Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 167 of 182
Found at i:50652822 original size:30 final size:29
Alignment explanation
Indices: 50652631--50652995 Score: 138
Period size: 30 Copynumber: 12.6 Consensus size: 29
50652621 AGCTCGGGGA
* *
50652631 TAAAATGGTAA-TTTTGGATACTTCAGGGG
1 TAAAATGGTAATTTTTGGA-AGTTCAAGGG
* *
50652660 CAAAAAT-ATAATTTTTGGAAGTTCAAGGG
1 -TAAAATGGTAATTTTTGGAAGTTCAAGGG
* * **
50652689 T-AAATGATAATTTATGGAAAGTTCGGGGG
1 TAAAATGGTAATTTTTGG-AAGTTCAAGGG
* * *
50652718 CAAAATGG-AATTTTTAGACA-TGCAAGGG
1 TAAAATGGTAATTTTTGGA-AGTTCAAGGG
* *
50652746 TAAAATGGTAATTTTTGGAAAATT-TAGGG
1 TAAAATGGTAATTTTTGG-AAGTTCAAGGG
* *
50652775 TAAAAAATGG-AACTTTTGGAAGTTCGAGGG
1 T--AAAATGGTAATTTTTGGAAGTTCAAGGG
** *
50652805 TAAAATGGTAATATTTTGGAAAAATCAA--A
1 TAAAATGGTAAT-TTTTGG-AAGTTCAAGGG
* *
50652834 AAAAATGG-AA-TTTTGGAAGTTCGA-GG
1 TAAAATGGTAATTTTTGGAAGTTCAAGGG
* *
50652860 TCAAAAATAG-AATTTTTGGAAAAATT--AGGG
1 T--AAAATGGTAATTTTTGG--AAGTTCAAGGG
*
50652890 TCAAAAT-GTAATTTTTGGAAAGTTCGAGGG
1 T-AAAATGGTAATTTTTGG-AAGTTCAAGGG
* ** **
50652920 TTAAAAT-ATGGTTTTTGGAAAGTTTGAGGG
1 -TAAAATGGTAATTTTTGG-AAGTTCAAGGG
* *
50652950 TTAAAAT-GTGATTTTTGAAAAGTTCAAGGG
1 -TAAAATGGTAATTTTTG-GAAGTTCAAGGG
*
50652980 TCAAAAT-GTGATTTTT
1 T-AAAATGGTAATTTTT
50652996 AAAAAGTTCG
Statistics
Matches: 262, Mismatches: 46, Indels: 54
0.72 0.13 0.15
Matches are distributed among these distances:
25 5 0.02
26 6 0.02
27 4 0.02
28 46 0.18
29 77 0.29
30 107 0.41
31 17 0.06
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (29 bp):
TAAAATGGTAATTTTTGGAAGTTCAAGGG
Found at i:50652883 original size:55 final size:57
Alignment explanation
Indices: 50652776--50652884 Score: 163
Period size: 56 Copynumber: 1.9 Consensus size: 57
50652766 AATTTAGGGT
*
50652776 AAAAAATGGAACTTTTGGAAGTTCGAGGGTAAAATGGTAATATTTTGGAAAAATCAA
1 AAAAAATGGAACTTTTGGAAGTTCGAGGGTAAAATAGTAATATTTTGGAAAAATCAA
50652833 AAAAAATGGAA-TTTTGGAAGTTCGA-GGTCAAAAATAG-AAT-TTTTGGAAAAAT
1 AAAAAATGGAACTTTTGGAAGTTCGAGGGT--AAAATAGTAATATTTTGGAAAAAT
50652885 TAGGGTCAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
55 15 0.31
56 17 0.35
57 17 0.35
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (57 bp):
AAAAAATGGAACTTTTGGAAGTTCGAGGGTAAAATAGTAATATTTTGGAAAAATCAA
Found at i:50652927 original size:59 final size:59
Alignment explanation
Indices: 50652669--50652995 Score: 207
Period size: 59 Copynumber: 5.6 Consensus size: 59
50652659 GCAAAAATAT
* * * * **
50652669 AATTTTTGGAAGTTCAAGGG-T-AAAT-GATAATTTATGG-AAAGTTCGGGGGCAAAATGG
1 AATTTTTGGAAGTTCGAGGGTTAAAATAG-TAATTTTTGGAAAAATT-AGGGTAAAAATGG
* * * * *
50652726 AATTTTTAGACA-TGCAAGGG-TAAAATGGTAATTTTTGGAAAATTTAGGGTAAAAAATGG
1 AATTTTTGGA-AGTTCGAGGGTTAAAATAGTAATTTTTGGAAAAATTAGGGT-AAAAATGG
* * * **
50652785 AACTTTTGGAAGTTCGAGGG-TAAAATGGTAATATTTTGGAAAAATCA--AAAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTTAAAATAGTAAT-TTTTGGAAAAATTAGGGTAAAAATGG
* * *
50652842 AA-TTTTGGAAGTTCGA-GGTCAAAAATAG-AATTTTTGGAAAAATTAGGGTCAAAATGT
1 AATTTTTGGAAGTTCGAGGGT-TAAAATAGTAATTTTTGGAAAAATTAGGGTAAAAATGG
** ** *
50652899 AATTTTTGGAAAGTTCGAGGGTTAAAATA-TGGTTTTTGGAAAGTTTGAGGGTTAAAATGTG
1 AATTTTTGG-AAGTTCGAGGGTTAAAATAGTAATTTTTGGAAAAATT-AGGGTAAAAATG-G
* * * *
50652960 -ATTTTTGAAAAGTTCAAGGGTCAAAAT-GTGATTTTT
1 AATTTTTG-GAAGTTCGAGGGTTAAAATAGTAATTTTT
50652996 AAAAAGTTCG
Statistics
Matches: 218, Mismatches: 33, Indels: 35
0.76 0.12 0.12
Matches are distributed among these distances:
55 15 0.07
56 17 0.08
57 41 0.19
58 24 0.11
59 65 0.30
60 56 0.26
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (59 bp):
AATTTTTGGAAGTTCGAGGGTTAAAATAGTAATTTTTGGAAAAATTAGGGTAAAAATGG
Found at i:50652974 original size:60 final size:59
Alignment explanation
Indices: 50652850--50652995 Score: 161
Period size: 60 Copynumber: 2.5 Consensus size: 59
50652840 GGAATTTTGG
* *
50652850 AAGTTCGA-GGTCAAAA-ATAGAATTTTTGGAAAAATTAGGGTCAAAATGTAATTTTTGGA
1 AAGTTCAAGGGTCAAAATAT-G-ATTTTTGGAAAAATTAGGGTCAAAATGTAATTTTTGAA
* * * ** * *
50652909 AAGTTCGAGGGTTAAAATATGGTTTTTGGAAAGTTTGAGGGTTAAAATGTGATTTTTGAA
1 AAGTTCAAGGGTCAAAATATGATTTTTGGAAAAATT-AGGGTCAAAATGTAATTTTTGAA
*
50652969 AAGTTCAAGGGTCAAAATGTGATTTTT
1 AAGTTCAAGGGTCAAAATATGATTTTT
50652996 AAAAAGTTCG
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
59 20 0.27
60 51 0.70
61 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (59 bp):
AAGTTCAAGGGTCAAAATATGATTTTTGGAAAAATTAGGGTCAAAATGTAATTTTTGAA
Found at i:50653001 original size:30 final size:30
Alignment explanation
Indices: 50652886--50653011 Score: 153
Period size: 30 Copynumber: 4.2 Consensus size: 30
50652876 TGGAAAAATT
* *
50652886 AGGGTCAAAATGTAATTTTTGGAAAGTTCG
1 AGGGTCAAAATGTGATTTTTGAAAAGTTCG
* * * * *
50652916 AGGGTTAAAATATGGTTTTTGGAAAGTTTG
1 AGGGTCAAAATGTGATTTTTGAAAAGTTCG
* *
50652946 AGGGTTAAAATGTGATTTTTGAAAAGTTCA
