Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007534.1 Corchorus capsularis cultivar CVL-1 contig07555, 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: 105509
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3983 original size:18 final size:18
Alignment explanation
Indices: 3960--3995 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3950 AAGGAGAAGA
3960 GGAAGAAGTGGTGGTTGT
1 GGAAGAAGTGGTGGTTGT
* *
3978 GGAAGACGTGTTGGTTGT
1 GGAAGAAGTGGTGGTTGT
3996 AGCAGCAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.47, T:0.31
Consensus pattern (18 bp):
GGAAGAAGTGGTGGTTGT
Found at i:5188 original size:12 final size:12
Alignment explanation
Indices: 5167--5206 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5157 GTTGTGGCCG
*
5167 GTTGCCCCATGC
1 GTTGCTCCATGC
*
5179 GTTGCTCCATAC
1 GTTGCTCCATGC
*
5191 GATGCTCCATGC
1 GTTGCTCCATGC
5203 GTTG
1 GTTG
5207 GCCGGTCATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.12, C:0.33, G:0.25, T:0.30
Consensus pattern (12 bp):
GTTGCTCCATGC
Found at i:5229 original size:30 final size:32
Alignment explanation
Indices: 5193--5279 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 32
5183 CTCCATACGA
* *
5193 TGCTCCATGCG-T-TGGCCGGTCATGGCTGGT
1 TGCTCCAAGCGATGTGGCCGGTCATGGCCGGT
5223 TGCTCCAAGCGATGGTGGCCGGTCATGGCCGGT
1 TGCTCCAAGCGAT-GTGGCCGGTCATGGCCGGT
5256 TGCTCCAAGCGATGGTGGCCGGTC
1 TGCTCCAAGCGAT-GTGGCCGGTC
5280 CTCAACTCCT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
30 10 0.19
31 1 0.02
33 41 0.79
ACGTcount: A:0.10, C:0.28, G:0.38, T:0.24
Consensus pattern (32 bp):
TGCTCCAAGCGATGTGGCCGGTCATGGCCGGT
Found at i:5244 original size:33 final size:33
Alignment explanation
Indices: 5205--5279 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
5195 CTCCATGCGT
*
5205 TGGCCGGTCATGGCTGGTTGCTCCAAGCGATGG
1 TGGCCGGTCATGGCCGGTTGCTCCAAGCGATGG
5238 TGGCCGGTCATGGCCGGTTGCTCCAAGCGATGG
1 TGGCCGGTCATGGCCGGTTGCTCCAAGCGATGG
5271 TGGCCGGTC
1 TGGCCGGTC
5280 CTCAACTCCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.11, C:0.27, G:0.40, T:0.23
Consensus pattern (33 bp):
TGGCCGGTCATGGCCGGTTGCTCCAAGCGATGG
Found at i:10784 original size:12 final size:12
Alignment explanation
Indices: 10769--10799 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10759 GGTTGCCCCG
10769 TGCGTTGCTCCA
1 TGCGTTGCTCCA
*
10781 TGCGATGCTCCA
1 TGCGTTGCTCCA
10793 TGCGTTG
1 TGCGTTG
10800 GCCGGTCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.29, G:0.29, T:0.32
Consensus pattern (12 bp):
TGCGTTGCTCCA
Found at i:16485 original size:38 final size:38
Alignment explanation
Indices: 16421--16514 Score: 163
Period size: 38 Copynumber: 2.5 Consensus size: 38
16411 GCATTTCAAT
16421 GCATTTGGTTCTA-TTTTAGTGTTGGTTAAGCTAATTC
1 GCATTTGGTTCTATTTTTAGTGTTGGTTAAGCTAATTC
16458 GCATTTGGTTCTATTTTTAGTGTTGGTTAAGCTAATTC
1 GCATTTGGTTCTATTTTTAGTGTTGGTTAAGCTAATTC
* *
16496 GCATCTGGTTTTATTTTTA
1 GCATTTGGTTCTATTTTTA
16515 TCCTTTTATG
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
37 13 0.24
38 41 0.76
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (38 bp):
GCATTTGGTTCTATTTTTAGTGTTGGTTAAGCTAATTC
Found at i:31128 original size:1 final size:1
Alignment explanation
Indices: 31122--31147 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
31112 GCAAAGGGTG
31122 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
31148 CTTTGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38935 original size:104 final size:106
