Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397283.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_31.0, 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: 1333793
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 10515 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:1204392 original size:15 final size:14
Alignment explanation
Indices: 1204368--1204414 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1204358 TAATGTTATA
1204368 TTTTTATTATAATT
1 TTTTTATTATAATT
*
1204382 TTTTATATTATAATA
1 TTTT-TATTATAATT
*
1204397 TTATT-TT-TAATT
1 TTTTTATTATAATT
1204409 TTTTTA
1 TTTTTA
1204415 AAAGATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 5 0.19
15 12 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTATTATAATT
Found at i:1207799 original size:22 final size:22
Alignment explanation
Indices: 1207774--1207815 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1207764 TTGGTGAGTT
1207774 GCATGATAGCATTGGTTGAGCC
1 GCATGATAGCATTGGTTGAGCC
1207796 GCATGATAGCATTGGTTGAG
1 GCATGATAGCATTGGTTGAG
1207816 TCTACAGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (22 bp):
GCATGATAGCATTGGTTGAGCC
Found at i:1225503 original size:26 final size:28
Alignment explanation
Indices: 1225467--1225524 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
1225457 ATAAGAATTT
1225467 ATTTGATTC-A-A-AATAAAAATATAAAA
1 ATTTGATTCAATATAATAAAAA-ATAAAA
1225493 ATTTGATTCAATATAATAAAAAATAAAA
1 ATTTGATTCAATATAATAAAAAATAAAA
1225521 ATTT
1 ATTT
1225525 ATTTTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.31
27 1 0.03
28 11 0.38
29 8 0.28
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
ATTTGATTCAATATAATAAAAAATAAAA
Found at i:1237167 original size:17 final size:17
Alignment explanation
Indices: 1237145--1237179 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1237135 TTTTAAATTT
*
1237145 AAGAAAAGGAGATTCGA
1 AAGAAAAAGAGATTCGA
1237162 AAGAAAAAGAGATTCGA
1 AAGAAAAAGAGATTCGA
1237179 A
1 A
1237180 CCTTAGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.26, T:0.11
Consensus pattern (17 bp):
AAGAAAAAGAGATTCGA
Found at i:1240511 original size:21 final size:19
Alignment explanation
Indices: 1240493--1240545 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
1240483 TAAGAAAAGG
1240493 AAAAGAATAAG--AAAAAA
1 AAAAGAATAAGAAAAAAAA
1240510 AAAAGAATAAGAAACAAAAAA
1 AAAAGAATAAG-AA-AAAAAA
1240531 AAAAGAATAAGAAAA
1 AAAAGAATAAGAAAA
1240546 GGAAAATCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 11 0.34
19 2 0.06
20 2 0.06
21 17 0.53
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (19 bp):
AAAAGAATAAGAAAAAAAA
Found at i:1240551 original size:17 final size:17
Alignment explanation
Indices: 1240479--1240545 Score: 80
Period size: 17 Copynumber: 3.7 Consensus size: 17
1240469 ACGTTTCAAT
**
1240479 AGAATAAGAAAAGGAAA
