Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018429.1 Corchorus olitorius cultivar O-4 contig18462, 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: 82864
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:2236 original size:4 final size:4
Alignment explanation
Indices: 2227--2280 Score: 99
Period size: 4 Copynumber: 13.5 Consensus size: 4
2217 ATTCGACTAA
*
2227 AAAG AAAG AAAG AAAA AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
2275 AAAG AA
1 AAAG AA
2281 GTCAAATTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:14930 original size:16 final size:16
Alignment explanation
Indices: 14911--14963 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
14901 CTTTTTGGTC
*
14911 ATTATACTTTATTAAT
1 ATTATATTTTATTAAT
14927 ATTA-ATTTTTAAATTAAT
1 ATTATA-TTTT--ATTAAT
14945 ATTATATTTTATTAAT
1 ATTATATTTTATTAAT
14961 ATT
1 ATT
14964 TTTTTGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 1 0.03
16 16 0.50
18 14 0.44
19 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATATTTTATTAAT
Found at i:14955 original size:18 final size:16
Alignment explanation
Indices: 14918--14963 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
14908 GTCATTATAC
14918 TTTATTAATATTAATT
1 TTTATTAATATTAATT
14934 TTTAAATTAATATT-ATAT
1 TTT--ATTAATATTAAT-T
14952 TTTATTAATATT
1 TTTATTAATATT
14964 TTTTTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 12 0.44
17 2 0.07
18 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATTAATATTAATT
Found at i:17319 original size:518 final size:517
Alignment explanation
Indices: 16342--17368 Score: 1930
Period size: 518 Copynumber: 2.0 Consensus size: 517
16332 TAAGGTACAA
*
16342 CCTTCATCAGGTCAGGTCCACTTCAATACATATCCAGCGGCTATGCTAGCTCTTTTAGCATTAAC
1 CCTTCATCAGGCCAGGTCCACTTCAATACATATCCAGCGGCTATGCTAGCTCTTTTAGCATTAAC
16407 GGGTGCAAAAAGTGCTGCCCAGTAGATATCTCCTCTTTTCTAAACTATTTTACTTTCTAGACAAT
66 GGGTGCAAAAAGTGCTGCCCAGTAGATATCTCCTCTTTTCTAAACTATTTTACTTTCTAGACAAT
* *
16472 TTATGTGTTGTGAATTTTATTTTCTATTTATCAAGTATTTTTATAATTTTTTTAACGATGCAGTG
131 TTATGTGCTGTGAATTTTATTTTCTATTTATCAAGTATTTTTATAATTCTTTTAACGATGCAGTG
*
16537 GAGAATTGTGAAGTAATGTCTTCCATTACAACAAATAAAACAACTAATTCATCATTGTGCAACAA
196 GAGAATTGTGAAGTAATGTCTTCCATTACAACAAATAAAACAACTAATTCATCATCGTGCAACAA
16602 TACTACTTCACAAGGTTAGACCTTCCTCACCATTTTTAAGATTTTATTTTATTTATGTTACTTAT
261 TACTACTTCACAAGGTTAGACCTTCCTCACCATTTTTAAGATTTTATTTTATTTATGTTACTTAT
*
16667 CTTGCTTTATATTATGAATGTTTTACAGGTAAAGAAAGAGGTCAACCTCCTAGATACGGATTTCT
326 CTTGCTTTATATTATGAATGTTTTACAGGTAAAAAAAGAGGTCAACCTCCTAGATACGGATTTCT
16732 TAATTATATTGAACAACAATTAAAGCATCTCGAGATAGAACCAAACAATTTTGTTATTCCAAAGA
391 TAATTATATTGAACAACAATTAAAGCATCTCGAGATAGAACCAAACAATTTTGTTATTCCAAAGA
16797 AGAGAAGAAAAATTGATTGGTTATGTATAGCTCAATCTACTCCTTTCGAAAAAGAGTGTTACT
456 AGAGAAGAAAAATTGATTGGTTATGTATAGCTCAATCTACTCCTTTC-AAAAAGAGTGTTACT
16860 CCTTCATCAGGCCAGGTCCACTTCAATACATATCCAGCGGCTATGCTAGCTCTTTTAGCATTAAC
1 CCTTCATCAGGCCAGGTCCACTTCAATACATATCCAGCGGCTATGCTAGCTCTTTTAGCATTAAC
