Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018069.1 Corchorus olitorius cultivar O-4 contig18102, 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: 119663
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:243 original size:31 final size:31
Alignment explanation
Indices: 180--243 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
170 AGAGTTTGTC
*
180 TTTATTTTCTTAATTAGGTTAGTATTATGCT
1 TTTATTTTCTTAATTAGGTTAGTATTAGGCT
* *
211 TTTATTTTCTTATTTTA-GTTAGTATTGGGCT
1 TTTATTTTCTTA-ATTAGGTTAGTATTAGGCT
242 TT
1 TT
244 ATGGGCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.19, C:0.06, G:0.14, T:0.61
Consensus pattern (31 bp):
TTTATTTTCTTAATTAGGTTAGTATTAGGCT
Found at i:2930 original size:29 final size:29
Alignment explanation
Indices: 2898--2968 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
2888 AGCCCAAATT
2898 AAAATTAAAATTTTATTTTAAGGGTTAGG
1 AAAATTAAAATTTTATTTTAAGGGTTAGG
*
2927 AAAATTAAAATTTTATTTTAAGGGTTATG
1 AAAATTAAAATTTTATTTTAAGGGTTAGG
2956 AAAATTAAAATTT
1 AAAATTAAAATTT
2969 GTAAAAGGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (29 bp):
AAAATTAAAATTTTATTTTAAGGGTTAGG
Found at i:3788 original size:14 final size:14
Alignment explanation
Indices: 3769--3802 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3759 TTTTATAATT
3769 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
3783 ATTTTATTTTTACT
1 ATTTTATTTTTACC
3797 ATTTTA
1 ATTTTA
3803 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:3850 original size:15 final size:15
Alignment explanation
Indices: 3830--3860 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3820 GATTAACCTA
3830 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
3845 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
3860 T
1 T
3861 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:6024 original size:21 final size:22
Alignment explanation
Indices: 5984--6024 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5974 GACAAACTCG
*
5984 TAACCCGAATAACCCGAGAAAA
1 TAACCCGAATAACCCAAGAAAA
*
6006 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
6025 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAAA
Found at i:7949 original size:15 final size:15
Alignment explanation
Indices: 7929--7959 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
7919 ACAATACATT
7929 AACTATCAAATAGAA
1 AACTATCAAATAGAA
7944 AACTATCAAATAGAA
1 AACTATCAAATAGAA
7959 A
1 A
7960 CAGGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:8002 original size:14 final size:14
Alignment explanation
Indices: 7983--8020 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
7973 ATAACCTTTT
7983 AAATAAAATAGTAA
1 AAATAAAATAGTAA
*
7997 AAATAAAATGGTAA
1 AAATAAAATAGTAA
8011 AAATAAAATA
1 AAATAAAATA
8021 ATTATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (14 bp):
AAATAAAATAGTAA
Found at i:14453 original size:38 final size:38
Alignment explanation
Indices: 14367--14453 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 38
14357 AGTGGATACT
* * ** *
14367 GGATAGTTAATTCCTATACCTTTTTTTTTATAATGAGT
1 GGATAATTAATTCCTATACCTTTTTTTTTAAAAAAAGA
* *
14405 GGATAGTTAATTTCTATACCTTTTTTTTTAAAAAAAGAA
1 GGATAATTAATTCCTATACCTTTTTTTTTAAAAAAAG-A
14444 GGA-AATTAAT
1 GGATAATTAAT
14454 AAAGGAACCT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 39 0.93
39 3 0.07
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (38 bp):
GGATAATTAATTCCTATACCTTTTTTTTTAAAAAAAGA
Found at i:16553 original size:11 final size:9
Alignment explanation
Indices: 16537--16561 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16527 CATGTTTCCT