1 AGAATAAGAAAAAAAAA
1240496 AGAATAAGAAAAAAAAA
1 AGAATAAGAAAAAAAAA
1240513 AGAATAAGAAACAAAAAAAAA
1 AGAATAAG----AAAAAAAAA
1240534 AGAATAAGAAAA
1 AGAATAAGAAAA
1240546 GGAAAATCAG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 27 0.61
21 17 0.39
ACGTcount: A:0.78, C:0.01, G:0.15, T:0.06
Consensus pattern (17 bp):
AGAATAAGAAAAAAAAA
Found at i:1240551 original size:21 final size:21
Alignment explanation
Indices: 1240504--1240544 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1240494 AAAGAATAAG
1240504 AAAAAAAAAAGAATAAGAAAC
1 AAAAAAAAAAGAATAAGAAAC
1240525 AAAAAAAAAAGAATAAGAAA
1 AAAAAAAAAAGAATAAGAAA
1240545 AGGAAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAAGAATAAGAAAC
Found at i:1266057 original size:40 final size:43
Alignment explanation
Indices: 1265958--1266057 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 43
1265948 CAACTTCTAA
* *
1265958 TAAAATAT-TAATATTAAATTAAAAAGTAAAATATTAATAGTT
1 TAAAATATCAAATATTAAATCAAAAAGTAAAATATTAATAGTT
* * *
1266000 TAAAATATTAAAAATTAAATCAAGAA-TAAAAT-TTAATA-TT
1 TAAAATATCAAATATTAAATCAAAAAGTAAAATATTAATAGTT
*
1266040 T-AAATGATCAATTATTAA
1 TAAAAT-ATCAAATATTAA
1266058 TAAAATAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
39 4 0.08
40 12 0.24
41 6 0.12
42 14 0.29
43 13 0.27
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (43 bp):
TAAAATATCAAATATTAAATCAAAAAGTAAAATATTAATAGTT
Found at i:1266300 original size:15 final size:15
Alignment explanation
Indices: 1266241--1266300 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
1266231 TTAAATTAAA
1266241 TAAAATATTAATATT
1 TAAAATATTAATATT
* * *
1266256 AAAAACATTAATAAT
1 TAAAATATTAATATT
*
1266271 TAAATTA-TAA-A--
1 TAAAATATTAATATT
1266282 TAAAATATTAATATT
1 TAAAATATTAATATT
1266297 TAAA
1 TAAA
1266301 TTATCTATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 2 0.06
14 3 0.09
15 20 0.59
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATTAATATT
Found at i:1266314 original size:41 final size:42
Alignment explanation
Indices: 1266237--1266327 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 42
1266227 ATATTTAAAT
1266237 TAAATAAAATATTAATATTAAAAACATTAATAATTAA-ATTA
1 TAAATAAAATATTAATATTAAAAACATTAATAATTAACATTA
* ** * *
1266278 TAAATAAAATATTAATATTTAAATTATCT-ATTATTAACATTT
1 TAAATAAAATATTAATATTAAAAACAT-TAATAATTAACATTA
1266320 TAAATAAA
1 TAAATAAA
1266328 TAATCAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 31 0.72
42 12 0.28
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (42 bp):
TAAATAAAATATTAATATTAAAAACATTAATAATTAACATTA
Found at i:1266337 original size:27 final size:28
Alignment explanation
Indices: 1266297--1266355 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
1266287 TATTAATATT
* * *
1266297 TAAATTATCTATTATTAACATTT-TAAA
1 TAAATAATCAATTATTAACATTTAAAAA
*
