Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008460.1 Hibiscus syriacus cultivar Beakdansim tig00111273_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: 2854393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 15
Found at i:2734573 original size:17 final size:18
Alignment explanation
Indices: 2734536--2734574 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2734526 ATGCTTTCTC
*
2734536 TCTTGTTTCTCTATTGAT
1 TCTTCTTTCTCTATTGAT
*
2734554 TCTTCTTTCT-TATTGTT
1 TCTTCTTTCTCTATTGAT
2734571 TCTT
1 TCTT
2734575 GTTGTTGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.08, C:0.18, G:0.08, T:0.67
Consensus pattern (18 bp):
TCTTCTTTCTCTATTGAT
Found at i:2734865 original size:45 final size:46
Alignment explanation
Indices: 2734796--2734902 Score: 139
Period size: 45 Copynumber: 2.3 Consensus size: 46
2734786 GGTGCACTAA
* * *
2734796 GAGTGCATCGATGCATGAAGTGCATT-TGATG-TTTCA-AAATAGCCT
1 GAGTGCATCGATGCATCAAATGCATTCT-ATGTTTTCATAAA-ACCCT
2734841 GAGTGCATCGATGCATCAAATGCATTCTATGTTTTCATAAAACCCT
1 GAGTGCATCGATGCATCAAATGCATTCTATGTTTTCATAAAACCCT
*
2734887 CAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
2734903 GGTATGTGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 27 0.49
46 25 0.45
47 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATCAAATGCATTCTATGTTTTCATAAAACCCT
Found at i:2737425 original size:24 final size:24
Alignment explanation
Indices: 2737398--2737445 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2737388 TAGGGGTGTT
2737398 TGAACTCGATTTTTACCGAACTAA
1 TGAACTCGATTTTTACCGAACTAA
*
2737422 TGAACTCGATTTTTATCGAACTAA
1 TGAACTCGATTTTTACCGAACTAA
2737446 CCGACCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (24 bp):
TGAACTCGATTTTTACCGAACTAA
Found at i:2737605 original size:25 final size:25
Alignment explanation
Indices: 2737571--2737631 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
2737561 GAAAACATTT
2737571 GATTCGGTTAACGGTTAATGGGAAA
1 GATTCGGTTAACGGTTAATGGGAAA
2737596 GATTCGGTTAACGGTTAATGGGAAA
1 GATTCGGTTAACGGTTAATGGGAAA
2737621 GATTCGGTTAA
1 GATTCGGTTAA
2737632 TAAAATTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (25 bp):
GATTCGGTTAACGGTTAATGGGAAA
Found at i:2738180 original size:117 final size:118
Alignment explanation
Indices: 2738020--2738245 Score: 400
Period size: 117 Copynumber: 1.9 Consensus size: 118
2738010 TCTAAGTTTT
*
2738020 TTATATTTTTTGTTTTAAAATTAAATTTAAATTCCTAAATTTTTCTTAGAATTGTATTATGTACT
1 TTATATTTTTTATTTTAAAATTAAATTTAAATTCCTAAATTTTTCTTAGAATTGTATTATGTACT
2738085 TCTAAGTTTTGAATTTTTT-AAAAATATTAATTTATCAATATATATATATAAA
66 TCTAAGTTTTGAATTTTTTAAAAAATATTAATTTATCAATATATATATATAAA
* *
2738137 TTATATTTTTTATTTTAAAATTAAATTTAAATTCCTAATTTTTTCTTAGATTTGTATTATGTACT
1 TTATATTTTTTATTTTAAAATTAAATTTAAATTCCTAAATTTTTCTTAGAATTGTATTATGTACT
2738202 TCTAAGTTTTGAATTTTTTAAAAAAAATATTAATTTATCAATAT
66 TCTAAGTTTTGAATTTTTT--AAAAAATATTAATTTATCAATAT
2738246 GAGATTCGGA
Statistics
Matches: 103, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
117 81 0.79
120 22 0.21
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (118 bp):
TTATATTTTTTATTTTAAAATTAAATTTAAATTCCTAAATTTTTCTTAGAATTGTATTATGTACT
TCTAAGTTTTGAATTTTTTAAAAAATATTAATTTATCAATATATATATATAAA
Found at i:2738322 original size:2 final size:2
Alignment explanation
Indices: 2738315--2738344 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2738305 ATAAACTTTA
2738315 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
2738345 TTATCTTTAT
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:2739268 original size:6 final size:6
Alignment explanation
Indices: 2739257--2739288 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2739247 CTGAGGCCTG
2739257 AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AG
1 AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AG
2739289 TGCAGAGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:2742571 original size:2 final size:2
Alignment explanation
Indices: 2742564--2742598 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2742554 TGAGCAACGC
2742564 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 A
