Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012301.1 Corchorus olitorius cultivar O-4 contig12334, 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: 68735
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:919 original size:24 final size:24
Alignment explanation
Indices: 887--943 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
877 TCGGGTCACG
887 CGCGACCCGGGTGCATGGCCAGGT
1 CGCGACCCGGGTGCATGGCCAGGT
911 CGCGACCCGGGTGCATGGCCAGGT
1 CGCGACCCGGGTGCATGGCCAGGT
935 CGCGACCCG
1 CGCGACCCG
944 TCATTCCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.12, C:0.37, G:0.40, T:0.11
Consensus pattern (24 bp):
CGCGACCCGGGTGCATGGCCAGGT
Found at i:18261 original size:20 final size:21
Alignment explanation
Indices: 18222--18263 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
18212 CCTCTCATGG
**
18222 AGCTTGGGATTTTCTTCATCA
1 AGCTTGGGATTTTCACCATCA
18243 AGCTT-GGATTTTCACCATCA
1 AGCTTGGGATTTTCACCATCA
18263 A
1 A
18264 ATATCTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
AGCTTGGGATTTTCACCATCA
Found at i:20961 original size:108 final size:109
Alignment explanation
Indices: 20769--20989 Score: 336
Period size: 108 Copynumber: 2.0 Consensus size: 109
20759 AAGAGGGAAT
* *
20769 TTAATAAACTACTTCGCTGTTTTTGGGAAGTATAGCACACGGGGTTCGGTATCACAAATATCAAC
1 TTAATAAACTACTCCGCTGTTTTTGGGAAGTAGAGCACACGGGGTTCGGTATCACAAATATCAAC
* * * * *
20834 CTTCGCGTCAGTCATGAACCAAACTTATGAGTATGCAAAGCATC
66 CTTCGCGTCAATCACGAACCAAAATTACGAGTATGCAAAGCACC
* * *
20878 TTAATAAACTACTCCTCTGTTTTT-GGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAT
1 TTAATAAACTACTCCGCTGTTTTTGGGAAGTAGAGCACACGGGGTTCGGTATCACAAATATCAAC
*
20942 CTTCGCGTCAATCACGAACCAAAATTACGATTATGCAAAGCACC
66 CTTCGCGTCAATCACGAACCAAAATTACGAGTATGCAAAGCACC
20986 TTAA
1 TTAA
20990 ATGCGTAAGT
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
108 79 0.78
109 22 0.22
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (109 bp):
TTAATAAACTACTCCGCTGTTTTTGGGAAGTAGAGCACACGGGGTTCGGTATCACAAATATCAAC
CTTCGCGTCAATCACGAACCAAAATTACGAGTATGCAAAGCACC
Found at i:22135 original size:20 final size:21
Alignment explanation
Indices: 22096--22137 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
22086 CCTCTCATGG
**
22096 AGCTTGGGATTTTCTTCATCA
1 AGCTTGGGATTTTCACCATCA
22117 AGCTT-GGATTTTCACCATCA
1 AGCTTGGGATTTTCACCATCA
22137 A
1 A
22138 ATATCTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
AGCTTGGGATTTTCACCATCA
Found at i:25109 original size:30 final size:30
Alignment explanation
Indices: 25073--25129 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
25063 CTTGCTTAGC
25073 AGATTGTT-CTTTATCCTTCTCTTCTTTGAT
1 AGATTGTTGC-TTATCCTTCTCTTCTTTGAT
* *
25103 AGATTGTTGCTTCTCTTTCTCTTCTTT
1 AGATTGTTGCTTATCCTTCTCTTCTTT
25130 CTCTGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.11, C:0.21, G:0.11, T:0.58
Consensus pattern (30 bp):
