Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020264.1 Corchorus olitorius cultivar O-4 contig20297, 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: 50629
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:11801 original size:31 final size:31
Alignment explanation
Indices: 11763--11880 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 31
11753 TCGACGCCAA
11763 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
* * * *
11794 GCCCTTATTTGAACCCTTATTTGGCCAAATTAAAAGATCAG
1 GCCCTTATTTG-A-GCAT-TTTGG-C-----AAACG-TTAG
* *
11835 ACCCTTATTTGAGCATTTTGGCAAACATTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
11866 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
11881 ATGAGCCTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
31 28 0.42
32 4 0.06
33 2 0.03
34 5 0.08
35 1 0.02
37 1 0.02
38 5 0.08
39 2 0.03
40 5 0.08
41 13 0.20
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAG
Found at i:13932 original size:29 final size:29
Alignment explanation
Indices: 13899--13959 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
13889 AATTGACGAC
13899 TTACTGTTAGTGTGTAAAATAAAAGGAAT
1 TTACTGTTAGTGTGTAAAATAAAAGGAAT
*
13928 TTACTGTTAGTGTGTAGAATAAAAGGAAT
1 TTACTGTTAGTGTGTAAAATAAAAGGAAT
13957 TTA
1 TTA
13960 TATAATTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.36
Consensus pattern (29 bp):
TTACTGTTAGTGTGTAAAATAAAAGGAAT
Found at i:14189 original size:58 final size:58
Alignment explanation
Indices: 14099--14214 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
14089 AAGTTAAATT
* * *
14099 AAAAGAAATATTGTTAGAATTTTAGGAAATGGAGTTTTACTTTGATTATAATCCAATG
1 AAAAGAAATATTGTTAAAATTCTACGAAATGGAGTTTTACTTTGATTATAATCCAATG
14157 AAAAGAAATATTGTTAAAATTCTACGAAATGGAGTTTTACTTTGATTATAATCCAATG
1 AAAAGAAATATTGTTAAAATTCTACGAAATGGAGTTTTACTTTGATTATAATCCAATG
14215 TTCTAAATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.37
Consensus pattern (58 bp):
AAAAGAAATATTGTTAAAATTCTACGAAATGGAGTTTTACTTTGATTATAATCCAATG
Found at i:16280 original size:118 final size:118
Alignment explanation
Indices: 16072--16308 Score: 465
Period size: 118 Copynumber: 2.0 Consensus size: 118
16062 ATTAAGAAAT
16072 TACCTTATATAACCTACTTACTAAACTACCAAACAAATAAATAAATATATAAACTAAACTCACAT
1 TACCTTATATAACCTACTTACTAAACTACCAAACAAATAAATAAATATATAAACTAAACTCACAT
*
16137 TTCATGAGACTTGAACCCAGGATCTCACTGTCCAGACACGGTGTACTCACCAG
66 TTCATGAGACTTGAACCCAGGATCTCACTGTCCAGACACGGTATACTCACCAG
16190 TACCTTATATAACCTACTTACTAAACTACCAAACAAATAAATAAATATATAAACTAAACTCACAT
1 TACCTTATATAACCTACTTACTAAACTACCAAACAAATAAATAAATATATAAACTAAACTCACAT
16255 TTCATGAGACTTGAACCCAGGATCTCACTGTCCAGACACGGTATACTCACCAG
66 TTCATGAGACTTGAACCCAGGATCTCACTGTCCAGACACGGTATACTCACCAG
16308 T
1 T
16309 TAAACTAACA
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (118 bp):
TACCTTATATAACCTACTTACTAAACTACCAAACAAATAAATAAATATATAAACTAAACTCACAT
TTCATGAGACTTGAACCCAGGATCTCACTGTCCAGACACGGTATACTCACCAG
Found at i:17983 original size:154 final size:153
Alignment explanation
Indices: 17704--18049 Score: 586
Period size: 154 Copynumber: 2.3 Consensus size: 153
17694 TTCTTTAAGT
* *
17704 CTAACTATAATCATTTTGGTGAGATTAGTCAACTGTGAAGTTTTTAGCTCATTTGACCACTTGTT
1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAACACTTGTT
*
17769 ATTTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGACAAACCTCAAAG
66 ATTTTGGGCCTTACGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGACAAACCTCAAAG
* *
17834 CTTTTCTTTTC-ATTGTTTATGGC
131 CTTTTC-TTTCAACTGTTTATAGC
17857 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT-GAACACTTGT
** *
17922 TATTTTGGGCCTTACGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAA
65 TATTTTGGGCCTTACGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGACAAACCTCAAA
17987 GCTTTTCTTTCAACTGTTTATAGC
130 GCTTTTCTTTCAACTGTTTATAGC
*
18011 CTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAA
1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
18050 TCAGCTTGGA
Statistics
Matches: 182, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
153 57 0.31
154 125 0.69
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (153 bp):
CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAACACTTGTT
ATTTTGGGCCTTACGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGACAAACCTCAAAG
CTTTTCTTTCAACTGTTTATAGC
Found at i:22302 original size:19 final size:20
Alignment explanation
Indices: 22266--22303 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
22256 TTACTATTAT
22266 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
22286 TTTT-AATTTCAAT-TTTTA
1 TTTTGAATTT-AATATTTTA
22304 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:22539 original size:44 final size:42
Alignment explanation
Indices: 22474--23166 Score: 233
Period size: 44 Copynumber: 15.9 Consensus size: 42
22464 CTGTGTGGTA
* * *
22474 ATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTT
1 ATCAAAATTTCAT-AGGTGGTTATCAAAATTTCAT-AGGAGGTT
* **
22518 ATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGAAATT
1 ATCAAAATTTCATAG-GTGGTTATCAAAATTTCATA-GGAGGTT
* ** * * *
22562 ATCCAAATTTCAGGGGAAGATTATCAAAATTTCATAGTGTGGTT
1 ATCAAAATTTCATAGG-TGGTTATCAAAATTTCATAG-GAGGTT
* *
22606 ACCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TAAGGAAGGTT
1 ATCAAAATTTCATAGG-T--GGTTATCAAAATTTCAT-AGG-AGGTT
** * * *
22652 ATTGAAATTTCATAGTGTGGTTATCACAATTTTATAGAAAGG-T
1 ATCAAAATTTCATAG-GTGGTTATCAAAATTTCATAG-GAGGTT
* * * *
22695 -T----A--TCATA-GAGATTATCAAAATGTCATAGCGAGCTT
1 ATCAAAATTTCATAGGTGGTTATCAAAATTTCATAG-GAGGTT
* *
22730 AT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAAGTT
1 ATCAA-AATTTCATAG-GTGGTTATCAAAATTTCAT-AGGAGGTT
* * *
22774 A-CTAATATTTCAT-GGGGATGTTATCAAAATTTCATAAGGAAGTT
1 ATC-AAAATTTCATAGGTG--GTTATCAAAATTTCAT-AGGAGGTT
* * * *
22818 A-CTAATATTTCAT-GGGGATGTTATCAAAATTTCGTAGTGTGTGGTT
1 ATC-AAAATTTCATAGGTG--GTTATCAAAATTTCATA--G-GAGGTT
** *
22864 ATCAAAATTTCATATGAAGGTTATAAAAGTCTCAATTTCATAAGGA-G-T
1 ATCAAAATTTCATA-GGTGGTTAT-CAA-----AATTTCAT-AGGAGGTT
* * ** *
22912 ACCAAAATTTGATAGAAGGTTATC-AAATCTCATA-GAGTGATT
1 ATCAAAATTTCATAGGTGGTTATCAAAATTTCATAGGAG-G-TT
* * * *
22954 ATCGAAATTTCATAGAGATCGGATTATAAAAATTT-ACAGGAAGATT
1 ATCAAAATTTCATAG-G-T-GG-TTATCAAAATTTCATAGG-AGGTT
* * *
23000 ATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAAGTT
1 ATCAAAATTTCATAG-GTGGTTATCAAAATTTCATAG-GAGGTT
* * * * * *
23044 ATC--AATTACGTAATGTGATTATCAAAATTTCATAGAGGGGTC
1 ATCAAAATTTCAT-AGGTGGTTATCAAAATTTCATAG-GAGGTT
* * * *
