Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012862.1 Corchorus olitorius cultivar O-4 contig12895, 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: 104241
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4598 original size:18 final size:17
Alignment explanation
Indices: 4569--4617 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
4559 GTAGTGATCA
4569 TATAACTAATAATAATTGT
1 TATAA-TAATAATAA-TGT
4588 TATAATAATAATAA-GT
1 TATAATAATAATAATGT
*
4604 T-TAATAATTATAAT
1 TATAATAATAATAAT
4618 AAGAAGATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (17 bp):
TATAATAATAATAATGT
Found at i:4722 original size:115 final size:115
Alignment explanation
Indices: 4588--4811 Score: 353
Period size: 115 Copynumber: 1.9 Consensus size: 115
4578 TAATAATTGT
* *
4588 TATAATAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACGTAAAAAAA-TGTTAGTATT
1 TATAATAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACGTAAAAAAATTATTAGTATC
*
4652 ATTTTAA-ATTTTTGTAATATGAAAAGAAAAACGTAATGACTAATGATATA
66 A-TTTAAGACTTTTGTAATATGAAAAGAAAAACGTAATGACTAATGATATA
* * *
4702 TATAACTAATAATAATTTTAATAATTATAATAATAAGTTGTTTAACGTAAAAAAATTATTAGTAT
1 TATAA-TAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACGTAAAAAAATTATTAGTAT
*
4767 CATTTAAGACTTTTGTAATATGGAAAGAAAAACGTAATGACTAAT
65 CATTTAAGACTTTTGTAATATGAAAAGAAAAACGTAATGACTAAT
4812 TCCTCAAAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
114 5 0.05
115 51 0.51
116 44 0.44
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (115 bp):
TATAATAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACGTAAAAAAATTATTAGTATC
ATTTAAGACTTTTGTAATATGAAAAGAAAAACGTAATGACTAATGATATA
Found at i:4853 original size:144 final size:142
Alignment explanation
Indices: 4673--4939 Score: 446
Period size: 144 Copynumber: 1.9 Consensus size: 142
4663 TTGTAATATG
*
4673 AAAAGAAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAA
1 AAAAAAAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAA
4738 GTTGTTTAACGTAAAAA-AATTATTAGTATCATTTAAGACTTTTGTAATATGGAAAGAAAAACGT
66 GTTGTTTAACGTAAAAATAATTATTA-T-T-ATTTAAGACTTTTGTAATATGGAAAGAAAAACGT
4802 AATGACTAATTCCTC
128 AATGACTAATTCCTC
4817 AAAAAAAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAA
1 AAAAAAAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAA
* * * * *
4882 GTTGTTTAATGTAAAAATAATTGTTATTATTTTAGACTTTTTTAATATGGAAATAAAA
66 GTTGTTTAACGTAAAAATAATTATTATTATTTAAGACTTTTGTAATATGGAAAGAAAA
4940 TCTGATTGGA
Statistics
Matches: 116, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
142 27 0.23
143 1 0.01
144 81 0.70
145 7 0.06
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (142 bp):
AAAAAAAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAA
GTTGTTTAACGTAAAAATAATTATTATTATTTAAGACTTTTGTAATATGGAAAGAAAAACGTAAT
GACTAATTCCTC
Found at i:13054 original size:17 final size:17
Alignment explanation
Indices: 13032--13068 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13022 AATGGAGTTT
13032 ATATATATAAATAAATA
1 ATATATATAAATAAATA
* *
13049 ATATATATATATATATA
1 ATATATATAAATAAATA
13066 ATA
1 ATA
13069 AAACTTGTAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATATATAAATAAATA
Found at i:20948 original size:2 final size:2
Alignment explanation
Indices: 20935--20971 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
20925 ACTAAAAATA
20935 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20972 TAGTTTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28501 original size:30 final size:31
Alignment explanation
Indices: 28467--28543 Score: 115
Period size: 30 Copynumber: 2.5 Consensus size: 31
28457 TAATGACAAA
28467 ATCAGAATTC-TCTCCTTCACAAACAAAGAG
1 ATCAGAATTCTTCTCCTTCACAAACAAAGAG
