Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017170.1 Corchorus olitorius cultivar O-4 contig17203, 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: 43555
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8224 original size:21 final size:19
Alignment explanation
Indices: 8177--8234 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
8167 CTGTTTAGCA
8177 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* * *
8196 ATTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
8217 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
8235 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:9202 original size:20 final size:19
Alignment explanation
Indices: 9165--9205 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
9155 AATGGGACTC
9165 TTCTTTTATTATTTTCATT
1 TTCTTTTATTATTTTCATT
9184 TTCTATTTA-TATTTGTCATT
1 TTCT-TTTATTATTT-TCATT
9204 TT
1 TT
9206 TTTCAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (19 bp):
TTCTTTTATTATTTTCATT
Found at i:13923 original size:27 final size:27
Alignment explanation
Indices: 13893--13988 Score: 113
Period size: 27 Copynumber: 3.6 Consensus size: 27
13883 CAATGGCGAC
*
13893 CTTCATTTGCATGATCAAACTGGTTTT
1 CTTCATTTTCATGATCAAACTGGTTTT
* * **
13920 CTTCATTTTCATGATGAAA-TAGGCTCC
1 CTTCATTTTCATGATCAAACT-GGTTTT
* *
13947 CTTCATTTCCATGACCAAACTGGTTTT
1 CTTCATTTTCATGATCAAACTGGTTTT
13974 CTTCATTTTCATGAT
1 CTTCATTTTCATGAT
13989 GAAATAGGCT
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
26 1 0.02
27 52 0.96
28 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (27 bp):
CTTCATTTTCATGATCAAACTGGTTTT
Found at i:13974 original size:54 final size:54
Alignment explanation
Indices: 13892--14014 Score: 228
Period size: 54 Copynumber: 2.3 Consensus size: 54
13882 ACAATGGCGA
* *
13892 CCTTCATTTGCATGATCAAACTGGTTTTCTTCATTTTCATGATGAAATAGGCTC
1 CCTTCATTTCCATGACCAAACTGGTTTTCTTCATTTTCATGATGAAATAGGCTC
13946 CCTTCATTTCCATGACCAAACTGGTTTTCTTCATTTTCATGATGAAATAGGCTC
1 CCTTCATTTCCATGACCAAACTGGTTTTCTTCATTTTCATGATGAAATAGGCTC
14000 CCTTCATTTCCATGA
1 CCTTCATTTCCATGA
14015 TATAAATCTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.40
Consensus pattern (54 bp):
CCTTCATTTCCATGACCAAACTGGTTTTCTTCATTTTCATGATGAAATAGGCTC
Found at i:14004 original size:27 final size:27
Alignment explanation
Indices: 13920--14015 Score: 113
Period size: 27 Copynumber: 3.6 Consensus size: 27
13910 AACTGGTTTT
*
13920 CTTCATTTTCATGATGAAATAGGCTCC
1 CTTCATTTCCATGATGAAATAGGCTCC
** * **
13947 CTTCATTTCCATGACCAAACT-GGTTTT
1 CTTCATTTCCATGATGAAA-TAGGCTCC
*
13974 CTTCATTTTCATGATGAAATAGGCTCC
1 CTTCATTTCCATGATGAAATAGGCTCC
14001 CTTCATTTCCATGAT
1 CTTCATTTCCATGAT
14016 ATAAATCTTC
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
26 1 0.02
27 52 0.96
28 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (27 bp):
CTTCATTTCCATGATGAAATAGGCTCC
Found at i:15673 original size:12 final size:12
Alignment explanation
Indices: 15658--15691 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15648 ACACTTAACC
15658 AAAAGAGAGAGA
1 AAAAGAGAGAGA
15670 AAAAGAGAGAGA
1 AAAAGAGAGAGA
* *
15682 CAGAGAGAGA
1 AAAAGAGAGA
15692 AGAAGAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (12 bp):
AAAAGAGAGAGA
