Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015093.1 Corchorus olitorius cultivar O-4 contig15126, 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: 82910
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:10764 original size:32 final size:32
Alignment explanation
Indices: 10713--10776 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
10703 CTAAGTTTAA
* *
10713 GGTGCTTACTTTCTGAATTTGC-AGGTGTTACT
1 GGTGCTTACATTCTAAATTTGCGA-GTGTTACT
10745 GGTGCTTACATTCTAAATTTGCGAGTGTTACT
1 GGTGCTTACATTCTAAATTTGCGAGTGTTACT
10777 TTCTTTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (32 bp):
GGTGCTTACATTCTAAATTTGCGAGTGTTACT
Found at i:12852 original size:22 final size:22
Alignment explanation
Indices: 12824--12865 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
12814 CTGTTTTTTT
12824 TTGTTTAGATTATCTTATATTC
1 TTGTTTAGATTATCTTATATTC
12846 TTGTTTAGATTATCTTATAT
1 TTGTTTAGATTATCTTATAT
12866 GCAGACTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.60
Consensus pattern (22 bp):
TTGTTTAGATTATCTTATATTC
Found at i:14878 original size:2 final size:2
Alignment explanation
Indices: 14871--14908 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14861 CGATTACTAG
14871 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14909 ATCCCAGTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21429 original size:16 final size:16
Alignment explanation
Indices: 21410--21444 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
21400 GACCTGGAAA
21410 ACCCAAAACCTGAATG
1 ACCCAAAACCTGAATG
*
21426 ACCCAAAACCTGAGTG
1 ACCCAAAACCTGAATG
21442 ACC
1 ACC
21445 TAAGGGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.34, G:0.14, T:0.11
Consensus pattern (16 bp):
ACCCAAAACCTGAATG
Found at i:22200 original size:85 final size:85
Alignment explanation
Indices: 22098--22256 Score: 266
Period size: 85 Copynumber: 1.9 Consensus size: 85
22088 GTAATATGGT
* *
22098 AAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAA
1 AAAATAAAATAGGTATAAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT-AA
22163 AT-TATAAAAGTAAAATAGTA
65 ATCTATAAAAGTAAAATAGTA
* *
22183 AAAATAAAATAGTTATAAGGATATTAAATTTGATTAAATAAAAATAGAGTTTTTAGTTGACTAAA
1 AAAATAAAATAGGTATAAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTAAA
22248 TCTATAAAA
66 TCTATAAAA
22257 ATTAAACAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
84 4 0.06
85 65 0.94
ACGTcount: A:0.52, C:0.01, G:0.13, T:0.34
Consensus pattern (85 bp):
AAAATAAAATAGGTATAAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTAAA
TCTATAAAAGTAAAATAGTA
Found at i:26793 original size:21 final size:22
Alignment explanation
Indices: 26751--26805 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
26741 TTTGATAATT
26751 AAATTTTGATAATCATCATATA
1 AAATTTTGATAATCATCATATA
* *
26773 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAATCATCATATA
*
26794 AAATTGTGATAA
1 AAATTTTGATAA
26806 ACTCCATAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAATCATCATATA
Found at i:26879 original size:21 final size:21
Alignment explanation
Indices: 26752--26929 Score: 69
Period size: 22 Copynumber: 8.3 Consensus size: 21
26742 TTGATAATTA
* * *
26752 AATTTTGATAATCATCATATAA
1 AATTTTGATAATCTTCCTAT-G
* *
26774 AATTTTGATAAT-TACCTATAA
1 AATTTTGATAATCTTCCTAT-G
* * *
