Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 30
Found at i:4429743 original size:45 final size:45
Alignment explanation
Indices: 4429687--4429884 Score: 254
Period size: 45 Copynumber: 4.4 Consensus size: 45
4429677 TTAATTTTAT
* * * *
4429687 CAACCCAATAATCAAAAGGAACTAGTCATTTGATTTTATTTTTCG
1 CAACACAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTGG
* * * * *
4429732 CAATACAATAATCGAAATGAACTAATCCTTTGATTTTATTTTTGG
1 CAACACAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTGG
* *
4429777 CAACACAATAATCGAAATGAACTAAT-ACTTTGATTTTACTTTTGG
1 CAACACAATAATCAAAAGGAACTAATCA-TTTGATTTTACTTTTGG
*
4429822 CAACACAATAATCAAAAGGAACTAATCCTTTGATTTTACTTTTGG
1 CAACACAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTGG
* *
4429867 TAACCCAATAATCAAAAG
1 CAACACAATAATCAAAAG
4429885 CCTTGAATTA
Statistics
Matches: 136, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (45 bp):
CAACACAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTGG
Found at i:4429809 original size:90 final size:90
Alignment explanation
Indices: 4429687--4429884 Score: 281
Period size: 90 Copynumber: 2.2 Consensus size: 90
4429677 TTAATTTTAT
* * * * *
4429687 CAACCCAATAATCAAAAGGAACTAGTCATTTGATTTTATTTTTCGCAATACAATAATCGAAATGA
1 CAACCCAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTCGCAACACAATAATCAAAAGGA
*
4429752 ACTAATCCTTTGATTTTATTTTTGG
66 ACTAATCCTTTGATTTTACTTTTGG
* * * *
4429777 CAACACAATAATCGAAATGAACTAAT-ACTTTGATTTTACTTTTGGCAACACAATAATCAAAAGG
1 CAACCCAATAATCAAAAGGAACTAATCA-TTTGATTTTACTTTTCGCAACACAATAATCAAAAGG
4429841 AACTAATCCTTTGATTTTACTTTTGG
65 AACTAATCCTTTGATTTTACTTTTGG
*
4429867 TAACCCAATAATCAAAAG
1 CAACCCAATAATCAAAAG
4429885 CCTTGAATTA
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 1 0.01
90 92 0.99
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (90 bp):
CAACCCAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTCGCAACACAATAATCAAAAGGA
ACTAATCCTTTGATTTTACTTTTGG
Found at i:4432055 original size:2 final size:2
Alignment explanation
Indices: 4432048--4432099 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4432038 GATCTAACCC
4432048 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
4432090 AT AT AT AT AT
1 AT AT AT AT AT
4432100 TAGAAAATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4433858 original size:18 final size:18
Alignment explanation
Indices: 4433823--4433856 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4433813 TGTTATTTAC
*
4433823 GTATCGTTACTCAAGGGA
1 GTATCGATACTCAAGGGA
4433841 GTATCGATAC-CAAGGG
1 GTATCGATACTCAAGGG
4433857 GATAGTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (18 bp):
GTATCGATACTCAAGGGA
Found at i:4436473 original size:24 final size:24
Alignment explanation
Indices: 4436441--4436491 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
4436431 ATCCAAGAGG
4436441 CCATTCAAAAAGTGTTATCAACGT
1 CCATTCAAAAAGTGTTATCAACGT
4436465 CCATTCAAAAAGTGTTATCAACGT
1 CCATTCAAAAAGTGTTATCAACGT
4436489 CCA
1 CCA
4436492 ACTGAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (24 bp):
CCATTCAAAAAGTGTTATCAACGT
Found at i:4438497 original size:29 final size:29
Alignment explanation
Indices: 4438454--4438536 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
4438444 CTCACCTAAC
4438454 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
4438484 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
4438513 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
4438537 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:4441692 original size:15 final size:15
Alignment explanation
Indices: 4441672--4441701 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4441662 CTTTCTCATA
4441672 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
4441687 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
4441702 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:4443032 original size:29 final size:29
Alignment explanation
Indices: 4442989--4443071 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
4442979 CTCACCTAAC
4442989 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
4443019 TAAATGATGTAAGCAATGCCATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
4443048 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
4443072 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:4445537 original size:17 final size:16
Alignment explanation
Indices: 4445515--4445549 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4445505 TTATGAGGTG
*
4445515 AAAATATTATTATTATA
1 AAAATATAATTATT-TA
4445532 AAAATATAATTATTTA
1 AAAATATAATTATTTA
4445548 AA
1 AA
4445550 CTAATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATATAATTATTTA
Found at i:4463496 original size:36 final size:36
Alignment explanation
Indices: 4463449--4463523 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
4463439 AGAAAACTCA
4463449 TATGAAATTTTCAAAAATAAAAAGCCTAACATTAGC
1 TATGAAATTTTCAAAAATAAAAAGCCTAACATTAGC
4463485 TATGAAATTTTCAAAAATAAAAAGCCTAACATTAGC
1 TATGAAATTTTCAAAAATAAAAAGCCTAACATTAGC
4463521 TAT
1 TAT
4463524 TTTCATCCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.29
Consensus pattern (36 bp):
TATGAAATTTTCAAAAATAAAAAGCCTAACATTAGC
Found at i:4467203 original size:26 final size:26
Alignment explanation
Indices: 4467170--4467229 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
4467160 TGGACATCAT
*
4467170 AAACATTGTTCCTTCAAAACATGTTG
1 AAACATTGTTCATTCAAAACATGTTG
*
4467196 AAATATTGTTCATTCAAAACATGTTG
1 AAACATTGTTCATTCAAAACATGTTG
4467222 AAACATTG
1 AAACATTG
4467230 ATTTATGGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (26 bp):
AAACATTGTTCATTCAAAACATGTTG
Found at i:4468592 original size:65 final size:65
Alignment explanation
Indices: 4468523--4468684 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
4468513 AATTAAATTG
* * *
4468523 AACATCGAATGCATTTCATGCATCGATGCACTTA-CCATGCACCAATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCAATGCACTCAGGATATTT-TG
4468586 AA
65 -A
* * * *
4468588 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCAATGCACTCAGGATATTTTGA
*
4468652 AACATCGAATGCACTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
4468685 TTAGTGAACC
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
64 32 0.37
65 51 0.59
66 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCAATGCACTCAGGATATTTTGA
Found at i:4469712 original size:2 final size:2
Alignment explanation
Indices: 4469697--4469752 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
4469687 AACAAAATAA
4469697 AT AT AT A- AT A- AT AT AT -T GAT 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
4469737 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
4469753 TTATGTTGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 46 0.92
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4470295 original size:84 final size:84
Alignment explanation
Indices: 4470179--4471057 Score: 1062
Period size: 84 Copynumber: 10.5 Consensus size: 84
4470169 AACTCAATAA
* * * * * ** *
4470179 TTTTTTTGTCAGATAGCCCTTCTTGCCTTGAGTTATGCTGTAAATGATGTTACTTTAAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
4470244 GTAATCGAACTCGTAGGTC
66 GTAATCGAACTCGAAGGTC
** * * *
4470263 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATATGCCTTTGAGCTAAAT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
4470328 GTAATAGAACTCGAAGATC
66 GTAATCGAACTCGAAGGTC
* * * * *
4470347 -TTTGTTGACAAATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTTGAGCTGAAT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
4470411 GTAATCAAACTCGAAGGT-
66 GTAATCGAACTCGAAGGTC
* * ** * * ** * *
4470429 ATTTGGTGATAGATAACCCTTCTAGCATTGAGTTATGTTATAAATGATGTGCCCTTGAGCTAAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
4470494 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* ** * * * * * * *
4470513 TTTGGCAGGTAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTTAAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
4470578 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * *
4470597 TTTTGTTGGCAGATAACTCTTCTTGCCTTGAGCTATACTGCAAATGTTGTGCCTTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
4470662 ATAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * *
4470681 TTTTGTTGGCATATAACCCTTCTAGCCTTGAGTTGTGCTGCAAATGATGTGCCTTGGAACTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
4470746 ATAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * *
4470765 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
4470830 GTAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * *
4470849 TTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
4470914 GTAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * *
4470933 TTTTGTTGGCAAATAACCCTTCTCA-CCTTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCT-AGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAG
* *
4470997 TGTAATCAAACTTGAAGGTC
65 TGTAATCGAACTCGAAGGTC
*
4471017 TTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
4471058 CAAAAGTTTC
Statistics
Matches: 693, Mismatches: 98, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
83 147 0.21
84 545 0.79
85 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
GTAATCGAACTCGAAGGTC
Found at i:4474593 original size:20 final size:20
Alignment explanation
Indices: 4474564--4474601 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4474554 CAGAACCCCA
*
4474564 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
4474584 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
4474602 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:4474637 original size:21 final size:21
Alignment explanation
Indices: 4474584--4474645 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
4474574 ATTCCCCTGT
4474584 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
**
4474607 GGGGGAATCGGTTCCCTCATG
1 GGGGGAATCGGTTCCCTCAAA
* *
4474628 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
4474646 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:4481989 original size:95 final size:94
Alignment explanation
Indices: 4481788--4482051 Score: 305
Period size: 95 Copynumber: 2.7 Consensus size: 94
4481778 AGCTAGTTGA
4481788 ATCCATAAAGCAGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAATATCATTGTA-TATAT
1 ATCCATAAAGC-GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAA-A-C-TT-TATTATAT
* * *
4481852 ATTATAATCATCTTTATCAGGCTAGCTAAATATT
61 ATTATAATAACCTTTATCAGACTAGCTAAATATT
* ** * *
4481886 ATCCATAAAGTCGAGGCGTTTAGTCAATTGCTCTAGCGGGACAACTCAAACTTTATTATATATTA
1 ATCCATAAAG-CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAAACTTTATTATATATTA
* *
4481951 TAATAACCTTTATCAGACTAGCTGAATCTT
65 TAATAACCTTTATCAGACTAGCTAAATATT
* * * * * *
4481981 ATCCATAAAGCCGGGGAGTTTAACCAATTGCTTTAGATGGATAACTTAAGCTTTATTGTATATAT
1 ATCCATAAAG-CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAAACTTTATTATATAT-T
4482046 ATAATA
64 ATAATA
4482052 TTATAATCTG
Statistics
Matches: 141, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
94 2 0.01
95 87 0.62
96 8 0.06
97 1 0.01
98 42 0.30
99 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (94 bp):
ATCCATAAAGCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAAACTTTATTATATATTAT
AATAACCTTTATCAGACTAGCTAAATATT
Found at i:4484943 original size:13 final size:13
Alignment explanation
Indices: 4484925--4484950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4484915 GTTTACCCTT
