Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007906.1 Corchorus capsularis cultivar CVL-1 contig07927, 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: 48661
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:571 original size:69 final size:70
Alignment explanation
Indices: 489--642 Score: 206
Period size: 69 Copynumber: 2.2 Consensus size: 70
479 TAATTAAAAT
* * * * * *
489 AGTAAAATGGTAAAATATAATAGTTATAAGGA-TATTAGATTTAATTATAT-AAAATTGAGTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGACT-TTAGATTTAATTAAATAAAAATAGAGTTTT
552 TAGTTG
65 TAGTTG
*
558 AGTAAAATAGTAAAATAAAATAATTATAAAGACTTTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGACTTTAGATTTAATTAAATAAAAATAGAGTTTTT
623 AGTTG
66 AGTTG
628 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
643 ACCTAAACAA
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
69 42 0.56
70 31 0.41
71 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.37
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGACTTTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Found at i:938 original size:2 final size:2
Alignment explanation
Indices: 933--966 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
923 TGGTATATTT
*
933 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
967 GATGATGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4605 original size:1 final size:1
Alignment explanation
Indices: 4599--4630 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
4589 TGCTTGAGAC
4599 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4631 AATTTATACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5775 original size:31 final size:32
Alignment explanation
Indices: 5699--5775 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 32
5689 AAAATTAAAA
*
5699 TTTAGGGTGCAAA-AAGTCCATTTACTTATAG
1 TTTAGGGTGCAAATTAGTCCATTTACTTATAG
* *
5730 TTTAGGGTGCAAATTA-TCCATTTGCTTATAT
1 TTTAGGGTGCAAATTAGTCCATTTACTTATAG
5761 TTTAGGGTGCAAATT
1 TTTAGGGTGCAAATT
5776 TTACATTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 41 0.98
32 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (32 bp):
TTTAGGGTGCAAATTAGTCCATTTACTTATAG
Found at i:19263 original size:9 final size:9
Alignment explanation
Indices: 19249--19274 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19239 GAGAGTGTTA
19249 CGTCTTCGT
1 CGTCTTCGT
19258 CGTCTTCGT
1 CGTCTTCGT
19267 CGTCTTCG
1 CGTCTTCG
19275 CCGATGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.35, G:0.23, T:0.42
Consensus pattern (9 bp):
CGTCTTCGT
Found at i:19783 original size:17 final size:17
Alignment explanation
Indices: 19730--19784 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
19720 ATCACCCCTT
* *
19730 AGATCACTAGTAATCTA
1 AGATCACTAGTGATCAA
*
19747 AGATCACCAGTGAT-ACA
1 AGATCACTAGTGATCA-A
*
19764 AGATCACTGGTGATCAA
1 AGATCACTAGTGATCAA
19781 AGAT
1 AGAT
19785 TACATGGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 30 0.97
18 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (17 bp):
AGATCACTAGTGATCAA
Found at i:19902 original size:17 final size:16
Alignment explanation