23086 AACAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTT
1 ATCAAAATTTCATAG-GTGGTTATCAAAATTTCAT-AGGAGGTT
* * * * *
23130 ATCAAATTTTCAAAATGTGATTACCAAAATTTCATAG
1 ATCAAAATTTC-ATAGGTGGTTATCAAAATTTCATAG
23167 TGGATATTTC
Statistics
Matches: 486, Mismatches: 105, Indels: 117
0.69 0.15 0.17
Matches are distributed among these distances:
34 18 0.04
35 1 0.00
36 6 0.01
38 3 0.01
39 1 0.00
40 9 0.02
42 50 0.10
43 22 0.05
44 239 0.49
45 16 0.03
46 74 0.15
47 19 0.04
48 17 0.03
49 1 0.00
50 1 0.00
51 1 0.00
52 7 0.01
53 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (42 bp):
ATCAAAATTTCATAGGTGGTTATCAAAATTTCATAGGAGGTT
Found at i:22572 original size:66 final size:68
Alignment explanation
Indices: 22466--23166 Score: 258
Period size: 66 Copynumber: 10.3 Consensus size: 68
22456 TCTTGTCTCT
* * * * * * *
22466 GTGTGGTAATCAAAATTTCATAAGA-TGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTTC
1 GTGTGGTTACCAAAATTTCATAGGACAGATTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
22529 ATA
66 ATA
* * *
22532 GTGTGGTTACCAAAATTTCATATGGA-A-ATTATCCAAATTTCA-GGGGAAGATTATCAAAATTT
1 GTGTGGTTACCAAAATTTCATA-GGACAGATTATCAAAATTTCATGAGGAAGGTTATCAAAATTT
22594 CATA
65 CATA
* * * **
22598 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TAAGGAAGGTTATTGAAATTT
1 GTGTGGTTACCAAAATTTCATAGGA-CAGATTATCAAAATTTCATGAGGAAGGTTATCAAAATTT
22662 CATA
65 CATA
* * * * *
22666 GTGTGGTTATCACAATTTTATAGAAAGGTTATCATAGAGATTATCAAAATGTCAT-AGCG-AGCT
1 GTGTGGTTACCAAAATTTCAT----AGG--A-C----AGATTATCAAAATTTCATGAG-GAAGGT
22729 TAT-AAGAATTTCATA
54 TATCAA-AATTTCATA
* * * *
22744 GTGTGGTTAACAAAATTTCATAAGGA-AG-TTA-CTAATATTTCATG-GGGATGTTATCAAAATT
1 GTGTGGTTACCAAAATTTCAT-AGGACAGATTATC-AAAATTTCATGAGGAAGGTTATCAAAATT
22805 TCATAA
64 TCAT-A
** * * * * * **
22811 G-GAAGTTACTAATATTTCATGGGGA-TG-TTATCAAAATTTCGT-AGTGTGTGGTTATCAAAAT
1 GTGTGGTTACCAAAATTTCAT-AGGACAGATTATCAAAATTTCATGAG-G-AAGGTTATCAAAAT
22872 TTCATA
63 TTCATA
* * * *** * * * *
22878 -TGAAGGTTA-TAAAAGTCTCAATTTCATAAGGAGTACCAAAATTTGAT-A-GAAGGTTATC-AA
1 GTG-TGGTTACCAAAA-TTTC-ATAGGA-CA-GATTATCAAAATTTCATGAGGAAGGTTATCAAA
*
22938 ATCTCATA
61 ATTTCATA
* * * * * * * *
22946 GAGTGATTATCGAAATTTCATAGAGATCGGATTATAAAAATTT-A-CAGGAAGATTATCAAAATT
1 GTGTGGTTACCAAAATTTCATAG-GA-CAGATTATCAAAATTTCATGAGGAAGGTTATCAAAATT
23009 TCATA
64 TCATA
* * * * * * * * *
23014 GTGTTGTTATCAAAATTTCAAAGCGA-AG-TTATC--AATTACGTAATG-TGATTATCAAAATTT
1 GTGTGGTTACCAAAATTTCATAG-GACAGATTATCAAAATTTCATGAGGAAGGTTATCAAAATTT
23074 CATA
65 CATA
* * * * * * * * * *
23078 GAGGGGTCAACAAAATTTTATA-GAGAGGTTATCAAAATTTCATAAAG-AGGTTATCAAATTTTC
1 GTGTGGTTACCAAAATTTCATAGGACAGATTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
*
23141 AAA
66 ATA
* *
23144 ATGTGATTACCAAAATTTCATAG
1 GTGTGGTTACCAAAATTTCATAG
23167 TGGATATTTC
Statistics
Matches: 477, Mismatches: 109, Indels: 97
0.70 0.16 0.14
Matches are distributed among these distances:
62 2 0.00
63 6 0.01
64 38 0.08
65 14 0.03
66 168 0.35
67 39 0.08
68 121 0.25
69 13 0.03
70 1 0.00
71 1 0.00
72 15 0.03
73 1 0.00
74 3 0.01
75 4 0.01
77 1 0.00
78 48 0.10
79 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (68 bp):
GTGTGGTTACCAAAATTTCATAGGACAGATTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
