Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021040.1 Corchorus olitorius cultivar O-4 contig21073, 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: 148684
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:712 original size:50 final size:50
Alignment explanation
Indices: 649--963 Score: 513
Period size: 50 Copynumber: 6.3 Consensus size: 50
639 TGTTTTGGCT
* * * *
649 TTTCCATACGAGTCGATTATCAACACAGGCATTTCCACAAGTCAAACTCG
1 TTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCG
* * *
699 TTTCCATATGAGTCAATTATCAACATAGTCTTTTCCACAAGCGAAACTCG
1 TTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCG
* * *
749 TTTCCATACGAGTCAATTATCAACACAGGCTTTTCTACAAGCCAAACTCA
1 TTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCG
*
799 TTTCCATACGAGTCAATTATCAACAAAGGCTTTTCCACAAGCCAAACTCG
1 TTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCG
*
849 TTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCA
1 TTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCG
*
899 TTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCC
1 TTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCG
949 TTTCCATACGAGTCA
1 TTTCCATACGAGTCA
964 TTTCAAACCT
Statistics
Matches: 246, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 246 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (50 bp):
TTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCG
Found at i:1150 original size:50 final size:50
Alignment explanation
Indices: 1019--1251 Score: 346
Period size: 50 Copynumber: 4.6 Consensus size: 50
1009 GCATTACCTT
*
1019 TTTTAAAGATTGAATTGGTAGACA-TTACAAAGGATAAGCGGAAGACGGTCG
1 TTTT-AAGATTGAATTGGTAGACAGTT-CAAAGGATAAGCGGAAGACGGTCC
*
1070 TTTTAAAGATTGAATTGGTAGATAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1121 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
1171 TTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCCGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
1221 TTTCAAGATT-AGATTGG-AGAACAATTCAAAG
1 TTTTAAGATTGA-ATTGGTAG-ACAGTTCAAAG
1252 AAATTGATCG
Statistics
Matches: 173, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
49 3 0.02
50 118 0.68
51 50 0.29
52 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:20726 original size:16 final size:16
Alignment explanation
Indices: 20705--20735 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20695 TAATAAAAGG
*
20705 TTTTTTTTTTCAAAAA
1 TTTTTTTTCTCAAAAA
20721 TTTTTTTTCTCAAAA
1 TTTTTTTTCTCAAAA
20736 CCATGTTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTTTTCTCAAAAA
Found at i:22085 original size:12 final size:12
Alignment explanation
Indices: 22066--22096 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
22056 TTATCCCCTC
22066 TCAATTTCTTTT
1 TCAATTTCTTTT
*
22078 TTAATTTCTTTT
1 TCAATTTCTTTT
22090 TCAATTT
1 TCAATTT
22097 ACCTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (12 bp):
TCAATTTCTTTT
Found at i:25899 original size:6 final size:6
Alignment explanation
Indices: 25888--25921 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
25878 CCCGAAGCAA
*
25888 CCCGAG CCCGAG CCCGAA CCCGA- CCCGAG CCCGA
1 CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGA
25922 AATAATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.21, C:0.53, G:0.26, T:0.00
Consensus pattern (6 bp):
CCCGAG
Found at i:25916 original size:17 final size:18
Alignment explanation
Indices: 25886--25922 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
25876 AACCCGAAGC
25886 AACCCGAGCCCGAGCCCG
