Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017056.1 Corchorus olitorius cultivar O-4 contig17089, 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: 72412
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1972 original size:6 final size:6
Alignment explanation
Indices: 1912--1971 Score: 111
Period size: 6 Copynumber: 10.0 Consensus size: 6
1902 GGCTGCACCG
1912 CAATCA CAATCA CAATCA CAATCA CAATCA CAATCA CAATCA CAATCA
1 CAATCA CAATCA CAATCA CAATCA CAATCA CAATCA CAATCA CAATCA
*
1960 CAATCA TAATCA
1 CAATCA CAATCA
1972 TCCGTTAACG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (6 bp):
CAATCA
Found at i:2127 original size:39 final size:38
Alignment explanation
Indices: 2001--2148 Score: 208
Period size: 38 Copynumber: 3.9 Consensus size: 38
1991 TCGAGTCTAG
2001 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* *
2038 CGAACAGTTTAACCCCCTGAGGCACGGTTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
2076 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* * *
2115 CCATCAGTTTAACCCCTTGAGGTACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
2149 ATGCACAGCC
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
37 6 0.06
38 59 0.60
39 33 0.34
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:4822 original size:32 final size:33
Alignment explanation
Indices: 4762--4824 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
4752 AACTTGTAAA
4762 GGCGTGATGAAGGCCCGTTTAACTTCATTGGAAC
1 GGCGTGATGAAGGCCCG-TTAACTTCATTGGAAC
4796 GGCGTGATGAAGGCCCG-TAACTTCATTGG
1 GGCGTGATGAAGGCCCGTTAACTTCATTGG
4825 TTGTAAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 12 0.41
34 17 0.59
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (33 bp):
GGCGTGATGAAGGCCCGTTAACTTCATTGGAAC
Found at i:5208 original size:21 final size:22
Alignment explanation
Indices: 5184--5230 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
5174 CATTGAAAAT
*
5184 CCAAATTTG-ATTTCTCAAGGC
1 CCAAATTTGCATATCTCAAGGC
* *
5205 CC-AATTTGCATATCTTAATGC
1 CCAAATTTGCATATCTCAAGGC
5226 CCAAA
1 CCAAA
5231 GAAGAGTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.29
21 13 0.62
22 2 0.10
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (22 bp):
CCAAATTTGCATATCTCAAGGC
Found at i:13143 original size:30 final size:29
Alignment explanation
Indices: 13070--13147 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
13060 TTGCATATTC
* * *
13070 TATCTTTCAATTG-TTGATTTGAATTGCCA
1 TATCTTGCTATTGATTGA-TTGAATTGCAA
13099 TATCTTGCTATTGATTGATTGAATTGCAA
1 TATCTTGCTATTGATTGATTGAATTGCAA
*
13128 TTAT-TTGTTAGTTGATTGAT
1 -TATCTTGCTA-TTGATTGAT
13148 AGATTGTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 26 0.62
30 16 0.38
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (29 bp):
TATCTTGCTATTGATTGATTGAATTGCAA
Found at i:15856 original size:21 final size:21
Alignment explanation
Indices: 15835--15876 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15825 GCCCACATGG
* *
15835 TTGCCTTGAGCACCCATGTGGT
1 TTGCC-TGAGAACCCAGGTGGT
15857 TTGCCTGAGAACCCAGGTGG
1 TTGCCTGAGAACCCAGGTGG
15877 GCAGTGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.26, G:0.31, T:0.26
Consensus pattern (21 bp):
TTGCCTGAGAACCCAGGTGGT
Found at i:15960 original size:76 final size:76
Alignment explanation
Indices: 15810--15961 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
15800 ACAAGGATCC
*
15810 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
*
15875 GGGCAGTGTCA
66 GGACAGTGTCA
* * * ** *
15886 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACTCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
15948 GATGGACTGTGTCA
63 GATGGACAGTGTCA
15962 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGACAGTGTCA
Found at i:17005 original size:16 final size:16
Alignment explanation
Indices: 16986--17016 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16976 GATGCAGTAA
16986 ATAATTGATGATTGGC
1 ATAATTGATGATTGGC
*
17002 ATAATTGCTGATTGG
1 ATAATTGATGATTGG
17017 AGAAATTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (16 bp):
ATAATTGATGATTGGC
Found at i:18452 original size:20 final size:20
Alignment explanation
Indices: 18427--18473 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
18417 TTTCTATTTA
18427 ATTGCTTTCGTGACAATCTT
1 ATTGCTTTCGTGACAATCTT
* * *
18447 ATTGCTTTCTTTATAATCTT
1 ATTGCTTTCGTGACAATCTT
18467 -TTGCTTT
1 ATTGCTTT
18474 TAATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
ATTGCTTTCGTGACAATCTT
Found at i:43798 original size:11 final size:11
Alignment explanation
