Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 51 of 131
Found at i:16893023 original size:43 final size:43
Alignment explanation
Indices: 16892975--16893257 Score: 313
Period size: 43 Copynumber: 6.6 Consensus size: 43
16892965 TTTTAGAAAT
*
16892975 AAACGCCACTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
16893018 AAACGCCGCTATAGAACAAGACCTTTCGCGGCGC-TTTCTCAA
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
16893060 AAACACCGCTAAAGAACAAGACCTTTAACGGCGCTTCTT-CTAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTT-TTCCCAC
**
16893103 AAACGCCGCTAAAGATA-AAGACCTTTAGCGGCATTTTTCCCAC
1 AAACGCCGCTAAAGA-ACAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * * * *
16893146 AAACGCCTCTATAGAACATGACCTTTAACGACGCTTTTTCCAT
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
16893189 AAACGACGCTAAAGAACAAGACCTTTAGAGGCGCTTTTTCTAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
* *
16893232 AAACGCCACTAAA-AACATGACCTTTA
1 AAACGCCGCTAAAGAACAAGACCTTTA
16893258 AAAAATATTT
Statistics
Matches: 197, Mismatches: 38, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
42 51 0.26
43 143 0.73
44 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:16893126 original size:85 final size:84
Alignment explanation
Indices: 16892975--16893258 Score: 329
Period size: 85 Copynumber: 3.3 Consensus size: 84
16892965 TTTTAGAAAT
* *
16892975 AAACGCCACTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAAGAC
1 AAACGCCACTAAAGAACAAGACCTTTAACGGCGCTTTT-CCACAAACGCCGCTAAAGAACAAGAC
* *
16893040 CTTTCGCGGCGCTTTCTCAA
65 CTTTAGCGGCGCTTTCTCAC
* * *
16893060 AAACACCGCTAAAGAACAAGACCTTTAACGGCGCTTCTTCTACAAACGCCGCTAAAGATA-AAGA
1 AAACGCCACTAAAGAACAAGACCTTTAACGGCGCTT-TTCCACAAACGCCGCTAAAGA-ACAAGA
** *
16893124 CCTTTAGCGGCATTTTTCCCAC
64 CCTTTAGCGGC-GCTTTCTCAC
* * * * * *
16893146 AAACGCCTCTATAGAACATGACCTTTAACGACGCTTTTTCCATAAACGACGCTAAAGAACAAGAC
1 AAACGCCACTAAAGAACAAGACCTTTAACGGCGC-TTTTCCACAAACGCCGCTAAAGAACAAGAC
* *
16893211 CTTTAGAGGCGCTTTTTCTAC
65 CTTTAGCGGCGCTTTCTC-AC
*
16893232 AAACGCCACTAAA-AACATGACCTTTAA
1 AAACGCCACTAAAGAACAAGACCTTTAA
16893259 AAAATATTTT
Statistics
Matches: 168, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
85 83 0.49
86 83 0.49
87 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.23
Consensus pattern (84 bp):
AAACGCCACTAAAGAACAAGACCTTTAACGGCGCTTTTCCACAAACGCCGCTAAAGAACAAGACC
TTTAGCGGCGCTTTCTCAC
Found at i:16893254 original size:128 final size:128
Alignment explanation
Indices: 16892975--16893257 Score: 394
Period size: 128 Copynumber: 2.2 Consensus size: 128
16892965 TTTTAGAAAT
*
16892975 AAACGCCACTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAAGAC
1 AAACGCCACTAAAGAACAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGAACAAGAC
** *
16893040 CTTTCGCGGCGCTTTCTCAAAAACACCGCTAAAGAACAAGACCTTTAACGGCGCTTCTTCTAC
66 CTTTAACGACGCTTTCTCAAAAACACCGCTAAAGAACAAGACCTTTAACGGCGCTTCTTCTAC
* * * *
16893103 AAACGCCGCTAAAGATA-AAGACCTTTAGCGGCATTTTTCCCACAAACGCCTCTATAGAACATGA
1 AAACGCCACTAAAGA-ACAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGAACAAGA
* * *
16893167 CCTTTAACGACGCTTTTTCCATAAACGA-CGCTAAAGAACAAGACCTTTAGA-GGCGCTTTTTCT
65 CCTTTAACGACGCTTTCT-CAAAAAC-ACCGCTAAAGAACAAGACCTTTA-ACGGCGCTTCTTCT
16893230 AC
127 AC
*
16893232 AAACGCCACTAAA-AACATGACCTTTA
1 AAACGCCACTAAAGAACAAGACCTTTA
16893258 AAAAATATTT
Statistics
Matches: 137, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
127 1 0.01
128 81 0.59
129 53 0.39
130 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.23
Consensus pattern (128 bp):
AAACGCCACTAAAGAACAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGAACAAGAC
CTTTAACGACGCTTTCTCAAAAACACCGCTAAAGAACAAGACCTTTAACGGCGCTTCTTCTAC
Found at i:16894258 original size:351 final size:350
Alignment explanation
Indices: 16893615--16894308 Score: 1264
Period size: 351 Copynumber: 2.0 Consensus size: 350
16893605 ATTCAAGTTC
* * *
16893615 TGACTAATATAAACGACCATGGAATGAAACATTAAATAACATTCCACTTGAAGAAGTGCTAAGCC
1 TGACTAAGATAAACGACCATGGAATGAAACATTAAATAACACTCCACTTGAAGAAATGCTAAGCC
16893680 TTGGCTTTTCCAGCTTGAAGAGATTGAATCCTCTGCTACACCTTCAATATCTAAAGGATGCAAAA
66 TTGGCTTTTCCAGCTTGAAGAGATTGAATCCTCTGCTACACCTTCAATATCTAAAGGATGCAAAA
16893745 CGAAATGATCAGATAAACCAACAAACTTGGTAAACAAGAGAGATGTTAAAAATAAAATATATATA
131 CGAAATGATCAGATAAACCAACAAACTTGGTAAACAAGAGAGATGTTAAAAATAAAATATATATA
*
16893810 TTAGATACATACGTACATATATATCTATATCGTTAGACACGTTAAAGATGTTAAAAAGACGTGAA
196 TTAGATACATACG-ACATATATATCTATATCGTTAGACACGTTAAAGATGTTAAAAAGACGTAAA
*
16893875 CATATGATAAAGACTTCTAAACTAAACCCAAACTCTTAGACACGTTACCCAGATTTAACATGGGT
260 CATATGATAAAGACTTCTAAACTAAACCCAAACTCTTACACACGTTACCCAGATTTAACATGGGT
16893940 ATATTAGATACATACATATATCTATA
325 ATATTAGATACATACATATATCTATA
* *
16893966 TGACTAAGATAAACGACCATGGAATGCAACATTAAATAACACTCTACTTGAAGAAATGCTAAGCC
1 TGACTAAGATAAACGACCATGGAATGAAACATTAAATAACACTCCACTTGAAGAAATGCTAAGCC
16894031 TTGGCTTTTCCAGCTTGAAGAGATTGAATCCTCTGCTACACCTTCAATATCTAAAGGATGCAAAA
66 TTGGCTTTTCCAGCTTGAAGAGATTGAATCCTCTGCTACACCTTCAATATCTAAAGGATGCAAAA
16894096 CGAAATGATCAGATAAACCAACAAACTTGGTAAACAAGAGAGATGTTAAAAATAAAATATATATA
131 CGAAATGATCAGATAAACCAACAAACTTGGTAAACAAGAGAGATGTTAAAAATAAAATATATATA
*
16894161 TTAGATACATAC-ACATACATATATCTATATCGTTAGACACGTTAAAGATGTTAAAAAGATGTAA
196 TTAGATACATACGACAT--ATATATCTATATCGTTAGACACGTTAAAGATGTTAAAAAGACGTAA
* *
16894225 ACATATGATAAAGACTTCTAAACTAAACCCAAACTCTTACACACGTTACCTAGATTTAGCATGGG
259 ACATATGATAAAGACTTCTAAACTAAACCCAAACTCTTACACACGTTACCCAGATTTAACATGGG
16894290 TATATTAGATACATACATA
324 TATATTAGATACATACATA
16894309 CATATATCTA
Statistics
Matches: 331, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
349 4 0.01
351 327 0.99
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (350 bp):
TGACTAAGATAAACGACCATGGAATGAAACATTAAATAACACTCCACTTGAAGAAATGCTAAGCC
TTGGCTTTTCCAGCTTGAAGAGATTGAATCCTCTGCTACACCTTCAATATCTAAAGGATGCAAAA
CGAAATGATCAGATAAACCAACAAACTTGGTAAACAAGAGAGATGTTAAAAATAAAATATATATA
TTAGATACATACGACATATATATCTATATCGTTAGACACGTTAAAGATGTTAAAAAGACGTAAAC
ATATGATAAAGACTTCTAAACTAAACCCAAACTCTTACACACGTTACCCAGATTTAACATGGGTA
TATTAGATACATACATATATCTATA
Found at i:16897820 original size:22 final size:21
Alignment explanation
Indices: 16897771--16897820 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
16897761 AAACCCCAAC
*
16897771 CCTTAAACCATAATCCATAAT
1 CCTTAAACCATAATCCATAAA
* *
16897792 CCCTAAACACATAATCCTTAAA
1 CCTTAAAC-CATAATCCATAAA
16897814 CCTTAAA
1 CCTTAAA
16897821 ATTTGGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
CCTTAAACCATAATCCATAAA
Found at i:16898252 original size:14 final size:14
Alignment explanation
Indices: 16898232--16898280 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
16898222 GATGGTAACA
*
16898232 CCTAAACCTTAAAC
1 CCTAAACCATAAAC
* *
16898246 TCTAAACCATATAC
1 CCTAAACCATAAAC
*
16898260 CCTAAACCAAAAAC
1 CCTAAACCATAAAC
16898274 CCTAAAC
1 CCTAAAC
16898281 TATAGTAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:16898610 original size:41 final size:41
Alignment explanation
Indices: 16898469--16898702 Score: 210
Period size: 41 Copynumber: 5.7 Consensus size: 41
16898459 CTCTGAGTAC
* * * *
16898469 TAGCGGCGCATTT-TAGAAAACGCCGCTAAAAG-TCTGATCTT
1 TAGCGGCGC-TTTCTAAAAAACGCCGCT-AAAGCCCTGAGCAT
16898510 TAGCGGCGCTTTCCT-AAAAACGCCGCTAAAGCCCT-AGCAT
1 TAGCGGCGCTTT-CTAAAAAACGCCGCTAAAGCCCTGAGCAT
* *
16898550 TAGCGACG-TTTCCTCAAAAACGCCGCTAAAGCCCTGAGCAT
1 TAGCGGCGCTTT-CTAAAAAACGCCGCTAAAGCCCTGAGCAT
* * * *
16898591 TAGTGGCGCTTTCTAAAAAACGCCGCTAAAAG-CCTAATCTT
1 TAGCGGCGCTTTCTAAAAAACGCCGCT-AAAGCCCTGAGCAT
* * ** *
16898632 TAGCAGCACTTTCTCGAAAACGCCGCTAAATCCCTGAGCAT
1 TAGCGGCGCTTTCTAAAAAACGCCGCTAAAGCCCTGAGCAT
* * * *
16898673 TAGCGGTGCTTCCTAAAATACGCCACTAAA
1 TAGCGGCGCTTTCTAAAAAACGCCGCTAAA
16898703 TCCCCGAAAG
Statistics
Matches: 157, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
39 6 0.04
40 40 0.25
41 103 0.66
42 8 0.05
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (41 bp):
TAGCGGCGCTTTCTAAAAAACGCCGCTAAAGCCCTGAGCAT
Found at i:16898660 original size:82 final size:82
Alignment explanation
Indices: 16898484--16898702 Score: 243
Period size: 82 Copynumber: 2.7 Consensus size: 82
16898474 GCGCATTTTA
* * *
16898484 GAAAACGCCGCTAAAAG-TCTGATCTTTAGCGGCGCTTTCCT-AAAAACGCCGCT-AAAGCCCTA
1 GAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCGCTTT-CTAAAAAACGCCGCTAAAAGCCCTA
16898546 GCATTAGCGACGTTTCCTC
64 GCATTAGCGACGTTTCCTC
* * *
16898565 AAAAACGCCGCTAAAGCCCTGAGCATTAGTGGCGCTTTCTAAAAAACGCCGCTAAAAG-CCTAAT
1 GAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAAGCCCT-AG
*
16898629 CTTTAGCAGCAC-TTT-CTC
65 CATTAGC-G-ACGTTTCCTC
* * * * *
16898647 GAAAACGCCGCTAAATCCCTGAGCATTAGCGGTGCTTCCTAAAATACGCCACTAAA
1 GAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAA
16898703 TCCCCGAAAG
Statistics
Matches: 118, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
80 6 0.05
81 43 0.36
82 63 0.53
83 4 0.03
84 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (82 bp):
GAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAAGCCCTAGC
ATTAGCGACGTTTCCTC
Found at i:16900074 original size:22 final size:22
Alignment explanation
Indices: 16900049--16900094 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
16900039 TTTCCCCTTC
*
16900049 CTTCCCTTCCTGTTCTCTTCTT
1 CTTCCCTTCCTCTTCTCTTCTT
* *
16900071 CTTCTCTTCTTCTTCTCTTCTT
1 CTTCCCTTCCTCTTCTCTTCTT
16900093 CT
1 CT
16900095 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.02, T:0.59
Consensus pattern (22 bp):
CTTCCCTTCCTCTTCTCTTCTT
Found at i:16900075 original size:11 final size:11
Alignment explanation
Indices: 16900061--16900094 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
16900051 TCCCTTCCTG
16900061 TTCTCTTCTTC
1 TTCTCTTCTTC
16900072 TTCTCTTCTTC
1 TTCTCTTCTTC
16900083 TTCTCTTCTTC
1 TTCTCTTCTTC
16900094 T
1 T
16900095 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
TTCTCTTCTTC
Found at i:16903768 original size:20 final size:17
Alignment explanation
Indices: 16903691--16903762 Score: 72
Period size: 17 Copynumber: 3.9 Consensus size: 17
16903681 TAATAATTTT
16903691 ACAAAAAAATTTATTTGA
1 ACAAAAAAA-TTATTTGA
* *
16903709 ACAGTGGAATAAAATAATTTAA
1 ACA----AA-AAAATTATTTGA
16903731 ACAAAAAAATTATTTGA
1 ACAAAAAAATTATTTGA
16903748 ACAAAAAAATTATTT
1 ACAAAAAAATTATTT
16903763 TTTGAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
17 25 0.56
18 5 0.11
22 11 0.24
23 4 0.09
ACGTcount: A:0.57, C:0.06, G:0.07, T:0.31
Consensus pattern (17 bp):
ACAAAAAAATTATTTGA
Found at i:16907641 original size:33 final size:33
Alignment explanation
Indices: 16907604--16907747 Score: 90
Period size: 33 Copynumber: 4.3 Consensus size: 33
16907594 TGATCCAACC
16907604 ATGGTCTTATGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTATGTTCATAGTGCCATAACCCAGTT
** * * * * *
16907637 ATGGTCTTATCATCAGAATGCCATAGCCTAGCT
1 ATGGTCTTATGTTCATAGTGCCATAACCCAGTT
* * ** * * * ** * *
16907670 ATAGTCTTACATATAAACACTACCATAGTCCAATC
1 ATGGTCTT--ATGTTCATAGTGCCATAACCCAGTT
* *
16907705 ATGGTATTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTATGTTCATAGTGCCATAACCCAGTT
16907738 ATGGTCTTAT
1 ATGGTCTTAT
16907748 CCTTCAATTC
Statistics
Matches: 74, Mismatches: 35, Indels: 4
0.65 0.31 0.04
Matches are distributed among these distances:
33 55 0.74
35 19 0.26
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (33 bp):
ATGGTCTTATGTTCATAGTGCCATAACCCAGTT
Found at i:16907702 original size:101 final size:101