ATA
Found at i:22636 original size:24 final size:22
Alignment explanation
Indices: 22477--22697 Score: 121
Period size: 22 Copynumber: 10.0 Consensus size: 22
22467 TGTGGTAATC
* *
22477 AAAATTTCATAAGATGGTTATT
1 AAAATTTCATAGGAAGGTTATT
* *
22499 ATAATTTCATGAGG-AGGTTATC
1 AAAATTTCAT-AGGAAGGTTATT
* **
22521 AAAATTTCATAGTG-TGGTTACC
1 AAAATTTCATAG-GAAGGTTATT
* *
22543 AAAATTTCATATGGAA-ATTATC
1 AAAATTTCATA-GGAAGGTTATT
* ** * *
22565 CAAATTTCAGGGGAAGATTATC
1 AAAATTTCATAGGAAGGTTATT
* **
22587 AAAATTTCATAGTG-TGGTTACC
1 AAAATTTCATAG-GAAGGTTATT
22609 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGGA--AGGTTATT
22633 AAAATTTC-TAAGGAAGGTTATT
1 AAAATTTCAT-AGGAAGGTTATT
* * *
22655 GAAATTTCATAGTG-TGGTTATC
1 AAAATTTCATAG-GAAGGTTATT
* * *
22677 ACAATTTTATAGAAAGGTTAT
1 AAAATTTCATAGGAAGGTTAT
22698 CATAGAGATT
Statistics
Matches: 156, Mismatches: 30, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
21 7 0.04
22 125 0.80
23 7 0.04
24 17 0.11
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTTATT
Found at i:22774 original size:22 final size:22
Alignment explanation
Indices: 22749--22850 Score: 82
Period size: 22 Copynumber: 4.6 Consensus size: 22
22739 TCATAGTGTG
22749 GTTAACAAAATTTCATAAGGAA
1 GTTAACAAAATTTCATAAGGAA
* ** *
22771 GTT-ACTAATATTTCATGGGGAT
1 GTTAAC-AAAATTTCATAAGGAA
*
22793 GTTATCAAAATTTCATAAGGAA
1 GTTAACAAAATTTCATAAGGAA
* ** *
22815 GTT-ACTAATATTTCATGGGGAT
1 GTTAAC-AAAATTTCATAAGGAA
*
22837 GTTATCAAAATTTC
1 GTTAACAAAATTTC
22851 GTAGTGTGTG
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
21 3 0.05
22 55 0.92
23 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
GTTAACAAAATTTCATAAGGAA
Found at i:23023 original size:22 final size:22
Alignment explanation
Indices: 22914--23168 Score: 117
Period size: 22 Copynumber: 11.7 Consensus size: 22
22904 TAAGGAGTAC
* *
22914 CAAAATTTGATAG-AAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * *
22935 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
22956 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGTGA--GG-TTAT
* * *
22981 AAAAATTT-ACAG-GAAGATTAT
1 CAAAATTTCATAGTG-AGGTTAT
**
23002 CAAAATTTCATAGTGTTGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
23024 CAAAATTTCAAAGCGAAGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * * *
23046 C--AATTACGTAATGTGATTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * *
23066 CAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGTGAGGTTAT
* *
23088 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
**
23110 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * * * *
23132 CAAATTTTCAAAATGTGATTAC
1 CAAAATTTCATAGTGAGGTTAT
23154 CAAAATTTCATAGTG
1 CAAAATTTCATAGTG
23169 GATATTTCTG
Statistics
Matches: 172, Mismatches: 52, Indels: 19
0.71 0.21 0.08
Matches are distributed among these distances:
20 21 0.12
21 18 0.10
22 116 0.67
23 2 0.01
24 5 0.03
25 10 0.06
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAT
Found at i:23295 original size:22 final size:21
Alignment explanation
Indices: 23248--23431 Score: 81
Period size: 22 Copynumber: 8.5 Consensus size: 21
23238 TTATGGAGTA
* *
23248 ATCAAAATTTCAAG-GAGGAT
1 ATCAAAATTTCATGTGAGGTT
