Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012085.1 Corchorus capsularis cultivar CVL-1 contig12106, 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: 39129
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:184 original size:41 final size:40
Alignment explanation
Indices: 137--335 Score: 143
Period size: 41 Copynumber: 4.8 Consensus size: 40
127 ACCCAATAAC
137 CAAAGTCCCCAAACACAATCATAACACATGGGCAACTCTTT
1 CAAAGTCCCCAAACACAATCATAACACA-GGGCAACTCTTT
* ** * * *
178 TAAAGTCTTCAAACACATTCATAACACAGAGGC-ATTCATAT
1 CAAAGTCCCCAAACACAATCATAACACAG-GGCAACTC-TTT
* *
219 CAAAGTCCCCAAGCACAATTATAACACACGGGCAATTCTCTTT
1 CAAAGTCCCCAAACACAATCATAACACA-GGGCAA--CTCTTT
* * * * * * * *
262 CAAAGTCCTCAAGCACATTCTTAACACAGAGACATCTATAT
1 CAAAGTCCCCAAACACAATCATAACACAG-GGCAACTCTTT
* *
303 CAAAGTCCCTAAACAC-AT-GTAACACAAGGGCAA
1 CAAAGTCCCCAAACACAATCATAACAC-AGGGCAA
336 TTTTCTCTAT
Statistics
Matches: 121, Mismatches: 29, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
39 9 0.07
40 7 0.06
41 71 0.59
42 3 0.02
43 29 0.24
44 2 0.02
ACGTcount: A:0.40, C:0.28, G:0.11, T:0.22
Consensus pattern (40 bp):
CAAAGTCCCCAAACACAATCATAACACAGGGCAACTCTTT
Found at i:343 original size:84 final size:84
Alignment explanation
Indices: 137--337 Score: 259
Period size: 84 Copynumber: 2.4 Consensus size: 84
127 ACCCAATAAC
* * * *
137 CAAAGTCCCCAAACACAATCATAACACATGGGCAA--CTCTTTTAAAGTCTTCAAACACATTCAT
1 CAAAGTCCCCAAACACAATTATAACACAAGGGCAATTCTCTTTCAAAGTCCTCAAACACATTCAT
*
200 AACACAGAGGCATTCATAT
66 AACACAGAGACATTCATAT
* * * *
219 CAAAGTCCCCAAGCACAATTATAACACACGGGCAATTCTCTTTCAAAGTCCTCAAGCACATTCTT
1 CAAAGTCCCCAAACACAATTATAACACAAGGGCAATTCTCTTTCAAAGTCCTCAAACACATTCAT
284 AACACAGAGACA-TCTATAT
66 AACACAGAGACATTC-ATAT
* *
303 CAAAGTCCCTAAACAC-A-TGTAACACAAGGGCAATT
1 CAAAGTCCCCAAACACAATTATAACACAAGGGCAATT
338 TTCTCTATAT
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
82 48 0.46
83 3 0.03
84 53 0.51
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.22
Consensus pattern (84 bp):
CAAAGTCCCCAAACACAATTATAACACAAGGGCAATTCTCTTTCAAAGTCCTCAAACACATTCAT
AACACAGAGACATTCATAT
Found at i:1669 original size:21 final size:21
Alignment explanation
Indices: 1643--1683 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1633 ATCAATTCCG
1643 GTGTAAAACAACTTGTTTTAT
1 GTGTAAAACAACTTGTTTTAT
1664 GTGTAAAACAACTTGTTTTA
1 GTGTAAAACAACTTGTTTTA
1684 CATCCTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (21 bp):
GTGTAAAACAACTTGTTTTAT
Found at i:6327 original size:29 final size:28
Alignment explanation
Indices: 6233--6326 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 28
6223 GCTCAAAAAT
*
6233 GCCCCTGAACTTATACAAAATGGTCAAATAA
1 GCCCCTGAACTT-T--AAAATGGCCAAATAA
* *
6264 GCCCCTGAACTTT-AATTGCAGCCGAATAA
1 GCCCCTGAACTTTAAAATG--GCCAAATAA
6293 GCCCCTGAACTCTTTAAAATGGCCAAATAA
1 GCCCCTGAA--CTTTAAAATGGCCAAATAA
6323 GCCC
1 GCCC
6327 TTTTTGGATG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
27 4 0.08
29 16 0.30
30 13 0.25
31 16 0.30
32 4 0.08
