Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014226.1 Corchorus olitorius cultivar O-4 contig14259, 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: 13476
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:4676 original size:15 final size:15
Alignment explanation
Indices: 4656--4684 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4646 CATATTTCAA
4656 TCATGAATTGAATCG
1 TCATGAATTGAATCG
4671 TCATGAATTGAATC
1 TCATGAATTGAATC
4685 ATCACCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (15 bp):
TCATGAATTGAATCG
Found at i:7204 original size:40 final size:40
Alignment explanation
Indices: 7074--7458 Score: 519
Period size: 40 Copynumber: 9.6 Consensus size: 40
7064 TTGAGGGCCC
*
7074 ATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAATTTGA
1 ATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAATTTGG
*
7115 ATGTGAATGAAGGCAAGTTCAATGTCATTTGGG--A-TTGG
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAATTTGG
* *
7153 ATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTGG
** *
7193 ATGTGAATAAGGCAAGTTCAATGTTGATTGGAAAATTT-G
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTGG
* *
7232 ATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTGG
** *
7272 ATGTGAATAAGGCAAGTTCAATGTTGATTGGAAAATTTGG
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTGG
* *
7312 ATGTGAATCAAGGCTAGTTCAATGTCAATTGGAAAATTTGG
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAATTTGG
* *
7353 ATGTGAATAAGGCAAGTTCAATGTTAATT-GGATAATTTGA
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGA-AATTTGG
* *
7393 ATGTGAATCAAGGCAAGTTCAATATCAATTGGGAAAGTTGG
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAATTTGG
7434 ATGTGAATCAAGGCAAGTTCAATGT
1 ATGTGAAT-AAGGCAAGTTCAATGT
7459 TGATAAGGAA
Statistics
Matches: 306, Mismatches: 29, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
37 24 0.08
38 11 0.04
39 38 0.12
40 115 0.38
41 115 0.38
42 3 0.01
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (40 bp):
ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTGG
Found at i:7375 original size:81 final size:80
Alignment explanation
Indices: 7074--7462 Score: 572
Period size: 81 Copynumber: 4.8 Consensus size: 80
7064 TTGAGGGCCC
* *
7074 ATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAATTTGAATGTGAATGAAGGCAAGTTCAATG
1 ATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTGGATGTGAAT-AAGGCAAGTTCAATG
* *
7139 -TCATTTGG--GA-TTGG
64 TTGA-TTGGAAAATTTGG
*
7153 ATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGTT
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGTT
7218 GATTGGAAAATTT-G
66 GATTGGAAAATTTGG
*
7232 ATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGTT
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGTT
7297 GATTGGAAAATTTGG
66 GATTGGAAAATTTGG
* * *
7312 ATGTGAATCAAGGCTAGTTCAATGTCAATTGGAAAATTTGGATGTGAATAAGGCAAGTTCAATGT
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGT
* * *
7377 TAATTGGATAATTTGA
65 TGATTGGAAAATTTGG
*
7393 ATGTGAATCAAGGCAAGTTCAATATCAATTGGGAAAGTTGGATGTGAATCAAGGCAAGTTCAATG
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTGGATGTGAAT-AAGGCAAGTTCAATG
7458 TTGAT
64 TTGAT
7463 AAGGAAAGTA
Statistics
Matches: 286, Mismatches: 17, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
77 19 0.07
78 40 0.14
79 87 0.30
80 11 0.04
81 110 0.38
82 19 0.07
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.31
Consensus pattern (80 bp):
ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGTT
GATTGGAAAATTTGG
Found at i:9593 original size:48 final size:48
Alignment explanation
Indices: 9517--9610 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
9507 ATTCTAAAGC
* * *
9517 TAACCATCATGAATTTCGGGTGCTAAAAATGACCTAGAATCCAAAGGT
1 TAACAATCATGAATTTCGAGTGCTAAAAATGACCTAAAATCCAAAGGT
*
9565 TAACAATCATGACTTTCGAGTGAC-AAAAATGACCTAAAATCCAAAG
1 TAACAATCATGAATTTCGAGTG-CTAAAAATGACCTAAAATCCAAAG
9611 ACAATCTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (48 bp):
TAACAATCATGAATTTCGAGTGCTAAAAATGACCTAAAATCCAAAGGT
Found at i:9640 original size:48 final size:48
Alignment explanation
Indices: 9530--9640 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
9520 CCATCATGAA
* * ** *
9530 TTTCGGGTGCTAAAAATGACCTAGAATCCAAAGGTTAACAATCATGAC
1 TTTCGGGTGCCAAAAATGACCTAAAATCCAAAGGACAACAATCACGAC
* * *
9578 TTTCGAGTGACAAAAATGACCTAAAATCCAAA-GACAATCTATCACGAC
1 TTTCGGGTGCCAAAAATGACCTAAAATCCAAAGGACAA-CAATCACGAC
*
9626 TTTTGGGTGCCAAAA
1 TTTCGGGTGCCAAAA
9641 TGGTCGAAAC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
47 3 0.06
48 48 0.94
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (48 bp):
TTTCGGGTGCCAAAAATGACCTAAAATCCAAAGGACAACAATCACGAC
Found at i:9734 original size:48 final size:48
Alignment explanation
Indices: 9694--9836 Score: 216
Period size: 48 Copynumber: 3.0 Consensus size: 48
9684 AAAATTGGTG
* *
9694 TAAAATCCGAAA-GCTAACCATCAGGACTTTTGAGGGTCAAAATTGACC
1 TAAAATCC-AAACGCTAACCATCACGACTTTTGGGGGTCAAAATTGACC
*
9742 TAAAACCCAAACGCTAACCATCACGACTTTTGGGGGTCAAAATTGACC
1 TAAAATCCAAACGCTAACCATCACGACTTTTGGGGGTCAAAATTGACC
* * *
9790 TAAAATCCAAAGGCTAACCATCACGACTGTCGGGGGTCAAAATTGAC
1 TAAAATCCAAACGCTAACCATCACGACTTTTGGGGGTCAAAATTGAC
9837 ATCATGCTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
47 3 0.03
48 84 0.97
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (48 bp):
TAAAATCCAAACGCTAACCATCACGACTTTTGGGGGTCAAAATTGACC
Found at i:10297 original size:49 final size:49
Alignment explanation
