Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_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: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 12 of 14
Found at i:2248494 original size:84 final size:84
Alignment explanation
Indices: 2248332--2248501 Score: 196
Period size: 84 Copynumber: 2.0 Consensus size: 84
2248322 TTCAACACAA
* * * * *
2248332 ACATTTGAGTTCGATTACACTCAACTCCAAGGCACCTCATTTACAATATAGCTCAAGGCAAGAAG
1 ACATTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAA
* * *
2248397 GGTTATTTGCCAACCAAAG
66 GGCTATCTACCAACCAAAG
* * * * * * * *
2248416 ACATTCGAGTTCGACTACTCTTAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAA
1 ACATTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAA
2248481 GGCTATCTACCAACCAAAG
66 GGCTATCTACCAACCAAAG
2248500 AC
1 AC
2248502 CTGACGAGTT
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (84 bp):
ACATTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAA
GGCTATCTACCAACCAAAG
Found at i:2249854 original size:20 final size:20
Alignment explanation
Indices: 2249829--2249881 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2249819 ATTGACGTGT
2249829 TTTCCCTTTAAATATTGTGC
1 TTTCCCTTTAAATATTGTGC
*
2249849 TTTCCCTTTAAATATTGTGT
1 TTTCCCTTTAAATATTGTGC
2249869 TTTCCCTTTAAAT
1 TTTCCCTTTAAAT
2249882 CTGTTTGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTCCCTTTAAATATTGTGC
Found at i:2250002 original size:11 final size:11
Alignment explanation
Indices: 2249981--2250069 Score: 57
Period size: 11 Copynumber: 8.4 Consensus size: 11
2249971 TTTATTTAAT
2249981 TTTTATT-TTA
1 TTTTATTATTA
2249991 TTTTATTATTA
1 TTTTATTATTA
*
2250002 TTTTACTA--A
1 TTTTATTATTA
2250011 CTTTTA-T-TTA
1 -TTTTATTATTA
*
2250021 TATTTGTTATCTA
1 T-TTTATTAT-TA
2250034 TTTTATT-TTA
1 TTTTATTATTA
2250044 TTATTATTATTA
1 TT-TTATTATTA
* *
2250056 TATTAATATT-
1 TTTTATTATTA
2250066 TTTT
1 TTTT
2250070 CTCTTTTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
9 3 0.05
10 23 0.37
11 24 0.38
12 10 0.16
13 3 0.05
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:2264129 original size:15 final size:16
Alignment explanation
Indices: 2264107--2264166 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 16
2264097 AATTATTAAT
2264107 TAAA-TTAAAAATAT-
1 TAAATTTAAAAATATA
* *
2264121 TCAATTTAAAATTATA
1 TAAATTTAAAAATATA
2264137 TAAATTTAAAATAAATATA
1 TAAATTT--AA-AAATATA
2264156 TAAAATTTAAA
1 T-AAATTTAAA
2264167 TTTATTTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 3 0.08
15 9 0.25
16 6 0.17
17 1 0.03
18 4 0.11
19 7 0.19
20 6 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATTTAAAAATATA
Found at i:2264531 original size:21 final size:21
Alignment explanation
Indices: 2264505--2264571 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
2264495 AGTTCTAAAA
2264505 ATTATAAAAAGTTATTAAATT
1 ATTATAAAAAGTTATTAAATT
*
2264526 ATTAT-AAAA--TA--AATTT
1 ATTATAAAAAGTTATTAAATT
* *
2264542 AATATAAATAGTTATTAAATT
1 ATTATAAAAAGTTATTAAATT
2264563 ATTATAAAA
1 ATTATAAAA
2264572 TAATCATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
16 8 0.23
17 3 0.09
18 2 0.06
19 2 0.06
20 4 0.11
21 16 0.46
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTATAAAAAGTTATTAAATT
Found at i:2264560 original size:22 final size:23
Alignment explanation
Indices: 2264535--2264586 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2264525 TATTATAAAA
* *
2264535 TAAATTTAATAT-AAATAGTTAT
1 TAAATTTAATATAAAATAATCAT
*
2264557 TAAA-TTATTATAAAATAATCAT
1 TAAATTTAATATAAAATAATCAT
2264579 TAAATTTA
1 TAAATTTA
2264587 TGATTGTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 16 0.64
23 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAATTTAATATAAAATAATCAT
Found at i:2270037 original size:20 final size:20
Alignment explanation
Indices: 2270012--2270063 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2270002 AACAAATGGT
2270012 AGTATCGATACTA-CTTAGAG
1 AGTATCGATACTATC-TAGAG
2270032 AGTATCGATACTATCTAGAG
1 AGTATCGATACTATCTAGAG
*
2270052 AGTATCAATACT
1 AGTATCGATACT
2270064 TCTCTTACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTATCTAGAG
Found at i:2271706 original size:229 final size:229
Alignment explanation
Indices: 2271305--2272025 Score: 1327
Period size: 229 Copynumber: 3.1 Consensus size: 229
2271295 GTTATATTGT
* * *
2271305 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
* *
2271369 ATCTTTGGTTAATATTGGTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAA
* * *
2271434 ATAATTTTGTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTA
130 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
2271499 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
2271534 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
2271599 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
2271664 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
2271729 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
*
2271763 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTATGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
2271828 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
*
2271893 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGAAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
2271958 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
*
2271992 AAAGTATATATCATTTTTATAAAAGTGTTCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
2272026 GTATAAAAGT
Statistics
Matches: 480, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
229 410 0.85
230 70 0.15
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (229 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:2272097 original size:20 final size:19
Alignment explanation
Indices: 2272074--2272120 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
2272064 CGATATACCA
2272074 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
2272094 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
2272114 GGTAAAA
1 GGTAAAA
2272121 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2272998 original size:23 final size:23
Alignment explanation
Indices: 2272967--2273030 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
2272957 ATAGGTAAAA
*
2272967 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2272990 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
2273013 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2273031 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2273480 original size:23 final size:23
Alignment explanation
Indices: 2273449--2273512 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2273439 ATAGGTAAAA
*
2273449 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCACTT
* **
2273472 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCACTT
2273495 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2273513 TTGTAAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCACTT
Found at i:2273705 original size:483 final size:481
Alignment explanation
Indices: 2272910--2273917 Score: 1901
Period size: 483 Copynumber: 2.1 Consensus size: 481
2272900 CAATTGCTTC
* *
2272910 AAAATGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATG
1 AAAAAGTATCGATCTTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATG
*
2272975 TAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGT
66 TAATAGGTAGCACTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGT
2273040 ATCTATCATTTTTATAAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCT
131 ATCTATCATTTTTATAAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCT
2273105 TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTA
196 TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTA
2273170 CGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTG
261 CGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTG
2273235 GTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTT
326 GTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTT
*
2273300 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAA
391 TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAA
2273364 TTGAAACATAAATTACATAACTTTAAAA
456 TTGAAACATAAATTACATAACTTT--AA
*
2273392 AAAAAGTATCGATCTTTTTTATAAAAAATATGGACACTTTCAATATAATAGGTAAAAATATGATG
1 AAAAAGTATCGATCTTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATG
2273457 TAATAGGTAGCACTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGT
66 TAATAGGTAGCACTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGT
* *
2273522 ATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATC
131 ATCTATCATTTTTATAAAAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATC
2273587 TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTT
195 TTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTT
2273652 ACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTT
260 ACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTT
2273717 GGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATT
325 GGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATT
2273782 TTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAA
390 TTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAA
2273847 ATTGAAACATAAATTACATAACTTTAA
455 ATTGAAACATAAATTACATAACTTTAA
*
2273874 AAAAATTATCGATCATTTTTTATAAAAAGTATGGACACTTTCAA
1 AAAAAGTATCGATC-TTTTTTATAAAAAGTATGGACACTTTCAA
2273918 CATATTATAA
Statistics
Matches: 514, Mismatches: 9, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
482 169 0.33
483 314 0.61
484 31 0.06
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (481 bp):
AAAAAGTATCGATCTTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATG
TAATAGGTAGCACTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGT
ATCTATCATTTTTATAAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCT
TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTA
CGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTG
GTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTT
TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAA
TTGAAACATAAATTACATAACTTTAA
Found at i:2281991 original size:11 final size:11
Alignment explanation
Indices: 2281977--2282010 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2281967 TAAATAAAAA
*
2281977 ATATTAAATAT
1 ATATTATATAT
*
2281988 ATATTATTTAT
1 ATATTATATAT
2281999 ATATTATATAT
1 ATATTATATAT
2282010 A
1 A
2282011 AATTTTAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATTATATAT
Found at i:2292424 original size:17 final size:17
Alignment explanation
Indices: 2292402--2292436 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2292392 TCGAGGTATG
2292402 TTCTGCAAGCACAATGA
1 TTCTGCAAGCACAATGA
2292419 TTCTGCAAGCACAATGA
1 TTCTGCAAGCACAATGA
2292436 T
1 T
2292437 CCTTTCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (17 bp):
TTCTGCAAGCACAATGA
Found at i:2294406 original size:23 final size:23
Alignment explanation
Indices: 2294380--2294424 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2294370 CACCACAACT
*
2294380 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
2294403 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2294425 ATATAATGAT
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:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:2297710 original size:21 final size:21
Alignment explanation
Indices: 2297659--2297711 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2297649 ATTATGACTA
2297659 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
2297680 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2297701 TCGCAATGCGA
1 TCGCAATGCGA
2297712 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2297784 original size:20 final size:20
Alignment explanation
Indices: 2297701--2297792 Score: 114
Period size: 20 Copynumber: 4.5 Consensus size: 20
2297691 TTTTCCCAAT
*
2297701 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2297721 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
2297742 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2297762 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
2297782 TCGCAATGCGA
1 TCGCAATGCGA
2297793 TTTACATAGC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
19 3 0.05
20 43 0.67
21 18 0.28
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2298059 original size:27 final size:27
Alignment explanation
Indices: 2298002--2298054 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2297992 CATCGCCGGC
* *
2298002 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
2298029 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
2298055 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:2298359 original size:19 final size:19
Alignment explanation
Indices: 2298310--2298380 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
2298300 TAGTTTCGAG
2298310 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
* *
2298330 AAT-AACTATCGCAATGCGA
1 AATGAA-AATCGCAACGCGA
2298349 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
2298368 AACCAAAATCGCA
1 AATGAAAATCGCA
2298381 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 29 0.67
20 14 0.33
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:2298386 original size:19 final size:19
Alignment explanation
Indices: 2298337--2298386 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2298327 GGAAATAACT
**
2298337 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAACCAAA
*
2298356 ATCGCAACGCGAAACCAAA
1 ATCGCAATGCGAAACCAAA
*
2298375 ATCGCATTGCGA
1 ATCGCAATGCGA
2298387 TTTTCATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAACCAAA
Found at i:2298398 original size:19 final size:19
Alignment explanation
Indices: 2298376--2298554 Score: 136
Period size: 19 Copynumber: 10.1 Consensus size: 19
2298366 GAAACCAAAA
*
2298376 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2298395 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2298409 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2298428 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2298442 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2298461 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2298475 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
2298494 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
2298514 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
* *
2298533 ATCTCGTTGCGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
2298553 TC
1 TC
2298555 AACCAAATGA
Statistics
Matches: 130, Mismatches: 13, Indels: 34
0.73 0.07 0.19
Matches are distributed among these distances:
14 30 0.23
16 8 0.06
17 9 0.07
19 50 0.38
20 33 0.25
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2298417 original size:14 final size:14
Alignment explanation
Indices: 2298398--2298486 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
2298388 TTTCATTTCG
2298398 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2298412 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2298431 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2298445 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2298464 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2298478 CGTTGCGAT
1 CGTTGCGAT
2298487 AGTCATTTCG
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 29 0.48
16 6 0.10
17 6 0.10
19 20 0.33
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2298423 original size:33 final size:33
Alignment explanation
Indices: 2298381--2298505 Score: 232
Period size: 33 Copynumber: 3.8 Consensus size: 33
2298371 CAAAATCGCA
2298381 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2298414 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2298447 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
2298480 TTGCGATAGTCATTTCGCGTTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
2298506 AGTCATTTTC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2298517 original size:20 final size:20
Alignment explanation
Indices: 2298478--2298545 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
2298468 GCGATTCTCT
2298478 CGTTGCGATAGTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
2298497 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
** * *
2298517 CGTTGCGATTCTCATTATCT
1 CGTTGCGATAGTCATTTTCG
2298537 CGTTGCGAT
1 CGTTGCGAT
2298546 TTTTATTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2300704 original size:42 final size:42
Alignment explanation
Indices: 2300644--2300736 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
2300634 GCCCGACTCG
* *
2300644 CCTATCATCCCTCAAGAGTCCAC-TCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCC-CTTCCTACCGTTCAAGAGGCC
* *
2300686 CCTATCATTCCTCGAGAGTCCCTTCCTACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCCTTCCTACCGTTCAAGAGGCC
* *
2300728 ACTGTCATC
1 CCTATCATC
2300737 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.26
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCCTTCCTACCGTTCAAGAGGCC
Found at i:2302148 original size:14 final size:14
Alignment explanation
Indices: 2302115--2302151 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2302105 GATTGTTTAA
2302115 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
**
2302129 GAGATTTGTAAAAG
1 TTGATTTGTAAAAG
2302143 TTGATTTGT
1 TTGATTTGT
2302152 TTAATTGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2302339 original size:19 final size:19
Alignment explanation
Indices: 2302258--2302328 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
2302248 AAAAAGTACT
*