2742599 AGTATGATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2743674 original size:28 final size:28
Alignment explanation
Indices: 2743637--2743700 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
2743627 GTAAGGTTAA
2743637 GTGAGCAATTAGAAAAATTGAAAGTTTG
1 GTGAGCAATTAGAAAAATTGAAAGTTTG
2743665 GTGAGCAATTAGAAAAATTGAAAGTTTG
1 GTGAGCAATTAGAAAAATTGAAAGTTTG
2743693 GTGAGCAA
1 GTGAGCAA
2743701 AATAGGAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.42, C:0.05, G:0.27, T:0.27
Consensus pattern (28 bp):
GTGAGCAATTAGAAAAATTGAAAGTTTG
Found at i:2750967 original size:23 final size:23
Alignment explanation
Indices: 2750941--2750985 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2750931 CACCACAGCT
*
2750941 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2750964 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2750986 ATAATGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2751219 original size:147 final size:144
Alignment explanation
Indices: 2750953--2751260 Score: 489
Period size: 147 Copynumber: 2.1 Consensus size: 144
2750943 TATAATTGCA
*
2750953 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATAATGATGTCCATAAGGACCACATAGAATT
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATAATAATGTCCATAAGGACCACATAGAATT
*
2751017 CCTTAAGAATCATAACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCA
65 CCTTAAGAATCATAACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCA
2751082 AAGAATATACATATGTC
130 AAG-A-ATACATATGTC
*
2751099 CCGAAGGACCGCGTAGAATTGCA-CGTAGTGCCATATAATAATGTCTATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCC--ATAATAATGTCCATAAGGACCACATAGAAT
2751163 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTC-TTCAAGACTTCACACATGTT
64 TCCTTAAGAATCATA-ACATATGCTAGGGATCA-AGTATGTGTCTTTCAAGACTTCACACATGTT
2751226 CCAAAGAATACATATGTC
127 CCAAAGAATACATATGTC
*
2751244 CCGAAGGATCGCGTAGA
1 CCGAAGGACCGCGTAGA
2751261 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 4, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
145 37 0.24
146 22 0.14
147 68 0.44
148 25 0.16
149 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (144 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATAATAATGTCCATAAGGACCACATAGAATTC
CTTAAGAATCATAACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAA
AGAATACATATGTC
Found at i:2752770 original size:21 final size:21
Alignment explanation
Indices: 2752746--2752786 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2752736 TGTTGTTCGT
* *
2752746 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2752767 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
2752787 TTGCCCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2756060 original size:23 final size:23
Alignment explanation
Indices: 2756034--2756078 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2756024 CACCACAGCT
*
2756034 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2756057 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2756079 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2756316 original size:149 final size:149
Alignment explanation
Indices: 2756046--2756360 Score: 562
Period size: 149 Copynumber: 2.1 Consensus size: 149
2756036 TATAATTGCA
*
2756046 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
*
2756110 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTATTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTATTTCAAGACTTCACACATGTT
2756175 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
*
2756195 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCTATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
2756260 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTTTCAAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTATTTCAAGACTTCACACATGTT
2756324 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
2756344 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
2756361 CCCTCGACTC
Statistics
Matches: 160, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
150 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTATTTCAAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:2757182 original size:21 final size:22
Alignment explanation