1 AACCCGAGCCCGAGCCCG
25904 AACCCGA-CCCGAGCCCG
1 AACCCGAGCCCGAGCCCG
25921 AA
1 AA
25923 ATAATTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.27, C:0.49, G:0.24, T:0.00
Consensus pattern (18 bp):
AACCCGAGCCCGAGCCCG
Found at i:26420 original size:31 final size:31
Alignment explanation
Indices: 26349--26420 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
26339 GTCTATCAGC
*
26349 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
26380 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
26410 GTTTTAATTTG
1 -TTTTAATTTG
26421 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:26902 original size:16 final size:16
Alignment explanation
Indices: 26877--26934 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
26867 CTACCCGAGA
*
26877 CCGAATCCGAAAATAC
1 CCGAACCCGAAAATAC
*
26893 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
26909 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
26925 TCGAACCCGA
1 CCGAACCCGA
26935 CTTAACTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.08
16 30 0.83
17 3 0.08
ACGTcount: A:0.40, C:0.38, G:0.14, T:0.09
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:26919 original size:32 final size:32
Alignment explanation
Indices: 26877--26960 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
26867 CTACCCGAGA
26877 CCGAATCCGAAAATACCCGAACCCGACATAAC
1 CCGAATCCGAAAATACCCGAACCCGACATAAC
* * *
26909 CCGAACCCGAAAATACTCGAACCCGACTTAAC
1 CCGAATCCGAAAATACCCGAACCCGACATAAC
** *
26941 TTGAGTCCGAAAATACCCGA
1 CCGAATCCGAAAATACCCGA
26961 GTCCGCTCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.13
Consensus pattern (32 bp):
CCGAATCCGAAAATACCCGAACCCGACATAAC
Found at i:28330 original size:178 final size:177
Alignment explanation
Indices: 28054--28385 Score: 447
Period size: 178 Copynumber: 1.9 Consensus size: 177
28044 CAGTTATCCA
* * *
28054 ATTAAGGTGATTTAAGTGTCTATTAGAAGATTGTTCCATGATCTACAATTTTCATGAAAGGCTCG
1 ATTAAGATGATTCAAGTGTCTATTAGAAGATTGTTCCATGATCTACAACTTTCATGAAAGGCTCG
* * * *
28119 AAAACTAAATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTCGTTTCGATTAACG
66 AAAACTAAATTTAATG-TTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTCATTTCGATTAACA
*
28183 GGAATAGACGGTCCACTTAATATTATATAACTTTTGTTCCAGAGGTCTG
129 GAAATAGACGGTCCACTTAATATTATATAACTTTTGTTCCAGAGGTCTG
* * *
28232 ATTAAGATGATTCAAGTGTCTCTT-GAAAGGTTTTTCCATGATCTACAACTTTCATG-AAGGACT
1 ATTAAGATGATTCAAGTGTCTATTAG-AAGATTGTTCCATGATCTACAACTTTCATGAAAGG-CT
* *
28295 CGAAAACTAAATTTAATAG-TCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTATTTCGGTTAA
64 CGAAAACTAAATTTAAT-GTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTCATTTCGATTAA
**
28359 CAGAAATAGACGGTTTACTTAATATTA
127 CAGAAATAGACGGTCCACTTAATATTA
28386 CATAGTTTGT
Statistics
Matches: 134, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
177 12 0.09
178 121 0.90
179 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (177 bp):
ATTAAGATGATTCAAGTGTCTATTAGAAGATTGTTCCATGATCTACAACTTTCATGAAAGGCTCG
AAAACTAAATTTAATGTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTCATTTCGATTAACAGA
AATAGACGGTCCACTTAATATTATATAACTTTTGTTCCAGAGGTCTG
Found at i:32415 original size:15 final size:15
Alignment explanation
Indices: 32391--32420 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32381 TGGAGGCAAA
*
32391 AGCTCTCAATGGCAT
1 AGCTCACAATGGCAT
32406 AGCTCACAATGGCAT
1 AGCTCACAATGGCAT
32421 CAAAAAATTC
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:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (15 bp):
