Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 15 of 18
Found at i:6204873 original size:39 final size:39
Alignment explanation
Indices: 6204814--6204891 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
6204804 CTACTAAATT
* * *
6204814 TTGTGCTGATTTTTAGCACATG-AGGGTTATGATTTTGGG
1 TTGTGCTGATTTTTAACACATGTA-AGCTATGATTTTGGG
*
6204853 TTGTGCTTATTTTTAACACATGTAAGCTATGATTTTGGG
1 TTGTGCTGATTTTTAACACATGTAAGCTATGATTTTGGG
6204892 CTATTGCTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.97
40 1 0.03
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGTGCTGATTTTTAACACATGTAAGCTATGATTTTGGG
Found at i:6208481 original size:28 final size:27
Alignment explanation
Indices: 6208345--6208494 Score: 93
Period size: 28 Copynumber: 5.4 Consensus size: 27
6208335 ATGTAACAAT
* * *
6208345 TTTTTTATCATGATGTGTGATAATTACA
1 TTTTTTAACATAATGTGTAATAATTA-A
* * * *
6208373 TCTTTTAACATTACGTATAATAATTAA
1 TTTTTTAACATAATGTGTAATAATTAA
* * * * *
6208400 ATCTTCAACATAATATATAATAATTATA
1 TTTTTTAACATAATGTGTAATAATTA-A
* * * * *
6208428 TATTTTTTACATGATATGTGACAATTATA
1 T-TTTTTAACATAATGTGTAATAATTA-A
*
6208457 TTTTTTAACATAACGTGTAATAATTAA
1 TTTTTTAACATAATGTGTAATAATTAA
*
6208484 ATTTTTAACAT
1 TTTTTTAACAT
6208495 GACACATCTT
Statistics
Matches: 92, Mismatches: 28, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
27 31 0.34
28 40 0.43
29 21 0.23
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (27 bp):
TTTTTTAACATAATGTGTAATAATTAA
Found at i:6214698 original size:17 final size:18
Alignment explanation
Indices: 6214664--6214703 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
6214654 GTAGAGAAAT
6214664 TTAAAAATTTAAAAAAAA
1 TTAAAAATTTAAAAAAAA
* *
6214682 TTAAAAA-TTGAATAAAA
1 TTAAAAATTTAAAAAAAA
6214699 TTAAA
1 TTAAA
6214704 TAGAGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
TTAAAAATTTAAAAAAAA
Found at i:6228175 original size:117 final size:116
Alignment explanation
Indices: 6228029--6228405 Score: 303
Period size: 117 Copynumber: 3.2 Consensus size: 116
6228019 ATATAAAACC
* * * *
6228029 TACTAAATTAATTAAATGCTTAATAACTAAAACATTTTTTCAATTCAAGTTGTCAAATTATATAA
1 TACTAATTTAATTAATTGCTTAATTACTAAAACATTTTTTCAATTCAA-TTGTCAAATTATTTAA
6228094 TTAATTTAATAAAATCTTAATTAATTTAAATATTTTTAAATTTTACTAAATT
65 TTAATTTAATAAAATCTTAATTAATTTAAATATTTTTAAATTTTACTAAATT
* * ** * ** * **
6228146 TACTATTTTAATTAATTGTTTAATTACTAATGCGTTACCTT-AATTCATTTAACTAAATTATTTA
1 TACTAATTTAATTAATTGCTTAATTACTAAAACATT-TTTTCAATTCAATTGTC-AAATTATTTA
* * * ** * * * * * *
6228210 ATTAACTGATTAGCACCTTCAGTAATTTAAATATTTTT-TATTTAAAT-AATAT
64 ATTAATTTAATAAAATCTTAATTAATTTAAATATTTTTAAATTTTACTAAAT-T
* *
6228262 TACTAATTTACTTAATTGCTTAATTACTAAAACATTGTTTGTTTGCACATGAT-AATTAGTTAAA
1 TACTAATTTAATTAATTGCTTAATTACTAAAACA---TTT-TTT-CA-AT--TCAATT-GTCAAA
* * * * * * *
6228326 TTATTTCACTAATTTAATAAAATCTTAATCAATTTGAATAATTATAAATTTTACTATATT
57 TTATTTAATTAATTTAATAAAATCTTAATTAATTTAAATATTTTTAAATTTTACTAAATT
6228386 TACTAATTTAATTAATTGCT
1 TACTAATTTAATTAATTGCT
6228406 AAAAATGTTA
Statistics
Matches: 189, Mismatches: 56, Indels: 23
0.71 0.21 0.09
Matches are distributed among these distances:
115 3 0.02
116 38 0.20
117 73 0.39
118 2 0.01
119 4 0.02
121 1 0.01
122 2 0.01
123 37 0.20
124 27 0.14
125 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (116 bp):
TACTAATTTAATTAATTGCTTAATTACTAAAACATTTTTTCAATTCAATTGTCAAATTATTTAAT
TAATTTAATAAAATCTTAATTAATTTAAATATTTTTAAATTTTACTAAATT
Found at i:6229911 original size:26 final size:27
Alignment explanation
Indices: 6229870--6229920 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
6229860 ATATAAGTTT
*
6229870 ATTTAATTTAAAATAA-AAATATAAAA
1 ATTTAATTTAAAATAACAAAAATAAAA
6229896 ATTTAA-TTAAATATAACAAAAATAA
1 ATTTAATTTAAA-ATAACAAAAATAA
6229921 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 10 0.45
27 7 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
ATTTAATTTAAAATAACAAAAATAAAA
Found at i:6230608 original size:20 final size:20
Alignment explanation
Indices: 6230583--6230623 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6230573 AGATAATTAT
*
6230583 TTAAAATGTAATTATTTAAA
1 TTAAAATATAATTATTTAAA
*
6230603 TTAAAATATAATTTTTTAAA
1 TTAAAATATAATTATTTAAA
6230623 T
1 T
6230624 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAAAATATAATTATTTAAA
Found at i:6230638 original size:19 final size:19
Alignment explanation
Indices: 6230616--6230655 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6230606 AAATATAATT
*
6230616 TTTTAAATAAATAAAAATA
1 TTTTAAACAAATAAAAATA
* *
6230635 TTTTGAACAAATAAAATTA
1 TTTTAAACAAATAAAAATA
6230654 TT
1 TT
6230656 AAATATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
TTTTAAACAAATAAAAATA
Found at i:6237592 original size:2 final size:2
Alignment explanation
Indices: 6237585--6237627 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6237575 GCAAGTGTTT
6237585 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6237627 T
1 T
6237628 GACTTTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6248462 original size:15 final size:16
Alignment explanation
Indices: 6248436--6248465 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6248426 NNNNNNNNTT
6248436 TTAAAAATTAAAATTA
1 TTAAAAATTAAAATTA
6248452 TTAAAAA-TAAAATT
1 TTAAAAATTAAAATT
6248466 CACATAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAAATTAAAATTA
Found at i:6252162 original size:36 final size:36
Alignment explanation
Indices: 6252088--6252163 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
6252078 TCACTCTTTG
* *
6252088 TGAACTTCTTGAGAAAGCCCATTGTCCTAATGTTTT
1 TGAACTTCTTGAGAAAGCCCATTATCCTAATGTATT
* ** *
6252124 TGAACTTCTTGAGATAGCCCATTATTTTTATGTATT
1 TGAACTTCTTGAGAAAGCCCATTATCCTAATGTATT
6252160 TGAA
1 TGAA
6252164 ACAGATTGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (36 bp):
TGAACTTCTTGAGAAAGCCCATTATCCTAATGTATT
Found at i:6255456 original size:31 final size:32
Alignment explanation
Indices: 6255420--6255492 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
6255410 CGACTCCTGA
*
6255420 CCCGATT-CCCCT-CAACCCCCCTCCCACGAGT
1 CCCGATTCCCCCTAC-ACCCCCCTCCCACGAAT
*
6255451 CCCGATTCCCCCTACCCCCCCCTCCCACGAAT
1 CCCGATTCCCCCTACACCCCCCTCCCACGAAT
*
6255483 CCCGACTCCC
1 CCCGATTCCC
6255493 GACCCGATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 7 0.19
32 29 0.78
33 1 0.03
ACGTcount: A:0.15, C:0.62, G:0.08, T:0.15
Consensus pattern (32 bp):
CCCGATTCCCCCTACACCCCCCTCCCACGAAT
Found at i:6255529 original size:29 final size:29
Alignment explanation
Indices: 6255496--6255555 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
6255486 GACTCCCGAC
6255496 CCGATTCCCCCCA-ACCCCCTCCCACTAGT
1 CCGATTCCCCCCACACCCCCTCCCAC-AGT
* *
6255525 CCGATTCCCCCTACCCCCCCTCCCACAGT
1 CCGATTCCCCCCACACCCCCTCCCACAGT
6255554 CC
1 CC
6255556 CACGAGTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.15, C:0.62, G:0.07, T:0.17
Consensus pattern (29 bp):
CCGATTCCCCCCACACCCCCTCCCACAGT
Found at i:6255567 original size:73 final size:75
Alignment explanation
Indices: 6255392--6255550 Score: 270
Period size: 75 Copynumber: 2.2 Consensus size: 75
6255382 ATTCTCCCGG
* *
6255392 CCCCCCTCCCACGAATCCCGACTCCTGACCCGATTCCCCTCAACCCCCCTCCCACGAGTCCCGAT
1 CCCCCCTCCCACGAATCCCGACTCCCGACCCGATTCCCCCCAACCCCCCTCCCACGAGTCCCGAT
6255457 TCCCCCTACC
66 TCCCCCTACC
*
6255467 CCCCCCTCCCACGAATCCCGACTCCCGACCCGATTCCCCCCAA-CCCCCTCCCACTAGT-CCGAT
1 CCCCCCTCCCACGAATCCCGACTCCCGACCCGATTCCCCCCAACCCCCCTCCCACGAGTCCCGAT
6255530 TCCCCCTA-C
66 TCCCCCTACC
6255539 CCCCCCTCCCAC
1 CCCCCCTCCCAC
6255551 AGTCCCACGA
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
72 13 0.16
73 13 0.16
74 14 0.17
75 41 0.51
ACGTcount: A:0.16, C:0.61, G:0.08, T:0.15
Consensus pattern (75 bp):
CCCCCCTCCCACGAATCCCGACTCCCGACCCGATTCCCCCCAACCCCCCTCCCACGAGTCCCGAT
TCCCCCTACC
Found at i:6257088 original size:2 final size:2
Alignment explanation
Indices: 6257075--6257113 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
6257065 CAGCCACATT
* *
6257075 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6257114 TTCTTGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6261775 original size:17 final size:17
Alignment explanation
Indices: 6261753--6261789 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6261743 TTACTATTAC
* *
6261753 ATATATATTTTTAATAT
1 ATATATACTTTAAATAT
6261770 ATATATACTTTAAATAT
1 ATATATACTTTAAATAT
6261787 ATA
1 ATA
