Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 10 of 133
Found at i:2654453 original size:32 final size:32
Alignment explanation
Indices: 2654412--2654480 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
2654402 ATTTTAATTC
2654412 TCTTGGTAGGATACCTTAAGGAAATTAAACTT
1 TCTTGGTAGGATACCTTAAGGAAATTAAACTT
2654444 TCTTGGTAGGATACCTTAAGGAAATTAAACTT
1 TCTTGGTAGGATACCTTAAGGAAATTAAACTT
2654476 TCTTG
1 TCTTG
2654481 CGAGATTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (32 bp):
TCTTGGTAGGATACCTTAAGGAAATTAAACTT
Found at i:2654739 original size:26 final size:25
Alignment explanation
Indices: 2654702--2654751 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
2654692 TTTAAACTCC
*
2654702 AAATATGTTAAATATCATTTATTAAT
1 AAATATGTTAAAAAT-ATTTATTAAT
2654728 AAATAT-TCTAAAAATATTTATTAA
1 AAATATGT-TAAAAATATTTATTAA
2654752 GATGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AAATATGTTAAAAATATTTATTAAT
Found at i:2663158 original size:18 final size:18
Alignment explanation
Indices: 2663135--2663171 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2663125 TTGAATCTAA
*
2663135 TTATATATTTTTTAATTT
1 TTATATATTTTTAAATTT
2663153 TTATATATTTTTAAATTT
1 TTATATATTTTTAAATTT
2663171 T
1 T
2663172 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATATATTTTTAAATTT
Found at i:2663165 original size:17 final size:18
Alignment explanation
Indices: 2663135--2663174 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
2663125 TTGAATCTAA
*
2663135 TTATATATTTTTTAATTT
1 TTATATATTTTTTAAATT
2663153 TTATATA-TTTTTAAATT
1 TTATATATTTTTTAAATT
2663170 TTATA
1 TTATA
2663175 AAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATATATTTTTTAAATT
Found at i:2663268 original size:22 final size:24
Alignment explanation
Indices: 2663221--2663273 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 24
2663211 AAATTAAAAA
*
2663221 TAAATTAATAAAATCAAATTTTATT
1 TAAATTAATAAAAT-AAATTTAATT
2663246 TAAATTAAT-AAAT-AATTTAATT
1 TAAATTAATAAAATAAATTTAATT
2663268 TAAATT
1 TAAATT
2663274 TTTATAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 14 0.52
24 4 0.15
25 9 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TAAATTAATAAAATAAATTTAATT
Found at i:2672505 original size:13 final size:13
Alignment explanation
Indices: 2672484--2672518 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2672474 TGTCTGATTC
*
2672484 AAATATAATATAT
1 AAATTTAATATAT
*
2672497 AAATTTAATATTT
1 AAATTTAATATAT
2672510 AAATTTAAT
1 AAATTTAAT
2672519 TCAAACTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTTAATATAT
Found at i:2674121 original size:20 final size:20
Alignment explanation
Indices: 2674084--2674122 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2674074 TTATATTTAA
* **
2674084 AATTATTAAAATTTAAAATT
1 AATTACTAAAATAAAAAATT
2674104 AATTACTAAAATAAAAAAT
1 AATTACTAAAATAAAAAAT
2674123 ATAACATTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTACTAAAATAAAAAATT
Found at i:2675186 original size:18 final size:18
Alignment explanation
Indices: 2675146--2675180 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2675136 ATAATAATAA
*
2675146 ATAAAAAAATGGATAAAG
1 ATAAAAAAAAGGATAAAG
2675164 ATAAAAAAAAGGATAAA
1 ATAAAAAAAAGGATAAA
2675181 ATTAAAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
ATAAAAAAAAGGATAAAG
Found at i:2675207 original size:25 final size:24
Alignment explanation
Indices: 2675159--2675208 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2675149 AAAAAATGGA
*
2675159 TAAAGATAAAAAAAAGGATAAAAT
1 TAAAGATAAAAAAAAGAATAAAAT
* *
2675183 TAAAGATTAATAAAAAGAATTAAAT
1 TAAAGA-TAAAAAAAAGAATAAAAT
2675208 T
1 T
2675209 GGTCATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (24 bp):
TAAAGATAAAAAAAAGAATAAAAT
Found at i:2676064 original size:21 final size:22
Alignment explanation
Indices: 2676031--2676083 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
2676021 TTTGCTCAAG
*
2676031 TTTAATATT-AAAATATT-ATTT
1 TTTAAT-TTAAAAATATTGATAT
*
2676052 TTTAATTTAAAAATGTTGATAT
1 TTTAATTTAAAAATATTGATAT
*
2676074 TTGAATTTAA
1 TTTAATTTAA
2676084 TTATTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 13 0.48
22 12 0.44
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTAATTTAAAAATATTGATAT
Found at i:2677348 original size:27 final size:28
Alignment explanation
Indices: 2677310--2677368 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
2677300 TAGTGGAAAG
2677310 TGTTTCATTATGTAAGTGG-TTTGGTAA
1 TGTTTCATTATGTAAGTGGTTTTGGTAA
2677337 TGTTTCATTATGTAAGTGGTTTTTGGTAA
1 TGTTTCATTATGTAAGTGG-TTTTGGTAA
2677366 TGT
1 TGT
2677369 GGTTGATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 19 0.63
29 11 0.37
ACGTcount: A:0.20, C:0.03, G:0.25, T:0.51
Consensus pattern (28 bp):
TGTTTCATTATGTAAGTGGTTTTGGTAA
Found at i:2680105 original size:43 final size:42
Alignment explanation
Indices: 2680040--2680126 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 42
2680030 TGCAATTGGT
*
2680040 TTTAGTTTTTAATCAGTTTTATAATGTGTCAATCTTAATGTC
1 TTTAGTTTTTAATCAATTTTATAATGTGTCAATCTTAATGTC
* *
2680082 TTTAGTTTTTAAATCAATTTTATAATGTGTTAGTCTTAATGTC
1 TTTAGTTTTT-AATCAATTTTATAATGTGTCAATCTTAATGTC
2680125 TT
1 TT
2680127 AATTTGAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 10 0.24
43 31 0.76
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.54
Consensus pattern (42 bp):
TTTAGTTTTTAATCAATTTTATAATGTGTCAATCTTAATGTC
Found at i:2686334 original size:14 final size:14
Alignment explanation
Indices: 2686315--2686344 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2686305 GCGTAGCTGG
*
2686315 AAGAAAGCATCTGA
1 AAGAAAGAATCTGA
2686329 AAGAAAGAATCTGA
1 AAGAAAGAATCTGA
2686343 AA
1 AA
2686345 CAGCTAACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.10, G:0.20, T:0.13
Consensus pattern (14 bp):
AAGAAAGAATCTGA
Found at i:2698112 original size:17 final size:17
Alignment explanation
Indices: 2698092--2698127 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2698082 TATTAATATT
2698092 TTAAATATTTTATAAAA
1 TTAAATATTTTATAAAA
*
2698109 TT-AATTTTTTATAAAA
1 TTAAATATTTTATAAAA
2698125 TTA
1 TTA
2698128 TATTGAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATATTTTATAAAA
Found at i:2705435 original size:3 final size:3
Alignment explanation
Indices: 2705427--2705453 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2705417 CAGAGAAAGA
2705427 AGT AGT AGT AGT AGT AGT AGT AGT AGT
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT
2705454 CTACGTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
AGT
Found at i:2706254 original size:2 final size:2
Alignment explanation
Indices: 2706247--2706287 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
2706237 TCCCATGACC
*
2706247 AT AT AT AT A- AT AT AT A- AT AT AC A- 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
2706286 AT
1 AT
2706288 TTAACTCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2708524 original size:2 final size:2
Alignment explanation
Indices: 2708517--2708553 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2708507 AAATAGGAAG
2708517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2708554 AATGGAAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2710444 original size:52 final size:52
Alignment explanation
Indices: 2710360--2710511 Score: 198
Period size: 52 Copynumber: 2.9 Consensus size: 52
2710350 ACAAGAAGAT
* * * * *
2710360 TTGCAAAAGAAGAATTCCAAGAGAAAAAAGATTCTTAATAGGTAAGTTTAAC
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTAAC
* *
2710412 TTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTTGAC
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTAAC
* * * *
2710464 TTACAGGAGAAGAATTCTAAGAGGAGAG-GATTCTTAATGGGCAAGTTT
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
2710512 GTATGGTTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 19 0.22
52 69 0.78
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (52 bp):
TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTAAC
Found at i:2711118 original size:24 final size:24
Alignment explanation
Indices: 2711091--2711136 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2711081 ATTCAAGATG
*
2711091 TGGAAGAGCCGATGGTTCGAGACA
1 TGGAAGAGCCGACGGTTCGAGACA
**
2711115 TGGAAGAGTTGACGGTTCGAGA
1 TGGAAGAGCCGACGGTTCGAGA
2711137 TATGAAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.39, T:0.20
Consensus pattern (24 bp):
TGGAAGAGCCGACGGTTCGAGACA
Found at i:2711529 original size:52 final size:52
Alignment explanation
Indices: 2711445--2711596 Score: 200
Period size: 52 Copynumber: 2.9 Consensus size: 52
2711435 ACAAGAAGAT
* * *
2711445 TTGCAAAAGAAGAATTCCAAGA-GAAAGAAGATTCTTAATAGGTAAGTTTAAC
1 TTGCAAGAGAAGAATTCTAAGAGGAAAG-AGATTCTTAATAGGCAAGTTTAAC
* *
2711497 TTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTTGAC
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTAAC
* * * *
2711549 TTACAGGAGAAGAATTCTAAGAGGAGAG-GATTCTTAATGGGCAAGTTT
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
2711597 GTATGGTTAT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
51 19 0.21
52 65 0.73
53 5 0.06
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (52 bp):
TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTAAC
Found at i:2712188 original size:25 final size:25
Alignment explanation
Indices: 2712160--2712207 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2712150 ATTCAAGATG
*
2712160 TGGGAAGAGCCGATGGTTCGAGACA
1 TGGGAAGAGCCGACGGTTCGAGACA
**
2712185 TGGGAAGAGTTGACGGTTCGAGA
1 TGGGAAGAGCCGACGGTTCGAGA
2712208 TATGAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.12, G:0.42, T:0.19
Consensus pattern (25 bp):
TGGGAAGAGCCGACGGTTCGAGACA
Found at i:2712600 original size:52 final size:52
Alignment explanation
Indices: 2712516--2712667 Score: 200
Period size: 52 Copynumber: 2.9 Consensus size: 52
2712506 ACAAGAAGAT
* * *
2712516 TTGCAAAAGAAGAATTCCAAGA-GAAAGAAGATTCTTAATAGGTAAGTTTAAC
1 TTGCAAGAGAAGAATTCTAAGAGGAAAG-AGATTCTTAATAGGCAAGTTTAAC
* *
2712568 TTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTTGAC
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTAAC
* * * *
2712620 TTACAGGAGAAGAATTCTAAGAGGAGAG-GATTCTTAATGGGCAAGTTT
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
2712668 GTATGGTTAT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
51 19 0.21
52 65 0.73
53 5 0.06
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (52 bp):
TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTAAC
Found at i:2714075 original size:2 final size:2
Alignment explanation
Indices: 2714068--2714096 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2714058 TTAATTTGGG
2714068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2714097 ACGATAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2715846 original size:24 final size:24
Alignment explanation
Indices: 2715814--2715859 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2715804 TCCGAAAACT
*
2715814 TAATCTCCAAACTATTCATGGACA
1 TAATCTCCAAACCATTCATGGACA
2715838 TAATCTCCAAACCATTCATGGA
1 TAATCTCCAAACCATTCATGGA
2715860 TATGCTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.28
Consensus pattern (24 bp):
TAATCTCCAAACCATTCATGGACA
Found at i:2717616 original size:150 final size:150
Alignment explanation
Indices: 2717345--2717645 Score: 539
Period size: 150 Copynumber: 2.0 Consensus size: 150
2717335 AGCCGGAAAA
* *
2717345 CCCATTTGTTGCGGGTCCTTCTTCTTGCTTTTTTCAAGTCTTTGTCGCTCAGGTTGTTAATGGTA
1 CCCATTTGTTGCGGGACCTTCTTCTTGCGTTTTTCAAGTCTTTGTCGCTCAGGTTGTTAATGGTA
*
2717410 ATGGAACTAACGAAAGACTTCAACCGTTGCACGGCGAGTTTTAGGGTGTCGTCGGGCCTGTTAGC
66 ATGGAACTAACGAAAGACTTCAACCGTTGCACGGCGAGTTTTAGGGTGTCGTCGGGCATGTTAGC
*
2717475 GAGGCAAACTCGGAACCACC
131 GAAGCAAACTCGGAACCACC
*
2717495 CCCATTTGTTGCGGGACCTTCTTCTTGCGTTTTTCAAGTCTTTGTCGCTCTGGTTGTTAATGGTA
1 CCCATTTGTTGCGGGACCTTCTTCTTGCGTTTTTCAAGTCTTTGTCGCTCAGGTTGTTAATGGTA
* *
2717560 ATGGAACTAACGAAAGACTTCAACCGTTGCATGGCGAGTTTTAGGGTGTCTTCGGGCATGTTAGC
66 ATGGAACTAACGAAAGACTTCAACCGTTGCACGGCGAGTTTTAGGGTGTCGTCGGGCATGTTAGC
2717625 GAAGCAAACTCGGAACCACC
131 GAAGCAAACTCGGAACCACC
2717645 C
1 C
2717646 TGGTTCAGTG
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 144 1.00
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.32
Consensus pattern (150 bp):
CCCATTTGTTGCGGGACCTTCTTCTTGCGTTTTTCAAGTCTTTGTCGCTCAGGTTGTTAATGGTA
ATGGAACTAACGAAAGACTTCAACCGTTGCACGGCGAGTTTTAGGGTGTCGTCGGGCATGTTAGC
GAAGCAAACTCGGAACCACC
Found at i:2719445 original size:2 final size:2
Alignment explanation
Indices: 2719438--2719466 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2719428 GCAAATGGGC
2719438 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2719467 AAAGTAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2722781 original size:14 final size:14
Alignment explanation
Indices: 2722762--2722798 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2722752 TAAGTAAGTA
2722762 TGGTGTTAAGGATT
1 TGGTGTTAAGGATT
2722776 TGGTGTTAAGGATT
1 TGGTGTTAAGGATT
2722790 TGGTGTTAA
1 TGGTGTTAA
2722799 TGACAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (14 bp):
TGGTGTTAAGGATT
Found at i:2725056 original size:12 final size:12
Alignment explanation
Indices: 2725039--2725068 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2725029 TCAGAAACAT
*
2725039 CATTCAATAAAC
1 CATTCAACAAAC
2725051 CATTCAACAAAC
1 CATTCAACAAAC
2725063 CATTCA
1 CATTCA
2725069 GTATACGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (12 bp):
CATTCAACAAAC
Found at i:2726644 original size:58 final size:58
Alignment explanation
Indices: 2726451--2726723 Score: 344
Period size: 58 Copynumber: 4.8 Consensus size: 58
2726441 TTATACAGAA
* * *
2726451 AAAATTGATACTTTCAATTTTT-TTCCAAAATATTTTTTAGAAA-CTTTAATTTTGAA-A
1 AAAATTGATACTTTCAATTTTTCTTCAAAAATATTTTTTAGAAAGC-TT-ATTTTCAAGG
* * * *
2726508 AAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTT-GAAAACTTATTTTAAAGG
1 AAAATTGATACTTTCAATTTTTCTTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGG
* * *
2726564 AAAATTGATATTTTAAACTTTTCTTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGG
1 AAAATTGATACTTTCAATTTTTCTTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGG
* * *
2726622 AAAATTGACACTTTTAATTTTTCCTT-AAAAATATTTTTTAGAAAGCTCATTTTCAAGG
1 AAAATTGATACTTTCAATTTTT-CTTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGG
2726680 AAAATTGATACTTTCAACTTTTTC-TCAAAAATATTTTTTAGAAA
1 AAAATTGATACTTTCAA-TTTTTCTTCAAAAATATTTTTTAGAAA
2726724 TAAATAAATA
Statistics
Matches: 191, Mismatches: 17, Indels: 15
0.86 0.08 0.07
Matches are distributed among these distances:
55 7 0.04
56 36 0.19
57 33 0.17
58 107 0.56
59 8 0.04
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (58 bp):
AAAATTGATACTTTCAATTTTTCTTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGG
Found at i:2726967 original size:16 final size:16
Alignment explanation
Indices: 2726946--2726995 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
2726936 TTTTAGTAGA
2726946 TCTCTCCTTCCCTCTC
1 TCTCTCCTTCCCTCTC
2726962 TCTCT-CTTCCCT-TC
1 TCTCTCCTTCCCTCTC
* *
2726976 TTTTTCTCTTCCCTCTC
1 TCTCTC-CTTCCCTCTC
2726993 TCT
1 TCT
2726996 AAACCAACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 5 0.18
15 7 0.25
16 12 0.43
17 4 0.14
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (16 bp):
TCTCTCCTTCCCTCTC
Found at i:2727614 original size:4 final size:4
Alignment explanation
Indices: 2727579--2727743 Score: 51
Period size: 4 Copynumber: 41.5 Consensus size: 4
2727569 AATTAAAAGA
* * * *
2727579 AAAT AATT AGAT AAAT AAA- AATAT TAAC AAAT AAAT -AA- AAAT GATAAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT -A-AAT
* * * * * *
2727627 AGAT AAAT GATAAT ATAT AAAT AGAT AAAT -AAT AAAT ACAT CAAT ATACT
1 AAAT AAAT -A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT
* * * * *
2727677 -AAC AGAT AAAT -AAT -AAT ATAT ATAT TAAT AAAT AGTAAT -AAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A--AAT AAAT AAAT
*
2727723 AAAT AAAT -AAT AAAT ACAT AA
1 AAAT AAAT AAAT AAAT AAAT AA
2727744 GATACAAAGA
Statistics
Matches: 115, Mismatches: 30, Indels: 32
0.65 0.17 0.18
Matches are distributed among these distances:
3 22 0.19
4 77 0.67
5 7 0.06
6 9 0.08
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:2727634 original size:14 final size:13
Alignment explanation
Indices: 2727612--2727737 Score: 62
Period size: 15 Copynumber: 8.8 Consensus size: 13
2727602 TTAACAAATA
2727612 AATAA-AAATGAT
1 AATAATAAATGAT
2727624 AATAGATAAATGAT
1 AATA-ATAAATGAT
2727638 AATATATAAATAGAT
1 AATA-ATAAAT-GAT
*
2727653 AAATAATAAATACAT
1 -AATAATAAAT-GAT
2727668 CAATATACTAACA-GAT
1 -AATA-A-TAA-ATGAT
2727684 AAATAATAATAT-AT
1 -AATAATAA-ATGAT
2727698 ATATTAATAAAT-AGT
1 A-A-TAATAAATGA-T
*
2727713 AATAATAAATAAAT
1 AATAATAAAT-GAT
2727727 AAATAATAAAT
1 -AATAATAAAT
2727738 ACATAAGATA
Statistics
Matches: 94, Mismatches: 6, Indels: 25
0.75 0.05 0.20
Matches are distributed among these distances:
12 4 0.04
13 10 0.11
14 29 0.31
15 36 0.38
16 11 0.12
17 3 0.03
18 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (13 bp):
AATAATAAATGAT
Found at i:2727664 original size:7 final size:7
Alignment explanation
Indices: 2727589--2727743 Score: 83
Period size: 7 Copynumber: 21.6 Consensus size: 7
2727579 AAATAATTAG
2727589 ATAAATA
1 ATAAATA
2727596 A-AAATA
1 ATAAATA
*
2727602 TTAACA-A
1 ATAA-ATA
2727609 ATAAATA
1 ATAAATA
*
2727616 A-AAATG
1 ATAAATA
2727622 AT-AATA
1 ATAAATA
*
2727628 GATAAATG
1 -ATAAATA
2727636 AT-AATA
1 ATAAATA
2727642 TATAAATA
1 -ATAAATA
2727650 GATAAATA
1 -ATAAATA
2727658 ATAAATA
