Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014898.1 Corchorus olitorius cultivar O-4 contig14931, 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: 104996
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:12686 original size:60 final size:60
Alignment explanation
Indices: 12599--12755 Score: 199
Period size: 60 Copynumber: 2.6 Consensus size: 60
12589 GACTGATTGC
* * * * * *
12599 TCAAATAGGTCCTTAATGTATGCGAAAATGTTCAATTTA-GGCCTCATGCTTTTAATTTGG
1 TCAAATAGGACCCTAACGTATGCGAAAATGATCAAATAAGGGCC-CATGCTTTTAATTTGG
* *
12659 TTAAATAGGACCCTAACGTACGCGAAAATGATCAAATAAGGGCCCATGCTTTTAATTTGG
1 TCAAATAGGACCCTAACGTATGCGAAAATGATCAAATAAGGGCCCATGCTTTTAATTTGG
* * *
12719 TCAAATAGGGCCCTAACGTATGCAAAAATGCTCAAAT
1 TCAAATAGGACCCTAACGTATGCGAAAATGATCAAAT
12756 GACGCCCTGA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 79 0.95
61 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (60 bp):
TCAAATAGGACCCTAACGTATGCGAAAATGATCAAATAAGGGCCCATGCTTTTAATTTGG
Found at i:13477 original size:19 final size:18
Alignment explanation
Indices: 13440--13487 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
13430 CTGGAATTAT
13440 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
* *
13458 TAATTATTT-TT-CAGAA
1 TAATTATTTATTAAATAA
13474 TAATTA-TTATTAAA
1 TAATTATTTATTAAA
13488 ATTCCCTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 11 0.44
17 3 0.12
18 9 0.36
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:15671 original size:59 final size:60
Alignment explanation
Indices: 15600--15727 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
15590 ACATTAGGGT
* * * ** * * * *
15600 CCTATTTGACCAAATTATAAGTATGAGGCCT-AATTGAGCATTTTCGCATACGTTAAGAC
1 CCTATTTAACCAAATTAAAAGCATGAAACCTAAATTGAACATTTCCGAATACATTAAGAC
15659 CCTATTTAACCAAATTAAAAGCATGAAACCTAAATTGAACATTTCCGAATACATTAAGAC
1 CCTATTTAACCAAATTAAAAGCATGAAACCTAAATTGAACATTTCCGAATACATTAAGAC
*
15719 CATATTTAA
1 CCTATTTAA
15728 ACAATTAGCC
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
59 26 0.45
60 32 0.55
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (60 bp):
CCTATTTAACCAAATTAAAAGCATGAAACCTAAATTGAACATTTCCGAATACATTAAGAC
Found at i:19535 original size:17 final size:18
Alignment explanation
Indices: 19506--19540 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
19496 TAATTGTACC
19506 ACCCAATTGAAAGTTTAA
1 ACCCAATTGAAAGTTTAA
19524 ACCCAA-TGAAAGTTTAA
1 ACCCAATTGAAAGTTTAA
19541 GAACTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (18 bp):
ACCCAATTGAAAGTTTAA
Found at i:27512 original size:21 final size:21
Alignment explanation
Indices: 27487--27526 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27477 GTTTCTCCCC
*
27487 TTTTCTCTCTTTTTACTTTGT
1 TTTTCCCTCTTTTTACTTTGT
* *
27508 TTTTCCCTTTTTTTCCTTT
1 TTTTCCCTCTTTTTACTTT
27527 CCTTTTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.23, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTCCCTCTTTTTACTTTGT
Found at i:27532 original size:21 final size:21
Alignment explanation
Indices: 27485--27532 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
27475 GGGTTTCTCC
*
27485 CCTTTTCTCTCTTTTTACTTT
1 CCTTTTCCCTCTTTTTACTTT
** * *
27506 GTTTTTCCCTTTTTTTCCTTT
1 CCTTTTCCCTCTTTTTACTTT
27527 CCTTTT
1 CCTTTT
27533 TTTTTATTAG
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (21 bp):
CCTTTTCCCTCTTTTTACTTT
Found at i:33343 original size:25 final size:25
Alignment explanation
Indices: 33312--33364 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
33302 GAGGGCATCT
*
33312 TCAATGTGATGCATCAAATTCTGCA
1 TCAATGTGATGCACCAAATTCTGCA
33337 TCAATGTGATGCACCAAATTCTGCA
1 TCAATGTGATGCACCAAATTCTGCA
33362 TCA
1 TCA
33365 TTTTTGTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (25 bp):
TCAATGTGATGCACCAAATTCTGCA
Found at i:37408 original size:2 final size:2
Alignment explanation
Indices: 37401--37438 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37391 TGAATGCATG
37401 AT AT 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 AT AT
37439 TTACAACTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43547 original size:15 final size:14
Alignment explanation
Indices: 43503--43549 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
43493 AGAATTCCTA
*
43503 TTTTCTTCTTTTTCA
1 TTTTCTTCTTTTT-T
43518 TTTTCTCTCTTTTTT
1 TTTTCT-TCTTTTTT
43533 TTTTCTGTCTTTTTT
1 TTTTCT-TCTTTTTT
43548 TT
1 TT
43550 GTGTTGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 22 0.76
16 7 0.24
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTTTTT
Found at i:43656 original size:6 final size:6
Alignment explanation
Indices: 43641--43673 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
43631 AGTCCAAGGA
43641 TTTTTG -TTTTG TTTTTG TTTTTG TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
43674 ATTCTGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:43673 original size:17 final size:17