16537 TATATATAC
1 TATATATAC
16546 TATATATAC
1 TATATATAC
16555 TATATAT
1 TATATAT
16562 TATTTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (9 bp):
TATATATAC
Found at i:22318 original size:17 final size:17
Alignment explanation
Indices: 22296--22330 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22286 TCCTATAATT
22296 AATTAAACTAATGTGAA
1 AATTAAACTAATGTGAA
22313 AATTAAACTAATGTGAA
1 AATTAAACTAATGTGAA
22330 A
1 A
22331 GCATGCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (17 bp):
AATTAAACTAATGTGAA
Found at i:23640 original size:45 final size:42
Alignment explanation
Indices: 23590--23683 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
23580 AGTAACAATT
* *
23590 AATATTAGTTTTATTTTGATGAATAATCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATAACCTAGAGAT--A-GAGTAG
*
23635 AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
1 AATATTAGCTTTATTTTGATGAATAACCTAGAGATAGAGTAG
23677 AAT-TTAG
1 AATATTAG
23684 ATAATGCACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 9 0.20
43 1 0.02
45 32 0.70
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATAACCTAGAGATAGAGTAG
Found at i:23974 original size:12 final size:12
Alignment explanation
Indices: 23959--23985 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23949 TAGAATATAA
23959 ATCATAATATCT
1 ATCATAATATCT
23971 ATCATAATATCT
1 ATCATAATATCT
23983 ATC
1 ATC
23986 TATACGTTAC
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:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (12 bp):
ATCATAATATCT
Found at i:24907 original size:20 final size:22
Alignment explanation
Indices: 24874--24915 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
24864 TTATATATTA
24874 TATATAAAATATATTTATAATC
1 TATATAAAATATATTTATAATC
24896 TATAT-AAA-ATATTTATAATC
1 TATATAAAATATATTTATAATC
24916 AATTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
21 3 0.15
22 5 0.25
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATAAAATATATTTATAATC
Found at i:25755 original size:12 final size:12
Alignment explanation
Indices: 25736--25772 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
25726 AGAGATGTTG
25736 TTATGCATATA-
1 TTATGCATATAC
25747 TTGATGCATATAC
1 TT-ATGCATATAC
25760 TTATGCATATAC
1 TTATGCATATAC
25772 T
1 T
25773 CAAAATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (12 bp):
TTATGCATATAC
Found at i:32972 original size:12 final size:12
Alignment explanation
Indices: 32955--32993 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
32945 GGAGATTTTC
32955 ATTCTAGAAATT
1 ATTCTAGAAATT
32967 ATTCTAGAAATT
1 ATTCTAGAAATT
32979 ATTCTAGAAATT
1 ATTCTAGAAATT
32991 ATT
1 ATT
32994 ATATGGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
ATTCTAGAAATT
Found at i:47962 original size:19 final size:19
Alignment explanation
Indices: 47938--47975 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
47928 TTCAGCATCA
* *
47938 ACACTCTCATTTTATAATT
1 ACACTCTAATATTATAATT
47957 ACACTCTAATATTATAATT
1 ACACTCTAATATTATAATT
47976 TATAAACCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (19 bp):
ACACTCTAATATTATAATT
Found at i:48725 original size:24 final size:22
Alignment explanation
Indices: 48694--48737 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
48684 AACTCAAAAT
48694 TAAATCCAACTAATAAAGATTAAA
1 TAAATCCAACTAA-AAA-ATTAAA
48718 TAAATCCAACTAAAAAATTA
1 TAAATCCAACTAAAAAATTA
48738 TGTTCCTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 3 0.15
24 13 0.65
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (22 bp):
TAAATCCAACTAAAAAATTAAA
