Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021771.1 Corchorus olitorius cultivar O-4 contig21804, 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: 56899
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2108 original size:126 final size:130
Alignment explanation
Indices: 1856--2116 Score: 329
Period size: 136 Copynumber: 2.0 Consensus size: 130
1846 ATTTTTCAAG
1856 TTTTGTTCAAGTTTCTTTCTTCTCATTCTCCTATTTTTTTTTCTACCTTTTATGATCACAAATCT
1 TTTTGTTCAAGTTTCTTTCTTCTCATTCTCCTATTTTTTTTTCTACCTTTTATGATCACAAATCT
1921 TATAATCTTATAGTACTCAATTTTTTTCCTGCTAGATGAGATGATTCTTTCATAGCCAATTTTAT
66 TATAATC---T--TACTCAATTTTTTTCC-GCTAGATGAGATGATTCTTTCATAGCCAATTTTAT
1986 CGCAAC
125 CGCAAC
**
1992 TTTTGTTCAAGTTTCTTTCTTCTCATTCTCCTCATTTTTTTCCTTCTACCTTTTATGATTGCAAA
1 TTTTGTTCAAGTTTCTTTCTTCTCATTCTCCT-ATTTTTTT--TTCTACCTTTTATGATCACAAA
* * * * *
2057 TGTTAT-A-C-TCCTCAA-TTTTTTCC-CT-G-TTAGATGATTCTTTTATAGCCAATTTTATTGC
63 TCTTATAATCTTACTCAATTTTTTTCCGCTAGATGAGATGATTCTTTCATAGCCAATTTTATCGC
2115 AA
128 AA
2117 ACATGTTAAA
Statistics
Matches: 115, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
126 31 0.27
127 1 0.01
128 2 0.02
130 8 0.07
131 6 0.05
136 32 0.28
137 9 0.08
138 1 0.01
139 25 0.22
ACGTcount: A:0.21, C:0.20, G:0.08, T:0.51
Consensus pattern (130 bp):
TTTTGTTCAAGTTTCTTTCTTCTCATTCTCCTATTTTTTTTTCTACCTTTTATGATCACAAATCT
TATAATCTTACTCAATTTTTTTCCGCTAGATGAGATGATTCTTTCATAGCCAATTTTATCGCAAC
Found at i:2934 original size:16 final size:16
Alignment explanation
Indices: 2909--2939 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2899 TATCAATCAG
2909 TATTAATGAAAATTTC
1 TATTAATGAAAATTTC
*
2925 TATTATTGAAAATTT
1 TATTAATGAAAATTT
2940 GATTTGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
TATTAATGAAAATTTC
Found at i:4337 original size:199 final size:199
Alignment explanation
Indices: 3989--4434 Score: 730
Period size: 199 Copynumber: 2.2 Consensus size: 199
3979 GATGGAGTAT
* * *
3989 TTAATTAATTATTAAATGGGGTATGTGTCAACTTCTTAACCCGTTTATGGAGTCCAAAATTTACA
1 TTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACA
* *
4054 CTGACAGTGTATTGTATAATAATCCCATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAG
66 CTGACAGTGTATTGTATAATAATCCCATAAGAAAAATTATACAATACACCGTCAATGGAGTTTAA
* **
4119 CAGACTGCATGTTCGGGGTTTAAGGCTTGACATGTGTCCCCTTAGGGAATATCTATTAATATTAA
131 CAGACTGCACGCGCGGGGTTTAAGGCTTGACATGTGTCCCCTTAGGGAATATCTATTAATATTAA
4184 ATAC
196 ATAC
* * *
4188 TTAATTAATTATAAAATGAGATATGTGTCAACTTCTTAACCCGCTTATGAAGTTCAAAATTTACA
1 TTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACA
**
4253 CTGACAGTGTATTGTATAATAATCTTATAAGAAAAATTATACAATACACCGTCAATGGAGTTTAA
66 CTGACAGTGTATTGTATAATAATCCCATAAGAAAAATTATACAATACACCGTCAATGGAGTTTAA
* * *
4318 CAGACTGCACGCGCGGGGTTTAAGGGTTGACATGTGTCCGCTTAGGGAATATGTATTAATATTAA
131 CAGACTGCACGCGCGGGGTTTAAGGCTTGACATGTGTCCCCTTAGGGAATATCTATTAATATTAA
*
4383 ATAT
196 ATAC
*
4387 TTAATTAATTATAAAATGGGGTATGTGTGAACTTCTTAACCCGCTTAT
1 TTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACCCGCTTAT
4435 AAATATTATT
Statistics
Matches: 227, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
199 227 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (199 bp):
TTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACA
CTGACAGTGTATTGTATAATAATCCCATAAGAAAAATTATACAATACACCGTCAATGGAGTTTAA
CAGACTGCACGCGCGGGGTTTAAGGCTTGACATGTGTCCCCTTAGGGAATATCTATTAATATTAA
ATAC
Found at i:4866 original size:13 final size:14
Alignment explanation
Indices: 4850--4887 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
4840 TAGCAAATAA
4850 CAATATTAAT-TTT
1 CAATATTAATATTT
4863 CAATTATTAATATTT
1 CAA-TATTAATATTT
4878 CAA-ATTAATA
1 CAATATTAATA
