Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018225.1 Corchorus olitorius cultivar O-4 contig18258, 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: 133783
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1143 original size:19 final size:18
Alignment explanation
Indices: 1099--1143 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
1089 TTTATAACTT
1099 TATATAT-ATAATATATA
1 TATATATAATAATATATA
1116 TATATATAATAATCATA-A
1 TATATATAATAAT-ATATA
1134 TAATATATAA
1 T-ATATATAA
1144 ACCTAAACGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.28
18 7 0.28
19 11 0.44
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TATATATAATAATATATA
Found at i:1528 original size:28 final size:28
Alignment explanation
Indices: 1482--1539 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1472 AGTAAAGGGA
*
1482 TTGAATTGAATCTGTCTACTACTCTTTC
1 TTGAATTGAATCTGCCTACTACTCTTTC
*
1510 TTGAATTGAATTTGCCTACTACTCTTTC
1 TTGAATTGAATCTGCCTACTACTCTTTC
1538 TT
1 TT
1540 CAGACTTGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (28 bp):
TTGAATTGAATCTGCCTACTACTCTTTC
Found at i:5908 original size:25 final size:25
Alignment explanation
Indices: 5869--5918 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
5859 TTGGGCTTTT
5869 TCGGGTTCGGCTATTTTCGAGCTCG
1 TCGGGTTCGGCTATTTTCGAGCTCG
*
5894 TCGGGTTCAGG-TATTTTCGGGCTCG
1 TCGGGTTC-GGCTATTTTCGAGCTCG
5919 GGTTATGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.08, C:0.22, G:0.34, T:0.36
Consensus pattern (25 bp):
TCGGGTTCGGCTATTTTCGAGCTCG
Found at i:5945 original size:16 final size:16
Alignment explanation
Indices: 5894--5951 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
5884 TTCGAGCTCG
5894 TCGGGTTCAGGTATTT
1 TCGGGTTCAGGTATTT
* * *
5910 TCGGGCTCGGGT-TATG
1 TCGGGTTCAGGTAT-TT
5926 TCGGGTTCAGGTATTT
1 TCGGGTTCAGGTATTT
5942 TCGGGTTCAG
1 TCGGGTTCAG
5952 TCTCGGGTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 1 0.03
16 32 0.94
17 1 0.03
ACGTcount: A:0.10, C:0.16, G:0.36, T:0.38
Consensus pattern (16 bp):
TCGGGTTCAGGTATTT
Found at i:5975 original size:6 final size:6
Alignment explanation
Indices: 5964--6008 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
5954 TCGGGTAGGA
* *
5964 TTCGGG TTCGGG TTCGGG CTCGGG -TCGGG TTCGGG TTCGAG TTCG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCG
6009 ATTTCAATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.02, C:0.20, G:0.47, T:0.31
Consensus pattern (6 bp):
TTCGGG
Found at i:5978 original size:29 final size:29
Alignment explanation
Indices: 5941--6007 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
5931 TTCAGGTATT
*
5941 TTCGGGTTCAGTCTCGGGTAGGATTCGGG
1 TTCGGGTTCAGGCTCGGGTAGGATTCGGG
* * *
5970 TTCGGGTTCGGGCTCGGGTCGGGTTCGGG
1 TTCGGGTTCAGGCTCGGGTAGGATTCGGG
*
5999 TTCGAGTTC
1 TTCGGGTTC
6008 GATTTCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.06, C:0.19, G:0.43, T:0.31
Consensus pattern (29 bp):
TTCGGGTTCAGGCTCGGGTAGGATTCGGG
Found at i:5980 original size:23 final size:23
Alignment explanation
Indices: 5941--6002 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
5931 TTCAGGTATT
*
5941 TTCGGGTTC-AGTCTCGGG-TAGG
1 TTCGGGTTCGGGT-TCGGGCTAGG
*
5963 ATTCGGGTTCGGGTTCGGGCTCGG
1 -TTCGGGTTCGGGTTCGGGCTAGG
*
5987 GTCGGGTTCGGGTTCG
1 TTCGGGTTCGGGTTCG
6003 AGTTCGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 29 0.85
24 5 0.15
ACGTcount: A:0.05, C:0.19, G:0.45, T:0.31
Consensus pattern (23 bp):
