Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014318.1 Corchorus capsularis cultivar CVL-1 contig14339, 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: 54935
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:670 original size:4 final size:4
Alignment explanation
Indices: 661--731 Score: 88
Period size: 4 Copynumber: 17.8 Consensus size: 4
651 TATGTGAGTG
* * * * *
661 TATA TATA TATA TATA TACA TACA TACA TATA TACA TATA CATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
709 CATA TATA TATA TATA TATA TAT
1 TATA TATA TATA TATA TATA TAT
732 TCTACTAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:672 original size:6 final size:6
Alignment explanation
Indices: 661--731 Score: 88
Period size: 6 Copynumber: 11.8 Consensus size: 6
651 TATGTGAGTG
* * * * *
661 TATATA TATATA TATATA CATACA TACATA TATACA TATACA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
709 CATATA TATATA TATATA TATAT
1 TATATA TATATA TATATA TATAT
732 TCTACTAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (6 bp):
TATATA
Found at i:691 original size:14 final size:14
Alignment explanation
Indices: 661--728 Score: 82
Period size: 14 Copynumber: 4.7 Consensus size: 14
651 TATGTGAGTG
* *
661 TATATATATATATA
1 TATACATATACATA
675 TATACATACATACATA
1 TATACAT--ATACATA
691 TATACATATACATA
1 TATACATATACATA
*
705 TATACATATATATA
1 TATACATATACATA
*
719 TATATATATA
1 TATACATATA
729 TATTCTACTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
14 35 0.73
16 13 0.27
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (14 bp):
TATACATATACATA
Found at i:694 original size:22 final size:22
Alignment explanation
Indices: 666--722 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
656 GAGTGTATAT
666 ATATATATATATACATACATAC
1 ATATATATATATACATACATAC
* *
688 ATATATACATATACATATATAC
1 ATATATATATATACATACATAC
710 ATATATATATATA
1 ATATATATATATA
723 TATATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATATATATATACATACATAC
Found at i:4324 original size:18 final size:18
Alignment explanation
Indices: 4289--4324 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4279 GCAGGCAAGT
*
4289 ATGAGTAGCAGGAGGAGC
1 ATGAGTAGCAAGAGGAGC
*
4307 ATGAGTAGCAAGATGAGC
1 ATGAGTAGCAAGAGGAGC
4325 TGGCGTGCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.39, T:0.14
Consensus pattern (18 bp):
ATGAGTAGCAAGAGGAGC
Found at i:11524 original size:20 final size:21
Alignment explanation
Indices: 11489--11527 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11479 AAATATTATA
*
11489 TTTATCCTATAATGGGTATTT
1 TTTATCCTAAAATGGGTATTT
11510 TTTAT-CTAAAATGGGTAT
1 TTTATCCTAAAATGGGTAT
11528 AATGGGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (21 bp):
TTTATCCTAAAATGGGTATTT
Found at i:11529 original size:29 final size:29
Alignment explanation
Indices: 11496--11555 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
11486 ATATTTATCC
*
11496 TATAATGGGTATTTTTTATCTAAAATGGG
1 TATAATGGGTAGTTTTTATCTAAAATGGG
11525 TATAATGGGTAGTTTTTATCTAAAATGGG
1 TATAATGGGTAGTTTTTATCTAAAATGGG
11554 TA
1 TA
11556 GTTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (29 bp):
TATAATGGGTAGTTTTTATCTAAAATGGG
Found at i:11727 original size:54 final size:54
Alignment explanation
Indices: 11659--11768 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
11649 ATATAGATAA
*
11659 TTTTAAAAATTCTTAAGAAAATAGCAATCTTATTTGTACTATATACTAGGGTTC
1 TTTTAAAAATTCTTAAGAAAATAGCAATCTTATTTGTAATATATACTAGGGTTC
11713 TTTTAAAAATTCTTAAGAAAATAGCAATCTTATTTGTAATATATACTAGGGTTC
1 TTTTAAAAATTCTTAAGAAAATAGCAATCTTATTTGTAATATATACTAGGGTTC
11767 TT
1 TT
11769 GCCTGAGTTG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (54 bp):
TTTTAAAAATTCTTAAGAAAATAGCAATCTTATTTGTAATATATACTAGGGTTC
Found at i:12022 original size:18 final size:19
