Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2445
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: 61034
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Found at i:662 original size:55 final size:55
Alignment explanation
Indices: 574--1444 Score: 981
Period size: 55 Copynumber: 15.4 Consensus size: 55
564 CTCCGTCCGC
* *
574 TTTTCAGTCCCCAAAGAGCAGGACGCCTTTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
628 TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
683 CCTTTCAATCCTCAAAGAGCAGGACACCTTTT-AAAGCCCACACAGGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * **
738 TTTTTTAGTCCTCAAAGAGTAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C---ACCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
799 CCTTTCAGTCCTCAAAGAGCAGGACACC-TTTCAAAGCCCACACAAGTTGGTGGTA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
854 TTTCCAGTCCTCAAAGAGCAGGACACCTTTT-AAAGCCCATACAGGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
** *
908 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C---ACCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
969 CCTTTCAGTCCCCAAAGAGCAGGACACC-TTTCAAAGCCCACACAAGTTTGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
1024 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTT-AAAGCCCACACAGGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
**
1079 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C---ACCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
1140 CCTTTCAGTCCTCAAAGAGCAGGACACC-TTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1195 TGTTCCAATCCTCAAAGAGCAGGACACCTTTT-AAAGCCCACATAGGTTGGTGGCA
1 T-TTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
**
1250 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C---ACCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1311 CCTTTCAGTCCCCAAAGAGCAGGACATCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1366 CCTTTCAGTCCTCAAAGAGCAGGACGCC-TTTCAAAGCCCACACGAGTTAGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1421 CTTTTTACTCCTCAATGAGCAGGA
1 -TTTTCAGTCCTCAAAGAGCAGGA
1445 TACAGTTTAT
Statistics
Matches: 707, Mismatches: 75, Indels: 69
0.83 0.09 0.08
Matches are distributed among these distances:
54 54 0.08
55 432 0.61
56 22 0.03
57 4 0.01
59 4 0.01
60 20 0.03
61 171 0.24
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (55 bp):
TTTTCAGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:821 original size:116 final size:110
Alignment explanation
Indices: 575--1444 Score: 1035
Period size: 116 Copynumber: 7.7 Consensus size: 110
565 TCCGTCCGCT
* * *
575 TTTCAGTCCCCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCT
*
640 CAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
66 CAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
685 TTTCAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTTAGTCCT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCT
* **
750 CAAAGAGTAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
66 CAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACC
* * *
801 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGTA-TTTCCAGTCCT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCT
* * **
865 CAAAGAGCAGGACACCTTTTAAAGCCCATACAGGTTGGTGGCATT
66 CAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC
** * **
910 TTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACCTTTC
1 TTTCAGTCCTCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCATTTTTC
* * * *
975 AGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTTGTGGCA-T
60 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
1025 TTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCC
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCC
**
1090 TCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
65 TCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACC
* * * *
1142 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATGTTCCAATCCT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCT
* * **
1207 CAAAGAGCAGGACACCTTTTAAAGCCCACATAGGTTGGTGGCATT
66 CAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC
** **
1252 TTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 TTTCAGTCCTCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCATTTTTC
* * *
1317 AGTCCCCAAAGAGCAGGACATCTCTTAAAGCCCACACAAGTTGGTGGCACC
60 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
1368 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTAGTGGCACTTTTT-ACTCC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTTCAGTCC
*
1432 TCAATGAGCAGGA
65 TCAAAGAGCAGGA
1445 TACAGTTTAT
Statistics
Matches: 652, Mismatches: 80, Indels: 56
0.83 0.10 0.07
Matches are distributed among these distances:
109 43 0.07
110 198 0.30
111 18 0.03
112 3 0.00
113 1 0.00
114 7 0.01
115 57 0.09
116 322 0.49
117 3 0.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (110 bp):
TTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCT
CAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:1112 original size:171 final size:171
Alignment explanation
Indices: 600--1445 Score: 1379
Period size: 171 Copynumber: 5.0 Consensus size: 171
590 AGCAGGACGC
*
600 CTTTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AA
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAA
*
662 AGCCCACACAAGTTGGTGGCACCTTT-CAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACAC
64 AGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACAC
* *
726 AGGTTGGTGGCATTTTTTAGTCCTCAAAGAGTAGGATGCTTTTT
128 AGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
770 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAG
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAG
* *
835 CCCACACAAGTTGGTGGTA-TTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCATACAGG
66 CCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGG
899 TTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
131 TTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
* *
940 CTTTTCAAAGCCCACACAGGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAG
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAG
* *
1005 CCCACACAAGTTTGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGG
66 CCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGG
1070 TTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
131 TTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
1111 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAG
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAG
* *
1176 CCCACACAAGTTGGTGGCA-TGTTCCAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACATAG
66 CCCACACAAGTTGGTGGCACT-TTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAG
1240 GTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
130 GTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
* *
1282 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACATCTCTT-AAA
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAA
* *
