Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012028.1 Corchorus capsularis cultivar CVL-1 contig12049, 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: 18675
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:132 original size:35 final size:35
Alignment explanation
Indices: 88--173 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
78 ATAATCAGTA
*
88 AAGAATAAAATAGTAATC-AGCAAAAGACAGCCATT
1 AAGAGTAAAATAGTAATCTA-CAAAAGACAGCCATT
* * ** *
123 AAGAGTAAAATAGTGATCTATAAAAGGTAGTCATT
1 AAGAGTAAAATAGTAATCTACAAAAGACAGCCATT
*
158 AAGAGTAAAACAGTAA
1 AAGAGTAAAATAGTAA
174 CCAGTGAGAG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 41 0.98
36 1 0.02
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.21
Consensus pattern (35 bp):
AAGAGTAAAATAGTAATCTACAAAAGACAGCCATT
Found at i:243 original size:15 final size:15
Alignment explanation
Indices: 225--281 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
215 ATCAGTAAGA
225 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
240 AGTAAAAAAAG-GAGC
1 AGT-AAAAGAGTAATC
*
255 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
269 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
282 AATGGTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
13 6 0.19
14 4 0.12
15 16 0.50
16 6 0.19
ACGTcount: A:0.58, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:295 original size:15 final size:16
Alignment explanation
Indices: 270--304 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
260 ATAGTAATCA
*
270 GTAAAAGAGTAAAATG
1 GTAAAAGAGTAAAAAG
286 GTAAAA-AGTAAAAAG
1 GTAAAAGAGTAAAAAG
301 GTAA
1 GTAA
305 TCAACAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (16 bp):
GTAAAAGAGTAAAAAG
Found at i:2222 original size:17 final size:17
Alignment explanation
Indices: 2200--2237 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2190 AATCGGCAGT
*
2200 CTTCTTCTTTTTCCTCC
1 CTTCTTCTTCTTCCTCC
*
2217 CTTCTTCTTCTTCCTCG
1 CTTCTTCTTCTTCCTCC
2234 CTTC
1 CTTC
2238 CCTCTTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (17 bp):
CTTCTTCTTCTTCCTCC
Found at i:7816 original size:87 final size:87
Alignment explanation
Indices: 7707--7887 Score: 272
Period size: 87 Copynumber: 2.1 Consensus size: 87
7697 AACCTTGTAA
* *
7707 ATTTTCTTGGTAAGCTTCTAAATTTATCATTAAACCTAAAAACTTATTAAATAGTTTTCTTAAAT
1 ATTTTTTTGGTAAGCTTATAAATTTATCATTAAACCTAAAAACTTATTAAATAGTTTTCTTAAAT
* * * *
7772 TTATTCATTCACGTTGTTTAAG
66 TTATTCAATCACCTCGTTAAAG
* * * *
7794 ATTTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAAT
1 ATTTTTTTGGTAAGCTTATAAATTTATCATTAAACCTAAAAACTTATTAAATAGTTTTCTTAAAT
7859 TTATTCAATCACCTCGTTAAAG
66 TTATTCAATCACCTCGTTAAAG
7881 ATTTTTT
1 ATTTTTT
7888 GTGATCTTAT
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (87 bp):
ATTTTTTTGGTAAGCTTATAAATTTATCATTAAACCTAAAAACTTATTAAATAGTTTTCTTAAAT
TTATTCAATCACCTCGTTAAAG
Found at i:9102 original size:12 final size:13
Alignment explanation
Indices: 9085--9121 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
9075 TTTATGCACC
9085 CAAAACATTTAT-
1 CAAAACATTTATA
9097 CAAAACATTT-TA
1 CAAAACATTTATA
*
