Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015760.1 Corchorus olitorius cultivar O-4 contig15793, 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: 59004
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1412 original size:50 final size:49
Alignment explanation
Indices: 1321--1418 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 49
1311 TAGCCAATGG
*
1321 TAAGTACAATCATTTTTTAATTCATTGTGTATATTAAATATGCTCTTGC
1 TAAGTACAATCATTTTTTAATTCATTGTGTAGATTAAATATGCTCTTGC
* * *
1370 TAAGTGCAATCATTTTTTAAATTCATTGTGTAGATTACATATGGTCTTG
1 TAAGTACAATCATTTTTT-AATTCATTGTGTAGATTAAATATGCTCTTG
1419 GAAATGCTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 17 0.39
50 27 0.61
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (49 bp):
TAAGTACAATCATTTTTTAATTCATTGTGTAGATTAAATATGCTCTTGC
Found at i:4570 original size:32 final size:32
Alignment explanation
Indices: 4529--4591 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
4519 ACCATTGAAT
* *
4529 TTCAAGACATTTTA-TCCCATGAACTTTCCAAG
1 TTCAAGACA-TTTAGTCCCATAAACTTCCCAAG
4561 TTCAAGACATTTAGTCCCATAAACTTCCCAA
1 TTCAAGACATTTAGTCCCATAAACTTCCCAA
4592 AGATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (32 bp):
TTCAAGACATTTAGTCCCATAAACTTCCCAAG
Found at i:9625 original size:12 final size:12
Alignment explanation
Indices: 9608--9633 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9598 ATTTTCCCCT
9608 AAAAAAAAAAGA
1 AAAAAAAAAAGA
9620 AAAAAAAAAAGA
1 AAAAAAAAAAGA
9632 AA
1 AA
9634 GAAACCCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:19481 original size:65 final size:65
Alignment explanation
Indices: 19367--19496 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
19357 GGAAAAACTG
* ** * * *
19367 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGATTAGTGCAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGACTAGTGCAGAAAATTGGAATC
* *
19432 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAAATTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGACTAGTGCAGAAAATTGGAATC
19497 AATAGCAAGC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGACTAGTGCAGAAAATTGGAATC
Found at i:23396 original size:17 final size:17
Alignment explanation
Indices: 23370--23404 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
23360 ATTACTATAC
*
23370 AATATGGATGAAATTTT
1 AATATAGATGAAATTTT
23387 AATATAGATGAAATTTT
1 AATATAGATGAAATTTT
23404 A
1 A
23405 TATTCACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (17 bp):
AATATAGATGAAATTTT
Found at i:28410 original size:7 final size:6
Alignment explanation
Indices: 28377--28444 Score: 65
Period size: 5 Copynumber: 11.8 Consensus size: 6
28367 CTCGTTTTGA
* *
28377 GAGCTC GAACTC GA-CTC GAGC-C GAGCTTC GAGCTC GA-CTC GA-CAC
1 GAGCTC GAGCTC GAGCTC GAGCTC GAGC-TC GAGCTC GAGCTC GAGCTC
28422 GAGCTC GAGC-C GAGCTTC GAGCT
1 GAGCTC GAGCTC GAGC-TC GAGCT
28445 ACTCGGTAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
5 24 0.45
6 19 0.36
7 10 0.19
ACGTcount: A:0.21, C:0.34, G:0.29, T:0.16
Consensus pattern (6 bp):
GAGCTC
Found at i:28412 original size:23 final size:22
Alignment explanation
Indices: 28377--28431 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
28367 CTCGTTTTGA
*
28377 GAGCTCGAACTCGACTCGAGC-C
1 GAGCTCGAGCTCGACTCGA-CAC
28399 GAGCTTCGAGCTCGACTCGACAC
1 GAGC-TCGAGCTCGACTCGACAC
28422 GAGCTCGAGC
1 GAGCTCGAGC
28432 CGAGCTTCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.22, C:0.35, G:0.29, T:0.15
Consensus pattern (22 bp):