AGATTGTTGCTTATCCTTCTCTTCTTTGAT
Found at i:26134 original size:17 final size:20
Alignment explanation
Indices: 26112--26150 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
26102 TTCTTTATTA
26112 TTGAGAA-T-CGTT-AGAAG
1 TTGAGAATTGCGTTAAGAAG
26129 TTGAGAATTGCGTTAAGAAG
1 TTGAGAATTGCGTTAAGAAG
26149 TT
1 TT
26151 TTCTATATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 4 0.21
20 7 0.37
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (20 bp):
TTGAGAATTGCGTTAAGAAG
Found at i:43390 original size:30 final size:30
Alignment explanation
Indices: 43334--43396 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
43324 ATGAAATTGA
*
43334 AAAAGATACACAAGGCTTTGTATTCTAATT
1 AAAAGATACACAAGGCTTTCTATTCTAATT
*
43364 AAAAGATACACAAGGCTTTCCT-TTCTAGTT
1 AAAAGATACACAAGGCTTT-CTATTCTAATT
43394 AAA
1 AAA
43397 CATTATCAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32
Consensus pattern (30 bp):
AAAAGATACACAAGGCTTTCTATTCTAATT
Found at i:44915 original size:45 final size:45
Alignment explanation
Indices: 44850--44959 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 45
44840 GGAGCTGCTC
* *
44850 CATCATCGTTCTCACATATCTCTTATTCAATCTCTATTGCTA-CT
1 CATCATCGTTCTGACATATCTCTTATTCAATCTCTACTGCTACCT
* * * ** *
44894 CTATCATCCTTCTGACTTATCTCTTCTTTTATCTTTACTGCTACCT
1 C-ATCATCGTTCTGACATATCTCTTATTCAATCTCTACTGCTACCT
*
44940 CATCATCGTTCTGACCTATC
1 CATCATCGTTCTGACATATC
44960 CCTTTCATCT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.02
45 50 0.93
46 3 0.06
ACGTcount: A:0.19, C:0.31, G:0.05, T:0.45
Consensus pattern (45 bp):
CATCATCGTTCTGACATATCTCTTATTCAATCTCTACTGCTACCT
Found at i:47534 original size:20 final size:21
Alignment explanation
Indices: 47511--47550 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
47501 TTTTTCTTTC
* *
47511 TTACTTTTTCTCTT-TGATTT
1 TTACTTGTTATCTTATGATTT
47531 TTACTTGTTATCTTATGATT
1 TTACTTGTTATCTTATGATT
47551 ATATGACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.12, G:0.07, T:0.65
Consensus pattern (21 bp):
TTACTTGTTATCTTATGATTT
Found at i:48659 original size:2 final size:2
Alignment explanation
Indices: 48652--48679 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48642 GGCACAGGAA
48652 AT 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 AT
48680 GTCTTTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51630 original size:49 final size:48
Alignment explanation
Indices: 51530--51651 Score: 147
Period size: 49 Copynumber: 2.5 Consensus size: 48
51520 AATTTTGTAC
* * * * * * **
51530 AAAAATTGATAAAAAGAGCAATGAAAAGTAAATATTCAATTTTGTCTT
1 AAAAATTGAGAAAAAGTGCAAGGAAAAATAAAGATTCAATTTCGTAGT
*
51578 AAAAATTGAGAAAAAGGTGCAAGGAAAAATAAAGGTTCAATTTCGTAGT
1 AAAAATTGAGAAAAA-GTGCAAGGAAAAATAAAGATTCAATTTCGTAGT
51627 AAAAATTGAGAAAAAGTGC-AGGAAA
1 AAAAATTGAGAAAAAGTGCAAGGAAA
51652 TGTAAAAGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
