Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 23 of 230
Found at i:6194729 original size:11 final size:11
Alignment explanation
Indices: 6194708--6194739 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
6194698 ATAATATCCA
6194708 AATAGTAATAAC
1 AATA-TAATAAC
6194720 AATATAATAAC
1 AATATAATAAC
6194731 AATATAATA
1 AATATAATA
6194740 GCAGAATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.28
Consensus pattern (11 bp):
AATATAATAAC
Found at i:6203442 original size:6 final size:6
Alignment explanation
Indices: 6203435--6203504 Score: 104
Period size: 6 Copynumber: 11.7 Consensus size: 6
6203425 CAAACCACAA
* * * *
6203435 CAACAA CAACAG CATCAG CAACAA CAACAA CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
6203483 CAACAG CAACAG CAACAG CAAC
1 CAACAG CAACAG CAACAG CAAC
6203505 GGGAACATGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.53, C:0.34, G:0.11, T:0.01
Consensus pattern (6 bp):
CAACAG
Found at i:6203463 original size:24 final size:24
Alignment explanation
Indices: 6203431--6203504 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
6203421 TCGGCAAACC
*
6203431 ACAACAACAACAACAGCATCAGCA
1 ACAACAACAACAACAGCAACAGCA
6203455 ACAACAACAACAACAGCAACAGCA
1 ACAACAACAACAACAGCAACAGCA
* *
6203479 ACAGCAACAGCAACAGCAACAGCA
1 ACAACAACAACAACAGCAACAGCA
6203503 AC
1 AC
6203505 GGGAACATGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.54, C:0.34, G:0.11, T:0.01
Consensus pattern (24 bp):
ACAACAACAACAACAGCAACAGCA
Found at i:6205614 original size:29 final size:31
Alignment explanation
Indices: 6205563--6205642 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 31
6205553 ATCTTACATG
* *
6205563 TTTATAATTTTTAAAAGATTAAATTA-AATT
1 TTTATTATTTTTAAAAGAGTAAATTACAATT
*
6205593 TTTATTATTTTT-AAAGGGTAAATTACAATT
1 TTTATTATTTTTAAAAGAGTAAATTACAATT
6205623 TTACTATTATTAATTTAAAA
1 TT--TATTATT--TTTAAAA
6205643 TTTTATAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 11 0.27
30 17 0.41
32 7 0.17
34 3 0.07
35 3 0.07
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (31 bp):
TTTATTATTTTTAAAAGAGTAAATTACAATT
Found at i:6209537 original size:29 final size:29
Alignment explanation
Indices: 6209498--6209553 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
6209488 CCAATTTAAG
6209498 AAAGGTAAACACGGGCCCGACCCAACTCT
1 AAAGGTAAACACGGGCCCGACCCAACTCT
*
6209527 AAAGGTAAACACGGGCCCGACTCAACT
1 AAAGGTAAACACGGGCCCGACCCAACT
6209554 TGCCTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.32, G:0.21, T:0.11
Consensus pattern (29 bp):
AAAGGTAAACACGGGCCCGACCCAACTCT
Found at i:6209758 original size:39 final size:41
Alignment explanation
Indices: 6209680--6209766 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 41
6209670 TAAAAAGTAT
* * * *
6209680 TTATATTAACAAATACTACCATAAATATAATAGATATTTT-C
1 TTATATTAAAAAACACTA-CATAAATATAATAAACATTTTAC
6209721 TTATATTAAAAAACACTA-ATAAATATAATAAACATTTTAC
1 TTATATTAAAAAACACTACATAAATATAATAAACATTTTAC
6209761 -TATATT
1 TTATATT
6209767 TAATATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 24 0.59
40 1 0.02
41 16 0.39
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAACACTACATAAATATAATAAACATTTTAC
Found at i:6215289 original size:19 final size:19
Alignment explanation
Indices: 6215265--6215304 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6215255 ATTTTTAAAA
6215265 AATTATATCTT-TATTTTTT
1 AATTAT-TCTTATATTTTTT
*
6215284 AATTATTTTTATATTTTTT
1 AATTATTCTTATATTTTTT
6215303 AA
1 AA
6215305 ATTTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
AATTATTCTTATATTTTTT
Found at i:6215525 original size:20 final size:20
Alignment explanation
Indices: 6215479--6215526 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
6215469 CTGTTTTTTA
*
6215479 TTTTATATATTATAATATAAT
1 TTTTA-ATATTATAACATAAT
*
6215500 TATTAATATTATGAACAT-AT
1 TTTTAATATTAT-AACATAAT
6215520 TTTTAAT
1 TTTTAAT
6215527 GGTTTGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTAATATTATAACATAAT
Found at i:6219935 original size:19 final size:20
Alignment explanation
Indices: 6219908--6219950 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
6219898 GTCCACGTGT
*
6219908 AATTCATAAAAAT-TTAAAA
1 AATTAATAAAAATATTAAAA
*
6219927 AATTAATAAAAATATTTAAA
1 AATTAATAAAAATATTAAAA
6219947 AATT
1 AATT
6219951 CAACAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTAATAAAAATATTAAAA
Found at i:6234684 original size:23 final size:22
Alignment explanation
Indices: 6234641--6234685 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
6234631 TTGATCTCAT
*
6234641 TTTTTTAAAAAAAATCAAATTA
1 TTTTTTAAAAAAAATAAAATTA
**
6234663 TTTTTTAACGAAAATAATAATTA
1 TTTTTTAAAAAAAATAA-AATTA
6234686 AAACATTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTTTTAAAAAAAATAAAATTA
Found at i:6238197 original size:33 final size:32
Alignment explanation
Indices: 6238112--6238301 Score: 100
Period size: 33 Copynumber: 5.7 Consensus size: 32
6238102 GTTTTCTTTG
** * *
6238112 TGCCATAGTCCAACTATGATCTTACA-CATGCAT
1 TGCCATAACCCAACTATGGTCTTACATCA-G-AA
* * * *
6238145 TACCATGACCCAACCATGGTCTTACATTC-GTAG
1 TGCCATAACCCAACTATGGTCTTACA-TCAG-AA
* * *
6238178 TGTCATAACTCAATTATGGTCTTATCATCAGAA
1 TGCCATAACCCAACTATGGTCTTA-CATCAGAA
*
6238211 TGCCATAACCCAACTATGGTCTTACTTAT-AAATA
1 TGCCATAACCCAACTATGGTCTTAC--ATCAGA-A
** *
6238245 CTGCCATAGTCCAACCATGGTCTTACATTCA-AA
1 -TGCCATAACCCAACTATGGTCTTACA-TCAGAA
**
6238278 TAGCCATAACCCAGTTATGGTCTT
1 T-GCCATAACCCAACTATGGTCTT
6238302 TTCATTAAAA
Statistics
Matches: 119, Mismatches: 27, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
32 2 0.02
33 85 0.71
34 8 0.07
35 24 0.20
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (32 bp):
TGCCATAACCCAACTATGGTCTTACATCAGAA
Found at i:6238259 original size:35 final size:34
Alignment explanation
Indices: 6238210--6238370 Score: 118
Period size: 35 Copynumber: 4.7 Consensus size: 34
6238200 TATCATCAGA
*
6238210 ATGCCATAACCCAACTATGGTCTTACTTATAAAT
1 ATGCCATAATCCAACTATGGTCTTACTTATAAAT
* * *
6238244 ACTGCCATAGTCCAACCATGGTCTTACATT-CAAAT
1 A-TGCCATAATCCAACTATGGTCTTAC-TTATAAAT
* **
6238279 A-GCCATAACCCAGTTATGGTCTT--TTCATTAAA-
1 ATGCCATAATCCAACTATGGTCTTACTT-A-TAAAT
* *
6238311 ATACCAT-ATCTCAGCTATGGTCTTACTTATAAAT
1 ATGCCATAATC-CAACTATGGTCTTACTTATAAAT
** *
6238345 ACTGCCATGGTCCAACCATGGTCTTA
1 A-TGCCATAATCCAACTATGGTCTTA
6238371 TCCGTCAATT
Statistics
Matches: 98, Mismatches: 17, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
30 2 0.02
32 3 0.03
33 40 0.41
34 3 0.03
35 46 0.47
36 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (34 bp):
ATGCCATAATCCAACTATGGTCTTACTTATAAAT
Found at i:6238286 original size:101 final size:101
Alignment explanation
Indices: 6238154--6238370 Score: 301
Period size: 101 Copynumber: 2.1 Consensus size: 101
6238144 TTACCATGAC
* * * * * *
6238154 CCAACCATGGTCTTACATTCGTAGTGTCATAACTCAATTATGGTCTTATCATCAGAATGCCATAA
1 CCAACCATGGTCTTACATTCGAAATGCCATAACCCAATTATGGTCTTATCATCAAAATACCATAA
6238219 CCCAACTATGGTCTTACTTATAAATACTGCCATAGT
66 CCCAACTATGGTCTTACTTATAAATACTGCCATAGT
* * *
6238255 CCAACCATGGTCTTACATTC-AAATAGCCATAACCCAGTTATGGTCTTTTCATTAAAATACCATA
1 CCAACCATGGTCTTACATTCGAAAT-GCCATAACCCAATTATGGTCTTATCATCAAAATACCATA
* * * *
6238319 TCTCAGCTATGGTCTTACTTATAAATACTGCCATGGT
65 ACCCAACTATGGTCTTACTTATAAATACTGCCATAGT
6238356 CCAACCATGGTCTTA
1 CCAACCATGGTCTTA
6238371 TCCGTCAATT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 2 0.02
101 100 0.98
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (101 bp):
CCAACCATGGTCTTACATTCGAAATGCCATAACCCAATTATGGTCTTATCATCAAAATACCATAA
CCCAACTATGGTCTTACTTATAAATACTGCCATAGT
Found at i:6238318 original size:33 final size:34
Alignment explanation
Indices: 6238212--6238334 Score: 101
Period size: 33 Copynumber: 3.6 Consensus size: 34
6238202 TCATCAGAAT
*
6238212 GCCATAACCCAACTATGGTC-TTAC-TTATAAATA
1 GCCATAACCCAGCTATGGTCTTTACATTA-AAATA
** * * *
6238245 CTGCCATAGTCCAACCATGGTC-TTACATTCAAATA
1 --GCCATAACCCAGCTATGGTCTTTACATTAAAATA
* *
6238280 GCCATAACCCAGTTATGGTCTTTTCATTAAAATA
1 GCCATAACCCAGCTATGGTCTTTACATTAAAATA
* *
6238314 -CCATATCTCAGCTATGGTCTT
1 GCCATAACCCAGCTATGGTCTT
6238335 ACTTATAAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
33 33 0.46
34 11 0.15
35 26 0.36
36 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (34 bp):
GCCATAACCCAGCTATGGTCTTTACATTAAAATA
Found at i:6242178 original size:16 final size:17
Alignment explanation
Indices: 6242159--6242190 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6242149 TTATTAAATC
6242159 ATATATTTAA-ATTAAA
1 ATATATTTAATATTAAA
6242175 ATATATTTAATATTAA
1 ATATATTTAATATTAA
6242191 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTTAATATTAAA
Found at i:6242254 original size:66 final size:63
Alignment explanation
Indices: 6242183--6242395 Score: 194
Period size: 61 Copynumber: 3.4 Consensus size: 63
6242173 AAATATATTT
6242183 AATATTAATTATTTAA-AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTA-TTAAGAATTTTA--TTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
6242247 AG
62 AG
* * * * * * *
6242249 AATATTAATTATTAAGAATTTTATTAA--ATTATATATTTTAATTAT-ATTATATTTA-ATAAT
1 AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATT-TGAGTAAATTCATATAAG
* * * *
6242309 AATTATGTTATT-TT-A-TATTTTA--CAGTATCATATATTATGGTTTGAGTAAATTCATATAAG
1 AA-TAT-TAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
6242369 AATATTAATTATTAAGAATTTTATTAA
1 AATATTAATTATTAAGAATTTTATTAA
6242396 ATTATATATT
Statistics
Matches: 113, Mismatches: 21, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 30 0.27
60 14 0.12
61 31 0.27
62 5 0.04
63 2 0.02
64 3 0.03
65 4 0.04
66 18 0.16
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (63 bp):
AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:6242269 original size:120 final size:120
