Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 12 of 50
Found at i:6510041 original size:18 final size:19
Alignment explanation
Indices: 6510005--6510043 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6509995 CTTGATCCCA
*
6510005 TTTTATTATAAATTTTATT
1 TTTTATTATAAATTCTATT
*
6510024 TTTTATTAT-CATTCTATT
1 TTTTATTATAAATTCTATT
6510042 TT
1 TT
6510044 ATTGGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATTATAAATTCTATT
Found at i:6511621 original size:29 final size:30
Alignment explanation
Indices: 6511576--6511635 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
6511566 GAATAATAAT
6511576 ATATACTTATTGTAT-AATTTATATTAAAAA
1 ATATACTTATTGTATAAATTTATA-TAAAAA
6511606 ATATA-TTATT-TCATAAAATTTATATAAAAA
1 ATATACTTATTGT-AT-AAATTTATATAAAAA
6511636 TAAATTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
28 1 0.04
29 7 0.26
30 11 0.41
31 8 0.30
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (30 bp):
ATATACTTATTGTATAAATTTATATAAAAA
Found at i:6512020 original size:22 final size:22
Alignment explanation
Indices: 6511986--6512047 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
6511976 AAAAATAAAC
*
6511986 AAAA-AAAAT-TAAATTATAAT
1 AAAATAAAATATAAATTAAAAT
*
6512006 AAAATAAAATATAAAGTAAAAT
1 AAAATAAAATATAAATTAAAAT
*
6512028 -AAATAAATAAATAAA-TAAAA
1 AAAATAAA-ATATAAATTAAAA
6512048 GAGAGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.11
21 17 0.47
22 15 0.42
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATAAAATATAAATTAAAAT
Found at i:6513332 original size:123 final size:123
Alignment explanation
Indices: 6513203--6513451 Score: 471
Period size: 123 Copynumber: 2.0 Consensus size: 123
6513193 TTGAAAATTT
6513203 TCACTTAAGAGAGGTAAAGAGTTACCTCTTCTAAGTGGGATTTTTTTTAAACGCGAAATTCGAGA
1 TCACTTAAGAGAGGTAAAGAGTTACCTCTTCTAAGTGGGATTTTTTTTAAACGCGAAATTCGAGA
6513268 CGAATTTTCACCGAAGCGTCGGGATAAATCCGAACTCCGAACTTCAATACCCATTAAC
66 CGAATTTTCACCGAAGCGTCGGGATAAATCCGAACTCCGAACTTCAATACCCATTAAC
*
6513326 TCACTTAAGAGAGGTAAAGAGTTACCTCTTCTAAGTGGGATTTTTTTTAAATGCGAAATTCGAGA
1 TCACTTAAGAGAGGTAAAGAGTTACCTCTTCTAAGTGGGATTTTTTTTAAACGCGAAATTCGAGA
* *
6513391 CGGATTTTCACCGAAGCGTCGGGATAAATCCGAACTCTGAACTTCAATACCCATTAAC
66 CGAATTTTCACCGAAGCGTCGGGATAAATCCGAACTCCGAACTTCAATACCCATTAAC
6513449 TCA
1 TCA
6513452 AATAATCGTT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (123 bp):
TCACTTAAGAGAGGTAAAGAGTTACCTCTTCTAAGTGGGATTTTTTTTAAACGCGAAATTCGAGA
CGAATTTTCACCGAAGCGTCGGGATAAATCCGAACTCCGAACTTCAATACCCATTAAC
Found at i:6522280 original size:59 final size:59
Alignment explanation
Indices: 6522210--6522651 Score: 536
Period size: 59 Copynumber: 7.7 Consensus size: 59
6522200 CATTAAAGAA
6522210 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
**
6522269 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAAAATTTTAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
* * *
6522328 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAAATAAGTCTAGGAA-TTTCATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
* * * * *
6522386 TTAAATTGAACC--TTGTGAGATAGGTCGAACTTAGATCAAGTCT--G-A---GAA-TT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
* * * *
6522436 TT-AATCAAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGT-TTGGAAATTTTAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGG-AATTTTAATTT
* * **
6522494 TT---TCGAACTTGTTGTGAGATAGATCGAGCCTAGATTAAGTCTAAAAATTTTAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAA--TT-T
* * * * *
6522553 TTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
6522612 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTA
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTA
6522652 NNNNNNNNNN
Statistics
Matches: 324, Mismatches: 42, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
49 7 0.02
50 5 0.02
51 25 0.08
52 1 0.00
53 1 0.00
54 2 0.01
56 67 0.21
57 3 0.01
58 24 0.07
59 145 0.45
60 1 0.00
62 43 0.13
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (59 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTT
Found at i:6522487 original size:51 final size:52
Alignment explanation
Indices: 6522326--6522651 Score: 201
Period size: 56 Copynumber: 5.8 Consensus size: 52
6522316 AAATTTTAAT
* *
6522326 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAAATAAGTCTAGGAATTTCA
1 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGT-TTGGAA----A
* * * * * *
6522383 TTTTTAAATTGAACC--TTGTGAGATAGGTCGAACTTAGATCAAGTCT-GAGAA
1 -TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTGGA-AA
* *
6522434 TTTT-AATCAAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTGGAAA
1 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTGGAAA
* * * * ** *
6522485 TTTTAATTTTTTCGAACTTGTTGTGAGATAGATCGAGCCTAGATTAAGTCTAAAAATTTTAATTT
1 TTTTAA----ATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAG--T-----TTGGAA--A
*
6522550 TGTTTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAA
1 T-TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTT-GG-A----AA
*
6522609 TATTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTA
1 T-TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTA
6522652 NNNNNNNNNN
Statistics
Matches: 207, Mismatches: 36, Indels: 49
0.71 0.12 0.17
Matches are distributed among these distances:
49 7 0.03
50 4 0.02
51 32 0.15
52 3 0.01
54 2 0.01
55 3 0.01
56 56 0.27
57 1 0.00
58 14 0.07
59 40 0.19
60 1 0.00
61 1 0.00
62 33 0.16
63 4 0.02
65 1 0.00
66 5 0.02
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (52 bp):
TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTGGAAA
Found at i:6522521 original size:56 final size:56
Alignment explanation
Indices: 6522443--6522651 Score: 222
Period size: 62 Copynumber: 3.6 Consensus size: 56
6522433 ATTTTAATCA
6522443 AACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTGGAAATTTTAATTTTTTCG
1 AACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTGGAAATTTTAATTTTTTCG
* * * * * **
6522499 AACTTGTTGTGAGATAGATCGAGCCTAGATTAAGTCTAAAAATTTTAATTTTGTTTAAATCG
1 AACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTGGAAATTTTAA--TT-TTT---TCG
* *
6522561 AACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGG-AATTTCAATATTTAAATCG
1 AACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTT-GGAAATTTTAAT-TTT--TTCG
* *
6522620 AACCTGTTGTGAGATAGGTCGAGCCTAGATTA
1 AACCTGTTATGAGATAGGTCGAGCCTAAATTA
6522652 NNNNNNNNNN
Statistics
Matches: 125, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
56 41 0.33
58 2 0.02
59 36 0.29
60 3 0.02
61 1 0.01
62 42 0.34
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (56 bp):
AACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTGGAAATTTTAATTTTTTCG
Found at i:6522574 original size:62 final size:59
Alignment explanation
Indices: 6522434--6522651 Score: 264
Period size: 56 Copynumber: 3.7 Consensus size: 59
6522424 AGTCTGAGAA
* *
6522434 TTTT-AATCAAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTGGAAATTTTAAT
1 TTTTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGAAATTTTAAT
* * * * * *
6522492 TTTT---TCGAACTTGTTGTGAGATAGATCGAGCCTAGATTAAGTCTAAAAATTTTAATTT
1 TTTTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGAAATTTTAA--T
* *
6522550 TGTTTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAAT
1 T-TTTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGAAATTTTAAT
* * *
6522610 ATTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTA
1 TTTTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTA
6522652 NNNNNNNNNN
Statistics
Matches: 135, Mismatches: 19, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
56 43 0.32
58 6 0.04
59 42 0.31
60 1 0.01
62 43 0.32
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (59 bp):
TTTTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGAAATTTTAAT
Found at i:6524993 original size:14 final size:14
Alignment explanation
Indices: 6524974--6525001 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6524964 GTGCATACGT
6524974 AAAACCAAATAAAA
1 AAAACCAAATAAAA
6524988 AAAACCAAATAAAA
1 AAAACCAAATAAAA
6525002 GACTCAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAACCAAATAAAA
Found at i:6552766 original size:2 final size:2
Alignment explanation
Indices: 6552759--6552785 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6552749 TAACAGACAG
6552759 AC 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 AC A
6552786 AAGCCACAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6553323 original size:2 final size:2
