Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020607.1 Corchorus olitorius cultivar O-4 contig20640, 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: 40238
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:412 original size:16 final size:15
Alignment explanation
Indices: 374--415 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
364 ACAGAGGTTG
374 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
389 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
404 ACTAGAAAACAA
1 AC-AGAAAACAA
416 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:7395 original size:16 final size:16
Alignment explanation
Indices: 7374--7404 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7364 AAGCAAATCA
*
7374 ATTTTATATTAGAATG
1 ATTTTATACTAGAATG
7390 ATTTTATACTAGAAT
1 ATTTTATACTAGAAT
7405 AAGTAATTAA
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:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (16 bp):
ATTTTATACTAGAATG
Found at i:7691 original size:26 final size:26
Alignment explanation
Indices: 7639--7697 Score: 111
Period size: 25 Copynumber: 2.3 Consensus size: 26
7629 AGAGTGCAAC
7639 AATGCCAACAATGTTAAATTACTAAA
1 AATGCCAACAATGTTAAATTACTAAA
7665 AATG-CAACAATGTTAAATTACTAAA
1 AATGCCAACAATGTTAAATTACTAAA
7690 AATGCCAA
1 AATGCCAA
7698 AGGTGCACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.25
Consensus pattern (26 bp):
AATGCCAACAATGTTAAATTACTAAA
Found at i:7904 original size:29 final size:29
Alignment explanation
Indices: 7784--7903 Score: 143
Period size: 29 Copynumber: 4.1 Consensus size: 29
7774 ATGTGAACTT
* *
7784 AAAATGACCAAAATGCCCCTAAATGTGCA
1 AAAATGACCAAAATGCCCCTGAATATGCA
* * *
7813 AAAATGACCATAATGCCCATGGATATGCA
1 AAAATGACCAAAATGCCCCTGAATATGCA
* * *
7842 GAAATGACAAAAATACCCCTGAATATGCA
1 AAAATGACCAAAATGCCCCTGAATATGCA
*
7871 GAAAA-GACCAAAATGCCCCTGAATGTGCA
1 -AAAATGACCAAAATGCCCCTGAATATGCA
7900 AAAA
1 AAAA
7904 ATAAGACCAT
Statistics
Matches: 75, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
28 4 0.05
29 68 0.91
30 3 0.04
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.17
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGAATATGCA
Found at i:10222 original size:29 final size:27
Alignment explanation
Indices: 10184--10259 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 27
10174 TGGGGGCATC
10184 CAGGGGCATTTTGGTCATTTACACATCT
1 CAGGGGCATTTTGGTCATTTACACAT-T
* ** *
10212 ACGGGGGCATTTTAATCATTTGCACATT
1 -CAGGGGCATTTTGGTCATTTACACATT
*
10240 CAGGGACATTTTGGTCATTT
1 CAGGGGCATTTTGGTCATTT
10260 TAAGTTCATA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 16 0.41
28 1 0.03
29 22 0.56
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTACACATT
Found at i:18063 original size:19 final size:19
Alignment explanation
Indices: 18006--18063 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
17996 AGTTAGATGG
18006 CTAAAATAAATAAAGGCCA
1 CTAAAATAAATAAAGGCCA
* ****
18025 CT--AAT-ATTAAAGTTGG
1 CTAAAATAAATAAAGGCCA
18041 CTAAAATAAATAAAGGCCA
