Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016165.1 Corchorus olitorius cultivar O-4 contig16198, 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: 67301
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:2738 original size:20 final size:20
Alignment explanation
Indices: 2709--2747 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2699 CATATAAAAT
* *
2709 AATAATAACTAATTTTTAAA
1 AATAACAACTAATTATTAAA
2729 AATAACAACTAATTATTAA
1 AATAACAACTAATTATTAA
2748 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAACAACTAATTATTAAA
Found at i:2842 original size:22 final size:21
Alignment explanation
Indices: 2794--2844 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2784 CGCGCGCAGA
* *
2794 TCGCGACCAAGCCGTGGTCGC
1 TCGCGACTAAGCCATGGTCGC
2815 TCGCGACTAAGCCATGGCTCAG-
1 TCGCGACTAAGCCATGG-TC-GC
2837 TCGCGACT
1 TCGCGACT
2845 GTGCTGCGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.58
22 10 0.38
23 1 0.04
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (21 bp):
TCGCGACTAAGCCATGGTCGC
Found at i:3586 original size:178 final size:179
Alignment explanation
Indices: 3270--3608 Score: 418
Period size: 178 Copynumber: 1.9 Consensus size: 179
3260 TATCCGATCA
* * *
3270 AGGTGATTTAAGTATCTATTAAAAGATTGTTCCATAATCTACAAATTTCATGAAGGACTCGTTAA
1 AGGTGATTCAAGTATCTATTAAAAGATTGTTCCATAATCTACAAATTTCATGAAGGAATCGTAAA
* * * * * *
3335 CTAAATTTAGCGTTTCAAGTATCAACAAAGCTTCCGAAAAATTAGTTGTTTCAGTTAACGAGAAT
66 CTAAATTTAACGTTTAAAGTATCAAAAAAACTTACAAAAAATTAGTTGTTTCAGTTAACGAGAAT
3400 GGACGGTCTACTT-A-ATATTACATAACTTTTGCTCTGGATGTCTGATTG
131 GGACGGTCTACTTAATATATTACATAA-TTTTGCTCTGGATGTCTGATTG
* * * * * *
3448 AGGTGATTCAAGTGTCTTTTAAAAGGTTGTTCCATTATCTACAACTATT-ATGAAGGAATTG-AA
1 AGGTGATTCAAGTATCTATTAAAAGATTGTTCCATAATCTACAAAT-TTCATGAAGGAATCGTAA
* * ** *
3511 AGCTAAATTTAATGTTTAAAGTAT-AAAAAATACTTACAAAAAATTAGTTGTTTCGGTTAGTGGG
65 A-CTAAATTTAACGTTTAAAGTATCAAAAAA-ACTTACAAAAAATTAGTTGTTTCAGTTAACGAG
*
3575 AATGTACGGTCTACTTAATATATTACATAATTTT
128 AATGGACGGTCTACTTAATATATTACATAATTTT
3609 CATATGTTTG
Statistics
Matches: 135, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
177 7 0.05
178 110 0.81
179 7 0.05
180 11 0.08
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (179 bp):
AGGTGATTCAAGTATCTATTAAAAGATTGTTCCATAATCTACAAATTTCATGAAGGAATCGTAAA
CTAAATTTAACGTTTAAAGTATCAAAAAAACTTACAAAAAATTAGTTGTTTCAGTTAACGAGAAT
GGACGGTCTACTTAATATATTACATAATTTTGCTCTGGATGTCTGATTG
Found at i:4666 original size:10 final size:9
Alignment explanation
Indices: 4634--4664 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4624 AGCTTGCTTC
*
4634 TTTTAATTT
1 TTTTATTTT
4643 TTTTATTTT
1 TTTTATTTT
4652 TTTTATTTT
1 TTTTATTTT
4661 TTTT
1 TTTT
4665 TACATAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTATTTT
Found at i:14110 original size:15 final size:16
Alignment explanation
Indices: 14082--14111 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14072 AATTTACTAC
14082 TGAAAATGAAAATTAA
1 TGAAAATGAAAATTAA
14098 TGAAAAT-AAAATTA
1 TGAAAATGAAAATTA
14112 TTACGTGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (16 bp):
TGAAAATGAAAATTAA
Found at i:16616 original size:22 final size:22
Alignment explanation
Indices: 16566--16696 Score: 70
Period size: 22 Copynumber: 5.9 Consensus size: 22
16556 TGTCTCTGTG
16566 TGGTTATTAAAATTTCATAAGA
1 TGGTTATTAAAATTTCATAAGA
* * *
16588 TGATTATTATAATTTCATGAGGA
1 TGGTTATTAAAATTTCAT-AAGA
* *
16611 -GGTTATCAAAATTCCAT-AG-
1 TGGTTATTAAAATTTCATAAGA
** * *
16630 TGTGATTACCAAAATTCCATAGGA
1 TG-G-TTATTAAAATTTCATAAGA
** *
16654 TCAGGTTATTAAAATTTTTTAGGA
1 T--GGTTATTAAAATTTCATAAGA
* *
16678 AGGTTATTGAAATTTCATA
1 TGGTTATTAAAATTTCATA
16697 GTACTATCAC
Statistics
