Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018325.1 Corchorus olitorius cultivar O-4 contig18358, 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: 13648
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:6092 original size:90 final size:90
Alignment explanation
Indices: 6034--6206 Score: 296
Period size: 90 Copynumber: 1.9 Consensus size: 90
6024 AAAGGATAAT
6034 AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGAT-
1 AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGATA
*
6098 AATGGTTGAAAATAAATAAAAAGATA
66 AATAGTT-AAAATAAATAAAAAGATA
*
6124 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGAT-
1 AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGATA
*
6188 AATAGTTAAAAAAAATAAA
66 AATAGTTAAAATAAATAAA
6207 TAAATAGTGA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 11 0.14
90 69 0.86
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.25
Consensus pattern (90 bp):
AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGATA
AATAGTTAAAATAAATAAAAAGATA
Found at i:6117 original size:36 final size:37
Alignment explanation
Indices: 6069--6227 Score: 122
Period size: 44 Copynumber: 3.8 Consensus size: 37
6059 GAAAATAAAT
*
6069 AAAAATAAATAAATAGTAAATAAATAGATAATGGTTG
1 AAAAATAAATAAATAGTAAATAAATAGATAATAGTTG
6106 AAAATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTG
1 --AA-AAAT---AA-ATAAATAGTAAATAAATAGATAATAGTTG
*
6150 AAAATAAATAAAAATAAATAAATAGTAAATAAATAGATAATAGTTAAA
1 ---------AAAAATAAATAAATAGTAAATAAATAGATAATAGTT--G
*
6198 AAAAATAAATAAATAGTGAATAAATA-ATAA
1 AAAAATAAATAAATAGTAAATAAATAGATAA
6228 AAAAAATCTT
Statistics
Matches: 102, Mismatches: 4, Indels: 29
0.76 0.03 0.21
Matches are distributed among these distances:
38 4 0.04
39 27 0.26
40 4 0.04
43 2 0.02
44 28 0.27
46 28 0.27
47 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.25
Consensus pattern (37 bp):
AAAAATAAATAAATAGTAAATAAATAGATAATAGTTG
Found at i:6228 original size:46 final size:46
Alignment explanation
Indices: 6034--6206 Score: 289
Period size: 46 Copynumber: 3.8 Consensus size: 46
6024 AAAGGATAAT
*
6034 AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
* *
6080 AATAGTAAATAAATAGATAATGGTTGAAAATAAAT-AAAA-AGATA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
6124 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
*
6170 AATAGTAAATAAATAGATAATAGTT-AAAAAAAATAAA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAA
6207 TAAATAGTGA
Statistics
Matches: 119, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
44 38 0.32
45 19 0.16
46 62 0.52
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.25
Consensus pattern (46 bp):
AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
Found at i:7913 original size:107 final size:107
Alignment explanation
Indices: 7751--8032 Score: 358
Period size: 107 Copynumber: 2.6 Consensus size: 107
7741 CATTTAAGAT
* * * *
7751 TCAACTCTGATCATCAAAAACGTCTTGGAATGACTGCACTGTATCAATTGAAGATCAACTCTGAT
1 TCAACTCTGATCATCAAAAACATCTTGGAATGACCGCACTGGATC-ATTGGAGATCAACTCTGAT
* * *
7816 CATTGAAAATTTCTTGGA-AAGACCGCACTAGATC-ATCT-GGGA
65 CATTGAAAACTTCTTGGATAA-ACCGCACAAGATCAAT-TAGAGA
7858 TCAACTCTGATC-TCTAAAAACATCTTGGAATGACCGCACTGGATCATCTGGAGATCAACTCTGA
1 TCAACTCTGATCATC-AAAAACATCTTGGAATGACCGCACTGGATCAT-TGGAGATCAACTCTGA
*
7922 TCATTGAAAACTTCTTGGATTAACCGCACAAGATCAATTAGAGA