Indices: 19856--19898 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
19846 CCAGATGACT
19856 AGTGATCTAAGATCACC
1 AGTGATC-AAGATCACC
19873 AGTGATGCAAGATCACC
1 AGTGAT-CAAGATCACC
*
19890 GGTGATCAA
1 AGTGATCAA
19899 AGATTACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (16 bp):
AGTGATCAAGATCACC
Found at i:19926 original size:118 final size:118
Alignment explanation
Indices: 19718--19939 Score: 381
Period size: 118 Copynumber: 1.9 Consensus size: 118
19708 GGGGCGTTTG
** *
19718 GGATCACCCCTTAGATCACTAGTAATCTAAGATCACCAGTGATACAAGATCACTGGTGATCAAAG
1 GGATCACCCCCCAGATCACTAGTAATCTAAGATCACCAGTGATACAAGATCACCGGTGATCAAAG
*
19783 ATTACATGGGTTTATGGTGGTAATCCAGATCACCCTTAGGGGGCGTTTGGTTA
66 ATTACATGGGTTTATGGTGGTAATCCAAATCACCCTTAGGGGGCGTTTGGTTA
* * *
19836 GGATCACCCCCCAGATGACTAGTGATCTAAGATCACCAGTGATGCAAGATCACCGGTGATCAAAG
1 GGATCACCCCCCAGATCACTAGTAATCTAAGATCACCAGTGATACAAGATCACCGGTGATCAAAG
19901 ATTACATGGGTTTATGGTGGTAATCCAAATCACCCTTAG
66 ATTACATGGGTTTATGGTGGTAATCCAAATCACCCTTAG
19940 AGGGATGATC
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 97 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (118 bp):
GGATCACCCCCCAGATCACTAGTAATCTAAGATCACCAGTGATACAAGATCACCGGTGATCAAAG
ATTACATGGGTTTATGGTGGTAATCCAAATCACCCTTAGGGGGCGTTTGGTTA
Found at i:20166 original size:130 final size:130
Alignment explanation
Indices: 19933--20168 Score: 341
Period size: 130 Copynumber: 1.8 Consensus size: 130
19923 ATCCAAATCA
19933 CCCTTAGAGGGATGATCAGGGGGTAATCCGGATTACCACACCAAACCAAAAAGTGTAACCAAACG
1 CCCTTAGAGGGATGATCAGGGGGTAATCCGGATTACCACACCAAACCAAAAAGTGTAACCAAACG
* * *
19998 AGATGATCTGAGATCACTTGTCAAGATCACCACAGGTGATCAAAGATCACCCCCAACCAAACGCC
66 AGATGATCTGAAATCACCTGACAAGATCACCACAGGTGATCAAAGATCACCCCCAACCAAACGCC
* * * * *
20063 CCCTTAGAGCGG-TGATTAGGGGGTAATCCTGATTATCACATCAAACCAAAAAGTGTAACCAAAT
1 CCCTTAGAG-GGATGATCAGGGGGTAATCCGGATTACCACACCAAACCAAAAAGTGTAACCAAAC
* * *
20127 GGGGTGATCTGAAATTACCT-ACAAAGATCACCACAGGTGATC
65 GAGATGATCTGAAATCACCTGAC-AAGATCACCACAGGTGATC
20169 TTGGGTGGTT
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
129 1 0.01
130 90 0.97
131 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (130 bp):
CCCTTAGAGGGATGATCAGGGGGTAATCCGGATTACCACACCAAACCAAAAAGTGTAACCAAACG
AGATGATCTGAAATCACCTGACAAGATCACCACAGGTGATCAAAGATCACCCCCAACCAAACGCC
Found at i:20675 original size:2 final size:2
Alignment explanation
Indices: 20668--20711 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
20658 AGTAGGAATA
*
20668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20710 AT
1 AT
20712 TACGAAAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23972 original size:141 final size:141
Alignment explanation
Indices: 23716--23983 Score: 401
Period size: 141 Copynumber: 1.9 Consensus size: 141
23706 AACAATCATC
* * * *
23716 CTTGGCTAACTCTGTAAGCTGCTTATGTGGGATAATTATCAAAAAAATATGAGGTCATTATGCCT
1 CTTGGCTAACTCTGTAAGCTACCTAAGTGGGATAATTATCAAAAAAATATGAGGTCATCATGCCT
* * * * *
23781 CATAACATTTTGGCAGGATGTTGCGTATTTAGGCTATTATAGATTTACTAAACAAAATTTATATT
66 CATAACATTTTGGCAGGATGTTGCGCATTTAGGCTATTAGAGAGTAACTAAACAAAAGTTATATT
