Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000479.1 Hibiscus syriacus cultivar Beakdansim tig00000907_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: 183264
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:427 original size:17 final size:19
Alignment explanation
Indices: 384--430 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
374 AATGTGGGGT
384 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
403 TAATTTTGTAT-AGATTTA
1 TAATTTTGTATAAGATTTA
421 T-ATTTTGTAT
1 TAATTTTGTAT
431 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.32
18 8 0.29
19 11 0.39
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1011 original size:195 final size:198
Alignment explanation
Indices: 658--1411 Score: 1156
Period size: 195 Copynumber: 3.9 Consensus size: 198
648 ACAATATGGC
*
658 AACA-GGTGCAACCATAAAGTGTCGATCCATATAAAAA-GTGTCGATCCCATAAACATCGAAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATAAAAAGGTGTCGATCCCAGAAACATCGAAACC
* * *
721 CATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTAT-AGCATACCGATTTT-T-AGAG
66 CATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTTATGAGAG
* *
783 ATTAGGTATATAATATGTATCAACACTTTTTAATTTTATGTCGATACTATTGGTCCAGAATGAAT
131 ATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAAT
848 GCA
196 GCA
*
851 AACAGGGTGC-ACCATAAAGTGTCGATCCATATATAAAAGGTGTTGATCCCAGAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATA-AAAAGGTGTCGATCCCAGAAACATCGAAAC
915 CCATAAGTATAATGTAATAGATAA-TTTTCAATCTAACCGGTATAAGTATACCGATTTTATGAGA
65 CCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTTATGAGA
* *
979 TATTA-GTATATAATATGTATCGACAC-TTTTAATTTTGTGTCGATACTATT-GTCCAAAATGAA
130 GATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAA
1041 TGC-
195 TGCA
* *
1044 AACAGGGTGCAACCAT-AAGTGTTGATCCATAT-AAAAGGTGTCAATCCCAGAAACATCG-AACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATAAAAAGGTGTCGATCCCAGAAACATCGAAACC
* *
1106 CATAAGT-TAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAG--TACCGGTTTTATGAGAG
66 CATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTTATGAGAG
1168 ATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAAT
131 ATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAAT
1233 GGCA
196 -GCA
* *
1237 AACATGGTGCAACCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAGAAACATCGAAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATAAAAAGGTGTCGATCCCAGAAACATCGAAACC
*
1302 CATAAGTATAATGTAATAGATAATTTTTTCAATCTAACC-GTATAAGTATACCAATTTTATGAGA
66 CATAAGTATAATGTAATAGATAA-TTTTTCAATCTAACCGGTATAAGTATACCGATTTTATGAGA
* * *
1366 TAATAGG--TGTAATAT-TA-CGACACTTTTTAATTTTGTGTCGATACTA
130 GATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
1412 ATTTAATATC
Statistics
Matches: 515, Mismatches: 26, Indels: 38
0.89 0.04 0.07
Matches are distributed among these distances:
188 19 0.04
189 35 0.07
190 57 0.11
191 36 0.07
192 2 0.00
193 67 0.13
194 61 0.12
195 135 0.26
196 34 0.07
197 35 0.07
198 15 0.03
199 19 0.04
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (198 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATAAAAAGGTGTCGATCCCAGAAACATCGAAACC
CATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTTATGAGAG
ATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAAT
GCA
Found at i:1216 original size:385 final size:384
Alignment explanation
Indices: 656--1411 Score: 1222
Period size: 386 Copynumber: 2.0 Consensus size: 384
646 TTACAATATG
* *
656 GCAACAGGTGCAACCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCATAAACATCGAAACC
1 GCAACAGGTGCAACCATAAAGTGTCGATCCATATAAAAAGTGTCAATCCCAGAAACATCGAAACC
721 CATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAGCATACCGATTTTTAGAGATT
66 CATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAG-ATACCGATTTTTAGAGATT
786 AGGTATATAATATGTATCAACACTTTTTAATTTTATGTCGATACTATTGGTCCAGAATGAAT-GC
130 AGGTATATAATATGTATCAACACTTTTTAATTTTATGTCGATACTATTGGTCCAGAATGAATGGC
* *
850 AAACAGGGTGC-ACCATAAAGTGTCGATCCATATATAAAAGGTGTTGATCCCAGAAACATCGAAA
195 AAACAGGGTGCAACCATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAGAAACATCGAAA
*
914 CCCATAAGTATAATGTAATAGATAA-TTTTCAATCTAACCGGTATAAGTATACCGATTTTATGAG
259 CCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACC-GTATAAGTATACCAATTTTATGAG
*
978 ATATTAGTATATAATATGTATCGACAC-TTTTAATTTTGTGTCGATACTATTGTCCAAAATGAAT
323 ATAATAG-ATATAATAT-TA-CGACACTTTTTAATTTTGTGTCGATACTATTGTCCAAAATGAAT
* *
1042 GCAACAGGGTGCAACCAT-AAGTGTTGATCCATATAAAAGGTGTCAATCCCAGAAACATCG-AAC
1 GCAACA-GGTGCAACCATAAAGTGTCGATCCATATAAAAAGTGTCAATCCCAGAAACATCGAAAC
* *
1105 CCATAAGT-TAATGTAATAGGTAATTTTTCAATCTAACCGGTATA-AGTACCGGTTTTATGAGAG
65 CCATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAGA-TACCGATTTT-T-AGAG
* *
1168 ATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAGAATGAAT
127 ATTAGGTATATAATATGTATCAACACTTTTTAATTTTATGTCGATACTATTGGTCCAGAATGAAT
*
1233 GGCAAACATGGTGCAACCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAGAAACATCGA
192 GGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAGAAACATCGA
1298 AACCCATAAGTATAATGTAATAGATAATTTTTTCAATCTAACCGTATAAGTATACCAATTTTATG
257 AACCCATAAGTATAATGTAATAGATAA-TTTTTCAATCTAACCGTATAAGTATACCAATTTTATG
* *
1363 AGATAATAGGTGTAATATTACGACACTTTTTAATTTTGTGTCGATACTA
321 AGATAATAGATATAATATTACGACACTTTTTAATTTTGTGTCGATACTA
1412 ATTTAATATC
Statistics
Matches: 346, Mismatches: 15, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
382 1 0.00
383 9 0.03
384 42 0.12
385 102 0.29
386 115 0.33
387 63 0.18
388 14 0.04
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (384 bp):
GCAACAGGTGCAACCATAAAGTGTCGATCCATATAAAAAGTGTCAATCCCAGAAACATCGAAACC
CATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAGATACCGATTTTTAGAGATTA
GGTATATAATATGTATCAACACTTTTTAATTTTATGTCGATACTATTGGTCCAGAATGAATGGCA
AACAGGGTGCAACCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAGAAACATCGAAACC
CATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGTATAAGTATACCAATTTTATGAGATA
ATAGATATAATATTACGACACTTTTTAATTTTGTGTCGATACTATTGTCCAAAATGAAT
Found at i:4454 original size:180 final size:176
Alignment explanation
Indices: 4236--4573 Score: 565
Period size: 180 Copynumber: 1.9 Consensus size: 176
4226 ATATCAACAT
4236 AAGTGTCGATACCTTTTCAAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTAAT
1 AAGTGTCGATACCTTTTCAAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTAAT
*
4301 A-GTAATTTTGTAATATAACCGGTATATATATACCGGTTTTATGAGAGAATAGGTCTACAACCTA
66 AGGTAA-TTTGTAATATAACC-GTATAAATATACC-G-TTTATGAGAGAATA-GTCTACAACCTA
4365 TATCGACAC-TTTTAATATTGTGTCGC-TACTTTATGTCCAATGGATGAAAA
126 TATCGACACTTTTTAATATTGTGTC-CATACTTTATGTCCAATGGATGAAAA
*
4415 AAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAA
1 AAGTGTCGATACCTTTTC-AAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTAA
*
4480 TAGGTAATTTGTAATATAACCGTATAAATATACCGTTTATGAGAGAATAGTCTATAACCTATATC
65 TAGGTAATTTGTAATATAACCGTATAAATATACCGTTTATGAGAGAATAGTCTACAACCTATATC
4545 GACACTTTTTAATATTGTGTCCATACTTT
130 GACACTTTTTAATATTGTGTCCATACTTT
4574 TAAGTAACGC
Statistics
Matches: 152, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
176 21 0.14
177 35 0.23
178 1 0.01
179 30 0.20
180 61 0.40
181 4 0.03
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (176 bp):
AAGTGTCGATACCTTTTCAAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTAAT
AGGTAATTTGTAATATAACCGTATAAATATACCGTTTATGAGAGAATAGTCTACAACCTATATCG
ACACTTTTTAATATTGTGTCCATACTTTATGTCCAATGGATGAAAA
Found at i:7593 original size:22 final size:22
Alignment explanation
Indices: 7549--7593 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
7539 ATTACATAAC
*
7549 TTTAAAAAAAGTATCGATTCTT
1 TTTAAAAAAAGTATCGATACTT
* *
7571 TTTACAAAAAGTATCTATACTT
1 TTTAAAAAAAGTATCGATACTT
7593 T
1 T
7594 CAACATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGATACTT
Found at i:7865 original size:21 final size:21
Alignment explanation
Indices: 7835--7876 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