1 CTAAAATAAATAAAGGCCA
18060 CTAA
1 CTAA
18064 CCACCAACTG
Statistics
Matches: 26, Mismatches: 10, Indels: 6
0.62 0.24 0.14
Matches are distributed among these distances:
16 8 0.31
17 3 0.12
18 3 0.12
19 12 0.46
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (19 bp):
CTAAAATAAATAAAGGCCA
Found at i:19952 original size:22 final size:22
Alignment explanation
Indices: 19927--19980 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
19917 AAATTGACAT
19927 GATTTCATGCCATGTAATCCCC
1 GATTTCATGCCATGTAATCCCC
*
19949 GATTTCATCCCATGTAATCCCC
1 GATTTCATGCCATGTAATCCCC
*
19971 AATTTCATGC
1 GATTTCATGC
19981 AGCAACATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.33
Consensus pattern (22 bp):
GATTTCATGCCATGTAATCCCC
Found at i:29908 original size:35 final size:35
Alignment explanation
Indices: 29867--30726 Score: 956
Period size: 35 Copynumber: 24.0 Consensus size: 35
29857 ATCTTTTGGG
* ** *
29867 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
*
29902 GATCAACTCTGATCATAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT--CAAAAACTTCTTGAAATGA
29939 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
29974 GATCAACTCTAATCATC-AAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
** *
30008 -ATCATTTCTGATCATCAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
30042 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
*
30077 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
30112 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
30147 GATCAACTCTAATCATC-AAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * *
30181 -ATCAATTCTGATCATCAAAAGCTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
30215 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
30250 GATCAACTCTAATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * * *
30285 GATCAACTCTGATCAACGAAAACTTCTTGATAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
30320 GATCAACTCTGATCATAAAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
30355 AATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
** **
30390 GATCAACTCTGATCAAAAAAAAAAAAACTTACTTGAACCGA
1 GATCAACTCTGATC-----ATCAAAAACTT-CTTGAAATGA
* * * *
30431 AATCAACTCTGATCATAAAAAAAAACTTACTTAAAAGGAA
1 GATCAACTCTGATCAT---CAAAAACTT-CTTGAAATG-A
* *
30471 GATCAACTCTGATCATAAAAAAACTTACTTGAAACGA
1 GATCAACTCTGATCAT-CAAAAACTT-CTTGAAATGA
* *
30508 GATCAACTCTGATCATAAAAAAAACTTACTTGAAAGGA
1 GATCAACTCTGATCAT--CAAAAACTT-CTTGAAATGA
*
30546 GATCAACTCTGATCA-CGAAAAAAAACTTTTTAGTAAATGA
1 GATCAACTCTGATCATC----AAAAACTTCTT-G-AAATGA
* * * *
30586 GATCAACTCTAATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
30621 GATCAACTCTGATCATCAAAAACTTCTTCAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * * *
30656 GATCAACTTTGATAATAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * *
30691 GATCAACTCTGATCATAAAAAAACTTCATGGAATGA
1 GATCAACTCTGATCAT-CAAAAACTTCTTGAAATGA
30727 CCGCACCGGT
Statistics
Matches: 721, Mismatches: 79, Indels: 49
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.04