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (28 bp):
GCCCCTGAACTTTAAAATGGCCAAATAA
Found at i:8306 original size:26 final size:28
Alignment explanation
Indices: 8277--8336 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
8267 CTAAACATGC
8277 AATGACCAGAATGCCCATGG-TG-CCGA
1 AATGACCAGAATGCCCATGGATGACCGA
* * *
8303 AATGACCAGCATGCCCCTGGATGACCGC
1 AATGACCAGAATGCCCATGGATGACCGA
8331 AATGAC
1 AATGAC
8337 TAATTAACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 18 0.62
27 2 0.07
28 9 0.31
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (28 bp):
AATGACCAGAATGCCCATGGATGACCGA
Found at i:8429 original size:21 final size:21
Alignment explanation
Indices: 8405--8445 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
8395 ACTGGTGGGC
8405 TTTACTTGCTGAGGAAGGCGT
1 TTTACTTGCTGAGGAAGGCGT
8426 TTTACTTGCTGAGGAAGGCG
1 TTTACTTGCTGAGGAAGGCG
8446 AACTCTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.34, T:0.32
Consensus pattern (21 bp):
TTTACTTGCTGAGGAAGGCGT
Found at i:8631 original size:17 final size:17
Alignment explanation
Indices: 8593--8625 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8583 CTCACAGTAC
*
8593 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGATA
8610 CTAGGTAGTATGAGAT
1 CTAGGTAGTATGAGAT
8626 GATAGGCTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.06, G:0.33, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGATA
Found at i:12287 original size:21 final size:22
Alignment explanation
Indices: 12248--12302 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
12238 CTTGGTCTTG
* *
12248 AGTCATTTG-TTCTTTAAG-TA
1 AGTCATTTGACTCCTTAAGTTA
*
12268 AGTCATTTGACTCCTTAAGTTG
1 AGTCATTTGACTCCTTAAGTTA
12290 AG-CATTTGACTCC
1 AGTCATTTGACTCC
12303 ATTATTCGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.30
21 18 0.60
22 3 0.10
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (22 bp):
AGTCATTTGACTCCTTAAGTTA
Found at i:14937 original size:9 final size:9
Alignment explanation
Indices: 14923--14947 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14913 AACAGCTTGG
14923 CGTGGAGGA
1 CGTGGAGGA
14932 CGTGGAGGA
1 CGTGGAGGA
14941 CGTGGAG
1 CGTGGAG
14948 CAGGATAGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.12, G:0.56, T:0.12
Consensus pattern (9 bp):
CGTGGAGGA
Found at i:15369 original size:135 final size:135
Alignment explanation
Indices: 15206--15500 Score: 418
Period size: 135 Copynumber: 2.2 Consensus size: 135
15196 AGAGGCAGAG
* * *
15206 CACCAAGCGGCTGTTGGTTTTGCCCCCCGAGTCCTTGCTCCCCAAGTCTTTCATCGATGAGACCA
1 CACCAAGCCGTTGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATGAGACCA
* * * * * *
15271 A-CTTGAGCCATGACCTGTTGATTGTTCACCTGATGGTTAACTTGTTG-AAGGGGAAGAGGACCG
66 ATC-TCAGCCATGACCTGTGGATTGTTCACCTGATGGTTAACCTGTTGAAAAGGCAA-AGCACCG
*
15334 GGCTGGG
129 GGCTGGA
15341 CACCAAGCAC-TTGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATGAGACC
1 CACCAAGC-CGTTGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATGAGACC
* * *
15405 AATCTCAGCCATGACTTGTGGGTTGTTCACCTGATGGTTGACCTGTTGAAAAGGCAAAGCACCGG
