Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 17
Found at i:1872764 original size:88 final size:89
Alignment explanation
Indices: 1872534--1872902 Score: 478
Period size: 89 Copynumber: 4.2 Consensus size: 89
1872524 GCAAATTATA
* * * *
1872534 GTAAGTATATTGGT-AAATAAGCTTACGAGCTTATTA-A-ATTATAGTAAGTATATTGGT-AAAT
1 GTAAGTATATTGATAAAATAAGCTTACGAGCTTA-GAGATATAATGGTAAGTATATTGGTAAAAT
* * *
1872595 AAGCTTACGAGCTTATGAAATTATA
65 AAGCTTACGAGCTTATGGAATAATG
* *
1872620 GTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAATGGTAAGTATATTGGTAAAATA
1 GTAAGTATATTGATAAAATAAGCTTACGAGCTTAGAGATATAATGGTAAGTATATTGGTAAAATA
*
1872685 AGCTTACGAGTTTATGGAATAATG
66 AGCTTACGAGCTTATGGAATAATG
* * * *
1872709 GTAAGTATATGGGTAAAATAAGCTTACGAGCTTATAGA-ATAATGGTAAGCATATTGGTAAAATA
1 GTAAGTATATTGATAAAATAAGCTTACGAGCTTAGAGATATAATGGTAAGTATATTGGTAAAATA
* * *
1872773 AGCTTATGAGCATATGTAATAATG
66 AGCTTACGAGCTTATGGAATAATG
* *
1872797 GTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAATGGTAAGTATATTGGTAAAATA
1 GTAAGTATATTGATAAAATAAGCTTACGAGCTTAGAGATATAATGGTAAGTATATTGGTAAAATA
* * *
1872862 AGCTTAGGAGCTTATGGATTAAATA
66 AGCTTACGAGCTTATGGAAT-AATG
*
1872887 GTATGTATATTGATAA
1 GTAAGTATATTGATAA
1872903 GAAATTTTAT
Statistics
Matches: 245, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
86 13 0.05
87 20 0.08
88 95 0.39
89 99 0.40
90 18 0.07
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (89 bp):
GTAAGTATATTGATAAAATAAGCTTACGAGCTTAGAGATATAATGGTAAGTATATTGGTAAAATA
AGCTTACGAGCTTATGGAATAATG
Found at i:1872843 original size:177 final size:175
Alignment explanation
Indices: 1872534--1872879 Score: 559
Period size: 177 Copynumber: 2.0 Consensus size: 175
1872524 GCAAATTATA
* * *
1872534 GTAAGTATATTGGTAAATAAGCTTACGAGCTTATTAAATTATAGTAAGTATATTGGTAAATAAGC
1 GTAAGTATATGGGTAAATAAGCTTACGAGCTTATTAAATAATAGTAAGCATATTGGTAAATAAGC
* *
1872599 TTACGAGCTTATGAAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAAT
66 TTACGAGCATATGAAATAATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAAT
*
1872664 GGTAAGTATATTGGTAAAATAAGCTTACGAGTTTATGGAATAATG
131 GGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
*
1872709 GTAAGTATATGGGTAAAATAAGCTTACGAGCTTA-TAGAATAATGGTAAGCATATTGGTAAAATA
1 GTAAGTATATGGGT-AAATAAGCTTACGAGCTTATTA-AATAATAGTAAGCATATTGGT-AAATA
* * *
1872773 AGCTTATGAGCATATGTAATAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTT
63 AGCTTACGAGCATATGAAATAATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTT
*
1872838 AATGGTAAGTATATTGGTAAAATAAGCTTAGGAGCTTATGGA
128 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
1872880 TTAAATAGTA
Statistics
Matches: 157, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
175 15 0.10
176 37 0.24
177 105 0.67
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (175 bp):
GTAAGTATATGGGTAAATAAGCTTACGAGCTTATTAAATAATAGTAAGCATATTGGTAAATAAGC
TTACGAGCATATGAAATAATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAAT
GGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
Found at i:1873395 original size:17 final size:18
Alignment explanation
Indices: 1873373--1873424 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
1873363 GCATCGGTAC
1873373 ACTGTTCACTGTTCACG-
1 ACTGTTCACTGTTCACGT
*
1873390 ACTGTTCACTGTTCAAGGT
1 ACTGTTCACTGTTC-ACGT
*
1873409 ATTGTTCACTGTTCAC
1 ACTGTTCACTGTTCAC
1873425 TATTCATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 14 0.47
18 3 0.10
19 13 0.43
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (18 bp):
ACTGTTCACTGTTCACGT
Found at i:1879688 original size:18 final size:18
Alignment explanation
Indices: 1879667--1879709 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1879657 TCATGCCCAG
1879667 AGTCGTGCCCATGTCTCC
1 AGTCGTGCCCATGTCTCC
1879685 AGTCGTGCCCATGTCTCC
1 AGTCGTGCCCATGTCTCC
*
1879703 AGCCGTG
1 AGTCGTG
1879710 ACCAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.37, G:0.26, T:0.26
Consensus pattern (18 bp):
AGTCGTGCCCATGTCTCC
Found at i:1881011 original size:304 final size:304
Alignment explanation
Indices: 1880447--1881361 Score: 1805
Period size: 304 Copynumber: 3.0 Consensus size: 304
1880437 AAACCATCTC
*
1880447 GGGTGTAACGTTAGCTTGTGCCTTGGGACTACTCATTGCATGGAGACTTGCCATTGTCATGATAG
1 GGGTGTAACGTTAGCTTGTGCCTTGGGACTATTCATTGCATGGAGACTTGCCATTGTCATGATAG
1880512 TAGTCCTACCCCTTCATCATCCTCTCCTTATTAGCTAGAATGGTCTTACTAAAAAGAATGTCCC-
66 TAGTCCTACCCCTTCATCATCCTCTCCTTATTAGCTAGAATGGTCTTACTAAAAAGAATGTCCCA
1880576 AAAAGCAATCGAAGCACACAAGAGAGCAACAAGCTTGCTACCGAGGCAATTTCCATCCACCGAAC
131 AAAAGCAATCGAAGCACACAAGAGAGCAACAAGCTTGCTACCGAGGCAATTTCCATCCACCGAAC
1880641 CATTACCGCCTTCTCATCTCAAGATTGAATCTTGAAAATGCTACAGAAGTCCCACGAGAGTCAAA
196 CATTACCGCCTTCTCATCTCAAGATTGAATCTTGAAAATGCTACAGAAGTCCCACGAGAGTCAAA
1880706 GAAAAGAGAATGTTAGACAATCTTGGTTTGCTGGTCTTGGACTT
261 GAAAAGAGAATGTTAGACAATCTTGGTTTGCTGGTCTTGGACTT
1880750 GGGTGTAACGTTAGCTTGTGCCTTGGGACTATTCATTGCATGGAGACTTGCCATTGTCATGATAG
1 GGGTGTAACGTTAGCTTGTGCCTTGGGACTATTCATTGCATGGAGACTTGCCATTGTCATGATAG
1880815 TAGTCCTACCCCTTCATCATCCTCTCCTTATTAGCTAGAATGGTCTTACTAAAAAGAATGTCCCA
66 TAGTCCTACCCCTTCATCATCCTCTCCTTATTAGCTAGAATGGTCTTACTAAAAAGAATGTCCCA
1880880 AAAAGCAATCGAAGCACACAAGAGAGCAACAAGCTTGCTACCGAGGCAATTTCCATCCACCGAAC
131 AAAAGCAATCGAAGCACACAAGAGAGCAACAAGCTTGCTACCGAGGCAATTTCCATCCACCGAAC
1880945 CATTACCGCCTTCTCATCTCAAGATTGAATCTTGAAAATGCTACAGAAGTCCCACGAGAGTCAAA
196 CATTACCGCCTTCTCATCTCAAGATTGAATCTTGAAAATGCTACAGAAGTCCCACGAGAGTCAAA
1881010 GAAAAGAGAATGTTAGACAATCTTGGTTTGCTGGTCTTGGACTT
261 GAAAAGAGAATGTTAGACAATCTTGGTTTGCTGGTCTTGGACTT
1881054 GGGTGTAACGTTAGCTTGTGCCTTGGGACTATTCATTGCATGGAGACTTGCCATTGTCATGATAG
1 GGGTGTAACGTTAGCTTGTGCCTTGGGACTATTCATTGCATGGAGACTTGCCATTGTCATGATAG
1881119 TAGTCCTACCCCTTCATCATCCTCTCCTTATTAGCTAGAATGGTCTTACTAAAAAGAATGTCCCA
66 TAGTCCTACCCCTTCATCATCCTCTCCTTATTAGCTAGAATGGTCTTACTAAAAAGAATGTCCCA
1881184 AAAAGCAATCGAAGCACACAAGAGAGCAACAAGCTTGCTACCGAGGCAATTTCCATCCACCGAAC
131 AAAAGCAATCGAAGCACACAAGAGAGCAACAAGCTTGCTACCGAGGCAATTTCCATCCACCGAAC
*
1881249 CATTACCGCCTTCTCATCTCAAGATTGAATCTTGAAAATGCTACAGAAGTCCCACGAGAGTCGAA
196 CATTACCGCCTTCTCATCTCAAGATTGAATCTTGAAAATGCTACAGAAGTCCCACGAGAGTCAAA
1881314 GAAAAGAGAATGTTAGACAATCTTGGTTTGCTGGTCTTGGACTT
261 GAAAAGAGAATGTTAGACAATCTTGGTTTGCTGGTCTTGGACTT
1881358 GGGT
1 GGGT
1881362 TGTCTCGATT
Statistics
Matches: 609, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
303 128 0.21
304 481 0.79
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (304 bp):
GGGTGTAACGTTAGCTTGTGCCTTGGGACTATTCATTGCATGGAGACTTGCCATTGTCATGATAG
TAGTCCTACCCCTTCATCATCCTCTCCTTATTAGCTAGAATGGTCTTACTAAAAAGAATGTCCCA
AAAAGCAATCGAAGCACACAAGAGAGCAACAAGCTTGCTACCGAGGCAATTTCCATCCACCGAAC
CATTACCGCCTTCTCATCTCAAGATTGAATCTTGAAAATGCTACAGAAGTCCCACGAGAGTCAAA
GAAAAGAGAATGTTAGACAATCTTGGTTTGCTGGTCTTGGACTT
Found at i:1881910 original size:13 final size:13
Alignment explanation
Indices: 1881889--1881921 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1881879 CCAAGAACCA
*
1881889 GCACTATTTTCCG
1 GCACAATTTTCCG
1881902 GCACAATTTTCCG
1 GCACAATTTTCCG
1881915 GCACAAT
1 GCACAAT
1881922 CAAGGAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (13 bp):
GCACAATTTTCCG
Found at i:1886449 original size:3 final size:3
Alignment explanation
Indices: 1886443--1886525 Score: 143
Period size: 3 Copynumber: 28.3 Consensus size: 3
1886433 CCATATTTTA
1886443 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1886490 ATT ATT ATT ATT A-T ATT ATT ATC ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1886526 AAATATTAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 4 0.05
3 72 0.95
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1886987 original size:28 final size:28
Alignment explanation
Indices: 1886946--1886999 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1886936 GAACCTGAAA
1886946 AAAAAAAGAAAAAAAAAAAAAAGAGACC
1 AAAAAAAGAAAAAAAAAAAAAAGAGACC
* * *
1886974 AAAAGAAGACAAAAAAAAAACAGAGA
1 AAAAAAAGAAAAAAAAAAAAAAGAGA
1887000 AATAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (28 bp):
AAAAAAAGAAAAAAAAAAAAAAGAGACC
Found at i:1888734 original size:15 final size:13
Alignment explanation
Indices: 1888714--1888751 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
1888704 ATGTTTTATT
1888714 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
1888729 TTATTTTATTTCA
1 TTATTTTATTTCA
1888742 TTA-TTTATTT
1 TTATTTTATTT
1888752 TACTGTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:1899350 original size:11 final size:11
Alignment explanation
Indices: 1899325--1899381 Score: 87
Period size: 11 Copynumber: 4.9 Consensus size: 11
1899315 ATTATGCTTG
1899325 AAGAAAAAAGGAA
1 AAGAAAAAA--AA
1899338 AAGAAAAAAAA
1 AAGAAAAAAAA
1899349 AAGAAAAAAAA
1 AAGAAAAAAAA
1899360 AAGAAGAAAAAA
1 AAGAA-AAAAAA
1899372 AAGAAAAAAA
1 AAGAAAAAAA
1899382 GGGGGTCAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 23 0.53
12 11 0.26
13 9 0.21
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1899356 original size:12 final size:12
Alignment explanation
Indices: 1899325--1899381 Score: 73
Period size: 12 Copynumber: 4.8 Consensus size: 12
1899315 ATTATGCTTG
*
1899325 AAGAAAAAAGGAA
1 AAGAAAAAA-AAA
1899338 AAG-AAAAAAAA
1 AAGAAAAAAAAA
1899349 AAG-AAAAAAAA
1 AAGAAAAAAAAA
*
1899360 AAGAAGAAAAAA
1 AAGAAAAAAAAA
1899372 AAGAAAAAAA
1 AAGAAAAAAA
1899382 GGGGGTCAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.40
12 21 0.52
13 3 0.08
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:1899369 original size:23 final size:22
Alignment explanation
Indices: 1899325--1899381 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 22
1899315 ATTATGCTTG
