Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:1483109 original size:20 final size:20
Alignment explanation
Indices: 1483086--1483141 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1483076 AAAATGTTAA
1483086 AAGAAAAAATAAAATAAATG
1 AAGAAAAAATAAAATAAATG
* * *
1483106 AAGAAAATATTAAAT---TT
1 AAGAAAAAATAAAATAAATG
1483123 AAGAAAAAATAATAATAAA
1 AAGAAAAAATAA-AATAAA
1483142 ATATAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 7
0.69 0.13 0.18
Matches are distributed among these distances:
17 11 0.41
18 3 0.11
20 13 0.48
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (20 bp):
AAGAAAAAATAAAATAAATG
Found at i:1483149 original size:18 final size:18
Alignment explanation
Indices: 1483083--1483178 Score: 59
Period size: 18 Copynumber: 5.3 Consensus size: 18
1483073 AAAAAAATGT
*
1483083 TAAAAGAAAAAATAA-AA
1 TAAAAGAGAAAATAATAA
* *
1483100 TAAATGAAGAAAATATTAAA
1 TAAAAG-AGAAAATAAT-AA
** *
1483120 TTTAAGAAAAAATAATAA
1 TAAAAGAGAAAATAATAA
* * * **
1483138 TAAAATATAAAAAAATGT
1 TAAAAGAGAAAATAATAA
*
1483156 TAAAAGAGAAAATAAAAA
1 TAAAAGAGAAAATAATAA
1483174 TAAAA
1 TAAAA
1483179 CAAAATAAAC
Statistics
Matches: 55, Mismatches: 21, Indels: 5
0.68 0.26 0.06
Matches are distributed among these distances:
17 5 0.09
18 37 0.67
19 8 0.15
20 5 0.09
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
TAAAAGAGAAAATAATAA
Found at i:1483153 original size:40 final size:37
Alignment explanation
Indices: 1483086--1483159 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
1483076 AAAATGTTAA
*
1483086 AAGAAAAAATAAAATAAATGAAGAAAATATTAAATTT
1 AAGAAAAAATAAAATAAATGAAAAAAATATTAAATTT
* *
1483123 AAGAAAAAATAATAATAAAATATAAAAAAATGTTAAA
1 AAGAAAAAATAA-AAT-AAAT-GAAAAAAATATTAAA
1483160 AGAGAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 12 0.39
38 3 0.10
39 4 0.13
40 12 0.39
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (37 bp):
AAGAAAAAATAAAATAAATGAAAAAAATATTAAATTT
Found at i:1483240 original size:6 final size:5
Alignment explanation
Indices: 1483164--1483239 Score: 53
Period size: 5 Copynumber: 13.8 Consensus size: 5
1483154 GTTAAAAGAG
* * *
1483164 AAAAT AAAAAT AAAAC AAAAT AAACT AAAAT AAAAA AAGAAGT GGGAAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AA-T ---AAAAT
*
1483215 AAAAAT AAAAC AAAAT AAAAT AAAA
1 -AAAAT AAAAT AAAAT AAAAT AAAA
1483240 AAGAAGTGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
5 39 0.70
6 12 0.21
8 1 0.02
9 2 0.04
10 2 0.04
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:1483240 original size:40 final size:44
Alignment explanation
Indices: 1483163--1483247 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 44
1483153 TGTTAAAAGA
1483163 GAAAATAAAAATAAAACAAAATAAACTAAAATAAAAAAAGAAGTGG
1 GAAAATAAAAATAAAAC--AATAAACTAAAATAAAAAAAGAAGTGG
1483209 GAAAATAAAAATAAAAC-A-AAA-TAAAAT-AAAAAAGAAGTG
1 GAAAATAAAAATAAAACAATAAACTAAAATAAAAAAAGAAGTG
1483248 TTAAATTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
40 12 0.31
41 6 0.15
42 3 0.08
43 1 0.03
46 17 0.44
ACGTcount: A:0.73, C:0.04, G:0.11, T:0.13
Consensus pattern (44 bp):
GAAAATAAAAATAAAACAATAAACTAAAATAAAAAAAGAAGTGG
Found at i:1483400 original size:18 final size:18
Alignment explanation
Indices: 1483379--1483421 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1483369 GTTGTTTTTA
* *
1483379 AAATAAAAGATAAGATTT
1 AAATAAAAGAAAAGAATT
* *
1483397 AAATAACAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1483415 AAATAAA
1 AAATAAA
1483422 TAATCTAAAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1484065 original size:2 final size:2
Alignment explanation
Indices: 1484053--1484082 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1484043 TAAAGATAAA
1484053 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1484083 CTAAATAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1486898 original size:18 final size:19
Alignment explanation
Indices: 1486851--1486899 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
1486841 ATGGATACTA
*
1486851 TATACATATACATGTACATG
1 TATACGTATACATGTA-ATG
*
1486871 TACACG--TACATGT-ATG
1 TATACGTATACATGTAATG
1486887 TATACGTATACAT
1 TATACGTATACAT
1486900 ATACCTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
16 8 0.33
18 12 0.50
20 4 0.17
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
TATACGTATACATGTAATG
Found at i:1488790 original size:39 final size:39
Alignment explanation
Indices: 1488746--1488827 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
1488736 ATTAGTTCTT
*
1488746 TTAGTTATTTTAATTATAATTTAAGGGAAAAATTGGATA
1 TTAGTTATTTTAATTATAATTTAAGGCAAAAATTGGATA
* *
1488785 TTAGTTCTTTTAATTATAATTTAAGGCATAAATTGGATA
1 TTAGTTATTTTAATTATAATTTAAGGCAAAAATTGGATA
1488824 TTAG
1 TTAG
1488828 GTTTTTTGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (39 bp):
TTAGTTATTTTAATTATAATTTAAGGCAAAAATTGGATA
Found at i:1491630 original size:42 final size:42
Alignment explanation
Indices: 1491571--1491653 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
1491561 CTCTTCGGAC
1491571 GCTGGGCTCTGAAAGAAGGGAGAAAT-CATGTTGGAATATGGT
1 GCTGGGCTCTGAAAGAAGGGAGAAATAC-TGTTGGAATATGGT
1491613 GCTGGGCTCTGAAAGAAGGGAGAAATACTGTTGGAATATGG
1 GCTGGGCTCTGAAAGAAGGGAGAAATACTGTTGGAATATGG
1491654 AGGAAGAGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.36, T:0.23
Consensus pattern (42 bp):
GCTGGGCTCTGAAAGAAGGGAGAAATACTGTTGGAATATGGT
Found at i:1492013 original size:3 final size:3
Alignment explanation
Indices: 1492001--1492064 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
1491991 GCCCATTTTT
* *
1492001 TTA TTAA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTG TTA TTAA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
* *
1492048 -AA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA
1492065 CAGGCCCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 1 0.02
3 43 0.86
4 6 0.12
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1493372 original size:22 final size:22
Alignment explanation
Indices: 1493342--1493384 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1493332 AATCCTATAT
1493342 ATATATATATATATATTTTAAA
1 ATATATATATATATATTTTAAA
* *
1493364 ATATTTATATCTATATTTTAA
1 ATATATATATATATATTTTAA
1493385 TATTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATATATATATATATTTTAAA
Found at i:1493532 original size:2 final size:2
Alignment explanation
Indices: 1493483--1493517 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1493473 AAATCTTACT
1493483 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1493518 CTTTAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1496440 original size:7 final size:7
Alignment explanation
Indices: 1496428--1496456 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1496418 TGTCATATAA
1496428 ATCACAT
1 ATCACAT
1496435 ATCACAT
1 ATCACAT
1496442 ATCACAT
1 ATCACAT
1496449 AT-ACAT
1 ATCACAT
1496455 AT
1 AT
1496457 AGACACATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCACAT
Found at i:1500608 original size:24 final size:24
Alignment explanation
Indices: 1500575--1500626 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1500565 GTTTAAATGA
* *
1500575 TAAACGAACACAGACAAACGAACG
1 TAAACAAACACAAACAAACGAACG
* *
1500599 TAAACAAACATAAACGAACGAACG
1 TAAACAAACACAAACAAACGAACG
1500623 TAAA
1 TAAA
1500627 ATTAATTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.21, G:0.13, T:0.08
Consensus pattern (24 bp):
TAAACAAACACAAACAAACGAACG
Found at i:1503463 original size:10 final size:10
Alignment explanation
Indices: 1503448--1503478 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1503438 TTATTCACTC
1503448 TCTTTTTTTT
1 TCTTTTTTTT
1503458 TC-TTTTTTT
1 TCTTTTTTTT
1503467 TCTTTTTTTT
1 TCTTTTTTTT
1503477 TC
1 TC
1503479 GAATCTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:1503465 original size:9 final size:9
Alignment explanation
Indices: 1503451--1503476 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1503441 TTCACTCTCT
1503451 TTTTTTTTC
1 TTTTTTTTC
1503460 TTTTTTTTC
1 TTTTTTTTC
1503469 TTTTTTTT
1 TTTTTTTT
1503477 TCGAATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1513480 original size:23 final size:23
Alignment explanation
Indices: 1513453--1513500 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1513443 TCCTTCACGC
1513453 AAGCTGCTGACTGAACCTTCTAG
1 AAGCTGCTGACTGAACCTTCTAG
*
1513476 AAGCTGCTGACTGGACCTTCTAG
1 AAGCTGCTGACTGAACCTTCTAG
1513499 AA
1 AA
1513501 ATTGTTGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (23 bp):
AAGCTGCTGACTGAACCTTCTAG
Found at i:1513509 original size:23 final size:23
Alignment explanation
Indices: 1513456--1513510 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1513446 TTCACGCAAG
*
1513456 CTGCTGACTGAACCTTCTAGAAG
1 CTGCTGACTGAACCTTCTAGAAA
*
1513479 CTGCTGACTGGACCTTCTAGAAA
1 CTGCTGACTGAACCTTCTAGAAA
* *
1513502 TTGTTGACT
1 CTGCTGACT
