Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001457.1 Hibiscus syriacus cultivar Beakdansim tig00002812_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70333
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5068 original size:15 final size:14
Alignment explanation
Indices: 5050--5093 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5040 ACTGAAATAG
*
5050 TTTTCGAAAATGAA
1 TTTTTGAAAATGAA
5064 TTTTTGAAAATGAA
1 TTTTTGAAAATGAA
* * *
5078 TTCTGGAAAATAAA
1 TTTTTGAAAATGAA
5092 TT
1 TT
5094 ACATTTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39
Consensus pattern (14 bp):
TTTTTGAAAATGAA
Found at i:8227 original size:22 final size:22
Alignment explanation
Indices: 8199--8272 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
8189 TCAATTTTAA
*
8199 TTTTTTCAATTTAGTTATTCAT
1 TTTTTTCATTTTAGTTATTCAT
* *
8221 TTTTTTCCTTTTTAATT-TT-AGT
1 TTTTTT-CATTTTAGTTATTCA-T
*
8243 ATTTTTTTATTTTAGTTATTCAT
1 -TTTTTTCATTTTAGTTATTCAT
8266 TTTTTTC
1 TTTTTTC
8273 TCTTTTAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
21 1 0.03
22 22 0.55
23 16 0.40
24 1 0.03
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTTTTCATTTTAGTTATTCAT
Found at i:8279 original size:23 final size:23
Alignment explanation
Indices: 8208--8279 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
8198 ATTTTTTCAA
8208 TTTAGTTATTCATTTTTTTC-CTT
1 TTTAGTTATTCATTTTTTTCTC-T
* *
8231 TTTAATT-TT-AGTATTTTTT-TAT
1 TTTAGTTATTCA-T-TTTTTTCTCT
8253 TTTAGTTATTCATTTTTTTCTCT
1 TTTAGTTATTCATTTTTTTCTCT
8276 TTTA
1 TTTA
8280 ATTTTAGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
21 1 0.03
22 16 0.41
23 21 0.54
24 1 0.03
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTAGTTATTCATTTTTTTCTCT
Found at i:8324 original size:39 final size:39
Alignment explanation
Indices: 8208--8306 Score: 101
Period size: 45 Copynumber: 2.4 Consensus size: 39
8198 ATTTTTTCAA
*
8208 TTTAGTTATTCATTTTTTTC-CTTTTTAATTTTAGTATTTTTTTAT
1 TTTAGTTATTCATTTTTTTCTC-TTTTAATTTTAG------TGTAT
8253 TTTAGTTATTCATTTTTTTCTCTTTTAATTTTAGTGTAT
1 TTTAGTTATTCATTTTTTTCTCTTTTAATTTTAGTGTAT
* *
8292 TTTATTTATTTATTT
1 TTTAGTTATTCATTT
8307 GTCTTTTCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
39 17 0.34
45 32 0.64
46 1 0.02
ACGTcount: A:0.18, C:0.06, G:0.05, T:0.71
Consensus pattern (39 bp):
TTTAGTTATTCATTTTTTTCTCTTTTAATTTTAGTGTAT
Found at i:10386 original size:22 final size:22
Alignment explanation
Indices: 10345--10411 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
10335 CTCGTATAAA
10345 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
10368 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
10390 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
10412 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:12119 original size:21 final size:21
Alignment explanation
Indices: 12095--12139 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12085 TCTTGTTCGT
* *
12095 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
12116 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
12137 TTG
1 TTG
12140 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:15888 original size:105 final size:105
Alignment explanation
Indices: 15404--16497 Score: 1509
Period size: 106 Copynumber: 10.6 Consensus size: 105
15394 AAAAGTTGTC
* *
15404 TGTCAACAAACAACTTCTCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCA
1 TGTCAA-AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*** * * **
15469 AGACAGTACAAGTTCAACTTCAAGACGAAGGGACTGCTGAC
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
15510 TGT------CAACTTCTTAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
1 TGTCAAAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
15569 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
15609 TGTC-AATA-AA-----CAATTT---A-CCAATTTCAACTTCACAACGAAGGATATTGGACTCAA
1 TGTCAAAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
*** * **
15663 GACAGTACAAGTTCAACTTCAAGACGAAGGGACCGCTGAC
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
15703 TGT------CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
1 TGTCAAAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
15762 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * **
15802 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTT
1 TGTCAAAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
*
15867 GACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
15907 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
1 TGTCAA-AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
15972 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-TGGT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
16012 TGTCAATAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAA-AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
16077 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * *
16118 TGTCAATAAATAATTTCCCAATTTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGGATTCC
1 TGTCAA-AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
16183 AGACAATGCAAGTTC-ACTTCACGACGAAGGGACCGCTGGT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * *
16223 TGTCAATAAACAATTTCTCAATCTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCG
1 TGTCAA-AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
16288 AGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
16329 TGTCAATAAACAATTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAA-AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
16394 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * * ** *
16435 TGTCAACAAACAATTTCCCAGTTCCAAAGCCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 TGTCAA-AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
16498 TGGAACAATA
Statistics
Matches: 895, Mismatches: 69, Indels: 48
