Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022887.1 Corchorus olitorius cultivar O-4 contig22920, 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: 37135
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:3877 original size:26 final size:26
Alignment explanation
Indices: 3841--3929 Score: 144
Period size: 26 Copynumber: 3.4 Consensus size: 26
3831 TTAAGTTAAA
* *
3841 AAGAGTTAAAATGGTATTCACTAATT
1 AAGAGTAAAAATGGTATTCAGTAATT
3867 AAGAGTAAAAATGGTATTCAGTAATT
1 AAGAGTAAAAATGGTATTCAGTAATT
3893 AAGAGTAAAAATGGTATTCAGTAATT
1 AAGAGTAAAAATGGTATTCAGTAATT
3919 AA-AGTTAAAAA
1 AAGAG-TAAAAA
3930 GAGTAAAGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 2 0.03
26 58 0.97
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (26 bp):
AAGAGTAAAAATGGTATTCAGTAATT
Found at i:3942 original size:35 final size:35
Alignment explanation
Indices: 3893--4149 Score: 365
Period size: 35 Copynumber: 7.3 Consensus size: 35
3883 TTCAGTAATT
3893 AAGAGTAAAAATGGTATTCAGTAATTAAAGTTAAA
1 AAGAGTAAAAATGGTATTCAGTAATTAAAGTTAAA
* *
3928 AAGAGTAAAGATGGTATTCAGTAATTAAAGATAAA
1 AAGAGTAAAAATGGTATTCAGTAATTAAAGTTAAA
*
3963 AAGAGTAAAAATGGTATTCAGTAATTATAGTTAAA
1 AAGAGTAAAAATGGTATTCAGTAATTAAAGTTAAA
* *
3998 AAGAATAAAAATGGTATTCAGTAATTAAAGATAAA
1 AAGAGTAAAAATGGTATTCAGTAATTAAAGTTAAA
4033 AAGAGTAAAAA-GGATATTCAGTAATTAAAGTTAAA
1 AAGAGTAAAAATGG-TATTCAGTAATTAAAGTTAAA
* *
4068 GAA-AGTAAAAATGAGGTATTCGGTAATTAGAGTTAAA
1 -AAGAGTAAAAAT--GGTATTCAGTAATTAAAGTTAAA
* **
4105 AAGAGTAAAAATGGTATTTAGTAATTGGAGTTAAA
1 AAGAGTAAAAATGGTATTCAGTAATTAAAGTTAAA
4140 AAGGAGTAAA
1 AA-GAGTAAA
4150 CAATATTGTT
Statistics
Matches: 200, Mismatches: 15, Indels: 13
0.88 0.07 0.06
Matches are distributed among these distances:
34 2 0.01
35 157 0.79
36 11 0.05
37 28 0.14
38 2 0.01
ACGTcount: A:0.51, C:0.02, G:0.19, T:0.27
Consensus pattern (35 bp):
AAGAGTAAAAATGGTATTCAGTAATTAAAGTTAAA
Found at i:4465 original size:36 final size:35
Alignment explanation
Indices: 4371--4870 Score: 610
Period size: 35 Copynumber: 14.0 Consensus size: 35
4361 AGTAAAAGGG
*
4371 CAGTAATTAAGTTAAAATGAGTAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAAT
*
4406 CAGTAGTTGAA-TTAAAAAGGAGTAAAAAAATGGTAAT
1 CAGTAATT-AAGTTAAAAA-GAGT-AAAAAATGGTAAT
* *
4443 TAGTAATTAAGCTAAAAAGAGTAAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAAGAGT-AAAAAATGGTAAT
* *
4479 CAGTAGTTGAGTTAAAAAGGAGTAAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAA-GAGT-AAAAAATGGTAAT
4516 CAGTAATTAAGTTAAAAAGAGTAAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAAGAGT-AAAAAATGGTAAT
*
4552 CAGTAATTAAGTTAGAAAGAGTAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAAT
* * *
4587 CAGCAATTAAATTAAAAGGAGTAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAAT
*
4622 CAGTAATTAAGTTAGAAAGAGTAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAAT
* * * * *
4657 AAGCAATTTAGTTAAAAGGAGT-AAAAATAGTAAT
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAAT
* * * * *
4691 CAATAGTTGAGTTAGAAAGAATAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAAT
* *
4726 CAGCAATTAAGTT-AAAAGAAGTAAAAAAAGGGTAAT
1 CAGTAATTAAGTTAAAAAG-AGT-AAAAAATGGTAAT
* *
4762 CAGTAATCAAGTTAAGAAAGGAGTAAAAAATAGTAAT
1 CAGTAATTAAGTTAA-AAA-GAGTAAAAAATGGTAAT
*
4799 CAGTAGTTAAGTTAAAAAGAGTAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAAT
* *
4834 CAGTAATCAAGTTAAAAAGACTAAAAAAAATGGTAAT
1 CAGTAATTAAGTTAAAAAGAGT--AAAAAATGGTAAT
4871 AAGTTATTGG
Statistics
Matches: 400, Mismatches: 52, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
34 29 0.07
35 162 0.41
36 105 0.26
37 97 0.24
38 6 0.01
39 1 0.00
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.24
Consensus pattern (35 bp):
CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAAT
Found at i:4494 original size:73 final size:70
Alignment explanation
Indices: 4371--4870 Score: 610
Period size: 73 Copynumber: 7.0 Consensus size: 70
4361 AGTAAAAGGG
* *
4371 CAGTAATTAAGTTAAAATGAGTAAAAAATGGTAATCAGTAGTTGAA-TTAAAAAGGAGTAAAAAA
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCAGTAATT-AAGTTAAAAA-GAGT-AAAAA
4435 ATGGTAAT
63 ATGGTAAT
* * * *
4443 TAGTAATTAAGCTAAAAAGAGTAAAAAAATGGTAATCAGTAGTTGAGTTAAAAAGGAGTAAAAAA
1 CAGTAATTAAGTTAAAAAGAGT-AAAAAATGGTAATCAGTAATTAAGTTAAAAA-GAGT-AAAAA
4508 ATGGTAAT
63 ATGGTAAT
*
4516 CAGTAATTAAGTTAAAAAGAGTAAAAAAATGGTAATCAGTAATTAAGTTAGAAAGAGTAAAAAAT
1 CAGTAATTAAGTTAAAAAGAGT-AAAAAATGGTAATCAGTAATTAAGTTAAAAAGAGTAAAAAAT
4581 GGTAAT
65 GGTAAT
* * * *
4587 CAGCAATTAAATTAAAAGGAGTAAAAAATGGTAATCAGTAATTAAGTTAGAAAGAGTAAAAAATG
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCAGTAATTAAGTTAAAAAGAGTAAAAAATG
4652 GTAAT
66 GTAAT
* * * * * * * * * *
4657 AAGCAATTTAGTTAAAAGGAGT-AAAAATAGTAATCAATAGTTGAGTTAGAAAGAATAAAAAATG
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCAGTAATTAAGTTAAAAAGAGTAAAAAATG
4721 GTAAT
66 GTAAT
* * *
4726 CAGCAATTAAGTT-AAAAGAAGTAAAAAAAGGGTAATCAGTAATCAAGTTAAGAAAGGAGTAAAA
1 CAGTAATTAAGTTAAAAAG-AGT-AAAAAATGGTAATCAGTAATTAAGTTAA-AAA-GAGTAAAA
*
4790 AATAGTAAT
62 AATGGTAAT
* * *
4799 CAGTAGTTAAGTTAAAAAGAGTAAAAAATGGTAATCAGTAATCAAGTTAAAAAGACTAAAAAAAA
1 CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCAGTAATTAAGTTAAAAAGAGT--AAAAAA
4864 TGGTAAT
64 TGGTAAT
4871 AAGTTATTGG
Statistics
Matches: 381, Mismatches: 37, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
68 4 0.01
69 56 0.15
70 70 0.18
71 55 0.14
72 66 0.17
73 125 0.33
74 5 0.01
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.24
Consensus pattern (70 bp):
CAGTAATTAAGTTAAAAAGAGTAAAAAATGGTAATCAGTAATTAAGTTAAAAAGAGTAAAAAATG
GTAAT
Found at i:5046 original size:57 final size:57
Alignment explanation
Indices: 4924--5083 Score: 205
Period size: 57 Copynumber: 2.8 Consensus size: 57
4914 AAATGGCGAT
** * * *
4924 TAGTAATGGGCTTAATTCAGAATAATTAAGTTAA-AAAAAAGTAAAAAAAAAATCAA
1 TAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAAAAAAATCAA
* * * ** *
4980 TAGTAATTAGCTTATTTCAGAGCAATTAAGTTAATCAAGAAGTAAATAAGCAATCAG
1 TAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAAAAAAATCAA
*
5037 TAGTAATTAGCATAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAA
1 TAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAA
5084 GGGTAATCAA
Statistics
Matches: 88, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
56 29 0.33
57 59 0.67
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.28
Consensus pattern (57 bp):
TAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAAAAAAATCAA
Found at i:5071 original size:19 final size:20
Alignment explanation
Indices: 4981--5081 Score: 56
Period size: 19 Copynumber: 5.2 Consensus size: 20
4971 AAAAATCAAT
*
4981 AGTAATT-AGCTTATTTCAG-
1 AGTAATTAAG-TTAATTCAGA
*
5000 AGCAATTAAGTTAA-TCAAGA
1 AGTAATTAAGTTAATTC-AGA
* * *
5020 AGTAAATAAG-CAA-TCAGT
1 AGTAATTAAGTTAATTCAGA
*
5038 AGTAATT-AGCATAATTCAG-
1 AGTAATTAAG-TTAATTCAGA
5057 AGTAATTAAGTTAA-TCAAGA
1 AGTAATTAAGTTAATTC-AGA
5077 AGTAA
1 AGTAA
5082 AAGGGTAATC
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
17 2 0.03
18 12 0.19
19 29 0.45
20 21 0.33
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.30
Consensus pattern (20 bp):
AGTAATTAAGTTAATTCAGA
Found at i:6328 original size:21 final size:20
Alignment explanation
Indices: 6295--6337 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
6285 TTGAGAAGAA
6295 AAAAAGAAGAAACAGGAAAAG
1 AAAAAGAAGAAAC-GGAAAAG
* * *
6316 AAAAAGTATAAACGTAAAAG
1 AAAAAGAAGAAACGGAAAAG
6336 AA
1 AA
6338 CAACAAGTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.70, C:0.05, G:0.19, T:0.07
Consensus pattern (20 bp):
AAAAAGAAGAAACGGAAAAG
Found at i:8330 original size:27 final size:28
Alignment explanation
Indices: 8289--8344 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
8279 TTTAAATATG
* * *
8289 TTTTTTTGATTGT-AAATTTTGTTGCTC
1 TTTTTTTAATGGTAAAATTTTATTGCTC
8316 TTTTTTTAATGGTAAAATTTTATTGCTC
1 TTTTTTTAATGGTAAAATTTTATTGCTC
8344 T
1 T
8345 ACAATAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.61
Consensus pattern (28 bp):
TTTTTTTAATGGTAAAATTTTATTGCTC
Found at i:12768 original size:33 final size:30
Alignment explanation
Indices: 12692--12770 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
12682 TGACCTAAAC
* *
12692 GTGTAAGTAGAAGGACTAAATTGATCTTTT
1 GTGTAAGTAGAGGGACCAAATTGATCTTTT
* *
12722 GT-TTAGTAGAGGGACCAAATTGATATTTTTT
1 GTGTAAGTAGAGGGACCAAATTG--ATCTTTT
12753 AGTGTAAGTAGAGGGACC
1 -GTGTAAGTAGAGGGACC
12771 TGCTAGGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 17 0.43
30 2 0.05
31 6 0.15
32 2 0.05
33 13 0.32
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.34
Consensus pattern (30 bp):
GTGTAAGTAGAGGGACCAAATTGATCTTTT
Found at i:26742 original size:22 final size:22
Alignment explanation
Indices: 26695--26745 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
26685 AAGAGACAAT
* *
26695 AGTCAAGAATGGGTAAAGAAGA
1 AGTCAAGAAAGGATAAAGAAGA
*
26717 AGTCAAGAAAGGATAGATGAAG-
1 AGTCAAGAAAGGATA-AAGAAGA
26739 AGTCAAG
1 AGTCAAG
26746 TATAGGTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.49, C:0.06, G:0.31, T:0.14
Consensus pattern (22 bp):
AGTCAAGAAAGGATAAAGAAGA
Found at i:26871 original size:54 final size:54
Alignment explanation