1513511 AGATGCCACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (23 bp):
CTGCTGACTGAACCTTCTAGAAA
Found at i:1516059 original size:20 final size:20
Alignment explanation
Indices: 1516034--1516141 Score: 144
Period size: 20 Copynumber: 5.4 Consensus size: 20
1516024 CTATTCCCTA
1516034 GTAATCTTTTATTCCCACTG
1 GTAATCTTTTATTCCCACTG
*
1516054 GTAATCTTTTATTTCCACTG
1 GTAATCTTTTATTCCCACTG
* *
1516074 ATAATCTTTTATTCTCACTG
1 GTAATCTTTTATTCCCACTG
** *
1516094 GTAATCTTACATTCTCACTG
1 GTAATCTTTTATTCCCACTG
**
1516114 GTAATCTTACATTCCCACTG
1 GTAATCTTTTATTCCCACTG
1516134 GTAATCTT
1 GTAATCTT
1516142 ACATTCCGTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.44
Consensus pattern (20 bp):
GTAATCTTTTATTCCCACTG
Found at i:1520341 original size:24 final size:24
Alignment explanation
Indices: 1520309--1520366 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
1520299 TTGCATGAAA
1520309 ACACGAAGAACATGAACAAATTAG
1 ACACGAAGAACATGAACAAATTAG
1520333 ACACGAAGAACATGAACAAATTAG
1 ACACGAAGAACATGAACAAATTAG
1520357 ACACGAAGAA
1 ACACGAAGAA
1520367 AAGGTGGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.55, C:0.17, G:0.17, T:0.10
Consensus pattern (24 bp):
ACACGAAGAACATGAACAAATTAG
Found at i:1520738 original size:21 final size:21
Alignment explanation
Indices: 1520714--1520758 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1520704 AAATAACCGG
* * *
1520714 ATTAACATAATATTTTAAGTA
1 ATTAACAGAAAATTTTAAATA
*
1520735 ATTACCAGAAAATTTTAAATA
1 ATTAACAGAAAATTTTAAATA
1520756 ATT
1 ATT
1520759 TTTATCAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (21 bp):
ATTAACAGAAAATTTTAAATA
Found at i:1523648 original size:33 final size:34
Alignment explanation
Indices: 1523592--1523674 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 34
1523582 TATTCAAATT
*
1523592 ATAATAATATATATATATATATATATTATAGTTA
1 ATAATAAAATATATATATATATATATTATAGTTA
1523626 ATAATAAAATATATATAT-TATATATTATAGTTA
1 ATAATAAAATATATATATATATATATTATAGTTA
* *
1523659 ATATTCAAAT-TATATA
1 ATAATAAAATATATATA
1523675 ATCATAAGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 6 0.13
33 23 0.50
34 17 0.37
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (34 bp):
ATAATAAAATATATATATATATATATTATAGTTA
Found at i:1524808 original size:15 final size:15
Alignment explanation
Indices: 1524788--1524821 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1524778 TGGTTAGCCA
1524788 TTTGAATTTTGGCCG
1 TTTGAATTTTGGCCG
*
1524803 TTTGAATTTTGGTCG
1 TTTGAATTTTGGCCG
1524818 TTTG
1 TTTG
1524822 GCCATGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.26, T:0.53
Consensus pattern (15 bp):
TTTGAATTTTGGCCG
Found at i:1525444 original size:21 final size:21
Alignment explanation
Indices: 1525420--1525466 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1525410 ATTCTGACTA
*
1525420 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCAATTTTCCAAAT
* *
1525441 TCGCGTTGCAATTTTCCTAAT
1 TCGCATTGCAATTTTCCAAAT
1525462 TCGCA
1 TCGCA
1525467 ATACGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCAATTTTCCAAAT
Found at i:1525487 original size:20 final size:20
Alignment explanation
Indices: 1525462--1525555 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
1525452 TTTTCCTAAT
*
1525462 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1525482 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1525503 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1525523 TCGCAATACAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1525543 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1525556 CTGACTATCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 44 0.73
21 16 0.27
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1526206 original size:20 final size:20
Alignment explanation
Indices: 1526133--1526223 Score: 103
Period size: 20 Copynumber: 4.6 Consensus size: 20
1526123 GCGATTCTGT
1526133 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
1526152 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
1526172 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
1526192 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
1526212 TGTTGCGATTTT
1 CGTTGCGATTTT
1526224 AAGTTTCAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
19 12 0.19
20 51 0.81
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:1526230 original size:20 final size:20
Alignment explanation
Indices: 1526187--1526230 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1526177 CGATAGTCAT
* *
1526187 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1526207 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1526227 TTTC
1 TTTC
1526231 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1528118 original size:20 final size:20
Alignment explanation
Indices: 1528093--1528232 Score: 129
Period size: 20 Copynumber: 6.6 Consensus size: 20
1528083 AGAATAGTTT
*
1528093 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
1528113 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
1528133 ACTATCGCAACGAGAAAATCG
1 ACTATCGCAACGCGAAAAT-G
*
1528154 TAACAACAAAATCGCAACGCGAAAATG
1 -----AC--TATCGCAACGCGAAAATG
*
1528181 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
**
1528201 ACTATCGC-ACTGCGAATTTG
1 ACTATCGCAAC-GCGAAAATG
*
1528221 ACTATCGTAACG
1 ACTATCGCAACG
1528233 AAAGAATCGC
Statistics
Matches: 100, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.01
20 76 0.76
21 3 0.03
22 2 0.02
26 2 0.02
27 1 0.01
28 15 0.15
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:1528300 original size:20 final size:20
Alignment explanation
Indices: 1528275--1528456 Score: 169
Period size: 20 Copynumber: 9.3 Consensus size: 20
1528265 GCGATTCTCT
**
1528275 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
1528295 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1528315 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1528335 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
** * *
1528355 TGTTACAATAGTCATTTTCGCG
1 CATTGCGATAGTCATTTT--CG
*
1528377 CATTGCGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
* **
1528393 --TTGTGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
1528411 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
1528431 CGTTGCTATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1528451 CGTTGC
1 CATTGC
1528457 AATTTTAAGT
Statistics
Matches: 135, Mismatches: 19, Indels: 16
0.79 0.11 0.09
Matches are distributed among these distances:
14 6 0.04
16 4 0.03
18 5 0.04
20 113 0.84
22 7 0.05
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:1528335 original size:40 final size:40
Alignment explanation
Indices: 1528277--1528456 Score: 192
Period size: 40 Copynumber: 4.6 Consensus size: 40
1528267 GATTCTCTCA
**
1528277 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCG
* *
1528317 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCG
* * *
1528357 TTACAATAGTCATTTTCGCGCATTGCGAT--TC----TCTCG
1 TTGCGATAGTCATTTT--CGCATTGCGATAGTCATTTTCGCG
* **
1528393 TTGTGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCG
* *
1528433 TTGCTATAGTCATTTTCGCGTTGC
1 TTGCGATAGTCATTTTCGCATTGC
1528457 AATTTTAAGT
Statistics
Matches: 112, Mismatches: 20, Indels: 16
0.76 0.14 0.11
Matches are distributed among these distances:
34 11 0.10
36 16 0.14
40 75 0.67
42 10 0.09
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (40 bp):
TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCG
Found at i:1529984 original size:14 final size:14
Alignment explanation
Indices: 1529965--1530000 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1529955 ATTGTTTAAT
1529965 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1529979 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1529993 TGATTTGT
1 TGATTTGT
1530001 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:1530245 original size:33 final size:34
Alignment explanation
Indices: 1530183--1530254 Score: 128
Period size: 33 Copynumber: 2.1 Consensus size: 34
1530173 ACTAAATTCG
1530183 CGTTGCGATTTTCATTTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTACGATTCTCT
*
1530217 CGTTGCGATTTTCATTTT-GCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTACGATTCTCT
1530250 CGTTG
1 CGTTG
1530255 ATATAGTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 19 0.51
34 18 0.49
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTACGATTCTCT
Found at i:1530265 original size:33 final size:34
Alignment explanation
Indices: 1530194--1530266 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 34
1530184 GTTGCGATTT
* **
1530194 TCATTTTCGCATTACGATTCTCTCGTTGCGATTT
1 TCATTTTCGCATTACGATTCTCTCGTTGAGATAG
* *
1530228 TCATTTT-GCATTGCGATTCTCTCGTTGATATAG
1 TCATTTTCGCATTACGATTCTCTCGTTGAGATAG
1530261 TCATTT
1 TCATTT
1530267 CCGCGTTGCG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 27 0.79
34 7 0.21
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.48
