Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 18 of 126
Found at i:4177713 original size:14 final size:14
Alignment explanation
Indices: 4177694--4177727 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
4177684 CAAATTTAAA
4177694 TGACGTCAAATAAG
1 TGACGTCAAATAAG
4177708 TGACGTCAAATAAG
1 TGACGTCAAATAAG
4177722 TGACGT
1 TGACGT
4177728 TTCATCAATT
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:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (14 bp):
TGACGTCAAATAAG
Found at i:4178283 original size:27 final size:27
Alignment explanation
Indices: 4178222--4178284 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
4178212 GTCTAAATTT
*
4178222 TTTTTTAATTATTAAAAAAAATCAAAA
1 TTTTTTAAATATTAAAAAAAATCAAAA
** *
4178249 AATATTAAAT-TTAAAAAAAATTCAAAA
1 TTTTTTAAATATTAAAAAAAA-TCAAAA
4178276 TTTTTTAAA
1 TTTTTTAAA
4178285 AAAATTTTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (27 bp):
TTTTTTAAATATTAAAAAAAATCAAAA
Found at i:4178304 original size:20 final size:19
Alignment explanation
Indices: 4178283--4178415 Score: 85
Period size: 20 Copynumber: 6.8 Consensus size: 19
4178273 AAATTTTTTA
4178283 AAAAAATTTTTAAAATTCT
1 AAAAAATTTTTAAAATTCT
4178302 -AAAAA-TTTTAAAATTTCT
1 AAAAAATTTTTAAAA-TTCT
* ** *
4178320 AAAAAGTTTAAAAAACATC-
1 AAAAAATTTTTAAAA-TTCT
* *
4178339 AAAAAAGTTTTAAGAACT-T
1 AAAAAATTTTTAA-AATTCT
**
4178358 ATAAAAATTTAAAATAATTCT
1 A-AAAAATTTTTAA-AATTCT
*
4178379 AAAAAATTTTAAAAAATTCT
1 AAAAAATTTT-TAAAATTCT
*
4178399 AAAAGAATGTTTAAAAT
1 AAAA-AATTTTTAAAAT
4178416 ATTTTTAAAA
Statistics
Matches: 87, Mismatches: 18, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
17 8 0.09
18 9 0.10
19 15 0.17
20 45 0.52
21 10 0.11
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAAAATTTTTAAAATTCT
Found at i:4178333 original size:10 final size:9
Alignment explanation
Indices: 4178283--4178402 Score: 62
Period size: 10 Copynumber: 12.4 Consensus size: 9
4178273 AAATTTTTTA
4178283 AAAAAATTT
1 AAAAAATTT
**
4178292 TTAAAATTCT
1 AAAAAATT-T
4178302 -AAAAATTT
1 AAAAAATTT
* *
4178310 TAAAATTTCT
1 AAAAAATT-T
*
4178320 AAAAAGTTT
1 AAAAAATTT
* *
4178329 AAAAAACATC
1 AAAAAA-TTT
4178339 AAAAAAGTTT
1 AAAAAA-TTT
* * *
4178349 TAAGAACTT
1 AAAAAATTT
4178358 ATAAAAATTT
1 A-AAAAATTT
4178368 AAAATAATTCT
1 AAAA-AATT-T
4178379 AAAAAATTTT
1 AAAAAA-TTT
4178389 AAAAAATTCT
1 AAAAAATT-T
4178399 AAAA
1 AAAA
4178403 GAATGTTTAA
Statistics
Matches: 84, Mismatches: 18, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
8 1 0.01
9 31 0.37
10 45 0.54
11 7 0.08
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAAATTT
Found at i:4178350 original size:39 final size:38
Alignment explanation
Indices: 4178302--4178402 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 38
4178292 TTAAAATTCT
*
4178302 AAAAATTTTAAAATTTCTAAAAAGTTTAAAA-AACATC-A
1 AAAAATTTTAAAAATTCTAAAAA-TTTAAAATAA-ATCTA
* * *
4178340 AAAAAGTTTTAAGAACTTATAAAAATTTAAAATAATTCTA
1 AAAAA-TTTTAA-AAATTCTAAAAATTTAAAATAAATCTA
4178380 AAAAATTTTAAAAAATTCTAAAA
1 AAAAATTTT-AAAAATTCTAAAA
4178403 GAATGTTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
38 5 0.09
39 28 0.53
40 20 0.38
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (38 bp):
AAAAATTTTAAAAATTCTAAAAATTTAAAATAAATCTA
Found at i:4178445 original size:20 final size:20
Alignment explanation
Indices: 4178279--4178445 Score: 70
Period size: 20 Copynumber: 8.6 Consensus size: 20
4178269 TTCAAAATTT
*
4178279 TTTA-AAAAAATTTTTAAAA
1 TTTATAAAAAATGTTTAAAA
*
4178298 -TTCT-AAAAAT-TTTAAAA
1 TTTATAAAAAATGTTTAAAA
*
4178315 TTTCT-AAAAA-GTTTAAAA
1 TTTATAAAAAATGTTTAAAA
***
4178333 AACATCAAAAAA-GTTTTAAGAA
1 TTTAT-AAAAAATG-TTTAA-AA
*
4178355 CTTAT-AAAAA--TTTAAAA
1 TTTATAAAAAATGTTTAAAA
*
4178372 TAATTCTAAAAAAT-TTTAAAAA
1 T--TTATAAAAAATGTTT-AAAA
* *
4178394 ATTCTAAAAGAATGTTTAAAA
1 TTTATAAAA-AATGTTTAAAA
**
4178415 TATT-TTTAAAATGTTTAAAA
1 T-TTATAAAAAATGTTTAAAA
4178435 TTTATAAAAAA
1 TTTATAAAAAA
4178446 ATTAATTTTA
Statistics
Matches: 116, Mismatches: 16, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
17 9 0.08
18 30 0.26
19 5 0.04
20 41 0.35
21 18 0.16
22 13 0.11
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (20 bp):
TTTATAAAAAATGTTTAAAA
Found at i:4178518 original size:19 final size:20
Alignment explanation
Indices: 4178491--4178539 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
4178481 AAAAATTAAT
* *
4178491 TTCTCAAAAATTT-TAAATAA
1 TTCT-AAAAATTTCAAAACAA
4178511 TTCTAAAAATTTCAAAACAA
1 TTCTAAAAATTTCAAAACAA
4178531 TTCTAAAAA
1 TTCTAAAAA
4178540 ACTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (20 bp):
TTCTAAAAATTTCAAAACAA
Found at i:4178860 original size:17 final size:19
Alignment explanation
Indices: 4178828--4178889 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 19
4178818 TCCTCGAAAT
4178828 TAAAAAAATGTCAAAAAAA
1 TAAAAAAATGTCAAAAAAA
*
4178847 TAAAAAAAT-T-AAAAATA
1 TAAAAAAATGTCAAAAAAA
* ** *
4178864 TAATAAAA-CCCAAAAAAG
1 TAAAAAAATGTCAAAAAAA
4178882 TAAAAAAA
1 TAAAAAAA
4178890 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 13 0.37
18 13 0.37
19 9 0.26
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.16
Consensus pattern (19 bp):
TAAAAAAATGTCAAAAAAA
Found at i:4178944 original size:36 final size:35
Alignment explanation
Indices: 4178883--4178954 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
4178873 CCAAAAAAGT
*
4178883 AAAAAAAAAATTTAAAAGTTCAAAAATATATAAAA
1 AAAAAAAAAATTTAAAAGTTAAAAAATATATAAAA
* *
4178918 AAAAATAAAAATTT-TAAGATTAAAAAATATGTAAAA
1 AAAAA-AAAAATTTAAAAG-TTAAAAAATATATAAAA
4178954 A
1 A
4178955 TTTATAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 8 0.25
36 24 0.75
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (35 bp):
AAAAAAAAAATTTAAAAGTTAAAAAATATATAAAA
Found at i:4179179 original size:11 final size:11
Alignment explanation
Indices: 4179147--4179204 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
4179137 AATTTTTAAG
4179147 TTTTAA-AATT
1 TTTTAAGAATT
*
4179157 TTCT-AGAA-T
1 TTTTAAGAATT
4179166 TTTT-AGAATT
1 TTTTAAGAATT
* *
4179176 TTTTAAAAATC
1 TTTTAAGAATT
*
4179187 TTTTCAGAATT
1 TTTTAAGAATT
4179198 TTTTAAG
1 TTTTAAG
4179205 TTTTTTTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
9 9 0.24
10 10 0.27
11 18 0.49
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.53
Consensus pattern (11 bp):
TTTTAAGAATT
Found at i:4182321 original size:121 final size:119
Alignment explanation
Indices: 4182177--4182469 Score: 290
Period size: 121 Copynumber: 2.4 Consensus size: 119
4182167 GCCAGAAATG
* * * * *
4182177 CCTTCAATAATCACTTACAAAAAATTCAATAAGGTTATTCAATGTGTTTTT-GACGAAAAATACC
1 CCTTGAATAATCCCTCATAAAAAATT-AAT-AGGTTATTCAATGTGTTTTTAG-CGAAAAACACC
4182241 TTGAATAATCTCCTGTCATTTTTTTAGGATTATTC-AAG-ATATTTTTGGC-CATAAACA
63 TTGAATAATCTCCTGTCATTTTTTTAGGATTATTCAAAGCAT-TTTTT-GCTCA-AAACA
** * * ** * * *
4182298 TTTTGAATAATCCCCTCA-CAAAAATTATATGAGGTTATTCAAGGCATTTCTAGCTAAAAACGCC
1 CCTTGAATAAT-CCCTCATAAAAAATTA-AT-AGGTTATTCAATGTGTTTTTAGCGAAAAACACC
* * *
4182362 TTGAATAATCTTCTGTCATTTTTTTTGGATTATTCAAAGCATTTTTTGCTGAAAACA
63 TTGAATAATCTCCTGTCATTTTTTTAGGATTATTCAAAGCATTTTTTGCTCAAAACA
*
4182419 CCTTGAATAATCCCTTATAAAAAATTGAATAGGATTATTCAATGTGTTTTT
1 CCTTGAATAATCCCTCATAAAAAATT-AATAGG-TTATTCAATGTGTTTTT
4182470 TTTATCAAAA
Statistics
Matches: 138, Mismatches: 25, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
120 9 0.07
121 112 0.81
122 15 0.11
123 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (119 bp):
CCTTGAATAATCCCTCATAAAAAATTAATAGGTTATTCAATGTGTTTTTAGCGAAAAACACCTTG
AATAATCTCCTGTCATTTTTTTAGGATTATTCAAAGCATTTTTTGCTCAAAACA
Found at i:4183239 original size:209 final size:209
Alignment explanation
Indices: 4182870--4183295 Score: 468
Period size: 209 Copynumber: 2.0 Consensus size: 209
4182860 AAATTAAAGG
* * * *
4182870 GGATTATTCAATGTATTTTTGGTAAAAAATGCTTTGAATAATCCTATTCAATTTTTTTAAGGGAT
1 GGATTA-TCAATGTATTTTTGGCAAAAAATGCATTGAATAATCATATTCAATTTTTGTAAGGGAT
* * * * * * * *
4182935 TATTCGAGGTATTTCTAGCTAAAAACATCTTTAATAATCCCTTGAAAAACCTTTTAAAATACTAA
65 TATTCAAGGCAGTTCTAACTAAAAACATCTTCAATAATCCCTTGAAAAAACTCTCAAAATACTAA
* * * * ** * *
4183000 AGAGAAGAATCGAACCTACAATCTTATGGTTAATATCTATATGCTCTAACTGA-TTGAGCTACTC
130 AGAGAAGAATCGAACCGACAACCTTATGGTTAATAGCCATATGCTCTAACCAACTT-AACTAATC
* *
4183064 TAGTGTTTTTGTTAAT
194 CAGTGTTTTTGTTAAC
* *
4183080 GGATTATCAA-GATATTTTTGGCCAAAAATGCATTGAATCATCATATTCAATATTTTGTAAGGGA
1 GGATTATCAATG-TATTTTTGGCAAAAAATGCATTGAATAATCATATTCAAT-TTTTGTAAGGGA
* * *
4183144 TTATTCAAGGCGGTTCTAAC-AAAAA-ATGCCTTCAATTATCCCTT-AAAAAACTCTCAAAATGC
64 TTATTCAAGGCAGTTCTAACTAAAAACAT--CTTCAATAATCCCTTGAAAAAACTCTCAAAATAC
* * * *
4183206 TAAAGGGAATG-ATTGAACCGACGACCTTATGGTTAATAGCCGTATGCTCTAACCAACTTAACTA
127 TAAAGAGAA-GAATCGAACCGACAACCTTATGGTTAATAGCCATATGCTCTAACCAACTTAACTA
4183270 ATCCAGTGTTTTTGTTAAC
191 ATCCAGTGTTTTTGTTAAC
4183289 GGATTAT
1 GGATTAT
4183296 TTAAGGTATT
Statistics
Matches: 179, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
208 3 0.02
209 128 0.72
210 48 0.27
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (209 bp):
GGATTATCAATGTATTTTTGGCAAAAAATGCATTGAATAATCATATTCAATTTTTGTAAGGGATT
ATTCAAGGCAGTTCTAACTAAAAACATCTTCAATAATCCCTTGAAAAAACTCTCAAAATACTAAA
GAGAAGAATCGAACCGACAACCTTATGGTTAATAGCCATATGCTCTAACCAACTTAACTAATCCA
GTGTTTTTGTTAAC
Found at i:4183360 original size:481 final size:478
Alignment explanation
Indices: 4182684--4183629 Score: 1089
Period size: 481 Copynumber: 2.0 Consensus size: 478
4182674 AAGGTATTTC
* * * *
4182684 CAAAAAATTCTTCAATAATCACTTGAAAAACTCTCAAAACGCTAGAGGGAGAGATTAACCTACAA
1 CAAAAAATCCTTCAATAATCACTTAAAAAACTCTCAAAACGCTAAAGGGAGAGATTAACCGACAA
* * * ** * *
4182749 CCTTATGATTAATAACCATATGCTTTAACCGACTAAATTGCTCTAATGTTTTTGTTAATAGATTA
66 CCTTATGATTAATAACCATATGCTCTAACCAACTAAACTAATCCAATGTTTTTGTTAACAGATTA
* ** * *** *
4182814 TTTAAGATGTTTTTGGTCAAAAACATCTTAAATAATTTTTTCATAAAAATTAAAGGGGATTATTC
131 TTTAAGATATTTTTGACCAAAAACACCTTAAATAATTCCCTCATAAAAATTAAAGGAGATTATTC