Alignment explanation
Indices: 11970--12014 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
11960 GGCTTTTTTA
* *
11970 CTTCCCTTTCATGGGG-CT
1 CTTCCCCTTAATGGGGTCT
11988 CTTCCCCTTAATGGGGTCT
1 CTTCCCCTTAATGGGGTCT
12007 C-TCCCCTT
1 CTTCCCCTT
12015 CCTGGGGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.07, C:0.38, G:0.18, T:0.38
Consensus pattern (19 bp):
CTTCCCCTTAATGGGGTCT
Found at i:18283 original size:11 final size:12
Alignment explanation
Indices: 18267--18298 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
18257 AATTTTGGAC
18267 ATATCTATA-CT
1 ATATCTATATCT
18278 ATATCTATATCT
1 ATATCTATATCT
18290 ATA-CTATAT
1 ATATCTATAT
18299 TAAAATGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATCTATATCT
Found at i:18287 original size:6 final size:6
Alignment explanation
Indices: 18267--18298 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
18257 AATTTTGGAC
18267 ATATCT ATA-CT ATATCT ATATCT ATA-CT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATAT
18299 TAAAATGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (6 bp):
ATATCT
Found at i:18509 original size:87 final size:87
Alignment explanation
Indices: 18405--18569 Score: 321
Period size: 87 Copynumber: 1.9 Consensus size: 87
18395 ATTCTTTTAA
18405 TTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAATCTCAACCAAAC
1 TTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAATCTCAACCAAAC
18470 TCCAAATTTTAATTTTAATTCT
66 TCCAAATTTTAATTTTAATTCT
18492 TTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAATCTCAACCAAAC
1 TTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAATCTCAACCAAAC
*
18557 TCCCAATTTTAAT
66 TCCAAATTTTAAT
18570 CTCAATTAAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (87 bp):
TTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAATCTCAACCAAAC
TCCAAATTTTAATTTTAATTCT
Found at i:20925 original size:13 final size:13
Alignment explanation
Indices: 20903--20935 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
20893 TTTAAAATAA
*
20903 ATATAAATTATAT
1 ATATATATTATAT
20916 ATATATATTATAT
1 ATATATATTATAT
20929 ATATATA
1 ATATATA
20936 CATTATCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:20929 original size:15 final size:15
Alignment explanation
Indices: 20903--20941 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
20893 TTTAAAATAA
*
20903 ATATAAATTATATAT
1 ATATACATTATATAT
20918 ATAT--ATTATATAT
1 ATATACATTATATAT
20931 ATATACATTAT
1 ATATACATTAT
20942 CAGTTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.59
15 9 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATACATTATATAT
Found at i:30403 original size:3 final size:3
Alignment explanation
Indices: 30388--30417 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30378 TGTCACTCTT
*
30388 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30418 AAATGTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:35395 original size:31 final size:32
Alignment explanation
Indices: 35360--35421 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
35350 TGTTTTCATT
* *
35360 ATTTTT-AGATTAATTAATATATCGAGATCTC
1 ATTTTTAAGATAAAATAATATATCGAGATCTC
*
35391 ATTTTTAAGATAAAATAATATATCTAGATCT
1 ATTTTTAAGATAAAATAATATATCGAGATCT
35422 AAAATCACGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (32 bp):
ATTTTTAAGATAAAATAATATATCGAGATCTC
Found at i:37259 original size:32 final size:31
Alignment explanation
Indices: 37184--37264 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
37174 TATCAGCGTC
* * *
37184 TTGGTCCGATGAGGCCA-TGCCACATGGCATT
1 TTGGTCCGACGTGG-CATTGCCACATGACATT
37215 TTGGTCCGACGTGGCATTGCCACATGACATTT
1 TTGGTCCGACGTGGCATTGCCACATGACA-TT
37247 TTGGTCAC-ACGTGGCATT
1 TTGGTC-CGACGTGGCATT
37265 ACTACGTCAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
30 2 0.05
31 23 0.52