1346 GCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAC-
65 GCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACA
* * *
1409 GAGTTAGTGGCACTTTTT-ACTCCTCAATGAGCAGGAT
129 G-GTTGGTGGCA-TTTTTCAGTCCTCAAAGAGCAGGAT
1446 ACAGTTTATT
Statistics
Matches: 640, Mismatches: 25, Indels: 21
0.93 0.04 0.03
Matches are distributed among these distances:
169 3 0.00
170 167 0.26
171 457 0.71
172 12 0.02
173 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (171 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAG
CCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGG
TTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
Found at i:2038 original size:21 final size:21
Alignment explanation
Indices: 2014--2070 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2004 AATTTATCCA
2014 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2035 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2056 AATGTATCGATACAT
1 AATGTATCGATACAT
2071 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2150 original size:19 final size:19
Alignment explanation
Indices: 2126--2193 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2116 AATTCAACAA
2126 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2145 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2160 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2177 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2194 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2165 original size:13 final size:13
Alignment explanation
Indices: 2147--2171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2137 ACATAAGTTT
2147 TGTATCGATACAA
1 TGTATCGATACAA
2160 TGTATCGATACA
1 TGTATCGATACA
2172 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2169 original size:32 final size:32
Alignment explanation
Indices: 2128--2190 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2118 TTCAACAATT
*
2128 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2160 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2191 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2251 original size:13 final size:13
Alignment explanation
Indices: 2233--2258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2223 CATTTTTCTG
2233 TGTATCGATACAT
1 TGTATCGATACAT
2246 TGTATCGATACAT
1 TGTATCGATACAT
2259 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2255 original size:33 final size:33
Alignment explanation
Indices: 2213--2279 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2203 GCCAAAGAAA
***
2213 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2246 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2279 T
1 T
2280 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:4832 original size:80 final size:82
Alignment explanation
Indices: 4661--4839 Score: 272
Period size: 80 Copynumber: 2.2 Consensus size: 82
4651 ATTTTCTATA
*
4661 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATAC
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
4726 TCCAACCCCGTTATTTC
66 TCCAACCCCGTTATTTC
*** * *
4743 CGAGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATAC
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
**
4806 TCCAACCTTGTTATTTC
66 TCCAACCCCGTTATTTC
4823 ATCGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
4840 CCCGTTACTT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 44 0.51
81 13 0.15
82 29 0.34
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (82 bp):
ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
TCCAACCCCGTTATTTC
Found at i:4846 original size:28 final size:28
Alignment explanation
Indices: 4800--4871 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
4790 TCACAGTCGA
** * **
4800 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
4828 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
4856 GGATACTCTAACCCCG
1 GGATACTCCAACCCCG
4872 GCTTTATTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.26
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:4945 original size:28 final size:29
Alignment explanation
Indices: 4905--4959 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
4895 TCTCATAATT
4905 GGGGATACTCCAACCCCG-TTATTTTTGA
1 GGGGATACTCCAACCCCGATTATTTTTGA
* *
4933 GGGGATACTCCAATCCCGATTTTTTTT
1 GGGGATACTCCAACCCCGATTATTTTT
4960 TCTAATCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGATTATTTTTGA
Found at i:4974 original size:79 final size:79
Alignment explanation
Indices: 4825--5027 Score: 219
Period size: 79 Copynumber: 2.6 Consensus size: 79
4815 GTTATTTCAT
* * * *
4825 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCTAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
4890 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * * ** *
4904 TGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
4968 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * *
4983 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
5028 TGTTATTATC
Statistics
Matches: 101, Mismatches: 22, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
78 3 0.03
79 98 0.97
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:6080 original size:53 final size:53
Alignment explanation
Indices: 6000--6116 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
5990 CGTCGCGACA
*
6000 GTATCGATACAGGACATTGGCAGTAGCCAAATTTGTATCGATACACACAATAT
1 GTATCGATACAGGACATTGGCAGTAGCCAAATTTGTATCGATACACAAAATAT
*
6053 GTATCGATACAGGTCATTGGCAGTAGCCAAATTTGTATCGATACACAAAATAT
1 GTATCGATACAGGACATTGGCAGTAGCCAAATTTGTATCGATACACAAAATAT
6106 GTATCGATACA
1 GTATCGATACA
6117 TTGGTAGTAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (53 bp):
GTATCGATACAGGACATTGGCAGTAGCCAAATTTGTATCGATACACAAAATAT
Found at i:6178 original size:13 final size:13
Alignment explanation
Indices: 6160--6198 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
6150 TCACTATTCA
6160 TGTATCGATACAT
1 TGTATCGATACAT
*
6173 TGTATCGATACAG
1 TGTATCGATACAT
6186 TGTATCGATACAT
1 TGTATCGATACAT
6199 CATAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7910 original size:30 final size:29
Alignment explanation
Indices: 7847--7933 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 29
7837 TTAAAAAAAA
* *
7847 AAAGTCCACGACCCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-AT-TTTTCTC
7878 AAAGTCCACGACTCAGTGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATTTT-TCTC
7908 AAAGTCCACGACTCAGTGGCATTTTT
1 AAAGTCCACGACTCAGTGGCATTTTT
7934 TCTTTAAAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
29 3 0.06
30 31 0.58
31 19 0.36
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (29 bp):
AAAGTCCACGACTCAGTGGCATTTTTCTC
Found at i:7974 original size:34 final size:33
Alignment explanation
Indices: 7936--8290 Score: 328
Period size: 34 Copynumber: 10.8 Consensus size: 33
7926 GCATTTTTTC
*
7936 TTTAAAGCCCACAACTCCATGGCACCTTGTTCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTT-TTCCT
* *
7970 TTT-AAGTCCACAACGCCGTGGCA-C----CCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTCCT
* * *
7997 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCAT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTCCT
*
8031 CTTT-AAGTCCACAACTCCGTGGCA-C----CCT
1 -TTTAAAGCCCACAACTCCGTGGCACCTTTTCCT
* * *
8059 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCAT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTCCT
*
8093 CTTT-AAGTCCACAACTCCGTGGCACCTTCTT-CT
1 -TTTAAAGCCCACAACTCCGTGGCACCTT-TTCCT
8126 TTTCAAAGCCCACAACTCCGTGGCACCTTCTT-CT
1 TTT-AAAGCCCACAACTCCGTGGCACCTT-TTCCT
8160 TTTCAAAGCCCACAACTCCGTGGCACCTTCTT-CT
1 TTT-AAAGCCCACAACTCCGTGGCACCTT-TTCCT
**
8194 TTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-C--TTTTCCT
* *
8230 TTTCAAAGCCCACAACTCCGTGGCACATTTTTCT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTCCT
*
8264 TTTAAAGCCCACAACTCTGTGGCACCT
1 TTTAAAGCCCACAACTCCGTGGCACCT
8291 ACAACTTTGT
Statistics
Matches: 268, Mismatches: 29, Indels: 49
0.77 0.08 0.14
Matches are distributed among these distances:
27 9 0.03
28 37 0.14
32 4 0.01
33 62 0.23
34 121 0.45
35 8 0.03
36 7 0.03
37 20 0.07
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.32
Consensus pattern (33 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTCCT
Found at i:8052 original size:62 final size:63
Alignment explanation
Indices: 7909--8453 Score: 365
Period size: 62 Copynumber: 8.5 Consensus size: 63
7899 TTTTGTCTCA
* * * * * * * * * *
7909 AAGTCCACGACTCAGTGGCATTTTTTCTTTAAAGCCCACAACTCCATGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTCT-TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATTTT
*
7973 AAGTCCACAACGCCGTGGCAC-C-CTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT
1 AAGTCCACAACTCCGTGGCACTCTCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCAT-TTT
8035 AAGTCCACAACTCCGTGGCAC-C-CTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT
1 AAGTCCACAACTCCGTGGCACTCTCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCAT-TTT
* * *
8097 AAGTCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC-TT
1 AAGTCCACAACTCCGTGGCA-C-TC-TCTTTT-AAAGCCCACAATTCCGTGGCACTTTTTTCATT
8161 TT
62 TT
* *
8163 CAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTT-TGTGGCACTCTTTTTT
1 --AAGTCCACAACTCCGTGGCA-C-TC-TCTTTTAAAGCCCACAA-TTCCGTGGCA--CTTTTTT
*
8227 CCTTTT
58 CATTTT
* * * * * *
8233 CAAAGCCCACAACTCCGTGGCACATTTTTCTTTTAAAGCCCACAACTCTGTGGCAC---CTACAA
1 --AAGTCCACAACTCCGTGGCAC---TCTCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTC-A
*
8295 CTTT
60 TTTT
** ** * *
8299 --GT-GGC-ACTCTC-TTTC-CT-T-TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC-TGTTT
1 AAGTCCACAACTC-CGTGGCACTCTCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCAT-TTT
* *
8355 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTT
1 -AAGTCCACAACTCCGTGGCACTC----T--CTTTT-AAAGCCCACAATTCCGTGGCACTTTTTT
8420 C-TTTT
58 CATTTT
*
8425 AAAGCCCACAACTCCGTGGCACTCT-TTTT
1 -AAGTCCACAACTCCGTGGCACTCTCTTTT
8454 CCCTTTTAAG
Statistics
Matches: 402, Mismatches: 41, Indels: 77
0.77 0.08 0.15
Matches are distributed among these distances:
54 25 0.06
55 1 0.00
56 4 0.01
57 2 0.00
59 2 0.00
60 8 0.02
61 37 0.09
62 88 0.22
63 5 0.01
64 17 0.04
65 3 0.01
66 7 0.02
67 24 0.06
68 59 0.15
69 8 0.02
70 81 0.20
71 31 0.08
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (63 bp):
AAGTCCACAACTCCGTGGCACTCTCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCATTTT
Found at i:8350 original size:87 final size:88
Alignment explanation
Indices: 8204--8376 Score: 287
Period size: 87 Copynumber: 2.0 Consensus size: 88
8194 TTTAAAGCCC
*
8204 ACAACTTTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACATTTTTCT-TTTA
1 ACAACTTTGTGGCACTCTTCTTTCCTTTTCAAAGCCCACAACTCCGTGGCACATTTTTCTGTTTA
*
8268 AAGCCCACAACTCTGTGGCACCT
66 AAGCCCACAACTCCGTGGCACCT
* *
8291 ACAACTTTGTGGCACTC-TCTTTCCTTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT
1 ACAACTTTGTGGCACTCTTCTTTCC-TTTTCAAAGCCCACAACTCCGTGGCACATTTTTCTGTTT
8355 AAAGCCCACAACTCCGTGGCAC
65 AAAGCCCACAACTCCGTGGCAC
8377 TCTTTTTCCC
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
86 6 0.08
87 50 0.62
88 24 0.30
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (88 bp):
ACAACTTTGTGGCACTCTTCTTTCCTTTTCAAAGCCCACAACTCCGTGGCACATTTTTCTGTTTA
AAGCCCACAACTCCGTGGCACCT
Found at i:8396 original size:71 final size:69
Alignment explanation
Indices: 8299--8485 Score: 295
Period size: 71 Copynumber: 2.7 Consensus size: 69
8289 CTACAACTTT
* *
8299 GTGGCACTCTCTTTCCTTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCAC
1 GTGGCACTCTTTTTCC-CTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCAC
8364 AACTCC
64 AACTCC
*
8370 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACA
1 GTGGCACTCTTTTTCCCTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACA
8435 ACTCC
65 ACTCC
* *
8440 GTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCCGTGGCATCTTT
1 GTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTT
8486 ATCCCTTCCT
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
68 22 0.20
70 43 0.39
71 44 0.40
ACGTcount: A:0.19, C:0.33, G:0.13, T:0.35
Consensus pattern (69 bp):
GTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAA
CTCC
Found at i:8485 original size:104 final size:104
Alignment explanation
Indices: 8061--8485 Score: 237
Period size: 104 Copynumber: 4.2 Consensus size: 104
8051 GGCACCCTTT
* * *
8061 TAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCTTCTT-
1 TAAAGCCCACAACTCCGTGGCACTTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* * *
8124 CTTTTCAAAGCCCACAACTCCGTGGCAC-CTTCT-T-CTTTTC
64 CCTTT-AAAGCCCACAACTCCGTGGCACTCTT-TATCCCTTCC
* * **
8164 -AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTC
1 TAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-C-TTTTTC
* *
8228 CTTTTCAAAGCCCACAACTCCGTGGCACAT-TTT-T--CTT-T
64 CCTTT-AAAGCCCACAACTCCGTGGCAC-TCTTTATCCCTTCC
* * **** * * **
8266 TAAAGCCCACAACTCTGTGGCACCTACAACTTTGT---G-GCAC-TCT-C-T--TTCC--TTT--
1 TAAAGCCCACAACTCCGTGGCACTTTTTTCTTT-TAAAGCCCACAACTCCGTGGCACCTTTTTCC
* **
8318 -TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTGTT--
65 CTTTAAAGCCCACAACTCCGTGGCACTCTTTATCCCTTCC
8354 TAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCA-CTTTT
1 TAAAGCCCACAACTCCGTGGCACT-TTTTT--CTTTT-AAAGCCCACAACTCCGTGGCACCTTTT
* * *
8418 TTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT--
62 TCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTATCCCTTCC
* *
8459 TTAAGTCCACAACTCCGTGGCATCTTT
1 TAAAGCCCACAACTCCGTGGCA-CTTT
8486 ATCCCTTCCT
Statistics
Matches: 257, Mismatches: 33, Indels: 62
0.73 0.09 0.18
Matches are distributed among these distances:
86 3 0.01
87 23 0.09
88 25 0.10
89 3 0.01
90 1 0.00
91 7 0.03
94 2 0.01
95 4 0.02
96 2 0.01
97 2 0.01
98 1 0.00
99 3 0.01
100 6 0.02
101 23 0.09
102 27 0.11
103 34 0.13
104 56 0.22
105 33 0.13
106 2 0.01
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (104 bp):
TAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCC
TTTAAAGCCCACAACTCCGTGGCACTCTTTATCCCTTCC
Found at i:8491 original size:34 final size:35
Alignment explanation
Indices: 8299--8505 Score: 253
Period size: 34 Copynumber: 5.9 Consensus size: 35
8289 CTACAACTTT
* *
8299 GTGGCACTCTCTTTCCTTTTTTAAAGCCCACAACTCC
1 GTGGCA-TCTTTTTCC-CTTTTAAAGCCCACAACTCC
*
8336 GTGGCACCTTTTT--CTGTTTAAAGCCCACAACTCC
1 GTGGCATCTTTTTCCCT-TTTAAAGCCCACAACTCC
8370 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCC
1 GTGGCA-TCTTTTTCCCTTTT-AAAGCCCACAACTCC
*
8407 GTGGCA-CTTTTT-TCTTTTAAAGCCCACAACTCC
1 GTGGCATCTTTTTCCCTTTTAAAGCCCACAACTCC
*
8440 GTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCC
1 GTGGCA-TCTTTTTCCCTTTTAAAGCCCACAACTCC
* *
8475 GTGGCATCTTTATCCCTTCCTAAAGCCCACA
1 GTGGCATCTTTTTCCCTT-TTAAAGCCCACA
8506 CAAGTCGGTG
Statistics
Matches: 150, Mismatches: 10, Indels: 21
0.83 0.06 0.12
Matches are distributed among these distances:
33 22 0.15
34 40 0.27
35 38 0.25
36 21 0.14
37 29 0.19
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (35 bp):
GTGGCATCTTTTTCCCTTTTAAAGCCCACAACTCC
Found at i:8526 original size:104 final size:101
Alignment explanation
Indices: 8313--8538 Score: 260
Period size: 104 Copynumber: 2.2 Consensus size: 101
8303 CACTCTCTTT
**
8313 CCTT-TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCAC
1 CCTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCAC
* *
8377 TCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCA
66 TCTTTATCCCTTCTCAAAGCCCACAACTCCGTGGCA
* * *
8413 CTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTG
1 C---CTTCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCCTTTAAAGCCCACAACTCCGTG
* *
8478 GCA-TCTTTATCCCTTC-CTAAAGCCCACACAAGTCGGTGGCAA
62 GCACTCTTTATCCCTTCTC-AAAG-CC-CACAACTCCGTGGC-A
**
8520 CCTTCTTCCAAAGCCCACA
1 CCTTCTTTTAAAGCCCACA
8539 CAAGTCGGTG
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
100 1 0.01
103 3 0.03
104 56 0.53
105 31 0.30
106 12 0.11
107 2 0.02
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (101 bp):
CCTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCAC
TCTTTATCCCTTCTCAAAGCCCACAACTCCGTGGCA
Found at i:8533 original size:33 final size:34
Alignment explanation
Indices: 8490--8556 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
8480 ATCTTTATCC
8490 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
8524 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
8557 TCTAAGCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 28 0.85
34 5 0.15
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.19
Consensus pattern (34 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
Found at i:8677 original size:49 final size:49
Alignment explanation
Indices: 8559--9071 Score: 641
Period size: 49 Copynumber: 10.7 Consensus size: 49
8549 GCAACCTTTC
* * *
8559 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
8611 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
8660 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
8703 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
8751 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
8794 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
8843 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
8886 TAAGTCCAATATCGCTGGCCTTGAATCAGCATAGTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
8935 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
8984 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
9036 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
9072 ACATCCTTTT
Statistics
Matches: 405, Mismatches: 36, Indels: 40
0.84 0.07 0.08
Matches are distributed among these distances:
43 116 0.29
45 3 0.01
46 1 0.00
47 1 0.00
48 40 0.10
49 165 0.41
50 2 0.00
51 2 0.00
52 75 0.19
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:8702 original size:21 final size:21
Alignment explanation
Indices: 8678--8744 Score: 50
Period size: 21 Copynumber: 3.1 Consensus size: 21
8668 ATGTAGCTGG
8678 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
8699 CCTTTAAGTC--CA-ATATCGCTGG
1 CCTTGAA-TCAGCACAT-TGGC--A
8721 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
8742 CCT
1 CCT
8745 CACCTTTAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 11 0.33
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:8720 original size:43 final size:43
Alignment explanation
Indices: 8657--9027 Score: 409
Period size: 43 Copynumber: 8.1 Consensus size: 43
8647 GCACCTTCAT
*
8657 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
8700 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG-----CAC
*
8748 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
8791 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
8838 ATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
8883 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAGTGGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C
* *
8927 TTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTC
1 -----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
8979 ATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
9024 CTTT
1 CTTT
9028 TCCATCTTTA
Statistics
Matches: 282, Mismatches: 26, Indels: 40
0.81 0.07 0.11
Matches are distributed among these distances:
43 121 0.43
44 1 0.00
45 2 0.01
47 1 0.00
48 41 0.15
49 115 0.41
52 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:8905 original size:92 final size:92
Alignment explanation
Indices: 8608--9080 Score: 714
Period size: 92 Copynumber: 5.0 Consensus size: 92
8598 CCTTTTCCAT
* * * *
8608 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
8673 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
8700 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
8764 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
8791 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
8856 GCTGGCCTTGACTCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
8883 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAGTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
8948 GCTGGCCTTGACTCAGCACATTGGCACCTTC
66 GCTGGCCTTGAATCAGCACATTGGCA----C
* * *
8979 ATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCA
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCA
*
9044 ATGTAGCTGGCCTTGAATCAGCACATTGACATC
61 ATGTAGCTGGCCTTGAATCAGCACATTGGCA-C
9077 CTTT
1 CTTT
9081 TTCATCATCT
Statistics
Matches: 353, Mismatches: 18, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
91 88 0.25
92 174 0.49
96 5 0.01
98 43 0.12
100 2 0.01
101 41 0.12
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:9111 original size:56 final size:53
Alignment explanation
Indices: 8883--9119 Score: 224
Period size: 49 Copynumber: 4.6 Consensus size: 53
8873 ACATTGGCAC
* * *
8883 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAGT-GGCACC--TT-T-AT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACA-TCGACACCTTTTCTCAT
* * * *
8932 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* *
