Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013256.1 Corchorus olitorius cultivar O-4 contig13289, 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: 40375
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5805 original size:2 final size:2
Alignment explanation
Indices: 5788--5921 Score: 82
Period size: 2 Copynumber: 74.5 Consensus size: 2
5778 ATAAAATAAA
*
5788 AT AT AC AT AT -T AT AT AT AT AT AT AT -T AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
5827 AT AT -T AT -T GT -T AT AT AT AT AT AT AT GT -T AT A- AA AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5864 AT AT AT AT -T AT -T AT AT AT -T AT -T GT -T AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5901 -T AT A- AA AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
5922 ACAACAATAT
Statistics
Matches: 111, Mismatches: 6, Indels: 30
0.76 0.04 0.20
Matches are distributed among these distances:
1 15 0.14
2 96 0.86
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5806 original size:15 final size:15
Alignment explanation
Indices: 5788--5822 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5778 ATAAAATAAA
5788 ATATACATATTATAT
1 ATATACATATTATAT
*
5803 ATATATATATTATAT
1 ATATACATATTATAT
5818 ATATA
1 ATATA
5823 TTATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATACATATTATAT
Found at i:5810 original size:13 final size:13
Alignment explanation
Indices: 5788--5921 Score: 93
Period size: 13 Copynumber: 10.5 Consensus size: 13
5778 ATAAAATAAA
*
5788 ATATACATATTAT
1 ATATATATATTAT
5801 ATATATATA-TATT
1 ATATATATATTA-T
5814 ATATATATATTAT
1 ATATATATATTAT
*
5827 ATAT-TATTGTTAT
1 ATATATA-TATTAT
5840 ATATATATA-TAT
1 ATATATATATTAT
* * ** *
5852 GT-TATAAAAAAA
1 ATATATATATTAT
5864 ATATATATTATTAT
1 ATATATA-TATTAT
*
5878 ATAT-TATTGTTAT
1 ATATATA-TATTAT
*
5891 ATATATATGTTAT
1 ATATATATATTAT
*
5904 A-AAATATA-TAT
1 ATATATATATTAT
5915 ATATATA
1 ATATATA
5922 ACAACAATAT
Statistics
Matches: 96, Mismatches: 16, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
11 9 0.09
12 19 0.20
13 56 0.58
14 12 0.12
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:5817 original size:26 final size:24
Alignment explanation
Indices: 5798--5898 Score: 61
Period size: 23 Copynumber: 4.3 Consensus size: 24
5788 ATATACATAT
5798 TATATATATATATATTA-TATATATA
1 TATATAT-TATATATTATTAT-TATA
*
5823 TTATATATTAT-TGTTA-TA-TATA
1 -TATATATTATATATTATTATTATA
** ** *
5845 TATATATGT-TATAAAAAAAATATA
1 TATATAT-TATATATTATTATTATA
*
5869 TAT-TATTATATATTATTGTTATA
1 TATATATTATATATTATTATTATA
5892 TATATAT
1 TATATAT
5899 GTTATAAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
21 8 0.14
22 8 0.14
23 16 0.28
24 16 0.28
25 3 0.05
26 7 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (24 bp):
TATATATTATATATTATTATTATA
Found at i:5857 original size:41 final size:41
Alignment explanation
Indices: 5798--5875 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
5788 ATATACATAT
* * * *
5798 TATATATATATATATTATATATATATTATATATTATTGTTA
1 TATATATATATATATTATAAAAAAAATATATATTATTGTTA
*
5839 TATATATATATATGTTATAAAAAAAATATATATTATT