28497 ATCAGAA-TCTTCTCCTTCACAAACAAAGAG
1 ATCAGAATTCTTCTCCTTCACAAACAAAGAG
*
28527 ATCGGAA-TCTTCCTCCT
1 ATCAGAATTCTT-CTCCT
28544 CGTCATACTC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 2 0.05
30 37 0.84
31 5 0.11
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.26
Consensus pattern (31 bp):
ATCAGAATTCTTCTCCTTCACAAACAAAGAG
Found at i:39452 original size:12 final size:12
Alignment explanation
Indices: 39435--39473 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
39425 GCTAAGTCCT
39435 TATAAAATTTTA
1 TATAAAATTTTA
*
39447 TATAAAATTATA
1 TATAAAATTTTA
39459 TTATAATAATTTTA
1 -TATAA-AATTTTA
39473 T
1 T
39474 TACTATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 11 0.48
13 6 0.26
14 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATAAAATTTTA
Found at i:44803 original size:57 final size:57
Alignment explanation
Indices: 44707--44925 Score: 278
Period size: 57 Copynumber: 3.8 Consensus size: 57
44697 AGTTAGAAAC
* *
44707 GCTCAACACCCTGAGATCTGAGCTCCGTAACTT-AGCACGTGTTGGCATAGAGTAAAT
1 GCTCAACACCCTGAGACCTGAGCTCCGT-ACTTAAGCACGTGTCGGCATAGAGTAAAT
* * * * *
44764 GCTCAACACTCTGAGACCTGAGCTCCGTACTTAATCACGTGTCGGCATGGAGTGATT
1 GCTCAACACCCTGAGACCTGAGCTCCGTACTTAAGCACGTGTCGGCATAGAGTAAAT
* * * * * * *
44821 GCTCAACACTCTGAAACCTGAGCTCTGTAATTAAGCACGTGTCAGCATACATTAAAT
1 GCTCAACACCCTGAGACCTGAGCTCCGTACTTAAGCACGTGTCGGCATAGAGTAAAT
* *
44878 GCTCAACACCCTGAGAACTGAGCTCCGTACTTGAGCACGTGTCGGCAT
1 GCTCAACACCCTGAGACCTGAGCTCCGTACTTAAGCACGTGTCGGCAT
44926 GAATACTTAT
Statistics
Matches: 137, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
56 4 0.03
57 133 0.97
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (57 bp):
GCTCAACACCCTGAGACCTGAGCTCCGTACTTAAGCACGTGTCGGCATAGAGTAAAT
Found at i:44907 original size:114 final size:114
Alignment explanation
Indices: 44707--44926 Score: 316
Period size: 114 Copynumber: 1.9 Consensus size: 114
44697 AGTTAGAAAC
* * ** *
44707 GCTCAACACCCTGAGATCTGAGCTCCGTAACTTAGCACGTGTTGGCATAGAGTAAATGCTCAACA
1 GCTCAACACCCTGAAACCTGAGCTCCGTAACTTAGCACGTGTCAGCATACAGTAAATGCTCAACA
* * *
44772 CTCTGAGACCTGAGCTCCGTACTTAATCACGTGTCGGCATGGAGTGATT
66 CCCTGAGAACTGAGCTCCGTACTTAAGCACGTGTCGGCATGGAGTGATT
* * *
44821 GCTCAACACTCTGAAACCTGAGCTCTGTAA-TTAAGCACGTGTCAGCATACATTAAATGCTCAAC
1 GCTCAACACCCTGAAACCTGAGCTCCGTAACTT-AGCACGTGTCAGCATACAGTAAATGCTCAAC
*
44885 ACCCTGAGAACTGAGCTCCGTACTTGAGCACGTGTCGGCATG
65 ACCCTGAGAACTGAGCTCCGTACTTAAGCACGTGTCGGCATG
44927 AATACTTATT
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
113 2 0.02
114 91 0.98
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (114 bp):
GCTCAACACCCTGAAACCTGAGCTCCGTAACTTAGCACGTGTCAGCATACAGTAAATGCTCAACA
CCCTGAGAACTGAGCTCCGTACTTAAGCACGTGTCGGCATGGAGTGATT
Found at i:48771 original size:86 final size:85
Alignment explanation
Indices: 48670--48845 Score: 264
Period size: 86 Copynumber: 2.1 Consensus size: 85
48660 ACAAATATAT
* *
48670 TTAAAAAATTATAATATATCTAA-GTTTTGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAG
1 TTAAAAAATTATAATATATCTAAGGTTTTGTAATTAAAACAAT-AAAATGGTAAAAATAAAATAG
*
48734 TTATAAAGAGATTAGATTAAAA
65 TTATAAAGAGATGAGATT-AAA
* * *
48756 TTAAAAACTTCTAATATATCTAAGGTTTTTTAATTAAAACAATAAAATGGTAAAAATAAAATAGT
1 TTAAAAAATTATAATATATCTAAGGTTTTGTAATTAAAACAATAAAATGGTAAAAATAAAATAGT
*
48821 TATAAAGAGATGAGATTTAA
66 TATAAAGAGATGAGATTAAA
48841 TTAAA
1 TTAAA
48846 TAAAATAGAG
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
85 7 0.09
86 59 0.72
87 16 0.20
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.34
Consensus pattern (85 bp):
TTAAAAAATTATAATATATCTAAGGTTTTGTAATTAAAACAATAAAATGGTAAAAATAAAATAGT
TATAAAGAGATGAGATTAAA
Found at i:50113 original size:42 final size:42
