Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018963.1 Corchorus olitorius cultivar O-4 contig18996, 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: 69070
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:4174 original size:3 final size:3
Alignment explanation
Indices: 4154--4198 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
4144 TTACCGGAAA
*
4154 AAG AAG AAT AA- AATG AAG AAG AAG AAG AAG AAG AAG AAG AGAG AA
1 AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG A-AG AA
4199 ACAAAAAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
2 2 0.05
3 31 0.82
4 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:4325 original size:35 final size:35
Alignment explanation
Indices: 4236--4329 Score: 134
Period size: 35 Copynumber: 2.7 Consensus size: 35
4226 GCTGGCCTGG
* *
4236 CGCGGCCCAACGCCTAGGCCAAGCGCGCGGGCCAG
1 CGCGGCCCAACGCCTAGGCCAGGCGCGCGGGCCAA
* * *
4271 CGTGGCCCAGCGCCCAGGCCAGGCGCGCGGGCCAA
1 CGCGGCCCAACGCCTAGGCCAGGCGCGCGGGCCAA
*
4306 CGCGGCCTAACGCCTAGGCCAGGC
1 CGCGGCCCAACGCCTAGGCCAGGC
4330 TTGGGCCCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.16, C:0.43, G:0.37, T:0.04
Consensus pattern (35 bp):
CGCGGCCCAACGCCTAGGCCAGGCGCGCGGGCCAA
Found at i:4381 original size:6 final size:6
Alignment explanation
Indices: 4372--4421 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
4362 AAAGAAAGAA
*
4372 AAGCCC AAGCCC AAGCCC AAGCCC AAGCCC TAGCCC AAGCCC AAGCCC
1 AAGCCC AAGCCC AAGCCC AAGCCC AAGCCC AAGCCC AAGCCC AAGCCC
4420 AA
1 AA
4422 TTTGGAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.34, C:0.48, G:0.16, T:0.02
Consensus pattern (6 bp):
AAGCCC
Found at i:5442 original size:27 final size:28
Alignment explanation
Indices: 5374--5442 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
5364 TTAAGGTGTC
* * * *
5374 AAAATTACTGTTTTGCCCTTGGTAGGCT
1 AAAATTACAGTTTTACCCCTGGTAGACT
*
5402 AAAATTACCA-TTTTACCCCTGGTTGACT
1 AAAATTA-CAGTTTTACCCCTGGTAGACT
5430 -AAATTACAGTTTT
1 AAAATTACAGTTTT
5443 TCTCTTAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
26 2 0.06
27 10 0.29
28 21 0.62
29 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (28 bp):
AAAATTACAGTTTTACCCCTGGTAGACT
Found at i:15434 original size:16 final size:16
Alignment explanation
Indices: 15413--15450 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
15403 CATTATTATA
15413 TTTTTTACTCTT-TTTC
1 TTTTTT-CTCTTCTTTC
*
15429 TTTTTTCTTTTCTTTC
1 TTTTTTCTCTTCTTTC
15445 TTTTTT
1 TTTTTT
15451 TAGTGCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTCTCTTCTTTC
Found at i:16264 original size:15 final size:15
Alignment explanation
Indices: 16239--16278 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
16229 CCAAGTTTTC
16239 TTTTTTC-TCTCTTT
1 TTTTTTCTTCTCTTT
16253 TTTTTTCTTCTCTTT
1 TTTTTTCTTCTCTTT
16268 TTTTTTCTTCT
1 TTTTTTCTTCT
16279 TCTTCCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTCTCTTT
Found at i:22094 original size:21 final size:22
Alignment explanation
Indices: 22058--22098 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
22048 GCATTATTTC
*
22058 TAAAACCAGGGGTCAAATTGAA
1 TAAAACCAGGGATCAAATTGAA
22080 TAAAA-CAGGGATCAAATTG
1 TAAAACCAGGGATCAAATTG
22099 CATTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (22 bp):
TAAAACCAGGGATCAAATTGAA
Found at i:23808 original size:13 final size:12
Alignment explanation
Indices: 23777--23804 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