Alignment explanation
Indices: 38745--38947 Score: 356
Period size: 104 Copynumber: 1.9 Consensus size: 106
38735 TCGAGGTCTA
38745 AAAAACCTGAATTTTGAATTCAAATTTATTCGACCAACAAAAAGAATTCAAACTTAATATATTCA
1 AAAAACCTGAATTTTGAATTCAAATTTA-T--ACCAACAAAAAGAATTCAAACTTAATATATTCA
*
38810 ATAATTCTAGTATTAGAAAGTATAAATTATTAATTTACCATGTC
63 ATAATTCTAGTATTAGAAAGTATAAATCATTAATTTACCATGTC
38854 AAAAA-CTGAATTTTGAATTCAAATTTA-ACCAACAAAAAGAATTCAAACTTAATATATTCAATA
1 AAAAACCTGAATTTTGAATTCAAATTTATACCAACAAAAAGAATTCAAACTTAATATATTCAATA
38917 ATTCTAGTATTAGAAAGTATAAATCATTAAT
66 ATTCTAGTATTAGAAAGTATAAATCATTAAT
38948 AATTTACCAT
Statistics
Matches: 93, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
104 66 0.71
108 22 0.24
109 5 0.05
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (106 bp):
AAAAACCTGAATTTTGAATTCAAATTTATACCAACAAAAAGAATTCAAACTTAATATATTCAATA
ATTCTAGTATTAGAAAGTATAAATCATTAATTTACCATGTC
Found at i:39332 original size:11 final size:11
Alignment explanation
Indices: 39308--39342 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
39298 TTGACAACGT
39308 AACAAAAACAA
1 AACAAAAACAA
* *
39319 AACGAAAACGA
1 AACAAAAACAA
39330 AACAAAAACAA
1 AACAAAAACAA
39341 AA
1 AA
39343 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:39699 original size:16 final size:16
Alignment explanation
Indices: 39678--39710 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39668 AAAACTCTGG
39678 CAAAAA-AGAAAATCAT
1 CAAAAAGAGAAAA-CAT
39694 CAAAAAGAGAAAACAT
1 CAAAAAGAGAAAACAT
39710 C
1 C
39711 TTTTATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.15, G:0.09, T:0.09
Consensus pattern (16 bp):
CAAAAAGAGAAAACAT
Found at i:40882 original size:2 final size:2
Alignment explanation
Indices: 40875--40908 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40865 CCTTTTACTG
40875 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
40909 ACACGTGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50060 original size:20 final size:21
Alignment explanation
Indices: 50035--50076 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
50025 AAATGGGATC
50035 AGTCAG-AAAAGTAAAAAGGT
1 AGTCAGCAAAAGTAAAAAGGT
*
50055 AGTCAGCAAAAGTAAAATGGT
1 AGTCAGCAAAAGTAAAAAGGT
50076 A
1 A
50077 AAAAAGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (21 bp):
AGTCAGCAAAAGTAAAAAGGT
Found at i:50179 original size:54 final size:58
Alignment explanation
Indices: 50070--50180 Score: 133
Period size: 54 Copynumber: 1.9 Consensus size: 58
50060 GCAAAAGTAA
* *
50070 AATGGTAAAAAAGTAAAGAGTAAAGTGATAATCAGAGTGATTAGAAAAGAGTAAAATATT
1 AATGGTAAAAAAGTAAAGAGTAAAG-GATAA-CAGAGAGATCAGAAAAGAGTAAAATATT
*
50130 AATGGT-AAAGAGTAAAGAGTAAA-G-TAA-AGAGAGATCAGTAAAA-AGTAAAAT
1 AATGGTAAAAAAGTAAAGAGTAAAGGATAACAGAGAGATCAG-AAAAGAGTAAAAT
50181 GGTAAAGAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
54 17 0.36
55 4 0.09
56 3 0.06
57 1 0.02
59 16 0.34
60 6 0.13
ACGTcount: A:0.55, C:0.02, G:0.23, T:0.21
Consensus pattern (58 bp):
AATGGTAAAAAAGTAAAGAGTAAAGGATAACAGAGAGATCAGAAAAGAGTAAAATATT
Found at i:50323 original size:22 final size:21
Alignment explanation
Indices: 50163--50402 Score: 217
Period size: 22 Copynumber: 11.3 Consensus size: 21
50153 GTAAAGAGAG
50163 ATCAGTAAAAAGTAAAATGGTA
1 ATCAGTAAAAAGTAAAA-GGTA
** *
50185 AAGAGT--AAAGTAAAAAGTA
1 ATCAGTAAAAAGTAAAAGGTA
50204 ATCAGTAAAGAA--AAAATGGTA
1 ATCAGTAAA-AAGTAAAA-GGTA
* * *