* * **
4182879 AATG-TATTTTTGGTA-AAAAATGCTTTGAATAATCCTAT-TCAATTTTTTTAAGGGATTATTCG
196 AA-GATATTTTTGGTACAAAAATACCTTGAATAATCCTATATCAATTTTTTTAAGGGATT-TAAG
* * * * *
4182941 AGGTATTTCTAGCTAAAAACATCTTTAATAATCCCTTGAAAAACCTTTTAAAATACTAAAGAGAA
259 ACGT-TTT-TAGCCAAAAACACCTTTAATAATCCCTTGAAAAACC-CTCAAAATACTAAAGA-AA
* * * * *
4183006 GA-ATCGAACCTACAATCTTATGGTTAATA-TCTATATGCTCTAACTGATTGAGCTACTCTAGTG
320 GATATCAAACCTACAACCTTATGATTAATAGTC-ATATGCTCTAACCGATTGAACTACTCTAGTG
* *
4183069 TTTTTGTTAATGGATTA-TC-AAGATATTTTTGGCCAAAAATGCATTGAATCATCATATTCAATA
384 TTTTTGTTAATGGATTATTCAAAG-TATTTTTGGCCAAAAATACATTGAATAATCATATTCAATA
**
4183132 TTTTGTAAGGGATTATTCAAGGCGGTTCTAA
448 TTTTGTAAAAGATTATTCAAGGCGGTTCTAA
* * *
4183163 CAAAAAATGCCTTCAATTATCCCTTAAAAAACTCTCAAAATGCTAAAGGGA-ATGATTGAACCGA
1 CAAAAAAT-CCTTCAATAATCACTTAAAAAACTCTCAAAACGCTAAAGGGAGA-GATT-AACCGA
* * * * * * *
4183227 CGACCTTATGGTTAATAGCCGTATGCTCTAACCAACTTAACTAATCCAGTGTTTTTGTTAACGGA
63 CAACCTTATGATTAATAACCATATGCTCTAACCAACTAAACTAATCCAATGTTTTTGTTAACAGA
* * * *
4183292 TTATTTAAGGTATTTTTTACCAAAAACACCTTGAATAATTCCCTCATAAAAATTGAAGGAGATTA
128 TTATTTAAGATATTTTTGACCAAAAACACCTTAAATAATTCCCTCATAAAAATTAAAGGAGATTA
** * *
4183357 TTCAAGATATTTTTTTTATCAAAAATACCTTGAATAATCTTTTATCAATTTTTTTAAGGGATTTA
193 TTCAAGATATTTTTGGTA-CAAAAATACCTTGAATAATCCTATATCAATTTTTTTAAGGGATTTA
* * * * * * *
4183422 AGACGTTTTTGGCCAAAAATACCTTTAATAATTCGTTGAAAAACCCTCAAAATGCTAGATAAAGA
257 AGACGTTTTTAGCCAAAAACACCTTTAATAATCCCTTGAAAAACCCTCAAAATACTAAAGAAAGA
* * **
4183487 TATCAAACCTACGACCTTATGATTAATAGTCATATGCTTTAACCGATTGAACTGTTCTAGTGTTT
322 TATCAAACCTACAACCTTATGATTAATAGTCATATGCTCTAACCGATTGAACTACTCTAGTGTTT
* ** * *
4183552 TTGTTAATGGATTATTCAAAGTATTTTTTGCCAAAAATATTTTGAATAATCCTATTCAATTTTTT
387 TTGTTAATGGATTATTCAAAGTATTTTTGGCCAAAAATACATTGAATAATCATATTCAATATTTT
4183617 GTAAAAGATTATT
452 GTAAAAGATTATT
4183630 TAAGATGTTT
Statistics
Matches: 385, Mismatches: 71, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
479 13 0.03
480 118 0.31
481 205 0.53
482 6 0.02
483 24 0.06
484 19 0.05
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (478 bp):
CAAAAAATCCTTCAATAATCACTTAAAAAACTCTCAAAACGCTAAAGGGAGAGATTAACCGACAA
CCTTATGATTAATAACCATATGCTCTAACCAACTAAACTAATCCAATGTTTTTGTTAACAGATTA
TTTAAGATATTTTTGACCAAAAACACCTTAAATAATTCCCTCATAAAAATTAAAGGAGATTATTC
AAGATATTTTTGGTACAAAAATACCTTGAATAATCCTATATCAATTTTTTTAAGGGATTTAAGAC
GTTTTTAGCCAAAAACACCTTTAATAATCCCTTGAAAAACCCTCAAAATACTAAAGAAAGATATC
AAACCTACAACCTTATGATTAATAGTCATATGCTCTAACCGATTGAACTACTCTAGTGTTTTTGT
TAATGGATTATTCAAAGTATTTTTGGCCAAAAATACATTGAATAATCATATTCAATATTTTGTAA
AAGATTATTCAAGGCGGTTCTAA
Found at i:4183689 original size:13 final size:12
Alignment explanation
Indices: 4183659--4183683 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4183649 AATACCTTCA
4183659 AAAATTTTTTGT
1 AAAATTTTTTGT
4183671 AAAATTTTTTGT
1 AAAATTTTTTGT
4183683 A
1 A
4183684 TGAATTATTG
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
AAAATTTTTTGT
Found at i:4183715 original size:64 final size:64
Alignment explanation
Indices: 4183609--4183760 Score: 164
Period size: 64 Copynumber: 2.4 Consensus size: 64
4183599 AATCCTATTC
** * * * *
4183609 AATTTTTTGTAAAAGATTATTTAAGATGTTTTTGTTCAAAAATACCTTCAAAAAT-TTTTTGTAA
1 AATTTTTTGTATGA-ATTATTGAAGATGTTTTTGTTCAAAAATACCTTCAAAAATCATTCTCTAA
* *
4183673 AATTTTTTGTATGAATTATTGAAGAT-TTTTTTTTACAGAAAATACCTTCAATAATCATTCTCTA
1 AATTTTTTGTATGAATTATTGAAGATGTTTTTGTT-CA-AAAATACCTTCAAAAATCATTCTCTA
4183737 A
64 A
* * *
4183738 AATTTTCTGAATGGATTATTGAA
1 AATTTTTTGTATGAATTATTGAA
4183761 TGCGTTTTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
62 7 0.09
63 13 0.18
64 28 0.38
65 26 0.35
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (64 bp):
AATTTTTTGTATGAATTATTGAAGATGTTTTTGTTCAAAAATACCTTCAAAAATCATTCTCTAA
Found at i:4183756 original size:65 final size:63
Alignment explanation
Indices: 4183623--4183760 Score: 161
Period size: 65 Copynumber: 2.2 Consensus size: 63
4183613 TTTTGTAAAA
* * * * * *
4183623 GATTATTTAAGATGTTTTTGTTCAAAAATACCTTCAAAAATTTTTTGTAAAATTTTTTGTATG
1 GATTATTGAAGATGTTTTTGTTCAAAAATACCTTCAAAAATATTCTCTAAAATTTTCTGAATG
* * *
4183686 AATTATTGAAGAT-TTTTTTTTACAGAAAATACCTTCAATAATCATTCTCTAAAATTTTCTGAAT
1 GATTATTGAAGATGTTTTTGTT-CA-AAAATACCTTCAAAAAT-ATTCTCTAAAATTTTCTGAAT
4183750 G
63 G
4183751 GATTATTGAA
1 GATTATTGAA
4183761 TGCGTTTTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
62 7 0.11
63 13 0.21
64 16 0.26
65 26 0.42
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (63 bp):
GATTATTGAAGATGTTTTTGTTCAAAAATACCTTCAAAAATATTCTCTAAAATTTTCTGAATG
Found at i:4187000 original size:16 final size:16
Alignment explanation
Indices: 4186979--4187024 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
4186969 TGATTAATAC
*
4186979 AATATTATTATTTTTA
1 AATATTATTATTTTAA
4186995 AATATTA--ATTTTAA
1 AATATTATTATTTTAA
4187009 AATATTATTATTTTAA
1 AATATTATTATTTTAA
4187025 TATTTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 13 0.48
16 14 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATATTATTATTTTAA
Found at i:4187005 original size:14 final size:13
Alignment explanation
Indices: 4186984--4187028 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
4186974 AATACAATAT
4186984 TATTATTTTTAAA
1 TATTATTTTTAAA
*
4186997 TATTAATTTTAAAA
1 TATT-ATTTTTAAA
*
4187011 TATTATTATTTTAA
1 TATTATT-TTTAAA
4187025 TATT
1 TATT
4187029 TTAATAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTTTTAAA
Found at i:4188036 original size:13 final size:13
Alignment explanation
Indices: 4188018--4188047 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
4188008 AGAAGAAAAA
4188018 AATTTTTTT-TTT
1 AATTTTTTTATTT
4188030 AATTTTTTTATTT
1 AATTTTTTTATTT
4188043 AATTT
1 AATTT
4188048 ATATATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
AATTTTTTTATTT
Found at i:4190560 original size:126 final size:126
Alignment explanation
Indices: 4190335--4190561 Score: 400
Period size: 126 Copynumber: 1.8 Consensus size: 126
4190325 CTCCGCTTAA
*
4190335 TGATGAATTTGATTACTGCTGGTCCAAAATTGAAGAGCTCCAACATAATAAACGAGCTCATAAAT
1 TGATGAATTTGATTACTGCTGGTCCAAAATTGAAGAACTCCAACATAATAAACGAGCTCATAAAT
*
4190400 TTTTTCAGGGACACAAACTTATTCTTTTCATTGGATTTTTTTATAAAATTCCAATCCTTTT
66 TTTTTCAGGGACACAAACATATTCTTTTCATTGGATTTTTTTATAAAATTCCAATCCTTTT
* *
4190461 TGATGAATTTGATTACTGCTGGTCCAATATTGAAGAACTCCAACATAATAAAGGAGCTCATAAAT
1 TGATGAATTTGATTACTGCTGGTCCAAAATTGAAGAACTCCAACATAATAAACGAGCTCATAAAT
* *
4190526 TTTTTCAGGGTCACAAACATGTTCTTTTCATTGGAT
66 TTTTTCAGGGACACAAACATATTCTTTTCATTGGAT
4190562 GACCTGTCCC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 95 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (126 bp):
TGATGAATTTGATTACTGCTGGTCCAAAATTGAAGAACTCCAACATAATAAACGAGCTCATAAAT
TTTTTCAGGGACACAAACATATTCTTTTCATTGGATTTTTTTATAAAATTCCAATCCTTTT
Found at i:4192368 original size:68 final size:68
Alignment explanation
Indices: 4192235--4192372 Score: 159
Period size: 68 Copynumber: 2.0 Consensus size: 68
4192225 CAAGTCGAAT
* ** * * * *
4192235 CTTTAATACCGGTGTTCGAACACATGGAGTTCATGGACGTGGCCAACCTCCGATCTGCCAGCAAT
1 CTTTAATACCGATGTTCGAACACAAAGAGTTCATAGACATGGCCAACCTCCAATCTGCCAACAAT
4192300 CTC
66 CTC
** * * * *
4192303 CTTTAATACCGATGTTCGAGTACAAAGAGTTGATAGACATGGCCAACCTCTAATTTGCTAACAAT
1 CTTTAATACCGATGTTCGAACACAAAGAGTTCATAGACATGGCCAACCTCCAATCTGCCAACAAT
4192368 CTC
66 CTC
4192371 CT
1 CT
4192373 CCCCAACAAC
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 57 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (68 bp):
CTTTAATACCGATGTTCGAACACAAAGAGTTCATAGACATGGCCAACCTCCAATCTGCCAACAAT
CTC
Found at i:4194012 original size:84 final size:84
Alignment explanation
Indices: 4193869--4194022 Score: 254
Period size: 84 Copynumber: 1.8 Consensus size: 84
4193859 CGATTGCTAC
* *
4193869 AATATACTCAGTATCTATAGTTGATAAAGTAACACACTTATGCAACTTAGACTACCAAGACATGG
1 AATATACTCAGCATCTATAGTTGATAAAGTAACACACTTATGCAACTTAGACTACCAAGACACGG
4193934 CTCCTGCTTTGGTTACTGT
66 CTCCTGCTTTGGTTACTGT
* ** *
4193953 AATATACTCAGCCTCTATAGTTGATAAAGTAACACACTTATGCAACTTAGACTGTCAAGATACGG
1 AATATACTCAGCATCTATAGTTGATAAAGTAACACACTTATGCAACTTAGACTACCAAGACACGG
4194018 CTCCT
66 CTCCT
4194023 TCTGTAAAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 64 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (84 bp):
AATATACTCAGCATCTATAGTTGATAAAGTAACACACTTATGCAACTTAGACTACCAAGACACGG
CTCCTGCTTTGGTTACTGT
Found at i:4199870 original size:11 final size:11
Alignment explanation
Indices: 4199856--4199894 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4199846 AAAATAATTC
4199856 TAAAAAATTTT
1 TAAAAAATTTT
4199867 TAAAAAAATTTT
1 T-AAAAAATTTT
* *
4199879 TAATATATTTT
1 TAAAAAATTTT
4199890 TAAAA
1 TAAAA
4199895 TGTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAAAAATTTT
Found at i:4199872 original size:12 final size:12
Alignment explanation
Indices: 4199857--4199894 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4199847 AAATAATTCT
4199857 AAAAAATTTTTA
1 AAAAAATTTTTA
4199869 AAAAAATTTTT-
1 AAAAAATTTTTA
* *
4199880 AATATATTTTTA
1 AAAAAATTTTTA
4199892 AAA
1 AAA
4199895 TGTTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAAAAATTTTTA
Found at i:4200045 original size:8 final size:9
Alignment explanation
Indices: 4199743--4200055 Score: 100
Period size: 10 Copynumber: 32.6 Consensus size: 9
4199733 ATTTTTTTAA
*
4199743 AAAAATTCT
1 AAAAATTTT
* *
4199752 AGAATTTTT
1 AAAAATTTT
*
4199761 AAATATTTTT
1 AAA-AATTTT
* *
4199771 TAAAATTAT
1 AAAAATTTT
4199780 AAAAATTTT
1 AAAAATTTT
4199789 -AAAATTTCT
1 AAAAATTT-T
*
4199798 AAAAGGTTTT
1 AAAA-ATTTT
**
4199808 AAAAACATT
1 AAAAATTTT
4199817 ACAAAAGTTTT
1 A-AAAA-TTTT
4199828 AAAAATTTAT
1 AAAAATTT-T
**
4199838 AAAAATTAA
1 AAAAATTTT
*
4199847 AAATAATTCTA
1 AAA-AATT-TT
4199858 AAAAATTTTT
1 AAAAA-TTTT
4199868 AAAAAAATTTTT
1 --AAAAA-TTTT
*
4199880 AATATATTTT
1 AA-AAATTTT
*
4199890 TAAAATGTTT
1 AAAAAT-TTT
4199900 -AAAATTTAT
1 AAAAATTT-T
4199909 AAAAA-TTT
1 AAAAATTTT