23767 GCCTTGAAAT
23777 ATGCAAAAAAAA
1 ATGCAAAAAAAA
23789 ATGCAAAAAAAA
1 ATGCAAAAAAAA
23801 ATGC
1 ATGC
23805 CAAAGGTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.11
Consensus pattern (12 bp):
ATGCAAAAAAAA
Found at i:23928 original size:27 final size:28
Alignment explanation
Indices: 23898--23971 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 28
23888 TGTGAACTTA
23898 AAATGACCAAAATGCCCCTGG-ATGTAC
1 AAATGACCAAAATGCCCCTGGAATGTAC
*
23925 AAATGACCAAAATGCCCCTGGAATGTGC
1 AAATGACCAAAATGCCCCTGGAATGTAC
* * *
23953 AGATGACTAAAATCCCCCT
1 AAATGACCAAAATGCCCCT
23972 AGGTGACTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.50
28 21 0.50
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGAATGTAC
Found at i:24774 original size:13 final size:12
Alignment explanation
Indices: 24755--24794 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
24745 CAAATTTAAA
24755 AAAAATGAAAAC
1 AAAAATGAAAAC
24767 AGAAAATGAAAAC
1 A-AAAATGAAAAC
24780 AAAAA-GAAAA-
1 AAAAATGAAAAC
24790 AAAAA
1 AAAAA
24795 CCACAAACGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
12 5 0.19
13 12 0.44
ACGTcount: A:0.80, C:0.05, G:0.10, T:0.05
Consensus pattern (12 bp):
AAAAATGAAAAC
Found at i:25821 original size:17 final size:17
Alignment explanation
Indices: 25799--25831 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
25789 CATTATGGTA
25799 TTGTAATTTTTTTTCTC
1 TTGTAATTTTTTTTCTC
25816 TTGTAATTTTTTTTCT
1 TTGTAATTTTTTTTCT
25832 TGGTTGAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.73
Consensus pattern (17 bp):
TTGTAATTTTTTTTCTC
Found at i:26474 original size:29 final size:28
Alignment explanation
Indices: 26417--26492 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 28
26407 TTCAGCACCG
* * * *
26417 AGTGCAAACCCACAC-TCAACAATCCCA
1 AGTGCAAACCCGCACTTGAACAAACACA
26444 AGTGCACAACCCGCACTTGAACAAACACA
1 AGTGCA-AACCCGCACTTGAACAAACACA
*
26473 AGTGCATAACCTGCACTTGA
1 AGTGCA-AACCCGCACTTGA
26493 TAAACCAAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 6 0.15
28 8 0.20
29 27 0.66
ACGTcount: A:0.38, C:0.34, G:0.13, T:0.14
Consensus pattern (28 bp):
AGTGCAAACCCGCACTTGAACAAACACA
Found at i:28179 original size:2 final size:2
Alignment explanation
Indices: 28172--28220 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
28162 TCCAGCGCTT
*
28172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA 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
28214 TA TA TA T
1 TA TA TA T
28221 CAGAGGTAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:52174 original size:54 final size:54
Alignment explanation
Indices: 52115--52275 Score: 259
Period size: 54 Copynumber: 3.0 Consensus size: 54
52105 CAATCTTTTA
* *
52115 AAGTTTTCAGAGATCTAAGTTGATGTTCAGATGACCCTGTGAGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* *
52169 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * *
52223 AAGTTTTCAGAGATCTAAGTTGATTTTCTGTTGACCCTGTGCGGTCTTTCATA
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATA
52276 AAGCCCTCTC
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (54 bp):
AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
Found at i:52560 original size:109 final size:108
Alignment explanation
Indices: 52360--52619 Score: 301
Period size: 109 Copynumber: 2.4 Consensus size: 108
52350 TTCAAATAAC
** * * * * * *
52360 CCAGTGCGGTCATTCCAAGAAGTTTTCTTTTATCGGAGTTGAT-CTCAGATGACCTAGTGTGGTC