Consensus pattern (34 bp):
TCATTTTCGCATTACGATTCTCTCGTTGAGATAG
Found at i:1530280 original size:20 final size:20
Alignment explanation
Indices: 1530257--1530363 Score: 162
Period size: 20 Copynumber: 5.3 Consensus size: 20
1530247 TCTCGTTGAT
1530257 ATAGTCATTTCCGCGTTGCG
1 ATAGTCATTTCCGCGTTGCG
*
1530277 ATAGTCATTTCTGCGTTGCG
1 ATAGTCATTTCCGCGTTGCG
1530297 ATAGTCATTTCCGCGTTGCG
1 ATAGTCATTTCCGCGTTGCG
* *
1530317 ATAGTCATTTCCGTGTTGTG
1 ATAGTCATTTCCGCGTTGCG
*
1530337 ATAGTTATATT-CGCGTTGCG
1 ATAGTCAT-TTCCGCGTTGCG
1530357 ATAGTCA
1 ATAGTCA
1530364 AATGAATGTC
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 76 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
ATAGTCATTTCCGCGTTGCG
Found at i:1532817 original size:24 final size:25
Alignment explanation
Indices: 1532769--1532823 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
1532759 CTGAAAAATC
1532769 ATCAAAATCCGAGTATTTGACCAAG
1 ATCAAAATCCGAGTATTTGACCAAG
* *
1532794 ATCAAAGTCCGGGTA-TTGACCAAG
1 ATCAAAATCCGAGTATTTGACCAAG
1532818 ATCAAA
1 ATCAAA
1532824 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (25 bp):
ATCAAAATCCGAGTATTTGACCAAG
Found at i:1532837 original size:24 final size:24
Alignment explanation
Indices: 1532786--1532837 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1532776 TCCGAGTATT
** *
1532786 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
1532810 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
1532834 TGAC
1 TGAC
1532838 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1533690 original size:20 final size:20
Alignment explanation
Indices: 1533665--1533731 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
1533655 AAATTCAGTA
1533665 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
1533685 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
1533705 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
1533725 TTGCGAT
1 TTGCGAT
1533732 TTACGTATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:1533741 original size:20 final size:20
Alignment explanation
Indices: 1533718--1533806 Score: 160
Period size: 20 Copynumber: 4.5 Consensus size: 20
1533708 CGATAGTCAG
*
1533718 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1533738 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1533758 ATTCGCATTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
1533778 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1533798 ATTCGCATT
1 ATTCGCATT
1533807 ACGAATTAGG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1533832 original size:21 final size:21
Alignment explanation
Indices: 1533808--1533852 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1533798 ATTCGCATTA
1533808 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* *
1533829 CGAATTTGGAAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
1533850 CGA
1 CGA
1533853 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:1541782 original size:2 final size:2
Alignment explanation
Indices: 1541777--1541817 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1541767 TTAATCATTA
1541777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1541818 ATGATATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1543272 original size:12 final size:12
Alignment explanation
Indices: 1543254--1543295 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
1543244 TTATGTTTGA
1543254 ATAAATATTATTT
1 ATAAATA-TATTT
1543267 -TAAATATATTT
1 ATAAATATATTT
1543278 ATAAATGATATTAT
1 ATAAAT-ATATT-T
1543292 ATAA
1 ATAA
1543296 TACCATCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.19
12 11 0.42
13 5 0.19
14 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
ATAAATATATTT
Found at i:1543470 original size:21 final size:22
Alignment explanation
Indices: 1543446--1543489 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1543436 ATTAAAATAA
*
1543446 TTTGTAAA-TTAATTTAATAGT
1 TTTGGAAAGTTAATTTAATAGT
* *
1543467 TTTGGAAAGTTATTTTAGTAGT
1 TTTGGAAAGTTAATTTAATAGT
1543489 T
1 T
1543490 CTAAAGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (22 bp):
TTTGGAAAGTTAATTTAATAGT
Found at i:1543625 original size:84 final size:83
Alignment explanation
Indices: 1543526--1543702 Score: 211
Period size: 84 Copynumber: 2.1 Consensus size: 83
1543516 TTATAATTTG
*
1543526 ATTTAAATAAATTAAA-ATCT-ATTTAATAATTTTGAATCATTAGGTAAT-AGAA-CCAAAATGA
1 ATTTAAATAAATTAAAGAT-TAATTTAAT-ATTTTGAATCATTAAGTAATGA-AATCCAAAAT-A
*
1543587 AATATTGAATTAAATAAATTATT
62 AATATTAAATT-AATAAATTATT
* * * * *
1543610 ATTTAAATGATTTAAAGATTAATTTAATATTTTGATTCATTAATTAATGAAATCTAAAATAAATA
1 ATTTAAATAAATTAAAGATTAATTTAATATTTTGAATCATTAAGTAATGAAATCCAAAATAAATA
1543675 TTAAATTAATAAATTATT
66 TTAAATTAATAAATTATT
1543693 A-TTAAATAAA
1 ATTTAAATAAA
1543703 AATAAAAAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
82 7 0.09
83 12 0.15
84 45 0.56
85 16 0.20
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (83 bp):
ATTTAAATAAATTAAAGATTAATTTAATATTTTGAATCATTAAGTAATGAAATCCAAAATAAATA
TTAAATTAATAAATTATT
Found at i:1543856 original size:16 final size:16
Alignment explanation
Indices: 1543835--1543876 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1543825 TTTATTAATT
1543835 AATTAATTATAGATTA
1 AATTAATTATAGATTA
*
1543851 AATTAAATT-TAGATTT
1 AATT-AATTATAGATTA
*
1543867 ATTTAATTAT
1 AATTAATTAT
1543877 TATATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
AATTAATTATAGATTA
Found at i:1545899 original size:42 final size:42
Alignment explanation
Indices: 1545853--1546087 Score: 173
Period size: 42 Copynumber: 5.7 Consensus size: 42
1545843 AAAATGATAC
* *
1545853 TTTAGCGGTGTTTTTTAAACAAACGCCGTAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTTAAACAAACGCCGTAATAGAGTGGCAA
* * *
1545895 TTTAGCGGCG-TTTATAGCAA-AAACGCCGTAATAGA-T-ACAT
1 TTTAGCGGCGTTTTTTA--AACAAACGCCGTAATAGAGTGGCAA
* * *
1545935 TTATAGTGGCGTTTTTTTAACAAACGCCGCAATAGAGTGGCAA
1 TT-TAGCGGCGTTTTTTAAACAAACGCCGTAATAGAGTGGCAA
* * ** *
1545978 TTTAGCGGCG-TTTTTACACAAACGCCGTGAT--AGTGTTAT
1 TTTAGCGGCGTTTTTTAAACAAACGCCGTAATAGAGTGGCAA
* * ** *
1546017 TTATAGTGGCGTTTGTTT-AACAAATGCCGCT-ATAGAGAAGAAA
1 TT-TAGCGGCGTTT-TTTAAACAAACGCCG-TAATAGAGTGGCAA
* *
1546060 TTTAGCGGCGTTTATAAAACAAACGCCG
1 TTTAGCGGCGTTTTTTAAACAAACGCCG
1546088 CAAATAGTAT
Statistics
Matches: 148, Mismatches: 31, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
39 7 0.05
40 12 0.08
41 58 0.39
42 60 0.41
43 11 0.07
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTAAACAAACGCCGTAATAGAGTGGCAA
Found at i:1545960 original size:41 final size:42
Alignment explanation
Indices: 1545862--1546045 Score: 130
Period size: 41 Copynumber: 4.5 Consensus size: 42
1545852 CTTTAGCGGT
* ** * *
1545862 GTTTTTTAAACAAACGCCGTAATAGAGTGGTAATT-TAGCGGC
1 GTTTTTTTAACAAACGCCGTAATAGA-TGACATTTATAGTGGC
***
1545904 GTTTATAGCAA-AAACGCCGTAATAGAT-ACATTTATAGTGGC
1 GTTT-TTTTAACAAACGCCGTAATAGATGACATTTATAGTGGC
* * * *
1545945 GTTTTTTTAACAAACGCCGCAATAGAGTGGCAATT-TAGCGGC
1 GTTTTTTTAACAAACGCCGTAATAGA-TGACATTTATAGTGGC
* **
1545987 G--TTTTTACACAAACGCCGTGATAG-TGTTATTTATAGTGGC
1 GTTTTTTTA-ACAAACGCCGTAATAGATGACATTTATAGTGGC
* *
1546027 GTTTGTTTAACAAATGCCG
1 GTTTTTTTAACAAACGCCG
1546046 CTATAGAGAA
Statistics
Matches: 111, Mismatches: 22, Indels: 19
0.73 0.14 0.12
Matches are distributed among these distances:
39 5 0.05
40 19 0.17
41 48 0.43
42 32 0.29
43 7 0.06
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (42 bp):
GTTTTTTTAACAAACGCCGTAATAGATGACATTTATAGTGGC
Found at i:1546030 original size:82 final size:81
Alignment explanation
Indices: 1545862--1546114 Score: 290
Period size: 82 Copynumber: 3.0 Consensus size: 81
1545852 CTTTAGCGGT
* * * * *
1545862 GTTTTTTAAACAAACGCCGTAATAGAGTGGTAATTTAGCGGCGTTTATAGCAAAAACGCCGTAAT
1 GTTTTTTTAACAAACGCCGCAATAGAGTGGAAATTTAGCGGCGTTTTTA-CACAAACGCCGTAAT
**
1545927 AGATACATTTATAGTGGC
65 AG-TTTATTTATAGTGGC
* *
1545945 GTTTTTTTAACAAACGCCGCAATAGAGTGGCAATTTAGCGGCGTTTTTACACAAACGCCGTGATA
1 GTTTTTTTAACAAACGCCGCAATAGAGTGGAAATTTAGCGGCGTTTTTACACAAACGCCGTAATA
1546010 GTGTTATTTATAGTGGC
66 GT-TTATTTATAGTGGC
* * * ** * * *
1546027 GTTTGTTTAACAAATGCCGCTATAGAGAAGAAATTTAGCGGCGTTTATAAAACAAACGCCGCAAA
1 GTTTTTTTAACAAACGCCGCAATAGAGTGGAAATTTAGCGGCGTTT-TTACACAAACGCCG-TAA
*
1546092 TAGTATTGTTTATAGTGGC
64 TAGT-TTATTTATAGTGGC
1546111 GTTT
1 GTTT
1546115 ATGCAAAAAA
Statistics
Matches: 147, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
81 1 0.01
82 67 0.46
83 57 0.39
84 22 0.15
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (81 bp):
GTTTTTTTAACAAACGCCGCAATAGAGTGGAAATTTAGCGGCGTTTTTACACAAACGCCGTAATA
GTTTATTTATAGTGGC
Found at i:1546150 original size:84 final size:82
Alignment explanation
Indices: 1545934--1546195 Score: 199
Period size: 82 Copynumber: 3.2 Consensus size: 82
1545924 AATAGATACA
* ** * * * ** * * * *
1545934 TTTATAGTGGCGTTTTTTTAACAAACGCCGCAATAGAGTGGCAATTTAGCGGCGTTTTTACACAA
1 TTTATAGTGGCGTTTATGCAAAAAATGCCGCTATAGAGAAGAAATATAGCGGCGTTTTAAAACAA