*
4199917 --AATTTTT
1 AAAAATTTT
*
4199924 AAAAAATATAT
1 -AAAAAT-TTT
*
4199935 AAAAATATT
1 AAAAATTTT
4199944 -AAAATTTT
1 AAAAATTTT
**
4199952 -TTAATTTAT
1 AAAAATTT-T
*
4199961 CAAAATTTTT
1 -AAAAATTTT
*
4199971 AAATAATTCT
1 AAA-AATTTT
*
4199981 AAAAATTTCA
1 AAAAATTT-T
*
4199991 AAACAATTCTA
1 AAA-AATT-TT
*
4200002 AAAAATTCT
1 AAAAATTTT
4200011 AAAAATTTTT
1 AAAAA-TTTT
*
4200021 GAAAAAATTATA
1 --AAAAATT-TT
*
4200033 AAAAAATTT
1 AAAAATTTT
4200042 AAAAATTTT
1 AAAAATTTT
4200051 AAAAA
1 AAAAA
4200056 AAGTTAGCTC
Statistics
Matches: 228, Mismatches: 44, Indels: 64
0.68 0.13 0.19
Matches are distributed among these distances:
6 2 0.01
7 3 0.01
8 22 0.10
9 68 0.30
10 86 0.38
11 30 0.13
12 17 0.07
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (9 bp):
AAAAATTTT
Found at i:4207948 original size:34 final size:33
Alignment explanation
Indices: 4207910--4208018 Score: 94
Period size: 34 Copynumber: 3.2 Consensus size: 33
4207900 CAGATTTTTA
*
4207910 ATTTAAAATTTCATTACCTCTGCTCAGAGGAGTT
1 ATTTAAAGTTTCATTACCTCTG-TCAGAGGAGTT
* * * * *
4207944 ATTTAAAGTGTCATAACCTCTAGTCAAAAGAGCT
1 ATTTAAAGTTTCATTACCTCT-GTCAGAGGAGTT
*
4207978 ATTTCAAAGTTTCA-TAGCCTCTAATCAGAGGAGTT
1 ATTT-AAAGTTTCATTA-CCTCT-GTCAGAGGAGTT
*
4208013 TTTTAA
1 ATTTAA
4208019 TTTCAAGAGC
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
34 33 0.56
35 26 0.44
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (33 bp):
ATTTAAAGTTTCATTACCTCTGTCAGAGGAGTT
Found at i:4208264 original size:40 final size:40
Alignment explanation
Indices: 4208184--4208265 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
4208174 GGATTTTTTT
* * *
4208184 AATTTAAAGTTTTATTACCTTTGGTCAAATGAGCCTTTTA
1 AATTTAAAGTTTTATTACCTCTGGTCAAATAAGCCATTTA
4208224 AATTTAAAGTTTCT-TTACCTCTGGTCAGAA-AAGCCATTTA
1 AATTTAAAGTTT-TATTACCTCTGGTCA-AATAAGCCATTTA
4208264 AA
1 AA
4208266 GTTTCATAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 34 0.92
41 3 0.08
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (40 bp):
AATTTAAAGTTTTATTACCTCTGGTCAAATAAGCCATTTA
Found at i:4209131 original size:19 final size:18
Alignment explanation
Indices: 4209103--4209150 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
4209093 CGTTTGTAAG
* *
4209103 ATTTTCTTTTTTCATTTT
1 ATTTTATTTTTTAATTTT
*
4209121 ATTTTTATTTTCTAATTTT
1 A-TTTTATTTTTTAATTTT
4209140 ATTTTATTTTT
1 ATTTTATTTTT
4209151 ATTATTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTATTTTTTAATTTT
Found at i:4209143 original size:24 final size:24
Alignment explanation
Indices: 4209103--4209153 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
4209093 CGTTTGTAAG
*
4209103 ATTTTCTTTTTTCATTTTATTTTT
1 ATTTTCTATTTTCATTTTATTTTT
4209127 ATTTTCTAATTTT-ATTTTATTTTT
1 ATTTTCT-ATTTTCATTTTATTTTT
4209151 ATT
1 ATT
4209154 ATTTGTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (24 bp):
ATTTTCTATTTTCATTTTATTTTT
Found at i:4209157 original size:19 final size:18
Alignment explanation
Indices: 4209103--4209157 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
4209093 CGTTTGTAAG
*
4209103 ATTTTCTTTTT-TCATTTT
1 ATTTTATTTTTAT-ATTTT
4209121 ATTTTTATTTTCTA-ATTTT
1 A-TTTTATTTT-TATATTTT
4209140 ATTTTATTTTTATTATTT
1 ATTTTATTTTTA-TATTT
4209158 GTTTAAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
17 2 0.06
18 10 0.32
19 18 0.58
20 1 0.03
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTATTTTTATATTTT
Found at i:4209203 original size:15 final size:15
Alignment explanation
Indices: 4209176--4209210 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
4209166 TTTTTTTACA
4209176 ATTTATGATTTATAAT
1 ATTTATGATTTAT-AT
4209192 ATTTAT-ATTTATAT
1 ATTTATGATTTATAT
4209206 ATTTA
1 ATTTA
4209211 CTAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 6 0.32
16 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
ATTTATGATTTATAT
Found at i:4209306 original size:3 final size:3
Alignment explanation
Indices: 4209298--4209336 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
4209288 GGATAAACAA
4209298 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4209337 TTAAGGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4209697 original size:2 final size:2
Alignment explanation
Indices: 4209690--4209715 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4209680 ATCATTACAA
4209690 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
4209716 TGGATTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4209780 original size:15 final size:16
Alignment explanation
Indices: 4209757--4209789 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4209747 AAAAACATAA
4209757 AAAGATTTA-TTAAAT
1 AAAGATTTATTTAAAT
*
4209772 AAAGGTTTATTTAAAT
1 AAAGATTTATTTAAAT
4209788 AA
1 AA
4209790 TAATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (16 bp):
AAAGATTTATTTAAAT
Found at i:4210203 original size:25 final size:25
Alignment explanation
Indices: 4210175--4210228 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
4210165 ATATTAACTT
4210175 TAAAACAAAAAATGTTTTTCATAAA
1 TAAAACAAAAAATGTTTTTCATAAA
***
4210200 TAAATTTAAAAATGTTTTTCATAAA
1 TAAAACAAAAAATGTTTTTCATAAA
4210225 TAAA
1 TAAA
4210229 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (25 bp):
TAAAACAAAAAATGTTTTTCATAAA
Found at i:4210229 original size:25 final size:26
Alignment explanation
Indices: 4210182--4210237 Score: 105
Period size: 25 Copynumber: 2.2 Consensus size: 26
4210172 CTTTAAAACA
4210182 AAAAATGTTTTTCATAAATAAA-TTT
1 AAAAATGTTTTTCATAAATAAATTTT
4210207 AAAAATGTTTTTCATAAATAAATTTT
1 AAAAATGTTTTTCATAAATAAATTTT
4210233 AAAAA
1 AAAAA
4210238 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 22 0.73
26 8 0.27
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
AAAAATGTTTTTCATAAATAAATTTT
Found at i:4213012 original size:3 final size:3
Alignment explanation
Indices: 4212961--4212992 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
4212951 GTATCAAAAA
*
4212961 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4212993 GACCATAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4223002 original size:103 final size:104
Alignment explanation
Indices: 4222818--4223047 Score: 383
Period size: 103 Copynumber: 2.2 Consensus size: 104
4222808 TGACTTTTGC
* * *
4222818 ATGC-CTCAACTAACTTGAGAATGCAATTTTATTTTTTCTTAGGCCTCAACAAAAGACCTTTACA
1 ATGCTCTCAACTAACTTGAGAATGCAATTCTATTTTTTCTAAGGCCTCAAAAAAAGACCTTTACA
4222882 AAACTTTTTATGTTCTTTTCCTACTTTTCAACATCCAAA
66 AAACTTTTTATGTTCTTTTCCTACTTTTCAACATCCAAA
4222921 ATGCTCTCAACTAACTTGAGAATG-AATTCTATTTTTTCTAAGGCCTCAAAAAAAGACCTTTACA
1 ATGCTCTCAACTAACTTGAGAATGCAATTCTATTTTTTCTAAGGCCTCAAAAAAAGACCTTTACA
* * *
4222985 AAACTTTTTGTGTTCTTTTCCTCCTTTTCAAGATCCAAA
66 AAACTTTTTATGTTCTTTTCCTACTTTTCAACATCCAAA
*
4223024 CTGCTCTCAACTAACTTGAGAATG
1 ATGCTCTCAACTAACTTGAGAATG
4223048 TTTACACCAA
Statistics
Matches: 119, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 100 0.84
104 19 0.16
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (104 bp):
ATGCTCTCAACTAACTTGAGAATGCAATTCTATTTTTTCTAAGGCCTCAAAAAAAGACCTTTACA
AAACTTTTTATGTTCTTTTCCTACTTTTCAACATCCAAA
Found at i:4225722 original size:6 final size:6
Alignment explanation
Indices: 4225711--4225737 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4225701 CAACTTCTTT
4225711 TTTTCC TTTTCC TTTTCC TTTTCC TTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTT
4225738 CTTTCCTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCC
Found at i:4233119 original size:19 final size:20
Alignment explanation
Indices: 4233082--4233123 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4233072 ATTATGTTAC
*
4233082 ATTTTTTGTTACTCATTTTA
1 ATTTTTTGTTAATCATTTTA
*
4233102 ATTTTTT-TTAATCTTTTTA
1 ATTTTTTGTTAATCATTTTA
4233121 ATT
1 ATT
4233124 CTTCCACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTTTTTGTTAATCATTTTA
Found at i:4234336 original size:10 final size:9
Alignment explanation
Indices: 4234301--4234398 Score: 56
Period size: 10 Copynumber: 9.7 Consensus size: 9
4234291 GCCCTTCTCA
4234301 TTTTTTATT
1 TTTTTTATT
4234310 TTTTGTT-TGT
1 TTTT-TTAT-T
*
4234320 GTTTTTACTT
1 TTTTTTA-TT
4234330 TTTTTTATT
1 TTTTTTATT
4234339 TTTGTGCTTATT
1 TTT-T--TTATT
4234351 TTATTTTATT
1 TT-TTTTATT
4234361 TGTTTTGT-TT
1 T-TTTT-TATT
4234371 TGTTTTTATTT
1 T-TTTTTA-TT
4234382 TGTTTTTATGT
1 T-TTTTTAT-T
4234393 TTTTTT
1 TTTTTT
4234399 TAGACTTAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 25
0.73 0.02 0.25
Matches are distributed among these distances:
9 13 0.18
10 37 0.50
11 15 0.20
12 8 0.11
13 1 0.01
ACGTcount: A:0.08, C:0.02, G:0.10, T:0.80
Consensus pattern (9 bp):
TTTTTTATT
Found at i:4234398 original size:22 final size:21
Alignment explanation
Indices: 4234308--4234400 Score: 82
Period size: 22 Copynumber: 4.3 Consensus size: 21
4234298 TCATTTTTTA
* *
4234308 TTTTTTGTTTGTGTTTTTACTT
1 TTTTTTATTT-TGTTTTTATTT
**
4234330 TTTTTTATTTTTGTGCTTATTT
1 TTTTTTA-TTTTGTTTTTATTT
*
4234352 TATTTTA-TTTGTTTTGT-TTT
1 TTTTTTATTTTGTTTT-TATTT
*
4234372 GTTTTTATTTTGTTTTTATGTT
1 TTTTTTATTTTGTTTTTAT-TT
4234394 TTTTTTA
1 TTTTTTA
4234401 GACTTAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
20 15 0.27
21 10 0.18
22 28 0.50
23 3 0.05
ACGTcount: A:0.09, C:0.02, G:0.11, T:0.78
Consensus pattern (21 bp):
TTTTTTATTTTGTTTTTATTT
Found at i:4234633 original size:35 final size:35
Alignment explanation
Indices: 4234520--4234635 Score: 85
Period size: 35 Copynumber: 3.3 Consensus size: 35
4234510 GTATTAACGC
* * *
4234520 AAGTCAAAAAATAAAGGACAACT-AGGACTAAATCGT
1 AAGTCAAAAAATAAA-GACGATTGA-GACAAAATCGT
** * * * *
4234556 AAGTTGAGAAATAAAGATGATTG-GA-ACAAAGCTAT
1 AAGTCAAAAAATAAAGACGATTGAGACA-AAATC-GT
*
4234591 AAATCAAAAAATAAAGACGATTGAGACAAAATCGT
1 AAGTCAAAAAATAAAGACGATTGAGACAAAATCGT
4234626 AAGTCAAAAA
1 AAGTCAAAAA
4234636 CAAAGATGAC
Statistics
Matches: 58, Mismatches: 17, Indels: 11
0.67 0.20 0.13
Matches are distributed among these distances:
34 6 0.10
35 33 0.57
36 18 0.31
37 1 0.02