*
16925 GGGTGCAAAAATTGCTGCCCAGTAGATATCTCCTCTTTTCTAAACTATTTTACTTTCTAGACAAT
66 GGGTGCAAAAAGTGCTGCCCAGTAGATATCTCCTCTTTTCTAAACTATTTTACTTTCTAGACAAT
16990 TTATGTGCTGTGTAATTTTATTTTCTATTTATCAAGTATTTTTATAA-TCTTTTAACGATGCAGT
131 TTATGTGCTGTG-AATTTTATTTTCTATTTATCAAGTATTTTTATAATTCTTTTAACGATGCAGT
17054 GGAGAATTGTGAAGTAATGTCTTCCATTACAACAAATAAAACAACTAATTCATCATCGTGCAACA
195 GGAGAATTGTGAAGTAATGTCTTCCATTACAACAAATAAAACAACTAATTCATCATCGTGCAACA
* * * *
17119 ATACTCCTTCACAAGGTTTGGCCTTCCTTACCATTTTTAAGATTTTATTTTATTTATGTTACTTA
260 ATACTACTTCACAAGGTTAGACCTTCCTCACCATTTTTAAGATTTTATTTTATTTATGTTACTTA
17184 TCTTGCTTTATATTATGAATGTTTTACAGGTAAAAAAAGAGGTCAACCTCCTAGATACGGATTTC
325 TCTTGCTTTATATTATGAATGTTTTACAGGTAAAAAAAGAGGTCAACCTCCTAGATACGGATTTC
*
17249 TTAATTATATTGAACAACAATTAAAGCATCTCGAGATAGAACCAAACAATTTTGTTGTTCCAAAG
390 TTAATTATATTGAACAACAATTAAAGCATCTCGAGATAGAACCAAACAATTTTGTTATTCCAAAG
17314 AAGAGAAGAAAAATTGATTGGTTATGTATAGCTCAATCTACTCCTTTCAAAAAGA
455 AAGAGAAGAAAAATTGATTGGTTATGTATAGCTCAATCTACTCCTTTCAAAAAGA
17369 CGTTACTACT
Statistics
Matches: 497, Mismatches: 11, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
517 7 0.01
518 456 0.92
519 34 0.07
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (517 bp):
CCTTCATCAGGCCAGGTCCACTTCAATACATATCCAGCGGCTATGCTAGCTCTTTTAGCATTAAC
GGGTGCAAAAAGTGCTGCCCAGTAGATATCTCCTCTTTTCTAAACTATTTTACTTTCTAGACAAT
TTATGTGCTGTGAATTTTATTTTCTATTTATCAAGTATTTTTATAATTCTTTTAACGATGCAGTG
GAGAATTGTGAAGTAATGTCTTCCATTACAACAAATAAAACAACTAATTCATCATCGTGCAACAA
TACTACTTCACAAGGTTAGACCTTCCTCACCATTTTTAAGATTTTATTTTATTTATGTTACTTAT
CTTGCTTTATATTATGAATGTTTTACAGGTAAAAAAAGAGGTCAACCTCCTAGATACGGATTTCT
TAATTATATTGAACAACAATTAAAGCATCTCGAGATAGAACCAAACAATTTTGTTATTCCAAAGA
AGAGAAGAAAAATTGATTGGTTATGTATAGCTCAATCTACTCCTTTCAAAAAGAGTGTTACT
Found at i:19573 original size:15 final size:15
Alignment explanation
Indices: 19543--19576 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19533 CATGGTAAAT
*
19543 TTTTTTCTAACCATA
1 TTTTTTCTAAACATA
*
19558 TTTTTTCTAAATATA
1 TTTTTTCTAAACATA
19573 TTTT
1 TTTT
19577 ATATTGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTCTAAACATA
Found at i:23797 original size:2 final size:2
Alignment explanation
Indices: 23790--23826 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23780 CCATAACTCC
23790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23827 GCATTAGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24152 original size:60 final size:60
Alignment explanation
Indices: 24059--24178 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
24049 TGATTCCGAA
*
24059 AATGCTGGCGAAGATCATGTTTCAATAAAGATAGTCGATGATACTCAGACTGATCATGAT
1 AATGCTGGCGAAGATCATGTTTCAACAAAGATAGTCGATGATACTCAGACTGATCATGAT
** * *
24119 AATGCTGGCGTTGATCATGTTTCAACAGAGATAGTCGATGATACTCAGACTGATGATGAT
1 AATGCTGGCGAAGATCATGTTTCAACAAAGATAGTCGATGATACTCAGACTGATCATGAT
24179 GCGGTGAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (60 bp):
