Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014459.1 Corchorus capsularis cultivar CVL-1 contig14480, 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: 194810
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:351 original size:200 final size:198
Alignment explanation
Indices: 5--581 Score: 793
Period size: 200 Copynumber: 2.9 Consensus size: 198
1 ATAC
* *
5 TTAATTAAATATTTAATAGTAATACATATTCCCAAAGGGGACACATGTAAACCCTTAAACCCCGC
1 TTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATG-AAACCCTTAAACCCCGC
** * ** *
70 TTGTGCAGTCTGCTAAACTCCAT-TGACGGTGCATTGTACGATTTTTCTTATAGGATTATAATAC
65 ACGTGCAGTCTGCTAAACT-CATCTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATAC
*
134 AATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTT
129 AATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCA-TT
199 TCATAA
193 TCATAA
205 TTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGAGAACCCTTAAACCCCCG
1 TTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGA-AACCCTTAAA-CCCCG
* *
270 CACGTGCAGTCTGCTAAACTCTTCTGACGG-GTATTGTATAATTTTTCTTATTGGATTATTATAC
64 CACGTGCAGTCTGCTAAACTCATCTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATAC
* *
334 AATACACTGTTAGTGTAAATTTTGGACTCAATAAGCGGGTTAAGAAGTTGACACATACCCCATTT
129 AATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTT
399 CATAA
194 CATAA
*
404 TTAATTAGTAAATATTTAATATTAGTACATATTCCCTAAGGGGACACATGACAACCCTTAAACCC
1 TTAA-T--TAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGA-AACCCTTAAACCC
* * * * * * * *
469 CACACGTGTAGCCTGTTAAACTCCA-CTAATGGTGTAATATATAATTTTTCTTATAGGA-TATTA
62 CGCACGTGCAGTCTGCTAAACT-CATCTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTA
* * * **
532 TATAATACACTATCAGTGTAAATTTTGGACTTCATAAGCATGTTAAGAAG
126 TACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAG
582 CTTTTGTGCT
Statistics
Matches: 337, Mismatches: 32, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
199 13 0.04
200 146 0.43
201 103 0.31
202 75 0.22
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (198 bp):
TTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGAAACCCTTAAACCCCGCA
CGTGCAGTCTGCTAAACTCATCTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAA
TACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCA
TAA
Found at i:1098 original size:13 final size:13
Alignment explanation
Indices: 1074--1113 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1064 ATGTCTCAAA
1074 ATATAT-ATATAT
1 ATATATAATATAT
1086 ATATATAATATAT
1 ATATATAATATAT
1099 ATAT-TCAATATAT
1 ATATAT-AATATAT
1112 AT
1 AT
1114 TTTCGTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.27
13 19 0.73
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:1113 original size:2 final size:2
Alignment explanation
Indices: 1074--1102 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1064 ATGTCTCAAA
1074 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1103 TCAATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2313 original size:49 final size:49
Alignment explanation
Indices: 2260--2367 Score: 198
Period size: 49 Copynumber: 2.2 Consensus size: 49
2250 AAAGATTAAA
2260 ACATAAAATTGTTACAAAATTGATCAAAACTAAAAATAAAAGGAGTAAG
1 ACATAAAATTGTTACAAAATTGATCAAAACTAAAAATAAAAGGAGTAAG
2309 ACATAAAATTGTTACAAAATTGATCAAAACTAAAAATAAAAGGAGTAAG
1 ACATAAAATTGTTACAAAATTGATCAAAACTAAAAATAAAAGGAGTAAG
2358 AGCTATAAAA
1 A-C-ATAAAA
2368 AGAGAATTCA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
49 50 0.88
50 1 0.02
51 6 0.11
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.22
Consensus pattern (49 bp):
ACATAAAATTGTTACAAAATTGATCAAAACTAAAAATAAAAGGAGTAAG
Found at i:3029 original size:22 final size:21
Alignment explanation
Indices: 2979--3030 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
2969 ATAAAAGCAG
2979 TGAAAAATCATGATATGTTGA
1 TGAAAAATCATGATATGTTGA
*
3000 TCATAAAATCATGATTATGGTT-A
1 TGA-AAAATCATGA-TAT-GTTGA
3023 TGAAAAAT
1 TGAAAAAT