47 6 0.09
48 18 0.28
49 40 0.62
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.24
Consensus pattern (48 bp):
AAAAATTGAGAAAAAGTGCAAGGAAAAATAAAGATTCAATTTCGTAGT
Found at i:55110 original size:2 final size:2
Alignment explanation
Indices: 55103--55127 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55093 AACCAAATGG
55103 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 T
55128 GTAATTTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55572 original size:44 final size:44
Alignment explanation
Indices: 55504--55627 Score: 176
Period size: 44 Copynumber: 2.8 Consensus size: 44
55494 TGACAATCAA
* * *
55504 ACCAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATACAAAGGTTATCAAAATTTCATAGTGTGGTT
* *
55548 ACCAAAATTTCATATAGAGGTTATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATACAAAGGTTATCAAAATTTCATAGTGTGGTT
* * *
55592 ATCAAAATTTCATACAAAGGTTACCACAATTTCATA
1 ACCAAAATTTCATACAAAGGTTATCAAAATTTCATA
55628 AAAAAGTTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (44 bp):
ACCAAAATTTCATACAAAGGTTATCAAAATTTCATAGTGTGGTT
Found at i:55613 original size:22 final size:22
Alignment explanation
Indices: 55504--55694 Score: 150
Period size: 22 Copynumber: 8.7 Consensus size: 22
55494 TGACAATCAA
* *
55504 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGAAAGGTT
* ***
55526 ATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATAGAAAGGTT
* *
55548 ACCAAAATTTCATATAGAGGTT
1 ACCAAAATTTCATAGAAAGGTT
* ***
55570 ATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATAGAAAGGTT
* *
55592 ATCAAAATTTCATACAAAGGTT
1 ACCAAAATTTCATAGAAAGGTT
* * *
55614 ACCACAATTTCATAAAAAAGTT
1 ACCAAAATTTCATAGAAAGGTT
* ** *
55636 ACCAAAATTTCTTAGGGATGTT
1 ACCAAAATTTCATAGAAAGGTT
**
55658 AATAAAATTTCATATGAAA-GTT
1 ACCAAAATTTCATA-GAAAGGTT
*
55680 AACAAAATTTCATAG
1 ACCAAAATTTCATAG
55695 GGAGGGAGGT
Statistics
Matches: 134, Mismatches: 34, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
21 1 0.01
22 131 0.98
23 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
ACCAAAATTTCATAGAAAGGTT
Found at i:55789 original size:22 final size:22
Alignment explanation
Indices: 55720--55796 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
55710 AAATTTGTGC
* **
55720 TTATCAAAATTTCCTAGGGAGG
1 TTATGAAAATTTTATAGGGAGG
**
55742 TTAACAAAATTTTATAGGGAGG
1 TTATGAAAATTTTATAGGGAGG
55764 TTATGAAAATTTTAT-GGAGAGG
1 TTATGAAAATTTTATAGG-GAGG
55786 TTATCGAAAAT
1 TTAT-GAAAAT
55797 ACATAGAGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
21 2 0.04
22 40 0.83
23 6 0.12
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (22 bp):
TTATGAAAATTTTATAGGGAGG
Found at i:55990 original size:22 final size:22
Alignment explanation
Indices: 55965--56017 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
55955 GAGGTTGTCG
55965 AAATTTCATAGTGTGATAATCA
1 AAATTTCATAGTGTGATAATCA
* * *
