Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008676.1 Corchorus capsularis cultivar CVL-1 contig08697, 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: 75742
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1467 original size:344 final size:346
Alignment explanation
Indices: 942--1634 Score: 1246
Period size: 345 Copynumber: 2.0 Consensus size: 346
932 TTATCAAATG
942 ATCCCTATACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTTTGGGTTGGACGATTGAACG
1 ATCCCTATACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTTTGGGTTGGACGATTGAACG
*
1007 TTTCGCCTTTAATTCTTTTATTTTTTTTGTTTTGTTTGTCCGATGAAGGTGATTCAAGTGCCTAT
66 TTTCGCCTTTAATTCTTTTA-TTTTTTTATTTTGTTTGTCCGATGAAGGTGATTCAAGTGCCTAT
*
1072 TAAAAGGTAATTTCATGATCTACAACTTCCATGAAGAACTCAAAAGTCAATTTTAATGTTTTGA-
130 TAAAAGGTAATTTCATGATCTACAACATCCATGAAGAACTCAAAAGTCAATTTTAATGTTTTGAT
*
1136 TCAAAAAAATGCTTCTGAAATTTTGTGGTCTCGATTGCCGATCTATTTGATATCGTATAAATTTC
195 TCAAAAAAATGCTTCTGAAATTTTGTGATCTCGATTGCCGATCTATTTGATATCGTATAAATTTC
*
1201 GGTCCACTTGTCTGATTGAGGTTGTTCAAGTGTCGATTAAAAAGTTATTGTGTGATCTACGACTT
260 GGTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGATTAAAAAGTTATTGTGTGATCTACGACTT
1266 TCGTTAAAGGCCTGAAAGCTGA
325 TCGTTAAAGGCCTGAAAGCTGA
1288 ATCCCTATACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTTTGGGTTGGACGATTGAACG
1 ATCCCTATACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTTTGGGTTGGACGATTGAACG
* * *
1353 TTTCGGCTTTAATTCTTTTA-TTTTTTATTTTGTTTGTCCGATTAAGGTGATTCAAGTGCTTATT
66 TTTCGCCTTTAATTCTTTTATTTTTTTATTTTGTTTGTCCGATGAAGGTGATTCAAGTGCCTATT
* *
1417 AAAAGTTAATTTCATGATCTACAACATCCATGAAGGACTCAAAAGTCAATTTTAATGTTTTGATT
131 AAAAGGTAATTTCATGATCTACAACATCCATGAAGAACTCAAAAGTCAATTTTAATGTTTTGATT
*
1482 CAAAAAAATGCTTCTGAAATTTTGTGATCTCGATTGCCGGTCTATTTGATATCGTATAAATTTCG
196 CAAAAAAATGCTTCTGAAATTTTGTGATCTCGATTGCCGATCTATTTGATATCGTATAAATTTCG
* *
1547 GTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTT
261 GTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGATTAAAAAGTTATTGTGTGATCTACGACTTT
*
1612 CGTTAAGGGCCTGAAAGCTGA
326 CGTTAAAGGCCTGAAAGCTGA
1633 AT
1 AT
1635 TTGATTAATG
Statistics
Matches: 333, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
344 101 0.30
345 148 0.44
346 84 0.25
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (346 bp):
ATCCCTATACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTTTGGGTTGGACGATTGAACG
TTTCGCCTTTAATTCTTTTATTTTTTTATTTTGTTTGTCCGATGAAGGTGATTCAAGTGCCTATT
AAAAGGTAATTTCATGATCTACAACATCCATGAAGAACTCAAAAGTCAATTTTAATGTTTTGATT
CAAAAAAATGCTTCTGAAATTTTGTGATCTCGATTGCCGATCTATTTGATATCGTATAAATTTCG
GTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGATTAAAAAGTTATTGTGTGATCTACGACTTT
CGTTAAAGGCCTGAAAGCTGA
Found at i:2148 original size:441 final size:439
Alignment explanation
Indices: 1288--2720 Score: 1796
Period size: 441 Copynumber: 3.3 Consensus size: 439
1278 TGAAAGCTGA
* * * * *
1288 ATCCCTATACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTTTGGGTTGGACGATTGAACG
1 ATCCCTATACTTTTATGCTTTATGCTATTTAATCCTTTACAAATTATGGGTTGGACGATTGAACG
* * * * *
1353 TTTCGGCTTTAATTCTTTTATTTTTTATTTTGTTTGTCCGATTAAGGTGATTCAAGTG-CTTATT
66 TTTCGACTTTAATTCTTTTATTTTTTGTTTTATTTGTCTGATCAAGGTGATTCAAGTGTC-TATT
* * * *
1417 AAAAGTTAATTTCATGATCTACAACATCCATGAAGGACTCAAAAGTCAATTTTAATGTTTTGATT