34 63 0.09
35 408 0.57
36 18 0.02
37 58 0.08
38 55 0.08
39 25 0.03
40 44 0.06
41 23 0.03
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
Found at i:30158 original size:173 final size:173
Alignment explanation
Indices: 29867--30711 Score: 1019
Period size: 173 Copynumber: 4.7 Consensus size: 173
29857 ATCTTTTGGG
* ** * *
29867 GATCAACTCTGACCATTGAAAACTTCTTGGAATGAGATCAACTCTGATCATAAAAAAAACTTCTT
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCAT--AAAAAACTTCTT
* * *
29932 GAAATGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAACTCTAATCATCAAAACT
64 GAAATGAGATCAACTCTGATCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAACT
**
29997 TCTTGAAACGAATCATTTCTGATCATCAAAAACTTCTTGAAAGGA
129 TCTTGAAACGAATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
*
30042 GATCAACTCTGATCATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAACTTCTTGA
* * *
30107 AATGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAACTCTAATCATCAAAACTTC
66 AATGAGATCAACTCTGATCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAACTTC
* *
30172 TTGAAACGAATCAATTCTGATCATCAAAAGCTTCTTGAAAGGA
131 TTGAAACGAATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
* **
30215 GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTAATCATCGAAAACTTCTTGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAACTTCTTGA
* * *
30280 AATGAGATCAACTCTGATCAACGAAAACTTCTTGATAGGAGATCAACTCTGATCATAAAAAACTT
66 AATGAGATCAACTCTGATCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCAT-AAAAACTT
* * *
30345 CTTGGAATGAAATCAACTCTGATCATCAAAAACTTCTTGAAACGA
130 CTTGAAACG-AATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
* * *
30390 GATCAACTCTGATCAAAAAAAAAAAAACTTACTTGAACCGAAATCAACTCTGATCATAAAAAAAA
1 GATCAACTCTGATC-----ATAAAAAACTT-CTTGAAACGAGATCAACTCTGATCAT---AAAAA
* * * *
30455 ACTTACTTAAAAGGAAGATCAACTCTGATCATAAAAAAACTTACTTGAAACGAGATCAACTCTGA
57 ACTT-CTTGAAATG-AGATCAACTCTGATCAT-CAAAAACTT-CTTGAAAGGAGATCAACTCTGA
* * *
30520 TCATAAAAAAAACTTACTTGAAAGGAGATCAACTCTGATCA-CGAAAAAAAACTTTTTAGTAAAT
118 TCAT---AAAAACTT-CTTGAAACGA-ATCAACTCTGATCATC----AAAAACTTCTT-G-AAAG
30584 GA
172 GA
* * * * *
30586 GATCAACTCTAATCA-ACGAAAACTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTC
1 GATCAACTCTGATCATA-AAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAACTTCTTG
* * * *
30650 AAACGAGATCAACTTTGATAATAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAA
65 AAATGAGATCAACTCTGATCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAA
30712 AACTTCATGG
Statistics
Matches: 594, Mismatches: 50, Indels: 47
0.86 0.07 0.07
Matches are distributed among these distances:
173 232 0.39
174 14 0.02
175 92 0.15
180 15 0.03
181 23 0.04
183 25 0.04
184 16 0.03
185 22 0.04
186 23 0.04
187 15 0.03
188 24 0.04
190 35 0.06
191 29 0.05
194 10 0.02
195 1 0.00
196 18 0.03
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (173 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAACTTCTTGA
AATGAGATCAACTCTGATCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAACTTC
TTGAAACGAATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
Found at i:30906 original size:161 final size:163
Alignment explanation
Indices: 30692--31028 Score: 441
Period size: 161 Copynumber: 2.1 Consensus size: 163
30682 TTGAAAGGAG
* *
30692 ATCAACTCTGATCATAAAAAAACTTCATGGAATGACCGCACCGGTTCATCTGGGGATCAACTCCG
1 ATCAACTCTGATCATAAAAAAACATCATGGAATGACCGCACCGGATCATCTGGGGATCAACTCCG
* *
30757 ATCACTGAAAACTTCTTTTG-AATGATCGCACTGGATCATTTAGGGATCAACTCTGATC--TCTA
66 ATCACTGAAAACTTC--TTGAAATGATCGCACTAGATCATTTAGGGATCAACTCTAATCATTC-A
*
30819 AAACTTATAGGAATGACCGCACTGGGCCATCT-GGA
128 AAACTTATAGGAATGACCGCACTGGACCATCTGGGA
** * * * *
30854 ATCAACTCTGATCA-ACGAAAACATCTTGGAATGACCGTACTGGATCATCTGGGGATCAACTCTG
1 ATCAACTCTGATCATAAAAAAACATCATGGAATGACCGCACCGGATCATCTGGGGATCAACTCCG
* * *
30918 ATCACTGAAAACTTCTTGAAATGATCGCACTATATCATTTGGGGATCAACTCTAATCATTCGAAA
66 ATCACTGAAAACTTCTTGAAATGATCGCACTAGATCATTTAGGGATCAACTCTAATCATTCAAAA
* * * * *
30983 CTTCTTGGAATGATCTCACTGGACCATCTGGGG
131 CTTATAGGAATGACCGCACTGGACCATCTGGGA
31016 ATCAACTCTGATC
1 ATCAACTCTGATC
31029 TCTAAAAACT
Statistics
Matches: 152, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
159 3 0.02
160 34 0.22
161 84 0.55
162 31 0.20
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (163 bp):
ATCAACTCTGATCATAAAAAAACATCATGGAATGACCGCACCGGATCATCTGGGGATCAACTCCG
ATCACTGAAAACTTCTTGAAATGATCGCACTAGATCATTTAGGGATCAACTCTAATCATTCAAAA
CTTATAGGAATGACCGCACTGGACCATCTGGGA
Found at i:30935 original size:54 final size:54
Alignment explanation
Indices: 30691--31201 Score: 366
Period size: 54 Copynumber: 9.5 Consensus size: 54
30681 CTTGAAAGGA
* * * *
30691 GATCAACTCTGATCA-TAAAAAAACTTCATGGAATGACCGCACCGGTTCATCTGGG
1 GATCAACTCTGATCACT--GAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * * *
30746 GATCAACTCCGATCACTGAAAACTTCTTTTGAATGATCGCACTGGATCATTTAGG
1 GATCAACTCTGATCACTGAAAACTTC-TTGGAATGACCGCACTGGATCATCTGGG
* * * **
30801 GATCAACTCTGATCTCT-AAAACTTATAGGAATGACCGCACTGGGCCATCT-GG
1 GATCAACTCTGATCACTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * *
30853 AATCAACTCTGATCAAC-GAAAACATCTTGGAATGACCGTACTGGATCATCTGGG
1 GATCAACTCTGATC-ACTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * ** *
30907 GATCAACTCTGATCACTGAAAACTTCTTGAAATGATCGCACTATATCATTTGGG
1 GATCAACTCTGATCACTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * * *
30961 GATCAACTCTAATCATTCG-AAACTTCTTGGAATGATCTCACTGGACCATCTGGG
1 GATCAACTCTGATCACT-GAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * ** * **
31015 GATCAACTCTGATCTCTAAAAACTTCTAT-GAAAGACAACACT-AAGTCATCTGAA
1 GATCAACTCTGATCACTGAAAACTTCT-TGGAATGACCGCACTGGA-TCATCTGGG
* * * * ***
31069 GATCAACT-T-ATCTCTGAAAGCTTCTAT-GAAAGACCGCACAAGG-TCATCTTAA
1 GATCAACTCTGATCACTGAAAACTTCT-TGGAATGACCGCAC-TGGATCATCTGGG
* * * * **
31121 AATCAACT-TAGATCTCTGAAAACTTCTAT-GAAAGACCGCACTGGGTCATCTGAA
1 GATCAACTCT-GATCACTGAAAACTTCT-TGGAATGACCGCACTGGATCATCTGGG
* *
31175 AATCAACT-TAGATCTCTGAAAACTTCT
1 GATCAACTCT-GATCACTGAAAACTTCT