55987 AAATTTCACAGTGTGGTTATCA
1 AAATTTCATAGTGTGATAATCA
*
56009 AATTTTCAT
1 AAATTTCAT
56018 GGGGAGGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
AAATTTCATAGTGTGATAATCA
Found at i:56026 original size:22 final size:22
Alignment explanation
Indices: 56001--56060 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
55991 TTCACAGTGT
*
56001 GGTTATCAAATTTTCATGGGGA
1 GGTTATCAAATTTTCATGAGGA
*
56023 GGTTATCGAAA-TTTCATGATGA
1 GGTTATC-AAATTTTCATGAGGA
*
56045 AGTTATCAAATTTTCA
1 GGTTATCAAATTTTCA
56061 AAATGTGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.09
22 27 0.82
23 3 0.09
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (22 bp):
GGTTATCAAATTTTCATGAGGA
Found at i:56071 original size:22 final size:22
Alignment explanation
Indices: 55983--56072 Score: 65
Period size: 22 Copynumber: 4.1 Consensus size: 22
55973 TAGTGTGATA
* * * *
55983 ATCAAAATTTCACAGTGTGGTT
1 ATCAAATTTTCATAATGAGGTT
***
56005 ATCAAATTTTCATGGGGAGGTT
1 ATCAAATTTTCATAATGAGGTT
* *
56027 ATCGAAA-TTTCATGATGAAGTT
1 ATC-AAATTTTCATAATGAGGTT
* *
56049 ATCAAATTTTCAAAATGTGGTT
1 ATCAAATTTTCATAATGAGGTT
56071 AT
1 AT
56073 TAATATTTCT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 3 0.06
22 48 0.89
23 3 0.06
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
ATCAAATTTTCATAATGAGGTT
Found at i:64969 original size:18 final size:18
Alignment explanation
Indices: 64932--64965 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64922 TTTTTAAGTA
64932 AAAATATAATATATAAAT
1 AAAATATAATATATAAAT
*
64950 AAAATTTAATAT-TAAA
1 AAAATATAATATATAAA
64966 ATAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATATAATATATAAAT
Found at i:65319 original size:44 final size:42
Alignment explanation
Indices: 65267--65387 Score: 178
Period size: 44 Copynumber: 2.9 Consensus size: 42
65257 CACGCGACGG
65267 CCACCCTTCCACGCGCTGCCAACTTTTGACGATCGCCAATCTTA
1 CCACCCTTCCACGCGCTGCCAACTTTTGACGATCGCCAATC--A
*
65311 CCACCCTTCCACACGCTGCCAACTTTTGACGATCGCCAATCA
1 CCACCCTTCCACGCGCTGCCAACTTTTGACGATCGCCAATCA
*
65353 --A--CTTCCACGCGCTGCCAACTTTTGACAATCGCCAA
1 CCACCCTTCCACGCGCTGCCAACTTTTGACGATCGCCAA
65388 CTTTAAATTG
Statistics
Matches: 74, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
38 32 0.43
40 1 0.01
42 1 0.01
44 40 0.54
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.23
Consensus pattern (42 bp):
CCACCCTTCCACGCGCTGCCAACTTTTGACGATCGCCAATCA
Found at i:65887 original size:123 final size:122
Alignment explanation
Indices: 65657--65920 Score: 336
Period size: 123 Copynumber: 2.1 Consensus size: 122
65647 TGAATGACCA
* * * *
65657 AGTATGGAAAATGATGATGCCCTCAAGGGGCCCAACGCAACAGGCGAGCGATCAGGCAAGGCAGA
1 AGTATGGAAAATGATGAAGCCCCCAAGGGGCCCAACGCAACAAGCAAGCGATCAGGCAAGGCAGA
* * *
65722 GCTCGACCTAGTATGGCCCCCGACCGGCAGATGAGCTGCAAAGACCATCCCTGTCTG
66 GCTCGACCTAGTATGGCCACCGACCGACAGACGAGCTGCAAAGACCATCCCTGTCTG
