Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008316.1 Hibiscus syriacus cultivar Beakdansim tig00111013_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: 2380696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1652082 original size:16 final size:17
Alignment explanation
Indices: 1652049--1652091 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1652039 CTAACGAAAA
1652049 TTAAAAAAAAAATCTTT
1 TTAAAAAAAAAATCTTT
* *
1652066 TTAAAATAATAAT-TTT
1 TTAAAAAAAAAATCTTT
1652082 TTAAACAAAA
1 TTAAA-AAAA
1652092 TTTTCTACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAAAAAAAATCTTT
Found at i:1655343 original size:23 final size:23
Alignment explanation
Indices: 1655317--1655390 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
1655307 AGAGAAGTTA
1655317 TTAAAGGTGCAATAGAACATACG
1 TTAAAGGTGCAATAGAACATACG
* ***
1655340 TTAAA--TGGAAT-GTAAGCATGTTA
1 TTAAAGGTGCAATAG-AA-CAT-ACG
1655363 TTAAAGGTGCAATAGAACATACG
1 TTAAAGGTGCAATAGAACATACG
1655386 TTAAA
1 TTAAA
1655391 TGGAATGTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 3 0.08
23 15 0.41
24 3 0.08
25 7 0.19
26 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.27
Consensus pattern (23 bp):
TTAAAGGTGCAATAGAACATACG
Found at i:1655366 original size:46 final size:46
Alignment explanation
Indices: 1655313--1655406 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1655303 AAACAGAGAA
1655313 GTTATTAAAGGTGCAATAGAACATACGTTAAATGGAATGTAAGCAT
1 GTTATTAAAGGTGCAATAGAACATACGTTAAATGGAATGTAAGCAT
1655359 GTTATTAAAGGTGCAATAGAACATACGTTAAATGGAATGTAAGCAT
1 GTTATTAAAGGTGCAATAGAACATACGTTAAATGGAATGTAAGCAT
1655405 GT
1 GT
1655407 ATGCCATTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (46 bp):
GTTATTAAAGGTGCAATAGAACATACGTTAAATGGAATGTAAGCAT
Found at i:1658695 original size:30 final size:30
Alignment explanation
Indices: 1658661--1658723 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1658651 TTAATGCAAT
1658661 ATGA-TTTGGACTTTGATTTCTAAAGGCTTA
1 ATGATTTTGGA-TTTGATTTCTAAAGGCTTA
**
1658691 ATGATTTTTTATTTGATTTCTAAAGGCTTA
1 ATGATTTTGGATTTGATTTCTAAAGGCTTA
1658721 ATG
1 ATG
1658724 TTATAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (30 bp):
ATGATTTTGGATTTGATTTCTAAAGGCTTA
Found at i:1672391 original size:21 final size:21
Alignment explanation
Indices: 1672357--1672409 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1672347 TTAATATTTG
* *
1672357 ATAATTTACA-AAATAATTAAT
1 ATAATTTTCATAAAT-ATAAAT
1672378 AT-ATTTTCATAAATATAAAT
1 ATAATTTTCATAAATATAAAT
1672398 ATAATTTTCATA
1 ATAATTTTCATA
1672410 TTTTATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATTTTCATAAATATAAAT
Found at i:1673068 original size:21 final size:22
Alignment explanation
Indices: 1673028--1673069 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1673018 TATTATTTTT
*
1673028 AAAATTTTATATTTCAATAAAA
1 AAAAGTTTATATTTCAATAAAA
1673050 AAAAGTTTATATTTC-ATAAA
1 AAAAGTTTATATTTCAATAAA
1673070 TCAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAGTTTATATTTCAATAAAA
Found at i:1673877 original size:32 final size:31
Alignment explanation
Indices: 1673838--1673897 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1673828 CAAATATTAC
*
1673838 AAAATAATATTAAAATTTATCGAATCATTGCA
1 AAAATAAT-TTAAAAGTTATCGAATCATTGCA
**
1673870 AAAATAATTTTTAAGTTATCGAATCATT
1 AAAATAATTTAAAAGTTATCGAATCATT
1673898 TTACAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (31 bp):
AAAATAATTTAAAAGTTATCGAATCATTGCA
Found at i:1675178 original size:2 final size:2
Alignment explanation
Indices: 1675171--1675203 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1675161 GCATAAAAAC
1675171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1675204 CTATTTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1680103 original size:15 final size:15
Alignment explanation
Indices: 1680083--1680117 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1680073 CCGTAGGACC
1680083 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1680098 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1680113 ACTAC
1 ACTAC
1680118 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:1686927 original size:15 final size:15
Alignment explanation
Indices: 1686907--1686941 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1686897 CCGTAGGACC
1686907 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1686922 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1686937 ACTAC
1 ACTAC
1686942 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:1691807 original size:6 final size:6
Alignment explanation
Indices: 1691796--1692727 Score: 1804
Period size: 6 Copynumber: 156.0 Consensus size: 6
1691786 GAGAAGGAAC
1691796 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1691844 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1691892 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1691940 ATATGT ATATGT ATATG- -TATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1691986 ATATGT ATATGT ATATGT ATATGTAT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATG--T ATATGT ATATGT ATATGT ATATGT
1692036 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692084 ATATG- -TATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692130 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692178 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692226 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692274 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692322 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692370 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692418 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692466 ATATGT ATATGT ATATGT ATATGT ATATG- -TATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692512 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692560 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692608 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692656 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1692704 ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT
1692728 CAAGCCATAA
Statistics
Matches: 918, Mismatches: 0, Indels: 16
0.98 0.00 0.02
Matches are distributed among these distances:
4 12 0.01
6 900 0.98
8 6 0.01
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:1696103 original size:24 final size:24
Alignment explanation
Indices: 1696067--1696189 Score: 142
Period size: 24 Copynumber: 5.1 Consensus size: 24
1696057 AGCAGGCATT
*
1696067 GCAACATTACCTACACTCGTTCGA
1 GCAACATTGCCTACACTCGTTCGA
1696091 GCAACATTGCCTACACTCGTTCGA
1 GCAACATTGCCTACACTCGTTCGA
* * **
1696115 GCAACATCGTCTATC-CTAATTCGA
1 GCAACATTGCCTA-CACTCGTTCGA
*
1696139 GCAACATTGCC-AGCCCTCGTTCGA
1 GCAACATTGCCTA-CACTCGTTCGA
* *
1696163 GCAACATTGCCTGCCCTCGTTCGA
1 GCAACATTGCCTACACTCGTTCGA
1696187 GCA
1 GCA
1696190 GGGCATAGTC
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.02
24 82 0.96
25 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (24 bp):
GCAACATTGCCTACACTCGTTCGA
Found at i:1702509 original size:6 final size:6
Alignment explanation
Indices: 1702498--1702526 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1702488 GATGAACGGA
1702498 TTCTCC TTCTCC TTCTCC TTCTCC TTCTC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTC
1702527 TATTGTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCTCC
Found at i:1702787 original size:15 final size:16
Alignment explanation
Indices: 1702763--1702797 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1702753 TTATAATCCA
*
1702763 ATAAATAATATA-TTT
1 ATAAAAAATATACTTT
1702778 ATAAAAAATATACTTT
1 ATAAAAAATATACTTT
1702794 ATAA
1 ATAA
1702798 TATTCTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAAAAATATACTTT
Found at i:1702873 original size:16 final size:18
Alignment explanation
Indices: 1702854--1702894 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
1702844 ATAATTAACT
1702854 TTTTAATAA-ATTTT-TA
1 TTTTAATAATATTTTATA
*
1702870 TTTTTATAATATTTTATA
1 TTTTAATAATATTTTATA
*
1702888 TTATAAT
1 TTTTAAT
1702895 CAGTATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 8 0.40
17 5 0.25
18 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTAATAATATTTTATA
Found at i:1702873 original size:17 final size:18
Alignment explanation
Indices: 1702853--1702889 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1702843 TATAATTAAC
1702853 TTTTTAATAA-ATTTT-TA
1 TTTTT-ATAATATTTTATA
1702870 TTTTTATAATATTTTATA
1 TTTTTATAATATTTTATA
1702888 TT
1 TT
1702890 ATAATCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 10 0.56
18 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTATAATATTTTATA
Found at i:1707246 original size:40 final size:40
Alignment explanation
Indices: 1707188--1707268 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
1707178 GATAACGCCA
1707188 AGAGATATTTCCGAAGGTATAACAATATTGAATCTTAACT
1 AGAGATATTTCCGAAGGTATAACAATATTGAATCTTAACT
* *
1707228 AGAGATATTTCCGGAGGTATAACATTATTGAATCTTAACT
1 AGAGATATTTCCGAAGGTATAACAATATTGAATCTTAACT
1707268 A
1 A
1707269 TTATGTCTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (40 bp):
AGAGATATTTCCGAAGGTATAACAATATTGAATCTTAACT
Found at i:1713644 original size:23 final size:23
Alignment explanation
Indices: 1713614--1713659 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1713604 CCTCAATTCT
1713614 ATAACAAAGAAAAGAAGTAAAGC
1 ATAACAAAGAAAAGAAGTAAAGC
*
1713637 ATAACAAAGAAATGAAGTAAAGC
1 ATAACAAAGAAAAGAAGTAAAGC
1713660 GTACCTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.63, C:0.09, G:0.17, T:0.11
Consensus pattern (23 bp):
ATAACAAAGAAAAGAAGTAAAGC
Found at i:1715572 original size:15 final size:15
Alignment explanation
Indices: 1715552--1715603 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1715542 TCGATAAAAA
1715552 ATTGATCAATTTGAT
