Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 29 of 29
Found at i:13318750 original size:5 final size:6
Alignment explanation
Indices: 13318729--13318758 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
13318719 CCAAACCCAA
*
13318729 AAAAAT AAAAAG AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
13318759 CATTTTGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:13319115 original size:38 final size:37
Alignment explanation
Indices: 13319073--13319156 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 37
13319063 ATCTAAAAAG
13319073 TTTTTAAATTAT-TTTAAAAAATTTTAAATAAAATTTTA
1 TTTTTAAATTATGTTTAAAAAATTTT--ATAAAATTTTA
** * *
13319111 TTTTT-AATTATGTTTAATTAATTTTATATATTTTTA
1 TTTTTAAATTATGTTTAAAAAATTTTATAAAATTTTA
13319147 -TTTTAAATTA
1 TTTTTAAATTA
13319157 AATAAATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 4 0.10
36 14 0.35
37 6 0.15
38 16 0.40
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (37 bp):
TTTTTAAATTATGTTTAAAAAATTTTATAAAATTTTA
Found at i:13319944 original size:28 final size:25
Alignment explanation
Indices: 13319909--13319974 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 25
13319899 GATTTAAATA
13319909 TTATAAATTTATATAATAATTATTATT
1 TTATAAATTTATATAAT--TTATTATT
* * *
13319936 TTATTAAATTCAAATAATTTTTTATT
1 TTA-TAAATTTATATAATTTATTATT
13319962 TTAT-AATTTATAT
1 TTATAAATTTATAT
13319975 TAGTATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
24 7 0.21
25 1 0.03
26 10 0.30
27 3 0.09
28 12 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTATAAATTTATATAATTTATTATT
Found at i:13343249 original size:129 final size:128
Alignment explanation
Indices: 13343004--13343259 Score: 406
Period size: 129 Copynumber: 2.0 Consensus size: 128
13342994 AAGTCAAAAT
*
13343004 TGTCTCCAGTGGTGTTTCCAGGATGTTTTGTTCATTGAACAAGAAGTCAGAAGCCTCTCCAGTTT
1 TGTCACCAGTGGTGTTTCCAGGATGTTTTGTTCATTGAACAAGAAGTCAGAAGCCTCTCCAGTTT
* * *
13343069 CCGCCACCAACGACAGAAACCTCCCTGTCATGGCAGATTCTGATGACAGGAACAAGGTTGAAAC
66 CCGCCACCAACAACAGAAACCTCCCTGTCATGGCAGATTCTAATGAAAGGAAC-AGGTTGAAAC
*
13343133 TGTCACCAGTGGTGTTTCCAGGATGTTTTGTTCATTGAACAAGAAGTCAGAAGCCTGTCCAGTTT
1 TGTCACCAGTGGTGTTTCCAGGATGTTTTGTTCATTGAACAAGAAGTCAGAAGCCTCTCCAGTTT
* * * *
13343198 CCGCCACCAACAACGGGAACCTCCCTGTCCA-GGGAGATTCTAATGAAAGGAACATGTTGAAA
66 CCGCCACCAACAACAGAAACCTCCCTGT-CATGGCAGATTCTAATGAAAGGAACAGGTTGAAA
13343260 TCCGCTTTTG
Statistics
Matches: 117, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
128 8 0.07
129 107 0.91
130 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (128 bp):
TGTCACCAGTGGTGTTTCCAGGATGTTTTGTTCATTGAACAAGAAGTCAGAAGCCTCTCCAGTTT
CCGCCACCAACAACAGAAACCTCCCTGTCATGGCAGATTCTAATGAAAGGAACAGGTTGAAAC
Found at i:13351639 original size:19 final size:19
Alignment explanation
Indices: 13351617--13351656 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13351607 AATTAAACTC
*
13351617 TATATTTTAAATAAAAAAT
1 TATATATTAAATAAAAAAT
* *
13351636 TATATATTAATTAATAAAT
1 TATATATTAAATAAAAAAT
13351655 TA
1 TA
13351657 AGTGTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATATTAAATAAAAAAT
Found at i:13362629 original size:21 final size:20
Alignment explanation
Indices: 13362591--13362631 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
13362581 TTAAAAACAT
* *
13362591 AAAATTATTTTTTTTTTTTA
1 AAAAATATTTTTTCTTTTTA
13362611 AAAAATATTTTTTACTTTTTA
1 AAAAATATTTTTT-CTTTTTA
13362632 GTTTAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
AAAAATATTTTTTCTTTTTA
Found at i:13383184 original size:54 final size:54
Alignment explanation
Indices: 13383102--13383209 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
13383092 GAAGATCAGT
*
13383102 AGGATTTGATTTTGTTGCACTGCCCACAGGCTTCTCAGGAGAACTGACTGCAGC
1 AGGATTTGATTTTGTTGCACTACCCACAGGCTTCTCAGGAGAACTGACTGCAGC
* *
13383156 AGGATTTGATTTTGTTGCATTACCCACAGTCTTCTCAGGAGAACTGACTGCAGC
1 AGGATTTGATTTTGTTGCACTACCCACAGGCTTCTCAGGAGAACTGACTGCAGC
13383210 TGCTACAGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (54 bp):
AGGATTTGATTTTGTTGCACTACCCACAGGCTTCTCAGGAGAACTGACTGCAGC
Found at i:13401935 original size:101 final size:101
Alignment explanation
Indices: 13401760--13401963 Score: 399
Period size: 101 Copynumber: 2.0 Consensus size: 101
13401750 NNNNNNNNNN
*
13401760 ACATTGTTCTTATCAAGTCCTCTATGTGGCAGCATTTGTTCATGCACTTATTAATTTATTGTTGC
1 ACATTGTTCTTATCAAGTCCTCTATGTGGCAGCATTTGTTCATGCACTCATTAATTTATTGTTGC
13401825 TTCATTGTGTTTATATTACCACAGGCAAAAGTTGAG
66 TTCATTGTGTTTATATTACCACAGGCAAAAGTTGAG
13401861 ACATTGTTCTTATCAAGTCCTCTATGTGGCAGCATTTGTTCATGCACTCATTAATTTATTGTTGC
1 ACATTGTTCTTATCAAGTCCTCTATGTGGCAGCATTTGTTCATGCACTCATTAATTTATTGTTGC
13401926 TTCATTGTGTTTATATTACCACAGGCAAAAGTTGAG
66 TTCATTGTGTTTATATTACCACAGGCAAAAGTTGAG
13401962 AC
1 AC
13401964 GTCTGGAGGT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.41
Consensus pattern (101 bp):
ACATTGTTCTTATCAAGTCCTCTATGTGGCAGCATTTGTTCATGCACTCATTAATTTATTGTTGC
TTCATTGTGTTTATATTACCACAGGCAAAAGTTGAG
Found at i:13416392 original size:2 final size:2
Alignment explanation
Indices: 13416387--13416415 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13416377 ATACATATAT
13416387 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
13416416 TATTTATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13420755 original size:41 final size:43
Alignment explanation
Indices: 13420697--13420784 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 43
13420687 ACCAATGAGT
*
13420697 AGAATTTCATCAGTCTTAGCACTGGT-AAAACCTCTTTATTGG
1 AGAATTTCATCAGTCTTAGCACTGGTAAAAACCTCTTCATTGG
13420739 AGAA-TTCATCAGTCTTAGCACTGGTAAAAACCTCTTCATTGG
1 AGAATTTCATCAGTCTTAGCACTGGTAAAAACCTCTTCATTGG
13420781 AGAA
1 AGAA
13420785 ACAAGTGCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 21 0.48