1 ATAAATA
2727665 CATCAATATA
1 -AT-AA-ATA
* *
2727675 CTAACA-G
1 ATAA-ATA
2727682 ATAAATA
1 ATAAATA
2727689 AT-AATA
1 ATAAATA
*
2727695 TATATATTA
1 -ATA-AATA
2727704 ATAAATA
1 ATAAATA
*
2727711 GT-AATA
1 ATAAATA
2727717 ATAAATAA
1 ATAAAT-A
2727725 ATAAATA
1 ATAAATA
2727732 ATAAATA
1 ATAAATA
2727739 CATAA
1 -ATAA
2727744 GATACAAAGA
Statistics
Matches: 114, Mismatches: 16, Indels: 35
0.69 0.10 0.21
Matches are distributed among these distances:
6 27 0.24
7 44 0.39
8 34 0.30
9 6 0.05
10 3 0.03
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (7 bp):
ATAAATA
Found at i:2727769 original size:74 final size:76
Alignment explanation
Indices: 2727629--2727806 Score: 179
Period size: 74 Copynumber: 2.4 Consensus size: 76
2727619 ATGATAATAG
* * * * * * *
2727629 ATAAAT-GATAATATATAAATAGATAAATAATAAATACATCAATATACTAACAGATAAATAATAA
1 ATAAATAGATAATATATAAATAAATAAATAATAAATACATCAAGATACAAACAAAAAAAAAAAAA
* *
2727693 TATATATATTA
66 TATAAATATAA
*
2727704 ATAAATAG-TAATA-ATAAATAAATAAATAATAAATACAT-AAGATACAAAGAAAAAAGAAAAAA
1 ATAAATAGATAATATATAAATAAATAAATAATAAATACATCAAGATACAAACAAAAAA-AAAAAA
2727766 ATATAAATATAA
65 ATATAAATATAA
* * * *
2727778 AAAAATATAGAATACA-AAATAAA-AAATAA
1 ATAAATAGATAATATATAAATAAATAAATAA
2727807 AATGGGCCTA
Statistics
Matches: 86, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
73 12 0.14
74 50 0.58
75 22 0.26
76 2 0.02
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.25
Consensus pattern (76 bp):
ATAAATAGATAATATATAAATAAATAAATAATAAATACATCAAGATACAAACAAAAAAAAAAAAA
TATAAATATAA
Found at i:2727781 original size:16 final size:17
Alignment explanation
Indices: 2727760--2727796 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2727750 AAGAAAAAAG
*
2727760 AAAAAAATATA-AATAT
1 AAAAAAATATAGAATAC
2727776 AAAAAAATATAGAATAC
1 AAAAAAATATAGAATAC
2727793 AAAA
1 AAAA
2727797 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAAAAATATAGAATAC
Found at i:2728075 original size:43 final size:42
Alignment explanation
Indices: 2727986--2728236 Score: 202
Period size: 42 Copynumber: 5.9 Consensus size: 42
2727976 TTGATCAAAA
* * * * *
2727986 CTCCTCTAAGCAGATGCTCAATGACTGTGAAAAACATAAACAAAG
1 CTCCTCTAATCAGAGGCTCAACGACT-T-TAAAA-ATAAATAAAG
* * *
2728031 CTCTTCTAGTCAGAGGCTCAACAACTTTAAAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACGACTTT-AAAAATAAATAAAG
* * *
2728074 CTCCCCTAAACAGAGGCTCAACGACTTTGAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACGACTTTAAAAATAAATAAAG
* * * *
2728116 CTCCTCTAATCAAAGGCTTAGCGACTTTGAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACGACTTTAAAAATAAATAAAG
* * * * ** *
2728158 CTCCGCTAATTAGAGGCTCAATGACTTTGGAAAGCAAAT--TG
1 CTCCTCTAATCAGAGGCTCAACGACTTT-AAAAATAAATAAAG
* * *
2728199 CTCCCCTAATCAGAGGCATC-ACAACTTTGAAAATAAAT
1 CTCCTCTAATCAGAGGC-TCAACGACTTTAAAAATAAAT
2728237 GGCTCATCTA
Statistics
Matches: 169, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
40 8 0.05
41 22 0.13
42 74 0.44
43 40 0.24
44 5 0.03
45 20 0.12
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.24
Consensus pattern (42 bp):
CTCCTCTAATCAGAGGCTCAACGACTTTAAAAATAAATAAAG
Found at i:2728119 original size:42 final size:42
Alignment explanation
Indices: 2728021--2728236 Score: 222
Period size: 42 Copynumber: 5.1 Consensus size: 42
2728011 TGTGAAAAAC
* ** * * *
2728021 ATAAACAAAGCTCTTCTAGTCAGAGGCTCAACAACTTTAAAAA
1 ATAAATAAAGCTCCCCTAATCAGAGGCTCAACGACTTT-GAAA
*
2728064 ATAAATAAAGCTCCCCTAAACAGAGGCTCAACGACTTTGAAA
1 ATAAATAAAGCTCCCCTAATCAGAGGCTCAACGACTTTGAAA
* * * *
2728106 ATAAATAAAGCTCCTCTAATCAAAGGCTTAGCGACTTTGAAA
1 ATAAATAAAGCTCCCCTAATCAGAGGCTCAACGACTTTGAAA
* * *
2728148 ATAAATAAAGCTCCGCTAATTAGAGGCTCAATGACTTTGGAAA
1 ATAAATAAAGCTCCCCTAATCAGAGGCTCAACGACTTT-GAAA
** * *
2728191 GCAAAT--TGCTCCCCTAATCAGAGGCATC-ACAACTTTGAAA
1 ATAAATAAAGCTCCCCTAATCAGAGGC-TCAACGACTTTGAAA
2728231 ATAAAT
1 ATAAAT
2728237 GGCTCATCTA
Statistics
Matches: 144, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
40 8 0.06
41 22 0.15
42 74 0.51
43 40 0.28
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (42 bp):
ATAAATAAAGCTCCCCTAATCAGAGGCTCAACGACTTTGAAA
Found at i:2729274 original size:13 final size:12
Alignment explanation
Indices: 2729258--2729301 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
2729248 CTTGAGTTTT
2729258 TTTTTTCATTCA
1 TTTTTTCATTCA
**
2729270 CTTTTTTTTTTCA
1 -TTTTTTCATTCA
2729283 TTTTTTCATTTCA
1 TTTTTTCA-TTCA
2729296 TTTTTT
1 TTTTTT
2729302 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTTCATTCA
Found at i:2729311 original size:25 final size:24
Alignment explanation
Indices: 2729254--2729315 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
2729244 TCGCCTTGAG
2729254 TTTTTTTTTTCATTCACTTTTTTT
1 TTTTTTTTTTCATTCACTTTTTTT
*
2729278 TTTCATTTTTTCATTTCA-TTTTTTT
1 TTT-TTTTTTTCA-TTCACTTTTTTT
2729303 TATTTTTTTTTCA
1 T-TTTTTTTTTCA
2729316 AGCATAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 3 0.09
25 24 0.73
26 6 0.18
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTTTTTTCATTCACTTTTTTT
Found at i:2733365 original size:27 final size:27
Alignment explanation
Indices: 2733314--2733376 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
2733304 TAATAATAAT
*
2733314 AATA-ATAATTATTATTATTTTTAAAAA
1 AATATATAATTATTATTA-TTATAAAAA
2733341 AATATATAATTATTAATTA-TATAAAAA
1 AATATATAATTATT-ATTATTATAAAAA
*
2733368 AACATATAA
1 AATATATAA
2733377 AAAAACAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 19 0.59
28 9 0.28
29 4 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATATAATTATTATTATTATAAAAA
Found at i:2733369 original size:29 final size:28
Alignment explanation
Indices: 2733314--2733375 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
2733304 TAATAATAAT
* **
2733314 AATA-ATAATTATTATTATTTTTAAAAA
1 AATATATAATTATTATTATATAAAAAAA
2733341 AATATATAATTATTAATTATATAAAAAAA
1 AATATATAATTATT-ATTATATAAAAAAA
*
2733370 CATATA
1 AATATA
2733376 AAAAAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.14
28 9 0.31
29 16 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
AATATATAATTATTATTATATAAAAAAA
Found at i:2733376 original size:12 final size:12
Alignment explanation
Indices: 2733359--2733383 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2733349 ATTATTAATT
2733359 ATATAAAAAAAC
1 ATATAAAAAAAC
2733371 ATATAAAAAAAC
1 ATATAAAAAAAC
2733383 A
1 A
2733384 AAAAACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
ATATAAAAAAAC
Found at i:2734894 original size:15 final size:15
Alignment explanation
Indices: 2734866--2734974 Score: 125
Period size: 16 Copynumber: 7.2 Consensus size: 15
2734856 AAACCCCATA
2734866 AAAATCCAAAATCCCT
1 AAAATCCAAAA-CCCT
* *
2734882 TAAATCCAAATCCCCT
1 AAAATCCAAA-ACCCT
*
2734898 AAAATCCGAAACCCTT
1 AAAATCCAAAACCC-T
2734914 AAAATCC-AAACCCT
1 AAAATCCAAAACCCT
2734928 AAAATCCAAAATCCCT
1 AAAATCCAAAA-CCCT
2734944 AAAATCC-AAACCCT
1 AAAATCCAAAACCCT
*
2734958 TAAAT-CAAAACCCT
1 AAAATCCAAAACCCT
2734972 AAA
1 AAA
2734975 CCTCAAAACC
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
13 1 0.01
14 25 0.31
15 15 0.19
16 40 0.49
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.18
Consensus pattern (15 bp):
AAAATCCAAAACCCT
Found at i:2734930 original size:30 final size:31
Alignment explanation
Indices: 2734866--2734971 Score: 141
Period size: 30 Copynumber: 3.5 Consensus size: 31
2734856 AAACCCCATA
2734866 AAAATCCAAAATCCCTT-AAATCCAAATCCCCT
1 AAAATCCAAAATCCCTTAAAATCCAAA--CCCT
*
2734898 AAAATCCGAAA-CCCTTAAAATCCAAACCCT
1 AAAATCCAAAATCCCTTAAAATCCAAACCCT
2734928 AAAATCCAAAATCCC-TAAAATCCAAACCCT
1 AAAATCCAAAATCCCTTAAAATCCAAACCCT
*
2734958 TAAAT-CAAAA-CCCT
1 AAAATCCAAAATCCCT
2734972 AAACCTCAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
28 3 0.04
29 5 0.07
30 33 0.49
31 8 0.12
32 19 0.28
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.19
Consensus pattern (31 bp):
AAAATCCAAAATCCCTTAAAATCCAAACCCT
Found at i:2734989 original size:14 final size:15
Alignment explanation
Indices: 2734962--2735027 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
2734952 AACCCTTAAA
*
2734962 TCAAAACCCTAAACC
1 TCAAAACCCAAAACC
*
2734977 TCAAAACCCAAACCC
1 TCAAAACCCAAAACC
2734992 T-AAAATCTCC-AAA-C
1 TCAAAA-C-CCAAAACC
*
2735006 TAAAAACCCAAAACC
1 TCAAAACCCAAAACC
2735021 -CAAAACC
1 TCAAAACC
2735028 TTCCATATCC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 2 0.05
14 16 0.38
15 22 0.52
16 2 0.05
ACGTcount: A:0.52, C:0.38, G:0.00, T:0.11
Consensus pattern (15 bp):
TCAAAACCCAAAACC
Found at i:2734991 original size:6 final size:7
Alignment explanation
Indices: 2734963--2735027 Score: 53
Period size: 7 Copynumber: 9.0 Consensus size: 7
2734953 ACCCTTAAAT
2734963 CAAAACC
1 CAAAACC
*
2734970 CTAAACC
1 CAAAACC
2734977 TCAAAACC
1 -CAAAACC
2734985 C-AAACC
1 CAAAACC