1899325 AAGAAAAAAGGAAAAGAAAAAAAA
1 AAGAAAAAA--AAAAGAAAAAAAA
1899349 AAGAAAAAAAAAAGAAGAAAAAA
1 AAGAAAAAAAAAAGAA-AAAAAA
1899372 AAGAAAAAAA
1 AAGAAAAAAA
1899382 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.22
23 16 0.50
24 9 0.28
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAAAAAGAAAAAAAA
Found at i:1900784 original size:83 final size:83
Alignment explanation
Indices: 1900505--1900783 Score: 479
Period size: 83 Copynumber: 3.4 Consensus size: 83
1900495 ATATCTTAGT
1900505 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1900570 TGATCTGGTTTGGCAGAA
66 TGATCTGGTTTGGCAGAA
* *
1900588 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGAAAGTATTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1900653 TGATCTGG-TTGGACAGAA
66 TGATCTGGTTTGG-CAGAA
*
1900671 CCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
1900736 TGATCTGGTTTGGTAGAA
66 TGATCTGGTTTGGCAGAA
* * *
1900754 CCAATCATTAAATTTGAAAGACGAATTTGC
1 CCAATCATTGAATTTGGAAGATGAATTTGC
1900784 TCATAGTAGA
Statistics
Matches: 185, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
82 4 0.02
83 177 0.96
84 4 0.02
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (83 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGCAGAA
Found at i:1901855 original size:112 final size:113
Alignment explanation
Indices: 1901615--1902377 Score: 1020
Period size: 112 Copynumber: 6.8 Consensus size: 113
1901605 ATTTTCAGAG
*
1901615 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAA-AAATTCATAATGAGAAGAATTT-T
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * *
1901678 TCAATTTTTTGCTTAAATTCATCCCTTGATGGATCAGTTTTTCCAGTT
66 TCAACTTTTTGCCTAAATTCATCACTTGATGGATCAGCTTTTCCAGTT
** *
1901726 CGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAA-AAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * *
1901790 TCAATTTTTTGCTTAAATTCATCCCTTGATGGATCAGCTTTTCCAGTT
66 TCAACTTTTTGCCTAAATTCATCACTTGATGGATCAGCTTTTCCAGTT
** * *
1901838 CGAGTTCATACTGAGAAGAACTCATCTGAAGAAAGAAGAA-AAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * *
1901902 TCAATTTTTTTGCTTAAATTCATCCCTTGATGGATCAGCTTTTCCAGTT
66 TCAA-CTTTTTGCCTAAATTCATCACTTGATGGATCAGCTTTTCCAGTT
** *
1901951 CGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * * * * **
1902016 TCAACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAG
66 TCAACTTTTTGCCTAAATTCATCACTTGATGGATCAGCTTTTCCAGTT
1902064 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * * * * **
1902129 TCAACCTTTTACCTAAATCCATCATTTAATGGATCATCTTTT-CAGAG
66 TCAACTTTTTGCCTAAATTCATCACTTGATGGATCAGCTTTTCCAGTT
1902176 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * * * * *
1902241 TCAACCTTTTACCTGAATTCATCAATTGATGGATTATCTTTTCCAG-A
66 TCAACTTTTTGCCTAAATTCATCACTTGATGGATCAGCTTTTCCAGTT
* *
1902288 AAAGTTCATAATGAGAAGAACTCATCTAAAG-AAGAAAGAAGAAGTTCATAATAAGAAGAATTTG
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AAGAAGAAGTTCATAATGAGAAGAATTTG
*
1902352 TTCAACTTTTTGCAT-AATTCTATCAC
65 TTCAACTTTTTGCCTAAATTC-ATCAC
1902378 AGAAGGAGAT
Statistics
Matches: 611, Mismatches: 35, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
111 68 0.11
112 296 0.48
113 220 0.36
114 27 0.04
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (113 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
TCAACTTTTTGCCTAAATTCATCACTTGATGGATCAGCTTTTCCAGTT
Found at i:1901983 original size:225 final size:225
Alignment explanation
Indices: 1901580--1902364 Score: 1109
Period size: 225 Copynumber: 3.5 Consensus size: 225
1901570 ATCAAAGATT
* *
1901580 TGAATCCATC-ATTCGATGGATCAACATTTT-CAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TGAATTCATCAATT-GATGGATCATC-TTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTG
1901643 AAGAAAGAAGAA-AAATTCATAATGAGAAGAATTT-TTCAATTTTTTGCTTAAATTCATCCCTTG
63 AAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATTTTTTGCTTAAATTCATCCCTTG
* *
1901706 ATGGATCAGTTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAA-AAAT
128 ATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGT
** * *
1901770 TCATAATGAGAAGAATTTGTTCAATTTTTTGCT
193 TCATAATGAGAAGAATTTGTTCAACCTTTTACC
* ** * *** *
1901803 TAAATTCATCCCTTGATGGATCAGCTTTTCCAGTTCGAGTTCATACTGAGAAGAACTCATCTGAA
1 TGAATTCATCAATTGATGGATCATCTTTTCCAG-AAAAGTTCATAATGAGAAGAACTCATCTGAA
1901868 GAAAGAAGAA-AAATTCATAATGAGAAGAATTTGTTCAATTTTTTTGCTTAAATTCATCCCTTGA
65 GAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-TTTTTTGCTTAAATTCATCCCTTGA
*
1901932 TGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
129 TGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
1901997 CATAATGAGAAGAATTTGTTCAACCTTTTACC
194 CATAATGAGAAGAATTTGTTCAACCTTTTACC
* *
1902029 TGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCAATTGATGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAA
* ** * * * ** *
1902094 GAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATCCATCATTTAAT
65 GAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATTTTTTGCTTAAATTCATCCCTTGAT
* ****
1902159 GGATCATCTTTT-CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
130 GGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTC
1902223 ATAATGAGAAGAATTTGTTCAACCTTTTACC
195 ATAATGAGAAGAATTTGTTCAACCTTTTACC
* *
1902254 TGAATTCATCAATTGATGGATTATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTAAAG
1 TGAATTCATCAATTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
1902319 -AAGAAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTTGC
66 AAAG-AAGAAGAAATTCATAATGAGAAGAATTTGTTCAATTTTTTGC
1902365 ATAATTCTAT
Statistics
Matches: 507, Mismatches: 46, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
222 4 0.01
223 83 0.16
224 76 0.15
225 191 0.38
226 126 0.25
227 27 0.05
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (225 bp):
TGAATTCATCAATTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATTTTTTGCTTAAATTCATCCCTTGATG
GATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
TAATGAGAAGAATTTGTTCAACCTTTTACC
Found at i:1902696 original size:3 final size:3
Alignment explanation
Indices: 1902690--1902796 Score: 182
Period size: 3 Copynumber: 36.3 Consensus size: 3
1902680 CCATATTTTA
*
1902690 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1902738 ATT ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1902784 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
1902797 AAAATATTAA
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
2 4 0.04
3 94 0.96
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1903251 original size:19 final size:21
Alignment explanation
Indices: 1903229--1903284 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
1903219 AAAAAGAAAA
1903229 AAAAGAAAAAACAGAGA-CC-
1 AAAAGAAAAAACAGAGAGCCG
* *
1903248 AAAAG-AAGAACATAGAGCCG
1 AAAAGAAAAAACAGAGAGCCG
1903268 AAGAA-AAAAAACAGAGA
1 AA-AAGAAAAAACAGAGA
1903285 AATAATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 9 0.31
19 7 0.24
20 2 0.07
21 11 0.38
ACGTcount: A:0.66, C:0.12, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAAGAAAAAACAGAGAGCCG
Found at i:1905926 original size:13 final size:13
Alignment explanation
Indices: 1905910--1905935 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1905900 TTTTATTAAA
1905910 AATTTTTAAAATT
1 AATTTTTAAAATT
1905923 AATTTTTAAAATT
1 AATTTTTAAAATT
1905936 TTGATTGAAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTTAAAATT
Found at i:1907020 original size:14 final size:14
Alignment explanation
Indices: 1907003--1907063 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 14
1906993 ACTTAAAAAG
1907003 TTTTTTGAAAAATA
1 TTTTTTGAAAAATA
*
1907017 TTTTTCATAAAATGAATTA
1 TTTTT--TGAAA--AA-TA
1907036 TATTTTTTGAAAAATA
1 T-T-TTTTGAAAAATA
1907052 TTTTTTGAAAAA
1 TTTTTTGAAAAA
1907064 CGTTTTACAG
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
14 15 0.39
15 1 0.03
16 7 0.18
17 2 0.05
18 2 0.05
19 7 0.18
20 1 0.03
21 3 0.08
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (14 bp):
TTTTTTGAAAAATA
Found at i:1907509 original size:31 final size:29
Alignment explanation
Indices: 1907441--1907571 Score: 72
Period size: 31 Copynumber: 4.3 Consensus size: 29
1907431 TTAATTTTTT
*
1907441 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
1907471 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
* * * * *
1907504 TTATATTAATTATTTATTAAAGTAATAGT-A
1 TTATATT--TTATTAATAAAAATATTAATAA
* * *
1907534 TTATATTATATT-TTAAATATATTAATTAA
1 TTATATTTTATTAATAAAAATATTAA-TAA
1907563 -TATATTTTA
1 TTATATTTTA
1907572 AATATCTTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 22
0.68 0.12 0.19
Matches are distributed among these distances:
27 7 0.09
28 13 0.17
29 1 0.01
30 9 0.12
31 22 0.29
32 6 0.08
33 19 0.25
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:1907556 original size:21 final size:21
Alignment explanation
Indices: 1907527--1907584 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
1907517 TTATTAAAGT
1907527 AATAGTATTATATTATATTTTA
1 AATA-TATTATATTATATTTTA
*
1907549 AATATATTAATTAATATATTTTA
1 AATATATT-A-TATTATATTTTA
*
1907572 AATATCTT-TATTA
1 AATATATTATATTA
1907585 AAATATTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.13
21 4 0.13
22 5 0.16
23 18 0.58
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
AATATATTATATTATATTTTA
Found at i:1907570 original size:23 final size:23
Alignment explanation
Indices: 1907540--1907591 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1907530 AGTATTATAT
1907540 TATATTTTAAATATATTAATTAA
1 TATATTTTAAATATATTAATTAA
* *
1907563 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAATATATTAATTAA
*
1907586 AATATT
1 TATATT
