Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019532.1 Corchorus olitorius cultivar O-4 contig19565, 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: 142361
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:534 original size:45 final size:45
Alignment explanation
Indices: 470--559 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
460 CGGAAGTACA
*
470 ATGGTTTTAGATCAGGGCTTAGTGGCAATAGGTAAACTGTTTGGT
1 ATGGTTTTAGATCAGGGCTTAGTAGCAATAGGTAAACTGTTTGGT
515 ATGGTTTTAGATCAGGGCTTAGTAGCAATAGGTAAACTGTTTGGT
1 ATGGTTTTAGATCAGGGCTTAGTAGCAATAGGTAAACTGTTTGGT
560 TGTGTGTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.36
Consensus pattern (45 bp):
ATGGTTTTAGATCAGGGCTTAGTAGCAATAGGTAAACTGTTTGGT
Found at i:6833 original size:51 final size:51
Alignment explanation
Indices: 6766--6883 Score: 236
Period size: 51 Copynumber: 2.3 Consensus size: 51
6756 TCAGCCTGTC
6766 CTTTCGACTTCTTCTTCTTTGAGCTGGATGATGGACCAGTATCCTGTTCTT
1 CTTTCGACTTCTTCTTCTTTGAGCTGGATGATGGACCAGTATCCTGTTCTT
6817 CTTTCGACTTCTTCTTCTTTGAGCTGGATGATGGACCAGTATCCTGTTCTT
1 CTTTCGACTTCTTCTTCTTTGAGCTGGATGATGGACCAGTATCCTGTTCTT
6868 CTTTCGACTTCTTCTT
1 CTTTCGACTTCTTCTT
6884 TTCATGTTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.45
Consensus pattern (51 bp):
CTTTCGACTTCTTCTTCTTTGAGCTGGATGATGGACCAGTATCCTGTTCTT
Found at i:9726 original size:173 final size:172
Alignment explanation
Indices: 9324--10156 Score: 1378
Period size: 173 Copynumber: 4.8 Consensus size: 172
9314 AGTAACAAAT
* * * *
9324 GACAAATTATTCAAGATTTTATTTTAATTTCGTTTGTTGTAATTCTATATATTATTTACACACGT
1 GACAAATTGTTCAAGATTTTATTTTAATTT-TTTTGTCGTAATTCTATACATTATTTACACACGT
* * *
9389 CTCACATGCAAATGCAAAGAGTAGAAAGTTGACATTATATTTGGTGAACAAAGTTGAATTGTATA
65 CACACATGCAAATGCAAAGAGTAGAAAGTTGACCTTATATTTGGTGAACAAAGTTGAATTATATA
*
9454 ATTTATTATATTGATGAGATAATCATTAAATTTTCATTCATTAAAC
130 A--T-TTATATTGATGAGATAAGCATTAAATTTTCATTCATTAAAC
*
9500 GACAAATTATTCAAGATTTTATTTTAATTTTGTTTGTCGTAATTCTATACATTATTTACACACGT
1 GACAAATTGTTCAAGATTTTATTTTAATTTT-TTTGTCGTAATTCTATACATTATTTACACACGT
9565 CACACATGCAAATGCAAAGAGTAGAAAGTTGACCTTATATTTGGTGAACAAAGTTGAATTATATA
65 CACACATGCAAATGCAAAGAGTAGAAAGTTGACCTTATATTTGGTGAACAAAGTTGAATTATATA
9630 ATTTATATTGATGAGATAAGCATTAAATTTTCATTCATTAAAC
130 ATTTATATTGATGAGATAAGCATTAAATTTTCATTCATTAAAC
*
9673 GACAAATTGTTCAAGATTTTATTTTAATTATTTTTGTCGTAATTCTGTACATTATTTACACACGT
1 GACAAATTGTTCAAGATTTTATTTTAATT-TTTTTGTCGTAATTCTATACATTATTTACACACGT
* * *
9738 CACACATGCAGATGCAAAGAGCAGAAAGTTGACGTTATATTTGGTGAACAAAGTTGAATTATATA
65 CACACATGCAAATGCAAAGAGTAGAAAGTTGACCTTATATTTGGTGAACAAAGTTGAATTATATA
9803 ATTTATATTGATGAGATAAGCATTAAATTTTCATTCATTAAAC
130 ATTTATATTGATGAGATAAGCATTAAATTTTCATTCATTAAAC
*
9846 GACAAATTGTTCAAGATTTTATTTTAATTATTTTTGTCGTAATTCTGTACATTATTTACACACGT
1 GACAAATTGTTCAAGATTTTATTTTAATT-TTTTTGTCGTAATTCTATACATTATTTACACACGT
* *
9911 CACACATGCAGATGCAAAGAGTAGAAAGTTGACCTTATATTTGGTGAACAAAGTTGAATTGTATA
65 CACACATGCAAATGCAAAGAGTAGAAAGTTGACCTTATATTTGGTGAACAAAGTTGAATTATATA
* *
9976 ATTTATATTGATGAGATAAACATTAAATTTTCATTCATTGAAC
130 ATTTATATTGATGAGATAAGCATTAAATTTTCATTCATTAAAC
* * *
10019 GACAAATTGTTCAAGATTTTATTTTAATTTCGTTTGTCGTAATCCTATACATTATTTACACACGC