Alignment explanation
Indices: 6242145--6242437 Score: 482
Period size: 120 Copynumber: 2.4 Consensus size: 120
6242135 AATTATTTTA
* * *
6242145 AATTTTATTAAATCATATATTTAAATTAAAATATATTTAATATTAATTAT-TTAAAATTT-TATT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
6242208 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
6242265 AATTTTATTAAATTATATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
6242330 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
6242385 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
6242438 TAAATATGAT
Statistics
Matches: 161, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
119 4 0.02
120 155 0.96
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:6242297 original size:18 final size:17
Alignment explanation
Indices: 6242266--6242300 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6242256 ATTATTAAGA
6242266 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
6242283 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
6242301 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:6242414 original size:18 final size:17
Alignment explanation
Indices: 6242386--6242420 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6242376 ATTATTAAGA
*
6242386 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
6242403 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
6242421 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:6242534 original size:147 final size:149
Alignment explanation
Indices: 6242374--6242648 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
6242364 ATAAGAATAT
*
6242374 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
6242439 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
6242502 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
6242521 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
6242586 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
6242649 CAATAATCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:6242561 original size:18 final size:17
Alignment explanation
Indices: 6242533--6242567 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6242523 ATTATTAAGA
*
6242533 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
6242550 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
6242568 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:6242818 original size:45 final size:44
Alignment explanation
Indices: 6242729--6242823 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
6242719 TTACACCTCT
* *
6242729 ATTACATTCAACCAAACACAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGATTTACTATTACACCTCTATTCC
** *
6242773 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACA-CAGATTTACTATTACACCTCTATTCC
6242818 ATTACA
1 ATTACA
6242824 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGATTTACTATTACACCTCTATTCC
Found at i:6242823 original size:16 final size:16
Alignment explanation
Indices: 6242804--6242855 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
6242794 GATTTGCTAT
* *
6242804 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
6242820 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
6242836 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
6242852 TACA
1 TACA
6242856 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:6244329 original size:25 final size:23
Alignment explanation
Indices: 6244285--6244345 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
6244275 TGGTATTTAA
*
6244285 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
6244309 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
6244334 ATATTATTAAAT
1 ATATAATTAAAT
6244346 GAATTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:6246095 original size:39 final size:39
Alignment explanation
Indices: 6246033--6246148 Score: 99
Period size: 45 Copynumber: 2.8 Consensus size: 39
6246023 TTACTGATCA
* * * *
6246033 GGCAC-TTATGTGCCGACTACTGTTACTGTTACCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACAGATTC
6246071 GGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGATTC
1 GGCACTTTGTGTGTCGAATAC---T---GTTACTGTTACAGATTC
* * * *
6246116 AGCACTTTGTGTGTTGAATAATGTCACTGTTAC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTAC
6246149 TATTACTGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
38 5 0.08
39 22 0.35
42 2 0.03
45 34 0.54
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (39 bp):
GGCACTTTGTGTGTCGAATACTGTTACTGTTACAGATTC
Found at i:6246160 original size:51 final size:45
Alignment explanation
Indices: 6246050--6246154 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
6246040 ATGTGCCGAC
* *
6246050 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGT
* * *
6246095 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATAATGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGT
* *
6246140 CACTGTTACTATTAC
1 TACTGTTACTGTTAC
6246155 TGTTACCATT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGT
Found at i:6248692 original size:17 final size:17
Alignment explanation
Indices: 6248670--6248778 Score: 87
Period size: 17 Copynumber: 6.5 Consensus size: 17
6248660 ACGACTATAC
6248670 TTTATATGCAAGTTGTG
1 TTTATATGCAAGTTGTG
** *
6248687 TTTATATGTGAGTTGTC
1 TTTATATGCAAGTTGTG
* *
6248704 TTTATATGTAAGCTG-G
1 TTTATATGCAAGTTGTG
* * *
6248720 GTTATATGCGAGTTGTA
1 TTTATATGCAAGTTGTG
* * * *
6248737 TGTATATGCGAGCTATG
1 TTTATATGCAAGTTGTG
*
6248754 TTTATACGCAAGTTGTG
1 TTTATATGCAAGTTGTG
6248771 -TTATATGC
1 TTTATATGC
6248779 GAACTGCGTT
Statistics
Matches: 69, Mismatches: 22, Indels: 3
0.73 0.23 0.03
Matches are distributed among these distances:
16 18 0.26
17 51 0.74
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (17 bp):
TTTATATGCAAGTTGTG
Found at i:6248733 original size:33 final size:34
Alignment explanation
Indices: 6248669--6248810 Score: 110
Period size: 33 Copynumber: 4.2 Consensus size: 34
6248659 AACGACTATA
* * *
6248669 CTTTATATGCAAGTTGTGTTTATATGTGAGTTGT
1 CTTTATATGCAAGCTGTGGTTATATGCGAGTTGT
*
6248703 CTTTATATGTAAGCTG-GGTTATATGCGAGTTGT
1 CTTTATATGCAAGCTGTGGTTATATGCGAGTTGT
* * * * * * *
6248736 ATGTATATGCGAGCTATGTTTATACGCAAGTTGT
1 CTTTATATGCAAGCTGTGGTTATATGCGAGTTGT
* * * * *
6248770 -GTTATATGCGAA-CTGCGTTTATATGTGTGTTGT
1 CTTTATATGC-AAGCTGTGGTTATATGCGAGTTGT
6248803 CTTTATAT
1 CTTTATAT
6248811 TCGAGCTATG
Statistics
Matches: 83, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
33 48 0.58
34 35 0.42
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (34 bp):
CTTTATATGCAAGCTGTGGTTATATGCGAGTTGT
Found at i:6248758 original size:50 final size:50
Alignment explanation
Indices: 6248671--6248780 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 50
6248661 CGACTATACT
* * * * * * * *
6248671 TTATATGCAAGTTGTGTTTATATGTGAGTTGTCTTTATATGTAAGCTGGG
1 TTATATGCGAGTTGTATGTATATGCGAGCTATCTTTATACGCAAGCTGGG
* * *
6248721 TTATATGCGAGTTGTATGTATATGCGAGCTATGTTTATACGCAAGTTGTG
1 TTATATGCGAGTTGTATGTATATGCGAGCTATCTTTATACGCAAGCTGGG
6248771 TTATATGCGA
1 TTATATGCGA
6248781 ACTGCGTTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.24, C:0.08, G:0.25, T:0.43
Consensus pattern (50 bp):
TTATATGCGAGTTGTATGTATATGCGAGCTATCTTTATACGCAAGCTGGG
Found at i:6248808 original size:50 final size:50
Alignment explanation
Indices: 6248686--6248809 Score: 122
Period size: 50 Copynumber: 2.5 Consensus size: 50
6248676 TGCAAGTTGT
* * ** *
6248686 GTTTATATGTGAGTTGTCTTTATATGTAAGCTGGGTTATATGCGAGTTGT
1 GTTTATATGTGAGTTGTCTTTATACGCAAGCTGGGTTATATGCGAACTGC
* * * * * * * *
6248736 ATGTATATGCGAGCTATGTTTATACGCAAGTTGTGTTATATGCGAACTGC
1 GTTTATATGTGAGTTGTCTTTATACGCAAGCTGGGTTATATGCGAACTGC
*
6248786 GTTTATATGTGTGTTGTCTTTATA
1 GTTTATATGTGAGTTGTCTTTATA
6248810 TTCGAGCTAT
Statistics
Matches: 54, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (50 bp):
GTTTATATGTGAGTTGTCTTTATACGCAAGCTGGGTTATATGCGAACTGC
Found at i:6254287 original size:9 final size:9
Alignment explanation
Indices: 6254270--6254300 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6254260 TCGAGTTGAT
6254270 TCGAATAAC
1 TCGAATAAC
*
6254279 TCGATTAAC
1 TCGAATAAC
6254288 TCGAATAAC
1 TCGAATAAC
6254297 TCGA
1 TCGA
6254301 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:6256363 original size:50 final size:50
Alignment explanation
Indices: 6256288--6256386 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
6256278 TTCAGAATTC
* *
6256288 TGACTTCTGATATATAAAACATAAGGAAGAATACGTTTTGTTGGTAAAAT
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTGGTTGGTAAAAT
* *
6256338 TGACTTCTGGTATATAAAACATAAGGAAGGATACATTTGGTTGGTAAAA
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTGGTTGGTAAAA
6256387 AACTGACTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (50 bp):
TGACTTCTGATATATAAAACATAAGGAAGAATACATTTGGTTGGTAAAAT
Found at i:6264988 original size:24 final size:24
Alignment explanation
Indices: 6264961--6265012 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
6264951 TGAGGGGGAG
6264961 TATTGAGAATCTTTGATTATTTGA
1 TATTGAGAATCTTTGATTATTTGA
6264985 TATTGAGAATCTTTGATTATTTGA
1 TATTGAGAATCTTTGATTATTTGA
6265009 TATT
1 TATT
6265013 ATTAAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.52
Consensus pattern (24 bp):
TATTGAGAATCTTTGATTATTTGA
Found at i:6274505 original size:15 final size:14
Alignment explanation
Indices: 6274474--6274503 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6274464 TCATATAAAA
6274474 TTATTAAAGATGAT
1 TTATTAAAGATGAT
*
6274488 TTATTTAAGATGAT
1 TTATTAAAGATGAT
6274502 TT
1 TT
6274504 TAAATTGGAA
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:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TTATTAAAGATGAT
Found at i:6274703 original size:16 final size:14
Alignment explanation