1 ATTGATCAATTTGAT
1715567 ATTGATCTAA-TTGAAAT
1 ATTGATC-AATTTG--AT
* *
1715584 ATTGATTAATATGAT
1 ATTGATCAATTTGAT
1715599 ATTGA
1 ATTGA
1715604 CATAGATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 17 0.55
16 4 0.13
17 10 0.32
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (15 bp):
ATTGATCAATTTGAT
Found at i:1729595 original size:59 final size:60
Alignment explanation
Indices: 1729479--1729607 Score: 179
Period size: 59 Copynumber: 2.2 Consensus size: 60
1729469 AAGTTTGAGG
* *
1729479 TTAGAATGAGCGTCATAATTTAGGGATGAAATTAGAATGTTCAAAAGTTTAAAGACTAAT
1 TTAGAATGAGCGTCATAATTTAGGGATGAAATTAAAATATTCAAAAGTTTAAAGACTAAT
* * * * *
1729539 TTAGAATGTGGGTCATAATTTA-GGATGAAATTAAAATATTTAAAAGTTTGATGACTAAT
1 TTAGAATGAGCGTCATAATTTAGGGATGAAATTAAAATATTCAAAAGTTTAAAGACTAAT
*
1729598 TTAAAATGAG
1 TTAGAATGAG
1729608 TGTAATAGTT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 40 0.67
60 20 0.33
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (60 bp):
TTAGAATGAGCGTCATAATTTAGGGATGAAATTAAAATATTCAAAAGTTTAAAGACTAAT
Found at i:1743915 original size:17 final size:17
Alignment explanation
Indices: 1743893--1743927 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1743883 ATAATTGAGT
*
1743893 ATATTATTGTAATAATA
1 ATATTATTATAATAATA
*
1743910 ATATTATTATATTAATA
1 ATATTATTATAATAATA
1743927 A
1 A
1743928 ATATATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATATTATTATAATAATA
Found at i:1744730 original size:19 final size:18
Alignment explanation
Indices: 1744706--1744748 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
1744696 ATTTTCAATA
1744706 TAAAATATAAAAAAATATT
1 TAAAATATAAAAAAAT-TT
**
1744725 TAAAATATATGAAAATTT
1 TAAAATATAAAAAAATTT
1744743 TAAAAT
1 TAAAAT
1744749 TTTAGGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TAAAATATAAAAAAATTT
Found at i:1746253 original size:2 final size:2
Alignment explanation
Indices: 1746246--1746275 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1746236 TAGTATCTAT
1746246 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
1746276 GGAATAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1747182 original size:20 final size:20
Alignment explanation
Indices: 1747157--1747194 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1747147 CGGTAAAGTG
1747157 TTACCTAAAATATTATTTTT
1 TTACCTAAAATATTATTTTT
*
1747177 TTACCTAAAATGTTATTT
1 TTACCTAAAATATTATTT
1747195 ACGCTAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.53
Consensus pattern (20 bp):
TTACCTAAAATATTATTTTT
Found at i:1747749 original size:21 final size:22
Alignment explanation
Indices: 1747708--1747749 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1747698 AAAATATAAA
1747708 TAATTTTTGTTTTTCTCTCTTG
1 TAATTTTTGTTTTTCTCTCTTG
1747730 TAATTTTTGTTTTTCT-TCTT
1 TAATTTTTGTTTTTCTCTCTT
1747750 TATGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.10, C:0.12, G:0.07, T:0.71
Consensus pattern (22 bp):
TAATTTTTGTTTTTCTCTCTTG
Found at i:1748496 original size:6 final size:6
Alignment explanation
Indices: 1748485--1749434 Score: 1823
Period size: 6 Copynumber: 160.2 Consensus size: 6
1748475 ACGACAATAA
1748485 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748533 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748581 TATATG TATATG TATATG TATA-G TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748628 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748676 TATATG TATATG TATATG --TATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748722 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748770 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748818 TATATG TATATG TATATG --TATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748864 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748912 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1748960 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATA-G
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749007 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATA--
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749053 TATA-G TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749100 TATATG TATATG TATATG TATATG TATATG --TATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749146 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749194 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749242 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749290 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749338 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749386 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1749434 T
1 T
1749435 TACACAATGT
Statistics
Matches: 934, Mismatches: 0, Indels: 20
0.98 0.00 0.02
Matches are distributed among these distances:
4 16 0.02
5 14 0.01
6 904 0.97
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:1751753 original size:14 final size:14
Alignment explanation
Indices: 1751734--1751780 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
1751724 GCCAAAATTT
1751734 TAAAATTTTAAAAC
1 TAAAATTTTAAAAC
*
1751748 TAAAATTGATAAAAC
1 TAAAATT-TTAAAAC
*
1751763 TAAAATATTAAAAC
1 TAAAATTTTAAAAC
1751777 TAAA
1 TAAA
1751781 TCAAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (14 bp):
TAAAATTTTAAAAC
Found at i:1752321 original size:18 final size:17
Alignment explanation
Indices: 1752300--1752335 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1752290 AAATTTTAAA
1752300 TAAAAAATATATAAAAAT
1 TAAAAAATATA-AAAAAT
*
1752318 TAAAATATATAAAAAAT
1 TAAAAAATATAAAAAAT
1752335 T
1 T
1752336 TAAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAATATAAAAAAT
Found at i:1753054 original size:31 final size:30
Alignment explanation
Indices: 1753018--1753113 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
1753008 TGTTCAAAAA
*
1753018 AGTTTGGGGACTAATTTAAAATGAAAATCAT
1 AGTTTGAGGACTAATTTAAAATG-AAATCAT
* * *
1753049 AGTTTGAGGA-TAAAATTAAAATG--TTCAAA
1 AGTTTGAGGACT-AATTTAAAATGAAATC-AT
*
1753078 AGTTTGAGGACTAATTTAAAATGATAGTCAT
1 AGTTTGAGGACTAATTTAAAATGA-AATCAT
1753109 AGTTT
1 AGTTT
1753114 ATGGATGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
28 2 0.04
29 21 0.40
30 2 0.04
31 25 0.48
32 2 0.04
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (30 bp):
AGTTTGAGGACTAATTTAAAATGAAATCAT
Found at i:1756061 original size:41 final size:41
Alignment explanation
Indices: 1756016--1756106 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
1756006 ACTGTAGACT
* *
1756016 ATCGCAATAACAAATGTAGACTATCGCAA-CGAATTTGGAAA
1 ATCGCAACAACAAATGTAGACTATCGCAACCGAA-ATGGAAA
*
1756057 ATCGCAACAACAACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACAACAAATGTAGACTATCGCAAC-CGAAATGGAAA
1756099 ATCGCAAC
1 ATCGCAAC
1756107 GCGAAATGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 27 0.60
42 14 0.31
43 4 0.09
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (41 bp):
ATCGCAACAACAAATGTAGACTATCGCAACCGAAATGGAAA
Found at i:1756086 original size:22 final size:22
Alignment explanation
Indices: 1755998--1756086 Score: 85
Period size: 22 Copynumber: 4.2 Consensus size: 22
1755988 TGAAAAATCA
*
1755998 CAACGACAACTGTAGACTATCG
1 CAACAACAACTGTAGACTATCG
* *
1756020 CAATAACAAATGTAGACTATCG
1 CAACAACAACTGTAGACTATCG
* * * **
1756042 CAAC--GAA-TTTGGAAAATCG
1 CAACAACAACTGTAGACTATCG
1756061 CAACAACAACTGTAGACTATCG
1 CAACAACAACTGTAGACTATCG
1756083 CAAC
1 CAAC
1756087 GCGAAATGGA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
19 12 0.24
20 2 0.04
21 2 0.04
22 34 0.68
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.19
Consensus pattern (22 bp):
CAACAACAACTGTAGACTATCG
Found at i:1756104 original size:20 final size:20
Alignment explanation
Indices: 1756079--1756134 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
1756069 ACTGTAGACT
1756079 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1756099 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1756119 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
1756135 CAACGCGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1762596 original size:23 final size:22
Alignment explanation
Indices: 1762557--1762601 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1762547 TTATTATATT
*
1762557 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
1762580 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
1762602 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:1762618 original size:18 final size:18
Alignment explanation
Indices: 1762571--1762609 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1762561 ATATTTTGTA
1762571 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
1762589 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
1762606 TTTA
1 TTTA
1762610 CTTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:1769070 original size:103 final size:103
Alignment explanation
Indices: 1768641--1769062 Score: 803
Period size: 103 Copynumber: 4.1 Consensus size: 103
1768631 GTCGAGGGTC
1768641 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1768706 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1768744 TATGTGGTCCTTCGGGAC--ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1768807 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1768845 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1768910 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1768948 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1769013 TTGATCCATAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1769051 TATGTGGTCCTT
1 TATGTGGTCCTT
1769063 ATGGACATTA
Statistics
Matches: 314, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
101 101 0.32
103 213 0.68
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1775023 original size:23 final size:23
Alignment explanation