1 AGGGTCAAAATGTGATTTTTGAAAAGTTCG
*
50652976 AGGGTCAAAATGTGATTTTTAAAAAGTTCG
1 AGGGTCAAAATGTGATTTTTGAAAAGTTCG
*
50653006 GGGGTC
1 AGGGTC
50653012 TAGGCAATAA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (30 bp):
AGGGTCAAAATGTGATTTTTGAAAAGTTCG
Found at i:50653788 original size:26 final size:24
Alignment explanation
Indices: 50653754--50653816 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 24
50653744 AAACTTGAAA
* *
50653754 TTAAGTTTAGAACAATATTTCAAATT
1 TTAAATTTAAAACAA-ATTT-AAATT
*
50653780 TTAAATTTAAAATAAATTTAAATT
1 TTAAATTTAAAACAAATTTAAATT
50653804 TAATAAATTTAAA
1 T--TAAATTTAAA
50653817 TTTAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 6 0.19
25 4 0.12
26 22 0.69
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (24 bp):
TTAAATTTAAAACAAATTTAAATT
Found at i:50653790 original size:6 final size:6
Alignment explanation
Indices: 50653779--50653822 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
50653769 TATTTCAAAT
*
50653779 TTTAAA TTTAAA -ATAAA TTTAAA TTT-AA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
50653823 ATAATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
3 1 0.03
4 2 0.06
5 6 0.19
6 23 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:50653801 original size:17 final size:17
Alignment explanation
Indices: 50653779--50653846 Score: 104
Period size: 17 Copynumber: 4.1 Consensus size: 17
50653769 TATTTCAAAT
50653779 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
50653796 TTTAAATTT--AATAAA
1 TTTAAATTTAAAATAAA
*
50653811 TTTAAATTTAAAATAAT
1 TTTAAATTTAAAATAAA
*
50653828 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
50653845 TT
1 TT
50653847 AAAAATACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
15 15 0.33
17 31 0.67
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:50653810 original size:15 final size:15
Alignment explanation
Indices: 50653779--50653821 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 15
50653769 TATTTCAAAT
50653779 TTTAAATTTAAAATAAA
1 TTTAAATTT--AATAAA
50653796 TTTAAATTTAATAAA
1 TTTAAATTTAATAAA
50653811 TTTAAATTTAA
1 TTTAAATTTAA
50653822 AATAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 17 0.65
17 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAATTTAATAAA
Found at i:50654520 original size:203 final size:204
Alignment explanation
Indices: 50654165--50654610 Score: 671
Period size: 203 Copynumber: 2.2 Consensus size: 204
50654155 TGGTTTGGTG
50654165 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATC----AGA-GACCGCATCACTTGTTTCAATCCG
* * * * * * *
50654230 CTTCTCTGTATTTCTTAAGGAAGACAGATCTGGTTCACTTCTTTGCATCTCATCAGGAAGGCAAC
61 ATTCTCTGTATCTCATAAGAAAGACAGATCTGGTCCACTTCTCTGCATCTCATCAAGAAGGCAAC
* * *
50654295 CACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
126 CACTTTATTGCTTCGACCTGCTTCCCAGTATCTCATCAGAAAGCTGAGGTTCGAAGATTTGCTCA
*
50654360 CTTTGAGCCTAGTT
191 CTTTGAGCCTAGCT
50654374 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAG-GACCGCATCACTTGTTTCAATCCGATTCT
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGAGACCGCATCACTTGTTTCAATCCGATTCT
* * * *
50654438 CTGTATCTCATCAGAAAGAC-GAATTTGGTCCACTTCTCTGTATCTCATCAAGAAGGTAACCACT
66 CTGTATCTCATAAGAAAGACAG-ATCTGGTCCACTTCTCTGCATCTCATCAAGAAGGCAACCACT
50654502 TTATTGCTTCGACCTGCTTCCCAGTATCTCATCAGAAAGCTGAGGTTCGAAGATTTGCTCACTTT
130 TTATTGCTTCGACCTGCTTCCCAGTATCTCATCAGAAAGCTGAGGTTCGAAGATTTGCTCACTTT
*
50654567 GAGCCTGGCT
195 GAGCCTAGCT
*
50654577 TCATTGATTTGGTCTTCTTCTCAGTATCTCATCA
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCA
50654611 AGAAGATGAC
Statistics
Matches: 219, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
202 1 0.00
203 183 0.84
205 2 0.01
209 33 0.15
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (204 bp):
TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGAGACCGCATCACTTGTTTCAATCCGATTCT
CTGTATCTCATAAGAAAGACAGATCTGGTCCACTTCTCTGCATCTCATCAAGAAGGCAACCACTT
TATTGCTTCGACCTGCTTCCCAGTATCTCATCAGAAAGCTGAGGTTCGAAGATTTGCTCACTTTG
AGCCTAGCT
Found at i:50655520 original size:44 final size:44
Alignment explanation
Indices: 50655431--50655520 Score: 103
Period size: 45 Copynumber: 2.1 Consensus size: 44
50655421 AACCTTTTGG
**
50655431 TTTCAAGACGCCCTTTACAAGTTTTCATCTTGACCTCTCTCTTT
1 TTTCAAGACGCCCTTTACAAGTTTTCATCTCAACCTCTCTCTTT
* * * *
50655475 TTTCGAGATGCCCTTTTACGAGTTTTCATCTCAATCT-TCT-TTT
1 TTTCAAGACGCCC-TTTACAAGTTTTCATCTCAACCTCTCTCTTT
50655518 TTT
1 TTT
50655521 AGGCGAAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
43 6 0.15
44 14 0.36
45 19 0.49
ACGTcount: A:0.17, C:0.26, G:0.10, T:0.48
Consensus pattern (44 bp):
TTTCAAGACGCCCTTTACAAGTTTTCATCTCAACCTCTCTCTTT
Found at i:50666456 original size:59 final size:59
Alignment explanation
Indices: 50666364--50666495 Score: 148
Period size: 59 Copynumber: 2.3 Consensus size: 59
50666354 GCTCGGGGAC
* * *