** *
1545999 ACGCCGTGATAGTGTTA
66 ACGCCGCAATAGTGTTG
* ** * *
1546016 TTTATAGTGGCGTTTGTTTAACAAATGCCGCTATAGAGAAGAAATTTAGCGGCGTTTATAAAACA
1 TTTATAGTGGCGTTTATGCAAAAAATGCCGCTATAGAGAAGAAATATAGCGGCGTTT-TAAAACA
*
1546081 AACGCCGCAAATAGTATTG
65 AACGCCGC-AATAGTGTTG
* * ** **
1546100 TTTATAGTGGCGTTTATGCAAAAAATGCCG-TAATAGATTAA-TAATATAGCGGATTTTGTAGGA
1 TTTATAGTGGCGTTTATGCAAAAAATGCCGCT-ATAGA-GAAGAAATATAGCGGCGTTT-TAAAA
1546163 -AAACGCCGCAATA-TGTTG
63 CAAACGCCGCAATAGTGTTG
*
1546181 TTTATCGTGGCGTTT
1 TTTATAGTGGCGTTT
1546196 TTATAAAAAC
Statistics
Matches: 150, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
81 18 0.12
82 55 0.37
83 22 0.15
84 53 0.35
85 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.33
Consensus pattern (82 bp):
TTTATAGTGGCGTTTATGCAAAAAATGCCGCTATAGAGAAGAAATATAGCGGCGTTTTAAAACAA
ACGCCGCAATAGTGTTG
Found at i:1547675 original size:41 final size:42
Alignment explanation
Indices: 1547603--1547833 Score: 245
Period size: 41 Copynumber: 5.5 Consensus size: 42
1547593 TAATTAGTGA
* * * * * *
1547603 CGTTTTTATCGAAAAATGCCGCTATAGACCACACTTTTGTGG
1 CGTTTGTATCAAAAAACGCCGCCATAAACCACACTTTTGCGG
* * *
1547645 CATTTGTAT-AAAAAACGCAGCCATAAACCACACTTTTACGG
1 CGTTTGTATCAAAAAACGCCGCCATAAACCACACTTTTGCGG
* * *
1547686 CATTTGTATCAAAAATA--CCGCCATAAACCATACTTTTTTACGG
1 CGTTTGTATCAAAAA-ACGCCGCCATAAACCACAC--TTTTGCGG
* * *
1547729 CGTTTGTATAAAAAAATGCCGCCATAAACCACACTTTTGCGA
1 CGTTTGTATCAAAAAACGCCGCCATAAACCACACTTTTGCGG
* *
1547771 CGTTTGTTTC-AAAAACGCCGCCATAGACCACACTTTTGCGG
1 CGTTTGTATCAAAAAACGCCGCCATAAACCACACTTTTGCGG
*
1547812 CGTTTGTATCAAAAAATGCCGC
1 CGTTTGTATCAAAAAACGCCGC
1547834 AATATGTTCA
Statistics
Matches: 159, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
41 85 0.53
42 37 0.23
43 22 0.14
44 15 0.09
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (42 bp):
CGTTTGTATCAAAAAACGCCGCCATAAACCACACTTTTGCGG
Found at i:1547753 original size:85 final size:82
Alignment explanation
Indices: 1547621--1547833 Score: 246
Period size: 85 Copynumber: 2.5 Consensus size: 82
1547611 TCGAAAAATG
* * ** * * * *
1547621 CCGCTATAGACCACACTTTTGTGGCATTTGTATAAAAAACGCAGCCATAAACCACACTTTTACGG
1 CCGCCATAAACCACACTTTTACGGCGTTTGTATAAAAAATGCCGCCATAAACCACACTTTTACGA
*
1547686 CATTTGTATCAAAAATA
66 CATTTGTATCAAAAACA
* *
1547703 CCGCCATAAACCATACTTTTTTACGGCGTTTGTATAAAAAAATGCCGCCATAAACCACACTTTTG
1 CCGCCATAAACCACAC--TTTTACGGCGTTTGTAT-AAAAAATGCCGCCATAAACCACACTTTTA
* * *
1547768 CGACGTTTGTTTCAAAAACG
63 CGACATTTGTATCAAAAACA
* *
1547788 CCGCCATAGACCACACTTTTGCGGCGTTTGTATCAAAAAATGCCGC
1 CCGCCATAAACCACACTTTTACGGCGTTTGTAT-AAAAAATGCCGC
1547834 AATATGTTCA
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
82 13 0.12
83 28 0.25
84 14 0.13
85 55 0.50
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (82 bp):
CCGCCATAAACCACACTTTTACGGCGTTTGTATAAAAAATGCCGCCATAAACCACACTTTTACGA
CATTTGTATCAAAAACA
Found at i:1552109 original size:21 final size:21
Alignment explanation
Indices: 1552085--1552161 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1552075 ATGAAGCAAG
1552085 GGAAGCAGAGAGAGCAGTAGC
1 GGAAGCAGAGAGAGCAGTAGC
* * *
1552106 GGAAGTAGAGAGAGCAATAAC
1 GGAAGCAGAGAGAGCAGTAGC
* ** *
1552127 AGAAGCAGCCAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGTAGC
1552148 GGAAGCAGAGAGAG
1 GGAAGCAGAGAGAG
1552162 AAACAGTGGC
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.42, C:0.16, G:0.39, T:0.04
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGTAGC
Found at i:1552175 original size:21 final size:21
Alignment explanation
Indices: 1552151--1552210 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
1552141 CAGCAGCGGA
* * *
1552151 AGCAGAGAGAGAAACAGTGGC
1 AGCACAGAGAGAAGCAGTGAC
* *
1552172 AGCACAGAGAGAGGCAGCGAC
1 AGCACAGAGAGAAGCAGTGAC
1552193 AGCACAGAGAGAAGCAGT
1 AGCACAGAGAGAAGCAGT
1552211 ATATCAGTAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.42, C:0.18, G:0.37, T:0.03
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGTGAC
Found at i:1552604 original size:44 final size:42
Alignment explanation
Indices: 1552544--1552626 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 42
1552534 GTTTGTCACA
*
1552544 AAAAACGCCATAATATACCATACATTTAGCGGCGTTTGTATCCT
1 AAAAACGCCATAATATA-C-GACATTTAGCGGCGTTTGTATCCT
* *
1552588 AAAAACGCCACT-ATATACGACCTTTAGCTGCGTTTGTAT
1 AAAAACGCCA-TAATATACGACATTTAGCGGCGTTTGTAT
1552627 GAAAAATATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 18 0.51
43 1 0.03
44 15 0.43
45 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (42 bp):
AAAAACGCCATAATATACGACATTTAGCGGCGTTTGTATCCT
Found at i:1552706 original size:85 final size:86
Alignment explanation
Indices: 1552617--1552793 Score: 214
Period size: 86 Copynumber: 2.1 Consensus size: 86
1552607 ACCTTTAGCT
* * * *
1552617 GCGTTTGTATGAAAAATATCGCAAAATATCAAC-CCTATTACGGCGTTTGCACT-AAAAACGCCG
1 GCGTTTGCAGGAAAAACATCGCAAAACATCAACACCTATTACGGCGTTTG-ACTGAAAAACGCCG
1552680 CTAAAAATCAACACCTACTGCG
65 CTAAAAATCAACACCTACTGCG
* * * * ** *
1552702 GCGTTAGCGGGAAAAACGTCGCAAAACATCAACACCTATTACGGCGTTTGTCTGCCAAACGTCGC
1 GCGTTTGCAGGAAAAACATCGCAAAACATCAACACCTATTACGGCGTTTGACTGAAAAACGCCGC
* *
1552767 TAAACATCAACACCTATTGCG
66 TAAAAATCAACACCTACTGCG
1552788 GCGTTT
1 GCGTTT
1552794 TTTGTTAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
85 28 0.37
86 48 0.63
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (86 bp):
GCGTTTGCAGGAAAAACATCGCAAAACATCAACACCTATTACGGCGTTTGACTGAAAAACGCCGC
TAAAAATCAACACCTACTGCG
Found at i:1552768 original size:86 final size:85
Alignment explanation
Indices: 1552635--1552792 Score: 228
Period size: 86 Copynumber: 1.8 Consensus size: 85
1552625 ATGAAAAATA
*
1552635 TCGCAAAATATCAACCCTATTACGGCGTTTGCACTAAAAACGCCGCTAAAAATCAACACCTACTG
1 TCGCAAAACATCAACCCTATTACGGCGTTTGCACTAAAAACGCCGCTAAAAATCAACACCTACTG
1552700 CGGCGTTAGCGGGAAAAACG
66 CGGCGTTAGCGGGAAAAACG
* ** * * *
1552720 TCGCAAAACATCAACACCTATTACGGCGTTTG-TCTGCCAAACGTCGCTAAACATCAACACCTAT
1 TCGCAAAACATCAAC-CCTATTACGGCGTTTGCACT-AAAAACGCCGCTAAAAATCAACACCTAC
1552784 TGCGGCGTT
64 TGCGGCGTT
1552793 TTTTGTTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
85 16 0.25
86 48 0.75
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (85 bp):
TCGCAAAACATCAACCCTATTACGGCGTTTGCACTAAAAACGCCGCTAAAAATCAACACCTACTG
CGGCGTTAGCGGGAAAAACG
Found at i:1552793 original size:43 final size:43
Alignment explanation
Indices: 1552635--1552793 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 43
1552625 ATGAAAAATA
* * * ***
1552635 TCGCAAAATATCAAC-CCTATTACGGCGTTTGCACTAAAAACG
1 TCGCTAAACATCAACACCTATTGCGGCGTTTGCGGGAAAAACG
* * * *
1552677 CCGCTAAAAATCAACACCTACTGCGGCGTTAGCGGGAAAAACG
1 TCGCTAAACATCAACACCTATTGCGGCGTTTGCGGGAAAAACG
* * * **
1552720 TCGCAAAACATCAACACCTATTACGGCGTTTGTC-TGCCAAACG
1 TCGCTAAACATCAACACCTATTGCGGCGTTTG-CGGGAAAAACG
1552763 TCGCTAAACATCAACACCTATTGCGGCGTTT
1 TCGCTAAACATCAACACCTATTGCGGCGTTT
1552794 TTTGTTAAAA
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
42 12 0.13
43 82 0.86
44 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
TCGCTAAACATCAACACCTATTGCGGCGTTTGCGGGAAAAACG
Found at i:1561992 original size:19 final size:21
Alignment explanation
Indices: 1561968--1562008 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1561958 GTATATATAT
*
1561968 AAATG-ATG-ATGCTATGGAA
1 AAATGAATGTATGATATGGAA
1561987 AAATGAATGTATGATATGGAA
1 AAATGAATGTATGATATGGAA
1562008 A
1 A
1562009 TGGAACGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 11 0.58
ACGTcount: A:0.46, C:0.02, G:0.24, T:0.27
Consensus pattern (21 bp):
AAATGAATGTATGATATGGAA
Found at i:1563442 original size:20 final size:20
Alignment explanation
Indices: 1563413--1563455 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1563403 ATTTCACCAC
*
1563413 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
* *
1563433 ATGCATCTATATGATCTTAA
1 ATGCAACTATATGATCCTAA
1563453 ATG
1 ATG
1563456 GGCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1570990 original size:20 final size:20
Alignment explanation
Indices: 1570961--1571003 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1570951 ATTTCACCAC
*
1570961 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
1570981 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
1571001 ATG
1 ATG
1571004 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1575287 original size:146 final size:147
Alignment explanation
Indices: 1575067--1575359 Score: 419
Period size: 146 Copynumber: 2.0 Consensus size: 147
1575057 AACGGTTGAG
** * * *
1575067 AAATTCAAATTTATACCAGTTGGAACTCGTCACGCTAGTGTGACGAGTTCTGTTTACAATAAAAT
1 AAATTCAAATTTATACCAGTTAAAACTCGTCACACCAGTGTGACGAGTTATGTTTACAATAAAAT
* * * *
1575132 AATATATATATTTTTAACAATGTTTTCTAAAATTCCAAAAAATTA-TTTTTATTA-AGACTCGTC
66 AATATATATATATTTAACAATGTTTTCTAAAATTCAAAAAAAATATTTTTTATTACA-ACTCATC
*
1575195 ATGCAAGCATGATGAGTC
130 ACGCAAGCATGATGAGTC
