Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024582.1 Corchorus olitorius cultivar O-4 contig24615, 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: 56497
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2155 original size:135 final size:135
Alignment explanation
Indices: 1913--2183 Score: 533
Period size: 135 Copynumber: 2.0 Consensus size: 135
1903 TTGAGTATAT
1913 TAGATTTGGGCCCAAAGCCCACTAGCCAATGGAGGCCCAGGCCTCATACAAGGTATATATATAGC
1 TAGATTTGGGCCCAAAGCCCACTAGCCAATGGAGGCCCAGGCCTCATACAAGGTATATATATAGC
1978 CAAGGTATGGCTCATAAACTCAGAACATAATATATGAGGAGAGAGCACAAGCTCACATAGAGGCT
66 CAAGGTATGGCTCATAAACTCAGAACATAATATATGAGGAGAGAGCACAAGCTCACATAGAGGCT
2043 TAGAC
131 TAGAC
*
2048 TAGATTTGGGCCCAAAGCCCACTAGCCATTGGAGGCCCAGGCCTCATACAAGGTATATATATAGC
1 TAGATTTGGGCCCAAAGCCCACTAGCCAATGGAGGCCCAGGCCTCATACAAGGTATATATATAGC
2113 CAAGGTATGGCTCATAAACTCAGAACATAATATATGAGGAGAGAGCACAAGCTCACATAGAGGCT
66 CAAGGTATGGCTCATAAACTCAGAACATAATATATGAGGAGAGAGCACAAGCTCACATAGAGGCT
2178 TAGAC
131 TAGAC
2183 T
1 T
2184 CTCTAACTCT
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 135 1.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (135 bp):
TAGATTTGGGCCCAAAGCCCACTAGCCAATGGAGGCCCAGGCCTCATACAAGGTATATATATAGC
CAAGGTATGGCTCATAAACTCAGAACATAATATATGAGGAGAGAGCACAAGCTCACATAGAGGCT
TAGAC
Found at i:2689 original size:2 final size:2
Alignment explanation
Indices: 2682--2706 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2672 GTCGCCGCTG
2682 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2707 AAATCATGCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2900 original size:58 final size:59
Alignment explanation
Indices: 2810--3000 Score: 251
Period size: 58 Copynumber: 3.3 Consensus size: 59
2800 CAAGAACGAC
** * * *
2810 CGAGCATCCCTCGGTCACACGACTTAGTGGGCATCCCCCACTCATGCAATAAG-AAAAT
1 CGAGCATCCCTCGGTCACACGACCCAATGGGCATCCCCCACTCACGCAAAAAGAAAAAT
* **
2868 CGAGCATCCCTCAGTCACACGACCCAATGGGCATCCCCCACTTGCGCAAAAAGAAAAAT
1 CGAGCATCCCTCGGTCACACGACCCAATGGGCATCCCCCACTCACGCAAAAAGAAAAAT
* ** *
2927 -GAGCATCCCTCGGTCACACAACCCAATGGGCATCCCCCACTTGCGCAAAAAGAAAAAA
1 CGAGCATCCCTCGGTCACACGACCCAATGGGCATCCCCCACTCACGCAAAAAGAAAAAT
*
2985 AGAGCATCCCTCGGTC
1 CGAGCATCCCTCGGTC
3001 GTACAACCTA
Statistics
Matches: 120, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
58 100 0.83
59 20 0.17
ACGTcount: A:0.32, C:0.35, G:0.18, T:0.15
Consensus pattern (59 bp):
CGAGCATCCCTCGGTCACACGACCCAATGGGCATCCCCCACTCACGCAAAAAGAAAAAT
Found at i:4106 original size:86 final size:84
Alignment explanation
Indices: 3789--4912 Score: 321
Period size: 83 Copynumber: 13.5 Consensus size: 84
3779 TCCAAGCTCT
* * * * *
3789 CGAAGTGGTAGTACGC-CTCAAAGTTCGCGAAAT-GGTAGTACACCCTCCAAGCTCTCGAAGTGG
1 CGAAGTGGTAGTACGCTCCCAAAGCTCGCG-AATCGGTAGAACCCCCTCCAAGCTCTCGAGGTGG
* * ***
3852 TAGTACGC-CTCAAAGTTCG
65 TAGTACACTCCCAAAGAGAG
* * * * * * * * * **
3871 CGAAATGGTAGTACAC-CCTCCAAGCTCTCGAAGT-GGTAGTA-CGCCTCAAAGTTCGCGAAATG
1 CGAAGTGGTAGTACGCTCC-CAAAGCTCGCGAA-TCGGTAGAACCCCCTCCAAGCTCTCGAGGTG
* * ****
3933 GTAGTACTC-CCTCCAAGCTCT
64 GTAGTACACTCC-CAAAGAGAG
* * *
3954 CGAAGTGGTAGTACGC-CTCC-AAGCTCGCGAATCGGTAGTACGCCCTCCAAGCTCTCGAGGTTG
1 CGAAGTGGTAGTACGCTC-CCAAAGCTCGCGAATCGGTAGAACCCCCTCCAAGCTCTCGAGGTGG
4017 TAGTACACTCCCAAAGAGAG
65 TAGTACACTCCCAAAGAGAG
*
4037 CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAATTGGTAGAACTCCCCCTCCAAGCTCTCGAGGTG
1 CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAATCGGTAGAA--CCCCCTCCAAGCTCTCGAGGTG
* *
4102 GTAGTACTCTCCCAAAGAGCG
64 GTAGTACACTCCCAAAGAGAG
* * ** * * * * * * * *
4123 TGAAGCGGTAGTACGCTCCCAAAGAGCGCGAAGCGGAAGTACGCTC-CCAACGAC-CGCGAAGCG
1 CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAATCGGTAGAACCCCCTCCAA-G-CTCTCGAGGTG
* * * **
4186 GTAGTACGCTCTCAAGGATCG
64 GTAGTACACTCCCAAAGAGAG
* * * ** * * * * * *
4207 CAAAGAGGTAGTACGCTCCCAAAGATCGCGAAGAGGTAGTACGCTCT-CAAGGCTCGCGAAGTGA
1 CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAATCGGTAGAACCCCCTCCAA-GCTCTCGAGGTGG
* * ****
4271 TAGAACGGCT-CC-AAGCTCT