50666364 AAAATGGTAA-TTTTGGACACTTCAGGGGCAAAAATTCAACTTTTT-GAAGTTTGAGG-A
1 AAAATGGTAATTTTTGGAAACTTCAGGGGCAAAAATGCAA-TTTTTGGAAGTTCGAGGTA
* *
50666421 TAAAATGGTAATTTTTGGAAAGTTC-GAGGGCAAAAATGGAATTTTTGGAAGTTCGAGGTCA
1 -AAAATGGTAATTTTTGGAAACTTCAG-GGGCAAAAATGCAATTTTTGGAAGTTCGAGGT-A
50666482 AAAATGG-AATTTTT
1 AAAATGGTAATTTTT
50666496 AGACATCCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
58 16 0.25
59 40 0.62
60 7 0.11
61 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAACTTCAGGGGCAAAAATGCAATTTTTGGAAGTTCGAGGTA
Found at i:50666475 original size:29 final size:29
Alignment explanation
Indices: 50666364--50666582 Score: 157
Period size: 29 Copynumber: 7.5 Consensus size: 29
50666354 GCTCGGGGAC
*
50666364 AAAATGGTAA-TTTTGGACACTTC-AGGGGCA
1 AAAATGG-AATTTTTGGA-AGTTCGA-GGGCA
** *
50666394 AAAATTCAACTTTTT-GAAGTTTGA-GG-A
1 AAAATGGAA-TTTTTGGAAGTTCGAGGGCA
50666421 TAAAATGGTAATTTTTGGAAAGTTCGAGGGCA
1 -AAAATGG-AATTTTTGG-AAGTTCGAGGGCA
*
50666453 AAAATGGAATTTTTGGAAGTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGCA
* * * *
50666482 AAAATGGAATTTTTAGACA-TCCAAGGG-T
1 AAAATGGAATTTTTGGA-AGTTCGAGGGCA
* *
50666510 AAAATGGTAATTTTTGGAAAATTCGAGGTCA
1 AAAATGG-AATTTTTGG-AAGTTCGAGGGCA
* * *
50666541 AAAATGAAACTTTTGGAAGTTCGAGGG-T
1 AAAATGGAATTTTTGGAAGTTCGAGGGCA
*
50666569 AAAATGGTATTTTT
1 AAAATGGAATTTTT
50666583 TTGGAAAAAT
Statistics
Matches: 149, Mismatches: 26, Indels: 30
0.73 0.13 0.15
Matches are distributed among these distances:
27 1 0.01
28 30 0.20
29 59 0.40
30 39 0.26
31 19 0.13
32 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGCA
Found at i:50666535 original size:59 final size:59
Alignment explanation
Indices: 50666453--50666614 Score: 179
Period size: 59 Copynumber: 2.8 Consensus size: 59
50666443 TTCGAGGGCA
*
50666453 AAAATGG-AATTTTTGG-AAGTTCGAGGTCAAAAATGGAATTTTTAGACA-TCCAAGGGT
1 AAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTTAGA-AGTCCAAGGGT
* * * * *
50666510 AAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAATGAAACTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTTAGAAGTCCAAGGGT
* * * *
50666569 AAAATGGTATTTTTTTGGAAAAATTTG-GATCAAAATTGGAATTTTT
1 AAAATGGTA-ATTTTTGG-AAAATTCGAGGTCAAAAATGGAATTTTT
50666615 GGAAAAATTA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 7 0.08
58 10 0.11
59 42 0.48
60 22 0.25
61 7 0.08
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTTAGAAGTCCAAGGGT
Found at i:50666583 original size:88 final size:87
Alignment explanation
Indices: 50666421--50666582 Score: 254
Period size: 88 Copynumber: 1.9 Consensus size: 87
50666411 AGTTTGAGGA
* * *
50666421 TAAAATGGTAATTTTTGGAAAGTTCGAGGGCAAAAATGGAATTTTTGGAAGTTCGAGGTCAAAAA
1 TAAAATGGTAATTTTTGGAAAATTCGAGGGCAAAAATGAAACTTTTGGAAGTTCGAGGT-AAAAA
50666486 TGGAATTTTTAGACATCCAAGGG
65 TGGAATTTTTAGACATCCAAGGG
*
50666509 TAAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAATGAAACTTTTGGAAGTTCGAGGGT-AAAA
1 TAAAATGGTAATTTTTGGAAAATTCGAGGGCAAAAATGAAACTTTTGGAAGTTCGA-GGTAAAAA
*
50666573 TGGTATTTTT
65 TGGAATTTTT
50666583 TTGGAAAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
87 13 0.19
88 52 0.76
89 3 0.04
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (87 bp):
TAAAATGGTAATTTTTGGAAAATTCGAGGGCAAAAATGAAACTTTTGGAAGTTCGAGGTAAAAAT
GGAATTTTTAGACATCCAAGGG
Found at i:50666628 original size:60 final size:58
Alignment explanation
Indices: 50666433--50666619 Score: 146
Period size: 59 Copynumber: 3.2 Consensus size: 58
50666423 AAATGGTAAT
* * * * * *
50666433 TTTTGGAAAGTTCGAGGGCAAAAATGG-AATTTTTGG-AAGTTCGAGGTCAAAAATGGAAT
1 TTTTGGAAA-TTC-AGGG-TAAAATGGTATTTTTTGGAAAATTCGAGATCAAAAATGAAAC
* * * * *
50666492 TTTTAGACATCCAAGGGTAAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAATGAAAC
1 TTTTGGAAATTC-AGGGTAAAATGGTATTTTTTGGAAAATTCGAGATCAAAAATGAAAC
* * * * *
50666551 TTTTGGAAGTTCGAGGGTAAAATGGTATTTTTTTGGAAAAATTTG-GATCAAAATTGGAAT
1 TTTTGGAAATTC-AGGGTAAAATGGTA-TTTTTTGG-AAAATTCGAGATCAAAAATGAAAC
50666611 TTTTGGAAA
1 TTTTGGAAA
50666620 AATTAGGGTC
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
57 7 0.07
58 15 0.14
59 49 0.47
60 26 0.25
61 7 0.07
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (58 bp):
TTTTGGAAATTCAGGGTAAAATGGTATTTTTTGGAAAATTCGAGATCAAAAATGAAAC
Found at i:50666689 original size:30 final size:30
Alignment explanation
Indices: 50666421--50666801 Score: 219
Period size: 30 Copynumber: 12.8 Consensus size: 30
50666411 AGTTTGAGGA
* *
50666421 TAAAATGGTAATTTTTGGAAAGTTCGAGGGC
1 TAAAAT-GTAATTTTTGGAAAGTTCAAGGGT
* * *
50666452 AAAAATGGAATTTTTGG-AAGTTCGA-GGT
1 TAAAATGTAATTTTTGGAAAGTTCAAGGGT
* * * * *
50666480 CAAAAATGGAATTTTTAGACA-TCCAAGGG-
1 -TAAAATGTAATTTTTGGAAAGTTCAAGGGT
* *
50666509 TAAAATGGTAATTTTTGGAAAATTCGA-GGT
1 TAAAAT-GTAATTTTTGGAAAGTTCAAGGGT
* * * *
50666539 CAAAAATGAAACTTTTGG-AAGTTCGAGGG-
1 -TAAAATGTAATTTTTGGAAAGTTCAAGGGT
* * * *
50666568 TAAAATGGTATTTTTTTGGAAAAATT--TGGAT
