Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016497.1 Corchorus olitorius cultivar O-4 contig16530, 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: 29417
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:3210 original size:24 final size:24
Alignment explanation
Indices: 3182--3231 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3172 GTATTTAGAG
3182 TAACTTGTAAGTTAAGTTTAGTTT
1 TAACTTGTAAGTTAAGTTTAGTTT
3206 TAACTTGTAAGTTAAGTTTAGTTT
1 TAACTTGTAAGTTAAGTTTAGTTT
3230 TA
1 TA
3232 GAATAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50
Consensus pattern (24 bp):
TAACTTGTAAGTTAAGTTTAGTTT
Found at i:3238 original size:29 final size:27
Alignment explanation
Indices: 3175--3255 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 27
3165 TCTAATCGTA
3175 TTTAGAGTAACTTGTAAGTTAAGTTTAG
1 TTTAGA-TAACTTGTAAGTTAAGTTTAG
3203 TTT---TAACTTGTAAGTTAAGTTTAG
1 TTTAGATAACTTGTAAGTTAAGTTTAG
* *
3227 TTTTAGAATAACTTATAATTTAAGTTTAG
1 -TTTAG-ATAACTTGTAAGTTAAGTTTAG
3256 CCCTGAATCA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
24 21 0.46
25 3 0.07
28 3 0.07
29 19 0.41
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (27 bp):
TTTAGATAACTTGTAAGTTAAGTTTAG
Found at i:6233 original size:12 final size:12
Alignment explanation
Indices: 6215--6244 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6205 ATGGAGCACA
6215 ACAGAGTCAAGG
1 ACAGAGTCAAGG
*
6227 GCAGAGTCAAGG
1 ACAGAGTCAAGG
6239 ACAGAG
1 ACAGAG
6245 GTTATATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.37, T:0.07
Consensus pattern (12 bp):
ACAGAGTCAAGG
Found at i:7176 original size:1 final size:1
Alignment explanation
Indices: 7170--7194 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
7160 GTAATTAGAG
7170 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
7195 AAATTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8105 original size:33 final size:33
Alignment explanation
Indices: 8048--8112 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
8038 CTCCTTTTTC
*
8048 TTATACATATAATATATACAACTAATATATATT
1 TTATACATATAATATATACAACTAACATATATT
* *
8081 TTATGCATATAAT-TAATACTACTAACATATAT
1 TTATACATATAATAT-ATACAACTAACATATAT
8113 ATAGTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.42
Consensus pattern (33 bp):
TTATACATATAATATATACAACTAACATATATT
Found at i:10046 original size:9 final size:9
Alignment explanation
Indices: 10032--10064 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
10022 GCATTTACCT
10032 TATTAACCC
1 TATTAACCC
10041 TATTAACCC
1 TATTAACCC
*
10050 CATTAACCC
1 TATTAACCC
10059 TATTAA
1 TATTAA
10065 TAGTAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (9 bp):
TATTAACCC
Found at i:11980 original size:22 final size:22
Alignment explanation
Indices: 11953--12530 Score: 197
Period size: 22 Copynumber: 26.2 Consensus size: 22
11943 ATTACACTAT
*
11953 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
11975 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** * *
11997 TTTTAATAACGATACTATGGAA
1 TTTTGATAACCTTCCTATGAAA
** ** **
12019 TTTCAATAATATTTTTAT--AA
1 TTTTGATAACCTTCCTATGAAA
** *
12039 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
12061 TTTT-ATTAACCTCCCTGA-GGAA
1 TTTTGA-TAACCTTCCT-ATGAAA
*
12083 TTTTGA-AGACC-TCATTATGAAA
1 TTTTGATA-ACCTTC-CTATGAAA
*
12105 TTTTGATAA-CTTCCCAATGAAA
1 TTTTGATAACCTT-CCTATGAAA
* ** *
12127 TTTTGATGACCAACACTATGAGA
1 TTTTGATAACCTTC-CTATGAAA
* *
12150 TGTTGATAACC-TCCATATGATA
1 TTTTGATAACCTTCC-TATGAAA
* * *
12172 TATTGATAACC-ACGTTATGAAAA
1 TTTTGATAACCTTC-CTATG-AAA
*
12195 TTTT-AAAACC-TCCATATG-AA
1 TTTTGATAACCTTCC-TATGAAA
*
12215 TTGTT-AGTAA--TTAC-ACTGAAA
1 TT-TTGA-TAACCTTCCTA-TGAAA
* * *
12236 TTTTGATAATCATACTATGAAA