Indices: 10232--10356 Score: 207
Period size: 49 Copynumber: 2.5 Consensus size: 49
10222 CTTACAGGTT
10232 CCCAAAATGGTCTAAAATCCAAAGGCTAACCATTACCACTTTCAGACAC
1 CCCAAAATGGTCTAAAATCCAAAGGCTAACCATTACCACTTTCAGACAC
*
10281 CCCAAAATGGTCTAAAATCCAAAGGCTAACCATTACGACTTTCAGACAC
1 CCCAAAATGGTCTAAAATCCAAAGGCTAACCATTACCACTTTCAGACAC
*
10330 CCCAAAATTGG-CGTAAATTCCAAAGGC
1 CCCAAAA-TGGTC-TAAAATCCAAAGGC
10357 GACTTTCGGG
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
49 56 0.78
50 16 0.22
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.20
Consensus pattern (49 bp):
CCCAAAATGGTCTAAAATCCAAAGGCTAACCATTACCACTTTCAGACAC
Found at i:10743 original size:96 final size:93
Alignment explanation
Indices: 10356--11173 Score: 503
Period size: 96 Copynumber: 8.6 Consensus size: 93
10346 ATTCCAAAGG
*** * * * *
10356 CGACTTTCGGGTGCCAAAAATGGAAAAAAAATTCAAATGCTAACCATCCCGACTTTCAGACCTCA
1 CGACTTTCGGG-GCCAAAAAT-GACCTAAAATTCAAAGGCTAACCATCACAACTTTCAGAGC-CA
* * *
10421 AAATTGG-CGTAAAATCTAAAGGTTAACCATCA
63 AAAATGGAC-TAAAATCCAAA-GCTAACCATCA
* * * * * * * **
10453 CGACTTTCGGGGTCAAAATTGAACTGAAATTTAAAGGCTAACCACCACGACTTTTGGGAGCCAAA
1 CGACTTTCGGGGCCAAAAATGACCTAAAATTCAAAGGCTAACCATCACAAC-TTTCAGAGCCAAA
* * *
10518 ACT-GACCAAAAATCCAGAAGGTAACCATCA
65 AATGGA-CTAAAATCCA-AAGCTAACCATCA
* * * *
10548 CGACTTTCGGGTGCAAAAAATGACCTAAAATTCAAAGGCTTATCATCACGAA-TTTCTGA-CCAA
1 CGACTTTCGGG-GCCAAAAATGACCTAAAATTCAAAGGCTAACCATCAC-AACTTTCAGAGCCAA
* **
10611 AATTGG-CGTAAAATAAAAACGCTAACCATCA
64 AAATGGAC-TAAAATCCAAA-GCTAACCATCA
* * * * * * *
10642 GGACTTTCGGGGACCAAAATTGGCCTAAAATCCAAAGACTATCTATCACAACTTTCAGATGCCAA
1 CGACTTTCGGGG-CCAAAAATGACCTAAAATTCAAAGGCTAACCATCACAACTTTCAGA-GCCAA
10707 AAATGGACTAAAATCCAAATGCTAACCATCA
64 AAATGGACTAAAATCCAAA-GCTAACCATCA
*** ** * * * * *
10738 CGACTTTCAACTGATAAAAATGA-ATTAAATGTCAAAGGCTAACCATCACGACTTTCCGA-CCCA
1 CGACTTTC-GGGGCCAAAAATGACCTAAAAT-TCAAAGGCTAACCATCACAACTTTCAGAGCCAA
* * * *
10801 AAATCGACGTGAAATCCAAAGGGTAATCATCA
64 AAATGGAC-TAAAATCCAAA-GCTAACCATCA
*** * * * * * *
10833 CGACTTTCCGACCCCAAAATTGACCTAAAATTCAAAGACTAACCATCACAACATTCGGGTGCAAA
1 CGACTTT-CGGGGCCAAAAATGACCTAAAATTCAAAGGCTAACCATCACAACTTTC-AGAGCCAA
10898 AAAT-GACCTAAAATCCAAAGACTAACCATCA
64 AAATGGA-CTAAAATCCAAAG-CTAACCATCA
* * * * **
10929 CGACTTTCGGGTGCCAAAAATGATCTAAAA-TCAAAAGGCTAACCATCACGACTTTCGGGGTGGT
1 CGACTTTCGGG-GCCAAAAATGACCTAAAATTC-AAAGGCTAACCATCACAACTTTC--AGAGCC
10993 AAAAAT-GACCTAAAATCCAAAAGCTAACCATCA
62 AAAAATGGA-CTAAAATCC-AAAGCTAACCATCA
* * * * * * * *
11026 CGACCTTCGGGGCC-AAAATCGGCTTAAAATACAAAGGCTAACCATTACGACTTACGAGACCCAA
1 CGACTTTCGGGGCCAAAAAT-GACCTAAAATTCAAAGGCTAACCATCACAACTTTC-AGAGCCAA
* *
11090 CAATGGCCT-AAATCCAAATGCTAACCAT-A
64 AAATGGACTAAAATCCAAA-GCTAACCATCA
