Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021705.1 Corchorus olitorius cultivar O-4 contig21738, 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: 14150
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Found at i:86 original size:39 final size:39
Alignment explanation
Indices: 32--715 Score: 1065
Period size: 39 Copynumber: 17.9 Consensus size: 39
22 AAACAGGTCA
*
32 ATTTATCAAGGTTGACTGGAAACAGGTCATCTTTTCAGC
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* *
71 ATTTACCATAGTTGACTGGAAACAGGTCATCTTTTCAG-
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
*
109 -TTTATTAAAG-TGACTGGAAACAGGTCATCTTTTCAGC
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
146 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* *
185 ATTTACCAAAGTTGATTGGAAACAGGTCATCTTTTCAG-
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
223 -TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
261 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* *
300 ATTTACCAAAGTTGATTGGAAACAGGTCATCTTTTCAG-
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* *
338 -TTTATCAAAATTGATTGGAAACAGGTCATCTTTTCAGC
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
*
376 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTTAGC
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
415 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG-
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
*
453 -TTTATCAAAAGTTGACTGGAAACAGGTCATCTTTTTAGC
1 ATTTATC-AAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* *
492 ATTTATCAAAGTTGATTGGAAACAGGTCGTCTTTTCAG-
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
*
530 -TTTATCAAAAGTTGACTGGAAACAGGTCATCTTTTTAGC
1 ATTTATC-AAAGTTGACTGGAAACAGGTCATCTTTTCAGC
569 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG-
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* *
607 -TTTATCAAAGTTGACTGGAAACAGGTTATCGTTTCAG-
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* *
644 A-TTATCAAAGTAGACTGGAAACAGGTCCTCTTTTCAGC
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
*
682 ATTTATCAAAGTTGATTGGAAACAGGTCATCTTT
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTT
716 CCTCAGTTTT
Statistics
Matches: 593, Mismatches: 36, Indels: 32
0.90 0.05 0.05
Matches are distributed among these distances:
36 26 0.04
37 156 0.26
38 68 0.11
39 331 0.56
40 12 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (39 bp):
ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
Found at i:306 original size:115 final size:115
Alignment explanation
Indices: 32--715 Score: 1085
Period size: 115 Copynumber: 6.0 Consensus size: 115
22 AAACAGGTCA
* *
32 ATTTATCAAGGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCATAGTTGACTGGAAACAGG
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCAAAGTTGACTGGAAACAGG
*
97 TCATCTTTTCAGTTTATTAAAG-TGACTGGAAACAGGTCATCTTTTCAGC
66 TCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
*
146 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCAAAGTTGATTGGAAACAGG
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCAAAGTTGACTGGAAACAGG
211 TCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
66 TCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
*
261 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCAAAGTTGATTGGAAACAGG
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCAAAGTTGACTGGAAACAGG
* *
326 TCATCTTTTCAGTTTATCAAAATTGATTGGAAACAGGTCATCTTTTCAGC
66 TCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* *
376 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTTAGCATTTATCAAAGTTGACTGGAAACAGG
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCAAAGTTGACTGGAAACAGG
*
441 TCATCTTTTCAGTTTATCAAAAGTTGACTGGAAACAGGTCATCTTTTTAGC
66 TCATCTTTTCAGTTTATC-AAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* * *
492 ATTTATCAAAGTTGATTGGAAACAGGTCGTCTTTTCAG--TTTATCAAAAGTTGACTGGAAACAG
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTA-CCAAAGTTGACTGGAAACAG
*
555 GTCATCTTTTTAGCATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG-
65 GTCATCTTTTCAG--TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
* * * *
607 -TTTATCAAAGTTGACTGGAAACAGGTTATCGTTTCAG-A-TTATCAAAGTAGACTGGAAACAGG
1 ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCAAAGTTGACTGGAAACAGG
* *
669 TCCTCTTTTCAGCATTTATCAAAGTTGATTGGAAACAGGTCATCTTT
66 TCATCTTTTCAG--TTTATCAAAGTTGACTGGAAACAGGTCATCTTT
716 CCTCAGTTTT
Statistics
Matches: 535, Mismatches: 29, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
113 62 0.12
114 123 0.23
115 250 0.47
116 94 0.18
117 6 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (115 bp):
ATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCAAAGTTGACTGGAAACAGG
TCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGC
Found at i:320 original size:154 final size:152
Alignment explanation
Indices: 32--715 Score: 1031
Period size: 154 Copynumber: 4.5 Consensus size: 152
22 AAACAGGTCA
* * * *
32 ATTTATCAAGGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCATAGTTGACTGGAAACAGG
1 ATTTATCAAAGTTGATTGGAAACAGGTCATCTTTTCAG-ATTTATCAAAGTTGACTGGAAACAGG
* *
97 TCATCTTTTCAG--TTTATTAAAG-TGACTGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTT
65 TCATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG--TTTACCAAAGTT
159 GACTGGAAACAGGTCATCTTTTCAG
128 GACTGGAAACAGGTCATCTTTTCAG
*
184 CATTTACCAAAGTTGATTGGAAACAGGTCATCTTTTCAG-TTTATCAAAGTTGACTGGAAACAGG
1 -ATTTATCAAAGTTGATTGGAAACAGGTCATCTTTTCAGATTTATCAAAGTTGACTGGAAACAGG
248 TCATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTACCAAAGTT
65 TCATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG--TTTACCAAAGTT
*
313 GATTGGAAACAGGTCATCTTTTCAG
128 GACTGGAAACAGGTCATCTTTTCAG
*
338 -TTTATCAAAATTGATTGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGG
1 ATTTATCAAAGTTGATTGGAAACAGGTCATCTTTTCAG-ATTTATCAAAGTTGACTGGAAACAGG
* *
402 TCATCTTTTTAGCATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAAGTTG
65 TCATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTA-CCAAAGTTG
*
467 ACTGGAAACAGGTCATCTTTTTAG
129 ACTGGAAACAGGTCATCTTTTCAG
*
491 CATTTATCAAAGTTGATTGGAAACAGGTCGTCTTTTCAG-TTTATCAAAAGTTGACTGGAAACAG
1 -ATTTATCAAAGTTGATTGGAAACAGGTCATCTTTTCAGATTTATC-AAAGTTGACTGGAAACAG
* *
555 GTCATCTTTTTAGCATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTG
64 GTCATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTACCAAAGTTG
* *
620 ACTGGAAACAGGTTATCGTTTCAG
129 ACTGGAAACAGGTCATCTTTTCAG
* * * *
644 A-TTATCAAAGTAGACTGGAAACAGGTCCTCTTTTCAGCATTTATCAAAGTTGATTGGAAACAGG