1 TATATATATATATATTATAAAAAAAATATATATTATT
5876 ATATATTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (41 bp):
TATATATATATATATTATAAAAAAAATATATATTATTGTTA
Found at i:5918 original size:77 final size:77
Alignment explanation
Indices: 5778--5921 Score: 181
Period size: 77 Copynumber: 1.9 Consensus size: 77
5768 TTTATTTATA
* * *
5778 ATAAAATAAAATATACATATTATATATATATATATTATATATATATTATATATTATTGTTATATA
1 ATAAAATAAAATATACATATTATATATATATATATTATATATATATTATAAAATATTGATATATA
5843 TATATATATGTT
66 TATATATATGTT
* *
5855 ATAAAA-AAAATATATATTATTATATAT-TAT-TGTTATATATATATGTTATAAAATA-T-ATAT
1 ATAAAATAAAATATACA-TATTATATATATATATATTATATATATA--TTATAAAATATTGATAT
5915 ATATATA
63 ATATATA
5922 ACAACAATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
75 22 0.37
76 13 0.22
77 24 0.41
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.48
Consensus pattern (77 bp):
ATAAAATAAAATATACATATTATATATATATATATTATATATATATTATAAAATATTGATATATA
TATATATATGTT
Found at i:6997 original size:51 final size:51
Alignment explanation
Indices: 6857--7049 Score: 257
Period size: 51 Copynumber: 3.8 Consensus size: 51
6847 AATTACCATA
* * ** *
6857 ATAATTATCTTTAATAATATAAAAAGATAATATGGTTAATAAATATAATCATC
1 ATAATTATCTCTAAT-ATATATATGGATAATATGGTTAAT-AATATAATCACC
*
6910 AT-ATCATCTCT-A-ATATATATGGATAATATGGTTAATAATATAATCACC
1 ATAATTATCTCTAATATATATATGGATAATATGGTTAATAATATAATCACC
* *
6958 ATAATTATCACTAATATATATATGGATAATATGGCTAATAATATAATCACC
1 ATAATTATCTCTAATATATATATGGATAATATGGTTAATAATATAATCACC
* *
7009 ATAACTATCTCTAATATATTTATGGATAATATGGTTAATAA
1 ATAATTATCTCTAATATATATATGGATAATATGGTTAATAA
7050 AGATAATGGG
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
48 13 0.10
49 28 0.23
50 1 0.01
51 73 0.59
52 7 0.06
53 2 0.02
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (51 bp):
ATAATTATCTCTAATATATATATGGATAATATGGTTAATAATATAATCACC
Found at i:7022 original size:27 final size:26
Alignment explanation
Indices: 6942--7024 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
6932 ATAATATGGT
6942 TAATAATATAATCACCATAATTATCAC
1 TAATAATATAATCACCATAA-TATCAC
** **
6969 TAAT-ATAT-AT-ATGGATAATATGGC
1 TAATAATATAATCA-CCATAATATCAC
*
6993 TAATAATATAATCACCATAACTATCTC
1 TAATAATATAATCACCATAA-TATCAC
7020 TAATA
1 TAATA
7025 TATTTATGGA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
24 9 0.21
25 10 0.23
26 10 0.23
27 14 0.33
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (26 bp):
TAATAATATAATCACCATAATATCAC
Found at i:9562 original size:48 final size:48
Alignment explanation
Indices: 9509--9625 Score: 189
Period size: 48 Copynumber: 2.4 Consensus size: 48
9499 TTCAGTATTT
* *
9509 TCTTCTGACTTTGGCTTGTAATCTTTTGTTTCGTAAGTGGTAGGCTTC
1 TCTTCTGACTTTGGCTTGTAATCTTTGGTTTCATAAGTGGTAGGCTTC
*
9557 TCTTCTGACTTTGGCTTGTAATCTTTGGTTTCATAAGTGGTAGGTTTC
1 TCTTCTGACTTTGGCTTGTAATCTTTGGTTTCATAAGTGGTAGGCTTC
* *
9605 TCTTCAGGCTTTGGCTTGTAA
1 TCTTCTGACTTTGGCTTGTAA
9626 GTGTCTGGCT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.47
Consensus pattern (48 bp):
TCTTCTGACTTTGGCTTGTAATCTTTGGTTTCATAAGTGGTAGGCTTC
Found at i:9851 original size:57 final size:57
Alignment explanation
Indices: 9777--9981 Score: 261