TTCGGGTTCGGGTTCGGGCTAGG
Found at i:5991 original size:17 final size:18
Alignment explanation
Indices: 5965--6008 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
5955 CGGGTAGGAT
5965 TCGGGTTCGGGTTCGGGC
1 TCGGGTTCGGGTTCGGGC
*
5983 TCGGG-TCGGGTTCGGGT
1 TCGGGTTCGGGTTCGGGC
*
6000 TCGAGTTCG
1 TCGGGTTCG
6009 ATTTCAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.02, C:0.20, G:0.48, T:0.30
Consensus pattern (18 bp):
TCGGGTTCGGGTTCGGGC
Found at i:8466 original size:16 final size:16
Alignment explanation
Indices: 8441--8481 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
8431 CCTCAAGCTC
*
8441 CTTTTTGAAATCTAAA
1 CTTTTAGAAATCTAAA
8457 CTTTTAGAAATCTAAA
1 CTTTTAGAAATCTAAA
8473 CTTTTAGAA
1 CTTTTAGAA
8482 TTCCTATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (16 bp):
CTTTTAGAAATCTAAA
Found at i:9935 original size:76 final size:74
Alignment explanation
Indices: 9839--9984 Score: 256
Period size: 76 Copynumber: 1.9 Consensus size: 74
9829 TAACCTCTAT
*
9839 AAATTAATAATTGGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTGTTAA
1 AAATTAATAATTGGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATTAA
9904 TTTATATGG
66 TTTATATGG
*
9913 AAATTAATAATGTTGGGACCATGAAAAATTATTAATTTAGAGATGTTATTAATTTATCGAGTATT
1 AAATTAATAA--TTGGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
9978 AATTTAT
64 AATTTAT
9985 GAAGGTTATA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
74 10 0.15
76 58 0.85
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (74 bp):
AAATTAATAATTGGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATTAA
TTTATATGG
Found at i:10846 original size:26 final size:26
Alignment explanation
Indices: 10817--10872 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
10807 TTATCAATTA
10817 GTTTTCACTTTCACG-TGATTCAATAT
1 GTTTTCACTTTC-CGATGATTCAATAT
***
10843 GTTTTTTTTTTCCGATGATTCAATAT
1 GTTTTCACTTTCCGATGATTCAATAT
10869 GTTT
1 GTTT
10873 AAATTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.54
Consensus pattern (26 bp):
GTTTTCACTTTCCGATGATTCAATAT
Found at i:11050 original size:76 final size:76
Alignment explanation
Indices: 10970--11115 Score: 206
Period size: 78 Copynumber: 1.9 Consensus size: 76
10960 CTTTTAGTTT
* *
10970 AAAAAATTT-AAATTT-TTGTTAAAATAAAAGAATAAATTTTAATTATAATAAATTATAAACTAC
1 AAAAAATTTAAAATTTCTTGTTAAAATAAAAGAATAAATTTTAATCACAATAAA-T-TAAACTAC
*
11033 CAATACACACCCC
64 AAATACACACCCC
* * *
11046 AAAAACTTTAAAATTTCTTGTTGAAATATAAGAATAAATTTTAATCACAATAAATTAAACTACAA
1 AAAAAATTTAAAATTTCTTGTTAAAATAAAAGAATAAATTTTAATCACAATAAATTAAACTACAA
11111 ATACA
66 ATACA
11116 TACTTTAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
76 22 0.35
77 7 0.11
78 33 0.53
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (76 bp):
AAAAAATTTAAAATTTCTTGTTAAAATAAAAGAATAAATTTTAATCACAATAAATTAAACTACAA
ATACACACCCC
Found at i:14106 original size:3 final size:3
Alignment explanation
Indices: 14098--14133 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
14088 AGTTGCTGAC
14098 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14134 ATAAATCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16244 original size:21 final size:21
Alignment explanation
Indices: 16192--16245 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
16182 GGGATTGGAG
* *
16192 TATTTA-TTTATCTTGTTGCT
1 TATTTATTTTATTTTCTTGCT
*
16212 TAATTT-TATTATTTTCTTGCT
1 T-ATTTATTTTATTTTCTTGCT
16233 TATTTATTTTATT
1 TATTTATTTTATT
