Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020864.1 Corchorus olitorius cultivar O-4 contig20897, 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: 95708
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:371 original size:26 final size:24
Alignment explanation
Indices: 338--388 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
328 ATTAATAATA
*
338 ATTATATAGATATTAATATTATTTTT
1 ATTATATAGATA-TAA-ATTAATTTT
364 ATTATATAGATATAAATTAATTTT
1 ATTATATAGATATAAATTAATTTT
388 A
1 A
389 CACATTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 9 0.38
25 3 0.12
26 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTATATAGATATAAATTAATTTT
Found at i:3434 original size:19 final size:18
Alignment explanation
Indices: 3404--3449 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
3394 TCATACTACT
3404 CAAACTAACTGACTCAAA
1 CAAACTAACTGACTCAAA
3422 CAAACTGAACTGACTC-AA
1 CAAACT-AACTGACTCAAA
*
3440 GAAACTAACT
1 CAAACTAACT
3450 AAAACCCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 13 0.50
19 9 0.35
ACGTcount: A:0.48, C:0.26, G:0.09, T:0.17
Consensus pattern (18 bp):
CAAACTAACTGACTCAAA
Found at i:5174 original size:60 final size:59
Alignment explanation
Indices: 5081--5239 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 59
5071 GCTAAATGCT
* * * *
5081 CAAATAAGGGCCTAACGTTTGCCAAATTGCTCAAATAAGGGCCTGGTCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTG-CAAAATGCTCAAATAAGGGCCCGATCCTTTAATTTGGC
* *
5141 CAAATAAGGGCCTAACGTTAATG-AAAATGCTCAAATAATGGCCCGATCCTTTAATTTTGC
1 CAAATAAGGGCCTAACGTT--TGCAAAATGCTCAAATAAGGGCCCGATCCTTTAATTTGGC
* ** *
5201 CAAATAAAGGCCTAATATTTGCCAAAATACTCAAATAAG
1 CAAATAAGGGCCTAACGTTTG-CAAAATGCTCAAATAAG
5240 AGCCTGACAT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
58 2 0.02
60 80 0.95
62 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTTGCAAAATGCTCAAATAAGGGCCCGATCCTTTAATTTGGC
Found at i:5318 original size:31 final size:31
Alignment explanation
Indices: 5283--5390 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 31
5273 TTTCGATATC
*
5283 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGAAAACGTT
** **
5314 AGGCCCTTATTTG-GCCAAATTAAAAAATCG--
1 AGGCCCTTATTTGAG-CATTTTGGAAAA-CGTT
**
5344 -GGCCCTTATTTGAGCATTTTGGAAAATATT
1 AGGCCCTTATTTGAGCATTTTGGAAAACGTT
5374 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
5391 ATTAGCCTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
29 20 0.33
30 2 0.03
31 36 0.60
32 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGAAAACGTT
Found at i:50368 original size:1 final size:1
Alignment explanation
Indices: 50364--50390 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
50354 AAAATTATAT
50364 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
50391 GAAGATGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:87516 original size:71 final size:71
Alignment explanation
Indices: 87357--87570 Score: 376
Period size: 71 Copynumber: 3.0 Consensus size: 71
87347 GGTAGCATCT
87357 CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTTTTCTTGATTTCGTTTTCTTCAGTTT
1 CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTTTTCTTGATTTCG-TTTCTTCAGTTT
87422 TAACTTC
65 TAACTTC
* * *
87429 CCTTCTAGATCCGATTTCTTGTATTTCTTTTCATC-TCGTTTTATTGATATCGTTTCTTCAGTTT
1 CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTC-TTTTCTTGATTTCGTTTCTTCAGTTT
87493 TAACTTC
65 TAACTTC
87500 CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTTTTCTTGATTTCGTTTCTTCAGTTTT
1 CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTTTTCTTGATTTCGTTTCTTCAGTTTT
87565 AACTTC
66 AACTTC