2302258 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2302277 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
**
2302296 ATCGCAAAACGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
2302315 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2302329 CTAAATTCGC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 45 0.98
20 1 0.02
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2302345 original size:19 final size:19
Alignment explanation
Indices: 2302258--2302339 Score: 96
Period size: 19 Copynumber: 4.3 Consensus size: 19
2302248 AAAAAGTACT
*
2302258 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
2302277 ATCGCAACGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
**
2302296 ATCGCAAAACGAAACTAAA
1 ATCGCAACGCGAAACTAAA
2302315 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
2302334 TTCGCA
1 ATCGCA
2302340 TTGCGATTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 55 0.98
20 1 0.02
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:2302376 original size:33 final size:32
Alignment explanation
Indices: 2302334--2302445 Score: 172
Period size: 33 Copynumber: 3.4 Consensus size: 32
2302324 CGAAACTAAA
2302334 TTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATT-CCTCGTTGCGATTTTCAT
*
2302367 TTCGCATTGCGAAATT-CGCGTTGCGATTTTCAT
1 TTCGCATTGCG--ATTCCTCGTTGCGATTTTCAT
2302400 TTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTC-CTCGTTGCGATTTTCAT
2302433 TTCGCATTGCGAT
1 TTCGCATTGCGAT
2302446 AGTAATTTCC
Statistics
Matches: 73, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
31 3 0.04
33 67 0.92
35 3 0.04
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (32 bp):
TTCGCATTGCGATTCCTCGTTGCGATTTTCAT
Found at i:2302378 original size:19 final size:19
Alignment explanation
Indices: 2302354--2302445 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
2302344 GATTCCCTCG
2302354 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
2302373 TTGCGA-----AATTCGCG
1 TTGCGATTTTCATTTCGCA
2302387 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2302406 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2302420 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2302439 TTGCGAT
1 TTGCGAT
2302446 AGTAATTTCC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 18 0.32
16 7 0.12
17 7 0.12
19 25 0.44
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2304750 original size:3 final size:3
Alignment explanation
Indices: 2304742--2304786 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
2304732 CGGGGACTTT
* * * *
2304742 TTC TTC TTC TTT TTC TTA TTC TTT TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2304787 AGGATTATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:2304755 original size:12 final size:12
Alignment explanation
Indices: 2304738--2304786 Score: 89
Period size: 12 Copynumber: 4.1 Consensus size: 12
2304728 TCTTCGGGGA
2304738 CTTTTTCTTCTT
1 CTTTTTCTTCTT
*
2304750 CTTTTTCTTATT
1 CTTTTTCTTCTT
2304762 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2304774 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2304786 C
1 C
2304787 AGGATTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2304757 original size:6 final size:6
Alignment explanation
Indices: 2304738--2304782 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
2304728 TCTTCGGGGA
* * *
2304738 CTTTTT CTTCTT CTTTTT CTTATT CTTTTT CTTCTT CTTTTT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTT
2304783 CTTCAGGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (6 bp):
CTTTTT
Found at i:2305812 original size:20 final size:21
Alignment explanation
Indices: 2305787--2305838 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2305777 TTTTCCTAAT
*
2305787 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
2305807 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2305828 TCGCAATGCGA
1 TCGCAATGCGA
2305839 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2305860 original size:20 final size:20
Alignment explanation
Indices: 2305827--2305900 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
2305817 AATTTGGAAA
* *
2305827 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
2305847 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
2305868 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
*
2305888 TTCGCAACGAGAT
1 ATCGCAACGAGAT
2305901 TTTGAAAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
21 14 0.33
22 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:2305912 original size:20 final size:20
Alignment explanation
Indices: 2305823--2305914 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
2305813 TGCGAATTTG
* * *
2305823 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATTCT
** **
2305843 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATTCT
*
2305863 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATTCT
*** *
2305884 GACTTTCGCAACGAGATTTT
1 GAAAATCGCAACGAGATTCT
2305904 GAAAATCGCAA
1 GAAAATCGCAA
2305915 TCATCTTCAA
Statistics
Matches: 53, Mismatches: 18, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
20 38 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
GAAAATCGCAACGAGATTCT
Found at i:2306137 original size:20 final size:20
Alignment explanation
Indices: 2306112--2306181 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
2306102 ATTCATTTGA
2306112 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
** *
2306132 CTATCGCAATTCG-AAATGAA
1 CTATCGCAACGCGAAAATG-G
** *
2306152 AAATCGAAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
2306172 CTATCGCAAC
1 CTATCGCAAC
2306182 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:2306232 original size:14 final size:14
Alignment explanation
Indices: 2306213--2306266 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2306203 GAAAATCGCA
2306213 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
2306227 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
2306244 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
2306260 TTGCGAT
1 TTGCGAT
2306267 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:2306232 original size:33 final size:33
Alignment explanation
Indices: 2306195--2306265 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
2306185 AAAATCGCAA
2306195 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
2306228 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
2306261 TGCGA
1 TGCGA
2306266 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:2307889 original size:41 final size:41
Alignment explanation
Indices: 2307844--2307935 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 41
2307834 CCTCTTCAAC
* *
2307844 GATGACAGTGGCCTCTTGAACTG-TGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAAC-GATGGAGGGGACTCTTGAGG
*
2307885 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGA-TGGAGGGGACTCTTGAGG
*
2307927 AATGACAGG
1 GATGACAGG
2307936 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
40 1 0.02
41 19 0.43
42 24 0.55
ACGTcount: A:0.22, C:0.15, G:0.40, T:0.23
Consensus pattern (41 bp):
GATGACAGGGGCCTCTTGAACGATGGAGGGGACTCTTGAGG
Found at i:2308322 original size:20 final size:20
Alignment explanation
Indices: 2308299--2308354 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
2308289 AAACTTACTT
2308299 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2308319 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
2308339 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
2308355 AAATCGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 6 0.18
20 27 0.82
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2308360 original size:19 final size:19
Alignment explanation
Indices: 2308338--2308429 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
2308328 GGAAATGGCT
2308338 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2308357 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
2308371 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2308390 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
2308404 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2308423 ATCGCAA
1 ATCGCAA
2308430 CGACAAAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.35
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 27 0.47
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2308461 original size:33 final size:33
Alignment explanation
Indices: 2308338--2308450 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
2308328 GGAAATGGCT
*
2308338 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2308371 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2308404 ATCGTAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
2308437 ATCACAACGCGAAA
1 ATCGCAATGCGAAA
2308451 CACAAATCGC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2308479 original size:19 final size:19
