Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007908.1 Corchorus capsularis cultivar CVL-1 contig07929, 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: 53369
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3374 original size:427 final size:427
Alignment explanation
Indices: 2568--3838 Score: 1989
Period size: 427 Copynumber: 3.0 Consensus size: 427
2558 GTAGCACATC
* *
2568 TAGATGAAATTGTATTGAAGACAATTACGTGAACTCAATTGCTCTGTACTATTTTTCCCTTATGT
1 TAGATGGAATTGTATTGAAGACAATTACATGAACTCAATTGCTCTGTACTATTTTTCCCTTATGT
* * *
2633 TCGGTTTTTATCCCATTGAGTTTTTCAACTTAAGGTTTTAAACGAGACAGCAGCCATAGTCCAAC
66 TCGGTTTTTATCCCATTGAGTTTTTCAACTTAAGGTTTT----TAGACAACATCCATAGTCCAAC
*
2698 TTGGCTCATTTGTGTTATCCTGAAGACAAATTGTAAAC-GTATGTGATTTGATGTACTATTTTTC
127 TTGGCTCATTTGTGTTATCCTGAAGACAAATTGTAAACAG-ATGTGATTTGATGTACTTTTTTTC
* * *
2762 CCCTTCTGGCCAGTTTTTGTCCCACTGGTCTTTCGGCTTAAGGTTTTTAATAAGACAATTGGCAT
191 CCCTTCTGGCCAGTTTTTGTCCCACTGGTCTTTTGACTTAAGGTTTTTAATGAGACAATTGGCAT
*
2827 ATGTCTAATTAGGTCATTTTAGTGGTGTTCAATCTAAGGGGAAGTGTTATAAAATAATGGACTTA
256 ATGTCTAATTAGGTCATTTTAGTGGTGTTCAATCTAAGGGGAAGTGTTATAGAATAATGGACTTA
* *
2892 TCGCCTCACAACATTCATTCATATGAATATTGAGTTATTATTTGATACATCGTCAGTGTAGTTTT
321 TCACCTCACAACATTCATCCATATGAATATTGAGTTATTATTTGATACATCGTCAGTGTAGTTTT
*
2957 TGGACTCCATAAGCGGGTTCAAATGTTGACAAGTACCCCATT
386 TGGACTCCACAAGCGGGTTCAAATGTTGACAAGTACCCCATT
* * *
2999 TAGATGGAATTGTATTGAAGAAAATTACATGAACTCAATTGCTCTGTAGTATTTTCCCCTTATGT
1 TAGATGGAATTGTATTGAAGACAATTACATGAACTCAATTGCTCTGTACTATTTTTCCCTTATGT
3064 TCGGTTTTTATCCCATTGAGTTTTTCAACTTAAGGTTTTTAGACAACATCCATAGTCCAACTTGG
66 TCGGTTTTTATCCCATTGAGTTTTTCAACTTAAGGTTTTTAGACAACATCCATAGTCCAACTTGG
* *
3129 CTCATTTGTGTTATCCTGAAGATAAATTGTAAACAGATATGATTTGATGTACTTTTTTTCCCCTT
131 CTCATTTGTGTTATCCTGAAGACAAATTGTAAACAGATGTGATTTGATGTACTTTTTTTCCCCTT
3194 CTGGCCAGTTTTTGTCCCACTGGTCTTTTGACTTAAGGTTTTTAATGAGACAATTGGCATATGTC
196 CTGGCCAGTTTTTGTCCCACTGGTCTTTTGACTTAAGGTTTTTAATGAGACAATTGGCATATGTC
3259 TAATTAGGTCATTTTAGTGGTGTTCAATCTAAGGGGAAGTGTTATAGAATAATGGACTTATCACC
261 TAATTAGGTCATTTTAGTGGTGTTCAATCTAAGGGGAAGTGTTATAGAATAATGGACTTATCACC
* *
3324 TCACAACATTCATCCGTATGAATATTGAGTTATTATTTGATACATCGTCAGTGTAGTTTTTGAAC
326 TCACAACATTCATCCATATGAATATTGAGTTATTATTTGATACATCGTCAGTGTAGTTTTTGGAC
*
3389 TCCACAAGTGGGTTCAAATGTTGACAAGTACCCCATT
391 TCCACAAGCGGGTTCAAATGTTGACAAGTACCCCATT
3426 TAGATGGAATTGTATTGAAGACAATTACATGAACTCAATTGCTCTGTACTATTTTTCCCTTATGT
1 TAGATGGAATTGTATTGAAGACAATTACATGAACTCAATTGCTCTGTACTATTTTTCCCTTATGT
3491 TCGG-----------TTGAGTTTTTCAACTTAAGGTTTTTA-ACGAGACAGTAGCCATAGTCCAA
66 TCGGTTTTTATCCCATTGAGTTTTTCAACTTAAGGTTTTTAGAC-A-ACA-T--CCATAGTCCAA
* *
3544 CTTGGCTCATTTGTATTATCCTTG-AGACAAATTGTGAACAGATGTGATTTGATGTAC-TTTTTT
126 CTTGGCTCATTTGTGTTATCC-TGAAGACAAATTGTAAACAGATGTGATTTGATGTACTTTTTTT
* * *
3607 -CCCTTCTGGTCAGTTTTTGTCCCACTGGTCTTTTGTCTTAAGGTTTTTAATGAGACAATTGCCA