64 TCATTGAAAACTTCTTGGATAAACCGCACAAGATCAATTAGAGA
* * * * *
7966 TCAACTCTAATCATCAAAAACTTCTTAGAATGACCGCACCGGATCATT-TAGGATCAACTCTGAT
1 TCAACTCTGATCATCAAAAACATCTTGGAATGACCGCACTGGATCATTGGA-GATCAACTCTGAT
8030 CAT
65 CAT
8033 AAAAAAAACT
Statistics
Matches: 155, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
106 5 0.03
107 102 0.66
108 46 0.30
109 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (107 bp):
TCAACTCTGATCATCAAAAACATCTTGGAATGACCGCACTGGATCATTGGAGATCAACTCTGATC
ATTGAAAACTTCTTGGATAAACCGCACAAGATCAATTAGAGA
Found at i:8003 original size:161 final size:161
Alignment explanation
Indices: 7729--8030 Score: 385
Period size: 161 Copynumber: 1.9 Consensus size: 161
7719 TTCTTAATCA
* * * *
7729 ACCGCACTGGATCATTTAAGATTCAACTCTGATCATCAAAAACGTCTTGGAATGACTGCACTGTA
1 ACCGCACTGGATCATTGAAGATTCAACTCTGATCATCAAAAACGTCTTGGAATAACCGCACAGTA
* ** * * * *
7794 TCAATTGAAGATCAACTCTGATCATTGAAAATTTCTTGGAAAGACCGCACTAGATCATCTGGGAT
66 TCAATTGAAGATCAACTCTAATCATCAAAAACTTCTTAGAAAGACCGCACCAGATCATCTAGGAT
7859 CAACTCTGATCTCTAAAAACATCTTGGAATG
131 CAACTCTGATCTCTAAAAACATCTTGGAATG
* ** * *
7890 ACCGCACTGGATCATCTGGAGA-TCAACTCTGATCATTGAAAACTTCTTGGATTAACCGCACAAG
1 ACCGCACTGGATCAT-TGAAGATTCAACTCTGATCATCAAAAACGTCTTGGAATAACCGCAC-AG
* * *
7954 -ATCAATT-AGAGATCAACTCTAATCATCAAAAACTTCTTAGAATGACCGCACCGGATCATTTAG
64 TATCAATTGA-AGATCAACTCTAATCATCAAAAACTTCTTAGAAAGACCGCACCAGATCATCTAG
8017 GATCAACTCTGATC
128 GATCAACTCTGATC
8031 ATAAAAAAAA
Statistics
Matches: 119, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
160 1 0.01
161 113 0.95
162 5 0.04
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (161 bp):
ACCGCACTGGATCATTGAAGATTCAACTCTGATCATCAAAAACGTCTTGGAATAACCGCACAGTA
TCAATTGAAGATCAACTCTAATCATCAAAAACTTCTTAGAAAGACCGCACCAGATCATCTAGGAT
CAACTCTGATCTCTAAAAACATCTTGGAATG
Found at i:8039 original size:54 final size:53
Alignment explanation
Indices: 7729--8038 Score: 325
Period size: 54 Copynumber: 5.8 Consensus size: 53
7719 TTCTTAATCA
* * *
7729 ACCGCACTGGATCATTTAAGATTCAACTCTGATCATCAAAAACGTCTTGGAATG
1 ACCGCACTGGATCATTTAGGA-TCAACTCTGATCATTAAAAACTTCTTGGAATG
* * * * * * *
7783 ACTGCACTGTATCAATTGAAGATCAACTCTGATCATTGAAAATTTCTTGGAAAG
1 ACCGCACTGGATC-ATTTAGGATCAACTCTGATCATTAAAAACTTCTTGGAATG
* * * *
7837 ACCGCACTAGATCATCTGGGATCAACTCTGATC-TCTAAAAACATCTTGGAATG
1 ACCGCACTGGATCATTTAGGATCAACTCTGATCAT-TAAAAACTTCTTGGAATG
* * * * *
7890 ACCGCACTGGATCATCTGGAGATCAACTCTGATCATTGAAAACTTCTTGGATTA
1 ACCGCACTGGATCATTTAG-GATCAACTCTGATCATTAAAAACTTCTTGGAATG
** * * * *
7944 ACCGCACAAGATCAATTAGAGATCAACTCTAATCATCAAAAACTTCTTAGAATG
1 ACCGCACTGGATCATTTAG-GATCAACTCTGATCATTAAAAACTTCTTGGAATG
* *
7998 ACCGCACCGGATCATTTAGGATCAACTCTGATCATAAAAAA
1 ACCGCACTGGATCATTTAGGATCAACTCTGATCATTAAAAA
8039 AACTTTTTGA
Statistics
Matches: 212, Mismatches: 40, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
52 1 0.00
53 68 0.32
54 135 0.64
55 8 0.04
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (53 bp):
ACCGCACTGGATCATTTAGGATCAACTCTGATCATTAAAAACTTCTTGGAATG
Found at i:8058 original size:37 final size:37
Alignment explanation
Indices: 8017--8505 Score: 692
Period size: 37 Copynumber: 13.4 Consensus size: 37
8007 GATCATTTAG
*
8017 GATCAACTCTGATCATAAAAAAAACTTTTTGAAACGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
8054 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