AATGCTGGCGAAGATCATGTTTCAACAAAGATAGTCGATGATACTCAGACTGATCATGAT
Found at i:39203 original size:18 final size:20
Alignment explanation
Indices: 39166--39205 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 20
39156 ATCTTCCTCC
39166 GCTACTCTTTGCTTTGTTATT
1 GCTACTCTTTGC-TTGTTATT
39187 GCTACT-TTTGC-TGTTATT
1 GCTACTCTTTGCTTGTTATT
39205 G
1 G
39206 TTCTTTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.10, C:0.17, G:0.17, T:0.55
Consensus pattern (20 bp):
GCTACTCTTTGCTTGTTATT
Found at i:39330 original size:6 final size:7
Alignment explanation
Indices: 39313--39339 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
39303 TTATTTTCCC
39313 TTTTTAA
1 TTTTTAA
39320 TTTTTAA
1 TTTTTAA
39327 TTTTTAA
1 TTTTTAA
39334 TTTTTA
1 TTTTTA
39340 TTATCTCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:42407 original size:20 final size:20
Alignment explanation
Indices: 42379--42421 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
42369 TTCCAGATTT
* *
42379 CTTTTTTCTCTTCTTATCTC
1 CTTTCTTCTCTTCTTAACTC
42399 CTTTCTTCTCTTCTTAACTC
1 CTTTCTTCTCTTCTTAACTC
42419 CTT
1 CTT
42422 ATTTTACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (20 bp):
CTTTCTTCTCTTCTTAACTC
Found at i:44787 original size:61 final size:61
Alignment explanation
Indices: 44715--44837 Score: 219
Period size: 61 Copynumber: 2.0 Consensus size: 61
44705 GGGAAGGAAT
* *
44715 AGGTAAAGTCAAGTTTCATGGGTATCAAGTTAAAGTCAATATTCTATTTATCAGGTATGGG
1 AGGTAAAGTCAAGTTACATGGGTATCAAGTTAAAGTCAATATTCTATTTATCACGTATGGG
*
44776 AGGTAAAGTCAAGTTACATGGGTATCAAGTTAAAGTCAATATTCTATTTATCACGTGTGGG
1 AGGTAAAGTCAAGTTACATGGGTATCAAGTTAAAGTCAATATTCTATTTATCACGTATGGG
44837 A
1 A
44838 AACATGTCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (61 bp):
AGGTAAAGTCAAGTTACATGGGTATCAAGTTAAAGTCAATATTCTATTTATCACGTATGGG
Found at i:52563 original size:22 final size:22
Alignment explanation
Indices: 52511--52553 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
52501 TAAATGAAAT
* *
52511 ATTCATATGAAATTATGATAAC
1 ATTCCTATTAAATTATGATAAC
52533 ATTCCTATTAAATTATGATAA
1 ATTCCTATTAAATTATGATAA
52554 TTACACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (22 bp):
ATTCCTATTAAATTATGATAAC
Found at i:52605 original size:22 final size:21
Alignment explanation
Indices: 52580--52958 Score: 149
Period size: 22 Copynumber: 17.1 Consensus size: 21
52570 GACCTCATGG
52580 AATTTTGATAACCTTCCTATGA
1 AATTTTGATAACC-TCCTATGA
* * *
52602 AATTTT-AGTAACGATACTATGG
1 AATTTTGA-TAAC-CTCCTATGA
* * **
52624 AATTTCGAGAACCTTATAT-A
1 AATTTTGATAACCTCCTATGA
** * *
52644 AATTTTTTTTAACCTTCTTATGG
1 AA-TTTTGATAACC-TCCTATGA
* *
52667 AATTTTGTTAACCTCCCTAAGA
1 AATTTTGATAACCT-CCTATGA
52689 AATTTTGA-AGACCTCACTATGA
1 AATTTTGATA-ACCTC-CTATGA
* *
52711 AATTTTGATAACTTACCAATGA
1 AATTTTGATAACCT-CCTATGA
* *
52733 AATTTTGATAACCAACACCATGA
1 AATTTTGATAACC-TC-CTATGA
* ** * *
52756 GATGCTAATAACCTCAATATGA
1 AATTTTGATAACCTC-CTATGA
* * * *
52778 TATATTGATAACCACGTTATGA
1 AATTTTGATAACCTC-CTATGA