50225 ATTAGTAAAGAGTAATA-GTA
1 ATCAGTAAAAAGTAAAAGGTA
* *
50245 ATCAGTAAGAAGT-AATGGTA
1 ATCAGTAAAAAGTAAAAGGTA
50265 ATCAGTTAGAAAAGTAAAAGGTA
1 ATCAG-TA-AAAAGTAAAAGGTA
*
50288 ATCAGTGAAAAGTAAAATGGTA
1 ATCAGTAAAAAGTAAAA-GGTA
*
50310 ATTAG-AAAAGAGTAAAAAGGTA
1 ATCAGTAAAA-AGT-AAAAGGTA
50332 ATCAGTAAAAAGTAAAATGGTA
1 ATCAGTAAAAAGTAAAA-GGTA
*
50354 ATTAGTAAAAAGTAAAAGAGTA
1 ATCAGTAAAAAGTAAAAG-GTA
*
50376 ATCAGTAAAGAGT-AAAGAGTA
1 ATCAGTAAAAAGTAAAAG-GTA
50397 ATCAGT
1 ATCAGT
50403 GAGGAAAAAA
Statistics
Matches: 179, Mismatches: 23, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
19 8 0.04
20 35 0.20
21 46 0.26
22 71 0.40
23 19 0.11
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCAGTAAAAAGTAAAAGGTA
Found at i:50345 original size:7 final size:7
Alignment explanation
Indices: 50274--50397 Score: 52
Period size: 7 Copynumber: 17.1 Consensus size: 7
50264 AATCAGTTAG
50274 AAAAGTA
1 AAAAGTA
*
50281 AAAGGTA
1 AAAAGTA
** *
50288 ATCAGTG
1 AAAAGTA
50295 AAAAGTA
1 AAAAGTA
*
50302 AAATGGTA
1 AAA-AGTA
**
50310 ATTAG-A
1 AAAAGTA
50316 AAAGAGTA
1 AAA-AGTA
50324 AAAAGGTA
1 AAAA-GTA
**
50332 ATCAGTA
1 AAAAGTA
50339 AAAAGTA
1 AAAAGTA
*
50346 AAATGGTA
1 AAA-AGTA
**
50354 ATTAGTA
1 AAAAGTA
50361 AAAAGTA
1 AAAAGTA
50368 AAAGAGTA
1 AAA-AGTA
**
50376 ATCAGTA
1 AAAAGTA
*
50383 AAGAGTA
1 AAAAGTA
*
50390 AAGAGTA
1 AAAAGTA
50397 A
1 A
50398 TCAGTGAGGA
Statistics
Matches: 83, Mismatches: 28, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
6 2 0.02
7 59 0.71
8 22 0.27
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.20
Consensus pattern (7 bp):
AAAAGTA
Found at i:50434 original size:7 final size:7
Alignment explanation
Indices: 50357--50579 Score: 109
Period size: 7 Copynumber: 31.9 Consensus size: 7
50347 AATGGTAATT
*
50357 AGTAAAA
1 AGTAAAG
50364 AGTAAAAG
1 AGT-AAAG
**
50372 AGTAATC
1 AGTAAAG
50379 AGTAAAG
1 AGTAAAG
50386 AGTAAAG
1 AGTAAAG
**
50393 AGTAATC
1 AGTAAAG
* *
50400 AGTGAGG
1 AGTAAAG
** *
50407 AAAAAAT
1 AGTAAAG
50414 AGTAAAG
1 AGTAAAG
50421 A-TAAAG
1 AGTAAAG
50427 AGTAAAG
1 AGTAAAG
50434 AGTAAAG
1 AGTAAAG
50441 AGTAAAG
1 AGTAAAG
**
50448 AGTAATC
1 AGTAAAG
50455 AGTAAAG
1 AGTAAAG
**
50462 AAAAAATG
1 AGTAAA-G
*
50470 -GCAAAG
1 AGTAAAG
50476 AGTAAAG
1 AGTAAAG
**
50483 AGTAATT
1 AGTAAAG
50490 AGTAAAG
1 AGTAAAG
* *
50497 A-AAAAT
1 AGTAAAG
*
50503 AGTAAGG
1 AGTAAAG
*
50510 AGTGAAG
1 AGTAAAG
**
50517 AGTAATC
1 AGTAAAG
50524 AGTAAA-
1 AGTAAAG
50530 ATGGTAAAG
1 A--GTAAAG
50539 -GATAAAG
1 AG-TAAAG
**
50546 AGTAATC
1 AGTAAAG
50553 AGTAAAG
1 AGTAAAG
50560 AAG-AAAG
1 -AGTAAAG
50567 -GTTAAAG
1 AG-TAAAG
50574 AGTAAA
1 AGTAAA
50580 ATATTAAGCA
Statistics
Matches: 156, Mismatches: 46, Indels: 28
0.68 0.20 0.12
Matches are distributed among these distances:
5 1 0.01
6 13 0.08
7 126 0.81
8 16 0.10
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:50458 original size:21 final size:20
Alignment explanation
Indices: 50115--50560 Score: 119
Period size: 22 Copynumber: 22.2 Consensus size: 20
50105 AGTGATTAGA
* * *
50115 AAAGAGTAAAATATTAATGGT
1 AAAGAGT-AAAGAGTAATAGT
50136 AAAGAGTAAAGAGTAA-AGT
1 AAAGAGTAAAGAGTAATAGT
** *
50155 AAAGAG-AGATCAGTAAAAAGT
1 AAAGAGTA-AAGAGT-AATAGT
50176 AAA-ATGGTAAAGAGTAA-AGT
1 AAAGA--GTAAAGAGTAATAGT
* **
50196 AAAAAGTAATCAGTAA-AG-
1 AAAGAGTAAAGAGTAATAGT
*
50214 AAA-A--AATG-GTAATTAGT
1 AAAGAGTAAAGAGTAA-TAGT
*
50231 AAAGAGT-AATAGTAATCAGT
1 AAAGAGTAAAGAGTAAT-AGT
*
