Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004635.1 Hibiscus syriacus cultivar Beakdansim tig00010375_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 155746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1613 original size:36 final size:36
Alignment explanation
Indices: 1505--1620 Score: 155
Period size: 35 Copynumber: 3.2 Consensus size: 36
1495 ACCAACTTGA
* *
1505 AAAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
1541 -AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
* * * *
1576 AAAAATAGTTTTTCAAAGTTTTGTAGATGTTT-GTTG
1 AAAAAT-GATTTTCAAAGTTTGGTAAATGTTTCTTTG
1612 AAAAATGAT
1 AAAAATGAT
1621 AATGGGATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 35 0.49
36 14 0.20
37 22 0.31
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.44
Consensus pattern (36 bp):
AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:6169 original size:37 final size:38
Alignment explanation
Indices: 6114--6197 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
6104 TGGTAACCAA
6114 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
6151 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
6188 -GTTGAAAAAT
1 CTTTGAAAAAT
6198 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:8478 original size:18 final size:18
Alignment explanation
Indices: 8455--8491 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8445 CCTATTTTTA
8455 TTTAATAAAAATAATATT
1 TTTAATAAAAATAATATT
* *
8473 TTTAATAAATATATTATT
1 TTTAATAAAAATAATATT
8491 T
1 T
8492 CAGGTCAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAATAAAAATAATATT
Found at i:9011 original size:17 final size:17
Alignment explanation
Indices: 8991--9024 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8981 ATTTTTATTG
8991 AATAAAAATAATATTTT
1 AATAAAAATAATATTTT
* *
9008 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
9025 GGGTCGGGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATAAAAATAATATTTT
Found at i:9547 original size:34 final size:34
Alignment explanation
Indices: 9478--9547 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 34
9468 AATTTAATTT
* *
9478 ATTTAAAAAGATATAATTACCTATTAATGTTAAA
1 ATTTAAAAAGATATAAATACCTATTAATGTAAAA
* * *
9512 ATTTAAAAATATAATAAATATCTTTTAAT-TAAAA
1 ATTTAAAAAGAT-ATAAATACCTATTAATGTAAAA
9546 AT
1 AT
9548 ATTTGGAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (34 bp):
ATTTAAAAAGATATAAATACCTATTAATGTAAAA
Found at i:13408 original size:19 final size:19
Alignment explanation
Indices: 13353--13395 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
13343 AATGATTTTA
13353 AAACTATAGAATGCACTAT
1 AAACTATAGAATGCACTAT
13372 AAACTATAGAATGCACTAT
1 AAACTATAGAATGCACTAT
13391 AAACT
1 AAACT
13396 TATTTAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (19 bp):
AAACTATAGAATGCACTAT
Found at i:20844 original size:58 final size:58
Alignment explanation
Indices: 20709--20967 Score: 294
Period size: 58 Copynumber: 4.5 Consensus size: 58
20699 AAGATTTTAC
* * * * *
20709 GAAAATAAATTCAACAACTTATTTTCTTCTACAAGATAAAAT-GTTCAAGATT-TCTAA
1 GAAAATAAATTCAACAATTTATTTTCTTTTACAAAACAAAATCATTCAAGATTCTC-AA
** * * *
20766 GAAAATAAATTTGACGATTTATTTTCTTTTACAAACCAAAATCATAT-AAGATTCACAA
1 GAAAATAAATTCAACAATTTATTTTCTTTTACAAAACAAAATCAT-TCAAGATTCTCAA
* * *
20824 GAAAATAAATTCAACAATTTA-TTTCTTTTTAGAAAACAAAATCATTTAAGATTCTTAA
1 GAAAATAAATTCAACAATTTATTTTC-TTTTACAAAACAAAATCATTCAAGATTCTCAA
20882 GAAAATAAATTCAACAATTTA-TTTCTTTTTACAAAACAAAATCATTCAAGATTCTCAA
1 GAAAATAAATTCAACAATTTATTTTC-TTTTACAAAACAAAATCATTCAAGATTCTCAA
* * **
20940 GAAAATATATTCAATAACGTATTTTCTT
1 GAAAATAAATTCAACAATTTATTTTCTT
20968 ACAAAGTTAG
Statistics
Matches: 172, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
57 39 0.23
58 127 0.74
59 6 0.03
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (58 bp):
GAAAATAAATTCAACAATTTATTTTCTTTTACAAAACAAAATCATTCAAGATTCTCAA
Found at i:22411 original size:71 final size:71
Alignment explanation
Indices: 22295--22437 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 71
22285 TCAAAATCTC
* * * *
22295 GAACTATCCCTTACCTTTGTTTATCACCGAAACAACAGCTAAATTCTGAGTTGTGTTTAACCTAG
1 GAACTATCCCTTACCTCTGTTTATCACCGAAAAAACAACTAAATTCTAAGTTGTGTTTAACCTAG
22360 AAGCTT
66 AAGCTT
* *
22366 GAACTATCCCTTACCTCTGTTTATCACCGAAAAAATAACTAAATTCTAAGTTGTGTTTCACCTAG
1 GAACTATCCCTTACCTCTGTTTATCACCGAAAAAACAACTAAATTCTAAGTTGTGTTTAACCTAG
22431 AAGCTT
66 AAGCTT
22437 G
1 G
22438 TCCATTGTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (71 bp):
GAACTATCCCTTACCTCTGTTTATCACCGAAAAAACAACTAAATTCTAAGTTGTGTTTAACCTAG
AAGCTT
Found at i:22570 original size:71 final size:71
Alignment explanation
Indices: 22489--22631 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 71
22479 ATGGTCTTTC
* * *
22489 GAACTATCCCTTACCTTTGTTTATCACAGGAAAAACAATTAAATTATGAGTTGTGTTTAACCTAG
1 GAACTATCCCTTACCTTTGTTTATCACAGAAAAAACAACTAAATTATGAGTTGTGTTTAACCTAA
22554 AAGCTT
66 AAGCTT
*
22560 GAACTATCCCTTACCTTTGTTTATCACTGAAAAAACAACTAAATTATGAGTTGTGTTTAACCTAA
1 GAACTATCCCTTACCTTTGTTTATCACAGAAAAAACAACTAAATTATGAGTTGTGTTTAACCTAA
22625 AAGCTT
66 AAGCTT
22631 G
1 G
22632 TCCATTGTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (71 bp):
GAACTATCCCTTACCTTTGTTTATCACAGAAAAAACAACTAAATTATGAGTTGTGTTTAACCTAA
AAGCTT
Found at i:22631 original size:194 final size:192
Alignment explanation
Indices: 22293--22678 Score: 630
Period size: 194 Copynumber: 2.0 Consensus size: 192
22283 TGTCAAAATC
* *
22293 TCGAACTATCCCTTACCTTTGTTTATCACCGAAACAACAGCTAAATTCTGAGTTGTGTTTAACCT
1 TCGAACTATCCCTTACCTTTGTTTATCACCGAAACAACAACTAAATTATGAGTTGTGTTTAACCT
* *
22358 AGAAGCTTGAACTATCCCTTACCTCTGTTTATCACCGAAAAAATAACTAAATTCTAAGTTGTGTT
66 AGAAGCTTGAACTATCCCTTACCTCTGTTTATCACCGAAAAAACAACTAAATTATAAGTTGTGTT
* *
22423 TCACCTAGAAGCTTGTCCATTGTTCACTATAAAAATTATGTCAAAGTCCATTGTTAATGGTCTT
131 TAACCTAAAAGCTTGTCCATTGTTCACTAT-AAAATTATGTCAAAGTCCATT-TTAATGGTCTT
* *
22487 TCGAACTATCCCTTACCTTTGTTTATCACAGGAAA-AACAATTAAATTATGAGTTGTGTTTAACC
1 TCGAACTATCCCTTACCTTTGTTTATCAC-CGAAACAACAACTAAATTATGAGTTGTGTTTAACC
* * *
22551 TAGAAGCTTGAACTATCCCTTACCTTTGTTTATCACTGAAAAAACAACTAAATTATGAGTTGTGT
65 TAGAAGCTTGAACTATCCCTTACCTCTGTTTATCACCGAAAAAACAACTAAATTATAAGTTGTGT
*
22616 TTAACCTAAAAGCTTGTCCATTGTTCTCTATAAAATTATGTCAAAGTCCATTTTAATGGTCTT
130 TTAACCTAAAAGCTTGTCCATTGTTCACTATAAAATTATGTCAAAGTCCATTTTAATGGTCTT
22679 AATAATATAA
Statistics
Matches: 179, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
192 11 0.06
193 21 0.12
194 143 0.80
195 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (192 bp):
TCGAACTATCCCTTACCTTTGTTTATCACCGAAACAACAACTAAATTATGAGTTGTGTTTAACCT
AGAAGCTTGAACTATCCCTTACCTCTGTTTATCACCGAAAAAACAACTAAATTATAAGTTGTGTT
TAACCTAAAAGCTTGTCCATTGTTCACTATAAAATTATGTCAAAGTCCATTTTAATGGTCTT
