Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015192.1 Corchorus olitorius cultivar O-4 contig15225, 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: 8420
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:63 original size:2 final size:2
Alignment explanation
Indices: 56--100 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
46 CTTTTCCCCC
56 TA TA 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 TA TA
98 TA T
1 TA T
101 TTTATATGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:613 original size:18 final size:18
Alignment explanation
Indices: 590--624 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
580 GTTAATACTA
590 AGTGAGAATGATAGTGAG
1 AGTGAGAATGATAGTGAG
*
608 AGTGAGAATGATGGTGA
1 AGTGAGAATGATAGTGA
625 AGTTGTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (18 bp):
AGTGAGAATGATAGTGAG
Found at i:1700 original size:12 final size:12
Alignment explanation
Indices: 1683--1713 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1673 CTCTAGTTAA
1683 TTACCCTTATTG
1 TTACCCTTATTG
1695 TTACCCTTATTG
1 TTACCCTTATTG
1707 TTACCCT
1 TTACCCT
1714 CAAATAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.29, G:0.06, T:0.48
Consensus pattern (12 bp):
TTACCCTTATTG
Found at i:2100 original size:107 final size:106
Alignment explanation
Indices: 1875--2137 Score: 433
Period size: 107 Copynumber: 2.5 Consensus size: 106
1865 TTTTTATTCT
* *
1875 TTTTAGAGATT-AAATAT--AACTAATGCCATTAAGTTTAGCCCCAAATTAAAATTTTAATTTAA
1 TTTTAGA-ATTAAAATATAAAACTAATGTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTAA
*
1937 TTTTAAGGTAAATTCCAAAATTAATAATTTATTGTTATAGGG
65 TTTTAAGGTAAATTCCAAAATTAATAATTTATTGTTATAGGA
1979 TTTTAGAATTAAAATATAAAACTAATGTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTAAT
1 TTTTAGAATTAAAATATAAAACTAATGTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTAAT
*
2044 TTTAAGGGTAAATTCTAAAATTAATAATTTATTGTTATAGGA
66 TTTAA-GGTAAATTCCAAAATTAATAATTTATTGTTATAGGA
*
2086 TTTTAGAATTAAAATATAAAACTAATGTCACTAAAGTTTAGCTCCAAATTAA
1 TTTTAGAATTAAAATATAAAACTAATGTCACT-AAGTTTAGCCCCAAATTAA
2138 TATATTTTTA
Statistics
Matches: 149, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
103 3 0.02
104 13 0.09
106 49 0.33
107 66 0.44
108 18 0.12
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.39
Consensus pattern (106 bp):
TTTTAGAATTAAAATATAAAACTAATGTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTAAT
TTTAAGGTAAATTCCAAAATTAATAATTTATTGTTATAGGA
Found at i:3400 original size:18 final size:19
Alignment explanation
Indices: 3361--3400 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
3351 GTGCTCCCGT
3361 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
3382 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