4484925 GAAAAAAATAAAA
1 GAAAAAAATAAAA
4484938 GAAAAAAATAAAA
1 GAAAAAAATAAAA
4484951 ATATATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
GAAAAAAATAAAA
Found at i:4486112 original size:2 final size:2
Alignment explanation
Indices: 4486033--4486095 Score: 87
Period size: 2 Copynumber: 32.0 Consensus size: 2
4486023 AACAAAATAA
4486033 AT AT AT A- AT A- AT AT AGT GAT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT AT
4486074 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
4486096 GCTATATGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.05
2 50 0.89
3 2 0.04
4 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4486880 original size:12 final size:12
Alignment explanation
Indices: 4486863--4486893 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4486853 TTAGCATAAA
4486863 CGGGTATCGGGC
1 CGGGTATCGGGC
4486875 CGGGTATCGGGC
1 CGGGTATCGGGC
4486887 CGGGTAT
1 CGGGTAT
4486894 ATATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.19
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:4486898 original size:2 final size:2
Alignment explanation
Indices: 4486891--4486989 Score: 59
Period size: 2 Copynumber: 53.0 Consensus size: 2
4486881 TCGGGCCGGG
* * * *
4486891 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
4486931 TA TA TT TA -A TT TA -A TT TA AA TT TA T- TA -A AA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4486968 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
4486990 ATAATTAATT
Statistics
Matches: 71, Mismatches: 19, Indels: 14
0.68 0.18 0.13
Matches are distributed among these distances:
1 7 0.10
2 64 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4486950 original size:41 final size:41
Alignment explanation
Indices: 4486898--4486976 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 41
4486888 GGGTATATAT
4486898 ATTTAAATTAAATATA-TAAATATTATATATATATATATTTA
1 ATTTAAATTAAATATATTAAA-ATTATATATATATATATTTA
* *
4486939 ATTTAATTTAAATTTATTAAAATTATATATATATATAT
1 ATTTAAATTAAATATATTAAAATTATATATATATATAT
4486977 ATATATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 31 0.89
42 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (41 bp):
ATTTAAATTAAATATATTAAAATTATATATATATATATTTA
Found at i:4495989 original size:27 final size:27
Alignment explanation
Indices: 4495943--4496010 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
4495933 GTTTAGGAAT
4495943 TATAGAGATA--ATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
4495968 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
4495995 TATAGAGATATGATTT
1 TATAGAGATATGATTT
4496011 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 10 0.24
27 31 0.76
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:4499760 original size:27 final size:27
Alignment explanation
Indices: 4499721--4499773 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
4499711 ATAGAGATGA
*
4499721 TTTGTTACTATTCCTATAGAGATATGG
1 TTTGTTACCATTCCTATAGAGATATGG
4499748 TTTGTTACCATTCCTATAGAGATATG
1 TTTGTTACCATTCCTATAGAGATATG
4499774 ATTTTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (27 bp):
TTTGTTACCATTCCTATAGAGATATGG
Found at i:4524091 original size:24 final size:24
Alignment explanation
Indices: 4524033--4524094 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
4524023 CGTTCGTGAA
4524033 CGTTCAGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* * *
4524057 CATTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
4524081 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
4524095 TAACCTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:4524368 original size:33 final size:33
Alignment explanation
Indices: 4524326--4524415 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
4524316 ATTTTCATTT
4524326 CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
1 CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
4524359 CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
1 CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
* *
4524392 CTGCAACAATTCGACAGAGCTTCA
1 CTGCAACGATTCGACGGAGCTTCA
4524416 TCTCTTTCCC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (33 bp):
CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
Found at i:4525667 original size:16 final size:16
Alignment explanation
Indices: 4525642--4525698 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
4525632 CCAACGTTTA
4525642 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
4525658 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
4525674 TCTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
4525690 TGTTCGTTT
1 TGTTCGTTT
4525699 TATTAAATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.07, C:0.12, G:0.21, T:0.60
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:4525784 original size:16 final size:16
Alignment explanation
Indices: 4525763--4525794 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4525753 AAAAAAATTT
4525763 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4525779 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4525795 CTTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:4528232 original size:20 final size:22
Alignment explanation
Indices: 4528196--4528253 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
4528186 TTCCCCTTGA
**
4528196 AGTGCATCGATATATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
4528216 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
4528239 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
4528254 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
22 1 0.03
23 3 0.09
24 13 0.41
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:4531800 original size:129 final size:126
Alignment explanation
Indices: 4531562--4531817 Score: 444
Period size: 129 Copynumber: 2.0 Consensus size: 126
4531552 AACTTCTTTC
4531562 ACATGTACCTGTAATCGGTAGCTTCTTTTCACGTAGTTCAGTCACTTTTCATATCATTCATTTAT
1 ACATGTACCTGTAATCGGTAGCTTCTTTTCACGTAGTTCAGTCACTTTTCATATCATTCATTTAT
4531627 CCATACATAATCTCTATCATATATACATTTCTTCACTTATCTCATAGTTATGTATCATATTACA
66 CCATACATAATCTCTATCATATATACA-TTCTTCACTTATCTCATAGTTA--TATCATATTACA
4531691 ACATGTACCTGTAATCAGGTAGCTTCTTTTCACGTAGTTCATGTCACTTTTCATATCATTCATTT
1 ACATGTACCTGTAATC-GGTAGCTTCTTTTCACGTAGTTCA-GTCACTTTTCATATCATTCATTT
4531756 ATCACATACATAATCTCTATCATATATACA-T-TTCACTTATCTCATAGTTATATCATATTACA
64 ATC-CATACATAATCTCTATCATATATACATTCTTCACTTATCTCATAGTTATATCATATTACA
4531818 TAATTACTTA
Statistics
Matches: 124, Mismatches: 0, Indels: 8
0.94 0.00 0.06
Matches are distributed among these distances:
127 12 0.10
129 35 0.28
130 25 0.20
131 26 0.21
132 26 0.21
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.42
Consensus pattern (126 bp):
ACATGTACCTGTAATCGGTAGCTTCTTTTCACGTAGTTCAGTCACTTTTCATATCATTCATTTAT
CCATACATAATCTCTATCATATATACATTCTTCACTTATCTCATAGTTATATCATATTACA
Found at i:4532273 original size:24 final size:20
Alignment explanation
Indices: 4532220--4532277 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
4532210 TCCCCCTTGA
*
4532220 AGTGCATCGATGTATTCTAC
1 AGTGCATCGATGCATTCTAC
4532240 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
4532263 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
4532278 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:4532364 original size:78 final size:78
Alignment explanation
Indices: 4532279--4532435 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
4532269 ATCGATGCAC
4532279 TACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAAGGGATGCATCGATGCACT
1 TACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAAGGGATGCATCGATGCACT
4532344 CCTTATGCATCAA
66 CCTTATGCATCAA
4532357 TACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAAGGGATGCATCGATGCACT
1 TACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAAGGGATGCATCGATGCACT
4532422 CCTTATGCATCAA
66 CCTTATGCATCAA
4532435 T
1 T
4532436 GCACCAATTG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (78 bp):
TACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAAGGGATGCATCGATGCACT
CCTTATGCATCAA
Found at i:4535258 original size:94 final size:94
Alignment explanation
Indices: 4535160--4535336 Score: 345
Period size: 94 Copynumber: 1.9 Consensus size: 94
4535150 ATAAGTCATT
4535160 ATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATATCATCATATATAAGTCATTT
1 ATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATATCATCATATATAAGTCATTT
*
4535225 ATGCTCACTCACATATACTATTATACTTC
66 ATACTCACTCACATATACTATTATACTTC
4535254 ATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATATCATCATATATAAGTCATTT
1 ATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATATCATCATATATAAGTCATTT
4535319 ATACTCACTCACATATAC
66 ATACTCACTCACATATAC
4535337 ATCAACATAT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 82 1.00
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (94 bp):
ATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATATCATCATATATAAGTCATTT
ATACTCACTCACATATACTATTATACTTC
Found at i:4535306 original size:50 final size:50
Alignment explanation
Indices: 4535155--4535307 Score: 135
Period size: 50 Copynumber: 3.2 Consensus size: 50
4535145 CATGTATAAG
*
4535155 TCATTATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATA
1 TCATCATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATA
* * * * * * *
4535205 TCATCATA--T-ATA-AGTC--ATT-TAT-GCTCACTCACATATAC-TATTA
1 TCATCATATCTCTTACATTCATATTCTATAACTTA-TAACAAATTCTTA-TA
*
4535248 TACTTCATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATA
1 T-CATCATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATA
4535299 TCATCATAT
1 TCATCATAT
4535308 ATAAGTCATT
Statistics
Matches: 74, Mismatches: 17, Indels: 24
0.64 0.15 0.21
Matches are distributed among these distances:
42 5 0.07
43 13 0.18
44 9 0.12
46 4 0.05
47 4 0.05
48 4 0.05
50 17 0.23
51 13 0.18
52 5 0.07
ACGTcount: A:0.35, C:0.20, G:0.01, T:0.44
Consensus pattern (50 bp):
TCATCATATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATA
Found at i:4536507 original size:64 final size:63
Alignment explanation
Indices: 4536420--4536560 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
4536410 TCTTTAACAT
* *
4536420 GTGCATCGATGCACTACCAATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACTACCAATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * ** *
4536483 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGTATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-AATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
*
4536547 GTGCAGCGATGCAC
1 GTGCATCGATGCAC
4536561 ATTCAATGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 20 0.30
64 46 0.70
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACCAATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:4540404 original size:20 final size:20
Alignment explanation
Indices: 4540379--4540416 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4540369 TCCCCCTTGA
4540379 AGTGCATCGATGTATTCTAC
1 AGTGCATCGATGTATTCTAC
4540399 AGTGCATCGATGTATTCT
1 AGTGCATCGATGTATTCT
4540417 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGTATTCTAC
Found at i:4540511 original size:64 final size:63
Alignment explanation
Indices: 4540428--4540564 Score: 161
Period size: 64 Copynumber: 2.2 Consensus size: 63
4540418 TAACATGTGA
* *
4540428 ATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGGGATGC
1 ATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGAG-TGC
* * * * *
4540492 ATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGAGTGC
1 ATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGAGTGC
*
4540555 ATCGAAGCAC
1 ATCGATGCAC
4540565 ATTCAATGTG
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
63 19 0.30
64 44 0.70
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (63 bp):
ATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGAGTGC
Found at i:4544423 original size:24 final size:20
Alignment explanation
Indices: 4544366--4544403 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4544356 TTCCCCTTGA
4544366 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
4544386 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
4544404 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:4544487 original size:64 final size:63
Alignment explanation
Indices: 4544411--4544551 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 63
4544401 TCTTTAACAT
* * *
4544411 GTGCATTGATGCACTACC-CATGGATCGATACACAAATTACCTTCGAT-TTT-TTCATTTTAAA-
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATGTTTCTTC--TTTAAAG
4544472 A
63 A
* * *
4544473 GGATGCATCGATGCACTCCTTATGCATCGATACACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 -G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
4544538 GTGCATCGATGCAC
1 GTGCATCGATGCAC
4544552 ATTCAATGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
63 16 0.24
64 44 0.66
65 4 0.06
66 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
Found at i:4548414 original size:2 final size:2
Alignment explanation
Indices: 4548407--4548434 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4548397 AGATTTTAGA
4548407 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
4548435 TATTTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4550686 original size:210 final size:210
Alignment explanation
Indices: 4550341--4551165 Score: 1013
Period size: 210 Copynumber: 3.9 Consensus size: 210
4550331 TCGCCTGATT
* ** *
4550341 TGCACAATCCA-CATATCAAAC-ATTCGTAGGTGACAGCGTTAGGTTTTACATTTCTCTGACTCA
1 TGCACAATCCATGA-ATCAAACAATT-GTAGGTGACAATGTTGGGTTTTACATTTCTCTGACTCA
* ** * *
4550404 TTACTTCCAACAAGGAAATGGCTTCTTC--TGTTCTTCCTTCCTTGCATAAAGTATCGATCAAAG
64 TTACTTCCAACATGGAAATGGCTTCTTCAATCCTCTT--TTCCTTGCATAAAGCATCGATTAAAG
* * ** *
4550467 AATTGAAAGTTACTGCATCAGGATGGACTCCTTCATTCATCATTCTATTGAGCAATCTTGTTGCT
127 AATTGAAAGTTACTACATCAGGATGGACTCCTCCATTCATCATTCTATCAAGCAAGCTTGTTGCT
*
4550532 TCTGCCCATTTATTTGAAC
192 TCTGCCCATTTATTTGAAG
* * *
4550551 TGCACAATGCATGAATTAAACAATTGTAGGTGACAATGTTGGGTATTACATTTCTCTGACTCATT
1 TGCACAATCCATGAATCAAACAATTGTAGGTGACAATGTTGGGTTTTACATTTCTCTGACTCATT
* * * ** * * * *
4550616 AGTTCCATCATGGAAATGGTTTCTTCTGTTCTCTTTTTCTTGCATAAAGCACCGATTAAAGAACT
66 ACTTCCAACATGGAAATGGCTTCTTCAATCCTCTTTTCCTTGCATAAAGCATCGATTAAAGAATT
* * *
4550681 GAAAGTTACTACATCAGGATGGACTCCTTCATTCATCATTCTATCAAGCAAGTTTGTTGCTTCTT
131 GAAAGTTACTACATCAGGATGGACTCCTCCATTCATCATTCTATCAAGCAAGCTTGTTGCTTCTG
*
4550746 TCCATTTATTTGAAG
196 CCCATTTATTTGAAG
** * * *
4550761 TGCACAATCCATTTATCAAACAATTGTATGTGACAATGTTGGGCTTTACATTTCTCTGTCTCATT
1 TGCACAATCCATGAATCAAACAATTGTAGGTGACAATGTTGGGTTTTACATTTCTCTGACTCATT
* ** *
4550826 ACTTCCAACATGGCAATGGAATCTTCAATCCTCTTTTCCTTGCATAAAGCATCAATTAAAGAATT
66 ACTTCCAACATGGAAATGGCTTCTTCAATCCTCTTTTCCTTGCATAAAGCATCGATTAAAGAATT
* * *
4550891 GAAGGTTACCACATCAGGATGGACTCCTCCATTCATCATACTATCAAGCAAGCTTGTTGCTTCTG
131 GAAAGTTACTACATCAGGATGGACTCCTCCATTCATCATTCTATCAAGCAAGCTTGTTGCTTCTG
*
4550956 TCCATTTATTTGAAG
196 CCCATTTATTTGAAG
* *
4550971 TGCACAATCCATGCATCAAACAATTGTAGGTGACAA---T-GGTTTTACATTTCTCTAACTCATT
1 TGCACAATCCATGAATCAAACAATTGTAGGTGACAATGTTGGGTTTTACATTTCTCTGACTCATT
* * * *
4551032 AGTTCGAACATGGAAATGGCTTCTTCAATCCTCCTTTT-CTTGCATAAAGCATTGATTATAGAAT
66 ACTTCCAACATGGAAATGGCTTCTTCAATCCT-CTTTTCCTTGCATAAAGCATCGATTAAAGAAT
* ** * * *
4551096 TGAAAGTTAGTACCCCAGGATGGACT-CTGCCATTCATCATCCTATCGAGCAAGCTTGTCGCTTC
130 TGAAAGTTACTACATCAGGATGGACTCCT-CCATTCATCATTCTATCAAGCAAGCTTGTTGCTTC
*
4551160 TTCCCA
194 TGCCCA
4551166 CCGTCCAGAA
Statistics
Matches: 533, Mismatches: 76, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
205 2 0.00
206 128 0.24
207 6 0.01
210 388 0.73
211 4 0.01
212 5 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (210 bp):
TGCACAATCCATGAATCAAACAATTGTAGGTGACAATGTTGGGTTTTACATTTCTCTGACTCATT
ACTTCCAACATGGAAATGGCTTCTTCAATCCTCTTTTCCTTGCATAAAGCATCGATTAAAGAATT
GAAAGTTACTACATCAGGATGGACTCCTCCATTCATCATTCTATCAAGCAAGCTTGTTGCTTCTG
CCCATTTATTTGAAG
Found at i:4552144 original size:21 final size:20
Alignment explanation
Indices: 4552117--4552215 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
4552107 AATCAGTTTC
4552117 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
4552138 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
4552159 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
4552179 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
4552200 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
4552216 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:4552244 original size:20 final size:20
Alignment explanation
Indices: 4552182--4552375 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
4552172 CGATTTTCCA
* ** *
4552182 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
4552202 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
4552222 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4552242 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
4552262 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
4552282 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4552302 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
4552322 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
4552342 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
4552363 AAATCGCAACGCG
1 AAATCGCAACGCG
4552376 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:4552266 original size:60 final size:60
Alignment explanation
Indices: 4552182--4552375 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
4552172 CGATTTTCCA
* ** * *
4552182 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
4552242 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
4552302 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
4552363 AAATCGCAACGCG
1 AAATCGCAACGCG
4552376 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:4552797 original size:33 final size:33
Alignment explanation
Indices: 4552758--4552828 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
4552748 TTCACTTAGA
*
4552758 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
4552791 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
4552824 TTTCA
1 TTTCA
4552829 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:4552952 original size:20 final size:20
Alignment explanation
Indices: 4552908--4553017 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
4552898 TGCAGAAGAG
*
4552908 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
4552929 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
4552949 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
4552970 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
4552984 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
4553003 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
4553018 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:4552965 original size:41 final size:38
Alignment explanation
Indices: 4552901--4553017 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
4552891 TTCAATTTGC
* *
4552901 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
4552939 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
4552980 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
4553013 AGAAT
1 AGAAT
4553018 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:4552987 original size:14 final size:14
Alignment explanation
Indices: 4552968--4553024 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4552958 GAGAAATGAA
4552968 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4552982 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4553001 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4553015 AATCGCAACG
1 AATCGCAACG
4553025 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4553000 original size:33 final size:33
Alignment explanation
Indices: 4552960--4553040 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
4552950 CGCAACGAGA
4552960 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4552993 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
4553026 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
4553041 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:4553058 original size:19 final size:19
Alignment explanation
Indices: 4553036--4553149 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
4553026 GAAACCAAAA
*
4553036 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4553055 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4553074 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
4553088 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
4553108 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
4553128 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
4553148 TC
1 TC
4553150 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 31 0.39
20 19 0.24
21 14 0.17
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4553111 original size:21 final size:21
Alignment explanation
Indices: 4553085--4553149 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
4553075 CGCGTTGCGA
4553085 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
4553106 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
4553126 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
4553147 TTC
1 TTC
4553150 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:4555011 original size:93 final size:93
Alignment explanation
Indices: 4554852--4555134 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
4554842 TAGATTGCTT
*
4554852 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4554917 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4554945 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4555010 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4555038 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4555103 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4555130 AGTAA
1 AGTAA
4555135 TGCAATCCAT
Statistics
Matches: 189, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 6 0.03
93 183 0.97
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:4555222 original size:19 final size:19
Alignment explanation
Indices: 4555182--4555310 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
4555172 TAGGTTACTT
* *
4555182 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
4555202 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
4555221 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
4555240 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
4555254 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
4555273 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
4555287 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
4555306 TCGCA
1 TCGCA
