Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 11 of 17
Found at i:2221598 original size:29 final size:29
Alignment explanation
Indices: 2221561--2221628 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
2221551 TGTTGAGTCT
2221561 CTCGACTATTAAAAATTACAAACTGATCA
1 CTCGACTATTAAAAATTACAAACTGATCA
* *
2221590 CTCTACTATTAAAAATTACAAACTGGTCA
1 CTCGACTATTAAAAATTACAAACTGATCA
2221619 CTCGACTATT
1 CTCGACTATT
2221629 TATTATGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (29 bp):
CTCGACTATTAAAAATTACAAACTGATCA
Found at i:2221981 original size:34 final size:34
Alignment explanation
Indices: 2221934--2222001 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
2221924 ATAGTCAATG
*
2221934 GATCATTTATGTACGTATACGTAAAATACTAAAA
1 GATCATTTATGTACCTATACGTAAAATACTAAAA
*
2221968 GATCATTTTTGTACCTATACGTAAAATACTAAAA
1 GATCATTTATGTACCTATACGTAAAATACTAAAA
2222002 TAAATATCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (34 bp):
GATCATTTATGTACCTATACGTAAAATACTAAAA
Found at i:2227947 original size:16 final size:16
Alignment explanation
Indices: 2227926--2227956 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2227916 CATCTCATCG
2227926 AGCACCACGTTTACCA
1 AGCACCACGTTTACCA
2227942 AGCACCACGTTTACC
1 AGCACCACGTTTACC
2227957 CGTTTGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.39, G:0.13, T:0.19
Consensus pattern (16 bp):
AGCACCACGTTTACCA
Found at i:2238196 original size:32 final size:31
Alignment explanation
Indices: 2238160--2238234 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
2238150 TCCGTATAAT
2238160 ATTATTTAAAATTAAAT-AGATAATTTAAAATA
1 ATTATTTAAAA-TAAATAAGATAATTTAAAA-A
* *
2238192 ATTATTTCAAATAAATAAGATGATTTAAAAA
1 ATTATTTAAAATAAATAAGATAATTTAAAAA
*
2238223 AATATTTTAAAA
1 ATTA-TTTAAAA
2238235 ATTTTTCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 9 0.24
32 28 0.76
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (31 bp):
ATTATTTAAAATAAATAAGATAATTTAAAAA
Found at i:2239220 original size:21 final size:21
Alignment explanation
Indices: 2239196--2239237 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2239186 AGAACGATGA
2239196 TTATAATTT-GAAAATACTTTT
1 TTATAATTTAGAAAATA-TTTT
**
2239217 TTATTTTTTAGAAAATATTTT
1 TTATAATTTAGAAAATATTTT
2239238 GTTGTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATAATTTAGAAAATATTTT
Found at i:2252435 original size:199 final size:198
Alignment explanation
Indices: 2252095--2252488 Score: 596
Period size: 199 Copynumber: 2.0 Consensus size: 198
2252085 TCCATCCTGC
* * * *
2252095 AAGTGAGCAAAGGTGGAAAAGCAAAACAGATCAGATATATGTGTATATATATCTTATGACCTCCA
1 AAGTGAGCAAAGGTGGAAAAGCAAAACAGACCAGATACATGTATATATATATCCTATGACCTCCA
* *
2252160 GGAACAAGATAAAGAAACGGAAAAGAATCAGCAATGCTCCTTTATGTTTCTGGAGAACCACGTTT
66 GGAACAAGATAAAGAAACGGAAAAGAATCAGCAATGCTCCTTTATCTATCTGGAGAACCACGTTT
* *
2252225 CATTAGTAAGTTTAATATCTCTTGACATG-GGGAAGTACAAAAGAACAAAAGAAGAGACACAACC
131 CACTAGTAAGTTTAATATCTCTTGACATGAGGCAA--ACAAAAGAACAAAAGAAGAGACACAACC
2252289 ACCGA
194 ACCGA
* *
2252294 AAGTGAGCAAAGGTGGAAAAGCAAAACA-ACCAAGGTACATGTATATCTATA-CGCTATGACCTC
1 AAGTGAGCAAAGGTGGAAAAGCAAAACAGACC-AGATACATGTATATATATATC-CTATGACCTC
*
2252357 CAGGAACAAGATAAAGAAACGGAAAAGAATCAGCAATGCTCCTTTATCTATCTGGAGAACCATGT
64 CAGGAACAAGATAAAGAAACGGAAAAGAATCAGCAATGCTCCTTTATCTATCTGGAGAACCACGT
** **
2252422 TTCACTAGTAAGTTTAATATCTCTTGATGTGAGGCAAATGAAAGAACAAAAGAAGAGACACAACC
129 TTCACTAGTAAGTTTAATATCTCTTGACATGAGGCAAACAAAAGAACAAAAGAAGAGACACAACC
2252487 AC
194 AC
2252489 TGTTGTGCCA
Statistics
Matches: 177, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
198 31 0.18
199 142 0.80
200 4 0.02
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (198 bp):
AAGTGAGCAAAGGTGGAAAAGCAAAACAGACCAGATACATGTATATATATATCCTATGACCTCCA
GGAACAAGATAAAGAAACGGAAAAGAATCAGCAATGCTCCTTTATCTATCTGGAGAACCACGTTT
CACTAGTAAGTTTAATATCTCTTGACATGAGGCAAACAAAAGAACAAAAGAAGAGACACAACCAC
CGA
Found at i:2258090 original size:46 final size:46
Alignment explanation
Indices: 2258038--2258127 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
2258028 ATCCAGACCT
*
2258038 TTAATACTTTGCATGCATCATTTATGATATTACTTACCATTGACTG
1 TTAATACTTTGCATGCATCATTTACGATATTACTTACCATTGACTG
* *
2258084 TTAATACTTTGCATGCATCATTTACGATATTGCTTAGCATTGAC
1 TTAATACTTTGCATGCATCATTTACGATATTACTTACCATTGAC
2258128 CTCCGGTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (46 bp):
TTAATACTTTGCATGCATCATTTACGATATTACTTACCATTGACTG
Found at i:2259576 original size:54 final size:54
Alignment explanation
Indices: 2259513--2259622 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
2259503 TAATAAGAGC
* *
2259513 CCTACATGTTAGGGGTGTTCAAATTAATCCGCTACCGTTAATTGTAACTATTAA
1 CCTACATGTTAGGGGTGTTCAAATTAATCCGCTACCGTTAATCGTAACAATTAA
* * * *
2259567 CCTACATGTTAGGGGTGTTTAAATTAATCTGTTACTGTTAATCGTAACAATTAA
1 CCTACATGTTAGGGGTGTTCAAATTAATCCGCTACCGTTAATCGTAACAATTAA
2259621 CC
1 CC
2259623 GATGTAACCG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (54 bp):
CCTACATGTTAGGGGTGTTCAAATTAATCCGCTACCGTTAATCGTAACAATTAA
Found at i:2280767 original size:21 final size:21
Alignment explanation
Indices: 2280741--2280803 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
2280731 TTTTGGTGCA
*
2280741 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
2280762 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
2280783 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
2280804 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:2280811 original size:21 final size:21
Alignment explanation
Indices: 2280785--2280824 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2280775 CCCCCTTTGA
*
2280785 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2280806 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2280825 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2284431 original size:22 final size:23
Alignment explanation
Indices: 2284402--2284453 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
2284392 GAGTCGAGGG
*
2284402 TTTCATAGGTCCTTCGGGACATA
1 TTTCATAGGTCCTTCGGGACAAA
2284425 -TTCATAGGTCCTTCGGGACAAA
1 TTTCATAGGTCCTTCGGGACAAA
2284447 TTTCATA
1 TTTCATA
2284454 TGCCACTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (23 bp):
TTTCATAGGTCCTTCGGGACAAA
Found at i:2285106 original size:25 final size:25
Alignment explanation
Indices: 2285072--2285145 Score: 121
Period size: 25 Copynumber: 3.0 Consensus size: 25
2285062 TTAACATTTT
*
2285072 GGTACTGTAGCAGGTTACTGTTCAC
1 GGTAATGTAGCAGGTTACTGTTCAC
*
2285097 GGTAATGTAGCAGGTTATTGTTCAC
1 GGTAATGTAGCAGGTTACTGTTCAC
*
2285122 GGTAATGTAGCAGGTGACTGTTCA
1 GGTAATGTAGCAGGTTACTGTTCA
2285146 TTACTGTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (25 bp):
GGTAATGTAGCAGGTTACTGTTCAC
Found at i:2288730 original size:29 final size:29
Alignment explanation
Indices: 2288697--2288752 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
2288687 GTAAACGCGT
2288697 TAGTTTTTAACATGGGTACTAAAATGAAA
1 TAGTTTTTAACATGGGTACTAAAATGAAA
2288726 TAGTTTTTAACATGGGTACTAAAATGA
1 TAGTTTTTAACATGGGTACTAAAATGA
2288753 TATAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (29 bp):
TAGTTTTTAACATGGGTACTAAAATGAAA
Found at i:2288764 original size:29 final size:29
Alignment explanation
Indices: 2288703--2288764 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2288693 GCGTTAGTTT
****
2288703 TTAACATGGGTACTAAAATGAAATAGTTT
1 TTAACATGGGTACTAAAATGAAATAAAAA
*
2288732 TTAACATGGGTACTAAAATGATATAAAAA
1 TTAACATGGGTACTAAAATGAAATAAAAA
2288761 TTAA
1 TTAA
2288765 ACGTTAGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (29 bp):
TTAACATGGGTACTAAAATGAAATAAAAA
Found at i:2291836 original size:31 final size:29
Alignment explanation
Indices: 2291795--2291859 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
2291785 AAAGAGGTCA
*
2291795 TTAAATTATTAATAAATTATATA-AACTATT
1 TTAAAATATTAATAAATTA-ATACAA-TATT
*
2291825 GTTAAAATATTAATACATTAATACAATATT
1 -TTAAAATATTAATAAATTAATACAATATT
2291855 TTAAA
1 TTAAA
2291860 TTAAAATGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 5 0.16
30 7 0.23
31 19 0.61
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (29 bp):
TTAAAATATTAATAAATTAATACAATATT
Found at i:2297961 original size:31 final size:31
Alignment explanation
Indices: 2297926--2298004 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
2297916 AAAAAGGGTT
2297926 AGGGGCCAAATTGCAACCCAAAGCCTAAA-TA
1 AGGGGCCAAATTGCAACCCAAAGCC-AAATTA
* * *** *
2297957 AGGGGTCAAATTGTAGTTCAAAGCCAAATTG
1 AGGGGCCAAATTGCAACCCAAAGCCAAATTA
2297988 AGGGGCCAAATTGCAAC
1 AGGGGCCAAATTGCAAC
2298005 AGAAAAAGGC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
30 3 0.08
31 34 0.92
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (31 bp):
AGGGGCCAAATTGCAACCCAAAGCCAAATTA
Found at i:2316777 original size:1 final size:1
Alignment explanation
Indices: 2316771--2316795 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2316761 TTGATTTTCC
2316771 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2316796 GCAGTGGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2321429 original size:92 final size:92