* * * * * *
11119 CGACCTTCGGATGTCAAAAATGGA-CTATAATTTAAAGGCTAACCATCACGACTTT
1 CGACTTTCGG-GGCCAAAAAT-GACCTAAAATTCAAAGGCTAACCATCACAACTTT
11174 TGAGGACAAA
Statistics
Matches: 565, Mismatches: 123, Indels: 69
0.75 0.16 0.09
Matches are distributed among these distances:
93 20 0.04
94 119 0.21
95 149 0.26
96 208 0.37
97 65 0.12
98 4 0.01
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (93 bp):
CGACTTTCGGGGCCAAAAATGACCTAAAATTCAAAGGCTAACCATCACAACTTTCAGAGCCAAAA
ATGGACTAAAATCCAAAGCTAACCATCA
Found at i:10902 original size:191 final size:188
Alignment explanation
Indices: 10356--11173 Score: 653
Period size: 191 Copynumber: 4.3 Consensus size: 188
10346 ATTCCAAAGG
* ** * *
10356 CGACTTTCGGGTGCCAAAAATGGAAAAAAAATTCAAATGCTAACCATCCCGACTTTCAGACCTCA
1 CGACTTTCGGGTG-AAAAAAT-G-AATTAAATTCAAAGGCTAACCATCACGACTTTCAGACC-CA
* * ** * * *
10421 AAATTGGCGTAAAATCTAAAGGTTAACCATCACGACTTT-CGGGGTCAAAATTGAACTGAAATTT
62 AAATTGGCGTAAAATCAAAAGGCTAACCATCACGACTTTCCGGGACCAAAATTGACCTAAAATTC
* * * * * * * *
10485 AAAGGCTAACCACCACGACTTTTGGGAGCCAAAACTGACCAAAAATCCAGAAGGTAACCATCA
127 AAAGACTAACCATCACAACTTTCGGGTGCCAAAAATGACCTAAAATCCA-AAGCTAACCATCA
* * * * * *
10548 CGACTTTCGGGTGCAAAAAATGACCTAAAATTCAAAGGCTTATCATCACGAATTTCTGA-CCAAA
1 CGACTTTCGGGTG-AAAAAATGA-ATTAAATTCAAAGGCTAACCATCACGACTTTCAGACCCAAA
* * * * * *
10612 ATTGGCGTAAAATAAAAACGCTAACCATCAGGACTTTCGGGGACCAAAATTGGCCTAAAATCCAA
64 ATTGGCGTAAAATCAAAAGGCTAACCATCACGACTTTCCGGGACCAAAATTGACCTAAAATTCAA
* * * *
10677 AGACTATCTATCACAACTTTCAGATGCCAAAAATGGA-CTAAAATCCAAATGCTAACCATCA
129 AGACTAACCATCACAACTTTCGGGTGCCAAAAAT-GACCTAAAATCCAAA-GCTAACCATCA
*** *
10738 CGACTTTCAACTGATAAAAATGAATTAAATGTCAAAGGCTAACCATCACGACTTTCCGACCCAAA
1 CGACTTTCGGGTGA-AAAAATGAATTAAAT-TCAAAGGCTAACCATCACGACTTTCAGACCCAAA
* * * * * * ***
10803 ATCGACGTGAAATCCAAAGGGTAATCATCACGACTTTCCGACCCCAAAATTGACCTAAAATTCAA
64 ATTGGCGTAAAATCAAAAGGCTAACCATCACGACTTTCCGGGACCAAAATTGACCTAAAATTCAA
* *
10868 AGACTAACCATCACAACATTCGGGTGCAAAAAATGACCTAAAATCCAAAGACTAACCATCA
129 AGACTAACCATCACAACTTTCGGGTGCCAAAAATGACCTAAAATCCAAAG-CTAACCATCA
* * * ****
10929 CGACTTTCGGGTGCCAAAAATG-ATCTAAAATCAAAAGGCTAACCATCACGACTTTCGGGGTGGT
1 CGACTTTCGGGTG-AAAAAATGAAT-TAAATTC-AAAGGCTAACCATCACGACTTTC--AGACCC
* * * * * * * *
10993 AAAAATGACCTAAAATCCAAAA-GCTAACCATCACGACCTT-CGGGGCCAAAATCGGCTTAAAAT
61 AAAATTGGCGTAAAAT-CAAAAGGCTAACCATCACGACTTTCCGGGACCAAAATTGACCTAAAAT
* * * * * * ** * *
11056 ACAAAGGCTAACCATTACGACTTACGAGACCCAACAATGGCCT-AAATCCAAATGCTAACCAT-A
125 TCAAAGACTAACCATCACAACTTTCGGGTGCCAAAAATGACCTAAAATCCAAA-GCTAACCATCA
* * * * * *
11119 CGACCTTCGGATGTCAAAAATGGACTATAATTTAAAGGCTAACCATCACGACTTT
1 CGACTTTCGGGTG-AAAAAATGAATTA-AATTCAAAGGCTAACCATCACGACTTT
11174 TGAGGACAAA
Statistics
