Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020173.1 Corchorus olitorius cultivar O-4 contig20206, 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: 63836
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:8752 original size:41 final size:41
Alignment explanation
Indices: 8682--8768 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
8672 GCCAACCCGG
*
8682 CAAGGCACAAAAGGAACAAGAGAGCCACACCAAGATAAGAGC
1 CAAGGCACAAAAGGAACAAGAGAGCCACACCAAG-CAAGAGC
* *
8724 CAAGGCACAAAAGG-CCAAGAGAGCCACACCATGCAAGAGC
1 CAAGGCACAAAAGGAACAAGAGAGCCACACCAAGCAAGAGC
8764 CAAGG
1 CAAGG
8769 TAAGACACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
40 11 0.26
41 17 0.40
42 14 0.33
ACGTcount: A:0.46, C:0.26, G:0.25, T:0.02
Consensus pattern (41 bp):
CAAGGCACAAAAGGAACAAGAGAGCCACACCAAGCAAGAGC
Found at i:13665 original size:106 final size:104
Alignment explanation
Indices: 13494--13754 Score: 380
Period size: 106 Copynumber: 2.5 Consensus size: 104
13484 AGTTTAGCCT
* *
13494 TAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATTTTTATTTTAAGGATAAATTTCAAAATT
1 TAATTTCACTAAGTTTAA-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
*
13559 AATAATTTATTGTTATAGGGTTTTATAAATAAAATACAAAAC
65 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* *
13601 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAACCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* * *
13666 ATAATGTTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* ** *
13705 TAA-TTCACTAAGTTTAACCTAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAACCCAAATTAAAATTTTATTTTTATTTTAAGGGT
13755 TAAAAAATTA
Statistics
Matches: 141, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
103 42 0.30
104 34 0.24
106 48 0.34
107 17 0.12
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAACCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:14609 original size:31 final size:29
Alignment explanation
Indices: 14574--14732 Score: 110
Period size: 31 Copynumber: 5.3 Consensus size: 29
14564 TGATGTCAAA
14574 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT--CAAACGTTAGG
* ** * **
14605 CCCTTGTTTG-GCCAAATT-AAAAGATCGGG
1 CCCTTATTTGAG-CATTTTCAAACG-TTAGG
14634 CCCTTATTTGAGCATTTTCAATAACGTTAGG
1 CCCTTATTTGAGCATTTTC-A-AACGTTAGG
** * *
14665 CCCTTATTTG-GCCAAATT-AAAAGATCAGG
1 CCCTTATTTGAG-CATTTTCAAACG-TTAGG
14694 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT--CAAACGTTAGG
14725 CCCTTATT
1 CCCTTATT
14733 AATACTTTTT
Statistics
Matches: 96, Mismatches: 20, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
28 7 0.07
29 35 0.36
30 4 0.04
31 43 0.45
32 7 0.07
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTCAAACGTTAGG
Found at i:14636 original size:29 final size:29
Alignment explanation
Indices: 14602--14703 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 29
14592 GGCAAACGTT
*
14602 AGGCCCTTGTTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
* ** *
14631 GGGCCCTTATTTGAG-CATTTTCAATAACG-TT
1 AGGCCCTTATTTG-GCCAAATT-AA-AA-GATC
14662 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
14691 AGGCCCTTATTTG
1 AGGCCCTTATTTG
14704 AGCATTTTGG
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
28 1 0.02
29 31 0.53
30 6 0.10
31 19 0.33
32 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:14646 original size:60 final size:60
Alignment explanation
Indices: 14574--14732 Score: 268
Period size: 60 Copynumber: 2.6 Consensus size: 60
14564 TGATGTCAAA
* *
14574 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTGTTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