0.88 0.07 0.05
Matches are distributed among these distances:
90 2 0.00
94 73 0.08
95 7 0.01
98 6 0.01
99 162 0.18
103 2 0.00
105 294 0.33
106 349 0.39
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (105 bp):
TGTCAAAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:15987 original size:211 final size:210
Alignment explanation
Indices: 15404--16497 Score: 1509
Period size: 211 Copynumber: 5.3 Consensus size: 210
15394 AAAAGTTGTC
*
15404 TGTCAACAAACAACTTCTCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCA
1 TGTCAAC-AACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
*** * * ** *
15469 AGACAGTACAAGTTCAACTTCAAGACGAAGGGACTGCTGACTGT------CAACTTCTTAATTTC
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACTTCTCAATTTC
15528 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
130 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
15593 CGAAGGGACCGCTGGT
195 CGAAGGGACCGCTGGT
*
15609 TGTCAA-TA-AA-----CAATTT---A-CCAATTTCAACTTCACAACGAAGGATATTGGACTCAA
1 TGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAA
*** * **
15663 GACAGTACAAGTTCAACTTCAAGACGAAGGGACCGCTGACTGT------CAACTTCTCAATTTCA
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACTTCTCAATTTCA
15722 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
131 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
15787 GAAGGGACCGCTGGT
196 GAAGGGACCGCTGGT
* **
15802 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTT
1 TGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAA
*
15867 GACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAACTTCTCAATTTC
* *
15932 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
130 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
15997 CGAAGGGACCG-TGGT
195 CGAAGGGACCGCTGGT
* * *
16012 TGTCAATAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAA-CAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
* * *
16077 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAATTT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAACTTCTCAATTT
* * *
16142 CTGAGCCAATTTCAACTTCACAACGAAGGATATTGGATTCCAGACAATGCAAGTTC-ACTTCACG
129 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
16206 ACGAAGGGACCGCTGGT
194 ACGAAGGGACCGCTGGT
* * * * * *
16223 TGTCAATAAACAATTTCTCAATCTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCG
1 TGTCAA-CAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
* * *
16288 AGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAACTTCTCAATTT
*
16353 CAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
129 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
16418 ACGAAGGGACCGCTGGT
194 ACGAAGGGACCGCTGGT
* * * * * ** *
16435 TGTCAACAAACAATTTCCCAGTTCCAAAGCCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 TGTCAAC-AACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
16498 TGGAACAATA
Statistics
Matches: 815, Mismatches: 52, Indels: 37
0.90 0.06 0.04
Matches are distributed among these distances:
193 179 0.22
194 2 0.00
195 2 0.00
197 6 0.01
200 6 0.01
202 2 0.00
203 2 0.00
204 71 0.09
205 6 0.01
210 30 0.04
211 431 0.53
212 78 0.10
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (210 bp):
TGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAA
GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACTTCTCAATTTCA
GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
GAAGGGACCGCTGGT
Found at i:18753 original size:22 final size:22
Alignment explanation
Indices: 18723--18796 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
18713 ATCAATTTTA
* *
18723 ATTTATTTCAATTTAGTTATTC
1 ATTTTTTTCATTTTAGTTATTC
* *
18745 ATTTTTTTCCTTTTTAATT-TT-
1 ATTTTTTT-CATTTTAGTTATTC
18766 AGTATTTTTT-ATTTTAGTTATTC
1 A-T-TTTTTTCATTTTAGTTATTC
18789 ATTTTTTT
1 ATTTTTTT
18797 TCTCTTTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 14 0.34
22 13 0.32
23 14 0.34
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (22 bp):
ATTTTTTTCATTTTAGTTATTC
Found at i:18766 original size:44 final size:44
Alignment explanation
Indices: 18716--18812 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
18706 TTAATCCATC
18716 AATTTTA-ATTTATTTCAATTTAGTTATTCATTTTTTTCCT-TTTT
1 AATTTTAGATTT-TTT-AATTTAGTTATTCATTTTTTTCCTCTTTT
* *
18760 AATTTTAGTATTTTTTATTTTAGTTATTCATTTTTTTTCTCTTTT
1 AATTTTAG-ATTTTTTAATTTAGTTATTCATTTTTTTCCTCTTTT
18805 AATTTTAG
1 AATTTTAG
18813 TGTATTTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
44 29 0.60
45 15 0.31
46 4 0.08
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (44 bp):
AATTTTAGATTTTTTAATTTAGTTATTCATTTTTTTCCTCTTTT
Found at i:18831 original size:44 final size:43
Alignment explanation
Indices: 18733--18831 Score: 144
Period size: 44 Copynumber: 2.3 Consensus size: 43
18723 ATTTATTTCA
*
18733 ATTTAGTTATTCATTTTTTTCCTTTTTAATTTTAGTATTTTTT
1 ATTTAGTTATTCATTTTTTTCCTTTTTAATTTTAGTATATTTT
* *
18776 ATTTTAGTTATTCATTTTTTTTCTCTTTTAATTTTAGTGTATTTT
1 A-TTTAGTTATTCATTTTTTTCCT-TTTTAATTTTAGTATATTTT
*
18821 ATTTATTTATT
1 ATTTAGTTATT
18832 TGTCTTTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
43 1 0.02
44 30 0.60
45 19 0.38
ACGTcount: A:0.19, C:0.06, G:0.05, T:0.70
Consensus pattern (43 bp):
ATTTAGTTATTCATTTTTTTCCTTTTTAATTTTAGTATATTTT
Found at i:21228 original size:7 final size:7
Alignment explanation
Indices: 21228--21264 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
21218 TCAAATCTCA
21228 AAATCAC
1 AAATCAC
21235 AAATCAC
1 AAATCAC
*
21242 AAAACAC
1 AAATCAC
21249 AAATCAC
1 AAATCAC
21256 AAATCAC
1 AAATCAC
21263 AA
1 AA
21265 TTTCATCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.62, C:0.27, G:0.00, T:0.11
Consensus pattern (7 bp):
AAATCAC
Found at i:21251 original size:14 final size:14
Alignment explanation
Indices: 21219--21264 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
21209 TTTTTCCTCT
