Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019184.1 Corchorus olitorius cultivar O-4 contig19217, 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: 21941
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:1167 original size:11 final size:11
Alignment explanation
Indices: 1151--1175 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1141 AGCTTTTATT
1151 TTCTGTTGGGC
1 TTCTGTTGGGC
1162 TTCTGTTGGGC
1 TTCTGTTGGGC
1173 TTC
1 TTC
1176 GGCTATTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.20, G:0.32, T:0.48
Consensus pattern (11 bp):
TTCTGTTGGGC
Found at i:2016 original size:18 final size:18
Alignment explanation
Indices: 1993--2043 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1983 AAAAATCCTA
1993 AAATAAAAAATAGAATT-C
1 AAATAAAAAA-AGAATTAC
2011 AAATAAAAAAAAGGAATTAC
1 AAAT-AAAAAAA-GAATTAC
2031 AAA-AAAAAAAGAA
1 AAATAAAAAAAGAA
2044 GAGTTTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
19 11 0.37
20 4 0.13
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.14
Consensus pattern (18 bp):
AAATAAAAAAAGAATTAC
Found at i:2021 original size:19 final size:20
Alignment explanation
Indices: 1993--2040 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1983 AAAAATCCTA
*
1993 AAATAAAAAATA-GAATT-C
1 AAATAAAAAAAAGGAATTAC
2011 AAATAAAAAAAAGGAATTAC
1 AAATAAAAAAAAGGAATTAC
2031 AAA-AAAAAAA
1 AAATAAAAAAA
2041 GAAGAGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.41
19 12 0.44
20 4 0.15
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (20 bp):
AAATAAAAAAAAGGAATTAC
Found at i:2022 original size:20 final size:19
Alignment explanation
Indices: 1992--2045 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
1982 CAAAAATCCT
*
1992 AAAATAAAAAATAGAATT-C
1 AAAA-AAAAAAAAGAATTAC
*
2011 AAATAAAAAAAAGGAATTAC
1 AAA-AAAAAAAAAGAATTAC
2031 AAAAAAAAAAGAAGA
1 AAAAAAAAAA-AAGA
2046 GTTTTCAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (19 bp):
AAAAAAAAAAAAGAATTAC
Found at i:7252 original size:14 final size:14
Alignment explanation
Indices: 7233--7260 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7223 AAGAAAAGTG
7233 AATGAAAAAATGAA
1 AATGAAAAAATGAA
7247 AATGAAAAAATGAA
1 AATGAAAAAATGAA
7261 GAGATAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATGAAAAAATGAA
Found at i:8322 original size:153 final size:141
Alignment explanation
Indices: 8179--8675 Score: 703
Period size: 153 Copynumber: 3.4 Consensus size: 141
8169 AGGTCTCAAT
*
8179 TCAGAATTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTTTGATA
1 TCAGAATTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATA
8244 AATCCTCCGGGTATCATTTCATTTCATTAAGTTTTAATCAAAGCTGTGTTTAAAGTTTCAAAATC
66 AATCCTCCGGGTATCATTTCATTTCATTAAGTTTTAATCAAAGCTGTGTTTAAA-TTTC--AAT-
8309 ACAACCTTGCTCAAGGTCTG
127 A-AACCTTGCTCAA-G---G
8329 AATTCAGAATTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTG
1 ---TCAGAATTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTG
*
8394 ATAAATCCTCCGGATATCATTTCATTTCATTAAGTTTTAATCAAAGCTGTGTTTAAATTTCAA-A
63 ATAAATCCTCCGGGTATCATTTCATTTCATTAAGTTTTAATCAAAGCTGTGTTTAAATTTCAATA
