Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012107.1 Corchorus olitorius cultivar O-4 contig12140, 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: 56605
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:792 original size:21 final size:21
Alignment explanation
Indices: 730--802 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
720 CCACTACCAA
* *
730 GCCACAACCGGCCATTCACCGT
1 GCCACCACCGGCCATAC-CCGT
** *
752 GCCACCACCGGTTAAACCCGT
1 GCCACCACCGGCCATACCCGT
*
773 GCCACCACCGGCCATGCCCGT
1 GCCACCACCGGCCATACCCGT
*
794 GCCATCACC
1 GCCACCACC
803 ATTCCAAGCC
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 29 0.71
22 12 0.29
ACGTcount: A:0.21, C:0.48, G:0.19, T:0.12
Consensus pattern (21 bp):
GCCACCACCGGCCATACCCGT
Found at i:2215 original size:26 final size:26
Alignment explanation
Indices: 2186--2273 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 26
2176 TATTTGTTAA
2186 TCTTTTGAATTGAGTGCTCTTATGAT
1 TCTTTTGAATTGAGTGCTCTTATGAT
* * *
2212 TC-TTTGATATTTTGATTTCATATTAT-ATT
1 TCTTTTGA-A--TTGAGTGC-TCTTATGA-T
2241 AATCTTTTGAATTGAGTGCTCTTATGAT
1 --TCTTTTGAATTGAGTGCTCTTATGAT
2269 TCTTT
1 TCTTT
2274 GTTATTTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 18
0.66 0.08 0.25
Matches are distributed among these distances:
25 5 0.11
26 8 0.17
28 13 0.28
29 13 0.28
31 3 0.06
32 5 0.11
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.55
Consensus pattern (26 bp):
TCTTTTGAATTGAGTGCTCTTATGAT
Found at i:2251 original size:57 final size:57
Alignment explanation
Indices: 2182--2301 Score: 231
Period size: 57 Copynumber: 2.1 Consensus size: 57
2172 TTGCTATTTG
2182 TTAATCTTTTGAATTGAGTGCTCTTATGATTCTTTGATATTTTGATTTCATATTATA
1 TTAATCTTTTGAATTGAGTGCTCTTATGATTCTTTGATATTTTGATTTCATATTATA
*
2239 TTAATCTTTTGAATTGAGTGCTCTTATGATTCTTTGTTATTTTGATTTCATATTATA
1 TTAATCTTTTGAATTGAGTGCTCTTATGATTCTTTGATATTTTGATTTCATATTATA
2296 TTAATC
1 TTAATC
2302 CTTAATATGT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (57 bp):
TTAATCTTTTGAATTGAGTGCTCTTATGATTCTTTGATATTTTGATTTCATATTATA
Found at i:11566 original size:36 final size:35
Alignment explanation
Indices: 11516--11632 Score: 166
Period size: 36 Copynumber: 3.3 Consensus size: 35
11506 TGCCTAAGAG
11516 GAAAAA-AAAACTGGACCTAAAATAGAGAGAGGTC
1 GAAAAAGAAAACTGGACCTAAAATAGAGAGAGGTC
11550 GAAAAAGAAAGACTGGACCTAAAATAGAGAGAGGTC
1 GAAAAAGAAA-ACTGGACCTAAAATAGAGAGAGGTC
* *
11586 AAAAAAGAAAAACTTGG-CCTAAAATAGAAAGAGGTC
1 GAAAAAG-AAAAC-TGGACCTAAAATAGAGAGAGGTC
11622 AGAAAAAGAAA
1 -GAAAAAGAAA
11633 TAAATAAAAG
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
34 6 0.08
35 3 0.04
36 54 0.72
37 12 0.16
ACGTcount: A:0.56, C:0.10, G:0.23, T:0.11
Consensus pattern (35 bp):
GAAAAAGAAAACTGGACCTAAAATAGAGAGAGGTC
Found at i:11941 original size:2 final size:2
Alignment explanation
Indices: 11929--11965 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
11919 CTATCTATTT