9109 CAAAGCATTTATA
1 CAAAACATTTATA
9122 TTAAAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 1 0.05
12 19 0.86
13 2 0.09
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (13 bp):
CAAAACATTTATA
Found at i:10226 original size:24 final size:23
Alignment explanation
Indices: 10194--10239 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
10184 ATTTCTTATT
10194 TTCCTTTTTCTCTTTCATTTTCTC
1 TTCCTTTTTCTCTTTC-TTTTCTC
*
10218 TTCCTTTTTCTTTTTCTTTTCT
1 TTCCTTTTTCTCTTTCTTTTCT
10240 TTATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (23 bp):
TTCCTTTTTCTCTTTCTTTTCTC
Found at i:11210 original size:6 final size:6
Alignment explanation
Indices: 11201--11245 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
11191 AAAAAAAGAA
*
11201 AAAAAG AAAAAGG AAAAAG -AAAAG AGAAAAG GAAAAG AAAAAG AA
1 AAAAAG AAAAA-G AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AA
11246 GTTTATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 5 0.15
6 18 0.53
7 11 0.32
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:11223 original size:19 final size:18
Alignment explanation
Indices: 11201--11245 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
11191 AAAAAAAGAA
11201 AAAAAGAAAAAGGAAAA-
1 AAAAAGAAAAAGGAAAAG
11218 AGAAAAGAGAAAAGGAAAAG
1 A-AAAAGA-AAAAGGAAAAG
11238 AAAAAGAA
1 AAAAAGAA
11246 GTTTATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 7 0.28
19 16 0.64
20 1 0.04
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAGGAAAAG
Found at i:14122 original size:36 final size:38
Alignment explanation
Indices: 14059--14879 Score: 264
Period size: 45 Copynumber: 21.0 Consensus size: 38
14049 TCATGAATTA
* ** * *
14059 ATCAAAGAACTTAATTCAGTATTATTAAGTAAATACAGT
1 ATCAAAG-TCTTAATTCAGGGTAATTAAGTAAACACAGT
14098 -T-AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
1 ATCAAAGTCTTAATTCAGGGTAATT-----AAGTAAACACAGT
14139 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTT
1 -A-TCAAAGTCTTAATTCAGGGTAATT-----AAGTAAACACAG-T
*
14185 AGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
1 A-TCAAAGTCTTAATTCAGGGTAATT-----AAGTAAACACAGT
*
14229 CAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
1 -A-TCAAAGTCTTAATTCAGGGTAATT-----AAGTAAACACAGT
**
14274 CAGTCAAAGTCTTAATTCAGGGTAATTAAG-AGAAGCAAACACA
1 -A-TCAAAGTCTTAATTCAGGGTAATTAAGTA-AA-C--ACAGT
*
14317 ATCGAAGTCTTAATTCAGGGTAATTAAGAAAATCAAACACA-T
1 ATCAAAGTCTTAATTCAGGGTAATTAAG----T-AAACACAGT
* * *
14359 -TTAAAGTCTCAATT--TGGTAATTAAGAAAAGTAAACACAG-
1 ATCAAAGTCTTAATTCAGGGTAATT-----AAGTAAACACAGT
* * * *
14398 -TCATAGACCTAATTTAGGGTAATTAAGTAAACACA-T
1 ATCAAAGTCTTAATTCAGGGTAATTAAGTAAACACAGT
* * * *
14434 -T-AGAGAACTTAATTCAGAGTAATTAAGTAAA-AGCTGT
1 ATCAAAG-TCTTAATTCAGGGTAATTAAGTAAACA-CAGT
*
14471 A--AAAGACTTAATTCAGGGTAATTAAGT-AA-A-AGT
1 ATCAAAGTCTTAATTCAGGGTAATTAAGTAAACACAGT
* * ** *
14504 AGTTAAAGGACTT-ATT-----TAAGAAAGTTAAATACA--
1 A-TCAAA-GTCTTAATTCAGGGTAATTAAG-TAAACACAGT
* * * *
14537 ATTAAAGAACTTAATTCTGGGTAATTAAGTAAAAACAGT
1 ATCAAAG-TCTTAATTCAGGGTAATTAAGTAAACACAGT
14576 -T-AAAGTACTTAATTCAGGGTAATTAAGTAAA-ATCAG-
1 ATCAAAGT-CTTAATTCAGGGTAATTAAGTAAACA-CAGT
