Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012049.1 Corchorus olitorius cultivar O-4 contig12082, 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: 19382
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:77 original size:48 final size:48
Alignment explanation
Indices: 6--458 Score: 753
Period size: 48 Copynumber: 9.4 Consensus size: 48
1 TATTC
6 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
* * *
54 TCAATAATTTATTCCTGTTTTGCCCTTCCTGGTAGGAAAGTGTTGTTT
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
* *
102 TCAGTATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTT
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
* * *
150 CCAATATTTTATTCATGTTTTGCCCTTCCCGTTAGGAAGGTGTTGTTT
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
198 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
*
246 TCAATATTTTATTCTTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
*
294 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAATGTGTTGTTT
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
* *
342 TCAATATTTTATTCATGTTTTGCCCTTCCTGGTAGGAAGGTGTTGTTT
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
* * * *
390 TCAATATTTTTTTCCTGTTTTGCCCTTCTCGGTAGGAAAGTGTGGTTT
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
*
438 TCAATATTTTATCCCTGTTTT
1 TCAATATTTTATTCCTGTTTT
459 CAATGTTTTG
Statistics
Matches: 375, Mismatches: 30, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 375 1.00
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.47
Consensus pattern (48 bp):
TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
Found at i:174 original size:96 final size:96
Alignment explanation
Indices: 6--786 Score: 872
Period size: 96 Copynumber: 8.2 Consensus size: 96
1 TATTC
*
6 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATAATTTATTCCTG
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTG
*
71 TTTTGCCCTTCCTGGTAGGAAAGTGTTGTTT
66 TTTTGCCCTTCCTGGTAGGAAGGTGTTGTTT
* * * *
102 TCAGTATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTCCAATATTTTATTCATG
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTG
* *
167 TTTTGCCCTTCCCGTTAGGAAGGTGTTGTTT
66 TTTTGCCCTTCCTGGTAGGAAGGTGTTGTTT
*
198 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCTTG
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTG
*
263 TTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
66 TTTTGCCCTTCCTGGTAGGAAGGTGTTGTTT
* *
294 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAATGTGTTGTTTTCAATATTTTATTCATG
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTG
359 TTTTGCCCTTCCTGGTAGGAAGGTGTTGTTT
66 TTTTGCCCTTCCTGGTAGGAAGGTGTTGTTT
* * * * *
390 TCAATATTTTTTTCCTGTTTTGCCCTTCTCGGTAGGAAAGTGTGGTTTTCAATATTTTATCCCTG
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTG
** * * **** * * ***
455 TTTT-CAATGT-TTTGT-TCCCGTTTTTCCCT
66 TTTTGCCCT-TCCTGGTAGGAAGGTGTTGTTT
*** *** * * ** ** *** *
484 TCCCGATCGGAAGGT-GTGGTTTT-CAATAT---TTTATCCA-----TGTTTTCAATGTTTTATT
1 TCAATAT-TTTA-TTCCT-GTTTTGCCCT-TCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATT
** * *
539 CCCATTTTGCCCTT-CTCGGTCGGAAGGTGTTGTTC
62 CCTGTTTTGCCCTTCCT-GGTAGGAAGGTGTTGTTT
* *
574 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATAATTTATTCATG
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTG
*
639 TTTTGCCCTTCCCGGTAGGAAGGTGTTGTTT
66 TTTTGCCCTTCCTGGTAGGAAGGTGTTGTTT
*
670 TCAATATTTTATTCATGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTG
1 TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTG
* * *
735 TTTTGCCCTT-TTCGGTAGGAAGATGTGGTTT
66 TTTTGCCCTTCCT-GGTAGGAAGGTGTTGTTT
*
766 TCAATATTTTATTCCTATTTT
1 TCAATATTTTATTCCTGTTTT
787 CAATGTTTTA
Statistics
Matches: 563, Mismatches: 102, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
88 30 0.05
89 8 0.01
90 8 0.01
91 3 0.01
93 3 0.01
94 9 0.02
95 8 0.01
96 493 0.88
97 1 0.00
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.47
Consensus pattern (96 bp):
TCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTG
TTTTGCCCTTCCTGGTAGGAAGGTGTTGTTT
Found at i:501 original size:68 final size:68
Alignment explanation
Indices: 385--594 Score: 294
Period size: 68 Copynumber: 3.1 Consensus size: 68
375 AGGAAGGTGT
* * * * *
385 TGTTTTCAATATTTTTTTCCTGTTTTGCCCTTCTCGGTAGGAAAGTGTGGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCTCGGTCGGAAGGTGTGGTTTTCAATATTTTAT
450 CCC
66 CCC
* * * *
453 TGTTTTCAATGTTTTGTTCCCGTTTTTCCCTTCCCGATCGGAAGGTGTGGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCTCGGTCGGAAGGTGTGGTTTTCAATATTTTAT
*
518 CCA
66 CCC
* * *
521 TGTTTTCAATGTTTTATTCCCATTTTGCCCTTCTCGGTCGGAAGGTGTTGTTCTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCTCGGTCGGAAGGTGTGGTTTTCAATATTTTAT
*
586 TCC
66 CCC
589 TGTTTT
1 TGTTTT
595 GCCCTTCCCG
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 124 1.00
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.50
Consensus pattern (68 bp):
TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCTCGGTCGGAAGGTGTGGTTTTCAATATTTTAT
CCC
Found at i:597 original size:48 final size:48
Alignment explanation
Indices: 521--786 Score: 406
Period size: 48 Copynumber: 5.5 Consensus size: 48
511 ATTTTATCCA
* ** * *
521 TGTTTTCAATGTTTTATTCCCATTTTGCCCTTCTCGGTCGGAAGGTGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
*
569 TGTTCTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
* *
617 TGTTTTCAATAATTTATTCATGTTTTGCCCTTCCCGGTAGGAAGGTGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
*
665 TGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTAGGAAGGTGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
** *
713 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTTTCGGTAGGAAGATGT
1 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
* *
761 GGTTTTCAATATTTTATTCCTATTTT
1 TGTTTTCAATATTTTATTCCTGTTTT
787 CAATGTTTTA
Statistics
Matches: 202, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 202 1.00
ACGTcount: A:0.16, C:0.17, G:0.19, T:0.47
Consensus pattern (48 bp):
TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
Found at i:643 original size:328 final size:328
Alignment explanation
Indices: 193--901 Score: 1177
Period size: 328 Copynumber: 2.2 Consensus size: 328
183 AGGAAGGTGT
* * *
193 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTCTCAATATTTTAT
* * *
258 TCTTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCC
66 TCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATAATTTATTCATGTTTTGCCCTTCC
* *
323 CGGTAGGAATGTGTTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCTGGTAGGAAGGTGTTGT
131 CGGTAGGAAGGTGTTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTAGGAAGGTGTTGT
*
388 TTTCAATATTTTTTTCCTGTTTTGCCCTTCTCGGTAGGAA-AGTGTGGTTTTCAATATTTTATCC
196 TTTCAATATTTTATTCCTGTTTTGCCCTTCTCGGTAGGAAGA-TGTGGTTTTCAATATTTTATCC
* * *
452 CTGTTTTCAATGTTTTGTTCCCGTTTTTCCCTTCCCGATCGGAAGGTGTGGTTTTCAATATTTTA
260 CTATTTTCAATGTTTTATTCCCGTTTTTCCCTTCCCGATCGGAAGGTGTGGTTCTCAATATTTTA
517 TCCA
325 TCCA