23268 ATCAAAATTTCATGTGAAGGTT
1 ATCAAAATTTCATGTG-AGGTT
*
23290 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCAT-G-TGAGGTT
* ** *
23312 TTCAAAATTTCATAAGAGATTT
1 ATCAAAATTTCATGTGAG-GTT
* * *
23334 ATCAAAA--TCATATAGTATGTAG
1 ATCAAAATTTCATGT-G-AGGT-T
* * *
23356 ATCAAAATTTCATAGGGCGATT
1 ATCAAAATTTCAT-GTGAGGTT
* *
23378 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCAT-GTGAGGTT
* *
23400 ATCAAAAAATCTCA-GGGAGGTT
1 ATC--AAAATTTCATGTGAGGTT
23422 ATCAAAATTT
1 ATCAAAATTT
23432 ATAGTTATCA
Statistics
Matches: 121, Mismatches: 29, Indels: 28
0.68 0.16 0.16
Matches are distributed among these distances:
20 25 0.21
21 3 0.02
22 76 0.63
23 3 0.02
24 14 0.12
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (21 bp):
ATCAAAATTTCATGTGAGGTT
Found at i:23455 original size:15 final size:15
Alignment explanation
Indices: 23417--23462 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
23407 AATCTCAGGG
23417 AGGTTATCAAAATTT
1 AGGTTATCAAAATTT
* *
23432 ATAGTTATCAAGATTT
1 A-GGTTATCAAAATTT
23448 AGGTTATCAAAATTT
1 AGGTTATCAAAATTT
23463 TATACGGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (15 bp):
AGGTTATCAAAATTT
Found at i:23464 original size:16 final size:16
Alignment explanation
Indices: 23417--23464 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
23407 AATCTCAGGG
23417 AGGTTATCAAAATTTAT
1 AGGTTATCAAAATTT-T
*
23434 A-GTTATCAAGA-TTT
1 AGGTTATCAAAATTTT
23448 AGGTTATCAAAATTTT
1 AGGTTATCAAAATTTT
23464 A
1 A
23465 TACGGAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 13 0.48
17 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (16 bp):
AGGTTATCAAAATTTT
Found at i:23477 original size:23 final size:23
Alignment explanation
Indices: 23451--23535 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
23441 AAGATTTAGG
23451 TTATCAAAATTTTATACGGAA-GT
1 TTATCAAAATTTTATA-GGAAGGT
23474 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGGT
* * *
23497 TTATTAAAATTTCATTGCG-AGG-
1 TTATCAAAATTTTATAG-GAAGGT
*
23519 TTATCACAATTTTATAG
1 TTATCAAAATTTTATAG
23536 TGTGATTACT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
22 17 0.32
23 35 0.66
24 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:23661 original size:22 final size:22
Alignment explanation
Indices: 23448--23698 Score: 112
Period size: 22 Copynumber: 11.3 Consensus size: 22
23438 ATCAAGATTT
* *
23448 AGGTTATCAAAATTTTATACGGA
1 AGGTTATCAAAATTTCATA-GGG
* * *
23471 AGTTTATCAAAATTTTATAGGA
1 AGGTTATCAAAATTTCATAGGG
* * *
23493 AGGTTTATTAAAATTTCATTGCG
1 AGG-TTATCAAAATTTCATAGGG
* * *
23516 AGGTTATCACAATTTTATAGTG
1 AGGTTATCAAAATTTCATAGGG
* * * * *
23538 TGATTA-CTAACAGTTCATATGG
1 AGGTTATC-AAAATTTCATAGGG
* * * **
23560 AGGTTTTTAAATTTTCATAACG
1 AGGTTATCAAAATTTCATAGGG
* * * *
23582 TGGTTATCAATATATCATATGG
1 AGGTTATCAAAATTTCATAGGG
** * *
23604 AGGTTATCATCATCTCATA-GT
1 AGGTTATCAAAATTTCATAGGG
*
23625 ATTGGTTATCAAAATTTCATAGTG
1 A--GGTTATCAAAATTTCATAGGG
* *
23649 AGGTCT-TCAAAATTCCTTAGGG
1 AGGT-TATCAAAATTTCATAGGG
* * *
23671 AGGTTAACAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGG
23693 AGGTTA
1 AGGTTA
23699 AAAGAAATTA
Statistics
Matches: 165, Mismatches: 55, Indels: 17
0.70 0.23 0.07
Matches are distributed among these distances:
