Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015870.1 Corchorus olitorius cultivar O-4 contig15903, 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: 53021
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3246 original size:2 final size:2
Alignment explanation
Indices: 3234--3279 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3224 GAGGTCCACT
*
3234 TA TA CA TA 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 TA TA TA TA
3276 TA TA
1 TA TA
3280 GATAGAGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:11734 original size:4 final size:4
Alignment explanation
Indices: 11720--11911 Score: 74
Period size: 4 Copynumber: 48.0 Consensus size: 4
11710 GACCAAAAAG
* * * *
11720 ATTT TTTT ATTT ATTT A-CT ATTT ATATT -TTT ATTT ATTA ATTT AGTT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
* * ** * *
11767 A-TT ATCT ATTT ATTT ACTATT ATCTA ATTT -TTT ACCT ACTT ATTT ATCT
1 ATTT ATTT ATTT ATTT A-T-TT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT
* * * ** * * *
11816 AATT ATCT ATAT ACCT ATTT ATCTT -TTT ATTT ATCT ATTAT TTTT ACTT
1 ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATT-T ATTT ATTT
* * * *
11865 ATTT -TTT AATTA ATTA ATTT ATTT ATTT ATCT A-TT ATTT TTTT ATTT
1 ATTT ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
11912 TAATATTTTT
Statistics
Matches: 137, Mismatches: 38, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
3 17 0.12
4 103 0.75
5 14 0.10
6 3 0.02
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:11789 original size:18 final size:18
Alignment explanation
Indices: 11766--11801 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
11756 TTAATTTAGT
11766 TATTATCT-ATTTATTTAC
1 TATTATCTAATTT-TTTAC
11784 TATTATCTAATTTTTTAC
1 TATTATCTAATTTTTTAC
11802 CTACTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATCTAATTTTTTAC
Found at i:14926 original size:26 final size:26
Alignment explanation
Indices: 14897--14956 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
14887 AAAAAAGGAG
*
14897 AAGAGAAGAAAAGAAAAGAAT-TGAAA
1 AAGAAAAGAAAA-AAAAGAATCTGAAA
* *
14923 AAGAAAAGGAAATAAAGAATCTGAAA
1 AAGAAAAGAAAAAAAAGAATCTGAAA
14949 AAGTAAAA
1 AAG-AAAA
14957 ATGAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 7 0.24
26 18 0.62
27 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.10
Consensus pattern (26 bp):
AAGAAAAGAAAAAAAAGAATCTGAAA
Found at i:16354 original size:53 final size:53
Alignment explanation
Indices: 16280--16478 Score: 265
Period size: 54 Copynumber: 3.7 Consensus size: 53
16270 GTACATGTGT
* * *
16280 TTAAAATGACTCAGTATGGTCTTTCATAGAAGTTTTCAGAGATCTAAATAGATC
1 TTAAGATGAC-CAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAATAGATC
*
16334 TTAAGATGACCAGTGTGGTCTTTCATAGAAGTTTTCA-AATATCTAAACAGATC
1 TTAAGATGACCAGTGTGGTCTTTCATAGAAGTTTTCAGAA-ATCTAAATAGATC
* *
16387 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAGTTGATC
1 TTAAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAATAGATC
* * *
16441 TTCAGATGACCTTGTGCGGTCTTTCATAAGAAGTTTTC
1 TTAAGATGACC-AGTGTGGTCTTTCAT-AGAAGTTTTC
16479 GATGATCAGA
Statistics
Matches: 130, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
52 1 0.01
53 49 0.38
54 68 0.52
55 12 0.09
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (53 bp):
TTAAGATGACCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAATAGATC
Found at i:16507 original size:35 final size:35
Alignment explanation
Indices: 16468--16755 Score: 391
Period size: 35 Copynumber: 8.3 Consensus size: 35
16458 GGTCTTTCAT
*
16468 AAGAAGTTTTCGATGATCAGAGTAGATCTCATTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* * *
16503 AAGAAGCTTTCTATGATCAGAGTTGATCTCGTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
*
16538 AAGAAGTTTT--ATGATCAGAGTTGATCTCCTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
**
16571 AAGAAGTTTTCGATGATCAGAGTTGATCTTGTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
** *
16606 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTT
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* * *