130 AAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAA-CCAATTTTAATGTTTTGATT
* * * * * * *
1482 CAAAAAAATGCTTCTGAAATTTTGTGATCTCGATTGCCGGTCTATTTGATATCGTATAAATTTCG
194 CTAAAAAATGCTTCTTAAATTTTGTGGTCTCGATTG-CAGTCTATTTAATATTGTATAATTTTCG
*
1547 GTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTT
258 GTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTTT
* * *
1612 CGTTAAGGGCCTGAAAGCTGAATTTGATTAATGATTTTCGTGGAGGGTTTCAAGAGGGAATTTTT
323 CGTTAAGGGCTTGAAAGCTGAATTTGATTAATGAGTTTCGTGGA-GGATTCAAGAGGGAATTTTT
*
1677 ATGTTTGGTCTCCATAAACAAATA-ATTTTTTTGTTGGATTATTCATCAAATG
387 ATGTTTGGTCTCCATAAACAAATATATTTTTTTGTTGGATTATTTATCAAATG
* * * * *
1729 ATCCATATACTTTTATGCTTTATGTTATTTAGTCCTTTCACAAATTCTGGATTGGACGATTGAAC
1 ATCCCTATACTTTTATGCTTTATGCTATTTAATCCTTT-ACAAATTATGGGTTGGACGATTGAAC
* * *
1794 GTTTCGACTTTAATTCTTTTATTTTTTGCTTTACTTATCTGATCAAGGTGATTCAAGTGTCTATT
65 GTTTCGACTTTAATTCTTTTATTTTTTGTTTTATTTGTCTGATCAAGGTGATTCAAGTGTCTATT
* * **
1859 AAAAGGTAATTTCATGATCTACAACTTTCATGAAGGATTCAAAACCAATTTTCATGTTTCAATTC
130 AAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAACCAATTTTAATGTTTTGATTC
*
1924 TAAAAAA-GACTTCTTAAATTTTGTGGTCTCGATTGTCAGTCTATCTAATATTGTATAATTTTCG
195 TAAAAAATG-CTTCTTAAATTTTGTGGTCTCGATTG-CAGTCTATTTAATATTGTATAATTTTCG
* * *
1988 ATCTACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGTGATTGTGTGATCTATGACTTT
258 GTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTTT
* *
2053 CGTCAAGGGCTTGAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGATTCGAGAGGGAATTTTTA
323 CGTTAAGGGCTTGAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGATTCAAGAGGGAATTTTTA
* * *
2118 TATTTGGTCTCCATAGACAAATATA-TTTTTTGCTGGATTATTTATCAAATG
388 TGTTTGGTCTCCATAAACAAATATATTTTTTTGTTGGATTATTTATCAAATG
* * * * *
2169 ATCCTTATACTTTTATGCTTTAAGCTATTTAATCATTTA-TAATTATGGGTTGGACGATTTAACG
1 ATCCCTATACTTTTATGCTTTATGCTATTTAATCCTTTACAAATTATGGGTTGGACGATTGAACG
** * * *
2233 CGTCG-CTTTTATT-TTTGTA---TCTGTTTTATTTGTCTGATCAAGGTGATTAAAGTGTCTATT
66 TTTCGACTTTAATTCTTT-TATTTTTTGTTTTATTTGTCTGATCAAGGTGATTCAAGTGTCTATT
* * ** *
2293 GAAAGGTAATCTCATGATCTACAACTTTCATGAAAAACTCAGAAGCCAATTTTAATGTTTTGATT
130 AAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCA-AAACCAATTTTAATGTTTTGATT
* * * *
2358 CTAAAAAATGTTTCTT-AA---CGTGGTTTCGATTGCCGATCTATTTAATATTGTATAATTTTCG
194 CTAAAAAATGCTTCTTAAATTTTGTGGTCTCGATTGCAG-TCTATTTAATATTGTATAATTTTCG
* **
2419 GTCCACTTGTCCGATTGAAGTTGTTCAAGTGTCACTTAAAAGGTTATTGTGTGATCTATGACTTT
258 GTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTTT
* * * *
2484 CATTAAGGG-TATGAAAGTTGAATTTTATTAATGAGTTTCATGGAGGATTCAAGAGGGAATTTTT
323 CGTTAAGGGCT-TGAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGATTCAAGAGGGAATTTTT
* * *
2548 ATGTTTTGTCTCCATAAAC-TA-AT-TTTTTTTGTTGGATTATTTATCTAATG
387 ATGTTTGGTCTCCATAAACAAATATATTTTTTTGTTGGATTATTTATCAAATG
* * * *
2598 A-CCCTCATACTTTTATGC-TCATGCTATTGAATCCTTTAC-AATTATAGGTTGGACGATTTAAC
1 ATCCCT-ATACTTTTATGCTTTATGCTATTTAATCCTTTACAAATTATGGGTTGGACGATTGAAC
** * ** *
2660 GCTTT-GACTTTTGTT-TTTGTATTTTTGTGTTCTATTTGTCCCATTAAGGTGATTCAAGTGT
65 G-TTTCGACTTTAATTCTTT-TATTTTT-TGTTTTATTTGTCTGATCAAGGTGATTCAAGTGT
2721 TTACAGGAAG
Statistics
Matches: 865, Mismatches: 109, Indels: 44
0.85 0.11 0.04
Matches are distributed among these distances:
428 43 0.05
429 53 0.06
430 4 0.00
431 167 0.19
