Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009135.1 Corchorus capsularis cultivar CVL-1 contig09156, 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: 85758
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1079 original size:20 final size:20
Alignment explanation
Indices: 1039--1080 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1029 TCTCACAAGA
* *
1039 TTCTAGCCGTTGGAGCTCTT
1 TTCTAGCCGTTAGAGCACTT
*
1059 TTCTAGCCGTTATAGCACTT
1 TTCTAGCCGTTAGAGCACTT
1079 TT
1 TT
1081 TCAACAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
TTCTAGCCGTTAGAGCACTT
Found at i:4302 original size:2 final size:2
Alignment explanation
Indices: 4297--4322 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4287 AAGAGAGGGC
4297 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
4323 TGCAATTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9390 original size:19 final size:20
Alignment explanation
Indices: 9353--9390 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9343 GCGTTTGGCA
*
9353 TTGTTGCCATTTTTGTTTTC
1 TTGTTGCCATTTTTCTTTTC
9373 TTGTTGCCA-TTTTCTTTT
1 TTGTTGCCATTTTTCTTTT
9391 TTTGGCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.05, C:0.16, G:0.13, T:0.66
Consensus pattern (20 bp):
TTGTTGCCATTTTTCTTTTC
Found at i:10737 original size:20 final size:20
Alignment explanation
Indices: 10712--10753 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
10702 GGATATCAAC
10712 TGTATTTCTGGCATGGGTGA
1 TGTATTTCTGGCATGGGTGA
10732 TGTATTTCTGGCATGGGTGA
1 TGTATTTCTGGCATGGGTGA
10752 TG
1 TG
10754 GCCATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (20 bp):
TGTATTTCTGGCATGGGTGA
Found at i:11441 original size:299 final size:297
Alignment explanation
Indices: 10902--11494 Score: 1080
Period size: 299 Copynumber: 2.0 Consensus size: 297
10892 AGAGAAACCG
* *
10902 AGATTTTGCTTTCTAAGAATGTCTCCGGCCATGTCCCTAAACCGAAGTTGTCGTTTGCCAAGCTG
1 AGATTTTGCTTTCCAAGAATGTCTCCGGCCATGTCCCTAAACCGAAGTTGTCGCTTGCCAAGCTG
*
10967 AGCATGATGCTCCAAAACCAGAGAGAGATTGTAGGAATAAAAGGTCACCATAGCTTGCAGAGCAG
66 AGCATGATGCTCCAAAACCACAGAGAGATTGTAGGAATAAAAGGTCACCATAGCTTGCAGAGCAG
11032 TAATCAAAAGTCCAGGCACCCAGCCAAGCAAGGACAGAGCAAAAGGGAAACCAAATATGACAGGG
131 TAATCAAAAGTCCAGGCACCCAGCCAAGCAAGGACAGAGCAAAAGGGAAACCAAATATGACAGGG
11097 CCAACAATAGATGTAATCAAATAATATCCACAGTGCAACCATGAACCTACAAAAGATACCTCTTA
196 CCAACAATAGATGTAATCAAATAATATCCACAGTGCAACCATGAACCT---AAAGATACCTCTTA
11162 CTCTGCTTTAGCCACCTTCTCCAATTGAGCAAGGTACCCA
258 CTCTGCTTTAGCCACCTTCTCCAATTGAGCAAGGTACCCA
11202 AGATTTTGCTTTCCAAGAATGTCTCCGGCCATGTCCCTAAACCGAAGTTGTCGCTTGCCAAGCTG
1 AGATTTTGCTTTCCAAGAATGTCTCCGGCCATGTCCCTAAACCGAAGTTGTCGCTTGCCAAGCTG
11267 AGCATGATGCTCC-AAACCACAGAGAGATTGTAGGAATAAAAGGTCACCATAGCTTGCAGAGCAG
66 AGCATGATGCTCCAAAACCACAGAGAGATTGTAGGAATAAAAGGTCACCATAGCTTGCAGAGCAG
* * *
11331 TAATCAAAAGTCCAGGCACCCAGCCAAGTAAGGACAGAGTAAAGGGGAAACCAAATATGACAGGG