Alignment explanation
Indices: 2308457--2308553 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
2308447 GAAACACAAA
2308457 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2308476 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2308492 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2308509 TCACATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2308525 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2308542 TCGCATTGCGAT
1 TCGCATTGCGAT
2308554 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 12 0.20
15 6 0.10
16 7 0.11
17 7 0.11
18 6 0.10
19 23 0.38
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2308498 original size:14 final size:14
Alignment explanation
Indices: 2308479--2308537 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2308469 TTTCATTTCG
2308479 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2308493 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
*
2308510 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
2308526 CGTTGCGATTTT
1 CGTTGCGATTTT
2308538 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 19 0.53
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 7 0.19
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2308504 original size:33 final size:33
Alignment explanation
Indices: 2308462--2308553 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
2308452 ACAAATCGCA
*
2308462 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
2308495 TTGCGATTTTCATTTCACATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2308528 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2308554 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2308592 original size:20 final size:20
Alignment explanation
Indices: 2308538--2308581 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2308528 TTGCGATTTT
*
2308538 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
2308557 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
2308577 CATTT
1 CATTT
2308582 TTGTGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:2309154 original size:18 final size:18
Alignment explanation
Indices: 2309127--2309172 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2309117 GGTCGATCAA
*
2309127 GTGATGGCTCTGGGTGAG
1 GTGATGGCTCTGGGTAAG
*
2309145 GTGATAGCTCTGGGTAAG
1 GTGATGGCTCTGGGTAAG
2309163 GTGATGGCTC
1 GTGATGGCTC
2309173 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.43, T:0.28
Consensus pattern (18 bp):
GTGATGGCTCTGGGTAAG
Found at i:2310538 original size:20 final size:20
Alignment explanation
Indices: 2310490--2310548 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2310480 AATAGTTTCT
* *
2310490 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
2310510 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
2310530 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
2310549 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:2310837 original size:22 final size:22
Alignment explanation
Indices: 2310811--2310854 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2310801 GATGGAGATA
2310811 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
2310833 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
2310855 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:2311102 original size:20 final size:20
Alignment explanation
Indices: 2311047--2311102 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2311037 GTATTATCTC
* *
2311047 GTTGCGAAAGTCAATATTGA
1 GTTGCAAAAGTCAGTATTGA
* *
2311067 GTTGCAAAATTAAGTATTGA
1 GTTGCAAAAGTCAGTATTGA
2311087 GTTGCAAAAGTCAGTA
1 GTTGCAAAAGTCAGTA
2311103 CCGCGTTGCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (20 bp):
GTTGCAAAAGTCAGTATTGA
Found at i:2311150 original size:20 final size:20
Alignment explanation
Indices: 2311095--2311155 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
2311085 GAGTTGCAAA
2311095 AGTCAGTACCGCGTTGCGATTT
1 AGTCAGTACCGCGTTGCGA--T
* * *
2311117 TGT-ATTATCGCGTTGCGAT
1 AGTCAGTACCGCGTTGCGAT
2311136 AGTCAGTACCGCGTTGCGAT
1 AGTCAGTACCGCGTTGCGAT
2311156 TTTCCAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.09
20 14 0.44
21 13 0.41
22 2 0.06
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (20 bp):
AGTCAGTACCGCGTTGCGAT
Found at i:2311179 original size:21 final size:21
Alignment explanation
Indices: 2311149--2311199 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
2311139 CAGTACCGCG
2311149 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
*
2311170 TTGTGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
2311191 TTGCGATTT
1 TTGCGATTT
2311200 ACTTATTCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.43
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:2311258 original size:21 final size:22
Alignment explanation
Indices: 2311206--2311258 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2311196 ATTTACTTAT
*
2311206 TCGCATTCCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2311227 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2311248 TCGCATTGCGA
1 TCGCATTGCGA
2311259 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2313446 original size:3 final size:3
Alignment explanation
Indices: 2313438--2313465 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2313428 TGTCATATAC
2313438 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2313466 AATAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2314822 original size:18 final size:18
Alignment explanation
Indices: 2314796--2314836 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2314786 AATATTTTAA
*
2314796 ATTTATTATTTAATTATT
1 ATTTTTTATTTAATTATT
* *
2314814 ATTTTTTATTTTATTTTT
1 ATTTTTTATTTAATTATT
2314832 ATTTT
1 ATTTT
2314837 AATTAGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:2316556 original size:29 final size:29
Alignment explanation
Indices: 2316514--2316576 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
2316504 AGAGAAATTT
2316514 AGTATAAGAGTATCGATACTCCTTTAATG
1 AGTATAAGAGTATCGATACTCCTTTAATG
2316543 AGTATAAGAGTATCGATACTCCTTTAATG
1 AGTATAAGAGTATCGATACTCCTTTAATG
2316572 AGTAT
1 AGTAT
2316577 CGATATCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (29 bp):
AGTATAAGAGTATCGATACTCCTTTAATG
Found at i:2316576 original size:21 final size:21
Alignment explanation
Indices: 2316550--2316623 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
2316540 ATGAGTATAA
*
2316550 GAGTATCGATACTCCTTTAAT
1 GAGTATCGATACTCCTCTAAT
* *
2316571 GAGTATCGATA-TCATGGGT-A-
1 GAGTATCGATACTCCT--CTAAT
2316591 GAGTATCGATACTCC-CTATAT
1 GAGTATCGATACTCCTCTA-AT
2316612 GAGTATCGATAC
1 GAGTATCGATAC
2316624 GAGGTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 1 0.02
20 15 0.35
21 26 0.60
22 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (21 bp):
GAGTATCGATACTCCTCTAAT
Found at i:2318857 original size:13 final size:13
Alignment explanation
Indices: 2318839--2318867 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2318829 CCTTGGCATC
2318839 AGCTTCTGTGGCG
1 AGCTTCTGTGGCG
2318852 AGCTTCTGTGGCG
1 AGCTTCTGTGGCG
2318865 AGC
1 AGC
2318868 ATCGGTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.24, G:0.38, T:0.28
Consensus pattern (13 bp):
AGCTTCTGTGGCG
Found at i:2322445 original size:23 final size:22
Alignment explanation
Indices: 2322407--2322451 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2322397 TAACATAAGC
2322407 TATATGATATGAGATAGATGAT
1 TATATGATATGAGATAGATGAT
* *
2322429 TATATGTATATGTGATATATGAT
1 TATATG-ATATGAGATAGATGAT
2322452 ATGTGGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (22 bp):
TATATGATATGAGATAGATGAT
Found at i:2323933 original size:21 final size:22
Alignment explanation
Indices: 2323909--2323949 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2323899 GTGGAATTAA
*
2323909 AGAATAAGAA-GTGTTAGAATG
1 AGAATAAGAACATGTTAGAATG
*
2323930 AGAATTAGAACATGTTAGAA
1 AGAATAAGAACATGTTAGAA
2323950 ATTGAGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (22 bp):
AGAATAAGAACATGTTAGAATG
Found at i:2324858 original size:18 final size:18
Alignment explanation
Indices: 2324835--2324900 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
2324825 AGGGATTATC
2324835 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
2324853 AGTGGTCCTTCAGAACAT
1 AGTGGTCCTTCGGGACAT
*
2324871 AATGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
2324889 AGTGGTCCTTCG
1 AGTGGTCCTTCG
2324901 AGATAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2337472 original size:22 final size:23
Alignment explanation
Indices: 2337442--2337486 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
2337432 TACCATTAAA
*
2337442 GTATGTTTTATGTTTTA-TATAT
1 GTATGTTTTATGTGTTATTATAT
