Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007085.1 Corchorus capsularis cultivar CVL-1 contig07106, 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: 26070
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Found at i:1298 original size:12 final size:12
Alignment explanation
Indices: 1281--1307 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1271 AATAGAAGTG
1281 AAAAAGAAAAGA
1 AAAAAGAAAAGA
1293 AAAAAGAAAAGA
1 AAAAAGAAAAGA
1305 AAA
1 AAA
1308 GTGAAGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:8343 original size:11 final size:11
Alignment explanation
Indices: 8324--8359 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
8314 ATTAATAGTG
8324 ATATTTGGAAA
1 ATATTTGGAAA
*
8335 ATATATGGAAA
1 ATATTTGGAAA
8346 ATTATTTGGAAA
1 A-TATTTGGAAA
8358 AT
1 AT
8360 TAATTGTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (11 bp):
ATATTTGGAAA
Found at i:8357 original size:12 final size:12
Alignment explanation
Indices: 8325--8361 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
8315 TTAATAGTGA
8325 TATTTGGAAAA-
1 TATTTGGAAAAT
*
8336 TATATGGAAAAT
1 TATTTGGAAAAT
8348 TATTTGGAAAAT
1 TATTTGGAAAAT
8360 TA
1 TA
8362 ATTGTCCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (12 bp):
TATTTGGAAAAT
Found at i:9276 original size:124 final size:125
Alignment explanation
Indices: 9052--9342 Score: 343
Period size: 124 Copynumber: 2.3 Consensus size: 125
9042 ACCTCGGGAA
* * * * * * *
9052 CCATGCTACTGACCTCCTTTGTTGATGAA-GAAAATGAACGTAGATTGAAGTGCCTCAGCAGCAC
1 CCATGCTGCTGACCTCCTTTGTTGATGAAGGATAA-G-ACTTTGGTTAAACTGCCTCAGCAGCAC
* * * * * * * *
9116 TTTCCAGCAGCGGGACCTCCTCCTCGGCAGAGTGACATGTCAGCAATGTCGCCCCAGGTTAG
64 TTTCCAACAGCGGAACCTCCTCCTCAGCAGAATGACACGTCAACAAGGTCGCACCAGGTTAG
* * *
9178 CCATGCTGCTGACCTCTTTTGTTGATGGAGGATAAGACTTTGGTTAAACTGCC-CAGTAGCACTT
1 CCATGCTGCTGACCTCCTTTGTTGATGAAGGATAAGACTTTGGTTAAACTGCCTCAGCAGCACTT
* * * * *
9242 TCTAACAGTGGAACCTCCTCCTCAGCAGAATGACACGTTAACAAGGTTGCACCGGGTTAG
66 TCCAACAGCGGAACCTCCTCCTCAGCAGAATGACACGTCAACAAGGTCGCACCAGGTTAG
9302 CCATGCTGCTGACCTCCTTTGTTGATGAAGGATAAGACTTT
1 CCATGCTGCTGACCTCCTTTGTTGATGAAGGATAAGACTTT
9343 TGGTACTACT
Statistics
Matches: 139, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
124 96 0.69
125 12 0.09
126 27 0.19
127 4 0.03
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.26
Consensus pattern (125 bp):
CCATGCTGCTGACCTCCTTTGTTGATGAAGGATAAGACTTTGGTTAAACTGCCTCAGCAGCACTT
TCCAACAGCGGAACCTCCTCCTCAGCAGAATGACACGTCAACAAGGTCGCACCAGGTTAG
Found at i:10485 original size:147 final size:147
Alignment explanation
Indices: 10301--10569 Score: 396
Period size: 147 Copynumber: 1.8 Consensus size: 147
10291 GACCGAAAAC
** * * *
10301 ATAAACTTTCCTATTAGTGAGCCCCACTATCAACATGTCTCGGATATTGCCATGTCAGCCTGTTG
1 ATAAACTCACCTATTAGTGAGCCCCACCATCAACATGTCTCGGATATTGCCACGTCAGCCTATTG
* *
10366 TGGGTCCCAACAGTGC-CAAATAGTGGGTTCGGCATCCCGGCAGAGGTCATGAACAGTGACCCTC
66 TGGGTCCCAACAGTGCTC-AATAGTGGGTCCGGCATCCCAGCAGAGGTCATGAACAGTGACCCTC
10430 CAGTAGGGGCGGAGAACA
130 CAGTAGGGGCGGAGAACA
* * * *
10448 ATAAACTCACCTATTAGTGAGCCCCACCATCAGCATGTCTCGGGTGTTGCCACGTCAGCTTATTG
1 ATAAACTCACCTATTAGTGAGCCCCACCATCAACATGTCTCGGATATTGCCACGTCAGCCTATTG
* * *
10513 TGGGTCCCAATAGTGCTCAATAGTGGGTCCGGCATCCCAGTAGGGGTCATGAACAGT
66 TGGGTCCCAACAGTGCTCAATAGTGGGTCCGGCATCCCAGCAGAGGTCATGAACAGT
10570 AGCTTTCCAA
Statistics
Matches: 107, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
147 106 0.99
148 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (147 bp):
ATAAACTCACCTATTAGTGAGCCCCACCATCAACATGTCTCGGATATTGCCACGTCAGCCTATTG
