Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019290.1 Corchorus olitorius cultivar O-4 contig19323, 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: 14527
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:2534 original size:9 final size:9
Alignment explanation
Indices: 2520--2546 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2510 AAATGGTTGC
2520 TTTGTTTTG
1 TTTGTTTTG
2529 TTTGTTTTG
1 TTTGTTTTG
2538 TTTGTTTTG
1 TTTGTTTTG
2547 ATGCTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (9 bp):
TTTGTTTTG
Found at i:7802 original size:70 final size:71
Alignment explanation
Indices: 7684--8070 Score: 297
Period size: 70 Copynumber: 5.4 Consensus size: 71
7674 ATTTCAGATG
* * *
7684 CTTCAGTTCATTTCAGTTGATCCAGGGC-AGTCTTTAT-TT-AGTTTATTTCAGTTGATACAGGG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGA-TCTTT-TCTTCAGTTTATTTCAATTGATCCAGGG
7746 CGACCTTT
64 CGACCTTT
* * * ** * * * *
7754 CTTCAGTTAATTTCAGTTGACCCAGGGCGGTC-TTTCTTCAACTCATTTCAGTTGACCCAGGGTG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGG-C
*
7818 GTCCTTAT
65 GACCTT-T
* *
7826 -TT-AGTTTATTTCAGTTGATCCAGGGGCGATCTTTTCTTCATTTTACTTCAATTGATCCAGGGC
1 CTTCAGTTTATTTCAGTTGATCCA-GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGC
*
7889 GATCTTTT
65 GA-CCTTT
* * * *
7897 CCTCAGTTTACTTCAATTTGATCCAGGGCGATCTTTTCTTCAGTTTATGTCAATTGATCCAGGGC
1 CTTCAGTTTATTTC-AGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGC
*
7962 GATCTTT
65 GACCTTT
* * * *
7969 CCTTCATTTCCTTCAATTT-A-TTCGATCCAGAGCGATCTTTTCTTCAGTTTATTTTAGTTGA-C
1 -CTTCA-GT--TT--ATTTCAGTT-GATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATC
* **
8031 CTAGGGTGGTCTTT
59 C-AGGGCGACCTTT
* * *
8045 CTTCAATTCATTTCAGTTGACCCAGG
1 CTTCAGTTTATTTCAGTTGATCCAGG
8071 TGATACGAAT
Statistics
Matches: 253, Mismatches: 43, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
68 1 0.00
69 4 0.02
70 68 0.27
71 23 0.09
72 35 0.14
73 52 0.21
74 11 0.04
75 9 0.04
76 47 0.19
78 3 0.01
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.41
Consensus pattern (71 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCG
ACCTTT
Found at i:7895 original size:36 final size:36
Alignment explanation
Indices: 7684--8019 Score: 258
Period size: 35 Copynumber: 9.3 Consensus size: 36
7674 ATTTCAGATG
* * *
7684 CTTCAGTTCATTTCAGTTGATCCAGGGC-AGTCTTTAT
1 CTTCAGTTTACTTCAATTGATCCAGGGCGA-TCTTT-T
* * * *
7721 -TT-AGTTTATTTCAGTTGATACAGGGCGA-CCTTT
1 CTTCAGTTTACTTCAATTGATCCAGGGCGATCTTTT
* * * * *
7754 CTTCAGTTAATTTCAGTTGACCCAGGGCGGTC-TTT
1 CTTCAGTTTACTTCAATTGATCCAGGGCGATCTTTT
** * * * * * * *
7789 CTTCAACTCATTTCAGTTGACCCAGGGTGGTCCTTAT
1 CTTCAGTTTACTTCAATTGATCCAGGGCGAT-CTTTT
* *
7826 -TT-AGTTTATTTCAGTTGATCCAGGGGCGATCTTTT
1 CTTCAGTTTACTTCAATTGATCCA-GGGCGATCTTTT
*
7861 CTTCATTTTACTTCAATTGATCCAGGGCGATCTTTT
1 CTTCAGTTTACTTCAATTGATCCAGGGCGATCTTTT
*
7897 CCTCAGTTTACTTCAATTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTACTTCAA-TTGATCCAGGGCGATCTTTT
*
7934 CTTCAGTTTA-TGTCAATTGATCCAGGGCGATCTTTC
1 CTTCAGTTTACT-TCAATTGATCCAGGGCGATCTTTT
* *
7970 CTTCA-TTTCCTTCAATTTATTCGATCCAGAGCGATCTTTT
1 CTTCAGTTTACTTC-A---ATT-GATCCAGGGCGATCTTTT
8010 CTTCAGTTTA
1 CTTCAGTTTA
8020 TTTTAGTTGA
Statistics
Matches: 251, Mismatches: 30, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
33 1 0.00
34 5 0.02
35 99 0.39
36 67 0.27
37 52 0.21
39 3 0.01
40 21 0.08
41 3 0.01
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (36 bp):
CTTCAGTTTACTTCAATTGATCCAGGGCGATCTTTT
Found at i:7929 original size:73 final size:74
Alignment explanation
Indices: 7840--8020 Score: 253
Period size: 73 Copynumber: 2.4 Consensus size: 74
7830 TTTATTTCAG
*
7840 TTGATCCAGGGGCGATCTTTTCTTCATTTTACT-TCAATTGATCCAGGGCGATCTTTTCC-TCAG
1 TTGATCCA-GGGCGATCTTTTCTTCAGTTTA-TGTCAATTGATCCAGGGCGATC-TTTCCTTCA-
7903 TTTACTTCAA-T-
62 TTTACTTCAATTA
*
7914 TTGATCCAGGGCGATCTTTTCTTCAGTTTATGTCAATTGATCCAGGGCGATCTTTCCTTCATTTC
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTATGTCAATTGATCCAGGGCGATCTTTCCTTCATTTA
7979 CTTCAATTTA
66 CTTCAA-TTA
*
7989 TTCGATCCAGAGCGATCTTTTCTTCAGTTTAT
1 TT-GATCCAGGGCGATCTTTTCTTCAGTTTAT
8021 TTTAGTTGAC
Statistics
Matches: 98, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
72 15 0.15
73 44 0.45
74 9 0.09
75 2 0.02
76 28 0.29
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.43
Consensus pattern (74 bp):
TTGATCCAGGGCGATCTTTTCTTCAGTTTATGTCAATTGATCCAGGGCGATCTTTCCTTCATTTA
CTTCAATTA
Found at i:8912 original size:21 final size:21
Alignment explanation
Indices: 8888--8962 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
8878 CTTAGGCAAT
*
8888 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
8909 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
8930 TCCAATGAGCTTGGAACATGC
1 TCCAATGAGCTTGGAACCTTC
8951 TCCAATGAGCTT
1 TCCAATGAGCTT
8963 CTTTCACATC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:10983 original size:26 final size:23
Alignment explanation
Indices: 10953--10999 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
10943 CTTGAAATTT
10953 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
10979 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
11000 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:11899 original size:21 final size:21
Alignment explanation
Indices: 11875--11966 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
11865 CTTAGGCAAT
*
11875 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
11896 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* * *
11917 TCGAATGAGCTTGGAACATGC
1 TCCAATGAGCTTGGAACCTTC
*
11938 TCCAATGAGCTTGG-ATCTTGC
1 TCCAATGAGCTTGGAACCTT-C
11959 TCCAATGA
1 TCCAATGA
11967 ACTCCTAGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 2 0.03