7825 GGTAAAGCGC
*
7835 TACCGGTTTTGTTATTTTTTT
1 TACCGATTTTGTTATTTTTTT
7856 TACCGATTTTGTTATTTTTTT
1 TACCGATTTTGTTATTTTTTT
7877 CAAGGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (21 bp):
TACCGATTTTGTTATTTTTTT
Found at i:7939 original size:113 final size:111
Alignment explanation
Indices: 7637--7973 Score: 541
Period size: 111 Copynumber: 3.0 Consensus size: 111
7627 TAATAAAACT
* * *
7637 GATTTTGTCATTTTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAAAGATCGATAC
1 GATTTTGTTATTTTTTT-CCTGTTATATTGTAAAGTATCAATCCTTTTTATAAAAGGATCGATAC
*
7702 TTTAATATATCAGGTAAAGCGCTATCGGTTTTGTTATTTTTTTTACC
65 TTTAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
* *
7749 GGTTTTGTTATTTTTTACCTGTTATATTGTAAAGTATCAATCC-TTTTATAAAAGGATCGATACT
1 GATTTTGTTATTTTTTTCCTGTTATATTGTAAAGTATCAATCCTTTTTATAAAAGGATCGATAC-
7813 TTTAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
65 TTTAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
** * *
7860 GATTTTGTTATTTTTTTCAAGGTATATTTGTAAAGTATCGATCCTTTTTATAAAAGGATCGATAC
1 GATTTTGTTATTTTTTTCCTGTTATA-TTGTAAAGTATCAATCCTTTTTATAAAAGGATCGATAC
7925 TTTCAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
65 TTT-AATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
7973 G
1 G
7974 GTTATATTAT
Statistics
Matches: 209, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
110 19 0.09
111 92 0.44
112 33 0.16
113 65 0.31
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (111 bp):
GATTTTGTTATTTTTTTCCTGTTATATTGTAAAGTATCAATCCTTTTTATAAAAGGATCGATACT
TTAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
Found at i:8007 original size:86 final size:86
Alignment explanation
Indices: 7895--8058 Score: 310
Period size: 86 Copynumber: 1.9 Consensus size: 86
7885 ATTTGTAAAG
*
7895 TATCGATCCTTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGT
1 TATCGATCATTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGT
7960 TATTTTTTTTACCGGTTATAT
66 TATTTTTTTTACCGGTTATAT
*
7981 TATCGATCATTTTTATAAAAGGATCGATACTTTCAATATATTAGGTAAAGCGCTACCGGTTTTGT
1 TATCGATCATTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGT
8046 TATTTTTTTTACC
66 TATTTTTTTTACC
8059 AGTTTTGTTA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (86 bp):
TATCGATCATTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGT
TATTTTTTTTACCGGTTATAT
Found at i:8076 original size:20 final size:21
Alignment explanation
Indices: 8034--8075 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
8024 GGTAAAGCGC
*
8034 TACCGGTTTTGTTATTTTTTT
1 TACCAGTTTTGTTATTTTTTT
8055 TACCAGTTTTGTTATTTTTTT
1 TACCAGTTTTGTTATTTTTTT
8076 ATCGGTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (21 bp):
TACCAGTTTTGTTATTTTTTT
Found at i:8083 original size:20 final size:21
Alignment explanation
Indices: 8034--8084 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
8024 GGTAAAGCGC
8034 TACCGGTTTTGTTATTTTTTT
1 TACCGGTTTTGTTATTTTTTT
*
8055 TACCAGTTTTGTTA-TTTTTT
1 TACCGGTTTTGTTATTTTTTT
*
8075 TATCGGTTTT
1 TACCGGTTTT
8085 ACCGAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.65
Consensus pattern (21 bp):
TACCGGTTTTGTTATTTTTTT
Found at i:8456 original size:22 final size:21
Alignment explanation
Indices: 8429--8469 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
8419 CAAATACAAT
8429 AAAATAATATTATTTATTAACA
1 AAAATAATATTATTT-TTAACA
8451 AAAATAATATTATTTTTAA
1 AAAATAATATTATTTTTAA
8470 AATATTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATAATATTATTTTTAACA
Found at i:8850 original size:23 final size:23
Alignment explanation
Indices: 8792--8851 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
8782 CTAGTAATTA
* *
8792 ATCTATTTTATTATATAAACGCT
1 ATCTAATTTATTATATAAACACT
* * *
8815 ACCT-ATTAAATTATATAAATACT
1 ATCTAATT-TATTATATAAACACT
8838 ATCTAATTTATTAT
1 ATCTAATTTATTAT
8852 TTTACTTGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
22 2 0.07
23 23 0.82
24 3 0.11
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (23 bp):
ATCTAATTTATTATATAAACACT
Found at i:8864 original size:87 final size:87
Alignment explanation
Indices: 8630--8864 Score: 294
Period size: 87 Copynumber: 2.7 Consensus size: 87
8620 GAATATGTCA
* * * * * *
8630 ATATAAGCGTTACATATTACATTATATAAGCACTACCTAATATGTTATTGTGCTTGATAACGTTT
1 ATATAAACGCTACCTATTACATTATATAAACACTACCTAATATATTATTGTGCTTGATAATGTTT
*
8695 CTTGTAATTAACTTATTTTATT
66 CTAGTAATTAACTTATTTTATT
** *
8717 ATATAAGA-GCTACCTATTACATTATATAAACGTTACCTAATATACTATTGTGCTTGATAATGTT
1 ATATAA-ACGCTACCTATTACATTATATAAACACTACCTAATATATTATTGTGCTTGATAATGTT
8781 TCTAGTAATTAA-TCTATTTTATT
65 TCTAGTAATTAACT-TATTTTATT
* * * * * *
8804 ATATAAACGCTACCTATTAAATTATATAAATACTATCTAATTTATTATTTTACTTGATAAT
1 ATATAAACGCTACCTATTACATTATATAAACACTACCTAATATATTATTGTGCTTGATAAT
8865 ATTTTCGATT
Statistics
Matches: 126, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
86 2 0.02
87 124 0.98
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTATATAAACACTACCTAATATATTATTGTGCTTGATAATGTTT
CTAGTAATTAACTTATTTTATT
Found at i:12846 original size:21 final size:20
Alignment explanation
Indices: 12801--12847 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
12791 GCCAACGAAC
*
12801 AAAAATGAAAATGCAAGATTA
1 AAAAATGAAAAT-CAAAATTA
12822 AAAAATGACAAAT-AAAATTA
1 AAAAATGA-AAATCAAAATTA
12842 TAAAAA
1 -AAAAA
12848 CCAAAATCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (20 bp):
AAAAATGAAAATCAAAATTA
Found at i:16778 original size:27 final size:28
Alignment explanation
Indices: 16745--16811 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
16735 AATGAAAAGT
* *
16745 CTAAAATACCCTTGAACTCTA-AAATGAC
1 CTAAAATACCCCTGAACT-GAGAAATGAC
*
16773 C-AAAATACCCCTGAAGTGAGAAATGAC
1 CTAAAATACCCCTGAACTGAGAAATGAC
16800 CTAAAATACCCC
1 CTAAAATACCCC
16812 AAAGCCATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.03
27 22 0.65
28 11 0.32
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.19
Consensus pattern (28 bp):
CTAAAATACCCCTGAACTGAGAAATGAC
Found at i:17753 original size:11 final size:11
Alignment explanation
Indices: 17737--17766 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
17727 CAAATATTTA
17737 GACTACATGTC
1 GACTACATGTC
17748 GACTACATGTC
1 GACTACATGTC
17759 GACTACAT
1 GACTACAT
17767 TCTATAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (11 bp):
GACTACATGTC
Found at i:19679 original size:20 final size:20
Alignment explanation
Indices: 19654--19704 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
19644 AATAATGTAG
19654 GTATCGATGCACTATACAGT
1 GTATCGATGCACTATACAGT
19674 GTATCGATGCACTATACAGT
1 GTATCGATGCACTATACAGT
19694 GTATCGATGCA
1 GTATCGATGCA
19705 TCCCTTAACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
GTATCGATGCACTATACAGT
Found at i:22412 original size:23 final size:24
Alignment explanation
Indices: 22378--22497 Score: 122
Period size: 24 Copynumber: 5.1 Consensus size: 24
22368 GAGTCGAGGG
* **
22378 TTCTACGCGGTCCTTTAGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
22402 -TCTATGTGGTCCTTCGGGAC-AT
1 TTCTACGTGGTCCTTCGGGACAAA
*
22424 TTCTACGTGGTCCTTCGAGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
*
22448 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
*
22472 TTCTATGTGG-CACTTCGGTG-CAAA
1 TTCTACGTGGTC-CTTCGG-GACAAA
22496 TT
1 TT
22498 ATATGAGCAG
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.01
23 35 0.44
24 43 0.54
25 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:22446 original size:46 final size:47
Alignment explanation
Indices: 22378--22469 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 47
22368 GAGTCGAGGG
* * *
22378 TTCTACGCGGTCCTTTAGGACAAA-TCTATGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTGAGGACAAATTCTACGCGGTCCTTCGGGACAT
*
22424 TTCTACGTGGTCCTTCGA-GACAAATTCTACGCGGTCCTTCGGGACA
1 TTCTACGCGGTCCTT-GAGGACAAATTCTACGCGGTCCTTCGGGACA
22470 AATTCTATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 20 0.50
47 20 0.50