65 AATCTCAGCCATGACCTGTGGATTGTTCACCTGATGGTTAACCTGTTGAAAAGGCAAAGCACCGG
15470 GCTGGA
130 GCTGGA
15476 CACCAAGCCGTTGTTGGTTTT-CCCC
1 CACCAAGCCGTTGTTGGTTTTGCCCC
15501 TCCAAGTCTT
Statistics
Matches: 143, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
134 5 0.03
135 131 0.92
136 7 0.05
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (135 bp):
CACCAAGCCGTTGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATGAGACCA
ATCTCAGCCATGACCTGTGGATTGTTCACCTGATGGTTAACCTGTTGAAAAGGCAAAGCACCGGG
CTGGA
Found at i:16083 original size:104 final size:105
Alignment explanation
Indices: 15903--16160 Score: 425
Period size: 104 Copynumber: 2.5 Consensus size: 105
15893 CCTTAAGAGG
15903 GAAGTCAA-A-TCTTGTTGAGTCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCGGTCGAGTGG
1 GAAGTCAACATTCTTG--GAGTCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCGGTCGAGTGG
*
15966 GACAGTCACCGAACAAATCTTAGAAGCAACGT-GCGGAGTGA
64 GACAGTCACCGAACAAATCTTAGAAGCAACGTCGCGAAGTGA
*
16007 GAAGTCAACATTCTTGGAGTCCCACCGGGCGTGCCAAAAGGAGATGTTGGTGCGGTCGAGTGGGA
1 GAAGTCAACATTCTTGGAGTCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCGGTCGAGTGGGA
*
16072 CAGTCACCGAACAAATTTTAGAAGCAACGTCGCGAAGTGA
66 CAGTCACCGAACAAATCTTAGAAGCAACGTCGCGAAGTGA
*
16112 GAAGTCAACATTCTTAGG-GTCCCACCAGGCGTGCCAAAAAGAGATGTTG
1 GAAGTCAACATTCTT-GGAGTCCCACCGGGCGTGCCAAAAAGAGATGTTG
16161 CGCCAAAAAT
Statistics
Matches: 145, Mismatches: 5, Indels: 7
0.92 0.03 0.04
Matches are distributed among these distances:
104 85 0.59
105 53 0.37
106 7 0.05
ACGTcount: A:0.29, C:0.21, G:0.31, T:0.19
Consensus pattern (105 bp):
GAAGTCAACATTCTTGGAGTCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCGGTCGAGTGGGA
CAGTCACCGAACAAATCTTAGAAGCAACGTCGCGAAGTGA
Found at i:20914 original size:21 final size:21
Alignment explanation
Indices: 20880--20920 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20870 ATTTATATAT
* * *
20880 AAAGATTGATTTTTTTAAGTA
1 AAAGATTCAATTTTTAAAGTA
20901 AAAGATTCAATTTTTAAAGT
1 AAAGATTCAATTTTTAAAGT
20921 GATTTGTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (21 bp):
AAAGATTCAATTTTTAAAGTA
Found at i:21006 original size:49 final size:49
Alignment explanation
Indices: 20943--21036 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
20933 AAAGTGGGTT
** *
20943 TTTTAATTAGAAGATGACTCTTTCAAGTAATTTGTAAATAGAGATGAAC
1 TTTTAATTAGAAGATGAAGCTTTCAAGTAATTTGTAAATAAAGATGAAC
* *
20992 TTTTAATT-GAAAGATTAAGCTTTTAAGTAATTTGTAAATAAAGAT
1 TTTTAATTAG-AAGATGAAGCTTTCAAGTAATTTGTAAATAAAGAT
21037 TGAGTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.03
49 38 0.97
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.39
Consensus pattern (49 bp):
TTTTAATTAGAAGATGAAGCTTTCAAGTAATTTGTAAATAAAGATGAAC
Found at i:21067 original size:50 final size:50
Alignment explanation
Indices: 20865--21088 Score: 150
Period size: 51 Copynumber: 4.4 Consensus size: 50
20855 TTAAGTTTTT
* * ** * * *
20865 AAGTAATTTATATATAAAGATTGATTTTTTTAAGTAAAAGATTCAATTTTTA