3400 T
1 T
3401 TATGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:6076 original size:111 final size:112
Alignment explanation
Indices: 5873--6097 Score: 407
Period size: 111 Copynumber: 2.0 Consensus size: 112
5863 CAATTTTGTG
*
5873 GTTTCTTGTTACTAAGCTAACTAGTTTCTAAAAGAATCATACAACTTCATTTCTTCTATGGCAGG
1 GTTTCTTGTTACTAAGCTAACTAGTTTCTAAAAGAATCATACAACTTCATTTCTTCCATGGCAGG
5938 GATGATGATAAAGGGGATGATGAGGCAACGAGAATAAGGTCCCATGT
66 GATGATGATAAAGGGGATGATGAGGCAACGAGAATAAGGTCCCATGT
*
5985 GTTTGTTG-TACTAAGCTAACTAGTTTCTAAAAGAATCATACAACTTCATTTCTTCCATGGCAGG
1 GTTTCTTGTTACTAAGCTAACTAGTTTCTAAAAGAATCATACAACTTCATTTCTTCCATGGCAGG
* *
6049 GATGATGATAAAGGGGATGATGAGGCAACGAGATTAAGGTCCCTTGT
66 GATGATGATAAAGGGGATGATGAGGCAACGAGAATAAGGTCCCATGT
6096 GT
1 GT
6098 CTCCATATAC
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
111 102 0.94
112 7 0.06
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (112 bp):
GTTTCTTGTTACTAAGCTAACTAGTTTCTAAAAGAATCATACAACTTCATTTCTTCCATGGCAGG
GATGATGATAAAGGGGATGATGAGGCAACGAGAATAAGGTCCCATGT
Found at i:6811 original size:43 final size:42
Alignment explanation
Indices: 6763--6854 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 42
6753 TATCCATATC
**
6763 AAATTTGAAAACTGCACTATGAAATTTTGATAACCACACAACG
1 AAATTTGAAAACTAAACTAT-AAATTTTGATAACCACACAACG
* * * *
6806 AAATTTTGATAACTAAACTATAAATTTTGATAACTATACTACG
1 AAA-TTTGAAAACTAAACTATAAATTTTGATAACCACACAACG
6849 AAATTT
1 AAATTT
6855 CGATAACCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.07
43 25 0.60
44 14 0.33
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.33
Consensus pattern (42 bp):
AAATTTGAAAACTAAACTATAAATTTTGATAACCACACAACG
Found at i:6832 original size:21 final size:22
Alignment explanation
Indices: 6778--6861 Score: 98
Period size: 22 Copynumber: 3.9 Consensus size: 22
6768 TGAAAACTGC
* * *
6778 ACTATGAAATTTTGATAACCAC
1 ACTACGAAATTTTGATAACTAA
*
6800 ACAACGAAATTTTGATAACTAA
1 ACTACGAAATTTTGATAACTAA
* *
6822 ACTA-TAAATTTTGATAACTAT
1 ACTACGAAATTTTGATAACTAA
*
6843 ACTACGAAATTTCGATAAC
1 ACTACGAAATTTTGATAAC
6862 CTCATGCTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 19 0.37
22 33 0.63
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (22 bp):
ACTACGAAATTTTGATAACTAA
Found at i:6860 original size:43 final size:44
Alignment explanation
Indices: 6778--6861 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
6768 TGAAAACTGC
*
6778 ACTATGAAATTTTGATAACCACACAACGAAATTTTGATAACTAA
1 ACTATGAAATTTTGATAACCACACAACGAAATTTCGATAACTAA
* * *
6822 ACTAT-AAATTTTGATAACTATACTACGAAATTTCGATAAC
1 ACTATGAAATTTTGATAACCACACAACGAAATTTCGATAAC
6862 CTCATGCTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 31 0.86
44 5 0.14
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (44 bp):