* *
2337464 GTATTTTTTTTGTGTTATTATAT
1 GTATGTTTTATGTGTTATTATAT
2337487 ATTACTTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (23 bp):
GTATGTTTTATGTGTTATTATAT
Found at i:2345849 original size:14 final size:14
Alignment explanation
Indices: 2345830--2345856 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2345820 TACATTTTCA
2345830 TTCTTCATTCTTTG
1 TTCTTCATTCTTTG
2345844 TTCTTCATTCTTT
1 TTCTTCATTCTTT
2345857 ACATTCATTT
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:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (14 bp):
TTCTTCATTCTTTG
Found at i:2349416 original size:22 final size:20
Alignment explanation
Indices: 2349388--2349449 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 20
2349378 GCTTGAAAAA
*
2349388 AAAAAGAATGAATGAAAAAGTG
1 AAAAAGAA--AATGAAAAAATG
2349410 AAAAAGAAAAAATGAAAAAAATG
1 AAAAAG--AAAATG-AAAAAATG
2349433 AAAAA-AAAATGAAAAAA
1 AAAAAGAAAATGAAAAAA
2349450 AAAGAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 6 0.17
20 6 0.17
22 10 0.28
23 12 0.33
24 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAAAGAAAATGAAAAAATG
Found at i:2349418 original size:14 final size:14
Alignment explanation
Indices: 2349401--2349514 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 14
2349391 AAGAATGAAT
*
2349401 GAAAAAGTGAAAAA
1 GAAAAAATGAAAAA
2349415 GAAAAAATGAAAAAAA
1 GAAAAAATG--AAAAA
2349431 TGAAAAAAAAATGAAAAA
1 -G---AAAAAATGAAAAA
2349449 -AAAAGAA--AAAAA
1 GAAAA-AATGAAAAA
**
2349461 GAAAAAA--AAAGG
1 GAAAAAATGAAAAA
*
2349473 GAAAAAAAGGAAAAA
1 G-AAAAAATGAAAAA
2349488 TGAAAAAATG-AAAA
1 -GAAAAAATGAAAAA
2349502 GAAAAAA-GAAAAA
1 GAAAAAATGAAAAA
2349515 TGAGGGTTCG
Statistics
Matches: 81, Mismatches: 6, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
12 12 0.15
13 25 0.31
14 14 0.17
15 10 0.12
16 6 0.07
17 1 0.01
18 5 0.06
20 8 0.10
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (14 bp):
GAAAAAATGAAAAA
Found at i:2349428 original size:9 final size:9
Alignment explanation
Indices: 2349416--2349468 Score: 63
Period size: 9 Copynumber: 5.7 Consensus size: 9
2349406 AGTGAAAAAG
2349416 AAAAAATGA
1 AAAAAATGA
2349425 AAAAAATGAAA
1 AAAAAATG--A
2349436 AAAAAATGAA
1 AAAAAATG-A
*
2349446 AAAAAAAGA
1 AAAAAATGA
2349455 AAAAAA-GA
1 AAAAAATGA
2349463 AAAAAA
1 AAAAAA
2349469 AAGGGAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
8 8 0.20
9 15 0.37
10 9 0.22
11 9 0.22
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (9 bp):
AAAAAATGA
Found at i:2349438 original size:11 final size:11
Alignment explanation
Indices: 2349416--2349480 Score: 70
Period size: 11 Copynumber: 6.4 Consensus size: 11
2349406 AGTGAAAAAG
2349416 AAAAAATG--A
1 AAAAAATGAAA
2349425 AAAAAATGAAA
1 AAAAAATGAAA
2349436 AAAAAATGAAA
1 AAAAAATGAAA
2349447 AAAAAA-G--A
1 AAAAAATGAAA
2349455 AAAAAA-GAAA
1 AAAAAATGAAA
*
2349465 AAAAAAGGGAAA
1 AAAAAA-TGAAA
2349477 AAAA
1 AAAA
2349481 GGAAAAATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.16
9 8 0.16
10 8 0.16
11 18 0.36
12 8 0.16
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:2349470 original size:10 final size:10
Alignment explanation
Indices: 2349424--2349487 Score: 69
Period size: 10 Copynumber: 6.4 Consensus size: 10
2349414 AGAAAAAATG
*
2349424 AAAAAAATGA
1 AAAAAAAAGA
2349434 AAAAAAAATGA
1 AAAAAAAA-GA
2349445 AAAAAAAAG-
1 AAAAAAAAGA
2349454 -AAAAAAAGA
1 AAAAAAAAGA
*
2349463 AAAAAAAAGGG
1 AAAAAAAA-GA
*
2349474 AAAAAAAGGA
1 AAAAAAAAGA
2349484 AAAA
1 AAAA
2349488 TGAAAAAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 8 0.17
10 20 0.43
11 18 0.39
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:2349505 original size:20 final size:18
Alignment explanation
Indices: 2349410--2349514 Score: 97
Period size: 20 Copynumber: 5.6 Consensus size: 18
2349400 TGAAAAAGTG
2349410 AAAAAGAAAAAATGAAAA
1 AAAAAGAAAAAATGAAAA
*
2349428 AAATGAAAAAAAAATGAAAA
1 AAA--AAGAAAAAATGAAAA
*
2349448 AAAAAGAAAAAAAGAAAA
1 AAAAAGAAAAAATGAAAA
**
2349466 AAAAAGGGAAAAAA--AGGA
1 AAAAA--GAAAAAATGAAAA
*
2349484 AAAATGAAAAAATGAAAAGA
1 AAAAAGAAAAAATG-AAA-A
2349504 AAAAAGAAAAA
1 AAAAAGAAAAA
2349515 TGAGGGTTCG
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
16 7 0.10
18 27 0.39
19 1 0.01
20 35 0.50
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAAATGAAAA
Found at i:2351131 original size:105 final size:105
Alignment explanation
Indices: 2350424--2351116 Score: 1206
Period size: 105 Copynumber: 6.6 Consensus size: 105
2350414 TCAACAACAA
* * *
2350424 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
2350489 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTATTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
2350529 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGTGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
2350594 CCTAAAGGATAAGGTTCGTAATGAGAAGAGCTTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
2350634 TCAAATCCACCACAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
2350699 CCTAAAGGATAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
2350739 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
2350804 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
2350844 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
2350909 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
2350949 TCAAATCCACCGCAGAAGGATGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
2351014 CTTAAAGGAGAAGGTTCGTAATGAGAAGAGTATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
* * * * *
2351054 TCAAATTCACCCCAGAAGGAGGTGAATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
1 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTC
2351117 ATCCGACAAA
Statistics
Matches: 564, Mismatches: 24, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 564 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (105 bp):
TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
Found at i:2352901 original size:22 final size:24
Alignment explanation
Indices: 2352871--2352916 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
2352861 TACCATTAAA
2352871 GTATGTTTTATGTT-TTA-TATAT
1 GTATGTTTTATGTTATTATTATAT
* *
2352893 GTATTTTTTGTGTTATTATTATAT
1 GTATGTTTTATGTTATTATTATAT
2352917 TTACTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 3 0.15
24 5 0.25
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.65
Consensus pattern (24 bp):
GTATGTTTTATGTTATTATTATAT
Found at i:2354234 original size:28 final size:29
Alignment explanation
Indices: 2354176--2354248 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
2354166 CTAATGTAAC
**
2354176 TTTTAGTCAAAATAAATACTAAAGTTAAT
1 TTTTAGTCAAAATAAATACTAAAAATAAT
*
2354205 TTTTA-TCAAAATAAATACATAAAAATATT
1 TTTTAGTCAAAATAAATAC-TAAAAATAAT
**
2354234 TTTTAACCAAAATAA
1 TTTTAGTCAAAATAA
2354249 GTAATCCACC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 13 0.34
29 17 0.45
30 8 0.21
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTTAGTCAAAATAAATACTAAAAATAAT
Found at i:2354467 original size:20 final size:20
Alignment explanation
Indices: 2354442--2354483 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2354432 ATGTATGACC
* *
2354442 TGACTATGTAATGGTATAAT
1 TGACTATGCAATGGCATAAT
2354462 TGACTATGCAATGGCATAAT
1 TGACTATGCAATGGCATAAT
2354482 TG
1 TG
2354484 CTTATAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (20 bp):
TGACTATGCAATGGCATAAT
Found at i:2364080 original size:23 final size:23
Alignment explanation
Indices: 2364054--2364111 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
2364044 TTTAACTTTT
2364054 ATGCATATTAAATAAATTTGTTC
1 ATGCATATTAAATAAATTTGTTC
**
2364077 ATGCATACCAAATAAATTTGTTC
1 ATGCATATTAAATAAATTTGTTC
*
2364100 ATGGATATTAAA
1 ATGCATATTAAA
2364112 CACAGTGGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (23 bp):
ATGCATATTAAATAAATTTGTTC
Found at i:2377524 original size:25 final size:25
Alignment explanation
Indices: 2377482--2377537 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
2377472 ACAAAATTAT
2377482 CAAAATAAATTAACAAAA-AGTCCAA
1 CAAAATAAATTAACAAAATA-TCCAA
*
2377507 CAAAATAAATTTTA-AAAATATCCAA
1 CAAAATAAA-TTAACAAAATATCCAA
*
2377532 CCAAAT
1 CAAAAT
2377538 TAACAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.61, C:0.16, G:0.02, T:0.21
Consensus pattern (25 bp):
CAAAATAAATTAACAAAATATCCAA
Found at i:2378062 original size:33 final size:32
Alignment explanation
Indices: 2378024--2378091 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
2378014 TCCTCCAGGA
* *
2378024 GGGGTCATATAACTC-TGTGACGGTGGTGGCGGC
1 GGGGTCATAAAAC-CAT-TGACGGTGGCGGCGGC
2378057 GGGGTCATAAAACCAATTGACGGTGGCGGCGGC
1 GGGGTCATAAAACC-ATTGACGGTGGCGGCGGC
2378090 GG
1 GG
2378092 TATCTGGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 1 0.03
33 29 0.94