131 TAATCAAAAGTCCAGGCACCCAGCCAAGCAAGGACAGAGCAAAAGGGAAACCAAATATGACAGGG
*
11396 CCAACAATAGATGTAATCAAATAATATCCACAGTGCAACCATGAACGTAAAGATACCTCTTACTC
196 CCAACAATAGATGTAATCAAATAATATCCACAGTGCAACCATGAACCTAAAGATACCTCTTACTC
*
11461 TGCTTTAGCCATCTTCTCCAATTGAGCAAGGTAC
261 TGCTTTAGCCACCTTCTCCAATTGAGCAAGGTAC
11495 ATCCGATCAA
Statistics
Matches: 285, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
296 50 0.18
299 159 0.56
300 76 0.27
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (297 bp):
AGATTTTGCTTTCCAAGAATGTCTCCGGCCATGTCCCTAAACCGAAGTTGTCGCTTGCCAAGCTG
AGCATGATGCTCCAAAACCACAGAGAGATTGTAGGAATAAAAGGTCACCATAGCTTGCAGAGCAG
TAATCAAAAGTCCAGGCACCCAGCCAAGCAAGGACAGAGCAAAAGGGAAACCAAATATGACAGGG
CCAACAATAGATGTAATCAAATAATATCCACAGTGCAACCATGAACCTAAAGATACCTCTTACTC
TGCTTTAGCCACCTTCTCCAATTGAGCAAGGTACCCA
Found at i:12181 original size:70 final size:70
Alignment explanation
Indices: 12066--12587 Score: 417
Period size: 70 Copynumber: 7.5 Consensus size: 70
12056 TTTCACTCTC
* *
12066 TGCACCACTATACCTTTATGTATAATAGGAATGCCACCACCACATAGAATTCTTACCAACCTTTA
1 TGCACCATTATACCTTGATGTATAATAGGAATGCCACCACCACATAGAATTCTTACCAACCTTTA
12131 TTCGA
66 TTCGA
* *
12136 TACACCATTATACCTTGATGTATAATAGGAATGCCGCCACCACATAGAATTCTTACCAACCTTTA
1 TGCACCATTATACCTTGATGTATAATAGGAATGCCACCACCACATAGAATTCTTACCAACCTTTA
12201 TTCGA
66 TTCGA
*
12206 TGCACCATTATACCTTGATGTATAATAGGAATGCCAGCCCTTTTACTGCAAAGTAGAAATTCCCA
1 TGCACCATTATACCTTGATGTATAATAGGAATGCCA--CC----AC--CACA-TAG-AATT--C-
* * *
12271 TCACCAACTTTTATGCAGA
53 TTACCAACCTTTATTC-GA
**** * *
12290 TGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTATGTATAGTATATT-ATA-CAA--
1 TGCACCATTATACCTTGATGTATAATAGGAATGCCACCACCA--CATAG-A-ATTCTTACCAACC
*
12351 ---ACT-G-
62 TTTATTCGA
*
12355 -GCACCACTATACC-T--T-TAT--TAGGAATGCCACCACCACATAGAATTCTTACCAACCTTTA
1 TGCACCATTATACCTTGATGTATAATAGGAATGCCACCACCACATAGAATTCTTACCAACCTTTA
12413 TTCGA
66 TTCGA
**** * ** *
12418 TGCACCATTATACCTTGATGTATAATAGGAATGCCA-C-TGTTAT-GTATAGTATAAC-ACAC--
1 TGCACCATTATACCTTGATGTATAATAGGAATGCCACCACCACATAGAATTCT-TACCAAC-CTT
* **
12477 AAACCG-
64 TATTCGA
* * * *
12483 -GCACCACTATACCTTTATGTATAGTAGGAATGCCACCGCCACATAGAATTCTTACCAACCTTTA
1 TGCACCATTATACCTTGATGTATAATAGGAATGCCACCACCACATAGAATTCTTACCAACCTTTA
12547 TTCGA
66 TTCGA
12552 TGCACCATTATACCTTGATGTATAATAGGAATGCCA
1 TGCACCATTATACCTTGATGTATAATAGGAATGCCA
12588 TCATTGCGAC
Statistics
Matches: 352, Mismatches: 57, Indels: 86
0.71 0.12 0.17
Matches are distributed among these distances:
54 3 0.01
55 3 0.01
56 7 0.02
58 13 0.04
60 3 0.01
61 3 0.01
62 1 0.00
63 1 0.00
64 56 0.16
65 2 0.01
66 10 0.03
67 13 0.04
68 13 0.04
69 1 0.00
70 143 0.41
72 2 0.01
73 3 0.01
74 1 0.00
76 3 0.01
77 4 0.01
78 7 0.02
79 3 0.01
80 4 0.01
82 2 0.01
83 13 0.04
84 38 0.11
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (70 bp):
TGCACCATTATACCTTGATGTATAATAGGAATGCCACCACCACATAGAATTCTTACCAACCTTTA
TTCGA