1 GACAAATTGTTCAAGATTTTATTTTAATTT-TTTTGTCGTAATTCTATACATTATTTACACACGT
* *
10084 CACACATGCAAATGCAAAGAGTAGAAAGTGGACCTTATATTTGGTGAACAAAATTGAATTATATA
65 CACACATGCAAATGCAAAGAGTAGAAAGTTGACCTTATATTTGGTGAACAAAGTTGAATTATATA
*
10149 ATATATAT
130 ATTTATAT
10157 ATATACTATA
Statistics
Matches: 628, Mismatches: 26, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
172 1 0.00
173 500 0.80
174 3 0.00
176 124 0.20
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.39
Consensus pattern (172 bp):
GACAAATTGTTCAAGATTTTATTTTAATTTTTTTGTCGTAATTCTATACATTATTTACACACGTC
ACACATGCAAATGCAAAGAGTAGAAAGTTGACCTTATATTTGGTGAACAAAGTTGAATTATATAA
TTTATATTGATGAGATAAGCATTAAATTTTCATTCATTAAAC
Found at i:10576 original size:223 final size:222
Alignment explanation
Indices: 10180--10587 Score: 642
Period size: 223 Copynumber: 1.8 Consensus size: 222
10170 TATTTTTAGT
* *
10180 TACCAAGGAAATTACTAAAAGGCCAAATTGAGGATTAATATGGTGTCATCTTTTGGCTGTTTTTG
1 TACCAAGGAAATTACTAAAAGGCCAAATTGAGGATTAATACGGTGCCATCTTTTGGCTGTTTTTG
* *
10245 GTCTTTTCTCACTTTTCATATGACTAAAAAGCCCCTCTGTGAGTTTCCCCACTTCCTTTTCCTGC
66 GTCTTTTCTCACTTTTCAAATGACTAAAAAGCCCCTCTATGAGTTTCCCCACTTCCTTTTCCTGC
* *
10310 TACCATTTTTTTTAATTACTCATTTCACTTCCTTAATTGTTTTTAATTAATGTTTCTTCTCCCCC
131 TACCATTTTTTGTAATTACCCATTTCACTTCCTTAATTGTTTTTAATTAATGTTTCTTCTCCCCC
10375 CTTTCTTTTTTCCTCTCACCAACTCAG
196 CTTTCTTTTTTCCTCTCACCAACTCAG
* * * * *
10402 TACCAGGGTAATTACTAAAAGGCCAAATTGAGGATTAATGCGGTGCCA-CATTTTGGTTTTTTTT
1 TACCAAGGAAATTACTAAAAGGCCAAATTGAGGATTAATACGGTGCCATC-TTTTGG---CTGTT
*
10466 TTTTGTCTTTTCTCACTTTTCAAATGACT-AAAAGCCCCTCTATGAGTTTCCCC-CTTCCTTTTC
62 TTTGGTCTTTTCTCACTTTTCAAATGACTAAAAAGCCCCTCTATGAGTTTCCCCACTTCCTTTTC
*
10529 CTGCTACCATTTTTTGTAATTACCCATTTCCCTTCCTTAATTGTTTTTAATTAATGTTT
127 CTGCTACCATTTTTTGTAATTACCCATTTCACTTCCTTAATTGTTTTTAATTAATGTTT
10588 AAGGCTTTTA
Statistics
Matches: 169, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
221 1 0.01
222 49 0.29
223 66 0.39
224 23 0.14
225 30 0.18
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.44
Consensus pattern (222 bp):
TACCAAGGAAATTACTAAAAGGCCAAATTGAGGATTAATACGGTGCCATCTTTTGGCTGTTTTTG
GTCTTTTCTCACTTTTCAAATGACTAAAAAGCCCCTCTATGAGTTTCCCCACTTCCTTTTCCTGC
TACCATTTTTTGTAATTACCCATTTCACTTCCTTAATTGTTTTTAATTAATGTTTCTTCTCCCCC
CTTTCTTTTTTCCTCTCACCAACTCAG
Found at i:16896 original size:5 final size:5
Alignment explanation
Indices: 16886--16910 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
16876 TTTCGCCGCG
16886 GGTCT GGTCT GGTCT GGTCT GGTCT
1 GGTCT GGTCT GGTCT GGTCT GGTCT
16911 ACCACTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
GGTCT
Found at i:17379 original size:35 final size:35
Alignment explanation
Indices: 17333--17403 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
17323 GAATCTTTGT
17333 TTATAAAATTTAGGGTTCGAGTCGTGTGGGTGATC
1 TTATAAAATTTAGGGTTCGAGTCGTGTGGGTGATC
*
17368 TTATAAGATTTAGGGTTCGAGTCGTGTGGGTGATC
1 TTATAAAATTTAGGGTTCGAGTCGTGTGGGTGATC
17403 T
1 T
17404 GTAAGTATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.21, C:0.08, G:0.32, T:0.38
Consensus pattern (35 bp):
TTATAAAATTTAGGGTTCGAGTCGTGTGGGTGATC
Found at i:28239 original size:31 final size:30
Alignment explanation
Indices: 28192--28249 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
