Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_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: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 22
Found at i:2732081 original size:20 final size:20
Alignment explanation
Indices: 2732054--2732142 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
2732044 ATGTGAAATT
2732054 TGTCCCGAAGAACCTATGTA
1 TGTCCCGAAGAACCTATGTA
*
2732074 TATCCCGAA-AGACCTATGTA
1 TGTCCCGAAGA-ACCTATGTA
* *
2732094 TGTCCCGAAGGACCTTTGTA
1 TGTCCCGAAGAACCTATGTA
* *
2732114 TGTCCCGAAGAACCTCTGTT
1 TGTCCCGAAGAACCTATGTA
2732134 TGTCCCGAA
1 TGTCCCGAA
2732143 TGACCTATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.02
20 59 0.98
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
TGTCCCGAAGAACCTATGTA
Found at i:2734125 original size:4 final size:4
Alignment explanation
Indices: 2734116--2734272 Score: 61
Period size: 4 Copynumber: 39.8 Consensus size: 4
2734106 AATTTAACAT
**
2734116 TTTA TTTA TTTA TTTA TTTA -TT- TTTA TTTTA TTTA TTTA TTCCC TTTGA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TT-TA TTT-A
* * **
2734165 TTTA TTTA -ATA TTT- TTCTA TTTT TTTAAA TTTA TTTTA TTT- TTCCC
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTT--A TTTA -TTTA TTTA TT-TA
*
2734211 TTGA TTTA TTTA TTTA TTT- TATTA -TTA -TTA -TTA -TTA TTATA TTT-
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TT-TA TTTA
2734255 TTATA TTT- TTT- TTTA TTT
1 TT-TA TTTA TTTA TTTA TTT
2734273 TTATCTAACA
Statistics
Matches: 121, Mismatches: 12, Indels: 40
0.70 0.07 0.23
Matches are distributed among these distances:
3 31 0.26
4 64 0.53
5 23 0.19
6 3 0.02
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:2734152 original size:9 final size:9
Alignment explanation
Indices: 2734114--2734273 Score: 72
Period size: 8 Copynumber: 17.6 Consensus size: 9
2734104 ATAATTTAAC
2734114 ATTTTATTT
1 ATTTTATTT
2734123 A-TTTATTT
1 ATTTTATTT
*
2734131 ATTTATTTTT
1 ATTT-TATTT
2734141 ATTTTATTT
1 ATTTTATTT
*
2734150 A-TTTATTCC
1 ATTTTATT-T
* *
2734159 CTTTGATTT
1 ATTTTATTT
2734168 ATTTAATATTT
1 ATTT--TATTT
*
2734179 -TTCTATTT
1 ATTTTATTT
2734187 -TTTTAAATTT
1 ATTTT--ATTT
2734197 ATTTTATTT
1 ATTTTATTT
2734206 -TTCCCTTGATTT
1 ATT---TT-ATTT
2734218 A-TTTATTT
1 ATTTTATTT
2734226 ATTTTA-TT
1 ATTTTATTT
2734234 ATTATTA-TT
1 ATT-TTATTT
*
2734243 ATTATTATAT
1 ATT-TTATTT
2734253 -TTTTATATT
1 ATTTTAT-TT
2734262 -TTTT-TTT
1 ATTTTATTT
2734269 ATTTT
1 ATTTT
2734274 TATCTAACAT
Statistics
Matches: 120, Mismatches: 12, Indels: 39
0.70 0.07 0.23
Matches are distributed among these distances:
7 2 0.02
8 43 0.36
9 40 0.33
10 20 0.17
11 10 0.08
12 5 0.04
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (9 bp):
ATTTTATTT
Found at i:2743131 original size:397 final size:397
Alignment explanation
Indices: 2742398--2743194 Score: 1558
Period size: 397 Copynumber: 2.0 Consensus size: 397
2742388 AGTGGTTATA
*
2742398 TTCGCGACTAACGTTGCAAGTTCGTCTGTATTTTTGTAGTGAAAATTGACGGTGGCATAATTGTT
1 TTCGCGACTAACATTGCAAGTTCGTCTGTATTTTTGTAGTGAAAATTGACGGTGGCATAATTGTT
* *
2742463 TTCTGGAATGTCTATCAAAATTTAACTCACCACTTCTGAGATCTGGTTTCAGGTCTATTTTATGA
66 TTCTGAAATGCCTATCAAAATTTAACTCACCACTTCTGAGATCTGGTTTCAGGTCTATTTTATGA
*
2742528 ACATTCAAGCCATCTTCTCATTTGTTTGTATATATTTTTACCTGCACTAGTAATTAAGTGCACTT
131 ACATTCAAGCCATCTTATCATTTGTTTGTATATATTTTTACCTGCACTAGTAATTAAGTGCACTT
2742593 TTAGGAATTTAAACAGATTTCAAGTATAGTTGTATGCCATCTGGTTAATTTGCTTTGCTCATAGC
196 TTAGGAATTTAAACAGATTTCAAGTATAGTTGTATGCCATCTGGTTAATTTGCTTTGCTCATAGC
2742658 TTCTGATCCTGAATGAATCAAGTTCGGTAAAAATATATCAATATAGAGATGCTATTGCATACTCT
261 TTCTGATCCTGAATGAATCAAGTTCGGTAAAAATATATCAATATAGAGATGCTATTGCATACTCT
2742723 GCTATGGTTTAGCACTTATTTAATTAGGTCATTTCTTCTTTTAGGCAAATCGTGTCAAAGCCATA
326 GCTATGGTTTAGCACTTATTTAATTAGGTCATTTCTTCTTTTAGGCAAATCGTGTCAAAGCCATA
2742788 GTGTTGC
391 GTGTTGC
2742795 TTCGCGACTAACATTGCAAGTTCGTCTGTATTTTTGTAGTGAAAATTGACGGTGGCATAATTGTT
1 TTCGCGACTAACATTGCAAGTTCGTCTGTATTTTTGTAGTGAAAATTGACGGTGGCATAATTGTT
2742860 TTCTGAAATGCCTATCAAAATTTAACTCACCACTTCTGAGATCTGGTTTCAGGTCTATTTTATGA
66 TTCTGAAATGCCTATCAAAATTTAACTCACCACTTCTGAGATCTGGTTTCAGGTCTATTTTATGA
2742925 ACATTCAAGCCATCTTATCATTTGTTTGTATATATTTTTACCTGCACTAGTAATTAAGTGCACTT
131 ACATTCAAGCCATCTTATCATTTGTTTGTATATATTTTTACCTGCACTAGTAATTAAGTGCACTT
2742990 TTAGGAATTTAAACAGATTTCAAGTATAGTTGTATGCCATCTGGTTAATTTGCTTTGCTCATAGC
196 TTAGGAATTTAAACAGATTTCAAGTATAGTTGTATGCCATCTGGTTAATTTGCTTTGCTCATAGC
2743055 TTCTGATCCTGAATGAATCAAGTTCGGTAAAAATATATCAATATAGAGATGCTATTGCATACTCT
261 TTCTGATCCTGAATGAATCAAGTTCGGTAAAAATATATCAATATAGAGATGCTATTGCATACTCT
2743120 GCTATGGTTTAGCACTTATTTAATTAGGTCATTTCTTCTTTTAGGCAAATCGTGTCAAAGCCATA
326 GCTATGGTTTAGCACTTATTTAATTAGGTCATTTCTTCTTTTAGGCAAATCGTGTCAAAGCCATA
2743185 GTGTTGC
391 GTGTTGC
2743192 TTC
1 TTC
2743195 TTGCATTAAC
Statistics
Matches: 396, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
397 396 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (397 bp):
TTCGCGACTAACATTGCAAGTTCGTCTGTATTTTTGTAGTGAAAATTGACGGTGGCATAATTGTT
TTCTGAAATGCCTATCAAAATTTAACTCACCACTTCTGAGATCTGGTTTCAGGTCTATTTTATGA
ACATTCAAGCCATCTTATCATTTGTTTGTATATATTTTTACCTGCACTAGTAATTAAGTGCACTT
TTAGGAATTTAAACAGATTTCAAGTATAGTTGTATGCCATCTGGTTAATTTGCTTTGCTCATAGC
TTCTGATCCTGAATGAATCAAGTTCGGTAAAAATATATCAATATAGAGATGCTATTGCATACTCT
GCTATGGTTTAGCACTTATTTAATTAGGTCATTTCTTCTTTTAGGCAAATCGTGTCAAAGCCATA
GTGTTGC
Found at i:2752902 original size:16 final size:18
Alignment explanation
Indices: 2752881--2752925 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
2752871 AACATTCCCA
2752881 GTAATCTTATTC-C-CTG
1 GTAATCTTATTCTCACTG
2752897 GTAATCTTACATTCTCACTG
1 GTAATCTT--ATTCTCACTG
2752917 GTAATCTTA
1 GTAATCTTA
2752926 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 5 0.20
19 1 0.04
20 11 0.44
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.42
Consensus pattern (18 bp):
GTAATCTTATTCTCACTG
Found at i:2754059 original size:72 final size:71
Alignment explanation
Indices: 2753867--2754107 Score: 209
Period size: 72 Copynumber: 3.3 Consensus size: 71
2753857 AGAAAGCAAT
* * * * *
2753867 TCAAAATTTTAAATATTGATACTTAATATATGATGATCAATACTTTTAAATATTTAAAAAGTTGA
1 TCAAAATTTAAAATATTAATACTT-ATAGATGATGATCGATACTTTTAAATATTGAAAAAGTTGA
*
2753932 -AGATAAGA
65 TA-A-AAAA
* * * ** * * *
2753940 TGAAAAGTTAAAACATCGATATTTATATTG-TAATGATCGATAATTTTAAATATTGAAAAAGTTG
1 TCAAAATTTAAAATATTAATACTTATA--GATGATGATCGATACTTTTAAATATTGAAAAAGTTG
2754004 ATAAAAAA
64 ATAAAAAA
* * * *
2754012 TCAAAATTTAAAATATTAATACTTATGCGATGATGATCGATACTTTTATATGTTGAAAAAATTGA
1 TCAAAATTTAAAATATTAATACTTAT-AGATGATGATCGATACTTTTAAATATTGAAAAAGTTGA
2754077 TAAAAATGA
65 TAAAAA--A
*
2754086 TCGATAA-TTAAAATATTAATAC
1 TC-AAAATTTAAAATATTAATAC
2754108 ATTTATTATG
Statistics
Matches: 135, Mismatches: 25, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
71 1 0.01
72 62 0.46
73 50 0.37
74 19 0.14
75 3 0.02
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.37
Consensus pattern (71 bp):
TCAAAATTTAAAATATTAATACTTATAGATGATGATCGATACTTTTAAATATTGAAAAAGTTGAT
AAAAAA
Found at i:2754771 original size:18 final size:18
Alignment explanation
Indices: 2754725--2754772 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
2754715 CAAGAAAAAT
* *
2754725 CAGATTGCCCAAGGGGTA
1 CAGATTCCCCCAGGGGTA
2754743 CAGATTCCCCCAGGGGTA
1 CAGATTCCCCCAGGGGTA
*
2754761 CCGATTCCCCCA
1 CAGATTCCCCCA
2754773 TGTCTAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (18 bp):
CAGATTCCCCCAGGGGTA
Found at i:2755159 original size:34 final size:32
Alignment explanation
Indices: 2755120--2755189 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2755110 TTTTGTAAAG
* *
2755120 GGGAAAGGTTATAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
*
2755154 GGGAAAGGTTATAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
2755186 GGGA
1 GGGA
2755190 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:2756074 original size:187 final size:186
Alignment explanation
Indices: 2755750--2756197 Score: 562
Period size: 187 Copynumber: 2.4 Consensus size: 186
2755740 TTAGCGACCA
* * * ** * *
2755750 ATAACATTCTTGGGCTCAACCTGATTTTTTATAGATATTTATAACATTTTAGCTTTTAATTTATT
1 ATAACATTCTTGAGCGCAATCAAATTTCTTATAGATATTTATAACATTTTAGCTTTTAACTTATT
** * * * * *
2755815 TTGTTCCCGTGAGAATGTTTAAGGCACTATCAGCTTAAACTCTAGTAATATTTTAGACAGAATCA
66 TTGTTATCGTGAAAATGTCTAAGGCACCATCAGCTTAAACTCTAGTAACATTTTAGACAGAACCA
* * *
2755880 ATTTTATTATAAAGAAAATTAACATTTCAGGTCGCAAACTACTTTCTTAGTGAAAC
131 ATTTTATTACAAAGAAAATTAACATTTCAGATCGCAAACTACTTTCTTAATGAAAC
* * *
2755936 ATAACATTCTTG-GATGCAATCAAATTTCTTATATATATTCATAACATTTTCAGCTTTTAACTTA
1 ATAACATTCTTGAG-CGCAATCAAATTTCTTATAGATATTTATAACATTTT-AGCTTTTAACTTA
* *
2756000 TTTTTGTTATCGTGAAAATGTCTAA-GCCCCATCAGCTTAAACTCTGGTAACATTTTA-A-ATGC
64 -TTTTGTTATCGTGAAAATGTCTAAGGCACCATCAGCTTAAACTCTAGTAACATTTTAGACA-G-
* * **
2756062 AACCAATTTTATTACAAAGAAAATTAACATTTCAGATCGTAATCTACTTTCTTAATGAGCC
126 AACCAATTTTATTACAAAGAAAATTAACATTTCAGATCGCAAACTACTTTCTTAATGAAAC
* *
2756123 ATAACATTCTTGAGCGCAATCAAATTTCTTTTAGATATTTATAATATTTTTAGCTTTTAACTTAT
1 ATAACATTCTTGAGCGCAATCAAATTTCTTATAGATATTTATAACA-TTTTAGCTTTTAACTTAT
2756188 TTTGTTATCG
65 TTTGTTATCG
2756198 ATACTTACAT
Statistics
Matches: 225, Mismatches: 30, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
185 2 0.01
186 53 0.24
187 145 0.64
188 25 0.11
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (186 bp):
ATAACATTCTTGAGCGCAATCAAATTTCTTATAGATATTTATAACATTTTAGCTTTTAACTTATT
TTGTTATCGTGAAAATGTCTAAGGCACCATCAGCTTAAACTCTAGTAACATTTTAGACAGAACCA
ATTTTATTACAAAGAAAATTAACATTTCAGATCGCAAACTACTTTCTTAATGAAAC
Found at i:2757092 original size:21 final size:23
Alignment explanation
Indices: 2757046--2757093 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2757036 ATTAAATACA
*
2757046 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
2757069 ATAATATAATATGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
2757092 AT
1 AT
