Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020468.1 Corchorus olitorius cultivar O-4 contig20501, 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: 29392
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:76 original size:29 final size:30
Alignment explanation
Indices: 34--106 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
24 AGTCTATTTT
*
34 CCTTCCCCTCGCAAAAACCAGAAAAAGTT-C
1 CCTTCCCC-GGCAAAAACCAGAAAAAGTTAC
*
64 CCTTCCCCGGCAAATACCAGAAAAAGTTAC
1 CCTTCCCCGGCAAAAACCAGAAAAAGTTAC
94 CCTTCCCCGGCAA
1 CCTTCCCCGGCAA
107 CGGCGCCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 18 0.45
30 22 0.55
ACGTcount: A:0.33, C:0.38, G:0.12, T:0.16
Consensus pattern (30 bp):
CCTTCCCCGGCAAAAACCAGAAAAAGTTAC
Found at i:207 original size:16 final size:15
Alignment explanation
Indices: 169--210 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
159 ACAGAGATTG
*
169 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
184 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
199 ACTAGAAAACAA
1 AC-AGAAAACAA
211 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:10807 original size:25 final size:23
Alignment explanation
Indices: 10779--10824 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
10769 CTTTTCTAAA
*
10779 ACGCAGAAACAAATTTTTTTTTATG
1 ACGCA-AAA-AAATTATTTTTTATG
*
10804 ACGCAAAAAACTTATTTTTTA
1 ACGCAAAAAAATTATTTTTTA
10825 GTAAAACGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 3 0.16
25 5 0.26
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (23 bp):
ACGCAAAAAAATTATTTTTTATG
Found at i:10857 original size:23 final size:24
Alignment explanation
Indices: 10827--10871 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
10817 ATTTTTTAGT
10827 AAAACGC-AAAACAAAAAAAATTA
1 AAAACGCAAAAACAAAAAAAATTA
*
10850 AAAACGCAAAAATAAAAAAAAT
1 AAAACGCAAAAACAAAAAAAAT
10872 ATTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.76, C:0.11, G:0.04, T:0.09
Consensus pattern (24 bp):
AAAACGCAAAAACAAAAAAAATTA
Found at i:11054 original size:15 final size:16
Alignment explanation
Indices: 11028--11057 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11018 GCAGAGGGTT
11028 AAGAAGAACAATTAAA
1 AAGAAGAACAATTAAA
11044 AAGAA-AACAATTAA
1 AAGAAGAACAATTAA
11058 TCTAGAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (16 bp):
AAGAAGAACAATTAAA
Found at i:12479 original size:11 final size:10
Alignment explanation
Indices: 12446--12493 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
12436 TTGAAATAAT
*
12446 TCTTCAAAAA
1 TCTTCAAATA
12456 TCTTC-AA-A
1 TCTTCAAATA
12464 TCTTCAAATTA
1 TCTTCAAA-TA
12475 TCTTCAAATA
1 TCTTCAAATA
12485 GTCTTCAAA
1 -TCTTCAAA
12494 CACGAACTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.18
9 4 0.12
10 7 0.21
11 17 0.50
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.38
Consensus pattern (10 bp):
TCTTCAAATA
Found at i:12479 original size:19 final size:18
Alignment explanation
Indices: 12446--12483 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
12436 TTGAAATAAT
12446 TCTTCAAAAATCTTCAAA
1 TCTTCAAAAATCTTCAAA
*
12464 TCTTCAAATTATCTTCAAA
1 TCTTCAAA-AATCTTCAAA
12483 T
1 T
12484 AGTCTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAA
Found at i:16186 original size:2 final size:2
Alignment explanation
Indices: 16179--16204 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16169 TTGGTATGGA
16179 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
16205 GGTTTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25923 original size:14 final size:14
Alignment explanation
Indices: 25904--25934 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
25894 TCCCTTAATT
25904 GCAGATGCTCCCTA
1 GCAGATGCTCCCTA
25918 GCAGATGCTCCCTA
1 GCAGATGCTCCCTA
25932 GCA
1 GCA
25935 TACTCTCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (14 bp):
GCAGATGCTCCCTA
Found at i:26670 original size:26 final size:27
Alignment explanation
Indices: 26618--26684 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
26608 CGGAATCTGG