28182 TTAATTCCCT
* * *
28192 TTTTGCCTCCTGAACTTGTATGATTTTGACG
1 TTTTGCCCCCTAAACTT-TATAATTTTGACG
28223 TTTTGCCCCCTAAACTTTATAATTTTG
1 TTTTGCCCCCTAAACTTTATAATTTTG
28250 GACATTTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.47
Consensus pattern (30 bp):
TTTTGCCCCCTAAACTTTATAATTTTGACG
Found at i:32032 original size:13 final size:13
Alignment explanation
Indices: 32014--32066 Score: 106
Period size: 13 Copynumber: 4.1 Consensus size: 13
32004 AAACAACTGA
32014 AAAGCACTTCTGG
1 AAAGCACTTCTGG
32027 AAAGCACTTCTGG
1 AAAGCACTTCTGG
32040 AAAGCACTTCTGG
1 AAAGCACTTCTGG
32053 AAAGCACTTCTGG
1 AAAGCACTTCTGG
32066 A
1 A
32067 TTTTCCGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:54271 original size:120 final size:115
Alignment explanation
Indices: 54057--54295 Score: 406
Period size: 120 Copynumber: 2.0 Consensus size: 115
54047 TGGAAAGAAC
54057 TGAACTATTACATATAAGATGACTGTTGCAAATTAAACTGGTTCCATTATGATTTTTTTTTTGGA
1 TGAACTATTACATATAAGATGACTGTTGCAAATTAAACTGGTTCCATTATGATTTTTTTTTTGGA
* *
54122 AGGGAACCAGAAACACTTTTGTTGCATACTTCATGTAACTTGAACCAAAT
66 AGGAAACCAGAAACACTTATGTTGCATACTTCATGTAACTTGAACCAAAT
*
54172 TGAACTATTACATAAGATAAGATGACTGTTGCAAATTAAACTGGTTCCATTATGGTTTTTTTCTT
1 TGAACTATTACAT---ATAAGATGACTGTTGCAAATTAAACTGGTTCCATTAT-GATTTTTT-TT
54237 TTGGAAGGAAACCAGAAACACTTATGTTGCATACTTCATGTAACTTGAACCAAAT
61 TTGGAAGGAAACCAGAAACACTTATGTTGCATACTTCATGTAACTTGAACCAAAT
54292 TGAA
1 TGAA
54296 TAACAAATCT
Statistics
Matches: 116, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
115 13 0.11
118 37 0.32
119 7 0.06
120 59 0.51
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (115 bp):
TGAACTATTACATATAAGATGACTGTTGCAAATTAAACTGGTTCCATTATGATTTTTTTTTTGGA
AGGAAACCAGAAACACTTATGTTGCATACTTCATGTAACTTGAACCAAAT
Found at i:60084 original size:11 final size:12
Alignment explanation
Indices: 60061--60085 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60051 CATTACCCCC
60061 AACCCGAAAAAA
1 AACCCGAAAAAA
60073 AACCCGAAAAAA
1 AACCCGAAAAAA
60085 A
1 A
60086 GGGCTTCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.24, G:0.08, T:0.00
Consensus pattern (12 bp):
AACCCGAAAAAA
Found at i:70906 original size:35 final size:35
Alignment explanation
Indices: 70860--70926 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
70850 TAAGTGGCTC
70860 GTTTCAGTTTAAACAGGTCTTAGGTTCGAGATCTT
1 GTTTCAGTTTAAACAGGTCTTAGGTTCGAGATCTT
70895 GTTTCAGTTTAAACAGGTCTTAGGTTCGAGAT
1 GTTTCAGTTTAAACAGGTCTTAGGTTCGAGAT
70927 TTTATGTACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (35 bp):
GTTTCAGTTTAAACAGGTCTTAGGTTCGAGATCTT
Found at i:74004 original size:17 final size:18
Alignment explanation
Indices: 73971--74004 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
73961 TATTCCCTCC
73971 TTTAAATACACAGGAAAA
1 TTTAAATACACAGGAAAA
*
73989 TTTAGATACA-AGGAAA
1 TTTAAATACACAGGAAA
74005 GAAATCATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.24
Consensus pattern (18 bp):
TTTAAATACACAGGAAAA
Found at i:86523 original size:7 final size:7
Alignment explanation
Indices: 86503--86540 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
86493 CAAATAGAGA
86503 TATATAT
1 TATATAT
86510 ATATATAT