Alignment explanation
Indices: 6553316--6553375 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
6553306 ACAGAGGGGA
* *
6553316 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AT A- ACT A- AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG
6553356 NAG AG AG AG AG AG AG AG AG A
1 -AG AG AG AG AG AG AG AG AG A
6553376 TACTAAGGCT
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
1 3 0.06
2 47 0.90
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.43, T:0.03
Consensus pattern (2 bp):
AG
Found at i:6553363 original size:29 final size:27
Alignment explanation
Indices: 6553327--6553383 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 27
6553317 GAGAGAGAGA
6553327 GAGAGAGAGAGAGAGAGAGATAACTAAG
1 GAGAGAGAGAGAGAGAGAGAT-ACTAAG
6553355 GNAGAGAGAGAGAGAGAGAGATACTAAG
1 G-AGAGAGAGAGAGAGAGAGATACTAAG
6553383 G
1 G
6553384 CTTACGTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.47, C:0.04, G:0.40, T:0.07
Consensus pattern (27 bp):
GAGAGAGAGAGAGAGAGAGATACTAAG
Found at i:6559001 original size:59 final size:60
Alignment explanation
Indices: 6558906--6559024 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 60
6558896 TGATTGGAAT
* ** * *
6558906 TTATTCTAGTCAATTTTACATTGATTTAATTAGAATGCTGCCAAACTACTTATTTTTTTC
1 TTATTCTAGTCAATTATACATTGAGCTAATTAGAATGCTACCAAACTACTTATTGTTTTC
* *
6558966 TTATTCTAGTCAA-TATACATTGAGCTAATTTGAATGCTACCAAACTGCTTATTGTTTTC
1 TTATTCTAGTCAATTATACATTGAGCTAATTAGAATGCTACCAAACTACTTATTGTTTTC
6559025 CTGATTAACT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
59 39 0.75
60 13 0.25
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (60 bp):
TTATTCTAGTCAATTATACATTGAGCTAATTAGAATGCTACCAAACTACTTATTGTTTTC
Found at i:6567918 original size:75 final size:73
Alignment explanation
Indices: 6567764--6568114 Score: 446
Period size: 75 Copynumber: 4.8 Consensus size: 73
6567754 AAGAATCAAC
* * ** * * * * *
6567764 TCGACCTAGAATCTCCAAGCCACTCTGTATTCTGTTCTCT-ACTCTCTCC-GTC-TTGCCTCTAC
1 TCGACCTAGAATCTCAAAGCCGCAATATATTCTGTTCTCTGTCTCTCTCCTTTCTTTACCTCCAC
6567826 CTTCACCT
66 CTTCACCT
* *
6567834 TCGACCTAGAATCTCAAAGCCGCAGTATATTCTGTTCTCTGCTCTTCTCTCCTTTCTTTATCTCC
1 TCGACCTAGAATCTCAAAGCCGCAATATATTCTGTTCTCTG-TC-TCTCTCCTTTCTTTACCTCC
6567899 ACCTTCACCT
64 ACCTTCACCT
* * * * * *
6567909 TCGACCTAGAATCT-ACAAGCCACTATGTATTCTGTTCTCT-ACTCTCT-CTGTCTTTACCTCTA
1 TCGACCTAGAATCTCA-AAGCCGCAATATATTCTGTTCTCTGTCTCTCTCCTTTCTTTACCTCCA
6567971 CCTTCACCT
65 CCTTCACCT
*
6567980 TCGACCTAAAATCTCAAAGCCGCAATATATTCTGTTCTCTGCTCTTCTCTCCTTTCTTTACCTCC
1 TCGACCTAGAATCTCAAAGCCGCAATATATTCTGTTCTCTG-TC-TCTCTCCTTTCTTTACCTCC
6568045 ACCTTCACCT
64 ACCTTCACCT
6568055 TCGACCTAGAATCTCAAAGCCGCAATATATTCTGTTCTCTG-CTCTCTCCTTTCTTTACCT
1 TCGACCTAGAATCTCAAAGCCGCAATATATTCTGTTCTCTGTCTCTCTCCTTTCTTTACCT
6568115 TTACCTTACC
Statistics
Matches: 244, Mismatches: 26, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
70 35 0.14
71 55 0.23
72 25 0.10
73 10 0.04
74 8 0.03
75 111 0.45
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.38
Consensus pattern (73 bp):
TCGACCTAGAATCTCAAAGCCGCAATATATTCTGTTCTCTGTCTCTCTCCTTTCTTTACCTCCAC
CTTCACCT
Found at i:6568017 original size:146 final size:145
Alignment explanation
Indices: 6567764--6568126 Score: 568
Period size: 146 Copynumber: 2.5 Consensus size: 145
6567754 AAGAATCAAC
* * *
6567764 TCGACCTAGAATCTCCAAGCCACTCTGTATTCTGTTCTCTACTCTCTCCGTC-TTGCCTCTACCT
1 TCGACCTAGAATCT-CAAGCCACTATGTATTCTGTTCTCTACTCTCTCTGTCTTTACCTCTACCT
* *
6567828 TCACCTTCGACCTAGAATCTCAAAGCCGCAGTATATTCTGTTCTCTGCTCTTCTCTCCTTTCTTT
65 TCACCTTCGACCTAAAATCTCAAAGCCGCAATATATTCTGTTCTCTGCTCTTCTCTCCTTTCTTT
*
6567893 ATCTCCACCTTCACCT
130 ACCTCCACCTTCACCT
6567909 TCGACCTAGAATCTACAAGCCACTATGTATTCTGTTCTCTACTCTCTCTGTCTTTACCTCTACCT
1 TCGACCTAGAATCT-CAAGCCACTATGTATTCTGTTCTCTACTCTCTCTGTCTTTACCTCTACCT
6567974 TCACCTTCGACCTAAAATCTCAAAGCCGCAATATATTCTGTTCTCTGCTCTTCTCTCCTTTCTTT
65 TCACCTTCGACCTAAAATCTCAAAGCCGCAATATATTCTGTTCTCTGCTCTTCTCTCCTTTCTTT
6568039 ACCTCCACCTTCACCT
130 ACCTCCACCTTCACCT
* * * * * *
6568055 TCGACCTAGAATCTCAAAGCCGCAATATATTCTGTTCTCTGCTCTCTCCTTTCTTTACCTTTACC
1 TCGACCTAGAATCTC-AAGCCACTATGTATTCTGTTCTCTACTCTCT-CTGTCTTTACCTCTACC
6568120 TT-ACCTT
64 TTCACCTT
6568127 TATTATTCAC
Statistics
Matches: 202, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
145 50 0.25
146 135 0.67
147 17 0.08
ACGTcount: A:0.18, C:0.35, G:0.09, T:0.38
Consensus pattern (145 bp):
TCGACCTAGAATCTCAAGCCACTATGTATTCTGTTCTCTACTCTCTCTGTCTTTACCTCTACCTT
CACCTTCGACCTAAAATCTCAAAGCCGCAATATATTCTGTTCTCTGCTCTTCTCTCCTTTCTTTA
CCTCCACCTTCACCT
Found at i:6578440 original size:17 final size:17
Alignment explanation
Indices: 6578401--6578443 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
6578391 TAACAATAAA
* *
6578401 TAAAAAAATAATTATTT
1 TAAAAATATTATTATTT
6578418 T-AAAATATTATTATTT
1 TAAAAATATTATTATTT
6578434 TAAAAATATT
1 TAAAAATATT
6578444 TTTTCATGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAATATTATTATTT
Found at i:6578504 original size:17 final size:18
Alignment explanation
Indices: 6578473--6578511 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6578463 AATTTTTTTA
*
6578473 TTTAAATAATTTTTAATT
1 TTTAAATAATATTTAATT
*
6578491 TTTAAA-AATATTTATTT
1 TTTAAATAATATTTAATT
6578508 TTTA
1 TTTA
6578512 TACCTTGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAATAATATTTAATT
Found at i:6580591 original size:2 final size:2
Alignment explanation
Indices: 6580575--6580608 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6580565 TTCTTCCCCT
6580575 TC TC -C TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6580609 CTTTTCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:6582514 original size:22 final size:22
Alignment explanation
Indices: 6582486--6582535 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
6582476 GAAATTGGAA
* *
6582486 AGAAAAAAGGAAAAATGAAAAT
1 AGAAAAAAAGAAAAATAAAAAT
*
6582508 AGAAAAAAATAAAAATAAAAAT
1 AGAAAAAAAGAAAAATAAAAAT
6582530 A-AAAAA
1 AGAAAAA
6582536 CATTATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (22 bp):
AGAAAAAAAGAAAAATAAAAAT
Found at i:6582580 original size:117 final size:118
Alignment explanation
Indices: 6582415--6582642 Score: 259
Period size: 117 Copynumber: 1.9 Consensus size: 118
6582405 TTTACTGTAT
* * *
6582415 AAAATATTATATTAGTATTTTAATAATAAATTACTAAACTAATAATATTTTAATA-AATAAAGAA
1 AAAACATTATATTAATATTTTAAGAATAAATTACTAAACTAATAATATTTTAATAGAA-AAAGAA
*
6582479 ATTGGAAAGA-AAAAA-GGAAAAATGAAAATAGA-AAAAAA-TAAAAATAAAAATAA
65 ATT-AAAAGAGAAAAATGG--AAATGAAAATAGAGAAAAAATTAAAAATAAAAATAA
* * * * * * * *
6582532 AAAACATTATTTTAATATTTTAAGAATAAATTATTACATTATTGATATTTTATTAGAAAAAGGAA
1 AAAACATTATATTAATATTTTAAGAATAAATTACTAAACTAATAATATTTTAATAGAAAAAGAAA
*
6582597 TTAAAAGAGAAAAATTGGAAATGCAAATAGAGAAAAAATTAAAAAT
66 TTAAAAGAGAAAAA-TGGAAATGAAAATAGAGAAAAAATTAAAAAT
6582643 TATTAATATT
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
116 5 0.05
117 70 0.76
118 8 0.09
119 9 0.10
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (118 bp):
AAAACATTATATTAATATTTTAAGAATAAATTACTAAACTAATAATATTTTAATAGAAAAAGAAA
TTAAAAGAGAAAAATGGAAATGAAAATAGAGAAAAAATTAAAAATAAAAATAA
Found at i:6582687 original size:22 final size:22
Alignment explanation
Indices: 6582662--6582706 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
6582652 TTAAACTTTG
6582662 ATATTTCAATAATAA-ATTATTA
1 ATATTTCAATAATAATA-TATTA
* *
6582684 ATATTTTAATGATAATATATTA
1 ATATTTCAATAATAATATATTA
6582706 A
1 A
6582707 ATTATTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATTTCAATAATAATATATTA
Found at i:6584177 original size:17 final size:18
Alignment explanation
Indices: 6584157--6584192 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6584147 ATTTAATTCA
6584157 TACATAAA-AAAATAAAT
1 TACATAAATAAAATAAAT
6584174 TACATAAATAAAATAAAT
1 TACATAAATAAAATAAAT
6584192 T
1 T
6584193 GAGTAAGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
TACATAAATAAAATAAAT
Found at i:6584179 original size:21 final size:21
Alignment explanation
Indices: 6584151--6584191 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6584141 TCATAAATTT
*
6584151 AATTCATACATAAAA-AAATA
1 AATTCATAAATAAAATAAATA
6584171 AATTACATAAATAAAATAAAT
1 AATT-CATAAATAAAATAAAT
6584192 TGAGTAAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (21 bp):
AATTCATAAATAAAATAAATA
Found at i:6584745 original size:40 final size:40