*
21219 CAAATCTCAAAATCA
1 CAAATCACAAAA-CA
21234 CAAATCACAAAACA
1 CAAATCACAAAACA
*
21248 CAAATCACAAATCA
1 CAAATCACAAAACA
21262 CAA
1 CAA
21265 TTTCATCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.13
Consensus pattern (14 bp):
CAAATCACAAAACA
Found at i:24732 original size:24 final size:24
Alignment explanation
Indices: 24699--24756 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
24689 ATGTTTTTAA
* * *
24699 TGTTAGTTTGATGTATTTGTGGAT
1 TGTTACTTTGATGAATTTATGGAT
*
24723 TGTTACTTTGGTGAATTTATGGAT
1 TGTTACTTTGATGAATTTATGGAT
24747 TGTTACTTTG
1 TGTTACTTTG
24757 CTTTTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.53
Consensus pattern (24 bp):
TGTTACTTTGATGAATTTATGGAT
Found at i:24991 original size:31 final size:31
Alignment explanation
Indices: 24949--25027 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
24939 GTTAACGAGC
24949 AACGAGCACGAGTCGAGCAATAATTTTTTTT
1 AACGAGCACGAGTCGAGCAATAATTTTTTTT
*
24980 AACGAGTACGAGTCGAGCAATAATTTTTTTT
1 AACGAGCACGAGTCGAGCAATAATTTTTTTT
* *
25011 AAAGTGCACGAGTCGAG
1 AACGAGCACGAGTCGAG
25028 TACTGCCTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (31 bp):
AACGAGCACGAGTCGAGCAATAATTTTTTTT
Found at i:31656 original size:50 final size:49
Alignment explanation
Indices: 31481--31701 Score: 358
Period size: 50 Copynumber: 4.5 Consensus size: 49
31471 TGATGAGTTC
* *
31481 TAAT-AAAAATATTTTTATTCAAAATTTTTGTCTCGATTTGATAAATTT
1 TAATAAAAAATATTTTTATTCAAAATTTTTATCTCAATTTGATAAATTT
31529 TAATAAAAAATATTTTTATTC-AAATTTTTATCTCAATTTGATAAATTT
1 TAATAAAAAATATTTTTATTCAAAATTTTTATCTCAATTTGATAAATTT
*
31577 TAATAAAAAATATTTTTATTCAAATTTTTTATCTCAATTTGATAAATTT
1 TAATAAAAAATATTTTTATTCAAAATTTTTATCTCAATTTGATAAATTT
*
31626 TAATAAAAAAATATTTTTATTCAAAATTTTTATCTCGATTTGATAAATTT
1 TAAT-AAAAAATATTTTTATTCAAAATTTTTATCTCAATTTGATAAATTT
31676 TAATAAAAAAATATATTTTATT-AAAA
1 TAAT-AAAAAATAT-TTTTATTCAAAA
31702 CTCACTACTT
Statistics
Matches: 164, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
48 50 0.30
49 46 0.28
50 61 0.37
51 7 0.04
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (49 bp):
TAATAAAAAATATTTTTATTCAAAATTTTTATCTCAATTTGATAAATTT
Found at i:35464 original size:18 final size:18
Alignment explanation
Indices: 35440--35484 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
35430 TAACGGAATG
*
35440 CAAGATTATCGACGGGAA
1 CAAGATTACCGACGGGAA
* *
35458 TAAGATTACCGATGGGAA
1 CAAGATTACCGACGGGAA
35476 CAAGATTAC
1 CAAGATTAC
35485 TGAGAATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (18 bp):
CAAGATTACCGACGGGAA
Found at i:36247 original size:20 final size:19
Alignment explanation
Indices: 36209--36247 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
36199 CAGGTCAAGA
*
36209 AATAATTTAATTTAAATAT
1 AATAATTAAATTTAAATAT
*
36228 AATAATTAAGATTTATATAT
1 AATAATTAA-ATTTAAATAT
36248 TGCACTAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AATAATTAAATTTAAATAT
Found at i:46394 original size:81 final size:83
Alignment explanation
Indices: 46266--46463 Score: 194
Period size: 84 Copynumber: 2.4 Consensus size: 83
46256 ATACGCATAT
* * *
46266 ATATATATATATAATAA-AATAAATAATATAAAAATAATACAAGTAATA-ATACAAGAATAATAA
1 ATATA-ATA-ATAATAATAAT-AATAATAT-AAAATAATACAAATAATATAAACAAGAAGAATAA
46329 AAAG-AAAGAGAA-AGTAAAAA
62 AAAGAAAAGAGAATAGTAAAAA
* *
46349 ATATAATAATAATAATAATAATAATATAAAAT-ATACATATATAATATAAATAAGTAGAATAAAA
1 ATATAATAATAATAATAATAATAATATAAAATAATACA-A-ATAATATAAACAAGAAGAATAAAA
* * *
46413 GGAAAATATAATAGTAAAAA
64 AGAAAAGAGAATAGTAAAAA
* *
46433 AAATAATAA-ATATAATAGTAATAATA-AAAAT
1 ATATAATAATA-ATAATAATAATAATATAAAAT
46464 GCAAAGAAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
79 5 0.05
80 6 0.06
81 20 0.20
82 20 0.20
83 17 0.17
84 30 0.31
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (83 bp):
ATATAATAATAATAATAATAATAATATAAAATAATACAAATAATATAAACAAGAAGAATAAAAAG
AAAAGAGAATAGTAAAAA
Found at i:47063 original size:37 final size:37
Alignment explanation
Indices: 47022--47118 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
47012 GGATCCTATC
*
47022 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCATATT
* * * * *
47059 TTTAGGAGTTTAAATCCTAGCAAAATTTTATCCTATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCATATT
*
47096 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTAAATCCTAGTAG
47119 GACGAAAAGG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAGAACTCTATCATATT
Found at i:47481 original size:164 final size:164
Alignment explanation
Indices: 47163--48854 Score: 1907
Period size: 164 Copynumber: 10.2 Consensus size: 164
47153 AGGTCTTTGG
* * * *
47163 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * *
47228 CGAACTCGAAGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGTTATTCTGTAATTGATGTG
66 CGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
47293 CCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
130 CCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
* * * *
47328 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCATTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * *
47393 CGAACTCGAAGGTCTTTGGTGACATATAACCCTTTTAGCCTTGAGTTATGCTATAAATGATGTGT
66 CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
47458 CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
131 CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
* * * *
47492 TTGGCAGATAGCCCTTCTCGACTTAAGCTTTGCTGCAAATGATGTGTCTTGGAGCTGATCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
47557 CGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGC
66 CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
47622 CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
131 CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
* * * * *
47656 TTGGCAGATATCCCTTCTCGACTTAAGCTATGTTGTAAATGATGCGTCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* ** * ** * ** *