Alignment explanation
Indices: 16907509--16907748 Score: 365
Period size: 101 Copynumber: 2.4 Consensus size: 101
16907499 AATTCATCCT
* * * * *
16907509 TTACATTCGTAGTGCCATAACCCAATTATGGTATTATCATCAGAATACCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATACCATAGCCCAGCTATAGT
* *
16907574 CTTACATATAAACACTGCCATGATCCAACCATGGTC
66 CTTACATATAAACACTACCATGATCCAACCATGGTA
* * *
16907610 TTATGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCTAGCTATAGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATACCATAGCCCAGCTATAGT
*
16907675 CTTACATATAAACACTACCAT-AGTCCAATCATGGTA
66 CTTACATATAAACACTACCATGA-TCCAACCATGGTA
16907711 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
16907749 CTTCAATTCA
Statistics
Matches: 126, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
100 1 0.01
101 125 0.99
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATACCATAGCCCAGCTATAGT
CTTACATATAAACACTACCATGATCCAACCATGGTA
Found at i:16909723 original size:31 final size:31
Alignment explanation
Indices: 16909665--16909730 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
16909655 TTTATACCAA
*
16909665 TAAAATAAAATAAAATAATAAAATATCTCAT
1 TAAAATAAAATAAAATAATAAAATATCTAAT
* **
16909696 TAAAATATTAATAAAATAAT-ATTTATCTAAT
1 TAAAATA-AAATAAAATAATAAAATATCTAAT
16909727 TAAA
1 TAAA
16909731 TAATTATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (31 bp):
TAAAATAAAATAAAATAATAAAATATCTAAT
Found at i:16910668 original size:87 final size:87
Alignment explanation
Indices: 16910560--16910741 Score: 192
Period size: 87 Copynumber: 2.1 Consensus size: 87
16910550 TAAATATTTA
* * * * *
16910560 GGGATTTATTCTCGCCGTTCAACGAATTTTATTCCAATTTTAATTTTATT-TCTAAAACGAG-TA
1 GGGATTTATTCTCGCCATTCAACGAA-TTTATTAC-ATTTTAATTTTATTGCCAAAAACGAGAAA
*
16910623 TT-AAATTAAAATAAAATCTGCTTT
64 TTAAAATT-AAATAAAATCTACTTT
* * * *
16910647 GGGATTTATTC-CTGTCATTCAATGGATTTATTACATTTTGATTTTATTGCCAAAAACGAGAAAT
1 GGGATTTATTCTC-GCCATTCAACGAATTTATTACATTTTAATTTTATTGCCAAAAACGAGAAAT
* *
16910711 TAAAATTAAATAAAATTTATTTT
65 TAAAATTAAATAAAATCTACTTT
16910734 GGGATTTA
1 GGGATTTA
16910742 CTCCAGCCGT
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
85 13 0.16
86 17 0.22
87 44 0.56
88 5 0.06
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (87 bp):
GGGATTTATTCTCGCCATTCAACGAATTTATTACATTTTAATTTTATTGCCAAAAACGAGAAATT
AAAATTAAATAAAATCTACTTT
Found at i:16910822 original size:84 final size:85
Alignment explanation
Indices: 16910708--16910870 Score: 247
Period size: 84 Copynumber: 1.9 Consensus size: 85
16910698 AAAAACGAGA
* * *
16910708 AATTAAAATTAAATAAAATTTATTTTGGGATTTACTCCAGCCGTTTAACAAGATTTTATTTGATT
1 AATTAAAATTAAATAAAATTTATTTCGGGATTTACTCCAGCCGTTTAACAAGATTTTATTCGATA
16910773 TTATTTCGTTTCCAGATTAG
66 TTATTTCGTTTCCAGATTAG
* * *
16910793 AATT-AAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTTATTCGATA
1 AATTAAAATTAAATAAAATTTATTTCGGGATTTACTCCAGCCGTTTAACAAGATTTTATTCGATA
* *
16910857 TTGTTTTGTTTCCA
66 TTATTTCGTTTCCA
16910871 AACAAAGACG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 66 0.94
85 4 0.06
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (85 bp):
AATTAAAATTAAATAAAATTTATTTCGGGATTTACTCCAGCCGTTTAACAAGATTTTATTCGATA
TTATTTCGTTTCCAGATTAG
Found at i:16910890 original size:84 final size:84
Alignment explanation
Indices: 16910713--16910931 Score: 239
Period size: 84 Copynumber: 2.6 Consensus size: 84
16910703 CGAGAAATTA
* * * * *
16910713 AAATTAAATAAAATTTATTTTGGGATTTACTCCAGCCGTTTAACAAGATTTTATTTGATTTTATT
1 AAATCAAATAAAATTTGTTTTGGGATTTATTCCAGCCGTTTAACAAGATTTTATTCGATATTATT
* ** *
16910778 TCGTTTCCAGATTAGAATT
66 TCGTTTCCAAAAAAGAAGT
* * * *
16910797 AAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTTATTCGATATTGTT
1 AAATCAAATAAAATTTGTTTTGGGATTTATTCCAGCCGTTTAACAAGATTTTATTCGATATTATT
* *
16910862 TTGTTTCCAAACAAAGACGT
66 TCGTTTCCAAA-AAAGAAGT
**
16910882 -AATCAAAT--AATTCTGTTTTGGGATTTATTCTTGCCGTTTAAC-AGATTTTA
1 AAATCAAATAAAATT-TGTTTTGGGATTTATTCCAGCCGTTTAACAAGATTTTA
16910932 ATTTGATGTA
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
82 12 0.10
83 26 0.22
84 74 0.64
85 4 0.03
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (84 bp):
AAATCAAATAAAATTTGTTTTGGGATTTATTCCAGCCGTTTAACAAGATTTTATTCGATATTATT
TCGTTTCCAAAAAAGAAGT
Found at i:16914633 original size:53 final size:52
Alignment explanation
Indices: 16914576--16914695 Score: 145
Period size: 53 Copynumber: 2.3 Consensus size: 52
16914566 CAATTTAAGC
*
16914576 TTTTATAATTTTTTAAAATAAATTTTATAAGCTTATATCAATTTTAATATTTT
1 TTTTATAATTTTTTAAAATAAATTTTATAAGCTTATAT-AATTTTAATAATTT
** * *
16914629 TTTTATAATTATTTT-TTATAATTTTTATAAGTTTATATAATTTTAATAATTT
1 TTTTATAATT-TTTTAAAATAAATTTTATAAGCTTATATAATTTTAATAATTT
* *
16914681 TTCT-TAATATTTTAA
1 TTTTATAATTTTTTAA
16914696 TATTTTATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
50 4 0.07
51 4 0.07
52 16 0.28
53 29 0.51
54 4 0.07
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.60
Consensus pattern (52 bp):
TTTTATAATTTTTTAAAATAAATTTTATAAGCTTATATAATTTTAATAATTT
Found at i:16914645 original size:13 final size:13
Alignment explanation
Indices: 16914627--16914651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16914617 TTTTAATATT
16914627 TTTTTTATAATTA
1 TTTTTTATAATTA
16914640 TTTTTTATAATT
1 TTTTTTATAATT
16914652 TTTATAAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTATAATTA
Found at i:16914655 original size:9 final size:9
Alignment explanation
Indices: 16914641--16914720 Score: 58
Period size: 9 Copynumber: 8.8 Consensus size: 9
16914631 TTATAATTAT
16914641 TTTTTATAA
1 TTTTTATAA
16914650 TTTTTATAA
1 TTTTTATAA
*
16914659 GTTTATATAA
1 -TTTTTATAA
*
16914669 TTTTAATAA
1 TTTTTATAA
*
16914678 TTTTTCTTAA
1 TTTTT-ATAA
*
16914688 TATTT-TAA
1 TTTTTATAA
16914696 TATTTTAT--
1 T-TTTTATAA
*
16914704 TTTTTAATAT
1 TTTTT-ATAA
16914714 TTTTTAT
1 TTTTTAT
16914721 GGGTAAAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
7 4 0.07
8 7 0.12
9 25 0.44
10 21 0.37
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:16914697 original size:8 final size:8
Alignment explanation
Indices: 16914684--16914716 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
16914674 ATAATTTTTC
16914684 TTAATATT
1 TTAATATT
16914692 TTAATATT
1 TTAATATT
*
16914700 TT-ATTTT
1 TTAATATT
16914707 TTAATATT
1 TTAATATT
16914715 TT
1 TT
16914717 TTATGGGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTAATATT
Found at i:16916056 original size:12 final size:12
Alignment explanation
Indices: 16916036--16916083 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
16916026 TTTTTTAAAT
16916036 TTATT-TTATTA
1 TTATTGTTATTA
*
16916047 ATATTGTTATTA
1 TTATTGTTATTA
*
16916059 TTATTATTA-TA
1 TTATTGTTATTA
16916070 TTATATGTTATTA
1 TTAT-TGTTATTA
16916083 T
1 T
16916084 CATTATACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 10 0.33
12 17 0.57
13 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (12 bp):
TTATTGTTATTA
Found at i:16916078 original size:24 final size:26
Alignment explanation
Indices: 16916036--16916089 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
16916026 TTTTTTAAAT
* *
16916036 TTATTTTATTAATATTGTTATTATTA
1 TTATTATATTAATATTGTTATTATCA
16916062 TTATTATATT-ATA-TGTTATTATCA
1 TTATTATATTAATATTGTTATTATCA
16916086 TTAT
1 TTAT
16916090 ACTTACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 14 0.54
25 3 0.12
26 9 0.35
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (26 bp):
TTATTATATTAATATTGTTATTATCA
Found at i:16927780 original size:22 final size:22
Alignment explanation
Indices: 16927752--16927796 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
16927742 GGGGTGTTAG
16927752 TGACAAAGCTTCATTGAACAAA
1 TGACAAAGCTTCATTGAACAAA
16927774 TGACAAAGCTTCATTGAACAAA
1 TGACAAAGCTTCATTGAACAAA
16927796 T
1 T
16927797 AAGCAGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (22 bp):
TGACAAAGCTTCATTGAACAAA
Found at i:16928634 original size:50 final size:50
Alignment explanation
Indices: 16928578--16928760 Score: 145
Period size: 50 Copynumber: 3.7 Consensus size: 50
16928568 TTGGCATTAC
*
16928578 AGTGGAAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCAGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGT
* * * * *** * * *
16928628 AGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACA-TAT
1 AGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGT
* ** * * **
16928677 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTTCCTAGTGGTGT
1 -AGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGT
* * *
16928728 AGT-GAAACAGATTGAAGCTACGACGGCAGATCT
1 AGTGGAAA-AGATTGAAGCCACAACGGCGGATCT
16928761 GGTTTCCCCG
Statistics
Matches: 97, Mismatches: 33, Indels: 6
0.71 0.24 0.04
Matches are distributed among these distances:
49 5 0.05
50 90 0.93
51 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (50 bp):
AGTGGAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGT
Found at i:16928790 original size:50 final size:50
Alignment explanation
Indices: 16928636--16928783 Score: 138
Period size: 50 Copynumber: 3.0 Consensus size: 50
16928626 GTAGTGGAAC
*
16928636 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATAT-CAATTAAAA
1 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACAT-TGCAGTTAAAA
* * * ** ** *** * * *
16928686 AGATTGAAGCCACAACGGCGGATCTTACTTTCCTAG-TGGTGTAGTGAAAC
1 AGATTGAAGCTACGACGGCAGATC-TGGTTTCCCCGACATTGCAGTTAAAA
16928736 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCAGTTAA
1 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCAGTTAA
16928784 GTAGATTAAA
Statistics
Matches: 69, Mismatches: 26, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
49 8 0.12
50 54 0.78
51 7 0.10
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCAGTTAAAA
Found at i:16928790 original size:100 final size:100
Alignment explanation
Indices: 16928583--16928774 Score: 330
Period size: 100 Copynumber: 1.9 Consensus size: 100
16928573 ATTACAGTGG
* *
16928583 AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTAGCAGTGTAGTGAAACAGATTGAAGCTA
16928648 CGACGGCAGATCTGGTTTCCCCGACATATCAATTA
66 CGACGGCAGATCTGGTTTCCCCGACATATCAATTA
* * **
16928683 AAAAGATTGAAGCCACAACGGCGGATCTTACTTTCCTAGTGGTGTAGTGAAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTAGCAGTGTAGTGAAACAGATTGAAGCTA
16928748 CGACGGCAGATCTGGTTTCCCCGACAT
66 CGACGGCAGATCTGGTTTCCCCGACAT
16928775 TGCAGTTAAG
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 86 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTAGCAGTGTAGTGAAACAGATTGAAGCTA
CGACGGCAGATCTGGTTTCCCCGACATATCAATTA
Found at i:16930426 original size:3 final size:3
Alignment explanation
Indices: 16930401--16930441 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
16930391 TTTTTTAAAT
* *
16930401 TTA TT- TTA TTA ATA TTG TTA TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16930442 ATGTCATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:16941637 original size:17 final size:16
Alignment explanation
Indices: 16941615--16941666 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 16
16941605 AAGCAGTTGT
16941615 GAAGTTAGACTGTTAAA
1 GAAGTTAG-CTGTTAAA
16941632 GAAGTTAGCTGTT-AA
1 GAAGTTAGCTGTTAAA
16941647 -AA---AGCTGTTAAA
1 GAAGTTAGCTGTTAAA
16941659 GAAGTTAG
1 GAAGTTAG
16941667 TTTGTTGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
11 7 0.23
12 2 0.07
13 2 0.07
14 2 0.07
15 2 0.07
16 7 0.23
17 8 0.27