Found at i:20394 original size:96 final size:96
Alignment explanation
Indices: 20230--20424 Score: 372
Period size: 96 Copynumber: 2.0 Consensus size: 96
20220 CTATGTTGTG
20230 GGTTCAAATCCCACTACCAACAAATCTTCTTTTAAAATTCAAATTTTGAAAGTCATTCAACATGT
1 GGTTCAAATCCCACTACCAACAAATCTTCTTTTAAAATTCAAATTTTGAAAGTCATTCAACATGT
20295 CAAGAACCGGTCAAAACCGATCCGATTCTCC
66 CAAGAACCGGTCAAAACCGATCCGATTCTCC
*
20326 GGTTCAACTCCCACTACCAACAAATCTTCTTTTAAAATTCAAATTTTGAAAGTCATTCAACATGT
1 GGTTCAAATCCCACTACCAACAAATCTTCTTTTAAAATTCAAATTTTGAAAGTCATTCAACATGT
*
20391 CAAGAACCGGTCAAAACCGATCCGATTCTTC
66 CAAGAACCGGTCAAAACCGATCCGATTCTCC
20422 GGT
1 GGT
20425 CCGATCAACA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (96 bp):
GGTTCAAATCCCACTACCAACAAATCTTCTTTTAAAATTCAAATTTTGAAAGTCATTCAACATGT
CAAGAACCGGTCAAAACCGATCCGATTCTCC
Found at i:21307 original size:105 final size:104
Alignment explanation
Indices: 21152--21419 Score: 439
Period size: 105 Copynumber: 2.6 Consensus size: 104
21142 TAAAATTTTG
* *
21152 ATTTTAATTTTGGCTAAACTTAGTG-AATTAGTTATATATTTTACTTCTAAAACCCTATAACAAT
1 ATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAACAAT
**
21216 ATTATTAATTATGGAATTTATTCTCAAAATAAAAATAAA
66 ATTATTAATTATGGAATTTACCCTCAAAATAAAAATAAA
21255 ATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAACAA
1 ATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAACAA
*
21320 TATTATTAATTATGGAATTTACCCTTAAAATAAAAATAAA
65 TATTATTAATTATGGAATTTACCCTCAAAATAAAAATAAA
* * *
21360 ATTTTAATTTAGGGCTAAACTTAGTGAAATTAATTTTGTATTTTATTTCTAAAACCCTAT
1 ATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTAT
21420 TTTGAAACTT
Statistics
Matches: 154, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
103 10 0.06
104 14 0.09
105 130 0.84
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (104 bp):
ATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAACAAT
ATTATTAATTATGGAATTTACCCTCAAAATAAAAATAAA
Found at i:22131 original size:45 final size:42
Alignment explanation
Indices: 22059--22152 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
22049 AGTGCATTAC
* *
22059 CTAA-ATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACTCCATCTCTAGATAATTCATAAAAATAAAA
*
22100 CTAATATTCTACTCCTCAATCTCTAGATAATTCATAAAAATAAAG
1 CTAATATTCTACT-C-C-ATCTCTAGATAATTCATAAAAATAAAA
22145 CTAATATT
1 CTAATATT
22153 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 1 0.02
44 1 0.02
45 32 0.70
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.34
Consensus pattern (42 bp):
CTAATATTCTACTCCATCTCTAGATAATTCATAAAAATAAAA
Found at i:24041 original size:2 final size:2
Alignment explanation
Indices: 24028--24067 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
24018 ACTAAAAATA
24028 AT AT AT AGT AT AT AT AT AT A- 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 AT AT
24068 GTATGCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24046 original size:13 final size:12
Alignment explanation
Indices: 24028--24067 Score: 64
Period size: 11 Copynumber: 3.3 Consensus size: 12
24018 ACTAAAAATA
24028 ATATATAGTATAT
1 ATATATA-TATAT
24041 ATATATA-ATAT
1 ATATATATATAT
24052 ATATATATATAT
1 ATATATATATAT
24064 ATAT
1 ATAT
24068 GTATGCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.42