Found at i:27145 original size:12 final size:13
Alignment explanation
Indices: 27128--27163 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27118 CGAGTCAAAC
27128 GAGTCAACTCG-T
1 GAGTCAACTCGTT
*
27140 GAGTCAACCCGTT
1 GAGTCAACTCGTT
27153 GAGTCAACTCG
1 GAGTCAACTCG
27164 AACAGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (13 bp):
GAGTCAACTCGTT
Found at i:28943 original size:6 final size:6
Alignment explanation
Indices: 28932--28959 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28922 TGAAAAGAAG
28932 AGAGGA AGAGGA AGAGGA AGAGGA AGAG
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAG
28960 AGCGTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:33539 original size:106 final size:106
Alignment explanation
Indices: 33344--34630 Score: 2074
Period size: 106 Copynumber: 12.1 Consensus size: 106
33334 AACCATGAGC
* * *
33344 ACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * * *
33409 ATAAACAA-TTTTCCACTTCTAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTC-AGAGCCAATTTCAACTTCACA
* * * *
33450 GCGAAGGATAGTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGTGACCGCTGATTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
33515 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
33556 ACGAATGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
33621 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* *
33662 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
33727 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
** * * *
33768 GTGAAGGATATAGGACTCCATACAACGCATGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
33833 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* * *
33874 GCGAAGGATATTGGACTCCATACAACGCATGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
33939 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
33980 GCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * *
34045 ATAAACAACTTCCCAATTTCATAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
34086 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
34151 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* * * *
34192 ACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAATGGACCGTTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * * *
34257 ATAAACAACTTCCCAATTTCATAGCCAATTTCAACTTCACG
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* *
34298 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
34363 ACAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* *
34404 ACGAAGGATATTGGACTCCAGACAACGCATGTTCGACTTCACGACGAAGGGACCGCTGGTTTTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
34469 AAAAACAACTTCTTAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
34510 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * * * *
34575 ATAAACAA-TTTTCCAGTTCCAGAGCCAATTTCAACTTCACG
66 ACAAACAACTTCT-CAATTTCAGAGCCAATTTCAACTTCACA
* *
34616 GCGGAGGATATTGGA
1 ACGAAGGATATTGGA
34631 GTTGGAACAA
Statistics
Matches: 1101, Mismatches: 78, Indels: 4
0.93 0.07 0.00
Matches are distributed among these distances:
105 3 0.00
106 1090 0.99
107 8 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (106 bp):
ACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
Found at i:35017 original size:84 final size:83
Alignment explanation
Indices: 34833--35247 Score: 322
Period size: 84 Copynumber: 5.0 Consensus size: 83
34823 TCTGCCAACA
* * * * * * * * * * *
34833 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAATGGCACATCATTTGCAACATAGCTTAAGTCGA
1 AAAGACCCTCGAGTTCGATTACACTCAGCTCAAGGGCACATCATTTACAGCATAACTCAAGGCTA
*
34898 GAAGGGCTATCTG---CC
66 GAAGGGTTATCTGTCACC
* * * *
34913 AAAGACCCCCGAGTTCGATTACACTCAGCCTCGAGGGCATATCATTTACAGTATAACTCAAGGCT
1 AAAGACCCTCGAGTTCGATTACACTCAG-CTCAAGGGCACATCATTTACAGCATAACTCAAGGCT
34978 AGAAGGGTTATCTGTCACC
65 AGAAGGGTTATCTGTCACC
* * * * * * * * * *
34997 AAAGACCTTCGAGTTTGATTACGCTCAGCTCCCA-GGCATATCATTTGCAGTACAACTTAAGTCT
1 AAAGACCCTCGAGTTCGATTACACTCAGCT-CAAGGGCACATCATTTACAGCATAACTCAAGGCT
* * * *
35061 AGAACGGTTGTCTGCCAACA
65 AGAAGGGTTATCTGTC-ACC
* * * * * * * * * * *
35081 AAAGACCTTTGAGTTCGACTACGCTTAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCCTCGAGTTCGATTACACTCAGCTCAAGGGCACATCATTTACAGCATAACTCAAGGCTA
* *
35146 GGAGGGCTATCTG---CC
66 GAAGGGTTATCTGTCACC
* * *
35161 AAAGACCCTCGAGTTCGATTACACTCAGCTTAAAGGGCACATTATTTACAGCATAACTCAATGCT
1 AAAGACCCTCGAGTTCGATTACACTCAGC-TCAAGGGCACATCATTTACAGCATAACTCAAGGCT
*
35226 AGAAGGGTTATATGTCACC
65 AGAAGGGTTATCTGTCACC
35245 AAA
1 AAA
35248 TTTTTAACTC
Statistics
Matches: 263, Mismatches: 61, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
80 48 0.18
81 76 0.29
83 43 0.16
84 96 0.37
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
AAAGACCCTCGAGTTCGATTACACTCAGCTCAAGGGCACATCATTTACAGCATAACTCAAGGCTA
GAAGGGTTATCTGTCACC
Found at i:36380 original size:4 final size:4
Alignment explanation
Indices: 36371--36422 Score: 65
Period size: 4 Copynumber: 13.8 Consensus size: 4
36361 TTTAATCATT
* *
36371 TTTA TTTA TTTA TTTA TTTA -TTA -TTA -TTA TATA TATA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
36416 TTTA TTT
1 TTTA TTT
36423 TTAATTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 9 0.20
4 36 0.80
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:36410 original size:29 final size:29
Alignment explanation
Indices: 36377--36447 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
36367 CATTTTTATT
36377 TATTTATTTATTTATTATT-ATTATATATA
1 TATTTATTTATTTATTATTAATTATA-ATA
* *
36406 TATTTATTTATTTATTTTTAATTTTAATA
1 TATTTATTTATTTATTATTAATTATAATA
* *
36435 TTTTTCTTTATTT
1 TATTTATTTATTT
36448 CTTTTAACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 32 0.86
30 5 0.14
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (29 bp):
TATTTATTTATTTATTATTAATTATAATA
Found at i:38022 original size:31 final size:31
Alignment explanation
Indices: 37984--38055 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
37974 TAAGACGACC
*
37984 CTTGGGTAGGCTCTGAGGCCCCGAGAACTTT
1 CTTGGGTAGGCTATGAGGCCCCGAGAACTTT
* *
38015 CTTGGGTAGGCTATGAGGCCCCGATAATTTT
1 CTTGGGTAGGCTATGAGGCCCCGAGAACTTT
38046 CTTGGGTAGG
1 CTTGGGTAGG
38056 ATTTCAGTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (31 bp):
CTTGGGTAGGCTATGAGGCCCCGAGAACTTT
Found at i:41730 original size:22 final size:23
Alignment explanation
Indices: 41705--41748 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
41695 AGTTTGACCC
41705 TTCAAAAATA-TTTTTATTAGTT
1 TTCAAAAATATTTTTTATTAGTT
*
41727 TTCAAAGATATTTTTTATTAGT
1 TTCAAAAATATTTTTTATTAGT
41749 ATGTGTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (23 bp):
TTCAAAAATATTTTTTATTAGTT
Found at i:42923 original size:63 final size:62