42 23 0.52
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (43 bp):
AGAATTTCATCAGTCTTAGCACTGGTAAAAACCTCTTCATTGG
Found at i:13437060 original size:2 final size:2
Alignment explanation
Indices: 13437055--13437084 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13437045 TTTTATTCAA
13437055 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
13437085 TACATATCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13448428 original size:20 final size:20
Alignment explanation
Indices: 13448403--13448440 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13448393 AGTGAGGAGC
13448403 CTAGATTTAGTTGGAGAATG
1 CTAGATTTAGTTGGAGAATG
*
13448423 CTAGATTTGGTTGGAGAA
1 CTAGATTTAGTTGGAGAA
13448441 GGAAGGTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (20 bp):
CTAGATTTAGTTGGAGAATG
Found at i:13449772 original size:2 final size:2
Alignment explanation
Indices: 13449765--13449789 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13449755 TACATTTTAA
13449765 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13449790 GTGTATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13475811 original size:68 final size:68
Alignment explanation
Indices: 13475695--13475830 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 68
13475685 GCACCCAGCA
* * *
13475695 GGCAACTATATCAAAACTTCCTCTAAAAGAGATACTAAACCAAGGATTCTTACTGGTTCGGGTCG
1 GGCAACTATATCAAAACTACCACTAAAAGAGATACTAAACCAAGGATTCTTACTGGATCGGGTCG
13475760 AGT
66 AGT
* * * * * *
13475763 GGCAATTATATCAAAACTACCACTAAAAGAGATATTCAATCAATGATTCTTACTTGATCGGGTCG
1 GGCAACTATATCAAAACTACCACTAAAAGAGATACTAAACCAAGGATTCTTACTGGATCGGGTCG
13475828 AGT
66 AGT
13475831 AATGTAAGAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (68 bp):
GGCAACTATATCAAAACTACCACTAAAAGAGATACTAAACCAAGGATTCTTACTGGATCGGGTCG
AGT
Found at i:13495171 original size:22 final size:23
Alignment explanation
Indices: 13495146--13495193 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
13495136 TTTTACATCA
13495146 AAAT-TTAAACTA-TTTATAATAT
1 AAATGTTAAA-TATTTTATAATAT
*
13495168 AAATGTTAAATATTTTTTAATAT
1 AAATGTTAAATATTTTATAATAT
13495191 AAA
1 AAA
13495194 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATGTTAAATATTTTATAATAT
Found at i:13500201 original size:13 final size:14
Alignment explanation
Indices: 13500178--13500211 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
13500168 TTAGTCCAAC
13500178 TTTATATTAATTTG
1 TTTATATTAATTTG
13500192 TTTA-ATTAATTTG
1 TTTATATTAATTTG
*
13500205 CTTATAT
1 TTTATAT
13500212 ATAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTATATTAATTTG
Found at i:13506447 original size:21 final size:21
Alignment explanation
Indices: 13506423--13506464 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
13506413 CGTTTGGTAA
13506423 GCCTTCTCTCTTTGTTTCTAC
1 GCCTTCTCTCTTTGTTTCTAC
13506444 GCCTTCTCTCTTTGTTTCTAC
1 GCCTTCTCTCTTTGTTTCTAC
13506465 ATTATGCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.33, G:0.10, T:0.52
Consensus pattern (21 bp):
GCCTTCTCTCTTTGTTTCTAC
Found at i:13508252 original size:3 final size:3
Alignment explanation
Indices: 13508244--13508268 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13508234 TTTAATATGA
13508244 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
13508269 TACTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13509383 original size:5 final size:5
Alignment explanation
Indices: 13509373--13509397 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13509363 TTTCATCATT
13509373 AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA
13509398 TTAATTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:13513440 original size:21 final size:21
Alignment explanation
Indices: 13513414--13513458 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
13513404 GTTGTTGTCC
13513414 GTTTCTTGGCCAATCAAGGGG
1 GTTTCTTGGCCAATCAAGGGG
13513435 GTTTCTTGGCCAATCAAGGGG
1 GTTTCTTGGCCAATCAAGGGG
13513456 GTT
1 GTT
13513459 CCTCTCGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (21 bp):
GTTTCTTGGCCAATCAAGGGG
Found at i:13515463 original size:36 final size:34
Alignment explanation
Indices: 13515423--13515503 Score: 103
Period size: 33 Copynumber: 2.4 Consensus size: 34
13515413 TAAAATAAAA
*
13515423 TAAAATAAAAAATAATCAATTAATCTTATCATATTT
1 TAAAATAAAAAATAATCAATTAAT-TT-TAATATTT
*
13515459 TAAAAT-AAAAATAATCAATTTATTTTAATATTT
1 TAAAATAAAAAATAATCAATTAATTTTAATATTT
*
13515492 TTAAA-AAAAAAT
1 TAAAATAAAAAAT
13515504 CAAAAAACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 17 0.41
34 2 0.05
35 16 0.39
36 6 0.15
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (34 bp):
TAAAATAAAAAATAATCAATTAATTTTAATATTT
Found at i:13515475 original size:35 final size:34
Alignment explanation
Indices: 13515423--13515503 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 34
13515413 TAAAATAAAA
*
13515423 TAAAATAAAAAATAATCAATTAATCTT-ATCATATTT
1 TAAAAT-AAAAATAATCAATTAATTTTAAT-AT-TTT
*
13515459 TAAAATAAAAATAATCAATTTATTTTAATATTTT
1 TAAAATAAAAATAATCAATTAATTTTAATATTTT
13515493 TAAAA-AAAAAT
1 TAAAATAAAAAT
13515504 CAAAAAACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 6 0.14
34 8 0.19
35 20 0.48
36 8 0.19
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (34 bp):
TAAAATAAAAATAATCAATTAATTTTAATATTTT
Found at i:13531508 original size:4 final size:4
Alignment explanation
Indices: 13531488--13531524 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
13531478 GAAAATGGAG
13531488 GAAA -AAA G-AA G-AA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
13531525 AGACGGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 9 0.29
4 22 0.71
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:13533203 original size:25 final size:26
