Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020729.1 Corchorus olitorius cultivar O-4 contig20762, 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: 154898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7048 original size:12 final size:14
Alignment explanation
Indices: 7010--7049 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
7000 TAGTTATGTC
*
7010 ACTTTAGTTTTGAG
1 ACTTTACTTTTGAG
7024 ACTTTACTTTTGAG
1 ACTTTACTTTTGAG
7038 A-TTTA-TTTTGAG
1 ACTTTACTTTTGAG
7050 TATGGTATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 7 0.28
13 4 0.16
14 14 0.56
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (14 bp):
ACTTTACTTTTGAG
Found at i:7807 original size:14 final size:13
Alignment explanation
Indices: 7790--7828 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
7780 TAGTTATGTC
7790 ACTTTAGTTTTGAG
1 ACTTTA-TTTTGAG
7804 ACTTTACTTTTGAG
1 ACTTTA-TTTTGAG
7818 A-TTTATTTTGA
1 ACTTTATTTTGA
7829 ATATGGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 6 0.25
13 4 0.17
14 14 0.58
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
ACTTTATTTTGAG
Found at i:7929 original size:780 final size:764
Alignment explanation
Indices: 6374--8181 Score: 3168
Period size: 780 Copynumber: 2.3 Consensus size: 764
6364 GGTTTGCGAG
* *
6374 ATTTGTGATGGATATCATCGACCATACTCAAAGGAATAAGGCTGCTGAAAATTCCTTGGCGCGGA
1 ATTTGTGATGGATATCTTCGACCATACTCAAAGGAATAAGGCTGCTGAAAATTCCTTGGCGCAGA
*
6439 AACAAGTTTTCCTCAATTTCTCATGGGTTCCTACATATAGTAGGAAGCTATTCAAACATGTTGAA
66 AACAAGTTTTCCTCAATTTCTCATGGGTTCCTACATTTAGTAGGAAGCTATTCAAACATGTTGAA
* * *
6504 TATGGAAAACATTTCAAGCATTGCTTTCTCTGAAACCCAAGCAAAAAAGCAAAGTACAAAAGAAG
131 TATGGCAAACATTTCAAGCATTGCTTTCTATGGAACCCAAGCAAAAAAGCAAAGTACAAAAGAAG
* *
6569 TTGCAAAGAAGCAAAACAGATATATAAGGATGATTTCAAGTGTTTCTTGAAATTCCCGCGTAACT
196 TTGGAAAGAAGCAAAACAGATATATAAGGATGATTTCAAGTGTTTCTTGAAATTCCTGCGTAACT
* *
6634 TTTTGTTCACCTCCATGAATCTGCTAGCTTAGATGAGATTGAGCACGTCACCGACTTTTTGTCAG
261 TTTTGTTCACCTCCATGAATCTGCTAGCTTAGATGAGATTGAGCAAGTCAACGACTTTTTGTCAG
* *
6699 GTTTTATGATATGTCTAATCTAAAATTTCAATTATTTAACTTGTTTCTTTGATGCTGAGTTTGAA
326 GTTTTATGA-ATGACTAATCTAAAATTTCAATTATTGAACTTGTTTCTTTGATGCTGAGTTTGAA
*
6764 GTAATTTTTTGCAAGTTATATGATGACTAATCCAAGATTCGTGGATTCAACATAGATCTTGTATC
390 GTAATTTTTTGCAAGTTATATGATGACTAATCCAAGATTCGTGGATTCAACATAAATCTTGTATC
* * *
6829 TGGCATACTTTTTGATGATGAGTTTAAGGGTGTGTTTGGAGAGCTGTTCAATTGTACTGATGGCT
455 TGGCAAACTTTTTGATGATAAGTTTAAAGGTGTGTTTGGAGAGCTGTTCAATTGTACTGATGGCT
6894 GACCTTGTTCTTCTGTTACGTCCCGTCCTCTTATTATGTCCCATCCTCTTCTTGTATGTAGGAGT
520 GACCTTGTTCTTCTGTTACGTCCCGTCCTCTTATTATGTCCCATCCTCTTCTTGTATGTAGGAGT
6959 ACAAATATGAGCTTTTAAAGACTCATTTTTCTTGTAGGCATTAGTTATGTCACTTTAGTTTTGAG
585 ACAAATATGAGCTTTTAAAGACTCATTTTTCTTGTAGGCATTAGTTATGTCACTTTAGTTTTGAG
*
7024 ACTTTACTTTTGAGATTTATTTTGAGTATGGTATCTTAATACTTTAAATTTATATAGTATTGTAT
650 ACTTTACTTTTGAGATTTATTTTGAATATGGTATCTTAATACTTTAAATTTATATAGTATTGTAT
7089 TGAAGTTTTGAATTATCTTGAATTGCTTAAATTAAACATATCTTTCCTCA
715 TGAAGTTTTGAATTATCTTGAATTGCTTAAATTAAACATATCTTTCCTCA
7139 ATTTGTGATGGATATCTTCGACCATACTCAAAGGAATAAGGCTGCTGAAAATTCCTTGGCGCAGA