1 -TATATAT
86518 TATATAT
1 TATATAT
86525 TATATAT
1 TATATAT
86532 TACTATAT
1 TA-TATAT
86540 T
1 T
86541 TTAGTGAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (7 bp):
TATATAT
Found at i:104110 original size:16 final size:16
Alignment explanation
Indices: 104089--104122 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
104079 ATTATTCACA
104089 AATATTACATCAGCAG
1 AATATTACATCAGCAG
* *
104105 AATATTACCTCAGTAG
1 AATATTACATCAGCAG
104121 AA
1 AA
104123 CACAATGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (16 bp):
AATATTACATCAGCAG
Found at i:115455 original size:33 final size:32
Alignment explanation
Indices: 115418--115481 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
115408 AAGCATGATT
115418 AATGAATT-ATTAGTAAAA-GAAAAGAATAAAGAG
1 AATGAATTGATTA--AAAAGGAAAAGAA-AAAGAG
*
115451 AATGATTTGATTAAAAAGGAAAAGAAAAAGA
1 AATGAATTGATTAAAAAGGAAAAGAAAAAGA
115482 AAGAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 9 0.32
33 15 0.54
34 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.20
Consensus pattern (32 bp):
AATGAATTGATTAAAAAGGAAAAGAAAAAGAG
Found at i:128427 original size:19 final size:19
Alignment explanation
Indices: 128403--128441 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
128393 AAAGTAACAT
128403 GAAAGA-AAGAGAGAGAAAG
1 GAAAGAGAAGAGA-AGAAAG
128422 GAAAGAGGAAGAGAAGAAAG
1 GAAAGA-GAAGAGAAGAAAG
128442 AATAGATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (19 bp):
GAAAGAGAAGAGAAGAAAG
Found at i:129335 original size:4 final size:4
Alignment explanation
Indices: 129326--129364 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
129316 CCTAAGTGAA
* * *
129326 AAAG AAAG AAAT TAAG AAAA AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
129365 CAGAGGAAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:129362 original size:20 final size:20
Alignment explanation
Indices: 129324--129364 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
129314 CTCCTAAGTG
**
129324 AAAAAGAAAGAAATTAAGAA
1 AAAAAGAAAGAAAGAAAGAA
129344 AAAAAGAAAGAAAGAAAGAA
1 AAAAAGAAAGAAAGAAAGAA
129364 A
1 A
129365 CAGAGGAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (20 bp):
AAAAAGAAAGAAAGAAAGAA
Found at i:130179 original size:5 final size:5
Alignment explanation
Indices: 130169--130204 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
130159 AGAGGGGGGG
*
130169 GAAAA GAAAA GAAAA GAAAA GAAAAA GAAGA GAAAA
1 GAAAA GAAAA GAAAA GAAAA G-AAAA GAAAA GAAAA
130205 CTATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:130196 original size:11 final size:11
Alignment explanation
Indices: 130170--130204 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
130160 GAGGGGGGGG
130170 AAAAGAAAAG-
1 AAAAGAAAAGA
130180 AAAAGAAAAGA
1 AAAAGAAAAGA
*
130191 AAAAGAAGAGA
1 AAAAGAAAAGA
130202 AAA
1 AAA
130205 CTATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:133307 original size:14 final size:14
Alignment explanation
Indices: 133288--133378 Score: 56
Period size: 14 Copynumber: 6.9 Consensus size: 14
133278 AATTCAAAGA
133288 AGTAAAGAGTAATC
1 AGTAAAGAGTAATC
133302 AGTAAA-AG-----
1 AGTAAAGAGTAATC
*
133310 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
133324 AGTAAAAGAGTAAT-