50251 -AAGAAGTAATG-GTAATCAGTT
1 AAAG-AGTAAAGAGTAAT-AG-T
*
50272 AGAAAAGTAAA-AGGTAATCAGT
1 A-AAGAGTAAAGA-GTAAT-AGT
*
50294 GAAA-AGTAAA-ATGGTAATTAGA
1 -AAAGAGTAAAGA--GTAA-TAGT
*
50316 AAAGAGTAAAAAGGTAATCAGT
1 AAAGAGTAAAGA-GTAAT-AGT
*
50338 AAAAAGTAAA-ATGGTAATTAGT
1 AAAGAGTAAAGA--GTAA-TAGT
*
50360 AAAAAGTAAAAGAGTAATCAGT
1 AAAGAGT-AAAGAGTAAT-AGT
50382 AAAGAGTAAAGAGTAATCAGT
1 AAAGAGTAAAGAGTAAT-AGT
*
50403 ---GAGGAAA-A--AATAGT
1 AAAGAGTAAAGAGTAATAGT
*
50417 AAAGA-TAAAGAGTAAAGAGT
1 AAAGAGTAAAGAGT-AATAGT
50437 AAAGAGTAAAGAGTAATCAGT
1 AAAGAGTAAAGAGTAAT-AGT
* *
50458 -AA-AG-AAA-A--AATGGC
1 AAAGAGTAAAGAGTAATAGT
50472 AAAGAGTAAAGAGTAATTAGT
1 AAAGAGTAAAGAGTAA-TAGT
* * *
50493 AAAGA-AAAATAGTAAGGAGT
1 AAAGAGTAAAGAGTAA-TAGT
* ** *
50513 GAAGAGTAATCAGTAAAATGGT
1 AAAGAGTAAAGAGT--AATAGT
50535 AAAG-GATAAAGAGTAATCAGT
1 AAAGAG-TAAAGAGTAAT-AGT
50556 AAAGA
1 AAAGA
50561 AGAAAGGTTA
Statistics
Matches: 328, Mismatches: 42, Indels: 109
0.68 0.09 0.23
Matches are distributed among these distances:
14 8 0.02
15 11 0.03
16 7 0.02
17 12 0.04
18 15 0.05
19 30 0.09
20 68 0.21
21 75 0.23
22 81 0.25
23 20 0.06
24 1 0.00
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.20
Consensus pattern (20 bp):
AAAGAGTAAAGAGTAATAGT
Found at i:50476 original size:35 final size:34
Alignment explanation
Indices: 50437--50529 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
50427 AGTAAAGAGT
*
50437 AAAGAGTAAAGAGTAATCAGTAAAGAAAAAATGGC
1 AAAGAGTAAAGAGTAATCAGTAAAG-AAAAATAGC
* *
50472 AAAGAGTAAAGAGTAATTAGTAAAGAAAAATAGT
1 AAAGAGTAAAGAGTAATCAGTAAAGAAAAATAGC
* *
50506 AAGGAGTGAAGAGTAATCAGTAAA
1 AAAGAGTAAAGAGTAATCAGTAAA
50530 ATGGTAAAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 28 0.54
35 24 0.46
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (34 bp):
AAAGAGTAAAGAGTAATCAGTAAAGAAAAATAGC
Found at i:50507 original size:55 final size:55
Alignment explanation
Indices: 50368--50497 Score: 188
Period size: 55 Copynumber: 2.3 Consensus size: 55
50358 GTAAAAAGTA
* * *
50368 AAAGAGTAATCAGTAAAGAGTAAAGAGTAATCAGTGAGGAAAAAATAGTAAAGAT
1 AAAGAGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAGAAAAAATAGCAAAGAT
** *
50423 AAAGAGTAAAGAGTAAAGAGTAAAGAGTAATCAGTAAAGAAAAAATGGCAAAGAGT
1 AAAGAGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAGAAAAAATAGCAAAGA-T
*
50479 AAAGAGTAATTAGTAAAGA
1 AAAGAGTAATCAGTAAAGA
50498 AAAATAGTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
55 48 0.73
56 18 0.27
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (55 bp):
AAAGAGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAGAAAAAATAGCAAAGAT
Found at i:50536 original size:29 final size:29
Alignment explanation
Indices: 50498--50578 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
50488 TTAGTAAAGA
*
50498 AAAATAGT-AAGGAGTGAAGAGTAATCAGT
1 AAAATAGTAAAGGA-TAAAGAGTAATCAGT
*
50527 AAAATGGTAAAGGATAAAGAGTAATCAGT
1 AAAATAGTAAAGGATAAAGAGTAATCAGT
*
50556 AAAGA-AG-AAAGGTTAAAGAGTAA
1 AAA-ATAGTAAAGGATAAAGAGTAA
50579 AATATTAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 15 0.33
29 25 0.54
30 6 0.13
ACGTcount: A:0.53, C:0.02, G:0.26, T:0.19
Consensus pattern (29 bp):
AAAATAGTAAAGGATAAAGAGTAATCAGT
Found at i:53684 original size:31 final size:31
Alignment explanation
Indices: 53646--53711 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
53636 CAAGTATAAC
*
53646 CTCCATTCGATTTCTTCATATTGGTGAAAAG
1 CTCCATTCGATTTCTTCATATCGGTGAAAAG