ACTATGAAATTTTGATAACCACACAACGAAATTTCGATAACTAA
Found at i:6924 original size:22 final size:21
Alignment explanation
Indices: 6878--7630 Score: 177
Period size: 22 Copynumber: 34.6 Consensus size: 21
6868 CTCACTATAA
* *
6878 AAATTTTGATAACCTCC-CTG
1 AAATTTTGATAACATCCTATG
6898 TAAATTTTTGATAACATCCTATG
1 -AAA-TTTTGATAACATCCTATG
* *
6921 AAATGTTGGTAAACA-CACTATG
1 AAATTTTGAT-AACATC-CTATG
* * *
6943 AGATTGTGATAACCATCTTATG
1 AAATTTTGATAA-CATCCTATG
*
6965 AAATTTTGATAACCA-CACTATA
1 AAATTTTGATAA-CATC-CTATG
* * *
6987 AAATTGTGATAATTATACTATG
1 AAATTTTGATAA-CATCCTATG
* * * *
7009 CAATTGTGATAACCTCCCTATA
1 AAATTTTGATAACAT-CCTATG
* * * *
7031 AAATTTTGATAACCTCTTTCTA
1 AAATTTTGATAACATC-CTATG
7053 AAATTTTGATAATCA-CACTATG
1 AAATTTTGATAA-CATC-CTATG
* *
7075 AAAATTTGATAACGTCCTACTAATG
1 AAATTTTGATAACAT-C--CT-ATG
*
7100 AAATTTTAATAATC-TCCCTATG
1 AAATTTTGATAA-CAT-CCTATG
** *
7122 AAATTTTGATAACCGCACAATG
1 AAATTTTGATAACATC-CTATG
** *
7144 AAATTTTGATAACCGCATAATG
1 AAATTTTGATAACATCCT-ATG
* *
7166 AAATTTCGATAACCTCTCTATG
1 AAATTTTGATAACATC-CTATG
* * *
7188 AAAATTTGAAAACCATACTATG
1 AAATTTTGATAA-CATCCTATG
* ****
7210 ATACCTCCCAATGAA-AT--T-T-
1 A-A-ATTTTGAT-AACATCCTATG
* *
7229 ---TTATAACT-ACA--CTATG
1 AAATTTTGA-TAACATCCTATG
* * * *
7245 AAAATTTGATAGCTTCATTATG
1 AAATTTTGATAACATC-CTATG
*
7267 AAAATTTGATAA-ACTCCCTATG
1 AAATTTTGATAACA-T-CCTATG
* *
7289 AAATTTTGAGAACCA-CGTAATG
1 AAATTTTGATAA-CATCCT-ATG
* * *
7311 AAATTTTGGT-ACCTCCCTATA
1 AAATTTTGATAACAT-CCTATG
*
7332 AAATATTGATAACCA-CACTATG
1 AAATTTTGATAA-CATC-CTATG
* ** *
7354 GAATTTTGATAATTTCCTTGTG
1 AAATTTTGATAACATCC-TATG
* * *
7376 AAATTTTGAGAACCTCACTGTG
1 AAATTTTGATAACATC-CTATG
* *
7398 AAATTTCGATAACCTCGCTATG
1 AAATTTTGATAACATC-CTATG
*
7420 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACAT-CCTATG
*
7442 AAAATTTGATAACCA-CACTATG
1 AAATTTTGATAA-CATC-CTATG
* *
7464 AAAGTTTGATAACGTTCCTATG
1 AAATTTTGATAAC-ATCCTATG
* * *
7486 AAATTTTAATAACTTCCCAATG
1 AAATTTTGATAACAT-CCTATG
* **
7508 AAATTTTGGTTTTCA-CACTATG
1 AAATTTT-GATAACATC-CTATG
* **
7530 AAATTTCGATAACCCCTCTATG
1 AAATTTTGATAACATC-CTATG
*
7552 AAATTTTGGTAATCA-CACTATG
1 AAATTTTGATAA-CATC-CTATG
*
7574 AAATTGTGATAACCA-CACTATG
1 AAATTTTGATAA-CATC-CTATG
* * *
7596 AAATTGTGATAACCTCAATATG
1 AAATTTTGATAACATC-CTATG
*
7618 ATATTTTGATAAC
1 AAATTTTGATAAC
7631 CGCACACACT
Statistics
Matches: 548, Mismatches: 124, Indels: 119
0.69 0.16 0.15
Matches are distributed among these distances:
13 1 0.00
14 5 0.01
15 2 0.00
18 1 0.00
19 4 0.01
20 2 0.00
21 42 0.08
22 445 0.81
23 22 0.04
24 5 0.01
25 18 0.03
26 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (21 bp):
AAATTTTGATAACATCCTATG
Found at i:7085 original size:66 final size:65
Alignment explanation
Indices: 6779--7631 Score: 520