47721 CGAACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATATG
66 CGAACTCGAAGGTCTTT-GGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* * * * * *
47786 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
130 CCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTC-T
* * * * * * *** *
47821 TTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCAGTAAATGATGTGCCCTCAAAGCTGAGTG
1 TT-G-G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCG
* * ** * * * * *
47886 TAATCGAACTCTG-GGGTCTTT-G-G-CAGATAGTCCTTCTCGACTTAAGCTATGCTGCAAATGA
62 TAGTCGAACTC-GAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
* * * * * *
47947 --TGCACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
126 TGTGC-CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
* * * * *
47985 TTGGTTGAAAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGATCG
1 TT-G--G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG
48050 TAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
62 TAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
48115 TGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
126 TGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
* *
48154 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGA-CGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
48218 CGAACTCGAAGGTCTTTGGTGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
66 CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
48283 CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
131 CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
* * * * *
48317 TTGGCAGATAGCCCTTCTCGACTTAAGCTTTACTGCAAATGATGTGTCTTGGAGCTGAGCGTTGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * *
48382 CGAACTCGAAGGTTTTTGGTGAAAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGC
66 CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
48447 CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
131 CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
* *
48481 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * * ** * * *
48546 CGAACTCGAAGGTCTTTGATTGGCAAATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATG
66 CGAACTCGAAGGTCTTTG-GTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* * * * * * *
48611 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATT
130 CCCTCGAAGCTGAGTGTAATCGAACTTGAGGGT-CT
* * * * * * * * *
48646 TTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTG
1 TT-G-G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCG
* * * * * * * *
48711 TAATCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
62 TAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
* * * * * * * * *
48773 GCG-TCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTT
127 GTGCCCTCGAAGCTGAGTGTAATCGAACTTG-AGG-GTCT
* * *
48812 GGTTGGAAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1 --TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
48855 TTGTCTTAAA
Statistics
Matches: 1334, Mismatches: 165, Indels: 56
0.86 0.11 0.04
Matches are distributed among these distances:
163 139 0.10
164 586 0.44
165 399 0.30
166 11 0.01
167 5 0.00
168 102 0.08
169 88 0.07
170 4 0.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (164 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
CCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
Found at i:47889 original size:249 final size:246
Alignment explanation
Indices: 47143--48854 Score: 1673
Period size: 249 Copynumber: 6.9 Consensus size: 246
47133 TTGACAGTAG
* *
47143 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * * * * *
47208 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGA
62 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAA
* * * * * * * * *
47273 GTTATTCTGTAATTGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTT-G-G-CAG
126 GTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * * * * * * * *
47335 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCATTGGAGCTGAGCGTAG
190 ATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCGAAGCTGAGCGTAA
* * * * * *
47392 TCGAACTCGAAGGTCTTTGGTGACATATAACCCTTTTAGCCTTGAGTTATGCTATAAATGATGTG
1 TCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
* * * * * * *
47457 TCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAG
63 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAG
* * *
47519 CTT-TGCTGCAAATGATGTGTCTTGGAGCTGATCGTAGTCGAACTCAAAGGTCTTTGGTGACAGA
127 -TTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
* * * * *
47583 TAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
191 TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTCGAAGCTGAGCGTAA
* * * * * * *
47640 TCGAACTTGAGGGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATGTTGTAAATGATGCGTCT
1 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCT
* *
47705 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCGATTTAAGTTA
66 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTA
* *
47770 TGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAA
130 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAA
* * * * * *
47835 CCCTTCTAGCCTTGAGTTATGCAGTAAATGATGTGCCCTCAAAGCTGAGTGTAA
194 CCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTCGAAGCTGAGCGTAA
* ** * * **
47889 TCGAACTCTG-GGGTCTTTGGCAGATAGTCCTTCTCGACTTAAGCTATGCTGCAAATGATGCACC
1 TCGAACTC-GAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCC
** *
47953 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGAAAGATAACCCTTCTCGATTTAAGTT
65 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTT
* *
48018 ATGCTGCAAATGATATGCCTTGGAGCTGATCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATA
129 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATA
* * * *
48083 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