3031 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.08
22 15 0.58
23 6 0.23
24 3 0.12
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (21 bp):
TGAAAAATCATGATATGTTGA
Found at i:5721 original size:30 final size:30
Alignment explanation
Indices: 5685--5745 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
5675 CTAAGTTATC
5685 TAAATTACCCTTGTTAGTGGTAGTAGAAAT
1 TAAATTACCCTTGTTAGTGGTAGTAGAAAT
5715 TAAATTACCCTTGTTAGTGGTAGTAGAAAT
1 TAAATTACCCTTGTTAGTGGTAGTAGAAAT
5745 T
1 T
5746 TAGTTGGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (30 bp):
TAAATTACCCTTGTTAGTGGTAGTAGAAAT
Found at i:8159 original size:2 final size:2
Alignment explanation
Indices: 8148--8180 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
8138 GTTTCATTAT
8148 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8181 ATGATATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13660 original size:4 final size:4
Alignment explanation
Indices: 13653--13687 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
13643 AAATAAACAA
13653 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
13688 AGCAGAGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:13840 original size:21 final size:20
Alignment explanation
Indices: 13816--13856 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
13806 AATCCATAAT
* *
13816 GTTGGTGTTGAGATTCTTGAG
1 GTTGGTATTGA-AATCTTGAG
13837 GTTGGTATTGAAATCTTGAG
1 GTTGGTATTGAAATCTTGAG
13857 ATTCTTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.05, G:0.34, T:0.41
Consensus pattern (20 bp):
GTTGGTATTGAAATCTTGAG
Found at i:13961 original size:24 final size:24
Alignment explanation
Indices: 13921--13966 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
13911 ATGTTCTTGT
* *
13921 TGAAATCCTTGAAGTTGGTGTTAA
1 TGAAATCCTCGAAGTTGATGTTAA
*
13945 TGAAATCCTCGATGTTGATGTT
1 TGAAATCCTCGAAGTTGATGTT
13967 CAAAACACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (24 bp):
TGAAATCCTCGAAGTTGATGTTAA
Found at i:14147 original size:17 final size:17
Alignment explanation
Indices: 14121--14190 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
14111 AGATCAAATA
14121 AATGTTAACTAAATACT
1 AATGTTAACTAAATACT
*
14138 AATTTTAACTAAATACT
1 AATGTTAACTAAATACT
* * *
14155 TATGTTCATTAAATACT
1 AATGTTAACTAAATACT
*
14172 AATGTTAACAAAATACT
1 AATGTTAACTAAATACT
14189 AA
1 AA
14191 CAACAACAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.37
Consensus pattern (17 bp):
AATGTTAACTAAATACT
Found at i:14841 original size:18 final size:18
Alignment explanation
Indices: 14818--14852 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
14808 TACAAACACT
14818 GAAATTGTTCATAAACAA
1 GAAATTGTTCATAAACAA
*
14836 GAAATTGTTCATGAACA
1 GAAATTGTTCATAAACA
14853 TGGTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (18 bp):
GAAATTGTTCATAAACAA
Found at i:17442 original size:87 final size:87
Alignment explanation
Indices: 17291--17459 Score: 302
Period size: 87 Copynumber: 1.9 Consensus size: 87
17281 TCATGATTCA
*
17291 TAGCAACTTGTAGTTAAAATAATTTTCTAAACATGAATGAACATTTGATTCAATAGTTTGATTGA
1 TAGCAACTTGTAGTTAAAATAATTTTCTAAACATGAATGAACATTTAATTCAATAGTTTGATTGA
17356 TATCTCTAACTAAGTTTTACTT
66 TATCTCTAACTAAGTTTTACTT
* * *
17378 TAGCGACTTGTAGTTAAAATCATTTTGTAAACATGAATGAACATTTAATTCAATAGTTTGATTGA
1 TAGCAACTTGTAGTTAAAATAATTTTCTAAACATGAATGAACATTTAATTCAATAGTTTGATTGA
17443 TATCTCTAACTAAGTTT
66 TATCTCTAACTAAGTTT
17460 GAATCCCTTC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (87 bp):
TAGCAACTTGTAGTTAAAATAATTTTCTAAACATGAATGAACATTTAATTCAATAGTTTGATTGA
TATCTCTAACTAAGTTTTACTT
Found at i:33736 original size:14 final size:11
Alignment explanation
Indices: 33704--33732 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
33694 TAACATAAAA
33704 TTTTTTTGTTC
1 TTTTTTTGTTC
33715 TTTTTTTGTTC
1 TTTTTTTGTTC
33726 TTTTTTT
1 TTTTTTT
33733 TTTGGCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTTTTGTTC
Found at i:34112 original size:31 final size:31
Alignment explanation