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.18
Consensus pattern (35 bp):
AAGTCAAAAAATAAAGACGATTGAGACAAAATCGT
Found at i:4234969 original size:34 final size:33
Alignment explanation
Indices: 4234915--4235035 Score: 91
Period size: 34 Copynumber: 3.5 Consensus size: 33
4234905 ATAAGTCGAG
* *
4234915 AAATAAATATGACTGGGATGAAATCGAAAGTCAT
1 AAATAAATATGA-TGAGATGAAATCGAAAGTCAA
* * * *
4234949 AAATAAATATGATAGAGATGAAGTCGTAAGTTAG
1 AAATAAATATGAT-GAGATGAAATCGAAAGTCAA
* * *
4234983 GAATAAAGATGATCGAGACGAAATC-ACAAGTCAAA
1 AAATAAATATGAT-GAGATGAAATCGA-AAGTC-AA
*
4235018 AAATAAAAATGATTGAGA
1 AAATAAATATGA-TGAGA
4235036 CTAAGCTGCA
Statistics
Matches: 68, Mismatches: 15, Indels: 7
0.76 0.17 0.08
Matches are distributed among these distances:
33 1 0.01
34 51 0.75
35 15 0.22
36 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (33 bp):
AAATAAATATGATGAGATGAAATCGAAAGTCAA
Found at i:4235048 original size:35 final size:33
Alignment explanation
Indices: 4235009--4235133 Score: 101
Period size: 35 Copynumber: 3.6 Consensus size: 33
4234999 GACGAAATCA
*
4235009 CAAGTCAAAAAATAAAAATGATTGAGACT-AAGC
1 CAAGTCAAAAAATAAAAATGAATGAGA-TAAAGC
* * *
4235042 TGCAAGTCGAGAAATAAAGAT-AACTGAGATAAAGC
1 --CAAGTCAAAAAATAAAAATGAA-TGAGATAAAGC
* * * *
4235077 CTAAGTCAGAAAATAAAGATGAATAAGATGAAGCC
1 C-AAGTCAAAAAATAAAAATGAATGAGATAAAG-C
4235112 ACAAGTCAAAAAATAAAAATGA
1 -CAAGTCAAAAAATAAAAATGA
4235134 CTACTAATCT
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
33 1 0.01
34 25 0.34
35 46 0.63
36 1 0.01
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.17
Consensus pattern (33 bp):
CAAGTCAAAAAATAAAAATGAATGAGATAAAGC
Found at i:4235106 original size:138 final size:139
Alignment explanation
Indices: 4234845--4235109 Score: 331
Period size: 138 Copynumber: 1.9 Consensus size: 139
4234835 CAGGTCAAAA
* * * * *
4234845 AATAAAGATGATGGAGATAAAACTATAAGTCAAAAAAAAAAAAATGATTGGGACTAAGCTATAAG
1 AATAAAGATGATCGAGAGAAAACTACAAGTCAAAAAAAAAAAAATGATTGAGACTAAGCTACAAG
* * * * * * *
4234910 TCGAGAAATAAATATGACTGGGATGAAATCGAAAGTCATAAATAAATATGATAGAGATGAAGTCG
66 TCGAGAAATAAAGATAACTGAGATGAAAGCCAAAGTCAAAAATAAAGATGATAGAGATGAAGTCG
4234975 TAAGTTAGG
131 TAAGTTAGG
* * *
4234984 AATAAAGATGATCGAGACGAAATC-ACAAGTC-AAAAAATAAAAATGATTGAGACTAAGCTGCAA
1 AATAAAGATGATCGAGA-GAAAACTACAAGTCAAAAAAAAAAAAATGATTGAGACTAAGCTACAA
*
4235047 GTCGAGAAATAAAGATAACTGAGAT-AAAGCCTAAGTCAGAAAATAAAGATGAATA-AGATGAAG
65 GTCGAGAAATAAAGATAACTGAGATGAAAGCCAAAGTCA-AAAATAAAGATG-ATAGAGATGAAG
4235110 CCACAAGTCA
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
137 10 0.09
138 68 0.64
139 25 0.23
140 4 0.04
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.20
Consensus pattern (139 bp):
AATAAAGATGATCGAGAGAAAACTACAAGTCAAAAAAAAAAAAATGATTGAGACTAAGCTACAAG
TCGAGAAATAAAGATAACTGAGATGAAAGCCAAAGTCAAAAATAAAGATGATAGAGATGAAGTCG
TAAGTTAGG
Found at i:4236496 original size:16 final size:16
Alignment explanation
Indices: 4236443--4236487 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
4236433 CTTCTATTTC
4236443 ATTTTTTCATTTTTTT
1 ATTTTTTCATTTTTTT
*
4236459 ATTTTTTTATTTTTTT
1 ATTTTTTCATTTTTTT
4236475 ATTTTTTCATTTT
1 ATTTTTTCATTTT
4236488 GCTTTTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.82
Consensus pattern (16 bp):
ATTTTTTCATTTTTTT
Found at i:4236501 original size:8 final size:8
Alignment explanation
Indices: 4236443--4236510 Score: 73
Period size: 8 Copynumber: 8.0 Consensus size: 8
4236433 CTTCTATTTC
*
4236443 ATTTTTTC
1 ATTTTTTT
4236451 ATTTTTTT
1 ATTTTTTT
4236459 ATTTTTTT
1 ATTTTTTT
4236467 ATTTTTTT
1 ATTTTTTT
*
4236475 ATTTTTTC
1 ATTTTTTT
4236483 ATTTTGCTTTT
1 A-TTT--TTTT
*
4236494 TTTGTTTTT
1 ATT-TTTTT
4236503 ATTTTTTT
1 ATTTTTTT
4236511 GTCTTTTCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
8 36 0.71
9 9 0.18
10 2 0.04
11 4 0.08
ACGTcount: A:0.10, C:0.04, G:0.03, T:0.82
Consensus pattern (8 bp):
ATTTTTTT
Found at i:4236511 original size:14 final size:14
Alignment explanation
Indices: 4236454--4236517 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
4236444 TTTTTTCATT
*
4236454 TTTTTATTTTTTTATT
1 TTTTTA-TTTTTT-TG
**
4236470 TTTTTATTTTTTCA
1 TTTTTATTTTTTTG
**
4236484 TTTTGCTTTTTTTG
1 TTTTTATTTTTTTG
4236498 TTTTTATTTTTTTG
1 TTTTTATTTTTTTG
4236512 TCTTTT
1 T-TTTT
4236518 CTTTCTCTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 23 0.59
15 10 0.26
16 6 0.15
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTTTTG
Found at i:4239511 original size:42 final size:43
Alignment explanation
Indices: 4239450--4239535 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 43
4239440 TGCACATCGC
* *
4239450 TAAACATTTAAGGCTTTTTTTAAG-GAAAAATGCCTTAAATGA
1 TAAACATTTAAAGCTTTTTTTAAGAAAAAAATGCCTTAAATGA
*
4239492 TAAACATTTAAAG-TGTTTTTTGAGAAAAAAATGCCTTAAATGA
1 TAAACATTTAAAGCT-TTTTTTAAGAAAAAAATGCCTTAAATGA
4239535 T
1 T
4239536 GATTATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 1 0.03
42 20 0.51
43 18 0.46
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (43 bp):
TAAACATTTAAAGCTTTTTTTAAGAAAAAAATGCCTTAAATGA
Found at i:4239705 original size:40 final size:42
Alignment explanation
Indices: 4239644--4239722 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 42
4239634 AAATGGTCAT
*
4239644 CATTGAAGGCATTTTTAAAG-A-AAACGCTTGAAATAATCAA
1 CATTGAAGACATTTTTAAAGAAGAAACGCTTGAAATAATCAA
* * *
4239684 CATTTAAGACATTTTTTAAGAAGAAACGCTTTAAATAAT
1 CATTGAAGACATTTTTAAAGAAGAAACGCTTGAAATAAT
4239723 GATCCTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 17 0.52
41 1 0.03
42 15 0.45
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (42 bp):
CATTGAAGACATTTTTAAAGAAGAAACGCTTGAAATAATCAA
Found at i:4244824 original size:16 final size:16
Alignment explanation
Indices: 4244803--4244837 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
4244793 TCGTTGAGTG
4244803 TCCTTTTTACGAGTAA
1 TCCTTTTTACGAGTAA
4244819 TCCTTTTTACGAGTAA
1 TCCTTTTTACGAGTAA
4244835 TCC
1 TCC
4244838 ATCCCCTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (16 bp):
TCCTTTTTACGAGTAA
Found at i:4246062 original size:23 final size:23
Alignment explanation
Indices: 4246009--4246062 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
4245999 TTAGTCTTTG
4246009 AAATTATT--AAATAATTTTGAT
1 AAATTATTAAAAATAATTTTGAT
**
4246030 TCATTATTAAAAATAATTTTAGAT
1 AAATTATTAAAAATAATTTT-GAT
4246054 AAATT-TTAA
1 AAATTATTAA
4246063 TTTTTCATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 6 0.23
23 14 0.54
24 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
AAATTATTAAAAATAATTTTGAT
Found at i:4252992 original size:20 final size:20
Alignment explanation
Indices: 4252969--4253006 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4252959 AAAAATTTAT
*
4252969 AAAAAAAAATAAAATAACAA
1 AAAAAAAAAGAAAATAACAA
4252989 AAAAAAAAAGAAAATAAC
1 AAAAAAAAAGAAAATAAC
4253007 CCTTTAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.84, C:0.05, G:0.03, T:0.08
Consensus pattern (20 bp):
AAAAAAAAAGAAAATAACAA
Found at i:4257307 original size:5 final size:5
Alignment explanation
Indices: 4257297--4257323 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4257287 CAGCAAACCA
4257297 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
4257324 TTTGGTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:4261328 original size:14 final size:14
Alignment explanation
Indices: 4261311--4261340 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4261301 CATTTTAACC
4261311 TTTTTT-TTTTCAT
1 TTTTTTCTTTTCAT
4261324 TTTTTTCTTTTCAT
1 TTTTTTCTTTTCAT
4261338 TTT
1 TTT
4261341 GATTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTTTCAT
Found at i:4262169 original size:42 final size:46
Alignment explanation
Indices: 4262112--4262197 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 46
4262102 ATTTTATTTT
*
4262112 ATTTATTGTTTAAAATTA-TT-TT-AA-GATAATATTTATTTATTA
1 ATTTATTGTTTAAAATTATTTATTAAACGATAATAATTATTTATTA
4262154 ATTTATCT-TTTAAAATTATTTATTAAACGATAATAATTATTTAT
1 ATTTAT-TGTTTAAAATTATTTATTAAACGATAATAATTATTTAT
4262198 ATTTTTCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
42 16 0.42
43 3 0.08
44 2 0.05
45 2 0.05
46 15 0.39
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (46 bp):
ATTTATTGTTTAAAATTATTTATTAAACGATAATAATTATTTATTA
Found at i:4269485 original size:14 final size:14
Alignment explanation
Indices: 4269466--4269492 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4269456 AATAATAAGG
4269466 ATTTATTTAAATAA
1 ATTTATTTAAATAA
4269480 ATTTATTTAAATA
1 ATTTATTTAAATA
4269493 TAATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTATTTAAATAA
Found at i:4270736 original size:12 final size:13
Alignment explanation
Indices: 4270713--4270755 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
4270703 CTAAAAGTAT
4270713 TTTATTTA--TTA
1 TTTATTTATTTTA
4270724 TTTA-TTATTTTA
1 TTTATTTATTTTA
4270736 TTTATTTATTTTA
1 TTTATTTATTTTA
4270749 -TTATTTA
1 TTTATTTA
4270756 GTTGGTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.10
11 4 0.14
12 14 0.48
13 8 0.28
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:4270740 original size:16 final size:15
Alignment explanation
Indices: 4270717--4270755 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
4270707 AAGTATTTTA
4270717 TTTA-TTATTTATTAT
1 TTTATTTATTTATT-T
4270732 TTTATTTATTTATTT
1 TTTATTTATTTATTT
4270747 TATTATTTA
1 T-TTATTTA
4270756 GTTGGTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTATTTATTT
Found at i:4275038 original size:2 final size:2
Alignment explanation
Indices: 4275033--4275069 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4275023 AAGAAAGAAC
4275033 GA GA GA GA GA GA GA GA GA GA GA GA G- GA G- GA G- GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4275070 TGGGTTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4279735 original size:19 final size:20
Alignment explanation
Indices: 4279697--4279740 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
4279687 AATTAATTTA