23846 AGCTAAGTTTG
131 AGCTAAGTTTG
* * * *
23857 CTTGGCTAACTTTGTAATCTACCTAAGTGGGATAATTATCGATAAAATATGAGGTCATCATGCCT
1 CTTGGCTAACTCTGTAAGCTACCTAAGTGGGATAATTATCAAAAAAATATGAGGTCATCATGCCT
* *
23922 CATAACATTTTGGCAGGATGTTGTGCATTTAGGCTATTGGAGAGTAACTAAACAAAAGTTAT
66 CATAACATTTTGGCAGGATGTTGCGCATTTAGGCTATTAGAGAGTAACTAAACAAAAGTTAT
23984 CTGTAAGCTG
Statistics
Matches: 112, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
141 112 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (141 bp):
CTTGGCTAACTCTGTAAGCTACCTAAGTGGGATAATTATCAAAAAAATATGAGGTCATCATGCCT
CATAACATTTTGGCAGGATGTTGCGCATTTAGGCTATTAGAGAGTAACTAAACAAAAGTTATATT
AGCTAAGTTTG
Found at i:24097 original size:117 final size:116
Alignment explanation
Indices: 23883--24100 Score: 346
Period size: 117 Copynumber: 1.9 Consensus size: 116
23873 ATCTACCTAA
* *
23883 GTGGGATAATTATCGATAAAATATGAGGTCATCATGCCTCATAACATTTTGGCAGGATGTTGTGC
1 GTGGGATAATTATCGAAAAAATATGAGGTCATCATGCCTCATAACATTTTGGCAGGATGTTGCGC
*
23948 ATTTAGGCTATTGGAGAGTAACTAAACAAAAGTTATCTGTAAGCTGCTTAT
66 ATTTAGGCTATTAGAGAGTAACTAAACAAAAGTTATCTGTAAGCTGCTTAT
*
23999 GTGGGATATATTATCGAAAAAATATGAGGTCATTATGCCTCATAACATTTTGGCAGGATGTTGCG
1 GTGGGATA-ATTATCGAAAAAATATGAGGTCATCATGCCTCATAACATTTTGGCAGGATGTTGCG
* * * * *
24064 TATTTAGGCTATTATAGATTTACTGAACAAAAGTTAT
65 CATTTAGGCTATTAGAGAGTAACTAAACAAAAGTTAT
24101 ATTAGCTAAG
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
116 8 0.09
117 84 0.91
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.34
Consensus pattern (116 bp):
GTGGGATAATTATCGAAAAAATATGAGGTCATCATGCCTCATAACATTTTGGCAGGATGTTGCGC
ATTTAGGCTATTAGAGAGTAACTAAACAAAAGTTATCTGTAAGCTGCTTAT
Found at i:24214 original size:258 final size:257
Alignment explanation
Indices: 23726--24241 Score: 960
Period size: 258 Copynumber: 2.0 Consensus size: 257
23716 CTTGGCTAAC
23726 TCTGTAAGCTGCTTATGTGGGATAATTATCAAAAAAATATGAGGTCATTATGCCTCATAACATTT
1 TCTGTAAGCTGCTTATGTGGGATAATTATCAAAAAAATATGAGGTCATTATGCCTCATAACATTT
*
23791 TGGCAGGATGTTGCGTATTTAGGCTATTATAGATTTACTAAACAAAATTTATATTAGCTAAGTTT
66 TGGCAGGATGTTGCGTATTTAGGCTATTATAGATTTACTAAACAAAAGTTATATTAGCTAAGTTT
*
23856 GCTTGGCTAACTTTGTAATCTACCTAAGTGGGATAATTATCGATAAAATATGAGGTCATCATGCC
131 GCTTGGCTAACTTTGTAAGCTACCTAAGTGGGATAATTATCGATAAAATATGAGGTCATCATGCC
**
23921 TCATAACATTTTGGCAGGATGTTGTGCATTTAGGCTATTGGAGAGTAACTAAACAAAAGTTA
196 TCATAACATTTTGGCAGGATGTTGTGCATTTAGGCTATTACAGAGTAACTAAACAAAAGTTA
*
23983 TCTGTAAGCTGCTTATGTGGGATATATTATCGAAAAAATATGAGGTCATTATGCCTCATAACATT
1 TCTGTAAGCTGCTTATGTGGGATA-ATTATCAAAAAAATATGAGGTCATTATGCCTCATAACATT
*
24048 TTGGCAGGATGTTGCGTATTTAGGCTATTATAGATTTACTGAACAAAAGTTATATTAGCTAAGTT
65 TTGGCAGGATGTTGCGTATTTAGGCTATTATAGATTTACTAAACAAAAGTTATATTAGCTAAGTT
24113 TGCTTGGCTAACTTTGTAAGCTACCTAAGTGGGATAATTATCGATAAAATATGAGGTCATCATGC
130 TGCTTGGCTAACTTTGTAAGCTACCTAAGTGGGATAATTATCGATAAAATATGAGGTCATCATGC
*
24178 CTCATAACATTTTTGCAGGATGTTGTGCATTTAGGCTATTACAGAGTAACTAAACAAAAGTTA
195 CTCATAACATTTTGGCAGGATGTTGTGCATTTAGGCTATTACAGAGTAACTAAACAAAAGTTA
24241 T
1 T
24242 ATTAGTTTGG
Statistics
Matches: 251, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