Indices: 1774986--1775049 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
1774976 TAGCTCGTAT
* *
1774986 AAATGCACCGGAGTGCCACATAG
1 AAATACACCGAAGTGCCACATAG
* * *
1775009 AATTACACCGAAGTGCCGCGTAG
1 AAATACACCGAAGTGCCACATAG
* *
1775032 AAATGCACCGTAGTGCCA
1 AAATACACCGAAGTGCCA
1775050 TATAAGATGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACATAG
Found at i:1776084 original size:20 final size:20
Alignment explanation
Indices: 1776046--1776086 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1776036 ATCAGATTGT
**
1776046 CCAGGGGGTACAGGTTCCCC
1 CCAGGGGGTACAGACTCCCC
*
1776066 CCAGGGGGTACCGACTCCCC
1 CCAGGGGGTACAGACTCCCC
1776086 C
1 C
1776087 TGTCTAACGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.41, G:0.32, T:0.12
Consensus pattern (20 bp):
CCAGGGGGTACAGACTCCCC
Found at i:1777385 original size:19 final size:20
Alignment explanation
Indices: 1777361--1777408 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1777351 AACGATTTTC
*
1777361 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1777380 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1777400 TTTTGAAAA
1 TTTTGAAAA
1777409 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1778887 original size:19 final size:19
Alignment explanation
Indices: 1778863--1778979 Score: 144
Period size: 19 Copynumber: 5.9 Consensus size: 19
1778853 GATTGTCCAG
1778863 GGGGTACAGATTCCCCCCA
1 GGGGTACAGATTCCCCCCA
1778882 GGGGTACAGATTCCCCCCA
1 GGGGTACAGATTCCCCCCA
* * *
1778901 GGGGGAATATATTTCCCCTCCA
1 -GGGGTACAGA-TTCCCC-CCA
1778923 GGGGTACAGATTCCCCCCA
1 GGGGTACAGATTCCCCCCA
* *
1778942 TGGGAACAGATTCCCCCCA
1 GGGGTACAGATTCCCCCCA
*
1778961 GGGGGTACCGATTCCCCCC
1 -GGGGTACAGATTCCCCCC
1778980 TGTCTAACGG
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
19 39 0.47
20 28 0.34
21 13 0.16
22 3 0.04
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.18
Consensus pattern (19 bp):
GGGGTACAGATTCCCCCCA
Found at i:1788196 original size:22 final size:22
Alignment explanation
Indices: 1788144--1788196 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1788134 CTATGTCACA
*
1788144 ACCAACAAACATCATCATTATT
1 ACCAACAAGCATCATCATTATT
1788166 ACCAACAAGCATCATCATTATT
1 ACCAACAAGCATCATCATTATT
1788188 ACCAACAAG
1 ACCAACAAG
1788197 ATATTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.45, C:0.28, G:0.04, T:0.23
Consensus pattern (22 bp):
ACCAACAAGCATCATCATTATT
Found at i:1788690 original size:25 final size:25
Alignment explanation
Indices: 1788662--1788735 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
1788652 CATAATAATC
1788662 TACAAATACACCAAAACCAACATAT
1 TACAAATACACCAAAACCAACATAT
* ** *
1788687 TAC-AAT-CAACGTAA-C-A-AT-C
1 TACAAATACACCAAAACCAACATAT
*
1788706 TACAAATACACCAAAACTAACATAT
1 TACAAATACACCAAAACCAACATAT
1788731 TACAA
1 TACAA
1788736 TCGTTCTTGA
Statistics
Matches: 34, Mismatches: 9, Indels: 12
0.62 0.16 0.22
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 6 0.18
22 1 0.03
23 6 0.18
24 5 0.15
25 8 0.24
ACGTcount: A:0.54, C:0.26, G:0.01, T:0.19
Consensus pattern (25 bp):
TACAAATACACCAAAACCAACATAT
Found at i:1788693 original size:44 final size:44
Alignment explanation
Indices: 1788620--1788737 Score: 184
Period size: 44 Copynumber: 2.7 Consensus size: 44
1788610 GTACTATTCC
* * *
1788620 ACAAATACACC-ATACTAACATATTCCAATCAACATAATAATCT
1 ACAAATACACCAAAACTAACATATTACAATCAACATAACAATCT
* *
1788663 ACAAATACACCAAAACCAACATATTACAATCAACGTAACAATCT
1 ACAAATACACCAAAACTAACATATTACAATCAACATAACAATCT
1788707 ACAAATACACCAAAACTAACATATTACAATC
1 ACAAATACACCAAAACTAACATATTACAATC
1788738 GTTCTTGAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 11 0.16
44 57 0.84
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21
Consensus pattern (44 bp):
ACAAATACACCAAAACTAACATATTACAATCAACATAACAATCT
Found at i:1798478 original size:32 final size:31
Alignment explanation
Indices: 1798432--1798540 Score: 130
Period size: 32 Copynumber: 3.5 Consensus size: 31
1798422 GTAAAATATT
1798432 AATAAATTTAATGATCATCTTGTAACAATTC
1 AATAAATTTAATGATCATCTTGTAACAATTC
* * *
1798463 AATAAGATTTAATGATTATTTTGTAATAATTC
1 AATAA-ATTTAATGATCATCTTGTAACAATTC
* * * *
1798495 GATAAATTTTAATGATCATC-TGTAGCATTTT
1 AATAAA-TTTAATGATCATCTTGTAACAATTC
1798526 AATAAATTTAATGAT
1 AATAAATTTAATGAT
1798541 AATTTTATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 9 0.14
31 18 0.28
32 38 0.58
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.43
Consensus pattern (31 bp):
AATAAATTTAATGATCATCTTGTAACAATTC
Found at i:1804788 original size:39 final size:39
Alignment explanation
Indices: 1804697--1804860 Score: 211
Period size: 39 Copynumber: 4.1 Consensus size: 39
1804687 GCCATACATC
*
1804697 TGCTGAGGATACATCGAACCCATCTGGCCTGCCGCTGGCATT
1 TGCTGAGGATACATTGAACCCATCT-GCC--CCGCTGGCATT
* * *
1804739 TGCTGTGGATAGATTGAACCTATCTGCCCCGCTGGCATT
1 TGCTGAGGATACATTGAACCCATCTGCCCCGCTGGCATT
* * *
1804778 TGGTGAGGATACATTGAACCCATCTGGCCCGCCGGCATT
1 TGCTGAGGATACATTGAACCCATCTGCCCCGCTGGCATT
* * *
1804817 TGCTGAGGATACATTGAACTCATCTGGCCAGCTGGCATT
1 TGCTGAGGATACATTGAACCCATCTGCCCCGCTGGCATT
1804856 TGCTG
1 TGCTG
1804861 TGGAAGCATG
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
39 84 0.78
41 3 0.03
42 21 0.19
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (39 bp):
TGCTGAGGATACATTGAACCCATCTGCCCCGCTGGCATT
Found at i:1815955 original size:17 final size:18
Alignment explanation
Indices: 1815935--1815975 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1815925 AAATTATATT
1815935 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
1815952 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
1815970 ATTAAA
1 AGTAAA
1815976 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:1816032 original size:10 final size:10
Alignment explanation
Indices: 1816017--1816041 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1816007 CTTAAATAAA
1816017 GAGAGTATTT
1 GAGAGTATTT
1816027 GAGAGTATTT
1 GAGAGTATTT
1816037 GAGAG
1 GAGAG
1816042 AATATGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (10 bp):
GAGAGTATTT
Found at i:1816186 original size:53 final size:52
Alignment explanation
Indices: 1816126--1816240 Score: 137
Period size: 51 Copynumber: 2.2 Consensus size: 52
1816116 TCTCTTGTAC
* *
1816126 CGCGCTATACCCCACGTGTCAGATAAACGT-GGCGTATAGCGCGG-ATCAGGGGG
1 CGCGCTATACCCCACGTGTAAG-T-AACGTCAGCGTATAGCGCGGTA-CAGGGGG
* * *
1816179 CGCGCTATA-CCCACGTGTAAGTCATGTCAGCGTATAGTGCGGTACAGGGGG
1 CGCGCTATACCCCACGTGTAAGTAACGTCAGCGTATAGCGCGGTACAGGGGG
1816230 CGCGCTATACC
1 CGCGCTATACC
1816241 TCACACGCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
50 3 0.06
51 29 0.54
52 13 0.24
53 9 0.17
ACGTcount: A:0.22, C:0.27, G:0.32, T:0.19
Consensus pattern (52 bp):
CGCGCTATACCCCACGTGTAAGTAACGTCAGCGTATAGCGCGGTACAGGGGG
Found at i:1826650 original size:16 final size:16
Alignment explanation
Indices: 1826629--1826663 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1826619 GTTAAGTTCC
1826629 TATTTTATCTAATAAA
1 TATTTTATCTAATAAA
1826645 TATTTTATCTAATAAA
1 TATTTTATCTAATAAA
1826661 TAT
1 TAT
1826664 GAATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTTATCTAATAAA
Found at i:1831165 original size:23 final size:23
Alignment explanation
Indices: 1831139--1831207 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
1831129 CACCACAGCT
*
1831139 CATATAAATGCACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
* * *
1831162 CATAGAATTGCACCGTAGTGCCG
1 CATAGAAATGCACCGAAGTGCCA
** * *
1831185 TGTAGAATTGCACCGTAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
1831208 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCCA
Found at i:1831394 original size:103 final size:103
Alignment explanation
Indices: 1831223--1831543 Score: 563
Period size: 103 Copynumber: 3.1 Consensus size: 103
1831213 TAATGTCCAT
* * *
1831223 AAGGACCACATATCATTCTTTAAGAATCATATAAATAT-ACTAGGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGAC-AAGGATCAAGTATGTGTCTCACC
1831287 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1831326 AATGACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGACAAGGATCAAGTATGTGTCTCACCA
1831391 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1831429 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGACAAGGATCAAGTATGTGTCTCACCA
1831494 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1831532 AAGGACAACATA
1 AAGGACCACATA
1831544 GACCCTCGAC
Statistics
Matches: 209, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
103 208 1.00
104 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGACAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1832750 original size:21 final size:21
Alignment explanation
Indices: 1832724--1832767 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1832714 ATTTTATTCG
* *
1832724 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1832745 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1832766 CT
1 CT
1832768 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1834629 original size:23 final size:23
Alignment explanation
Indices: 1834595--1834663 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
1834585 CACCACAGGT
*
1834595 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
1834618 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1834641 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1834664 AATAAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1836371 original size:63 final size:63
Alignment explanation
Indices: 1836312--1836472 Score: 173
Period size: 63 Copynumber: 2.5 Consensus size: 63
1836302 CCCTTAACAT
* * *
1836312 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTT-TAATCTTAAAGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCTAATCTTAAA--G
* * * * ** * * *