Alignment explanation
Indices: 43641--43672 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43631 AGTCCAAGGA
43641 TTTTTGTTTTGTTTTTG
1 TTTTTGTTTTGTTTTTG
43658 TTTTTGTTTT-TTTTT
1 TTTTTGTTTTGTTTTT
43673 TATTCTGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (17 bp):
TTTTTGTTTTGTTTTTG
Found at i:45901 original size:28 final size:29
Alignment explanation
Indices: 45846--45903 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
45836 CAAAGACTCA
**
45846 AACAAAATTAATTAAAAAGGGTTAGGCCC
1 AACAAAATTAATTAAAAAGGGAGAGGCCC
* *
45875 AACAAGATTAATT-GAAAGGGAGAGGCCC
1 AACAAAATTAATTAAAAAGGGAGAGGCCC
45903 A
1 A
45904 GCAGGGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.17
Consensus pattern (29 bp):
AACAAAATTAATTAAAAAGGGAGAGGCCC
Found at i:46259 original size:65 final size:64
Alignment explanation
Indices: 46155--46668 Score: 452
Period size: 65 Copynumber: 7.9 Consensus size: 64
46145 GTGTCTACAT
** * * *
46155 GATAAAGACCTGTCTGAGGTC-GAATTTAAAACTGAGAAAGACCTGTTTGAGGTCTAAAACTGAA
1 GATAAAGACCTGTCTGAGGTCTGAAACTGAAA--GAGAAAGACCTGTCTGAGGTCTGAAACTGAA
46219 A
64 A
* ** * *
46220 GATAAAGACCTGTCCGAGGTC-GAATTTAAGAACGAGAAAGACCTGTCTGAGGTCTGAAACTAAA
1 GATAAAGACCTGTCTGAGGTCTGAAACT--GAAAGAGAAAGACCTGTCTGAGGTCTGAAACTGAA
46284 A
64 A
* * ** *
46285 CTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTC-GAATTTAAA
1 --GATAAAGACCTGTCTGAGGTCTGAAACTGAAAGAGAAAGACCTGTCTGAGGTCTGAAACTGAA
46349 A
64 A
** * * * ** *
46350 CTGCGAAAGACCTGTCTGAGGTCTGAAACTGAAAGATAAAGACTTGTCTGAGGT-AGAATTTAAA
1 --GATAAAGACCTGTCTGAGGTCTGAAACTGAAAGAGAAAGACCTGTCTGAGGTCTGAAACTGAA
46414 A
64 A
* * * **
46415 CTGAGAAAAACCTGTCTGAGGTCTGAAACTGAAAGATAAAGACCTGT-TCGAGGTC-GAATTTAA
1 --GATAAAGACCTGTCTGAGGTCTGAAACTGAAAGAGAAAGACCTGTCT-GAGGTCTGAAACT--
*
46478 GAAC
61 GAAA
* * *
46482 GAGAAAGACTTGTCTGAGGTCTGAAACTAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAA
1 GATAAAGACCTGTCTGAGGTCTGAAACTGAAA--GAGAAAGACCTGTCTGAGGTCTGAAACTGAA
46547 A
64 A
** * *
46548 GATAAAGACCTGTCTGAGGTC-GAATTTAAAACTGAGAAAGACCTTTCTGAGGTCTGAAACTGAA
1 GATAAAGACCTGTCTGAGGTCTGAAACTGAAA--GAGAAAGACCTGTCTGAGGTCTGAAACTGAA
46612 A
64 A
** * *
46613 GATAAAGACCTGTCTGAGGTCTG-ATTTGAAAGAGAAAGACCTGCCTAAGGT-TGAAA
1 GATAAAGACCTGTCTGAGGTCTGAAACTGAAAGAGAAAGACCTGTCTGAGGTCTGAAA
46669 TTAAAAACTG
Statistics
Matches: 397, Mismatches: 37, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
62 5 0.01
63 17 0.04
64 1 0.00
65 278 0.70
66 46 0.12
67 41 0.10
68 9 0.02
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (64 bp):
GATAAAGACCTGTCTGAGGTCTGAAACTGAAAGAGAAAGACCTGTCTGAGGTCTGAAACTGAAA
Found at i:46430 original size:164 final size:162
Alignment explanation
Indices: 46158--46683 Score: 763
Period size: 164 Copynumber: 3.2 Consensus size: 162
46148 TCTACATGAT
* *
46158 AAAGACCTGTCTGAGGTCGAATTTAAAACTGAGAAAGACCTGTTTGAGGTCTAAAACTGAAAGAT
1 AAAGACCTGTCTGAGGTCGAATTTAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAT
* *
46223 AAAGACCTGTCCGAGGTCGAATTTAAGAAC-GAGAAAGACCTGTCTGAGGTCTGAAACTAAAACT
66 AAAGACCTGTCTGAGGTCGAATTTAA-AACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAA--
* ** *
46287 GAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAT
128 GATAAAGACCTGTCTGAGGTCTGAATTTGAAAGAG
*
46322 AAAGACCTGTCTGAGGTCGAATTTAAAACTGCGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAT
1 AAAGACCTGTCTGAGGTCGAATTTAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAT
* * *
46387 AAAGACTTGTCTGAGGTAGAATTTAAAACTGAGAAAAACCTGTCTGAGGTCTGAAACTGAAAGAT
66 AAAGACCTGTCTGAGGTCGAATTTAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAT
*
46452 AAAGACCTGT-TCGAGGTC-GAATTTAAGAACGAG
131 AAAGACCTGTCT-GAGGTCTGAATTT--GAAAGAG
* **
46485 AAAGACTTGTCTGAGGTCTGAAACTAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGA
1 AAAGACCTGTCTGAGGTC-GAATTTAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGA
*
46550 TAAAGACCTGTCTGAGGTCGAATTTAAAACTGAGAAAGACCTTTCTGAGGTCTGAAACTGAAAGA
65 TAAAGACCTGTCTGAGGTCGAATTTAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGA
46615 TAAAGACCTGTCTGAGGTCTG-ATTTGAAAGAG
130 TAAAGACCTGTCTGAGGTCTGAATTTGAAAGAG
* * * *
46647 AAAGACCTGCCTAAGGTTGAAATTAAAAACTGAGAAA
1 AAAGACCTGTCTGAGGTCG-AATTTAAAACTGAGAAA
46684 AGATGACCTG
Statistics
Matches: 325, Mismatches: 29, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
161 6 0.02
162 52 0.16
163 25 0.08
164 240 0.74
165 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (162 bp):
AAAGACCTGTCTGAGGTCGAATTTAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAT
AAAGACCTGTCTGAGGTCGAATTTAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAT
AAAGACCTGTCTGAGGTCTGAATTTGAAAGAG
Found at i:46556 original size:229 final size:229
Alignment explanation
Indices: 46155--46632 Score: 875
Period size: 229 Copynumber: 2.1 Consensus size: 229
46145 GTGTCTACAT