TGGGTCCCAACAGTGCTCAATAGTGGGTCCGGCATCCCAGCAGAGGTCATGAACAGTGACCCTCC
AGTAGGGGCGGAGAACA
Found at i:10827 original size:92 final size:92
Alignment explanation
Indices: 10653--11117 Score: 664
Period size: 92 Copynumber: 5.1 Consensus size: 92
10643 GAGTAGATCA
* * * * *
10653 ATGATGGTGAATAAAATATCATAACAAGGAAGACTAGTTGAGAGATATAGGGCGCTCAAATCACC
1 ATGATAGTGAATAATACATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
10718 AGCGGCATAATGCCTTGCCATGCCTTG
66 AGCGGCATAATGCCTTGCCATGCCTTG
* * * *
10745 ATGGTAGT-AGATAATACATCATAACAGGGAAGACTAGGTTAGAGCTATAGGGTGCTCAAATCAC
1 ATGATAGTGA-ATAATACATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCAC
* *
10809 CAGAGGCATAGTGCCTTGCCATGCCTTG
65 CAGCGGCATAATGCCTTGCCATGCCTTG
* * * *
10837 ATGATGGTGAATAATATATCATAACGAGGAAGACTGGGTGAGAGCTATAGGGCGCTCAAATCACC
1 ATGATAGTGAATAATACATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
* * *
10902 GGCGGCATAATGCCTTACCATGCCTTA
66 AGCGGCATAATGCCTTGCCATGCCTTG
* *
10929 ATGATAGT-AGATAATACATCATAACTAGGAAGACTAGGTGAGAGCTATAGGACGCTCAAATCAC
1 ATGATAGTGA-ATAATACATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCAC
*
10993 CAGCGGCATAGTGCCTTGCCATGCCTTG
65 CAGCGGCATAATGCCTTGCCATGCCTTG
* *
11021 ATGATGGTGAATAATATATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
1 ATGATAGTGAATAATACATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
* * *
11086 GGCGGCATAATGCCTTGCGATGCTTTG
66 AGCGGCATAATGCCTTGCCATGCCTTG
11113 ATGAT
1 ATGAT
11118 CATGATGGGT
Statistics
Matches: 328, Mismatches: 41, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
91 2 0.01
92 324 0.99
93 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (92 bp):
ATGATAGTGAATAATACATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
AGCGGCATAATGCCTTGCCATGCCTTG
Found at i:10962 original size:184 final size:184
Alignment explanation
Indices: 10653--11101 Score: 765
Period size: 184 Copynumber: 2.4 Consensus size: 184
10643 GAGTAGATCA
* * *
10653 ATGATGGTGAATAAAATATCATAACAAGGAAGACTAGTTGAGAGATATAGGGCGCTCAAATCACC
1 ATGATGGTGAATAATATATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
* * * *
10718 AGCGGCATAATGCCTTGCCATGCCTTGATGGTAGTAGATAATACATCATAACAGGGAAGACTAGG
66 GGCGGCATAATGCCTTACCATGCCTTAATGATAGTAGATAATACATCATAACAGGGAAGACTAGG
* **
10783 TTAGAGCTATAGGGTGCTCAAATCACCAGAGGCATAGTGCCTTGCCATGCCTTG
131 TGAGAGCTATAGGACGCTCAAATCACCAGAGGCATAGTGCCTTGCCATGCCTTG
* *
10837 ATGATGGTGAATAATATATCATAACGAGGAAGACTGGGTGAGAGCTATAGGGCGCTCAAATCACC
1 ATGATGGTGAATAATATATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
10902 GGCGGCATAATGCCTTACCATGCCTTAATGATAGTAGATAATACATCATAACTA-GGAAGACTAG
66 GGCGGCATAATGCCTTACCATGCCTTAATGATAGTAGATAATACATCATAAC-AGGGAAGACTAG
*
10966 GTGAGAGCTATAGGACGCTCAAATCACCAGCGGCATAGTGCCTTGCCATGCCTTG
130 GTGAGAGCTATAGGACGCTCAAATCACCAGAGGCATAGTGCCTTGCCATGCCTTG
11021 ATGATGGTGAATAATATATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
1 ATGATGGTGAATAATATATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
11086 GGCGGCATAATGCCTT
66 GGCGGCATAATGCCTT
11102 GCGATGCTTT
Statistics
Matches: 249, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
184 248 1.00
185 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (184 bp):
ATGATGGTGAATAATATATCATAACAAGGAAGACTAGGTGAGAGCTATAGGGCGCTCAAATCACC
GGCGGCATAATGCCTTACCATGCCTTAATGATAGTAGATAATACATCATAACAGGGAAGACTAGG
TGAGAGCTATAGGACGCTCAAATCACCAGAGGCATAGTGCCTTGCCATGCCTTG
Found at i:15355 original size:30 final size:31
Alignment explanation
Indices: 15301--15365 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
15291 AACTTTATGT
*
15301 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
*