1 ATTTGTGATGGATATCTTCGACCATACTCAAAGGAATAAGGCTGCTGAAAATTCCTTGGCGCAGA
7204 AACAAGTTTTCCTCAATTTCTCATGGGTTCCTACATTTAGTAGGAAGCTAAGCAATTCAAACATG
66 AACAAGTTTTCCTCAATTTCTCATGGGTTCCTACATTTAGTAGGAAGCT-----ATTCAAACATG
*
7269 TTGAATATGGCAAACATTTCAAGCATTGCTTTCTTTGGAACCCAAGCAAAAAAGCAAAGTACAAA
126 TTGAATATGGCAAACATTTCAAGCATTGCTTTCTATGGAACCCAAGCAAAAAAGCAAAGTACAAA
7334 AGAAGTTGGAAAGAAGCAAAACAGATATATAAGGATGATTTCAAGTGTTTCTTGAAATTCCTGCG
191 AGAAGTTGGAAAGAAGCAAAACAGATATATAAGGATGATTTCAAGTGTTTCTTGAAATTCCTGCG
*
7399 TAACTTTATTGTTCACCTCCATGAATCTGCTAGCTTAGATGAGATTGAGCAAGTCAACGATTTTT
256 TAACTTT-TTGTTCACCTCCATGAATCTGCTAGCTTAGATGAGATTGAGCAAGTCAACGACTTTT
7464 TGTCAGGTTTTATG-ATGACTAATCTAAAATTTCAATTATTGAACTTGTTTCTTTGATGCTGAGT
320 TGTCAGGTTTTATGAATGACTAATCTAAAATTTCAATTATTGAACTTGTTTCTTTGATGCTGAGT
7528 TTGAAGTAATTTTTTGCAAGTTATATGATGACTAATCCAAGATTTCGTGGATTCAACATAAATCT
385 TTGAAGTAATTTTTTGCAAGTTATATGATGACTAATCCAAGA-TTCGTGGATTCAACATAAATCT
*
7593 TGTATCTGGCAAACTTTTTGATGATAAGTTTAAAGGTGTGTTTGGAGAGTTGTTCAATTGTACTG
449 TGTATCTGGCAAACTTTTTGATGATAAGTTTAAAGGTGTGTTTGGAGAGCTGTTCAATTGTACTG
* * * * *
7658 ATGGCTGACCTTGGCTGACCTTGTTCTTGTCTTATGTTCTGTCCTCTTGTTATGTCCCATCCTCT
514 ATGGCTGACC-T---TG---TTCTTC-TG--TTACGTCCCGTCCTCTTATTATGTCCCATCCTCT
* *
7723 TCTTGTATGTAGGGGTACAAATATGAGCTTTTAAAGACTCCTTTTTCTTGTAGGCATTAGTTATG
569 TCTTGTATGTAGGAGTACAAATATGAGCTTTTAAAGACTCATTTTTCTTGTAGGCATTAGTTATG
7788 TCACTTTAGTTTTGAGACTTTACTTTTGAGATTTATTTTGAATATGGTATCTTAATACTTTAAAT
634 TCACTTTAGTTTTGAGACTTTACTTTTGAGATTTATTTTGAATATGGTATCTTAATACTTTAAAT
* *
7853 TTATATGGTATTGTATTGAAGTTTTGAATTATCTTGAATTGCTTAAATTAAGCATATCTTTCCTC
699 TTATATAGTATTGTATTGAAGTTTTGAATTATCTTGAATTGCTTAAATTAAACATATCTTTCCTC
7918 A
764 A
7919 ATTTGTGATGGATATCTTCGACCATACTCAAAGGAATAAGGCTGCTGAAAATTCCTTGGCGCAGA
1 ATTTGTGATGGATATCTTCGACCATACTCAAAGGAATAAGGCTGCTGAAAATTCCTTGGCGCAGA
* *
7984 AACAAGCTTTCCTCAATTTCTCATGGGTTCCTACATTTAGTAGGAAGCTATTCAAACATGCTGAA
66 AACAAGTTTTCCTCAATTTCTCATGGGTTCCTACATTTAGTAGGAAGCTATTCAAACATGTTGAA
8049 TATGGCAAACATTTCAAGCATTGCTTTCTATGGAACCCAAGCAAAAAAGCAAAGTACAAAAGAAG
131 TATGGCAAACATTTCAAGCATTGCTTTCTATGGAACCCAAGCAAAAAAGCAAAGTACAAAAGAAG
8114 TTGGAAAGAAGCAAAACAGATATATAAGGATGATTTCAAGTGTTTCTTGAAATTCCTGCGTAACT
196 TTGGAAAGAAGCAAAACAGATATATAAGGATGATTTCAAGTGTTTCTTGAAATTCCTGCGTAACT
8179 TTT
261 TTT
8182 ACTCTCACAT
Statistics
Matches: 995, Mismatches: 31, Indels: 25
0.95 0.03 0.02
Matches are distributed among these distances:
765 111 0.11
769 90 0.09
770 235 0.24
771 69 0.07
774 3 0.00
775 146 0.15
777 5 0.01
778 2 0.00
780 334 0.34
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (764 bp):
ATTTGTGATGGATATCTTCGACCATACTCAAAGGAATAAGGCTGCTGAAAATTCCTTGGCGCAGA
AACAAGTTTTCCTCAATTTCTCATGGGTTCCTACATTTAGTAGGAAGCTATTCAAACATGTTGAA
TATGGCAAACATTTCAAGCATTGCTTTCTATGGAACCCAAGCAAAAAAGCAAAGTACAAAAGAAG
TTGGAAAGAAGCAAAACAGATATATAAGGATGATTTCAAGTGTTTCTTGAAATTCCTGCGTAACT
TTTTGTTCACCTCCATGAATCTGCTAGCTTAGATGAGATTGAGCAAGTCAACGACTTTTTGTCAG
GTTTTATGAATGACTAATCTAAAATTTCAATTATTGAACTTGTTTCTTTGATGCTGAGTTTGAAG
TAATTTTTTGCAAGTTATATGATGACTAATCCAAGATTCGTGGATTCAACATAAATCTTGTATCT