16246 GTTACTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.69
Consensus pattern (21 bp):
TATTTATTTTATTTTCTTGCT
Found at i:17062 original size:17 final size:17
Alignment explanation
Indices: 17018--17063 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
17008 CACCCCCCAA
17018 ATCACTAGTGATGCAAG
1 ATCACTAGTGATGCAAG
* *
17035 ATCACCAGTGATGCGAG
1 ATCACTAGTGATGCAAG
*
17052 ATCACTGGTGAT
1 ATCACTAGTGAT
17064 CAAAGATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (17 bp):
ATCACTAGTGATGCAAG
Found at i:20843 original size:29 final size:30
Alignment explanation
Indices: 20780--20844 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
20770 AAGGGCTAGA
* * *
20780 TTATTTGGCCAAATTTGGTACTTCAGAAGT
1 TTATTTGGCCAAAATTGGAACTTCAGAAGC
* *
20810 TTATTTGGCCAAAATT-GAATTTCAGGAGC
1 TTATTTGGCCAAAATTGGAACTTCAGAAGC
20839 TTATTT
1 TTATTT
20845 AACTGTTGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (30 bp):
TTATTTGGCCAAAATTGGAACTTCAGAAGC
Found at i:37236 original size:71 final size:71
Alignment explanation
Indices: 37120--37268 Score: 235
Period size: 71 Copynumber: 2.1 Consensus size: 71
37110 ACATCGGGCC
** *
37120 TTTAATAGGATCTAAATTGAGCATTTTCGCAACTGGCTAGCCCTTCAATAAACATTTAGCCCTAT
1 TTTAATAGGATCTAAATTGAGCATTTTCGCAACCAGCTAACCCTTCAATAAACATTTAGCCCTAT
37185 ACAATT
66 ACAATT
* *
37191 TTTAATAGGATCTAAATTGAGCATTTTCGCAACCAGCTAACCCTTCAATGAACATTTAGTCCTAT
1 TTTAATAGGATCTAAATTGAGCATTTTCGCAACCAGCTAACCCTTCAATAAACATTTAGCCCTAT
*
37256 ATAATT
66 ACAATT
37262 TATTAAT
1 T-TTAAT
37269 GGTTGGTGCA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
71 66 0.93
72 5 0.07
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (71 bp):
TTTAATAGGATCTAAATTGAGCATTTTCGCAACCAGCTAACCCTTCAATAAACATTTAGCCCTAT
ACAATT
Found at i:39375 original size:16 final size:18
Alignment explanation
Indices: 39342--39388 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
39332 TAGTGAATAC
* *
39342 TATATATATACATTTGTA
1 TATATATATATATGTGTA
39360 TAT-TA-ATATATGTGTA
1 TATATATATATATGTGTA
39376 TATATATATATAT
1 TATATATATATAT
39389 ATTATATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 12 0.48
17 4 0.16
18 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (18 bp):
TATATATATATATGTGTA
Found at i:41242 original size:3 final size:3
Alignment explanation
Indices: 41234--41263 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41224 ATGGACAGCT
41234 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
41264 AACAGTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42668 original size:6 final size:6
Alignment explanation
Indices: 42657--42681 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42647 TGTTGTTCAA
42657 CTCTGC CTCTGC CTCTGC CTCTGC C
1 CTCTGC CTCTGC CTCTGC CTCTGC C
42682 GCCCACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.16, T:0.32
Consensus pattern (6 bp):
CTCTGC
Found at i:46519 original size:13 final size:13
Alignment explanation
Indices: 46501--46534 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
46491 ACAACATAAT
46501 AATCAATTTGAAA
1 AATCAATTTGAAA
46514 AATCAATTTGAAA
1 AATCAATTTGAAA
46527 AATCAATT
1 AATCAATT
46535 AATTTTACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (13 bp):
AATCAATTTGAAA
Found at i:47682 original size:31 final size:31
Alignment explanation
Indices: 47647--47708 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
47637 AAAGTCATTA
* *
47647 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
47678 ATGAATATTGTAAATATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
47709 TTCTCTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (31 bp):
ATGAATATTGTAAATATTCATGAATCAAGAG
Found at i:49210 original size:14 final size:15
Alignment explanation
Indices: 49191--49220 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
49181 CATTTGTTCA
49191 TTGTATATTT-TTTT
1 TTGTATATTTCTTTT
49205 TTGTATATTTCTTTT
1 TTGTATATTTCTTTT
49220 T
1 T
49221 CACGAATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (15 bp):
TTGTATATTTCTTTT
Found at i:50235 original size:2 final size:2
Alignment explanation
Indices: 50230--50264 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
50220 CCAACTTCTT
50230 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50265 GATTGCCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52484 original size:2 final size:2
Alignment explanation
Indices: 52477--52514 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
52467 TCTTTTACAC
52477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
52515 ATCGGCCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58789 original size:6 final size:6
Alignment explanation
Indices: 58780--58812 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
58770 TGCTACTGTA
*
58780 TTGTTT TTGTTT TTGTTT TTGTTT TTTTTT TTG
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTG
58813 CAAAATGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTGTTT
Found at i:60963 original size:2 final size:2
Alignment explanation
Indices: 60956--60992 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
60946 TTTCGAGTAT
60956 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
60993 TAGAACTTTC
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:62889 original size:15 final size:15
Alignment explanation
Indices: 62869--62908 Score: 66
Period size: 13 Copynumber: 2.8 Consensus size: 15
62859 TCAAATAATT
62869 ACCCTATATATATAA
1 ACCCTATATATATAA
62884 ACCC--TATATATAA
1 ACCCTATATATATAA
62897 ACCCTATATATA
1 ACCCTATATATA
62909 AACCCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.57
15 10 0.43
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (15 bp):
ACCCTATATATATAA
Found at i:62893 original size:13 final size:13
Alignment explanation
Indices: 62875--62914 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
62865 AATTACCCTA
62875 TATATATAAACCC
1 TATATATAAACCC
62888 TATATATAAACCC
1 TATATATAAACCC
62901 TATATATAAACCC
1 TATATATAAACCC
62914 T
1 T
62915 TTAATTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (13 bp):
TATATATAAACCC
Found at i:64832 original size:2 final size:2
Alignment explanation
Indices: 64825--64853 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
64815 TTTTCCTAAC
64825 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64854 GCGAATTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:64911 original size:47 final size:47
Alignment explanation
Indices: 64842--64935 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
64832 TATATATATA
64842 TATATATTATATGCGAATTAGGTGAAGGTGCGGAAAGAGAGGGATTC
1 TATATATTATATGCGAATTAGGTGAAGGTGCGGAAAGAGAGGGATTC
64889 TATATATTATATGCGAATTAGGTGAAGGTGCGGAAAGAGAGGGATTC
1 TATATATTATATGCGAATTAGGTGAAGGTGCGGAAAGAGAGGGATTC
64936 GAACCCTCGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (47 bp):
TATATATTATATGCGAATTAGGTGAAGGTGCGGAAAGAGAGGGATTC
Found at i:66809 original size:16 final size:16