Indices: 6274667--6274699 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
6274657 TTAAAATTTC
6274667 AATATTG-AAAAAA
1 AATATTGAAAAAAA
6274680 AATATTGAAAAAAA
1 AATATTGAAAAAAA
6274694 AATATT
1 AATATT
6274700 TTGAGCTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (14 bp):
AATATTGAAAAAAA
Found at i:6283208 original size:23 final size:24
Alignment explanation
Indices: 6283164--6283210 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6283154 TTTTTTTTAA
* * *
6283164 TTTCGAATTTAAATCGAGTTAAAT
1 TTTCGAATTCAAATCAACTTAAAT
6283188 TTTCGAATTCAAAT-AACTTAAAT
1 TTTCGAATTCAAATCAACTTAAAT
6283211 AAATCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (24 bp):
TTTCGAATTCAAATCAACTTAAAT
Found at i:6292510 original size:7 final size:6
Alignment explanation
Indices: 6292491--6292522 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
6292481 CGTTTTGATT
*
6292491 AATAAA AATAAA AATAAA AATAAA AATTAA AA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AA
6292523 CATGAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:6295301 original size:35 final size:36
Alignment explanation
Indices: 6295221--6295292 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
6295211 TAAACATTAA
* ***
6295221 AAAATTATTTTAAAAATAAAAAAATAAAAATATTTT
1 AAAAGTATTTTAAAAATAAAAAAATAAAAATAAAAT
*
6295257 AAAAGTATTTT-AAAATTAAAAAATAAAAATAAAAT
1 AAAAGTATTTTAAAAATAAAAAAATAAAAATAAAAT
6295292 A
1 A
6295293 TATATATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (36 bp):
AAAAGTATTTTAAAAATAAAAAAATAAAAATAAAAT
Found at i:6297121 original size:19 final size:19
Alignment explanation
Indices: 6297072--6297123 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
6297062 TTCTCATAAA
6297072 AAATATTAAAAA-ATTATG
1 AAATATTAAAAATATTATG
* * * *
6297090 AAAAATCATAAATATTATT
1 AAATATTAAAAATATTATG
6297109 AAATATTAAAAATAT
1 AAATATTAAAAATAT
6297124 ACAATCACAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATATTAAAAATATTATG
Found at i:6304202 original size:24 final size:24
Alignment explanation
Indices: 6304150--6304202 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
6304140 CTAATTTTTT
* *
6304150 AGAA-TAATATATTTAAATTTTAA
1 AGAATTAATATATTTAAAGTGTAA
*
6304173 AAAATTAATATTATTTAAAGTGT-A
1 AGAATTAATA-TATTTAAAGTGTAA
6304197 AGAATT
1 AGAATT
6304203 GCATTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.12
24 11 0.46
25 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (24 bp):
AGAATTAATATATTTAAAGTGTAA
Found at i:6307686 original size:27 final size:27
Alignment explanation
Indices: 6307559--6307690 Score: 156
Period size: 27 Copynumber: 4.9 Consensus size: 27
6307549 TTTCATCTCC
* *
6307559 TAGGGGCATTTCGATCATTTTACCCTA
1 TAGGGGTATTTCGGTCATTTTACCCTA
* *
6307586 TGGGGGTATTTCGGCCATTTTACCCTA
1 TAGGGGTATTTCGGTCATTTTACCCTA
* * *
6307613 TAGGGGTATTTCAGTCATTTAACCTTA
1 TAGGGGTATTTCGGTCATTTTACCCTA
** *
6307640 TAATGGTATTTCGGTCATTTCACCCTA
1 TAGGGGTATTTCGGTCATTTTACCCTA
* *
6307667 TAGGGGTATTTTGGTTATTTTACC
1 TAGGGGTATTTCGGTCATTTTACC
6307691 TATTTTTGGG
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (27 bp):
TAGGGGTATTTCGGTCATTTTACCCTA
Found at i:6308316 original size:73 final size:73
Alignment explanation
Indices: 6308197--6308339 Score: 234
Period size: 73 Copynumber: 2.0 Consensus size: 73
6308187 GAAAATCAAT
*
6308197 TGTCGAAACCATCTTTTCCAAAATTTGAAAAAATGGGGATCGACTTTTAAAATGAAAGCTGGAGT
1 TGTCGAAACCATCTTTTCCAAAATTTGAAAAAATGGGGATCGACTTTTAAAATGAAAACTGGAGT
6308262 CGCCAAGC
66 CGCCAAGC
**
6308270 TGTCGAAACCATCTTTTCTGAAATTTG-AAAAATAGGGGATCGACTTTTAAAATGAAAACTGGAG
1 TGTCGAAACCATCTTTTCCAAAATTTGAAAAAAT-GGGGATCGACTTTTAAAATGAAAACTGGAG
*
6308334 TTGCCA
65 TCGCCA
6308340 CCGATCTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
72 6 0.09
73 59 0.91
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (73 bp):
TGTCGAAACCATCTTTTCCAAAATTTGAAAAAATGGGGATCGACTTTTAAAATGAAAACTGGAGT
CGCCAAGC
Found at i:6309222 original size:27 final size:26
Alignment explanation
Indices: 6309166--6309223 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
6309156 GTTAACACTT
* *
6309166 AAAAACTAAAGAATTTAAAGTTCATC
1 AAAAACTAAAGAAATTAAAGTGCATC
* * *
6309192 AAAACACTAAATAAATTAATGTGCATG
1 AAAA-ACTAAAGAAATTAAAGTGCATC
6309219 AAAAA
1 AAAAA
6309224 TGTGTGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.24
Consensus pattern (26 bp):
AAAAACTAAAGAAATTAAAGTGCATC
Found at i:6311405 original size:84 final size:85
Alignment explanation
Indices: 6311317--6311684 Score: 235
Period size: 84 Copynumber: 4.4 Consensus size: 85
6311307 TATCGACTTC
*
6311317 AATCTGCTCCACTGTGACTTCAAGGG-GATAAGACTCGATACGATCTGCTCCACTACTGCTT-AG
1 AATCTGCTCCACTGTGACTTC-AGGGAGATAAGACTCGATTCGATCTGCTCCACTACTGCTTCAG
6311380 GGAGATAAGATCTATTCTTTT
65 GGAGATAAGATCTATTCTTTT
** * * * * *
6311401 AATCTGCTCCACTGCAACTTCAGGGAGATAGGA-TTGATTTCTCAGTCTGCCCCACT-GTGACTT
1 AATCTGCTCCACTGTGACTTCAGGGAGATAAGACTCGA-TTC-GA-TCTGCTCCACTACTG-CTT
* *
6311464 CAAGGG-GATAAGACTCGATGC----
62 C-AGGGAGATAAGA-TCTATTCTTTT
* * * * ** * * **
6311485 GATCTGCTCCACTACTG-CTT-AGGGAGATAAGATCTATTGTTTTAATCCGCTCCACTGCAACTT
1 AATCTGCTCCACT-GTGACTTCAGGGAGATAAGA-C--TCGATTCGATCTGCTCCACTACTGCTT
* *
6311548 CAGGGAGATAGGAT-TAATT-TTTC
62 CAGGGAGATAAGATCT-ATTCTTTT
* * * *
6311571 AGTCTGCCCCACTGTGACTTCAAGGG-GATAAGACTCGATGCGATCTGCTCCACTACTGCTT-AA
1 AATCTGCTCCACTGTGACTTC-AGGGAGATAAGACTCGATTCGATCTGCTCCACTACTGCTTCAG
*
6311634 GGAGATAAGATCTATTGTTTT
65 GGAGATAAGATCTATTCTTTT
** **
6311655 AATCCACTCCACTGCAACTTCAGGGAGATA
1 AATCTGCTCCACTGTGACTTCAGGGAGATA
6311685 GGATTGATTT
Statistics
Matches: 210, Mismatches: 48, Indels: 52
0.68 0.15 0.17
Matches are distributed among these distances:
83 43 0.20
84 102 0.49
85 6 0.03
86 29 0.14
87 17 0.08
88 13 0.06
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (85 bp):
AATCTGCTCCACTGTGACTTCAGGGAGATAAGACTCGATTCGATCTGCTCCACTACTGCTTCAGG
GAGATAAGATCTATTCTTTT
Found at i:6311411 original size:43 final size:44
Alignment explanation
Indices: 6311359--6311684 Score: 159
Period size: 43 Copynumber: 7.7 Consensus size: 44
6311349 ACTCGATACG
6311359 ATCTGCTCCACTACTGCTT-AGGGAGATAAGATCTATTCTTTTA
1 ATCTGCTCCACTACTGCTTCAGGGAGATAAGATCTATTCTTTTA
* ** * * *
6311402 ATCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TGATT-TCTCA
1 ATCTGCTCCACTACTGCTTCAGGGAGATAAGATCT-ATTCTTTTA
* * * * * *
6311445 GTCTGCCCCACT-GTGACTTCAAGGG-GATAAGACTCGATGC----G
1 ATCTGCTCCACTACTG-CTTC-AGGGAGATAAGA-TCTATTCTTTTA
*
6311486 ATCTGCTCCACTACTGCTT-AGGGAGATAAGATCTATTGTTTTA
1 ATCTGCTCCACTACTGCTTCAGGGAGATAAGATCTATTCTTTTA
* * ** * *
6311529 ATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TAATT-TTTCA
1 ATCTGCTCCACTACTGCTTCAGGGAGATAAGATCT-ATTCTTTTA
* * * * * *
6311572 GTCTGCCCCACT-GTGACTTCAAGGG-GATAAGACTCGATGC----G
1 ATCTGCTCCACTACTG-CTTC-AGGGAGATAAGA-TCTATTCTTTTA
* *
6311613 ATCTGCTCCACTACTGCTT-AAGGAGATAAGATCTATTGTTTTA
1 ATCTGCTCCACTACTGCTTCAGGGAGATAAGATCTATTCTTTTA
** * **
6311656 ATCCACTCCACTGCAACTTCAGGGAGATA
1 ATCTGCTCCACTACTGCTTCAGGGAGATA
6311685 GGATTGATTT
Statistics
Matches: 204, Mismatches: 52, Indels: 53
0.66 0.17 0.17
Matches are distributed among these distances:
39 15 0.07
40 14 0.07
41 26 0.13
42 4 0.02
43 93 0.46
44 52 0.25
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTCAGGGAGATAAGATCTATTCTTTTA
Found at i:6311506 original size:127 final size:127
Alignment explanation
Indices: 6311274--6311697 Score: 690
Period size: 127 Copynumber: 3.3 Consensus size: 127
6311264 TGGCGTTTCG
* * ** * *
6311274 ATCCACTCCACTGCAA-TGTCGGGGAGATAGGATT-ATCGACTTCAATCTGCTCCACTGTGACTT
1 ATCCGCTCCACTGCAACT-TCAGGGAGATAGGATTGAT-TTC-TCAGTCTGCCCCACTGTGACTT
* *
6311337 CAAGGGGATAAGACTCGATACGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTCTTTTA
63 CAAGGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTA
*
6311402 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTCAGTCTGCCCCACTGTGACTTCAA
1 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTCAGTCTGCCCCACTGTGACTTCAA
6311467 GGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTA
66 GGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTA
* *
6311529 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAATTTTTCAGTCTGCCCCACTGTGACTTCAA
1 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTCAGTCTGCCCCACTGTGACTTCAA
*
6311594 GGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTATTGTTTTA
66 GGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTA
*
6311656 ATCCACTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTC
1 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTC
6311698 CTGTTTGCTC
Statistics
Matches: 278, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
127 245 0.88
128 30 0.11
129 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (127 bp):
ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTCAGTCTGCCCCACTGTGACTTCAA
GGGGATAAGACTCGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTA
Found at i:6311841 original size:87 final size:87
Alignment explanation
Indices: 6311750--6311922 Score: 231
Period size: 87 Copynumber: 2.0 Consensus size: 87
6311740 TCCAACCTAT
* * * *
6311750 TCCACTACTGGTCAGGGACATAGGACTT-GTGGCTTAAATCTGTTTCCCTACTCCTGGGAAAGAT
1 TCCACTACTGCTCAGGGACATAAGA-TTAATGGCTTAAACCTGTTTCCCTACTCCTGGGAAAGAT
* *
6311814 AAGATTCGCCGTTTTGGATCTGC
65 AAGATTCGCCGTCTTCGATCTGC
* * * * *
6311837 TCCACTATTGCTTAGGGAGATAAGATTAATGGCTTAAACCTGTTTCCCTACTCCTGGGGAAGATG
1 TCCACTACTGCTCAGGGACATAAGATTAATGGCTTAAACCTGTTTCCCTACTCCTGGGAAAGATA
6311902 AGATTCGCCGTCTTCGATCTG
66 AGATTCGCCGTCTTCGATCTG
6311923 TTTCCCTACT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
86 2 0.03
87 72 0.97
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (87 bp):
TCCACTACTGCTCAGGGACATAAGATTAATGGCTTAAACCTGTTTCCCTACTCCTGGGAAAGATA
AGATTCGCCGTCTTCGATCTGC
