Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017649.1 Corchorus olitorius cultivar O-4 contig17682, 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: 66416
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:635 original size:36 final size:36
Alignment explanation
Indices: 588--657 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 36
578 GAGATTTTGG
588 AGAAATATGATAAT-CAAAATTACAAAAAATGTAATA
1 AGAAATATGAT-ATCCAAAATTACAAAAAATGTAATA
624 AGAAATATGATATCCAAAATTACAAAAAATGTAA
1 AGAAATATGATATCCAAAATTACAAAAAATGTAA
658 GGTTACTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (36 bp):
AGAAATATGATATCCAAAATTACAAAAAATGTAATA
Found at i:1405 original size:182 final size:182
Alignment explanation
Indices: 1098--1445 Score: 615
Period size: 182 Copynumber: 1.9 Consensus size: 182
1088 TTACTAATGT
*
1098 TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTTTAGTAGATTAC
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTAC
*
1163 TCAAGTAATTAAATTGGTAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
66 TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
1228 AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCGAAAAAAAAAA
131 AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCGAAAAAAAAAA
* * *
1280 TATTAAGAATGTAAGGATTGGTAAATACAATTTTAATAACTTTTTTAGCTTTTATAGTAGATTAC
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTAC
* * *
1345 TTAAGTAATTAAATTGGCAACTTTCATTATTGATCATACAAAGTTACTAAAATTAATAAGGATGT
66 TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
*
1410 AAGATTATTTGAATCTAGATAGTACTATAATGTTTT
131 AAGATTACTTGAATCTAGATAGTACTATAATGTTTT
1446 CATAACTTTT
Statistics
Matches: 157, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 157 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (182 bp):
TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTAC
TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCGAAAAAAAAAA
Found at i:3172 original size:95 final size:95
Alignment explanation
Indices: 3067--3248 Score: 328
Period size: 95 Copynumber: 1.9 Consensus size: 95
3057 AAATTGATAA
*
3067 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTAATTAATATTTAACTTCGTTCTTAGTAGCC
1 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTAATTAATATTTAACTTCGTTCTTAATAGCC
3132 CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
66 CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
* *
3162 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCC
1 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTAATTAATATTTAACTTCGTTCTTAATAGCC
*
3227 CTGTAGTTTTTTTAGTAAATTC
66 CTGTAGTTCTTTTAGTAAATTC
3249 AAATAAGAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 83 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (95 bp):
TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTAATTAATATTTAACTTCGTTCTTAATAGCC
CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
Found at i:3578 original size:30 final size:30
Alignment explanation
Indices: 3544--3618 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
3534 TGCCATAGTG
*
3544 AATAGTAAGACAGATTTCGGCCAAAAAAAA
1 AATAGTAAGACAGATTCCGGCCAAAAAAAA
*
3574 AATAGTAATACAGATTCCGGCCAAAAAAAA
1 AATAGTAAGACAGATTCCGGCCAAAAAAAA
3604 AATAGTAAGACAGAT
1 AATAGTAAGACAGAT
3619 GGTTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.17
Consensus pattern (30 bp):
AATAGTAAGACAGATTCCGGCCAAAAAAAA
Found at i:4164 original size:22 final size:24
Alignment explanation
Indices: 4129--4182 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
4119 ATAAATGTTG
* *
4129 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
4151 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
4174 CTTGATAAT
1 C-TGATAAT
4183 ATCTAGCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:9927 original size:78 final size:78
Alignment explanation
Indices: 9836--10004 Score: 286
Period size: 78 Copynumber: 2.2 Consensus size: 78
9826 TTGTTTAAAC
* *