Period size: 57 Copynumber: 3.6 Consensus size: 57
9767 GTAGGCTTTT
* * * * *
9777 CTTCCGGCTTTTG-CTTGTAAGTGTTTGGCTTTGCATCATAGTTAGCCTTTACATCTA
1 CTTCGGGC-TTTGCCTTGTAAGTGTCTGGCTTTGCACCATAGTTAGACTTTACATCTC
* * *
9834 CTTCGAGCTTTGCCTTGTAAGTGTCTGGCTTTGCACCATAGTTAGGCTTTACTTCTC
1 CTTCGGGCTTTGCCTTGTAAGTGTCTGGCTTTGCACCATAGTTAGACTTTACATCTC
* * *
9891 CTTCGGGCTTTGGCC-TGTAACTGTCTGGCTTTGCACCATAGTTAGACTTTGCGTCTC
1 CTTCGGGCTTT-GCCTTGTAAGTGTCTGGCTTTGCACCATAGTTAGACTTTACATCTC
* *
9948 CTTCGGGCTTTGTCTCGTAAGTGTCTGGCTTTGC
1 CTTCGGGCTTTGCCTTGTAAGTGTCTGGCTTTGC
9982 TTCTCCTTCA
Statistics
Matches: 130, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
56 6 0.05
57 121 0.93
58 3 0.02
ACGTcount: A:0.13, C:0.24, G:0.23, T:0.40
Consensus pattern (57 bp):
CTTCGGGCTTTGCCTTGTAAGTGTCTGGCTTTGCACCATAGTTAGACTTTACATCTC
Found at i:9987 original size:39 final size:39
Alignment explanation
Indices: 9937--10020 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
9927 CATAGTTAGA
* * *
9937 CTTTGCGTCTCCTTCGGGCTTTGTCTCGTAAGTGTCTGG
1 CTTTGCGTCTCCTTCAGGCTTTGACTCGTAACTGTCTGG
* *
9976 CTTTGCTTCTCCTTCAGGCTTTGACTTGTAACTGTCTGG
1 CTTTGCGTCTCCTTCAGGCTTTGACTCGTAACTGTCTGG
10015 CTTTGC
1 CTTTGC
10021 ACCATAGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (39 bp):
CTTTGCGTCTCCTTCAGGCTTTGACTCGTAACTGTCTGG
Found at i:10018 original size:21 final size:20
Alignment explanation
Indices: 9953--10020 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
9943 GTCTCCTTCG
* *
9953 GGCTTTGTCTCGTAAGTGTCT
1 GGCTTTG-CTTGTAACTGTCT
* * *
9974 GGCTTTGCTTCT-CCT-TCA
1 GGCTTTGCTTGTAACTGTCT
9992 GGCTTTGACTTGTAACTGTCT
1 GGCTTTG-CTTGTAACTGTCT
10013 GGCTTTGC
1 GGCTTTGC
10021 ACCATAGTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
18 9 0.25
19 5 0.14
20 6 0.17
21 16 0.44
ACGTcount: A:0.09, C:0.24, G:0.25, T:0.43
Consensus pattern (20 bp):
GGCTTTGCTTGTAACTGTCT
Found at i:10075 original size:39 final size:39
Alignment explanation
Indices: 10031--10115 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
10021 ACCATAGTTA
*
10031 GGCTTTGATTCTCCTT-TGGGCTTTGGCTTGTAATTGTCT
1 GGCTTTGATTCTCCTTCT-GGCTTTGGCTTGTAAGTGTCT
* *
10070 TGCTTTGTTTCTCCTTCTGGCTTTGGCTTGTAAGTGTCT
1 GGCTTTGATTCTCCTTCTGGCTTTGGCTTGTAAGTGTCT
10109 GGCTTTG
1 GGCTTTG
10116 CGACATAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 40 0.98
40 1 0.02
ACGTcount: A:0.06, C:0.19, G:0.26, T:0.49
Consensus pattern (39 bp):
GGCTTTGATTCTCCTTCTGGCTTTGGCTTGTAAGTGTCT
Found at i:10133 original size:153 final size:151
Alignment explanation
Indices: 9777--10159 Score: 371
Period size: 153 Copynumber: 2.5 Consensus size: 151
9767 GTAGGCTTTT
* * * * *
9777 CTTCCGGCTTTTGCTTGTAAGTGTTTGGCTTTGCATCATAGTTAGCCTTTACATCTACTTCGAGC
1 CTTCAGGC-TTTGCTTGTAAGTGTCTGGCTTTGCA-CATAGTTAGCCTTTGCTTCTCCTTCG-GC
* *
9842 TTTGCCTTGTAAGTGTCTGGCTTTGCACCATAGTTAGGCTTTACTTCTCCTTCGGGCTTTGGCCT
63 TTTGACTTGTAACTGTCTGGCTTTGCACCATAGTTAGGCTTTACTTCTCCTTCGGGCTTTGGCCT
9907 GTAACTGTCTGGCTTTGCACCATA
128 GTAACTGTCTGGCTTTGCACCATA
* * * * ** * * * * *
9931 GTT-AGACTTTGCGTCT-CCT-TCGGGCTTTGTCTCGTAAGTGTCTGGCTTTGCTTCTCCTTCAG