1 AGT-AAAGAGTAATC
* **
133338 AGTAGTA-AGTAAAG
1 AGTA-AAGAGTAATC
133352 AGTAAAGAGTAATC
1 AGTAAAGAGTAATC
133366 AAG-AAAGAGTAAT
1 -AGTAAAGAGTAAT
133379 AATAGTCAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
8 6 0.10
9 1 0.02
13 9 0.15
14 32 0.54
15 11 0.19
ACGTcount: A:0.55, C:0.03, G:0.22, T:0.20
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:133316 original size:7 final size:7
Alignment explanation
Indices: 133283--133363 Score: 51
Period size: 7 Copynumber: 11.3 Consensus size: 7
133273 ATTAAAATTC
133283 AAAGAAGT
1 AAAG-AGT
133291 AAAGAGT
1 AAAGAGT
**
133298 AATCAGT
1 AAAGAGT
133305 AAAAGAGT
1 -AAAGAGT
*
133313 AAAGAAT
1 AAAGAGT
**
133320 AATCAGT
1 AAAGAGT
133327 AAAAGAGT
1 -AAAGAGT
133335 AATAGTAGT
1 AA-AG-AGT
133344 --A-AGT
1 AAAGAGT
133348 AAAGAGT
1 AAAGAGT
133355 AAAGAGT
1 AAAGAGT
133362 AA
1 AA
133364 TCAAGAAAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
4 3 0.05
6 2 0.04
7 32 0.57
8 16 0.29
9 3 0.05
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.19
Consensus pattern (7 bp):
AAAGAGT
Found at i:133350 original size:21 final size:21
Alignment explanation
Indices: 133295--133439 Score: 106
Period size: 21 Copynumber: 7.0 Consensus size: 21
133285 AGAAGTAAAG
*
133295 AGTAATCAGTAAAAGAGTAA-
1 AGTAATAAGTAAAAGAGTAAT
*
133315 AGAATAATCAGTAAAAGAGTAAT
1 AG--TAATAAGTAAAAGAGTAAT
* *
133338 AGTAGTAAGT-AAAGAGTAAAG
1 AGTAATAAGTAAAAGAGT-AAT
133359 AGTAATCAAG--AAAGAGTAAT
1 AGTAAT-AAGTAAAAGAGTAAT
* * * *
133379 AATAGTCAGT-AAAGAGTAAAC
1 AGTAATAAGTAAAAGAGT-AAT
133400 AGTAATCAAG--AAAGAGTAAT
1 AGTAAT-AAGTAAAAGAGTAAT
*
133420 AGTAATCAGTAAAAGAGTAA
1 AGTAATAAGTAAAAGAGTAA
133440 ACAATAAACA
Statistics
Matches: 101, Mismatches: 14, Indels: 19
0.75 0.10 0.14
Matches are distributed among these distances:
19 4 0.04
20 30 0.30
21 42 0.42
22 23 0.23
23 2 0.02
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.20
Consensus pattern (21 bp):
AGTAATAAGTAAAAGAGTAAT
Found at i:133390 original size:41 final size:42
Alignment explanation
Indices: 133295--133440 Score: 199
Period size: 41 Copynumber: 3.5 Consensus size: 42
133285 AGAAGTAAAG
* *
133295 AGTAATCAGTAAAAGAGTAAAGAATAATC-AGTAAAAGAGTAAT
1 AGTAGTCAGTAAAAGAGTAAAGAGTAATCAAG--AAAGAGTAAT
*
133338 AGTAGTAAGT-AAAGAGTAAAGAGTAATCAAGAAAGAGTAAT
1 AGTAGTCAGTAAAAGAGTAAAGAGTAATCAAGAAAGAGTAAT
* *
133379 AATAGTCAGT-AAAGAGTAAACAGTAATCAAGAAAGAGTAAT
1 AGTAGTCAGTAAAAGAGTAAAGAGTAATCAAGAAAGAGTAAT
*
133420 AGTAATCAGTAAAAGAGTAAA
1 AGTAGTCAGTAAAAGAGTAAA
133441 CAATAAACAA
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
41 56 0.60
42 27 0.29
43 10 0.11
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.20
Consensus pattern (42 bp):
AGTAGTCAGTAAAAGAGTAAAGAGTAATCAAGAAAGAGTAAT
Found at i:133535 original size:28 final size:27
Alignment explanation
Indices: 133499--133613 Score: 74
Period size: 25 Copynumber: 3.9 Consensus size: 27
133489 GTCAAAGAGT
*
133499 AAAATTTGGGTTATTAAA-AGATAAAAAG
1 AAAATTT-GGTAATTAAAGAG-TAAAAAG
133527 AAAATTTGGTAATTAAAGAGTAAAAAAGTAAAAAG
1 AAAATTTGGTAATT-AA-AG------AGTAAAAAG
* *
133562 AAGAATTTGGTTAATTAAAGAGTTAAATG
1 AA-AATTTGG-TAATTAAAGAGTAAAAAG
133591 --AATTTGGTAATTAAAGAGTAAAA