21 4 0.02
22 109 0.66
23 51 0.31
24 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGG
Found at i:29966 original size:2 final size:2
Alignment explanation
Indices: 29917--29947 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29907 GATGACAGTA
29917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29948 CTCGAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31369 original size:56 final size:56
Alignment explanation
Indices: 31283--31390 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
31273 TCAAATATCA
*
31283 AGTGACATGTTGTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCTTCG
1 AGTGACATGTTGTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCAAGGCTTCG
* * *
31339 AGTGACATGTTTTTTATTAGATGCCTAAAAAAAGACGTTTTAGAACCGAGGC
1 AGTGACATGTTGTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCAAGGC
31391 ATGATGCTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (56 bp):
AGTGACATGTTGTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCAAGGCTTCG
Found at i:34822 original size:90 final size:89
Alignment explanation
Indices: 34715--34892 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 89
34705 ACACATGAAT
**
34715 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTTCAAGTTATTGAT
1 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
34780 AATATTTAAAAATTAAAAAGGACAC
66 AATATTT-AAAATTAAAAAGGACAC
* *
34805 ATGATATATAATTCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
1 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
34870 AATATTTAAAATTAAAAAGGACA
66 AATATTTAAAATTAAAAAGGACA
34893 TTTTAGATAT
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
89 16 0.19
90 68 0.81
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (89 bp):
ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
AATATTTAAAATTAAAAAGGACAC
Found at i:35814 original size:5 final size:5
Alignment explanation
Indices: 35804--35835 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
35794 ACTGATGTAC
*
35804 TATAT TATAT TATAT TATAT TATAT TAAAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TA
35836 CATTTTACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:38075 original size:13 final size:13
Alignment explanation
Indices: 38057--38083 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38047 GTCCAAGTAG
38057 TAATTATGATGAT
1 TAATTATGATGAT
38070 TAATTATGATGAT
1 TAATTATGATGAT
38083 T
1 T
38084 GGTTGGACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TAATTATGATGAT
Found at i:39563 original size:27 final size:28
Alignment explanation
Indices: 39527--39579 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
39517 AGTAGTTTTC
39527 TAAAGTTATTAAAA-AAATTA-AAAGTT
1 TAAAGTTATTAAAATAAATTATAAAGTT
39553 TAAAGATTATTAAAATAAATTATAAAG
1 TAAAG-TTATTAAAATAAATTATAAAG
39580 CTAGTAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.21
27 9 0.38
28 6 0.25
29 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (28 bp):
TAAAGTTATTAAAATAAATTATAAAGTT
Found at i:40420 original size:12 final size:12
Alignment explanation
Indices: 40403--40427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40393 TTTATCAATC
40403 TATATTTAATTT
1 TATATTTAATTT
40415 TATATTTAATTT
1 TATATTTAATTT
40427 T
1 T
