Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013814.1 Corchorus olitorius cultivar O-4 contig13847, 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: 50439
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:777 original size:54 final size:54
Alignment explanation
Indices: 707--997 Score: 291
Period size: 54 Copynumber: 5.4 Consensus size: 54
697 TCTTTTAAAG
* *
707 TTTTCAGAGATCTAAGTTAATTTTCAAATGACCCTGTGCGGTCTTTCATAGAAT
1 TTTTCAGAGATCTAAGTTGATCTTCAAATGACCCTGTGCGGTCTTTCATAGAAT
* * * * * * * *
761 TTTTCATAGATTTAAGTTGATCTTGAGATGACACC-GTACGGTCTTTTAAAGAAG
1 TTTTCAGAGATCTAAGTTGATCTTCAAATGAC-CCTGTGCGGTCTTTCATAGAAT
* * *
815 TTTCCAGAGA--TAAGTTGATGTTCAAATGACCCTGTGCAGTCTTTCATAGAAT
1 TTTTCAGAGATCTAAGTTGATCTTCAAATGACCCTGTGCGGTCTTTCATAGAAT
* * * * * *
867 TTTTCAAAGATCGAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCACACAAG
1 TTTTCAGAGATCTAAGTTGATCTTCAAATGACCCTGTGCGGTCTTTCATAGAAT
* * * * ** *
921 TTTTCAGAGATCTAAGATGATCTTCAGATGATCCGGTGTTGTTTTTCATAGAAGT
1 TTTTCAGAGATCTAAGTTGATCTTCAAATGACCCTGTGCGGTCTTTCATAGAA-T
* *
976 TTTTTAGAGATCAAAGTTGATC
1 TTTTCAGAGATCTAAGTTGATC
998 CCTAGATGAT
Statistics
Matches: 189, Mismatches: 43, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
51 2 0.01
52 39 0.21
54 127 0.67
55 21 0.11
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (54 bp):
TTTTCAGAGATCTAAGTTGATCTTCAAATGACCCTGTGCGGTCTTTCATAGAAT
Found at i:909 original size:106 final size:107
Alignment explanation
Indices: 704--997 Score: 331
Period size: 106 Copynumber: 2.7 Consensus size: 107
694 CAATCTTTTA
* * * *
704 AAGTTTTCAGAGATCTAAGTTAATTTTCAAATGACCCTGTGCGGTCTTTCATAGAATTTTTCATA
1 AAGTTTTCAGAGA-CTAAGTTGATCTTCAAATGACCCTGTGCAGTCTTTCATAGAATTTTTCAAA
** * * *
769 GATTTAAGTTGATCTTGAGATGACACCGTACGGTCTTTTAAAG
65 GATCAAAGTTGATCTTCAGATGACACCGTACGGTCTTTCAAAC
* *
812 AAGTTTCCAGAGA-TAAGTTGATGTTCAAATGACCCTGTGCAGTCTTTCATAGAATTTTTCAAAG
1 AAGTTTTCAGAGACTAAGTTGATCTTCAAATGACCCTGTGCAGTCTTTCATAGAATTTTTCAAAG
* * *
876 ATCGAAGTTGATCTTCAGATGAC-CCTGTGCGGTCTTTCACAC
66 ATCAAAGTTGATCTTCAGATGACACC-GTACGGTCTTTCAAAC
* * * * ** * * *
918 AAGTTTTCAGAGATCTAAGATGATCTTCAGATGATCCGGTGTTGTTTTTCATAGAAGTTTTTTAG
1 AAGTTTTCAGAGA-CTAAGTTGATCTTCAAATGACCCTGTGCAGTCTTTCATAGAA-TTTTTCAA
983 AGATCAAAGTTGATC
64 AGATCAAAGTTGATC
998 CCTAGATGAT
Statistics
Matches: 158, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
105 2 0.01
106 91 0.58
108 45 0.28
109 20 0.13
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (107 bp):
AAGTTTTCAGAGACTAAGTTGATCTTCAAATGACCCTGTGCAGTCTTTCATAGAATTTTTCAAAG
ATCAAAGTTGATCTTCAGATGACACCGTACGGTCTTTCAAAC
Found at i:1133 original size:54 final size:54
Alignment explanation
Indices: 984--1265 Score: 325
Period size: 54 Copynumber: 5.2 Consensus size: 54
974 GTTTTTTAGA
* * * * * *
984 GATCAAAGTTGATCCCTAGATGATCCGGTGTGATCATTTCAAGAAGTTTTCAAT
1 GATCAGAGTTGATCTCAAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAAT
* ** * *
1038 GGTCAGAGTTGATC-CCTGATGATCCAATGTGGTCATTCCAAGAAGCTTTCAAT
1 GATCAGAGTTGATCTCAAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAAT
* * *
1091 GATCAAAGTTGATCTCAAGATGATCCAGTGTGGTCGTTCCAAGAAGTTTCCAAT
1 GATCAGAGTTGATCTCAAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAAT
* * * *
1145 GATTAGAGTTGATCTCCAA-TTGATCTAGTATGGTCATTCCAAGAAGTTTTCAAT
1 GATCAGAGTTGATCT-CAAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAAT
* * * * *
1199 GATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCGTTTCAAGAAGTTTTCGAT
1 GATCAGAGTTGATCTCAAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAAT
*
1253 GATCAGGGTTGAT
1 GATCAGAGTTGAT
1266 TTGCACATTA
Statistics
Matches: 191, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
53 46 0.24
54 142 0.74
55 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (54 bp):
GATCAGAGTTGATCTCAAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAAT
Found at i:1211 original size:108 final size:107
Alignment explanation
Indices: 984--1265 Score: 368
Period size: 108 Copynumber: 2.6 Consensus size: 107
974 GTTTTTTAGA
* * * * * *
984 GATCAAAGTTGATCCCTAGATGATCCGGTGTGATCATTTCAAGAAGTTTTCAATGGTCAGAGTTG
1 GATCAAAGTTGATCTCAAGATGATCCAGTGTGGTCGTTTCAAGAAGTTTTCAATGATCAGAGTTG
* *
1049 ATCCCTGATGATCCAATGTGGTCATTCCAAGAAGCTTTCAAT
66 ATCCCTAATGATCCAATATGGTCATTCCAAGAAGCTTTCAAT
* * *
1091 GATCAAAGTTGATCTCAAGATGATCCAGTGTGGTCGTTCCAAGAAGTTTCCAATGATTAGAGTTG
1 GATCAAAGTTGATCTCAAGATGATCCAGTGTGGTCGTTTCAAGAAGTTTTCAATGATCAGAGTTG
* * *
1156 ATCTCC-AATTGATCTAGTATGGTCATTCCAAGAAGTTTTCAAT
66 ATC-CCTAA-TGATCCAATATGGTCATTCCAAGAAGCTTTCAAT
* * * * *
1199 GATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCGTTTCAAGAAGTTTTCGATGATCAGGGTTG
1 GATCAAAGTTGATCTCAAGATGATCCAGTGTGGTCGTTTCAAGAAGTTTTCAATGATCAGAGTTG
1264 AT
66 AT
1266 TTGCACATTA
Statistics
Matches: 151, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
107 60 0.40
108 91 0.60
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (107 bp):
GATCAAAGTTGATCTCAAGATGATCCAGTGTGGTCGTTTCAAGAAGTTTTCAATGATCAGAGTTG
ATCCCTAATGATCCAATATGGTCATTCCAAGAAGCTTTCAAT
Found at i:8927 original size:16 final size:15
Alignment explanation
Indices: 8901--8930 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
8891 TTAGGATTAG
8901 TTATTTTATTTTTTA
1 TTATTTTATTTTTTA
8916 TTATTATTATTTTTT
1 TTATT-TTATTTTTT
8931 GGACATGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTATTTTTTA
Found at i:9216 original size:14 final size:14
Alignment explanation
Indices: 9193--9222 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9183 ATCATGCTTT
*
9193 TTTATTTAATTAGG
1 TTTATCTAATTAGG
9207 TTTATCTAATTAGG
1 TTTATCTAATTAGG
9221 TT
1 TT
9223 AAACAAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (14 bp):
TTTATCTAATTAGG
Found at i:14602 original size:43 final size:44
Alignment explanation
Indices: 14555--14657 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 44
