Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 15
Found at i:1820150 original size:30 final size:30
Alignment explanation
Indices: 1820114--1820172 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1820104 AGAATATGTA
1820114 AATATTAAGGACAAAATGTATAATTATACC
1 AATATTAAGGACAAAATGTATAATTATACC
*
1820144 AATATTAAGGACCAAATGTATAATTATAC
1 AATATTAAGGACAAAATGTATAATTATAC
1820173 TAATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (30 bp):
AATATTAAGGACAAAATGTATAATTATACC
Found at i:1823420 original size:2 final size:2
Alignment explanation
Indices: 1823415--1823441 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1823405 TTATAGTGTG
1823415 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1823442 TCCTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1830783 original size:114 final size:114
Alignment explanation
Indices: 1830583--1830922 Score: 662
Period size: 114 Copynumber: 3.0 Consensus size: 114
1830573 CTTCTTCCGC
*
1830583 TTTGTTAGCAGTAACCAAACTTGCATTGTTTCTGTATGTTTTTTACTTGTACTAGGTGCACTTTT
1 TTTGTTAGCAGTAACCAAACTTGCATTGTTTCTGTATGTTTTTTACTTGTACTACGTGCACTTTT
1830648 TCTTTAATGACGTTGATTTTTGTGTTTATGGGATCAGGAGCTGAATGTT
66 TCTTTAATGACGTTGATTTTTGTGTTTATGGGATCAGGAGCTGAATGTT
*
1830697 TTTGTTAGCAGTAACCAAACTTGCATTGTTTCTGTATGTTTTTTACTTGTACTACGTGCAATTTT
1 TTTGTTAGCAGTAACCAAACTTGCATTGTTTCTGTATGTTTTTTACTTGTACTACGTGCACTTTT
1830762 TCTTTAATGACGTTGATTTTTGTGTTTATGGGATCAGGAGCTGAATGTT
66 TCTTTAATGACGTTGATTTTTGTGTTTATGGGATCAGGAGCTGAATGTT
1830811 TTTGTTAGCAGTAACCAAACTTGCATTGTTTCTGTATGTTTTTTACTTGTACTACGTGCACTTTT
1 TTTGTTAGCAGTAACCAAACTTGCATTGTTTCTGTATGTTTTTTACTTGTACTACGTGCACTTTT
1830876 TCTTTAATGACGTTGATTTTTGTGTTTATGGGATCAGGAGCTGAATG
66 TCTTTAATGACGTTGATTTTTGTGTTTATGGGATCAGGAGCTGAATG
1830923 CCAACAGACC
Statistics
Matches: 223, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 223 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.46
Consensus pattern (114 bp):
TTTGTTAGCAGTAACCAAACTTGCATTGTTTCTGTATGTTTTTTACTTGTACTACGTGCACTTTT
TCTTTAATGACGTTGATTTTTGTGTTTATGGGATCAGGAGCTGAATGTT
Found at i:1834357 original size:55 final size:55
Alignment explanation
Indices: 1834293--1834397 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
1834283 CTCACATTAG
* *
1834293 TCGATCAATTAATAGATCTCACATTACCATTTTATTTATCAAGATGTTTAACCAT
1 TCGACCAATTAATAGATCTCACATTACCATTTTACTTATCAAGATGTTTAACCAT
* * * * *
1834348 TCGACCAATTAATTGATCTCACATTAGCTTTTTGCTTATCAATATGTTTA
1 TCGACCAATTAATAGATCTCACATTACCATTTTACTTATCAAGATGTTTA
1834398 TATATTTCTC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (55 bp):
TCGACCAATTAATAGATCTCACATTACCATTTTACTTATCAAGATGTTTAACCAT
Found at i:1838744 original size:22 final size:22
Alignment explanation
Indices: 1838719--1838773 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
1838709 TAAGTATTAG
1838719 TGTTAGTTTATTTA-TCGTAAAA
1 TGTTAGTTTATTTATTCGT-AAA
* *
1838741 TGTTAATTTA-ATATTCGTAAA
1 TGTTAGTTTATTTATTCGTAAA
1838762 TG-T-GTTTATTTA
1 TGTTAGTTTATTTA
1838774 GTATTCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 4 0.15
20 3 0.11
21 7 0.26
22 13 0.48
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.53
Consensus pattern (22 bp):
TGTTAGTTTATTTATTCGTAAA
Found at i:1838772 original size:23 final size:22
Alignment explanation
Indices: 1838733--1838779 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1838723 AGTTTATTTA
1838733 TCGTAAAATGTTAATTTAATAT
1 TCGTAAAATGTTAATTTAATAT
* * *
1838755 TCGTAAATGTGTTTATTTAGTAT
1 TCGTAAA-ATGTTAATTTAATAT
1838778 TC
1 TC
1838780 ATTTAAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (22 bp):
TCGTAAAATGTTAATTTAATAT
Found at i:1839013 original size:20 final size:20
Alignment explanation
Indices: 1838988--1839044 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1838978 GCGATTTTCC
* *
1838988 TAAATCTCAATGCGATTACG
1 TAAATCGCAATGCGAATACG
1839008 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
1839028 TAAATCGCAATGCGAAT
1 TAAATCGCAATGCGAAT
1839045 CTGACTATCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.25
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:1839264 original size:22 final size:22
Alignment explanation
Indices: 1839239--1839300 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
1839229 GGCGACATCC
1839239 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1839261 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
* *
1839279 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1839301 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1839552 original size:12 final size:12
Alignment explanation
Indices: 1839535--1839567 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
1839525 GAAGTTAGTA
1839535 TTTGTCTTTTTT
1 TTTGTCTTTTTT
1839547 TTTGTC-TTTTT
1 TTTGTCTTTTTT
1839558 TTTGTCTTTT
1 TTTGTCTTTT
1839568 GGTTGAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (12 bp):
TTTGTCTTTTTT
Found at i:1839670 original size:20 final size:20
Alignment explanation
Indices: 1839645--1839693 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1839635 CAACGAGTGA
1839645 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1839665 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1839685 ATCGCAACG
1 ATCGCAACG
1839694 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1839776 original size:20 final size:20
Alignment explanation
Indices: 1839706--1839792 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
1839696 AGAATCGCAA
1839706 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
1839725 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
1839745 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1839765 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
1839785 TGCGATTT
1 TGCGATTT
1839793 AAAGTTTCAG
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 9 0.15
20 50 0.85
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1839800 original size:20 final size:20
Alignment explanation
Indices: 1839757--1839800 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1839747 CGATAGTCAT
** *
1839757 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
1839777 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
1839797 TTTC
1 TTTC
1839801 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:1841703 original size:20 final size:20
Alignment explanation
Indices: 1841678--1841761 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
1841668 AGAATAGTTT
1841678 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1841698 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1841718 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1841734 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1841752 ACAATCGCAA
1 ACTATCGCAA
1841762 CGAAAGAATC
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
14 7 0.13
16 4 0.07
17 4 0.07
18 4 0.07
20 36 0.65
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1841747 original size:34 final size:34
Alignment explanation
Indices: 1841701--1841793 Score: 143
Period size: 34 Copynumber: 2.8 Consensus size: 34
1841691 GAAAATGACT
* * *
1841701 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACAATCGCAACGAAAGA
1841735 ATCGCAATGCGAAAATGACAATCGCAACGAAAGA
1 ATCGCAATGCGAAAATGACAATCGCAACGAAAGA
*
1841769 ATCGCAATGCG-AAATGAAAATCGCA
1 ATCGCAATGCGAAAATGACAATCGCA
1841794 TTGCGATTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 13 0.24
34 42 0.76
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACAATCGCAACGAAAGA
Found at i:1841833 original size:20 final size:20
Alignment explanation
Indices: 1841808--1841894 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
1841798 GATTCTCTCG
**
1841808 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1841828 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1841848 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1841868 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1841888 TTGCGAT
1 TTGCGAT
1841895 TTTAAGTTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1842418 original size:18 final size:19
Alignment explanation
Indices: 1842379--1842420 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1842369 CTCACCTGTC
1842379 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1842400 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1842418 ATC
1 ATC
1842421 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1842451 original size:20 final size:21
Alignment explanation
Indices: 1842402--1842478 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
1842392 CCTCCCCTAT
*
1842402 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGTCCCCTATCA-C
*
1842424 C-CTCAAGAGTCCCCT-TCAC
1 CGTTCAAGAGTCCCCTATCAC
* * *
1842443 CGTTCAAGAGTCCACTGTCAT
1 CGTTCAAGAGTCCCCTATCAC
*
1842464 CGTTGAAGAGGTCCC
1 CGTTCAAGA-GTCCC
1842479 TCCCAACATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 23 0.51
22 5 0.11
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGTCCCCTATCAC
Found at i:1842472 original size:21 final size:20
Alignment explanation
Indices: 1842426--1842473 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1842416 CTATCATCCC
*
1842426 TCAAGAGTCCCCTTCACCGT
1 TCAAGAGTCCACTTCACCGT
*
1842446 TCAAGAGTCCACTGTCATCGT
1 TCAAGAGTCCACT-TCACCGT
*
1842467 TGAAGAG
1 TCAAGAG
1842474 GTCCCTCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (20 bp):
TCAAGAGTCCACTTCACCGT