8981 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * *
9033 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACA-CC-TTTTC-TCAT
* * * *
9089 CTTTAAGCCCAATATCGTTGGCCATGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
9120 ACATATTGGC
Statistics
Matches: 159, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
48 3 0.02
49 80 0.50
52 41 0.26
53 2 0.01
54 5 0.03
56 28 0.18
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
Found at i:11326 original size:30 final size:29
Alignment explanation
Indices: 11263--11349 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 29
11253 AAAAAAAAAA
* *
11263 AAAGTCCACGACCCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-AT-TTTTCTC
11294 AAAGTCCACGACTCAGTGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATTTT-TCTC
*
11324 AAAGTCCACGACTCAATGGCATTTTT
1 AAAGTCCACGACTCAGTGGCATTTTT
11350 TCTTTAAAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 3 0.06
30 30 0.58
31 19 0.37
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (29 bp):
AAAGTCCACGACTCAGTGGCATTTTTCTC
Found at i:11413 original size:27 final size:27
Alignment explanation
Indices: 11383--11595 Score: 138
Period size: 34 Copynumber: 7.0 Consensus size: 27
11373 GCACCTTGTT
* *
11383 CCTTTTAAGTCCACAACGCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
11410 CCTTTTAAAGCCCACAATTCCGTGGCAC
1 CCTTTT-AAGCCCACAACTCCGTGGCAC
* *
11438 TTTTTTCATCTTTAAGTCCACAACTCCGTGGCAC
1 ------CCT-TTTAAGCCCACAACTCCGTGGCAC
*
11472 CCTTTTAAAGCCCACAATTCCGTGGCAC
1 CCTTTT-AAGCCCACAACTCCGTGGCAC
* *
11500 TTTTTTCATCTTTAAGTCCACAACTCCGTGGCAC
1 ------CCT-TTTAAGCCCACAACTCCGTGGCAC
*
11534 CCGTTTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
11561 CTTCTTCTTTCCAAAGCCCACAACTCCGTGGCAC
1 C--C-T-TTT---AAGCCCACAACTCCGTGGCAC
11595 C
1 C
11596 TTCTTCTTTT
Statistics
Matches: 147, Mismatches: 16, Indels: 39
0.73 0.08 0.19
Matches are distributed among these distances:
27 33 0.22
28 40 0.27
29 1 0.01
31 3 0.02
34 64 0.44
35 6 0.04
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.28
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAC
Found at i:11420 original size:61 final size:62
Alignment explanation
Indices: 11352--11595 Score: 334
Period size: 62 Copynumber: 4.0 Consensus size: 62
11342 GCATTTTTTC
* * * *
11352 TTTAAAGCCCACAACTCCATGGCACCTTGTTCCT-TTTAAGTCCACAACGCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
* *
11413 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
* * *
11475 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
* * *
11537 TTT-AAGCCCACAACTCCGTGGCACCTTCTTC-T-TTCCAAAGCCCACAACTCCGTGGCACC
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCATCTT--TAAGTCCACAACTCCGTGGCACC
11596 TTCTTCTTTT
Statistics
Matches: 168, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
59 2 0.01
60 1 0.01
61 75 0.45
62 90 0.54
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (62 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
Found at i:11459 original size:34 final size:34
Alignment explanation
Indices: 11421--11533 Score: 139
Period size: 34 Copynumber: 3.5 Consensus size: 34
11411 CTTTTAAAGC
*
11421 CCACAATTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCATCTTTAAGT
** *
11455 CCACAACTCCGTGGCACCCTTTT-A-----AAGC
1 CCACAACTCCGTGGCACTTTTTTCATCTTTAAGT
*
11483 CCACAATTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCATCTTTAAGT
11517 CCACAACTCCGTGGCAC
1 CCACAACTCCGTGGCAC
11534 CCGTTTAAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
28 23 0.36
29 1 0.02
33 1 0.02
34 39 0.61
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.32
Consensus pattern (34 bp):
CCACAACTCCGTGGCACTTTTTTCATCTTTAAGT
Found at i:11498 original size:123 final size:122
Alignment explanation
Indices: 11352--11595 Score: 330
Period size: 123 Copynumber: 2.0 Consensus size: 122
11342 GCATTTTTTC
* *
11352 TTTAAAGCCCACAACTCCATGGCACCTTGTTCCT-TTTAAGTCCACAACGCCGTGGCACCCTTTT
1 TTTAAAGCCCACAACTCCATGGCACCTTGTTCATCTTTAAGTCCACAACGCCGTGGCACCCGTTT
* * * * *
11416 AAAGCCCACAATTCCGTGGCACTTTTTTCATCTT-TAAGTCCACAACTCCGTGGCACCCT
66 -AAGCCCACAACTCCGTGGCACCTTCTTC-T-TTCAAAGCCCACAACTCCGTGGCACCCT
* * * * *
11475 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCGTTT
1 TTTAAAGCCCACAACTCCATGGCACCTTGTTCATCTTTAAGTCCACAACGCCGTGGCACCCGTTT
11540 AAGCCCACAACTCCGTGGCACCTTCTTCTTTCCAAAGCCCACAACTCCGTGGCACC
66 AAGCCCACAACTCCGTGGCACCTTCTTCTTT-CAAAGCCCACAACTCCGTGGCACC
11596 TTCTTCTTTT
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
121 2 0.02
122 1 0.01
123 75 0.71
124 28 0.26
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (122 bp):
TTTAAAGCCCACAACTCCATGGCACCTTGTTCATCTTTAAGTCCACAACGCCGTGGCACCCGTTT
AAGCCCACAACTCCGTGGCACCTTCTTCTTTCAAAGCCCACAACTCCGTGGCACCCT
Found at i:11583 original size:34 final size:34
Alignment explanation
Indices: 11540--11611 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
11530 GCACCCGTTT
11540 AAGCCCACAACTCCGTGGCACCTTCTTCTTTCCA
1 AAGCCCACAACTCCGTGGCACCTTCTTCTTTCCA
*
11574 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTCTTCTTTCCA
11608 AAGC
1 AAGC
11612 TCGAATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.22, C:0.39, G:0.12, T:0.26
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACCTTCTTCTTTCCA
Found at i:11801 original size:33 final size:33
Alignment explanation
Indices: 11764--11830 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11754 TTCAACGATT
11764 TGTATCGATACATAAAATCTTGTATCGATACAA
1 TGTATCGATACATAAAATCTTGTATCGATACAA
*** *
11797 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATCTTGTATCGATACAA
11830 T
1 T
11831 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATCTTGTATCGATACAA
Found at i:11802 original size:13 final size:13
Alignment explanation
Indices: 11784--11808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11774 CATAAAATCT
11784 TGTATCGATACAA
1 TGTATCGATACAA
11797 TGTATCGATACA
1 TGTATCGATACA
11809 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11889 original size:13 final size:13
Alignment explanation
Indices: 11871--11895 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11861 ATTACTCAAA
11871 TGTATCGATACAT
1 TGTATCGATACAT
11884 TGTATCGATACA
1 TGTATCGATACA
11896 CCGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11960 original size:52 final size:52
Alignment explanation
Indices: 11904--12023 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
11894 CACCGATCTT
* *
11904 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
*
11956 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
12008 TGTATCGATACATGCA
1 TGTATCGATACATGCA
12024 AGTAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
Found at i:17574 original size:3 final size:3
Alignment explanation
Indices: 17561--17590 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
17551 CTTCATCCGA
*
17561 ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
17591 TTCCTCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:19298 original size:13 final size:13