87571 GCTTTGTTTT
Statistics
Matches: 134, Mismatches: 6, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
71 86 0.64
72 48 0.36
ACGTcount: A:0.14, C:0.21, G:0.09, T:0.57
Consensus pattern (71 bp):
CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTTTTCTTGATTTCGTTTCTTCAGTTTT
AACTTC
Found at i:90385 original size:45 final size:45
Alignment explanation
Indices: 90304--90390 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
90294 GGATAGTTTG
* *
90304 AGCACTCGGCAATCATGCAGCCAAAGCTCTCTTTGATTTCCTTAA
1 AGCACTCGGCAATCATGCAGCCAAAGCTCTCCTTGATCTCCTTAA
* * * * * *
90349 AGCATTCGGCAATCATGGATCCTAGGCTTTCCTTGATCTCCT
1 AGCACTCGGCAATCATGCAGCCAAAGCTCTCCTTGATCTCCT
90391 GCACGTTGTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (45 bp):
AGCACTCGGCAATCATGCAGCCAAAGCTCTCCTTGATCTCCTTAA
Found at i:91384 original size:99 final size:99
Alignment explanation
Indices: 91245--91427 Score: 348
Period size: 99 Copynumber: 1.8 Consensus size: 99
91235 GTGTCTGTCT
*
91245 TCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTTCC
1 TCCTCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTTCC
91310 TCTGTCTTCTCGTGTACCTTTGTGTCCTCTTCCA
66 TCTGTCTTCTCGTGTACCTTTGTGTCCTCTTCCA
*
91344 TCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTTCC
1 TCCTCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTTCC
91409 TCTGTCTTCTCGTGTACCT
66 TCTGTCTTCTCGTGTACCT
91428 CCGTGCCTGT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 82 1.00
ACGTcount: A:0.04, C:0.39, G:0.20, T:0.38
Consensus pattern (99 bp):
TCCTCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTTCC
TCTGTCTTCTCGTGTACCTTTGTGTCCTCTTCCA
Found at i:91412 original size:62 final size:62
Alignment explanation
Indices: 91335--91996 Score: 836
Period size: 62 Copynumber: 11.4 Consensus size: 62
91325 ACCTTTGTGT
*
91335 CCTCTTCCATCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
* *
91397 CCTCTTCCTTCCTCTGTCTTCTCGTGTACCTCCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
* *
91459 CCTCTTCCTTCCTCTGTCTTCCCGTGTACC-T--T--CTGTTGGCCTCGCTTCCT----T--
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
* * *
91510 CCTCTGT-CTT-C-CTGT-GTACC-T-T--C-G--TGCCTGTTGGCCTCGCCTCCTGCGGAGG
1 CCTCT-TCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
* *
91562 CCTCTTCCTTCCTCTGTCTTCCCGTGTACC-T--T--CTGTTGGCCTCGCTTCCT----T--
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
* * *
91613 CCTCTGT-CTT-C-CTGT-GTACC-T-T--C-G--TGCCTGTTGGCCTCGCCTCCTGCGGAGG
1 CCTCT-TCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
91665 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
91727 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
* *
91789 CCTCTTCCTTCATCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGTGGAGG
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
*
91851 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGG
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
* *
91913 CCTCTTCCTTCATCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGG
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
91975 CCTCTTCCTTCCTCTGTCTTCC
1 CCTCTTCCTTCCTCTGTCTTCC
91997 TTCCTCTGTC
Statistics
Matches: 531, Mismatches: 32, Indels: 74
0.83 0.05 0.12
Matches are distributed among these distances:
44 4 0.01
46 36 0.07
47 2 0.00
48 6 0.01
49 8 0.02
50 2 0.00
51 18 0.03
52 18 0.03
53 2 0.00
54 8 0.02
55 6 0.01
56 2 0.00
57 36 0.07
59 4 0.01
62 379 0.71
ACGTcount: A:0.03, C:0.40, G:0.21, T:0.35
Consensus pattern (62 bp):
CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
Found at i:91490 original size:22 final size:22