26795 AATTGTGATAAAC-TCCATAAG
1 AATTTTGATAATCTTCC-TATG
* * **
26816 AAACTTTGATAACCTAACTATG
1 -AATTTTGATAATCTTCCTATG
* *
26838 AAATTTTAATAAACTTTCCTATG
1 -AATTTTGATAATC-TTCCTATG
26861 TAATTTTG-TAATCTTCCTATG
1 -AATTTTGATAATCTTCCTATG
* *
26882 ATTTTTGATAATC-TCTCTGTG
1 AATTTTGATAATCTTC-CTATG
** *
26903 AGATTTTCTTAATCTCCCTAT-
1 A-ATTTTGATAATCTTCCTATG
26924 AATTTT
1 AATTTT
26930 TTGATACTAT
Statistics
Matches: 118, Mismatches: 29, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
20 13 0.11
21 37 0.31
22 54 0.46
23 14 0.12
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (21 bp):
AATTTTGATAATCTTCCTATG
Found at i:29619 original size:28 final size:28
Alignment explanation
Indices: 29587--29651 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 28
29577 TCTAAATTTC
29587 TATTATTTTAATAATGG-AATAATTA-AAA
1 TATTATTTTAATAATGGTAAT--TTAGAAA
29615 TATTA-TTTAATAATGGTAATTTAGAAA
1 TATTATTTTAATAATGGTAATTTAGAAA
29642 TATATATTTT
1 TAT-TATTTT
29652 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
26 3 0.09
27 17 0.52
28 10 0.30
29 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.48
Consensus pattern (28 bp):
TATTATTTTAATAATGGTAATTTAGAAA
Found at i:35054 original size:17 final size:17
Alignment explanation
Indices: 35032--35067 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35022 CCCTGGCAAT
*
35032 ATATATACCATCTGGCA
1 ATATATACCATATGGCA
*
35049 ATATATACCTTATGGCA
1 ATATATACCATATGGCA
35066 AT
1 AT
35068 TACCCTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (17 bp):
ATATATACCATATGGCA
Found at i:35145 original size:27 final size:27
Alignment explanation
Indices: 35083--35146 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
35073 TCTTGCACCA
35083 TCTT-GCAATAACATGTGGCAATTACCC
1 TCTTAGCAAT-ACATGTGGCAATTACCC
*
35110 TCTTA-CAATACTATGTGGCAATTACCT
1 TCTTAGCAATAC-ATGTGGCAATTACCC
35137 TC-TAGCAATA
1 TCTTAGCAATA
35147 TCAATACCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (27 bp):
TCTTAGCAATACATGTGGCAATTACCC
Found at i:49296 original size:35 final size:35
Alignment explanation
Indices: 49253--49322 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
49243 TTTGAGTTTG
49253 CTTTCTTAGGGCCTTTAGTTAGGCAATTGGGGTAT
1 CTTTCTTAGGGCCTTTAGTTAGGCAATTGGGGTAT
49288 CTTTCTTAGGGCCTTTAGTTAGGCAATTGGGGTAT
1 CTTTCTTAGGGCCTTTAGTTAGGCAATTGGGGTAT
49323 ACTCAACACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (35 bp):
CTTTCTTAGGGCCTTTAGTTAGGCAATTGGGGTAT
Found at i:50754 original size:46 final size:46
Alignment explanation
Indices: 50682--51500 Score: 849
Period size: 46 Copynumber: 18.3 Consensus size: 46
50672 TGCAAGAAGA
* * * *
50682 TACCATATAGAGAATTATTTCTGAAGATGGGTGCTCACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
*
50728 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTTACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
* * * *
50774 TACCGTATAAAGTATTTTTTCTGAAAAAAGGTGCTCACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
* * * *
50820 TACCATATAGAGCATTATTTCTGAAGAAGAGTGCTCACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
* **
50866 TACCGTATAGAGAATTCCTTT-TGAAGAAATGTGCTCACATAAGAG-
1 TACCGTATAGAGTATT-CTTTCTGAAGAAGGGTGCTCACATAAGAGC
*
50911 ---C---T--AGTATTCGTTCTGAAGAAGGGTGCTCACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
** *
50949 TACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