65 TAGTAC-ACTCCCAAAGAGAG
* * * * * * * * * * * **
4290 CGAGGTGGTAGTATGCTCTCAAGGATCGCAAAGT-GGTAGTA-CGCCTCAAAGTTCACGAAATGG
1 CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAA-TCGGTAGAACCCCCTCCAAGCTCTCGAGGTGG
* * ****
4353 TAGTACGC-CCTCCAAGTTCT
65 TAGTACACTCC-CAAAGAGAG
* * ** * * * * * ** * * *
4373 CGAGGTGGTAGTACTCTCCCAAAGAGCGTGAAGCGGTAGTACGCTCC-CAAAGAGCGCGAAGCGG
1 CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAATCGGTAGAAC-CCCCTCCAAGCTCTCGAGGTGG
* * * **
4437 AAGTACGCTCCC-ACGACCG
65 TAGTACACTCCCAAAGAGAG
* * * * * ** * * * * * * *
4456 CGAAGCGGTAGTACGCTCTCAAGGATCGCAAAGAGGTAGTACGCTCC-CAAAGATCGCGAAGAGG
1 CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAATCGGTAGAAC-CCCCTCCAAGCTCTCGAGGTGG
** * * **
4520 TAGTATGCTCTCAAGGATCG
65 TAGTACACTCCCAAAGAGAG
* * * * *
4540 CAAAGTGGTAGTACGGCT--CAAAGTTCGCGAAAT-GGTAGTACACCCTCCAAGCTCTCGAAGTG
1 CGAAGTGGTAGTAC-GCTCCCAAAGCTCGCG-AATCGGTAGAACCCCCTCCAAGCTCTCGAGGTG
* * ***
4602 GTAGTACGC-CTCAAAGTTCG
64 GTAGTACACTCCCAAAGAGAG
* * * * * * * * * **
4622 CGAAATGGTAGTACAC-CCTCCAAGCTCTCGAAGT-GGTAGTA-CGCCTCAAAGTTCGCGAAATG
1 CGAAGTGGTAGTACGCTCC-CAAAGCTCGCGAA-TCGGTAGAACCCCCTCCAAGCTCTCGAGGTG
* * ****
4684 GTAGTACTC-CCTCCAAGCTCT
64 GTAGTACACTCC-CAAAGAGAG
* * *
4705 CGAAGTGGTAGTACGC-CTCC-AAGCTCGTGAATCGGTAGTACGCCCTCCAAGCTCTCGAGGTGG
1 CGAAGTGGTAGTACGCTC-CCAAAGCTCGCGAATCGGTAGAACCCCCTCCAAGCTCTCGAGGTGG
*
4768 TAGTACGCTCCCAAAGAGAG
65 TAGTACACTCCCAAAGAGAG
*
4788 CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAATTGGTAGAACTCCCCCTCCAAGCTCTCGAGGTG
1 CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAATCGGTAGAA--CCCCCTCCAAGCTCTCGAGGTG
* * * **
4853 GTAGTACGCTCTCAAGGATCG
64 GTAGTACACTCCCAAAGAGAG
* * * *
4874 CAAAGAGGTAGTACGCTCCCAACGAC-CGCGAAGCGGTAG
1 CGAAGTGGTAGTACGCTCCCAAAG-CTCGCGAATCGGTAG
4913 TACGCTCCCA
Statistics
Matches: 813, Mismatches: 186, Indels: 82
0.75 0.17 0.08
Matches are distributed among these distances:
81 6 0.01
82 140 0.17
83 345 0.42
84 167 0.21
85 12 0.01
86 142 0.17
87 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (84 bp):
CGAAGTGGTAGTACGCTCCCAAAGCTCGCGAATCGGTAGAACCCCCTCCAAGCTCTCGAGGTGGT
AGTACACTCCCAAAGAGAG
Found at i:4354 original size:55 final size:55
Alignment explanation
Indices: 3595--5184 Score: 652
Period size: 55 Copynumber: 28.4 Consensus size: 55
3585 TAAAGAGCGT
* * * * ** * * * *
3595 GAAGCGGTAGTATGCTCCCAAAGAGCGCGAAGCGGAAGTACGCTCCCAACGACCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * *
3651 GAAGCGGTAGTAAGCTCTCAAGGATCGC-AAAGAGGTAGTACGCTCCCAAAGATCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAA-TGGTAGTACGCTCTCAAGGATCGC
* * * * * * *
3707 GAAGGGGTAGTATGCTCTCAAGGATCGC-AAAGTGATAGTACG-GCTCAAAGTTCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAA-TGGTAGTACGCTCTCAAGGATCGC
* * * * * * * *
3762 GAAATGGTAGTACACCCTCCAAGCTCTCGAAGTGGTAGTACGC-CTCAAAGTTCGC
1 GAAGTGGTAGTAC-GCCTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * * * *
3817 GAAATGGTAGTACACCCTCCAAGCTCTCGAAGTGGTAGTACGC-CTCAAAGTTCGC
1 GAAGTGGTAGTAC-GCCTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * * * *
3872 GAAATGGTAGTACACCCTCCAAGCTCTCGAAGTGGTAGTACGC-CTCAAAGTTCGC
1 GAAGTGGTAGTAC-GCCTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * * *
3927 GAAATGGTAGTACTCCCTCCAAGCTCTCGAAGTGGTAGTACGC-CTCCAA-GCTCGC
1 GAAGTGGTAGTAC-GCCTCAAAGATCGCGAAATGGTAGTACGCTCT-CAAGGATCGC
* * * ** * * * * **
3982 GAA-TCGGTAGTACGCCCTCCAAGCTCTCGAGGTTGTAGTACACTCCCAAAGAGAGC
1 GAAGT-GGTAGTACG-CCTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * * * *
4038 GAAGTGGTAGTACGCTCCCAAAGCTCGCGAATTGGTAGAACTCCCCCTCCAA-GCTCTC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAGTA--CGCTCT-CAAGGATCGC
* * * * * ** * * *
4096 GAGGTGGTAGTACTCTCCCAAAGAGCGTGAAGCGGTAGTACGCTCCCAAAGAGCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * **
4152 GAAGCGGAAGTACGCTCCCAACGACCGCGAAGCGGTAGTACGCTCTCAAGGATCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * *
4208 AAAGAGGTAGTACGCTCCCAAAGATCGCGAAGA-GGTAGTACGCTCTCAAGGCTCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAA-ATGGTAGTACGCTCTCAAGGATCGC
* * * * * * ** *
4264 GAAGTGATAGAACGGCTCCAAGCTCTCGAGGTGGTAGTATGCTCTCAAGGATCGC
1 GAAGTGGTAGTACGCCTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * *
4319 AAAGTGGTAGTACGCCTCAAAGTTCACGAAATGGTAGTACGCCCTCCAA-GTTCTC
1 GAAGTGGTAGTACGCCTCAAAGATCGCGAAATGGTAGTACGCTCT-CAAGGATCGC
* * * * * ** * * *
4374 GAGGTGGTAGTACTCTCCCAAAGAGCGTGAAGCGGTAGTACGCTCCCAAAGAGCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * **
4430 GAAGCGGAAGTACG-CTCCCACGACCGCGAAGCGGTAGTACGCTCTCAAGGATCGC
1 GAAGTGGTAGTACGCCT-CAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * *
4485 AAAGAGGTAGTACGCTCCCAAAGATCGCGAAGA-GGTAGTATGCTCTCAAGGATCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAA-ATGGTAGTACGCTCTCAAGGATCGC
* * * * * * *
4541 AAAGTGGTAGTACGGCTCAAAGTTCGCGAAATGGTAGTACACCCTCCAA-GCTCTC
1 GAAGTGGTAGTACGCCTCAAAGATCGCGAAATGGTAGTACGCTCT-CAAGGATCGC
* * * * *
4596 GAAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAGTACACCCTCCAA-GCTCTC
1 GAAGTGGTAGTACGCCTCAAAGATCGCGAAATGGTAGTACGCTCT-CAAGGATCGC
* * * * *
4651 GAAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAGTACTCCCTCCAA-GCTCTC
1 GAAGTGGTAGTACGCCTCAAAGATCGCGAAATGGTAGTACGCTCT-CAAGGATCGC
* * * * * *
4706 GAAGTGGTAGTACGCCTCCAAGCTCGTG-AATCGGTAGTACGCCCTCCAA-GCTCTC
1 GAAGTGGTAGTACGCCTCAAAGATCGCGAAAT-GGTAGTACGCTCT-CAAGGATCGC
* * ** * * * *
4761 GAGGTGGTAGTACGCTCCCAAAGAGAGCGAAGTGGTAGTACGCTCCCAAAGCTCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * * **
4817 GAATTGGTAGAACTCCCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATCGC
1 GAAGTGGTAG---TACGCCTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * * * * ** * *
4875 AAAGAGGTAGTACGCTCCCAACGACCGCGAAGCGGTAGTACGCTCCCAAAGATCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* * ** * *
4931 GAAGAGGTAGTACGCTCTCGAAGA-C-AAAAATGCGTAGTACGCTCCCAAAGAGCGGAGCGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATG-GTAGTACGCTCTC--A-A--GGATCGC
* * * * * * * * * *
4991 GAAGCGGTAGTACGCTCCCAAAGCTCGCGAATTGATAGAACACCCCCTCCAA-GCTCTC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAG--TACGCTCT-CAAGGATCGC
* * * * * * *
5049 GAGGTGGTAGTACGCTCTCAAGGATCGCAAAAAGGTAGTACGCTC-CCAGAGAGCGT
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAGTACGCTCTCAAG-GATCGC
* * * *** * * * *
5105 GAAGCGGTAGTACGCTCCCAAAGACCGCGAAGCAGTGGTACGCTCCCAAAGATTGC
1 GAAGTGGTAGTACGC-CTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
* *
5161 GAAGAGGTAGTACGCTCTCGAAGA
1 GAAGTGGTAGTACGC-CTCAAAGA
5185 CAAAAATGCG
Statistics
Matches: 1227, Mismatches: 259, Indels: 96
0.78 0.16 0.06
Matches are distributed among these distances:
54 11 0.01
55 594 0.48
56 462 0.38
57 7 0.01
58 107 0.09
59 6 0.00
60 25 0.02
61 5 0.00
62 5 0.00
63 4 0.00
64 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (55 bp):
GAAGTGGTAGTACGCCTCAAAGATCGCGAAATGGTAGTACGCTCTCAAGGATCGC
Found at i:5040 original size:202 final size:200
Alignment explanation
Indices: 4101--5177 Score: 745
Period size: 194 Copynumber: 5.5 Consensus size: 200
4091 CTCTCGAGGT
* * * * * *
4101 GGTAGTACTCTCCCAAAGAGCGTGAAGCGGTAGTACGCTCCCAAAGAGCGCGAAGCGGAAGTACG
1 GGTAGTACGCTCCC-AAGACCGCGAAGCGGTAGTACGCTCCCAAAGATCGCGAAGAGGTAGTACG
* * ** * * *
4166 CTCCCAACGAC-CGCGAAGCGGTAGTACGCTCTC--A-AG-GATCGCAAAGAGGTAGTACGCTCC
65 CTCTCAAAG-CTCGCGAAATGGTAGTACGCTCCCAAAGAGCGA-CGCGAAGTGGTAGTACGCTCC
* ** * * * * * * *
4226 CAAAGATCGCGAAGAGGTAG--TACGCTCT-CAAGGCTCGCGAAGTGATAGAACGGCTC-CAA-G
128 CAAAGCTCGCGAATTGGTAGAACACCCCCTCCAA-GCTCTCGAGGTGGTAGTAC-GCTCTCAAGG
* * * * *
4286 CTCTCGAGGT
191 ATCGCAAAGA
* * * * * * * *
4296 GGTAGTATGCTCTCAAGGATCGCAAAGTGGTAGTACGC-CTCAAAGTTCACGAA-ATGGTAGTAC
1 GGTAGTACGCTCCCAA-GACCGCGAAGCGGTAGTACGCTCCCAAAGATCGCGAAGA-GGTAGTAC
* * * * ** * * *
4359 GCCCTCCAAGTTCTCGAGGTGGTAGTACTCTCCCAAAGA--G-CGTGAAGCGGTAGTACGCTCCC
64 GCTCTCAAAGCTCGCGAAATGGTAGTACGCTCCCAAAGAGCGACGCGAAGTGGTAGTACGCTCCC
** ** * * * * * * * * *
4421 AAAGAGCGCGAAGCGGAAGTACGCTCCC-ACGA-C-CGCGAAGCGGTAGTACGCTCTCAAGGATC
