Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007888.1 Corchorus capsularis cultivar CVL-1 contig07909, 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: 72954
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10115 original size:21 final size:21
Alignment explanation
Indices: 10091--10136 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
10081 TTGGCATTAA
10091 GGTTGCAATTTGAAAAAAT-TT
1 GGTTGCAATTTG-AAAAATCTT
*
10112 GGTTGCAGTTTGAAAAATCTT
1 GGTTGCAATTTGAAAAATCTT
10133 GGTT
1 GGTT
10137 TGGAAAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (21 bp):
GGTTGCAATTTGAAAAATCTT
Found at i:18306 original size:25 final size:28
Alignment explanation
Indices: 18270--18332 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
18260 AAATAGAACT
18270 TAGCCCAATAGA-TT-TTTTTT-AGGTA
1 TAGCCCAATAGATTTCTTTTTTGAGGTA
*
18295 TGGCCCAATAGATTTCTTTTTTGAGGTA
1 TAGCCCAATAGATTTCTTTTTTGAGGTA
18323 TAGCCCAATA
1 TAGCCCAATA
18333 AAATGTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 11 0.33
26 2 0.06
27 6 0.18
28 14 0.42
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (28 bp):
TAGCCCAATAGATTTCTTTTTTGAGGTA
Found at i:18578 original size:1 final size:1
Alignment explanation
Indices: 18572--18601 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
18562 AATAATTTGC
18572 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18602 CCCTACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19856 original size:30 final size:28
Alignment explanation
Indices: 19785--19862 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
19775 GAACTTACAC
*
19785 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAAAGGCCAAATAAGCCCCTGAACTCT
**
19813 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T
19844 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
19863 TTTTCTGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.07
29 21 0.51
30 13 0.32
31 1 0.02
32 3 0.07
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Found at i:24707 original size:21 final size:19
Alignment explanation
Indices: 24682--24729 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
24672 CCCAAAGTGA
*
24682 AAACAGAGCAAAGCAGGGGGG
1 AAACAGAGCAAAACA--GGGG
*
24703 AAACAGAGGAAAACAGGGG
1 AAACAGAGCAAAACAGGGG
24722 AAACAGAG
1 AAACAGAG
24730 AGGAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.48
21 13 0.52
ACGTcount: A:0.50, C:0.12, G:0.38, T:0.00
Consensus pattern (19 bp):
AAACAGAGCAAAACAGGGG
Found at i:26258 original size:8 final size:8
Alignment explanation
Indices: 26245--26269 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
26235 ATCCAAATGG
26245 AATCATGC
1 AATCATGC
26253 AATCATGC
1 AATCATGC
26261 AATCATGC
1 AATCATGC
26269 A
1 A
26270 TAAAACAAAT
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:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (8 bp):
AATCATGC
Found at i:27226 original size:2 final size:2
Alignment explanation
Indices: 27219--27255 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
27209 ATACAAAGTC
27219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27256 CTAGCTAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28186 original size:70 final size:70
Alignment explanation
Indices: 28104--28336 Score: 288
Period size: 70 Copynumber: 3.2 Consensus size: 70
28094 TTGTTTAGGT
* * *
