Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014777.1 Corchorus capsularis cultivar CVL-1 contig14798, 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: 141080
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:3266 original size:9 final size:9
Alignment explanation
Indices: 3254--3288 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
3244 CCTCCTTCCC
3254 CATTTCTTT
1 CATTTCTTT
3263 CATTTCTTT
1 CATTTCTTT
*
3272 CTTTTCTTT
1 CATTTCTTT
3281 C-TTTCTTT
1 CATTTCTTT
3289 TTTTTATGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (9 bp):
CATTTCTTT
Found at i:3289 original size:13 final size:14
Alignment explanation
Indices: 3256--3289 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
3246 TCCTTCCCCA
3256 TTTC-TTTCATTTC
1 TTTCTTTTCATTTC
3269 TTTCTTTTC-TTTC
1 TTTCTTTTCATTTC
3282 TTTCTTTT
1 TTTCTTTT
3290 TTTTATGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCATTTC
Found at i:3792 original size:11 final size:11
Alignment explanation
Indices: 3776--3811 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
3766 ATTTATTCAT
*
3776 TATTAATTAAC
1 TATTAATTAGC
3787 TATTAATTAGC
1 TATTAATTAGC
3798 TATTAATTAGC
1 TATTAATTAGC
3809 TAT
1 TAT
3812 AGTATGATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:4007 original size:13 final size:13
Alignment explanation
Indices: 3989--4028 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
3979 ATTTATTCAT
3989 TATTAATTAACTA
1 TATTAATTAACTA
4002 TATTAATTAGA-TA
1 TATTAATTA-ACTA
*
4015 TATTAATTAGCTA
1 TATTAATTAACTA
4028 T
1 T
4029 TAATTAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 23 0.96
14 1 0.04
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (13 bp):
TATTAATTAACTA
Found at i:4243 original size:24 final size:24
Alignment explanation
Indices: 4216--4265 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4206 ATTTATTCAT
4216 TATTAATTAACTATTAATTAGATA
1 TATTAATTAACTATTAATTAGATA
*
4240 TATTAATTAGCTATTAATTAGATA
1 TATTAATTAACTATTAATTAGATA
4264 TA
1 TA
4266 GTATAATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (24 bp):
TATTAATTAACTATTAATTAGATA
Found at i:4245 original size:13 final size:13
Alignment explanation
Indices: 4227--4265 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
4217 ATTAATTAAC
4227 TATTAATTAGATA
1 TATTAATTAGATA
*
4240 TATTAATTAG--C
1 TATTAATTAGATA
4251 TATTAATTAGATA
1 TATTAATTAGATA
4264 TA
1 TA
4266 GTATAATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 10 0.45
13 12 0.55
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (13 bp):
TATTAATTAGATA
Found at i:4260 original size:11 final size:11
Alignment explanation
Indices: 4216--4260 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
4206 ATTTATTCAT
*
4216 TATTAATTAAC
1 TATTAATTAGC
*
4227 TATTAATTAGATA
1 TATTAATTAG--C
4240 TATTAATTAGC
1 TATTAATTAGC
4251 TATTAATTAG
1 TATTAATTAG
4261 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 19 0.66
13 10 0.34
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:4330 original size:225 final size:226
Alignment explanation
Indices: 3787--4405 Score: 1141
Period size: 225 Copynumber: 2.7 Consensus size: 226