1266324 TAAATAATCAATTATTAATATTTAAAAA
1 TAAATAATCAATTATTAACATTTAAAAA
1266352 TAAA
1 TAAA
1266356 ATCAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAATAATCAATTATTAACATTTAAAAA
Found at i:1266358 original size:26 final size:27
Alignment explanation
Indices: 1266307--1266360 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
1266297 TAAATTATCT
*
1266307 ATTATTAACATTTTAAATAAATAATCA
1 ATTATTAACATTTTAAATAAAAAATCA
*
1266334 ATTATTAATA-TTTAAA-AATAAAATCA
1 ATTATTAACATTTTAAATAA-AAAATCA
1266360 A
1 A
1266361 ATAAAGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 13 0.54
27 9 0.38
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (27 bp):
ATTATTAACATTTTAAATAAAAAATCA
Found at i:1266596 original size:17 final size:17
Alignment explanation
Indices: 1266574--1266606 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1266564 TATTGTTACC
*
1266574 AACCAAATACTGCTATA
1 AACCAAATACTACTATA
1266591 AACCAAATACTACTAT
1 AACCAAATACTACTAT
1266607 CAAATTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.24, G:0.03, T:0.24
Consensus pattern (17 bp):
AACCAAATACTACTATA
Found at i:1279617 original size:8 final size:9
Alignment explanation
Indices: 1279603--1279627 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1279593 ATACAAATAA
1279603 AAAAAAAAG
1 AAAAAAAAG
1279612 AAAAAAAAG
1 AAAAAAAAG
1279621 AAAAAAA
1 AAAAAAA
1279628 TTATGTCTTC
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1284971 original size:27 final size:27
Alignment explanation
Indices: 1284932--1285156 Score: 165
Period size: 27 Copynumber: 8.4 Consensus size: 27
1284922 CTGAGGTAAT
* *
1284932 TGCTGTTGTTGCAGCTGGGGAAGCTGC
1 TGCTGCTGCTGCAGCTGGGGAAGCTGC
* * * *
1284959 GGCTGCTGCTGCAGTTGTGGAAGTTGC
1 TGCTGCTGCTGCAGCTGGGGAAGCTGC
* *
1284986 TGCTGTTGCTGCATCTGGGGCAA-CTGC
1 TGCTGCTGCTGCAGCTGGGG-AAGCTGC
* * *
1285013 TGTTGTTGTTGCAGCT-GGGATAGCTGC
1 TGCTGCTGCTGCAGCTGGGGA-AGCTGC
*
1285040 TGCTGCTG-T--AGCTGTGGAAGCTGC
1 TGCTGCTGCTGCAGCTGGGGAAGCTGC
* ** ** * *
1285064 TGCTGCTGCTGCTGCTGTAGCTGCGGA
1 TGCTGCTGCTGCAGCTGGGGAAGCTGC
* * *
1285091 TGCTGCTGCTGTAGCTGTGGATGCTGC
1 TGCTGCTGCTGCAGCTGGGGAAGCTGC
* *
1285118 TGCTGCTGTTGCAGCTGAGGG-AGCTGA
1 TGCTGCTGCTGCAGCTG-GGGAAGCTGC
1285145 TGCTGCTGCTGC
1 TGCTGCTGCTGC
1285157 TGTTGCAGCT
Statistics
Matches: 154, Mismatches: 36, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
24 18 0.12
25 5 0.03
26 5 0.03
27 122 0.79
28 4 0.03
ACGTcount: A:0.10, C:0.21, G:0.38, T:0.31
Consensus pattern (27 bp):
TGCTGCTGCTGCAGCTGGGGAAGCTGC
Found at i:1285052 original size:24 final size:24
Alignment explanation
Indices: 1285025--1285126 Score: 91
Period size: 24 Copynumber: 4.0 Consensus size: 24
1285015 TTGTTGTTGC
1285025 AGCTG-GGATAGCTGCTGCTGCTGT
1 AGCTGTGGA-AGCTGCTGCTGCTGT
1285049 AGCTGTGGAAGCTGCTGCTGCTGCT
1 AGCTGTGGAAGCTGCTGCTGCTG-T