8091 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
* *
8128 GATCAACTCTGATCATAAAAAAAAATTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
*
8165 GATCAACTCTGATCATAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
** *
8202 GATCAACTCTGATC--AACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
8237 GATCAACTCTGATCAT--AAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
*
8272 TATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
8309 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
* *
8346 GATTAACTCTGATCATAAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT-AAAAAAAACTTCTTGAAACGA
* * *
8384 GAACAACTCTGATC---ACAAACACTTCTTGAAA-GTA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACG-A
* * *
8418 GATCAACTTTGATCATAAAAAAAACTTCTTGAAATGT
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
* ** * *
8455 GAACAACTCTGATCAT--CGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
*
8490 GATCAACTTTGATCAT
1 GATCAACTCTGATCAT
8506 CGAAAACTTC
Statistics
Matches: 410, Mismatches: 32, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
33 1 0.00
34 28 0.07
35 92 0.22
37 256 0.62
38 33 0.08
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (37 bp):
GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
Found at i:8279 original size:181 final size:182
Alignment explanation
Indices: 8017--8505 Score: 711
Period size: 181 Copynumber: 2.7 Consensus size: 182
8007 GATCATTTAG
* * *
8017 GATCAACTCTGATCATAAAAAAAACTTTTTGAAACGAGATCAACTCTGATCATAAAAAAAACTTC
1 GATCAACTCTGATC---AACAAAACTTCTTGAAAGGAGATCAACTCTGATCAT-AAAAAAACTTC
*
8082 TTGAAACGAGATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
62 TTGAAACGATATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
*
8147 AAAAAATTCTTGAAAGGAGATCAACTCTGATCAT-AAAAAAAACTTCTTGAAATGA
127 AAAAAATTCTTGAAACGAGATCAACTCTGATCATAAAAAAAAACTTCTTGAAATGA
8202 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTGATCAT-AAAAAACTTCTTG
1 GATCAACTCTGATCAAC-AAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAAACTTCTTG
8266 AAACGATATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAA
65 AAACGATATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAA
* *
8331 AACTTCTTGAAACGAGATTAACTCTGATCATAAAAAAAAACTTCTTGAAATGA
130 AAATTCTTGAAACGAGATCAACTCTGATCATAAAAAAAAACTTCTTGAAATGA
* * *
8384 GAACAACTCTGATC-ACAAACACTTCTTGAAAGTAGATCAACTTTGATCATAAAAAAAACTTCTT
1 GATCAACTCTGATCAACAAA-ACTTCTTGAAAGGAGATCAACTCTGATCAT-AAAAAAACTTCTT
* * ** * * *
8448 GAAATG-TGAACAACTCTGATCAT--CGAAAACTTCTTGGAATGAGATCAACTTTGATCAT
64 GAAACGAT-ATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCAT
8506 CGAAAACTTC
Statistics
Matches: 281, Mismatches: 17, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
180 3 0.01
181 165 0.59
182 37 0.13
183 62 0.22
185 14 0.05
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (182 bp):
GATCAACTCTGATCAACAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAAACTTCTTGA
AACGATATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAAA
AATTCTTGAAACGAGATCAACTCTGATCATAAAAAAAAACTTCTTGAAATGA
Found at i:8286 original size:218 final size:217
Alignment explanation
Indices: 8017--8505 Score: 732
Period size: 218 Copynumber: 2.2 Consensus size: 217
8007 GATCATTTAG
*
8017 GATCAACTCTGATCATAAAAAAAACTTTTTGAAACGAGATCAACTCTGATCATAAAAAAAACTTC
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAAAACTTC
8082 TTGAAACGAGATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
64 TTGAAACGAGATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
*
8147 AAAAAA-TTCTTGAAAGGAGATCAACTCTGATCATAAAAAAAACTTCTTGAAA-TGAGATCAACT
129 AAAAAACTTCTTGAAAGGAGAACAACTCTGATC---AAAAAAACTTCTTGAAAGT-AGATCAACT
**
8210 CTGATC-AACGAAAACTTCTTGAAAGGA
190 CTGATCAAAAAAAAACTTCTTGAAAGGA
*
8237 GATCAACTCTGATCATAAAAAACTTCTTGAAACGATATCAACTCTGATCATAAAAAAAACTTCTT
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAAAACTTCTT
*
8302 GAAACGAGATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATTAACTCTGATCATAAAAA
66 GAAACGAGATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAA
* * * *
8367 AAAACTTCTTGAAATGAGAACAACTCTGATCACAAACACTTCTTGAAAGTAGATCAACTTTGATC
131 AAAACTTCTTGAAAGGAGAACAACTCTGATCAAAAAAACTTCTTGAAAGTAGATCAACTCTGATC
* *
8432 ATAAAAAAAACTTCTTGAAATGT
196 A-AAAAAAAACTTCTTGAAAGGA
* ** * * *
8455 GAACAACTCTGATCATCGAAAACTTCTTGGAATGAGATCAACTTTGATCAT
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCAT
8506 CGAAAACTTC
Statistics
Matches: 246, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
216 29 0.12
217 1 0.00
218 176 0.72
219 24 0.10
220 16 0.07
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (217 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAAAACTTCTT
GAAACGAGATCAACTCTGATCATAAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAA
AAAACTTCTTGAAAGGAGAACAACTCTGATCAAAAAAACTTCTTGAAAGTAGATCAACTCTGATC
AAAAAAAAACTTCTTGAAAGGA
Found at i:8645 original size:54 final size:54
Alignment explanation
Indices: 8554--8813 Score: 337
Period size: 54 Copynumber: 4.8 Consensus size: 54
8544 GATCAACTCT
* * * * ***
8554 GATCTCTAAAAACTTCTTTGAAAGACCGCACGGGGTCATCTGAAGATCAACTTA
1 GATCTCTAAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTA
* * *
8608 GATTTCTAAAAACTTCTATGAAAGACCATA-TCAGGTCATCTTAAGATCTGTTTA
1 GATCTCTAAAAACTTCTATGAAAGACCACACT-GGGTCATCTTAAGATCTGTTTA
*
8662 GATCTCTGAAAAA-TTCTATGAAAGACCACACTGGGTAATCTTAAGATCTGTTTA
1 GATCTCT-AAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTA
*
8716 GATCTTTGAAAAA-TTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTA
1 GATCTCT-AAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTA
* * *
8770 GATCTCTGAAAACTTCTATGAAAGACCACACTAGGTCATTTTAA
1 GATCTCTAAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
8814 ACACTTGTAC
Statistics
Matches: 182, Mismatches: 20, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
53 4 0.02
54 172 0.95
55 6 0.03
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (54 bp):
GATCTCTAAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTA
Found at i:11806 original size:39 final size:38
Alignment explanation
Indices: 11763--11842 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 38
11753 CATGTATAAA
* * *
11763 ATGCATCTATTTACAAATGACAATGA-TAATGCATGATGG
1 ATGCATATATATACAAATG--AATGACAAATGCATGATGG
*
11802 ATGCATATATATACAAGTGAATGACAAATGCATGATGG
1 ATGCATATATATACAAATGAATGACAAATGCATGATGG
11840 ATG
1 ATG
11843 TGTGAATTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 5 0.14
38 15 0.42
39 16 0.44
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (38 bp):
ATGCATATATATACAAATGAATGACAAATGCATGATGG
Found at i:13328 original size:4 final size:4
Alignment explanation
Indices: 13319--13514 Score: 51
Period size: 4 Copynumber: 50.8 Consensus size: 4