Matches: 502, Mismatches: 106, Indels: 38
0.78 0.16 0.06
Matches are distributed among these distances:
189 44 0.09
190 157 0.31
191 200 0.40
192 69 0.14
193 28 0.06
194 4 0.01
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (188 bp):
CGACTTTCGGGTGAAAAAATGAATTAAATTCAAAGGCTAACCATCACGACTTTCAGACCCAAAAT
TGGCGTAAAATCAAAAGGCTAACCATCACGACTTTCCGGGACCAAAATTGACCTAAAATTCAAAG
ACTAACCATCACAACTTTCGGGTGCCAAAAATGACCTAAAATCCAAAGCTAACCATCA
Found at i:11076 original size:47 final size:46
Alignment explanation
Indices: 10383--11349 Score: 377
Period size: 48 Copynumber: 20.3 Consensus size: 46
10373 AAATGGAAAA
* * * * * ** *
10383 AAAATTCAAATGCTAACCATCCCGACTTTCAGACCTCAAAATTGGCGT
1 AAAATCCAAAGGCTAACCATCACGACCTTCGGGGC-CAAAA-TGGCCT
* * * * **
10431 AAAATCTAAAGGTTAACCATCACGACTTTCGGGGTCAAAATTGAACT
1 AAAATCCAAAGGCTAACCATCACGACCTTCGGGGCCAAAA-TGGCCT
* ** * * * * *
10478 GAAATTTAAAGGCTAACCACCACGACTTTTGGGAGCCAAAACTGACCA
1 AAAATCCAAAGGCTAACCATCACGACCTTCGGG-GCCAAAA-TGGCCT
* * *
10526 AAAATCCAGAAGG-TAACCATCACGACTTTCGGGTGCAAAAAATGACCT
1 AAAATCCA-AAGGCTAACCATCACGACCTTCGGG-GC-CAAAATGGCCT
* * * ** * * *
10574 AAAATTCAAAGGCTTATCATCACGAATTTC-TGACCAAAATTGGCGT
1 AAAATCCAAAGGCTAACCATCACGACCTTCGGGGCCAAAA-TGGCCT
** * * *
10620 AAAATAAAAACGCTAACCATCAGGACTTTCGGGGACCAAAATTGGCCT
1 AAAATCCAAAGGCTAACCATCACGACCTTCGGGG-CCAAAA-TGGCCT
* * * * * ** *
10668 AAAATCCAAAGACTATCTATCACAACTTTCAGATGCCAAAAATGGACT
1 AAAATCCAAAGGCTAACCATCACGACCTTC-GGGGCC-AAAATGGCCT
* * ** *** **
10716 AAAATCCAAATGCTAACCATCACGACTTTCAACTGATAAAAAT-GAAT
1 AAAATCCAAAGGCTAACCATCACGACCTTC--GGGGCCAAAATGGCCT
* * * * ** * *
10763 TAAATGTCAAAGGCTAACCATCACGACTTTCCGACCCAAAATCGACGT
1 AAAAT-CCAAAGGCTAACCATCACGACCTTCGGGGCCAAAAT-GGCCT
* * * * *** *
10811 GAAATCCAAAGGGTAATCATCACGACTTTCCGACCCCAAAATTGACCT
1 AAAATCCAAAGGCTAACCATCACGACCTT-CGGGGCCAAAA-TGGCCT
* * * * * *
10859 AAAATTCAAAGACTAACCATCACAACATTCGGGTGCAAAAAATGACCT
1 AAAATCCAAAGGCTAACCATCACGACCTTCGGG-GC-CAAAATGGCCT
* * **
10907 AAAATCCAAAGACTAACCATCACGACTTTCGGGTGCCAAAAATGATCT
1 AAAATCCAAAGGCTAACCATCACGACCTTCGGG-GCC-AAAATGGCCT
* * ** *
10955 AAAATCAAAAGGCTAACCATCACGACTTTCGGGGTGGTAAAAATGACCT
1 AAAATCCAAAGGCTAACCATCACGACCTTC--GG-GGCCAAAATGGCCT
* *
11004 AAAATCCAAAAGCTAACCATCACGACCTTCGGGGCCAAAATCGGCTT
1 AAAATCCAAAGGCTAACCATCACGACCTTCGGGGCCAAAAT-GGCCT
* * **
11051 AAAATACAAAGGCTAACCATTACGA-CTTACGAGACCCAACAATGGCCT
1 AAAATCCAAAGGCTAACCATCACGACCTT-CG-GGGCCAA-AATGGCCT
* * * *
11099 -AAATCCAAATGCTAACCAT-ACGACCTTCGGATGTCAAAAATGGACT
1 AAAATCCAAAGGCTAACCATCACGACCTTCGG--GGCCAAAATGGCCT
* ** * * * *
11145 ATAATTTAAAGGCTAACCATCACGACTTTTGAGGACAAAAATTGGCCT
1 AAAATCCAAAGGCTAACCATCACGACCTTCG-GGGCCAAAA-TGGCCT
*** ** * * * *
11193 AAAATCTTTAGGCTAAATATAAC-AACTTATGGGAACCAAAAATGGCCT