Indices: 34071--34168 Score: 106
Period size: 31 Copynumber: 3.2 Consensus size: 31
34061 AAAAAGTCGT
* *
34071 GCCACATGTACCAAAAAGTGACACATGTCAC
1 GCCACGTGTACCAAAAAGTGACACATGGCAC
* *
34102 GCCACGTGTACCAAAAAGTGACACGTGGCAT
1 GCCACGTGTACCAAAAAGTGACACATGGCAC
** * * * *
34133 GCCACGTGTTTCAAAAAATGGCACGTGGCAT
1 GCCACGTGTACCAAAAAGTGACACATGGCAC
34164 GCCAC
1 GCCAC
34169 ATGCATAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGTGACACATGGCAC
Found at i:53105 original size:6 final size:6
Alignment explanation
Indices: 53091--53129 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
53081 GAAAACAAAC
* *
53091 TGAAAA TGAACA TGAAAA TGAACA TGAAAA TGAAAA TGA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TGA
53130 GATGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.59, C:0.05, G:0.18, T:0.18
Consensus pattern (6 bp):
TGAAAA
Found at i:53108 original size:12 final size:12
Alignment explanation
Indices: 53091--53129 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
53081 GAAAACAAAC
53091 TGAAAATGAACA
1 TGAAAATGAACA
53103 TGAAAATGAACA
1 TGAAAATGAACA
*
53115 TGAAAATGAAAA
1 TGAAAATGAACA
53127 TGA
1 TGA
53130 GATGTAAACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.59, C:0.05, G:0.18, T:0.18
Consensus pattern (12 bp):
TGAAAATGAACA
Found at i:59874 original size:6 final size:6
Alignment explanation
Indices: 59863--59889 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
59853 GAAAACAAAC
59863 TGAAAA TGAAAA TGAAAA TGAAAA TGA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGA
59890 GATGTAAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAAAA
Found at i:70221 original size:3 final size:3
Alignment explanation
Indices: 70213--70244 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
70203 TTTACCCAAA
70213 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
70245 ATATATCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:88347 original size:31 final size:32
Alignment explanation
Indices: 88312--88373 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
88302 CCCAAACAGC
88312 ACTG-TGACGTGGACATG-CCACATCAGCTTTT
1 ACTGTTGACGTGG-CATGTCCACATCAGCTTTT
*
88343 ACTGTTGACGTGGCATGTCCACATTAGCTTT
1 ACTGTTGACGTGGCATGTCCACATCAGCTTT
88374 CACTAGGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (32 bp):
ACTGTTGACGTGGCATGTCCACATCAGCTTTT
Found at i:88596 original size:31 final size:31
Alignment explanation
Indices: 88554--88613 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
88544 CTGTGAGGTT
*
88554 GGGGAGAGATTGAGCCGATTTTGTAAATTAA
1 GGGGAGAGATTGAGCCGATTTTATAAATTAA
* *
88585 GGGGGGAGATTGAGCTGATTTTATAAATT
1 GGGGAGAGATTGAGCCGATTTTATAAATT
88614 CATAGGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (31 bp):
GGGGAGAGATTGAGCCGATTTTATAAATTAA
Found at i:96816 original size:18 final size:18
Alignment explanation
Indices: 96793--96829 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
96783 GAAGGGTGAC
96793 ATGTGTCCTATAGGAACT
1 ATGTGTCCTATAGGAACT
96811 ATGTGTCCTATAGGAACT
1 ATGTGTCCTATAGGAACT
96829 A
1 A
96830 GATTGAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (18 bp):
ATGTGTCCTATAGGAACT
Found at i:100213 original size:8 final size:8
Alignment explanation
Indices: 100200--100225 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
100190 CTACCTACCT
100200 AACAAATA
1 AACAAATA
100208 AACAAATA
1 AACAAATA
100216 AACAAATA
1 AACAAATA
100224 AA
1 AA
100226 TTAAACCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AACAAATA
Found at i:100779 original size:53 final size:53
Alignment explanation
Indices: 100716--100822 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
100706 TTGTTATCAT
*
100716 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAGAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
100769 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
100822 T
1 T
100823 AAAACAGCCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
Found at i:125962 original size:246 final size:245