1 CTTCAGGCTTTGCTTGTAAGTGTCTGGCTTTG-CACAT-AGT-T-AGCCTTTGCTTCTCCTTC-G
*
9993 GCTTTGACTTGTAACTGTCTGGCTTTGCACCATAGTTAGGCTTTGA-TTCTCCTTTGGGCTTTGG
61 GCTTTGACTTGTAACTGTCTGGCTTTGCACCATAGTTAGGCTTT-ACTTCTCCTTCGGGCTTTGG
* * * *** *
10057 CTTGTAATTGTCTTGCTTTGTTTC-TC
125 CCTGTAACTGTCTGGCTTTGCACCATA
* *
10083 CTTCTGGCTTTGGCTTGTAAGTGTCTGGCTTTGCGACATAGTTAGCCTTTGCTTCTCCTTCGGGG
1 CTTCAGGCTTT-GCTTGTAAGTGTCTGGCTTTGC-ACATAGTTAGCCTTTGCTTCTCCTTC-GGC
10148 TTTGACTTGTAA
63 TTTGACTTGTAA
10160 TTTTGTTCAG
Statistics
Matches: 178, Mismatches: 40, Indels: 23
0.74 0.17 0.10
Matches are distributed among these distances:
150 10 0.06
151 5 0.03
152 11 0.06
153 127 0.71
154 9 0.05
155 5 0.03
156 11 0.06
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (151 bp):
CTTCAGGCTTTGCTTGTAAGTGTCTGGCTTTGCACATAGTTAGCCTTTGCTTCTCCTTCGGCTTT
GACTTGTAACTGTCTGGCTTTGCACCATAGTTAGGCTTTACTTCTCCTTCGGGCTTTGGCCTGTA
ACTGTCTGGCTTTGCACCATA
Found at i:10157 original size:96 final size:96
Alignment explanation
Indices: 9878--10161 Score: 390
Period size: 96 Copynumber: 3.0 Consensus size: 96
9868 ACCATAGTTA
* * *
9878 GGCTTTACTTCTCCTTCGGGCTTTGGCCTGTAACTGTCTGGCTTTGCACCATAGTTAGACTTTGC
1 GGCTTTGCTTCTCCTTCAGGCTTTGGCTTGTAACTGTCTGGCTTTGCACCATAGTTAGACTTTGC
* * * *
9943 GTCTCCTTCGGGCTTTGTCTCGTAAGTGTCT
66 TTCTCCTTCGGGCTTTGACTTGTAATTGTCT
* * *
9974 GGCTTTGCTTCTCCTTCAGGCTTTGACTTGTAACTGTCTGGCTTTGCACCATAGTTAGGCTTTGA
1 GGCTTTGCTTCTCCTTCAGGCTTTGGCTTGTAACTGTCTGGCTTTGCACCATAGTTAGACTTTGC
* *
10039 TTCTCCTTTGGGCTTTGGCTTGTAATTGTCT
66 TTCTCCTTCGGGCTTTGACTTGTAATTGTCT
* * * * *
10070 TGCTTTGTTTCTCCTTCTGGCTTTGGCTTGTAAGTGTCTGGCTTTGCGA-CATAGTTAGCCTTTG
1 GGCTTTGCTTCTCCTTCAGGCTTTGGCTTGTAACTGTCTGGCTTTGC-ACCATAGTTAGACTTTG
*
10134 CTTCTCCTTCGGGGTTTGACTTGTAATT
65 CTTCTCCTTCGGGCTTTGACTTGTAATT
10162 TTGTTCAGGC
Statistics
Matches: 166, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 165 0.99
97 1 0.01
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.43
Consensus pattern (96 bp):
GGCTTTGCTTCTCCTTCAGGCTTTGGCTTGTAACTGTCTGGCTTTGCACCATAGTTAGACTTTGC
TTCTCCTTCGGGCTTTGACTTGTAATTGTCT
Found at i:11063 original size:30 final size:32
Alignment explanation
Indices: 11023--11091 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 32
11013 GATCGTTTAA
*
11023 TCTTTTTTTTTTATTGT-C-TATAATTGGTTT
1 TCTTTCTTTTTTATTGTGCATATAATTGGTTT
*
11053 TCTTTCTTTTTTTTTGTGGCAATATAATTGGTTT
1 TCTTTCTTTTTTATTGT-GC-ATATAATTGGTTT
11087 TCTTT
1 TCTTT
11092 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 15 0.45
32 1 0.03
34 17 0.52
ACGTcount: A:0.13, C:0.09, G:0.12, T:0.67
Consensus pattern (32 bp):
TCTTTCTTTTTTATTGTGCATATAATTGGTTT
Found at i:15049 original size:15 final size:15
Alignment explanation
Indices: 15029--15064 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
15019 TAAAAAGGTT
15029 TTCAAAATCCAAAAA
1 TTCAAAATCCAAAAA
*
15044 TTCAAAATTCAAAAA
1 TTCAAAATCCAAAAA
15059 TT-AAAA
1 TTCAAAA
15065 AAAAAAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (15 bp):
TTCAAAATCCAAAAA
Found at i:15151 original size:37 final size:37
Alignment explanation
Indices: 15110--15195 Score: 129