2734991 CTAAAATCTC
1 C-AAAA-C-C
*
2735001 C-AAACT
1 CAAAACC
*
2735007 AAAAACC
1 CAAAACC
2735014 CAAAACC
1 CAAAACC
2735021 CAAAACC
1 CAAAACC
2735028 TTCCATATCC
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
6 6 0.13
7 25 0.54
8 12 0.26
9 1 0.02
10 2 0.04
ACGTcount: A:0.52, C:0.38, G:0.00, T:0.09
Consensus pattern (7 bp):
CAAAACC
Found at i:2734996 original size:29 final size:27
Alignment explanation
Indices: 2734963--2735027 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
2734953 ACCCTTAAAT
*
2734963 CAAAACCCTAAACCTCAAAACCC-AAACC
1 CAAAACCC-AAA-CTAAAAACCCAAAACC
2734991 CTAAAATCTCCAAACTAAAAACCCAAAACC
1 C-AAAA-C-CCAAACTAAAAACCCAAAACC
2735021 CAAAACC
1 CAAAACC
2735028 TTCCATATCC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
27 1 0.03
28 2 0.06
29 17 0.53
30 10 0.31
31 2 0.06
ACGTcount: A:0.52, C:0.38, G:0.00, T:0.09
Consensus pattern (27 bp):
CAAAACCCAAACTAAAAACCCAAAACC
Found at i:2739715 original size:21 final size:24
Alignment explanation
Indices: 2739689--2739735 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 24
2739679 CTAAGTTTAA
2739689 GGGTCT-CTAA-AGAATA-GGTTC
1 GGGTCTACTAACAGAATAGGGTTC
2739710 GGGTCTACTAACCAGAATAGGGTTC
1 GGGTCTACTAA-CAGAATAGGGTTC
2739735 G
1 G
2739736 AGAGTTCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.27
22 4 0.18
24 6 0.27
25 6 0.27
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (24 bp):
GGGTCTACTAACAGAATAGGGTTC
Found at i:2740279 original size:58 final size:59
Alignment explanation
Indices: 2740036--2740371 Score: 405
Period size: 58 Copynumber: 5.7 Consensus size: 59
2740026 TTTTGTGCAG
* * * * * **
2740036 GAAAAATTAATACTTTCAAC-TTTTCTCCAAAATA-TTTTTTAGAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTTTTGAAAATTTATTTTTAA
*
2740093 GAAAAATTGATACTTTCAAC-TTTTCTTCAAAAAAACCTTTTTTTGAAAATTTATTTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTC-TCAAAAATA-CTTTTTTTGAAAATTTA-TTTTTAA
* * *
2740154 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTTTTGAAAATTTATTTTTAA
* * * * **
2740213 GGAAAATTGATACTTTCAACTTTTT-TCCAAAAATA-TTTTTTGGAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCT-CAAAAATACTTTTTTTGAAAATTTATTTTTAA
*
2740271 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA-ACTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTTTTGAAAATTTATTTTTAA
* * *
2740329 GGAAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTTTTT
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTTTT
2740372 ACAGTTCCTA
Statistics
Matches: 241, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
57 25 0.10
58 103 0.43
59 46 0.19
60 30 0.12
61 33 0.14
62 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTTTTGAAAATTTATTTTTAA
Found at i:2741842 original size:80 final size:80
Alignment explanation
Indices: 2741709--2741874 Score: 244
Period size: 80 Copynumber: 2.1 Consensus size: 80
2741699 GCAGTGCTAG
* * *
2741709 GGCTGGGAGAAAATCAAACACATTGGGCAGACCCAAAGTCTCTATTATTTCTGAGATAACGTGCT
1 GGCTGGGAGAAAATCAAACACATTGAGCAGACCCAAAGTCTCTATTATTTCTGAGATAACGTACC
*
2741774 TGAGCTTGGTGCCAA
66 TGAACTTGGTGCCAA
* * *
2741789 GGCTGGGAGAAAATCAGAA-ATATTGAGTAGACCCAAAGTCTCTATTATTTCTGAGATGACGTAC
1 GGCTGGGAGAAAATCA-AACACATTGAGCAGACCCAAAGTCTCTATTATTTCTGAGATAACGTAC
2741853 CTGAACTTGGTGCCAA
65 CTGAACTTGGTGCCAA
*
2741869 GACTGG
1 GGCTGG
2741875 CCCTGGCATC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 75 0.97
81 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (80 bp):
GGCTGGGAGAAAATCAAACACATTGAGCAGACCCAAAGTCTCTATTATTTCTGAGATAACGTACC
TGAACTTGGTGCCAA
Found at i:2741989 original size:13 final size:13
Alignment explanation
Indices: 2741971--2741995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2741961 GGCGATCCAG
2741971 CCTTGCTGTATAA
1 CCTTGCTGTATAA
2741984 CCTTGCTGTATA
1 CCTTGCTGTATA
2741996 TATAGTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (13 bp):
CCTTGCTGTATAA
Found at i:2742532 original size:13 final size:13
Alignment explanation
Indices: 2742511--2742540 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2742501 AAAAAATGAT
2742511 AAATATGAAATAA
1 AAATATGAAATAA
*
2742524 AAATTTGAAATAA
1 AAATATGAAATAA
2742537 AAAT
1 AAAT
2742541 GAATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (13 bp):
AAATATGAAATAA
Found at i:2744071 original size:31 final size:31
Alignment explanation
Indices: 2743968--2744070 Score: 154
Period size: 31 Copynumber: 3.3 Consensus size: 31
2743958 TACAAATGTT
2743968 GCTAATATAGTGACGTTTTATAGAAAACGCA
1 GCTAATATAGTGACGTTTTATAGAAAACGCA
* *
2743999 GCTAATATAGTGACATTTTATAGAAAATGCA
1 GCTAATATAGTGACGTTTTATAGAAAACGCA
* *
2744030 ACTAATATAGCT-ACGTTTTATAGAAAACGCG
1 GCTAATATAG-TGACGTTTTATAGAAAACGCA
2744061 GCTAATATAG
1 GCTAATATAG
2744071 CAGCATTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
31 63 0.98
32 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (31 bp):
GCTAATATAGTGACGTTTTATAGAAAACGCA
Found at i:2744080 original size:31 final size:31
Alignment explanation
Indices: 2743983--2744080 Score: 119
Period size: 31 Copynumber: 3.2 Consensus size: 31
2743973 TATAGTGACG
*
2743983 TTTTATAGAAAACGCAGCTAATATAG-TGACA
1 TTTTATAGAAAACGCAGCTAATATAGCAG-CA
* * *
2744014 TTTTATAGAAAATGCAACTAATATAGCTA-CG
1 TTTTATAGAAAACGCAGCTAATATAGC-AGCA
*
2744045 TTTTATAGAAAACGCGGCTAATATAGCAGCA
1 TTTTATAGAAAACGCAGCTAATATAGCAGCA
2744076 TTTTA
1 TTTTA
2744081 CAAATGTTGG
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.02
31 55 0.98
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (31 bp):
TTTTATAGAAAACGCAGCTAATATAGCAGCA
Found at i:2744511 original size:6 final size:6
Alignment explanation
Indices: 2744500--2744550 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
2744490 GTTTTTTGTT
2744500 AATAAA AATAAAA AATAAAA AATAAA AA-AAA TAA-AAA AGATAAA AATAAA
1 AATAAA AAT-AAA AAT-AAA AATAAA AATAAA -AATAAA A-ATAAA AATAAA
2744550 A
1 A
2744551 TGATTTAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 4 0.10
6 20 0.49
7 17 0.41
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (6 bp):
AATAAA
Found at i:2744513 original size:7 final size:7
Alignment explanation
Indices: 2744503--2744550 Score: 60
Period size: 7 Copynumber: 6.4 Consensus size: 7
2744493 TTTTGTTAAT
2744503 AAAAATA
1 AAAAATA
2744510 AAAAATA
1 AAAAATA
2744517 AAAAATAAA
1 AAAAAT--A
2744526 AAAAATA
1 AAAAATA
*
2744533 AAAAAGA
1 AAAAATA
2744540 TAAAAATA
1 -AAAAATA
2744548 AAA
1 AAA
2744551 TGATTTAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
7 23 0.64
8 6 0.17
9 7 0.19
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2744527 original size:15 final size:15
Alignment explanation
Indices: 2744503--2744550 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 15
2744493 TTTTGTTAAT
2744503 AAAAAT-AAAAAATA
1 AAAAATAAAAAAATA
2744517 AAAAATAAAAAAAATA
1 AAAAAT-AAAAAAATA
* *
2744533 AAAAAGATAAAAATA
1 AAAAATAAAAAAATA
2744548 AAA
1 AAA
2744551 TGATTTAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 6 0.20
15 11 0.37
16 13 0.43
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:2744528 original size:9 final size:9
Alignment explanation
Indices: 2744500--2744545 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
2744490 GTTTTTTGTT
2744500 AATAAAAATA
1 AATAAAAA-A
*
2744510 AAAAATAAAA
1 AATAA-AAAA
2744520 AATAAAAAA
1 AATAAAAAA
2744529 AATAAAAAA
1 AATAAAAAA
*
2744538 GATAAAAA
1 AATAAAAA
2744546 TAAAATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 20 0.62
10 9 0.28
11 3 0.09
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.13
Consensus pattern (9 bp):
AATAAAAAA
Found at i:2744533 original size:23 final size:24
Alignment explanation
Indices: 2744503--2744550 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
2744493 TTTTGTTAAT
*
2744503 AAAAATAAAAAATA-AAAAATAAA
1 AAAAATAAAAAAGATAAAAATAAA
2744526 AAAAATAAAAAAGATAAAAATAAA
1 AAAAATAAAAAAGATAAAAATAAA
2744550 A
1 A
2744551 TGATTTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.12
Consensus pattern (24 bp):
AAAAATAAAAAAGATAAAAATAAA
Found at i:2745052 original size:12 final size:11
Alignment explanation
Indices: 2745027--2745061 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2745017 AGAATAAGAG
*
2745027 AAAAGAGAAAA
1 AAAAGAAAAAA
2745038 AAAAGAAAGAAA
1 AAAAGAAA-AAA
2745050 AAAAGAAAAAA
1 AAAAGAAAAAA
2745061 A
1 A
2745062 TCTATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:2746477 original size:11 final size:11
Alignment explanation
Indices: 2746461--2746485 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2746451 GACCAATCTC
2746461 TGATGAACTTT
1 TGATGAACTTT
2746472 TGATGAACTTT
1 TGATGAACTTT
2746483 TGA
1 TGA
2746486 CAACTCAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (11 bp):
TGATGAACTTT
Found at i:2746873 original size:5 final size:5
Alignment explanation