Alignment explanation
Indices: 13533167--13533216 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
13533157 AGATGCTTTA
*
13533167 AATAATTATATATAT-TAAACATATT
1 AATAATTATATATATCTAAAAATATT
13533192 AATAA-TATTATATATCTAAAAATAT
1 AATAATTA-TATATATCTAAAAATAT
13533217 ATTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 2 0.09
25 12 0.55
26 8 0.36
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
AATAATTATATATATCTAAAAATATT
Found at i:13533228 original size:17 final size:18
Alignment explanation
Indices: 13533208--13533246 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
13533198 ATTATATATC
13533208 TAAAAATATATTATT-AA
1 TAAAAATATATTATTCAA
* *
13533225 TAAAAATCTATTTTTCAA
1 TAAAAATATATTATTCAA
13533243 TAAA
1 TAAA
13533247 TTAACAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAAATATATTATTCAA
Found at i:13537856 original size:18 final size:19
Alignment explanation
Indices: 13537833--13537870 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13537823 TAAATATAAA
*
13537833 TTTAATT-TTTATATTATT
1 TTTAATTATTTAAATTATT
13537851 TTTAATTATTTAAATTATT
1 TTTAATTATTTAAATTATT
13537870 T
1 T
13537871 AATCAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTATTTAAATTATT
Found at i:13561387 original size:16 final size:16
Alignment explanation
Indices: 13561362--13561411 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
13561352 TTGCCTTCAA
13561362 TTTGTAATAATAAACAT
1 TTTGT-ATAATAAACAT
* *
13561379 TTTTTATAAGAAA-A-
1 TTTGTATAATAAACAT
13561393 TTTGTATTAATAAACAT
1 TTTGTA-TAATAAACAT
13561410 TT
1 TT
13561412 GACTATGAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.19
15 7 0.27
16 8 0.31
17 6 0.23
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (16 bp):
TTTGTATAATAAACAT
Found at i:13574095 original size:2 final size:2
Alignment explanation
Indices: 13574088--13574143 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
13574078 GACAAGGGTA
* * *
13574088 AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT TT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13574130 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
13574144 TTATGTTTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:13589129 original size:2 final size:2
Alignment explanation
Indices: 13589122--13589147 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13589112 GTTGAATTGA
13589122 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
13589148 TCATGGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13590398 original size:100 final size:99
Alignment explanation
Indices: 13590255--13590457 Score: 298
Period size: 100 Copynumber: 2.0 Consensus size: 99
13590245 CAAGAATTTA
* * *
13590255 TAACCAATTTATGATTAGTTACAATAAAATAAATAAAAGGAAAATGACCCGCAACTGAATTTTTC
1 TAACCAATTTATGATTAGTTAAAATAAAATAAATAAAAGGAAAAGGACCCGCAACTGAATTTTCC
*** *
13590320 TTTTTTTTTTTCTCAATTTCAATGTATTAATAATC
66 CCCTTTTGTTT-TCAATTTCAATGTATTAATAATC
*
13590355 TAACCAATTTATGATTAGTTAAAATAAAATAAATAAAAGGAAAAGGGCCCGCAACTGAATTTTCC
1 TAACCAATTTATGATTAGTTAAAATAAAATAAATAAAAGGAAAAGGACCCGCAACTGAATTTTCC
* * *
13590420 CCCTTTTGTTTTCAATTTTAGTGTATTAATGATC
66 CCCTTTTGTTTTCAATTTCAATGTATTAATAATC
13590454 TAAC
1 TAAC
13590458 ACAAATTGCT
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 24 0.26
100 68 0.74
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (99 bp):
TAACCAATTTATGATTAGTTAAAATAAAATAAATAAAAGGAAAAGGACCCGCAACTGAATTTTCC
CCCTTTTGTTTTCAATTTCAATGTATTAATAATC
Found at i:13603579 original size:14 final size:14
Alignment explanation
Indices: 13603560--13603586 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13603550 CTCTTCAATT
13603560 TAATTTAATCGAAA
1 TAATTTAATCGAAA
13603574 TAATTTAATCGAA
1 TAATTTAATCGAA
13603587 TTCAAATTTA
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:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
TAATTTAATCGAAA
Found at i:13610721 original size:30 final size:31
Alignment explanation
Indices: 13610641--13610721 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 31
13610631 GATTATGTTG
* * * *
13610641 TTAATTTTATTTAATAAAAAATTAAAATTAT
1 TTAATTTTTTTTTATGAAAAATTAAAATAAT
* * *
13610672 TTAATAATTTTATTA-GAAAAATT-TAATAAT
1 TTAAT-TTTTTTTTATGAAAAATTAAAATAAT
13610702 TTAATTTTTTTTTATGAAAA
1 TTAATTTTTTTTTATGAAAA
13610722 CATAAATTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 7 0.18
30 15 0.38
31 12 0.31
32 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (31 bp):
TTAATTTTTTTTTATGAAAAATTAAAATAAT
Found at i:13648528 original size:2 final size:2
Alignment explanation
Indices: 13648521--13648555 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
13648511 ATGTTTAAAC
* *
13648521 TA TA TA TA TA TA TA TA TA TA TA TG TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13648556 TTAATTAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:13656185 original size:81 final size:81
Alignment explanation
Indices: 13656043--13656238 Score: 245
Period size: 81 Copynumber: 2.4 Consensus size: 81
13656033 TGTAAAGCTA
* * *
13656043 TTAATAATATAATTCCATCGATTCGATTATTGTTTTATAAAAATCAATAAATGAATGTAAA-TTG
1 TTAA-AATATAATTCAATCGATTTGATTATTGTTTTATAAAAATCAATAAATGAATATAAATTTG
*
13656107 AATTT-GATTATTTTAATT
65 --TTTAGATTATTTTAAAT
* * * *
13656125 TTAAAGTATAATTCAATCGATTTGATTGTT-TTTTATAAAAATTAATAGATGGAATATAAATTTG
1 TTAAAATATAATTCAATCGATTTGATTATTGTTTTATAAAAATCAATAAAT-GAATATAAATTTG
13656189 TTTAGATTATTTTAAAT
65 TTTAGATTATTTTAAAT
* *
13656206 TTAAAATATAATTAAATCGATTTAATTATTGTT
1 TTAAAATATAATTCAATCGATTTGATTATTGTT
13656239 AATTTTAAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
80 21 0.21
81 68 0.69
82 9 0.09
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.46
Consensus pattern (81 bp):