* *
11929 TA TA AA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11966 TATTACAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:12560 original size:57 final size:57
Alignment explanation
Indices: 12488--12870 Score: 344
Period size: 57 Copynumber: 6.6 Consensus size: 57
12478 TTCCCTTCTC
* * *
12488 TTTTAAAATCCTGTTCGAGGTCTCTAGTAGAGAGTTTTTGTTTCAAATTTTGGTTCA
1 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTTGTTTCAAATCTTGGTTCA
* ** * **
12545 TTTTTAAATCTTGTTCGAGGTCTCTGGTAGAGAGTTTTTAATCCAAAAATCTT-GTCTTG
1 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTTGTTTC--AAATCTTGGT-TCA
* * * *
12604 TTTTTAAAATCCTATTCGAGGTCTCTCGTAGAG-GATTTCTGTTTCAAATTTTGGTTCA
1 TTTTT-AAATCCTGTTCGAGGTCTCTGGTAGAGAG-TTTTTGTTTCAAATCTTGGTTCA
*** * * **
12662 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTGTCTTGT
1 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTTGTTTC-AAATCTTG-GTTCA
* *
12721 TTTTTAAAATCCTGTTTGAGGTTTCTGGTAGAGAGTTTTCTGCTTTCAAATCTT-GTTC-
1 TTTTT-AAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTT-TG-TTTCAAATCTTGGTTCA
* *** * *
12779 TTTTTAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTCCACTTTGAAATCTT-GTTCT
1 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTT-TTGTTTCAAATCTTGGTTCA
* * * *
12836 TTTTTAAATCCGGCTCGAGGTCTCTGATCGAGAGT
1 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGT
12871 CTGCATCTCA
Statistics
Matches: 263, Mismatches: 49, Indels: 28
0.77 0.14 0.08
Matches are distributed among these distances:
56 14 0.05
57 128 0.49
58 27 0.10
59 24 0.09
60 61 0.23
61 7 0.03
62 2 0.01
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (57 bp):
TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTTGTTTCAAATCTTGGTTCA
Found at i:12790 original size:174 final size:172
Alignment explanation
Indices: 12488--12870 Score: 391
Period size: 174 Copynumber: 2.2 Consensus size: 172
12478 TTCCCTTCTC
* * *** * * *
12488 TTTTAAAATCCTGTTCGAGGTCTCTAGTAGAGAGTTTTTGTTTCAAATTTTGGTTCATTTTTAAA
1 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAATCTTGCTTCATTTTTAAA
* *
12553 TCTTGTTCGAGGTCTCTGGTAGAGAGTTTTTAATCCAAAAATCTTGTCTTGTTTTTAAAATCCT-
66 TCCTGTTCGAGGTCTCTGGTAGAGAGTTTTTAATCC-AAAATCTTG-CTTCTTTTTAAAATCCTG
** *
12617 ATTCGAGGTCTCTCGTAGAG-GATTT-CTGTTTCAAATTTTGGTTCA
129 A-TCGAGGTCTCTCGTAGAGAG-TTTCCACTTTCAAATCTT-GTTCA
**
12662 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTGTCTTGTTTTTTA
1 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCC-AAATCTTG-CTTCATTTTT-
* * ** *
12727 AAATCCTGTTTGAGGTTTCTGGTAGAGAGTTTTCTGCTTTC-AAATCTTG-TTCTTTTT-AAATC
63 AAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTT-T-AATCCAAAATCTTGCTTCTTTTTAAAATC
* * *
12789 CTGATCGAGGTCTCTGGTAGAGAGTTTCCACTTTGAAATCTTGTTCT
126 CTGATCGAGGTCTCTCGTAGAGAGTTTCCACTTTCAAATCTTGTTCA
* * * *
12836 TTTTTAAATCCGGCTCGAGGTCTCTGATCGAGAGT
1 TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGT
12871 CTGCATCTCA
Statistics
Matches: 174, Mismatches: 27, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
174 100 0.57
175 26 0.15
176 7 0.04
177 38 0.22
178 1 0.01
179 2 0.01
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (172 bp):
TTTTTAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAATCTTGCTTCATTTTTAAA
TCCTGTTCGAGGTCTCTGGTAGAGAGTTTTTAATCCAAAATCTTGCTTCTTTTTAAAATCCTGAT
CGAGGTCTCTCGTAGAGAGTTTCCACTTTCAAATCTTGTTCA
Found at i:12832 original size:117 final size:118
Alignment explanation
Indices: 12488--12815 Score: 504
Period size: 117 Copynumber: 2.8 Consensus size: 118
12478 TTCCCTTCTC
12488 TTTTAAAATCCTGTTCGAGGTCTCTAGTAGAGAGTTTT-TGTTTCAAATTTTGGTTCATTTTTAA
1 TTTTAAAATCCTGTTCGAGGTCTCTAGTAGAGAGTTTTCTGTTTCAAATTTTGGTTCATTTTTAA
* *
12552 ATCTTGTTCGAGGTCTCTGGTAGAGAGTTTTTAATCCAAAAATCTTGTCTTG-T
66 ATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAAT-CAAAAATCTTGTCTTGTT
* * *
12605 TTTTAAAATCCTATTCGAGGTCTCTCGTAGAG-GATTTCTGTTTCAAATTTTGGTTCATTTTTAA
1 TTTTAAAATCCTGTTCGAGGTCTCTAGTAGAGAGTTTTCTGTTTCAAATTTTGGTTCATTTTTAA
*
12669 ATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTGTCTTGTT
66 ATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCAAAAATCTTGTCTTGTT
* * * *
12722 TTTTAAAATCCTGTTTGAGGTTTCTGGTAGAGAGTTTTCTGCTTTCAAATCTT-GTTC-TTTTTA
1 TTTTAAAATCCTGTTCGAGGTCTCTAGTAGAGAGTTTTCTG-TTTCAAATTTTGGTTCATTTTTA
*
12785 AATCCTGATCGAGGTCTCTGGTAGAGAGTTT
65 AATCCTGTTCGAGGTCTCTGGTAGAGAGTTT
12816 CCACTTTGAA
Statistics
Matches: 194, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
116 19 0.10
117 154 0.79
118 11 0.06
119 10 0.05
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (118 bp):
TTTTAAAATCCTGTTCGAGGTCTCTAGTAGAGAGTTTTCTGTTTCAAATTTTGGTTCATTTTTAA
ATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCAAAAATCTTGTCTTGTT
Found at i:13328 original size:66 final size:66
Alignment explanation
Indices: 13251--13374 Score: 214
Period size: 66 Copynumber: 1.9 Consensus size: 66
13241 GTTCATTAGG
*
13251 CATGCTTATATTTATTTTCTTTT-TATTTTCCTTTGTTCATTAACCATATACATTTAGTCCATTA
1 CATGCTTATATTTATTTTCTTTTCT-TTTTCCTTTGCTCATTAACCATATACATTTAGTCCATTA
13315 AC
65 AC
*
13317 CATGTTTATATTTATTTTCTTTTCTTTTTCCTTTGCTCATTAACCATATACATTTAGT
1 CATGCTTATATTTATTTTCTTTTCTTTTTCCTTTGCTCATTAACCATATACATTTAGT
13375 GACACCTGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
66 54 0.98
67 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (66 bp):
CATGCTTATATTTATTTTCTTTTCTTTTTCCTTTGCTCATTAACCATATACATTTAGTCCATTAA
C
Found at i:19718 original size:17 final size:19
Alignment explanation
Indices: 19691--19725 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19681 GAGAATTTTT
19691 TTTTATTTTAA-AACGCAA
1 TTTTATTTTAAGAACGCAA
19709 TTTT-TTTTAAGAACGCA
1 TTTTATTTTAAGAACGCA
19726 GAACACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (19 bp):
TTTTATTTTAAGAACGCAA
Found at i:22794 original size:26 final size:25