190 CCCCTTCTGGCCAGTTTTTGTCCCACTGGTCTTTTGACTTAAGGTTTTTAATGAGACAATTGGCA
* * * *
3671 TATGTCTAGTTAGGCCATTTTAGTGGTGTTCAATCTAAAGGGAAGTGTTATAGAATAATGAACTT
255 TATGTCTAATTAGGTCATTTTAGTGGTGTTCAATCTAAGGGGAAGTGTTATAGAATAATGGACTT
* * * * *
3736 ATCACCCCCACAACATTCATCCATATTAATATTGAGTTATTATTTGATACATCATTAGTGCAGTT
320 ATCA-CCTCACAACATTCATCCATATGAATATTGAGTTATTATTTGATACATCGTCAGTGTAG-T
*
3801 TTTTGGACTTCACAAGCGGGTTCAAATGTTGACAAGTA
383 TTTTGGACTCCACAAGCGGGTTCAAATGTTGACAAGTA
3839 TCTCATTTCA
Statistics
Matches: 787, Mismatches: 44, Indels: 29
0.92 0.05 0.03
Matches are distributed among these distances:
415 2 0.00
416 27 0.03
417 3 0.00
418 127 0.16
419 58 0.07
420 97 0.12
421 2 0.00
427 371 0.47
428 1 0.00
431 99 0.13
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (427 bp):
TAGATGGAATTGTATTGAAGACAATTACATGAACTCAATTGCTCTGTACTATTTTTCCCTTATGT
TCGGTTTTTATCCCATTGAGTTTTTCAACTTAAGGTTTTTAGACAACATCCATAGTCCAACTTGG
CTCATTTGTGTTATCCTGAAGACAAATTGTAAACAGATGTGATTTGATGTACTTTTTTTCCCCTT
CTGGCCAGTTTTTGTCCCACTGGTCTTTTGACTTAAGGTTTTTAATGAGACAATTGGCATATGTC
TAATTAGGTCATTTTAGTGGTGTTCAATCTAAGGGGAAGTGTTATAGAATAATGGACTTATCACC
TCACAACATTCATCCATATGAATATTGAGTTATTATTTGATACATCGTCAGTGTAGTTTTTGGAC
TCCACAAGCGGGTTCAAATGTTGACAAGTACCCCATT
Found at i:5970 original size:282 final size:284
Alignment explanation
Indices: 5416--5982 Score: 1048
Period size: 282 Copynumber: 2.0 Consensus size: 284
5406 ACAATTTGGC
* *
5416 TAAACTCCTCACCCATTTGATTAAACACCAATTTGGATAAATTTCAAAACCTCAAGCCTCCTAAA
1 TAAACTCCTCACCCATTTGATTAAACACCAATTTGGATAAATTTCAAAACCCCAAGCCCCCTAAA
5481 ATCAGGTACCAAGTTCCCATGAATCAAACTGATCATCTCTTCTCAAAAGATATTTCAATTTTGTT
66 ATCAGGTACCAAGTTCCCATGAATCAAACTGATCATCTCTTCTCAAAAGATATTTCAATTTTGTT
5546 TAGACTTTTCTTTTTGGGGCATTTTTCAGGGAAAATTGATTGGCGGGCCTGAGAGAGGAGGGTGA
131 TAGACTTTTCTTTTTGGGGCATTTTTCAGGGAAAATTGATTGGCGGGCCTGAGAGAGGAGGGTGA
5611 GTAGGCTGAGTATAGATTGAAATTGGAAGCTTTCATCGGATATTGTCGCCGAAATCAATCTTGAA
196 GTAGGCTGAGTATAGATTGAAATTGGAAGCTTTCATCGGATATTGTCGCCGAAATCAATCTTGAA
5676 GGGTGGCGGTTTTGGGAGTTTTGT
261 GGGTGGCGGTTTTGGGAGTTTTGT
5700 TAAACTCCTCACCCATTTGATTAAACACCAATTTGGATAAATTTCAAAACCCCAAGCCCCCTAAA
1 TAAACTCCTCACCCATTTGATTAAACACCAATTTGGATAAATTTCAAAACCCCAAGCCCCCTAAA
**
5765 ATCAGGTACCAAGTTCCCATGAATCAATTTGATCATCTCTTCTCAAAAGATATTTCAA-TTTGTT
66 ATCAGGTACCAAGTTCCCATGAATCAAACTGATCATCTCTTCTCAAAAGATATTTCAATTTTGTT
* *
5829 TAGGCTTTTCTTTTTGGGGCA-TTTTCAGGGAAAATTGATTGGTGGGCCTGAGAGAGGAGGGTGA
131 TAGACTTTTCTTTTTGGGGCATTTTTCAGGGAAAATTGATTGGCGGGCCTGAGAGAGGAGGGTGA
* *
5893 GTAGGCTGAGTATAGATTGAAATTGGAAGCTTTCATCGGATATTGTCGTCGGAATCAATCTTGAA
196 GTAGGCTGAGTATAGATTGAAATTGGAAGCTTTCATCGGATATTGTCGCCGAAATCAATCTTGAA
5958 GGGTGGCGGTTTTGGGAGTTTTGT
261 GGGTGGCGGTTTTGGGAGTTTTGT
5982 T
1 T
5983 TAGAGTTGAT
Statistics
Matches: 275, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
282 130 0.47
283 26 0.09