34 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (32 bp):
GGGGTCATAAAACCATTGACGGTGGCGGCGGC
Found at i:2379833 original size:15 final size:17
Alignment explanation
Indices: 2379814--2379850 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
2379804 AAAAAATAAT
2379814 TAAATAAAATA-TTAAA
1 TAAATAAAATACTTAAA
*
2379830 -AAATTAAATACTTAAA
1 TAAATAAAATACTTAAA
2379846 TAAAT
1 TAAAT
2379851 TACTAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 5 0.28
17 4 0.22
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATAAAATACTTAAA
Found at i:2380618 original size:10 final size:10
Alignment explanation
Indices: 2380599--2380638 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
2380589 TTCACCACAC
2380599 CAAATCCTCT
1 CAAATCCTCT
*
2380609 CAAATTCTCT
1 CAAATCCTCT
2380619 CAAATCCTCT
1 CAAATCCTCT
*
2380629 CAAATTCTCT
1 CAAATCCTCT
2380639 TACTTCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:2380624 original size:20 final size:20
Alignment explanation
Indices: 2380599--2380638 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2380589 TTCACCACAC
2380599 CAAATCCTCTCAAATTCTCT
1 CAAATCCTCTCAAATTCTCT
2380619 CAAATCCTCTCAAATTCTCT
1 CAAATCCTCTCAAATTCTCT
2380639 TACTTCTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (20 bp):
CAAATCCTCTCAAATTCTCT
Found at i:2380745 original size:13 final size:13
Alignment explanation
Indices: 2380698--2380749 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
2380688 ATTTTGTTAG
2380698 TATTTTATTTAAT
1 TATTTTATTTAAT
*
2380711 TATTTAAATTTTTTAA-
1 TA-TT---TTATTTAAT
2380727 TATTTTATTTAAT
1 TATTTTATTTAAT
2380740 TATTTTATTT
1 TATTTTATTT
2380750 TTTTGCAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
12 7 0.22
13 12 0.38
14 2 0.06
15 2 0.06
16 2 0.06
17 7 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:2380751 original size:29 final size:29
Alignment explanation
Indices: 2380687--2380753 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
2380677 TTCTATTTAA
* *
2380687 TATTTTGTTAGTATTTTATTTAATTATTT
1 TATTTTTTTAATATTTTATTTAATTATTT
* *
2380716 AAATTTTTTAATATTTTATTTAATTATTT
1 TATTTTTTTAATATTTTATTTAATTATTT
2380745 TATTTTTTT
1 TATTTTTTT
2380754 GCAGTTATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (29 bp):
TATTTTTTTAATATTTTATTTAATTATTT
Found at i:2380753 original size:21 final size:22
Alignment explanation
Indices: 2380698--2380753 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
2380688 ATTTTGTTAG
**
2380698 TATTTTATTTAATTATTTAAAT
1 TATTTTATTTTTTTATTTAAAT
* *
2380720 T-TTTTAATATTTTATTT-AAT
1 TATTTTATTTTTTTATTTAAAT
2380740 TATTTTATTTTTTT
1 TATTTTATTTTTTT
2380754 GCAGTTATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.15
21 22 0.81
22 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TATTTTATTTTTTTATTTAAAT
Found at i:2382608 original size:3 final size:3
Alignment explanation
Indices: 2382593--2382637 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
2382583 TATATGCTCC
* * *
2382593 TGA TGA CGA TGA TGA TGA TGG TGA TGA TGA CGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2382638 CAGTGAGGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.31, C:0.04, G:0.36, T:0.29
Consensus pattern (3 bp):
TGA
Found at i:2386499 original size:30 final size:30
Alignment explanation
Indices: 2386463--2386557 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
2386453 ATCAAAGGTA
* * *
2386463 AGAGGATTGTGGGGTGATATTTACGGGTTG
1 AGAGGATTGTTGTGTGATGTTTACGGGTTG
*
2386493 AGAGGATTGTTGTGTGATGTTTTCGGGTTG
1 AGAGGATTGTTGTGTGATGTTTACGGGTTG
*
2386523 AGAGGATTGTTGTGTGAATGTTTACGGGGTG
1 AGAGGATTGTTGTGTG-ATGTTTACGGGTTG
2386554 AGAG
1 AGAG
2386558 CATTTCATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 42 0.72
31 16 0.28
ACGTcount: A:0.19, C:0.03, G:0.42, T:0.36
Consensus pattern (30 bp):
AGAGGATTGTTGTGTGATGTTTACGGGTTG
Found at i:2392511 original size:2 final size:2
Alignment explanation
Indices: 2392504--2392545 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2392494 GGACTTGACA
2392504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2392546 TCATTAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2393465 original size:23 final size:23
Alignment explanation
Indices: 2393420--2393465 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2393410 AAAATAGAAA
*
2393420 ATATTATTTATTATGTAAAAAAT
1 ATATTATTTATTATCTAAAAAAT
*
2393443 ATATTA-TTATATATCTAACAAAT
1 ATATTATTTAT-TATCTAAAAAAT
2393466 TTTCTGAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATTATTTATTATCTAAAAAAT
Found at i:2395972 original size:18 final size:18
Alignment explanation
Indices: 2395949--2395984 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2395939 TCAAAGTTAT
2395949 GTGGCCACTGTAGAGGTG
1 GTGGCCACTGTAGAGGTG
2395967 GTGGCCACTGTAGAGGTG
1 GTGGCCACTGTAGAGGTG
2395985 AAGGCCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.44, T:0.22
Consensus pattern (18 bp):
GTGGCCACTGTAGAGGTG
Found at i:2395990 original size:18 final size:18
Alignment explanation
Indices: 2395951--2395992 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2395941 AAAGTTATGT
**
2395951 GGCCACTGTAGAGGTGGT
1 GGCCACTGTAGAGGTGAA
2395969 GGCCACTGTAGAGGTGAA
1 GGCCACTGTAGAGGTGAA
2395987 GGCCAC
1 GGCCAC
2395993 AATAGAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.17
Consensus pattern (18 bp):
GGCCACTGTAGAGGTGAA
Found at i:2409083 original size:21 final size:21
Alignment explanation
Indices: 2409054--2409138 Score: 134
Period size: 21 Copynumber: 4.0 Consensus size: 21
2409044 ATATAAATTG
* *
2409054 TGTATCGATGCACTGCTATAA
1 TGTACCGATGCACTGCTACAA
2409075 TGTACCGATGCACTGCTACAA
1 TGTACCGATGCACTGCTACAA
2409096 TGTACCGATGCACTGCTACAA
1 TGTACCGATGCACTGCTACAA
* *
2409117 TGAACCGATACACTGCTACAA
1 TGTACCGATGCACTGCTACAA
2409138 T
1 T
2409139 AACTTCCGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (21 bp):
TGTACCGATGCACTGCTACAA
Found at i:2409831 original size:32 final size:32
Alignment explanation
Indices: 2409713--2409904 Score: 275
Period size: 32 Copynumber: 6.1 Consensus size: 32
2409703 ACTCATATAA
*
2409713 TAAT-CTGTTCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
*
2409744 TAA-ATTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* *
2409775 TAA-ACTAAT-CATATGTCTCGAAAGACATAGG
1 TAATACT-GTCCATATGTCCCGAAAGACATAGG
* *
2409806 TAATACTGTCTATATGTCCCAAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
*
2409838 TAATACCGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
*
2409870 TAATAATGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
2409902 TAA
1 TAA
2409905 ACCCTTGACT
Statistics
Matches: 143, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
31 58 0.41
32 85 0.59
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (32 bp):
TAATACTGTCCATATGTCCCGAAAGACATAGG
Found at i:2412126 original size:23 final size:22
Alignment explanation
Indices: 2412078--2412126 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2412068 ACAGAATGTC
2412078 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
2412099 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
2412122 AAGGA
1 AAGGA
2412127 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:2413785 original size:103 final size:103
Alignment explanation
Indices: 2413606--2413825 Score: 370
Period size: 103 Copynumber: 2.1 Consensus size: 103
2413596 GGTCTACGCA
2413606 GTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
* **
2413671 CTTGGCATATGTATATGATTCTTAAGGAATGATATGTG
66 CCTAACATATGTATATGATTCTTAAGGAATGATATGTG
* *
2413709 GTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATACATACTTGATC
1 GTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
*
2413774 CCTAATATATGTATATGATTCTTAAGGAATGATATGTG
66 CCTAACATATGTATATGATTCTTAAGGAATGATATGTG
2413812 GTCCTT-ATGGACAT
1 GTCCTTCA-GGACAT
2413826 TATTATATGG
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
CCTAACATATGTATATGATTCTTAAGGAATGATATGTG
Found at i:2413860 original size:23 final size:23
Alignment explanation
Indices: 2413834--2413893 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2413824 ATTATTATAT
*
2413834 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
* *
2413857 GGCACTACGGTGAAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
2413880 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
2413894 TTTATATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2416994 original size:19 final size:21
Alignment explanation
Indices: 2416954--2416999 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2416944 TTGTTCGTAG
2416954 GTATCGATACTAAGCTCTTTA
1 GTATCGATACTAAGCTCTTTA
*
2416975 GTATTGATACT-AGC-CTTTA
1 GTATCGATACTAAGCTCTTTA
2416994 GGTATC
1 -GTATC
2417000 AATATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 5 0.23