40428 TATCATTTAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTAATTT
Found at i:41290 original size:142 final size:143
Alignment explanation
Indices: 41120--41406 Score: 486
Period size: 142 Copynumber: 2.0 Consensus size: 143
41110 TATGTTATAT
* *
41120 TATATATGTTCTTGATCATTTTTAGCAACACATAGTTTACAAATCTAATAATTAGTTGCTTATGC
1 TATATATGTTCTTGATAATTTTTAGCAACACATAGTTTACAAATCTAATAATTACTTGCTTATGC
* *
41185 TGGTTTTGAACTTACAAAAACAAATGATCAAAATTAT-AAATATAGATGCTAATATATATTGTGG
66 TGGTTTTGAACTTACAAAAACAAATGATCAAAATTATAAAATATAGATGCTAACATATATTGTGA
41249 CTTGGCTAAAAAA
131 CTTGGCTAAAAAA
*
41262 TATATATGTTCTTGATAATTTTTAGCAACACATAGTTTATAAATCTAATAATTACTTGCTTATGC
1 TATATATGTTCTTGATAATTTTTAGCAACACATAGTTTACAAATCTAATAATTACTTGCTTATGC
* * * *
41327 TGGTTTTGAACTTACCAAAACAAATGATCGAAATTATAAAATATATATGCTAACATATGTTGTGA
66 TGGTTTTGAACTTACAAAAACAAATGATCAAAATTATAAAATATAGATGCTAACATATATTGTGA
41392 CTTGGCTAAAAAA
131 CTTGGCTAAAAAA
41405 TA
1 TA
41407 CATGAAGAGT
Statistics
Matches: 135, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
142 97 0.72
143 38 0.28
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (143 bp):
TATATATGTTCTTGATAATTTTTAGCAACACATAGTTTACAAATCTAATAATTACTTGCTTATGC
TGGTTTTGAACTTACAAAAACAAATGATCAAAATTATAAAATATAGATGCTAACATATATTGTGA
CTTGGCTAAAAAA
Found at i:41571 original size:28 final size:28
Alignment explanation
Indices: 41529--41602 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 28
41519 AACACTTGCG
*
41529 AGTTCAGGGGGCAAACATCCAAAAT-TAA
1 AGTTTAGGGGGCAAACAT-CAAAATCTAA
*
41557 AGTTTAGGGGCCAAAACATCAAAATCGTAA
1 AGTTTAGGGGGC-AAACATCAAAATC-TAA
41587 AGGTTTAGGGGGCAAA
1 A-GTTTAGGGGGCAAA
41603 AAGGGCATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 16 0.41
29 6 0.15
30 7 0.18
31 10 0.26
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.19
Consensus pattern (28 bp):
AGTTTAGGGGGCAAACATCAAAATCTAA
Found at i:41596 original size:31 final size:29
Alignment explanation
Indices: 41541--41603 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
41531 TTCAGGGGGC
41541 AAACATCCAAAATTAAAGTTTAGGGGCCA
1 AAACATCCAAAATTAAAGTTTAGGGGCCA
*
41570 AAACAT-CAAAATCGTAAAGGTTTAGGGGGCA
1 AAACATCCAAAAT--TAAA-GTTTAGGGGCCA
41601 AAA
1 AAA
41604 AGGGCATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 6 0.20
29 6 0.20
30 4 0.13
31 14 0.47
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (29 bp):
AAACATCCAAAATTAAAGTTTAGGGGCCA
Found at i:42136 original size:30 final size:30
Alignment explanation
Indices: 42102--42193 Score: 184
Period size: 30 Copynumber: 3.1 Consensus size: 30
42092 CTATTCCTCC
42102 TGGCGTTTATAATCTCTGATTATTGATTAA
1 TGGCGTTTATAATCTCTGATTATTGATTAA
42132 TGGCGTTTATAATCTCTGATTATTGATTAA
1 TGGCGTTTATAATCTCTGATTATTGATTAA
42162 TGGCGTTTATAATCTCTGATTATTGATTAA
1 TGGCGTTTATAATCTCTGATTATTGATTAA
42192 TG
1 TG
42194 AAAGTGATTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (30 bp):
TGGCGTTTATAATCTCTGATTATTGATTAA
Found at i:49310 original size:4 final size:4
Alignment explanation
Indices: 49301--49326 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
49291 TTTCGGTCAA
49301 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
49327 CTTAAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Done.