Alignment explanation
Indices: 2321272--2321467 Score: 365
Period size: 92 Copynumber: 2.1 Consensus size: 92
2321262 ACCGGTCTAT
2321272 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
* *
2321337 CTATCCATAACAATATAACAAGTAAAA
66 CGATCCATAACAATATAACAAGCAAAA
2321364 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
*
2321429 CGATCCATAACAATATAACAGGCAAAA
66 CGATCCATAACAATATAACAAGCAAAA
2321456 AAATGACAAAAC
1 AAATGACAAAAC
2321468 CAGTCTATAA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 101 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (92 bp):
AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
CGATCCATAACAATATAACAAGCAAAA
Found at i:2321550 original size:204 final size:209
Alignment explanation
Indices: 2321200--2321738 Score: 741
Period size: 204 Copynumber: 2.5 Consensus size: 209
2321190 TTGTCGGTTT
* * * * *
2321200 GTGTCGATATTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGAAAAAAAATGACAAAACC
2321265 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 -GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* *
2321330 AATGTATCTATCCATAACAATATAAC-A-A-G-TAAA-A-AAATGACAAAACAGGTAAAGCGCTA
130 AATGTATCGATCCATAACAATATAACAATATGAAAAACATAAATGACAAAACAGGTAAAGCGCTA
2321389 CCGGATATATTGAA-A
195 CCGGATATATT-AATA
*
2321404 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGCAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGAAAAAAAATGACAAAACC
*
2321469 AGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTGTCGATACTTTATAAA
66 -GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
2321534 AATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTATAAATGACAAAA
130 AATGTATCGATCCATAACAATATAAC-------AATATGA-AAAA-----C-ATAAATGACAAAA
*
2321599 CAGGTAAAGCGCTACCGGATATGTTAATA
181 CAGGTAAAGCGCTACCGGATATATTAATA
* *
2321628 ATGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGG-AAAAAAAATGACAAAAC
*
2321693 CGATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGA
65 CG-TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGA
2321739 TAGTATTAAT
Statistics
Matches: 297, Mismatches: 15, Indels: 25
0.88 0.04 0.07
Matches are distributed among these distances:
204 148 0.50
212 1 0.00
213 1 0.00
214 1 0.00
216 3 0.01
223 3 0.01
224 82 0.28
225 58 0.20
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (209 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGAAAAAAAATGACAAAACC
GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
ATGTATCGATCCATAACAATATAACAATATGAAAAACATAAATGACAAAACAGGTAAAGCGCTAC
CGGATATATTAATA
Found at i:2321767 original size:112 final size:112
Alignment explanation
Indices: 2321364--2321738 Score: 637
Period size: 112 Copynumber: 3.3 Consensus size: 112
2321354 ACAAGTAAAA
2321364 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
*
2321429 CGATCCATAACAATATAACAGGCAAAAAAATGACAAAACC-AGTCTAT
66 CGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGA-TCTAT
*
2321476 AAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
* *
2321541 CGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTAT
66 CGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATCTAT
* *
2321588 AAATGACAAAACAGGTAAAGCGCTACCGGATATGTT-AATAATGTCGATACTTTATAAAAATGTA
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAA-AGTGTCGATACTTTATAAAAATGTA
*
2321652 TCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAACCGATCTAT
65 TCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAACCGATCTAT
*
2321701 AAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGA
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGA
2321739 TAGTATTAAT
Statistics
Matches: 249, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
111 2 0.01
112 188 0.76
113 58 0.23
114 1 0.00
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (112 bp):
AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
CGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATCTAT
Found at i:2321946 original size:182 final size:182
Alignment explanation
Indices: 2321629--2322081 Score: 665
Period size: 182 Copynumber: 2.5 Consensus size: 182
2321619 ATGTTAATAA
* * * *
2321629 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAACC
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGAT-AAAAATATGACAAAATC
** * ** * *
2321694 GATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTATTAATACTTTATTAT
65 GATCTCGAAATGACAAAACCGGTAAAGAACTACCAGATATGTTGATAGTATCAATACTTTATTAT
* * * * *
2321759 AAGTATCGACATTTTTTGAATTTAAAAGAGAATAAGTTATAGTGCTAATAAAG
130 AAGTATCGACATTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAG
*
2321812 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGACTAAATCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGACAAAATCG
* * * *
2321877 GTCTCGAAATGATAAAACCGGTAAAGAACTACCAGATATGTTGATAGTGTCGATACTTTATTATA
66 ATCTCGAAATGACAAAACCGGTAAAGAACTACCAGATATGTTGATAGTATCAATACTTTATTATA
2321942 AGTATCGACATTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAG
131 AGTATCGACATTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAG
* * *
2321994 TGTCAATACTTTATAAAAATGTATCGATTCATAATAATATAACA-AGTAAAAATATGACAAAATC
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGA-TAAAAATATGACAAAATC
2322058 GATCTCGAAATGACAAAACCGGTA
65 GATCTCGAAATGACAAAACCGGTA
2322082 GTAAAAAAGT
Statistics
Matches: 242, Mismatches: 27, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
181 1 0.00
182 196 0.81
183 45 0.19
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (182 bp):
TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGACAAAATCG
ATCTCGAAATGACAAAACCGGTAAAGAACTACCAGATATGTTGATAGTATCAATACTTTATTATA
AGTATCGACATTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAG
Found at i:2324428 original size:18 final size:18
Alignment explanation
Indices: 2324399--2324445 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
2324389 TATGTCTCTT
*
2324399 ATTTATTTATTTAATTT-TA
1 ATTTA-TTATTT-ATTTAAA
2324418 ATTTATTATTTATTTAAA
1 ATTTATTATTTATTTAAA
2324436 ATTTATTATT
1 ATTTATTATT
2324446 GTTAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTATTATTTATTTAAA
Found at i:2324752 original size:17 final size:17
Alignment explanation
Indices: 2324727--2324761 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2324717 ATTTTGATTA
2324727 ATAAAATTTTAAAATTT
1 ATAAAATTTTAAAATTT
*
2324744 ATAATATTTTAAAATTT
1 ATAAAATTTTAAAATTT
2324761 A
1 A
2324762 AAGACCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAAAATTTTAAAATTT
Found at i:2324925 original size:13 final size:13
Alignment explanation
Indices: 2324901--2324936 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2324891 CATGATATTA
*
2324901 AAATAGAAAATAC
1 AAATATAAAATAC
*
2324914 AACTATAAAATAC
1 AAATATAAAATAC
2324927 AAATATAAAA
1 AAATATAAAA
2324937 ATTATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.19
Consensus pattern (13 bp):
AAATATAAAATAC
Found at i:2332648 original size:16 final size:17
Alignment explanation
Indices: 2332617--2332652 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2332607 ATCCCAAGAA
*
2332617 ACCCCTCCACAAGTGTC
1 ACCCCTCCAAAAGTGTC
2332634 ACCCCT-CAAAAGTGTC
1 ACCCCTCCAAAAGTGTC
2332650 ACC
1 ACC
2332653 ACTGAGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.28, C:0.44, G:0.11, T:0.17
Consensus pattern (17 bp):
ACCCCTCCAAAAGTGTC
Found at i:2334414 original size:20 final size:21
Alignment explanation
Indices: 2334360--2334416 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
2334350 ATCACAGTCG
2334360 ATAATATA-ATTATA-TTATC
1 ATAATATATATTATATTTATC
* *
2334379 ATGGAACATATTTTATATTTAT-
1 AT--AATATATATTATATTTATC
2334401 ATAATATATATTATAT
1 ATAATATATATTATAT
2334417 AAAGTTGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.07
20 12 0.40
21 5 0.17
22 7 0.23
23 4 0.13
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (21 bp):
ATAATATATATTATATTTATC
Found at i:2339658 original size:2 final size:2
Alignment explanation
Indices: 2339651--2339718 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
2339641 AATTTAAACA
2339651 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
2339693 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
2339719 GAGTTAAATC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2343420 original size:51 final size:50
Alignment explanation
Indices: 2343279--2343423 Score: 191
Period size: 51 Copynumber: 2.8 Consensus size: 50
2343269 TCATATTATA
* *
2343279 AAAAAAATGTAGCACTTAACACATACTTACATCGGTGTAAGTGAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTACA-CTGTGTAAGTAAATAAAAT
* * * *
2343330 AAAAAAGTATATCACTTAACACATACTTACAACAGTGTAAGTAAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTAC-ACTGTGTAAGTAAATAAAAT
* *
2343381 AAAAAAATGTAGAACTTAACACATATTTACACTGATGTAAGTA
1 AAAAAAATGTAGCACTTAACACATACTTACACTG-TGTAAGTA
2343424 TATACATCTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
50 3 0.04
51 77 0.95
52 1 0.01
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (50 bp):
AAAAAAATGTAGCACTTAACACATACTTACACTGTGTAAGTAAATAAAAT
Found at i:2344263 original size:16 final size:17
Alignment explanation