Indices: 43774--43808 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
43764 AGTAAAACTG
*
43774 AAAAGTAAATA
1 AAAAGTAAAGA
*
43785 AAAAGAAAAGA
1 AAAAGTAAAGA
43796 AAAAGTAAAGA
1 AAAAGTAAAGA
43807 AA
1 AA
43809 GCAAACCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (11 bp):
AAAAGTAAAGA
Found at i:44528 original size:25 final size:25
Alignment explanation
Indices: 44460--44529 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
44450 GTGATGAACA
44460 AGAG-AAA-AAGCGCGGAGCTTTTG
1 AGAGAAAATAAGCGCGGAGCTTTTG
* * *
44483 AGAGAAAATAAGTGTGAAGCTTTTG
1 AGAGAAAATAAGCGCGGAGCTTTTG
*
44508 AGAGAAAATAAGCACGGAGCTT
1 AGAGAAAATAAGCGCGGAGCTT
44530 GGTTTTTTGC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 4 0.11
24 3 0.08
25 31 0.82
ACGTcount: A:0.40, C:0.10, G:0.30, T:0.20
Consensus pattern (25 bp):
AGAGAAAATAAGCGCGGAGCTTTTG
Found at i:48614 original size:7 final size:7
Alignment explanation
Indices: 48604--48628 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48594 ATTAAAAAAT
48604 AAAAGGA
1 AAAAGGA
48611 AAAAGGA
1 AAAAGGA
48618 AAAAGGA
1 AAAAGGA
48625 AAAA
1 AAAA
48629 TTTGCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:54736 original size:25 final size:26
Alignment explanation
Indices: 54696--54744 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
54686 GTCCATATTT
*
54696 ATTTTTTAAAT-TAAAATAATAATTAA
1 ATTTTTTAAATAAAAAATAA-AATTAA
54722 ATTTTTT-AATAAAAAATAAAATT
1 ATTTTTTAAATAAAAAATAAAATT
54745 TAAACATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTTTTAAATAAAAAATAAAATTAA
Found at i:54894 original size:29 final size:30
Alignment explanation
Indices: 54841--54901 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
54831 GTTCTAATTA
* *
54841 ATGTATACATATGAATTATTCAATTTTATT
1 ATGTATAAATATGAATTATTCAATTATATT
54871 ATGTATAAATAT-AATTAATT-AATTATATT
1 ATGTATAAATATGAATT-ATTCAATTATATT
54900 AT
1 AT
54902 ATTATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (30 bp):
ATGTATAAATATGAATTATTCAATTATATT
Found at i:55081 original size:42 final size:43
Alignment explanation
Indices: 55031--55124 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
55021 AGTGTATTAC
* *
55031 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAATG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
55072 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
55117 TTAATATT
1 CTAATATT
55125 AATAGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:55723 original size:293 final size:294
Alignment explanation
Indices: 55197--55784 Score: 939
Period size: 293 Copynumber: 2.0 Consensus size: 294
55187 AATCTTGATC
** *
55197 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTATAGCATTAATCCTTTGGATTCCGGTAG
1 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTATAGCAGCAATCCTTTGGATTCCGGCAG
* *
55262 AGGAGTTGAACCGGTAAACCCTAATATCAACACACAATTCATATGTAATTAAAACACACTTAATC
66 AGGAGTTGAACCAGTAAACCCTAATATCAACACACAATTAATATGTAATTAAAACACACTTAATC
* * *
55327 ATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGAGAGGAAATTCATCGA
131 ATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGAGAGAAAATTCATCAA
* ** *
55392 GGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGAC-AAAACAAAAGTCAAAAGGGGGCACCACAT
196 GGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAACCAAAAGGAGGCACCACAT
*
55456 TAATCCTCAATTTGGCCTTT-AGTAATTTCCATA
261 TAATCCTCAATTTGGCCTTTAAGTAATTTCAATA
*
55489 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCAGCAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTATAGCAGCAATCCTTTGG-ATTCCGGCA
* * * * *
55554 GATGAGTTGAACTATTAAATCCTAATATTAACACACAATTAATATGTAATTAAAACACACTTAAT
65 GAGGAGTTGAACCAGTAAACCCTAATATCAACACACAATTAATATGTAATTAAAACACACTTAAT
55619 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAA-AGGAGAAAATTCATC
130 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGA-GAGAAAATTCATC
* * *
55683 AAGGGCCTTTTTAGTCACTCGAAAAGTGAGAAAAGACAAAAAAAAAAACCAGAAGGAGGCACCAT
194 AAGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAACCAAAAGGAGGCACCAC
55748 ATTAATCCTCAATTTGGCCTTTAAGTAATTTCAATA
259 ATTAATCCTCAATTTGGCCTTTAAGTAATTTCAATA
55784 G
1 G
55785 TCACTAAAAA
Statistics
Matches: 270, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
292 53 0.20
293 161 0.60
294 43 0.16
295 13 0.05
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.25
Consensus pattern (294 bp):
GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTATAGCAGCAATCCTTTGGATTCCGGCAG
AGGAGTTGAACCAGTAAACCCTAATATCAACACACAATTAATATGTAATTAAAACACACTTAATC
ATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGAGAGAAAATTCATCAA
GGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAACCAAAAGGAGGCACCACAT
TAATCCTCAATTTGGCCTTTAAGTAATTTCAATA
Found at i:55816 original size:3 final size:3
Alignment explanation
Indices: 55810--55853 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
55800 TATAGTATAT
55810 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
55854 GTCCCTCCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:58725 original size:13 final size:13
Alignment explanation
Indices: 58707--58732 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58697 AAGATCTCAG
58707 CAAAAATCATCAC
1 CAAAAATCATCAC
58720 CAAAAATCATCAC
1 CAAAAATCATCAC
58733 TCATGCTAAG
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:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:59209 original size:22 final size:23
Alignment explanation
Indices: 59179--59221 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
59169 ATAAAGTTAG
59179 ATTTCATGAGCAT-GAAAACCTA
1 ATTTCATGAGCATAGAAAACCTA
* *
59201 ATTTGATGAGGATAGAAAACC
1 ATTTCATGAGCATAGAAAACC
59222 CTAGCAAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (23 bp):
ATTTCATGAGCATAGAAAACCTA
Found at i:65945 original size:30 final size:30
Alignment explanation
Indices: 65861--65933 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
65851 CAGAAATTAT
* *
65861 AGGCCC-GAAAATAATAGGCTCAGATGAGGC
1 AGGCCCAG-AAATAATAGGCTCAGATAAGAC
65891 AGGCCCAGAAATAATAGGCTCAGATAAGAC
1 AGGCCCAGAAATAATAGGCTCAGATAAGAC
*
65921 AGGCCCATAAATA
1 AGGCCCAGAAATA
65934 CTTGGTTCAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 38 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.14
Consensus pattern (30 bp):
AGGCCCAGAAATAATAGGCTCAGATAAGAC
Found at i:71618 original size:2 final size:2
Alignment explanation
Indices: 71600--71639 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
71590 ATGATCATAG
*
71600 AT AT AGT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71640 AGTCTAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:71838 original size:108 final size:107
Alignment explanation
Indices: 71669--71885 Score: 398
Period size: 108 Copynumber: 2.0 Consensus size: 107
71659 TTGATCTGAA
71669 ATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCACTTAAAGGGTAAACATGTATTTA
1 ATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCACTTAAAGGGTAAACATGTATTTA
71734 TCAAATTAAACTTTTAATTAAGGTTCAATATGTAATTTCATTT
66 TCAAATTAAACTTTTAATT-AGGTTCAATATGTAATTTCATTT
* * *
71777 ATATGTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAAGGGTACACATGTATTTA
1 ATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCACTTAAAGGGTAAACATGTATTTA
71842 TCAAATTAAACTTTTAATTAGGTTCAATATGTAATTTCATTT
66 TCAAATTAAACTTTTAATTAGGTTCAATATGTAATTTCATTT
71884 AT
1 AT
71886 CAATTAAATT
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 25 0.24
108 81 0.76
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (107 bp):
ATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCACTTAAAGGGTAAACATGTATTTA
TCAAATTAAACTTTTAATTAGGTTCAATATGTAATTTCATTT
Found at i:71967 original size:21 final size:21
Alignment explanation
Indices: 71943--72006 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
71933 GTAATATATA
71943 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* **
71964 TAATTAAATGTAATA-TT--A-
1 TAA-TAACTAAAATACTTACAT
71982 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
72003 TAAT
1 TAAT
72007 TAAATTCTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
17 8 0.25
18 5 0.16
19 1 0.03
20 1 0.03
21 9 0.28
22 8 0.25
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Found at i:71971 original size:18 final size:18
Alignment explanation
Indices: 71950--72010 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
71940 ATATAATAAC
71950 TAAAATACTTACATTAAT
1 TAAAATACTTACATTAAT
* * *
71968 TAAATGTAATA-TTATAATAAC
1 T-AA---AATACTTACATTAAT
71989 TAAAATACTTACATTAAT
1 TAAAATACTTACATTAAT
72007 TAAA
1 TAAA
72011 TTCTTAGGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
17 4 0.12
18 12 0.38
19 2 0.06
20 2 0.06
21 8 0.25
22 4 0.12
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAAATACTTACATTAAT
Found at i:71988 original size:39 final size:40
Alignment explanation
Indices: 71931--72011 Score: 155
Period size: 39 Copynumber: 2.0 Consensus size: 40
71921 TTTAATTCCT
71931 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
71971 ATGTAATAT-TATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
72010 AT
1 AT
72012 TCTTAGGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 32 0.78
40 9 0.22
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.