1907592 ACAAGATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATTTTAAATATATTAATTAA
Found at i:1907740 original size:31 final size:30
Alignment explanation
Indices: 1907695--1907795 Score: 88
Period size: 29 Copynumber: 3.5 Consensus size: 30
1907685 AAATTTTATT
1907695 AATA-ATT-TATTATATACTATTAAAATAAA
1 AATATATTATATTATATA-TATTAAAATAAA
* *
1907724 AATATATTATATTATAT-TATTATAAT-AT
1 AATATATTATATTATATATATTAAAATAAA
* * *
1907752 AATTTATTATTTTATTATATATTAAAA-ATA
1 AATATATTATATTA-TATATATTAAAATAAA
*
1907782 TA-ATATTATATTAT
1 AATATATTATATTAT
1907796 TAAAAATATT
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
28 14 0.25
29 24 0.42
30 11 0.19
31 8 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (30 bp):
AATATATTATATTATATATATTAAAATAAA
Found at i:1907741 original size:26 final size:26
Alignment explanation
Indices: 1907702--1907794 Score: 70
Period size: 26 Copynumber: 3.6 Consensus size: 26
1907692 ATTAATAATT
1907702 TATTATA-TACTATTAAAATAAAAATA
1 TATTATATTA-TATTAAAATAAAAATA
** *
1907728 TATTATATTATATTATTATAATATAATT
1 TATTATATTATATTAAAATAA-A-AATA
*
1907756 TATTAT-TT-TATTATATATTAAAAATA
1 TATTATATTATATTA-A-AATAAAAATA
1907782 TA--ATATTATATTA
1 TATTATATTATATTA
1907795 TTAAAAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
24 2 0.04
25 2 0.04
26 31 0.58
27 6 0.11
28 12 0.23
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTATATTATATTAAAATAAAAATA
Found at i:1907759 original size:23 final size:23
Alignment explanation
Indices: 1907724--1907770 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1907714 TTAAAATAAA
1907724 AATATATTATATTATATTATTAT
1 AATATATTATATTATATTATTAT
*
1907747 AATATAATT-TATTATTTTATTAT
1 AATAT-ATTATATTATATTATTAT
1907770 A
1 A
1907771 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATATTATATTATATTATTAT
Found at i:1907808 original size:23 final size:24
Alignment explanation
Indices: 1907765--1907841 Score: 90
Period size: 23 Copynumber: 3.3 Consensus size: 24
1907755 TTATTATTTT
1907765 ATTATA-TATTAAAAATA-TAAT-
1 ATTATATTATTAAAAATATTAATA
1907786 ATTATATTATTAAAAATATTAATA
1 ATTATATTATTAAAAATATTAATA
* * *
1907810 AATATATT-TTAAATATTTTAATA
1 ATTATATTATTAAAAATATTAATA
1907833 ATTAATATT
1 ATT-ATATT
1907842 TTGATTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 6 0.12
22 11 0.23
23 19 0.40
24 12 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTATATTATTAAAAATATTAATA
Found at i:1907826 original size:52 final size:52
Alignment explanation
Indices: 1907720--1907881 Score: 129
Period size: 54 Copynumber: 3.1 Consensus size: 52
1907710 ACTATTAAAA
* **
1907720 TAAAAATATATTATATTATATTATTATAATATAATTTATTATTTTATTATATAT
1 TAAAAATATA-TATATTATATTATTAAAATATAATAAATTATTTTA-TATATAT
* *
1907774 TAAAAATATA-ATATTATATTATTAAAAATATTAATAAATATATTTTAAATATTT
1 TAAAAATATATATATTATATTATT-AAAATA-TAATAAAT-TATTTTATATATAT
* * * *
1907828 TAATAAT-TA-ATATT-T-TGATTAAAATGATATTAAAATATTTT-TATTGATAT
1 TAAAAATATATATATTATATTATTAAAAT-ATAATAAATTATTTTATA-T-ATAT
1907878 TAAA
1 TAAA
1907882 TTCATAAAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
48 1 0.01
49 7 0.08
50 17 0.19
51 5 0.06
52 14 0.16
53 12 0.13
54 27 0.30
55 7 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (52 bp):
TAAAAATATATATATTATATTATTAAAATATAATAAATTATTTTATATATAT
Found at i:1914277 original size:17 final size:18
Alignment explanation
Indices: 1914251--1914320 Score: 52
Period size: 21 Copynumber: 3.6 Consensus size: 18
1914241 CGACCCGACC
*
1914251 CAAAATAATATATTTATT
1 CAAAAAAATATATTTATT
1914269 -AAAAAAATATTATTTTTATT
1 CAAAAAAATA-TA--TTTATT
1914289 CAATAAAAATATGAATTTAATT
1 CAA-AAAAATAT--ATTT-ATT
*
1914311 GAAAAAAATA
1 CAAAAAAATA
1914321 ATATATAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
17 8 0.19
18 2 0.05
20 6 0.14
21 13 0.31
22 12 0.29
23 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (18 bp):
CAAAAAAATATATTTATT
Found at i:1914277 original size:20 final size:21
Alignment explanation
Indices: 1914252--1914326 Score: 75
Period size: 22 Copynumber: 3.6 Consensus size: 21
1914242 GACCCGACCC
1914252 AAAATAATATATTTATT-AAA
1 AAAATAATATATTTATTCAAA
* *
1914272 AAAATATTATTTTTATTCAATA
1 AAAATAATATATTTATTCAA-A
*
1914294 AAAAT-ATGA-ATTTAATTGAAA
1 AAAATAAT-ATATTT-ATTCAAA
1914315 AAAATAATATAT
1 AAAATAATATAT
1914327 AGAGGGATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 15 0.34
21 13 0.30
22 16 0.36
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAATAATATATTTATTCAAA
Found at i:1918174 original size:15 final size:16
Alignment explanation
Indices: 1918154--1918187 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1918144 AAAAAGGGGG
1918154 AAATAATAA-AATAAT
1 AAATAATAATAATAAT
*
1918169 AAATAATAATAGTAAT
1 AAATAATAATAATAAT
1918185 AAA
1 AAA
1918188 GATAAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:1923500 original size:12 final size:12
Alignment explanation
Indices: 1923483--1923511 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1923473 AGGGGTATGC
1923483 GAAAACTAGAGA
1 GAAAACTAGAGA
1923495 GAAAACTAGAGA
1 GAAAACTAGAGA
1923507 GAAAA
1 GAAAA
1923512 ATAAGATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.24, T:0.07
Consensus pattern (12 bp):
GAAAACTAGAGA
Found at i:1924696 original size:26 final size:28
Alignment explanation
Indices: 1924637--1924697 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 28
1924627 AGTATTGCTA
*
1924637 AGCTCGACTCGACTCGAAAACTCTGAAATGG
1 AGCTCGACTCGACTCGAAAACTCTG--A-CG
1924668 AGCTCGACTCGACTCGAAAACTC-G-CG
1 AGCTCGACTCGACTCGAAAACTCTGACG
1924694 AGCT
1 AGCT
1924698 TAAAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 23 0.79
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.18
Consensus pattern (28 bp):
AGCTCGACTCGACTCGAAAACTCTGACG
Found at i:1925624 original size:21 final size:21
Alignment explanation
Indices: 1925595--1925680 Score: 145
Period size: 21 Copynumber: 4.1 Consensus size: 21
1925585 ATTCTGACTA
*
1925595 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
1925616 TCGCGTTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
1925637 TCGCGTTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
* *
1925658 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTCCCAAAT
1925679 TC
1 TC
1925681 ACAATGTGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATTTCCCAAAT
Found at i:1925711 original size:20 final size:20
Alignment explanation
Indices: 1925682--1925812 Score: 165
Period size: 20 Copynumber: 6.5 Consensus size: 20
1925672 TCCTAATTCA
*
1925682 CAATGTGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
** * *
1925702 CAATGCGAATTTGGAAAATCA
1 CAATGCGAA-TACGTAAATCG
*
1925723 CAATGCGATTACGTAAATCG
1 CAATGCGAATACGTAAATCG
1925743 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
1925763 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
1925783 CAATGCGAATATG-ACAATCG
1 CAATGCGAATACGTA-AATCG
*
1925803 CAACGCGAAT
1 CAATGCGAAT
1925813 CTGACAATCG
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 80 0.83
21 15 0.16
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:1925817 original size:20 final size:20
Alignment explanation
Indices: 1925697--1925846 Score: 114
Period size: 20 Copynumber: 7.5 Consensus size: 20
1925687 TGAATACGTA
* *
1925697 AATCGCAATGCGAATTTGGAA
1 AATCGCAATGCGAATCT-GAC
* *
1925718 AATCACAATGCGATTAC-GTA-
1 AATCGCAATGCGAAT-CTG-AC
1925738 AATCGCAATGCGAATAC-GTA-
1 AATCGCAATGCGAAT-CTG-AC
1925758 AATCGCAATGCGAATAC-GTA-
1 AATCGCAATGCGAAT-CTG-AC
*
1925778 AATCGCAATGCGAATATGAC
1 AATCGCAATGCGAATCTGAC
*
1925798 AATCGCAACGCGAATCTGAC
1 AATCGCAATGCGAATCTGAC
* *
1925818 AATCGCAATGAGATTCTGAC
1 AATCGCAATGCGAATCTGAC
*
1925838 TATCGCAAT
1 AATCGCAAT
1925847 ACTGAATTTC
Statistics
Matches: 113, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.01
20 98 0.87
21 14 0.12
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGAATCTGAC
Found at i:1926714 original size:24 final size:24
Alignment explanation
Indices: 1926687--1926740 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1926677 GTATTCGAAA
1926687 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1926711 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1926735 TTTGAT
1 TTTGAT
1926741 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1929169 original size:14 final size:14
Alignment explanation
Indices: 1929150--1929176 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1929140 TCATTTGATT
1929150 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1929164 ATCGCAACGCGAA
1 ATCGCAACGCGAA
1929177 TATGACTATC
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:0.41, C:0.30, G:0.22, T:0.07
Consensus pattern (14 bp):
ATCGCAACGCGAAA
Found at i:1929189 original size:20 final size:20
Alignment explanation
Indices: 1929164--1929252 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
1929154 CAACGCGAAA
1929164 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
1929184 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* * *
1929204 ATCTCAACGTGGAATTGACT
1 ATCGCAACGCGGAAATGACT
1929224 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
1929244 ATCGCAACG
1 ATCGCAACG
1929253 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:1929329 original size:34 final size:34
Alignment explanation
Indices: 1929291--1929386 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
1929281 CAAAATTTCG
1929291 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
1929325 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* ** * *
1929358 CGTTACGATAATCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
1929387 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:1931002 original size:42 final size:42