* *
26618 ATTTTGAGTTTCGAACATGACATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
26645 ATTTTGAGTTTTGAA-ATGAAATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
*
26671 ATTTTGACTTTTGA
1 ATTTTGAGTTTTGA
26685 CTTTTGACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTGAGTTTTGAACATGAAATGCAA
Found at i:26684 original size:7 final size:7
Alignment explanation
Indices: 26672--26698 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
26662 GAAATGCAAA
26672 TTTTGAC
1 TTTTGAC
26679 TTTTGAC
1 TTTTGAC
26686 TTTTGAC
1 TTTTGAC
26693 TTTTGA
1 TTTTGA
26699 AATGTTGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (7 bp):
TTTTGAC
Found at i:26727 original size:7 final size:7
Alignment explanation
Indices: 26714--26783 Score: 113
Period size: 7 Copynumber: 10.0 Consensus size: 7
26704 TGAGATGCAG
26714 GTTTTGA
1 GTTTTGA
*
26721 ATTTTGA
1 GTTTTGA
*
26728 ATTTTGA
1 GTTTTGA
*
26735 GTTTTTA
1 GTTTTGA
26742 GTTTTGA
1 GTTTTGA
26749 GTTTTGA
1 GTTTTGA
26756 GTTTTGA
1 GTTTTGA
26763 GTTTTGA
1 GTTTTGA
26770 GTTTTGA
1 GTTTTGA
26777 GTTTTGA
1 GTTTTGA
26784 ATTATGAGCA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (7 bp):
GTTTTGA
Found at i:26738 original size:21 final size:21
Alignment explanation
Indices: 26714--26791 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
26704 TGAGATGCAG
*
26714 GTTTTGAATTTTGAATTTTGA
1 GTTTTGAATTTTGAGTTTTGA
* *
26735 GTTTTTAGTTTTGAGTTTTGA
1 GTTTTGAATTTTGAGTTTTGA
*
26756 GTTTTGAGTTTTGAGTTTTGA
1 GTTTTGAATTTTGAGTTTTGA
*
26777 GTTTTGAATTATGAG
1 GTTTTGAATTTTGAG
26792 CAATGAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.19, C:0.00, G:0.24, T:0.56
Consensus pattern (21 bp):
GTTTTGAATTTTGAGTTTTGA
Found at i:27105 original size:55 final size:54
Alignment explanation
Indices: 27038--27475 Score: 182
Period size: 54 Copynumber: 8.1 Consensus size: 54
27028 CATTAAAAAT
* * * *
27038 TCAACTTTGATCAT-GGAAACCTTTCTTGGAACGACC-CATTGGGTCAATTTAGAGA
1 TCAACTCTGATCATCGGAAA-C-TTCTTGGAACGACCACAATGGATCAACTTA-AGA
* *
27093 TCAACTCTGATCATCGTAAACTTCTTGGAATGACCACAATGGATCAACTTAAGA
1 TCAACTCTGATCATCGGAAACTTCTTGGAACGACCACAATGGATCAACTTAAGA
** * * *
27147 TCAACT-TAGATTTTTGAAAACTTCTATGGAA-GACCACACA--GAGTC-ATTTGAAGA
1 TCAACTCT-GATCATCGGAAACTTCT-TGGAACGACCACA-ATGGA-TCAACTT-AAGA
** * ** * * *
27201 TCAACTAAGA-CCTCTAAAAGCTTCTAT-GAAAGACCACACTGGATCATCTTAAGA
1 TCAACTCTGATCATCGGAAA-CTTCT-TGGAACGACCACAATGGATCAACTTAAGA
* * * * *
27255 TCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCACACT-GTTCATCTTAAGA
1 TCAACTCT-GATCATC-GGAAACTTCT-TGGAACGACCACAATGGATCAACTTAAGA
* * * *
27308 TCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCACACTGGATCATCTTAAGA
1 TCAACTCT-GATCATC-GGAAACTTCT-TGGAACGACCACAATGGATCAACTTAAGA
* * * * *
27362 TCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCACACTGGTTCATCTTAAGA
1 TCAACTCT-GATCATC-GGAAACTTCT-TGGAACGACCACAATGGATCAACTTAAGA
* * * * *
27416 TCAAAT-TAGGTC-TCTGAAAACTTCTAT-GAAAGACCACAGTGGATCAACTTAAGA
1 TCAACTCT-GATCATC-GGAAACTTCT-TGGAACGACCACAATGGATCAACTTAAGA
27470 TCAACT
1 TCAACT
27476 TTCTAGAGAG
Statistics
Matches: 336, Mismatches: 30, Indels: 35
0.84 0.07 0.09
Matches are distributed among these distances:
53 66 0.20
54 225 0.67
55 41 0.12
56 4 0.01
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACTCTGATCATCGGAAACTTCTTGGAACGACCACAATGGATCAACTTAAGA
Found at i:27148 original size:54 final size:54
Alignment explanation
Indices: 27110--27476 Score: 501
Period size: 54 Copynumber: 6.8 Consensus size: 54
27100 TGATCATCGT
* * * *
27110 AAACTTCT-TGGAATGACCACAATGGATCAACTTAAGATCAACTTAGATTTTTGA
1 AAACTTCTAT-GAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
* * * * *
27164 AAACTTCTATGGAAGACCACAC-AGAGTC-ATTTGAAGATCAACTAAGACCTCT-A
1 AAACTTCTATGAAAGACCACACTGGA-TCAACTT-AAGATCAACTTAGATCTCTGA
*
27217 AAAGCTTCTATGAAAGACCACACTGGATCATCTTAAGATCAACTTAGATCTCTGA
1 AAA-CTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
* *
27272 AAACTTCTATGAAAGACCACACT-GTTCATCTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