TTAAAATATAATTCAATCGATTTGATTATTGTTTTATAAAAATCAATAAATGAATATAAATTTGT
TTAGATTATTTTAAAT
Found at i:13667283 original size:16 final size:17
Alignment explanation
Indices: 13667264--13667296 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13667254 TACTAATAGG
13667264 TTATAATATAT-TTATA
1 TTATAATATATGTTATA
*
13667280 TTATTATATATGTTATA
1 TTATAATATATGTTATA
13667297 ACTTTGAAAT
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:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATAATATATGTTATA
Found at i:13683131 original size:6 final size:6
Alignment explanation
Indices: 13683120--13683161 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
13683110 TTTGATTCTC
* *
13683120 TCTCTT TCTCTT TCTCTT TCTC-- TCTCTC TCTCTT CCTCTT TC
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TC
13683162 CTAGTGTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
4 4 0.13
6 27 0.87
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (6 bp):
TCTCTT
Found at i:13683136 original size:16 final size:16
Alignment explanation
Indices: 13683115--13683158 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
13683105 ACGTTTTTGA
* *
13683115 TTCTCTCTCTTTCTCT
1 TTCTCTTTCTCTCTCT
13683131 TTCTCTTTCTCTCTCT
1 TTCTCTTTCTCTCTCT
* *
13683147 CTCTCTTCCTCT
1 TTCTCTTTCTCT
13683159 TTCCTAGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (16 bp):
TTCTCTTTCTCTCTCT
Found at i:13683143 original size:22 final size:22
Alignment explanation
Indices: 13683115--13683161 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
13683105 ACGTTTTTGA
* *
13683115 TTCTCTCTCTTTCTCTTTCTCT
1 TTCTCTCTCTCTCTCTTCCTCT
13683137 TTCTCTCTCTCTCTCTTCCTCT
1 TTCTCTCTCTCTCTCTTCCTCT
13683159 TTC
1 TTC
13683162 CTAGTGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (22 bp):
TTCTCTCTCTCTCTCTTCCTCT
Found at i:13683225 original size:7 final size:7
Alignment explanation
Indices: 13683190--13683218 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
13683180 GTGTTGTCTC
13683190 TCTTTCT
1 TCTTTCT
13683197 TCTTTCT
1 TCTTTCT
13683204 TCTTTCT
1 TCTTTCT
13683211 TCTTTCT
1 TCTTTCT
13683218 T
1 T
13683219 TCATCTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TCTTTCT
Found at i:13693071 original size:21 final size:21
Alignment explanation
Indices: 13693045--13693085 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13693035 GTATGTTTTA
13693045 TATTATTATG-TAATTAAATAT
1 TATTATTATGCTAA-TAAATAT
*
13693066 TATTATTTTGCTAATAAATA
1 TATTATTATGCTAATAAATA
13693086 AATTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TATTATTATGCTAATAAATAT
Found at i:13694551 original size:25 final size:25
Alignment explanation
Indices: 13694517--13694581 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
13694507 TAATATATAT
13694517 TTATACTTATTAATATTATCAA-TAA-A
1 TTATA-TTATTAATA-TAT-AATTAATA
13694543 TGT-TATTATTAATATATAATTAATA
1 T-TATATTATTAATATATAATTAATA
13694568 TTATATTATTAATA
1 TTATATTATTAATA
13694582 AAAAATGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
23 2 0.06
24 7 0.20
25 22 0.63
26 3 0.09
27 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (25 bp):
TTATATTATTAATATATAATTAATA
Found at i:13700261 original size:16 final size:17
Alignment explanation
Indices: 13700240--13700271 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13700230 AAGAGACATC
13700240 TCTTTTTT-CTTTTTTT
1 TCTTTTTTCCTTTTTTT
13700256 TCTTTTTTCCTTTTTT
1 TCTTTTTTCCTTTTTT
13700272 GGAGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TCTTTTTTCCTTTTTTT
Found at i:13700295 original size:30 final size:31
Alignment explanation
Indices: 13700252--13700311 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
13700242 TTTTTTCTTT
* *
13700252 TTTTTCTTTTTTCCTTTTTTGGAGTATTTTC
1 TTTTTCTTTTTTCCTTTTTTCGAGGATTTTC
13700283 TTTTTC-TTTTTCCTTTTTTCGAGGATTTT
1 TTTTTCTTTTTTCCTTTTTTCGAGGATTTT
13700312 AATTACTACG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.07, C:0.13, G:0.10, T:0.70
Consensus pattern (31 bp):
TTTTTCTTTTTTCCTTTTTTCGAGGATTTTC
Found at i:13702685 original size:18 final size:17
Alignment explanation
Indices: 13702651--13702700 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 17
13702641 TTTAAATAAA
13702651 TATATAAAAAATATATT
1 TATATAAAAAATATATT
13702668 TATTAATAAAAAAT-TATT
1 TA-T-ATAAAAAATATATT
13702686 TATATAAAAAA-ATAT
1 TATATAAAAAATATAT
13702701 GTACACATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 11 0.37
17 3 0.10
18 7 0.23
19 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATAAAAAATATATT
Found at i:13720794 original size:2 final size:2
Alignment explanation
Indices: 13720787--13720812 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13720777 TTTTATTTAA
13720787 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
13720813 CCACATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13758908 original size:24 final size:23
Alignment explanation
Indices: 13758864--13758908 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
13758854 GGCAAACTGG
* *
13758864 TAGAATTGCTCTCACAATTGTTT
1 TAGAATTCCTCTAACAATTGTTT
*
13758887 TAGAATTTCCTCTAACACTTGT
1 TAGAA-TTCCTCTAACAATTGT
13758909 GATCCAGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (23 bp):
TAGAATTCCTCTAACAATTGTTT
Found at i:13764490 original size:399 final size:400
Alignment explanation
Indices: 13763244--13764728 Score: 1558
Period size: 401 Copynumber: 3.7 Consensus size: 400
13763234 CAGCTCTGTG
* * * ** *
13763244 GTTGCAGAGGAAGATGATAAAGAAAGGTGTTGTTCCTGATGTGCTTACACACAATTATCTTCTAA
1 GTTGCGGAGGAAGATGATAAAGAAAGGTATTATTCCTGACATACTTACACACAATTATCTTCTAA
* * * * *
13763309 ATGGCTTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTATTAGGGAGATGCTAGAAATT
66 ATGGCCTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTTTTAGTGAGATGATAGAAAAT