* * * *
52800 AAATTTAAAAACGTCCATATG-
1 AATTTTGATAACCTCC-TATGA
* * *
52821 AATTGTT-AGTAATCACACTCTGA
1 AATT-TTGA-TAACCTC-CTATGA
*
52844 AATTTTGATAACCACACTATGA
1 AATTTTGATAACCTC-CTATGA
* *
52866 AATTGTGATAACCTCGTTATGA
1 AATTTTGATAACCTC-CTATGA
52888 AATTTTGATAAACCTTCCTAT-A
1 AATTTTGAT-AACC-TCCTATGA
* *
52910 ATATTTTCATAAACCTCCCTATAA
1 A-ATTTTGAT-AACCT-CCTATGA
52934 AATTTTGATAACCTCCTTATGA
1 AATTTTGATAACCTCC-TATGA
52956 AAT
1 AAT
52959 CCTGACTACA
Statistics
Matches: 266, Mismatches: 66, Indels: 50
0.70 0.17 0.13
Matches are distributed among these distances:
20 2 0.01
21 21 0.08
22 183 0.69
23 56 0.21
24 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (21 bp):
AATTTTGATAACCTCCTATGA
Found at i:53026 original size:80 final size:81
Alignment explanation
Indices: 52887--53038 Score: 193
Period size: 80 Copynumber: 1.9 Consensus size: 81
52877 CCTCGTTATG
* * *
52887 AAATTTTGATAAACCTTCCTATAATATTTTCATAAACCTCCCTATAAAATTTTGATAACCTCCTT
1 AAATTTTGATAAACCTCCCTATAATATTTTCATAAACCTCCCCATAAAATTTAGATAACCTCCTT
52952 ATGAAATCCTGACTAC
66 ATGAAATCCTGACTAC
* * * *
52968 AAATTTTGAT-AACCTCCCTATGATTTTTTTGAT-AACCTCCCCATGAAATATTAG-TAACCTCC
1 AAATTTTGATAAACCTCCCTAT-AATATTTTCATAAACCTCCCCATAAAAT-TTAGATAACCTCC
*
53030 TTGTGAAAT
64 TTATGAAAT
53039 TTTGTTAACC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
80 40 0.66
81 21 0.34
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.38
Consensus pattern (81 bp):
AAATTTTGATAAACCTCCCTATAATATTTTCATAAACCTCCCCATAAAATTTAGATAACCTCCTT
ATGAAATCCTGACTAC
Found at i:53088 original size:22 final size:22
Alignment explanation
Indices: 53050--53091 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
53040 TTGTTAACCA
53050 CTATGAAATTCTTATAATCTTG
1 CTATGAAATTCTTATAATCTTG
*
53072 CTATGACATT-TTGATAATCT
1 CTATGAAATTCTT-ATAATCT
53092 CTTTGATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (22 bp):
CTATGAAATTCTTATAATCTTG
Found at i:53131 original size:22 final size:22
Alignment explanation
Indices: 53106--53238 Score: 112
Period size: 22 Copynumber: 6.0 Consensus size: 22
53096 GATAACCTTT
* *
53106 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACCACA
53128 CTATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
53151 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* * *
53172 CTACGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * *
53193 CTCATAAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
53216 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
53238 C
1 C
53239 AGAGACAAGA
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 5 0.06
22 75 0.87
23 4 0.05
24 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:53143 original size:44 final size:44
Alignment explanation
Indices: 53093--53234 Score: 155
Period size: 44 Copynumber: 3.2 Consensus size: 44
53083 TGATAATCTC
* *
53093 TTTGATAACCTTTCTATAAAATTGTGATAACCACACTATGAAAT
1 TTTGATAACCTTCCTATAAAATTATGATAACCACACTATGAAAT
* * * * *