1 TAAAAT-GTA-ATTTTTGG-AAAGTTCAAGGGT
* * *
50666599 CAAAATTGGAATTTTTGGAAAAATT--AGGGT
1 TAAAA-TGTAATTTTTGG-AAAGTTCAAGGGT
* ** *
50666629 CAAAATGTAATTTTTAAAAAGCTT-AGGGGT
1 TAAAATGTAATTTTTGGAAAG-TTCAAGGGT
*
50666659 TAAAATGTAATTTTTGGAAAGTTTAAGGGT
1 TAAAATGTAATTTTTGGAAAGTTCAAGGGT
* * *
50666689 TAAAATATTATTTTTAGAAAGTTCAAGGGT
1 TAAAATGTAATTTTTGGAAAGTTCAAGGGT
* * *
50666719 TAAAATATTATTTTTAGAAAGTTCAAGGGT
1 TAAAATGTAATTTTTGGAAAGTTCAAGGGT
* * *
50666749 TAAAATGTGATTTTTGAAAAGTTAAAGGGT
1 TAAAATGTAATTTTTGGAAAGTTCAAGGGT
* * * *
50666779 CAAAACGTGATTTTTGAAAAGTT
1 TAAAATGTAATTTTTGGAAAGTT
50666802 TGAGGGTCTT
Statistics
Matches: 284, Mismatches: 49, Indels: 35
0.77 0.13 0.10
Matches are distributed among these distances:
28 15 0.05
29 62 0.22
30 186 0.65
31 16 0.06
32 5 0.02
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (30 bp):
TAAAATGTAATTTTTGGAAAGTTCAAGGGT
Found at i:50667554 original size:55 final size:56
Alignment explanation
Indices: 50667495--50667601 Score: 139
Period size: 55 Copynumber: 1.9 Consensus size: 56
50667485 AAAAAACCAC
50667495 TTTGATTTCCTTC-CCTTTAAAAAAAATCCTTTTC-CTTTTCATTTC-TTAAAACTGT
1 TTTGATTT-CTTCTCCTTTAAAAAAAA-CCTTTTCTCTTTTCATTTCTTTAAAACTGT
* ***
50667550 TTTGATTTTTTCTCCTTTTTTAAAAACCTTTTCTCTTTTCATTTCTTTAAAA
1 TTTGATTTCTTCTCCTTTAAAAAAAACCTTTTCTCTTTTCATTTCTTTAAAA
50667602 ATTGTTTCGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 10 0.22
55 29 0.64
56 6 0.13
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.54
Consensus pattern (56 bp):
TTTGATTTCTTCTCCTTTAAAAAAAACCTTTTCTCTTTTCATTTCTTTAAAACTGT
Found at i:50669650 original size:24 final size:22
Alignment explanation
Indices: 50669622--50669672 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
50669612 TCAATTTGAA
*
50669622 TTTTAAATATTAATGGGTATTGGG
1 TTTTAAATATTAA-AGGT-TTGGG
*
50669646 TTTTAAATTTTAAAGGTTTGGG
1 TTTTAAATATTAAAGGTTTGGG
50669668 TTTTA
1 TTTTA
50669673 TGAGCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
23 3 0.12
24 12 0.48
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (22 bp):
TTTTAAATATTAAAGGTTTGGG
Found at i:50678933 original size:37 final size:37
Alignment explanation
Indices: 50678883--50678956 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
50678873 GCCTTTCAAA
50678883 GCAAATTTATTTTTGACATGGAAAGTTTGGAAATATT
1 GCAAATTTATTTTTGACATGGAAAGTTTGGAAATATT
50678920 GCAAATTTATTTTTGACATGGAAAGTTTGGAAATATT
1 GCAAATTTATTTTTGACATGGAAAGTTTGGAAATATT
50678957 CATTGGTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (37 bp):
GCAAATTTATTTTTGACATGGAAAGTTTGGAAATATT
Found at i:50681449 original size:5 final size:5
Alignment explanation
Indices: 50681405--50681442 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
50681395 TCTAGGTCAA
50681405 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
50681443 TAATTTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:50681680 original size:18 final size:18
Alignment explanation
Indices: 50681657--50681695 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50681647 GGTGTGTAGT
50681657 AATTTTAAA-ATATTTTAA
1 AATTTTAAATAT-TTTTAA
*
50681675 AATTTTGAATATTTTTAA
1 AATTTTAAATATTTTTAA
50681693 AAT
1 AAT
50681696 ACTAGTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTTTAAATATTTTTAA
Found at i:50688560 original size:32 final size:31
Alignment explanation
Indices: 50688516--50688575 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
50688506 TCGTCAAAGT
50688516 CTTTTTACGGCCATAAATGAAAACATATAGA
1 CTTTTTACGGCCATAAATGAAAACATATAGA
* *
50688547 CTTTTGTATGGCCATAAATGAGAACATAT
1 CTTTT-TACGGCCATAAATGAAAACATAT
50688576 TTCTTAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (31 bp):
CTTTTTACGGCCATAAATGAAAACATATAGA
Found at i:50688580 original size:82 final size:82
Alignment explanation
Indices: 50688443--50688635 Score: 359
Period size: 82 Copynumber: 2.4 Consensus size: 82
50688433 ATATAACATA
*
50688443 GCCATAAATGAAAACATATAGACTTTTGTATGGCCATAAATGAGAACACATTTCTTAACTAAGTC
1 GCCATAAATGAAAACATATAGACTTTTGTATGGCCATAAATGAGAACACATTTCTTAACAAAGTC
*
50688508 GTCAAAGTCTTTTTACG
66 ATCAAAGTCTTTTTACG
*
50688525 GCCATAAATGAAAACATATAGACTTTTGTATGGCCATAAATGAGAACATATTTCTTAACAAAGTC
1 GCCATAAATGAAAACATATAGACTTTTGTATGGCCATAAATGAGAACACATTTCTTAACAAAGTC
50688590 ATCAAAGTCTTTTTACG
66 ATCAAAGTCTTTTTACG
50688607 GCCATAAATGAAAACATATAGACTTTTGT
1 GCCATAAATGAAAACATATAGACTTTTGT
50688636 CGACGACCCA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 108 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (82 bp):
GCCATAAATGAAAACATATAGACTTTTGTATGGCCATAAATGAGAACACATTTCTTAACAAAGTC
ATCAAAGTCTTTTTACG
Found at i:50697079 original size:17 final size:17
Alignment explanation
Indices: 50697041--50697073 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
50697031 ATAATTAATA
50697041 ATTA-ATAAAATATTAG
1 ATTATATAAAATATTAG