Alignment explanation
Indices: 1930923--1931015 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1930913 CCTCTTCAAC
* * *
1930923 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
1930965 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
1931007 GATGACAGG
1 GATGACAGG
1931016 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1931518 original size:20 final size:20
Alignment explanation
Indices: 1931495--1931543 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1931485 GAAACTTAAA
1931495 ATCGCAACGCGAAAATGAAT
1 ATCGCAACGCGAAAATGAAT
* *
1931515 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGAAT
*
1931535 GTCGCAACG
1 ATCGCAACG
1931544 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGAAT
Found at i:1931553 original size:34 final size:34
Alignment explanation
Indices: 1931515--1931667 Score: 119
Period size: 34 Copynumber: 4.4 Consensus size: 34
1931505 GAAAATGAAT
*
1931515 ATCGCAATGCGAAAATGACTGTCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
** * * *
1931549 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
* * * *
1931582 ATCTCAACGTGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AGA-GA
* **
1931620 CTATCGCAATACGAATTTGACTATCGCAACGAGAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
*
1931656 ATCACAATGCGA
1 ATCGCAATGCGA
1931668 TTTTCATTTC
Statistics
Matches: 89, Mismatches: 23, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
33 24 0.27
34 34 0.38
36 3 0.03
37 4 0.04
38 3 0.03
40 21 0.24
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.18
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
Found at i:1931617 original size:20 final size:20
Alignment explanation
Indices: 1931592--1931648 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1931582 ATCTCAACGT
*
1931592 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAATAC
1931612 GAAAATGACTATCGCAATAC
1 GAAAATGACTATCGCAATAC
**
1931632 GAATTTGACTATCGCAA
1 GAAAATGACTATCGCAA
1931649 CGAGAGAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (20 bp):
GAAAATGACTATCGCAATAC
Found at i:1931723 original size:20 final size:20
Alignment explanation
Indices: 1931695--1931871 Score: 175
Period size: 20 Copynumber: 9.5 Consensus size: 20
1931685 GATTCTTTCG
**
1931695 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1931715 TTCCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1931735 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1931755 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1931775 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
* **
1931789 TTGTGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1931808 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
1931822 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1931842 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1931862 TTGCGATAGT
1 TTGCGATAGT
1931872 AAACTATTCT
Statistics
Matches: 134, Mismatches: 9, Indels: 28
0.78 0.05 0.16
Matches are distributed among these distances:
14 13 0.10
16 12 0.09
17 6 0.04
18 5 0.04
19 6 0.04
20 92 0.69
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1933765 original size:20 final size:20
Alignment explanation
Indices: 1933742--1933796 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1933732 CTGAAACTTT
1933742 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
1933762 AAATTGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
1933782 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
1933797 TTTGACTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1933854 original size:33 final size:34
Alignment explanation
Indices: 1933784--1933856 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
1933774 GAAAATGACT
* **
1933784 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
*
1933818 ATCGCAACGCGAA-ATGAAAATCGCAATGACAA-A
1 ATCGCAACGCGAATATGAAAATCGCAACG-CAAGA
1933851 ATCGCA
1 ATCGCA
1933857 TTGCGATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 18 0.53
34 16 0.47
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
Found at i:1934242 original size:22 final size:22
Alignment explanation
Indices: 1934180--1934245 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
1934170 TGACCGTGAA
* *
1934180 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
1934202 TGATATCGTCGGCGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1934224 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1934246 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1934450 original size:20 final size:20
Alignment explanation
Indices: 1934441--1934571 Score: 199
Period size: 20 Copynumber: 6.5 Consensus size: 20
1934431 CGATAGTTAG
1934441 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1934461 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT
1934481 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1934501 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
1934522 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1934542 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1934562 ATTCGCATTG
1 ATTCGCATTG
1934572 TAAATTAGGA
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
20 83 0.85
21 15 0.15
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1934547 original size:61 final size:60
Alignment explanation
Indices: 1934443--1934571 Score: 195
Period size: 61 Copynumber: 2.1 Consensus size: 60
1934433 ATAGTTAGAT
** *
1934443 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACTTATTCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
* * *
1934503 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGA-TTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
1934564 TCGCATTG
1 TCGCATTG
1934572 TAAATTAGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 11 0.18
61 51 0.82
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (60 bp):
TCGCATTGCGATTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
Found at i:1938705 original size:52 final size:52
Alignment explanation
Indices: 1938640--1938798 Score: 309
Period size: 52 Copynumber: 3.1 Consensus size: 52
1938630 TACTGAACAA
1938640 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
*
1938692 TATGTTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1938744 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1938796 TAT
1 TAT
1938799 TTTGTTGTTA
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 105 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (52 bp):
TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
Found at i:1941909 original size:43 final size:42
Alignment explanation
Indices: 1941841--1941974 Score: 187
Period size: 43 Copynumber: 3.1 Consensus size: 42
1941831 TAATTAGCGA
* *
1941841 CGTTTGTATCCAAAAATGCCACTATAGATCTGACCTTTTGCAG
1 CGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC-G
1941884 CGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
1 CGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
* * * *
1941926 ACGTTTGTTTCCAAAAACGCCGTTGTAGGTCTGACCTTTTGCGG
1 -CGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC-G
1941970 CGTTT
1 CGTTT
1941975 TGCACTAGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
42 1 0.01
43 81 0.98
44 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (42 bp):
CGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
Found at i:1941987 original size:43 final size:42
Alignment explanation
Indices: 1941851--1941993 Score: 137
Period size: 43 Copynumber: 3.3 Consensus size: 42
1941841 CGTTTGTATC
* * * *
1941851 CAAAAATGCCACTATAGATCTGACCTTTTGCAGCG-TTTGTA
1 CAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTGCA
* *
1941892 TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGACGTTTGTTTC-
1 --CAAAAACGCCGCTATAGATCTGACCTTTTGCGGCG-TT-TTGCA
* * *
1941937 CAAAAACGCCGTTGTAGGTCTGACCTTTTGCGGCGTTTTGCA
1 CAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTGCA
*
1941979 CTAGAAACGCCGCTA
1 C-AAAAACGCCGCTA
1941994 ATTCTCAACC
Statistics
Matches: 81, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
41 3 0.04
42 3 0.04
43 72 0.89
45 1 0.01
46 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (42 bp):
CAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTGCA
Found at i:1942276 original size:43 final size:42
Alignment explanation
Indices: 1942025--1942251 Score: 145
Period size: 43 Copynumber: 5.3 Consensus size: 42
1942015 GTTTTCGATA
* * * * **
1942025 AAAACGCCGCTAAAAAACATAA-CTTACTGCGGCATTTTTGGG
1 AAAACGCCGCTAAATAACA-AATCCTATTGCGGCGTTTTTCAG
* * * * * *
1942067 AAAAACGTCGCAAAATATCAAAACCTATTGCGGCGGTTTTAAG
1 -AAAACGCCGCTAAATAACAAATCCTATTGCGGCGTTTTTCAG
* * ** * *
1942110 TAAAACGTCGCTACATCTCAAAACC-ATTTACGGCGTTTTTTCTA-
1 -AAAACGCCGCTAAATAACAAATCCTA-TTGCGGCG-TTTTTC-AG
* * * ** *
1942154 AAAACGCCGTTAAACATCAACGCCTATTGCGGCGTTTTTCTG
1 AAAACGCCGCTAAATAACAAATCCTATTGCGGCGTTTTTCAG
1942196 ACAAACGCCGCTAAATAACAAATCCTATTGCGGCGTTTGTTCAG
1 A-AAACGCCGCTAAATAACAAATCCTATTGCGGCGTTT-TTCAG
1942240 AAAACGCCGCTA
1 AAAACGCCGCTA
1942252 TATGTTGTAA
Statistics
Matches: 144, Mismatches: 32, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
42 10 0.07
43 123 0.85
44 10 0.07
45 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (42 bp):
AAAACGCCGCTAAATAACAAATCCTATTGCGGCGTTTTTCAG
Found at i:1945423 original size:36 final size:35
Alignment explanation
Indices: 1945312--1945420 Score: 157
Period size: 35 Copynumber: 3.1 Consensus size: 35
1945302 CAACTTTGAA
* *
1945312 AAAATGGTTTTCAAAGTTTAGTAAATGTTTCTTTG
1 AAAATTGTTTTCAAAGTTTGGTAAATGTTTCTTTG
*