GGCAAACTTTTTGATGATAAGTTTAAAGGTGTGTTTGGAGAGCTGTTCAATTGTACTGATGGCTG
ACCTTGTTCTTCTGTTACGTCCCGTCCTCTTATTATGTCCCATCCTCTTCTTGTATGTAGGAGTA
CAAATATGAGCTTTTAAAGACTCATTTTTCTTGTAGGCATTAGTTATGTCACTTTAGTTTTGAGA
CTTTACTTTTGAGATTTATTTTGAATATGGTATCTTAATACTTTAAATTTATATAGTATTGTATT
GAAGTTTTGAATTATCTTGAATTGCTTAAATTAAACATATCTTTCCTCA
Found at i:9128 original size:14 final size:13
Alignment explanation
Indices: 9111--9149 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
9101 TAGTTATGTC
9111 ACTTTAGTTTTGAG
1 ACTTTA-TTTTGAG
9125 ACTTTACTTTTGAG
1 ACTTTA-TTTTGAG
9139 A-TTTATTTTGA
1 ACTTTATTTTGA
9150 ATATGGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 6 0.25
13 4 0.17
14 14 0.58
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
ACTTTATTTTGAG
Found at i:10800 original size:17 final size:16
Alignment explanation
Indices: 10778--10811 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10768 CTTAATTTCT
10778 TATTTCATCTTTTTAAA
1 TATTTC-TCTTTTTAAA
*
10795 TATTTCTTTTTTTAAA
1 TATTTCTCTTTTTAAA
10811 T
1 T
10812 GTTCAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTCTCTTTTTAAA
Found at i:11024 original size:31 final size:29
Alignment explanation
Indices: 10957--11039 Score: 107
Period size: 28 Copynumber: 2.8 Consensus size: 29
10947 CAATCTTACA
*
10957 AGTAGAGAGACTAAATTGA-TCGGTTTTT
1 AGTAGAGGGACTAAATTGATTCGGTTTTT
*
10985 AGTAGAGGGACTAAATTGATTC-TTTTGTGT
1 AGTAGAGGGACTAAATTGATTCGGTTT-T-T
11015 ATGTAGAGGGACTAAATTGATTCGG
1 A-GTAGAGGGACTAAATTGATTCGG
11040 GTTATATGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 21 0.45
29 3 0.06
30 2 0.04
31 21 0.45
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (29 bp):
AGTAGAGGGACTAAATTGATTCGGTTTTT
Found at i:14428 original size:21 final size:21
Alignment explanation
Indices: 14402--14443 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
14392 TACCGGAGGA
14402 GATTATAAATGGAAGAAAGGC
1 GATTATAAATGGAAGAAAGGC
*
14423 GATTATATATGGAAGAAAGGC
1 GATTATAAATGGAAGAAAGGC
14444 CCTAATCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21
Consensus pattern (21 bp):
GATTATAAATGGAAGAAAGGC
Found at i:15714 original size:24 final size:24
Alignment explanation
Indices: 15682--15729 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
15672 CTTCAGCTGA
15682 TCTTTTTGCTATTGCTGATCCAAT
1 TCTTTTTGCTATTGCTGATCCAAT
15706 TCTTTTTGCTATTGCTGATCCAAT
1 TCTTTTTGCTATTGCTGATCCAAT
15730 CCTGCCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.12, T:0.50
Consensus pattern (24 bp):
TCTTTTTGCTATTGCTGATCCAAT
Found at i:17261 original size:21 final size:21
Alignment explanation
Indices: 17235--17277 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
17225 CATCAGCACC
* *
17235 AACCGACGACACCGAGACCGA
1 AACCGACGAAACCGAAACCGA
17256 AACCGACGAAACCGAAACCGA
1 AACCGACGAAACCGAAACCGA
17277 A
1 A
17278 TGGATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.35, G:0.21, T:0.00
Consensus pattern (21 bp):
AACCGACGAAACCGAAACCGA
Found at i:17355 original size:21 final size:20
Alignment explanation