12 8 0.31
13 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
ATATATATATAT
Found at i:27382 original size:29 final size:30
Alignment explanation
Indices: 27327--27384 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
27317 GGAGGCTGAA
* ***
27327 ATTGATAGTTTAGGGGGCAATTTGTCCAAG
1 ATTGATAGTTTAGGGGACAAAGCGTCCAAG
27357 ATTGA-AGTTTAGGGGACAAAGCGTCCAA
1 ATTGATAGTTTAGGGGACAAAGCGTCCAA
27385 CTGGTATGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.28
Consensus pattern (30 bp):
ATTGATAGTTTAGGGGACAAAGCGTCCAAG
Found at i:27483 original size:29 final size:31
Alignment explanation
Indices: 27449--27517 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
27439 GAAAGTTTAT
* *
27449 GGGGCAAAATGTCCAAA-ATT-GAAGTTCAG
1 GGGGCAAAATGTCCAAACATTACAAGTTAAG
* *
27478 GTGGCAAAATTTCCAAACATTACAAGTTAAG
1 GGGGCAAAATGTCCAAACATTACAAGTTAAG
27509 GGGGCAAAA
1 GGGGCAAAA
27518 AGGATATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 15 0.45
30 3 0.09
31 15 0.45
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (31 bp):
GGGGCAAAATGTCCAAACATTACAAGTTAAG
Found at i:27642 original size:304 final size:304
Alignment explanation
Indices: 27093--27993 Score: 1520
Period size: 304 Copynumber: 3.0 Consensus size: 304
27083 TAAATGGACG
* * *
27093 TTTTGCCCCCTGAACTTGTACGGTTTGGATGTTTTCCCCCCT-AAGAGTTTATGGGGCAAAATGT
1 TTTTGCCCCCTGAACTTGTACGGTTCGGACGTTTTGCCCCCTGAA-AGTTTATGGGGCAAAATGT
* * * * *
27157 TCAAAATTAAAGTTCAGGTGGTAAAATGTCCAAACATTACAAGTTGAGGGGGCAAAAAGGATATT
65 CCAAAATTGAAGTTCAGGTGGCAAAATTTCCAAACATTACAAGTTAAGGGGGCAAAAAGGATATT
**
27222 AAACTGTCCGATGTGGCACGCCACATCAGCAGGGTTGCGGCGCCGTTAGTCATGTGGGTCACATG
130 AAACTGTCCGATGTGGCACGCCACATCAGCACCGTTGCGGCGCCGTTAGTCATGTGGGTCACATG
*
27287 ACTAACGGTTCATTATAGTGAGGGGGCAACGGAGGCTGAAATTGATAGTTTAGGGGGCAATTTGT
195 ACTAACGGTTCATTATAGTGAGGGGGCAACGGAGGCTGAAATTGATAGTTTATGGGGCAATTTGT
27352 CCAAGATTGAAGTTTAGGGGACAAAGCGTCCAACTGGTATGTCCA
260 CCAAGATTGAAGTTTAGGGGACAAAGCGTCCAACTGGTATGTCCA
27397 TTTTGCCCCCTGAACTTGTACGGTTCGGACGTTTTGCCCCCTGAAAGTTTATGGGGCAAAATGTC
1 TTTTGCCCCCTGAACTTGTACGGTTCGGACGTTTTGCCCCCTGAAAGTTTATGGGGCAAAATGTC
27462 CAAAATTGAAGTTCAGGTGGCAAAATTTCCAAACATTACAAGTTAAGGGGGCAAAAAGGATATTA
66 CAAAATTGAAGTTCAGGTGGCAAAATTTCCAAACATTACAAGTTAAGGGGGCAAAAAGGATATTA
*
27527 AACTGTCCGATGTGGCACGCCACATCAGCACCGTTGCGGCACCGTTAGTCATGTGGGTCACATGA
131 AACTGTCCGATGTGGCACGCCACATCAGCACCGTTGCGGCGCCGTTAGTCATGTGGGTCACATGA
*
27592 CTAATGGTTCATTATAGTGAGGGGGCAACGGAGGCTGAAATTGATAGTTTATGGGGCAATTTGTC
196 CTAACGGTTCATTATAGTGAGGGGGCAACGGAGGCTGAAATTGATAGTTTATGGGGCAATTTGTC
**
27657 CAAGATTGAAGTTTAGGGGACAAAGTATCCAACTGGTATGTCCA
261 CAAGATTGAAGTTTAGGGGACAAAGCGTCCAACTGGTATGTCCA
27701 TTTTGCCCCCTGAACTTGTACGGTTCGGACGTTTTGCCCCCTGAAAGTTTATGGGGCAAAATGTC
1 TTTTGCCCCCTGAACTTGTACGGTTCGGACGTTTTGCCCCCTGAAAGTTTATGGGGCAAAATGTC
*
27766 CAAAATTGAAGTTCAGGTGGCAAAATTTCCAAACATTACAAGTTAAGGAGGCAAAAAGGATATTA
66 CAAAATTGAAGTTCAGGTGGCAAAATTTCCAAACATTACAAGTTAAGGGGGCAAAAAGGATATTA
* * *
27831 AACTGTCCGATGTGGCACGCCATATCAGCACCGTTGCGGCGCAGTTAGTCACGTGGGTCACATGA
131 AACTGTCCGATGTGGCACGCCACATCAGCACCGTTGCGGCGCCGTTAGTCATGTGGGTCACATGA
* * * * * *
27896 TTAACGGTTCA--CTAGTGTGGAGGCAACGGAGGCTGAAATTGATAGTTTATGAGGCAATTTATC
196 CTAACGGTTCATTATAGTGAGGGGGCAACGGAGGCTGAAATTGATAGTTTATGGGGCAATTTGTC