Period size: 37 Copynumber: 2.3 Consensus size: 37
15100 AATTTAGCTC
15110 TTTTCAAATTAGGAAAGTTCCCATCAAGTTTTTC-AAG
1 TTTTCAAATTAGGAAAGTTCCCATCAAG-TTTTCAAAG
*
15147 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAG
1 TTTTCAAATTAGGAAAGTTCCCATCAAGTTTTCAAAG
* *
15184 TATTCAATTTAG
1 TTTTCAAATTAG
15196 CTCTTTTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 5 0.11
37 39 0.89
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (37 bp):
TTTTCAAATTAGGAAAGTTCCCATCAAGTTTTCAAAG
Found at i:15174 original size:28 final size:28
Alignment explanation
Indices: 15142--15286 Score: 90
Period size: 28 Copynumber: 5.5 Consensus size: 28
15132 ATCAAGTTTT
15142 TCAAGTTTTCAAATTGGGAAAGTTCCCA
1 TCAAGTTTTCAAATTGGGAAAGTTCCCA
* **** * **
15170 TCAAGTTTTCAAAGTATTCAATTTAGC-
1 TCAAGTTTTCAAATTGGGAAAGTTCCCA
15197 TC---TTTTCAAATTGGGAAAGTTCCCA
1 TCAAGTTTTCAAATTGGGAAAGTTCCCA
* * *** * *
15222 CCAAGTTTTCAAAGTATTAAATTTACC-
1 TCAAGTTTTCAAATTGGGAAAGTTCCCA
15249 TC---TTTTCAAATTGGGAAAGTTCCCA
1 TCAAGTTTTCAAATTGGGAAAGTTCCCA
*
15274 CCAAGTTTTCAAA
1 TCAAGTTTTCAAA
15287 GTATTCAATT
Statistics
Matches: 78, Mismatches: 31, Indels: 16
0.62 0.25 0.13
Matches are distributed among these distances:
24 30 0.38
25 2 0.03
27 3 0.04
28 43 0.55
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (28 bp):
TCAAGTTTTCAAATTGGGAAAGTTCCCA
Found at i:15204 original size:52 final size:52
Alignment explanation
Indices: 15147--15346 Score: 337
Period size: 52 Copynumber: 3.8 Consensus size: 52
15137 GTTTTTCAAG
*
15147 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGCTC
1 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCAAAGTATTCAATTTAGCTC
* *
15199 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCAAAGTATTAAATTTACCTC
1 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCAAAGTATTCAATTTAGCTC
*
15251 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCAAAGTATTCAATTTAGTTC
1 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCAAAGTATTCAATTTAGCTC
* * *
15303 TATTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAA
1 TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCAAAGTATTCAA
15347 ATTGGGAAAG
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 139 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (52 bp):
TTTTCAAATTGGGAAAGTTCCCACCAAGTTTTCAAAGTATTCAATTTAGCTC
Found at i:15346 original size:37 final size:37
Alignment explanation
Indices: 15305--15521 Score: 183
Period size: 37 Copynumber: 5.7 Consensus size: 37
15295 TTTAGTTCTA
*
15305 TTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTT
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTTCATAGTT
* * *
15342 TTCAAATTGGGAAAGTTCCCATTAAGTCTTCATGGTT
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTTCATAGTT
* *
15379 TTCAAATTGGAATTGGGAAAGTTCCCATCAAGTCTTCATGGTT
1 TTC--A----AATTGGGAAAGTTCCCATCAAGTTTTCATAGTT
* *
15422 TTCAAATTTGGGAAAGCTCCCATC-AGGTTT--TAGTT
1 TTCAAA-TTGGGAAAGTTCCCATCAAGTTTTCATAGTT
* * *
15457 TTCAATTTAGGGAAAGTTCCCGTC-A-TTTTCGGTTTTAGTT
1 TTCAAATT-GGGAAAGTTCCCATCAAGTTTTC----ATAGTT
*
15497 TTCAAAGTGGGAAAGTTCCCATCAA
1 TTCAAATTGGGAAAGTTCCCATCAA