14634 CCCTTATTTGAGCATTTT--CAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
1 CCCTTATTTGAGCATTTTGGC-A-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
14694 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATT
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATT
14733 AATACTTTTT
Statistics
Matches: 93, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 89 0.96
61 1 0.01
62 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
Found at i:15532 original size:21 final size:21
Alignment explanation
Indices: 15508--15555 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
15498 TGTAAAAACT
*
15508 TTTTTGGGAAGCTCATAAGCA
1 TTTTTAGGAAGCTCATAAGCA
* * *
15529 TTTTTAGTAAGCTTATAAGCC
1 TTTTTAGGAAGCTCATAAGCA
15550 TTTTTA
1 TTTTTA
15556 TTAGTAACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (21 bp):
TTTTTAGGAAGCTCATAAGCA
Found at i:16332 original size:13 final size:13
Alignment explanation
Indices: 16314--16340 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16304 CCATGCTATT
16314 TTTCAATAAAGTA
1 TTTCAATAAAGTA
16327 TTTCAATAAAGTA
1 TTTCAATAAAGTA
16340 T
1 T
16341 CGACTGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTCAATAAAGTA
Found at i:16846 original size:20 final size:20
Alignment explanation
Indices: 16823--16868 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
16813 TAACTTTTCC
*
16823 CAATTTTCTTTAAGATGATA
1 CAATTTTCTTTAAGAGGATA
*
16843 CAATTTTCTTTGAGAGGATA
1 CAATTTTCTTTAAGAGGATA
16863 CAATTT
1 CAATTT
16869 CAGATTACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (20 bp):
CAATTTTCTTTAAGAGGATA
Found at i:18070 original size:31 final size:31
Alignment explanation
Indices: 17970--18070 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
17960 AAGTACCTAA
* *
17970 TTAGTCCCTGTACTATAGAAAAAAGATCAAT
1 TTAGTCCCTCTACTATTGAAAAAAGATCAAT
* * ***
18001 TTAGTCCCT-TCATTA-TCAAATCTG-TCAAT
1 TTAGTCCCTCT-ACTATTGAAAAAAGATCAAT
*
18030 TTAGTCCCTCTACTATTGAAAAGAGATCAAT
1 TTAGTCCCTCTACTATTGAAAAAAGATCAAT
18061 TTAGTCCCTC
1 TTAGTCCCTC
18071 CGTGAAATGG
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
29 17 0.31
30 11 0.20
31 27 0.49
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (31 bp):
TTAGTCCCTCTACTATTGAAAAAAGATCAAT
Found at i:18921 original size:31 final size:31
Alignment explanation
Indices: 18886--18986 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
18876 CCATTTCACG
*
18886 GAGGGACTAAATTGATCTCTTTTCAATAGTA
1 GAGGGACTAAATTGATCTATTTTCAATAGTA
* * * * *
18917 GAGGGACTAAATTGA-CAAATTT-GATAATG
1 GAGGGACTAAATTGATCTATTTTCAATAGTA
* *
18946 GAGGGACTAAATTGATCTTTTTTCTATAGTA
1 GAGGGACTAAATTGATCTATTTTCAATAGTA
*
18977 CAGGGACTAA
1 GAGGGACTAA
18987 TCAGGTACTT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 19 0.35
30 8 0.15
31 28 0.51
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (31 bp):
GAGGGACTAAATTGATCTATTTTCAATAGTA
Found at i:20035 original size:3 final size:3
Alignment explanation
Indices: 20029--20060 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
20019 TCTCCTGTTG
20029 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20061 CACAATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:32233 original size:13 final size:13
Alignment explanation
Indices: 32215--32241 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32205 AGCAGAGCAC
32215 GGAGCATGTGTTA
1 GGAGCATGTGTTA
32228 GGAGCATGTGTTA
1 GGAGCATGTGTTA
32241 G
1 G
32242 AAGTCAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.41, T:0.30
Consensus pattern (13 bp):