* * *
50995 TACCGTATAAAGTATTCTTTCTGAAAAAGGGTGCTTACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
*
51041 TACCATATAGATTATAGAGCATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
1 TACC-----G--TATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
* **
51094 TACCGTATAGAGAATTCCTTT-TGAAGAAATGTGCTCACATAAGAG-
1 TACCGTATAGAGTATT-CTTTCTGAAGAAGGGTGCTCACATAAGAGC
* *
51139 ---C---T--AGTATTCATTCTGAAGAAGGGTGCTCACATAAGAAC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
** * *
51177 TACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCACATAAGAAC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
* * * *
51223 TACCATATAAAGTATTCTTTCTGAAAAATGGTGCTCACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
* *
51269 TACCATATAGAGCATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
* * **
51315 TACCGTATAGAGAATTCCTTT-TGAAAAAATGTGCTCACATAAGAG-
1 TACCGTATAGAGTATT-CTTTCTGAAGAAGGGTGCTCACATAAGAGC
*
51360 ---C---T--AGTATTCATTCTGAAGAAGGGTGCTCACATAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
** * *
51398 TACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCACGTAAGAGC
1 TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
* *
51444 TACCGTATAGAGAATTCCTTTC-GAAGAAGTGTGCTCAC--AAGAGC
1 TACCGTATAGAGTATT-CTTTCTGAAGAAGGGTGCTCACATAAGAGC
*
51488 TACTGTATAGAGT
1 TACCGTATAGAGT
51501 TTAAGATGCA
Statistics
Matches: 654, Mismatches: 78, Indels: 84
0.80 0.10 0.10
Matches are distributed among these distances:
36 9 0.01
37 79 0.12
39 3 0.00
41 3 0.00
42 3 0.00
44 20 0.03
46 478 0.73
47 16 0.02
48 1 0.00
51 1 0.00
53 41 0.06
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (46 bp):
TACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGC
Found at i:51029 original size:129 final size:131
Alignment explanation
Indices: 50682--51445 Score: 610
Period size: 129 Copynumber: 5.7 Consensus size: 131
50672 TGCAAGAAGA
* * * *
50682 TACCATATAGAGA-ATTATTTCTGAAGATGGGTGCTCACATAAGAGCTACCGTATAGAGTATTCT
1 TACCATATAGA-ATATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATATAAAGTATTCT
* * * *
50746 TTCTGAAGAAGGGTGCTTACATAAGAGCTACCGTATAAAGTATTTTTTCTGAAAAAAGGTGCTCA
65 TTCTGAAGAAGGGTGCTCACATAAGAGCTA--G-AT--A--ATTCTTTCTGAAGAAGGGTGCTCA
50811 CATAAGAGC
123 CATAAGAGC
** * * * * *
50820 TACCATATAGAGCATTATTTCTGAAGAAGAGTGCTCACATAAGAGCTACCGTATAGAGAATTCCT
1 TACCATATAGAATATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATATAAAGTATT-CT
** *
50885 TT-TGAAGAAATGTGCTCACATAAGAGCTAG-T-ATTCGTTCTGAAGAAGGGTGCTCACATAAGA
65 TTCTGAAGAAGGGTGCTCACATAAGAGCTAGATAATTCTTTCTGAAGAAGGGTGCTCACATAAGA
50947 GC
130 GC
* *
50949 TACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCGTATAAAGTATTCTT
1 TACCATATAGAATATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATATAAAGTATTCTT
* *
51014 TCTGAAAAAGGGTGCTTACATAAGAGCTACCATATAGATTATAGAGCATTCTTTCTGAAGAAGGG
66 TCTGAAGAAGGGTGCTCACATAAGAG----C---TAG---AT--A--ATTCTTTCTGAAGAAGGG
51079 TGCTCACATAAGAGC
117 TGCTCACATAAGAGC
* **
51094 TACCGTATAGAGA-ATTCCTTT-TGAAGAAATGTGCTCACATAAGAG----C---T--AGTATTC
1 TACCATATAGA-ATATT-CTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATATAAAGTATTC
* * *
51148 ATTCTGAAGAAGGGTGCTCACATAAGAACTACCACATAGAATATTCTTTCTGAAGAAGGGTGCTC
64 TTTCTGAAGAAGGGTGCTCACATAAGAGCT---AGAT---A-ATTCTTTCTGAAGAAGGGTGCTC