6261790 AAGATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATACTTTAAATAT
Found at i:6272945 original size:25 final size:25
Alignment explanation
Indices: 6272924--6273017 Score: 161
Period size: 25 Copynumber: 3.8 Consensus size: 25
6272914 ACTTGACATT
6272924 TGAAGTTGTTAATACAAGTGACACC
1 TGAAGTTGTTAATACAAGTGACACC
6272949 TGAAGTTGTTAATACAAGTGACACC
1 TGAAGTTGTTAATACAAGTGACACC
6272974 TGAAGTTGTTAATACAAGTGACACC
1 TGAAGTTGTTAATACAAGTGACACC
* * *
6272999 TAAAATTGTTAATATAAGT
1 TGAAGTTGTTAATACAAGT
6273018 CCAAATGGGA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (25 bp):
TGAAGTTGTTAATACAAGTGACACC
Found at i:6273389 original size:68 final size:68
Alignment explanation
Indices: 6273316--6273448 Score: 248
Period size: 68 Copynumber: 2.0 Consensus size: 68
6273306 GTTGATGAGC
6273316 AAAATAAAGAATTTCTTTGCATTACCTCTTATAAGATGGGCTAAAAGACCATCCATGAGAAGCTG
1 AAAATAAAGAATTTCTTTGCATTACCTCTTATAAGATGGGCTAAAAGACCATCCATGAGAAGCTG
6273381 AAA
66 AAA
* *
6273384 AAAATAAAGAATTTCTTTGCATTACTTCTTATAAGATGGGCTAGAAGACCATCCATGAGAAGCTG
1 AAAATAAAGAATTTCTTTGCATTACCTCTTATAAGATGGGCTAAAAGACCATCCATGAGAAGCTG
6273449 GAAGCTTCAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (68 bp):
AAAATAAAGAATTTCTTTGCATTACCTCTTATAAGATGGGCTAAAAGACCATCCATGAGAAGCTG
AAA
Found at i:6277278 original size:15 final size:15
Alignment explanation
Indices: 6277260--6277313 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
6277250 TATCTTGATA
6277260 AATTAATTTATAATT
1 AATTAATTTATAATT
*
6277275 AATTAATGTATGAATT
1 AATTAATTTAT-AATT
*
6277291 AA-TAAATTATTAATT
1 AATTAATTTA-TAATT
*
6277306 TATTAATT
1 AATTAATT
6277314 AAATAATATC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 20 0.65
16 11 0.35
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (15 bp):
AATTAATTTATAATT
Found at i:6277295 original size:23 final size:22
Alignment explanation
Indices: 6277264--6277320 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
6277254 TTGATAAATT
*
6277264 AATTTATAATTAATTAATGTATG
1 AATTAATAATT-ATTAATGTATG
* *
6277287 AATTAATAAATTATTAATTTATT
1 AATTAAT-AATTATTAATGTATG
6277310 AATTAAATAAT
1 AATT-AATAAT
6277321 ATCTTGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
AATTAATAATTATTAATGTATG
Found at i:6279681 original size:38 final size:38
Alignment explanation
Indices: 6279639--6279715 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
6279629 TTGCTGAATT
* * *
6279639 TGAATCTGCGCGTATTGAGAATGACTGAATTGCTAGTA
1 TGAATCTGCACATATTGAGAATGACTGAACTGCTAGTA
* *
6279677 TGAATCTGCACATATTGAGAATGATTGAACTGCTGGTA
1 TGAATCTGCACATATTGAGAATGACTGAACTGCTAGTA
6279715 T
1 T
6279716 TAGTTGTCGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (38 bp):
TGAATCTGCACATATTGAGAATGACTGAACTGCTAGTA
Found at i:6282799 original size:30 final size:30
Alignment explanation
Indices: 6282763--6282822 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
6282753 TTGGTTTGGT
*
6282763 TTGAGACAATAAT-GTCTTGTGGAGGAGATG
1 TTGAGACAAT-ATCATCTTGTGGAGGAGATG
*
6282793 TTGAGACGATATCATCTTGTGGAGGAGATG
1 TTGAGACAATATCATCTTGTGGAGGAGATG
6282823 GTTCGATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.28, C:0.08, G:0.33, T:0.30
Consensus pattern (30 bp):
TTGAGACAATATCATCTTGTGGAGGAGATG
Found at i:6283737 original size:261 final size:261
Alignment explanation
Indices: 6283261--6283758 Score: 811
Period size: 261 Copynumber: 1.9 Consensus size: 261
6283251 TTACATTTAC
6283261 AAGAATGAAGCTTCGGCTTTCATTCTCCAAAAGATTCTTGGATTAATTTGAAGAACCAATAATAT
1 AAGAATGAAGCTTCGGCTTTCATTCTCCAAAAGATTCTTGGATTAATTTGAAGAACCAATAATAT
* *
6283326 ATAGACTTTATGTTTTTTTTTTCTTATAAAATGGTTGCATTTTAATTTAATAATTAAAAATTATT
66 ATAGACTTAATG-TTTTATTTTCTTATAAAATGGTTGCATTTTAATTTAATAATTAAAAATTATT
* * *
6283391 AATTAAATTATATATAACATATTTTGTTTAGATAATATCGATTAATAATGAAATTTATCTACATA
130 AATTAAATTATACATAAAATATTTTGTTTAGATAATATCGATTAATAATGAAATTTATCAACATA
**
6283456 TCTACCCGTTCACATACATTCTCACTCACACATTATATTATAAAATATTAAAATTTTATTTACTA
195 TCTACCCACTCACATACATTCTCACTCACACATTATATTATAAAATATTAAAATTTTATTTACTA
6283521 TT
260 TT
*
6283523 AAGAATGAAGCTTCGGCTTTCA-TCTTCCAAAAGATTCTTGGATTAATTTGAAGAACCAATATTA
1 AAGAATGAAGCTTCGGCTTTCATTC-TCCAAAAGATTCTTGGATTAATTTGAAGAACCAATAATA
* *
6283587 TATAGACTTAATG-TTTATTTTCTTGTGAAAATGGTTGCATTTTAATTTAATAATTCAAAATTAT
65 TATAGACTTAATGTTTTATTTTCTTAT-AAAATGGTTGCATTTTAATTTAATAATTAAAAATTAT
* * *
6283651 TAATTAATTTATACATAAAATCTTTTGTTTAGATAATATCGATTAATAATGAAATTTATCAATAT
129 TAATTAAATTATACATAAAATATTTTGTTTAGATAATATCGATTAATAATGAAATTTATCAACAT
* * *
6283716 ATCTACCTACTCACGTACATTCTCGCTCACACATTATATTATA
194 ATCTACCCACTCACATACATTCTCACTCACACATTATATTATA
6283759 TGTATCACAT
Statistics
Matches: 218, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
260 11 0.05
261 135 0.62
262 72 0.33
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (261 bp):
AAGAATGAAGCTTCGGCTTTCATTCTCCAAAAGATTCTTGGATTAATTTGAAGAACCAATAATAT
ATAGACTTAATGTTTTATTTTCTTATAAAATGGTTGCATTTTAATTTAATAATTAAAAATTATTA
ATTAAATTATACATAAAATATTTTGTTTAGATAATATCGATTAATAATGAAATTTATCAACATAT
CTACCCACTCACATACATTCTCACTCACACATTATATTATAAAATATTAAAATTTTATTTACTAT
T
Found at i:6290038 original size:17 final size:17
Alignment explanation
Indices: 6290011--6290044 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6290001 ATATCAAAAT
6290011 AATCAAATTTACTAATTG
1 AATCAAATTTAC-AATTG
6290029 AATC-AATTTACAATTG
1 AATCAAATTTACAATTG
6290045 TTAGAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (17 bp):
AATCAAATTTACAATTG
Found at i:6296683 original size:21 final size:20
Alignment explanation
Indices: 6296659--6296697 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6296649 ATTTTACATT
6296659 TTTTTTAAATTTAAAATATAA
1 TTTTTT-AATTTAAAATATAA
*
6296680 TTTTTTATTTTAAAATAT
1 TTTTTTAATTTAAAATAT
6296698 TTTATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTAATTTAAAATATAA
Found at i:6296700 original size:15 final size:14
Alignment explanation
Indices: 6296681--6296719 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
6296671 AAAATATAAT
6296681 TTTTTATTTTAAAA
1 TTTTTATTTTAAAA
*
6296695 TATTTTATATTAAAA
1 T-TTTTATTTTAAAA
*
6296710 TTATTATTTT
1 TTTTTATTTT
6296720 TAATATCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTATTTTAAAA
Found at i:6298092 original size:28 final size:28
Alignment explanation
Indices: 6298058--6298112 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
6298048 GATTGAAATT
*
6298058 TTATTTATATTTAATGCAATTTATTTGC
1 TTATTTATACTTAATGCAATTTATTTGC
* * *
6298086 TTATTTATGCTTGATGTAATTTATTTG
1 TTATTTATACTTAATGCAATTTATTTG
6298113 TTTGTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.58
Consensus pattern (28 bp):
TTATTTATACTTAATGCAATTTATTTGC
Found at i:6302094 original size:21 final size:21
Alignment explanation
Indices: 6302070--6302131 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
6302060 GGGTTGGTTG
6302070 TTGGGGTTAAGCATTGGGCCA
1 TTGGGGTTAAGCATTGGGCCA
* ***
6302091 TT--GG---AGTATTGGGTTG
1 TTGGGGTTAAGCATTGGGCCA
6302107 TTGGGGTTAAGCATTGGGCCA
1 TTGGGGTTAAGCATTGGGCCA
6302128 TTGG
1 TTGG
6302132 AGTATTGGGT
Statistics
Matches: 28, Mismatches: 8, Indels: 10
0.61 0.17 0.22
Matches are distributed among these distances:
16 10 0.36
18 2 0.07
19 2 0.07
21 14 0.50
ACGTcount: A:0.16, C:0.10, G:0.40, T:0.34
Consensus pattern (21 bp):
TTGGGGTTAAGCATTGGGCCA
Found at i:6302106 original size:37 final size:37
Alignment explanation
Indices: 6302065--6302142 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
6302055 TTTGGGGGTT
6302065 GGTTGTTGGGGTTAAGCATTGGGCCATTGGAGTATTG
1 GGTTGTTGGGGTTAAGCATTGGGCCATTGGAGTATTG
6302102 GGTTGTTGGGGTTAAGCATTGGGCCATTGGAGTATTG
1 GGTTGTTGGGGTTAAGCATTGGGCCATTGGAGTATTG
6302139 GGTT
1 GGTT
6302143 CAATAGAGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.15, C:0.08, G:0.41, T:0.36
Consensus pattern (37 bp):
GGTTGTTGGGGTTAAGCATTGGGCCATTGGAGTATTG
Found at i:6304597 original size:12 final size:13
Alignment explanation
Indices: 6304579--6304608 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
6304569 TTTCTAGGTT
6304579 ATCTCACTCAAGC
1 ATCTCACTCAAGC
6304592 -TCTCACTCAAGC
1 ATCTCACTCAAGC
6304604 ATCTC
1 ATCTC
6304609 TGCCCTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.27, C:0.40, G:0.07, T:0.27
Consensus pattern (13 bp):
ATCTCACTCAAGC
Found at i:6308215 original size:27 final size:27
Alignment explanation
Indices: 6308177--6308228 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