1 AAAATTTGGTAATTAAAGAGTAAAA
133614 GAGTAAAAAG
Statistics
Matches: 72, Mismatches: 4, Indels: 25
0.71 0.04 0.25
Matches are distributed among these distances:
25 15 0.21
26 7 0.10
27 6 0.08
28 9 0.12
29 8 0.11
35 11 0.15
36 11 0.15
37 5 0.07
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (27 bp):
AAAATTTGGTAATTAAAGAGTAAAAAG
Found at i:133569 original size:36 final size:37
Alignment explanation
Indices: 133514--133584 Score: 119
Period size: 36 Copynumber: 1.9 Consensus size: 37
133504 TTGGGTTATT
133514 AAAAGATAAAAAGAAAATTTGG-TAATTAAAGAGTAA
1 AAAAGATAAAAAGAAAATTTGGTTAATTAAAGAGTAA
133550 AAAAG-TAAAAAGAAGAATTTGGTTAATTAAAGAGT
1 AAAAGATAAAAAGAA-AATTTGGTTAATTAAAGAGT
133585 TAAATGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 9 0.27
36 12 0.36
37 12 0.36
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (37 bp):
AAAAGATAAAAAGAAAATTTGGTTAATTAAAGAGTAA
Found at i:133579 original size:64 final size:64
Alignment explanation
Indices: 133501--133840 Score: 473
Period size: 64 Copynumber: 5.4 Consensus size: 64
133491 CAAAGAGTAA
*
133501 AATTTGGGTT-ATTAAA-AGATAAAAAGAAAATTTGGTAATTAAAGAGTAAAAAAGTAAAAAGAA
1 AATTT-GGTTAATTAAAGAG-TAAAAAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAA
133564 G
64 G
* *
133565 AATTTGGTTAATTAAAGAGTTAAATG--AATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGGAA-
1 AATTTGGTTAATTAAAGAGTAAAAAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAA-GAAG
* * *
133627 ATTTTGGGTAATTAAA-AGATAAAGAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAG
1 AATTTGGTTAATTAAAGAG-TAAAAAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAG
* *
133691 AATTTGGTTAATTAAAGAGTAAAATG--AATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAA
1 AATTTGGTTAATTAAAGAGTAAAAAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAG
* * *
133753 AATTTGGGTAATTAAA-AGATTAAGAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAG
1 AATTTGGTTAATTAAAGAG-TAAAAAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAG
133817 AATTTGGTTAATTAAAGAGTAAAA
1 AATTTGGTTAATTAAAGAGTAAAA
133841 TGAATTTGGA
Statistics
Matches: 243, Mismatches: 21, Indels: 24
0.84 0.07 0.08
Matches are distributed among these distances:
61 4 0.02
62 103 0.42
63 10 0.04
64 120 0.49
65 6 0.02
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (64 bp):
AATTTGGTTAATTAAAGAGTAAAAAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAG
Found at i:133603 original size:62 final size:62
Alignment explanation
Indices: 133529--133862 Score: 462
Period size: 62 Copynumber: 5.3 Consensus size: 62
133519 ATAAAAAGAA
*
133529 AATTTGGTAATTAAAGAGTAAAAAAGTAAAAAGAAGAATTTGGTTAATTAAAGAGTTAAATG
1 AATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAGAATTTGGTTAATTAAAGAGTTAAATG
* * * *
133591 AATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGGAA-ATTTTGGGTAATTAAA-AGATAAAGAG
1 AATTTGGTAATTAAAGAGTAAAAGAGTAAAAA-GAAGAATTTGGTTAATTAAAGAGTTAAA-TG
*
133653 AAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAGAATTTGGTTAATTAAAGAGTAAAATG
1 --AATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAGAATTTGGTTAATTAAAGAGTTAAATG
* *
133717 AATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAAAATTTGGGTAATTAAA-AGATTAAGA-G