*
51213 ACATAAGAAC
122 ACATAAGAGC
* * * *
51223 TACCATATA-AAGTATTCTTTCTGAAAAATGGTGCTCACATAAGAGCTACCATATAGAGCATTCT
1 TACCATATAGAA-TATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATATAAAGTATTCT
* **
51287 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTT-TGAAAAAATGTGCTC
65 TTCTGAAGAAGGGTGCTCACATAAGAGCTA--G-AT----AATT-CTTTCTGAAGAAGGGTGCTC
51351 ACATAAGAG-
122 ACATAAGAGC
* *
51360 ---C---TAG--TATTCATTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAA-TATTCT
1 TACCATATAGAATATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATATA-AAGTATTCT
*
51416 TTCTGAAGAAGGGTGCTCACGTAAGAGCTA
65 TTCTGAAGAAGGGTGCTCACATAAGAGCTA
51446 CCGTATAGAG
Statistics
Matches: 524, Mismatches: 58, Indels: 97
0.77 0.09 0.14
Matches are distributed among these distances:
127 1 0.00
128 9 0.02
129 244 0.47
130 2 0.00
131 2 0.00
132 2 0.00
133 2 0.00
134 2 0.00
135 1 0.00
136 36 0.07
138 141 0.27
139 9 0.02
140 1 0.00
141 1 0.00
145 66 0.13
146 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (131 bp):
TACCATATAGAATATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATATAAAGTATTCTT
TCTGAAGAAGGGTGCTCACATAAGAGCTAGATAATTCTTTCTGAAGAAGGGTGCTCACATAAGAG
C
Found at i:51389 original size:221 final size:220
Alignment explanation
Indices: 50700--51499 Score: 1291
Period size: 221 Copynumber: 3.6 Consensus size: 220
50690 AGAGAATTAT
* ** * *
50700 TTCTGAAGATGGGTGCTCACATAAGAGCTACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTTA
1 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCA
*
50765 CATAAGAGCTACCGTATAAAGTATTTTTTCTGAAAAAAGGTGCTCACATAAGAGCTACCATATAG
66 CATAAGAGCTACCGTATAAAGTATTCTTTCTG-AAAAAGGTGCTCACATAAGAGCTACCATATAG
* *
50830 AGCATTATTTCTGAAGAAGAGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTTGAAGAAA
130 AGCATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTTGAAGAAA
*
50895 TGTGCTCACATAAGAGCTAGTATTCG
195 TGTGCTCACATAAGAGCTAGTATTCA
50921 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCA
1 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCA
*
50986 CATAAGAGCTACCGTATAAAGTATTCTTTCTGAAAAAGGGTGCTTACATAAGAGCTACCATATAG
66 CATAAGAGCTACCGTATAAAGTATTCTTTCTGAAAAA-GGTGCTCACATAAGAGCTACC------
51051 ATTATAGAGCATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTT
124 A-TATAGAGCATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTT
51116 GAAGAAATGTGCTCACATAAGAGCTAGTATTCA
188 GAAGAAATGTGCTCACATAAGAGCTAGTATTCA
*
51149 TTCTGAAGAAGGGTGCTCACATAAGAACTACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCA
1 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCA
* *
51214 CATAAGAACTACCATATAAAGTATTCTTTCTGAAAAATGGTGCTCACATAAGAGCTACCATATAG
66 CATAAGAGCTACCGTATAAAGTATTCTTTCTGAAAAA-GGTGCTCACATAAGAGCTACCATATAG
*
51279 AGCATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTTGAAAAAA
130 AGCATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTTGAAGAAA
51344 TGTGCTCACATAAGAGCTAGTATTCA
195 TGTGCTCACATAAGAGCTAGTATTCA
51370 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCA
1 TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCA
* * * * **
51435 CGTAAGAGCTACCGTATAGAGAATTCCTTTC-GAAGAAGTGTGCTCAC--AAGAGCTACTGTATA
66 CATAAGAGCTACCGTATAAAGTATT-CTTTCTGAAAAAG-GTGCTCACATAAGAGCTACCATATA
51497 GAG
129 GAG
51500 TTTAAGATGC
Statistics