Indices: 2344228--2344268 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
2344218 TATGGGATGA
2344228 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
2344245 AAAAAT-GTATTTATT-T
1 AAAAATAGTA-TTATTGT
2344261 AAATAATA
1 AAA-AATA
2344269 TTTTACTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:2347882 original size:21 final size:21
Alignment explanation
Indices: 2347831--2347883 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2347821 ATTCTGACTA
2347831 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
2347852 TTGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
2347873 TCGCAATGCGA
1 TCGCATTGCGA
2347884 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2347898 original size:20 final size:20
Alignment explanation
Indices: 2347873--2347986 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
2347863 TTTTCCTAAT
2347873 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2347893 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
2347914 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2347934 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2347954 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2347974 TCGCAATGTGAAT
1 TCGCAATGCGAAT
2347987 CTGACTATCG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
20 68 0.81
21 16 0.19
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2347966 original size:40 final size:40
Alignment explanation
Indices: 2347873--2348004 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
2347863 TTTTCCTAAT
* **
2347873 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAA-TACGAAAA
*
2347914 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
* **
2347954 TCGCAATGCGAATACGTAAATCGCAATGTGAAT-CTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GAAAA
2347994 TCGCAATGCGA
1 TCGCAATGCGA
2348005 TTTACATAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 50 0.61
41 31 0.38
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
Found at i:2348590 original size:33 final size:34
Alignment explanation
Indices: 2348542--2348614 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
2348532 ACTATCGCAA
* * *
2348542 TGCGATTCTGTCGTTGCGAT-TTTCATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTTAAATTCGCGT
2348575 TGCGATTCT-TACGTTGCGATAGTTAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTTAAATTCGCGT
2348609 TGCGAT
1 TGCGAT
2348615 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 18 0.51
34 16 0.46
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTTAAATTCGCGT
Found at i:2348625 original size:20 final size:20
Alignment explanation
Indices: 2348586--2348650 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
2348576 GCGATTCTTA
* **
2348586 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCATTTTCG
2348606 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
2348626 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
2348646 TGTTG
1 CGTTG
2348651 TGATTTAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2348655 original size:20 final size:20
Alignment explanation
Indices: 2348602--2348656 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
2348592 GATAGTTAAA
* **
2348602 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
2348622 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
2348642 TTCGTGTTGTGATTT
1 TTCGTGTTGCGATTT
2348657 AAAGTTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.51
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:2350559 original size:20 final size:20
Alignment explanation
Indices: 2350534--2350768 Score: 210
Period size: 20 Copynumber: 12.4 Consensus size: 20
2350524 AATAGTTTAT
2350534 TATCGCAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
2350554 TATCGCAAAGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
* *
2350574 TATTGCAA--CG-AGA-GA-
1 TATCGCAATGCGAAAATGAC
* *
2350589 -ATCGCAATGTG-AAATGAA
1 TATCGCAATGCGAAAATGAC
*
2350607 AATCGCAA--C-AACAA--A-
1 TATCGCAATGCGAA-AATGAC
*
2350622 -ATCGCAATGCGAAAATAAC
1 TATCGCAATGCGAAAATGAC
*
2350641 TATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
* * *
2350661 TATCGCAACGCAAAAATGAT
1 TATCGCAATGCGAAAATGAC
* *
2350681 TATCACAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
2350701 TATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
2350721 TATCGCAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
** *
2350741 TATCGCAATGCGAATTTGAT
1 TATCGCAATGCGAAAATGAC
2350761 TATCGCAA
1 TATCGCAA
2350769 CGAAAGAATC
Statistics
Matches: 182, Mismatches: 19, Indels: 28
0.79 0.08 0.12
Matches are distributed among these distances:
14 13 0.07
16 9 0.05
17 7 0.04
18 5 0.03
19 7 0.04
20 141 0.77
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (20 bp):
TATCGCAATGCGAAAATGAC
Found at i:2350843 original size:20 final size:20
Alignment explanation
Indices: 2350815--2350881 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
2350805 GATTCTCTCG
* *
2350815 TTGCAATAGTTAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
2350835 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
2350855 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
2350875 TTGCGAT
1 TTGCGAT
2350882 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:2351403 original size:18 final size:19
Alignment explanation
Indices: 2351364--2351407 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
2351354 CTCACCTGTC
2351364 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
2351385 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
2351403 ATCGT
1 ATCGT
2351408 CCCTCAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
21 13 0.57
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.25
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:2353035 original size:33 final size:34
Alignment explanation
Indices: 2352998--2353073 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
2352988 GGAAATGACT
2352998 ATCGCAACGAGAGAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
*
2353031 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
2353065 ATCGCAACG
1 ATCGCAACG
2353074 CGAAAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 25 0.61
34 16 0.39
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
Found at i:2353150 original size:33 final size:34
Alignment explanation
Indices: 2353088--2353163 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
2353078 AATAAATTCG
2353088 CGTTGCGATTTTCATTTTCACATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCACATTGCGATTCACT
* *
2353122 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCACATTGCGATTCACT
2353155 CGTTGCGAT
1 CGTTGCGAT
2353164 AGTCAATTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 26 0.65
34 14 0.35
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCACATTGCGATTCACT
Found at i:2353180 original size:20 final size:20
Alignment explanation
Indices: 2353155--2353249 Score: 156
Period size: 20 Copynumber: 4.8 Consensus size: 20
2353145 GCGATTCTCT
2353155 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
2353175 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
2353195 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
2353215 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCA-ATTCCG
2353235 CGTTGCGATAGTCAA
1 CGTTGCGATAGTCAA
2353250 ATGAATGTCT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
19 1 0.01
20 67 0.96
21 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:2355723 original size:24 final size:24
Alignment explanation
Indices: 2355672--2355726 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2355662 AAAATCCGAG
**
2355672 TATTGACCAAGATCAAAGTCAGGG
1 TATTGACCAAGATCAAAGTCAGAA
*
2355696 TATTGACCAAGATCAAATTTC-GAA
1 TATTGACCAAGATCAAA-GTCAGAA
2355720 TATTGAC
1 TATTGAC
2355727 TAGTACTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCAGAA
Found at i:2356583 original size:20 final size:20
Alignment explanation
Indices: 2356558--2356608 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2356548 TTCAGTATTA
2356558 CGATAGTCAGAATCTCGTTG
1 CGATAGTCAGAATCTCGTTG
*
2356578 CGATAGTCAAAATCTCGTTG
1 CGATAGTCAGAATCTCGTTG
*
2356598 CGATTGTCAGA
1 CGATAGTCAGA
2356609 TTCGCATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (20 bp):
CGATAGTCAGAATCTCGTTG
Found at i:2359418 original size:206 final size:206
Alignment explanation
Indices: 2359064--2359481 Score: 818
Period size: 206 Copynumber: 2.0 Consensus size: 206
2359054 ATTCTTTTAG
2359064 ATCGAACGTAGCTTAAAAATTAAATAAACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACT
1 ATCGAACGTAGCTTAAAAATTAAATAAACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACT
2359129 AGGACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAA
66 AGGACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAA
2359194 ATACTCGGATCGAATGAACTCGACTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACG
131 ATACTCGGATCGAATGAACTCGACTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACG
2359259 AGCTACTCGAT
196 AGCTACTCGAT
2359270 ATCGAACGTAGCTTAAAAATTAAATAAACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACT
1 ATCGAACGTAGCTTAAAAATTAAATAAACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACT
2359335 AGGACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAA
66 AGGACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAA
*
2359400 ATACTCGGATCGAATGAACTCGATTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACG
131 ATACTCGGATCGAATGAACTCGACTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACG
2359465 AGCTACTCGAT
196 AGCTACTCGAT
2359476 ACTCGA
1 A-TCGA
2359482 CTCGAAACGC
Statistics
Matches: 210, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
206 206 0.98
207 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (206 bp):
ATCGAACGTAGCTTAAAAATTAAATAAACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACT
AGGACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAA
ATACTCGGATCGAATGAACTCGACTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACG
AGCTACTCGAT
Found at i:2359564 original size:11 final size:11
Alignment explanation
Indices: 2359548--2359610 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
2359538 AAAATTACAT
2359548 TATTAAAAATA
1 TATTAAAAATA
2359559 TATTAAAAATA
1 TATTAAAAATA
* ***
2359570 CATTATTGATA
1 TATTAAAAATA
*
2359581 -CTTATAAAAT-
1 TATTA-AAAATA
2359591 T-TTAAAAATA
1 TATTAAAAATA
2359601 TATTAAAAAT
1 TATTAAAAAT
2359611 TCTATAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 5 0.12
10 7 0.17
11 28 0.70
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:2359781 original size:14 final size:14
Alignment explanation
Indices: 2359742--2359781 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
2359732 ACCCTAAACC
*
2359742 TAAACCCTAAAGTA
1 TAAACCCTAAATTA
2359756 TAAACCCTAAATTA
1 TAAACCCTAAATTA
2359770 TAAACCCTAAAT
1 TAAACCCTAAAT
2359782 CTACGACCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.23, G:0.03, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAATTA
Found at i:2359964 original size:21 final size:21
Alignment explanation
Indices: 2359938--2359986 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2359928 CCCTTATCCC
*
2359938 AAACCCTAAGCCATAAGTCCT
1 AAACCCTAAGCCATAAGCCCT
*
2359959 AAACCCTAAGCCCTAAGCCCT
1 AAACCCTAAGCCATAAGCCCT
2359980 AAACCCT
1 AAACCCT
2359987 TAATTCGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.39, G:0.08, T:0.16
Consensus pattern (21 bp):
AAACCCTAAGCCATAAGCCCT
Found at i:2359968 original size:14 final size:14
Alignment explanation
Indices: 2359938--2359986 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
2359928 CCCTTATCCC
*
2359938 AAACCCTAAGCCAT
1 AAACCCTAAGCCCT
** *
2359952 AAGTCCTAAACCCT
1 AAACCCTAAGCCCT
*
2359966 AAGCCCTAAGCCCT
1 AAACCCTAAGCCCT
2359980 AAACCCT
1 AAACCCT
2359987 TAATTCGATT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.37, C:0.39, G:0.08, T:0.16
Consensus pattern (14 bp):
AAACCCTAAGCCCT
Found at i:2361368 original size:11 final size:11
Alignment explanation
Indices: 2361352--2361420 Score: 102
Period size: 11 Copynumber: 6.2 Consensus size: 11
2361342 TGGTGAGCAC
2361352 TCGAGTTTGAA
1 TCGAGTTTGAA
2361363 TCGAGTTTGAA
1 TCGAGTTTGAA
2361374 TCGAGTTTGAA
1 TCGAGTTTGAA
* *
2361385 TTGAGTTTGTA
1 TCGAGTTTGAA
*
2361396 TCGAGCTTGAA
1 TCGAGTTTGAA
2361407 TCGAGCTTTGAA
1 TCGAG-TTTGAA
2361419 TC
1 TC
2361421 AAGCTTGAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
11 44 0.86
12 7 0.14
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.38
Consensus pattern (11 bp):
TCGAGTTTGAA
Found at i:2361428 original size:11 final size:11
Alignment explanation
Indices: 2361352--2361428 Score: 82
Period size: 11 Copynumber: 6.9 Consensus size: 11
2361342 TGGTGAGCAC
*
2361352 TCGAGTTTGAA
1 TCGAGCTTGAA
*
2361363 TCGAGTTTGAA
1 TCGAGCTTGAA
*
2361374 TCGAGTTTGAA
1 TCGAGCTTGAA
* * *
2361385 TTGAGTTTGTA
1 TCGAGCTTGAA
2361396 TCGAGCTTGAA
1 TCGAGCTTGAA
2361407 TCGAGCTTTGAA
1 TCGAGC-TTGAA
*
2361419 TCAAGCTTGA
1 TCGAGCTTGA
2361429 GTCTCGAGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
11 49 0.83
12 10 0.17
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:2363244 original size:29 final size:29
Alignment explanation
Indices: 2363211--2363280 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2363201 ATGATCTTAA
2363211 GCAGAAACATGACATGAA-A-TAAATCACAT
1 GCAGAAACATGAC--GAAGATTAAATCACAT
* *
2363240 GCAGAAACAGGACGAAGATTAAATCTCAT
1 GCAGAAACATGACGAAGATTAAATCACAT
*
2363269 GCATAAACATGA
1 GCAGAAACATGA
2363281 AGAGGAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 3 0.09
28 1 0.03
29 31 0.89
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (29 bp):
GCAGAAACATGACGAAGATTAAATCACAT
Found at i:2365956 original size:2 final size:2
Alignment explanation
Indices: 2365949--2366024 Score: 99
Period size: 2 Copynumber: 40.5 Consensus size: 2
2365939 CTGCCCCGAT
2365949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2365990 TT TA TA TA TT TA TA -A T- TA -A TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2366025 TTTCGGGTTA
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
1 5 0.08
2 61 0.92
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2368387 original size:20 final size:20
Alignment explanation
Indices: 2368362--2368454 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
2368352 TTTTCCCAAT
2368362 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
2368382 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
2368402 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
2368423 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
2368444 TCGCAATGCGA
1 TCGCAATGCGA
2368455 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:2368404 original size:41 final size:41
Alignment explanation
Indices: 2368359--2368454 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
2368349 CGATTTTCCC
*
2368359 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
2368400 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
2368441 AAATCGCAATGCGA
1 AATTCGCAATGCGA
2368455 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:2368467 original size:41 final size:41
Alignment explanation
Indices: 2368381--2368515 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
2368371 GAATAAGTAA
* * * *
2368381 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
2368422 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
2368463 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
2368504 TTCGCAACGCGA
1 ATCGCAACGCGA
2368516 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:2368468 original size:20 final size:20
Alignment explanation
Indices: 2368443--2368537 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
2368433 AATTGAGAAA
*
2368443 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2368463 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2368484 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2368504 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2368524 TTCGCAACGCGATA
1 ATCGCAACGCGATA
2368538 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2369057 original size:20 final size:20
Alignment explanation
Indices: 2369032--2369069 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2369022 CGATTCTCTC
2369032 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
2369052 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
2369070 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:2370409 original size:18 final size:18
Alignment explanation
Indices: 2370388--2370432 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2370378 TCCACTTCGG
*
2370388 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
2370406 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
2370424 GAGCCATCA
1 GAGCCATCA
2370433 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2370930 original size:20 final size:20
Alignment explanation
Indices: 2370905--2370950 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2370895 TAGTTTACTT
2370905 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
2370925 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
2370945 TCGCAA
1 TCGCAA
2370951 TGAGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:2370959 original size:19 final size:20
Alignment explanation
Indices: 2370916--2370971 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
2370906 CGCAACACGA
*
2370916 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCAG
* *
2370936 AAATGGCTATCGCAATG-AG
1 AAATGACTATCGCAACGCAG
**
2370955 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
2370972 ACAAAATCGC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:2370979 original size:14 final size:14
Alignment explanation
Indices: 2370960--2371017 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2370950 ATGAGAAATG
2370960 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2370974 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2370990 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2371006 AAAATCGCAACG
1 AAAATCGCAACG
2371018 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2371002 original size:32 final size:33