* * *
46155 GATAAAGACCTGTCTGAGGTCGAATTTAAAACTGAGAAAGACCTGTTTGAGGTCTAAAACTGAAA
1 GATAAAGACCTGTCTGAGGTAGAATTTAAAACTGAGAAAAACCTGTCTGAGGTCTAAAACTGAAA
46220 GATAAAGACCTGTCCGAGGTCGAATTTAAGAACGAGAAAGACCTGTCTGAGGTCTGAAACTAAAA
66 GATAAAGACCTGTCCGAGGTCGAATTTAAGAACGAGAAAGACCTGTCTGAGGTCTGAAACTAAAA
46285 CTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAATTTAAAA
131 CTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAATTTAAAA
*
46350 CTGCGAAAGACCTGTCTGAGGTCTGAAACTGAAA
196 CTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAA
* *
46384 GATAAAGACTTGTCTGAGGTAGAATTTAAAACTGAGAAAAACCTGTCTGAGGTCTGAAACTGAAA
1 GATAAAGACCTGTCTGAGGTAGAATTTAAAACTGAGAAAAACCTGTCTGAGGTCTAAAACTGAAA
* *
46449 GATAAAGACCTGTTCGAGGTCGAATTTAAGAACGAGAAAGACTTGTCTGAGGTCTGAAACTAAAA
66 GATAAAGACCTGTCCGAGGTCGAATTTAAGAACGAGAAAGACCTGTCTGAGGTCTGAAACTAAAA
46514 CTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAATTTAAAA
131 CTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAATTTAAAA
*
46579 CTGAGAAAGACCTTTCTGAGGTCTGAAACTGAAA
196 CTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAA
46613 GATAAAGACCTGTCTGAGGT
1 GATAAAGACCTGTCTGAGGT
46633 CTGATTTGAA
Statistics
Matches: 239, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
229 239 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.23
Consensus pattern (229 bp):
GATAAAGACCTGTCTGAGGTAGAATTTAAAACTGAGAAAAACCTGTCTGAGGTCTAAAACTGAAA
GATAAAGACCTGTCCGAGGTCGAATTTAAGAACGAGAAAGACCTGTCTGAGGTCTGAAACTAAAA
CTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAATTTAAAA
CTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAA
Found at i:46727 original size:39 final size:39
Alignment explanation
Indices: 46680--47037 Score: 476
Period size: 39 Copynumber: 9.2 Consensus size: 39
46670 TAAAAACTGA
* * * * *
46680 GAAAAGATGACCTGGTTCCAGTCAACCTTGGTAACTACT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* *
46719 GAAAAGATGACCTGTTTCCAATCAACTTTGATAAATACT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
46758 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
46797 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
46836 GAAAAGATGACCTGTTTCCAGTCAA-TCTTGATAACTGCT
1 GAAAAGATGACCTGTTTCCAGTCAACT-TTGATAAATGCT
**
46875 GAAAGAGATGACCTGCCTCCAGTCAACTTTGATAAATGCT
1 GAAA-AGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
46915 GAAAAGATGACCTGTTTCCAGTCAA-TCTTGATAACTGCT
1 GAAAAGATGACCTGTTTCCAGTCAACT-TTGATAAATGCT
* * *
46954 GAAAGAGATGACCTGCTTCCAGTCAACTTTAATAACT--T
1 GAAA-AGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* * * *
46992 G-AAGGAAGACCTGTTTCCAGTCAACTTTGATAAGTACT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
47030 G-AAAGATG
1 GAAAAGATG
47038 TTCTAAAACA
Statistics
Matches: 288, Mismatches: 23, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
36 27 0.09
37 2 0.01
38 11 0.04
39 184 0.64
40 62 0.22
41 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (39 bp):
GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
Found at i:47202 original size:98 final size:105
Alignment explanation
Indices: 47072--47285 Score: 282
Period size: 108 Copynumber: 2.1 Consensus size: 105
47062 AATTGAAGCA
* *
47072 TTGAA-AAAAGACTACACTGGATCGTTGAAGTAAATTGATGCATTG-AG-G-A-ATTGAAACTG-
1 TTGAAGAAAAGACCACACTGGATCGTTGAAGTAAACTGATGCATTGAAGAGAATATTGAAACTGA
*
47131 A-AATTGAAATATTGAAATTGAAGCATTGAAGGATTGAAT
66 AGAATTGAAATATTGAAATTGAAACATTGAAGGATTGAAT
47170 TTGAAGAAAA-ACCACACTGGATCGTTGAAGTAAACTGATGCATTGAAGAATTGAAATATTGAAA
1 TTGAAGAAAAGACCACACTGGATCGTTGAAGTAAACTGATGCATTGAAG-A--G-AATATTGAAA
* * *
47234 TTGAAGAATTGAAGTATTGAAATTTAAACATTGAAGGATTGAAT
62 CTGAAGAATTGAAATATTGAAATTGAAACATTGAAGGATTGAAT
47278 TTGAAGAA
1 TTGAAGAA
47286 TTGAAATTGA
Statistics
Matches: 99, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
98 38 0.38
99 6 0.06
103 1 0.01
105 1 0.01
106 9 0.09
107 1 0.01
108 43 0.43
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (105 bp):
TTGAAGAAAAGACCACACTGGATCGTTGAAGTAAACTGATGCATTGAAGAGAATATTGAAACTGA
AGAATTGAAATATTGAAATTGAAACATTGAAGGATTGAAT
Found at i:47224 original size:8 final size:7
Alignment explanation
Indices: 47211--47720 Score: 149
Period size: 8 Copynumber: 70.7 Consensus size: 7
47201 AAACTGATGC
47211 ATTGAAGA
1 ATTGAA-A
47219 ATTGAAA
1 ATTGAAA
47226 TATTG-AA
1 -ATTGAAA
47233 ATTGAAGA
1 ATTGAA-A
*
47241 ATTGAAGT
1 ATTGAA-A
47249 ATTG-AA
1 ATTGAAA
*
47255 ATTTAAA
1 ATTGAAA
*
47262 CATTGAAGG
1 -ATTGAA-A
47271 ATTG-AA
1 ATTGAAA
*
47277 TTTGAAGA
1 ATTGAA-A
47285 ATTG-AA
1 ATTGAAA
*
47291 ATTGAACC
1 ATTGAA-A
*
47299 ATTGAAGG
1 ATTGAA-A
47307 ATTG-AA
1 ATTGAAA
*
47313 TTTGAAGA
1 ATTGAA-A
47321 ATTGAAA
1 ATTGAAA
*
47328 ACTTGAACC
1 A-TTGAA-A
*
47337 ATTGAAGG
1 ATTGAA-A
47345 ATTG-AA
1 ATTGAAA
*
47351 TTTGAAGA
1 ATTGAA-A
47359 ATTGAAA
1 ATTGAAA
* *
47366 ACT-AGA
1 ATTGAAA
47372 ATTGAAA
1 ATTGAAA