65779 AGTATAGG-AAATGATGAAGCCCCCAAGGGGCCCAACGCCAACAAGCAAGCGATCAGGCAAGGTC
1 AGTAT-GGAAAATGATGAAGCCCCCAAGGGGCCCAACG-CAACAAGCAAGCGATCAGGCAAGG-C
* * * * **
65843 -GAGCTCGACCTAGTATGGCCATCGACCGACAGGCGATC-GACAAAGACCATCCCTGACCA
63 AGAGCTCGACCTAGTATGGCCACCGACCGACAGACGAGCTG-CAAAGACCATCCCTGTCTG
*
65902 AGTATGGGAAAAAGATGAA
1 AGTAT-GGAAAATGATGAA
65921 ACACTCGCAG
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
122 33 0.27
123 79 0.65
124 10 0.08
ACGTcount: A:0.32, C:0.27, G:0.28, T:0.13
Consensus pattern (122 bp):
AGTATGGAAAATGATGAAGCCCCCAAGGGGCCCAACGCAACAAGCAAGCGATCAGGCAAGGCAGA
GCTCGACCTAGTATGGCCACCGACCGACAGACGAGCTGCAAAGACCATCCCTGTCTG
Found at i:65958 original size:56 final size:56
Alignment explanation
Indices: 65872--65978 Score: 189
Period size: 56 Copynumber: 1.9 Consensus size: 56
65862 CATCGACCGA
65872 CAGGCGATCGACAAAGACCATCCCTGACCAAGTATGGGAAAAAGATGAAACACTCG
1 CAGGCGATCGACAAAGACCATCCCTGACCAAGTATGGGAAAAAGATGAAACACTCG
*
65928 CAGGCGATCGAC-ATGAACCATCCCTGACCAAGTATGGGAAAAAGATGAAAC
1 CAGGCGATCGACAAAG-ACCATCCCTGACCAAGTATGGGAAAAAGATGAAAC
65979 CCTCCTAAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
55 2 0.04
56 47 0.96
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.13
Consensus pattern (56 bp):
CAGGCGATCGACAAAGACCATCCCTGACCAAGTATGGGAAAAAGATGAAACACTCG
Found at i:66107 original size:20 final size:20
Alignment explanation
Indices: 66060--66108 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
66050 ACCTTGGCCT
66060 GAGGAGAATGATCCCCAAGGA
1 GAGGAGAATGATCCCC-AGGA
* *
66081 AAGGAGAATGCTCCCC-GTGA
1 GAGGAGAATGATCCCCAG-GA
66101 GAGGAGAA
1 GAGGAGAA
66109 CGATAACGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 9 0.38
21 14 0.58
ACGTcount: A:0.37, C:0.18, G:0.35, T:0.10
Consensus pattern (20 bp):
GAGGAGAATGATCCCCAGGA
Found at i:66144 original size:25 final size:25
Alignment explanation
Indices: 66116--66206 Score: 164
Period size: 25 Copynumber: 3.6 Consensus size: 25
66106 GAACGATAAC
* *
66116 GCTCGCCGAACGCGAAGCGGAGAAG
1 GCTCGCCGAGCGCCAAGCGGAGAAG
66141 GCTCGCCGAGCGCCAAGCGGAGAAG
1 GCTCGCCGAGCGCCAAGCGGAGAAG
66166 GCTCGCCGAGCGCCAAGCGGAGAAG
1 GCTCGCCGAGCGCCAAGCGGAGAAG
66191 GCTCGCCGAGCGCCAA
1 GCTCGCCGAGCGCCAA
66207 ACATAGATCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.24, C:0.33, G:0.38, T:0.04
Consensus pattern (25 bp):
GCTCGCCGAGCGCCAAGCGGAGAAG
Found at i:66363 original size:25 final size:25
Alignment explanation
Indices: 66341--66388 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
66331 CACGAAGCGT
66341 AGAACGCTCGCCGAGCGCCAAGCAG
1 AGAACGCTCGCCGAGCGCCAAGCAG
* *
66366 AGAATGCTCGTCGAGCGCCAAGC
1 AGAACGCTCGCCGAGCGCCAAGC
66389 TTAGCAGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.33, G:0.31, T:0.08
Consensus pattern (25 bp):
AGAACGCTCGCCGAGCGCCAAGCAG
Found at i:66965 original size:18 final size:18
Alignment explanation