**
4279697 AAATAAAATTTTAGTTTATT
1 AAATAAAAACTTAGTTTATT
4279717 AAATAAAAACTTA-TTTATT
1 AAATAAAAACTTAGTTTATT
4279736 AAATA
1 AAATA
4279741 TATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AAATAAAAACTTAGTTTATT
Found at i:4279950 original size:13 final size:14
Alignment explanation
Indices: 4279932--4279962 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4279922 ACTTAAATTT
4279932 ATTTGAT-TTGAAA
1 ATTTGATGTTGAAA
4279945 ATTTGATGTTGAAA
1 ATTTGATGTTGAAA
4279959 ATTT
1 ATTT
4279963 AATTGGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (14 bp):
ATTTGATGTTGAAA
Found at i:4280080 original size:6 final size:6
Alignment explanation
Indices: 4280069--4280095 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4280059 TTTATAAAAT
4280069 TATAAA TATAAA TATAAA TATAAA TAT
1 TATAAA TATAAA TATAAA TATAAA TAT
4280096 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TATAAA
Found at i:4285695 original size:18 final size:18
Alignment explanation
Indices: 4285660--4285720 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
4285650 TGAAAAATTA
*
4285660 CTAAAAAT-GACA-GTTT
1 CTAAAAATAGAAAGGTTT
4285676 CTAAAAATAGAAAGGTTT
1 CTAAAAATAGAAAGGTTT
*
4285694 CTAAAAATAAAAAGGTTT
1 CTAAAAATAGAAAGGTTT
4285712 CTAAAAATA
1 CTAAAAATA
4285721 AAAAAAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
16 8 0.20
17 3 0.07
18 30 0.73
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (18 bp):
CTAAAAATAGAAAGGTTT
Found at i:4285721 original size:18 final size:18
Alignment explanation
Indices: 4285672--4285724 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
4285662 AAAAATGACA
*
4285672 GTTTCTAAAAATAGAAAG
1 GTTTCTAAAAATAAAAAG
4285690 GTTTCTAAAAATAAAAAG
1 GTTTCTAAAAATAAAAAG
4285708 GTTTCTAAAAATAAAAA
1 GTTTCTAAAAATAAAAA
4285725 AAATTACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (18 bp):
GTTTCTAAAAATAAAAAG
Found at i:4287006 original size:21 final size:22
Alignment explanation
Indices: 4286982--4287025 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
4286972 AAATGTGTTT
*
4286982 ACAAATTAAAGGA-AAATTAAA
1 ACAAACTAAAGGATAAATTAAA
* *
4287003 ACAAGCTAAAGGATAACTTAAA
1 ACAAACTAAAGGATAAATTAAA
4287025 A
1 A
4287026 GAACAATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
ACAAACTAAAGGATAAATTAAA
Found at i:4292507 original size:17 final size:17
Alignment explanation
Indices: 4292478--4292512 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4292468 GATCTATGAG
4292478 TAAAATAATATTTTTAA
1 TAAAATAATATTTTTAA
4292495 TAAAA-AATAATTTTTAA
1 TAAAATAAT-ATTTTTAA
4292512 T
1 T
4292513 TTTTAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATAATATTTTTAA
Found at i:4292520 original size:19 final size:20
Alignment explanation
Indices: 4292498--4292545 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
4292488 TTTTTAATAA
*
4292498 AAAATAATTTTTAAT-TTTT
1 AAAATAATTTTGAATGTTTT
* *
4292517 AAAATGATATTGAATGTTTT
1 AAAATAATTTTGAATGTTTT
*
4292537 AAAAAAATT
1 AAAATAATT
4292546 GGATTTTTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
AAAATAATTTTGAATGTTTT
Found at i:4296473 original size:2 final size:2
Alignment explanation
Indices: 4296466--4296501 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4296456 CCTTTTCGTC
4296466 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4296502 TCCTTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4303636 original size:27 final size:27
Alignment explanation
Indices: 4303598--4303649 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
4303588 ATGAAACGGA
* *
4303598 GCATCACATACCAATTGATTTCTGCAT
1 GCATCACATACCAACTGAATTCTGCAT
4303625 GCATCACATACCAACTGAATTCTGC
1 GCATCACATACCAACTGAATTCTGC
4303650 TTCTTGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (27 bp):
GCATCACATACCAACTGAATTCTGCAT
Found at i:4308874 original size:15 final size:15
Alignment explanation
Indices: 4308856--4308887 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4308846 GTTGTTGTTA
*
4308856 TTGATTTTGTTTATG
1 TTGATGTTGTTTATG
4308871 TTGATGTTGTTTATG
1 TTGATGTTGTTTATG
4308886 TT
1 TT
4308888 TGTAAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.22, T:0.66
Consensus pattern (15 bp):
TTGATGTTGTTTATG
Found at i:4308892 original size:69 final size:69
Alignment explanation
Indices: 4308805--4308956 Score: 295
Period size: 69 Copynumber: 2.2 Consensus size: 69
4308795 AATATGACGG
4308805 TGTTAGTTTATGTTTGTAAAATGAATTAGTGGATTGTTGTTGTTGTTGTTATTGATTTTGTTTAT
1 TGTT-GTTTATGTTTGTAAAATGAATTAGTGGATTGTTGTTGTTGTTGTTATTGATTTTGTTTAT
4308870 GTTGA
65 GTTGA
4308875 TGTTGTTTATGTTTGTAAAATGAATTAGTGGATTGTTGTTGTTGTTGTTATTGATTTTGTTTATG
1 TGTTGTTTATGTTTGTAAAATGAATTAGTGGATTGTTGTTGTTGTTGTTATTGATTTTGTTTATG
4308940 TTGA
66 TTGA
4308944 TGTTGTTTATGTT
1 TGTTGTTTATGTT
4308957 GTTGTTATTG
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 78 0.95
70 4 0.05
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.57
Consensus pattern (69 bp):
TGTTGTTTATGTTTGTAAAATGAATTAGTGGATTGTTGTTGTTGTTGTTATTGATTTTGTTTATG
TTGA
Found at i:4308912 original size:33 final size:33
Alignment explanation
Indices: 4308805--4308914 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 33
4308795 AATATGACGG
4308805 TGTTAGTTTATGTTTGTAAAATGAATTAGTGGAT
1 TGTT-GTTTATGTTTGTAAAATGAATTAGTGGAT
* * * *
4308839 TGTTGTTGT-TG-TTGT-TATTGATTTTGTTTATGTTGA-
1 TGTTGTT-TATGTTTGTAAAATGA-----ATTA-GTGGAT
4308875 TGTTGTTTATGTTTGTAAAATGAATTAGTGGAT
1 TGTTGTTTATGTTTGTAAAATGAATTAGTGGAT
4308908 TGTTGTT
1 TGTTGTT
4308915 GTTGTTGTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 23
0.65 0.09 0.26
Matches are distributed among these distances:
31 4 0.07
32 8 0.14
33 15 0.26
34 5 0.09
35 1 0.02
36 12 0.21
37 8 0.14
38 4 0.07
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.55
Consensus pattern (33 bp):
TGTTGTTTATGTTTGTAAAATGAATTAGTGGAT
Found at i:4308943 original size:15 final size:15
Alignment explanation
Indices: 4308925--4308962 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4308915 GTTGTTGTTA
*
4308925 TTGATTTTGTTTATG
1 TTGATGTTGTTTATG
4308940 TTGATGTTGTTTATG
1 TTGATGTTGTTTATG
*
4308955 TTGTTGTT
1 TTGATGTT
4308963 ATTGTTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.00, G:0.24, T:0.66
Consensus pattern (15 bp):
TTGATGTTGTTTATG
Found at i:4310319 original size:18 final size:18
Alignment explanation
Indices: 4310263--4310320 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
4310253 TTTTAGGTTG
* * *
4310263 TTAATTGCTTTGTTAATT
1 TTAATTACTTTATTAATA
* *
4310281 TTAATTATATGTTATTGATA
1 TTAATTA-CT-TTATTAATA
4310301 TTAATTACTTTATTAATA
1 TTAATTACTTTATTAATA
4310319 TT
1 TT
4310321 TTGTAGCGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
18 16 0.52
19 2 0.06
20 13 0.42
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (18 bp):
TTAATTACTTTATTAATA
Found at i:4312667 original size:48 final size:48
Alignment explanation
Indices: 4312611--4312707 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
4312601 TTCCCAACTC
4312611 AAAGGTTTTAATCACAATCACAAAACCATTATCTTTTCCACCTTACCT
1 AAAGGTTTTAATCACAATCACAAAACCATTATCTTTTCCACCTTACCT
4312659 AAAGGTTTTAATCACAATCACAAAACCATTATCTTTTCCACCTTACCT
1 AAAGGTTTTAATCACAATCACAAAACCATTATCTTTTCCACCTTACCT
4312707 A
1 A
4312708 GTCCACGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (48 bp):
AAAGGTTTTAATCACAATCACAAAACCATTATCTTTTCCACCTTACCT
Found at i:4312720 original size:48 final size:48
Alignment explanation
Indices: 4312620--4312720 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
4312610 CAAAGGTTTT
******
4312620 AATCACAATCACAAAACCATTATCTTTTCCACCTTACCTAAAGGTTTT
1 AATCACAATCACAAAACCATTATCTTTTCCACCTTACCTAAACCACGA
**
4312668 AATCACAATCACAAAACCATTATCTTTTCCACCTTACCTAGTCCACGA
1 AATCACAATCACAAAACCATTATCTTTTCCACCTTACCTAAACCACGA
4312716 AATCA
1 AATCA
4312721 AGGCTTCTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.30
Consensus pattern (48 bp):
AATCACAATCACAAAACCATTATCTTTTCCACCTTACCTAAACCACGA
Found at i:4313171 original size:34 final size:34
Alignment explanation
Indices: 4313033--4313191 Score: 105
Period size: 34 Copynumber: 4.7 Consensus size: 34
4313023 ATGTTATCAT
* * * *
4313033 ATATGCATATTCGAAAAT-CATATTGTATTATCAA
1 ATATGCATATCCGATAATGCATAATG-ATTTTCAA
*
4313067 ATATGCATATCC-A-AGATGCAT-ATGCATTATT-AG
1 ATATGCATATCCGATA-ATGCATAATG-ATT-TTCAA
** ** **
4313100 ATACACATATCTTATAATGCATAATGATTTTTGA
1 ATATGCATATCCGATAATGCATAATGATTTTCAA
*
4313134 ATATTCATATCCGATAATGCA-ATATGATTTTCAA
1 ATATGCATATCCGATAATGCATA-ATGATTTTCAA
* *
4313168 ATATGCATATTCGATAATGTATAA
1 ATATGCATATCCGATAATGCATAA
4313192 ATATTACTGG
Statistics
Matches: 97, Mismatches: 19, Indels: 18
0.72 0.14 0.13
Matches are distributed among these distances:
32 1 0.01
33 21 0.22
34 70 0.72
35 5 0.05
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.38
Consensus pattern (34 bp):
ATATGCATATCCGATAATGCATAATGATTTTCAA
Found at i:4313457 original size:20 final size:20
Alignment explanation
Indices: 4313434--4313472 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4313424 TTAATAATTA
* *
4313434 TTTCAATGATTTATGGTTTG
1 TTTCAAAGATTTAGGGTTTG
4313454 TTTCAAAGATTTAGGGTTT
1 TTTCAAAGATTTAGGGTTT
4313473 ATGATATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTCAAAGATTTAGGGTTTG
Found at i:4326403 original size:23 final size:24
Alignment explanation
Indices: 4326349--4326404 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
4326339 TGCAATGAAC
4326349 AAATTTAAAATGGAATTTAAACTA
1 AAATTTAAAATGGAATTTAAACTA
* * * *
4326373 AAA-GTAAAGTGGAA-TTGAAGTA
1 AAATTTAAAATGGAATTTAAACTA
4326395 AAATTTAAAA
1 AAATTTAAAA
4326405 GCAGATAATG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
22 9 0.36
23 13 0.52
24 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (24 bp):
AAATTTAAAATGGAATTTAAACTA
Found at i:4332542 original size:17 final size:16
Alignment explanation
Indices: 4332522--4332555 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4332512 TATAATTAAC
4332522 TATTTAAATTTTAAAAA