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (47 bp):
TTCTACGCGGTCCTTGAGGACAAATTCTACGCGGTCCTTCGGGACAT
Found at i:22459 original size:24 final size:24
Alignment explanation
Indices: 22378--22476 Score: 105
Period size: 23 Copynumber: 4.2 Consensus size: 24
22368 GAGTCGAGGG
*
22378 TTCTACGCGGTCCTT-TAGGACAAA
1 TTCTACGCGGTCCTTCGA-GACAAA
* * * *
22402 -TCTATGTGGTCCTTCGGGAC-AT
1 TTCTACGCGGTCCTTCGAGACAAA
*
22424 TTCTACGTGGTCCTTCGAGACAAA
1 TTCTACGCGGTCCTTCGAGACAAA
*
22448 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCGAGACAAA
22472 TTCTA
1 TTCTA
22477 TGTGGCACTT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.02
23 33 0.53
24 28 0.45
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.31
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGAGACAAA
Found at i:23253 original size:32 final size:32
Alignment explanation
Indices: 23185--23274 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
23175 CCTAATGTTA
* * *
23185 CCTTGGGTAGGCTCTGAGGCCCCAAGGCATTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTC
**
23217 CCTTGGGTAGGCTCTAAGGCCCCAAGGTGCTC
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTC
* * *
23249 CCTTGGGTAGGCCCTCATGCCCCAAG
1 CCTTGGGTAGGCTCTAAGGCCCCAAG
23275 ATATTCCATA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTC
Found at i:24277 original size:23 final size:23
Alignment explanation
Indices: 24247--24290 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
24237 CATTATAAAG
*
24247 ATATAATCAGATTCAATATCTGA
1 ATATAATCAGATCCAATATCTGA
24270 ATATAATCAGATCCAATATCT
1 ATATAATCAGATCCAATATCT
24291 ATTGTGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (23 bp):
ATATAATCAGATCCAATATCTGA
Found at i:36550 original size:16 final size:16
Alignment explanation
Indices: 36525--36567 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
36515 AACGTCTTTT
36525 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
36541 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
36558 ACAAAAATTT
1 AAAAAAATTT
36568 GGTCTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:39264 original size:25 final size:26
Alignment explanation
Indices: 39226--39349 Score: 188
Period size: 25 Copynumber: 5.0 Consensus size: 26
39216 AGTTAGGGGA
*
39226 TTAGGG-TTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCTAAATCTGAT
39250 TTAGGGTTTGAAACCCT-AATCTGAT
1 TTAGGGTTTGAAACCCTAAATCTGAT
39275 TTAGGGTTTGAAACCCT-AATCTGAT
1 TTAGGGTTTGAAACCCTAAATCTGAT
*
39300 TTAGGGTTTGAAACCCTAAA-CTAAT
1 TTAGGGTTTGAAACCCTAAATCTGAT
39325 TTAGGGTTTGAAACCCT-AATCTGAT
1 TTAGGGTTTGAAACCCTAAATCTGAT
39350 AGGTTGGTTC
Statistics
Matches: 93, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
24 11 0.12
25 80 0.86
26 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (26 bp):
TTAGGGTTTGAAACCCTAAATCTGAT
Found at i:39486 original size:3 final size:3
Alignment explanation
Indices: 39478--39529 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
39468 ATATATAATT
* *
39478 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA AAA TTA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
39523 TATA TAA
1 TA-A TAA
39530 AAAGACCCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 1 0.02
3 35 0.83
4 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39747 original size:40 final size:40
Alignment explanation
Indices: 39682--39851 Score: 115
Period size: 40 Copynumber: 4.0 Consensus size: 40
39672 TTGGTTGTTG
* * * *
39682 GGGACGACACTGCTCCTACGTGATGAAGAAATCTGGTCAA
1 GGGATGACACGGCTCATACGCGATGAAGAAATCTGGTCAA
**
39722 GGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTCATCTTTAAGAA
1 GGGATGACACGGCTCATACGCGATGAAGAAATCTGG---TC------AA
* * * * * *
39771 GGGTGATAACTCGGTTCCTACGTGATGAGGAAATCTGGTCAA
1 -GG-GATGACACGGCTCATACGCGATGAAGAAATCTGGTCAA
**
39813 GGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTCA
1 GGGATGACACGGCTCATACGCGATGAAGAAATCTGGTCA
39852 TCTTTAAGAA
Statistics
Matches: 97, Mismatches: 22, Indels: 22
0.69 0.16 0.16
Matches are distributed among these distances:
40 59 0.61
41 2 0.02
42 2 0.02
43 2 0.02
48 2 0.02
49 2 0.02
50 2 0.02
51 26 0.27
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (40 bp):
GGGATGACACGGCTCATACGCGATGAAGAAATCTGGTCAA
Found at i:39850 original size:91 final size:91
Alignment explanation
Indices: 39695--39896 Score: 377
Period size: 91 Copynumber: 2.2 Consensus size: 91
39685 ACGACACTGC
*
39695 TCCTACGTGATGAAGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
1 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
39760 ATCTTTAAGAAGGGTGATAACTCGGT
66 ATCTTTAAGAAGGGTGATAACTCGGT
39786 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
1 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
* *
39851 ATCTTTAAGAAGGGTGATAATTTGGT
66 ATCTTTAAGAAGGGTGATAACTCGGT
39877 TCCTACGTGATGAGGAAATC
1 TCCTACGTGATGAGGAAATC
39897 CGATTATCTA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 108 1.00
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (91 bp):
TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
ATCTTTAAGAAGGGTGATAACTCGGT
Found at i:40033 original size:141 final size:137
Alignment explanation
Indices: 39786--40085 Score: 340
Period size: 141 Copynumber: 2.2 Consensus size: 137
39776 ATAACTCGGT
* * **
39786 TCCTACGTGATGAGGAAATCT-G--GTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTG
1 TCCTACGTGATGAGGAAGTCTGGTCGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTG
* * * *
39848 GTCATCTTTAAGAAGGGTGATAATTTGGTTCCTACGTGATGAGGAAATCCGATTAT-CTAAGGTT
66 GCCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAAGCCGATTATCCTAAGGTT
39912 GACACGGC
131 GACAC-GC
* * *
39920 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
1 TCCTACGTGATGAGGAAGTCTGGTCGTC-AA-GG--GATGACACGGCTCATACACGATGAAGAAC
* ** * *
39985 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
62 TCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAAGCCGATTATCCTAA
* *
40050 TGTTGACACTC
127 GGTTGACACGC
*
40061 TCCTATGTGATGAGG-AGATCTGGTC
1 TCCTACGTGATGAGGAAG-TCTGGTC
40086 AGTTGATGTT
Statistics
Matches: 138, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
134 20 0.14
135 1 0.01
137 3 0.02
138 2 0.01
139 2 0.01
140 2 0.01
141 96 0.70
142 12 0.09
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.28
Consensus pattern (137 bp):
TCCTACGTGATGAGGAAGTCTGGTCGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTG
GCCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAAGCCGATTATCCTAAGGTT
GACACGC
Found at i:41065 original size:7 final size:8
Alignment explanation
Indices: 41036--41072 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
41026 TCCTTTATTT
41036 ATTTTTTC
1 ATTTTTTC
*
41044 TTCTTTTTC
1 AT-TTTTTC
41053 ATTTTTTC
1 ATTTTTTC
41061 ATTTTTTC
1 ATTTTTTC
41069 ATTT
1 ATTT
41073 CCTCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTC
Found at i:54199 original size:25 final size:25
Alignment explanation
Indices: 54158--54231 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
54148 CATTAGGGGA
* * *
54158 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
54182 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
54207 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
54232 GGGGTGGTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 6 0.13
25 40 0.87
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:54333 original size:3 final size:3
Alignment explanation
Indices: 54325--54367 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
54315 ATTTGTAAAT
* **
54325 TAA TAA TAA TAA TAG TAA TAA TAA T-A TAA CGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
54368 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55464 original size:121 final size:121
Alignment explanation
Indices: 55239--55644 Score: 449
Period size: 120 Copynumber: 3.4 Consensus size: 121
55229 ACGTGTGTAT
* * * * *
55239 CTAAATTATCAATTTTGATCCGTTTTAACA-TCTAAA-TTT-TATTTTTTT---AATCATATCTA