Indices: 17291--17356 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
17281 ATTTATATAT
*
17291 TATAATTATAT-TATATATA
1 TATAATTATATATATAAATA
* *
17310 TAATTAATTATA-AAACAAATA
1 T-A-TAATTATATATATAAATA
17331 TATAATTATATATATAAATA
1 TATAATTATATATATAAATA
17351 CTATAA
1 -TATAA
17357 AAAAAACATT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 9 0.24
20 9 0.24
21 19 0.51
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAATTATATATATAAATA
Found at i:17438 original size:21 final size:20
Alignment explanation
Indices: 17413--17461 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
17403 AGGACCGACC
17413 CACCGATCGAGAAACCGTTTA
1 CACCGATCGA-AAACCGTTTA
* * *
17434 TACCGACCCTAAAACCGTTTA
1 CACCGA-TCGAAAACCGTTTA
17455 CACCGAT
1 CACCGAT
17462 GCACCGTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20
Consensus pattern (20 bp):
CACCGATCGAAAACCGTTTA
Found at i:26054 original size:21 final size:19
Alignment explanation
Indices: 26028--26084 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 19
26018 CACTGCTCTA
26028 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
*
26047 ACATAATCTAATCTGTACAGT
1 --ATAATCTCATCTGTACAGT
*
26068 GTAATCTCATCTGTACA
1 ATAATCTCATCTGTACA
26085 ATTACTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:49352 original size:22 final size:22
Alignment explanation
Indices: 49327--49369 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
49317 CCATTAAGGC
*
49327 TTGGGTGAGCCCAAGCGAGAAA
1 TTGGGTGAGCCCAAGCAAGAAA
49349 TTGGGTGAGCCCAAGCAAGAA
1 TTGGGTGAGCCCAAGCAAGAA
49370 GTTGTCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.14
Consensus pattern (22 bp):
TTGGGTGAGCCCAAGCAAGAAA
Found at i:50458 original size:33 final size:33
Alignment explanation
Indices: 50385--50458 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
50375 ACTGATACCA
* ** *
50385 CCCTAGGAGTGCGGCACTGACCATGACGTGCCG
1 CCCTAGGAGGGCGGCACCAACCATGACATGCCG
* * *
50418 CCGTAGGAGGGCGGCACCAACCATGTCATGTCG
1 CCCTAGGAGGGCGGCACCAACCATGACATGCCG
50451 CCCTAGGA
1 CCCTAGGA
50459 CATGACATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.15
Consensus pattern (33 bp):
CCCTAGGAGGGCGGCACCAACCATGACATGCCG
Found at i:50599 original size:19 final size:19
Alignment explanation
Indices: 50553--50589 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50543 AATTATTATT
*
50553 AATTATAATTAATAATAAC
1 AATTAAAATTAATAATAAC
*
50572 AATTTAAATTAATAATAA
1 AATTAAAATTAATAATAA
50590 TTAATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAATTAATAATAAC
Found at i:66791 original size:6 final size:6
Alignment explanation
Indices: 66782--66808 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
66772 ACATCTATTC
66782 CAGCTT CAGCTT CAGCTT CAGCTT CAG
1 CAGCTT CAGCTT CAGCTT CAGCTT CAG
66809 GATTGTGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.30
Consensus pattern (6 bp):
CAGCTT
Found at i:74217 original size:48 final size:48
Alignment explanation
Indices: 74161--74258 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
74151 ATGCACATGG
74161 ACTATGAGTTTTGCTTAAATCTTATGATTATATCAAAATAATGAACAA