9836 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATATTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATACTTATAAAT
9900 ATTTTATTTTACCA
65 ATTTTATTTTACCA
* *
9914 TTTTACTATTTTACTCAACTAAAAACTCTTTTTTTATTTAATTAAATCTAATATCCTTATAAATA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATACTTATAAATA
9979 TTTTATTTTACCA
66 TTTTATTTTACCA
9992 TTTTACTATTTTA
1 TTTTACTATTTTA
10005 ATTTAAATAC
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
78 84 0.98
79 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.53
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATACTTATAAATA
TTTTATTTTACCA
Found at i:11438 original size:22 final size:22
Alignment explanation
Indices: 11397--11438 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11387 GTTTCTAATA
* * *
11397 TTCTTGGGTCATTTGCGTTAAC
1 TTCTCGGGTCATTCGAGTTAAC
11419 TTCTCGGGTCATTCGAGTTA
1 TTCTCGGGTCATTCGAGTTA
11439 TGTGTTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (22 bp):
TTCTCGGGTCATTCGAGTTAAC
Found at i:11934 original size:31 final size:31
Alignment explanation
Indices: 11896--12003 Score: 125
Period size: 31 Copynumber: 3.5 Consensus size: 31
11886 TTAGACTAAT
11896 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * ***
11927 TGCTCAAATAAGGGCCTGATC-TTT--TATTT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAAAA
11956 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
11987 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
12004 GGCGTCGAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
28 2 0.03
29 18 0.30
30 4 0.07
31 35 0.57
32 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:12083 original size:31 final size:31
Alignment explanation
Indices: 12045--12145 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
12035 TGACGCCAGA
12045 CCCTTATTTGAGCATTTTTTATAACGTTAGG
1 CCCTTATTTGAGCATTTTTTATAACGTTAGG
** * * *
12076 CCCTTATTTG-GCCA--AATTA-AAAGATCGG
1 CCCTTATTTGAG-CATTTTTTATAACGTTAGG
**
12104 ACCCTTATTTGAGCATTTTCGATAACGTTAGG
1 -CCCTTATTTGAGCATTTTTTATAACGTTAGG
12136 CCCTTATTTG
1 CCCTTATTTG
12146 GCCAAATTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 6 0.12
29 15 0.29
30 2 0.04
31 23 0.44
32 6 0.12
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.39
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTTTATAACGTTAGG
Found at i:12136 original size:60 final size:60
Alignment explanation
Indices: 12043--12204 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
12033 ACTGACGCCA
**
12043 GACCCTTATTTGAGCATTTTTTATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
12103 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* * *
12163 G-CCCTTATTTGAGCATTTTGGCA-AATGTTAGACCCTTATTTG
1 GACCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
12205 AGCAATTAGC
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
59 36 0.38
60 60 0.62
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (60 bp):
GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:12171 original size:28 final size:28
Alignment explanation
Indices: 12074--12173 Score: 103
Period size: 28 Copynumber: 3.4 Consensus size: 28
12064 TATAACGTTA
12074 GGCCCTTATTTGGCCAAATTAAAAGATC
1 GGCCCTTATTTGGCCAAATTAAAAGATC
** * * *
12102 GGACCCTTATTTGAG-CATTTTCGATAACGTTA
1 GG-CCCTTATTTG-GCCAAATT--A-AAAGATC
12134 GGCCCTTATTTGGCCAAATTAAAAGATC
1 GGCCCTTATTTGGCCAAATTAAAAGATC
12162 GGCCCTTATTTG
1 GGCCCTTATTTG
12174 AGCATTTTGG
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 18 0.32
29 15 0.27
30 2 0.04
31 15 0.27
32 6 0.11
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (28 bp):
GGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:14684 original size:18 final size:19
Alignment explanation
Indices: 14648--14687 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
14638 CTGGGAAGTC
14648 AACATATATAGCAAAGAACA
1 AACATATATA-CAAAGAACA
*
14668 AACATATATA-AAGGAACA
1 AACATATATACAAAGAACA
14686 AA
1 AA
14688 ACAAAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (19 bp):
AACATATATACAAAGAACA