** *
521 TGTTTTCAATGTTTTATTCCCATTTTGCCCTTCTCGGTCGGAAGGTGTTGTTCTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTCTCAATATTTTAT
586 TCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATAATTTATTCATGTTTTGCCCTTCC
66 TCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATAATTTATTCATGTTTTGCCCTTCC
651 CGGTAGGAAGGTGTTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTAGGAAGGTGTTGT
131 CGGTAGGAAGGTGTTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTAGGAAGGTGTTGT
* *
716 TTTCAATATTTTATTCCTGTTTTGCCCTTTTCGGTAGGAAGATGTGGTTTTCAATATTTTATTCC
196 TTTCAATATTTTATTCCTGTTTTGCCCTTCTCGGTAGGAAGATGTGGTTTTCAATATTTTATCCC
* * *
781 TATTTTCAATGTTTTATTCCCGTTTTTCCTTTCCCGGTCGGAAGGTGTTGTTCTCAATATTTTAT
261 TATTTTCAATGTTTTATTCCCGTTTTTCCCTTCCCGATCGGAAGGTGTGGTTCTCAATATTTTAT
* *
846 TCT
326 CCA
* * *
849 TGTTTTCAATGTTTTATTCTTGTTTTGCCCTTCCCCGTCGGAAGGGGTTGTTC
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTC
902 CTATTCTCTT
Statistics
Matches: 352, Mismatches: 28, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
328 351 1.00
329 1 0.00
ACGTcount: A:0.15, C:0.18, G:0.19, T:0.48
Consensus pattern (328 bp):
TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTCTCAATATTTTAT
TCCTGTTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATAATTTATTCATGTTTTGCCCTTCC
CGGTAGGAAGGTGTTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTAGGAAGGTGTTGT
TTTCAATATTTTATTCCTGTTTTGCCCTTCTCGGTAGGAAGATGTGGTTTTCAATATTTTATCCC
TATTTTCAATGTTTTATTCCCGTTTTTCCCTTCCCGATCGGAAGGTGTGGTTCTCAATATTTTAT
CCA
Found at i:786 original size:20 final size:20
Alignment explanation
Indices: 763--800 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
753 GAAGATGTGG
763 TTTTCAATATTTTATTCCTA
1 TTTTCAATATTTTATTCCTA
*
783 TTTTCAATGTTTTATTCC
1 TTTTCAATATTTTATTCC
801 CGTTTTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.16, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTCAATATTTTATTCCTA
Found at i:806 original size:20 final size:20
Alignment explanation
Indices: 762--806 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
752 GGAAGATGTG
*
762 GTTTTCAATATTTTATTCCT
1 GTTTTCAATATTTTATTCCC
* *
782 ATTTTCAATGTTTTATTCCC
1 GTTTTCAATATTTTATTCCC
802 GTTTT
1 GTTTT
807 TCCTTTCCCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.60
Consensus pattern (20 bp):
GTTTTCAATATTTTATTCCC
Found at i:857 original size:20 final size:20
Alignment explanation
Indices: 828--874 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
818 TCGGAAGGTG
*
828 TTGTTCTCAATATTTTATTC
1 TTGTTTTCAATATTTTATTC
*
848 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATATTTTATTC
868 TTGTTTT
1 TTGTTTT
875 GCCCTTCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.11, G:0.09, T:0.66
Consensus pattern (20 bp):
TTGTTTTCAATATTTTATTC
Found at i:889 original size:68 final size:68
Alignment explanation
Indices: 712--901 Score: 245
Period size: 68 Copynumber: 2.8 Consensus size: 68
702 TAGGAAGGTG
* ** * * * *
712 TTGTTTTCAATATTTTATTCCTGTTTTGCCCTTTTCGGTAGGAAGATGTGGTTTTCAATATTTTA
1 TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTCTCAATATTTTA
777 TTC
66 TTC
* * * * *
780 CTATTTTCAATGTTTTATTCCCGTTTTTCCTTTCCCGGTCGGAAGGTGTTGTTCTCAATATTTTA
1 TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTCTCAATATTTTA
845 TTC
66 TTC
* * *
848 TTGTTTTCAATGTTTTATTCTTGTTTTGCCCTTCCCCGTCGGAAGGGGTTGTTC
1 TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTC
902 CTATTCTCTT
Statistics
Matches: 102, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 102 1.00
ACGTcount: A:0.14, C:0.18, G:0.17, T:0.51