Indices: 2746863--2746902 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
2746853 TTTTTGGTAT
*
2746863 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTT TATTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTT
2746903 TTAAGTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:2748783 original size:22 final size:22
Alignment explanation
Indices: 2748758--2748802 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2748748 AAGGCCATGT
2748758 GCTTACTTTGAGGTCAAAAGCG
1 GCTTACTTTGAGGTCAAAAGCG
2748780 GCTTACTTTGAGGTCAAAAGCG
1 GCTTACTTTGAGGTCAAAAGCG
2748802 G
1 G
2748803 ACCGACTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (22 bp):
GCTTACTTTGAGGTCAAAAGCG
Found at i:2749534 original size:3 final size:3
Alignment explanation
Indices: 2749528--2749556 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2749518 TTGTTTGTAA
2749528 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2749557 AGAAAGTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2750648 original size:2 final size:2
Alignment explanation
Indices: 2750641--2750713 Score: 86
Period size: 2 Copynumber: 39.0 Consensus size: 2
2750631 TCCCATGACC
2750641 AT AT AT AT A- AT AT AT A- AT AT AT GAT AT AT A- AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
*
2750680 AT AT A- AT AT AC A- 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
2750714 TTAACTCTAA
Statistics
Matches: 63, Mismatches: 1, Indels: 14
0.81 0.01 0.18
Matches are distributed among these distances:
1 6 0.10
2 55 0.87
3 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2750655 original size:7 final size:7
Alignment explanation
Indices: 2750643--2750712 Score: 106
Period size: 7 Copynumber: 10.0 Consensus size: 7
2750633 CCATGACCAT
2750643 ATATATA
1 ATATATA
2750650 ATATATA
1 ATATATA
*
2750657 ATATATG
1 ATATATA
2750664 ATATATA
1 ATATATA
2750671 ATATATA
1 ATATATA
2750678 ATATATA
1 ATATATA
*
2750685 ATATACA
1 ATATATA
2750692 ATATAT-
1 ATATATA
2750698 ATATATA
1 ATATATA
2750705 TATATATA
1 -ATATATA
2750713 TTTAACTCTA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
6 6 0.11
7 44 0.77
8 7 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:2752064 original size:18 final size:18
Alignment explanation
Indices: 2752049--2752084 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2752039 AGGAATGTAG
2752049 GTTACAAAAGCGATGTCA
1 GTTACAAAAGCGATGTCA
* *
2752067 GTTTCAAAAGGGATGTCA
1 GTTACAAAAGCGATGTCA
2752085 CTCAATCAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (18 bp):
GTTACAAAAGCGATGTCA
Found at i:2752642 original size:2 final size:2
Alignment explanation
Indices: 2752635--2752664 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2752625 AAATAGGAAG
2752635 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
2752665 GGAAGGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2755372 original size:2 final size:2
Alignment explanation
Indices: 2755365--2755399 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2755355 TTAATTTGGG
* *
2755365 AT AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2755400 AACACTCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:2757119 original size:24 final size:24
Alignment explanation
Indices: 2757087--2757132 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2757077 TCCGAAAACT
*
2757087 TAATCTCCAAACTATTCATGGACA
1 TAATCTCCAAACCATTCATGGACA
2757111 TAATCTCCAAACCATTCATGGA
1 TAATCTCCAAACCATTCATGGA
2757133 TATGCTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.28
Consensus pattern (24 bp):
TAATCTCCAAACCATTCATGGACA
Found at i:2758897 original size:150 final size:150
Alignment explanation
Indices: 2758622--2758922 Score: 530
Period size: 150 Copynumber: 2.0 Consensus size: 150
2758612 GCCGGAAAAA
* *
2758622 CCCATTTGTTGCGGGACCTTCTTTTTGCGTTTTTCAAGTCTTTGTCGTTCTGGTTGTTAATGGTA
1 CCCATTTGTTGCGGGACCTTCTTCTTGCGTTTTTCAAGTCTTTGTCGCTCTGGTTGTTAATGGTA
** *
2758687 ATGGAACTATCGAAAGACTTCAACCGTTGCATGGCGAGTCTTAGGGTGTCTTCGGACATGTTAGC
66 AAAGAACTAACGAAAGACTTCAACCGTTGCATGGCGAGTCTTAGGGTGTCTTCGGACATGTTAGC
2758752 GAAGCAAACTCGGAACCACC
131 GAAGCAAACTCGGAACCACC
*
2758772 CCCATTTGTTGCGGGACCTTCTTCTTGCGTTTTTCGAGTCTTTGTCGCTCTGGTTGTTAATGGTA
1 CCCATTTGTTGCGGGACCTTCTTCTTGCGTTTTTCAAGTCTTTGTCGCTCTGGTTGTTAATGGTA
* *
2758837 AAAGAACTAACGAAAGACTTCAACCGTTGCATGGCGAGTGTTAGGGTGTCTTCGGGCATGTTAGC
66 AAAGAACTAACGAAAGACTTCAACCGTTGCATGGCGAGTCTTAGGGTGTCTTCGGACATGTTAGC
2758902 GAAGCAAACTCGGAACCACC
131 GAAGCAAACTCGGAACCACC
2758922 C
1 C
2758923 TGGTTCAGTG
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 143 1.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (150 bp):
CCCATTTGTTGCGGGACCTTCTTCTTGCGTTTTTCAAGTCTTTGTCGCTCTGGTTGTTAATGGTA
AAAGAACTAACGAAAGACTTCAACCGTTGCATGGCGAGTCTTAGGGTGTCTTCGGACATGTTAGC
GAAGCAAACTCGGAACCACC
Found at i:2760617 original size:2 final size:2
Alignment explanation
Indices: 2760612--2760636 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2760602 AAAAATTATC
2760612 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2760637 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2760641 original size:2 final size:2
Alignment explanation
Indices: 2760636--2760668 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2760626 ATATATATAT
2760636 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2760669 AGGAATTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2762205 original size:24 final size:24
Alignment explanation
Indices: 2762166--2762251 Score: 131
Period size: 24 Copynumber: 3.6 Consensus size: 24
2762156 TAAATTTTTC
2762166 ATTA-AAT-TTTTTTTCAATTACA
1 ATTATAATATTTTTTTCAATTACA
2762188 ATTATAATATTTTTTTCAATTACA
1 ATTATAATATTTTTTTCAATTACA
*
2762212 ATTATAATATTTTTTTTCAATCACA
1 ATTATAATA-TTTTTTTCAATTACA
*
2762237 ATTATAATAATTTTT
1 ATTATAATATTTTTT
2762252 ATTACTATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
22 4 0.07
23 3 0.05
24 29 0.49
25 23 0.39
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTATAATATTTTTTTCAATTACA
Found at i:2762225 original size:25 final size:25
Alignment explanation
Indices: 2762171--2762251 Score: 137
Period size: 25 Copynumber: 3.3 Consensus size: 25
2762161 TTTTCATTAA
2762171 ATTTTTTTTCAATTACAATTATAAT
1 ATTTTTTTTCAATTACAATTATAAT
2762196 A-TTTTTTTCAATTACAATTATAAT
1 ATTTTTTTTCAATTACAATTATAAT
*
2762220 ATTTTTTTTCAATCACAATTATAAT
1 ATTTTTTTTCAATTACAATTATAAT
*
2762245 AATTTTT
1 ATTTTTT
2762252 ATTACTATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
24 24 0.45
25 29 0.55
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTTTTTTCAATTACAATTATAAT
Found at i:2763069 original size:18 final size:18
Alignment explanation
Indices: 2763046--2763081 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2763036 AATAACCCTA
2763046 GGACTATATAATGGGGTG
1 GGACTATATAATGGGGTG
2763064 GGACTATATAATGGGGTG
1 GGACTATATAATGGGGTG
2763082 CCATTTGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.39, T:0.28
Consensus pattern (18 bp):
GGACTATATAATGGGGTG
Found at i:2764633 original size:46 final size:46
Alignment explanation
Indices: 2764583--2764678 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 46
2764573 CAAAAAACAA
*
2764583 AAAAAAAAATTTCTAAA-TGGACCAAAATGGTGAAAAATTTAGAAAT
1 AAAAAAAAATTTCTAAACCGG-CCAAAATGGTGAAAAATTTAGAAAT
* *
2764629 AAAAAAAATTTTCTAAACCGGCCTAAATGGTGAAAAATTTAGAAAT
1 AAAAAAAAATTTCTAAACCGGCCAAAATGGTGAAAAATTTAGAAAT
2764675 AAAA
1 AAAA
2764679 CTTGTAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.24
Consensus pattern (46 bp):
AAAAAAAAATTTCTAAACCGGCCAAAATGGTGAAAAATTTAGAAAT
Found at i:2765695 original size:8 final size:7
Alignment explanation
Indices: 2765674--2765826 Score: 70
Period size: 8 Copynumber: 21.6 Consensus size: 7
2765664 AAAATCACTT
2765674 ATAATAA
1 ATAATAA
*
2765681 TAAAATAA
1 -ATAATAA
2765689 ACTAAT-A
1 A-TAATAA
2765696 A-AATAA
1 ATAATAA
*
2765702 ACAAATAA
1 A-TAATAA
2765710 ATAATAA
1 ATAATAA
*
2765717 TTAATTAA
1 ATAA-TAA
* *
2765725 TTAATTA
1 ATAATAA
2765732 A-AATAA
1 ATAATAA
2765738 ACTAAT-A
1 A-TAATAA
2765745 A-AATAA
1 ATAATAA
*
2765751 ACAAATAA
1 A-TAATAA
*
2765759 TTAATAA
1 ATAATAA
*
2765766 TTAATTAA
1 ATAA-TAA
* *
2765774 TTAATTA
1 ATAATAA
2765781 A-AATAA
1 ATAATAA
2765787 ACTAATAA
1 A-TAATAA
2765795 ACTAAT-A
1 A-TAATAA
2765802 A-AATAA
1 ATAATAA
2765808 ACTAATAA
1 A-TAATAA
2765816 ATAATAA
1 ATAATAA
2765823 ATAA
1 ATAA
2765827 GCCTAGCATA
Statistics
Matches: 117, Mismatches: 12, Indels: 33
0.72 0.07 0.20
Matches are distributed among these distances:
5 9 0.08
6 16 0.14
7 38 0.32
8 54 0.46
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAATAA
Found at i:2765738 original size:49 final size:49
Alignment explanation
Indices: 2765681--2765820 Score: 228
Period size: 49 Copynumber: 2.8 Consensus size: 49