Found at i:1843855 original size:14 final size:14
Alignment explanation
Indices: 1843836--1843871 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1843826 ATTGTTTAAT
1843836 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1843850 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1843864 TGATTTGT
1 TGATTTGT
1843872 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:1844030 original size:33 final size:34
Alignment explanation
Indices: 1843973--1844068 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 34
1843963 AAAACAAAAT
* **
1843973 ATCGCAACGCGAAAATGACTATCGCAACGA-TAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGT-GA
1844007 ATCGCAATGCG-AAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGTGA
1844040 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
1844069 CAAACTAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 29 0.51
34 28 0.49
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGTGA
Found at i:1844165 original size:236 final size:237
Alignment explanation
Indices: 1843865--1844510 Score: 1195
Period size: 237 Copynumber: 2.7 Consensus size: 237
1843855 TGTAAATGTT
*
1843865 GATTTGTTTAATTGATGTGTACCTAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGA
1 GATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGA
* * *
1843930 TTTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAAAATATCGCAACGCGAAAATGACTAT
66 TTTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTAT
*
1843995 CGCAACGATAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
131 CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1844060 ATCGCAACG-CAAACTAATTTCGCGTTGCGATTTTCATTTTC
196 ATCGCAACGTCAAACTAATTTCGCGTTGCGATTTTCATTTTC
*
1844101 GATTTGTTTAATTTATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGA
1 GATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGA
1844166 TTTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTAT
66 TTTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTAT
*
1844231 CGCAACGAGAGAATTGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
131 CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
* *
1844296 ATCGCAACGTGAAACTAATTTTGCGTTGCGATTTTCATTTTC
196 ATCGCAACGTCAAACTAATTTCGCGTTGCGATTTTCATTTTC
*
1844338 GATTTGTTTAATTGATGTGTACATAATATTTGTTCTTGTTTAATTGATTGAAATGTAATAGTTGA
1 GATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGA
1844403 TTTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTAT
66 TTTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTAT
1844468 CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
131 CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
1844511 TTTCGCGTTG
Statistics
Matches: 397, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
236 197 0.50
237 200 0.50
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.33
Consensus pattern (237 bp):
GATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGA
TTTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTAT
CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
ATCGCAACGTCAAACTAATTTCGCGTTGCGATTTTCATTTTC
Found at i:1844297 original size:34 final size:33
Alignment explanation
Indices: 1844209--1844304 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
1844199 AAAACAGACT
* **
1844209 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
1844243 ATTGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1844276 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1844305 TGAAACTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1844496 original size:33 final size:34
Alignment explanation
Indices: 1844446--1844509 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
1844436 AAAACAGACT
**
1844446 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
*
1844480 ATCGCAATGC-GAAATGAAAATCGCAACGAG
1 ATCGCAACGCGGAAATGAAAATCGCAACGAG
1844510 TTTTCGCGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1844568 original size:33 final size:33
Alignment explanation
Indices: 1844516--1844649 Score: 133
Period size: 33 Copynumber: 3.8 Consensus size: 33
1844506 CGAGTTTTCG
1844516 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
** *
1844550 CGTTGCGATTTTCATTTCGCATTGTAATTTTCATTT
1 CGTTGCGATTTTCATTTCGCATTGCGA--TTCA-CT
*
1844586 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CG--TTGCGATTTTCATTTCGCATTGCGATTCACT
* ** *
1844621 CATTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
1844650 AGTCAATTCT
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
33 24 0.29
34 24 0.29
35 6 0.07
36 6 0.07
38 23 0.28
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:1844613 original size:19 final size:19
Alignment explanation
Indices: 1844511--1844616 Score: 132
Period size: 19 Copynumber: 5.8 Consensus size: 19
1844501 CGCAACGAGT
*
1844511 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1844530 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
1844548 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
**
1844564 TTTCGCATTGTAATTTTCA
1 TTTCGCATTGCGATTTTCA
1844583 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1844602 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
1844617 CTCTCATTGC
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 3 0.04
18 4 0.05
19 42 0.57
20 12 0.16
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:1844648 original size:20 final size:20
Alignment explanation
Indices: 1844623--1844709 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
1844613 GATTCTCTCA
1844623 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
* * *
1844643 TTGCGATAGTCAATTCTGCA
1 TTGCGATAGTCATTTCCGCG
* *
1844663 TTGTGATAGTCATTTCCGTG
1 TTGCGATAGTCATTTCCGCG
1844683 TTGCGATAGTCATATT-CGCG
1 TTGCGATAGTCAT-TTCCGCG
1844703 TTGCGAT
1 TTGCGAT
1844710 TTCCGCGTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 54 0.96
21 2 0.04
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:1844671 original size:40 final size:41
Alignment explanation
Indices: 1844621--1844709 Score: 137
Period size: 40 Copynumber: 2.2 Consensus size: 41
1844611 GCGATTCTCT
1844621 CATTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCTG
1 CATTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCTG
* *
1844661 CATTGTGATAGTCATTTCCGTGTTGCGATAGTCATATTC-G
1 CATTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCTG
*
1844701 CGTTGCGAT
1 CATTGCGAT
1844710 TTCCGCGTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCTG
Found at i:1850910 original size:18 final size:18
Alignment explanation
Indices: 1850872--1850910 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1850862 GCCACCGCAA
* *
1850872 CCATTTATGATGTCACAG
1 CCATATATGATGCCACAG
*
1850890 CCATATATGATGCCACCG
1 CCATATATGATGCCACAG
1850908 CCA
1 CCA
1850911 CCGCCACCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (18 bp):
CCATATATGATGCCACAG
Found at i:1851218 original size:12 final size:12
Alignment explanation
Indices: 1851197--1851227 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1851187 TCAGGATGAT
*
1851197 GACGACGACGAC
1 GACGATGACGAC
1851209 GACGATGACGAC
1 GACGATGACGAC
1851221 GACGATG
1 GACGATG
1851228 GTGATGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.35, T:0.06
Consensus pattern (12 bp):
GACGATGACGAC
Found at i:1858592 original size:22 final size:22
Alignment explanation
Indices: 1858567--1858618 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1858557 ACATCACATA
1858567 TATTAAAGGTATGGATGTTCAT
1 TATTAAAGGTATGGATGTTCAT
1858589 TATTAAAGGTATGGATGTTCAT
1 TATTAAAGGTATGGATGTTCAT
1858611 TATTAAAG
1 TATTAAAG
1858619 AATTGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (22 bp):
TATTAAAGGTATGGATGTTCAT
Found at i:1861839 original size:19 final size:19
Alignment explanation
Indices: 1861815--1861865 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1861805 ACCAACTAAA
1861815 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
1861834 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
*
1861853 TCGCAACGCGATC
1 TCGCAATGCGATC
1861866 TCCGGTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (19 bp):
TCGCAATGCGATCGATAAT
Found at i:1861942 original size:21 final size:21
Alignment explanation
Indices: 1861913--1861959 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1861903 ATTCTGACTA
1861913 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1861934 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
1861955 TCGCA
1 TCGCA
1861960 ACGCGATTAC
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:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1863016 original size:126 final size:125
Alignment explanation
Indices: 1862786--1863041 Score: 446
Period size: 126 Copynumber: 2.0 Consensus size: 125
1862776 AACAGAAAAA
1862786 ATTGTGAGTACTAATCAGTATTCGAAATTTGATCTTGGTCAATACCCGGACTTTGATCTTAGTCA
1 ATTGTGAGTACTAATCAGTATTCGAAATTTGATCTTGGTCAATACCCGGACTTTGATCTTAGTCA
1862851 ATACTTGGATTTTGATGATTTTTCAGAAGAAGAAACAGACCATGCGT-GTAATGATTTTGAT
66 ATACTTGGATTTTGATGATTTTTCAGAAGAAGAAACAGACCATGCGTGGT-ATGA-TTTGAT
1862912 ATTGTGAGTACTAATCAGTATTCGAAATTTGATCTTGGTCAATAACCCCGGACTTTGATCTTAGT
1 ATTGTGAGTACTAATCAGTATTCGAAATTTGATCTTGGTCAAT-A-CCCGGACTTTGATCTTAGT
1862977 CAATACTTGGATTTTGATGATTTTTCAGAAG-A-AAACAGACCATGCGTGGGTATGATTTGAT
64 CAATACTTGGATTTTGATGATTTTTCAGAAGAAGAAACAGACCATGCGT-GGTATGATTTGAT
1863038 ATTG
1 ATTG