14545 CATAGTTAGG
* * * * *
14555 TTATCAAAGTCTCTTATGGAGTTTATCACAATTTTATA-GGTAA
1 TTATCAAAATCTCATATGGAGGTTATCAAAATTTGATAGGGTAA
* * *
14598 TTATCAAAATTTCATATGGTGGTTATCAAAATTTGATAGGGTAG
1 TTATCAAAATCTCATATGGAGGTTATCAAAATTTGATAGGGTAA
*
14642 TTATCAAAATTTCATA
1 TTATCAAAATCTCATA
14658 AAAATATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 31 0.61
44 20 0.39
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.41
Consensus pattern (44 bp):
TTATCAAAATCTCATATGGAGGTTATCAAAATTTGATAGGGTAA
Found at i:14603 original size:21 final size:22
Alignment explanation
Indices: 14577--14657 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
14567 CTTATGGAGT
* * *
14577 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTCATAGGGTAG
* *
14598 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTCATAGGGTAG
*
14620 TTATCAAAATTTGATAGGGTAG
1 TTATCAAAATTTCATAGGGTAG
14642 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
14658 AAAATATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 14 0.27
22 37 0.73
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGTAG
Found at i:14624 original size:22 final size:21
Alignment explanation
Indices: 14538--14657 Score: 96
Period size: 22 Copynumber: 5.5 Consensus size: 21
14528 GGAAAGTATT
*
14538 AAAATTTCATAGTTAGGTTATC
1 AAAATTTCATAGGT-GGTTATC
* * * * *
14560 AAAGTCTCTTATGGAGTTTATC
1 AAAATTTCATA-GGTGGTTATC
* * **
14582 ACAATTTTATAGGTAATTATC
1 AAAATTTCATAGGTGGTTATC
14603 AAAATTTCATATGGTGGTTATC
1 AAAATTTCATA-GGTGGTTATC
* *
14625 AAAATTTGATAGGGTAGTTATC
1 AAAATTTCATA-GGTGGTTATC
14647 AAAATTTCATA
1 AAAATTTCATA
14658 AAAATATTCA
Statistics
Matches: 74, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
21 16 0.22
22 57 0.77
23 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (21 bp):
AAAATTTCATAGGTGGTTATC
Found at i:14865 original size:30 final size:32
Alignment explanation
Indices: 14806--14872 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
14796 AAAGCTTTTC
**
14806 TAAATTTAACCATCACTAATCGCGGAAAAAAA
1 TAAATTTAACCATCACTAATCGCCAAAAAAAA
14838 -AAATTTAACCATCACT-ATCGCCAAAAAAAA
1 TAAATTTAACCATCACTAATCGCCAAAAAAAA
14868 TAAAT
1 TAAAT
14873 GATATCACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.22
Consensus pattern (32 bp):
TAAATTTAACCATCACTAATCGCCAAAAAAAA
Found at i:21120 original size:35 final size:35
Alignment explanation
Indices: 21081--21168 Score: 144
Period size: 33 Copynumber: 2.6 Consensus size: 35
21071 GCTACCATTC
*
21081 GTGTATTTTCATTGTATTATATAGGTTATAAATTA
1 GTGTATTTTCATTGTATTATATAGATTATAAATTA
21116 GTGTATTTTCATTGTA-T-TATAGATTATAAATTA
1 GTGTATTTTCATTGTATTATATAGATTATAAATTA
*
21149 GTGTATTTTCTTTGTATTAT
1 GTGTATTTTCATTGTATTAT
21169 GGATTTTGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
33 30 0.61
34 2 0.04
35 17 0.35
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.55
Consensus pattern (35 bp):