Matches: 544, Mismatches: 25, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
219 16 0.03
220 6 0.01
221 303 0.56
222 6 0.01
227 1 0.00
228 212 0.39
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (220 bp):
TTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTCTGAAGAAGGGTGCTCA
CATAAGAGCTACCGTATAAAGTATTCTTTCTGAAAAAGGTGCTCACATAAGAGCTACCATATAGA
GCATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTTGAAGAAAT
GTGCTCACATAAGAGCTAGTATTCA
Found at i:51463 original size:129 final size:127
Alignment explanation
Indices: 51233--51489 Score: 406
Period size: 129 Copynumber: 2.0 Consensus size: 127
51223 TACCATATAA
* * * *
51233 AGTATTCTTTCTGAAAAATGGTGCTCACATAAGAGCTACCATATAGAGCATTCTTTCTGAAGAAG
1 AGTATTCATTCTGAAAAAGGGTGCTCACATAAGAGCTACCACATAGAACATTCTTTCTGAAGAAG
*
51298 GGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTTGAAAAAATGTGCTCACATAAGAGCT
66 GGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTCGAAAAAATGTGCTCAC--AAGAGCT
* *
51362 AGTATTCATTCTGAAGAAGGGTGCTCACATAAGAGCTACCACATAGAATATTCTTTCTGAAGAAG
1 AGTATTCATTCTGAAAAAGGGTGCTCACATAAGAGCTACCACATAGAACATTCTTTCTGAAGAAG
* * *
51427 GGTGCTCACGTAAGAGCTACCGTATAGAGAATTCCTTTCGAAGAAGTGTGCTCACAAGAGCT
66 GGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTCGAAAAAATGTGCTCACAAGAGCT
51489 A
1 A
51490 CTGTATAGAG
Statistics
Matches: 118, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
127 8 0.07
129 110 0.93
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (127 bp):
AGTATTCATTCTGAAAAAGGGTGCTCACATAAGAGCTACCACATAGAACATTCTTTCTGAAGAAG
GGTGCTCACATAAGAGCTACCGTATAGAGAATTCCTTTCGAAAAAATGTGCTCACAAGAGCT
Found at i:51698 original size:36 final size:36
Alignment explanation
Indices: 51651--51782 Score: 156
Period size: 36 Copynumber: 3.7 Consensus size: 36
51641 AGTGGCATCA
51651 AAGGCCAGCGGCATTATAGCCAAATATTGGGCGACT
1 AAGGCCAGCGGCATTATAGCCAAATATTGGGCGACT
* * * *
51687 AAGGCCAGCGGCTTTACAGCCAATTATTGGGTGACT
1 AAGGCCAGCGGCATTATAGCCAAATATTGGGCGACT
* * * * * *
51723 TAGGCCATCAGCATTATGGCCAAGTATTAGGCGACT
1 AAGGCCAGCGGCATTATAGCCAAATATTGGGCGACT
* *
51759 TAGGCCATCGGCATTATAGCCAAA
1 AAGGCCAGCGGCATTATAGCCAAA
51783 GACAGAGCAA
Statistics
Matches: 80, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (36 bp):
AAGGCCAGCGGCATTATAGCCAAATATTGGGCGACT
Found at i:51972 original size:31 final size:32
Alignment explanation
Indices: 51937--52024 Score: 126
Period size: 31 Copynumber: 2.8 Consensus size: 32
51927 GATAGTTTGC
*
51937 CAACACCATGTGGAAGATGGTGTACTTCTT-A
1 CAACACCATATGGAAGATGGTGTACTTCTTGA
*
51968 CAACATCATATGGAAGATGGTGTACTTCTTGA
1 CAACACCATATGGAAGATGGTGTACTTCTTGA
*
52000 TAACACCATATGGAAGA-GGATGTAC
1 CAACACCATATGGAAGATGG-TGTAC
52025 CCTTCGACAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 30 0.59
32 21 0.41
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (32 bp):
CAACACCATATGGAAGATGGTGTACTTCTTGA
Found at i:52092 original size:51 final size:51
Alignment explanation
Indices: 52033--52200 Score: 192
Period size: 51 Copynumber: 3.3 Consensus size: 51
52023 ACCCTTCGAC
*
52033 ATTGGAAGGAGGTGATAGTTCGCCAACTCCATATACAAAAGACTTCATAAT
1 ATTGGAAGGAGGTGATAGTTCGCCAACACCATATACAAAAGACTTCATAAT
* * * *
52084 ATTGGAAGGAGGTGATATTTTGCGAACACCATATGCAAAAGACTTCATAAT
1 ATTGGAAGGAGGTGATAGTTCGCCAACACCATATACAAAAGACTTCATAAT
* * * * * * * ** *
52135 ATTGGAAAGAGGTGATATTTTGCGAACACCATATGCAAGAGGCTTCAGGAC