Alignment explanation
Indices: 6584701--6584780 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
6584691 CTACATAAGA
* *
6584701 AAGTGAAATGTACATGTTGAGGCCCCAACTTACCCCAACT
1 AAGTGAAATGCACATGTTGAGCCCCCAACTTACCCCAACT
* * *
6584741 AAGTGACATGCACATGTTTAGCCCCCAACTTACCCTAACT
1 AAGTGAAATGCACATGTTGAGCCCCCAACTTACCCCAACT
6584781 TTAATTCTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (40 bp):
AAGTGAAATGCACATGTTGAGCCCCCAACTTACCCCAACT
Found at i:6584827 original size:56 final size:56
Alignment explanation
Indices: 6584741--6584955 Score: 280
Period size: 56 Copynumber: 3.9 Consensus size: 56
6584731 TACCCCAACT
* *
6584741 AAGTGACATGCACATGTTTAGCCCCCAACTTACCCTAACTTTAATTCTACATAAGA
1 AAGTGACATGTACATGTTTAGCCCCCAACTTACCCCAACTTTAATTCTACATAAGA
** **
6584797 AAGTGACATGTACATGTTTAGCCCCCAACTTTTAGCCCCCAAC-TT-A--C--CCCAACT
1 AAGTGACATGTACATGTTTAGCCCCCAAC--TTA--CCCCAACTTTAATTCTACATAAGA
* *
6584851 AAGTGACATGTACATGTTTGGGCCCCAACTTACCCCAACTTTAATTCTACATAAGA
1 AAGTGACATGTACATGTTTAGCCCCCAACTTACCCCAACTTTAATTCTACATAAGA
6584907 AAGTGACATGTACATGTTTAGCCCCCAACTTACCCCAACTTTAATTCTA
1 AAGTGACATGTACATGTTTAGCCCCCAACTTACCCCAACTTTAATTCTA
6584956 GATGTTGATC
Statistics
Matches: 135, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
50 7 0.05
51 2 0.01
52 4 0.03
54 31 0.23
56 79 0.59
58 4 0.03
59 2 0.01
60 6 0.04
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (56 bp):
AAGTGACATGTACATGTTTAGCCCCCAACTTACCCCAACTTTAATTCTACATAAGA
Found at i:6584832 original size:14 final size:14
Alignment explanation
Indices: 6584813--6584841 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6584803 CATGTACATG
6584813 TTTAGCCCCCAACT
1 TTTAGCCCCCAACT
6584827 TTTAGCCCCCAACT
1 TTTAGCCCCCAACT
6584841 T
1 T
6584842 ACCCCAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.41, G:0.07, T:0.31
Consensus pattern (14 bp):
TTTAGCCCCCAACT
Found at i:6584916 original size:110 final size:110
Alignment explanation
Indices: 6584723--6584937 Score: 394
Period size: 110 Copynumber: 2.0 Consensus size: 110
6584713 CATGTTGAGG
*
6584723 CCCCAACTTACCCCAACTAAGTGACATGCACATGTTTAGCCCCCAACTTACCCTAACTTTAATTC
1 CCCCAACTTACCCCAACTAAGTGACATGCACATGTTTAGCCCCCAACTTACCCCAACTTTAATTC
6584788 TACATAAGAAAGTGACATGTACATGTTTAGCCCCCAACTTTTAGC
66 TACATAAGAAAGTGACATGTACATGTTTAGCCCCCAACTTTTAGC
* * *
6584833 CCCCAACTTACCCCAACTAAGTGACATGTACATGTTTGGGCCCCAACTTACCCCAACTTTAATTC
1 CCCCAACTTACCCCAACTAAGTGACATGCACATGTTTAGCCCCCAACTTACCCCAACTTTAATTC
6584898 TACATAAGAAAGTGACATGTACATGTTTAGCCCCCAACTT
66 TACATAAGAAAGTGACATGTACATGTTTAGCCCCCAACTT
6584938 ACCCCAACTT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 101 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.27
Consensus pattern (110 bp):
CCCCAACTTACCCCAACTAAGTGACATGCACATGTTTAGCCCCCAACTTACCCCAACTTTAATTC
TACATAAGAAAGTGACATGTACATGTTTAGCCCCCAACTTTTAGC
Found at i:6590873 original size:18 final size:18
Alignment explanation
Indices: 6590852--6590888 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6590842 TGTCACGTAT
* *
6590852 ACACGTTTAAACACGATA
1 ACACGATTAAACACAATA
6590870 ACACGATTAAACACAATA
1 ACACGATTAAACACAATA
6590888 A
1 A
6590889 TACCATTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.22, G:0.08, T:0.19
Consensus pattern (18 bp):
ACACGATTAAACACAATA
Found at i:6590896 original size:18 final size:18
Alignment explanation
Indices: 6590858--6590896 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6590848 GTATACACGT
* *
6590858 TTAAACACGATAACACGA
1 TTAAACACAATAACACCA
*
6590876 TTAAACACAATAATACCA
1 TTAAACACAATAACACCA
6590894 TTA
1 TTA
6590897 GATAAACGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.23
Consensus pattern (18 bp):
TTAAACACAATAACACCA
Found at i:6591301 original size:7 final size:7
Alignment explanation
Indices: 6591289--6591319 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
6591279 ACTAGTTAGT
6591289 GCAAGTA
1 GCAAGTA
6591296 GCAAGTA
1 GCAAGTA
6591303 GCAAGTA
1 GCAAGTA
*
6591310 GCAAGCA
1 GCAAGTA
6591317 GCA
1 GCA
6591320 GCTCACTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.42, C:0.19, G:0.29, T:0.10
Consensus pattern (7 bp):
GCAAGTA
Found at i:6600503 original size:2 final size:2
Alignment explanation
Indices: 6600496--6600520 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6600486 TCCGTTATGA
6600496 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6600521 ATTATGGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6623772 original size:2 final size:2
Alignment explanation
Indices: 6623767--6623806 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6623757 TTCTTTTTTG
6623767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6623807 TTGTATACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6624590 original size:5 final size:5
Alignment explanation
Indices: 6624580--6624609 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
6624570 AATACGTGCA
6624580 TAATT TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT
6624610 AATCTGATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:6629863 original size:3 final size:3
Alignment explanation
Indices: 6629857--6629898 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
6629847 CACTCAACAA
*
6629857 CTT CTT CTT CTT CTT CTT CTT CTT CCT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
6629899 GTTCCCAGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:6634900 original size:20 final size:19
Alignment explanation
Indices: 6634852--6634890 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6634842 AGGTAAATTT
6634852 ATAAGAAGT-AATCATAAAA
1 ATAA-AAGTAAATCATAAAA
6634871 ATAAAAGTAAATCATAAAA
1 ATAAAAGTAAATCATAAAA
6634890 A
1 A
6634891 AAATTAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (19 bp):
ATAAAAGTAAATCATAAAA
Found at i:6637312 original size:15 final size:16
Alignment explanation
Indices: 6637292--6637322 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6637282 TTTTTTCACC
6637292 CTTTCTCT-TCTTTTG
1 CTTTCTCTATCTTTTG
6637307 CTTTCTCTATCTTTTG
1 CTTTCTCTATCTTTTG
6637323 ATCGTTTTTT
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:0.03, C:0.26, G:0.06, T:0.65
Consensus pattern (16 bp):
CTTTCTCTATCTTTTG
Found at i:6644581 original size:2 final size:2
Alignment explanation
Indices: 6644574--6644611 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6644564 ATTATCCCCG
6644574 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6644612 TTTCCTCACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6646231 original size:156 final size:157
Alignment explanation
Indices: 6646070--6646372 Score: 437
Period size: 157 Copynumber: 1.9 Consensus size: 157
6646060 TGGATGTCAT
* * * * *
6646070 ATTAGTAAGAGATGATATAAATTTTGAATATATAAATATG-ATTTTTTTTTATAAATTATGTTTT
1 ATTAGTAAAAAATGAAATAAACTTTGAATATATAAATATGTATTTTTTTTTATAAATTATGTCTT
* * * * * *
6646134 TTGAATTGAAAATATTTGATTTTTTATGGCAATATTGATTTGGGTTGAAAAATGAGAAATTCAAG
66 TTGAATTGAAAATATTTAATTTCTTATGACAACATTGATTTGGGTTGAAAAATCAGAAATTCAAA
*
6646199 AAATAAAAACTTTGATTTATACAACAC
131 AAACAAAAACTTTGATTTATACAACAC
* * * *
6646226 ATTAGTAAAAAATGAAATAAACTTTGAATATATAAATATGTGTTTTTTTTTATTAGTTGTGTCTT
1 ATTAGTAAAAAATGAAATAAACTTTGAATATATAAATATGTATTTTTTTTTATAAATTATGTCTT
* *
6646291 TTGAATTGAAAATATTTAATTTCTTATGACAACATTGGTTTGGGTTGGAAAATCAGAAATTCAAA
66 TTGAATTGAAAATATTTAATTTCTTATGACAACATTGATTTGGGTTGAAAAATCAGAAATTCAAA
6646356 AAACAAAAACTTTGATT
131 AAACAAAAACTTTGATT
6646373 AGGCCGATAT
Statistics
Matches: 128, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
156 36 0.28
157 92 0.72
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (157 bp):
ATTAGTAAAAAATGAAATAAACTTTGAATATATAAATATGTATTTTTTTTTATAAATTATGTCTT
TTGAATTGAAAATATTTAATTTCTTATGACAACATTGATTTGGGTTGAAAAATCAGAAATTCAAA
AAACAAAAACTTTGATTTATACAACAC
Found at i:6646386 original size:2 final size:2
Alignment explanation
Indices: 6646379--6646403 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6646369 GATTAGGCCG
6646379 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6646404 ATAAATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6646434 original size:2 final size:2
Alignment explanation
Indices: 6646427--6646455 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6646417 CCCAACNCCG
6646427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6646456 AAATACATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6646460 original size:50 final size:47