1 CTAAACTATCAGTTTTGATCCATTTTAATACT-TAAACTTTCAATTTTTTTCAAAATCATATCTA
* * * ***
55298 ATATTAAAATTTTGTTTCATTTTAGTA-TTCATCATTAAAAACTTAATACG-TTAGTAC
65 ATGTT-TAATTTTGTTTCATTTTAGTACTT-GTCATTAAAAACTTAACGTGTTTAGTAC
* * * *
55355 CTAAATTATTAGTTTTGACCCATTTTAATA-TCTAAACTTTTAATTTTTTTCAAAATCATATCTA
1 CTAAACTATCAGTTTTGATCCATTTTAATACT-TAAACTTTCAATTTTTTTCAAAATCATATCTA
* * *
55419 ACGTTTAATTTTTATTTCATTTTAGTACTTGTCGA-TAAAAACTTAACGTGTTTAGTAT
65 ATGTTTAA-TTTTGTTTCATTTTAGTACTTGTC-ATTAAAAACTTAACGTGTTTAGTAC
* *
55477 CTAAACTATCAGTTTTGATCTATTTTAATACTTAAACTTTCAA-TTTTTTCAAAA-CTATACCTA
1 CTAAACTATCAGTTTTGATCCATTTTAATACTTAAACTTTCAATTTTTTTCAAAATC-ATATCTA
* **
55540 ATGTTTAATTTTGTTTCATCTTAGTACCCGTCATTAAAAACTTAACGTGTTTAGTAC
65 ATGTTTAATTTTGTTTCATTTTAGTACTTGTCATTAAAAACTTAACGTGTTTAGTAC
*
55597 CTAAACTATCAGTTTTGATCCATTTTAATACTTAAACTTCCAATTTTT
1 CTAAACTATCAGTTTTGATCCATTTTAATACTTAAACTTTCAATTTTT
55645 ACAAAACTTA
Statistics
Matches: 248, Mismatches: 29, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
116 31 0.12
117 3 0.01
118 8 0.03
119 1 0.00
120 86 0.35
121 73 0.29
122 45 0.18
123 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (121 bp):
CTAAACTATCAGTTTTGATCCATTTTAATACTTAAACTTTCAATTTTTTTCAAAATCATATCTAA
TGTTTAATTTTGTTTCATTTTAGTACTTGTCATTAAAAACTTAACGTGTTTAGTAC
Found at i:55601 original size:120 final size:121
Alignment explanation
Indices: 55305--55652 Score: 454
Period size: 120 Copynumber: 2.9 Consensus size: 121
55295 CTAATATTAA
* * *** * *
55305 AATTTTGTTTCATTTTAGTATTCATCATTAAAAACTTAATACG-TTAGTACCTAAATTATTAGTT
1 AATTTTGTTTCATTTTAGTACTCGTCATTAAAAACTTAACGTGTTTAGTACCTAAACTATCAGTT
* * *
55369 TTGACCCATTTTAATA-TCTAAACTTTTAATTTTTTTCAAAA-TCATATCTAACGTTT
66 TTGATCCATTTTAATACT-TAAACTTTCAA-TTTTTTCAAAACTCATACCTAACGTTT
* * *
55425 AATTTTTATTTCATTTTAGTACTTGTCGA-TAAAAACTTAACGTGTTTAGTATCTAAACTATCAG
1 AA-TTTTGTTTCATTTTAGTACTCGTC-ATTAAAAACTTAACGTGTTTAGTACCTAAACTATCAG
* *
55489 TTTTGATCTATTTTAATACTTAAACTTTCAATTTTTTCAAAACT-ATACCTAATGTTT
64 TTTTGATCCATTTTAATACTTAAACTTTCAATTTTTTCAAAACTCATACCTAACGTTT
* *
55546 AATTTTGTTTCATCTTAGTACCCGTCATTAAAAACTTAACGTGTTTAGTACCTAAACTATCAGTT
1 AATTTTGTTTCATTTTAGTACTCGTCATTAAAAACTTAACGTGTTTAGTACCTAAACTATCAGTT
* *
55611 TTGATCCATTTTAATACTTAAACTTCCAATTTTTACAAAACT
66 TTGATCCATTTTAATACTTAAACTTTCAATTTTTTCAAAACT
55653 TAACGTTAAG
Statistics
Matches: 199, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
119 1 0.01
120 97 0.49
121 56 0.28
122 44 0.22
123 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (121 bp):
AATTTTGTTTCATTTTAGTACTCGTCATTAAAAACTTAACGTGTTTAGTACCTAAACTATCAGTT
TTGATCCATTTTAATACTTAAACTTTCAATTTTTTCAAAACTCATACCTAACGTTT
Found at i:57093 original size:29 final size:29
Alignment explanation
Indices: 57051--57108 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
57041 CGTACTGATA
57051 CTCAAACTCTGTTTCAATGTCCATTGCAC
1 CTCAAACTCTGTTTCAATGTCCATTGCAC
57080 CTCAAACTCTGTTTCAATGTCCATTGCAC
1 CTCAAACTCTGTTTCAATGTCCATTGCAC
57109 ACCGAAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.34
Consensus pattern (29 bp):
CTCAAACTCTGTTTCAATGTCCATTGCAC
Found at i:62866 original size:29 final size:29
Alignment explanation
Indices: 62806--62889 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
62796 CCGTTGACCA
* ** *
62806 GTGCTATTCTGGGAAATT-ATTCAATTTTG
1 GTGCTATTATGGG-AATTAATTCAAAATGG
62835 GTGCTATTATGGGAATTAATTCAAAATGG
1 GTGCTATTATGGGAATTAATTCAAAATGG
* * *
62864 GTGTTATTTTGGTAATTAATTCAAAA
1 GTGCTATTATGGGAATTAATTCAAAA
62890 AGGGGTGATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 4 0.09
29 43 0.91
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (29 bp):
GTGCTATTATGGGAATTAATTCAAAATGG
Found at i:62902 original size:30 final size:29
Alignment explanation
Indices: 62834--62902 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
62824 ATTCAATTTT
* * *
62834 GGTGCTATTATGGGAATTAATTCAAAATG
1 GGTGATATTTTGGGAATTAATTCAAAAGG
* *
62863 GGTGTTATTTTGGTAATTAATTCAAAAAGG
1 GGTGATATTTTGGGAATTAATTC-AAAAGG
62893 GGTGATATTT
1 GGTGATATTT
62903 CTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.39
Consensus pattern (29 bp):
GGTGATATTTTGGGAATTAATTCAAAAGG
Found at i:69987 original size:17 final size:18
Alignment explanation
Indices: 69937--70006 Score: 99
Period size: 17 Copynumber: 4.0 Consensus size: 18
69927 TGACCGGTCA
*
69937 CGACCTGACCCGTTGACC
1 CGACCCGACCCGTTGACC
* *
69955 CGACCCTACCCATTGACC
1 CGACCCGACCCGTTGACC
69973 CGA-CCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
69990 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
70007 GGTGCTATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
17 24 0.52
18 22 0.48
ACGTcount: A:0.19, C:0.47, G:0.20, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:70105 original size:30 final size:29
Alignment explanation
Indices: 70037--70110 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
70027 TTCGATTTTT
* * *
70037 GTGCTATTATGGGAATTAATTCAAAATGG
1 GTGCTATTTTGGTAATTAATTCAAAAGGG
* *
70066 CTACTATTTTGGTAATTAATTCAAAAAGGG
1 GTGCTATTTTGGTAATTAATTC-AAAAGGG
*
70096 GTGCTATTTTTGTAA
1 GTGCTATTTTGGTAA
70111 AATGGTTGAC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (29 bp):
GTGCTATTTTGGTAATTAATTCAAAAGGG
Found at i:72512 original size:13 final size:13
Alignment explanation
Indices: 72494--72521 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
72484 ATTTTAAGAT
72494 ATACCGATGAACA
1 ATACCGATGAACA
72507 ATACCGATGAACA
1 ATACCGATGAACA
72520 AT
1 AT
72522 GATGGAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.18
Consensus pattern (13 bp):
ATACCGATGAACA
Found at i:73020 original size:14 final size:14
Alignment explanation
Indices: 73003--73037 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
72993 TTGTTTCATT
73003 GAAAATGTTTTCCG
1 GAAAATGTTTTCCG
73017 GAAAATGTTTTCCG
1 GAAAATGTTTTCCG
*
73031 TAAAATG
1 GAAAATG
73038 AATTACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (14 bp):
GAAAATGTTTTCCG
Found at i:73250 original size:30 final size:31
Alignment explanation
Indices: 73201--73287 Score: 92
Period size: 33 Copynumber: 2.8 Consensus size: 31
73191 AAATATTAAA
* **
73201 ATAA-TTTATT-ATTAAAATATTAT-TTTTT
1 ATAATTTTATTAATAAAAATATTATATTGGT
73229 ATAATTTTATTAATAAAAATATTAATATTGGT
1 ATAATTTTATTAATAAAAATATT-ATATTGGT
73261 AT-ATTTTATTGAAATAAAAATATTATA
1 ATAATTTTATT--AATAAAAATATTATA
73288 AATTATATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
28 4 0.08
29 6 0.12
30 10 0.20
31 10 0.20
32 8 0.16
33 12 0.24
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
ATAATTTTATTAATAAAAATATTATATTGGT
Found at i:73295 original size:31 final size:29
Alignment explanation
Indices: 73190--73296 Score: 73
Period size: 30 Copynumber: 3.7 Consensus size: 29
73180 TATTATTTTT
*
73190 AAAATATTAA-AA-TA-A-TTTATT-ATT
1 AAAATATTAATAATTATATTTTATTAATA
* **
73214 AAAATATTATTTTTTATAATTTTATTAATA
1 AAAATATTAATAATTAT-ATTTTATTAATA
*
73244 AAAATATTAATATTGGTATATTTTATTGAAATA
1 AAAATATTAATAAT--TATATTTTATT--AATA
73277 AAAATATT-ATAAATTATATT
1 AAAATATTAAT-AATTATATT
73297 AATTATTTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
24 9 0.14
26 2 0.03
28 1 0.02
29 6 0.09
30 14 0.22
31 14 0.22
32 5 0.08
33 14 0.22
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
AAAATATTAATAATTATATTTTATTAATA
Found at i:73370 original size:23 final size:23
Alignment explanation
Indices: 73326--73370 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
73316 AGTGTTATAT
*
73326 TATATTTTAAAAATGTTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
73349 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
73371 AAATATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:73376 original size:23 final size:23
Alignment explanation
Indices: 73327--73395 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
73317 GTGTTATATT
* * * **
73327 ATATTTTAAAAATGTTAATTAGT
1 ATATTTTAAATATATTTATTAAA
73350 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
