Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019447.1 Corchorus olitorius cultivar O-4 contig19480, 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: 18784
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:134 original size:2 final size:2
Alignment explanation
Indices: 127--170 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
117 CCCACCACAC
127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
169 TA
1 TA
171 AAACTACTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1381 original size:27 final size:26
Alignment explanation
Indices: 1326--1387 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
1316 TCTAAATTTC
*
1326 TATTATTTTAATAATTCAATAATTAAAA
1 TATTA-TTTAATAATGCAAT-ATTAAAA
1354 TATTATTTAATAATGGCAAT-TTAGAAA
1 TATTATTTAATAAT-GCAATATTA-AAA
1381 TA-TATTT
1 TATTATTT
1388 GAAAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 8 0.26
27 14 0.45
28 9 0.29
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (26 bp):
TATTATTTAATAATGCAATATTAAAA
Found at i:2194 original size:15 final size:15
Alignment explanation
Indices: 2174--2203 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2164 TTTGTATCCC
*
2174 AAATTGGTCTTTCCT
1 AAATTGGTCTCTCCT
2189 AAATTGGTCTCTCCT
1 AAATTGGTCTCTCCT
2204 CAACGTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.43
Consensus pattern (15 bp):
AAATTGGTCTCTCCT
Found at i:2772 original size:22 final size:23
Alignment explanation
Indices: 2747--2801 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
2737 ATTACACTAT
*
2747 TTTTGATGACCTTCTTAT-AAAA
1 TTTTGATAACCTTCTTATGAAAA
2769 TTTTGATAACCTTCTTATGAAAA
1 TTTTGATAACCTTCTTATGAAAA
*
2792 TTTTAATAAC
1 TTTTGATAAC
2802 GATACTACGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (23 bp):
TTTTGATAACCTTCTTATGAAAA
Found at i:2800 original size:23 final size:22
Alignment explanation
Indices: 2755--2801 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
2745 ATTTTTGATG
*
2755 ACCTTCTTATAAAATTTTGATA
1 ACCTTCTTATAAAATTTTAATA
2777 ACCTTCTTATGAAAATTTTAATA
1 ACCTTCTTAT-AAAATTTTAATA
2800 AC
1 AC
2802 GATACTACGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (22 bp):
ACCTTCTTATAAAATTTTAATA
Found at i:3036 original size:20 final size:21
Alignment explanation
Indices: 2985--3037 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
2975 CCTCCATATG
* *
2985 AATTGTTAGTAATCACACTCTGG
1 AATTGTGA-TAATCACAC-CTGA
*
3008 AATTTTGATAATCACA-CTGA
1 AATTGTGATAATCACACCTGA
3028 AATTGTGATA
1 AATTGTGATA
3038 GCCTCGCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.46
22 8 0.31
23 6 0.23
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (21 bp):
AATTGTGATAATCACACCTGA
Found at i:3076 original size:23 final size:23
Alignment explanation
Indices: 3049--3111 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
3039 CCTCGCTATG
* *
3049 AAATTTTGATAAATCTTCCAATA
1 AAATTTTGATAAACCTCCCAATA
*
3072 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCAATA
3095 AAATTTTGAT-AACCTCC
1 AAATTTTGATAAACCTCC
3112 TTATGAAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 7 0.19
23 30 0.81
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCAATA
Found at i:3111 original size:22 final size:22
Alignment explanation
Indices: 2848--3290 Score: 195
Period size: 22 Copynumber: 20.5 Consensus size: 22
2838 TTTTTAAATT
* *
2848 TATGAAATTTTGTTAACCTCTC
1 TATGAAATTTTGATAACCTCCC
* *
2870 TGA-GGAATTTTGA-AGACCTCGC
1 T-ATGAAATTTTGATA-ACCTCCC
*
2892 TATGAAATTTTGATAA-CTAACAC
1 TATGAAATTTTGATAACCT--CCC
* * *
2915 TATGAGATGTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * * **
2937 TATGATATATTGATAACCACAT
1 TATGAAATTTTGATAACCTCCC
* ** * *
2959 TATGAAAATTAAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * *
2981 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAACCTCCC
* * *
3003 TCTGGAATTTTGATAA--TCAC
1 TATGAAATTTTGATAACCTCCC