Alignment explanation
Indices: 125497--126007 Score: 659
Period size: 246 Copynumber: 2.1 Consensus size: 245
125487 CTTTTAATTG
* * * *
125497 ACCTCAGATTCCTTACCAGATGAAGCATTTTCAGCAACCTTAGAATCTGGGTCACTCTCATTTGC
1 ACCTCAGATTCCTTCCCTGAGGAAGCATTTTCAGCAACCTTAGAATCTGAGTCACTCTCATTTGC
* * * * * *
125562 CACTGATAACCCGTTTCTTAGTGATCTTTGGCTTGTCGACGCCTCTGTTTCATCCTTGCAGCAAT
66 CACTGATAACCCATCTCCTACTGATCTTTGGCTTGTCGACGCCTCTGCTTCATCCTTGCAGCAAC
* * * ** *
125627 GCTGTCTGGGCTATGTTCCATCGCAGAGGCAGGCCTCTTCTTAAGCTTTGGGCTAGTCTCTGATG
131 ACTGTCTGGGCTATGATCCATAGCAGAAACAGGCCTCTTCTTAAGCTTTGGGCTACTCTCTGATG
*
125692 CAATATAGCCTTCACCTATATTGTCATTAGCATT-GTGCATCTCCTTCTTA
196 CAATATAGCCTTCACCTATATTGTCATTAGC-TTCATGCATCTCCTTCTTA
* * * * *
125742 ACTTCAGGTTCCTTCCCTGAGGAAGCATTTTCAGCAACCTTTGAATCTGATTTACTCTCATTTGC
1 ACCTCAGATTCCTTCCCTGAGGAAGCATTTTCAGCAACCTTAGAATCTGAGTCACTCTCATTTGC
** * *
125807 CACTGATAATTCATGCTCCTCCTGATCTTT-GCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCA
66 CACTGATAACCCAT-CTCCTACTGATCTTTGGC-TTGTCGACGCCTCTGCTTCATCCTTGCAGCA
* *
125871 ACACTGTCTGGGCTTTGATCCGTAGCAGAAACA-GCCTGCTTCTTAAGCTTTGGGCTACTCTCTG
129 ACACTGTCTGGGCTATGATCCATAGCAGAAACAGGCCT-CTTCTTAAGCTTTGGGCTACTCTCTG
* * * * *
125935 ATGCAATATAGCCTTTACCTTTATTGTCGTTGGCTTCATGCATTTCCTTCTTA
193 ATGCAATATAGCCTTCACCTATATTGTCATTAGCTTCATGCATCTCCTTCTTA
*
125988 ACCTCAGATTCCTTCACTGA
1 ACCTCAGATTCCTTCCCTGA
126008 CAATTCATGC
Statistics
Matches: 226, Mismatches: 36, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
245 75 0.33
246 151 0.67
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (245 bp):
ACCTCAGATTCCTTCCCTGAGGAAGCATTTTCAGCAACCTTAGAATCTGAGTCACTCTCATTTGC
CACTGATAACCCATCTCCTACTGATCTTTGGCTTGTCGACGCCTCTGCTTCATCCTTGCAGCAAC
ACTGTCTGGGCTATGATCCATAGCAGAAACAGGCCTCTTCTTAAGCTTTGGGCTACTCTCTGATG
CAATATAGCCTTCACCTATATTGTCATTAGCTTCATGCATCTCCTTCTTA
Found at i:126152 original size:195 final size:195
Alignment explanation
Indices: 125807--126180 Score: 640
Period size: 195 Copynumber: 1.9 Consensus size: 195
125797 TCTCATTTGC
*
125807 CACTGATAATTCATGCTCCTCCTGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
1 CACTGACAATTCATGCTCCTCCTGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
*
125872 CACTGTCTGGGCTTTGATCCGTAGCAGAAACAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
66 CACTGTCTGGGCTTTGATACGTAGCAGAAACAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
* * *
125937 GCAATATAGCCTTTACCTTTATTGTCGTTGGCTTCATGCATTTCCTTCTTAACCTCAGATTCCTT
131 GCAATACAGCCTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCTTAACCTCAGATTCCTT
*
126002 CACTGACAATTCATGCTCTTCCTGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
1 CACTGACAATTCATGCTCCTCCTGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
* * * * *
126067 TACTGTTTGGGCTTTGATACGTAGCAGAAGCAGGCTGCTTCTTAGGCTTTGGGCTACTCTCTGAT
66 CACTGTCTGGGCTTTGATACGTAGCAGAAACAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
*
126132 GCAATACAGTCTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCT
131 GCAATACAGCCTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCT
126181 CTTGGACTAG
Statistics
Matches: 167, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
195 167 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (195 bp):
CACTGACAATTCATGCTCCTCCTGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
CACTGTCTGGGCTTTGATACGTAGCAGAAACAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
GCAATACAGCCTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCTTAACCTCAGATTCCTT
Found at i:128068 original size:96 final size:97
Alignment explanation
Indices: 127882--128080 Score: 310
Period size: 96 Copynumber: 2.0 Consensus size: 97
127872 ATAAAGGTGA
*
127882 AAGACTAAAACACCTAAACTTTCTTTATTATAATTGAACCGACTCCATTAGAGCTTTAGGACATT
1 AAGACTAAAACACCTAAACTTTCATTATTATAATTGAACCG----C-TTAGAGCTTTAGGACATT
*
127947 TATGAGGAGAAACTCCTAATATCAGTAGCTAAGAATG
61 AATGAGGAGAAACTCCTAATATCAGTAGCTAAGAATG