4555311 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:4555261 original size:33 final size:32
Alignment explanation
Indices: 4555218--4555310 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
4555208 CGCGAAACCA
**
4555218 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
4555250 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
4555283 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
4555311 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:4555308 original size:52 final size:52
Alignment explanation
Indices: 4555182--4555310 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
4555172 TAGGTTACTT
**
4555182 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
4555234 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
4555287 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
4555311 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:4555328 original size:19 final size:19
Alignment explanation
Indices: 4555306--4555478 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
4555296 GAAACCAAAA
*
4555306 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4555325 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
4555341 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
4555358 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
4555374 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
4555391 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
4555410 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
4555429 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
4555448 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
4555468 TCGTGTTGCGA
1 TCGCGTTGCGA
4555479 AAGTAAACTA
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
19 79 0.62
20 12 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4555347 original size:14 final size:14
Alignment explanation
Indices: 4555328--4555384 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4555318 TTTCATTTCG
4555328 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
4555342 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
4555359 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
4555375 CGTTGCGATT
1 CGTTGCGATT
4555385 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:4555436 original size:38 final size:38
Alignment explanation
Indices: 4555306--4555478 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
4555296 GAAACCAAAA
*
4555306 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
4555341 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
4555374 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
4555410 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
4555448 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
4555479 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
33 56 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:4557422 original size:14 final size:14
Alignment explanation
Indices: 4557403--4557438 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4557393 ATTGTTTAAT
4557403 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
4557417 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
4557431 TGATTTGT
1 TGATTTGT
4557439 GTAATTGATG
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:4557561 original size:19 final size:19
Alignment explanation
Indices: 4557545--4557642 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
4557535 AAAAATGACT
4557545 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4557564 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4557583 ATCGCAA--CGAAA-G--A
1 ATCGCAATGCGAAATGAAA
4557597 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4557616 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4557636 ATCGCAA
1 ATCGCAA
4557643 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 8 0.11
16 6 0.08
17 6 0.08
19 35 0.49
20 16 0.23
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4557674 original size:53 final size:53
Alignment explanation
Indices: 4557545--4557661 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
4557535 AAAAATGACT
*
4557545 ATCGCAATGCGAAATGAAAATCACAATGC-GAAATGAAAATCGCAACGAAAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGA
*
4557597 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGA
4557650 ATCGCAATGCGA
1 ATCGCAATGCGA
4557662 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 28 0.45
53 34 0.55
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGA
Found at i:4557679 original size:19 final size:19
Alignment explanation
Indices: 4557651--4557853 Score: 203
Period size: 19 Copynumber: 11.7 Consensus size: 19
4557641 AACGAGAGAA
* *
4557651 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
4557670 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
4557686 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
4557703 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4557722 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
4557738 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
4557755 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4557774 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
4557790 TCG--TTGCGATTTTCATTT
1 TCGCATTGCGATTTTCA-TT
4557808 TCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATT
*
4557825 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
4557841 TCGCATTGCGATT
1 TCGCATTGCGATT
4557854 CTCTCGTTGC
Statistics
Matches: 153, Mismatches: 10, Indels: 42
0.75 0.05 0.20
Matches are distributed among these distances:
14 29 0.19
16 23 0.15
17 18 0.12
18 4 0.03
19 67 0.44
20 12 0.08
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:4557694 original size:33 final size:33
Alignment explanation
Indices: 4557657--4557875 Score: 201
Period size: 33 Copynumber: 6.5 Consensus size: 33
4557647 AGAATCGCAA
4557657 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
* *
4557690 TGCGATTTTCATTTCGCATTGCGATT-T-TCAT
1 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
* *** * * *
4557721 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTAATT-TCGCATTGCGA--TTC-TCTCG--T
*
4557761 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
* *
4557794 TGCGATTTTCATTTTCGCATTGCGATTTTCAT-GT
1 TGCGATTTT-AATTTCGCATTGCGATTCTC-TCGT
* *
4557828 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
*
4557861 TGCGATTGTAATTTC
1 TGCGATTTTAATTTC
4557876 CGTGTTGCGA
Statistics
Matches: 148, Mismatches: 26, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
31 6 0.04
32 8 0.05
33 75 0.51
34 27 0.18
35 7 0.05
36 3 0.02
37 1 0.01
38 11 0.07
39 6 0.04
40 4 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
Found at i:4557714 original size:52 final size:52
Alignment explanation
Indices: 4557651--4557825 Score: 323
Period size: 52 Copynumber: 3.3 Consensus size: 52
4557641 AACGAGAGAA
* *
4557651 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
4557703 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
4557755 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA-TT
4557808 TCGCATTGCGATTTTCAT
1 TCGCATTGCGATTTTCAT
4557826 GTTGGGATTT
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
52 100 0.83
53 20 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:4559575 original size:20 final size:20
Alignment explanation
Indices: 4559547--4559776 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
4559537 AAATTTCAGT
* * *
4559547 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
4559567 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
4559587 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
4559607 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
4559627 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
4559647 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
4559667 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
4559687 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
4559707 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
4559727 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
4559747 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
4559767 GTTGCGATTT
1 GTTGCGATTT
4559777 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:4559793 original size:21 final size:21
Alignment explanation
Indices: 4559763--4559845 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
4559753 ATTTTCATAT
*
4559763 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
4559784 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
4559805 TCGCATTGCGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
4559826 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
4559846 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:4559836 original size:42 final size:43
Alignment explanation
Indices: 4559743--4559841 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
4559733 ATTTATGTGT
*
4559743 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
** *
4559784 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-TAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGGAA-AA
*
4559826 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
4559842 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
Found at i:4567507 original size:20 final size:20
Alignment explanation
Indices: 4567484--4567540 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
4567474 TCACAACGCA
*
4567484 AATATGTAAATCGCAACGAT
1 AATATGTAAATCGCAACGAG
*
4567504 AATATGTAAATCGCAACGCG
1 AATATGTAAATCGCAACGAG
*
4567524 AATTTGTAAATCGCAAC
1 AATATGTAAATCGCAAC
4567541 ACAGAAGTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (20 bp):
AATATGTAAATCGCAACGAG
Found at i:4567557 original size:20 final size:21
Alignment explanation
Indices: 4567534--4567581 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
4567524 AATTTGTAAA
4567534 TCGCAACACAGAA-GTCAAAT
1 TCGCAACACAGAATGTCAAAT
* *
4567554 TCGCAACACGGAATTTCAAAT
1 TCGCAACACAGAATGTCAAAT
4567575 TCGCAAC
1 TCGCAAC
4567582 GCGAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.19
Consensus pattern (21 bp):
TCGCAACACAGAATGTCAAAT
Found at i:4567574 original size:21 final size:20
Alignment explanation
Indices: 4567514--4567702 Score: 100
Period size: 20 Copynumber: 9.4 Consensus size: 20
4567504 AATATGTAAA
* *
4567514 TCGCAACGCGAATTTGTAAA-
1 TCGCAACACGAATTT-CAAAT
*
4567534 TCGCAACACAGAA-GTCAAAT
1 TCGCAACAC-GAATTTCAAAT
4567554 TCGCAACACGGAATTTCAAAT
1 TCGCAACAC-GAATTTCAAAT
* **
4567575 TCGCAACGCGAATTT-ATTTT
1 TCGCAACACGAATTTCA-AAT
** ***
4567595 TCATAACAC-AAGTTTCCTTT
1 TCGCAACACGAA-TTTCAAAT
* *
4567615 TCGCAACAAGATTTTCTAAA-
1 TCGCAACACGAATTTC-AAAT
**
4567635 TCGCAACACGAATTTTGAAT
1 TCGCAACACGAATTTCAAAT
* * *
4567655 TCGCAACTCGATTTTCGAAT
1 TCGCAACACGAATTTCAAAT
* * *
4567675 TCACAACACGAATTTTAATT
1 TCGCAACACGAATTTCAAAT
4567695 TCGCAACA
1 TCGCAACA
4567703 ACTTTTATTT
Statistics
Matches: 127, Mismatches: 33, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
19 8 0.06
20 101 0.80
21 18 0.14
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (20 bp):
TCGCAACACGAATTTCAAAT
Found at i:4567589 original size:20 final size:20
Alignment explanation
Indices: 4567430--4567589 Score: 82
Period size: 20 Copynumber: 8.0 Consensus size: 20
4567420 AAATGACCAA
*
4567430 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACGCGAATTT
* * * *
4567449 CAAATTCGTAACTCGAAATC