Matches: 82, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
20 2 0.02
21 1 0.01
22 58 0.71
23 4 0.05
24 15 0.18
25 1 0.01
26 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAAGA
Found at i:17005 original size:22 final size:22
Alignment explanation
Indices: 16940--17145 Score: 101
Period size: 22 Copynumber: 9.6 Consensus size: 22
16930 GTGATAATCG
*
16940 AAATTTCATAGAGATCCGATTATCA
1 AAATTTCATAGTGAT--G-TTATCA
*
16965 AAATTT-ATAG-GAAGATTATCA
1 AAATTTCATAGTGATG-TTATCA
*
16986 AAATTTCATAGTGTTGTTATC-
1 AAATTTCATAGTGATGTTATCA
* *
17007 AAA----A-AGCGAGGTTATCA
1 AAATTTCATAGTGATGTTATCA
* *
17024 AAATTACATAATG-TGATTATCA
1 AAATTTCATAGTGATG-TTATCA
* * * *
17046 AAATTTCATAGAG-GGTCAACA
1 AAATTTCATAGTGATGTTATCA
* * *
17067 AAATTTTATAGAGAAGTTATCA
1 AAATTTCATAGTGATGTTATCA
* *
17089 AAATTTCATAGAGAGGTTATCA
1 AAATTTCATAGTGATGTTATCA
* * * *
17111 AATTTTCAAAATG-TGATTACCA
1 AAATTTCATAGTGATG-TTATCA
17133 AAATTTCATAGTG
1 AAATTTCATAGTG
17146 TTTTTTTTGG
Statistics
Matches: 140, Mismatches: 30, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
16 9 0.06
17 4 0.03
21 36 0.26
22 77 0.55
23 4 0.03
24 4 0.03
25 6 0.04
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
AAATTTCATAGTGATGTTATCA
Found at i:17113 original size:21 final size:22
Alignment explanation
Indices: 16729--17118 Score: 190
Period size: 22 Copynumber: 17.9 Consensus size: 22
16719 TGGTTATCAA
* *
16729 AGAGATTATCAAAATGTCATAG
1 AGAGGTTATCAAAATTTCATAG
16751 CA-AGGTTAT-AAGAATTTCATA-
1 -AGAGGTTATCAA-AATTTCATAG
* *
16772 ATGTGGTTAACAAAATTTCATA-
1 A-GAGGTTATCAAAATTTCATAG
* * *
16794 AGGAGGTTA-CTAATATTCCATGG
1 A-GAGGTTATC-AAAATTTCATAG
*
16817 GGAGGTTATCAAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
* *
16839 TGTGGTTATCAAAATTTCATATG
1 AGAGGTTATCAAAATTTCATA-G
*
16862 A-AGGTTATAAAAGTCTCAATTTCATA-
1 AGAGGTTAT-CAA-----AATTTCATAG
* * *
16888 AGAAG-TACCAAAATTTGATAG
1 AGAGGTTATCAAAATTTCATAG
*
16909 A-AGGTTATC-AAATCTCATAG
1 AGAGGTTATCAAAATTTCATAG
* * * *
16929 AGTGATAATCGAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
*
16951 AGATCCGATTATCAAAATTT-ATAG
1 AGA---GGTTATCAAAATTTCATAG
*
16975 -GAAGATTATCAAAATTTCATAG
1 AG-AGGTTATCAAAATTTCATAG
* **
16997 TGTTGTTATC-AAA----A-AG
1 AGAGGTTATCAAAATTTCATAG
* *
17013 CGAGGTTATCAAAATTACATA-
1 AGAGGTTATCAAAATTTCATAG
* *
17034 ATGTGATTATCAAAATTTCATAG
1 A-GAGGTTATCAAAATTTCATAG
* * *
17057 AG-GGTCAACAAAATTTTATAG
1 AGAGGTTATCAAAATTTCATAG
*
17078 AGAAGTTATCAAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
*
17100 AGAGGTTATCAAATTTTCA
1 AGAGGTTATCAAAATTTCA
17119 AAATGTGATT
Statistics
Matches: 280, Mismatches: 53, Indels: 69
0.70 0.13 0.17
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
20 21 0.08
21 47 0.17
22 156 0.56
23 10 0.04
24 5 0.02
25 14 0.05
26 3 0.01
27 2 0.01
28 9 0.03
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (22 bp):
AGAGGTTATCAAAATTTCATAG
Found at i:17273 original size:22 final size:22
Alignment explanation
Indices: 17245--17371 Score: 96
Period size: 22 Copynumber: 5.7 Consensus size: 22
17235 GGGAGGATAC
17245 CAAAATTTCATATGAAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
** *
17267 CAAAATTTCATAGTTTA-GTTTT
1 CAAAATTTCATA-TGAAGGTTAT
* *
17289 CAAAATTTCATAAGAGGGTTAT
1 CAAAATTTCATATGAAGGTTAT
* * * *
17311 GAAAATTTCATA-GTATGTAGAT
1 CAAAATTTCATATGAAGGT-TAT
* * * *
17333 CAAAATTTCATAGGGAGATTAA
1 CAAAATTTCATATGAAGGTTAT
17355 CAAAATTTCATAATGAA
1 CAAAATTTCAT-ATGAA
17372 ATTTATTTAG
Statistics
Matches: 79, Mismatches: 21, Indels: 9
0.72 0.19 0.08
Matches are distributed among these distances:
21 3 0.04
22 68 0.86
23 8 0.10
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATATGAAGGTTAT
Found at i:17300 original size:44 final size:44
Alignment explanation