2757094 TTACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:2764679 original size:6 final size:6
Alignment explanation
Indices: 2764643--2764693 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
2764633 CATCTAAAAC
* * * * *
2764643 TCAGCA CCAGCA CCAGCA CCAGCA TCAGCA TCAGCA TCAACA TCAACA
1 TCAGCA TCAGCA TCAGCA TCAGCA TCAGCA TCAGCA TCAGCA TCAGCA
2764691 TCA
1 TCA
2764694 ACATGCACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.37, C:0.39, G:0.12, T:0.12
Consensus pattern (6 bp):
TCAGCA
Found at i:2764686 original size:12 final size:12
Alignment explanation
Indices: 2764662--2764697 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2764652 GCACCAGCAC
*
2764662 CAGCATCAGCAT
1 CAGCATCAACAT
2764674 CAGCATCAACAT
1 CAGCATCAACAT
*
2764686 CAACATCAACAT
1 CAGCATCAACAT
2764698 GCACTAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (12 bp):
CAGCATCAACAT
Found at i:2765683 original size:2 final size:2
Alignment explanation
Indices: 2765676--2765708 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2765666 TAATTGAAAT
2765676 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 T
2765709 TGTTTTAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2765859 original size:24 final size:25
Alignment explanation
Indices: 2765832--2765882 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
2765822 AATTCAAAAT
2765832 AATTTTATAAATTT-TTAAT-ATTTA
1 AATTTTAT-AATTTATTAATAATTTA
2765856 AATTTTATAATTTATTAATAATTTA
1 AATTTTATAATTTATTAATAATTTA
2765881 AA
1 AA
2765883 GAAGTTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.20
24 13 0.52
25 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AATTTTATAATTTATTAATAATTTA
Found at i:2767391 original size:38 final size:38
Alignment explanation
Indices: 2767343--2767425 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
2767333 CACTGAATAT
*
2767343 TTGTCCCGAAGGACCACTACGCCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTACGCCCCGAAGGACCACTGA
* * * *
2767381 TTGTTCCGAAGAACCACTATGTCTCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTACGCCCCGAAGGACCACTGA
*
2767419 TTATCCC
1 TTGTCCC
2767426 TCGACTCTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTACGCCCCGAAGGACCACTGA
Found at i:2767414 original size:18 final size:18
Alignment explanation
Indices: 2767344--2767416 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
2767334 ACTGAATATT
2767344 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
2767362 CGCCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
2767381 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
2767400 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2767417 GATTATCCCT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 29 0.66
19 2 0.05
20 13 0.30
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2768004 original size:24 final size:20
Alignment explanation
Indices: 2767949--2768006 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 20
2767939 AATGAAGGTA
2767949 TGCATCGATGCACTCTACAG
1 TGCATCGATGCACTCTACAG
* *
2767969 TGTATCGATGCATTTCTTACCAGG
1 TGCATCGATGCA-CTC-TA-CA-G
2767993 TGCATCGATGCACT
1 TGCATCGATGCACT
2768007 ACCTGTGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 11 0.37
21 2 0.07
22 2 0.07
23 3 0.10
24 12 0.40
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCACTCTACAG
Found at i:2772099 original size:18 final size:20
Alignment explanation
Indices: 2772069--2772114 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
2772059 ATAATATATA
*
2772069 TTAAAAAGAAA-ACACAAA-T
1 TTAAAAATAAACACA-AAACT
*
2772088 TTAAAAATAAACCCAAAACT
1 TTAAAAATAAACACAAAACT
2772108 TTAAAAA
1 TTAAAAA
2772115 CCTTCATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.65, C:0.13, G:0.02, T:0.20
Consensus pattern (20 bp):
TTAAAAATAAACACAAAACT
Found at i:2772819 original size:29 final size:30
Alignment explanation
Indices: 2772786--2772843 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
2772776 GGCCTTTTTT
*
2772786 CAGTTTAGTGTCTAATATTT-ATTTCGTTC
1 CAGTTTAGTGTCTAACATTTCATTTCGTTC
* * *
2772815 CAGTTTGGTTTCTAACGTTTCATTTCGTT
1 CAGTTTAGTGTCTAACATTTCATTTCGTT
2772844 ACTCATTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.52
Consensus pattern (30 bp):
CAGTTTAGTGTCTAACATTTCATTTCGTTC
Found at i:2783997 original size:14 final size:14
Alignment explanation
Indices: 2783978--2784013 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2783968 AGTTTAAGAA
2783978 ATTTGAGTCGAATT
1 ATTTGAGTCGAATT
*
2783992 ATTTGAGTCGAGTT
1 ATTTGAGTCGAATT
*
2784006 ATTCGAGT
1 ATTTGAGT
2784014 TTTTATACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (14 bp):
ATTTGAGTCGAATT
Found at i:2784839 original size:155 final size:156
Alignment explanation
Indices: 2784354--2784884 Score: 648
Period size: 156 Copynumber: 3.4 Consensus size: 156
2784344 CAAATGAAGT
* * * * * * * * * *
2784354 TACATATGTATTCTATTGTGGTATATGGA-CATGTGGTTTAAATTTGGTAAATAACATACTCAAA
1 TACACATGTATTCTACTATGGTTTA-GGAGCATGTGGCTCAAACTTGGTAAA-AAAAGACTTAAA
*
2784418 ATAAATGACAAATTGAA-AGAATAAGGAGATTATGAAAAATTAA-GACTAAATTGAAAAATAAAA
64 ATAAATGACGAATTGAAGA-AATAAGGAGATTATGAAAAATTAAGGACTAAATTGAAAAATAAAA
2784481 AAATTGTTATCAAAAAGAGGAATTGAAAG
128 AAATTGTTATCAAAAAGAGGAATTGAAAG
* * * * * *
2784510 TACACATGTATTCTACTATGATTTAAGAGCATGTGGCTCAAATTTGATTAAAAAAATACCTAAAA
1 TACACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAACTTG-GTAAAAAAAGACTTAAAA
* * *
2784575 TAAATGACGAAATGAAGAAATAAAGAGATTAT-AAAAATTAAAGGACTAAATTGGAAAATAAAAA
65 TAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATT-AAGGACTAAATTGAAAAATAAAAA
*
2784639 AATTGTTA-CAAAAGGAGGAATTGAAAG
129 AATTGTTATCAAAAAGAGGAATTGAAAG
*
2784666 TACACATGTATT-TGACTATGGTTTAGGAGCATGTGACTCAAA-TTGGTAAAAAAAGACTTAAAA
1 TACACATGTATTCT-ACTATGGTTTAGGAGCATGTGGCTCAAACTTGGTAAAAAAAGACTTAAAA
*
2784729 TAAATGATGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAAT-AAAA
65 TAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATT-AAGGACTAAATTGAAAAATAAAAA
* *
2784793 ACTTGTTATCAAAAAGAGGAATTGAGAG
129 AATTGTTATCAAAAAGAGGAATTGAAAG
* ** * * * *
2784821 TAGACATACATTCTACTATAGTTTAGGAGCAT-TGGTTCAAACTTGATAAAAATAGACTTAAAAT
1 TACACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAACTTGGTAAAAAAAGACTTAAAAT
2784885 GAAGGATGGA
Statistics
Matches: 326, Mismatches: 39, Indels: 21
0.84 0.10 0.05
Matches are distributed among these distances:
154 62 0.19
155 101 0.31
156 130 0.40
157 33 0.10
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (156 bp):
TACACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAACTTGGTAAAAAAAGACTTAAAAT
AAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTAAGGACTAAATTGAAAAATAAAAAAA
TTGTTATCAAAAAGAGGAATTGAAAG
Found at i:2784902 original size:155 final size:154
Alignment explanation
Indices: 2784415--2784906 Score: 638
Period size: 155 Copynumber: 3.2 Consensus size: 154
2784405 TAACATACTC
**
2784415 AAAATAAATGACAAATTGAA-AGAATAAGGAGATTATGAAAAATTAA-GACTAAATTGAAAAATA
1 AAAATAAATGATGAATTGAAGA-AATAAGGAGATTATGAAAAATTAAGGACTAAATTGAAAAATA
*
2784478 AAAAAATTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATGATTTAAGAGCATG
65 AAAAAATTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG-TTTAGGAGCATG
* *
2784543 TGGCTCAAATTTGATTAAAAAAATACCT
129 TGGCTCAAA-TTGA-TAAAAAAAGACTT
* * * *
2784571 AAAATAAATGACGAAATGAAGAAATAAAGAGATTAT-AAAAATTAAAGGACTAAATTGGAAAATA
1 AAAATAAATGATGAATTGAAGAAATAAGGAGATTATGAAAAATT-AAGGACTAAATTGAAAAATA
*
2784635 AAAAAATTGTTA-CAAAAGGAGGAATTGAAAGTACACATGTATT-TGACTATGGTTTAGGAGCAT
65 AAAAAATTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCT-ACTAT-GTTTAGGAGCAT
* *
2784698 GTGACTCAAATTGGTAAAAAAAGACTT
128 GTGGCTCAAATTGATAAAAAAAGACTT
2784725 AAAATAAATGATGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAAT-
1 AAAATAAATGATGAATTGAAGAAATAAGGAGATTATGAAAAATT-AAGGACTAAATTGAAAAATA
* * * **
2784789 AAAAACTTGTTATCAAAAAGAGGAATTGAGAGTAGACATACATTCTACTATAGTTTAGGAGCAT-
65 AAAAAATTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTAT-GTTTAGGAGCATG
* *
2784853 TGGTTCAAACTTGATAAAAATAGACTT
129 TGGCTCAAA-TTGATAAAAAAAGACTT
* * * *
2784880 AAAATGAAGGATGGATTTAAGAAATAA
1 AAAATAAATGATGAATTGAAGAAATAA
2784907 TGAAATCAGT
Statistics
Matches: 297, Mismatches: 30, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
154 62 0.21
155 117 0.39
156 88 0.30
157 30 0.10
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (154 bp):
AAAATAAATGATGAATTGAAGAAATAAGGAGATTATGAAAAATTAAGGACTAAATTGAAAAATAA
AAAAATTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATGTTTAGGAGCATGTG
GCTCAAATTGATAAAAAAAGACTT
Found at i:2785473 original size:21 final size:22
Alignment explanation
Indices: 2785443--2785576 Score: 138
Period size: 21 Copynumber: 6.2 Consensus size: 22
2785433 GATTTACATA
* *
2785443 TTCGCATTGCGA-TAGTCCAAG
1 TTCGCGTTGCGATTATTCCAAG
2785464 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAG
*
2785487 TT--CGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAG
2785508 TT--CGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAG
*
2785529 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAG
2785552 TT--CGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAG
2785573 TTCG
1 TTCG
2785577 TTGCGGTAGT
Statistics
Matches: 101, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
21 71 0.70
23 30 0.30
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
TTCGCGTTGCGATTATTCCAAG
Found at i:2785530 original size:65 final size:65
Alignment explanation
Indices: 2785458--2785581 Score: 230
Period size: 65 Copynumber: 1.9 Consensus size: 65
2785448 ATTGCGATAG
*
2785458 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
*
2785523 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTTCGTTGCG
1 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCG
2785582 GTAGTCCAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (65 bp):
TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