28104 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
28168 ATTTTA
65 ATTTTA
*
28174 TTTTACTATTTTACTCAACTAAAAACTCTTTTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-T-A-TA
*
28239 TTATATTTTACCA
62 AT-TATTTT---A
* * *
28252 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
28317 TTATA
66 TTTTA
*
28322 TTTTACCATTTTACT
1 TTTTACTATTTTACT
28337 ATTTTAATTA
Statistics
Matches: 142, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
70 62 0.44
71 5 0.04
72 1 0.01
73 6 0.04
74 5 0.04
75 7 0.05
76 1 0.01
77 2 0.01
78 53 0.37
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:28257 original size:78 final size:78
Alignment explanation
Indices: 28104--28342 Score: 352
Period size: 78 Copynumber: 3.2 Consensus size: 78
28094 TTGTTTAGGT
* * *
28104 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
28164 AAT-TATTTT---A
65 ATTATATTTTACCA
*
28174 TTTTACTATTTTACTCAACTAAAAACTCTTTTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
28239 TTATATTTTACCA
66 TTATATTTTACCA
*
28252 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
28317 TTATATTTTACCA
66 TTATATTTTACCA
28330 TTTTACTATTTTA
1 TTTTACTATTTTA
28343 ATTAAAAAAA
Statistics
Matches: 153, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
70 47 0.31
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
78 90 0.59
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.50
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACCA
Found at i:28496 original size:60 final size:60
Alignment explanation
Indices: 28431--28591 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 60
28421 GCTAATTGCT
* * ****
28431 CAAATAAGGGCCTAACGTTTGACAAAATGCTTAAATAAGGGTTTGATCTATT-AATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCT-TTGAATTTGGC
*
28491 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
* *
28551 TAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
28592 ACTGTCTCAC
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 2 0.02
60 88 0.98
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
Found at i:28571 original size:29 final size:30
Alignment explanation
Indices: 28483--28572 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 30
28473 TTGATCTATT
* * *
28483 AATTTGGCCAAATAAGGACCTAACGTTTGCC
1 AATTTGGCTAAATAAGGGCCTAATGTTTG-C
** ** *
28514 AAAAT-GCTCAAATAAGGGCCCCATCTTTG-
1 AATTTGGCT-AAATAAGGGCCTAATGTTTGC
28543 AATTTGGCTAAATAAGGGCCTAATGTTTGC
1 AATTTGGCTAAATAAGGGCCTAATGTTTGC
28573 CAAAATGCTC
Statistics
Matches: 43, Mismatches: 13, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
29 20 0.47
30 5 0.12
31 18 0.42
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (30 bp):
AATTTGGCTAAATAAGGGCCTAATGTTTGC
Found at i:28591 original size:31 final size:31
Alignment explanation
Indices: 28491--28591 Score: 109
Period size: 31 Copynumber: 3.3 Consensus size: 31
28481 TTAATTTGGC
* *
28491 CAAATAAGGACCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
** * **
28522 CAAATAAGGGCCCCATCTTTG--AATTTGGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAAT-GCT
28552 -AAATAAGGGCCTAATGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
28582 CAAATAAGGG
1 CAAATAAGGG
28592 ACTGTCTCAC
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 20 0.37
30 6 0.11
31 28 0.52
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCT
Found at i:28662 original size:31 final size:30
Alignment explanation
Indices: 28624--28725 Score: 113
Period size: 31 Copynumber: 3.4 Consensus size: 30
28614 TTGACACCAT
28624 GCCCTTATTTGAGCATTTTCGATAACGTTAG
1 GCCCTTATTTGAGCATTTTCGATAA-GTTAG
**
28655 GCCCTTATTTG-GCCAAATT--ATAAGATT-G
1 GCCCTTATTTGAG-CATTTTCGATAAG-TTAG
28683 AGCCCTTATTTGAGCATTTTCGATAAAGTTAG
1 -GCCCTTATTTGAGCATTTTCGAT-AAGTTAG
28715 GCCCTTATTTG
1 GCCCTTATTTG
28726 GCCAAATTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
28 2 0.03
29 21 0.36
30 2 0.03
31 30 0.51
32 4 0.07
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (30 bp):
GCCCTTATTTGAGCATTTTCGATAAGTTAG
Found at i:28688 original size:29 final size:28
Alignment explanation
Indices: 28655--28754 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 28
28645 ATAACGTTAG
28655 GCCCTTATTTGGCCAAATTATAAGATTGA
1 GCCCTTATTTGGCCAAATTATAAGATT-A
**
28684 GCCCTTATTTGAG-CATTTTCGATAA-AGTTA
1 GCCCTTATTTG-GCCAAATT--ATAAGA-TTA
* *
28714 GGCCCTTATTTGGCCAAATTAAAAGATCA
1 -GCCCTTATTTGGCCAAATTATAAGATTA
28743 GACCCTTATTTG
1 G-CCCTTATTTG
28755 AGCATTTTGA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
28 1 0.02
29 30 0.53
30 5 0.09
31 21 0.37
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (28 bp):
GCCCTTATTTGGCCAAATTATAAGATTA
Found at i:28700 original size:60 final size:59
Alignment explanation
Indices: 28624--28785 Score: 236
Period size: 60 Copynumber: 2.7 Consensus size: 59
28614 TTGACACCAT
* *
28624 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTATAAGATTGA
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA-TCA
*
28684 GCCCTTATTTGAGCATTTTCGATAAAGTTAGGCCCTTATTTGGCCAAATTAAAAGATCA
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCA
* * *
28743 GACCCTTATTTGAGCATTTT-GACAAACGTTAGACCCTTGTTTG
1 G-CCCTTATTTGAGCATTTTCGA-TAACGTTAGGCCCTTATTTG
28786 AGCAATTAGT
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
59 5 0.05
60 88 0.95
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (59 bp):
GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCA
Found at i:28780 original size:31 final size:29
Alignment explanation
Indices: 28625--28789 Score: 106
Period size: 31 Copynumber: 5.5 Consensus size: 29
28615 TGACACCATG
* *
28625 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTT-GA-AAAGTTAGA
** *
28656 CCCTTATTTG-GCCAAATT-ATAAGATT-GA
1 CCCTTATTTGAG-CATTTTGAAAAG-TTAGA
*
28684 GCCCTTATTTGAGCATTTTCGATAAAGTTAGG
1 -CCCTTATTTGAGCATTTT-GA-AAAGTTAGA
** *
28716 CCCTTATTTG-GCCAAATT-AAAAGATCAGA
1 CCCTTATTTGAG-CATTTTGAAAAG-TTAGA
28745 CCCTTATTTGAGCATTTTGACAAACGTTAGA
1 CCCTTATTTGAGCATTTTGA-AAA-GTTAGA
*
28776 CCCTTGTTTGAGCA
1 CCCTTATTTGAGCA
28790 ATTAGTCATT
Statistics
Matches: 103, Mismatches: 17, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
28 7 0.07
29 35 0.34
30 5 0.05
31 51 0.50
32 5 0.05
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAAAGTTAGA
Found at i:43958 original size:21 final size:22
Alignment explanation
Indices: 43913--43959 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
43903 TAGTGTAATT
***
43913 AAAAACTTGGATCCTTCCCTCG
1 AAAAACTTGGATCCTTAAATCG
43935 AAAAACTTGGATCCTTAAAT-G
1 AAAAACTTGGATCCTTAAATCG
43956 AAAA
1 AAAA
43960 GGTTGCAACG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (22 bp):
AAAAACTTGGATCCTTAAATCG
Found at i:44838 original size:41 final size:41