Period size: 66 Copynumber: 13.0 Consensus size: 65
6769 GAAAACTGCA
* * **
6779 CTATGAAATTTTGATAACCACACAACGAAATTTTGATAA-CTAAACTAT-AAATTTTGATAA-CT
1 CTATGAAATTTTGATAACCACACTATGAAA-TTTGATAACCT-CCCTATGAAATTTTGATAACCT
**
6841 ATA
64 -CC
* * * *
6844 CTACGAAATTTCGATAACCTCATGCTCACTATAAAAATTTTGATAACCTCCCTGT-AAATTTTTG
1 CTATGAAATTTTGATAA-C-CA----CACTAT-GAAA-TTTGATAACCTCCCTATGAAA-TTTTG
*
6908 ATAACAT-C
57 ATAACCTCC
* * * * * *
6916 CTATGAAATGTTGGTAAACACACTATGAGATTGTGATAACCAT-CTTATGAAATTTTGATAACCA
1 CTATGAAATTTTGATAACCACACTATGAAATT-TGATAACC-TCCCTATGAAATTTTGATAACCT
*
6980 CA
64 CC
* * ** * * *
6982 CTATAAAATTGTGATAATTATACTATGCAATTGTGATAACCTCCCTATAAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACCACACTATGAAATT-TGATAACCTCCCTATGAAATTTTGATAACCTC
*
7047 T
65 C
* * * * * * *
7048 TTCTAAAATTTTGATAATCACACTATGAAAATTTGATAACGTCCTACTAATGAAATTTTAATAAT
1 CTATGAAATTTTGATAACCACACTATG-AAATTTGATAACCTCC--CT-ATGAAATTTTGATAAC
7113 CTCC
62 CTCC
* * * * *
7117 CTATGAAATTTTGATAACCGCACAATGAAATTTTGATAACC-GCATAATGAAATTTCGATAACCT
1 CTATGAAATTTTGATAACCACACTATGAAA-TTTGATAACCTCCCT-ATGAAATTTTGATAACCT
*
7181 CT
64 CC
* * * * *
7183 CTATGAAAATTTGA-AA--AC-C-AT--ACTATGAT-ACCTCCCAATGAAATTTTTATAA-CTAC
1 CTATGAAATTTTGATAACCACACTATGAAATTTGATAACCTCCCTATGAAATTTTGATAACCT-C
*
7239 A
65 C
* * ** * * * *
7240 CTATGAAAATTTGATAGCTTCATTATGAAAATTTGATAAACTCCCTATGAAATTTTGAGAACC-A
1 CTATGAAATTTTGATAACCACACTATG-AAATTTGATAACCTCCCTATGAAATTTTGATAACCTC
7304 C
65 C
* * * * * * * * **
7305 GTAATGAAATTTTGGT-ACCTCCCTATAAAATATTGATAACCACACTATGGAATTTTGATAATTT
1 CT-ATGAAATTTTGATAACCACACTATGAAAT-TTGATAACCTCCCTATGAAATTTTGATAACCT
7369 CC
64 CC
* * * * * *
7371 TTGTGAAATTTTGAGAACCTCACTGTGAAATTTCGATAACCTCGCTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACCACACTATGAAATTT-GATAACCTCCCTATGAAATTTTGATAACCTC
7436 C
65 C
* * * * *
7437 CTATGAAAATTTGATAACCACACTATGAAAGTTTGATAACGTTCCTATGAAATTTTAATAACTTC
1 CTATGAAATTTTGATAACCACACTATGAAA-TTTGATAACCTCCCTATGAAATTTTGATAACCTC
7502 C
65 C
* * *** * * *
7503 CAATGAAATTTTGGTTTTCACACTATGAAATTTCGATAACC-CCTCTATGAAATTTTGGTAATCA
1 CTATGAAATTTTGATAACCACACTATGAAATTT-GATAACCTCC-CTATGAAATTTTGATAACCT
*
7567 CA
64 CC
* ** *
7569 CTATGAAATTGTGATAACCACACTATGAAATTGTGATAACCTCAATATGATATTTTGATAACC
1 CTATGAAATTTTGATAACCACACTATGAAATT-TGATAACCTCCCTATGAAATTTTGATAACC
7632 GCACACACTA
Statistics
Matches: 602, Mismatches: 144, Indels: 83
0.73 0.17 0.10
Matches are distributed among these distances:
56 2 0.00
57 31 0.05
58 7 0.01
59 1 0.00
60 1 0.00
61 2 0.00
62 3 0.00
63 1 0.00
64 6 0.01
65 94 0.16
66 341 0.57
67 12 0.02
68 6 0.01
69 46 0.08
70 2 0.00
71 4 0.01
72 31 0.05
73 11 0.02
74 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (65 bp):