Alignment explanation
Indices: 6646376--6646470 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 47
6646366 TTTGATTAGG
6646376 CCGATATATATATATATATATATATATAATAAATACATAGACCCAAC
1 CCGATATATATATATATATATATATATAATAAATACATAGACCCAAC
6646423 NCCGATATATATATATATATATATATATATATAAAATACATAGACCCA
1 -CCGATATATATATATATATATATATATA-AT-AAATACATAGACCCA
6646471 CAAAAACTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 28 0.62
49 2 0.04
50 15 0.33
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.33
Consensus pattern (47 bp):
CCGATATATATATATATATATATATATAATAAATACATAGACCCAAC
Found at i:6652159 original size:6 final size:6
Alignment explanation
Indices: 6652148--6652173 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6652138 GGGTATTCAA
6652148 AGCCAT AGCCAT AGCCAT AGCCAT AG
1 AGCCAT AGCCAT AGCCAT AGCCAT AG
6652174 TTGTAGCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (6 bp):
AGCCAT
Found at i:6653333 original size:4 final size:4
Alignment explanation
Indices: 6653324--6653350 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6653314 CCATTACCAT
6653324 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
6653351 TTCAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:6656799 original size:15 final size:15
Alignment explanation
Indices: 6656779--6656808 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6656769 TGTTACAATG
*
6656779 TAATATTATTATAAA
1 TAATATGATTATAAA
6656794 TAATATGATTATAAA
1 TAATATGATTATAAA
6656809 AAAGATAAAA
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:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TAATATGATTATAAA
Found at i:6665505 original size:22 final size:23
Alignment explanation
Indices: 6665454--6665517 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
6665444 GAAGATGAAC
6665454 AATTAATTTAAATTTTT-TTATTA
1 AATTAA-TTAAATTTTTATTATTA
6665477 AATTTAATTAAATTTTTATT-TTA
1 AA-TTAATTAAATTTTTATTATTA
* *
6665500 AATTAAATAAGTTTTTAT
1 AATTAATTAAATTTTTAT
6665518 GATAAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 14 0.38
23 17 0.46
24 6 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AATTAATTAAATTTTTATTATTA
Found at i:6665524 original size:22 final size:20
Alignment explanation
Indices: 6665468--6665517 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
6665458 AATTTAAATT
*
6665468 TTTTTATTAAATTTAATTAAA
1 TTTTTATTAAA-TTAAATAAA
*
6665489 TTTTTATTTTAAATTAAATAAG
1 TTTTTA--TTAAATTAAATAAA
6665511 TTTTTAT
1 TTTTTAT
6665518 GATAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 13 0.52
23 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTATTAAATTAAATAAA
Found at i:6665685 original size:30 final size:30
Alignment explanation
Indices: 6665649--6665710 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
6665639 CAAAAAAGAT
* *
6665649 TTATTTAACTCAAACTATAAATATAAAAAC
1 TTATTTAACTCAAAATAAAAATATAAAAAC
** *
6665679 TTATTTAGTTCAAAATAAAAATATAAATAC
1 TTATTTAACTCAAAATAAAAATATAAAAAC
6665709 TT
1 TT
6665711 GATTAAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (30 bp):
TTATTTAACTCAAAATAAAAATATAAAAAC
Found at i:6670494 original size:29 final size:29
Alignment explanation
Indices: 6670437--6670494 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
6670427 GATGAATCAG
* *
6670437 GTGCCTCAAGTTTCTACTCACATTTCTTA
1 GTGCCTCAAATTTCTACTCACATTACTTA
* *
6670466 GTGCCTCAAATTTCTACTTACGTTACTTA
1 GTGCCTCAAATTTCTACTCACATTACTTA
6670495 ATTTAGGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.41
Consensus pattern (29 bp):
GTGCCTCAAATTTCTACTCACATTACTTA
Found at i:6671443 original size:99 final size:98
Alignment explanation
Indices: 6671273--6671467 Score: 336
Period size: 99 Copynumber: 2.0 Consensus size: 98
6671263 TTTAGCCTCA
* * *
6671273 ACTAAATCTAAGTTCAATCTACACTTTTAATGCTGCATAAACAGATCAAGGTGATACTTCGTTTC
1 ACTAAATCTAAGTTCAATCAACACTTTTAATGCTGCATAAACAGATAAAGGTGATACTTCATTTC
6671338 TTCAATATGAAATAAATTTCATTAAATCAAAGT
66 TTCAATATGAAATAAATTTCATTAAATCAAAGT
6671371 ACTAAATCTAAGTTCAATCAACACTTTTTAATGCTGCATAAACAGATAAAGGTGATACTTCATTT
1 ACTAAATCTAAGTTCAATCAACAC-TTTTAATGCTGCATAAACAGATAAAGGTGATACTTCATTT
**
6671436 CTTCAATATGAAATGTATTTCATTAAATCAAA
65 CTTCAATATGAAATAAATTTCATTAAATCAAA
6671468 TTATTTCTTC
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 23 0.25
99 68 0.75
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (98 bp):
ACTAAATCTAAGTTCAATCAACACTTTTAATGCTGCATAAACAGATAAAGGTGATACTTCATTTC
TTCAATATGAAATAAATTTCATTAAATCAAAGT
Found at i:6673839 original size:16 final size:15
Alignment explanation
Indices: 6673811--6673853 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
6673801 AATTAATTAT
6673811 ATTAAAAATATATACAA
1 ATTAAAAA-ATATA-AA
6673828 ATTAAAAAATATAAA
1 ATTAAAAAATATAAA
*
6673843 AGTAAAAAATA
1 ATTAAAAAATA
6673854 ATTAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.48
16 5 0.20
17 8 0.32
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (15 bp):
ATTAAAAAATATAAA
Found at i:6675285 original size:80 final size:80
Alignment explanation
Indices: 6675147--6675307 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 80
6675137 AGAGTTTGTT
* *
6675147 TATTGTGATTTAGCTCGATATTTACAAAGGGAGTGTTCAATGTATCACACTTCCTAATCCTAGCT
1 TATTGCGAATTAGCTCGATATTTACAAAGGGAGTGTTCAATGTATCACACTTCCTAATCCTAGCT
*
6675212 TTTAAGTTGGTTCAA
66 CTTAAGTTGGTTCAA
** * *
6675227 TATTGCGAATTAGCTCGATATTTATGAAGGGAGTGTTCAATGTATCGCACTTCTTAATCCTAGCT
1 TATTGCGAATTAGCTCGATATTTACAAAGGGAGTGTTCAATGTATCACACTTCCTAATCCTAGCT
6675292 CTTAAGTTGGTTCAA
66 CTTAAGTTGGTTCAA
6675307 T
1 T
6675308 TTAGAGACGA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (80 bp):
TATTGCGAATTAGCTCGATATTTACAAAGGGAGTGTTCAATGTATCACACTTCCTAATCCTAGCT
CTTAAGTTGGTTCAA
Found at i:6677016 original size:9 final size:9
Alignment explanation
Indices: 6676971--6677016 Score: 51
Period size: 8 Copynumber: 5.2 Consensus size: 9
6676961 TACACGTTCA
6676971 AACACGA-T
1 AACACGATT
6676979 AACACGATT
1 AACACGATT
6676988 AAACACGA-T
1 -AACACGATT
* *
6676997 AATATGATT
1 AACACGATT
6677006 AACACGATT
1 AACACGATT
6677015 AA
1 AA
6677017 TTAAATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
8 12 0.39
9 12 0.39
10 7 0.23
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (9 bp):
AACACGATT
Found at i:6677017 original size:18 final size:18
Alignment explanation
Indices: 6676970--6677013 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
6676960 ATACACGTTC
*
6676970 AAACACGATAACACGATT
1 AAACACGATAATACGATT
*
6676988 AAACACGATAATATGATT
1 AAACACGATAATACGATT
6677006 -AACACGAT
1 AAACACGAT
6677014 TAATTAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.20
Consensus pattern (18 bp):
AAACACGATAATACGATT
Found at i:6679765 original size:19 final size:20
Alignment explanation
Indices: 6679737--6679787 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
6679727 AGAGGGATAT
6679737 TTTTTAAAAAATTGATGTGA
1 TTTTTAAAAAATTGATGTGA
6679757 TTTTTAAAAAATTGATGTGA
1 TTTTTAAAAAATTGATGTGA
6679777 TTTTTAAAAAA
1 TTTTTAAAAAA
6679788 AGAGAAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (20 bp):
TTTTTAAAAAATTGATGTGA
Found at i:6681918 original size:14 final size:14
Alignment explanation
Indices: 6681899--6681927 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6681889 CAAAAATTAT
6681899 AACTTATAAAAAAA
1 AACTTATAAAAAAA
6681913 AACTTATAAAAAAA
1 AACTTATAAAAAAA
6681927 A
1 A
6681928 TTTTACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AACTTATAAAAAAA
Found at i:6682866 original size:14 final size:14
Alignment explanation
Indices: 6682847--6682876 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6682837 AATAAAATTA
*
6682847 TATTTTAATTTAAT
1 TATTTTAATTGAAT
6682861 TATTTTAATTGAAT
1 TATTTTAATTGAAT
6682875 TA
1 TA
6682877 ATCACCTAAT
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:0.03, T:0.60
Consensus pattern (14 bp):
TATTTTAATTGAAT
Found at i:6687000 original size:79 final size:80
Alignment explanation
Indices: 6686899--6687057 Score: 221
Period size: 79 Copynumber: 2.0 Consensus size: 80
6686889 TGCATAACTC
* * * * * * *
6686899 AGTATTTTTTTAATAGGCTGTCTTATTAATACTTTATGTAGATTCTCCTGGCAATCTTTTTTTCT
1 AGTATTTTTTTAAGAGGCTGTCTTATGAATACTGTATGTAGAGTCTCCTGGAAATCATTTTTACT
6686964 CTCTAGGATTTATGT
66 CTCTAGGATTTATGT
* *
6686979 AGTATTTTTTTAAGA-GTTGTCTTATGAATACTGTGTGTAGAGTCTCCTGGAAATCATTTTTACT
1 AGTATTTTTTTAAGAGGCTGTCTTATGAATACTGTATGTAGAGTCTCCTGGAAATCATTTTTACT
*
6687043 CTCTTGGATTTATGT
66 CTCTAGGATTTATGT