4888 CTTATGGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 7 0.30
15 6 0.26
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
CAATATTAATATTT
Found at i:5251 original size:22 final size:22
Alignment explanation
Indices: 5226--5272 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
5216 GCCTAAGTTA
5226 ATAAGATTAACACATATTTGGG
1 ATAAGATTAACACATATTTGGG
5248 ATAAGATTAACACATATTTGGG
1 ATAAGATTAACACATATTTGGG
5270 ATA
1 ATA
5273 TATAATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.32
Consensus pattern (22 bp):
ATAAGATTAACACATATTTGGG
Found at i:5998 original size:21 final size:20
Alignment explanation
Indices: 5974--6012 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5964 GTTTTACCAG
*
5974 TTACAATAAAAGTTAAATAGT
1 TTACAA-AAAAGCTAAATAGT
*
5995 TTACTAAAAAGCTAAATA
1 TTACAAAAAAGCTAAATA
6013 AGATAATCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (20 bp):
TTACAAAAAAGCTAAATAGT
Found at i:6471 original size:16 final size:18
Alignment explanation
Indices: 6439--6472 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6429 ACCTAGTTAA
6439 ATATATAATATGATGTAC
1 ATATATAATATGATGTAC
6457 ATATAT-ATATG-TGTAC
1 ATATATAATATGATGTAC
6473 CCAGTAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (18 bp):
ATATATAATATGATGTAC
Found at i:8385 original size:20 final size:20
Alignment explanation
Indices: 8349--8387 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
8339 TTGGAAATGA
*
8349 AATATTAATGTATTATTGTG
1 AATATTAATGTAATATTGTG
8369 AATACTTAAT-TAATATTGT
1 AATA-TTAATGTAATATTGT
8388 CTATATCAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (20 bp):
AATATTAATGTAATATTGTG
Found at i:8741 original size:184 final size:184
Alignment explanation
Indices: 8425--8772 Score: 472
Period size: 184 Copynumber: 1.9 Consensus size: 184
8415 AATAAAGATA
* ** *
8425 GCTTGGATGATAATCATGATCAAGATGAGCATAGTGAAAGTTCTGAATCCCATGAAGCAGTTGAT
1 GCTTGGATGATAATCATGATCAAGACGAGCATAGTGAAAGGACTCAATCCCATGAAGCAGTTGAT
** *
8490 GAGAGTAATTCATCTGAAGATGAGGTCAGACTGCTGTTTACTATTTTAAAAAACAAGATTTCTTT
66 GAGAGTAATTCATCTGAAGATGAGGTCAGACTGCTGTTTACTATTAGAAAAAACAAGATTCCTTT
**
8555 TGGATTCTTACATTTCTATTTTGGCTTAACAGGTTGATGGAGGCAGTGTTGATG
131 TGGATTCTTACACCTCTATTTTGGCTTAACAGGTTGATGGAGGCAGTGTTGATG
* *
8609 GCTTGGATGATAATCATGATGAATACGAGCATAGTGAAAGCGAC-CAATCCCATGAAGCAGTTGA
1 GCTTGGATGATAATCATGATCAAGACGAGCATAGTGAAAG-GACTCAATCCCATGAAGCAGTTGA
* * *
8673 TGAGAGTGATTCATCTGAAGATGAGGTCAGGCATGCCT-TTTAGC-ATTAGAAAGTAA-AAG-TT
65 TGAGAGTAATTCATCTGAAGATGAGGTCAGAC-TG-CTGTTTA-CTATTAGAAA-AAACAAGATT
* *
8734 CCTTTTGGGTTCTTACACCTCTCTTTTGGCTTAACAGGT
126 CCTTTTGGATTCTTACACCTCTATTTTGGCTTAACAGGT
8773 GGCTCCTCGA
Statistics
Matches: 143, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
184 122 0.85
185 16 0.11
186 5 0.03
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.32
Consensus pattern (184 bp):
GCTTGGATGATAATCATGATCAAGACGAGCATAGTGAAAGGACTCAATCCCATGAAGCAGTTGAT
GAGAGTAATTCATCTGAAGATGAGGTCAGACTGCTGTTTACTATTAGAAAAAACAAGATTCCTTT
TGGATTCTTACACCTCTATTTTGGCTTAACAGGTTGATGGAGGCAGTGTTGATG
Found at i:20856 original size:1 final size:1
Alignment explanation
Indices: 20850--20894 Score: 72
Period size: 1 Copynumber: 45.0 Consensus size: 1
20840 ATTCCCCTTG
**
20850 TTTTTTTTTTTTTTTTTTGCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20895 CTTGTAGCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.02, G:0.02, T:0.96
Consensus pattern (1 bp):
T
Found at i:25133 original size:28 final size:29
Alignment explanation
Indices: 25102--25158 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
25092 TATCTTTTGC
25102 TTTT-GGGACAAAATAATCCCTTATGTTT
1 TTTTGGGGACAAAATAATCCCTTATGTTT
*