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (16 bp):
GAAGTTAGCTGTTAAA
Found at i:16947535 original size:48 final size:48
Alignment explanation
Indices: 16947471--16947726 Score: 266
Period size: 48 Copynumber: 5.3 Consensus size: 48
16947461 GGAATTGAGC
* *
16947471 TAATGTACCTAATTTATATTACAAAGTTTGTTCTTCATTTTAATGTTG
1 TAATGTATCTAATTTATATTACAAAGTTTGTTCTTCGTTTTAATGTTG
* * * *
16947519 TAATATTTCTAATTTATATTACAAAGTTTGTCCCTCGTTTTAATGTTG
1 TAATGTATCTAATTTATATTACAAAGTTTGTTCTTCGTTTTAATGTTG
16947567 TAATGTATCTAATTTATATTACAAAGTTTGTT-TCTCGTTTTAATGTTG
1 TAATGTATCTAATTTATATTACAAAGTTTGTTCT-TCGTTTTAATGTTG
** * ***
16947615 TAATGTATCTAATTTATGACCATAAAGTTTGTTCCAAGTTTTAATGTTG
1 TAATGTATCTAATTTAT-ATTACAAAGTTTGTTCTTCGTTTTAATGTTG
* ** * ***
16947664 CAAT-TAATCTAATTTATGACCATAAAGTTTGTTCCAAGTTTTAATGTTG
1 TAATGT-ATCTAATTTAT-ATTACAAAGTTTGTTCTTCGTTTTAATGTTG
*
16947713 CAAT-TAATCTAATT
1 TAATGT-ATCTAATT
16947727 AAATAAATAA
Statistics
Matches: 187, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
48 103 0.55
49 84 0.45
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (48 bp):
TAATGTATCTAATTTATATTACAAAGTTTGTTCTTCGTTTTAATGTTG
Found at i:16948142 original size:12 final size:12
Alignment explanation
Indices: 16948125--16948224 Score: 101
Period size: 12 Copynumber: 8.3 Consensus size: 12
16948115 TATACGACCA
16948125 CTCGGGCTCTAG
1 CTCGGGCTCTAG
16948137 CTCGGGCTCTAG
1 CTCGGGCTCTAG
*
16948149 CTCGGGCTCTGG
1 CTCGGGCTCTAG
** * *
16948161 CTCTTGCTTTGG
1 CTCGGGCTCTAG
* *
16948173 CTCGGGCTTTGG
1 CTCGGGCTCTAG
**
16948185 CTCTAGCTCTAG
1 CTCGGGCTCTAG
*
16948197 CTCGGCCTCTAG
1 CTCGGGCTCTAG
*
16948209 CTCGGGCTCTGG
1 CTCGGGCTCTAG
16948221 CTCG
1 CTCG
16948225 TATGCCCCAA
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 73 1.00
ACGTcount: A:0.05, C:0.33, G:0.32, T:0.30
Consensus pattern (12 bp):
CTCGGGCTCTAG
Found at i:16948164 original size:6 final size:6
Alignment explanation
Indices: 16948129--16948223 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
16948119 CGACCACTCG
* * * * * * *
16948129 GGCTCT AGCTCG GGCTCT AGCTCG GGCTCT GGCTCT TGCTTT GGCTCG
1 GGCTCT GGCTCT GGCTCT GGCTCT GGCTCT GGCTCT GGCTCT GGCTCT
* * * * *
16948177 GGCTTT GGCTCT AGCTCT AGCTC- GGCCTCT AGCTCG GGCTCT GGCTC
1 GGCTCT GGCTCT GGCTCT GGCTCT GG-CTCT GGCTCT GGCTCT GGCTC
16948224 GTATGCCCCA
Statistics
Matches: 65, Mismatches: 22, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
5 1 0.02
6 63 0.97
7 1 0.02
ACGTcount: A:0.05, C:0.33, G:0.32, T:0.31
Consensus pattern (6 bp):
GGCTCT
Found at i:16948858 original size:14 final size:14
Alignment explanation
Indices: 16948839--16948871 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16948829 CAAATTACAT
16948839 GTTAGAATAATATC
1 GTTAGAATAATATC
16948853 GTTAGAATAATATC
1 GTTAGAATAATATC
*
16948867 ATTAG
1 GTTAG
16948872 CAAAAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (14 bp):
GTTAGAATAATATC
Found at i:16950454 original size:16 final size:16
Alignment explanation
Indices: 16950435--16950506 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
16950425 ATAACATGCC
*
16950435 AAATAAATTACATAAA
1 AAATAAATCACATAAA
16950451 AAATAAATCA-ATAAA
1 AAATAAATCACATAAA
* *
16950466 CCTAAA-ACA-CACATAAC
1 ---AAATAAATCACATAAA
*
16950483 AAATAAATTACATAAAA
1 AAATAAATCACAT-AAA
16950500 AAATAAA
1 AAATAAA
16950507 ACATTCTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
14 3 0.07
15 7 0.16
16 15 0.35
17 15 0.35
18 3 0.07
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAATCACATAAA
Found at i:16951669 original size:20 final size:21
Alignment explanation
Indices: 16951625--16951669 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
16951615 AGCACTTAGG
* *
16951625 TTTTTATAGGAAAAACTTGAA
1 TTTTTATAGGAAAAAATTCAA
16951646 TTTTTATA-GAAAAAATTC-A
1 TTTTTATAGGAAAAAATTCAA
16951665 TTTTT
1 TTTTT
16951670 CTTTTTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 8 0.36
21 8 0.36
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (21 bp):
TTTTTATAGGAAAAAATTCAA
Found at i:16952059 original size:32 final size:32
Alignment explanation
Indices: 16952023--16952094 Score: 101
Period size: 31 Copynumber: 2.2 Consensus size: 32
16952013 AATGGTAAAT
* *
16952023 TAACAACCGATGACTAAAATGATAAAAA-TATG
1 TAACAACAG-TGACTAAAATGATAAAAAGTAAG
*
16952055 TAACAATAGTGACTAAAATGATAAAAAGTAAG
1 TAACAACAGTGACTAAAATGATAAAAAGTAAG
16952087 TAACAACA
1 TAACAACA
16952095 ATTCTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 18 0.51
32 17 0.49
ACGTcount: A:0.56, C:0.11, G:0.12, T:0.21
Consensus pattern (32 bp):
TAACAACAGTGACTAAAATGATAAAAAGTAAG
Found at i:16952070 original size:31 final size:32
Alignment explanation
Indices: 16952033--16952092 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
16952023 TAACAACCGA
*
16952033 TGACTAAAATGATAAAAA-TATGTAACAATAG
1 TGACTAAAATGATAAAAAGTAAGTAACAATAG
16952064 TGACTAAAATGATAAAAAGTAAGTAACAA
1 TGACTAAAATGATAAAAAGTAAGTAACAA
16952093 CAATTCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (32 bp):
TGACTAAAATGATAAAAAGTAAGTAACAATAG
Found at i:16953399 original size:16 final size:16
Alignment explanation
Indices: 16953378--16953408 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16953368 GATAACAAAA
16953378 AAAAGCTAACCATGGG
1 AAAAGCTAACCATGGG
16953394 AAAAGCTAACCATGG
1 AAAAGCTAACCATGG
16953409 ATGTATGAAC
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:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (16 bp):
AAAAGCTAACCATGGG
Found at i:16960641 original size:44 final size:43
Alignment explanation
Indices: 16960531--16960645 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 43
16960521 ATATCATACA
* *
16960531 ATGCCAACGTCCTAGACGTGGTCTTACATGAAATCACCTAACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACCTAACG
* *
16960574 ATGCC-ACTGTCTCAAACAG-GGTCTTACACGTAAATCA-C-AAGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACG-AAATCACCTAA--CG
16960618 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
16960646 TGATAACACA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
42 4 0.07
43 23 0.39
44 30 0.51
45 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACCTAACG
Found at i:16988542 original size:14 final size:16
Alignment explanation
Indices: 16988523--16988559 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
16988513 GTACATCTTC
*
16988523 ATACATATATAC-A-T
1 ATACATATAAACTATT
16988537 ATACATATAAACTATT
1 ATACATATAAACTATT
16988553 ATACATA
1 ATACATA
16988560 CAATGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 11 0.55
15 1 0.05
16 8 0.40
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (16 bp):
ATACATATAAACTATT
Found at i:16989302 original size:41 final size:41
Alignment explanation
Indices: 16989257--16989353 Score: 140
Period size: 41 Copynumber: 2.4 Consensus size: 41
16989247 CAGAAAATTG
* *
16989257 GCATTAAGCCTGGTAGATGTAAAGTCTGAAATATTTCACCA
1 GCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCA
* **
16989298 GCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTTCACTG
1 GCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCA
*
16989339 GCATTAAGCTTGCTA
1 GCATTAAGCCTGCTA
16989354 AGCATAGAGC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (41 bp):
GCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCA
Found at i:16989368 original size:41 final size:41
Alignment explanation
Indices: 16989257--16989369 Score: 111
Period size: 41 Copynumber: 2.8 Consensus size: 41
16989247 CAGAAAATTG
* ** * *
16989257 GCATTAAGCCTGGTAGATGTAAAGTCTGAAATATTTCACCA
1 GCATTAAGCCTGCTAGACATAAAGCCTGAATTATTTCACCA
* * **
16989298 GCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTTCACTG
1 GCATTAAGCCTGCTAGACATAAAGCCTGAATTATTTCACCA
* *
16989339 GCATTAAGCTTGCTA-AGCATAGAGCCTGAAT
1 GCATTAAGCCTGCTAGA-CATAAAGCCTGAAT
16989370 AACTCAGATA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 1 0.02
41 61 0.98
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (41 bp):
GCATTAAGCCTGCTAGACATAAAGCCTGAATTATTTCACCA
Found at i:16996057 original size:40 final size:40
Alignment explanation
Indices: 16996013--16996249 Score: 318
Period size: 40 Copynumber: 5.9 Consensus size: 40
16996003 GCGTGTTTTG
* * *
16996013 GTTGGACCAGCTCTTATGAGCTTTTGTTTGGCGTGTTACA
1 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTGTTACA
16996053 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTGTTAC-
1 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTGTTACA
* * *
16996092 GATTGGATCAGCTCTTATGAGTTTCTGTCTAGTGTGCTT-CA
1 G-TTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTG-TTACA
* *
16996133 GGTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTGTTACG
1 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTGTTACA
* *
16996173 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTACTT-CG
1 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGT-GTTACA
* *
16996213 GGTGGATCAGCTCTTATGAGCTTCTGTCTGGTGTGTT
1 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTGTT
16996250 CGGTGGATCT
Statistics
Matches: 176, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
39 5 0.03
40 166 0.94
41 5 0.03
ACGTcount: A:0.14, C:0.16, G:0.29, T:0.41
Consensus pattern (40 bp):
GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTGTTACA
Found at i:16996139 original size:80 final size:80
Alignment explanation
Indices: 16996014--16996249 Score: 350
Period size: 80 Copynumber: 3.0 Consensus size: 80
16996004 CGTGTTTTGG
* * *
16996014 TTGGACCAGCTCTTATGAGCTTT-TGTTTGGCGTG-TTACAGTTGGATCAGCTCTTATGAGCTTC
1 TTGGATCAGCTCTTATGAG-TTTCTGTTTGGTGTGCTT-CAGGTGGATCAGCTCTTATGAGCTTC
16996077 TGTTTGGTGTGTTACGA
64 TGTTTGGTGTGTTACGA
* *
16996094 TTGGATCAGCTCTTATGAGTTTCTGTCTAGTGTGCTTCAGGTGGATCAGCTCTTATGAGCTTCTG
1 TTGGATCAGCTCTTATGAGTTTCTGTTTGGTGTGCTTCAGGTGGATCAGCTCTTATGAGCTTCTG
*
16996159 TTTGGTGTGTTACGG
66 TTTGGTGTGTTACGA
* * *
16996174 TTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTACTTCGGGTGGATCAGCTCTTATGAGCTTCTG
1 TTGGATCAGCTCTTATGAGTTTCTGTTTGGTGTGCTTCAGGTGGATCAGCTCTTATGAGCTTCTG
*
16996239 TCTGGTGTGTT
66 TTTGGTGTGTT
16996250 CGGTGGATCT
Statistics
Matches: 142, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
79 3 0.02
80 137 0.96
81 2 0.01
ACGTcount: A:0.14, C:0.17, G:0.28, T:0.42
Consensus pattern (80 bp):
TTGGATCAGCTCTTATGAGTTTCTGTTTGGTGTGCTTCAGGTGGATCAGCTCTTATGAGCTTCTG
TTTGGTGTGTTACGA
Found at i:16996206 original size:120 final size:118
Alignment explanation
Indices: 16996015--16996258 Score: 373
Period size: 120 Copynumber: 2.1 Consensus size: 118
16996005 GTGTTTTGGT
* *
16996015 TGGACCAGCTCTTATGAGCTTTTGTTTGGCGTGTTACAGTTGGATCAGCTCTTATGAGCTTCTGT
1 TGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTACAGTTGGATCAGCTCTTATGAGCTTCTGT
* * *
16996080 TTGGTGT-GTTACGATTGGATCAGCTCTTATGAGTTTCTGTCTAGTGTGCTTCAGG
66 TTGGTGTACTT-CGAGTGGATCAGCTCTTATGAGCTTCTGTCTAGTGTG-TTC-GG
* *
16996135 TGGATCAGCTCTTATGAGCTTCTGTTTGGTGTGTTACGGTTGGATCAGCTCTTATGAGCTTCTGT
1 TGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTACAGTTGGATCAGCTCTTATGAGCTTCTGT
* *
16996200 TTGGTGTACTTCGGGTGGATCAGCTCTTATGAGCTTCTGTCTGGTGTGTTCGG
66 TTGGTGTACTTCGAGTGGATCAGCTCTTATGAGCTTCTGTCTAGTGTGTTCGG
16996253 TGGATC
1 TGGATC
16996259 TGACGATGTA
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
118 8 0.07
119 3 0.03
120 101 0.89
121 2 0.02
ACGTcount: A:0.14, C:0.17, G:0.29, T:0.41
Consensus pattern (118 bp):
TGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTACAGTTGGATCAGCTCTTATGAGCTTCTGT
