Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018252.1 Corchorus olitorius cultivar O-4 contig18285, 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: 86057
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:12599 original size:2 final size:2
Alignment explanation
Indices: 12592--12655 Score: 51
Period size: 2 Copynumber: 31.5 Consensus size: 2
12582 GTTCAAGTAT
* * * *
12592 TA TA TA TA TA TA TA TA TA TA TA T- TA TT TT TA GTGA CTA GA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A -TA TA TA
12634 T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
12656 TAATTTTAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
1 2 0.04
2 46 0.88
3 2 0.04
4 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12639 original size:41 final size:42
Alignment explanation
Indices: 12594--12679 Score: 147
Period size: 41 Copynumber: 2.0 Consensus size: 42
12584 TCAAGTATTA
*
12594 TATATATATATATATATATATTATTTTTAGTGACTA-GAAAT
1 TATATATATATATATATATATTAATTTTAGTGACTAGGAAAT
12635 TATATATATATATATATATATTAATTTTAGTGACTATGGAAAT
1 TATATATATATATATATATATTAATTTTAGTGACTA-GGAAAT
12678 TA
1 TA
12680 CTTAAAAATG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
41 35 0.83
43 7 0.17
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (42 bp):
TATATATATATATATATATATTAATTTTAGTGACTAGGAAAT
Found at i:17929 original size:14 final size:14
Alignment explanation
Indices: 17910--17937 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17900 CCAATGCAAA
17910 AGATTTCAACTTAT
1 AGATTTCAACTTAT
17924 AGATTTCAACTTAT
1 AGATTTCAACTTAT
17938 TTGCTCCAGG
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:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
AGATTTCAACTTAT
Found at i:18397 original size:19 final size:19
Alignment explanation
Indices: 18369--18419 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
18359 ACAATACAAG
*
18369 TTTA-TTTTAATTTATTCA
1 TTTATTTTTAATTAATTCA
*
18387 TTTATTTTTAATTAATTTA
1 TTTATTTTTAATTAATTCA
18406 -TTATTATTTAATTA
1 TTTATT-TTTAATTA
18420 TAATAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTTTAATTAATTCA
Found at i:19434 original size:9 final size:9
Alignment explanation
Indices: 19420--19453 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
19410 TTATCTCAAC
19420 AACAAGAAG
1 AACAAGAAG
19429 AACAAGAAG
1 AACAAGAAG
19438 AACAAGAAG
1 AACAAGAAG
*
19447 AAGAAGA
1 AACAAGA
19454 GCAGCCATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.68, C:0.09, G:0.24, T:0.00
Consensus pattern (9 bp):
AACAAGAAG
Found at i:19484 original size:21 final size:21
Alignment explanation
Indices: 19460--19500 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
19450 AAGAGCAGCC
19460 ATCTTCTCATCATCCAAAGCA
1 ATCTTCTCATCATCCAAAGCA
19481 ATCTTCTCATCATCCAAAGC
1 ATCTTCTCATCATCCAAAGC
19501 CATGATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (21 bp):
ATCTTCTCATCATCCAAAGCA
Found at i:25371 original size:1 final size:1
Alignment explanation
Indices: 25365--25400 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
25355 CAACTAGATT
25365 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25401 CCACGCACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:33212 original size:7 final size:7