1836376 GTGTATCGAT-CACTTCTTATGCATCGATGCACTAATTGCATTCGATGTTTCTATTTTTAAGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCTAATCTTAA-AG
1836439 GTGCATCGATGCACTTCCTATGCATCGATACACA
1 GTGCATCGATGCACTTCCTATGCATCGATACACA
1836473 CTGAATAATT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
63 42 0.54
64 36 0.46
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCTAATCTTAAAG
Found at i:1836796 original size:12 final size:12
Alignment explanation
Indices: 1836779--1836803 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1836769 CCTTCACAAG
1836779 TCCAATTTAACT
1 TCCAATTTAACT
1836791 TCCAATTTAACT
1 TCCAATTTAACT
1836803 T
1 T
1836804 ATCAACTTTC
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:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TCCAATTTAACT
Found at i:1841594 original size:20 final size:20
Alignment explanation
Indices: 1841569--1841608 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1841559 TCGGATATAC
1841569 TTTATCGATATGGAGAGCGA
1 TTTATCGATATGGAGAGCGA
1841589 TTTATCGATATGGAGAGCGA
1 TTTATCGATATGGAGAGCGA
1841609 GATTGGGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (20 bp):
TTTATCGATATGGAGAGCGA
Found at i:1856260 original size:30 final size:30
Alignment explanation
Indices: 1856192--1856266 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
1856182 TGTTAGATGG
* *
1856192 GGTAGGTCGCCATGCACGCCTAGCGACCTA
1 GGTAGGTCGCCATGCACGCCCAACGACCTA
**
1856222 -CCAGGTCGCCATGCACGCCCAACGACCTA
1 GGTAGGTCGCCATGCACGCCCAACGACCTA
1856251 GGTAGGTCGCCATGCA
1 GGTAGGTCGCCATGCA
1856267 ATCCATGCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (30 bp):
GGTAGGTCGCCATGCACGCCCAACGACCTA
Found at i:1857059 original size:27 final size:28
Alignment explanation
Indices: 1857021--1857075 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
1857011 ATTCATAGAT
*
1857021 TGCATGGCGACCT-TTGGTCGTTGGGCG
1 TGCATGGCGACCTGTAGGTCGTTGGGCG
1857048 TGCATGGCGACCTGGTAGGTCGTTGGGC
1 TGCATGGCGACCT-GTAGGTCGTTGGGC
1857076 ATGGCGACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.52
29 12 0.48
ACGTcount: A:0.09, C:0.22, G:0.42, T:0.27
Consensus pattern (28 bp):
TGCATGGCGACCTGTAGGTCGTTGGGCG
Found at i:1857880 original size:29 final size:29
Alignment explanation
Indices: 1857835--1857921 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
1857825 GTGTTGGCCG
* *
1857835 TAGGTCGCCATGCCTTCTAGACGACCTAC
1 TAGGTCGCCATGTCTTCCAGACGACCTAC
* *
1857864 TAGGTCGCCATGTCTTCCGGGCGACCTAC
1 TAGGTCGCCATGTCTTCCAGACGACCTAC
* *
1857893 TAGGTCGCCATGTCTTCCCGACGAGCTAC
1 TAGGTCGCCATGTCTTCCAGACGACCTAC
1857922 AAGAGATTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.17, C:0.34, G:0.24, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGTCTTCCAGACGACCTAC
Found at i:1859512 original size:17 final size:17
Alignment explanation
Indices: 1859490--1859530 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1859480 TTATATAAAC
1859490 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
1859507 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
*
1859524 ATATGAT
1 TTATGAT
1859531 TACTCTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:1859557 original size:51 final size:52
Alignment explanation
Indices: 1859500--1859597 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 52
1859490 TTATGATAAT
* *
1859500 TAAATTATTATGATAATTAAATTAATATGATTAC-TCTTTGAAATTTTATCA
1 TAAATTATTATGATAATCAAATTAATATAATTACTTCTTTGAAATTTTATCA
*
1859551 TAAATTATTATGATAATCAAATTAATATAATTACTTTTTTGAAATTT
1 TAAATTATTATGATAATCAAATTAATATAATTACTTCTTTGAAATTT
1859598 AATTTTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
51 32 0.74
52 11 0.26
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (52 bp):
TAAATTATTATGATAATCAAATTAATATAATTACTTCTTTGAAATTTTATCA
Found at i:1859626 original size:18 final size:16
Alignment explanation
Indices: 1859593--1859650 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 16
1859583 ACTTTTTTGA
1859593 AATTTAATTTTATATT
1 AATTTAATTTTATATT
1859609 AATTATAATTTGTATATTAT
1 AATT-TAATTT-TATA-T-T
*
1859629 AAATTTAATCTTTATGTT
1 -AATTTAAT-TTTATATT
1859647 AATT
1 AATT
1859651 CCAATTCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
16 4 0.11
17 10 0.29
18 5 0.14
19 2 0.06
20 8 0.23
21 6 0.17
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (16 bp):
AATTTAATTTTATATT
Found at i:1860448 original size:20 final size:20
Alignment explanation
Indices: 1860415--1860455 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1860405 AACACGTACA
* *
1860415 AATATCAAACAGAAGTAAAC
1 AATATAAAACAGAAGCAAAC
*
1860435 AATATAAAATAGAAGCAAAC
1 AATATAAAACAGAAGCAAAC
1860455 A
1 A
1860456 GAATCAAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.12, G:0.10, T:0.15
Consensus pattern (20 bp):
AATATAAAACAGAAGCAAAC
Found at i:1861254 original size:21 final size:21
Alignment explanation
Indices: 1861230--1861269 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1861220 ACTTCTGTTG
*
1861230 ACATTACCTAAAACAGCAATC
1 ACATAACCTAAAACAGCAATC
*
1861251 ACATAACCTAACACAGCAA
1 ACATAACCTAAAACAGCAA
1861270 GATAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.30, G:0.05, T:0.15
Consensus pattern (21 bp):
ACATAACCTAAAACAGCAATC
Found at i:1862696 original size:15 final size:15
Alignment explanation
Indices: 1862678--1862778 Score: 51
Period size: 15 Copynumber: 6.2 Consensus size: 15
1862668 TCTTATCCCT
1862678 ATAAAATTTATATTA
1 ATAAAATTTATATTA
1862693 ATAAATTATTTATAATTAA
1 ATAAA--ATTTAT-ATT-A
1862712 TATTAAAATAATTATA-TA
1 -A-TAAAAT--TTATATTA
* * *
1862730 TTATAATTAATATTA
1 ATAAAATTTATATTA
* *
1862745 ATATAATTAATATTA
1 ATAAAATTTATATTA
* *
1862760 ATATTAACTTATATTA
1 ATA-AAATTTATATTA
1862776 ATA
1 ATA
1862779 TAATATAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
14 4 0.06
15 24 0.34
16 18 0.26
17 6 0.09
18 4 0.06
19 4 0.06
20 2 0.03
21 8 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAAAATTTATATTA
Found at i:1862737 original size:28 final size:27
Alignment explanation
Indices: 1862682--1862759 Score: 99
Period size: 28 Copynumber: 3.0 Consensus size: 27
1862672 ATCCCTATAA
* *
1862682 AATTTATATTAATA-AATT-AT-TTAT
1 AATTAATATTAAAATAATTAATATTAT
1862706 AATTAATATTAAAATAATTATATATTAT
1 AATTAATATTAAAATAATTA-ATATTAT
*
1862734 AATTAATATTAATATAATTAATATTA
1 AATTAATATTAAAATAATTAATATTA
1862760 ATATTAACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
24 12 0.26
25 4 0.09
27 8 0.17
28 23 0.49
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATTAATATTAAAATAATTAATATTAT
Found at i:1862744 original size:6 final size:6
Alignment explanation
Indices: 1862707--1862813 Score: 54
Period size: 6 Copynumber: 18.3 Consensus size: 6
1862697 ATTATTTATA
1862707 ATTAAT ATTAAAAT AATTATAT ATT-AT AATTAAT ATTAAT A-T-A- ATTAAT
1 ATTAAT ATT--AAT -ATTA-AT ATTAAT -ATTAAT ATTAAT ATTAAT ATTAAT
* * *
1862756 ATTAAT ATTAA- CTT-AT ATTAAT A-TAAT A-TAAT TTGTAAT -TT-GT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT-TAAT ATTAAT
1862799 AATTAAT ATTAAT AT
1 -ATTAAT ATTAAT AT
1862814 AAAATATAGT
Statistics
Matches: 80, Mismatches: 5, Indels: 32
0.68 0.04 0.27
Matches are distributed among these distances:
3 1 0.01
4 4 0.05
5 18 0.22
6 38 0.47
7 11 0.14
8 5 0.06
9 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (6 bp):
ATTAAT
Found at i:1862777 original size:31 final size:31
Alignment explanation
Indices: 1862705--1862815 Score: 122
Period size: 28 Copynumber: 3.6 Consensus size: 31
1862695 AAATTATTTA
* *
1862705 TAATTAATATTAAAATAATT-ATA-TATTA-
1 TAATTAATATTAATATAATTAATATTAATAT
1862733 TAATTAATATTAATATAATTAATATTAATAT
1 TAATTAATATTAATATAATTAATATTAATAT
* *
1862764 TAACTT-ATATTAATATAATATAATTTGTAATTT
1 TAA-TTAATATTAATATAAT-TAATAT-TAATAT
1862797 GTAATTAATATTAATATAA
1 -TAATTAATATTAATATAA
1862816 AATATAGTGC
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
28 19 0.27
29 3 0.04
30 4 0.06
31 16 0.23
32 7 0.10
33 7 0.10
34 15 0.21
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (31 bp):
TAATTAATATTAATATAATTAATATTAATAT
Found at i:1862891 original size:18 final size:17
Alignment explanation
Indices: 1862878--1862929 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 17
1862868 AGTATAGTTA
1862878 ATATAGTTTATATATACC
1 ATATAGTTTATATATA-C
1862896 ATATAGTTTATATATAC
1 ATATAGTTTATATATAC
*
1862913 TATATAGGTTATATATA
1 -ATATAGTTTATATATA
1862930 GTAATGAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (17 bp):
ATATAGTTTATATATAC
Found at i:1862977 original size:18 final size:18
Alignment explanation
Indices: 1862956--1863380 Score: 220
Period size: 18 Copynumber: 24.6 Consensus size: 18
1862946 TGTATATACC
* *
1862956 ATATACTATGTAGGTTAT
1 ATATACTATATAGTTTAT
**
1862974 ATATACTA-AT-GAACTAT
1 ATATACTATATAG-TTTAT
*
1862991 ATA-A-TATATAGTTTAC
1 ATATACTATATAGTTTAT
1863007 ATATACTATATAGTTTAT
1 ATATACTATATAGTTTAT
*
1863025 ATATACTA-AT-G--AACT
1 ATATACTATATAGTTTA-T
*
1863040 ATATAATATATAGTTTAT
1 ATATACTATATAGTTTAT
**
1863058 ATATACTA-AT-GAAATAT
1 ATATACTATATAG-TTTAT
* *
1863075 ATATAATGTATAGTTTAT
1 ATATACTATATAGTTTAT
*
1863093 ATATACTATATAGGTTAT
1 ATATACTATATAGTTTAT
* * * * *
1863111 ATATAGTTTGTA-TATACC
1 ATATACTATATAGTTTA-T
* * *
1863129 ATAAATTATATAGGTTAT
1 ATATACTATATAGTTTAT
*
1863147 ATATACTA-AT-G--AACT
1 ATATACTATATAGTTTA-T
* * *
1863162 ATATAATAAATAGTTTAC
1 ATATACTATATAGTTTAT
1863180 ATATACTATATAGTTTAT
1 ATATACTATATAGTTTAT
*
1863198 ATATACTA-AT-G--AACT
1 ATATACTATATAGTTTA-T
*
1863213 ATATAATATATAGTTTAT
1 ATATACTATATAGTTTAT
**
1863231 ATATACTA-AT-GAAATAT
1 ATATACTATATAG-TTTAT
*
1863248 ATATA-TATATA-TATAT
1 ATATACTATATAGTTTAT
* *
1863264 ATATAATGTATAGTTTAT
1 ATATACTATATAGTTTAT
*
1863282 ATATACCATATAGCTTATAT
1 ATATACTATATAG-TT-TAT
* *
1863302 ATATATTATATAGGTTAT
1 ATATACTATATAGTTTAT
* *
1863320 ATATAGTA-AT-G--AACT
1 ATATACTATATAGTTTA-T
* *
1863335 ATATAATATATAGTTTGT
1 ATATACTATATAGTTTAT
*