31202 ATGAAAGACC
Statistics
Matches: 376, Mismatches: 65, Indels: 31
0.80 0.14 0.07
Matches are distributed among these distances:
52 57 0.15
53 53 0.14
54 213 0.57
55 52 0.14
56 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (54 bp):
GATCAACTCTGATCACTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
Found at i:31136 original size:106 final size:107
Alignment explanation
Indices: 31016--31213 Score: 301
Period size: 106 Copynumber: 1.9 Consensus size: 107
31006 CCATCTGGGG
*
31016 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACTAAGTCATCTGAAGATCAACTT-AT
1 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACTAAGTCATCTGAAAATCAACTTAAT
*
31080 CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
66 CTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTTAAA
* ** **
31122 ATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAAAATCAACTTAG
1 ATCAACTCT-GATCTCTAAAAACTTCTATGAAAGACAACACTAAGTCATCTGAAAATCAACTTA-
31186 ATCTCTGAAAACTTCTATGAAAGACCGC
64 ATCTCTGAAAACTTCTATGAAAGACCGC
31214 CCAGGGCTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 1 0.01
106 54 0.66
108 27 0.33
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (107 bp):
ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACTAAGTCATCTGAAAATCAACTTAAT
CTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTTAAA
Found at i:31326 original size:92 final size:93
Alignment explanation
Indices: 31137--31327 Score: 235
Period size: 92 Copynumber: 2.1 Consensus size: 93
31127 CTTAGATCTC
** *
31137 TGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAAAATCAACTTAGATCTCTGAAAACTTCT
1 TGAAAACTTCTATGAAAGACCGCAAAGGGTCATCTGAAAATCAACTTAAATCTCTGAAAACTTCT
* * ***
31202 ATGAAAGACCGCCCAGGGCTTAGATCTT
66 ATGAAAGACCACACAGGGCTTAGATAGG
* * * *
31230 TGAAAGCTTCTATGATAGACCGCAAAGGGTC-TCTTAAGATCAACTTAAATCTCTGAAAACTTCT
1 TGAAAACTTCTATGAAAGACCGCAAAGGGTCATCTGAAAATCAACTTAAATCTCTGAAAACTTCT
31294 ATGAAAGACCACACATGGTGCTT-GA-AGG
66 ATGAAAGACCACACA-GG-GCTTAGATAGG
31322 TGAAAA
1 TGAAAA
31328 GATCGCACTG
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
92 48 0.58
93 31 0.37
94 4 0.05
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (93 bp):
TGAAAACTTCTATGAAAGACCGCAAAGGGTCATCTGAAAATCAACTTAAATCTCTGAAAACTTCT
ATGAAAGACCACACAGGGCTTAGATAGG
Found at i:32486 original size:37 final size:38
Alignment explanation
Indices: 32417--32488 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
32407 TTGAAATTTT
* ** * *
32417 TTTTTCTCTTTTGAAAATATTGCACTTTGAGGAAAACG
1 TTTTTCTCTTTTGAAAAGATCACACCTAGAGGAAAACG
32455 TTTTT-TCTTTTGAAAAGATCACACCTAGAGGAAA
1 TTTTTCTCTTTTGAAAAGATCACACCTAGAGGAAA
32489 GTTTCATTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 24 0.83
38 5 0.17
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (38 bp):
TTTTTCTCTTTTGAAAAGATCACACCTAGAGGAAAACG
Found at i:35768 original size:13 final size:15
Alignment explanation
Indices: 35736--35765 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
35726 TAAATAGGAA
35736 AATAAGTTAAAAAAG