Indices: 2757141--2757182 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2757131 ATTCAATTTT
*
2757141 ATATAACTCCTATAATCTTCTC
1 ATATAACTCATATAATCTTCTC
2757163 ATATAACTTCATA-AAT-TTCT
1 ATATAAC-TCATATAATCTTCT
2757183 ATCATATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAACTCATATAATCTTCTC
Found at i:2757874 original size:21 final size:21
Alignment explanation
Indices: 2757850--2757890 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2757840 TGTTGTTCGT
* *
2757850 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2757871 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
2757891 TTGCCCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2759185 original size:31 final size:31
Alignment explanation
Indices: 2759147--2759302 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
2759137 AGGGTCGAGG
2759147 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2759178 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2759209 ATTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
2759240 GCTTACCTATGTTCTTCGGGACATATAGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2759271 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2759302 G
1 G
2759303 GTCATTCGGG
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2760012 original size:22 final size:22
Alignment explanation
Indices: 2759987--2760040 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
2759977 TATTGTTCAA
*
2759987 TACTGTTCATTACTGTTCACGG
1 TACTGTTCATTAATGTTCACGG
*
2760009 TACTATTCATTAATGTTCACGG
1 TACTGTTCATTAATGTTCACGG
2760031 TACTGTTCAT
1 TACTGTTCAT
2760041 ACCGTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (22 bp):
TACTGTTCATTAATGTTCACGG
Found at i:2760026 original size:32 final size:32
Alignment explanation
Indices: 2759966--2760027 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2759956 GAATTTTTTC
* * *
2759966 ACTGTTCACGGTATTGTTCAATACTGTTCATT
1 ACTGTTCACGGTACTATTCAATAATGTTCATT
*
2759998 ACTGTTCACGGTACTATTCATTAATGTTCA
1 ACTGTTCACGGTACTATTCAATAATGTTCA
2760028 CGGTACTGTT
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:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (32 bp):
ACTGTTCACGGTACTATTCAATAATGTTCATT
Found at i:2761541 original size:32 final size:32
Alignment explanation
Indices: 2761473--2761543 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
2761463 TAAGGCGACC
* * * *
2761473 CTTGGGT-AGGCTCTGCGGCCCTGAGATTTTT
1 CTTGGGTAAGCCTCTGCGGCCCCGAGAATTGT
* *
2761504 ATTGGGTAAGCCTCTGTGGCCCCGAGAATTGT
1 CTTGGGTAAGCCTCTGCGGCCCCGAGAATTGT
2761536 CTTGGGTA
1 CTTGGGTA
2761544 GGTTCTTAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.14, C:0.21, G:0.32, T:0.32
Consensus pattern (32 bp):
CTTGGGTAAGCCTCTGCGGCCCCGAGAATTGT
Found at i:2763228 original size:62 final size:62
Alignment explanation
Indices: 2763152--2763274 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 62
2763142 ACAAATGATC
* * ** *
2763152 GTAAACTATCACCTCATCTA-TTTCTAAAATTCTAATCGTCTCCAGATTTCAATCCCAGAAAA
1 GTAAACTATCACCTCATCAATTTTCGAAAA-TCTAATCACCTCCAAATTTCAATCCCAGAAAA
* * *
2763214 GTAAACTATCACCTCGTCAATTTTCGAAGATCTAATCACCTCCAAATTTCAATCCCGGAAA
1 GTAAACTATCACCTCATCAATTTTCGAAAATCTAATCACCTCCAAATTTCAATCCCAGAAA
2763275 GATATAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 45 0.87
63 7 0.13
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30
Consensus pattern (62 bp):
GTAAACTATCACCTCATCAATTTTCGAAAATCTAATCACCTCCAAATTTCAATCCCAGAAAA
Found at i:2775117 original size:16 final size:18
Alignment explanation
Indices: 2775096--2775140 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2775086 ATGGAATTGG
2775096 ATTCCAATTCC-T-ACAA
1 ATTCCAATTCCTTCACAA
*
2775112 ATTCCAATTCCTTCACAG
1 ATTCCAATTCCTTCACAA
2775130 ATTCCAATTCC
1 ATTCCAATTCC
2775141 CTCATAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.33
Consensus pattern (18 bp):
ATTCCAATTCCTTCACAA
Found at i:2782998 original size:14 final size:14
Alignment explanation
Indices: 2782979--2783007 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2782969 TGCACTTTTG
2782979 CCCGGTCTCCCCCA
1 CCCGGTCTCCCCCA
2782993 CCCGGTCTCCCCCA
1 CCCGGTCTCCCCCA
2783007 C
1 C