* *
1575213 AAATTCAAATTTATACCAGTTAAAACTCGTCATACCAGTGTGACGAGTTATGTTTCCAATAAAAT
1 AAATTCAAATTTATACCAGTTAAAACTCGTCACACCAGTGTGACGAGTTATGTTTACAATAAAAT
* *
1575278 AATATATATATATTTAACAATTTTTTTTAAAATTCAAAAAAAATATTTTTTATTACAACTCATCA
66 AATATATATATATTTAACAATGTTTTCTAAAATTCAAAAAAAATATTTTTTATTACAACTCATCA
**
1575343 CGCGGGCATGATGAGTC
131 CGCAAGCATGATGAGTC
1575360 CCTTAATATA
Statistics
Matches: 129, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
146 98 0.76
147 30 0.23
148 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (147 bp):
AAATTCAAATTTATACCAGTTAAAACTCGTCACACCAGTGTGACGAGTTATGTTTACAATAAAAT
AATATATATATATTTAACAATGTTTTCTAAAATTCAAAAAAAATATTTTTTATTACAACTCATCA
CGCAAGCATGATGAGTC
Found at i:1576542 original size:50 final size:50
Alignment explanation
Indices: 1576448--1576542 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 50
1576438 TGCACATGAA
* ***
1576448 GACTTTGGCGCCAAGATGAACAAGCACATCACCATTCGGGCAAGGAATAT
1 GACTTTGGCGCCAAGATGAACAAACACATCACCATTCAACCAAGGAATAT
* *
1576498 GACTTTGGTGCCAAGATGAACAAACATATCACCATTCAACCAAGG
1 GACTTTGGCGCCAAGATGAACAAACACATCACCATTCAACCAAGG
1576543 GGAGGTTGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (50 bp):
GACTTTGGCGCCAAGATGAACAAACACATCACCATTCAACCAAGGAATAT
Found at i:1580176 original size:36 final size:36
Alignment explanation
Indices: 1580136--1580224 Score: 108
Period size: 36 Copynumber: 2.4 Consensus size: 36
1580126 CTTAATGTTT
*
1580136 TTATTTAATTGTTT-GAATTGTAATGTTTGTATTTAA
1 TTATTTAATTATTTAG-ATTGTAATGTTTGTATTTAA
* *
1580172 TTATTTTATTATTTAGATTGTAATGTTTTTATTTAA
1 TTATTTAATTATTTAGATTGTAATGTTTGTATTTAA
*
1580208 TTTTCTTAATGTATTTA
1 TTAT-TTAAT-TATTTA
1580225 TCGTTTCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
36 34 0.76
37 5 0.11
38 6 0.13
ACGTcount: A:0.27, C:0.01, G:0.10, T:0.62
Consensus pattern (36 bp):
TTATTTAATTATTTAGATTGTAATGTTTGTATTTAA
Found at i:1583255 original size:27 final size:25
Alignment explanation
Indices: 1583225--1583284 Score: 59
Period size: 25 Copynumber: 2.3 Consensus size: 25
1583215 TTCTCCTAAT
* *
1583225 TAAATAAATAGTATACAAATTAAAATA
1 TAAATAAATACTA-A-AAATTAAAAAA
1583252 TAAACT-AATACTAAAAATTAAAAAA
1 TAAA-TAAATACTAAAAATTAAAAAA
1583277 TACAATAA
1 TA-AATAA
1583285 TTTAAATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
25 13 0.46
26 4 0.14
27 10 0.36
28 1 0.04
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.27
Consensus pattern (25 bp):
TAAATAAATACTAAAAATTAAAAAA
Found at i:1584966 original size:15 final size:16
Alignment explanation
Indices: 1584948--1584984 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1584938 AACATATTCT
1584948 AAAAAAA-GAAAAACA
1 AAAAAAAGGAAAAACA
1584963 AAAAAAAGGGAAAAACA
1 AAAAAAA-GGAAAAACA
1584980 AAAAA
1 AAAAA
1584985 CAGGTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
17 13 0.65
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAGGAAAAACA
Found at i:1589248 original size:19 final size:19
Alignment explanation
Indices: 1589203--1589274 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
1589193 TACGTTGGGC
*
1589203 TATGAATCT-AAAATTGAGC
1 TATGAATCTGAAAA-TGAGT
**
1589222 TACAAATCTGAAAATGAGT
1 TATGAATCTGAAAATGAGT
** *
1589241 TATGAATCAAAAAAATGAAT
1 TATGAATC-TGAAAATGAGT
1589261 TATGAATCTGAAAA
1 TATGAATCTGAAAA
1589275 GAAAGAAAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 21 0.51
20 20 0.49
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (19 bp):
TATGAATCTGAAAATGAGT
Found at i:1589274 original size:20 final size:20
Alignment explanation
Indices: 1589226--1589274 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1589216 TTGAGCTACA
*
1589226 AATCTG-AAAATGAGTTATG
1 AATCTGAAAAATGAATTATG
**
1589245 AATCAAAAAAATGAATTATG
1 AATCTGAAAAATGAATTATG
1589265 AATCTGAAAA
1 AATCTGAAAA
1589275 GAAAGAAAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.27
Consensus pattern (20 bp):
AATCTGAAAAATGAATTATG
Found at i:1592289 original size:75 final size:76
Alignment explanation
Indices: 1592166--1592351 Score: 267
Period size: 75 Copynumber: 2.5 Consensus size: 76
1592156 TAAATAGTGA
* *
1592166 GGTACCGATACACCTCATAGGGTGTACCGATAGCCCTATGCAAATTTTGGCT-CTGAG-AAAACA
1 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTATGCAAATTTTGGCTAC-GAGAAAAACA
1592229 GAATGCCAAATG
65 GAATGCCAAATG
1592241 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTATG-ACAATTTTGGCTACGAGAAAAACA
1 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTATGCA-AATTTTGGCTACGAGAAAAACA
*
1592305 GAATGCCCAATG
65 GAATGCCAAATG
* *
1592317 GGTACCGATACCCCT--TAGAG-GTACCAATACCCCTA
1 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTA
1592352 GTCATTTAAC
Statistics
Matches: 103, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
73 14 0.14
74 5 0.05
75 51 0.50
76 33 0.32
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (76 bp):
GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTATGCAAATTTTGGCTACGAGAAAAACAG
AATGCCAAATG
Found at i:1598097 original size:21 final size:21
Alignment explanation
Indices: 1598071--1598124 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1598061 TTTGCACCAT
* *
1598071 GTATCGATACCCCCTTTATAG
1 GTATCGATACCCCCATGATAG
*
1598092 GTATCGATACCCCCATGCTAG
1 GTATCGATACCCCCATGATAG
1598113 GTATCGATACCC
1 GTATCGATACCC
1598125 TTTCAACGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (21 bp):
GTATCGATACCCCCATGATAG
Found at i:1598161 original size:23 final size:22
Alignment explanation
Indices: 1598113--1598170 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
1598103 CCCATGCTAG
1598113 GTATCGATA-CCCTTTCAACGT
1 GTATCGATACCCCTTTCAACGT
* * *
1598134 ATATCGATACCCTCTTTGAATGT
1 GTATCGATACCC-CTTTCAACGT
1598157 GTATCGATACCCCT
1 GTATCGATACCCCT
1598171 ATAAGGGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 8 0.26
22 4 0.13
23 19 0.61
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (22 bp):
GTATCGATACCCCTTTCAACGT
Found at i:1600885 original size:76 final size:76
Alignment explanation
Indices: 1600759--1600945 Score: 308
Period size: 76 Copynumber: 2.5 Consensus size: 76
1600749 TAAATAGGGA
1600759 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAG
1 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAG
*
1600824 AATGTCAAATG
66 AATGCCAAATG
*
1600835 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAT
1 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAG
*
1600900 AATGCCCAATG
66 AATGCCAAATG
* *
1600911 GGTACCAATACCCC-C-TAGAG-GTACCGATACCCCTA
1 GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTA
1600946 GTCATTTAAC
Statistics
Matches: 106, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
73 15 0.14
74 4 0.04
75 1 0.01
76 86 0.81
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (76 bp):
GGTACCGATACCCCTCATAGGGTGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAG
AATGCCAAATG
Found at i:1605401 original size:19 final size:19
Alignment explanation
Indices: 1605377--1605442 Score: 114
Period size: 19 Copynumber: 3.5 Consensus size: 19
1605367 TACATTGGAC
1605377 TATGAATCTAAAAATGAGT
1 TATGAATCTAAAAATGAGT
*
1605396 TATGAATCTGAAAATGAGT
1 TATGAATCTAAAAATGAGT
*
1605415 TATGAATCAAAAAATGAGT
1 TATGAATCTAAAAATGAGT
1605434 TATGAATCT
1 TATGAATCT
1605443 TGAAAGAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (19 bp):
TATGAATCTAAAAATGAGT
Found at i:1613947 original size:18 final size:18
Alignment explanation
Indices: 1613907--1613948 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1613897 AAACAGAGTG
**
1613907 ATTTTAATAAAATATTTT
1 ATTTTAATAAAATATTCA
1613925 ATTTTAATAAAATA-TCA
1 ATTTTAATAAAATATTCA
1613942 AGTTTTA
1 A-TTTTA
1613949 GGGTTTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTTAATAAAATATTCA
Found at i:1622605 original size:17 final size:17
Alignment explanation
Indices: 1622583--1622621 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1622573 TTGGATCCGC
1622583 CATTAATGATGTGAAAT
1 CATTAATGATGTGAAAT
1622600 CATTAATGATGTGAAAT
1 CATTAATGATGTGAAAT
1622617 CATTA
1 CATTA
1622622 CAGATCAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (17 bp):
CATTAATGATGTGAAAT
Found at i:1623053 original size:8 final size:8
Alignment explanation
Indices: 1623040--1623080 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
1623030 CTCATTTTTA
1623040 GAGAATTT
1 GAGAATTT
1623048 GAGAATTT
1 GAGAATTT
*
1623056 -AGAGTTT
1 GAGAATTT
1623063 GAGAATTT
1 GAGAATTT
1623071 GAGAATTT
1 GAGAATTT
1623079 GA
1 GA
1623081 AAGCTTGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1623065 original size:15 final size:16
Alignment explanation
Indices: 1623040--1623080 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
1623030 CTCATTTTTA
1623040 GAGAATTTGAGAATTT
1 GAGAATTTGAGAATTT
*
1623056 -AGAGTTTGAGAATTT
1 GAGAATTTGAGAATTT
1623071 GAGAATTTGA
1 GAGAATTTGA
1623081 AAGCTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (16 bp):
GAGAATTTGAGAATTT