20 7 0.32
21 10 0.45
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (21 bp):
GTATCGATACTAAGCTCTTTA
Found at i:2421120 original size:21 final size:21
Alignment explanation
Indices: 2421091--2421130 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2421081 AGTCAGCGTC
*
2421091 ACTGGCTCCAAAGCTAGCTTG
1 ACTGGCTCCAAAGATAGCTTG
*
2421112 ACTGTCTCCAAAGATAGCT
1 ACTGGCTCCAAAGATAGCT
2421131 CGATTGTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (21 bp):
ACTGGCTCCAAAGATAGCTTG
Found at i:2425166 original size:58 final size:58
Alignment explanation
Indices: 2425104--2425219 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 58
2425094 TCTTTCTTTG
* * *
2425104 TTGGATTTTATGAATCTTCTAAATATTTTGGCAAACATTTTCA-TTTCTTCATCTTTTT
1 TTGGACTTCATGAATCTTCTAAATATTTTGGCAAACATTGTCACTTT-TTCATCTTTTT
*
2425162 TTGGACTTCATGAATCTTCTAAATGTTTTGGCAAACATTGTCACTTTTTCATCTTTTT
1 TTGGACTTCATGAATCTTCTAAATATTTTGGCAAACATTGTCACTTTTTCATCTTTTT
2425220 CCTCACTAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 50 0.94
59 3 0.06
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.51
Consensus pattern (58 bp):
TTGGACTTCATGAATCTTCTAAATATTTTGGCAAACATTGTCACTTTTTCATCTTTTT
Found at i:2428490 original size:2 final size:2
Alignment explanation
Indices: 2428483--2428515 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2428473 CATAATGAAT
2428483 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
2428516 CATGTAAAAA
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:2428813 original size:39 final size:39
Alignment explanation
Indices: 2428770--2428866 Score: 144
Period size: 39 Copynumber: 2.5 Consensus size: 39
2428760 GAACAAATTC
2428770 TTCTCATTATGAACTTCTTCTTCCTCTTCAGA-TAAGTTA
1 TTCTCATTATGAACTTCTTCTTCCTCTTCA-ATTAAGTTA
* * *
2428809 TTCTCATTATGAATTTCTTCTTCTTCTTCAATTGAGTTA
1 TTCTCATTATGAACTTCTTCTTCCTCTTCAATTAAGTTA
2428848 TTCTCATTATGAAC-TCTTC
1 TTCTCATTATGAACTTCTTC
2428867 CTTGAAATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
38 6 0.11
39 47 0.89
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (39 bp):
TTCTCATTATGAACTTCTTCTTCCTCTTCAATTAAGTTA
Found at i:2429085 original size:2 final size:2
Alignment explanation
Indices: 2429078--2429104 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2429068 CATAATGAAT
2429078 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2429105 TCATGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2444667 original size:32 final size:32
Alignment explanation
Indices: 2444631--2444707 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 32
2444621 ACAAAGTTTA
*
2444631 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
2444663 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
2444696 CGATAATTGAAA
1 CGATAATTGAAA
2444708 CAAAGTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.27
33 30 0.73
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:2444721 original size:21 final size:21
Alignment explanation
Indices: 2444696--2444737 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2444686 CTTCCAAGTT
2444696 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2444717 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
2444738 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2455528 original size:378 final size:378
Alignment explanation
Indices: 2454785--2455539 Score: 1281
Period size: 378 Copynumber: 2.0 Consensus size: 378
2454775 TCTCCTAGAG
2454785 AGCACACATCATAAAGAGAAGATCTCACGCAACTACTCTAATTAAAGATTCTGAGACTCTACGTC
1 AGCACACATCATAAAGAGAAGATCTCACGCAACTACTCTAATTAAAGATTCTGAGACTCTACGTC
**
2454850 TTGCACTCACTAACGTTACCACCATTGAGCATCTGATGACAACTACGCTAATTAATCGACCCTTA
66 TTGCACTCACTAACACTACCACCATTGAGCATCTGATGACAACTACGCTAATTAATCGACCCTTA
2454915 AGGTACTTAATCTCCTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTAAACTAT
131 AGGTACTTAATCTCCTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTAAACTAT
*
2454980 TATGTGTTGTATATAGCTCGTTCTTATATATCAACACGAAAATAACAATGACGAAGTTAGGGTCA
196 TATGTGCTG-ATATAGCTCGTTCTTATATATCAACACGAAAATAACAATGACGAAGTTAGGGTCA
*
2455045 AAAACTCAAACTCTTACTTAATCACATATACAATTTATGGTGTAATCTGAAGTCAAACAACATCC
260 AAAACTCAAACTCTTACTTAAT-ACATATACAAATTATGGTGTAATCTGAAGTCAAACAACATCC
2455110 CAAGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGAGGA-ACCTACAC
324 CAAGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGAGGAGACCTACAC
*
2455164 AGCACACATCAT-AAGAGAATATCTCACGCAACTGCACTCTAATTTAAAGATTCTGAGACTCTAC
1 AGCACACATCATAAAGAGAAGATCTCACGCAACT--ACTCTAA-TTAAAGATTCTGAGACTCTAC
2455228 GTCTTGCACTCACTAACACTACCACCATTGAGCTATCTGATGACAACTAGCGCTAATTAATCGAC
63 GTCTTGCACTCACTAACACTACCACCATTGAGC-ATCTGATGACAACTA-CGCTAATTAATCGAC
*
2455293 CCTTAAGGTACTTAATCTCTTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTAA
126 CCTTAAGGTACTTAATCTCCTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTAA
*
2455358 ACTATTATGTGCTG-TATAGCTCGTTC-T-TATATCAACACGAAAATAACAA-GATGAAGTTTAG
191 ACTATTATGTGCTGATATAGCTCGTTCTTATATATCAACACGAAAATAACAATGACGAAG-TTAG
* **
2455419 GGTCGAAAACTCAAACTCTTACTTAAT-CATATACATAATTATGGTGTAATCTGAAGTCAAACGG
255 GGTCAAAAACTCAAACTCTTACTTAATACATATACA-AATTATGGTGTAATCTGAAGTCAAACAA
*
2455483 CATCCCAAGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGATGAGACCTA
319 CATCCCAAGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGAGGAGACCTA
2455540 AAACACTCAC
Statistics
Matches: 357, Mismatches: 11, Indels: 16
0.93 0.03 0.04
Matches are distributed among these distances:
377 8 0.02
378 101 0.28
379 69 0.19
380 8 0.02
381 64 0.18
382 15 0.04
383 92 0.26
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (378 bp):
AGCACACATCATAAAGAGAAGATCTCACGCAACTACTCTAATTAAAGATTCTGAGACTCTACGTC
TTGCACTCACTAACACTACCACCATTGAGCATCTGATGACAACTACGCTAATTAATCGACCCTTA
AGGTACTTAATCTCCTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTAAACTAT
TATGTGCTGATATAGCTCGTTCTTATATATCAACACGAAAATAACAATGACGAAGTTAGGGTCAA
AAACTCAAACTCTTACTTAATACATATACAAATTATGGTGTAATCTGAAGTCAAACAACATCCCA
AGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGAGGAGACCTACAC
Found at i:2457716 original size:44 final size:45
Alignment explanation
Indices: 2457668--2457753 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
2457658 AACATATCTC
2457668 AAATACCTCAGGCGAGGTCCA-GTCACACAACATCGACACCTCCT
1 AAATACCTCAGGCGAGGTCCAGGTCACACAACATCGACACCTCCT
* * * * *
2457712 AAATACCTTAGGCTAGGTCCAGGTCATATAGCATCGACACCT
1 AAATACCTCAGGCGAGGTCCAGGTCACACAACATCGACACCT
2457754 TACTTGGCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 19 0.53
45 17 0.47
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (45 bp):
AAATACCTCAGGCGAGGTCCAGGTCACACAACATCGACACCTCCT
Found at i:2462340 original size:12 final size:12
Alignment explanation
Indices: 2462325--2462356 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2462315 AAAGTGAGGA
2462325 AAAAGAAAAAGT
1 AAAAGAAAAAGT
2462337 AAAAGAAAAAGT
1 AAAAGAAAAAGT
2462349 AAAA-AAAA
1 AAAAGAAAA
2462357 TTAATTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (12 bp):
AAAAGAAAAAGT
Found at i:2462662 original size:17 final size:17
Alignment explanation
Indices: 2462626--2462671 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
2462616 AATTATTTAT
* *
2462626 AAAATAAAATAAAAATA
1 AAAATAAAATTAAAAGA
*
2462643 AAAATAAAATTAAAGGA
1 AAAATAAAATTAAAAGA
*
2462660 AAAAGAAAATTA
1 AAAATAAAATTA
2462672 TTATTTATGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
AAAATAAAATTAAAAGA
Found at i:2465648 original size:23 final size:24
Alignment explanation
Indices: 2465603--2465657 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
2465593 TTGCCAGCTG
2465603 TCCTTTTTACAAAATATCTTTTTA
1 TCCTTTTTACAAAATATCTTTTTA
*
2465627 TCCTTTTTACAAAATATCTTTTTG
1 TCCTTTTTACAAAATATCTTTTTA
2465651 TCCTTTT
1 TCCTTTT
2465658 CTACGCTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.18, G:0.02, T:0.56
Consensus pattern (24 bp):
TCCTTTTTACAAAATATCTTTTTA
Found at i:2467341 original size:20 final size:21
Alignment explanation
Indices: 2467302--2467341 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2467292 AAGGTTGCAC
*
2467302 TATCGATACTGCTTCTTAGAG
1 TATCGATACTGCTCCTTAGAG
*
2467323 TATCGATACTTC-CCTTAGA
1 TATCGATACTGCTCCTTAGA
2467342 AAATACCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TATCGATACTGCTCCTTAGAG
Found at i:2467400 original size:20 final size:20
Alignment explanation
Indices: 2467363--2467400 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2467353 ATTCATCCTA
* *
2467363 GTTCATCCAGTATTGATATT
1 GTTCATCCAATATCGATATT
2467383 GTTCATCCAATATCGATA
1 GTTCATCCAATATCGATA
2467401 CTCGAACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (20 bp):
GTTCATCCAATATCGATATT
Found at i:2468036 original size:64 final size:65
Alignment explanation
Indices: 2467878--2468039 Score: 236