Alignment explanation
Indices: 42837--43003 Score: 155
Period size: 60 Copynumber: 2.7 Consensus size: 62
42827 CTCAATTATA
* **
42837 AAGGTAGAAAATAAGGATTATTTTATAAAATTGAAAAAAAAAAATTA-GAGACCTTTAATAATT
1 AAGGTAGAAAATTAGGACAATTTTATAAAATTGAAAAAAAAAAA-TAGGAG-CCTTTAATAATT
* * * * *
42900 AAGGTAGAAAATTAGGACAATTTTTGTACAATT---TAAAAACAATAGGAGCTTTTAATAATT
1 AAGGTAGAAAATTAGGACAA-TTTTATAAAATTGAAAAAAAAAAATAGGAGCCTTTAATAATT
* * * *
42960 AAGTTAG-AAAGTATGGACAAATTTATAAAATTGAAAGAAAAAAA
1 AAGGTAGAAAATTA-GGACAATTTTATAAAATTGAAAAAAAAAAA
43004 CCCTTAGAGA
Statistics
Matches: 82, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
59 14 0.17
60 25 0.30
61 10 0.12
62 6 0.07
63 17 0.21
64 10 0.12
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.29
Consensus pattern (62 bp):
AAGGTAGAAAATTAGGACAATTTTATAAAATTGAAAAAAAAAAATAGGAGCCTTTAATAATT
Found at i:43895 original size:2 final size:2
Alignment explanation
Indices: 43888--43944 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
43878 TCGGGCCGGG
* * * *
43888 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43928 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
43945 TTAATTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:44090 original size:35 final size:36
Alignment explanation
Indices: 44037--44121 Score: 136
Period size: 35 Copynumber: 2.4 Consensus size: 36
44027 ATCAAACCCG
*
44037 TCCCCGTCCCCGTCCCCGTTTAACATAAACGGTTTT
1 TCCCCGTCCCCGTTCCCGTTTAACATAAACGGTTTT
* *
44073 T-TCCGTCCCCGTTCCCGTTTAGCATAAACGGTTTT
1 TCCCCGTCCCCGTTCCCGTTTAACATAAACGGTTTT
44108 TCCCCGTCCCCGTT
1 TCCCCGTCCCCGTT
44122 TAATTCGATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 32 0.73
36 12 0.27
ACGTcount: A:0.13, C:0.39, G:0.15, T:0.33
Consensus pattern (36 bp):
TCCCCGTCCCCGTTCCCGTTTAACATAAACGGTTTT
Found at i:45455 original size:2 final size:2
Alignment explanation
Indices: 45450--45478 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45440 AAAAAGGAAA
45450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45479 AAAGCTACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45900 original size:2 final size:2
Alignment explanation
Indices: 45893--45946 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
45883 ATATTAAAGA
45893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
45935 AT A- AT AA AT AT A
1 AT AT AT AT AT AT A
45947 GTAAAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:46015 original size:18 final size:17
Alignment explanation
Indices: 45994--46036 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
45984 ATATATACAT
45994 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
46012 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
46029 ATAA-AATA
1 ATAATAATA
46037 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:46441 original size:37 final size:38
Alignment explanation
Indices: 46391--46495 Score: 142
Period size: 37 Copynumber: 2.8 Consensus size: 38
46381 GTGCTTGTGG
* * * *
46391 ATCCTATATTTAGGAATTTAAATCTTAGTAGAAC-TCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTCT
* *
46428 ATCCTATTTTTAGGAGTTTGAATCCTAGCA-AACTTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTCT
46465 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
46496 GACGAAAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 3 0.05
37 56 0.95
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (38 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTCT
Found at i:47342 original size:105 final size:105
Alignment explanation
Indices: 47039--47670 Score: 898
Period size: 105 Copynumber: 6.0 Consensus size: 105
47029 ACATTGTTTC
* * ** *
47039 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCT-AGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * * *
47103 ACCAGCCGTCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
47145 GAGTCCAATATCATTTGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTG-TTGACAA
* *
47205 GCAGCGGTCCCTTCGTCATGGAGTTGAACTTGCGTTGTCTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
47246 GAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
47311 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
47351 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
47416 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
47456 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
47521 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
47561 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
47626 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
47667 GAGT
1 GAGT
47671 GTCACGATAT
Statistics
Matches: 480, Mismatches: 38, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
100 3 0.01
101 76 0.16
102 7 0.01
103 1 0.00
105 306 0.64
106 86 0.18
107 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:47910 original size:36 final size:36
Alignment explanation
Indices: 47870--47945 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
47860 TGTTTGGAGA
* * *
47870 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
47906 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
47942 GAAA
1 GAAA
47946 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:48014 original size:39 final size:39
Alignment explanation
Indices: 47957--48033 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
47947 GTTTTCAATG
* * *
47957 TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
1 TTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAAT
* *
47996 TTTATGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAA
1 TTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAA
48034 AATCATTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (39 bp):
TTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAAT
Found at i:48120 original size:39 final size:39
Alignment explanation
Indices: 48066--48140 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
48056 TCAATGTTTA
* *
48066 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
48105 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
48141 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:48179 original size:105 final size:104
Alignment explanation
Indices: 47845--48163 Score: 511
Period size: 105 Copynumber: 3.1 Consensus size: 104
47835 TTCGTTAAAT
** *
47845 TGTTTTCAAAT-TTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGG
1 TGTTTTC-AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGG
* *
47906 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
65 GAAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
*
47946 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTATGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