* *
13763374 GGACCACCTCCCAACCGTGTGACCTACAACACCTTTATCAAGGGATGTTGTCTTTCAAATGATGT
131 GGTCCACCTCCAAACCGTGTGACCTACAACACCTTTATCAAGGGATGTTGTCTTTC-AATGATGT
*
13763439 GGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCGTGGTATCAGGCCAAATAGTGTTACTT
195 GGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCGTGGTATCAGGCCAAATAGAGTTACTT
* * *
13763504 GTAGTATTCTTGTGCATAAATTGTGCAAGGGACATCTTTTGAGAGATGCTACAAAGCTTCTCGGG
260 GTAGTATACTTGTGCATAAATTGTGCAAGAGACATCTTTT-AGAGATGCTACAAAGCTTCTTGGG
* * *
13763569 AAGATGCTAAGGGAGGACAATGGTGTAGCCATAATTCAGGTTTTATGTTCAGATGGGAAGTTGGG
324 AAGATGTTAAGGGAGGACAATGGTGAAGCCATAATTCAGGTTTTATGTTCGGATGGGAAGTTGGG
13763634 ATCAGCTCTAAT
389 ATCAGCTCTAAT
* * *
13763646 GTTGCGGAGGAAGCTGATACAGAAAGGTATTATTCCTGACATACTTGCACACAATTATCTTCT-A
1 GTTGCGGAGGAAGATGATAAAGAAAGGTATTATTCCTGACATACTTACACACAATTATCTTCTAA
* * * *
13763710 ATGGCCTGTGCAAAATAGGCGACAT-GA-ACAGAGCAGATTGTCTTTTTTGTGAGATGATAGAAA
66 ATGGCCTGTGCAAAAAAGGTGACATGGAGA-AG-GCAGATTGGCTTTTTAGTGAGATGATAGAAA
* * * * * * * **
13763773 AAGGCCCACCTCCAAACCGTTTGACTTACCACACTTTTATCAAGGGCTACTGTCTTAT-ACATGA
129 ATGGTCCACCTCCAAACCGTGTGACCTACAACACCTTTATCAAGGGATGTTGTCTT-TCA-ATGA
* * * * * * * * ** * *
13763837 TTTGGATAAAGCTCTCTATCTTTTCT-CAGCTATGGCCAGCTGTTCTATTAGACCAAATAGAGTT
192 TGTGGATAAAGCCCTTTATATGTTCTCCA-CTATGACTAGCCGTGGTATCAGGCCAAATAGAGTT
* * ** ** *** ** *
13763901 ACTTGTAGCATACTTATGCATGCATTGTTG-AAGAGAGGTCTAGAAAGAGATGCTATGAAGTTTC
256 ACTTGTAGTATACTTGTGCATAAATTG-TGCAAGAGACATCT-TTTAGAGATGCTACAAAGCTTC
* * * * * * * * * * *
13763965 TT-GGAGTGATTTTAAGTGATGATAATGCTGGACAGATAGCCATGATTAAAGATTTGTG-TCTGG
319 TTGGGA-AGATGTTAAGGGAGGACAA---TGG--TGA-AGCCATAATTCAGGTTTTATGTTC-GG
* * *
13764028 A-GCAGAAGTTAGGAGCAGCTCT-AT
376 ATG-GGAAGTTGGGATCAGCTCTAAT
* * ** *
13764052 GGTTGCGGAGGGAGATGATAAAGAAAGGTGTTATTCCTGATGTGCTTACACACAATTATCTTCTA
1 -GTTGCGGAGGAAGATGATAAAGAAAGGTATTATTCCTGACATACTTACACACAATTATCTTCTA
* * *
13764117 AATGGCTTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTTTTAG-GACATGCTA-AGAA
65 AATGGCCTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTTTTAGTGAGATGATAGA-AA
* * * *
13764180 ATTGTCCACCTCCCAACCATGTGACCTACAACACCTTTATC-AGGGATGTTGCCTTTCAATGATG
129 ATGGTCCACCTCCAAACCGTGTGACCTACAACACCTTTATCAAGGGATGTTGTCTTTCAATGATG
** * *
13764244 TGGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCACGGTATCAGGCCAAATAGGGTTACA
194 TGGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCGTGGTATCAGGCCAAATAGAGTTACT
* *
13764309 TGTAGTATGCTTGTGCATAAATTGTGCAAGAGACATCTTCTTAGAGATGCTCCAAAGCTTCTTGG
259 TGTAGTATACTTGTGCATAAATTGTGCAAGAGACATCTT-TTAGAGATGCTACAAAGCTTCTTGG
13764374 GAAGATGTTAAGGGAGGACAATGGTGAAGCCATAATTCAGGTTTTATGTTCGGATGGGAAGTTGG
323 GAAGATGTTAAGGGAGGACAATGGTGAAGCCATAATTCAGGTTTTATGTTCGGATGGGAAGTTGG
13764439 GATCAGCTCTAAT
388 GATCAGCTCTAAT
** *
13764452 GTTGCGGAGGAAGATGATGCAGAAAGGTATTATTCCTGACATACTTGCACACAATTATCTTCTAA
1 GTTGCGGAGGAAGATGATAAAGAAAGGTATTATTCCTGACATACTTACACACAATTATCTTCTAA
* * * * * *
13764517 ATGGCCTGTGCAAAATAGGTGACATGAAGAAAGCAGATTGTCTTTTTCGTGAGATGATAGAAAAG
66 ATGGCCTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTTTTAGTGAGATGATAGAAAAT
* * * ** *
13764582 GGTCCACCTCCAAACCGTGTGACTTACAACACTTTTATCAAGGGCTACTGTCTTAT-AGATGATA
131 GGTCCACCTCCAAACCGTGTGACCTACAACACCTTTATCAAGGGATGTTGTCTT-TCA-ATGATG
* * * * * * * ** ** * *
13764646 TGGATAAAGCTCTATATCTTTTCTCCGCTATGGCCAGTTGTTCTATTAGGCCTAATAGAGTTACT
194 TGGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCGTGGTATCAGGCCAAATAGAGTTACT
** *
13764711 TGTAACATACTTATGCAT
259 TGTAGTATACTTGTGCAT
13764729 GCATTGTTGA
Statistics
Matches: 856, Mismatches: 193, Indels: 68
0.77 0.17 0.06
Matches are distributed among these distances:
399 136 0.16
400 61 0.07
401 218 0.25
402 128 0.15
404 5 0.01
405 112 0.13
406 23 0.03
407 130 0.15
408 38 0.04
409 4 0.00
410 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (400 bp):
GTTGCGGAGGAAGATGATAAAGAAAGGTATTATTCCTGACATACTTACACACAATTATCTTCTAA
ATGGCCTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTTTTAGTGAGATGATAGAAAAT
GGTCCACCTCCAAACCGTGTGACCTACAACACCTTTATCAAGGGATGTTGTCTTTCAATGATGTG
GATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCGTGGTATCAGGCCAAATAGAGTTACTTG
TAGTATACTTGTGCATAAATTGTGCAAGAGACATCTTTTAGAGATGCTACAAAGCTTCTTGGGAA
GATGTTAAGGGAGGACAATGGTGAAGCCATAATTCAGGTTTTATGTTCGGATGGGAAGTTGGGAT
CAGCTCTAAT
Found at i:13764793 original size:807 final size:809
Alignment explanation
Indices: 13763175--13764793 Score: 2771
Period size: 807 Copynumber: 2.0 Consensus size: 809
13763165 CTTTGAAAGC
*
13763175 TGATAATGCTGGACAGATAGCCATGATTAAAGATTTGTGTTTGGAGCAGAAGTTAGGAGCAGCTC
1 TGATAATGCTGGACAGATAGCCATGATTAAAGATTTGTGTCTGGAGCAGAAGTTAGGAGCAGCTC
* *
13763240 TGTGGTTGCAGAGGAAGATGATAAAGAAAGGTGTTGTTCCTGATGTGCTTACACACAATTATCTT
66 TATGGTTGCAGAGGAAGATGATAAAGAAAGGTGTTATTCCTGATGTGCTTACACACAATTATCTT
*
13763305 CTAAATGGCTTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTATTAGGGAGATGCTAGA
131 CTAAATGGCTTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTATTAGGGACATGCTAGA
* *
13763370 AATTGGACCACCTCCCAACCGTGTGACCTACAACACCTTTATCAAGGGATGTTGTCTTTCAAATG
196 AATTGGACCACCTCCCAACCATGTGACCTACAACACCTTTATCAAGGGATGTTGCCTTTCAAATG
** *
13763435 ATGTGGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCGTGGTATCAGGCCAAATAGTGTT
261 ATGTGGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCACGGTATCAGGCCAAATAGGGTT
* * *
13763500 ACTTGTAGTATTCTTGTGCATAAATTGTGCAAGGGACATCTTTTGAGAGATGCTACAAAGCTTCT
326 ACATGTAGTATGCTTGTGCATAAATTGTGCAAGAGACATCTTTTGAGAGATGCTACAAAGCTTCT
*
13763565 CGGGAAGATGCTAAGGGAGGACAATGGTGTAGCCATAATTCAGGTTTTATGTTCAGATGGGAAGT
391 CGGGAAGATGCTAAGGGAGGACAATGGTGAAGCCATAATTCAGGTTTTATGTTCAGATGGGAAGT
*