1863042 GTTAATACCC
Statistics
Matches: 126, Mismatches: 0, Indels: 8
0.94 0.00 0.06
Matches are distributed among these distances:
126 68 0.54
127 6 0.05
128 52 0.41
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (125 bp):
ATTGTGAGTACTAATCAGTATTCGAAATTTGATCTTGGTCAATACCCGGACTTTGATCTTAGTCA
ATACTTGGATTTTGATGATTTTTCAGAAGAAGAAACAGACCATGCGTGGTATGATTTGAT
Found at i:1865535 original size:33 final size:33
Alignment explanation
Indices: 1865485--1865666 Score: 193
Period size: 33 Copynumber: 5.3 Consensus size: 33
1865475 GGAAATTACT
*
1865485 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
* * ** *
1865518 ATCGTAACGTGAAAATCGCAACACGAATATGAAT
1 ATCGCAACGAGAAAATCGCAATGCGAA-ATGAAA
*
1865552 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAACG-AG-AA--A--ATCGCAATGCGAAATGAAA
*
1865591 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
** *
1865624 ATCGCAACGAGGGAATCTGCAAAGCGAAATGAAA
1 ATCGCAACGAGAAAATC-GCAATGCGAAATGAAA
1865658 ATCGCAACG
1 ATCGCAACG
1865667 CGAATTTAGT
Statistics
Matches: 126, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
33 57 0.45
34 37 0.29
35 2 0.02
36 2 0.02
37 1 0.01
38 2 0.02
39 14 0.11
40 11 0.09
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:1865550 original size:20 final size:19
Alignment explanation
Indices: 1865498--1865670 Score: 106
Period size: 19 Copynumber: 9.7 Consensus size: 19
1865488 GCAACGAGAG
*
1865498 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1865517 AATCGTAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
*
1865531 AATCGCAACACGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* *
1865551 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
1865571 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1865590 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
1865604 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
**
1865623 AATCGCAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
*
1865637 AATCTGCAAAGCGAAATGAA
1 AATC-GCAACGCGAAATGAA
1865657 AATCGCAACGCGAA
1 AATCGCAACGCGAA
1865671 TTTAGTTTCG
Statistics
Matches: 121, Mismatches: 15, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
14 26 0.21
15 6 0.05
16 4 0.03
17 8 0.07
18 1 0.01
19 41 0.34
20 32 0.26
21 3 0.02
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1865731 original size:33 final size:33
Alignment explanation
Indices: 1865676--1865755 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
1865666 GCGAATTTAG
* * *
1865676 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
1865709 TTTCGCATTGTGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
1865742 TTTTGCATTGCGAT
1 TTTCGCATTGCGAT
1865756 AGTCATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.11, C:0.19, G:0.21, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:1867276 original size:21 final size:21
Alignment explanation
Indices: 1867210--1867276 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1867200 GTGAATCGGG
*
1867210 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1867230 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1867252 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1867273 CTCT
1 CTCT
1867277 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1867295 original size:42 final size:41
Alignment explanation
Indices: 1867210--1867332 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1867200 GTGAATCGGG
* * * *
1867210 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1867252 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1867294 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1867333 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1867831 original size:19 final size:17
Alignment explanation
Indices: 1867809--1867866 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 17
1867799 AAATCGCAAC
1867809 GCGATTATAGTTTCGCGTT
1 GCGATT-TA-TTTCGCGTT
1867828 GCGATTT-TTT--CGTT
1 GCGATTTATTTCGCGTT
1867842 GCGATTTTCATTTCGCGTT
1 GCGA-TTT-ATTTCGCGTT
1867861 GCGATT
1 GCGATT
1867867 CTCTCGTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 8 0.24
15 3 0.09
16 3 0.09
17 3 0.09
18 3 0.09
19 14 0.41
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.47
Consensus pattern (17 bp):
GCGATTTATTTCGCGTT
Found at i:1867841 original size:14 final size:14
Alignment explanation
Indices: 1867824--1867882 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1867814 TATAGTTTCG
1867824 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
1867838 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TTT
* *
1867855 CGCGTTGCGATTCTCT
1 --CGTTGCGATTTTTT
1867871 CGTTGCGATTTT
1 CGTTGCGATTTT
1867883 CATTTAGCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 19 0.51
15 3 0.08
16 2 0.05
17 3 0.08
18 2 0.05
19 8 0.22
ACGTcount: A:0.08, C:0.20, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:1867856 original size:33 final size:33
Alignment explanation
Indices: 1867819--1867898 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1867809 GCGATTATAG
* *
1867819 TTTCGCGTTGCGATTTTTTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1867852 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
1867885 TTTAGCGTTGCGAT
1 TTTCGCGTTGCGAT
1867899 AGTCATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:1867895 original size:19 final size:18
Alignment explanation
Indices: 1867823--1867898 Score: 69
Period size: 19 Copynumber: 4.6 Consensus size: 18
1867813 TTATAGTTTC
1867823 GCGTTGCGA-TTT--TTT
1 GCGTTGCGATTTTCATTT
1867838 -CGTTGCGATTTTCATTT
1 GCGTTGCGATTTTCATTT
*
1867855 CGCGTTGCGA--TTC-TCT
1 -GCGTTGCGATTTTCATTT
1867871 -CGTTGCGATTTTCATTT
1 GCGTTGCGATTTTCATTT
1867888 AGCGTTGCGAT
1 -GCGTTGCGAT
1867899 AGTCATTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
14 16 0.33
15 3 0.06
16 5 0.10
17 8 0.16
19 17 0.35
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.46
Consensus pattern (18 bp):
GCGTTGCGATTTTCATTT
Found at i:1868131 original size:94 final size:94
Alignment explanation
Indices: 1867985--1868364 Score: 629
Period size: 94 Copynumber: 4.1 Consensus size: 94
1867975 ATGGATTGCA
* * * *
1867985 TTAC-TTCAAACAAAAGATAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1868049 TTAGCAGAATTGGCAGCAACCGAGCAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
1868078 TTACTTTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACGCAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1868143 TTAGCAGAATTAGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1868172 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1868237 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1868266 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1868330 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1868360 TTACT
1 TTACT
1868365 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
93 23 0.09
94 247 0.91
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1870094 original size:20 final size:20
Alignment explanation
Indices: 1870069--1870124 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1870059 TGAAATAAAA
*
1870069 ATCGCAACGAGAGAATGATT
1 ATCGCAACGAGAGAATGACT
*
1870089 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
1870109 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
1870125 CGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:1870233 original size:20 final size:20
Alignment explanation
Indices: 1870180--1870247 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
1870170 AGATTCTCTC
* * *
1870180 GTTGCGATAGTCATTTCCGC
1 GTTGCGATATTCATTTTCGT
*
1870200 GTTGCGATAATCATTTTCGT
1 GTTGCGATATTCATTTTCGT
* *
1870220 GTTGCGATTTTCATTTTCAT
1 GTTGCGATATTCATTTTCGT
1870240 GTTGCGAT
1 GTTGCGAT
1870248 TTTAAGTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (20 bp):
GTTGCGATATTCATTTTCGT
Found at i:1870834 original size:20 final size:20
Alignment explanation
Indices: 1870809--1871141 Score: 360
Period size: 20 Copynumber: 16.4 Consensus size: 20
1870799 TTAAAAATCG
*
1870809 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACT
* **
1870829 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGGATACT
*
1870850 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACT
* * *
1870870 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACT
* *
1870890 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACT
* *
1870910 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACT
*
1870930 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACT
* **
1870950 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGGATACT
*
1870971 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACT
* * *
1870991 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACT
* *
1871011 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACT
* *
1871031 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACT
* *
1871051 CGCTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACT
* **
1871071 CGTTGCGATTTTACGTATGGT
1 CGTTGCGA-TTTACGGATACT
*
1871092 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACT
1871112 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACT
1871133 CGTTGCGAT
1 CGTTGCGAT
1871142 AGTCAGAATC
Statistics
Matches: 250, Mismatches: 59, Indels: 8
0.79 0.19 0.03
Matches are distributed among these distances:
20 183 0.73
21 67 0.27
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACT
Found at i:1870841 original size:40 final size:41
Alignment explanation
Indices: 1870804--1871126 Score: 417
Period size: 40 Copynumber: 8.0 Consensus size: 41
1870794 GCGTTTTAAA
*
1870804 AATCGCGTTGCGATTTACGGATACACGTTGCGATTTTACGT
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
* *
1870845 -ATTGTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGT
1 AATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
* * *
1870885 ATTCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGT
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
* *
1870925 ATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
* *
1870966 -ATTGTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGT
1 AATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
* * *
1871006 ATTCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGT
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
* * *
1871046 ATTCTCGCTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
*
1871087 -ATGGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
1 AATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACG
1871127 GATACTCGTT
Statistics
Matches: 251, Mismatches: 24, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
40 148 0.59
41 103 0.41
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
Found at i:1871023 original size:121 final size:121
Alignment explanation
Indices: 1870809--1871141 Score: 603
Period size: 121 Copynumber: 2.7 Consensus size: 121
1870799 TTAAAAATCG
*
1870809 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1870874 GCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
66 GCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1870930 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1870995 GCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
66 GCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
* * *
1871051 CGCTGCGATTTACGGATACGCGTTGCGATTTTACGTATGGTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
* *
1871116 GCGATTTTACGGATACTCGTTGCGAT
66 GCGA-TTTACGTATTCTCGTTGCGAT
1871142 AGTCAGAATC
Statistics
Matches: 205, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
121 186 0.91
122 19 0.09
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (121 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
GCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
Found at i:1871177 original size:20 final size:20
Alignment explanation
Indices: 1871154--1871202 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1871144 TCAGAATCGT
*
1871154 GTTGCGATTTAT-ATGTTCGC
1 GTTGCGATTT-TCATATTCGC
*
1871174 GTTGTGATTTTCATATTCGC
1 GTTGCGATTTTCATATTCGC
1871194 GTTGCGATT
1 GTTGCGATT
1871203 CTGGAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.47
Consensus pattern (20 bp):
GTTGCGATTTTCATATTCGC
Found at i:1871305 original size:20 final size:19
Alignment explanation
Indices: 1871252--1871305 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1871242 ATTCTTCATA
1871252 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* ** *
1871271 AACTGATTTGTGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
1871292 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
1871306 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:1874134 original size:21 final size:21
Alignment explanation
Indices: 1874096--1874135 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1874086 ATAATTTTAT
* **
1874096 TCTCATGATTTTTTTAAATAA
1 TCTCATGATTATCCTAAATAA
1874117 TCTCATGATTATCCTAAAT
1 TCTCATGATTATCCTAAAT
1874136 GAATAATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (21 bp):
TCTCATGATTATCCTAAATAA
Found at i:1874542 original size:2 final size:2
Alignment explanation
Indices: 1874537--1874574 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1874527 AAAAAGGAGA
1874537 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
1874575 TTAAAAAAGT
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:1875870 original size:20 final size:20
Alignment explanation
Indices: 1875838--1875876 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1875828 AGATGAACAA
1875838 TTAATAAATTGTTGTTATTT
1 TTAATAAATTGTTGTTATTT
1875858 TTAA-AAATATGTTGTTATT
1 TTAATAAAT-TGTTGTTATT
1875877 AAAATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
TTAATAAATTGTTGTTATTT
Found at i:1880072 original size:15 final size:15
Alignment explanation
Indices: 1880052--1880086 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1880042 CTATAGGACC
1880052 ACTACGTCCCGAAAG
1 ACTACGTCCCGAAAG
*
1880067 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAAG
1880082 ACTAC
1 ACTAC
1880087 AATACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.20, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAAG
Found at i:1887066 original size:19 final size:20
Alignment explanation
Indices: 1887042--1887080 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1887032 TATGTGTAAC
*
1887042 CATATATTTCATA-TCATAT
1 CATATATTGCATATTCATAT
1887061 CATATATTGCATATTCATAT
1 CATATATTGCATATTCATAT
1887081 GTCATTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (20 bp):
CATATATTGCATATTCATAT
Found at i:1887545 original size:18 final size:18
Alignment explanation
Indices: 1887522--1887556 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1887512 TTTCCTTTAG
1887522 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
1887540 GGGGAATCGATACCCCC
1 GGGGAATCGATACCCCC
1887557 TGGACATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.29, T:0.11
Consensus pattern (18 bp):
GGGGAATCGATACCCCCA
Found at i:1893678 original size:20 final size:20
Alignment explanation
Indices: 1893628--1893679 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1893618 TAGTTGAAAA
*
1893628 TCGCATTGCGGTTTTCCATT
1 TCGCATTGCGATTTTCCATT
**
1893648 TCGCAACGCGATTTTCCATT
1 TCGCATTGCGATTTTCCATT
*
1893668 TCGCGTTGCGAT
1 TCGCATTGCGAT
1893680 AATCTACAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.27, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTTCCATT
Found at i:1893698 original size:22 final size:22
Alignment explanation
Indices: 1893671--1893723 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1893661 TTCCATTTCG
1893671 CGTTGCGATAATCTACAGTTGT
1 CGTTGCGATAATCTACAGTTGT
* *
1893693 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAATCTACAGTTGT
1893715 CGTTGCGAT
1 CGTTGCGAT
1893724 TTTTCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAATCTACAGTTGT
Found at i:1894391 original size:6 final size:6
Alignment explanation
Indices: 1894380--1894405 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1894370 GGACGGGCCG
1894380 GGTCGT GGTCGT GGTCGT GGTCGT GG
1 GGTCGT GGTCGT GGTCGT GGTCGT GG
1894406 AGATCGCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.54, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1895448 original size:14 final size:15
Alignment explanation
Indices: 1895424--1895452 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1895414 TAAATATAAT
1895424 ATATAATTTTTAAAA
1 ATATAATTTTTAAAA
1895439 ATAT-ATTTTTAAAA
1 ATATAATTTTTAAAA
1895453 GTAAGATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATAATTTTTAAAA
Found at i:1896031 original size:23 final size:24
Alignment explanation
Indices: 1895986--1896031 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1895976 TTGTTATTCG
**
1895986 TGGATGAAACTTTAAAGTTATTGT
1 TGGATGAAACTTTAAAGAGATTGT
*
1896010 TGGATGAAAC-TTAATGAGATTG
1 TGGATGAAACTTTAAAGAGATTG
1896032 AAGAATGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (24 bp):
TGGATGAAACTTTAAAGAGATTGT
Found at i:1900487 original size:13 final size:13
Alignment explanation
Indices: 1900469--1900495 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1900459 TTCGGTCGGC
1900469 CACCGAACTAGTT
1 CACCGAACTAGTT
1900482 CACCGAACTAGTT
1 CACCGAACTAGTT
1900495 C
1 C
1900496 GGTCAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (13 bp):
CACCGAACTAGTT
Found at i:1901422 original size:23 final size:22
Alignment explanation
Indices: 1901349--1901422 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
1901339 ACACTGATTC
* *
1901349 AAATTAAAATAATTAGATA-TT
1 AAATTAAATTAATTAAATATTT
*
1901370 -ATTTAAATTAATTAAATATTT
1 AAATTAAATTAATTAAATATTT
* *
1901391 GAATCAAATTAATTAAA-ATATT
1 AAATTAAATTAATTAAATAT-TT
1901413 AAATGTAAAT
1 AAAT-TAAAT
1901423 GTTTGAATCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 15 0.36
21 4 0.10
22 19 0.45
23 4 0.10
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (22 bp):
AAATTAAATTAATTAAATATTT
Found at i:1901468 original size:20 final size:20
Alignment explanation
Indices: 1901432--1901471 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1901422 TGTTTGAATC
*
1901432 AAATTAATTAGATATTATTT
1 AAATTAATTAGAAATTATTT
1901452 AAATTAATT-GTAAATTATTT
1 AAATTAATTAG-AAATTATTT
1901472 TTTTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATTAATTAGAAATTATTT
Found at i:1904119 original size:33 final size:33
Alignment explanation
Indices: 1904082--1904180 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
1904072 ATTTGGCAAG
1904082 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* * *
1904115 TTGGAAATTTCATCTTAGTTGGTGGTCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
1904148 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