14612 -TC-AAGTACTTAATTCAGGGTAATTAAGTAAA-AGCAG-
1 ATCAAAGT-CTTAATTCAGGGTAATTAAGTAAACA-CAGT
* * * * *
14648 -T-AAAGAACTTAATTCAGGGCAATTAAGTAAAGAAAGC
1 ATCAAAG-TCTTAATTCAGGGTAATTAAGTAAACACAGT
* * * * *
14685 AGTTAAAGAACTTAATTCAGGGTAATTAAGTAAAGAAAGC
1 A-TCAAAG-TCTTAATTCAGGGTAATTAAGTAAACACAGT
* * * * * *
14725 AGTTAAAGAACTTAATTCATGGTAATTAAGTAAAGAAAGC
1 A-TCAAAG-TCTTAATTCAGGGTAATTAAGTAAACACAGT
* * * * * *
14765 AGTTAAAGAACTTAATTCAGGGTAATTTAGTAAATAAAGC
1 A-TCAAAG-TCTTAATTCAGGGTAATTAAGTAAACACAGT
**
14805 AGT-AAAGTACTTAATTCAGGCAAATTAAGTAAA-AGCAGT
1 A-TCAAAGT-CTTAATTCAGGGTAATTAAGTAAACA-CAGT
* * *
14844 -T-AAAATACTTAATTTAGGGTAATTAAGTAAGCACAG
1 ATCAAAGT-CTTAATTCAGGGTAATTAAGTAAACACAG
14880 ACTTAATTTC
Statistics
Matches: 662, Mismatches: 56, Indels: 130
0.78 0.07 0.15
Matches are distributed among these distances:
31 7 0.01
32 10 0.02
33 9 0.01
34 1 0.00
35 8 0.01
36 140 0.21
37 80 0.12
38 10 0.02
39 52 0.08
40 120 0.18
41 57 0.09
42 1 0.00
43 6 0.01
44 5 0.01
45 152 0.23
46 3 0.00
47 1 0.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (38 bp):
ATCAAAGTCTTAATTCAGGGTAATTAAGTAAACACAGT
Found at i:14155 original size:45 final size:45
Alignment explanation
Indices: 14094--14400 Score: 438
Period size: 45 Copynumber: 7.0 Consensus size: 45
14084 TAAGTAAATA
*
14094 CAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
1 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
14139 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
1 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
* *
14184 TAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
1 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
*
14229 CAGTCAAAATCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
1 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
* *
14274 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAGAAGCAAACACA--
1 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
*
14317 -A-TCGAAGTCTTAATTCAGGGTAATTAAGAAAA-TCAAACACA-T
1 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGT-AAACACAGT
* * *
14359 ---TTAAAGTCTCAATT--TGGTAATTAAGAAAAGTAAACACAGT
1 CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
14399 CA
1 CA
14401 TAGACCTAAT
Statistics
Matches: 242, Mismatches: 14, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
39 21 0.09
40 2 0.01
41 47 0.19
42 1 0.00
45 171 0.71
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (45 bp):
CAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGT
Found at i:14695 original size:40 final size:39
Alignment explanation
Indices: 14407--14873 Score: 475
Period size: 36 Copynumber: 12.5 Consensus size: 39
14397 GTCATAGACC
* * *
14407 TAATTTAGGGTAATTAAGT-AAACA-CA-TTAGAGAACT
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTTAAAGAACT
* * *
14443 TAATTCAGAGTAATTAAGT--AAAAGCTGTAAAAG-ACT
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTTAAAGAACT
* *
14479 TAATTCAGGGTAATTAAGT--AAAAGTAGTTAAAGGACT
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTTAAAGAACT
** * * *
14516 T-ATT-----TAAGAAAGTTAAATA-CAATTAAAGAACT