73373 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
73396 TATTAAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 27 0.71
24 11 0.29
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:73433 original size:19 final size:19
Alignment explanation
Indices: 73365--73445 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
73355 TTAAATATAT
73365 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
73384 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
73403 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
73423 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
73441 -TATTA
1 TTATTA
73446 TTTCTATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:73943 original size:19 final size:21
Alignment explanation
Indices: 73891--73944 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
73881 TAGTGTGATA
73891 TGGCAACAAATAGAGATGTAG
1 TGGCAACAAATAGAGATGTAG
73912 TGGCAACAAATAGAGATGTAG
1 TGGCAACAAATAGAGATGTAG
73933 TGG-AA-AAATAGA
1 TGGCAACAAATAGA
73945 TGGAAATGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.21
20 2 0.06
21 24 0.73
ACGTcount: A:0.46, C:0.07, G:0.28, T:0.19
Consensus pattern (21 bp):
TGGCAACAAATAGAGATGTAG
Found at i:96415 original size:28 final size:28
Alignment explanation
Indices: 96360--96415 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
96350 TATATATATA
* * *
96360 TTATTACTTTTATTATTTTTATTCTTTT
1 TTATTACTATTATTATTTATATTATTTT
* *
96388 TTATTACTATTCTTATTTATTTTATTTT
1 TTATTACTATTATTATTTATATTATTTT
96416 ATTTTTCTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (28 bp):
TTATTACTATTATTATTTATATTATTTT
Found at i:97416 original size:24 final size:24
Alignment explanation
Indices: 97376--97421 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
97366 ACTCACACAA
*
97376 TTTTTTTCATTTATGTAGTTTCTT
1 TTTTTTTCATTTATGTACTTTCTT
* *
97400 TTTTTTTCTTTTTTGTACTTTC
1 TTTTTTTCATTTATGTACTTTC
97422 GTCATTTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.74
Consensus pattern (24 bp):
TTTTTTTCATTTATGTACTTTCTT
Found at i:102222 original size:3 final size:3
Alignment explanation
Indices: 102214--102292 Score: 70
Period size: 3 Copynumber: 26.0 Consensus size: 3
102204 GTATTTTATT
* * * *
102214 TAA TAA TAA TAA TAT TTA T-A TAA TATA TGA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* **
102259 TATT TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
102293 AAGTAAACTA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.03
3 54 0.90
4 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:102612 original size:45 final size:45
Alignment explanation
Indices: 102548--103167 Score: 1010
Period size: 45 Copynumber: 13.8 Consensus size: 45
102538 TAAAATCTCA
*
102548 TTTGAAAACATCTTGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
102593 TTTGAAAACTTCCTGCACTGAAGGGCTTAC-GAATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAG-ATGACCCGAAGGT
** **
102638 TTTGAAAACATTATGCACTGAAGATCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
**
102683 TTTGAAAACATTATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
102728 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACTCAAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
102773 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
** *
102818 TTTGAAAACATCCTAAACTTAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
102863 TTTGAAAACATCCTGCACTGAAGGGCTTACGGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
102908 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGGCCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
102953 TTTGAAAACATCCTACACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
102998 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
**
103043 TTTGAAAACATCCTGCACTGAAGGGCTTATGGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
103088 TTTGAAAACATCATGCATTGAAGGGCTTA-AGGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACA-GATGACCCGAAGGT
*
103133 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATG
103168 GTGGGAAATA
Statistics
Matches: 536, Mismatches: 35, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
44 1 0.00
45 533 0.99
46 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (45 bp):
TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:103851 original size:22 final size:20
Alignment explanation
Indices: 103823--103877 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 20
103813 AATAAAGCTT
103823 TCATCTTTGAAGAGAGAATATA
1 TCATCTTTGAAGA-A-AATATA
*
103845 TCATCTTTG-AGAAAATTTA
1 TCATCTTTGAAGAAAATATA
103864 TCATCTTTGAAGAA
1 TCATCTTTGAAGAA
103878 TGTAGATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 14 0.45
20 5 0.16
21 3 0.10
22 9 0.29
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (20 bp):
TCATCTTTGAAGAAAATATA
Found at i:104286 original size:53 final size:54
Alignment explanation
Indices: 104205--104341 Score: 177
Period size: 53 Copynumber: 2.6 Consensus size: 54
104195 ATAATCACTG
* * * * *
104205 GTTCGTAAAACATGTGACAATACATTCATCATTTCTCGTGGCTTAT-GCCCGGT
1 GTTCGTAAAGCATTTGACAACACATTCATCATTTCTCGTGGCTTATAGCCAGAT
* * * * *
104258 TTTCGTAAAGCTTTTGATAACACATTCATCATTTCTTGTGGCTTCTAGCCAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCATTTCTCGTGGCTTATAGCCAGAT
104312 GTTCGTAAAGCATTTGACAACACATTCATC
1 GTTCGTAAAGCATTTGACAACACATTCATC
104342 TTTTTCTGTG
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
53 38 0.54
54 32 0.46
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAGCATTTGACAACACATTCATCATTTCTCGTGGCTTATAGCCAGAT
Found at i:104352 original size:54 final size:52
Alignment explanation
Indices: 104205--104359 Score: 175
Period size: 54 Copynumber: 2.9 Consensus size: 52
104195 ATAATCACTG
* * * * * *
104205 GTTCGTAAAACATGTGACAATACATTCATCATTTCTCGTGGCTTATGCCCGGT
1 GTTCGTAAAGCATTTGACAACACATTCATCATTTCT-GTGGCTTCTGCCAGAT
* * *
104258 TTTCGTAAAGCTTTTGATAACACATTCATCATTTCTTGTGGCTTCTAGCCAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCATTTC-TGTGGCTTCT-GCCAGAT
* *
104312 GTTCGTAAAGCATTTGACAACACATTCATCTTTTTCTGTGGTTTCTGC
1 GTTCGTAAAGCATTTGACAACACATTCATC-ATTTCTGTGGCTTCTGC
104360 ACAAATTTCT
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
53 39 0.46
54 42 0.49
55 4 0.05
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (52 bp):
GTTCGTAAAGCATTTGACAACACATTCATCATTTCTGTGGCTTCTGCCAGAT
Found at i:107980 original size:32 final size:32
Alignment explanation
Indices: 107928--107989 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
107918 GAAGAAATGA
* *
107928 TTGTTATGCTCACCTTGTAGAAATACTTCTCG
1 TTGTTATGATCACCTCGTAGAAATACTTCTCG
* *
107960 TTGTTATGATCATCTCGTAGAGATACTTCT
1 TTGTTATGATCACCTCGTAGAAATACTTCT
107990 TGTTTCTAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (32 bp):
TTGTTATGATCACCTCGTAGAAATACTTCTCG
Found at i:111121 original size:172 final size:172
Alignment explanation
Indices: 110834--111191 Score: 682
Period size: 172 Copynumber: 2.1 Consensus size: 172
110824 TTGTTCTTTT
110834 GAATCATCCTGAAACTTTTTTACTTGATCAATCATATTTTGTTGTGTCTCAATAAATTGCTCTTG
1 GAATCATCCTGAAACTTTTTTACTTGATCAATCATATTTTGTTGTGTCTCAATAAATTGCTCTTG
110899 CAGTTTCTCGATTCTACCAACCCTTGCTAAAATCTCATTCATGGCTATTATCCTTCTTTTAGGAA
66 CAGTTTCTCGATTCTACCAACCCTTGCTAAAATCTCATTCATGGCTATTATCCTTCTTTTAGGAA
110964 GACCAAGTTTAGCTCCACTTTGATTTAAAAAATTCTGTCATGG
131 GACCAAGTTTAGCTCCACTTTGATTTAAAAAATTCTGTCAT-G
111007 GAATCATCCTGAAAC-TTTTTACTTGATCAATCATATTTTGTTGTGTCTCAATAAATTGCTCTTG
1 GAATCATCCTGAAACTTTTTTACTTGATCAATCATATTTTGTTGTGTCTCAATAAATTGCTCTTG
111071 CAGTTTCTCGATTCTACCAACCCTTGCTAAAATCTCATTCATGGCTATTATCCTTCTTTTAGGAA
66 CAGTTTCTCGATTCTACCAACCCTTGCTAAAATCTCATTCATGGCTATTATCCTTCTTTTAGGAA
111136 GACCAAGTTTAGCTCCACTTTGATTTAAAAAATTCTGTCATG
131 GACCAAGTTTAGCTCCACTTTGATTTAAAAAATTCTGTCATG
*
111178 GAATCCTCCCTGAA
1 GAATCAT-CCTGAA
111192 TTATTCCCAT
Statistics
Matches: 183, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
171 7 0.04
172 161 0.88