2765671 CTTATAATAA
2765681 TAAAATAAACTAATAAAATAAACAAATAAATAATAATTAATTAATTAAT
1 TAAAATAAACTAATAAAATAAACAAATAAATAATAATTAATTAATTAAT
*
2765730 TAAAATAAACTAATAAAATAAACAAATAATTAATAATTAATTAATTAAT
1 TAAAATAAACTAATAAAATAAACAAATAAATAATAATTAATTAATTAAT
* *
2765779 TAAAATAAACTAATAAACTAATA-AAATAAACTAATAAATAAT
1 TAAAATAAACTAATAAAATAA-ACAAATAAA-TAATAATTAAT
2765821 AAATAAGCCT
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
49 74 0.87
50 11 0.13
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (49 bp):
TAAAATAAACTAATAAAATAAACAAATAAATAATAATTAATTAATTAAT
Found at i:2773349 original size:177 final size:177
Alignment explanation
Indices: 2773046--2773402 Score: 624
Period size: 177 Copynumber: 2.0 Consensus size: 177
2773036 GAAAAAGACA
* * *
2773046 TATGAGGTAAGATTTGGATCCTTGAAAAAGGATATTTTTCAATATTATGAACAATTTGTAAAACT
1 TATGAGCTAAGATTTGGATCCTTGAAAAAGGATATTTTTCAATATTAGGAACAATTTGTAAAACC
2773111 TTCGGGTGTAATCTTCTATAATTTCTTCTGATGATCAATAAAACCTCTAAACATGTTGTTGAAGA
66 TTCGGGTGTAATCTTCTATAATTTCTTCTGATGATCAATAAAACCTCTAAACATGTTGTTGAAGA
* * *
2773176 GTTTTTTTTATTTCTCAAAGTTGTTAAGCTTTTATTTAGAAGAGCCT
131 GCTTTTCTTATTTCTCAAAGTTGTTAAGCCTTTATTTAGAAGAGCCT
* *
2773223 TATGAGCTAAGATTTGGATCCTTGAAAAAGGGTATTTTTCAATATTAGGAACAATTTGTAAGACC
1 TATGAGCTAAGATTTGGATCCTTGAAAAAGGATATTTTTCAATATTAGGAACAATTTGTAAAACC
* *
2773288 TTCGGGTGTAATCTTTTATAATTTCTTCTGATGATCAATAAAACCTCTAGACATGTTGTTGAAGA
66 TTCGGGTGTAATCTTCTATAATTTCTTCTGATGATCAATAAAACCTCTAAACATGTTGTTGAAGA
2773353 GCTTTTCTTATTTCTCAAAGTTGTTAAGCCTTTATTTAGAAGAGCCT
131 GCTTTTCTTATTTCTCAAAGTTGTTAAGCCTTTATTTAGAAGAGCCT
2773400 TAT
1 TAT
2773403 TTATTTTTCA
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
177 170 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (177 bp):
TATGAGCTAAGATTTGGATCCTTGAAAAAGGATATTTTTCAATATTAGGAACAATTTGTAAAACC
TTCGGGTGTAATCTTCTATAATTTCTTCTGATGATCAATAAAACCTCTAAACATGTTGTTGAAGA
GCTTTTCTTATTTCTCAAAGTTGTTAAGCCTTTATTTAGAAGAGCCT
Found at i:2773515 original size:44 final size:43
Alignment explanation
Indices: 2773420--2773537 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 43
2773410 TCAAAAGTTG
* * *
2773420 TTAAACGAGCATTATTTGTTTTTCAAAGTCATTAAGCATCTGC
1 TTAAAAGAGCCTTATTTATTTTTCAAAGTCATTAAGCATCTGC
* *
2773463 TTAGAAGAGCCTTATTTATTTTTCAAAAGTCATTAAGTC-TCTGT
1 TTAAAAGAGCCTTATTTATTTTTC-AAAGTCATTAAG-CATCTGC
*
2773507 TTAAAAGAGTCTTATTTATTTTTCAAAGTCA
1 TTAAAAGAGCCTTATTTATTTTTCAAAGTCA
2773538 ATGAGCCTCT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 27 0.41
44 38 0.58
45 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (43 bp):
TTAAAAGAGCCTTATTTATTTTTCAAAGTCATTAAGCATCTGC
Found at i:2773553 original size:43 final size:43
Alignment explanation
Indices: 2773420--2773554 Score: 162
Period size: 43 Copynumber: 3.1 Consensus size: 43
2773410 TCAAAAGTTG
* * * * *
2773420 TTAAACGAGCATTATTTGTTTTTCAAAGTCATTAAGCATCTGC
1 TTAAAAGAGCCTTATTTATTTTTCAAAGTCATTAAGCCTCTGT
* *
2773463 TTAGAAGAGCCTTATTTATTTTTCAAAAGTCATTAAGTCTCTGT
1 TTAAAAGAGCCTTATTTATTTTTC-AAAGTCATTAAGCCTCTGT
* * * *
2773507 TTAAAAGAGTCTTATTTATTTTTCAAAGTCAATGAGCCTCTAT
1 TTAAAAGAGCCTTATTTATTTTTCAAAGTCATTAAGCCTCTGT
2773550 TTAAA
1 TTAAA
2773555 GTAGTTTTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 40 0.51
44 38 0.49
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (43 bp):
TTAAAAGAGCCTTATTTATTTTTCAAAGTCATTAAGCCTCTGT
Found at i:2778700 original size:14 final size:13
Alignment explanation
Indices: 2778665--2778706 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2778655 TTTTTAGAAA
*
2778665 TTTTA-TTAATTA
1 TTTTATTTAATTT
2778677 TTTTATTTAATTT
1 TTTTATTTAATTT
2778690 TTTTAATTTAAATTT
1 TTTT-ATTT-AATTT
2778705 TT
1 TT
2778707 GAAGGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 4 0.15
15 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTTAATTT
Found at i:2780010 original size:18 final size:18
Alignment explanation
Indices: 2779959--2780011 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 18
2779949 GACTATGTTT
* *
2779959 TTTTTTTTTTGTGCACTA
1 TTTTTTTGTTGTGTACTA
*
2779977 TTTTTTTGGGTGTGTGTATTA
1 TTTTTTT--GT-TGTGTACTA
2779998 TTTTTTTGTTGTGT
1 TTTTTTTGTTGTGT
2780012 TTGGGGAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 12 0.41
19 2 0.07
20 1 0.03
21 14 0.48
ACGTcount: A:0.08, C:0.04, G:0.21, T:0.68
Consensus pattern (18 bp):
TTTTTTTGTTGTGTACTA
Found at i:2780484 original size:8 final size:8
Alignment explanation
Indices: 2780469--2780535 Score: 70
Period size: 8 Copynumber: 8.9 Consensus size: 8
2780459 TATTTTTTAA
2780469 TATTTTTG
1 TATTTTTG
2780477 TATTTTTG
1 TATTTTTG
*
2780485 TA-TATTG
1 TATTTTTG
*
2780492 TA-TATTG
1 TATTTTTG
*
2780499 TA-TATTG
1 TATTTTTG
*
2780506 TA-TATTG
1 TATTTTTG
2780513 TATTTTTG
1 TATTTTTG
2780521 TATTTTTG
1 TATTTTTG
2780529 TATTTTT
1 TATTTTT
2780536 TAATTAATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
7 27 0.48
8 29 0.52
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (8 bp):
TATTTTTG
Found at i:2780501 original size:14 final size:14
Alignment explanation
Indices: 2780482--2780515 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
2780472 TTTTGTATTT
2780482 TTGTATATTGTATA
1 TTGTATATTGTATA
2780496 TTGTATATTGTATA
1 TTGTATATTGTATA
2780510 TTGTAT
1 TTGTAT
2780516 TTTTGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (14 bp):
TTGTATATTGTATA
Found at i:2781015 original size:48 final size:50
Alignment explanation
Indices: 2780951--2781093 Score: 159
Period size: 48 Copynumber: 2.9 Consensus size: 50
2780941 AGGCTTAACA
2780951 ATTTTG-AAAAAGCTCATCTCAGCAGAGGCACAACAACTTTAAAATT-T-
1 ATTTTGAAAAAAGCTCATCTCAGCAGAGGCACAACAACTTTAAAATTCTC
*** *
2780998 ATTTTGAAAAAAGCTCATCTCAGCAGAGATTCAACAACTTTAGAATTCTC
1 ATTTTGAAAAAAGCTCATCTCAGCAGAGGCACAACAACTTTAAAATTCTC
* * * * **
2781048 ATATT-AGAAAAAGCTCCTCTCAACAGAGGCGCAATGACTTTAAAAT
1 ATTTTGA-AAAAAGCTCATCTCAGCAGAGGCACAACAACTTTAAAAT
2781094 AAACCATAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
47 6 0.08
48 36 0.46
49 2 0.03
50 35 0.44
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (50 bp):
ATTTTGAAAAAAGCTCATCTCAGCAGAGGCACAACAACTTTAAAATTCTC
Found at i:2781785 original size:76 final size:75
Alignment explanation
Indices: 2781287--2781788 Score: 515
Period size: 75 Copynumber: 6.5 Consensus size: 75
2781277 TTTTTTTTAG
* * * * * *
2781287 TAATACTTGGATATCTCCACCGAGTGATTTTGAAGATGTCTTGGATTTCACCACCACGAAAATGC
1 TAATACTCGGATATCACCACCGAG-AACTTTGAAAATGTCTTGGATATCACCA-CA--AAAA---
* *
2781352 AAATGCAAATTTAAACTT
59 AAATG-AAATTCATACTT
* * * *
2781370 CAA-ACTCGGATATCACCACCGATTG-ATTTTAAAAATATCTTGGATATCACCACCAAGAAAATA
1 TAATACTCGGATATCACCACCGA--GAACTTTGAAAATGTCTTGGATATCACCA-C-A-AAAA-A
* *
2781433 CAAGTGCAAATTTAAACTT
60 -AA-TG-AAATTCATACTT
* * *
2781452 TAA-ACTCGGATATCACCACCGATTAATTTTGAAAATGTCTTGGATATCACCACCAAAAAAATGA
1 TAATACTCGGATATCACCACCGA-GAACTTTGAAAATGTCTTGGATATCACCACAAAAAAAATGA
2781516 AATTCATACTT
65 AATTCATACTT
* * * * *
2781527 TAATACTCAGATATCACCACTGAGAACTTTGAAAATGTCTTGGATATCACTACTAAGAAAATGAA
1 TAATACTCGGATATCACCACCGAGAACTTTGAAAATGTCTTGGATATCACCACAAAAAAAATGAA
*
2781592 AGTCATACTT
66 ATTCATACTT
* * * * *
2781602 TAATACTAGGATATCACCACCGAGAATTTTGAAAATGTCTTGGATATCACCACCAAGAAAATAAA
1 TAATACTCGGATATCACCACCGAGAACTTTGAAAATGTCTTGGATATCACCACAAAAAAAATGAA
*
2781667 ATTCACACTT
66 ATTCATACTT
2781677 TAATACTCGGATATCACCACCGAGAACTTTTGAAAATGTCTTGGATATCACCACAAAAAAAAATG
1 TAATACTCGGATATCACCACCGAGAAC-TTTGAAAATGTCTTGGATATCACCAC-AAAAAAAATG
2781742 AAATTCATACTT
64 AAATTCATACTT
* **
2781754 TAATACTCGAATATCACCATTGAGAACTTTGAAAA
1 TAATACTCGGATATCACCACCGAGAACTTTGAAAA
2781789 CAATTTATCA
Statistics
Matches: 369, Mismatches: 41, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
75 150 0.41
76 53 0.14
77 44 0.12
78 1 0.00
79 4 0.01
80 1 0.00
81 4 0.01
82 108 0.29
83 3 0.01
84 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (75 bp):
TAATACTCGGATATCACCACCGAGAACTTTGAAAATGTCTTGGATATCACCACAAAAAAAATGAA
ATTCATACTT
Found at i:2782050 original size:35 final size:36
Alignment explanation
Indices: 2781972--2782054 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 36
2781962 ATACCATTAT
2781972 GATGCAAATGTCTTCTCTTAAAATGATTATGCAAATGA
1 GATGCAAATGTCTTCTCTTAAAATG--TATGCAAATGA
* * *
2782010 AATGCAAATGTCTTTTCTTAAAATG-ATGCACATGA
1 GATGCAAATGTCTTCTCTTAAAATGTATGCAAATGA
2782045 GATGCAAATG
1 GATGCAAATG
2782055 AAATACAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 18 0.44
38 23 0.56
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (36 bp):
GATGCAAATGTCTTCTCTTAAAATGTATGCAAATGA
Found at i:2782072 original size:46 final size:46
Alignment explanation
Indices: 2782000--2782099 Score: 164
Period size: 46 Copynumber: 2.2 Consensus size: 46
2781990 TAAAATGATT
* *
2782000 ATGCAAATGAAATGCAAATGTCTTTTCTTAAAATGATGCACATGAG