21 60 0.97
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:12129 original size:36 final size:36
Alignment explanation
Indices: 12088--12744 Score: 615
Period size: 36 Copynumber: 18.5 Consensus size: 36
12078 GTGGTCCTTA
*
12088 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * *
12124 TTCAGTTTATTTCGATTTGATCCAGGGCGATC-CTTA
1 TTCAGTTTATTTC-AGTTGATCCAGGGCGATCTTTTC
* * * * * * *
12160 TTCAATTCATTTCAGTTGACCCAGGGTGGTC-CTTA
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* *
12195 TTCAGTTTATTTCATTTGATCTAGGGCGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* *
12231 TTCATTTTACTTCAGTTGATCCAGGGCGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * *
12267 TTCAGTTTACTTCAATTTGATCCAGGGCGATTTTTTC
1 TTCAGTTTATTTC-AGTTGATCCAGGGCGATCTTTTC
*
12304 TTCAGTTT-TTGTCAATTGATCCAGGGCGATCTTTTC
1 TTCAGTTTATT-TCAGTTGATCCAGGGCGATCTTTTC
** * *
12340 TTCA-TTTCCTTCAATTGATCCAGGGTGAT-TTTTCC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT-C
*
12375 TTCAGTTTA-TTC----GATCCAGGGCGATATTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * * *
12406 TTCAGTTTATTTCAGCTGACCCAGGGTGGTC-TTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * * * * *
12441 TTCAATTCATTTCAGCTGACCCAGGGGTGGTC-TTTC
1 TTCAGTTTATTTCAGTTGATCCA-GGGCGATCTTTTC
* * * * * * *
12477 TTCAGTTCATTTCAGTTAACCCAGGGTGGTC-CTTA
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
*
12512 TTCAGTTTATTTCAGTCGATCCAGGGCGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * * ** *
12548 TTCATTTTACTTCAGTTGATCTAGATCAATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
*
12584 TTCAGTTTATTTCAGTTGATCCAGGTCGAT-TTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * * * * *
12619 TTCAGTATATTTTAGTTGACCCAGAGCG-GCCTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
* * * *
12654 TTCAATTAATTTCAGTGGATCCATGGCGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
*
12690 TTCAGTTTATTTCAGTTGATCCAGAGCGATCTTTTC
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
*
12726 TGCAGTTTATTTCAGTTGA
1 TTCAGTTTATTTCAGTTGA
12745 CCGCAAATTT
Statistics
Matches: 517, Mismatches: 87, Indels: 34
0.81 0.14 0.05
Matches are distributed among these distances:
31 22 0.04
32 7 0.01
34 4 0.01
35 183 0.35
36 254 0.49
37 47 0.09
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (36 bp):
TTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
Found at i:12418 original size:71 final size:74
Alignment explanation
Indices: 12208--12418 Score: 198
Period size: 73 Copynumber: 2.9 Consensus size: 74
12198 AGTTTATTTC
* *
12208 ATTTGATCTAGGGCGATCTTTT-CTTCATTTTACT-TCAGTTGATCCAGGGCGATCTTTTCTTCA
1 ATTTGATCCAGGGCGAT-TTTTCCTTCAGTTTA-TGTCA---GATCCAGGGCGATCTTTTCTTCA
12271 GTTTA----CTTCA
61 GTTTATTTCCTTCA
* *
12281 ATTTGATCCAGGGCGATTTTTTCTTCAGTTTTTGTCAATTGATCCAGGGCGATCTTTTCTTC---
1 ATTTGATCCAGGGCGATTTTTCCTTCAGTTTATGTC-A--GATCCAGGGCGATCTTTTCTTCAGT