15332 TTTCCAATTGTACCCTT-TTTTTAAATCATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
15362 TTTC
1 TTTC
15366 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.26, C:0.20, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:15372 original size:31 final size:31
Alignment explanation
Indices: 15307--15372 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
15297 ATGTTTTCCG
*
15307 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCAA
*
15338 ATTGTACCCTT-TTTTTAAATCATATTTCTAA
1 ATTGTACCCTTATTTTTAAAACATATTTC-AA
15369 ATTG
1 ATTG
15373 CCATTACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCAA
Found at i:15424 original size:18 final size:19
Alignment explanation
Indices: 15375--15427 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
15365 CTAAATTGCC
*
15375 ATTACTAAATAATGTTTTTA
1 ATTACTAAATTAT-TTTTTA
* **
15395 ATTATTCCATTATTTTTTA
1 ATTACTAAATTATTTTTTA
15414 ATTA-TAAATTATTT
1 ATTACTAAATTATTT
15428 CATTATATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 9 0.33
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTACTAAATTATTTTTTA
Found at i:15489 original size:22 final size:22
Alignment explanation
Indices: 15455--15561 Score: 74
Period size: 22 Copynumber: 4.9 Consensus size: 22
15445 ATTTTACTAT
* *
15455 GGTTATTATAATTCCATGAG-GA
1 GGTTATCAAAATTCCAT-AGTGA
* *
15477 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTCCATAGTGA
* *
15499 GGTTACCAAAATTTCATAGTGTA
1 GGTTATCAAAATTCCATAGTG-A
* * * *
15522 -GTTACCAAAATTTCATAGAGT
1 GGTTATCAAAATTCCATAGTGA
* *
15543 GGTTACCAAAATTTCATAG
1 GGTTATCAAAATTCCATAG
15562 GATCAAGTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
21 2 0.03
22 72 0.97
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTCCATAGTGA
Found at i:15531 original size:44 final size:44
Alignment explanation
Indices: 15478--15561 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
15468 CCATGAGGAG
* *
15478 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGTGTA
1 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGTGTA
15522 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAG
1 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAG
15562 GATCAAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (44 bp):
GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGTGTA
Found at i:15592 original size:46 final size:44
Alignment explanation
Indices: 15478--15593 Score: 139
Period size: 44 Copynumber: 2.6 Consensus size: 44
15468 CCATGAGGAG
15478 GTTATCAAAATTTCATA-GTGTGGTTACCAAAATTTCATAGTGTA
1 GTTATCAAAATTTCATAGGT-TGGTTACCAAAATTTCATAGTGTA
*
15522 GTTACCAAAATTTCATAGAG-TGGTTACCAAAATTTCATAG-GATCAA
1 GTTATCAAAATTTCATAG-GTTGGTTACCAAAATTTCATAGTG-T--A
* *
15568 GTTATTAAAATTTCTTAGGTTGGTTA
1 GTTATCAAAATTTCATAGGTTGGTTA
15594 TTGCAATTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
43 1 0.02
44 37 0.60
45 1 0.02
46 23 0.37
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGGTTGGTTACCAAAATTTCATAGTGTA
Found at i:15784 original size:22 final size:22
Alignment explanation
Indices: 15679--16041 Score: 125
Period size: 22 Copynumber: 16.3 Consensus size: 22
15669 AGGTTATACG
* *
15679 AATTTCATA-GTATGGTTAACAA
1 AATTTCATATG-AAGGTTATCAA
15701 AATTTCAT-TAGAAGGTTA-CTAA
1 AATTTCATAT-GAAGGTTATC-AA
* * *
15723 TACTTCAT-TGGGAGGTTATCAA
1 AATTTCATAT-GAAGGTTATCAA
* *
15745 AATTTTATAGTGTA-GTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
15767 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
* * *
15788 AAGTCTCAATTTCAT-AAGGAGTACCAA
1 AA-TTTC-A--T-ATGAAGG-TTATCAA
*
15815 AATTTGATA-GAAGGTTATC-A
1 AATTTCATATGAAGGTTATCAA
* *
15835 AATCTCATA-G-AGTGATTATCGA