6687058 TGATAAATTG
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
79 55 0.80
80 14 0.20
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (80 bp):
AGTATTTTTTTAAGAGGCTGTCTTATGAATACTGTATGTAGAGTCTCCTGGAAATCATTTTTACT
CTCTAGGATTTATGT
Found at i:6692472 original size:3 final size:3
Alignment explanation
Indices: 6692464--6692490 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6692454 AATCGCAAGG
6692464 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
6692491 GGGAGGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6692948 original size:2 final size:2
Alignment explanation
Indices: 6692941--6692978 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6692931 ATAACGGAAG
6692941 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
6692979 CATCTACTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6699773 original size:2 final size:2
Alignment explanation
Indices: 6699768--6699802 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6699758 TCTCTCTCTC
6699768 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
6699803 TATGTATCTA
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:6710777 original size:20 final size:19
Alignment explanation
Indices: 6710734--6710777 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
6710724 TTTTTACTGC
* *
6710734 AGATATTTGAAATATCCAT
1 AGATATATGAAATATACAT
*
6710753 GGATATATGAATATATACAT
1 AGATATATGAA-ATATACAT
6710773 AGATA
1 AGATA
6710778 ATTTGTCGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (19 bp):
AGATATATGAAATATACAT
Found at i:6723871 original size:2 final size:2
Alignment explanation
Indices: 6723864--6723909 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
6723854 CCTTAAGCTG
*
6723864 CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6723905 CT CT C
1 CT CT C
6723910 CCTCCAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:6741217 original size:45 final size:45
Alignment explanation
Indices: 6741160--6741253 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
6741150 ATTAAATTTA
* *
6741160 AATAATACTAAATAATATTCTTTGTTACATTTATTATA-TTCAAAT
1 AATAATACTAAATAATATTCTTTATAACATTTATTATAGTT-AAAT
* *
6741205 AATAATATTAAATAATATTCTTTATAATATTTATTATAGTTAAAT
1 AATAATACTAAATAATATTCTTTATAACATTTATTATAGTTAAAT
6741250 AATA
1 AATA
6741254 TTAATATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 42 0.95
46 2 0.05
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (45 bp):
AATAATACTAAATAATATTCTTTATAACATTTATTATAGTTAAAT
Found at i:6741220 original size:10 final size:10
Alignment explanation
Indices: 6741205--6741279 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
6741195 ATATTCAAAT
6741205 AATAATATTA
1 AATAATATTA
*
6741215 AATAATATTCTT
1 AATAATA-T-TA
*
6741227 TATAATATT-
1 AATAATATTA
* *
6741236 TATTATAGTTA
1 AATAATA-TTA
6741247 AATAATATT-
1 AATAATATTA
6741256 AAT-ATATTA
1 AATAATATTA
6741265 AATAATATTTA
1 AATAATA-TTA
6741276 AATA
1 AATA
6741280 TTTTCACCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.09
9 12 0.23
10 15 0.28
11 14 0.26
12 7 0.13
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (10 bp):
AATAATATTA
Found at i:6741267 original size:18 final size:19
Alignment explanation
Indices: 6741228--6741273 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
6741218 AATATTCTTT
*
6741228 ATAATATTTATTATAGTTAA
1 ATAATA-TTAATATAGTTAA
6741248 ATAATATTAATATA-TTAA
1 ATAATATTAATATAGTTAA
6741266 ATAATATT
1 ATAATATT
6741274 TAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
19 7 0.28
20 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATAATATTAATATAGTTAA
Found at i:6741272 original size:12 final size:11
Alignment explanation
Indices: 6741195--6741279 Score: 56
Period size: 11 Copynumber: 8.0 Consensus size: 11
6741185 TACATTTATT
*
6741195 ATATTCAAATA
1 ATATTTAAATA
6741206 ATAATATTAAATA
1 AT-AT-TTAAATA
**
6741219 ATATTCTTTATA
1 ATATT-TAAATA
*
6741231 ATATTT--ATT
1 ATATTTAAATA
*
6741240 ATAGTTAAATA
1 ATATTTAAATA
6741251 ATA-TT-AAT-
1 ATATTTAAATA
6741259 ATA-TTAAATA
1 ATATTTAAATA
6741269 ATATTTAAATA
1 ATATTTAAATA
6741280 TTTTCACCTT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
8 5 0.08
9 13 0.22
10 5 0.08
11 16 0.27
12 13 0.22
13 8 0.13
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (11 bp):
ATATTTAAATA
Found at i:6741280 original size:18 final size:18
Alignment explanation
Indices: 6741228--6741281 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
6741218 AATATTCTTT
*
6741228 ATAATATTTATTATAGTTAA
1 ATAATATTTA-AATA-TTAA
6741248 ATAATA-TTAATATATTAA
1 ATAATATTTAA-ATATTAA
6741266 ATAATATTTAAATATT
1 ATAATATTTAAATATT
6741282 TTCACCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 15 0.48
19 10 0.32
20 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATAATATTTAAATATTAA
Found at i:6741676 original size:2 final size:2
Alignment explanation
Indices: 6741669--6741695 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6741659 CATTCACTAA
6741669 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6741696 CATACCTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6750886 original size:65 final size:64
Alignment explanation
Indices: 6750782--6750907 Score: 243
Period size: 65 Copynumber: 2.0 Consensus size: 64
6750772 GACTCGTGGT
6750782 GCCAAAATCAGCATATGCCATTAACTATTGATATATATATATATATATATATAATTATAAGTAA
1 GCCAAAATCAGCATATGCCATTAACTATTGATATATATATATATATATATATAATTATAAGTAA
6750846 NGCCAAAATCAGCATATGCCATTAACTATTGATATATATATATATATATATATAATTATAAG
1 -GCCAAAATCAGCATATGCCATTAACTATTGATATATATATATATATATATATAATTATAAG
6750908 AATTATGACC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (64 bp):
GCCAAAATCAGCATATGCCATTAACTATTGATATATATATATATATATATATAATTATAAGTAA
Found at i:6757006 original size:2 final size:2
Alignment explanation
Indices: 6757001--6757043 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
6756991 GCATTACTTT
*
6757001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6757042 TA
1 TA
6757044 GATTAGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6757399 original size:7 final size:8
Alignment explanation
Indices: 6757373--6757404 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
6757363 TCATCTTGAA
6757373 TTTATAAT
1 TTTATAAT
6757381 TTTATAAT
1 TTTATAAT
6757389 TTTATAAT
1 TTTATAAT
6757397 TTATATAA
1 TT-TATAA
6757405 GAAATTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTATAAT
Found at i:6765719 original size:2 final size:2
Alignment explanation
Indices: 6765712--6765744 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6765702 TTCTTTGGAC
6765712 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
6765745 TAGTTTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6780575 original size:13 final size:14
Alignment explanation
Indices: 6780557--6780585 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6780547 TATTTATATT
6780557 TTATTTT-TTAAAA
1 TTATTTTATTAAAA
6780570 TTATTTTATTAAAA
1 TTATTTTATTAAAA
6780584 TT
1 TT
6780586 GACGTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTTATTAAAA
Found at i:6788524 original size:41 final size:41
Alignment explanation
Indices: 6788479--6788556 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
6788469 ATAATAATTG
*
6788479 AGTTAAGTGTTCAGCTACATAATTTAAATTATTTTTTGATC
1 AGTTAAGTGTTCAGATACATAATTTAAATTATTTTTTGATC
* *
6788520 AGTTAAGTGTTCAGATACCTAATTTGAATTATTTTTT
1 AGTTAAGTGTTCAGATACATAATTTAAATTATTTTTT
6788557 TGTCAATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (41 bp):
AGTTAAGTGTTCAGATACATAATTTAAATTATTTTTTGATC
Found at i:6788728 original size:40 final size:41
Alignment explanation
Indices: 6788667--6788744 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
6788657 TTAAAGTTTA
* * *
6788667 AAGAAGCAATTAAAAAATTAAATTGAAAATATG-TTCAAAT
1 AAGAAACAATTAAAAAATTAAAATAAAAATATGATTCAAAT
* *
6788707 AAGAAACAATTATAAAGTTAAAATAAAAATATGATTCA
1 AAGAAACAATTAAAAAATTAAAATAAAAATATGATTCA
6788745 CATTAAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.27
Consensus pattern (41 bp):
AAGAAACAATTAAAAAATTAAAATAAAAATATGATTCAAAT
Found at i:6796263 original size:31 final size:31
Alignment explanation
Indices: 6796225--6796286 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
6796215 ACTTATATAC
6796225 TACTATTGCTTTAAGCACTACAAAATGAAAG
1 TACTATTGCTTTAAGCACTACAAAATGAAAG
*
6796256 TACTATTGCTTTAAGCACTACGAAATGAAAG
1 TACTATTGCTTTAAGCACTACAAAATGAAAG