127984 AAGACTAAAACACCTAAACTTTCATTATTATAATTGAACCG-TTAGAGCTTTAGGACATTAATGA
1 AAGACTAAAACACCTAAACTTTCATTATTATAATTGAACCGCTTAGAGCTTTAGGACATTAATGA
* *
128048 GGAGAAACTTCTAATCTCAGTAGCTAAGAATG
66 GGAGAAACTCCTAATATCAGTAGCTAAGAATG
128080 A
1 A
128081 TGTAATTAGA
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
96 53 0.57
102 40 0.43
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (97 bp):
AAGACTAAAACACCTAAACTTTCATTATTATAATTGAACCGCTTAGAGCTTTAGGACATTAATGA
GGAGAAACTCCTAATATCAGTAGCTAAGAATG
Found at i:131427 original size:246 final size:245
Alignment explanation
Indices: 130974--131482 Score: 695
Period size: 246 Copynumber: 2.1 Consensus size: 245
130964 TTAATTGACT
* * * * *
130974 TCAGATTCCTTACCAGATGAAGCATTTTCAGCAACCTTAGAATCTGGGCCACTCTCATTTGCCAC
1 TCAGATTCCTTCCCTGATAAAGCATTTTCAGCAACCTTAGAATCTGAGCCACTCTCATATGCCAC
* * * *
131039 TGATAACCTGTCTTCTTAGTTATCTTTGGCTTGTCGACGCCTTTGTTTCATCCTTGCAGCAATAC
66 TGATAACATGTCTTCTCAG-TATCTTTGGCTTGTCGACGCCTTTGCTTCATCCTTGCAGCAACAC
* * * *
131104 TGTCTGGGCTATGTTCCATCGCAGAGGCAAGCCTCTTCTTAAGCTTTGGGCTAGTCTCTGATGCA
130 TGTCTGGGCTATGATCCATAGCAGAAGCAAGCCTCTTCTTAAGCTTTGGGCTACTCTCTGATGCA
*
131169 ATATAGCCTTCACCTTTATTGTCATTAGCATT-GTGCATTTCCTTCTTAACC
195 ATATAGCCTTCACCTTTATTGTCATTAGC-TTCATGCATTTCCTTCTTAACC
* * ***
131220 TCAGGTTCCTTCCCTGATAAAGCATTTTCAGCAACCTTTGAATCTGATTTACTCTCATATGCCAC
1 TCAGATTCCTTCCCTGATAAAGCATTTTCAGCAACCTTAGAATCTGAGCCACTCTCATATGCCAC
*
131285 TGATAATTCATGCTCTTC-CCG-ATCTTT-GCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
66 TGATAA--CATG-TCTTCTCAGTATCTTTGGC-TTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
* * *
131347 CACTGTCTGGGGTTTGATCCATAGCAGAAGC-ATCCTGCTTCTTAAGCTTTGGGCTACTCTCTGA
127 CACTGTCTGGGCTATGATCCATAGCAGAAGCAAGCCT-CTTCTTAAGCTTTGGGCTACTCTCTGA
*
131411 TGCAATATAGCCTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCTTAACC
191 TGCAATATAGCCTTCACCTTTATTGTCATTAGCTTCATGCATTTCCTTCTTAACC
*
131466 TCAGATTCCTTCACTGA
1 TCAGATTCCTTCCCTGA
131483 CAATTCATGC
Statistics
Matches: 231, Mismatches: 26, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
245 8 0.03
246 214 0.93
248 4 0.02
249 5 0.02
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.37
Consensus pattern (245 bp):
TCAGATTCCTTCCCTGATAAAGCATTTTCAGCAACCTTAGAATCTGAGCCACTCTCATATGCCAC
TGATAACATGTCTTCTCAGTATCTTTGGCTTGTCGACGCCTTTGCTTCATCCTTGCAGCAACACT
GTCTGGGCTATGATCCATAGCAGAAGCAAGCCTCTTCTTAAGCTTTGGGCTACTCTCTGATGCAA
TATAGCCTTCACCTTTATTGTCATTAGCTTCATGCATTTCCTTCTTAACC
Found at i:131621 original size:195 final size:195
Alignment explanation
Indices: 131282--131668 Score: 695
Period size: 195 Copynumber: 2.0 Consensus size: 195
131272 TCTCATATGC
*
131282 CACTGATAATTCATGCTCTTCCCGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
1 CACTGACAATTCATGCTCTTCCCGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
* * *
131347 CACTGTCTGGGGTTTGATCCATAGCAGAAGCATCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
66 CACTGTCTGGGCTTTGATCCATAGCAGAAACAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
*
131412 GCAATATAGCCTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCTTAACCTCAGATTCCTT
131 GCAATATAGCCTTCACCTGTATTGTCATTGGCTTCATGCATTTCCTTCTTAACCTCAGATTCCTT
*
131477 CACTGACAATTCATGCTCTTCCTGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
1 CACTGACAATTCATGCTCTTCCCGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
*
131542 CACTGTCTGGGCTTTGAT-CAGTAGCAGAAACAGCCTGCTTCTTAAGCTTTGGGCTACTCTTTGA
66 CACTGTCTGGGCTTTGATCCA-TAGCAGAAACAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGA
131606 TGCAATATAGCCTTCACCTGTATTGTCATTGGCTTCATGCATTTCCTTCTTAACCTCAGATTC
130 TGCAATATAGCCTTCACCTGTATTGTCATTGGCTTCATGCATTTCCTTCTTAACCTCAGATTC
131669 TATCCCTGAT
Statistics
Matches: 184, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
194 2 0.01
195 182 0.99
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (195 bp):
CACTGACAATTCATGCTCTTCCCGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