1 AATAAGTTAAAAAAG
35751 AATAA-TTAAAAAAG
1 AATAAGTTAAAAAAG
35765 A
1 A
35766 TAAATAGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
AATAAGTTAAAAAAG
Found at i:35790 original size:24 final size:24
Alignment explanation
Indices: 35763--35823 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
35753 TAATTAAAAA
*
35763 AGATAAATAGGTATAGAG-ATAAAT
1 AGATAAATAGGTACAGAGAAT-AAT
*
35787 AGATAAATAGATACAGAGAATAAT
1 AGATAAATAGGTACAGAGAATAAT
35811 AGATAAATAGGTA
1 AGATAAATAGGTA
35824 ACTAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.23
Consensus pattern (24 bp):
AGATAAATAGGTACAGAGAATAAT
Found at i:35848 original size:4 final size:4
Alignment explanation
Indices: 35839--35988 Score: 55
Period size: 4 Copynumber: 38.2 Consensus size: 4
35829 AAATAATAAT
** * * * *
35839 AATA AATA AATA AAT- AATA GCTA GATT AATAA AAAA AATA AAT- AGTA
1 AATA AATA AATA AATA AATA AATA AATA AAT-A AATA AATA AATA AATA
* * * * *
35886 AATA AATA GAT- AATA ATTAA AATA AAAA AATA AA-A GATA AAT- AGTA
1 AATA AATA AATA AATA AAT-A AATA AATA AATA AATA AATA AATA AATA
* ** *
35932 AATA AATA GAT- AATA GTTGAA AATA AATA AA-A AGATA AAT- AGTA AATA
1 AATA AATA AATA AATA AAT--A AATA AATA AATA A-ATA AATA AATA AATA
*
35980 AATA GATA A
1 AATA AATA A
35989 TAGTTAAAAA
Statistics
Matches: 103, Mismatches: 30, Indels: 26
0.65 0.19 0.16
Matches are distributed among these distances:
3 17 0.17
4 77 0.75
5 7 0.07
6 2 0.02
ACGTcount: A:0.67, C:0.01, G:0.08, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:35858 original size:46 final size:43
Alignment explanation
Indices: 35805--36039 Score: 147
Period size: 43 Copynumber: 5.3 Consensus size: 43
35795 AGATACAGAG
*
35805 AATAATAGATAAATAGGTAACTAAAAATAAT-AATAATAAATAAATA
1 AATAATAGATAAAT---TAA-TAAAAAAAATAAATAATAAATAAATA
* * *
35851 AATAATAGCTAGATTAATAAAAAAAATAAATAGTAAATAAATA
1 AATAATAGATAAATTAATAAAAAAAATAAATAATAAATAAATA
* * * *
35894 GATAATA-ATTAAAATAAAAAAATAAAAGATAAATAGTAAATAAATA
1 AATAATAGA-T-AAATTAATAAA-AAAA-ATAAATAATAAATAAATA
* * * * *
35940 GATAATAGTTGAAAATAA-ATAAAAAGATAAATAGTAAATAAATA
1 AATAATAGAT-AAATTAATA-AAAAAAATAAATAATAAATAAATA
* * * * *
35984 GATAATAGTTAAA--AAAAATAAAAAGAGAAATAGTAAATAAATA
1 AATAATAGATAAATTAATAA-AAAAA-ATAAATAATAAATAAATA
* *
36027 GATAATAGTTAAA
1 AATAATAGATAAA
36040 AAAATAAATA
Statistics
Matches: 163, Mismatches: 16, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
41 3 0.02
42 14 0.09
43 57 0.35
44 36 0.22
45 8 0.05
46 45 0.28
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.25
Consensus pattern (43 bp):
AATAATAGATAAATTAATAAAAAAAATAAATAATAAATAAATA
Found at i:35889 original size:43 final size:43
Alignment explanation
Indices: 35836--36047 Score: 241
Period size: 43 Copynumber: 4.8 Consensus size: 43
35826 TAAAAATAAT
* * * *
35836 AATAATAAATAAATAAATAATAGCTAGATTAATAAAAAAA-ATA
1 AATAGTAAATAAATAGATAATAGTTAGA-AAATAAAAAAAGATA
* * *
35879 AATAGTAAATAAATAGATAATAATTAAAATAAAAAAATAAAAGATA
1 AATAGTAAATAAATAGATAATAGTT-AGA-AAATAAA-AAAAGATA