Found at i:1623389 original size:128 final size:128
Alignment explanation
Indices: 1623161--1623767 Score: 1088
Period size: 128 Copynumber: 4.7 Consensus size: 128
1623151 ACTATTCACA
* * *
1623161 TGAAGGCACGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
1623226 TTATGTCACTCATGTCCCTCGAGAACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
1623289 TGAAGGCGCTTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATATTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1623354 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
1623417 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1623482 TTATGTCACTCATGTCCCTCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
1623545 TGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1623610 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
1623673 TGAAGGCGCGTTCTCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1623738 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
1623768 GATGGATTGT
Statistics
Matches: 458, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 458 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:1624202 original size:34 final size:34
Alignment explanation
Indices: 1624163--1624235 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
1624153 TAAGTTGAAA
1624163 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATGTTAAATTTCGAATACTATAATTTATAT
* * *
1624197 TTTAATTTTAAATTTCGAATAGTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1624231 TTTAA
1 TTTAA
1624236 AAACATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACTATAATTTATAT
Found at i:1624790 original size:21 final size:21
Alignment explanation
Indices: 1624766--1624864 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
1624756 AACCCTGCGA
*
1624766 GCTAGGCATGTAACCTGGCGG
1 GCTAGGAATGTAACCTGGCGG
*
1624787 GCTAGGAATGTAACCCT-GCGA
1 GCTAGGAATGTAA-CCTGGCGG
*
1624808 GCTCGGAATGTAACCTGGCGG
1 GCTAGGAATGTAACCTGGCGG
*
1624829 GCTAGGAATGTAACCCT-GCAG
1 GCTAGGAATGTAA-CCTGGCGG
1624850 GCTCA-GAATGTAACC
1 GCT-AGGAATGTAACC
1624865 CTGCGGAGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.07
21 56 0.82
22 7 0.10
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.19
Consensus pattern (21 bp):
GCTAGGAATGTAACCTGGCGG
Found at i:1624819 original size:42 final size:42
Alignment explanation
Indices: 1624756--1624864 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
1624746 TATGGTATAA
* *
1624756 AACCCTGCGAGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGAGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1624798 AACCCTGCGAGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGAGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
*
1624840 AACCCTGC-AGGCTCAGAATGTAACC
1 AACCCTGCGA-GCTCGGAATGTAACC
1624865 CTGCGGAGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
41 1 0.02
42 62 0.98
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.18
Consensus pattern (42 bp):
AACCCTGCGAGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:1624900 original size:21 final size:21
Alignment explanation
Indices: 1624874--1624921 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1624864 CCTGCGGAGA
*
1624874 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
1624895 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
1624916 GGGCAT
1 TGGCAT
1624922 GTACCCCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.25
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:1626484 original size:17 final size:17
Alignment explanation
Indices: 1626447--1626500 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1626437 ACATTATAAA
* *
1626447 AAATT-AAAATTAATAT
1 AAATTAAAAATAAATTT
* * *
1626463 AAATTTATAATAACTTT
1 AAATTAAAAATAAATTT
1626480 AAATTAAAAATAAATTT
1 AAATTAAAAATAAATTT
1626497 AAAT
1 AAAT
1626501 ATTAACATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTAAAAATAAATTT
Found at i:1626695 original size:33 final size:31
Alignment explanation
Indices: 1626644--1626731 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 31
1626634 TTAATAATTC
*
1626644 TAAATAAATAATAATTATATAAATATTATTTAA
1 TAAAAAAATAATAATTATATAAATA-TA-TTAA
* *
1626677 TAAAAAAATAATATTTATATAATTATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
1626708 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
1626732 AAAATACTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 6 0.13
32 18 0.39
33 22 0.48
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:1626702 original size:30 final size:33
Alignment explanation
Indices: 1626644--1626721 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
1626634 TTAATAATTC
*
1626644 TAAATAAATAATAATTATATAAATATTAT-TTAA
1 TAAAAAAATAAT-ATTATATAAATATTATATTAA
*
1626677 TAAAAAAATAATATT-TATATA-ATTATATTAA
1 TAAAAAAATAATATTATATAAATATTATATTAA
*
1626708 TATAAAATATAATA
1 TA-AAAAAATAATA
1626722 ACTATTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 5 0.12
31 11 0.28
32 13 0.32
33 11 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TAAAAAAATAATATTATATAAATATTATATTAA
Found at i:1638510 original size:21 final size:21
Alignment explanation
Indices: 1638468--1638525 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
1638458 GCTACAGTGG
* * *
1638468 CATATGAAATGGTTGTGGTGC
1 CATATGAAACGATTGCGGTGC
* *
1638489 CATCTGATACGATTGCGGTGC
1 CATATGAAACGATTGCGGTGC
1638510 CATATGAAACGATTGC
1 CATATGAAACGATTGC
1638526 AGAATATACA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (21 bp):
CATATGAAACGATTGCGGTGC
Found at i:1644609 original size:32 final size:32
Alignment explanation
Indices: 1644550--1644620 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1644540 TACATTATAA
* * *
1644550 ATTATGTATATATGTTTTATATCATTATTTTT
1 ATTATATATATATATTTTATATCATTATTATT
* *
1644582 CTTATATATATATATTGTT-TATTATTATTATT
1 ATTATATATATATATT-TTATATCATTATTATT
1644614 ATTATAT
1 ATTATAT
1644621 TTTTTATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (32 bp):
ATTATATATATATATTTTATATCATTATTATT
Found at i:1644788 original size:2 final size:2
Alignment explanation
Indices: 1644781--1644819 Score: 60
Period size: 2 Copynumber: 18.5 Consensus size: 2
1644771 TAAATACTAT
1644781 TA TA TA TA TA TA TA TA TA TA TA CTA CTA 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 T
1644820 GCATATGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 31 0.86
3 5 0.14
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1644825 original size:26 final size:26
Alignment explanation
Indices: 1644774--1644825 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1644764 TTTTATTTAA
* *
1644774 ATACTATTATATATATATATATATAT
1 ATACTACTATATATATATATACATAT
*
1644800 ATACTACTATATATATATATGCATAT
1 ATACTACTATATATATATATACATAT
1644826 GTTTTACTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (26 bp):
ATACTACTATATATATATATACATAT
Found at i:1644972 original size:18 final size:17
Alignment explanation
Indices: 1644945--1644986 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1644935 TTAGTTGTAT
1644945 TTATTTTTTC-TGTTTTA
1 TTATTTTTTCAT-TTTTA
1644962 TTATTTATTTCATTTTTA
1 TTATTT-TTTCATTTTTA
1644980 TT-TTTTT
1 TTATTTTT
1644987 GGGTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 9 0.39
18 11 0.48
19 1 0.04
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (17 bp):
TTATTTTTTCATTTTTA
Found at i:1651930 original size:18 final size:19
Alignment explanation
Indices: 1651903--1651940 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1651893 GGCAAACAAG
1651903 TTTTCTTA-TTTCATTCATT
1 TTTTCTTATTTTC-TTCATT
1651922 TTTTC-TATTTTCTTCATT
1 TTTTCTTATTTTCTTCATT
1651940 T
1 T
1651941 CAGTACTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCTTATTTTCTTCATT
Found at i:1656859 original size:2 final size:2
Alignment explanation
Indices: 1656848--1656880 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1656838 TTTTTCAATC
1656848 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1656881 ACAATATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1657055 original size:85 final size:86
Alignment explanation
Indices: 1656904--1657072 Score: 225
Period size: 85 Copynumber: 2.0 Consensus size: 86
1656894 AAATACAATC
* ** * *
1656904 ATGACACACGAATGTGTGTCATCTTTTTTTAATGACGTGTACTTCAATGACACGCAATGTAAGTC
1 ATGACACACAAATGTGTGTCATCTTAATTTAATGACGCGGACTTCAATGACACGCAATGTAAGTC
* *
1656969 ATACATGCGTGTCATAAATTT
66 ATAAATGCGCGTCATAAATTT
* * *
1656990 ATGACACACAAATGTGTGTCATCTTAATTT-ATGACGCGGGCTTCAATGACGCTCAATG-AATGT
1 ATGACACACAAATGTGTGTCATCTTAATTTAATGACGCGGACTTCAATGACACGCAATGTAA-GT
1657053 CATAAATGCGCGTCATAAAT
65 CATAAATGCGCGTCATAAAT
1657073 GTGTGTCATA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
84 2 0.03
85 43 0.60
86 27 0.38
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (86 bp):
ATGACACACAAATGTGTGTCATCTTAATTTAATGACGCGGACTTCAATGACACGCAATGTAAGTC
ATAAATGCGCGTCATAAATTT
Found at i:1657067 original size:13 final size:13