16641 AAGAAGTTTTCGATGATCAAAGTTGATCTCCTTTG
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* ** *
16676 AAAAAGTTTTTTATGATCAGAGTTGATCTCCTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* *
16711 AAGAAGTTTTTGTTGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
16746 AAGAAGTTTT
1 AAGAAGTTTT
16756 TTTATGATCA
Statistics
Matches: 224, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
33 32 0.14
35 192 0.86
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (35 bp):
AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
Found at i:16650 original size:70 final size:70
Alignment explanation
Indices: 16468--16768 Score: 435
Period size: 70 Copynumber: 4.3 Consensus size: 70
16458 GGTCTTTCAT
** * * *
16468 AAGAAGTTTTCGATGATCAGAGTAGATCTCATTTCAAGAAGCTTTCTATGATCAGAGTTGATCTC
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
16533 GTTTC
66 GTTTC
* *
16538 AAGAAG--TTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
16601 GTTTC
66 GTTTC
* *
16606 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTTAAGAAGTTTTCGATGATCAAAGTTGATCTC
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* *
16671 CTTTG
66 GTTTC
* * * *
16676 AAAAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTGTTGATCAGAGTTGATCTC
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
*
16741 ATTTC
66 GTTTC
16746 AAGAAGTTTTTTTATGATCAGAG
1 AAGAAG-TTTTTTATGATCAGAG
16769 AAGTTTTTTA
Statistics
Matches: 206, Mismatches: 22, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
68 61 0.30
70 129 0.63
71 16 0.08
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (70 bp):
AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
GTTTC
Found at i:16783 original size:18 final size:20
Alignment explanation
Indices: 16747--16786 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
16737 TCTCATTTCA
16747 AGAAGTTTTTTTATGATCAG
1 AGAAGTTTTTTTATGATCAG
16767 AGAAG-TTTTTTAT-ATCAG
1 AGAAGTTTTTTTATGATCAG
16785 AG
1 AG
16787 TTGATCTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 8 0.40
20 5 0.25
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (20 bp):
AGAAGTTTTTTTATGATCAG
Found at i:16841 original size:226 final size:228
Alignment explanation
Indices: 16544--16981 Score: 684
Period size: 226 Copynumber: 1.9 Consensus size: 228
16534 TTTCAAGAAG
* *
16544 TTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTTGTTTCAAG
1 TTTTATGATCAGAGTTGATCTCCTTTCAAAAAGTTTT--ATGATCAGAGTTGATCTCGTTTCAAG
*
16609 AAGTTTTTTATGATCAGAGTTGATCTCATTTTAAGAAGTTTTCGATGATCAAAGTTGATCTCCTT
64 AAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAAAGTTGATCTCCTT
* * * *
16674 TGAAAAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTGTTGATCAGAGTTGATC
129 TCAAAAAGTTTTTTATAATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATAAGAGTTGATC
16739 -TCATTTCAAGAAGTTTTTTTATGATCAGAGAAGTT
194 TTC-TTTCAAGAAGTTTTTTTATGATCAGAGAAGTT
* *
16774 TTTTAT-ATCAGAGTTGATCTCGTTTCAAAAAGTTTT-TTATCAGAGTTGATCTCGTTTCAAGAA
1 TTTTATGATCAGAGTTGATCTCCTTTCAAAAAGTTTTATGATCAGAGTTGATCTCGTTTCAAGAA
* * * * *
16837 GTTTTTTATGATCAGAGTTTATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTTATCTCCTTTC
66 GTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAAAGTTGATCTCCTTTC
* *
16902 AAGAAGTTTTTTATAATCAGAGTTTATCTCCTTTCAAGAAGTTTTCGTTGATAAGAGTTGATCTT
131 AAAAAGTTTTTTATAATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATAAGAGTTGATCTT
16967 CTTTCAAGAAGTTTT
196 CTTTCAAGAAGTTTT
16982 CGATGATCAG
Statistics
Matches: 191, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
226 155 0.81
227 2 0.01
229 28 0.15
230 6 0.03
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (228 bp):
TTTTATGATCAGAGTTGATCTCCTTTCAAAAAGTTTTATGATCAGAGTTGATCTCGTTTCAAGAA
GTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAAAGTTGATCTCCTTTC
AAAAAGTTTTTTATAATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATAAGAGTTGATCTT
CTTTCAAGAAGTTTTTTTATGATCAGAGAAGTT
Found at i:16861 original size:35 final size:35
Alignment explanation
Indices: 16767--17069 Score: 357
Period size: 35 Copynumber: 8.8 Consensus size: 35
16757 TTATGATCAG