1 AAGTAATTTGTAAATAAAGATTGA-ACTTTTAATTGAAAGATT-AATCTTTA
* * *** * * *
20917 AAGTGATTTGTAAATAAA-AGTGGGTTTTTTAATT-AGAAGATGACTCTTTC
1 AAGTAATTTGTAAATAAAGA-TTGAACTTTTAATTGA-AAGATTAATCTTTA
* * *
20967 AAGTAATTTGTAAATAGAGA-TGAACTTTTAATTGAAAGATTAAGCTTTT
1 AAGTAATTTGTAAATAAAGATTGAACTTTTAATTGAAAGATTAATCTTTA
** *
21016 AAGTAATTTGTAAATAAAGATTGAGTTTTTAGTTGGAAA-ATTAAATCTTTA
1 AAGTAATTTGTAAATAAAGATTGAACTTTTAATT-GAAAGATT-AATCTTTA
* * *
21067 AAGTATTTTGTGAATAAGGATT
1 AAGTAATTTGTAAATAAAGATT
21089 AAATGTTTTA
Statistics
Matches: 136, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
49 38 0.28
50 36 0.26
51 45 0.33
52 17 0.12
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (50 bp):
AAGTAATTTGTAAATAAAGATTGAACTTTTAATTGAAAGATTAATCTTTA
Found at i:21669 original size:35 final size:34
Alignment explanation
Indices: 21630--22094 Score: 515
Period size: 35 Copynumber: 13.7 Consensus size: 34
21620 AGTAATAAGA
*
21630 AACTTAATTCAGGGCAATTAAGTAAGTCAGTGAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGT-AAT
* *
21665 AACTTAATTCAGGGTAATTAAGTAAATCAGCAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* *
21699 ---TTAATTCAGGGTAATTAAGTAAGT-AATAGGT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTA-AT
21730 AACTTAATTCAGGGTAATTAAGT---T-AGTAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* * * *
21760 CAACTTAATTCGGGGTAATTAGGTAATTCAGTGATT
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGT-AAT
21796 AACTTAATTCAGGGTAA-T---TAAGTCAGTAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* * *
21826 CAACTTAATTCAGGGTAATTAGGTAATTCAGTGATT
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGT-AAT
* *
21862 AACTTAATTCAAGGTAATTAAGTGAGTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-T
* *
21897 AACTTAATTCAGAGTAATTAAGTAATTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-T
*
21932 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
21966 CAACTTAATTCAGGGTAATTAAGTAAGTCAATAAGT
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-T
* * *
22002 ACCTTAATTCAGGGTAATTAAGTGAGTCAGTTAGT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAG-TAAT
* *
22037 AACTTAATTCATGGTAATTAAGT-AGTTCAATAAGT
1 AACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA-T
22072 AACTTAATTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
22095 TTAGTAAGAA
Statistics
Matches: 368, Mismatches: 40, Indels: 44
0.81 0.09 0.10
Matches are distributed among these distances:
30 5 0.01
31 74 0.20
32 1 0.00
34 31 0.08
35 250 0.68
36 7 0.02
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (34 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
Found at i:21811 original size:27 final size:27
Alignment explanation
Indices: 21781--21845 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 27
21771 GGGGTAATTA
* *
21781 GGTAATTCAGTGATTAACTTAATTCAG
1 GGTAATTCAGTAATCAACTTAATTCAG
21808 GGTAATTAAGTCAGTAATCAACTTAATTCAG
1 GGTAA-T---TCAGTAATCAACTTAATTCAG
21839 GGTAATT
1 GGTAATT
21846 AGGTAATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
27 6 0.19
28 1 0.03