*
47379 A-TGAAGC
1 ATTGAA-A
47386 ATTGAAA
1 ATTGAAA
47393 TATTG-AA
1 -ATTGAAA
47400 ATTGAAGA
1 ATTGAA-A
47408 ATTGAAA
1 ATTGAAA
**
47415 CATTGAGGG
1 -ATTGA-AA
47424 ATTG-AA
1 ATTGAAA
*
47430 TTTGAAGA
1 ATTGAA-A
47438 ATTG-AA
1 ATTGAAA
47444 ATTGAAA
1 ATTGAAA
47451 CATTGAAA
1 -ATTGAAA
47459 TATTG-AA
1 -ATTGAAA
47466 ATTGAAGA
1 ATTGAA-A
*
47474 ACTG-AA
1 ATTGAAA
47480 ATTGAAA
1 ATTGAAA
*
47487 CATTGAATG
1 -ATTGAA-A
47496 ATTG-AA
1 ATTGAAA
* *
47502 TTTCAAGA
1 ATTGAA-A
47510 ATTGAAAA
1 ATTG-AAA
47518 ATTG--A
1 ATTGAAA
*
47523 ATT-TAA
1 ATTGAAA
*
47529 ATTGAAGC
1 ATTGAA-A
47537 ATTGAAA
1 ATTGAAA
47544 TATTG-AA
1 -ATTGAAA
47551 ATTGAAA
1 ATTGAAA
**
47558 CATTGAGGG
1 -ATTGA-AA
47567 ATTG-AA
1 ATTGAAA
* *
47573 TTTGAAG
1 ATTGAAA
47580 ATCTG-AA
1 AT-TGAAA
47587 ATTGAAA
1 ATTGAAA
47594 CATTGAAA
1 -ATTGAAA
47602 TATTG-AA
1 -ATTGAAA
*
47609 ATTGGAGA
1 ATT-GAAA
47617 ATTG-AA
1 ATTGAAA
47623 ATTGAAA
1 ATTGAAA
*
47630 CATTGAAGG
1 -ATTGAA-A
47639 ATTG-AA
1 ATTGAAA
* *
47645 TTTGATGA
1 ATTGA-AA
*
47653 ACTGAAAA
1 ATTG-AAA
47661 ATTG--A
1 ATTGAAA
47666 ATTG-AA
1 ATTGAAA
*
47672 ATTGAAGC
1 ATTGAA-A
47680 ATTGAAA
1 ATTGAAA
47687 TATTG-AA
1 -ATTGAAA
47694 ATTGAAGA
1 ATTGAA-A
47702 ATTG-AA
1 ATTGAAA
47708 ATTGAAA
1 ATTGAAA
47715 CATTGA
1 -ATTGA
47721 GGGATTGGAT
Statistics
Matches: 373, Mismatches: 65, Indels: 128
0.66 0.11 0.23
Matches are distributed among these distances:
5 9 0.02
6 89 0.24
7 66 0.18
8 205 0.55
9 4 0.01
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (7 bp):
ATTGAAA
Found at i:47305 original size:36 final size:36
Alignment explanation
Indices: 47242--47659 Score: 404
Period size: 36 Copynumber: 11.4 Consensus size: 36
47232 AATTGAAGAA
* *
47242 TTGAAGTATTGAAATTTAAACATTGAAGGATTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
*
47278 TTGAAGAATTGAAATTGAACCATTGAAGGATTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
*
47314 TTGAAGAATTGAAAACTTGAACCATTGAAGGATTGAAT
1 TTGAAGAATTG-AAA-TTGAAACATTGAAGGATTGAAT
* * * *
47352 TTGAAGAATTGAAAACTAGAATTGAAAATGAAGCATTGAAAT
1 TTGAAGAATTG-AAA-TTGAA---ACATTGAAGGATTG-AAT
*
47394 ATTG-A-AATTGAAGAATTGAAACATTGAGGGATTGAAT
1 -TTGAAGAATTG-A-AATTGAAACATTGAAGGATTGAAT
** *
47431 TTGAAGAATTGAAATTGAAACATTGAAATATTGAAA
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
* *
47467 TTGAAGAACTGAAATTGAAACATTGAATGATTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
* * *
47503 TTCAAGAATTGAAAAATTG--A-ATTTAA--ATTGAAGCA
1 TTGAAGAATTG--AAATTGAAACATTGAAGGATTGAA--T
*
47538 TTGAA-ATATTGAAATTGAAACATTGAGGGATTGAAT
1 TTGAAGA-ATTGAAATTGAAACATTGAAGGATTGAAT
** *
47574 TTGAAG-ATCTGAAATTGAAACATTGAAATATTGAAA
1 TTGAAGAAT-TGAAATTGAAACATTGAAGGATTGAAT
*
47610 TTGGAGAATTGAAATTGAAACATTGAAGGATTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
* *
47646 TTGATGAACTGAAA
1 TTGAAGAATTGAAA
47660 AATTGAATTG
Statistics
Matches: 319, Mismatches: 40, Indels: 46
0.79 0.10 0.11
Matches are distributed among these distances:
33 12 0.04
34 1 0.00
35 16 0.05
36 181 0.57
37 10 0.03
38 69 0.22
41 21 0.07
42 6 0.02
43 3 0.01
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.31
Consensus pattern (36 bp):
TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAT
Found at i:47683 original size:85 final size:85
Alignment explanation
Indices: 47583--47763 Score: 308
Period size: 85 Copynumber: 2.1 Consensus size: 85
47573 TTTGAAGATC
* *
47583 TGAAATTGAAACATTGAAATATTGAAATTGGAGAATTGAAATTGAAACATTGAAGGATTGAATTT
1 TGAAATTGAAGCATTGAAATATTGAAATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTT
*
47648 GATGAACTGAAAAATTGAAT
66 GAAGAACTGAAAAATTGAAT
* *
47668 TGAAATTGAAGCATTGAAATATTGAAATTGAAGAATTGAAATTGAAACATTGAGGGATTGGATTT
1 TGAAATTGAAGCATTGAAATATTGAAATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTT
*
47733 GAAGAATTGAAAAATTGAAT
66 GAAGAACTGAAAAATTGAAT
47753 TGAAATTGAAG
1 TGAAATTGAAG
47764 AAAGACCACA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 90 1.00
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (85 bp):
TGAAATTGAAGCATTGAAATATTGAAATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTT
GAAGAACTGAAAAATTGAAT
Found at i:47710 original size:36 final size:36
Alignment explanation
Indices: 47664--47744 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
47654 CTGAAAAATT
* *
47664 GAATTGAAATTGAAGCATTGAAATATTGAAATTGAA
1 GAATTGAAATTGAAACATTGAAAGATTGAAATTGAA
** * *
47700 GAATTGAAATTGAAACATTGAGGGATTGGATTTGAA
1 GAATTGAAATTGAAACATTGAAAGATTGAAATTGAA
47736 GAATTGAAA
1 GAATTGAAA
47745 AATTGAATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.30
Consensus pattern (36 bp):
GAATTGAAATTGAAACATTGAAAGATTGAAATTGAA
Found at i:47720 original size:22 final size:20
Alignment explanation
Indices: 47211--47714 Score: 159
Period size: 22 Copynumber: 23.7 Consensus size: 20
47201 AAACTGATGC
47211 ATTGAAGAATTGAAATATTG-AA