1 CAAATTCGCAACGCGAATTT
* * *
4567469 CAATTTCACAACGCAAATATGT
1 CAAATTCGCAACGCGAAT-T-T
**
4567491 -AAA-TCGCAACGATAATATGT
1 CAAATTCGCAACGCGAAT-T-T
4567511 -AAA-TCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
* * *
4567529 GTAAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAACGC-GAATTT
*
4567549 CAAATTCGCAACACGGAATTT
1 CAAATTCGCAACGC-GAATTT
4567570 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
4567590 ATTTTTCATA
Statistics
Matches: 109, Mismatches: 24, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
18 1 0.01
19 17 0.16
20 71 0.65
21 20 0.18
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:4567658 original size:40 final size:40
Alignment explanation
Indices: 4567613--4567703 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
4567603 CAAGTTTCCT
* *
4567613 TTTCGCAACAAGATTTTCTAAATCGCAACACGAATTTTGAA
1 TTTCGCAACAAGATTTTCGAAATCACAACACGAATTTT-AA
** *
4567654 -TTCGCAACTCGATTTTCGAATTCACAACACGAATTTTAA
1 TTTCGCAACAAGATTTTCGAAATCACAACACGAATTTTAA
4567693 TTTCGCAACAA
1 TTTCGCAACAA
4567704 CTTTTATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.05
40 40 0.95
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (40 bp):
TTTCGCAACAAGATTTTCGAAATCACAACACGAATTTTAA
Found at i:4567894 original size:16 final size:15
Alignment explanation
Indices: 4567859--4567897 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
4567849 TCCCCATCTC
*
4567859 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
4567874 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
4567890 TAATTTTT
1 TAATTTTT
4567898 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:4571438 original size:21 final size:21
Alignment explanation
Indices: 4571414--4571513 Score: 89
Period size: 21 Copynumber: 4.8 Consensus size: 21
4571404 GTGGGAGGGA
4571414 CCTCTTGAACGATGACGGGGG
1 CCTCTTGAACGATGACGGGGG
* *
4571435 CCTCTTGAACGGTG-GGAGGGG
1 CCTCTTGAACGATGACG-GGGG
* ** *
4571456 CCTCTTGAAAGATGATAGTGG
1 CCTCTTGAACGATGACGGGGG
*
4571477 CCTCTTGAATGAT-A-GGAGAGG
1 CCTCTTGAACGATGACGG-G-GG
4571498 CCTCTTGAACGATGAC
1 CCTCTTGAACGATGAC
4571514 ATGTGAATCG
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
19 1 0.02
20 2 0.03
21 58 0.94
22 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGACGGGGG
Found at i:4571453 original size:42 final size:41
Alignment explanation
Indices: 4571394--4571514 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 41
4571384 GTGAATCGGG
* *
4571394 CTCTTAAATGGTGGGAGGGACCTCTTGAACGATGACGGGGGC
1 CTCTTGAATGGTGGGAGGG-CCTCTTGAACGATGACAGGGGC
* * * *
4571436 CTCTTGAACGGTGGGAGGGGCCTCTTGAAAGATGATAGTGGC
1 CTCTTGAATGGTGGGA-GGGCCTCTTGAACGATGACAGGGGC
* *
4571478 CTCTTGAATGATAGGAGAGGCCTCTTGAACGATGACA
1 CTCTTGAATGGTGGGAG-GGCCTCTTGAACGATGACA
4571515 TGTGAATCGG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 62 0.94
43 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGCCTCTTGAACGATGACAGGGGC
Found at i:4571876 original size:63 final size:63
Alignment explanation
Indices: 4571806--4571927 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
4571796 CATAGAGCGA
* * *
4571806 CTACCTCATCACGTAAAG-TAGATACCTCA-CTACGTAAAGCACCATTGTCATCGCGTAAAACCT
1 CTACCTCACCACGTAAAGATAG-TACCTCATC-ACGCAAAGCACCATTGTCATCACGTAAAACCT
* * *
4571869 CTACCTCACCACGTAAAGATTGTACCTCATCACGCAATGCACCATTGTCGTCACGTAAA
1 CTACCTCACCACGTAAAGATAGTACCTCATCACGCAAAGCACCATTGTCATCACGTAAA
4571928 GTACCGACCT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
63 48 0.94
64 3 0.06
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (63 bp):
CTACCTCACCACGTAAAGATAGTACCTCATCACGCAAAGCACCATTGTCATCACGTAAAACCT
Found at i:4573684 original size:19 final size:20
Alignment explanation
Indices: 4573610--4573681 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
4573600 TCTGAAACTT
4573610 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
4573630 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
4573650 AAAATCGCAACGC-AAAATG
1 AAAATCGCAACGCGAAAATG
4573669 AAAATCGCAACGC
1 AAAATCGCAACGC
4573682 AAATTTCATT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 19 0.37
20 33 0.63
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:4573757 original size:20 final size:20
Alignment explanation
Indices: 4573685--4573746 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
4573675 GCAACGCAAA
4573685 TTTCATTTTCGCAACGTTGCGAT
1 TTTCATTTTCG---CGTTGCGAT
4573708 TTTCATTTTCGCGTTGCGAT
1 TTTCATTTTCGCGTTGCGAT
*
4573728 TTTCATTTTCGTGTTGCGA
1 TTTCATTTTCGCGTTGCGA
4573747 ATTTAAGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 27 0.71
23 11 0.29
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (20 bp):
TTTCATTTTCGCGTTGCGAT
Found at i:4574273 original size:20 final size:20
Alignment explanation
Indices: 4574248--4574308 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 20
4574238 TTTCAAATTT
**
4574248 GAAAATAAAATTCGCGTTGC
1 GAAAATAAAACGCGCGTTGC
*
4574268 GAAAAT-AAACGCGCTTTGC
1 GAAAATAAAACGCGCGTTGC
*
4574287 GAAAAT-AAACGCGCTTTGC
1 GAAAATAAAACGCGCGTTGC
4574306 GAA
1 GAA
4574309 TTTGACTTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 32 0.84
20 6 0.16
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
GAAAATAAAACGCGCGTTGC
Found at i:4574288 original size:19 final size:19
Alignment explanation
Indices: 4574264--4574308 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
4574254 AAAATTCGCG
4574264 TTGCGAAAATAAACGCGCT
1 TTGCGAAAATAAACGCGCT
4574283 TTGCGAAAATAAACGCGCT
1 TTGCGAAAATAAACGCGCT
4574302 TTGCGAA
1 TTGCGAA
4574309 TTTGACTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (19 bp):
TTGCGAAAATAAACGCGCT
Found at i:4574345 original size:20 final size:20
Alignment explanation
Indices: 4574322--4574411 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
4574312 GACTTCTGTA
4574322 TTGCGATTTACATAATCGCG
1 TTGCGATTTACATAATCGCG
* **
4574342 TTGCGATTTACATATTATCG
1 TTGCGATTTACATAATCGCG
* *
4574362 TTGCGATTTACCTACTCGCG
1 TTGCGATTTACATAATCGCG
* * *
4574382 TTGTGAATTTGA-AAAACCGCG
1 TTGCG-ATTT-ACATAATCGCG
4574403 TTGCGATTT
1 TTGCGATTT
4574412 TGGAACCTGT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
20 41 0.75
21 13 0.24
22 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACATAATCGCG
Found at i:4574703 original size:2 final size:2
Alignment explanation
Indices: 4574696--4574725 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4574686 TTGATAGGTC
4574696 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4574726 GCCATTGAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4576498 original size:22 final size:22
Alignment explanation
Indices: 4576445--4576491 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
4576435 GGAAAGGAAT
4576445 ATGATTGCAAAGACCTTATAGA
1 ATGATTGCAAAGACCTTATAGA
4576467 ATGATTGCAAAGACCTTATAGA
1 ATGATTGCAAAGACCTTATAGA
4576489 ATG
1 ATG
4576492 TGTGCAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (22 bp):
ATGATTGCAAAGACCTTATAGA
Found at i:4579431 original size:32 final size:32
Alignment explanation
Indices: 4579312--4579434 Score: 117
Period size: 31 Copynumber: 3.9 Consensus size: 32
4579302 CTTCGGCAAC
* * * * *
4579312 TGTCCATAGGTCCCGAAGAACCTAGGTAA-AC
1 TGTCCATATGTTCCGTAGAACATAGGTAATAT
* *
4579343 TATCCATATGTTCCTTAGAACATAGGT-ATAT
1 TGTCCATATGTTCCGTAGAACATAGGTAATAT
* * *
4579374 TGTCCATATGTCCCG-AAAGACATAGGTAATTT
1 TGTCCATATGTTCCGTAGA-ACATAGGTAATAT
*
4579406 TGTCCATATGTTCCGTAGAATATAGGTAA
1 TGTCCATATGTTCCGTAGAACATAGGTAA
4579435 ATCCTCGACT
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
30 3 0.04
31 42 0.58
32 26 0.36
33 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (32 bp):
TGTCCATATGTTCCGTAGAACATAGGTAATAT
Found at i:4581974 original size:13 final size:13
Alignment explanation
Indices: 4581956--4581981 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4581946 TTACAGACGC
4581956 GCATATGAAGACT
1 GCATATGAAGACT
4581969 GCATATGAAGACT
1 GCATATGAAGACT
4581982 ATTCAACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:4584569 original size:61 final size:61
Alignment explanation
Indices: 4584492--4584654 Score: 213
Period size: 61 Copynumber: 2.7 Consensus size: 61
4584482 GTATGTACAT
* * *
4584492 ATAGTTTGGGATGAAATTGGAATGTTTAAAAAGTTTGGGGATTAATTTAGAATAAA-GGTC
1 ATAGTTTGGGATGAAATTGAAATATTTAAAAAGTTTGGGGATTAATTTAGAATAAATAGTC
* * * *
4584552 ATAGTTTGGGGATGAAATTGAAATATTCAAAATGTTTGAGGATTGATTTAGAATAAATAGTC
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAAGTTTGGGGATTAATTTAGAATAAATAGTC
* *
4584614 ATAGTTTAGGGATAAAATTGAAATATTTAAAAA-TTTAGGGA
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAAGTTTGGGGA
4584655 CCAATTCAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
60 7 0.08
61 49 0.56
62 32 0.36
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (61 bp):
ATAGTTTGGGATGAAATTGAAATATTTAAAAAGTTTGGGGATTAATTTAGAATAAATAGTC
Found at i:4585154 original size:38 final size:38
Alignment explanation
Indices: 4585106--4585191 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 38
4585096 AAGTACTTAA
4585106 TTAAAGAATATGT-TAAATT-ATAGTTTAAAAGC-ATAAT-T
1 TTAAA-AATAT-TCTAAATTAAT-GTTTAAAA-CAATAATCT
*
4585144 TTAAGAAATATTCTTAATTAATGTTTAAAACAATAATCT
1 TTAA-AAATATTCTAAATTAATGTTTAAAACAATAATCT
4585183 TTAAAAATA
1 TTAAAAATA
4585192 AATTCATGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
37 2 0.05
38 32 0.76
39 8 0.19
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (38 bp):
TTAAAAATATTCTAAATTAATGTTTAAAACAATAATCT
Found at i:4586046 original size:21 final size:21
Alignment explanation
Indices: 4586022--4586090 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
4586012 ATAAAATTAT
4586022 TAATTATTAAAATATATTTAA
1 TAATTATTAAAATATATTTAA
* ** *
4586043 TAATTTTTTTAATAT-TATAA
1 TAATTATTAAAATATATTTAA
*
4586063 TAATATACTTAAATTATATTATAA
1 TAAT-TA-TTAAAATATATT-TAA
4586087 TAAT
1 TAAT
4586091 ATAAGATACT
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
20 8 0.23
21 13 0.37
22 6 0.17
23 1 0.03
24 7 0.20
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTATTAAAATATATTTAA
Found at i:4586147 original size:27 final size:28
Alignment explanation
Indices: 4586111--4586165 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
4586101 ATATTTTTAT
4586111 TTTTAATATTATATAATAAATTAATAAA
1 TTTTAATATTATATAATAAATTAATAAA
* * *
4586139 TTTT-ATATTATTTATTAACTTAATAAA
1 TTTTAATATTATATAATAAATTAATAAA
4586166 AATAATACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTAATATTATATAATAAATTAATAAA
Found at i:4586212 original size:27 final size:27
Alignment explanation
Indices: 4586158--4586217 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
4586148 ATTTATTAAC
4586158 TTAATAAAAATAATACTATTAAATTA-
1 TTAATAAAAATAATACTATTAAATTAT
*
4586184 TTAATAACAAATAATATTATT-AATGTAT
1 TTAATAA-AAATAATACTATTAAAT-TAT
4586212 TTAATA
1 TTAATA
4586218 TTAATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 10 0.33
27 14 0.47
28 6 0.20
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (27 bp):
TTAATAAAAATAATACTATTAAATTAT
Found at i:4586553 original size:14 final size:14
Alignment explanation
Indices: 4586530--4586562 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4586520 CAAACATCGT
4586530 AAAATATTTTCTA-
1 AAAATATTTTCTAG
4586543 AAAACTATTTTCTAG
1 AAAA-TATTTTCTAG
4586558 AAAAT
1 AAAAT
4586563 GTAATTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAATATTTTCTAG
Found at i:4591476 original size:210 final size:210
Alignment explanation
Indices: 4591206--4592015 Score: 1051
Period size: 210 Copynumber: 3.9 Consensus size: 210
4591196 CCAGTTGCCT
* *
4591206 TCGCCTATAATTCTTTGATTCATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTTG
1 TCGCCTACAATTCCTTGATTCATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTTG
** * *
4591271 CTAAATAGAATGATGAATGAAAGAGACAATCCTAATGTAGTAACTTTCAATTCTTTTATCAATGC
66 CTTCATAGAATGATGAATGAAAGAGTCAATCCTGATGTAGTAACTTTCAATTCTTTTATCAATGC
* *
4591336 TTTATGTAGGGAAAAGAGAACCGAAGAAGCCAATACCATGTTGGGACTAATGTGTCAAAGAAATG
131 TTTATGCAGGGAAAAGAGAACCGAAGAAGCCAATACCATGTTGGAACTAATGTGTCAAAGAAATG
* * *
4591401 TAAAAGCAGACATCC
196 TAAAACCAGACGTCG
* *
4591416 TCGTCTACAATTCCTTGATTCATGGATTTTGTCATTTAGGGAAATGGGAAGAAGCGACAAGTTTG
1 TCGCCTACAATTCCTTGATTCATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTTG
*
4591481 CTTCATAGAATGATGAATGAAAGAGTCAATCCTGATATAGTAACTTTCAATTCTTTTATCAATGC
66 CTTCATAGAATGATGAATGAAAGAGTCAATCCTGATGTAGTAACTTTCAATTCTTTTATCAATGC
* * *
4591546 TTTATGCAGGGAAAAGAGAACCGAAAAAGCC-ATGACCATGTCGGAACTAATGCGTCAAAGAAAT
131 TTTATGCAGGGAAAAGAGAACCGAAGAAGCCAAT-ACCATGTTGGAACTAATGTGTCAAAGAAAT
* *
4591610 GTAAAACCTGACGTTG
195 GTAAAACCAGACGTCG
*
4591626 TCACCTACAATT-C-TGAGTT-ATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTT
1 TCGCCTACAATTCCTTGA-TTCATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTT
* ** * * *
4591688 GCTCCATAGAATGATGAATGAAAGAGTTGATCCTGATGTTGTGACCTTCAATTCTTTTATCAATG
65 GCTTCATAGAATGATGAATGAAAGAGTCAATCCTGATGTAGTAACTTTCAATTCTTTTATCAATG
* * *
4591753 CTTTATGCAGGGGAAAGAGAACCGAAGAAGCCAATTCCATGTTGGAACTGATGTGTCAAAGAAAT
130 CTTTATGCAGGGAAAAGAGAACCGAAGAAGCCAATACCATGTTGGAACTAATGTGTCAAAGAAAT
*
4591818 GTAAAACCAAACGTCG
195 GTAAAACCAGACGTCG
* * * **
4591834 T-GACCTACAATTCTTTGATTCACGGATTTTGTCATTTAGGGAAATGGGAAGAAGCGATGAGTTT
1 TCG-CCTACAATTCCTTGATTCATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTT
* * * * * * * * *
4591898 GCTTGATATG-ATGATGAATGAAGGAGTCCAT-CTGGATGTTGTGACCTTCAGTTCATTAATCAA
65 GCTTCATA-GAATGATGAATGAAAGAGTCAATCCT-GATGTAGTAACTTTCAATTCTTTTATCAA
* * ** * * *
4591961 TTG-TTTATGCAAGGAAAAGAGGACTAAAGAAGCCATTACAATGTTTGAACTAATG
128 -TGCTTTATGCAGGGAAAAGAGAACCGAAGAAGCCAATACCATGTTGGAACTAATG
4592016 ATTCAGAGAG
Statistics
Matches: 528, Mismatches: 62, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
208 182 0.34
209 11 0.02
210 332 0.63
211 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (210 bp):
TCGCCTACAATTCCTTGATTCATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTTG
CTTCATAGAATGATGAATGAAAGAGTCAATCCTGATGTAGTAACTTTCAATTCTTTTATCAATGC
TTTATGCAGGGAAAAGAGAACCGAAGAAGCCAATACCATGTTGGAACTAATGTGTCAAAGAAATG
TAAAACCAGACGTCG
Found at i:4592013 original size:418 final size:416
Alignment explanation
Indices: 4591227--4592050 Score: 1136
Period size: 418 Copynumber: 2.0 Consensus size: 416
4591217 TCTTTGATTC
4591227 ATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTTGCTAAATAGAATGATGAATGAA
1 ATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTTGCTAAATAGAATGATGAATGAA
* *
4591292 AGAGACAATCCTAATGTAGTAACTTTCAATTCTTTTATCAATGCTTTATGTAGGGAAAAGAGAAC
66 AGAGACAATCCTAATGTAGTAACCTTCAATTCTTTTATCAATGCTTTATGCAGGGAAAAGAGAAC
* * * *
4591357 CGAAGAAGCCAATACCATGTTGGGACTAATGTGTCAAAGAAATGTAAAAGCAGACATCCTCGTCT
131 CGAAGAAGCCAATACCATGTTGGAACTAATGTGTCAAAGAAATGTAAAACCAAACATCCTCGCCT
*
4591422 ACAATTCCTTGATTCATGGATTTTGTCATTTAGGGAAATGGGAAGAAGCGACAAGTTTGCTTCAT
196 ACAATTCCTTGATTCACGGATTTTGTCATTTAGGGAAATGGGAAGAAGCGACAAGTTTGCTTCAT
* * *
4591487 AGAATGATGAATGAAAGAGTCAATCCTGATATAGTAACTTTCAATTCTTTTATCAATGCTTTATG
261 AGAATGATGAATGAAAGAGTCAATCCTGATATAGTAACCTTCAATTCATTAATCAATGCTTTATG
* * *
4591552 CAGGGAAAAGAGAACCGAAAAAGCCATGACCATGTCGGAACTAATGCGTCAAAGAAATGTAAAAC
326 CAAGGAAAAGAGAACCGAAAAAGCCATGACAATGTCGGAACTAATGAGTCAAAGAAA--TAAAAC
* *
4591617 CTGACGTTGTCACCTACAATTCTGAGTT
389 CCGACATTGTCACCTACAATTCTGAGTT
**
4591645 ATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTTGCTCCATAGAATGATGAATGAA
1 ATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTTGCTAAATAGAATGATGAATGAA
*** * * * *
4591710 AGAGTTGATCCTGATGTTGTGACCTTCAATTCTTTTATCAATGCTTTATGCAGGGGAAAGAGAAC
66 AGAGACAATCCTAATGTAGTAACCTTCAATTCTTTTATCAATGCTTTATGCAGGGAAAAGAGAAC
* * * *
4591775 CGAAGAAGCCAATTCCATGTTGGAACTGATGTGTCAAAGAAATGTAAAACCAAACGTCGT-GACC
131 CGAAGAAGCCAATACCATGTTGGAACTAATGTGTCAAAGAAATGTAAAACCAAACATCCTCG-CC
* ** *
4591839 TACAATTCTTTGATTCACGGATTTTGTCATTTAGGGAAATGGGAAGAAGCGATGAGTTTGCTTGA
195 TACAATTCCTTGATTCACGGATTTTGTCATTTAGGGAAATGGGAAGAAGCGACAAGTTTGCTTCA
* * * * * *
4591904 TATG-ATGATGAATGAAGGAGTCCAT-CTGGATGTTGTGACCTTCAGTTCATTAATCAATTG-TT
260 TA-GAATGATGAATGAAAGAGTCAATCCT-GATATAGTAACCTTCAATTCATTAATCAA-TGCTT
* * * ** * * *
4591966 TATGCAAGGAAAAGAGGA-CTAAAGAAGCCATTACAATGTTTGAACTAATGATTCAGAGAGATAA
322 TATGCAAGGAAAAGAGAACCGAAA-AAGCCATGACAATGTCGGAACTAATGAGTCAAAGAAATAA
4592030 AACCCGACATTGTCACCTACA
386 AACCCGACATTGTCACCTACA
4592051 GTTGTTTAAT
Statistics
Matches: 355, Mismatches: 46, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
416 22 0.06
417 7 0.02
418 323 0.91
419 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (416 bp):
ATGGATTTTGTCATTCAGGGAAATGGGAAGAAGCGACAAGTTTGCTAAATAGAATGATGAATGAA
AGAGACAATCCTAATGTAGTAACCTTCAATTCTTTTATCAATGCTTTATGCAGGGAAAAGAGAAC
CGAAGAAGCCAATACCATGTTGGAACTAATGTGTCAAAGAAATGTAAAACCAAACATCCTCGCCT
ACAATTCCTTGATTCACGGATTTTGTCATTTAGGGAAATGGGAAGAAGCGACAAGTTTGCTTCAT
AGAATGATGAATGAAAGAGTCAATCCTGATATAGTAACCTTCAATTCATTAATCAATGCTTTATG
CAAGGAAAAGAGAACCGAAAAAGCCATGACAATGTCGGAACTAATGAGTCAAAGAAATAAAACCC
GACATTGTCACCTACAATTCTGAGTT
Found at i:4600284 original size:2 final size:2
Alignment explanation
Indices: 4600211--4600264 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
4600201 AATTTTAAAA
* * *
4600211 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT TT AT CT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4600252 AT TT A- AT AT AT AT
1 AT AT AT AT AT AT AT
4600265 TTCAATAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4604104 original size:12 final size:12
Alignment explanation
Indices: 4604087--4604118 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
4604077 ATAATTGCGC
4604087 TATATTTTTTTT
1 TATATTTTTTTT
4604099 TATATTTTTTTT
1 TATATTTTTTTT
4604111 T-TATTTTT
1 TATATTTTT
4604119 GATTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TATATTTTTTTT
Found at i:4605094 original size:31 final size:31
Alignment explanation
Indices: 4605059--4605126 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
4605049 TGATGACCAC
*
4605059 ATCTTAATTATATAAAAACAAAAGTGA-TAAT
1 ATCTTAATTAAATAAAAACAAAAGTGACT-AT
*
4605090 ATCTTAATTAAATAAAAACGAAAGTGACTAT
1 ATCTTAATTAAATAAAAACAAAAGTGACTAT
4605121 ATCTTA
1 ATCTTA
4605127 TGTTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.32
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGACTAT
Found at i:4612887 original size:47 final size:47
Alignment explanation
Indices: 4612830--4612933 Score: 172
Period size: 47 Copynumber: 2.2 Consensus size: 47
4612820 GAGGATTGTC
* * *
4612830 CGATAACCGGACGTACATTCTCGTACGTTGAAACGGAGGATTACCGT
1 CGATAACCGGACGTACATTCTCGTACATTGAAACGGAGGATGACCAT
*
4612877 CGATAACCGGACGTACATTCTCGTACATTGAAACGGAGGATGCCCAT
1 CGATAACCGGACGTACATTCTCGTACATTGAAACGGAGGATGACCAT
4612924 CGATAACCGG
1 CGATAACCGG
4612934 TCTTGTACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (47 bp):
CGATAACCGGACGTACATTCTCGTACATTGAAACGGAGGATGACCAT
Found at i:4613630 original size:76 final size:76
Alignment explanation
Indices: 4613548--4613850 Score: 321
Period size: 76 Copynumber: 3.9 Consensus size: 76
4613538 ATTGTTGCGT
* *
4613548 CCAATAATGTCATGGTTCACTAAGAAATATGTTGTTATCTGTAATGTTAATA-TTTTATTAATAA
1 CCAAGAATGTCATAGTTCACTAAGAAATATGTTGTTATCTG-AATGTTAATATTTTTATTAATAA
*
4613612 AATAGGTTATGC
65 AATAGGTTACGC
* * * *
4613624 CCAATAATGTCATGGTTCACTAATAAATATGTT-TTGATCTGAAATATTAATATTTTTATTAATA
1 CCAAGAATGTCATAGTTCACTAAGAAATATGTTGTT-ATCTG-AATGTTAATATTTTTATTAATA
4613688 AAAT-GTGTTACGC
64 AAATAG-GTTACGC
* * *
4613701 CCAAGAATGTCATAGTTCATTAAGAAATA-GATTACGAATAT-AGAATGTTAATATTTTTATTAA
1 CCAAGAATGTCATAGTTCACTAAGAAATATG-TT--G-TTATCTGAATGTTAATATTTTTATTAA
* *
4613764 TAAAATAAGTTACGA
62 TAAAATAGGTTACGC
* ** * *
4613779 CCAAGAATGTCATAGTTCACTAAGAAATAGGTTGCGATATAGAATGTTTATA-TTTTATTAATAA
1 CCAAGAATGTCATAGTTCACTAAGAAATATGTTGTTATCT-GAATGTTAATATTTTTATTAATAA
*
4613843 AATGGGTT
65 AATAGGTT
4613851 GTTCACTAAG
Statistics
Matches: 195, Mismatches: 20, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
75 4 0.02
76 67 0.34
77 58 0.30
78 61 0.31
79 2 0.01
80 2 0.01
81 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (76 bp):
CCAAGAATGTCATAGTTCACTAAGAAATATGTTGTTATCTGAATGTTAATATTTTTATTAATAAA
ATAGGTTACGC
Found at i:4613729 original size:77 final size:75
Alignment explanation
Indices: 4613548--4613847 Score: 320
Period size: 78 Copynumber: 3.9 Consensus size: 75
4613538 ATTGTTGCGT
* * * *
4613548 CCAATAATGTCATGGTTCACTAAGAAATATG-TT-GTTATCTGTAATGTTAATATTTTATTAATA
1 CCAAGAATGTCATAGTTCACTAAGAAATATGTTTCGATAT-AG-AATGTTAATATTTTATTAATA
*
4613611 AAATAGGTTATGC
64 AAAT-GGTTACGC
* * * * * *
4613624 CCAATAATGTCATGGTTCACTAATAAATATGTTTTGATCT-GAAATATTAATATTTTTATTAATA
1 CCAAGAATGTCATAGTTCACTAAGAAATATGTTTCGATATAG-AATGTTAATA-TTTTATTAATA
4613688 AAATGTGTTACGC
64 AAATG-GTTACGC
* *
4613701 CCAAGAATGTCATAGTTCATTAAGAAATA-GATTACGAATATAGAATGTTAATATTTTTATTAAT
1 CCAAGAATGTCATAGTTCACTAAGAAATATG-TTTCG-ATATAGAATGTTAATA-TTTTATTAAT
* *
4613765 AAAATAAGTTACGA
63 AAAAT-GGTTACGC
* * *
4613779 CCAAGAATGTCATAGTTCACTAAGAAATAGGTTGCGATATAGAATGTTTATATTTTATTAATAAA
1 CCAAGAATGTCATAGTTCACTAAGAAATATGTTTCGATATAGAATGTTAATATTTTATTAATAAA
4613844 ATGG
66 ATGG
4613848 GTTGTTCACT
Statistics
Matches: 195, Mismatches: 20, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
75 1 0.01
76 57 0.29
77 66 0.34
78 69 0.35
79 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (75 bp):
CCAAGAATGTCATAGTTCACTAAGAAATATGTTTCGATATAGAATGTTAATATTTTATTAATAAA
ATGGTTACGC
Found at i:4613736 original size:37 final size:38
Alignment explanation
Indices: 4613694--4613808 Score: 108
Period size: 40 Copynumber: 3.0 Consensus size: 38
4613684 AATAAAATGT
*
4613694 GTTACGCCCAAGAATGTCATAGTTCATTAAGAAATAGA
1 GTTACGACCAAGAATGTCATAGTTCATTAAGAAATAGA
** * * * *
4613732 -TTACGAATATAGAATGTTAATATTTTTATTAATAAAATA-A
1 GTTACGACCA-AGAATG-TCATA-GTTCATTAA-GAAATAGA
*
4613772 GTTACGACCAAGAATGTCATAGTTCACTAAGAAATAG
1 GTTACGACCAAGAATGTCATAGTTCATTAAGAAATAG
4613809 GTTGCGATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
37 11 0.19
38 12 0.21
39 8 0.14
40 14 0.25
41 12 0.21
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (38 bp):
GTTACGACCAAGAATGTCATAGTTCATTAAGAAATAGA
Found at i:4613823 original size:37 final size:37
Alignment explanation
Indices: 4613704--4613825 Score: 111
Period size: 37 Copynumber: 3.2 Consensus size: 37
4613694 GTTACGCCCA
*
4613704 AGAATGTCATAGTTCATTAAGAAATAGATTACGAATAT
1 AGAATGTCATAGTTCATTAAGAAATAGGTTACG-ATAT
* * * * * *
4613742 AGAATGTTAATATTTTTATTAATAAAATAAGTTACGACCA-
1 AGAATG-TCATA-GTTCATTAA-GAAATAGGTTACGA-TAT
* *
4613782 AGAATGTCATAGTTCACTAAGAAATAGGTTGCGATAT
1 AGAATGTCATAGTTCATTAAGAAATAGGTTACGATAT
4613819 AGAATGT
1 AGAATGT
4613826 TTATATTTTA
Statistics
Matches: 64, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
36 1 0.02