1 AAAATCCAAAGGCTAACCATCACGACCTT-CGGG-GCC-AAAATGGCCT
* ** *
11241 AAAATCCAAAGAC-AATCCATCACGAGTTTCGAAGGCCAAAATTGGCCT
1 AAAATCCAAAGGCTAA-CCATCACGACCTTCG-GGGCCAAAA-TGGCCT
* * * * * * *
11289 AAAATACAAATGCTAATCATCATGA-CTTACATGTGCTCAAAATGACCT
1 AAAATCCAAAGGCTAACCATCACGACCTT-C-GGGGC-CAAAATGGCCT
11337 AAAATCCAAAGGC
1 AAAATCCAAAGGC
11350 ATGACTTTCA
Statistics
Matches: 704, Mismatches: 172, Indels: 86
0.73 0.18 0.09
Matches are distributed among these distances:
45 5 0.01
46 57 0.08
47 160 0.23
48 403 0.57
49 75 0.11
50 3 0.00
51 1 0.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (46 bp):
AAAATCCAAAGGCTAACCATCACGACCTTCGGGGCCAAAATGGCCT
Found at i:11530 original size:221 final size:221
Alignment explanation
Indices: 11147--11592 Score: 883
Period size: 221 Copynumber: 2.0 Consensus size: 221
11137 AATGGACTAT
11147 AATTTAAAGGCTAACCATCACGACTTTTGAGGACAAAAATTGGCCTAAAATCTTTAGGCTAAATA
1 AATTTAAAGGCTAACCATCACGACTTTTGAGGACAAAAATTGGCCTAAAATCTTTAGGCTAAATA
*
11212 TAACAACTTATGGGAACCAAAAATGGCCTAAAATCCAAAGACAATCCATCACGAGTTTCGAAGGC
66 TAACAACTTATGGGAACCAAAAATGGCCTAAAATCCAAAGACAATCCATCACGAATTTCGAAGGC
11277 CAAAATTGGCCTAAAATACAAATGCTAATCATCATGACTTACATGTGCTCAAAATGACCTAAAAT
131 CAAAATTGGCCTAAAATACAAATGCTAATCATCATGACTTACATGTGCTCAAAATGACCTAAAAT
11342 CCAAAGGCATGACTTTCAGATCCCCA
196 CCAAAGGCATGACTTTCAGATCCCCA
11368 AATTTAAAGGCTAACCATCACGACTTTTGAGGACAAAAATTGGCCTAAAATCTTTAGGCTAAATA
1 AATTTAAAGGCTAACCATCACGACTTTTGAGGACAAAAATTGGCCTAAAATCTTTAGGCTAAATA
11433 TAACAACTTATGGGAACCAAAAATGGCCTAAAATCCAAAGACAATCCATCACGAATTTCGAAGGC
66 TAACAACTTATGGGAACCAAAAATGGCCTAAAATCCAAAGACAATCCATCACGAATTTCGAAGGC
11498 CAAAATTGGCCTAAAATACAAATGCTAATCATCATGACTTACATGTGCTCAAAATGACCTAAAAT
131 CAAAATTGGCCTAAAATACAAATGCTAATCATCATGACTTACATGTGCTCAAAATGACCTAAAAT
11563 CCAAAGGCATGACTTTCAGATCCCCA
196 CCAAAGGCATGACTTTCAGATCCCCA
11589 AATT
1 AATT
11593 GGCGTAAAAT
Statistics
Matches: 224, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 224 1.00
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (221 bp):
AATTTAAAGGCTAACCATCACGACTTTTGAGGACAAAAATTGGCCTAAAATCTTTAGGCTAAATA
TAACAACTTATGGGAACCAAAAATGGCCTAAAATCCAAAGACAATCCATCACGAATTTCGAAGGC
CAAAATTGGCCTAAAATACAAATGCTAATCATCATGACTTACATGTGCTCAAAATGACCTAAAAT
CCAAAGGCATGACTTTCAGATCCCCA
Found at i:11625 original size:88 final size:87
Alignment explanation
Indices: 11500--11659 Score: 200
Period size: 88 Copynumber: 1.8 Consensus size: 87
11490 TCGAAGGCCA
* * *
11500 AAATTGGCCTAAAATACAAATGCTAATCATCATGACTTAC-ATGTGCTCAAAA-TGACCTAAAAT
1 AAATTGGCCTAAAATACAAATGCTAAACATCACGACTTACGA-G-G-TCAAAATTGACCCAAAAT
11563 CCAAAGGCATGACTTTCAGATCCCC
63 CCAAAGGCATGACTTTCAGATCCCC
* * * *
11588 AAATTGGCGTAAAATCCAAA-GGTAAACAATCACGACTTTCGAGGTCAAAATTGACCCAAAATCC