257 24 0.10
258 227 0.90
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (257 bp):
TCTGTAAGCTGCTTATGTGGGATAATTATCAAAAAAATATGAGGTCATTATGCCTCATAACATTT
TGGCAGGATGTTGCGTATTTAGGCTATTATAGATTTACTAAACAAAAGTTATATTAGCTAAGTTT
GCTTGGCTAACTTTGTAAGCTACCTAAGTGGGATAATTATCGATAAAATATGAGGTCATCATGCC
TCATAACATTTTGGCAGGATGTTGTGCATTTAGGCTATTACAGAGTAACTAAACAAAAGTTA
Found at i:24240 original size:141 final size:142
Alignment explanation
Indices: 23985--24246 Score: 409
Period size: 141 Copynumber: 1.9 Consensus size: 142
23975 AAAAGTTATC
* * * *
23985 TGTAAGCTGCTTATGTGGGATATATTATCGAAAAAATATGAGGTCATTATGCCTCATAACATTTT
1 TGTAAGCTACCTAAGTGGGATATATTATCGAAAAAATATGAGGTCATCATGCCTCATAACATTTT
* * * * *
24050 GGCAGGATGTTGCGTATTTAGGCTATTATAGATTTACTGAACAAAAGTTATATTAGCTAAGTTTG
66 GGCAGGATGTTGCGCATTTAGGCTATTACAGAGTAACTAAACAAAAGTTATATTAGCTAAGTTTG
24115 CTTGGCTAACTT
131 CTTGGCTAACTT
*
24127 TGTAAGCTACCTAAGTGGGATA-ATTATCGATAAAATATGAGGTCATCATGCCTCATAACATTTT
1 TGTAAGCTACCTAAGTGGGATATATTATCGAAAAAATATGAGGTCATCATGCCTCATAACATTTT
* *
24191 TGCAGGATGTTGTGCATTTAGGCTATTACAGAGTAACTAAACAAAAGTTATATTAG
66 GGCAGGATGTTGCGCATTTAGGCTATTACAGAGTAACTAAACAAAAGTTATATTAG
24247 TTTGGAGCTT
Statistics
Matches: 108, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
141 89 0.82
142 19 0.18
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (142 bp):
TGTAAGCTACCTAAGTGGGATATATTATCGAAAAAATATGAGGTCATCATGCCTCATAACATTTT
GGCAGGATGTTGCGCATTTAGGCTATTACAGAGTAACTAAACAAAAGTTATATTAGCTAAGTTTG
CTTGGCTAACTT
Found at i:25006 original size:22 final size:22
Alignment explanation
Indices: 24962--25006 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
24952 ATTGCAAAAA
*
24962 GCACTCACATTTCATATGCTAT
1 GCACTCACATTTCATAAGCTAT
*
24984 GCACTCA-ATTTCAATAAGTTAT
1 GCACTCACATTTC-ATAAGCTAT
25006 G
1 G
25007 ACAATAAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (22 bp):
GCACTCACATTTCATAAGCTAT
Found at i:26656 original size:58 final size:58
Alignment explanation
Indices: 26591--26743 Score: 234
Period size: 58 Copynumber: 2.6 Consensus size: 58
26581 CAATTACCCC
** * *
26591 GAATTAAGCTAATTGTTACTGCTTACTCCTTTTACTTCTTGGTTAACTTAATCGCTCT
1 GAATTAAGCTAATTACTACTGTTTACTCCTTTTACTTCTTGATTAACTTAATCGCTCT
* *
26649 GAATTAAGCTAATTACTACTATTTACTCCTTTTACTTCTTGATTAACTTAATTGCTCT
1 GAATTAAGCTAATTACTACTGTTTACTCCTTTTACTTCTTGATTAACTTAATCGCTCT
* *
26707 GAATTTAGCTAATTACTATTGTTTACTCCTTTTACTT
1 GAATTAAGCTAATTACTACTGTTTACTCCTTTTACTT
26744 TTACTTCTTG
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 86 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (58 bp):
GAATTAAGCTAATTACTACTGTTTACTCCTTTTACTTCTTGATTAACTTAATCGCTCT
Found at i:26804 original size:44 final size:44
Alignment explanation
Indices: 26730--26874 Score: 224
Period size: 44 Copynumber: 3.4 Consensus size: 44
26720 TACTATTGTT
* *
26730 TACTCCTTTTACTTTTAC---TTCTTGATTACCAATTTACTGCG
1 TACTCCTTTTACTTTTACTGTTTTTTAATTACCAATTTACTGCG
26771 TACTCCTTTTACTTTTACTGTTTTTTAATTACCAATTTACTGCG
1 TACTCCTTTTACTTTTACTGTTTTTTAATTACCAATTTACTGCG
* **
26815 TACTCCTTTTACTTTTACTGTTTTTTAATTACCAACTTACTGAT