Alignment explanation
Indices: 19280--19304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19270 ACAATGAGCA
19280 TGTATCGATACAT
1 TGTATCGATACAT
19293 TGTATCGATACA
1 TGTATCGATACA
19305 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:26161 original size:21 final size:19
Alignment explanation
Indices: 26137--26192 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
26127 TTCAACAGTT
26137 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAA-AGT-AA
* **
26158 TGTATCGATACATAAGTGT
1 TGTATCGATACAAAAGTAA
26177 TGTATCGATACAAAAG
1 TGTATCGATACAAAAG
26193 CTACTCTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
20 3 0.10
21 13 0.42
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:39428 original size:19 final size:19
Alignment explanation
Indices: 39404--39503 Score: 98
Period size: 19 Copynumber: 5.9 Consensus size: 19
39394 AATTCAACGA
39404 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
39423 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
39438 --TGTATCAATACATAAGT
1 TTTGTATCGATACATAAGT
39455 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
39470 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
39487 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
39504 TTAGCTACTG
Statistics
Matches: 67, Mismatches: 2, Indels: 24
0.72 0.02 0.26
Matches are distributed among these distances:
13 21 0.31
15 4 0.06
17 4 0.06
19 38 0.57
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:39442 original size:32 final size:32
Alignment explanation
Indices: 39406--39500 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
39396 TTCAACGATT
39406 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
39438 TGTATCAATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
39470 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTTTTGTATCGATACA
39501 TAATTAGCTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:39443 original size:13 final size:13
Alignment explanation
Indices: 39425--39481 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
39415 ACATAAGTTT
39425 TGTATCGATACAA
1 TGTATCGATACAA
*
39438 TGTATCAATACATAA
1 TGTATCGATAC--AA
39453 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
39470 TGTATCGATACA
1 TGTATCGATACA
39482 TAAGTATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:39580 original size:33 final size:33
Alignment explanation
Indices: 39523--39589 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
39513 GCCAAGGAAA
***
39523 TGTATCGATACATTTTTCTGTGTATCAATACAT
1 TGTATCGATACATGGATCTGTGTATCAATACAT
* *
39556 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCAATACAT
39589 T
1 T
39590 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCAATACAT
Found at i:42114 original size:28 final size:27
Alignment explanation
Indices: 42047--42115 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
42037 CTTCACAATC
**
42047 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
42074 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
42102 GGGGATACTCCAAC
1 GGGGATACTCCAAC
42116 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:42175 original size:52 final size:51
Alignment explanation
Indices: 42102--42271 Score: 175
Period size: 52 Copynumber: 3.3 Consensus size: 51
42092 TTATTTCCGA
*
42102 GGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATC-CTAAAACACCAATTTTTCCACAATC
** * **
42154 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATCCT-AAAACACCAATTTTTCC-ACAATC
* * *
42206 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTA--TCCTAAAACACCAATTTTTCCACAATC
*
42258 GAGGATACTCCAAC
1 GGGGATACTCCAAC
42272 CTCGTTATTT
Statistics
Matches: 96, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
51 10 0.10
52 69 0.72
53 12 0.12
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATCCTAAAACACCAATTTTTCCACAATC
Found at i:42255 original size:104 final size:103
Alignment explanation
Indices: 41935--42270 Score: 288
Period size: 104 Copynumber: 3.2 Consensus size: 103
41925 ATCAATTCTC
* * * * *
41935 CACAATCGAGGATATTCCAGCTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGAGGATACTCCA-ATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
*
41999 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * * ** * * * ** * *
42040 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTCCGA
1 CACAATCGAGGATACTCCAATCCGGTTTTATTTTC---AAAACACCAATTTTCCTTTA-AT-C--
* * *
42102 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT
* *
42146 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGAGGATACTCCAATCC-GGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
42211 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
42251 CACAATCGAGGATACTCCAA
1 CACAATCGAGGATACTCCAA
42271 CCTCGTTATT
Statistics
Matches: 176, Mismatches: 39, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
103 6 0.03
104 44 0.25
105 34 0.19
106 19 0.11
107 38 0.22
108 7 0.04
109 28 0.16
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (103 bp):
CACAATCGAGGATACTCCAATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:42291 original size:28 final size:28
Alignment explanation
Indices: 42255--42331 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
42245 ATTTTTCACA
* * *
42255 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
42283 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
42311 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
42332 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:42300 original size:212 final size:212
Alignment explanation
Indices: 41933--42338 Score: 629
Period size: 212 Copynumber: 1.9 Consensus size: 212
41923 TTATCAATTC
* * *
41933 TCCACAATCGAGGATATTCCAGCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAGATCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
41998 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * *
42063 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
42128 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * *
42145 TCCACAATCGGGGATACTCCA-ATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAGATCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
42209 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
42272 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
42337 AT
193 AT
42339 TCCCAAAATA
Statistics
Matches: 176, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 31 0.18
212 110 0.62
213 35 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAGATCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:42397 original size:107 final size:107
Alignment explanation
Indices: 41993--42410 Score: 288
Period size: 107 Copynumber: 3.9 Consensus size: 107
41983 TTCTATAATC
* * * * *
41993 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCC
* *
42058 AACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTCCGA
64 AACCCCGTTATTTCA-CGGGGATACTCCAACCCCGTTACTTCCGA
* * * * * * * *