Found at i:6311945 original size:87 final size:87
Alignment explanation
Indices: 6311779--6312035 Score: 322
Period size: 87 Copynumber: 3.0 Consensus size: 87
6311769 ATAGGACTTG
* * *
6311779 TGGCTTAAATCTGTTTCCCTACTCCTGGGAAAGATAAGATTCGCCGTTTTGGATCTG-CTCCACT
1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTGGATCTGTTTCC-CT
* *
6311843 ATTGCTTAGGG-AGATAAGATTAA
65 ACT-CTTGGGGAAGATAAGATTAA
* * *
6311866 TGGCTTAAACCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCTGTTTCCCTA
1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTGGATCTGTTTCCCTA
**
6311931 CTCTTGGGGAAGATAAGATTCG
66 CTCTTGGGGAAGATAAGATTAA
* *** * *
6311953 TAGCTCGGATTTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCAG-CTTGGATCTGTTTCCCTA
1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTGGATCTGTTTCCCTA
*
6312017 CTCCTGGGGAAGATAAGAT
66 CTCTTGGGGAAGATAAGAT
6312036 CCGTAATATT
Statistics
Matches: 148, Mismatches: 20, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
86 41 0.28
87 104 0.70
88 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (87 bp):
TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTGGATCTGTTTCCCTA
CTCTTGGGGAAGATAAGATTAA
Found at i:6311982 original size:43 final size:43
Alignment explanation
Indices: 6311876--6312035 Score: 241
Period size: 43 Copynumber: 3.7 Consensus size: 43
6311866 TGGCTTAAAC
* *
6311876 CTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTC-GAT
1 CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCAG-C-TCGGAT
* *
6311920 CTGTTTCCCTACTCTTGGGGAAGATAAGATTCGTAGCTCGGAT
1 CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCAGCTCGGAT
* *
6311963 TTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCAGCTTGGAT
1 CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCAGCTCGGAT
6312006 CTGTTTCCCTACTCCTGGGGAAGATAAGAT
1 CTGTTTCCCTACTCCTGGGGAAGATAAGAT
6312036 CCGTAATATT
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
42 2 0.02
43 72 0.68
44 32 0.30
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (43 bp):
CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCAGCTCGGAT
Found at i:6313273 original size:14 final size:13
Alignment explanation
Indices: 6313250--6313307 Score: 64
Period size: 15 Copynumber: 4.2 Consensus size: 13
6313240 AGCCTCTCCA
6313250 TTTTACTTTTCATT
1 TTTTA-TTTTCATT
6313264 TTTTCATTTTCATTT
1 TTTT-ATTTTCA-TT
6313279 TTTTATTTTTCATCT
1 TTTTA-TTTTCAT-T
6313294 TTTTATTTT-ATT
1 TTTTATTTTCATT
6313306 TT
1 TT
6313308 ATTGTCTCGT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 2 0.05
14 16 0.40
15 19 0.47
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTCATT
Found at i:6313282 original size:15 final size:14
Alignment explanation
Indices: 6313250--6313307 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
6313240 AGCCTCTCCA
6313250 TTTTACTTTTCATTT
1 TTTTA-TTTTCATTT
*
6313265 TTTCATTTTCATTT
1 TTTTATTTTCATTT
*
6313279 TTTTATTTTTCATCT
1 TTTTA-TTTTCATTT
6313294 TTTTATTTT-ATTT
1 TTTTATTTTCATTT
6313307 T
1 T
6313308 ATTGTCTCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 4 0.11
14 17 0.45
15 17 0.45
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTTCATTT
Found at i:6313288 original size:29 final size:28
Alignment explanation
Indices: 6313250--6313307 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
6313240 AGCCTCTCCA
6313250 TTTTACTTTTCAT-TTTTTCATTTTCATTT
1 TTTTACTTTTCATCTTTTT-ATTTT-ATTT
*
6313279 TTTTATTTTTCATCTTTTTATTTTATTT
1 TTTTACTTTTCATCTTTTTATTTTATTT
6313307 T
1 T
6313308 ATTGTCTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 17 0.63
30 5 0.19
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTACTTTTCATCTTTTTATTTTATTT
Found at i:6317543 original size:73 final size:73
Alignment explanation
Indices: 6317419--6317573 Score: 256
Period size: 73 Copynumber: 2.1 Consensus size: 73
6317409 ATCCCCAGTG
* *
6317419 GAGTCGCCAAGCTATCGAAACCATCTTTTCTGAAATTTGAAAAAACGGGGATCGACTTTTAAAAC
1 GAGTCGCCAAGCTATCGAAACCATCTTTTCTGAAATTGGAAAAAACAGGGATCGACTTTTAAAAC
6317484 GAAAACTA
66 GAAAACTA
* * *
6317492 GAGTCGCCAAGCTGTCGAAACCATCTTTTCTGAAATTGGAAAAAATAGGGATCGACTTTTAAAAT
1 GAGTCGCCAAGCTATCGAAACCATCTTTTCTGAAATTGGAAAAAACAGGGATCGACTTTTAAAAC
*
6317557 GAAAACTG
66 GAAAACTA
6317565 GAGTCGCCA
1 GAGTCGCCA
6317574 CCGATCTTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (73 bp):
GAGTCGCCAAGCTATCGAAACCATCTTTTCTGAAATTGGAAAAAACAGGGATCGACTTTTAAAAC
GAAAACTA
Found at i:6318455 original size:27 final size:26
Alignment explanation
Indices: 6318399--6318456 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
6318389 GTTAACACTT
* *
6318399 AAAAACTAAAGAATTTAAAGTTCATC
1 AAAAACTAAAGAAATTAAAGTGCATC
* * *
6318425 AAAACACTAAATAAATTAATGTGCATG
1 AAAA-ACTAAAGAAATTAAAGTGCATC
6318452 AAAAA
1 AAAAA
6318457 TGTATGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.24
Consensus pattern (26 bp):
AAAAACTAAAGAAATTAAAGTGCATC
Found at i:6319522 original size:11 final size:10
Alignment explanation
Indices: 6319496--6319529 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
6319486 AAAAAAGAAA
6319496 AAAATAAAA-
1 AAAATAAAAG
6319505 AAAATAAAAG
1 AAAATAAAAG
6319515 AAACATAAAAG
1 AAA-ATAAAAG
6319526 AAAA
1 AAAA
6319530 CAGAGAGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 4 0.17
11 10 0.43
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (10 bp):
AAAATAAAAG
Found at i:6331557 original size:4 final size:4
Alignment explanation
Indices: 6331548--6331614 Score: 55
Period size: 4 Copynumber: 16.2 Consensus size: 4
6331538 CTAACTTTTC
* * *
6331548 TCTT TCTT TCTT TCTCT T-TT TCTT TCCTT TCTT TCCT TCTC TGTT TCGTT
1 TCTT TCTT TCTT TCT-T TCTT TCTT T-CTT TCTT TCTT TCTT TCTT TC-TT
* *
6331598 TCTT TCTC TCAT TCTT T
1 TCTT TCTT TCTT TCTT T
6331615 ATCTATTTCT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
3 2 0.04
4 37 0.76
5 10 0.20
ACGTcount: A:0.01, C:0.28, G:0.03, T:0.67
Consensus pattern (4 bp):
TCTT
Found at i:6331566 original size:21 final size:21
Alignment explanation
Indices: 6331542--6331606 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
6331532 GAAACCCTAA
6331542 CTTTTCTCTTTCTTTCTTTCT
1 CTTTTCTCTTTCTTTCTTTCT
6331563 CTTTT-TCTTTCCTTTCTTTC-
1 CTTTTCTCTTT-CTTTCTTTCT
* *
6331583 CTTCTCTGTTTCGTTTCTTTCT
1 CTTTTCTCTTTC-TTTCTTTCT
6331605 CT
1 CT
6331607 CATTCTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 10 0.26
21 26 0.68
22 2 0.05
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (21 bp):
CTTTTCTCTTTCTTTCTTTCT
Found at i:6331579 original size:25 final size:26
Alignment explanation
Indices: 6331544--6331604 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
6331534 AACCCTAACT
* *
6331544 TTTCTCTTTCTTTCTTTCTCTTTTTC-
1 TTTC-CTTTCTTTCCTTCTCTGTTTCG
6331570 TTTCCTTTCTTTCCTTCTCTGTTTCG
1 TTTCCTTTCTTTCCTTCTCTGTTTCG
6331596 TTT-CTTTCT
1 TTTCCTTTCT
6331605 CTCATTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTCCTTTCTTTCCTTCTCTGTTTCG
Found at i:6331612 original size:25 final size:25
Alignment explanation
Indices: 6331548--6331612 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
6331538 CTAACTTTTC
* *
6331548 TCTTTCTTTCTTTCTCTTTTTC-TT
1 TCTTTCTTTCATTCTCTGTTTCGTT
*
6331572 TCCTTTCTTTCCTTCTCTGTTTCGTT
1 T-CTTTCTTTCATTCTCTGTTTCGTT
*
6331598 TCTTTCTCTCATTCT
1 TCTTTCTTTCATTCT
6331613 TTATCTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.03
25 31 0.89
26 3 0.09
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (25 bp):
TCTTTCTTTCATTCTCTGTTTCGTT
Found at i:6331647 original size:5 final size:5
Alignment explanation
Indices: 6331637--6331678 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
6331627 TTCTTTTACT
6331637 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
6331679 CTTAACTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:6332891 original size:21 final size:22
Alignment explanation
Indices: 6332849--6332898 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
6332839 CTTTTATTCG
* *
6332849 AAACATGTGATTTAATGGCTAA
1 AAACATGTGATTTAAAGACTAA
*
6332871 AAACATG-GCTTTAAAGACTAA
1 AAACATGTGATTTAAAGACTAA
6332892 ATAACAT
1 A-AACAT
6332899 TTAAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (22 bp):
AAACATGTGATTTAAAGACTAA
Found at i:6333121 original size:9 final size:9
Alignment explanation
Indices: 6333107--6333132 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6333097 AGTTGGGACT
6333107 TTGGGAGAG
1 TTGGGAGAG
6333116 TTGGGAGAG
1 TTGGGAGAG
6333125 TTGGGAGA
1 TTGGGAGA
6333133 ATAAAAGGAC
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:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (9 bp):
TTGGGAGAG
Found at i:6335272 original size:15 final size:16
Alignment explanation
Indices: 6335244--6335274 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6335234 TTAATAAAAG
6335244 TATTTTTAATTAATAT
1 TATTTTTAATTAATAT
6335260 TATTTTT-ATTAATAT
1 TATTTTTAATTAATAT
6335275 ACTAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAATTAATAT
Found at i:6336512 original size:22 final size:22
Alignment explanation
Indices: 6336486--6336549 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
6336476 TATTTTTCAC
*
6336486 TATTGTTTTGCTGCCATTTTGA
1 TATTGTTTTGCTACCATTTTGA
*
6336508 TATTGTTTTGCTACCATTTTGC
1 TATTGTTTTGCTACCATTTTGA
* * *
6336530 TATTATATTGCTACTATTTT
1 TATTGTTTTGCTACCATTTT
6336550 ATTGTTATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.56
Consensus pattern (22 bp):
TATTGTTTTGCTACCATTTTGA
Found at i:6338891 original size:31 final size:31
Alignment explanation
Indices: 6338856--6338923 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
6338846 TTTTGGGTTC
* *
6338856 AATTTGATACCTAAGCTTCACACTTTTTAC-T
1 AATTTGACACCTAAACTTCACACTTTTT-CTT
* * *
6338887 AATTTCACACTTAAACTTGACACTTTTTCTT
1 AATTTGACACCTAAACTTCACACTTTTTCTT