53677 CTCCATTCGATTTCTTCATATCGGTGAAAAG
1 CTCCATTCGATTTCTTCATATCGGTGAAAAG
53708 CTCC
1 CTCC
53712 TTTTTCTCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (31 bp):
CTCCATTCGATTTCTTCATATCGGTGAAAAG
Found at i:56696 original size:71 final size:71
Alignment explanation
Indices: 56580--56714 Score: 261
Period size: 71 Copynumber: 1.9 Consensus size: 71
56570 TCCATGGCGT
*
56580 TGCTTAATTCTGCAAATCTCCTTCCTTATGCTTGATGCTTTGTGTGCAGGAAAGTACTTTTCCAA
1 TGCTTAATTCCGCAAATCTCCTTCCTTATGCTTGATGCTTTGTGTGCAGGAAAGTACTTTTCCAA
56645 GAACTG
66 GAACTG
56651 TGCTTAATTCCGCAAATCTCCTTCCTTATGCTTGATGCTTTGTGTGCAGGAAAGTACTTTTCCA
1 TGCTTAATTCCGCAAATCTCCTTCCTTATGCTTGATGCTTTGTGTGCAGGAAAGTACTTTTCCA
56715 CCAACTGTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (71 bp):
TGCTTAATTCCGCAAATCTCCTTCCTTATGCTTGATGCTTTGTGTGCAGGAAAGTACTTTTCCAA
GAACTG
Found at i:57608 original size:34 final size:33
Alignment explanation
Indices: 57570--57639 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 33
57560 AAAATAGCAA
* * *
57570 TTTTTTTT-T-GAAAAATCGGAAAAAGGAAAAAC
1 TTTTTTTTATAGAAAAAACAGAAAAA-CAAAAAC
57602 TTTTTTTTATAGAAAAAACAGAAAAACAAAAAC
1 TTTTTTTTATAGAAAAAACAGAAAAACAAAAAC
57635 TTTTT
1 TTTTT
57640 AGAGCAGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 8 0.24
33 12 0.36
34 13 0.39
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (33 bp):
TTTTTTTTATAGAAAAAACAGAAAAACAAAAAC
Found at i:67911 original size:20 final size:21
Alignment explanation
Indices: 67886--67927 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
67876 AAATGAGATC
67886 AGTCAG-AAAAGTAAAAAGGT
1 AGTCAGCAAAAGTAAAAAGGT
*
67906 AGTCAGCAAAAGTAAAATGGT
1 AGTCAGCAAAAGTAAAAAGGT
67927 A
1 A
67928 AAAAAGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (21 bp):
AGTCAGCAAAAGTAAAAAGGT
Found at i:68164 original size:22 final size:22
Alignment explanation
Indices: 68010--68235 Score: 152
Period size: 22 Copynumber: 10.6 Consensus size: 22
68000 AAAAGAGACC
* **
68010 AGTAAAAAGTAAAATGGTAAAG
1 AGTAAAAAGTAAAAAGGTAATT
*
68032 AGT--AAAGTAAAAA-GTAATC
1 AGTAAAAAGTAAAAAGGTAATT
*
68051 AGT--AAAG-AAAAAGTGGTAATC
1 AGTAAAAAGTAAAAA--GGTAATT
* * *
68072 AGTAAAGAGT-AATA-GTAATC
1 AGTAAAAAGTAAAAAGGTAATT
* * *
68092 AGTAAGAAGT--AATGGTAATC
1 AGTAAAAAGTAAAAAGGTAATT
*
68112 AGTCAGAAAAGT-AAAAGGTAATC
1 AGT-A-AAAAGTAAAAAGGTAATT
* **
68135 AGTGAAAAGTAAATTGGTAATT
1 AGTAAAAAGTAAAAAGGTAATT
* *
68157 AGAAAAAAGTAAAAAGGTAATC
1 AGTAAAAAGTAAAAAGGTAATT
*
68179 AGTAAAAAGTAAAATGGTAATT
1 AGTAAAAAGTAAAAAGGTAATT
68201 AGTAAAAAGT-AAAAGAGTAATT
1 AGTAAAAAGTAAAAAG-GTAATT
*
68223 AGTAAAGAGTAAA
1 AGTAAAAAGTAAA
68236 GAGTAATCAG
Statistics
Matches: 166, Mismatches: 25, Indels: 25
0.77 0.12 0.12
Matches are distributed among these distances:
18 5 0.03
19 12 0.07
20 32 0.19
21 20 0.12
22 77 0.46
23 20 0.12
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.22
Consensus pattern (22 bp):
AGTAAAAAGTAAAAAGGTAATT
Found at i:68170 original size:7 final size:7
Alignment explanation
Indices: 68160--68241 Score: 56
Period size: 7 Copynumber: 11.3 Consensus size: 7
68150 GGTAATTAGA
68160 AAAAAGT
1 AAAAAGT
68167 AAAAAGGT
1 AAAAA-GT
**
68175 AATCAGT
1 AAAAAGT
68182 AAAAAGT
1 AAAAAGT
*
68189 AAAATGGT
1 AAAA-AGT
**
68197 AATTAGT
1 AAAAAGT
68204 AAAAAGT
1 AAAAAGT
68211 AAAAGAGT
1 AAAA-AGT
**
68219 AATTAGT
1 AAAAAGT
*
68226 AAAGAGT
1 AAAAAGT
*
68233 AAAGAGT
1 AAAAAGT
68240 AA
1 AA