*
27325 AAACTTCTATGAAAGACCACACTGGATCATCTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
* * * *
27379 AAACTTCTATGAAAGACCACACTGGTTCATCTTAAGATCAAATTAGGTCTCTGA
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
*
27433 AAACTTCTATGAAAGACCACAGTGGATCAACTTAAGATCAACTT
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTT
27477 TCTAGAGAGA
Statistics
Matches: 281, Mismatches: 24, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
53 61 0.22
54 211 0.75
55 9 0.03
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (54 bp):
AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
Found at i:27364 original size:161 final size:162
Alignment explanation
Indices: 27110--27476 Score: 537
Period size: 161 Copynumber: 2.3 Consensus size: 162
27100 TGATCATCGT
* * * *
27110 AAACTTCT-TGGAATGACCACAATGGATCAACTTAAGATCAACTTAGATTTTTGAAAACTTCTAT
1 AAACTTCTAT-GAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTAT
*
27174 GGAAGACCACACAGAGTCATTTGAAGATCAACTAAGACCTCT-AAAAGCTTCTATGAAAGACCAC
65 GAAAGACCACACAGAGTCATTTGAAGATCAACTAAGACCTCTGAAAA-CTTCTATGAAAGACCAC
*
27238 ACTGGATCATCTTAAGATCAACTTAGATCTCTGA
129 ACTGGATCATCTTAAGATCAAATTAGATCTCTGA
* *
27272 AAACTTCTATGAAAGACCACACT-GTTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATG
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATG
* * *
27336 AAAGACCACACTG-GATCATCTT-AAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCAC
66 AAAGACCACACAGAG-TCAT-TTGAAGATCAACTAAGACCTCTGAAAACTTCTATGAAAGACCAC
* *
27399 ACTGGTTCATCTTAAGATCAAATTAGGTCTCTGA
129 ACTGGATCATCTTAAGATCAAATTAGATCTCTGA
*
27433 AAACTTCTATGAAAGACCACAGTGGATCAACTTAAGATCAACTT
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTT
27477 TCTAGAGAGA
Statistics
Matches: 184, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
160 1 0.01
161 139 0.76
162 43 0.23
163 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (162 bp):
AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATG
AAAGACCACACAGAGTCATTTGAAGATCAACTAAGACCTCTGAAAACTTCTATGAAAGACCACAC
TGGATCATCTTAAGATCAAATTAGATCTCTGA
Found at i:27629 original size:37 final size:37
Alignment explanation
Indices: 27584--28078 Score: 446
Period size: 37 Copynumber: 13.4 Consensus size: 37
27574 TATTTTAAAG
* * *
27584 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* * * ** * *
27621 AAAAACCTAAACAGGAATTTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGATA
* * *
27658 AGACACTTAAACAGGTACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* ** *
27695 AGAAACCTAAACAGGGACCTTAAACAAAAATTTTGACA
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGATA
* * * *
27733 AGAAACCTAAACAAGCACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* * * * * *
27770 AGAAACCTAAACATGGATCTTACAC-ATGATTTTGATG
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGATA
* * * *
27807 AGACACCTAAATAGGGAACTTAAATAAAGATTT-AGTA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGA-TA
* * * * * *
27844 AGAAACCTAAACATGAATCTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGATA
* * * *
27881 AGACACCTAAACAGGGATCTTGAACCA-GATTTCGATG
1 AGACACCTAAACAGGGACCTTAAACAAGGATTT-GATA
*
27918 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
27955 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* * * *
27992 AGGCACCTAAACAGGAATCTTGAACAA-GATTTTGATGA
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGAT-A
*
28030 A-ACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
28066 AGACACCTAAACA
1 AGACACCTAAACA
28079 AAAATCTTGA
Statistics
Matches: 371, Mismatches: 73, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
36 15 0.04
37 310 0.84
38 46 0.12
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (37 bp):
AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
Found at i:27669 original size:74 final size:74
Alignment explanation
Indices: 27583--28106 Score: 608
Period size: 74 Copynumber: 7.1 Consensus size: 74
27573 GTATTTTAAA
* * * *
27583 GAGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAAAAACCTAAACAGGAATTTTGAACAA