284 119 0.43
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (284 bp):
TAAACTCCTCACCCATTTGATTAAACACCAATTTGGATAAATTTCAAAACCCCAAGCCCCCTAAA
ATCAGGTACCAAGTTCCCATGAATCAAACTGATCATCTCTTCTCAAAAGATATTTCAATTTTGTT
TAGACTTTTCTTTTTGGGGCATTTTTCAGGGAAAATTGATTGGCGGGCCTGAGAGAGGAGGGTGA
GTAGGCTGAGTATAGATTGAAATTGGAAGCTTTCATCGGATATTGTCGCCGAAATCAATCTTGAA
GGGTGGCGGTTTTGGGAGTTTTGT
Found at i:9761 original size:157 final size:155
Alignment explanation
Indices: 9568--9953 Score: 390
Period size: 156 Copynumber: 2.5 Consensus size: 155
9558 CTTCTCACCT
* *
9568 CAAACTGTCCTTAAATGAAAAACTAGCATAAATTTTTTCATTCTAAGTCTGAATGAGCTGAAATT
1 CAAAATGTCCTTAAATGAAAAACTAGCAT-AAGTTTTTCATTCTAAGTCTGAATGAG-TGAAATT
* *
9633 TCACCAAG-GGACTTAGATTCTCTCCAAAAGACTATG-GAAAAAATTCTAAGTAAAACCGAGCTC
64 TCACCAAGAGG-CTTAGATTATCTCCAAAAGACTATGAGAAAAAA-TCTAAGTAAAACCGAACTC
* * * * *
9696 GCCTTG-ATGGTGAACTTGGTTTCTCTC-C
127 -CCTAGCATAGAGAACTTGGTTTCACACAC
* * * * * *
9724 CTGAAGTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGTTAATTT
1 C-AAAATGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATG-AGTGAA-AT
* * *
9788 TTCACC-AGTAGGCTTATATTATCTCCACAAGGCTATGAGAAAAAATCTAAGTAAAACCGAACTC
63 TTCACCAAG-AGGCTTAGATTATCTCCAAAAGACTATGAGAAAAAATCTAAGTAAAACCGAACTC
* * *
9852 TCTAGCATAGAGAAGTTGGTTTGACACAC
127 CCTAGCATAGAGAACTTGGTTTCACACAC
* * * **
9881 CAAAATATCCTTAATTGAAAAACTTGCATAAGTTTTTCA-TCTTAAGTCTGTTTGAGATGAAATT
1 CAAAATGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTC-TAAGTCTGAATGAG-TGAAATT
9945 TCACCAAGA
64 TCACCAAGA
9954 TGACATATAT
Statistics
Matches: 187, Mismatches: 31, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
155 13 0.07
156 131 0.70
157 43 0.23
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (155 bp):
CAAAATGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGTGAAATTTC
ACCAAGAGGCTTAGATTATCTCCAAAAGACTATGAGAAAAAATCTAAGTAAAACCGAACTCCCTA
GCATAGAGAACTTGGTTTCACACAC
Found at i:10690 original size:17 final size:17
Alignment explanation
Indices: 10663--10702 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
10653 ATAAACAGTG
*
10663 ATATATAAAATTTCATCT
1 ATAT-TAAAATTTCATCC
10681 ATATTAAAATTTCATCC
1 ATATTAAAATTTCATCC
10698 ATATT
1 ATATT
10703 GTATAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTAAAATTTCATCC
Found at i:11084 original size:87 final size:87
Alignment explanation
Indices: 10955--11122 Score: 243
Period size: 88 Copynumber: 1.9 Consensus size: 87
10945 AAAACTTTAG
* *
10955 TTTTATTTAATTAAATCTAATTCTTTATAACTATTTTATTTTTA-C-TATTTTACTATTTTAATT
1 TTTTAATTAAATAAATCTAATTCTTTATAACTATTTTATTTTTATCAT-TTTTACTATTTTAATT
*
11018 AAAAAAGTTAGATATATTAGAAT
65 AAAAAACTTAGATATATTAGAAT
11041 TTTTAATTAAATATAAT-TAATCTCTTTATAACTATTTTATTTTTATCATTTTTACTATTTTAAT
1 TTTTAATTAAATA-AATCTAAT-TCTTTATAACTATTTTATTTTTATCATTTTTACTATTTTAAT
* *
11105 TACATAACTTAGATATAT
64 TAAAAAACTTAGATATAT