13763630 TGGGATCAGCTCTAATGTTGCGGAGGAAGCTGATACAGAAAGGTATTATTCCTGACATACTTGCA
456 TGGGATCAGCTCTAATGTTGCGGAGGAAGATGATACAGAAAGGTATTATTCCTGACATACTTGCA
* *
13763695 CACAATTATCTTCTAATGGCCTGTGCAAAATAGGCGACATGAACAGAGCAGATTGTCTTTTTTGT
521 CACAATTATCTTCTAATGGCCTGTGCAAAATAGGCGACATGAACAAAGCAGATTGTCTTTTTCGT
* *
13763760 GAGATGATAGAAAAAGGCCCACCTCCAAACCGTTTGACTTACCACACTTTTATCAAGGGCTACTG
586 GAGATGATAGAAAAAGGCCCACCTCCAAACCGTGTGACTTACAACACTTTTATCAAGGGCTACTG
* *
13763825 TCTTATACATGATTTGGATAAAGCTCTCTATCTTTTCTCAGCTATGGCCAGCTGTTCTATTAGAC
651 TCTTATACATGATATGGATAAAGCTCTATATCTTTTCTCAGCTATGGCCAGCTGTTCTATTAGAC
*
13763890 CAAATAGAGTTACTTGTAGCATACTTATGCATGCATTGTTGAAGAGAGGTCTAGAAAGAGATGCT
716 CAAATAGAGTTACTTGTAACATACTTATGCATGCATTGTTGAAGAGAGGTCTAGAAAGAGATGCT
** * *
13763955 ATGAAGTTTCTTGGAGTGATTTTAAGTGA
781 ATGAACCTTCTTAGAGAGATTTTAAGTGA
13763984 TGATAATGCTGGACAGATAGCCATGATTAAAGATTTGTGTCTGGAGCAGAAGTTAGGAGCAGCTC
1 TGATAATGCTGGACAGATAGCCATGATTAAAGATTTGTGTCTGGAGCAGAAGTTAGGAGCAGCTC
* *
13764049 TATGGTTGCGGAGGGAGATGATAAAGAAAGGTGTTATTCCTGATGTGCTTACACACAATTATCTT
66 TATGGTTGCAGAGGAAGATGATAAAGAAAGGTGTTATTCCTGATGTGCTTACACACAATTATCTT
*
13764114 CTAAATGGCTTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTTTTA-GGACATGCTAAG
131 CTAAATGGCTTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTATTAGGGACATGCT-AG
*
13764178 AAATT-GTCCACCTCCCAACCATGTGACCTACAACACCTTTATC-AGGGATGTTGCCTTTC-AAT
195 AAATTGGACCACCTCCCAACCATGTGACCTACAACACCTTTATCAAGGGATGTTGCCTTTCAAAT
13764240 GATGTGGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCACGGTATCAGGCCAAATAGGGT
260 GATGTGGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCACGGTATCAGGCCAAATAGGGT
*
13764305 TACATGTAGTATGCTTGTGCATAAATTGTGCAAGAGACATCTTCTT-AGAGATGCTCCAAAGCTT
325 TACATGTAGTATGCTTGTGCATAAATTGTGCAAGAGACATCTT-TTGAGAGATGCTACAAAGCTT
* * *
13764369 CTTGGGAAGATGTTAAGGGAGGACAATGGTGAAGCCATAATTCAGGTTTTATGTTCGGATGGGAA
389 CTCGGGAAGATGCTAAGGGAGGACAATGGTGAAGCCATAATTCAGGTTTTATGTTCAGATGGGAA
*
13764434 GTTGGGATCAGCTCTAATGTTGCGGAGGAAGATGATGCAGAAAGGTATTATTCCTGACATACTTG
454 GTTGGGATCAGCTCTAATGTTGCGGAGGAAGATGATACAGAAAGGTATTATTCCTGACATACTTG
* *
13764499 CACACAATTATCTTCTAAATGGCCTGTGCAAAATAGGTGACATGAAGAAAGCAGATTGTCTTTTT
519 CACACAATTATCTTCT-AATGGCCTGTGCAAAATAGGCGACATGAACAAAGCAGATTGTCTTTTT
* *
13764564 CGTGAGATGATAGAAAAGGGTCCACCTCCAAACCGTGTGACTTACAACACTTTTATCAAGGGCTA
583 CGTGAGATGATAGAAAAAGGCCCACCTCCAAACCGTGTGACTTACAACACTTTTATCAAGGGCTA
* * *
13764629 CTGTCTTATAGATGATATGGATAAAGCTCTATATCTTTTCTCCGCTATGGCCAGTTGTTCTATTA
648 CTGTCTTATACATGATATGGATAAAGCTCTATATCTTTTCTCAGCTATGGCCAGCTGTTCTATTA
* * **
13764694 GGCCTAATAGAGTTACTTGTAACATACTTATGCATGCATTGTTGAAGAGAGGTCTATTAAGAGAT
713 GACCAAATAGAGTTACTTGTAACATACTTATGCATGCATTGTTGAAGAGAGGTCTAGAAAGAGAT
13764759 GCTATGAACCTTCTTAGAGAGATTTTAAGTGA
778 GCTATGAACCTTCTTAGAGAGATTTTAAGTGA
13764791 TGA
1 TGA
13764794 CAATTCGAAA
Statistics
Matches: 762, Mismatches: 45, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
806 262 0.34
807 273 0.36
808 44 0.06
809 183 0.24
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (809 bp):
TGATAATGCTGGACAGATAGCCATGATTAAAGATTTGTGTCTGGAGCAGAAGTTAGGAGCAGCTC
TATGGTTGCAGAGGAAGATGATAAAGAAAGGTGTTATTCCTGATGTGCTTACACACAATTATCTT
CTAAATGGCTTGTGCAAAAAAGGTGACATGGAGAAGGCAGATTGGCTTATTAGGGACATGCTAGA
AATTGGACCACCTCCCAACCATGTGACCTACAACACCTTTATCAAGGGATGTTGCCTTTCAAATG
ATGTGGATAAAGCCCTTTATATGTTCTCCACTATGACTAGCCACGGTATCAGGCCAAATAGGGTT
ACATGTAGTATGCTTGTGCATAAATTGTGCAAGAGACATCTTTTGAGAGATGCTACAAAGCTTCT
CGGGAAGATGCTAAGGGAGGACAATGGTGAAGCCATAATTCAGGTTTTATGTTCAGATGGGAAGT
TGGGATCAGCTCTAATGTTGCGGAGGAAGATGATACAGAAAGGTATTATTCCTGACATACTTGCA
CACAATTATCTTCTAATGGCCTGTGCAAAATAGGCGACATGAACAAAGCAGATTGTCTTTTTCGT
GAGATGATAGAAAAAGGCCCACCTCCAAACCGTGTGACTTACAACACTTTTATCAAGGGCTACTG
TCTTATACATGATATGGATAAAGCTCTATATCTTTTCTCAGCTATGGCCAGCTGTTCTATTAGAC
CAAATAGAGTTACTTGTAACATACTTATGCATGCATTGTTGAAGAGAGGTCTAGAAAGAGATGCT
ATGAACCTTCTTAGAGAGATTTTAAGTGA
Found at i:13767917 original size:3 final size:3
Alignment explanation
Indices: 13767909--13767941 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
13767899 AAAAGGGGGG
13767909 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
13767942 TGCAGGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:13769297 original size:12 final size:12
Alignment explanation
Indices: 13769280--13769304 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13769270 GTTTAAATAC
13769280 CCCCCACCTTAA
1 CCCCCACCTTAA
13769292 CCCCCACCTTAA
1 CCCCCACCTTAA
13769304 C
1 C
13769305 TATCAAATAA
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:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCCCCACCTTAA
Found at i:13775921 original size:2 final size:2
Alignment explanation
Indices: 13775914--13775946 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13775904 CCCATCTGCC
13775914 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
13775947 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13795294 original size:2 final size:2
Alignment explanation
Indices: 13795282--13795325 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
13795272 TTCGAATCTG
* *
13795282 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
13795324 TC
1 TC
13795326 CAGGCAGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:13795476 original size:3 final size:3
Alignment explanation
Indices: 13795468--13795493 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13795458 NNNNNNNNNN
13795468 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
13795494 GCCAGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:13798248 original size:2 final size:2
Alignment explanation
Indices: 13798241--13798268 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13798231 ATTAATGTGC
