Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022211.1 Corchorus olitorius cultivar O-4 contig22244, 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: 57609
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:43 original size:33 final size:33
Alignment explanation
Indices: 1--122 Score: 235
Period size: 33 Copynumber: 3.7 Consensus size: 33
*
1 TGCCGCCCCAGGAGGACGGCACCACCATGGTCA
1 TGCCGCCCCAGGAGGGCGGCACCACCATGGTCA
34 TGCCGCCCCAGGAGGGCGGCACCACCATGGTCA
1 TGCCGCCCCAGGAGGGCGGCACCACCATGGTCA
67 TGCCGCCCCAGGAGGGCGGCACCACCATGGTCA
1 TGCCGCCCCAGGAGGGCGGCACCACCATGGTCA
100 TGCCGCCCCAGGAGGGCGGCACC
1 TGCCGCCCCAGGAGGGCGGCACC
123 GGTTATTTTT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.18, C:0.40, G:0.34, T:0.08
Consensus pattern (33 bp):
TGCCGCCCCAGGAGGGCGGCACCACCATGGTCA
Found at i:239 original size:29 final size:28
Alignment explanation
Indices: 200--255 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
190 GTTATTCCAC
*
200 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
229 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
256 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:4451 original size:13 final size:13
Alignment explanation
Indices: 4433--4459 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4423 AAACGGAAAA
4433 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
4446 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
4459 T
1 T
4460 TTAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:8119 original size:438 final size:440
Alignment explanation
Indices: 7317--8263 Score: 1544
Period size: 438 Copynumber: 2.2 Consensus size: 440
7307 TTTTGTCGGT
* * * *
7317 TTATTTATCAAATGATTCATATACTTTTATACTTTATGCTATTTAGTCCCTCACAATTTCTGGGT
1 TTATTTATCAAATGATCCTTAGACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTCTGGGT
* *
7382 TGGACGACTAAATGTTTCGGCTTTAATTCTTTTATTTTTTGTTTTGCTTGTCCGATCAAGGTGAT
66 TGGACGACTAAACGTTTCGGCTTTAATTCTTTTATTTTTTCTTTTGCTTGTCCGATCAAGGTGAT
* * * * *
7447 TCAAGTGTCTATTAAAACTTAATTTCGTGATCTACAACTTTCATGAAGGACTCAAAAGTCAATTT
131 TCAAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATGAAGGACTCAAAAGCCAAATT
*
7512 TAATGTTTTGATTTTAAAAAATACTTTTGAAATTTTGTGGTCTTGATTGCCGGTCTATTTGATAT
196 TAATGTTTTGATTTTAAAAAATACTTTTGAAATTTTGTGGTCTTGATTGCCGGTATATTTGATAT
* * **
7577 CGTATAATTTTTGTTCCATTTGTTTGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGT
261 CGTATAATTTTTGTCCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGT
*
7642 GATCTATGGCTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGGTTCAA
326 GATCTACGGCTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGGTTCAA
7707 GAGGGAATTTTTATGTTTGGTCTCCATAAACAAATA-TTTTTTTGCTGGA
391 GAGGGAATTTTTATGTTTGGTCTCCATAAACAAATATTTTTTTTGCTGGA
*
7756 TTATTTATCAAATGATCCTTAGACTTTTGTGCTTTATGCTATTTAGTCCCTCACAATTTCTGGGT
1 TTATTTATCAAATGATCCTTAGACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTCTGGGT
* *
7821 TGGACGACTGAACGTTTTGGCTTTAATTCTTTTA-TTTTTCTTTTGCTTGTCCGATCAAGGTGAT
66 TGGACGACTAAACGTTTCGGCTTTAATTCTTTTATTTTTTCTTTTGCTTGTCCGATCAAGGTGAT
* *
7885 TCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTCCATGATGGACTCAAAAGCCAAATT
131 TCAAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATGAAGGACTCAAAAGCCAAATT
*
7950 TAATGTTTTGATTTTAAAAAATGCTTTTGAAATTTTGTGGTCTTGATTGCCGGTATATTTGATAT
196 TAATGTTTTGATTTTAAAAAATACTTTTGAAATTTTGTGGTCTTGATTGCCGGTATATTTGATAT
*
8015 CGTATAATTTTT-TGCCCACTTGTCCGATTGTGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTG
261 CGTATAATTTTTGT-CCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTG
* *
8079 TGATCTACGGTTTTTGTTAAGGG-TCTCAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGGTTC
325 TGATCTACGGCTTTCGTTAAGGGCT-TCAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGGTTC
8143 AAGAGGGAATTTTTATGTTTGGTCTCCATAAACAAATATTTTTTTTGCTGGA
389 AAGAGGGAATTTTTATGTTTGGTCTCCATAAACAAATATTTTTTTTGCTGGA
* * * * * * *
8195 TTATTTATCAAATGATCCTCAGATTTTTATGTTTTATGCTATTTAATCCCTTATAA-TTATGGGT
1 TTATTTATCAAATGATCCTTAGACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTCTGGGT
8259 TGGAC
66 TGGAC
8264 CATTTAATGC
Statistics
Matches: 471, Mismatches: 34, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
437 2 0.00
438 316 0.67
439 153 0.32
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (440 bp):
TTATTTATCAAATGATCCTTAGACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTCTGGGT
TGGACGACTAAACGTTTCGGCTTTAATTCTTTTATTTTTTCTTTTGCTTGTCCGATCAAGGTGAT
TCAAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATGAAGGACTCAAAAGCCAAATT
TAATGTTTTGATTTTAAAAAATACTTTTGAAATTTTGTGGTCTTGATTGCCGGTATATTTGATAT
CGTATAATTTTTGTCCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGT
GATCTACGGCTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGGTTCAA
GAGGGAATTTTTATGTTTGGTCTCCATAAACAAATATTTTTTTTGCTGGA
Found at i:9062 original size:20 final size:20
Alignment explanation
Indices: 9037--9076 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9027 ATCTGCATAT
9037 ATTTGTAATCCTACTCGTAC
1 ATTTGTAATCCTACTCGTAC
9057 ATTTGTAATCCTACTCGTAC
1 ATTTGTAATCCTACTCGTAC
9077 GTAATATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (20 bp):
ATTTGTAATCCTACTCGTAC
Found at i:9259 original size:21 final size:21
Alignment explanation
Indices: 9233--9282 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
9223 TGCTAGGAGT
9233 TCATTGGAGCAA-GTTTCAAGC
1 TCATTGGAG-AAGGTTTCAAGC
9254 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTTCAAGC
9275 TCATTGGA
1 TCATTGGA
9283 ATTGCCCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (21 bp):
TCATTGGAGAAGGTTTCAAGC
Found at i:9558 original size:65 final size:65
Alignment explanation
Indices: 9476--9600 Score: 232
Period size: 65 Copynumber: 1.9 Consensus size: 65
9466 GTTTGCTATT
* *
9476 GATTCCAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTGCACTAGCCCAAGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
9541 GATTCAAACTTTCTGCACTAGCCCAAGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGT
1 GATTCAAACTTTCTGCACTAGCCCAAGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGT
9601 AGGAGCAGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.22
Consensus pattern (65 bp):
GATTCAAACTTTCTGCACTAGCCCAAGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
Found at i:18509 original size:28 final size:29
Alignment explanation
Indices: 18469--18524 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
18459 ACCTGTAAGA
* *
18469 AGAGGGACTAAATTGA-TTGTTCTTGTAT
1 AGAGGAACCAAATTGACTTGTTCTTGTAT
*
18497 AGAGGAACCAAATTGACTTTTTCTTGTA
1 AGAGGAACCAAATTGACTTGTTCTTGTA
18525 AGTACAGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (29 bp):
AGAGGAACCAAATTGACTTGTTCTTGTAT
Found at i:19465 original size:42 final size:43
Alignment explanation
Indices: 19414--19501 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 43
19404 TGCATTACCT
* *
19414 AAATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTA
1 AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
19456 AAATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTA
1 AAATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTA
19501 A
1 A
19502 TATTAATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 8 0.20
45 33 0.80
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.31
Consensus pattern (43 bp):
AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
Found at i:20534 original size:22 final size:21
Alignment explanation
Indices: 20509--20567 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
20499 AACACTATTA
20509 AATAAACATAATACATATTAAT
1 AATAAACATAATA-ATATTAAT
*
20531 AATATAA-AT-ATAACATTAAT
1 AATA-AACATAATAATATTAAT
20551 AAT-AACATAATATATAT
1 AATAAACATAATA-ATAT
20568 ATATATCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 13 0.42
21 6 0.19
22 6 0.19
23 2 0.06
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAAACATAATAATATTAAT
Found at i:21625 original size:13 final size:13
Alignment explanation
Indices: 21607--21631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21597 TTGAAATTCC
21607 AAATAATATTTAT
1 AAATAATATTTAT
21620 AAATAATATTTA
1 AAATAATATTTA
21632 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:22380 original size:22 final size:22
Alignment explanation
Indices: 22335--22380 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
22325 TAACAAATTT
* * *
22335 TTAACAAATTTTCATAAGATGG
1 TTAACAAAATTTCATAAAAAGG
22357 TTAACAAAATTTCATAAAAAGG
1 TTAACAAAATTTCATAAAAAGG
22379 TT
1 TT
22381 TTCGAAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
TTAACAAAATTTCATAAAAAGG
Found at i:22521 original size:22 final size:22
Alignment explanation
Indices: 22445--22522 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
22435 AATCTGGAGA
* *
22445 TTATCGAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGT
* * *
22467 TTATTAAGATTTCATAGAGATGT
1 TTATCAAAATTTCATAGTG-TGT
* * *
22490 AT-TCACAATTTTATAGTGTGT
1 TTATCAAAATTTCATAGTGTGT
22511 TTATCAAAATTT
1 TTATCAAAATTT
22523 GATATGAATA
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.83
23 3 0.07
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGT
Found at i:23813 original size:45 final size:44
Alignment explanation
Indices: 23751--23838 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 44
23741 CTAAATTCTA
* *
23751 CTCCATCTTTAGGTAATTCATCAAAATAAAGCTAATATTCAATTC
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT-AATTC
23796 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTAATT
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTAATT
23839 GTAACTTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 4 0.10
45 37 0.90
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (44 bp):
CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTAATTC
Found at i:26040 original size:2 final size:2
Alignment explanation
Indices: 26027--26065 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
26017 ATTAAAAATA
26027 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26066 TATTAAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26883 original size:16 final size:17
Alignment explanation
Indices: 26850--26883 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
26840 CTCGAGGTTT
26850 TGAGGTTTCAGTTATATA
1 TGAGGTTTCAG-TATATA
26868 TGAGGTTTCA-TATATA
1 TGAGGTTTCAGTATATA
26884 AGCCATAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAGGTTTCAGTATATA
Found at i:28547 original size:5 final size:5
Alignment explanation
Indices: 28537--28570 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
28527 TCTCTTATGT
28537 ATATA ATATA ATATA ATATA ATAT- ATAT- ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
28571 GTAATATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:29031 original size:2 final size:2
Alignment explanation
Indices: 29016--29048 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
29006 TCTTATTGTA
*
29016 AT AT AT TT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29049 TATTATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:38044 original size:14 final size:15
Alignment explanation
Indices: 38025--38060 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
38015 GACCTTTAAT
38025 TATAAAAA-AAATTA
1 TATAAAAATAAATTA
38039 TATAAAAATAAATT-
1 TATAAAAATAAATTA
38053 T-TAAAAAT
1 TATAAAAAT
38061 TATGTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.33
14 9 0.43
15 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TATAAAAATAAATTA
Found at i:39816 original size:31 final size:32
Alignment explanation
Indices: 39779--39852 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
39769 TTCAAATCGC
* * *
39779 GACAATTTATTCCAT-AAATTTTCAAATTCAG
1 GACAATTTATCCCATCAAATTTCCAAATTAAG
* *
39810 GACAATTTGTCCCATCAACTTTCCAAATTAAG
1 GACAATTTATCCCATCAAATTTCCAAATTAAG
*
39842 AACAATTTATC
1 GACAATTTATC
39853 TCCCGGTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 13 0.37
32 22 0.63
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (32 bp):
GACAATTTATCCCATCAAATTTCCAAATTAAG
Found at i:49611 original size:21 final size:21
Alignment explanation
Indices: 49585--49673 Score: 133
Period size: 21 Copynumber: 4.2 Consensus size: 21
49575 TACATACATG
* **
49585 GTCAAACCACAAAGGATGATA
1 GTCAAACCCCAAAGTTTGATA
*
49606 GTCAAACCCCAAATTTTGATA
1 GTCAAACCCCAAAGTTTGATA
49627 GTCAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAAGTTTGATA
*
49648 GTCAAACCCCAAATTTTGATA
1 GTCAAACCCCAAAGTTTGATA
49669 GTCAA
1 GTCAA
49674 CACGTTAAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (21 bp):
GTCAAACCCCAAAGTTTGATA
Found at i:49647 original size:42 final size:42
Alignment explanation
Indices: 49585--49673 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
49575 TACATACATG
49585 GTCAAACCACAAAGGATGATAGTCAAACCCCAAATTTTGATA
1 GTCAAACCACAAAGGATGATAGTCAAACCCCAAATTTTGATA
* **
49627 GTCAAACCCCAAAGTTTGATAGTCAAACCCCAAATTTTGATA
1 GTCAAACCACAAAGGATGATAGTCAAACCCCAAATTTTGATA
49669 GTCAA
1 GTCAA
49674 CACGTTAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (42 bp):
GTCAAACCACAAAGGATGATAGTCAAACCCCAAATTTTGATA
Found at i:52664 original size:2 final size:2
Alignment explanation
Indices: 52657--52683 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52647 AAAACTTTAT
52657 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52684 TAAGAAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53431 original size:51 final size:50
Alignment explanation
Indices: 53372--53472 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 50
53362 TGCTAATCAA
53372 ATATCTATATATTATTTTTAGTTACCAGGGAAATTACTAAAAGGCCAAAT
1 ATATCTATATATTATTTTTAGTTACCAGGGAAATTACTAAAAGGCCAAAT
53422 ATATACTATATATTATTTTTAGTTACCAGGGAAATTACTAAAAGGCCAAAT
1 ATAT-CTATATATTATTTTTAGTTACCAGGGAAATTACTAAAAGGCCAAAT
53473 TGAGGATTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 4 0.08
51 46 0.92
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (50 bp):
ATATCTATATATTATTTTTAGTTACCAGGGAAATTACTAAAAGGCCAAAT
Found at i:56546 original size:18 final size:18
Alignment explanation
Indices: 56523--56568 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
56513 TGAAATTAAT
56523 TAATTATTAATTAAATAA
1 TAATTATTAATTAAATAA
** *
56541 TAATTATTTTTTGAATAA
1 TAATTATTAATTAAATAA
*
56559 TTATTATTAA
1 TAATTATTAA
56569 ATTTCTAGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTAATTAAATAA
Done.