1 AATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAGAATTTGGTTAATTAAAGAG-TTAA-ATG
*
133779 AAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAGAATTTGGTTAATTAAAGAGTAAAATG
1 --AATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAGAATTTGGTTAATTAAAGAGTTAAATG
* *
133843 AATTTGG-AGTAAAAGAGTAA
1 AATTTGGTAATTAAAGAGTAA
133863 TGGGTTAATT
Statistics
Matches: 242, Mismatches: 18, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
61 19 0.08
62 107 0.44
63 8 0.03
64 101 0.42
65 7 0.03
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (62 bp):
AATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAAGAATTTGGTTAATTAAAGAGTTAAATG
Found at i:133633 original size:126 final size:126
Alignment explanation
Indices: 133499--133862 Score: 640
Period size: 126 Copynumber: 2.9 Consensus size: 126
133489 GTCAAAGAGT
* * *
133499 AAAATTTGGGTTATTAAAAGATAAAAAGAAAATTTGGTAATTAAAGAGTAAAAAAGTAAAAAGAA
1 AAAATTTGGGTAATTAAAAGATAAAGAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAA
* *
133564 GAATTTGGTTAATTAAAGAGTTAAATGAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGG
66 GAATTTGGTTAATTAAAGAGTAAAATGAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGA
*
133625 AAATTTTGGGTAATTAAAAGATAAAGAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAA
1 AAAATTTGGGTAATTAAAAGATAAAGAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAA
133690 GAATTTGGTTAATTAAAGAGTAAAATGAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGA
66 GAATTTGGTTAATTAAAGAGTAAAATGAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGA
*
133751 AAAATTTGGGTAATTAAAAGATTAAGAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAA
1 AAAATTTGGGTAATTAAAAGATAAAGAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAA
* *
133816 GAATTTGGTTAATTAAAGAGTAAAATGAATTTGG-AGTAAAAGAGTAA
66 GAATTTGGTTAATTAAAGAGTAAAATGAATTTGGTAATTAAAGAGTAA
133863 TGGGTTAATT
Statistics
Matches: 228, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
125 11 0.05
126 217 0.95
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.27
Consensus pattern (126 bp):
AAAATTTGGGTAATTAAAAGATAAAGAGAAAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGAA
GAATTTGGTTAATTAAAGAGTAAAATGAATTTGGTAATTAAAGAGTAAAAGAGTAAAAAGA
Found at i:133639 original size:37 final size:35
Alignment explanation
Indices: 133578--133714 Score: 125
Period size: 37 Copynumber: 4.1 Consensus size: 35
133568 TTGGTTAATT
* *
133578 AAAGAGTTAAATG-AATTT-GGTAATTAAAGAGTA
1 AAAGAGTAAAAAGAAATTTGGGTAATTAAAGAGTA
133611 AAAGAGTAAAAAGGAAATTTTGGGTAATTAAA-AG-A
1 AAAGAGTAAAAA-GAAA-TTTGGGTAATTAAAGAGTA
133646 TAAAGAG-----A-AAATTT-GGTAATTAAAGAGTA
1 -AAAGAGTAAAAAGAAATTTGGGTAATTAAAGAGTA
*
133675 AAAGAGTAAAAAGAAGAATTTGGTTAATTAAAGAGTA
1 AAAGAGTAAAAAG-A-AATTTGGGTAATTAAAGAGTA
133712 AAA
1 AAA
133715 TGAATTTGGT
Statistics
Matches: 85, Mismatches: 3, Indels: 28
0.73 0.03 0.24
Matches are distributed among these distances:
27 10 0.12
28 11 0.13
29 4 0.05
31 1 0.01
33 11 0.13
34 1 0.01
35 4 0.05
36 16 0.19
37 27 0.32
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (35 bp):
AAAGAGTAAAAAGAAATTTGGGTAATTAAAGAGTA
Found at i:133732 original size:25 final size:26
Alignment explanation