1 TTTTGATAACCTTCCTATGAAA
*
12258 TTGTGATAACC-TCGCTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
*
12280 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
12303 TTTTGATAAACC-TCGCTATGAAA
1 TTTTGAT-AACCTTC-CTATGAAA
*
12326 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
12349 TTTTGATAAACC-TCCTTAT-AAA
1 TTTTGAT-AACCTTCC-TATGAAA
* ** *
12371 ATTT-ATAAAATT-TTGAT-AACA
1 TTTTGATAACCTTCCT-ATGAA-A
* ** *
12392 TCCTTATGA-AATCTTGATAACTACAAA
1 T--TT-TGATAACCTTCCT-A-T-GAAA
*
12419 TTTTGATAACCTCCCTATG-AA
1 TTTTGATAACCTTCCTATGAAA
* *
12440 TGTTTGATAACCCTCTTATGAAA
1 T-TTTGATAACCTTCCTATGAAA
* **
12463 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-TCCTATGAAA
* *
12485 TTTTGATAACCTTCATAAGAAA
1 TTTTGATAACCTTCCTATGAAA
*
12507 TTTTGATATCC-TCCT-TGAAA
1 TTTTGATAACCTTCCTATGAAA
12527 TTTT
1 TTTT
12531 AATTACTCCA
Statistics
Matches: 423, Mismatches: 84, Indels: 100
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.00
20 39 0.09
21 29 0.07
22 222 0.52
23 103 0.24
24 13 0.03
25 10 0.02
26 1 0.00
27 2 0.00
28 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:12178 original size:45 final size:45
Alignment explanation
Indices: 12098--12183 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
12088 AAGACCTCAT
* * * *
12098 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATGACCAACAC
1 TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
* *
12143 TATGAGATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCCA-ATGAAATATTGATAACCA
12184 CGTTATGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 3 0.09
45 31 0.91
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
Found at i:12374 original size:46 final size:46
Alignment explanation
Indices: 12231--12362 Score: 205
Period size: 46 Copynumber: 2.9 Consensus size: 46
12221 GTAATTACAC
* * * * *
12231 TGAAATTTTGAT-AATCATACTATGAAATTGTGAT-AACCTCGCTA
1 TGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCGCTA
12275 TGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCGCTA
1 TGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCGCTA
12321 TGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTC
1 TGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTC
12363 CTTATAAAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 12 0.15
45 17 0.21
46 52 0.64
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (46 bp):
TGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCGCTA
Found at i:12382 original size:32 final size:31
Alignment explanation
Indices: 12342--12403 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
12332 TAAACCTTCC
*
12342 TATAAAATTTTGATAAACCTCCTTATAAAATT
1 TATAAAATTTTGAT-AACATCCTTATAAAATT
*
12374 TATAAAATTTTGATAACATCCTTATGAAAT
1 TATAAAATTTTGATAACATCCTTATAAAAT
12404 CTTGATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (31 bp):
TATAAAATTTTGATAACATCCTTATAAAATT
Found at i:12465 original size:44 final size:44
Alignment explanation
Indices: 12416--13053 Score: 131
Period size: 44 Copynumber: 14.8 Consensus size: 44
12406 TGATAACTAC
* *
12416 AAATTTTGATAACCTCCCTATG-AATGTTTGATAACCCTCTTATG
1 AAATTTTGATAACCTCCCTATGAAAT-TTTGATAACCCTCATAAG
* ** *
12460 AAATTTTGA-AAACTAAACTATGAAATTTTGATAACCTTCATAAG
1 AAATTTTGATAACCT-CCCTATGAAATTTTGATAACCCTCATAAG
* * * * * *
12504 AAATTTTGATATCCT-CCT-TGAAATTTTAATTACTC-CAAAATA
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTCATAA-G
* * * * * *
12546 AAAGTTTAATAACCTTCC-A--AAA-TTTGGTAACCAT-ACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTCA-TAAG
* *
12586 AAATTTTTATAACCTCCCCA-G-AA-----AT-ACCACT-AT-A-
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACC-CTCATAAG
* * * ** * * ** ** *