50697057 ATTATATAAATATATTA
1 ATTATATAAA-ATATTA
50697074 TTTATAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTATATAAAATATTAG
Found at i:50697170 original size:16 final size:15
Alignment explanation
Indices: 50697140--50697173 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
50697130 TATCTTTAAA
50697140 TTTTTTGCTAGTTTT
1 TTTTTTGCTAGTTTT
50697155 TTTTTTGTCTA-TTTT
1 TTTTTTG-CTAGTTTT
50697170 TTTT
1 TTTT
50697174 ATTTTAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.06, C:0.06, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTTTGCTAGTTTT
Found at i:50704612 original size:24 final size:24
Alignment explanation
Indices: 50704562--50704613 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
50704552 TTTTAAAAAA
* * *
50704562 TATAAATATATATAATTTATAATT
1 TATAAATACATATAATATATAAAT
50704586 TATAAATACATA-AATATATTAAAT
1 TATAAATACATATAATATA-TAAAT
50704610 TATA
1 TATA
50704614 TATTTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAAATACATATAATATATAAAT
Found at i:50704913 original size:29 final size:28
Alignment explanation
Indices: 50704880--50704942 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
50704870 TTCCATTTTC
*
50704880 AATTT-CTTAATCATAAATATTTTTTATTT
1 AATTTACTTAATCATAAA-A-ATTTTATTT
*
50704909 AATTTTACTTTATCATAAAAATTTTATTT
1 AA-TTTACTTAATCATAAAAATTTTATTT
50704938 AATTT
1 AATTT
50704943 TTATTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.10
29 12 0.40
30 4 0.13
31 11 0.37
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (28 bp):
AATTTACTTAATCATAAAAATTTTATTT
Found at i:50713987 original size:24 final size:24
Alignment explanation
Indices: 50713926--50713988 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
50713916 TAGAGTAATA
* * * *
50713926 AGAGTTTGACTCAAATAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
50713950 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
50713974 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
50713989 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:50715973 original size:24 final size:24
Alignment explanation
Indices: 50715916--50715978 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
50715906 TAGAGTAATA
* *
50715916 AGAGTTTAACTCAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
50715940 AGAATTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
50715964 AGAGTTTAATTGAAA
1 AGAGTTTAATTGAAA
50715979 AATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.25
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:50726372 original size:20 final size:22
Alignment explanation
Indices: 50726328--50726378 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
50726318 TTTTATTATT
*
50726328 TATTTTT-ATTTTATTATTTGC
1 TATTTTTAATTTAATTATTTGC
50726349 -ATTTTTAATTTAATT-TTT-C
1 TATTTTTAATTTAATTATTTGC
50726368 TA-TTTTAATTT
1 TATTTTTAATTT
50726379 TTTTCCCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 7 0.26
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTTTTAATTTAATTATTTGC
Found at i:50729139 original size:12 final size:11
Alignment explanation
Indices: 50729121--50729154 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
50729111 AAAAAATTAG
50729121 TATATTTATTT
1 TATATTTATTT
50729132 TCATATTTATTT
1 T-ATATTTATTT
50729144 TAT-TTTATTT
1 TATATTTATTT
50729154 T
1 T
50729155 TAATTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.36
11 3 0.14
12 11 0.50
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (11 bp):
TATATTTATTT
Found at i:50729147 original size:17 final size:17
Alignment explanation
Indices: 50729125--50729166 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
50729115 AATTAGTATA
50729125 TTTATTTTCATATTT-AT
1 TTTATTTT-ATATTTAAT
*
50729142 TTTATTTTATTTTTAAT
1 TTTATTTTATATTTAAT
50729159 TTTATTTT
1 TTTATTTT
50729167 TGCAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTATATTTAAT
Found at i:50729160 original size:12 final size:11
Alignment explanation
Indices: 50729125--50729167 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
50729115 AATTAGTATA
*
50729125 TTTATTTTCAT
1 TTTATTTTTAT
50729136 ATTTA-TTTTAT
1 -TTTATTTTTAT
50729147 TTTATTTTTAAT
1 TTTATTTTT-AT
50729159 TTTATTTTT
1 TTTATTTTT
50729168 GCAATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 4 0.14
11 9 0.32
12 15 0.54
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:50731172 original size:23 final size:23
Alignment explanation
Indices: 50731146--50731266 Score: 147
Period size: 23 Copynumber: 5.2 Consensus size: 23
50731136 ACACTAGCGC
50731146 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
50731169 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
50731192 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
50731217 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
* *
50731240 GCTCTCTGATTAGCACTTTGTAT
1 GCTCTCTGATTAGCACTGTGTGT