Indices: 17245--17366 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
17235 GGGAGGATAC
* *
17245 CAAAATTTCATATGAAGGTTATCAAAATTTCATAGT-T-TAGTTTT
1 CAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAG--AT
* *
17289 CAAAATTTCATAAGAGGGTTATGAAAATTTCATAGTATGTAGAT
1 CAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAGAT
* * * *
17333 CAAAATTTCATAGGGAGATTAACAAAATTTCATA
1 CAAAATTTCATAAGAAGGTTATCAAAATTTCATA
17367 ATGAAATTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
44 62 0.94
45 1 0.02
46 3 0.05
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (44 bp):
CAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAGAT
Found at i:17400 original size:8 final size:8
Alignment explanation
Indices: 17383--17415 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
17373 TTTATTTAGA
17383 TCAAAATT
1 TCAAAATT
*
17391 TCATAATT
1 TCAAAATT
17399 TCAAAATT
1 TCAAAATT
17407 TCAAAATT
1 TCAAAATT
17415 T
1 T
17416 GATATGTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (8 bp):
TCAAAATT
Found at i:20013 original size:4 final size:4
Alignment explanation
Indices: 20004--20072 Score: 138
Period size: 4 Copynumber: 17.2 Consensus size: 4
19994 TGTTGTGTTA
20004 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
20052 TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG T
20073 GATGGGTGTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 65 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:21917 original size:18 final size:18
Alignment explanation
Indices: 21880--21923 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
21870 TTTTTTTCTT
**
21880 TCCTTTTTAATTAATATA
1 TCCTTTTTAAGCAATATA
*
21898 TCCTTTTTAAGCAATTTA
1 TCCTTTTTAAGCAATATA
21916 T-CTTTTTA
1 TCCTTTTTA
21924 CCGGCCAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.27, C:0.14, G:0.02, T:0.57
Consensus pattern (18 bp):
TCCTTTTTAAGCAATATA
Found at i:30200 original size:6 final size:6
Alignment explanation
Indices: 30182--30241 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
30172 AAAGGAGAAG
* * *
30182 AGAAAA A-ACAAA AGAAAAA AGGAAA AGAAAA AG-AAA ATAAAA CGAAAA
1 AGAAAA AGA-AAA AG-AAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
30230 AG-AAA AGAAAA A
1 AGAAAA AGAAAA A
30242 AGCCATGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
5 10 0.23
6 27 0.63
7 5 0.12
8 1 0.02
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:30207 original size:13 final size:13
Alignment explanation
Indices: 30172--30213 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
30162 TCGGGTTGAG
30172 AAAGGAGAAGAGAAA
1 AAAGGA-AA-AGAAA
*
30187 AAA-CAAAAGAAA
1 AAAGGAAAAGAAA
30199 AAAGGAAAAGAAA
1 AAAGGAAAAGAAA
30212 AA
1 AA
30214 GAAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 8 0.33
13 12 0.50
14 1 0.04
15 3 0.12
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGGAAAAGAAA
Found at i:30228 original size:17 final size:16
Alignment explanation
Indices: 30198--30240 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
30188 AACAAAAGAA
30198 AAAAGGAAAAGAAAAAG
1 AAAA-GAAAAGAAAAAG
*
30215 AAAATAAAACGAAAAAG
1 AAAAGAAAA-GAAAAAG
30232 AAAAGAAAA
1 AAAAGAAAA
30241 AAGCCATGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:30243 original size:12 final size:12
Alignment explanation
Indices: 30177--30240 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 12
30167 TTGAGAAAGG
*
30177 AGAAGAGAAAAA
1 AGAAAAGAAAAA
*
30189 ACAAAAGAAAAA
1 AGAAAAGAAAAA
30201 AGGAAAAG-AAAA
1 A-GAAAAGAAAAA
*
30213 AGAAAA-TAAAA
1 AGAAAAGAAAAA
* *
30224 CGAAAA-AGAAA
1 AGAAAAGAAAAA
30235 AGAAAA
1 AGAAAA
30241 AAGCCATGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
11 22 0.51
12 16 0.37
13 5 0.12