1 TATTT-AATTTTAAAAA
*
4332539 TATTTATTTTTAAAAA
1 TATTTAATTTTAAAAA
4332555 T
1 T
4332556 TATAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTAATTTTAAAAA
Found at i:4332572 original size:25 final size:26
Alignment explanation
Indices: 4332527--4332577 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
4332517 TTAACTATTT
* *
4332527 AAATTTTAAAAATATTTATTT-TTAA
1 AAATTATAAAAATATTAATTTATTAA
4332552 AAATTATAAAAAT-TTGAATTTATTAA
1 AAATTATAAAAATATT-AATTTATTAA
4332578 TAATGATGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 2 0.09
25 16 0.73
26 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
AAATTATAAAAATATTAATTTATTAA
Found at i:4335526 original size:2 final size:2
Alignment explanation
Indices: 4335521--4335546 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4335511 TCTCTTCTAC
4335521 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
4335547 GTAGATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4345281 original size:2 final size:2
Alignment explanation
Indices: 4345274--4345306 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4345264 AACACCCTTG
*
4345274 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4345307 GTATGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4349780 original size:159 final size:149
Alignment explanation
Indices: 4349302--4349930 Score: 827
Period size: 157 Copynumber: 4.0 Consensus size: 149
4349292 GCCTATGGGG
*
4349302 TTTTGAGAAAGTAGAGTGAAATAGCGACCAAAATGGAGAGCTTGATGTAAGTTAGGAGAGAGGAA
1 TTTTGAGAAAGTAGAGT-AAATAGCGACAAAAATGGAGAGC------T-AGTTAGGAGAGAGGAA
* * * *
4349367 GCCCGCTGTTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGAATATATATATTTTTTT
58 GCCCGCTGCTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGG-ATATTTTTTTTTTTTT
4349432 TTTATAAATACGTTGAAAGTAAACTTTA
122 TTTATAAATACGTTGAAAGTAAACTTTA
*
4349460 TTTTGAGAAAGTAGAGTGAATAGCGACAAAAATGGAGAGCTTGATGTAAGTTAGGAGAGAGGAAG
1 TTTTGAGAAAGTAGAGTAAATAGCGACAAAAATGGAGAGC------T-AGTTAGGAGAGAGGAAG
*
4349525 CCCGCTGTTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGA-A---TTTTTTTTTTTT
59 CCCGCTGCTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGATATTTTTTTTTTTTTTT
4349586 TATAAATACGTTGAAAGTAAACTTTA
124 TATAAATACGTTGAAAGTAAACTTTA
*
4349612 TTTTGAGAAAGTAGAGTAAATAGCGACAAAAATTGAGAGC-AGTTAGGAGAGAGGAAGCCCGCTG
1 TTTTGAGAAAGTAGAGTAAATAGCGACAAAAATGGAGAGCTAGTTAGGAGAGAGGAAGCCCGCTG
*
4349676 TTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGAATATATATATATATATATATATTT
66 CTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGG---ATAT-T-T-T-T-T-T-T-TTT
4349741 TTTTTATAAATACGTTGAAAGTAAACTTTA
120 TTTTTATAAATACGTTGAAAGTAAACTTTA
*
4349771 TTTTGAGAAAGTAGAGTTAATAGCGACAAAAATGGAGAGCTTGATGTAAGTTAGGAGAGAGGAAG
1 TTTTGAGAAAGTAGAGTAAATAGCGACAAAAATGGAGAGC------T-AGTTAGGAGAGAGGAAG
4349836 CCCGCTGCTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGATATTTTTTTTTTTTTTT
59 CCCGCTGCTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGATATTTTTTTTTTTTTTT
4349901 TATAAATACGTTGAAAGTAAACTTTA
124 TATAAATACGTTGAAAGTAAACTTTA
4349927 TTTT
1 TTTT
4349931 AGATTTTTTT
Statistics
Matches: 439, Mismatches: 9, Indels: 48
0.89 0.02 0.10
Matches are distributed among these distances:
144 64 0.15
147 1 0.00
148 1 0.00
152 74 0.17
154 1 0.00
155 2 0.00
156 39 0.09
157 95 0.22
158 19 0.04
159 72 0.16
160 1 0.00
161 1 0.00
162 1 0.00
163 1 0.00
164 4 0.01
167 63 0.14
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (149 bp):
TTTTGAGAAAGTAGAGTAAATAGCGACAAAAATGGAGAGCTAGTTAGGAGAGAGGAAGCCCGCTG
CTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGATATTTTTTTTTTTTTTTTATAAAT
ACGTTGAAAGTAAACTTTA
Found at i:4349896 original size:311 final size:301
Alignment explanation
Indices: 4349351--4349930 Score: 1016
Period size: 311 Copynumber: 1.9 Consensus size: 301
4349341 GCTTGATGTA
4349351 AGTTAGGAGAGAGGAAGCCCGCTGTTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGA
1 AGTTAGGAGAGAGGAAGCCCGCTGTTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGA
4349416 ATATATATATTTTTTTTTTATAAATACGTTGAAAGTAAACTTTATTTTGAGAAAGTAGAGTGAAT
66 ATATATATATTTTTTTTTTATAAATACGTTGAAAGTAAACTTTATTTTGAGAAAGTAGAGTGAAT
*
4349481 AGCGACAAAAATGGAGAGCTTGATGTAAGTTAGGAGAGAGGAAGCCCGCTGTTAGCGTTTAATTT
131 AGCGACAAAAATGGAGAGCTTGATGTAAGTTAGGAGAGAGGAAGCCCGCTGCTAGCGTTTAATTT
4349546 GGATTTTGGGAATTGGATTCCGGTGGAATTTTTTTTTTTTTATAAATACGTTGAAAGTAAACTTT
196 GGATTTTGGGAATTGGATTCCGGTGGAATTTTTTTTTTTTTATAAATACGTTGAAAGTAAACTTT
4349611 ATTTTGAGAAAGTAGAGTAAATAGCGACAAAAATTGAGAGC
261 ATTTTGAGAAAGTAGAGTAAATAGCGACAAAAATTGAGAGC
4349652 AGTTAGGAGAGAGGAAGCCCGCTGTTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGA
1 AGTTAGGAGAGAGGAAGCCCGCTGTTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGG-
4349717 ATATATATATATATATATATATTTTTTTTATAAATACGTTGAAAGTAAACTTTATTTTGAGAAAG
65 ------A-ATATATATAT-T-TTTTTTTTATAAATACGTTGAAAGTAAACTTTATTTTGAGAAAG
*
4349782 TAGAGTTAATAGCGACAAAAATGGAGAGCTTGATGTAAGTTAGGAGAGAGGAAGCCCGCTGCTAG
121 TAGAGTGAATAGCGACAAAAATGGAGAGCTTGATGTAAGTTAGGAGAGAGGAAGCCCGCTGCTAG
4349847 CGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGATATTTTTTTTTTTTTTTTATAAATACGT
186 CGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGA-A---TTTTTTTTTTTTTATAAATACGT
4349912 TGAAAGTAAACTTTATTTT
247 TGAAAGTAAACTTTATTTT
4349931 AGATTTTTTT
Statistics
Matches: 263, Mismatches: 2, Indels: 14
0.94 0.01 0.05
Matches are distributed among these distances:
301 64 0.24
308 1 0.00
309 10 0.04
310 1 0.00
311 144 0.55
312 1 0.00
315 42 0.16
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.36
Consensus pattern (301 bp):
AGTTAGGAGAGAGGAAGCCCGCTGTTAGCGTTTAATTTGGATTTTGGGAATTGGATTCCGGTGGA
ATATATATATTTTTTTTTTATAAATACGTTGAAAGTAAACTTTATTTTGAGAAAGTAGAGTGAAT
AGCGACAAAAATGGAGAGCTTGATGTAAGTTAGGAGAGAGGAAGCCCGCTGCTAGCGTTTAATTT
GGATTTTGGGAATTGGATTCCGGTGGAATTTTTTTTTTTTTATAAATACGTTGAAAGTAAACTTT
ATTTTGAGAAAGTAGAGTAAATAGCGACAAAAATTGAGAGC
Found at i:4350221 original size:6 final size:6
Alignment explanation
Indices: 4350212--4350237 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4350202 TTTGTTTAAA
4350212 TAAAAT TAAAAT TAAAAT TAAAAT TA
1 TAAAAT TAAAAT TAAAAT TAAAAT TA
4350238 TTTAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAAAT
Found at i:4357111 original size:17 final size:17
Alignment explanation
Indices: 4357074--4357116 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4357064 TAAACTTTAT
* *
4357074 AATATTTTTTCATGAAT
1 AATATTTTTTCAGGAAG
*
4357091 AATATTTTTTCAGGTAG
1 AATATTTTTTCAGGAAG
4357108 AATAATTTT
1 AAT-ATTTT
4357117 GACATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (17 bp):
AATATTTTTTCAGGAAG
Found at i:4360824 original size:13 final size:14
Alignment explanation
Indices: 4360799--4360836 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
4360789 TTATTTTCTA
4360799 AAAAATGATTTTTG
1 AAAAATGATTTTTG
4360813 AAAAATGATTTTTG
1 AAAAATGATTTTTG
4360827 AAAAAT-ATTT
1 AAAAATGATTT
4360837 ACATTTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (14 bp):
AAAAATGATTTTTG
Found at i:4360983 original size:25 final size:26
Alignment explanation
Indices: 4360951--4361009 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
4360941 TTAATATAAC
4360951 TATTAAAATAT-TAAAAATAATTTAT
1 TATTAAAATATATAAAAATAATTTAT
** *
4360976 TATTAAAATATATTGAAATTATTTAT
1 TATTAAAATATATAAAAATAATTTAT
4361002 TATTAAAA
1 TATTAAAA
4361010 AAATTATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
TATTAAAATATATAAAAATAATTTAT
Found at i:4361055 original size:19 final size:18
Alignment explanation
Indices: 4360995--4361071 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
4360985 ATATTGAAAT
*
4360995 TATTTATTATTAAAA-AA
1 TATTTAATATTAAAATAA
*
4361012 -A-TTATATGTTAATAATAA
1 TATTTA-ATATTAA-AATAA
*
4361030 TATTTAATATTAAAATAT
1 TATTTAATATTAAAATAA
4361048 TATGTTAATA-TAAAA-AA
1 TAT-TTAATATTAAAATAA
*
4361065 TACTTAA
1 TATTTAA
4361072 AATAAAACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.06
16 10 0.21
17 5 0.10
18 14 0.29
19 13 0.27
20 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (18 bp):
TATTTAATATTAAAATAA
Found at i:4361135 original size:26 final size:27
Alignment explanation
Indices: 4361106--4361167 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
4361096 TATTATTTAT
4361106 TAATATATTAATAGAT-TATT-TATTAA
1 TAATATATTAATA-ATATATTGTATTAA
*
4361132 TAATAT-TTATTAATATATTGTATTAA
1 TAATATATTAATAATATATTGTATTAA
*
4361158 TAGTATATTA
1 TAATATATTA
4361168 TTTATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 2 0.06
25 9 0.29
26 17 0.55
27 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
TAATATATTAATAATATATTGTATTAA
Found at i:4361173 original size:18 final size:17
Alignment explanation
Indices: 4361094--4361385 Score: 103
Period size: 18 Copynumber: 16.7 Consensus size: 17
4361084 TATTATTCTT
4361094 TATATTATTTATTAATA
1 TATATTATTTATTAATA
* * *
4361111 TATTAATAGATTATTTAT-
1 TA-TATTA-TTTATTAATA
*
4361129 TAATAATATTTATT-A-A
1 T-ATATTATTTATTAATA
*
4361145 TATA-T-TGTATTAATA
1 TATATTATTTATTAATA
4361160 GTATATTATTTATTAATAA
1 -TATATTATTTATTAAT-A
4361179 TATATTATTTATTCATATA
1 TATATTATTTATT-A-ATA
4361198 TTATTATAATATTTATTAAT-
1 -TA-TAT--TATTTATTAATA
* * *
4361218 TAAATTAATAATATTTAT-
1 TATATT-AT-TTATTAATA
*
4361236 TATGTTATTTATTAATA
1 TATATTATTTATTAATA
*
4361253 TAATATTATATATTAATA
1 T-ATATTATTTATTAATA
* * **
4361271 TCTTATAATATTATTTCCTA
1 T-ATATTAT-TTA-TTAATA
4361291 -ATATTATTTATT-A-A
1 TATATTATTTATTAATA
*
4361305 TATATTA--TAAT-AT-
1 TATATTATTTATTAATA
*
4361318 TAT-TTATTAATATAATA
1 TATATTATTTAT-TAATA
*
4361335 T-TATTCATTTATCAATAAA
1 TATATT-ATTTATTAAT--A
4361354 TATTATTTATTTATTAATA
1 TA-TA-TTATTTATTAATA
4361373 TAATATTATTTAT
1 T-ATATTATTTAT
4361386 AAGTAAAATT
Statistics
Matches: 208, Mismatches: 30, Indels: 73
0.67 0.10 0.23
Matches are distributed among these distances:
12 3 0.01
13 12 0.06
14 4 0.02
15 11 0.05
16 18 0.09
17 22 0.11
18 81 0.39
19 21 0.10
20 9 0.04
21 16 0.08
22 3 0.01
23 8 0.04