48011 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
48051 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
48116 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
48155 TGTTTTCAA
1 TGTTTTCAA
48164 GAGAAACTGT
Statistics
Matches: 202, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
100 3 0.01
101 43 0.21
103 2 0.01
104 54 0.27
105 100 0.50
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:48319 original size:36 final size:36
Alignment explanation
Indices: 48279--48392 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
48269 CTTTCGAGTG
* *
48279 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * * * **
48315 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
*
48351 AAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TCTTGTTTTAAGA
48387 AAAACA
1 AAAACA
48393 AATTTGAGTG
Statistics
Matches: 58, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:48371 original size:72 final size:74
Alignment explanation
Indices: 48234--48408 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 74
48224 TAAAATCTTC
** * *
48234 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
48298 CAAA-TCTTGTT
64 CAAAGT-ATGTT
*
48309 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
48372 AAGTATGTT
66 AAGTATGTT
*
48381 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
48409 TCATCTGCAT
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
72 48 0.53
73 15 0.17
75 8 0.09
76 19 0.21
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
AAGTATGTT
Found at i:49863 original size:183 final size:183
Alignment explanation
Indices: 49548--50084 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
49538 ATCAGGTTTA
*
49548 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
49613 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
49677 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * *
49731 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
49796 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCAAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
49861 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
49914 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAACAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * *
49979 GCCAAGTGTCCGAGCAGTGTCAGAGTTTGAACATAATCCATTCATAAAGCCAAGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
50044 TCCTCTATAACCAATTGCTTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
50085 CGGATTTAAT
Statistics
Matches: 336, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
183 335 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:54684 original size:18 final size:17
Alignment explanation
Indices: 54663--54705 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
54653 ATATATACAT
54663 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
54681 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
54698 ATAA-AATA
1 ATAATAATA
54706 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:54713 original size:60 final size:59
Alignment explanation
Indices: 54589--54713 Score: 128
Period size: 62 Copynumber: 2.1 Consensus size: 59
54579 ATATTAAAGA
* * * * *
54589 ATATATATATATATAATAATAAAATATAGTCAAAAAATAAATGAAAATAATTTAATATATAT
1 ATATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATAA--TAATATACAT
*
54651 ATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-AATATCCAT
1 ATATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAATAATATACAT
54711 ATA
1 ATA
54714 ATAAATAAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
60 10 0.19
62 21 0.39
63 9 0.17
64 3 0.06
65 11 0.20
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (59 bp):
ATATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATAATAATATACAT
Found at i:62198 original size:36 final size:36
Alignment explanation
Indices: 62156--62230 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
62146 TATTCAAAAG
**
62156 TTAAAACCTCTTTTACCATTCAGTCTTAAATAGATT
1 TTAAAACCTCTTTTACCATTCAAACTTAAATAGATT
*
62192 TTAAAACTTCTTTTACCATTCAAACTTAAATAGATT
1 TTAAAACCTCTTTTACCATTCAAACTTAAATAGATT
62228 TTA
1 TTA
62231 TTTTAATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (36 bp):
TTAAAACCTCTTTTACCATTCAAACTTAAATAGATT
Found at i:66666 original size:23 final size:24
Alignment explanation
Indices: 66634--66686 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
66624 ATAGTCTAAT
*
66634 AATATTTTAATAAAGATATT-TAA
1 AATATATTAATAAAGATATTATAA
* * *
66657 AATATATTAATTAATATTTTATAA
1 AATATATTAATAAAGATATTATAA
66681 AATATA
1 AATATA
66687 ATATAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AATATATTAATAAAGATATTATAA
Found at i:66685 original size:22 final size:22
Alignment explanation
Indices: 66617--66696 Score: 58
Period size: 23 Copynumber: 3.5 Consensus size: 22
66607 ATGTATTTAT
* * *
66617 TAATATAATAGTCTAATAATATTT
1 TAATATAATATTTTAA-AATA-TA
*
66641 TAATA-AAGATATTTAAAATATA
1 TAATATAATAT-TTTAAAATATA
66663 TTAAT-TAATATTTTATAAA-ATA
1 -TAATATAATATTTTA-AAATATA
66685 TAATATAATATT
1 TAATATAATATT
66697 ATTACTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 4 0.09
22 15 0.33
23 18 0.39
24 9 0.20
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (22 bp):
TAATATAATATTTTAAAATATA
Found at i:66700 original size:35 final size:35
Alignment explanation
Indices: 66617--66700 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 35
66607 ATGTATTTAT
*
66617 TAATATAATAGT-CTAATAATATTTTAATAAAGATA
1 TAATATAATA-TATTAATAATATTTTAATAAAGATA
* *
66652 T-TTAAAATATATTAATTAATATTTT-ATAAA-ATA
1 TAATATAATATATTAA-TAATATTTTAATAAAGATA
66685 TAATATAATATTATTA
1 TAATATAATA-TATTA
66701 CTTTAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
33 5 0.12
34 20 0.50
35 15 0.38
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (35 bp):
TAATATAATATATTAATAATATTTTAATAAAGATA
Found at i:68589 original size:6 final size:6
Alignment explanation
Indices: 68580--68609 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
68570 ACCATTACCA
68580 TCACCT TCACCT TCACCT TCACCT TCACCT
1 TCACCT TCACCT TCACCT TCACCT TCACCT
68610 CAACCAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TCACCT
Found at i:68855 original size:9 final size:9
Alignment explanation
Indices: 68816--68857 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
68806 TCCCCTAAAA
68816 TTTTTATAT
1 TTTTTATAT
*
68825 TTTATATAT
1 TTTTTATAT
**
68834 TTTAGATAT
1 TTTTTATAT
68843 TTTTTATAT
1 TTTTTATAT
68852 TTTTTA
1 TTTTTA
68858 GTTGAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTATAT
Found at i:71558 original size:35 final size:35
Alignment explanation
Indices: 71511--71580 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
71501 TCGGGTGTGG
*