2783008 TATTGCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.66, G:0.14, T:0.14
Consensus pattern (14 bp):
CCCGGTCTCCCCCA
Found at i:2788209 original size:34 final size:34
Alignment explanation
Indices: 2788166--2788239 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
2788156 CTAGAGTTGG
2788166 AAGTTAAATTTGACTTGT-CAATGGTCTAATTAAA
1 AAGTTAAATTTGACTT-TCCAATGGTCTAATTAAA
2788200 AAGTTAAATTTGACTTTCCAATGGTCTAATTAAA
1 AAGTTAAATTTGACTTTCCAATGGTCTAATTAAA
2788234 AAGTTA
1 AAGTTA
2788240 GAAGCCATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 1 0.03
34 38 0.97
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (34 bp):
AAGTTAAATTTGACTTTCCAATGGTCTAATTAAA
Found at i:2788621 original size:24 final size:22
Alignment explanation
Indices: 2788581--2788657 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
2788571 ATGCAATTAA
2788581 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
2788600 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
2788623 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
2788644 TGCATCGATGCACT
1 TGCATCGATGCACT
2788658 TCAAGGGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:2789696 original size:23 final size:23
Alignment explanation
Indices: 2789640--2789696 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
2789630 CTTATATGGA
*
2789640 ACTTCGGTGCATTTCTACGCGGC
1 ACTTCGGTGCAATTCTACGCGGC
* * *
2789663 ACTACGATGCAATTCTACGTGGC
1 ACTTCGGTGCAATTCTACGCGGC
2789686 ACTTCGGTGCA
1 ACTTCGGTGCA
2789697 TCTATACGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGCGGC
Found at i:2793006 original size:24 final size:22
Alignment explanation
Indices: 2792966--2793042 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
2792956 ATGTAATTAA
2792966 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
2792985 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
2793008 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
2793029 TGCATCGATGCACT
1 TGCATCGATGCACT
2793043 TCAAGGGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:2794035 original size:23 final size:23
Alignment explanation
Indices: 2794002--2794062 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2793992 AATCTTATAT
2794002 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
2794025 GGCACTACGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
2794048 GGCACTTCGGTGCAT
1 GGCACTTCGGTGCAT
2794063 CTATATGAGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:2798851 original size:79 final size:77
Alignment explanation
Indices: 2798733--2798892 Score: 223
Period size: 79 Copynumber: 2.1 Consensus size: 77
2798723 TTAACAATAG
* *
2798733 AAAATGAGGGGTAAAATAAAATAAATTAAAATCTAAAGGCCTAAATAGGTAATT-TCCCCATTAT
1 AAAATGAGGGGGAAAATAAAATAAATTAAAATCTAAAGGCCTAAATAGATAATTGT-CCCATTAT
2798797 TCATTAATGATAA
65 TCATTAATGATAA
* ***
2798810 AAAATTGAGGGGGAAAATCAAAATAAATTAAAATTTAAAGGCCTAAATAGATAATTGTCTTGTTA
1 AAAA-TGAGGGGGAAAAT-AAAATAAATTAAAATCTAAAGGCCTAAATAGATAATTGTCCCATTA
*
2798875 TTCTTTAATGATAA
64 TTCATTAATGATAA
2798889 AAAA
1 AAAA
2798893 ATTGGTGGGG
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
77 4 0.05
78 12 0.16
79 56 0.77
80 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (77 bp):
AAAATGAGGGGGAAAATAAAATAAATTAAAATCTAAAGGCCTAAATAGATAATTGTCCCATTATT
CATTAATGATAA
Found at i:2799706 original size:43 final size:43
Alignment explanation
Indices: 2799645--2799730 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
2799635 GATGACACCT
* *
2799645 AGGAAAATAAATTTAATAAATATAAACAAATTTAATTATCTAA
1 AGGAAAATAAATTTAATAAATATAAAAAAAATTAATTATCTAA
2799688 AGGAAAATAAATTTAATAAATATAAAAAAAATTAATTATCTAA
1 AGGAAAATAAATTTAATAAATATAAAAAAAATTAATTATCTAA
2799731 TTATAGATAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.31
Consensus pattern (43 bp):
AGGAAAATAAATTTAATAAATATAAAAAAAATTAATTATCTAA
Found at i:2799780 original size:17 final size:19
Alignment explanation
Indices: 2799747--2799781 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2799737 ATAGATACAT
2799747 GTTACAATTTAATTAAATG
1 GTTACAATTTAATTAAATG
2799766 GTTA-AATTT-ATTAAAT
1 GTTACAATTTAATTAAAT
2799782 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (19 bp):
GTTACAATTTAATTAAATG