8458 AACCTTGCTCAAGG
128 AACCTTGCTCAAGG
* *
8472 TC-GAGTTTGCATTTGTAAGTCCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATA
1 TCAGAATTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATA
* * ** **
8536 AATCCTCCGGGTATCATCTCATTTCATCAAGTTTCTTAATCAAATTTACGTTTAAATTTCAATAA
66 AATCCTCCGGGTATCATTTCATTTCATTAAG-TT-TTAATCAAAGCTGTGTTTAAATTTCAATAA
* *
8601 ACCTCGTTCAAGG
129 ACCTTGCTCAAGG
** * *
8614 TCA-AATTTGCATTTGTAAGACCTCTAGGCACAATTTCAGTAACCTCTGGGTATTAATTCTGA
1 TCAGAATTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGA
8676 CAGGTCCTCC
Statistics
Matches: 321, Mismatches: 19, Indels: 19
0.89 0.05 0.05
Matches are distributed among these distances:
139 88 0.27
140 4 0.01
141 23 0.07
142 68 0.21
143 1 0.00
146 1 0.00
147 12 0.04
148 1 0.00
150 2 0.01
152 4 0.01
153 117 0.36
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (141 bp):
TCAGAATTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATA
AATCCTCCGGGTATCATTTCATTTCATTAAGTTTTAATCAAAGCTGTGTTTAAATTTCAATAAAC
CTTGCTCAAGG
Found at i:8833 original size:40 final size:39
Alignment explanation
Indices: 8789--9446 Score: 548
Period size: 40 Copynumber: 16.7 Consensus size: 39
8779 AGTCAATTTT
* *
8789 AATCCTATTCATGATCATTGCTTTATCAAATTAATTTATA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTA-A
* * *
8829 AATCCTATTCATGATCATTTCTTTATCAAATTAATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTT-AA
* * * *
8869 AATCCTGCTCAGGATCATTGGTTTATCAAATTAA-TCAC
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTAA
* * * *
8907 AATCCTATTCAGAATCATTGCTTTATTCATCAAATTAAATTCAG
1 AATCCTACTCAGGATCATTGC--T-TT-ATCAAATT-AATTTAA
* * *
8951 AATCCTATTCAGGATCATTGCTTTATCAGATTAATTTCAG
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTT-AA
* * * * * *
8991 AATCCTGCTCAGGATCATTGCTTTA-CCAGTCAATAT-C
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTAA
* * * * * *
9028 AATCCCATTCATGATCATTTCTTTATCAAATTAA-TCAC
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTAA
*
9066 ATTCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTT-AA
* *
9106 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCTA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTT-AA
* *
9146 AATCCTGCTCAGGATCATTGCTTAATCAAATTAATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTT-AA
*
9186 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAT
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTT-AA
*
9226 AATCGTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTT-AA
** * * **
9266 AATCCTACTCAAAATCAGTGCTTTACCAAATTAATTTTTTG
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAA--TTTAA
* * * * *
9307 AATCCTATTCAGGATCATTTCTTTATC-AATCAATGT-C
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTAA
* * * * **
9344 CATCCTATTCAGGATCATT-ATTGTATC-AA-TCATTTCGG
1 AATCCTACTCAGGATCATTGCTT-TATCAAATTAATTT-AA
* * ***
9382 AATCCTGCTCAGGATCATTTCTTTATC-AGCCAATTT--
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTAA
* *
9418 AATCCTATTCAGGATCATTTCTTTATCAA
1 AATCCTACTCAGGATCATTGCTTTATCAA
9447 TCAATTTCCA
Statistics