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTTAAAGAACT
* *
14548 TAATTCTGGGTAATTAAGT-AAAAA-CAGTTAAAGTACT
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTTAAAGAACT
* * *
14585 TAATTCAGGGTAATTAAGT--AAAATCAG-TCAAGTACT
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTTAAAGAACT
14621 TAATTCAGGGTAATTAAGT--AAAAGCAG-TAAAGAACT
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTTAAAGAACT
*
14657 TAATTCAGGGCAATTAAGTAAAGAAAGCAGTTAAAGAACT
1 TAATTCAGGGTAATTAAGTAAA-AAAGCAGTTAAAGAACT
14697 TAATTCAGGGTAATTAAGTAAAGAAAGCAGTTAAAGAACT
1 TAATTCAGGGTAATTAAGTAAA-AAAGCAGTTAAAGAACT
*
14737 TAATTCATGGTAATTAAGTAAAGAAAGCAGTTAAAGAACT
1 TAATTCAGGGTAATTAAGTAAA-AAAGCAGTTAAAGAACT
* *
14777 TAATTCAGGGTAATTTAGTAAATAAAGCAG-TAAAGTACT
1 TAATTCAGGGTAATTAAGTAAA-AAAGCAGTTAAAGAACT
**
14816 TAATTCAGGCAAATTAAGT--AAAAGCAGTTAAA-ATACT
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTTAAAGA-ACT
*
14853 TAATTTAGGGTAATTAAGTAA
1 TAATTCAGGGTAATTAAGTAA
14874 GCACAGACTT
Statistics
Matches: 371, Mismatches: 40, Indels: 37
0.83 0.09 0.08
Matches are distributed among these distances:
31 7 0.02
32 11 0.03
33 6 0.02
35 3 0.01
36 123 0.33
37 68 0.18
38 8 0.02
39 31 0.08
40 114 0.31
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (39 bp):
TAATTCAGGGTAATTAAGTAAAAAAGCAGTTAAAGAACT
Found at i:14756 original size:80 final size:75
Alignment explanation
Indices: 14407--14873 Score: 466
Period size: 80 Copynumber: 6.3 Consensus size: 75
14397 GTCATAGACC
* * * * * *
14407 TAATTTAGGGTAATTAAGT-AAACA-CATTAGAGAACTTAATTCAGAGTAATTAAGTAAAAGCTG
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAG
*
14470 TAAAAG-ACT
66 TTAAAGAACT
* * **
14479 TAATTCAGGGTAATTAAGT--AAAAGTAGTTAAAGGACTT-ATT-----TAAGAAAGTTAAATA-
1 TAATTCAGGGTAATTAAGTAAAAAAGCAG-TAAAGAACTTAATTCAGGGTAATTAAG-TAAA-AG
*
14535 CAATTAAAGAACT
63 CAGTTAAAGAACT
* * *
14548 TAATTCTGGGTAATTAAGT-AAAAA-CAGTTAAAGTACTTAATTCAGGGTAATTAAGTAAAATCA
1 TAATTCAGGGTAATTAAGTAAAAAAGCAG-TAAAGAACTTAATTCAGGGTAATTAAGTAAAAGCA
* *
14611 G-TCAAGTACT
65 GTTAAAGAACT
*
14621 TAATTCAGGGTAATTAAGT--AAAAGCAGTAAAGAACTTAATTCAGGGCAATTAAGTAAAGAAAG
1 TAATTCAGGGTAATTAAGTAAAAAAGCAGTAAAGAACTTAATTCAGGGTAATTAAGT--A-AAAG
14684 CAGTTAAAGAACT
63 CAGTTAAAGAACT
*
14697 TAATTCAGGGTAATTAAGTAAAGAAAGCAGTTAAAGAACTTAATTCATGGTAATTAAGTAAAGAA
1 TAATTCAGGGTAATTAAGTAAA-AAAGCAG-TAAAGAACTTAATTCAGGGTAATTAAGT--A-AA
14762 AGCAGTTAAAGAACT
61 AGCAGTTAAAGAACT
* * **
14777 TAATTCAGGGTAATTTAGTAAATAAAGCAGTAAAGTACTTAATTCAGGCAAATTAAGTAAAAGCA
1 TAATTCAGGGTAATTAAGTAAA-AAAGCAGTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGCA
14842 GTTAAA-ATACT
65 GTTAAAGA-ACT
*
14853 TAATTTAGGGTAATTAAGTAA
1 TAATTCAGGGTAATTAAGTAA
14874 GCACAGACTT
Statistics
Matches: 337, Mismatches: 35, Indels: 42
0.81 0.08 0.10
Matches are distributed among these distances:
67 6 0.02
68 10 0.03
69 34 0.10
70 7 0.02
71 3 0.01
72 52 0.15
73 37 0.11
74 7 0.02
75 13 0.04
76 60 0.18
77 1 0.00
78 1 0.00
79 31 0.09
80 75 0.22
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (75 bp):
TAATTCAGGGTAATTAAGTAAAAAAGCAGTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAG
TTAAAGAACT
Found at i:14917 original size:41 final size:41
Alignment explanation
Indices: 14872--15200 Score: 433
Period size: 41 Copynumber: 8.5 Consensus size: 41
14862 GTAATTAAGT
14872 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
*
14913 AAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTAAAGAC
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
* * *
14954 AAGCACAGACTTAA-TTC-A-G--GGTAATTAAGTAAAG-T
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
*
14989 GAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
15030 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
* * *
15071 AAGCACAGACTTAA-TTC-A-G--GGTAATTAAGTAAAG-T
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
15106 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
* * *
15147 AAGCACAGACTTAA-TTC-A-G--GGTAATTAAGTAAAG-T
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
15182 AAGCACAGACTTAATTTCA
1 AAGCACAGACTTAATTTCA
15201 CAAGAATTAA
Statistics
Matches: 255, Mismatches: 19, Indels: 32
0.83 0.06 0.10
Matches are distributed among these distances:
35 41 0.16
36 47 0.18
37 2 0.01
38 5 0.02
39 3 0.01
40 35 0.14
41 122 0.48
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (41 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
Found at i:14944 original size:76 final size:76
Alignment explanation
Indices: 14864--15200 Score: 348
Period size: 76 Copynumber: 4.4 Consensus size: 76
14854 AATTTAGGGT
14864 AATTAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
1 AATTAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAA-T
*
14929 TCAAGG-AAAGA
65 TCAAGGTAATGA
* * * **
14940 AATTAGGTAAAGACAAGCACAGACTTAA-TTC-A-G--GGTAATTAAGTAAAG-TGAGCACAGAC
1 AA-T---T-AAG-TAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
*
14999 TTAATTTCAAGG-AAGGA
60 TTAA-TTCAAGGTAATGA
*
15016 AATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
1 AA-T---T-AAG-TAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
* *
15081 TTAATTCAGGGTAATTA
60 TTAATTCAAGGTAATGA
* *
15098 AGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
1 AATTAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
* *
15163 CAGGGTAATTA
66 CAAGGTAATGA
* *
15174 AGTAAAGTAAGCACAGACTTAATTTCA
1 AATTAAGTAAGCACAGACTTAATTTCA
15201 CAAGAATTAA
Statistics
Matches: 232, Mismatches: 16, Indels: 26
0.85 0.06 0.09
Matches are distributed among these distances:
76 150 0.65
77 20 0.09
78 1 0.00
79 2 0.01
80 2 0.01
81 26 0.11
82 31 0.13
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.22
Consensus pattern (76 bp):
AATTAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
CAAGGTAATGA
Found at i:15012 original size:117 final size:115
Alignment explanation
Indices: 14850--15197 Score: 561
Period size: 117 Copynumber: 3.1 Consensus size: 115
14840 CAGTTAAAAT
*
14850 ACTTAATTTAGGGTAATTAAGT--A--AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG
1 ACTTAATTCAGGGTAATTAAGTAAAGTAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG
14911 ACAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTAAAGACAAGCACAG
66 ACAAGCACAGACTTAATTTCAAGG-AAGAAATTAGGTAAAGACAAGCACAG