50731263 GCTC
1 GCTC
50731267 AGTACTTTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
22 4 0.05
23 61 0.72
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:50731215 original size:48 final size:46
Alignment explanation
Indices: 50731146--50731266 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
50731136 ACACTAGCGC
* *
50731146 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
50731192 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
* *
50731240 GCTCTCTGATTAGCACTTTGTATGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
50731267 AGTACTTTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
46 25 0.37
48 41 0.61
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:50731295 original size:39 final size:39
Alignment explanation
Indices: 50731231--50731305 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
50731221 TCCGATTAGC
*
50731231 ACTTCGTGTGCTCTCTGATTAGCACTTTGTATGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTATGCTCAGT
* * *
50731270 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTATGCTC
50731306 TCTGTTGCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTATGCTCAGT
Found at i:50731300 original size:23 final size:23
Alignment explanation
Indices: 50731265--50731358 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
50731255 CTTTGTATGC
*
50731265 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
50731288 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
50731311 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
50731336 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
50731358 T
1 T
50731359 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:50737620 original size:23 final size:23
Alignment explanation
Indices: 50737594--50737714 Score: 147
Period size: 23 Copynumber: 5.2 Consensus size: 23
50737584 ACACTAGCGC
50737594 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
50737617 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
50737640 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
50737665 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
* *
50737688 GCTCTCTGATTAGCACTTTGTAT
1 GCTCTCTGATTAGCACTGTGTGT
50737711 GCTC
1 GCTC
50737715 AGTACTTTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
22 4 0.05
23 61 0.72
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:50737663 original size:48 final size:46
Alignment explanation
Indices: 50737594--50737714 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
50737584 ACACTAGCGC
* *
50737594 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
50737640 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
* *
50737688 GCTCTCTGATTAGCACTTTGTATGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
50737715 AGTACTTTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
46 25 0.37
48 41 0.61
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:50737743 original size:39 final size:39
Alignment explanation
Indices: 50737679--50737753 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
50737669 TCCGATTAGC
*
50737679 ACTTCGTGTGCTCTCTGATTAGCACTTTGTATGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTATGCTCAGT
* * *
50737718 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTATGCTC
50737754 TCTGTTGCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTATGCTCAGT
Found at i:50737748 original size:23 final size:23
Alignment explanation
Indices: 50737713--50737806 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
50737703 CTTTGTATGC
*
50737713 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
50737736 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
50737759 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
50737784 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
50737806 T
1 T
50737807 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:50739311 original size:46 final size:46
Alignment explanation
Indices: 50739244--50739335 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
50739234 ATATTAACCA
50739244 ATGATCCATATATTTGTGGTATATTTACCCCTTTATTGACTCCCTT
1 ATGATCCATATATTTGTGGTATATTTACCCCTTTATTGACTCCCTT
50739290 ATGATCCATATATTTGTGGTATATTTACCCCTTTATTGACTCCCTT
1 ATGATCCATATATTTGTGGTATATTTACCCCTTTATTGACTCCCTT
50739336 TTTGTCGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (46 bp):
ATGATCCATATATTTGTGGTATATTTACCCCTTTATTGACTCCCTT
Found at i:50739437 original size:17 final size:16
Alignment explanation
Indices: 50739414--50739453 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
50739404 TATTATTTAG
**
50739414 AAAAAAAATGTCGAAA
1 AAAAAAAATGAAGAAA
50739430 AGAAAAAAATGAAGAAA
1 A-AAAAAAATGAAGAAA
50739447 AAAAAAA
1 AAAAAAA
50739454 GAATTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAAAAAATGAAGAAA
Found at i:50740985 original size:15 final size:15
Alignment explanation