* * *
3023 -ACTGAAATTGTGATAGCCTCGC
1 TA-TGAAATTTTGATAACCTCCC
* *
3045 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTCCC
* *
3068 AATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCC
* *
3091 TATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCTCCC
*
3113 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTCCC
*
3130 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
** **
3151 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCC
* *
3173 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCC
* * *
3195 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCCC
*
3217 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CC
* **
3239 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CCC
* *
3261 TAAGAAATTTTGATATCCTCCC
1 TATGAAATTTTGATAACCTCCC
3283 --TGAAATTT
1 TATGAAATTT
3291 GATTACTCCA
Statistics
Matches: 310, Mismatches: 83, Indels: 58
0.69 0.18 0.13
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
20 21 0.07
21 16 0.05
22 193 0.62
23 65 0.21
24 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:3221 original size:44 final size:43
Alignment explanation
Indices: 2848--3994 Score: 229
Period size: 44 Copynumber: 26.7 Consensus size: 43
2838 TTTTTAAATT
* * * * *
2848 TATGAAATTTTGTTAACCTCTCTGA-GGAATTTTGA-AGACCTCGC
1 TATGAAATTTTGATAACATCACT-ATGAAATTTTGATA-A-CTCCC
* * * *
2892 TATGAAATTTTGATAACTAACACTATGAGATGTTGATAACCTCCA
1 TATGAAATTTTGATAAC-ATCACTATGAAATTTTGATAA-CTCCC
* * * * ** * *
2937 TATGATATATTGATAACCA-CATTATGAAAATTAAAAAACCTCCA
1 TATGAAATTTTGATAA-CATCACTATGAAATTTTGATAA-CTCCC
* * *
2981 TATG-AATTGTT-AGTAATCA-CACTCTGGAATTTTGATAA-TCAC
1 TATGAAATT-TTGA-TAA-CATCACTATGAAATTTTGATAACTCCC
* * * * *
3023 -ACTGAAATTGTGATAGCCTCGCTATGAAATTTTGATAAATCTTCC
1 TA-TGAAATTTTGATAACATCACTATGAAATTTTGAT-AA-CTCCC
* * * * * *
3068 AATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGAT-AACATCACTATGAAATTTTGATAA-CTCCC
*
3113 TATGAAATCTTGATAAC-T-AC----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACATCACTATGAAATTTTGATAA-CTCCC
** * * *
3151 TATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACATCACTATGAAATTTTGATAA-CTCCC
*
3195 TATGAAATTTTGATCTACAT-ACTATGAAATTTTGATAAC-CCTC
1 TATGAAATTTTGAT-AACATCACTATGAAATTTTGATAACTCC-C
* * * *
3238 TTATGAAATTTTGAAAAC-TAAACTAAGAAATTTTGATATCCTCCC
1 -TATGAAATTTTGATAACAT-CACTATGAAATTTTGATA-ACTCCC
* * * * *
3283 --TGAAA-TTTGATTAC-TC-CATAATAAAAGTTTAATAAC-CTTC
1 TATGAAATTTTGATAACATCAC-T-ATGAAATTTTGATAACTC-CC
*
3323 T-T--AA-TTTGGTAACCAT-ACTATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAA-CATCACTATGAAATTTTGATAA-CTCCC
* * *
3363 CA-G-AA-----AT-AC--CACTATGAAATTTTGGTAA-TCACAT
1 TATGAAATTTTGATAACATCACTATGAAATTTTGATAACTC-C-C
* * ** *
3397 TTTGAAAATTTGATAACCAT-TTTATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAA-CATCACTATGAAATTTTGATAA-CTCCC
* * * ** * *
3441 TAT-AAAATTTGTTGACCCCTCTATGAAATTTTGATAA-TCACAT
1 TATGAAATTTTGATAACATCACTATGAAATTTTGATAACTC-C-C
* * * *
3484 TATGTAATTTTGATAACAACACTATGAAATTTTGATAATTTTCC
1 TATGAAATTTTGATAACATCACTATGAAATTTTGATAA-CTCCC
* *
3528 TAT-AAATTTTGATAATCCGATCTCTATGAAATTTCGATAA-TCACTC
1 TATGAAATTTTGATAA--C-ATCACTATGAAATTTTGATAACTC-C-C
* * * * * *
3574 TATGAGA-TTTGATAACCT-TCTATCAAATTTTGGT-ACTCCT
1 TATGAAATTTTGATAACATCACTATGAAATTTTGATAACTCCC
* * *
3614 TATGAAATTGAGACTTTTATAACCTTCA-TATGAAATTTTGATAAC-CACAA
1 TATGAAA-T-----TTTGATAA-CATCACTATGAAATTTTGATAACTC-C-C
**
3664 TAAAAAATTTTGATAACCA-CACTATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAA-CATCACTATGAAATTTTGATAAC-TCCC
* * * * *
3708 CATGAAATATT-AGTAACCTC-CTTATGAAATTTTGTTAACTACAC
1 TATGAAATTTTGA-TAACATCAC-TATGAAATTTTGATAACT-CCC
* * **
3752 TATGAAATTCTTG-TAACCTCGCTATGGCATTTTGATAA-T--C
1 TATGAAATT-TTGATAACATCACTATGAAATTTTGATAACTCCC
* * * * *
3792 --T----CTTTGATAACCTTTA-TATAAAATTGTGATAAC-CACAC
1 TATGAAATTTTGATAA-CATCACTATGAAATTTTGATAACTC-C-C