1 ATTTATCAAAGTTGATTGGAAACAGGTCATCTTTTCAG-ATTTATCAAAGTTGACTGGAAACAGG
708 TCATCTTT
65 TCATCTTT
716 CCTCAGTTTT
Statistics
Matches: 495, Mismatches: 25, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
151 68 0.14
152 66 0.13
153 114 0.23
154 212 0.43
155 35 0.07
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (152 bp):
ATTTATCAAAGTTGATTGGAAACAGGTCATCTTTTCAGATTTATCAAAGTTGACTGGAAACAGGT
CATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTACCAAAGTTGAC
TGGAAACAGGTCATCTTTTCAG
Found at i:766 original size:31 final size:31
Alignment explanation
Indices: 731--913 Score: 158
Period size: 32 Copynumber: 5.7 Consensus size: 31
721 GTTTTAACTT
731 CGACCTCAGACAGGTCTTTATC-TTTCAAATC
1 CGACCTCAGACAGGT-TTTATCATTTCAAATC
* *
762 CGACCTCAGACAGGTTTTCCTCAGTT-AAATTC
1 CGACCTCAGACAGGTTTT-ATCATTTCAAA-TC
* *
794 CGACCTTAGACGGGTCTTTATC-TTTCAAATC
1 CGACCTCAGACAGGT-TTTATCATTTCAAATC
* *
825 CGACCTCAGACAGGTTTTCCTCAGTTT-AATTC
1 CGACCTCAGACAGGTTTT-ATCA-TTTCAAATC
* *
857 CGACCTCAGACAGGTCTTTCTCAATTTTTAAATTC
1 CGACCTCAGACAGGT-TTTATC-A-TTTCAAA-TC
*
892 CGACCTCAGATAGGTTGTTATC
1 CGACCTCAGACAGGTT-TTATC
914 TTCCAAACTC
Statistics
Matches: 125, Mismatches: 14, Indels: 22
0.78 0.09 0.14
Matches are distributed among these distances:
30 6 0.05
31 39 0.31
32 44 0.35
33 13 0.10
34 3 0.02
35 20 0.16
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (31 bp):
CGACCTCAGACAGGTTTTATCATTTCAAATC
Found at i:816 original size:63 final size:63
Alignment explanation
Indices: 713--907 Score: 266
Period size: 63 Copynumber: 3.0 Consensus size: 63
703 ACAGGTCATC
*
713 TTTCCTCAGTTTTAACTT-CGACCTCAGACAGGTCTTTATCTTTCAAATCCGACCTCAGACAGGT
1 TTTCCTCAG--TTAAATTCCGACCTCAGACAGGTCTTTATCTTTCAAATCCGACCTCAGACAGGT
* *
777 TTTCCTCAGTTAAATTCCGACCTTAGACGGGTCTTTATCTTTCAAATCCGACCTCAGACAGGT
1 TTTCCTCAGTTAAATTCCGACCTCAGACAGGTCTTTATCTTTCAAATCCGACCTCAGACAGGT
* * * *
840 TTTCCTCAGTTTAATTCCGACCTCAGACAGGTCTTTCTCAATTTTTAAATTCCGACCTCAGATAG
1 TTTCCTCAGTTAAATTCCGACCTCAGACAGGTCTTTATC---TTTCAAA-TCCGACCTCAGACAG
905 GT
62 GT
907 T
1 T
908 GTTATCTTCC
Statistics
Matches: 117, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
62 6 0.05
63 79 0.68
64 9 0.08
66 6 0.05
67 17 0.15
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (63 bp):
TTTCCTCAGTTAAATTCCGACCTCAGACAGGTCTTTATCTTTCAAATCCGACCTCAGACAGGT
Found at i:864 original size:32 final size:33
Alignment explanation
Indices: 711--906 Score: 176
Period size: 31 Copynumber: 6.0 Consensus size: 33
701 AAACAGGTCA
*
711 TCTTTCCTCAGTTTTAACTT-CGACCTCAGACAGG
1 TCTTT-CTCAGTTTCAA-TTCCGACCTCAGACAGG
* *
745 TCTTTATC--TTTCAAATCCGACCTCAGACAGG
1 TCTTTCTCAGTTTCAATTCCGACCTCAGACAGG
* * *
776 T-TTTCCTCAG-TTAAATTCCGACCTTAGACGGG
1 TCTTT-CTCAGTTTCAATTCCGACCTCAGACAGG
* *
808 TCTTTATC--TTTCAAATCCGACCTCAGACAGG
1 TCTTTCTCAGTTTCAATTCCGACCTCAGACAGG
839 T-TTTCCTCAGTTT-AATTCCGACCTCAGACAGG
1 TCTTT-CTCAGTTTCAATTCCGACCTCAGACAGG
* * *
871 TCTTTCTCAATTTTTAAATTCCGACCTCAGATAGG
1 TCTTTCTC-A-GTTTCAATTCCGACCTCAGACAGG
906 T
1 T
907 TGTTATCTTC
Statistics
Matches: 132, Mismatches: 17, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
30 7 0.05
31 43 0.33
32 43 0.33
33 12 0.09
34 8 0.06
35 19 0.14
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.35
Consensus pattern (33 bp):
TCTTTCTCAGTTTCAATTCCGACCTCAGACAGG