GTGTATTTTCATTGTATTATATAGATTATAAATTA
Found at i:24642 original size:2 final size:2
Alignment explanation
Indices: 24637--24696 Score: 53
Period size: 2 Copynumber: 33.0 Consensus size: 2
24627 ACACACACAC
*
24637 AT AT AT AT AT AT AT A- AT A- AT AT AT AT A- AC AT AT AGT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
24676 AT -T A- AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
24697 TCACACACTT
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
1 7 0.14
2 40 0.82
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:26113 original size:17 final size:17
Alignment explanation
Indices: 26091--26138 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
26081 TTTTAAAAGA
26091 ATAAAAAAAATAATTA-T
1 ATAAAAAAAA-AATTATT
*
26108 ATAAAAAGAAAATTTATT
1 ATAAAAA-AAAAATTATT
*
26126 ATAAATAAAAAAT
1 ATAAAAAAAAAAT
26139 CGTGCCTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAAAAAAAATTATT
Found at i:29404 original size:25 final size:25
Alignment explanation
Indices: 29349--29402 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29339 TAGTGGATTG
*
29349 TAAAATAAATTGAATAATTAAGACA
1 TAAAATAAATTGAAGAATTAAGACA
* *
29374 TTAAATAAATTTAAGAATTAA-ACA
1 TAAAATAAATTGAAGAATTAAGACA
29398 TAAAA
1 TAAAA
29403 ATTCAAGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30
Consensus pattern (25 bp):
TAAAATAAATTGAAGAATTAAGACA
Found at i:29461 original size:8 final size:9
Alignment explanation
Indices: 29436--29467 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
29426 CGAGTGCTAG
29436 ACCCGAAAA
1 ACCCGAAAA
29445 ACCCGAAAA
1 ACCCGAAAA
29454 ACCC--AAA
1 ACCCGAAAA
29461 ACCCGAA
1 ACCCGAA
29468 TGATCAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.53, C:0.38, G:0.09, T:0.00
Consensus pattern (9 bp):
ACCCGAAAA
Found at i:31199 original size:30 final size:30
Alignment explanation
Indices: 31165--31234 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
31155 GACTATGATC
31165 AAGAGGATGAGGAGACTGATGAAGAGGACG
1 AAGAGGATGAGGAGACTGATGAAGAGGACG
*
31195 AAGAGGATGAGGAGACTGATGAAGAGTACG
1 AAGAGGATGAGGAGACTGATGAAGAGGACG
31225 AAGAGGATGA
1 AAGAGGATGA
31235 AGATGTAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.41, C:0.06, G:0.41, T:0.11
Consensus pattern (30 bp):
AAGAGGATGAGGAGACTGATGAAGAGGACG
Found at i:32778 original size:123 final size:123
Alignment explanation
Indices: 32556--32802 Score: 467
Period size: 123 Copynumber: 2.0 Consensus size: 123
32546 TGGAACTCGG
*
32556 AAAAGCAATAAAAAGAAGGTTAAAAGTAGGGATGGGGCTTTGAAAAATGGTAGTAATTCAGCTCA
1 AAAAGCAATAAAAAGAAGGTTAAAAGTAGGGATGGGGCTTCGAAAAATGGTAGTAATTCAGCTCA
32621 GCAAACATCAACAACAGTTGGTCAGCTTGCACCTAATGAGAACCAACATGATTTCTCC
66 GCAAACATCAACAACAGTTGGTCAGCTTGCACCTAATGAGAACCAACATGATTTCTCC
*
32679 AAAAGCAATAAAAAGAAGGTTAAAAGTAGGGTTGGGGCTTCGAAAAATGGTAGTAATTCAGCTCA
1 AAAAGCAATAAAAAGAAGGTTAAAAGTAGGGATGGGGCTTCGAAAAATGGTAGTAATTCAGCTCA
*