Matches: 516, Mismatches: 82, Indels: 43
0.80 0.13 0.07
Matches are distributed among these distances:
36 30 0.06
37 45 0.09
38 76 0.15
39 18 0.03
40 284 0.55
41 26 0.05
42 12 0.02
43 2 0.00
44 23 0.04
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (39 bp):
AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTAA
Found at i:8888 original size:80 final size:80
Alignment explanation
Indices: 8789--9591 Score: 599
Period size: 80 Copynumber: 10.3 Consensus size: 80
8779 AGTCAATTTT
* * * * *
8789 AATCCTATTCATGATCATTGCTTTATCAAATTAATTTATAAATCCTATTCATGATCATTTCTTTA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTATAAATCCTACTCAGGATCATTGCTTTA
8854 TCAAATTAATTTCAA
66 TCAAATTAATTTCAA
* * * * * *
8869 AATCCTGCTCAGGATCATTGGTTTATCAAATTAA-TCA-CAATCCTATTCAGAATCATTGCTTTA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTATAAATCCTACTCAGGATCATTGC--T-
* *
8932 TTCATCAAATTAAATTCAG
63 TT-ATCAAATTAATTTCAA
* * * *
8951 AATCCTATTCAGGATCATTGCTTTATCAGATTAATTTCA-GAATCCTGCTCAGGATCATTGCTTT
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTT-ATAAATCCTACTCAGGATCATTGCTTT
* * * *
9015 A-CCAGTCAATATC--
65 ATCAAATTAATTTCAA
* * * * * * *
9028 AATCCCATTCATGATCATTTCTTTATCAAATTAA-TCA-CATTCCTACTCAGGATCATTGCTTTA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTATAAATCCTACTCAGGATCATTGCTTTA
9091 TCAAATTAATTTCAA
66 TCAAATTAATTTCAA
* * * *
9106 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCTAAATCCTGCTCAGGATCATTGCTTAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTATAAATCCTACTCAGGATCATTGCTTTA
9171 TCAAATTAATTTCAA
66 TCAAATTAATTTCAA
*
9186 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAT-AATCGTACTCAGGATCATTGCTTT
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTT-ATAAATCCTACTCAGGATCATTGCTTT
9250 ATCAAATTAATTTCAA
65 ATCAAATTAATTTCAA
** * * * * * *
9266 AATCCTACTCAAAATCAGTGCTTTACCAAATTAATTTTTTGAATCCTATTCAGGATCATTTCTTT
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAA-TTTATAAATCCTACTCAGGATCATTGCTTT
* *
9331 ATC-AATCAATGTC--
65 ATCAAATTAATTTCAA
* * * * *** * *
9344 CATCCTATTCAGGATCATT-ATTGTATC-AA-TCATTTCGGAATCCTGCTCAGGATCATTTCTTT
1 AATCCTACTCAGGATCATTGCTT-TATCAAATTAATTTATAAATCCTACTCAGGATCATTGCTTT
***
9406 ATC-AGCCAATTT---
65 ATCAAATTAATTTCAA
* * * ** * *
9418 AATCCTATTCAGGATCATTTCTTTATC-AATCAA-TT-TCCATCCTATTCAGGATCGTTG-TTGT
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTATAAATCCTACTCAGGATCATTGCTT-T
* *
9479 ATC-AA-TCATTTCAG
65 ATCAAATTAATTTCAA
* * * * * * * * * *
9493 AATCCTGCTCAGGATCGTTTCTCTGT--TATTCAA-TTCT-AATCCTATTTAGGATCATTTTCTT
1 AATCCTACTCAGGATCATTGCTTTATCAAATT-AATTTATAAATCCTACTCAGGATCA-TTGCTT
*
9554 TATC-AATCAATTTC--
64 TATCAAATTAATTTCAA
*
9568 AATCCTATTCAGGATCATTGCTTT
1 AATCCTACTCAGGATCATTGCTTT
9592 TCGAATCCTA
Statistics
Matches: 587, Mismatches: 110, Indels: 57
0.78 0.15 0.08
Matches are distributed among these distances:
72 6 0.01
73 20 0.03
74 28 0.05
75 120 0.20
76 20 0.03
77 41 0.07
78 64 0.11
79 10 0.02
80 181 0.31
81 32 0.05
82 45 0.08
83 1 0.00
84 19 0.03
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (80 bp):
AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTATAAATCCTACTCAGGATCATTGCTTTA
TCAAATTAATTTCAA
Found at i:9354 original size:37 final size:37
Alignment explanation
Indices: 8781--9591 Score: 475
Period size: 40 Copynumber: 20.9 Consensus size: 37
8771 TTTTTACCAG
* * *
8781 TCAATTTTAATCCTATTCATGATCATTGCTTTATCAAA
1 TCAATTTCAATCCTATTCAGGATCATTTCTTTATC-AA
* * *
8819 TTAATTTATAAATCCTATTCATGATCATTTCTTTATCAAA
1 TCAA-TT-TCAATCCTATTCAGGATCATTTCTTTATC-AA
* ** **
8859 TTAATTTCAAAATCCTGCTCAGGATCATTGGTTTATCAAA
1 TCAATTTC--AATCCTATTCAGGATCATTTCTTTATC-AA
* ** * *
8899 TTAATCACAATCCTATTCAGAATCATTGCTTTATTC-A
1 TCAATTTCAATCCTATTCAGGATCATTTCTTTA-TCAA
*
8936 TCAAATTAAATTCAGAATCCTATTCAGGATCATTGCTTTATCAGA
1 TC-AA-T---TTC--AATCCTATTCAGGATCATTTCTTTATCA-A
* ** * * *
8981 TTAATTTCAGAATCCTGCTCAGGATCATTGCTTTACCAG
1 TCAATTTC--AATCCTATTCAGGATCATTTCTTTATCAA
* * *
9020 TCAATATCAATCCCATTCATGATCATTTCTTTATCAAA
1 TCAATTTCAATCCTATTCAGGATCATTTCTTTATC-AA
* ** * * *
9058 TTAATCACATTCCTACTCAGGATCATTGCTTTATCAAA
1 TCAATTTCAATCCTATTCAGGATCATTTCTTTATC-AA
* ** *
9096 TTAATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAA
1 TCAATTTC--AATCCTATTCAGGATCATTTCTTTATC-AA
* ** * *
9136 TTAATTTCTAAATCCTGCTCAGGATCATTGCTTAATCAAA
1 TCAATTTC--AATCCTATTCAGGATCATTTCTTTATC-AA
* * *
9176 TTAATTTCAAAATCCTACTCAGGATCATTGCTTTATCAAA
1 TCAATTTC--AATCCTATTCAGGATCATTTCTTTATC-AA
* * * *
9216 TTAATTTCATAATCGTACTCAGGATCATTGCTTTATCAAA
1 TCAATTTC--AATCCTATTCAGGATCATTTCTTTATC-AA
* * ** * * *
9256 TTAATTTCAAAATCCTACTCAAAATCAGTGCTTTACCAAA
1 TCAATTTC--AATCCTATTCAGGATCATTTCTTTATC-AA
* *
9296 TTAATTTTTTGAATCCTATTCAGGATCATTTCTTTATCAA
1 TCAA---TTTCAATCCTATTCAGGATCATTTCTTTATCAA
* * *
9336 TCAATGTCCATCCTATTCAGGATCATTAT-TGTATCAA
1 TCAATTTCAATCCTATTCAGGATCATT-TCTTTATCAA
** *
9373 TC-ATTTCGGAATCCTGCTCAGGATCATTTCTTTATCAG
1 TCAATTTC--AATCCTATTCAGGATCATTTCTTTATCAA
*
9411 CCAATTT-AATCCTATTCAGGATCATTTCTTTATCAA
1 TCAATTTCAATCCTATTCAGGATCATTTCTTTATCAA
* * *
9447 TCAATTTCCATCCTATTCAGGATCGTTGT-TGTATCAA
1 TCAATTTCAATCCTATTCAGGATCATT-TCTTTATCAA
** * * * * *
9484 TC-ATTTCAGAATCCTGCTCAGGATCGTTTCTCTGTTAT
1 TCAATTTC--AATCCTATTCAGGATCATTTCTTTATCAA
*
9522 TCAA-TTCTAATCCTATTTAGGATCATTTTCTTTATCAA
1 TCAATTTC-AATCCTATTCAGGATCA-TTTCTTTATCAA
*
9560 TCAATTTCAATCCTATTCAGGATCATTGCTTT
1 TCAATTTCAATCCTATTCAGGATCATTTCTTT
9592 TCGAATCCTA
Statistics
Matches: 638, Mismatches: 102, Indels: 67
0.79 0.13 0.08
Matches are distributed among these distances:
36 41 0.06
37 99 0.16
38 142 0.22
39 21 0.03
40 279 0.44
41 21 0.03
42 1 0.00
43 6 0.01
44 26 0.04
45 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (37 bp):
TCAATTTCAATCCTATTCAGGATCATTTCTTTATCAA
Found at i:9435 original size:111 final size:112
Alignment explanation
Indices: 9307--9586 Score: 436
Period size: 111 Copynumber: 2.5 Consensus size: 112
9297 TAATTTTTTG
*
9307 AATCCTATTCAGGATCATTTCTTTATCAATCAATGTCCATCCTATTCAGGATCATTATTGTATCA
1 AATCCTATTCAGGATCATTTCTTTATCAATCAATTTCCATCCTATTCAGGATCATTATTGTATCA
* *
9372 ATCATTTCGGAATCCTGCTCAGGATCATTTCTTTATCAGCCAATT-T
66 ATCATTTCAGAATCCTGCTCAGGATCATTTCTCTATCAGCCAATTCT