1945347 AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATTGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* *
1945382 AAAATTGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 AAAATTG-TTTTCAAAGTTTGGTAAATGTTTCTTTG
1945417 AAAA
1 AAAA
1945421 ATTATAATGG
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 46 0.68
36 22 0.32
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (35 bp):
AAAATTGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:1945864 original size:16 final size:16
Alignment explanation
Indices: 1945832--1945865 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1945822 ACTATTTACG
**
1945832 TGAATAGTAAATTTTT
1 TGAATAGTAAAAATTT
1945848 TGAATAGTAAAAATTT
1 TGAATAGTAAAAATTT
1945864 TG
1 TG
1945866 TTGGTGATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
TGAATAGTAAAAATTT
Found at i:1949886 original size:21 final size:21
Alignment explanation
Indices: 1949862--1949922 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1949852 AACTTTGAAA
1949862 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
* *
1949883 AAAT--ATTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1949897 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1949918 AAATG
1 AAATG
1949923 TTTCTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.14
19 4 0.14
20 3 0.10
21 10 0.34
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1949967 original size:35 final size:35
Alignment explanation
Indices: 1949861--1949969 Score: 166
Period size: 35 Copynumber: 3.1 Consensus size: 35
1949851 CAACTTTGAA
*
1949861 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1949896 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
1949931 AAAATTGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 AAAA-TGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1949966 AAAA
1 AAAA
1949970 CTTATAATAG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 45 0.65
36 24 0.35
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:1950641 original size:23 final size:23
Alignment explanation
Indices: 1950611--1950660 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1950601 GCTACCATAG
1950611 GGTGCTTGAGTGCAATTTTATTT
1 GGTGCTTGAGTGCAATTTTATTT
1950634 GGTGCTTGAGTGCAATTTTATTT
1 GGTGCTTGAGTGCAATTTTATTT
1950657 GGTG
1 GGTG
1950661 TAGTTCAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.16, C:0.08, G:0.30, T:0.46
Consensus pattern (23 bp):
GGTGCTTGAGTGCAATTTTATTT
Found at i:1952090 original size:12 final size:12
Alignment explanation
Indices: 1952056--1952090 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1952046 TATCATGTTC
**
1952056 TCATATCACAGG
1 TCATATCACATA
1952068 TCATATCACATA
1 TCATATCACATA
1952080 TCATATCACAT
1 TCATATCACAT
1952091 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1958748 original size:15 final size:15
Alignment explanation
Indices: 1958725--1958772 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
1958715 CGTAGGACTC
1958725 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1958740 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
*
1958755 CTACATCCCGAAAGA
1 CTACATCCCGAAGGA
1958770 CTA
1 CTA
1958773 TTATACCCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:1958951 original size:12 final size:12
Alignment explanation
Indices: 1958917--1958951 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1958907 TATCATGTTC
**
1958917 TCATATCACAGG
1 TCATATCACATA
1958929 TCATATCACATA
1 TCATATCACATA
1958941 TCATATCACAT
1 TCATATCACAT
1958952 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1961634 original size:27 final size:27
Alignment explanation
Indices: 1961547--1961637 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 27
1961537 GAATTTGTCT
*
1961547 CGTAGAACTAC-TATGTCTCGAAGGACCA
1 CGTAGAAC-ACATATGTC-CGTAGGACCA
* *
1961575 CATAGAACACATATATCCTGTAGGACCA
1 CGTAGAACACATATGTCC-GTAGGACCA
1961603 CGTAGAACACATATGTCCGTAGGACCA
1 CGTAGAACACATATGTCCGTAGGACCA
*
1961630 TGTAGAAC
1 CGTAGAAC
1961638 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 19 0.35
28 36 0.65
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (27 bp):
CGTAGAACACATATGTCCGTAGGACCA
Found at i:1962462 original size:55 final size:54
Alignment explanation
Indices: 1962379--1962504 Score: 207
Period size: 55 Copynumber: 2.3 Consensus size: 54
1962369 TCGAATTACC
*
1962379 CAGTGTACGATACATAAATAGCACTCGATGTTTTGAGGGTATCGATACACTCCT
1 CAGTGTACGATACACAAATAGCACTCGATGTTTTGAGGGTATCGATACACTCCT
* *
1962433 CAGTGTACTGATACACAAATGGCATTCGATGTTTTGAGGGTATCGATACACTCCT
1 CAGTGTAC-GATACACAAATAGCACTCGATGTTTTGAGGGTATCGATACACTCCT
1962488 CAGTGTACCGATACACA
1 CAGTGTA-CGATACACA
1962505 CTCATACAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
54 8 0.12
55 58 0.87
56 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (54 bp):
CAGTGTACGATACACAAATAGCACTCGATGTTTTGAGGGTATCGATACACTCCT
Found at i:1962563 original size:54 final size:54
Alignment explanation
Indices: 1962499--1962602 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
1962489 AGTGTACCGA
1962499 TACACACTCATACAAATACACATGTTCAACTCATGAGGTATC-AGTACCCTTAGG
1 TACACACTCATACAAATACACATGTTCAACTCATGAGGTATCGA-TACCCTTAGG
*
1962553 TACACACTCATACAAATACACATGTTTAACTCATGAGGTATCGATACCCT
1 TACACACTCATACAAATACACATGTTCAACTCATGAGGTATCGATACCCT
1962603 CCTAAGGGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
54 47 0.98
55 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.27
Consensus pattern (54 bp):
TACACACTCATACAAATACACATGTTCAACTCATGAGGTATCGATACCCTTAGG
Found at i:1965797 original size:27 final size:28
Alignment explanation
Indices: 1965742--1965821 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
1965732 GTAGGACCAC
* * * *
1965742 TATGTCCCGAATGACCACATAAAACACA
1 TATGTCCCGTAGGACCACGTAGAACACA
*
1965770 TATGTCCTGTAGGA-CACGTAGAACACA
1 TATGTCCCGTAGGACCACGTAGAACACA
1965797 TATGTCCCGTAGGACCACGTAGAAC
1 TATGTCCCGTAGGACCACGTAGAAC
1965822 CTTTGACTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 24 0.53
28 21 0.47
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (28 bp):
TATGTCCCGTAGGACCACGTAGAACACA
Found at i:1966397 original size:16 final size:16
Alignment explanation
Indices: 1966372--1966402 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1966362 GTCTTAATTC
1966372 CTTAACATAATGTACA
1 CTTAACATAATGTACA
*
1966388 CTTAATATAATGTAC
1 CTTAACATAATGTAC
1966403 TCATCTGGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (16 bp):
CTTAACATAATGTACA
Found at i:1966773 original size:55 final size:55
Alignment explanation
Indices: 1966669--1966812 Score: 173
Period size: 55 Copynumber: 2.6 Consensus size: 55
1966659 TCATACTTGG
* * * *
1966669 GGGTATCGATACACTCCCCAGTATACTGATACACAAACAACACTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAACAACACTCGATGTTTTAA
* * *** * *
1966724 GGGTACCGATACACTCCTCAGTGTACCGATACATAAATGGCATTTGATGTTTTAA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAACAACACTCGATGTTTTAA
*
1966779 GGGTATCG-TACACTCCTCAGCGTACCGATACACA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACA
1966813 CTCATACAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
54 24 0.32
55 51 0.68
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAACAACACTCGATGTTTTAA
Found at i:2001321 original size:7 final size:7
Alignment explanation
Indices: 2001309--2001333 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2001299 CCAACCCAAA
2001309 AAAAAAG
1 AAAAAAG
2001316 AAAAAAG
1 AAAAAAG
2001323 AAAAAAG
1 AAAAAAG
2001330 AAAA
1 AAAA
2001334 GCAATATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2012833 original size:42 final size:42
Alignment explanation
Indices: 2012786--2012899 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 42
2012776 TTTTCTCGAA
* * * *
2012786 TTCTCGTATTTATTTTACGTAATTCATTTTTTAAAAAATATT
1 TTCTCGTATTTGTTTCACGTAATTCGTTTTTCAAAAAATATT
* **
2012828 TTCTCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATT
1 TTCTCGTATTTGTTTCACGTAATTCGTTTTTCAAAAAATATT
2012870 TTC-CTGTATTTGTTTCACGTAATTCGTTTT
1 TTCTC-GTATTTGTTTCACGTAATTCGTTTT
2012900 CCGGAACGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.02
42 62 0.98
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.54
Consensus pattern (42 bp):
TTCTCGTATTTGTTTCACGTAATTCGTTTTTCAAAAAATATT
Found at i:2013124 original size:31 final size:29
Alignment explanation
Indices: 2013089--2013159 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 29
2013079 AAATATTATT
*
2013089 TATTA-ATTTATTAATATTTATAATAATATAA
1 TATTATATTT-TTAAT-TTTAT-ATAAAATAA
2013120 TATTATATTTTTAATTTTATATAAAATAA
1 TATTATATTTTTAATTTTATATAAAATAA
2013149 TCAATTATATT
1 T--ATTATATT
2013160 ATAATAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 9 0.25
30 5 0.14
31 18 0.50
32 4 0.11
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTATATTTTTAATTTTATATAAAATAA
Found at i:2013224 original size:30 final size:31
Alignment explanation
Indices: 2013185--2013268 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 31
2013175 ATTATATTTT
2013185 TATTTTAATAATATATAATAAAAAAATTATA
1 TATTTTAATAATATATAATAAAAAAATTATA
** *
2013216 TA-TTTAATAATGA-ATAAT--ATTATTTATA
1 TATTTTAATAAT-ATATAATAAAAAAATTATA
*
2013244 TATTTTAATAATATTTTAATAAAAA
1 TATTTTAATAATA-TATAATAAAAA
2013269 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
28 10 0.24
29 9 0.22
30 18 0.44
31 3 0.07
32 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
TATTTTAATAATATATAATAAAAAAATTATA
Found at i:2013224 original size:59 final size:57
Alignment explanation
Indices: 2013106--2013268 Score: 162
Period size: 59 Copynumber: 2.9 Consensus size: 57
2013096 TTATTAATAT
**
2013106 TTATAATAATAT-AATATTATATTTTTAATTTT-AT-ATA-A-AAT-AATCAATTATA