1 TACTCCTTTTACTTTTACTGTTTTTTAATTACCAATTTACTGCG
26859 TACTCCTTTTACTTTT
1 TACTCCTTTTACTTTT
26875 GCTCCTTTAG
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
41 18 0.19
44 78 0.81
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.52
Consensus pattern (44 bp):
TACTCCTTTTACTTTTACTGTTTTTTAATTACCAATTTACTGCG
Found at i:26929 original size:32 final size:32
Alignment explanation
Indices: 26893--26976 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
26883 AGGAATTTTT
*
26893 TGATTACTTCTTTTACTTTTACTTCACTCTGC
1 TGATTACTTCTTTTACTTTTACTTAACTCTGC
*
26925 TGATTACTTCTTTTACTTTTACTTAATTCTGC
1 TGATTACTTCTTTTACTTTTACTTAACTCTGC
26957 TGATTACTTCTTTTACTTTT
1 TGATTACTTCTTTTACTTTT
26977 TCTCTTAGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (32 bp):
TGATTACTTCTTTTACTTTTACTTAACTCTGC
Found at i:26945 original size:104 final size:103
Alignment explanation
Indices: 26848--27048 Score: 226
Period size: 104 Copynumber: 2.0 Consensus size: 103
26838 TTTAATTACC
** ** * *
26848 AACT-TACTGATTACTCCTTTTACTTTTGCTCCT-TTAGGAATTTTTTGATTACTTCTTTTACTT
1 AACTCTACTGATTACTCCTTTTACTTTTGCTCCTATTACCAATTTACTGATCACTTCTTTTACCT
** * *
26911 TTACTTCACTCTGCTGATTACTTCTTTTACTTTTACTT
66 TTACCCCACTCTACTGATTACTTCTTTTACTTTTAATT
* * * * * *
26949 AATTCTGCTGATTACTTCTTTTACTTTTTCTCTTAGTTACCAATTTACTGCTCACTTCTTTTACC
1 AACTCTACTGATTACTCCTTTTACTTTTGCTCCTA-TTACCAATTTACTGATCACTTCTTTTACC
*
27014 TTTACCCCATTCTACTGATTACTTCTTTTACTTTT
65 TTTACCCCACTCTACTGATTACTTCTTTTACTTTT
27049 TTAGCTTAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
101 3 0.04
102 25 0.31
104 53 0.65
ACGTcount: A:0.18, C:0.23, G:0.06, T:0.53
Consensus pattern (103 bp):
AACTCTACTGATTACTCCTTTTACTTTTGCTCCTATTACCAATTTACTGATCACTTCTTTTACCT
TTACCCCACTCTACTGATTACTTCTTTTACTTTTAATT
Found at i:27235 original size:55 final size:56
Alignment explanation
Indices: 27114--27236 Score: 162
Period size: 55 Copynumber: 2.2 Consensus size: 56
27104 TTTTTAGTTT
* *
27114 AATTTAACTAATTACTGTTTACTCTTCTTTCCTTTACTTTTTAGTGTAATTTCTCAG
1 AATTAAACTAATTACTGTTTAC-CTTCTTTCCTTTACTTTTTAGTGTAATTGCTCAG
* *
27171 AATTAAACTAATTACTGTTTA-C-TCTTTCTTTTACTTCTTTAGCT-TAATTGCTCTG
1 AATTAAACTAATTACTGTTTACCTTCTTTCCTTTACTT-TTTAG-TGTAATTGCTCAG
27226 AATTAAACTAA
1 AATTAAACTAA
27237 CTGCTGATTG
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
54 13 0.22
55 26 0.43
56 1 0.02
57 20 0.33
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (56 bp):
AATTAAACTAATTACTGTTTACCTTCTTTCCTTTACTTTTTAGTGTAATTGCTCAG
Found at i:34986 original size:30 final size:30
Alignment explanation
Indices: 34950--35014 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
34940 AAAGGGTCAA
34950 ATGGCCGGTTGTACCCGGATGGCC-CATGCG
1 ATGGCCGGTTGTACCCGG-TGGCCTCATGCG
** *
34980 ATGGCCGGTTGTGGCCGGTTGCCTCATGCG
1 ATGGCCGGTTGTACCCGGTGGCCTCATGCG
35010 ATGGC
1 ATGGC
35015 GCATGCGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.11, C:0.28, G:0.38, T:0.23
Consensus pattern (30 bp):
ATGGCCGGTTGTACCCGGTGGCCTCATGCG
Found at i:35036 original size:14 final size:14
Alignment explanation
Indices: 35005--35044 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