53137 TTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTACGGAAT
1 TTTGATAACCTTCC-TATAAAATTATGATAACCACACTATGAAAT
* *
53181 TTTGATAACC-TCCTCATAAAATTATAATAACCATC-TTATGAAAT
1 TTTGATAACCTTCCT-ATAAAATTATGATAACCA-CACTATGAAAT
53225 TTTGATAACC
1 TTTGATAACC
53235 ACACAGAGAC
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
43 5 0.06
44 74 0.91
45 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (44 bp):
TTTGATAACCTTCCTATAAAATTATGATAACCACACTATGAAAT
Found at i:53432 original size:19 final size:20
Alignment explanation
Indices: 53401--53438 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
53391 TATTGACATT
53401 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
53420 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
53439 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:54403 original size:27 final size:26
Alignment explanation
Indices: 54348--54409 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
54338 TCTAAATTTC
*
54348 TATTATTTTAATAGTGGAATAATTAAAA
1 TATTA-TTTAATAATGGAAT-ATTAAAA
54376 TATTATTTAATAATGGCAAT-TTAGAAA
1 TATTATTTAATAATGG-AATATTA-AAA
54403 TA-TATTT
1 TATTATTT
54410 GTCAAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 8 0.26
27 15 0.48
28 8 0.26
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
TATTATTTAATAATGGAATATTAAAA
Found at i:55110 original size:2 final size:2
Alignment explanation
Indices: 55103--55154 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
55093 TTCGTAGTTT
* * *
55103 TA TA TA TA CTA TA GA TA TA TA TA TA GA TA TA TA TA TA TA CT- TT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
55146 TA TA TA TA T
1 TA TA TA TA T
55155 TCATTGGATG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
1 1 0.02
2 38 0.90
3 3 0.07
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:55129 original size:12 final size:12
Alignment explanation
Indices: 55104--55139 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
55094 TCGTAGTTTT
55104 ATATATACTATAG
1 ATATATA-TATAG
55117 ATATATATATAG
1 ATATATATATAG
55129 ATATATATATA
1 ATATATATATA
55140 TACTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (12 bp):
ATATATATATAG
Found at i:56682 original size:11 final size:12
Alignment explanation
Indices: 56657--56687 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
56647 TATTTTTTGA
56657 TTAAAAAATATT
1 TTAAAAAATATT
56669 TTAAAAAATA-T
1 TTAAAAAATATT
56680 TTAAAAAA
1 TTAAAAAA
56688 AAAGTGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:58330 original size:29 final size:30
Alignment explanation
Indices: 58288--58353 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
58278 CATTAATGGT
** *
58288 CAAATAAGTTCTTGAA-TTTCAATTTTGGC
1 CAAATAAGCGCTTGAACTATCAATTTTGGC
*
58317 CAAATAAGCGCTTGAACTATCAATTTTTGC
1 CAAATAAGCGCTTGAACTATCAATTTTGGC
*
58347 CATATAA
1 CAAATAA
58354 ACCCTTCTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (30 bp):
CAAATAAGCGCTTGAACTATCAATTTTGGC
Found at i:66113 original size:35 final size:35