Found at i:2785539 original size:44 final size:44
Alignment explanation
Indices: 2785468--2785576 Score: 204
Period size: 44 Copynumber: 2.5 Consensus size: 44
2785458 TCCAAGTTCG
2785468 CGTTGCGATTTATTCCAAGTT--CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATT
2785510 CGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATT
2785554 CGTTGCGATTTATTCCAAGTTCG
1 CGTTGCGATTTATTCCAAGTTCG
2785577 TTGCGGTAGT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
42 21 0.32
44 44 0.68
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.41
Consensus pattern (44 bp):
CGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:2785577 original size:21 final size:21
Alignment explanation
Indices: 2785458--2785581 Score: 194
Period size: 21 Copynumber: 5.7 Consensus size: 21
2785448 ATTGCGATAG
2785458 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTAT
2785481 TCCAAGTTCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATTTAT
*
2785502 TCCAAATTCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATTTAT
2785523 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTAT
*
2785546 TCCAAATTCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATTTAT
2785567 TCCAAGTTCGTTGCG
1 TCCAAGTTCGTTGCG
2785582 GTAGTCCAAA
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
21 67 0.71
23 28 0.29
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (21 bp):
TCCAAGTTCGTTGCGATTTAT
Found at i:2785684 original size:6 final size:6
Alignment explanation
Indices: 2785673--2785708 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
2785663 GCAGACACAT
2785673 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
2785709 CGAGACGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:2786389 original size:21 final size:21
Alignment explanation
Indices: 2786364--2786427 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
2786354 AATATGTAAA
2786364 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
2786385 TCGCATTGCG--A-TCCAAGT
1 TCGCATTGCGATAGTCGAAGT
2786403 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
2786424 TCGC
1 TCGC
2786428 GTTACGAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 16 0.42
19 1 0.03
20 1 0.03
21 20 0.53
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:2788546 original size:20 final size:20
Alignment explanation
Indices: 2788521--2788558 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2788511 TTTGGTTCAC
2788521 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
2788541 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
2788559 GGAATAGGAT
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:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:2790131 original size:27 final size:26
Alignment explanation
Indices: 2790100--2790153 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
2790090 TGTTATAGAT
* *
2790100 TAAAAAAATCTATCATTTAAATTTATA
1 TAAAAAAATATAACATTTAAA-TTATA
2790127 TAAAAAAATATAACATTTAAATTATA
1 TAAAAAAATATAACATTTAAATTATA
2790153 T
1 T
2790154 TTACACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (26 bp):
TAAAAAAATATAACATTTAAATTATA
Found at i:2790362 original size:2 final size:2
Alignment explanation
Indices: 2790357--2790389 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2790347 AAAAACAAAG
2790357 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 A
2790390 AAAGATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2797786 original size:23 final size:21
Alignment explanation
Indices: 2797741--2797786 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
2797731 TATTTTTAAC
**
2797741 AAAAAAAATTATTTAAAGTAT
1 AAAAAAAATTATTTAAAAAAT
2797762 AAAAAAAAGTTAATTTAAAAAAT
1 AAAAAAAA-TT-ATTTAAAAAAT
2797785 AA
1 AA
2797787 TTTAGTCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 2 0.10
23 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAAAAATTATTTAAAAAAT
Found at i:2809095 original size:2 final size:2
Alignment explanation
Indices: 2809088--2809125 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2809078 TTCTCACTTC
2809088 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2809126 GTTGTTGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2823228 original size:17 final size:17
Alignment explanation
Indices: 2823206--2823243 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2823196 AGATTACTAA
2823206 AATTATTTTATATGCAG
1 AATTATTTTATATGCAG
*
2823223 AATTATTTTATATGCAT
1 AATTATTTTATATGCAG
2823240 AATT
1 AATT
2823244 TTATAATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (17 bp):
AATTATTTTATATGCAG
Found at i:2824180 original size:3 final size:3
Alignment explanation
Indices: 2824172--2824211 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2824162 ACCCTAAAAG
2824172 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2824212 GATGATCATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2833315 original size:54 final size:53
Alignment explanation
Indices: 2833150--2833360 Score: 181
Period size: 54 Copynumber: 3.9 Consensus size: 53
2833140 TTGAATTAAC
* * * * **
2833150 GATTGAGCACCTCTGTGCTTCAATCGACAAACTGACACCTCTGTGCAGTTAAAAAT
1 GATTGAACACCTCTGTGCTTCAATCTAGAATCTGACACCTCTGTGC--TT-TGAAT
* * * * *
2833206 GATTGAGCACCTCTGTGCTT-TATCTAGAATTTGGCACATCTGTGCTTTGTAAT
1 GATTGAACACCTCTGTGCTTCAATCTAGAATCTGACACCTCTGTGCTTTG-AAT
* *
2833259 GATTGAACACCTGTGTGCTTCAATCTAGAATCTGCCACCTCTGTGCTTTGAGAT
1 GATTGAACACCTCTGTGCTTCAATCTAGAATCTGACACCTCTGTGCTTTGA-AT
* * * * * ** *
2833313 GATTAAACACCTATGTGTTTCAATATAGGATCTGTTACCTCCGTGCTT
1 GATTGAACACCTCTGTGCTTCAATCTAGAATCTGACACCTCTGTGCTT
2833361 CAATCTAGGA
Statistics
Matches: 129, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
53 24 0.19
54 67 0.52
55 18 0.14
56 20 0.16
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (53 bp):
GATTGAACACCTCTGTGCTTCAATCTAGAATCTGACACCTCTGTGCTTTGAAT
Found at i:2833386 original size:28 final size:28
Alignment explanation
Indices: 2833324--2833388 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
2833314 ATTAAACACC
* *
2833324 TATGTGTTTCAATATAGGATCTGTTACC
1 TATGTGCTTCAATATAGGATCTGTTACA
** *
2833352 TCCGTGCTTCAATCTAGGATCTAG-TACA
1 TATGTGCTTCAATATAGGATCT-GTTACA
2833380 TATGTGCTT
1 TATGTGCTT
2833389 TAAAATGATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (28 bp):
TATGTGCTTCAATATAGGATCTGTTACA
Found at i:2834779 original size:59 final size:60
Alignment explanation
Indices: 2834658--2834802 Score: 168
Period size: 59 Copynumber: 2.4 Consensus size: 60
2834648 AGTCAAATGG
* * * *
2834658 TCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAACAACAACCTATAGTTAAGGGA
1 TCATTTTGTAACTTTTAATAGTCGATAGACTCAACAAAACAACAACCTATAATTAAGGGA
* ** * *
2834718 TCATTTTGTAACTTTTAATAGTCGATA-ACTCAACAAAGCTGCATCCTATAATT-AGATGA
1 TCATTTTGTAACTTTTAATAGTCGATAGACTCAACAAAACAACAACCTATAATTAAG-GGA
* *
2834777 TCACTTTGTAATTTTTAATAGTCGAT
1 TCATTTTGTAACTTTTAATAGTCGAT
2834803 TGCTTAAAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
58 2 0.03
59 47 0.64
60 24 0.33
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (60 bp):
TCATTTTGTAACTTTTAATAGTCGATAGACTCAACAAAACAACAACCTATAATTAAGGGA
Found at i:2836217 original size:61 final size:61
Alignment explanation
Indices: 2836114--2836269 Score: 258
Period size: 61 Copynumber: 2.6 Consensus size: 61
2836104 CGAACGAGAG
*
2836114 AACAACAACAATGAGTAAGCAATCAAGGCTCGGCAATTACCATGCACACCAGATCATTTTA
1 AACAACAGCAATGAGTAAGCAATCAAGGCTCGGCAATTACCATGCACACCAGATCATTTTA
* *
2836175 AACAGCAGCAATGAGCAAGCAATCAAGGCTCGGCAATTACCATGCACACCAGATCATTTTA
1 AACAACAGCAATGAGTAAGCAATCAAGGCTCGGCAATTACCATGCACACCAGATCATTTTA
* * *
2836236 AACAACAGCAACGAGTACGCAATCGAGGCTCGGC
1 AACAACAGCAATGAGTAAGCAATCAAGGCTCGGC
2836270 TAAATGAGCA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 87 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (61 bp):
AACAACAGCAATGAGTAAGCAATCAAGGCTCGGCAATTACCATGCACACCAGATCATTTTA
Found at i:2841846 original size:38 final size:39
Alignment explanation
Indices: 2841804--2841879 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
2841794 ATTTATATAA
2841804 AAAAATATGAT-AATTATATAATATTTTAAGTTG-TAATT
1 AAAAATATGATCAA-TATATAATATTTTAAGTTGATAATT
* *
2841842 AAAAATATTATCAATATATAATATTTTAGGTTGATAAT
1 AAAAATATGATCAATATATAATATTTTAAGTTGATAAT
2841880 GAATATCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 28 0.82
39 6 0.18
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.43
Consensus pattern (39 bp):
AAAAATATGATCAATATATAATATTTTAAGTTGATAATT
Found at i:2842478 original size:2 final size:2
Alignment explanation
Indices: 2842473--2842516 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
2842463 ATCCTTGATA
* *
2842473 AT AT AT AT AT AT AT AT AT AC AC AT -T 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
2842514 AT A
1 AT A
2842517 AATTTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2843281 original size:152 final size:153
Alignment explanation
Indices: 2843064--2843369 Score: 605
Period size: 152 Copynumber: 2.0 Consensus size: 153
2843054 ATGAAGAAAA
2843064 TATAATAGAAAAAACAAGGGTTTACTCTCTTAATTATTTAGGGTTTTAGAATCAGCATCAATTGT
1 TATAATAGAAAAAACAAGGGTTTACTCTCTTAATTATTTAGGGTTTTAGAATCAGCATCAATTGT
2843129 AATTTAAGATAGATATTACTATTGTGTTATAAATATTTTCAAAATTTAAGTTTATCTGACGGTCA
66 AATTTAAGATAGATATTACTATTGTGTTATAAATATTTTCAAAATTTAAGTTTATCTGACGGTCA
2843194 AATGATTTTCATGTT-AAAGAAT
131 AATGATTTTCATGTTAAAAGAAT
2843216 TATAATAGAAAAAACAAGGGTTTACTCTCTTAATTATTTAGGGTTTTAGAATCAGCATCAATTGT
1 TATAATAGAAAAAACAAGGGTTTACTCTCTTAATTATTTAGGGTTTTAGAATCAGCATCAATTGT
2843281 AATTTAAGATAGATATTACTATTGTGTTATAAATATTTTCAAAATTTAAGTTTATCTGACGGTCA
66 AATTTAAGATAGATATTACTATTGTGTTATAAATATTTTCAAAATTTAAGTTTATCTGACGGTCA
2843346 AATGATTTTCATGTTAAAAGAAT
131 AATGATTTTCATGTTAAAAGAAT
2843369 T
1 T
2843370 TAAGTTTGAT
Statistics
Matches: 153, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 145 0.95
153 8 0.05
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (153 bp):