Alignment explanation
Indices: 44781--44862 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
44771 TTTTAGATTA
44781 TTCCATCACGGTTAAAGGGTTGATTTGATATAAGTATGAAT
1 TTCCATCACGGTTAAAGGGTTGATTTGATATAAGTATGAAT
44822 TTCCATCACGGTTAAAGGGTTGATTTGATATAAGTATGAAT
1 TTCCATCACGGTTAAAGGGTTGATTTGATATAAGTATGAAT
44863 CGATATTGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (41 bp):
TTCCATCACGGTTAAAGGGTTGATTTGATATAAGTATGAAT
Found at i:47542 original size:20 final size:21
Alignment explanation
Indices: 47517--47558 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
47507 TCTTGAGTTC
*
47517 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGAAATTGTGAGT
47537 TACTCTCACGAAATTGTGAGT
1 TACTCTCACGAAATTGTGAGT
47558 T
1 T
47559 TTTTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
TACTCTCACGAAATTGTGAGT
Found at i:47739 original size:198 final size:197
Alignment explanation
Indices: 47401--47801 Score: 793
Period size: 198 Copynumber: 2.0 Consensus size: 197
47391 CTAATTGTTC
47401 AGTTATCTATATATATACCCTCAAATAACTTAACTAATTGCCATCGGGCATTTGGCCTGATGGTA
1 AGTTATCTATATATATACCCTCAAATAACTTAACTAATTGCCATCGGGCATTTGGCCTGATGGTA
47466 GAGTGCTGGATTCTTAATTCCAATATACCTGGATCATGAGATCTTGAGTTCTACTCTCACGGAAT
66 GAGTGCTGGATTCTTAATTCCAATATACCTGGATCATGAGATCTTGAGTTCTACTCTCACGGAAT
47531 GTGAGTTACTCTCACGAAATTGTGAGTTTTTTTTGTAATTTATTTGTTTGTGTATTTAATATGTT
131 GTGAGTTACTCTCACGAAATTGTGAG-TTTTTTTGTAATTTATTTGTTTGTGTATTTAATATGTT
47596 GGT
195 GGT
47599 AGTTATCTATATATATACCCTCAAATAACTTAACTAATTGCCATCGGGCATTTGGCCTGATGGTA
1 AGTTATCTATATATATACCCTCAAATAACTTAACTAATTGCCATCGGGCATTTGGCCTGATGGTA
47664 GAGTGCTGGATTCTTAATTCCAATATACCTGGATCATGAGATCTTGAGTTCTACTCTCACGGAAT
66 GAGTGCTGGATTCTTAATTCCAATATACCTGGATCATGAGATCTTGAGTTCTACTCTCACGGAAT
47729 GTGAGTTACTCTCACGAAATTGTGAGTTTTTTTGTAATTTATTTGTTTGTGTATTTAATATGTTG
131 GTGAGTTACTCTCACGAAATTGTGAGTTTTTTTGTAATTTATTTGTTTGTGTATTTAATATGTTG
47794 GT
196 GT
47796 AGTTAT
1 AGTTAT
47802 AGATAGTGAA
Statistics
Matches: 203, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
197 47 0.23
198 156 0.77
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (197 bp):
AGTTATCTATATATATACCCTCAAATAACTTAACTAATTGCCATCGGGCATTTGGCCTGATGGTA
GAGTGCTGGATTCTTAATTCCAATATACCTGGATCATGAGATCTTGAGTTCTACTCTCACGGAAT
GTGAGTTACTCTCACGAAATTGTGAGTTTTTTTGTAATTTATTTGTTTGTGTATTTAATATGTTG
GT
Found at i:47740 original size:20 final size:21
Alignment explanation
Indices: 47715--47756 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
47705 TCTTGAGTTC
*
47715 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGAAATTGTGAGT
47735 TACTCTCACGAAATTGTGAGT
1 TACTCTCACGAAATTGTGAGT
47756 T
1 T
47757 TTTTTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
TACTCTCACGAAATTGTGAGT
Found at i:47887 original size:44 final size:44
Alignment explanation
Indices: 47824--47911 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
47814 TAGAGATAAT
*
47824 TTGTAAATAGGGAATTCAATGTATTAGCACGATAATCGTGTGGG
1 TTGTAAATAGGAAATTCAATGTATTAGCACGATAATCGTGTGGG
47868 TTGTAAATAGGAAATTCAATGTATTAGCACGATAATCGTGTGGG
1 TTGTAAATAGGAAATTCAATGTATTAGCACGATAATCGTGTGGG
47912 GCGGGACTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (44 bp):
TTGTAAATAGGAAATTCAATGTATTAGCACGATAATCGTGTGGG
Found at i:52078 original size:37 final size:37
Alignment explanation