30 1 0.03
31 24 0.75
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCAGTAATCAACTTAATTCAG
Found at i:21922 original size:8 final size:8
Alignment explanation
Indices: 21840--21933 Score: 53
Period size: 8 Copynumber: 11.0 Consensus size: 8
21830 TTAATTCAGG
*
21840 GTAATTAG
1 GTAATTAA
*
21848 GTAATTCA
1 GTAATTAA
*
21856 GTGATTAA
1 GTAATTAA
*
21864 CTTAATTCAA
1 -GTAATT-AA
21874 GGTAATTAA
1 -GTAATTAA
* * *
21883 GTGAGTCA
1 GTAATTAA
21891 GTAATTAA
1 GTAATTAA
*
21899 CTTAATTCAGA
1 -GTAATT-A-A
21910 GTAATTAA
1 GTAATTAA
*
21918 GTAATTCA
1 GTAATTAA
21926 GTAATTAA
1 GTAATTAA
21934 CTTAATTCAG
Statistics
Matches: 63, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
8 37 0.59
9 12 0.19
10 13 0.21
11 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36
Consensus pattern (8 bp):
GTAATTAA
Found at i:25179 original size:30 final size:30
Alignment explanation
Indices: 25104--25272 Score: 115
Period size: 30 Copynumber: 5.9 Consensus size: 30
25094 GGCATGTATC
* * *
25104 CTTTT-GTGCACGTGGCATGCCACGTGCCA
1 CTTTTGGTACACGTGGCGTGCCACGTGTCA
* ** * *
25133 TTTTTGAAACATGTGGCATGCCACGTGTCA
1 CTTTTGGTACACGTGGCGTGCCACGTGTCA
* *
25163 CTTTTGGTACACGTGGCGTGACATGTGTCA
1 CTTTTGGTACACGTGGCGTGCCACGTGTCA
*
25193 CCTTTTGGTACA--T---GTGACAC--G--A
1 -CTTTTGGTACACGTGGCGTGCCACGTGTCA
* * *
25215 CTTTTTGGTACATGTGGCGTGTCACATGTCA
1 C-TTTTGGTACACGTGGCGTGCCACGTGTCA
25246 CTTTTTGGTACACGTGGCGTGCCACGT
1 C-TTTTGGTACACGTGGCGTGCCACGT
25273 CGGACACCGT
Statistics
Matches: 110, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
21 1 0.01
22 11 0.10
24 2 0.02
26 6 0.05
27 6 0.05
29 6 0.05
30 42 0.38
31 36 0.33
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (30 bp):
CTTTTGGTACACGTGGCGTGCCACGTGTCA
Found at i:25207 original size:19 final size:21
Alignment explanation
Indices: 25183--25230 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
25173 ACGTGGCGTG
*
25183 ACATGTGTCAC-C-TTTTGGT
1 ACATGTGACACACTTTTTGGT
25202 ACATGTGACACGACTTTTTGGT
1 ACATGTGACAC-ACTTTTTGGT
25224 ACATGTG
1 ACATGTG
25231 GCGTGTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
21 1 0.04
22 14 0.56
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (21 bp):
ACATGTGACACACTTTTTGGT
Found at i:26800 original size:15 final size:15
Alignment explanation
Indices: 26782--26811 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26772 AGAAAGAGAT
*
26782 TAAAAATAACAATTA
1 TAAAAAAAACAATTA
26797 TAAAAAAAACAATTA
1 TAAAAAAAACAATTA
26812 ATCTAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAAAAACAATTA
Found at i:28391 original size:31 final size:30
Alignment explanation
Indices: 28353--28486 Score: 110
Period size: 31 Copynumber: 4.4 Consensus size: 30
28343 GATGGCTAAC
28353 TGCTCAAATAAGGGCCCAACGTTTACAAAAA
1 TGCTCAAATAAGGGCCCAACG-TTACAAAAA
* * *
28384 TGCTCAAATAAGGGTCCAAAG--AAAAAATA
1 TGCTCAAATAAGGGCCCAACGTTACAAAA-A
* * * *
28413 TGCTCAAATTAGGGCCCAATGTTTGCGAAAA
1 TGCTCAAATAAGGGCCCAACG-TTACAAAAA
* * * *
28444 TACTCAAATAAAGACCCAACGTTGCAAAAA
1 TGCTCAAATAAGGGCCCAACGTTACAAAAA