3777 ATTAATTAAC
* *
3787 TATTAATTAGCTATTAATTAGCTATAGTATGATGGATGGTTAAGGAGGGGCTTTAAATTAATCTG
1 TATTAATTAGCTATTAATTAGATATAGTATAATGGATGGTTAAGGAGGGGCTTTAAATTAATCTG
*
3852 TTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACCGGGTTAAAAGTTGAAAGGGCTT
66 TTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTT
*
3917 GTTAGTAATTTGCACAGGGGACAAAAAATAATATATAACTAAAAAAATTCAAATTGAATTGAATT
131 GTTAGTAATTTGCATAGGGGAC-AAAAATAATATATAACTAAAAAAATTCAAATTGAATTGAATT
3982 TATTCATTATTAATTAACTATATTAATTAGATA
195 TATTCATTATTAATTAAC-ATATTAATTAGATA
4015 TATTAATTAGCTATTAATTAGATATAGTATAATGGATGGTTAAGGAGGGGCTTTAAATTAATCTG
1 TATTAATTAGCTATTAATTAGATATAGTATAATGGATGGTTAAGGAGGGGCTTTAAATTAATCTG
*
4080 TTAGATGTGAGAAATTACTAAAATGGGGCGATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTT
66 TTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTT
4145 GTTAGTAATTTGCATAGGGGACAAAAATAATATATAACTAAAAAAATTCAAATTGAATTGAATTT
131 GTTAGTAATTTGCATAGGGGACAAAAATAATATATAACTAAAAAAATTCAAATTGAATTGAATTT
4210 ATTCATTATTAATTAAC-TATTAATTAGATA
196 ATTCATTATTAATTAACATATTAATTAGATA
*
4240 TATTAATTAGCTATTAATTAGATATAGTATAATGGATGGTTAAGGAGGGGCTTTAAATTAATCTA
1 TATTAATTAGCTATTAATTAGATATAGTATAATGGATGGTTAAGGAGGGGCTTTAAATTAATCTG
*
4305 TTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGCCACCAGGTTAAAAGTTGAAAGGGCTT
66 TTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTT
*
4370 GTTAGTAATTTGCATAGGAGACAAAAATAATATATA
131 GTTAGTAATTTGCATAGGGGACAAAAATAATATATA
4406 GTATATATAA
Statistics
Matches: 382, Mismatches: 9, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
225 175 0.46
227 60 0.16
228 147 0.38
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (226 bp):
TATTAATTAGCTATTAATTAGATATAGTATAATGGATGGTTAAGGAGGGGCTTTAAATTAATCTG
TTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTT
GTTAGTAATTTGCATAGGGGACAAAAATAATATATAACTAAAAAAATTCAAATTGAATTGAATTT
ATTCATTATTAATTAACATATTAATTAGATA
Found at i:9565 original size:2 final size:2
Alignment explanation
Indices: 9558--9588 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9548 TTTTGACAAT
9558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9589 TAAGTACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17819 original size:155 final size:156
Alignment explanation
Indices: 17646--18055 Score: 415
Period size: 156 Copynumber: 2.6 Consensus size: 156
17636 TTCGAGCCTT
* **
17646 CCTTCATGGTGAACTAGGTTTCACACCCCGAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
1 CCTTGATGGTGAACTAGGTTTCACACCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
*
17711 CATTCTAAGTCTGATTGAGATGAAACTTTGCCAC-AG-GACTTAGATT-CTCTCCA-AAAGACTA
66 CATTCTAAGTC-AATTGAGATGAAACTTTGCCACTAGAGACTTAGATTACTC-CCATAAAG-CTA
*
17772 T-AAAAAAATTCCAAGTAAAACCGAGCTCC
128 TGAAAAAAATTCCAAGTAAAACCGAACT-C
*** ** *
17801 CCTTGATGGTGAACTAGGTTTCTGTCCCTAAACTGTCCTTAAATGAAAAGTTAGCTTAAGTTTTT
1 CCTTGATGGTGAACTAGGTTTCACACCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
* * * * *
17866 CATTCTACGTCCAA-TGAAGCTG-ATC-TT-CCACTAGTAGGCTTAGATTACTCCCATAAAGTTA
66 CATTCTAAGT-CAATTG-AGATGAAACTTTGCCACTAG-AGACTTAGATTACTCCCATAAAGCTA
* **
17927 TGGAAAAAATTCTTAGTAAAACCGAACTC
