Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009687.1 Corchorus capsularis cultivar CVL-1 contig09708, 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: 20675
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4605 original size:49 final size:48
Alignment explanation
Indices: 4556--5035 Score: 479
Period size: 49 Copynumber: 9.9 Consensus size: 48
4546 AATCCCGTTA
4556 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTT
* * *
4604 ATTTCCCAAAATGCCCTTCCCAGACGGTAGGCATTTGATTTTACCCGTT
1 -TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTT
* *
4653 TTTCCCAAAATGCCCTTCCCGGACGGATGGCATTTGATTTTACCCGTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTT
* *
4701 ATTTCCCAAAATGCCCTTCCTGGACGGAAGGCATTTGATTTTACCTGGTA
1 -TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCT-GTT
* * * *
4751 TTTCCCAAAATGCCCTTTCCGGACGGAAGGTATTTGATTTCACTTGTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTT
* * * * * *
4799 TTTCCCAAAACGCCCTTCCCGGACGGAAGTCA-CTAATCCTTACTTGTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGAT-TTTACCTGTT
* * *
4847 TTTCCCAAAATGCCCTTCCCGGACGGGAGGCACTT-ATTTTACTTGCTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG-TT
* * * * **
4895 TTT-TCAAAACTGACCTTCCTGGACGGAAGACGCTT-ATTTTTACTCACT-TT
1 TTTCCCAAAA-TGCCCTTCCCGGACGGAAGGCATTTGA-TTTTA--C-CTGTT
* * * * *
4945 TTTCCCAAAGTGCCCTTCCCGGACGGAAGGCA-CTAATTTCCACTTGCTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTT-TACCTG-TT
* ** * *
4994 TTTCCTAAAACACCCTTCCCGGATGGAAGGCA-TTAATTTTAC
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTAC
5036 TCGCGTTTTC
Statistics
Matches: 364, Mismatches: 52, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
47 16 0.04
48 143 0.39
49 172 0.47
50 27 0.07
51 5 0.01
52 1 0.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (48 bp):
TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTT
Found at i:4814 original size:146 final size:146
Alignment explanation
Indices: 4549--4981 Score: 489
Period size: 146 Copynumber: 3.0 Consensus size: 146
4539 CCTCTCAAAT
*
4549 CCCGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTATTTCCCAAA
1 CCCGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGGTATTTCCCAAA
* * *
4614 ATGCCCTTCCCAGACGGTAGGCATTTGATTTTACCCGTTTTTCCCAAAATGCCCTTCCCGGACGG
66 ATGCCCTTCCCAGACGGAAGGCATTTGATTTCACCCGTTTTTCCCAAAACGCCCTTCCCGGACGG
* * * *
4679 ATGGCATTTGAT-TTTA
131 AAGGCA-CTAATCCTTA
*
4695 CCCGTTATTTCCCAAAATGCCCTTCCTGGACGGAAGGCATTTGATTTTACCTGGTATTTCCCAAA
1 CCCGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGGTATTTCCCAAA
* * * **
4760 ATGCCCTTTCCGGACGGAAGGTATTTGATTTCACTTGTTTTTCCCAAAACGCCCTTCCCGGACGG
66 ATGCCCTTCCCAGACGGAAGGCATTTGATTTCACCCGTTTTTCCCAAAACGCCCTTCCCGGACGG
*
4825 AAGTCACTAATCCTTA
131 AAGGCACTAATCCTTA
** * * * * **
4841 CTTGTT-TTTCCCAAAATGCCCTTCCCGGACGGGAGGCACTT-ATTTTACTTGCT-TTTTTCAAA
1 CCCGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGGTATTTCCCAAA
* ** * ** * * **
4903 ACTGACCTTCCTGGACGGAAGACGCTT-ATTTTTACTCACTTTTTTCCCAAAGTGCCCTTCCCGG
66 A-TGCCCTTCCCAGACGGAAGGCATTTGA-TTTCAC-C-CGTTTTTCCCAAAACGCCCTTCCCGG
4967 ACGGAAGGCACTAAT
127 ACGGAAGGCACTAAT
4982 TTCCACTTGC
Statistics
Matches: 244, Mismatches: 38, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
143 9 0.04
144 33 0.14
145 35 0.14
146 167 0.68
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.33
Consensus pattern (146 bp):
CCCGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGGTATTTCCCAAA
ATGCCCTTCCCAGACGGAAGGCATTTGATTTCACCCGTTTTTCCCAAAACGCCCTTCCCGGACGG
AAGGCACTAATCCTTA
Found at i:4990 original size:146 final size:142
Alignment explanation
Indices: 4556--5067 Score: 445
Period size: 146 Copynumber: 3.5 Consensus size: 142
4546 AATCCCGTTA
4556 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTATTTCCCAAAATGCCCT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTT-TTT-CCAAAATGCCCT
* * * * *
4621 TCCCAGACGGTAGGCATT-TGATTTTAC-C-CGTTTTTCCCAAAATGCCCTTCCCGGACGGATGG
64 T-CCGGACGG-AAGCGTTAT--TTTTACTCACTTTTTTCCCAAAATGCCCTTCCCGGACGGAAGG
* * * **
4683 CATTTGATTT-TACCCGTT
125 CA-CTAATTTCCACTTGTT
* *
4701 ATTTCCCAAAATGCCCTTCCTGGACGGAAGGCATTTGATTTTACCTGGTATTTCCCAAAATGCCC
1 -TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCT-GT-TTTTCCAAAATGCCC
*
4766 TTTCCGGACGGAAG-G-TATTTGATT--TCACTTGTTTTTCCCAAAACGCCCTTCCCGGACGGAA
63 -TTCCGGACGGAAGCGTTATTT--TTACTCAC-T-TTTTTCCCAAAATGCCCTTCCCGGACGGAA
*
4827 GTCACTAA--TCCTTACTTGTT
123 GGCACTAATTTCC--ACTTGTT
* * * * *
4847 TTTCCCAAAATGCCCTTCCCGGACGGGAGGCACTT-ATTTTACTTGCTTTTTTCAAAACTGACCT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG-TTTTTCCAAAA-TGCCCT
*
4911 TCCTGGACGGAAGACGCTTATTTTTACTCACTTTTTTCCCAAAGTGCCCTTCCCGGACGGAAGGC
64 TCC-GGACGGAAG-CG-TTATTTTTACTCACTTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGC
4976 ACTAATTTCCACTTGCTT
126 ACTAATTTCCACTTG-TT
* ** * * * **
4994 TTTCCTAAAACACCCTTCCCGGATGGAAGGCA-TTAATTTTACTCGCGTTTTCTTAAAAATGCCC
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTAC-C-TGTTTT-TCCAAAATGCCC
5058 TTTCCGGACG
63 -TTCCGGACG
5068 AAAGGCAAGT
Statistics
Matches: 303, Mismatches: 33, Indels: 58
0.77 0.08 0.15
Matches are distributed among these distances:
142 2 0.01
143 16 0.05
144 26 0.09
145 36 0.12
146 143 0.47
147 43 0.14
148 26 0.09
149 11 0.04
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (142 bp):
TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTTTTCCAAAATGCCCTTC
CGGACGGAAGCGTTATTTTTACTCACTTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
TTTCCACTTGTT
Found at i:5057 original size:98 final size:95
Alignment explanation
Indices: 4561--5074 Score: 337
Period size: 97 Copynumber: 5.3 Consensus size: 95
4551 CGTTATTTCC
* * * * **
4561 CAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG-TTATTTCCCAAAATGCCCTTCCC
1 CAAAATGCCCTTCCCGGACGGAAGGCA-CTAATTTCACTTGCTT-TTT-CCAAAACACCCTTCCC
* * * * * *
4625 AGACGGTAGGCATTTGATTTTACCCGTTTTTC-C
63 GGACGGAAGGCA-TTAATTTTACTCGCTTTTCTT
* * * * ** ** *
4658 CAAAATGCCCTTCCCGGACGGATGGCATTTGATTTTACCCG-TTATTTCCCAAAATGCCCTTCCT
1 CAAAATGCCCTTCCCGGACGGAAGGCA-CTAATTTCACTTGCTT-TTT-CCAAAACACCCTTCCC
* * *
4722 GGACGGAAGGCATTTGATTTTAC-CTGGTATTTC-C
63 GGACGGAAGGCA-TTAATTTTACTC-GCT-TTTCTT
* * * * *
4756 CAAAATGCCCTTTCCGGACGGAAGGTATTTGATTTCACTTG-TTTTTCCCAAAACGCCCTTCCCG
1 CAAAATGCCCTTCCCGGACGGAAGGCA-CTAATTTCACTTGCTTTTT-CCAAAACACCCTTCCCG
* * * * * *
4820 GACGGAAGTCACTAATCCTTACTTGTTTTTC-C
64 GACGGAAGGCATTAAT-TTTACTCGCTTTTCTT
* * * * *
4852 CAAAATGCCCTTCCCGGACGGGAGGCACTTATTTTACTTGCTTTTTTCAAAACTGA-CCTTCCTG
1 CAAAATGCCCTTCCCGGACGGAAGGCACTAATTTCACTTGCTTTTTCCAAAAC--ACCCTTCCCG
* *
4916 GACGGAAGACGC-TTATTTTTACTCACTTTT-TT
64 GACGGAAG--GCATTAATTTTACTCGCTTTTCTT
*
4948 CCCAAAGTGCCCTTCCCGGACGGAAGGCACTAATTTCCACTTGCTTTTTCCTAAAACACCCTTCC
1 --CAAAATGCCCTTCCCGGACGGAAGGCACTAATTT-CACTTGCTTTTTCC-AAAACACCCTTCC
*
5013 CGGATGGAAGGCATTAATTTTACTCGCGTTTTCTT
62 CGGACGGAAGGCATTAATTTTACTCGC-TTTTCTT
* * *
5048 AAAAATGCCCTTTCCGGACGAAAGGCA
1 CAAAATGCCCTTCCCGGACGGAAGGCA
5075 AGTTCACTTT