14962 ACTTAATTCAGGGTAATTAAGTAAAGTGAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
1 ACTTAATTCAGGGTAATTAAGTAAAGT-AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
15027 GACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAG
65 GACAAGCACAGACTTAATTTCAAGGAA-GAAATTAGGTAAAGACAAGCACAG
15079 ACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
1 ACTTAATTCAGGGTAATTAAGTAAAGT-AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA
* * *
15144 GACAAGCACAGACTTAA-TTC-AGG--GTAATTAAGTAAAG-TAAGCACAG
65 GACAAGCACAGACTTAATTTCAAGGAAGAAATTAGGTAAAGACAAGCACAG
15190 ACTTAATT
1 ACTTAATT
15198 TCACAAGAAT
Statistics
Matches: 225, Mismatches: 5, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
111 16 0.07
112 33 0.15
114 1 0.00
115 3 0.01
116 5 0.02
117 167 0.74
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.23
Consensus pattern (115 bp):
ACTTAATTCAGGGTAATTAAGTAAAGTAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG
ACAAGCACAGACTTAATTTCAAGGAAGAAATTAGGTAAAGACAAGCACAG
Found at i:15228 original size:36 final size:34
Alignment explanation
Indices: 15169--15286 Score: 94
Period size: 36 Copynumber: 3.3 Consensus size: 34
15159 AATTCAGGGT
* * * * *
15169 AATTAAGTAAAGTAAGCACAGACTTAATTTCACAAG
1 AATTAAGTAAAATCAGTAAAGACTTAA-TCCA-AAG
15205 AATTAAGTAAAATCAGTAAAGACTTAATCCAAAG
1 AATTAAGTAAAATCAGTAAAGACTTAATCCAAAG
* * *
15239 ATGATTAAGTAAGATCAGTCAAA-ACTTAACCCAAGGG
1 A--ATTAAGTAAAATCAGT-AAAGACTTAATCCAA-AG
*
15276 GATTAAGTAAA
1 AATTAAGTAAA
15287 GCACAGACTT
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
34 4 0.06
35 12 0.18
36 48 0.71
37 4 0.06
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (34 bp):
AATTAAGTAAAATCAGTAAAGACTTAATCCAAAG
Found at i:15333 original size:37 final size:37
Alignment explanation
Indices: 15292--15391 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 37
15282 GTAAAGCACA
* **
15292 GACTTGATTCCAAGGAAGGGAATTATGTAGAGTTAAG
1 GACTTAATTCCAAGGAAGGGAATTAAATAGAGTTAAG
* * *
15329 GACTTAATTCTAAGGAAGCGAAATAAATAGAGTTAAG
1 GACTTAATTCCAAGGAAGGGAATTAAATAGAGTTAAG
* * *
15366 GACTTAATTTCAAGTAAGGAAATTAA
1 GACTTAATTCCAAGGAAGGGAATTAA
15392 GTCAAGTTAG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (37 bp):
GACTTAATTCCAAGGAAGGGAATTAAATAGAGTTAAG
Found at i:15423 original size:32 final size:32
Alignment explanation
Indices: 15386--15457 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
15376 CAAGTAAGGA
15386 AATTAAGTCAAGT-TAGGG-GCTTAATTCAGGGT
1 AATTAAGTCAAGTCT-GGGAG-TTAATTCAGGGT
* *
15418 GATTAAGTCAGGTCTGGGAGTTAATTCAGGGT
1 AATTAAGTCAAGTCTGGGAGTTAATTCAGGGT
15450 AATTAAGT
1 AATTAAGT
15458 AGTGTCAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (32 bp):
AATTAAGTCAAGTCTGGGAGTTAATTCAGGGT
Found at i:15479 original size:37 final size:37
Alignment explanation
Indices: 15433--15551 Score: 154
Period size: 36 Copynumber: 3.3 Consensus size: 37
15423 AGTCAGGTCT
* *
15433 GGGAGTTAATTCAGGGTAATTAAGTAGTGTCAATAAA
1 GGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
*
15470 GGGACTTAATTCAGGGTAATTAAGCAGCGTCAAT-AA