*
16767 AGAAGTTTTTTAT-ATCAGAGTTGATCTCGTTTCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCA
* *
16801 AAAAG-TTTTT-T-ATCAGAGTTGATCTCGTTTCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCA
*
16833 AGAAGTTTTTTATGATCAGAGTTTATCTCCTTTCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCA
* *
16868 AGAAGTTTTCGT-TGATCAGAGTTTATCTCCTTTCA
1 AGAAGTTTT-TTATGATCAGAGTTGATCTCCTTTCA
* *
16903 AGAAGTTTTTTATAATCAGAGTTTATCTCCTTTCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCA
* * *
16938 AGAAGTTTTCGT-TGATAAGAGTTGATCTTCTTTCA
1 AGAAGTTTT-TTATGATCAGAGTTGATCTCCTTTCA
** *
16973 AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCA
* * * *
17008 AGAAGTTTTTGATGATCAGAATTGATCTCATTCCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCA
** *
17043 AGAAGTTTTCAATGGTCAGAGTTGATC
1 AGAAGTTTTTTATGATCAGAGTTGATC
17070 CTAAGATGAT
Statistics
Matches: 237, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
32 26 0.11
33 10 0.04
34 6 0.03
35 193 0.81
36 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (35 bp):
AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCA
Found at i:16910 original size:70 final size:70
Alignment explanation
Indices: 16767--17069 Score: 398
Period size: 70 Copynumber: 4.4 Consensus size: 70
16757 TTATGATCAG
* * *
16767 AGAAGTTTTTTAT-ATCAGAGTTGATCTCGTTTCAAAAAGTTTT--TT-ATCAGAGTTGATCTCG
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCC
16828 TTTCA
66 TTTCA
* *
16833 AGAAGTTTTTTATGATCAGAGTTTATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTTATCTCC
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCC
16898 TTTCA
66 TTTCA
* * * *
16903 AGAAGTTTTTTATAATCAGAGTTTATCTCCTTTCAAGAAGTTTTCGTTGATAAGAGTTGATCTTC
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCC
16968 TTTCA
66 TTTCA
** * * * * *
16973 AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTGATGATCAGAATTGATCTCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCC
*
17038 TTCCA
66 TTTCA
** *
17043 AGAAGTTTTCAATGGTCAGAGTTGATC
1 AGAAGTTTTTTATGATCAGAGTTGATC
17070 CTAAGATGAT
Statistics
Matches: 210, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
66 13 0.06
67 27 0.13
69 2 0.01
70 168 0.80
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (70 bp):
AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCC
TTTCA
Found at i:17102 original size:54 final size:54
Alignment explanation
Indices: 17035--17484 Score: 564
Period size: 54 Copynumber: 8.3 Consensus size: 54
17025 AGAATTGATC
* *
17035 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCTAAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTGCGG
*
17089 TCATTCTAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTGCGG
* **
17143 TCATTCGAAGAAGTTTTTGATGATCAGAGTTGAT-CTCCAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCT-CAGATGATCCAGTGCGG
* * * * * *
17197 TCCTTACAAGAAGTTTTTAATAATCAGAGTTGATCCTCATATGATCCAGTGCGA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTGCGG
* * * * * * *
17251 TGATACCAAGAAGTTTTCAATGGTCCGAGTTGATCCTCAAATGATCTAGTGTGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTGCGG
* * **
17305 TCATTCCAAGAAACTTAT-AATGATCAGAGTTGATCCTTTGATGATCCAGTGCGG
1 TCATTCCAAG-AAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTGCGG
*
17359 TCATTCCAAGAAGTTTTCAATGATCAGATTTGATCCTCAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTGCGG
** * ** *
17413 TCATTAGAAAAAGTTTTTGATGATTAGAGTTGAT-CTCCAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCT-CAGATGATCCAGTGCGG
* *
17467 TCCTTACAAGAAGTTTTC
1 TCATTCCAAGAAGTTTTC
17485 GAGTGCGGTT
Statistics
Matches: 339, Mismatches: 52, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
53 9 0.03
54 323 0.95
55 7 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (54 bp):
TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTGCGG
Found at i:17504 original size:26 final size:26
Alignment explanation
Indices: 17460--17510 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
17450 CAGATGATCC
17460 AGTGCGGTCCTTACAAGAAGTTTTCG
1 AGTGCGGTCCTTACAAGAAGTTTTCG
* * *
17486 AGTGCGGTTCTTCCGAGAAGTTTTC