Found at i:51003 original size:32 final size:31
Alignment explanation
Indices: 50967--51028 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
50957 ATATATTAAT
*
50967 AATCAAAAT-GAGTTTTTACAACCATAGCATAC
1 AATCAAAATAGA-TTTTTAC-ACCATACCATAC
50999 AATCAAAATAGATTTTTACACCATACCATA
1 AATCAAAATAGATTTTTACACCATACCATA
51029 TAACTAGTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 10 0.36
32 16 0.57
33 2 0.07
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.29
Consensus pattern (31 bp):
AATCAAAATAGATTTTTACACCATACCATAC
Found at i:53260 original size:49 final size:49
Alignment explanation
Indices: 53203--53321 Score: 229
Period size: 49 Copynumber: 2.4 Consensus size: 49
53193 TTGGTGAATC
53203 TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
1 TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
53252 TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
1 TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
*
53301 TTTAAGTCTTAATCGGGTAAT
1 TTTAAGCCTTAATCGGGTAAT
53322 CTTATCTAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (49 bp):
TTTAAGCCTTAATCGGGTAATTGATTTGTTAAGTTAACAATAGGGGTAA
Found at i:53540 original size:15 final size:15
Alignment explanation
Indices: 53520--53550 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53510 TTGTTTCTAG
53520 TTTAATTGCTTTCTT
1 TTTAATTGCTTTCTT
*
53535 TTTAATTGTTTTCTT
1 TTTAATTGCTTTCTT
53550 T
1 T
53551 CAACCTCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTAATTGCTTTCTT
Found at i:57607 original size:21 final size:22
Alignment explanation
Indices: 57572--57615 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
57562 AGAGCACGAA
*
57572 AATGGAGCCTCTTGATG-GCTTG
1 AATGGAGCATCTTGA-GAGCTTG
57594 AATGGAG-ATCTTGAGAGCTTG
1 AATGGAGCATCTTGAGAGCTTG
57615 A
1 A
57616 GAAACAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 12 0.60
22 7 0.35
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.30
Consensus pattern (22 bp):
AATGGAGCATCTTGAGAGCTTG
Found at i:59344 original size:59 final size:60
Alignment explanation
Indices: 59265--59482 Score: 289
Period size: 64 Copynumber: 3.5 Consensus size: 60
59255 GGGTTTCTCA
* * * *
59265 ATCACCAATGCCTTGTCAC-ATAGTGGGCTTTGTAAATAAGGTGAGATG-CATATTGCCCG
1 ATCACCAATGTCTTGCCACAATAGTGGGCTTTGTAAATAAGGTGAGA-GACATAATGCTCG
59324 ATCACCAATGTCTTGCCACATAGTATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCG
1 ATCACCAATGTCTTGCCAC--A--ATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCG
59388 ATCACCAATGTCTTGCCACATAGTATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCG
1 ATCACCAATGTCTTGCCAC--A--ATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCG
*
59452 ATTACCAATGTCTTGCCAC-ATAGTGGGCTTT
1 ATCACCAATGTCTTGCCACAATAGTGGGCTTT
59483 ATGATGAATC
Statistics
Matches: 148, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
59 29 0.20
63 1 0.01
64 118 0.80
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (60 bp):
ATCACCAATGTCTTGCCACAATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCG
Found at i:59365 original size:64 final size:64
Alignment explanation
Indices: 59284--59475 Score: 341
Period size: 64 Copynumber: 3.0 Consensus size: 64
59274 GCCTTGTCAC
* *
59284 ATAGTGGGCTTTGTAAATAAGGTGAGATG-CATATTGCCCGATCACCAATGTCTTGCCACATAGT
1 ATAGTGGGCTTTGTAAATAAGGTGAGA-GACATAATGCTCGATCACCAATGTCTTGCCACATAGT
59348 ATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCGATCACCAATGTCTTGCCACATAGT
1 ATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCGATCACCAATGTCTTGCCACATAGT
*
59412 ATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCGATTACCAATGTCTTGCCACATAGT