6796287 GTGCTGAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (31 bp):
TACTATTGCTTTAAGCACTACAAAATGAAAG
Found at i:6799146 original size:76 final size:75
Alignment explanation
Indices: 6799020--6799166 Score: 215
Period size: 76 Copynumber: 1.9 Consensus size: 75
6799010 AATATATTCC
* * *
6799020 TGGTAATATGCGGGCAGTTGTTGGCTGATAAGAGAGTTGACCCTCCTTTAAAGACTTGAAACCGG
1 TGGTAATATGCGGGCAGTTGTTGGCTGAAAAGAGAGTTGACCATCCTTTAAAGACTCGAAA-CGG
6799085 GACCAAATAGG
65 GACCAAATAGG
** *
6799096 TGGTAATATGCTGGGCA-TTGTTGGCTGAAAAGAGAGTTGACCATTGTTTAAAGACTCGAAACTG
1 TGGTAATATGC-GGGCAGTTGTTGGCTGAAAAGAGAGTTGACCATCCTTTAAAGACTCGAAACGG
6799160 GACCAAA
65 GACCAAA
6799167 GAGGCATTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 9 0.14
76 50 0.78
77 5 0.08
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.26
Consensus pattern (75 bp):
TGGTAATATGCGGGCAGTTGTTGGCTGAAAAGAGAGTTGACCATCCTTTAAAGACTCGAAACGGG
ACCAAATAGG
Found at i:6808140 original size:7 final size:7
Alignment explanation
Indices: 6808128--6808184 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
6808118 CGTTATAATT
6808128 AAAATAA
1 AAAATAA
*
6808135 AAAATATT
1 AAAATA-A
6808143 AAAATAA
1 AAAATAA
* *
6808150 AATATAT
1 AAAATAA
*
6808157 AATAT-A
1 AAAATAA
6808163 AAAATAA
1 AAAATAA
6808170 AAAAT-A
1 AAAATAA
6808176 AAAATAA
1 AAAATAA
6808183 AA
1 AA
6808185 TAAAATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
6 10 0.24
7 25 0.61
8 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATAA
Found at i:6808145 original size:15 final size:14
Alignment explanation
Indices: 6808127--6808325 Score: 99
Period size: 13 Copynumber: 14.1 Consensus size: 14
6808117 ACGTTATAAT
6808127 TAAAATAAAAAATA
1 TAAAATAAAAAATA
*
6808141 TTAAAATAAAATATA
1 -TAAAATAAAAAATA
*
6808156 TAATAT-AAAAATA
1 TAAAATAAAAAATA
* *
6808169 AAAAATAAAAATAAAA
1 TAAAAT-AAAA-AATA
6808185 TAAAATATAAGAAAT-
1 TAAAATA-AA-AAATA
* *
6808200 TAAAATGTATATAATA
1 TAAAA--TAAAAAATA
**
6808216 T-AGGTAAAAAAT-
1 TAAAATAAAAAATA
*
6808228 TAAAATAAAATATA
1 TAAAATAAAAAATA
*
6808242 TAATATAAAAAAT-
1 TAAAATAAAAAATA
* *
6808255 TATATTAAAAAA-A
1 TAAAATAAAAAATA
*
6808268 TAAAATATATAAGAT-
1 TAAAATA-A-AAAATA
*
6808283 TATAATAAAAAATA
1 TAAAATAAAAAATA
*
6808297 -AAAATAAAATATA
1 TAAAATAAAAAATA
* * *
6808310 TGATATTAAAAATA
1 TAAAATAAAAAATA
6808324 TA
1 TA
6808326 TTTAGAGATG
Statistics
Matches: 134, Mismatches: 34, Indels: 33
0.67 0.17 0.16
Matches are distributed among these distances:
12 1 0.01
13 53 0.40
14 28 0.21
15 35 0.26
16 14 0.10
17 3 0.02
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
TAAAATAAAAAATA
Found at i:6808152 original size:20 final size:19
Alignment explanation
Indices: 6808127--6808205 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 19
6808117 ACGTTATAAT
6808127 TAAAATAAAAAATATTAAAA
1 TAAAATAAAAAA-ATTAAAA
* * *
6808147 TAAAATATATAATATAAAAA
1 TAAAATA-AAAAAATTAAAA
6808167 TAAAA-AATAAAAA-TAAAA
1 TAAAATAA-AAAAATTAAAA
*
6808185 TAAAATATAAGAAATTAAAA
1 TAAAATA-AAAAAATTAAAA
6808205 T
1 T
6808206 GTATATAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
18 10 0.21
19 9 0.19
20 25 0.53
21 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.25
Consensus pattern (19 bp):
TAAAATAAAAAAATTAAAA
Found at i:6808159 original size:33 final size:33
Alignment explanation
Indices: 6808121--6808204 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
6808111 TTTGTAACGT
6808121 TATAAT-T-AAAATAAAAAATATTAAAATAAAATA
1 TATAATATAAAAATAAAAAATA--AAAATAAAATA
6808154 TATAATATAAAAATAAAAAATAAAAATAAAATA
1 TATAATATAAAAATAAAAAATAAAAATAAAATA
*
6808187 -A-AATATAAGAAATTAAAA
1 TATAATATAA-AAATAAAAA
6808205 TGTATATAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 7 0.15
32 9 0.19
33 17 0.36
34 1 0.02
35 13 0.28
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (33 bp):
TATAATATAAAAATAAAAAATAAAAATAAAATA
Found at i:6808204 original size:53 final size:52
Alignment explanation
Indices: 6808127--6808256 Score: 138
Period size: 53 Copynumber: 2.4 Consensus size: 52
6808117 ACGTTATAAT
* *
6808127 TAAAATAAAAAATATTAAAA-TAAAA-TATATAATATAAAAATAAAAAATAAAAA
1 TAAAATAAAATATA-AAAAATTAAAAGTATATAATAT--AAATAAAAAATAAAAA
* ** *
6808180 TAAAATAAAATATAAGAAATTAAAATGTATATAATATAGGTAAAAAATTAAAA
1 TAAAATAAAATATAAAAAATTAAAA-GTATATAATATAAATAAAAAATAAAAA
6808233 TAAAATATATAATATAAAAAATTA
1 TAAAATA-A-AATATAAAAAATTA
6808257 TATTAAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
52 3 0.05
53 38 0.58
54 1 0.02
55 23 0.35
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (52 bp):
TAAAATAAAATATAAAAAATTAAAAGTATATAATATAAATAAAAAATAAAAA
Found at i:6808319 original size:28 final size:27
Alignment explanation
Indices: 6808233--6808321 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 27
6808223 AAAATTAAAA
* * *
6808233 TAAAATATATAATATAAAAAATTATAT
1 TAAAAAATAAAATATAAAAGATTATAT
* *
6808260 TAAAAAAATAAAATATATAAGATTATAA
1 T-AAAAAATAAAATATAAAAGATTATAT
*
6808288 TAAAAAATAAAA-ATAAAATATATGATAT
1 TAAAAAATAAAATATAAAAGAT-T-ATAT
6808316 TAAAAA
1 TAAAAA
6808322 TATATTTAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.14
27 13 0.25
28 31 0.61
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
TAAAAAATAAAATATAAAAGATTATAT
Found at i:6808323 original size:27 final size:31
Alignment explanation
Indices: 6808151--6808321 Score: 82
Period size: 33 Copynumber: 5.3 Consensus size: 31
6808141 TTAAAATAAA
* * * * * *
6808151 ATATATAATATAAAAATAAAAAATAAAAATA
1 ATATAAAAAATAAAAATAAAATATATAGATT
* * * * *
6808182 AAATAAAATATAAGAAATTAAAATGTATATAAT
1 ATATAAAAAATAA-AAA-TAAAATATATAGATT
*
6808215 ATAGGTAAAAAATTAAAATAAAATATATA-A-T
1 ATA--TAAAAAATAAAAATAAAATATATAGATT
*
6808246 ATAAAAAATTATATTAAAAAAATAAAATATATAAGATT
1 ATATAAAA--A-A-T--AAAAATAAAATATAT-AGATT
6808284 ATAATAAAAAATAAAAATAAAATATAT-GA-T
1 AT-ATAAAAAATAAAAATAAAATATATAGATT
6808314 AT-TAAAAA
1 ATATAAAAA
6808322 TATATTTAGA
Statistics
Matches: 111, Mismatches: 15, Indels: 31
0.71 0.10 0.20
Matches are distributed among these distances:
28 6 0.05
29 4 0.04
30 3 0.03
31 18 0.16
32 5 0.05
33 37 0.33
34 3 0.03
35 23 0.21
36 2 0.02
37 2 0.02
38 3 0.03
39 5 0.05
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (31 bp):
ATATAAAAAATAAAAATAAAATATATAGATT
Found at i:6808547 original size:15 final size:15
Alignment explanation
Indices: 6808509--6808552 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6808499 TGTTATTTTT
6808509 TTTACAATCACATTA
1 TTTACAATCACATTA
* ** *
6808524 CTTGTAATCATATTA
1 TTTACAATCACATTA
6808539 TTTACAATCACATT
1 TTTACAATCACATT
6808553 GCATTGTAAA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.43
Consensus pattern (15 bp):
TTTACAATCACATTA
Found at i:6812274 original size:22 final size:22
Alignment explanation
Indices: 6812249--6812293 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
6812239 TGAACTTTGC
6812249 ACATCTTGAAGCAAGCGGCTCT
1 ACATCTTGAAGCAAGCGGCTCT
*
6812271 ACATCTTGAAGCAAGTGGCTCT
1 ACATCTTGAAGCAAGCGGCTCT
6812293 A
1 A
6812294 TGATCCTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
ACATCTTGAAGCAAGCGGCTCT
Found at i:6822892 original size:18 final size:18
Alignment explanation
Indices: 6822866--6822900 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6822856 TTTAAGAGGG
*
6822866 TAATGGAGAAAATTTTTT
1 TAATAGAGAAAATTTTTT
*
6822884 TAATAGAGAATATTTTT
1 TAATAGAGAAAATTTTT
6822901 GAAACAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (18 bp):
TAATAGAGAAAATTTTTT
Found at i:6826021 original size:3 final size:3
Alignment explanation
Indices: 6826013--6826050 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6826003 TCAGCTACAG
6826013 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6826051 CAGTAAACCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6833096 original size:15 final size:15
Alignment explanation
Indices: 6833059--6833098 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
6833049 GTTTAGCAAA
*
6833059 CACCACCACCTCCTC
1 CACCACCACCGCCTC
*
6833074 CACAACCACCGCCTC
1 CACCACCACCGCCTC
*
6833089 CTCCACCACC
1 CACCACCACC
6833099 ACCGCTGCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.65, G:0.03, T:0.10
Consensus pattern (15 bp):
CACCACCACCGCCTC
Found at i:6833102 original size:18 final size:18
Alignment explanation
Indices: 6833059--6833103 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6833049 GTTTAGCAAA
*
6833059 CACCACCACCTCCTCCAC
1 CACCACCGCCTCCTCCAC
*
6833077 AACCACCGCCTCCTCCAC
1 CACCACCGCCTCCTCCAC
6833095 CACCACCGC