1 GGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
* *
15506 GGGACTTAATTCAAGGTAATTAAGT-GGGATCAATAAA
1 GGGACTTAATTCAGGGTAATTAAGTAGCG-TCAATAAA
*
15543 -GAACTTAAT
1 GGGACTTAAT
15552 CTAAAAAGAG
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 2 0.03
36 38 0.52
37 33 0.45
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (37 bp):
GGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
Found at i:15515 original size:36 final size:35
Alignment explanation
Indices: 15400--15529 Score: 151
Period size: 37 Copynumber: 3.7 Consensus size: 35
15390 AAGTCAAGTT
* *
15400 AGGGGCTTAATTCAGGGTGATTAAGTCAGGTC--T-
1 AGGGACTTAATTCAGGGTAATTAAG-CAGGTCAATA
* *
15433 -GGGAGTTAATTCAGGGTAATTAAGTAGTGTCAATAA
1 AGGGACTTAATTCAGGGTAATTAAGCAG-GTCAAT-A
15469 AGGGACTTAATTCAGGGTAATTAAGCAGCGTCAATA
1 AGGGACTTAATTCAGGGTAATTAAGCAG-GTCAATA
*
15505 AGGGACTTAATTCAAGGTAATTAAG
1 AGGGACTTAATTCAGGGTAATTAAG
15530 TGGGATCAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
31 2 0.02
32 24 0.29
34 1 0.01
36 25 0.30
37 31 0.37
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (35 bp):
AGGGACTTAATTCAGGGTAATTAAGCAGGTCAATA
Found at i:15539 original size:73 final size:69
Alignment explanation
Indices: 15400--15551 Score: 175
Period size: 73 Copynumber: 2.2 Consensus size: 69
15390 AAGTCAAGTT
* * * * *
15400 AGGGGCTTAATTCAGGGTGATTAAGTCAGGTCTGGGAGTTAATTCAGGGTAATTAAGTAGTGTCA
1 AGGGACTTAATTCAGGGTAATTAAGTCAGGTCTGGGACTTAATTCAAGGTAATTAAGTAGGGTCA
15465 ATAA
66 ATAA
15469 AGGGACTTAATTCAGGGTAATTAAG-CAGCGTCAATAAGGGACTTAATTCAAGGTAATTAAGT-G
1 AGGGACTTAATTCAGGGTAATTAAGTCAG-GTC--T--GGGACTTAATTCAAGGTAATTAAGTAG
15532 GGATCAATAA
61 GG-TCAATAA
*
15542 A-GAACTTAAT
1 AGGGACTTAAT
15552 CTAAAAAGAG
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
68 3 0.04
69 26 0.37
71 1 0.01
72 10 0.14
73 31 0.44
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (69 bp):
AGGGACTTAATTCAGGGTAATTAAGTCAGGTCTGGGACTTAATTCAAGGTAATTAAGTAGGGTCA
ATAA
Found at i:16243 original size:19 final size:19
Alignment explanation
Indices: 16219--16261 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
16209 CACCCTTACT
*
16219 CCAAATTTTACTTTATATC
1 CCAAATTTTAATTTATATC
16238 CCAAATTTTAATTTATATC
1 CCAAATTTTAATTTATATC
*
16257 TCAAA
1 CCAAA
16262 AGTAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (19 bp):
CCAAATTTTAATTTATATC
Found at i:18198 original size:19 final size:19
Alignment explanation
Indices: 18174--18216 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
18164 CACCCTTACT
18174 CCAAATTTTAATTTATATC
1 CCAAATTTTAATTTATATC
18193 CCAAATTTTAATTTATATC
1 CCAAATTTTAATTTATATC
*
18212 TCAAA
1 CCAAA
18217 AGTAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (19 bp):
CCAAATTTTAATTTATATC
Found at i:18224 original size:19 final size:19
Alignment explanation
Indices: 18183--18225 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
18173 TCCAAATTTT
** *
18183 AATTTATATCCCAAATTTT
1 AATTTATATCCCAAAAGTA
*
18202 AATTTATATCTCAAAAGTA
1 AATTTATATCCCAAAAGTA
18221 AATTT
1 AATTT
18226 TATGGTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (19 bp):
AATTTATATCCCAAAAGTA
Done.