1 ATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCGATCACCAATGTCTTGCCACATAGT
59476 GGGCTTTATG
Statistics
Matches: 124, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
63 1 0.01
64 123 0.99
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (64 bp):
ATAGTGGGCTTTGTAAATAAGGTGAGAGACATAATGCTCGATCACCAATGTCTTGCCACATAGT
Found at i:59840 original size:18 final size:18
Alignment explanation
Indices: 59817--59862 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
59807 TAATTATTTG
*
59817 TGAATAATGGGCTTTTAA
1 TGAATAATGGGATTTTAA
* *
59835 TGAATAGTGGGATTTTGA
1 TGAATAATGGGATTTTAA
59853 TGAAGTAATG
1 TGAA-TAATG
59863 CCCTTTGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (18 bp):
TGAATAATGGGATTTTAA
Found at i:73870 original size:18 final size:18
Alignment explanation
Indices: 73847--73881 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
73837 AATTAATATG
73847 AGAAAAAAGAAGAAAAAT
1 AGAAAAAAGAAGAAAAAT
*
73865 AGAAAAGAGAAGAAAAA
1 AGAAAAAAGAAGAAAAA
73882 ATCTTTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (18 bp):
AGAAAAAAGAAGAAAAAT
Found at i:77407 original size:13 final size:12
Alignment explanation
Indices: 77389--77423 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
77379 TTGGGTTTAC
77389 TTTTTCTTTTCTT
1 TTTTTCTTTT-TT
77402 TTTTTCTTTTTT
1 TTTTTCTTTTTT
77414 TTTTTGCTTT
1 TTTTT-CTTT
77424 GATTAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:79461 original size:32 final size:32
Alignment explanation
Indices: 79425--79488 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
79415 TTTTTAACCC
79425 CTTATTCGATACTCACATTAGATTCAAATTAT
1 CTTATTCGATACTCACATTAGATTCAAATTAT
79457 CTTATTCGATACTCACATTAGATTCAAATTAT
1 CTTATTCGATACTCACATTAGATTCAAATTAT
79489 TTTAGAATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (32 bp):
CTTATTCGATACTCACATTAGATTCAAATTAT
Found at i:89671 original size:52 final size:52
Alignment explanation
Indices: 89588--89687 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
89578 TACATAAGCA
*
89588 TGGAGGTTGCAGGCCGGTTCTTCAATCATCTGCGATACATATGCAGAGAGCT
1 TGGAGGTTGCAGGCCGGTTCTTCAATCATCTGCGAAACATATGCAGAGAGCT
89640 TGGAGGTTGCAGGCCGGTTCTTCAA-CTATCTGCGAAACATATGCAGAG
1 TGGAGGTTGCAGGCCGGTTCTTCAATC-ATCTGCGAAACATATGCAGAG
89688 GCCAGTTCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 1 0.02
52 45 0.98
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (52 bp):
TGGAGGTTGCAGGCCGGTTCTTCAATCATCTGCGAAACATATGCAGAGAGCT
Found at i:93936 original size:14 final size:14
Alignment explanation
Indices: 93917--93944 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
93907 GAATAAGTTC
93917 TAATCAAATAATGT
1 TAATCAAATAATGT
93931 TAATCAAATAATGT
1 TAATCAAATAATGT
93945 CTTCTTCTTG
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:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
TAATCAAATAATGT
Found at i:94343 original size:18 final size:18
Alignment explanation
Indices: 94320--94356 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
94310 AAATAAGTAG
94320 ATTAAGGCAAGATAATAA
1 ATTAAGGCAAGATAATAA
94338 ATTAAGGCAAGATAATAA
1 ATTAAGGCAAGATAATAA
94356 A
1 A
94357 AAGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.16, T:0.22
Consensus pattern (18 bp):
ATTAAGGCAAGATAATAA
Found at i:96419 original size:88 final size:86
Alignment explanation
Indices: 96262--96435 Score: 303
Period size: 88 Copynumber: 2.0 Consensus size: 86
96252 ATTCAATTAC
96262 TGTGGAATCTCAATTTCCTCTATGGGCCTATAAATATATATCTTGTTTACTTGGGGAGCTATCCA
1 TGTGGAATCTCAATTTCCTCTATGGGCCTATAAATATATATCTTGTTTACTTGGGGAGCTATCCA