173 15 0.08
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (172 bp):
GAATCATCCTGAAACTTTTTTACTTGATCAATCATATTTTGTTGTGTCTCAATAAATTGCTCTTG
CAGTTTCTCGATTCTACCAACCCTTGCTAAAATCTCATTCATGGCTATTATCCTTCTTTTAGGAA
GACCAAGTTTAGCTCCACTTTGATTTAAAAAATTCTGTCATG
Found at i:111579 original size:43 final size:43
Alignment explanation
Indices: 111499--111584 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
111489 TCGTGCATCA
* *
111499 AACAAAACTTTACATATAAGGGACAACTTTCAGTCCTATCTTC
1 AACAAAACTTTACATATAAGGGACAACTTTCACTCCTAACTTC
* * *
111542 AACAAAACTTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTACATATAAGGGACAACTTTCACTCCTAACTTC
111585 TCTAAAGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.30
Consensus pattern (43 bp):
AACAAAACTTTACATATAAGGGACAACTTTCACTCCTAACTTC
Found at i:115214 original size:22 final size:22
Alignment explanation
Indices: 115170--115237 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
115160 ATTTTATTTA
115170 ATAATAATAATATATATATAATAT
1 ATAATAATAATA-ATA-ATAATAT
* *
115194 ATGATACTAATAATAATAATAT
1 ATAATAATAATAATAATAATAT
*
115216 TTAATAATAATAATAATAATAT
1 ATAATAATAATAATAATAATAT
115238 TTTTAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 26 0.67
23 3 0.08
24 10 0.26
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (22 bp):
ATAATAATAATAATAATAATAT
Found at i:115220 original size:16 final size:16
Alignment explanation
Indices: 115164--115230 Score: 82
Period size: 16 Copynumber: 4.1 Consensus size: 16
115154 GCTTGTATTT
115164 TATTTAATAATAATAA
1 TATTTAATAATAATAA
* *
115180 TATATATATAATATATGA
1 TATTTA-ATAATA-ATAA
*
115198 TA-CTAATAATAATAA
1 TATTTAATAATAATAA
115213 TATTTAATAATAATAA
1 TATTTAATAATAATAA
115229 TA
1 TA
115231 ATAATATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 5 0.12
16 25 0.58
17 8 0.19
18 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
TATTTAATAATAATAA
Found at i:115247 original size:3 final size:3
Alignment explanation
Indices: 115168--115236 Score: 75
Period size: 3 Copynumber: 21.7 Consensus size: 3
115158 GTATTTTATT
* * *
115168 TAA TAA TAA TAA TATA TATA TAA TATA TGA TAC TAA TAA TAA TAA TATT
1 TAA TAA TAA TAA TA-A TA-A TAA TA-A TAA TAA TAA TAA TAA TAA TA-A
115217 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
115237 TTTTTAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
3 46 0.81
4 11 0.19
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:116718 original size:63 final size:65
Alignment explanation
Indices: 116559--116729 Score: 274
Period size: 65 Copynumber: 2.7 Consensus size: 65
116549 TTTTTGCATC
* *
116559 TTTAAGAGCCAATTTCAACTTCACAACGAAGGGTATTGGACTCAACAAACAACTTTCTAGTTTCA
1 TTTAAGAGTCAATTTCAACTTCACAACGAAGGGTATTGGACTCAACAAACAACTTTCCAGTTTCA
* * *
116624 TTTAAGAGTCAATTTCAACTTAACAATGAAGGATATTGGACTCAACAAA-AACTTTCCAGTTTCA
1 TTTAAGAGTCAATTTCAACTTCACAACGAAGGGTATTGGACTCAACAAACAACTTTCCAGTTTCA
*
116688 -TTCAGAGTCAATTTCAACTTCACAACGAAGGGTATTGGACTC
1 TTTAAGAGTCAATTTCAACTTCACAACGAAGGGTATTGGACTC
116730 GAAGCGACAC
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
63 38 0.39
64 14 0.14
65 45 0.46
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (65 bp):
TTTAAGAGTCAATTTCAACTTCACAACGAAGGGTATTGGACTCAACAAACAACTTTCCAGTTTCA
Found at i:116881 original size:121 final size:120
Alignment explanation
Indices: 116737--117221 Score: 612
Period size: 121 Copynumber: 4.0 Consensus size: 120
116727 CTCGAAGCGA
* * *
116737 CACAAGCAACTTACTCGAGATTGGATTACAACTTCACGACGAAGGATATCCAATTCAAGGATCAA
1 CACAAGCAA-TTACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAA
* * * *
116802 CTTCACAACGAATGAGCCATCTACAATTTCAACTTCACGACGAAGGATATCGTGCC
65 CTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
* * * *
116858 CACAAGCAAGTTACTCAAGATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAATGCTTAA
1 CACAAGCAA-TTACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAA
*
116923 CTTCACAACGAATGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
65 CTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
* * *
116979 CACCATAAC-ATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCTAATTCAAGGCT
1 CA-CA-AGCAATT-A-CTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCT
* * * **
117043 CAAATTCTCAATGAAGGGGCCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGGT
62 CAACTTCACAACGAAGGGG-CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
* * ** * *
117103 CACTAGTAACATCCCTCTTTAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTAAAGGCT
1 CACAAG-CA-ATTACTC--TAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCT
* *
117168 CAACTTCATAACGAAGGGGACATCCACGATTTCAACTTCACGACGAAGGATATC
62 CAACTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATC
117222 CAACTCAAAG
Statistics
Matches: 317, Mismatches: 37, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
121 115 0.36
122 5 0.02
123 63 0.20
124 74 0.23
125 60 0.19
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (120 bp):
CACAAGCAATTACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAAC
TTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
Found at i:117175 original size:248 final size:244
Alignment explanation
Indices: 116754--117221 Score: 666
Period size: 248 Copynumber: 1.9 Consensus size: 244
116744 AACTTACTCG
* *
116754 AGATTGGATTACAACTTCACGACGAAGGATATCCAATTCAAGGATCAACTTCACAACGAATGAGC
1 AGATTGGATTACAACTTCACGACGAAGGATATCCAATTCAAGGATCAAATTCACAACGAAGGAGC
* * *
116819 CATCTACAATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAAGTTACTCAAGATTGGAT
66 CATCCACAATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAAATCACTCAAGATTGGAT
* * * * * * *
116884 TTCAACTTCACGATGAAGGATATCCAATTCAATGCTTAACTTCACAACGAATGGGCCATCCACGA
131 TTCAACTTCACAACGAAGGATATCCAATTAAAGGCTCAACTTCACAACGAAGGGGACATCCACGA
116949 TTTCAACTTCACGACGAAGGATATCGTGCCCACCATAACATTCATCTTT
196 TTTCAACTTCACGACGAAGGATATCGTGCCCACCATAACATTCATCTTT
* * * * * *
116998 AGATTGGATTTCAACTTCACGACGAAGGATATCTAATTCAAGGCTCAAATTCTCAATGAAGGGGC
1 AGATTGGATTACAACTTCACGACGAAGGATATCCAATTCAAGGATCAAATTCACAACGAAGGAG-
* ** * * * *
117063 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGGTCACTAGTAACATCCCTCTTTAGATT
65 CCATCCACAATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAA-ATCACTC--AAGATT
*
117128 GGATTTCAACTTCACAACGAAGGATATCCAATTAAAGGCTCAACTTCATAACGAAGGGGACATCC
127 GGATTTCAACTTCACAACGAAGGATATCCAATTAAAGGCTCAACTTCACAACGAAGGGGACATCC
117193 ACGATTTCAACTTCACGACGAAGGATATC
192 ACGATTTCAACTTCACGACGAAGGATATC
117222 CAACTCAAAG
Statistics
Matches: 194, Mismatches: 26, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
244 56 0.29
245 43 0.22
246 4 0.02
248 91 0.47
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (244 bp):
AGATTGGATTACAACTTCACGACGAAGGATATCCAATTCAAGGATCAAATTCACAACGAAGGAGC
CATCCACAATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAAATCACTCAAGATTGGAT
TTCAACTTCACAACGAAGGATATCCAATTAAAGGCTCAACTTCACAACGAAGGGGACATCCACGA
TTTCAACTTCACGACGAAGGATATCGTGCCCACCATAACATTCATCTTT
Found at i:119115 original size:13 final size:12
Alignment explanation
Indices: 119056--119114 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
119046 TATATATATA
*
119056 TTATATTTTAT-
1 TTATTTTTTATC
*
119067 TTATTATTTATTC
1 TTATTTTTTA-TC
119080 TT-TTTTTACTATTC
1 TTATTTTT--TA-TC
119094 TTATTTTTTATC
1 TTATTTTTTATC
119106 TTATTTTTT
1 TTATTTTTT
119115 TCTACTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.20
12 16 0.40
13 4 0.10
14 7 0.17
15 5 0.12
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.75
Consensus pattern (12 bp):
TTATTTTTTATC
Found at i:119115 original size:31 final size:30
Alignment explanation
Indices: 119059--119120 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
119049 ATATATATTA
*
119059 TATTTTATTTATTATTTATTCTTTTTTTAC
1 TATTTTATTTATTATTTATTCTTTTTCTAC
*
119089 TATTCTTATTTTTTATCTTATT-TTTTTCTAC
1 TATT-TTATTTATTAT-TTATTCTTTTTCTAC
119120 T
1 T
119121 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 19 0.68