Alignment explanation
Indices: 1657051--1657095 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
1657041 CTCAATGAAT
1657051 GTCATAAATGCGC
1 GTCATAAATGCGC
* *
1657064 GTCATAAATGTGT
1 GTCATAAATGCGC
1657077 GTCATAAATGCGC
1 GTCATAAATGCGC
*
1657090 GACATA
1 GTCATA
1657096 GATTTATGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:1657073 original size:26 final size:26
Alignment explanation
Indices: 1657044--1657095 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1657034 AATGACGCTC
*
1657044 AATGAATGTCATAAATGCGCGTCATA
1 AATGAATGTCATAAATGCGCGACATA
**
1657070 AATGTGTGTCATAAATGCGCGACATA
1 AATGAATGTCATAAATGCGCGACATA
1657096 GATTTATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (26 bp):
AATGAATGTCATAAATGCGCGACATA
Found at i:1659613 original size:11 final size:11
Alignment explanation
Indices: 1659592--1659647 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
1659582 CCCTAAATTG
1659592 AAAAGAAAAG-
1 AAAAGAAAAGA
1659602 AAAAGAAAAAGA
1 AAAAG-AAAAGA
1659614 AAAAGAAAAGA
1 AAAAGAAAAGA
**
1659625 AAAAGTGAA-A
1 AAAAGAAAAGA
1659635 AAAAGAAAA-A
1 AAAAGAAAAGA
1659645 AAA
1 AAA
1659648 TTAGGTGGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
10 17 0.43
11 18 0.45
12 5 0.12
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:1659619 original size:17 final size:16
Alignment explanation
Indices: 1659592--1659644 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
1659582 CCCTAAATTG
1659592 AAAAGAAAAGAAAAGA
1 AAAAGAAAAGAAAAGA
1659608 AAAAGAAAAAGAAAAGA
1 AAAAG-AAAAGAAAAGA
*
1659625 AAAAGTGAAA-AAAAGA
1 AAAAG-AAAAGAAAAGA
1659641 AAAA
1 AAAA
1659645 AAATTAGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 15 0.44
17 19 0.56
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAGAAAAGA
Found at i:1659644 original size:6 final size:5
Alignment explanation
Indices: 1659591--1659627 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
1659581 ACCCTAAATT
1659591 GAAAA GAAAA GAAAA GAAAAA GAAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA G-AAAA G-AAAA GAAAA GAAAA
1659628 AGTGAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:1661359 original size:2 final size:2
Alignment explanation
Indices: 1661348--1661380 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1661338 TCATTCATAC
1661348 AT AT -T 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
1661381 TATTTTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1662086 original size:20 final size:20
Alignment explanation
Indices: 1662061--1662100 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1662051 AATTTTTGCA
* *
1662061 ACCGATGAACGGCGGCCGAC
1 ACCGATCAACGACGGCCGAC
1662081 ACCGATCAACGACGGCCGAC
1 ACCGATCAACGACGGCCGAC
1662101 GAGGCAACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.38, G:0.30, T:0.05
Consensus pattern (20 bp):
ACCGATCAACGACGGCCGAC
Found at i:1662221 original size:6 final size:6
Alignment explanation
Indices: 1662210--1662237 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1662200 GTTTCGATTT
1662210 TGAAAA TGAAAA TGAAAA TGAAAA TGAA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGAA
1662238 GTTGGGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (6 bp):
TGAAAA
Found at i:1662542 original size:5 final size:5
Alignment explanation
Indices: 1662534--1662710 Score: 141
Period size: 5 Copynumber: 34.6 Consensus size: 5
1662524 TTTTTGTCTC
* * *
1662534 TTTAT TTTA- TTTA- TTTATT TTTAT TTT-C TTTAT TATAT TTT-C TTTAT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1662581 TTTAT TTTAT TTTAT TTTATTT TTTAT TTTA- TTTAT CTTTAT TTTA-
1 TTTAT TTTAT TTTAT TTTA--T TTTAT TTTAT TTTAT -TTTAT TTTAT
* * *
1662627 TTTAT TTTAT TTTTT CTTTAT TTTAT TTTCT TTATTT TTTAT CTTTAT
1 TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TT-TAT TTTAT -TTTAT
* * *
1662675 TATTTT CTTTAT CTTAT TTTCT TTATAT TTTAT TTT
1 T-TTAT -TTTAT TTTAT TTTAT TT-TAT TTTAT TTT
1662711 TTCCTTGACC
Statistics
Matches: 140, Mismatches: 17, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
4 22 0.16
5 80 0.57
6 32 0.23
7 6 0.04
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:1662548 original size:9 final size:9
Alignment explanation
Indices: 1662534--1662709 Score: 118
Period size: 9 Copynumber: 19.3 Consensus size: 9
1662524 TTTTTGTCTC
1662534 TTTATTTTA
1 TTTATTTTA
*
1662543 TTTATTTATT
1 TTTATTT-TA
*
1662553 TTTATTTTC
1 TTTATTTTA
*
1662562 TTTATTATA
1 TTTATTTTA
1662571 TTT-TCTTTA
1 TTTAT-TTTA
1662580 TTTTATTTTA
1 -TTTATTTTA
1662590 TTTTATTTTA
1 -TTTATTTTA
1662600 -TT-TTTTA
1 TTTATTTTA
*
1662607 TTTTATTTATC
1 -TTTATTT-TA
1662618 TTTATTTTA
1 TTTATTTTA
1662627 TTTATTTTA
1 TTTATTTTA
*
1662636 TTTTTTCTTTA
1 -TTTAT-TTTA
*
1662647 TTTTATTTTC
1 -TTTATTTTA
1662657 TTTA-TTT-
1 TTTATTTTA
1662664 TTTATCTTTA
1 TTTAT-TTTA
*
1662674 -TTATTTTC
1 TTTATTTTA
*
1662682 TTTATCTTA
1 TTTATTTTA
1662691 TTT-TCTTTA
1 TTTAT-TTTA
1662700 --TATTTTA
1 TTTATTTTA
1662707 TTT
1 TTT
1662710 TTTCCTTGAC
Statistics
Matches: 135, Mismatches: 14, Indels: 36
0.73 0.08 0.19
Matches are distributed among these distances:
7 14 0.10
8 11 0.08
9 57 0.42
10 42 0.31
11 11 0.08
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1662695 original size:14 final size:14
Alignment explanation
Indices: 1662509--1662710 Score: 190
Period size: 14 Copynumber: 14.5 Consensus size: 14
1662499 ATTTTTACTA
*
1662509 TTATTTTCTTTTTCT
1 TTATTTTCTTTAT-T
*
1662524 TTTTTGTCTCTTTATT
1 TTATT-T-TCTTTATT
*
1662540 TTA-TTTATTTATTT
1 TTATTTTCTTTA-TT
1662554 TTATTTTCTTTATT
1 TTATTTTCTTTATT
*
1662568 ATATTTTCTTTATT
1 TTATTTTCTTTATT
*
1662582 TTATTTTATTTTATT
1 TTATTTT-CTTTATT
1662597 TTA-TTT-TTTATT
1 TTATTTTCTTTATT
1662609 TTATTTATCTTTATT
1 TTATTT-TCTTTATT
1662624 TTATTTAT-TTTA--
1 TTATTT-TCTTTATT
1662636 TT-TTTTCTTTATT
1 TTATTTTCTTTATT
1662649 TTATTTTCTTTATT
1 TTATTTTCTTTATT
*
1662663 TT-TTATCTTTA--
1 TTATTTTCTTTATT
*
1662674 TTATTTTCTTTATC
1 TTATTTTCTTTATT
1662688 TTATTTTCTTTATATT
1 TTATTTTC-TT-TATT
1662704 TTATTTT
1 TTATTTT
1662711 TTCCTTGACC
Statistics
Matches: 159, Mismatches: 11, Indels: 33
0.78 0.05 0.16
Matches are distributed among these distances:
10 1 0.01
11 9 0.06
12 19 0.12
13 17 0.11
14 56 0.35
15 37 0.23
16 14 0.09
17 6 0.04
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTTTCTTTATT
Found at i:1662777 original size:14 final size:13
Alignment explanation
Indices: 1662756--1662798 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1662746 TCTTTAAGAT
1662756 TTTTATTTTTTTA
1 TTTTATTTTTTTA
1662769 TTTTCATTTTTTATA
1 TTTT-ATTTTTT-TA
* *
1662784 TATTGTTTTTTTA
1 TTTTATTTTTTTA
1662797 TT
1 TT
1662799 ATTTTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 7 0.28
14 13 0.52
15 5 0.20
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:1662810 original size:15 final size:14
Alignment explanation
Indices: 1662754--1662810 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 14
1662744 CCTCTTTAAG
1662754 ATTTTTATTTTT-TT
1 ATTTTT-TTTTTATT
1662768 ATTTTCATTTTTTATAT
1 ATTTT--TTTTTTAT-T
*
1662785 ATTGTTTTTTTATT
1 ATTTTTTTTTTATT
1662799 ATTTTTTCTTTT
1 ATTTTTT-TTTT
1662811 TGCTTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 12 0.33
15 17 0.47
16 2 0.06
17 5 0.14
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (14 bp):
ATTTTTTTTTTATT
Found at i:1666601 original size:104 final size:105
Alignment explanation
Indices: 1666482--1666672 Score: 258
Period size: 105 Copynumber: 1.8 Consensus size: 105
1666472 TTTGGTCGCT
* *
1666482 AAAATTCTCAATGTGACAATATTTATGGCCAT-AAATATATTTTCAATGTCAAATAAATTCATTA
1 AAAATTCTCAATGTGACAACATTTATGGCCATAAAATATATTTTCAATGTCAAATAAATTCATCA
* * *
1666546 TATTTTCTATTGATAATAGTGTCAAACATCAGGTCATTGA
66 TAATTTCTATTGACAACAGTGTCAAACATCAGGTCATTGA
* * * ** ***
1666586 AAAATTCTTATTGTGACAACATTTGTGGTTATAAAATATATTTTTTGTGTCAAATAAATTCATCA
1 AAAATTCTCAATGTGACAACATTTATGGCCATAAAATATATTTTCAATGTCAAATAAATTCATCA
1666651 TAATTTCTATTGACAACAGTGT
66 TAATTTCTATTGACAACAGTGT
1666673 TGAACATTTG
Statistics
Matches: 73, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
104 26 0.36
105 47 0.64
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (105 bp):
AAAATTCTCAATGTGACAACATTTATGGCCATAAAATATATTTTCAATGTCAAATAAATTCATCA
TAATTTCTATTGACAACAGTGTCAAACATCAGGTCATTGA
Found at i:1666694 original size:105 final size:104
Alignment explanation
Indices: 1666482--1666694 Score: 246
Period size: 105 Copynumber: 2.0 Consensus size: 104
1666472 TTTGGTCGCT
* *
1666482 AAAATTCTCAATGTGACAATATTTATGGCCATAAATATATTTTCAATGTCAAATAAATTCATTAT
1 AAAATTCTCAATGTGACAACATTTATGGCCATAAATATATTTTCAATGTCAAATAAATTCATCAT
* * * * *
1666547 ATTTTCTATTGATAATAGTGTCAAACATCAGGTCATTGA
66 AATTTCTATTGACAACAGTGTCAAACATCAGGTCACTAA
* * * ** ***
1666586 AAAATTCTTATTGTGACAACATTTGTGGTTATAAAATATATTTTTTGTGTCAAATAAATTCATCA
1 AAAATTCTCAATGTGACAACATTTATGGCCAT-AAATATATTTTCAATGTCAAATAAATTCATCA