15522 AAGCATTTTT
Statistics
Matches: 149, Mismatches: 16, Indels: 27
0.78 0.08 0.14
Matches are distributed among these distances:
34 5 0.03
35 23 0.15
37 42 0.28
38 16 0.11
39 15 0.10
40 12 0.08
41 1 0.01
43 35 0.23
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (37 bp):
TTCAAATTGGGAAAGTTCCCATCAAGTTTTCATAGTT
Found at i:15397 original size:43 final size:43
Alignment explanation
Indices: 15346--15429 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
15336 AAAGTTTTCA
*
15346 AATTGGGAAAGTTCCCATTAAGTCTTCATGGTTTTCAAATTGG
1 AATTGGGAAAGTTCCCATCAAGTCTTCATGGTTTTCAAATTGG
15389 AATTGGGAAAGTTCCCATCAAGTCTTCATGGTTTTCAAATT
1 AATTGGGAAAGTTCCCATCAAGTCTTCATGGTTTTCAAATT
15430 TGGGAAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (43 bp):
AATTGGGAAAGTTCCCATCAAGTCTTCATGGTTTTCAAATTGG
Found at i:16446 original size:12 final size:13
Alignment explanation
Indices: 16425--16456 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
16415 AAAATATTCA
16425 AATC-AATCAATC
1 AATCTAATCAATC
16437 AAT-TAATCAATC
1 AATCTAATCAATC
16449 AATCTAAT
1 AATCTAAT
16457 ATATATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (13 bp):
AATCTAATCAATC
Found at i:17250 original size:224 final size:224
Alignment explanation
Indices: 16854--17376 Score: 868
Period size: 224 Copynumber: 2.3 Consensus size: 224
16844 ACGGATGGTG
* * *
16854 TATTTTTTATATTTAAACCCACTGAAAATGCGTTCACATTTACAGAGAAAAAAAACAATCTATAA
1 TATTTATTATATTTAAACCCACAGAAAACGCGTTCACATTTACAGAGAAAAAAAACAATCTATAA
*
16919 AAATTGACTCTACATATTATTTTTGTAACCAGGTGAAATTACTAAATGCTCCTGCTAACTTTTAA
66 AAATTGACTCTACATATTATTTTTGTAACCAGGTGAAATTACTAAATGCTCATGCTAACTTTTAA
* * *
16984 CCTGGGATGACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCAATTTGT
131 CCTAGGACGACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCAATTCGT
* *
17049 ATTCCATCACTCTATAACCTCATAAATCA
196 ATTCAATCACTCTATAACCTCATAAATAA
*
17078 TATTTATTATATTTAAACCCACAGAAAACGCGTTCAAATTTACAGAG-AAAAAAACAATCTATAA
1 TATTTATTATATTTAAACCCACAGAAAACGCGTTCACATTTACAGAGAAAAAAAACAATCTATAA
* *
17142 AAATTGACTCTACATATTATTTTTGTAACCAGGTGAAATTACTAAATGCTCATTCTGACTTTTAA
66 AAATTGACTCTACATATTATTTTTGTAACCAGGTGAAATTACTAAATGCTCATGCTAACTTTTAA
* *
17207 CCTCAGGACGACCTTATTGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCGATTCG
131 CCT-AGGACGACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCAATTCG
*
17272 TATTTAATCACTCTATAACCTCATAAATAA
195 TATTCAATCACTCTATAACCTCATAAATAA
* * *
17302 TATTTATTATATTTAAACCTACAGAAAACGTGTTCACATTTACAGAGCAAAAAAACAATCTATAA
1 TATTTATTATATTTAAACCCACAGAAAACGCGTTCACATTTACAGAGAAAAAAAACAATCTATAA
17367 AAATTGACTC
66 AAATTGACTC
17377 ATATGATAAT
Statistics
Matches: 279, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
223 82 0.29
224 170 0.61
225 27 0.10
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (224 bp):
TATTTATTATATTTAAACCCACAGAAAACGCGTTCACATTTACAGAGAAAAAAAACAATCTATAA
AAATTGACTCTACATATTATTTTTGTAACCAGGTGAAATTACTAAATGCTCATGCTAACTTTTAA
CCTAGGACGACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCAATTCGT
ATTCAATCACTCTATAACCTCATAAATAA
Found at i:18619 original size:18 final size:18