32 5 0.18
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.73
Consensus pattern (30 bp):
TATTTTATTTATTATTTATTCTTTTTCTAC
Found at i:119126 original size:2 final size:2
Alignment explanation
Indices: 119121--119172 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
119111 TTTTTCTACT
* *
119121 TA TA TA TA TA TT TT TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
119162 TA TA TA TA TA T
1 TA TA TA TA TA T
119173 TTTATTTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:119135 original size:23 final size:23
Alignment explanation
Indices: 119120--119172 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
119110 TTTTTTCTAC
119120 TTATATATATATTTTTATATATA
1 TTATATATATATTTTTATATATA
* *
119143 TTATATATATATATATATATATA
1 TTATATATATATTTTTATATATA
119166 -TATATAT
1 TTATATAT
119173 TTTATTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATATATATATTTTTATATATA
Found at i:121353 original size:19 final size:18
Alignment explanation
Indices: 121331--121369 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
121321 TATGAATCTC
121331 AAATTAAATACTTAAATTT
1 AAATTAAATA-TTAAATTT
* *
121350 AAATTTAATATTTAATTT
1 AAATTAAATATTAAATTT
121368 AA
1 AA
121370 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTAAATATTAAATTT
Found at i:130686 original size:38 final size:39
Alignment explanation
Indices: 130602--130704 Score: 122
Period size: 38 Copynumber: 2.7 Consensus size: 39
130592 GTATATATAT
* **
130602 AACGTATATAAGATATAGTTTTG--AATTTTTTTTCCGAA
1 AACGTATATAATATATAGTTTTGAAAACATTTTTT-CGAA
*
130640 AACATATATAATATATAGTTTTGAAAACATTTTTT-GAA
1 AACGTATATAATATATAGTTTTGAAAACATTTTTTCGAA
* *
130678 ATCGTATATAATATATAGGTTTGAAAA
1 AACGTATATAATATATAGTTTTGAAAA
130705 TATATATAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 48 0.86
40 8 0.14
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.42
Consensus pattern (39 bp):
AACGTATATAATATATAGTTTTGAAAACATTTTTTCGAA
Found at i:130710 original size:25 final size:25
Alignment explanation
Indices: 130682--130729 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
130672 TTTGAAATCG
130682 TATATAATATATAGGTTTGAAAATA
1 TATATAATATATAGGTTTGAAAATA
*
130707 TATATAATATATAGTTTTGAAAA
1 TATATAATATATAGGTTTGAAAA
130730 CATCTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (25 bp):
TATATAATATATAGGTTTGAAAATA
Found at i:130710 original size:63 final size:63
Alignment explanation
Indices: 130637--130767 Score: 210
Period size: 63 Copynumber: 2.1 Consensus size: 63
130627 TTTTTTTTCC
*
130637 GAAAACATATATAATATATAGTTTTGAAAACATTTTTTG-AAATCGTATATAATATATAGGTTT
1 GAAAACATATATAATATATAGTTTTGAAAACATCTTTTGAAAAT-GTATATAATATATAGGTTT
* *
130700 GAAAATATATATAATATATAGTTTTGAAAACATCTTTTGAAAATGTATATAATATATAGTTTT
1 GAAAACATATATAATATATAGTTTTGAAAACATCTTTTGAAAATGTATATAATATATAGGTTT
*
130763 TAAAA
1 GAAAA
130768 AATACTTTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 59 0.94
64 4 0.06
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (63 bp):
GAAAACATATATAATATATAGTTTTGAAAACATCTTTTGAAAATGTATATAATATATAGGTTT
Found at i:130739 original size:38 final size:39
Alignment explanation
Indices: 130697--130794 Score: 139
Period size: 38 Copynumber: 2.6 Consensus size: 39
130687 AATATATAGG
*
130697 TTTGAAAATATATATAATATATAGTTTTGAAAACAT-CT
1 TTTGAAAATATATATAATATATAGTTTTGAAAAAATACT
* *
130735 TTTGAAAATGTATATAATATATAGTTTTTAAAAAATACT
1 TTTGAAAATATATATAATATATAGTTTTGAAAAAATACT
*
130774 TTTG-AAA-ACATATAATATATA
1 TTTGAAAATATATATAATATATA
130795 ATTTAAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
37 12 0.22
38 36 0.67
39 6 0.11
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (39 bp):
TTTGAAAATATATATAATATATAGTTTTGAAAAAATACT
Found at i:130878 original size:9 final size:9
Alignment explanation
Indices: 130853--130891 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
130843 ATAGTTATTA
130853 TTATTATAT
1 TTATTATAT
130862 TTACATTATAT
1 TT--ATTATAT
130873 TTATTATAT
1 TTATTATAT
130882 TTATT-TAT
1 TTATTATAT
130890 TT
1 TT
130892 TGTTTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.18
9 14 0.50
11 9 0.32
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATTATAT
Found at i:130888 original size:13 final size:12
Alignment explanation
Indices: 130850--130921 Score: 58
Period size: 13 Copynumber: 5.9 Consensus size: 12
130840 TATATAGTTA
*
130850 TTATTATTATAT
1 TTATTATTTTAT
* *
130862 TTA-CATTATAT
1 TTATTATTTTAT
130873 TTATTATATTTAT
1 TTATTAT-TTTAT
*
130886 TTATTTTGTTTAT
1 TTATTAT-TTTAT
*
130899 TTTTTATTTTTAT
1 TTATTA-TTTTAT
130912 TT-TTATTTTA
1 TTATTATTTTA
130922 GGCTCAAAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
11 15 0.30
12 8 0.16
13 26 0.52
14 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (12 bp):
TTATTATTTTAT
Found at i:130890 original size:17 final size:17
Alignment explanation
Indices: 130833--130919 Score: 60
Period size: 16 Copynumber: 5.2 Consensus size: 17
130823 GAAAACACAT
*
130833 TTTATATTA-TATAGTTA
1 TTTAT-TTATTATATTTA
130850 -TTA-TTATTATATTTACA
1 TTTATTTATTATATTT--A
130867 TTATATTTATTATATTTA
1 TT-TATTTATTATATTTA
*
130885 TTTATTT-TGTTTATTT-
1 TTTATTTAT-TATATTTA
*
130901 TTTATTT-TTATTTTTA
1 TTTATTTATTATATTTA
130917 TTT
1 TTT
130920 TAGGCTCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.05
15 11 0.19
16 15 0.26
17 12 0.21
18 4 0.07
19 2 0.03
20 11 0.19
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTATTTATTATATTTA
Found at i:130910 original size:6 final size:6
Alignment explanation
Indices: 130870--130920 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
130860 ATTTACATTA
*
130870 TATTTAT TATATT TATTTAT T-TTGTT TATTTTT TATTTT TATTTT TATTTT
1 TATTT-T TATTTT TATTT-T TATT-TT TA-TTTT TATTTT TATTTT TATTTT
130921 AGGCTCAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 25 0.66
7 11 0.29
8 2 0.05
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:136099 original size:11 final size:11
Alignment explanation
Indices: 136083--136108 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
136073 AGCAAATAAA
136083 ACATAATAATT
1 ACATAATAATT
136094 ACATAATAATT
1 ACATAATAATT
136105 ACAT
1 ACAT
136109 GCCACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (11 bp):
ACATAATAATT
Found at i:146886 original size:38 final size:37
Alignment explanation
Indices: 146844--147038 Score: 248
Period size: 38 Copynumber: 5.1 Consensus size: 37
146834 ATATATAACG
* *
146844 TATATAAGAAATAGTTTTGAAAACATTTTTCGAAAACA
1 TATATAATATATAGTTTTGAAAACATTTTT-GAAAACA
* * *
146882 TATATAATATATATTTTTAAAAACATTTTTTGAAAACG
1 TATATAATATATAGTTTTGAAAACA-TTTTTGAAAACA
146920 TATATAATATATAGTTTTGAAAACATTTTTTGAAAACA
1 TATATAATATATAGTTTTGAAAACA-TTTTTGAAAACA
* *
146958 TATATAATATATAGTTTTGAAAACATCTTTTAAAAACG
1 TATATAATATATAGTTTTGAAAACAT-TTTTGAAAACA
*
146996 TATATAATATATAGTTTTTAACAA-ATACTTTTGAAAACA
1 TATATAATATATAGTTTTGAA-AACAT--TTTTGAAAACA
147035 TATA
1 TATA
147039 GTATATAATT
Statistics
Matches: 140, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
37 1 0.01
38 118 0.84
39 21 0.15
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (37 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAACA
Found at i:146935 original size:76 final size:75
Alignment explanation
Indices: 146840--147038 Score: 283
Period size: 76 Copynumber: 2.6 Consensus size: 75
146830 GTATATATAT
* * *
146840 AACGTATATAAGAAATAGTTTTGAAAACATTTTTCGAAAACATATATAATATATATTTTTAAAAA
1 AACGTATATAATATATAGTTTTGAAAACATTTTT-GAAAACATATATAATATATAGTTTTAAAAA
* *
146905 CATTTTTTGAA
65 CATCTTTTAAA
*
146916 AACGTATATAATATATAGTTTTGAAAACATTTTTTGAAAACATATATAATATATAGTTTTGAAAA
1 AACGTATATAATATATAGTTTTGAAAACA-TTTTTGAAAACATATATAATATATAGTTTTAAAAA
146981 CATCTTTTAAA
65 CATCTTTTAAA
*
146992 AACGTATATAATATATAGTTTTTAACAA-ATACTTTTGAAAACATATA
1 AACGTATATAATATATAGTTTTGAA-AACAT--TTTTGAAAACATATA
147039 GTATATAATT
Statistics
Matches: 112, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