Alignment explanation
Indices: 66071--66140 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
66061 ACATATTAAG
66071 TTTTAATTGTTATAATTTAATATAAAAGGAAATAT
1 TTTTAATTGTTATAATTTAATATAAAAGGAAATAT
66106 TTTTAATTGTTATAATTTAATATAAAAGGAAATAT
1 TTTTAATTGTTATAATTTAATATAAAAGGAAATAT
66141 CTAAAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (35 bp):
TTTTAATTGTTATAATTTAATATAAAAGGAAATAT
Found at i:67875 original size:14 final size:14
Alignment explanation
Indices: 67856--67883 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
67846 AAAGTTACTA
67856 ATATTGCTAGATAT
1 ATATTGCTAGATAT
67870 ATATTGCTAGATAT
1 ATATTGCTAGATAT
67884 GTAAAGTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
ATATTGCTAGATAT
Found at i:69998 original size:18 final size:19
Alignment explanation
Indices: 69975--70024 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
69965 AACGTTGAAA
*
69975 TATAACCTTA-ATTTTTTT
1 TATAACCTTATAGTTTTTT
*
69993 TATAACGTCTATAGTTTTTT
1 TATAACCT-TATAGTTTTTT
70013 TAGTAACCTTAT
1 TA-TAACCTTAT
70025 TAGATGTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 7 0.27
19 2 0.08
20 12 0.46
21 5 0.19
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (19 bp):
TATAACCTTATAGTTTTTT
Found at i:71335 original size:21 final size:20
Alignment explanation
Indices: 71294--71343 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
71284 AGTTTTATTG
71294 TATTATTT-ATGATAATTTT
1 TATTATTTAATGATAATTTT
71313 TATTAATTTAATG-TAAGTTTT
1 TATT-ATTTAATGATAA-TTTT
71334 TATTATTTAA
1 TATTATTTAA
71344 AATAGAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 11 0.39
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
TATTATTTAATGATAATTTT
Found at i:79095 original size:27 final size:27
Alignment explanation
Indices: 79065--79118 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
79055 ACCACAGCAT
79065 TAGTTGG-CGACATCCCATAAACAGGGC
1 TAGTTGGCCG-CATCCCATAAACAGGGC
* *
79092 TAGTTGGCCGCCTCCCATAAAGAGGGC
1 TAGTTGGCCGCATCCCATAAACAGGGC
79119 CCGGACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.19
Consensus pattern (27 bp):
TAGTTGGCCGCATCCCATAAACAGGGC
Found at i:79889 original size:30 final size:30
Alignment explanation
Indices: 79855--79916 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
79845 GGAAACCTTA
* *
79855 CCATCAGCCGTTGAAGCCGTCAAATTTTTG
1 CCATCACCCGTCGAAGCCGTCAAATTTTTG
* *
79885 CCATCACCCGTCGCAGGCGTCAAATTTTTG
1 CCATCACCCGTCGAAGCCGTCAAATTTTTG
79915 CC
1 CC
79917 TTGCGCACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.27
Consensus pattern (30 bp):
CCATCACCCGTCGAAGCCGTCAAATTTTTG
Found at i:82544 original size:22 final size:22
Alignment explanation
Indices: 82516--82559 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
82506 TTTTCCTGTT
82516 TCAACCTTCATCGGGGTC-AAAC
1 TCAACCTTC-TCGGGGTCGAAAC
*
82538 TCAACCTTCTCTGGGTCGAAAC
1 TCAACCTTCTCGGGGTCGAAAC
82560 AGGATTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (22 bp):
TCAACCTTCTCGGGGTCGAAAC
Done.