CACTGTCTGGGCTTTGATCCATAGCAGAAACAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
GCAATATAGCCTTCACCTGTATTGTCATTGGCTTCATGCATTTCCTTCTTAACCTCAGATTCCTT
Found at i:131883 original size:441 final size:441
Alignment explanation
Indices: 131060--131901 Score: 1388
Period size: 441 Copynumber: 1.9 Consensus size: 441
131050 CTTCTTAGTT
* * * *
131060 ATCTTTGGCTTGTCGACGCCTTTGTTTCATCCTTGCAGCAATACTGTCTGGGCTATGTTCCATCG
1 ATCTTTGGCTTGTCGACGCCTTTGCTTCATCCTTGCAGCAACACTGTCTGGGCTATGATCCATAG
** * *
131125 CAGAGGCAAGCCTCTTCTTAAGCTTTGGGCTAGTCTCTGATGCAATATAGCCTTCACCTTTATTG
66 CAGAAACAAGCCTCTTCTTAAGCTTTGGGCTACTCTCTGATGCAATATAGCCTTCACCTGTATTG
* *
131190 TCATTAGCATTGTGCATTTCCTTCTTAACCTCAGGTTCCTTCCCTGATAAAGCATTTTCAGCAAC
131 TCATTAGCATTATGCATTTCCTTCTTAACCTCAGATTCCTTCCCTGATAAAGCATTTTCAGCAAC
*
131255 CTTTGAATCTGATTTACTCTCATATGCCACTGATAATTCATGCTCTTCCCGATCTTTGCTTTGTC
196 CTTTGAATCTGATTTACTCTCATATGCCACTGATAATCCATGCTCTTCCCGATCTTTGCTTTGTC
* *
131320 GACGCCTTTGCTTCATCCTTGCAGCAACACTGTCTGGGGTTTGATCCATAGCAGAAGCATCCTGC
261 GACGCCTTTGCTTCATCCTTGCAGCAACACTGTCTGGGCTTTGATCCATAGCAGAAGCAGCCTGC
* *
131385 TTCTTAAGCTTTGGGCTACTCTCTGATGCAATATAGCCTTCACCTTTATTGTCATTGGCTTCATG
326 TTCTTAAGCTTTGGGCTACTCTCTGATGCAATATAGCCTTCACCTTTATTATCATTGGCTCCATG
131450 CATTTCCTTCTTAACCTCAGATTCCTTCACTGACAATTCATGCTCTTCCTG
391 CATTTCCTTCTTAACCTCAGATTCCTTCACTGACAATTCATGCTCTTCCTG
*
131501 ATCTTT-GCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAACACTGTCTGGGCTTTGAT-CAGT
1 ATCTTTGGC-TTGTCGACGCCTTTGCTTCATCCTTGCAGCAACACTGTCTGGGCTATGATCCA-T
*
131564 AGCAGAAAC-AGCCTGCTTCTTAAGCTTTGGGCTACTCTTTGATGCAATATAGCCTTCACCTGTA
64 AGCAGAAACAAGCCT-CTTCTTAAGCTTTGGGCTACTCTCTGATGCAATATAGCCTTCACCTGTA
* *
131628 TTGTCATTGGC-TTCATGCATTTCCTTCTTAACCTCAGATT-CTATCCCTGATGAAGCATTTTCA
128 TTGTCATTAGCATT-ATGCATTTCCTTCTTAACCTCAGATTCCT-TCCCTGATAAAGCATTTTCA
* *
131691 GCAACCTTTGAATCTGATTTACTCTCATTTGCCACTGATAATCCATGCTCTTCCTGATCTTTGCT
191 GCAACCTTTGAATCTGATTTACTCTCATATGCCACTGATAATCCATGCTCTTCCCGATCTTTGCT
*
131756 TTGTCGACGCCTTTGCTTCATCCTTGCAGCAATACTGTCTGGGCTTTGATCCATAGCAGAAGCAG
256 TTGTCGACGCCTTTGCTTCATCCTTGCAGCAACACTGTCTGGGCTTTGATCCATAGCAGAAGCAG
* *
131821 GCTGCTTCTTAAGCTTTGGTCTACTCTCTGATGCAATATAGCCTTCACCTTTATTATCATTGGCT
321 CCTGCTTCTTAAGCTTTGGGCTACTCTCTGATGCAATATAGCCTTCACCTTTATTATCATTGGCT
131886 CCATGCATTTCCTTCT
386 CCATGCATTTCCTTCT
131902 CTTGGACTAG
Statistics
Matches: 372, Mismatches: 24, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
440 13 0.03
441 359 0.97
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (441 bp):
ATCTTTGGCTTGTCGACGCCTTTGCTTCATCCTTGCAGCAACACTGTCTGGGCTATGATCCATAG
CAGAAACAAGCCTCTTCTTAAGCTTTGGGCTACTCTCTGATGCAATATAGCCTTCACCTGTATTG
TCATTAGCATTATGCATTTCCTTCTTAACCTCAGATTCCTTCCCTGATAAAGCATTTTCAGCAAC
CTTTGAATCTGATTTACTCTCATATGCCACTGATAATCCATGCTCTTCCCGATCTTTGCTTTGTC
GACGCCTTTGCTTCATCCTTGCAGCAACACTGTCTGGGCTTTGATCCATAGCAGAAGCAGCCTGC
TTCTTAAGCTTTGGGCTACTCTCTGATGCAATATAGCCTTCACCTTTATTATCATTGGCTCCATG
CATTTCCTTCTTAACCTCAGATTCCTTCACTGACAATTCATGCTCTTCCTG
Found at i:139614 original size:5 final size:5
Alignment explanation
Indices: 139604--139630 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
139594 CCAATTTCCC
139604 CCAAA CCAAA CCAAA CCAAA CCAAA CC
1 CCAAA CCAAA CCAAA CCAAA CCAAA CC
139631 CCACATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAA
Found at i:139823 original size:1 final size:1
Alignment explanation
Indices: 139817--139845 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
139807 TTTCATTAGG
139817 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
139846 AATTTTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:146451 original size:21 final size:21
Alignment explanation
Indices: 146422--146500 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 21
146412 GCAGTTACAA
* *
146422 TTTCCACAGCAACAGCAACCG
1 TTTCAACAGCAGCAGCAACCG
*
146443 TTTCAACAGCAGCAGCAGCCG
1 TTTCAACAGCAGCAGCAACCG
*
146464 TTTCAGCAGCAGCAGCAA-C-
1 TTTCAACAGCAGCAGCAACCG
*