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (12 bp):
AGAAAAGAAAAA
Found at i:38650 original size:2 final size:2
Alignment explanation
Indices: 38643--38678 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
38633 TCGACCTAGC
38643 AT AT AT AT AT AT AT AT AT 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
38679 CAAGCCTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47021 original size:22 final size:22
Alignment explanation
Indices: 46993--47037 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
46983 TGTCCTTATA
* *
46993 ACTATTTCATTTTTATCGTTTT
1 ACTATTTCACTTTTATAGTTTT
*
47015 ACTATTTTACTTTTATAGTTTT
1 ACTATTTCACTTTTATAGTTTT
47037 A
1 A
47038 TTCAACTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.62
Consensus pattern (22 bp):
ACTATTTCACTTTTATAGTTTT
Found at i:47034 original size:93 final size:93
Alignment explanation
Indices: 46930--47100 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
46920 CATTATTTAA
* *
46930 ACTTTTATAGTTTTAGTCAACTAAAAACTCTAATTTTGTTTAATTAAATCTAATGTCCTTATAAC
1 ACTTTTATAGTTTTAGTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATAAC
46995 TATTTCATTTTTATCGTTTTACTATTTT
66 TATTTCATTTTTATCGTTTTACTATTTT
* * *
47023 ACTTTTATAGTTTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTATAGTTTTAGTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATAAC
*
47088 TATTTTATTTTTA
66 TATTTCATTTTTA
47101 CCATATTACT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.52
Consensus pattern (93 bp):
ACTTTTATAGTTTTAGTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTCATTTTTATCGTTTTACTATTTT
Found at i:47433 original size:129 final size:129
Alignment explanation
Indices: 47214--47469 Score: 365
Period size: 129 Copynumber: 2.0 Consensus size: 129
47204 GTTTAAACTC
47214 TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATT
1 TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTTATAACTATT
** *
47279 TAATTTTTACCATTTTACTGTTTTAATT-AAAAACTT-ATATATTAGAATTTTTTAAATATACTT
65 TAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAATTTTTAAAATATACTT
* *
47342 TTATAGTTTTACTCAACTTAAAACTCTATTTTTTTTATTTAATTAAATCTAATAT-TTATACCTA
1 TTATAGTTTTACTCAACTAAAAACTCTA---TTTTTATTTAATTAAATCTAATATCTTATAACTA
* * * *
47406 TTTTATTTTTATCATTTTACTAATTTAATTAAAAAATTTAGATATATTATAATTTTTAAAATAT
63 TTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTA-ATATATTAGAATTTTTAAAATAT
47470 TTTTCTTAAA
Statistics
Matches: 113, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
128 27 0.24
129 34 0.30
130 7 0.06
131 24 0.21
132 21 0.19
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (129 bp):
TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTATAACTATTT
AATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAATTTTTAAAATATACTT
Found at i:48040 original size:38 final size:38
Alignment explanation
Indices: 47989--48069 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
47979 GTCAGGCGGG
47989 TTCGGGTTTTGGCCTCAGGTTAATCTGGTTCTTGGTCA
1 TTCGGGTTTTGGCCTCAGGTTAATCTGGTTCTTGGTCA
48027 TTCGGGTTTTGGCCTCAGGTTAATCTGGTTCTTGGTCA
1 TTCGGGTTTTGGCCTCAGGTTAATCTGGTTCTTGGTCA
*
48065 CTCGG
1 TTCGG
48070 ATCAATTGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.10, C:0.20, G:0.30, T:0.41
Consensus pattern (38 bp):
TTCGGGTTTTGGCCTCAGGTTAATCTGGTTCTTGGTCA
Found at i:51055 original size:12 final size:12
Alignment explanation
Indices: 51038--51062 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51028 TAATGCAGCA
51038 TGACAATTTGAT
1 TGACAATTTGAT
51050 TGACAATTTGAT
1 TGACAATTTGAT
51062 T
1 T
51063 AATTGATGGT
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:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TGACAATTTGAT
Found at i:51314 original size:5 final size:5