CTATGAAATTTTGATAACCACACTATGAAATTTGATAACCTCCCTATGAAATTTTGATAACCTCC
Found at i:7167 original size:44 final size:42
Alignment explanation
Indices: 6756--7631 Score: 345
Period size: 44 Copynumber: 20.0 Consensus size: 42
6746 AATTAAATAT
* *
6756 CCATATCAAA-TTTGA-AAACTGCACTATGAAATTTTGATAAC
1 CCATATGAAATTTTGATAACCT-CACTATGAAATTTTGATAAC
* * *
6797 CACACAACGAAATTTTGATAA-CTAAACTAT-AAATTTTGATAA-
1 C-CA-TATGAAATTTTGATAACCT-CACTATGAAATTTTGATAAC
* * *
6839 CTATACTACGAAATTTCGATAACCTCATGCTCACTATAAAAATTTTGATAAC
1 CCATA-T--GAAATTTTGATAA---C---CTCACTAT-GAAATTTTGATAAC
** * * *
6891 CTC-CCTGTAAATTTTTGATAACATC-CTATGAAATGTTGGTAAAC
1 C-CATATG-AAA-TTTTGATAACCTCACTATGAAATTTTGAT-AAC
* * * *
6935 ACACTATGAGATTGTGATAACCATC-TTATGAAATTTTGATAAC
1 CCA-TATGAAATTTTGATAACC-TCACTATGAAATTTTGATAAC
* * * * * *
6978 CACACTATAAAATTGTGATAA-TTATACTATGCAATTGTGATAACC
1 C-CA-TATGAAATTTTGATAACCT-CACTATGAAATTTTGATAA-C
* * ** * *
7023 TCCCTATAAAATTTTGATAACCTCTTTCTAAAATTTTGATAATC
1 -CCATATGAAATTTTGATAACCTCACTATGAAATTTTGATAA-C
* * * *
7067 ACACTATGAAAATTTGATAACGTCCTACTAATGAAATTTTAATAATC
1 CCA-TATGAAATTTTGATAACCT-C-ACT-ATGAAATTTTGATAA-C
* * *
7114 TCCCTATGAAATTTTGATAACCGCACAATGAAATTTTGATAAC
1 -CCATATGAAATTTTGATAACCTCACTATGAAATTTTGATAAC
* * * *
7157 CGCATAATGAAATTTCGATAACCTCTCTATGAAAATTTGA-AAA
1 C-CAT-ATGAAATTTTGATAACCTCACTATGAAATTTTGATAAC
* * *
7200 CCATACT---A---TGAT-ACCTCCCAATGAAATTTTTATAAC
1 CCATA-TGAAATTTTGATAACCTCACTATGAAATTTTGATAAC
* * * * * *
7236 TACACTATGAAAATTTGATAGCTTCATTATGAAAATTTGATAAAC
1 -CCA-TATGAAATTTTGATAACCTCACTATGAAATTTTGAT-AAC
* * * *
7281 TCCCTATGAAATTTTGAGAA-C-CACGTAATGAAATTTTGGTACC
1 -CCATATGAAATTTTGATAACCTCAC-T-ATGAAATTTTGATAAC
* * * * * *
7324 TCCCTATAAAATATTGATAACCACACTATGGAATTTTGATAATTT
1 -CCATATGAAATTTTGATAACCTCACTATGAAATTTTGATAA--C
* * * * *
7369 CCTTGTGAAATTTTGAGAACCTCACTGTGAAATTTCGATAAC
1 CCATATGAAATTTTGATAACCTCACTATGAAATTTTGATAAC
* * *
7411 CTCGCTATGAAATTTTGATAACCTCCCTATGAAAATTTGATAAC
1 C-C-ATATGAAATTTTGATAACCTCACTATGAAATTTTGATAAC
* * *
7455 CACACTATGAAAGTTTGATAACGTTC-CTATGAAATTTTAATAACTTC
1 C-CA-TATGAAATTTTGATAAC-CTCACTATGAAATTTTGATAA---C
* *** * *
7502 CCA-ATGAAATTTTGGTTTTCACACTATGAAATTTCGATAACC
1 CCATATGAAATTTTGATAACCTCACTATGAAATTTTGATAA-C
* * * * *
7544 CCTCTATGAAATTTTGGTAATCACACTATGAAATTGTGATAAC
1 CC-ATATGAAATTTTGATAACCTCACTATGAAATTTTGATAAC
* * *
7587 CACACTATGAAATTGTGATAACCTCAATATGATATTTTGATAAC
1 C-CA-TATGAAATTTTGATAACCTCACTATGAAATTTTGATAAC
7631 C
1 C
7632 GCACACACTA
Statistics
Matches: 621, Mismatches: 147, Indels: 131
0.69 0.16 0.15
Matches are distributed among these distances:
35 16 0.03
36 5 0.01
37 3 0.00
38 2 0.00
39 1 0.00
40 2 0.00
41 3 0.00
42 15 0.02
43 96 0.15
44 384 0.62
45 22 0.04
46 5 0.01
47 32 0.05
48 2 0.00
49 6 0.01
50 5 0.01
51 21 0.03