1 ATTGAA-AATTG-AA-ATTGAAA
47233 ATTGAAGAATTGAAGTATTG-AA
1 ATTGAA-AATTGAA--ATTGAAA
*
47255 ATTTAAACATTGAAGGATTG-AA
1 ATTGAAA-ATTGAA--ATTGAAA
* *
47277 TTTGAAGAATTGAAATTGAACC
1 ATTGAA-AATTGAAATTGAA-A
* *
47299 ATTGAAGGATTGAATTTGAAGA
1 ATTGAA-AATTGAAATTGAA-A
*
47321 ATTGAAAACTTGAACCATTGAAGG
1 ATTGAAAA-TTGAA--ATTGAA-A
*
47345 ATTG-AATTTGAAGAATTGAAA
1 ATTGAAAATTG-A-AATTGAAA
* * * *
47366 ACT-AGAATTGAAAATGAAGC
1 ATTGAAAATTGAAATTGAA-A
47386 ATTGAAATATTGAAATTGAAGA
1 ATTGAAA-ATTGAAATTGAA-A
*
47408 ATTGAAACATTGAGGGATTG-AA
1 ATTGAAA-ATTGA--AATTGAAA
*
47430 TTTGAAGAATTGAAATTGAAA
1 ATTGAA-AATTGAAATTGAAA
47451 CATTG-AAA-T---ATTG-AA
1 -ATTGAAAATTGAAATTGAAA
*
47466 ATTGAAGAACTGAAATTGAAA
1 ATTGAA-AATTGAAATTGAAA
* * *
47487 CATTGAATGATTGAATTTCAAGA
1 -ATTGAA-AATTGAAATTGAA-A
*
47510 ATTGAAAAATTG-AATT-TAA
1 ATTG-AAAATTGAAATTGAAA
*
47529 ATTGAAGCATTGAAATATTG-AA
1 ATTGAA-AATTG-AA-ATTGAAA
*
47551 ATTGAAACATTGAGGGATTG-AA
1 ATTGAAA-ATTGA--AATTGAAA
* *
47573 TTTGAAGATCTGAAATTGAAA
1 ATTGAAAAT-TGAAATTGAAA
*
47594 CATTGAAATATTGAAATTGGAGA
1 -ATTGAAA-ATTGAAATT-GAAA
*
47617 ATTG-AAATTGAAACATTGAAGG
1 ATTGAAAATTG-AA-ATTGAA-A
* *
47639 ATTG-AATTTGATGAACTGAAAA
1 ATTGAAAATTGA--AATTG-AAA
*
47661 ATTG--AATTGAAATTGAAGC
1 ATTGAAAATTGAAATTGAA-A
47680 ATTGAAATATTGAAATTGAAGA
1 ATTGAAA-ATTGAAATTGAA-A
47702 ATTG-AAATTGAAA
1 ATTGAAAATTGAAA
47715 CATTGAGGGA
Statistics
Matches: 375, Mismatches: 55, Indels: 106
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.01
15 3 0.01
16 6 0.02
17 1 0.00
18 4 0.01
19 24 0.06
20 33 0.09
21 42 0.11
22 226 0.60
23 17 0.05
24 15 0.04
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.31
Consensus pattern (20 bp):
ATTGAAAATTGAAATTGAAA
Found at i:50437 original size:14 final size:13
Alignment explanation
Indices: 50412--50468 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
50402 TTAAAAACTC
50412 AAAACC-TTTTTG
1 AAAACCATTTTTG
50424 AAAACTCATTTTTG
1 AAAAC-CATTTTTG
*
50438 AAAACCTTTTCTTG
1 AAAACCATTT-TTG
50452 AAAA-CATTTTTTG
1 AAAACCA-TTTTTG
50465 AAAA
1 AAAA
50469 ATACTTCTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 5 0.13
13 13 0.33
14 21 0.54
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (13 bp):
AAAACCATTTTTG
Found at i:50459 original size:26 final size:26
Alignment explanation
Indices: 50412--50468 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
50402 TTAAAAACTC
50412 AAAACCTTTTTGAAAACTCA-TTTTTG
1 AAAACCTTTTTGAAAAC-CATTTTTTG
50438 AAAACCTTTTCTTGAAAA-CATTTTTTG
1 AAAACC-TTT-TTGAAAACCATTTTTTG
50465 AAAA
1 AAAA
50469 ATACTTCTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 8 0.29
27 13 0.46
28 7 0.25
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (26 bp):
AAAACCTTTTTGAAAACCATTTTTTG
Found at i:51066 original size:37 final size:39
Alignment explanation
Indices: 50996--51073 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 39
50986 TTCAAAAGAA
*
50996 TCTAGTTTATCTTTTTTCGTTCAAAACACACTTGTTTAT
1 TCTAGTTTATCTATTTTCGTTCAAAACACACTTGTTTAT
*
51035 TCTAGTTTATC-ATTTT-GTTCAAAACATACTTGTTTAT
1 TCTAGTTTATCTATTTTCGTTCAAAACACACTTGTTTAT
51072 TC
1 TC
51074 AAAAGAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 22 0.59
38 4 0.11
39 11 0.30
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (39 bp):
TCTAGTTTATCTATTTTCGTTCAAAACACACTTGTTTAT
Found at i:54984 original size:15 final size:14
Alignment explanation
Indices: 54964--55010 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
54954 AGAATTCCTA
54964 TTTTCTTCTTTTTCT
1 TTTTCTTCTTTTT-T
54979 TTTTCTCTCTTTTTT
1 TTTTCT-TCTTTTTT
*
54994 TTGTCTT-TTTTATT
1 TTTTCTTCTTTT-TT
55008 TTT
1 TTT
55011 GTGTTGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 4 0.14
14 5 0.18
15 12 0.43
16 7 0.25
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTCTTCTTTTTT
Found at i:56929 original size:28 final size:29
Alignment explanation
Indices: 56874--56931 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
56864 CAAAGTCTCA
**
56874 AACAAAATTAATTAAAAAGGGTTAGGCCC
1 AACAAAATTAATTAAAAAGGGAGAGGCCC
* *
56903 AACAAGATTAATT-GAAAGGGAGAGGCCC
1 AACAAAATTAATTAAAAAGGGAGAGGCCC
56931 A
1 A
56932 GCAGGGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.17
Consensus pattern (29 bp):
AACAAAATTAATTAAAAAGGGAGAGGCCC
Found at i:58081 original size:15 final size:17
Alignment explanation
Indices: 58056--58087 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
58046 CACCATCACA
58056 ATTTGCATCTT-TTCCT
1 ATTTGCATCTTCTTCCT
58072 ATTT-CATCTTCTTCCT
1 ATTTGCATCTTCTTCCT
58088 CTATGAGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.12, C:0.28, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTGCATCTTCTTCCT
Found at i:68088 original size:22 final size:22
Alignment explanation
Indices: 68063--68126 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
68053 ATTAAGCTAG