Found at i:1198 original size:20 final size:20
Alignment explanation
Indices: 1141--1204 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
1131 TTGAGTATAG
* *
1141 ATTTGAAGATTTGAAGTTCGT
1 ATTTGAAGATTTGAAG-ACTT
*
1162 GTTTGAAGACCATTTGAAGACTT
1 ATTTGAAG---ATTTGAAGACTT
1185 ATTTGAAGATTTGAAGACTT
1 ATTTGAAGATTTGAAGACTT
1205 TGAAGAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 12 0.33
21 7 0.19
23 9 0.25
24 8 0.22
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (20 bp):
ATTTGAAGATTTGAAGACTT
Found at i:9888 original size:25 final size:25
Alignment explanation
Indices: 9849--9915 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
9839 GGTTTCAGGT
*
9849 AGGAAGAAAGAAGGAGGAGAAGAAG
1 AGGAAGAAAGAAGGAGGAAAAGAAG
*
9874 AGGAAGAAA-AGAGGAGGAAAAGAAA
1 AGGAAGAAAGA-AGGAGGAAAAGAAG
* *
9899 AAGAA-AAATAAGGAGGA
1 AGGAAGAAAGAAGGAGGA
9916 GACGACGTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 11 0.30
25 26 0.70
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.01
Consensus pattern (25 bp):
AGGAAGAAAGAAGGAGGAAAAGAAG
Found at i:9896 original size:22 final size:22
Alignment explanation
Indices: 9862--9905 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9852 AAGAAAGAAG
**
9862 GAGGAGAAGAAGAGGAAGAAAA
1 GAGGAGAAGAAGAAAAAGAAAA
9884 GAGGAGGAA-AAGAAAAAGAAAA
1 GAGGA-GAAGAAGAAAAAGAAAA
9906 ATAAGGAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (22 bp):
GAGGAGAAGAAGAAAAAGAAAA
Found at i:10648 original size:22 final size:21
Alignment explanation
Indices: 10619--10693 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
10609 AAGAAAGAGA
10619 AATCAGAAGTAAAGGGAAAAGT
1 AATCAGAAGTAAA-GGAAAAGT
* *
10641 AATGAGAAGTAGAAGGAAGAGT
1 AATCAGAAGTA-AAGGAAAAGT
* *
10663 AATCAGGAGTAAAAGAAAGAGT
1 AATCAGAAGTAAAGGAAA-AGT
*
10685 AATTAGAAG
1 AATCAGAAG
10694 AGTAATTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.12
22 36 0.84
23 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.29, T:0.15
Consensus pattern (21 bp):
AATCAGAAGTAAAGGAAAAGT
Found at i:10668 original size:44 final size:44
Alignment explanation
Indices: 10605--10693 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
10595 AAGCTAGGAG
*
10605 GTAGAAGAAAGAGAAATCAGAAGTAAAGGGAAA-AGTAATGAGAA
1 GTAGAAGAAAGAGAAATCAGAAGTAAA-AGAAAGAGTAATGAGAA
* * * *
10649 GTAGAAGGAAGAGTAATCAGGAGTAAAAGAAAGAGTAATTAGAA
1 GTAGAAGAAAGAGAAATCAGAAGTAAAAGAAAGAGTAATGAGAA
10693 G
1 G
10694 AGTAATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 4 0.10
44 35 0.90
ACGTcount: A:0.54, C:0.02, G:0.30, T:0.13
Consensus pattern (44 bp):
GTAGAAGAAAGAGAAATCAGAAGTAAAAGAAAGAGTAATGAGAA
Found at i:10785 original size:47 final size:47
Alignment explanation
Indices: 10733--10992 Score: 394
Period size: 47 Copynumber: 5.5 Consensus size: 47
10723 GAAGCAAAGC
* *
10733 AGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGGGCAAGAGAAGA
1 AGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGA
*
10780 AGAAAATAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGA
1 AGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGA
*
10827 AGAAAACAATTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGA
1 AGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGA
* * * * *
10874 AAAAAACAATTTAATTCTGGCTAATTAAACTAAAAAGTAAGAGAAGA