128 TGAAAAAAATTCCAAGTAAAACCGAACTC
* * * * * * *
17956 CCTAGCATAGAGAAGTTGGTTTGACACCCTAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTT
1 CCTTG-ATGGTGAACTAGGTTTCACACCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTT
* * *
18021 TCATACTAACTCCAATTGAGATGAAACTTGGCCAC
65 TCATTCTAAGT-CAATTGAGATGAAACTTTGCCAC
18056 GACCGTAGGG
Statistics
Matches: 204, Mismatches: 38, Indels: 22
0.77 0.14 0.08
Matches are distributed among these distances:
152 4 0.02
153 4 0.02
154 4 0.02
155 90 0.44
156 93 0.46
157 4 0.02
158 1 0.00
159 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (156 bp):
CCTTGATGGTGAACTAGGTTTCACACCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
CATTCTAAGTCAATTGAGATGAAACTTTGCCACTAGAGACTTAGATTACTCCCATAAAGCTATGA
AAAAAATTCCAAGTAAAACCGAACTC
Found at i:19941 original size:27 final size:27
Alignment explanation
Indices: 19880--19948 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 27
19870 ATGACGTGGG
19880 TTTTCTTTTTT-TTTT-TTTTCTCTTT
1 TTTTCTTTTTTCTTTTCTTTTCTCTTT
* *
19905 TATTC-CTTTTCTTTTCTTTT-TCTGTT
1 TTTTCTTTTTTCTTTTCTTTTCTCT-TT
*
19931 TTTTCTTTTTTCTCTTCT
1 TTTTCTTTTTTCTTTTCT
19949 CCTTCTTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
24 4 0.11
25 11 0.31
26 10 0.29
27 10 0.29
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (27 bp):
TTTTCTTTTTTCTTTTCTTTTCTCTTT
Found at i:21222 original size:57 final size:53
Alignment explanation
Indices: 21123--21235 Score: 190
Period size: 57 Copynumber: 2.1 Consensus size: 53
21113 GCGATTTATG
21123 TTTATAAAGGAATTTTTTAAAAAAATTTTTCCAAAAATCCACGTCATTTGGTC
1 TTTATAAAGGAATTTTTTAAAAAAATTTTTCCAAAAATCCACGTCATTTGGTC
21176 TTTATAAAGGAATTTTTTTTAAAAAAATTTTTTTCCAAAAATCCACGTCATTTGGTC
1 TTTATAAAGGAA--TTTTTTAAAAAAA--TTTTTCCAAAAATCCACGTCATTTGGTC
21233 TTT
1 TTT
21236 TAGCCACGTG
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
53 12 0.21
55 13 0.23
57 31 0.55
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (53 bp):
TTTATAAAGGAATTTTTTAAAAAAATTTTTCCAAAAATCCACGTCATTTGGTC
Found at i:31443 original size:13 final size:13
Alignment explanation
Indices: 31425--31452 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31415 TCTATGTTTC
31425 TGCTTTACGAATA
1 TGCTTTACGAATA
31438 TGCTTTACGAATA
1 TGCTTTACGAATA
31451 TG
1 TG
31453 ATATTTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGCTTTACGAATA
Found at i:37798 original size:20 final size:20
Alignment explanation
Indices: 37773--37815 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
37763 ACAAGTATGG
**
37773 ACTTAACGAAGCGGTTAGTT
1 ACTTAACGAAGCCATTAGTT
*
37793 ACTTAACGTAGCCATTAGTT
1 ACTTAACGAAGCCATTAGTT
37813 ACT
1 ACT
37816 ACTAACTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (20 bp):
ACTTAACGAAGCCATTAGTT
Found at i:61687 original size:63 final size:55
Alignment explanation
Indices: 61619--61777 Score: 218
Period size: 63 Copynumber: 2.8 Consensus size: 55
61609 GCCTGTATGC
61619 ATAAATATTCTATTGAACCTAGTCATATTTATATATGAATTTAAAGCATATCAAAATTTATAT
1 ATAAATATTCTATTGAACCTAGTCATATTTATATATGAATTTAAAGC--AT----A-TT-TAT
61682 ATAAATATTCTATTGAACCTAGTCATATTTATATATGAATTTAAAGCATATTTAT