Found at i:12587 original size:134 final size:128
Alignment explanation
Indices: 12273--12587 Score: 504
Period size: 134 Copynumber: 2.4 Consensus size: 128
12263 AATTCCCATC
* *
12273 ACCAACTTTTATGCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTATGTATA
1 ACCAACCTTTATTC-GATGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTATGTATA
** * *
12338 GTATATTATACAAACTGGCACCACTATACCTTTATTAGGAATGCCACCACCACATAGAATTCTT
65 GTATAACACACAAACCGGCACCACTATACCTTTATTAGGAATGCCACCACCACATAGAATTCTT
12402 ACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTATGTATAG
1 ACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTATGTATAG
*
12467 TATAACACACAAACCGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCGCCACATAGAAT
66 TATAACACACAAACCGGCACCACTATACC--T-T-TAT--TAGGAATGCCACCACCACATAGAAT
12532 TCTT
125 TCTT
12536 ACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCA
1 ACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCA
12588 TCATTGCGAC
Statistics
Matches: 173, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
128 76 0.44
129 12 0.07
130 1 0.01
131 1 0.01
132 3 0.02
134 80 0.46
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (128 bp):
ACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTATGTATAG
TATAACACACAAACCGGCACCACTATACCTTTATTAGGAATGCCACCACCACATAGAATTCTT
Found at i:17862 original size:41 final size:41
Alignment explanation
Indices: 17789--17931 Score: 126
Period size: 50 Copynumber: 3.2 Consensus size: 41
17779 ACATTTATGG
*
17789 GATAATTATGGTGATTATA-TAATTAACCATATTATCCATAGA
1 GATAATTAT-G-GATTATATTTATTAACCATATTATCCATAGA
17831 GATAATTATGGATTATATTTATTAACCATATTATCTACATAAATATTAGA
1 GATAATTATGGATTATATTTATTAACCATATTATC--C------A-TAGA
** ** *
17881 GATAATTATGGATTATATTTATTAGTCATATTATCTTTAAA
1 GATAATTATGGATTATATTTATTAACCATATTATCCATAGA
17922 GATAATTATG
1 GATAATTATG
17932 ACAATTATCA
Statistics
Matches: 85, Mismatches: 6, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
40 7 0.08
41 30 0.35
42 9 0.11
43 1 0.01
49 1 0.01
50 37 0.44
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (41 bp):
GATAATTATGGATTATATTTATTAACCATATTATCCATAGA
Found at i:20805 original size:6 final size:6
Alignment explanation
Indices: 20796--20866 Score: 60
Period size: 6 Copynumber: 12.2 Consensus size: 6
20786 CACAAAACCA
* *
20796 AAAAAC AAAAA- AACAAA- AAGAAC ACAAAAC -AAAAC AAAAAC AAAAGC
1 AAAAAC AAAAAC AA-AAAC AAAAAC A-AAAAC AAAAAC AAAAAC AAAAAC
* *
20843 AGAAAC AAAAAG AAAAA- AAAAAC A
1 AAAAAC AAAAAC AAAAAC AAAAAC A
20867 TATGTTTTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
5 14 0.26
6 35 0.66
7 4 0.08
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:20814 original size:16 final size:16
Alignment explanation
Indices: 20789--20840 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
20779 GTTCAGTCAC
*
20789 AAAACCAAAAAACAAA
1 AAAACAAAAAAACAAA
20805 AAAACAAAAAGAACACAA