GAGCTCGAGCTCGACTCGACAC
Found at i:28988 original size:20 final size:20
Alignment explanation
Indices: 28963--29018 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
28953 ATGAATGGTC
28963 GTCGACGGTGAAGGATAAGT
1 GTCGACGGTGAAGGATAAGT
*
28983 GTCGACGGTGAAGGATGAGT
1 GTCGACGGTGAAGGATAAGT
*
29003 GTCTACGGTGAAGGAT
1 GTCGACGGTGAAGGAT
29019 TGGGGTACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.11, G:0.41, T:0.21
Consensus pattern (20 bp):
GTCGACGGTGAAGGATAAGT
Found at i:29373 original size:21 final size:22
Alignment explanation
Indices: 29349--29390 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
29339 TCGAGCTCGG
*
29349 CTCGAAATTT-TTCGAGTCGAA
1 CTCGAAATTTCTTCAAGTCGAA
*
29370 CTCGAATTTTCTTCAAGTCGA
1 CTCGAAATTTCTTCAAGTCGA
29391 GCCCGAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (22 bp):
CTCGAAATTTCTTCAAGTCGAA
Found at i:29573 original size:36 final size:36
Alignment explanation
Indices: 29524--29595 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
29514 TAGGGAAGTA
29524 AACTTTGTACTTCACCCCTCTGGTTGAACTAGTCTC
1 AACTTTGTACTTCACCCCTCTGGTTGAACTAGTCTC
* *
29560 AACTTTGTTCTTCATCCCTCTGGTTGAACTAGTCTC
1 AACTTTGTACTTCACCCCTCTGGTTGAACTAGTCTC
29596 CATGAAAGAC
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:0.18, C:0.29, G:0.14, T:0.39
Consensus pattern (36 bp):
AACTTTGTACTTCACCCCTCTGGTTGAACTAGTCTC
Found at i:29840 original size:53 final size:53
Alignment explanation
Indices: 29758--29859 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 53
29748 ACTATGGGGA
**
29758 TAAAGCTCTTTCAACAATGATTTTCTCCATTCACAAGACTCGAACCCGAAGGG
1 TAAAGCTCTCCCAACAATGATTTTCTCCATTCACAAGACTCGAACCCGAAGGG
* *
29811 TAAAGCTCTCCCAACAATGATTTTGTCCATTCACAAGACTTGAACCCGA
1 TAAAGCTCTCCCAACAATGATTTTCTCCATTCACAAGACTCGAACCCGA
29860 GACCTTACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (53 bp):
TAAAGCTCTCCCAACAATGATTTTCTCCATTCACAAGACTCGAACCCGAAGGG
Found at i:35087 original size:30 final size:30
Alignment explanation
Indices: 35053--35115 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
35043 TACTAGTACT
35053 AAACTAAGTACAAATAT-TCTGCCAAAAAAA
1 AAACTAAGTACAAATATAT-TGCCAAAAAAA
*
35083 AAACTAAGTACTAATATATTGCCAAAAAAA
1 AAACTAAGTACAAATATATTGCCAAAAAAA
35113 AAA
1 AAA
35116 AAAACTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.21
Consensus pattern (30 bp):
AAACTAAGTACAAATATATTGCCAAAAAAA
Found at i:36475 original size:21 final size:22
Alignment explanation
Indices: 36415--36475 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
36405 TCAAATTTTG
36415 ATATT-TTTAAGTATGAAAAGAA
1 ATATTATTTAAGTAT-AAAAGAA
36437 ATATTATTT--GCTCA-AAAAGAA
1 ATATTATTTAAG-T-ATAAAAGAA
36458 ATATTATTTAAGT-TAAAA
1 ATATTATTTAAGTATAAAA
36476 TTTTCTCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
21 21 0.64
22 7 0.21
23 5 0.15
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (22 bp):
ATATTATTTAAGTATAAAAGAA
Found at i:44061 original size:11 final size:11
Alignment explanation
Indices: 44047--44077 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
44037 AATCTACTTA
44047 AATCTTCAGAT
1 AATCTTCAGAT
*
44058 AATCTCCAGAT
1 AATCTTCAGAT
44069 AATCTTCAG
1 AATCTTCAG
44078 TTGAAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (11 bp):
AATCTTCAGAT
Found at i:48872 original size:12 final size:11
Alignment explanation
Indices: 48845--48920 Score: 52
Period size: 12 Copynumber: 6.7 Consensus size: 11
48835 AATCATTTAA
48845 TAATTATATAT
1 TAATTATATAT
48856 T-ATTATATAT
1 TAATTATATAT