*
96327 TAATTTCCAAGCAAATTAGAA
66 TAATTTCCAAACAAATTAGAA
* *
96348 TGTGGAATCTCAATTTCCTCTATGGGTCTATATATGTATATATCTTGTTTACTTGGGGAGCTATC
1 TGTGGAATCTCAATTTCCTCTATGGGCCTATA-A-ATATATATCTTGTTTACTTGGGGAGCTATC
96413 CATAATTTCCAAACAAATTAGAA
64 CATAATTTCCAAACAAATTAGAA
96436 CCAATGAATT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
86 31 0.37
87 1 0.01
88 51 0.61
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (86 bp):
TGTGGAATCTCAATTTCCTCTATGGGCCTATAAATATATATCTTGTTTACTTGGGGAGCTATCCA
TAATTTCCAAACAAATTAGAA
Found at i:101652 original size:226 final size:225
Alignment explanation
Indices: 101201--101657 Score: 815
Period size: 226 Copynumber: 2.0 Consensus size: 225
101191 CTGGATAGTC
*
101201 ATCAATATATTAGCAGTTAGTGCAATGCTACCAAAATCACCTCGAGAACTTAAGTATGATTTTGG
1 ATCAATATATTAGCAGTTAGTGCAATACTACCAAAATCACCTCGAGAACTTAAGTATGATTTTGG
*
101266 CATAAATAAACAGAGTGCACAGAGTCATAGCAGAGTCTTGACATCACATTTTGCAGCCTGTTTCA
66 CATAAATAAACAGAGTGCACAGAGTCATAGCAGAGTCTCGACATCACATTTTGCAGCCTGTTTCA
*
101331 AAAATCATCATGTTGCTCAACTCACAAACATTTCAAAACAGGATTTTGACTACAGCTTCTAAATT
131 AAAATCATCATGTTGCTCAACTCACAAACATGTCAAAACAGGATTTTGACTACAGCTTCTAAATT
101396 GAAGCTTGGGAAATAGGTAAGTCAGCATAG
196 GAAGCTTGGGAAATAGGTAAGTCAGCATAG
** *
101426 ATCAATATATTAGCAGTTAGTGCAATACTACTGAAATCACCTCGAGCACTTAAGTATGATTTTGG
1 ATCAATATATTAGCAGTTAGTGCAATACTACCAAAATCACCTCGAGAACTTAAGTATGATTTTGG
* *
101491 CATAAATAAACAGAGTTCACAGAGTCATAGCAGAGTCTCGACATCACAGTTTTGCAGCTTGTTTC
66 CATAAATAAACAGAGTGCACAGAGTCATAGCAGAGTCTCGACATCACA-TTTTGCAGCCTGTTTC
*
101556 GAAAATCATCATGTTGCTCAACTCACAAACATGTCAAAACAGGATTTTGACTACAGCTTCTAAAT
130 AAAAATCATCATGTTGCTCAACTCACAAACATGTCAAAACAGGATTTTGACTACAGCTTCTAAAT
*
101621 TGAAGCTTGGGAAATAGTTAAGTCAGCATAG
195 TGAAGCTTGGGAAATAGGTAAGTCAGCATAG
101652 ATCAAT
1 ATCAAT
101658 CTTTCCAAAT
Statistics
Matches: 221, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
225 107 0.48
226 114 0.52
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (225 bp):
ATCAATATATTAGCAGTTAGTGCAATACTACCAAAATCACCTCGAGAACTTAAGTATGATTTTGG
CATAAATAAACAGAGTGCACAGAGTCATAGCAGAGTCTCGACATCACATTTTGCAGCCTGTTTCA
AAAATCATCATGTTGCTCAACTCACAAACATGTCAAAACAGGATTTTGACTACAGCTTCTAAATT
GAAGCTTGGGAAATAGGTAAGTCAGCATAG
Found at i:105681 original size:5 final size:5
Alignment explanation
Indices: 105671--105698 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
105661 ATTTCCTTCC
105671 ATTTA ATTTA ATTTA ATTTA ATTTA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATT
105699 GTTATTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTTA
Found at i:107223 original size:66 final size:65
Alignment explanation
Indices: 107112--107347 Score: 204
Period size: 66 Copynumber: 3.5 Consensus size: 65
107102 TCCAACGTAG
* * * * *
107112 AAATATTGATAACCACACCGCGAAAATTTGATAACCTCATTGTGAAATTTCGATAACCTCCCTAT
1 AAAT-TTGATAACCACACCGTGAAATTTTGATAACCACATTGTGAAA-TTCGATAACCACACTAT
107177 GA
64 GA
** *
107179 AAATTTGATAACCACAATGTGAAATTTTGATAACCACATTGTGAAATTCTGATAACCACACAATG
1 AAATTTGATAACCACACCGTGAAATTTTGATAACCACATTGTGAAATTC-GATAACCACACTATG
107244 A
65 A
** * ** * * * * * *
107245 AGTTTTGATAACCTCATTGTCTATGAAATTTTGATAATCACATTATAAAATT-GGTAATCGCACT
1 AAATTTGATAACCACA----CCGTGAAATTTTGATAACCACATTGTGAAATTCGATAACCACACT
107309 ATGA
62 ATGA
* *
107313 AAATTTTGATAACCACACCATGAAATTTCGATAAC
1 AAA-TTTGATAACCACACCGTGAAATTTTGATAAC
107348 TTACCTATAA
Statistics
Matches: 137, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
65 18 0.13
66 63 0.46
67 4 0.03
68 13 0.09
69 12 0.09
70 27 0.20
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (65 bp):