11123 ATTATAATGT
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
86 15 0.21
87 26 0.36
88 31 0.42
89 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.54
Consensus pattern (87 bp):
TTTTAATTAAATAAATCTAATTCTTTATAACTATTTTATTTTTATCATTTTTACTATTTTAATTA
AAAAACTTAGATATATTAGAAT
Found at i:19156 original size:22 final size:22
Alignment explanation
Indices: 19130--19174 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
19120 CAGAAATATT
19130 GTCCCTCTTTTGAAAATAAAAG
1 GTCCCTCTTTTGAAAATAAAAG
19152 GTCCCTCTTTTGAAAATAAAAG
1 GTCCCTCTTTTGAAAATAAAAG
19174 G
1 G
19175 AGTCCTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (22 bp):
GTCCCTCTTTTGAAAATAAAAG
Found at i:20330 original size:41 final size:41
Alignment explanation
Indices: 20273--20512 Score: 358
Period size: 41 Copynumber: 5.9 Consensus size: 41
20263 ATTTTCGTTT
20273 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCA
1 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCA
*** *
20314 ATTCAAGATTGAGTCATCGAGACACTTGAATTAAATTATCA
1 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCA
*
20355 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAGATTATCA
1 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCA
*** *
20396 ATTCAAGATTGAGTCATCGAAACCCTTGAATTAAATTATCA
1 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCA
20437 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCA
1 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCA
* *
20478 ATTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 ATTCAAGAACAAGTCA-TCGAGACCCTTGAATTAAAT
20513 CAAATCAAAT
Statistics
Matches: 178, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
40 15 0.08
41 161 0.90
42 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (41 bp):
ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCA
Found at i:20410 original size:82 final size:82
Alignment explanation
Indices: 20273--20485 Score: 399
Period size: 82 Copynumber: 2.6 Consensus size: 82
20263 ATTTTCGTTT
*
20273 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGACA
1 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAAACA
20338 CTTGAATTAAATTATCA
66 CTTGAATTAAATTATCA
* *
20355 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAGATTATCAATTCAAGATTGAGTCATCGAAACC
1 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAAACA
20420 CTTGAATTAAATTATCA
66 CTTGAATTAAATTATCA
20437 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGA
1 ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGA
20486 CCAAGTCATT
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 127 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (82 bp):
ATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAAACA
CTTGAATTAAATTATCA
Found at i:23165 original size:41 final size:40
Alignment explanation
Indices: 23109--23195 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 40
