Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015239.1 Kokia drynarioides strain JFW-HI SEQ_130284, 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: 106099
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Warning! 261 characters in sequence are not A, C, G, or T
Found at i:165 original size:37 final size:38
Alignment explanation
Indices: 105--197 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 38
95 CGGATAGATT
*
105 CGATGAGGTACTGGGTACCACTTTA-CTTCG-ACTAGGC
1 CGATGAGGCACTGGGTACCACTTTATCTTCGAACTA-GC
* ** *
142 CGATGAGACACTGGGTATTACTTTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTACCACTTTA-T-CTTCGAACTAGC
182 CGATGAGGCACTGGGT
1 CGATGAGGCACTGGGT
198 GTCATTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 21 0.46
40 21 0.46
41 4 0.09
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (38 bp):
CGATGAGGCACTGGGTACCACTTTATCTTCGAACTAGC
Found at i:9211 original size:4 final size:4
Alignment explanation
Indices: 9202--9269 Score: 66
Period size: 4 Copynumber: 16.8 Consensus size: 4
9192 AATAAACGGA
* * *
9202 AAAG AAAG AAAGG AAAG AAAG AAAG AAAG GAAG AATG AGAGG AAAG AAAG
1 AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG
* *
9252 -AAG AAGG AAAA AAAG AAA
1 AAAG AAAG AAAG AAAG AAA
9270 ATGTGTTTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.81
5 7 0.13
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:9224 original size:17 final size:16
Alignment explanation
Indices: 9202--9269 Score: 66
Period size: 17 Copynumber: 4.2 Consensus size: 16
9192 AATAAACGGA
*
9202 AAAGAAAGAAAGGAAAG
1 AAAGAAGGAAA-GAAAG
* *
9219 AAAGAAAGAAAGGAAG
1 AAAGAAGGAAAGAAAG
*
9235 AATGAGAGGAAAGAAAG
1 AAAGA-AGGAAAGAAAG
*
9252 -AAGAAGGAAAAAAAG
1 AAAGAAGGAAAGAAAG
9267 AAA
1 AAA
9270 ATGTGTTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
15 10 0.23
16 13 0.30
17 20 0.47
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.01
Consensus pattern (16 bp):
AAAGAAGGAAAGAAAG
Found at i:9244 original size:29 final size:27
Alignment explanation
Indices: 9203--9269 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
9193 ATAAACGGAA
9203 AAGAAAGAAAGGAAAGAAAGAAAGAAAGG
1 AAGAAAGAAAGGAAAGAAAG-AAG-AAGG
* *
9232 AAGAATGAGAGGAAAGAAAGAAGAAGG
1 AAGAAAGAAAGGAAAGAAAGAAGAAGG
*
9259 AAAAAAAGAAA
1 -AAGAAAGAAA
9270 ATGTGTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 4 0.12
28 10 0.31
29 18 0.56
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (27 bp):
AAGAAAGAAAGGAAAGAAAGAAGAAGG
Found at i:10886 original size:711 final size:701
Alignment explanation
Indices: 9524--10935 Score: 2734
Period size: 711 Copynumber: 2.0 Consensus size: 701
9514 AAAAATTTTT
9524 GACGTTGTGGGAGAAGGATCTCGAAACTTTTCTACAAGTTTCCAGTTTCGATAGATCCCATCAAA
1 GACGTTGTGGGAGAAGGATCTCGAAACTTTTCTACAAGTTTCCAGTTTCGATAGATCCCATCAAA
9589 TTCACCGAGATGGAACTTGTAGACGACGAAGACGTGGAGACAATGATCGCTCTTTATTGTTCGAA
66 TTCACCGAGATGGAACTTGTAGACGACGAAGACGTGGAGACAATGATCGCTCTTTATTGTTCGAA
9654 TCAAAGTGACCCAAATGCACCAGTTCAATTGTTTGCTGAGTTAGTTGATGTGAAACCTTTACAAA
131 TCAAAGTGACCCAAATGCACCAGTTCAATTGTTTGCTGAGTTAGTTGATGTGAAACCTTTACAAA
9719 ATGAAGATTTAACTCCGTGTATGGTGGTTCCAGTATCGTACATTGAAAGTCAATCAATCGTACGT
196 ATGAAGATTTAACTCCGTGTATGGTGGTTCCAGTATCGTACATTGAAAGTCAATCAATCGTACGT
9784 GGGCTAGACATCGATCTTAATGCTGCTGCACCCGAGAATGATGCAGATCAAGATGGTGGATATGA
261 GGGCTAGACATCGATCTTAATGCTGCTGCACCCGAGAATGATGCAGATCAAGATGGTGGATATGA
9849 TAGTAGTATTCCTTCTGATAATGAAGTCAATATTGATAGTGATCCGGATGTGGATGAGGTCTCAG
326 TAGTAGTATTCCTTCTGATAATGAAGTCAATATTGATAGTGATCCGGATGTGGATGAGGTCTCAG
9914 ATGATATTAACGAAGAAGGGGCGAATGACGATGAATATCCAGTTACACATATTGTGATGCACAAT
391 ATGATATTAACGAAGAAGGGGCGAATGACGATGAATATCCAGTTACACATATTGTGATGCACAAT
9979 AATCCTCTTGGGGCACACATGTCGCTTATAAACTCCGATGCGACACATGCCGAGTTCGCGGAATA
456 AATCCTCTTGGGGCACACATGTCGCTTATAAACTCCGATGCGACACATGCCGAGTTCGCGGAATA
10044 CCTTGAAATAGTACCTGCTCACCGATTGACCGTAGCAGCAGATTGTGAAGAGTTGTTTGTGGGCC
521 CCTTGAAATAGTACCTGCTCACCGATTGACCGTAGCAGCAGATTGTGAAGAGTTGTTTGTGGGCC
10109 AAAAATTTTAATCCAAGGAAGAATGCATATTTGCTATTAAGCGATATAGCATGAATGTGTCGATA
586 AAAAATTTTAATCCAAGGAAGAATGCATATTTGCTATTAAGCGATATAGCATGAATGTGTCGATA
10174 GACTACAAAGTCGCAGTGTCTAAACCGACATTGTATATTGGAGAGTGCTGG
651 GACTACAAAGTCGCAGTGTCTAAACCGACATTGTATATTGGAGAGTGCTGG
10225 NNNNNNNNNNGACGTTGTGGGAGAAGGATCTCGAAACTTTTCTACAAGTTTCCAGTTTCGATAGA
1 ----------GACGTTGTGGGAGAAGGATCTCGAAACTTTTCTACAAGTTTCCAGTTTCGATAGA
10290 TCCCATCAAATTCACCGAGATGGAACTTGTAGACGACGAAGACGTGGAGACAATGATCGCTCTTT
56 TCCCATCAAATTCACCGAGATGGAACTTGTAGACGACGAAGACGTGGAGACAATGATCGCTCTTT
10355 ATTGTTCGAATCAAAGTGACCCAAATGCACCAGTTCAATTGTTTGCTGAGTTAGTTGATGTGAAA
121 ATTGTTCGAATCAAAGTGACCCAAATGCACCAGTTCAATTGTTTGCTGAGTTAGTTGATGTGAAA
10420 CCTTTACAAAATGAAGATTTAACTCCGTGTATGGTGGTTCCAGTATCGTACATTGAAAGTCAATC
186 CCTTTACAAAATGAAGATTTAACTCCGTGTATGGTGGTTCCAGTATCGTACATTGAAAGTCAATC
10485 AATCGTACGTGGGCTAGACATCGATCTTAATGCTGCTGCACCCGAGAATGATGCAGATCAAGATG
251 AATCGTACGTGGGCTAGACATCGATCTTAATGCTGCTGCACCCGAGAATGATGCAGATCAAGATG
10550 GTGGATATGATAGTAGTATTCCTTCTGATAATGAAGTCAATATTGATAGTGATCCGGATGTGGAT
316 GTGGATATGATAGTAGTATTCCTTCTGATAATGAAGTCAATATTGATAGTGATCCGGATGTGGAT
10615 GAGGTCTCAGATGATATTAACGAAGAAGGGGCGAATGACGATGAATATCCAGTTACACATATTGT
381 GAGGTCTCAGATGATATTAACGAAGAAGGGGCGAATGACGATGAATATCCAGTTACACATATTGT
10680 GATGCACAATAATCCTCTTGGGGCACACATGTCGCTTATAAACTCCGATGCGACACATGCCGAGT
446 GATGCACAATAATCCTCTTGGGGCACACATGTCGCTTATAAACTCCGATGCGACACATGCCGAGT
10745 TCGCGGAATACCTTGAAATAGTACCTGCTCACCGATTGACCGTAGCAGCAGATTGTGAAGAGTTG
511 TCGCGGAATACCTTGAAATAGTACCTGCTCACCGATTGACCGTAGCAGCAGATTGTGAAGAGTTG
10810 TTTGTGGGCCAAAAATTTTAATCCAAGGAAGAATGCATATTTGCTATTAAGCGATATAGCATGAA
576 TTTGTGGGCCAAAAATTTTAATCCAAGGAAGAATGCATATTTGCTATTAAGCGATATAGCATGAA
10875 TGTGTCGATAGACTACAAAGTCGCAGTGTCTAAACCGACATTGTATATTGGAGAGTGCTGG
641 TGTGTCGATAGACTACAAAGTCGCAGTGTCTAAACCGACATTGTATATTGGAGAGTGCTGG
10936 NNNNNNNNNN
Statistics
Matches: 701, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
711 701 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (701 bp):
GACGTTGTGGGAGAAGGATCTCGAAACTTTTCTACAAGTTTCCAGTTTCGATAGATCCCATCAAA
TTCACCGAGATGGAACTTGTAGACGACGAAGACGTGGAGACAATGATCGCTCTTTATTGTTCGAA
TCAAAGTGACCCAAATGCACCAGTTCAATTGTTTGCTGAGTTAGTTGATGTGAAACCTTTACAAA
ATGAAGATTTAACTCCGTGTATGGTGGTTCCAGTATCGTACATTGAAAGTCAATCAATCGTACGT
GGGCTAGACATCGATCTTAATGCTGCTGCACCCGAGAATGATGCAGATCAAGATGGTGGATATGA
TAGTAGTATTCCTTCTGATAATGAAGTCAATATTGATAGTGATCCGGATGTGGATGAGGTCTCAG
ATGATATTAACGAAGAAGGGGCGAATGACGATGAATATCCAGTTACACATATTGTGATGCACAAT
AATCCTCTTGGGGCACACATGTCGCTTATAAACTCCGATGCGACACATGCCGAGTTCGCGGAATA
CCTTGAAATAGTACCTGCTCACCGATTGACCGTAGCAGCAGATTGTGAAGAGTTGTTTGTGGGCC
AAAAATTTTAATCCAAGGAAGAATGCATATTTGCTATTAAGCGATATAGCATGAATGTGTCGATA
GACTACAAAGTCGCAGTGTCTAAACCGACATTGTATATTGGAGAGTGCTGG
Found at i:11247 original size:78 final size:77
Alignment explanation
Indices: 11157--11438 Score: 244
Period size: 78 Copynumber: 3.6 Consensus size: 77
11147 AAAATCACCG
* * *
11157 TCAGCCAATCTCTTACTCCGAGCTTCGGGTAGATTGCAGCCATTCAATCTCTTACCCCGAGTTTG
1 TCAGCCAATCTCTTAC-CCGAGCTTCGGGTAGATTGCAGCCATTCGATCTATTACCCCGAGCTTG
11222 GGGTCGATCTCCA
65 GGGTCGATCTCCA
* * * * * * * ** * *
11235 TCAGCTAATCTCTTACCCCAAGCCTCGAGTAGATTACAGCCTTTCGATCTTTTACCCTTACCCT-
1 TCAGCCAATCTCTTA-CCCGAGCTTCGGGTAGATTGCAGCCATTCGATCTATTACCCCGAGCTTG
*
11299 GGGACAGATCAT-CA
65 GGGTC-GATC-TCCA
* * * * *
11313 TCAGCCAATCTCTTACCTCGATCTTAGGGCAAATTGCAGCCATTCGATCTATTACCCCGAGCCTG
1 TCAGCCAATCTCTTACC-CGAGCTTCGGGTAGATTGCAGCCATTCGATCTATTACCCCGAG-CTT
* *
11378 GGGGTAGATCACCA
64 GGGGTCGATCTCCA
* * * * *
11392 TCAGCCAATCTCTTACCTCGATCATGGGGCAGATTGCAGGCATTCGA
1 TCAGCCAATCTCTTACC-CGAGCTTCGGGTAGATTGCAGCCATTCGA
11439 AGCAATAAAG
Statistics
Matches: 160, Mismatches: 37, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
77 6 0.04
78 99 0.62
79 52 0.32
80 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (77 bp):
TCAGCCAATCTCTTACCCGAGCTTCGGGTAGATTGCAGCCATTCGATCTATTACCCCGAGCTTGG
GGTCGATCTCCA
Found at i:11863 original size:6 final size:6
Alignment explanation
Indices: 11852--11935 Score: 70
Period size: 6 Copynumber: 14.7 Consensus size: 6
11842 GACCCATTTG
* * *
11852 TTAAAT TTAAAT TT-AAT TTAAGT TTAAAT TT-AGT TTAAAT ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