Indices: 52037--52110 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
52027 TAACTAAGAT
52037 GAGAAACAAGTTTATAGTCAATGTGTTATAAAAACAA
1 GAGAAACAAGTTTATAGTCAATGTGTTATAAAAACAA
52074 GAGAAACAAGTTTATAGTCAATGTGTTATAAAAACAA
1 GAGAAACAAGTTTATAGTCAATGTGTTATAAAAACAA
52111 AGTCTAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (37 bp):
GAGAAACAAGTTTATAGTCAATGTGTTATAAAAACAA
Found at i:59185 original size:76 final size:73
Alignment explanation
Indices: 59058--59201 Score: 225
Period size: 76 Copynumber: 1.9 Consensus size: 73
59048 AAAAGTTCAT
* * *
59058 GATGAAATTTGTTTAATTTCTTGAGTTTATGTTTGGTGATTGGGAATGGATTATAGATATGTTTA
1 GATGAAATTTGTTTAATTTCTTGAGTTGATGTTTGGTGATTGGGAAGGGATTATAGATATGTTCA
59123 GAATTTAC
66 GAATTTAC
*
59131 GATGAAATTTGTTTAATTTTTTGTTAAGTTGATGTTTGGTGATTGGGAAGGGATTATAGATATGT
1 GATGAAATTTGTTTAATTTCTTG---AGTTGATGTTTGGTGATTGGGAAGGGATTATAGATATGT
59196 TCAGAA
63 TCAGAA
59202 GTGAAAATGA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
73 22 0.34
76 42 0.66
ACGTcount: A:0.28, C:0.02, G:0.25, T:0.45
Consensus pattern (73 bp):
GATGAAATTTGTTTAATTTCTTGAGTTGATGTTTGGTGATTGGGAAGGGATTATAGATATGTTCA
GAATTTAC
Found at i:59880 original size:5 final size:5
Alignment explanation
Indices: 59853--59898 Score: 67
Period size: 5 Copynumber: 9.2 Consensus size: 5
59843 AATCTGAAGA
*
59853 AAAAG GAAAG AAAA- AAAAGG AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG A
59899 GAAAAGAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 4 0.11
5 29 0.78
6 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:59914 original size:14 final size:14
Alignment explanation
Indices: 59891--59933 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
59881 AGAAAAGAAA
*
59891 AGAAAAGAGAAAAG
1 AGAAAAGAGAAATG
*
59905 AGAAATGAGAAATGG
1 AGAAAAGAGAAAT-G
59920 AGAAAAGA-AAATG
1 AGAAAAGAGAAATG
59933 A
1 A
59934 AACGAGGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 2 0.08
14 15 0.60
15 8 0.32
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (14 bp):
AGAAAAGAGAAATG
Found at i:60263 original size:22 final size:24
Alignment explanation
Indices: 60237--60280 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
60227 ATAACTTTTG
60237 TATATTTCT-A-ATACCAAAGATA
1 TATATTTCTCATATACCAAAGATA
*
60259 TATATTTTTCATATACCAAAGA
1 TATATTTCTCATATACCAAAGA
60281 CAACTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 10 0.53
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (24 bp):
TATATTTCTCATATACCAAAGATA
Found at i:64268 original size:24 final size:24
Alignment explanation
Indices: 64236--64298 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
64226 AATCCAGGAC
64236 AGGGGAATCAAAATGCCATTGTTG
1 AGGGGAATCAAAATGCCATTGTTG
64260 AGGGGAATCAAAATGCCATTGTTG
1 AGGGGAATCAAAATGCCATTGTTG
*
64284 TGGGGAATCAAAATG
1 AGGGGAATCAAAATG
64299 GGGGAATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.35, C:0.11, G:0.30, T:0.24
Consensus pattern (24 bp):
AGGGGAATCAAAATGCCATTGTTG
Found at i:64304 original size:14 final size:14
Alignment explanation
Indices: 64285--64312 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64275 CCATTGTTGT
64285 GGGGAATCAAAATG
1 GGGGAATCAAAATG
64299 GGGGAATCAAAATG
1 GGGGAATCAAAATG
64313 CCGTTGTTAA
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:0.43, C:0.07, G:0.36, T:0.14
Consensus pattern (14 bp):
GGGGAATCAAAATG