1904181 TGCACATGGG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 43 0.74
34 15 0.26
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:1907741 original size:34 final size:33
Alignment explanation
Indices: 1907650--1907748 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1907640 ATTTGGCAAG
1907650 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
1907683 TT-GAAAATTTCATCTTAGTTGGTGGCCAACTTA
1 TTGGAAAA-TTCATCTTGGTTGGTGGCCAACTTA
*
1907716 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
1907749 TGTACATGTG
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
32 5 0.08
33 34 0.57
34 21 0.35
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:1912203 original size:18 final size:19
Alignment explanation
Indices: 1912168--1912204 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1912158 TACGGAATGT
1912168 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1912188 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1912205 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1912377 original size:15 final size:15
Alignment explanation
Indices: 1912359--1912389 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1912349 AAATTCTAAA
1912359 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1912374 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1912389 T
1 T
1912390 CTATTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1915350 original size:20 final size:19
Alignment explanation
Indices: 1915325--1915383 Score: 84
Period size: 20 Copynumber: 3.1 Consensus size: 19
1915315 CTAGACTACC
1915325 AGGAAAAGAATCAAAAGCAA
1 AGGAAAA-AATCAAAAGCAA
*
1915345 AGG-AAAAATAAAAAGCAA
1 AGGAAAAAATCAAAAGCAA
1915363 AGGAAAATAATCAAAAGCAA
1 AGGAAAA-AATCAAAAGCAA
1915383 A
1 A
1915384 AGCAAAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 14 0.40
19 6 0.17
20 15 0.43
ACGTcount: A:0.68, C:0.08, G:0.17, T:0.07
Consensus pattern (19 bp):
AGGAAAAAATCAAAAGCAA
Found at i:1917100 original size:2 final size:2
Alignment explanation
Indices: 1917093--1917137 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1917083 TGTCCGTGCA
1917093 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
1917135 AT A
1 AT A
1917138 CTTAAGGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1925235 original size:23 final size:22
Alignment explanation
Indices: 1925209--1925253 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1925199 CAATTCATGA
*
1925209 TTTTATTGATTTTTTTAGTATTT
1 TTTTATTGA-ATTTTTAGTATTT
*
1925232 TTTTTTTGAATTTTTAGTATTT
1 TTTTATTGAATTTTTAGTATTT
1925254 CCTTCTATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (22 bp):
TTTTATTGAATTTTTAGTATTT
Found at i:1931512 original size:23 final size:23
Alignment explanation
Indices: 1931486--1931534 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1931476 TAACTCTACT
*
1931486 TTTATGACACGATTTTC-TATGTC
1 TTTATAACACG-TTTTCTTATGTC
*
1931509 TTTATAATACGTTTTCTTATGTC
1 TTTATAACACGTTTTCTTATGTC
1931532 TTT
1 TTT
1931535 TGATATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.55
Consensus pattern (23 bp):
TTTATAACACGTTTTCTTATGTC
Found at i:1932504 original size:29 final size:30
Alignment explanation
Indices: 1932450--1932507 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1932440 TAAATTACAT
1932450 TTTTAGTATCTAAACTATTATTTTTTTTTA
1 TTTTAGTATCTAAACTATTATTTTTTTTTA
* *
1932480 TTTTGGTATCTAAA-TCTTATTTTTTTTT
1 TTTTAGTATCTAAACTATTATTTTTTTTT
1932508 CAAATCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (30 bp):
TTTTAGTATCTAAACTATTATTTTTTTTTA
Found at i:1934336 original size:60 final size:60
Alignment explanation
Indices: 1934217--1934364 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 60
1934207 TTGATGAAAT
* * *
1934217 TTTGGGGATGAAATTAAAATATTCAAAAGTTTGAAGATCAATCTAGAATGAGGGACATAA
1 TTTGGGGATGAAATTAAAATATTCAAAAGTTTGAAGATCAATCTAAAATAAAGGACATAA
* * * * * * *
1934277 TTTGGTGATGAAATTGAAATATTTAAAAGTTT-AAGAATTAATTTAAAATAAATGTCATAA
1 TTTGGGGATGAAATTAAAATATTCAAAAGTTTGAAG-ATCAATCTAAAATAAAGGACATAA
*** *
1934337 TTTGAAAATAAAATTAAAATATTCAAAA
1 TTTGGGGATGAAATTAAAATATTCAAAA
1934365 ATTTAATAAC
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 3 0.04
60 68 0.96
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (60 bp):
TTTGGGGATGAAATTAAAATATTCAAAAGTTTGAAGATCAATCTAAAATAAAGGACATAA
Found at i:1941470 original size:18 final size:19
Alignment explanation
Indices: 1941427--1941472 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1941417 CTTCTTATTT
*
1941427 TTATTTTAATTGCTTCTAC
1 TTATTTTAATCGCTTCTAC
*
1941446 TTA-TTTAATCGCTTTTA-
1 TTATTTTAATCGCTTCTAC
1941463 TTATTTTAAT
1 TTATTTTAAT
1941473 ATTTTATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.61
Consensus pattern (19 bp):
TTATTTTAATCGCTTCTAC
Found at i:1942606 original size:17 final size:18
Alignment explanation
Indices: 1942560--1942606 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
1942550 CTATTGAGAA
1942560 AAAAATTAAAATATATCAAT
1 AAAAA-TAAAATATA-CAAT
1942580 AATAAA-AAAATATA-AAT
1 AA-AAATAAAATATACAAT
1942597 AAAAATAAAA
1 AAAAATAAAA
1942607 AGATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.12
17 9 0.36
19 8 0.32
20 2 0.08
21 3 0.12
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATAAAATATACAAT
Found at i:1949760 original size:27 final size:27
Alignment explanation
Indices: 1949726--1949782 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1949716 AAAATATATT
*
1949726 TATATAAATGTATATT-ATAT-TTAGATG
1 TATATAAA-ATATATTCATATATTA-ATG
1949753 TATATAAAATATATTCATATATTAATG
1 TATATAAAATATATTCATATATTAATG
1949780 TAT
1 TAT
1949783 GAATCATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 6 0.22
27 18 0.67
28 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (27 bp):
TATATAAAATATATTCATATATTAATG
Found at i:1949765 original size:21 final size:21
Alignment explanation
Indices: 1949714--1949767 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
1949704 CAATATACGA
*
1949714 ATAAAATATATTTATATAAAT
1 ATAAAATATATTTAGATAAAT
* * * **
1949735 GTATATTATATTTAGATGTAT
1 ATAAAATATATTTAGATAAAT
1949756 ATAAAATATATT
1 ATAAAATATATT
1949768 CATATATTAA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (21 bp):
ATAAAATATATTTAGATAAAT
Found at i:1949810 original size:17 final size:17
Alignment explanation
Indices: 1949782--1949814 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1949772 TATTAATGTA
1949782 TGAATCATTTATATTTTT
1 TGAATCATTTAT-TTTTT
1949800 TGAAT-ATTTATTTTT
1 TGAATCATTTATTTTT
1949815 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATCATTTATTTTTT
Found at i:1950332 original size:23 final size:21
Alignment explanation
Indices: 1950306--1950352 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1950296 GTGTCACCAA
1950306 TAACACATATCATGATCATGTGT
1 TAACACATATCA-GATCATG-GT
* *
1950329 TAACACATGTCAGATCCTGGT
1 TAACACATATCAGATCATGGT
1950350 TAA
1 TAA
1950353 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (21 bp):
TAACACATATCAGATCATGGT
Found at i:1950483 original size:130 final size:130
Alignment explanation
Indices: 1950279--1950526 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
1950269 AATTTTCTTC
**
1950279 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCAAACACATGTCAGAT
** *
1950344 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAAGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAAGACCAAATTGATAGCATATATAAA
* * * *
1950409 TAATTAGGTGGTGACATGTGTCATCAATGACACGTGTCATGATCATGTGCAAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCAAACACATGTCAGAT
*
1950474 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAAGACCAAATTGAT
1950527 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCAAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAAGACCAAATTGATAGCATATATAAA
Found at i:1950968 original size:35 final size:35
Alignment explanation
Indices: 1950922--1950997 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
1950912 AATTGAATTT
*
1950922 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTATTTTGGAAATTAGGGTTTAGAATGA
*
1950957 AATTGAATTATTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTATTTTGGAAATTAGGGTTTAGAATGA
1950992 AATTGA
1 AATTGA
1950998 GGTCTGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.41
Consensus pattern (35 bp):
AATTGAATTATTTTGGAAATTAGGGTTTAGAATGA
Found at i:1961250 original size:21 final size:20
Alignment explanation
Indices: 1961223--1961321 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1961213 AATCAGTTTC
1961223 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1961244 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1961265 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1961285 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1961306 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1961322 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1961314 original size:20 final size:20
Alignment explanation
Indices: 1961289--1961521 Score: 317
Period size: 20 Copynumber: 11.6 Consensus size: 20
1961279 GATTTTCCAG
* ** *
1961289 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1961309 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1961329 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1961349 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1961369 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1961389 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1961409 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1961429 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1961449 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1961469 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