68063 GAAGTAGAAGAAAGGGTAATCA
1 GAAGTAGAAGAAAGGGTAATCA
* **
68085 GAAGTAGAAGGAAGAATAATCA
1 GAAGTAGAAGAAAGGGTAATCA
* *
68107 GAAGTAAAAAAAAGGGTAAT
1 GAAGTAGAAGAAAGGGTAAT
68127 TAAAAGAGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.55, C:0.03, G:0.28, T:0.14
Consensus pattern (22 bp):
GAAGTAGAAGAAAGGGTAATCA
Found at i:68332 original size:75 final size:76
Alignment explanation
Indices: 68207--68348 Score: 189
Period size: 75 Copynumber: 1.9 Consensus size: 76
68197 GAGTAGAAGA
* * ** * *
68207 AGAAGTAAAGCAGAAGTTTGTTTAATTCTGGGCAATTAAACTAAAGAGTAAAAGAGGAAGAGTTT
1 AGAAGTAAAGCAGAAGGTAGTTTAATTCCAGGCAATTAAACTAAAGAGTAAAAGAAGAAGAGATT
68272 AGAGAAAAAGG
66 AGAGAAAAAGG
* *
68283 AGAAGTAAA-CAGAGGGTAGTTTAATTCCAGGTAATTAAACT-AAGTAGTAAAAGAAGAAGAGAT
1 AGAAGTAAAGCAGAAGGTAGTTTAATTCCAGGCAATTAAACTAAAG-AGTAAAAGAAGAAGAGAT
68346 TAG
65 TAG
68349 TTTAATTCCA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
74 3 0.05
75 45 0.79
76 9 0.16
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.23
Consensus pattern (76 bp):
AGAAGTAAAGCAGAAGGTAGTTTAATTCCAGGCAATTAAACTAAAGAGTAAAAGAAGAAGAGATT
AGAGAAAAAGG
Found at i:68391 original size:44 final size:46
Alignment explanation
Indices: 68299--68484 Score: 281
Period size: 44 Copynumber: 4.1 Consensus size: 46
68289 AAACAGAGGG
68299 TAGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCCAGGTAATTAAACTAA-TAGTAAAAGAAGAAGAGAT
*
68346 TAGTTTAATTCCAGGTAATTGAACT-A-AGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCCAGGTAATTAAACTAATAGTAAAAGAAGAAGAGAT
* *
68390 TAGTTTAATTCTAGGTAATTAAACT-A-AGTAAAAGGAGAAGAGAT
1 TAGTTTAATTCCAGGTAATTAAACTAATAGTAAAAGAAGAAGAGAT
* *
68434 TAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGAG
1 TAGTTTAATTCCAGGTAATTAAACT-AATAGTAAAAGAAGAAGAGAT
68481 TAGT
1 TAGT
68485 AAAGGAAGAA
Statistics
Matches: 130, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
44 84 0.65
46 2 0.02
47 44 0.34
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.28
Consensus pattern (46 bp):
TAGTTTAATTCCAGGTAATTAAACTAATAGTAAAAGAAGAAGAGAT
Found at i:68503 original size:19 final size:19
Alignment explanation
Indices: 68462--68503 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
68452 TTAAACTAAA
*
68462 TAGTAAAAGAAGAAGAGAG
1 TAGTAAAAGAAGAAGAAAG
* *
68481 TAGTAAAGGAAGAAGAAAT
1 TAGTAAAAGAAGAAGAAAG
68500 TAGT
1 TAGT
68504 TTAATTCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.17
Consensus pattern (19 bp):
TAGTAAAAGAAGAAGAAAG
Found at i:68522 original size:66 final size:65
Alignment explanation
Indices: 68420--68602 Score: 274
Period size: 59 Copynumber: 2.9 Consensus size: 65
68410 AAACTAAGTA
*
68420 AAAGG-AGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGAGTAG
1 AAAGGAAGAAGAAATTAGTTTAATTCTAGG-AATTAAACTAAATAGTAAAAGAAGAAGAGAGTAG
68484 T
65 T
68485 AAAGGAAGAAGAAATTAGTTTAATTCTAGGACATTAAACTAAATAGT------A-AAGAGAGTAG
1 AAAGGAAGAAGAAATTAGTTTAATTCTAGGA-ATTAAACTAAATAGTAAAAGAAGAAGAGAGTAG
68543 T
65 T
68544 AAAGGAAGAAGAAATTAGTTTAATTCTAGGAAATTAAACTAAATAGTAAAAGAAGAAGA
1 AAAGGAAGAAGAAATTAGTTTAATTCTAGG-AATTAAACTAAATAGTAAAAGAAGAAGA
68603 AATTAGTTTA
Statistics
Matches: 107, Mismatches: 1, Indels: 19
0.84 0.01 0.15
Matches are distributed among these distances:
59 56 0.52
60 2 0.02
65 7 0.07
66 42 0.39
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.24
Consensus pattern (65 bp):
AAAGGAAGAAGAAATTAGTTTAATTCTAGGAATTAAACTAAATAGTAAAAGAAGAAGAGAGTAGT
Found at i:68609 original size:47 final size:47
Alignment explanation
Indices: 68548--69530 Score: 940
Period size: 47 Copynumber: 20.6 Consensus size: 47
68538 AGTAGTAAAG
** * * * *
68548 GAAGAAGAAATTAGTTTAATTCTAGGAAATTAAACTAAATAGTAAAA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
** * *
68595 GAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACT-AAGTAGTAAAA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAG-AGCAAAA
* ***** * *
68642 GAATAAGGGCTTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAAGTAAAA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAA--AG-----AGCAAAA
* * * *
68696 GAAGAAGAAAAAAGCTTAATTCCGGGTAATTAAACTAAAGAGCAAGA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
68743 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAA-AA
* * *
68791 -AAGAATAAAAGAGTTTAATTCTGGGTAATTAAACTAAAAATTAAGAAAAGAA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACT--AAA--GAG-CAA-AA
* ** *
68843 GAAAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAAATTAAGA
1 G--AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
*
68892 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
68939 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAA-AA
* *
68987 -AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAGCTAAAGAGCAAGA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
* * *