*
28474 TTACTCAAATAAG
1 -TGCTCAAATAAG
28487 TCCTTGTCGT
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
28 5 0.06
29 19 0.23
30 8 0.10
31 47 0.57
32 3 0.04
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCCAACGTTACAAAAA
Found at i:28599 original size:28 final size:28
Alignment explanation
Indices: 28567--28653 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 28
28557 ATTTTCACAA
*
28567 TGTTGGGTCCTGATTGGAGCATTTTTTT
1 TGTTGGGTCCTGATTTGAGCATTTTTTT
* * *
28595 TGTTGGGCCCTTATTTGAGCAATTTTTGTAA
1 TGTTGGGTCCTGATTTGAGC-ATTTTT-T-T
* *
28626 TATTGGGTCTTGATTTGAG-ATTTTTTT
1 TGTTGGGTCCTGATTTGAGCATTTTTTT
28653 T
1 T
28654 CTTTAAACTC
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
27 1 0.02
28 18 0.38
29 12 0.26
30 1 0.02
31 15 0.32
ACGTcount: A:0.15, C:0.09, G:0.24, T:0.52
Consensus pattern (28 bp):
TGTTGGGTCCTGATTTGAGCATTTTTTT
Found at i:29819 original size:32 final size:33
Alignment explanation
Indices: 29765--29869 Score: 110
Period size: 32 Copynumber: 3.2 Consensus size: 33
29755 TGTCCCAAGA
* *
29765 GGGCGGCTT-ACCGT-GGCGAAGCCGCCCCACTT
1 GGGCGGCTTCACCATCGGC-AAGCCGCCCCACTG
* *
29797 GGGAGGCTTCGCCA-CGGCAAGCCGCCCTCA-TG
1 GGGCGGCTTCACCATCGGCAAGCCGCCC-CACTG
* *
29829 GGGCGGCTTCACCATGGGCAGGCCGCCCCACTG
1 GGGCGGCTTCACCATCGGCAAGCCGCCCCACTG
29862 GGGCGGCT
1 GGGCGGCT
29870 CGGCTATTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
32 32 0.53
33 28 0.47
ACGTcount: A:0.12, C:0.37, G:0.37, T:0.13
Consensus pattern (33 bp):
GGGCGGCTTCACCATCGGCAAGCCGCCCCACTG
Found at i:30000 original size:33 final size:32
Alignment explanation
Indices: 29963--30058 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 32
29953 GGCGGTTGAG
29963 CCATGGCCAAGCCGCACTCCTGGGGCGGCACTA
1 CCATGGCCAAGCCGC-CTCCTGGGGCGGCACTA
* * *
29996 CCATGGCCAGGCCGCCTCCCTGGGGCAGCCCTA
1 CCATGGCCAAGCCGCCT-CCTGGGGCGGCACTA
*
30029 CCATGG--ATAGACCGCCCCCTGGGGCGGCAC
1 CCATGGCCA-AG-CCGCCTCCTGGGGCGGCAC
30059 CGGTACTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
31 1 0.02
32 14 0.26
33 38 0.72
ACGTcount: A:0.16, C:0.42, G:0.31, T:0.11
Consensus pattern (32 bp):
CCATGGCCAAGCCGCCTCCTGGGGCGGCACTA
Found at i:30189 original size:33 final size:33
Alignment explanation
Indices: 30094--30252 Score: 216
Period size: 33 Copynumber: 4.9 Consensus size: 33
30084 AAAAAGCCTT
* * *
30094 GCCGCCCTAGTGGGGCGGCT-AGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* **
30126 GCCGTCCTAGTGGGGCGG-TTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
30158 GCTGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
30191 GCCGTCTTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
30224 ACCGTCCTAGTGGGGAGGCTCCG-CGTGGC
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGC
30253 TAAGAGCAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
31 1 0.01
32 51 0.44
33 64 0.55
ACGTcount: A:0.12, C:0.28, G:0.43, T:0.17
Consensus pattern (33 bp):
GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:30370 original size:86 final size:86