71511 GTGTGGGTGTTGGGTACAGGTATGGTTAGATTTTA
1 GTGTGGGAGTTGGGTACAGGTATGGTTAGATTTTA
*
71546 GTGTGGGAGTTGGGTACAGGTATGGTTTGATTTTA
1 GTGTGGGAGTTGGGTACAGGTATGGTTAGATTTTA
71581 CTAAGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.17, C:0.03, G:0.40, T:0.40
Consensus pattern (35 bp):
GTGTGGGAGTTGGGTACAGGTATGGTTAGATTTTA
Found at i:79268 original size:3 final size:3
Alignment explanation
Indices: 79248--79333 Score: 138
Period size: 3 Copynumber: 28.3 Consensus size: 3
79238 TCGGGCTTAA
*
79248 ATT ATT A-T ACTT ATTT ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT
1 ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
79294 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
79334 ATTTTGTTTA
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
2 2 0.03
3 71 0.91
4 5 0.06
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:81132 original size:2 final size:2
Alignment explanation
Indices: 81125--81154 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
81115 GTTTTTATGC
81125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81155 TCGTATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83035 original size:32 final size:32
Alignment explanation
Indices: 82994--83082 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 32
82984 ATATTAAATG
*
82994 ATTTTTTTCCTTTTGTTTGTGTACATTAA-CT
1 ATTTATTTCCTTTTGTTTGTGTACATTAACCT
* *
83025 AATTTATTTCCTTTT-TTTATGTACACTAACCT
1 -ATTTATTTCCTTTTGTTTGTGTACATTAACCT
* *
83057 ATTTATTTTCTTTTGATTGTGT-CATT
1 ATTTATTTCCTTTTGTTTGTGTACATT
83083 TTTCATCATT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
31 28 0.58
32 20 0.42
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60
Consensus pattern (32 bp):
ATTTATTTCCTTTTGTTTGTGTACATTAACCT
Found at i:89460 original size:15 final size:15
Alignment explanation
Indices: 89442--89476 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
89432 AGGAAGAAAA
*
89442 AGAAAATAATCAAAG
1 AGAAAATAAACAAAG
89457 AGAAAATAAACAAAG
1 AGAAAATAAACAAAG
89472 -GAAAA
1 AGAAAA
89477 GGGACAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.71, C:0.06, G:0.14, T:0.09
Consensus pattern (15 bp):
AGAAAATAAACAAAG
Found at i:89621 original size:9 final size:11
Alignment explanation
Indices: 89588--89623 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
89578 GAAGATCATG
89588 GAGCATCTAGA
1 GAGCATCTAGA
89599 GAGCATCTAGA
1 GAGCATCTAGA
*
89610 GAGCATCAAGA
1 GAGCATCTAGA
89621 GAG
1 GAG
89624 AGACACGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.39, C:0.17, G:0.31, T:0.14
Consensus pattern (11 bp):
GAGCATCTAGA
Found at i:90538 original size:32 final size:32
Alignment explanation
Indices: 90502--90571 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
90492 ATATTTAAAT
* * *
90502 ATTCAATAGCGAATGTTGAGGCATCTTTGGAG
1 ATTCAAGAGCGAATATTGAGGCATCTATGGAG
* * *
90534 ATTCAAGATCGAATATTGGGGCATCTATGGGG
1 ATTCAAGAGCGAATATTGAGGCATCTATGGAG
90566 ATTCAA
1 ATTCAA
90572 CATTATGATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (32 bp):
ATTCAAGAGCGAATATTGAGGCATCTATGGAG
Found at i:90768 original size:21 final size:21
Alignment explanation
Indices: 90744--90796 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
90734 AATCTTTAAG
*
90744 TTTGTTTCTTTGGAAACAATT
1 TTTGTCTCTTTGGAAACAATT
90765 TTTGTCTCTTTGGAAACAATT
1 TTTGTCTCTTTGGAAACAATT
90786 TTTGTCTCTTT
1 TTTGTCTCTTT
90797 TGAGACAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (21 bp):
TTTGTCTCTTTGGAAACAATT
Found at i:91190 original size:46 final size:46
Alignment explanation
Indices: 90950--91214 Score: 194
Period size: 46 Copynumber: 6.0 Consensus size: 46
90940 AACCAGCAGT
* * * * *
90950 CCTAGATAACCAGTCGTTCTTATCACGTAGAAATCGTGTTATCACC
1 CCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCACC
* *** * * *
90996 CTTAGATGGTCTGTCGTCCTCATCACGTAGGAACCGTG---TCATC
1 CCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCACC
* * * * * * *
91039 CCTAG---ACCAAAT-TTCCTCATCATGTATGAACCATGTCA--ACT
1 CCTAGATAACC-AGTCATCCTCATCACGTAGGAACCGTGTTATCACC
* * * *
91080 CC-AGATAATCAGTCGTCCTCATCACATAGGAACCGTGTTACCA-C
1 CCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCACC
*
91124 CCTAGATAACCAG-CTATCCTCATCTCGTAGGAACCGTGTTATCACC
1 CCTAGATAACCAGTC-ATCCTCATCACGTAGGAACCGTGTTATCACC
* *
91170 CCTAGATAACCAGTCATCCTCAACACGTAGGAACCATGTTATCAC
1 CCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCAC
91215 TTCCTAAAGA
Statistics
Matches: 167, Mismatches: 38, Indels: 28
0.72 0.16 0.12
Matches are distributed among these distances:
40 22 0.13
41 4 0.02
42 2 0.01
43 30 0.18
44 3 0.02
45 35 0.21
46 70 0.42
47 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (46 bp):
CCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCACC
Found at i:91383 original size:135 final size:134
Alignment explanation
Indices: 91193--91470 Score: 416
Period size: 135 Copynumber: 2.1 Consensus size: 134
91183 TCATCCTCAA
*
91193 CACGTAGGAACCATGTTATCACTTCCTAAAGATGACCAAGAACTCTTCATCACGTATGAGCAGTG
1 CACGTATGAACCATGTTATCACTTCCTAAAGATGACCAAGAACTCTTCATCACGTATGAGCAGTG
* * * *
91258 TCATCCCCTGACAAGATTTCCTCATTATTTAGGAGTCGTGCCAACCCTT-GATAACCAGAACTCC
66 TCATCCCCTGACAAGATTTCCTCATTATATAGGAGCCATGCCAACCCTTAGACAACCAGAACT-C
91322 TT-AT
130 TTCAT
* *
91326 CACGTATGAACCGTGTTATCACACTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAG
1 CACGTATGAACCATGTTAT--CACTTCCTAAAGATGACCAAGAACTCTTCATCACGTATGAGCAG
* * *
91391 TGTCATCCCCTGATAAGATTTCCTCATTATATAGGAGCCATGTCAACCCTTAGACGACCAGAACT
64 TGTCATCCCCTGACAAGATTTCCTCATTATATAGGAGCCATGCCAACCCTTAGACAACCAGAACT
91456 CTTCAT
129 CTTCAT
*
91462 CGCGTATGA
1 CACGTATGA
91471 GTCGTGTCGT
Statistics
Matches: 130, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
133 17 0.13
135 92 0.71
136 21 0.16
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (134 bp):
CACGTATGAACCATGTTATCACTTCCTAAAGATGACCAAGAACTCTTCATCACGTATGAGCAGTG
TCATCCCCTGACAAGATTTCCTCATTATATAGGAGCCATGCCAACCCTTAGACAACCAGAACTCT
TCAT
Found at i:91645 original size:3 final size:3
Alignment explanation
Indices: 91629--91695 Score: 109
Period size: 3 Copynumber: 22.3 Consensus size: 3
91619 CCGAGCTTAA
*
91629 ATT ATT A-T ACTT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
91674 ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
91696 ATTTTGTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.93
4 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:93498 original size:2 final size:2
Alignment explanation
Indices: 93491--93562 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
93481 GTTTTTATGC
93491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93563 GAAACATTAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95262 original size:3 final size:3