Alignment explanation
Indices: 33200--33254 Score: 94
Period size: 7 Copynumber: 8.0 Consensus size: 7
33190 ACAGATATAG
33200 TATAGAT
1 TATAGAT
33207 TATAGAT
1 TATAGAT
33214 TATAGAT
1 TATAGAT
33221 TATAGAT
1 TATAGAT
33228 TATAGAT
1 TATAGAT
33235 TATAGAT
1 TATAGAT
*
33242 TATGGA-
1 TATAGAT
33248 TATAGAT
1 TATAGAT
33255 AGATAAGTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
6 5 0.11
7 40 0.89
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (7 bp):
TATAGAT
Found at i:45809 original size:18 final size:18
Alignment explanation
Indices: 45786--45824 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
45776 ACGTAATAGA
45786 TAATTATTTGATGTATTG
1 TAATTATTTGATGTATTG
45804 TAATTATTTGATGTATTG
1 TAATTATTTGATGTATTG
45822 TAA
1 TAA
45825 GTGTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (18 bp):
TAATTATTTGATGTATTG
Found at i:46600 original size:3 final size:3
Alignment explanation
Indices: 46579--46627 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
46569 CTACTGAGTC
*
46579 ATT ATT -TT ATT ATT CTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
46626 AT
1 AT
46628 ATATACTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:48636 original size:42 final size:43
Alignment explanation
Indices: 48589--48678 Score: 130
Period size: 45 Copynumber: 2.1 Consensus size: 43
48579 CATTACATAA
*
48589 ATTCTA-CTCCATCTCTGGATAATTCATCAAAATAAA-TCTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGT-TAAT
48631 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGTTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGTTAAT
48676 ATT
1 ATT
48679 AATTGTTGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 6 0.14
45 36 0.84
46 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGTTAAT
Found at i:50874 original size:31 final size:32
Alignment explanation
Indices: 50837--50907 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
50827 ATTAAAATGG
*
50837 TAAAAATAAAATATTTA-TAAATTTAATTAAA
1 TAAAAATAAAATATTTATTAAATTTAATCAAA
* * *
50868 TAAAAATAGAATTTTTATTGAATTTAATCAAA
1 TAAAAATAAAATATTTATTAAATTTAATCAAA
50900 TAAAAATA
1 TAAAAATA
50908 TAGTTTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 15 0.43
32 20 0.57
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (32 bp):
TAAAAATAAAATATTTATTAAATTTAATCAAA
Found at i:50901 original size:32 final size:31
Alignment explanation
Indices: 50837--50916 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
50827 ATTAAAATGG
* *
50837 TAAAAATAAAATATTTATAAATTTAATTAAA
1 TAAAAATAAAATTTTTATAAATTTAATCAAA
* *
50868 TAAAAATAGAATTTTTATTGAATTTAATCAAA
1 TAAAAATAAAATTTTTA-TAAATTTAATCAAA
* *
50900 TAAAAATATAGTTTTTA
1 TAAAAATAAAATTTTTA
50917 GTATAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 15 0.36
32 27 0.64
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (31 bp):
TAAAAATAAAATTTTTATAAATTTAATCAAA
Found at i:51164 original size:167 final size:166
Alignment explanation
Indices: 50883--51218 Score: 525
Period size: 167 Copynumber: 2.0 Consensus size: 166
50873 ATAGAATTTT
*
50883 TATTGAATTTAATCAAATAAAAATATAGTTTTTAGTATAATAAAACTGTAAAAGTTTTTTTTTTT
1 TATTGAATTTAATCAAATAAAAATATAGTTTTTAGTAGAATAAAACTGTAAAAG---TTTTTTTT