TATAATAGAAAAAACAAGGGTTTACTCTCTTAATTATTTAGGGTTTTAGAATCAGCATCAATTGT
AATTTAAGATAGATATTACTATTGTGTTATAAATATTTTCAAAATTTAAGTTTATCTGACGGTCA
AATGATTTTCATGTTAAAAGAAT
Found at i:2846897 original size:26 final size:26
Alignment explanation
Indices: 2846868--2846923 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
2846858 TGTTGCCATT
2846868 TTTAGCAAAACATAAGTTGTTAAATA
1 TTTAGCAAAACATAAGTTGTTAAATA
2846894 TTTAGCAAAACATAAGTTGTTAAATA
1 TTTAGCAAAACATAAGTTGTTAAATA
2846920 TTTA
1 TTTA
2846924 TACGCTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (26 bp):
TTTAGCAAAACATAAGTTGTTAAATA
Found at i:2848335 original size:24 final size:23
Alignment explanation
Indices: 2848299--2848345 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2848289 CAATCCCATT
* *
2848299 AACCAAAACAAATTACTAAATAA
1 AACCAAAACAAATAAATAAATAA
*
2848322 AACCAAAAATAAATAAATAAATAA
1 AACC-AAAACAAATAAATAAATAA
2848346 CTTAAAGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (23 bp):
AACCAAAACAAATAAATAAATAA
Found at i:2848387 original size:14 final size:14
Alignment explanation
Indices: 2848368--2848394 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2848358 AAGACCGGGA
2848368 AGAGGAAGAAAAGG
1 AGAGGAAGAAAAGG
2848382 AGAGGAAGAAAAG
1 AGAGGAAGAAAAG
2848395 AAGCTGCTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAGGAAGAAAAGG
Found at i:2854079 original size:165 final size:165
Alignment explanation
Indices: 2853807--2854137 Score: 626
Period size: 165 Copynumber: 2.0 Consensus size: 165
2853797 TTGAAATTTG
*
2853807 TCCCTTGTGTTACTTGACACAACTTCTGCTAAGTGTAGAATGAATGGTTTTGAGGCTACGCTGTT
1 TCCCTTGTGTTACTTGACACAACTTCTGCTAAGTGCAGAATGAATGGTTTTGAGGCTACGCTGTT
2853872 CGATTCCGCAGGTTTGGGTGAGCAACATAAAAATTAAATATATTGTTGAGCTCGTTAGCCTATAC
66 CGATTCCGCAGGTTTGGGTGAGCAACATAAAAATTAAATATATTGTTGAGCTCGTTAGCCTATAC
2853937 CTCATGGATATGTTTTAGTTGTGTGATATAATGCC
131 CTCATGGATATGTTTTAGTTGTGTGATATAATGCC
* *
2853972 TCCCTTGTGTTACTTGACACAACTTCTGCTAAGTGCAGAATGAATTGTTTTGAGGCTACGTTGTT
1 TCCCTTGTGTTACTTGACACAACTTCTGCTAAGTGCAGAATGAATGGTTTTGAGGCTACGCTGTT
*
2854037 CGATTCCGCAGGTTTGGGTGAGCAACATAAAAATTAAATATATTGTTGAGCTCGTTATCCTATAC
66 CGATTCCGCAGGTTTGGGTGAGCAACATAAAAATTAAATATATTGTTGAGCTCGTTAGCCTATAC
2854102 CTCATGGATATGTTTTAGTTGTGTGATATAATGCC
131 CTCATGGATATGTTTTAGTTGTGTGATATAATGCC
2854137 T
1 T
2854138 TTCAACAGTT
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 162 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (165 bp):
TCCCTTGTGTTACTTGACACAACTTCTGCTAAGTGCAGAATGAATGGTTTTGAGGCTACGCTGTT
CGATTCCGCAGGTTTGGGTGAGCAACATAAAAATTAAATATATTGTTGAGCTCGTTAGCCTATAC
CTCATGGATATGTTTTAGTTGTGTGATATAATGCC
Found at i:2861388 original size:28 final size:28
Alignment explanation
Indices: 2861356--2861411 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2861346 AATCACCCGT
2861356 CATGTGGTCACTTGTGCCTGAATCAACA
1 CATGTGGTCACTTGTGCCTGAATCAACA
2861384 CATGTGGTCACTTGTGCCTGAATCAACA
1 CATGTGGTCACTTGTGCCTGAATCAACA
2861412 ATCCAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (28 bp):
CATGTGGTCACTTGTGCCTGAATCAACA
Found at i:2862375 original size:22 final size:22
Alignment explanation
Indices: 2862347--2862393 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2862337 CAATCGATGA
2862347 CATGTGATGGAAGAGGAGCCTG
1 CATGTGATGGAAGAGGAGCCTG
2862369 CATGTGATGGAAGAGGAGCCTG
1 CATGTGATGGAAGAGGAGCCTG
2862391 CAT
1 CAT
2862394 CTGTGGTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.19
Consensus pattern (22 bp):
CATGTGATGGAAGAGGAGCCTG
Found at i:2862604 original size:17 final size:17
Alignment explanation
Indices: 2862584--2862638 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
2862574 ACTGTGTGAA
*
2862584 GAGCGACGCTGTGACAG
1 GAGCGACGCTGCGACAG
** * *
2862601 GAGCGGTGCTGCGAGAA
1 GAGCGACGCTGCGACAG
*
2862618 GAGCAACGCTGCGACAG
1 GAGCGACGCTGCGACAG
2862635 GAGC
1 GAGC
2862639 AGCGCTACAA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.25, C:0.24, G:0.42, T:0.09
Consensus pattern (17 bp):
GAGCGACGCTGCGACAG
Found at i:2862652 original size:34 final size:34
Alignment explanation
Indices: 2862581--2862671 Score: 101
Period size: 34 Copynumber: 2.7 Consensus size: 34
2862571 AGTACTGTGT
* * * * * *
2862581 GAAGAGCGACGCTGTGACAGGAGCGGTGCTGCGA
1 GAAGAGCAACGCTGCGACAGGAGCAGCGCTACAA
2862615 GAAGAGCAACGCTGCGACAGGAGCAGCGCTACAA
1 GAAGAGCAACGCTGCGACAGGAGCAGCGCTACAA
* * *
2862649 GAAGAGTAACGCTACGACGGGAG
1 GAAGAGCAACGCTGCGACAGGAG
2862672 TGGCGCAGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.31, C:0.22, G:0.38, T:0.09
Consensus pattern (34 bp):
GAAGAGCAACGCTGCGACAGGAGCAGCGCTACAA
Found at i:2864897 original size:17 final size:17
Alignment explanation
Indices: 2864875--2864918 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
2864865 AACAGGAAGA
*
2864875 TGTTTATGTTTTGCCTT
1 TGTTTATGTTTGGCCTT
*
2864892 TGTTTATGGTTGGCCTT
1 TGTTTATGTTTGGCCTT
2864909 TGTCTTATGT
1 TGT-TTATGT
2864919 GCACTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.07, C:0.11, G:0.23, T:0.59
Consensus pattern (17 bp):
TGTTTATGTTTGGCCTT
Found at i:2867050 original size:23 final size:25
Alignment explanation
Indices: 2867006--2867051 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2866996 ATCAAGAATT
*
2867006 TATTCAATTTAAATTTAGTTTTAAA
1 TATTCAATTGAAATTTAGTTTTAAA
2867031 TATT-AATTGAAA-TTAGTTTTA
1 TATTCAATTGAAATTTAGTTTTA
2867052 GTTTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (25 bp):
TATTCAATTGAAATTTAGTTTTAAA
Found at i:2875388 original size:12 final size:12
Alignment explanation
Indices: 2875371--2875403 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2875361 ACCTACTCAG
2875371 GATGATGACGAT
1 GATGATGACGAT
2875383 GATGATGGA-GAT
1 GATGAT-GACGAT
2875395 GATGATGAC
1 GATGATGAC
2875404 AACGAGGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.11
12 15 0.79
13 2 0.11
ACGTcount: A:0.33, C:0.06, G:0.36, T:0.24
Consensus pattern (12 bp):
GATGATGACGAT
Found at i:2875662 original size:35 final size:33
Alignment explanation
Indices: 2875623--2875709 Score: 86
Period size: 35 Copynumber: 2.5 Consensus size: 33
2875613 GTATTTCAGT
2875623 TAATTTTGTTGA-TTACCATTTAATATCAGTTATTG
1 TAATTTTGTTGATTTACCATTTAATA-C--TTATTG
* *
2875658 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTG-T-TGATTTACCATTTAATACTTATTG
*
2875693 TAAGTTTGTTGTATTTA
1 TAATTTTGTTG-ATTTA
2875710 AAATTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
33 1 0.02
34 6 0.14
35 19 0.44
36 1 0.02
37 3 0.07
38 13 0.30
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (33 bp):
TAATTTTGTTGATTTACCATTTAATACTTATTG
Found at i:2880117 original size:21 final size:21
Alignment explanation
Indices: 2880093--2880238 Score: 129
Period size: 21 Copynumber: 7.1 Consensus size: 21
2880083 GCAAATTCGC
2880093 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
2880114 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
*
2880134 -TTTCTATTTCGCGTTGCGATA
1 GTTGC-ATTTCGCGTTGCGATA
* **
2880155 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
2880175 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
2880196 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
2880216 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
2880237 GT
1 GT
2880239 CTACAGTTGT
Statistics
Matches: 93, Mismatches: 27, Indels: 10
0.72 0.21 0.08
Matches are distributed among these distances:
19 2 0.02
20 43 0.46
21 46 0.49
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:2880125 original size:41 final size:39
Alignment explanation
Indices: 2880097--2880238 Score: 221
Period size: 41 Copynumber: 3.5 Consensus size: 39
2880087 ATTCGCGTTG
2880097 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG--TTTC
*
2880138 TATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG--TTTC
2880179 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG--TTTC
2880220 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
2880239 CTACAGTTGT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (39 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGTTTC
Found at i:2880147 original size:20 final size:20
Alignment explanation
Indices: 2880098--2880235 Score: 114
Period size: 20 Copynumber: 6.8 Consensus size: 20
2880088 TTCGCGTTGC
* *
2880098 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
** *
2880119 AAATCGCGTTGCGATTTTCT
1 ATTTCGCGTTGCGATTTTCA
* *
2880139 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
** *
2880160 AAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCA
* *
2880180 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
** *
2880201 AAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCA
2880221 ATTTCGCGTTGCGAT
1 ATTTCGCGTTGCGAT
2880236 AGTCTACAGT
Statistics
Matches: 88, Mismatches: 27, Indels: 5
0.73 0.22 0.04
Matches are distributed among these distances:
20 45 0.51
21 43 0.49
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
ATTTCGCGTTGCGATTTTCA
Found at i:2880905 original size:28 final size:28
Alignment explanation
Indices: 2880865--2880943 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
2880855 TCTCGTCTTG
2880865 GGTCGGGTCGGGTCGGGGTCGGGGTCGT
1 GGTCGGGTCGGGTCGGGGTCGGGGTCGT
*
2880893 GGTCGGGTCGGGTCGGGGTCGTGGTCGT
1 GGTCGGGTCGGGTCGGGGTCGGGGTCGT
*
2880921 GGTCGTGGTCGTGGTCGTGGTCG
1 GGTCG-GGTCG-GGTCGGGGTCG
2880944 TGGCTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 32 0.68
29 5 0.11
30 10 0.21
ACGTcount: A:0.00, C:0.18, G:0.57, T:0.25
Consensus pattern (28 bp):
GGTCGGGTCGGGTCGGGGTCGGGGTCGT
Found at i:2880944 original size:6 final size:6
Alignment explanation
Indices: 2880865--2880946 Score: 109
Period size: 6 Copynumber: 14.3 Consensus size: 6
2880855 TCTCGTCTTG
* * *
2880865 GGTCG- GGTCG- GGTCGG GGTCGG GGTCGT GGTCG- GGTCG- GGTCGG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2880909 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GG