129 AAAGCTCGCGAATTGGTAGAACACCCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATC
4483 GCAAAGA
194 GCAAAGA
* * * * * * *
4490 GGTAGTACGCTCCCAAAGATCGCGAAGAGGTAGTATGCTCTCAAGGATCGCAAAGTGGTAGTACG
1 GGTAGTACGCTCCC-AAGACCGCGAAGCGGTAGTACGCTCCCAAAGATCGCGAAGAGGTAGTACG
* * * * * * *
4555 -GCTCAAAGTTCGCGAAATGGTAGTACAC-CCTC-CA-AGC-TCTCGAAGTGGTAGTACGC-CTC
65 CTCTCAAAGCTCGCGAAATGGTAGTACGCTCC-CAAAGAGCGACGCGAAGTGGTAGTACGCTCCC
* * * * * *
4614 AAAGTTCGCGAAATGGTAGTACA--CCCTCCAAGCTCTCGAAGTGGTAGTACGC-CTCAAAGTTC
129 AAAGCTCGCGAATTGGTAGAACACCCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATC
*
4676 GCGAAA-T
194 GC-AAAGA
* * * * * * **
4683 GGTAGTACTCCCTCCAAG-CTCTCGAAGTGGTAGTACGC-CTCC-AAGCTCGTGAATCGGTAGTA
1 GGTAGTACGCTC-CCAAGAC-CGCGAAGCGGTAGTACGCTC-CCAAAGATCGCGAAGAGGTAGTA
* * * **
4745 CGCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCCCAAAGA--GA-GCGAAGTGGTAGTACGCTCC
63 CGCTCTCAAAGCTCGCGAAATGGTAGTACGCTCCCAAAGAGCGACGCGAAGTGGTAGTACGCTCC
*
4807 CAAAGCTCGCGAATTGGTAGAACTCCCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGAT
128 CAAAGCTCGCGAATTGGTAGAACACCCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGAT
4872 CGCAAAGA
193 CGCAAAGA
4880 GGTAGTACGCTCCCAACGACCGCGAAGCGGTAGTACGCTCCCAAAGATCGCGAAGAGGTAGTACG
1 GGTAGTACGCTCCCAA-GACCGCGAAGCGGTAGTACGCTCCCAAAGATCGCGAAGAGGTAGTACG
* * ** *
4945 CTCTCGAAG-AC-AAAAATGCGTAGTACGCTCCCAAAGAGCGGAGCGCGAAGCGGTAGTACGCTC
65 CTCTCAAAGCTCGCGAAATG-GTAGTACGCTCCCAAAGAGC-GA-CGCGAAGTGGTAGTACGCTC
*
5008 CCAAAGCTCGCGAATTGATAGAACACCCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGA
127 CCAAAGCTCGCGAATTGGTAGAACACCCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGA
*
5073 TCGCAAAAA
192 TCGCAAAGA
* * * *
5082 GGTAGTACGCTCCCAGAGAGCGTGAAGCGGTAGTACGCTCCCAAAGACCGCGAAGCA-GTGGTAC
1 GGTAGTACGCTCCCA-AGACCGCGAAGCGGTAGTACGCTCCCAAAGATCGCGAAG-AGGTAGTAC
* * *
5146 GCTCCCAAAGATTGCGAAGA-GGTAGTACGCTC
64 GCTCTCAAAGCTCGCGAA-ATGGTAGTACGCTC
5178 TCGAAGACAA
Statistics
Matches: 695, Mismatches: 137, Indels: 92
0.75 0.15 0.10
Matches are distributed among these distances:
191 3 0.00
192 24 0.03
193 116 0.17
194 198 0.28
195 51 0.07
196 45 0.06
197 59 0.08
198 27 0.04
200 2 0.00
202 153 0.22
203 13 0.02
204 3 0.00
205 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.18
Consensus pattern (200 bp):
GGTAGTACGCTCCCAAGACCGCGAAGCGGTAGTACGCTCCCAAAGATCGCGAAGAGGTAGTACGC
TCTCAAAGCTCGCGAAATGGTAGTACGCTCCCAAAGAGCGACGCGAAGTGGTAGTACGCTCCCAA
AGCTCGCGAATTGGTAGAACACCCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATCGC
AAAGA
Found at i:5184 original size:28 final size:28
Alignment explanation
Indices: 3573--5177 Score: 750
Period size: 28 Copynumber: 57.4 Consensus size: 28
3563 AAAAAAGGGC
* * * * *
3573 GTAGAACGCTCCTAAAGAGCGTGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * *
3601 GTAGTATGCTCCCAAAGAGCGCGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * *
3629 GAAGTACGCTCCCAACGACCGCGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * *
3657 GTAGTAAGCTCTCAAGGATCGCAAAGAG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
*
3685 GTAGTACGCTCCCAAAGATCGCGAAGGG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * * *
3713 GTAGTATGCTCTCAAGGATCGCAAAGTG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* *
3741 ATAGTACGGCT--CAAAGTTCGCGAA-ATG
1 GTAGTAC-GCTCCCAAAGATCGCGAAGA-G
* * * * *
3768 GTAGTACAC-CCTCCAAGCTCTCGAAGTG
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
* *
3796 GTAGTACGC-CTCAAAGTTCGCGAA-ATG
1 GTAGTACGCTCCCAAAGATCGCGAAGA-G
* * * * *
3823 GTAGTACAC-CCTCCAAGCTCTCGAAGTG
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
* *
3851 GTAGTACGC-CTCAAAGTTCGCGAA-ATG
1 GTAGTACGCTCCCAAAGATCGCGAAGA-G
* * * * *
3878 GTAGTACAC-CCTCCAAGCTCTCGAAGTG
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
* *
3906 GTAGTACGC-CTCAAAGTTCGCGAA-ATG
1 GTAGTACGCTCCCAAAGATCGCGAAGA-G
* * * * *
3933 GTAGTACTC-CCTCCAAGCTCTCGAAGTG
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
* **
3961 GTAGTACGC-CTCC-AAGCTCGCGAATCG