1 AAATTGGCCTAAAATACAAATGCTAAAC-ATCACGACTTACGAGGTCAAAATTGACCCAAAATCC
11652 AAAGGCAT
65 AAAGGCAT
11660 CACTACTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
86 6 0.10
87 26 0.42
88 29 0.47
89 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (87 bp):
AAATTGGCCTAAAATACAAATGCTAAACATCACGACTTACGAGGTCAAAATTGACCCAAAATCCA
AAGGCATGACTTTCAGATCCCC
Found at i:11729 original size:48 final size:46
Alignment explanation
Indices: 11672--11827 Score: 161
Period size: 48 Copynumber: 3.2 Consensus size: 46
11662 CTACTTTTAG
* * *
11672 GTGCCAAAAATGATTGAAAATCCAAAGACTGATCATCACGACTTTCGA
1 GTGCTAAAAATGACT-AAAATCCAAAGACT-AACATCACGACTTTCGA
* * * * *
11720 GTGCTAAAAATGGCCTAAAAATCCAAAGGCTAACCATGACAACTTTTGA
1 GTGCTAAAAAT-GACT-AAAATCCAAAGACTAA-CATCACGACTTTCGA
11769 GTG-TAAAAAATGACCTAAAATCCAAAGACTAACTATCACGACTTTCGA
1 GTGCT-AAAAATGA-CTAAAATCCAAAGACTAAC-ATCACGACTTTCGA
11817 GTGCTAAAAAT
1 GTGCTAAAAAT
11828 AGTCTAAAGT
Statistics
Matches: 88, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
47 1 0.01
48 48 0.55
49 39 0.44
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (46 bp):
GTGCTAAAAATGACTAAAATCCAAAGACTAACATCACGACTTTCGA
Found at i:11765 original size:49 final size:48
Alignment explanation
Indices: 11688--11827 Score: 183
Period size: 49 Copynumber: 2.9 Consensus size: 48
11678 AAAATGATTG
* * *
11688 AAAATCCAAAGACTGATCATCACGACTTTCGAGTGCTAAAAATGGCCT
1 AAAATCCAAAGACTAACCATCACGACTTTCGAGTGCTAAAAATGACCT
* * * *
11736 AAAAATCCAAAGGCTAACCATGACAACTTTTGAGTG-TAAAAAATGACCT
1 -AAAATCCAAAGACTAACCATCACGACTTTCGAGTGCT-AAAAATGACCT
*
11785 AAAATCCAAAGACTAACTATCACGACTTTCGAGTGCTAAAAAT
1 AAAATCCAAAGACTAACCATCACGACTTTCGAGTGCTAAAAAT
11828 AGTCTAAAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
48 37 0.48
49 40 0.52
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (48 bp):
AAAATCCAAAGACTAACCATCACGACTTTCGAGTGCTAAAAATGACCT
Found at i:11835 original size:48 final size:48
Alignment explanation
Indices: 11688--11835 Score: 167
Period size: 48 Copynumber: 3.1 Consensus size: 48
11678 AAAATGATTG
* *
11688 AAAATCCAAAGACTGA-TCATCACGACTTTCGAGTGCTAAAAATGGCCT
1 AAAATCCAAAGACTAACT-ATCACGACTTTCGAGTGCTAAAAATAGCCT
* * * * *
11736 AAAAATCCAAAGGCTAACCATGACAACTTTTGAGTG-TAAAAA-ATGACCT
1 -AAAATCCAAAGACTAACTATCACGACTTTCGAGTGCTAAAAATA-G-CCT
*
11785 AAAATCCAAAGACTAACTATCACGACTTTCGAGTGCTAAAAATAGTCT
1 AAAATCCAAAGACTAACTATCACGACTTTCGAGTGCTAAAAATAGCCT
11833 AAA
1 AAA
11836 GTCTAAAGGT
Statistics
Matches: 81, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
48 42 0.52
49 38 0.47
50 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (48 bp):
AAAATCCAAAGACTAACTATCACGACTTTCGAGTGCTAAAAATAGCCT
Found at i:13206 original size:332 final size:333