1961490 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1961510 AATCGCAACGCG
1 AATCGCAACGCG
1961522 ATTTTTAAAG
Statistics
Matches: 189, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 169 0.89
21 19 0.10
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1961929 original size:33 final size:33
Alignment explanation
Indices: 1961890--1961960 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1961880 TTCACGTAGA
*
1961890 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGAGAT
*
1961923 TTTCATTTCGCGTTGCTATTCTCTCGTTGAGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGAGAT
1961956 TTTCA
1 TTTCA
1961961 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCGATTCTCTCGTTGAGAT
Found at i:1961938 original size:19 final size:18
Alignment explanation
Indices: 1961888--1961938 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 18
1961878 ATTTCACGTA
1961888 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
*
1961906 GA-TTC---TCTCGTTGC
1 GATTTCATTTCGCGTTGC
1961920 GATTTTCATTTCGCGTTGC
1 GA-TTTCATTTCGCGTTGC
1961939 TATTCTCTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
14 10 0.38
16 3 0.12
17 3 0.12
18 2 0.08
19 8 0.31
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.45
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:1962066 original size:21 final size:21
Alignment explanation
Indices: 1962040--1962116 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
1962030 TGCAGAAGAG
1962040 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
1962061 TCGCAACGCGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
1962081 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
1962103 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1962117 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.19
21 30 0.62
22 9 0.19
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1962177 original size:14 final size:14
Alignment explanation
Indices: 1962158--1962214 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1962148 TTTCATTTCG
1962158 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1962172 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1962191 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1962205 CGTTGCGATT
1 CGTTGCGATT
1962215 TTCATTTATC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1962183 original size:33 final size:33
Alignment explanation
Indices: 1962141--1962263 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1962131 CAAAATCGCA
1962141 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1962174 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1962207 TTGCGATTTTCATTTATCTCGTTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTTGC----G--ATTCTCTCG
1962248 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1962264 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 8 0.10
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1962228 original size:21 final size:21
Alignment explanation
Indices: 1962202--1962262 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 21
1962192 GTTGCGATTC
1962202 TCTCGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTA
** *
1962223 TCTCGTTGCGATAGTCA-TTC
1 TCTCGTTGCGATTTTCATTTA
1962243 TCTCGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
1962263 CAACCAAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.49
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTA
Found at i:1962248 original size:20 final size:20
Alignment explanation
Indices: 1962198--1962254 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
1962188 TCGCGTTGCG
**
1962198 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATAGTC
*
1962218 ATTTATCTCGTTGCGATAGTC
1 A-TTCTCTCGTTGCGATAGTC
1962239 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
1962255 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:1964243 original size:19 final size:20
Alignment explanation
Indices: 1964187--1964249 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
1964177 TAGTTTACTT
* **
1964187 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACACAAAA
1964207 TCGCAACGC--AACGACAAAA
1 TCGCAACGCGAAAC-ACAAAA
1964226 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACACAAAA
1964245 TCGCA
1 TCGCA
1964250 TTGCGATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.08
19 23 0.62
20 8 0.22
21 3 0.08
ACGTcount: A:0.46, C:0.30, G:0.14, T:0.10
Consensus pattern (20 bp):
TCGCAACGCGAAACACAAAA
Found at i:1964272 original size:19 final size:19
Alignment explanation
Indices: 1964245--1964384 Score: 146
Period size: 19 Copynumber: 7.6 Consensus size: 19
1964235 GAAACCAAAA
*
1964245 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1964264 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1964283 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1964299 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1964316 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1964335 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1964354 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1964374 TCGTGTTGCGA
1 TCGCGTTGCGA
1964385 AAGTAAACTA
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
14 7 0.07
16 5 0.05
17 5 0.05
19 69 0.70
20 12 0.12
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1964308 original size:33 final size:35
Alignment explanation
Indices: 1964266--1964366 Score: 134
Period size: 33 Copynumber: 2.9 Consensus size: 35
1964256 TTTTCATTTC
*
1964266 TCGTTGCGATTTTCATTTCGCATTGCGATTCT-G-
1 TCGTTGCGATTTTCATTTCGCGTTGCGATTCTGGT
*
1964299 TCGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTTT
1 TCGTTGCGATTTTCATTTCGCGTTGCGATTCTGG--T
*
1964336 CTCGTTGCGATTCTCATTTCGCGTTGCGATT
1 -TCGTTGCGATTTTCATTTCGCGTTGCGATT
1964367 TTAAGTTTCG
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
33 30 0.50
34 1 0.02
38 29 0.48
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.47
Consensus pattern (35 bp):
TCGTTGCGATTTTCATTTCGCGTTGCGATTCTGGT
Found at i:1964312 original size:52 final size:52
Alignment explanation
Indices: 1964250--1964349 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
1964240 CAAAATCGCA
*
1964250 TTGCGATTTTCATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGTCG
** * *
1964302 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCT
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCT
1964350 CATTTCGCGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.10, C:0.20, G:0.21, T:0.49
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGTCG
Found at i:1966328 original size:14 final size:14
Alignment explanation
Indices: 1966309--1966344 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1966299 ATTGTTTAAT
1966309 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1966323 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1966337 TGATTTGT
1 TGATTTGT
1966345 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1966486 original size:19 final size:19
Alignment explanation
Indices: 1966451--1966534 Score: 115
Period size: 19 Copynumber: 4.6 Consensus size: 19
1966441 AAAAATGACT
1966451 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1966471 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1966490 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1966504 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1966523 ATCGCAATGCGA
1 ATCGCAATGCGA
1966535 TTTTCATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 31 0.54
20 10 0.18
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1966567 original size:20 final size:19
Alignment explanation
Indices: 1966524--1966714 Score: 205
Period size: 19 Copynumber: 10.7 Consensus size: 19
1966514 GAAATGAAAA
*
1966524 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1966543 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
1966562 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1966579 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1966596 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1966615 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1966632 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1966649 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1966668 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1966686 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1966702 TCGCATTGCGATT
1 TCGCATTGCGATT
1966715 CTCTCGTTGC
Statistics
Matches: 145, Mismatches: 9, Indels: 36
0.76 0.05 0.19
Matches are distributed among these distances:
14 23 0.16
16 12 0.08
17 13 0.09
18 6 0.04
19 55 0.38
20 36 0.25
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1966593 original size:53 final size:53
Alignment explanation
Indices: 1966530--1966714 Score: 327
Period size: 53 Copynumber: 3.5 Consensus size: 53
1966520 AAAATCGCAA
*
1966530 TGCGATTTTCATTTCGCATTGCGATTTTTATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1966583 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
1966636 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGT
*