48866 GTAATTATATA-
1 -TAATTATATAT
48877 T-ATCTA-ATAT
1 TAAT-TATATAT
*
48887 TATTTTATATAT
1 TA-ATTATATAT
*
48899 ATATAATATATATT
1 -TA-ATTATATA-T
48913 TAATTATA
1 TAATTATA
48921 AATATTACTA
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
9 5 0.10
10 13 0.25
11 4 0.08
12 18 0.35
13 11 0.21
14 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (11 bp):
TAATTATATAT
Found at i:48894 original size:21 final size:22
Alignment explanation
Indices: 48848--48913 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
48838 CATTTAATAA
* * *
48848 TTATATAT-TATTATATATGTAA
1 TTATATATATATAATATATAT-T
*
48870 TTATATATATCTAATAT-TATT
1 TTATATATATATAATATATATT
48891 TTATATATATATAATATATATT
1 TTATATATATATAATATATATT
48913 T
1 T
48914 AATTATAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 16 0.43
22 15 0.41
23 6 0.16
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATATATATATAATATATATT
Found at i:48914 original size:21 final size:20
Alignment explanation
Indices: 48848--48927 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 20
48838 CATTTAATAA
*
48848 TTATATAT-TATTATATATGTAA
1 TTATATATATA-TA-ATAT-TAT
*
48870 TTATATATATCTAATATTATT
1 TTATATATATATAATATTA-T
48891 TTATATATATATAATATATAT
1 TTATATATATATAATAT-TAT
48912 TTA-AT-TATA-AATATTA
1 TTATATATATATAATATTA
48928 CTAAACGATC
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
17 2 0.04
18 5 0.10
19 4 0.08
20 4 0.08
21 24 0.46
22 12 0.23
23 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (20 bp):
TTATATATATATAATATTAT
Found at i:49854 original size:16 final size:17
Alignment explanation
Indices: 49818--49859 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
49808 CTTCTCCAAC
49818 CTTCAACAAACAACAATTT
1 CTTCAACAAACAAC-A-TT
49837 CTTCAACAAACAAC-TT
1 CTTCAACAAACAACATT
49853 CTTCAAC
1 CTTCAAC
49860 CTTGAATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.39
19 14 0.61
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (17 bp):
CTTCAACAAACAACATT
Found at i:49981 original size:40 final size:40
Alignment explanation
Indices: 49935--50011 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
49925 AAGATTTACA
*
49935 AGTTTTAGATCTAGATCTATTGAAATGGTTTGAATTTGAT
1 AGTTTTAGATCTAGATCTATTGAAATAGTTTGAATTTGAT
* *
49975 AGTTTTAGATCTAGATCTGTTGAAATATTTTGAATTT
1 AGTTTTAGATCTAGATCTATTGAAATAGTTTGAATTT
50012 CGGGTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.47
Consensus pattern (40 bp):
AGTTTTAGATCTAGATCTATTGAAATAGTTTGAATTTGAT
Found at i:50076 original size:33 final size:33
Alignment explanation
Indices: 50034--50102 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
50024 GGAGTTGACA
*
50034 GCCACGGCGCTGCCGCCCCAGCTA-GGCGGCGTT
1 GCCACGGCGCTGCCG-CCCAGCTAGGGCGGCATT
50067 GCCACGGCGCTGCCGCCCAGCTAGGGCGGCATT
1 GCCACGGCGCTGCCGCCCAGCTAGGGCGGCATT
50100 GCC
1 GCC
50103 CCTTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.10, C:0.42, G:0.36, T:0.12
Consensus pattern (33 bp):
GCCACGGCGCTGCCGCCCAGCTAGGGCGGCATT
Found at i:52350 original size:18 final size:18
Alignment explanation
Indices: 52320--52365 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
52310 TAAATAAATC
52320 ATTTCTTTGACTTATTAT
1 ATTTCTTTGACTTATTAT
52338 ATTTCCTTT-ACTTATTAT
1 ATTT-CTTTGACTTATTAT
*
52356 GTTTTCTTTG
1 -ATTTCTTTG
52366 TTTCTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.17, C:0.13, G:0.07, T:0.63
Consensus pattern (18 bp):
ATTTCTTTGACTTATTAT
Found at i:53080 original size:14 final size:14