1 AAAACAAAAA-AACA-AA
20823 AACAA-AACAAAAACAAA
1 AA-AACAA-AAAAACAAA
20840 A
1 A
20841 GCAGAAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.29
17 7 0.23
18 10 0.32
19 5 0.16
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAAACAAA
Found at i:20833 original size:29 final size:28
Alignment explanation
Indices: 20795--20866 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
20785 TCACAAAACC
20795 AAAAAACAAAAAAACAAAA-AGAACACAA
1 AAAAAACAAAAAAACAAAACAGAA-ACAA
20823 AACAAAAC--AAAAACAAAAGCAGAAACAA
1 AA-AAAACAAAAAAACAAAA-CAGAAACAA
20851 AAAGAAA-AAAAAAACA
1 AAA-AAACAAAAAAACA
20867 TATGTTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
27 11 0.29
28 11 0.29
29 16 0.42
ACGTcount: A:0.81, C:0.14, G:0.06, T:0.00
Consensus pattern (28 bp):
AAAAAACAAAAAAACAAAACAGAAACAA
Found at i:20848 original size:12 final size:11
Alignment explanation
Indices: 20787--20866 Score: 58
Period size: 11 Copynumber: 7.3 Consensus size: 11
20777 AAGTTCAGTC
*
20787 ACAAAACCAAA
1 ACAAAAACAAA
20798 A-AACAAA-AAA
1 ACAA-AAACAAA
* *
20808 ACAAAAAGAAC
1 ACAAAAACAAA
20819 AC-AAAACAAA
1 ACAAAAACAAA
20829 ACAAAAACAAA
1 ACAAAAACAAA
*
20840 AGCAGAAACAAAA
1 A-CAAAAAC-AAA
* *
20853 AGAAAAAAAAA
1 ACAAAAACAAA
20864 ACA
1 ACA
20867 TATGTTTTCA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
10 17 0.31
11 23 0.43
12 10 0.19
13 4 0.07
ACGTcount: A:0.79, C:0.16, G:0.05, T:0.00
Consensus pattern (11 bp):
ACAAAAACAAA
Found at i:20918 original size:39 final size:40
Alignment explanation
Indices: 20875--20950 Score: 145
Period size: 39 Copynumber: 1.9 Consensus size: 40
20865 CATATGTTTT
20875 CATATACAACAACAATGGCCTATGTCG-CCATATATACAA
1 CATATACAACAACAATGGCCTATGTCGCCCATATATACAA
20914 CATATACAACAACAATGGCCTATGTCGCCCATATATA
1 CATATACAACAACAATGGCCTATGTCGCCCATATATA
20951 TTAAATGGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 27 0.75
40 9 0.25
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (40 bp):
CATATACAACAACAATGGCCTATGTCGCCCATATATACAA
Found at i:21095 original size:29 final size:29
Alignment explanation
Indices: 20991--21083 Score: 114
Period size: 29 Copynumber: 3.1 Consensus size: 29
20981 ACTATTACCT
* *
20991 TGGCCTATGACGCCACTCCATATATACAAAAA
1 TGGCCTATGATGCCA---CATATATATAAAAA
* *
21023 TGGCCTATGATGCCACACATATATAACAA
1 TGGCCTATGATGCCACATATATATAAAAA
*
21052 TGGCCTATGATGCCACATATATATAATAA
1 TGGCCTATGATGCCACATATATATAAAAA
21081 TGG
1 TGG
21084 TTTATGTTGC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 41 0.75
32 14 0.25
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.26
Consensus pattern (29 bp):
TGGCCTATGATGCCACATATATATAAAAA
Found at i:21283 original size:88 final size:88
Alignment explanation
Indices: 21162--21567 Score: 527
Period size: 88 Copynumber: 4.6 Consensus size: 88
21152 TTAAAAAATA
* * *
21162 TTTTCATTGCCGCTAATCAAAGCGAGCTAAATATCTAAATGTTCCCTCCAAGTAAG-AGAATCTT