Alignment explanation
Indices: 51304--51342 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
51294 CAAAAAGGAA
51304 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
51343 AATTTCTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:53174 original size:129 final size:127
Alignment explanation
Indices: 53002--53232 Score: 304
Period size: 129 Copynumber: 1.8 Consensus size: 127
52992 TTTTGAATTG
* * *
53002 AAATGATAAAAATAAAATAATTACAAAAATATTGCATTTAATTAAATGAAAATACAATTTTTAAC
1 AAATGATAAAAATAAAATAATTACAAAAATATTACATTCAATTAAAT-AAAATA-AACTTTTAAC
* * * *
53067 ATAATAAAATCGT-AAAACA-TTAAACAATGACATTTAAAATATTAAAAAAAATTCTAAAATAGT
64 AGAATAAAA-C-TAAAAAAATTTAAAAAATGACATATAAAATATTAAAAAAAATTCTAAAATAGT
53130 A
127 A
* * * * *
53131 AAATGGTAAAAATAAAATAGTTATAAAAATATTATATTCAATTAAATAAAATAAACTTTTAATAG
1 AAATGATAAAAATAAAATAATTACAAAAATATTACATTCAATTAAATAAAATAAACTTTTAACAG
53196 AATAAAACTAAAAAAATTTAAAAAATGACATATAAAA
66 AATAAAACTAAAAAAATTTAAAAAATGACATATAAAA
53233 AAATATTAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
125 1 0.01
126 6 0.07
127 34 0.39
128 6 0.07
129 41 0.47
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.30
Consensus pattern (127 bp):
AAATGATAAAAATAAAATAATTACAAAAATATTACATTCAATTAAATAAAATAAACTTTTAACAG
AATAAAACTAAAAAAATTTAAAAAATGACATATAAAATATTAAAAAAAATTCTAAAATAGTA
Found at i:53306 original size:13 final size:13
Alignment explanation
Indices: 53285--53320 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
53275 GATAATTCTT
53285 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
53298 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
53311 TCTGACCCTC
1 TTTGACCCTC
53321 ATAATAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.42, G:0.08, T:0.33
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:53374 original size:36 final size:36
Alignment explanation
Indices: 53322--53391 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
53312 CTGACCCTCA
*
53322 TAATAATTAAGATAATAAATTAAA-TCGAGGTTTAGC
1 TAATAATTAAGATAATAAATCAAATTC-AGGTTTAGC
*
53358 TAATAATTAAGGTAATAAATCAAATTCAGGTTTA
1 TAATAATTAAGATAATAAATCAAATTCAGGTTTA
53392 ACTTCTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 29 0.94
37 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (36 bp):
TAATAATTAAGATAATAAATCAAATTCAGGTTTAGC
Found at i:53585 original size:2 final size:2
Alignment explanation
Indices: 53578--53618 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
53568 TTTTGTAGTC
*
53578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53619 ACTAATTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:55728 original size:129 final size:129
Alignment explanation
Indices: 55586--55847 Score: 393
Period size: 129 Copynumber: 2.0 Consensus size: 129
55576 GTCATTTAAT
* *
55586 AAATATATTTTAAAAATTCTAATATATCTAAG-TTTTTTAATTAAATTAGTAAAATGGTAAAAAT
1 AAATATA-TTAAAAAATTCTAATATA--TAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT
* * * *
55650 AAAATAGGTATAAAGATATTAGATTTTA-TACAATAGAAATAGAGTTTTTAGTTGAGTAAAATTA
63 AAAATAGGTATAAAGATATTAGATTTAATTA-AATAAAAATAGAGTTTTTAGTTAAGTAAAACTA
55714 TAA
127 TAA
55717 AAATATATTAAAAAATTCTAATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
1 AAATATATTAAAAAATTCTAATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
* * *
55782 TTAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAA
66 ATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAA
55846 AA
1 AA
55848 GTTTAACTAA
Statistics
Matches: 120, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
128 4 0.03
129 90 0.75
130 19 0.16
131 7 0.06
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (129 bp):
AAATATATTAAAAAATTCTAATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
ATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAA
Found at i:57338 original size:25 final size:22
Alignment explanation
Indices: 57310--57357 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
57300 ATTCTAAATA
57310 TATTATATAATAATATATATTGGTT
1 TATTATAT-AT-ATATATA-TGGTT
*
57335 TATTCTATATATATATATGGTT
1 TATTATATATATATATATGGTT
57357 T
1 T
57358 TCTCCCAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 7 0.32
24 2 0.09
25 7 0.32
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.54
Consensus pattern (22 bp):
TATTATATATATATATATGGTT
Found at i:59044 original size:2 final size:2
Alignment explanation
Indices: 59039--59071 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59029 ATATAAACCT
59039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59072 GTTTGTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59618 original size:107 final size:105
Alignment explanation
Indices: 59444--59707 Score: 415
Period size: 107 Copynumber: 2.5 Consensus size: 105
59434 TAAGTTTAGC
* *
59444 CTTAATTTCACTAAATTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAA
1 CTTAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAA
59509 TTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAA
65 TTAATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAA
*
59552 CTTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAAT
1 CTTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
* *
59617 TAATAATATTGTTATAGGGTTTTAGAAATAAAATATATAA
66 TAATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAA
** *
59657 C-TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 CTTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
59708 TAGAAAAATT
Statistics
Matches: 148, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
103 44 0.30
104 3 0.02
105 33 0.22
107 49 0.33
108 19 0.13
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (105 bp):
CTTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
TAATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAA
Found at i:63097 original size:19 final size:18
Alignment explanation
Indices: 63044--63098 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
63034 TTCAGCTTTA
63044 GGCTTGCA-TTAGGACATTG
1 GGCTTGCATTTAGG-CA-TG
* *
63063 GGCTTGCATATGGGCATG
1 GGCTTGCATTTAGGCATG
63081 GAGCTTGCATTTAGGCAT
1 G-GCTTGCATTTAGGCAT
63099 TTTAGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 3 0.10
19 24 0.80
20 3 0.10
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (18 bp):
GGCTTGCATTTAGGCATG
Found at i:66357 original size:36 final size:37
Alignment explanation
Indices: 66297--66703 Score: 448
Period size: 36 Copynumber: 11.2 Consensus size: 37
66287 ATGAATCAGT
66297 CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
1 CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
* * *
66334 CATAGACTTAA-TTCAAGGTAATTAAGT-AAATC-AG
1 CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
66368 TCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
1 -CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
* * * *
66406 CACAGACTTAA-TTCAAGGTAATCAGGTAAAATCAAA
1 CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
* * *
66442 CACAGACTTAA-TTCAAGGTAATTAAGT-AAATCAAG
1 CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
* *
66477 CAAAGAATTAATTTCAAGGAAATTGGGTAAGAA-CAAG
1 CAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAG
66514 CAAAGACTTAATTTCAAGGAAATTAGGTAAGAA-CAAG
1 CAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAG
* * * *
66551 CACAA-ACTTAA-TTCAGGGTAATTAAGT-AAAGC-AG
1 CA-AAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
*
66585 TCAAAGACGTAATTTCAAGGAAATTAGGTAAAATCAAG
1 -CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