TTGGTGTACTTCGAGTGGATCAGCTCTTATGAGCTTCTGTCTAGTGTGTTCGG
Found at i:16998202 original size:23 final size:23
Alignment explanation
Indices: 16998167--16998232 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
16998157 CGGTTTTGGG
* * *
16998167 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACAAAATGGTAATGCGA
* *
16998190 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACAAAATGGTAATGCGA
* *
16998213 TTTGGTACGAAATGTTAATG
1 TTTGGTACAAAATGGTAATG
16998233 GTTCAAAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (23 bp):
TTTGGTACAAAATGGTAATGCGA
Found at i:17020793 original size:23 final size:24
Alignment explanation
Indices: 17020751--17020795 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
17020741 GTACATTTAT
* *
17020751 TTTTATAATAAATAACTTAAAAAC
1 TTTTATAATAAAAAAATTAAAAAC
17020775 TTTTA-AATAAAAAAATTAAAA
1 TTTTATAATAAAAAAATTAAAA
17020796 TAAATGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
TTTTATAATAAAAAAATTAAAAAC
Found at i:17034677 original size:45 final size:45
Alignment explanation
Indices: 17034585--17034697 Score: 133
Period size: 45 Copynumber: 2.5 Consensus size: 45
17034575 GCATCTAGTA
*
17034585 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAATC
* **
17034630 TTATC-CTCCTGAAGTTGCAGT-GAGGCAGGCTAAAG-ATGGCAAATC
1 TTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGCAAAGCAAATC
*
17034675 TTATCTCCCTGAAGTTGCGGTGG
1 TTATCTCCCTGAAGTTGCAGTGG
17034698 CGCGGATTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
44 3 0.05
45 50 0.86
46 5 0.09
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAATC
Found at i:17034709 original size:45 final size:45
Alignment explanation
Indices: 17034585--17034710 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 45
17034575 GCATCTAGTA
* *
17034585 TTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAAGCAAGTC
1 TTATCTCCCTGAAGTTGCAGTGG-GCGGACTAAAGCAAAGCAAATC
**
17034630 TTATC-CTCCTGAAGTTGCAGTGAGGCAGG-CTAAAG-ATGGCAAATC
1 TTATCTC-CCTGAAGTTGCAGTG-GGC-GGACTAAAGCAAAGCAAATC
* *
17034675 TTATCTCCCTGAAGTTGCGGTGGCGCGGATTAAAGC
1 TTATCTCCCTGAAGTTGCAGTGG-GCGGACTAAAGC
17034711 CGACAGTGGA
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
44 4 0.06
45 57 0.85
46 6 0.09
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAGTGGGCGGACTAAAGCAAAGCAAATC
Found at i:17034964 original size:44 final size:44
Alignment explanation
Indices: 17034867--17034972 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
17034857 GAAGATGGCA
* * *
17034867 AATCTTATCTCCCTGAAGTTACGGTGGAGCAAATTAAAGCTGAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAAATTAAACCTCAT
* ***
17034911 AATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACCTCA-
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAAATT-AAACCTCAT
* *
17034955 GATCTTATCTCTCTGAAG
1 AATCTTATCTCCCTGAAG
17034973 ATGCAGAGAG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 45 0.88
45 6 0.12
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTACAGTGGAGCAAATTAAACCTCAT
Found at i:17035119 original size:44 final size:43
Alignment explanation
Indices: 17035041--17035152 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 43
17035031 AGCAAAGCAA
*
17035041 ATCTTATCTCCCTGAAGTTGCAGCGGAACAGATTA-AAGCCGACA-
1 ATCTTATCTCCCTGAAGTTGCAG-TGAACAGATTATAA-CC-ACAG
*
17035085 AT-TCTATCTCCCTGAAGTTGCAGTGAAGCGGATTATAACCACAG
1 ATCT-TATCTCCCTGAAGTTGCAGTGAA-CAGATTATAACCACAG
*
17035129 ATCTTATCTCTCTGAAGTTGCAGT
1 ATCTTATCTCCCTGAAGTTGCAGT
17035153 AGAGTAGATC
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
43 7 0.12
44 50 0.83
45 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTGAACAGATTATAACCACAG
Found at i:17035132 original size:173 final size:175
Alignment explanation
Indices: 17034864--17035236 Score: 502
Period size: 173 Copynumber: 2.1 Consensus size: 175
17034854 ACTGAAGATG
* * * * * *
17034864 GCAAATCTTATCTCCCTGAAGTTACGGTGGAGCAAATTAAAGCTGATAATCCTATCTCCCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGCGGAACAAATTAAAGCCGACAATCCTATCTCCCTGAAG
* * * **
17034929 TTACAGTGGAGTGGATTAAAACCTCAGATCTTATCTCTCTGAAGATGCAG-AGAGTAGATCGTAT
66 TTACAGTGAAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGATGCAGTAGAGTAGATCACAT
* *
17034993 CTAGTCTT-ATCTCCCTGAAGTTGTAGTGGAGCAAACT-AAGCAAA
131 CGAGTCTTAATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAG-AAA
* *
17035037 GCAAATCTTATCTCCCTGAAGTTGCAGCGGAACAGATTAAAGCCGACAATTCTATCTCCCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGCGGAACAAATTAAAGCCGACAATCCTATCTCCCTGAAG
* * *
17035102 TTGCAGTGAAGCGGATTATAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCACAT
66 TTACAGTGAAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGATGCAGTAGAGTAGATCACAT
* *
17035167 CGGGTCTTAATCTCCCTGAAGTTGCAGTGGAGTAAACTCAAGAAA
131 CGAGTCTTAATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAA
* *
17035212 GCAAGTCTTATC-CCCTTGAAATTGC
1 GCAAATCTTATCTCCC-TGAAGTTGC
17035237 TGTGGGACAG
Statistics
Matches: 174, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
173 101 0.58
174 21 0.12
175 49 0.28
176 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (175 bp):
GCAAATCTTATCTCCCTGAAGTTGCAGCGGAACAAATTAAAGCCGACAATCCTATCTCCCTGAAG
TTACAGTGAAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGATGCAGTAGAGTAGATCACAT
CGAGTCTTAATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAA
Found at i:17035269 original size:175 final size:173
Alignment explanation
Indices: 17034864--17035284 Score: 481
Period size: 173 Copynumber: 2.4 Consensus size: 173
17034854 ACTGAAGATG
* * * * * * * *
17034864 GCAAATCTTATCTCCCTGAAGTTACGGTGGAGCAAATTAAAGCTGATAATCCTATCTCCCTGAAG
1 GCAAATCTTATCTCCCTGAAATTGCAGCGGAACAGACTAAAGCAGATAATCCTATCTCCCTGAAG
* * * **
17034929 TTACAGTGGAGTGGATTAAAACCTCAGATCTTATCTCTCTGAAGATGCAGAGAGTAGATCGTATC
66 TTACAGTGAAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGATGCAGAGAGTAGATCACATC
* *
17034994 TAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAAACTAAGCAAA
131 GAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGCAAA
* * * * *
17035037 GCAAATCTTATCTCCCTGAAGTTGCAGCGGAACAGATTAAAGCCGACAATTCTATCTCCCTGAAG
1 GCAAATCTTATCTCCCTGAAATTGCAGCGGAACAGACTAAAGCAGATAATCCTATCTCCCTGAAG
* * *
17035102 TTGCAGTGAAGCGGATTATAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCACAT
66 TTACAGTGAAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGATGCAG-AGAGTAGATCACAT
* *
17035167 CGGGTCTTAATCTCCCTGAAGTTGCAGTGGAGTAAACTCAAG-AAA
130 CGAGTCTT-ATCTCCCTGAAGTTGCAGTGGAGCAAACT-AAGCAAA
* * * * *
17035212 GCAAGTCTTATC-CCCTTGAAATTGCTGTGGGACAGACTAAA-CATATTAATCCTATCT-CCTCG
1 GCAAATCTTATCTCCC-TGAAATTGCAGCGGAACAGACTAAAGCAGA-TAATCCTATCTCCCT-G
*
17035274 ATGTTACAGTG
63 AAGTTACAGTG
17035285 GAGTGGATCG
Statistics
Matches: 210, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
173 101 0.48
174 26 0.12
175 80 0.38
176 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (173 bp):
GCAAATCTTATCTCCCTGAAATTGCAGCGGAACAGACTAAAGCAGATAATCCTATCTCCCTGAAG
TTACAGTGAAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGATGCAGAGAGTAGATCACATC
GAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGCAAA
Found at i:17039157 original size:5 final size:6
Alignment explanation
Indices: 17039141--17039166 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17039131 TGGATAATAC
17039141 ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT
17039167 GTTAAATATT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:17045005 original size:20 final size:20
Alignment explanation
Indices: 17044980--17045071 Score: 68
Period size: 20 Copynumber: 4.6 Consensus size: 20
17044970 ATTTTTTATC
17044980 ATTTTAATAAATATTATATA
1 ATTTTAATAAATATTATATA
17045000 ATTTT-AT-AATATTCTATATA
1 ATTTTAATAAATA-T-TATATA
**
17045020 ATTTCCA-AAATATTATA-A
1 ATTTTAATAAATATTATATA
*
17045038 TATTTTCATAACATATTA-ATA
1 -ATTTTAATAA-ATATTATATA
*
17045059 ATGTATAATAAAT
1 AT-TTTAATAAAT
17045072 TTTCTAAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
18 5 0.08
19 13 0.22
20 23 0.39
21 18 0.31
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (20 bp):
ATTTTAATAAATATTATATA
Found at i:17046254 original size:3 final size:3
Alignment explanation
Indices: 17046246--17046283 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
17046236 TCCTCACGCT
*
17046246 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCT TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
17046284 TTCATGGTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:17053133 original size:41 final size:41
Alignment explanation
Indices: 17053088--17053171 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
17053078 CAGAAAGCGC
*
17053088 CGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCATT
1 CGCAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCATT
17053129 CGCAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCATT
1 CGCAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCATT
17053170 CG
1 CG
17053172 GGGATTTAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.19
Consensus pattern (41 bp):
CGCAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCATT
Found at i:17053227 original size:86 final size:81
Alignment explanation
Indices: 17053132--17053357 Score: 290
Period size: 72 Copynumber: 2.8 Consensus size: 81
17053122 GAGCATTCGC
* *
17053132 AAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCATTCGGGGATTTAGCGGCATTTTTGAGGAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCATTCGGGGATTTAGCGGCGTTTTTGAGGAA
17053197 GCGCCGCCAAAAACGCCGCAA
66 GCG--G---AAAACGCCGCAA
*
17053218 AAAAAACCTAAGCTCAACGACGCCGTTTTCTGAGCATTC-GGGATTTAGCGGCGTTTTT---G-A
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCATTCGGGGATTTAGCGGCGTTTTTGAGGAA
*
17053278 ---GAAAGCGCCGC-A
66 GCGGAAAACGCCGCAA
* *
17053290 AAAAAACCTAAGCCCAATGACGTCGTTTTCTGAGCATTCGGGGATTTAGCGGCGTTTTTGAGGAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCATTCGGGGATTTAGCGGCGTTTTTGAGGAA
17053355 GCG
66 GCG
17053358 TCGCTAATGC
Statistics
Matches: 125, Mismatches: 7, Indels: 22
0.81 0.05 0.14
Matches are distributed among these distances:
72 37 0.30
73 28 0.22
76 2 0.02
77 1 0.01
81 1 0.01
82 1 0.01
85 18 0.14
86 37 0.30
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (81 bp):
AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCATTCGGGGATTTAGCGGCGTTTTTGAGGAA
GCGGAAAACGCCGCAA
Found at i:17053284 original size:85 final size:86
Alignment explanation
Indices: 17053132--17053294 Score: 274
Period size: 86 Copynumber: 1.9 Consensus size: 86
17053122 GAGCATTCGC
*
17053132 AAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCATTCGGGGATTTAGCGGCATTTTTGAGGAA
1 AAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCATTCGGGGATTTAGCGGCATTTTTGAGAAA
*
17053197 GCGCCGCCAAAAACGCCGCAA
66 GCGCCGCAAAAAACGCCGCAA
* * *
17053218 AAAAAACCTAAGCTCAACGACGCCGTTTTCTGAGCATTC-GGGATTTAGCGGCGTTTTTGAGAAA
1 AAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCATTCGGGGATTTAGCGGCATTTTTGAGAAA
17053282 GCGCCGCAAAAAA
66 GCGCCGCAAAAAA
17053295 ACCTAAGCCC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
85 35 0.49
86 37 0.51
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (86 bp):
AAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCATTCGGGGATTTAGCGGCATTTTTGAGAAA
GCGCCGCAAAAAACGCCGCAA
Found at i:17053514 original size:73 final size:73
Alignment explanation
Indices: 17053386--17053617 Score: 286