1 TTTT-ATTGCCGCTAATCAAAGCAAGCTCAATATCTAAATGCTCCCTCCAAGT-AGTAGAATCTT
*
21226 TTCTCCTTGTAGAGGTCGAAAGCAC
64 TTCTCCTTGTAGAGGTTGAAAGCAC
*
21251 TTTTATTGCTGCTAA-CAAAGGCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTT
1 TTTTATTGCCGCTAATCAAA-GCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTT
*
21315 TCTCCTTGTAGAGGTTGAAAACAC
65 TCTCCTTGTAGAGGTTGAAAGCAC
* *
21339 TTTTATTGCTGCTAA-CAAAGGCAAACTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTT
1 TTTTATTGCCGCTAATCAAA-GCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTT
21403 TCTCCTTGTAGAGGTTGAAAGCAC
65 TCTCCTTGTAGAGGTTGAAAGCAC
* * * *
21427 TCTTATTTGCCGCTAATCAAAGCGAGCTTAATATCTATATGCTCCCTCCAAGTAGTAGAATCATT
1 TTTTA-TTGCCGCTAATCAAAGCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATC---
21492 TTTTCTCCTTGTAGAGGTTGAAAGCAC
62 TTTTCTCCTTGTAGAGGTTGAAAGCAC
** * * *
21519 TTTCCTTGCAGCT-ATCAAAGCGAGCT-TATCATCTAAATG-TCTCCTCCAA
1 TTTTATTGCCGCTAATCAAAGCAAGCTCAAT-ATCTAAATGCTC-CCTCCAA
21568 AATGAACTTC
Statistics
Matches: 288, Mismatches: 20, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
87 6 0.02
88 160 0.56
89 54 0.19
90 32 0.11
91 7 0.02
92 29 0.10
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (88 bp):
TTTTATTGCCGCTAATCAAAGCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTT
CTCCTTGTAGAGGTTGAAAGCAC
Found at i:22963 original size:66 final size:66
Alignment explanation
Indices: 22883--23014 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
22873 TTGCAAAAGG
22883 GATTTGGCAGTTTTGAGAAAAACAAACAAATATGTATATACATGATGTATATATTTTGTAAAGAA
1 GATTTGGCAGTTTTGAGAAAAACAAACAAATATGTATATACATGATGTATATATTTTGTAAAGAA
22948 A
66 A
22949 GATTTGGCAGTTTTGAGAAAAACAAACAAATATGTATATACATGATGTATATATTTTGTAAAGAA
1 GATTTGGCAGTTTTGAGAAAAACAAACAAATATGTATATACATGATGTATATATTTTGTAAAGAA
23014 A
66 A
23015 AGCTTCACGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (66 bp):
GATTTGGCAGTTTTGAGAAAAACAAACAAATATGTATATACATGATGTATATATTTTGTAAAGAA
A
Found at i:23125 original size:1 final size:1
Alignment explanation
Indices: 23119--23157 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
23109 AATTCACGTT
23119 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23158 GAGGCAAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:23252 original size:30 final size:30
Alignment explanation
Indices: 23218--23287 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
23208 CACCCCTGCA
23218 ACAGGTAATACCCACGTGGTTACACACGTT
1 ACAGGTAATACCCACGTGGTTACACACGTT
*
23248 ACAGGTAATACCCACTTGGTTACACACGTT
1 ACAGGTAATACCCACGTGGTTACACACGTT
*
23278 ATAGGTAATA
1 ACAGGTAATA
23288 ACCTGTAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (30 bp):
ACAGGTAATACCCACGTGGTTACACACGTT
Found at i:23318 original size:16 final size:16
Alignment explanation
Indices: 23297--23354 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
23287 AACCTGTAAC
23297 TGGTAATACATGTTGT
1 TGGTAATACATGTTGT
* *