**
1285074 -GCTGCTGTAGCTGCGGATGCTGCTGCTGT
1 AGCTG-TG--GAAGC---TGCTGCTGCTGT
*
1285103 AGCTGTGGATGCTGCTGCTGCTGT
1 AGCTGTGGAAGCTGCTGCTGCTGT
1285127 TGCAGCTGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
24 35 0.53
25 6 0.09
27 7 0.11
29 3 0.05
30 15 0.23
ACGTcount: A:0.10, C:0.23, G:0.37, T:0.30
Consensus pattern (24 bp):
AGCTGTGGAAGCTGCTGCTGCTGT
Found at i:1285062 original size:33 final size:33
Alignment explanation
Indices: 1285025--1285096 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
1285015 TTGTTGTTGC
*
1285025 AGCTG-GGATAGCTGCTGCTGCTGTAGCTGTGGA
1 AGCTGCGGAT-GCTGCTGCTGCTGTAGCTGCGGA
* *
1285058 AGCTGCTGCTGCTGCTGCTGCTGTAGCTGCGGA
1 AGCTGCGGATGCTGCTGCTGCTGTAGCTGCGGA
*
1285091 TGCTGC
1 AGCTGC
1285097 TGCTGTAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.11, C:0.24, G:0.38, T:0.28
Consensus pattern (33 bp):
AGCTGCGGATGCTGCTGCTGCTGTAGCTGCGGA
Found at i:1285065 original size:3 final size:3
Alignment explanation
Indices: 1285059--1285158 Score: 62
Period size: 3 Copynumber: 33.3 Consensus size: 3
1285049 AGCTGTGGAA
* *
1285059 GCT GCT GCT GCT GCT GCT GCT G-T AGCT GCG GAT GCT GCT GCT G-T
1 GCT GCT GCT GCT GCT GCT GCT GCT -GCT GCT GCT GCT GCT GCT GCT
* * * ** ** *
1285103 AGCT G-T GGAT GCT GCT GCT GCT GTT GCA GCT GAG GGA GCT GAT GCT
1 -GCT GCT -GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1285149 GCT GCT GCT G
1 GCT GCT GCT G
1285159 TTGCAGCTGA
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
2 3 0.04
3 68 0.92
4 3 0.04
ACGTcount: A:0.08, C:0.24, G:0.38, T:0.30
Consensus pattern (3 bp):
GCT
Found at i:1285086 original size:21 final size:21
Alignment explanation
Indices: 1285062--1285122 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
1285052 TGTGGAAGCT
*
1285062 GCTGCTGCTGCTGCTGCTGTA
1 GCTGCTGATGCTGCTGCTGTA
*
1285083 GCTGCGGATGCTGCTGCTGTA
1 GCTGCTGATGCTGCTGCTGTA
1285104 GCTG-TGGATGCTGCTGCTG
1 GCTGCT-GATGCTGCTGCTG
1285123 CTGTTGCAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.07, C:0.25, G:0.38, T:0.31
Consensus pattern (21 bp):
GCTGCTGATGCTGCTGCTGTA
Found at i:1285095 original size:81 final size:81
Alignment explanation
Indices: 1284938--1285239 Score: 216
Period size: 81 Copynumber: 3.7 Consensus size: 81
1284928 TAATTGCTGT
* * * *
1284938 TGTTGCAGCTGGGGA-AGCTGCGGCTGCTGCTGCAGTTGTGGAAGTTGCTGCTGTTGCTGCAT-C
1 TGTTGCAGCTGAGGATAGCT---GCTGCTGCTGCAGCTGTGGAAGCTGCTGCTGCTGCTGC-TGC
* * *
1285001 TG-G-GGC-AACTGCTGTTGT
62 TGAGCTGCGGA-TGCTGTTGC
*
1285019 TGTTGCAGCTG-GGATAGCTGCTGCTGCTGTAGCTGTGGAAGCTGCTGCTGCTGCTGCTGCTGTA
1 TGTTGCAGCTGAGGATAGCTGCTGCTGCTGCAGCTGTGGAAGCTGCTGCTGCTGCTGCTGCTG-A
*
1285083 GCTGCGGATGCTGCTGC
65 GCTGCGGATGCTGTTGC
* * * * *
1285100 TG-T--AGCTGTGGAT-GCTGCTGCTGCTGTTGCAGCTGAGGGAGCTGATGCTGCTGCTGCTGTT
1 TGTTGCAGCTGAGGATAGCTGCTGCTGC---TGCAGCTGTGGAAGCTGCTGCTGCTGCTGCTGCT