Alignment explanation
Indices: 91465--91532 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
91455 GAGGCCTCTT
91465 CCTTCCTCTGTCTTCCCGTGTA
1 CCTTCCTCTGTCTTCCCGTGTA
* * * *
91487 CCTT-CTGTTGGCCTCGC-T-T-
1 CCTTCCT-CTGTCTTCCCGTGTA
*
91506 CCTTCCTCTGTCTTCCTGTGTA
1 CCTTCCTCTGTCTTCCCGTGTA
91528 CCTTC
1 CCTTC
91533 GTGCCTGTTG
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 9 0.28
20 4 0.12
21 4 0.12
22 15 0.47
ACGTcount: A:0.03, C:0.40, G:0.15, T:0.43
Consensus pattern (22 bp):
CCTTCCTCTGTCTTCCCGTGTA
Found at i:91579 original size:103 final size:104
Alignment explanation
Indices: 91400--91945 Score: 648
Period size: 103 Copynumber: 4.9 Consensus size: 104
91390 GCGGAGGCCT
*
91400 CTTCCTTCCTCTGTCTT-CTCGTGTACCTCCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCT
1 CTTCCTTCCTCTGTCTTCCT-GTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCT
91464 TCCTTCCTCTGTCTTCCCGTGTACCTTCTGTTGGCCTCG-
65 TCCTTCCTCTGTCTTCCCGTGTACCTTCTGTTGGCCTCGC
91503 CTTCCTTCCTCTGTCTTCCTGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
1 CTTCCTTCCTCTGTCTTCCTGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
91568 CCTTCCTCTGTCTTCCCGTGTACCTTCTGTTGGCCTCG-
66 CCTTCCTCTGTCTTCCCGTGTACCTTCTGTTGGCCTCGC
91606 CTTCCTTCCTCTGTCTTCCTGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
1 CTTCCTTCCTCTGTCTTCCTGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
91671 CCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGC
66 CCTTCCTCTGTCTTCCCGTGTACC-T--T--CTGTTGGCCTCGC
*
91715 CTCCTGCGGAGGCCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTC
1 CT--T--------C-C-T--T-CCTCTGTCTTCCTGTGTACCTTCGTGCCTGTTGGCCTCGCCTC
*
91780 CTGCGGAGGCCTCTTCCTTCATCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTG
51 CTGCGGAGGCCTCTTCCTTCCTCTGTCTTCCCGTGTACC-T--T--CTGTT-G----GCCT-C--
91845 TGGAGGC
103 -----GC
* *
91852 CTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTC
1 CT--TCCTTCCTCTGTCTTCCTGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTC
*
91917 TTCCTTCATCTGTCTTCCCGTGTACCTTC
64 TTCCTTCCTCTGTCTTCCCGTGTACCTTC
91946 GTGCCTGCTG
Statistics
Matches: 403, Mismatches: 5, Indels: 54
0.87 0.01 0.12
Matches are distributed among these distances:
103 188 0.47
104 3 0.01
106 1 0.00
108 12 0.03
109 2 0.00
111 1 0.00
119 2 0.00
120 1 0.00
121 2 0.00
123 2 0.00
124 173 0.43
125 2 0.00
127 1 0.00
128 1 0.00
129 5 0.01
130 1 0.00
137 6 0.01
ACGTcount: A:0.03, C:0.40, G:0.21, T:0.36
Consensus pattern (104 bp):
CTTCCTTCCTCTGTCTTCCTGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
CCTTCCTCTGTCTTCCCGTGTACCTTCTGTTGGCCTCGC
Found at i:91593 original size:22 final size:22
Alignment explanation
Indices: 91568--91635 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
91558 GAGGCCTCTT
91568 CCTTCCTCTGTCTTCCCGTGTA
1 CCTTCCTCTGTCTTCCCGTGTA
* * * *
91590 CCTT-CTGTTGGCCTCGC-T-T-
1 CCTTCCT-CTGTCTTCCCGTGTA
*
91609 CCTTCCTCTGTCTTCCTGTGTA
1 CCTTCCTCTGTCTTCCCGTGTA
91631 CCTTC
1 CCTTC
91636 GTGCCTGTTG
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 9 0.28
20 4 0.12
21 4 0.12
22 15 0.47
ACGTcount: A:0.03, C:0.40, G:0.15, T:0.43
Consensus pattern (22 bp):
CCTTCCTCTGTCTTCCCGTGTA
Found at i:91920 original size:186 final size:185
Alignment explanation
Indices: 91335--91996 Score: 929
Period size: 186 Copynumber: 3.8 Consensus size: 185
91325 ACCTTTGTGT
*
91335 CCTCTTCCATCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCT
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCT
* *
91400 CTTCCTTCCTCTGTCTTCTCGTGTACCTCCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