23313 TGGTAATACCT-TGTGAC
1 TGGTAATACATGT-TG-T
23330 TGGTAATACATGTTGT
1 TGGTAATACATGTTGT
23346 TGGTAATAC
1 TGGTAATAC
23355 CCTATGAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 1 0.03
16 21 0.60
17 12 0.34
18 1 0.03
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (16 bp):
TGGTAATACATGTTGT
Found at i:23332 original size:33 final size:32
Alignment explanation
Indices: 23281--23355 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 32
23271 ACACGTTATA
23281 GGTAATAACCTGTAACTGGTAATACATGTTGTT
1 GGTAAT-ACCTGTAACTGGTAATACATGTTGTT
*
23314 GGTAATACCTTGTGACTGGTAATACATGTTGTT
1 GGTAATACC-TGTAACTGGTAATACATGTTGTT
23347 GGTAATACC
1 GGTAATACC
23356 CTATGAACTG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 3 0.08
33 37 0.93
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (32 bp):
GGTAATACCTGTAACTGGTAATACATGTTGTT
Found at i:24041 original size:41 final size:41
Alignment explanation
Indices: 23955--24047 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 41
23945 ATATTTATGG
*
23955 GATAATTATGGTGATTATATAATTAACCATATTATCCATAGA
1 GATAATTAT-GTGATTATATAATTAACCATATTATCCATAAA
* ** **
23997 GATAATTATG-GATTATATTTATTAGTCATATTATCTTTAAA
1 GATAATTATGTGATTATA-TAATTAACCATATTATCCATAAA
24038 GATAATTATG
1 GATAATTATG
24048 ACAATTATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 7 0.16
41 28 0.64
42 9 0.20
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (41 bp):
GATAATTATGTGATTATATAATTAACCATATTATCCATAAA
Found at i:24996 original size:13 final size:13
Alignment explanation
Indices: 24962--24995 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
24952 GCATATAATA
24962 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
*
24975 CTTTCTTTTCTTT
1 TTTTCTTTTCTTT
24988 TTTT-TTTT
1 TTTTCTTTT
24996 TAATATTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:45570 original size:1 final size:1
Alignment explanation
Indices: 45564--45588 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
45554 TTATAGTTAG
45564 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
45589 GCATTTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:64275 original size:19 final size:19
Alignment explanation
Indices: 64251--64310 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
64241 TAAGCAAGTC
64251 GGTAATCAACTTAATTCAG
1 GGTAATCAACTTAATTCAG
* * * *
64270 GGTAATTAA-GTGAGTCA-
1 GGTAATCAACTTAATTCAG
64287 -GTAATCAACTTAATTCAG
1 GGTAATCAACTTAATTCAG
64305 GGTAAT
1 GGTAAT
64311 TAAGAGAGTT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 7 0.23
17 5 0.17
18 5 0.17
19 13 0.43
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (19 bp):
GGTAATCAACTTAATTCAG
Found at i:64333 original size:70 final size:70
Alignment explanation
Indices: 64201--64384 Score: 250
Period size: 70 Copynumber: 2.6 Consensus size: 70
64191 ATAAGCAACT
* **
64201 TAATTAAGTGAGTCAGTAAACAACTTTAATTCAGGGTAATTAAGCAAGTCGGTAATCAACTTAAT