* * *
27959 CAAAATTAAAGTTTAGGGGACAAAGCGTTCAACTG
261 CAAGATTGAAGTTTAGGGGACAAAGCGTCCAACTG
27994 ATATAAGTTC
Statistics
Matches: 564, Mismatches: 32, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
302 77 0.14
304 485 0.86
305 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (304 bp):
TTTTGCCCCCTGAACTTGTACGGTTCGGACGTTTTGCCCCCTGAAAGTTTATGGGGCAAAATGTC
CAAAATTGAAGTTCAGGTGGCAAAATTTCCAAACATTACAAGTTAAGGGGGCAAAAAGGATATTA
AACTGTCCGATGTGGCACGCCACATCAGCACCGTTGCGGCGCCGTTAGTCATGTGGGTCACATGA
CTAACGGTTCATTATAGTGAGGGGGCAACGGAGGCTGAAATTGATAGTTTATGGGGCAATTTGTC
CAAGATTGAAGTTTAGGGGACAAAGCGTCCAACTGGTATGTCCA
Found at i:27787 original size:29 final size:31
Alignment explanation
Indices: 27755--27821 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
27745 AAGTTTATGG
* * *
27755 GGCAAAATGTCCAAA-ATT-GAAGTTCAGGT
1 GGCAAAATGTCCAAACATTACAAGTTAAGGA
*
27784 GGCAAAATTTCCAAACATTACAAGTTAAGGA
1 GGCAAAATGTCCAAACATTACAAGTTAAGGA
27815 GGCAAAA
1 GGCAAAA
27822 AGGATATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.44
30 3 0.09
31 15 0.47
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (31 bp):
GGCAAAATGTCCAAACATTACAAGTTAAGGA
Found at i:29229 original size:46 final size:45
Alignment explanation
Indices: 29144--29238 Score: 109
Period size: 46 Copynumber: 2.1 Consensus size: 45
29134 GTTATCACAC
* * * *
29144 TGAGTTCCTTCAATCAACATTTCTCCACATAGCATATTATCAATT
1 TGAGGTCCTTCAATCAACATTACTCCAAATAGCACATTATCAATT
* * * *
29189 TGAGGTCCATTCATTCAACATTACTCCAAATGGTACATTATCAGTT
1 TGAGGTCC-TTCAATCAACATTACTCCAAATAGCACATTATCAATT
29235 TGAG
1 TGAG
29239 TGCTCCATGT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 7 0.17
46 34 0.83
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (45 bp):
TGAGGTCCTTCAATCAACATTACTCCAAATAGCACATTATCAATT
Found at i:31538 original size:15 final size:15
Alignment explanation
Indices: 31514--31543 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31504 AAAGCTACGG
31514 TTTTTCAATACATAT
1 TTTTTCAATACATAT
*
31529 TTTTTTAATACATAT
1 TTTTTCAATACATAT
31544 ATCATTATAT
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:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTTCAATACATAT
Found at i:32663 original size:52 final size:54
Alignment explanation
Indices: 32563--32671 Score: 195
Period size: 52 Copynumber: 2.0 Consensus size: 54
32553 ACTTCTTCTA
32563 AAGATTAGGAAACTAATTAAAAACAACAGACTACAAAAACATATAAAGGAAAGAT
1 AAGATTAGGAAACTAATT-AAAACAACAGACTACAAAAACATATAAAGGAAAGAT
32618 AAGATTAGGAAACTAATT-AAA-AACAGACTACAAAAACATATAAAGGAAAGAT
1 AAGATTAGGAAACTAATTAAAACAACAGACTACAAAAACATATAAAGGAAAGAT
32670 AA
1 AA
32672 ACATCATCAG
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 33 0.61
53 3 0.06
55 18 0.33
ACGTcount: A:0.61, C:0.10, G:0.13, T:0.17
Consensus pattern (54 bp):
AAGATTAGGAAACTAATTAAAACAACAGACTACAAAAACATATAAAGGAAAGAT
Found at i:32785 original size:15 final size:15
Alignment explanation
Indices: 32765--32795 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32755 TCGTCACCAA
*
32765 CCTCATTCTTAGAAC
1 CCTCATTCTCAGAAC
32780 CCTCATTCTCAGAAC
1 CCTCATTCTCAGAAC
32795 C
1 C
32796 AGATTCCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.39, G:0.06, T:0.29