6308167 TTTTTTATTC
*
6308177 TTTAAATATTAATAATTTAT-ATTTTA
1 TTTAAATATTAATAATGTATCATTTTA
6308203 TTTATAATATTAATAATGTATCATTT
1 TTTA-AATATTAATAATGTATCATTT
6308229 AAATATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 15 0.65
28 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTAAATATTAATAATGTATCATTTTA
Found at i:6308375 original size:159 final size:151
Alignment explanation
Indices: 6308177--6308464 Score: 220
Period size: 159 Copynumber: 1.8 Consensus size: 151
6308167 TTTTTTATTC
* * * *
6308177 TTTAAATATTAATAATTTATATTTTATTTATAATATTAATAA-TGTATCATTTAAATATTAATAT
1 TTTAAATATTAATAATTTACAATTGATTTAAAATATTAATAATTG-ATCATTTAAATATTAATAT
* * * **********
6308241 TTTATTTATAATTAAATCATTAATATTATAAAATACTANNNNNNNNNNTATAATTTAAATGTTAT
65 TTTATTTATAATTTAATCATTAATATT-GAAAATAATAATATTTAATTTATAATTTAAATGTTAT
6308306 TATGATTCTTTATTTTTATTTTATTTTATT-
129 TATGA-----T-TTTTTA-TTT-TTTTATTC
*
6308336 TTTAAATATTAATAATTTACAATTGATTTAAAATATTAATAATTGGTCATTTAAATATTAATATT
1 TTTAAATATTAATAATTTACAATTGATTTAAAATATTAATAATTGATCATTTAAATATTAATATT
* * * ** * * * *
6308401 TTATGTATAATTTAATTATTAAAATTTTCAAATATTAACATTTTATTTATAATTTAAATATTAT
66 TTATTTATAATTTAATCATTAATA-TTGAAAATAATAATATTTAATTTATAATTTAAATGTTAT
6308465 AATACTTAAA
Statistics
Matches: 105, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
159 101 0.96
160 4 0.04
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.51
Consensus pattern (151 bp):
TTTAAATATTAATAATTTACAATTGATTTAAAATATTAATAATTGATCATTTAAATATTAATATT
TTATTTATAATTTAATCATTAATATTGAAAATAATAATATTTAATTTATAATTTAAATGTTATTA
TGATTTTTTATTTTTTTATTC
Found at i:6308434 original size:42 final size:43
Alignment explanation
Indices: 6308388--6308489 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 43
6308378 TTGGTCATTT
* * *
6308388 AAATATTAATATTTTATGTATAATTTAATTATTAAAAT-TTTC
1 AAATATTAATATTTTATGTATAATTTAAATATTAAAATACTTA
* * *
6308430 AAATATTAACATTTTATTTATAATTTAAATATTATAATACTTA
1 AAATATTAATATTTTATGTATAATTTAAATATTAAAATACTTA
6308473 AAATATTAATACTTTTA
1 AAATATTAATA-TTTTA
6308490 ATTAATTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 34 0.67
43 12 0.24
44 5 0.10
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (43 bp):
AAATATTAATATTTTATGTATAATTTAAATATTAAAATACTTA
Found at i:6308631 original size:14 final size:15
Alignment explanation
Indices: 6308614--6308647 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6308604 TAACTTAACA
6308614 ATTTAAAA-ATTAAT
1 ATTTAAAATATTAAT
6308628 ATTTTAAAATATTAAT
1 A-TTTAAAATATTAAT
6308644 ATTT
1 ATTT
6308648 TCTTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.06
15 10 0.56
16 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAAATATTAAT
Found at i:6308633 original size:15 final size:16
Alignment explanation
Indices: 6308615--6308648 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
6308605 AACTTAACAA
6308615 TTTAAAA-ATTAATAT
1 TTTAAAATATTAATAT
6308630 TTTAAAATATTAATAT
1 TTTAAAATATTAATAT
6308646 TTT
1 TTT
6308649 CTTTATAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAATATTAATAT
Found at i:6308662 original size:26 final size:26
Alignment explanation
Indices: 6308633--6308720 Score: 167
Period size: 26 Copynumber: 3.4 Consensus size: 26
6308623 TTAATATTTT
6308633 AAAATATTAATATTTTCTTTATAATC
1 AAAATATTAATATTTTCTTTATAATC
6308659 AAAATATTAATATTTTCTTTATAATC
1 AAAATATTAATATTTTCTTTATAATC
*
6308685 AAAATATTAATATTTTCTTTATAATT
1 AAAATATTAATATTTTCTTTATAATC
6308711 AAAATATTAA
1 AAAATATTAA
6308721 AATATTAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (26 bp):
AAAATATTAATATTTTCTTTATAATC
Found at i:6310933 original size:28 final size:29
Alignment explanation
Indices: 6310902--6310956 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
6310892 ATTTTAAAAA
*
6310902 ATTTAAATATATTTTTAT-TTTTTATTAT
1 ATTTAAATAAATTTTTATATTTTTATTAT
*
6310930 ATTTAATTAAATTTTTATATTTTTATT
1 ATTTAAATAAATTTTTATATTTTTATT
6310957 TTGAACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
ATTTAAATAAATTTTTATATTTTTATTAT
Found at i:6311196 original size:30 final size:29
Alignment explanation
Indices: 6311160--6311231 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 29
6311150 TACTATTAAT
*
6311160 TATAAAAATTTATTTGATATAAAATAAAAA
1 TATAAAAATTTATTT-AAATAAAATAAAAA
* **
6311190 TATAAAAATTTAATTAAATCTAATAAAAA
1 TATAAAAATTTATTTAAATAAAATAAAAA
6311219 -ATAAAAATTTATT
1 TATAAAAATTTATT
6311232 AAAAGTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 12 0.32
29 11 0.30
30 14 0.38
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
TATAAAAATTTATTTAAATAAAATAAAAA
Found at i:6312680 original size:30 final size:30
Alignment explanation
Indices: 6312646--6312705 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
6312636 TGAGAGAAAA
* *
6312646 AAAAGTCATACAATTTAATTTTATACTTAC
1 AAAAGTCATACAACTTAATTTTAGACTTAC
*
6312676 AAAAGTCATCCAACTTAATTTTAGACTTAC
1 AAAAGTCATACAACTTAATTTTAGACTTAC
6312706 TTTCTTGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAAGTCATACAACTTAATTTTAGACTTAC
Found at i:6325465 original size:24 final size:24
Alignment explanation
Indices: 6325438--6325492 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
6325428 GAAGGTAGAA
6325438 ATGTCATATGACCATAAGCATGTC
1 ATGTCATATGACCATAAGCATGTC
6325462 ATGTCATATGACCATAAGCATGTC
1 ATGTCATATGACCATAAGCATGTC
6325486 ATGTCAT
1 ATGTCAT
6325493 CATCCAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (24 bp):
ATGTCATATGACCATAAGCATGTC
Found at i:6329018 original size:3 final size:3
Alignment explanation
Indices: 6329010--6329043 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
6329000 CTAGAACAGC
* *
6329010 ATG ATG ATG GTG ATG ATG ATG ATG AGG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
6329044 CTTTGTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:6348097 original size:3 final size:3
Alignment explanation
Indices: 6348089--6348117 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6348079 CTTTTAAAGA
6348089 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6348118 AACCTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6352292 original size:4 final size:4
Alignment explanation
Indices: 6352285--6352322 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
6352275 AAATTGTCAC
6352285 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
6352323 ATCATTGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:6352584 original size:25 final size:25
Alignment explanation
Indices: 6352556--6352622 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
6352546 TTTAAAAAAT
*
6352556 ATTAAATATATTTTTATTATTTTTA
1 ATTAAATATATTTTTATTATTTTAA
* *
6352581 ATTAAATTTTATATTT-TTATTTTAA
1 ATTAAA-TATATTTTTATTATTTTAA
6352606 ATTAAATATATTTTTAT
1 ATTAAATATATTTTTAT
6352623 AATTAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 7 0.20
25 21 0.60
26 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTAAATATATTTTTATTATTTTAA
Found at i:6352605 original size:20 final size:20
Alignment explanation
Indices: 6352567--6352628 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
6352557 TTAAATATAT
6352567 TTTTATTATTTTTA-ATTAAA
1 TTTTA-TATTTTTATATTAAA
*
6352587 TTTTATATTTTTATTTTAAA
1 TTTTATATTTTTATATTAAA
*
6352607 TTAAATATATTTTTATAATTAA
1 TT--TTATATTTTTAT-ATTAA
6352629 TTATAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 8 0.23
20 12 0.34
22 11 0.31
23 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTATATTTTTATATTAAA
Found at i:6352619 original size:16 final size:18
Alignment explanation
Indices: 6352600--6352633 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6352590 TATATTTTTA
6352600 TTTTA-AATTAAATATAT
1 TTTTATAATTAAATATAT
*
6352617 TTTTATAATTAATTATA
1 TTTTATAATTAAATATA
6352634 AATTAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTATAATTAAATATAT
Found at i:6352634 original size:10 final size:10
Alignment explanation
Indices: 6352619--6352652 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
6352609 AAATATATTT
6352619 TTATAATTAA
1 TTATAATTAA
6352629 TTATAAATTAA
1 TTAT-AATTAA
*
6352640 TTATTATTAA
1 TTATAATTAA
6352650 TTA
1 TTA
6352653 AAATATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTATAATTAA
Found at i:6352644 original size:43 final size:41
Alignment explanation
Indices: 6352597--6352683 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 41
6352587 TTTTATATTT
6352597 TTATT-TTAAATTAAATATATT-TTTATAATTAATTATAAATTAA