6338918 AATTTG
1 AATTTG
6338924 GTACTTAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (31 bp):
AATTTGACACCTAAACTTCACACTTTTTCTT
Found at i:6339458 original size:32 final size:32
Alignment explanation
Indices: 6339421--6339490 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
6339411 AGCTTAGGTG
6339421 CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
1 CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
* *** * *
6339453 CCAAATTGGGCCTAAAATATTAAGTTTAAGTA
1 CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
6339485 CCAAAT
1 CCAAAT
6339491 ATTATATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (32 bp):
CCAAATTAGGAAAAAAATACTAAGTTCAAGTA
Found at i:6340813 original size:11 final size:11
Alignment explanation
Indices: 6340782--6340821 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
6340772 AATCTGCTAT
6340782 TTTTTTTGTTA
1 TTTTTTTGTTA
**
6340793 TTTTAATGTTA
1 TTTTTTTGTTA
*
6340804 TTTTTTTGTTG
1 TTTTTTTGTTA
6340815 TTTTTTT
1 TTTTTTT
6340822 ACCTATTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (11 bp):
TTTTTTTGTTA
Found at i:6341088 original size:13 final size:13
Alignment explanation
Indices: 6341054--6341089 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
6341044 TTATATACAC
6341054 TTAAAAATT-ATA
1 TTAAAAATTAATA
6341066 -TAAAAA-TAATA
1 TTAAAAATTAATA
6341077 TTAAAAATTAATA
1 TTAAAAATTAATA
6341090 CGTGTAGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.05
11 9 0.43
12 6 0.29
13 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAATTAATA
Found at i:6342389 original size:30 final size:29
Alignment explanation
Indices: 6342353--6342414 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
6342343 ACTTAACAAG
6342353 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAA-AAAATTAA
* *
6342383 CAAATGTCTTTAAAATAATAATAAATTAA
1 CAAATGTCTCTAAAATAATAAAAAATTAA
6342412 CAA
1 CAA
6342415 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.29
Consensus pattern (29 bp):
CAAATGTCTCTAAAATAATAAAAAATTAA
Found at i:6351768 original size:73 final size:73
Alignment explanation
Indices: 6351649--6351792 Score: 225
Period size: 73 Copynumber: 2.0 Consensus size: 73
6351639 ATTGTCTCAG
* * * *
6351649 GGTAGGTCACTTTATAACCTTACCCTCAATTGGGAGCATGCAATTGTTATCAATACCTTGTCATA
1 GGTAGGTCACTTTATAACCTTACCCTCAATTGGGAGCAAGAAATTGTTATCAATACATTGCCATA
6351714 ACACACAT
66 ACACACAT
** *
6351722 GGTAGGTCACTTTATAACCTTACCCTTGATTGGGGGCAAGAAATTGTTATCAATACATTGCCATA
1 GGTAGGTCACTTTATAACCTTACCCTCAATTGGGAGCAAGAAATTGTTATCAATACATTGCCATA
6351787 ACACAC
66 ACACAC
6351793 CTTGCCACCC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (73 bp):
GGTAGGTCACTTTATAACCTTACCCTCAATTGGGAGCAAGAAATTGTTATCAATACATTGCCATA
ACACACAT
Found at i:6353038 original size:18 final size:17
Alignment explanation
Indices: 6353017--6353065 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
6353007 ATATATAAAA
6353017 TATAAAAAAT-ATATATTT
1 TATAAAAAATCA-A-ATTT
*
6353035 TATAAAACATCAAATTT
1 TATAAAAAATCAAATTT
*
6353052 TATAAAATATCAAA
1 TATAAAAAATCAAA
6353066 GATTTATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 17 0.61
18 10 0.36
19 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
TATAAAAAATCAAATTT
Found at i:6353051 original size:17 final size:17
Alignment explanation
Indices: 6353031--6353065 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6353021 AAAAATATAT
6353031 ATTTTATAAAACATCAA
1 ATTTTATAAAACATCAA
*
6353048 ATTTTATAAAATATCAA
1 ATTTTATAAAACATCAA
6353065 A
1 A
6353066 GATTTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTTATAAAACATCAA
Found at i:6371188 original size:27 final size:27
Alignment explanation
Indices: 6371144--6371195 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
6371134 GTATATATAT
6371144 ATTTAAGTCCATAATCTAACATTTTCC
1 ATTTAAGTCCATAATCTAACATTTTCC
* *
6371171 ATTTAAGTCCTTAGTCTAACATTTT
1 ATTTAAGTCCATAATCTAACATTTT
6371196 TCTTGTTCTT
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:0.19, G:0.06, T:0.44
Consensus pattern (27 bp):
ATTTAAGTCCATAATCTAACATTTTCC
Found at i:6373039 original size:21 final size:21
Alignment explanation
Indices: 6373013--6373060 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6373003 ATCTCTGAAT
*
6373013 AAATTGAATAAATTTTGAAGA
1 AAATTGAATAAATTCTGAAGA
* * *
6373034 ACATTGCATCAATTCTGAAGA
1 AAATTGAATAAATTCTGAAGA
6373055 AAATTG
1 AAATTG
6373061 TTCTTCAATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
AAATTGAATAAATTCTGAAGA
Found at i:6377395 original size:3 final size:3
Alignment explanation
Indices: 6377387--6377431 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
6377377 TTTTTGCATA
* * * *
6377387 ATG ATG ATG GTG GTG GTG GTG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
6377432 CCATTTGCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:6380235 original size:18 final size:17
Alignment explanation
Indices: 6380184--6380235 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
6380174 GCAACCCAAT
*
6380184 TTTATTTTATTTTCTTA
1 TTTATTTTATTTTTTTA
**
6380201 TTTATTTTAATAATTTTA
1 TTTATTTT-ATTTTTTTA
6380219 TTTATCTTTATTTTTTT
1 TTTAT-TTTATTTTTTT
6380236 TGTTCTAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 8 0.29
18 17 0.61
19 3 0.11
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTATTTTTTTA
Found at i:6393866 original size:15 final size:15
Alignment explanation
Indices: 6393846--6393874 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6393836 AAACAGGATA
6393846 TAAATGAGTAAATAG
1 TAAATGAGTAAATAG
6393861 TAAATGAGTAAATA
1 TAAATGAGTAAATA
6393875 ATAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (15 bp):
TAAATGAGTAAATAG
Found at i:6395833 original size:50 final size:49
Alignment explanation
Indices: 6395757--6395940 Score: 224
Period size: 50 Copynumber: 3.7 Consensus size: 49
6395747 CTGTTCACCA
* * *
6395757 GGGAAGTAAGATTTGCTATTGTAGCTTCAATCTATTTAACTGCAATGTC
1 GGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC
* ** ** *
6395806 GGGTAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
1 GGG-AAGCAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC
* * *
6395856 AGAGAAGTAAGATTCGCTGTTTTAGCTTCAATCTATTTAACTGCAATGTC
1 -GGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC
*
6395906 GGGGAAGCAAGATTCGTTGTTGTAGCTTCAATCTA
1 -GGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTA
6395941 AAATTTTTAT
Statistics
Matches: 110, Mismatches: 23, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
49 3 0.03
50 105 0.95
51 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (49 bp):
GGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC
Found at i:6395932 original size:100 final size:100
Alignment explanation
Indices: 6395754--6395939 Score: 318
Period size: 100 Copynumber: 1.9 Consensus size: 100
6395744 GATCTGTTCA
* * *
6395754 CCAGGGAAGTAAGATTTGCTATTGTAGCTTCAATCTATTTAACTGCAATGTCGGGTAAGCAAGAT
1 CCAGAGAAGTAAGATTCGCTATTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGAT
6395819 TCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCG
66 TCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCG
* *
6395854 CCAGAGAAGTAAGATTCGCTGTTTTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGAT
1 CCAGAGAAGTAAGATTCGCTATTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGAT
*
6395919 TCGTTGTTGTAGCTTCAATCT
66 TCGCTGTTGTAGCTTCAATCT
6395940 AAAATTTTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 80 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (100 bp):
CCAGAGAAGTAAGATTCGCTATTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGAT
TCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCG
Found at i:6407579 original size:43 final size:44
Alignment explanation
Indices: 6407480--6407586 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 44
6407470 GTGGAATAGA
6407480 TTATCT-TCTTGAAGTTGCAGTGGAGTAGATTAAAGACAACAATC
1 TTATCTCTC-TGAAGTTGCAGTGGAGTAGATTAAAGACAACAATC
* * * ***
6407524 CTATCTCGCTGAAGTTGCAGTGG-GTGGATTAAA-ACCTTAGATC
1 TTATCTCTCTGAAGTTGCAGTGGAGTAGATTAAAGACAACA-ATC
6407567 TTATCTCTCTGAAGTTGCAG
1 TTATCTCTCTGAAGTTGCAG
6407587 AGAGCAGATC
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 3 0.06
43 30 0.57
44 19 0.36
45 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (44 bp):
TTATCTCTCTGAAGTTGCAGTGGAGTAGATTAAAGACAACAATC
Found at i:6409123 original size:24 final size:25
Alignment explanation
Indices: 6409051--6409142 Score: 77
Period size: 24 Copynumber: 3.8 Consensus size: 25
6409041 CTTATTTTTG
*
6409051 TATTATAATATA-AT-TACTATTATTT
1 TATTTTAATATATATGTA-TATTA-TT
* *
6409076 TATTTTTATTTATATGTA-ATTATT
1 TATTTTAATATATATGTATATTATT
*
6409100 T-TTTATAATCTATATGTATA-TATT
1 TATTT-TAATATATATGTATATTATT
*
6409124 TATTTTAGTATATATGTAT
1 TATTTTAATATATATGTAT
6409143 GTATACATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
23 3 0.05
24 31 0.56
25 17 0.31
26 2 0.04
27 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
TATTTTAATATATATGTATATTATT
Found at i:6420235 original size:26 final size:25
Alignment explanation
Indices: 6420181--6420235 Score: 58
Period size: 26 Copynumber: 2.1 Consensus size: 25
6420171 AGTTTTTCCC
* *
6420181 TTTTGAAATAGGGAAAATGTCATCCT
1 TTTTGAAATAAGGAAAATATCAT-CT
6420207 TTTTGAAACTAAGGAATAATATCAT-T
1 TTTTGAAA-TAAGGAA-AATATCATCT
6420233 TTT
1 TTT
6420236 GTTATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 12 0.48
27 6 0.24
28 7 0.28
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (25 bp):
TTTTGAAATAAGGAAAATATCATCT
Found at i:6424582 original size:100 final size:100
Alignment explanation
Indices: 6424409--6424616 Score: 389
Period size: 100 Copynumber: 2.1 Consensus size: 100
6424399 TTCAGTTTTC
*
6424409 ACAAATTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTATA
1 ACAAACTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTATA
*
6424474 GCGGTTCGCATTGTAATAATGCATGTACCTTGACA
66 GCGGTTCGCATTGTAATAATGCAAGTACCTTGACA
*
6424509 ACAAACTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTGTA
1 ACAAACTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTATA
6424574 GCGGTTCGCATTGTAATAATGCAAGTACCTTGACA
66 GCGGTTCGCATTGTAATAATGCAAGTACCTTGACA
6424609 ACAAACTT
1 ACAAACTT
6424617 ACAGCGAACA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 105 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (100 bp):
ACAAACTTCACTTCATGGCTTAGAGTTCCTTTTACATATCATAGAACCCTTTTTACTACTCTATA
GCGGTTCGCATTGTAATAATGCAAGTACCTTGACA
Found at i:6426299 original size:21 final size:21
Alignment explanation
Indices: 6426273--6426316 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6426263 TTTTACCAAA
6426273 AATGTGTA-TTGGACTAAATTG
1 AATGTG-AGTTGGACTAAATTG
* *
6426294 AATGTGAGTTGTATTAAATTG
1 AATGTGAGTTGGACTAAATTG
6426315 AA
1 AA
6426317 CTAAATTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (21 bp):
AATGTGAGTTGGACTAAATTG
Found at i:6426741 original size:49 final size:48
Alignment explanation
Indices: 6426685--6426900 Score: 159
Period size: 49 Copynumber: 4.4 Consensus size: 48
6426675 ATTCTGTTAT
* * *
6426685 TTGGCTCTCTTGAGCTTCCCGTTTATGGCTCGTATGAGCTTCCCGATAA
1 TTGGCTCTCATGAGCTTCCCGATAATGGCTC-TATGAGCTTCCCGATAA
*** * *
6426734 TTGGCTCTC-TAGAGCTTCTTAATAATTGGCTCTCATGAGCTTTCTGATAA
1 TTGGCTCTCAT-GAGCTTCCCGATAA-TGGCTCT-ATGAGCTTCCCGATAA
* * * * **
6426784 TAGGATCTCGTGAGCTTCCTGATTAATGGCTCTCCGAAGCTTCCCGAT-A
1 TTGGCTCTCATGAGCTTCCCGA-TAATGGCTCTATG-AGCTTCCCGATAA
* * * * *
6426833 TTGGCTCGCATGAGCTTCTCGATTATGGCTCTTATGAGCTTCTCGTTACA
1 TTGGCTCTCATGAGCTTCCCGATAATGGCTC-TATGAGCTTCCCGATA-A
*
6426883 -TGGCTCACATGAGCTTCC
1 TTGGCTCTCATGAGCTTCC
6426901 TGTTATAAGG
Statistics
Matches: 130, Mismatches: 28, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
48 18 0.14
49 55 0.42
50 53 0.41
51 4 0.03
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (48 bp):
TTGGCTCTCATGAGCTTCCCGATAATGGCTCTATGAGCTTCCCGATAA
Found at i:6426748 original size:25 final size:26
Alignment explanation
Indices: 6426685--6426900 Score: 129
Period size: 25 Copynumber: 8.8 Consensus size: 26
6426675 ATTCTGTTAT
* *
6426685 TTGGCTCTCT-TGAGCTTCCCGTTTA
1 TTGGCTCTCTATGAGCTTCCCGATAA
*
6426710 -TGGCTC-GTATGAGCTTCCCGATAA
1 TTGGCTCTCTATGAGCTTCCCGATAA
***
6426734 TTGGCTCTCTA-GAGCTTCTTAATAA
1 TTGGCTCTCTATGAGCTTCCCGATAA
* *
6426759 TTGGCTCTC-ATGAGCTTTCTGATAA
1 TTGGCTCTCTATGAGCTTCCCGATAA
* * * *
6426784 TAGGATCTC-GTGAGCTTCCTGATTAA
1 TTGGCTCTCTATGAGCTTCCCGA-TAA
*
6426810 -TGGCTCTC--CGAAGCTTCCCGAT-A
1 TTGGCTCTCTATG-AGCTTCCCGATAA
* * *
6426833 TTGGCTCGC-ATGAGCTTCTCGATTA
1 TTGGCTCTCTATGAGCTTCCCGATAA
* *
6426858 -TGGCTCT-TATGAGCTTCTCGTTACA
1 TTGGCTCTCTATGAGCTTCCCGATA-A
*
6426883 -TGGCTCAC-ATGAGCTTCC
1 TTGGCTCTCTATGAGCTTCC
6426901 TGTTATAAGG
Statistics
Matches: 153, Mismatches: 26, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
23 2 0.01
24 58 0.38
25 88 0.58
26 5 0.03
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (26 bp):
TTGGCTCTCTATGAGCTTCCCGATAA
Found at i:6426783 original size:50 final size:49
Alignment explanation
Indices: 6426651--6426802 Score: 128
Period size: 50 Copynumber: 3.1 Consensus size: 49
6426641 CGCAAGGGCA
* * * * *
6426651 TCCCATTAATTAGCTCTCATGAGCATTCTGTTATTTGGCTCTCTTGAGCT
1 TCCCAATAATTGGCTCTCATGAGCTTTCTGATAATTGGCTCTC-TGAGCT
** * * *
6426701 TCCCGTTTA-TGGCTCGT-ATGAGCTTCCCGATAATTGGCTCTCTAGAGCT
1 TCCCAATAATTGGCTC-TCATGAGCTTTCTGATAATTGGCTCTCT-GAGCT
** * *
6426750 TCTTAATAATTGGCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCT
1 TCCCAATAATTGGCTCTCATGAGCTTTCTGATAATTGGCTCTC-TGAGCT
6426800 TCC
1 TCC
6426803 TGATTAATGG
Statistics
Matches: 79, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
48 1 0.01
49 35 0.44
50 42 0.53
51 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (49 bp):
TCCCAATAATTGGCTCTCATGAGCTTTCTGATAATTGGCTCTCTGAGCT
Found at i:6426814 original size:50 final size:49
Alignment explanation
Indices: 6426663--6426873 Score: 157
Period size: 49 Copynumber: 4.3 Consensus size: 49
6426653 CCATTAATTA
* * * * *
6426663 GCTCTCATGAGCATTCTGTTATTTGGCTCTCTTGAGCTTCCCG-TTTATG
1 GCTCTCATGAGCTTTCTGATAATTGGCTCTC-TGAGCTTCCTGATTAATG
* * * *
6426712 GCTCGT-ATGAGCTTCCCGATAATTGGCTCTCTAGAGCTT-CTTAATAATTG
1 GCTC-TCATGAGCTTTCTGATAATTGGCTCTCT-GAGCTTCCTGATTAA-TG
* *
6426762 GCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCTTCCTGATTAATG
1 GCTCTCATGAGCTTTCTGATAATTGGCTCTC-TGAGCTTCCTGATTAATG
* * * *
6426812 GCTCTC-CGAAGCTTCCCGAT-ATTGGCTCGCATGAGCTT-CTCGATT-ATG
1 GCTCTCATG-AGCTTTCTGATAATTGGCTCTC-TGAGCTTCCT-GATTAATG
*
6426860 GCTCTTATGAGCTT
1 GCTCTCATGAGCTT
6426874 CTCGTTACAT
Statistics
Matches: 128, Mismatches: 24, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
48 17 0.13
49 53 0.41
50 51 0.40
51 7 0.05
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (49 bp):
GCTCTCATGAGCTTTCTGATAATTGGCTCTCTGAGCTTCCTGATTAATG
Found at i:6426836 original size:99 final size:99
Alignment explanation
Indices: 6426657--6426873 Score: 235
Period size: 99 Copynumber: 2.2 Consensus size: 99
6426647 GGCATCCCAT
* * * * * * * * *
6426657 TAATTAGCTCTCATGAGCATTCTGTTATTTGGCTCTCTTGAGCTTCCCGTTTATGGCTCGTATGA
1 TAATTGGCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCTTCCCGTTAATGGCTCGTACGA
* *
6426722 GCTTCCCGATAATTGGCTCTC-TAGAGCTTCTTAA
66 GCTTCCCGATAATTGGCTCGCAT-GAGCTTCTCAA
* *
6426756 TAATTGGCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCTTCCTGATTAATGGCTC-TCCG
1 TAATTGGCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCTTCCCG-TTAATGGCTCGTACG
*
6426820 AAGCTTCCCGAT-ATTGGCTCGCATGAGCTTCTCGA
65 -AGCTTCCCGATAATTGGCTCGCATGAGCTTCTCAA
* *
6426855 TTA-TGGCTCTTATGAGCTT
1 TAATTGGCTCTCATGAGCTT
6426874 CTCGTTACAT
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
98 15 0.15
99 63 0.64
100 21 0.21
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (99 bp):
TAATTGGCTCTCATGAGCTTTCTGATAATAGGATCTCGTGAGCTTCCCGTTAATGGCTCGTACGA
GCTTCCCGATAATTGGCTCGCATGAGCTTCTCAA
Found at i:6426905 original size:25 final size:25
Alignment explanation
Indices: 6426834--6426948 Score: 85
Period size: 25 Copynumber: 4.6 Consensus size: 25
6426824 TTCCCGATAT
*
6426834 TGGCTCGCATGAGCTTCTCGATT--A
1 TGGCTCACATGAGCTTCTCG-TTACA
**
6426858 TGGCTCTTATGAGCTTCTCGTTACA
1 TGGCTCACATGAGCTTCTCGTTACA
*
6426883 TGGCTCACATGAGCTTC-CTGTTATA
1 TGGCTCACATGAGCTTCTC-GTTACA
* * * * * *
6426908 AGGCTCAAAAGAGATACTCGTTTATA
1 TGGCTCACATGAGCTTCTCG-TTACA
6426934 T-GCTCACATGAGCTT
1 TGGCTCACATGAGCTT
6426949 TCCTGAATAT
Statistics
Matches: 71, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
23 2 0.03
24 19 0.27
25 44 0.62
26 6 0.08
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCTCGTTACA
Found at i:6441438 original size:3 final size:3
Alignment explanation
Indices: 6441430--6441468 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
6441420 GTTCAGGTCA
6441430 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6441469 CAATAATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6441749 original size:41 final size:41
Alignment explanation
Indices: 6441662--6441779 Score: 164
Period size: 41 Copynumber: 2.8 Consensus size: 41
6441652 GAAAAACGCT
* * *
6441662 GCTAAAGAACATGATTTTTAGCGGCGCATTTTTCTAAGCACA
1 GCTAAAGAACATGATCTTTAGCGGCG-TTTTTTTTAAGCACA
* * *
6441704 GCTAAAGAACATGATCTTTAGAGGCGTTTTTTTTAAGCGCC
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTAAGCACA
6441745 GCTAAAGAACATGATCTTTAGCGGCGTTTATTTTT
1 GCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTT
6441780 GTAAACGCTA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 39 0.57
42 29 0.43
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (41 bp):
GCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTAAGCACA
Found at i:6447754 original size:16 final size:15
Alignment explanation
Indices: 6447717--6447746 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6447707 GAAATAGTTT
6447717 CAAAA-AATAAACTC
1 CAAAACAATAAACTC
6447731 CAAAACAATAAACTC
1 CAAAACAATAAACTC
6447746 C
1 C
6447747 CTAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (15 bp):
CAAAACAATAAACTC
Found at i:6450879 original size:30 final size:30
Alignment explanation
Indices: 6450843--6450901 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
6450833 ATTTAAAGAG
*
6450843 ATTGCTTGCAAGTCAAGTTAAACAAAATAT
1 ATTGCTTACAAGTCAAGTTAAACAAAATAT
6450873 ATTGCTTACAAGTCAAGTTAAACAAAATA
1 ATTGCTTACAAGTCAAGTTAAACAAAATA
6450902 CATTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (30 bp):
ATTGCTTACAAGTCAAGTTAAACAAAATAT
Found at i:6459456 original size:295 final size:295
Alignment explanation
Indices: 6458926--6459519 Score: 1161
Period size: 295 Copynumber: 2.0 Consensus size: 295
6458916 AACACCACAA
6458926 ATTACAAGCAACAGCGGCGATTACCCAAAAGCGCCGCAAATGAGTTAGGTAAACGGTACCATTTT
1 ATTACAAGCAACAGCGGCGATTACCCAAAAGCGCCGCAAATGAGTTAGGTAAACGGTACCATTTT
6458991 CATGGTCAGATTCAAAGACATTAGTGGTGCTTCAATGAAAACGCCGCAAAAGACAAACATTAGCG
66 CATGGTCAGATTCAAAGACATTAGTGGTGCTTCAATGAAAACGCCGCAAAAGACAAACATTAGCG
6459056 GCGCTTTATCCAGAAGCGCCGCAAAAGTGATTAACAGACGATGCCGTATTGATTTACGTTTGATT
131 GCGCTTTATCCAGAAGCGCCGCAAAAGTGATTAACAGACGATGCCGTATTGATTTACGTTTGATT
6459121 ACATTAGTGGCGTTTATAAGTAAACGCCGCAAAAGATCCTGTATTCGCGGCGCGTTCACAAAAGC
196 ACATTAGTGGCGTTTATAAGTAAACGCCGCAAAAGATCCTGTATTCGCGGCGCGTTCACAAAAGC
6459186 GCCACAAATTTTTCCAGCGAACGACGCCGTTTTCT
261 GCCACAAATTTTTCCAGCGAACGACGCCGTTTTCT
*
6459221 ATTACAAGCAACAGCGGCGATTACCCAAAAGCGCCGCAAATGAGTTAGGTAAACGGTACCGTTTT
1 ATTACAAGCAACAGCGGCGATTACCCAAAAGCGCCGCAAATGAGTTAGGTAAACGGTACCATTTT
6459286 CATGGTCAGATTCAAAGACATTAGTGGTGCTTCAATGAAAACGCCGCAAAAGACAAACATTAGCG