37 18 0.28
38 12 0.19
39 8 0.12
40 14 0.22
41 11 0.17
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (37 bp):
AGAATGTCATAGTTCATTAAGAAATAGGTTACGATAT
Found at i:4613890 original size:58 final size:59
Alignment explanation
Indices: 4613793--4613910 Score: 184
Period size: 58 Copynumber: 2.0 Consensus size: 59
4613783 GAATGTCATA
* * *
4613793 GTTCACTAAGAAATAGGTTGCGATATAGAATGTTTATA-TTTTATTAATAAAATGGGTT
1 GTTCACTAAGAAATAGGTTGCAATATAGAATATTAATATTTTTATTAATAAAATGGGTT
* *
4613851 GTTCACTAAGAAATAGGTTGTAATATGGAATATTAATATTTTTATTAATAAAATGGGTT
1 GTTCACTAAGAAATAGGTTGCAATATAGAATATTAATATTTTTATTAATAAAATGGGTT
4613910 G
1 G
4613911 GCTCAAGAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 33 0.61
59 21 0.39
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (59 bp):
GTTCACTAAGAAATAGGTTGCAATATAGAATATTAATATTTTTATTAATAAAATGGGTT
Found at i:4613957 original size:134 final size:134
Alignment explanation
Indices: 4613715--4613985 Score: 359
Period size: 134 Copynumber: 2.0 Consensus size: 134
4613705 GAATGTCATA
* *
4613715 GTTCATTAAGAAATAGATTACGAATATAGAATGTTAATATTTTTATTAATAAAATAAGTTACGAC
1 GTTCACTAAGAAATAGATTA-GAATATAGAATATTAATATTTTTATTAATAAAATAAGTTA-GAC
* *
4613780 CAAGAATGTCATAGTTCACTAAGAAATAGGTTGCGATATAGAATGTTTATA-TTTTATTAATAAA
64 CAAGAATGTCACAGTTCACTAAGAAATAGGTTGCGATATAGAAT-TTAATATTTTTATTAATAAA
*
4613844 ATGGGTT
128 ATGAGTT
* * ** *
4613851 GTTCACTAAGAAATAGGTT-GTAATATGGAATATTAATATTTTTATTAATAAAATGGGTT-GGCT
1 GTTCACTAAGAAATAGATTAG-AATATAGAATATTAATATTTTTATTAATAAAATAAGTTAGAC-
* * *
4613914 CAAGAATGTCACGGTTCACTAATAAATAGGTTGCGATCTAGAATTTAATATTTTTATTAATAAAA
64 CAAGAATGTCACAGTTCACTAAGAAATAGGTTGCGATATAGAATTTAATATTTTTATTAATAAAA
4613979 TGAGTT
129 TGAGTT
4613985 G
1 G
4613986 CACACAAGAA
Statistics
Matches: 119, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
133 7 0.06
134 61 0.51
135 34 0.29
136 17 0.14
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (134 bp):
GTTCACTAAGAAATAGATTAGAATATAGAATATTAATATTTTTATTAATAAAATAAGTTAGACCA
AGAATGTCACAGTTCACTAAGAAATAGGTTGCGATATAGAATTTAATATTTTTATTAATAAAATG
AGTT
Found at i:4613994 original size:76 final size:76
Alignment explanation
Indices: 4613851--4613998 Score: 208
Period size: 76 Copynumber: 1.9 Consensus size: 76
4613841 AAAATGGGTT
* * * * *
4613851 GTTCACTAAGAAATAGGTTGTAATATGGAATATTAATATTTTTATTAATAAAATGGGTTGGCTCA
1 GTTCACTAAGAAATAGGTTGCAATATAGAATATTAATATTTTTATTAATAAAATGAGTTGACACA
4613916 AGAATGTCACG
66 AGAATGTCACG
* * *
4613927 GTTCACTAATAAATAGGTTGCGATCTAGAAT-TTAATATTTTTATTAATAAAATGAGTTGCACAC
1 GTTCACTAAGAAATAGGTTGCAATATAGAATATTAATATTTTTATTAATAAAATGAGTTG-ACAC
4613991 AAGAATGT
65 AAGAATGT
4613999 TATAGTTTAC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 27 0.43
76 36 0.57
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (76 bp):
GTTCACTAAGAAATAGGTTGCAATATAGAATATTAATATTTTTATTAATAAAATGAGTTGACACA
AGAATGTCACG
Found at i:4614229 original size:75 final size:77
Alignment explanation
Indices: 4614137--4614283 Score: 201
Period size: 79 Copynumber: 1.9 Consensus size: 77
4614127 AGAAGGTTGC
* * * *
4614137 AAAGTATCGATATTTTTCCAAAAGTATCG-A-TTTAACTTCGAAAGTTAAAATATCA-TTTTCTA
1 AAAGTATCGATAGTTTTCCAAAAATATCGAACTTTAAATTCAAAAGTTAAAATATCATTTTTC-A
4614199 TTTTTTTAATTTG
65 TTTTTTTAATTTG
*
4614212 AAAGTATCGATAGTTTTCCAAAAATATCGATACTTTTAAATTTAAAAGTTAAAATATCATTTTTC
1 AAAGTATCGATAGTTTTCCAAAAATATCGA-AC-TTTAAATTCAAAAGTTAAAATATCATTTTTC
4614277 ATTTTTT
64 ATTTTTT
4614284 GAAAAAAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
75 27 0.44
77 1 0.02
79 29 0.47
80 5 0.08
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (77 bp):
AAAGTATCGATAGTTTTCCAAAAATATCGAACTTTAAATTCAAAAGTTAAAATATCATTTTTCAT
TTTTTTAATTTG
Found at i:4622981 original size:77 final size:77
Alignment explanation
Indices: 4622888--4623178 Score: 318
Period size: 77 Copynumber: 3.8 Consensus size: 77
4622878 CTTGTGCAAA
* * * * *
4622888 CTATTTTTTTAATAAAAATATTAACATTCTATATCGTAACCTATTTATAAGTGAACCATGTTATT
1 CTATTTTATTAATAAAAATATTAACATTCTATATTGTAACCTATTTCTTAGTGAACCATGATATT
* **
4622953 TTTGGGCACAAC
66 CTTGGGCGTAAC
* * *
4622965 CTATTTTATTAAT-AAAATATTAACATTAC-ATATTGTAACCTATTTCTTAGTGAACCACGACAA
1 CTATTTTATTAATAAAAATATTAACATT-CTATATTGTAACCTATTTCTTAGTGAACCATGATAT
4623028 TCTTGGGCGTAAC
65 TCTTGGGCGTAAC
* * * * * *
4623041 CCATTTTATTAATAAAAATATTAACATTTTAGATTGCAACATATTTCTTAGTGAATCATGATATT
1 CTATTTTATTAATAAAAATATTAACATTCTATATTGTAACCTATTTCTTAGTGAACCATGATATT
*
4623106 CTTGGGTGTAACC
66 CTTGGGCGTAA-C
* * * * ** *
4623119 CT-TTTTATTAATAAAAATATTAACATTCCAAATCGCAACCGGTTTCTTAGTGATCCATGA
1 CTATTTTATTAATAAAAATATTAACATTCTATATTGTAACCTATTTCTTAGTGAACCATGA
4623179 CATTTTTAGG
Statistics
Matches: 179, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
76 63 0.35
77 114 0.64
78 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (77 bp):
CTATTTTATTAATAAAAATATTAACATTCTATATTGTAACCTATTTCTTAGTGAACCATGATATT
CTTGGGCGTAAC
Found at i:4623594 original size:185 final size:185
Alignment explanation
Indices: 4623121--4623572 Score: 554
Period size: 186 Copynumber: 2.4 Consensus size: 185
4623111 GTGTAACCCT
* *
4623121 TTTTATTAATAAAAATATTAACATTCCAAATCGCAACCGGTTTCTTAGTG-ATCCATGACATTTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTGTTTCTTAGTGAAT-CATGACATTTT
* ** *
4623185 TAGGCATAATCGTATTTTTTATATATATTCATAATATTTTCAGTTTTTAACTTATTTTCTTATTG
65 TAGGCACAA-CCCATTTTTTATATATATTCATAACATTTTCAGTTTTTAACTTATTTTCTTATTG
* *
4623250 TGAGAAAATACAATGGTCCATCATATTAAACTGTGGTAACATTTTAGGCGCAATCCA
129 TGAGAAAATACAATGCTCCATCAGATTAAACTGTGGTAACATTTTAGGCGCAATCCA
* * * * *
4623307 TTATATTAATAAAAATATTAACATTCTAGATCACAACTTGTTTCTTAGTGAACCATGACATTTTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTGTTTCTTAGTGAATCATGACATTTTT
* *
4623372 AGACGCAA-CCATATTTCTTATATATATTCATAACATTTTCAGTTTTTAACTTATTTTCTTATTG
66 AGGCACAACCCAT-TTT-TTATATATATTCATAACATTTTCAGTTTTTAACTTATTTTCTTATTG
* * * * * * * *
4623436 TG-GGAAATTCAACT-CTCCATTAGCTTAAATTGTGGTAACATTTTAGGTG-TAGCTCA
129 TGAGAAAATACAA-TGCTCCATCAGATTAAACTGTGGTAACATTTTAGGCGCAATC-CA
* * * * *
4623492 TTTTATTAATAAAAATATTAGCATTCCAGATCGCAACCTATTTCTTAGTGAATCATAACATTCTC
1 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTGTTTCTTAGTGAATCATGACATTTTT
*
4623557 GGGCACAACCCATTTT
66 AGGCACAACCCATTTT
4623573 ATTAACAAAA
Statistics
Matches: 224, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
184 4 0.02
185 105 0.47
186 114 0.51
187 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (185 bp):
TTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTGTTTCTTAGTGAATCATGACATTTTT
AGGCACAACCCATTTTTTATATATATTCATAACATTTTCAGTTTTTAACTTATTTTCTTATTGTG
AGAAAATACAATGCTCCATCAGATTAAACTGTGGTAACATTTTAGGCGCAATCCA
Found at i:4623960 original size:77 final size:76
Alignment explanation
Indices: 4623754--4623986 Score: 258
Period size: 76 Copynumber: 3.1 Consensus size: 76
4623744 GGCACAATCC
* * * * * *
4623754 ATTTTATT-A-AAAAATACTAATATTCTAGGTCGCAACTTATTTCTTAGTGAACTATGACATTCT
1 ATTTTATTAATAAAAATATTAACATTC-AGATCGCAACATATTTCTTAATGAACCATGACATTCT
**
4623817 TGGGCACAACAC-
65 TGGGTGCAAC-CT
* * * *
4623829 GTTTTATTAATAAAAA-ATTAACATTCCAGATCTCAATATATTTCTTAATGAACCATGATATTCT
1 ATTTTATTAATAAAAATATTAACATT-CAGATCGCAACATATTTCTTAATGAACCATGACATTCT
4623893 TGGGTGCAACCT
65 TGGGTGCAACCT
* *
4623905 ATTTTATTAATAAAAATATTAACATTACAGATCGCAACATATTTCTTAATAAACCATGACATTTT
1 ATTTTATTAATAAAAATATTAACATT-CAGATCGCAACATATTTCTTAATGAACCATGACATTCT
*
4623970 TAGGTGCAACCAT
65 TGGGTGCAACC-T
4623983 ATTT
1 ATTT
4623987 CTTATATTCA
Statistics
Matches: 132, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
75 8 0.06
76 61 0.46
77 58 0.44
78 5 0.04
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (76 bp):
ATTTTATTAATAAAAATATTAACATTCAGATCGCAACATATTTCTTAATGAACCATGACATTCTT
GGGTGCAACCT
Found at i:4630725 original size:2 final size:2
Alignment explanation
Indices: 4630718--4630768 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
4630708 ACAAATCTTA
*
4630718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4630760 AT AT AT AT A
1 AT AT AT AT A
4630769 CTTTTCAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4631053 original size:36 final size:35
Alignment explanation
Indices: 4631013--4631319 Score: 215
Period size: 36 Copynumber: 8.7 Consensus size: 35
4631003 CTTGAAAATG
* *
4631013 ATTTTTAAAAAATATATAATATAGTTTTTTGAAAAT
1 ATTTTTAAAAAATATATAATATAG-TTTTTAAAAAC
* * * *
4631049 ATTTTT---AAA-A-GT-GTATAGTTTTTGAAAAT
1 ATTTTTAAAAAATATATAATATAGTTTTTAAAAAC
* *
4631078 ATTTTTGAAAATATATATAATATATGGTTTTAAAAA-
1 ATTTTT-AAAAAATATATAATATA-GTTTTTAAAAAC
*
4631114 ATATTTTAAAAAAACATATATATTATATAG-TTTAAAAAAC
1 AT-TTTT--AAAAA-ATATATA--ATATAGTTTTTAAAAAC
* * *
4631154 A-TTTTGAAATATATATAATATGATTTTTTAAAAAC
1 ATTTTTAAAAAATATATAATAT-AGTTTTTAAAAAC
*
4631189 ATTTTTAAAATATATATAATATATGGTTTTTAAAAAC
1 ATTTTTAAAAAATATATAATATA--GTTTTTAAAAAC
* *
4631226 A-TTTTGAAAAATGTATAATGTATAGTTTTT-AAAAC
1 ATTTTTAAAAAATATATAA--TATAGTTTTTAAAAAC
* * * *
4631261 A-TTTTGAAAACTATATAATATAGGATTTTGAAAAC
1 ATTTTTAAAAAATATATAATATA-GTTTTTAAAAAC
4631296 ATTTTTAAAAATATATATAATATA
1 ATTTTTAAAAA-ATATATAATATA
4631320 TAATTTTAAA
Statistics
Matches: 222, Mismatches: 24, Indels: 49
0.75 0.08 0.17
Matches are distributed among these distances:
29 17 0.08
30 5 0.02
31 1 0.00
32 1 0.00
33 13 0.06
34 7 0.03
35 46 0.21
36 62 0.28
37 36 0.16
38 12 0.05
39 15 0.07
40 2 0.01
41 5 0.02
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (35 bp):
ATTTTTAAAAAATATATAATATAGTTTTTAAAAAC
Found at i:4631068 original size:30 final size:30
Alignment explanation
Indices: 4631032--4631088 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
4631022 AAATATATAA
4631032 TATAGTTTTTTGAAAATATTTTT-AAAAGTG
1 TATAG-TTTTTGAAAATATTTTTGAAAAGTG
4631062 TATAGTTTTTGAAAATATTTTTGAAAA
1 TATAGTTTTTGAAAATATTTTTGAAAA
4631089 TATATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (30 bp):
TATAGTTTTTGAAAATATTTTTGAAAAGTG
Found at i:4631084 original size:12 final size:12
Alignment explanation
Indices: 4631038--4631091 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 12
4631028 ATAATATAGT
4631038 TTTTTGAAAATA
1 TTTTTGAAAATA
*
4631050 TTTTTAAAAGTGTATA
1 TTTTTGAAA----ATA
4631066 GTTTTTGAAAATA
1 -TTTTTGAAAATA
4631079 TTTTTGAAAATA
1 TTTTTGAAAATA
4631091 T
1 T
4631092 ATATAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
12 21 0.60
13 3 0.09
16 3 0.09
17 8 0.23
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (12 bp):
TTTTTGAAAATA
Found at i:4631094 original size:29 final size:30
Alignment explanation
Indices: 4631031--4631094 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
4631021 AAAATATATA
4631031 ATATAGTTTTTTGAAAATATTTTTAAAAGT
1 ATATAGTTTTTTGAAAATATTTTTAAAAGT
*
4631061 GTATAG-TTTTTGAAAATATTTTTGAAAA-T
1 ATATAGTTTTTTGAAAATATTTTT-AAAAGT
4631090 ATATA
1 ATATA
4631095 TAATATATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (30 bp):
ATATAGTTTTTTGAAAATATTTTTAAAAGT
Found at i:4631326 original size:37 final size:37
Alignment explanation
Indices: 4631062--4631348 Score: 254
Period size: 35 Copynumber: 7.8 Consensus size: 37
4631052 TTTAAAAGTG
* *
4631062 TATAGTTTTTGAAAATATTTTTGAAAATATATATAATA
1 TATAG-TTTTAAAAACATTTTTGAAAATATATATAATA
* * * *
4631100 TATGGTTTTAAAAA-ATATTTTAAAAAAACATATATATTA
1 TATAGTTTTAAAAACAT-TTTT--GAAAATATATATAATA
*
4631139 TATAGTTTAAAAAACA-TTTTG-AAATATATATAATA
1 TATAGTTTTAAAAACATTTTTGAAAATATATATAATA