AGCTCACAATGGCAT
Found at i:43112 original size:25 final size:25
Alignment explanation
Indices: 43078--43126 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
43068 GATTAGTTTG
43078 TAGAGACCGAGCGAGAGTGCTCAAT
1 TAGAGACCGAGCGAGAGTGCTCAAT
43103 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
43127 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAT
Found at i:44271 original size:5 final size:5
Alignment explanation
Indices: 44261--44294 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
44251 AATTATACTG
44261 TTATA TTATA -TATA TATATA TTATA TTATA TTAT
1 TTATA TTATA TTATA T-TATA TTATA TTATA TTAT
44295 TATTGACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:46781 original size:22 final size:22
Alignment explanation
Indices: 46756--46830 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 22
46746 TCAAAAAATT
*
46756 ATAGGGAGATTAACAAAATCTC
1 ATAGGGAGGTTAACAAAATCTC
* *
46778 ATAGTGAGGTTATCAAAA-CTC
1 ATAGGGAGGTTAACAAAATCTC
* *
46799 ATAGGGAGGTT-ATAAAATTTC
1 ATAGGGAGGTTAACAAAATCTC
*
46820 ATAGGAAGGTT
1 ATAGGGAGGTT
46831 TATTAAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
20 4 0.09
21 25 0.57
22 15 0.34
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (22 bp):
ATAGGGAGGTTAACAAAATCTC
Found at i:46801 original size:21 final size:22
Alignment explanation
Indices: 46756--46954 Score: 104
Period size: 22 Copynumber: 9.1 Consensus size: 22
46746 TCAAAAAATT
* *
46756 ATAGGGAGATTAACAAAATCTC
1 ATAGGGAGGTTATCAAAATCTC
*
46778 ATAGTGAGGTTATCAAAA-CTC
1 ATAGGGAGGTTATCAAAATCTC
*
46799 ATAGGGAGGTTAT-AAAATTTC
1 ATAGGGAGGTTATCAAAATCTC
* * * *
46820 ATAGGAAGGTTTATTAAAATTTA
1 ATAGGGAGG-TTATCAAAATCTC
** * * *
46843 ATAGTTAGATTATCAAAGTTTC
1 ATAGGGAGGTTATCAAAATCTC
* * * *
46865 ATATGGAGTTTATCACAATTTC
1 ATAGGGAGGTTATCAAAATCTC
* *
46887 ATAGGTTA--TTATCAAAATTTC
1 ATAGG-GAGGTTATCAAAATCTC
** * *
46908 ATA-ACATGGTTATCAAAATTTA
1 ATAGGGA-GGTTATCAAAATCTC
*
46930 ATAGGGTA-GTTATCAAAATTTC
1 ATAGGG-AGGTTATCAAAATCTC
46952 ATA
1 ATA
46955 AAATCGAAAC
Statistics
Matches: 140, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.01
20 4 0.03
21 40 0.29
22 80 0.57
23 14 0.10
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
ATAGGGAGGTTATCAAAATCTC
Found at i:46885 original size:44 final size:45
Alignment explanation
Indices: 46828--46955 Score: 140
Period size: 43 Copynumber: 2.9 Consensus size: 45
46818 TCATAGGAAG
* * **
46828 GTTTATTAAAATTTAATA-GTTAGATTATCAAAGTTTCATATGGA-
1 GTTTATCAAAATTTAATAGGTTAGATTATCAAAATTTCATA-ACAT
* *
46872 GTTTATCACAATTTCATAGGTT--ATTATCAAAATTTCATAACAT
1 GTTTATCAAAATTTAATAGGTTAGATTATCAAAATTTCATAACAT
* *
46915 GGTTATCAAAATTTAATAGGGTAG-TTATCAAAATTTCATAA
1 GTTTATCAAAATTTAATAGGTTAGATTATCAAAATTTCATAA
46956 AATCGAAACA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 1 0.01
43 34 0.49
44 32 0.46
45 3 0.04
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.41
Consensus pattern (45 bp):
GTTTATCAAAATTTAATAGGTTAGATTATCAAAATTTCATAACAT
Found at i:50778 original size:27 final size:27
Alignment explanation
Indices: 50748--50818 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
50738 GGTCATCCAT
50748 GGGCATTTTGGTCATTTGCACATTCAG
1 GGGCATTTTGGTCATTTGCACATTCAG
*
50775 GGGCATTTTGGTCATTTGCATATTCAG
1 GGGCATTTTGGTCATTTGCACATTCAG
*
50802 GGGGATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
50819 AAAGTTCACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTGCACATTCAG
Found at i:69838 original size:14 final size:14
Alignment explanation