* *
50948 TGCAACAGTAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTCTAATA
63 TGAAACAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTCTAAT-
*
51013 ATATAGTAATAAAACTGTAAA-AGTTTTTTTGGCAACAGTAAA
127 A-ATAG-AATAAAACTATAAATA-TTTTTTTGGCAACAGTAAA
* *
51055 TATTGAATTTAATTAAAT-AAAATATATTTTTTAGTAGAATAAAACTGTAAAAG-TTTTTTTTGA
1 TATTGAATTTAATCAAATAAAAATATAGTTTTTAGTAGAATAAAACTGTAAAAGTTTTTTTTTGA
*
51118 AACAATATAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTCTAATAATA
66 AACAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTCTAATAATA
51183 GAATAAAACTATAAATATTTTTTTGGCAACAGTAAA
131 GAATAAAACTATAAATATTTTTTTGGCAACAGTAAA
51219 ACTATAAAAT
Statistics
Matches: 156, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
164 32 0.21
165 5 0.03
166 1 0.01
167 68 0.44
171 33 0.21
172 17 0.11
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (166 bp):
TATTGAATTTAATCAAATAAAAATATAGTTTTTAGTAGAATAAAACTGTAAAAGTTTTTTTTTGA
AACAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTCTAATAATA
GAATAAAACTATAAATATTTTTTTGGCAACAGTAAA
Found at i:51227 original size:92 final size:92
Alignment explanation
Indices: 51089--51272 Score: 289
Period size: 92 Copynumber: 2.0 Consensus size: 92
51079 TATTTTTTAG
* * * *
51089 TAGAATAAAACTGTAAAAGTTTTTTTTGAAACAATATAACTGTAAAAGTTTAAACAATGTCATTT
1 TAGAATAAAACTATAAAAGTTTTTTTGGAAACAATAAAACTATAAAAGTTTAAACAATGTCATTT
51154 AAGAAATATATGTAAAAATTCTAATAA
66 AAGAAATATATGTAAAAATTCTAATAA
* * *
51181 TAGAATAAAACTATAAATA-TTTTTTTGGCAACAGTAAAACTATAAAATTTTAAACAATGTCATT
1 TAGAATAAAACTATAAA-AGTTTTTTTGGAAACAATAAAACTATAAAAGTTTAAACAATGTCATT
51245 TAAGAAATATATGTAAAAATTCTAATAA
65 TAAGAAATATATGTAAAAATTCTAATAA
51273 ATCTAAGTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 83 0.99
93 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (92 bp):
TAGAATAAAACTATAAAAGTTTTTTTGGAAACAATAAAACTATAAAAGTTTAAACAATGTCATTT
AAGAAATATATGTAAAAATTCTAATAA
Found at i:51970 original size:17 final size:18
Alignment explanation
Indices: 51948--51983 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
51938 AACCAATAAG
51948 ACTAATATA-TTTAAAAA
1 ACTAATATATTTTAAAAA
51965 ACTAATATATTTTAAAAA
1 ACTAATATATTTTAAAAA
51983 A
1 A
51984 GTACCTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
ACTAATATATTTTAAAAA
Found at i:52475 original size:59 final size:60
Alignment explanation
Indices: 52308--52467 Score: 243
Period size: 59 Copynumber: 2.7 Consensus size: 60
52298 CGACGCCAGG
* *
52308 TCCTTATTTGAACATTTTGGCAAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGAG
1 TCCTTATTTGAACATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAC
* *
52368 TCCTTATTTGAACATTTTGGCAAATGTTAGG-CCTTATTTGGTCAAATTAAAAGATCAGAC
1 TCCTTATTTGAACATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC-GAC
* *
52428 T-CTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 TCCTTATTTGAACATTTTGGCAAACGTTAGGCCCTTATTTG
52468 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
59 49 0.54
60 42 0.46
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (60 bp):
TCCTTATTTGAACATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAC
Found at i:59011 original size:78 final size:78
Alignment explanation
Indices: 58911--59067 Score: 235