Consensus pattern (15 bp):
CCTCATTCTCAGAAC
Found at i:34570 original size:11 final size:11
Alignment explanation
Indices: 34554--34579 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34544 GTTTTAGATC
34554 TTTTCTTCTAG
1 TTTTCTTCTAG
34565 TTTTCTTCTAG
1 TTTTCTTCTAG
34576 TTTT
1 TTTT
34580 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:35349 original size:22 final size:20
Alignment explanation
Indices: 35323--35370 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
35313 GCCATAGATC
* *
35323 TTAATTTACTTTGCTTTGTTT
1 TTAATTTA-ATTGCTTTCTTT
*
35344 TCTAATATAATTGCTTTCTTT
1 T-TAATTTAATTGCTTTCTTT
35365 TTAATT
1 TTAATT
35371 GTTTTCTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.18
21 12 0.55
22 6 0.27
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.62
Consensus pattern (20 bp):
TTAATTTAATTGCTTTCTTT
Found at i:35753 original size:15 final size:15
Alignment explanation
Indices: 35733--35763 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35723 CCGTCACCAA
35733 CCTCATTCTCAGAAC
1 CCTCATTCTCAGAAC
35748 CCTCATTCTCAGAAC
1 CCTCATTCTCAGAAC
35763 C
1 C
35764 AGAACCCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.42, G:0.06, T:0.26
Consensus pattern (15 bp):
CCTCATTCTCAGAAC
Found at i:36874 original size:15 final size:15
Alignment explanation
Indices: 36851--36881 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36841 CCGTCACCAA
36851 CCTCATTCTCAGAAC
1 CCTCATTCTCAGAAC
*
36866 CCTCTTTCTCAGAAC
1 CCTCATTCTCAGAAC
36881 C
1 C
36882 AGAACCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.42, G:0.06, T:0.29
Consensus pattern (15 bp):
CCTCATTCTCAGAAC
Found at i:37981 original size:15 final size:15
Alignment explanation
Indices: 37961--37991 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37951 CTGTCACCAA
*
37961 CCTCATTCTCAGAAC
1 CCTCATTCTCAAAAC
37976 CCTCATTCTCAAAAC
1 CCTCATTCTCAAAAC
37991 C
1 C
37992 AGAACCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.42, G:0.03, T:0.26
Consensus pattern (15 bp):
CCTCATTCTCAAAAC
Found at i:39078 original size:15 final size:15
Alignment explanation
Indices: 39058--39088 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39048 CCGTCACCAA
39058 CCTCATTCTCAAAAC
1 CCTCATTCTCAAAAC
*
39073 CCTCATTCTCAGAAC
1 CCTCATTCTCAAAAC
39088 C
1 C
39089 AGAACCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.42, G:0.03, T:0.26
Consensus pattern (15 bp):
CCTCATTCTCAAAAC
Found at i:40188 original size:15 final size:15
Alignment explanation
Indices: 40168--40198 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40158 CCGTCACCAA
40168 CCTCATTCTCAAAAC
1 CCTCATTCTCAAAAC
*
40183 CCTCATTCTCAGAAC
1 CCTCATTCTCAAAAC
40198 C
1 C
40199 AGAACCTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.42, G:0.03, T:0.26
Consensus pattern (15 bp):
CCTCATTCTCAAAAC
Found at i:41302 original size:15 final size:15
Alignment explanation
Indices: 41282--41312 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41272 CTGTCACCAA
41282 CCTCATTCTCAAAAC
1 CCTCATTCTCAAAAC
*
41297 CCTCATTCTCAGAAC
1 CCTCATTCTCAAAAC
41312 C
1 C
41313 AGAACCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.42, G:0.03, T:0.26
Consensus pattern (15 bp):
CCTCATTCTCAAAAC
Done.