Statistics
Matches: 349, Mismatches: 50, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
95 16 0.05
96 62 0.18
97 124 0.36
98 110 0.32
99 30 0.09
100 7 0.02
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (95 bp):
CAAAATGCCCTTCCCGGACGGAAGGCACTAATTTCACTTGCTTTTTCCAAAACACCCTTCCCGGA
CGGAAGGCATTAATTTTACTCGCTTTTCTT
Found at i:8401 original size:17 final size:17
Alignment explanation
Indices: 8376--8422 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
8366 AGGAGGTCAT
*
8376 CGAAAGACGTCGTTTGA
1 CGAAGGACGTCGTTTGA
8393 CGAAGGACGTCG-TTGA
1 CGAAGGACGTCGTTTGA
* *
8409 AGAAGGAAGTCGTT
1 CGAAGGACGTCGTT
8423 GGTGTGGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (17 bp):
CGAAGGACGTCGTTTGA
Found at i:10908 original size:36 final size:36
Alignment explanation
Indices: 10861--10932 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
10851 CCCTCAGTTC
10861 CTTATTATAAGTCATGGATAACTAAAATCAACCAAG
1 CTTATTATAAGTCATGGATAACTAAAATCAACCAAG
10897 CTTATTATAAGTCATGGATAACTAAAATCAACCAAG
1 CTTATTATAAGTCATGGATAACTAAAATCAACCAAG
10933 AGAAGTAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (36 bp):
CTTATTATAAGTCATGGATAACTAAAATCAACCAAG
Found at i:12062 original size:29 final size:29
Alignment explanation
Indices: 12020--12095 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
12010 GAGCAAGCTT
12020 GTGAGATGAGTGATATCTCTGAGAGATGC
1 GTGAGATGAGTGATATCTCTGAGAGATGC
*
12049 GTGAGATGAGTGATATCTCTGAGAGATGT
1 GTGAGATGAGTGATATCTCTGAGAGATGC
* *
12078 TTGAGATAAGTGATATCT
1 GTGAGATGAGTGATATCT
12096 GTCTGAAGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.29, C:0.08, G:0.32, T:0.32
Consensus pattern (29 bp):
GTGAGATGAGTGATATCTCTGAGAGATGC
Found at i:13489 original size:18 final size:18
Alignment explanation
Indices: 13466--13509 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
13456 ATATAACAAT
*
13466 AATAATTATTATTCTGA-A
1 AATAATTATTATT-TAATA
13484 AATAATTATTATTTAATA
1 AATAATTATTATTTAATA
13502 AATAATTA
1 AATAATTA
13510 ATAATTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AATAATTATTATTTAATA
Found at i:15508 original size:22 final size:22
Alignment explanation
Indices: 15483--16119 Score: 201
Period size: 22 Copynumber: 29.6 Consensus size: 22
15473 ATGATCCCAT
15483 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
15505 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
15527 TAT-AGAATTTCGAGAACCTTTT
1 TATGA-AATTTTGATAACCTTCC
** *
15549 TAT-AAATTTTTTTTAACCTAT-T
1 TATGAAA-TTTTGATAACCT-TCC
* * *
15571 TATGAAATTTGGTTATCC-TCAC
1 TATGAAATTTTGATAACCTTC-C
* * ***
15593 TAAGGAATTTTGA-AGACCTAAA
1 TATGAAATTTTGATA-ACCTTCC
15615 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
15636 TAATG-AATTTTGATAA-CTTCC
1 T-ATGAAATTTTGATAACCTTCC
15657 TAATG-AATTTTGATAA-CTTCCC
1 T-ATGAAATTTTGATAACCTT-CC
* * **
15679 AAT-CAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
15701 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
15722 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
15745 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
15766 ATATG-AATTGTTAATAATC-ACAC
1 -TATGAAATT-TTGATAACCTTC-C
* * * **
15789 TTTGAAATTTTGATAATCATAA
1 TATGAAATTTTGATAACCTTCC
*
15811 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
15833 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
15856 TAT----TTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
15875 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
15897 TATGAAATCTTAATAA-----C