1 TAATTAAGTGAGTCAGTAATCAAC-TTAATTCAGGGTAATTAAGCAAGTCAATAATCAACTTAAT
64266 TCAGGG
65 TCAGGG
*
64272 TAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAG-AGAGTTAATAAGT-AACTTAA
1 TAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGCA-AGTCAATAA-TCAACTTAA
64335 TTCAGGG
64 TTCAGGG
*
64342 TAATTAAGT-AGTTCACTAAGT-AACTTAATTCAGGGTAATTAAG
1 TAATTAAGTGAG-TCAGTAA-TCAACTTAATTCAGGGTAATTAAG
64385 TTTAGTAAGA
Statistics
Matches: 104, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
69 3 0.03
70 76 0.73
71 25 0.24
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (70 bp):
TAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGCAAGTCAATAATCAACTTAATT
CAGGG
Found at i:64385 original size:35 final size:34
Alignment explanation
Indices: 64201--64385 Score: 221
Period size: 35 Copynumber: 5.3 Consensus size: 34
64191 ATAAGCAACT
*
64201 TAATTAAGTGAGTCAGTAAACAACTTTAATTCAGGG
1 TAATTAAGT-AGTCAGTAATCAAC-TTAATTCAGGG
* *
64237 TAATTAAGCAAGTCGGTAATCAACTTAATTCAGGG
1 TAATTAAG-TAGTCAGTAATCAACTTAATTCAGGG
64272 TAATTAAGTGAGTCAGTAATCAACTTAATTCAGGG
1 TAATTAAGT-AGTCAGTAATCAACTTAATTCAGGG
* * *
64307 TAATTAAGAGAGTTAATAAGT-AACTTAATTCAGGG
1 TAATTAAG-TAGTCAGTAA-TCAACTTAATTCAGGG
*
64342 TAATTAAGTAGTTCACTAAGT-AACTTAATTCAGGG
1 TAATTAAGTAG-TCAGTAA-TCAACTTAATTCAGGG
64377 TAATTAAGT
1 TAATTAAGT
64386 TTAGTAAGAA
Statistics
Matches: 133, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
34 2 0.02
35 110 0.83
36 21 0.16
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (34 bp):
TAATTAAGTAGTCAGTAATCAACTTAATTCAGGG
Found at i:64451 original size:56 final size:57
Alignment explanation
Indices: 64365--64506 Score: 146
Period size: 56 Copynumber: 2.5 Consensus size: 57
64355 CACTAAGTAA
* * * * * *
64365 CTTAATTCAGGGTAATTAAGTTTAG-TAAGAAGCAGAGACTAGGGAA-AATAAAAT-GG
1 CTTAATTCAGGGTAATTGAG-TCAGTTAAGAACCAAAGA-AAGAGAACAATAAAATGGG
* * *
64421 CTTAATTCAGGGTAATTGAGTCAGTTAAGAACCAAATAAAGATAATCAATAATATGGG
1 CTTAATTCAGGGTAATTGAGTCAGTTAAGAACCAAAGAAAGAGAA-CAATAAAATGGG
*
64479 CTTAATTCAGGGTAATTGGGTCAGTTAA
1 CTTAATTCAGGGTAATTGAGTCAGTTAA
64507 AAAATAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
55 7 0.10
56 29 0.40
57 7 0.10
58 29 0.40
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (57 bp):
CTTAATTCAGGGTAATTGAGTCAGTTAAGAACCAAAGAAAGAGAACAATAAAATGGG
Found at i:69341 original size:24 final size:24
Alignment explanation
Indices: 69309--69388 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
69299 GTCCCTCCCT
*
69309 TCGATCTCTCTCTCCTCTAGGTAA
1 TCGATCTCTCTCTCCTCAAGGTAA
*
69333 TCGATCTCTCTCTCCTCCA-GTCAA
1 TCGATCTCTCTCTCCTCAAGGT-AA
* *
69357 TTGATCTCTCTCTCC-CAAGTTAA
1 TCGATCTCTCTCTCCTCAAGGTAA
69380 TC-ATCTCTC
1 TCGATCTCTC
69389 ACTCTCCTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
22 7 0.14
23 7 0.14
24 35 0.71
ACGTcount: A:0.17, C:0.36, G:0.09, T:0.38
Consensus pattern (24 bp):
TCGATCTCTCTCTCCTCAAGGTAA
Done.