13798241 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
13798269 CTCAACTCCA
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:13801709 original size:2 final size:2
Alignment explanation
Indices: 13801702--13801726 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13801692 CTCTGAAAAG
13801702 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13801727 GTAGCAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13828403 original size:2 final size:2
Alignment explanation
Indices: 13828396--13828427 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13828386 CATGGGGGAA
13828396 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
13828428 GTCTCTCTGC
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:13831809 original size:3 final size:3
Alignment explanation
Indices: 13831801--13831831 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
13831791 TTGCCACCAA
13831801 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13831832 CAATTGTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13832864 original size:8 final size:8
Alignment explanation
Indices: 13832853--13832879 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
13832843 ATTTCTGGAC
13832853 CCTACATG
1 CCTACATG
13832861 CCTACATG
1 CCTACATG
13832869 CCTACATG
1 CCTACATG
13832877 CCT
1 CCT
13832880 TACTTTACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.41, G:0.11, T:0.26
Consensus pattern (8 bp):
CCTACATG
Found at i:13845810 original size:18 final size:18
Alignment explanation
Indices: 13845776--13845810 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13845766 CTAGCTCATA
**
13845776 AGCAAAACAAACTCTAAG
1 AGCAAAACAAAAGCTAAG
13845794 AGCAAAACAAAAGCTAA
1 AGCAAAACAAAAGCTAA
13845811 AAAAGGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.11, T:0.09
Consensus pattern (18 bp):
AGCAAAACAAAAGCTAAG
Found at i:13855705 original size:32 final size:32
Alignment explanation
Indices: 13855659--13855724 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
13855649 GTAGGAGGAG
* *
13855659 GAGATTTTTTATTGTGCTCTCTAACGAGAGCA
1 GAGATTTCTGATTGTGCTCTCTAACGAGAGCA
*
13855691 GAGATTTCTGATTGTTCTCTCTAACGAGAGCA
1 GAGATTTCTGATTGTGCTCTCTAACGAGAGCA
13855723 GA
1 GA
13855725 AGGCCGGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.35
Consensus pattern (32 bp):
GAGATTTCTGATTGTGCTCTCTAACGAGAGCA
Found at i:13858023 original size:2 final size:2
Alignment explanation
Indices: 13858016--13858042 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13858006 TATGAATGTT
13858016 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13858043 TCATTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13860436 original size:29 final size:29
Alignment explanation
Indices: 13860394--13860451 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
13860384 TCATAGTAAA
13860394 ATATGTTTTCGTTCGATAGTAGCCTCATT
1 ATATGTTTTCGTTCGATAGTAGCCTCATT
*
13860423 ATATGTTTTCGTTCTATAGTAGCCTCATT
1 ATATGTTTTCGTTCGATAGTAGCCTCATT
13860452 GACAATCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.47
Consensus pattern (29 bp):
ATATGTTTTCGTTCGATAGTAGCCTCATT
Found at i:13879602 original size:159 final size:159
Alignment explanation
Indices: 13879124--13879602 Score: 816
Period size: 159 Copynumber: 3.0 Consensus size: 159
13879114 AAACTTGTAG
* * * *
13879124 TATATCTAAAGAACACGGGTGTGAATACTTAAGTATGTTGATAGCATATG-ATGGTCCATTCATG
1 TATATCTAAAGAACACGGGAGTGAATACTTAAGTATGTTGATAGGATATGCCT-ATCCATTCATG
**
13879188 ATAAATTACTAAGTAATAGTAATATGATTCGAGAATACAATATGATGTGATGCTACCAAATATTA
65 ATAAATTACTAAGTAATAGTAATATGATTCGAGAATATGATATGATGTGATGCTACCAAATATTA
13879253 ATGGTAATGGTAACTCAAACAGATGACTGA
130 ATGGTAATGGTAACTCAAACAGATGACTGA
*
13879283 CATATCTAAAGAACACGGGAGTGAATACTTAAGTATGTTGATAGGATATGCCTATCCATTCATGA
1 TATATCTAAAGAACACGGGAGTGAATACTTAAGTATGTTGATAGGATATGCCTATCCATTCATGA
*
13879348 TAAATTACTAAGTAATAGTAATATGATTCGAGAATATGATATGATGTGATGCTACCAAATATCAA
66 TAAATTACTAAGTAATAGTAATATGATTCGAGAATATGATATGATGTGATGCTACCAAATATTAA
*
13879413 TGGTAATGGTAACTCAAACAGATGATTGA
131 TGGTAATGGTAACTCAAACAGATGACTGA
*
13879442 TATATCTAAAGAACACGGGAGTGAATACTTAAGTATGTTGATAGGATATGCCTATCCACTCATGA
1 TATATCTAAAGAACACGGGAGTGAATACTTAAGTATGTTGATAGGATATGCCTATCCATTCATGA
*
13879507 TAAATTACTAAGTAATAGTAATATGATTCGAGAATATGATATGATGTGATGCTACCAATTATTAA
66 TAAATTACTAAGTAATAGTAATATGATTCGAGAATATGATATGATGTGATGCTACCAAATATTAA
* * *
13879572 TGGTAATGGTAAATTAAACAGACGACTGA
131 TGGTAATGGTAACTCAAACAGATGACTGA
13879601 TA
1 TA
13879603 GTAAGGAAAT
Statistics
Matches: 302, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
159 301 1.00
160 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (159 bp):
TATATCTAAAGAACACGGGAGTGAATACTTAAGTATGTTGATAGGATATGCCTATCCATTCATGA
TAAATTACTAAGTAATAGTAATATGATTCGAGAATATGATATGATGTGATGCTACCAAATATTAA
TGGTAATGGTAACTCAAACAGATGACTGA
Found at i:13881650 original size:2 final size:2
Alignment explanation
Indices: 13881645--13881671 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13881635 CATCTAAAGC
13881645 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13881672 GTAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13886040 original size:30 final size:30
Alignment explanation
Indices: 13886004--13886074 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
13885994 TAACTTTTGT
13886004 AACTCCATTTTGTCTATTCTCAAGTCCCTG
1 AACTCCATTTTGTCTATTCTCAAGTCCCTG
*
13886034 AACTCCACTTTGTCTATTCTCAAGTCCCTG
1 AACTCCATTTTGTCTATTCTCAAGTCCCTG
13886064 AACTCCATTTT
1 AACTCCATTTT
13886075 TTTCCATCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.21, C:0.31, G:0.08, T:0.39
Consensus pattern (30 bp):
AACTCCATTTTGTCTATTCTCAAGTCCCTG
Found at i:13892900 original size:15 final size:15
Alignment explanation