Period size: 73 Copynumber: 3.2 Consensus size: 73
17053376 TTAGTGGCGT
** * * *
17053386 TTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAATGACGCCGTTTTCTAAGCATTCGGGGATTT
1 TTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACAACACCGTTTTCTGACCATTCGGGGATTT
17053450 AGCGGCAA
66 AGCGGCAA
*
17053458 TTTTGAGAAAGTGCCGCAAAAAAACCTAAGCCCAACAACACCGTTTTCTGACCATTCGGGGATTT
1 TTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACAACACCGTTTTCTGACCATTCGGGGATTT
***
17053523 AGCGGTGT
66 AGCGGCAA
* * * ** *
17053531 TTTTGAGAAAGCACCGCAAGAAAACCTAAGCCCAACAACACTGTTTTCTGATCTTTTTGGGGATT
1 TTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACAACACCGTTTTCTGA-CCATTCGGGGATT
**
17053596 TAGCGGCGT
65 TAGCGGCAA
*
17053605 TTTTAAGAAAGCG
1 TTTTGAGAAAGCG
17053618 TCGCTAATGC
Statistics
Matches: 139, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
72 16 0.12
73 94 0.68
74 29 0.21
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (73 bp):
TTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACAACACCGTTTTCTGACCATTCGGGGATTT
AGCGGCAA
Found at i:17053662 original size:260 final size:260
Alignment explanation
Indices: 17053211--17053713 Score: 742
Period size: 260 Copynumber: 1.9 Consensus size: 260
17053201 CGCCAAAAAC
* * * *
17053211 GCCGCAAAAAAAACCTAAGCTCAACGACGCCGTTTTCTGAGCATTCGGGATTTAGCGGCGTTTTT
1 GCCGCAAAAAAAACCTAAGCCCAACAACACCGTTTTCTGACCATTCGGGATTTAGCGGCGTTTTT
* ** *
17053276 GAGAAAGCGCCGCAAAAAAACCTAAGCCCAATGACGTCGTTTTCTGAGCATTCGGGGATTTAGCG
66 GAGAAAGCACCGCAAAAAAACCTAAGCCCAACAACCTCGTTTTCTGAGCATTCGGGGATTTAGCG
* * * *
17053341 GCGTTTTTGAGGAAGCGTCGCTAATGCACAGGGCTTTAGTGGCGTTTTTGAGAAAGCGCCGC-AA
131 GCGTTTTTAAGAAAGCGTCGCTAATGCACAGGGCTTTAGCGGCGTTTTTGACAAAGCGCCGCAAA
* *
17053405 AAAACCTAAGCCCAATGACGCCGTTTTCTAAGCATTCGGGGATTTAGCGGCAATTTTGAGAAAGT
196 AAAACCTAAGCCCAACGACGCCGTTTTCTAACCATTCGGGGATTTAGCGGCAATTTTGAGAAAGT
*
17053470 GCCGC-AAAAAAACCTAAGCCCAACAACACCGTTTTCTGACCATTCGGGGATTTAGCGGTGTTTT
1 GCCGCAAAAAAAACCTAAGCCCAACAACACCGTTTTCTGACCATTC-GGGATTTAGCGGCGTTTT
* * * *
17053534 TGAGAAAGCACCGCAAGAAAACCTAAGCCCAACAACACT-GTTTTCTGATCTTTTTGGGGATTTA
65 TGAGAAAGCACCGCAAAAAAACCTAAGCCCAACAAC-CTCGTTTTCTGAGC-ATTCGGGGATTTA
* *
17053598 GCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGACAATGCGCCGC
128 GCGGCGTTTTTAAGAAAGCGTCGCTAATGCACAGGGCTTTAGCGGCGTTTTTGACAAAGCGCCGC
* * *
17053663 AAAAAAACCTAAGCCCAACGACGTCGTTTTCTGACCTTTCGGGGATTTAGC
193 AAAAAAACCTAAGCCCAACGACGCCGTTTTCTAACCATTCGGGGATTTAGC
17053714 AGCGTTTTTA
Statistics
Matches: 216, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
258 36 0.17
259 64 0.30
260 71 0.33
261 45 0.21
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (260 bp):
GCCGCAAAAAAAACCTAAGCCCAACAACACCGTTTTCTGACCATTCGGGATTTAGCGGCGTTTTT
GAGAAAGCACCGCAAAAAAACCTAAGCCCAACAACCTCGTTTTCTGAGCATTCGGGGATTTAGCG
GCGTTTTTAAGAAAGCGTCGCTAATGCACAGGGCTTTAGCGGCGTTTTTGACAAAGCGCCGCAAA
AAAACCTAAGCCCAACGACGCCGTTTTCTAACCATTCGGGGATTTAGCGGCAATTTTGAGAAAGT
Found at i:17053751 original size:114 final size:113
Alignment explanation
Indices: 17053520--17053857 Score: 453
Period size: 114 Copynumber: 2.9 Consensus size: 113
17053510 CATTCGGGGA
* * * * * *
17053520 TTTAGCGGTGTTTTTGAGAAAGCACCGCAAGAAAACCTAAGCCCAACAAC-ACTGTTTTCTGATC
1 TTTAGCGGCGTTTTTGA-CAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTC-GTTTTCTGA-C
* * *
17053584 TTTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCAGGGC
63 CTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
17053635 TTTAGCGGCGTTTTTGACAATGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGACCT
1 TTTAGCGGCGTTTTTGACAA-GCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGACCT
*
17053700 TTCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
** * * *
17053749 TTTAGCGGCGTTTTTGGTAGAGCGCCGCTAAAAGACATAAGCCCAACGACGTCGTTTTCTGACCT
1 TTTAGCGGCGTTTTTGACA-AGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGACCT
* * *
17053814 TTCGGAGGATTTAGCGGCGTTTTTAATACAGCGCCACTAATGCT
65 TTCGG-GGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCT
17053858 TTGGGATCCC
Statistics
Matches: 200, Mismatches: 19, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
114 113 0.56
115 86 0.43
116 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (113 bp):
TTTAGCGGCGTTTTTGACAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGACCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:17055089 original size:52 final size:52
Alignment explanation
Indices: 17055004--17055108 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
17054994 GCAAAACGAC
*
17055004 TATACTTTAGTGGCGCTTCAGCAAAAATTGCCACAAATAGGTTTTAATAGTT
1 TATACTTTAGTGGCGCTTCAGCAAAAATCGCCACAAATAGGTTTTAATAGTT
*
17055056 TATACTTTAGTGGCGCTTCAGCAGAAATCGCCACAAATAGGTTTTAATAGTT
1 TATACTTTAGTGGCGCTTCAGCAAAAATCGCCACAAATAGGTTTTAATAGTT
17055108 T
1 T
17055109 CCGAAATGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (52 bp):
TATACTTTAGTGGCGCTTCAGCAAAAATCGCCACAAATAGGTTTTAATAGTT
Found at i:17060508 original size:87 final size:87
Alignment explanation
Indices: 17060354--17060519 Score: 226
Period size: 87 Copynumber: 1.9 Consensus size: 87
17060344 AGGTTCAAAG
* * * * *
17060354 GAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAACGAGGGAAGCAAAGGCTATAG
1 GAAATATGAAGAACTCCAGCTACAACGTAAACCAGAGGCGGCAACGAGAGAAGCAAACGCTACAG
17060419 CG-AGAGAAGCAGAGTTTAAAAA
66 CGAAG-GAAGCAGAGTTTAAAAA
* * * * *
17060441 GAAATATGAAGAACTCCAGCTACAACGTAAACCAGATGTGGCATCGAGAGAAGCAGACGCTGCAG
1 GAAATATGAAGAACTCCAGCTACAACGTAAACCAGAGGCGGCAACGAGAGAAGCAAACGCTACAG
17060506 CGAAGGAAGCAGAG
66 CGAAGGAAGCAGAG
17060520 CAGAGCAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
87 66 0.97
88 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (87 bp):
GAAATATGAAGAACTCCAGCTACAACGTAAACCAGAGGCGGCAACGAGAGAAGCAAACGCTACAG
CGAAGGAAGCAGAGTTTAAAAA
Found at i:17060981 original size:42 final size:42
Alignment explanation
Indices: 17060935--17061165 Score: 144
Period size: 42 Copynumber: 5.5 Consensus size: 42
17060925 AAAGTGTCGT
* *** *
17060935 TAAAGAACATGTTCTTTAGCGGCGCATATTCACAAACGCCAC
1 TAAAGATCATGTTCTTTAGCGGCGCATAGAAAAAAACGCCAC
* * * *
17060977 TAAAGATCATGTCCTTTAGCGGCACTTAGAAAAAAACGCCGC
1 TAAAGATCATGTTCTTTAGCGGCGCATAGAAAAAAACGCCAC
* * **** **** **
17061019 TAAAGATCTTGTTCTTTAGCGGCG-TTCTTTAGCGGCGTTTAGGC
1 TAAAGATCATGTTCTTTAGCGGCGCATAGAAAAAAACG-CCA--C
* * *
17061063 TAAAGATCATGTTCTTTAGCGGCGCTTATG--AAAAATGCCGC
1 TAAAGATCATGTTCTTTAGCGGCGCATA-GAAAAAAACGCCAC
* * * * *
17061104 TAAAGATCATGTCCTTTAGTGGCGCTTAGAAAAAAATGCCGC
1 TAAAGATCATGTTCTTTAGCGGCGCATAGAAAAAAACGCCAC
17061146 TAAAGATCATGTTCTTTAGC
1 TAAAGATCATGTTCTTTAGC
17061166 AGCGTTCTTT
Statistics
Matches: 144, Mismatches: 38, Indels: 14
0.73 0.19 0.07
Matches are distributed among these distances:
40 1 0.01
41 32 0.22
42 83 0.58
44 26 0.18
45 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (42 bp):
TAAAGATCATGTTCTTTAGCGGCGCATAGAAAAAAACGCCAC
Found at i:17061047 original size:13 final size:13
Alignment explanation
Indices: 17061029--17061057 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17061019 TAAAGATCTT
17061029 GTTCTTTAGCGGC
1 GTTCTTTAGCGGC
17061042 GTTCTTTAGCGGC
1 GTTCTTTAGCGGC
17061055 GTT
1 GTT
17061058 TAGGCTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.21, G:0.31, T:0.41
Consensus pattern (13 bp):
GTTCTTTAGCGGC
Found at i:17061116 original size:127 final size:128
Alignment explanation
Indices: 17060935--17061179 Score: 384
Period size: 127 Copynumber: 1.9 Consensus size: 128
17060925 AAAGTGTCGT
*
17060935 TAAAGAACATGTTCTTTAGCGGCGCATATTCACAAACGCCACTAAAGATCATGTCCTTTAGCGGC
1 TAAAGAACATGTTCTTTAGCGGCGCATATTCAAAAACGCCACTAAAGATCATGTCCTTTAGCGGC
* *
17061000 ACTTAGAAAAAAACGCCGCTAAAGATCTTGTTCTTTAGCGGCGTTCTTTAGCGGCGTTTAGGC
66 ACTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGTTCTTTAGCGGCGTTTAGGC
* * * * * *
17061063 TAAAGATCATGTTCTTTAGCGGCGCTTA-TGAAAAATGCCGCTAAAGATCATGTCCTTTAGTGGC
1 TAAAGAACATGTTCTTTAGCGGCGCATATTCAAAAACGCCACTAAAGATCATGTCCTTTAGCGGC
* *
17061127 GCTTAGAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCAGCGTTCTTTAGCG
66 ACTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGTTCTTTAGCG
17061180 ACGCTTATGA
Statistics
Matches: 106, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
127 80 0.75
128 26 0.25
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (128 bp):
TAAAGAACATGTTCTTTAGCGGCGCATATTCAAAAACGCCACTAAAGATCATGTCCTTTAGCGGC
ACTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGTTCTTTAGCGGCGTTTAGGC
Found at i:17061204 original size:55 final size:55
Alignment explanation
Indices: 17061117--17061220 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
17061107 AGATCATGTC
* * * *
17061117 CTTTAGTGGCGCTTAGAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCAGCGTT
1 CTTTAGCGACGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCAGCGTT
*
17061172 CTTTAGCGACGCTTATG-AAAAAACGCCACTAAAGATCATGTTTTTTAGC
1 CTTTAGCGACGCTTA-GAAAAAAACGCCACTAAAGATCATGTTCTTTAGC
17061221 GGCGCTTAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
55 42 0.98
56 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (55 bp):
CTTTAGCGACGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCAGCGTT
Found at i:17061235 original size:42 final size:42
Alignment explanation
Indices: 17061171--17061266 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
17061161 TTAGCAGCGT
* * *
17061171 TCTTTAGCGACGCTTATGAAAAAACGCCACTAAAGATCATGT
1 TCTTTAGCGGCGCTTATGAAAAAACGCCACTAAAGAACATGA
* *
17061213 TTTTTAGCGGCGCTTA-GAAAAAAACGCCGCTAAAGAACATGA
1 TCTTTAGCGGCGCTTATG-AAAAAACGCCACTAAAGAACATGA
17061255 TCTTTAGCGGCG
1 TCTTTAGCGGCG
17061267 TTTTTGTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (42 bp):
TCTTTAGCGGCGCTTATGAAAAAACGCCACTAAAGAACATGA
Found at i:17061242 original size:97 final size:96
Alignment explanation
Indices: 17061073--17061268 Score: 293
Period size: 97 Copynumber: 2.0 Consensus size: 96
17061063 TAAAGATCAT
* * * *
17061073 GTTCTTTAGCGGCGCTTATGAAAAATGCCGCTAAAGATCATGTCCTTTAGTGGCGCTTAGAAAAA
1 GTTCTTTAGCGACGCTTATGAAAAACGCCACTAAAGATCATGTCCTTTAGCGGCGCTTAGAAAAA
* * *
17061138 AATGCCGCTAAAGATCATGTTCTTTAGCAGC
66 AACGCCGCTAAAGAACATGATCTTTAGCAGC
**
17061169 GTTCTTTAGCGACGCTTATGAAAAAACGCCACTAAAGATCATGTTTTTTAGCGGCGCTTAGAAAA
1 GTTCTTTAGCGACGCTTATG-AAAAACGCCACTAAAGATCATGTCCTTTAGCGGCGCTTAGAAAA
*
17061234 AAACGCCGCTAAAGAACATGATCTTTAGCGGC
65 AAACGCCGCTAAAGAACATGATCTTTAGCAGC
17061266 GTT
1 GTT
17061269 TTTGTTTGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
96 19 0.21
97 70 0.79
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (96 bp):
GTTCTTTAGCGACGCTTATGAAAAACGCCACTAAAGATCATGTCCTTTAGCGGCGCTTAGAAAAA
AACGCCGCTAAAGAACATGATCTTTAGCAGC
Found at i:17061512 original size:43 final size:43
Alignment explanation
Indices: 17061447--17061691 Score: 307
Period size: 43 Copynumber: 5.7 Consensus size: 43
17061437 ACACAAATGT
* * *
17061447 CGCTAAAAGAACATGA-CATTTAGTGGCGTTTGCGGAAGAAGCGC
1 CGCT-AAAGAACATGATC-TTTAGCGGCGTTTGTGGAAAAAGCGC
17061491 CGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGAAAAAGCGC
1 CGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGAAAAAGCGC
* *
17061534 CGCTAAGGAACATGATCTTTAGCGGCGTTTGTGGAAAAAGCAC
1 CGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGAAAAAGCGC
* * *
17061577 CGCTAAAGAACATGATCTTTAGCGGCGTTTGTTGAGAAAGAGC
1 CGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGAAAAAGCGC
* * *
17061620 CGCTAAAGAACATGACCTTTAGCGGCTTTTTTAGG-AAAA-CGC
1 CGCTAAAGAACATGATCTTTAGCGGCGTTTGT-GGAAAAAGCGC
* * * *
17061662 CGCTAAACACCCTGACCTTTAGCGGCGTTT
1 CGCTAAAGAACATGATCTTTAGCGGCGTTT
17061692 ATTTATAAAC
Statistics
Matches: 179, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 28 0.16
43 145 0.81
44 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (43 bp):
CGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGAAAAAGCGC
Found at i:17062833 original size:19 final size:19
Alignment explanation
Indices: 17062793--17062834 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
17062783 ATTACAAAAT
* *
17062793 AATTCAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
17062812 AATTAAAAAT-ATTTATAGA
1 AATTAAAAATAATTTATA-A
17062831 AATT
1 AATT
17062835 TCAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:17069890 original size:53 final size:53
Alignment explanation
Indices: 17069819--17069920 Score: 186
Period size: 53 Copynumber: 1.9 Consensus size: 53
17069809 GAAATTTAAA
*
17069819 ACCAACTTAGTATATGAATACAGAGTGTCATTGAGTTAGTATTAAAATTCTAG
1 ACCAACTTAGTATATGAATACAGAGTGTCATGGAGTTAGTATTAAAATTCTAG
*
17069872 ACCAACTTAGTATATGAATACGGAGTGTCATGGAGTTAGTATTAAAATT
1 ACCAACTTAGTATATGAATACAGAGTGTCATGGAGTTAGTATTAAAATT
17069921 TTGTTAGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (53 bp):
ACCAACTTAGTATATGAATACAGAGTGTCATGGAGTTAGTATTAAAATTCTAG
Found at i:17079029 original size:14 final size:16
Alignment explanation
Indices: 17079011--17079053 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
17079001 AAGTCAAGCT
17079011 TAATATTATTATATTAA
1 TAATA-TATTATATTAA
*
17079028 TAATATATTATATATAT
1 TAATATATTATAT-TAA
17079045 TAATA-ATTA
1 TAATATATTA
17079054 ACGTTTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATATTATATTAA
Found at i:17079036 original size:11 final size:11
Alignment explanation
Indices: 17079020--17079051 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
17079010 TTAATATTAT
17079020 TATATTAATAA
1 TATATTAATAA
17079031 TATATT-AT-A
1 TATATTAATAA
17079040 TATATTAATAA
1 TATATTAATAA
17079051 T
1 T
17079052 TAACGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 7 0.37
10 4 0.21
11 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATATTAATAA
Found at i:17079045 original size:20 final size:19
Alignment explanation
Indices: 17079013--17079051 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
17079003 GTCAAGCTTA
17079013 ATATTATTATATTAATAAT
1 ATATTATTATATTAATAAT
17079032 ATATTATATATATTAATAAT
1 ATATTAT-TATATTAATAAT
17079052 TAACGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTATTATATTAATAAT
Found at i:17092446 original size:24 final size:24
Alignment explanation
Indices: 17092395--17092454 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
17092385 TCACAAAGTT
* ** **
17092395 CACTATCACTATCATCATAGTTTG
1 CACTATTACTATCATCATAACTCC
17092419 CACTATTACTATCATCATAACTCC
1 CACTATTACTATCATCATAACTCC
17092443 CACTATTACTAT
1 CACTATTACTAT
17092455 AAACTTCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (24 bp):
CACTATTACTATCATCATAACTCC
Found at i:17094160 original size:16 final size:16
Alignment explanation
Indices: 17094130--17094171 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
17094120 TTAGTTATTA
17094130 AATTAA-TTT-TAATT
1 AATTAATTTTCTAATT
17094144 AATTAATTTTCTAATT
1 AATTAATTTTCTAATT
*
17094160 AAATAATTTTCT
1 AATTAATTTTCT
17094172 CAACCCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 3 0.12
16 16 0.64
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTAATTTTCTAATT
Found at i:17100101 original size:15 final size:15
Alignment explanation
Indices: 17100081--17100119 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
17100071 ATCGTTAAAA
17100081 TTATTATCATTGTAT
1 TTATTATCATTGTAT
17100096 TTATTA-CTATTGTAT
1 TTATTATC-ATTGTAT
*
17100111 TTGTTATCA
1 TTATTATCA
17100120 CAATATTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (15 bp):
TTATTATCATTGTAT
Found at i:17103862 original size:24 final size:24
Alignment explanation
Indices: 17103833--17103878 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17103823 TAGAACAGTC
* *
17103833 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
17103857 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
17103879 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:17112178 original size:44 final size:45
Alignment explanation
Indices: 17112115--17112235 Score: 158
Period size: 45 Copynumber: 2.7 Consensus size: 45
17112105 GATCGCATCT
17112115 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT-AGCA
* * *
17112159 AGTCTTATC-CTCCTAAAGTTGCAGTGGGGCAGACTAAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCA
**
17112204 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
17112236 GTTAAAGCCG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
43 1 0.02
44 31 0.47
45 32 0.48
46 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCA
Found at i:17112340 original size:44 final size:42
Alignment explanation
Indices: 17112277--17112788 Score: 237
Period size: 44 Copynumber: 11.8 Consensus size: 42
17112267 TATCGCATTT
17112277 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* *
17112321 AGTCTTATTCTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA
1 AGTCTTA-TCTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * *
17112366 AATCTTATCTCCCTGAAGTTGCAGTGAAGCA-AATTA-AAGCCGA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * * * *
17112409 TAATCCTATCTCCCTGAAGTTGTAGTGGATCGGATTAA-AACCTT
1 -AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * * * * ***
17112453 GGATCTTATCTCTCTG-AGTTGTAG-AGAGCAGAC--CGCATTT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
17112493 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
1 AGTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACT-AAGAAGCA
*
17112537 AGTCTTATTCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTA-TCTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * *
17112582 AATCTTATCTTCTTGAAGTTGCAGTGTAGCAGA-TTA-AAGCCGA
1 AGTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * *
17112625 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AATCCT
1 -AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAA-GCA
* ** * * * * *
17112669 TGATCTTATCTCTCTGAAGTTGCAG-AAAGCATA-T-CGCATCT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
17112710 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
1 AGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
17112754 AGTCTTATCCTCCTGAAGTTGCAGTGCGA-CAGACT
1 AGTCTTAT-CTCCTGAAGTTGCAGTG-GAGCAGACT
17112789 GAATGAACAA
Statistics
Matches: 357, Mismatches: 71, Indels: 80
0.70 0.14 0.16
Matches are distributed among these distances:
39 11 0.03
40 31 0.09
41 19 0.05
42 12 0.03
43 24 0.07
44 181 0.51
45 77 0.22
46 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (42 bp):
AGTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:17112375 original size:162 final size:162
Alignment explanation
Indices: 17112106--17112429 Score: 549
Period size: 162 Copynumber: 2.0 Consensus size: 162
17112096 CAGAGAGCAG
17112106 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTC
1 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTC
* * *
17112171 CTAAAGTTGCAGTGGGGCAGACTAAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAG
66 CTAAAGTTGCAGTGAGGCAGACTAAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAA
*
17112236 GTTAAAGCCGATAATCCTATCTCCCTAAAGTT
131 ATTAAAGCCGATAATCCTATCTCCCTAAAGTT
* *
17112268 ATCGCATTTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATTCTC
1 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTC
* * * *
17112333 CTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAA
66 CTAAAGTTGCAGTGAGGCAGACTAAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAA
*
17112398 ATTAAAGCCGATAATCCTATCTCCCTGAAGTT
131 ATTAAAGCCGATAATCCTATCTCCCTAAAGTT
17112430 GTAGTGGATC
Statistics
Matches: 151, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 151 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (162 bp):
ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTC
CTAAAGTTGCAGTGAGGCAGACTAAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAA
ATTAAAGCCGATAATCCTATCTCCCTAAAGTT
Found at i:17112525 original size:216 final size:217
Alignment explanation
Indices: 17112270--17112791 Score: 843
Period size: 216 Copynumber: 2.4 Consensus size: 217
17112260 CTAAAGTTAT
*
17112270 CGCATTTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATTCTCCT
1 CGCATTTAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATTCTCCT
*
17112335 GAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAAAT
66 GAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAAAT
* *
17112400 TAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGATCGGATTAAAA-CCTTGGATCTTATCT
131 TAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCCTT-GATCTTATCT
* *
17112464 CTCTG-AGTTGTAGAGAGCAGAC
195 CTCTGAAGTTGCAGAAAGCAGAC
*
17112486 CGCATTTAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGTCTTATTCTCCT
1 CGCATTTAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATTCTCCT
* * * *
17112551 GAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCTTGAAGTTGCAGTGTAGCAGAT
66 GAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAAAT
17112616 TAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCCTTGATCTTATCTC
131 TAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCCTTGATCTTATCTC
* *
17112681 TCTGAAGTTGCAGAAAGCATAT
196 TCTGAAGTTGCAGAAAGCAGAC
* * *
17112703 CGCATCTAGTCTTATC-TCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTCC
1 CGCATTTAGTCTTATCTTCC-TGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATTCTCC
* *
17112767 TGAAGTTGCAGTGCGACAGACTGAA
65 TGAAGTTGCAGTGAGGCAGACTGAA
17112792 TGAACAAATC
Statistics
Matches: 284, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
216 188 0.66
217 96 0.34
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (217 bp):
CGCATTTAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATTCTCCT
GAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAAAT
TAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCCTTGATCTTATCTC
TCTGAAGTTGCAGAAAGCAGAC
Found at i:17112773 original size:172 final size:173
Alignment explanation
Indices: 17112537--17112865 Score: 386
Period size: 172 Copynumber: 1.9 Consensus size: 173
17112527 TAAATAAGCA
** * *
17112537 AGTCTTATTCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCTTGAAGTT
1 AGTCTTATTCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATAACAAATCTTATCCTCCTGAAGTT
* * * *
17112602 GCAGTGTAG-CAGA-TTAAAG-CCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
66 GCAGTG-AGACAGACTGAAAGAAC-A-AATCCTATCTCCCTAAAGTTACAGTGGAGCGGATTAAA
*
17112664 ATCCTTGA-TCTTATCTCTCTGAAGTTGCAGAAAGCATATCGCATCT
128 AT-CATGAGTCTTATCTCTCTGAAGTTGCAGAAAGCATATCGCATCT
*
17112710 AGTCTTA-TCTCCTTGAAGTTGCAGTG-GAGCAGACT-AAG-TAAACAAGTCTTATCCTCCTGAA
1 AGTCTTATTCTCC-TGAAGTTGCAGTGAG-GCAGACTGAAGAT-AACAAATCTTATCCTCCTGAA
* * * * * *
17112771 GTTGCAGTGCGACAGACTGAATGAACAAATCCTGTCTCCCTAAAGTTATAGTGGAGTGGATTAGA
63 GTTGCAGTGAGACAGACTGAAAGAACAAATCCTATCTCCCTAAAGTTACAGTGGAGCGGATTAAA
*
17112836 ATGATGAGTCTTATCTCTCTGAAGTTGCAG
128 ATCATGAGTCTTATCTCTCTGAAGTTGCAG
17112866 CAGAGTAGAT
Statistics
Matches: 132, Mismatches: 17, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
171 5 0.04