** * * * * *
3830 TATGAAATTTCAATAACCTTC-CTAAGAAGTTTTAATAACCTGATCC
1 TATGAAATTTTGATAA-CATCACTATGAAATTTTGATAA-CT--CCC
* *
3876 TATGAAATTTTGATAACCA-CATTATGAAATTTTGATAGCCTTCCC
1 TATGAAATTTTGATAA-CATCACTATGAAATTTTGATA-AC-TCCC
* *
3921 -ATGAAATTTTGATAACTTC-CATATGAAATTTTGGTAAC-CACAC
1 TATGAAATTTTGATAACATCAC-TATGAAATTTTGATAACTC-C-C
* *
3964 TATGGAATTTTGATAACCTC-CTCATGAAATT
1 TATGAAATTTTGATAACATCACT-ATGAAATT
3995 ATAATAACCA
Statistics
Matches: 808, Mismatches: 178, Indels: 234
0.66 0.15 0.19
Matches are distributed among these distances:
32 2 0.00
33 4 0.00
34 33 0.04
35 4 0.00
36 3 0.00
37 1 0.00
38 33 0.04
39 23 0.03
40 16 0.02
41 33 0.04
42 48 0.06
43 69 0.09
44 342 0.42
45 74 0.09
46 88 0.11
47 11 0.01
48 15 0.02
49 4 0.00
50 5 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (43 bp):
TATGAAATTTTGATAACATCACTATGAAATTTTGATAACTCCC
Found at i:3448 original size:22 final size:22
Alignment explanation
Indices: 3399--3794 Score: 183
Period size: 22 Copynumber: 17.9 Consensus size: 22
3389 AATCACATTT
* *
3399 TGAAAATTTGATAACCAT-TTTA
1 TGAAATTTTGATAACC-TCTCTA
3421 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
3443 T-AAAATTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
3464 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* ** *
3486 TGTAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
3508 TGAAATTTTGATAA-TTTTCCTA
1 TGAAATTTTGATAACCTCT-CTA
3530 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * *
3554 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
3576 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* *
3596 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
*
3616 TGAAATTGAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* **
3644 TGAAATTTTGATAACCACAATA
1 TGAAATTTTGATAACCTCTCTA
** * *
3666 AAAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* * *
3688 TGAAATTTTGATAACTTCCCCA
1 TGAAATTTTGATAACCTCTCTA
*
3710 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* *
3732 TGAAATTTTGTTAA-CTACACTA
1 TGAAATTTTGATAACCT-CTCTA
*
3754 TGAAATTCTTG-TAACCTCGCTA
1 TGAAATT-TTGATAACCTCTCTA
** *
3776 TGGCATTTTGATAATCTCT
1 TGAAATTTTGATAACCTCT
3795 TTGATAACCT
Statistics
Matches: 284, Mismatches: 59, Indels: 62
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 51 0.18
22 175 0.62
23 7 0.02
24 5 0.02
25 13 0.05
26 4 0.01
27 2 0.01
28 10 0.04
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:3531 original size:87 final size:89
Alignment explanation
Indices: 3374--3589 Score: 226
Period size: 87 Copynumber: 2.4 Consensus size: 89
3364 AGAAATACCA
* * * ***
3374 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCATTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACAACACTATGAAATTTTGATAACCTC
* *
3439 TCTATAAAATTTGTTGA-CC-CCT
66 TCTATAAAATTTGATAATCCACCT
* * * *
3461 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACAACACTATGAAATTTTGATAA-TTT
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACAACACTATGAAATTTTGATAACCTC
* *
3525 TCCTATAAATTTTGATAATCCGATCT
66 T-CTATAAAATTTGATAATCC-ACCT
* *
3551 CTATGAAATTTCGATAATCAC-TCTATG-AGATTTGATAAC
1 CTATGAAATTTTGATAATCACAT-TATGAAAATTTGATAAC
3590 CTTCTATCAA
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
86 2 0.02
87 66 0.62
88 2 0.02
89 11 0.10
90 26 0.24
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (89 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACAACACTATGAAATTTTGATAACCTC
TCTATAAAATTTGATAATCCACCT
Found at i:3837 original size:22 final size:21
Alignment explanation
Indices: 3812--4027 Score: 153
Period size: 22 Copynumber: 9.8 Consensus size: 21
3802 CCTTTATATA
*
3812 AAATTGTGATAACCACACTATG
1 AAATTTTGATAACCAC-CTATG
** * *
3834 AAATTTCAATAACCTTCCTAAG
1 AAATTTTGATAACC-ACCTATG
* *
3856 AAGTTTTAATAACCTGATCCTATG
1 AAATTTTGATAACC--A-CCTATG
*
3880 AAATTTTGATAACCACATTATG