1 TATGAAATTTTGATAACCTTCC
* * *
15914 TA-CAAATTTTGATAACATCCC
1 TATGAAATTTTGATAACCTTCC
** *
15935 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
15957 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
15979 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
16001 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * * **
16023 TGTGAAATTGTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
16045 TATGAAATTTTAATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
16067 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
16088 -CTG-AATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
16107 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
16120 TACTCCATAA
Statistics
Matches: 454, Mismatches: 118, Indels: 88
0.69 0.18 0.13
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
19 35 0.08
20 12 0.03
21 71 0.16
22 281 0.62
23 41 0.09
24 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:15646 original size:21 final size:21
Alignment explanation
Indices: 15620--15694 Score: 132
Period size: 21 Copynumber: 3.6 Consensus size: 21
15610 CTAAATATGA
15620 AATTTTGATAACTTCCTAATG
1 AATTTTGATAACTTCCTAATG
15641 AATTTTGATAACTTCCTAATG
1 AATTTTGATAACTTCCTAATG
* *
15662 AATTTTGATAACTTCCCAATC
1 AATTTTGATAACTTCCTAATG
15683 AATTTTGATAAC
1 AATTTTGATAAC
15695 CAACACTATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (21 bp):
AATTTTGATAACTTCCTAATG
Found at i:15888 original size:23 final size:22
Alignment explanation
Indices: 15815--15890 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 22
15805 TCATAATATG
* *
15815 AAATTGTGAT-AACCTCGCTAT
1 AAATTTTGATAAACCTCCCTAT
* *
15836 GAAATTTTGATAAATCTTCCTAT
1 -AAATTTTGATAAACCTCCCTAT
15859 ---TTTTGATAAACCTCCCTAT
1 AAATTTTGATAAACCTCCCTAT
15878 AAAATTTTGATAA
1 -AAATTTTGATAA
15891 CTTTCTTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
19 17 0.40
22 9 0.21
23 17 0.40
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAAACCTCCCTAT
Found at i:16125 original size:19 final size:20
Alignment explanation
Indices: 16069--16119 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
16059 AACCTTCATA
16069 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
16089 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
16108 TGAAATTTTGAT
1 TGAAATTTTGAT
16120 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:16258 original size:22 final size:22
Alignment explanation
Indices: 16231--16476 Score: 176
Period size: 22 Copynumber: 11.2 Consensus size: 22
16221 ATTTTAAAAA
*
16231 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* * *
16253 TTTGATAACTTCTTTATAAAAT
1 TTTGATAACCTCTCTATGAAAT
* * *
16275 TTTGTTGACCCCTCTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* * * *
16297 TCTGATAATCACAT-TATGTAAT
1 TTTGATAACCTC-TCTATGAAAT
* *
16319 TTTGATAACCTCGCTTTGAAAT
1 TTTGATAACCTCTCTATGAAAT
** *
16341 TTTGATAACAACACTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
16363 TTTGATAATCTTTCTAT-AAAT
1 TTTGATAACCTCTCTATGAAAT
* *
16384 TTTGATAATCAGATCTCTCTGAAAT
1 TTTGATAA-C--CTCTCTATGAAAT
* * *
16409 TTCGATAATCACTCTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* * * *
16431 TTCGATAATCACTCTATGAGA-
1 TTTGATAACCTCTCTATGAAAT
*
16452 TTTGATAACCT-TCTATCAAAT
1 TTTGATAACCTCTCTATGAAAT
16473 TTTG
1 TTTG
16477 GTACTCCTTG
Statistics
Matches: 173, Mismatches: 44, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
20 7 0.04
21 24 0.14
22 125 0.72
23 1 0.01
24 5 0.03
25 11 0.06