1 AGTGCGGTCCTTACAAGAAGTTTTC
17511 AAAGTTGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (26 bp):
AGTGCGGTCCTTACAAGAAGTTTTCG
Found at i:17595 original size:54 final size:55
Alignment explanation
Indices: 17513--17682 Score: 276
Period size: 54 Copynumber: 3.2 Consensus size: 55
17503 AAGTTTTCAA
* *
17513 AGTTGA-CCTCTAGATGATCCGTTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
1 AGTTGATCTTCTAGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
17567 AGTTGATCTTC-AGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
1 AGTTGATCTTCTAGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
* *
17621 AGTTGATC-TCTAGATGATCCAGTGTGGTC-TTTCAAGAAGTTTTCGATGATCAG
1 AGTTGATCTTCTAGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
17674 AGTTGATCT
1 AGTTGATCT
17683 CCAATTTGAT
Statistics
Matches: 109, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
53 33 0.30
54 73 0.67
55 3 0.03
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (55 bp):
AGTTGATCTTCTAGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
Found at i:17712 original size:108 final size:108
Alignment explanation
Indices: 17513--17713 Score: 273
Period size: 108 Copynumber: 1.9 Consensus size: 108
17503 AAGTTTTCAA
*
17513 AGTTGACCTCTAGATGATCCGTTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTTC
1 AGTTGACCTCTAGATGATCCGTTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCC
* * ** *
17578 AGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
66 AGATGATCCAGTATGGTCACTCCAAGAAGTTTTCGAAGATCAG
* *
17621 AGTTGATCTCTAGATGATCCAG-TGTGGTC-TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 AGTTGACCTCTAGATGATCC-GTTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTC
*
17684 CA-ATTTGATCTAGTATGGTCACTCCAAGAA
65 CAGA--TGATCCAGTATGGTCACTCCAAGAA
17714 AAGTTTCCGT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
106 1 0.01
107 34 0.42
108 45 0.56
109 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (108 bp):
AGTTGACCTCTAGATGATCCGTTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCC
AGATGATCCAGTATGGTCACTCCAAGAAGTTTTCGAAGATCAG
Found at i:19168 original size:8 final size:8
Alignment explanation
Indices: 19120--19200 Score: 56
Period size: 8 Copynumber: 10.0 Consensus size: 8
19110 TTTTACCTAC
19120 CTATTTAT
1 CTATTTAT
*
19128 CTAATTAT
1 CTATTTAT
* *
19136 CTATATAC
1 CTATTTAT
19144 CTATTTAT
1 CTATTTAT
*
19152 CTTTTTAT
1 CTATTTAT
* *
19160 TTATCTAT
1 CTATTTAT
*
19168 -TATTTTT
1 CTATTTAT
*
19175 ACTTATTTTT
1 -C-TATTTAT
19185 CTATTTAT
1 CTATTTAT
*
19193 TTATTTAT
1 CTATTTAT
19201 TTATCTATTA
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
7 5 0.09
8 43 0.77
9 1 0.02
10 7 0.12
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (8 bp):
CTATTTAT
Found at i:19195 original size:4 final size:4
Alignment explanation
Indices: 19145--19221 Score: 54
Period size: 4 Copynumber: 19.2 Consensus size: 4
19135 TCTATATACC
* * *
19145 TATT TATCT T-TT TATT TATC TATT ATTTT TACT TATT T-TT CTATT TATT
1 TATT TAT-T TATT TATT TATT TATT -TATT TATT TATT TATT -TATT TATT
*
19194 TATT TATT TATC TA-T TACTT T-TT TATT T
1 TATT TATT TATT TATT TA-TT TATT TATT T
19222 TAATATTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
3 9 0.16
4 39 0.68
5 9 0.16
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:19209 original size:12 final size:12
Alignment explanation
Indices: 19121--19204 Score: 66
Period size: 12 Copynumber: 7.2 Consensus size: 12
19111 TTTACCTACC
*
19121 TATTTATCTAAT
1 TATTTATCTATT
* * **
19133 TATCTATATACC
1 TATTTATCTATT
*
19145 TATTTATCTTTT
1 TATTTATCTATT
19157 TATTTATCTA-T
1 TATTTATCTATT
*
19168 TATTT-T-TACT
1 TATTTATCTATT
*
19178 TATTTTTCTATT
1 TATTTATCTATT
*
19190 TATTTATTTATT
1 TATTTATCTATT
19202 TAT
1 TAT
19205 CTATTACTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
9 2 0.04
10 7 0.12
11 7 0.12
12 40 0.71
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTATCTATT
Found at i:22195 original size:16 final size:16
Alignment explanation
Indices: 22174--22206 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22164 GCCAAAAAAT