Found at i:67276 original size:16 final size:18
Alignment explanation
Indices: 67255--67297 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
67245 GTGAGATTGA
67255 ATATTTAAAT-AATT-AG
1 ATATTTAAATAAATTAAG
*
67271 ATATTTAAGTAAATTAAG
1 ATATTTAAATAAATTAAG
*
67289 ATGTTTAAA
1 ATATTTAAA
67298 GTATGAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
ATATTTAAATAAATTAAG
Found at i:67608 original size:123 final size:123
Alignment explanation
Indices: 67464--67711 Score: 318
Period size: 123 Copynumber: 2.0 Consensus size: 123
67454 AATTTGGTTA
* * * *
67464 ATAAATTTTAAATTTAAGTTAAAATATAAT-TCGATCGATTGACCGATATATTTCGGTTCGGTTA
1 ATAAATTTAAAATTTAAGTTAAAATATAATCT-GATCGATTAACCGAAATACTTCGGTTCGGTTA
* * *
67528 ATGTTCGGAATAAGATACTTCGGATCGGTTAATGATTTACAAAAAATAGTGTTCAGTTC
65 ATATTCGGAATAAGATACTTCGGATCGATTAACGATTTACAAAAAATAGTGTTCAGTTC
* * * * * *
67587 ATAAATTTAAAATTTATGTTAAAATATCATCTGGTTGGTTAACCGAAATACTTCGGTTCGGTTGA
1 ATAAATTTAAAATTTAAGTTAAAATATAATCTGATCGATTAACCGAAATACTTCGGTTCGGTTAA
* * * * *
67652 TATTCGGAATAGGATACTTCGGTTCGATTAACGTTTTACAAAAAATAGTTTTCGGTTC
66 TATTCGGAATAAGATACTTCGGATCGATTAACGATTTACAAAAAATAGTGTTCAGTTC
67710 AT
1 AT
67712 TTGGTTAGTA
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
123 105 0.99
124 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (123 bp):
ATAAATTTAAAATTTAAGTTAAAATATAATCTGATCGATTAACCGAAATACTTCGGTTCGGTTAA
TATTCGGAATAAGATACTTCGGATCGATTAACGATTTACAAAAAATAGTGTTCAGTTC
Found at i:68827 original size:22 final size:22
Alignment explanation
Indices: 68799--68865 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
68789 TAAAGCATTC
68799 ATTTGAATATTTGATTCAATTA
1 ATTTGAATATTTGATTCAATTA
*
68821 ATTTGAAAATATTT-A-TCAAAT-
1 ATTTG--AATATTTGATTCAATTA
68842 ATTTGAATATTTGATTCAAATTA
1 ATTTGAATATTTGATTC-AATTA
68865 A
1 A
68866 AGTATTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 7 0.19
20 1 0.03
21 7 0.19
22 13 0.35
23 2 0.05
24 7 0.19
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (22 bp):
ATTTGAATATTTGATTCAATTA
Found at i:71203 original size:162 final size:162
Alignment explanation
Indices: 70930--71256 Score: 577
Period size: 162 Copynumber: 2.0 Consensus size: 162
70920 CCACCTTGTG
**
70930 TTATGATCCATTCTTGGTACGCCGCAAGGAAGCTGGAGACTTAGAACCCCTGAGGTCGATGACTT
1 TTATGATCCATTCTTGGTACGCCGCAAGGAAGCTGGAGACTTAGAACCCCTGAGGTCGATGACCC
70995 CACCAAGAGACCCCTTTTTCTAAATATTAAAAAAAAAGATTGTTGCCGGGATTGGACTTTTGTCA
66 CACCAAGAGACCCCTTTTTCTAAATATTAAAAAAAAAGATTGTTGCCGGGATTGGACTTTTGTCA
*
71060 CGCGGTGATAGGCAAGGATACTCATTACAATA
131 CGCGGTGATAGGCAAGGATACTCATCACAATA
* *
71092 TTATGATCCATTCTTGGTACGCCGCAAGGAAGCTGGAGACTTAGAGCCCTTGAGGTCGATGACCC
1 TTATGATCCATTCTTGGTACGCCGCAAGGAAGCTGGAGACTTAGAACCCCTGAGGTCGATGACCC
71157 CTACCAAGAGACCCCTTTTTCTAAATATTTAAAAAAAAA-A-TGTTGCCGGGATTGGACTTTTGT
66 C-ACCAAGAGACCCCTTTTTCTAAATA-TTAAAAAAAAAGATTGTTGCCGGGATTGGACTTTTGT
71220 CACGCGGTGATAGGCAAGGATACTCATCACAATA
129 CACGCGGTGATAGGCAAGGATACTCATCACAATA
71254 TTA
1 TTA
71257 CAACAACCAT
Statistics
Matches: 158, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
162 121 0.77
163 26 0.16
164 11 0.07
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (162 bp):
TTATGATCCATTCTTGGTACGCCGCAAGGAAGCTGGAGACTTAGAACCCCTGAGGTCGATGACCC
CACCAAGAGACCCCTTTTTCTAAATATTAAAAAAAAAGATTGTTGCCGGGATTGGACTTTTGTCA
CGCGGTGATAGGCAAGGATACTCATCACAATA
Done.