2880947 CTTTTTTTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
5 20 0.27
6 53 0.73
ACGTcount: A:0.00, C:0.17, G:0.57, T:0.26
Consensus pattern (6 bp):
GGTCGT
Found at i:2881079 original size:61 final size:62
Alignment explanation
Indices: 2880999--2881115 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 62
2880989 AAAATGGAAA
*
2880999 ATCGCAACGTAAAATGGAAAATCGCAACGCGAAATGGAAAATCGCAACGC-AATTTTCAACT
1 ATCGCAACGCAAAATGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTTCAACT
* *
2881060 ATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGAATTT
1 ATCGCAACGCAAAATGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGAATTT
2881116 GCGATAGTGG
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 47 0.90
62 5 0.10
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (62 bp):
ATCGCAACGCAAAATGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTTCAACT
Found at i:2881110 original size:20 final size:20
Alignment explanation
Indices: 2880973--2881112 Score: 174
Period size: 20 Copynumber: 7.0 Consensus size: 20
2880963 GCAACGAATT
**
2880973 TGGAAAATCGCAACGTAAAA
1 TGGAAAATCGCAACGCGAAA
**
2880993 TGGAAAATCGCAACGTAAAA
1 TGGAAAATCGCAACGCGAAA
2881013 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
*
2881033 TGGAAAATCGCAACGC-AATT
1 TGGAAAATCGCAACGCGAA-A
** * *
2881053 TTCAACTATCGCAACGCGAAC
1 TGGAA-AATCGCAACGCGAAA
2881074 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
2881094 TGGAAAATCGCAACGCGAA
1 TGGAAAATCGCAACGCGAA
2881113 TTTGCGATAG
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 89 0.84
21 13 0.12
22 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:2888476 original size:14 final size:12
Alignment explanation
Indices: 2888457--2888490 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
2888447 TAATAATTAA
2888457 TTAATAATTTTT
1 TTAATAATTTTT
2888469 ATTAAATAATTTTT
1 -TT-AATAATTTTT
2888483 TTAATAAT
1 TTAATAAT
2888491 CTAATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 4 0.20
14 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAATAATTTTT
Found at i:2890736 original size:21 final size:21
Alignment explanation
Indices: 2890698--2890747 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2890688 GAAAAAATCG
*
2890698 GATATCCGAAATTTCGGATCA
1 GATATCCGAAATTCCGGATCA
*
2890719 GATATCCG-AATATCCGGATCC
1 GATATCCGAAAT-TCCGGATCA
2890740 GA-ATCCGA
1 GATATCCGA
2890748 TTTTTTTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
GATATCCGAAATTCCGGATCA
Found at i:2894280 original size:18 final size:18
Alignment explanation
Indices: 2894257--2894309 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
2894247 AACTTTGTGC
*
2894257 CCACTGCAGAGGTGAAGT
1 CCACTGCAGAAGTGAAGT
2894275 CCACTGCAGAAGTGAAGT
1 CCACTGCAGAAGTGAAGT
*
2894293 CCACTGTAGAAGTGAAG
1 CCACTGCAGAAGTGAAG
2894310 GCTACAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.30, T:0.17
Consensus pattern (18 bp):
CCACTGCAGAAGTGAAGT
Found at i:2899392 original size:40 final size:40
Alignment explanation
Indices: 2899315--2899800 Score: 261
Period size: 41 Copynumber: 11.9 Consensus size: 40
2899305 CATTTCTAGA
* * * * *
2899315 ACAAACGCCGGTAAAGACTCGTACTATAGCGGCGTTTTTAT
1 ACAAACGCCGCTAAATAAT-GTACTTTAGTGGCGTTTTTAT
* *
2899356 AAAAACGCCGCTAAATAATGTTCTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAATAATGTACTTTAGTGGCGTTTTTAT
* * * * *
2899396 ACAAACGCCGCTAAA-GA-CTAATTTAGTGGCATTTTTGT
1 ACAAACGCCGCTAAATAATGTACTTTAGTGGCGTTTTTAT
* ***
2899434 ACAAACGCCGCTATAGTACGA-GT-CTTTACCAGCGTTTTTTAT
1 ACAAACGCCGCTA-AATA--ATGTACTTTAGTGGCG-TTTTTAT
* * * ** *
2899476 ACAAACGCTGCTATAGACTCAT-T-CTATAGCAGCGTTTTTAC
1 ACAAACGCCGCTA-A-A-TAATGTACTTTAGTGGCGTTTTTAT
* *
2899517 AGAAACGCCGCTAAATAATTTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAATAATGTACTTTAGTGGCGTTTTTAT
* * * * *
2899557 ACAAACGCCGCGAAAGACTGTAATTTAGTGGCGTTTTTAGA
1 ACAAACGCCGCTAAATAATGTACTTTAGTGGCGTTTTTA-T
** ** * *
2899598 ACAAACGCCTTTGTAGACTCGTGA-TTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAATAAT-GT-ACTTTAGTGGCGTTTTTAT
* * *
2899639 ACAAGCGCCGCTATAGT-ATG-AGTCTTTAGCGGCGTTTTTTAT
1 ACAAACGCCGCTA-AATAATGTA--CTTTAGTGGCG-TTTTTAT
* * * **
2899681 ACAAACGTCGCTAAATACTCGTACTATAGTGGTATTTTTAT
1 ACAAACGCCGCTAAATAAT-GTACTTTAGTGGCGTTTTTAT
* ** * * * * *
2899722 ATAAATACCTCAAAATAATGTACTTTAGTGGCATTTTAAGC
1 ACAAACGCCGCTAAATAATGTACTTTAGTGGCGTTTTTA-T
* * *
2899763 ACAAACGCCGCCAGATACTCGTACTTTAGTGGCGTTTT
1 ACAAACGCCGCTAAATAAT-GTACTTTAGTGGCGTTTT
2899801 AAGCACAAAC
Statistics
Matches: 337, Mismatches: 85, Indels: 45
0.72 0.18 0.10
Matches are distributed among these distances:
38 33 0.10
39 4 0.01
40 98 0.29
41 104 0.31
42 94 0.28
43 2 0.01
44 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (40 bp):
ACAAACGCCGCTAAATAATGTACTTTAGTGGCGTTTTTAT
Found at i:2899509 original size:42 final size:42
Alignment explanation
Indices: 2899427--2899529 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
2899417 TTTAGTGGCA
* * *
2899427 TTTTTGTACAAACGCCGCTATAGTACGAGTCTTTACCAGCGT
1 TTTTTATACAAACGCCGCTATAGTACCAGTCTATACCAGCGT
* * *
2899469 TTTTTATACAAACGCTGCTATAG-ACTCATTCTATAGCAGCG-
1 TTTTTATACAAACGCCGCTATAGTAC-CAGTCTATACCAGCGT
* *
2899510 TTTTTACAGAAACGCCGCTA
1 TTTTTATACAAACGCCGCTA
2899530 AATAATTTAC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 19 0.37
42 32 0.63
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (42 bp):
TTTTTATACAAACGCCGCTATAGTACCAGTCTATACCAGCGT
Found at i:2899604 original size:81 final size:79
Alignment explanation
Indices: 2899315--2899606 Score: 245
Period size: 81 Copynumber: 3.6 Consensus size: 79
2899305 CATTTCTAGA
* * *
2899315 ACAAACGCCG-GTAAAGACTCGTACTATAGCGGCGTTTTTATAA-AAACGCCGCTAAATAATGTT
1 ACAAACGCCGCG-AAAGACT--TAATTTAGCGGCGTTTTTAGAACAAACGCCGCTAAATAAT-TT
2899378 CTTTAGTGGCGTTTTTAT
62 CTTTAGTGGCGTTTTTAT
* * * * * *
2899396 ACAAACGCCGCTAAAGAC-TAATTTAGTGGCATTTTT-GTACAAACGCCGCTATAGTACGA-GTC
1 ACAAACGCCGCGAAAGACTTAATTTAGCGGCGTTTTTAGAACAAACGCCGCTA-AATA--ATTTC
***
2899458 TTTACCAGCGTTTTTTAT
63 TTTAGTGGCG-TTTTTAT
* * * * * * * *
2899476 ACAAACGCTGCTATAGACTCATTCTATAGCAGCGTTTTTA-CAGAAACGCCGCTAAATAATTTAC
1 ACAAACGCCGCGAAAGACTTAAT-T-TAGCGGCGTTTTTAGAACAAACGCCGCTAAATAATTT-C
2899540 TTTAGTGGCGTTTTTAT
63 TTTAGTGGCGTTTTTAT
*
2899557 ACAAACGCCGCGAAAGACTGTAATTTAGTGGCGTTTTTAGAACAAACGCC
1 ACAAACGCCGCGAAAGACT-TAATTTAGCGGCGTTTTTAGAACAAACGCC
2899607 TTTGTAGACT
Statistics
Matches: 162, Mismatches: 35, Indels: 28
0.72 0.16 0.12
Matches are distributed among these distances:
77 1 0.01
78 25 0.15
79 12 0.07
80 36 0.22
81 52 0.32
82 14 0.09
83 22 0.14
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (79 bp):
ACAAACGCCGCGAAAGACTTAATTTAGCGGCGTTTTTAGAACAAACGCCGCTAAATAATTTCTTT
AGTGGCGTTTTTAT
Found at i:2899627 original size:42 final size:40
Alignment explanation
Indices: 2899314--2899649 Score: 146
Period size: 40 Copynumber: 8.3 Consensus size: 40
2899304 GCATTTCTAG
* * *
2899314 AACAAACGCCG-GTAAAGACTCGTACTATAGCGGCGTTTTTA
1 AACAAACGCCGCG-AAAGACT-GTAATTTAGTGGCGTTTTTA
* * * **
2899355 TAA-AAACGCCGCTAAATAATGTTCTTTAGTGGCGTTTTTA
1 -AACAAACGCCGCGAAAGACTGTAATTTAGTGGCGTTTTTA
* * * *
2899395 TACAAACGCCGCTAAAGAC--TAATTTAGTGGCATTTTTG
1 AACAAACGCCGCGAAAGACTGTAATTTAGTGGCGTTTTTA
* * * * * ***
2899433 TACAAACGCCGCTATAGTACGAGT-CTTTACCAGCGTTTTTTA
1 AACAAACGCCGCGAAAG-AC-TGTAATTTAGTGGCG-TTTTTA
* * * * * * **
2899475 TACAAACGCTGCTATAGACT-CATTCTATAGCAGCGTTTTTA
1 AACAAACGCCGCGAAAGACTGTAAT-T-TAGTGGCGTTTTTA
* * * * * * *
2899516 CAGAAACGCCGCTAAATAATTTACTTTAGTGGCGTTTTTA
1 AACAAACGCCGCGAAAGACTGTAATTTAGTGGCGTTTTTA
*
2899556 TACAAACGCCGCGAAAGACTGTAATTTAGTGGCGTTTTTA
1 AACAAACGCCGCGAAAGACTGTAATTTAGTGGCGTTTTTA
** * *
2899596 GAACAAACGCCTTTG-TAGACTCGTGATTTAGTGGCGTTTTTA
1 -AACAAACGCC-GCGAAAGACT-GTAATTTAGTGGCGTTTTTA
* *
2899638 TACAAGCGCCGC
1 AACAAACGCCGC
2899650 TATAGTATGA
Statistics
Matches: 229, Mismatches: 51, Indels: 30
0.74 0.16 0.10
Matches are distributed among these distances:
38 31 0.14
39 3 0.01
40 77 0.34
41 65 0.28
42 53 0.23
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (40 bp):
AACAAACGCCGCGAAAGACTGTAATTTAGTGGCGTTTTTA
Found at i:2899740 original size:205 final size:202
Alignment explanation
Indices: 2899335--2899819 Score: 506
Period size: 205 Copynumber: 2.4 Consensus size: 202
2899325 GTAAAGACTC
* * * * * * *
2899335 GTACTATAGCGGCGTTTTTATAAAAACGCCGCTAAATAATGTTCTTTAGTGGCGTTTTTA-TACA
1 GTACTTTAGTGGCGTTTTTATACAAACGCCGCCAAATACTGTACTTTAGTGGCGTTTTTAGAACA
*
2899399 AACGCCGCTAAAGACTAATTTAGTGGCATTTTTGTACAAACGCCGCTATAGTACGAGTCTTTACC
66 AACGCCGCTAAAGACTAATTTAGTGGCATTTTTATACAAACGCCGCTATAGTACGAGTCTTTACC
* * * * *
2899464 AGCGTTTTTTATACAAACGCTGCTATAGACTCATTCTATAGCAGCGTTTTTACAGAAACGCCGCT
131 AGCGTTTTTTATACAAACGCTGCTAAAGACTCATACTATAGCAGCATTTTTACAGAAACACCGCA
2899529 AAATAAT
196 AAATAAT
* * * *
2899536 TTACTTTAGTGGCGTTTTTATACAAACGCCGCGAAAGACTGTAATTTAGTGGCGTTTTTAGAACA
1 GTACTTTAGTGGCGTTTTTATACAAACGCCGCCAAATACTGTACTTTAGTGGCGTTTTTAGAACA
** ** * * * *
2899601 AACGCCTTTGTAGACTCGTGATTTAGTGGCGTTTTTATACAAGCGCCGCTATAGTATGAGTCTTT
66 AACGCCGCTAAAGA--C-TAATTTAGTGGCATTTTTATACAAACGCCGCTATAGTACGAGTCTTT
* * * * ** * * * *
2899666 AGCGGCGTTTTTTATACAAACG-TCGCTAAATACTCGTACTATAGTGGTATTTTTATATAAATAC
128 ACCAGCGTTTTTTATACAAACGCT-GCTAAAGACTCATACTATAGCAGCATTTTTACAGAAACAC
*
2899730 CTCAAAATAAT
192 CGCAAAATAAT
* * * * * *
2899741 GTACTTTAGTGGCATTTTAAGCACAAACGCCGCCAGATACTCGTACTTTAGTGGCGTTTTAAGCA
1 GTACTTTAGTGGCGTTTTTA-TACAAACGCCGCCAAATACT-GTACTTTAGTGGCGTTTTTAGAA
* *
2899806 CAAACACCACTAAA
64 CAAACGCCGCTAAA
2899820 TACTCGTACT
Statistics
Matches: 227, Mismatches: 50, Indels: 8
0.80 0.18 0.03
Matches are distributed among these distances:
201 51 0.22
202 13 0.06
204 2 0.01
205 116 0.51
206 16 0.07
207 29 0.13
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (202 bp):
GTACTTTAGTGGCGTTTTTATACAAACGCCGCCAAATACTGTACTTTAGTGGCGTTTTTAGAACA
AACGCCGCTAAAGACTAATTTAGTGGCATTTTTATACAAACGCCGCTATAGTACGAGTCTTTACC