66 CATGGTCAGATTCAAAGACATTAGTGGTGCTTCAATGAAAACGCCGCAAAAGACAAACATTAGCG
*
6459351 GCGCTTTATCCAGAAGCTCCGCAAAAGTGATTAACAGACGATGCCGTATTGATTTACGTTTGATT
131 GCGCTTTATCCAGAAGCGCCGCAAAAGTGATTAACAGACGATGCCGTATTGATTTACGTTTGATT
6459416 ACATTAGTGGCGTTTATAAGTAAACGCCGCAAAAGATCCTGTATTCGCGGCGCGTTCACAAAAGC
196 ACATTAGTGGCGTTTATAAGTAAACGCCGCAAAAGATCCTGTATTCGCGGCGCGTTCACAAAAGC
*
6459481 GCCACAAATTTTTCCCGCGAACGACGCCGTTTTCT
261 GCCACAAATTTTTCCAGCGAACGACGCCGTTTTCT
6459516 ATTA
1 ATTA
6459520 AATTTTATAG
Statistics
Matches: 296, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
295 296 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (295 bp):
ATTACAAGCAACAGCGGCGATTACCCAAAAGCGCCGCAAATGAGTTAGGTAAACGGTACCATTTT
CATGGTCAGATTCAAAGACATTAGTGGTGCTTCAATGAAAACGCCGCAAAAGACAAACATTAGCG
GCGCTTTATCCAGAAGCGCCGCAAAAGTGATTAACAGACGATGCCGTATTGATTTACGTTTGATT
ACATTAGTGGCGTTTATAAGTAAACGCCGCAAAAGATCCTGTATTCGCGGCGCGTTCACAAAAGC
GCCACAAATTTTTCCAGCGAACGACGCCGTTTTCT
Found at i:6460617 original size:21 final size:21
Alignment explanation
Indices: 6460591--6460641 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
6460581 TACGATTTAG
6460591 GGTTTAGGGGATAAGGGTTAT
1 GGTTTAGGGGATAAGGGTTAT
*
6460612 GGTTTAGGGGATAAGGGTTGT
1 GGTTTAGGGGATAAGGGTTAT
6460633 GGTTTAGGG
1 GGTTTAGGG
6460642 TCTAGGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (21 bp):
GGTTTAGGGGATAAGGGTTAT
Found at i:6462090 original size:22 final size:22
Alignment explanation
Indices: 6462063--6462109 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
6462053 GTCTTTCTAC
6462063 TTAGGTTTAATCAGTATAAAAT
1 TTAGGTTTAATCAGTATAAAAT
*
6462085 TTAGGTTTAATTAGTATAAAAT
1 TTAGGTTTAATCAGTATAAAAT
6462107 TTA
1 TTA
6462110 AGAAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (22 bp):
TTAGGTTTAATCAGTATAAAAT
Found at i:6463333 original size:18 final size:18
Alignment explanation
Indices: 6463310--6463354 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
6463300 AAACAAATTT
6463310 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
6463328 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
*
6463346 TAACTTATA
1 TAAATTATA
6463355 AATATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTATATAACTTACA
Found at i:6463339 original size:9 final size:9
Alignment explanation
Indices: 6463314--6463354 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
6463304 AAATTTTAAA
6463314 TTATATAAC
1 TTATATAAC
* *
6463323 TTACATAAA
1 TTATATAAC
6463332 TTATATAAC
1 TTATATAAC
*
6463341 TTACATAAC
1 TTATATAAC
6463350 TTATA
1 TTATA
6463355 AATATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
TTATATAAC
Found at i:6463585 original size:231 final size:232
Alignment explanation
Indices: 6463301--6463815 Score: 987
Period size: 232 Copynumber: 2.2 Consensus size: 232
6463291 TTTATTAGTA
*
6463301 AACAAATTTTAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATAT
1 AACAATTTTTAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATAT
6463366 ACATTTTTAATATATA-TTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTT
66 ACATTTTTAATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTT
6463430 ACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATAATACATATCTTAAA
131 ACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATAATACATATCTTAAA
6463495 TAACATACAATACATAAACTTACATATAAACTTGCAT
196 TAACATACAATACATAAACTTACATATAAACTTGCAT
* *
6463532 AACAATTTTTAAATTGTATAACTTACATAAAATATATAACTTACATAACTTATAAATATTTATAT
1 AACAATTTTTAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATAT
6463597 ACATTTTTAATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTT
66 ACATTTTTAATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTT
6463662 ACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATAATACATATCTTAAA
131 ACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATAATACATATCTTAAA
6463727 TAACATACAATACATAAACTTACATATAAACTTGCAT
196 TAACATACAATACATAAACTTACATATAAACTTGCAT
*
6463764 AATAATTTTTAAATTATATAACTTACATAAATTATATAACTTACATAACTTA
1 AACAATTTTTAAATTATATAACTTACATAAATTATATAACTTACATAACTTA
6463816 CATACCTTAC
Statistics
Matches: 277, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
231 78 0.28
232 199 0.72
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (232 bp):
AACAATTTTTAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATAT
ACATTTTTAATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTT
ACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATAATACATATCTTAAA
TAACATACAATACATAAACTTACATATAAACTTGCAT
Found at i:6463627 original size:17 final size:18
Alignment explanation
Indices: 6463607--6463640 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6463597 ACATTTTTAA
6463607 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
6463624 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
6463641 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:6463811 original size:9 final size:9
Alignment explanation
Indices: 6463781--6464223 Score: 433
Period size: 9 Copynumber: 49.2 Consensus size: 9
6463771 TTTAAATTAT
6463781 ATAACTTAC
1 ATAACTTAC
* *
6463790 ATAAATTAT
1 ATAACTTAC
6463799 ATAACTTAC
1 ATAACTTAC
6463808 ATAACTTAC
1 ATAACTTAC
*
6463817 ATACCTTAC
1 ATAACTTAC
* *
6463826 ATAAATTAA
1 ATAACTTAC
6463835 ATAACTTAC
1 ATAACTTAC
6463844 ATAACTTAC
1 ATAACTTAC
*
6463853 ATAACTTAA
1 ATAACTTAC
6463862 ATAACTTAC
1 ATAACTTAC
6463871 ATAA--TAC
1 ATAACTTAC
*
6463878 ATAACCTAC
1 ATAACTTAC
*
6463887 CTAACTTAC
1 ATAACTTAC
6463896 ATAACTTAC
1 ATAACTTAC
*
6463905 ATAACTTAA
1 ATAACTTAC
6463914 ATAACTTAC
1 ATAACTTAC
6463923 ATAA--TAC
1 ATAACTTAC
*
6463930 ATAACCTAC
1 ATAACTTAC
* *
6463939 CTAACTTAA
1 ATAACTTAC
* *
6463948 ATTATTTAC
1 ATAACTTAC
6463957 ATAA--TAC
1 ATAACTTAC
6463964 ATAACTTAGTAC
1 ATAAC-T--TAC
*
6463976 ATAATTTAC
1 ATAACTTAC
6463985 ATAA--TAC
1 ATAACTTAC
6463992 ATAACTTATAC
1 ATAAC-T-TAC
6464003 ATAACTTAC
1 ATAACTTAC
** *
6464012 ATATTTTTTTC
1 ATA--ACTTAC
6464023 -TAAATTGCTTAC
1 AT-AA---CTTAC
* *
6464035 ATAAATTAT
1 ATAACTTAC
6464044 ATAACTTAC
1 ATAACTTAC
6464053 ATAACTTAC
1 ATAACTTAC
* *
6464062 ATAAATTAA
1 ATAACTTAC
6464071 ATAACTTAC
1 ATAACTTAC
6464080 ATAACTTAC
1 ATAACTTAC
*
6464089 ATAACATAC
1 ATAACTTAC
*
6464098 ATAACTTAA
1 ATAACTTAC
6464107 ATAACTTAC
1 ATAACTTAC
6464116 ATAACTTAC
1 ATAACTTAC
*
6464125 ATATCTTAC
1 ATAACTTAC
6464134 ATAACTTAC
1 ATAACTTAC
* *
6464143 ATAAATTAA
1 ATAACTTAC
6464152 ATAACTTAC
1 ATAACTTAC
6464161 ATAACTTAC
1 ATAACTTAC
*
6464170 ATAAATTAC
1 ATAACTTAC
6464179 ATAACTTAC
1 ATAACTTAC
6464188 ATAACTTAC
1 ATAACTTAC
6464197 ATAA--TAC
1 ATAACTTAC
6464204 ATAACCTT-C
1 ATAA-CTTAC
*
6464213 CTAACTTAC
1 ATAACTTAC
6464222 AT
1 AT
6464224 TATTGTCTAA
Statistics
Matches: 356, Mismatches: 54, Indels: 48
0.78 0.12 0.10
Matches are distributed among these distances:
7 35 0.10
8 3 0.01
9 289 0.81
10 3 0.01
11 13 0.04
12 12 0.03
13 1 0.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAACTTAC
Found at i:6463894 original size:232 final size:231
Alignment explanation
Indices: 6463417--6464146 Score: 664
Period size: 232 Copynumber: 3.1 Consensus size: 231
6463407 ATTTATCAAT
6463417 CATAGCATAACTTACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATAA
1 CATA-CATAACTTACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATAA
*
6463482 TACATATCTTAAATAACATACAATACATAAACTTACATATAAACTTGCATAACAATTTTTAAATT
65 TACATATCTTAAATAACATACAATACATAAACTTACATATAAACTTGCATAATAATTTTTAAATT
* * * * * * **
6463547 GTATAACTTACATAAAATATATAACTTACATAACTTATAAATATTTATATACATT-TTTAA--TA
130 ATATAACTTACATAAATTATATAACTTACATAAC-T-TACATAATTAAATAAATTAAATAACTTA
* ** * *** * * **
6463609 TATATTTTTA-A-AA-TCTATATTTTTTTCAAAATTTATCAA
193 CATA-ACTTACATAACT-TAAATAACTTACATAATACAT-AA
6463648 TCATAGCATAACTTACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATA
1 -CATA-CATAACTTACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATA
6463713 ATACATATCTTAAATAACATACAATACATAAACTTACATATAAACTTGCATAATAATTTTTAAAT
64 ATACATATCTTAAATAACATACAATACATAAACTTACATATAAACTTGCATAATAATTTTTAAAT
* *
6463778 TATATAACTTACATAAATTATATAACTTACATAACTTACATACCTTACATAAATTAAATAACTTA
129 TATATAACTTACATAAATTATATAACTTACATAACTTACATA-ATTAAATAAATTAAATAACTTA
6463843 CATAACTTACATAACTTAAATAACTTACATAATACATAA
193 CATAACTTACATAACTTAAATAACTTACATAATACATAA
* * * *
6463882 CCTACCTAACTTACATAACTTACATAACTTAAAT-AACTTACATAATACATAACCTACCTA-ACT
1 CATACATAACTTACATAAC-T-CA-AA-TT-TATCAA--T-CAT-AT-CATAACTTA--TATA--
* * ** * *
6463945 TAAATTATTTACATAATACATAACTTAGTACATAATTTACATAATACAT-AACTTATACAT-AAC
52 T-AA--ACTTACATAATACATATCTTA--A-ATAACATAC--AATACATAAACTTACATATAAAC
* * **
6464008 TTACAT-AT--TTTTT---TCTAAATTGCTTACATAAATTATATAACTTACATAACTTACATAAA
109 TTGCATAATAATTTTTAAAT-TATATAACTTACATAAATTATATAACTTACATAACTTACAT-AA
* * * *
6464067 TTAAATAACTTACATAACTTACATAACATACATAACTTAAATAACTTACATAACTTACATAT
172 TTAAATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTACATAA--TACATAA
*
6464129 CTTACATAACTTACATAA
1 CATACATAACTTACATAA
6464147 ATTAAATAAC
Statistics
Matches: 423, Mismatches: 42, Indels: 51
0.82 0.08 0.10
Matches are distributed among these distances:
230 5 0.01
231 10 0.02
232 178 0.42
233 7 0.02
234 10 0.02
235 17 0.04
236 5 0.01
237 2 0.00
238 1 0.00
239 3 0.01
240 2 0.00
241 8 0.02
242 1 0.00
243 2 0.00
244 2 0.00
245 89 0.21
246 1 0.00
247 46 0.11
249 3 0.01
250 15 0.04
251 9 0.02
252 7 0.02
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (231 bp):
CATACATAACTTACATAACTCAAATTTATCAATCATATCATAACTTATATATAAACTTACATAAT
ACATATCTTAAATAACATACAATACATAAACTTACATATAAACTTGCATAATAATTTTTAAATTA
TATAACTTACATAAATTATATAACTTACATAACTTACATAATTAAATAAATTAAATAACTTACAT
AACTTACATAACTTAAATAACTTACATAATACATAA
Found at i:6469766 original size:21 final size:21
Alignment explanation