11898 TT-ATT TTGAAT TTAAA- TT-CAT TATAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTAA
11936 TTAAAAATTA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
4 1 0.02
5 16 0.26
6 41 0.67
7 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:11877 original size:17 final size:17
Alignment explanation
Indices: 11852--11937 Score: 102
Period size: 17 Copynumber: 5.1 Consensus size: 17
11842 GACCCATTTG
11852 TTAAATTTAAATTTAAT
1 TTAAATTTAAATTTAAT
* *
11869 TTAAGTTTAAATTTAGT
1 TTAAATTTAAATTTAAT
* *
11886 TTAAATATAAATTTATT
1 TTAAATTTAAATTTAAT
* *
11903 TTGAATTTAAA-TTCAT
1 TTAAATTTAAATTTAAT
11919 TATAAATTTAAATTTAAT
1 T-TAAATTTAAATTTAAT
11937 T
1 T
11938 AAAAATTATA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
16 4 0.07
17 47 0.84
18 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAAATTTAAATTTAAT
Found at i:13370 original size:36 final size:36
Alignment explanation
Indices: 13313--13415 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
13303 GGTATTTATA
* * * *
13313 GGGCATCAAAACGACGTCGTTTTGGCCTTGGTGCCT
1 GGGCCTCAAAACGACGCCGTTTTGGCCTTAGTGCCC
13349 GGGCCTCAAAACGACGCCGTTTTGGCCTTAGTGCCC
1 GGGCCTCAAAACGACGCCGTTTTGGCCTTAGTGCCC
* * *
13385 AGGCCTAAAAATGACGCCGTTTTGAGCCTTA
1 GGGCCTCAAAACGACGCCGTTTTG-GCCTTA
13416 CCCATTTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 53 0.90
37 6 0.10
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (36 bp):
GGGCCTCAAAACGACGCCGTTTTGGCCTTAGTGCCC
Found at i:13939 original size:29 final size:29
Alignment explanation
Indices: 13813--13998 Score: 164
Period size: 30 Copynumber: 6.3 Consensus size: 29
13803 TAAAAGGTCC
* *
13813 CTAAACTTTCCAAAAATCACATTTTAGCCC-
1 CTAAACTTTTC-AAAATTACATTTT-GCCCT
* ** *
13843 CTAAACTTTTCCAAAATTGCATTTTAACCA
1 CTAAACTTTT-CAAAATTACATTTTGCCCT
* *
13873 CTAAACTTTTCCAAAATTTCATTTTCCCCT
1 CTAAACTTTT-CAAAATTACATTTTGCCCT
13903 -TAAACTTTTCAAAATTACATTTTGCCCT
1 CTAAACTTTTCAAAATTACATTTTGCCCT
* *
13931 CTAATCTTTTCAAAAATTACATTTTTACCC-
1 CTAAACTTTTC-AAAATTACA-TTTTGCCCT
* *
13961 CCAAACTTCTTTAAAATTACATTTTTGCCCT
1 CTAAACTT-TTCAAAATTACA-TTTTGCCCT
13992 C-AAACTT
1 CTAAACTT
13999 CAAAAAATTA
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
28 17 0.13
29 20 0.15
30 84 0.64
31 11 0.08
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (29 bp):
CTAAACTTTTCAAAATTACATTTTGCCCT
Found at i:13940 original size:58 final size:59
Alignment explanation
Indices: 13813--14019 Score: 210
Period size: 58 Copynumber: 3.5 Consensus size: 59
13803 TAAAAGGTCC
* * * ** *
13813 CTAAACTTTCCAAAAATCACA-TTTTAGCCCCTAAACTTTTCCAAAATTGCATTTTAACCA
1 CTAAACTTTTCAAAAATTACATTTTTA-CCCCTAAACTTTT-CAAAATTACATTTTGCCCT
* *
13873 CTAAACTTTTCCAAAATTTCA-TTTT-CCCCTTAAACTTTTCAAAATTACATTTTGCCCT
1 CTAAACTTTTCAAAAATTACATTTTTACCCC-TAAACTTTTCAAAATTACATTTTGCCCT
* * *
13931 CTAATCTTTTCAAAAATTACATTTTTACCCCCAAACTTCTTTAAAATTACATTTTTGCCCT
1 CTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTT-TTCAAAATTACA-TTTTGCCCT
*
13992 C-AAAC--TTCAAAAAATTAAATTTTTACCC
1 CTAAACTTTTC-AAAAATTACATTTTTACCC
14020 TCGAACTTCT
Statistics
Matches: 126, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
58 40 0.32
59 37 0.29
60 39 0.31
61 10 0.08
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (59 bp):
CTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTTTCAAAATTACATTTTGCCCT
Found at i:13967 original size:88 final size:89
Alignment explanation
Indices: 13814--13985 Score: 215
Period size: 88 Copynumber: 1.9 Consensus size: 89
13804 AAAAGGTCCC
* * *
13814 TAAACTTTCCAAAAATCACATTTTAGCCCCTAAACTTTTCCAAAATTGCATTTTAACCACTAAAC
1 TAAACTTTCCAAAAATCACATTTTAGCCCCTAAACTTTTCAAAAATTACATTTTAACCACCAAAC
*
13879 TT-TTCCAAAATTTCATTTTCCCCT
66 TTCTT-CAAAATTACATTTTCCCCT
* * * * *
13903 TAAACTTTTC-AAAATTACATTTT-GCCCTCTAATCTTTTCAAAAATTACATTTTTACCCCCAAA
1 TAAACTTTCCAAAAATCACATTTTAGCCC-CTAAACTTTTCAAAAATTACATTTTAACCACCAAA
*
13966 CTTCTTTAAAATTACATTTT
65 CTTCTTCAAAATTACATTTT
13986 TGCCCTCAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
87 4 0.06
88 56 0.79
89 11 0.15
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (89 bp):
TAAACTTTCCAAAAATCACATTTTAGCCCCTAAACTTTTCAAAAATTACATTTTAACCACCAAAC
TTCTTCAAAATTACATTTTCCCCT
Found at i:14006 original size:29 final size:29
Alignment explanation
Indices: 13811--14281 Score: 178
Period size: 29 Copynumber: 16.3 Consensus size: 29
13801 CTTAAAAGGT
*
13811 CCCT-AAACTTTCCAAAAATCACA-TTTTA
1 CCCTCAAAC-TTCCAAAAATTACATTTTTA
* *
13839 GCCC-CTAAACTTTTCC-AAAATTGCATTTTAA
1 -CCCTC-AAAC--TTCCAAAAATTACATTTTTA
* *
13870 CCACT-AAACTTTTCC-AAAATTTCA-TTTTC
1 CC-CTCAAAC--TTCCAAAAATTACATTTTTA
* * *
13899 CCCTTAAACTTTTC-AAAATTACA-TTTTG
1 CCCTCAAAC-TTCCAAAAATTACATTTTTA
* *
13927 CCCTCTAATCTTTTCAAAAATTACATTTTTA
1 CCCTC-AAAC-TTCCAAAAATTACATTTTTA
* ** *
13958 CCCCCAAACTTCTTTAAAATTACATTTTTG
1 CCCTCAAACTTC-CAAAAATTACATTTTTA
* *
13988 CCCTCAAACTTCAAAAAATTAAATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* * *
14017 CCCTCGAACTTCTAAAAATCACATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* * * * *
14046 GACC-CGAACATCCAAAAATCATATTTTTA
1 -CCCTCAAACTTCCAAAAATTACATTTTTA
*
14075 CCCTCAAACATCCAAAAATTAC-TATTTTA
1 CCCTCAAACTTCCAAAAATTACAT-TTTTA
* * *
14104 TCC-CAAA-TATCTAAAAAGATTATCATTTTGA
1 CCCTCAAACT-TC-CAAAA-ATTA-CATTTTTA
* * *
14135 CTC-CAAACTTTTCTAAAATTACCA-TTTTA
1 CCCTCAAAC-TTCCAAAAATTA-CATTTTTA
* * * *
14164 CCCACGAACGTCCAAAAATTGCATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* *
14193 ---T---ACATCCAAAAATTACCA-TTTTG
1 CCCTCAAACTTCCAAAAATTA-CATTTTTA
* * **
14216 CCCTCGAACATCCAAATTTTACCATTTTT-
1 CCCTCAAACTTCCAAAAATTA-CATTTTTA
* * *
14245 CCCTCAAATTTCCAAAAATCACATTTTCA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
*
14274 ACCTCAAA
1 CCCTCAAA
14282 TTTTAAGAAA
Statistics
Matches: 344, Mismatches: 66, Indels: 64
0.73 0.14 0.14
Matches are distributed among these distances:
23 16 0.05
24 2 0.01
26 1 0.00
28 39 0.11
29 164 0.48
30 88 0.26
31 31 0.09
32 2 0.01
33 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTTA
Found at i:14008 original size:59 final size:60
Alignment explanation
Indices: 13904--14044 Score: 166
Period size: 59 Copynumber: 2.4 Consensus size: 60
13894 TTTTCCCCTT
* * *
13904 AAACTT-TTCAAAATTACA-TTTTGCCCTCTAATCTTTTCAAAAATTACATTTTTACCCCC
1 AAACTTCTTAAAAATTACATTTTTGCCCTCTAAAC-TTTCAAAAATTAAATTTTTACCCCC
* *
13963 AAACTTCTTTAAAATTACATTTTTGCCCTC-AAAC-TTCAAAAAATTAAATTTTTACCCTC
1 AAACTTCTTAAAAATTACATTTTTGCCCTCTAAACTTTC-AAAAATTAAATTTTTACCCCC
* *
14022 GAACTTC-TAAAAATCACATTTTT
1 AAACTTCTTAAAAATTACATTTTT
14045 AGACCCGAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
58 17 0.24
59 31 0.43
60 14 0.19
61 10 0.14
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (60 bp):
AAACTTCTTAAAAATTACATTTTTGCCCTCTAAACTTTCAAAAATTAAATTTTTACCCCC
Found at i:14329 original size:29 final size:30
Alignment explanation
Indices: 14246--14330 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
14236 ACCATTTTTC
14246 CCTCAAA-TTTCCAAAAA-TCACATTTTCAA
1 CCTCAAATTTTCCAAAAATTCA-ATTTTCAA
*
14275 CCTCAAATTTT--AAGAAAGTTCGATTTT-AA
1 CCTCAAATTTTCCAA-AAA-TTCAATTTTCAA
*
14304 TCTCAAATTTTCCAAAAATTCAATTTT
1 CCTCAAATTTTCCAAAAATTCAATTTT
14331 GTTCCCCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
28 2 0.04
29 30 0.64
30 11 0.23
31 4 0.09
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (30 bp):
CCTCAAATTTTCCAAAAATTCAATTTTCAA
Found at i:23726 original size:29 final size:27
Alignment explanation
Indices: 23664--24123 Score: 359
Period size: 29 Copynumber: 15.7 Consensus size: 27
23654 TTCGAACATC
23664 CGGGAGTAAAATGGTAATTTTTGGAAGTGT
1 CGGG-GTAAAATGG-AATTTTTGGAAGT-T
23694 CGGGGTCAAAAAT-GAGATTTTTGGAAGTT
1 CGGGGT--AAAATGGA-ATTTTTGGAAGTT
*
23723 CGGGGTAAAATGGTAATTTTAGGAAGTT
1 CGGGGTAAAATGG-AATTTTTGGAAGTT
23751 CGAGGGTAAAATGGTAATTTTTGGAAGTTT
1 CG-GGGTAAAATGG-AATTTTTGGAAG-TT
* * *
23781 CGAGGTTAAAAATGGGACTTTTGGAAGTT
1 CG-GGGT-AAAATGGAATTTTTGGAAGTT
*
23810 CGAGGTAAAATGGTAATTTTTGGAAGTTT
1 CGGGGTAAAATGG-AATTTTTGGAAG-TT
* *
23839 CGAGGTAAAAATGGGATTTTTGGAAGTT
1 CGGGGT-AAAATGGAATTTTTGGAAGTT
23867 CGGGGGTAAAATGGTAATTTTTGGAAGTTT
1 C-GGGGTAAAATGG-AATTTTTGGAAG-TT
*** * *
23897 TAAGGTCAAAAATGGGATTTTTGGAAATT