35925 AATAGTAAATAAATAGATAATAGTT-GAAAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAGAAAAT-AA-AAAAAGATA
* *
35969 AATAGTAAATAAATAGATAATAGTTA-AAAAAAATAAAAAGAGA
1 AATAGTAAATAAATAGATAATAGTTAGAAAATAA-AAAAAGATA
*
36012 AATAGTAAATAAATAGATAATAGTTAAAAAAATAAA
1 AATAGTAAATAAATAGATAATAGTT-AGAAAATAAA
36048 TAGTGAATAA
Statistics
Matches: 148, Mismatches: 13, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
43 60 0.41
44 50 0.34
45 11 0.07
46 27 0.18
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (43 bp):
AATAGTAAATAAATAGATAATAGTTAGAAAATAAAAAAAGATA
Found at i:35890 original size:39 final size:39
Alignment explanation
Indices: 35836--36049 Score: 116
Period size: 39 Copynumber: 5.1 Consensus size: 39
35826 TAAAAATAAT
* *
35836 AATAATAA-ATAAATAAATA-ATAGCTAGATTAATA-AAAAA
1 AATAA-AAGATAAATAAATAGATA-ATA-ATTAAAATAAAAA
35875 AATAAATAG-TAAATAAATAGATAATAATTAAAATAAAAA
1 AATAAA-AGATAAATAAATAGATAATAATTAAAATAAAAA
*
35914 AATAAAAGATAAATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAA
1 AATAAAAG------A-TAAATAAATAGATAATAATT-AAAAT--A-AAAA
* *
35964 AGATAAATAG-TAAATAAATAGATAATAGTTAAAAAAAATAAA
1 A-ATAAA-AGATAAATAAATAGATAATAATT-AAAATAA-AAA
* * * *
36006 AAGAGAAATAGTAAATAAATAGATAATAGTTAAAA-AAATA
1 AATA-AAAGA-TAAATAAATAGATAATAATTAAAATAAAAA
36046 AATA
1 AATA
36050 GTGAATAAAT
Statistics
Matches: 144, Mismatches: 9, Indels: 43
0.73 0.05 0.22
Matches are distributed among these distances:
38 9 0.06
39 29 0.20
40 8 0.06
41 6 0.04
42 11 0.08
43 20 0.14
44 24 0.17
46 19 0.13
47 5 0.03
49 1 0.01
50 5 0.03
51 5 0.03
52 2 0.01
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (39 bp):
AATAAAAGATAAATAAATAGATAATAATTAAAATAAAAA
Found at i:36066 original size:19 final size:18
Alignment explanation
Indices: 36011--36062 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
36001 ATAAAAAGAG
36011 AAATAGTAAATAAATAGAT
1 AAATAGTAAATAAATA-AT
*
36030 -AATAGTTAA-AAA-AAT
1 AAATAGTAAATAAATAAT
*
36045 AAATAGTGAATAAATAAT
1 AAATAGTAAATAAATAAT
36063 TAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 2 0.07
16 9 0.32
17 6 0.21
18 11 0.39
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (18 bp):
AAATAGTAAATAAATAAT
Found at i:36465 original size:25 final size:27
Alignment explanation
Indices: 36416--36466 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
36406 TAAAACTATT
36416 AAGAATTAAAGTAATCCTAAATTAATTA
1 AAGAATTAAAG-AATCCTAAATTAATTA
*
36444 AAGAATTAAA-AA-CCTATATTAAT
1 AAGAATTAAAGAATCCTAAATTAAT
36467 CAAATCTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 2 0.09
28 10 0.45
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (27 bp):
AAGAATTAAAGAATCCTAAATTAATTA
Found at i:38846 original size:34 final size:34
Alignment explanation
Indices: 38757--38846 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 34
38747 TGATTCTAAC
* * *
38757 ATTTTCAAGCGTTAGAGATTGTACTGGTTAGTTG
1 ATTTTCATGCGTTACAGATTGTACTAGTTAGTTG
* * * * *
38791 ATTTTCGTGCATTATAGATTGTACTAGTTGGTTT
1 ATTTTCATGCGTTACAGATTGTACTAGTTAGTTG
*