Indices: 133690--133739 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
133680 GTAAAAAGAA
133690 GAATTTGGTTAATTAAAGAGTAAAAT
1 GAATTTGGTTAATTAAAGAGTAAAAT
133716 GAATTTGG-TAATTAAAGAGTAAAA
1 GAATTTGGTTAATTAAAGAGTAAAA
133740 GAGTAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (26 bp):
GAATTTGGTTAATTAAAGAGTAAAAT
Found at i:133932 original size:26 final size:25
Alignment explanation
Indices: 133903--133995 Score: 93
Period size: 27 Copynumber: 3.6 Consensus size: 25
133893 TGAATTTGGA
133903 AAAAGAAATTTGGATAATTAAAGAGT
1 AAAAGAAATTTGG-TAATTAAAGAGT
133929 AAAATG-AA-TTGGTAATTAAA-AGGT
1 AAAA-GAAATTTGGTAATTAAAGA-GT
* *
133953 AAAAAATGAATTTGGTGATTAAAGAGT
1 AAAAGA--AATTTGGTAATTAAAGAGT
*
133980 AAAAGAAAATTGGTAA
1 AAAAGAAATTTGGTAA
133996 ATTTGGTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
23 1 0.02
24 14 0.25
25 12 0.22
26 8 0.15
27 19 0.35
28 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (25 bp):
AAAAGAAATTTGGTAATTAAAGAGT
Found at i:134310 original size:20 final size:21
Alignment explanation
Indices: 134272--134317 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
134262 GAGAAGAGGT
**
134272 AAAAATGAAATGTTGGTAATC
1 AAAAATGAAATGTCAGTAATC
*
134293 AAAAATGAAAT-TCAGTAATT
1 AAAAATGAAATGTCAGTAATC
134313 AAAAA
1 AAAAA
134318 GGGGTAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (21 bp):
AAAAATGAAATGTCAGTAATC
Found at i:136033 original size:14 final size:13
Alignment explanation
Indices: 135998--136025 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
135988 TCAACCCCAA
135998 TTTTAAAAAGCAC
1 TTTTAAAAAGCAC
136011 TTTTAAAAAGCAC
1 TTTTAAAAAGCAC
136024 TT
1 TT
136026 CTTCAAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (13 bp):
TTTTAAAAAGCAC
Found at i:137325 original size:2 final size:2
Alignment explanation
Indices: 137318--137349 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
137308 CGAAAGGATA
137318 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
137350 ATTAGTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:138888 original size:21 final size:21
Alignment explanation
Indices: 138864--138905 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
138854 TCACAAAGAA
138864 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
*
138885 GTTTCAAGCTCATTGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
138906 CCTAAGGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.36
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:140493 original size:18 final size:19
Alignment explanation
Indices: 140467--140505 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
140457 CTTGTAGTTT
* *
140467 AATCGAAAAATAT-AAAAA
1 AATCAAAAAAAATGAAAAA
140485 AATCAAAAAAAATGAAAAA
1 AATCAAAAAAAATGAAAAA
140504 AA
1 AA
140506 ATTTCGACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (19 bp):
AATCAAAAAAAATGAAAAA
Found at i:140840 original size:21 final size:21
Alignment explanation
Indices: 140814--140854 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
140804 TTTAAACCCT
140814 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
140835 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
140855 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Done.