Alignment explanation
Indices: 2370944--2371034 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
2370934 GGAAATGGCT
* *
2370944 ATCGCAATGAGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2370977 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2371009 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2371035 TGGCGTTGCG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2371028 original size:19 final size:19
Alignment explanation
Indices: 2370905--2371034 Score: 75
Period size: 19 Copynumber: 7.3 Consensus size: 19
2370895 TAGTTTACTT
* **
2370905 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
2370925 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
* *
2370945 TCGCAATGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2370964 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2370978 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
2370996 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2371010 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2371029 TCGCAA
1 TCGCAA
2371035 TGGCGTTGCG
Statistics
Matches: 86, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
14 20 0.23
15 1 0.01
16 6 0.07
17 1 0.01
18 11 0.13
19 23 0.27
20 23 0.27
21 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2371057 original size:14 final size:14
Alignment explanation
Indices: 2371038--2371095 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2371028 ATCGCAATGG
2371038 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2371052 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2371068 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2371084 CGTTGCGATTTT
1 CGTTGCGATTTT
2371096 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2371078 original size:32 final size:33
Alignment explanation
Indices: 2371037--2371111 Score: 134
Period size: 32 Copynumber: 2.3 Consensus size: 33
2371027 AATCGCAATG
2371037 GCGTTGCGATTTTGTCGTTGCGA-TTTCATTTC
1 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTC
2371069 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTC
*
2371102 GCATTGCGAT
1 GCGTTGCGAT
2371112 AGCCATTTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 23 0.56
33 18 0.44
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (33 bp):
GCGTTGCGATTTTGTCGTTGCGATTTTCATTTC
Found at i:2371110 original size:19 final size:19
Alignment explanation
Indices: 2371052--2371169 Score: 77
Period size: 20 Copynumber: 6.4 Consensus size: 19
2371042 GCGATTTTGT
2371052 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2371070 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
2371084 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
2371103 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
* **
2371123 CTTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
2371142 TGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
2371162 TGTTGCGA
1 CGTTGCGA
2371170 AAGTAAACTA
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 11 0.14
19 24 0.30
20 30 0.38
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2373035 original size:14 final size:14
Alignment explanation
Indices: 2373016--2373051 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2373006 ATTGTTTAAT
2373016 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2373030 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2373044 TGATTTGT
1 TGATTTGT
2373052 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2373631 original size:14 final size:14
Alignment explanation
Indices: 2373599--2373632 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2373589 GATTGTTTAA
2373599 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
2373613 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
2373627 TTGATT
1 TTGATT
2373633 GTTTAATTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2374199 original size:14 final size:14
Alignment explanation
Indices: 2374180--2374215 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2374170 ATTGTTTAAT
2374180 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2374194 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2374208 TGATTTGT
1 TGATTTGT
2374216 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2374424 original size:581 final size:584
Alignment explanation
Indices: 2372767--2374588 Score: 3405
Period size: 581 Copynumber: 3.1 Consensus size: 584
2372757 TGGTAAGTCA
2372767 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACA-ATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
2372832 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
65 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAAT-TTTGGTTT
2372897 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
129 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
2372962 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTTAATTGATTTGTAAA
194 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTTAATTGATTTGTAAA
2373027 AGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAA-TTTGTTGAAATGTAATAGTT
259 AGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTTGTTGAAATGTAATAGTT
*
2373091 GATTTGTTGATTTTCAATATGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCT
324 GATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCT
***
2373156 ATCGCAACGAGAAAATCGCAATGCGAAATGAAATTTCGCATTGCGATTTTCTCGTTGCGATAACC
389 ATCGCAACGAGAAAATCGCAATGCG--ATTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACC
2373221 ATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAA
452 ATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAA
2373286 TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACA
517 TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACA
2373351 C--
582 CAT
2373352 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACA-ATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
*
2373417 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATATTGGTTTC
65 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATTTTGGTTTC
2373482 TGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCTT
130 TGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCTT
2373547 GATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTTAATTGATTTGTAAAA
195 GATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTTAATTGATTTGTAAAA
2373612 GATGATTTGTAAATGTTGA-TTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGTT
260 GATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTT-TGTTGAAATGTAATAGTT
*
2373676 GATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGC-AAACAGACTATCGCAACGCGAAATGGTT
324 GATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCT
2373740 ATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACCA
389 ATCGCAACGAGAAAATCGCAATGCGA-TTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACCA
2373805 TTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAAT
453 TTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAAT
2373870 GTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACAC
518 GTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACAC
2373935 AT
583 AT
*
2373937 AATGCAAGTTTTGTTAAC-ATATACTCC-TTTGGTTTGAAAATGTTTGGTTAAGTACCTATAATT
1 AATGCAAGTTTTGTTAACAATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
2374000 CAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTG-TTGAGCAAATTTTGGTTT-T
66 CAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATTTTGGTTTCT
*
2374063 GCATG-TAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCTTG
131 GCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCTTG
2374127 ATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAAAA
196 ATTCAATAATTGATGAAGAAATAAGAATTATTATTA-TTTTTGATTGTTTAATTGATTTGTAAAA
2374192 GATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTATGTTGAAATGTAATAGTT
260 GATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTT-TGTTGAAATGTAATAGTT
2374257 GATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCT
324 GATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCT
2374322 ATCGCAACGAGAAAATCGCAATGCGATTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACCAT
389 ATCGCAACGAGAAAATCGCAATGCGATTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACCAT
*
2374387 TTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACATATCATAGCAATG
454 TTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAATG
2374452 TTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACA
519 TTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACA
2374517 T
584 T
2374518 AATGCAAGTTTTGTTAAC-ATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
1 AATGCAAGTTTTGTTAACAATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
2374582 CAATAAT
66 CAATAAT
2374589 AATTGTTAAA
Statistics
Matches: 1215, Mismatches: 13, Indels: 21
0.97 0.01 0.02
Matches are distributed among these distances:
579 95 0.08
580 52 0.04
581 293 0.24
582 175 0.14
583 197 0.16
584 211 0.17
585 192 0.16
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (584 bp):
AATGCAAGTTTTGTTAACAATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATT
CAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATTTTGGTTTCT
GCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCTTG
ATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTTAATTGATTTGTAAAAG
ATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTTGTTGAAATGTAATAGTTGA
TTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCTAT
CGCAACGAGAAAATCGCAATGCGATTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACCATTT
TCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAATGTT
CAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
Found at i:2375695 original size:12 final size:12
Alignment explanation
Indices: 2375678--2375702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2375668 ATATAATCCT
2375678 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2375690 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2375702 G
1 G
2375703 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2377976 original size:22 final size:19
Alignment explanation
Indices: 2377951--2378070 Score: 62
Period size: 19 Copynumber: 6.7 Consensus size: 19
2377941 CTTAATGTCC
2377951 ATCGCAACGCGGAAACGACAAA
1 ATCGCAACGC-GAAACG--AAA
* *
2377973 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAACGAAA
*
2377992 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAACGAAA
* *
2378006 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAACGAAA
**
2378025 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAACGAAA
* *
2378039 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAACGAAA
2378058 ATCGCAACGCGAA
1 ATCGCAACGCGAA
2378071 TTTAATTTCG
Statistics
Matches: 79, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.24
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 34 0.43
21 5 0.06
22 9 0.11
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAACGAAA
Found at i:2377994 original size:19 final size:19
Alignment explanation
Indices: 2377970--2378070 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 19
2377960 CGGAAACGAC
2377970 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
2377989 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
*
2378003 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
2378022 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
**
2378036 GGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
2378055 AAAATCGCAACGCGAA
1 AAAATCGCAATGCGAA
2378071 TTTAATTTCG
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
14 19 0.29
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 34 0.52
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:2378009 original size:33 final size:33
Alignment explanation
Indices: 2377972--2378066 Score: 181
Period size: 33 Copynumber: 2.9 Consensus size: 33
2377962 GAAACGACAA
2377972 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
2378005 AATCGCAATGCGAAATGAAAATCGCAACGAGGG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
2378038 AATCGCAATGCGAAATGAAAATCGCAACG
1 AATCGCAATGCGAAATGAAAATCGCAACG
2378067 CGAATTTAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:2378088 original size:19 final size:20
Alignment explanation
Indices: 2378066--2378108 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2378056 AAATCGCAAC
2378066 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
2378085 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
2378105 GCGA
1 GCGA
2378109 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:2378093 original size:14 final size:14
Alignment explanation
Indices: 2378094--2378127 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2378084 TGCGATTTTC
2378094 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
2378108 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
2378122 ATTTTC
1 ATTTTC
2378128 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:2378266 original size:14 final size:14
Alignment explanation
Indices: 2378247--2378283 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2378237 CATCAATTAA
2378247 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2378261 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2378275 ACAAATCAA
1 ACAAATCAA
2378284 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2379754 original size:42 final size:41
Alignment explanation
Indices: 2379666--2379757 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
2379656 CCTCTTCAAC
* * * * *
2379666 GATGACAGTGGCCTCTTGAACGGTGGGAGGGACTCTCGAGG
1 GATGATAGGGGCCTCTTCAACGATAGGAGGGACTCTCGAGG
* *
2379707 AATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGG
1 GATGATAGGGGCCTCTTCAACGATAGGAG-GGACTCTCGAGG
2379749 GATGATAGG
1 GATGATAGG
2379758 CGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 23 0.55
42 19 0.45
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (41 bp):
GATGATAGGGGCCTCTTCAACGATAGGAGGGACTCTCGAGG
Found at i:2381861 original size:19 final size:19
Alignment explanation
Indices: 2381744--2381947 Score: 185
Period size: 19 Copynumber: 11.1 Consensus size: 19
2381734 TCTTTTGGTT
*
2381744 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2381763 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2381783 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
2381801 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
2381817 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
2381835 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2381850 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
2381870 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2381889 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2381908 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
* *
2381927 GAAATGAAAAGCGCAATGC
1 GAAATGAAAATCGCAACGC
2381946 GA
1 GA
2381948 TTTGGTTTCG
Statistics
Matches: 156, Mismatches: 16, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
14 19 0.12
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 80 0.51
20 45 0.29
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2381904 original size:58 final size:57
Alignment explanation
Indices: 2381839--2381947 Score: 173
Period size: 58 Copynumber: 1.9 Consensus size: 57
2381829 GCGACCAGAC
* *
2381839 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATGAAAAGCGCAACGCGAAATTAA
* *
2381897 AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAAGCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAAGCGCAACGCGA
2381948 TTTGGTTTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 20 0.43
58 27 0.57
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (57 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAAGCGCAACGCGAAATTAA
Found at i:2381918 original size:38 final size:38
Alignment explanation
Indices: 2381744--2381947 Score: 185
Period size: 33 Copynumber: 5.6 Consensus size: 38
2381734 TCTTTTGGTT
* *
2381744 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
2381783 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
2381817 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
2381850 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
* *
2381889 GAAATTAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
* *
2381927 GAAATGAAAAGCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
2381948 TTTGGTTTCG
Statistics
Matches: 141, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
33 42 0.30
34 16 0.11
35 2 0.01
38 40 0.28
39 27 0.19
40 14 0.10
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:2381966 original size:18 final size:18
Alignment explanation
Indices: 2381943--2381985 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2381933 AAAAGCGCAA
*
2381943 TGCGATTTGGTTTCGCGT
1 TGCGATTTGATTTCGCGT
*
2381961 TGCGATTTTATTTCGCGT
1 TGCGATTTGATTTCGCGT
2381979 TGCGATT
1 TGCGATT
2381986 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTGATTTCGCGT
Found at i:2382570 original size:20 final size:20
Alignment explanation
Indices: 2382545--2382658 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
2382535 CGCTAAGTAA
* *
2382545 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
2382565 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
2382585 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
2382606 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2382626 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2382646 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2382659 TTTCTCAATT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 67 0.84
21 13 0.16
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2382647 original size:61 final size:61
Alignment explanation
Indices: 2382545--2382661 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
2382535 CGCTAAGTAA
* * * *
2382545 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTATT
* * *
2382606 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
2382662 CTCAATTTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTATT
Found at i:2382677 original size:61 final size:61
Alignment explanation
Indices: 2382545--2382679 Score: 166