* * * *
66623 CAGAGACTTAA-TTCACGGTAATTAAGT-AAATC-AG
1 CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
*
66657 TCAAAGACTTAATTTCAAGGAAATTAGGTAAAATTAAG
1 -CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
*
66695 CACAGACTT
1 CAAAGACTT
66704 TGTCGAAACG
Statistics
Matches: 313, Mismatches: 39, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
34 10 0.03
35 55 0.18
36 140 0.45
37 98 0.31
38 10 0.03
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (37 bp):
CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAG
Found at i:66407 original size:72 final size:72
Alignment explanation
Indices: 66290--66703 Score: 566
Period size: 72 Copynumber: 5.7 Consensus size: 72
66280 TGCATCCATG
*
66290 AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCATAGACTTAATTCAAGGTAA
1 AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTCAAGGTAA
66355 TTAAGTA
66 TTAAGTA
66362 AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTCAAGGTAA
1 AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTCAAGGTAA
* *
66427 TCAGGTAA
66 TTAAGT-A
** * * * * * *
66435 AATCAAACACAGACTTAA-TTCAAGGTAATTAAGT-AAATCAAGCAAAGAATTAATTTCAAGGAA
1 AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAA-TTCAAGGTA
**
66498 ATTGGGTA
65 ATTAAGTA
* * *
66506 AGAACAAG-CAAAGACTTAATTTCAAGGAAATTAGGTAAGAA-CAAGCACAAACTTAATTCAGGG
1 A-ATC-AGTCAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAGCACAGACTTAATTCAAGG
66569 TAATTAAGTA
63 TAATTAAGTA
* * * *
66579 AAGCAGTCAAAGACGTAATTTCAAGGAAATTAGGTAAAATCAAGCAGAGACTTAATTCACGGTAA
1 AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTCAAGGTAA
66644 TTAAGTA
66 TTAAGTA
*
66651 AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATTAAGCACAGACTT
1 AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTT
66704 TGTCGAAACG
Statistics
Matches: 299, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
71 23 0.08
72 216 0.72
73 45 0.15
74 13 0.04
75 2 0.01
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (72 bp):
AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTCAAGGTAA
TTAAGTA
Found at i:66676 original size:217 final size:217
Alignment explanation
Indices: 66297--66688 Score: 626
Period size: 217 Copynumber: 1.8 Consensus size: 217
66287 ATGAATCAGT
* *
66297 CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCATAGACTTAATTCAAGGTAATTAAGTA
1 CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAAACTTAATTCAAGGTAATTAAGTA
* *
66362 AATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTCAAGGTAA
66 AAGCAGTCAAAGACGTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTCAAGGTAA
* * *
66427 TCAGGTAAAATCAAACACAGACTTAATTCAAGGTAATTAAGTAAATCAAGCAAAGAATTAATTTC
131 TCAAGTAAAATCAAACAAAGACTTAATTCAAGGAAATTAAGTAAATCAAGCAAAGAATTAATTTC
66492 AAGGAAATTGGGTAAGAACAAG
196 AAGGAAATTGGGTAAGAACAAG
*
66514 CAAAGACTTAATTTCAAGGAAATTAGGTAAGAA-CAAGCACAAACTTAATTCAGGGTAATTAAGT
1 CAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAGCACAAACTTAATTCAAGGTAATTAAGT
* *
66578 AAAGCAGTCAAAGACGTAATTTCAAGGAAATTAGGTAAAATCAAGCAGAGACTTAATTCACGGTA
65 AAAGCAGTCAAAGACGTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTCAAGGTA
* ** *
66643 ATTAAGT-AAATCAGTCAAAGACTTAATTTCAAGGAAATTAGGTAAA
130 ATCAAGTAAAATCAAACAAAGACTTAA-TTCAAGGAAATTAAGTAAA
66689 ATTAAGCACA
Statistics
Matches: 159, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
216 16 0.10
217 141 0.89
218 2 0.01
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (217 bp):
CAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAAACTTAATTCAAGGTAATTAAGTA
AAGCAGTCAAAGACGTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTCAAGGTAA
TCAAGTAAAATCAAACAAAGACTTAATTCAAGGAAATTAAGTAAATCAAGCAAAGAATTAATTTC
AAGGAAATTGGGTAAGAACAAG
Done.