1 TTATAATAATATAAATATTATATTTTT-ATTTTAATAATATATAATAAAAAAATTATA
2013158 TTATAATAATATAAGATATTATATTTTTATTTTAATAATATATAATAAAAAAATTATA
1 TTATAATAATATAA-ATATTATATTTTTATTTTAATAATATATAATAAAAAAATTATA
* * *
2013216 TATTTAATAATGA-ATAATATTAT-TTATATATTTTAATAATATTTTAATAAAAA
1 T-TATAATAAT-ATA-AATATTATATT-TTTATTTTAATAATA-TATAATAAAAA
2013269 TATTTAAAAT
Statistics
Matches: 94, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
52 12 0.13
53 6 0.06
54 15 0.16
55 3 0.03
56 1 0.01
57 3 0.03
58 12 0.13
59 30 0.32
60 12 0.13
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (57 bp):
TTATAATAATATAAATATTATATTTTTATTTTAATAATATATAATAAAAAAATTATA
Found at i:2013257 original size:11 final size:11
Alignment explanation
Indices: 2013228--2013265 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2013218 TTTAATAATG
2013228 AATAATATTATT
1 AATAATATT-TT
*
2013240 TAT-ATATTTT
1 AATAATATTTT
2013250 AATAATATTTT
1 AATAATATTTT
2013261 AATAA
1 AATAA
2013266 AAATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.74
12 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATATTTT
Found at i:2013286 original size:23 final size:23
Alignment explanation
Indices: 2013260--2013304 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2013250 AATAATATTT
2013260 TAATAAAAATATTTAAAATATAC
1 TAATAAAAATATTTAAAATATAC
* * *
2013283 TAATTAATATTTTTAAAATATA
1 TAATAAAAATATTTAAAATATA
2013305 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAAATATTTAAAATATAC
Found at i:2013439 original size:18 final size:18
Alignment explanation
Indices: 2013416--2013470 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
2013406 TACTATTTAA
2013416 TAATAAATAAATTATTTT
1 TAATAAATAAATTATTTT
**
2013434 TAAT-AATAAAAAATTTT
1 TAATAAATAAATTATTTT
2013451 TATGATAAATAATATTATTT
1 TA--ATAAATAA-ATTATTT
2013471 ATTTTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 13 0.45
18 4 0.14
19 2 0.07
20 5 0.17
21 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAATAAATAAATTATTTT
Found at i:2013472 original size:19 final size:19
Alignment explanation
Indices: 2013399--2013472 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
2013389 TAATAAAATT
*
2013399 ATAAA-AATACTATTTAATA
1 ATAAATAATATTATTT-ATA
*
2013418 ATAAATAA-ATTATTTTTA
1 ATAAATAATATTATTTATA
* * *
2013436 ATAATAAAAAATT-TTTATG
1 ATAA-ATAATATTATTTATA
2013455 ATAAATAATATTATTTAT
1 ATAAATAATATTATTTAT
2013473 TTTATTTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
18 12 0.27
19 27 0.61
20 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (19 bp):
ATAAATAATATTATTTATA
Found at i:2013629 original size:14 final size:14
Alignment explanation
Indices: 2013595--2013635 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2013585 AAATGTAATT
*
2013595 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
2013609 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
* *
2013623 CGTTTTCCAGAAA
1 CATTTTCCGGAAA
2013636 TGTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:2013680 original size:29 final size:30
Alignment explanation
Indices: 2013637--2013709 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
2013627 TTCCAGAAAT
*
2013637 GTAATTCATTTTTCAG-AATTTAAATTCCA
1 GTAATTCATTTTTCAGTAATTCAAATTCCA
* **
2013666 TTAATTCATTTTTCAGTAATTCAAATTGTA
1 GTAATTCATTTTTCAGTAATTCAAATTCCA
2013696 GTAATTCATTTTTC
1 GTAATTCATTTTTC
2013710 GAAAAACTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 15 0.39
30 23 0.61
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (30 bp):
GTAATTCATTTTTCAGTAATTCAAATTCCA
Found at i:2013685 original size:15 final size:15
Alignment explanation
Indices: 2013637--2013709 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
2013627 TTCCAGAAAT
2013637 GTAATTCATTTTTCA
1 GTAATTCATTTTTCA
* ** *
2013652 G-AATTTAAATTCCA
1 GTAATTCATTTTTCA
*
2013666 TTAATTCATTTTTCA
1 GTAATTCATTTTTCA
* *
2013681 GTAATTCAAATTGT-A
1 GTAATTC-ATTTTTCA
2013696 GTAATTCATTTTTC
1 GTAATTCATTTTTC
2013710 GAAAAACTAA
Statistics
Matches: 41, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
14 13 0.32
15 24 0.59
16 4 0.10
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (15 bp):
GTAATTCATTTTTCA
Found at i:2013790 original size:16 final size:16
Alignment explanation
Indices: 2013771--2013801 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2013761 AGAATAACCT
2013771 ATTTATTTGATCATTC
1 ATTTATTTGATCATTC
*
2013787 ATTTATTTTATCATT
1 ATTTATTTGATCATT
2013802 TGATTAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTATTTGATCATTC
Found at i:2017553 original size:27 final size:26
Alignment explanation
Indices: 2017523--2017580 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
2017513 GGAAACTTTC
*
2017523 AATTTGTTTGAAA-AAAAAACACTGTTA
1 AATTT-TTT-AAAGAAAAAACACTATTA
**
2017550 AATTTTTTAAAGTTAAAACACTATTA
1 AATTTTTTAAAGAAAAAACACTATTA
2017576 AATTT
1 AATTT
2017581 AATTAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 3 0.11
26 19 0.70
27 5 0.19
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (26 bp):
AATTTTTTAAAGAAAAAACACTATTA
Found at i:2018409 original size:13 final size:13
Alignment explanation
Indices: 2018391--2018416 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2018381 TTTCATCTCA
2018391 TGCTTATAACTTG
1 TGCTTATAACTTG
2018404 TGCTTATAACTTG
1 TGCTTATAACTTG
2018417 GACATTCAAA
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:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
TGCTTATAACTTG
Found at i:2023254 original size:12 final size:12
Alignment explanation
Indices: 2023226--2023259 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2023216 ATGTGAAAGG
*
2023226 AATAAATAAATAC
1 AATAAA-AAATAA
2023239 AATAAAAAATAA
1 AATAAAAAATAA
2023251 AATAAAAAA
1 AATAAAAAA
2023260 ATCTCCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:2024386 original size:23 final size:23
Alignment explanation
Indices: 2024360--2024410 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
2024350 AATAACATAT
**
2024360 TAGGTA-CTGCTTATATAATGTAA
1 TAGGTAGC-GCTTATATAATAAAA
2024383 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
2024406 TAGGT
1 TAGGT
2024411 TAATTACTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:2024464 original size:23 final size:23
Alignment explanation
Indices: 2024438--2024495 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2024428 ATTAAGCACA
* *
2024438 ATAATATATTAGATATCGCTTAT
1 ATAATATAATAGATATCACTTAT
* *
2024461 ATAATGTAATAGGTATCACTTAT
1 ATAATATAATAGATATCACTTAT
*
2024484 ATAATAAAATAG
1 ATAATATAATAG
2024496 GTTAATTACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGATATCACTTAT
Found at i:2024494 original size:87 final size:86
Alignment explanation
Indices: 2024348--2024584 Score: 384
Period size: 87 Copynumber: 2.7 Consensus size: 86
2024338 ATTACCAAGT
2024348 ACAATAACATATTAGGTACTGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTA
1 ACAATAACATATTAGGTAC-GCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTA
* *
2024413 ATTACTAGAAACATTATTAAGC
65 ATTACTAGAAACATTATCAAAC
* * * *
2024435 ACAATAATATATTAGATATCGCTTATATAATGTAATAGGTATCACTTATATAATAAAATAGGTTA
1 ACAATAACATATTAGGTA-CGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTA
2024500 ATTACTAGAAACATTATCAAAC
65 ATTACTAGAAACATTATCAAAC
*
2024522 ACAATAACATATTAGGTAGCGCTTATATAATGTAATATGTAGCGCTTATATAATAAAATAGGT
1 ACAATAACATATTAGGTA-CGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGT
2024585 AGCGCTTATA
Statistics
Matches: 137, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
87 136 0.99
88 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (86 bp):
ACAATAACATATTAGGTACGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAA
TTACTAGAAACATTATCAAAC
Found at i:2024551 original size:23 final size:23
Alignment explanation
Indices: 2024534--2024607 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
2024524 AATAACATAT
**
2024534 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
2024557 TATGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
*
2024580 TAGGTAGCGCTTATATAATAAAT
1 TAGGTAGCGCTTATATAATAAAA
2024603 TAGGT
1 TAGGT
2024608 TAATTACTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:2024568 original size:110 final size:110
Alignment explanation
Indices: 2024454--2024691 Score: 368
Period size: 110 Copynumber: 2.2 Consensus size: 110
2024444 TATTAGATAT
** *
2024454 CGCTTATATAATGTAATAGGTATCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCA
1 CGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCA
* * *
2024519 AACACAATAACATATTAGGTAGCGCTTATATAATGTAATATGTAG
66 AACACAATAACATATTAGGTAGCACTTATATAATGTAATAGGTAA
* * *
2024564 CGCTTATATAATAAAATAGGTAGCGCTTATATAATAAATTAGGTTAATTACTGGAAACATTATCA
1 CGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCA
* *
2024629 AGCACAATAACATATTAGGTATCACTTATATAATGTAATAGGTAA
66 AACACAATAACATATTAGGTAGCACTTATATAATGTAATAGGTAA
*
2024674 CACTTATATAATAAAATA
1 CGCTTATATAATAAAATA
2024692 TGTTAATTAC
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 116 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (110 bp):
CGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCA
AACACAATAACATATTAGGTAGCACTTATATAATGTAATAGGTAA
Found at i:2024660 original size:87 final size:87
Alignment explanation
Indices: 2024560--2024789 Score: 361
Period size: 87 Copynumber: 2.6 Consensus size: 87
2024550 AATGTAATAT
* ** *
2024560 GTAGCGCTTATATAATAAAATAGGTAGCGCTTATATAATAAATTAGGTTAATTACTGGAAACATT
1 GTAGCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATT
2024625 ATCAAGCACAATAACATATTAG
66 ATCAAGCACAATAACATATTAG
* * * *
2024647 GTATCACTTATATAATGTAATAGGTAACACTTATATAATAAAATATGTTAATTACTGGAAACATT