1863353 ATATATTATATAGTTTAT
1 ATATACTATATAGTTTAT
1863371 ATATACTATA
1 ATATACTATA
1863381 GTATAAATTA
Statistics
Matches: 305, Mismatches: 65, Indels: 74
0.69 0.15 0.17
Matches are distributed among these distances:
14 4 0.01
15 34 0.11
16 34 0.11
17 51 0.17
18 159 0.52
19 9 0.03
20 14 0.05
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (18 bp):
ATATACTATATAGTTTAT
Found at i:1863044 original size:17 final size:17
Alignment explanation
Indices: 1863022--1863079 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
1863012 CTATATAGTT
*
1863022 TATATATACTAATGAAC
1 TATATATACTAATGAAA
**
1863039 TATATA-A-TATAT-AGT
1 TATATATACTA-ATGAAA
1863054 TTATATATACTAATGAAA
1 T-ATATATACTAATGAAA
1863072 TATATATA
1 TATATATA
1863080 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 16 0.50
18 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAA
Found at i:1863054 original size:51 final size:51
Alignment explanation
Indices: 1862896--1863065 Score: 238
Period size: 51 Copynumber: 3.4 Consensus size: 51
1862886 TATATATACC
* *
1862896 ATATAGTTTATATATACTATATAGGTTATATATAGTAATGAACTATAT--T
1 ATATAGTTTACATATACTATATAGGTTATATATACTAATGAACTATATAAT
* * * *
1862945 TTGTA-TATACCATATACTATGTAGGTTATATATACTAATGAACTATATAAT
1 ATATAGTTTA-CATATACTATATAGGTTATATATACTAATGAACTATATAAT
*
1862996 ATATAGTTTACATATACTATATAGTTTATATATACTAATGAACTATATAAT
1 ATATAGTTTACATATACTATATAGGTTATATATACTAATGAACTATATAAT
*
1863047 ATATAGTTTATATATACTA
1 ATATAGTTTACATATACTA
1863066 ATGAAATATA
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
48 3 0.03
49 38 0.36
51 61 0.58
52 3 0.03
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (51 bp):
ATATAGTTTACATATACTATATAGGTTATATATACTAATGAACTATATAAT
Found at i:1863078 original size:35 final size:33
Alignment explanation
Indices: 1863007--1863357 Score: 153
Period size: 33 Copynumber: 10.7 Consensus size: 33
1862997 TATAGTTTAC
* *
1863007 ATATACTATATAGTTTATATATACTAATGAACT
1 ATATAATATATAGTTTATATATACTAATGAAAT
1863040 ATATAATATATAGTTTATATATACTAATGAAATAT
1 ATATAATATATAGTTTATATATACTAATG-AA-AT
*
1863075 ATATAATGTATAGTTTATATATACT-AT---AT
1 ATATAATATATAGTTTATATATACTAATGAAAT
** * * *
1863104 AGGTTATATATAGTTTGTATATAC-CAT---A-
1 ATATAATATATAGTTTATATATACTAATGAAAT
* *
1863132 A-AT--TATATAGGTTATATATACTAATGAACT
1 ATATAATATATAGTTTATATATACTAATGAAAT
* * **
1863162 ATATAATAAATAGTTTACATATACTATATAGTTTAT
1 ATATAATATATAGTTTATATATACTA-AT-G-AAAT
* * * * * *
1863198 ATATACTA-ATGAACTATATAATATA-TAGTTTATAT
1 ATATAATATAT--AGTTTAT-ATATACTA-ATGAAAT
* * *
1863233 ATACTAATGAAATA-TATATATATA-T-AT-ATAT
1 ATA-TAAT-ATATAGTTTATATATACTAATGAAAT
* * *
1863264 ATATAATGTATAGTTTATATATACCATATAGCTTATAT
1 ATATAATATATAGTTTATATATA-C-TA-A--TGAAAT
* * * *
1863302 ATATATTATATAGGTTATATATAGTAATGAACT
1 ATATAATATATAGTTTATATATACTAATGAAAT
*
1863335 ATATAATATATAGTTTGTATATA
1 ATATAATATATAGTTTATATATA
1863358 TTATATAGTT
Statistics
Matches: 247, Mismatches: 42, Indels: 58
0.71 0.12 0.17
Matches are distributed among these distances:
25 16 0.06
26 2 0.01
27 1 0.00
28 1 0.00
29 27 0.11
30 14 0.06
31 9 0.04
32 1 0.00
33 69 0.28
34 12 0.05
35 41 0.17
36 14 0.06
37 9 0.04
38 31 0.13
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (33 bp):
ATATAATATATAGTTTATATATACTAATGAAAT
Found at i:1863126 original size:51 final size:52
Alignment explanation
Indices: 1863039--1863385 Score: 175
Period size: 51 Copynumber: 6.7 Consensus size: 52
1863029 ACTAATGAAC
* * * * * *
1863039 TATATAATATATAGTTTATATATACTAATGAAATATATATAATGTATAGTTTA
1 TATATACTATATAGATTATATATAGTATTG-TATATATATAATATATAGTTTA
* * *
1863092 TATATACTATATAGGTTATATATAGT-TTGTATATACCATAAATTATATAGGTTA
1 TATATACTATATAGATTATATATAGTATTGTATATA-TAT-AA-TATATAGTTTA
* * * * * *
1863146 TATATACTA-AT-GAACTATATAATA-AATAGTTTACATATACTATATAGTTTA
1 TATATACTATATAG-ATTATAT-ATAGTATTGTATATATATAATATATAGTTTA
* *
1863197 TATATACTA-AT-GAACTATATAATATA-TAGTT-TATATATACTAATGAAATA-TATA
1 TATATACTATATAG-A-T-TAT-ATATAGTA-TTGTATATATA-TAAT-ATATAGTTTA
* * * **
1863251 TATATA-TATATATA-TATA-AT-GTATAGTTTATATATACCATATAGCTTATA
1 TATATACTATATAGATTATATATAGTATTGTATATATATAATATATAG-TT-TA
* * * *
1863301 TATATATTATATAGGTTATATATAGTAATG-A-ACTATATAATATATAGTTTG
1 TATATACTATATAGATTATATATAGTATTGTATA-TATATAATATATAGTTTA
* * * *
1863352 TATATATTATATAGTTTATATATACTATAGTATA
1 TATATACTATATAGATTATATATAGTATTGTATA
1863386 AATTATTTTA
Statistics
Matches: 224, Mismatches: 44, Indels: 52
0.70 0.14 0.16
Matches are distributed among these distances:
47 4 0.02
48 3 0.01
49 12 0.05
50 9 0.04
51 65 0.29
52 14 0.06
53 64 0.29
54 49 0.22
55 4 0.02
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (52 bp):
TATATACTATATAGATTATATATAGTATTGTATATATATAATATATAGTTTA
Found at i:1863163 original size:173 final size:171
Alignment explanation
Indices: 1862939--1863378 Score: 659
Period size: 173 Copynumber: 2.5 Consensus size: 171
1862929 AGTAATGAAC
* * *
1862939 TATATTTTGTATATACCATATACTATGTAGGTTATATATACTAATGAACTATATAATATATAGTT
1 TATAATTTGTATATACCATATATTATATAGGTTATATATACTAATGAACTATATAATATATAGTT
1863004 TACATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATG
66 TACATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATG
* * *
1863069 AAATATATATAATGTATAGTTTATATATACTATATAGGTTATA
131 AAATATATAT-ATATATA-TATATATATAATATATAGGTTATA
* * *
1863112 TATAGTTTGTATATACCATAAATTATATAGGTTATATATACTAATGAACTATATAATAAATAGTT
1 TATAATTTGTATATACCATATATTATATAGGTTATATATACTAATGAACTATATAATATATAGTT
1863177 TACATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATG
66 TACATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATG
* *
1863242 AAATATATATATATATATATATATATAATGTATAGTTTATA
131 AAATATATATATATATATATATATATAATATATAGGTTATA
* * *
1863283 TATACCATATAGCT-TATA-TATATATTATATAGGTTATATATAGTAATGAACTATATAATATAT
1 TATA--AT-TTG-TATATACCATATATTATATAGGTTATATATACTAATGAACTATATAATATAT
** *
1863346 AGTTTGTATATATTATATAGTTTATATATACTA
62 AGTTTACATATACTATATAGTTTATATATACTA
1863379 TAGTATAAAT
Statistics
Matches: 244, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
171 24 0.10
172 6 0.02
173 207 0.85
174 6 0.02
175 1 0.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (171 bp):
TATAATTTGTATATACCATATATTATATAGGTTATATATACTAATGAACTATATAATATATAGTT
TACATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATG
AAATATATATATATATATATATATATAATATATAGGTTATA
Found at i:1863216 original size:122 final size:119
Alignment explanation
Indices: 1863013--1863235 Score: 299
Period size: 122 Copynumber: 1.8 Consensus size: 119
1863003 TTACATATAC
* * *
1863013 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAAATATATA
1 TATATAGGTTATATATACTAATGAACTATATAATAAATAGTTTACATATACTAATGAAATATATA
*
1863078 TAATGTATAGTTTATATATACTATATAGGTTATATATAGTTTGTATATACCATAAAT
66 TAATGTATAG-CTATATA-A-TATATAGGTTATATATAGTTTGTATATACCATAAAT
**
1863135 TATATAGGTTATATATACTAATGAACTATATAATAAATAGTTTACATATACTATATAGTTTATAT
1 TATATAGGTTATATATACTAATGAACTATATAATAAATAGTTTACATATACTA-AT-G-AAATAT
*
1863200 ATACTAATG-A-A-CTATATAATATATAGTTTATATATA
63 ATA-TAATGTATAGCTATATAATATATAGGTTATATATA
1863236 CTAATGAAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
120 16 0.18
121 1 0.01
122 56 0.62
123 2 0.02
124 2 0.02
125 8 0.09
126 5 0.06
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (119 bp):
TATATAGGTTATATATACTAATGAACTATATAATAAATAGTTTACATATACTAATGAAATATATA
TAATGTATAGCTATATAATATATAGGTTATATATAGTTTGTATATACCATAAAT
Found at i:1863217 original size:2 final size:2
Alignment explanation
Indices: 1863212--1863590 Score: 76
Period size: 2 Copynumber: 184.0 Consensus size: 2
1863202 ACTAATGAAC
* *
1863212 TA TA TA -A TA TA TA GTT TA TA TA TA CTA -A TGA AA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA T-A TA TA TA TA TA
* * * **
1863253 TA TA TA TA TA TA TA TA -A TG TA TA GTT TA TA TA TA CCA TA TA GC
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA
**
1863296 T- TA TA TA TA TA T- TA TA TA GG T- TA TA TA TA GTA -A TGA -A CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA -TA
* * *
1863336 TA TA -A TA TA TA GTT TG TA TA TA T- TA TA TA GTT TA TA TA TA CTA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * * *
1863379 TA GTA TA AA T- TA T- TT TA TA TA GTA TA TA AA TA TCA -A CTA TGG
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA -TA T-A
* * * * * *
1863421 TA TA TA GTT TA TA TGG TT TT TA TA TA TA GT- TCA TA TG TA AA T-
1 TA TA TA -TA TA TA T-A TA TA TA TA TA TA -TA T-A TA TA TA TA TA
* *
1863463 TA TA CTA TA TA GTA TA TA T- TG TT TA TA TA TA -A TA TA TA GTA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * **
1863504 TA TA AA TA TA AA CTA TA GTA TG TA TA TA TA TA GG TCA TA TA TA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA T-A TA TA TA
* *
1863547 AA CTA TA TA GTA TA TA AA TA TCA -A CTA TA -A TA TA TA TA TA TA
1 TA -TA TA TA -TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA
1863589 TA
1 TA
1863591 GGTCATATGT
Statistics
Matches: 275, Mismatches: 53, Indels: 98
0.65 0.12 0.23
Matches are distributed among these distances:
1 19 0.07
2 216 0.79
3 40 0.15
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1863217 original size:17 final size:17
Alignment explanation
Indices: 1863195--1863271 Score: 51
Period size: 17 Copynumber: 4.8 Consensus size: 17
1863185 CTATATAGTT
*
1863195 TATATATACTAATGAAC
1 TATATATACTAATGAAA
**
1863212 TATATA-A-TATAT-AGT
1 TATATATACTA-ATGAAA
1863227 TTATATATACTAATGAAA
1 T-ATATATACTAATGAAA
*
1863245 TATATATA-T-AT-ATA
1 TATATATACTAATGAAA
1863259 TATATATA-TAATG
1 TATATATACTAATG
1863272 TATAGTTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
14 11 0.23
15 8 0.17
16 9 0.19
17 16 0.33
18 4 0.08
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (17 bp):
TATATATACTAATGAAA
Found at i:1863248 original size:122 final size:113
Alignment explanation
Indices: 1863013--1863357 Score: 295