68242 TCAGTGAAGA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
7 44 0.76
8 14 0.24
ACGTcount: A:0.59, C:0.01, G:0.20, T:0.21
Consensus pattern (7 bp):
AAAAAGT
Found at i:68187 original size:44 final size:43
Alignment explanation
Indices: 68009--68235 Score: 216
Period size: 44 Copynumber: 5.3 Consensus size: 43
67999 AAAAAGAGAC
** *
68009 CAGTAAAAAGTAAAATGGTAA--AGAGTAAAGTAAAAAGTAAT
1 CAGTAAAAAGTAAAATGGTAATCAGAAAAAAGTAAAAGGTAAT
* * * *
68050 CAGTAAAGAA--AAAGTGGTAATCAGTAAAGAGTAATA-GTAAT
1 CAGTAAA-AAGTAAAATGGTAATCAGAAAAAAGTAAAAGGTAAT
* *
68091 CAGTAAGAAGT--AATGGTAATCAGTCAGAAAAGTAAAAGGTAAT
1 CAGTAAAAAGTAAAATGGTAATCAG--AAAAAAGTAAAAGGTAAT
* * *
68134 CAGTGAAAAGTAAATTGGTAATTAGAAAAAAGTAAAAAGGTAAT
1 CAGTAAAAAGTAAAATGGTAATCAGAAAAAAGT-AAAAGGTAAT
* *
68178 CAGTAAAAAGTAAAATGGTAATTAGTAAAAAGTAAAAGAGTAAT
1 CAGTAAAAAGTAAAATGGTAATCAGAAAAAAGTAAAAG-GTAAT
* *
68222 TAGTAAAGAGTAAA
1 CAGTAAAAAGTAAA
68236 GAGTAATCAG
Statistics
Matches: 152, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
40 22 0.14
41 18 0.12
42 19 0.12
43 26 0.17
44 57 0.38
45 10 0.07
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.22
Consensus pattern (43 bp):
CAGTAAAAAGTAAAATGGTAATCAGAAAAAAGTAAAAGGTAAT
Found at i:68198 original size:15 final size:14
Alignment explanation
Indices: 68160--68241 Score: 56
Period size: 15 Copynumber: 5.6 Consensus size: 14
68150 GGTAATTAGA
68160 AAAAAGTAAAAAGGT
1 AAAAAGTAAAAA-GT
**
68175 AATCAGTAAAAAGT
1 AAAAAGTAAAAAGT
* **
68189 AAAATGGTAATTAGT
1 AAAA-AGTAAAAAGT
68204 AAAAAGTAAAAGAGT
1 AAAAAGTAAAA-AGT
** *
68219 AATTAGTAAAGAGT
1 AAAAAGTAAAAAGT
*
68233 AAAGAGTAA
1 AAAAAGTAA
68242 TCAGTGAAGA
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
14 18 0.36
15 32 0.64
ACGTcount: A:0.59, C:0.01, G:0.20, T:0.21
Consensus pattern (14 bp):
AAAAAGTAAAAAGT
Found at i:68251 original size:21 final size:21
Alignment explanation
Indices: 68037--68398 Score: 166
Period size: 22 Copynumber: 17.0 Consensus size: 21
68027 TAAAGAGTAA
*
68037 AGTAAAAAGTAATCAGTAAAG
1 AGTAAAGAGTAATCAGTAAAG
* *
68058 A-AAAAGTGGTAATCAGTAAAG
1 AGTAAAG-AGTAATCAGTAAAG
*
68079 AGT-AATAGTAATCAGT-AAG
1 AGTAAAGAGTAATCAGTAAAG
* *
68098 AAGTAATG-GTAATCAGTCAGAAA
1 -AGTAAAGAGTAATCAGT-A-AAG
68121 AGTAAA-AGGTAATCAGTGAAA-
1 AGTAAAGA-GTAATCAGT-AAAG
* * *
68142 AGTAAATTG-GTAATTAGAAAAA
1 AGTAAA--GAGTAATCAGTAAAG
* *
68164 AGTAAAAAGGTAATCAGTAAAA
1 AGTAAAGA-GTAATCAGTAAAG
* *
68186 AGTAAA-ATGGTAATTAGTAAAA
1 AGTAAAGA--GTAATCAGTAAAG
*
68208 AGTAAAAGAGTAATTAGTAAAG
1 AGT-AAAGAGTAATCAGTAAAG
*
68230 AGTAAAGAGTAATCAGTGAAGAAAAAAT
1 AGTAAAGAGTAATCAGT-------AAAG
68258 AGTAAAGAGTAATCAGTAAAG
1 AGTAAAGAGTAATCAGTAAAG
68279 AGTAAAGAGTAATCAGT-AA-
1 AGTAAAGAGTAATCAGTAAAG
* *
68298 AG-AAA-A--AATGA-CAAAG
1 AGTAAAGAGTAATCAGTAAAG
*
68314 AGTAAAGAGTAATTAGTAAAG
1 AGTAAAGAGTAATCAGTAAAG
* * ** *
68335 A-AAAATAGTAAGGAGTGAAG
1 AGTAAAGAGTAATCAGTAAAG
** *
68355 AGTAATCAGTAAAAT-GGTAAAG
1 AGTAAAGAGT--AATCAGTAAAG
68377 TA-TAAAGAGTAATCAGTAAAG
1 -AGTAAAGAGTAATCAGTAAAG
68398 A
1 A
68399 AGAAATGTTA
Statistics
Matches: 265, Mismatches: 39, Indels: 75
0.70 0.10 0.20
Matches are distributed among these distances:
15 6 0.02
16 2 0.01
17 4 0.02
18 4 0.02
19 5 0.02
20 49 0.18
21 77 0.29
22 79 0.30
23 18 0.07
24 1 0.00
28 20 0.08
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.21
Consensus pattern (21 bp):
AGTAAAGAGTAATCAGTAAAG
Found at i:68276 original size:49 final size:50