Alignment explanation
Indices: 22719--22818 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 25
22709 TTAATTTTAA
*
22719 AAAAAAATAATTTGTGTTTTGCATTTT
1 AAAAAAA-AATTTGT-TTTTGCGTTTT
* *
22746 GAAAAAAAAAGATTCTTTTTGCGTTTT
1 -AAAAAAAAA-TTTGTTTTTGCGTTTT
*
22773 CAAAAAAAAATTTGTTTCTGCGTTCTT
1 -AAAAAAAAATTTGTTTTTGCGTT-TT
*
22800 AGAAACAAAAATTTCTTTT
1 A-AAA-AAAAATTTGTTTT
22819 ATTTTCTATC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
26 12 0.20
27 26 0.44
28 21 0.36
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (25 bp):
AAAAAAAAATTTGTTTTTGCGTTTT
Found at i:27211 original size:11 final size:11
Alignment explanation
Indices: 27191--27225 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
27181 CATCAAGGTT
*
27191 ATATCGAAAAA
1 ATATCAAAAAA
27202 ATATCAAAAAA
1 ATATCAAAAAA
*
27213 ATATAAAAAAA
1 ATATCAAAAAA
27224 AT
1 AT
27226 TTCGACCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (11 bp):
ATATCAAAAAA
Found at i:28858 original size:41 final size:41
Alignment explanation
Indices: 28708--28895 Score: 123
Period size: 41 Copynumber: 4.6 Consensus size: 41
28698 CAATTTTAAC
* ** * *
28708 ATAAATATTCTAAATCAGGGGGCAAATTGCATCAAACAATAA
1 ATAAA-ATCCTAAATCAGGGACCAAATTGAATCAAATAATAA
* ** * * * *
28750 ATAACATTTTAAATTAGGGACCAAGTTGAATGAAATCACACAA
1 ATAAAATCCTAAATCAGGGACCAAATTGAATCAAAT-A-ATAA
* * *
28793 ATAAAGA---AAAAT-AAGGACCAAATTGAATCAAATAGTAA
1 ATAAA-ATCCTAAATCAGGGACCAAATTGAATCAAATAATAA
* * *
28831 CTAAAATCCTAAATCAGGGACTAAATTGTATCAAATAATAA
1 ATAAAATCCTAAATCAGGGACCAAATTGAATCAAATAATAA
* * *
28872 ATAGACTCCTAAATTAGGGACCAA
1 ATAAAATCCTAAATCAGGGACCAA
28896 TGTGAAAACG
Statistics
Matches: 111, Mismatches: 28, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
37 1 0.01
38 6 0.05
39 1 0.01
40 22 0.20
41 68 0.61
42 5 0.05
43 7 0.06
44 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.23
Consensus pattern (41 bp):
ATAAAATCCTAAATCAGGGACCAAATTGAATCAAATAATAA
Found at i:31603 original size:29 final size:28
Alignment explanation
Indices: 31535--31611 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
31525 AATAAACTTA
31535 AAATGACCAAAATGCCCCT-GAATATGC
1 AAATGACCAAAATGCCCCTAGAATATGC
* * *
31562 AAATGACTAAAATGCCCCTAGATTCTTG-
1 AAATGACCAAAATGCCCCTAGAAT-ATGC
31590 AGAATGACCAAAATGCCCCTAG
1 A-AATGACCAAAATGCCCCTAG
31612 TTGATCCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 18 0.42
28 4 0.09
29 21 0.49
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.21
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTAGAATATGC
Found at i:32058 original size:35 final size:35
Alignment explanation
Indices: 32007--32313 Score: 352
Period size: 35 Copynumber: 8.8 Consensus size: 35
31997 TGAGTTCATA
* * *
32007 TTGAAGAGGCTGCACCGAGTTATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* * *
32042 TTGAAGATGCTACACCGAGTCATC-CAAGATCATTT
1 TTGAAGATGCTACACCGAGTCATCTGAA-TTCATCT
* * *
32077 TTGAAGATGCTACACCAAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
32112 TTGAAGATGCTACACCGAGTCATCTGAAGTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* *
32147 TTGAAAATGCTACACCGAGTCATCTG-ATCTCATTT
1 TTGAAGATGCTACACCGAGTCATCTGAAT-TCATCT
* * *
32182 TTGAAGATGCTACACCGAGTCATATGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
** *
32217 TT-AAGGATGCTACACTAAGTCATCTGAGTTCATCT
1 TTGAA-GATGCTACACCGAGTCATCTGAATTCATCT
* * *
32252 TTGAAGATGCTACACCGAGTCATCTGGATAT-AACC
1 TTGAAGATGCTACACCGAGTCATCTGAAT-TCATCT
*
32287 TTGAAAATGCTACACCGAGTCATCTGA
1 TTGAAGATGCTACACCGAGTCATCTGA
32314 GAAGATGGTA
Statistics
Matches: 228, Mismatches: 37, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
34 5 0.02
35 217 0.95
36 6 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
Found at i:32189 original size:105 final size:105
Alignment explanation
Indices: 32007--32312 Score: 411
Period size: 105 Copynumber: 2.9 Consensus size: 105
31997 TGAGTTCATA
* * * * ** *
32007 TTGAAGAGGCTGCACCGAGTTATCTGAATTCATCTTTGAAGATGCTACACCGAGTCATCCAAGAT
1 TTGAAGATGCTACACCGAGTCATCTGAAGTCATCTTTGAAGATGCTACACCGAGTCATCTGATAT
*
32072 CATTTTTGAAGATGCTACACCAAGTCATCTGGATTCAACT
66 CATTTTTGAAGATGCTACACCGAGTCATCTGGATTCAACT
* *
32112 TTGAAGATGCTACACCGAGTCATCTGAAGTCATCTTTGAAAATGCTACACCGAGTCATCTGATCT
1 TTGAAGATGCTACACCGAGTCATCTGAAGTCATCTTTGAAGATGCTACACCGAGTCATCTGATAT
*
32177 CATTTTTGAAGATGCTACACCGAGTCATATGGATTCAACT
66 CATTTTTGAAGATGCTACACCGAGTCATCTGGATTCAACT
**
32217 TT-AAGGATGCTACACTAAGTCATCTG-AGTTCATCTTTGAAGATGCTACACCGAGTCATCTGGA
1 TTGAA-GATGCTACACCGAGTCATCTGAAG-TCATCTTTGAAGATGCTACACCGAGTCATCT-GA
*** *
32280 TAT-AACCTTGAAAATGCTACACCGAGTCATCTG
63 TATCATTTTTGAAGATGCTACACCGAGTCATCTG
32313 AGAAGATGGT
Statistics
Matches: 178, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
104 4 0.02
105 170 0.96
106 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (105 bp):
TTGAAGATGCTACACCGAGTCATCTGAAGTCATCTTTGAAGATGCTACACCGAGTCATCTGATAT
CATTTTTGAAGATGCTACACCGAGTCATCTGGATTCAACT
Found at i:32427 original size:69 final size:69
Alignment explanation
Indices: 32329--32485 Score: 217
Period size: 69 Copynumber: 2.3 Consensus size: 69
32319 TGGTAATGCA
* * * * * * *
32329 TCGTATGGAAATGAACTGTGGCTTGTGGAAAAGC-CTATGCTGCCTGGATGGAAGCAAGGTTTGA
1 TCGTATGGAAACG-AGTTTGGCTTATGGAAAAGCAC-ATGCTACCTGGATGGAACCAAGGCTTGA
32393 ACTGAC
64 ACTGAC
*
32399 TCGTATGGAAACGAGTTTGGCTTATGGAAAAGCACATGCTACTTGGATGGAACCAAGGCTTGAAC
1 TCGTATGGAAACGAGTTTGGCTTATGGAAAAGCACATGCTACCTGGATGGAACCAAGGCTTGAAC
32464 TGAC
66 TGAC
32468 TCGTATGGAAACGAGTTT
1 TCGTATGGAAACGAGTTT
32486 AGTCTTGGAA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
69 65 0.83
70 13 0.17
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (69 bp):
TCGTATGGAAACGAGTTTGGCTTATGGAAAAGCACATGCTACCTGGATGGAACCAAGGCTTGAAC
TGAC
Found at i:32702 original size:50 final size:50
Alignment explanation
Indices: 32618--32753 Score: 191