* *
9418 AATCCTATTCAGGATCATTTCTTTATCAATCAATTTCCATCCTATTCAGGATCGTTGTTGTATCA
1 AATCCTATTCAGGATCATTTCTTTATCAATCAATTTCCATCCTATTCAGGATCATTATTGTATCA
* * * **
9483 ATCATTTCAGAATCCTGCTCAGGATCGTTTCTCTGTTATTCAATTCT
66 ATCATTTCAGAATCCTGCTCAGGATCATTTCTCTATCAGCCAATTCT
* *
9530 AATCCTATTTAGGATCATTTTCTTTATCAATCAATTTCAATCCTATTCAGGATCATT
1 AATCCTATTCAGGATCA-TTTCTTTATCAATCAATTTCCATCCTATTCAGGATCATT
9587 GCTTTTCGAA
Statistics
Matches: 154, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
111 100 0.65
112 17 0.11
113 37 0.24
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (112 bp):
AATCCTATTCAGGATCATTTCTTTATCAATCAATTTCCATCCTATTCAGGATCATTATTGTATCA
ATCATTTCAGAATCCTGCTCAGGATCATTTCTCTATCAGCCAATTCT
Found at i:9602 original size:27 final size:26
Alignment explanation
Indices: 9564--9618 Score: 101
Period size: 27 Copynumber: 2.1 Consensus size: 26
9554 TATCAATCAA
9564 TTTCAATCCTATTCAGGATCATTGCT
1 TTTCAATCCTATTCAGGATCATTGCT
9590 TTTCGAATCCTATTCAGGATCATTGCT
1 TTTC-AATCCTATTCAGGATCATTGCT
9617 TT
1 TT
9619 GTGAGTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (26 bp):
TTTCAATCCTATTCAGGATCATTGCT
Found at i:10900 original size:31 final size:30
Alignment explanation
Indices: 10860--10922 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
10850 AAGGCAAGGT
**
10860 CACTGCACACCAACCCTTGCACACTGCACA
1 CACTGCACACCAACCCTTAAACACTGCACA
10890 CACTGTCACACCAACCCTTAAACACTGCACA
1 CACTG-CACACCAACCCTTAAACACTGCACA
10921 CA
1 CA
10923 ACAAACAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.33, C:0.44, G:0.08, T:0.14
Consensus pattern (30 bp):
CACTGCACACCAACCCTTAAACACTGCACA
Found at i:13189 original size:19 final size:20
Alignment explanation
Indices: 13167--13219 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
13157 AAAAATCCTA
13167 AAATAAAAAAA-AAGAATTC
1 AAATAAAAAAAGAAGAATTC
*
13186 AAATAAAAAAAGAA-ATTTC
1 AAATAAAAAAAGAAGAATTC
13205 AAA-AAAAAAAGAAGA
1 AAATAAAAAAAGAAGA
13220 GTTTTCAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 10 0.32
19 19 0.61
20 2 0.06
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (20 bp):
AAATAAAAAAAGAAGAATTC
Found at i:13193 original size:17 final size:17
Alignment explanation
Indices: 13171--13217 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 17
13161 ATCCTAAAAT
13171 AAAAAAAAAGAA-TTCA
1 AAAAAAAAAGAATTTCA
13187 AATAAAAAAAGAAATTTCA
1 AA-AAAAAAAG-AATTTCA
13206 AAAAAAAAAGAA
1 AAAAAAAAAGAA
13218 GAGTTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.07
17 10 0.36
18 10 0.36
19 6 0.21
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (17 bp):
AAAAAAAAAGAATTTCA
Found at i:13214 original size:21 final size:21
Alignment explanation
Indices: 13166--13228 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
13156 CAAAAATCCT
13166 AAAATAAAAAAAAAG-AA-TTC
1 AAAA-AAAAAAAAAGAAATTTC
*
13186 --AAATAAAAAAAGAAATTTC
1 AAAAAAAAAAAAAGAAATTTC
* **
13205 AAAAAAAAAAGAAGAGTTTTC
1 AAAAAAAAAAAAAGAAATTTC
13226 AAA
1 AAA
13229 CCTAAAAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 9 0.26
18 4 0.12
19 3 0.09
21 18 0.53