Indices: 13892882--13892926 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
13892872 ACAAGAAGAA
13892882 GAAGAAGAAGACGAG
1 GAAGAAGAAGACGAG
*
13892897 GAAGAAGAAG-GGAG
1 GAAGAAGAAGACGAG
*
13892911 G-AG-GGAAGACGAG
1 GAAGAAGAAGACGAG
13892924 GAA
1 GAA
13892927 TTGATGGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
12 4 0.16
13 6 0.24
14 5 0.20
15 10 0.40
ACGTcount: A:0.49, C:0.04, G:0.47, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGACGAG
Found at i:13902859 original size:7 final size:7
Alignment explanation
Indices: 13902847--13902879 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
13902837 ATTTCAATCT
13902847 ATTCTTC
1 ATTCTTC
13902854 ATTCTTC
1 ATTCTTC
*
13902861 ATTCTTT
1 ATTCTTC
13902868 ATTCTTC
1 ATTCTTC
13902875 -TTCTT
1 ATTCTT
13902880 GTTTCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (7 bp):
ATTCTTC
Found at i:13922368 original size:27 final size:27
Alignment explanation
Indices: 13922338--13922396 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
13922328 TAAAAGTGCT
**
13922338 TAAGGGAGTTTTAAGCACGAAAGCATC
1 TAAGGGAGTTCCAAGCACGAAAGCATC
* *
13922365 TAAGGGGGTTCCAAGCGCGAAAGCATC
1 TAAGGGAGTTCCAAGCACGAAAGCATC
13922392 TAAGG
1 TAAGG
13922397 TGTTTCAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.19
Consensus pattern (27 bp):
TAAGGGAGTTCCAAGCACGAAAGCATC
Found at i:13922414 original size:26 final size:26
Alignment explanation
Indices: 13922356--13922434 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
13922346 TTTTAAGCAC
*
13922356 GAAAGCATCTAAGGGGGTTCCAAGCGC
1 GAAAGCATCTAA-GGGGTTCCAAGCGA
* *
13922383 GAAAGCATCTAAGGTGTTTCAAGCGTA
1 GAAAGCATCTAAGGGGTTCCAAGCG-A
* *
13922410 G-AAGCATCGAAGGGATGTCCAAGCG
1 GAAAGCATCTAAGGGGT-TCCAAGCG
13922435 CGGAAGTGCC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 23 0.53
27 20 0.47
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.18
Consensus pattern (26 bp):
GAAAGCATCTAAGGGGTTCCAAGCGA
Found at i:13923380 original size:19 final size:19
Alignment explanation
Indices: 13923356--13923400 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
13923346 TGACAAGCAC
* *
13923356 GTTCTCCATTATTGAATGT
1 GTTCTCCATGATTGAACGT
*
13923375 GTTCTCTATGATTGAACGT
1 GTTCTCCATGATTGAACGT
13923394 GTTCTCC
1 GTTCTCC
13923401 TAACTACTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (19 bp):
GTTCTCCATGATTGAACGT
Found at i:13937802 original size:39 final size:39
Alignment explanation
Indices: 13937748--13937860 Score: 136
Period size: 39 Copynumber: 2.9 Consensus size: 39
13937738 TTTCCGATCA
* *
13937748 CCTACTTCAACTTCACTGCTTAGCAATGCTAAGCTGGAC
1 CCTACTTCAACTTCACTGCTTAACAATGCTAAGCCGGAC
* * * *
13937787 CCTACTTCAACTTCACTTCTTAACAATACTAATCCGGGC
1 CCTACTTCAACTTCACTGCTTAACAATGCTAAGCCGGAC
* * * *
13937826 TCTACTTCAACTTCACCGCTTACCAATGTTAAGCC
1 CCTACTTCAACTTCACTGCTTAACAATGCTAAGCC
13937861 AGAATCTAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.27, C:0.33, G:0.11, T:0.30
Consensus pattern (39 bp):
CCTACTTCAACTTCACTGCTTAACAATGCTAAGCCGGAC
Found at i:13942946 original size:20 final size:20
Alignment explanation
Indices: 13942901--13942948 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
13942891 GTGTATTTAA
* *
13942901 TTATTGATATTTGAGTATTT
1 TTATTGAGATTTCAGTATTT
*
13942921 TGATTGAGATTTCAG-ATTAT
1 TTATTGAGATTTCAGTATT-T
13942941 TTATTGAG
1 TTATTGAG
13942949 TGATTTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.52
Consensus pattern (20 bp):
TTATTGAGATTTCAGTATTT
Found at i:13947938 original size:26 final size:26
Alignment explanation
Indices: 13947900--13947949 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
13947890 TCAGGTCATA
*
13947900 TCTCTTTTCTTGCTACAAAAGCACCT
1 TCTCATTTCTTGCTACAAAAGCACCT
* *
13947926 TCTCATTTGTTGCTATAAAAGCAC
1 TCTCATTTCTTGCTACAAAAGCAC
13947950 TTTCAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (26 bp):
TCTCATTTCTTGCTACAAAAGCACCT
Found at i:13949378 original size:7 final size:7
Alignment explanation
Indices: 13949366--13949405 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
13949356 TTCATATTTA
13949366 TGAAGTG
1 TGAAGTG
13949373 TGAAGTG
1 TGAAGTG
13949380 TGAAGTG
1 TGAAGTG
13949387 TGAAGTG
1 TGAAGTG
13949394 TGAAGTG
1 TGAAGTG
13949401 TGAAG
1 TGAAG
13949406 CGTGTGAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.30, C:0.00, G:0.42, T:0.28
Consensus pattern (7 bp):
TGAAGTG
Found at i:13958901 original size:14 final size:14
Alignment explanation
Indices: 13958879--13958911 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
13958869 ATTAGGAATC
*
13958879 GTTCAGGGTTTGGG
1 GTTCGGGGTTTGGG
13958893 GTTCGGGGTTTGGG
1 GTTCGGGGTTTGGG
13958907 GTTCG
1 GTTCG
13958912 AGTTTTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.09, G:0.52, T:0.36
Consensus pattern (14 bp):
GTTCGGGGTTTGGG
Found at i:13958918 original size:14 final size:14
Alignment explanation
Indices: 13958885--13958918 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13958875 AATCGTTCAG
*
13958885 GGTTTGGGGTTCGG
1 GGTTTGGGGTTCGA
13958899 GGTTTGGGGTTCGA
1 GGTTTGGGGTTCGA
*
13958913 GTTTTG
1 GGTTTG
13958919 AGTTTTGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.06, G:0.50, T:0.41
Consensus pattern (14 bp):
GGTTTGGGGTTCGA
Found at i:13958950 original size:29 final size:28
Alignment explanation
Indices: 13958897--13958959 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
13958887 TTTGGGGTTC
* * *
13958897 GGGGTTTGGGGTTCGAGTTTTGAGTTTT
1 GGGGTTTGGGATTCGAGGTTCGAGTTTT
13958925 GGGGTTTAGGGATTCGAGGTTCGAGTTTT
1 GGGGTTT-GGGATTCGAGGTTCGAGTTTT
*
13958954 GAGGTT
1 GGGGTT
13958960 CGGGGTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.11, C:0.05, G:0.43, T:0.41
Consensus pattern (28 bp):
GGGGTTTGGGATTCGAGGTTCGAGTTTT
Done.