34995 CGGTTGCCTC
*
35005 ATGCGATGG-C-GC
1 ATGCGATGGTCGGT
35017 ATGCGATGGTCGGT
1 ATGCGATGGTCGGT
35031 ATGCGATGGTCGGT
1 ATGCGATGGTCGGT
35045 TGTGGCCGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.36
13 1 0.04
14 15 0.60
ACGTcount: A:0.15, C:0.17, G:0.42, T:0.25
Consensus pattern (14 bp):
ATGCGATGGTCGGT
Found at i:35310 original size:41 final size:42
Alignment explanation
Indices: 35265--35343 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
35255 TACACCAGTG
*
35265 AGATTGGTT-CGGT-GAGAGTAAAATTGGTTACTGTACATGTT
1 AGATTGGTTACGGTACAGA-TAAAATTGGTTACTGTACATGTT
* * *
35306 AGATTTGTTACTGTACAGATAAAATTTGTTACTGTACA
1 AGATTGGTTACGGTACAGATAAAATTGGTTACTGTACA
35344 GATGAGAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 8 0.25
42 21 0.66
43 3 0.09
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (42 bp):
AGATTGGTTACGGTACAGATAAAATTGGTTACTGTACATGTT
Found at i:35317 original size:21 final size:21
Alignment explanation
Indices: 35283--35346 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
35273 TCGGTGAGAG
*
35283 TAAAATTGGTTACTGTACATG-
1 TAAAATTTGTTACTGTACA-GA
* *
35304 TTAGATTTGTTACTGTACAGA
1 TAAAATTTGTTACTGTACAGA
35325 TAAAATTTGTTACTGTACAGA
1 TAAAATTTGTTACTGTACAGA
35346 T
1 T
35347 GAGAATATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (21 bp):
TAAAATTTGTTACTGTACAGA
Found at i:37240 original size:127 final size:128
Alignment explanation
Indices: 37092--37346 Score: 503
Period size: 128 Copynumber: 2.0 Consensus size: 128
37082 CCACGCCATT
37092 TTCTTTTTCTTTTTATCTTTCGAATTCTAATGGAGACAAGTTTGCATATTACC-TTTTTTTTTGA
1 TTCTTTTTCTTTTTATCTTTCGAATTCTAATGGAGACAAGTTTGCATATTACCTTTTTTTTTTGA
37156 CAGTAAGAAAGGAAGTTTGCATATTACCTTTAGGGAGTGCTTTTCTTGGATGGGGTTAGATAC
66 CAGTAAGAAAGGAAGTTTGCATATTACCTTTAGGGAGTGCTTTTCTTGGATGGGGTTAGATAC
37219 TTCTTTTTCTTTTTATCTTTCGAATTCTAATGGAGACAAGTTTGCATATTACCTTTTTTTTTTGA
1 TTCTTTTTCTTTTTATCTTTCGAATTCTAATGGAGACAAGTTTGCATATTACCTTTTTTTTTTGA
37284 CAGTAAGAAAGGAAGTTTGCATATTACCTTTAGGGAGTGCTTTTCTTGGATGGGGTTAGATAC
66 CAGTAAGAAAGGAAGTTTGCATATTACCTTTAGGGAGTGCTTTTCTTGGATGGGGTTAGATAC
37347 CTCATCAAGG
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 53 0.42
128 74 0.58
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.44
Consensus pattern (128 bp):
TTCTTTTTCTTTTTATCTTTCGAATTCTAATGGAGACAAGTTTGCATATTACCTTTTTTTTTTGA
CAGTAAGAAAGGAAGTTTGCATATTACCTTTAGGGAGTGCTTTTCTTGGATGGGGTTAGATAC
Found at i:38346 original size:16 final size:16
Alignment explanation
Indices: 38317--38350 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38307 GCAATGACTA
38317 CAGAAAAAAACAAAAT
1 CAGAAAAAAACAAAAT
* *
38333 CAGAATAAACCAAAAT
1 CAGAAAAAAACAAAAT
38349 CA
1 CA
38351 TTTACCTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.09
Consensus pattern (16 bp):
CAGAAAAAAACAAAAT
Found at i:38670 original size:19 final size:20
Alignment explanation
Indices: 38646--38703 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
38636 CTATTTAGAA
38646 ACTGTACAAATGAGATTA-C
1 ACTGTACAAATGAGATTAGC
* *
38665 ACTGTACAAATTAGATTAGGT
1 ACTGTACAAATGAGATTA-GC