1 AAATTTTGATAACCAC-CTATG
* * *
3902 AAATTTTGATAGCCTTCCCATG
1 AAATTTTGATAACC-ACCTATG
**
3924 AAATTTTGATAACTTCCATATG
1 AAATTTTGATAACCACC-TATG
*
3946 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCAC-CTATG
* *
3968 GAATTTTGATAACCTCCTCATG
1 AAATTTTGATAACCACCT-ATG
* * * *
3990 AAATTATAATAACCATCTTATA
1 AAATTTTGATAACCA-CCTATG
4012 AAATTTTGATAACCAC
1 AAATTTTGATAACCAC
4028 ACAGAGACAA
Statistics
Matches: 151, Mismatches: 34, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
21 7 0.05
22 122 0.81
23 5 0.03
24 17 0.11
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.35
Consensus pattern (21 bp):
AAATTTTGATAACCACCTATG
Found at i:3973 original size:66 final size:66
Alignment explanation
Indices: 3798--4029 Score: 252
Period size: 66 Copynumber: 3.5 Consensus size: 66
3788 AATCTCTTTG
* * ** * * *
3798 ATAACCTTTATATAAAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAGAAGTTTT
1 ATAACCTTCATATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTT
3863 A
66 A
* * * *
3864 ATAACCTGATCCTATGAAATTTTGATAACCACATTATGAAATTTTGATAGCCTTCCCATGAAATT
1 ATAACCT--TCATATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
*
3929 TTG
64 TTA
* * *
3932 ATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATT
1 ATAACCTT-CATATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATT
*
3995 ATA
64 TTA
* *
3998 ATAACCATCTTATAAAATTTTGATAACCACAC
1 ATAACCTTCATATAAAATTTTGATAACCACAC
4030 AGAGACAAGA
Statistics
Matches: 138, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
65 4 0.03
66 79 0.57
67 4 0.03
68 51 0.37
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (66 bp):
ATAACCTTCATATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTT
A
Found at i:4230 original size:20 final size:20
Alignment explanation
Indices: 4192--4230 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4182 TATTGACATT
4192 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
4212 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
4231 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:10133 original size:14 final size:14
Alignment explanation
Indices: 10114--10151 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
10104 GAAATTTAAT
10114 AATAATTATTCAAA
1 AATAATTATTCAAA
10128 AATAATTATTCAAA
1 AATAATTATTCAAA
10142 AATAATTATT
1 AATAATTATT
10152 ATTTAATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAATTATTCAAA
Found at i:11293 original size:20 final size:21
Alignment explanation
Indices: 11270--11308 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11260 AAATTGATTA
*
11270 AATTAGCCA-AAAATTAAGGG
1 AATTAACCATAAAATTAAGGG
*
11290 AATTAATCATAAAATTAAG
1 AATTAACCATAAAATTAAG
11309 TCCTAATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (21 bp):
AATTAACCATAAAATTAAGGG
Found at i:13384 original size:15 final size:16
Alignment explanation
Indices: 13364--13402 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
13354 AATAAAAATA
13364 TTTTGTTTTATTTTT-
1 TTTTGTTTTATTTTTG
*
13379 TTTTGTTTTGTTTTTG
1 TTTTGTTTTATTTTTG
13395 TTTT-TTTT
1 TTTTGTTTT
13403 TTCAAAAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (16 bp):
TTTTGTTTTATTTTTG
Found at i:13389 original size:20 final size:20
Alignment explanation
Indices: 13364--13402 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
13354 AATAAAAATA
13364 TTTTGTTTTAT-TTTTTTTTG
1 TTTTGTTTT-TGTTTTTTTTG
13384 TTTTGTTTTTGTTTTTTTT
1 TTTTGTTTTTGTTTTTTTT
13403 TTCAAAAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (20 bp):
TTTTGTTTTTGTTTTTTTTG
Found at i:13404 original size:11 final size:11
Alignment explanation
Indices: 13374--13404 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
13364 TTTTGTTTTA
13374 TTTTTTTTTGT
1 TTTTTTTTTGT
*
13385 TTTGTTTTTGT
1 TTTTTTTTTGT
13396 TTTTTTTTT
1 TTTTTTTTT
13405 CAAAAGCCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTGT
Done.