1 TTATTATT-AATTAAA-ATATTATTTAT-ATTAATTATAAA-TAA
* *
6352640 TTATTATTAATTAAAATATTATTTATATTTATTATTAATAA
1 TTATTATTAATTAAAATATTATTTATATTAATTATAAATAA
6352681 TTA
1 TTA
6352684 AAATATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
41 6 0.15
42 15 0.38
43 17 0.43
44 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (41 bp):
TTATTATTAATTAAAATATTATTTATATTAATTATAAATAA
Found at i:6352648 original size:21 final size:21
Alignment explanation
Indices: 6352619--6352683 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
6352609 AAATATATTT
*
6352619 TTATAATTAATTATAAATTAA
1 TTATTATTAATTATAAATTAA
* *
6352640 TTATTATTAATTAAAATATTAT
1 TTATTATTAATTATAA-ATTAA
* *
6352662 TTA-TATTTATTATTAA-TAA
1 TTATTATTAATTATAAATTAA
6352681 TTA
1 TTA
6352684 AAATATTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
19 5 0.14
20 1 0.03
21 23 0.64
22 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTATTAATTATAAATTAA
Found at i:6352671 original size:25 final size:25
Alignment explanation
Indices: 6352556--6352677 Score: 70
Period size: 25 Copynumber: 5.2 Consensus size: 25
6352546 TTTAAAAAAT
6352556 ATTAAATATATT-TTTATTATTT-TTA
1 ATTAAA-ATATTATTTA-TATTTATTA
* * * *
6352581 ATTAAATTTTATATTTTTATTT-TAA
1 ATTAAAATAT-TATTTATATTTATTA
6352606 ATTAAATATATT-TTTATA---ATTA
1 ATTAAA-ATATTATTTATATTTATTA
* *
6352628 ATTATAA-ATTA-AT-TA-TTATTA
1 ATTAAAATATTATTTATATTTATTA
6352649 ATTAAAATATTATTTATATTTATT-
1 ATTAAAATATTATTTATATTTATTA
6352673 ATTAA
1 ATTAA
6352678 TAATTAAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
19 2 0.03
20 4 0.05
21 11 0.15
22 11 0.15
23 1 0.01
24 14 0.19
25 26 0.35
26 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTAAAATATTATTTATATTTATTA
Found at i:6352693 original size:25 final size:25
Alignment explanation
Indices: 6352556--6352694 Score: 60
Period size: 25 Copynumber: 5.6 Consensus size: 25
6352546 TTTAAAAAAT
**
6352556 ATTAAATATATT-TTTATTATTTTTA
1 ATTAAA-ATATTATTTATTATTAATA
* * *
6352581 ATT-AAATTTTATATTTTTATT-TTAA
1 ATTAAAATATTAT-TTATTATTAAT-A
6352606 ATT-AAATA-TATTT-TTA-TAATTA
1 ATTAAAATATTATTTATTATTAA-TA
* *
6352628 ATTATAA-ATTAATTATTATTAATTAA
1 ATTAAAATATTATTTATTATTAA-T-A
* ** *
6352654 AATATTATTTATATTTATTATTAATA
1 ATTAAAATAT-TATTTATTATTAATA
6352680 ATTAAAATATTATTT
1 ATTAAAATATTATTT
6352695 GTGATTTTAT
Statistics
Matches: 88, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
21 1 0.01
22 8 0.09
23 13 0.15
24 11 0.12
25 28 0.32
26 13 0.15
27 2 0.02
28 12 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTAAAATATTATTTATTATTAATA
Found at i:6353240 original size:2 final size:2
Alignment explanation
Indices: 6353233--6353257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6353223 AGAGACAGAA
6353233 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
6353258 AAACAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:6354372 original size:18 final size:18
Alignment explanation
Indices: 6354346--6354407 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
6354336 TTTTGAGTAG
*
6354346 TTATTTTTATTAAAAAAA
1 TTATATTTATTAAAAAAA
* **
6354364 TTATATTTATTCAAAATG
1 TTATATTTATTAAAAAAA
6354382 TTATATATT-TGTATAAAAAA
1 TTATAT-TTAT-TA-AAAAAA
6354402 TTATAT
1 TTATAT
6354408 CTTTGCTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
18 21 0.62
19 3 0.09
20 10 0.29
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (18 bp):
TTATATTTATTAAAAAAA
Found at i:6366247 original size:2 final size:2
Alignment explanation
Indices: 6366240--6366270 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6366230 TCATGTGTTC
6366240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6366271 GGGTTGATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6374476 original size:15 final size:15
Alignment explanation
Indices: 6374456--6374486 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6374446 AGTTTTATAT
*
6374456 ATTTAATAATTAAAA
1 ATTTAAAAATTAAAA
6374471 ATTTAAAAATTAAAA
1 ATTTAAAAATTAAAA
6374486 A
1 A
6374487 GTGACGACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTTAAAAATTAAAA
Found at i:6380392 original size:22 final size:21
Alignment explanation
Indices: 6380349--6380392 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
6380339 ATTGATTAAG
*
6380349 AAATGATACAAAAAACCCGAC
1 AAATGATACAAAAAACCAGAC
6380370 AAATGA-ACAAAATGAACCAGAC
1 AAATGATACAAAA--AACCAGAC
6380392 A
1 A
6380393 TGAGCTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.09
Consensus pattern (21 bp):
AAATGATACAAAAAACCAGAC
Found at i:6382824 original size:110 final size:110
Alignment explanation
Indices: 6382710--6382930 Score: 331
Period size: 110 Copynumber: 2.0 Consensus size: 110
6382700 TATTTTTTTA
* * *
6382710 TTACATTCAATCAAATCTTTATAT-TTTTATTTTAAATTAAATATATTCTTATAATTAATAG-TG
1 TTACATTCAATCAAACCCTTATATATTTT-TTTAAAATTAAATATATTCTTATAATTAA-AGATG
*
6382773 GATTAATTGTGGTTAGTTAAAATA-ACACTTATTATTTTGATATCATG
64 GATTAATTGTGATTAGTTAAAATATA-ACTTATTATTTTGATATCATG
* *
6382820 TTACATTCAATCAAACCCTTATATATTTTTTTAAAATTAAATATATTCTTATAATTAACGATTGA
1 TTACATTCAATCAAACCCTTATATATTTTTTTAAAATTAAATATATTCTTATAATTAAAGATGGA
*
6382885 TTAATTGTGATTAGTTAAAATATAATTTATTATTTTGATATCATG
66 TTAATTGTGATTAGTTAAAATATAACTTATTATTTTGATATCATG
6382930 T
1 T
6382931 GATGCTGACA
Statistics
Matches: 101, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
109 1 0.01
110 95 0.94
111 5 0.05
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (110 bp):
TTACATTCAATCAAACCCTTATATATTTTTTTAAAATTAAATATATTCTTATAATTAAAGATGGA
TTAATTGTGATTAGTTAAAATATAACTTATTATTTTGATATCATG
Found at i:6385931 original size:18 final size:17
Alignment explanation
Indices: 6385891--6385933 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
6385881 TCTTTTGAGT
*
6385891 AGTTATTTTTATTAAAA
1 AGTTATATTTATTAAAA
*
6385908 AATTATATTTATTCAAAA
1 AGTTATATTTATT-AAAA
*
6385926 TGTTATAT
1 AGTTATAT
6385934 ATTTGTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
AGTTATATTTATTAAAA
Found at i:6390932 original size:105 final size:105
Alignment explanation
Indices: 6390750--6390960 Score: 404
Period size: 105 Copynumber: 2.0 Consensus size: 105
6390740 ATATTATATA
6390750 TATATATATATTCTTCAATCCAGTTGTGCATGATACCTAGTCTGACACTTGGTATAGAATAGATT
1 TATATATATATTCTTCAATCCAGTTGTGCATGATACCTAGTCTGACACTTGGTATAGAATAGATT
6390815 CTGTGTGTCTTCTTGATTTCTATTGAGAAAGTATGCTACC
66 CTGTGTGTCTTCTTGATTTCTATTGAGAAAGTATGCTACC
*
6390855 TATATATATATTCTTCAATCCAGTTGTGCATGATACCTAGTCTGACTCTTGGTATAGAATAGATT
1 TATATATATATTCTTCAATCCAGTTGTGCATGATACCTAGTCTGACACTTGGTATAGAATAGATT
*
6390920 CTTTGTGTCTTCTTGATTTCTATTGAGAAAGTATGCTACC
66 CTGTGTGTCTTCTTGATTTCTATTGAGAAAGTATGCTACC
6390960 T
1 T
6390961 GTGAACATGC
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (105 bp):
TATATATATATTCTTCAATCCAGTTGTGCATGATACCTAGTCTGACACTTGGTATAGAATAGATT
CTGTGTGTCTTCTTGATTTCTATTGAGAAAGTATGCTACC
Found at i:6397512 original size:3 final size:3
Alignment explanation
Indices: 6397504--6397531 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6397494 CATAATCTCC
6397504 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
6397532 CTTGATGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:6402405 original size:33 final size:36
Alignment explanation
Indices: 6402361--6402450 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 36
6402351 TTTTTGAGCC
* *
6402361 GGAAATTAGGTCAAGACTCG-TGGAAGG-GGGGGG-
1 GGAAATCAGGTCAAGACTCGCGGGAAGGTGGGGGGT
** *
6402394 GGAAATCAGGTCGGGACTCGCGGGAGGGTGGGGGGT
1 GGAAATCAGGTCAAGACTCGCGGGAAGGTGGGGGGT
* *
6402430 GGGAATCAGGTCAAGATTCGC
1 GGAAATCAGGTCAAGACTCGC
6402451 AGGAGGGGGG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
33 17 0.38
34 5 0.11
35 6 0.13
36 17 0.38
ACGTcount: A:0.23, C:0.13, G:0.48, T:0.16
Consensus pattern (36 bp):
GGAAATCAGGTCAAGACTCGCGGGAAGGTGGGGGGT
Found at i:6402456 original size:36 final size:37
Alignment explanation
Indices: 6402386--6402457 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
6402376 ACTCGTGGAA
** *
6402386 GGGGGGGGGGAAATCAGGTCGGGACTCGCGGGAGGGT
1 GGGGGGGGGGAAATCAGGTCAAGACTCGCAGGAGGGT
* *
6402423 GGGGGGTGGG-AATCAGGTCAAGATTCGCAGGAGGG
1 GGGGGGGGGGAAATCAGGTCAAGACTCGCAGGAGGG
6402458 GGGAAGGAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 21 0.70
37 9 0.30
ACGTcount: A:0.19, C:0.12, G:0.56, T:0.12
Consensus pattern (37 bp):
GGGGGGGGGGAAATCAGGTCAAGACTCGCAGGAGGGT
Found at i:6403331 original size:29 final size:29
