCTCTATAGCGGCGTTTGTTAAAAAA
1 ACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTT-AAAAA
* * * ** *
45702 ACGCCACTATAAATA--ACACTATCACGACGTTTGTGT-AAAA
1 ACGCCGCTA-AATTACTACTCTATTGCGGCGTTTGT-TAAAAA
*
45742 ACGCCGCTAAATTACCACTCTATTGCGGCGTTTGTTAAAAAA
1 ACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTT-AAAAA
* * * *
45784 ACGCCACT--ATTAACGTA-TCTATTACGGCGTGTTTGCT-ATAA
1 ACGCCGCTAAATT-AC-TACTCTATTGCGGC--GTTTGTTAAAAA
*
45825 ACGCCGCTAAATTACTACTCTATTGTGGCGTTTGTTTAAAAA
1 ACGCCGCTAAATTACTACTCTATTGCGGCGTTTG-TTAAAAA
*
45867 ATGCCGCTAAA
1 ACGCCGCTAAA
45878 GTATCATTTT
Statistics
Matches: 136, Mismatches: 25, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
39 4 0.03
40 21 0.15
41 54 0.40
42 45 0.33
43 12 0.09
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (41 bp):
ACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTTAAAAA
Found at i:45855 original size:42 final size:43
Alignment explanation
Indices: 45738--45877 Score: 116
Period size: 42 Copynumber: 3.3 Consensus size: 43
45728 ACGTTTGTGT
* *
45738 AAAAACGCCGCTAAATTACCACTCTATTGCGGC--GTTTGTTAA
1 AAAAACGCCGCTAAATTACTACTCTATTGCGGCGTGTTTGCT-A
* *
45780 AAAAACGCCACT--ATTAACGTA-TCTATTACGGCGTGTTTGCT-
1 AAAAACGCCGCTAAATT-AC-TACTCTATTGCGGCGTGTTTGCTA
* * *
45821 ATAAACGCCGCTAAATTACTACTCTATTGTGGC--GTTTGTTTA
1 AAAAACGCCGCTAAATTACTACTCTATTGCGGCGTGTTTG-CTA
*
45863 AAAAATGCCGCTAAA
1 AAAAACGCCGCTAAA
45878 GTATCATTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
40 8 0.10
41 25 0.32
42 36 0.46
43 9 0.12
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (43 bp):
AAAAACGCCGCTAAATTACTACTCTATTGCGGCGTGTTTGCTA
Done.