Indices: 50740948--50740986 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
50740938 TTATGTGTGC
*
50740948 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
50740963 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
50740977 TTAATTCTTG
1 TTAATTCTTG
50740987 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:50744828 original size:22 final size:22
Alignment explanation
Indices: 50744803--50744846 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
50744793 ACACACCCTA
50744803 AATATAAACTTAATTATTTAGG
1 AATATAAACTTAATTATTTAGG
50744825 AATATAAACTTAATTATTTAGG
1 AATATAAACTTAATTATTTAGG
50744847 GTGTGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (22 bp):
AATATAAACTTAATTATTTAGG
Found at i:50744886 original size:17 final size:16
Alignment explanation
Indices: 50744864--50744912 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
50744854 ATAATTTTAA
50744864 AATATTTTAAAATGTT
1 AATATTTTAAAATGTT
**
50744880 GAATATTTTTAAAATACT
1 -AATA-TTTTAAAATGTT
*
50744898 AATATGTTAAAATGT
1 AATATTTTAAAATGT
50744913 ATTGTTTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 8 0.31
17 8 0.31
18 10 0.38
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (16 bp):
AATATTTTAAAATGTT
Found at i:50753843 original size:16 final size:16
Alignment explanation
Indices: 50753826--50753856 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
50753816 TATAGAAAAT
50753826 TTTA-AAAAATATAAA
1 TTTATAAAAATATAAA
50753841 TTTATAAAAATATAAA
1 TTTATAAAAATATAAA
50753857 GTTGCTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTATAAAAATATAAA
Found at i:50756830 original size:13 final size:13
Alignment explanation
Indices: 50756801--50756862 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
50756791 TAAACCAAAT
*
50756801 TTTTCAAAAGTAT
1 TTTTCAAAAGTAC
*
50756814 TTTTCAAAATTAC
1 TTTTCAAAAGTAC
* * *
50756827 TTTTCTAACGCAC
1 TTTTCAAAAGTAC
* *
50756840 TTTTTAAAAGAAC
1 TTTTCAAAAGTAC
*
50756853 TTCTCAAAAG
1 TTTTCAAAAG
50756863 CAATACTAAA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAGTAC
Found at i:50758491 original size:9 final size:9
Alignment explanation
Indices: 50758477--50758501 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
50758467 CGCGTTAGAC
50758477 TATTATAAT
1 TATTATAAT
50758486 TATTATAAT
1 TATTATAAT
50758495 TATTATA
1 TATTATA
50758502 TACATAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATAAT
Found at i:50763380 original size:2 final size:2
Alignment explanation
Indices: 50763375--50763400 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50763365 TATGCTTTAG
50763375 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
50763401 TATGTGAGAA
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:50767592 original size:34 final size:34
Alignment explanation
Indices: 50767554--50767620 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
50767544 AATAAGGAAA
50767554 CAATATACACAAATCCCATAAATAACTCCTAACT
1 CAATATACACAAATCCCATAAATAACTCCTAACT
* *
50767588 CAATATATACAAATCCCATAAATTACTCCTAAC
1 CAATATACACAAATCCCATAAATAACTCCTAAC
50767621 ACCTCCCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.25
Consensus pattern (34 bp):
CAATATACACAAATCCCATAAATAACTCCTAACT
Found at i:50773154 original size:8 final size:8
Alignment explanation
Indices: 50773114--50773211 Score: 60
Period size: 8 Copynumber: 11.5 Consensus size: 8
50773104 AAAACTCGTA
50773114 AAAATTAT
1 AAAATTAT
50773122 AAAATATAT
1 AAAAT-TAT
50773131 AGAAA-TAT
1 A-AAATTAT
*
50773139 AGAA--AT
1 AAAATTAT
50773145 AAAATTAT
1 AAAATTAT
50773153 AAAATTTTAT
1 AAAA--TTAT
*
50773163 AAAGTTGAGT
1 AAAATT-A-T
50773173 GAAAATTAT
1 -AAAATTAT
50773182 AAAA-TAT
1 AAAATTAT
50773189 AAAATTAGT
1 AAAATTA-T
50773198 AAAAATATAT
1 -AAAAT-TAT
50773208 AAAA
1 AAAA
50773212 ATTACCGTAC
Statistics
Matches: 73, Mismatches: 4, Indels: 25
0.72 0.04 0.25
Matches are distributed among these distances:
6 5 0.07
7 9 0.12
8 23 0.32
9 11 0.15
10 18 0.25
11 7 0.10
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (8 bp):
AAAATTAT
Found at i:50773194 original size:15 final size:17
Alignment explanation
Indices: 50773174--50773206 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
50773164 AAGTTGAGTG
50773174 AAAATTA-T-AAAATAT
1 AAAATTAGTAAAAATAT
50773189 AAAATTAGTAAAAATAT
1 AAAATTAGTAAAAATAT
50773206 A
1 A
50773207 TAAAAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAATTAGTAAAAATAT
Found at i:50773208 original size:26 final size:26
Alignment explanation
Indices: 50773145--50773211 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
50773135 ATATAGAAAT
* *
50773145 AAAATTATAAAATTTTATAAAGTTGAGTG
1 AAAATTATAAAA---TATAAAATTGAGTA
50773174 AAAATTATAAAATATAAAATT-AGTA
1 AAAATTATAAAATATAAAATTGAGTA
50773199 AAAATATATAAAA
1 AAAAT-TATAAAA
50773212 ATTACCGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 8 0.23