ACGTcount: A:0.70, C:0.05, G:0.08, T:0.17
Consensus pattern (21 bp):
AAAAAAAAAAAAAGAAATTTC
Found at i:13215 original size:18 final size:17
Alignment explanation
Indices: 13171--13217 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 17
13161 ATCCTAAAAT
13171 AAAAAAAAAG-AATTCA
1 AAAAAAAAAGAAATTCA
13187 AATAAAAAAAGAAATTTCA
1 AA-AAAAAAAGAAA-TTCA
13206 AAAAAAAAAGAA
1 AAAAAAAAAGAA
13218 GAGTTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.07
17 8 0.29
18 12 0.43
19 6 0.21
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (17 bp):
AAAAAAAAAGAAATTCA
Found at i:17985 original size:132 final size:132
Alignment explanation
Indices: 17767--18294 Score: 616
Period size: 132 Copynumber: 4.0 Consensus size: 132
17757 GAAGTTATAG
* * * *
17767 TCTTTTCGCAACGACTTTTGTTAGTTGTTGTTTAATATATTTTACAAATTGGTTTTTGAAGCGAC
1 TCTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGGTTTTCGCAGCGAC
* * * * *
17832 CTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGATAGATTAAGTCGTTGCGAAATCTT
66 CATGAAAGTCGCTACAAAAAACATAATTACTTTTGAAACGACAAATTAAGTCGCTGCGAAATCTT
17897 AA
131 AA
* * *
17899 ACTTTTCGCAACGACTTTTGTTAGTCGTTACTTCATATATTTTACAAATTGGTTTTCGCAGCGAC
1 TCTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGGTTTTCGCAGCGAC
*
17964 CATGAAAGTCGCTACAAAAAACATAATTACTTTTGAAGAC-ACAAATTAAGTCGCTGCGGAATCT
66 CATGAAAGTCGCTACAAAAAACATAATTACTTTTGAA-ACGACAAATTAAGTCGCTGCGAAATCT
*
18028 TAC
130 TAA
***** * *
18031 TCTTTTCGCAACGACTAACAATAGTCGTTGCTTAATATATTTTACAAATTGGTTTTCCCAACGAC
1 TCTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGGTTTTCGCAGCGAC
* * * * *
18096 CTTGAAAGTCACTACAAAAAACGTAATTACCTTT-AAAGCGACAAATTAAGTCGCTGTGAAATCT
66 CATGAAAGTCGCTACAAAAAACATAATTACTTTTGAAA-CGACAAATTAAGTCGCTGCGAAATCT
*
18160 GAA
130 TAA
* * * * * *
18163 TCTTTTCGCAACGACCTTCTGTTAGTCATTGCTTAATATATTTTCCAAAATGATTTTTGCAGCGA
1 TCTTTTCGCAACGA-CTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGGTTTTCGCAGCGA
* * * * * *
18228 -TATTTAAAGTTGCTACAAAAATA-A-ACATTATTTTTGAAAAGACAAATTAAGTCACTGCGAAA
65 CCA-TGAAAGTCGCTACAAAAA-ACATA-ATTACTTTTGAAACGACAAATTAAGTCGCTGCGAAA
18290 TCTTA
127 TCTTA
18295 TTTTAGTCAC
Statistics
Matches: 332, Mismatches: 56, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
130 1 0.00
131 3 0.01
132 238 0.72
133 86 0.26
134 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (132 bp):
TCTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGGTTTTCGCAGCGAC
CATGAAAGTCGCTACAAAAAACATAATTACTTTTGAAACGACAAATTAAGTCGCTGCGAAATCTT
AA
Found at i:19888 original size:29 final size:27
Alignment explanation
Indices: 19856--19935 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 27
19846 TTAGGATTAC
19856 CTAGGGGCATTTTGGTCATTTTCAAAAAT
1 CTAGGGGCATTTTGGTCATTTT--AAAAT
* * *
19885 CTAGGGGCATTTTAGTCATTTGTATAGT
1 CTAGGGGCATTTTGGTCATTT-TAAAAT
19913 -TAGGGGCATTTTGGTCATTTTAA
1 CTAGGGGCATTTTGGTCATTTTAA
19936 GTCCACACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.04
27 19 0.42
28 3 0.07
29 20 0.44
30 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (27 bp):
CTAGGGGCATTTTGGTCATTTTAAAAT
Done.