432 1 0.00
433 29 0.03
434 74 0.09
435 32 0.04
436 4 0.00
437 9 0.01
438 24 0.03
439 1 0.00
440 98 0.11
441 207 0.24
442 118 0.14
443 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (439 bp):
ATCCCTATACTTTTATGCTTTATGCTATTTAATCCTTTACAAATTATGGGTTGGACGATTGAACG
TTTCGACTTTAATTCTTTTATTTTTTGTTTTATTTGTCTGATCAAGGTGATTCAAGTGTCTATTA
AAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAACCAATTTTAATGTTTTGATTCT
AAAAAATGCTTCTTAAATTTTGTGGTCTCGATTGCAGTCTATTTAATATTGTATAATTTTCGGTC
CACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTTTCGT
TAAGGGCTTGAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGATTCAAGAGGGAATTTTTATGT
TTGGTCTCCATAAACAAATATATTTTTTTGTTGGATTATTTATCAAATG
Found at i:26439 original size:39 final size:39
Alignment explanation
Indices: 26396--26609 Score: 229
Period size: 39 Copynumber: 5.6 Consensus size: 39
26386 TAGAAAGAGT
*
26396 AGAAGCATCAGCAGGAGCCCAGCTAGAGCACATTCTCGA
1 AGAAGCATCAGCAGGAGCCCAGCTAGAGCACATTCTCAA
* * **
26435 AGAAGCATCGGCAGGAGCCCTGCTAGAGCACATTCTCCC
1 AGAAGCATCAGCAGGAGCCCAGCTAGAGCACATTCTCAA
* *
26474 AGAAGCATCGGTAGGAGCCCAG-TAAGAGCACATTCTCAA
1 AGAAGCATCAGCAGGAGCCCAGCT-AGAGCACATTCTCAA
* * * * *
26513 AGAAGCCTTAGCAGGAGCCCAGTTAGAGCACATTCCCGA
1 AGAAGCATCAGCAGGAGCCCAGCTAGAGCACATTCTCAA
* * * *
26552 AGAAG---CAGCAGGAGCCCAGTTCGATCACGTTCTCAA
1 AGAAGCATCAGCAGGAGCCCAGCTAGAGCACATTCTCAA
* *
26588 AGAAGCATTAGCAGGAGACCAG
1 AGAAGCATCAGCAGGAGCCCAG
26610 TTTCTAGAAG
Statistics
Matches: 148, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
36 30 0.20
38 1 0.01
39 116 0.78
40 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.26, T:0.14
Consensus pattern (39 bp):
AGAAGCATCAGCAGGAGCCCAGCTAGAGCACATTCTCAA
Found at i:26769 original size:36 final size:36
Alignment explanation
Indices: 26729--26823 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 36
26719 ACCTTCAAAA
* *
26729 AGAAGCTTAAGTAGAAGCCCAGGGAGATCTTCTCGG
1 AGAAGCATAAGTAGAAGCCCAGGAAGATCTTCTCGG
* * * *
26765 AGAAGCACT-AGCAGAAGTCCTGTAAGATCTTCTCGG
1 AGAAGCA-TAAGTAGAAGCCCAGGAAGATCTTCTCGG
* *
26801 AGAAGCATAAGTAGGAGCTCAGG
1 AGAAGCATAAGTAGAAGCCCAGG
26824 CAGGGCTCCT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
35 1 0.02
36 43 0.96
37 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (36 bp):
AGAAGCATAAGTAGAAGCCCAGGAAGATCTTCTCGG
Found at i:30082 original size:108 final size:107
Alignment explanation
Indices: 29899--30110 Score: 336
Period size: 108 Copynumber: 2.0 Consensus size: 107
29889 ATTAATCGAA
* * * *
29899 TATATTAATTCTTCAACAAAATAATCCGGCTTTACATTATAAATTTTAAGGTTGGGATATTCGGA
1 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
* *
29964 AAAAAGAAAACAAAA-AATTGATTTAAGGATATTGTTAATTAAT
66 AAAAAAAAAACAAAACAATTGA--TAAAGATATTGTTAATTAAT
*
30007 TATATTAATTCTTGAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
1 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
30072 AAAAAAAAAACAAAACAATTGATAAAGATATTGTTAATT
66 AAAAAAAAAACAAAACAATTGATAAAGATATTGTTAATT
30111 GATTTTTACA
Statistics
Matches: 96, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
107 16 0.17
108 74 0.77
109 6 0.06
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (107 bp):
TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
AAAAAAAAAACAAAACAATTGATAAAGATATTGTTAATTAAT
Found at i:31486 original size:37 final size:37