Alignment explanation
Indices: 95237--95316 Score: 87
Period size: 3 Copynumber: 27.7 Consensus size: 3
95227 TTTTCATTTT
*
95237 TTA TT- TTA TT- TTA TT- TATA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
95280 TTA TAA TTA TAA TTA TTA TTA TTA TTA ATA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
95317 TAATATTACA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
2 7 0.11
3 57 0.88
4 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:95732 original size:21 final size:20
Alignment explanation
Indices: 95707--95762 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
95697 TGCGAGCAAG
95707 AGAGACAGAGACAGAGACAAA
1 AGAGA-AGAGACAGAGACAAA
*
95728 AGAGATAGAGACAGAGAGAAA
1 AGAGA-AGAGACAGAGACAAA
95749 AGAG-AGAGACAGAG
1 AGAGAAGAGACAGAG
95763 CCGGAGAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.30
21 23 0.70
ACGTcount: A:0.55, C:0.09, G:0.34, T:0.02
Consensus pattern (20 bp):
AGAGAAGAGACAGAGACAAA
Found at i:96476 original size:29 final size:30
Alignment explanation
Indices: 96417--96476 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
96407 ATATTTAGGA
*
96417 TAAATAACATATTTAATTCCTTAATTTTAT
1 TAAATAACATATTTAATTCCCTAATTTTAT
* *
96447 TAAATAATAT-TTTAA-TCCCTAGTTTATAT
1 TAAATAACATATTTAATTCCCTAATTT-TAT
96476 T
1 T
96477 TTTAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 8 0.31
29 9 0.35
30 9 0.35
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (30 bp):
TAAATAACATATTTAATTCCCTAATTTTAT
Found at i:108406 original size:16 final size:16
Alignment explanation
Indices: 108380--108424 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
108370 TTTGAATACA
*
108380 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
108397 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
108412 ATTCAATTTATTT
1 ATTCAATTTATTT
108425 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:109304 original size:83 final size:83
Alignment explanation
Indices: 109165--110096 Score: 1609
Period size: 83 Copynumber: 11.1 Consensus size: 83
109155 GAATAAGTGC
*
109165 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAATCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
109230 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
109248 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
* *
109313 CATTGAATTTAGAAGAGG
66 CATTGAATTTGGAAGATG
*
109331 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
109396 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
*
109414 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
109479 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* *
109497 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGATAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
* *
109562 CATTGAATTTAGAAGAGG
66 CATTGAATTTGGAAGATG
*
109580 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
109645 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
*
109663 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
109728 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
*
109746 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGACAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
109811 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
109829 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-CAGAACCAA-
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
109892 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
* *
109910 AATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
109975 CATTGAATTTGGAAGATG
66 CATTGAATTTGGAAGATG
*
109993 AATTTGCTCATAGTATAAGCAAGCATCTTCTGGAAGTGTTCTTT-AGTTATCTGATCTGGTTTGG
1 AATTTGCTC-----AT-----AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGA
*
110057 CAGAACCAACCATTGAATTTGGAAGATG
56 CAGAACCAATCATTGAATTTGGAAGATG
110085 AATTTGCTCATA
1 AATTTGCTCATA
110097 TAGAAATAAG
Statistics
Matches: 815, Mismatches: 22, Indels: 25
0.95 0.03 0.03
Matches are distributed among these distances:
81 71 0.09
82 19 0.02
83 642 0.79
87 2 0.00
88 2 0.00
92 56 0.07
93 23 0.03
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
AATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAAT
CATTGAATTTGGAAGATG
Found at i:110059 original size:92 final size:99
Alignment explanation
Indices: 109918--110159 Score: 365
Period size: 92 Copynumber: 2.5 Consensus size: 99
109908 TGAATTTGCT
*
109918 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAACCATTGAAT
*
109983 TTGGAAGATGAATTTGCTC-ATAG-TATAA-G-C
66 TTGGAAGATGAATTTGCTCAATAGAAATAAGGAC
110013 -A-AGCATCTTCTGGAAGTGTTCTTT-AGTTATCTGATCTGGTTTGGCAGAACCAACCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAACCATTGAAT
110075 TTGGAAGATGAATTTGCTCATATAGAAATAAGGAAATTC
66 TTGGAAGATGAATTTGCTCA-ATAGAAATAAGG--A--C
110114 AATAGCATC-TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
110160 TAGACTACAA
Statistics
Matches: 133, Mismatches: 2, Indels: 16
0.88 0.01 0.11
Matches are distributed among these distances:
92 56 0.42
93 23 0.17
94 5 0.04
95 4 0.03
96 1 0.01
101 1 0.01
102 17 0.13
103 26 0.20
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (99 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAACCATTGAAT
TTGGAAGATGAATTTGCTCAATAGAAATAAGGAC
Found at i:111038 original size:111 final size:108
Alignment explanation
Indices: 110860--111394 Score: 722
Period size: 108 Copynumber: 4.9 Consensus size: 108
110850 TAGCAAAGAT
*
110860 TCAAATCCATCATTGATGGA--GCTTTTCCAGTTCGAGTTCAT-ATGAGAAGAACTCATCTGAAG
1 TCAAATCCATCATTGATGGATCACTTTTCCAG-T-GAGTTCATAATGAGAAGAACTCATCTGAAG
*
110922 GAGGAAGAAGAAG-TCATAATGAGAAGAATTTGTTCAACCTTTTGC
64 AAGGAAGAA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
110967 TCAAATCCATCACTTGATGGATCACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCCATCA-TTGATGGATCACTTTTCCAG-T-GAGTTCATAATGAGAAGAACTCATCTGAA
111032 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
63 GAAGGAAGAA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
111079 TC-AATCCATCATTGATGGATCAACATTGCCAG-AAGTTCATAATGAGAAGAACTCGTCATCTGA
1 TCAAATCCATCATTGATGGATC-ACTTTTCCAGTGAGTTCATAATGAGAAGAA--C-TCATCTGA
111142 AGAAGGAAG-AAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62 AGAAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
111187 TCAAAT-C-TCACTTGATGGATCAGCTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 TCAAATCCATCA-TTGATGGATCA-CTTTTCCAGTGAGTTCATAATGAGAAGAACTCATCTGAAG
111250 AAGGAAGAAAAGTTCATAATGAGAAGAACTTTGTTCAA-CTTTTGC
64 AAGGAAGAAAAGTTCATAATGAGAAGAA-TTTGTTCAACCTTTTGC
* *
111295 -CAGAT-CATCATTGATGGATCAACATTTCCAGT-AGTTCATAATGAGAAGAACTCGTCATCTGA
1 TCAAATCCATCATTGATGGATC-ACTTTTCCAGTGAGTTCATAATGAGAAGAA--C-TCATCTGA
*
111357 AG-ATGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAA
62 AGAAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAA
111395 TTTTGAAATA
Statistics
Matches: 395, Mismatches: 12, Indels: 42
0.88 0.03 0.09
Matches are distributed among these distances:
106 35 0.09
107 52 0.13
108 133 0.34
109 42 0.11
110 32 0.08
111 67 0.17
112 34 0.09
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (108 bp):
TCAAATCCATCATTGATGGATCACTTTTCCAGTGAGTTCATAATGAGAAGAACTCATCTGAAGAA
GGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:111734 original size:174 final size:179
Alignment explanation
Indices: 111516--111868 Score: 562
Period size: 179 Copynumber: 2.0 Consensus size: 179
111506 CAGAGAAGAC
111516 TTATTCAACCTTTGAAGATCTATCACAAAAGAAAAAGGTCAACATCATCCCCAGC-GAAAGTTCA
1 TTATTCAACCTTTGAAGATCTATCACAAAAGAAAAAGGTCAACATCATCCCCAGCGGAAAGTTCA
*
111580 TAAT-G-AGAACTCATCTGA-AGAGAGAGAAGAATTATTCAATCTCCATACTAATCAAGTGAAAT
66 TAATAGAAGAACTCACCTGACAGAGAGAGAAGAATTATTCAATCTCCATACTAATCAAGTGAAAT
111642 CAAATG-AAAAAA-TTAT-ATC-TTT-TCTTTGCTCTATTCTTATAGAA
131 CAAATGAAAAAAACTTATCATCTTTTCTCTTTGCTCTATTCTTATAGAA
111686 TTATTCAACCTTTTGAATGATTCTATCACAGAAAGAAAAAGGTCAACATCATCCCCAGCGGAAAG
1 TTATTCAACC-TTTGAA-GA-TCTATCACA-AAAGAAAAAGGTCAACATCATCCCCAGCGGAAAG
111751 TTCATAATGAGAAGAACTCACCTGACAGAGAGAGAAGAATTATTCAATCTCCATACTAATCAAGT
62 TTCATAAT-AGAAGAACTCACCTGACAGAGAGAGAAGAATTATTCAATCTCCATACTAATCAAGT
111816 GAAATCAAATGAAAAAAAAACTTATCATCTTTTCGTCTTTGCTCTATTCTTAT
126 GAAATCAAATG--AAAAAAACTTATCATCTTTTC-TCTTTGCTCTATTCTTAT
111869 TAAGAATAAG
Statistics
Matches: 165, Mismatches: 1, Indels: 17
0.90 0.01 0.09
Matches are distributed among these distances:
170 10 0.06
171 6 0.04
172 2 0.01
173 9 0.05
174 28 0.17
175 13 0.08
177 1 0.01
178 12 0.07
179 50 0.30
182 6 0.04
183 4 0.02
184 3 0.02
185 3 0.02
187 18 0.11
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (179 bp):
TTATTCAACCTTTGAAGATCTATCACAAAAGAAAAAGGTCAACATCATCCCCAGCGGAAAGTTCA
TAATAGAAGAACTCACCTGACAGAGAGAGAAGAATTATTCAATCTCCATACTAATCAAGTGAAAT
CAAATGAAAAAAACTTATCATCTTTTCTCTTTGCTCTATTCTTATAGAA
Found at i:111937 original size:3 final size:3
Alignment explanation
Indices: 111914--111990 Score: 77
Period size: 3 Copynumber: 25.7 Consensus size: 3
111904 TTTTCATTTT
* *
111914 TTA TT- TTA TTT TTA TTTA TTA TTA TTA TAA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
111958 ATA TAA TTA TAA TTA TTA TTA TTA TATA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT
111991 TAATATTACA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 4 0.07
3 51 0.84
4 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:111972 original size:26 final size:26
Alignment explanation
Indices: 111919--111998 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 26
111909 ATTTTTTATT
* *
111919 TTATTTTTATT-TATTATTATTATAA
1 TTATTATTATTATAATATTATTATAA
*
111944 TTATTATTATTATAATATAATTATAA
1 TTATTATTATTATAATATTATTATAA
111970 TTATTATTATTAT-ATATTATT-TAA
1 TTATTATTATTATAATATTATTATAA
111994 -TATTA
1 TTATTA
111999 CAAGCCCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.10
24 3 0.06
25 17 0.34
26 25 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTATTATTATAATATTATTATAA
Found at i:111976 original size:23 final size:22
Alignment explanation
Indices: 111929--111989 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
111919 TTATTTTTAT
* * *
111929 TTATTATTAT-TATAATTATTA
1 TTATTATAATATATTATAATTA
111950 TTATTATAATATAATTATAATTA
1 TTATTATAATAT-ATTATAATTA
*
111973 TTATTATTATATATTAT
1 TTATTATAATATATTAT
111990 TTAATATTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.26
22 6 0.18
23 19 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTATAATATATTATAATTA
Found at i:112389 original size:6 final size:6
Alignment explanation
Indices: 112378--112432 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
112368 TGCGAGCAAG
* * *
112378 AGAGAC AGAGAC AGAGAC A-A-A- AGAGAC AGAGAC AGAGAG AAAGAG
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC
112423 AGAGAC AGAG
1 AGAGAC AGAG
112433 CCGGGAAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
3 1 0.02
4 2 0.05
5 2 0.05
6 37 0.88
ACGTcount: A:0.55, C:0.11, G:0.35, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:112403 original size:21 final size:20
Alignment explanation
Indices: 112378--112432 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
112368 TGCGAGCAAG
112378 AGAGACAGAGACAGAGACAAA
1 AGAGACAGAGACAGAGA-AAA
*
112399 AGAGACAGAGACAGAGAGAA
1 AGAGACAGAGACAGAGAAAA
112419 AGAG--AGAGACAGAG
1 AGAGACAGAGACAGAG
112433 CCGGGAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 10 0.30
20 6 0.18
21 17 0.52
ACGTcount: A:0.55, C:0.11, G:0.35, T:0.00
Consensus pattern (20 bp):
AGAGACAGAGACAGAGAAAA
Found at i:113340 original size:13 final size:13
Alignment explanation
Indices: 113324--113370 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
113314 ATATAATAAA
113324 TAAATATTTATTT
1 TAAATATTTATTT
*
113337 TAAATAAATTATTT
1 TAAAT-ATTTATTT
113351 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
113364 TCAATAT
1 TAAATAT
113371 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:116939 original size:24 final size:24
Alignment explanation
Indices: 116912--116957 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
116902 TGTTCGATCA
116912 TTTATATGTTCGCGAACATGTTAG
1 TTTATATGTTCGCGAACATGTTAG
**
116936 TTTATATGTTCTTGAACATGTT
1 TTTATATGTTCGCGAACATGTT
116958 GATTTGCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (24 bp):
TTTATATGTTCGCGAACATGTTAG
Found at i:119972 original size:158 final size:156
Alignment explanation
Indices: 119506--120010 Score: 596
Period size: 158 Copynumber: 3.3 Consensus size: 156
119496 CCTGATTTTA
* * * * * * *
119506 TTATTTCTTCAATT-ACTCCTTCATTTTAAGTCATTTTTTTACTAAATTTGAACCACGTGCTCAT
1 TTATTTCTTCAATTCA-TCATTTATTTTAAGTCCTTTTTTTACCAAATTTGAGCCACATGCTCCT
* * * *
119570 AAATCATAGCATAATACATGTTTACTTTCAATTTCTCTTTTTGATA-ACAATTTTTTATTTTTCA
65 AAA-CATAGTAGAATACATGTGTACTTTCAATTTCTCTTTTTGGTACA-AATTTTTTATTTTTCA
119634 ATTTAGTCCTTCAATTTTTCATAATCTCC
128 ATTTAGTCCTTCAATTTTTCATAATCTCC
* * * ** * *
119663 TTATTTCTTCCATTCGTCATTTATTTTAAGT-CTATTTTTACCAAATTTGAGTTATATGCACCTA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCCTTTTTTTACCAAATTTGAGCCACATGCTCCTA
* * * * * *
119727 AAC---GTAGAATGCATTTGTACTTTCAATTCCTCTTTTT-G-ATAATTTTTTTATTTTTTAATT
66 AACATAGTAGAATACATGTGTACTTTCAATTTCTCTTTTTGGTACAAATTTTTTATTTTTCAATT
*
119787 TAGTCCTTCAAATTTTT-ATAATATCC
131 TAGTCCTTC-AATTTTTCATAATCTCC
* * *
119813 TTATTTCTTCAATTCATTATTTATTTTAAATCCTTTTTTTACCAAATGTGAGCCACATGCTCCTA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCCTTTTTTTACCAAATTTGAGCCACATGCTCCTA
119878 AACCATAGTAGAATACATGTGTACTTTCAATTTCTCTTTTTGGTTACAAATTTTTTATTTTTCAA