1 CACCACCGC
6833104 TGCTGCCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.64, G:0.04, T:0.09
Consensus pattern (18 bp):
CACCACCGCCTCCTCCAC
Found at i:6833956 original size:17 final size:17
Alignment explanation
Indices: 6833934--6833969 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
6833924 AAGCAGGACC
6833934 ATTCAACAGAAAATACT
1 ATTCAACAGAAAATACT
6833951 ATTCAACAGAAAATACT
1 ATTCAACAGAAAATACT
6833968 AT
1 AT
6833970 AAAATATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (17 bp):
ATTCAACAGAAAATACT
Found at i:6836487 original size:2 final size:2
Alignment explanation
Indices: 6836480--6836525 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6836470 TCTGTCCAAA
6836480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6836522 AT AT
1 AT AT
6836526 TTCACCACCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6850166 original size:11 final size:11
Alignment explanation
Indices: 6850150--6850195 Score: 92
Period size: 11 Copynumber: 4.2 Consensus size: 11
6850140 TGACTTACTG
6850150 GTGATGCTAAT
1 GTGATGCTAAT
6850161 GTGATGCTAAT
1 GTGATGCTAAT
6850172 GTGATGCTAAT
1 GTGATGCTAAT
6850183 GTGATGCTAAT
1 GTGATGCTAAT
6850194 GT
1 GT
6850196 AATTGCTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.37
Consensus pattern (11 bp):
GTGATGCTAAT
Found at i:6856785 original size:16 final size:16
Alignment explanation
Indices: 6856764--6856799 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
6856754 CTTTTTCTTT
6856764 TAAAAAATAAA-TAAAC
1 TAAAAAA-AAATTAAAC
6856780 TAAAAAAAAATTAAAC
1 TAAAAAAAAATTAAAC
6856796 TAAA
1 TAAA
6856800 TAGGCACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAAAAAATTAAAC
Found at i:6857010 original size:23 final size:26
Alignment explanation
Indices: 6856963--6857012 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
6856953 ATGTTTATAA
*
6856963 ATTTTTATCAAAATAAAAATTTTATT
1 ATTTTTATCAAAATAAAAATCTTATT
6856989 ATTTTTA-CAAAA-AAAAA-CTTATT
1 ATTTTTATCAAAATAAAAATCTTATT
6857012 A
1 A
6857013 AAATAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 5 0.22
25 5 0.22
26 7 0.30
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTTTATCAAAATAAAAATCTTATT
Found at i:6867911 original size:10 final size:10
Alignment explanation
Indices: 6867890--6867933 Score: 70
Period size: 10 Copynumber: 4.2 Consensus size: 10
6867880 AAAAATAAAT
6867890 ATTTTATTTAA
1 ATTTT-TTTAA
6867901 ATTTTTTTAA
1 ATTTTTTTAA
6867911 ATTTTTTTAA
1 ATTTTTTTAA
6867921 ATTTTTTTCAA
1 ATTTTTTT-AA
6867932 AT
1 AT
6867934 ATTATGCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:6878519 original size:14 final size:14
Alignment explanation
Indices: 6878497--6878531 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
6878487 AAATTGTTTG
6878497 ATAAATTTTCTTTT
1 ATAAATTTTCTTTT
* *
6878511 ATAAGTTTTTTTTT
1 ATAAATTTTCTTTT
6878525 ATAAATT
1 ATAAATT
6878532 ATAATTTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (14 bp):
ATAAATTTTCTTTT
Found at i:6884935 original size:2 final size:2
Alignment explanation
Indices: 6884928--6884953 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6884918 ATCCTCTTAT
6884928 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
6884954 CTCCTCACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6887595 original size:45 final size:44
Alignment explanation
Indices: 6887541--6887845 Score: 329
Period size: 43 Copynumber: 6.9 Consensus size: 44
6887531 TCTTTGGACA
* *
6887541 AAAATATTATTAAATTGTAATAAAAGGTATATTTATGTTTTGGTG
1 AAAATATTATTAAATTATAATAAAAGGTATATTTAT-TTTTGATG
* * * * *
6887586 AAAATATTATT-TATTATAATAGAGGGT-TCTTTTTTTTTTGATG
1 AAAATATTATTAAATTATAATAAAAGGTAT-ATTTATTTTTGATG
* * * *
6887629 AAAAATATTTTTAAATTATAAT-AAA-GCATATTTTTGTATTTGGGTG
1 -AAAATATTATTAAATTATAATAAAAGGTATATTTAT-T-TTT-GATG
* *
6887675 AAAATATTATTAAATTATAATAAAGGGTAGATTTA-TTTTGATG
1 AAAATATTATTAAATTATAATAAAAGGTATATTTATTTTTGATG
* *
6887718 AAAATATTATTAAATTATAATAAAGGGTAGATTTA-TTTTGATG
1 AAAATATTATTAAATTATAATAAAAGGTATATTTATTTTTGATG
6887761 AAAATATTATTAAATTATAATAAAAGGTA-ATTTTATCTTTTGAT-
1 AAAATATTATTAAATTATAATAAAAGGTATA-TTTAT-TTTTGATG
*
6887805 ATAAATATTATTAAATTATAATAAAAGGTATTTTTATTTTT
1 A-AAATATTATTAAATTATAATAAAAGGTATATTTATTTTT
6887846 TTATAAAACA
Statistics
Matches: 224, Mismatches: 22, Indels: 29
0.81 0.08 0.11
Matches are distributed among these distances:
42 1 0.00
43 92 0.41
44 37 0.17
45 83 0.37
46 5 0.02
47 6 0.03
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (44 bp):
AAAATATTATTAAATTATAATAAAAGGTATATTTATTTTTGATG
Found at i:6887841 original size:88 final size:88
Alignment explanation
Indices: 6887541--6887844 Score: 352
Period size: 88 Copynumber: 3.5 Consensus size: 88
6887531 TCTTTGGACA
* * *
6887541 AAAATATTATTAAATTGTAATAAAAGGTATATTTATGTTTTGGTGAAAATATTATT-TATTATAA
1 AAAATATTATTAAATTATAATAAAAGGTAT-TTTATATTTTGGTGAAAATATTATTAAATTATAA
* ** *
6887605 TAGAGGGTTCTTTTTTTTTTGATG
65 TAAAGGGTAATTTTATTTTTGATG
* * * *
6887629 AAAAATATTTTTAAATTATAAT-AAAGCATATTTTTGTATTTGGGTGAAAATATTATTAAATTAT
1 -AAAATATTATTAAATTATAATAAAAG-GTA-TTTTATATTTTGGTGAAAATATTATTAAATTAT
6887693 AATAAAGGGTAGA-TTTA-TTTTGATG
63 AATAAAGGGTA-ATTTTATTTTTGATG
* ** *
6887718 AAAATATTATTAAATTATAATAAAGGGTAGATT-TATTTTGATGAAAATATTATTAAATTATAAT
1 AAAATATTATTAAATTATAATAAAAGGTATTTTATATTTTGGTGAAAATATTATTAAATTATAAT
*
6887782 AAAAGGTAATTTTATCTTTTGAT-
66 AAAGGGTAATTTTAT-TTTTGATG
6887805 ATAAATATTATTAAATTATAATAAAAGGTATTTT-TATTTT
1 A-AAATATTATTAAATTATAATAAAAGGTATTTTATATTTT
6887845 TTTATAAAAC
Statistics
Matches: 184, Mismatches: 22, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
85 1 0.01
86 40 0.22
87 3 0.02
88 68 0.37
89 54 0.29
90 18 0.10
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (88 bp):
AAAATATTATTAAATTATAATAAAAGGTATTTTATATTTTGGTGAAAATATTATTAAATTATAAT
AAAGGGTAATTTTATTTTTGATG
Found at i:6887872 original size:45 final size:45
Alignment explanation
Indices: 6887520--6887873 Score: 235
Period size: 45 Copynumber: 8.0 Consensus size: 45
6887510 ATGCCATTTT
* * * * * *
6887520 AGGTTATTTTGTCTTTGGACAAAAATATTATTAAATTGTAATAAA
1 AGGTAATTTTATCTTTTGATAAAAAAATTATTAAATTATAATAAA
* * * * * *
6887565 AGGT-ATATTTATGTTTTGGTGAAAATATTATT-TATTATAATAGA
1 AGGTAAT-TTTATCTTTTGATAAAAAAATTATTAAATTATAATAAA
* ** * * *
6887609 GGGTTCTTTT-TTTTTTGATGAAAAATATTTTTAAATTATAAT-AA
1 AGGTAATTTTATCTTTTGAT-AAAAAAATTATTAAATTATAATAAA
* * * * * * * *
6887653 AGCATATTTTTGTATTTGGGTGAAAATATTATTAAATTATAATAAA
1 AG-GTAATTTTATCTTTTGATAAAAAAATTATTAAATTATAATAAA
* * *
6887699 GGGTAGA-TTTA--TTTTGATGAAAATATTATTAAATTATAATAAA
1 AGGTA-ATTTTATCTTTTGATAAAAAAATTATTAAATTATAATAAA
* * *
6887742 GGGTAGA-TTTA--TTTTGATGAAAATATTATTAAATTATAATAAA
1 AGGTA-ATTTTATCTTTTGATAAAAAAATTATTAAATTATAATAAA
* *
6887785 AGGTAATTTTATCTTTTGATATAAATATTATTAAATTATAATAAA
1 AGGTAATTTTATCTTTTGATAAAAAAATTATTAAATTATAATAAA
* * * *
6887830 AGGTATTTTTATTTTTTTATAAAACAAATT-TTAAATTTTAATAA
1 AGGTAATTTTATCTTTTGATAAAA-AAATTATTAAATTATAATAA
6887874 TTAATTTTTT
Statistics
Matches: 256, Mismatches: 41, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
42 1 0.00
43 88 0.34
44 29 0.11
45 125 0.49
46 13 0.05
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.46
Consensus pattern (45 bp):
AGGTAATTTTATCTTTTGATAAAAAAATTATTAAATTATAATAAA
Found at i:6887882 original size:21 final size:20
Alignment explanation
Indices: 6887858--6887908 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
6887848 ATAAAACAAA
*
6887858 TTTTAAATTTTAATAATTAAT
1 TTTTTAATTTTAAT-ATTAAT
* **
6887879 TTTTTATTTTTTCTATTAAT
1 TTTTTAATTTTAATATTAAT
6887899 TTTTTAATTT
1 TTTTTAATTT
6887909 ATTGTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTAATTTTAATATTAAT
Found at i:6889526 original size:16 final size:16
Alignment explanation
Indices: 6889505--6889535 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6889495 TTCTTTTCCA
6889505 AGTACATTGAATGGCC
1 AGTACATTGAATGGCC
6889521 AGTACATTGAATGGC
1 AGTACATTGAATGGC
6889536 TCTTTGAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (16 bp):
AGTACATTGAATGGCC
Found at i:6898045 original size:2 final size:2
Alignment explanation
Indices: 6898032--6898075 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
6898022 AAATTAAAGG
*
6898032 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6898074 AT
1 AT
6898076 GGGTTTCCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6906425 original size:21 final size:21
Alignment explanation