1 GTAGTACGCTC-CCAAAGATCGCGAAGAG
* * * * **
3988 GTAGTACGC-CCTCCAAGCTCTCGAGGTT
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
* ** *
4016 GTAGTACACTCCCAAAGAGAGCGAAGTG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* **
4044 GTAGTACGCTCCCAAAGCTCGCGAATTG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * * * * * *
4072 GTAGAACTCCCCCTCCAAGCTCTCGAGGTG
1 GTAGTAC-GCTCC-CAAAGATCGCGAAGAG
* * * *
4102 GTAGTACTCTCCCAAAGAGCGTGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* *
4130 GTAGTACGCTCCCAAAGAGCGCGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * *
4158 GAAGTACGCTCCCAACGACCGCGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * *
4186 GTAGTACGCTCTCAAGGATCGCAAAGAG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
4214 GTAGTACGCTCCCAAAGATCGCGAAGAG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * *
4242 GTAGTACGCTCTCAAGGCTCGCGAAGTG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * * * *
4270 ATAGAACGGCT-CC-AAGCTCTCGAGGTG
1 GTAGTAC-GCTCCCAAAGATCGCGAAGAG
* * * * *
4297 GTAGTATGCTCTCAAGGATCGCAAAGTG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * *
4325 GTAGTACGC-CTCAAAGTTCACGAA-ATG
1 GTAGTACGCTCCCAAAGATCGCGAAGA-G
* * * * *
4352 GTAGTACGC-CCTCCAAGTTCTCGAGGTG
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
* * * *
4380 GTAGTACTCTCCCAAAGAGCGTGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* *
4408 GTAGTACGCTCCCAAAGAGCGCGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * *
4436 GAAGTACGCTCCC-ACGACCGCGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * *
4463 GTAGTACGCTCTCAAGGATCGCAAAGAG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
4491 GTAGTACGCTCCCAAAGATCGCGAAGAG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * * *
4519 GTAGTATGCTCTCAAGGATCGCAAAGTG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
*
4547 GTAGTACGGCT--CAAAGTTCGCGAA-ATG
1 GTAGTAC-GCTCCCAAAGATCGCGAAGA-G
* * * * *
4574 GTAGTACAC-CCTCCAAGCTCTCGAAGTG
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
* *
4602 GTAGTACGC-CTCAAAGTTCGCGAA-ATG
1 GTAGTACGCTCCCAAAGATCGCGAAGA-G
* * * * *
4629 GTAGTACAC-CCTCCAAGCTCTCGAAGTG
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
* *
4657 GTAGTACGC-CTCAAAGTTCGCGAA-ATG
1 GTAGTACGCTCCCAAAGATCGCGAAGA-G
* * * * *
4684 GTAGTACTC-CCTCCAAGCTCTCGAAGTG
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
* * **
4712 GTAGTACGC-CTCC-AAGCTCGTGAATCG
1 GTAGTACGCTC-CCAAAGATCGCGAAGAG
* * * * *
4739 GTAGTACGC-CCTCCAAGCTCTCGAGGTG
1 GTAGTACGCTCC-CAAAGATCGCGAAGAG
** *
4767 GTAGTACGCTCCCAAAGAGAGCGAAGTG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* **
4795 GTAGTACGCTCCCAAAGCTCGCGAATTG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * * * * * *
4823 GTAGAACTCCCCCTCCAAGCTCTCGAGGTG
1 GTAGTAC-GCTCC-CAAAGATCGCGAAGAG
* * *
4853 GTAGTACGCTCTCAAGGATCGCAAAGAG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * *
4881 GTAGTACGCTCCCAACGACCGCGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
4909 GTAGTACGCTCCCAAAGATCGCGAAGAG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * *
4937 GTAGTACGCTCTCGAAGA---CAAAAATG
1 GTAGTACGCTCCCAAAGATCGCGAAGA-G
* *
4963 CGTAGTACGCTCCCAAAGAGCGGAGCGCGAAGCG
1 -GTAGTACGCTCCC-AA-A---GATCGCGAAGAG
* **
4997 GTAGTACGCTCCCAAAGCTCGCGAATTG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * * * * * * *
5025 ATAGAACACCCCCTCCAAGCTCTCGAGGTG
1 GTAGTAC-GCTCC-CAAAGATCGCGAAGAG
* * * *
5055 GTAGTACGCTCTCAAGGATCGCAAAAAG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
* * * *
5083 GTAGTACGCTCCCAGAGAGCGTGAAGCG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
*
5111 GTAGTACGCTCCCAAAGACCGCGAAGCA-
1 GTAGTACGCTCCCAAAGATCGCGAAG-AG
* *
5139 GTGGTACGCTCCCAAAGATTGCGAAGAG
1 GTAGTACGCTCCCAAAGATCGCGAAGAG
5167 GTAGTACGCTC
1 GTAGTACGCTC
5178 TCGAAGACAA
Statistics
Matches: 1203, Mismatches: 313, Indels: 122
0.73 0.19 0.07
Matches are distributed among these distances:
25 4 0.00
26 8 0.01
27 252 0.21
28 830 0.69
29 34 0.03
30 53 0.04
31 1 0.00
32 4 0.00
33 13 0.01
34 1 0.00