1 AATTTCATATGAAG-G-TTATCAA
* *
15857 AATTTCATAAAGATATGATTATCAA
1 AATTTCAT-ATGA-A-GGTTATCAA
*
15882 AATTT-ATATGAAGATTATCAA
1 AATTTCATATGAAGGTTATCAA
**
15903 AATTTCATAGTG-TTGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
* *
15925 AATTTCA-AAGCGAGGTTATCAA
1 AATTTCATATG-AAGGTTATCAA
* * *
15947 AATTACATAATG-TGATTATCAA
1 AATTTCAT-ATGAAGGTTATCAA
* * *
15969 AATTTCATA-GAGGGGTCAACAA
1 AATTTCATATGA-AGGTTATCAA
*
15991 AATTT--TATAAAGATGTTATCAA
1 AATTTCATATGAAG--GTTATCAA
*
16013 AATTTCATA-AAGAGGTTATCAA
1 AATTTCATATGA-AGGTTATCAA
*
16035 ATTTTCA
1 AATTTCA
16042 AAATCTGATT
Statistics
Matches: 260, Mismatches: 44, Indels: 74
0.69 0.12 0.20
Matches are distributed among these distances:
19 2 0.01
20 15 0.06
21 33 0.13
22 157 0.60
23 14 0.05
24 10 0.04
25 17 0.07
26 7 0.03
27 5 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:15892 original size:18 final size:19
Alignment explanation
Indices: 15869--15907 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
15859 TTTCATAAAG
15869 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
15887 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
15908 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:15966 original size:44 final size:44
Alignment explanation
Indices: 15828--16041 Score: 168
Period size: 44 Copynumber: 4.8 Consensus size: 44
15818 TTGATAGAAG
* * * * * *
15828 GTTATC-AAATCTCATAGAGTGATTATCGAAATTTCATAAAGATAT
1 GTTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG--AT
* * * *
15873 GATTATCAAAATTT-ATATGA-AGATTATCAAAATTTCATAGTGTT
1 G-TTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGAT
* *
15917 GTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATG-T
1 GTTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAT
* * * * * *
15960 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAT
1 G-TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAT
*
16005 GTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCA
1 GTTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCA
16042 AAATCTGATT
Statistics
Matches: 134, Mismatches: 27, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
43 16 0.12
44 83 0.62
45 4 0.03
46 24 0.18
47 7 0.05
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
GTTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAT
Found at i:15992 original size:66 final size:66
Alignment explanation
Indices: 15893--16041 Score: 165
Period size: 66 Copynumber: 2.3 Consensus size: 66
15883 ATTTATATGA
* ** * * *
15893 AGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAA
*
15957 TG
65 AG
* * * *
15959 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
16024 G
66 G
* *
16025 AGGTTATCAAATTTTCA
1 AGATTATCAAAATTTCA
16042 AAATCTGATT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 66 0.97
67 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
G
Found at i:15994 original size:88 final size:88
Alignment explanation
Indices: 15900--16066 Score: 221
Period size: 88 Copynumber: 1.9 Consensus size: 88
15890 TGAAGATTAT
** * * * *
15900 CAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATCTGATT
15964 ATC-AAAATTTCATAGAGGGGTCAA
65 A-CAAAAATTTCATAGAGGGGTCAA
* * *
15988 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATCTGATTA
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATCTGATTA
16053 CAAAAATTTCATAG
66 CAAAAATTTCATAG
16067 TGGTATTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 1 0.01
88 65 0.96
89 2 0.03
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (88 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATCTGATTA
CAAAAATTTCATAGAGGGGTCAA
Found at i:16174 original size:20 final size:20
Alignment explanation
Indices: 16149--16216 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
16139 ATGGAGTAAT
*
16149 CAAAATTTTAAGGAGGATAC
1 CAAAATTTCAAGGAGGATAC
* *
16169 CAAAA-TTCAGGGAGGATAT
1 CAAAATTTCAAGGAGGATAC
*
16188 CAAAA-TTC-AGTGAGGATAT
1 CAAAATTTCAAG-GAGGATAC
16207 CAAAATTTCA
1 CAAAATTTCA
16217 TATGAAGGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 1 0.02
19 32 0.78
20 8 0.20
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (20 bp):
CAAAATTTCAAGGAGGATAC
Found at i:16182 original size:19 final size:19
Alignment explanation
Indices: 16160--16213 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
16150 AAAATTTTAA
*
16160 GGAGGATACCAAAATTCAG
1 GGAGGATATCAAAATTCAG
16179 GGAGGATATCAAAATTCAG
1 GGAGGATATCAAAATTCAG
*
16198 TGAGGATATCAAAATT
1 GGAGGATATCAAAATT
16214 TCATATGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (19 bp):
GGAGGATATCAAAATTCAG
Found at i:16232 original size:22 final size:22
Alignment explanation
Indices: 16204--16368 Score: 120
Period size: 22 Copynumber: 7.5 Consensus size: 22
16194 TCAGTGAGGA
16204 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
16226 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
16248 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
16270 TATCAAAATTTCATA-GCATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
16291 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
16314 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
16336 TATCAAAAAATCATAAGGAGCT
1 TATCAAAATTTCATATGAAGGT
16358 TATCAAAATTT
1 TATCAAAATTT
16369 GTAGTTATCA
Statistics
Matches: 109, Mismatches: 28, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
21 5 0.05
22 97 0.89
23 7 0.06
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:16297 original size:66 final size:66
Alignment explanation
Indices: 16198--16343 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 66
16188 CAAAATTCAG
* * * ** **
16198 TGAGGATATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAG-TTTTCAAAATTTCAT
1 TGAGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCATAG-GGAGATTAACAAAATTTCAT
16262 AA
65 AA
* *
16264 -GAGGGTTATCAAAATTTCATA-GCATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCA
1 TGA-GGTTATCAAAATTTCATATGAAGGT-GATCAAAATTTCATAGGGAGATTAACAAAATTTCA
16327 TAA
64 TAA
16330 TGAGGTTATCAAAA
1 TGAGGTTATCAAAA
16344 AATCATAAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
65 8 0.12
66 57 0.85
67 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (66 bp):
TGAGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
A
Found at i:16298 original size:44 final size:43
Alignment explanation
Indices: 16204--16368 Score: 133
Period size: 44 Copynumber: 3.8 Consensus size: 43
16194 TCAGTGAGGA
* * * *
16204 TATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAG
1 TATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTGTAG
*
16247 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGCATGTAG
1 -TATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAG--TGTAG
* *
16293 -ATCAAAATTTCAT-AG-GGAGATTAACAAAATTTCATAATG-AGG
1 TATCAAAATTTCATAAGAGG-G-TTATCAAAATTTCATAGTGTA-G
** *
16335 TTATCAAAAAATCATAAG-GAGCTTATCAAAATTT
1 -TATCAAAATTTCATAAGAG-GGTTATCAAAATTT
16369 GTAGTTATCA
Statistics
Matches: 100, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
41 1 0.01
42 5 0.05
43 3 0.03
44 83 0.83
45 3 0.03
46 5 0.05
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTGTAG
Found at i:16488 original size:22 final size:22
Alignment explanation