22174 CCAAAACCCGAATGAC
1 CCAAAACCCGAATGAC
*
22190 CCAAAACCCGAGTGAC
1 CCAAAACCCGAATGAC
22206 C
1 C
22207 TGAGGCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.39, G:0.15, T:0.06
Consensus pattern (16 bp):
CCAAAACCCGAATGAC
Found at i:22280 original size:31 final size:31
Alignment explanation
Indices: 22241--22311 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
22231 GACCCGAGAC
*
22241 CCGAATGACCTGAACTTAGATAATCCGAAAT
1 CCGAATGACCTGAACCTAGATAATCCGAAAT
* * *
22272 TCGAATGACCTGAACCTAGATGATCTGAAAT
1 CCGAATGACCTGAACCTAGATAATCCGAAAT
22303 CCGAATGAC
1 CCGAATGAC
22312 GTGAGAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (31 bp):
CCGAATGACCTGAACCTAGATAATCCGAAAT
Found at i:26291 original size:22 final size:22
Alignment explanation
Indices: 26266--26312 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
26256 TTTATAGTTG
*
26266 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
26288 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
26310 AGT
1 AGT
26313 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:26291 original size:93 final size:94
Alignment explanation
Indices: 26189--26375 Score: 295
Period size: 95 Copynumber: 2.0 Consensus size: 94
26179 GCTTTTTAAT
* *
26189 TAAATTAGTAATATCGTAAAAATAAAATAGGTATAAGG-ATATTAGATTTAATTAAATAAAAATA
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGAATATTAGATTTAATTAAATAAAAATA
*
26253 GAGTTTATAGTTGAGTAAAACTATAAAAG
66 GAGTTTATAGTTGACTAAAACTATAAAAG
* * *
26282 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATATTAGATTTAGTTAAATAAAAAT
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGA-ATATTAGATTTAATTAAATAAAAAT
*
26347 AGAGTTTTTAGTTGACTAAAACTATAAAA
65 AGAGTTTATAGTTGACTAAAACTATAAAA
26376 ATATAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
93 34 0.40
95 51 0.60
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (94 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGAATATTAGATTTAATTAAATAAAAATA
GAGTTTATAGTTGACTAAAACTATAAAAG
Found at i:26449 original size:31 final size:31
Alignment explanation
Indices: 26411--26472 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
26401 ATATTCAAAA
* *
26411 AATAAGGGTATAATAGGCTATTCAAAAGTTT
1 AATAAGGGTAAAATAGGCGATTCAAAAGTTT
26442 AATAAGGGTAAAATAGGCGATTCAAAAGTTT
1 AATAAGGGTAAAATAGGCGATTCAAAAGTTT
26473 TACAAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (31 bp):
AATAAGGGTAAAATAGGCGATTCAAAAGTTT
Found at i:29547 original size:27 final size:26
Alignment explanation
Indices: 29516--29591 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 26
29506 CTTAAGTTGT
*
29516 CAAAATTACTATTTTGCCCTTGGTCAG
1 CAAAATTAC-ATTTTGCCCTTGGTCAA
* * *
29543 CAAAAATTACCATTTTACCCCTGGTTAA
1 C-AAAATTA-CATTTTGCCCTTGGTCAA
*
29571 CTAAATTACAGTTTTGCCCTT
1 CAAAATTACA-TTTTGCCCTT
29592 AAATGCCGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
26 2 0.05
27 15 0.38
28 21 0.54
29 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (26 bp):
CAAAATTACATTTTGCCCTTGGTCAA
Found at i:31018 original size:2 final size:2
Alignment explanation
Indices: 31006--31051 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
30996 TCAGTAAGTA
31006 AT AT CAT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31048 AT AT
1 AT AT
31052 CAAAAGCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52227 original size:79 final size:79
Alignment explanation
Indices: 52143--52289 Score: 242
Period size: 79 Copynumber: 1.9 Consensus size: 79
52133 TTAAAATGCT
*
52143 AAAAATAAAATAATTATAAA-ATATTGAATTTAATTAAATGAAAATAGAATTTTTAGTAGAATAA
1 AAAAATAAAATAATTATAAAGATATTAAATTTAATTAAAT-AAAATAGAATTTTTAGTAGAATAA
52207 AACTCTATATTTTGA
65 AACTCTATATTTTGA
* * *
52222 AAAAATAAAGTAATTATAAAGATATTAAATTTAATTGAATAAAATAGAGTTTTTAGTAGAATAAA
1 AAAAATAAAATAATTATAAAGATATTAAATTTAATTAAATAAAATAGAATTTTTAGTAGAATAAA
52287 ACT
66 ACT
52290 ATAATAGTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 46 0.73
80 17 0.27
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (79 bp):
AAAAATAAAATAATTATAAAGATATTAAATTTAATTAAATAAAATAGAATTTTTAGTAGAATAAA
ACTCTATATTTTGA
Done.