Period size: 65 Copynumber: 2.5 Consensus size: 65
2467868 GAATAAATTG
* * * * *
2467878 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
* * * *
2467943 AACATCGATTGCATTTTATGCATCAATGCACACACCATGCATCGATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
2468007 AACATCGAATGCATTTTATGCATCGATGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
2468040 TTAGTGCACC
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
64 37 0.43
65 49 0.57
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:2468053 original size:64 final size:64
Alignment explanation
Indices: 2467878--2468057 Score: 227
Period size: 64 Copynumber: 2.8 Consensus size: 64
2467868 GAATAAATTG
* * * *
2467878 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACT-CATGCATCGATGCACTCAGGTCTTAATCAA
* * * * *
2467943 AACATCGATTGCATTTTATGCATCAATGCACACACCATGCATCGATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACAC-TCATGCATCGATGCACTCAGGTCTTAATCAA
* *
2468007 AACATCGAATGCATTTTATGCATCGATGCACACTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACACTCA-TGCATCGATGCACT
2468058 AAGTGTTCCA
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.01
64 50 0.51
65 48 0.48
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACTCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:2473482 original size:44 final size:44
Alignment explanation
Indices: 2473399--2473495 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
2473389 TTGTGCATAA
* * *
2473399 TGCATCGATACACTGAATAGTGTATCGATGCATCCCCTTGAATG
1 TGCATCGATACACTGAAGAGTGCACCGATGCATCCCCTTGAATG
*
2473443 TGCATCGATACATCATGAAGA-TGCACCGATGCA-CTCCTTGAATG
1 TGCATCGATACA-C-TGAAGAGTGCACCGATGCATCCCCTTGAATG
2473487 TGCATCGAT
1 TGCATCGAT
2473496 GCACAAGGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 31 0.66
45 11 0.23
46 5 0.11
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTGAAGAGTGCACCGATGCATCCCCTTGAATG
Found at i:2473490 original size:23 final size:23
Alignment explanation
Indices: 2473412--2473499 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 23
2473402 ATCGATACAC
* *
2473412 TGAATAGTGTATCGATGCATCCCCT
1 TGAAT-GTGCATCGATGCA-CTCCT
* *
2473437 TGAATGTGCATCGATACA-T-CA
1 TGAATGTGCATCGATGCACTCCT
*
2473458 TGAA-GATGCACCGATGCACTCCT
1 TGAATG-TGCATCGATGCACTCCT
2473481 TGAATGTGCATCGATGCAC
1 TGAATGTGCATCGATGCAC
2473500 AAGGCCATAC
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 15 0.29
22 1 0.02
23 17 0.33
24 12 0.24
25 5 0.10
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (23 bp):
TGAATGTGCATCGATGCACTCCT
Found at i:2483561 original size:31 final size:31
Alignment explanation
Indices: 2483507--2483585 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
2483497 TAGTTTATCC
*
2483507 ATTAATATTTAACT-AAAGTTTAAGGATCAA
1 ATTAATATTTACCTAAAAGTTTAAGGATCAA
*
2483537 ATTGATATTTTACCTAAAAG-TTAAGGATCAA
1 ATTAATA-TTTACCTAAAAGTTTAAGGATCAA
*
2483568 ATTAATATTTATCTAAAA
1 ATTAATATTTACCTAAAA
2483586 ATAATGTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 16 0.37
31 23 0.53
32 4 0.09
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (31 bp):
ATTAATATTTACCTAAAAGTTTAAGGATCAA
Found at i:2520614 original size:2 final size:2
Alignment explanation
Indices: 2520602--2520641 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2520592 TCATTTATCC
*
2520602 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2520642 CATTTGTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2521922 original size:32 final size:32
Alignment explanation
Indices: 2521862--2521936 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
2521852 GCATCTTTAA
* *
2521862 AGATTCAACAGTAAATGTTGGGGCATATTTGG
1 AGATTCAACATTAAATATTGGGGCATATTTGG
* * *
2521894 AGATTCAACATTGAATATTGTGGTATATTTGG
1 AGATTCAACATTAAATATTGGGGCATATTTGG
*
2521926 GGATTCAACAT
1 AGATTCAACAT
2521937 CCTGATGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (32 bp):
AGATTCAACATTAAATATTGGGGCATATTTGG
Found at i:2522549 original size:43 final size:43
Alignment explanation
Indices: 2522496--2522633 Score: 186
Period size: 43 Copynumber: 3.2 Consensus size: 43
2522486 GTCATCCGCA
2522496 ATTTCAACTCCACGACGGAGGATATCGTACCCATACATCCACG
1 ATTTCAACTCCACGACGGAGGATATCGTACCCATACATCCACG
* * * * * *
2522539 ATTTTAACTCCACGACTGAGGATATCATACCAACAGATCCACG
1 ATTTCAACTCCACGACGGAGGATATCGTACCCATACATCCACG
* * *
2522582 ATTTCAACTCCACAACGGAGGATATCGTGCCCATACATTCACG
1 ATTTCAACTCCACGACGGAGGATATCGTACCCATACATCCACG
*
2522625 GTTTCAACT
1 ATTTCAACT
2522634 TCACAACGAA
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (43 bp):
ATTTCAACTCCACGACGGAGGATATCGTACCCATACATCCACG
Found at i:2522954 original size:43 final size:43
Alignment explanation
Indices: 2522871--2522965 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
2522861 GCCATCCACA
*
2522871 ATTTCAACTCCACGACGGAGGATATCGTACCCACGAATCCATG
1 ATTTCAACTCCACGACGGAGGATATCATACCCACGAATCCATG
* * *
2522914 ATTTTAACTCCACGACGGAGGATATCATGCCCAC-ACATCCACG
1 ATTTCAACTCCACGACGGAGGATATCATACCCACGA-ATCCATG
*
2522957 GTTTCAACT
1 ATTTCAACT
2522966 TCATGACGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.02
43 44 0.98
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (43 bp):
ATTTCAACTCCACGACGGAGGATATCATACCCACGAATCCATG
Found at i:2522959 original size:332 final size:334
Alignment explanation
Indices: 2522531--2523235 Score: 943
Period size: 332 Copynumber: 2.1 Consensus size: 334
2522521 CGTACCCATA
* *
2522531 CATCCACGATTTTAACTCCACGACTGAGGATATCATACCAACAGATCCACGATTTCAACTCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCAACAGATCCACGATTTCAACTCCACA
* * * * *
2522596 ACGGAGGATATCGTGCCCATACATTCACGGTTTCAACTTCACAACGAAGGGAATCGTATACACGA
66 ACGGAGGATATCATGCCCACACATCCACGGTTTCAACTTCACAACGAAGGGAATCGTACACACAA
* * *
2522661 GCAGCATCCATCTCTTGATTGGATTTCAACTTCATGACGAAGGATATCCAACTCAAAGAATGAGT
131 GCAGCATCCATCTCTAGATTGGATTTCAACTTCAGGACGAAGGATATCCAACTCAAAGAAGGAGT
* **
2522726 GTCTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCG
196 GTCTGTCAATAAACTTTCCAGTTTCAGAGCCAACTTCAACTTCACGAAGAAGGATATTGGACTCG
* *
2522791 AAACAA-C-AC-AAGCTTGGATTTCAACTTCACGATGAAGGATATTCAAGTT-GCTCAACTTCAC
261 AAACAAGCAACTAA-CTTGGATTTCAACTTCACGACGAAGGATATCCAA-TTAGCTCAACTTCAC
*
2522852 GACGAATGGGC
324 GACGAAGGGGC
* * * * *
2522863 CATCCACAATTTCAACTCCACGACGGAGGATATCGTACCCAC-GAATCCATGATTTTAACTCCAC
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCAACAG-ATCCACGATTTCAACTCCAC
* **
2522927 GACGGAGGATATCATGCCCACACATCCACGGTTTCAACTTCATGACGAAGGGAATCGTACACACA
65 AACGGAGGATATCATGCCCACACATCCACGGTTTCAACTTCACAACGAAGGGAATCGTACACACA
* * * * * *
2522992 AGCATCATCTATCTCTAGGTTGGATTTCAACTTCAGGACGAATGATATCCAACTCAGAGAGGGAG
130 AGCAGCATCCATCTCTAGATTGGATTTCAACTTCAGGACGAAGGATATCCAACTCAAAGAAGGAG
* * * *
2523057 TGTTTGTCAATAAACTTTCCAGTTTCATAGTCAACTTCAACTTCACGAAGAAGGATATTGGCCTC
195 TGTCTGTCAATAAACTTTCCAGTTTCAGAGCCAACTTCAACTTCACGAAGAAGGATATTGGACTC
* * *
2523122 GAAACAATGCAACTTAACTTGGATTTCAACTTCTCGACGAAGGATATCCAATTCAAGGTTTAACT
260 GAAACAA-GCAAC-TAACTTGGATTTCAACTTCACGACGAAGGATATCCAATT--A-GCTCAACT
*
2523187 TCACGACGAAGGGGT
320 TCACGACGAAGGGGC
* *
2523202 CATCCACGATTTCAACTTCACGACGAAGGATATC
1 CATCCACGATTTCAACTCCACGACGGAGGATATC
2523236 CAATTCGAGG
Statistics
Matches: 322, Mismatches: 41, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
331 1 0.00
332 233 0.72
334 1 0.00
335 4 0.01
336 31 0.10
337 2 0.01
339 50 0.16
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (334 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCATACCAACAGATCCACGATTTCAACTCCACA
ACGGAGGATATCATGCCCACACATCCACGGTTTCAACTTCACAACGAAGGGAATCGTACACACAA
GCAGCATCCATCTCTAGATTGGATTTCAACTTCAGGACGAAGGATATCCAACTCAAAGAAGGAGT
GTCTGTCAATAAACTTTCCAGTTTCAGAGCCAACTTCAACTTCACGAAGAAGGATATTGGACTCG
AAACAAGCAACTAACTTGGATTTCAACTTCACGACGAAGGATATCCAATTAGCTCAACTTCACGA
CGAAGGGGC
Found at i:2523187 original size:34 final size:35
Alignment explanation
Indices: 2523143--2523301 Score: 129
Period size: 32 Copynumber: 4.8 Consensus size: 35
2523133 ACTTAACTTG
*
2523143 GATTTCAACTTCTCGACGAAGGATATCCAATTCAA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAA
* ** * *
2523178 GGTTT-AACTTCACGACGAAGG-GGT-C-ATCCAC
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAA
*
2523209 GATTTCAACTTCACGACGAAGGATATCCAATTCGA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAA
** * * * *
2523244 G-GCTCAACTTCACAATGAATGG--GT-C-ATTCAC
1 GATTTCAACTTCACGACGAA-GGATATCCAATTCAA
2523275 GATTTCAACTTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
2523302 GTGCTCATTT
Statistics
Matches: 91, Mismatches: 24, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
31 15 0.16
32 32 0.35
33 4 0.04
34 30 0.33
35 10 0.11
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (35 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAA
Done.