AGCGTTTTTTATACAAACGCTGCTAAAGACTCATACTATAGCAGCATTTTTACAGAAACACCGCA
AAATAAT
Found at i:2899788 original size:42 final size:42
Alignment explanation
Indices: 2899693--2899831 Score: 138
Period size: 42 Copynumber: 3.4 Consensus size: 42
2899683 AAACGTCGCT
* * * * * * * *
2899693 AAATACTCGTACTATAGTGGTATTTTTA-TATAAATACCTCA
1 AAATACTCGTACTTTAGTGGCATTTTAAGCACAAACACCACC
* * *
2899734 AAATAAT-GTACTTTAGTGGCATTTTAAGCACAAACGCCGCC
1 AAATACTCGTACTTTAGTGGCATTTTAAGCACAAACACCACC
* * *
2899775 AGATACTCGTACTTTAGTGGCGTTTTAAGCACAAACACCACT
1 AAATACTCGTACTTTAGTGGCATTTTAAGCACAAACACCACC
2899817 AAATACTCGTACTTT
1 AAATACTCGTACTTT
2899832 TTAATCCGTA
Statistics
Matches: 79, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
40 17 0.22
41 18 0.23
42 44 0.56
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (42 bp):
AAATACTCGTACTTTAGTGGCATTTTAAGCACAAACACCACC
Found at i:2902737 original size:21 final size:21
Alignment explanation
Indices: 2902713--2902767 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2902703 TGATTTATTA
**
2902713 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
2902734 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
2902755 TTATGGATGTCAA
1 TTATGGATTTCAA
2902768 ATTTATTGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:2902933 original size:43 final size:43
Alignment explanation
Indices: 2902883--2902979 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
2902873 GAAGTAATTA
*
2902883 GCGGCGTTTGTATCT-TAAAACGCCGCTATAGA-TATGACCTTTT
1 GCGGCGTTTGT-TCTAAAAAACGCCGCTATAGACTA-GACCTTTT
* * *
2902926 GCGGCGTTTGTTCTAAAAAATGCCGCTATATACTAGATCTTTT
1 GCGGCGTTTGTTCTAAAAAACGCCGCTATAGACTAGACCTTTT
*
2902969 GCGGTGTTTGT
1 GCGGCGTTTGT
2902980 GGGAAAAACG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 3 0.06
43 42 0.89
44 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.37
Consensus pattern (43 bp):
GCGGCGTTTGTTCTAAAAAACGCCGCTATAGACTAGACCTTTT
Found at i:2902987 original size:43 final size:43
Alignment explanation
Indices: 2902899--2902995 Score: 99
Period size: 43 Copynumber: 2.3 Consensus size: 43
2902889 TTTGTATCTT
* *
2902899 AAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCTAA
1 AAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTGCGAA
* * * * *
2902942 AAAATGCCGCTATATACTA-GATCTTTTGCGGTGTTTGTG-GGA
1 AAAACGCCGCTATAGA-TATGACCTTTTGCGGCGTTTGTGCGAA
*
2902984 AAAACGCTGCTA
1 AAAACGCCGCTA
2902996 AATCTCAACA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
42 11 0.25
43 31 0.70
44 2 0.05
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (43 bp):
AAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTGCGAA
Found at i:2903014 original size:43 final size:43
Alignment explanation
Indices: 2902967--2903063 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
2902957 ACTAGATCTT
* *
2902967 TTGCGGTGTTTGTGGGAAAAACGCTGCTAAATCTCAACACCTA
1 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* *
2903010 TTGCGGTGTTTGTTGGACAAACGCCGCTAAATATCAACACCTA
1 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
*
2903053 TTGCGGCGTTT
1 TTGCGGTGTTT
2903064 TTTGTTACCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (43 bp):
TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
Found at i:2919958 original size:23 final size:23
Alignment explanation
Indices: 2919924--2920010 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
2919914 ACATATTATA
2919924 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
2919947 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
2919970 CGGTC-CTTCGG-GACAAAATTCTACG
1 TGG-CACTACGGTG-C--AATTCTACG
2919995 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
2920011 AATTTATATG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 2 0.04
25 16 0.31
26 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:2927609 original size:17 final size:18
Alignment explanation
Indices: 2927578--2927611 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2927568 CGAAAAATAG
2927578 TATTATCAGATAATAATT
1 TATTATCAGATAATAATT
2927596 TATTATCA-ATAATAAT
1 TATTATCAGATAATAAT
2927612 ATTTTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
TATTATCAGATAATAATT
Found at i:2927783 original size:29 final size:27
Alignment explanation
Indices: 2927751--2927836 Score: 91
Period size: 29 Copynumber: 3.0 Consensus size: 27
2927741 TCTTTGTGAT
*
2927751 TTATTCAAAATTATATACTTAATAAAATA
1 TTATACAAAATT-TA-ACTTAATAAAATA
*
2927780 TTATACAAATAATTTAATTTAATAAAATA
1 TTATAC-AA-AATTTAACTTAATAAAATA
*
2927809 TTATACAAATAATTTAATTTAATAAAAT
1 TTATAC-AA-AATTTAACTTAATAAAAT
2927837 TTGAGTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
29 45 0.85
30 4 0.08
31 4 0.08
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (27 bp):
TTATACAAAATTTAACTTAATAAAATA
Found at i:2927796 original size:24 final size:27
Alignment explanation
Indices: 2927769--2927836 Score: 100
Period size: 29 Copynumber: 2.4 Consensus size: 27
2927759 AATTATATAC
2927769 TTAATAAAATATTATACAAATAATTTAAT
1 TTAATAAAATATTATAC-AATAA-TTAAT
2927798 TTAATAAAATATTATACAAATAATTTAAT
1 TTAATAAAATATTATAC-AATAA-TTAAT
2927827 TTAATAAAAT
1 TTAATAAAAT
2927837 TTGAGTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
TTAATAAAATATTATACAATAATTAAT
Found at i:2927877 original size:16 final size:16
Alignment explanation
Indices: 2927854--2927904 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2927844 ATTAAAATTA
2927854 TTTT-ATATTTTATAT
1 TTTTAATATTTTATAT
*
2927869 TTTTAATATTTAATA-
1 TTTTAATATTTTATAT
*
2927884 TATTAATTATTTTATAAT
1 TTTTAA-TATTTTAT-AT
2927902 TTT
1 TTT
2927905 GTGAGGTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 9 0.32
16 16 0.57
17 1 0.04
18 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAATATTTTATAT
Found at i:2928044 original size:17 final size:17
Alignment explanation
Indices: 2928022--2928054 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2928012 TGAGATCATA
2928022 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
2928039 ATATTATATTTTATAT
1 ATATTATATTTTATAT
2928055 AAATGAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:2933436 original size:39 final size:39
Alignment explanation
Indices: 2933382--2933458 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
2933372 GACTAGCCTA
*
2933382 GTATCAGAGAAGACAGACAGGAGAAGAGGCTCTTTGTCC
1 GTATCAGAGAAGACAGACAGGAGAAAAGGCTCTTTGTCC
2933421 GTATCAGAGAAGACAGACAGGAGAAAAGGCTCTTTGTC
1 GTATCAGAGAAGACAGACAGGAGAAAAGGCTCTTTGTC
2933459 AGAAACTACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (39 bp):
GTATCAGAGAAGACAGACAGGAGAAAAGGCTCTTTGTCC
Found at i:2939999 original size:45 final size:45
Alignment explanation
Indices: 2939948--2940042 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
2939938 TTAAAATGAT
2939948 ATGTTATTTATGGTGATACAATTTTATTAATAAAATTACCAAAAA
1 ATGTTATTTATGGTGATACAATTTTATTAATAAAATTACCAAAAA
2939993 ATGTTATTTATGGTGATACAATTTTATTAATAAAATTACCAAAAA
1 ATGTTATTTATGGTGATACAATTTTATTAATAAAATTACCAAAAA
2940038 ATGTT
1 ATGTT
2940043 CCAACAACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.41
Consensus pattern (45 bp):
ATGTTATTTATGGTGATACAATTTTATTAATAAAATTACCAAAAA
Found at i:2940970 original size:13 final size:15
Alignment explanation
Indices: 2940942--2940970 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2940932 AAAAATATTT
2940942 TTTTAAAATAATATA
1 TTTTAAAATAATATA
2940957 TTTTAAAATAATAT
1 TTTTAAAATAATAT
2940971 TGACACGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAAAATAATATA
Found at i:2946358 original size:20 final size:20
Alignment explanation
Indices: 2946315--2946358 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2946305 ACTGACAATG
* * **
2946315 AACCGGCTGAAAACCGGTTG
1 AACCGACTGAAAACCAGTAA
2946335 AACCGACTGAAAACCAGTAA
1 AACCGACTGAAAACCAGTAA
2946355 AACC
1 AACC
2946359 AGGGTGAACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.11
Consensus pattern (20 bp):
AACCGACTGAAAACCAGTAA
Found at i:2946387 original size:30 final size:29
Alignment explanation
Indices: 2946324--2946399 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 29
2946314 GAACCGGCTG
* *
2946324 AAAACCGGTTGAACCGACTGAAAACCAGT
1 AAAACCGGGTGAACCGACTGAAAACCAGC
* * *
2946353 AAAACCAGGGTGAACCGGCTGAAATCTAGC
1 AAAACC-GGGTGAACCGACTGAAAACCAGC
*
2946383 AAAACCGGTTTGAACCG
1 AAAACCGG-GTGAACCG
2946400 TCGGTTCACT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 8 0.21
30 31 0.79
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (29 bp):
AAAACCGGGTGAACCGACTGAAAACCAGC
Found at i:2951099 original size:32 final size:32
Alignment explanation
Indices: 2951005--2951128 Score: 92
Period size: 31 Copynumber: 3.9 Consensus size: 32
2950995 CCTTAAGGGA
*
2951005 ACATCTTAGGGCC-TGAGAGTCTACCCAAG-AT
1 ACATCTTAGGGCCGTG-GAGCCTACCCAAGAAT
* * * * * * *
2951036 AGATTTTGGGGTCGTGGGGCCCACCTAAGAAT
1 ACATCTTAGGGCCGTGGAGCCTACCCAAGAAT
* *
2951068 ACATCTTAGGGCCGTGGGGCCTACCCGAGAAT
1 ACATCTTAGGGCCGTGGAGCCTACCCAAGAAT
* * * *
2951100 -GATCTCAGGGCCGTAGAGCCTACCTAAGA
1 ACATCTTAGGGCCGTGGAGCCTACCCAAGA
2951129 GTCACATTAG
Statistics
Matches: 70, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
31 41 0.59
32 29 0.41
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (32 bp):
ACATCTTAGGGCCGTGGAGCCTACCCAAGAAT
Found at i:2952099 original size:31 final size:29
Alignment explanation
Indices: 2952070--2952177 Score: 109
Period size: 28 Copynumber: 3.9 Consensus size: 29
2952060 ACATTTTTAC
2952070 AAAAAAAATTCCCAAAATGTCACCGTTTT
1 AAAAAAAATTCCCAAAATGTCACCGTTTT
* * * ***
2952099 AAAAATAATTACCAGAATGTCATTATTTT
1 AAAAAAAATTCCCAAAATGTCACCGTTTT
*
2952128 -TAAAAAATTCCCAAAATGTCA-C-TATTT
1 AAAAAAAATTCCCAAAATGTCACCGT-TTT
2952155 AAAAAAAA--CCCAAAATGTCACCG
1 AAAAAAAATTCCCAAAATGTCACCG
2952178 GGTCGGGTCG
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
26 13 0.21
27 4 0.06
28 23 0.37
29 23 0.37
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (29 bp):