Indices: 66942--66988 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
66932 TGATCGATAT
66942 CGTCACTATCATCAATAG
1 CGTCACTATCATCAATAG
66960 CGTCACTATCATCAATAG
1 CGTCACTATCATCAATAG
66978 CGTCACTATCA
1 CGTCACTATCA
66989 CTATCATCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.28
Consensus pattern (18 bp):
CGTCACTATCATCAATAG
Found at i:67275 original size:62 final size:62
Alignment explanation
Indices: 67178--67338 Score: 223
Period size: 62 Copynumber: 2.6 Consensus size: 62
67168 GCAGAGCGAA
* * *
67178 AAGGAGAGGAGAATGCTCCCCGTGAGAGGAGAACGATCGCCAATCGCCAAATGTAAATTCAT
1 AAGGAGAGGAGAATGCTCCCCGTGAGAGGAGAACGATCGCCAATCGCCAAACGTAAATCCAC
* * * * *
67240 AAGGAGAGGAGAATGCTCCCCGTGAGAGGAGAACGATCGTCGATCGCCAAGCGTAGATCCGC
1 AAGGAGAGGAGAATGCTCCCCGTGAGAGGAGAACGATCGCCAATCGCCAAACGTAAATCCAC
** *
67302 AAGGAGAGGAGAATGCTCTTCGTGAGAGGAAAACGAT
1 AAGGAGAGGAGAATGCTCCCCGTGAGAGGAGAACGAT
67339 AACGCTCGCC
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 88 1.00
ACGTcount: A:0.34, C:0.20, G:0.32, T:0.15
Consensus pattern (62 bp):
AAGGAGAGGAGAATGCTCCCCGTGAGAGGAGAACGATCGCCAATCGCCAAACGTAAATCCAC
Found at i:67536 original size:25 final size:24
Alignment explanation
Indices: 67480--67574 Score: 73
Period size: 25 Copynumber: 3.7 Consensus size: 24
67470 GTAGAACGGT
* *
67480 CGCCGAATGCGAAGCGGAGAACCC
1 CGCCGAGTGCCAAGCGGAGAACCC
*
67504 TCGTCGAGTGCCAAGCGGAGAACGCC
1 -CGCCGAGTGCCAAGCGGAGAAC-CC
*
67530 CGCCGAGTGAGTGCCAAGCGGAGAACACT
1 CGCC----GAGTGCCAAGCGGAGAAC-CC
* *
67559 CGCCGAGCGCAAAGCG
1 CGCCGAGTGCCAAGCG
67575 TAGATCCCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
25 32 0.56
26 2 0.04
29 23 0.40
ACGTcount: A:0.26, C:0.32, G:0.35, T:0.07
Consensus pattern (24 bp):
CGCCGAGTGCCAAGCGGAGAACCC
Found at i:67551 original size:29 final size:29
Alignment explanation
Indices: 67509--67565 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
67499 AACCCTCGTC
*
67509 GAGTGCCAAGCGGAGAACGCCCGCCGAGT
1 GAGTGCCAAGCGGAGAACACCCGCCGAGT
*
67538 GAGTGCCAAGCGGAGAACACTCGCCGAG
1 GAGTGCCAAGCGGAGAACACCCGCCGAG
67566 CGCAAAGCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.37, T:0.07
Consensus pattern (29 bp):
GAGTGCCAAGCGGAGAACACCCGCCGAGT
Found at i:67653 original size:164 final size:160
Alignment explanation
Indices: 67343--67690 Score: 482
Period size: 164 Copynumber: 2.1 Consensus size: 160
67333 AACGATAACG
* * * * *
67343 CTCGCCGAGCGCCAAGCGGAGAACTCCCGCCGAGTGAGTGCCAAGTGGAGAACGCTCGCCGATCG
1 CTCGCCGAGTGCCAAGCGGAGAACGCCCGCCGAGTGAGTGCCAAGCGGAGAACACTCGCCGAGCG
* *
67408 CGGAGATCCCCAAGGAAAGGAAAATGCTCCCCGTGAGAGGAGGACGATCGCCGATCGCAAATGTA
66 CGGAGATCCCCAAGGAAAGGAAAATGCTCCCCGTGAGAGGAGAAAGATCGCCGATCGCAAATGTA
* *
67473 GAACGGTCGCCGAATGCGAAGCGGAGAACC
131 GAACGCTCGCCGAATGCGAAACGGAGAACC
*
67503 CTCGTCGAGTGCCAAGCGGAGAACGCCCGCCGAGTGAGTGCCAAGCGGAGAACACTCGCCGAGCG
1 CTCGCCGAGTGCCAAGCGGAGAACGCCCGCCGAGTGAGTGCCAAGCGGAGAACACTCGCCGAGCG