32744 GCAAACATCAACAACAGTTGGTCAGCTTGTACCTAATGAGAACCAACATGATTTCTCC
66 GCAAACATCAACAACAGTTGGTCAGCTTGCACCTAATGAGAACCAACATGATTTCTCC
32802 A
1 A
32803 CAGTTTCAGC
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (123 bp):
AAAAGCAATAAAAAGAAGGTTAAAAGTAGGGATGGGGCTTCGAAAAATGGTAGTAATTCAGCTCA
GCAAACATCAACAACAGTTGGTCAGCTTGCACCTAATGAGAACCAACATGATTTCTCC
Found at i:33487 original size:6 final size:6
Alignment explanation
Indices: 33476--33526 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
33466 AACCATTTCA
*
33476 TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGA TCGAGG TCGAGG
1 TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG
33524 TCG
1 TCG
33527 CTTTACGGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.18, C:0.18, G:0.47, T:0.18
Consensus pattern (6 bp):
TCGAGG
Found at i:44298 original size:60 final size:64
Alignment explanation
Indices: 44222--44391 Score: 181
Period size: 60 Copynumber: 2.6 Consensus size: 64
44212 ATCTCAGCAA
* *
44222 CATTTTTACAACCAACAGAAACATCATTACAAGGAAGAGAAGAATTAG-A-AAC-AA-AA-TCAG
1 CATTTTTACAAACAACAGAAACATCATTACAAGGAA-AGAAGAATCAGAACAACGAACAACTCAG
*
44282 CATTTTTACAAACAACATG-AACGTCATTACAAGGAAATGAAGAATCAGAAGCAACAGGAACAAT
1 CATTTTTACAAACAACA-GAAACATCATTACAAGGAAA-GAAGAATCAGAA-CAAC--GAACAA-
44346 CTCAG
60 CTCAG
* *
44351 CATTTTTACAAGCAACAAAAACATCATTACAAGGAACAGAA
1 CATTTTTACAAACAACAGAAACATCATTACAAGGAA-AGAA
44392 ATGGTATTGG
Statistics
Matches: 91, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
59 1 0.01
60 41 0.45
61 2 0.02
63 3 0.03
66 2 0.02
67 2 0.02
69 39 0.43
70 1 0.01
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (64 bp):
CATTTTTACAAACAACAGAAACATCATTACAAGGAAAGAAGAATCAGAACAACGAACAACTCAG
Found at i:48033 original size:82 final size:82
Alignment explanation
Indices: 47871--48039 Score: 250
Period size: 82 Copynumber: 2.1 Consensus size: 82
47861 TCTAAAACCT
* * *
47871 TCAAACTAAAACCTTAAATTTTCAAAAAAATCTTGAAGCAAATCATGGCGGATTTCATTCGTGGC
1 TCAAATTAAAACCTCAAAATTTCAAAAAAATCTTGAAGCAAATCATGGCGGATTTCATTCGTGGC
* *
47936 AGAGGCAAAGGATTGAA
66 AGACGAAAAGGATTGAA
* *
47953 TCAAATTAAAACCTCAAAATTTCAAAACAATCTTGAAGCAAATCATGGCGGATTTCGTTCGTGGC
1 TCAAATTAAAACCTCAAAATTTCAAAAAAATCTTGAAGCAAATCATGGCGGATTTCATTCGTGGC
**
48018 AGACGAAAATTATTGAA
66 AGACGAAAAGGATTGAA
48035 T-AAAT
1 TCAAAT
48040 AAATAAATAA
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 4 0.05
82 74 0.95
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.27
Consensus pattern (82 bp):
TCAAATTAAAACCTCAAAATTTCAAAAAAATCTTGAAGCAAATCATGGCGGATTTCATTCGTGGC
AGACGAAAAGGATTGAA
Found at i:48048 original size:12 final size:13
Alignment explanation
Indices: 48033--48064 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
48023 AAAATTATTG
48033 AATAAATAAA-TA
1 AATAAATAAATTA
48045 AATAAATAAATTA
1 AATAAATAAATTA
48058 AA-AAATA
1 AATAAATA
48065 TTCGAGGCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AATAAATAAATTA
Done.