Found at i:2802074 original size:47 final size:44
Alignment explanation
Indices: 2801992--2802089 Score: 142
Period size: 47 Copynumber: 2.1 Consensus size: 44
2801982 AAAATATGTG
* *
2801992 CAATTTTCAGTAATAAGTATATATTACAGGTAAGGACTTCAATT
1 CAATTTTCAGTAATAAGTATATATTACAGATAAGGACTTAAATT
2802036 CAATTTTCAGTAATAAGTAGTATGTATTACAGATAAGGACTTAAATT
1 CAATTTTCAGTAATAAGTA-TA--TATTACAGATAAGGACTTAAATT
2802083 CATATTT
1 CA-ATTT
2802090 CTGAAAGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
44 19 0.40
45 2 0.04
47 23 0.48
48 4 0.08
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (44 bp):
CAATTTTCAGTAATAAGTATATATTACAGATAAGGACTTAAATT
Found at i:2804470 original size:25 final size:26
Alignment explanation
Indices: 2804436--2804485 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
2804426 TCCTTTAGGG
* *
2804436 AATTATTTTATGT-TTTTTGAAGTTA
1 AATTATTTTAGGTGTGTTTGAAGTTA
*
2804461 AATTCTTTTAGGTGTGTTTGAAGTT
1 AATTATTTTAGGTGTGTTTGAAGTT
2804486 TTGAATGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.24, C:0.02, G:0.18, T:0.56
Consensus pattern (26 bp):
AATTATTTTAGGTGTGTTTGAAGTTA
Found at i:2807014 original size:21 final size:21
Alignment explanation
Indices: 2806988--2807104 Score: 78
Period size: 21 Copynumber: 5.4 Consensus size: 21
2806978 TTTGGTTTTT
2806988 AATATATATATATAGTTTTG-
1 AATATATATATATAGTTTTGA
*
2807008 AA-ATATATATATAGTTTTTA
1 AATATATATATATAGTTTTGA
* **
2807028 AATATCAATATATATTATATATTTTT
1 AATAT--ATATATA-TA-GT-TTTGA
** * *
2807054 TTTAAACATATATAGTTTTGA
1 AATATATATATATAGTTTTGA
*
2807075 AATATATATTATATA-TTTTAA
1 AATATATA-TATATAGTTTTGA
2807096 AATATATAT
1 AATATATAT
2807105 GGTTTTATTG
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
19 16 0.22
20 5 0.07
21 22 0.30
22 7 0.09
23 9 0.12
24 8 0.11
25 1 0.01
26 6 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (21 bp):
AATATATATATATAGTTTTGA
Found at i:2807038 original size:19 final size:19
Alignment explanation
Indices: 2806982--2807110 Score: 86
Period size: 19 Copynumber: 7.3 Consensus size: 19
2806972 TGTTATTTTG
2806982 GTTTTTAATATATATATATA
1 GTTTTTAA-ATATATATATA
*
2807002 GTTTTGAAATATATATATA
1 GTTTTTAAATATATATATA
2807021 GTTTTTAAATATCA-ATATA
1 GTTTTTAAATAT-ATATATA
*
2807040 --TATT--ATATAT-T-T-
1 GTTTTTAAATATATATATA
*
2807052 -TTTTT-AA-ACATATATA
1 GTTTTTAAATATATATATA
*
2807068 GTTTTGAAATATATATTATA
1 GTTTTTAAATATATA-TATA
*
2807088 -TATTTTAAA-ATATATATG
1 GT-TTTTAAATATATATATA
2807106 GTTTT
1 GTTTT
2807111 ATTGAAAATA
Statistics
Matches: 87, Mismatches: 9, Indels: 28
0.70 0.07 0.23
Matches are distributed among these distances:
13 7 0.08
14 4 0.05
15 5 0.06
17 7 0.08
18 8 0.09
19 38 0.44
20 18 0.21
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (19 bp):
GTTTTTAAATATATATATA
Found at i:2807087 original size:20 final size:21
Alignment explanation
Indices: 2807062--2807158 Score: 74
Period size: 21 Copynumber: 4.5 Consensus size: 21
2807052 TTTTTAAACA
*
2807062 TATATAGTTTTGAAATATATAT
1 TATATA-TTTTAAAATATATAT
2807084 TATATATTTTAAAATATATAT
1 TATATATTTTAAAATATATAT
* * *
2807105 GGT-TTTA-TTGAAAATACATAT
1 --TATATATTTTAAAATATATAT
*
2807126 TATATATTTCGAATAATATATTAT
1 TATATATTT-TAA-AATATA-TAT
2807150 TAT-TATTTT
1 TATATATTTT
2807159 CTTTTTATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 28 0.46
22 12 0.20
23 11 0.18
24 6 0.10
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (21 bp):
TATATATTTTAAAATATATAT
Found at i:2807166 original size:14 final size:14
Alignment explanation
Indices: 2807144--2807193 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2807134 TCGAATAATA
*
2807144 TATTATTATTATTT
1 TATTTTTATTATTT
*
2807158 TCTTTTTATT-TATT
1 TATTTTTATTAT-TT
2807172 TATTTTTA-TATTT
1 TATTTTTATTATTT
2807185 TAATTTTTA
1 T-ATTTTTA
2807194 GGTCCATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.17
14 25 0.83
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTATTATTT
Found at i:2809195 original size:21 final size:20
Alignment explanation
Indices: 2809151--2809224 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
2809141 GCAGCCTTCG
*
2809151 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
* **