1 CCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATCACCTAGTGCGATC
* *
52424 ATTCCAAGAAGTTTTTAGAGATTAAAGTTGATCCCTAAATGAT
66 ATTCCAAGAAGTTTTTAGAGATCAAAGTTGATCCCCAAATGAT
* *
52467 CCAGTGCGGTCAGTCCAAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGTTCATCC-AGTGCGA
1 CCAGTGCGGTCATTCC-AAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATCA-CCTAGTGCGA
* * *
52531 TCATTTCAAGAAGTTTTTAGTGATCAAAGTTGATCCCCAGATGAT
64 TCATTCCAAGAAGTTTTTAGAGATCAAAGTTGATCCCCAAATGAT
* * * *
52576 CTAGTG-GGATAATTTCAAGAAATTTTCAATGATCAGAGTTGATC
1 CCAGTGCGG-TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
52620 TCATTTCAAG
Statistics
Matches: 129, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
107 15 0.12
108 52 0.40
109 60 0.47
110 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (108 bp):
CCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATCACCTAGTGCGATC
ATTCCAAGAAGTTTTTAGAGATCAAAGTTGATCCCCAAATGAT
Found at i:52562 original size:54 final size:54
Alignment explanation
Indices: 52360--52619 Score: 229
Period size: 54 Copynumber: 4.8 Consensus size: 54
52350 TTCAAATAAC
* ** * ** *
52360 CCAGTGCGGTCATTCCAAGAAGTTTTCTTTTATCGGAGTTGAT-CTCAGATGA-
1 CCAGTGCGATCATTCCAAGAAGTTTTCAATGATCAAAGTTGATCCCCAGATGAT
* * * * * *
52412 CCTAGTGTGGTCATTCCAAGAAGTTTTTAGA-GATTAAAGTTGATCCCTAAATGAT
1 CC-AGTGCGATCATTCCAAGAAGTTTTCA-ATGATCAAAGTTGATCCCCAGATGAT
* * * * *
52467 CCAGTGCGGTCAGTCCAAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGTTCAT
1 CCAGTGCGATCATTCC-AAGAAGTTTTCAATGATCAAAGTTGATCCCCAGATGAT
* * *
52522 CCAGTGCGATCATTTCAAGAAGTTTTTAGTGATCAAAGTTGATCCCCAGATGAT
1 CCAGTGCGATCATTCCAAGAAGTTTTCAATGATCAAAGTTGATCCCCAGATGAT
* * * * * *
52576 CTAGTGGGATAATTTCAAGAAATTTTCAATGATCAGAGTTGATC
1 CCAGTGCGATCATTCCAAGAAGTTTTCAATGATCAAAGTTGATC
52620 TCATTTCAAG
Statistics
Matches: 167, Mismatches: 35, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
52 2 0.01
53 32 0.19
54 89 0.53
55 44 0.26
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
CCAGTGCGATCATTCCAAGAAGTTTTCAATGATCAAAGTTGATCCCCAGATGAT
Found at i:52627 original size:35 final size:35
Alignment explanation
Indices: 52587--53320 Score: 1026
Period size: 35 Copynumber: 20.9 Consensus size: 35
52577 TAGTGGGATA
* *
52587 ATTTCAAGAAATTTTCAATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
*
52622 ATTTCAAGGAAGTTTTCGATGATCAGAGTTGATATC
1 ATTTCAA-GAAGTTTTCGATGATCAGAGTTGATCTC
*
52658 ATTTCAAGAAGTTTT-AATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* *
52692 ATTTCGAGAAAGTTTTCGATGATCAAAGTTGATCTC
1 ATTTCAAG-AAGTTTTCGATGATCAGAGTTGATCTC
*
52728 ATTTCAAGAAGTTTCCGATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
*
52763 ATTTTAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* * **
52798 CTTTGAAGAAGTTTTTTATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* * *
52833 CTTTCAAGAAGTTTTCGTTGATCAGAGTTGAACTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
**
52868 ATTTCAAGAAGTTTTTTTATGATCAGAGTTGATCTC
1 ATTTCAAGAAG-TTTTCGATGATCAGAGTTGATCTC
* *
52904 CTTTCAAGAAGTTTTTCGATGATCAGAGTTTATCTC
1 ATTTCAAGAAG-TTTTCGATGATCAGAGTTGATCTC
* **
52940 GTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
52975 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* *
53010 GTTTCAAGAAGTTTTTGATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* **
53045 GTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
53080 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* **