12343 --ATTTCCTTCA
63 TTATTTCCTTCA
* *
12353 A-TTGATCCAGGGTGATTTTTCCTTCAGTTTAT-TC-GATCCAGGGCGATATTTTCTTCAGTTTA
1 ATTTGATCCAGGGCGATTTTTCCTTCAGTTTATGTCAGATCCAGGGCGATCTTTTCTTCAGTTTA
12415 TTTC
66 TTTC
12419 AGCTGACCCA
Statistics
Matches: 119, Mismatches: 7, Indels: 26
0.78 0.05 0.17
Matches are distributed among these distances:
66 21 0.18
68 1 0.01
70 2 0.02
71 33 0.28
72 11 0.09
73 50 0.42
74 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (74 bp):
ATTTGATCCAGGGCGATTTTTCCTTCAGTTTATGTCAGATCCAGGGCGATCTTTTCTTCAGTTTA
TTTCCTTCA
Found at i:12465 original size:102 final size:102
Alignment explanation
Indices: 12217--12483 Score: 236
Period size: 102 Copynumber: 2.5 Consensus size: 102
12207 CATTTGATCT
* * ** * *
12217 AGGGCGATCTTTTCTTCATTTTACTTCAGTTGATCCA-GGGCGATCTTTTCTTCAGTTTACTTCA
1 AGGGCGATCTTTTCTTCA-ATTCCTTCAACTGACCCAGGGGTGATC-TTTCTTCAGTTTA-TTC-
* * *
12281 ATTTGATCCAGGGCGATTTTTTCTTCAGTTTTTGTCAATTGATCC
62 ----GATCCAGGGCGATATTTTCTTCAGTTTTTGTCAACTGACCC
* * * *
12326 AGGGCGATCTTTTCTTCATTTCCTTCAATTGATCCA-GGGTGATTTTTCCTTCAGTTTATTCGAT
1 AGGGCGATCTTTTCTTCAATTCCTTCAACTGACCCAGGGGTGATCTTT-CTTCAGTTTATTCGAT
*
12390 CCAGGGCGATATTTTCTTCAGTTTATT-TCAGCTGACCC
65 CCAGGGCGATATTTTCTTCAGTTT-TTGTCAACTGACCC
* * * * *
12428 AGGGTGGTC-TTTCTTCAATTCATTTCAGCTGACCCAGGGGTGGTCTTTCTTCAGTT
1 AGGGCGATCTTTTCTTCAATTC-CTTCAACTGACCCAGGGGTGATCTTTCTTCAGTT
12484 CATTTCAGTT
Statistics
Matches: 137, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
101 11 0.08
102 59 0.43
103 11 0.08
107 6 0.04
108 32 0.23
109 18 0.13
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (102 bp):
AGGGCGATCTTTTCTTCAATTCCTTCAACTGACCCAGGGGTGATCTTTCTTCAGTTTATTCGATC
CAGGGCGATATTTTCTTCAGTTTTTGTCAACTGACCC
Found at i:12548 original size:71 final size:71
Alignment explanation
Indices: 12075--12744 Score: 545
Period size: 71 Copynumber: 9.5 Consensus size: 71
12065 GCACATCACT
* * * *
12075 AGGGTGGTCCTTATTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCGAT
1 AGGGTGATCCTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTC-AG
12140 TTGATCC
65 TTGATCC
* * * * * * * * * *
12147 AGGGCGATCCTTATTCAATTCATTTCAGTTGACCCAGGGTGGTC-CTTATTCAGTTTATTTCATT
1 AGGGTGATCCTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGT
*
12211 TGATCT
66 TGATCC
* * * * *
12217 AGGGCGATCTTTTCTTCATTTTACTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTACTTCAA
1 AGGGTGATC-CTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTC-A
*
12282 TTTGATCC
64 GTTGATCC
* ** * **
12290 AGGGCGATTTTTTCTTCAGTTT-TTGTCAATTGATCCAGGGCGATCTTTTCTTCA-TTTCCTTCA
1 AGGGTGA-TCCTTCTTCAGTTTATT-TCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCA
*
12353 ATTGATCC
64 GTTGATCC
** *
12361 AGGGTGATTTTTCCTTCAGTTTA-TTC----GATCCAGGGCGATATTTTCTTCAGTTTATTTCAG
1 AGGGTGATCCTT-CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAG
* *