2809171 TGCATTGATGCACAACCTTGA
1 TGCATCGATGCACAA-CAGGA
2809192 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACA-ACAGGA
2809212 TGCATCGATGCAC
1 TGCATCGATGCAC
2809225 TAATTGCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 29 0.63
21 16 0.35
22 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:2809291 original size:42 final size:43
Alignment explanation
Indices: 2809245--2809342 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 43
2809235 CGGTGTTTGA
*
2809245 GTGCATGGATGCACTGCATGG-TGCATCG-ATGCACTAGT-GCAG
1 GTGCATGGATGCACTGCAGGGATGCAT-GAATGCACT-GTAGCAG
**
2809287 GTGCATGGATGCACTGCAGGGATGCATGAATGCACTGTAGGGG
1 GTGCATGGATGCACTGCAGGGATGCATGAATGCACTGTAGCAG
2809330 GTGCATGGATGCA
1 GTGCATGGATGCA
2809343 TTTTGATACC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 23 0.46
43 27 0.54
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (43 bp):
GTGCATGGATGCACTGCAGGGATGCATGAATGCACTGTAGCAG
Found at i:2809341 original size:22 final size:21
Alignment explanation
Indices: 2809245--2809342 Score: 94
Period size: 22 Copynumber: 4.6 Consensus size: 21
2809235 CGGTGTTTGA
*
2809245 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
*
2809265 GTGCATCGATGCACT--AGTGCAG
1 GTGCATGGATGCACTGCAG-G--G
2809287 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
* * *
2809308 ATGCATGAATGCACTGTAGGGG
1 GTGCATGGATGCACTGCA-GGG
2809330 GTGCATGGATGCA
1 GTGCATGGATGCA
2809343 TTTTGATACC
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.02
20 14 0.22
21 16 0.25
22 29 0.46
23 1 0.02
24 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:2809919 original size:9 final size:10
Alignment explanation
Indices: 2809883--2809923 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
2809873 TGATCTTAAA
2809883 ACACAATTTT
1 ACACAATTTT
*
2809893 ACATAATTTT
1 ACACAATTTT
*
2809903 AC-CAAATTT
1 ACACAATTTT
2809912 ACACAATTTT
1 ACACAATTTT
2809922 AC
1 AC
2809924 TCATTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (10 bp):
ACACAATTTT
Found at i:2810644 original size:21 final size:21
Alignment explanation
Indices: 2810618--2810661 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2810608 CTGAAGCCGG
*
2810618 AGGAGGAGCACGAGAGGAGCT
1 AGGAGGAGCACGAGAGGAACT
* *
2810639 AGGAGGAGCTCGTGAGGAACT
1 AGGAGGAGCACGAGAGGAACT
2810660 AG
1 AG
2810662 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.45, T:0.09
Consensus pattern (21 bp):
AGGAGGAGCACGAGAGGAACT
Found at i:2818009 original size:21 final size:21
Alignment explanation
Indices: 2817982--2818038 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2817972 TAGGAGCGTC
2817982 AGTGCATCGATGCATATCCAT
1 AGTGCATCGATGCATATCCAT
*
2818003 GGTGCATCGATGCATATCCAT
1 AGTGCATCGATGCATATCCAT
*
2818024 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
2818039 CCGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (21 bp):
AGTGCATCGATGCATATCCAT
Found at i:2819847 original size:19 final size:21
Alignment explanation
Indices: 2819800--2819847 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
2819790 TCTAAATCAT
*
2819800 TTTTCAAAATTTCATTTTGGC
1 TTTTCAAAATCTCATTTTGGC
*
2819821 TTTT-AAAATCT-ATTTTTG-
1 TTTTCAAAATCTCATTTTGGC
2819839 TTTTCAAAA
1 TTTTCAAAA
2819848 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 6 0.25
21 4 0.17
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTTCAAAATCTCATTTTGGC
Found at i:2821025 original size:21 final size:21
Alignment explanation
Indices: 2820991--2821030 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2820981 TGTTGTATAT
*
2820991 AGCCTTTTGGGAT-GTTTTGG
1 AGCCTTTGGGGATGGTTTTGG
2821011 AGCCGTTTGGGGATGGTTTT
1 AGCC-TTTGGGGATGGTTTT
2821031 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.10, C:0.10, G:0.38, T:0.42
Consensus pattern (21 bp):
AGCCTTTGGGGATGGTTTTGG
Found at i:2821172 original size:20 final size:20
Alignment explanation
Indices: 2821143--2821215 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
2821133 GCAGCCTTCG
* *
2821143 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGAAGGA
*
2821163 TGCATCGATGCACAGAAAGA
1 TGCATCGATGCACAGAAGGA
2821183 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGAAGGA
2821203 TGCATCGATGCAC