35 3 0.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (28 bp):
GTAGTACGCTCCCAAAGATCGCGAAGAG
Found at i:17386 original size:81 final size:80
Alignment explanation
Indices: 17286--17434 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 80
17276 CAATATTGAC
* *
17286 ATTTGTTACAGATGAACCAAGCATCCTGTTACGAATTGAGTTTAC-TTTGAATAACATATATTTG
1 ATTTGTTACAGATGAACCAAGCATCCTGTTACCAATTGAGTTTACGTTTGAACAAC--ATATTTG
17350 AGCAAATTAATTGTCAT
64 AGCAAATTAATTGTCAT
* * *
17367 ATTTGTTACAGGTGAACCAAGTATCCTGTTACCAGTTGAGTTTACGTTTGAACAACATATTTGAG
1 ATTTGTTACAGATGAACCAAGCATCCTGTTACCAATTGAGTTTACGTTTGAACAACATATTTGAG
17432 CAA
66 CAA
17435 CCGCCTCCTC
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 12 0.19
81 41 0.66
82 9 0.15
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (80 bp):
ATTTGTTACAGATGAACCAAGCATCCTGTTACCAATTGAGTTTACGTTTGAACAACATATTTGAG
CAAATTAATTGTCAT
Found at i:20974 original size:22 final size:21
Alignment explanation
Indices: 20929--20974 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
20919 GAGAACCCTT
* * *
20929 TTATAAATTTTTTTAATCTTC
1 TTATAAATTTTGTTAACCTCC
20950 TTATGAAATTTTGTTAACCTCC
1 TTAT-AAATTTTGTTAACCTCC
20972 TTA
1 TTA
20975 AGGAATATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (21 bp):
TTATAAATTTTGTTAACCTCC
Found at i:21142 original size:22 final size:22
Alignment explanation
Indices: 21117--21163 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
21107 GAATTGCTAG
* *
21117 TAATCACATTCTAAAATTTTGA
1 TAATCACATTATAAAATTGTGA
*
21139 TAATCACATTATGAAATTGTGA
1 TAATCACATTATAAAATTGTGA
21161 TAA
1 TAA
21164 CCTCGCTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (22 bp):
TAATCACATTATAAAATTGTGA
Found at i:21248 original size:38 final size:38
Alignment explanation
Indices: 21197--21269 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
21187 CTTCCCTATA
*
21197 AAATTTTAATAACCTCCTTATGAAATCTTGATAACTAC
1 AAATTTTAATAACCTCCCTATGAAATCTTGATAACTAC
* **
21235 AAATTTTGATAACCTCCCTATGATTTCTTGATAAC
1 AAATTTTAATAACCTCCCTATGAAATCTTGATAAC
21270 CTCATTATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (38 bp):
AAATTTTAATAACCTCCCTATGAAATCTTGATAACTAC
Found at i:21300 original size:22 final size:22
Alignment explanation
Indices: 21130--21396 Score: 162
Period size: 22 Copynumber: 12.5 Consensus size: 22
21120 TCACATTCTA
* * **
21130 AAATTTTGATAATCACATTATG
1 AAATTTTGATAACCTCCCTATG
* *
21152 AAATTGTGATAACCTCGCTAT-
1 AAATTTTGATAACCTCCCTATG
* * *
21173 ACAATTTTAATAAACTTCCCTATA
1 A-AATTTTGAT-AACCTCCCTATG
* *
21197 AAATTTTAATAACCTCCTTATG
1 AAATTTTGATAACCTCCCTATG
* *
21219 AAATCTTGATAA-----CTA-C
1 AAATTTTGATAACCTCCCTATG
21235 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
* **
21257 -ATTTCTTGATAACCTCATTATG
1 AAATT-TTGATAACCTCCCTATG
* *
21279 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
*
21301 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CCTATG
* **
21323 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CCCTATG
* * *
21345 AAATTTAGATAACCTTCATATG
1 AAATTTTGATAACCTCCCTATG
**
21367 AAATTTTGATATTCTCCC--TG
1 AAATTTTGATAACCTCCCTATG
21387 AAATTTTGAT
1 AAATTTTGAT
21397 TACTCCATAG
Statistics
Matches: 187, Mismatches: 43, Indels: 32
0.71 0.16 0.12
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
20 12 0.06
21 11 0.06
22 125 0.67
23 25 0.13
24 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:22425 original size:2 final size:2
Alignment explanation
Indices: 22414--22442 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
22404 AAATTAAAAT
22414 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22443 AATAAGTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:22968 original size:20 final size:18
Alignment explanation
Indices: 22936--22973 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
22926 AATTATAATC
22936 AAAAAAAAAAAGAAAAAG
1 AAAAAAAAAAAGAAAAAG
22954 AAAAAGAAAAGAAGAAAAAG
1 AAAAA-AAAA-AAGAAAAAG
22974 TAACCATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAAAAAG
Found at i:27015 original size:30 final size:30