AAATTTGATAACCACACCGTGAAATTTTGATAACCACATTGTGAAATTCGATAACCACACTATGA
Found at i:107340 original size:22 final size:22
Alignment explanation
Indices: 107111--107347 Score: 163
Period size: 22 Copynumber: 10.6 Consensus size: 22
107101 CTCCAACGTA
* ***
107111 GAAATATTGATAACCACACCGC
1 GAAATTTTGATAACCACACTAT
* * * *
107133 GAAAATTTGATAACCTCATTGT
1 GAAATTTTGATAACCACACTAT
* * *
107155 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* * *
107177 GAAAATTTGATAACCACAATGT
1 GAAATTTTGATAACCACACTAT
* *
107199 GAAATTTTGATAACCACATTGT
1 GAAATTTTGATAACCACACTAT
* *
107221 GAAATTCTGATAACCACACAAT
1 GAAATTTTGATAACCACACTAT
* *
107243 GAAGTTTTGATAACCTCATTGTCTAT
1 GAAATTTTGATAACCACA----CTAT
* *
107269 GAAATTTTGATAATCACATTAT
1 GAAATTTTGATAACCACACTAT
* * * *
107291 -AAA-ATTGGTAATCGCACTAT
1 GAAATTTTGATAACCACACTAT
*
107311 GAAAATTTTGATAACCACACCAT
1 G-AAATTTTGATAACCACACTAT
*
107334 GAAATTTCGATAAC
1 GAAATTTTGATAAC
107348 TTACCTATAA
Statistics
Matches: 167, Mismatches: 41, Indels: 14
0.75 0.18 0.06
Matches are distributed among these distances:
20 13 0.08
21 3 0.02
22 120 0.72
23 13 0.08
26 18 0.11
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:107569 original size:22 final size:22
Alignment explanation
Indices: 107544--107721 Score: 105
Period size: 22 Copynumber: 8.0 Consensus size: 22
107534 TAAAATTTCA
*
107544 ATAACCTTCGTATGAAATTTTG
1 ATAACCTTCATATGAAATTTTG
* * * *
107566 ATAATCTCCATAAGAGATTTTG
1 ATAACCTTCATATGAAATTTTG
**
107588 ATAACCTTTTTTTTATGAAATTTTG
1 ATAACC---TTCATATGAAATTTTG
*
107613 GTAACC-TCTATATGAAATTTTG
1 ATAACCTTC-ATATGAAATTTTG
* *
107635 ATAA--TTACACTACGAAGTTTTG
1 ATAACCTT-CA-TATGAAATTTTG
* *
107657 ATAAAC-TCATATAAAATTTTG
1 ATAACCTTCATATGAAATTTTG
* * *
107678 GTAACC-ACACTATGAAATTTTA
1 ATAACCTTCA-TATGAAATTTTG
* *
107700 ATAACCTTCCTATGTAATTTTG
1 ATAACCTTCATATGAAATTTTG
107722 GTTTGATTGT
Statistics
Matches: 115, Mismatches: 30, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
21 18 0.16
22 79 0.69
23 2 0.02
25 16 0.14
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (22 bp):
ATAACCTTCATATGAAATTTTG
Found at i:107688 original size:43 final size:44
Alignment explanation
Indices: 107604--107703 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 44
107594 TTTTTTTTAT
* * * **
107604 GAAATTTTGGTAACCTCTATATGAAATTTTGATAATTACACTAC
1 GAAATTTTGATAAACTCTATATAAAATTTTGATAACCACACTAC
* * *
107648 GAAGTTTTGATAAACTC-ATATAAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAAACTCTATATAAAATTTTGATAACCACACTAC
*
107691 GAAATTTTAATAA
1 GAAATTTTGATAA
107704 CCTTCCTATG
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
43 32 0.70
44 14 0.30
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (44 bp):
GAAATTTTGATAAACTCTATATAAAATTTTGATAACCACACTAC
Found at i:109533 original size:22 final size:22
Alignment explanation
Indices: 109457--109700 Score: 124
Period size: 22 Copynumber: 11.1 Consensus size: 22
109447 CTCCAATGTA
* *
109457 GAAATATT-GATAACCACATTTT
1 GAAAT-TTCGATAACCACACTAT
109479 GCAAATTT-GATAACCTA-A-TAT
1 G-AAATTTCGATAACC-ACACTAT
* * *
109500 CAAATTTCGATAACCTCCCTAT
1 GAAATTTCGATAACCACACTAT
* *
109522 GAAAATTCGATAACCACACTGT
1 GAAATTTCGATAACCACACTAT
* *
109544 GAAATTTGGGTAACCACACTAT
1 GAAATTTCGATAACCACACTAT
* * * *
109566 GAAATTTCGATAATCTCAGTGT
1 GAAATTTCGATAACCACACTAT
* **
109588 GAAATTTTGATAATCTGC-CTAT
1 GAAATTTCGATAA-CCACACTAT
* ** *
109610 AAAATTTTAATAATCACACTAAAT
1 GAAATTTCGATAACCACACT--AT
* * *
109634 -AAAATT-GGTAACCGCACTAT
1 GAAATTTCGATAACCACACTAT
* * *
109654 GAAAATTTTGATAATCACACCAT
1 G-AAATTTCGATAACCACACTAT
* *
109677 GAAATTTCGATAACCTCCCTAT