Found at i:15769 original size:31 final size:31
Alignment explanation
Indices: 15727--15903 Score: 219
Period size: 31 Copynumber: 5.7 Consensus size: 31
15717 GGTGTCCGAC
* * *
15727 GTGGCATGCCACGTGTACCAAAAAGTGAAAT
1 GTGGCACGCCACGTGTACAAAAAAGTGACAT
15758 GTGGCACGCCACGTGTACAAAAAAGTGACAT
1 GTGGCACGCCACGTGTACAAAAAAGTGACAT
15789 GTGGCACGCCACGTGTACAAAAAAGTGACAT
1 GTGGCACGCCACGTGTACAAAAAAGTGACAT
*
15820 GTGGCACGCCACGTGTACAAAAAAGTGACAC
1 GTGGCACGCCACGTGTACAAAAAAGTGACAT
** * * * * *
15851 GTATCATGCTATGTGTACCAAAAAGTGACAC
1 GTGGCACGCCACGTGTACAAAAAAGTGACAT
* * * *
15882 ATGGCATGCTACGTGCACAAAA
1 GTGGCACGCCACGTGTACAAAA
15904 GGATACGTGC
Statistics
Matches: 130, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 130 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (31 bp):
GTGGCACGCCACGTGTACAAAAAAGTGACAT
Found at i:15824 original size:62 final size:62
Alignment explanation
Indices: 15725--15903 Score: 241
Period size: 62 Copynumber: 2.9 Consensus size: 62
15715 ATGGTGTCCG
*
15725 ACGTGGCATGCCACGTGTACCAAAAAGTGAAATGTGGCACGCCACGTGTACAAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGACATGTGGCACGCCACGTGTACAAAAAAGTGAC
* * *
15787 ATGTGGCACGCCACGTGTACAAAAAAGTGACATGTGGCACGCCACGTGTACAAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGACATGTGGCACGCCACGTGTACAAAAAAGTGAC
** * * ** * * *
15849 ACGTATCATGCTATGTGTACCAAAAAGTGACACATGGCATGCTACGTGCACAAAA
1 ACGTGGCATGCCACGTGTACCAAAAAGTGACATGTGGCACGCCACGTGTACAAAA
15904 GGATACGTGC
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 101 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (62 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGACATGTGGCACGCCACGTGTACAAAAAAGTGAC
Found at i:18476 original size:28 final size:27
Alignment explanation
Indices: 18434--18488 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
18424 TTTTTATTTG
*
18434 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
18460 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
18489 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Found at i:19584 original size:21 final size:22
Alignment explanation
Indices: 19558--19600 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19548 CAAAAAGTAT
*
19558 TTTCC-TAAATAAATTAAATTC
1 TTTCCTTAAAAAAATTAAATTC
19579 TTTCCTTAAAAAAATTAAATTC
1 TTTCCTTAAAAAAATTAAATTC
19601 ATGCTTGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTCCTTAAAAAAATTAAATTC
Found at i:19739 original size:13 final size:13
Alignment explanation
Indices: 19710--19748 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
19700 TGAAAAAACT
*
19710 TGCTTTGGAAGAAG
1 TGCTTTTGAA-AAG
19724 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
19737 TGCTTTTTAAAA
1 TGCTTTTGAAAA
19749 TTGGGGTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:20806 original size:27 final size:27
Alignment explanation
Indices: 20776--20828 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
20766 GAAGTTACGT
20776 TTAAGGTAGAGATGGGAGAAGAATAGC
1 TTAAGGTAGAGATGGGAGAAGAATAGC
* *
20803 TTAAGGTCGAGATGGGAGAGGAATAG
1 TTAAGGTAGAGATGGGAGAAGAATAG
20829 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.40, T:0.19
Consensus pattern (27 bp):
TTAAGGTAGAGATGGGAGAAGAATAGC
Found at i:26815 original size:2 final size:2
Alignment explanation
Indices: 26808--26841 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
26798 GTATACATAA
26808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26842 CACAAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29086 original size:40 final size:41
Alignment explanation
Indices: 29010--29101 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 41
29000 TTCCCCATTG
29010 TTAAAGGATATTTAAGAATATATTATTTAAAGGATTTATCT
1 TTAAAGGATATTTAAGAATATATTATTTAAAGGATTTATCT
* * * *
29051 TTGAAGGATATTTAA-AATGTATTTTTTAAAGGATTTATTT
1 TTAAAGGATATTTAAGAATATATTATTTAAAGGATTTATCT
29091 TTAAAGGATAT
1 TTAAAGGATAT
29102 ATTATGATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 32 0.70
41 14 0.30