193 ACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTCGAAGCTGAGCGTAA
* * * *
48138 TCGAACTTGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
1 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCT
* * * * * *
48203 TGGAGCTGA-CGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACTCTTCTAGCCTTGAGTTAT
66 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* * * * * * * *
48267 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTT-G-G-CAGATAGC
131 GCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAAC
* * * * * **
48329 CCTTCTCGACTTAAGCTT-TACTGCAAATGATGTGTCTTGGAGCTGAGCGTTG
195 CCTTCTAGACTTAAG-TTATGCTGCAAATGATGTGCCTCGAAGCTGAGCGTAA
* * * * * *
48381 TCGAACTCGAAGGTTTTTGGTGAAAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
* * * * * * *
48446 CCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAG
63 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAG
* * * * *
48508 CTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGATTGGCAAA
127 TTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG-GTGACAGA
* * * * * *
48573 TAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
191 TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCGAAGCTGAGCGTAA
* * * * *
48629 TCGAACTCGAAGGTATTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGGT-CTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * * * * *
48694 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAA
62 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAA
* * * *
48756 GCTATGCTGCAAATGATGCGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGGA-A
126 GTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T-GACA
* *
48820 GATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
189 GATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
48855 TTGTCTTAAA
Statistics
Matches: 1256, Mismatches: 175, Indels: 64
0.84 0.12 0.04
Matches are distributed among these distances:
243 27 0.02
244 117 0.09
245 108 0.09
246 44 0.04
247 92 0.07
248 261 0.21
249 605 0.48
250 2 0.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (246 bp):
TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCT
TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACC
CTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCGAAGCTGAGCGTAA
Found at i:48730 original size:825 final size:826
Alignment explanation
Indices: 47139--48854 Score: 3042
Period size: 825 Copynumber: 2.1 Consensus size: 826
47129 TGTGTTGACA
* *
47139 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGTAAATG
1 GTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
*
47204 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACATATAACCCTTCTAGCC
66 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCC
* *
47269 TTGAGTTATTCTGTAATTGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCA
131 TTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCA
*
47334 GATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCATTGGAGCTGAGCGTAGTCGAACT
196 GATAACCCTTCTCGACTTAAGCTATACTGCAAATGATATGCATTGGAGCTGAGCGTAGTCGAACT
* * *
47399 CGAAGGTCTTTGGTGACATATAACCCTTTTAGCCTTGAGTTATGCTATAAATGATGTGTCCTCGA
261 CGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGA
*
47464 AGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTTTGCTGCA
326 AGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTTTACTGCA
* *
47529 AATGATGTGTCTTGGAGCTGATCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTA
391 AATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGAAAGATAACCCTTCTA
**
47594 GCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTG
456 GCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTG
* * * *
47659 GCAGATATCCCTTCTCGACTTAAGCTATGTTGTAAATGATGCGTCTTGGAGCTGAGCGTAGTCGA
521 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGA
* *
47724 ACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATATGCCT
586 ACTCGAAGGTCTTTAGTTGGCAAATAACCCTTCTCGATTTAAGTTATGCTACAAATGATATGCCT
*
47789 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTA
651 TGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTA
*
47854 TGCAGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCTGGGGTCTTTGGCAGATAGTCC
716 TGCAGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCTGGGGTCTTTGGCAGATAGCCC
47919 TTCTCGACTTAAGCTATGCTGCAAATGATGCACCTTGGAGCTGAGC
781 TTCTCGACTTAAGCTATGCTGCAAATGATGCACCTTGGAGCTGAGC
*
47965 GTAGTCGAACTCGAAGGTCTTTGGTTGAAAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1 GTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
*
48030 ATATGCCTTGGAGCTGATCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCC
66 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCC
48095 TTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCA
131 TTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCA
* * *
48160 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGA-CGTAGTCGAACT
196 GATAACCCTTCTCGACTTAAGCTATACTGCAAATGATATGCATTGGAGCTGAGCGTAGTCGAACT
* *
48224 CGAAGGTCTTTGGTGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
261 CGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGA
48289 AGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTTTACTGCA
326 AGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTTTACTGCA
* * *
48354 AATGATGTGTCTTGGAGCTGAGCGTTGTCGAACTCGAAGGTTTTTGGTGAAAGATAACCCTTCTA
391 AATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGAAAGATAACCCTTCTA
48419 GCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTG
456 GCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTG
48484 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGA
521 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGA
*
48549 ACTCGAAGGTCTTT-GATTGGCAAATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCC
586 ACTCGAAGGTCTTTAG-TTGGCAAATAACCCTTCTCGATTTAAGTTATGCTACAAATGATATGCC