172 94 0.71
173 32 0.24
174 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (173 bp):
AGTCTTATTCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATAACAAATCTTATCCTCCTGAAGTT
GCAGTGAGACAGACTGAAAGAACAAATCCTATCTCCCTAAAGTTACAGTGGAGCGGATTAAAATC
ATGAGTCTTATCTCTCTGAAGTTGCAGAAAGCATATCGCATCT
Found at i:17114753 original size:15 final size:15
Alignment explanation
Indices: 17114733--17114771 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
17114723 ATCGTTAAAA
17114733 TTATTATCATTGTAT
1 TTATTATCATTGTAT
17114748 TTATTA-CTATTGTAT
1 TTATTATC-ATTGTAT
*
17114763 TTGTTATCA
1 TTATTATCA
17114772 CAATATTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (15 bp):
TTATTATCATTGTAT
Found at i:17116447 original size:17 final size:17
Alignment explanation
Indices: 17116427--17116468 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
17116417 AAAAAACTTT
17116427 AAAAATATAA-AAAATG
1 AAAAATATAATAAAATG
17116443 CAAAAA-ATAATAAAATG
1 -AAAAATATAATAAAATG
*
17116460 ATAAATATA
1 AAAAATATA
17116469 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAATATAATAAAATG
Found at i:17116681 original size:85 final size:86
Alignment explanation
Indices: 17116571--17116741 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 86
17116561 AAATTATAAA
17116571 AATCATATTATTAAATATTTTATAAATTGTTGTAACTTAATAGAGTGTACCTTCTCTAATCACAT
1 AATCATATTATTAAATATTTTATAAATTGTTGTAACTTAATAGAGTGTACCTTCTCTAATCACAT
17116636 GTAAAATATTAAAAAATTGAT
66 GTAAAATATTAAAAAATTGAT
17116657 AATCATATTA-TAAATATTTTATAAATTGTTGTAACTTAATAGAGTGTACCTTCTCTAATCACAT
1 AATCATATTATTAAATATTTTATAAATTGTTGTAACTTAATAGAGTGTACCTTCTCTAATCACAT
17116721 GTAAAATATTAAAAAATTGAT
66 GTAAAATATTAAAAAATTGAT
17116742 TTAAAACTTG
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 75 0.88
86 10 0.12
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.40
Consensus pattern (86 bp):
AATCATATTATTAAATATTTTATAAATTGTTGTAACTTAATAGAGTGTACCTTCTCTAATCACAT
GTAAAATATTAAAAAATTGAT
Found at i:17124043 original size:150 final size:151
Alignment explanation
Indices: 17123850--17124208 Score: 512
Period size: 152 Copynumber: 2.4 Consensus size: 151
17123840 AATTTAGTGT
* * *
17123850 GTATTTTTATTGAAAGTAAGAAAA-TTGGAAAAAAAATACGAACAAATGGCCGAAATAAGG-ATT
1 GTATTTTT-TTAAAAGTAATAAAATTTGGAAAAAAAATACGAACAAAGGGCCGAAATAAGGTATT
17123913 TTTTT-AATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATG
65 TTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATG
17123977 CAAAATAAAAAAATTAAAAAATA
130 CAAAATAAAAAAATT-AAAAATA
* * *
17124000 GTATTTTTTTAAAAGTAATAAAATTTGAGGAAAAAAA-ACGAACATAGGGCCGAAATAAGGTTTT
1 GTATTTTTTTAAAAGTAATAAAATTTG-GAAAAAAAATACGAACAAAGGGCCGAAATAAGGTATT
*
17124064 TTTTTAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAATATAATGTACTAAAATAATG
65 TTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATG
* **
17124129 TAAAATTTAAAAATTAAAAATA
130 CAAAATAAAAAAATTAAAAATA
* ** *
17124151 ATATATTTTTTAAAAGTAATAAAA-TCCGAAAAAAAGATACGAACAAAGGGCCAAAATA
1 GTAT-TTTTTTAAAAGTAATAAAATTTGGAAAAAAA-ATACGAACAAAGGGCCGAAATA
17124209 CGAACAATTG
Statistics
Matches: 186, Mismatches: 16, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
149 13 0.07
150 39 0.21
151 27 0.15
152 107 0.58
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.30
Consensus pattern (151 bp):
GTATTTTTTTAAAAGTAATAAAATTTGGAAAAAAAATACGAACAAAGGGCCGAAATAAGGTATTT
TTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGC
AAAATAAAAAAATTAAAAATA
Found at i:17138755 original size:58 final size:58
Alignment explanation
Indices: 17138548--17138828 Score: 233
Period size: 59 Copynumber: 4.8 Consensus size: 58
17138538 CTCAATTGTG
* * * ** * * * *
17138548 TTATATTTCAAAATTTTCTTAAGTATAAAAAAGCTCACGGAGTAACATCCCCGGCTGTG
1 TTATCTTTCAAGATTTTCTTAAGTATAAAACAGCTCGTGGAGTAACAT-CTCAGCTATA
* * * * * * *
17138607 TTAT-TTGTCAAAATTTTCTTAAGTATAAAATAGCTCTTGGAGTAACATTCCCATCTGTG
1 TTATCTT-TCAAGATTTTCTTAAGTATAAAACAGCTCGTGGAGTAACA-TCTCAGCTATA
* * *
17138666 TTATCTTTCAAAATTTTCTTAAGTATAAAACAACTCGTAGAGTAACATCTCAGCTATA
1 TTATCTTTCAAGATTTTCTTAAGTATAAAACAGCTCGTGGAGTAACATCTCAGCTATA
* * * * * * *
17138724 TTATCTTTCGAGATTTTCTTAAGTATGAAACAGCTTGTGGATTCACAGCTTCAG-TTTA
1 TTATCTTTCAAGATTTTCTTAAGTATAAAACAGCTCGTGGAGTAACATC-TCAGCTATA
* * * *
17138782 TTATCTTTCAAGATTTTTCTTGAGTATAAAATAGCTCGCGGATTAAC
1 TTATCTTTCAAGA-TTTTCTTAAGTATAAAACAGCTCGTGGAGTAAC
17138829 GTTCCCAACT
Statistics
Matches: 187, Mismatches: 30, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
58 64 0.34
59 120 0.64
60 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (58 bp):
TTATCTTTCAAGATTTTCTTAAGTATAAAACAGCTCGTGGAGTAACATCTCAGCTATA
Found at i:17143431 original size:21 final size:21
Alignment explanation
Indices: 17143389--17143433 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17143379 TTTATTGCTT
* *
17143389 AAAATAATTAAAATTTAAATA
1 AAAATAAGTAAAATATAAATA
17143410 AAAATAAGTAAAA-ATAATATA
1 AAAATAAGTAAAATATAA-ATA
17143431 AAA
1 AAA
17143434 TGTAAATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATAAGTAAAATATAAATA
Found at i:17145298 original size:6 final size:6
Alignment explanation
Indices: 17145262--17145321 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
17145252 AGCAAAAGCA
* *
17145262 AAAACA AAAACA AAAAC- -AAACT -AAACT -AAACT AAAACT AAAACT
1 AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT
17145306 AAAACT AAAACT AAAA
1 AAAACT AAAACT AAAA
17145322 TCTATCAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.08
5 10 0.19
6 38 0.73
ACGTcount: A:0.72, C:0.17, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAACT
Found at i:17149116 original size:7 final size:7
Alignment explanation
Indices: 17149106--17149143 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
17149096 AGAAAAGTAA
17149106 AAAAAAG
1 AAAAAAG
17149113 AAAAAAG
1 AAAAAAG
17149120 AAAAAAG
1 AAAAAAG
17149127 AAAAAAG
1 AAAAAAG
*
17149134 AAAAGAG
1 AAAAAAG
17149141 AAA
1 AAA
17149144 CCATGGATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:17153239 original size:58 final size:58
Alignment explanation
Indices: 17153168--17153280 Score: 208
Period size: 58 Copynumber: 1.9 Consensus size: 58
17153158 TTAAAAATAG
* *
17153168 AAAATTTTTAAAATAAAGACAATACTCGTATTTAGGATTTTCAAGAAAATTGAGCTAA
1 AAAATTTTCAAAATAAAGACAATACTCGTATTTAGGATTTTCAAAAAAATTGAGCTAA
17153226 AAAATTTTCAAAATAAAGACAATACTCGTATTTAGGATTTTCAAAAAAATTGAGC
1 AAAATTTTCAAAATAAAGACAATACTCGTATTTAGGATTTTCAAAAAAATTGAGC
17153281 CCTAACGTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (58 bp):
AAAATTTTCAAAATAAAGACAATACTCGTATTTAGGATTTTCAAAAAAATTGAGCTAA
Found at i:17157023 original size:16 final size:16
Alignment explanation
Indices: 17157002--17157037 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
17156992 CAAATTTTTC
17157002 AAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
*
17157018 AAAAAAAAGAAGAAAG
1 AAAAAAAAGAAAAAAG
17157034 AAAA
1 AAAA
17157038 TGGAGAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:17158433 original size:88 final size:88
Alignment explanation
Indices: 17158284--17158818 Score: 793
Period size: 88 Copynumber: 6.1 Consensus size: 88
17158274 AGCGGATCAG
* * * * * *
17158284 TGAAGATAACAGATCTTGGCTTCCTGTACTGGCAGTGAAGCAGATCAAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCT
* *
17158349 CCCTGGGTTGTAGTGGAGTAGGT
66 CCCTGGGTCGTAGTGGAGCAGGT
* * * *
17158372 TGAAGATAGCAAATCTTGCCTTCCTGCATCAACAGTGAAGCAGATCGAAGATACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCT
*
17158437 CCCTGGGTTGTAGTGGAGCAGGT
66 CCCTGGGTCGTAGTGGAGCAGGT
* *
17158460 TGAAGATAGCAGATCTTGCCTTCCTATACCGACAGTGAAGCGGATCGAAGATACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCT
* *
17158525 CCCAGGGTCGTAGTGGAGTAGGT
66 CCCTGGGTCGTAGTGGAGCAGGT
*
17158548 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCGGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCT
*
17158613 TCCTGGGTCGTAGTGGAGCAGGT
66 CCCTGGGTCGTAGTGGAGCAGGT
* * * *
17158636 TGAAGATAGAAGATATTGCCTTCCTGTACCGACAGTGAAACAGATCGAAGATACTAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCT
*
17158701 CCCTGGGTCGTAGTGGAGCAAGT
66 CCCTGGGTCGTAGTGGAGCAGGT
**
17158724 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTATCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCT
* **
17158789 CCCT-GGTCAGCAGTGGAATAGGT
66 CCCTGGGTC-GTAGTGGAGCAGGT
17158812 TGAAGAT
1 TGAAGAT
17158819 TGAGAATTCT
Statistics
Matches: 403, Mismatches: 43, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
87 4 0.01
88 399 0.99
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCT
CCCTGGGTCGTAGTGGAGCAGGT
Found at i:17158838 original size:44 final size:44
Alignment explanation
Indices: 17158784--17159073 Score: 299
Period size: 44 Copynumber: 6.7 Consensus size: 44
17158774 ATACCAGCCT
*
17158784 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCC
* * *
17158828 TATCTCCCTGGGCAGTAGTGGAATAGATT--A-A---AGAATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCC
* * * * * * * *
17158866 TATCTCTCTGGACAACAGTGGAATAGGTTAAAGATCGTGATTCT
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCC
* *
17158910 TATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGAGAATTC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCC
* * * *
17158954 TATCTCCTTGGGCAGCAGTGGAATAGATTGAAGATTGTAG-GTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTG-AGAATCC
* * *
17158998 TATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTGTGAACCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCC
* *
17159042 TATCTCCCTGAG-CAACAGTGGAGTAGGTTGAA
1 TATCTCCCTG-GTCAGCAGTGGAATAGGTTGAA
17159074 AATAACAGAT
Statistics
Matches: 201, Mismatches: 36, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
38 30 0.15
40 1 0.00
41 2 0.01
42 1 0.00
43 1 0.00
44 163 0.81
45 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCC
Found at i:17158931 original size:126 final size:131
Alignment explanation
Indices: 17158781--17159073 Score: 400
Period size: 126 Copynumber: 2.3 Consensus size: 131
17158771 AAGATACCAG
* *
17158781 CCTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGTAG
1 CCTTATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAG
* *
17158846 TGGAATAGATT-AA-A-G-A-ATCCTATCTCTCTGGACAACAGTGGAATAGGTTAAAGATCGTGA
66 TGGAATAGATTGAAGATGTAGATCCTATCTCCCTGGACAACAGTGGAATAAGTTAAAGATCGTGA
*
17158906 T
131 A
* *
17158907 TCTTATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCTTGGGCAGCAG
1 CCTTATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAG
* * * * *
17158972 TGGAATAGATTGAAGATTGTAGGTCCTATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTGTG
66 TGGAATAGATTGAAGA-TGTAGATCCTATCTCCCTGGACAACAGTGGAATAAGTTAAAGATCGTG
17159037 AA
130 AA
* *
17159039 CCCTATCTCCCTGAG-CAACAGTGGAGTAGGTTGAA
1 CCTTATCTCCCTG-GTCAACAGTGGAATAGGTTGAA
17159074 AATAACAGAT
Statistics
Matches: 145, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
126 72 0.50
127 2 0.01
128 1 0.01
130 1 0.01
131 1 0.01
132 67 0.46
133 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (131 bp):
CCTTATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAG
TGGAATAGATTGAAGATGTAGATCCTATCTCCCTGGACAACAGTGGAATAAGTTAAAGATCGTGA
A
Found at i:17161230 original size:3 final size:3
Alignment explanation
Indices: 17161222--17161247 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17161212 TAAAGGATGT
17161222 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