66 CTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
91465 CCTTCCTCTGTCTTCCCGTGTACC-T--T--CTGTTGGCCTCG-CT--T------
131 CCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGGGAGG
*
91506 CCT-T-----CCTCTGTCTTCCTGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCT
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCT
*
91565 CTTCCTTCCTCTGTCTTCCCGTGTACC-T--T--CTGTTGGCCTCG-CT--T-------CCTT--
66 CTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
*
91613 ----CCTCTGTCTTCCTGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG
131 CCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTG-GGAGG
91665 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCT
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCT
91730 CTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
66 CTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
*
91795 CCTTCATCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGTGGAGG
131 CCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTG-GGAGG
*
91851 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
1 CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCT
* *
91916 CTTCCTTCATCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTT
66 CTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
91981 CCTTCCTCTGTCTTCC
131 CCTTCCTCTGTCTTCC
91997 TTCCTCTGTC
Statistics
Matches: 435, Mismatches: 14, Indels: 69
0.84 0.03 0.13
Matches are distributed among these distances:
144 19 0.04
145 1 0.00
147 1 0.00
149 12 0.03
150 5 0.01
152 1 0.00
157 1 0.00
159 5 0.01
160 13 0.03
162 1 0.00
165 161 0.37
166 1 0.00
168 1 0.00
170 13 0.03
171 5 0.01
173 1 0.00
180 3 0.01
186 191 0.44
ACGTcount: A:0.03, C:0.40, G:0.21, T:0.35
Consensus pattern (185 bp):
CCTCTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCT
CTTCCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTT
CCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGGGAGG
Found at i:91996 original size:14 final size:14
Alignment explanation
Indices: 91977--92007 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
91967 TGCGGAGGCC
91977 TCTTCCTTCCTCTG
1 TCTTCCTTCCTCTG
91991 TCTTCCTTCCTCTG
1 TCTTCCTTCCTCTG
92005 TCT
1 TCT
92008 GTCATGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.06, T:0.52
Consensus pattern (14 bp):
TCTTCCTTCCTCTG
Found at i:93096 original size:37 final size:37
Alignment explanation
Indices: 93046--93121 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
93036 AATGGCTCAC
93046 TTAGTCTTAATTTCATTATCAAGTCTATTATAATGAA
1 TTAGTCTTAATTTCATTATCAAGTCTATTATAATGAA
93083 TTAGTCTTAATTTCATTATCAAGTCTATTATAATGAA
1 TTAGTCTTAATTTCATTATCAAGTCTATTATAATGAA
93120 TT
1 TT
93122 GTATGAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (37 bp):
TTAGTCTTAATTTCATTATCAAGTCTATTATAATGAA
Found at i:94587 original size:325 final size:321
Alignment explanation
Indices: 93647--94780 Score: 1291
Period size: 325 Copynumber: 3.6 Consensus size: 321
93637 CTAAGACTTG
* * ** * *
93647 TTGAAATATCTATATTCATCGAATCAAAT-TCCAGCCAAATTTGATTTAACGATTTATTTTTACA
1 TTGAAATATCTATATTCATCGAACCAAATCT-CAGCCACATTAAATTTAACGATTTGTTTTTACG
* * * **
93711 AGCATATGAATCTTATTTCGTTTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACAATATT
65 AGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCCG-AAAAAAATGGAAAAATGATATT
* * * * * * *
93776 AGTAGCGTGAAAAACCCCTCAAT-TTTTTGGCGTTGAACTATATATTTTTTATGACTATTGTCGC
129 AGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* ** * * *
93840 AAAAAATTGAGAAAAAATTTTTCGTCTCAGTTTTTAG-CC-AA-C--AT-CGT----GT-ACG--