*
1285161 GCAGCTGAGGGA-GCTGTTGC
63 G-AGCTG-CGGATGCTGTTGC
* * * * * *
1285181 TGCTGCAAG-TGAGG-GAGCTGTTGTTGTTGCAACTGTGGAAGCTGCTGCTGCTGCTGCTG
1 TGTTGC-AGCTGAGGATAGCTGCTGCTGCTGCAGCTGTGGAAGCTGCTGCTGCTGCTGCTG
1285240 TTGTTGCAGC
Statistics
Matches: 180, Mismatches: 25, Indels: 32
0.76 0.11 0.14
Matches are distributed among these distances:
77 1 0.01
78 53 0.29
79 4 0.02
80 5 0.03
81 98 0.54
82 5 0.03
84 12 0.07
85 2 0.01
ACGTcount: A:0.11, C:0.21, G:0.38, T:0.30
Consensus pattern (81 bp):
TGTTGCAGCTGAGGATAGCTGCTGCTGCTGCAGCTGTGGAAGCTGCTGCTGCTGCTGCTGCTGAG
CTGCGGATGCTGTTGC
Found at i:1285097 original size:33 final size:33
Alignment explanation
Indices: 1285035--1285101 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1285025 AGCTGGGATA
*
1285035 GCTGCTGCTGCTGTAGCTGTGGAAGCTGCTGCT
1 GCTGCTGCTGCTGTAGCTGCGGAAGCTGCTGCT
*
1285068 GCTGCTGCTGCTGTAGCTGCGGATGCTGCTGCT
1 GCTGCTGCTGCTGTAGCTGCGGAAGCTGCTGCT
1285101 G
1 G
1285102 TAGCTGTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.07, C:0.25, G:0.37, T:0.30
Consensus pattern (33 bp):
GCTGCTGCTGCTGTAGCTGCGGAAGCTGCTGCT
Found at i:1285143 original size:18 final size:18
Alignment explanation
Indices: 1285122--1285185 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
1285112 TGCTGCTGCT
1285122 GCTGTTGCAGCTGAGGGA
1 GCTGTTGCAGCTGAGGGA
* * **
1285140 GCTGATGCTGCT---GCT
1 GCTGTTGCAGCTGAGGGA
1285155 GCTGTTGCAGCTGAGGGA
1 GCTGTTGCAGCTGAGGGA
*
1285173 GCTGTTGCTGCTG
1 GCTGTTGCAGCTG
1285186 CAAGTGAGGG
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
15 11 0.32
18 23 0.68
ACGTcount: A:0.11, C:0.20, G:0.41, T:0.28
Consensus pattern (18 bp):
GCTGTTGCAGCTGAGGGA
Found at i:1285147 original size:33 final size:33
Alignment explanation
Indices: 1285110--1285186 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
1285100 TGTAGCTGTG
1285110 GATGCTGCTGCTGCTGTTGCAGCTGAGGGAGCT
1 GATGCTGCTGCTGCTGTTGCAGCTGAGGGAGCT
1285143 GATGCTGCTGCTGCTGTTGCAGCTGAGGGAGCT
1 GATGCTGCTGCTGCTGTTGCAGCTGAGGGAGCT
*
1285176 GTTGCTGCTGC
1 GATGCTGCTGC
1285187 AAGTGAGGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.22, G:0.39, T:0.29
Consensus pattern (33 bp):
GATGCTGCTGCTGCTGTTGCAGCTGAGGGAGCT
Found at i:1285176 original size:24 final size:24
Alignment explanation
Indices: 1285149--1285239 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1285139 AGCTGATGCT
*
1285149 GCTGCTGCTGTTGCAGCTGAGGGA
1 GCTGCTGCTGCTGCAGCTGAGGGA
*
1285173 GCTGTTGCTGCTGCAAG-TGAGGGA
1 GCTGCTGCTGCTGC-AGCTGAGGGA
* * * * * *
1285197 GCTGTTGTTGTTGCAACTGTGGAA
1 GCTGCTGCTGCTGCAGCTGAGGGA
*
1285221 GCTGCTGCTGCTGCTGCTG
1 GCTGCTGCTGCTGCAGCTG
1285240 TTGTTGCAGC
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.94
25 2 0.04
ACGTcount: A:0.12, C:0.20, G:0.38, T:0.30
Consensus pattern (24 bp):
GCTGCTGCTGCTGCAGCTGAGGGA