Alignment explanation
Indices: 31444--31514 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
31434 ACATGATTAT
* *
31444 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
31481 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
31515 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:33939 original size:37 final size:37
Alignment explanation
Indices: 33897--33967 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
33887 ACATGATTAT
* *
33897 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
33934 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
33968 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:38535 original size:3 final size:3
Alignment explanation
Indices: 38525--38575 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
38515 ACTGTTGTTT
*
38525 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TCA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38572 TAA T
1 TAA T
38576 TCACTTGCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:59985 original size:31 final size:31
Alignment explanation
Indices: 59950--60018 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
59940 AGTTTTGTAA
*
59950 AACTTTTGAAACGCCTATTGTACCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
* *
59981 AACTTTTGAAATGCCTATTATATCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
60012 AACTTTT
1 AACTTTT
60019 ACAGTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (31 bp):
AACTTTTGAAACGCCTATTATACCCTTATTT
Found at i:60746 original size:22 final size:22
Alignment explanation
Indices: 60718--60759 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
60708 GTTTATAATA
*
60718 TTCTCGGATCATTTGGGTTAAC
1 TTCTCGGATCATTCGGGTTAAC
60740 TTCTCGGATCATTCGGGTTA
1 TTCTCGGATCATTCGGGTTA
60760 TATGTTTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (22 bp):
TTCTCGGATCATTCGGGTTAAC
Found at i:61158 original size:20 final size:20
Alignment explanation
Indices: 61143--61180 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
61133 AATTTATTTG
61143 TTTTTTTCTTCTTTTACCTT
1 TTTTTTTCTTCTTTTACCTT
61163 TTTTTTTCTTCTTTTACC
1 TTTTTTTCTTCTTTTACC
61181 AATATATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTTCTTCTTTTACCTT
Found at i:64487 original size:53 final size:53
Alignment explanation
Indices: 64429--64594 Score: 138
Period size: 53 Copynumber: 3.2 Consensus size: 53
64419 TTTTGGATAT
64429 ATTAAATTTTTTTAATATACAGTTTTATTCTACTAAAAACTCTATTTTCATTA
1 ATTAAATTTTTTTAATATACAGTTTTATTCTACTAAAAACTCTATTTTCATTA
* * * *
64482 ATTAAATTCAATATTTTATATTTTAC--TATTT-TTC-AATAAAAA-TTTGGA-TAT-ATTA
1 ATTAAATT---T-TTTTA-A-TATACAGT-TTTATTCTACTAAAAACTCT--ATTTTCATTA
64537 A--AAA--TTTTTAATATACAGTTTTATTCTACTAAAAACTCTATTTTCATTA
1 ATTAAATTTTTTTAATATACAGTTTTATTCTACTAAAAACTCTATTTTCATTA
64586 ATTAAATTT
1 ATTAAATTT
64595 AATATTTTAT
Statistics
Matches: 85, Mismatches: 8, Indels: 40
0.64 0.06 0.30
Matches are distributed among these distances:
45 4 0.05
46 4 0.05
47 10 0.12
48 10 0.12
49 7 0.08
51 3 0.04
53 12 0.14
55 7 0.08
56 10 0.12
57 10 0.12
58 4 0.05
59 4 0.05
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (53 bp):
ATTAAATTTTTTTAATATACAGTTTTATTCTACTAAAAACTCTATTTTCATTA
Found at i:64513 original size:104 final size:104
Alignment explanation
Indices: 64397--64605 Score: 382