66 AA-CATAGTAGAATACATGTGTACTTTCAATTTCTCTTTTTGG-TACAAATTTTTTATTTTTCAA
*
119943 TTTAGTCCTTCAGTTTTTCATAATCTCC
129 TTTAGTCCTTCAATTTTTCATAATCTCC
* ** *
119971 TTATTCCTTCAATTTGTCATTTATTTTAAGTTCTTTTTTT
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCCTTTTTTT
120011 TTTTACCAAA
Statistics
Matches: 288, Mismatches: 48, Indels: 23
0.80 0.13 0.06
Matches are distributed among these distances:
150 62 0.22
151 37 0.13
152 29 0.10
155 32 0.11
156 26 0.09
157 32 0.11
158 70 0.24
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.51
Consensus pattern (156 bp):
TTATTTCTTCAATTCATCATTTATTTTAAGTCCTTTTTTTACCAAATTTGAGCCACATGCTCCTA
AACATAGTAGAATACATGTGTACTTTCAATTTCTCTTTTTGGTACAAATTTTTTATTTTTCAATT
TAGTCCTTCAATTTTTCATAATCTCC
Found at i:120254 original size:21 final size:20
Alignment explanation
Indices: 120224--120263 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
120214 TCCTTAAAAT
120224 ATAATATTATGAATATATTTC
1 ATAATATTAT-AATATATTTC
* *
120245 ATAATTTTATATTATATTT
1 ATAATATTATAATATATTT
120264 TATTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
ATAATATTATAATATATTTC
Found at i:128536 original size:16 final size:18
Alignment explanation
Indices: 128515--128552 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
128505 AACGTCTTTT
128515 AAAAACA-ATTTTAAGA-
1 AAAAACATATTTTAAGAC
*
128531 AAAAACATTTTTTAAGAC
1 AAAAACATATTTTAAGAC
128549 AAAA
1 AAAA
128553 GTTAGTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAACATATTTTAAGAC
Found at i:128966 original size:14 final size:15
Alignment explanation
Indices: 128947--128980 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
128937 TTTAAGAAAA
128947 TATAATAA-AATATT
1 TATAATAATAATATT
128961 TATAATAATAATATT
1 TATAATAATAATATT
128976 T-TAAT
1 TATAAT
128981 CCTTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATAATAATATT
Found at i:129365 original size:19 final size:19
Alignment explanation
Indices: 129327--129365 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
129317 ATTTTAAAAG
*
129327 TTTTTTTATAATATATAAT
1 TTTTTTTATAATATACAAT
129346 TTTTTTTAGTAA-ATACAAT
1 TTTTTTTA-TAATATACAAT
129365 T
1 T
129366 GAAATATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTTTATAATATACAAT
Found at i:129419 original size:2 final size:2
Alignment explanation
Indices: 129414--129450 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
129404 AAATTAATGT
*
129414 TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
129451 TAACATGACT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:129451 original size:12 final size:12
Alignment explanation
Indices: 129417--129456 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
129407 TTAATGTTAT
*
129417 ATATATATATATAT
1 ATATATAT-TA-AC
129431 ATATATATTAAC
1 ATATATATTAAC
129443 ATATATATTAAC
1 ATATATATTAAC
129455 AT
1 AT
129457 GACTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 15 0.60
13 2 0.08
14 8 0.32
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATATATTAAC
Found at i:130793 original size:15 final size:16
Alignment explanation
Indices: 130775--130819 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
130765 ATATATGTAT
130775 TAATAATA-ATAATAA
1 TAATAATATATAATAA
130790 TAATAA-ATATAAT-A
1 TAATAATATATAATAA
130804 T-ATATATATATAATAA
1 TAATA-ATATATAATAA
130820 ATCCCAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.12
14 4 0.15
15 18 0.69
16 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATATATAATAA
Found at i:132135 original size:11 final size:10
Alignment explanation
Indices: 132095--132160 Score: 54
Period size: 9 Copynumber: 7.1 Consensus size: 10
132085 ACCCTCCTTC
132095 TTCA-TTTTT
1 TTCATTTTTT
132104 TT-ATTTTTT
1 TTCATTTTTT
*
132113 TTTA-TTTTT
1 TTCATTTTTT
*
132122 TTCCTTTTTCT
1 TTCATTTTT-T
132133 TTCA-TTTTT
1 TTCATTTTTT
132142 TT-A-TTTTT
1 TTCATTTTTT
*
132150 TCCATTTTTT
1 TTCATTTTTT
132160 T
1 T
132161 CTTCAATCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
8 8 0.17
9 20 0.43
10 15 0.32
11 4 0.09
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (10 bp):
TTCATTTTTT
Found at i:132158 original size:10 final size:10
Alignment explanation
Indices: 132097--132161 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 10
132087 CCTCCTTCTT
132097 CATTTTTTT-
1 CATTTTTTTC
*
132106 -ATTTTTTTT
1 CATTTTTTTC
*
132115 TATTTTTTTC
1 CATTTTTTTC
*
132125 C-TTTTTCTTT
1 CATTTTT-TTC
132135 CATTTTTTT-
1 CATTTTTTTC
132144 -A-TTTTTTC
1 CATTTTTTTC
132152 CATTTTTTTC
1 CATTTTTTTC
132162 TTCAATCATA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
7 6 0.13
8 9 0.20
9 6 0.13
10 20 0.43
11 5 0.11
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (10 bp):
CATTTTTTTC
Found at i:147984 original size:17 final size:18
Alignment explanation
Indices: 147962--148000 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
147952 AACGTCTTTT
147962 AAAAACA-ATTTTAAGAA
1 AAAAACATATTTTAAGAA
*
147979 AAAAACATTTTTTAAGAA
1 AAAAACATATTTTAAGAA
147997 AAAA
1 AAAA
148001 GTTAGTCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAACATATTTTAAGAA
Found at i:148409 original size:19 final size:18
Alignment explanation
Indices: 148364--148410 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
148354 TTTTTACATG
148364 AAATAATATAATAATTTT
1 AAATAATATAATAATTTT
*
148382 AAGAAAATATAA-AATATTT
1 AA-ATAATATAATAAT-TTT
148401 ATAATAATAT
1 A-AATAATAT
148411 TTTAATCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 5 0.21
19 18 0.75
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATAATATAATAATTTT
Found at i:150192 original size:12 final size:13
Alignment explanation
Indices: 150177--150225 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
150167 ATATGTATTA
150177 ATAATA-ATAAAT
1 ATAATATATAAAT
150189 ATAATATAT-AAT
1 ATAATATATAAAT
*
150201 ATATATATATATAT
1 ATA-ATATATAAAT
150215 ATATATATATA
1 ATA-ATATATA
150226 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
12 12 0.36
13 8 0.24
14 13 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAATATATAAAT
Found at i:150204 original size:2 final size:2
Alignment explanation
Indices: 150187--150226 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
150177 ATAATAATAA
150187 AT AT A- AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
150227 TTTTTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:150323 original size:20 final size:20
Alignment explanation
Indices: 150298--150337 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
150288 TCCTTCTTAA
150298 TTGTTCTTGTAGTCGTAGAT
1 TTGTTCTTGTAGTCGTAGAT
150318 TTGTTCTTGTAGTCGTAGAT
1 TTGTTCTTGTAGTCGTAGAT
150338 GTAGCAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (20 bp):
TTGTTCTTGTAGTCGTAGAT
Done.