17161248 TATTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17163394 original size:5 final size:5
Alignment explanation
Indices: 17163386--17163498 Score: 82
Period size: 5 Copynumber: 21.0 Consensus size: 5
17163376 TAGTAGATGA
* * *
17163386 GATAG GATAT GATAT GATAAGA GATAT GATGT GATAT GATAT GAGATAT
1 GATAT GATAT GATAT GAT-A-T GATAT GATAT GATAT GATAT --GATAT
* * * * *
17163435 GATAT GAAATGT GCTAC GACAT GATAT GAAAT CCGATAT GATAT GATAT
1 GATAT G--ATAT GATAT GATAT GATAT GATAT --GATAT GATAT GATAT
17163484 GATAT GATAT GATAT
1 GATAT GATAT GATAT
17163499 AAGATATGCT
Statistics
Matches: 85, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
5 67 0.79
6 2 0.02
7 16 0.19
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (5 bp):
GATAT
Found at i:17163411 original size:12 final size:11
Alignment explanation
Indices: 17163396--17163438 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
17163386 GATAGGATAT
17163396 GATATGATAAGA
1 GATATGAT-AGA
*
17163408 GATATGAT-GT
1 GATATGATAGA
17163418 GATATGATATGA
1 GATATGATA-GA
17163430 GATATGATA
1 GATATGATA
17163439 TGAAATGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.33
Consensus pattern (11 bp):
GATATGATAGA
Found at i:17163437 original size:17 final size:17
Alignment explanation
Indices: 17163417--17163506 Score: 76
Period size: 17 Copynumber: 5.4 Consensus size: 17
17163407 AGATATGATG
17163417 TGATATGATATGAGATA
1 TGATATGATATGAGATA
* * *
17163434 TGATATGAAATGTGCTA
1 TGATATGATATGAGATA
* * * *
17163451 CGACATGATATGAAATC
1 TGATATGATATGAGATA
*
17163468 CGATATGATAT--GATA
1 TGATATGATATGAGATA
*
17163483 TGATATGATATGATATA
1 TGATATGATATGAGATA
*
17163500 AGATATG
1 TGATATG
17163507 CTTCGATATA
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
15 12 0.22
17 43 0.78
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (17 bp):
TGATATGATATGAGATA
Found at i:17163504 original size:22 final size:22
Alignment explanation
Indices: 17163385--17163506 Score: 95
Period size: 22 Copynumber: 5.3 Consensus size: 22
17163375 GTAGTAGATG
*
17163385 AGATAGGATATGATATGATA-A
1 AGATATGATATGATATGATATA
* *
17163406 GAGATATGATGTGATATGATATG
1 -AGATATGATATGATATGATATA
* *
17163429 AGATATGATATGAAATG-TGCTA
1 AGATATGATATGATATGAT-ATA
* * *
17163451 CGACATGATATGAAATCCGATATGA
1 AGATATGATATGATAT--GATAT-A
17163476 TATGATATGATATGATATGATATA
1 -A-GATATGATATGATATGATATA
17163500 AGATATG
1 AGATATG
17163507 CTTCGATATA
Statistics
Matches: 79, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
21 1 0.01
22 54 0.68
23 1 0.01
24 3 0.04
25 7 0.09
27 13 0.16
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (22 bp):
AGATATGATATGATATGATATA
Found at i:17163536 original size:22 final size:22
Alignment explanation
Indices: 17163475--17163536 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
17163465 ATCCGATATG
* * *
17163475 ATATGATATGATATGATATGAT
1 ATATGATATGCTATGATATAAA
*
17163497 ATAAGATATGCT-TCGATATAAA
1 ATATGATATGCTAT-GATATAAA
*
17163519 ATCTGATATGCTATGATA
1 ATATGATATGCTATGATA
17163537 CATTTTGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.37
Consensus pattern (22 bp):
ATATGATATGCTATGATATAAA
Found at i:17164321 original size:8 final size:8
Alignment explanation
Indices: 17164308--17164334 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17164298 TGAACATACG
17164308 TGTATATT
1 TGTATATT
17164316 TGTATATT
1 TGTATATT
17164324 TGTATATT
1 TGTATATT
17164332 TGT
1 TGT
17164335 TTTGATGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (8 bp):
TGTATATT
Found at i:17165539 original size:17 final size:17
Alignment explanation
Indices: 17165517--17165549 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17165507 TTATATATTC
17165517 TAATTAA-ATTTTATAAA
1 TAATTAATA-TTTATAAA
17165534 TAATTAATATTTATAA
1 TAATTAATATTTATAA
17165550 TTTATATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTAATATTTATAAA
Found at i:17165654 original size:13 final size:13
Alignment explanation
Indices: 17165621--17165654 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17165611 TTCTCAAAAG
17165621 CACTTTTCCACAA
1 CACTTTTCCACAA
*
17165634 CACATTTCCACAA
1 CACTTTTCCACAA
*
17165647 TACTTTTC
1 CACTTTTC
17165655 AAAAGCACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (13 bp):
CACTTTTCCACAA
Found at i:17167522 original size:14 final size:14
Alignment explanation
Indices: 17167503--17167531 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17167493 TATATGAAGT
17167503 TAGTTTACTGAGAA
1 TAGTTTACTGAGAA
17167517 TAGTTTACTGAGAA
1 TAGTTTACTGAGAA
17167531 T
1 T
17167532 GGTATAGAAA
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:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (14 bp):
TAGTTTACTGAGAA
Found at i:17172442 original size:76 final size:76
Alignment explanation
Indices: 17172350--17172520 Score: 236
Period size: 76 Copynumber: 2.2 Consensus size: 76
17172340 ATGTAAAAAT
* * *
17172350 AGTAGACATGCTTAACATGTATTCAATTCAACAGTAGCAGTAGACATGCTTAACATGTAT-TGGG
1 AGTAGACATGTTTAACATGTATTCAATTCAACAATAACAGTAGACATGCTTAACAT-TATCTGGG
17172414 TTCAACAGTAAC
65 TTCAACAGTAAC
* * * *
17172426 AGTAGACATGTTTAACATGTATTCAGTTCAACAATAACAGTAGGCATGCTTAACATTTTCTTGGT
1 AGTAGACATGTTTAACATGTATTCAATTCAACAATAACAGTAGACATGCTTAACATTATCTGGGT
*
17172491 TCAAGAGTAAC
66 TCAACAGTAAC
* *
17172502 AGTAGGCATGTTGAACATG
1 AGTAGACATGTTTAACATG
17172521 CAATTGGTAA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 2 0.02
76 82 0.98
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (76 bp):
AGTAGACATGTTTAACATGTATTCAATTCAACAATAACAGTAGACATGCTTAACATTATCTGGGT
TCAACAGTAAC
Found at i:17172528 original size:38 final size:38
Alignment explanation
Indices: 17172350--17172520 Score: 204
Period size: 38 Copynumber: 4.5 Consensus size: 38
17172340 ATGTAAAAAT
** *
17172350 AGTAGACATGCTTAACATGTATTCAATTCAACAGTAGC
1 AGTAGACATGCTTAACATGTATTCGGTTCAACAGTAAC
*
17172388 AGTAGACATGCTTAACATGTATTGGGTTCAACAGTAAC
1 AGTAGACATGCTTAACATGTATTCGGTTCAACAGTAAC
* * *
17172426 AGTAGACATGTTTAACATGTATTCAGTTCAACAATAAC
1 AGTAGACATGCTTAACATGTATTCGGTTCAACAGTAAC
* *
17172464 AGTAGGCATGCTTAACAT-T-TTCTTGGTTCAAGAGTAAC
1 AGTAGACATGCTTAACATGTATTC--GGTTCAACAGTAAC
*
17172502 AGTAGGCATG-TTGAACATG
1 AGTAGACATGCTT-AACATG
17172521 CAATTGGTAA
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
36 3 0.03
37 3 0.03
38 110 0.95
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTCGGTTCAACAGTAAC
Found at i:17174710 original size:6 final size:6
Alignment explanation
Indices: 17174694--17174727 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
17174684 TTAATATAAA
17174694 AAAAAG AAAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAA
17174728 GAGAGAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:17174914 original size:2 final size:2
Alignment explanation
Indices: 17174903--17174939 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
17174893 TTCTTCTTCT
17174903 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
17174940 TAATTCTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:17177791 original size:18 final size:18
Alignment explanation
Indices: 17177750--17177787 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
17177740 GAGAACAAAG
*
17177750 AATAAATAAAAAATTATA
1 AATAAATAAGAAATTATA
17177768 AATAAATAAGAAA-TATA
1 AATAAATAAGAAATTATA
17177785 AAT
1 AAT
17177788 TAAAAAGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAAATAAGAAATTATA
Found at i:17178906 original size:99 final size:99
Alignment explanation
Indices: 17178800--17178999 Score: 391
Period size: 99 Copynumber: 2.0 Consensus size: 99
17178790 TTCTTTATTC
17178800 TTTTTGGATTCCAATTGCAATTGAAGTTATCGTTGCAAATGTTAAAGAAAATCCCACTTTCGCGC
1 TTTTTGGATTCCAATTGCAATTGAAGTTATCGTTGCAAATGTTAAAGAAAATCCCACTTTCGCGC
*
17178865 ACAAATTGATACTAAAATGGATTTATTTTCTTAT
66 ACAAATTGATACCAAAATGGATTTATTTTCTTAT
17178899 TTTTTGGATTCCAATTGCAATTGAAGTTATCGTTGCAAATGTTAAAGAAAATCCCACTTTCGCGC
1 TTTTTGGATTCCAATTGCAATTGAAGTTATCGTTGCAAATGTTAAAGAAAATCCCACTTTCGCGC
17178964 ACAAATTGATACCAAAATGGATTTATTTTCTTAT
66 ACAAATTGATACCAAAATGGATTTATTTTCTTAT
17178998 TT
1 TT
17179000 CCTTCTTTTA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (99 bp):
TTTTTGGATTCCAATTGCAATTGAAGTTATCGTTGCAAATGTTAAAGAAAATCCCACTTTCGCGC
ACAAATTGATACCAAAATGGATTTATTTTCTTAT
Found at i:17183574 original size:3 final size:3
Alignment explanation
Indices: 17183566--17183601 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
17183556 TTATTTGTGT
17183566 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17183602 GCTTGTTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17184157 original size:17 final size:16
Alignment explanation
Indices: 17184132--17184180 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
17184122 TGTGTGCGAG
17184132 CCCCCTGTTATGCGGA
1 CCCCCTGTTATGCGGA
17184148 CCCCCATGTTATGC-GA
1 CCCCC-TGTTATGCGGA
17184164 CCCCCTG-TATTGCGGA
1 CCCCCTGTTA-TGCGGA
17184180 C
1 C
17184181 ACTTAGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.07
15 5 0.17
16 15 0.50
17 8 0.27
ACGTcount: A:0.14, C:0.39, G:0.22, T:0.24
Consensus pattern (16 bp):
CCCCCTGTTATGCGGA
Found at i:17184480 original size:27 final size:27
Alignment explanation
Indices: 17184430--17184494 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
17184420 ATGCCTGAGT
* *
17184430 TGCGAACCCATATAGGTGAGCCCT-TA
1 TGCGAACCCATATAGGCGACCCCTGTA
* *
17184456 TGCGAACCCCCTATAGGCGACCCCTGTG
1 TGCGAA-CCCATATAGGCGACCCCTGTA
*
17184484 TGCGAAACCAT
1 TGCGAACCCAT
17184495 GAGTGTAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 6 0.19
27 18 0.58
28 7 0.23
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (27 bp):
TGCGAACCCATATAGGCGACCCCTGTA
Found at i:17184739 original size:23 final size:23
Alignment explanation
Indices: 17184709--17184756 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
17184699 TGATTTTTAG
*
17184709 TACATGATTTAAG-ATGTGAACCC
1 TACATGA-TAAAGTATGTGAACCC
*
17184732 TACATGATAAAGTATTTGAACCC
1 TACATGATAAAGTATGTGAACCC
17184755 TA
1 TA
17184757 TATATTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (23 bp):
TACATGATAAAGTATGTGAACCC
Found at i:17186713 original size:42 final size:42
Alignment explanation
Indices: 17186662--17186929 Score: 396
Period size: 42 Copynumber: 6.4 Consensus size: 42
17186652 CAGTGCCTAT
*
17186662 CAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * * *
17186704 CAGACTTAATGCCAGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
17186746 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
17186788 CAGGCTTAATGCTGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* *
17186830 CAGACTTAATACCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
17186872 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
17186913 CAGGC-TAAGTGCCGGTG
1 CAGGCTTAA-TGCCGGTG
17186930 TACTGAATCA
Statistics
Matches: 205, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
40 3 0.01
41 30 0.15
42 172 0.84
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
Found at i:17191610 original size:21 final size:21
Alignment explanation
Indices: 17191562--17191620 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
17191552 CCATGTAACC
*
17191562 TTGTCACATGGACGTGTGTCT
1 TTGTCACATGGACGTGTGCCT
*** *
17191583 CAATCACATGGCCGTGTGCCT
1 TTGTCACATGGACGTGTGCCT
*
17191604 TTGTCACATGGGCGTGT
1 TTGTCACATGGACGTGT
17191621 CACTCCCCAC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (21 bp):
TTGTCACATGGACGTGTGCCT
Done.