1 CGGGGT--AAAATGGAATTTTTGGAAGTT
23926 CGAGGGTAAAATGGTAATTTTTGGAAGTTT
1 CG-GGGTAAAATGG-AATTTTTGGAAG-TT
* *
23956 TGGGGTCAAAAATGGGAA-TTTTGTAAGTT
1 CGGGGT--AAAAT-GGAATTTTTGGAAGTT
*
23985 CTAGGGTAAAATGGTAATTTTTGGAAGTTT
1 C-GGGGTAAAATGG-AATTTTTGGAAG-TT
*
24015 TGGGGTCAAAAATGGGAA-TTTTGGAAGTT
1 CGGGGT--AAAAT-GGAATTTTTGGAAGTT
24044 CGAGGGTAAAATGGTAATTTTTGGAAGTTT
1 CG-GGGTAAAATGG-AATTTTTGGAAG-TT
* * * *
24074 TGGGGTCAAAAATGGGATTTTTAGAAATGT
1 CGGGGT--AAAATGGAATTTTTGGAAGT-T
*
24104 GGGGGTAAAATGGTAATTTT
1 CGGGGTAAAATGG-AATTTT
24124 CAGACAGTTT
Statistics
Matches: 357, Mismatches: 36, Indels: 75
0.76 0.08 0.16
Matches are distributed among these distances:
27 16 0.04
28 65 0.18
29 127 0.36
30 105 0.29
31 40 0.11
32 4 0.01
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (27 bp):
CGGGGTAAAATGGAATTTTTGGAAGTT
Found at i:23810 original size:59 final size:59
Alignment explanation
Indices: 23671--24123 Score: 582
Period size: 59 Copynumber: 7.7 Consensus size: 59
23661 ATCCGGGAGT
* * *
23671 AAAATGGTAATTTTTGGAAGTGTCG-GGGTCAAAAAT-G-AGATTTTTGGAAG-TTCGGGGT--
1 AAAATGGGAA-TTTTGGAAGT-TCGAGGGT--AAAATGGTA-ATTTTTGGAAGTTTTGAGGTCA
* * *
23729 AAAATGGTAATTTTAGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGGAATTTT-GGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCA
* *
23789 AAAATGGGACTTTTGGAAGTTCGA-GGTAAAATGGTAATTTTTGGAAGTTTCGAGGT-A
1 AAAATGGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCA
* * *
23846 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTTAAGGTCA
1 AAAATGGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCA
* * *
23905 AAAATGGGATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCA
* * *
23964 AAAATGGGAATTTTGTAAGTTCTAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCA
*
24023 AAAATGGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCA
* * * *
24082 AAAATGGGATTTTTAGAAATGT-GGGGGTAAAATGGTAATTTT
1 AAAATGGGAATTTTGGAAGT-TCGAGGGTAAAATGGTAATTTT
24124 CAGACAGTTT
Statistics
Matches: 364, Mismatches: 21, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
56 5 0.01
57 42 0.12
58 90 0.25
59 214 0.59
60 13 0.04
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (59 bp):
AAAATGGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCA
Found at i:25949 original size:17 final size:18
Alignment explanation
Indices: 25940--26050 Score: 117
Period size: 17 Copynumber: 6.5 Consensus size: 18
25930 AAATAAATTT
25940 TAAATTTAAATTT-ATAA
1 TAAATTTAAATTTCATAA
*
25957 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTTCATAA
*
25974 CAAATTTAAATTT-ATAA
1 TAAATTTAAATTTCATAA
*
25991 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTTCATAA
*
26008 CAAATTTAAATTT-ATAA
1 TAAATTTAAATTTCATAA
* * *
26025 TAAACTT-AATTTTAAAA
1 TAAATTTAAATTTCATAA
26042 TAAATTTAA
1 TAAATTTAA
26051 GTTGATTGGG
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
16 7 0.09
17 67 0.87
18 3 0.04
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTCATAA
Found at i:26050 original size:34 final size:34
Alignment explanation
Indices: 25941--26033 Score: 177
Period size: 34 Copynumber: 2.7 Consensus size: 34
25931 AATAAATTTT
25941 AAATTTAAATTTATAATAAATTTAAATTTCAACC
1 AAATTTAAATTTATAATAAATTTAAATTTCAACC
25975 AAATTTAAATTTATAATAAATTTAAATTTCAACC
1 AAATTTAAATTTATAATAAATTTAAATTTCAACC
*
26009 AAATTTAAATTTATAATAAACTTAA
1 AAATTTAAATTTATAATAAATTTAA
26034 TTTTAAAATA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.41
Consensus pattern (34 bp):
AAATTTAAATTTATAATAAATTTAAATTTCAACC
Found at i:26649 original size:208 final size:208
Alignment explanation
Indices: 26353--26814 Score: 681
Period size: 208 Copynumber: 2.2 Consensus size: 208
26343 TCTATACCTT
* * * **
26353 ATCAGGAAGACAAATTTGGTTCACTTCTTAGTATCTCATCGGGAAGCTAACCTTTTATTGCTTTG
1 ATCAGGAAGACGAATTTGGTACACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCA
* * * * *
26418 ACCTGCTTCTCAATGTTTCATCAGGAAGTTGGGGTTTGAAGATTTTGCTCGTTTCGAGCCTCGTT
66 ACCTGCTTCTCAATGTCTCATCAGGAAGCTGAGGTTTGAAGATTTTGCTCGTTTCAAGCCTCGCT
* *
26483 TGGGTTTGATTTAGTCTTCTTCTCAGTATCTTATTCGAAAGATGACCGCATCGTTTTTAATTCGC
131 TGGGTTTAATTTAGTCTTCTTCTCAGTATCTTATCCGAAAGATGACCGCATCGTTTTTAATTCGC
26548 TTCTCCGTATCTC
196 TTCTCCGTATCTC
* * * * *
26561 ATCAGTAAGACGAATTTGGTACACCTCTCAGTATCTCATCAAGAAGCTAACCTTTTGTTGCTTCA
1 ATCAGGAAGACGAATTTGGTACACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCA
** * * *
26626 ATTTGCTTCTTAGTGTCTCATCAGGAAGCTGATGTTTGAAGATTTTGCTCGTTTCAAGCCTCGCT
66 ACCTGCTTCTCAATGTCTCATCAGGAAGCTGAGGTTTGAAGATTTTGCTCGTTTCAAGCCTCGCT
* * * *
26691 TGGGTTTAATTTAGTCTTCTTCTCAGTATCTTGTCCGGAAGATGATCGCATCGTTTTTAATTTGC
131 TGGGTTTAATTTAGTCTTCTTCTCAGTATCTTATCCGAAAGATGACCGCATCGTTTTTAATTCGC
*
26756 TTCTTCGTATCTC
196 TTCTCCGTATCTC
26769 ATCAGGAAGACGAATTTGGTACACTTCTTAGTATCTCATCAGGAAG
1 ATCAGGAAGACGAATTTGGTACACTTCTTAGTATCTCATCAGGAAG
26815 ACGAGTTTGG
Statistics
Matches: 223, Mismatches: 31, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
208 223 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (208 bp):
ATCAGGAAGACGAATTTGGTACACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCA
ACCTGCTTCTCAATGTCTCATCAGGAAGCTGAGGTTTGAAGATTTTGCTCGTTTCAAGCCTCGCT
TGGGTTTAATTTAGTCTTCTTCTCAGTATCTTATCCGAAAGATGACCGCATCGTTTTTAATTCGC
TTCTCCGTATCTC
Found at i:26805 original size:37 final size:37
Alignment explanation
Indices: 26755--26851 Score: 158
Period size: 37 Copynumber: 2.6 Consensus size: 37
26745 TTTTAATTTG
*
26755 CTTCTTCGTATCTCATCAGGAAGACGAATTTGGTACA
1 CTTCTTAGTATCTCATCAGGAAGACGAATTTGGTACA
* *
26792 CTTCTTAGTATCTCATCAGGAAGACGAGTTTGGTTCA
1 CTTCTTAGTATCTCATCAGGAAGACGAATTTGGTACA
*
26829 CTTCTCAGTATCTCATCAGGAAG
1 CTTCTTAGTATCTCATCAGGAAG
26852 CTAACCTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (37 bp):
CTTCTTAGTATCTCATCAGGAAGACGAATTTGGTACA
Found at i:27153 original size:204 final size:204
Alignment explanation
Indices: 26803--27395 Score: 1015
Period size: 204 Copynumber: 2.9 Consensus size: 204
26793 TTCTTAGTAT
*
26803 CTCATCAGGAAGACGAGTTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCT
1 CTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCT
*
26868 TCGACCTGCTTCTCAGTGTCTCATCAGGAAGGCGGGGTTCGAAGATTTCGCTTGTTTTGACCCTC
66 TCGACCTGCTTCTCAGTGTCTCATCAGGAAGGCGGGGTTCGAAGATTTCGCTCGTTTTGACCCTC
*
26933 GTTTGGATCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCT
131 GTTTGGATCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCACT
26998 CCTCTGTAC
196 CCTCTGTAC
*
27007 CTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCC
1 CTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCT
* * * * *
27072 TCGACCCGCTTCTCAATGTCTCTTCAGGAAGGCGGGGTTCAAAGATTTCGCTCGTTTTGAGCCTC
66 TCGACCTGCTTCTCAGTGTCTCATCAGGAAGGCGGGGTTCGAAGATTTCGCTCGTTTTGACCCTC
* **
27137 GTTTGGATCTTCTTCTCAGGGTCTCATCAGGAAGATGATCACATCGCTGTTTGGATCAATTCACT
131 GTTTGGATCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCACT
27202 CCTCTGTAC
196 CCTCTGTAC
* *
27211 CTCATCAGGAAGACGAATTTGGTTCACTTCTTAGTATCTCATCAGGAAGCTAACTTTTTATTGCT
1 CTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCT
* * *
27276 TCGACCTGCTTCTTAGTGTCTCATCAGGAAGGCGGGATTCGAAGATTTAGCTCGTTTTGACCCTC
66 TCGACCTGCTTCTCAGTGTCTCATCAGGAAGGCGGGGTTCGAAGATTTCGCTCGTTTTGACCCTC
* *
27341 GTTTGGGTCTTCTTCTCAGTGTCTTATCAGGAAGATGATCACATCGCTGTTTGTT
131 GTTTGGATCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTGTTTGTT
27396 AAATCACAAT
Statistics
Matches: 361, Mismatches: 28, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
204 361 1.00
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (204 bp):
CTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCT
TCGACCTGCTTCTCAGTGTCTCATCAGGAAGGCGGGGTTCGAAGATTTCGCTCGTTTTGACCCTC
GTTTGGATCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCACT
CCTCTGTAC
Found at i:28650 original size:13 final size:13
Alignment explanation
Indices: 28632--28658 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28622 AAGACTGCTT
28632 CCATACCGTATGC
1 CCATACCGTATGC
28645 CCATACCGTATGC
1 CCATACCGTATGC
28658 C
1 C
28659 AATGAGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (13 bp):
CCATACCGTATGC
Found at i:39350 original size:29 final size:30
Alignment explanation
Indices: 39287--39667 Score: 249