* * * *
67568 CAAAGCGTAGAT-CCCTAGGAGAGGAGAATGCTCCCCGTGAGAGGAGAAAGATCGCTGATCGCAA
66 C---G-G-AGATCCCCAAGGAAAGGAAAATGCTCCCCGTGAGAGGAGAAAGATCGCCGATCGCAA
*
67632 ATGTAGAACGCTCGCCGAATGCGAAACGGAGAACG
126 ATGTAGAACGCTCGCCGAATGCGAAACGGAGAACC
* * *
67667 CTCGCCAAATGCGAAGCGGAGAAC
1 CTCGCCGAGTGCCAAGCGGAGAAC
67691 ACTCGTCGAG
Statistics
Matches: 164, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
160 60 0.37
163 1 0.01
164 99 0.60
165 4 0.02
ACGTcount: A:0.29, C:0.28, G:0.33, T:0.11
Consensus pattern (160 bp):
CTCGCCGAGTGCCAAGCGGAGAACGCCCGCCGAGTGAGTGCCAAGCGGAGAACACTCGCCGAGCG
CGGAGATCCCCAAGGAAAGGAAAATGCTCCCCGTGAGAGGAGAAAGATCGCCGATCGCAAATGTA
GAACGCTCGCCGAATGCGAAACGGAGAACC
Found at i:67664 original size:25 final size:25
Alignment explanation
Indices: 67636--67695 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
67626 TCGCAAATGT
*
67636 AGAACGCTCGCCGAATGCGAAACGG
1 AGAACGCTCGCCAAATGCGAAACGG
*
67661 AGAACGCTCGCCAAATGCGAAGCGG
1 AGAACGCTCGCCAAATGCGAAACGG
*
67686 AGAACACTCG
1 AGAACGCTCG
67696 TCGAGCATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.33, C:0.28, G:0.30, T:0.08
Consensus pattern (25 bp):
AGAACGCTCGCCAAATGCGAAACGG
Found at i:67781 original size:29 final size:29
Alignment explanation
Indices: 67704--67783 Score: 115
Period size: 29 Copynumber: 2.8 Consensus size: 29
67694 CGTCGAGCAT
* * * *
67704 CAAGCAGAAAACGCCCGCCAAGTGAGTGC
1 CAAGCGGAGAACGCTCGCCGAGTGAGTGC
*
67733 CAAGCGGAGAACGCTCGCCGAGTGAGTTC
1 CAAGCGGAGAACGCTCGCCGAGTGAGTGC
67762 CAAGCGGAGAACGCTCGCCGAG
1 CAAGCGGAGAACGCTCGCCGAG
67784 CGCAAAACGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.29, C:0.30, G:0.33, T:0.09
Consensus pattern (29 bp):
CAAGCGGAGAACGCTCGCCGAGTGAGTGC
Found at i:68022 original size:36 final size:36
Alignment explanation
Indices: 67947--68027 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
67937 CGAGGTTACG
* * *
67947 AATGGAGAATGCTCCCCATAAATGAGTAGATCGCAC
1 AATGGAGAATGCTCCACATAAAGGAGTAGATCACAC
* *
67983 AATGGAGAATGCTCCACATAAGGGAGTAGATCACGC
1 AATGGAGAATGCTCCACATAAAGGAGTAGATCACAC
*
68019 AATGAAGAA
1 AATGGAGAA
68028 CGTCGATCGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.17
Consensus pattern (36 bp):
AATGGAGAATGCTCCACATAAAGGAGTAGATCACAC
Found at i:68100 original size:58 final size:58
Alignment explanation
Indices: 67983--68100 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 58
67973 TAGATCGCAC
* * * * * **
67983 AATGGAGAATGCTCCACATAAGGGAGTAGATCACGCAATGAAGAACGTCGATCGTGCG
1 AATGGAGAATGCTCCACATAAAGGAGCAGATCACGCAATGAAAAACGCCGACCACGCG
* * * *
68041 AATGGAGTATGCTCCCCATAAAGGAGCAGATCGCGCAATGAAAAATGCCGACCACGCG
1 AATGGAGAATGCTCCACATAAAGGAGCAGATCACGCAATGAAAAACGCCGACCACGCG
68099 AA
1 AA
68101 ATGAAGTTCG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.15
Consensus pattern (58 bp):
AATGGAGAATGCTCCACATAAAGGAGCAGATCACGCAATGAAAAACGCCGACCACGCG
Done.