Alignment explanation
Indices: 12581--13270 Score: 987
Period size: 332 Copynumber: 2.1 Consensus size: 333
12571 TACTTTACAG
* * * *
12581 TTTTTCGCTAAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGAGTTTTGGCAGAAAGATGC
1 TTTTTGGCTAAAAACGCGTTTCGGGGCCCTAACTCAGTTTTGCATGAGTTTTGGAAGAAAAATGC
* * * *
12646 CTCGAAATATTTGTATTCATCAAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTAC
66 CTCGAAATATATATATTCATCAAACCAAAATCTCAGCCACAATGGATTTAAGGATTTATTTTTAC
* * * *
12711 GAGCATCTGAATCTTGTTTCAATTAAATTAGAAATAAATTCGGAAAAATTTGGAAAAACGATATT
131 CAGCATCTGAATCTTGTTTCAATTAAATTAGAAATAAATTCAGAAAAATATGGAAAAACAATATT
* * *
12776 AGAAGCATGAAAAACCCTATAATACTTTTGGTGTTGAATTATATGATTTTACTGAGTATTGTGGC
196 AGAAGCACGAAAAACCCTATAATACTTTTGGCGTTGAATTATATGATTTTACAGAGTATTGTGGC
*
12841 AAAATTGGGGAAAAAACTTCTCTGGTCAGTTTTTTGCAAAATTTTAGCTGAAATAGTGTTCTAAC
261 AAAATTGGGGAAAAAACTTCTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATAGTGTTCTAAC
12906 AATCACGA
326 AATCACGA
* *
12914 TTTTTGGCTAAAAACGCGTTTCGGGGCTCTAACTCAGTTTTGCATGATTTTTGGAAGAAAAACT-
1 TTTTTGGCTAAAAACGCGTTTCGGGGCCCTAACTCAGTTTTGCATGAGTTTTGGAAGAAAAA-TG
* * *
12978 CCTCGAAATATATATATTCATCTAATC-AAATCTTAGCCACAATGGATTTAAGGATTTATTTTTA
65 CCTCGAAATATATATATTCATCAAACCAAAATCTCAGCCACAATGGATTTAAGGATTTATTTTTA
* * *
13042 CCAGTATCTGAATCTTGTTTCGATTTAATTA-ATAATAAATTCAGAAAAA-ATGGAAAAACAATA
130 CCAGCATCTGAATCTTGTTTCAATTAAATTAGA-AATAAATTCAGAAAAATATGGAAAAACAATA
* * ** *
13105 TTAGAAGCGCGAAAAACCCT-TCATTGGTTTTGGCGTTGAATTATATGATTTTCCAGAGTATTGT
194 TTAGAAGCACGAAAAACCCTAT-AATACTTTTGGCGTTGAATTATATGATTTTACAGAGTATTGT
* *
13169 GGCAAAAAATTGGGG-GAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATAGTGTT
258 GGC--AAAATTGGGGAAAAAACTTCTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATAGTGTT
* *
13233 CTAACCATCACGG
321 CTAACAATCACGA
*
13246 TTTTTGGCTAAAGACGCGTTTCGGG
1 TTTTTGGCTAAAAACGCGTTTCGGG
13271 AAATAAATTC
Statistics
Matches: 318, Mismatches: 34, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
330 1 0.00
331 70 0.22
332 157 0.49
333 89 0.28
334 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (333 bp):
TTTTTGGCTAAAAACGCGTTTCGGGGCCCTAACTCAGTTTTGCATGAGTTTTGGAAGAAAAATGC
CTCGAAATATATATATTCATCAAACCAAAATCTCAGCCACAATGGATTTAAGGATTTATTTTTAC
CAGCATCTGAATCTTGTTTCAATTAAATTAGAAATAAATTCAGAAAAATATGGAAAAACAATATT
AGAAGCACGAAAAACCCTATAATACTTTTGGCGTTGAATTATATGATTTTACAGAGTATTGTGGC
AAAATTGGGGAAAAAACTTCTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATAGTGTTCTAAC
AATCACGA
Found at i:13455 original size:2 final size:2
Alignment explanation
Indices: 13448--13476 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13438 AGACTTCTCG
13448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.