1 ATAAATATTCTATTGAACCTAGTCATATTTATATATGAATTTAAAGCATATTTAT
61737 -T---TATTCTATTGAACCTAGTCATATTTATATATGAATTTAAA
1 ATAAATATTCTATTGAACCTAGTCATATTTATATATGAATTTAAA
61778 ACATCAAAAT
Statistics
Matches: 96, Mismatches: 0, Indels: 12
0.89 0.00 0.11
Matches are distributed among these distances:
51 40 0.42
54 1 0.01
55 3 0.03
56 2 0.02
57 1 0.01
61 2 0.02
63 47 0.49
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.43
Consensus pattern (55 bp):
ATAAATATTCTATTGAACCTAGTCATATTTATATATGAATTTAAAGCATATTTAT
Found at i:61735 original size:23 final size:24
Alignment explanation
Indices: 61702--61777 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 24
61692 TATTGAACCT
61702 AGTCATATTTATATATGAATTTAA
1 AGTCATATTTATATATGAATTTAA
* ** *
61726 AG-CATATTTATTTATTCTATTGAA
1 AGTCATATTTATATA-TGAATTTAA
61750 CCTAGTCATATTTATATATGAATTTAA
1 ---AGTCATATTTATATATGAATTTAA
61777 A
1 A
61778 ACATCAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
23 11 0.28
24 9 0.23
27 8 0.21
28 11 0.28
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (24 bp):
AGTCATATTTATATATGAATTTAA
Found at i:61762 original size:28 final size:28
Alignment explanation
Indices: 61686--61768 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
61676 TTATATATAA
61686 ATATTCTATTGAACCTAGTCATATTTAT
1 ATATTCTATTGAACCTAGTCATATTTAT
** *
61714 ATA-TGAATTTAA---AG-CATATTTAT
1 ATATTCTATTGAACCTAGTCATATTTAT
*
61737 TTATTCTATTGAACCTAGTCATATTTAT
1 ATATTCTATTGAACCTAGTCATATTTAT
61765 ATAT
1 ATAT
61769 GAATTTAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
23 11 0.26
24 8 0.19
27 8 0.19
28 15 0.36
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (28 bp):
ATATTCTATTGAACCTAGTCATATTTAT
Found at i:61824 original size:32 final size:28
Alignment explanation
Indices: 61771--61829 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 28
61761 TTATATATGA
61771 ATTTAAAACATCAAAATTAAGTTCCATTC
1 ATTTAAAACATCAAAATTAAG-TCCATTC
*
61800 ATTTAAGAAGCATGAAAAGTTAAGTCCATT
1 ATTTAA-AA-CATCAAAA-TTAAGTCCATT
61830 TAGGGCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 2 0.08
31 13 0.50
32 5 0.19
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (28 bp):
ATTTAAAACATCAAAATTAAGTCCATTC
Found at i:61962 original size:104 final size:104
Alignment explanation
Indices: 61777--61964 Score: 358
Period size: 104 Copynumber: 1.8 Consensus size: 104
61767 ATGAATTTAA
*
61777 AACATCAAAATTAAGTTCCATTCATTTAAGAAGCATGAAAAGTTAAGTCCATTTAGGGCTAAAAG
1 AACAGCAAAATTAAGTTCCATTCATTTAAGAAGCATGAAAAGTTAAGTCCATTTAGGGCTAAAAG
61842 TTACAAGGACAGCAATTAGTCTTAGTATTCGAATGCTTT
66 TTACAAGGACAGCAATTAGTCTTAGTATTCGAATGCTTT
61881 AACAGCAAAATTAAGTTCCATTCATTTAAGAAGCATGAAAAGTTAAGTCCATTTAGGGCTAAAAG
1 AACAGCAAAATTAAGTTCCATTCATTTAAGAAGCATGAAAAGTTAAGTCCATTTAGGGCTAAAAG
*
61946 TTCCAAGGACAGCAATTAG
66 TTACAAGGACAGCAATTAG
61965 GCTAAAAGTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 82 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (104 bp):
AACAGCAAAATTAAGTTCCATTCATTTAAGAAGCATGAAAAGTTAAGTCCATTTAGGGCTAAAAG
TTACAAGGACAGCAATTAGTCTTAGTATTCGAATGCTTT
Found at i:61972 original size:27 final size:27