Period size: 122 Copynumber: 2.9 Consensus size: 113
1863003 TTACATATAC
* **
1863013 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTA-AT-GAAATATA
1 TATATAG-TTATATATACTAATGAACTATATAATAAATAGTTTATATATACTATATAGTTATATA
* * * * *
1863076 TATAATGTATAGTTTATATATACTATATAGGTTATATATAGTTTGTATATACCATAAA
65 TATAATG-A-A--CTATATA-A-TATATAGTTTATATATACTATG-A-ATA-TATAAA
*
1863134 TTATATAGGTTATATATACTAATGAACTATATAATAAATAGTTTACATATACTATATAGTTTATA
1 -TATATA-GTTATATATACTAATGAACTATATAATAAATAGTTTATATATACTATATAG-TTATA
*
1863199 TATACTAATGAACTATATAATATATAGTTTATATATACTAATGAA-ATATATA
63 TATA-TAATGAACTATATAATATATAGTTTATATATACT-ATGAATATATAAA
* * *
1863251 TATATA-TATATATATA-TAATGTATAGTTTATATATACCATATAGCTTATATATATATTATATA
1 TATATAGT-TATATATACTAATG-A-ACTATATA-ATA--A-ATAG-TT-TATATATACTATATA
*
1863314 GGTTATATATAGTAATGAACTATATAATATATAGTTTGTATATA
57 -GTTATATATA-TAATGAACTATATAATATATAGTTTATATATA
1863358 TTATATAGTT
Statistics
Matches: 191, Mismatches: 16, Indels: 32
0.80 0.07 0.13
Matches are distributed among these distances:
114 6 0.03
115 9 0.05
116 12 0.06
117 7 0.04
118 1 0.01
119 2 0.01
120 22 0.12
121 5 0.03
122 108 0.57
123 4 0.02
124 2 0.01
125 8 0.04
126 5 0.03
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (113 bp):
TATATAGTTATATATACTAATGAACTATATAATAAATAGTTTATATATACTATATAGTTATATAT
ATAATGAACTATATAATATATAGTTTATATATACTATGAATATATAAA
Found at i:1863445 original size:122 final size:122
Alignment explanation
Indices: 1863180--1863446 Score: 269
Period size: 122 Copynumber: 2.2 Consensus size: 122
1863170 AATAGTTTAC
* *
1863180 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAAA
1 ATATATTATATGGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAAA
* * * * * *
1863245 TATATATATATATATATATATATAATGTATAGTTTATATATACCATATAGCTTATAT
66 TATATATATATATATAAATATATAATATATAGTATATAAATACAATATAGCGTATAT
* * *
1863302 ATATATTATATAGG-TTATATATAGTAATGAACTATATAATATATAGTTTGTATATATTATAT-A
1 ATATATTATAT-GGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTA-ATGA
** **
1863365 GTTTATATATACTATAGTATAAAT-TATTTTATATAGTATATAAATATCAACTAT-G-GTATAT
64 -AATATATATA-TATA-TATAAATATATAATATATAGTATATAAATA-CAA-TATAGCGTATAT
* *
1863426 A-GT-TTATATGGTTTTTATATA
1 ATATATTATATGGTTTATATATA
1863447 TAGTTCATAT
Statistics
Matches: 120, Mismatches: 17, Indels: 16
0.78 0.11 0.10
Matches are distributed among these distances:
121 2 0.02
122 67 0.56
123 12 0.10
124 27 0.22
125 9 0.08
126 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (122 bp):
ATATATTATATGGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAAA
TATATATATATATATAAATATATAATATATAGTATATAAATACAATATAGCGTATAT
Found at i:1863481 original size:25 final size:27
Alignment explanation
Indices: 1863442--1863507 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
1863432 TATGGTTTTT
1863442 ATATATAGT-TCATA-TGTAAAT-TATA
1 ATATATAGTAT-ATATTGTAAATATATA
* **
1863467 CTATATAGTATATATTGTTTATATATA
1 ATATATAGTATATATTGTAAATATATA
1863494 ATATATAGTATATA
1 ATATATAGTATATA
1863508 AATATAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 11 0.32
26 6 0.18
27 17 0.50
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (27 bp):
ATATATAGTATATATTGTAAATATATA
Found at i:1863531 original size:33 final size:31
Alignment explanation
Indices: 1863486--1863641 Score: 96
Period size: 33 Copynumber: 5.1 Consensus size: 31
1863476 ATATATTGTT
*
1863486 TATATA-TA-ATATATAGTATATAAATATAAAC
1 TATATAGTATATATATAG-AT-CAAATATAAAC
* *
1863517 TATAGTATGTATATATATAGGTCATATATAAAC
1 TATA-TA-GTATATATATAGATCAAATATAAAC
* *
1863550 TATATAGTATATA-A-ATATCAACTAT--A-
1 TATATAGTATATATATAGATCAAATATAAAC
* * *
1863576 -ATATA-TATATATATAGGTCATATGTAAAC
1 TATATAGTATATATATAGATCAAATATAAAC
* * *
1863605 TATATAGTTTATATATATAGTTCATATGTAAAC
1 TATATAG--TATATATATAGATCAAATATAAAC
1863638 TATA
1 TATA
1863642 ATTCATATGT
Statistics
Matches: 99, Mismatches: 13, Indels: 24
0.73 0.10 0.18
Matches are distributed among these distances:
24 6 0.06
25 6 0.06
26 6 0.06
27 1 0.01
28 1 0.01
29 7 0.07
30 6 0.06
31 11 0.11
32 4 0.04
33 40 0.40
34 3 0.03
35 8 0.08
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (31 bp):
TATATAGTATATATATAGATCAAATATAAAC
Found at i:1863554 original size:55 final size:55
Alignment explanation
Indices: 1863458--1863623 Score: 210
Period size: 55 Copynumber: 3.0 Consensus size: 55
1863448 AGTTCATATG
* * * * *
1863458 TAAATTATACTATATAGTATATATTGTTTATATAT-AA-TATATAGTATATAAATA
1 TAAACTATAATATATA-TATATATAGGTCATATATAAACTATATAGTATATAAATA
* *
1863512 TAAACTATAGTATGTATATATATAGGTCATATATAAACTATATAGTATATAAATA
1 TAAACTATAATATATATATATATAGGTCATATATAAACTATATAGTATATAAATA
* * * *
1863567 TCAACTATAATATATATATATATAGGTCATATGTAAACTATATAGTTTATATATA
1 TAAACTATAATATATATATATATAGGTCATATATAAACTATATAGTATATAAATA
1863622 TA
1 TA
1863624 GTTCATATGT
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
53 15 0.15
54 15 0.15
55 67 0.69
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (55 bp):
TAAACTATAATATATATATATATAGGTCATATATAAACTATATAGTATATAAATA
Found at i:1863691 original size:18 final size:18
Alignment explanation
Indices: 1863620--1863756 Score: 67
Period size: 18 Copynumber: 7.7 Consensus size: 18
1863610 AGTTTATATA
1863620 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
*
1863638 TATAATTCATATGTAAATATCAAC
1 TATAGTTCATATG----TA--AAC
1863662 TATAGCTT-ATATGTAAAC
1 TATAG-TTCATATGTAAAC
*
1863680 TATAGTTCATATATAAA-
1 TATAGTTCATATGTAAAC
** * *
1863697 TATCA-ACCTTA-GTATA-
1 TAT-AGTTCATATGTAAAC
* *
1863713 TATA-TT--TATATATA-
1 TATAGTTCATATGTAAAC
1863727 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
1863745 TATAGTTCATAT
1 TATAGTTCATAT
1863757 ATATAATATA
Statistics
Matches: 92, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.02
14 8 0.09
15 3 0.03
16 6 0.07
17 14 0.15
18 41 0.45
20 2 0.02
22 2 0.02
24 12 0.13
25 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:1863715 original size:42 final size:42
Alignment explanation
Indices: 1863620--1863703 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
1863610 AGTTTATATA
*
1863620 TATAG-TTCATATGTAAACTATAATTCATATGTAAATATCAAC
1 TATAGCTT-ATATGTAAACTATAATTCATATATAAATATCAAC
*
1863662 TATAGCTTATATGTAAACTATAGTTCATATATAAATATCAAC
1 TATAGCTTATATGTAAACTATAATTCATATATAAATATCAAC
1863704 CTTAGTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 37 0.95
43 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (42 bp):
TATAGCTTATATGTAAACTATAATTCATATATAAATATCAAC
Found at i:1863766 original size:18 final size:18
Alignment explanation
Indices: 1863719--1863766 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1863709 TATATATATT
1863719 TATATAT-ATATAGTTCA
1 TATATATAATATAGTTCA
*
1863736 TATGTA-AACTATAGTTCA
1 TATATATAA-TATAGTTCA
1863754 TATATATAATATA
1 TATATATAATATA
1863767 TAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.23
18 18 0.69
19 2 0.08
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
TATATATAATATAGTTCA
Found at i:1863777 original size:33 final size:32
Alignment explanation
Indices: 1863740--1863806 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
1863730 AGTTCATATG
*
1863740 TAAACTATAGTTCATATATATAATATATAAATA
1 TAAACTATAGTTCATATAGATAATATA-AAATA
* *
1863773 TAAACTATAGTTTATATAGATAGTATAAAATA
1 TAAACTATAGTTCATATAGATAATATAAAATA
1863805 TA
1 TA
1863807 GTATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (32 bp):
TAAACTATAGTTCATATAGATAATATAAAATA
Found at i:1863789 original size:29 final size:27
Alignment explanation
Indices: 1863756--1863856 Score: 95
Period size: 29 Copynumber: 3.7 Consensus size: 27
1863746 ATAGTTCATA
1863756 TATATAATATATAAATATAAACTATAGTT
1 TATATAA-ATATAAATATAAA-TATAGTT
*
1863785 TATATAGATAGT--ATA-AAATATAG--
1 TATATAAATA-TAAATATAAATATAGTT
* *
1863808 TATATAAATATAAATTATAGTATGTAGTT
1 TATATAAATATAAA-TATA-AATATAGTT
1863837 TATATAAATATAAATATAAA
1 TATATAAATATAAATATAAA
1863857 CCCTAAACCC
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
22 1 0.02
23 9 0.15
24 1 0.02
25 7 0.12
26 4 0.07
27 9 0.15
28 7 0.12
29 21 0.36
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (27 bp):
TATATAAATATAAATATAAATATAGTT
Found at i:1863809 original size:12 final size:13
Alignment explanation
Indices: 1863756--1863819 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
1863746 ATAGTTCATA
1863756 TATATAATATATA-
1 TATATAA-ATATAG
*
1863769 AATATAAACTATAG
1 TATATAAA-TATAG
* * *
1863783 TTTATATAGATAG
1 TATATAAATATAG
1863796 TATA-AAATATAG
1 TATATAAATATAG
1863808 TATATAAATATA
1 TATATAAATATA
1863820 AATTATAGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
12 11 0.28
13 24 0.60
14 5 0.12
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (13 bp):
TATATAAATATAG
Found at i:1863827 original size:20 final size:20
Alignment explanation
Indices: 1863757--1863830 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
1863747 TAGTTCATAT
*
1863757 ATATAATATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
1863777 CTATAGTTTATATAGATAGTATAAA
1 ATATAG--TATATA-A-A-TATAAA
1863802 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
1863822 TTATAGTAT
1 ATATAGTAT
1863831 GTAGTTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
20 18 0.40
21 1 0.02
22 7 0.16
23 7 0.16
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:1863893 original size:22 final size:20
Alignment explanation
Indices: 1863867--1863906 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1863857 CCCTAAACCC
1863867 TAAACCATATATATTATATATA
1 TAAACCATATA-ATT-TATATA
*
1863889 TAAACTATATAATTTATA
1 TAAACCATATAATTTATA
1863907 CAATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAACCATATAATTTATATA
Found at i:1863906 original size:18 final size:18
Alignment explanation
Indices: 1863894--1863947 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
1863884 ATATATAAAC