12620 AAATTTTGGTAATCACATTTTGAAAATTTGATAACTTTTTTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTCATAAG
* * * * *
12664 AAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTC-TATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGAT-AACCCTCATAAG
* * ** * **
12708 AAATTTTGATAATCACATTATGTAATTTTGATAA-CCTCGATTTG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTC-ATAAG
** * * * * *
12752 AAATTTTGATAACAACACTATGAAATTTTGATAATCTTCCT-AT
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTCATAAG
* * * *
12795 AAATTTTGATAATCCGATCTCTATGAAATTTCGATAATCACTC-TATG
1 AAATTTTGATAA-CC--TCCCTATGAAATTTTGATAA-CCCTCATAAG
* * * * *
12842 AGA-TTTGATAACCT-TCTATCAAATTTTGGT-ACTCCTTATGAAATTG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAAC-CCTCAT--AA--G
* * * * * *
12888 AGACTTTT-ATAACCTTCATATGAAATTTTGATAA-TCACACTAAA
1 A-AATTTTGATAACCTCCCTATGAAATTTTGATAACCCTCA-TAAG
* * *
12932 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCAT--G
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAA-C-CCTCATAAG
* * * * * *
12976 AAATATT-AGTAACCTTCATATGAAATTTTGTTAA-CCACACTATG
1 AAATTTTGA-TAACCTCCCTATGAAATTTTGATAACCCTCA-TAAG
* *
13020 AAATTCTT-ATAACCTCACTATGACATTTTGATAA
1 AAATT-TTGATAACCTCCCTATGAAATTTTGATAA
13054 TCTCTTTGAT
Statistics
Matches: 422, Mismatches: 121, Indels: 102
0.65 0.19 0.16
Matches are distributed among these distances:
34 12 0.03
35 1 0.00
36 6 0.01
37 3 0.01
40 23 0.05
41 21 0.05
42 47 0.11
43 28 0.07
44 200 0.47
45 17 0.04
46 31 0.07
47 16 0.04
48 16 0.04
49 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTCATAAG
Found at i:12689 original size:22 final size:22
Alignment explanation
Indices: 12640--13058 Score: 241
Period size: 22 Copynumber: 18.9 Consensus size: 22
12630 AATCACATTT
* * * *
12640 TGAAAATTTGATAACTTTTTTA
1 TGAAATTTTGATAACCTCTCTA
12662 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
12684 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
12706 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* ** *
12728 TGTAATTTTGATAACCTCGATT
1 TGAAATTTTGATAACCTCTCTA
** *
12750 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
*
12772 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
12794 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * *
12818 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
12840 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* *
12860 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
*
12880 TGAAATTGAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* * *
12908 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCTCTA
** * *
12930 AAAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
12952 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTCTA
*
12974 TGAAATATT-AGTAACCT-TCATA
1 TGAAATTTTGA-TAACCTCTC-TA
* * *
12996 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
13018 TGAAATTCTT-ATAACCTCACTA
1 TGAAATT-TTGATAACCTCTCTA
* *
13040 TGACATTTTGATAATCTCT
1 TGAAATTTTGATAACCTCT
13059 TTGATAACCT
Statistics
Matches: 303, Mismatches: 67, Indels: 54
0.71 0.16 0.13
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 30 0.10
22 217 0.72
23 5 0.02
24 6 0.02
25 12 0.04
26 4 0.01
27 2 0.01
28 10 0.03
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:12977 original size:66 final size:67
Alignment explanation
Indices: 12907--13290 Score: 226
Period size: 66 Copynumber: 5.6 Consensus size: 67
12897 TAACCTTCAT
* *
12907 ATGAAATTTTGATAA-TCACACTAAAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCC
1 ATGAAATTTTAATAACTCACACTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCC
12971 CC
66 CC
* * * * *
12973 ATGAAATATTAGTAAC-CTTCA-TATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCT
1 ATGAAATTTTAATAACTC-ACACTATAAAATTTTGATAACCACACTATGAAATT-TTGATAACCT
* *
13035 CACT
64 CCCC
* * * * * *
13039 ATGACATTTTGATAATCTCTTTGATAACCTTTCTATAAAATTGTGATCACCACACTATGAAATGT
1 ATGAAATTTTAATAA-CTC-------A-C--ACTATAAAATTTTGATAACCACACTATGAAATTT
** * *
13104 CAATAACCTTCCT
55 TGATAACCTCCCC
* * * ** * * * *
13117 AAGAAATTTAAATAACCTGATTCTATGAAATTTTGGTAACCACACTAAGAAATTTTGATAACCTT
1 ATGAAATTTTAATAA-CTCACACTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTC
**
13182 CAA
65 CCC
* * * *
13185 ATTAAATTTTTATAACTTC-CA-TATAAAATTTTGGTAACCACACTATGAAATTTCGATAACCTC
1 ATGAAATTTTAATAAC-TCACACTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTC
*
13248 CTC
65 CCC
* * *
13251 ATGAAATTATAATAAC-CA-TCTAATAAAATTTTGATTACCA
1 ATGAAATTTTAATAACTCACACT-ATAAAATTTTGATAACCA
13291 TACAGAGTCA
Statistics
Matches: 238, Mismatches: 60, Indels: 40
0.70 0.18 0.12
Matches are distributed among these distances:
64 1 0.00
65 1 0.00
66 129 0.54
67 6 0.03
68 50 0.21
71 1 0.00
75 1 0.00
77 1 0.00
78 48 0.20
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (67 bp):
ATGAAATTTTAATAACTCACACTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCC
CC
Found at i:13235 original size:22 final size:22
Alignment explanation
Indices: 13139--13290 Score: 89
Period size: 22 Copynumber: 6.9 Consensus size: 22
13129 TAACCTGATT
*
13139 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
13161 CTAAGAAATTTTGATAACCTTCA
1 CTATGAAATTTTGATAACC-ACA
* * *
13184 -AATTAAATTTTTATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
* *
13206 -TATAAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
13227 CTATGAAATTTCGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * *
13248 CTCATGAAATTATAATAACCA-T
1 CT-ATGAAATTTTGATAACCACA
* *
13270 CTAATAAAATTTTGATTACCA
1 CT-ATGAAATTTTGATAACCA
13291 TACAGAGTCA
Statistics
Matches: 99, Mismatches: 24, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
20 1 0.01
21 4 0.04
22 91 0.92
23 2 0.02
24 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:16403 original size:6 final size:6
Alignment explanation
Indices: 16394--16441 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
16384 ATTTTGCTTT
* * *
16394 TACACA TACATA TACATA TACATA TACATA T-CATG T-CATA AACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
16440 TA
1 TA
16442 TCGTTCCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
5 7 0.19
6 29 0.81
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (6 bp):
TACATA
Found at i:17467 original size:17 final size:20
Alignment explanation
Indices: 17447--17486 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
17437 AACTATATTA
17447 TTTTGG-GAAA-AAAAAA-T
1 TTTTGGTGAAAGAAAAAAGT
17464 TTTTGGTGAAAGAAAAAAGT
1 TTTTGGTGAAAGAAAAAAGT
17484 TTT
1 TTT
17487 AAAAACAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 4 0.20
19 6 0.30
20 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (20 bp):
TTTTGGTGAAAGAAAAAAGT
Found at i:25146 original size:42 final size:42
Alignment explanation
Indices: 25087--25170 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
25077 GGTAAGTCTT
*
25087 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTATAAATTAAGAAATACTCAAATCAAATCATA
* *
25129 GAAAATTCTTTGTAAATTAAGAAATACTCAAATCAAATCATA
1 GAAAATTCTCTATAAATTAAGAAATACTCAAATCAAATCATA
25171 ATCCTTAGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTATAAATTAAGAAATACTCAAATCAAATCATA
Found at i:25496 original size:13 final size:13
Alignment explanation
Indices: 25478--25503 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25468 AACATTTAGT
25478 ATATATTTTCAGC
1 ATATATTTTCAGC
25491 ATATATTTTCAGC
1 ATATATTTTCAGC
25504 GAAAGAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
ATATATTTTCAGC
Done.