146483 -TTCAACAGCAGCAACAAC
1 TTTCAACAGCAGCAGCAAC
146501 AACAACTGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.30
20 1 0.02
21 34 0.68
ACGTcount: A:0.34, C:0.34, G:0.18, T:0.14
Consensus pattern (21 bp):
TTTCAACAGCAGCAGCAACCG
Found at i:146486 original size:18 final size:18
Alignment explanation
Indices: 146449--146500 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
146439 ACCGTTTCAA
***
146449 CAGCAGCAGCAGCCGTTT
1 CAGCAGCAGCAGCAACTT
146467 CAGCAGCAGCAGCAACTT
1 CAGCAGCAGCAGCAACTT
* *
146485 CAACAGCAGCAACAAC
1 CAGCAGCAGCAGCAAC
146501 AACAACTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.35, G:0.21, T:0.10
Consensus pattern (18 bp):
CAGCAGCAGCAGCAACTT
Found at i:156778 original size:32 final size:32
Alignment explanation
Indices: 156740--156803 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
156730 ACATTAGGAA
156740 ACAGATGGTGAAGAAAGAGAGACATTTTGTGC
1 ACAGATGGTGAAGAAAGAGAGACATTTTGTGC
156772 ACAGATGGTGAAGAAAGAGAGACATTTTGTGC
1 ACAGATGGTGAAGAAAGAGAGACATTTTGTGC
156804 TAGTCCATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.31, T:0.22
Consensus pattern (32 bp):
ACAGATGGTGAAGAAAGAGAGACATTTTGTGC
Found at i:161305 original size:178 final size:176
Alignment explanation
Indices: 160816--161316 Score: 472
Period size: 177 Copynumber: 2.8 Consensus size: 176
160806 TTAACACTAT
* * * ** *
160816 ATAATTTTCGTTCCGGATATCCGATCAAGGTGATTCAAGTATTTATTAAAAGGTTGTTCCATGAT
1 ATAATTTTTGTTCCAGATGTCCGATTGAGGTGATTCAAGTATCTATTAAAAGGTTGTTCCATGAT
* * * *
160881 TTACAACTTTCATGAAGGATTCAAAAAT-TGAATTTAATGTTT-AAAGTATCAAAATTACTT-TC
66 CTACAACTTTCATGAAGGATTC-GAAATCTAAATTTAATGTTTCAAA-TAACAAAATT-CTTCT-
* * * *
160943 GAAAAATTAGTTGTTTCGGTTAATGGGAATGGACATTCCACCTAATATTA
127 GAAAATTTAGTTGTTTCGGTTAACGAGAATGGACAGTCCACCTAATATTA
* * * * * * * * ** *
160993 ATAACTTTTGCTCCAGATGTCTGATTGAGGTAATTAAACTGTCTCTTAAAAGGTTGTTTTATTAT
1 ATAATTTTTGTTCCAGATGTCCGATTGAGGTGATTCAAGTATCTATTAAAAGGTTGTTCCATGAT
* * * * * * * * * **
161058 CTACAACTTTCATTAAGAATTTGAAAGCTAAGTTTAATGTTTCGAGTAAAAAAAATGCTTCCAAA
66 CTACAACTTTCATGAAGGATTCGAAATCTAAATTTAATGTTTCAAAT-AACAAAATTCTTCTGAA
* * *
161123 AATTTAGTTGTTTCGGTTAGCGAGAATGGACGGTCCACTTAATATTA
130 AATTTAGTTGTTTCGGTTAACGAGAATGGACAGTCCACCTAATATTA
* * *
161170 CATAATTTTTGTTCCAAATGTCCGATTGAGGTGATTCAAGTACCTGTTAAAAGGTTGTTCCATGA
1 -ATAATTTTTGTTCCAGATGTCCGATTGAGGTGATTCAAGTATCTATTAAAAGGTTGTTCCATGA
* * * *
161235 TCTACGACTTTCATGAAGGACTCGAAATCTAAATTTGAAT-TTTCAAATACCAGGAATTCTTCTG
65 TCTACAACTTTCATGAAGGATTCGAAATCTAAATTT-AATGTTTCAAATAACA-AAATTCTTCTG
*
161299 AAAATTT-GTTATTTCGGT
128 AAAATTTAGTTGTTTCGGT
161317 GGATTTTTGA
Statistics
Matches: 249, Mismatches: 68, Indels: 14
0.75 0.21 0.04
Matches are distributed among these distances:
176 3 0.01
177 136 0.55
178 107 0.43
179 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (176 bp):
ATAATTTTTGTTCCAGATGTCCGATTGAGGTGATTCAAGTATCTATTAAAAGGTTGTTCCATGAT
CTACAACTTTCATGAAGGATTCGAAATCTAAATTTAATGTTTCAAATAACAAAATTCTTCTGAAA
ATTTAGTTGTTTCGGTTAACGAGAATGGACAGTCCACCTAATATTA
Found at i:165066 original size:19 final size:17
Alignment explanation
Indices: 165042--165079 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
165032 TATTCTACAC
165042 TAATTAGTTAGCAGTTAGT
1 TAATTAGTTAG-A-TTAGT
165061 TAATTAGTTAGATTAGT
1 TAATTAGTTAGATTAGT
165078 TA
1 TA
165080 GCTATGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (17 bp):
TAATTAGTTAGATTAGT
Found at i:166584 original size:23 final size:25
Alignment explanation
Indices: 166552--166604 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
166542 ACATCAGAAA
166552 TTTTTGGG-C-CACTCCCACCATTTT
1 TTTTTGGGCCACACTCCCACCA-TTT
*
166576 TTTTTGGCCACACACTCCCACCATTT
1 TTTTTGGGC-CACACTCCCACCATTT
166602 TTT
1 TTT
166605 AGGGCATGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
26 7 0.28
27 11 0.44
ACGTcount: A:0.15, C:0.34, G:0.09, T:0.42
Consensus pattern (25 bp):
TTTTTGGGCCACACTCCCACCATTT
Found at i:176801 original size:24 final size:25