1 TGCATCGATGCAC
2821216 TAATTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.33, C:0.22, G:0.29, T:0.16
Consensus pattern (20 bp):
TGCATCGATGCACAGAAGGA
Found at i:2821305 original size:21 final size:20
Alignment explanation
Indices: 2821236--2821334 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
2821226 CGGTGTTTGA
*
2821236 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
2821256 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
*
2821278 GTGCATGGATGCATTGCAGG
1 GTGCATGGATGCACTGCAGG
2821298 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
2821320 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2821335 TTGACACCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.22
21 30 0.43
22 16 0.23
23 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:2821435 original size:29 final size:29
Alignment explanation
Indices: 2821414--2821471 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
2821404 AAACTTTGAA
2821414 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
2821443 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
2821472 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:2821461 original size:30 final size:30
Alignment explanation
Indices: 2821414--2821473 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
2821404 AAACTTTGAA
2821414 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
2821443 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
2821474 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:2823053 original size:121 final size:119
Alignment explanation
Indices: 2822783--2823002 Score: 323
Period size: 121 Copynumber: 1.8 Consensus size: 119
2822773 TCTCCGATAC
* *
2822783 TTCAGAGTTAAATTTAATAATATTATTTATAAGTTACAAAGTTCAATCCATTAAATTAAACATAT
1 TTCAAAGTTAAATGTAAT-ATATTATTTATAAGTTACAAAGTTCAATCCATTAAATTAAACATAT
* * ** ** *
2822848 TTTATGAAATTAACTTAATATTTATTCCTTCTTCAGATTGTTTTTAAATATTTTTA
65 TTTATGAAATTAACTTAATATTTATTCCTTATTCAGATGGTCATT-AATACCTTCA
2822904 TTCAAAGTTAAATGTAATAATATTATTTATAAGTTACAAAGTTCAATCCATTAAATTAAACATAT
1 TTCAAAGTTAAATGTAAT-ATATTATTTATAAGTTACAAAGTTCAATCCATTAAATTAAACATAT
*
2822969 TTTATGAAATTAACTTAATATTTATTCTTTATTC
65 TTTATGAAATTAACTTAATATTTATTCCTTATTC
2823003 TTAATGGTCA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 95 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (119 bp):
TTCAAAGTTAAATGTAATATATTATTTATAAGTTACAAAGTTCAATCCATTAAATTAAACATATT
TTATGAAATTAACTTAATATTTATTCCTTATTCAGATGGTCATTAATACCTTCA
Found at i:2830789 original size:11 final size:11
Alignment explanation
Indices: 2830751--2830787 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
2830741 AAATTTTGGC
2830751 TTTTTTGCCTT
1 TTTTTTGCCTT
2830762 TTTTTTGCCTT
1 TTTTTTGCCTT
2830773 TTTTTTG--TT
1 TTTTTTGCCTT
2830782 TTTTTT
1 TTTTTT
2830788 TTTTGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 8 0.31
11 18 0.69
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (11 bp):
TTTTTTGCCTT
Found at i:2840094 original size:35 final size:35
Alignment explanation
Indices: 2840028--2840145 Score: 103
Period size: 35 Copynumber: 3.4 Consensus size: 35
2840018 AGTTTGCATC
* * * * *
2840028 GATTCAAGTTGAATGGAATGAAGCATCGCACTTTT
1 GATTCAAGTAGAAAGGAAGGAAACATCGCACTTCT
* *
2840063 GATTCTAGTAGAAAGGAAGGAAACATTGCACTTCT
1 GATTCAAGTAGAAAGGAAGGAAACATCGCACTTCT
* * * **
2840098 GATTCAAGTCGAACGGAAGTAGGCATCGCACTT-T
1 GATTCAAGTAGAAAGGAAGGAAACATCGCACTTCT
*
2840132 CGATTCAACTAGAA
1 -GATTCAAGTAGAA
2840146 CAGATGGTTT
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
34 1 0.02
35 65 0.98
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (35 bp):
GATTCAAGTAGAAAGGAAGGAAACATCGCACTTCT
Found at i:2841340 original size:14 final size:14
Alignment explanation
Indices: 2841321--2841369 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
2841311 TAGATATTAA
2841321 TTTTAATATTAATT
1 TTTTAATATTAATT
2841335 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
2841345 ATTAAATATTAATT
1 TTTTAATATTAATT
2841359 TTTTAATATTA
1 TTTTAATATTA
2841370 TATTATAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 6 0.22
13 1 0.04
14 15 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:2841445 original size:20 final size:19