Alignment explanation
Indices: 50054--50144 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
50044 AACAACAATT
50054 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
*
50096 AATATTAGCTTTATTTTGTTGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
50138 AAT-TTAG
1 AATATTAG
50145 GTAATGCACT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
Found at i:54189 original size:11 final size:11
Alignment explanation
Indices: 54165--54199 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
54155 TTGACAGCAC
54165 AACAAAAACAA
1 AACAAAAACAA
* *
54176 AACGAAAACGA
1 AACAAAAACAA
54187 AACAAAAACAA
1 AACAAAAACAA
54198 AA
1 AA
54200 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:56118 original size:22 final size:22
Alignment explanation
Indices: 56092--56145 Score: 54
Period size: 28 Copynumber: 2.2 Consensus size: 22
56082 TTACAATTAC
56092 ACCAAATGATAATCAATTCCAT
1 ACCAAATGATAATCAATTCCAT
56114 ACCAATTACAAATGATAATCAATTCCAT
1 A-C-----CAAATGATAATCAATTCCAT
56142 ACCA
1 ACCA
56146 TTGAAACCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
22 3 0.12
23 1 0.04
27 1 0.04
28 21 0.81
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (22 bp):
ACCAAATGATAATCAATTCCAT
Found at i:61019 original size:181 final size:184
Alignment explanation
Indices: 60715--61077 Score: 572
Period size: 181 Copynumber: 2.0 Consensus size: 184
60705 TCGTGGATTT
60715 GGAGAAGAAAGGGGAAGAATACCTCAAGTCCCAGGCATTCAGATTCGTCGACGGTGGGCGAACGG
1 GGAGAAGAAAGGGGAAGAATACCTCAAGTCCCAGGCATTCAGATTCGTCGACGGTGGGCGAACGG
*
60780 AGGGGCGACCATCGGGGATTTGGAAATGAAGGAGGCAGAGGGAGAGAGTGAAACAGAGTT-G-A-
66 AGGGGCGACCATCGGGGATTTGAAAATGAAGGAGGCAGAGGGAGAGAGTGAAACAGAGTTAGAAT
* *
60842 GA-GAGCTCGAGCAAAAGAGGGAATTAGGGATTAGGTTTATGAAAATTTAAGAAA
131 GAGGAGCTCGAGCAAAAGAGGGAATTAGGGAATAGGATTA-GAAAATTTAAGAAA
*** * *
60896 GGAGAAGAAAGGGGAAGAATGGGTCAAGTCTCAGGCATTCAGATTCGTCGACGGTGGGCGAATGG
1 GGAGAAGAAAGGGGAAGAATACCTCAAGTCCCAGGCATTCAGATTCGTCGACGGTGGGCGAACGG
* *
60961 AGGGGCGACCATCGTGGATTTGAAAATGAAGGAGGCGGAGGGAGAGAGTGAAACAGAGTTGAGAA
66 AGGGGCGACCATCGGGGATTTGAAAATGAAGGAGGCAGAGGGAGAGAGTGAAACAGAGTT-AGAA
61026 CTTGAGGAGCTCGAGCAAAAGAGGGAATTAGGGAATAGGATTAGAAAATTTA
130 --TGAGGAGCTCGAGCAAAAGAGGGAATTAGGGAATAGGATTAGAAAATTTA
61078 GGAATTTTTA
Statistics
Matches: 165, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
181 117 0.71
183 1 0.01
184 1 0.01
187 11 0.07
188 35 0.21
ACGTcount: A:0.35, C:0.11, G:0.37, T:0.17
Consensus pattern (184 bp):
GGAGAAGAAAGGGGAAGAATACCTCAAGTCCCAGGCATTCAGATTCGTCGACGGTGGGCGAACGG
AGGGGCGACCATCGGGGATTTGAAAATGAAGGAGGCAGAGGGAGAGAGTGAAACAGAGTTAGAAT
GAGGAGCTCGAGCAAAAGAGGGAATTAGGGAATAGGATTAGAAAATTTAAGAAA
Found at i:64876 original size:16 final size:16
Alignment explanation
Indices: 64855--64886 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
64845 CATGCAAATA
64855 ACAAAGATAAATTTTG
1 ACAAAGATAAATTTTG
64871 ACAAAGATAAATTTTG
1 ACAAAGATAAATTTTG
64887 CCCCCTCTCA
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:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (16 bp):
ACAAAGATAAATTTTG
Found at i:65392 original size:30 final size:30
Alignment explanation
Indices: 65358--65420 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
65348 TATAGCTCAT
* *
65358 AGATTTCATATTTACAAGAACATTTACAAG
1 AGATTTCACATTTACAAGAACAATTACAAG
*
65388 AGATTTCACATTTACAAGAACAATTATAAG
1 AGATTTCACATTTACAAGAACAATTACAAG
65418 AGA
1 AGA
65421 AGAAGTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (30 bp):
AGATTTCACATTTACAAGAACAATTACAAG
Found at i:67100 original size:68 final size:69
Alignment explanation
Indices: 66991--67128 Score: 217
Period size: 68 Copynumber: 2.0 Consensus size: 69