Period size: 78 Copynumber: 2.0 Consensus size: 78
58901 AACGCGGTCA
* * * *
58911 TGACCAACGCCCCCGGCGTCCGCCAAGCGGTCCAATAGAAGGGCAGCCTCCT-CACCACCAACGT
1 TGACCAACACCCCCGGCCTCCGCCAACCGGTCCAACAGAAGGGCAGCCTCCTCCA-CACCAACGT
58975 CCACAGCCACTTGG
65 CCACAGCCACTTGG
* *
58989 TGACCAACACTCCCGGCCTCCGCCAACCGGTCCAACAGAGGGGCAGCCTCCTCCACACCAACGTC
1 TGACCAACACCCCCGGCCTCCGCCAACCGGTCCAACAGAAGGGCAGCCTCCTCCACACCAACGTC
*
59054 TACAGCCACTTGG
66 CACAGCCACTTGG
59067 T
1 T
59068 CCATCTCCGC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
78 69 0.97
79 2 0.03
ACGTcount: A:0.23, C:0.43, G:0.22, T:0.13
Consensus pattern (78 bp):
TGACCAACACCCCCGGCCTCCGCCAACCGGTCCAACAGAAGGGCAGCCTCCTCCACACCAACGTC
CACAGCCACTTGG
Found at i:66889 original size:87 final size:87
Alignment explanation
Indices: 66736--66911 Score: 266
Period size: 87 Copynumber: 2.0 Consensus size: 87
66726 ACCCTTTTTT
66736 TTCAAATATATTTCTAAATTTCCATTGCTAAATAATATTTTAATTATTTCATCAATAAAAAATAG
1 TTCAAATATATTTCTAAATTTCCATTGCTAAATAATATTTTAATTATTTCATCAATAAAAAATAG
66801 AAATTTAGATTATCTTCATTAA
66 AAATTTAGATTATCTTCATTAA
* * * * * *
66823 TTCATATATATTTCTAAATTGT-CATT-ATCAAATAATATTTTATTTATTTCATTAATACAAACT
1 TTCAAATATATTTCTAAATT-TCCATTGCT-AAATAATATTTTAATTATTTCATCAATAAAAAAT
66886 AGAAATTTAGATTATCTTCATTAA
64 AGAAATTTAGATTATCTTCATTAA
66910 TT
1 TT
66912 AGGACCCAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
86 1 0.01
87 79 0.98
88 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.46
Consensus pattern (87 bp):
TTCAAATATATTTCTAAATTTCCATTGCTAAATAATATTTTAATTATTTCATCAATAAAAAATAG
AAATTTAGATTATCTTCATTAA
Found at i:67164 original size:221 final size:220
Alignment explanation
Indices: 66781--67223 Score: 805
Period size: 221 Copynumber: 2.0 Consensus size: 220
66771 TATTTTAATT
* *
66781 ATTTCATCAATAAAAAATAGAAATTTAGATTATCTTCATTAATTCATATATATTTCTAAATTGTC
1 ATTTCATCAATAAAAAATAGAAATTTAGATTATATTCATTAATTCAAATATATTTCTAAATTGTC
*
66846 ATTATCAAATAATATTTTATTTATTTCATTAATACAAACTAGAAATTTAGATTATCTTCATTAAT
66 ATTATCAAATAATATTTTATTTATTTCATTAATAAAAACTAGAAATTTAGATTATCTTCATTAAT
*
66911 TAGGACCCAACGTTGCCAATAGGAATGCTCCACATCATCTTTAGCATCTGAATTTTCGTCCAAAA
131 TAGGACCCAACGTGGCCAATAGGAATGCTCCACATCATC-TTAGCATCTGAATTTTCGTCCAAAA
*
66976 CATTCTCCAAGTTGGTTTAGGAGAAG
195 CATTCTCCAAATTGGTTTAGGAGAAG
*
67002 ATTTCATTAATAAAAAATAGAAATTTAGATTATATTCATTAATTCAAATATATTTCTAAATTGTC
1 ATTTCATCAATAAAAAATAGAAATTTAGATTATATTCATTAATTCAAATATATTTCTAAATTGTC
*
67067 ATTATTAAATAATATTTTATTTATTTCATTAATAAAAACTAGAAATTTAGATTATCTTCATTAAT
66 ATTATCAAATAATATTTTATTTATTTCATTAATAAAAACTAGAAATTTAGATTATCTTCATTAAT
*
67132 TAGGACCCAACGTGGCCAATAGGAATGCTCCACATTATCTTAGCATCTGAATTTTCGTCCAAAAC
131 TAGGACCCAACGTGGCCAATAGGAATGCTCCACATCATCTTAGCATCTGAATTTTCGTCCAAAAC
67197 ATTCTCCAAATTGGTTTAGGAGAAG
196 ATTCTCCAAATTGGTTTAGGAGAAG
67222 AT
1 AT
67224 CAATTCTATC
Statistics
Matches: 214, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
220 52 0.24
221 162 0.76
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (220 bp):
ATTTCATCAATAAAAAATAGAAATTTAGATTATATTCATTAATTCAAATATATTTCTAAATTGTC
ATTATCAAATAATATTTTATTTATTTCATTAATAAAAACTAGAAATTTAGATTATCTTCATTAAT
TAGGACCCAACGTGGCCAATAGGAATGCTCCACATCATCTTAGCATCTGAATTTTCGTCCAAAAC