Alignment explanation
Indices: 68204--68318 Score: 175
Period size: 49 Copynumber: 2.4 Consensus size: 50
68194 GGTAATTAGT
* *
68204 AAAA-AGTAAAAGAGTAATTAGTAAAGAGTAAAGAGTAATCAGTGAAGAA
1 AAAATAGTAAAAGAGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAGAA
68253 AAAATAGT-AAAGAGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAGAA
1 AAAATAGTAAAAGAGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAGAA
68302 AAAAT-G-ACAAAGAGTAA
1 AAAATAGTA-AAAGAGTAA
68319 AGAGTAATTA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
48 1 0.02
49 57 0.93
50 3 0.05
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.17
Consensus pattern (50 bp):
AAAATAGTAAAAGAGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAGAA
Found at i:68322 original size:7 final size:7
Alignment explanation
Indices: 68201--68398 Score: 89
Period size: 7 Copynumber: 28.1 Consensus size: 7
68191 AATGGTAATT
*
68201 AGTAAAA
1 AGTAAAG
68208 AGTAAAAG
1 AGT-AAAG
**
68216 AGTAATT
1 AGTAAAG
68223 AGTAAAG
1 AGTAAAG
68230 AGTAAAG
1 AGTAAAG
**
68237 AGTAATC
1 AGTAAAG
*
68244 AGTGAAG
1 AGTAAAG
** *
68251 AAAAAAT
1 AGTAAAG
68258 AGTAAAG
1 AGTAAAG
**
68265 AGTAATC
1 AGTAAAG
68272 AGTAAAG
1 AGTAAAG
68279 AGTAAAG
1 AGTAAAG
**
68286 AGTAATC
1 AGTAAAG
68293 AGTAAAG
1 AGTAAAG
**
68300 AAAAAATG
1 AGTAAA-G
*
68308 A-CAAAG
1 AGTAAAG
68314 AGTAAAG
1 AGTAAAG
**
68321 AGTAATT
1 AGTAAAG
68328 AGTAAAG
1 AGTAAAG
* *
68335 A-AAAAT
1 AGTAAAG
*
68341 AGTAAGG
1 AGTAAAG
*
68348 AGTGAAG
1 AGTAAAG
**
68355 AGTAATC
1 AGTAAAG
68362 AGTAAA-
1 AGTAAAG
68368 ATGGTAAAG
1 A--GTAAAG
68377 TA-TAAAG
1 -AGTAAAG
**
68384 AGTAATC
1 AGTAAAG
68391 AGTAAAG
1 AGTAAAG
68398 A
1 A
68399 AGAAATGTTA
Statistics
Matches: 134, Mismatches: 48, Indels: 18
0.67 0.24 0.09
Matches are distributed among these distances:
6 8 0.06
7 112 0.84
8 13 0.10
10 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.22, T:0.19
Consensus pattern (7 bp):
AGTAAAG
Found at i:68374 original size:29 final size:29
Alignment explanation
Indices: 68336--68396 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
68326 TTAGTAAAGA
*
68336 AAAATAGT-AAGGAGTGAAGAGTAATCAGT
1 AAAATAGTAAAGGA-TAAAGAGTAATCAGT
* *
68365 AAAATGGTAAAGTATAAAGAGTAATCAGT
1 AAAATAGTAAAGGATAAAGAGTAATCAGT
68394 AAA
1 AAA
68397 GAAGAAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.21
Consensus pattern (29 bp):
AAAATAGTAAAGGATAAAGAGTAATCAGT
Found at i:68698 original size:16 final size:17
Alignment explanation
Indices: 68668--68700 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
68658 ACAAAAGAAA
*
68668 AAGAAAAAGTCAGTTTT
1 AAGAAAAAATCAGTTTT
68685 AAGAAAAAAT-AGTTTT
1 AAGAAAAAATCAGTTTT
68701 GAAGGCATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.30
Consensus pattern (17 bp):
AAGAAAAAATCAGTTTT
Found at i:86164 original size:46 final size:45
Alignment explanation
Indices: 86110--86237 Score: 137
Period size: 39 Copynumber: 3.0 Consensus size: 45
86100 TTTGGCCCAT
86110 ATAACTTTTGGGCTTTCCTTGTCATTAAAGGATATTAAT-GAATGAA
1 ATAACTTTTGGGCTTTCCTTGTCATTAAAGGAT-TTAATAG-ATGAA
*
86156 ATAACTTTTGGGCTTTTCTTGTCATT----G--TTAATAGATGAA
1 ATAACTTTTGGGCTTTCCTTGTCATTAAAGGATTTAATAGATGAA
* * *
86195 ATGACTTTTGGGCTTTCCTTGT-AATAAAGGATTTTAATTGATG
1 ATAACTTTTGGGCTTTCCTTGTCATTAAAGGA-TTTAATAGATG
86238 GAACTTAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 17
0.76 0.05 0.19
Matches are distributed among these distances:
38 2 0.03