1 ATGCAAATGAAATACAAATGTCTTTTCTTAAAATGATGCACATGAA
* *
2782046 ATGCAAATGAAATACAAATGTTTTTTCTTAAAATGATGCATATGAA
1 ATGCAAATGAAATACAAATGTCTTTTCTTAAAATGATGCACATGAA
2782092 ATGCAAAT
1 ATGCAAAT
2782100 ATCTCTTCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (46 bp):
ATGCAAATGAAATACAAATGTCTTTTCTTAAAATGATGCACATGAA
Found at i:2782336 original size:21 final size:21
Alignment explanation
Indices: 2782292--2782345 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
2782282 AAATCTTTTC
*
2782292 TTTGCTGTTCATTTTCATCAAT
1 TTTGCT-TTCTTTTTCATCAAT
2782314 TTTGCTTTCTTTATTCA-CAAT
1 TTTGCTTTCTTT-TTCATCAAT
* *
2782335 TTGGATTTCTT
1 TTTGCTTTCTT
2782346 GACTTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (21 bp):
TTTGCTTTCTTTTTCATCAAT
Found at i:2783012 original size:7 final size:7
Alignment explanation
Indices: 2783008--2783048 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
2782998 TTCATTTTTC
2783008 TTTTT-T
1 TTTTTAT
2783014 TTTTTACCT
1 TTTTTA--T
2783023 TTTTTAT
1 TTTTTAT
2783030 TTTTTAT
1 TTTTTAT
2783037 TTTTTAT
1 TTTTTAT
2783044 TTTTT
1 TTTTT
2783049 TGATGATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.16
7 20 0.62
9 7 0.22
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:2788505 original size:22 final size:21
Alignment explanation
Indices: 2788473--2788522 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
2788463 TATTAATAAC
* *
2788473 AAAA-TTTAAAATAACCAAACT
1 AAAATTTTAAAAAAACCAAA-A
*
2788494 AAAATTTTAAAAAAATCAAAA
1 AAAATTTTAAAAAAACCAAAA
2788515 AAAATTTT
1 AAAATTTT
2788523 TTTACTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATTTTAAAAAAACCAAAA
Found at i:2789561 original size:37 final size:37
Alignment explanation
Indices: 2789498--2789603 Score: 149
Period size: 37 Copynumber: 2.8 Consensus size: 37
2789488 CAGCATGGTA
* * *
2789498 GTTCAGGAGTGTTGATGGGGTGGATAAGTTTTGCATG
1 GTTCAAGAGTGCTGATGGGGTAGATAAGTTTTGCATG
* *
2789535 GTTTAAGAGTGCTGATAGGGTAGATAAGTTTTGCATG
1 GTTCAAGAGTGCTGATGGGGTAGATAAGTTTTGCATG
*
2789572 GTTCAAAAGTGCTGATGGGGTAGATAAAGTTT
1 GTTCAAGAGTGCTGATGGGGTAGAT-AAGTTT
2789604 GCAGGGTATG
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
37 54 0.90
38 6 0.10
ACGTcount: A:0.25, C:0.06, G:0.35, T:0.34
Consensus pattern (37 bp):
GTTCAAGAGTGCTGATGGGGTAGATAAGTTTTGCATG
Found at i:2789749 original size:8 final size:8
Alignment explanation
Indices: 2789676--2789749 Score: 64
Period size: 8 Copynumber: 9.6 Consensus size: 8
2789666 CAACCCCCTT
*
2789676 TTTTTGTT
1 TTTTTGTA
*
2789684 TTTTTATA
1 TTTTTGTA
2789692 TTTTTGTA
1 TTTTTGTA
*
2789700 TTTTTATA
1 TTTTTGTA
*
2789708 TTTTTTTA
1 TTTTTGTA
*
2789716 -TATTGTA
1 TTTTTGTA
*
2789723 -TATTGTA
1 TTTTTGTA
*
2789730 GTTTTGTA
1 TTTTTGTA
2789738 -TTTTGTA
1 TTTTTGTA
2789745 TTTTT
1 TTTTT
2789750 ATTTAATTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
7 19 0.34
8 37 0.66
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (8 bp):
TTTTTGTA
Found at i:2797766 original size:2 final size:2
Alignment explanation
Indices: 2797759--2797792 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2797749 AGTTATTTAA
2797759 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
2797793 TACCTTAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2799964 original size:9 final size:9
Alignment explanation
Indices: 2799950--2799975 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2799940 ATTGCTGATC
2799950 TCAACATCT
1 TCAACATCT
2799959 TCAACATCT
1 TCAACATCT
2799968 TCAACATC
1 TCAACATC
2799976 ATCCGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (9 bp):
TCAACATCT
Found at i:2804571 original size:12 final size:12
Alignment explanation
Indices: 2804554--2804579 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2804544 TATATATATA
2804554 TAATTAAAAAAT
1 TAATTAAAAAAT
2804566 TAATTAAAAAAT
1 TAATTAAAAAAT
2804578 TA
1 TA
2804580 TTTTTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATTAAAAAAT
Found at i:2805855 original size:2 final size:2
Alignment explanation
Indices: 2805848--2805885 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2805838 TTCATGTGGG
2805848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2805886 ATTTAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2808430 original size:2 final size:2
Alignment explanation
Indices: 2808418--2808449 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2808408 ATTTTTCATG
*
2808418 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2808450 ATTTAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2833160 original size:15 final size:16
Alignment explanation
Indices: 2833124--2833162 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2833114 TCATATCATG
2833124 AGCAAAAATTGCCAAC
1 AGCAAAAATTGCCAAC
**
2833140 TCCAAAAATTGCC-AC
1 AGCAAAAATTGCCAAC
2833155 AGCAAAAA
1 AGCAAAAA
2833163 AATGAAGAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.51, C:0.26, G:0.10, T:0.13
Consensus pattern (16 bp):
AGCAAAAATTGCCAAC
Found at i:2835910 original size:2 final size:2
Alignment explanation
Indices: 2835903--2835930 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2835893 AACGAAAAAT
2835903 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2835931 ATTACGTCAA
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):
TA
Found at i:2838141 original size:20 final size:19
Alignment explanation
Indices: 2838107--2838154 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
2838097 GTGGAAGTTT
2838107 TTTTTATGTTTTTTT-TTCTA
1 TTTTT-TGTTTTTTTATT-TA
*
2838127 TTTTTTGTTTCTTTTATTTT
1 TTTTTTGTTT-TTTTATTTA
2838147 TTTTTTGT
1 TTTTTTGT
2838155 CTGTGGGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 5 0.20
20 18 0.72
21 2 0.08
ACGTcount: A:0.06, C:0.04, G:0.06, T:0.83
Consensus pattern (19 bp):
TTTTTTGTTTTTTTATTTA
Found at i:2839773 original size:30 final size:31
Alignment explanation
Indices: 2839739--2839796 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2839729 TATCATATTA
*
2839739 ATTAAT-AAATTTATAATTTAAGTATCACAC
1 ATTAATGAAATTTAAAATTTAAGTATCACAC
**
2839769 ATTAATGATTTTTAAAATTTAAGTATCA
1 ATTAATGAAATTTAAAATTTAAGTATCA
2839797 GATTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (31 bp):
ATTAATGAAATTTAAAATTTAAGTATCACAC
Found at i:2839819 original size:31 final size:30
Alignment explanation
Indices: 2839748--2839821 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
2839738 AATTAATAAA
2839748 TTTATAATTTAAGTATCACACATTAATGATT
1 TTTATAATTTAAGTAT-ACACATTAATGATT
* *
2839779 TTTAAAATTTAAGTAT-CAGATTAAAT-ATT
1 TTTATAATTTAAGTATACACATT-AATGATT
2839808 TCATTATAATTTAA
1 T--TTATAATTTAA
2839822 AATTGTTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 9 0.24
30 3 0.08
31 25 0.68
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (30 bp):
TTTATAATTTAAGTATACACATTAATGATT
Found at i:2840756 original size:14 final size:14
Alignment explanation
Indices: 2840718--2840769 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2840708 AATTGCAAAT
*
2840718 TAAATCTTAAA-TA
1 TAAATATTAAATTA
**
2840731 TAAATAAAAAATTA
1 TAAATATTAAATTA
2840745 TAAATATTAAATTTA
1 TAAATATTAAA-TTA
2840760 TCAAATATTA
1 T-AAATATTA
2840770 TTTTTTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 8 0.26
14 11 0.35
15 4 0.13
16 8 0.26
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATATTAAATTA
Found at i:2840781 original size:16 final size:16
Alignment explanation
Indices: 2840742--2840788 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2840732 AAATAAAAAA
2840742 TTATAAATATTA-AAT
1 TTATAAATATTATAAT
**
2840757 TTATCAAATATTATTTT
1 TTAT-AAATATTATAAT
2840774 TTATAAATTATTATA
1 TTATAAA-TATTATA
2840789 TAAATCAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 11 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATAAATATTATAAT
Found at i:2860768 original size:17 final size:19
Alignment explanation
Indices: 2860748--2860782 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2860738 TTATAGTTTA
2860748 AATTTTTA-ATT-TATATT
1 AATTTTTATATTATATATT
2860765 AATTTTTATATTATATAT
1 AATTTTTATATTATATAT
2860783 AGATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTTATATTATATATT
Found at i:2861830 original size:2 final size:2
Alignment explanation
Indices: 2861823--2861849 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2861813 GACCGTCATA
2861823 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2861850 ACTGAATCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2864338 original size:52 final size:52
Alignment explanation
Indices: 2864281--2864383 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
2864271 AAAAAGCAAG
*
2864281 TTGAAATAATATGTATTCTACTACAATCATAAATGTCATTTAACATCAAGCA
1 TTGAAATAATATGTATTCTACTACAATCATAAATGTCATTCAACATCAAGCA
* *
2864333 TTGAAATAATATTTATTCTGCTACAATCATAAATGTCATTCAACATCAAGC