48613 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGGTGACAGATAACCCTTCTAGCCTTGAGTT
650 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGGTGACAGATAACCCTTCTAGCCTTGAGTT
** *
48678 ATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-GAGGGTCTTTGGCAGATAGC
715 ATGCAGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCTG-GGGTCTTTGGCAGATAGC
**
48742 CCTTCTCGACTTAAGCTATGCTGCAAATGATGCGTCTTGGAGCTGAGC
779 CCTTCTCGACTTAAGCTATGCTGCAAATGATGCACCTTGGAGCTGAGC
*
48790 GTAGTCGAACTCGAAGGTATTTGGTTGGAAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1 GTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
48855 TTGTCTTAAA
Statistics
Matches: 848, Mismatches: 40, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
824 2 0.00
825 610 0.72
826 236 0.28
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (826 bp):
GTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCC
TTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCA
GATAACCCTTCTCGACTTAAGCTATACTGCAAATGATATGCATTGGAGCTGAGCGTAGTCGAACT
CGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGA
AGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTTTACTGCA
AATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGAAAGATAACCCTTCTA
GCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTG
GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTAGTTGGCAAATAACCCTTCTCGATTTAAGTTATGCTACAAATGATATGCCT
TGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTA
TGCAGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCTGGGGTCTTTGGCAGATAGCCC
TTCTCGACTTAAGCTATGCTGCAAATGATGCACCTTGGAGCTGAGC
Found at i:55253 original size:16 final size:15
Alignment explanation
Indices: 55228--55257 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
55218 TTGTGAGGCC
55228 GGTTGTCCCGGGATG
1 GGTTGTCCCGGGATG
55243 GGTTAGTCCCGGGAT
1 GGTT-GTCCCGGGAT
55258 TATCGGCCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.20, G:0.43, T:0.27
Consensus pattern (15 bp):
GGTTGTCCCGGGATG
Found at i:55556 original size:72 final size:72
Alignment explanation
Indices: 55473--55727 Score: 222
Period size: 72 Copynumber: 3.5 Consensus size: 72
55463 AAAAACATTA
* *
55473 TTTTAAAACTATATATAATATACATTTCAAAAATATTTTTTAAAATCATATATTATAAAATTTTA
1 TTTTAAAACTATATATAATATATATTTCAAAAATATTTTTTAAAATCATATATTATAAAATTTTT
55538 AAAAATG
66 AAAAATG
* * * **
55545 CTTTT-AAACTATATGTTATATAGT-TTTC-AAAA-ATGTTTTAAAA-C-TATATTAT-ATGTTT
1 -TTTTAAAACTATATATAATATA-TATTTCAAAAATATTTTTTAAAATCATATATTATAAAATTT
*
55603 TTAAAATTG
64 TTAAAAATG
* * * ** * *
55612 TTTTTTCAAAAATTATATATTATATATATTTTCAAAAATGTTTTAAAAAATTATATATTATATAA
1 --TTTT--AAAACTATATATAATATATA-TTTCAAAAATATTTTTTAAAATCATATATTATAAAA
55677 TTTTTAAAAATG
61 TTTTTAAAAATG
*
55689 TTTTAAAA--ACTATATAATATATTTTTTCAAAAATATTTT
1 TTTTAAAACTA-TATATAATATA-TATTTCAAAAATATTTT
55728 GAAAACTACA
Statistics
Matches: 145, Mismatches: 23, Indels: 29
0.74 0.12 0.15
Matches are distributed among these distances:
67 11 0.08
68 12 0.08
69 1 0.01
70 11 0.08
71 20 0.14
72 47 0.32
73 13 0.09
74 7 0.05
75 4 0.03
76 8 0.06
77 11 0.08
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (72 bp):
TTTTAAAACTATATATAATATATATTTCAAAAATATTTTTTAAAATCATATATTATAAAATTTTT
AAAAATG
Found at i:55634 original size:38 final size:36
Alignment explanation
Indices: 55473--55760 Score: 216
Period size: 35 Copynumber: 7.9 Consensus size: 36
55463 AAAAACATTA
* * ** *
55473 TTTT-AAAACTATATATAATATACATTTCAAAAATAT
1 TTTTAAAAATTATATATTATATATTTTTCAAAAAT-G
* * * * *
55509 TTTTTAAAATCATATATTATAAAATTTTAAAAAATG
1 TTTTAAAAATTATATATTATATATTTTTCAAAAATG
* * *
55545 CTTTT--AAACTATATGTTATATAGTTTTCAAAAATG
1 -TTTTAAAAATTATATATTATATATTTTTCAAAAATG
* * *
55580 TTTT-AAAA--CTATATTATATGTTTTT-AAAATTG
1 TTTTAAAAATTATATATTATATATTTTTCAAAAATG
55612 TTTTTTCAAAAATTATATATTATATATATTTTCAAAAATG
1 --TTTT-AAAAATTATATATTATATAT-TTTTCAAAAATG
55652 TTTTAAAAAATTATATATTATATAATTTTT-AAAAATG
1 TTTT-AAAAATTATATATTATAT-ATTTTTCAAAAATG
* * *
55689 TTTTAAAAACTATATAATATAT-TTTTTCAAAAATA
1 TTTTAAAAATTATATATTATATATTTTTCAAAAATG
* * *
55724 TTTTGAAAACTACATATTATATACGTATTTTCAAAAA
1 TTTTAAAAATTATATATTATATA--T-TTTTCAAAAA
55761 CCATTTGTAA
Statistics
Matches: 206, Mismatches: 29, Indels: 31
0.77 0.11 0.12
Matches are distributed among these distances:
32 6 0.03
33 13 0.06
34 13 0.06
35 52 0.25
36 24 0.12
37 38 0.18
38 38 0.18
39 16 0.08
40 6 0.03
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTTAAAAATTATATATTATATATTTTTCAAAAATG
Found at i:55638 original size:40 final size:40
Alignment explanation
Indices: 55594--55727 Score: 142
Period size: 38 Copynumber: 3.5 Consensus size: 40
55584 AAAACTATAT
* * *
55594 TATATGTTTTTAAAATTGTTTTTTCAAAAATTATATATTA
1 TATATATTTTTAAAAATGTTTTTTAAAAAATTATATATTA
*
55634 TATATATTTTCAAAAATG--TTTTAAAAAATTATATATTA
1 TATATATTTTTAAAAATGTTTTTTAAAAAATTATATATTA
*
55672 TATA-ATTTTTAAAAATG--TTTT-AAAAACTATATA--A
1 TATATATTTTTAAAAATGTTTTTTAAAAAATTATATATTA
*
55706 TATAT-TTTTTCAAAAATATTTT
1 TATATATTTTT-AAAAATGTTTT
55728 GAAAACTACA
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
34 10 0.12
35 6 0.07
36 11 0.13
37 18 0.22
38 23 0.28
40 15 0.18
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (40 bp):
TATATATTTTTAAAAATGTTTTTTAAAAAATTATATATTA
Found at i:55780 original size:2 final size:2
Alignment explanation
Indices: 55773--55799 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55763 ATTTGTAAAC
55773 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55800 CTTCAAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55783 original size:109 final size:107
Alignment explanation
Indices: 55549--55784 Score: 237
Period size: 109 Copynumber: 2.2 Consensus size: 107
55539 AAAATGCTTT
* * * *
55549 TAAACTATATGTTATATAGTTTTCAAAAATGTTTTAAAACTATATTATATGTTTTTAAAATTGTT