*
38686 ACTGTACATATGAGATTA
1 ACTGTACAAATGAGATTA
38704 TTAGAGCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
ACTGTACAAATGAGATTAGC
Found at i:39296 original size:16 final size:15
Alignment explanation
Indices: 39256--39312 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
39246 TTCGAACCAT
*
39256 ATGACCCGAAACTGAAA
1 ATGACCCG-AAC-CAAA
*
39273 AAGACCCGAACCAAA
1 ATGACCCGAACCAAA
*
39288 ATTGACCCGAACCCAA
1 A-TGACCCGAACCAAA
39304 ATGACCCGA
1 ATGACCCGA
39313 CATTTGAGCG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 12 0.34
16 16 0.46
17 7 0.20
ACGTcount: A:0.44, C:0.32, G:0.16, T:0.09
Consensus pattern (15 bp):
ATGACCCGAACCAAA
Found at i:40075 original size:24 final size:24
Alignment explanation
Indices: 40043--40091 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
40033 ACAACGCGTT
40043 TGAACAAAATATATTTTGAAATAC
1 TGAACAAAATATATTTTGAAATAC
40067 TGAACAAAATATATTTTGAAATAC
1 TGAACAAAATATATTTTGAAATAC
40091 T
1 T
40092 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (24 bp):
TGAACAAAATATATTTTGAAATAC
Found at i:42034 original size:28 final size:25
Alignment explanation
Indices: 41965--42020 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
41955 AAGAAAAAAA
*
41965 AAAGTCTAGTAAATTTAATCAAATCC
1 AAAGTCTA-TTAATTTAATCAAATCC
41991 AAAGTCTATT--TTTAATCAAATCC
1 AAAGTCTATTAATTTAATCAAATCC
42014 AAAGTCT
1 AAAGTCT
42021 CTGGTGAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 20 0.69
25 1 0.03
26 8 0.28
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (25 bp):
AAAGTCTATTAATTTAATCAAATCC
Found at i:42488 original size:2 final size:2
Alignment explanation
Indices: 42481--42505 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42471 TTATTCTAAA
42481 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 A
42506 GAAAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44775 original size:3 final size:3
Alignment explanation
Indices: 44767--44797 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
44757 TCAAATTCTG
44767 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
44798 TAATAACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:46259 original size:13 final size:13
Alignment explanation
Indices: 46243--46268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46233 TCTTTTACCC
46243 TTCACTTTGGATG
1 TTCACTTTGGATG
46256 TTCACTTTGGATG
1 TTCACTTTGGATG
46269 ACATGTTAGG
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:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
TTCACTTTGGATG
Found at i:47117 original size:2 final size:2
Alignment explanation
Indices: 47110--47135 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47100 TAAGATGCCA
47110 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
47136 GGATTAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47218 original size:2 final size:2
Alignment explanation
Indices: 47213--47240 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47203 ATAAACACCA
47213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47241 GGAATAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.