12421 CTGACCC
65 TTGATCC
* * * * * * * * *
12428 AGGGTGGTCTTTCTTCAATTCATTTCAGCTGACCCAGGGGTGGTC-TTTCTTCAGTTCATTTCAG
1 AGGGTGATCCTTCTTCAGTTTATTTCAGTTGATCCA-GGGCGATCTTTTCTTCAGTTTATTTCAG
* *
12492 TTAACCC
65 TTGATCC
* * * * *
12499 AGGGTGGTCCTTATTCAGTTTATTTCAGTCGATCCAGGGCGATCTTTTCTTCATTTTACTTCAGT
1 AGGGTGATCCTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGT
*
12564 TGATCT
66 TGATCC
* * * * * *
12570 A-GATCAATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGTCGAT-TTTTCTTCAGTATATTTTA
1 AGGGT-GATC-CTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCA
*
12633 GTTGACCC
64 GTTGATCC
* * * * * * *
12641 AGAGCG-GCCTTTCTTCAATTAATTTCAGTGGATCCATGGCGATCTTTTCTTCAGTTTATTTCAG
1 AGGGTGATCC-TTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAG
12705 TTGATCC
65 TTGATCC
* * * *
12712 AGAGCGATCTTTTCTGCAGTTTATTTCAGTTGA
1 AGGGTGATC-CTTCTTCAGTTTATTTCAGTTGA
12745 CCGCAAATTT
Statistics
Matches: 483, Mismatches: 93, Indels: 44
0.78 0.15 0.07
Matches are distributed among these distances:
66 30 0.06
67 25 0.05
70 61 0.13
71 198 0.41
72 114 0.24
73 54 0.11
74 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (71 bp):
AGGGTGATCCTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGT
TGATCC
Found at i:13047 original size:30 final size:30
Alignment explanation
Indices: 12928--13037 Score: 166
Period size: 30 Copynumber: 3.7 Consensus size: 30
12918 TTGTCAATTT
* *
12928 TTTTAATCCTGGTTGAGGATCATTGCTTTA
1 TTTTAATCCTGATTTAGGATCATTGCTTTA
* *
12958 TTTTTATCCTAATTTAGGATCATTGCTTTA
1 TTTTAATCCTGATTTAGGATCATTGCTTTA
*
12988 TTTTCATCCTGATTTAGGATCATTGCTTTA
1 TTTTAATCCTGATTTAGGATCATTGCTTTA
*
13018 TTTTAATCCTGGTTTAGGAT
1 TTTTAATCCTGATTTAGGAT
13038 AATCACTTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (30 bp):
TTTTAATCCTGATTTAGGATCATTGCTTTA
Found at i:13047 original size:60 final size:60
Alignment explanation
Indices: 12928--13052 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
12918 TTGTCAATTT
* * * **
12928 TTTTAATCCTGGTTGAGGATCATTGCTTTATTTTTATCCTAATTTAGGATCATTGCTTTA
1 TTTTAATCCTGATTGAGGATCATTGCTTTATTTTAATCCTAATTTAGGATAATCACTTTA
* * **
12988 TTTTCATCCTGATTTAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATAATCACTTTA
1 TTTTAATCCTGATTGAGGATCATTGCTTTATTTTAATCCTAATTTAGGATAATCACTTTA
*
13048 GTTTA
1 TTTTA
13053 TTTGAATCGT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (60 bp):
TTTTAATCCTGATTGAGGATCATTGCTTTATTTTAATCCTAATTTAGGATAATCACTTTA
Found at i:13851 original size:16 final size:17
Alignment explanation
Indices: 13830--13867 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
13820 AATACAAAAA
13830 AAAAAAATGCAAAT-GC
1 AAAAAAATGCAAATAGC
*
13846 AAAAAAATGGAAATAGC
1 AAAAAAATGCAAATAGC
13863 AAAAA
1 AAAAA
13868 TACAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.68, C:0.08, G:0.13, T:0.11
Consensus pattern (17 bp):
AAAAAAATGCAAATAGC
Done.