25130 TTTTGGGGACAAATTAATCCCTTATGTTT
1 TTTTGGGGACAAAATAATCCCTTATGTTT
25159 CAAAAATGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (29 bp):
TTTTGGGGACAAAATAATCCCTTATGTTT
Found at i:25342 original size:30 final size:31
Alignment explanation
Indices: 25306--25365 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
25296 GGGACTAATT
*
25306 TCCCAAAA-AAAAATATAACGGATTTTTTTG
1 TCCCAAAAGAAAAACATAACGGATTTTTTTG
*
25336 TCCCAAAAGAAAAACATAAGGGATTTTTTT
1 TCCCAAAAGAAAAACATAACGGATTTTTTT
25366 AGTATTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (31 bp):
TCCCAAAAGAAAAACATAACGGATTTTTTTG
Found at i:27746 original size:27 final size:27
Alignment explanation
Indices: 27698--27751 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
27688 TTATAACTAT
**
27698 TTATATTTACCATTTTTTTTTTGAAAA
1 TTATATTTACCATTTTAATTTTGAAAA
* *
27725 TTATCTTTACCATTTTAATTTTTAAAA
1 TTATATTTACCATTTTAATTTTGAAAA
27752 ATGAGTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.57
Consensus pattern (27 bp):
TTATATTTACCATTTTAATTTTGAAAA
Found at i:27944 original size:30 final size:31
Alignment explanation
Indices: 27877--27934 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
27867 TATAAAAAAA
* * *
27877 ATCCCATATGTTTTTCTTTTGGGACAAAATG
1 ATCCCTTATATTTTTCTTATGGGACAAAATG
27908 ATCCCTTATATTTTT-TTATGGGACAAA
1 ATCCCTTATATTTTTCTTATGGGACAAA
27935 TTAGTCCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (31 bp):
ATCCCTTATATTTTTCTTATGGGACAAAATG
Found at i:28089 original size:29 final size:31
Alignment explanation
Indices: 28047--28120 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 31
28037 CTCATTTTTG
* * **
28047 AAACGTAAGAGATTAATTTATC-CCGAAA-A
1 AAACATAAGGGATTAATTTATCACAAAAACA
* *
28076 AAATATAAGGGATTATTTTATCACAAAAACA
1 AAACATAAGGGATTAATTTATCACAAAAACA
28107 AAACATAAGGGATT
1 AAACATAAGGGATT
28121 TTTTTGGGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 18 0.50
30 4 0.11
31 14 0.39
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.26
Consensus pattern (31 bp):
AAACATAAGGGATTAATTTATCACAAAAACA
Found at i:28645 original size:23 final size:23
Alignment explanation
Indices: 28593--28645 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
28583 ATGTTCGTTT
28593 ATATTATATATATTATATATATA
1 ATATTATATATATTATATATATA
* *
28616 ATAATTATAT-TTTTATTTATATAA
1 AT-ATTATATATATTATATATAT-A
28640 ATATTA
1 ATATTA
28646 AAATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTATATATATTATATATATA
Found at i:28654 original size:18 final size:18
Alignment explanation
Indices: 28633--28693 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
28623 TATTTTTATT
28633 TATATAAATATTAAAATA
1 TATATAAATATTAAAATA
* **
28651 TATATAATTATATCTTATCT-
1 TATATAA--ATAT-TAAAATA
28671 TATATAAATATTAAAATA
1 TATATAAATATTAAAATA
28689 TATAT
1 TATAT
28694 TATTCGTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 3 0.09
18 16 0.48
20 11 0.33
21 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATAAATATTAAAATA
Found at i:28658 original size:38 final size:38
Alignment explanation
Indices: 28609--28693 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 38
28599 TATATATTAT
*
28609 ATATATAATAATTATATTTTTAT-TTATATAAATATTAAA
1 ATATAT-ATAATTATA-TCTTATCTTATATAAATATTAAA
28648 ATATATATAATTATATCTTATCTTATATAAATATTAAA
1 ATATATATAATTATATCTTATCTTATATAAATATTAAA
28686 ATATATAT
1 ATATATAT
28694 TATTCGTGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
37 5 0.11
38 33 0.75
39 6 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (38 bp):
ATATATATAATTATATCTTATCTTATATAAATATTAAA
Found at i:29025 original size:19 final size:19
Alignment explanation
Indices: 28997--29036 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28987 GAATAATGAA