69033 GAAGAAGAAAACAGTTTAATTCTGGGCAATTACACTAAAGAGCAAGAA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAA-AA
* * *
69081 -AAAAAG-AAAGCAGTTTAATTCTGGATAATTAAACT--A-AG--AAT
1 GAAGAAGAAAAG-AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
* *
69122 TAAGAAGAAAAGAGTTTAATTCCT-GGTAATTAAACTAAAGAGCAAGA
1 GAAGAAGAAAAGAGTTTAATT-CTGGGTAATTAAACTAAAGAGCAAAA
* * *
69169 GAAGAAGAGAACAGTTTAATTCTGGTTAATTAAACTAAAGAGCAAGAA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAA-AA
* * *
69217 -AAGAAG-GAAGCAGTTTTATTCTGGGTAATTAAACT--A-A--AAAT
1 GAAGAAGAAAAG-AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
* * *
69258 TAAGAAGAAAAGAGTTTAATTCCGGGTAATTAAACTAAAGAGCAAGA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
** * * ** *
69305 GAAGAAGAAATCAGTTTAATTATGGGTAATTAAAACTAAAAATTAAGA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATT-AAACTAAAGAGCAAAA
* *
69353 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
* * * **
69400 GAAGAAGTGAACGGATATTAGTTTAATTCTGGGTAATTAAAATAAATAATAAAA
1 GAAGAA--GAA---A-A-GAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
* * * *
69454 GAAGAAGAAAATAGCTTAATTCCGGGTAATTAAACTAAAGAGCAAGA
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
* *
69501 GAAGAAGAAAACAGTTTGATTCTGGGTAAT
1 GAAGAAGAAAAGAGTTTAATTCTGGGTAAT
69531 CAAGCTAAGA
Statistics
Matches: 797, Mismatches: 92, Indels: 94
0.81 0.09 0.10
Matches are distributed among these distances:
41 2 0.00
42 56 0.07
43 9 0.01
44 5 0.01
45 5 0.01
46 11 0.01
47 521 0.65
48 47 0.06
49 9 0.01
50 4 0.01
51 4 0.01
52 11 0.01
53 4 0.01
54 75 0.09
55 34 0.04
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (47 bp):
GAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAA
Found at i:68846 original size:8 final size:8
Alignment explanation
Indices: 68833--68857 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
68823 ACTAAAAATT
68833 AAGAAAAG
1 AAGAAAAG
68841 AAGAAAAG
1 AAGAAAAG
68849 AAGAAAAG
1 AAGAAAAG
68857 A
1 A
68858 GTTTAATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AAGAAAAG
Found at i:69184 original size:136 final size:136
Alignment explanation
Indices: 68846--69541 Score: 824
Period size: 136 Copynumber: 5.0 Consensus size: 136
68836 AAAAGAAGAA
* ** *
68846 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAAATTAAGAGAAGAAGAAAAGAGTTTAA
1 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAA
*
68911 TTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTA
66 TTCTGGGTAATTAAACTAAAGAGCAAGAAAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACT-
**
68976 AAGAGCAAGAA
130 -A-AG-AA-TT
*
68987 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAGCTAAAGAGCAAGAGAAGAAGAAAACAGTTTAA
1 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAA
* * * *
69052 TTCTGGGCAATTACACTAAAGAGCAAGAAAAAAAG-AAAGCAGTTTAATTCTGGATAATTAAACT
66 TTCTGGGTAATTAAACTAAAGAGCAAGAAAAGAAGAAAAG-AGTTTAATTCTGGGTAATTAAACT
69116 AAGAATT
130 AAGAATT
*
69123 AAGAAGAAAAGAGTTTAATTCCT-GGTAATTAAACTAAAGAGCAAGAGAAGAAGAGAACAGTTTA
1 AAGAAGAAAAGAGTTTAATT-CTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTA
* * *
69187 ATTCTGGTTAATTAAACTAAAGAGCAAGAAAAGAAG-GAAGCAGTTTTATTCTGGGTAATTAAAC
65 ATTCTGGGTAATTAAACTAAAGAGCAAGAAAAGAAGAAAAG-AGTTTAATTCTGGGTAATTAAAC
*
69251 TAAAAATT
129 TAAGAATT
* *
69259 AAGAAGAAAAGAGTTTAATTCCGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAATCAGTTTAA
1 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAA
* * ** *
69324 TTATGGGTAATTAAAACTAAAAATTAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACT
66 TTCTGGGTAATT-AAACTAAAGAGCAAGAAAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACT
*
69389 AA-ATAGTAA
130 AAGA-A-T-T
* * ** *
69398 AAGAAGAAGTGAACGGATATTAGTTTAATTCTGGGTAATTAAAATAAATAATAAAAGAAGAAGAA
1 AAGAAGAA---AA--G-----AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAA
* * * * * *
69463 AATAGCTTAATTCCGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTGATTCTGGGT
56 AACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAAAAGAAGAAAAGAGTTTAATTCTGGGT
* *
69528 AATCAAGCTAAGAA
121 AATTAAACTAAGAA
69542 GAAAGAGTAA
Statistics
Matches: 484, Mismatches: 52, Indels: 31
0.85 0.09 0.05
Matches are distributed among these distances:
135 1 0.00
136 194 0.40
137 49 0.10
138 6 0.01
139 9 0.02
140 4 0.01
141 114 0.24
142 2 0.00
144 1 0.00
148 48 0.10
149 56 0.12
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (136 bp):
AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAA
TTCTGGGTAATTAAACTAAAGAGCAAGAAAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTA
AGAATT
Found at i:69554 original size:22 final size:20
Alignment explanation
Indices: 69526--69626 Score: 58
Period size: 22 Copynumber: 4.4 Consensus size: 20
69516 TTGATTCTGG
69526 GTAATCAAGCTAAGAAGAAAGA
1 GTAATCAAG-TAA-AAGAAAGA
*
69548 GTAATCAGAGTAAAAGGAAGA
1 GTAATCA-AGTAAAAGAAAGA
* *
69569 GCAATCAAAAGCAAAATAAAGAGTAAGA