Alignment explanation
Indices: 18592--18630 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
18582 TACATCACTT
18592 CTCTCATTTTCATTTTAC
1 CTCTCATTTTCATTTTAC
*
18610 CTCTCGTTTTCATTTTAC
1 CTCTCATTTTCATTTTAC
18628 CTC
1 CTC
18631 AAAAAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.31, G:0.03, T:0.54
Consensus pattern (18 bp):
CTCTCATTTTCATTTTAC
Found at i:19188 original size:29 final size:29
Alignment explanation
Indices: 19153--19255 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 29
19143 ATGACAGATC
*
19153 TTAAGCAATAATTGTCATAAATGTCAAAA
1 TTAAGCAATAATGGTCATAAATGTCAAAA
* * ** **
19182 TTAAGCATTAATCGGTGA-AATCATAACAGATTC
1 TTAAGCAATAAT-GGTCATAA--ATGTCA-A-AA
19215 TTAAGCAATAATGGTCATAAATGTCAAAA
1 TTAAGCAATAATGGTCATAAATGTCAAAA
*
19244 TTAAGCATTAAT
1 TTAAGCAATAAT
19256 CGATGAAATT
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
29 24 0.44
30 4 0.07
31 8 0.15
32 5 0.09
33 13 0.24
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (29 bp):
TTAAGCAATAATGGTCATAAATGTCAAAA
Found at i:19248 original size:62 final size:61
Alignment explanation
Indices: 19108--19292 Score: 307
Period size: 61 Copynumber: 3.0 Consensus size: 61
19098 TTAGAATTTG
* *
19108 ATAAATGTCAAAATTAAGCATTAGTCGGTGAAATCATGACAGATCTTAAGCAATAATTGTC
1 ATAAATGTCAAAATTAAGCATTAATCGGTGAAATCATGACAGATCTTAAGCAATAATGGTC
*
19169 ATAAATGTCAAAATTAAGCATTAATCGGTGAAATCATAACAGATTCTTAAGCAATAATGGTC
1 ATAAATGTCAAAATTAAGCATTAATCGGTGAAATCATGACAGA-TCTTAAGCAATAATGGTC
* * *
19231 ATAAATGTCAAAATTAAGCATTAATCGATGAAATTATGACAAATCTTAAGCAATAATGGTC
1 ATAAATGTCAAAATTAAGCATTAATCGGTGAAATCATGACAGATCTTAAGCAATAATGGTC
19292 A
1 A
19293 GATCATAAGT
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
61 60 0.52
62 56 0.48
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (61 bp):
ATAAATGTCAAAATTAAGCATTAATCGGTGAAATCATGACAGATCTTAAGCAATAATGGTC
Found at i:19358 original size:39 final size:39
Alignment explanation
Indices: 19304--19390 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
19294 ATCATAAGTC
** *
19304 ATTTTGCAGATAAATCGGTGGTAAATTGGAATTAAAGAT
1 ATTTTGCAGATAAATCGGCAGTAAATCGGAATTAAAGAT
*
19343 ATTTTGCAGATAAATCGGCAGTAAATCGGATTTAAAGAT
1 ATTTTGCAGATAAATCGGCAGTAAATCGGAATTAAAGAT
19382 ATTTTGCAG
1 ATTTTGCAG
19391 CATTGTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (39 bp):
ATTTTGCAGATAAATCGGCAGTAAATCGGAATTAAAGAT
Found at i:20994 original size:17 final size:17
Alignment explanation
Indices: 20968--21011 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
20958 CCATCTACCT
* *
20968 ACCAAATACACAAATTA
1 ACCAATTACACAAATAA
20985 ACCAATTACACAAATAA
1 ACCAATTACACAAATAA
*
21002 ACAAATTACA
1 ACCAATTACA
21012 AACTAAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.18
Consensus pattern (17 bp):
ACCAATTACACAAATAA
Found at i:29195 original size:15 final size:15
Alignment explanation
Indices: 29177--29220 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
29167 GTTGGATGCA
29177 GCTTGGTTTGATGTT
1 GCTTGGTTTGATGTT
* * *
29192 GCTTAGTTGGAGGTT
1 GCTTGGTTTGATGTT
29207 GCTTGGTTTGATGT
1 GCTTGGTTTGATGT