75 1 0.01
76 89 0.79
77 22 0.20
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.40
Consensus pattern (75 bp):
AACGTATATAATATATAGTTTTGAAAACATTTTTGAAAACATATATAATATATAGTTTTAAAAAC
ATCTTTTAAA
Found at i:147123 original size:17 final size:16
Alignment explanation
Indices: 147090--147144 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
147080 ACACATTTTA
147090 TATTA-TATAGTT-TT
1 TATTATTATAGTTATT
147104 TATTATTATAGTTATAT
1 TATTATTATAGTTAT-T
*
147121 TA-TATT-TATTTATT
1 TATTATTATAGTTATT
147135 TATTTATTAT
1 TA-TTATTAT
147145 TTTATTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 8 0.24
15 13 0.38
16 9 0.26
17 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
TATTATTATAGTTATT
Found at i:147144 original size:11 final size:12
Alignment explanation
Indices: 147102--147150 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
147092 TTATATAGTT
147102 TTTATTATTATA
1 TTTATTATTATA
*
147114 GTTA-TATTATA
1 TTTATTATTATA
147125 TTTATTTATT-TA
1 TTTA-TTATTATA
*
147137 TTTATTATTTTA
1 TTTATTATTATA
147149 TT
1 TT
147151 CTTTATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 15 0.47
12 13 0.41
13 4 0.12
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTATTATTATA
Found at i:147148 original size:12 final size:12
Alignment explanation
Indices: 147102--147160 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
147092 TTATATAGTT
*
147102 TTTATTATTATA
1 TTTATTATTTTA
* *
147114 GTTA-TATTATA
1 TTTATTATTTTA
147125 TTTATT-TATTTA
1 TTTATTAT-TTTA
147137 TTTATTATTTTA
1 TTTATTATTTTA
147149 TTCT-TTATTTTA
1 TT-TATTATTTTA
147161 GGCCCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 11 0.28
12 27 0.68
13 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:151727 original size:12 final size:13
Alignment explanation
Indices: 151710--151738 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
151700 ACTTTAGGAT
151710 ATAAATACACA-C
1 ATAAATACACATC
151722 ATAAATACACATC
1 ATAAATACACATC
151735 ATAA
1 ATAA
151739 TATAAAAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAATACACATC
Found at i:159982 original size:36 final size:36
Alignment explanation
Indices: 159902--159972 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
159892 GATTTTCCGA
* * *
159902 GATTGGTTGGGATTTGGTGTGATTTTTATTGATTTT
1 GATTTGTTTGGATTTGGTGTGATTTTTACTGATTTT
*
159938 GATTTGTTTGGATTTGGT-TGTTTTTTACTGATTTT
1 GATTTGTTTGGATTTGGTGTGATTTTTACTGATTTT
159973 TTCTCTGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 15 0.48
36 16 0.52
ACGTcount: A:0.13, C:0.01, G:0.27, T:0.59
Consensus pattern (36 bp):
GATTTGTTTGGATTTGGTGTGATTTTTACTGATTTT
Found at i:160549 original size:61 final size:61
Alignment explanation
Indices: 160479--160623 Score: 193
Period size: 61 Copynumber: 2.4 Consensus size: 61
160469 TTACTAGGTA
* * *
160479 AGAAACTTTGAAAATCACTTTATTACTTTTCAAA-ATTTTCATTTTCTGAAAATTCTAAATG
1 AGAAACTTTGAAAATCACTTTATCACTTTTCAAATA-TTTCATTTTCTAAAAATACTAAATG
** * *
160540 AGAAACTTTGAAAATTGCTTTCTCATTTTTCAAATATTTCATTTTCTAAAAATACTAAATG
1 AGAAACTTTGAAAATCACTTTATCACTTTTCAAATATTTCATTTTCTAAAAATACTAAATG
* *
160601 AGAAAATTTGAAAATCTCTTTAT
1 AGAAACTTTGAAAATCACTTTAT
160624 GTAACACCCC
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
61 71 0.99
62 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (61 bp):
AGAAACTTTGAAAATCACTTTATCACTTTTCAAATATTTCATTTTCTAAAAATACTAAATG
Found at i:162040 original size:20 final size:22
Alignment explanation
Indices: 162015--162072 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
162005 TTCCCCTTGA
162015 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
162035 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
162058 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
162073 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:165352 original size:16 final size:15
Alignment explanation
Indices: 165328--165380 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
165318 ACTTGATATG
165328 TTCTCTTTTTTCTTC
1 TTCTCTTTTTTCTTC
165343 TTCT-TCTTTTTCTTC
1 TTCTCT-TTTTTCTTC
165358 -TCT-TTTTTTCTTC
1 TTCTCTTTTTTCTTC
165371 TTCTCTTTTT
1 TTCTCTTTTT
165381 CTTTATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.26
14 8 0.23
15 18 0.51
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TTCTCTTTTTTCTTC
Found at i:165358 original size:27 final size:27
Alignment explanation
Indices: 165328--165383 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
165318 ACTTGATATG
165328 TTCTC-TTTTTTCTTCTTCTTCTTTTTC
1 TTCTCTTTTTTTCTTCTTC-TCTTTTTC
165355 TTCTCTTTTTTTCTTCTTCTCTTTTTC
1 TTCTCTTTTTTTCTTCTTCTCTTTTTC
165382 TT
1 TT
165384 TATTTTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (27 bp):
TTCTCTTTTTTTCTTCTTCTCTTTTTC
Found at i:165393 original size:16 final size:15
Alignment explanation
Indices: 165331--165398 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 15
165321 TGATATGTTC
*
165331 TCTTTTTTCTTCTTCT
1 TCTTTTTT-TTCTTTT
165347 TCTTTTTCTTCTCTTTT
1 TCTTTTT-TT-TCTTTT
*
165364 T-TTCTTCTTCTCTTTT
1 TCTT-TT-TTTTCTTTT
165380 TCTTTATTTTTCTTTT
1 TCTTT-TTTTTCTTTT
165396 TCT
1 TCT
165399 ATTTCTATCT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
16 29 0.67
17 13 0.30
18 1 0.02
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TCTTTTTTTTCTTTT
Found at i:165403 original size:22 final size:20
Alignment explanation
Indices: 165335--165404 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 20
165325 ATGTTCTCTT
* *
165335 TTTTCTTCTTCTTCTTTTTC
1 TTTTCTTTTTTTTCTTTTTC
*
165355 TTCTC-TTTTTTTCTTCTTCTC
1 TTTTCTTTTTTTTCTT-TT-TC
165376 TTTTTCTTTATTTTTCTTTTTC
1 -TTTTCTTT-TTTTTCTTTTTC
165398 TATTTCT
1 T-TTTCT
165405 ATCTTGAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
19 8 0.20
20 6 0.15
21 3 0.08
22 11 0.28
23 4 0.10
24 8 0.20
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTTTTTCTTTTTC
Found at i:168694 original size:2 final size:2
Alignment explanation
Indices: 168689--168729 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
168679 ATCACACATC
168689 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
168730 CATTTGTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:168958 original size:32 final size:30
Alignment explanation
Indices: 168884--168973 Score: 117
Period size: 32 Copynumber: 2.9 Consensus size: 30
168874 GAATGACCTA
* * *
168884 TCCATATGTTCCGACGAACATAGGTAACTG
1 TCCATATGTCCCGAAGGACATAGGTAACTG
*
168914 TCCATATATCCCGAAGGACATAGGTAATCATG
1 TCCATATGTCCCGAAGGACATAGGTAA-C-TG
*
168946 TCCATATGTCCCGAACGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGGTAAC
168974 CCTCGACTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 23 0.44
31 2 0.04
32 27 0.52
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
TCCATATGTCCCGAAGGACATAGGTAACTG
Found at i:169352 original size:2 final size:2
Alignment explanation
Indices: 169345--169423 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
169335 GGCTTATCTT
169345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
169387 TA TA TA TA TA 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 TA TA TA TA TA T
169424 TCACAACTTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:172012 original size:19 final size:19
Alignment explanation
Indices: 171988--172034 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
171978 GTCAAAATTA
171988 ACTTATCAATAATTTACTT
1 ACTTATCAATAATTTACTT
*
172007 ACTTATCAATAATTTAGTT
1 ACTTATCAATAATTTACTT
172026 ACTTATCAA
1 ACTTATCAA
172035 ATTCGCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (19 bp):
ACTTATCAATAATTTACTT
Found at i:177776 original size:2 final size:2
Alignment explanation
Indices: 177771--177827 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
177761 ATCACACATC
177771 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
177813 AT AT AT -T AC AT AT AT
1 AT AT AT AT AT AT AT AT
177828 TGTATTCAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.