1863894 TATATAATTTATACAATA
1 TATATAATTTATACAATA
* *
1863912 TATATTATTTATA-ATTA
1 TATATAATTTATACAATA
* *
1863929 TACATAATATATA-AATA
1 TATATAATTTATACAATA
1863946 TA
1 TA
1863948 AATTGGTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATAATTTATACAATA
Found at i:1864068 original size:27 final size:28
Alignment explanation
Indices: 1864022--1864090 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
1864012 ATATATAAAC
* **
1864022 TATATAGTATTATAGTTTATACATGGTA
1 TATATAGTATTATACTTTATACATAATA
1864050 TATATAGT-TTATACTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
1864077 TATATA-TATATATA
1 TATATAGTAT-TATA
1864091 TATAAACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.03
27 23 0.64
28 12 0.33
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:1864081 original size:2 final size:2
Alignment explanation
Indices: 1864074--1864168 Score: 77
Period size: 2 Copynumber: 46.0 Consensus size: 2
1864064 TTTATACATA
* *
1864074 AT AT AT AT AT AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* * * *
1864117 AT AC AT AT ACT CT AT AT AT AA ACT AT AT AGT TT AT AT -T AT AT
1 AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
1864159 AT AT AT AT AT
1 AT AT AT AT AT
1864169 TAGTTGTTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
1 2 0.03
2 67 0.91
3 5 0.07
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1864113 original size:22 final size:21
Alignment explanation
Indices: 1864077--1864169 Score: 93
Period size: 22 Copynumber: 4.4 Consensus size: 21
1864067 ATACATAATA
*
1864077 TATATATATATATATATAAAC
1 TATATATTTATATATATAAAC
1864098 TATATAGTTTATATATATAATAC
1 TATATA-TTTATATATATAA-AC
* *
1864121 -ATATA-CTCTATATATAAAC
1 TATATATTTATATATATAAAC
*
1864140 TATATAGTTTATATTATATATA-
1 TATATA-TTTATA-TATATAAAC
1864162 TATATATT
1 TATATATT
1864170 AGTTGTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.03
20 15 0.25
21 8 0.13
22 26 0.43
23 9 0.15
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATATTTATATATATAAAC
Found at i:1864139 original size:42 final size:44
Alignment explanation
Indices: 1864074--1864168 Score: 142
Period size: 42 Copynumber: 2.2 Consensus size: 44
1864064 TTTATACATA
* *
1864074 ATATATATATA-TATATATATAAACTATATAGTTTATA-TATAT
1 ATATACATATACTCTATATATAAACTATATAGTTTATATTATAT
1864116 A-ATACATATACTCTATATATAAACTATATAGTTTATATTATAT
1 ATATACATATACTCTATATATAAACTATATAGTTTATATTATAT
*
1864159 ATATATATAT
1 ATATACATAT
1864169 TAGTTGTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 8 0.17
42 26 0.55
43 6 0.13
44 7 0.15
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (44 bp):
ATATACATATACTCTATATATAAACTATATAGTTTATATTATAT
Found at i:1864555 original size:210 final size:209
Alignment explanation
Indices: 1864193--1865008 Score: 1217
Period size: 210 Copynumber: 3.8 Consensus size: 209
1864183 TTTTTTATCA
* *
1864193 ACTTATTACTTATTTCTATTTATT-AATTGGCTCATAACTTTTTAAATGAGTATAATTTAGTACA
1 ACTTATTACTTATTTCTATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAC-
*
1864257 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-TTTGTGTTGTTC
64 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATTTGTGTTGTTT
1864321 AATATATTTAAATTTTTATTTGTAATGTT-ATATTTGTTCAATTTAGTCCTCCAAATTTCATTTG
129 AATATATTTAAATTTTTATTTGTAAT-TTCATATTTGTTCAATTTAGTCCTCCAAATTT-ATTTG
* **
1864385 TACCTGAAATTGACCCAT
192 CATATGAAATTGACCCAT
1864403 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
*
1864468 GTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCAATTTGATCCCT-TTTGTGTTGTTTA
66 -TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATTTGTGTTGTTTA
1864532 ATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAAATTTATTTGCA
130 ATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCC-AAATTTATTTGCA
1864597 TATGAAATTGACCCAT
194 TATGAAATTGACCCAT
1864613 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * *
1864678 TTAGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTG
66 TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-AT---T-TGTGTTG
* * *
1864743 TTTAATTTATTAAAAATTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATT
126 TTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA-TTTATT
* *
1864808 TGCATATGAAAGTGATCCAT
190 TGCATATGAAATTGACCCAT
* * * *
1864828 AATTATTACTTAATTCTATTTTTTTAATTGGCTCATAACTTTTTAAATGGGTATAATTTAGTACT
1 ACTTATTACTTATTTCTA-TTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAC-
* *
1864893 TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCACCAATGTGTGT
64 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-----ATTTGTGT
* *
1864958 TGCTTAATTTATTTAAATTTTTTATTTGTAATTTCATATTTGTTCAATTTA
124 TGTTTAATATATTTAAA-TTTTTATTTGTAATTTCATATTTGTTCAATTTA
1865009 ATTCTTAAAT
Statistics
Matches: 561, Mismatches: 27, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
209 52 0.09
210 252 0.45
211 7 0.01
214 4 0.01
215 99 0.18
216 43 0.08
217 70 0.12
218 32 0.06
221 2 0.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (209 bp):
ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATTTGTGTTGTTTAA
TATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTATTTGCATA
TGAAATTGACCCAT
Found at i:1867033 original size:107 final size:108
Alignment explanation
Indices: 1866845--1867053 Score: 384
Period size: 107 Copynumber: 1.9 Consensus size: 108
1866835 TTTTTTTTTT
*
1866845 ACTTGTTTGGAACTCATAAAATTAAACATAAAAAATATAAATTTTTGGGGTTCAAAAACTTACTC
1 ACTTGTTTGAAACTCATAAAATTAAACAT-AAAAATATAAATTTTTGGGGTTCAAAAACTTACTC
1866910 GAATTTGAGATGTTTGTTTTCTATTCAAATGAAGAGTTTTCTTA
65 GAATTTGAGATGTTTGTTTTCTATTCAAATGAAGAGTTTTCTTA
*
1866954 ACTTGTTTGAAACTCATAAAATTAAACAT-AAAATATAAATTTTTGGGGTTCAAAAACTTGCTCG
1 ACTTGTTTGAAACTCATAAAATTAAACATAAAAATATAAATTTTTGGGGTTCAAAAACTTACTCG
1867018 AATTTGAGATGTTTGTTTTCTATTCAAATGAAGAGT
66 AATTTGAGATGTTTGTTTTCTATTCAAATGAAGAGT
1867054 AATTTTCTTG
Statistics
Matches: 98, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
107 70 0.71
109 28 0.29
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (108 bp):
ACTTGTTTGAAACTCATAAAATTAAACATAAAAATATAAATTTTTGGGGTTCAAAAACTTACTCG
AATTTGAGATGTTTGTTTTCTATTCAAATGAAGAGTTTTCTTA
Found at i:1871045 original size:21 final size:23
Alignment explanation
Indices: 1870994--1871045 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1870984 GATTCCCCTG
1870994 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTTCCCCTTCA
**
1871017 AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGAATCGGTTCCCCTTCA
1871038 TGGGGGGA
1 TGGGGGGA
1871046 TCGATTCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCCCCTTCA
Found at i:1874906 original size:22 final size:21
Alignment explanation
Indices: 1874864--1874903 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1874854 GAGTTTGTTT
*
1874864 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1874885 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1874904 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1877627 original size:21 final size:21
Alignment explanation
Indices: 1877593--1877706 Score: 115
Period size: 21 Copynumber: 5.5 Consensus size: 21
1877583 ATACTGACTA
* * *
1877593 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
1877614 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
1877634 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
* * *
1877655 TCGCATTGTGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
1877675 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
*
1877696 TCGCAATGCGA
1 TCGCATTGCGA
1877707 ATTAGGAAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 33 0.45
21 41 0.55
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:1877637 original size:20 final size:20
Alignment explanation
Indices: 1877612--1877688 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
1877602 AATTTTCCTA
1877612 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
1877632 ATTCGCGTTGCGATTTTCAT
1 ATTCGCATTGCGATTTACGT
*
1877652 AATTCGCATTGTGATTTACGT
1 -ATTCGCATTGCGATTTACGT
*
1877673 ATTCGCGTTGCGATTT
1 ATTCGCATTGCGATTT
1877689 TCATAATTCG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 31 0.66
21 16 0.34
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1877648 original size:41 final size:41
Alignment explanation
Indices: 1877603--1877706 Score: 181
Period size: 41 Copynumber: 2.5 Consensus size: 41
1877593 TCGCAATGCA
*
1877603 ATTTTCCTAATTCGCATTGCGATTTACGTATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCGATTTACGTATTCGCGTTGCG
*
1877644 ATTTTCATAATTCGCATTGTGATTTACGTATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCGATTTACGTATTCGCGTTGCG
*
1877685 ATTTTCATAATTCGCAATGCGA
1 ATTTTCATAATTCGCATTGCGA
1877707 ATTAGGAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (41 bp):
ATTTTCATAATTCGCATTGCGATTTACGTATTCGCGTTGCG
Found at i:1877720 original size:21 final size:21
Alignment explanation
Indices: 1877696--1877749 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1877686 TTTTCATAAT
*
1877696 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
1877717 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
1877737 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1877750 CTTACTATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:1878315 original size:20 final size:21
Alignment explanation
Indices: 1878280--1878340 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
1878270 GAATAGTTTC
*
1878280 GAGAATGAAAATCGCAACGCG
1 GAGAATAAAAATCGCAACGCG
** *
1878301 GA-AATAACTATCGCAACG-A
1 GAGAATAAAAATCGCAACGCG
1878320 GAGAATAAAAATCGCAACGCG
1 GAGAATAAAAATCGCAACGCG
1878341 AAACCAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (21 bp):
GAGAATAAAAATCGCAACGCG
Found at i:1878349 original size:20 final size:19
Alignment explanation
Indices: 1878287--1878354 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