Period size: 61 Copynumber: 2.2 Consensus size: 61
2382535 CGCTAAGTAA
* * * * *
2382545 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTAATT
* * *
2382606 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT-T-AATT
2382669 -T-GCGTTGCGAT
1 ATCGCGTTGCGAT
2382680 TTACTTATTC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
61 58 0.92
62 2 0.03
63 3 0.05
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTAATT
Found at i:2382692 original size:41 final size:41
Alignment explanation
Indices: 2382647--2382742 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
2382637 ATAGTCAGTA
* * *
2382647 TCGCATTGCGATTTTCTCAATTTGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
*
2382688 TCGCATTACGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2382729 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2382743 GGGAAAATCG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2382730 original size:20 final size:20
Alignment explanation
Indices: 2382647--2382739 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
2382637 ATAGTCAGTA
*
2382647 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* * *
2382668 TTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* * *
2382688 TCGCATTACGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
2382709 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
2382729 TCGCATTGCGA
1 TCGCATTGCGA
2382740 ATTGGGAAAA
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 26 0.47
21 29 0.53
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:2386435 original size:34 final size:29
Alignment explanation
Indices: 2386396--2386467 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
2386386 CATATTATGA
2386396 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
2386425 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
2386454 TACATGACATGAAT
1 TACATGACATGAAT
2386468 ATACAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:2386523 original size:30 final size:30
Alignment explanation
Indices: 2386489--2386547 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
2386479 GTTATATGAG
* *
2386489 CTATGTGATAAAGGTATGTAAATGATATGC
1 CTATGTGATAAAGGTATGGAAATAATATGC
2386519 CTATGTGATAAAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
2386548 TCTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGC
Found at i:2386858 original size:24 final size:24
Alignment explanation
Indices: 2386793--2386860 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
2386783 CAATATTATA
*
2386793 TGGCACTACGGTGCAAAATTCTACG
1 TGGCACTTCGGTGC-AAATTCTACG
* *
2386818 CGGTC-CTTTGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-CAAATTCTACG
2386842 TGGCACTTCGGTGCAAATT
1 TGGCACTTCGGTGCAAATT
2386861 TATACGAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
23 1 0.03
24 24 0.71
25 8 0.24
26 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:2392188 original size:27 final size:28
Alignment explanation
Indices: 2392158--2392232 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 28
2392148 CATTCCATAT
2392158 TATGA-TACATGACATGAATTCATATTA
1 TATGATTACATGACATGAATTCATATTA
2392185 TATGTATTACATGACATGAATTCATATTA
1 TATG-ATTACATGACATGAATTCATATTA
2392214 TAT-ATTACATGACATGAAT
1 TATGATTACATGACATGAAT
2392233 ATGCAGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
27 20 0.43
28 1 0.02
29 25 0.54
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (28 bp):
TATGATTACATGACATGAATTCATATTA
Found at i:2392287 original size:30 final size:30
Alignment explanation
Indices: 2392253--2392311 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
2392243 AGTATATGAG
* *
2392253 CTATGTGATAAAGGTATGTAAATGATATGC
1 CTATGTGATAAAGGTATGGAAATAATATGC
2392283 CTATGTGATAAAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
2392312 TCTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGC
Found at i:2392622 original size:24 final size:24
Alignment explanation
Indices: 2392557--2392624 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
2392547 CAATATTATA
*
2392557 TGGCACTACGGTGCAAAATTCTACG
1 TGGCACTTCGGTGC-AAATTCTACG
* *
2392582 CGGTC-CTTTGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-CAAATTCTACG
2392606 TGGCACTTCGGTGCAAATT
1 TGGCACTTCGGTGCAAATT
2392625 TATACGAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
23 1 0.03
24 24 0.71
25 8 0.24
26 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:2394638 original size:38 final size:38
Alignment explanation
Indices: 2394594--2394679 Score: 163
Period size: 38 Copynumber: 2.3 Consensus size: 38
2394584 AAACCTTTAT
2394594 ATCTCATTTTCATCTTTCACTTTCATATCCAGTTTCAC
1 ATCTCATTTTCATCTTTCACTTTCATATCCAGTTTCAC
2394632 ATCTCATTTTCATCTTTCACTTTCATATCCAGTTTCAC
1 ATCTCATTTTCATCTTTCACTTTCATATCCAGTTTCAC
*
2394670 ATTTCATTTT
1 ATCTCATTTT
2394680 TCATAATTCG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.21, C:0.27, G:0.02, T:0.50
Consensus pattern (38 bp):
ATCTCATTTTCATCTTTCACTTTCATATCCAGTTTCAC
Found at i:2394792 original size:19 final size:18
Alignment explanation
Indices: 2394738--2394789 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
2394728 TTGTTTCTGG
2394738 ACTCATAACTTATTTCAT
1 ACTCATAACTTATTTCAT
* *
2394756 ATTCATAATTTAATTTCAT
1 ACTCATAACTT-ATTTCAT
*
2394775 ACTCATAGCTTATTT
1 ACTCATAACTTATTT
2394790 TCAATTTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (18 bp):
ACTCATAACTTATTTCAT
Found at i:2397557 original size:29 final size:30
Alignment explanation
Indices: 2397525--2397594 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
2397515 GGTCAAAATA
* *
2397525 CCTAAATTTTGAA-AATTACACTTTT-GATC
1 CCTAAATTTTAAAGAATTACACTTTTAG-CC
* *
2397554 CCTAAACGTTTAAAGAATTACCCTTTTAGCC
1 CCTAAA-TTTTAAAGAATTACACTTTTAGCC
2397585 CCTAAATTTT
1 CCTAAATTTT
2397595 TCCTAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
29 6 0.18
30 8 0.24
31 18 0.55
32 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (30 bp):
CCTAAATTTTAAAGAATTACACTTTTAGCC
Found at i:2399209 original size:112 final size:111
Alignment explanation
Indices: 2399043--2399259 Score: 407
Period size: 112 Copynumber: 1.9 Consensus size: 111
2399033 GTAAAGGGTT
*
2399043 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
*
2399108 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGATAGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGATAGAATGA
2399154 TATGTGGTCCTTCGGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATA
1 TATGTGGTCCTTC-GGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATA
2399219 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGATA
65 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGATA
2399260 TGTGGTCCTT
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
111 13 0.13
112 90 0.87
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (111 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGATAGAATGA
Found at i:2399318 original size:23 final size:23
Alignment explanation
Indices: 2399285--2399347 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
2399275 CATTATTAAT
2399285 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2399308 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
2399331 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
2399348 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2405475 original size:20 final size:20
Alignment explanation
Indices: 2405450--2405487 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2405440 GAATGCTAGA
*
2405450 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
2405470 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
2405488 TAATAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:2406191 original size:103 final size:103
Alignment explanation
Indices: 2405966--2406183 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
2405956 ATAGAGGGTT
*
2405966 TATGTGGTCCTTCGGGACATATATGTATTCTTTTGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
* *
2406031 TTGATCCTTGGTATATGTATATGATTCTTAATGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
2406069 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
2406134 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
2406172 TATGTGGTCCTT
1 TATGTGGTCCTT
2406184 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:2406233 original size:23 final size:23
Alignment explanation
Indices: 2406200--2406262 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
2406190 ATTATTATAT
2406200 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2406223 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
2406246 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
2406263 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2408552 original size:2 final size:2
Alignment explanation
Indices: 2408545--2408579 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2408535 TTGATTTTAT
*
2408545 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2408580 TTTTTGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2412922 original size:29 final size:30
Alignment explanation