Alignment explanation
Indices: 6403277--6403336 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
6403267 ATCATGTATA
* *
6403277 TATTTAATTAATTATATCATATTTATGTT
1 TATTTAATTAATTATATAATATTTATATT
6403306 TATTT-ATATAATTAT-TAATATCTTATATT
1 TATTTAAT-TAATTATATAATAT-TTATATT
6403335 TA
1 TA
6403337 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (29 bp):
TATTTAATTAATTATATAATATTTATATT
Found at i:6405960 original size:24 final size:24
Alignment explanation
Indices: 6405911--6405962 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
6405901 ATATATTAAA
* * *
6405911 AAAATTTAAAACTTTTATGAAGAT
1 AAAATTTAAAACTTCTATAAAAAT
6405935 AAAATTATAAAACTTCTA-AAAAAT
1 AAAATT-TAAAACTTCTATAAAAAT
6405959 AAAA
1 AAAA
6405963 CTAAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAATTTAAAACTTCTATAAAAAT
Found at i:6406086 original size:13 final size:13
Alignment explanation
Indices: 6406068--6406099 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6406058 AAATATAAAA
*
6406068 ATATTATTTTATT
1 ATATTATTATATT
6406081 ATATTATTATATT
1 ATATTATTATATT
6406094 ATATTA
1 ATATTA
6406100 ATAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTATTATATT
Found at i:6411124 original size:30 final size:30
Alignment explanation
Indices: 6411090--6411150 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
6411080 TAAGGATCAT
6411090 AAGTAATGGCAACTAACTTTTGATGATAAA
1 AAGTAATGGCAACTAACTTTTGATGATAAA
6411120 AAGTAATGGCAACTAACTTTTGATGATAAA
1 AAGTAATGGCAACTAACTTTTGATGATAAA
6411150 A
1 A
6411151 GATGAAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (30 bp):
AAGTAATGGCAACTAACTTTTGATGATAAA
Found at i:6411169 original size:2 final size:2
Alignment explanation
Indices: 6411162--6411186 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6411152 ATGAAGGAAA
6411162 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
6411187 AGTAACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6419132 original size:23 final size:23
Alignment explanation
Indices: 6419106--6419163 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
6419096 AATTGAATAA
*
6419106 TTGTGTCT-TATGGAAACAAACAG
1 TTGTGTCTGT-TGAAAACAAACAG
*
6419129 TTGTGTCTGTTGAAAACATACAG
1 TTGTGTCTGTTGAAAACAAACAG
*
6419152 TTGTGTATGTTG
1 TTGTGTCTGTTG
6419164 GGAGAAGACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (23 bp):
TTGTGTCTGTTGAAAACAAACAG
Found at i:6421679 original size:5 final size:5
Alignment explanation
Indices: 6421669--6421693 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6421659 AAAGCATGAA
6421669 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
6421694 CCAAGCAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:6423379 original size:33 final size:32
Alignment explanation
Indices: 6423329--6423413 Score: 82
Period size: 33 Copynumber: 2.5 Consensus size: 32
6423319 AAACAAATTA
*
6423329 AAATAAAATATATAATATAAAAAA-TATATTAAAG
1 AAATAAAATA-A-AATATAAAAAATTATAAT-AAG
* * *
6423363 AAATAAAGATAAAATATATAAGATTATAATAAT
1 AAATAAA-ATAAAATATAAAAAATTATAATAAG
6423396 AAATAAAAATAAAATATA
1 AAAT-AAAATAAAATATA
6423414 TGACATTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
33 25 0.57
34 16 0.36
35 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (32 bp):
AAATAAAATAAAATATAAAAAATTATAATAAG
Found at i:6423650 original size:15 final size:15
Alignment explanation
Indices: 6423630--6423673 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
6423620 TTATTTTCTC
*
6423630 TACAATCACATTGCT
1 TACAATCACATTACT
6423645 TACAATCACATTACT
1 TACAATCACATTACT
*
6423660 TGCAATCACATTAC
1 TACAATCACATTAC
6423674 CTGTAATCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (15 bp):
TACAATCACATTACT
Found at i:6423681 original size:15 final size:15
Alignment explanation
Indices: 6423632--6423686 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
6423622 ATTTTCTCTA
* * *
6423632 CAATCACATTGCTTA
1 CAATCACATTACCTG
*
6423647 CAATCACATTACTTG
1 CAATCACATTACCTG
6423662 CAATCACATTACCTG
1 CAATCACATTACCTG
*
6423677 TAATCACATT
1 CAATCACATT
6423687 GTATTGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (15 bp):
CAATCACATTACCTG
Found at i:6427138 original size:54 final size:54
Alignment explanation
Indices: 6427056--6427162 Score: 178
Period size: 54 Copynumber: 2.0 Consensus size: 54
6427046 CTTGGAAAAT
*
6427056 AGAAAAACTCTCAATCTGCAGCTGAAGGCTGTCAAACAACAGGTATCTCATCTG
1 AGAAAAACTCTCAATCTGCAGCTGAAGGCCGTCAAACAACAGGTATCTCATCTG
* * *
6427110 AGAAAAGCTCTCAATCTGCAGCTGAAGGCCGTCAAACTACAGGTTTCTCATCT
1 AGAAAAACTCTCAATCTGCAGCTGAAGGCCGTCAAACAACAGGTATCTCATCT
6427163 TCTTGAACCC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (54 bp):
AGAAAAACTCTCAATCTGCAGCTGAAGGCCGTCAAACAACAGGTATCTCATCTG
Found at i:6441417 original size:27 final size:27
Alignment explanation
Indices: 6441387--6441456 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
6441377 TGATGGTGAT
*
6441387 GATGAATATGATGCTAAGTTTGATGAC
1 GATGAAGATGATGCTAAGTTTGATGAC
* * *
6441414 GATGAAGAGGATAG-TGAGTTTGATGAT
1 GATGAAGATGAT-GCTAAGTTTGATGAC
*
6441441 GATGAAGATGAGGCTA
1 GATGAAGATGATGCTA
6441457 TCAACATTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
26 1 0.03
27 32 0.94
28 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.33, T:0.29
Consensus pattern (27 bp):
GATGAAGATGATGCTAAGTTTGATGAC
Found at i:6444318 original size:35 final size:34
Alignment explanation
Indices: 6444256--6444368 Score: 136
Period size: 34 Copynumber: 3.3 Consensus size: 34
6444246 AGAATGCTTC
*
6444256 ACTACGTGATTGAACCAATACACATCAAACATTT
1 ACTACGTGATTGAACCAATATACATCAAACATTT
* * *
6444290 ACTACGTGATTGGAACCAATGTATATCAAACATTC
1 ACTACGTGATT-GAACCAATATACATCAAACATTT
* ** *
6444325 ACTACATGATCAAACCAACATACATCAAACATTT
1 ACTACGTGATTGAACCAATATACATCAAACATTT
*
6444359 ACTAAGTGAT
1 ACTACGTGAT
6444369 CAAACAAGCA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 37 0.57
35 28 0.43
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.27
Consensus pattern (34 bp):
ACTACGTGATTGAACCAATATACATCAAACATTT
Found at i:6444369 original size:34 final size:34
Alignment explanation
Indices: 6444268--6444387 Score: 109
Period size: 34 Copynumber: 3.5 Consensus size: 34
6444258 TACGTGATTG
* * * **
6444268 AACCAATACACATCAAACATTTACTACGTGATTGG
1 AACCAACATACATCAAACATTTACTAAGTGA-TCA
** * *
6444303 AACCAATGTATATCAAACATTCACTACA-TGATCA
1 AACCAACATACATCAAACATTTACTA-AGTGATCA
6444337 AACCAACATACATCAAACATTTACTAAGTGATCA
1 AACCAACATACATCAAACATTTACTAAGTGATCA
*
6444371 AA-CAAGCATATATCAAA
1 AACCAA-CATACATCAAA
6444388 GAACTAAAGT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
33 4 0.06
34 41 0.59
35 25 0.36
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (34 bp):
AACCAACATACATCAAACATTTACTAAGTGATCA
Found at i:6446927 original size:2 final size:2
Alignment explanation
Indices: 6446881--6446912 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6446871 CCTCAATTTC
*
6446881 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6446913 TCTCTTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6449542 original size:4 final size:4
Alignment explanation
Indices: 6449533--6449569 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
6449523 CATGAGGATT
6449533 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
6449570 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (4 bp):
TCTA
Found at i:6455601 original size:2 final size:2
Alignment explanation
Indices: 6455594--6455628 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6455584 TCAAGTGCTT
6455594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6455629 TACGAGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6456367 original size:18 final size:19
Alignment explanation
Indices: 6456344--6456382 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6456334 TAAAAAGTAT
* *
6456344 TTAATAA-ATATTTTTTTG
1 TTAATAATAAATTCTTTTG
6456362 TTAATAATAAATTCTTTTG
1 TTAATAATAAATTCTTTTG
6456381 TT
1 TT
6456383 CACAATGGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TTAATAATAAATTCTTTTG
Found at i:6463423 original size:17 final size:17
Alignment explanation
Indices: 6463401--6463435 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6463391 GTTAGCAAAG
6463401 TTCTAAAATAATTTAAT
1 TTCTAAAATAATTTAAT
**
6463418 TTCTAATCTAATTTAAT
1 TTCTAAAATAATTTAAT
6463435 T
1 T
6463436 ATTTAAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (17 bp):