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (41 bp):
TTAAAGGATATTTAAGAATATATTATTTAAAGGATTTATCT
Found at i:29093 original size:15 final size:15
Alignment explanation
Indices: 29027--29104 Score: 58
Period size: 15 Copynumber: 5.5 Consensus size: 15
29017 ATATTTAAGA
29027 ATATATTATTTAAAGG
1 ATATATT-TTTAAAGG
* * *
29043 ATTTATCTTTGAAGG
1 ATATATTTTTAAAGG
* *
29058 --ATA-TTTAAAATG
1 ATATATTTTTAAAGG
29070 -TAT-TTTTTAAAGG
1 ATATATTTTTAAAGG
*
29083 ATTTATTTTTAAAGG
1 ATATATTTTTAAAGG
29098 ATATATT
1 ATATATT
29105 ATGATGATAT
Statistics
Matches: 46, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
12 5 0.11
13 11 0.24
14 2 0.04
15 23 0.50
16 5 0.11
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (15 bp):
ATATATTTTTAAAGG
Found at i:29835 original size:22 final size:22
Alignment explanation
Indices: 29808--29850 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29798 GGAAACACAG
**
29808 GACAAGACCTGGGCAGGAGTTA
1 GACAAGACCTGCCCAGGAGTTA
*
29830 GACAAGTCCTGCCCAGGAGTT
1 GACAAGACCTGCCCAGGAGTT
29851 GTTGCGGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.33, T:0.16
Consensus pattern (22 bp):
GACAAGACCTGCCCAGGAGTTA
Found at i:42094 original size:26 final size:26
Alignment explanation
Indices: 42065--42122 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
42055 ATTGCATTTT
*
42065 GAAAATAAGAACAGTATTAGTATTAA
1 GAAAATAAGAACAATATTAGTATTAA
42091 GAAAATAAGAACAATATTAGTATTAA
1 GAAAATAAGAACAATATTAGTATTAA
42117 GAAAAT
1 GAAAAT
42123 GAGGCTTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.57, C:0.03, G:0.14, T:0.26
Consensus pattern (26 bp):
GAAAATAAGAACAATATTAGTATTAA
Found at i:43854 original size:17 final size:17
Alignment explanation
Indices: 43822--43855 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43812 ATTAAAGCAG
*
43822 AAATCAAAAGAAAAAGA
1 AAATCAAAACAAAAAGA
*
43839 AAATCAAAACAGAAAGA
1 AAATCAAAACAAAAAGA
43856 GACCCATACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
AAATCAAAACAAAAAGA
Found at i:47525 original size:19 final size:18
Alignment explanation
Indices: 47488--47527 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
47478 TCCTTGAAAT
47488 AATTCTTCATTGATCTTC
1 AATTCTTCATTGATCTTC
47506 AATTCTTCAAATTG-TCTTC
1 AATTCTTC--ATTGATCTTC
47525 AAT
1 AAT
47528 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (18 bp):
AATTCTTCATTGATCTTC
Found at i:56135 original size:21 final size:21
Alignment explanation
Indices: 56109--56148 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56099 CAACAAAAAG
* *
56109 GGAGATGCTTCCTTCCTCCTA
1 GGAGATGCCTCCTACCTCCTA
56130 GGAGATGCCTCCTACCTCC
1 GGAGATGCCTCCTACCTCC
56149 CAAGAGGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.38, G:0.20, T:0.28
Consensus pattern (21 bp):
GGAGATGCCTCCTACCTCCTA
Found at i:57359 original size:44 final size:45
Alignment explanation
Indices: 57279--57377 Score: 182
Period size: 44 Copynumber: 2.2 Consensus size: 45
57269 AAGTGGTAGA
*
57279 TGAGGAAATTACGCTCGGGGGGCAACTTTCTAACCACTCTGACTC
1 TGAGGAAGTTACGCTCGGGGGGCAACTTTCTAACCACTCTGACTC
57324 TGAGGAAGTTACGCTC-GGGGGCAACTTTCTAACCACTCTGACTC
1 TGAGGAAGTTACGCTCGGGGGGCAACTTTCTAACCACTCTGACTC
57368 TGAGGAAGTT
1 TGAGGAAGTT
57378 GACGACTCCA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 38 0.72
45 15 0.28
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.25
Consensus pattern (45 bp):
TGAGGAAGTTACGCTCGGGGGGCAACTTTCTAACCACTCTGACTC
Found at i:58788 original size:51 final size:51
Alignment explanation
Indices: 58704--58806 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
58694 TTCATATTTT
* * ** *
58704 TCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGTTTCTC
1 TCTTGTTCAAATCTTGTCTCAGGACACAAAAACACTCTATTAGTGTTTCTC
* * * *
58755 TCTTGTTCAAATCTTGTCTCCGGACATAAAAACACTGTATTCGTGTTTCTC
1 TCTTGTTCAAATCTTGTCTCAGGACACAAAAACACTCTATTAGTGTTTCTC
58806 T
1 T
58807 TTCATAAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (51 bp):
TCTTGTTCAAATCTTGTCTCAGGACACAAAAACACTCTATTAGTGTTTCTC
Done.