Alignment explanation
Indices: 53061--53087 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53051 TTGTATTCTC
53061 TAATGTACAATATG
1 TAATGTACAATATG
53075 TAATGTACAATAT
1 TAATGTACAATAT
53088 ATAGCACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (14 bp):
TAATGTACAATATG
Found at i:54833 original size:19 final size:19
Alignment explanation
Indices: 54805--54845 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54795 CACCTGCGGA
*
54805 AATAATTAATGAAT-ACATT
1 AATAAATAAT-AATAACATT
54824 AATAAATAATAATAACATT
1 AATAAATAATAATAACATT
54843 AAT
1 AAT
54846 TAATTAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
AATAAATAATAATAACATT
Found at i:56202 original size:14 final size:14
Alignment explanation
Indices: 56183--56209 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56173 CCGCCAAGCA
56183 TGGGCGGCCTAACG
1 TGGGCGGCCTAACG
56197 TGGGCGGCCTAAC
1 TGGGCGGCCTAAC
56210 CAAGGCCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.30, G:0.41, T:0.15
Consensus pattern (14 bp):
TGGGCGGCCTAACG
Found at i:56235 original size:33 final size:33
Alignment explanation
Indices: 56198--56271 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
56188 GGCCTAACGT
* *
56198 GGGCGGCCTAACCAAGGCCATGCCGCCCACCGA
1 GGGCGGCATAACCAAGGCCATACCGCCCACCGA
* * * *
56231 GGGCGGCATTACCATGGCCATACCGCCCTCCTA
1 GGGCGGCATAACCAAGGCCATACCGCCCACCGA
56264 GGGCGGCA
1 GGGCGGCA
56272 CCGAGAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.19, C:0.39, G:0.31, T:0.11
Consensus pattern (33 bp):
GGGCGGCATAACCAAGGCCATACCGCCCACCGA
Found at i:57744 original size:22 final size:22
Alignment explanation
Indices: 57719--57928 Score: 90
Period size: 22 Copynumber: 9.5 Consensus size: 22
57709 TGTATCTGTG
57719 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
57741 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
57764 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
** *
57785 TGGTTGCCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
57808 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
57829 AGGTTACCAAAATTTCA-CAGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
57851 TGGTTACCAAAATTTC-TTAGAA
1 TGGTTATCAAAATTTCATAAG-A
* **
57873 AGGTTATTGAAATTTCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* * * *
57895 TGATTATCACAATTTTATAAAAA
1 TGGTTATCAAAATTTCAT-AAGA
*
57918 AGGTTATCAAA
1 TGGTTATCAAA
57929 GAGATTATCA
Statistics
Matches: 135, Mismatches: 41, Indels: 23
0.68 0.21 0.12
Matches are distributed among these distances:
20 1 0.01
21 4 0.03
22 113 0.84
23 15 0.11
24 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:57789 original size:44 final size:44
Alignment explanation
Indices: 57720--57845 Score: 121
Period size: 44 Copynumber: 2.9 Consensus size: 44
57710 GTATCTGTGT
* ** *
57720 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCAT-ATGGA
* *
57764 GGTTATCAAAATTCCAT-AGTGTGGTTGCCAAAATTTCATATGGA
1 GGTTATCAAAATTCCATAAG-ATGGTTACCAAAATTTCATATGGA
* * ** *
57808 AGTTATCAAAATTTCATGGGAAGGTTACCAAAATTTCA
1 GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCA
57846 CAGTGTGGTT
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
43 3 0.04
44 63 0.94
45 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCATATGGA
Found at i:57879 original size:66 final size:66
Alignment explanation
Indices: 57716--57890 Score: 203
Period size: 66 Copynumber: 2.7 Consensus size: 66
57706 TCTTGTATCT
* * * *