39 30 0.43
40 1 0.01
42 2 0.03
45 9 0.13
46 25 0.36
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (45 bp):
ATAACTTTTGGGCTTTCCTTGTCATTAAAGGATTTAATAGATGAA
Found at i:88293 original size:25 final size:26
Alignment explanation
Indices: 88263--88311 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
88253 CAAATTGTCC
88263 TTCCTTTCATCTTAA-TTTCTTTTTT
1 TTCCTTTCATCTTAATTTTCTTTTTT
*
88288 TTCCTTTTATCTTAATTTTCTTTT
1 TTCCTTTCATCTTAATTTTCTTTT
88312 GACCAAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (26 bp):
TTCCTTTCATCTTAATTTTCTTTTTT
Found at i:90050 original size:32 final size:32
Alignment explanation
Indices: 90014--90079 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
90004 TTTTAGTTAG
90014 ATATTCTATTTACTTATTTGTTTATGAATATT
1 ATATTCTATTTACTTATTTGTTTATGAATATT
* *
90046 ATATTCTATTTACTTATTTGTTTCTGAGTATT
1 ATATTCTATTTACTTATTTGTTTATGAATATT
90078 AT
1 AT
90080 GAAGAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (32 bp):
ATATTCTATTTACTTATTTGTTTATGAATATT
Found at i:91208 original size:75 final size:76
Alignment explanation
Indices: 91118--91270 Score: 209
Period size: 75 Copynumber: 2.0 Consensus size: 76
91108 GGCTTTTTTT
* * * *
91118 GATTTATGATAGAAAACATAGAGATTAAATAATCGAAATTAGATG-TTGGGAATTATGCATCAAA
1 GATTTATGATAGAAAACAGAGAGATTAAATAATAGAAATTAGATGTTTGGCAATAATGCATCAAA
*
91182 AAGTCATTTAG
66 AAGTCATTGAG
* * * *
91193 GATTTATGCTAGAAAATAGAGAGATTAGATAATAGAAATTAGATGTTTGGCAATAATGTATCAAA
1 GATTTATGATAGAAAACAGAGAGATTAAATAATAGAAATTAGATGTTTGGCAATAATGCATCAAA
*
91258 GAGTCATTGAG
66 AAGTCATTGAG
91269 GA
1 GA
91271 ATGATTGCTC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
75 40 0.60
76 27 0.40
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (76 bp):
GATTTATGATAGAAAACAGAGAGATTAAATAATAGAAATTAGATGTTTGGCAATAATGCATCAAA
AAGTCATTGAG
Found at i:94547 original size:55 final size:53
Alignment explanation
Indices: 94488--94664 Score: 187
Period size: 55 Copynumber: 3.2 Consensus size: 53
94478 AATAGCTTGA
94488 TCCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAAAATTGG
1 TCCTGATGGTGTTG-CTTCAA-TTATCATTCAGATCATCTGGACCAAAAAATTGG
** * * * * *
94543 TCCTGATGGTGTTG--TCAATTAAAAATTACTAAAATCATCGGGACTAATAAATTGA
1 TCCTGATGGTGTTGCTTCAATT-ATCATT-C--AGATCATCTGGACCAAAAAATTGG
*
94598 TCTTGATGGTGTTGTCTTCAATTTATCATTCAGATCATCTGGACCAAAAAATTGG
1 TCCTGATGGTGTTG-CTTCAA-TTATCATTCAGATCATCTGGACCAAAAAATTGG
*
94653 TCCTAATGGTGT
1 TCCTGATGGTGT
94665 AATATTTAAT
Statistics
Matches: 97, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
51 2 0.02
52 8 0.08
53 1 0.01
55 75 0.77
57 1 0.01
58 8 0.08
59 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (53 bp):
TCCTGATGGTGTTGCTTCAATTATCATTCAGATCATCTGGACCAAAAAATTGG
Found at i:101996 original size:18 final size:17
Alignment explanation
Indices: 101973--102008 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
101963 CTCAACCTAA
101973 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
101991 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
102008 A
1 A
102009 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:102485 original size:10 final size:10
Alignment explanation
Indices: 102470--102494 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
102460 TAACTTCAAT
102470 TATGGACTTA
1 TATGGACTTA
102480 TATGGACTTA
1 TATGGACTTA
102490 TATGG
1 TATGG
102495 GCTGAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (10 bp):
TATGGACTTA
Done.