1 GAAATTTCGATAACCACACTAT
109699 GA
1 GA
109701 GAATGAAACT
Statistics
Matches: 165, Mismatches: 45, Indels: 24
0.71 0.19 0.10
Matches are distributed among these distances:
20 8 0.05
21 10 0.06
22 123 0.75
23 22 0.13
24 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (22 bp):
GAAATTTCGATAACCACACTAT
Found at i:109743 original size:22 final size:23
Alignment explanation
Indices: 109713--109805 Score: 95
Period size: 22 Copynumber: 4.2 Consensus size: 23
109703 ATGAAACTGT
* *
109713 GATATCCTCTCTAT-ATATTTTC
1 GATAACCTCTCTATAAAATTTTC
*
109735 GATAACCTCTCCATAAAATTTTC
1 GATAACCTCTCTATAAAATTTTC
*
109758 -ATAACCTCCCTATAAAATTTT-
1 GATAACCTCTCTATAAAATTTTC
* **
109779 GTTAACCTCTCTAGGAAATTTT-
1 GATAACCTCTCTATAAAATTTTC
109801 GATAA
1 GATAA
109806 GCACAAATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
22 52 0.88
23 7 0.12
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (23 bp):
GATAACCTCTCTATAAAATTTTC
Found at i:109914 original size:22 final size:22
Alignment explanation
Indices: 109832--109935 Score: 97
Period size: 22 Copynumber: 4.7 Consensus size: 22
109822 CCTCCCTCCC
* * *
109832 TATGAAATTTTGGTAGCCTCTG
1 TATGAAATTTTGATAACCTCTA
109854 TATGAAATTTTGATAA-CTAC-A
1 TATGAAATTTTGATAACCT-CTA
*
109875 TTATGAAGTTTTGATAACCTCTA
1 -TATGAAATTTTGATAACCTCTA
* *
109898 TATGAAATTTTGGTAACCAC-A
1 TATGAAATTTTGATAACCTCTA
*
109919 CTACGAAATTTTGATAA
1 -TATGAAATTTTGATAA
109936 TCGTTCTATG
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
21 3 0.04
22 62 0.91
23 3 0.04
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTA
Found at i:109955 original size:44 final size:44
Alignment explanation
Indices: 109835--109935 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 44
109825 CCCTCCCTAT
* * * * * * *
109835 GAAATTTTGGTAGCCTCTGTATGAAATTTTGATAACTACATTAT
1 GAAATTTTGATAACCTCTATATGAAATTTTGGTAACCACACTAC
*
109879 GAAGTTTTGATAACCTCTATATGAAATTTTGGTAACCACACTAC
1 GAAATTTTGATAACCTCTATATGAAATTTTGGTAACCACACTAC
109923 GAAATTTTGATAA
1 GAAATTTTGATAA
109936 TCGTTCTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (44 bp):
GAAATTTTGATAACCTCTATATGAAATTTTGGTAACCACACTAC
Found at i:110738 original size:1 final size:1
Alignment explanation
Indices: 110728--110886 Score: 75
Period size: 1 Copynumber: 159.0 Consensus size: 1
110718 CAATTACGTA
* * * * * * * * * *
110728 TTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * * *
110793 GTTTTTGTTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTGTTTTGTTTTGTTTTTGTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
110858 GTTTTTGTTTTTGTTTTTGTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
110887 ACAAAAGCTA
Statistics
Matches: 104, Mismatches: 54, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 104 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (1 bp):
T
Found at i:110739 original size:6 final size:6
Alignment explanation
Indices: 110728--110886 Score: 269
Period size: 6 Copynumber: 27.7 Consensus size: 6
110718 CAATTACGTA
110728 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
110776 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG -TTTTG -TTTTG -TTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
110821 -TTTTG TTTTTG -TTTTG -TTTTG TTTTTG TTTTTG -TTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
110865 TTTTTG TTTTTG TTTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTT
110887 ACAAAAGCTA
Statistics
Matches: 150, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
5 35 0.23
6 115 0.77
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTTG
Done.