AAAAAAAATTCCCAAAATGTCACCGTTTT
Found at i:2952117 original size:29 final size:30
Alignment explanation
Indices: 2952042--2952135 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 30
2952032 ACCTTTTTTT
* *
2952042 AATAATTACCAAAATATCACATTTTTACAAA
1 AATAATTACCAAAATGTCACAGTTTTA-AAA
* * *
2952073 AAAAATTCCCAAAATGTCACCGTTTT-AAA
1 AATAATTACCAAAATGTCACAGTTTTAAAA
* * *
2952102 AATAATTACCAGAATGTCATTATTTTTAAAA
1 AATAATTACCAAAATGTCA-CAGTTTTAAAA
2952133 AAT
1 AAT
2952136 TCCCAAAATG
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 19 0.38
30 4 0.08
31 27 0.54
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (30 bp):
AATAATTACCAAAATGTCACAGTTTTAAAA
Found at i:2952146 original size:28 final size:28
Alignment explanation
Indices: 2952072--2952175 Score: 113
Period size: 26 Copynumber: 3.8 Consensus size: 28
2952062 ATTTTTACAA
** *
2952072 AAAAAATTCCCAAAATGTCACCGTTTTA
1 AAAAAATTCCCAAAATGTCACTATTTTT
* * *
2952100 AAAATAATTACCAGAATGTCATTATTTTT
1 AAAA-AATTCCCAAAATGTCACTATTTTT
2952129 AAAAAATTCCCAAAATGTCACTA--TTT
1 AAAAAATTCCCAAAATGTCACTATTTTT
**
2952155 AAAAAAAACCCAAAATGTCAC
1 AAAAAATTCCCAAAATGTCAC
2952176 CGGGTCGGGT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 22 0.34
28 20 0.31
29 22 0.34
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (28 bp):
AAAAAATTCCCAAAATGTCACTATTTTT
Found at i:2952194 original size:18 final size:18
Alignment explanation
Indices: 2952171--2952225 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
2952161 AACCCAAAAT
2952171 GTCACCGGGTCGGGTCGG
1 GTCACCGGGTCGGGTCGG
*
2952189 GTCACCGGGTC-GGAC-G
1 GTCACCGGGTCGGGTCGG
*
2952205 GTCAACGGGTCGGGTCGG
1 GTCACCGGGTCGGGTCGG
2952223 GTC
1 GTC
2952226 GGGTCGAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 11 0.34
17 6 0.19
18 15 0.47
ACGTcount: A:0.09, C:0.27, G:0.47, T:0.16
Consensus pattern (18 bp):
GTCACCGGGTCGGGTCGG
Found at i:2958477 original size:32 final size:32
Alignment explanation
Indices: 2958383--2958477 Score: 95
Period size: 32 Copynumber: 3.0 Consensus size: 32
2958373 CCCTAATGGA
*
2958383 ACATCTTAGGGCC-TGAGAGCCTACCCAAG-AT
1 ACATCTTAGGGCCGTG-GGGCCTACCCAAGAAT
* * * * * *
2958414 AGATTTTGGGGTCGTGGGGCCCACCTAAGAAT
1 ACATCTTAGGGCCGTGGGGCCTACCCAAGAAT
*
2958446 ACATCTTAGGGCCGTGGGGCCTACCCGAGAAT
1 ACATCTTAGGGCCGTGGGGCCTACCCAAGAAT
2958478 GATTTCAGGG
Statistics
Matches: 48, Mismatches: 14, Indels: 3
0.74 0.22 0.05
Matches are distributed among these distances:
31 19 0.40
32 29 0.60
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.21
Consensus pattern (32 bp):
ACATCTTAGGGCCGTGGGGCCTACCCAAGAAT
Found at i:2959431 original size:29 final size:28
Alignment explanation
Indices: 2959390--2959525 Score: 114
Period size: 29 Copynumber: 4.7 Consensus size: 28
2959380 TCCACTGTCG
*
2959390 AAAATTACAAAAATATCACCTTTTTAAA
1 AAAATTACCAAAATATCACCTTTTTAAA
* * *
2959418 AATAATTATCAAAATTTCA-TTGTTTTACAA
1 AA-AATTACCAAAATATCACCT-TTTTA-AA
* * *
2959448 AAAATTCCCAAAATGTCACCGTTTTAAA
1 AAAATTACCAAAATATCACCTTTTTAAA
* * *
2959476 AATAATTACCAGAATGTCACTGTTTTTAAA
1 AA-AATTACCAAAATATCAC-CTTTTTAAA
2959506 AAAATT-CCTAAAATATCACC
1 AAAATTACC-AAAATATCACC
2959526 GGGTCGGGTC
Statistics
Matches: 85, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
28 9 0.11
29 63 0.74
30 13 0.15
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAATTACCAAAATATCACCTTTTTAAA
Found at i:2959461 original size:58 final size:58
Alignment explanation
Indices: 2959390--2959526 Score: 177
Period size: 58 Copynumber: 2.4 Consensus size: 58
2959380 TCCACTGTCG
* * * * *
2959390 AAAATTACAAAAATATCACCTTTTTAAAAATAATTATCAAAATTTCATTG-TTTTACAA
1 AAAATTCCAAAAATATCACCGTTTTAAAAATAATTACCAAAATGTCACTGTTTTTA-AA
* * *
2959448 AAAATTCCCAAAATGTCACCGTTTTAAAAATAATTACCAGAATGTCACTGTTTTTAAA
1 AAAATTCCAAAAATATCACCGTTTTAAAAATAATTACCAAAATGTCACTGTTTTTAAA
*
2959506 AAAATTCCTAAAATATCACCG
1 AAAATTCCAAAAATATCACCG
2959527 GGTCGGGTCG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 63 0.93
59 5 0.07
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (58 bp):
AAAATTCCAAAAATATCACCGTTTTAAAAATAATTACCAAAATGTCACTGTTTTTAAA
Found at i:2959573 original size:19 final size:19
Alignment explanation
Indices: 2959549--2959585 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2959539 CAACAGGTCG
2959549 GGTCAAACCGGCTCAGACC
1 GGTCAAACCGGCTCAGACC
* *
2959568 GGTCAAACTGGTTCAGAC
1 GGTCAAACCGGCTCAGAC
2959586 ATGCAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGCTCAGACC
Found at i:2963007 original size:30 final size:31
Alignment explanation
Indices: 2962941--2963007 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
2962931 TTTATTTTTT
* * *
2962941 ATTTGACCCTTAAAATTTATATAAATTATTA
1 ATTTGACCCTTAAAATTTAGATAAAATATCA
*
2962972 TTTTGACCCTT-AAATTTAGATAAAATATCA
1 ATTTGACCCTTAAAATTTAGATAAAATATCA
2963002 ATTTGA
1 ATTTGA
2963008 TCATTGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.43
Consensus pattern (31 bp):
ATTTGACCCTTAAAATTTAGATAAAATATCA
Found at i:2963378 original size:2 final size:2
Alignment explanation
Indices: 2963371--2963399 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2963361 TGCTCTAAAG
2963371 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 A
2963400 AATAATGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2964795 original size:95 final size:96
Alignment explanation
Indices: 2964696--2964878 Score: 278
Period size: 97 Copynumber: 1.9 Consensus size: 96
2964686 TTCGAGCTTC
* *
2964696 AATTGAGCTAAGTCTAAGAATGTTTCGAGTTCAA-ATTTTTAGAGCTCGAGATTCAATTTTTTAT
1 AATTGAGCTAAGTCTAAGAATATTTCGAGTCCAAGATTTTTAGAGCTCGAGATTCAATTTTTTAT
2964760 TTTGAGTTGAGTTTGAAAATTTTTAAACTTT
66 TTTGAGTTGAGTTTGAAAATTTTTAAACTTT
* * ** * *
2964791 AATTGAGCTAAGTCTAAGAATATTTTGAGTCCAAGTTTTTTTCTAGCTTGAGATTTAATTTTTTA
1 AATTGAGCTAAGTCTAAGAATATTTCGAGTCCAAG-ATTTTTAGAGCTCGAGATTCAATTTTTTA
2964856 TTTTGAGTTGAGTTTGAAAATTT
65 TTTTGAGTTGAGTTTGAAAATTT
2964879 AAAGATCACT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 31 0.40
97 47 0.60
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.46
Consensus pattern (96 bp):
AATTGAGCTAAGTCTAAGAATATTTCGAGTCCAAGATTTTTAGAGCTCGAGATTCAATTTTTTAT
TTTGAGTTGAGTTTGAAAATTTTTAAACTTT
Found at i:2966846 original size:31 final size:31
Alignment explanation
Indices: 2966785--2966846 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2966775 GTTTTATAGA
* *
2966785 TTTAAATAATTTATTTATATAAATTATAATT
1 TTTAAATAATTTATTTAGATAAAATATAATT
*
2966816 TTTAAATTATTTATTTAGATGAAAAT-TAATT
1 TTTAAATAATTTATTTAGAT-AAAATATAATT
2966847 CATGCTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTAAATAATTTATTTAGATAAAATATAATT
Found at i:2967035 original size:32 final size:33
Alignment explanation
Indices: 2966999--2967063 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
2966989 TTTATATAGA
*
2966999 TTTAAATAATTTATTTTATAT-AAATTA-TAATT
1 TTTAAATAATTTA-TTTAGATGAAATTATTAATT
*
2967031 TTTAAATTATTTATTTAGATGAAATTATTAATT
1 TTTAAATAATTTATTTAGATGAAATTATTAATT
2967064 CATGCTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 6 0.21
32 18 0.62
33 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (33 bp):
TTTAAATAATTTATTTAGATGAAATTATTAATT
Found at i:2978459 original size:2 final size:2
Alignment explanation
Indices: 2978452--2978504 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2978442 CATGCTCAGG
2978452 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2978494 TC TC TC TC TC T
1 TC TC TC TC TC T
2978505 ACTTAATTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2986382 original size:13 final size:13
Alignment explanation
Indices: 2986366--2986391 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2986356 TGGATATGCC
2986366 CCTCCTATATAAT
1 CCTCCTATATAAT
2986379 CCTCCTATATAAT
1 CCTCCTATATAAT
2986392 TGTCCCGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
CCTCCTATATAAT
Found at i:2988052 original size:30 final size:31
Alignment explanation
Indices: 2988016--2988078 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
2988006 AAAACATAAT
2988016 ATATGGTCACTTTT-G-TTTTATTTAATTAAG
1 ATATGGTCA-TTTTCGTTTTTATTTAATTAAG
2988046 ATATGGTCATTTTCGTTTTTATTTAATTAAG
1 ATATGGTCATTTTCGTTTTTATTTAATTAAG
2988077 AT
1 AT
2988079 GTGATCACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 4 0.13
30 10 0.32
31 17 0.55
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.54
Consensus pattern (31 bp):
ATATGGTCATTTTCGTTTTTATTTAATTAAG
Found at i:2988709 original size:8 final size:8
Alignment explanation
Indices: 2988689--2988731 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
2988679 TATATTATAG
2988689 ATTTTTAA
1 ATTTTTAA
2988697 A-TTTTAA
1 ATTTTTAA
2988704 ATTTTTAGA
1 ATTTTTA-A
*
2988713 ATTTTTTAT
1 A-TTTTTAA
2988722 ATTTTTAA
1 ATTTTTAA
2988730 AT
1 AT
2988732 AATATAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 7 0.23
8 14 0.47
9 3 0.10
10 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (8 bp):
ATTTTTAA
Found at i:2988827 original size:21 final size:20
Alignment explanation
Indices: 2988803--2988841 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2988793 ATATAATTAT
2988803 ATATATATATATTAACTTAAA
1 ATATATATATA-TAACTTAAA
* *
2988824 ATATTTTTATATAACTTA
1 ATATATATATATAACTTA
2988842 TTAAATATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATATATATAACTTAAA
Found at i:2990540 original size:12 final size:11
Alignment explanation
Indices: 2990506--2990547 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
2990496 CCACAGTTTG
2990506 TTTCTTTTC-T
1 TTTCTTTTCTT
*
2990516 TTGCTTTTCTT
1 TTTCTTTTCTT
*
2990527 TTTCGTTTTTTT
1 TTTC-TTTTCTT
2990539 TTTCTTTTC
1 TTTCTTTTC
2990548 CATCTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.31
11 8 0.31
12 10 0.38
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:2998526 original size:165 final size:166
Alignment explanation
Indices: 2998254--2998571 Score: 514
Period size: 165 Copynumber: 1.9 Consensus size: 166