32 18 0.41
33 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.30
Consensus pattern (31 bp):
TTGGTCCGACGTGGCATTGCCACATGACATT
Found at i:40178 original size:437 final size:437
Alignment explanation
Indices: 39278--40178 Score: 1106
Period size: 437 Copynumber: 2.1 Consensus size: 437
39268 TCGAGTAAGA
* *
39278 AAATAAGAAAATAGTT-GTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTCCATG
1 AAATAAGAAAATA-TTAGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTCAACG
* * *
39342 AAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAGACCATACAGTAACCTTTT
65 AAACTCGTAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTCGTAAACCATACAATAACCTTTT
* * * * * * *
39407 AACCGACACTTGAATAACTTTAATTGGACATGTGGATCGAAAGTTATATGGTATTAAATAGACCA
130 AACCGACACTTCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCA
* * * * *
39472 ACAATCGAAACAACCAAATTTAGGAAGCATTTTTTTGAATTGAAACATAAAAAATTACTTTTGAG
195 ACAATCAAAACAACAAAATTTAGGAACCATTTTTTAGAATTCAAACATAAAAAATTACTTTTGAG
** * *
39537 TCCTTCCTGAAAGTTGTAAATCATGAAATTACCTTTTAATAGACAAATGTATCAACTTAATCGGA
260 TCCTTAATGAAAATTGTAAATCATGAAATTACCTTTTAATAGACAAATGAATCAACTTAATCGGA
* * *
39602 CAAATAGAACAAAAAATAAAAAAATAAAGCTTAAACGTCAGATTAAGATAGAATTTGTAAAGGAC
325 CAAATAGAACAAAAAATAAAAAAATAAAGCTCAAACGTCAAATTAACATAGAATTTGTAAAGGAC
* * * *
39667 TAAGTAGTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATCC
390 TAAATAGCATAAAGTAGAAAAGTATGAGGATCATTAGATAAATAATCC
* * *
39715 AAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTT-AACCCTTAACGA
1 AAATAAGAAAATATTAGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTCAACGA
* * *
39779 AACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTT
66 AACTCGTAGATCAAA-TTAACTTTCGGGTCCTTCATGAAAGTCGTAAACCATACAATAACCTTTT
39844 AACCGACACTTCAATAACTTCAATCGGACATGTGGA-CAAAAAATTATACGATATTAAATTA-AC
130 AACCGACACTTCAATAACTTCAATCGGACATGTGGATC-AAAAATTATACGATATTAAA-TAGAC
** * * * * **
39907 CGGCAATCAAAACCACAAAATTTCGGAACCATTTTTTAGAA-TCAACACAT-TAAGATTGGTTTT
193 CAACAATCAAAACAACAAAATTTAGGAACCATTTTTTAGAATTCAA-ACATAAAAAATT-ACTTT
* * *** *
39970 TGAGTTCTTAATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACGCTTGAATCACCTTAAT
256 TGAGTCCTTAATGAAAATTGTAAATCATGAAATTACCTTTTAATAGACAAATGAATCAACTTAAT
* * * * *
40035 CGGACAAATAGAA-AAAAAATACAAAAATAAAAGC-CAACGCGTTAAATCGTCCAACCTATAA-T
321 CGGACAAATAGAACAAAAAATAAAAAAAT-AAAGCTCAA-ACGTCAAAT--T--AACATAGAATT
*
40097 TGTAAAGGACTAAATAGCATAAAGTATAAAAGTATGAGGATCATTAGATAAATAATCC
380 TGTAAAGGACTAAATAGCATAAAGTAGAAAAGTATGAGGATCATTAGATAAATAATCC
* *
40155 -AAT-A-AAAGTATTAGTTTATGGAGA
1 AAATAAGAAAATATTAGTTAATGGAGA
40179 ATGTGCCCCA
Statistics
Matches: 395, Mismatches: 57, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
436 51 0.13
437 277 0.70
438 3 0.01
439 4 0.01
440 54 0.14
441 6 0.02
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (437 bp):
AAATAAGAAAATATTAGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTCAACGA
AACTCGTAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTCGTAAACCATACAATAACCTTTTA
ACCGACACTTCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAA
CAATCAAAACAACAAAATTTAGGAACCATTTTTTAGAATTCAAACATAAAAAATTACTTTTGAGT
CCTTAATGAAAATTGTAAATCATGAAATTACCTTTTAATAGACAAATGAATCAACTTAATCGGAC
AAATAGAACAAAAAATAAAAAAATAAAGCTCAAACGTCAAATTAACATAGAATTTGTAAAGGACT
AAATAGCATAAAGTAGAAAAGTATGAGGATCATTAGATAAATAATCC
Found at i:40385 original size:2 final size:2
Alignment explanation
Indices: 40378--40407 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40368 TGTATTTGTG
40378 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40408 AAATATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41910 original size:17 final size:17
Alignment explanation
Indices: 41890--41922 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41880 GCAACCTATC