23099 CCATCTTCAC
* *
23109 CCTCCTAATAATTAAG-TAAATAAACTAAATGCAGGTTTAG
1 CCTCCTAATAATTAAGCT-AAGAAACTAAATACAGGTTTAG
*
23149 CCTCCATAATAATTAAGCTAAGAAATTAAATACAGGTTTAG
1 CCTCC-TAATAATTAAGCTAAGAAACTAAATACAGGTTTAG
23190 CC-CCTA
1 CCTCCTA
23196 GTTATAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 2 0.05
40 7 0.17
41 32 0.76
42 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.29
Consensus pattern (40 bp):
CCTCCTAATAATTAAGCTAAGAAACTAAATACAGGTTTAG
Found at i:24991 original size:37 final size:37
Alignment explanation
Indices: 24941--25017 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
24931 TTTGAGGAGG
*
24941 CAAGCTTTCTCAAATATAATATTGTCTGACTATTTCA
1 CAAGCTTTCTCAAATACAATATTGTCTGACTATTTCA
24978 CAAGCTTTCTCAAATACAATATTGTCTGACTATTTCA
1 CAAGCTTTCTCAAATACAATATTGTCTGACTATTTCA
25015 CAA
1 CAA
25018 ACAAGTTGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (37 bp):
CAAGCTTTCTCAAATACAATATTGTCTGACTATTTCA
Found at i:34689 original size:11 final size:11
Alignment explanation
Indices: 34673--34698 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34663 CCTCTAGTAC
34673 ATTTCAATATA
1 ATTTCAATATA
34684 ATTTCAATATA
1 ATTTCAATATA
34695 ATTT
1 ATTT
34699 TCATGAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTCAATATA
Found at i:48294 original size:14 final size:15
Alignment explanation
Indices: 48275--48325 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 15
48265 CCCGACCGAC
48275 ATATAT-TTTAATAT
1 ATATATATTTAATAT
*
48289 ATATATATATAATAT
1 ATATATATTTAATAT
*
48304 -TTTATATTTAAT-T
1 ATATATATTTAATAT
48317 ATATATATT
1 ATATATATT
48326 ATGTTTTAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 1 0.03
14 23 0.74
15 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATATTTAATAT
Found at i:49132 original size:15 final size:16
Alignment explanation
Indices: 49112--49142 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49102 TTTTAATTAC
49112 ATTATAC-CATCATAT
1 ATTATACTCATCATAT
49127 ATTATACTCATCATAT
1 ATTATACTCATCATAT
49143 TTCCATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATACTCATCATAT
Found at i:51551 original size:18 final size:18
Alignment explanation
Indices: 51530--51566 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
51520 AACTTTCAAC
51530 ACTGCCCCGGCCCCAGCA
1 ACTGCCCCGGCCCCAGCA
*
51548 ACTGCCCCTGCCCCAGCA
1 ACTGCCCCGGCCCCAGCA
51566 A
1 A
51567 GAAGGCCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.54, G:0.19, T:0.08
Consensus pattern (18 bp):
ACTGCCCCGGCCCCAGCA
Found at i:52908 original size:14 final size:14
Alignment explanation
Indices: 52889--52916 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52879 ATTAAAGGAC
52889 ATTAAATTAGTTTA
1 ATTAAATTAGTTTA
52903 ATTAAATTAGTTTA
1 ATTAAATTAGTTTA
52917 GACCCAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTAAATTAGTTTA
Done.