Alignment explanation
Indices: 66790--66824 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
66780 AAGAAAGAGA
66790 AAATACGCTA-ATAAAT
1 AAATACGCTAGA-AAAT
66806 AAATACGCTAGAAAAT
1 AAATACGCTAGAAAAT
66822 AAA
1 AAA
66825 ATACCCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (16 bp):
AAATACGCTAGAAAAT
Found at i:69548 original size:36 final size:36
Alignment explanation
Indices: 69508--69579 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
69498 AGGTCACTAT
*
69508 TTTTATTTTTCTTACATGAGAACATGAAATTGAAAG
1 TTTTATTTTTCTTACATAAGAACATGAAATTGAAAG
*
69544 TTTTATTTTTCTTACATAAGAACATTAAATTGAAAG
1 TTTTATTTTTCTTACATAAGAACATGAAATTGAAAG
69580 GTTACACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTTATTTTTCTTACATAAGAACATGAAATTGAAAG
Found at i:70323 original size:25 final size:25
Alignment explanation
Indices: 70289--70337 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
70279 CCAAACAATC
70289 TTGAGCACTCTCGCTCGGTCTCTAA
1 TTGAGCACTCTCGCTCGGTCTCTAA
70314 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
70338 CAAACTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAA
Found at i:70663 original size:7 final size:7
Alignment explanation
Indices: 70651--70675 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
70641 AATTGCACCA
70651 AATCTTC
1 AATCTTC
70658 AATCTTC
1 AATCTTC
70665 AATCTTC
1 AATCTTC
70672 AATC
1 AATC
70676 AATTCTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (7 bp):
AATCTTC
Found at i:74642 original size:15 final size:16
Alignment explanation
Indices: 74609--74647 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
74599 GGCCGAATTT
74609 AAAGGAAAGGAAAAGA
1 AAAGGAAAGGAAAAGA
74625 AAAGGAAA-G-AAAGAA
1 AAAGGAAAGGAAAAG-A
74640 AAAGGAAA
1 AAAGGAAA
74648 ACTAAGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 10 0.45
16 8 0.36
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AAAGGAAAGGAAAAGA
Found at i:75564 original size:21 final size:21
Alignment explanation
Indices: 75538--75593 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
75528 TAGCGGAAGC
75538 TTTTAAGTAACTAGAGTTAAA
1 TTTTAAGTAACTAGAGTTAAA
* *
75559 TTTTAAGTGATTAGAGTTAAA
1 TTTTAAGTAACTAGAGTTAAA
75580 TTTTAAGTAACTAG
1 TTTTAAGTAACTAG
75594 CAAATGCAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (21 bp):
TTTTAAGTAACTAGAGTTAAA
Found at i:81119 original size:1 final size:1
Alignment explanation
Indices: 81113--81157 Score: 72
Period size: 1 Copynumber: 45.0 Consensus size: 1
81103 ACTTATCTAG
* *
81113 TTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTATTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
81158 CGGAAGCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.02, C:0.00, G:0.02, T:0.96
Consensus pattern (1 bp):
T
Found at i:81638 original size:41 final size:39
Alignment explanation
Indices: 81573--81707 Score: 117
Period size: 41 Copynumber: 3.3 Consensus size: 39
81563 GTGTTCAACA
**
81573 TGGTCCCTGATTTAGGATACTATTTTTTATCTGATGCAATT
1 TGGTCCCTGATTTA-GATTTTATTTTTTAT-TGATGCAATT
* * ***
81614 TGGTCCCTGATTTAGTATTTTATTTTTAATTTATGCGGCT
1 TGGTCCCTGATTTAG-ATTTTATTTTTTATTGATGCAATT
* * * **
81654 TAGTCCCTGATTCAAGATTTTGTTTACTATTTGATGCAATT
1 TGGTCCCTGATT-TAGATTTTATTTTTTA-TTGATGCAATT
81695 TGGTCCCTGATTT
1 TGGTCCCTGATTT
81708 TAGAAATACG
Statistics
Matches: 72, Mismatches: 19, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
40 27 0.38
41 45 0.62
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (39 bp):