1 ACTATGAGTTTTGCTTAAATCTTATGATTATATCAAAATAATGAACAA
*
74209 ACTATGAGTTTTGCTTAAATCTTATGATTTTATCAAAATAATGAACAA
1 ACTATGAGTTTTGCTTAAATCTTATGATTATATCAAAATAATGAACAA
74257 AC
1 AC
74259 AAACGATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (48 bp):
ACTATGAGTTTTGCTTAAATCTTATGATTATATCAAAATAATGAACAA
Found at i:75292 original size:1 final size:1
Alignment explanation
Indices: 75286--75320 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
75276 AGCTTTCAAG
*
75286 TTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
75321 AAAAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:81664 original size:31 final size:30
Alignment explanation
Indices: 81629--81690 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
81619 AACAGCCCAT
81629 AAAGCCCAATACTAA-CTAAAATAAGAAAATA
1 AAAGCCCAATACTAACCT-AAATAA-AAAATA
*
81660 AAAGCCTAATACTAACCTAAATAAAAAATA
1 AAAGCCCAATACTAACCTAAATAAAAAATA
81690 A
1 A
81691 TGACAGAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 20 0.69
32 2 0.07
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (30 bp):
AAAGCCCAATACTAACCTAAATAAAAAATA
Found at i:83216 original size:31 final size:30
Alignment explanation
Indices: 83181--83242 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
83171 AACAGCCCAT
83181 AAAGCCCAATACTAA-CTAAAATAAGAAAATA
1 AAAGCCCAATACTAACCT-AAATAA-AAAATA
*
83212 AAAGCCTAATACTAACCTAAATAAAAAATA
1 AAAGCCCAATACTAACCTAAATAAAAAATA
83242 A
1 A
83243 TGACATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 20 0.69
32 2 0.07
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (30 bp):
AAAGCCCAATACTAACCTAAATAAAAAATA
Found at i:84827 original size:45 final size:45
Alignment explanation
Indices: 84763--84852 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
84753 TCAGGTTCGA
*
84763 GACCTTGCGTACGCAGCTGCTCATATTGGGAGACTCACCCACCAT
1 GACCTTGCGTACGCAGCTGCCCATATTGGGAGACTCACCCACCAT
84808 GACCTTGCGTACGCAGCTGCCCATATTGGGAGACTCACCCACCAT
1 GACCTTGCGTACGCAGCTGCCCATATTGGGAGACTCACCCACCAT
84853 AACCAGGTGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (45 bp):
GACCTTGCGTACGCAGCTGCCCATATTGGGAGACTCACCCACCAT
Found at i:84907 original size:67 final size:67
Alignment explanation
Indices: 84799--84930 Score: 264
Period size: 67 Copynumber: 2.0 Consensus size: 67
84789 TGGGAGACTC
84799 ACCCACCATGACCTTGCGTACGCAGCTGCCCATATTGGGAGACTCACCCACCATAACCAGGTGCG
1 ACCCACCATGACCTTGCGTACGCAGCTGCCCATATTGGGAGACTCACCCACCATAACCAGGTGCG
84864 TG
66 TG
84866 ACCCACCATGACCTTGCGTACGCAGCTGCCCATATTGGGAGACTCACCCACCATAACCAGGTGCG
1 ACCCACCATGACCTTGCGTACGCAGCTGCCCATATTGGGAGACTCACCCACCATAACCAGGTGCG
84931 CGACGCGGGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.17
Consensus pattern (67 bp):
ACCCACCATGACCTTGCGTACGCAGCTGCCCATATTGGGAGACTCACCCACCATAACCAGGTGCG
TG
Found at i:85040 original size:14 final size:14
Alignment explanation
Indices: 84999--85042 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
84989 AAAAAAATCT
84999 AATTGGTTTTAAAAA
1 AATTGGTTTT-AAAA
* *
85014 AATT-CTTTCAAAA
1 AATTGGTTTTAAAA
85027 AATTGGTTTTAAAA
1 AATTGGTTTTAAAA
85041 AA
1 AA