Period size: 50 Copynumber: 2.7 Consensus size: 50
32608 AGGTTTGAAC
* * **
32618 TGACCCGTATGGAAACGAATTTGGCTTGCAGAAAAGCCTATGCTGCTAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGCTGCTAAT
*
32668 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGCTAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGCTGCTAAT
* * * *
32718 TGACTCGTCTGGAAACGAGTTCGACTTATGGAAAAG
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
32754 TCAAAGCATT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGCTGCTAAT
Found at i:36660 original size:12 final size:12
Alignment explanation
Indices: 36643--36669 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
36633 CACCTGACAG
36643 ACCTAGAAACTA
1 ACCTAGAAACTA
36655 ACCTAGAAACTA
1 ACCTAGAAACTA
36667 ACC
1 ACC
36670 ACAACAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.30, G:0.07, T:0.15
Consensus pattern (12 bp):
ACCTAGAAACTA
Found at i:38312 original size:41 final size:41
Alignment explanation
Indices: 38162--38349 Score: 125
Period size: 41 Copynumber: 4.6 Consensus size: 41
38152 CAATTTTAAC
* ** * *
38162 ATAAATATTCTAAATCAGGGGGCAAATTGCATCAAACAATAA
1 ATAAA-ATCCTAAATCAGGGACCAAATTGAATCAAATAATAA
* * * * *
38204 ATAACAA-CTTAAATTAGGGACCAAGTTGAATGAAATCACACAA
1 ATAA-AATCCTAAATCAGGGACCAAATTGAATCAAAT-A-ATAA
* * *
38247 ATAAAGA---AAAAT-AAGGACCAAATTGAATCAAATAGTAA
1 ATAAA-ATCCTAAATCAGGGACCAAATTGAATCAAATAATAA
* * *
38285 CTAAAATCCTAAATCAGGGACTAAATTGTATCAAATAATAA
1 ATAAAATCCTAAATCAGGGACCAAATTGAATCAAATAATAA
* * *
38326 ATAGACTCCTAAATTAGGGACCAA
1 ATAAAATCCTAAATCAGGGACCAA
38350 TGTGAAAACA
Statistics
Matches: 111, Mismatches: 27, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
37 1 0.01
38 6 0.05
39 1 0.01
40 22 0.20
41 65 0.59
42 7 0.06
43 9 0.08
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.22
Consensus pattern (41 bp):
ATAAAATCCTAAATCAGGGACCAAATTGAATCAAATAATAA
Found at i:41061 original size:29 final size:28
Alignment explanation
Indices: 40993--41069 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
40983 AATGAACTTA
40993 AAATGACCAAAATGCCCCT-GAATGTGC
1 AAATGACCAAAATGCCCCTAGAATGTGC
* * *
41020 AAATGACTAAAATGCCCCTAGATTCTTG-
1 AAATGACCAAAATGCCCCTAGAAT-GTGC
41048 AGAATGACCAAAATGCCCCTAG
1 A-AATGACCAAAATGCCCCTAG
41070 TTGATCCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 18 0.42
28 4 0.09
29 21 0.49
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTAGAATGTGC
Found at i:41326 original size:21 final size:21
Alignment explanation
Indices: 41302--41346 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41292 TTGGAGCTCA
*
41302 TTGAATTCAAAATTATGGTTC
1 TTGAATTCAAAATTAGGGTTC
*
41323 TTGAGTTCAAAATTAGGGTTC
1 TTGAATTCAAAATTAGGGTTC
41344 TTG
1 TTG
41347 GTTGATTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (21 bp):
TTGAATTCAAAATTAGGGTTC
Found at i:53497 original size:42 final size:43
Alignment explanation
Indices: 53438--53617 Score: 258