42102 GGGGATACTCCAACTCCG-GTTT-TATCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTC-CAAAAATACCAATTTCT-CACAATCGAGGATACTCC
** * * ** * *
42165 AATCCTGGTTTTATTTTCA-----AAACGCCAATTTTCCTTTA-AT-C--
64 AA-CCCCG--TTA-TTTCACGGGGATACTCCAA--CCCCGTTACTTCCGA
* * *
42206 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
42271 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTTCA-CGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * *
42314 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
42378 CCCCGTTATTTTCGA-GGGGATACTCCAATCCCG
66 CCCCGTTA-TTTC-ACGGGGATACTCCAACCCCG
42411 ATTTTTTTTT
Statistics
Matches: 245, Mismatches: 41, Indels: 48
0.73 0.12 0.14
Matches are distributed among these distances:
100 5 0.02
101 3 0.01
103 4 0.02
104 42 0.17
105 18 0.07
106 20 0.08
107 92 0.38
108 37 0.15
109 18 0.07
110 3 0.01
112 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCACGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:42434 original size:79 final size:79
Alignment explanation
Indices: 42285--42489 Score: 232
Period size: 79 Copynumber: 2.6 Consensus size: 79
42275 GTTATTTCAT
* * *
42285 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
42350 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
42364 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
42428 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * * *
42443 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCCACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
42490 TTATTATCTC
Statistics
Matches: 105, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
78 3 0.03
79 102 0.97
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:53475 original size:16 final size:17
Alignment explanation
Indices: 53449--53492 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
53439 CCTTCTCTTA
*
53449 AAAAAAAAAAAAAAAAC
1 AAAAAACAAAAAAAAAC
53466 -AAAAACAAAAAAAAAC
1 AAAAAACAAAAAAAAAC
53482 AAAAAACAAAA
1 AAAAAACAAAA
53493 CAAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAACAAAAAAAAAC
Found at i:53475 original size:17 final size:18
Alignment explanation
Indices: 53448--53492 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
53438 ACCTTCTCTT
*
53448 AAAAAAAAAAAAAAAAAC
1 AAAAAACAAAAAAAAAAC
53466 -AAAAAC-AAAAAAAAAC
1 AAAAAACAAAAAAAAAAC
53482 AAAAAACAAAA
1 AAAAAACAAAA
53493 CAAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 10 0.42
17 11 0.46
18 3 0.12
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAAAAAAC
Found at i:53478 original size:22 final size:22
Alignment explanation
Indices: 53449--53502 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
53439 CCTTCTCTTA
*
53449 AAAAAAAAAAAAAAAACAAAAAC
1 AAAAAAAAACAAAAAAC-AAAAC
53472 AAAAAAAAACAAAAAACAAAAC
1 AAAAAAAAACAAAAAACAAAAC
*
53494 AAAGAAAAA
1 AAAAAAAAA
53503 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (22 bp):
AAAAAAAAACAAAAAACAAAAC
Found at i:53502 original size:17 final size:16
Alignment explanation
Indices: 53450--53502 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
53440 CTTCTCTTAA
53450 AAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAC
*
53466 AAAAACAAAAAAAAAC
1 AAAAAAAAAAAAAAAC
* * *
53482 AAAAAACAAAACAAAG
1 AAAAAAAAAAAAAAAC
53498 AAAAA
1 AAAAA
53503 GAGAGAAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAC
Found at i:53517 original size:1 final size:1
Alignment explanation
Indices: 53448--53502 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
53438 ACCTTCTCTT
* * * * * *
53448 AAAAAAAAAAAAAAAAACAAAAACAAAAAAAAACAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53503 GAGAGAAAAG
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:54548 original size:29 final size:29
Alignment explanation
Indices: 54516--54603 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
54506 CCTCTTAAAG
54516 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
** * *
54545 CCCA-A-AGAG-CAG-GACACCTCTTAAAG--
1 CCCACACA-AGTTGGTGGCACCT-TT-CAGTC
54571 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
54600 CCCA
1 CCCA
54604 AAGAGCAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
26 10 0.24
27 9 0.21
28 9 0.21
29 14 0.33
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.19
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:54570 original size:55 final size:55
Alignment explanation
Indices: 54486--55328 Score: 1256
Period size: 55 Copynumber: 15.3 Consensus size: 55
54476 TCCGCTTTTT
54486 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
54541 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
54596 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
54651 AGTCCTCAAAGAGAAGCACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
54706 AGTCCCCAAAGAGCAGGGCACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
54761 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
54816 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
54871 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
54926 AGTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
54981 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCTACACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
55036 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
55091 AGTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
55146 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
55201 ATTCCCCAAAGAGTAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
55256 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
55311 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
55329 TACAGTTTAT
Statistics
Matches: 727, Mismatches: 48, Indels: 26
0.91 0.06 0.03
Matches are distributed among these distances:
54 15 0.02
55 698 0.96
56 14 0.02
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:55208 original size:29 final size:29
Alignment explanation
Indices: 55176--55256 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 29
55166 CCTCTTAAAG
**
55176 CCCACACAAGTTGGTGGCACCTTTCATTC
1 CCCACACAAGTTGGTGGCACCTTTCAAAC
* * *
55205 CCCA-A-AGAG-TAG-GACACCTTTCAAAG
1 CCCACACA-AGTTGGTGGCACCTTTCAAAC
55231 CCCACACAAGTTGGTGGCACCTTTCA
1 CCCACACAAGTTGGTGGCACCTTTCA
55257 GTCCTCAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
26 14 0.35
27 6 0.15
28 6 0.15
29 14 0.35
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAAAC
Found at i:55874 original size:19 final size:19
Alignment explanation
Indices: 55850--55917 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
55840 AATTCAACGA
55850 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
55869 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
55884 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
55901 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
55918 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:55888 original size:32 final size:32
Alignment explanation
Indices: 55852--55914 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
55842 TTCAACGATT
*