Alignment explanation
Indices: 26981--27070 Score: 153
Period size: 30 Copynumber: 3.0 Consensus size: 30
26971 ACGCCAAATC
*
26981 AACTCTCCGCGTGTTTGTCTTCTCTTTCAA
1 AACTCTCCGCGAGTTTGTCTTCTCTTTCAA
*
27011 AACTCTCCGCGAGTTTGTCTTCTATTTCAA
1 AACTCTCCGCGAGTTTGTCTTCTCTTTCAA
*
27041 AACTCTCTGCGAGTTTGTCTTCTCTTTCAA
1 AACTCTCCGCGAGTTTGTCTTCTCTTTCAA
27071 TTTCGTCTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.17, C:0.28, G:0.13, T:0.42
Consensus pattern (30 bp):
AACTCTCCGCGAGTTTGTCTTCTCTTTCAA
Found at i:28726 original size:25 final size:25
Alignment explanation
Indices: 28698--28749 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
28688 TCTCTTTATT
*
28698 TCATTTCTCAAATTCATTTTAATGG
1 TCATTTCTCAAATTCATTCTAATGG
*
28723 TCATTTCTCAATTTCATTCTAATGG
1 TCATTTCTCAAATTCATTCTAATGG
28748 TC
1 TC
28750 CAAGACCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (25 bp):
TCATTTCTCAAATTCATTCTAATGG
Found at i:28986 original size:2 final size:2
Alignment explanation
Indices: 28979--29003 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28969 AAATATACAA
28979 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29004 GAAATTGGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32338 original size:52 final size:52
Alignment explanation
Indices: 32201--32446 Score: 404
Period size: 52 Copynumber: 4.7 Consensus size: 52
32191 CAGGTTTAAG
*
32201 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCT-T
1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCT
* * *
32252 TTTTCAAATTGGGAAAGTTCCCATCAAATCTTCAAAGTATTCAATCTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCA-CCAGTTTTCAAAGTATTCAATCTAGCTCT
*
32305 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTTTTCAATCTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCT
*
32357 TTTTCAAATTGGGAAAGTTCCCACCAATTTTCAAAGTATTCAATCTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCT
*
32409 GTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGT
1 -TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGT
32447 TTTTAAATTG
Statistics
Matches: 180, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
51 23 0.13
52 98 0.54
53 59 0.33
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (52 bp):
TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCT
Found at i:32449 original size:36 final size:33
Alignment explanation
Indices: 32409--32510 Score: 116
Period size: 36 Copynumber: 2.9 Consensus size: 33
32399 ATCTAGCTCT
*
32409 GTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAA
1 GTTTTCAAATTGGGAAAGTTCCCGTCAGTTTT---A
*
32445 GTTTTTAAATTGGGAAAGTTCCCGTCAGGTTTTA
1 GTTTTCAAATTGGGAAAGTTCCCGTCA-GTTTTA
*
32479 GTTTTC-AATTCAGGCAAAGTTCCCGTCAGTTT
1 GTTTTCAAATT--GGGAAAGTTCCCGTCAGTTT
32511 CGGTTTCAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
33 4 0.07
34 10 0.17
35 15 0.25
36 25 0.42
37 5 0.08
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (33 bp):
GTTTTCAAATTGGGAAAGTTCCCGTCAGTTTTA
Found at i:45424 original size:11 final size:12
Alignment explanation
Indices: 45408--45439 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
45398 GAAATTCATG
45408 TTTGAAGACT-A
1 TTTGAAGACTAA
45419 TTTGAAGA-TAA
1 TTTGAAGACTAA
45430 TTTGAAGACT
1 TTTGAAGACT
45440 TGAAGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Found at i:45444 original size:19 final size:18
Alignment explanation
Indices: 45420--45455 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
45410 TGAAGACTAT
45420 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
45439 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
45456 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:48154 original size:30 final size:30
Alignment explanation
Indices: 48120--48179 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
48110 ACGCCAAATC
*
48120 AACTCTCCGCGAGTTTGTCTTCTCTTTCAA
1 AACTCTCCGCGAGTTTGTATTCTCTTTCAA
*
48150 AACTCTTCGCGAGTTTGTATTCTCTTTCAA
1 AACTCTCCGCGAGTTTGTATTCTCTTTCAA
48180 TTTCGTCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.42