*
28997 AAGAATAGAGCACATAATT
1 AAGAAAAGAGCACATAATT
*
29016 AAGAAAAGAGCAGATAATT
1 AAGAAAAGAGCACATAATT
29035 AA
1 AA
29037 AATGCTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.17
Consensus pattern (19 bp):
AAGAAAAGAGCACATAATT
Found at i:41423 original size:107 final size:104
Alignment explanation
Indices: 41302--41590 Score: 404
Period size: 107 Copynumber: 2.8 Consensus size: 104
41292 AGGTTTTTTA
* *
41302 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTC
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTA
*
41367 ATTCTTATTTTAAGGGTAAATTTCAAAATTAATAATTTATTG
66 ATT-TTATTTTAAGGGTAAATTCCAAAATTAATAA--TATTG
*
41409 TTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAA-TTT
* *
41474 ATTTTTATTTTAAGGGTAAATTCCATAATTAATAATATTG
65 AATTTTATTTTAAGGGTAAATTCCAAAATTAATAATATTG
* * * * * *
41514 TTATAGGG-TTTGGAAATAAAATATATAACTAA-TTCGCTAAGTTTA-ACCCAAATTAGAATTAA
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATT-T
41576 AATTTTATTTTAAGG
65 AATTTTATTTTAAGG
41591 CTTAGAAAAA
Statistics
Matches: 166, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
101 2 0.01
102 25 0.15
103 12 0.07
104 21 0.13
105 13 0.08
107 88 0.53
108 5 0.03
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (104 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTA
ATTTTATTTTAAGGGTAAATTCCAAAATTAATAATATTG
Found at i:42315 original size:23 final size:24
Alignment explanation
Indices: 42285--42343 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
42275 GAAGGATTTG
* * *
42285 GAGAATTATTAAAGAA-ATCCTCT
1 GAGAATTATTAAAAAAGATCCACA
42308 GAGAATTATTAAAAAAGATCCACA
1 GAGAATTATTAAAAAAGATCCACA
*
42332 GAGGATTATTAA
1 GAGAATTATTAA
42344 TTATTAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.27
Consensus pattern (24 bp):
GAGAATTATTAAAAAAGATCCACA
Found at i:44405 original size:15 final size:15
Alignment explanation
Indices: 44385--44413 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44375 TTTAGATAAA
44385 TAATTAATTAATTAC
1 TAATTAATTAATTAC
44400 TAATTAATTAATTA
1 TAATTAATTAATTA
44414 ACGTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTAATTAATTAC
Found at i:44438 original size:11 final size:11
Alignment explanation
Indices: 44383--44438 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
44373 TTTTTAGATA
44383 AATAATTAATT
1 AATAATTAATT
* *
44394 AATTACTAATT
1 AATAATTAATT
*
44405 AATTAATTAACGT
1 AA-TAATTAA-TT
44418 -ATATATTAATT
1 AATA-ATTAATT
44429 AATAATTAAT
1 AATAATTAAT
44439 ATAAGTATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
11 20 0.57
12 14 0.40
13 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (11 bp):
AATAATTAATT
Found at i:45430 original size:12 final size:12
Alignment explanation
Indices: 45410--45449 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
45400 TGTCCGTTCT
45410 CAAAGCCAAATC
1 CAAAGCCAAATC
*
45422 CAAATCCAAATC
1 CAAAGCCAAATC
* *
45434 CAAAGCTAAAGC
1 CAAAGCCAAATC
45446 CAAA
1 CAAA
45450 AGAAAGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.53, C:0.30, G:0.07, T:0.10
Consensus pattern (12 bp):
CAAAGCCAAATC
Found at i:52236 original size:51 final size:51
Alignment explanation
Indices: 52160--52260 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
52150 TGCTTAGCCT
* *
52160 TGTTATGTCTTATAACTATATATGCTGCTTTATCAATGGCTTCTTTATGTC
1 TGTTATGTCTTATAACTATATATGCTGCTTTATCAACGGCTTCTTCATGTC
* *
52211 TGTTATGTGTTATAACTGTATATGCTGCTTTATCAACGGCTTCTTCATGT
1 TGTTATGTCTTATAACTATATATGCTGCTTTATCAACGGCTTCTTCATGT
52261 TGCTCACATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.48
Consensus pattern (51 bp):
TGTTATGTCTTATAACTATATATGCTGCTTTATCAACGGCTTCTTCATGTC
Done.