Indices: 69819--69847 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
69809 TGAATATTTG
69819 TCTGCATTTGGTAT
1 TCTGCATTTGGTAT
69833 TCTGCATTTGGTAT
1 TCTGCATTTGGTAT
69847 T
1 T
69848 AAGTTGGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.52
Consensus pattern (14 bp):
TCTGCATTTGGTAT
Found at i:87879 original size:51 final size:51
Alignment explanation
Indices: 87778--87886 Score: 118
Period size: 51 Copynumber: 2.2 Consensus size: 51
87768 GTTCATCAAA
**
87778 TTTT-TCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTCATAGTGT
* *
87828 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACTGTACAT-GTGT
1 TTTTCTCTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCT-CATAGTGT
*
87879 TTCTCTCT
1 TTTTCTCT
87887 CAGAAATAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
50 6 0.12
51 42 0.84
52 2 0.04
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (51 bp):
TTTTCTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTCATAGTGT
Found at i:88416 original size:13 final size:13
Alignment explanation
Indices: 88398--88435 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
88388 GTTATAATAG
88398 ATTTTCAAGGGTA
1 ATTTTCAAGGGTA
88411 ATTTTCAAGGGTA
1 ATTTTCAAGGGTA
88424 A--TTCAAGGGTA
1 ATTTTCAAGGGTA
88435 A
1 A
88436 CTAACCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
13 14 0.56
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (13 bp):
ATTTTCAAGGGTA
Found at i:88624 original size:2 final size:2
Alignment explanation
Indices: 88617--88650 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
88607 ACAATAATGG
88617 AT AT AT 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 AT AT AT
88651 TTTTTTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91668 original size:15 final size:16
Alignment explanation
Indices: 91638--91671 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
91628 TACTTTGCTC
91638 TGTTTTCTAGTTTAAT
1 TGTTTTCTAGTTTAAT
*
91654 TGTTTTCT-TTTTAAT
1 TGTTTTCTAGTTTAAT
91669 TGT
1 TGT
91672 GATTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (16 bp):
TGTTTTCTAGTTTAAT
Found at i:96899 original size:24 final size:21
Alignment explanation
Indices: 96844--96898 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
96834 CGCCCATTCA
*
96844 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCTAAGC
*
96865 CCGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
*
96886 CCGTGCCATCACC
1 CCGTGCCACCACC
96899 ATTCCATGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:100268 original size:15 final size:16
Alignment explanation
Indices: 100241--100270 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
100231 TTTACTCTGT
100241 TTTCTTGTTTAATTGC
1 TTTCTTGTTTAATTGC
100257 TTTCTT-TTTAATTG
1 TTTCTTGTTTAATTG
100271 TGATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.13, C:0.10, G:0.10, T:0.67
Consensus pattern (16 bp):
TTTCTTGTTTAATTGC
Found at i:101505 original size:11 final size:11
Alignment explanation
Indices: 101456--101503 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
101446 TGGTGCGCAG
*
101456 CATGGCCGGGT
1 CATGGCCGGGC
101467 CATGGCCGGGC
1 CATGGCCGGGC
*
101478 CATGGCCTGGC
1 CATGGCCGGGC
*
101489 CATGTCCGGGC
1 CATGGCCGGGC
101500 CATG
1 CATG
101504 TCTTGGTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.10, C:0.33, G:0.40, T:0.17
Consensus pattern (11 bp):
CATGGCCGGGC
Found at i:108312 original size:51 final size:51
Alignment explanation
Indices: 108253--108361 Score: 218
Period size: 51 Copynumber: 2.1 Consensus size: 51