Found at i:1285200 original size:33 final size:33
Alignment explanation
Indices: 1285110--1285200 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 33
1285100 TGTAGCTGTG
* **
1285110 GATGCTGCTGCTGCTGTTGCAGCTGAGGGAGCT
1 GATGCTGCTGCAGCTGAGGCAGCTGAGGGAGCT
* **
1285143 GATGCTGCTGCTGCTGTTGCAGCTGAGGGAGCT
1 GATGCTGCTGCAGCTGAGGCAGCTGAGGGAGCT
* *
1285176 GTTGCTGCTGCAAG-TGAGGGAGCTG
1 GATGCTGCTGC-AGCTGAGGCAGCTG
1285201 TTGTTGTTGC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
33 51 0.98
34 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.41, T:0.26
Consensus pattern (33 bp):
GATGCTGCTGCAGCTGAGGCAGCTGAGGGAGCT
Found at i:1285320 original size:30 final size:30
Alignment explanation
Indices: 1285227--1285330 Score: 145
Period size: 30 Copynumber: 3.5 Consensus size: 30
1285217 GGAAGCTGCT
1285227 GCTGCTGCTGCTGTTGTTGCAGCTGTGGAA
1 GCTGCTGCTGCTGTTGTTGCAGCTGTGGAA
**
1285257 GGGGCTGCTGCTGTTGTTGCAGCTGTGGAA
1 GCTGCTGCTGCTGTTGTTGCAGCTGTGGAA
* * * *
1285287 GCTGCTGCTGCTGCTGTTGCAGTTGCGGCA
1 GCTGCTGCTGCTGTTGTTGCAGCTGTGGAA
*
1285317 GCTGTTGCTGCTGT
1 GCTGCTGCTGCTGT
1285331 AGCTGTGGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.08, C:0.21, G:0.38, T:0.33
Consensus pattern (30 bp):
GCTGCTGCTGCTGTTGTTGCAGCTGTGGAA
Found at i:1285349 original size:24 final size:24
Alignment explanation
Indices: 1285322--1285367 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1285312 CGGCAGCTGT
1285322 TGCTGCTGTAGCTG-TGGTTGCATC
1 TGCTGCTGTAGCTGCT-GTTGCATC
* *
1285346 TGCTGGTGTTGCTGCTGTTGCA
1 TGCTGCTGTAGCTGCTGTTGCA
1285368 ATTGTTGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.07, C:0.20, G:0.35, T:0.39
Consensus pattern (24 bp):
TGCTGCTGTAGCTGCTGTTGCATC
Found at i:1293572 original size:36 final size:36
Alignment explanation
Indices: 1293523--1293594 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1293513 GGCTTTTACA
1293523 AGTCAATTACTCATTCATCAAGCAGTAAGTGCAAAT
1 AGTCAATTACTCATTCATCAAGCAGTAAGTGCAAAT
* *
1293559 AGTCAATTCCTCATTCATCAAGTAGTAAGTGCAAAT
1 AGTCAATTACTCATTCATCAAGCAGTAAGTGCAAAT
1293595 GATCATAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (36 bp):
AGTCAATTACTCATTCATCAAGCAGTAAGTGCAAAT
Found at i:1295532 original size:3 final size:3
Alignment explanation
Indices: 1295524--1295559 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1295514 TAAAAAAGCT
*
1295524 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1295560 ATTTCACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:1309105 original size:12 final size:12
Alignment explanation
Indices: 1309088--1309112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1309078 GAAGCCCTCG
1309088 CTTCTCCCCCCC
1 CTTCTCCCCCCC
1309100 CTTCTCCCCCCC
1 CTTCTCCCCCCC
1309112 C
1 C
1309113 CAAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (12 bp):
CTTCTCCCCCCC
Done.