57716 GTGTGGTTATCAAAATTTCATA-AGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAGA-AAGGTTATTAAAATTTCATGAGGAGGTTACCAAAATTCCA
*
57780 TA
65 CA
* * * *
57782 GTGTGGTTGCCAAAATTTCATATGGAA-GTTATCAAAATTTCATG-GGAAGGTTACCAAAATTTC
1 GTGTGGTTACCAAAATTTCATA-GAAAGGTTATTAAAATTTCATGAGG-AGGTTACCAAAATTCC
57845 ACA
64 ACA
* *
57848 GTGTGGTTACCAAAATTTCTTAGAAAGGTTATTGAAATTTCAT
1 GTGTGGTTACCAAAATTTCATAGAAAGGTTATTAAAATTTCAT
57891 AATGTGATTA
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
65 5 0.05
66 85 0.93
67 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAGAAAGGTTATTAAAATTTCATGAGGAGGTTACCAAAATTCCAC
A
Found at i:58045 original size:22 final size:22
Alignment explanation
Indices: 57933--58374 Score: 141
Period size: 22 Copynumber: 20.6 Consensus size: 22
57923 ATCAAAGAGA
* * * *
57933 TTATCAAAATGTCATAGCAAGA
1 TTATCAAAATTTCATAGGATGG
57955 TTAT-AAGAATTTCATAGTG-TGG
1 TTATCAA-AATTTCATAG-GATGG
**
57977 TTAAAAAAATTTCATATGGA-GG
1 TTATCAAAATTTCATA-GGATGG
* *
57999 TTA-CTAATATTTCATTGGGAT-G
1 TTATC-AAAATTTCA-TAGGATGG
*
58021 TTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATAGGATGG
* * *
58043 TTA-CCAAA--T--TAGGAAGC
1 TTATCAAAATTTCATAGGATGG
* * *
58060 TTATTAAACTTTTACTATGGA--G
1 TTATCAAAATTTCA-TA-GGATGG
* *
58082 TAATCAAAATTTCA-GGGA-GG
1 TTATCAAAATTTCATAGGATGG
* * *
58102 ATATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAGGATGG
** *
58124 TTATCAAAATTTCATAGTTTAG
1 TTATCAAAATTTCATAGGATGG
* * *
58146 TTTTCAAATTTTCATAGTAT-G
1 TTATCAAAATTTCATAGGATGG
* *
58167 TAGATCAAAATTTCATAGTAT-G
1 T-TATCAAAATTTCATAGGATGG
* *
58189 TAGATCAAAATTTCATAGGGA-GA
1 T-TATCAAAATTTCATA-GGATGG
* *
58212 TTAACAAAATTTCATAATGA-GG
1 TTATCAAAATTTCAT-AGGATGG
**
58234 TTATCAAAAAATCATAGGGA-GG
1 TTATCAAAATTTCATA-GGATGG
*
58256 TTATCAAAA-TT--T--G-TAG
1 TTATCAAAATTTCATAGGATGG
* *
58272 CTATCAAGATTTCATAAGGA-GG
1 TTATCAAAATTTCAT-AGGATGG
*
58294 TTATCAAAATTTTATAGGGA-GG
1 TTATCAAAATTTCATA-GGATGG
*
58316 TTTATCAAAATTTTATAGCGA-GG
1 -TTATCAAAATTTCATAG-GATGG
* * *
58339 TTATCACAACTTCATAGTG-TGA
1 TTATCAAAATTTCATAG-GATGG
*
58361 CTATCAAAATTTCA
1 TTATCAAAATTTCA
58375 GTGTGTGATA
Statistics
Matches: 317, Mismatches: 66, Indels: 74
0.69 0.14 0.16
Matches are distributed among these distances:
16 9 0.03
17 10 0.03
18 2 0.01
19 6 0.02
20 14 0.04
21 17 0.05
22 225 0.71
23 31 0.10
24 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGATGG
Found at i:58316 original size:82 final size:83
Alignment explanation
Indices: 58192--58344 Score: 200
Period size: 82 Copynumber: 1.9 Consensus size: 83
58182 TAGTATGTAG
* * *
58192 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG-TTATCAAAAAATCATAGGGAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGCGAGG
58256 TTATCAAAATTTGTAGCT
66 TTATCAAAATTTGTAGCT
* * * * * ** *
58274 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGCGAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGCGAGG
58339 TTATCA
66 TTATCA
58345 CAACTTCATA
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
82 35 0.59
83 24 0.41
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (83 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGCGAGG
TTATCAAAATTTGTAGCT
Found at i:58937 original size:39 final size:40
Alignment explanation
Indices: 58881--58961 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
58871 TTAAATTCCT
58881 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
58921 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
58960 AT
1 AT
58962 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.