Indices: 2412890--2412952 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
2412880 AGTTACAATT
* **
2412890 AAGTCACTCAATTAATTGA-TGTAACGATC
1 AAGTAACTCAATTAATTGATTGTAAAAATC
*
2412919 AAGTAACTTAATTAATTGATTGTAAAAATC
1 AAGTAACTCAATTAATTGATTGTAAAAATC
2412949 AAGT
1 AAGT
2412953 TACGTGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (30 bp):
AAGTAACTCAATTAATTGATTGTAAAAATC
Found at i:2419355 original size:21 final size:21
Alignment explanation
Indices: 2419331--2419380 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2419321 ACCATAAACA
2419331 TTATTATTTCTACCGGTTTTG
1 TTATTATTTCTACCGGTTTTG
* *
2419352 TTATTTTTTCTATCGGTTTTG
1 TTATTATTTCTACCGGTTTTG
2419373 TTATTATT
1 TTATTATT
2419381 AGATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.10, G:0.12, T:0.64
Consensus pattern (21 bp):
TTATTATTTCTACCGGTTTTG
Found at i:2421943 original size:31 final size:31
Alignment explanation
Indices: 2421905--2421990 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
2421895 GTTTTGAAAA
*
2421905 AAAATTGAAAGTTTAGGTACTAAAACGGACC
1 AAAATTGATAGTTTAGGTACTAAAACGGACC
*
2421936 AAAATTGATAGTTTAGGTACTAAAATGGACC
1 AAAATTGATAGTTTAGGTACTAAAACGGACC
* *
2421967 GAAACTGATAGTTTAGGTACTAAA
1 AAAATTGATAGTTTAGGTACTAAA
2421991 TATGTTAAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (31 bp):
AAAATTGATAGTTTAGGTACTAAAACGGACC
Found at i:2425869 original size:20 final size:21
Alignment explanation
Indices: 2425844--2425895 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2425834 TTTTCCCAAT
2425844 TCGCAATGCGAATAAGT-AAA
1 TCGCAATGCGAATAAGTAAAA
* **
2425864 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCGAATAAGTAAAA
2425885 TCGCAATGCGA
1 TCGCAATGCGA
2425896 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATAAGTAAAA
Found at i:2425908 original size:41 final size:41
Alignment explanation
Indices: 2425881--2426018 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
2425871 GCGAATTGGT
*
2425881 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
2425922 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAAT-AC
** * * *
2425964 --TTTCGCAACGCGATTCTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
2426003 AGAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
2426019 TTTCAAAGTT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.39
41 47 0.57
42 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:2425909 original size:20 final size:20
Alignment explanation
Indices: 2425884--2425998 Score: 133
Period size: 20 Copynumber: 5.7 Consensus size: 20
2425874 AATTGGTAAA
*
2425884 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2425904 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
2425925 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2425945 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2425965 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
2425985 TTCGCAACGAGATA
1 ATCGCAACGCGATA
2425999 ATACAGAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.77
21 15 0.18
22 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2426171 original size:12 final size:12
Alignment explanation
Indices: 2426152--2426185 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2426142 CTCTCTGGCG
2426152 ACATCCGTTCCT
1 ACATCCGTTCCT
*
2426164 ATATCCGTTCCT
1 ACATCCGTTCCT
2426176 ACATCC-TTCC
1 ACATCCGTTCC
2426186 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:2428055 original size:19 final size:19
Alignment explanation
Indices: 2428033--2428124 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
2428023 AGAAATTACT
2428033 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2428052 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
2428066 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2428085 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
2428099 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2428118 ATCGCAA
1 ATCGCAA
2428125 CGAGGGAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 19 0.35
15 4 0.07
16 1 0.02
17 2 0.04
18 4 0.07
19 25 0.45
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2428080 original size:33 final size:33
Alignment explanation
Indices: 2428033--2428159 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
2428023 AGAAATTACT
2428033 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2428066 ATCGCAATGTGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2428098 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
2428132 ATCGCAATACGAAATAAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2428160 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2428116 original size:66 final size:66
Alignment explanation
Indices: 2428034--2428166 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
2428024 GAAATTACTA
** * *
2428034 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATAAAAATCACAACGCGAAT
2428099 T
66 T
*
2428100 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATACGAAATAAAAATCACAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATAAAAATCACAACGCGAAT
2428165 T
66 T
2428166 T
1 T
2428167 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATAAAAATCACAACGCGAAT
T
Found at i:2428341 original size:14 final size:14
Alignment explanation
Indices: 2428322--2428358 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2428312 CATCAATTAA
2428322 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2428336 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2428350 ACAAATCAA
1 ACAAATCAA
2428359 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2429774 original size:21 final size:21
Alignment explanation
Indices: 2429709--2429774 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
2429699 TGAATCAGGA
*
2429709 TCTTGAATGGTGGGA-GGGACC
1 TCTTGAACGGTGGGAGGGGA-C
* * ** * *
2429730 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGGTGGGAGGGGAC
2429751 TCTTGAACGGTGGGAGGGGAC
1 TCTTGAACGGTGGGAGGGGAC
2429772 TCT
1 TCT
2429775 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (21 bp):
TCTTGAACGGTGGGAGGGGAC
Found at i:2430223 original size:91 final size:90
Alignment explanation
Indices: 2430048--2430232 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
2430038 ATTTCAAACT
*
2430048 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
2430113 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
2430141 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
2430205 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
2430232 T
1 T
2430233 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:2432001 original size:33 final size:33
Alignment explanation
Indices: 2431944--2432042 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
2431934 ACGAGATAAT
2431944 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
2431978 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
2432011 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
2432043 CGAAATGAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:2432036 original size:19 final size:19
Alignment explanation
Indices: 2431919--2432064 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
2431909 TCTTTTGGTT
* * *
2431919 GAAATGAAAAGCGCAACGA
1 GAAATGAGAATCGCAACGC
2431938 GATAATGAGAATCGCAACGC
1 GA-AATGAGAATCGCAACGC
**
2431958 GGAAATGACTATCGCAA--C
1 -GAAATGAGAATCGCAACGC
2431976 G--A-GAGAATCGCAACGC
1 GAAATGAGAATCGCAACGC
** *
2431992 GAAATGACTATCGCGA--C
1 GAAATGAGAATCGCAACGC
2432009 G--A-GAGAATCGCAACGC
1 GAAATGAGAATCGCAACGC
*
2432025 GAAATGAAAATCGCAACGC
1 GAAATGAGAATCGCAACGC
*
2432044 GAAATGAGAATCGCAATGC
1 GAAATGAGAATCGCAACGC
2432063 GA
1 GA
2432065 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 42 0.42
20 26 0.26
21 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.12
Consensus pattern (19 bp):
GAAATGAGAATCGCAACGC
Found at i:2432082 original size:19 final size:19
Alignment explanation
Indices: 2432060--2432107 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2432050 AGAATCGCAA
*
2432060 TGCGATTTTGGTTTC-GCGT
1 TGCGATTTT-ATTTCTGCGT
*
2432079 TGCGATAGTTATTTCTGCGT
1 TGCGAT-TTTATTTCTGCGT
2432099 TGCGATTTT
1 TGCGATTTT
2432108 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.10, C:0.15, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTATTTCTGCGT
Found at i:2432651 original size:20 final size:20
Alignment explanation
Indices: 2432626--2432678 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2432616 GCACTATGTA
2432626 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
2432646 AATCGCGTTACGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2432666 TATCTCGTTGCGA
1 AATCGCGTTGCGA
2432679 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2432713 original size:21 final size:20
Alignment explanation
Indices: 2432689--2432740 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2432679 TTTTGTATTA
*
2432689 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
2432710 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
2432730 TCGCATTGCGA
1 TCGCATTGCGA
2432741 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Done.