1 GAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAA
27648 GATTTTGAT
66 GATTTTGAT
* * * * *
27657 GAGACACTTAAACAGGTACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGACCTTAAACAA
1 GAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAAC-A
* *
27722 AAATTTTGAC
65 AGATTTTGAT
* * * *
27732 AAGAAACCTAAACAAGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGG-ATCTT-ACAC
1 GAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACA-GGAATCTTGA-AC
*
27795 ATGATTTTGAT
64 AAGATTTTGAT
* * * *
27806 GAGACACCTAAATAGGGAACTTAAATAAAGATTT-AGTAAGAAACCTAAACATGAATCTTGAACA
1 GAGACACCTAAACAGGGACCTTAAATAAGGATTTGA-TAAGAAACCTAAACAGGAATCTTGAACA
27870 AGATTTTGAT
65 AGATTTTGAT
* * ** * * * * * *
27880 GAGACACCTAAACAGGGATCTTGAACCA-GATTTCGATGAGACACCTAAACAGGGACCTTAAATA
1 GAGACACCTAAACAGGGACCTTAAATAAGGATTT-GATAAGAAACCTAAACAGGAATCTTGAACA
27944 AGGA-TTTGAT
65 A-GATTTTGAT
* * **
27954 AAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGGCACCTAAACAGGAATCTTGAACAA
1 GAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAA
28019 GATTTTGAT
66 GATTTTGAT
* * **
28028 GAAACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAAAAATCTTGAACAA
1 GAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAA
*
28093 GGTTTTGAT
66 GATTTTGAT
28102 GAGAC
1 GAGAC
28107 TGAATTTTGT
Statistics
Matches: 382, Mismatches: 57, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
73 9 0.02
74 301 0.79
75 70 0.18
76 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (74 bp):
GAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAA
GATTTTGAT
Found at i:27704 original size:111 final size:110
Alignment explanation
Indices: 27584--28106 Score: 552
Period size: 111 Copynumber: 4.7 Consensus size: 110
27574 TATTTTAAAG
* * * * *
27584 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAAAAACCTAAACAGGAATTTTGAACAAG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAAGAATCTTGAACAAG
* * *
27649 ATTTTGATGAGACACTTAAACAGGTACCTTAAATAAGGA-TTTGATA
66 ATTTTGATGAGACACCTAAACAGG-ATCTTAAACAA-GATTTTGATA
* * ** * * * * *
27695 AGAAACCTAAACAGGGACCTTAAACAAAAATTTTGACAAGAAACCTAAACAAGCACCTTAAATAA
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAGAAACCTAAACAAGAATCTTGAACAA
* * * * *
27760 GGA-TTTGATAAGAAACCTAAACATGGATCTTACACATGATTTTGATG
65 -GATTTTGATGAGACACCTAAACA-GGATCTTAAACAAGATTTTGATA
* * * *
27807 AGACACCTAAATAGGGAACTTAAATAAAGATTT-AGTAAGAAACCTAAACATGAATCTTGAACAA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGA-TAAGAAACCTAAACAAGAATCTTGAACAA
* * * *
27871 GATTTTGATGAGACACCTAAACAGGGATCTTGAACCAGATTTCGATG
65 GATTTTGATGAGACACCTAAACA-GGATCTTAAACAAGATTTTGATA
* * * * *
27918 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGGACCTTAAACAAG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAAGAATCTTGAACAA-
* * *
27983 GA-TTTGATAAGGCACCTAAACAGGAATCTTGAACAAGATTTTGATGA
65 GATTTTGATGAGACACCTAAACAGG-ATCTTAAACAAGATTTTGAT-A
* *
28030 A-ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAAAAATCTTGAACAAG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAAGAATCTTGAACAAG
*
28094 GTTTTGATGAGAC
66 ATTTTGATGAGAC
28107 TGAATTTTGT
Statistics
Matches: 339, Mismatches: 62, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
110 6 0.02
111 245 0.72
112 84 0.25
113 4 0.01
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.24
Consensus pattern (110 bp):
AGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAAGAATCTTGAACAAG
ATTTTGATGAGACACCTAAACAGGATCTTAAACAAGATTTTGATA
Found at i:29181 original size:29 final size:30
Alignment explanation
Indices: 29149--29215 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
29139 CCTTTTGATT
29149 TTTTCTTTATTT-CTTTCCCTTTTTTTCAC
1 TTTTCTTTATTTGCTTTCCCTTTTTTTCAC
* * **
29178 TTTT-TTTCTTTGCTTTCTCTTTTTTTCTT
1 TTTTCTTTATTTGCTTTCCCTTTTTTTCAC
29207 TTTTCTTTA
1 TTTTCTTTA
29216 GATTGCTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.19
29 22 0.71
30 3 0.10
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.75
Consensus pattern (30 bp):
TTTTCTTTATTTGCTTTCCCTTTTTTTCAC
Done.