Alignment explanation
Indices: 176774--176823 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
176764 TATTTCATTT
176774 ACCGCTTC-ATTCATCTCATCCCTC
1 ACCGCTTCAATTCATCTCATCCCTC
*
176798 ACCGCTTCAGATTCATCTCTTCCCTC
1 ACCGCTTCA-ATTCATCTCATCCCTC
176824 TTTTGCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.35
26 15 0.65
ACGTcount: A:0.16, C:0.44, G:0.06, T:0.34
Consensus pattern (25 bp):
ACCGCTTCAATTCATCTCATCCCTC
Found at i:179130 original size:126 final size:125
Alignment explanation
Indices: 178894--179140 Score: 413
Period size: 126 Copynumber: 2.0 Consensus size: 125
178884 TTGACATACA
* *
178894 ACAATAACGTTATATCCTGAAACCACACTTTTGTAACGTTTGATTCTGAATTGAACATTTGGCAA
1 ACAATAACGTTATATCCTGAAACCACACTTTTATAACGTTTGATCCTGAATTGAACATTTGGCAA
*
178959 ACGTTATATCTTGAATTGAGCATTTAGCCAATTATAATTGCTCACAATTGCACCATGCTC
66 ACGTTATATCCTGAATTGAGCATTTAGCCAATTATAATTGCTCACAATTGCACCATGCTC
* * *
179019 ACAATAACGTTATATCCTGAAATCACACTTTTATAACTTTTGATCCTGAGTTGAACATTTGGGCA
1 ACAATAACGTTATATCCTGAAACCACACTTTTATAACGTTTGATCCTGAATTGAACATTT-GGCA
* *
179084 AACGTTATATCCTGAATTGAGTATTTAGCCAATTATAATTGCTCACAATTGCCCCAT
65 AACGTTATATCCTGAATTGAGCATTTAGCCAATTATAATTGCTCACAATTGCACCAT
179141 CCTCTATACA
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
125 55 0.49
126 58 0.51
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (125 bp):
ACAATAACGTTATATCCTGAAACCACACTTTTATAACGTTTGATCCTGAATTGAACATTTGGCAA
ACGTTATATCCTGAATTGAGCATTTAGCCAATTATAATTGCTCACAATTGCACCATGCTC
Found at i:185203 original size:28 final size:29
Alignment explanation
Indices: 185147--185203 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
185137 ATGTTTTCCA
* *
185147 ATTGTACCCATTTTTTTAAAATATTTTTCG
1 ATTGTACCCA-TTTTTTAAAACATATTTCG
185177 ATTGTACCC-TTTTTTAAAACATATTTC
1 ATTGTACCCATTTTTTAAAACATATTTC
185204 TAAATTGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 16 0.64
30 9 0.36
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (29 bp):
ATTGTACCCATTTTTTAAAACATATTTCG
Found at i:185367 original size:37 final size:37
Alignment explanation
Indices: 185325--185419 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
185315 ATTTTGCTTT
185325 TTTGTTTCCAACGTCCTATTTAATTTTGGC-TTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTT-GCTTTTTGTC
* ** *
185362 TTTGTTTTCAACGTTGTATTTAATTTTGCTTTTTGTT
1 TTTGTTTCCAACGTCCTATTTAATTTTGCTTTTTGTC
* *
185399 TTTGTCTCCAACATCCTATTT
1 TTTGTTTCCAACGTCCTATTT
185420 GGGCTTAGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
36 2 0.04
37 46 0.96
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.57
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTTTGTC
Found at i:190122 original size:14 final size:14
Alignment explanation
Indices: 190103--190129 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
190093 CTATAATTCT
190103 AGTGACAAAAAGAA
1 AGTGACAAAAAGAA
190117 AGTGACAAAAAGA
1 AGTGACAAAAAGA
190130 CTGACTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.07
Consensus pattern (14 bp):
AGTGACAAAAAGAA
Found at i:191485 original size:24 final size:25
Alignment explanation
Indices: 191453--191505 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
191443 TTGAATGATT
*
191453 GAGATTTG-AAAGTTTGAAGGTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
* *
191477 GAGAATTGAAAATTTTGAAGTTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
191502 -AGAA
1 GAGAA
191506 AAGGACAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (25 bp):
GAGAATTGAAAAGTTTGAAGGTTGA
Found at i:194763 original size:11 final size:12
Alignment explanation
Indices: 194734--194772 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
194724 AAAATTAAAG
194734 AAGAACAAGAAAGA
1 AAGAA-AAGAAA-A
194748 AAGAAAA-AAAA
1 AAGAAAAGAAAA
194759 AAGAAAAGAAAA
1 AAGAAAAGAAAA
194771 AA
1 AA
194773 AGATGAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 9 0.38
13 2 0.08
14 5 0.21
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAGAAAAGAAAA
Done.