Alignment explanation
Indices: 2841385--2841446 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
2841375 TAGATATTTA
*
2841385 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
2841404 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
2841422 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
2841442 ATTTT
1 ATTTT
2841447 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:2842095 original size:31 final size:31
Alignment explanation
Indices: 2842060--2842119 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2842050 TAGCTCTATG
* *
2842060 AATTATTTAAATTTTAGTATT-CTAAAACTAA
1 AATTATTTAAATCTCAGTATTGC-AAAACTAA
2842091 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
2842120 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:2843615 original size:6 final size:6
Alignment explanation
Indices: 2843599--2843654 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
2843589 CATAACGTTC
* *
2843599 TATTTT T-TTTT TATTTT TATTTT TGTAGTT TA-TTT TATTTT TA-TTT
1 TATTTT TATTTT TATTTT TATTTT TAT-TTT TATTTT TATTTT TATTTT
2843645 TA-TTT TATTT
1 TATTTT TATTT
2843655 CTTTGTGCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 19 0.45
6 20 0.48
7 3 0.07
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:2843849 original size:9 final size:9
Alignment explanation
Indices: 2843800--2843848 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
2843790 TTAATCTTCT
2843800 TTTTATTTA
1 TTTTATTTA
* *
2843809 TTCTATTTC
1 TTTTATTTA
*
2843818 TTTTACTTTG
1 TTTTA-TTTA
2843828 TTTTATTTA
1 TTTTATTTA
2843837 TTTTA-TTA
1 TTTTATTTA
2843845 TTTT
1 TTTT
2843849 TTGTGTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
8 7 0.21
9 19 0.56
10 8 0.24
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTATTTA
Found at i:2843983 original size:4 final size:4
Alignment explanation
Indices: 2843974--2844011 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
2843964 ACACTCAATC
*
2843974 TTTA TTTA TTTA TTTA TTT- TTTA TTTA GTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
2844012 GGGTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2843998 original size:15 final size:15
Alignment explanation
Indices: 2843978--2844011 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2843968 TCAATCTTTA
*
2843978 TTTATTTATTTATTT
1 TTTATTTAGTTATTT
2843993 TTTATTTAGTTATTT
1 TTTATTTAGTTATTT
2844008 TTTA
1 TTTA
2844012 GGGTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTATTTAGTTATTT
Found at i:2844795 original size:2 final size:2
Alignment explanation
Indices: 2844788--2844826 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2844778 TCAAAGAATA
2844788 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 A
2844827 ATTCTCACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2846379 original size:2 final size:2
Alignment explanation
Indices: 2846372--2846399 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2846362 AGTGTGACAA
2846372 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2846400 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2847942 original size:2 final size:2
Alignment explanation
Indices: 2847935--2847964 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2847925 ACTCTTAGAT
2847935 TA TA TA TA TA -A 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 T
2847965 TCAGCATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2848839 original size:20 final size:20
Alignment explanation
Indices: 2848814--2848851 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2848804 CAAAATTGCA
2848814 TAGGGGTATCGGTACCCTAT
1 TAGGGGTATCGGTACCCTAT
2848834 TAGGGGTATCGGTACCCT
1 TAGGGGTATCGGTACCCT
2848852 CTGGGCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (20 bp):
TAGGGGTATCGGTACCCTAT
Found at i:2851031 original size:18 final size:17
Alignment explanation
Indices: 2851008--2851041 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2850998 ATTTTAACAA
2851008 TTTTGATCAAATCTTGTG
1 TTTTGATCAAAT-TTGTG
*
2851026 TTTTGATGAAATTTGT
1 TTTTGATCAAATTTGT
2851042 TGTAGAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (17 bp):
TTTTGATCAAATTTGTG
Done.