Period size: 104 Copynumber: 2.0 Consensus size: 104
64387 TATTTTTACC
* **
64397 ATTTTACTATTTTTCAATAAAATTTTGGATATATTAAATTTTTTTAATATACAGTTTTATTCTAC
1 ATTTTACTATTTTTCAATAAAAATTTGGATATATTAAAAATTTTTAATATACAGTTTTATTCTAC
64462 TAAAAACTCTATTTTCATTAATTAAATTCAATATTTTAT
66 TAAAAACTCTATTTTCATTAATTAAATTCAATATTTTAT
64501 ATTTTACTATTTTTCAATAAAAATTTGGATATATTAAAAATTTTTAATATACAGTTTTATTCTAC
1 ATTTTACTATTTTTCAATAAAAATTTGGATATATTAAAAATTTTTAATATACAGTTTTATTCTAC
*
64566 TAAAAACTCTATTTTCATTAATTAAATTTAATATTTTAT
66 TAAAAACTCTATTTTCATTAATTAAATTCAATATTTTAT
64605 A
1 A
64606 ATTATTTTAT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (104 bp):
ATTTTACTATTTTTCAATAAAAATTTGGATATATTAAAAATTTTTAATATACAGTTTTATTCTAC
TAAAAACTCTATTTTCATTAATTAAATTCAATATTTTAT
Found at i:64626 original size:25 final size:25
Alignment explanation
Indices: 64598--64666 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
64588 TAAATTTAAT
**
64598 ATTTTATAATTATTTTATTTTTACC
1 ATTTTATAATTATTTTATTTACACC
* * *
64623 ATTTTA-ATTTATTGTGATTTACATC
1 ATTTTATAATTATT-TTATTTACACC
64648 -TTTTATAATTATTTTATTT
1 ATTTTATAATTATTTTATTT
64667 GACTTATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
24 16 0.46
25 19 0.54
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (25 bp):
ATTTTATAATTATTTTATTTACACC
Found at i:70564 original size:17 final size:17
Alignment explanation
Indices: 70542--70576 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
70532 ATTTACACCG
70542 CCAGTGTATCAAATAAT
1 CCAGTGTATCAAATAAT
70559 CCAGTGTATCAAATAAT
1 CCAGTGTATCAAATAAT
70576 C
1 C
70577 ACCCTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (17 bp):
CCAGTGTATCAAATAAT
Found at i:70910 original size:201 final size:201
Alignment explanation
Indices: 70559--70982 Score: 814
Period size: 201 Copynumber: 2.1 Consensus size: 201
70549 ATCAAATAAT
70559 CCAGTGTATCAAATAATCACCCTTTCTTAAAGGCAAATTATACAATACACCGTCAGTGGAGTTTA
1 CCAGTGTATCAAATAATCACCCTTTCTTAAAGGCAAATTATACAATACACCGTCAGTGGAGTTTA
70624 GCAGACTACACAAGCGGGTCCTCAAGGGTGACATGTGTCCCCTAGGGACTAGATTGAAAAATTTA
66 GCAGACTACACAAGCGGGTCCTCAAGGGTGACATGTGTCCCCTAGGGACTAGATTGAAAAATTTA
70689 AACTTGATTAATTAAAAAAATGGACATATGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTT
131 AACTTGATTAATTAAAAAAATGGACATATGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTT
70754 ACACCG
196 ACACCG
70760 CCAGTGTATCAAATAATCACCCTTTCTTAAAGGCAAATTATACAATACACCGTCAGTGGAGTTTA
1 CCAGTGTATCAAATAATCACCCTTTCTTAAAGGCAAATTATACAATACACCGTCAGTGGAGTTTA
*
70825 GCAGACTACACAAGCGGGTCCTCAAGGGTGACATGTGTCTCCTAGGGACTAGATTGAAAAATTTA
66 GCAGACTACACAAGCGGGTCCTCAAGGGTGACATGTGTCCCCTAGGGACTAGATTGAAAAATTT-
*
70890 AAACTTGATTAATT-AAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATT
130 AAACTTGATTAATTAAAAAAATGGACATATGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATT
70954 TACACCG
195 TACACCG
70961 CCAGTGTATCAAATAATCACCC
1 CCAGTGTATCAAATAATCACCC
70983 CATATAGCAT
Statistics
Matches: 220, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
201 206 0.94
202 14 0.06
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (201 bp):
CCAGTGTATCAAATAATCACCCTTTCTTAAAGGCAAATTATACAATACACCGTCAGTGGAGTTTA
GCAGACTACACAAGCGGGTCCTCAAGGGTGACATGTGTCCCCTAGGGACTAGATTGAAAAATTTA
AACTTGATTAATTAAAAAAATGGACATATGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTT
ACACCG
Done.