TGGTCCCTGATTTAGATTTTATTTTTTATTGATGCAATT
Found at i:82268 original size:17 final size:17
Alignment explanation
Indices: 82246--82295 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
82236 TCAAAATTTG
82246 AAGAAAAGAGAAAAAAA
1 AAGAAAAGAGAAAAAAA
82263 AAGAAAAGA-AAAGAAAA
1 AAGAAAAGAGAAA-AAAA
*
82280 ATGAAAA-ATGAAAAAA
1 AAGAAAAGA-GAAAAAA
82296 TGGAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 4 0.14
17 22 0.76
18 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (17 bp):
AAGAAAAGAGAAAAAAA
Found at i:83144 original size:17 final size:17
Alignment explanation
Indices: 83122--83154 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
83112 GAAGAAGATT
83122 TTCACAAAGGAACAATC
1 TTCACAAAGGAACAATC
*
83139 TTCACAATGGAACAAT
1 TTCACAAAGGAACAAT
83155 ATTCTTTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (17 bp):
TTCACAAAGGAACAATC
Found at i:83564 original size:16 final size:17
Alignment explanation
Indices: 83545--83578 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
83535 GCCCAACCCT
*
83545 AATAATATCC-AAACTG
1 AATAATAACCTAAACTG
83561 AATAATAACCTAAACTG
1 AATAATAACCTAAACTG
83578 A
1 A
83579 GATAGGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.24
Consensus pattern (17 bp):
AATAATAACCTAAACTG
Found at i:86397 original size:13 final size:13
Alignment explanation
Indices: 86379--86408 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
86369 TAAAGGCTTA
*
86379 TTCATGGCTTGTT
1 TTCATGGCTTGTC
86392 TTCATGGCTTGTC
1 TTCATGGCTTGTC
86405 TTCA
1 TTCA
86409 ATCCTTCGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (13 bp):
TTCATGGCTTGTC
Found at i:101298 original size:21 final size:21
Alignment explanation
Indices: 101256--101299 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
101246 AAAAATCGAA
* *
101256 AACCCTAATCTCAAAGCTTAG
1 AACCCTAATCTCAAACCCTAG
101277 AACCCTAAT-TCAAAACCCTAG
1 AACCCTAATCTC-AAACCCTAG
101298 AA
1 AA
101300 ATTCAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (21 bp):
AACCCTAATCTCAAACCCTAG
Found at i:107188 original size:23 final size:23
Alignment explanation
Indices: 107146--107189 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
107136 AAACCAGTCC
*
107146 CCAAATTCTGGTCTGATACAGTG
1 CCAAATTCTGGTCAGATACAGTG
*
107169 CCAAATTCTGGTCAGTTACAG
1 CCAAATTCTGGTCAGATACAG
107190 AGGGAGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (23 bp):
CCAAATTCTGGTCAGATACAGTG
Found at i:113638 original size:50 final size:49
Alignment explanation
Indices: 113572--113762 Score: 238
Period size: 50 Copynumber: 3.8 Consensus size: 49
113562 GTTTTACAAT
* *
113572 AAGATTGCATTCCATTTGTGAGTCCAAGGTCAAAATTCGCTTTTTATAAG
1 AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCA-AAG
** * *
113622 AAGATTGCATTCCATTTACGAGTTCAAGATCAAAATTCGCTTTTCAAAAC
1 AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTC-AAAG
* ** *
113672 AAAATTGTTTTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAAAG
1 AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
* * *
113721 TAGGATTGCATTCCATTTGTGAGTCTAAGATCAAAACTCGCT
1 -AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCT
113763 CTTCGAGGGG
Statistics
Matches: 118, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
49 3 0.03
50 114 0.97
51 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (49 bp):
AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
Found at i:113754 original size:100 final size:100