** **
1666651 TAATTTCTATTGACAACAGTGTTGAACATTTGGTCACTAA
65 TAATTTCTATTGACAACAGTGTCAAACATCAGGTCACTAA
1666691 AAAA
1 AAAA
1666695 ATAGATTTTT
Statistics
Matches: 89, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
104 26 0.29
105 63 0.71
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (104 bp):
AAAATTCTCAATGTGACAACATTTATGGCCATAAATATATTTTCAATGTCAAATAAATTCATCAT
AATTTCTATTGACAACAGTGTCAAACATCAGGTCACTAA
Found at i:1666703 original size:74 final size:74
Alignment explanation
Indices: 1666618--1666767 Score: 221
Period size: 74 Copynumber: 2.0 Consensus size: 74
1666608 TTGTGGTTAT
* * * * *
1666618 AAAATATATTTTTTGTGTCAAATAAATTCATCATAATTTCTATTGACAAC-AGTGTTGAACATTT
1 AAAATAGATTTTTAGTGTCAAACAAATTCATCACAATTTCTATTGA-AACTAGTGTCGAACATTT
1666682 GGTCACTAAA
65 GGTCACTAAA
* *
1666692 AAAATAGATTTTTAGTTTCAAACAAATTCATCACAATTTTTATTGAAACTAGTGTCGAACATTTG
1 AAAATAGATTTTTAGTGTCAAACAAATTCATCACAATTTCTATTGAAACTAGTGTCGAACATTTG
1666757 GTCACTAAA
66 GTCACTAAA
1666766 AA
1 AA
1666768 GTACTTAGTG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 3 0.04
74 65 0.96
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (74 bp):
AAAATAGATTTTTAGTGTCAAACAAATTCATCACAATTTCTATTGAAACTAGTGTCGAACATTTG
GTCACTAAA
Found at i:1666865 original size:178 final size:178
Alignment explanation
Indices: 1666530--1666871 Score: 386
Period size: 178 Copynumber: 1.9 Consensus size: 178
1666520 ATTTTCAATG
* * * * *
1666530 TCAAATAAATTCATTATATTTTCTATTGATAATAGTGTCAAACATCAGGTCATTGAAAAATTCTT
1 TCAAACAAATTCATCAAATTTTCTATTGATAATAGTGTCAAACATCAGGTCACTGAAAAATACTT
* ** * *** * *
1666595 ATTGTGACAACATTTGTGGTTATAAAATATATTTTTTGTGTCAAATAAATTCATCATAATTTCTA
66 AGTGTGACAACATTCATGGTTACAAAATATATTTTCAATGTCAAACAAATTCATCACAATTTCTA
* ** *
1666660 TTGACAACAGTGTTGAACATTTGGTCACTAAAAAAATAGATTTTTAGTT
131 TTGACAACAGCGGCGAACATATGGTCAC-AAAAAAATAGATTTTTAGTT
* **
1666709 TCAAACAAATTCATCACAATTTT-TATTGA-AACTAGTGTCGAACATTTGGTCACT-AAAAAGTA
1 TCAAACAAATTCATCA-AATTTTCTATTGATAA-TAGTGTCAAACATCAGGTCACTGAAAAA-TA
*
1666771 CTTAGTGTGACAACATTCAT-GTTACAAAATATATTTTCAATGTCGAACAAATTCATCACAATTT
63 CTTAGTGTGACAACATTCATGGTTACAAAATATATTTTCAATGTCAAACAAATTCATCACAATTT
* ** *
1666835 CTATTGATAGTAGCGGCGAATATATGGTCACAAAAAA
128 CTATTGACAACAGCGGCGAACATATGGTCACAAAAAA
1666872 TTAACAATTG
Statistics
Matches: 134, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
177 6 0.04
178 67 0.50
179 56 0.42
180 5 0.04
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (178 bp):
TCAAACAAATTCATCAAATTTTCTATTGATAATAGTGTCAAACATCAGGTCACTGAAAAATACTT
AGTGTGACAACATTCATGGTTACAAAATATATTTTCAATGTCAAACAAATTCATCACAATTTCTA
TTGACAACAGCGGCGAACATATGGTCACAAAAAAATAGATTTTTAGTT
Found at i:1667442 original size:45 final size:47
Alignment explanation
Indices: 1667352--1667442 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 47
1667342 AATTACGATT
*
1667352 TCTTTTTAATTATCTTTTAATTTGAAATATTTAAAAAGATATAAATA
1 TCTTTTCAATTATCTTTTAATTTGAAATATTTAAAAAGATATAAATA
1667399 TCTTTTCAA-TATC-TTTAATATT-AAA-ATTTAAAAAGATAATAAAT
1 TCTTTTCAATTATCTTTTAAT-TTGAAATATTTAAAAAGAT-ATAAAT
1667443 TTATTTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 12 0.29
45 15 0.37
46 6 0.15
47 8 0.20
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (47 bp):
TCTTTTCAATTATCTTTTAATTTGAAATATTTAAAAAGATATAAATA
Found at i:1667484 original size:34 final size:35
Alignment explanation
Indices: 1667412--1667505 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 35
1667402 TTTCAATATC
*
1667412 TTTAATATTAAAATTTAAAAAGATAATAAATTTAT
1 TTTAATATTAAAATTTAAAAAGATAATAAATCTAT
*
1667447 TTTAAT-TTAAAATATTCAAAAAGAT-ATAACTCT-T
1 TTTAATATTAAAAT-TT-AAAAAGATAATAAATCTAT
* * * *
1667481 TTTACTATTCAAACTTAAATAGATA
1 TTTAATATTAAAATTTAAAAAGATA
1667506 TTATGTTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
33 7 0.14
34 15 0.31
35 19 0.39
36 8 0.16
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (35 bp):
TTTAATATTAAAATTTAAAAAGATAATAAATCTAT
Found at i:1681058 original size:38 final size:40
Alignment explanation
Indices: 1681016--1681104 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 40
1681006 TTATTCATTT
*
1681016 ATATTCAAACTCT-AAAAGATAAT-ATA-TTTTAATTTGAA
1 ATATTCAAA-TCTAAAAAGATAATAATACTTTTAATTTAAA
* *
1681054 ATATTTAAATTTAAAAAGATAATAAATATCTTTTAATTTAAA
1 ATATTCAAATCTAAAAAGATAAT-AATA-CTTTTAATTTAAA
1681096 ATATTCAAA
1 ATATTCAAA
1681105 AGATATAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
37 2 0.05
38 18 0.43
40 3 0.07
42 19 0.45
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (40 bp):
ATATTCAAATCTAAAAAGATAATAATACTTTTAATTTAAA
Found at i:1681230 original size:71 final size:69
Alignment explanation
Indices: 1681053--1681280 Score: 205
Period size: 71 Copynumber: 3.3 Consensus size: 69
1681043 TTTAATTTGA
* * * * *
1681053 AATATTTAAATTTAAA-AAGATAATAAATATCTTTTAATTTAAAATATTCAAAAGATATA-AACT
1 AATATTCAAAGTTAAATAA-ATAATAAATAACTTTTAATTTGAAATATTCAAAAGATATATTA-T
1681116 CCTTTT
64 CCTTTT
* * ** * ** *
1681122 ACTATTCAAACTTAAATTGATATTATGTTAATTTTTAATTTGAAATATTCAAAAGTATATGATTA
1 AATATTCAAAGTTAAATAAATAATA-AATAACTTTTAATTTGAAATATTCAAAAG-ATAT-ATTA
1681187 T-CTTTT
63 TCCTTTT
*
1681193 AATATTCAAAGTTAAATAAATAATAAATAACTATTTAATTTGACATATTCAAAAGA-ATAATTAT
1 AATATTCAAAGTTAAATAAATAATAAATAACT-TTTAATTTGAAATATTCAAAAGATAT-ATTAT
**
1681257 CCTACT
64 CCTTTT
*
1681263 AATATT-TAAGTTAAATAA
1 AATATTCAAAGTTAAATAA
1681281 TATCTTTTAA
Statistics
Matches: 127, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
69 36 0.28
70 38 0.30
71 50 0.39
72 2 0.02
73 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (69 bp):
AATATTCAAAGTTAAATAAATAATAAATAACTTTTAATTTGAAATATTCAAAAGATATATTATCC
TTTT
Found at i:1681501 original size:2 final size:2
Alignment explanation
Indices: 1681494--1681531 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1681484 AACTTCATAA
1681494 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
1681532 TACCTCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1686416 original size:14 final size:14
Alignment explanation
Indices: 1686397--1686429 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1686387 TGCGGCGAGG
1686397 AGACAATGTTAGCT
1 AGACAATGTTAGCT
1686411 AGACAATGTTAGCT
1 AGACAATGTTAGCT
1686425 AGACA
1 AGACA
1686430 GTTACTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (14 bp):
AGACAATGTTAGCT
Found at i:1686845 original size:23 final size:23
Alignment explanation
Indices: 1686815--1686872 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1686805 TACTATGTAG
* *
1686815 AAACAGAGTTTTCCCGCTCTGGT
1 AAACAGAGTTTTCCAGCTCTAGT
1686838 AAACAGAGTTTTCCAGCTCTAGT
1 AAACAGAGTTTTCCAGCTCTAGT
*
1686861 AAATAGAGTTTT
1 AAACAGAGTTTT
1686873 TTATTCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (23 bp):
AAACAGAGTTTTCCAGCTCTAGT
Found at i:1688474 original size:12 final size:12
Alignment explanation
Indices: 1688443--1688478 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1688433 ATGCCATTAA
*
1688443 AAATATATATTT
1 AAATATATTTTT
1688455 AAAT-TATTTTT
1 AAATATATTTTT
1688466 AAATATATTTTT
1 AAATATATTTTT
1688478 A
1 A
1688479 TAAGTTTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATATATTTTT
Found at i:1690196 original size:70 final size:70
Alignment explanation
Indices: 1690070--1690238 Score: 232
Period size: 70 Copynumber: 2.4 Consensus size: 70
1690060 TTAAAGAGAT
* ** * *
1690070 AATATCTTTTAATTTCAAATATTCAAAA-GGTATAATTATCATACTAATATTCAAATTAGAGAGA
1 AATATCTTTTAATTTAAAATATTCAAAATAATATAATTACCATACTAATATTCAAATTAAAGAGA
*
1690134 TAATA
66 CAATA
* * * *
1690139 AATATATTTTAATTTAAAATATTTAAAATAATATAATTACCTTATTAATATTCAAATTAAAGAGA
1 AATATCTTTTAATTTAAAATATTCAAAATAATATAATTACCATACTAATATTCAAATTAAAGAGA
1690204 CAATA
66 CAATA
*
1690209 AATATCTTTTAATTTAGAATATTCAAAATA
1 AATATCTTTTAATTTAAAATATTCAAAATA
1690239 TGATATTAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
69 25 0.29
70 61 0.71
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (70 bp):
AATATCTTTTAATTTAAAATATTCAAAATAATATAATTACCATACTAATATTCAAATTAAAGAGA
CAATA
Found at i:1693553 original size:2 final size:2
Alignment explanation
Indices: 1693546--1693588 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1693536 CTATGTTAAG
*
1693546 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1693588 T
1 T
1693589 TTGAAATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1697435 original size:54 final size:54
Alignment explanation
Indices: 1697353--1697469 Score: 234
Period size: 54 Copynumber: 2.2 Consensus size: 54
1697343 TGGTAAGGCG
1697353 TGCCCACGCCTTAACTGTAGACTTCTTCTGCGATAGCTCAAGATGAATAAGTCA
1 TGCCCACGCCTTAACTGTAGACTTCTTCTGCGATAGCTCAAGATGAATAAGTCA
1697407 TGCCCACGCCTTAACTGTAGACTTCTTCTGCGATAGCTCAAGATGAATAAGTCA
1 TGCCCACGCCTTAACTGTAGACTTCTTCTGCGATAGCTCAAGATGAATAAGTCA
1697461 TGCCCACGC
1 TGCCCACGC
1697470 TTTATGCAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (54 bp):
TGCCCACGCCTTAACTGTAGACTTCTTCTGCGATAGCTCAAGATGAATAAGTCA
Done.