Indices: 6906396--6906453 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 21
6906386 GATTCTCGAC
*
6906396 TTTACCCAACAAACAACAAACT
1 TTTA-CCAACAAACAAAAAACT
*
6906418 TGTT-CCAA-AAAAAAAAAACT
1 T-TTACCAACAAACAAAAAACT
6906438 TTTACCCAACAAACAA
1 TTTA-CCAACAAACAA
6906454 TACAAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 8 0.28
22 6 0.21
23 2 0.07
ACGTcount: A:0.53, C:0.26, G:0.02, T:0.19
Consensus pattern (21 bp):
TTTACCAACAAACAAAAAACT
Found at i:6911415 original size:22 final size:22
Alignment explanation
Indices: 6911356--6911409 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
6911346 TTCTTGTAAT
6911356 AAGAAAAAGAAGTGTTGCAAAC
1 AAGAAAAAGAAGTGTTGCAAAC
6911378 AAGAAAAAGAAGTGTTGCAAAC
1 AAGAAAAAGAAGTGTTGCAAAC
*
6911400 AAGTAAAAGA
1 AAGAAAAAGA
6911410 TATGTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.57, C:0.07, G:0.22, T:0.13
Consensus pattern (22 bp):
AAGAAAAAGAAGTGTTGCAAAC
Found at i:6917027 original size:18 final size:18
Alignment explanation
Indices: 6917006--6917075 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
6916996 ATAGAGATAA
6917006 AAAATTAAAAATTATATT
1 AAAATTAAAAATTATATT
*
6917024 AAAATT-ATAATTATAATT
1 AAAATTAAAAATTAT-ATT
*
6917042 ATAATTATAAAAATTGATATTT
1 A-AAAT-TAAAAATT-ATA-TT
*
6917064 CAAATTAAAAAT
1 AAAATTAAAAAT
6917076 CACACTAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 7 0.17
18 10 0.24
19 3 0.07
20 8 0.20
21 9 0.22
22 4 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (18 bp):
AAAATTAAAAATTATATT
Found at i:6917049 original size:6 final size:6
Alignment explanation
Indices: 6917015--6917051 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
6917005 AAAAATTAAA
*
6917015 AATTAT -ATTAA AATTAT AATTAT AATTAT AATTAT AA
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AA
6917052 AAATTGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTAT
Found at i:6917603 original size:20 final size:23
Alignment explanation
Indices: 6917563--6917605 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 23
6917553 TCCTCCCTCT
6917563 ATTGATTCTTCTAGTTTTCTCCC
1 ATTGATTCTTCTAGTTTTCTCCC
6917586 ATTG-TTCTTCT-G-TTTCTCCC
1 ATTGATTCTTCTAGTTTTCTCCC
6917606 CTGATTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 7 0.35
23 4 0.20
ACGTcount: A:0.09, C:0.28, G:0.09, T:0.53
Consensus pattern (23 bp):
ATTGATTCTTCTAGTTTTCTCCC
Found at i:6930518 original size:28 final size:27
Alignment explanation
Indices: 6930459--6930525 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
6930449 ATTTATACTT
*
6930459 TATTTATGTAATTTATTTGTTTATTTA
1 TATTTATGTAATTTATTTGTTTATTCA
*
6930486 TATTTGATGTAATTTATTTTTATTATTCA
1 TATTT-ATGTAATTTATTTGT-TTATTCA
6930515 -ATTTATG-AATT
1 TATTTATGTAATT
6930526 AAATCATTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 4 0.11
27 8 0.22
28 18 0.50
29 6 0.17
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.63
Consensus pattern (27 bp):
TATTTATGTAATTTATTTGTTTATTCA
Found at i:6931222 original size:19 final size:20
Alignment explanation
Indices: 6931181--6931227 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
6931171 ATGAACACAA
* *
6931181 TATTTGAAAAAAATTTTGAAT
1 TATTTTAAAAAAATTAT-AAT
6931202 TATTTTAAAAAAATTAT-AT
1 TATTTTAAAAAAATTATAAT
6931221 TATTTTA
1 TATTTTA
6931228 TTACGTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.38
21 15 0.62
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
TATTTTAAAAAAATTATAAT
Found at i:6949229 original size:10 final size:10
Alignment explanation
Indices: 6949214--6949241 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6949204 TTTTGATGAA
6949214 ATGCATTTGT
1 ATGCATTTGT
6949224 ATGCATTTGT
1 ATGCATTTGT
6949234 ATGCATTT
1 ATGCATTT
6949242 CTCTTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (10 bp):
ATGCATTTGT
Found at i:6956489 original size:10 final size:10
Alignment explanation
Indices: 6956437--6956491 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
6956427 CTTAAATTTG
6956437 TTTATTTTAAA
1 TTTATTTT-AA
*
6956448 TTCATTTTAA
1 TTTATTTTAA
*
6956458 -TTGTTTT-A
1 TTTATTTTAA
6956466 TTTAATTTTAAA
1 TTT-ATTTT-AA
6956478 TTTATTTTAA
1 TTTATTTTAA
6956488 TTTA
1 TTTA
6956492 GTGAGGGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
8 1 0.03
9 7 0.19
10 12 0.33
11 12 0.33
12 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTATTTTAA
Found at i:6960328 original size:15 final size:15
Alignment explanation
Indices: 6960308--6960337 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6960298 AACAATATCT
6960308 AATATTAATTAATTA
1 AATATTAATTAATTA
*
6960323 AATATTAGTTAATTA
1 AATATTAATTAATTA
6960338 TCCACAAATA
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AATATTAATTAATTA
Found at i:6963560 original size:37 final size:37
Alignment explanation
Indices: 6963510--6963585 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
6963500 TGTGGAGTTG
6963510 TGGGAATAGATTTTGAGGGCACACGATTGAGGATGTA
1 TGGGAATAGATTTTGAGGGCACACGATTGAGGATGTA
*
6963547 TGGGAATATATTTTGAGGGCACACGATTGAGGATGTA
1 TGGGAATAGATTTTGAGGGCACACGATTGAGGATGTA
6963584 TG
1 TG
6963586 ATGCTGTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.34, T:0.29
Consensus pattern (37 bp):
TGGGAATAGATTTTGAGGGCACACGATTGAGGATGTA
Found at i:6966591 original size:35 final size:35
Alignment explanation
Indices: 6966539--6966629 Score: 94
Period size: 37 Copynumber: 2.5 Consensus size: 35
6966529 TACAATTGTC
6966539 TATTTTTTTATCATTTTTATTATT-TAATTCTTATTT
1 TATTTTTTTAT--TTTTTATTATTATAATTCTTATTT
* * *
6966575 TCATTTTTTTATTTTTTATTGTTATATTTTTTATTT
1 T-ATTTTTTTATTTTTTATTATTATAATTCTTATTT
6966611 TATTTCTTATTATTATTTT
1 TATTT-TT-TTATT-TTTT
6966630 TTCATACTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
35 14 0.30
36 14 0.30
37 15 0.32
38 4 0.09
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (35 bp):
TATTTTTTTATTTTTTATTATTATAATTCTTATTT
Found at i:6966599 original size:27 final size:25
Alignment explanation
Indices: 6966552--6966631 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 25
6966542 TTTTTTATCA
* *
6966552 TTTTTATTATTTAATTCTTATTTTCATT
1 TTTTTATT-TTTTATTATTATTTT--TT
*
6966580 TTTTTATTTTTTATTGTTATATTTTT
1 TTTTTATTTTTTATTATTAT-TTTTT
*
6966606 TATTTTATTTCTTATTATTATTTTTT
1 T-TTTTATTTTTTATTATTATTTTTT
6966632 CATACTTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.17
27 27 0.59
28 11 0.24
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (25 bp):
TTTTTATTTTTTATTATTATTTTTT
Found at i:6966602 original size:15 final size:14
Alignment explanation
Indices: 6966579--6966677 Score: 55
Period size: 14 Copynumber: 6.9 Consensus size: 14
6966569 TTATTTTCAT
*
6966579 TTTTTTATTTTTTA
1 TTTTATATTTTTTA
6966593 TTGTTATATTTTTTA
1 TT-TTATATTTTTTA
*
6966608 -TTT-TATTTCTTA
1 TTTTATATTTTTTA
6966620 TTATTAT-TTTTTCATA
1 TT-TTATATTTTT--TA
* *
6966636 CTTTACATTTTTTA
1 TTTTATATTTTTTA
*
6966650 TTCTAT-TGTTATTTA
1 TTTTATAT-TT-TTTA
6966665 -TTTATTATTTTTT
1 TTTTA-TATTTTTT
6966678 GAGTGATTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
12 8 0.12
13 4 0.06
14 22 0.34
15 22 0.34
16 9 0.14
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTATATTTTTTA
Found at i:6966620 original size:12 final size:13
Alignment explanation
Indices: 6966546--6966628 Score: 52
Period size: 12 Copynumber: 6.7 Consensus size: 13
6966536 GTCTATTTTT
*
6966546 TTATCATTT-TTA
1 TTATTATTTCTTA
*
6966558 TTATTTAATTCTTA
1 TTA-TTATTTCTTA
6966572 TT-TTCATTT-TT-
1 TTATT-ATTTCTTA
* * *
6966583 TTATTTTTTATTG
1 TTATTATTTCTTA
*
6966596 TTA-TATTTTTTA
1 TTATTATTTCTTA
6966608 TT-TTATTTCTTA
1 TTATTATTTCTTA
6966620 TTATTATTT
1 TTATTATTT
6966629 TTTCATACTT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
11 5 0.09
12 29 0.53
13 16 0.29
14 5 0.09
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.73
Consensus pattern (13 bp):
TTATTATTTCTTA
Found at i:6966624 original size:22 final size:22
Alignment explanation
Indices: 6966579--6966651 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
6966569 TTATTTTCAT
* *
6966579 TTTTTTATTTTTTATTGTTATA
1 TTTTTTATTTTATATTCTTATA
6966601 TTTTTTATTTTAT-TTCTTATTA
1 TTTTTTATTTTATATTCTTA-TA
* * * *
6966623 TTATTT-TTTCATACT-TTACA
1 TTTTTTATTTTATATTCTTATA
6966643 TTTTTTATT
1 TTTTTTATT
6966652 CTATTGTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
20 6 0.15
21 15 0.37
22 20 0.49
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.74
Consensus pattern (22 bp):
TTTTTTATTTTATATTCTTATA
Done.