55852 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
55884 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
55915 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:55889 original size:13 final size:13
Alignment explanation
Indices: 55871--55895 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55861 ACATAAGTTT
55871 TGTATCGATACAA
1 TGTATCGATACAA
55884 TGTATCGATACA
1 TGTATCGATACA
55896 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:55975 original size:13 final size:13
Alignment explanation
Indices: 55957--55982 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55947 CATTTTTCTG
55957 TGTATCGATACAT
1 TGTATCGATACAT
55970 TGTATCGATACAT
1 TGTATCGATACAT
55983 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:55979 original size:33 final size:33
Alignment explanation
Indices: 55937--56003 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
55927 GCCAAGGAAA
***
55937 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
55970 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
56003 T
1 T
56004 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:58411 original size:51 final size:53
Alignment explanation
Indices: 58342--58683 Score: 205
Period size: 52 Copynumber: 6.5 Consensus size: 53
58332 AGTTTATCAA
* * * * *
58342 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
58393 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
58447 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * *
58505 TAT-TTC-CGA--GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * *
58554 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
58607 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
58659 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
58684 CTCGTTATTT
Statistics
Matches: 225, Mismatches: 37, Indels: 57
0.71 0.12 0.18
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 6 0.03
51 35 0.16
52 79 0.35
53 33 0.15
54 33 0.15
55 22 0.10
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:58526 original size:28 final size:27
Alignment explanation
Indices: 58459--58527 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
58449 CTTCACAATC
**
58459 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
58486 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
58514 GGGGATACTCCAAC
1 GGGGATACTCCAAC
58528 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:58537 original size:109 final size:105
Alignment explanation
Indices: 58405--58799 Score: 327
Period size: 109 Copynumber: 3.7 Consensus size: 105
58395 TTCTATAATC
*
58405 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
58470 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGA
63 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTA-TTCCGA
* * *
58514 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
** * ** * * * ** * *
58578 ATCCTGGTTTTATTTTC---AAAACGCCAATTTTCCTTTAAT-C--
64 A-CCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTCCGA
* *
58618 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* *
58683 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTCTACTTCCGA
65 CCCCGTTA-ATCATCGGGGATACTCCAACCCCG-T-TA-TTCCGA
* ** * * *** * * *
58728 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
58793 CCCGTTA
66 CCCGTTA
58800 TTTTCGAGGG
Statistics
Matches: 223, Mismatches: 45, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
102 2 0.01
103 7 0.03
104 44 0.20
105 15 0.07
106 21 0.09
107 36 0.16
108 10 0.04
109 67 0.30
110 21 0.09
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.30
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTCCGA
Found at i:58667 original size:104 final size:103
Alignment explanation
Indices: 58347--58682 Score: 297
Period size: 104 Copynumber: 3.2 Consensus size: 103
58337 ATCAATTCTC
* * * *
58347 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGAGGATACTCCAA-TCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
*
58411 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * * ** * * * ** * *
58452 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTCCGA
1 CACAATCGAGGATACTCCAATCCGGTTTTATTTTC---AAAACACCAATTTTCCTTTA-AT-C--
* * *
58514 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT
* *
58558 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGAGGATACTCCAATCC-GGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
58623 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
58663 CACAATCGAGGATACTCCAA
1 CACAATCGAGGATACTCCAA
58683 CCTCGTTATT
Statistics
Matches: 177, Mismatches: 38, Indels: 33
0.71 0.15 0.13
Matches are distributed among these distances:
103 6 0.03
104 44 0.25
105 35 0.20
106 19 0.11
107 38 0.21
108 7 0.04
109 28 0.16
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (103 bp):
CACAATCGAGGATACTCCAATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:58712 original size:212 final size:214
Alignment explanation
Indices: 58345--58752 Score: 628
Period size: 212 Copynumber: 1.9 Consensus size: 214
58335 TTATCAATTC
* *
58345 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
58410 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * *
58475 CGTTAATCATCGGGGATACTCCAACCCCG-T-TATTTCCGAGGGGATACTCCAACTCCGGTTTTA
131 CGTTAATCATCGGGGATACTCCAACCCCGTTCTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
58538 TCGCTAAAACACTAATTTT
196 TCGCTAAAACACTAATTTT
* * * *
58557 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
58621 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
58684 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTCTACTTCCGAGGGGATACTCCAACCCCGGCT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTCTACTTCCGAGGGGATACTCCAACCCCGGCT
58749 TTAT
193 TTAT
58753 TCCCAAAATA
Statistics
Matches: 177, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
211 31 0.18
212 79 0.45
213 36 0.20
214 31 0.18
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (214 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTCTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
TCGCTAAAACACTAATTTT
Found at i:58869 original size:80 final size:79
Alignment explanation
Indices: 58697--58904 Score: 211
Period size: 80 Copynumber: 2.6 Consensus size: 79
58687 GTTATTTCAT
* *
58697 CGGGGATACTCCAACCCCGTTCTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT
1 CGGGGATACTCCAACCCCG-T-TATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT
* * *
58762 ATTGATTTCTCATAAT
64 ATCGATTTCTCACAAC
* * ** * ** *
58778 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTTC-TAATC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG-GCTTTATTCCCAAAAT-
58842 ATCGATTTCTCACAAC
64 ATCGATTTCTCACAAC
* * * * *
58858 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCCACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
58905 TTATTATCTC
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
79 27 0.26
80 60 0.57
81 18 0.17
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
CGATTTCTCACAAC
Done.