GGAGCATGTGTTA
Found at i:37759 original size:22 final size:20
Alignment explanation
Indices: 37721--37762 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
37711 TCGCTCGGTC
*
37721 TCTACAAACAAATAATCACA
1 TCTACAAACAAACAATCACA
37741 TCTATCAAACCAAACAATCACA
1 TCTA-CAAA-CAAACAATCACA
37763 CACACACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (20 bp):
TCTACAAACAAACAATCACA
Found at i:38831 original size:25 final size:25
Alignment explanation
Indices: 38797--38844 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
38787 CAAACAATCA
38797 TGAGCACTCTCGCTCGGTCTCTATT
1 TGAGCACTCTCGCTCGGTCTCTATT
*
38822 TGAGCACTCTCGCTCGGTTTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
38845 CAAACCAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.31, G:0.21, T:0.35
Consensus pattern (25 bp):
TGAGCACTCTCGCTCGGTCTCTATT
Found at i:39551 original size:16 final size:17
Alignment explanation
Indices: 39521--39554 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39511 TAAGATAAGG
39521 TGTACATATAAATTATA
1 TGTACATATAAATTATA
*
39538 TGTA-ATATATATTATA
1 TGTACATATAAATTATA
39554 T
1 T
39555 ATTAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
TGTACATATAAATTATA
Found at i:41220 original size:16 final size:16
Alignment explanation
Indices: 41199--41230 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41189 CTTTAGAAGA
41199 AACTCATATAAACAAT
1 AACTCATATAAACAAT
41215 AACTCATATAAACAAT
1 AACTCATATAAACAAT
41231 CTGAGTGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (16 bp):
AACTCATATAAACAAT
Found at i:42888 original size:25 final size:25
Alignment explanation
Indices: 42854--42902 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
42844 CCCAACAATC
42854 TTGAGCACTCTCGCTCAGTCTCTAA
1 TTGAGCACTCTCGCTCAGTCTCTAA
*
42879 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCAGTCTCTA
42903 CAAACTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCAGTCTCTAA
Found at i:45099 original size:18 final size:18
Alignment explanation
Indices: 45076--45110 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
45066 ATGTCCAACA
*
45076 ATTCATTTTCTTCCTTCC
1 ATTCATGTTCTTCCTTCC
45094 ATTCATGTTCTTCCTTC
1 ATTCATGTTCTTCCTTC
45111 GAGGTTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.31, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTCATGTTCTTCCTTCC
Found at i:45554 original size:154 final size:159
Alignment explanation
Indices: 45333--45650 Score: 448
Period size: 159 Copynumber: 2.0 Consensus size: 159
45323 TTCAACTGTT
* **
45333 GAGGTATGCTAATTAAAAAGTTTTCCATATTTTTGCATCATTGCTTTTGGAAGATTTCTTTCTAA
1 GAGGTATGCTAATT-AAAAGTTTTACATATTTTTGCATCACAGCTTTTGGAAGATTTCTTTCTAA
* *
45398 TTCTTATATTTC-T-T-TAGGGAATACAATTTTTACTTAGCCACAAGAAGATTGAAGTGGATAAG
65 TTCTTATATTTCTTATATAGGGAATACAATTTTTACTTAGCCACAAGAAAATTGAAGTGGATAAA
* *
45460 CTTTCAATATTTTACAATTTGACCCTTTTG
130 CTTCCAATATTTTACAATTTGACCCATTTG
*
45490 GAGGTATGCTAATT-AAAGTTTTACATA-TTTTGCATCACAGCTTTTGGAAGTTTTCTTTCTAAT
1 GAGGTATGCTAATTAAAAGTTTTACATATTTTTGCATCACAGCTTTTGGAAGATTTCTTTCTAAT
* * * * * *
45553 TCTTGTATTTCTTTATAATAGGGTATACAATTTTTGCTTGGCCTCAAGAAAATTGAGGTGGATAA
66 TCTTATATTTC-TTAT-ATAGGGAATACAATTTTTACTTAGCCACAAGAAAATTGAAGTGGATAA
45618 ACTTCCAATATTTTACAATTTGACCCATTTG
129 ACTTCCAATATTTTACAATTTGACCCATTTG
45649 GA
1 GA
45651 ATTGGCAGTA
Statistics
Matches: 142, Mismatches: 14, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
154 43 0.30
155 12 0.08
156 1 0.01
157 15 0.11
159 71 0.50
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (159 bp):