85043 AAAAAGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 8 0.33
14 12 0.50
15 4 0.17
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.39
Consensus pattern (14 bp):
AATTGGTTTTAAAA
Found at i:85041 original size:15 final size:15
Alignment explanation
Indices: 84999--85043 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
84989 AAAAAAATCT
84999 AATTGGTTTTAAAAA
1 AATTGGTTTTAAAAA
* *
85014 AATT--CTTTCAAAA
1 AATTGGTTTTAAAAA
85027 AATTGGTTTTAAAAA
1 AATTGGTTTTAAAAA
85042 AA
1 AA
85044 AAAAGTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (15 bp):
AATTGGTTTTAAAAA
Found at i:100603 original size:2 final size:2
Alignment explanation
Indices: 100587--100621 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
100577 AATCATTTTC
100587 AT AT A- AT AGT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
100622 ATAGTATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:101976 original size:31 final size:31
Alignment explanation
Indices: 101934--102094 Score: 189
Period size: 31 Copynumber: 5.2 Consensus size: 31
101924 GCACGTGACA
* *
101934 TGCCACGTGTCACTTTTTGGTACACACGGCG
1 TGCCACATGTCACTTTTTGGTACACATGGCG
** *
101965 TGATACATGTCACTTTTTGGTACACGTGGCG
1 TGCCACATGTCACTTTTTGGTACACATGGCG
* * *
101996 TGCCACATGTCGCTTTTCGGTACA-AGTGGTG
1 TGCCACATGTCACTTTTTGGTACACA-TGGCG
* *
102027 TGCCACATGTCACTTTTTGGTATACGTGGCG
1 TGCCACATGTCACTTTTTGGTACACATGGCG
* * *
102058 TGCCACATGTCGCTTTTTGGTACACGTGGCA
1 TGCCACATGTCACTTTTTGGTACACATGGCG
102089 TGCCAC
1 TGCCAC
102095 GTCGGACACC
Statistics
Matches: 109, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
31 109 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (31 bp):
TGCCACATGTCACTTTTTGGTACACATGGCG
Found at i:102093 original size:62 final size:62
Alignment explanation
Indices: 101925--102094 Score: 223
Period size: 62 Copynumber: 2.7 Consensus size: 62
101915 TCCTTTTGTG
* * * * ** **
101925 CACGTGACATGCCACGTGTCACTTTTTGGTACACACGGCGTGATACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGCGTGCCACATGTCACTTTTTGGTA
* * *
101987 CACGTGGCGTGCCACATGTCGCTTTTCGGTACAAGTGGTGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGCGTGCCACATGTCACTTTTTGGTA
* *
102049 TACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGCATGCCAC
1 CACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGCGTGCCAC
102095 GTCGGACACC
Statistics
Matches: 92, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 92 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (62 bp):
CACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGCGTGCCACATGTCACTTTTTGGTA
Found at i:102110 original size:62 final size:61
Alignment explanation
Indices: 101982--102110 Score: 143
Period size: 62 Copynumber: 2.1 Consensus size: 61
101972 TGTCACTTTT
** ****
101982 TGGTACACGTGGCGTGCCACATGTCGCTTTTCGGTACAAGTGGTGTGCCACATGTCACTTTT
1 TGGTACACGTGGCGTGCCACATGTCGCTTTTCGGTACAAGTGGCATGCCACA-GTCACACCA
* * *
102044 TGGTATACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGCATGCCAC-GTCGGACACCA
1 TGGTACACGTGGCGTGCCACATGTCGCTTTTCGGTACAAGTGGCATGCCACAGTC--ACACCA
102106 TGGTA
1 TGGTA