TTCTAAAATAATTTAAT
Found at i:6466329 original size:19 final size:19
Alignment explanation
Indices: 6466307--6466343 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6466297 AAAGAAAGGA
6466307 GAAAAA-AGAAAAATGAAAT
1 GAAAAATAG-AAAATGAAAT
6466326 GAAAAATAGAAAATGAAA
1 GAAAAATAGAAAATGAAA
6466344 GGGCGAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (19 bp):
GAAAAATAGAAAATGAAAT
Found at i:6466534 original size:3 final size:3
Alignment explanation
Indices: 6466528--6466552 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6466518 AAAAAAACTT
6466528 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
6466553 GTTTAAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6467351 original size:33 final size:33
Alignment explanation
Indices: 6467277--6467351 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
6467267 TGTCATGTCG
* *
6467277 TATTAACATGTCATGTAATCATCAATTACGATA
1 TATTAACATGTCACGTAATCATCAATTACGACA
* * *
6467310 TATCAACATGTCACGTCATCATCAATTATGACA
1 TATTAACATGTCACGTAATCATCAATTACGACA
*
6467343 TTTTAACAT
1 TATTAACAT
6467352 ATCATATTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (33 bp):
TATTAACATGTCACGTAATCATCAATTACGACA
Found at i:6467589 original size:12 final size:11
Alignment explanation
Indices: 6467567--6467596 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
6467557 AATTTTTATT
6467567 TAATTATAAAAA
1 TAATT-TAAAAA
6467579 TAATTTAAAAA
1 TAATTTAAAAA
6467590 TAATTTA
1 TAATTTA
6467597 TTTTATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATTTAAAAA
Found at i:6468294 original size:24 final size:23
Alignment explanation
Indices: 6468251--6468298 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
6468241 AATGTTATTG
*
6468251 TTACACATCATATACTAAAACATA
1 TTACACATCATATACGAAAA-ATA
6468275 TTACACATCATATTA-GAAAAATA
1 TTACACATCATA-TACGAAAAATA
6468298 T
1 T
6468299 ATTGTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 16 0.73
25 2 0.09
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (23 bp):
TTACACATCATATACGAAAAATA
Found at i:6468356 original size:79 final size:79
Alignment explanation
Indices: 6468273--6468461 Score: 184
Period size: 79 Copynumber: 2.3 Consensus size: 79
6468263 TACTAAAACA
* * * * * *
6468273 TATTACACATCATATTAGAAAAATATATTGTTTTTATACT-TTATATACAAAAACATGTTACAC-
1 TATTACACATCATATTAAAAAAAAATATTATTATTACA-TGCTATATACAAAAACATGTTACACG
6468336 CATAGTTAAAAAAGGT
65 CATA-TTAAAAAAGGT
* * * *
6468352 TATTATACATCATGTTAAAAAAAAATATTATTATTACATGCTATGTACAAAAACTTGTTACACGT
1 TATTACACATCATATTAAAAAAAAATATTATTATTACATGCTATATACAAAAACATGTTACACG-
**
6468417 CATATTAAAAAATATTAT
65 CATATT-AAAAA-A-GGT
*
6468435 TATTACACATCATGTTCAAAAAAAAAT
1 TATTACACATCATATT-AAAAAAAAAT
6468462 TGTTACACTT
Statistics
Matches: 90, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
78 1 0.01
79 51 0.57
80 2 0.02
81 9 0.10
82 1 0.01
83 16 0.18
84 10 0.11
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (79 bp):
TATTACACATCATATTAAAAAAAAATATTATTATTACATGCTATATACAAAAACATGTTACACGC
ATATTAAAAAAGGT
Found at i:6469427 original size:2 final size:2
Alignment explanation
Indices: 6469420--6469455 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6469410 AAAATAGACA
*
6469420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6469456 CTAGATAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6469614 original size:3 final size:3
Alignment explanation
Indices: 6469606--6469641 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
6469596 CACTTCAACA
*
6469606 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6469642 TTAACAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:6474938 original size:16 final size:17
Alignment explanation
Indices: 6474903--6474935 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6474893 TTGCACTAGT
*
6474903 TTTTTTTAAATAAATAA
1 TTTTTTTAAAAAAATAA
6474920 TTTTTTTAAAAAAATA
1 TTTTTTTAAAAAAATA
6474936 TTTAAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTTTTAAAAAAATAA
Found at i:6476396 original size:2 final size:2
Alignment explanation
Indices: 6476389--6476415 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6476379 CACATAGGTG
6476389 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6476416 GACTAATCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6477489 original size:23 final size:23
Alignment explanation
Indices: 6477459--6477506 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
6477449 TATGTTACTC
6477459 TGCTATTGTGTTTTTGGGTCATT
1 TGCTATTGTGTTTTTGGGTCATT
*
6477482 TGCTATTGTGTTTTTGGGTTATT
1 TGCTATTGTGTTTTTGGGTCATT
6477505 TG
1 TG
6477507 ATTAATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.08, C:0.06, G:0.27, T:0.58
Consensus pattern (23 bp):
TGCTATTGTGTTTTTGGGTCATT
Found at i:6482170 original size:32 final size:31
Alignment explanation
Indices: 6482110--6482168 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
6482100 ATTCCCCCGG
*
6482110 CCCCCTTCCCACGAGTCCCGATTCCCCCTTA
1 CCCCCCTCCCACGAGTCCCGATTCCCCCTTA
*
6482141 CCCCCCTCCCACGAGTTCCGATTCCCCC
1 CCCCCCTCCCACGAGTCCCGATTCCCCC
6482169 CTGCCTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.12, C:0.58, G:0.10, T:0.20
Consensus pattern (31 bp):
CCCCCCTCCCACGAGTCCCGATTCCCCCTTA
Found at i:6484777 original size:11 final size:11
Alignment explanation
Indices: 6484761--6484808 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
6484751 TTAAAATCAC
6484761 AAAAATAAAAT
1 AAAAATAAAAT
6484772 AAAAATAAAAT
1 AAAAATAAAAT
*
6484783 GAAAAACAAAAT
1 -AAAAATAAAAT
* *
6484795 AGAAAGAAAA-
1 AAAAATAAAAT
6484805 AAAA
1 AAAA
6484809 GAAATAATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 3 0.09
11 19 0.59
12 10 0.31
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.10
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:6484787 original size:17 final size:16
Alignment explanation
Indices: 6484762--6484808 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
6484752 TAAAATCACA
6484762 AAAAT-AAAATAAAAAT
1 AAAATGAAAA-AAAAAT
6484778 AAAATGAAAAACAAAAT
1 AAAATGAAAAA-AAAAT
6484795 AGAAA-GAAAAAAAA
1 A-AAATGAAAAAAAA
6484809 GAAATAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.32
17 16 0.57
18 3 0.11
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAATGAAAAAAAAAT
Found at i:6484793 original size:23 final size:23
Alignment explanation
Indices: 6484761--6484804 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6484751 TTAAAATCAC
* *
6484761 AAAAATAAAATAAAAATAAAATG
1 AAAAACAAAATAAAAAGAAAATG
*
6484784 AAAAACAAAATAGAAAGAAAA
1 AAAAACAAAATAAAAAGAAAA
6484805 AAAAGAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (23 bp):
AAAAACAAAATAAAAAGAAAATG
Found at i:6500476 original size:38 final size:38
Alignment explanation
Indices: 6500425--6500497 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
6500415 CCCTCTCTGT
6500425 CCAAGCATTCTCTCTCCTTCTCTCATTAAATTTTCGAC
1 CCAAGCATTCTCTCTCCTTCTCTCATTAAATTTTCGAC
6500463 CCAAGCATTCTCTCTCCTTCTCTCATTAAATTTTC
1 CCAAGCATTCTCTCTCCTTCTCTCATTAAATTTTC
6500498 TCCATTAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.21, C:0.34, G:0.04, T:0.41
Consensus pattern (38 bp):
CCAAGCATTCTCTCTCCTTCTCTCATTAAATTTTCGAC
Found at i:6501654 original size:30 final size:30
Alignment explanation
Indices: 6501620--6501678 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
6501610 AATGTCTTAC
6501620 ATTAAAGGTTGTATAAATAATAACTAATTA
1 ATTAAAGGTTGTATAAATAATAACTAATTA
6501650 ATTAAAGGTTGTATAAATAATAACTAATT
1 ATTAAAGGTTGTATAAATAATAACTAATT
6501679 TAAACAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.37
Consensus pattern (30 bp):
ATTAAAGGTTGTATAAATAATAACTAATTA
Found at i:6501696 original size:30 final size:30
Alignment explanation
Indices: 6501623--6501685 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
6501613 GTCTTACATT
**
6501623 AAAGGTTGTATAAATAATAACTAATTAATT
1 AAAGGTTGTATAAATAATAACTAATTAAAC
6501653 AAAGGTTGTATAAATAATAACTAATTTAAAC
1 AAAGGTTGTATAAATAATAACTAA-TTAAAC
6501684 AA
1 AA
6501686 TATGTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (30 bp):
AAAGGTTGTATAAATAATAACTAATTAAAC
Found at i:6501793 original size:17 final size:17
Alignment explanation
Indices: 6501771--6501825 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
6501761 TAGTAATATT
6501771 TATGTATAAATTAAGTA
1 TATGTATAAATTAAGTA
*
6501788 TATGTATACA-TAA-TA
1 TATGTATAAATTAAGTA
*