ATTCTCCAAATTGGTTTAGGAGAAG
Found at i:69762 original size:21 final size:22
Alignment explanation
Indices: 69692--69811 Score: 79
Period size: 22 Copynumber: 5.5 Consensus size: 22
69682 AGTTTATTAA
*
69692 AAAATTTCATA-GTTAGGTTATC
1 AAAATTTCATATGGTA-GTTATC
* * *
69714 AAAGTCTCTTATGG-AGTTTATC
1 AAAATTTCATATGGTAG-TTATC
* *
69736 ACAATTTTATA-GGTAAG-TATC
1 AAAATTTCATATGGT-AGTTATC
*
69757 AAAATTTCATATGGTGGTTATC
1 AAAATTTCATATGGTAGTTATC
* *
69779 AAAATTTGATACT-GTAGTTACC
1 AAAATTTCATA-TGGTAGTTATC
*
69801 GAAATTTCATA
1 AAAATTTCATA
69812 AAAGTATTCA
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
21 17 0.23
22 53 0.72
23 4 0.05
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (22 bp):
AAAATTTCATATGGTAGTTATC
Found at i:73463 original size:23 final size:22
Alignment explanation
Indices: 73395--73478 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
73385 TCTCACAGAG
* *
73395 AGGTTATGAAAA-ATCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
73416 AGATTA-CAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* **
73437 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATCAAAATTTCATAGGA
*
73460 AGGTTATCAAAGTTTCATA
1 AGGTTATCAAAATTTCATA
73479 TTTCATAAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 4 0.08
21 15 0.29
22 17 0.33
23 15 0.29
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:73506 original size:22 final size:21
Alignment explanation
Indices: 73478--73552 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 21
73468 AAAGTTTCAT
*
73478 ATTTCATAAGTAAATTATCAAA
1 ATTTCATAAGT-AGTTATCAAA
*
73500 ATTTCATAACGTGGTTATCAAA
1 ATTTCATAA-GTAGTTATCAAA
*
73522 ATTTAATAAGTTAGTTATCAAA
1 ATTTCATAAG-TAGTTATCAAA
73544 ATTTCATAA
1 ATTTCATAA
73553 AAATATTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 43 0.93
23 2 0.04
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (21 bp):
ATTTCATAAGTAGTTATCAAA
Found at i:74937 original size:124 final size:128
Alignment explanation
Indices: 74797--75052 Score: 387
Period size: 124 Copynumber: 2.0 Consensus size: 128
74787 CATTGTTTAA
*
74797 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
74858 -TGATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTGATTTTTACCATTTTACTATTTT-ATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
74921 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--C
* ** *
74986 TATTTTATTTTTACCATTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTCAATA
64 TA-TTGATTTTTACCATTTTACTATTTTATTAAAAAAACTTATATATATTAGAATTTTTTAAATA
75051 T
128 T
75052 A
1 A
75053 TTTCTTTAAA
Statistics
Matches: 118, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
124 54 0.46
125 1 0.01
126 1 0.01
127 1 0.01
130 2 0.02
131 36 0.31
132 23 0.19
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:76716 original size:28 final size:28
Alignment explanation
Indices: 76684--76739 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
76674 ATCAAAATTA
76684 TTTTGGTACTTTGTTAGTTTACTAATAG
1 TTTTGGTACTTTGTTAGTTTACTAATAG
*
76712 TTTTGGTGCTTTGTTAGTTTACTAATAG
1 TTTTGGTACTTTGTTAGTTTACTAATAG
76740 GGAGAGGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.54
Consensus pattern (28 bp):
TTTTGGTACTTTGTTAGTTTACTAATAG
Done.