66981 ACGTTTGAAA
* * *
66991 TGCATTGTCTTTATATGTAATTTTAGTATTTGGATGTAATTAATGGTGTTCATATTA-TTTTTCC
1 TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGTTCACATCATTTTTTCC
67055 TTAG
66 TTAG
*
67059 TGCATTGTCTTTATATGTAATTTTAGCA-TTGAGATGTAATTAATGGTGTTCCCATCATTTTTTC
1 TGCATTGTCTTTATATGTAATTTTAGCATTTG-GATGTAATTAATGGTGTTCACATCATTTTTTC
67123 CTTAG
65 CTTAG
67128 T
1 T
67129 TGTTAGTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
67 3 0.05
68 49 0.77
69 12 0.19
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (69 bp):
TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGTTCACATCATTTTTTCC
TTAG
Found at i:67219 original size:2 final size:2
Alignment explanation
Indices: 67212--67241 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
67202 TTGTATTTTC
67212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67242 AAACAGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76566 original size:11 final size:11
Alignment explanation
Indices: 76550--76575 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
76540 AGATAATTTC
76550 TTTTCTTCTAG
1 TTTTCTTCTAG
76561 TTTTCTTCTAG
1 TTTTCTTCTAG
76572 TTTT
1 TTTT
76576 TTAGGTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:77807 original size:13 final size:13
Alignment explanation
Indices: 77786--77817 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
77776 CTACTAACAA
77786 TTTTCTTTTGAGT
1 TTTTCTTTTGAGT
*
77799 TTTTTTTTTGAGT
1 TTTTCTTTTGAGT
77812 TTTTCT
1 TTTTCT
77818 AGGAAGCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.75
Consensus pattern (13 bp):
TTTTCTTTTGAGT
Found at i:80229 original size:21 final size:21
Alignment explanation
Indices: 80164--80231 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
80154 CCATTGCCAA
*
80164 GCCACTACCGGCCATTCACCGT
1 GCCACTACCGGCCATGC-CCGT
* ** *
80186 GCCACCACCGGTTAAGCCCGT
1 GCCACTACCGGCCATGCCCGT
*
80207 GCCACTACCGGCCATGCCTGT
1 GCCACTACCGGCCATGCCCGT
80228 GCCA
1 GCCA
80232 TCGCCATTCC
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.18, C:0.44, G:0.22, T:0.16
Consensus pattern (21 bp):
GCCACTACCGGCCATGCCCGT
Found at i:83157 original size:11 final size:11
Alignment explanation
Indices: 83141--83166 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
83131 AGATAATTTC
83141 TTTTCTTCTAG
1 TTTTCTTCTAG
83152 TTTTCTTCTAG
1 TTTTCTTCTAG
83163 TTTT
1 TTTT
83167 TTAGGCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:89726 original size:5 final size:5
Alignment explanation
Indices: 89712--89743 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
89702 AATTAAGATT
89712 AAAA- AAAAG AAAAG AAAAG -AAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
89744 TATGAGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:89729 original size:14 final size:14
Alignment explanation
Indices: 89712--89743 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
89702 AATTAAGATT
89712 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
*
89726 AAAAGAAAGAAAAG
1 AAAAAAAAGAAAAG
89740 AAAA
1 AAAA
89744 TATGAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:95066 original size:41 final size:43
Alignment explanation
Indices: 95017--95109 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
95007 AGTGCATTAC
* * *
95017 CTAA-ATTCTA-CT-CATCTCTAGGTAATTCATCAAAATAAAT
1 CTAATATTCTACCTCCATCGCTAGATAATTCATCAAAATAAAG
*
95057 CTAATATTCTACTCCTCCATCGCTAGATTATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCGCTAGATAATTCATCAAAATAAAG
95102 CTAATATT
1 CTAATATT
95110 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
40 4 0.09
41 6 0.14
44 2 0.05
45 32 0.73
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCGCTAGATAATTCATCAAAATAAAG
Done.