6501803 TATTTATACAATT-AGATA
1 TATGTATA-AATTAAG-TA
6501821 TATGT
1 TATGT
6501826 TCATAACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 9 0.30
16 5 0.17
17 10 0.33
18 6 0.20
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (17 bp):
TATGTATAAATTAAGTA
Found at i:6501800 original size:21 final size:23
Alignment explanation
Indices: 6501753--6501800 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
6501743 AAAGTTTATT
* **
6501753 ATAAATTATAGTAATATTTATGT
1 ATAAATTATAGTAATATGTATAC
6501776 ATAAATTA-AGT-ATATGTATAC
1 ATAAATTATAGTAATATGTATAC
6501797 ATAA
1 ATAA
6501801 TATATTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 11 0.50
22 3 0.14
23 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (23 bp):
ATAAATTATAGTAATATGTATAC
Found at i:6502577 original size:16 final size:18
Alignment explanation
Indices: 6502546--6502585 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
6502536 TAACAAAAAA
6502546 TTATAAAAATTATAATAT
1 TTATAAAAATTATAATAT
* *
6502564 TTATAAAATATAATAAAAT
1 TTATAAAA-ATTATAATAT
6502583 TTA
1 TTA
6502586 CTTATTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATAAAAATTATAATAT
Found at i:6505010 original size:34 final size:34
Alignment explanation
Indices: 6504965--6505031 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
6504955 TCTTCCTCAA
*
6504965 TAGAGTGCATTGAATCTTATTTATCTTAGAAAAG
1 TAGAGTACATTGAATCTTATTTATCTTAGAAAAG
*
6504999 TAGAGTACATTGAATCTTATTTTTCTTAGAAAA
1 TAGAGTACATTGAATCTTATTTATCTTAGAAAA
6505032 AACGCTAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (34 bp):
TAGAGTACATTGAATCTTATTTATCTTAGAAAAG
Found at i:6514890 original size:14 final size:13
Alignment explanation
Indices: 6514866--6514904 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
6514856 TTATATTTGA
*
6514866 TGTTATTATTATT
1 TGTTATAATTATT
6514879 TGGTTATAATTATT
1 T-GTTATAATTATT
6514893 T-TTATAATTATT
1 TGTTATAATTATT
6514905 GATTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 11 0.46
13 1 0.04
14 12 0.50
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATAATTATT
Found at i:6516885 original size:32 final size:32
Alignment explanation
Indices: 6516844--6516988 Score: 110
Period size: 32 Copynumber: 5.1 Consensus size: 32
6516834 GAGAAGAAAA
6516844 GCTACATAATTTGTAGATTTATTGATAAGTTT
1 GCTACATAATTTGTAGATTTATTGATAAGTTT
* * *
6516876 GCTACATAATTT-T--A--TGTGGA-AA---A
1 GCTACATAATTTGTAGATTTATTGATAAGTTT
6516899 GCTACATAATTTGTAGATTTATTGATAAGTTT
1 GCTACATAATTTGTAGATTTATTGATAAGTTT
* * *
6516931 GCTACATAATTT-T--A--TGTGGA-AA---A
1 GCTACATAATTTGTAGATTTATTGATAAGTTT
6516954 GCTACATAATTTGTAGATTTATTGATAAGTTT
1 GCTACATAATTTGTAGATTTATTGATAAGTTT
6516986 GCT
1 GCT
6516989 CTGGTGATAA
Statistics
Matches: 83, Mismatches: 12, Indels: 36
0.63 0.09 0.27
Matches are distributed among these distances:
23 24 0.29
24 2 0.02
26 6 0.07
27 8 0.10
28 8 0.10
29 6 0.07
31 2 0.02
32 27 0.33
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.43
Consensus pattern (32 bp):
GCTACATAATTTGTAGATTTATTGATAAGTTT
Found at i:6516923 original size:55 final size:55
Alignment explanation
Indices: 6516839--6516988 Score: 300
Period size: 55 Copynumber: 2.7 Consensus size: 55
6516829 GCACTGAGAA
6516839 GAAAAGCTACATAATTTGTAGATTTATTGATAAGTTTGCTACATAATTTTATGTG
1 GAAAAGCTACATAATTTGTAGATTTATTGATAAGTTTGCTACATAATTTTATGTG
6516894 GAAAAGCTACATAATTTGTAGATTTATTGATAAGTTTGCTACATAATTTTATGTG
1 GAAAAGCTACATAATTTGTAGATTTATTGATAAGTTTGCTACATAATTTTATGTG
6516949 GAAAAGCTACATAATTTGTAGATTTATTGATAAGTTTGCT
1 GAAAAGCTACATAATTTGTAGATTTATTGATAAGTTTGCT
6516989 CTGGTGATAA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 95 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (55 bp):
GAAAAGCTACATAATTTGTAGATTTATTGATAAGTTTGCTACATAATTTTATGTG
Found at i:6525576 original size:29 final size:29
Alignment explanation
Indices: 6525502--6525577 Score: 70
Period size: 31 Copynumber: 2.6 Consensus size: 29
6525492 TTCATTAATT
*
6525502 ATAAGAGTTTATTTG-ACTCAAAATAAAA
1 ATAAAAGTTTATTTGAACTCAAAATAAAA
6525530 ATATAAAGATTTGA-TTGAACAT-AACAA-AAAA
1 ATA-AAAG-TTT-ATTTGAAC-TCAA-AATAAAA
6525561 ATAAAAGTTTATTTGAA
1 ATAAAAGTTTATTTGAA
6525578 TTTTTTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
28 4 0.10
29 11 0.28
30 10 0.25
31 12 0.30
32 3 0.08
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.32
Consensus pattern (29 bp):
ATAAAAGTTTATTTGAACTCAAAATAAAA
Found at i:6527240 original size:15 final size:15
Alignment explanation
Indices: 6527220--6527249 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6527210 TATCTCAAAC
6527220 ATAAGTAATAATTTT
1 ATAAGTAATAATTTT
*
6527235 ATAAGTTATAATTTT
1 ATAAGTAATAATTTT
6527250 TGTAATGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
ATAAGTAATAATTTT
Found at i:6527884 original size:344 final size:339
Alignment explanation
Indices: 6527220--6528351 Score: 1254
Period size: 344 Copynumber: 3.3 Consensus size: 339
6527210 TATCTCAAAC
* * *
6527220 ATAAGTAATAATTTTATAAGTTATAATTTTTGTAATGTTAATACAAAATAGAAAGTAAGTATGTT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
* * * *
6527285 TATATTTAAAG----TGTACATATACTAAAAGAATTTTAGTATATATAATAGTAATTATATTTCT
66 TATATTTAAAGTATATATATATATACTAAAAGTATTTTAATATATATAATAGTAATTATA-TTCT
*** * * ** * *
6527346 TATAAATGACCTCAATGTATTTAAAGTATACGTATTAAAAGATATTACAAATCAATTAATAATCA
130 TATAAATGACC-CAGCATATATAAAGCATATATATTAAAAGATATTACAAGTTAATTAATAATCA
* * * *
6527411 TAGTTTCATTAATTAATTTAATTAACTATATGAATTTGTCCTTAATTATATAAAATTAAAAAAAT
194 TAGTTTCATGAATTAATTTAATTAACTATATGGATTTGTCTTTAATTATATGAAATTAAAAAAA-
* * * * *
6527476 AACTAGGTTTCATAACTATTCTAATCTCTCAACTTCTCTTTAGATTTATATATTATA--ATATAT
258 AAATA-GTTTCAAAACTATTCTAATCTCACAACTTCTCTTAAG-TTTATATATTATAGTTTATAT
6527539 AAACAAAGGTATATATATT
321 AAACAAAGGTATATATATT
*
6527558 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAATAAATATGTT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
6527623 TATATTTAAAGTACATATATATATATACTAAAAGTATTTTAATATATATAATAGTAATTATATTC
66 TATATTTAAAGT--ATATATATATATACTAAAAGTATTTTAATATATATAATAGTAATTATATT-
*
6527688 CTTATAAATGACCCTAGCATATATAAAGCATATATATTAAAAGATATCACAAGTTAATTAATAAT
128 CTTATAAATGACCC-AGCATATATAAAGCATATATATTAAAAGATATTACAAGTTAATTAATAAT
* * *
6527753 TATAATTTCATGAATTAATTTAATTAACTATCTGGATTTGTCTTTAATTATATGAAA-TAAAAAA
192 CATAGTTTCATGAATTAATTTAATTAACTATATGGATTTGTCTTTAATTATATGAAATTAAAAAA
*
6527817 AAAATAGTTTCAAAACTATTCTAATCTCACAACTTCTCTTGAAGTTTATCTATTATATGTTTATA
257 AAAATAGTTTCAAAACTATTCTAATCTCACAACTTCTCTT-AAGTTTATATATTATA-GTTTATA
6527882 TAAACAAAGGTATATATATATATATATATTATAT
320 TAAACAAAGG------------TATATA-TAT-T
* * *
6527916 ATATATTATATTTAATAGTTTTATAAGTTATAATTTTTTTAATGTTAATACAAAATAGCAAGTAA
1 ATA-ATTA-A--T-A-A-TTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAA
* *
6527981 ATATGTTTATATTTAAAGTATATATATACA-A--AAAA-TATTTTAGTATATCTATAATAGTAAT
59 ATATGTTTATATTTAAAGTATATATATATATACTAAAAGTATTTTA--ATATATATAATAGTAAT
* * * *
6528042 TATATATCTTATAAATTA-ACA-CAATATATAAA-CTATATATATGAAAAGACATTACAAGTTAA
122 TATAT-TCTTATAAATGACCCAGC-ATATATAAAGC-ATATATATTAAAAGATATTACAAGTTAA
* * *
6528104 TTAATAATCATAGTTTCATGAATTAATTTAATTAACTATATAGATTTATCTTTAATT-TCTAGAA
184 TTAATAATCATAGTTTCATGAATTAATTTAATTAACTATATGGATTTGTCTTTAATTATAT-GAA
* * * * *
6528168 ATTAAAAAAAAGAAGTTAGGTTCTAAAATTATTCTAATCTCAAAAGCTT-TCTTTAAATATATAT
248 ATTAAAAAAAA-AA--TAGTTTC-AAAACTATTCTAATCTCACAA-CTTCTC-TTAAGTTTATAT
* *
6528232 ATTATAAGTTTATATAAACAATGGTATATTTATT
307 ATTAT-AGTTTATATAAACAAAGGTATATATATT
* * *
6528266 ATAATTAATAATTTTATAAGTTATAATTTTTATAATATTAACACAAAATAGAAAGTAAATATATT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
6528331 TAT-TTTAAAAGTATATATATA
66 TATATTT-AAAGTATATATATA
6528352 ATAGTAATTA
Statistics
Matches: 685, Mismatches: 61, Indels: 91
0.82 0.07 0.11
Matches are distributed among these distances:
338 72 0.11
341 44 0.06
342 9 0.01
343 77 0.11
344 159 0.23
345 1 0.00
346 1 0.00
348 1 0.00
349 4 0.01
350 4 0.01
351 3 0.00
352 5 0.01
356 6 0.01
357 3 0.00
358 8 0.01
359 102 0.15
360 15 0.02
361 33 0.05
362 3 0.00
363 17 0.02
364 50 0.07
365 68 0.10
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (339 bp):
ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
TATATTTAAAGTATATATATATATACTAAAAGTATTTTAATATATATAATAGTAATTATATTCTT
ATAAATGACCCAGCATATATAAAGCATATATATTAAAAGATATTACAAGTTAATTAATAATCATA
GTTTCATGAATTAATTTAATTAACTATATGGATTTGTCTTTAATTATATGAAATTAAAAAAAAAA