Alignment explanation
Indices: 61937--61991 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
61927 GTCCATTTAG
*
61937 GGCTAAAAGTTCCAAGGACAGCAATTA
1 GGCTAAAAGTTACAAGGACAGCAATTA
*
61964 GGCTAAAAGTTACAAGGACATCAATTA
1 GGCTAAAAGTTACAAGGACAGCAATTA
61991 G
1 G
61992 TCTTAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (27 bp):
GGCTAAAAGTTACAAGGACAGCAATTA
Found at i:75916 original size:58 final size:58
Alignment explanation
Indices: 75845--75960 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
75835 AGCTCAGTAT
75845 CTGGTAATCACATTAAACTCTGATTAATTTAAGATCGAGTCACGTTGAACTTCAAACA
1 CTGGTAATCACATTAAACTCTGATTAATTTAAGATCGAGTCACGTTGAACTTCAAACA
* * * * * *
75903 CTGGTAATTACATTGAATTTTGATTAATTTAAGATCGAGTCACGTTTAATTTCAAACA
1 CTGGTAATCACATTAAACTCTGATTAATTTAAGATCGAGTCACGTTGAACTTCAAACA
75961 AAACAAAGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (58 bp):
CTGGTAATCACATTAAACTCTGATTAATTTAAGATCGAGTCACGTTGAACTTCAAACA
Found at i:92904 original size:5 final size:5
Alignment explanation
Indices: 92897--92934 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
92887 TGTGGGTGAG
*
92897 ACAGG ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACA
1 ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACA
92935 TTGCAGTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.58, C:0.21, G:0.21, T:0.00
Consensus pattern (5 bp):
ACAGA
Found at i:94754 original size:29 final size:29
Alignment explanation
Indices: 94710--94768 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
94700 AAAGCGGAGG
*
94710 CGAATAAGGAGTGGGAGAGGTTACAGGTA
1 CGAATAAGGAGCGGGAGAGGTTACAGGTA
* *
94739 CGAATAAGGAGCGGGAGATGTTATAGGTA
1 CGAATAAGGAGCGGGAGAGGTTACAGGTA
94768 C
1 C
94769 TCATGATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.39, T:0.19
Consensus pattern (29 bp):
CGAATAAGGAGCGGGAGAGGTTACAGGTA
Found at i:102327 original size:2 final size:2
Alignment explanation
Indices: 102320--102347 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
102310 AAGGGAAATA
102320 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
102348 TAATGCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102931 original size:4 final size:4
Alignment explanation
Indices: 102922--102959 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
102912 TTGTCGAGAT
102922 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
102960 TTATTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:102954 original size:11 final size:11
Alignment explanation
Indices: 102926--102971 Score: 69
Period size: 10 Copynumber: 4.3 Consensus size: 11
102916 CGAGATTTTA
102926 TTTATTTATTT
1 TTTATTTATTT
102937 ATTTATTTATTT
1 -TTTATTTATTT
102949 TTTATTTA-TT
1 TTTATTTATTT
102959 TTTATTT-TTT
1 TTTATTTATTT
102969 TTT
1 TTT
102972 TCATATGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 14 0.42
11 8 0.24
12 11 0.33
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:102961 original size:12 final size:12
Alignment explanation
Indices: 102920--102972 Score: 60
Period size: 11 Copynumber: 4.7 Consensus size: 12
102910 GTTTGTCGAG
102920 ATTTTATTTATTT
1 ATTTT-TTTATTT
*
102933 ATTTATTTATTT