108243 CAATGGTCTT
108253 CAAATCTTCAAATCATCTTCAATGAGTCTTCAAACACGAACTTCGATTCTC
1 CAAATCTTCAAATCATCTTCAATGAGTCTTCAAACACGAACTTCGATTCTC
108304 CAAATCTTCAAATCATCTTCAATGAGTCTTCAAACACGAACTTCGATTCTC
1 CAAATCTTCAAATCATCTTCAATGAGTCTTCAAACACGAACTTCGATTCTC
108355 CAAATCT
1 CAAATCT
108362 ATACTCAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (51 bp):
CAAATCTTCAAATCATCTTCAATGAGTCTTCAAACACGAACTTCGATTCTC
Found at i:113323 original size:18 final size:18
Alignment explanation
Indices: 113297--113331 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
113287 CCTGGCGAGG
*
113297 TGCATCATTGCCATTCTT
1 TGCACCATTGCCATTCTT
*
113315 TGCACCATTTCCATTCT
1 TGCACCATTGCCATTCT
113332 GCACAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.31, G:0.09, T:0.43
Consensus pattern (18 bp):
TGCACCATTGCCATTCTT
Found at i:115360 original size:17 final size:18
Alignment explanation
Indices: 115338--115372 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
115328 CCCTTATCCT
115338 TAATTGAAAACTT-TTAA
1 TAATTGAAAACTTGTTAA
115355 TAATTGAAAACTTGTTAA
1 TAATTGAAAACTTGTTAA
115373 AAGTTTATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (18 bp):
TAATTGAAAACTTGTTAA
Found at i:116993 original size:2 final size:2
Alignment explanation
Indices: 116988--117013 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
116978 TTTATGTAAC
116988 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
117014 GGCCAAAAAA
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:121531 original size:17 final size:16
Alignment explanation
Indices: 121488--121531 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
121478 TTTTTTTTTC
121488 TTTTATTT-GTTCTTT
1 TTTTATTTAGTTCTTT
*
121503 TTTTGCTTTAGTTCTTT
1 TTTT-ATTTAGTTCTTT
121520 TTTTATTCTAGT
1 TTTTATT-TAGT
121532 GAGTAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.17
16 5 0.21
17 15 0.62
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.73
Consensus pattern (16 bp):
TTTTATTTAGTTCTTT
Found at i:126004 original size:34 final size:34
Alignment explanation
Indices: 125964--126028 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
125954 TAACTTGTAA
*
125964 AGGCGTGATGAAGGCCCGTTTAACTTCATTGAAT
1 AGGCGTGATGAAGGCCCGTGTAACTTCATTGAAT
*
125998 AGGCGTGATGAAGGCCTGTGTAACTTCATTG
1 AGGCGTGATGAAGGCCCGTGTAACTTCATTG
126029 GTTGTAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (34 bp):
AGGCGTGATGAAGGCCCGTGTAACTTCATTGAAT
Found at i:129064 original size:17 final size:17
Alignment explanation
Indices: 129039--129075 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
129029 GTTGTCTTCG
*
129039 CTTTCAAAGCCCATTTC
1 CTTTCAAAGCCCATCTC
*
129056 CTTTTAAAGCCCATCTC
1 CTTTCAAAGCCCATCTC
129073 CTT
1 CTT
129076 CCTATTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (17 bp):
CTTTCAAAGCCCATCTC
Found at i:140985 original size:2 final size:2
Alignment explanation
Indices: 140978--141008 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
140968 ATTTGTCTCT
140978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
141009 TCTCTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:144755 original size:21 final size:21
Alignment explanation
Indices: 144729--144778 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
144719 TGCTAGGAGT
144729 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
144750 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
144771 TCATTGGA
1 TCATTGGA
144779 ATTAACTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.