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TTTGATAACCTCTCTATGAAAT
Found at i:16273 original size:44 final size:45
Alignment explanation
Indices: 16201--16391 Score: 153
Period size: 44 Copynumber: 4.4 Consensus size: 45
16191 GAAATACCAC
** * *
16201 TATGAAATTTTTCTAA-TCACATTTTAAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACTCACATTATAAAATTTTGATAACCTCTT
* * * * * *
16245 TATGAAATTTTGATAACT-TCTTTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACTCACATTATAAAATTTTGATAACCTCTT
* ** *
16289 TATGAAATTCTGATAA-TCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACTCACATTATAAAATTTTGATAACCTC-TT
* * * *
16334 T-TGAAATTTTGATAAC-AACACTATGAAATTTTGATAATCT-TT
1 TATGAAATTTTGATAACTCACATTATAAAATTTTGATAACCTCTT
16376 CTAT-AAATTTTGATAA
1 -TATGAAATTTTGATAA
16392 TCAGATCTCT
Statistics
Matches: 115, Mismatches: 26, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
42 1 0.01
43 14 0.12
44 98 0.85
45 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.43
Consensus pattern (45 bp):
TATGAAATTTTGATAACTCACATTATAAAATTTTGATAACCTCTT
Found at i:16447 original size:68 final size:66
Alignment explanation
Indices: 16286--16460 Score: 171
Period size: 68 Copynumber: 2.6 Consensus size: 66
16276 TTGTTGACCC
* * * *
16286 CTCTATGAAA-TTCTGATAATCACAT-TATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAA
1 CTCTATGAAATTTC-GATAATCAC-TCTATGAAATTTTGATAACATCGCTCTGAAATTTCGATAA
16349 CAA
64 CAA
* * ** *
16352 CACTATGAAATTTTGATAATCTTTCTAT-AAATTTTGATAATCAGATCTCTCTGAAATTTCGATA
1 CTCTATGAAATTTCGATAATCACTCTATGAAATTTTGATAA-C--ATCGCTCTGAAATTTCGATA
16416 ATC-A
63 A-CAA
*
16420 CTCTATGAAATTTCGATAATCACTCTATGAGA-TTTGATAAC
1 CTCTATGAAATTTCGATAATCACTCTATGAAATTTTGATAAC
16461 CTTCTATCAA
Statistics
Matches: 88, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
65 12 0.14
66 20 0.23
67 3 0.03
68 50 0.57
69 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (66 bp):
CTCTATGAAATTTCGATAATCACTCTATGAAATTTTGATAACATCGCTCTGAAATTTCGATAACA
A
Found at i:16564 original size:22 final size:22
Alignment explanation
Indices: 16514--16564 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
16504 TAACCTTCAT
* *
16514 ATGAAATTTTGATAATCACACT
1 ATGAAATTTTGATAACCACACC
* *
16536 ATAAAATTTTGATAACCACCCC
1 ATGAAATTTTGATAACCACACC
16558 ATGAAAT
1 ATGAAAT
16565 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:16770 original size:22 final size:22
Alignment explanation
Indices: 16664--16803 Score: 79
Period size: 22 Copynumber: 6.3 Consensus size: 22
16654 TTGTGATAAT
* * **
16664 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATAAAATTTTGA
* * *
16686 TAACCAACCTA-AGAGATTTTAA
1 TAACCATCCTATA-AAATTTTGA
* * *
16708 TAACCTGATCCTATGAAATTATGG
1 TAACC--ATCCTATAAAATTTTGA
* *
16732 TAATCA-CACTATGAAATTTTGA
1 TAACCATC-CTATAAAATTTTGA
* *
16754 TAACC-TCCTCATAAAATTATAA
1 TAACCATCCT-ATAAAATTTTGA
*
16776 TAACCATCCTATGAAATTTTGA
1 TAACCATCCTATAAAATTTTGA
16798 TAACCA
1 TAACCA
16804 CATAGAGACA
Statistics
Matches: 90, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
21 3 0.03
22 69 0.77
23 4 0.04
24 14 0.16
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
TAACCATCCTATAAAATTTTGA
Found at i:17006 original size:19 final size:20
Alignment explanation
Indices: 16975--17012 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
16965 TATTGACATT
16975 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
16994 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
17013 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Done.