Alignment explanation
Indices: 30225--30394 Score: 322
Period size: 86 Copynumber: 2.0 Consensus size: 86
30215 CGTGGCAGAA
*
30225 CCGTCCTAGTGGGGAGGCTCCGCGTGGCTAAGAGCAAAAGTGAAAAAGTGGCAAAGGTCAAAGGG
1 CCGTCCTAGTGGGGAGGCTCCGCGTGGCTAAGAGCAAAAGTGAAAAAGTGGCAAAGGTCAAAGAG
30290 CAAAAGTGTAAAAAATGGGGC
66 CAAAAGTGTAAAAAATGGGGC
*
30311 CCGTCCTAGTGGGGAGGCTCCGCGTGGCTAAGGGCAAAAGTGAAAAAGTGGCAAAGGTCAAAGAG
1 CCGTCCTAGTGGGGAGGCTCCGCGTGGCTAAGAGCAAAAGTGAAAAAGTGGCAAAGGTCAAAGAG
30376 CAAAAGTGTAAAAAATGGG
66 CAAAAGTGTAAAAAATGGG
30395 ACGGTGAATA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.35, C:0.16, G:0.35, T:0.14
Consensus pattern (86 bp):
CCGTCCTAGTGGGGAGGCTCCGCGTGGCTAAGAGCAAAAGTGAAAAAGTGGCAAAGGTCAAAGAG
CAAAAGTGTAAAAAATGGGGC
Found at i:30785 original size:2 final size:2
Alignment explanation
Indices: 30778--30806 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30768 GTTCAAACAT
30778 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 T
30807 CCAACTTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34230 original size:16 final size:16
Alignment explanation
Indices: 34209--34248 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
34199 GAACTCGAAT
*
34209 CCGAAAAAGTTCA-AAC
1 CCGAAAAA-ATCAGAAC
34225 CCGAAAAAATCAGAAC
1 CCGAAAAAATCAGAAC
34241 CCGAAAAA
1 CCGAAAAA
34249 TCTGAAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.55, C:0.25, G:0.12, T:0.07
Consensus pattern (16 bp):
CCGAAAAAATCAGAAC
Found at i:34247 original size:15 final size:15
Alignment explanation
Indices: 34209--34264 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
34199 GAACTCGAAT
34209 CCGAAAAAGTTCA-AAC
1 CCGAAAAA--TCAGAAC
34225 CCGAAAAAATCAGAAC
1 CCG-AAAAATCAGAAC
*
34241 CCGAAAAATCTGAAAC
1 CCGAAAAATCAG-AAC
*
34257 CTGAAAAA
1 CCGAAAAA
34265 ACCTGAACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 11 0.31
16 19 0.54
17 5 0.14
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (15 bp):
CCGAAAAATCAGAAC
Found at i:34264 original size:17 final size:17
Alignment explanation
Indices: 34221--34271 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
34211 GAAAAAGTTC
*
34221 AAACCCGAAAAAATCAG
1 AAACCCGAAAAAATCTG
34238 -AACCCG-AAAAATCTG
1 AAACCCGAAAAAATCTG
* *
34253 AAACCTGAAAAAACCTG
1 AAACCCGAAAAAATCTG
34270 AA
1 AA
34272 CTCGAACCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 8 0.28
16 11 0.38
17 10 0.34
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.10
Consensus pattern (17 bp):
AAACCCGAAAAAATCTG
Found at i:35263 original size:19 final size:19
Alignment explanation
Indices: 35205--35268 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 19
35195 ATGTGAAGAT
* *
35205 AGGCCAGGTGGAAATATCAG
1 AGGCCACGTGG-AATATTAG
35225 AGGCCACGTGGAATTATTAG
1 AGGCCACGTGGAA-TATTAG
35245 AGGCCACGTGGAATATTAG
1 AGGCCACGTGGAATATTAG
35264 -GGCCA
1 AGGCCA
35269 TGTCATCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.12
19 8 0.20
20 28 0.68
ACGTcount: A:0.31, C:0.17, G:0.33, T:0.19
Consensus pattern (19 bp):
AGGCCACGTGGAATATTAG
Done.