1 AGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGA
* *
10921 AGAAAAAAGTTTAATTCGGGGTAATTAAACTAAAGAGCAAGAGAAGA
1 AGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGA
* * *
10968 AGAAAATAGTCTAATTCTCGGTAAT
1 AGAAAACAGTTTAATTCTGGGTAAT
10993 CAAGCTAAGC
Statistics
Matches: 194, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 194 1.00
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.23
Consensus pattern (47 bp):
AGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGA
Found at i:11031 original size:22 final size:22
Alignment explanation
Indices: 11003--11223 Score: 270
Period size: 22 Copynumber: 10.1 Consensus size: 22
10993 CAAGCTAAGC
11003 AGTAAAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
*
11025 AGTAAAAGAAAGAGTAATCAGG
1 AGTAAAAGAAAGAGTAATCAGA
* *
11047 AGTAAAAGGAAGAGTAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
* *
11069 AGCAGAAGAAAGAGTAATCAG-
1 AGTAAAAGAAAGAGTAATCAGA
*
11090 AGTGAAAA-AGAAGAGTAATCAAA
1 AGT-AAAAGA-AAGAGTAATCAGA
*
11113 AGCAAAAGAAAGAGTAATCA-A
1 AGTAAAAGAAAGAGTAATCAGA
*
11134 AGTAAAA-AGAAGAGTAATCAAA
1 AGTAAAAGA-AAGAGTAATCAGA
* *
11156 AGCAAAAGAAAGAGTAATCAGG
1 AGTAAAAGAAAGAGTAATCAGA
* *
11178 AGCAGAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
*
11200 AGTAAAAGACAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
11222 AG
1 AG
11224 ATTAGAGTAA
Statistics
Matches: 171, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.01
21 21 0.12
22 145 0.85
23 4 0.02
ACGTcount: A:0.57, C:0.07, G:0.24, T:0.12
Consensus pattern (22 bp):
AGTAAAAGAAAGAGTAATCAGA
Found at i:11171 original size:109 final size:110
Alignment explanation
Indices: 11006--11219 Score: 319
Period size: 109 Copynumber: 2.0 Consensus size: 110
10996 GCTAAGCAGT
** * *
11006 AAAAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAGGAGTAAAAGGAAGAGTAATCAAAAG
1 AAAAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAAAAGCAAAAGAAAGAGTAATCAAAAG
11071 CAGAAGAAAGAGTAATCAG-AGTGAAAAAGA-AGAGTAATCAAAAGC
66 CAGAAGAAAGAGTAATCAGAAGT--AAAAGACAGAGTAATCAAAAGC
**
11116 AAAAGAAAGAGTAATCA-AAGTAAAA-AGAAGAGTAATCAAAAGCAAAAGAAAGAGTAATCAGGA
1 AAAAGAAAGAGTAATCAGAAGTAAAAGA-AAGAGTAATCAAAAGCAAAAGAAAGAGTAATCAAAA
11179 GCAGAAGAAAGAGTAATCAGAAGTAAAAGACAGAGTAATCA
65 GCAGAAGAAAGAGTAATCAGAAGTAAAAGACAGAGTAATCA
11220 GAAGATTAGA
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
108 7 0.07
109 68 0.72
110 20 0.21
ACGTcount: A:0.58, C:0.07, G:0.23, T:0.12
Consensus pattern (110 bp):
AAAAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAAAAGCAAAAGAAAGAGTAATCAAAAG
CAGAAGAAAGAGTAATCAGAAGTAAAAGACAGAGTAATCAAAAGC
Found at i:11266 original size:47 final size:47
Alignment explanation
Indices: 11197--11292 Score: 126
Period size: 47 Copynumber: 2.0 Consensus size: 47
11187 AAGAGTAATC
*
11197 AGAAGTAAAAGACAGAGTAATCAGAAGATTAGAG-TAATTAAGCTA-AA
1 AGAAGTAAAAGACAGAGTAATCAGAAG-TAAG-GTTAATTAAGCTACAA
*
11244 AGAAGTAAAA-ACAAGAGTAATCAGTAGTAAGGTTAATTAAGCTACAA
1 AGAAGTAAAAGAC-AGAGTAATCAGAAGTAAGGTTAATTAAGCTACAA
11291 AG
1 AG
11293 TAAAAATCAG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
45 1 0.02
46 16 0.36
47 27 0.61
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.20
Consensus pattern (47 bp):
AGAAGTAAAAGACAGAGTAATCAGAAGTAAGGTTAATTAAGCTACAA
Done.