1 TTGAAATAATATGTATTCTACTACAATCATAAATGTCATTCAACATCAAGC
2864384 TCATCATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.35
Consensus pattern (52 bp):
TTGAAATAATATGTATTCTACTACAATCATAAATGTCATTCAACATCAAGCA
Found at i:2867763 original size:3 final size:3
Alignment explanation
Indices: 2867755--2867789 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2867745 GAAGCTTTTC
*
2867755 TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2867790 CTTATGTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:2868897 original size:125 final size:124
Alignment explanation
Indices: 2868595--2869131 Score: 545
Period size: 125 Copynumber: 4.3 Consensus size: 124
2868585 ATTAAGGCGT
* ** * * * *
2868595 TTTTTTACACAAACATCTTAATTGATGAT-ATTTTAAAATTATAAAACCGATTAATT-AAGATGT
1 TTTTGTACACAAACGCCTTAATTGATAATCA-ATT-AAATTATAAAACTGATCAATTAAAG-TGT
* * *
2868658 TTGTGTACAGAAACGTCTTAATTGATCTATTTTAAAAATTATAATGATTGATCAATTAAAGCA
63 TTGTGTAAAGAAATGTCTTAATTGATCTATTTTTAAAATTATAATGATTGATCAATTAAAG-A
* *
2868721 TTTTTGTACACAAACGCCTTAATTGATCATCAATTAAATTATAAAATTGATCAATTAAAGTGTTT
1 -TTTTGTACACAAACGCCTTAATTGATAATCAATTAAATTATAAAACTGATCAATTAAAGTGTTT
* * * *
2868786 GTGTATAGAAATGTCTTCATTGATCTATTTTTAAAATTAT-TTAATTGATCAATTAAAGA
65 GTGTAAAGAAATGTCTTAATTGATCTATTTTTAAAATTATAATGATTGATCAATTAAAGA
* * *
2868845 GTTTATGTATACAAACGCCTTAATTGATAATCAATTAAATTATAAAACTGATCAATTAAGGTTTT
1 -TTT-TGTACACAAACGCCTTAATTGATAATCAATTAAATTATAAAACTGATCAATTAAAGTGTT
* *
2868910 TGTGTAAAGAAATGCCTTAATTGATCTATTTTTAAAATTATAATGATTGATCAATTAAATCA
64 TGTGTAAAGAAATGTCTTAATTGATCTATTTTTAAAATTATAATGATTGATCAATTAAA-GA
* * *
2868972 TTGTTGTACACAAAC-CCCTAATTGATCTAA-C-TTTAAATTATAAAACTGATCAATTAAAGTTT
1 TT-TTGTACACAAACGCCTTAATTGA--TAATCAATTAAATTATAAAACTGATCAATTAAAGTGT
*** * * *
2869034 TTGTGTACAA-AAACACCTTAATTGATC-A-ATTAAATAATTATAATGATT-ATCAATTAAGGTG
63 TTGTGTA-AAGAAATGTCTTAATTGATCTATTTTTAA-AATTATAATGATTGATCAATTAA--AG
*
2869095 T
124 A
* ** * *
2869096 TTTTGTATACAAACGAGTTAATTGATCATCACTTAA
1 TTTTGTACACAAACGCCTTAATTGATAATCAATTAA
2869132 GGCTTTTATA
Statistics
Matches: 352, Mismatches: 43, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
122 2 0.01
123 25 0.07
124 31 0.09
125 169 0.48
126 89 0.25
127 35 0.10
128 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (124 bp):
TTTTGTACACAAACGCCTTAATTGATAATCAATTAAATTATAAAACTGATCAATTAAAGTGTTTG
TGTAAAGAAATGTCTTAATTGATCTATTTTTAAAATTATAATGATTGATCAATTAAAGA
Found at i:2869119 original size:187 final size:186
Alignment explanation
Indices: 2868626--2869131 Score: 479
Period size: 187 Copynumber: 2.7 Consensus size: 186
2868616 TTGATGATAT
* * * * *
2868626 TTTAAAATTATAAAACCGATTAATT-AAGATGTTTGTGTACAGAAACGTCTTAATTGATCTATTT
1 TTTAAAATTATAAAACTGATCAATTAAAG-TGTTTGTGTACAAAAACGCCTTAATTGATC-A-AT
** *
2868690 TAAA-AATTATAATGATTGATCAATTAAAGCATTTTTGTACACAAACGCCTTAATTGATCATCAA
63 TAAATAATTATAATGATT-ATCAATT-AAGGTTTTTTGTAAACAAACGCCTTAATTGATCATCAA
** * * ** * * **
2868754 TTAAATTATAAAATTGATCAATTAAAGTGTTTGTGTATAGAAATGTCTTCATTGATCTATT
126 TTAAATTATAAAATTGATCAATTAAAGTCATTGTGTACACAAATCCCCTAATTGATCTAAC
** * * * * * *
2868815 TTTAAAATTATTTAATTGATCAATTAAAGAGTTTATGTATACAAACGCCTTAATTGAT-AATCAA
1 TTTAAAATTATAAAACTGATCAATTAAAGTGTTTGTGTACAAAAACGCCTTAATTGATCAATTAA
* * * * * **
2868879 TTAAATTATAA-AACTGATCAATTAAGGTTTTTGTGTAAAGAAATGCCTTAATTGATCTAT-TTT
66 AT-AATTATAATGA-TTATCAATTAAGGTTTTT-TGTAAACAAACGCCTTAATTGATC-ATCAAT
*
2868942 TAAAATTATAATGATTGATCAATTAAA-TCATTGTTGTACACAAA-CCCCTAATTGATCTAAC
127 T-AAATTATAA-AATTGATCAATTAAAGTCATTG-TGTACACAAATCCCCTAATTGATCTAAC
* *
2869003 TTT-AAATTATAAAACTGATCAATTAAAGTTTTTGTGTACAAAAACACCTTAATTGATCAATTAA
1 TTTAAAATTATAAAACTGATCAATTAAAGTGTTTGTGTACAAAAACGCCTTAATTGATCAATTAA
* ** *
2869067 ATAATTATAATGATTATCAATTAAGGTGTTTTTGTATACAAACGAGTTAATTGATCATCACTTAA
66 ATAATTATAATGATTATCAATTAAGGT-TTTTTGTAAACAAACGCCTTAATTGATCATCAATTAA
2869132 GGCTTTTATA
Statistics
Matches: 251, Mismatches: 53, Indels: 29
0.75 0.16 0.09
Matches are distributed among these distances:
186 14 0.06
187 119 0.47
188 49 0.20
189 66 0.26
190 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (186 bp):
TTTAAAATTATAAAACTGATCAATTAAAGTGTTTGTGTACAAAAACGCCTTAATTGATCAATTAA
ATAATTATAATGATTATCAATTAAGGTTTTTTGTAAACAAACGCCTTAATTGATCATCAATTAAA
TTATAAAATTGATCAATTAAAGTCATTGTGTACACAAATCCCCTAATTGATCTAAC
Found at i:2869123 original size:62 final size:63
Alignment explanation
Indices: 2868580--2869122 Score: 382
Period size: 62 Copynumber: 8.7 Consensus size: 63
2868570 TTACAAAAAA
* * * ** * * * **
2868580 GATCAATTAAGGCGTTTTTTTACACAAACATCTTAATTGATGATATTTTAAAATTATAA-AACC
1 GATCAATTAAAGTGTTTTTGTACACAAACGCCTTAATTGAT-CTAATTAAAAATTATAATAATT
* * * * * *
2868643 GATTAATT-AAGATGTTTGTGTACAGAAACGTCTTAATTGATCTATTTTAAAAATTATAATGATT
1 GATCAATTAAAG-TGTTTTTGTACACAAACGCCTTAATTGATCTA-ATTAAAAATTATAATAATT
**
2868707 GATCAATTAAAGCATTTTTGTACACAAACGCCTTAATTGATCATCAATT--AAATTATAA-AATT
1 GATCAATTAAAGTGTTTTTGTACACAAACGCCTTAATTGATC-T-AATTAAAAATTATAATAATT
* * * * * * * * *
2868769 GATCAATTAAAGTGTTTGTGTATAGAAATGTCTTCATTGATCTATTTTTAAAATTAT-TTAATT
1 GATCAATTAAAGTGTTTTTGTACACAAACGCCTTAATTGATCTA-ATTAAAAATTATAATAATT
* * * * *
2868832 GATCAATTAAAGAGTTTATGTATACAAACGCCTTAATTGA--TAATCAATTAAATTATAA-AACT
1 GATCAATTAAAGTGTTTTTGTACACAAACGCCTTAATTGATCTAATTAA--AAATTATAATAATT
* * * * * * *
2868894 GATCAATTAAGGT-TTTTGTGTAAAGAAATGCCTTAATTGATCTATTTTTAAAATTATAATGATT
1 GATCAATTAAAGTGTTTT-TGTACACAAACGCCTTAATTGATCTA-ATTAAAAATTATAATAATT
* * * * *
2868958 GATCAATTAAA-TCATTGTTGTACACAAAC-CCCTAATTGATCTAACTT-TAAATTATAA-AACT
1 GATCAATTAAAGT-GTTTTTGTACACAAACGCCTTAATTGATCTAA-TTAAAAATTATAATAATT
* * *
2869019 GATCAATTAAAGT-TTTTGTGTACAAAAACACCTTAATTGATC-AATTAAATAATTATAATGATT
1 GATCAATTAAAGTGTTTT-TGTACACAAACGCCTTAATTGATCTAATTAAA-AATTATAATAATT
* * **
2869082 -ATCAATTAAGGTGTTTTTGTATACAAACGAGTTAATTGATC
1 GATCAATTAAAGTGTTTTTGTACACAAACGCCTTAATTGATC
2869123 ATCACTTAAG
Statistics
Matches: 378, Mismatches: 74, Indels: 57
0.74 0.15 0.11
Matches are distributed among these distances:
60 8 0.02
61 34 0.09
62 140 0.37
63 129 0.34
64 55 0.15
65 11 0.03
66 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (63 bp):
GATCAATTAAAGTGTTTTTGTACACAAACGCCTTAATTGATCTAATTAAAAATTATAATAATT
Found at i:2890291 original size:22 final size:22
Alignment explanation
Indices: 2890263--2890307 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2890253 AAAAAAAAAC
2890263 CCAGAATGTCAAACTCCAAATG
1 CCAGAATGTCAAACTCCAAATG
2890285 CCAGAATGTCAAACTCCAAATG
1 CCAGAATGTCAAACTCCAAATG
2890307 C
1 C
2890308 TTGCATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.18
Consensus pattern (22 bp):
CCAGAATGTCAAACTCCAAATG
Found at i:2896215 original size:13 final size:14
Alignment explanation
Indices: 2896174--2896220 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2896164 AATTTTAAAA
*
2896174 AAATATATATTAAT
1 AAATATATTTTAAT
* *
2896188 ATATATATTTAAAT
1 AAATATATTTTAAT
2896202 AAATAT-TTTTAAT
1 AAATATATTTTAAT
2896215 AAATAT
1 AAATAT
2896221 CTAAAAATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATATATTTTAAT
Found at i:2896803 original size:18 final size:19
Alignment explanation
Indices: 2896768--2896802 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2896758 AATTTAAAAT
2896768 TAAATAAAATTAAATTTTG
1 TAAATAAAATTAAATTTTG
2896787 TAAA-AAAA-TAAATTTT
1 TAAATAAAATTAAATTTT
2896803 TTCATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
TAAATAAAATTAAATTTTG
Found at i:2896811 original size:17 final size:17
Alignment explanation
Indices: 2896770--2896812 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2896760 TTTAAAATTA
2896770 AATAAAATTAAATTTTGT
1 AATAAAA-TAAATTTTGT
* *
2896788 AAAAAAATAAATTTTTT
1 AATAAAATAAATTTTGT
*
2896805 CATAAAAT
1 AATAAAAT
2896813 TTAAAACTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AATAAAATAAATTTTGT
Found at i:2897398 original size:27 final size:27
Alignment explanation
Indices: 2897357--2897416 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
2897347 TTTTTTATTG
* *
2897357 TTTATTTTAAATTTATC-ATATGATAAA
1 TTTATTTTAAATTTACCAACATGA-AAA
**
2897384 TTTATTTTATTTTTACCAACATGAAAA
1 TTTATTTTAAATTTACCAACATGAAAA
2897411 TTTATT
1 TTTATT
2897417 AAAATAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (27 bp):
TTTATTTTAAATTTACCAACATGAAAA
Found at i:2897978 original size:18 final size:20
Alignment explanation
Indices: 2897955--2898000 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
2897945 TTGAATTCTT
2897955 ATATTTTAAT-AAATTATCA
1 ATATTTTAATCAAATTATCA
*
2897974 A-A-TTTAATCAAATTATTA
1 ATATTTTAATCAAATTATCA
2897992 ATATTTTAA
1 ATATTTTAA
2898001 ATTTTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 6 0.26
18 10 0.43
19 2 0.09
20 5 0.22
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATTTTAATCAAATTATCA
Done.