1 ATTGGAAGGAGGTGATAGTTCGCCAACACCATATACAAAAGACTTCATAAT
*
52186 GTTGGAAGGAGGTGA
1 ATTGGAAGGAGGTGA
52201 GACTTCGCTA
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 104 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (51 bp):
ATTGGAAGGAGGTGATAGTTCGCCAACACCATATACAAAAGACTTCATAAT
Found at i:52223 original size:30 final size:30
Alignment explanation
Indices: 52187--52277 Score: 148
Period size: 30 Copynumber: 3.0 Consensus size: 30
52177 CTTCAGGACG
*
52187 TTGGAAGGAGGTGAGACTTCGCTAACAGCA
1 TTGGAAGGAGGTGAGACTTCGCTAACACCA
52217 TTGGAAGGAGGTGAGACTTCGCTAACACCA
1 TTGGAAGGAGGTGAGACTTCGCTAACACCA
*
52247 TTGGAAGGAGGTG-GTACTTCGCGAACACCA
1 TTGGAAGGAGGTGAG-ACTTCGCTAACACCA
52277 T
1 T
52278 ATGCTTTTGA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 1 0.02
30 57 0.98
ACGTcount: A:0.29, C:0.19, G:0.32, T:0.21
Consensus pattern (30 bp):
TTGGAAGGAGGTGAGACTTCGCTAACACCA
Found at i:52314 original size:44 final size:44
Alignment explanation
Indices: 52264--52410 Score: 161
Period size: 44 Copynumber: 3.6 Consensus size: 44
52254 GAGGTGGTAC
* *
52264 TTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
1 TTCGCAAACACCATATGCCTTTGACATTGAAAGAGGGTGATAGT
*
52308 TTCGCGAACACCATATGCCTTTGACATTGAAAGA----G---G-
1 TTCGCAAACACCATATGCCTTTGACATTGAAAGAGGGTGATAGT
* **
52344 --CACAAACACCATATGTATTTGACATTGAAAGAGGGTGATAGT
1 TTCGCAAACACCATATGCCTTTGACATTGAAAGAGGGTGATAGT
*
52386 CTCGCAAACACCATATGCCTTTGAC
1 TTCGCAAACACCATATGCCTTTGAC
52411 GTCGCAGTTG
Statistics
Matches: 85, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
34 28 0.33
37 1 0.01
38 1 0.01
40 1 0.01
41 1 0.01
44 53 0.62
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
TTCGCAAACACCATATGCCTTTGACATTGAAAGAGGGTGATAGT
Found at i:52594 original size:19 final size:19
Alignment explanation
Indices: 52570--52641 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
52560 GCCTTTATTG
52570 TCGCGAATACCATACCATA
1 TCGCGAATACCATACCATA
* * *
52589 TCGCGAGTACCATGCCTCTA
1 TCGCGAATACCATACC-ATA
*
52609 GCGTCGCGAATACCATACCACA
1 ---TCGCGAATACCATACCATA
*
52631 TCGCGAGTACC
1 TCGCGAATACC
52642 GTCGCGAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 24 0.59
20 2 0.05
22 1 0.02
23 14 0.34
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.19
Consensus pattern (19 bp):
TCGCGAATACCATACCATA
Found at i:52645 original size:31 final size:31
Alignment explanation
Indices: 52610--52672 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
52600 ATGCCTCTAG
52610 CGTCGCGAATACCATACCACATCGCGAGTAC
1 CGTCGCGAATACCATACCACATCGCGAGTAC
52641 CGTCGCGAATACCATACCACATCGCGAGTAC
1 CGTCGCGAATACCATACCACATCGCGAGTAC
52672 C
1 C
52673 ATATGCCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.37, G:0.19, T:0.16
Consensus pattern (31 bp):
CGTCGCGAATACCATACCACATCGCGAGTAC
Found at i:52829 original size:53 final size:53
Alignment explanation
Indices: 52767--52920 Score: 254
Period size: 53 Copynumber: 2.9 Consensus size: 53
52757 TGTTTGAAGC
* * * *
52767 GAATGCCACATGCTTTTGACGTTGCGAATACCACATCGCAAATACCATATCGA
1 GAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCAAATACCACATCGA
* *
52820 GAATGCCACATGCCTTTGACATCGCGAATACCACATTGCAAATACCACATCGC
1 GAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCAAATACCACATCGA
52873 GAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCAAATACCAC
1 GAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCAAATACCAC
52921 CACATGCCTT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 94 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (53 bp):
GAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCAAATACCACATCGA
Found at i:52853 original size:25 final size:25
Alignment explanation
Indices: 52815--52908 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
52805 CAAATACCAT
* *
52815 ATCGAGAATGCCACATGCCTTTGAC
1 ATCGCGAATACCACATGCCTTTGAC
* ***
52840 ATCGCGAATACCACATTGCAAATACCAC
1 ATCGCGAATACCACA-TGC--CTTTGAC
*
52868 ATCGCGAATGCCACATGCCTTTGAC
1 ATCGCGAATACCACATGCCTTTGAC
*
52893 GTCGCGAATACCACAT
1 ATCGCGAATACCACAT
52909 TGCAAATACC
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
25 30 0.57
26 3 0.06
27 3 0.06
28 17 0.32
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (25 bp):
ATCGCGAATACCACATGCCTTTGAC
Found at i:52863 original size:14 final size:14
Alignment explanation
Indices: 52838--52883 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
52828 CATGCCTTTG
*
52838 ACATCGCGAATACC
1 ACATCGCAAATACC
*
52852 ACATTGCAAATACC
1 ACATCGCAAATACC
* *
52866 ACATCGCGAATGCC
1 ACATCGCAAATACC
52880 ACAT
1 ACAT
52884 GCCTTTGACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (14 bp):
ACATCGCAAATACC
Found at i:53507 original size:110 final size:110
Alignment explanation
Indices: 53329--53541 Score: 383
Period size: 110 Copynumber: 1.9 Consensus size: 110
53319 TTTTAAGTTG
53329 CATAGGCTAGAAGTATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAACACTCCTAAG
1 CATAGGCTAGAAGTATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAACACTCCTAAG
53394 GGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTAATGGGCTA
66 GGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTAATGGGCTA
* * *
53439 CATAGGCTTGAA-TCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACTAGTGCAGCACTCCTAA
1 CATAGGCTAGAAGT-ATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAACACTCCTAA
53503 GGGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTAA
65 GGGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTAA
53542 CAAGGAAGGG
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
109 1 0.01
110 98 0.99
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (110 bp):
CATAGGCTAGAAGTATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAACACTCCTAAG
GGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTAATGGGCTA
Found at i:57856 original size:45 final size:45
Alignment explanation
Indices: 57765--57857 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 45
57755 AGCAACAATT
* ** * * *
57765 AATATTAACTTTATTTTGATGAATTATTTAGAGATGGAGGAGTAG
1 AATATTAACTTTATTTTAATGAATTACCTAGAGACGGAAGACTAG
* *
57810 AATATTAGCTTTATTTTAATGAATTACCTAGAGACGGAATACTAG
1 AATATTAACTTTATTTTAATGAATTACCTAGAGACGGAAGACTAG
57855 AAT
1 AAT
57858 TTTGGTAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (45 bp):
AATATTAACTTTATTTTAATGAATTACCTAGAGACGGAAGACTAG
Found at i:79045 original size:2 final size:2
Alignment explanation
Indices: 79038--79067 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
79028 TCAGGATACA
79038 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79068 CAATAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.