1 GTAGCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATT
2024712 ATCAAGCACAATAACATATTAG
66 ATCAAGCACAATAACATATTAG
* * *
2024734 GTAGCGCTTATATAACGTAATAGATAGCGCTTATATAATAAAATAGGTTAATTACT
1 GTAGCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACT
2024790 TAATTTGTTA
Statistics
Matches: 128, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 128 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (87 bp):
GTAGCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATT
ATCAAGCACAATAACATATTAG
Found at i:2024691 original size:23 final size:23
Alignment explanation
Indices: 2024644--2024691 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2024634 AATAACATAT
* **
2024644 TAGGTATCACTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
2024667 TAGGTAACACTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
2024690 TA
1 TA
2024692 TGTTAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.35
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:2024710 original size:197 final size:197
Alignment explanation
Indices: 2024368--2024781 Score: 695
Period size: 197 Copynumber: 2.1 Consensus size: 197
2024358 ATTAGGTACT
** *
2024368 GCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATTAA
1 GCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAA
* * *
2024433 GCACAATAATATATTAGATATCGCTTATATAATGTAATAGGTATCACTTATATAATAAAATAGGT
66 GCACAATAACATATTAGATATCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGT
*
2024498 TAATTACTAGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTATATAATGTAATATG-T
131 TAATTACTAGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTATATAACGTAATA-GAT
2024562 AGC
195 AGC
* *
2024565 GCTTATATAATAAAATAGGTAGCGCTTATATAATAAATTAGGTTAATTACTGGAAACATTATCAA
1 GCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAA
* *
2024630 GCACAATAACATATTAGGTATCACTTATATAATGTAATAGGTAACACTTATATAATAAAATATGT
66 GCACAATAACATATTAGATATCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGT
* *
2024695 TAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGATA
131 TAATTACTAGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTATATAACGTAATAGATA
2024760 GC
196 GC
2024762 GCTTATATAATAAAATAGGT
1 GCTTATATAATAAAATAGGT
2024782 TAATTACTTA
Statistics
Matches: 203, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
196 1 0.00
197 202 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (197 bp):
GCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAA
GCACAATAACATATTAGATATCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGT
TAATTACTAGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTATATAACGTAATAGATA
GC
Found at i:2024748 original size:23 final size:23
Alignment explanation
Indices: 2024722--2024771 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2024712 ATCAAGCACA
* *
2024722 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
*
2024745 ATAACGTAATAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
2024768 ATAA
1 ATAA
2024772 TAAAATAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:2024778 original size:23 final size:23
Alignment explanation
Indices: 2024735--2024779 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2024725 ACATATTAGG
**
2024735 TAGCGCTTATATAACGTAATAGA
1 TAGCGCTTATATAACAAAATAGA
*
2024758 TAGCGCTTATATAATAAAATAG
1 TAGCGCTTATATAACAAAATAG
2024780 GTTAATTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (23 bp):
TAGCGCTTATATAACAAAATAGA
Found at i:2025351 original size:20 final size:23
Alignment explanation
Indices: 2025301--2025346 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2025291 TTACAAAGGA
2025301 TAAC-AAT-ATAATATTATTTAT
1 TAACAAATAATAATATTATTTAT
2025322 TAACAAATAATAATATTATTT-T
1 TAACAAATAATAATATTATTTAT
2025344 TAA
1 TAA
2025347 AATAAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.17
22 7 0.30
23 12 0.52
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TAACAAATAATAATATTATTTAT
Found at i:2025707 original size:192 final size:192
Alignment explanation
Indices: 2025353--2025778 Score: 475
Period size: 192 Copynumber: 2.2 Consensus size: 192
2025343 TTAAAATAAA
*
2025353 ACATTGCAAATTTATCTATTACATTATAATTATCGGTTTCGATGTTTTGGGATCGATATAATTTT
1 ACATTGCAAATTTACCTATTACA-TATAATTATCGGTTTCGATGTTTTGGGATCGATAT-ATTTT
* * *
2025418 AAATGTATCGACACTTTATGTGGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAA
64 AAATGTATCGACACTTTATGTGGCACCTCGTTGGACATTCATTATGAAAAAAAGTATCGACACAA
*
2025483 ACTTAAAATGTTCGATACATTATGTAGACCTATTTTCTCATAAAACCGTATATTTATACCGAGT
129 ACTTAAAATGTTCGATACATTATGTAGACCTATTCTCTCATAAAACCGTATATTTATACCGAGT
* *
2025547 ACATTGTAAATTTACCTATT-C-TA-AATTATCGG-TTCGATGTTTTTGTGATCGATACT-TTTA
1 ACATTGCAAATTTACCTATTACATATAATTATCGGTTTCGATG-TTTTGGGATCGATA-TATTT-
*
2025607 ATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGACA-TCATTAT-AAACAAAATGTATCGA
63 -TAAATGTATCGACACTTTATGTG-GCACCTCGTTGGACATTCATTATGAAA-AAAA-GTATCGA
*** * * * * *
2025670 CAC-TTTTTAAATTGTGTCGATACATTATGTTGACCTATTCTCTCATAAAATC-AATA-TTATAA
124 CACAAACTTAAAATGT-TCGATACATTATGTAGACCTATTCTCTCATAAAACCGTATATTTATAC
2025732 CG-GTT
188 CGAG-T
* * *
2025737 ATATTGTAAA---CCCTATTACATTATAATTATCGGTTTCGATGT
1 ACATTGCAAATTTACCTATTACA-TATAATTATCGGTTTCGATGT
2025779 ACATATGTGT
Statistics
Matches: 200, Mismatches: 18, Indels: 31
0.80 0.07 0.12
Matches are distributed among these distances:
187 6 0.03
188 1 0.00
189 11 0.05
190 43 0.22
191 57 0.28
192 63 0.31
193 1 0.00
194 18 0.09
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (192 bp):
ACATTGCAAATTTACCTATTACATATAATTATCGGTTTCGATGTTTTGGGATCGATATATTTTAA
ATGTATCGACACTTTATGTGGCACCTCGTTGGACATTCATTATGAAAAAAAGTATCGACACAAAC
TTAAAATGTTCGATACATTATGTAGACCTATTCTCTCATAAAACCGTATATTTATACCGAGT
Found at i:2026045 original size:21 final size:21
Alignment explanation
Indices: 2025985--2026045 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
2025975 AATAATATTA
* **
2025985 AATAAATATTCTAATATT-TT
1 AATAAATATTATTTTATTGTT
*
2026005 AAAAAATATTATTATT-TTGTT
1 AATAAATATTATT-TTATTGTT
2026026 AATAAATATTATTTTATTGT
1 AATAAATATTATTTTATTGT
2026046 ATTTGATGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (21 bp):
AATAAATATTATTTTATTGTT
Found at i:2033706 original size:29 final size:29
Alignment explanation
Indices: 2033674--2033747 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 29
2033664 AGTTTGTGGG
2033674 GTTTTTTATAAATAAATTATTTTT-TCAAA
1 GTTTTTTATAAA-AAATTATTTTTATCAAA
*
2033703 GTTTTTT-TAAAATAA-TATTTTTATTAAA
1 GTTTTTTATAAAA-AATTATTTTTATCAAA
*
2033731 -TTTTTTAAAAAAAATTA
1 GTTTTTTATAAAAAATTA
2033748 AAAATATAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 16 0.41
28 16 0.41
29 7 0.18
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (29 bp):
GTTTTTTATAAAAAATTATTTTTATCAAA
Found at i:2033721 original size:27 final size:29
Alignment explanation
Indices: 2033675--2033747 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 29
2033665 GTTTGTGGGG
2033675 TTTTTTATAAATAAATTATTTTT-TCAAAGT
1 TTTTTTA-AAATAAATTATTTTTATCAAA-T
*
2033705 TTTTTTAAAAT-AA-TATTTTTATTAAA-
1 TTTTTTAAAATAAATTATTTTTATCAAAT
*
2033731 TTTTTTAAAAAAAATTA
1 TTTTTTAAAATAAATTA
2033748 AAAATATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 10 0.26
27 9 0.24
28 8 0.21
29 4 0.11
30 7 0.18
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (29 bp):
TTTTTTAAAATAAATTATTTTTATCAAAT
Found at i:2034191 original size:172 final size:172
Alignment explanation
Indices: 2033989--2034334 Score: 676
Period size: 172 Copynumber: 2.0 Consensus size: 172
2033979 CTTAAAATTG
2033989 TATCAATTCAATCATGTCTATAAAACTTTTAACAATTTTCTTGATTAAGTGTCAAATTTTCTTCA
1 TATCAATTCAATCATGTCTATAAAACTTTTAACAATTTTCTTGATTAAGTGTCAAATTTTCTTCA
2034054 TCAAGTTGTCTTTTCATTTCAATTCTTTTCATGCCTACTATATGAAAGCTACTTAAGACATAATT
66 TCAAGTTGTCTTTTCATTTCAATTC-TTTCATGCCTACTATATGAAAGCTACTTAAGACATAATT
2034119 TACATACAACTTTGAGAAGAAAGAGACTT-AAAAAATTCCTTT
130 TACATACAACTTTGAGAAGAAAGAGACTTAAAAAAATTCCTTT
2034161 TATCAATTCAATCATGTCTATAAAACTTTTAACAATTTTCTTGATTAAGTGTCAAATTTTCTTCA
1 TATCAATTCAATCATGTCTATAAAACTTTTAACAATTTTCTTGATTAAGTGTCAAATTTTCTTCA
2034226 TCAAGTTGTCTTTTCATTTCAATTCTTTCATGCCTACTATATGAAAGCTACTTAAGACATAATTT
66 TCAAGTTGTCTTTTCATTTCAATTCTTTCATGCCTACTATATGAAAGCTACTTAAGACATAATTT
2034291 ACATACAACTTTGAGAAGAAAGAGACTTAAAAAAATTCCTTT
131 ACATACAACTTTGAGAAGAAAGAGACTTAAAAAAATTCCTTT
2034333 TA
1 TA
2034335 AATTCATTAT
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
171 68 0.39
172 105 0.61
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (172 bp):
TATCAATTCAATCATGTCTATAAAACTTTTAACAATTTTCTTGATTAAGTGTCAAATTTTCTTCA
TCAAGTTGTCTTTTCATTTCAATTCTTTCATGCCTACTATATGAAAGCTACTTAAGACATAATTT
ACATACAACTTTGAGAAGAAAGAGACTTAAAAAAATTCCTTT
Found at i:2039989 original size:30 final size:31
Alignment explanation
Indices: 2039926--2039995 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
2039916 TAATTTTTTG
2039926 ATTTAGTGATCAAAATAAAACCATTCTTATA
1 ATTTAGTGATCAAAATAAAACCATTCTTATA
2039957 ATTTAGTGATCAAAATAAAACCATTC-TATA
1 ATTTAGTGATCAAAATAAAACCATTCTTATA
2039987 ATTTAGTGA
1 ATTTAGTGA
2039996 ATATATATCG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (31 bp):
ATTTAGTGATCAAAATAAAACCATTCTTATA
Found at i:2041021 original size:17 final size:19
Alignment explanation
Indices: 2040994--2041033 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
2040984 ATATGAAGAA
2040994 AAATAGAAG-AAAAGAGGG
1 AAATAGAAGAAAAAGAGGG
2041012 AAAT-GAAGAAAAAGAGGG
1 AAATAGAAGAAAAAGAGGG
2041030 AAAT
1 AAAT
2041034 TAGATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (19 bp):
AAATAGAAGAAAAAGAGGG
Found at i:2043713 original size:13 final size:13