Indices: 16441--16633 Score: 87
Period size: 22 Copynumber: 8.7 Consensus size: 22
16431 ATAGAAAAAT
* * *
16441 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGTGA
*
16463 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
* *
16485 TTATCAAAATTTTAAAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
16507 TTA-CTAACAA-TTCATA-TG-GA
1 TTATC-AA-AATTTCATAGTGTGA
* * * * ** *
16527 GGTTTTTAAATTTTTATAAAGTGG
1 --TTATCAAAATTTCATAGTGTGA
* *
16551 TTATCAATATATCATA-TG-GA
1 TTATCAAAATTTCATAGTGTGA
* *
16571 GGTTATCAACATCTCATAGTGTTGA
1 --TTATCAAAATTTCATAGTG-TGA
*
16596 TTATCAAAATTTCAT--TGGGAA
1 TTATCAAAATTTCATAGTGTG-A
16617 GTTATCAAAATTTCATA
1 -TTATCAAAATTTCATA
16634 TTGAGGTCTT
Statistics
Matches: 127, Mismatches: 28, Indels: 31
0.68 0.15 0.17
Matches are distributed among these distances:
20 4 0.03
21 8 0.06
22 94 0.74
23 18 0.14
24 1 0.01
25 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:16610 original size:23 final size:22
Alignment explanation
Indices: 16550--16677 Score: 71
Period size: 22 Copynumber: 5.8 Consensus size: 22
16540 TTATAAAGTG
* * * *
16550 GTTATCAATATATCATATGGAG
1 GTTATCAAAATTTCATAGGGAA
* * * **
16572 GTTATCAACATCTCATAGTGTT
1 GTTATCAAAATTTCATAGGGAA
*
16594 GATTATCAAAATTTCATTGGGAA
1 G-TTATCAAAATTTCATAGGGAA
** *
16617 GTTATCAAAATTTCATATTGAG
1 GTTATCAAAATTTCATAGGGAA
* *
16639 GTCT-TCAAAA-TTCTTTAGGGAG
1 GT-TATCAAAATTTC-ATAGGGAA
*
16661 GTTAACAAAATTTCATA
1 GTTATCAAAATTTCATA
16678 AGAAAGTTTA
Statistics
Matches: 80, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
21 4 0.05
22 56 0.70
23 20 0.25
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAA
Found at i:16742 original size:22 final size:21
Alignment explanation
Indices: 16711--16763 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
16701 AGGATTCTTG
* *
16711 AAATTCCATAGTACCATTATCA
1 AAATTTCATAGGA-CATTATCA
**
16733 AAATTTCATAGGAGGTTATCA
1 AAATTTCATAGGACATTATCA
16754 AAATTTCATA
1 AAATTTCATA
16764 ATGGGATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (21 bp):
AAATTTCATAGGACATTATCA
Found at i:16891 original size:2 final size:2
Alignment explanation
Indices: 16884--16914 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16874 CTAAAACTAG
16884 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
16915 TGTTCTAAGA
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:17789 original size:2 final size:2
Alignment explanation
Indices: 17782--17808 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17772 ACAAATTGGA
17782 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 A
17809 GTAGGTAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19031 original size:33 final size:33
Alignment explanation
Indices: 18989--19091 Score: 116
Period size: 33 Copynumber: 3.1 Consensus size: 33
18979 ATCTAGGCAC
*
18989 GGAGACGTCCCCGGAGGGCACCCCAACACGGTG
1 GGAGGCGTCCCCGGAGGGCACCCCAACACGGTG
*** *
19022 GGAGGCGTCCCCGGAGGGCGTTCCACCACGGTG
1 GGAGGCGTCCCCGGAGGGCACCCCAACACGGTG
* * * * *
19055 GGAGGCATTCCCGGAGGGCCCCCCATCATGGTG
1 GGAGGCGTCCCCGGAGGGCACCCCAACACGGTG
19088 GGAG
1 GGAG
19092 ACGCCTCTGT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.17, C:0.33, G:0.40, T:0.11
Consensus pattern (33 bp):
GGAGGCGTCCCCGGAGGGCACCCCAACACGGTG
Found at i:19580 original size:13 final size:13
Alignment explanation
Indices: 19562--19588 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19552 ATATTTGGCC
19562 TAGTGGCAAGAGG
1 TAGTGGCAAGAGG
19575 TAGTGGCAAGAGG
1 TAGTGGCAAGAGG
19588 T
1 T
19589 TTGGAAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.44, T:0.19
Consensus pattern (13 bp):
TAGTGGCAAGAGG
Done.