Period size: 30 Copynumber: 12.7 Consensus size: 30
39277 ATCCGAGAGT
*
39287 AAAATGGTAATTTTTGGAAGTGTTC--GGGTAA
1 AAAATGG-AATTTTTGGAA--GTTCGAGGGTCA
39318 AAAAT-GAGATTTTTGGAAGTTCGAGGGT-A
1 AAAATGGA-ATTTTTGGAAGTTCGAGGGTCA
* *
39347 AAAATGGTAATTTTAGGAAGTTTGAGGGT--
1 AAAATGG-AATTTTTGGAAGTTCGAGGGTCA
* * *
39376 TAAATGGTAATTTTTTGAAGTTTCGA-GGTCT
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGTCA
* * *
39407 AAAGTGGGATTTTTGGAAGTTCGGGGGT--
1 AAAATGGAATTTTTGGAAGTTCGAGGGTCA
* * *
39435 AAAATGGTAAATTTTAGAAGTTTCGAGGATCA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGTCA
39467 AAAATGGGAATTTTTTGGAAGTTTCGA-GGTCA
1 AAAAT-GGAA-TTTTTGGAAG-TTCGAGGGTCA
* * * *
39499 AAATTGGGATTTTTAGAAATTCGAGGGT--
1 AAAATGGAATTTTTGGAAGTTCGAGGGTCA
*
39527 AAAATGGTAATTTTTGGAAGTTTAGAGGGT--
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGTCA
***
39557 AAAATGGTAA-TTTTGGAAGTTTTTGGGTCA
1 AAAATGG-AATTTTTGGAAGTTCGAGGGTCA
* *
39587 AAAATGGGATTTTTGGAAGTTTTG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTCA
* * *
39617 AAAATGGGATTTTTAGAAATTCGAGGGT--
1 AAAATGGAATTTTTGGAAGTTCGAGGGTCA
39645 AAAATGGTAATTTTTGGATAGTT
1 AAAATGG-AATTTTTGGA-AGTT
39668 TAGGGACCTC
Statistics
Matches: 285, Mismatches: 40, Indels: 51
0.76 0.11 0.14
Matches are distributed among these distances:
28 29 0.10
29 75 0.26
30 133 0.47
31 17 0.06
32 15 0.05
33 16 0.06
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTCA
Found at i:39425 original size:59 final size:60
Alignment explanation
Indices: 39326--39670 Score: 263
Period size: 59 Copynumber: 5.8 Consensus size: 60
39316 AAAAAATGAG
* * * *
39326 ATTTTTGGAAG-TTCGAGGGT-AAAAATGGTAATTTTAGGAAGTTT-GAGGGTTAAATGGTA
1 ATTTTTAGAAGTTTCGA-GGTCAAAAATGG-GATTTTTGGAAGTTTAGAGGGTAAAATGGTA
* * * * *
39385 ATTTTTTGAAGTTTCGAGGTCTAAAGTGGGATTTTTGGAAG-TTCGGGGGTAAAATGGTA
1 ATTTTTAGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTAGAGGGTAAAATGGTA
* * *
39444 AATTTTAGAAGTTTCGAGGATCAAAAATGGGAATTTTTTGGAAGTTTCGA-GGTCAAAATTGG-G
1 ATTTTTAGAAGTTTCGAGG-TCAAAAATGGG-A-TTTTTGGAAGTTTAGAGGGT-AAAA-TGGTA
* *
39507 ATTTTTAGAA-ATTCGAGGGT--AAAATGGTAATTTTTGGAAGTTTAGAGGGTAAAATGGTA
1 ATTTTTAGAAGTTTCGA-GGTCAAAAATGG-GATTTTTGGAAGTTTAGAGGGTAAAATGGTA
* * * *
39566 A-TTTTGGAAGTTTTTG-GGTCAAAAATGGGATTTTTGGAAGTTTTG-GGGTCAAAAATGG-G
1 ATTTTTAGAAG-TTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTAGAGGGT--AAAATGGTA
* *
39625 ATTTTTAGAA-ATTCGAGGGT--AAAATGGTAATTTTTGGATAGTTTAG
1 ATTTTTAGAAGTTTCGA-GGTCAAAAATGG-GATTTTTGGA-AGTTTAG
39671 GGACCTCCGA
Statistics
Matches: 233, Mismatches: 29, Indels: 47
0.75 0.09 0.15
Matches are distributed among these distances:
58 29 0.12
59 98 0.42
60 64 0.27
61 1 0.00
62 19 0.08
63 19 0.08
64 3 0.01
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (60 bp):
ATTTTTAGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTAGAGGGTAAAATGGTA
Found at i:39633 original size:118 final size:122
Alignment explanation
Indices: 39415--39670 Score: 389
Period size: 118 Copynumber: 2.1 Consensus size: 122
39405 CTAAAGTGGG
* *
39415 ATTTTTGGAAG-TTCGGGGGTAAAATGGTAAATTTTAGAAGTTTCGAGGATCAAAAATGGGAATT
1 ATTTTTGGAAGTTTAGAGGGTAAAATGGTAAATTTTAGAAGTTTCGAGGATCAAAAATGGGAATT
*
39479 TTTTGGAAGTTTCGAGGTCAAAATTGGGATTTTTAGAAATTCGAGGGTAAAATGGTA
66 TTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTAGAAATTCGAGGGTAAAATGGTA
* *
39536 ATTTTTGGAAGTTTAGAGGGTAAAATGGT-AATTTTGGAAGTTTTTG-GG-TCAAAAATGGG-A-
1 ATTTTTGGAAGTTTAGAGGGTAAAATGGTAAATTTTAGAAG-TTTCGAGGATCAAAAATGGGAAT
* *
39596 TTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAATTCGAGGGTAAAATGGTA
65 TTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTAGAAATTCGAGGGTAAAATGGTA
39654 ATTTTTGGATAGTTTAG
1 ATTTTTGGA-AGTTTAG
39671 GGACCTCCGA
Statistics
Matches: 125, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
118 64 0.51
119 8 0.06
120 11 0.09
121 23 0.18
122 19 0.15
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (122 bp):
ATTTTTGGAAGTTTAGAGGGTAAAATGGTAAATTTTAGAAGTTTCGAGGATCAAAAATGGGAATT
TTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTAGAAATTCGAGGGTAAAATGGTA
Found at i:41481 original size:17 final size:18
Alignment explanation
Indices: 41474--41550 Score: 72
Period size: 17 Copynumber: 4.5 Consensus size: 18
41464 AAATAAATTT
*
41474 TAAATTTAAATTT-ATAA
1 TAAATTTAAATTTAAGAA
* *
41491 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTTAAGAA
*
41508 CAAATTTAAATTT-AGAA
1 TAAATTTAAATTTAAGAA
* *
41525 TAAACTTAATTTTAA-AA
1 TAAATTTAAATTTAAGAA
41542 TAAATTTAA
1 TAAATTTAA
41551 GTTGATTGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 1 0.02
17 47 0.94
18 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTAAGAA
Found at i:41547 original size:34 final size:34
Alignment explanation
Indices: 41474--41550 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
41464 AAATAAATTT
* * * *
41474 TAAATTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
* *
41508 CAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
41542 TAAATTTAA
1 TAAATTTAA
41551 GTTGATTGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
Found at i:42741 original size:51 final size:51
Alignment explanation
Indices: 42678--42779 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
42668 GGCAGTTCAA
*
42678 ATTTTGAGCAAAAAATGGGCATGTAATGGTCTTATGTTGAAAAATATCCTT
1 ATTTTGAGCAAAAAATGGGCATGTAATGGTCTTATGTTGAAAAAGATCCTT
*
42729 ATTTTGATCAAAAAATGGGCATGTAATGGTCTTATGTTGAAAAAGATCCTT
1 ATTTTGAGCAAAAAATGGGCATGTAATGGTCTTATGTTGAAAAAGATCCTT
42780 TTCATACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (51 bp):
ATTTTGAGCAAAAAATGGGCATGTAATGGTCTTATGTTGAAAAAGATCCTT
Found at i:43986 original size:100 final size:97
Alignment explanation
Indices: 43726--44091 Score: 294
Period size: 100 Copynumber: 3.7 Consensus size: 97
43716 GATTAGTGAA
* * * ** * * *
43726 ACATCAAATCATATACCCCTAAAGTTACAATAGATC-AGATTGAAACCATAATAACAAATTTTAT
1 ACATCAAATCCTATATCCCTAAAGTT-GAAGGGATCGA-ATTAAAACTACAATAACAAATTTTAT
43790 CTCCCTAAAGATGCAGTGGAGCAAGATGAAGC-A-
64 CTCCCTAAAGATGCAGT-GAGCAAGATGAAGCTAC
* * *
43823 ACATTAAATCCTATATCCCTGAAGTTGCAGGGATCGAATTAAAACTACAATAACAAATCTTTATC
1 ACATCAAATCCTATATCCCTAAAGTTGAAGGGATCGAATTAAAACTACAATAACAAAT-TTTATC
* * *
43888 TCTCTGAAGTTGCAGTAGAGCAAGATGAAGCTACC
65 TCCCTAAAGATGCAGT-GAGCAAGATGAAGCTA-C
* * * * * *
43923 ACATCAAATCCTATACCCCTAAAGTTGTAATGGG-TTGGATTGAAGCTACAGA-AGCAAATTTTA
1 ACATCAAATCCTATATCCCTAAAGTTG-AA-GGGATCGAATTAAAACTACA-ATAACAAATTTTA
* * * *
43986 TCTCCCTAAAGATGTAGTGTAGCAATATAAAGTTAC
63 TCTCCCTAAAGATGCAGTG-AGCAAGATGAAGCTAC
* * * * **
44022 GACATCAAATCCTATATCCCTACAGTTACAATGGATC-AGATTGAAAACTACAACAACAAACCTT
1 -ACATCAAATCCTATATCCCTAAAGTT-GAAGGGATCGA-ATT-AAAACTACAATAACAAATTTT
44086 ATCTCC
62 ATCTCC
44092 TTGAAGTTGT
Statistics
Matches: 212, Mismatches: 42, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
96 23 0.11
97 56 0.26
98 1 0.00
99 4 0.02
100 85 0.40
101 39 0.18
102 4 0.02
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (97 bp):
ACATCAAATCCTATATCCCTAAAGTTGAAGGGATCGAATTAAAACTACAATAACAAATTTTATCT
CCCTAAAGATGCAGTGAGCAAGATGAAGCTAC
Found at i:46382 original size:58 final size:59
Alignment explanation
Indices: 46312--46456 Score: 188
Period size: 59 Copynumber: 2.5 Consensus size: 59
46302 GTGAGTTCAG
* * *
46312 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGT-AAAATGT-ATTTTGGAAAAGATT-A
1 GGGTCAAAATGTAATTTTGGAAAAGTTTA-GGGTCAAAATGTAATTCTAGAAAAGATTGA
* * *
46369 TGGGTCAAAATGTAATTTTAGAAAAGTTTATGGTCAAAATGTAATTCTAGAAAAGTTTGA
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTAGGGTCAAAATGTAATTCTAGAAAAGATTGA
*
46429 GGGTCAAAATGTAATTCTGGAAAAGTTT
1 GGGTCAAAATGTAATTTTGGAAAAGTTT
46457 GAGGACCTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 3 0.04
58 34 0.45
59 38 0.50
60 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.34
Consensus pattern (59 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTAGGGTCAAAATGTAATTCTAGAAAAGATTGA
Found at i:46460 original size:30 final size:29
Alignment explanation
Indices: 46312--46456 Score: 186
Period size: 30 Copynumber: 5.0 Consensus size: 29
46302 GTGAGTTCAG
*
46312 GGGTTAAAATGTAATTTTGGAAAAGTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTA
*
46341 GGGGT-AAAATGT-ATTTTGGAAAAGATTA