Consensus pattern (30 bp):
AACTCTCCGCGAGTTTGTATTCTCTTTCAA
Found at i:49313 original size:3 final size:3
Alignment explanation
Indices: 49305--49368 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
49295 GTATGACAAC
*
49305 TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49353 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
49369 AAGATTTTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:51063 original size:19 final size:19
Alignment explanation
Indices: 51037--51084 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
51027 AATTAATCAT
51037 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
51055 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
* *
51074 CTTATAAATTA
1 TTTATATATTA
51085 CTCCTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:52652 original size:53 final size:53
Alignment explanation
Indices: 52591--52697 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
52581 AAATTTAGGG
**
52591 TCTAGTAAGGTTTGTCCTCAATTATAAGGTTAATTAGATAAGCATTAGTAGCA
1 TCTAGTAAGGAATGTCCTCAATTATAAGGTTAATTAGATAAGCATTAGTAGCA
*
52644 TCTAGTAAGGAATGTCCTCAATTATAAGGTTAATTAGATAAGGATTAGTAGCA
1 TCTAGTAAGGAATGTCCTCAATTATAAGGTTAATTAGATAAGCATTAGTAGCA
52697 T
1 T
52698 AATCCTTGCC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.35
Consensus pattern (53 bp):
TCTAGTAAGGAATGTCCTCAATTATAAGGTTAATTAGATAAGCATTAGTAGCA
Found at i:53916 original size:21 final size:22
Alignment explanation
Indices: 53870--53916 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
53860 TAGAATAAAA
* *
53870 AAATTTACATAAACTTAATTAG
1 AAATTTACATAAACTTAATCAC
*
53892 AAATTTACA-AAATTTAATCAC
1 AAATTTACATAAACTTAATCAC
53913 AAAT
1 AAAT
53917 AAAAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (22 bp):
AAATTTACATAAACTTAATCAC
Found at i:54174 original size:21 final size:22
Alignment explanation
Indices: 54134--54180 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
54124 TAGAATAAAA
*
54134 AAATTTACATAAACTTAATCAG
1 AAATTTACATAAACTTAATCAC
*
54156 AAATTTACA-AAATTTAATCAC
1 AAATTTACATAAACTTAATCAC
54177 AAAT
1 AAAT
54181 AAAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (22 bp):
AAATTTACATAAACTTAATCAC
Found at i:55081 original size:2 final size:2
Alignment explanation
Indices: 55076--55109 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55066 GGTTAAATAA
55076 AT AT AT AT 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 AT AT AT AT
55110 CAACTTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55361 original size:127 final size:128
Alignment explanation
Indices: 55222--55480 Score: 339
Period size: 127 Copynumber: 2.0 Consensus size: 128
55212 CATTATTTAA
* * *
55222 ACTTTTATAGTTTTATTCAACTAAAAACTCTAATTTTATTTATTTAAATCTAATA-TC-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATTCTTATCTA
55283 -TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATTAGAATTTTTTAAAT
66 TTGATTTTTACCATTTTACTATTTTAATTAAAAAAC---T-TATATATATTAGAATTTTTTAAAT
55347 AT
127 AT
**
55349 ACTTTTACAGTTTTACTCAACTAAAAACTCTTTTTTTATTTAATTAAATCTAATATTCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATTCTTAT--C
* * * *
55414 TATTTTATTTTTACCATTTTATTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATA
64 TA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
55479 T
128 T
55480 A
1 A
55481 TTTCTTAAAT
Statistics
Matches: 115, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
127 50 0.43
128 2 0.02
129 1 0.01
130 1 0.01
131 27 0.23
132 1 0.01
133 2 0.02
135 31 0.27
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATTCTTATCTA
TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:55502 original size:14 final size:13
Alignment explanation
Indices: 55466--55504 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
55456 TATATATTAG
55466 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
55479 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
55493 AATTTTTTAAAT
1 AATTTTTTAAAT
55505 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Done.