1 ATTTTTTTATTT
102945 A-TTTTTTATTT
1 ATTTTTTTATTT
102956 A--TTTTTATTT
1 ATTTTTTTATTT
102966 -TTTTTTT
1 ATTTTTTT
102973 CATATGGTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 9 0.25
11 15 0.42
12 8 0.22
13 4 0.11
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
ATTTTTTTATTT
Found at i:104328 original size:12 final size:12
Alignment explanation
Indices: 104251--104364 Score: 90
Period size: 12 Copynumber: 9.5 Consensus size: 12
104241 ACTGTTTCTG
*
104251 AATCTGAACAGCC
1 AATCTGGACAG-C
104264 AAT-TGGACAGC
1 AATCTGGACAGC
*
104275 CATCTGGACAGC
1 AATCTGGACAGC
*
104287 AAT-TCGGGCAGC
1 AATCT-GGACAGC
* *
104299 CATCTGGACAAC
1 AATCTGGACAGC
*
104311 ACTCTGGACAGC
1 AATCTGGACAGC
*
104323 AATCTGGTCAG-
1 AATCTGGACAGC
104334 AATTCTGGACAGC
1 AA-TCTGGACAGC
* * *
104347 GATCAGGACAAC
1 AATCTGGACAGC
104359 AATCTG
1 AATCTG
104365 TGGCTGCAGA
Statistics
Matches: 78, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
11 6 0.08
12 67 0.86
13 5 0.06
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (12 bp):
AATCTGGACAGC
Found at i:105648 original size:40 final size:40
Alignment explanation
Indices: 105604--105688 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
105594 TTCCATAAAC
105604 CATTTTGTCTGTT-ATTATTGTTTGGTTGTGTTAGATTCTG
1 CATTTT-TCTGTTGATTATTGTTTGGTTGTGTTAGATTCTG
105644 CATTTTTCTGTTGATTATTGTTTGGTTGTGTTAGATTCTG
1 CATTTTTCTGTTGATTATTGTTTGGTTGTGTTAGATTCTG
*
105684 AATTT
1 CATTT
105689 GAGGTTGGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
39 6 0.14
40 37 0.86
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.58
Consensus pattern (40 bp):
CATTTTTCTGTTGATTATTGTTTGGTTGTGTTAGATTCTG
Found at i:106718 original size:2 final size:2
Alignment explanation
Indices: 106701--106747 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
106691 TATGTTCTTT
*
106701 TA TA TG TA TA TA -A TA TA TA TA TA TA T- TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
106740 TA TA TA TA
1 TA TA TA TA
106748 GTAATTTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:106853 original size:54 final size:55
Alignment explanation
Indices: 106795--106898 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 55
106785 ACTAATACTC
* ** *
106795 TTTACCAACG-CCTGTAAATCATATACCGACGGATTAATTAATG-AAAAAATACCT
1 TTTACCAACGACC-CTAAATCATATACAAACGGATTAACTAATGCAAAAAATACCT
*
106849 TTTACCAACGACCCTAAATCCTATACAAACGGATTAACTAATGCAAAAAA
1 TTTACCAACGACCCTAAATCATATACAAACGGATTAACTAATGCAAAAAA
106899 CGATTTACCT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
54 35 0.81
55 8 0.19
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (55 bp):
TTTACCAACGACCCTAAATCATATACAAACGGATTAACTAATGCAAAAAATACCT
Found at i:125066 original size:39 final size:39
Alignment explanation
Indices: 125012--125129 Score: 236
Period size: 39 Copynumber: 3.0 Consensus size: 39
125002 AGACTAGCGA
125012 TGAACTTGTCACATTAAACACAATGTCAATTTCAAAGGG
1 TGAACTTGTCACATTAAACACAATGTCAATTTCAAAGGG
125051 TGAACTTGTCACATTAAACACAATGTCAATTTCAAAGGG
1 TGAACTTGTCACATTAAACACAATGTCAATTTCAAAGGG
125090 TGAACTTGTCACATTAAACACAATGTCAATTTCAAAGGG
1 TGAACTTGTCACATTAAACACAATGTCAATTTCAAAGGG