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (17 bp):
TATATTATTTATTAATA
Found at i:4361244 original size:30 final size:30
Alignment explanation
Indices: 4361202--4361267 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
4361192 CATATATTAT
*
4361202 TATAATAT-TTATTAATTAA-ATTAATAATA
1 TATATTATGTTATTAATTAATA-TAATAATA
* * *
4361231 TTTATTATGTTATTTATTAATATAATATTA
1 TATATTATGTTATTAATTAATATAATAATA
4361261 TATATTA
1 TATATTA
4361268 ATATCTTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 6 0.20
30 23 0.77
31 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TATATTATGTTATTAATTAATATAATAATA
Found at i:4361245 original size:34 final size:37
Alignment explanation
Indices: 4361093--4361337 Score: 149
Period size: 36 Copynumber: 6.7 Consensus size: 37
4361083 TTATTATTCT
*
4361093 TTATATTATTTATT-A-AT-ATATTAATAGAT-TATTTA
1 TTATAATATTTATTAATATAATATTAATA-ATATA-TTA
*
4361128 TTAATAATATTTATTAATAT-AT-TGTATTAATAGTA-TA
1 TT-ATAATATTTATTAATATAATAT-TAATAATA-TATTA
* * * * *
4361165 TTAT-TTA-TTAATAATATATTATTTATTCATATATTA
1 TTATAATATTTATTAATATAATA-TTAATAATATATTA
4361201 TTATAATATTTATTAAT-TAA-ATTAATAATAT-TTA
1 TTATAATATTTATTAATATAATATTAATAATATATTA
** * *
4361235 TTATGTTATTTATTAATATAATATTATATATTA-ATATC
1 TTATAATATTTATTAATATAATATTA-ATAATATAT-TA
* * *
4361273 TTATAATATTATTTCCTAATATTAT-TTATTAATATATTA
1 TTATAATATT-TAT--TAATATAATATTAATAATATATTA
* *
4361312 TAATATTATTTATTAATATAATATTA
1 TTATAATATTTATTAATATAATATTA
4361338 TTCATTTATC
Statistics
Matches: 162, Mismatches: 26, Indels: 42
0.70 0.11 0.18
Matches are distributed among these distances:
34 27 0.17
35 18 0.11
36 39 0.24
37 22 0.14
38 26 0.16
39 17 0.10
40 5 0.03
41 8 0.05
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (37 bp):
TTATAATATTTATTAATATAATATTAATAATATATTA
Found at i:4361315 original size:23 final size:23
Alignment explanation
Indices: 4361095--4361385 Score: 108
Period size: 23 Copynumber: 12.5 Consensus size: 23
4361085 ATTATTCTTT
4361095 ATATTATTTATTAATATATTA-A
1 ATATTATTTATTAATATATTATA
*
4361117 TAGATTATTTATTAATAATATTTATTA
1 -ATATTATTTATTAAT-ATA-TTA-TA
*
4361144 ATA-TATTGTATTAATAGTA-TATT
1 ATATTATT-TATTAATA-TATTATA
*
4361167 AT-TTA-TTAATAATATATTAT-
1 ATATTATTTATTAATATATTATA
* * * *
4361187 TTATTCATATATTATTATAATAT-
1 ATATT-ATTTATTAATATATTATA
* *
4361210 TTATTAATTAAATTAATA-A-TAT-
1 ATATT-ATT-TATTAATATATTATA
* * *
4361232 TTATTATGTTATTTAT-TAATATA
1 ATATTAT-TTATTAATATATTATA
* *
4361255 ATATTATATATTAATATCTTATA
1 ATATTATTTATTAATATATTATA
**
4361278 ATATTATTTCCTAATATTATTTATTA
1 ATATTATTTATTAATA-TA-TTA-TA
4361304 ATA-TA-TTA-TAATATTATTTATTA
1 ATATTATTTATTAATA-TA-TTA-TA
* * * *
4361327 ATATAATATTATTCATTTATCAATAA
1 ATATTAT-TTATTAATATAT-TAT-A
* *
4361353 ATATTATTTATTTAT-TAATATA
1 ATATTATTTATTAATATATTATA
4361375 ATATTATTTAT
1 ATATTATTTAT
4361386 AAGTAAAATT
Statistics
Matches: 209, Mismatches: 33, Indels: 53
0.71 0.11 0.18
Matches are distributed among these distances:
20 3 0.01
21 20 0.10
22 32 0.15
23 82 0.39
24 17 0.08
25 22 0.11
26 29 0.14
27 4 0.02
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (23 bp):
ATATTATTTATTAATATATTATA
Found at i:4361330 original size:49 final size:49
Alignment explanation
Indices: 4361095--4361385 Score: 173
Period size: 49 Copynumber: 6.0 Consensus size: 49
4361085 ATTATTCTTT
* *
4361095 ATATTATTTATTAATATATTA-ATAGATTATTTATTAATAATATTTATTA
1 ATATTATTTATTAATATATTATA-ATATTATTTATTAATATTATTTATTA
* * *
4361144 ATA-TATTGTATTAATAGTA-TATTAT-TTATTAATAATATATTATTTATTCA
1 ATATTATT-TATTAATA-TATTATAATATTATTTATTA-ATATTATTTATT-A
* * *
4361194 TATATTA-TTA-TAATAT-TTATTA-ATTA--AATTAATAATATTTATT-
1 -ATATTATTTATTAATATATTATAATATTATTTATTAATATTATTTATTA
* * **
4361237 ATGTTATTTATTAATATAATATTATATATTAATATCT-TATAATATTATTTCCTA
1 ATATTATTTATTAATATATTA-TA-ATATT-AT-T-TAT-TAATATTATTTATTA
* *
4361291 ATATTATTTATTAATATATTATAATATTATTTATTAATATAATATTATTC
1 ATATTATTTATTAATATATTATAATATTATTTATTAATATTAT-TTATTA
* * * *
4361341 AT-TTA-TCAATAA-ATATTAT-TTATTTATTAATATAATATTATTTAT
1 ATATTATTTATTAATATATTATAATA-TTATTTAT-TAATATTATTTAT
4361386 AAGTAAAATT
Statistics
Matches: 191, Mismatches: 25, Indels: 54
0.71 0.09 0.20
Matches are distributed among these distances:
42 5 0.03
43 3 0.02
44 6 0.03
45 13 0.07
46 7 0.04
47 19 0.10
48 37 0.19
49 43 0.23
50 12 0.06
51 6 0.03
52 8 0.04
53 13 0.07
54 19 0.10
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (49 bp):
ATATTATTTATTAATATATTATAATATTATTTATTAATATTATTTATTA
Found at i:4362545 original size:24 final size:24
Alignment explanation
Indices: 4362492--4362539 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
4362482 AACAATTTAG
*
4362492 CAACAACTTTTCTCTAGCAAATTT
1 CAACAACTTTTCACTAGCAAATTT
4362516 CAACAACTTTTCACTAGCAAATTT
1 CAACAACTTTTCACTAGCAAATTT
4362540 TCACAATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (24 bp):
CAACAACTTTTCACTAGCAAATTT
Found at i:4378063 original size:20 final size:21
Alignment explanation
Indices: 4378026--4378069 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
4378016 AAAGACAATC
4378026 AGATTTCACTTACATTCTTAT
1 AGATTTCACTTACATTCTTAT
4378047 AGATTTCACTT-CATTCTTAT
1 AGATTTCACTTACATTCTTAT
4378067 AGA
1 AGA
4378070 GAGCAGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (21 bp):
AGATTTCACTTACATTCTTAT
Found at i:4380659 original size:22 final size:21
Alignment explanation
Indices: 4380622--4380671 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
4380612 AATTGTTAAT
*
4380622 TTTAATTTTATAATTTTATAA
1 TTTAATTTTATAATTTTACAA
*
4380643 TTTAATTTTATGCATTTTACAA
1 TTTAATTTTAT-AATTTTACAA
*
4380665 TTAAATT
1 TTTAATT
4380672 ATAAGCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTAATTTTATAATTTTACAA
Found at i:4382122 original size:14 final size:16
Alignment explanation
Indices: 4382093--4382125 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
4382083 GCATCTTAAA
4382093 ATTATAATTATTTTAT
1 ATTATAATTATTTTAT
4382109 ATTATAA-T-TTTTAT
1 ATTATAATTATTTTAT
4382123 ATT
1 ATT
4382126 TTTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTATAATTATTTTAT
Found at i:4385186 original size:30 final size:31
Alignment explanation
Indices: 4385109--4385187 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
4385099 AATTATTTAT
4385109 GTTAAGAACTTATTT-AGATAAAAGTTAAAA
1 GTTAAGAACTTATTTGAGATAAAAGTTAAAA
** *
4385139 GTTTAAGGGCTTGTTTGA-ATATAAA-TTAAAA
1 G-TTAAGAACTTATTTGAGATA-AAAGTTAAAA
*
4385170 GTTAAGAATTTATTTGAG
1 GTTAAGAACTTATTTGAG
4385188 TGCAAATCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
30 13 0.34
31 21 0.55
32 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.38
Consensus pattern (31 bp):
GTTAAGAACTTATTTGAGATAAAAGTTAAAA
Found at i:4385468 original size:30 final size:32
Alignment explanation
Indices: 4385398--4385473 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
4385388 TATTTATATC
*
4385398 AAGAACTTATTT-AGATAAAAGTTAAAAGTTT
1 AAGAATTTATTTGAGATAAAAGTTAAAAGTTT
**
4385429 AAGGGTTTATTTGA-ATATAAA-TTAAAAG-TT
1 AAGAATTTATTTGAGATA-AAAGTTAAAAGTTT
4385459 AAGAATTTATTTGAG
1 AAGAATTTATTTGAG
4385474 TGCAAATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
30 14 0.38
31 19 0.51
32 4 0.11
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.38
Consensus pattern (32 bp):
AAGAATTTATTTGAGATAAAAGTTAAAAGTTT
Found at i:4390539 original size:33 final size:34
Alignment explanation
Indices: 4390476--4390539 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
4390466 AAAGCCCCAA
*
4390476 AATTTTTAAAAAATATAATATTTTGGATTTTTTG
1 AATTTTTAAAAAATATAATATTTAGGATTTTTTG
*
4390510 AATTTTT-AAAAATATCAA-ATTTAGTATTTT
1 AATTTTTAAAAAATAT-AATATTTAGGATTTT
4390540 CAAAAACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (34 bp):
AATTTTTAAAAAATATAATATTTAGGATTTTTTG
Found at i:4390667 original size:22 final size:20
Alignment explanation
Indices: 4390639--4390692 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
4390629 AAGTATTGCA
4390639 AAAAAATAAATTTAGGATTTTT
1 AAAAAATAAA--TAGGATTTTT
*
4390661 AAAAAATTGAAATATGATTTTT
1 AAAAAA-T-AAATAGGATTTTT
*
4390683 AATAAATAAA
1 AAAAAATAAA
4390693 AGAAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 20 0.71
23 1 0.04
24 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
AAAAAATAAATAGGATTTTT
Found at i:4390688 original size:25 final size:25
Alignment explanation
Indices: 4390660--4390714 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
4390650 TTAGGATTTT
*
4390660 TAAAAAATTGAAATATGA-TTTTTAA
1 TAAAAAA-AGAAATATGACTTTTTAA
*
4390685 TAAATAAAAGAAATATTACTTTTTAA
1 TAAA-AAAAGAAATATGACTTTTTAA
4390711 -AAAA
1 TAAAA
4390715 TAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
26 10 0.38
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (25 bp):
TAAAAAAAGAAATATGACTTTTTAA
Found at i:4390715 original size:26 final size:25
Alignment explanation
Indices: 4390654--4390719 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
4390644 ATAAATTTAG
*
4390654 GATTTTTAAAAAAT---TGAAATAT
1 GATTTTTAAAAAATAAAAGAAATAT
*
4390676 GATTTTTAATAAATAAAAGAAATAT
1 GATTTTTAAAAAATAAAAGAAATAT
*
4390701 TACTTTTTAAAAAATAAAA
1 GA-TTTTTAAAAAATAAAA
4390720 TATTATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.36
25 8 0.22
26 15 0.42
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (25 bp):
GATTTTTAAAAAATAAAAGAAATAT
Found at i:4399341 original size:18 final size:18
Alignment explanation
Indices: 4399299--4399336 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4399289 ATAAAAACAA
*
4399299 AAAATAATAAAATAATTT
1 AAAATAATAAAAAAATTT
4399317 AAAATAATAAAACAAATTT
1 AAAATAATAAAA-AAATTT
4399336 A
1 A
4399337 GATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATAATAAAAAAATTT
Found at i:4399927 original size:28 final size:29
Alignment explanation
Indices: 4399870--4399928 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
4399860 ATAAATTTTC
*
4399870 ATACTTCTATTGTACTTAAATAAGCCTTT
1 ATACTTCTATTGTACTCAAATAAGCCTTT
4399899 ATACTTCTATTGTAC-CAAATAAGCCTTT
1 ATACTTCTATTGTACTCAAATAAGCCTTT