194 AAAAAATTCAGAAAAAA-AATTCATGTCAGTTTTTAGCCCAAATCGTATAC-TAACCATCACGTT
* * * * ** * **
93892 TTT-GGCTAAAAACGCGTTTTGGGGCCTCGACTCAGTTTTGCATGATTTTTTGCTTAAAAACTTT
257 TTTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCC
* * * **
93956 TTGAAATATCTATATTCATCGAACCAAATGC-AAGCCACAATAGACAT-ACTGATTTGTTTTTAC
1 TTGAAATATCTATATTCATCGAACCAAAT-CTCAGCCACATTAAATTTAAC-GATTTGTTTTTAC
* * * *
94019 GAGCATCTGAATCTTGTTTCGATTTAATTTGAAATTAATT-CGGAAAAAATGGAAAAATAATATT
64 GAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCCGAAAAAAATGGAAAAATGATATT
** * * * * *
94083 AGAAGCGTGAAAAGACCATCAATCTTTTGGGTGTTGAATTATAAATGTTTTCTGAGTATTGTGGC
129 AGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* * * ** *
94148 AAAAAATTCAGGAAAAAGAATTCAGGTAAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTT
194 AAAAAATTCA-GAAAAAAAATTCATGTCAGTTTTTAGCCCAAATCGTATACTAACCATCAC-GTT
* * * *
94213 TTTGGGCTAAAAACGAGTTTCGGGGGCCCAGGCTCAGCTTTGCATGATTTTTGGCAGAACGACTC
257 TTTGGGCTAAAAACGCGTTTC-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
94278 C
321 C
* * * *
94279 GTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAAATTGAAGGATTTGTTTTTACGA
1 TTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTAAATTTAACGATTTGTTTTTACGA
* * *
94344 GCATCTGAATCTTGTTTTGATTTAATTAGAAATTGATTCCGAAAAAAATTGGAAAAAATGATATT
66 GCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCCGAAAAAAA-TGG-AAAAATGATATT
*
94409 AGAAGCGTGAAAATCCCGTCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGC
129 AGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC
*
94474 AAAAAATTCAGAAAAAAAATTCTTGTCAGTTTTTAGCCCAAATCGTATACTAACCATCACGATTT
194 AAAAAATTCAGAAAAAAAATTCATGTCAGTTTTTAGCCCAAATCGTATACTAACCATCACG-TTT
*
94539 TTGGGCTAAAAACGCGTTTCGGAGGCCCCGGCTCAGTTTTGCATGATTTTTGGTAGAAAGACTCC
258 TTGGGCTAAAAACGCGTTTCGG-GGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCC
* * * **
94604 TTGAAATATCTACATTCATCGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGA
1 TTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTAAATTTAACGATTTGTTTTTACGA
* *
94669 GCATCCGAATCTTATTTCG-TTTAAATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATTA
66 GCATCTGAATCTTATTTCGATTT-AATTAGAAATTAATTCCGAAAAAAATGGAAAAATGATATTA
** *
94733 GAAGCACGAAAATCCCGTCAATATTTTTGGCGTTGAATTATATATTTT
130 GAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATTTT
94781 GCTACATGTT
Statistics
Matches: 692, Mismatches: 104, Indels: 44
0.82 0.12 0.05
Matches are distributed among these distances:
307 39 0.06
308 58 0.08
309 91 0.13
310 2 0.00
311 1 0.00
313 2 0.00
314 1 0.00
317 1 0.00
318 2 0.00
319 1 0.00
321 3 0.00
322 16 0.02
323 177 0.26
324 18 0.03
325 201 0.29
326 79 0.11
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (321 bp):
TTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTAAATTTAACGATTTGTTTTTACGA
GCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCCGAAAAAAATGGAAAAATGATATTAG
AAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAA
AAAATTCAGAAAAAAAATTCATGTCAGTTTTTAGCCCAAATCGTATACTAACCATCACGTTTTTG
GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCC
Found at i:95533 original size:314 final size:318
Alignment explanation
Indices: 94943--95598 Score: 853
Period size: 314 Copynumber: 2.1 Consensus size: 318
94933 TATTTTGGGC
* * *
94943 GTTGAATTATAAATTTTTTCTAAGTATTGTGGCGAAAAATTCAGGAAAAAAAATTTGGGTCAGTT
1 GTTGAATTATATATTTTTTCTAAGTATTGTGGCAAAAAATTCAGAAAAAAAAATTTGGGTCAGTT
** *
95008 TTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTTGGGCTAAAAACGAGTTTCGGGGGCCCAG
66 TTTAGCCCAAATCGTGTACTAACCATCACGGATTTTTGGGCTAAAAACGAGTTTC--GGG--CAG