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTA
*
46369 TGGGTCAAAATGTAATTTTAGAAAAGTTTA
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTA
* * *
46399 TGGTCAAAATGTAATTCTAGAAAAGTTTGA
1 GGGTCAAAATGTAATTTTGGAAAAGTTT-A
*
46429 GGGTCAAAATGTAATTCTGGAAAAGTTT
1 GGGTCAAAATGTAATTTTGGAAAAGTTT
46457 GAGGACCTAT
Statistics
Matches: 104, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
28 19 0.18
29 40 0.38
30 45 0.43
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.34
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTA
Found at i:47427 original size:30 final size:30
Alignment explanation
Indices: 47393--47453 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
47383 GAAAATAATA
* *
47393 AATAAGCAATTAA-TAAATACATTATTATAT
1 AATAAACAA-TAAGTAAATACATTAATATAT
* *
47423 AATAAATAATAAGTAAATATATTAATATAT
1 AATAAACAATAAGTAAATACATTAATATAT
47453 A
1 A
47454 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (30 bp):
AATAAACAATAAGTAAATACATTAATATAT
Found at i:47528 original size:101 final size:103
Alignment explanation
Indices: 47349--47555 Score: 262
Period size: 101 Copynumber: 2.0 Consensus size: 103
47339 TGGCTTTTTT
*
47349 TATTTTTATTTATTAAAATGTTTTGAATTTCGCAGAAAATAATAAATAAGCAATTAATAAATACA
1 TATTTTTATTTATTAAAACGTTTTGAATTTCGCAGAAAATAATAAATAAGCAATTAATAAATACA
* *
47414 TTATTATATAATAAATA-ATAAGTAAATATATTAATATA
66 TTACTATATAATAAATAGATAA-TAAACATATTAATATA
* * * *
47452 TATTTTT-TTT-TTAAAAACGTTTTGAATTTC-CAAGAGAATAATAAATGAGC-ATTAATGAGTA
1 TATTTTTATTTATT-AAAACGTTTTGAATTTCGC-AGAAAATAATAAATAAGCAATTAATAAATA
** *
47513 TGTTACTATATAATAAATAGTTAATAAACATATTAATATA
64 CATTACTATATAATAAATAGATAATAAACATATTAATATA
47553 TAT
1 TAT
47556 ACTTAAATAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
101 46 0.51
102 38 0.42
103 7 0.08
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (103 bp):
TATTTTTATTTATTAAAACGTTTTGAATTTCGCAGAAAATAATAAATAAGCAATTAATAAATACA
TTACTATATAATAAATAGATAATAAACATATTAATATA
Found at i:57102 original size:30 final size:28
Alignment explanation
Indices: 57029--57103 Score: 55
Period size: 30 Copynumber: 2.5 Consensus size: 28
57019 GGTCAAAACA
57029 TAATTTTGGAAAAGTTT-AGTGG-TAAAATTG
1 TAATTTTGG-AAA-TTTAAG-GGTTAAAA-TG
*
57059 TAATTATGAGAAATTTAAGGGTTAAAATG
1 TAATTTTG-GAAATTTAAGGGTTAAAATG
*
57088 TGATTTTAAGGAAATT
1 TAATTTT--GGAAATT
57104 GGGATTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
29 12 0.32
30 23 0.62
31 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.39
Consensus pattern (28 bp):
TAATTTTGGAAATTTAAGGGTTAAAATG
Found at i:57169 original size:30 final size:29
Alignment explanation
Indices: 57128--57441 Score: 323
Period size: 30 Copynumber: 10.6 Consensus size: 29
57118 AAATGTTAAG
* *
57128 GGGTCAAAATGTAATTTTGGGAAAATTTTA
1 GGGTTAAAATGTAATTTT-GGAAAAGTTTA
*
57158 GGGTTAAAATGTTATTTTAGG-AAAGTTTAA
1 GGGTTAAAATGTAATTTT-GGAAAAGTTT-A
* * *
57188 GTGTCAAAATGTGATTTTGGAAAAGTTT-
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
*
57216 GAGGTTAAAATGTAATTTTGGAAAGGTTTAA
1 G-GGTTAAAATGTAATTTTGGAAAAGTTT-A
* *
57247 GGGTTAAAATGTAACTTTAGAAAA-TATTA
1 GGGTTAAAATGTAATTTTGGAAAAGT-TTA
*
57276 GGGGTTAAAATGTAATTTTGGAAAAGATTA
1 -GGGTTAAAATGTAATTTTGGAAAAGTTTA
* *
57306 GGGGTTAAAATGTATTTTTAGAAAA-TATTA
1 -GGGTTAAAATGTAATTTTGGAAAAGT-TTA
57336 GGGTTAAAATGTAATTTTGGAAAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
* *
57365 AGGTTAAAATGTAATTTTAGAAAAGTTT-
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
* *
57393 GGGCTCAAAAATGTAGTTTTGGAAAAGTTTA
1 GGG-T-TAAAATGTAATTTTGGAAAAGTTTA
* * *
57424 GGATCAAAATATAATTTT
1 GGGTTAAAATGTAATTTT
57442 AAAGAAGTTC
Statistics
Matches: 239, Mismatches: 32, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
28 3 0.01
29 96 0.40
30 137 0.57
31 3 0.01
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTA
Found at i:57404 original size:59 final size:58
Alignment explanation
Indices: 57133--57450 Score: 335
Period size: 59 Copynumber: 5.4 Consensus size: 58
57123 TTAAGGGGTC
* * * *
57133 AAAATGTAATTTTGGGAAAATTTTAGGGTTAAAATGTTATTTTAGG-AAAGTTTAAGTGTC
1 AAAATGTAATTTT-AGAAAAGTTTAGGGTTAAAATGTAATTTT-GGAAAAGTTTAAG-GTT
* * *
57193 AAAATGTGATTTTGGAAAAGTTT-GAGGTTAAAATGTAATTTTGGAAAGGTTTAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAG-GGTTAAAATGTAATTTTGGAAAAGTTTAA-GGTT
* * *
57252 AAAATGTAACTTTAGAAAA-TATTAGGGGTTAAAATGTAATTTTGGAAAAGATTAGGGGTT
1 AAAATGTAATTTTAGAAAAGT-TTA-GGGTTAAAATGTAATTTTGGAAAAGTTTA-AGGTT
*
57312 AAAATGTATTTTTAGAAAA-TATTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGTT
1 AAAATGTAATTTTAGAAAAGT-TTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGTT
* * *
57370 AAAATGTAATTTTAGAAAAGTTT-GGGCTCAAAAATGTAGTTTTGGAAAAGTTT-AGGATC
1 AAAATGTAATTTTAGAAAAGTTTAGGG-T-TAAAATGTAATTTTGGAAAAGTTTAAGG-TT
*
57429 AAAATATAATTTTA-AAGAAGTT
1 AAAATGTAATTTTAGAA-AAGTT
57451 CAAGGACCTA
Statistics
Matches: 226, Mismatches: 20, Indels: 25
0.83 0.07 0.09
Matches are distributed among these distances:
57 3 0.01
58 34 0.15
59 123 0.54
60 65 0.29
61 1 0.00
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.37
Consensus pattern (58 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGTT
Found at i:61549 original size:22 final size:20
Alignment explanation
Indices: 61503--61550 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
61493 TCAAATTAAC
*
61503 TATTTCAATATTATTTTATT
1 TATTTTAATATTATTTTATT
* *
61523 AATTTTAATATTTTATTTAGTT
1 TATTTTAATATTAT-TTTA-TT
61545 TATTTT
1 TATTTT
61551 TATAAATAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 11 0.50
21 4 0.18
22 7 0.32
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTTAATATTATTTTATT
Found at i:61781 original size:7 final size:7
Alignment explanation
Indices: 61769--61816 Score: 96
Period size: 7 Copynumber: 6.9 Consensus size: 7
61759 GTGTTAAGTT
61769 AGAAGCA
1 AGAAGCA
61776 AGAAGCA
1 AGAAGCA
61783 AGAAGCA
1 AGAAGCA
61790 AGAAGCA
1 AGAAGCA
61797 AGAAGCA
1 AGAAGCA
61804 AGAAGCA
1 AGAAGCA
61811 AGAAGC
1 AGAAGC
61817 GGAACTTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.56, C:0.15, G:0.29, T:0.00
Consensus pattern (7 bp):
AGAAGCA
Found at i:62245 original size:18 final size:19
Alignment explanation
Indices: 62224--62275 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
62214 ATTAATTTAC
62224 TATTTAATTTTTTAATT-A
1 TATTTAATTTTTTAATTGA
*
62242 TATTTAA-TTTTTATGTTGA
1 TATTTAATTTTTTA-ATTGA
*
62261 TATTTATTTTTTTAA
1 TATTTAATTTTTTAA
62276 ATTTGATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 7 0.25
20 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TATTTAATTTTTTAATTGA
Found at i:62449 original size:20 final size:20
Alignment explanation
Indices: 62424--62465 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
62414 AATTAGATTT
62424 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATATTAA
**
62444 ATTTAAGTTAAAAATATTAA
1 ATTTAAAATAAAAATATTAA
62464 AT
1 AT
62466 ATTTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATTTAAAATAAAAATATTAA
Found at i:62676 original size:21 final size:21
Alignment explanation
Indices: 62627--62690 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 21
62617 TAAATTTTTT
*
62627 AATAAAATTTT-AAATA-TATA
1 AATAAAATTTTAAAAAATTA-A
*
62647 ATTATAAATTTTAAAAAATTAA
1 AATA-AAATTTTAAAAAATTAA
* *
62669 AATAAAA-TATAAAAAATAAA
1 AATAAAATTTTAAAAAATTAA
62689 AA
1 AA
62691 AGTGTTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 16 0.44
21 10 0.28
22 8 0.22
23 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAAATTTTAAAAAATTAA
Found at i:62801 original size:21 final size:22
Alignment explanation
Indices: 62769--62809 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
62759 TAAAAAAATA
62769 TTTTTACAATTTTTTATAATTT
1 TTTTTACAATTTTTTATAATTT
*
62791 TTTTTAC-ATTTTTTGTAAT
1 TTTTTACAATTTTTTATAAT
62810 AATATTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTACAATTTTTTATAATTT
Found at i:62882 original size:18 final size:17
Alignment explanation
Indices: 62861--62904 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
62851 TTTTTGTAAA
62861 TTTTATTTTTTTATATAT
1 TTTTATTTTTTT-TATAT
*
62879 TTTTCTTATTTTTTATAT
1 TTTTATT-TTTTTTATAT
*
62897 ATTTATTT
1 TTTTATTT
62905 ATATTTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTTTTTTATAT
Found at i:62892 original size:20 final size:20
Alignment explanation
Indices: 62861--62921 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
62851 TTTTTGTAAA
62861 TTTTAT-TTTTTTATATATT
1 TTTTATATTTTTTATATATT
62880 TTTCT-TATTTTTTATATATT
1 TTT-TATATTTTTTATATATT
*
62900 TATTTATATTTTTCATAT-TT
1 T-TTTATATTTTTTATATATT
62920 TT
1 TT
62922 AATGTGTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 5 0.14
20 19 0.51
21 13 0.35
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTATATTTTTTATATATT
Found at i:62936 original size:28 final size:30
Alignment explanation
Indices: 62872--62938 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
62862 TTTATTTTTT
* *
62872 TATATATTTTTCTTATTTTTTATATATTTA
1 TATATATTTTTCATATTTTTTATATATGTA
* *
62902 TTTATATTTTTCATA-TTTTTA-ATGTGTA
1 TATATATTTTTCATATTTTTTATATATGTA
62930 TATATATTT
1 TATATATTT
62939 AATAAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 13 0.41
29 6 0.19
30 13 0.41
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (30 bp):
TATATATTTTTCATATTTTTTATATATGTA
Found at i:64046 original size:229 final size:229
Alignment explanation
Indices: 63645--64072 Score: 811
Period size: 229 Copynumber: 1.9 Consensus size: 229
63635 ATGTGTCAAG
63645 TTTATTGTTAGGGTAAACTACATCCAAGGTCACACTTAAATAGAGTTTGTCCTATTTTGGCCACT
1 TTTATTGTTAGGGTAAACTACATCCAAGGTCACACTTAAATAGAGTTTGTCCTATTTTGGCCACT
63710 TTAATTTTTTTTCTCAATTTAATCACTCTAAATAAGATAATTATTTGAACTAGTCAATGCCGTTA
66 TTAATTTTTTTTCTCAATTTAATCACTCTAAATAAGATAATTATTTGAACTAGTCAATGCCGTTA
63775 AAAATTTTGTTAATCCACTAACAAATTATTGACGTGACATATTAACCAATTAAAAGACGAGATAT
131 AAAATTTTGTTAATCCACTAACAAATTATTGACGTGACATATTAACCAATTAAAAGACGAGATAT
63840 GAAACTTTTTTTTTTTTTTACTCTTGACTAAAAC
196 GAAACTTTTTTTTTTTTTTACTCTTGACTAAAAC
* *
63874 TTTATTGTTAGGGTAAACTACATCCAAGGTCACACTTAAATAGAGTTTGTCCTATTTTGGTCATT
1 TTTATTGTTAGGGTAAACTACATCCAAGGTCACACTTAAATAGAGTTTGTCCTATTTTGGCCACT
* *
63939 TTAATTTTTTTTCTCAATTTAATCACTCTAAATAGGATAATTATTTGAACTAGTCAATGTCGTTA
66 TTAATTTTTTTTCTCAATTTAATCACTCTAAATAAGATAATTATTTGAACTAGTCAATGCCGTTA
*
64004 AATATTTTGTTAATCCACTAACAAATTATTGACGTGACATATTAACCAATTAAAAGACGAGATAT
131 AAAATTTTGTTAATCCACTAACAAATTATTGACGTGACATATTAACCAATTAAAAGACGAGATAT
64069 GAAA
196 GAAA
64073 AAAAAAAAAA
Statistics
Matches: 194, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
229 194 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (229 bp):
TTTATTGTTAGGGTAAACTACATCCAAGGTCACACTTAAATAGAGTTTGTCCTATTTTGGCCACT
TTAATTTTTTTTCTCAATTTAATCACTCTAAATAAGATAATTATTTGAACTAGTCAATGCCGTTA
AAAATTTTGTTAATCCACTAACAAATTATTGACGTGACATATTAACCAATTAAAAGACGAGATAT
GAAACTTTTTTTTTTTTTTACTCTTGACTAAAAC
Found at i:65391 original size:92 final size:92
Alignment explanation
Indices: 65234--65488 Score: 263
Period size: 92 Copynumber: 2.8 Consensus size: 92
65224 GGGACGGTTT
* *
65234 AAGTACTCAATTGAGTGCAAAA-AATAATCA-TGGACTTAATT-TATTTTTTTTTGAAAAAGTTT
1 AAGTACCCAATTGAGTGCAAAATAA-AAACAGTGG-CTTAATTGT-TTTTTTTTTGAAAAAGTTT
* *
65296 GAGGGTTTTTTTGATGCATTTTGAAAATTC
63 GAGGGCTTTTTTGATGCATTATGAAAATTC
* ****
65326 AAGTACCCAATTGAGTGCAAAATAAAAGCAGTGGCTTAATTGCTTTTTTTTTTTTTTAA-TTTGA
1 AAGTACCCAATTGAGTGCAAAATAAAAACAGTGGCTTAATTG-TTTTTTTTTTGAAAAAGTTTGA
*
65390 GGGCTTTTTTGATGCATTATGAAAGTTC
65 GGGCTTTTTTGATGCATTATGAAAATTC
* * * * * * * *
65418 AAATATCCAAGTAAATGCAAAATAAAAACAGAGGTTTAATTG--ATTTTTTTGAAAAAGTTTGAG
1 AAGTACCCAATTGAGTGCAAAATAAAAACAGTGGCTTAATTGTTTTTTTTTTGAAAAAGTTTGAG
65481 GG-TTTTTT
66 GGCTTTTTT
65489 ACACTATTAA
Statistics
Matches: 136, Mismatches: 22, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
89 15 0.11
90 8 0.06
92 96 0.71
93 16 0.12
94 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (92 bp):
AAGTACCCAATTGAGTGCAAAATAAAAACAGTGGCTTAATTGTTTTTTTTTTGAAAAAGTTTGAG
GGCTTTTTTGATGCATTATGAAAATTC
Found at i:66543 original size:31 final size:31
Alignment explanation
Indices: 66508--66632 Score: 98
Period size: 31 Copynumber: 4.2 Consensus size: 31
66498 TTTGTATATG
*
66508 AACTTGATATTTTTTTTTAATTTGGTATTTA
1 AACTTGATATTTTTTTTTAATTTGGTACTTA
* * *
66539 AACTT--T-TTTTTGTTCAATTTGGTACTCA
1 AACTTGATATTTTTTTTTAATTTGGTACTTA
* * ** *
66567 AACTTGACACTTTTTCCTAATTTGGTACCTA
1 AACTTGATATTTTTTTTTAATTTGGTACTTA
* * *
66598 AACTTG-TCA-CTTTTTTTAAGTTGATACTTA
1 AACTTGAT-ATTTTTTTTTAATTTGGTACTTA
66628 AACTT
1 AACTT
66633 TTTAGGATCC
Statistics
Matches: 71, Mismatches: 19, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
28 23 0.32
29 1 0.01
30 20 0.28
31 27 0.38
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.51
Consensus pattern (31 bp):
AACTTGATATTTTTTTTTAATTTGGTACTTA
Found at i:66557 original size:28 final size:26
Alignment explanation
Indices: 66517--66571 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
66507 GAACTTGATA
* *
66517 TTTTTTTTTAATTTGGTATTTAAACT
1 TTTTTTTTTAATTTGGTACTCAAACT
66543 TTTTTTTGTTCAATTTGGTACTCAAACT
1 TTTTTTT-TT-AATTTGGTACTCAAACT
66571 T
1 T
66572 GACACTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 2 0.08
28 16 0.64
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (26 bp):
TTTTTTTTTAATTTGGTACTCAAACT
Found at i:66940 original size:60 final size:60
Alignment explanation
Indices: 66836--67023 Score: 197
Period size: 60 Copynumber: 3.1 Consensus size: 60
66826 ATAAATTTAG
* * *
66836 GTACTAAATTGAATCTTAAAAAAA-TCTTAGGTA-TCAAATTAGGAAAAAACTGTCAAGTTCAT
1 GTACTAAATTGGATC-AAAAAAAAGT-TTAGGTACT-AAATTAGGAAAAAA-TGTCAAGTTCAA
* * *
66898 GTACTAAATTGGATC-CAAAAAAGTTTAAGTACTAAATTAGGAAAAAGTGTCAAGTTCAA
1 GTACTAAATTGGATCAAAAAAAAGTTTAGGTACTAAATTAGGAAAAAATGTCAAGTTCAA
* * * *
66957 GTACCAAATTGGGTCAAAAAAAAGTTTAGGTACTAAAATA--AAAAAATGTCAAATTCAA
1 GTACTAAATTGGATCAAAAAAAAGTTTAGGTACTAAATTAGGAAAAAATGTCAAGTTCAA
* *
67015 ATACCAAAT
1 GTACTAAAT
67024 ATTATATTAA
Statistics
Matches: 110, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
58 24 0.22
59 24 0.22
60 46 0.42
61 2 0.02
62 14 0.13
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (60 bp):
GTACTAAATTGGATCAAAAAAAAGTTTAGGTACTAAATTAGGAAAAAATGTCAAGTTCAA
Found at i:67008 original size:58 final size:57
Alignment explanation
Indices: 66879--67023 Score: 173
Period size: 59 Copynumber: 2.5 Consensus size: 57
66869 TCAAATTAGG
* * * * *
66879 AAAAAACTGTCAAGTTCATGTACTAAATTGGATCCAAAAAAGTTTAAGTACTAAATT
1 AAAAAAATGTCAAGTTCAAGTACCAAATTGGATCAAAAAAAGTTTAAGTACTAAAAT
* * *
66936 AGGAAAAAGTGTCAAGTTCAAGTACCAAATTGGGTCAAAAAAAAGTTTAGGTACTAAAAT
1 A--AAAAAATGTCAAGTTCAAGTACCAAATTGGATC-AAAAAAAGTTTAAGTACTAAAAT
* *
66996 AAAAAAATGTCAAATTCAAATACCAAAT
1 AAAAAAATGTCAAGTTCAAGTACCAAAT
67024 ATTATATTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
57 1 0.01
58 24 0.32
59 29 0.39
60 21 0.28
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.26
Consensus pattern (57 bp):
AAAAAAATGTCAAGTTCAAGTACCAAATTGGATCAAAAAAAGTTTAAGTACTAAAAT
Found at i:73570 original size:24 final size:21
Alignment explanation
Indices: 73517--73588 Score: 58
Period size: 24 Copynumber: 3.3 Consensus size: 21
73507 AAATGAAAAG
*
73517 AAATAAATA-AAT-AATAGATA
1 AAATAAA-ACAATAAATAAATA
73537 AAATAAAACAAAATAAAATAAATA
1 AAATAAAAC--AAT-AAATAAATA
**
73561 AAATGCAACAATAAATAAATA
1 AAATAAAACAATAAATAAATA
73582 ATAATAA
1 A-AATAA
73589 TAAAATATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 1 0.02
20 7 0.17
21 10 0.24
22 9 0.22
24 14 0.34
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (21 bp):
AAATAAAACAATAAATAAATA
Found at i:73578 original size:21 final size:19
Alignment explanation
Indices: 73537--73614 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 19
73527 ATAATAGATA
73537 AAATAAAACAAAATAAAAT
1 AAATAAAACAAAATAAAAT
73556 AAATAAAATGCAACAAT-AAAT
1 AAATAAAA--CAA-AATAAAAT
* *
73577 AAATAATA-ATAATAAAAT
1 AAATAAAACAAAATAAAAT
73595 ATGTAATAAAGACAAAATAA
1 A---AATAAA-ACAAAATAA
73615 TTAAAAGGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
17 3 0.07
18 6 0.13
19 8 0.17
21 19 0.41
22 4 0.09
23 6 0.13
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.21
Consensus pattern (19 bp):
AAATAAAACAAAATAAAAT
Found at i:76280 original size:31 final size:31
Alignment explanation
Indices: 76242--76384 Score: 97
Period size: 31 Copynumber: 4.3 Consensus size: 31
76232 CCTTTTACAT
*