Indices: 26809--26924 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
26799 CGATCTTTTA
* *
26809 AAGTTTTCAGAGATTTAAACAGATCTTAAGATGACCCAGTGTAATCCTTCATAG
1 AAGTTTTCAGAGATCTAAACAGATCATAAGATGACCCAGTGTAATCCTTCATAG
* ** **
26863 AAGTTTTCAGAGATCTAAACAGATCATAAGATGACCTAGTGTGGTTTTTCATAG
1 AAGTTTTCAGAGATCTAAACAGATCATAAGATGACCCAGTGTAATCCTTCATAG
26917 AAGTTTTC
1 AAGTTTTC
26925 GATGATCAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (54 bp):
AAGTTTTCAGAGATCTAAACAGATCATAAGATGACCCAGTGTAATCCTTCATAG
Found at i:26954 original size:35 final size:35
Alignment explanation
Indices: 26909--27290 Score: 597
Period size: 35 Copynumber: 10.9 Consensus size: 35
26899 TAGTGTGGTT
26909 TTTCATAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCA-AGAAGTTTTCGATGATCAGAGTTGATCTCG
* *
26945 TTTCAAGAAGTTTTCAATTATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
*
26980 TTTTAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
* *
27015 TTTCAATAAGTTTTCGATGAT-TGAAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAG-AGTTGATCTCG
* *
27050 TTTCAAGAAATTTTCGATAATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
*
27085 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
*
27120 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
* * * *
27155 TTTCAAGAAGTTTTGGAAGATCATAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
*
27190 TTTCAAGAAGTTTTCGATGATCAAAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
*
27225 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
27260 TTTCAAGAAGTTTT-GATGATCAGAGTTGATC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATC
27291 CCTAAATGAT
Statistics
Matches: 320, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
34 18 0.06
35 296 0.93
36 6 0.02
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
Found at i:27318 original size:53 final size:53
Alignment explanation
Indices: 27263--27900 Score: 657
Period size: 53 Copynumber: 11.9 Consensus size: 53
27253 GATCTCCTTT
* *
27263 CAAGAAGTTTT-GATGATCAGAGTTGATCCCTAAATGATCCAGTGCGGTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTC
* ** * * * * *
27316 CAAGAAATTTTCTTTGATTAGAGTTTATCTCAGAT-AACCAGTGCGATCATTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTC
* * * * *
27368 CAAAAAGTTTTC-AGTGATCAGAGCTGATCCCAGATGATTCAGTGTGGTCATTT
1 CAAGAAGTTTTCGA-TGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTC
* ** *
27421 CAACAAGTTTTCTTTGATCAGAGTTGATCCTAGATGA-CCGAGTGCGGTCATTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCCCAGATGATCC-AGTGCGGTCATTC
* * *
27474 CAAGAGGTTTCTAGA-GATCAGAGTTGATCCCTAGATGATCCAGTGCAGTCATTC
1 CAAGAAGTTT-TCGATGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTC
* * * *
27528 CAAAGAAGTTTTCAATGATCAGAGTTGATTCCCAGATGATCTAGTGCGGCCATTT
1 C-AAGAAGTTTTCGATGATCAGAGTTGA-TCCCAGATGATCCAGTGCGGTCATTC
*
27583 GAAGAAGTTTTC-AGTGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTC
1 CAAGAAGTTTTCGA-TGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTC
* * * *
27636 CAAGAAGTTTTCGTTGATCAGAGTTGATCCCAAATGATGCAGTGCAGTCATTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTC
** * * *
27689 CAAGAAGTTTTTAATGATCAAAGTTGATCTCCAGATTATCCAGTGCGGTCGTTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTC
* * ** *
27743 TAAGAAGTTTTTC-ATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTTGTTT
1 CAAGAAG-TTTTCGATGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTC
* *
27797 CAAGAAGTTTTCGATGATCAGAGTTGATCTCCA-ATTGATCTAGTGCGGTCGTTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATC-CCAGA-TGATCCAGTGCGGTCATTC
* *
27851 CAAGAAG-TTTCGATGATCAAAGTTAATCTCCA-ATTTGATCCAGTGCGGTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATC-CCAGA--TGATCCAGTGCGGTC
27901 GTTTTAAGGA
Statistics
Matches: 491, Mismatches: 76, Indels: 35
0.82 0.13 0.06
Matches are distributed among these distances:
52 42 0.09
53 217 0.44
54 184 0.37
55 44 0.09
56 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (53 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTC
Found at i:27646 original size:215 final size:211
Alignment explanation
Indices: 27263--27883 Score: 700
Period size: 215 Copynumber: 2.9 Consensus size: 211
27253 GATCTCCTTT
* * *
27263 CAAGAAGTTT-TGATGATCAGAGTTGATCCCTAAATGATCCAGTGCGGTCATTTCAAGAAATTTT
1 CAAGAAGTTTCTAATGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCA-TTCAAGAAGTTTT
* * * * * * * *
27327 CTTTGATTAGAGTTTATCTCAGAT-AACCAGTGCGATCATTCCAAAAAGTTTTCAGTGATCAGAG
65 C-ATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAGTGATCAGAG
* * * * * * * *
27391 CTGATCCCAGATGATTCAGTGTGGTCATTTCAACAAGTTTTCTTTGATCAGAGTTGATCCTAGAT
129 TTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGTTGATCAGAGTTGATCCCAAAT
*
27456 GAC-CGAGTGCGGTCATTC
194 GACGC-AGTGCAGTCATTC
* *
27474 CAAGAGGTTTCTAGA-GATCAGAGTTGATCCCTAGATGATCCAGTGCAGTCATTCCAAAGAAGTT
1 CAAGAAGTTTCTA-ATGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATT-C-AAGAAGTT
* * *
27538 TTCAATGATCAGAGTTGATTCCCAGATGATCTAGTGCGGCCATTTGAAGAAGTTTTCAGTGATCA
63 TTC-ATGATCAGAGTTGA-TCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAGTGATCA
27603 GAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGTTGATCAGAGTTGATCCCA
126 GAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGTTGATCAGAGTTGATCCCA
*
27668 AATGATGCAGTGCAGTCATTC
191 AATGACGCAGTGCAGTCATTC
* * * *
27689 CAAGAAGTTTTTAATGATCAAAGTTGATCTCC-AGATTATCCAGTGCGGTCGTTCTAAGAAGTTT
1 CAAGAAGTTTCTAATGATCAGAGTTGATC-CCTAGATGATCCAGTGCGGTCATTC-AAGAAG-TT
* **
27753 TTCATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTTGTTTCAAGAAGTTTTC-GATGATCA
63 TTCATGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAG-TGATCA
* * * * *
27817 GAGTTGATCTCCA-ATTGATCTAGTGCGGTCGTTCCAAGAAG-TTTCGATGATCAAAGTTAATCT
126 GAGTTGATC-CCAGA-TGATCCAGTGCGGTCATTCCAAGAAGTTTTCGTTGATCAGAGTTGATC-
27880 CCAA
188 CCAA
27884 TTTGATCCAG
Statistics
Matches: 350, Mismatches: 45, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
211 11 0.03
212 36 0.10
213 25 0.07
214 93 0.27
215 182 0.52
216 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (211 bp):
CAAGAAGTTTCTAATGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCAAGAAGTTTTC
ATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCAGTGATCAGAGTT
GATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGTTGATCAGAGTTGATCCCAAATGA
CGCAGTGCAGTCATTC
Found at i:27890 original size:108 final size:107
Alignment explanation
Indices: 27260--27904 Score: 554
Period size: 108 Copynumber: 6.0 Consensus size: 107
27250 GTTGATCTCC
* * * * *
27260 TTTCAAGAAGTTTTGATGATCAGAGTTGATC-CCTA-AATGATCCAGTGCGGTCATTTCAAGAAA
1 TTTCAAGAAGTTTTCATGATCAGAGTTGATCTCC-AGATTGATCCAGTGCGGTCGTTCCAAGAAG
** * * * * *
27323 TTTTCTTTGATTAGAGTTTATCT-CAGAT-AACCAGTGCGATCA
65 TTTTCGATGATCAGAGTTGATCTCCA-ATGATCCAGTGCGGTCG
* * * * * * * *
27365 TTCCAAAAAGTTTTCAGTGATCAGAGCTGATC-CCAGA-TGATTCAGTGTGGTCATTTCAACAAG
1 TTTCAAGAAGTTTTCA-TGATCAGAGTTGATCTCCAGATTGATCCAGTGCGGTCGTTCCAAGAAG
** * *
27428 TTTTCTTTGATCAGAGTTGATC-CTAGATGA-CCGAGTGCGGTCA
65 TTTTCGATGATCAGAGTTGATCTCCA-ATGATCC-AGTGCGGTCG
* * * * *
27471 TTCCAAG-AGGTTTCTAGAGATCAGAGTTGATC-CCTAGA-TGATCCAGTGCAGTCATTCCAAAG
1 TTTCAAGAAGTTTTC-A-TGATCAGAGTTGATCTCC-AGATTGATCCAGTGCGGTCGTTCC-AAG
* * * *
27533 AAGTTTTCAATGATCAGAGTTGAT-TCCCAGATGATCTAGTGCGGCCA
62 AAGTTTTCGATGATCAGAGTTGATCT-CCA-ATGATCCAGTGCGGTCG
* *
27580 TTTGAAGAAGTTTTCAGTGATCAGAGTTGATC-CCAGA-TGATCCAGTGCGGTCATTCCAAGAAG
1 TTTCAAGAAGTTTTCA-TGATCAGAGTTGATCTCCAGATTGATCCAGTGCGGTCGTTCCAAGAAG
* * * *
27643 TTTTCGTTGATCAGAGTTGATC-CCAAATGATGCAGTGCAGTCA
65 TTTTCGATGATCAGAGTTGATCTCC-AATGATCCAGTGCGGTCG
* * * *
27686 TTCCAAGAAGTTTTTAATGATCAAAGTTGATCTCCAGATT-ATCCAGTGCGGTCGTTCTAAGAAG
1 TTTCAAGAAG-TTTTCATGATCAGAGTTGATCTCCAGATTGATCCAGTGCGGTCGTTCCAAGAAG
* *
27750 TTTTTC-ATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTTG
65 -TTTTCGATGATCAGAGTTGATCTCCA-ATGATCCAGTGCGGTCG
*
27794 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCCA-ATTGATCTAGTGCGGTCGTTCCAAGAAG
1 TTTCAAGAAGTTTTC-ATGATCAGAGTTGATCTCCAGATTGATCCAGTGCGGTCGTTCCAAGAAG
* *
27858 -TTTCGATGATCAAAGTTAATCTCCAATTTGATCCAGTGCGGTCG
65 TTTTCGATGATCAGAGTTGATCTCCAA--TGATCCAGTGCGGTCG
27902 TTT
1 TTT
27905 TAAGGAAAGT
Statistics
Matches: 457, Mismatches: 58, Indels: 47
0.81 0.10 0.08
Matches are distributed among these distances:
105 68 0.15
106 92 0.20
107 118 0.26
108 133 0.29
109 39 0.09
110 7 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (107 bp):
TTTCAAGAAGTTTTCATGATCAGAGTTGATCTCCAGATTGATCCAGTGCGGTCGTTCCAAGAAGT
TTTCGATGATCAGAGTTGATCTCCAATGATCCAGTGCGGTCG
Found at i:30430 original size:6 final size:6
Alignment explanation
Indices: 30407--30442 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
30397 CACAGTATAA
* *
30407 ATAGAT ATAGTT ACAGAT ATAGAT ATAGAT ATAGAT
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT
30443 GTGTTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (6 bp):
ATAGAT
Found at i:36073 original size:2 final size:2
Alignment explanation
Indices: 36068--36092 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36058 AAATTACTAC
36068 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
36093 GTTTCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.