41890 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
41907 ACCTCATACTACCTAG
1 ACCTCATACTACCTAG
41923 GTACTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:46237 original size:44 final size:43
Alignment explanation
Indices: 46197--46301 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 43
46187 AATCATACGA
*
46197 AGATTA-CAAAATTTCATA-GGAAGGTTTATTACAATTTCATAGTT
1 AGATTATCAAAATTTCATATGG-A-GTTTATCACAATTTCATAG-T
*
46241 AGATTATCAAAGTTTCATATGGAGTTTATCACAATTTCATAGGT
1 AGATTATCAAAATTTCATATGGAGTTTATCACAATTTCATA-GT
46285 AG-TTATCAAAATTTCAT
1 AGATTATCAAAATTTCAT
46302 TGGGTGGTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
43 14 0.25
44 26 0.47
45 13 0.24
46 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (43 bp):
AGATTATCAAAATTTCATATGGAGTTTATCACAATTTCATAGT
Found at i:46292 original size:21 final size:22
Alignment explanation
Indices: 46206--46301 Score: 99
Period size: 22 Copynumber: 4.4 Consensus size: 22
46196 AAGATTACAA
* *
46206 AATTTCATAGGAAGGTTTATTAC
1 AATTTCATAGGTA-GTTTATCAC
* *
46229 AATTTCATAGTTAGATTATCA-
1 AATTTCATAGGTAGTTTATCAC
46250 AAGTTTCATATGG-AGTTTATCAC
1 AA-TTTCATA-GGTAGTTTATCAC
*
46273 AATTTCATAGGTAG-TTATCAA
1 AATTTCATAGGTAGTTTATCAC
46294 AATTTCAT
1 AATTTCAT
46302 TGGGTGGTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
21 18 0.29
22 30 0.48
23 14 0.23
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (22 bp):
AATTTCATAGGTAGTTTATCAC
Found at i:46313 original size:43 final size:44
Alignment explanation
Indices: 46197--46314 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 44
46187 AATCATACGA
* ** * *
46197 AGATTA-CAAAATTTCATAGGAAGGTTTATTACAATTTCATAGTT
1 AGATTATCAAAATTTCATTGGGTGG-TTATCACAATTTCATAGGT
*
46241 AGATTATCAAAGTTTCATATGGAGT--TTATCACAATTTCATAGGT
1 AGATTATCAAAATTTCAT-TGG-GTGGTTATCACAATTTCATAGGT
46285 AG-TTATCAAAATTTCATTGGGTGGTTATCA
1 AGATTATCAAAATTTCATTGGGTGGTTATCA
46315 AAATAGGGTA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
41 2 0.03
42 3 0.05
43 20 0.32
44 25 0.40
45 10 0.16
46 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (44 bp):
AGATTATCAAAATTTCATTGGGTGGTTATCACAATTTCATAGGT
Found at i:46314 original size:22 final size:21
Alignment explanation
Indices: 46244--46318 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
46234 CATAGTTAGA
*
46244 TTATCAAAGTTTCATATGGAGT-
1 TTATCAAAATTTCAT-TGG-GTG
* *
46266 TTATCACAATTTCA-TAGGTAG
1 TTATCAAAATTTCATTGGGT-G
46287 TTATCAAAATTTCATTGGGTGG
1 TTATCAAAATTTCATTGGGT-G
46309 TTATCAAAAT
1 TTATCAAAAT
46319 AGGGTAGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 13 0.30
22 27 0.61
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (21 bp):
TTATCAAAATTTCATTGGGTG
Found at i:49115 original size:27 final size:26
Alignment explanation
Indices: 49072--49130 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
49062 TTGAGGGACT
* * *
49072 TGTTTTTATTACTATTTTTAATAAAG
1 TGTTTTTATAAATATTTTTAATAAAA
*
49098 TGTTTTTATAAATGATTTTTATTAAAA
1 TGTTTTTATAAAT-ATTTTTAATAAAA
49125 TGTTTT
1 TGTTTT
49131 GGGTGCATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (26 bp):
TGTTTTTATAAATATTTTTAATAAAA
Found at i:49569 original size:15 final size:15
Alignment explanation
Indices: 49549--49582 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
49539 ATTGGATTTA
49549 TTATTACTAA-TTGTT
1 TTATTA-TAACTTGTT
49564 TTATTATAACTTGTT
1 TTATTATAACTTGTT
49579 TTAT
1 TTAT
49583 AAGTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (15 bp):
TTATTATAACTTGTT
Found at i:50202 original size:2 final size:2
Alignment explanation
Indices: 50197--50224 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50187 GGCTATGACC
50197 AT AT AT 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
50225 TTAGTAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.