125129 T
1 T
125130 ATTATTTTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (39 bp):
TGAACTTGTCACATTAAACACAATGTCAATTTCAAAGGG
Found at i:126369 original size:19 final size:21
Alignment explanation
Indices: 126345--126397 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
126335 TTTATAACTG
*
126345 TTTGGTGTAATGAT-TC-TTT
1 TTTGGTGTAATGATATCATTA
*
126364 TTTGGTGTAATGGTATCATTA
1 TTTGGTGTAATGATATCATTA
126385 TTTGGTGTAATGA
1 TTTGGTGTAATGA
126398 AAAATCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.45
20 2 0.07
21 14 0.48
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.51
Consensus pattern (21 bp):
TTTGGTGTAATGATATCATTA
Found at i:134478 original size:34 final size:34
Alignment explanation
Indices: 134435--134504 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
134425 CATGGGTCGC
134435 GCCCAGATCGTGACCCACCATTGGGCGGGTCCGG
1 GCCCAGATCGTGACCCACCATTGGGCGGGTCCGG
* *
134469 GCCCGGATCGTGACCCACCATTGGGCGGGTCTGG
1 GCCCAGATCGTGACCCACCATTGGGCGGGTCCGG
134503 GC
1 GC
134505 GCGACCCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.13, C:0.34, G:0.37, T:0.16
Consensus pattern (34 bp):
GCCCAGATCGTGACCCACCATTGGGCGGGTCCGG
Found at i:134935 original size:20 final size:20
Alignment explanation
Indices: 134910--134947 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
134900 TAGTCCAAAG
134910 GGGGACGGTGA-TTAGTAAAA
1 GGGGACGGT-ATTTAGTAAAA
134930 GGGGACGGTATTTAGTAA
1 GGGGACGGTATTTAGTAA
134948 TTCACGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.32, C:0.05, G:0.39, T:0.24
Consensus pattern (20 bp):
GGGGACGGTATTTAGTAAAA
Found at i:135891 original size:2 final size:2
Alignment explanation
Indices: 135886--135922 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
135876 AACTTTTTTT
135886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
135923 TTCTTTGCAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:137284 original size:32 final size:32
Alignment explanation
Indices: 137248--137359 Score: 115
Period size: 32 Copynumber: 3.5 Consensus size: 32
137238 GAACCCGCCC
* *
137248 GACCCGAGAGCCGAATGACCCGTAACCC-AGAT
1 GACCCGAAACCCGAATGACCCGTAACCCGAG-T
137280 GACCCGAAACCCGAATGACCCGTAACCCGAGT
1 GACCCGAAACCCGAATGACCCGTAACCCGAGT
* **
137312 GACCTGTGACCCG-A-GACCCGTATGACCCGTA-T
1 GACCCGAAACCCGAATGACCCGTA--ACCCG-AGT
137344 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
137360 AACTCGAGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
30 8 0.12
31 1 0.02
32 53 0.80
33 4 0.06
ACGTcount: A:0.29, C:0.36, G:0.23, T:0.12
Consensus pattern (32 bp):
GACCCGAAACCCGAATGACCCGTAACCCGAGT
Found at i:137307 original size:16 final size:16
Alignment explanation
Indices: 137258--137359 Score: 102
Period size: 16 Copynumber: 6.4 Consensus size: 16
137248 GACCCGAGAG
137258 CCGAATGACCCGTAAC
1 CCGAATGACCCGTAAC
*
137274 CC-AGATGACCCGAAAC
1 CCGA-ATGACCCGTAAC
137290 CCGAATGACCCGTAAC
1 CCGAATGACCCGTAAC
* * *
137306 CCGAGTGACCTGTGAC
1 CCGAATGACCCGTAAC
137322 CCG-A-GACCCGTATGAC
1 CCGAATGACCCGTA--AC
* *
137338 CCGTATGACCCGAAAC
1 CCGAATGACCCGTAAC
137354 CCGAAT
1 CCGAAT
137360 AACTCGAGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