Consensus pattern (68 bp):
TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTCTCAATATTTTA
TTC
Found at i:3226 original size:23 final size:21
Alignment explanation
Indices: 3189--3231 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
3179 CTCCTTTTCC
*
3189 TTTTCCTTTTCTTTTTCTCTT
1 TTTTCCTTTTCTTTTCCTCTT
3210 TTTTCCTCCTTTCTTTTCCTCT
1 TTTTCCT--TTTCTTTTCCTCT
3232 CCTGGCCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCCTTTTCTTTTCCTCTT
Found at i:6082 original size:5 final size:5
Alignment explanation
Indices: 6061--6095 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
6051 CAAGTACAAA
6061 AAAAT AATAAT -AAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT
6096 TCTGCAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 3 0.11
5 22 0.79
6 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:8380 original size:15 final size:15
Alignment explanation
Indices: 8360--8392 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
8350 GGGCAGCTAG
8360 CAGCTGCCTGTTGAT
1 CAGCTGCCTGTTGAT
8375 CAGCTGCCTGTTGAT
1 CAGCTGCCTGTTGAT
8390 CAG
1 CAG
8393 TAGAAGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.30
Consensus pattern (15 bp):
CAGCTGCCTGTTGAT
Found at i:8578 original size:51 final size:51
Alignment explanation
Indices: 8502--8655 Score: 308
Period size: 51 Copynumber: 3.0 Consensus size: 51
8492 TCATTCACCT
8502 ATTTTAACATGTAACAATGATTTAGAACAAGCAAGAAGAAAGCAAATATAG
1 ATTTTAACATGTAACAATGATTTAGAACAAGCAAGAAGAAAGCAAATATAG
8553 ATTTTAACATGTAACAATGATTTAGAACAAGCAAGAAGAAAGCAAATATAG
1 ATTTTAACATGTAACAATGATTTAGAACAAGCAAGAAGAAAGCAAATATAG
8604 ATTTTAACATGTAACAATGATTTAGAACAAGCAAGAAGAAAGCAAATATAG
1 ATTTTAACATGTAACAATGATTTAGAACAAGCAAGAAGAAAGCAAATATAG
8655 A
1 A
8656 GAGAGAATAG
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 103 1.00
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.23
Consensus pattern (51 bp):
ATTTTAACATGTAACAATGATTTAGAACAAGCAAGAAGAAAGCAAATATAG
Found at i:9453 original size:30 final size:30
Alignment explanation
Indices: 9410--9467 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
9400 GCTGCTGCAA
* *
9410 CAACTAATTCTCTCACCACCCAACTTTCAG
1 CAACTAATCCTCTCAACACCCAACTTTCAG
* *
9440 CAACTGATCCTCTCAACACCCAGCTTTC
1 CAACTAATCCTCTCAACACCCAACTTTC
9468 TTCTCAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.41, G:0.05, T:0.26
Consensus pattern (30 bp):
CAACTAATCCTCTCAACACCCAACTTTCAG
Found at i:13978 original size:22 final size:21
Alignment explanation
Indices: 13953--14006 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
13943 GAAGTTCGTG
13953 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
13975 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
13994 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
14007 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:18844 original size:21 final size:21
Alignment explanation
Indices: 18818--18930 Score: 183
Period size: 21 Copynumber: 5.4 Consensus size: 21
18808 TGCTAGGAGT
18818 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
18839 TCATTGGAGTAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
18860 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
18881 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
18902 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
18923 TCATTGGA
1 TCATTGGA
18931 ATTGCCTAAG
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
20 1 0.01
21 85 0.99
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.