102111 GAGCCATTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 3 0.05
62 53 0.95
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (61 bp):
TGGTACACGTGGCGTGCCACATGTCGCTTTTCGGTACAAGTGGCATGCCACAGTCACACCA
Found at i:115783 original size:32 final size:32
Alignment explanation
Indices: 115742--115829 Score: 176
Period size: 32 Copynumber: 2.8 Consensus size: 32
115732 AACTTGACAA
115742 CATTTGGAAGCTATGTTTTTTTTTTTTTGCAC
1 CATTTGGAAGCTATGTTTTTTTTTTTTTGCAC
115774 CATTTGGAAGCTATGTTTTTTTTTTTTTGCAC
1 CATTTGGAAGCTATGTTTTTTTTTTTTTGCAC
115806 CATTTGGAAGCTATGTTTTTTTTT
1 CATTTGGAAGCTATGTTTTTTTTT
115830 ATCCCATCCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (32 bp):
CATTTGGAAGCTATGTTTTTTTTTTTTTGCAC
Found at i:124601 original size:5 final size:5
Alignment explanation
Indices: 124591--124625 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
124581 ACCTGTTCAT
*
124591 GGCCG GGCCG GGCCG GGTTCG GGCCG GGCCG GGCC
1 GGCCG GGCCG GGCCG GG-CCG GGCCG GGCCG GGCC
124626 TAGCCTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.00, C:0.37, G:0.57, T:0.06
Consensus pattern (5 bp):
GGCCG
Found at i:126122 original size:11 final size:11
Alignment explanation
Indices: 126106--126131 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
126096 TTTCTTAATC
126106 GGGCCGGGCTT
1 GGGCCGGGCTT
126117 GGGCCGGGCTT
1 GGGCCGGGCTT
126128 GGGC
1 GGGC
126132 TTTTGCTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.27, G:0.58, T:0.15
Consensus pattern (11 bp):
GGGCCGGGCTT
Found at i:131928 original size:14 final size:15
Alignment explanation
Indices: 131909--131942 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
131899 TCATCTCCTT
*
131909 AGAAATTTTAAGT-A
1 AGAAATTATAAGTAA
131923 AGAAATTATAAGTAA
1 AGAAATTATAAGTAA
131938 AGAAA
1 AGAAA
131943 GTGAAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (15 bp):
AGAAATTATAAGTAA
Found at i:133831 original size:13 final size:14
Alignment explanation
Indices: 133812--133838 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
133802 ACTACAAAAA
133812 AAAAAAAATTAAAG
1 AAAAAAAATTAAAG
133826 AAAAAAAATTAAA
1 AAAAAAAATTAAA
133839 CTGAAACTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAAAAAATTAAAG
Found at i:134141 original size:7 final size:7
Alignment explanation
Indices: 134129--134164 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
134119 TGGTGGTGGT
134129 GGCAGAA
1 GGCAGAA
134136 GGCAGAA
1 GGCAGAA
134143 GGCAGAA
1 GGCAGAA
*
134150 GGCAGAC
1 GGCAGAA
134157 GGCAGAA
1 GGCAGAA
134164 G
1 G
134165 TAGCTATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.39, C:0.17, G:0.44, T:0.00
Consensus pattern (7 bp):
GGCAGAA
Found at i:146469 original size:27 final size:27
Alignment explanation
Indices: 146439--146492 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
146429 ATTGGCCACT
*
146439 GTACTAAATGCAGAGCCAATAAGGTTA
1 GTACTAAATGCAGAGCCAACAAGGTTA
146466 GTACTAAATGCAGAGCCAACAAGGTTA
1 GTACTAAATGCAGAGCCAACAAGGTTA
146493 AACTGTCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (27 bp):
GTACTAAATGCAGAGCCAACAAGGTTA
Done.