2998244 TAACATGCAT
**
2998254 AATAGCTTTGAACACATTTGAAAAACCATCTAGATTCATCCAAACATTTCAATGTTTGAATTTTA
1 AATAGCTTTGAACACAGCTGAAAAACCATCTAGATTCATCCAAACATTTCAATGTTTGAATTTTA
* * * * *
2998319 ATTTTAGAAACTTACTGATTTAATCATATATACCATTTCAGCCTATAAATATC-AGAACAATTCT
66 ATTTCAGAAACTGACTGATTTAATCATACAGACAATTTCAGCCTATAAATATCAAGAACAATTCT
2998383 TTCACAATCTTTTATGCTTGAATAATAGGCACAATA
131 TTCACAATCTTTTATGCTTGAATAATAGGCACAATA
*
2998419 AATAGCTTTGAACACAGCTGAAAAACCATCTAGATTCATCCAAACGTTT-AACTGTTTGAATTTT
1 AATAGCTTTGAACACAGCTGAAAAACCATCTAGATTCATCCAAACATTTCAA-TGTTTGAATTTT
*
2998483 AATTTCAGAAACTGACTGATTTAATCATACAGACAATTTCAGCCTATAAATATCATAATAACAAT
65 AATTTCAGAAACTGACTGATTTAATCATACAGACAATTTCAGCCTATAAATATC--AAGAACAAT
2998548 TCTTTCACAATCTTTTATGCTTGA
128 TCTTTCACAATCTTTTATGCTTGA
2998572 GAAAAATCAT
Statistics
Matches: 140, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
164 2 0.01
165 107 0.76
168 31 0.22
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (166 bp):
AATAGCTTTGAACACAGCTGAAAAACCATCTAGATTCATCCAAACATTTCAATGTTTGAATTTTA
ATTTCAGAAACTGACTGATTTAATCATACAGACAATTTCAGCCTATAAATATCAAGAACAATTCT
TTCACAATCTTTTATGCTTGAATAATAGGCACAATA
Found at i:2999243 original size:30 final size:28
Alignment explanation
Indices: 2999209--2999286 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 28
2999199 GTGTATAAAT
*
2999209 ACTTAAATTCATAATATTTTATATATATTA
1 ACTTAAATT-AAAATATTTTATAT-TATTA
2999239 ACTTAAA--AAAATATATTT-TATTATTA
1 ACTTAAATTAAAATAT-TTTATATTATTA
*
2999265 ACTTAATTTAAAAATATTTTAT
1 ACTTAAATT-AAAATATTTTAT
2999287 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
26 11 0.27
27 9 0.22
28 6 0.15
29 8 0.20
30 7 0.17
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (28 bp):
ACTTAAATTAAAATATTTTATATTATTA
Found at i:2999277 original size:29 final size:27
Alignment explanation
Indices: 2999221--2999286 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 27
2999211 TTAAATTCAT
2999221 AATATTTTATATATATTAACTTAAAAA
1 AATATTTTATATATATTAACTTAAAAA
2999248 AATATATTT-TAT-TATTAACTTAATTTAAA
1 AATAT-TTTATATATATTAACTTAA---AAA
2999277 AATATTTTAT
1 AATATTTTAT
2999287 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
26 11 0.32
27 8 0.24
28 6 0.18
29 9 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (27 bp):
AATATTTTATATATATTAACTTAAAAA
Found at i:2999300 original size:27 final size:28
Alignment explanation
Indices: 2999221--2999287 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
2999211 TTAAATTCAT
*
2999221 AATAT-TTTATATATATTAACTTAA--AAA
1 AATATATTT-TAT-TATTAACTTAATTTAA
2999248 AATATATTTTATTATTAACTTAATTTAA
1 AATATATTTTATTATTAACTTAATTTAA
2999276 AA-ATATTTTATT
1 AATATATTTTATT
2999288 TTTATTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 11 0.31
27 18 0.50
28 7 0.19
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
AATATATTTTATTATTAACTTAATTTAA
Found at i:3000567 original size:20 final size:19
Alignment explanation
Indices: 3000530--3000590 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
3000520 GTATCGATCC
*
3000530 AAAACGAT-ATACCAGGTAA
1 AAAACGATAAAACC-GGTAA
* * *
3000549 AAATATGATAAAATCGGTATC
1 AAA-ACGATAAAACCGGTA-A
3000570 AAAACGATAAAACCGGTAA
1 AAAACGATAAAACCGGTAA
3000589 AA
1 AA
3000591 GGTTACCGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 5 0.16
20 21 0.66
21 6 0.19
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAACGATAAAACCGGTAA
Found at i:3000747 original size:20 final size:19
Alignment explanation
Indices: 3000724--3000770 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
3000714 CGATATAACA
3000724 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
3000744 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
3000764 GGTAAAA
1 GGTAAAA
3000771 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:3000749 original size:180 final size:182
Alignment explanation
Indices: 3000331--3000802 Score: 691
Period size: 180 Copynumber: 2.6 Consensus size: 182
3000321 GATCCAAATT
* * *
3000331 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTAT-AGAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCA-AAATGAT
* * * *
3000395 AAAACCGGT-AAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
65 AAAACCGGTAAAAG-GATACCGGATATATTAAAAGTGTCGATAC-TTAATATAAGGATCGACACT
* * *
3000459 TCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTAA
128 TCGTGAATTTAAAAGAGAAACAATTTTAAAGCCTATAAAGTGTCGATACTTTTAA
* * *
3000514 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAATCGGTATCAAAACGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
3000579 AAACCGGTAAAAGGTTACCGGATATATTAAAAGTGTCGATACTT-ATATAAGGATCGACACTTTG
66 AAACCGGTAAAAGGATACCGGATATATTAAAAGTGTCGATACTTAATATAAGGATCGACACTTCG
** *
3000643 TGAATTTAAAAGAGAAACAATTTTAGCGCCTATAATGTGTCGATAC-TTTAA
131 TGAATTTAAAAGAGAAACAATTTTAAAGCCTATAAAGTGTCGATACTTTTAA
* *
3000694 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
3000759 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTT
66 AAACCGGTAAAAGGATACCGGATATATTAAAAGTGTCGATACTT
3000803 TCGTAAGTAC
Statistics
Matches: 262, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
180 106 0.40
181 59 0.23
182 2 0.01
183 90 0.34
184 5 0.02
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAAGGATACCGGATATATTAAAAGTGTCGATACTTAATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAACAATTTTAAAGCCTATAAAGTGTCGATACTTTTAA
Found at i:3000772 original size:17 final size:19
Alignment explanation
Indices: 3000733--3000775 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3000723 AGGTAAAAAT
3000733 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
3000753 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
3000770 ATGATA
1 ATGATA
3000776 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:3003006 original size:21 final size:21
Alignment explanation
Indices: 3002982--3003025 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3002972 AAGACAATCA
*
3002982 AGAGTTGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
3003003 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
3003024 AG
1 AG
3003026 GCATAAGGGG
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:0.41, C:0.09, G:0.32, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:3003101 original size:33 final size:33
Alignment explanation
Indices: 3003059--3003124 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3003049 AAATAGATGG
*
3003059 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
3003092 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
3003125 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:3004939 original size:19 final size:19
Alignment explanation
Indices: 3004915--3004963 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3004905 AATGTAGGGT
3004915 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3004934 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
3004953 TATTTTTGTAT
1 TAATTTTGTAT
3004964 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3005423 original size:199 final size:199
Alignment explanation
Indices: 3005082--3005655 Score: 1096
Period size: 199 Copynumber: 2.9 Consensus size: 199
3005072 CAATATGGCC
*
3005082 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
3005147 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
3005212 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCTAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
3005277 TGGAA
195 TGGAA
3005282 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
3005347 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
3005412 AATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
3005477 GGAA
196 GGAA
3005481 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
* *
3005546 CAAAAGTATAATGTAATATGTAAATTTTCAATCTAAACGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
3005611 AATATGTCTAAATAATGTGTCGACAC-TTTTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
3005656 CTAATTTAAA
Statistics
Matches: 370, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
198 19 0.05
199 290 0.78
200 61 0.16
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
GGAA
Found at i:3007128 original size:6 final size:6
Alignment explanation
Indices: 3007117--3007210 Score: 62
Period size: 6 Copynumber: 15.7 Consensus size: 6
3007107 CAAGCGGTCA
* ** * * * *
3007117 ATGAAG ATGAAG CTGGCG ATGAAT ATGACG ATGATG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * * * *
3007165 CTGACG ATGAAG ATGATG ACGATG ATGATG ATGATG ATGAAG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
3007211 TGATCCAAAT
Statistics
Matches: 68, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.22
Consensus pattern (6 bp):
ATGAAG
Found at i:3007139 original size:12 final size:12
Alignment explanation
Indices: 3007117--3007210 Score: 80
Period size: 12 Copynumber: 7.8 Consensus size: 12
3007107 CAAGCGGTCA
*
3007117 ATGAAGATGAAG
1 ATGACGATGAAG
* * *
3007129 CTGGCGATGAAT
1 ATGACGATGAAG
*
3007141 ATGACGATGATG
1 ATGACGATGAAG
3007153 ATGACGATGAAG
1 ATGACGATGAAG
*
3007165 CTGACGATGAAG
1 ATGACGATGAAG
* * *
3007177 ATGATGACGATG
1 ATGACGATGAAG
* *
3007189 ATGATGATGATG
1 ATGACGATGAAG
*
3007201 ATGAAGATGA
1 ATGACGATGA
3007211 TGATCCAAAT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 66 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:3007202 original size:9 final size:9
Alignment explanation
Indices: 3007141--3007214 Score: 76
Period size: 9 Copynumber: 8.2 Consensus size: 9
3007131 GGCGATGAAT
*
3007141 ATGACGATG
1 ATGATGATG
*
3007150 ATGATGACG
1 ATGATGATG
* *
3007159 ATGAAGCTG
1 ATGATGATG
* *
3007168 ACGATGAAG
1 ATGATGATG
*
3007177 ATGATGACG
1 ATGATGATG
3007186 ATGATGATG
1 ATGATGATG
3007195 ATGATGATG
1 ATGATGATG
*
3007204 AAGATGATG
1 ATGATGATG
3007213 AT
1 AT
3007215 CCAAATAAGT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.36, C:0.07, G:0.32, T:0.24
Consensus pattern (9 bp):
ATGATGATG
Done.