*
4631174 TGAT-TTTTTAAAAACATTTTT-AAAATATATATAATA
1 T-ATAGTTTTAAAAACATTTTTGAAAATATATATAATA
* * *
4631210 TATGGTTTTTAAAAACA-TTTTGAAAA-ATGTATAATG
1 TATAG-TTTTAAAAACATTTTTGAAAATATATATAATA
* *
4631246 TATAGTTTTTAAAACA-TTTTGAAAA-CTATATAATA
1 TATAGTTTTAAAAACATTTTTGAAAATATATATAATA
* * *
4631281 TA-GGATTTTGAAAACATTTTTAAAAATATATATAATA
1 TATAG-TTTTAAAAACATTTTTGAAAATATATATAATA
* * *
4631318 TATAATTTT-AAAATATTATTTGAAAGTATAT
1 TATAGTTTTAAAAACATT-TTTGAAAATATAT
4631349 TATATGATTT
Statistics
Matches: 205, Mismatches: 29, Indels: 31
0.77 0.11 0.12
Matches are distributed among these distances:
34 1 0.00
35 63 0.31
36 54 0.26
37 53 0.26
38 8 0.04
39 25 0.12
40 1 0.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (37 bp):
TATAGTTTTAAAAACATTTTTGAAAATATATATAATA
Found at i:4637176 original size:106 final size:105
Alignment explanation
Indices: 4636973--4637634 Score: 731
Period size: 106 Copynumber: 6.5 Consensus size: 105
4636963 GACGAAGGGG
* * * * *
4636973 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGC
1 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGT
* * * **
4637038 TCAACTTCAC-AGCGAAGGGGCAGTTGACTGTCAACAAACAA
66 TCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAA-AAACAA
*
4637079 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
1 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGT
*
4637144 TCAACTTCACGACGAAGGGACCGCTGGTTGTC-AATA-AA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAA
* * * *
4637182 -----CAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCAAAAGC
1 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGT
* * * * **
4637238 TCAACTTCACAACGAAGGGGCGGTTGACTGTCAACAAACAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAA
* * *
4637279 CTTCTCAATTTCAGAGCCAATTTTAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGT
1 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGT
* *
4637344 TCAACTTCACGACGATGGGACCGCTAGTTGTCAATAAACAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAA
* *
4637385 TTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACACAAGT
1 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGT
*
4637450 TCAACTTCACGACGAAGGGACCGCTGGTTGTC-AATA-AA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAA
* * *
4637488 -----CAATTTC----CCAATTTCAACTTCACAACAAAAGATATTGGGCTCCAGACAACACAAGT
1 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGT
* *
4637544 TCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAATAA
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAA
* * * * * ** *
4637585 TTTCCCAGTTCCAAAGCCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
4637635 TGGAACAATA
Statistics
Matches: 472, Mismatches: 59, Indels: 50
0.81 0.10 0.09
Matches are distributed among these distances:
94 147 0.31
95 2 0.00
96 4 0.01
97 4 0.01
98 14 0.03
102 12 0.03
103 4 0.01
104 4 0.01
105 2 0.00
106 278 0.59
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (105 bp):
CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGT
TCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAA
Found at i:4637213 original size:200 final size:200
Alignment explanation
Indices: 4636989--4637591 Score: 782
Period size: 200 Copynumber: 3.0 Consensus size: 200
4636979 AATTTCAGAG
*
4636989 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGCGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGCGAA
*
4637054 GGGGCAGTTGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
66 GGGGCAGTTGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAG
4637119 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
4637184 ATTTC
196 ATTTC
* *
4637189 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCAAAAGCTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGCGAA
* * *
4637254 GGGGCGGTTGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTTAACTTCACAACGAATG
66 GGGGCAGTTGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAG
* *
4637319 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGATGGGACCGCTAGTTGTCAATAAACA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-A
4637384 ATTTCTCAATTTC
193 A-----CAATTTC
* * * *
4637397 AGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACACAAGTTCAACTTCAC-G
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAG
* * * ** *
4637461 ACGAAGGGACCGCTGGTTGTC-A-ATA-AA-----CAATTTC----CCAATTTCAACTTCACAAC
62 -CGAAGGGGCAGTTGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
* * * *
4637514 AAAAGATATTGGGCTCCAGACAACACAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAAT
126 GAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
*
4637579 AAATAATTTC
191 AAACAATTTC
4637589 CCA
1 CCA
4637592 GTTCCAAAGC
Statistics
Matches: 361, Mismatches: 29, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
188 3 0.01
192 6 0.02
197 2 0.01
198 1 0.00
200 258 0.71
202 1 0.00
203 2 0.01
204 7 0.02
208 7 0.02
209 2 0.01
210 2 0.01
211 1 0.00
212 69 0.19
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (200 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGCGAA
GGGGCAGTTGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAG
ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
ATTTC
Found at i:4637550 original size:306 final size:306
Alignment explanation
Indices: 4636973--4637634 Score: 934
Period size: 306 Copynumber: 2.2 Consensus size: 306
4636963 GACGAAGGGG
* *
4636973 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGC
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
* *
4637038 TCAACTTCACAGCGAAGGGGCAGTTGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTC
66 TCAACTTCACAGCGAAGGGACAGTAGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTC
*
4637103 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
131 AACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGC
* * *
4637168 TGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCA
196 TGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACAAAAGATATTGGACTCAAGACAACA
4637233 AAAGCTCAACTTCACAACGAAGGGGCGGTTGACTGTCAACAAACAA
261 AAAGCTCAACTTCACAACGAAGGGGCGGTTGACTGTCAACAAACAA
* * * * * *
4637279 CTTCTCAATTTCAGAGCCAATTTTAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
* * * * *
4637344 TCAACTTCAC-GACGATGGGACCGCTAG-TTGTCAATAAACAATTTCTCAATTTCAGAGCCAATT
66 TCAACTTCACAG-CGAAGGGACAG-TAGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
*
4637407 TCAACTTCACAACGAATGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACC
129 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACC
* *
4637472 GCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACAAAAGATATTGGGCTCCAGACAA
194 GCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACAAAAGATATTGGACTCAAGACAA
* * * * * ** * *
4637537 CACAAGTTCAACTTCACGACGAAGGGATC-GCTGGTTGTCAATAAATAA
259 CAAAAGCTCAACTTCACAACGAAGGG-GCGGTTGACTGTCAACAAACAA
* * * * ** *
4637585 TTTCCCAGTTCCAAAGCCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
4637635 TGGAACAATA
Statistics
Matches: 312, Mismatches: 41, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
305 1 0.00
306 308 0.99
307 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (306 bp):
CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
TCAACTTCACAGCGAAGGGACAGTAGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTC
AACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGC
TGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACAAAAGATATTGGACTCAAGACAACA
AAAGCTCAACTTCACAACGAAGGGGCGGTTGACTGTCAACAAACAA
Found at i:4638113 original size:165 final size:165
Alignment explanation
Indices: 4637835--4638745 Score: 1333
Period size: 165 Copynumber: 5.5 Consensus size: 165
4637825 TCTGCCAACA
* * * *
4637835 AAAGACCTTTGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
1 AAAGACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTCG
*
4637900 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTACATCATT
66 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
4637965 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
131 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
*
4638000 AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGGCACATCATTTGCAGCATAACTTAAGTCG
1 AAAGACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTCG
* * *
4638065 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCAAAGGCTCATCATT
66 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
4638130 TGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
131 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
* * * * *
4638165 AAAGACC-CCAGAGGTCGATTACACTCAACTTCGAGGGAACATCATTTGCAGCATAACTTAAGTC
1 AAAGACCTTC-GAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTC
* *
4638229 GAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
65 GAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* *
4638294 TTGCAGCATAGCTTAAGTTGAAAAGGGCTATCTGCC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
* *
4638330 AGAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGGCACATCATTTGCAGCATAACTTAAGTCG
1 AAAGACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTCG
* *
4638395 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGACACATCAT
66 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
*
4638459 TTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTGCC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
** * * *
4638495 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGAACATCATTTGCAGCATAACTTAACTCG
1 AAAGACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTCG
* * *
4638560 AGAAGGGTTATCTGCCAATCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCATATCATT
66 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * * * *
4638625 TGCAGTACAACTTAAGTCTAAAAGGGTTGTCTGCCAAC
131 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C
* * * * * *
4638663 AAAAGACCTTTGAGTTCGACTACGCTTAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTC
1 -AAAGACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTC
*
4638727 GAGAAGGGCTATCTGCCAA
65 GAGAAGGGTTATCTGCCAA
4638746 AGACCCCCGA
Statistics
Matches: 669, Mismatches: 69, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
164 4 0.01
165 589 0.88
166 5 0.01
168 48 0.07
169 23 0.03
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
AAAGACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTCG
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
Found at i:4639419 original size:30 final size:30
Alignment explanation
Indices: 4639385--4639441 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
4639375 AAATATATAA
4639385 TATAGTTTTTTGAAAATATTTTT-AAAAGTG
1 TATAG-TTTTTGAAAATATTTTTGAAAAGTG
4639415 TATAGTTTTTGAAAATATTTTTGAAAA
1 TATAGTTTTTGAAAATATTTTTGAAAA
4639442 TATATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (30 bp):
TATAGTTTTTGAAAATATTTTTGAAAAGTG
Found at i:4639437 original size:12 final size:12
Alignment explanation
Indices: 4639391--4639444 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 12
4639381 ATAATATAGT
4639391 TTTTTGAAAATA
1 TTTTTGAAAATA
*
4639403 TTTTTAAAAGTGTATA
1 TTTTTGAAA----ATA
4639419 GTTTTTGAAAATA
1 -TTTTTGAAAATA
4639432 TTTTTGAAAATA
1 TTTTTGAAAATA
4639444 T
1 T
4639445 ATATAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
12 21 0.60
13 3 0.09
16 3 0.09
17 8 0.23
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (12 bp):
TTTTTGAAAATA
Done.