1878277 TTCGAGAATG
1878287 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
1878307 ACTATCGCAACGAGAGAATA
1 AAAATCGCAACGCGA-AATA
**
1878327 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1878346 AAAATCGCA
1 AAAATCGCA
1878355 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.49, C:0.24, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1878420 original size:20 final size:20
Alignment explanation
Indices: 1878397--1878443 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1878387 GTTGCAATAG
1878397 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
1878417 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
1878437 TCATTTC
1 TCATTTC
1878444 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:1883139 original size:20 final size:20
Alignment explanation
Indices: 1883079--1883144 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
1883069 TAGTTTACTT
* * **
1883079 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGACTA
*
1883099 TCGCAACGCGAAAATGACTA
1 TCGCAACACGAAAATGACTA
*
1883119 TCGCAACACGAAAATGGCTA
1 TCGCAACACGAAAATGACTA
1883139 TCGCAA
1 TCGCAA
1883145 TGCGAAATGC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.42, C:0.26, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1883150 original size:20 final size:20
Alignment explanation
Indices: 1883098--1883151 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1883088 GAAACTTAAA
1883098 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1883118 ATCGCAACACGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
1883138 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1883152 TGCAAATCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1883420 original size:18 final size:18
Alignment explanation
Indices: 1883394--1883438 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1883384 GTTGATCAGA
**
1883394 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGACGAGG
*
1883412 TGATAGCTCTGGACGAGG
1 TGATGGCTCTGGACGAGG
1883430 TGATGGCTC
1 TGATGGCTC
1883439 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGACGAGG
Found at i:1884782 original size:20 final size:19
Alignment explanation
Indices: 1884757--1884830 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
1884747 AATAGTTTCT
*
1884757 GAAAATGAAAATCGCAACAC
1 GAAAAT-AAAATCGCAACGC
*
1884777 GAAAATAACTATCGCAACGC
1 GAAAATAA-AATCGCAACGC
** **
1884797 GAATTTGACTATCGCAACGC
1 GAAAAT-AAAATCGCAACGC
*
1884817 GAAACTAAAATCGC
1 GAAAATAAAATCGC
1884831 GTTGCGATTC
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 8 0.19
20 34 0.79
21 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (19 bp):
GAAAATAAAATCGCAACGC
Found at i:1885302 original size:20 final size:20
Alignment explanation
Indices: 1885277--1885348 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
1885267 ATTATGTATT
1885277 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
1885297 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
1885317 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
1885337 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1885349 TTTTGTATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:1893029 original size:287 final size:286
Alignment explanation
Indices: 1892403--1893045 Score: 799
Period size: 287 Copynumber: 2.3 Consensus size: 286
1892393 GTAAATTTTG
* *
1892403 ATAAAAATATAATTTTAAGGACTAGATTGAACAAACATGAAATTACAAACT--GA---AAATAAA
1 ATAAAAATATAATTTTAAGGACTAAATTGAACAAACATGAAATTACAAACTAAAATTTAAATAAA
* * *
1892463 TTAGAA-AACACGCAGGGTTGAGCGATCAAATTGGAACAATTGTAAAATGTGAAGATGAAATTAA
66 TTA-AACAACACACA-GG-TGAGCGATCAAATCGAAACAATTGTAAAATGTGAAGATGAAATTAA
* * **
1892527 TATAAAAATGAATTAATTGCATCTATTTAAAAAGTTGGTGAACAAAAGTTTATAGAGTTTGGAGA
128 TATAAAAACGAATAAATTGCATCTATTTAAAAAGTTAATGAACAAAAGTTTATAGAGTTTGGAGA
* * * * *
1892592 TTATGATATAATTTATAGAGTTTGAAATAAAGTTTGTGATGTGGTTTATAGGGTTTGGAGTAATT
193 TTATGATAGAATTTATAGAGTTTGAAATAAAGTTTATGATGTGATTTATAAGGTTTGAAGTAATT
* * ** *
1892657 TAAAAAAAATAAGTATGTTCCAATTTCAT
258 AAAAAAAAATAAATATGAGCCAATTTCAA
* ** * *
1892686 ATAAAAATATCATTTTAAAAAGTAAATTGAACAAACATGAAATTACAAATTAAAATTTAAATAAA
1 ATAAAAATATAATTTTAAGGACTAAATTGAACAAACATGAAATTACAAACTAAAATTTAAATAAA
* *
1892751 TTAAACAACACACA-G-G-G-G-TCAAATCGAAACAATTGTAAAATGTGGAGCTGAAATTAATAT
66 TTAAACAACACACAGGTGAGCGATCAAATCGAAACAATTGTAAAATGTGAAGATGAAATTAATAT
*
1892811 AAAAAACGAACTAAATTGCAT-TCATTTAAAAAGTTAATGAACAAAATTTTATA-AGGTTTTGGA
131 -AAAAACGAA-TAAATTGCATCT-ATTTAAAAAGTTAATGAACAAAAGTTTATAGA-G-TTTGGA
* *
1892874 GATTATGATAGAGATTTATAGGGTTTGAAATGAAGTTTATGATGTGATTTATAAGGTTTGAAGTA
191 GATTATGATAGA-ATTTATAGAGTTTGAAATAAAGTTTATGATGTGATTTATAAGGTTTGAAGT-
1892939 AATTAAAAAAAATATAAATATGAGCCAATTTCAA
254 AATTAAAAAAAA-ATAAATATGAGCCAATTTCAA
* * * *
1892973 ATAAAAATATAATTTTAAGGATTAAATTGAACAAACATAAAATTTCAAACTAAAATTTAAATAAT
1 ATAAAAATATAATTTTAAGGACTAAATTGAACAAACATGAAATTACAAACTAAAATTTAAATAAA
1893038 TTAAACAA
66 TTAAACAA
1893046 AATAAAGTGA
Statistics
Matches: 309, Mismatches: 37, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
281 38 0.12
282 11 0.04
283 83 0.27
284 18 0.06
285 46 0.15
286 12 0.04
287 84 0.27
288 17 0.06
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (286 bp):
ATAAAAATATAATTTTAAGGACTAAATTGAACAAACATGAAATTACAAACTAAAATTTAAATAAA
TTAAACAACACACAGGTGAGCGATCAAATCGAAACAATTGTAAAATGTGAAGATGAAATTAATAT
AAAAACGAATAAATTGCATCTATTTAAAAAGTTAATGAACAAAAGTTTATAGAGTTTGGAGATTA
TGATAGAATTTATAGAGTTTGAAATAAAGTTTATGATGTGATTTATAAGGTTTGAAGTAATTAAA
AAAAAATAAATATGAGCCAATTTCAA
Found at i:1901234 original size:20 final size:20
Alignment explanation
Indices: 1901209--1901247 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1901199 ATGTAAATCG
*
1901209 CAACACAGAAGTCAAATTCA
1 CAACACAGAAATCAAATTCA
1901229 CAACACAGAAATCAAATTC
1 CAACACAGAAATCAAATTC
1901248 GTAAAGCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.26, G:0.08, T:0.15
Consensus pattern (20 bp):
CAACACAGAAATCAAATTCA
Found at i:1901834 original size:14 final size:14
Alignment explanation
Indices: 1901815--1901842 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1901805 TTGCGTTGTG
1901815 ATTTTCATTTTCGT
1 ATTTTCATTTTCGT
1901829 ATTTTCATTTTCGT
1 ATTTTCATTTTCGT
1901843 GTTGCGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (14 bp):
ATTTTCATTTTCGT
Found at i:1901854 original size:20 final size:20
Alignment explanation
Indices: 1901831--1901873 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1901821 ATTTTCGTAT
1901831 TTTCATTTTCGTGTTGCGAA
1 TTTCATTTTCGTGTTGCGAA
1901851 TTTCATTTTCGTGTTGCGAA
1 TTTCATTTTCGTGTTGCGAA
1901871 TTT
1 TTT
1901874 AAGTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (20 bp):
TTTCATTTTCGTGTTGCGAA
Found at i:1903565 original size:21 final size:21
Alignment explanation
Indices: 1903536--1903585 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1903526 GTTAAGGGAG
* * *
1903536 TTACATGATGAGGTTAGTGCT
1 TTACGTGATGAGGTCAGTACT
*
1903557 TTGCGTGATGAGGTCAGTACT
1 TTACGTGATGAGGTCAGTACT
1903578 TTACGTGA
1 TTACGTGA
1903586 CGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:1903626 original size:21 final size:22
Alignment explanation
Indices: 1903602--1903697 Score: 58
Period size: 21 Copynumber: 4.5 Consensus size: 22
1903592 TGGTGCATGG
1903602 CGTGATGAGGTACGGT-CTTTA
1 CGTGATGAGGTACGGTACTTTA
* * **
1903623 CGTGGTGAGGTA-GATGTTTTA
1 CGTGATGAGGTACGGTACTTTA
* ** * *
1903644 CGCGATGA-CAATGGTGCTTTA
1 CGTGATGAGGTACGGTACTTTA
*
1903665 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTA-CGGTACTTTA
1903686 CGTGATGAGGTA
1 CGTGATGAGGTA
1903698 GCCGCTCTAC
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
20 3 0.05
21 51 0.93
22 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.33, T:0.33
Consensus pattern (22 bp):
CGTGATGAGGTACGGTACTTTA
Found at i:1903674 original size:63 final size:63
Alignment explanation
Indices: 1903555--1903698 Score: 150
Period size: 63 Copynumber: 2.3 Consensus size: 63
1903545 GAGGTTAGTG
* ** * *
1903555 CTTTGCGTGATGAGGTCAG-TACTTTACGTGACGACAATGGTGCATGGCGTGATGAGGTA-CGGT
1 CTTTACGTGATGAGGT-AGATGTTTTACGCGACGACAATGGTGCATGACGTGATGAGGTATC--T
1903618 -
63 A
* * * * *
1903618 CTTTACGTGGTGAGGTAGATGTTTTACGCGATGACAATGGTGCTTTACGTGGTGAGGTATCTA
1 CTTTACGTGATGAGGTAGATGTTTTACGCGACGACAATGGTGCATGACGTGATGAGGTATCTA
1903681 CTTTACGTGATGAGGTAG
1 CTTTACGTGATGAGGTAG
1903699 CCGCTCTACG
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
62 3 0.04
63 63 0.94
64 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.32
Consensus pattern (63 bp):
CTTTACGTGATGAGGTAGATGTTTTACGCGACGACAATGGTGCATGACGTGATGAGGTATCTA
Found at i:1904021 original size:21 final size:21
Alignment explanation
Indices: 1903985--1904063 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
1903975 GATTCACTTG
*
1903985 TCATCTTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
1904006 -CTATCGTTCAAAAGGCCCCTT
1 TC-ATCGTTCAAGAGGCCCCTC
*
1904027 TCATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1904048 TCATCGTTCAAGAGGC
1 TCATCGTTCAAGAGGC
1904064 TCTTCCCACC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
20 1 0.02
21 47 0.96
22 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1904077 original size:42 final size:42
Alignment explanation
Indices: 1903991--1904082 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
1903981 CTTGTCATCT
* *
1903991 TTCAAGAGGCCCCTCCTATCGTTCAAAAGGCCCCTTTCATCA
1 TTCAAGAGGCCCCTCCTATCGTTCAAAAGGCCCCTTCCACCA
* *
1904033 TTCAAGAGGCCCCT-CTCATCGTTCAAGAGG-CTCTTCCCACCA
1 TTCAAGAGGCCCCTCCT-ATCGTTCAAAAGGCCCCTT-CCACCA
1904075 TTCAAGAG
1 TTCAAGAG
1904083 CCTGATTCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 6 0.14
42 38 0.86
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.25
Consensus pattern (42 bp):
TTCAAGAGGCCCCTCCTATCGTTCAAAAGGCCCCTTCCACCA
Done.