TAGTTTCAAAACTATTCTAATCTCACAACTTCTCTTAAGTTTATATATTATAGTTTATATAAACA
AAGGTATATATATT
Found at i:6527897 original size:2 final size:2
Alignment explanation
Indices: 6527892--6527926 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
6527882 TAAACAAAGG
6527892 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6527927 TTAATAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:6527916 original size:11 final size:11
Alignment explanation
Indices: 6527892--6527926 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
6527882 TAAACAAAGG
6527892 TATATATA-TA
1 TATATATATTA
6527902 TATATATATTA
1 TATATATATTA
6527913 TATATATATTA
1 TATATATATTA
6527924 TAT
1 TAT
6527927 TTAATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATATATTA
Found at i:6528284 original size:15 final size:15
Alignment explanation
Indices: 6528259--6528301 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
6528249 ACAATGGTAT
6528259 ATTTATTATAATTAATA
1 ATTT-TTATAATT-ATA
6528276 A-TTTTATAAGTTATA
1 ATTTTTATAA-TTATA
6528291 ATTTTTATAAT
1 ATTTTTATAAT
6528302 ATTAACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 11 0.46
16 12 0.50
17 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTTTTATAATTATA
Found at i:6528299 original size:359 final size:362
Alignment explanation
Indices: 6527548--6528300 Score: 959
Period size: 359 Copynumber: 2.1 Consensus size: 362
6527538 TAAACAAAGG
6527548 TATATATATTATAATTAATAA-TTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAA
1 TATATATATTATAATT-ATAATTTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAA
*
6527612 ATAAATATGTTTATATTTAAAGTACATATATATATATACTAAAAGTATTTTAATATATATAATAG
65 ATAAATATGTTTATATTTAAAGTA-ATATATATACATAC-AAAAGTATTTTAATATATATAATAG
* * * *
6527677 TAATTATATTCCTTATAAATGACCCTAGCATATATAAAGCATATATATTAAAAGATATCACAAGT
128 TAATTATATTCCTTATAAATAACACTA-CATATATAAAGCATATATATGAAAAGACATCACAAGT
* * * *
6527742 TAATTAATAATTATAATTTCATGAATTAATTTAATTAACTATCTGGATTTGTCTTTAATTATATG
192 TAATTAATAATCATAATTTCATGAATTAATTTAATTAACTATATAGATTTATCTTTAATTATATG
* * * * *
6527807 AAATAAAAAAAAAATAGTTTCAAAACTATTCTAATCTCACAACTTCTCTTGAAGTTTATCTATTA
257 AAATAAAAAAAAAATAGGTTCAAAACTATTCTAATCTCAAAACTTCTCTTGAAATATATATATTA
*
6527872 TATGTTTATATAAACAAAGGTATATATATATATATATATTA
322 TAAGTTTATATAAACAAAGGTATATATATATATATATATTA
* * *
6527913 TATATATATTAT-ATT-TAATAGTTTTATAAGTTATAATTTTTTTAATGTTAATACAAAATAGCA
1 TATATATATTATAATTATAAT--TTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAA
* *
6527976 AGTAAATATGTTTATATTTAAAGT-ATATATATACA-A-AAAA-TATTTTAGTATATCTATAATA
64 AATAAATATGTTTATATTTAAAGTAATATATATACATACAAAAGTATTTTA--ATATATATAATA
*
6528037 GTAATTATATAT-CTTATAAATTAACAC-A-ATATATAAA-CTATATATATGAAAAGACATTACA
127 GTAATTATAT-TCCTTATAAA-TAACACTACATATATAAAGC-ATATATATGAAAAGACATCACA
*
6528098 AGTTAATTAATAATCATAGTTTCATGAATTAATTTAATTAACTATATAGATTTATCTTTAATT-T
189 AGTTAATTAATAATCATAATTTCATGAATTAATTTAATTAACTATATAGATTTATCTTTAATTAT
* * *
6528162 CTAGAAATTAAAAAAAAGAAGTTAGGTTCTAAAATTATTCTAATCTCAAAAGCTT-TCTTTAAAT
254 AT-GAAA-TAAAAAAAA-AA--TAGGTTC-AAAACTATTCTAATCTCAAAA-CTTCTCTTGAAAT
*
6528226 ATATATATTATAAGTTTATATAAACAATGGTATAT-T-TAT-TATA-ATTA
312 ATATATATTATAAGTTTATATAAACAAAGGTATATATATATATATATATTA
*
6528273 -ATA-ATTTTATAAGTTATAATTTTTATAA
1 TATATATATTATAA-TTATAATTTTTATAA
6528301 TATTAACACA
Statistics
Matches: 343, Mismatches: 27, Indels: 42
0.83 0.07 0.10
Matches are distributed among these distances:
358 9 0.03
359 109 0.32
360 19 0.06
361 40 0.12
362 12 0.03
363 17 0.05
364 60 0.17
365 77 0.22
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (362 bp):
TATATATATTATAATTATAATTTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAA
TAAATATGTTTATATTTAAAGTAATATATATACATACAAAAGTATTTTAATATATATAATAGTAA
TTATATTCCTTATAAATAACACTACATATATAAAGCATATATATGAAAAGACATCACAAGTTAAT
TAATAATCATAATTTCATGAATTAATTTAATTAACTATATAGATTTATCTTTAATTATATGAAAT
AAAAAAAAAATAGGTTCAAAACTATTCTAATCTCAAAACTTCTCTTGAAATATATATATTATAAG
TTTATATAAACAAAGGTATATATATATATATATATTA
Found at i:6528913 original size:53 final size:54
Alignment explanation
Indices: 6528826--6528934 Score: 175
Period size: 53 Copynumber: 2.0 Consensus size: 54
6528816 CTCATATTAC
* *
6528826 CACCAAATTGAGTATATGGACTTGTTATCAGAATTCCACTTCAATTCCACTTTA
1 CACCAAATTGAGTATATGGACTTGTTATCAGAATTCCACTCCAATCCCACTTTA
**
6528880 CACCAAATTGAGTA-ATGGACTTGTTATTTGAATTCCACTCCAATCCCACTTTA
1 CACCAAATTGAGTATATGGACTTGTTATCAGAATTCCACTCCAATCCCACTTTA
6528933 CA
1 CA
6528935 AACAAATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 37 0.73
54 14 0.27
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (54 bp):
CACCAAATTGAGTATATGGACTTGTTATCAGAATTCCACTCCAATCCCACTTTA
Found at i:6531372 original size:7 final size:7
Alignment explanation
Indices: 6531362--6531390 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
6531352 TTTTTCCCTT
6531362 GCAGTGG
1 GCAGTGG
6531369 GCAGTGG
1 GCAGTGG
6531376 GCAGTGG
1 GCAGTGG
6531383 GCAGTGG
1 GCAGTGG
6531390 G
1 G
6531391 ATGCTGCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.59, T:0.14
Consensus pattern (7 bp):
GCAGTGG
Found at i:6538986 original size:26 final size:26
Alignment explanation
Indices: 6538949--6539000 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
6538939 AATGGAAGAG
*
6538949 AAATAATGTATAAAATATAAATAATT
1 AAATAATGTATAAAAGATAAATAATT
* *
6538975 AAAT-ATGATATACAAGATTAATAATT
1 AAATAATG-TATAAAAGATAAATAATT
6539001 TTTTTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (26 bp):
AAATAATGTATAAAAGATAAATAATT
Found at i:6542692 original size:40 final size:41
Alignment explanation
Indices: 6542605--6542694 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
6542595 GTGATTGAAA
6542605 ATTCTTTTTTATCCCAATAAGTTTGAGTATCTATAATTGCT
1 ATTCTTTTTTATCCCAATAAGTTTGAGTATCTATAATTGCT
6542646 ATTCTTTTTTATCCCAATAAGTTTGAGTATCTATAATTGCT
1 ATTCTTTTTTATCCCAATAAGTTTGAGTATCTATAATTGCT
6542687 A-TCTTTTT
1 ATTCTTTTT
6542695 CATATGCAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 7 0.14
41 42 0.86
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (41 bp):
ATTCTTTTTTATCCCAATAAGTTTGAGTATCTATAATTGCT
Found at i:6552321 original size:15 final size:17
Alignment explanation
Indices: 6552301--6552338 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
6552291 AGTATAAACT
6552301 AAAATTAAAAT-AAT-C
1 AAAATTAAAATCAATAC
*
6552316 AAAATTAAACTCAATAC
1 AAAATTAAAATCAATAC
6552333 AAAATT
1 AAAATT
6552339 GCACATGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 3 0.15
17 7 0.35
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATTAAAATCAATAC
Found at i:6552905 original size:90 final size:90
Alignment explanation
Indices: 6552776--6553005 Score: 307
Period size: 90 Copynumber: 2.6 Consensus size: 90
6552766 GAATGTCTCC
* * * * **
6552776 GATGGAGGTTCACACAAGTTCATAACGAAAGCCTCATCTTTCCATAAATCTTTAATCGAGGCCGG
1 GATGGAGGTTCCCACAAATTCATAACGGAAGCCTCATCTTTCCATAAATCTTTAACCGACACCGG
* * *
6552841 CTCGAACGTTTTCTTCCATGAGTCT
66 CTCGAACGTCTCCTTCCATGAGTCA
* * *
6552866 GATGGAGGTTCCCACAAATTCACAACGGAAGCCTCATCTTTCCATGAATCTTTAGCCGACACCGG
1 GATGGAGGTTCCCACAAATTCATAACGGAAGCCTCATCTTTCCATAAATCTTTAACCGACACCGG
*
6552931 CTCGAAGGTCTCCTTCCATGAGTCA
66 CTCGAACGTCTCCTTCCATGAGTCA
* * * *
6552956 GATGGAAGTTCCCACAAATCCATAACAGAAGCCTGATCTTTCCATAAATC
1 GATGGAGGTTCCCACAAATTCATAACGGAAGCCTCATCTTTCCATAAATC
6553006 GGCATGGACA
Statistics
Matches: 121, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 121 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (90 bp):
GATGGAGGTTCCCACAAATTCATAACGGAAGCCTCATCTTTCCATAAATCTTTAACCGACACCGG
CTCGAACGTCTCCTTCCATGAGTCA
Found at i:6554788 original size:12 final size:13
Alignment explanation
Indices: 6554757--6554789 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
6554747 AGGTTAATTA
6554757 AATTATTATTTTGT
1 AATT-TTATTTTGT
6554771 AATTTTATTTTG-
1 AATTTTATTTTGT
6554783 AATTTTA
1 AATTTTA
6554790 AAATTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 8 0.42
14 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (13 bp):
AATTTTATTTTGT
Found at i:6560151 original size:14 final size:14
Alignment explanation
Indices: 6560134--6560168 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6560124 TATCAAATAA
6560134 CAAAATTAATTAAC
1 CAAAATTAATTAAC
*
6560148 CAAAAATAATTAAC
1 CAAAATTAATTAAC
6560162 CAAAATT
1 CAAAATT
6560169 TAACCTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (14 bp):
CAAAATTAATTAAC
Done.