52 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (42 bp):
CCATATGAAATTTTGATAACCTCACTATGAAATTTTGATAAC
Found at i:7288 original size:101 final size:101
Alignment explanation
Indices: 7113--7303 Score: 240
Period size: 101 Copynumber: 1.9 Consensus size: 101
7103 TTTTAATAAT
* * *
7113 CTCCCTATGAAATTTTGATAACCGCACAATGAAATTTTGATAACCGCATAATGAAATTTCGATAA
1 CTCCCAATGAAATTTTGATAACCACACAATGAAAATTTGATAACCGCATAATGAAATTTCGATAA
* *
7178 CCTCTCTATGAAAATTTGAAAACCATACTATGATAC
66 ACTCCCTATGAAAATTTGAAAACCATACTATGATAC
* * * * ** *
7214 CTCCCAATGAAATTTTTATAACTACACTATGAAAATTTGATAGCTTCATTATGAAAATTT-GATA
1 CTCCCAATGAAATTTTGATAACCACACAATGAAAATTTGATAACCGCATAATG-AAATTTCGATA
* *
7278 AACTCCCTATGAAATTTTGAGAACCA
65 AACTCCCTATGAAAATTTGAAAACCA
7304 CGTAATGAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
101 69 0.92
102 6 0.08
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (101 bp):
CTCCCAATGAAATTTTGATAACCACACAATGAAAATTTGATAACCGCATAATGAAATTTCGATAA
ACTCCCTATGAAAATTTGAAAACCATACTATGATAC
Found at i:7631 original size:22 final size:22
Alignment explanation
Indices: 7220--7682 Score: 316
Period size: 22 Copynumber: 21.1 Consensus size: 22
7210 ATACCTCCCA
*
7220 ATGAAATTTTTATAA-CTACACT
1 ATGAAATTTTGATAACCT-CACT
* * * *
7242 ATGAAAATTTGATAGCTTCATT
1 ATGAAATTTTGATAACCTCACT
* * *
7264 ATGAAAATTTGATAAACTCCCT
1 ATGAAATTTTGATAACCTCACT
*
7286 ATGAAATTTTGAGAA-C-CACGT
1 ATGAAATTTTGATAACCTCAC-T
* *
7307 AATGAAATTTTGGT-ACCTCCCT
1 -ATGAAATTTTGATAACCTCACT
* * *
7329 ATAAAATATTGATAACCACACT
1 ATGAAATTTTGATAACCTCACT
* **
7351 ATGGAATTTTGATAATTTC-CTT
1 ATGAAATTTTGATAACCTCAC-T
* *
7373 GTGAAATTTTGAGAACCTCACT
1 ATGAAATTTTGATAACCTCACT
* * *
7395 GTGAAATTTCGATAACCTCGCT
1 ATGAAATTTTGATAACCTCACT
*
7417 ATGAAATTTTGATAACCTCCCT
1 ATGAAATTTTGATAACCTCACT
* *
7439 ATGAAAATTTGATAACCACACT
1 ATGAAATTTTGATAACCTCACT
* *
7461 ATGAAAGTTTGATAACGTTC-CT
1 ATGAAATTTTGATAAC-CTCACT
* * * *
7483 ATGAAATTTTAATAACTTCCCA
1 ATGAAATTTTGATAACCTCACT
* *** *
7505 ATGAAATTTTGGTTTTCACACT
1 ATGAAATTTTGATAACCTCACT
* * *
7527 ATGAAATTTCGATAACCCCTCT
1 ATGAAATTTTGATAACCTCACT
* * *
7549 ATGAAATTTTGGTAATCACACT
1 ATGAAATTTTGATAACCTCACT
* *
7571 ATGAAATTGTGATAACCACACT
1 ATGAAATTTTGATAACCTCACT
* *
7593 ATGAAATTGTGATAACCTCAAT
1 ATGAAATTTTGATAACCTCACT
* *
7615 ATGATATTTTGATAACCGCACACACT
1 ATGAAATTTTGATAA---C-CTCACT
*
7641 ATGAAATTTTGATTA-CT---T
1 ATGAAATTTTGATAACCTCACT
* *
7659 ATGAATTTTTGACAACCTCACT
1 ATGAAATTTTGATAACCTCACT
7681 AT
1 AT
7683 ATATGAAAAT
Statistics
Matches: 340, Mismatches: 83, Indels: 36
0.74 0.18 0.08
Matches are distributed among these distances:
18 13 0.04
19 2 0.01
20 2 0.01
21 18 0.05
22 282 0.83
23 5 0.01
25 1 0.00
26 17 0.05
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCACT
Done.