1 TAAACTATAT-ATATATAATTTTCAAAAATGTTTTAAAACTATATTATATGTTTTTAAAA-TATA
* * ***
55614 TTTTCAAAAATTATATATTATATATATTTTCAAAAATGTTTTAA
64 TTTTCAAAAACTACATATTATATATATTTTCAAAAACCATTTAA
* * *
55658 AAAATTATATATTATATAATTTTTAAAAATGTTTTAAAAACTATATAATATAT-TTTTTCAAAA-
1 TAAACTATATA-TATATAATTTTCAAAAATGTTTT-AAAACTATAT--TATATGTTTTT-AAAAT
* *
55721 ATATTTT-GAAAACTACATATTATATACGTATTTTCAAAAACCATTT-G
61 ATATTTTCAAAAACTACATATTATATA--TATTTTCAAAAACCATTTAA
55768 TAAACTATATATATATA
1 TAAACTATATATATATA
55785 TATATATATA
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
109 51 0.49
110 24 0.23
111 20 0.19
112 9 0.09
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (107 bp):
TAAACTATATATATATAATTTTCAAAAATGTTTTAAAACTATATTATATGTTTTTAAAATATATT
TTCAAAAACTACATATTATATATATTTTCAAAAACCATTTAA
Found at i:61347 original size:123 final size:121
Alignment explanation
Indices: 61057--61398 Score: 479
Period size: 123 Copynumber: 2.8 Consensus size: 121
61047 TAAGAATGAC
* * * * * *
61057 AATGTTGATGTTTATATGTCTCCTTCTGCGATAGAGTCAAGGAAAATGTTGAACAAGTTCTTCAT
1 AATGTTGATG-TTATATATCTTCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAG
61122 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTATTACGAACTCCTTCTGGA
65 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTATTACGAACTCCTTCTGGA
* * * ** *
61179 AATGTTGATGTTGTTTTATC-TCATTTTATGATAGAGTCAAACAAAAGGTTGAATAAGTTCTTCA
1 AATGTTGATGTT-ATATATCTTC-TTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCA
* * *
61243 GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTATGAACTCCTTTTGGA
64 GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTC-TATTACGAACTCCTTCTGGA
*
61302 AATGTTGATGCTACTATATCTTCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAG
1 AATGTTGATGTTA-TATATCTTCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAG
*
61367 ATTATGAACTTCTTCTTCCTCTTTAGATGAGT
65 ATTATGAACTTCTTCTTCCTCTTCAGATGAGT
61399 CCAAGTGTTT
Statistics
Matches: 192, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
121 3 0.02
122 84 0.44
123 103 0.54
124 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (121 bp):
AATGTTGATGTTATATATCTTCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAGA
TTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTATTACGAACTCCTTCTGGA
Found at i:62338 original size:36 final size:36
Alignment explanation
Indices: 62298--62412 Score: 133
Period size: 36 Copynumber: 3.2 Consensus size: 36
62288 TTTATCTCAA
62298 TTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
1 TTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
** ** * * * *
62334 TTGAGAAAGTTTCACTTGAAATAACAAT-TTATCTCAC
1 TTGAGATTGTTTTTCTTAAAACAA-ACTGTT-TCTCGC
62371 TTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
1 TTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
62407 TTGAGA
1 TTGAGA
62413 AAATTTCACT
Statistics
Matches: 60, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
36 33 0.55
37 27 0.45
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (36 bp):
TTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
Found at i:62355 original size:73 final size:73
Alignment explanation
Indices: 62269--62466 Score: 342
Period size: 73 Copynumber: 2.7 Consensus size: 73
62259 AAAGATTTTC
*
62269 GTTTCACTTGAAATAGCAATTTATCTCAATTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
1 GTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
62334 TTGAGAAA
66 TTGAGAAA
*
62342 GTTTCACTTGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
1 GTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
62407 TTGAGAAA
66 TTGAGAAA
* * * *
62415 ATTTCACTCGAAATAGAAATTTATCTCACTTGAAATTGTTTTTCTTAAAACA
1 GTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
62467 TTTCCTGAAA
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 118 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (73 bp):
GTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGC
TTGAGAAA
Found at i:62375 original size:37 final size:36
Alignment explanation
Indices: 62269--62447 Score: 119
Period size: 37 Copynumber: 4.9 Consensus size: 36
62259 AAAGATTTTC
* * **
62269 GTTTCACTTGAAATAGCAATTTATCTCAATTGAGATT
1 GTTTCACTTGAAATA-AAATTTATCTCACTTGAGAAA
** * * * *
62306 GTTTTTCTTAAAACAAACTGTT-TCTCGCTTGAGAAA
1 GTTTCACTTGAAATAAAAT-TTATCTCACTTGAGAAA
**
62342 GTTTCACTTGAAATAACAATTTATCTCACTTGAGATT
1 GTTTCACTTGAAATAA-AATTTATCTCACTTGAGAAA
** * * * *
62379 GTTTTTCTTAAAACAAACTGTT-TCTCGCTTGAGAAA
1 GTTTCACTTGAAATAAAAT-TTATCTCACTTGAGAAA
* *
62415 ATTTCACTCGAAATAGAAATTTATCTCACTTGA
1 GTTTCACTTGAAATA-AAATTTATCTCACTTGA
62448 AATTGTTTTT
Statistics
Matches: 102, Mismatches: 34, Indels: 12
0.69 0.23 0.08
Matches are distributed among these distances:
36 50 0.49
37 52 0.51
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (36 bp):
GTTTCACTTGAAATAAAATTTATCTCACTTGAGAAA
Found at i:62572 original size:73 final size:73
Alignment explanation
Indices: 62487--62683 Score: 349
Period size: 73 Copynumber: 2.7 Consensus size: 73
62477 GAGTTCGTAA
* * *
62487 TAAGAAAAACAATCTAAAGTGAGATAAATTGCTATTTCGAGTGAAATTTTCTCAAGCGAGAAACA
1 TAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAGAAACA
62552 ATTTGTTT
66 ATTTGTTT
62560 TAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAGAAACA
1 TAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAGAAACA
*
62625 GTTTGTTT
66 ATTTGTTT
*
62633 CAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTC
1 TAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTC
62684 CCCAGCGGAG
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 119 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (73 bp):
TAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAGAAACA
ATTTGTTT
Found at i:62636 original size:36 final size:35
Alignment explanation
Indices: 62521--62683 Score: 105
Period size: 36 Copynumber: 4.5 Consensus size: 35