29221 GAATGCAGCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.09, C:0.07, G:0.36, T:0.48
Consensus pattern (15 bp):
GCTTGGTTTGATGTT
Found at i:32454 original size:15 final size:15
Alignment explanation
Indices: 32418--32483 Score: 78
Period size: 15 Copynumber: 4.4 Consensus size: 15
32408 CTGATATGAG
* *
32418 GAATCCACACTATCA
1 GAATCCCCATTATCA
32433 GAATCCCCATTATCA
1 GAATCCCCATTATCA
*
32448 GAATCCCCATAATCA
1 GAATCCCCATTATCA
* *
32463 GGAGCCCCATTATCA
1 GAATCCCCATTATCA
*
32478 GGATCC
1 GAATCC
32484 TCATCCTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.21
Consensus pattern (15 bp):
GAATCCCCATTATCA
Found at i:32676 original size:18 final size:18
Alignment explanation
Indices: 32653--32698 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
32643 TTATTGTGAG
*
32653 CATTCTCAGCTTCCTCAC
1 CATTCTCACCTTCCTCAC
* *
32671 CATTCTCACCTTGCTGAC
1 CATTCTCACCTTCCTCAC
32689 CATTCTCACC
1 CATTCTCACC
32699 ATCATTCGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.43, G:0.07, T:0.33
Consensus pattern (18 bp):
CATTCTCACCTTCCTCAC
Found at i:33447 original size:14 final size:15
Alignment explanation
Indices: 33428--33463 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
33418 TTACAAAACC
33428 CATAAAAAAC-AATA
1 CATAAAAAACAAATA
*
33442 CATAAAAACCAAATA
1 CATAAAAAACAAATA
33457 CATAAAA
1 CATAAAA
33464 CTTACCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (15 bp):
CATAAAAAACAAATA
Found at i:34265 original size:43 final size:42
Alignment explanation
Indices: 34204--34319 Score: 142
Period size: 47 Copynumber: 2.6 Consensus size: 42
34194 CATATAGCCC
*
34204 TAGGACAAGGAATTCTAATTATTTAAGAACCTCCTAACTTGAA
1 TAGGACAAGGAGTTCTAATTATTTAAGAA-CTCCTAACTTGAA
34247 TAGGACAAGGAGTTCTAATATAATTAATTAAGAACTCCTAACTTGAA
1 TAGGACAAGGAGTTCTAAT-T-A-T--TTAAGAACTCCTAACTTGAA
* * *
34294 TAGGACAAAGAGTTCCAATTAATTAA
1 TAGGACAAGGAGTTCTAATTATTTAA
34320 TTTTACTTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
42 4 0.06
43 18 0.28
44 1 0.02
45 2 0.03
46 2 0.03
47 30 0.47
48 7 0.11
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (42 bp):
TAGGACAAGGAGTTCTAATTATTTAAGAACTCCTAACTTGAA
Found at i:34298 original size:47 final size:47
Alignment explanation
Indices: 34219--34321 Score: 163
Period size: 47 Copynumber: 2.2 Consensus size: 47
34209 CAAGGAATTC
* * *
34219 TAATTATTTAAGAACCTCCTAACTTGAATAGGACAAGGAGTTCTAAT
1 TAATTAATTAAGAACCTCCTAACTTGAATAGGACAAAGAGTTCCAAT
34266 ATAATTAATTAAGAA-CTCCTAACTTGAATAGGACAAAGAGTTCCAAT
1 -TAATTAATTAAGAACCTCCTAACTTGAATAGGACAAAGAGTTCCAAT
34313 TAATTAATT
1 TAATTAATT
34322 TTACTTGTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
46 9 0.17
47 30 0.58
48 13 0.25
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (47 bp):
TAATTAATTAAGAACCTCCTAACTTGAATAGGACAAAGAGTTCCAAT
Found at i:39409 original size:14 final size:14
Alignment explanation
Indices: 39390--39419 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39380 GATGTTTTCC
*
39390 ATATATTGCTAGCT
1 ATATATAGCTAGCT
39404 ATATATAGCTAGCT
1 ATATATAGCTAGCT
39418 AT
1 AT
39420 CAACTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (14 bp):
ATATATAGCTAGCT
Done.