14 6 0.09
15 1 0.01
16 54 0.77
17 2 0.03
18 7 0.10
ACGTcount: A:0.29, C:0.36, G:0.22, T:0.13
Consensus pattern (16 bp):
CCGAATGACCCGTAAC
Found at i:137308 original size:39 final size:38
Alignment explanation
Indices: 137265--137342 Score: 86
Period size: 39 Copynumber: 2.0 Consensus size: 38
137255 GAGCCGAATG
137265 ACCC-GTAACCCAGATGACCCGAAACCCGAATGACCCGTA
1 ACCCAGTAA-CCAG-TGACCCGAAACCCGAATGACCCGTA
* * * *
137304 ACCCGAGTGACCTGTGACCCGAGACCCGTATGACCCGTA
1 ACCC-AGTAACCAGTGACCCGAAACCCGAATGACCCGTA
137343 TGACCCGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
39 27 0.82
40 3 0.09
41 3 0.09
ACGTcount: A:0.28, C:0.37, G:0.22, T:0.13
Consensus pattern (38 bp):
ACCCAGTAACCAGTGACCCGAAACCCGAATGACCCGTA
Found at i:137315 original size:48 final size:48
Alignment explanation
Indices: 137248--137359 Score: 120
Period size: 48 Copynumber: 2.3 Consensus size: 48
137238 GAACCCGCCC
* *
137248 GACCCGAGAGCCGAATGACCCGTAACCCAGATGACCCG-A-AACCCGAAT
1 GACCCGAAACCCGAATGACCCGTAACCC-GA-GACCCGTATAACCCGAAT
* * * * * *
137296 GACCCGTAACCCGAGTGACCTGTGACCCGAGACCCGTATGACCCGTAT
1 GACCCGAAACCCGAATGACCCGTAACCCGAGACCCGTATAACCCGAAT
137344 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
137360 AACTCGAGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
46 6 0.12
47 3 0.06
48 43 0.83
ACGTcount: A:0.29, C:0.36, G:0.23, T:0.12
Consensus pattern (48 bp):
GACCCGAAACCCGAATGACCCGTAACCCGAGACCCGTATAACCCGAAT
Found at i:137330 original size:23 final size:23
Alignment explanation
Indices: 137288--137357 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
137278 ATGACCCGAA
*
137288 ACCCGAATGACCCGTAACCCGAGTG
1 ACCCGTATGACCCG-AACCCGA-TG
*
137313 A-CC-TGTGACCCGAGACCCGTATG
1 ACCCGTATGACCCGA-ACCCG-ATG
137336 ACCCGTATGACCCGAAACCCGA
1 ACCCGTATGACCCG-AACCCGA
137358 ATAACTCGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
22 1 0.03
23 15 0.41
24 6 0.16
25 14 0.38
26 1 0.03
ACGTcount: A:0.27, C:0.37, G:0.23, T:0.13
Consensus pattern (23 bp):
ACCCGTATGACCCGAACCCGATG
Found at i:138217 original size:16 final size:16
Alignment explanation
Indices: 138196--138252 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
138186 AACCCGTCCA
138196 ACCCGAGACTCGGTA-G
1 ACCCGAGACTC-GTATG
* *
138212 ACCCGAGACCCGAATG
1 ACCCGAGACTCGTATG
*
138228 ACCCGAAACTCGTATG
1 ACCCGAGACTCGTATG
138244 ACCCGAGAC
1 ACCCGAGAC
138253 CCGGATACCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 2 0.06
16 32 0.94
ACGTcount: A:0.30, C:0.35, G:0.25, T:0.11
Consensus pattern (16 bp):
ACCCGAGACTCGTATG
Found at i:138232 original size:32 final size:31
Alignment explanation
Indices: 138196--138265 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 31
138186 AACCCGTCCA
*
138196 ACCCGAGACTCGGTA-GACCCGAGACCCGAAT
1 ACCCGAAACTC-GTATGACCCGAGACCCGAAT
*
138227 GACCCGAAACTCGTATGACCCGAGACCCGGAT
1 -ACCCGAAACTCGTATGACCCGAGACCCGAAT
138259 ACCCGAA
1 ACCCGAA
138266 TGACTCGAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 10 0.29
32 25 0.71
ACGTcount: A:0.30, C:0.36, G:0.24, T:0.10
Consensus pattern (31 bp):
ACCCGAAACTCGTATGACCCGAGACCCGAAT
Done.