* * * * *
95073 GCTCAGCTTTGCATGATTTTTGGCAGAACGACTCCGTGAAATATCTATATTCATCTAACCAAATC
127 GCT---CTTTGCATGATTTTTGGCAGAAAGACTCCGTGAAATATATACATTCACCGAACCAAATC
* * * *
95138 TCAGCCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTCTAATTTAATTAGA
189 CCAGCCACATTAAATTGAACGATTTGTTTTTACGAGCATCCGAATCTTATTCTAATTTAATTAGA
* ** *
95203 AATTGATTTCGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAATCCTGTCAATCTTTTTGG
254 AATTGAATTCGAAAAAAA-TGGAAAAATGATATTAGAAGCACGAAAATCCCGTCAATCTTTTTGG
95268 A
318 A
* *
95269 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAATAAATTCT-TGTCAG
1 GTTGAATTATATATTTTTTCTAAGTATTGTGGCAAAAAATTCAGAAAAAA-AAATT-TGGGTCAG
*
95333 TTTTTAGCCCAAATCGTGTACTAACCATCAC-GATTTTTGGGCTAAAAACGCGTTTC-GG-A-G-
64 TTTTTAGCCCAAATCGTGTACTAACCATCACGGATTTTTGGGCTAAAAACGAGTTTCGGGCAGGC
* * *
95393 T-TTTGCATGATTTTTGGTAGAAAGACTCCTTGAAGTATATACATTCACCGAACCAAATCCCAGC
129 TCTTTGCATGATTTTTGGCAGAAAGACTCCGTGAAATATATACATTCACCGAACCAAATCCCAGC
* ** * **
95457 GACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATT-TCGTTTAAATTAGAAATT
194 CACATTAAATTGAACGATTTGTTTTTACGAGCATCCGAATCTTATTCTAATTT-AATTAGAAATT
*
95521 -AATTCGGAAAAAAATGGAAAAATGATATTAGAAGCACGAAAATCCCGTCAATCTTTTTGGT
258 GAATTC-GAAAAAAATGGAAAAATGATATTAGAAGCACGAAAATCCCGTCAATCTTTTTGGA
95582 GTTGAATTATATATTTT
1 GTTGAATTATATATTTT
95599 GCTACATGTT
Statistics
Matches: 294, Mismatches: 32, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
313 68 0.23
314 112 0.38
318 1 0.00
319 1 0.00
320 1 0.00
323 2 0.01
326 69 0.23
327 39 0.13
328 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (318 bp):
GTTGAATTATATATTTTTTCTAAGTATTGTGGCAAAAAATTCAGAAAAAAAAATTTGGGTCAGTT
TTTAGCCCAAATCGTGTACTAACCATCACGGATTTTTGGGCTAAAAACGAGTTTCGGGCAGGCTC
TTTGCATGATTTTTGGCAGAAAGACTCCGTGAAATATATACATTCACCGAACCAAATCCCAGCCA
CATTAAATTGAACGATTTGTTTTTACGAGCATCCGAATCTTATTCTAATTTAATTAGAAATTGAA
TTCGAAAAAAATGGAAAAATGATATTAGAAGCACGAAAATCCCGTCAATCTTTTTGGA
Found at i:95692 original size:818 final size:818
Alignment explanation
Indices: 94107--95708 Score: 2859
Period size: 818 Copynumber: 1.9 Consensus size: 818
94097 ACCATCAATC
* * *
94107 TTTTGGGTGTTGAATTATAAATGTTTTCTGAGTATTGTGGCAAAAAATTCAGGAAAAAGAATTCA
1 TTTTGGGCGTTGAATTATAAATGTTTTCTAAGTATTGTGGCAAAAAATTCAGGAAAAAAAATTCA
94172 GGTAAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGAGTTTCGGG
66 GGTAAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGAGTTTCGGG
94237 GGCCCAGGCTCAGCTTTGCATGATTTTTGGCAGAACGACTCCGTGAAATATCTATATTCATCTAA
131 GGCCCAGGCTCAGCTTTGCATGATTTTTGGCAGAACGACTCCGTGAAATATCTATATTCATCTAA
* *
94302 CCAAATCTCAGCCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTT
196 CCAAATCTCAGCCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTCTAATTT
94367 AATTAGAAATTGATTCCGAAAAAAATTGGAAAAAATGATATTAGAAGCGTGAAAATCCCGTCAAT
261 AATTAGAAATTGATTCCGAAAAAAATTGGAAAAAATGATATTAGAAGCGTGAAAATCCCGTCAAT
94432 CTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAATTCT
326 CTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAATTCT
94497 TGTCAGTTTTTAGCCCAAATCGTATACTAACCATCACGATTTTTGGGCTAAAAACGCGTTTCGGA
391 TGTCAGTTTTTAGCCCAAATCGTATACTAACCATCACGATTTTTGGGCTAAAAACGCGTTT----
* *
94562 GGCCCCGGCTCAGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCATCGAA
452 ----CCGG--CAGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATATACATTCACCGAA
94627 CCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCGTTTA
511 CCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCGTTTA
94692 AATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCACGAAAATCCCGTCAATAT
576 AATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCACGAAAATCCCGTCAATAT
94757 TTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAGAAAGA
641 TTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAGAAAGA
94822 TATTGCAGCAAATTGAAACTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAGGGTCC
706 TATTGCAGCAAATTGAAACTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAGGGTCC
94887 GTTTGACTCAGCTTATTTAACAGCTTATCTACTGAAAAAGGCTTAATA
771 GTTTGACTCAGCTTATTTAACAGCTTATCTACTGAAAAAGGCTTAATA
* * **
94935 TTTTGGGCGTTGAATTATAAATTTTTTCTAAGTATTGTGGCGAAAAATTCAGGAAAAAAAATTTG
1 TTTTGGGCGTTGAATTATAAATGTTTTCTAAGTATTGTGGCAAAAAATTCAGGAAAAAAAATTCA
*
95000 GGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTTGGGCTAAAAACGAGTTTCGG
66 GGTAAGTTTTTAGCTGAAATCGTGTACTAACCATCACGG-TTTTTGGGCTAAAAACGAGTTTCGG
95065 GGGCCCAGGCTCAGCTTTGCATGATTTTTGGCAGAACGACTCCGTGAAATATCTATATTCATCTA
130 GGGCCCAGGCTCAGCTTTGCATGATTTTTGGCAGAACGACTCCGTGAAATATCTATATTCATCTA
95130 ACCAAATCTCAGCCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTCTAATT
195 ACCAAATCTCAGCCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTCTAATT
* *
95195 TAATTAGAAATTGATTTCGAAAAAAATTGG-AAAAATGATATTAGAAGCGTGAAAATCCTGTCAA
260 TAATTAGAAATTGATTCCGAAAAAAATTGGAAAAAATGATATTAGAAGCGTGAAAATCCCGTCAA
95259 TCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAATAAAT
325 TCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAG-AAAAA-AAAT
*
95324 TCTTGTCAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTGGGCTAAAAACGCGTTT-
388 TCTTGTCAGTTTTTAGCCCAAATCGTATACTAACCATCACGATTTTTGGGCTAAAAACGCGTTTC
*
95388 CGG-AGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAGTATATACATTCACCGAACCAAATC
453 CGGCAGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATATACATTCACCGAACCAAATC
95452 CCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCGTTTAAATTAGA
518 CCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCGTTTAAATTAGA
* *
95517 AATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCACGAAAATCCCGTCAATCTTTTTGGT
583 AATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCACGAAAATCCCGTCAATATTTTTGGC
* *
95582 GTTGAATTATATATTTTGCTACATGTTAAATTCCTTTAAGAATGGTGAATTAGAAAGATATTGCT
648 GTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAGAAAGATATTGCA
***
95647 GCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAGGGTCCGTTT
713 GCAAATTGAAACTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAGGGTCCGTTT
Statistics
Matches: 748, Mismatches: 23, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
818 308 0.41
821 3 0.00
828 183 0.24
829 187 0.25
830 67 0.09
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (818 bp):
TTTTGGGCGTTGAATTATAAATGTTTTCTAAGTATTGTGGCAAAAAATTCAGGAAAAAAAATTCA
GGTAAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGAGTTTCGGG
GGCCCAGGCTCAGCTTTGCATGATTTTTGGCAGAACGACTCCGTGAAATATCTATATTCATCTAA
CCAAATCTCAGCCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTCTAATTT
AATTAGAAATTGATTCCGAAAAAAATTGGAAAAAATGATATTAGAAGCGTGAAAATCCCGTCAAT
CTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAATTCT
TGTCAGTTTTTAGCCCAAATCGTATACTAACCATCACGATTTTTGGGCTAAAAACGCGTTTCCGG
CAGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATATACATTCACCGAACCAAATCCCA
GCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCGTTTAAATTAGAAAT
TAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCACGAAAATCCCGTCAATATTTTTGGCGTT
GAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAGAAAGATATTGCAGCA
AATTGAAACTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAGGGTCCGTTTGACTCA
GCTTATTTAACAGCTTATCTACTGAAAAAGGCTTAATA
Done.