GAGGTATGCTAATTAAAAGTTTTACATATTTTTGCATCACAGCTTTTGGAAGATTTCTTTCTAAT
TCTTATATTTCTTATATAGGGAATACAATTTTTACTTAGCCACAAGAAAATTGAAGTGGATAAAC
TTCCAATATTTTACAATTTGACCCATTTG
Found at i:47797 original size:78 final size:77
Alignment explanation
Indices: 47668--47841 Score: 215
Period size: 78 Copynumber: 2.2 Consensus size: 77
47658 TGATTTAAAC
* * * *
47668 TTTTATAGTTTTACTCAACTAAAAACTCTATATTCGTTTGATTAAATCTAATATCTTTATAACTA
1 TTTTATA-TTTTACTTAACTAAAAACTCTATATTCATTTAATTAAATCTAATATCTTTAAAACTA
*
47733 TTTTATTTTACCA
65 TTTTAGTTTACCA
* * *
47746 TTTTAGTATTTTACTTAATTAAAAACTCTAT-TGTTATTTAATTAAATCTAATATTTTTAAAACT
1 TTTTA-TATTTTACTTAACTAAAAACTCTATAT-TCATTTAATTAAATCTAATATCTTTAAAACT
*
47810 GTTTTAGTTTACCA
64 ATTTTAGTTTACCA
*
47824 TTTTACTATTTTAATTAA
1 TTTTA-TATTTTACTTAA
47842 AAAAATGATA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 1 0.01
78 80 0.96
79 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (77 bp):
TTTTATATTTTACTTAACTAAAAACTCTATATTCATTTAATTAAATCTAATATCTTTAAAACTAT
TTTAGTTTACCA
Found at i:49047 original size:17 final size:17
Alignment explanation
Indices: 49025--49057 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
49015 TCATTACATC
49025 AATTAA-AATTATAAATT
1 AATTAATAA-TATAAATT
49042 AATTAATAATATAAAT
1 AATTAATAATATAAAT
49058 ATCCATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAATAATATAAATT
Found at i:54735 original size:154 final size:155
Alignment explanation
Indices: 54432--54715 Score: 403
Period size: 154 Copynumber: 1.8 Consensus size: 155
54422 TTCAACTGTT
* *
54432 GAGGTATGCTAATTAAAGTTTTCGATATATTGCATATCATTGCTTTTGGAAGATTTCTTTCTAAT
1 GAGGTATGCTAATTAAAGTTTTCCATATATTGCA-ATCACTGCTTTTGGAAGATTTCTTTCTAAT
* * * *
54497 TCTTTTGTTTCTTTACGGAATACAATTTTTACTTAGCCACAAGAAGATTGAGGTCGATAAGCTTT
65 TCTTGTGTTTCTTTACGGAATACAATCTTTACTTAGCCACAAGAAAATTGAGGTCGATAAGATTT
54562 CAAAACCTTACAATTTGACCCTTTTG
130 CAAAACCTTACAATTTGACCCTTTTG
* * *
54588 GAGGTATGCTGATTAAAGTTTTCCATATTTTGC-ATCACTGCTTTTGGAAGTTTTCTTTCTAATT
1 GAGGTATGCTAATTAAAGTTTTCCATATATTGCAATCACTGCTTTTGGAAGATTTCTTTCTAATT
* * * * *
54652 CTTGTGTTTCTTTA-GCGTATACAATCTTTGCTTAGCCTCACGAAAATTGAGGTGGATAA-ATTT
66 CTTGTGTTTCTTTACG-GAATACAATCTTTACTTAGCCACAAGAAAATTGAGGTCGATAAGATTT
54715 C
130 C
54716 CAATATTCTA
Statistics
Matches: 113, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
153 5 0.04
154 78 0.69
156 30 0.27
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (155 bp):
GAGGTATGCTAATTAAAGTTTTCCATATATTGCAATCACTGCTTTTGGAAGATTTCTTTCTAATT
CTTGTGTTTCTTTACGGAATACAATCTTTACTTAGCCACAAGAAAATTGAGGTCGATAAGATTTC
AAAACCTTACAATTTGACCCTTTTG
Found at i:55303 original size:30 final size:27
Alignment explanation
Indices: 55218--55300 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
55208 GTTAATTTAG
55218 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
55245 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
*
55275 ACTTATTATTATAATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
55301 TTAGTGGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Found at i:58397 original size:6 final size:6
Alignment explanation
Indices: 58386--58469 Score: 145
Period size: 6 Copynumber: 14.2 Consensus size: 6
58376 GTATACTAAT
58386 ATACTA ATACTA ATACTA ATACTA ATACTA ATACT- ATACTA ATACTA
1 ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA
58433 ATACTA ATACTA ATACTA ATACTA ATA-TA TATACTA A
1 ATACTA ATACTA ATACTA ATACTA ATACTA -ATACTA A
58470 ATAGTATTAG
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
5 7 0.09
6 66 0.88
7 2 0.03
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
ATACTA
Done.