Alignment explanation
Indices: 2043679--2043728 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
2043669 GACCTACTCG
2043679 TTTCAAAAGCATT
1 TTTCAAAAGCATT
2043692 TCTT-AAAAGCATT
1 T-TTCAAAAGCATT
* *
2043705 TTTCCAAAGCACT
1 TTTCAAAAGCATT
2043718 TTTCAAAAGCA
1 TTTCAAAAGCA
2043729 AAGCCAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (13 bp):
TTTCAAAAGCATT
Found at i:2046423 original size:71 final size:72
Alignment explanation
Indices: 2046340--2046484 Score: 274
Period size: 71 Copynumber: 2.0 Consensus size: 72
2046330 AAGAAGGAAT
2046340 GGTATGAATAACTTGAAGATAAGGAGCGCTGCCATC-AAAGGGCTGAAATTGAAAGTAAATCATT
1 GGTATGAATAACTTGAAGATAAGGAGCGCTGCCATCAAAAGGGCTGAAATTGAAAGTAAATCATT
2046404 TCAGCAG
66 TCAGCAG
2046411 GGTATGAATAACTTGAAGATAAGGAGCGCTGCCATCAGAAAGGGCTGAAATTGAAAGTAAATCAT
1 GGTATGAATAACTTGAAGATAAGGAGCGCTGCCATCA-AAAGGGCTGAAATTGAAAGTAAATCAT
2046476 TTCAGCAG
65 TTCAGCAG
2046484 G
1 G
2046485 TATCCAGGAA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 36 0.50
73 36 0.50
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (72 bp):
GGTATGAATAACTTGAAGATAAGGAGCGCTGCCATCAAAAGGGCTGAAATTGAAAGTAAATCATT
TCAGCAG
Found at i:2046979 original size:34 final size:34
Alignment explanation
Indices: 2046936--2047004 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2046926 ACAAAGGTTA
2046936 ATGGAATTCTCATATCAGAAAGCTGCAAATATCT
1 ATGGAATTCTCATATCAGAAAGCTGCAAATATCT
2046970 ATGGAATTCTCATATCAGAAAGCTGCAAATATCT
1 ATGGAATTCTCATATCAGAAAGCTGCAAATATCT
2047004 A
1 A
2047005 CCATTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (34 bp):
ATGGAATTCTCATATCAGAAAGCTGCAAATATCT
Found at i:2056001 original size:54 final size:53
Alignment explanation
Indices: 2055830--2055997 Score: 209
Period size: 54 Copynumber: 3.2 Consensus size: 53
2055820 TGGAGGCGCA
* * *
2055830 GGAGTTGGGGCCTTATACGGGGGTGTTGGAG-CTTTGGTTGGGGGTGCTGGTGCA
1 GGAGTTGGGGACTTATA-TGGGGTGTTGGAGCCTTT-GTTGGGGGTGCTGGTGCT
* *
2055884 GGAGTTGGGGACTTATATATGGG-GTTGGAGCC-TTGCTGGGGGTGCTGGTGCT
1 GGAGTTGGGGACTTATAT-GGGGTGTTGGAGCCTTTGTTGGGGGTGCTGGTGCT
*
2055936 GTAGTTGGAGG-CTTATATGGCGGTGTTGGAGCCTTTGTTGGGGGTGCTGGTGCT
1 GGAGTTGG-GGACTTATATGG-GGTGTTGGAGCCTTTGTTGGGGGTGCTGGTGCT
2055990 GGAGTTGG
1 GGAGTTGG
2055998 AGGCATGACT
Statistics
Matches: 99, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
51 1 0.01
52 32 0.32
53 20 0.20
54 46 0.46
ACGTcount: A:0.10, C:0.11, G:0.48, T:0.32
Consensus pattern (53 bp):
GGAGTTGGGGACTTATATGGGGTGTTGGAGCCTTTGTTGGGGGTGCTGGTGCT
Found at i:2057246 original size:42 final size:42
Alignment explanation
Indices: 2057193--2057286 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
2057183 TCCACTCTAT
* *
2057193 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATC-TTCCTCGAAGAGGT-CCCTCCCAC
* * *
2057235 CGTTCAAGAGGCCACTGTCTTCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCTTCCTCGAAGAGGTCCCTCCCAC
*
2057277 CATTCAAGAG
1 CGTTCAAGAG
2057287 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 5 0.11
42 37 0.84
43 2 0.05
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCTTCCTCGAAGAGGTCCCTCCCAC
Found at i:2058666 original size:13 final size:14
Alignment explanation
Indices: 2058635--2058669 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2058625 ATTGTTTAAT
2058635 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
2058649 TGATTTGTAAAA-G
1 TGATTTGTAAAAGG
2058662 TGATTTGT
1 TGATTTGT
2058670 TTAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2058812 original size:14 final size:14
Alignment explanation
Indices: 2058793--2058849 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2058783 GCGAAATGAA
2058793 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2058807 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2058826 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2058840 AATCGCAACG
1 AATCGCAACG
2058850 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2058820 original size:33 final size:33
Alignment explanation
Indices: 2058775--2058864 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
2058765 CAAAAGTACT
*
2058775 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2058808 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
2058841 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
2058865 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2058834 original size:19 final size:19
Alignment explanation
Indices: 2058775--2058835 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
2058765 CAAAAGTACT
*
2058775 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2058794 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
2058808 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2058827 ATCGCAACG
1 ATCGCAACG
2058836 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2058914 original size:33 final size:32
Alignment explanation
Indices: 2058864--2058989 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
2058854 ATTAAATTCG
2058864 CGTTGCGA-TTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
2058896 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2058929 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
2058962 CGTTGTGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2058990 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
31 3 0.04
32 8 0.10
33 70 0.83
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2058954 original size:66 final size:65
Alignment explanation
Indices: 2058857--2058988 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 65
2058847 ACGCGAAATT
*
2058857 AAATTCGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
* *
2058922 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2058987 G
65 G
2058988 A
1 A
2058989 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 14 0.22
66 49 0.78
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:2060976 original size:12 final size:12
Alignment explanation
Indices: 2060959--2060983 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2060949 TCTTCGGGGA
2060959 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2060971 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2060983 C
1 C
2060984 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2062034 original size:21 final size:20
Alignment explanation
Indices: 2061991--2062038 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2061981 TTTTCCTAAT
*
2061991 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
2062011 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
2062032 TCGCAAT
1 TCGCAAT
2062039 ACGATTCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:2062116 original size:20 final size:20
Alignment explanation
Indices: 2062069--2062118 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2062059 GAGATAATAC
2062069 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
2062089 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
2062109 AAAATCGCAA
1 AAAATCGCAA
2062119 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:2062426 original size:20 final size:20
Alignment explanation
Indices: 2062331--2062418 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
2062321 CAACGGGGAA
2062331 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
2062351 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
2062371 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
2062391 ATTGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
2062411 ATCGCAAC
1 ATCGCAAC
2062419 TAGAAAATCG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.09
20 44 0.81
21 5 0.09
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:2062486 original size:19 final size:19
Alignment explanation
Indices: 2062445--2062531 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
2062435 GAAATGAAAA
2062445 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
2062461 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2062478 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2062497 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
2062516 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
2062532 TCGTTGCGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 47 0.73
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2062517 original size:38 final size:33
Alignment explanation
Indices: 2062445--2062541 Score: 140
Period size: 38 Copynumber: 2.8 Consensus size: 33
2062435 GAAATGAAAA
2062445 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
2062478 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
2062516 TCGCATTGCGATTTTCTCGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
2062542 AGTCAGTTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
33 23 0.40
35 3 0.05
36 3 0.05
38 29 0.50
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:2062687 original size:14 final size:14
Alignment explanation
Indices: 2062668--2062704 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2062658 CATCAATTAA
2062668 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2062682 ACAAATCATCTTTT
1 ACAAATCAACATTT
2062696 ACAAATCAA
1 ACAAATCAA
2062705 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2064597 original size:20 final size:19
Alignment explanation
Indices: 2064574--2064641 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
2064564 GAAACTTAAA
2064574 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
2064594 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
2064614 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
2064633 ATCGCAACG
1 ATCGCAACG
2064642 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Done.