1966689 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
1966715 CTCTCGTTGC
Statistics
Matches: 128, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
53 127 0.99
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:1966736 original size:33 final size:33
Alignment explanation
Indices: 1966548--1966728 Score: 145
Period size: 33 Copynumber: 5.2 Consensus size: 33
1966538 TCATTTCGCA
*
1966548 TTGCGATTTTTATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
1966582 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
1966619 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
*
1966654 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1966688 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1966721 TTGCGATT
1 TTGCGATT
1966729 GTAATTTCCG
Statistics
Matches: 116, Mismatches: 16, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
31 4 0.03
32 7 0.06
33 44 0.38
34 30 0.26
35 4 0.03
36 3 0.03
37 2 0.02
38 2 0.02
39 8 0.07
40 3 0.03
41 9 0.08
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1966743 original size:53 final size:53
Alignment explanation
Indices: 1966530--1966747 Score: 232
Period size: 53 Copynumber: 4.1 Consensus size: 53
1966520 AAAATCGCAA
* * *
1966530 TGCGATTTTCATTTCGCATTGCGATTTTTATTTCCGCATTGCGA-TTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT-GT
* *
1966583 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT-GT
* * *
1966636 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTCCATGT
* * * *
1966689 TGGGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGTGT
1 TGCGATTTTCATTTCGCATTGCGATT-T-TCAGTTCCGCATTGCAATTTCCATGT
1966742 TGCGAT
1 TGCGAT
1966748 AGTCAAATGC
Statistics
Matches: 151, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
53 141 0.93
54 8 0.05
55 2 0.01
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTCCATGT
Found at i:1969029 original size:12 final size:12
Alignment explanation
Indices: 1969012--1969036 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1969002 TCTTCGGGGA
1969012 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1969024 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1969036 C
1 C
1969037 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1969245 original size:24 final size:24
Alignment explanation
Indices: 1969211--1969257 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1969201 CTGAAACATC
1969211 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1969235 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1969258 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1969978 original size:20 final size:20
Alignment explanation
Indices: 1969950--1970138 Score: 209
Period size: 20 Copynumber: 9.4 Consensus size: 20
1969940 AAATTTCAGT
* * *
1969950 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1969970 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1969990 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1970010 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1970030 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1970050 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1970070 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1970090 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1970110 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1970130 GTTGCGATT
1 GTTGCGATT
1970139 CTGGAAAATC
Statistics
Matches: 149, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1983954 original size:21 final size:21
Alignment explanation
Indices: 1983930--1983982 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1983920 TTAAAAGGAG
1983930 GGATTACATTATTCCAGCAAT
1 GGATTACATTATTCCAGCAAT
1983951 GGATTACATTATTCCAGCAAT
1 GGATTACATTATTCCAGCAAT
*
1983972 GGATTCCATTA
1 GGATTACATTA
1983983 AAGGAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (21 bp):
GGATTACATTATTCCAGCAAT
Found at i:1993229 original size:85 final size:85
Alignment explanation
Indices: 1992964--1993356 Score: 501
Period size: 85 Copynumber: 4.7 Consensus size: 85
1992954 TTGCGCATAG
* * *
1992964 CTTAAGTCAAGAAGGGCTATCTG-C--C-AAAGACC-CCGAGTTCGATTACACTCAGCTTCGAGG
1 CTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGG
*
1993024 GCACATCATTTGCAGCATAA
66 GCACATCATTTGCAGCACAA
* * * * * *
1993044 CTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAG
1 CTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGG
* *
1993108 GCATATCATTTACAGCACAA
66 GCACATCATTTGCAGCACAA
* **
1993128 CTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
1 CTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGG
* *
1993193 ACATATCATTTGCAGCACAA
66 GCACATCATTTGCAGCACAA
* * * *
1993213 CTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGATTACGCTCAGCTTCGAGG
1 CTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGG
*
1993278 GCACATCATTTGCAGCATAA
66 GCACATCATTTGCAGCACAA
* * * * *
1993298 CTCAAGGCTACAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTACACTCAGCT
1 CTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCT
1993357 CAGAGGCAAA
Statistics
Matches: 269, Mismatches: 38, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
80 21 0.08
81 1 0.00
83 1 0.00
84 79 0.29
85 167 0.62
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (85 bp):
CTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGG
GCACATCATTTGCAGCACAA
Found at i:1993238 original size:169 final size:170
Alignment explanation
Indices: 1992989--1993356 Score: 542
Period size: 169 Copynumber: 2.2 Consensus size: 170
1992979 GCTATCTGCC
* *
1992989 AAAGA-CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
1 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTGCAGCACAACTTAAGTCG
*
1993053 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCAT
66 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCAT
* * * *
1993117 TTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACA
131 TTACAGCACAACTCAAGGCTACAAGGGTTATCTGCCAACA
* *
1993157 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACATATCATTTGCAGCACAACTTAAGTCT
1 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTGCAGCACAACTTAAGTCG
* * * * *
1993222 AGAAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGATTACGCTCAGCTTCGAGGGCACATCAT
66 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCAT
* * * *
1993287 TTGCAGCATAACTCAAGGCTACAAGGGTTATCTGTCACCA
131 TTACAGCACAACTCAAGGCTACAAGGGTTATCTGCCAACA
**
1993327 AAAGACCTTCGAGTTCGATTACACTCAGCT
1 AAAGACCCCCGAGTTCGATTACACTCAGCT
1993357 CAGAGGCAAA
Statistics
Matches: 178, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
168 5 0.03
169 101 0.57
170 72 0.40
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (170 bp):
AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTGCAGCACAACTTAAGTCG
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCAT
TTACAGCACAACTCAAGGCTACAAGGGTTATCTGCCAACA
Found at i:1994124 original size:106 final size:106
Alignment explanation
Indices: 1993849--1994431 Score: 988
Period size: 106 Copynumber: 5.5 Consensus size: 106
1993839 TCTTATTTTA
**
1993849 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTTGACAACGCATGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
* *
1993914 GACGAAGGGACCACTGGTTGTCAAC-AACAACTTCCCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATT
**
1993954 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTTGACAACGCATGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
1994019 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATT
*
1994060 TCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
*
1994125 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAAT
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATT
*
1994166 TCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
*
1994231 GACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATT
* *
1994272 TTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
* * * *
1994337 GATGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATT
* * *
1994378 TCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCATG
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATG
1994432 GGACCGCTGG
Statistics
Matches: 456, Mismatches: 21, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
105 89 0.20
106 367 0.80
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (106 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATT
Found at i:1994246 original size:212 final size:212
Alignment explanation
Indices: 1993849--1994814 Score: 1565
Period size: 212 Copynumber: 4.6 Consensus size: 212
1993839 TCTTATTTTA
**
1993849 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTTGACAACGCATGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
*
1993914 GACGAAGGGACCACTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
**
1993978 CGAAGGATATTGGACTCTTGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1994043 CAAACAACTTCTCAATT
196 CAAACAACTTCTCAATT
*
1994060 TCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
* *
1994125 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
*
1994190 CAAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1994255 TAAACAACTTCTCAATT
196 CAAACAACTTCTCAATT
* *
1994272 TTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
* * * * *
1994337 GATGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAG
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
1994402 CGAAGGATATTGGACTCCAGAC-A---ATG--C-A--T---------GGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1994449 CAAACAACTTCTCAATT
196 CAAACAACTTCTCAATT
*
1994466 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
* * *
1994531 GACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCTCAATTTCAGAGCCAATTTAAAACTTCACA
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT-CAACTTCACA
*
1994596 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCA
130 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1994661 ACAAACAACTTCTCAATT
195 ACAAACAACTTCTCAATT
* *
1994679 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
*
1994744 GACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
1994809 CGAAGG
131 CGAAGG
1994815 GAATCGTGCA
Statistics
Matches: 695, Mismatches: 40, Indels: 39
0.90 0.05 0.05
Matches are distributed among these distances:
194 145 0.21
195 31 0.04
196 1 0.00
199 3 0.00
201 1 0.00
202 1 0.00
203 1 0.00
204 1 0.00
205 1 0.00
206 1 0.00
208 3 0.00
211 87 0.13
212 272 0.39
213 147 0.21
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (212 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
CGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAAACAACTTCTCAATT
Found at i:1994456 original size:88 final size:88
Alignment explanation
Indices: 1994343--1994519 Score: 309
Period size: 88 Copynumber: 2.0 Consensus size: 88
1994333 TCACGATGAA
* *
1994343 GGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGG
1 GGGACCACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
*
1994408 ATATTGGACTCCAGACAATGCAT
66 ATATTGGACTCCAGACAACGCAT
* *
1994431 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
1 GGGACCACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
1994496 ATATTGGACTCCAGACAACGCAT
66 ATATTGGACTCCAGACAACGCAT
1994519 G
1 G
1994520 TTCAACTTCA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (88 bp):
GGGACCACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
ATATTGGACTCCAGACAACGCAT
Found at i:1994634 original size:107 final size:106
Alignment explanation
Indices: 1994431--1994814 Score: 687
Period size: 106 Copynumber: 3.6 Consensus size: 106
1994421 GACAATGCAT
*
1994431 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
1 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
1994496 ATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAA
66 ATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAA
* *
1994537 GGGACCGCTGGTTGTCAACAAAAAACTTCTCAATTTCAGAGCCAATTTAAAACTTCACAACGAAG
1 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT-CAACTTCACAACGAAG
1994602 GATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAA
65 GATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAA
*
1994644 GGGACTGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
1 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
1994709 ATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
66 ATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAA
* *
1994750 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
1 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
1994815 GAATCGTGCA
Statistics
Matches: 266, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
106 164 0.62
107 102 0.38
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
ATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAA
Found at i:1994779 original size:407 final size:406
Alignment explanation
Indices: 1994025--1994814 Score: 1445
Period size: 407 Copynumber: 1.9 Consensus size: 406
1994015 TCACGACGAA
1994025 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAG
1 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAG
*
1994090 ATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
66 ATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAA
*
1994155 ACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCATG
131 ACTTCTCAAATTCAGAGCCAATTTAAACTTCACAACAAAGGATATTGGACTCCAGACAACGCATG
* *
1994220 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTTAGAGCCAATTT
196 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
1994285 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCA
261 CAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCA
* *
1994350 CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
326 CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1994415 ACTCCAGACAATGCAT
391 ACTCCAGACAATGCAT
* *
1994431 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
1 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAG
1994496 ATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAA
66 ATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAA
* *
1994561 ACTTCTCAATTTCAGAGCCAATTTAAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAT
131 ACTTCTCAAATTCAGAGCCAATTT-AAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAT
*
1994626 GTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
195 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
1994691 TCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
260 TCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
*
1994756 GCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
325 ACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
1994815 GAATCGTGCA
Statistics
Matches: 369, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
406 150 0.41
407 219 0.59
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (406 bp):
GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAG
ATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAA
ACTTCTCAAATTCAGAGCCAATTTAAACTTCACAACAAAGGATATTGGACTCCAGACAACGCATG
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCA
CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
ACTCCAGACAATGCAT
Found at i:1995468 original size:15 final size:16
Alignment explanation
Indices: 1995448--1995477 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1995438 TACATGTTAT
1995448 TATATTATA-TCATTA
1 TATATTATATTCATTA
1995463 TATATTATATTCATT
1 TATATTATATTCATT
1995478 TGCTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTATATTCATTA
Found at i:1998713 original size:13 final size:14
Alignment explanation
Indices: 1998674--1998713 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1998664 AATGAACGTA
1998674 AACGAACACAAACG
1 AACGAACACAAACG
* *
1998688 AGCGAACATAAACG
1 AACGAACACAAACG
1998702 AAC-AACACAAAC
1 AACGAACACAAAC
1998714 ACAAAAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.57, C:0.28, G:0.12, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:2019257 original size:21 final size:21
Alignment explanation
Indices: 2019231--2019271 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2019221 GACTATCACA
2019231 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
*
2019252 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTTCCAAATTCGC
2019272 AATGAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCG
Found at i:2019310 original size:20 final size:20
Alignment explanation
Indices: 2019287--2019392 Score: 178
Period size: 20 Copynumber: 5.3 Consensus size: 20
2019277 GAATATGTAA
*
2019287 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
2019307 ATCGCAACGCG-TTCTGACT
1 ATCGCAACGCGATTCTGACT
2019326 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
2019346 ATCGCAACAAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2019366 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2019386 ATCGCAA
1 ATCGCAA
2019393 TACTGAATTT
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
19 18 0.22
20 62 0.77
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2020218 original size:24 final size:24
Alignment explanation
Indices: 2020191--2020244 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2020181 GTATTCGAAA
2020191 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2020215 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2020239 TTTGAT
1 TTTGAT
2020245 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2020462 original size:14 final size:13
Alignment explanation
Indices: 2020438--2020472 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
2020428 AAAAAAGAAG
2020438 AAGAAAATCCCCA
1 AAGAAAATCCCCA
*
2020451 AAGAAAAGTCCCCG
1 AAGAAAA-TCCCCA
2020465 AAGAAAAT
1 AAGAAAAT
2020473 GCCACGGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.54, C:0.23, G:0.14, T:0.09
Consensus pattern (13 bp):
AAGAAAATCCCCA
Found at i:2022700 original size:20 final size:20
Alignment explanation
Indices: 2022675--2022743 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
2022665 CAACGCGGAA
2022675 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
2022695 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
2022715 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
2022735 ATCGCAACG
1 ATCGCAACG
2022744 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:2022754 original size:14 final size:14
Alignment explanation
Indices: 2022735--2022788 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
2022725 GGAAATGACT
2022735 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2022749 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
2022768 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
2022782 ATCGCAA
1 ATCGCAA
2022789 TGCAAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Done.