53115 GTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
*
53150 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* * *
53185 GTTTCAAGAAGTTGTT---TTATCAGAGTTTATCTC
1 ATTTCAAGAAGTT-TTCGATGATCAGAGTTGATCTC
*
53218 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* ** *
53253 GTTTCAAGAAGTTTTTTATGATCATAGTTGATCTC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* *
53288 CTTTCAAGAAGTTTTCAATGATCAGAGTTGATC
1 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
53321 CCTAGATGAT
Statistics
Matches: 627, Mismatches: 64, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
32 2 0.00
33 27 0.04
34 24 0.04
35 454 0.72
36 120 0.19
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (35 bp):
ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
Found at i:53406 original size:53 final size:53
Alignment explanation
Indices: 53292--53605 Score: 330
Period size: 54 Copynumber: 5.8 Consensus size: 53
53282 GATCTCCTTT
*
53292 CAAGAAGTTTTCAATGATCAGAGTTGATCCCTAGATGATCCAGTGCAGTCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGATCCC-AAATGATCCAGTGCAGTCATTC
53346 CAAGAAGTTTTCAATGATCAGAGTTGATCCCAAATGATCCAGTGCAGTCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGATCCCAAATGATCCAGTGCAGTCATTC
* * * * * *
53399 CAAGAAGTTTTTAGA-GATCAGAGTTGAT-CCAGATGATCTAGTGCGGTCTTTT
1 CAAGAAGTTTTCA-ATGATCAGAGTTGATCCCAAATGATCCAGTGCAGTCATTC
* * * * * *
53451 CAAGAAATTTTCAATGATCAGAGTTGATCTTCAATTGATACAATGCAGTCATTA
1 CAAGAAGTTTTCAATGATCAGAGTTGATC-CCAAATGATCCAGTGCAGTCATTC
* ** *
53505 CAATAAGTTTTCAATGATCAGAGTTGATTTTCAATTTGATCCAGTGC-GATCATTC
1 CAAGAAGTTTTCAATGATCAGAGTTGA-TCCCAA-ATGATCCAGTGCAG-TCATTC
* * **
53560 CAAGAAAGGTTTCCATGATCTAG-GTTGAATCTTAAATGATCCAGTG
1 CAAG-AAGTTTTCAATGATC-AGAGTTG-ATCCCAAATGATCCAGTG
53606 TGGTTGATTA
Statistics
Matches: 220, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
51 1 0.00
52 43 0.20
53 46 0.21
54 77 0.35
55 29 0.13
56 21 0.10
57 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (53 bp):
CAAGAAGTTTTCAATGATCAGAGTTGATCCCAAATGATCCAGTGCAGTCATTC
Found at i:56621 original size:24 final size:24
Alignment explanation
Indices: 56593--56638 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
56583 GCGCCACCTC
*
56593 CTTCTC-CTTTGTATGGAGTTTTCT
1 CTTCTCTC-TTGTAAGGAGTTTTCT
*
56617 CTTCTTTCTTGTAAGGAGTTTT
1 CTTCTCTCTTGTAAGGAGTTTT
56639 ACATGAGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.54
Consensus pattern (24 bp):
CTTCTCTCTTGTAAGGAGTTTTCT
Found at i:68819 original size:16 final size:18
Alignment explanation
Indices: 68788--68820 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
68778 TAGAAATTTA
68788 GTATTTTGCGTTCCAAAG
1 GTATTTTGCGTTCCAAAG
68806 GTATTTT-C-TTCCAAA
1 GTATTTTGCGTTCCAAA
68821 ATCACTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (18 bp):
GTATTTTGCGTTCCAAAG
Found at i:68943 original size:50 final size:50
Alignment explanation
Indices: 68884--69070 Score: 320
Period size: 50 Copynumber: 3.7 Consensus size: 50
68874 CGAATGATTT
* *
68884 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * * *
68934 GGCTTTTCCACAAGTCGAACTCGTTTCCATACGAGTCAACTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
68984 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
69034 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTC
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTC
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 129 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Done.