Indices: 6469737--6469784 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
6469727 CAACAACTTA
* * *
6469737 AAGCTGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
6469758 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
6469779 AAGCAG
1 AAGCAG
6469785 CGATAGAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.46, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:6470273 original size:42 final size:43
Alignment explanation
Indices: 6470201--6470296 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 43
6470191 CATACCAAAC
* *
6470201 AGTGGCGTTTGTGAAATAAGCGCCGCTAAAGAACACTACTTTT
1 AGTGGCGTTTTTGAAACAAGCGCCGCTAAAGAACACTACTTTT
*
6470244 AGTGGCGTTTTTG-AACAAGCGCCGCTAAAGAACATTACTTTT
1 AGTGGCGTTTTTGAAACAAGCGCCGCTAAAGAACACTACTTTT
*
6470286 AGAGGCGTTTT
1 AGTGGCGTTTT
6470297 ATTCCAAAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 37 0.76
43 12 0.24
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (43 bp):
AGTGGCGTTTTTGAAACAAGCGCCGCTAAAGAACACTACTTTT
Found at i:6470396 original size:42 final size:42
Alignment explanation
Indices: 6470217--6470510 Score: 346
Period size: 43 Copynumber: 7.0 Consensus size: 42
6470207 GTTTGTGAAA
* **
6470217 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGTGGCGTTTTTGAAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TCC
* *
6470260 -AAGCGCCGCTAAAGAACATTA-CTTTTAGAGGCGTTTTATTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCC
* * ** * *
6470302 AAAGCACCGCTAAAGAACATGAGATTTCGCGGTGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTCC
*
6470345 TAAGTGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
*
6470387 TAAGCGCCGCTAAAGAACATGATCTTTCGCGGCGTTTTTT-C
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* *
6470428 TATGCGCCGCTACAGAACATGATCTTTAGCGGCGTTTATTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTCC
*
6470471 TTAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
6470511 TGTGTAAGCA
Statistics
Matches: 220, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
41 36 0.16
42 87 0.40
43 93 0.42
44 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
Found at i:6470495 original size:126 final size:127
Alignment explanation
Indices: 6470217--6470510 Score: 355
Period size: 126 Copynumber: 2.3 Consensus size: 127
6470207 GTTTGTGAAA
* * *
6470217 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGTGGCGTTTTTGAACAAGCGCCGCTAAAGAACATT
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TACAAGCGCCGCTAAAGAACATG
* * *
6470280 ACTTTTAGAGGCGTTTTATTCCAAAGCACCGCTAAAGAACATGAGATTTCGCGGTGTTTTTTTCC
63 ACTTTTAGAGGCGTTTTATTCCAAAGCACCGCTAAAGAACATGAGATTTAGCGGCGTTTATTTCC
* *
6470345 TAAGTGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGA-
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTAC-AAGCGCCGCTAAAGAACATGAC
* * * * * * **
6470409 TCTTTCGCGGCGTTTT-TT-CTATGCGCCGCTACAGAACATGATCTTTAGCGGCGTTTATTTCC
65 T-TTTAGAGGCGTTTTATTCCAAAGCACCGCTAAAGAACATGAGATTTAGCGGCGTTTATTTCC
*
6470471 TTAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
6470511 TGTGTAAGCA
Statistics
Matches: 144, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
126 73 0.51
127 5 0.03
128 65 0.45
129 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (127 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACAAGCGCCGCTAAAGAACATGACT
TTTAGAGGCGTTTTATTCCAAAGCACCGCTAAAGAACATGAGATTTAGCGGCGTTTATTTCC
Found at i:6472459 original size:17 final size:17
Alignment explanation
Indices: 6472439--6472474 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
6472429 GATTGTATTG
6472439 ATTTACATGTTGTACGC
1 ATTTACATGTTGTACGC
*
6472456 ATTTACATGTTGTATGC
1 ATTTACATGTTGTACGC
6472473 AT
1 AT
6472475 CAAGCTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (17 bp):
ATTTACATGTTGTACGC
Found at i:6482870 original size:16 final size:16
Alignment explanation
Indices: 6482837--6482870 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6482827 TGAGAGTGTT
* *
6482837 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
6482853 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
6482869 AA
1 AA
6482871 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:6485699 original size:21 final size:21
Alignment explanation
Indices: 6485673--6485713 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6485663 AGACGAGCAA
* *
6485673 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
6485694 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
6485714 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:6487652 original size:16 final size:16
Alignment explanation
Indices: 6487619--6487652 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6487609 GGAGATTGTT
* *
6487619 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
6487635 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
6487651 AA
1 AA
6487653 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:6492857 original size:18 final size:18
Alignment explanation
Indices: 6492834--6492869 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6492824 TTTTTTATTC
*
6492834 TTTTTTTAAATAAAATTA
1 TTTTTTAAAATAAAATTA
*
6492852 TTTTTTAAAATGAAATTA
1 TTTTTTAAAATAAAATTA
6492870 GTGACCAAAA
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTTTAAAATAAAATTA
Found at i:6505834 original size:9 final size:9
Alignment explanation
Indices: 6505820--6505856 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
6505810 TATAGTTTGA
6505820 TATTCGAAT
1 TATTCGAAT
6505829 TATTCGAAT
1 TATTCGAAT
6505838 TATTC-AAGT
1 TATTCGAA-T
6505847 TATTCGAAT
1 TATTCGAAT
6505856 T
1 T
6505857 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6509270 original size:42 final size:41
Alignment explanation
Indices: 6509195--6509305 Score: 136
Period size: 41 Copynumber: 2.7 Consensus size: 41
6509185 GTTTACAAAC
* * *
6509195 AAAAATGCCGATAAAGA--ATGGTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGATAAAGACCATGTTCTTTAGAGGCGCTTAG-A
*
6509235 AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGA
1 AAAAACGCCGATAAAGACCATGTTCTTTAGAGGCGCTTAGA
* * *
6509276 GAAAACACCGTTAAAGACCATGTTCTTTAG
1 AAAAACGCCGATAAAGACCATGTTCTTTAG
6509306 CGGTGTACAT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 15 0.24
41 28 0.45
42 19 0.31
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (41 bp):
AAAAACGCCGATAAAGACCATGTTCTTTAGAGGCGCTTAGA
Found at i:6509293 original size:41 final size:42
Alignment explanation
Indices: 6509216--6509305 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 42
6509206 TAAAGAATGG
* *
6509216 TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGT
1 TCTTTAGAGGCGCTTAGAAAAAAACACCGCTAAAGACCATGT
* *
6509258 TCTTTAGAGGCGCTTAG-AGAAAACACCGTTAAAGACCATGT
1 TCTTTAGAGGCGCTTAGAAAAAAACACCGCTAAAGACCATGT
6509299 TCTTTAG
1 TCTTTAG
6509306 CGGTGTACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 28 0.64
42 16 0.36
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
TCTTTAGAGGCGCTTAGAAAAAAACACCGCTAAAGACCATGT
Found at i:6509783 original size:21 final size:21
Alignment explanation
Indices: 6509720--6509785 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
6509710 CTCTATTCTA
* * *
6509720 CTTCTCTCACTGCAGCCTCTA
1 CTTCCCTCGCTGCAGCCTCTG
*
6509741 CTTCCCTCGCTGCAGCCCCTG
1 CTTCCCTCGCTGCAGCCTCTG
*
6509762 CTTCCCTCGCTGCCGCCTCTG
1 CTTCCCTCGCTGCAGCCTCTG
6509783 CTT
1 CTT
6509786 TAAGTTGTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.06, C:0.48, G:0.15, T:0.30
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCTG
Found at i:6515018 original size:29 final size:29
Alignment explanation
Indices: 6514985--6515048 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
6514975 TAGTCCCTTT
* *
6514985 TATTTTAT-TTTTCTTTCAATTTCGCCCTA
1 TATTTTATGTTTTATTTCAATTTAGCCC-A
*
6515014 TATTTT-TGTTTTATTTCGATTTAGCCCA
1 TATTTTATGTTTTATTTCAATTTAGCCCA
6515042 TATTTTA
1 TATTTTA
6515049 GCAATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (29 bp):
TATTTTATGTTTTATTTCAATTTAGCCCA
Found at i:6515068 original size:3 final size:3
Alignment explanation
Indices: 6515060--6515137 Score: 79
Period size: 3 Copynumber: 26.3 Consensus size: 3
6515050 CAATTTTATG
* *
6515060 TTA TTA TTA TTA TTA TTA TTA TT- TTAA ATA TTA TTA TTA GT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* ** *
6515104 CTA TTA TTA TTA TGG TTA TTA TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6515138 CGTTAGTATT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
2 3 0.05
3 56 0.93
4 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:6532097 original size:40 final size:40
Alignment explanation
Indices: 6532053--6532152 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
6532043 CCGTTGTATT
6532053 TTATTTTTTGCGGCGTTTTTCCTGGAAACGCCGCTAATGC
1 TTATTTTTTGCGGCGTTTTTCCTGGAAACGCCGCTAATGC
* * ** *
6532093 TTATTTTTTGAGGCG-ATTTCCTTTAAGCGCCGCTAATGC
1 TTATTTTTTGCGGCGTTTTTCCTGGAAACGCCGCTAATGC
* **
6532132 TCGATTTTTACCGGCGTTTTT
1 T-TATTTTTTGCGGCGTTTTT
6532153 TGTATAAACG
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
39 21 0.44
40 24 0.50
41 3 0.06
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (40 bp):
TTATTTTTTGCGGCGTTTTTCCTGGAAACGCCGCTAATGC
Found at i:6532113 original size:39 final size:40
Alignment explanation
Indices: 6532053--6532132 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 40
6532043 CCGTTGTATT
* *
6532053 TTATTTTTTGCGGCGTTTTTCCTGGAAACGCCGCTAATGC
1 TTATTTTTTGAGGCGTATTTCCTGGAAACGCCGCTAATGC
** *
6532093 TTATTTTTTGAGGCG-ATTTCCTTTAAGCGCCGCTAATGC
1 TTATTTTTTGAGGCGTATTTCCTGGAAACGCCGCTAATGC
6532132 T
1 T
6532133 CGATTTTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 21 0.60
40 14 0.40
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (40 bp):
TTATTTTTTGAGGCGTATTTCCTGGAAACGCCGCTAATGC
Done.