38825 ATTTTCATGCGTTACAAATTGT
1 ATTTTCATGCGTTACAGATTGT
38847 TTTGGTTAGC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (34 bp):
ATTTTCATGCGTTACAGATTGTACTAGTTAGTTG
Found at i:38913 original size:84 final size:85
Alignment explanation
Indices: 38791--38958 Score: 239
Period size: 84 Copynumber: 2.0 Consensus size: 85
38781 TGGTTAGTTG
* * * **
38791 ATTTTCGTGCATTATAGATTGTACTAGTTGGTTTATTTTCATG-CGTTACAAATTGTTTTGGTTA
1 ATTTTCATGCATTATAGATGGTACTAGTTGGTTGATTTTCATGACGTTACAAATTGTTTTCATTA
* *
38855 GCTAATTCTATCAATTTCAT
66 GCTAATTCTAACAACTTCAT
* * *
38875 ATTTTCATGCATTATGGATGGTACTAGTTGGTTGATTTTCATGACTTTATAAATTGTTTTCATTA
1 ATTTTCATGCATTATAGATGGTACTAGTTGGTTGATTTTCATGACGTTACAAATTGTTTTCATTA
38940 GCTAATTCTAACAACTTCA
66 GCTAATTCTAACAACTTCA
38959 GACGTTACAG
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 39 0.53
85 34 0.47
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (85 bp):
ATTTTCATGCATTATAGATGGTACTAGTTGGTTGATTTTCATGACGTTACAAATTGTTTTCATTA
GCTAATTCTAACAACTTCAT
Found at i:39182 original size:65 final size:66
Alignment explanation
Indices: 39069--39234 Score: 208
Period size: 65 Copynumber: 2.5 Consensus size: 66
39059 TTTAATATTT
* * * * *
39069 TAACATTTTCAGGCATTACAGATTATACTGGTTTGTCAATACTAACATTTTAGGCATT-CAGATT
1 TAACATTTTCAAGCGTTACAGATTATACTAGTTGGCCAATACTAACATTTTAGGCATTACAGATT
39133 C
66 C
* * * *
39134 TAACATTTTCAAGCGTTACAGATTATATTAGTTGGCCGATTCTTACATTTTAGGCATTACAGATT
1 TAACATTTTCAAGCGTTACAGATTATACTAGTTGGCCAATACTAACATTTTAGGCATTACAGATT
39199 C
66 C
** * *
39200 TAACATTTTCAAATGTTACAAATTGTACTAGTTGG
1 TAACATTTTCAAGCGTTACAGATTATACTAGTTGG
39235 TTGATTTTCA
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 49 0.57
66 37 0.43
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (66 bp):
TAACATTTTCAAGCGTTACAGATTATACTAGTTGGCCAATACTAACATTTTAGGCATTACAGATT
C
Found at i:39408 original size:118 final size:118
Alignment explanation
Indices: 39195--39475 Score: 339
Period size: 118 Copynumber: 2.4 Consensus size: 118
39185 AGGCATTACA
* * ** * * * * * *
39195 GATTCTAACATTTTCAAATGTTACAAATTGTACTAGTTGGTTGATTTTCATGCGTTACAGATTGT
1 GATTCCAACATTTTTAGGTGTTACAAGTTGTACTGGTTGGCTAATTTTCATGCCTTACACATTGT
* * *
39260 ATAGATTGGTTGATTGTAACATTTCTAGGCGTTACAAATTGTACTTGTTGACT
66 ATAGATTGGCTGATTCTAACATTTCTAGGCGTTACAAATTGTACTAGTTGACT
* * *
39313 GATTCCAACTTTTTTAGGTGTTACAAGTTGTATTGGTTGGCTAATTTTCATGCCTTGCACATTGT
1 GATTCCAACATTTTTAGGTGTTACAAGTTGTACTGGTTGGCTAATTTTCATGCCTTACACATTGT
* * * *
39378 GTTGATTGGCTGATTCTAATATTT-TCAGGCGTTACTAATTGTACTAGTTGACT
66 ATAGATTGGCTGATTCTAACATTTCT-AGGCGTTACAAATTGTACTAGTTGACT
* * *
39431 GATTCTAACATTTTTAGGCGTTACAAGTTGTACCGGTTGGCTAAT
1 GATTCCAACATTTTTAGGTGTTACAAGTTGTACTGGTTGGCTAAT
39476 GCTTACAAAA
Statistics
Matches: 137, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
117 1 0.01
118 136 0.99
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (118 bp):
GATTCCAACATTTTTAGGTGTTACAAGTTGTACTGGTTGGCTAATTTTCATGCCTTACACATTGT
ATAGATTGGCTGATTCTAACATTTCTAGGCGTTACAAATTGTACTAGTTGACT
Done.