1 GTAATC--AAG-----TAAA-AGAAAGA
69597 GTAATCAGAAGTAAAAGAAAGA
1 GTAATC--AAGTAAAAGAAAGA
69619 GTAATCAA
1 GTAATCAA
69627 AAGATTAGAG
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
20 2 0.03
21 12 0.19
22 24 0.38
23 7 0.11
27 4 0.06
28 15 0.23
ACGTcount: A:0.56, C:0.08, G:0.22, T:0.14
Consensus pattern (20 bp):
GTAATCAAGTAAAAGAAAGA
Found at i:69597 original size:28 final size:28
Alignment explanation
Indices: 69565--69622 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
69555 GAGTAAAAGG
*
69565 AAGAGCAATCAAAAGCAAAATAAAGAGT
1 AAGAGCAATCAAAAGCAAAAGAAAGAGT
* * *
69593 AAGAGTAATCAGAAGTAAAAGAAAGAGT
1 AAGAGCAATCAAAAGCAAAAGAAAGAGT
69621 AA
1 AA
69623 TCAAAAGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.60, C:0.07, G:0.21, T:0.12
Consensus pattern (28 bp):
AAGAGCAATCAAAAGCAAAAGAAAGAGT
Found at i:79778 original size:17 final size:17
Alignment explanation
Indices: 79731--79783 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
79721 ATTTCTCCCT
* *
79731 TTCTCCATATTCTCTTC
1 TTCTCCATATTCTTTTG
79748 TTCTCCATATTCTTTTG
1 TTCTCCATATTCTTTTG
*
79765 TTCTCTATATTCTTTTG
1 TTCTCCATATTCTTTTG
79782 TT
1 TT
79784 TCTCTATTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.11, C:0.25, G:0.04, T:0.60
Consensus pattern (17 bp):
TTCTCCATATTCTTTTG
Found at i:79798 original size:16 final size:17
Alignment explanation
Indices: 79731--79790 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
79721 ATTTCTCCCT
* * *
79731 TTCTCCATATTCTCTTC
1 TTCTCTATATTCTTTTG
*
79748 TTCTCCATATTCTTTTG
1 TTCTCTATATTCTTTTG
79765 TTCTCTATATTCTTTTG
1 TTCTCTATATTCTTTTG
79782 TTTCTCTAT
1 -TTCTCTAT
79791 TCTATTGTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 31 0.79
18 8 0.21
ACGTcount: A:0.12, C:0.25, G:0.03, T:0.60
Consensus pattern (17 bp):
TTCTCTATATTCTTTTG
Found at i:80016 original size:31 final size:31
Alignment explanation
Indices: 79978--80037 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
79968 CAAAAAGATC
* *
79978 GAGATTGAAACTTTAATTATACAAGTCTACG
1 GAGATTGAAACTTGAATCATACAAGTCTACG
*
80009 GAGATTGAAAGTTGAATCATACAAGTCTA
1 GAGATTGAAACTTGAATCATACAAGTCTA
80038 AGGTTAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (31 bp):
GAGATTGAAACTTGAATCATACAAGTCTACG
Found at i:80116 original size:32 final size:34
Alignment explanation
Indices: 80072--80139 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
80062 GTTTAATTAA
* *
80072 CATGCATGATCT-CTTCTTCGACCTTTC-TTTAT
1 CATGCATAATCTCCTCCTTCGACCTTTCTTTTAT
*
80104 CATGCATAATCTCCTCCTTCTACCTTTCTTTTAT
1 CATGCATAATCTCCTCCTTCGACCTTTCTTTTAT
80138 CA
1 CA
80140 ATAAAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 11 0.35
33 13 0.42
34 7 0.23
ACGTcount: A:0.18, C:0.31, G:0.06, T:0.46
Consensus pattern (34 bp):
CATGCATAATCTCCTCCTTCGACCTTTCTTTTAT
Found at i:83472 original size:300 final size:300
Alignment explanation
Indices: 82956--83558 Score: 1197
Period size: 300 Copynumber: 2.0 Consensus size: 300
82946 TCATCTGCAT
*
82956 CTTCTGCCTCGTCCGAGTCTTTATACACTGTAAGATCAAAATTCTGCTCCTTGTTGATCTTGAGA
1 CTTCTGCCTAGTCCGAGTCTTTATACACTGTAAGATCAAAATTCTGCTCCTTGTTGATCTTGAGA
83021 CCATGGAATAAAGTGACTTTTAAGTATCGAAGTACCCTTTTAACTGCTGTGAGATGAGTTTGAGT
66 CCATGGAATAAAGTGACTTTTAAGTATCGAAGTACCCTTTTAACTGCTGTGAGATGAGTTTGAGT
83086 CGGCTTATGCATGAATTGAGATAACTTATTCACTGCAAGGGAGATGTCCGGTCTTGTGATATTGA
131 CGGCTTATGCATGAATTGAGATAACTTATTCACTGCAAGGGAGATGTCCGGTCTTGTGATATTGA
83151 GATACTGAAGTGAACCAAGTATTTTCCTATATTCTTCAGCATCTGCTGCAGCTGTACCATCATGA
196 GATACTGAAGTGAACCAAGTATTTTCCTATATTCTTCAGCATCTGCTGCAGCTGTACCATCATGA
83216 AGTTTCAATGAAATTGAAGTAGACAATGGTGTGTTTGTAG
261 AGTTTCAATGAAATTGAAGTAGACAATGGTGTGTTTGTAG
83256 CTTCTGCCTAGTCCGAGTCTTTATACACTGTAAGATCAAAATTCTGCTCCTTGTTGATCTTGAGA
1 CTTCTGCCTAGTCCGAGTCTTTATACACTGTAAGATCAAAATTCTGCTCCTTGTTGATCTTGAGA
83321 CCATGGAATAAAGTGACTTTTAAGTATCGAAGTACCCTTTTAACTGCTGTGAGATGAGTTTGAGT
66 CCATGGAATAAAGTGACTTTTAAGTATCGAAGTACCCTTTTAACTGCTGTGAGATGAGTTTGAGT
83386 CGGCTTATGCATGAATTGAGATAACTTATTCACTGCAAGGGAGATGTCCGGTCTTGTGATATTGA
131 CGGCTTATGCATGAATTGAGATAACTTATTCACTGCAAGGGAGATGTCCGGTCTTGTGATATTGA
83451 GATACTGAAGTGAACCAAGTATTTTCCTATATTCTTCAGCATCTGCTGCAGCTGTACCATCATGA
196 GATACTGAAGTGAACCAAGTATTTTCCTATATTCTTCAGCATCTGCTGCAGCTGTACCATCATGA
83516 AGTTTCAATGAAATTGAAGTAGACAATGGTGTGTTTGTAG
261 AGTTTCAATGAAATTGAAGTAGACAATGGTGTGTTTGTAG
83556 CTT
1 CTT
83559 TGACCCCTGC
Statistics
Matches: 302, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
300 302 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (300 bp):
CTTCTGCCTAGTCCGAGTCTTTATACACTGTAAGATCAAAATTCTGCTCCTTGTTGATCTTGAGA
CCATGGAATAAAGTGACTTTTAAGTATCGAAGTACCCTTTTAACTGCTGTGAGATGAGTTTGAGT
CGGCTTATGCATGAATTGAGATAACTTATTCACTGCAAGGGAGATGTCCGGTCTTGTGATATTGA
GATACTGAAGTGAACCAAGTATTTTCCTATATTCTTCAGCATCTGCTGCAGCTGTACCATCATGA
AGTTTCAATGAAATTGAAGTAGACAATGGTGTGTTTGTAG
Done.