62511 TAAATTGCTA
* *
62521 TTTCGAGTGAAATTTTCTCAAGCGAGAAACAATTTG
1 TTTCAAGTGAAACTTTCTCAAGCGAGAAAC-ATTTG
* ** ** * *
62557 TTTTAAGAAAAACAATCTCAAGTGAGATAA-ATTGCTA
1 TTTCAAGTGAAACTTTCTCAAGCGAGA-AACATT--TG
62594 TTTCAAGTGAAACTTTCTCAAGCGAGAAACAGTTTG
1 TTTCAAGTGAAACTTTCTCAAGCGAGAAACA-TTTG
** ** * *
62630 TTTCAAGAAAAACAATCTCAAGTGAGATAA-ATTGCTA
1 TTTCAAGTGAAACTTTCTCAAGCGAGA-AACATT--TG
62667 TTTCAAGTGAAACTTTC
1 TTTCAAGTGAAACTTTC
62684 CCCAGCGGAG
Statistics
Matches: 93, Mismatches: 26, Indels: 15
0.69 0.19 0.11
Matches are distributed among these distances:
35 5 0.05
36 45 0.48
37 41 0.44
38 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (35 bp):
TTTCAAGTGAAACTTTCTCAAGCGAGAAACATTTG
Found at i:62673 original size:37 final size:37
Alignment explanation
Indices: 62488--62673 Score: 159
Period size: 37 Copynumber: 5.1 Consensus size: 37
62478 AGTTCGTAAT
*
62488 AAGAAAAACAATCTAAAGTGAGATAAATTGCTATTTC
1 AAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTC
* ** *** * *
62525 GAGTGAAATTTTCTCAAGCGAGAAACAATTTG-T-TTT-
1 AAGAAAAACAATCTCAAGTGAGATA-AA-TTGCTATTTC
62561 AAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTC
1 AAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTC
** ** * *
62598 AAGTGAAACTTTCTCAAGCGAGA-AACAGTT--TGTTTC
1 AAGAAAAACAATCTCAAGTGAGATAA-A-TTGCTATTTC
62634 AAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTC
1 AAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTC
62671 AAG
1 AAG
62674 TGAAACTTTC
Statistics
Matches: 110, Mismatches: 29, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
34 3 0.03
35 5 0.05
36 46 0.42
37 48 0.44
38 5 0.05
39 3 0.03
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (37 bp):
AAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTC
Found at i:63419 original size:2 final size:2
Alignment explanation
Indices: 63412--63447 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
63402 ATTTAATTAA
*
63412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63448 GACTAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:64889 original size:19 final size:19
Alignment explanation
Indices: 64865--64905 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
64855 CAGAAATTGT
64865 TTGAAGGTGTATCGATGCA
1 TTGAAGGTGTATCGATGCA
64884 TTGAAGGTGTATCGATGCA
1 TTGAAGGTGTATCGATGCA
64903 TTG
1 TTG
64906 GTAGTGCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.34
Consensus pattern (19 bp):
TTGAAGGTGTATCGATGCA
Found at i:64916 original size:19 final size:19
Alignment explanation
Indices: 64865--64921 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
64855 CAGAAATTGT
*
64865 TTGAAGGTGTATCGATGCA
1 TTGAAGGTGCATCGATGCA
*
64884 TTGAAGGTGTATCGATGCA
1 TTGAAGGTGCATCGATGCA
*
64903 TTGGTA-GTGCATCGATGCA
1 TT-GAAGGTGCATCGATGCA
64922 CTCTTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 33 0.94
20 2 0.06
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.32
Consensus pattern (19 bp):
TTGAAGGTGCATCGATGCA
Found at i:65006 original size:64 final size:63
Alignment explanation
Indices: 64894--65113 Score: 241
Period size: 64 Copynumber: 3.5 Consensus size: 63
64884 TTGAAGGTGT
** **
64894 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAA-AAA-ACATCGAATGCAATTTGTG
64957 C
63 C
* *
64958 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAA-AAAACATCGAATGCAATTTGTGC
* * * * *
65022 ATCGATGCATAAGTCA-TGCATCGATGCAT-CCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAAGT-AGTGCATCGATGCATCCCATTAATAA-AAAACATCGAATGCAATTTGTGC
* *
65085 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
65114 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
62 1 0.01
63 51 0.38
64 77 0.57
65 6 0.04
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAAAAACATCGAATGCAATTTGTGC
Found at i:65091 original size:63 final size:63
Alignment explanation
Indices: 64938--65113 Score: 223
Period size: 63 Copynumber: 2.8 Consensus size: 63
64928 TAAAATAAAT
* *
64938 ACATCGAATGCAATTTGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAA
1 ACATCGAATGC-ATTTATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAAGGAA
* *
65002 ACATCGAATGCAATTAGTGCATCGATGCATAAGTCA-TGCATCGATGCAT-CCAGTAATAA-TAC
1 ACATCGAATGCATTTA-TGCATCGATGCATAAGT-AGTGCATCGATGCATCCCAGTAATAAGGA-
65064 A
63 A
* * *
65065 ACATCGAATACATTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCA-TTTATGCATCGATGCATAAGTAGTGCATCGATGCAT
65114 ACCTTCATTA
Statistics
Matches: 99, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
62 2 0.02
63 52 0.53
64 44 0.44
65 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (63 bp):
ACATCGAATGCATTTATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAAGGAA
Found at i:66079 original size:103 final size:103
Alignment explanation
Indices: 65854--66071 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
65844 GTCGAGGGTC
65854 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
65919 TTGATCCTTGACATATATATATGATTCTTAAGGAATGA
66 TTGATCCTAGACATATATATATGATTCTTAAGGAATGA
65957 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
66022 TTGATCCCTAG-TATATGTATATGATTCTTAAGGAATGA
66 TTGAT-CCTAGACATATATATATGATTCTTAAGGAATGA
66060 TATGTGGTCCTT
1 TATGTGGTCCTT
66072 ATGGACATTA
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 107 0.96
104 4 0.04
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTAGACATATATATATGATTCTTAAGGAATGA
Found at i:66121 original size:23 final size:23
Alignment explanation
Indices: 66088--66150 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
66078 ATTATTATAT
66088 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
66111 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
66134 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
66151 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Done.