4399927 AT
1 AT
4399929 TCTTTGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (29 bp):
ATACTTCTATTGTACTCAAATAAGCCTTT
Found at i:4400015 original size:30 final size:30
Alignment explanation
Indices: 4399980--4400111 Score: 108
Period size: 30 Copynumber: 4.4 Consensus size: 30
4399970 ATCAATTTAT
*
4399980 GTTAAGGGCTTATTTAGG-TGTAAATTAAAA
1 GTTAAGGGCTTATTT-GGATGCAAATTAAAA
* * * * *
4400010 ATTAAGAGTTTATTTGGATACAAATTAAAT
1 GTTAAGGGCTTATTTGGATGCAAATTAAAA
* *
4400040 TTTAAGGGCTTATTTGGATGCAAAATAAAA
1 GTTAAGGGCTTATTTGGATGCAAATTAAAA
* * ** *
4400070 GTTAAGAGCTCATTTAAATG-TAA-TAAAA
1 GTTAAGGGCTTATTTGGATGCAAATTAAAA
4400098 GTATAAGGGCTTAT
1 GT-TAAGGGCTTAT
4400112 CTAAATAAAG
Statistics
Matches: 80, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
28 7 0.09
29 13 0.16
30 60 0.75
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (30 bp):
GTTAAGGGCTTATTTGGATGCAAATTAAAA
Found at i:4400117 original size:29 final size:28
Alignment explanation
Indices: 4400063--4400117 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
4400053 TTGGATGCAA
*
4400063 AATAAAAGTTAAGAGCTCATTTAAATGT
1 AATAAAAGTTAAGAGCTCATCTAAATGT
* *
4400091 AATAAAAGTATAAGGGCTTATCTAAAT
1 AATAAAAGT-TAAGAGCTCATCTAAAT
4400118 AAAGAACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (28 bp):
AATAAAAGTTAAGAGCTCATCTAAATGT
Found at i:4401679 original size:15 final size:15
Alignment explanation
Indices: 4401661--4401706 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
4401651 AAAAGAAAGT
*
4401661 AAAGAAAAAACAAAA
1 AAAGAAAAGACAAAA
*
4401676 AAAGAGAAAGAGAAAA
1 AAAGA-AAAGACAAAA
*
4401692 AATGAAAAGACAAAA
1 AAAGAAAAGACAAAA
4401707 GAAGTGAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.02
Consensus pattern (15 bp):
AAAGAAAAGACAAAA
Found at i:4404670 original size:112 final size:109
Alignment explanation
Indices: 4404510--4404712 Score: 271
Period size: 112 Copynumber: 1.8 Consensus size: 109
4404500 TTATTTCATC
* * * ** *
4404510 ATTTGGGCCAAATTAAAATTTTTTTTTTGAATTTCTAAGTTTTCCACCATTTGGGCCTGTTTAGA
1 ATTTGGGCCAAATTAAAATTTTTCTTTTGAATTTCTAAATTTTCCACCATTTGGACCCATTTAAA
*
4404575 AATTCTCTTTATTTCTTTCTTTTTTTTATTTCTAAATTTTTCACT
66 AATTCTCTTTATTTCTCT-TTTTTTTTATTTCTAAATTTTTCACT
* * *
4404620 ATTTGGGTCAATTTAGAAATATTTTCTTTTGAATTTCTAAATTTTTCACCATTTGGACCCATTTA
1 ATTTGGGCCAAATTA-AAAT-TTTTCTTTTGAATTTCTAAATTTTCCACCATTTGGACCCATTTA
* *
4404685 AAAATTTTTTTTATTTCTCTTTTTTTTT
64 AAAATTCTCTTTATTTCTCTTTTTTTTT
4404713 GGAAAGAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
110 13 0.16
111 12 0.15
112 54 0.68
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.55
Consensus pattern (109 bp):
ATTTGGGCCAAATTAAAATTTTTCTTTTGAATTTCTAAATTTTCCACCATTTGGACCCATTTAAA
AATTCTCTTTATTTCTCTTTTTTTTTATTTCTAAATTTTTCACT
Found at i:4404684 original size:50 final size:47
Alignment explanation
Indices: 4404594--4404696 Score: 129
Period size: 50 Copynumber: 2.2 Consensus size: 47
4404584 TATTTCTTTC
* **
4404594 TTTTTTTT--ATTTCTAAATTTTTCACTATTTGGGTCAATTTAGAAATA
1 TTTTTTTTGAATTTCTAAATTTTTCACCATTTGGACCAATTTA-AAA-A
*
4404641 TTTTCTTTTGAATTTCTAAATTTTTCACCATTTGGACCCATTTAAAAA
1 TTTT-TTTTGAATTTCTAAATTTTTCACCATTTGGACCAATTTAAAAA
4404689 TTTTTTTT
1 TTTTTTTT
4404697 ATTTCTCTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
47 8 0.16
48 9 0.18
49 3 0.06
50 29 0.59
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (47 bp):
TTTTTTTTGAATTTCTAAATTTTTCACCATTTGGACCAATTTAAAAA
Found at i:4406049 original size:14 final size:13
Alignment explanation
Indices: 4406021--4406067 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
4406011 TTATTATCTT
4406021 AAAAT-AAAATCA
1 AAAATAAAAATCA
*
4406033 AAAATCAAAAATTA
1 AAAAT-AAAAATCA
4406047 AAAATAAAAAT-A
1 AAAATAAAAATCA
*
4406059 AGAATAAAA
1 AAAATAAAA
4406068 TAAAATAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 14 0.45
13 6 0.19
14 11 0.35
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (13 bp):
AAAATAAAAATCA
Found at i:4406833 original size:22 final size:21
Alignment explanation
Indices: 4406782--4407203 Score: 254
Period size: 21 Copynumber: 19.0 Consensus size: 21
4406772 GGTTTCACAT
4406782 CTCAAAGATTCTCATTTAAAA
1 CTCAAAGATTCTCATTTAAAA
* *
4406803 TTCAAAGATTCCCATTTAAAGA
1 CTCAAAGATTCTCATTTAAA-A
* *
4406825 CACAAAGATTCTTATTTGAAAA
1 CTCAAAGATTCTCATTT-AAAA
* * *
4406847 CTCAAAAATTCTTATTTGAAA
1 CTCAAAGATTCTCATTTAAAA
4406868 CTCAAAGATT-TACATTTAAAAA
1 CTCAAAGATTCT-CATTT-AAAA
**
4406890 CTCAAAGATTCTTGTTTAAAA
1 CTCAAAGATTCTCATTTAAAA
4406911 CTCAAAGATTCTCATTTGAAAA
1 CTCAAAGATTCTCATTT-AAAA
* *
4406933 CTCAAAGATTTTCATTTGAAA
1 CTCAAAGATTCTCATTTAAAA
* * * *
4406954 CTAAAAAATTCTTATTTGAAATTTT
1 CTCAAAGATTCTCATTT-AAA---A
* * *
4406979 CTTAAAGGTTCTCATTTAAGA
1 CTCAAAGATTCTCATTTAAAA
* *
4407000 CTTAAAGATTCTCATTTGAGAATTT
1 CTCAAAGATTCTCATTT-A-AA--A
* *
4407025 CTTAAAGATTCTCATTTAAGA
1 CTCAAAGATTCTCATTTAAAA
* **
4407046 TTCAAAGATTCTCATTTGAGGATTT
1 CTCAAAGATTCTCATTT-A--A-AA
* * *
4407071 CTTAAAGATTTTCATTTAAGA
1 CTCAAAGATTCTCATTTAAAA
* *
4407092 CTTAAAGATTCTCATTTGAAGATTT
1 CTCAAAGATTCTCATTT-AA-A--A
* * *
4407117 CTTAAAGATTTTCATTTAAGA
1 CTCAAAGATTCTCATTTAAAA
*
4407138 C-AAAAGATTCTCATTTAAAGA
1 CTCAAAGATTCTCATTTAAA-A
* * * *
4407159 TTTCTTAAAAATTTTCATTTAAGA
1 ---CTCAAAGATTCTCATTTAAAA
*
4407183 CTCAAAGATTCTTATTTAAAA
1 CTCAAAGATTCTCATTTAAAA
4407204 ATTTTTTAAA
Statistics
Matches: 312, Mismatches: 62, Indels: 54
0.73 0.14 0.13
Matches are distributed among these distances:
20 16 0.05
21 134 0.43
22 73 0.23
23 6 0.02
24 9 0.03
25 74 0.24
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTAAAA
Found at i:4406874 original size:65 final size:64
Alignment explanation
Indices: 4406782--4406974 Score: 237
Period size: 65 Copynumber: 3.0 Consensus size: 64
4406772 GGTTTCACAT
* * **
4406782 CTCAAAGATTCTCATTTAAAATTCAAAGATTCCCATTTAAAGACACAAAGATTCTTATTTGAAAA
1 CTCAAAGATTCTCATTTGAAACTCAAAGATTTACATTTAAA-ACACAAAGATTCTTATTTGAAAA
* * * *
4406847 CTCAAAAATTCTTATTTGAAACTCAAAGATTTACATTTAAAAACTCAAAGATTCTTGTTT-AAAA
1 CTCAAAGATTCTCATTTGAAACTCAAAGATTTACATTT-AAAACACAAAGATTCTTATTTGAAAA
* * *
4406911 CTCAAAGATTCTCATTTGAAAACTCAAAGATTTTCATTTGAAACTA-AAAAATTCTTATTTGAAA
1 CTCAAAGATTCTCATTTG-AAACTCAAAGATTTACATTTAAAAC-ACAAAGATTCTTATTTGAAA
4406975 TTTTCTTAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
64 36 0.33
65 70 0.64
66 3 0.03
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (64 bp):
CTCAAAGATTCTCATTTGAAACTCAAAGATTTACATTTAAAACACAAAGATTCTTATTTGAAAA
Found at i:4407011 original size:46 final size:45
Alignment explanation
Indices: 4406785--4407228 Score: 376
Period size: 46 Copynumber: 9.9 Consensus size: 45
4406775 TTCACATCTC
* * **
4406785 AAAGATTCTCATTT-AAAATTC--AAAGATTCCCATTTAAAGACAC
1 AAAGATTCTCATTTGAAATTTCTTAAAGATTCTCATTT-AAGACTT
* * * * * *
4406828 AAAGATTCTTATTTGAAA--ACTCAAAAATTCTTATTTGAA-ACTC
1 AAAGATTCTCATTTGAAATTTCTTAAAGATTCTCATTT-AAGACTT
** * ** * *
4406871 AAAGATT-TACATTT-AAA-AACTCAAAGATTCTTGTTTAAAACTC
1 AAAGATTCT-CATTTGAAATTTCTTAAAGATTCTCATTTAAGACTT
* * * *
4406914 AAAGATTCTCATTTGAAA--ACTCAAAGATTTTCATTTGAA-ACTA
1 AAAGATTCTCATTTGAAATTTCTTAAAGATTCTCATTT-AAGACTT
* * *
4406957 AAAAATTCTTATTTGAAATTTTCTTAAAGGTTCTCATTTAAGACTT
1 AAAGATTCTCATTTGAAA-TTTCTTAAAGATTCTCATTTAAGACTT
4407003 AAAGATTCTCATTTGAGAATTTCTTAAAGATTCTCATTTAAGA-TT
1 AAAGATTCTCATTTGA-AATTTCTTAAAGATTCTCATTTAAGACTT
* *
4407048 CAAAGATTCTCATTTGAGGATTTCTTAAAGATTTTCATTTAAGACTT
1 -AAAGATTCTCATTTGA-AATTTCTTAAAGATTCTCATTTAAGACTT
* *
4407095 AAAGATTCTCATTTGAAGATTTCTTAAAGATTTTCATTTAAGAC-A
1 AAAGATTCTCATTTGAA-ATTTCTTAAAGATTCTCATTTAAGACTT
* * * *
4407140 AAAGATTCTCATTTAAAGATTTCTTAAAAATTTTCATTTAAGACTC
1 AAAGATTCTCATTTGAA-ATTTCTTAAAGATTCTCATTTAAGACTT
* * *
4407186 AAAGATTCTTATTTAAAAATTTTTTAAAGATTCTCATTTAAGA
1 AAAGATTCTCATTT-GAAATTTCTTAAAGATTCTCATTTAAGA
4407229 AATTAAGATT
Statistics
Matches: 347, Mismatches: 35, Indels: 35
0.83 0.08 0.08
Matches are distributed among these distances:
42 7 0.02
43 93 0.27
44 22 0.06
45 46 0.13
46 172 0.50
47 7 0.02
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (45 bp):
AAAGATTCTCATTTGAAATTTCTTAAAGATTCTCATTTAAGACTT
Found at i:4407237 original size:137 final size:138
Alignment explanation
Indices: 4406782--4407240 Score: 384
Period size: 137 Copynumber: 3.4 Consensus size: 138
4406772 GGTTTCACAT
* * *
4406782 CTCAAAGATTCTCATTT-AAAA-TTC--AAAGATTCCCATTTAAAGACA-CAAAGATTCTTATTT
1 CTCAAAGATTCTCATTTAAAAATTTCTTAAAGATTCTCATTT-AAGA-ATTAAAGATTCTCATTT
* * * * * * * *
4406842 GAAA---ACTCAAAAATTCTTATTTGAA-ACTCAAAGATT-TACATTTAA-AA--ACTCAAAGAT
64 GAAATTTTCTTAAAGATTCTCATTT-AAGACTAAAAGATTCT-CATTTAAGAATTTCTTAAAAAT
** *
4406899 TCTTGTTTAAAA
127 TCTCATTTAAGA
* * * * * * *
4406911 CTCAAAGATTCTCATTTGAAAA---CTCAAAGATTTTCATTTGAA-ACTAAAAAATTCTTATTTG
1 CTCAAAGATTCTCATTTAAAAATTTCTTAAAGATTCTCATTT-AAGAATTAAAGATTCTCATTTG
* * * *
4406972 AAATTTTCTTAAAGGTTCTCATTTAAGACTTAAAGATTCTCATTTGAGAATTTCTTAAAGATTCT
65 AAATTTTCTTAAAGATTCTCATTTAAGACTAAAAGATTCTCATTTAAGAATTTCTTAAAAATTCT
4407037 CATTTAAGA
130 CATTTAAGA
* * ** * *
4407046 TTCAAAGATTCTCATTTGAGGATTTCTTAAAGATTTTCATTTAAGACTTAAAGATTCTCATTTGA
1 CTCAAAGATTCTCATTTAAAAATTTCTTAAAGATTCTCATTTAAGAATTAAAGATTCTCATTTGA
* *
4407111 AGA-TTTCTTAAAGATTTTCATTTAAGAC-AAAAGATTCTCATTTAA-AGATTTCTTAAAAATTT
66 A-ATTTTCTTAAAGATTCTCATTTAAGACTAAAAGATTCTCATTTAAGA-ATTTCTTAAAAATTC
4407173 TCATTTAAGA
129 TCATTTAAGA
* *
4407183 CTCAAAGATTCTTATTTAAAAATTTTTTAAAGATTCTCATTTAAGAAATT-AAGATTCT
1 CTCAAAGATTCTCATTTAAAAATTTCTTAAAGATTCTCATTTAAG-AATTAAAGATTCT
4407241 TATCAAAAGA
Statistics
Matches: 272, Mismatches: 39, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
128 1 0.00
129 35 0.13
130 18 0.07
131 2 0.01
132 29 0.11
133 3 0.01
135 36 0.13
136 1 0.00
137 86 0.32
138 60 0.22
139 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (138 bp):
CTCAAAGATTCTCATTTAAAAATTTCTTAAAGATTCTCATTTAAGAATTAAAGATTCTCATTTGA
AATTTTCTTAAAGATTCTCATTTAAGACTAAAAGATTCTCATTTAAGAATTTCTTAAAAATTCTC
ATTTAAGA
Done.