13309 GGATAATAAT
* **
13319 AATA AATA AATA GAT- AATA GTTGA AAATA AAT- AA-A AATA AATA AAT-
1 AATA AATA AATA AATA AATA AAT-A AA-TA AATA AATA AATA AATA AATA
* * * ** *
13365 AGTA AATA AATA GAT- AATG GTTGA AAATA AATA AA-A AGATA AAT- AGTA
1 AATA AATA AATA AATA AATA AAT-A A-ATA AATA AATA A-ATA AATA AATA
* ** *
13413 AATA AATA GAT- AATA GTTGAA AATA AAT- AA-A AATA AATA AAT- AGTA
1 AATA AATA AATA AATA AAT--A AATA AATA AATA AATA AATA AATA AATA
* ** * * *
13459 AATA AATA GAT- AATA GTTA AAAA AATA AATA AAT- AGTG AATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
13504 AATA AAAA AAT
1 AATA AATA AAT
13515 CTTTTTGGTC
Statistics
Matches: 133, Mismatches: 38, Indels: 42
0.62 0.18 0.20
Matches are distributed among these distances:
3 29 0.22
4 92 0.69
5 8 0.06
6 4 0.03
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:13376 original size:90 final size:90
Alignment explanation
Indices: 13316--13487 Score: 296
Period size: 90 Copynumber: 1.9 Consensus size: 90
13306 AAAGGATAAT
13316 AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGAT-
1 AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGATA
*
13380 AATGGTTGAAAATAAATAAAAAGATA
66 AATAGTT-AAAATAAATAAAAAGATA
*
13406 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGAT-
1 AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGATA
13470 AATAGTTAAAA-AAATAAA
66 AATAGTTAAAATAAATAAA
13488 TAAATAGTGA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
88 7 0.09
89 4 0.05
90 69 0.86
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (90 bp):
AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATAAATAGTAAATAAATAGATA
AATAGTTAAAATAAATAAAAAGATA
Found at i:13399 original size:36 final size:37
Alignment explanation
Indices: 13351--13508 Score: 129
Period size: 44 Copynumber: 3.8 Consensus size: 37
13341 GAAAATAAAT
*
13351 AAAAATAAATAAATAGTAAATAAATAGATAATGGTTG
1 AAAAATAAATAAATAGTAAATAAATAGATAATAGTTG
13388 AAAATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTG
1 --AA-AAAT---AA-ATAAATAGTAAATAAATAGATAATAGTTG
*
13432 AAAATAAATAAAAATAAATAAATAGTAAATAAATAGATAATAGTTAA
1 ---------AAAAATAAATAAATAGTAAATAAATAGATAATAGTT-G
*
13479 AAAAATAAATAAATAGTGAATAAATA-ATAA
1 AAAAATAAATAAATAGTAAATAAATAGATAA
13509 AAAAATCTTT
Statistics
Matches: 102, Mismatches: 4, Indels: 28
0.76 0.03 0.21
Matches are distributed among these distances:
37 4 0.04
38 25 0.25
39 2 0.02
40 4 0.04
43 2 0.02
44 28 0.27
46 28 0.27
47 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.25
Consensus pattern (37 bp):
AAAAATAAATAAATAGTAAATAAATAGATAATAGTTG
Found at i:13493 original size:46 final size:46
Alignment explanation
Indices: 13316--13487 Score: 289
Period size: 46 Copynumber: 3.8 Consensus size: 46
13306 AAAGGATAAT
*
13316 AATAATAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
* *
13362 AATAGTAAATAAATAGATAATGGTTGAAAATAAAT-AAAA-AGATA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
13406 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
13452 AATAGTAAATAAATAGATAATAGTT-AAAA-AAATAAA
1 AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAA
13488 TAAATAGTGA
Statistics
Matches: 119, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
44 45 0.38
45 12 0.10
46 62 0.52
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (46 bp):
AATAGTAAATAAATAGATAATAGTTGAAAATAAATAAAAATAAATA
Done.