76242 TTTATTTATTTAGCAAGATTTTATTTATTTA
1 TTTATTTATTTAGCAAGATTTTAATTATTTA
* * *
76273 TTTATTTATTTTGCATGATTTTAATTATTTTTG
1 TTTATTTATTTAGCAAGATTTTAATTA--TTTA
* ** *
76306 TTTGTTTATTTAATATGATTTTTAATTATTGATTTTA
1 TTTATTTATTTAGCAAGA-TTTT-A--ATT-A-TTTA
* * * *
76343 TTTGTTTAATTAGCATGATTTTAATTAATTA
1 TTTATTTATTTAGCAAGATTTTAATTATTTA
76374 TTTTATTTATT
1 -TTTATTTATT
76385 ATTCATTGGT
Statistics
Matches: 89, Mismatches: 15, Indels: 15
0.75 0.13 0.13
Matches are distributed among these distances:
31 27 0.30
32 9 0.10
33 20 0.22
34 4 0.04
35 2 0.02
36 4 0.04
37 22 0.25
38 1 0.01
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.64
Consensus pattern (31 bp):
TTTATTTATTTAGCAAGATTTTAATTATTTA
Found at i:76347 original size:37 final size:35
Alignment explanation
Indices: 76246--76381 Score: 140
Period size: 37 Copynumber: 4.0 Consensus size: 35
76236 TTACATTTTA
* *
76246 TTTATTTAGCAAGATTTT-A-T-TTA-TTTATTTA
1 TTTATTTAGCATGATTTTAATTATTATTTTATTTG
* *
76277 TTTATTTTGCATGATTTTAATTA-T-TTTTGTTTG
1 TTTATTTAGCATGATTTTAATTATTATTTTATTTG
**
76310 TTTATTTAATATGATTTTTAATTATTGATTTTATTTG
1 TTTATTTAGCATGA-TTTTAATTATT-ATTTTATTTG
*
76347 TTTAATTAGCATGATTTTAATTAATTATTTTATTT
1 TTTATTTAGCATGATTTTAATT-ATTATTTTATTT
76382 ATTATTCATT
Statistics
Matches: 85, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
31 16 0.19
32 1 0.01
33 19 0.22
34 9 0.11
35 1 0.01
36 17 0.20
37 22 0.26
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.63
Consensus pattern (35 bp):
TTTATTTAGCATGATTTTAATTATTATTTTATTTG
Found at i:85339 original size:91 final size:91
Alignment explanation
Indices: 85184--85369 Score: 363
Period size: 91 Copynumber: 2.0 Consensus size: 91
85174 CATTACTTGT
85184 CCAATCCTCCAGTTTTGATGCCACCGAATCCAGACAAATCTTTGATCTTATACTTAGTCATATAC
1 CCAATCCTCCAGTTTTGATGCCACCGAATCCAGACAAATCTTTGATCTTATACTTAGTCATATAC
85249 GAAAACTATATAAGATGTGTATTAGG
66 GAAAACTATATAAGATGTGTATTAGG
*
85275 CCAATCCTCCAGTTTTGATGCCACCGAATCCAGACAAATCTTTGATCTTATACTTGGTCATATAC
1 CCAATCCTCCAGTTTTGATGCCACCGAATCCAGACAAATCTTTGATCTTATACTTAGTCATATAC
85340 GAAAACTATATAAGATGTGTATTAGG
66 GAAAACTATATAAGATGTGTATTAGG
85366 CCAA
1 CCAA
85370 CATGATGAGT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (91 bp):
CCAATCCTCCAGTTTTGATGCCACCGAATCCAGACAAATCTTTGATCTTATACTTAGTCATATAC
GAAAACTATATAAGATGTGTATTAGG
Found at i:87816 original size:30 final size:30
Alignment explanation
Indices: 87777--87877 Score: 136
Period size: 30 Copynumber: 3.5 Consensus size: 30
87767 AGTGGTCATC
87777 ATCAA-GTTTGCTAACTTTAGCGATTCCTG
1 ATCAATGTTTGCTAACTTTAGCGATTCCTG
*
87806 ATCAATGTTTGCTAACTTTAGCGATT--TT
1 ATCAATGTTTGCTAACTTTAGCGATTCCTG
*** *
87834 ATTTCTTTTTGCTAACTTTAGCGATTCCTG
1 ATCAATGTTTGCTAACTTTAGCGATTCCTG
87864 ATCAATGTTTGCTA
1 ATCAATGTTTGCTA
87878 TTTTTTGACC
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
28 23 0.39
29 5 0.08
30 31 0.53
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.45
Consensus pattern (30 bp):
ATCAATGTTTGCTAACTTTAGCGATTCCTG
Found at i:88973 original size:101 final size:99
Alignment explanation
Indices: 88802--89015 Score: 241
Period size: 101 Copynumber: 2.1 Consensus size: 99
88792 TTAATAAAGA
* *
88802 AAGATGAAGCTACAAAACCAAATCCTATACCCCTGAAGTTGCAATGGGTTGAATTAAAGTCATGA
1 AAGATAAAGCTACAAAACCAAATCCTATACCCCTGAAGTTGCAATGGATTGAATTAAAGTCAT-A
* * * *
88867 AAACAAATCTTTATCTCCCTAAAGTTGTAGTGGAGT
65 AAACAAATC-TTATCTCCCTAAAGATATAATGGAGC
* * * * * * * *
88903 AAGATAAAGCTACAACATCAAATTCTATATCCCTGAAGTTGTAATGGATTGGATTGAGGCTACAT
1 AAGATAAAGCTACAAAACCAAATCCTATACCCCTGAAGTTGCAATGGATTGAATTAAAG-T-CAT
* *
88968 -TAACAAGTCTTATCTCCCTAAAGATATAATGGAGC
64 AAAACAAATCTTATCTCCCTAAAGATATAATGGAGC
89003 AAGATAAAGCTAC
1 AAGATAAAGCTAC
89016 GATATTGAAT
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
100 35 0.37
101 56 0.59
102 1 0.01
103 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (99 bp):
AAGATAAAGCTACAAAACCAAATCCTATACCCCTGAAGTTGCAATGGATTGAATTAAAGTCATAA
AACAAATCTTATCTCCCTAAAGATATAATGGAGC
Found at i:89036 original size:100 final size:101
Alignment explanation
Indices: 88802--89048 Score: 257
Period size: 100 Copynumber: 2.5 Consensus size: 101
88792 TTAATAAAGA
* * * * * * * *
88802 AAGATGAAGCTACAAAACCAAATCCTATACCCCTGAAGTTGCAATGGGTTGAATTAAAG-T-CAT
1 AAGATAAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAATGGATTGGATTGAGGCTACAT
* * * * *
88865 GAAAACAAATCTTTATCTCCCTAAAGTTGTAGTGGAGT
66 --TAACAAATCTTTATCTCCCTAAAGATATAATGGAGC
* *
88903 AAGATAAAGCTACAACATCAAATTCTATATCCCTGAAGTTGTAATGGATTGGATTGAGGCTACAT
1 AAGATAAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAATGGATTGGATTGAGGCTACAT
*
88968 TAACAAGTC-TTATCTCCCTAAAGATATAATGGAGC
66 TAACAAATCTTTATCTCCCTAAAGATATAATGGAGC
* * ** * *
89003 AAGATAAAGCTACGATATTGAATCCTATCTCCCTGAGGTTGCAATG
1 AAGATAAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAATG
89049 AAAGTGGATA
Statistics
Matches: 120, Mismatches: 24, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
100 60 0.50
101 56 0.47
102 1 0.01
103 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (101 bp):
AAGATAAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAATGGATTGGATTGAGGCTACAT
TAACAAATCTTTATCTCCCTAAAGATATAATGGAGC
Found at i:90589 original size:27 final size:26
Alignment explanation
Indices: 90533--90589 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
90523 TTTACATTTT
* *
90533 ATTTATTTATTAGCAAGATTTTATTT
1 ATTTATTTATTAGCAAGATTTTAATC
* *
90559 ATTTATTTATTTTGCATGATTTTAATC
1 ATTTATTTA-TTAGCAAGATTTTAATC
90586 ATTT
1 ATTT
90590 TTGTTTGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (26 bp):
ATTTATTTATTAGCAAGATTTTAATC
Found at i:92801 original size:16 final size:16
Alignment explanation
Indices: 92780--92815 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
92770 GAACTTTAAA
*
92780 TTTTTTTATTTTTTAT
1 TTTTTTTATATTTTAT
*
92796 TTTTTTTGTATTTTAT
1 TTTTTTTATATTTTAT
92812 TTTT
1 TTTT
92816 CTCTTTGGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTTTATATTTTAT
Found at i:93706 original size:96 final size:97
Alignment explanation
Indices: 93531--93716 Score: 261
Period size: 96 Copynumber: 1.9 Consensus size: 97
93521 GGAAAGGATG
* * * * * *
93531 TTCGATTATCTCGATTTGAGGAAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCG
1 TTCGATTATCTCAATTTAAAGAAAAGATTGCACCTAGTAAGTTAAGACGCAAATTTTCAAAATCG
*
93596 AAGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AAGATAAAGAAACATTGCCTCGATTAAGGGTA
*
93628 TTCGATTATTTCAATTTAAAGAAAA-ATTGCACCTAGTAAGTTAAGACGCAAATTTTCAAAACTC
1 TTCGATTATCTCAATTTAAAGAAAAGATTGCACCTAGTAAGTTAAGACGCAAATTTTCAAAA-TC
93692 GAA-ATAACAG-AACATTGCCTCGATT
65 GAAGATAA-AGAAACATTGCCTCGATT
93717 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
96 52 0.66
97 27 0.34
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (97 bp):
TTCGATTATCTCAATTTAAAGAAAAGATTGCACCTAGTAAGTTAAGACGCAAATTTTCAAAATCG
AAGATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:94522 original size:205 final size:205
Alignment explanation
Indices: 93901--94744 Score: 1213
Period size: 205 Copynumber: 4.1 Consensus size: 205
93891 TTGATGATTA
* * * *
93901 AGGAAGATGACTGCGTCGTTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGATGAATTTGG
1 AGGAAGATGACCGTGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGG
* * * *
93966 TCCGCTTCTCAGTATCTCATCAGGAAGCTAACCTTTTGTTGCTTTGACCTGCTTCTCAGTGTCTC
66 TCCACTTCTCAGTATCCCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTC
* *
94031 ATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGTGCGGGTTTGATTTGGTCTTCTTCTCA
131 ATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGCGAGTTTGATTTGGTCTTCTTCTCA
94096 GTATCTTATC
196 GTATCTTATC
* * * ** * *
94106 AGGAAGATGACCGCGTTGTTTGCTTCAATTCGCTTCTCTGTATCTTGTTAGGAAGATGAATTTGG
1 AGGAAGATGACCGTGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGG
* * * * *
94171 TCCACTTCTCAGTATCCCATCAAGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCT
66 TCCACTTCTCAGTATCCCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTGCTTCTCAGTGTCT
* * * *
94236 CATCAGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTC
130 CATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGCGAGTTTGATTTGGTCTTCTTCTC
94301 AGTAT-TTCATC
195 AGTATCTT-ATC
* *
94312 AGGAAGATGACCGTGTCGTTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGA
1 AGGAAGATGACCGTGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGG
* *
94377 TCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTGTTGCTTCGACCTGCTTCTCAGTGTCTC
66 TCCACTTCTCAGTATCCCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTC
* * *
94442 ATCAGGAAGTTGGGGTTCGAAGATTTACTCACATCGAGTGCGAGTTTGATTTGGTCTTCTTCTTA
131 ATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGCGAGTTTGATTTGGTCTTCTTCTCA
*
94507 GTATCTTACC
196 GTATCTTATC
* * * *
94517 AGGAAGATGACCGTGTTGTTTGCTTCAATTCGCTTCTTTGTATCTCGTCAGGAAGACGAATTTGG
1 AGGAAGATGACCGTGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGG
* *
94582 TCCACTTCTCAGTATCCCATCAGGAAGCTAACCTTTTATTGTTTCGACCTGCTTCTTAGTGTCTC
66 TCCACTTCTCAGTATCCCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTC
* * ** ** *
94647 ATCAGGAAGCTGGGGTTCGAAGATTTGCTCACACCGAGCATGAGTTTGATTTATTCTTCTTTTCA
131 ATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGCGAGTTTGATTTGGTCTTCTTCTCA
* *
94712 GTGTCTCATC
196 GTATCTTATC
*
94722 AGGAAGATGACAGTGTCGTTTGT
1 AGGAAGATGACCGTGTCGTTTGT
94745 GGATAATCAG
Statistics
Matches: 570, Mismatches: 66, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
205 385 0.68
206 185 0.32
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (205 bp):
AGGAAGATGACCGTGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGG
TCCACTTCTCAGTATCCCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTC
ATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGCGAGTTTGATTTGGTCTTCTTCTCA
GTATCTTATC
Found at i:104585 original size:95 final size:96
Alignment explanation
Indices: 104411--104591 Score: 240
Period size: 95 Copynumber: 1.9 Consensus size: 96
104401 GGAAAGGATG
* *
104411 TTCGATTATCTCGATTTGAGGAAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATCG
1 TTCGATTATCTCAATTTGAAGAAAA-GTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATCG
*
104476 AAGATAAGAAAACATTACCTCAATTAAGGGTA
65 AAGATAACAAAACATTACCTCAATTAAGGGTA
* * * * * *
104508 TTCGATTATTTCAATTTGAATAAAA-TTGCACCTAGTAAGTTAAGGTGCAAATTTTTGAAACTCT
1 TTCGATTATCTCAATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAAA-TTTTCAAAATCG
*
104572 AA-ATAACAGAACATTACCTC
65 AAGATAACAAAACATTACCTC
104592 GATTTTAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
95 41 0.56
96 11 0.15
97 21 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCAATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATCGA
AGATAACAAAACATTACCTCAATTAAGGGTA
Found at i:104864 original size:27 final size:28
Alignment explanation
Indices: 104813--104874 Score: 108
Period size: 27 Copynumber: 2.2 Consensus size: 28
104803 AAATGAGACT
104813 TTTTGGATACTCGGGGGTAAAATGGTAA
1 TTTTGGATACTCGGGGGTAAAATGGTAA
*
104841 TTTTGGATTCTC-GGGGTAAAATGGTAA
1 TTTTGGATACTCGGGGGTAAAATGGTAA
104868 TTTTGGA
1 TTTTGGA
104875 AAATTTAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 22 0.67
28 11 0.33
ACGTcount: A:0.26, C:0.06, G:0.31, T:0.37
Consensus pattern (28 bp):
TTTTGGATACTCGGGGGTAAAATGGTAA
Found at i:104998 original size:59 final size:58
Alignment explanation
Indices: 104912--105404 Score: 441
Period size: 59 Copynumber: 8.4 Consensus size: 58
104902 TTAGACATTT
* * * *
104912 GAGGGT-AAAAGGGTAATTTTAAG-AGTTTAGAGGTCGAAAATGAAGA-TTTTGGAGGTTC
1 GAGGGTAAAAATGG-AATTTTTAGAAGTTTA-AGGTCAAAAATG-AGATTTTTGGAAGTTC
* * *
104970 AAGGGTAAAAATGGCATTTTTAGAAGTTTCAAGGGT-AAAAATG-GTATTTTTGGAAGTTT
1 GAGGGTAAAAATGGAATTTTTAGAAGTTT-AA-GGTCAAAAATGAG-ATTTTTGGAAGTTC
** * *
105029 TTGGGTCAAAAATGGAATTTTTAGAAGTTTCAAGGTCAAAAATGGGATTTTTGGAAGTTTT
1 GAGGGT-AAAAATGGAATTTTTAGAAGTTT-AAGGTCAAAAATGAGATTTTTGGAAG-TTC
* * * *
105090 G-GGTTCAAAATAGAATTTTTGGAAGTTTCAAGGTCAAAAAT-AGAATTTTTGGAAGTTTC
1 GAGGGTAAAAATGGAATTTTTAGAAGTTT-AAGGTCAAAAATGAG-ATTTTTGGAAG-TTC
* * ** * * *
105149 GAGGTTAAAAAT-GAGATTTTTGGAAGTTTTGGGGTTAAAAATGAAATTTTTGGAAGTTTT
1 GAGGGTAAAAATGGA-ATTTTTAGAAG-TTTAAGGTCAAAAATGAGATTTTTGGAAG-TTC
* * * * *
105209 G-GGTTCAAAATGGAATTTTTGGAAGTTTTAATGTCAAAAATGGGATTTTTGGAAGTTC
1 GAGGGTAAAAATGGAATTTTTAGAAG-TTTAAGGTCAAAAATGAGATTTTTGGAAGTTC
* * *
105267 GAGGGTAAAAATGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTC
1 GAGGGTAAAAATGGAATTTTTAGAAGTTT-AAGGTCAAAAATGAGATTTTTGGAAGTTC
* * *
105326 GAGGGTAAAAATGAAATTTTTGGAAGTTTCGAGGTCAAAAAT-ATGATTTTTGGAAGTTC
1 GAGGGTAAAAATGGAATTTTTAGAAGTTT-AAGGTCAAAAATGA-GATTTTTGGAAGTTC
105385 G-GGGTAAAAATGGAATTTTT
1 GAGGGTAAAAATGGAATTTTT
105405 GGACAGTTCG
Statistics
Matches: 374, Mismatches: 42, Indels: 38
0.82 0.09 0.08
Matches are distributed among these distances:
57 1 0.00
58 38 0.10
59 231 0.62
60 96 0.26
61 8 0.02
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (58 bp):
GAGGGTAAAAATGGAATTTTTAGAAGTTTAAGGTCAAAAATGAGATTTTTGGAAGTTC
Found at i:105003 original size:30 final size:30
Alignment explanation
Indices: 104958--105412 Score: 404
Period size: 30 Copynumber: 15.4 Consensus size: 30
104948 AAAATGAAGA
* *
104958 TTTTGG-AGGTTCAAGGGTAAAAATGGCAT
1 TTTTGGAAGTTTCAAGGGTAAAAATGGAAT
* *
104987 TTTTAGAAGTTTCAAGGGTAAAAATGGTAT
1 TTTTGGAAGTTTCAAGGGTAAAAATGGAAT
**
105017 TTTTGGAAGTTT-TTGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCAAGGGT-AAAAATGGAAT
* *
105047 TTTTAGAAGTTTCAA-GGTCAAAAATGGGAT
1 TTTTGGAAGTTTCAAGGGT-AAAAATGGAAT
* * *
105077 TTTTGGAAGTTT--TGGGTTCAAAATAGAAT
1 TTTTGGAAGTTTCAAGGG-TAAAAATGGAAT
*
105106 TTTTGGAAGTTTCAA-GGTCAAAAATAGAAT
1 TTTTGGAAGTTTCAAGGGT-AAAAATGGAAT
* *
105136 TTTTGGAAGTTTCGAGGTTAAAAAT-GAGAT
1 TTTTGGAAGTTTCAAGGGTAAAAATGGA-AT
** *
105166 TTTTGGAAGTTT-TGGGGTTAAAAATGAAAT
1 TTTTGGAAGTTTCAAGGG-TAAAAATGGAAT
* *
105196 TTTTGGAAGTTT--TGGGTTCAAAATGGAAT
1 TTTTGGAAGTTTCAAGGG-TAAAAATGGAAT
* * *
105225 TTTTGGAAGTTTTAA-TGTCAAAAATGGGAT
1 TTTTGGAAGTTTCAAGGGT-AAAAATGGAAT
*
105255 TTTTGGAAG-TTCGAGGGTAAAAATGGAAT
1 TTTTGGAAGTTTCAAGGGTAAAAATGGAAT
* * * *
105284 TTTTAGAAGTTTCGAGGTTAAAAATGGGAT
1 TTTTGGAAGTTTCAAGGGTAAAAATGGAAT
* *
105314 TTTTGGAAG-TTCGAGGGTAAAAATGAAAT
1 TTTTGGAAGTTTCAAGGGTAAAAATGGAAT
* *
105343 TTTTGGAAGTTTCGA-GGTCAAAAATATG-AT
1 TTTTGGAAGTTTCAAGGGT-AAAAAT-GGAAT
*
105373 TTTTGGAAG-TTC-GGGGTAAAAATGGAAT
1 TTTTGGAAGTTTCAAGGGTAAAAATGGAAT
105401 TTTTGGACAGTT
1 TTTTGGA-AGTT
105413 CGGGGACCTC
Statistics
Matches: 356, Mismatches: 46, Indels: 47
0.79 0.10 0.10
Matches are distributed among these distances:
27 1 0.00
28 15 0.04
29 121 0.34
30 216 0.61
31 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.36
Consensus pattern (30 bp):
TTTTGGAAGTTTCAAGGGTAAAAATGGAAT
Found at i:105115 original size:89 final size:86
Alignment explanation
Indices: 104958--105412 Score: 438
Period size: 89 Copynumber: 5.1 Consensus size: 86
104948 AAAATGAAGA
* * * * *
104958 TTTTGG-AGGTTCAAGGGTAAAAATGGCATTTTTAGAAGTTTCAAGGGTAAAAATGGTATTTTTG
1 TTTTGGAAGTTTCAA-GGTAAAAATGGGATTTTTGGAAGTTTC--GGGTAAAAATAGAATTTTTG
105022 GAAGTTTTTGGGTCAAAAATGGAAT
63 GAAG-TTTTGGGTCAAAAATGGAAT
* * *
105047 TTTTAGAAGTTTCAAGGTCAAAAATGGGATTTTTGGAAGTTTTGGGTTCAAAATAGAATTTTTGG
1 TTTTGGAAGTTTCAAGGT-AAAAATGGGATTTTTGGAAGTTTCGGG-TAAAAATAGAATTTTTGG
** *
105112 AAGTTTCAAGGTCAAAAATAGAAT
64 AAGTTT-TGGGTCAAAAATGGAAT
* * *
105136 TTTTGGAAGTTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTTGGGGTTAAAAAT-GAAATTTTT
1 TTTTGGAAGTTTCAAGG-TAAAAATGGGATTTTTGGAAG-TTTCGGG-TAAAAATAG-AATTTTT
105200 GGAAGTTTTGGGTTC-AAAATGGAAT
62 GGAAGTTTTGGG-TCAAAAATGGAAT
* * * *
105225 TTTTGGAAGTTTTAATGTCAAAAATGGGATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTA
1 TTTTGGAAGTTTCAAGGT-AAAAATGGGATTTTTGGAAGTTTC--GGGTAAAAATAGAATTTTTG
* * *
105289 GAAGTTTCGAGGTTAAAAATGGGAT
63 GAAGTTTTG-GGTCAAAAATGGAAT
* **
105314 TTTTGGAAG-TTCGAGGGTAAAAATGAAATTTTTGGAAGTTTCGAGGTCAAAAATATG-ATTTTT
1 TTTTGGAAGTTTC-AAGGTAAAAATGGGATTTTTGGAAGTTTCG-GGT-AAAAATA-GAATTTTT
**
105377 GGAAGTTCGGGGT-AAAAATGGAAT
62 GGAAGTTTTGGGTCAAAAATGGAAT
105401 TTTTGGACAGTT
1 TTTTGGA-AGTT
105413 CGGGGACCTC
Statistics
Matches: 307, Mismatches: 38, Indels: 42
0.79 0.10 0.11
Matches are distributed among these distances:
87 20 0.07
88 58 0.19
89 169 0.55
90 60 0.20
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.36
Consensus pattern (86 bp):
TTTTGGAAGTTTCAAGGTAAAAATGGGATTTTTGGAAGTTTCGGGTAAAAATAGAATTTTTGGAA
GTTTTGGGTCAAAAATGGAAT
Done.