Period size: 42 Copynumber: 4.2 Consensus size: 43
53428 AGCAACAATT
* *
53438 AATATTAGGTTTATTTTGATGAATTACCTAGAGAT-GGAGTAA
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGGAGTAG
53480 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT-G-GGAGTAG
* * *
53525 AATATTAACTTTATTTTGATGAATTACCTAGAAATGGAGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGG-GAGTAG
*
53569 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT-GAAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGGAGTAG
53611 AAT-TTAG
1 AATATTAG
53618 GTAATACTCT
Statistics
Matches: 125, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
41 4 0.03
42 41 0.33
43 2 0.02
44 39 0.31
45 39 0.31
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (43 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGGAGTAG
Found at i:53537 original size:45 final size:45
Alignment explanation
Indices: 53438--53604 Score: 261
Period size: 45 Copynumber: 3.8 Consensus size: 45
53428 AGCAACAATT
*
53438 AATATTAGGTTTATTTTGATGAATTACCTAGAGAT---GGAGTAA
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAA
*
53480 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAA
* * *
53525 AATATTAACTTTATTTTGATGAATTACCTAGAAATGGA-GAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAA
53569 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
53605 AAGTAGAATT
Statistics
Matches: 115, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
42 34 0.30
44 39 0.34
45 42 0.37
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAA
Found at i:53599 original size:89 final size:87
Alignment explanation
Indices: 53438--53604 Score: 280
Period size: 89 Copynumber: 1.9 Consensus size: 87
53428 AGCAACAATT
** *
53438 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGTAAAATATTAGCTTTATTTTGATGAA
1 AATATTAACTTTATTTTGATGAATTACCTAGAAATGGAGTAAAATATTAGCTTTATTTTGATGAA
53503 TTACCTAGAGATGGAGGAGTAG
66 TTACCTAGAGATGGAGGAGTAG
*
53525 AATATTAACTTTATTTTGATGAATTACCTAGAAATGGAGAGTATAATATTAGCTTTATTTTGATG
1 AATATTAACTTTATTTTGATGAATTACCTAGAAAT-G-GAGTAAAATATTAGCTTTATTTTGATG
53590 AATTACCTAGAGATG
64 AATTACCTAGAGATG
53605 AAGTAGAATT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
87 32 0.43
88 1 0.01
89 41 0.55
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (87 bp):
AATATTAACTTTATTTTGATGAATTACCTAGAAATGGAGTAAAATATTAGCTTTATTTTGATGAA
TTACCTAGAGATGGAGGAGTAG
Found at i:53817 original size:47 final size:47
Alignment explanation
Indices: 53744--53838 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
53734 CTTACTAACC
*
53744 GACTTAAACAACTACAAAAAATTAGCCCTAATAAGAAGATGACTGCA
1 GACTTAAACAACTACAAAAAAATAGCCCTAATAAGAAGATGACTGCA
53791 GACTTAAACAACTACAAAAAAATAGCCCTAATAAGAAGATGACTGCA
1 GACTTAAACAACTACAAAAAAATAGCCCTAATAAGAAGATGACTGCA
53838 G
1 G
53839 CGCAAGCGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.18
Consensus pattern (47 bp):
GACTTAAACAACTACAAAAAAATAGCCCTAATAAGAAGATGACTGCA
Done.