Alignment explanation
Indices: 113581--113762 Score: 269
Period size: 100 Copynumber: 1.8 Consensus size: 100
113571 TAAGATTGCA
* * *
113581 TTCCATTTGTGAGTCCAAGGTCAAAATTCGCTTTTTATAAGAAGATTGCATTCCATTTACGAGTT
1 TTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCATAAGAAGATTGCATTCCATTTACGAGTT
*
113646 CAAGATCAAAATTCGCTTTTCAAAACAAAATTGTT
66 CAAGATCAAAACTCGCTTTTCAAAACAAAATTGTT
* **
113681 TTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCA-AAGTAGGATTGCATTCCATTTGTGAG-
1 TTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCATAAG-AAGATTGCATTCCATTTACGAGT
113744 TCTAAGATCAAAACTCGCT
65 TC-AAGATCAAAACTCGCT
113763 CTTCGAGGGG
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
99 5 0.07
100 68 0.93
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (100 bp):
TTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCATAAGAAGATTGCATTCCATTTACGAGTT
CAAGATCAAAACTCGCTTTTCAAAACAAAATTGTT
Found at i:114665 original size:69 final size:69
Alignment explanation
Indices: 114592--115254 Score: 1001
Period size: 69 Copynumber: 9.6 Consensus size: 69
114582 TTCCATGAGT
* *
114592 CAAACTCGTTTCCATGCGAGTCAATTCAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCAC
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCAC
114657 AAGC
66 AAGC
* *
114661 CAAACTCGTTTCCATACGAGTCAGTCCAAGCCTTGGCTCCATCCAAGCAACATGGGCTTTTCCAC
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCAC
*
114726 AACC
66 AAGC
* **
114730 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTCATCCAAGCAACATAAGCTTTTCCAC
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCAC
114795 AAGC
66 AAGC
* ** **
114799 AAAACTCGTTTCCATACGAGTCAGTAAAAGCCTTGGTTCCATCCAAGGC-ACATAAGC-TTTCCA
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAA-GCAACATGGGCTTTTCCA
114862 CAAGC
65 CAAGC
*
114867 AAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC--CATGTAGGCTTTTCC
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATG--GGCTTTTCC
114930 ATCAAGC
64 A-CAAGC
*
114937 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTAACATGGGCTTTTCCAC
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCAC
115002 AAGC
66 AAGC
* **
115006 CAAACTCGTTTCCATACGAGTCAGTCCAAGCCTTGACTCCATCCAAGCAACATGGGCTTTTCCAC
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCAC
*
115071 AACC
66 AAGC
* **
115075 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTCATCCAAGCAACATAAGCTTTTCCAC
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCAC
115140 AAGC
66 AAGC
* * * *
115144 AAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCACGTAGGCTTTTCCAT
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCA-
115209 CAAGC
65 CAAGC
* *
115214 CAAACTCGTTTCCATACGAGTTAGTTTAAGCCTTGGTTCCA
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA
115255 CCTAAACAGG
Statistics
Matches: 545, Mismatches: 41, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
66 3 0.01
67 2 0.00
68 57 0.10
69 373 0.68
70 106 0.19
72 4 0.01
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (69 bp):
CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGGGCTTTTCCAC
AAGC
Found at i:133127 original size:14 final size:15
Alignment explanation
Indices: 133108--133136 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
133098 GACAGAAAGC
133108 AATTAAAC-AGAAAA
1 AATTAAACTAGAAAA
133122 AATTAAACTAGAAAA
1 AATTAAACTAGAAAA
133137 CAAAGCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (15 bp):
AATTAAACTAGAAAA
Done.