26 15 0.43
29 12 0.34
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (26 bp):
AAAATTATAAAATATAAAATTGAGTA
Found at i:50773520 original size:18 final size:17
Alignment explanation
Indices: 50773466--50773521 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
50773456 TTTTAAATAT
*
50773466 TTTAT-TTTTTATTAAAA
1 TTTATATTTTTATT-ATA
50773483 TTTAATCATTTTTATT-TA
1 TTT-AT-ATTTTTATTATA
50773501 TTTATATTTTTATATATA
1 TTTATATTTTTAT-TATA
50773519 TTT
1 TTT
50773522 TTACCACATG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
16 8 0.24
17 6 0.18
18 11 0.33
20 8 0.24
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATATTTTTATTATA
Found at i:50773795 original size:88 final size:89
Alignment explanation
Indices: 50773608--50773826 Score: 225
Period size: 88 Copynumber: 2.5 Consensus size: 89
50773598 TAACAGTCAA
* * * *
50773608 AGGGTCTTTTTT-ATGCATTTTGATAGTTTAAGTATCTAATTGTGTGGAAAAAAAAAAGGAGTTT
1 AGGG-CTTTTTTGATGTATTTTGAAAGTTTAAGTATCCAATTGAGTGGAAAAAAAAAAGGAGTTT
*
50773672 AATTGCCTTTTTTTGAAAAAGTTGG
65 AATTGACTTTTTTTGAAAAAGTTGG
* * *
50773697 A-GGATATTTTTGATGTATTTTGAAAGTTT-AGTATCCAATTGAGTGTAAAAAAAAACTAGGGGT
1 AGGGCT-TTTTTGATGTATTTTGAAAGTTTAAGTATCCAATTGAGTGGAAAAAAAAA--AGGAGT
* *
50773760 TTAA-TGAC-TTTTTTGAAAAATTTTG
63 TTAATTGACTTTTTTTGAAAAAGTTGG
* * * * *
50773785 AGGGCTTTTTTGATCT-TTTTTAAAGTTCAAATACCCAATTGA
1 AGGGCTTTTTTGATGTATTTTGAAAGTTTAAGTATCCAATTGA
50773827 ATAAAAAAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
87 11 0.10
88 66 0.61
89 22 0.20
90 9 0.08
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (89 bp):
AGGGCTTTTTTGATGTATTTTGAAAGTTTAAGTATCCAATTGAGTGGAAAAAAAAAAGGAGTTTA
ATTGACTTTTTTTGAAAAAGTTGG
Found at i:50794358 original size:25 final size:25
Alignment explanation
Indices: 50794327--50794382 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
50794317 ACTAAATCAA
* * *
50794327 TTTTAATAGTCTATATGTTTTTAAT
1 TTTTAATAATCTATATATTTATAAT
*
50794352 TTTTAATAATTTATATATTTATAAT
1 TTTTAATAATCTATATATTTATAAT
50794377 TTTTAA
1 TTTTAA
50794383 ATGATTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTTAATAATCTATATATTTATAAT
Found at i:50796158 original size:16 final size:17
Alignment explanation
Indices: 50796137--50796174 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
50796127 AATTTGACTG
50796137 TTATAACAAAAT-GTTA
1 TTATAACAAAATAGTTA
* *
50796153 TTATAACATAATAGTTG
1 TTATAACAAAATAGTTA
50796170 TTATA
1 TTATA
50796175 GAGAAAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (17 bp):
TTATAACAAAATAGTTA
Found at i:50797184 original size:76 final size:76
Alignment explanation
Indices: 50797058--50797211 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
50797048 ATGCACAGAC
50797058 AGCGTTTCACATCACTTCAATTACTAGTGGACAGGCATGTAGGTCCAACCCACATAAGATATAAA
1 AGCGTTTCACATCACTTCAATTACTAGTGGACAGGCATGTAGGTCCAACCCACATAAGATATAAA
50797123 GGCATGGATGG
66 GGCATGGATGG
50797134 AGCGTTTCACATCACTTCAATTACTAGTGGACAGGCATGTAGGTCCAACCCACATAAGATATAAA
1 AGCGTTTCACATCACTTCAATTACTAGTGGACAGGCATGTAGGTCCAACCCACATAAGATATAAA
50797199 GGCATGGATGG
66 GGCATGGATGG
50797210 AG
1 AG
50797212 TCTTTTTATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (76 bp):
AGCGTTTCACATCACTTCAATTACTAGTGGACAGGCATGTAGGTCCAACCCACATAAGATATAAA
GGCATGGATGG
Found at i:50797259 original size:18 final size:18
Alignment explanation
Indices: 50797238--50797276 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50797228 ATAATTTAAC
50797238 ATTTTAAAATT-TATTTTA
1 ATTTTAAAATTATA-TTTA
*
50797256 ATTTTAATATTATATTTA
1 ATTTTAAAATTATATTTA
50797274 ATT
1 ATT
50797277 AAGAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTAAAATTATATTTA
Found at i:50798977 original size:24 final size:24
Alignment explanation
Indices: 50798919--50798981 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
50798909 AAAAGTTCTA
* *
50798919 ATTATGAAAAGAAATAACAAAAAT
1 ATTATGATAATAAATAACAAAAAT
* *
50798943 TTTATGATAATAAATAACAAATAT
1 ATTATGATAATAAATAACAAAAAT
*
50798967 ATTATGTTAATAAAT
1 ATTATGATAATAAAT
50798982 TCTTAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.33
Consensus pattern (24 bp):
ATTATGATAATAAATAACAAAAAT
Found at i:50799239 original size:36 final size:37
Alignment explanation
Indices: 50799174--50799260 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 37
50799164 GACTTCGTTG
* *
50799174 GGCTTATAGACTTCACCAAAACTTATAGAGTTCATCA
1 GGCTTATAGACTTCACCAAAACTCATAGAGTTAATCA
**
50799211 GGCTTATAGACTTTGCC-AAACTCATAGAGTTAATCA
1 GGCTTATAGACTTCACCAAAACTCATAGAGTTAATCA
* * *
50799247 AGCATATTGACTTC
1 GGCTTATAGACTTC
50799261 GTCGACTCTA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 27 0.64
37 15 0.36
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (37 bp):
GGCTTATAGACTTCACCAAAACTCATAGAGTTAATCA
Found at i:50805387 original size:18 final size:19
Alignment explanation
Indices: 50805350--50805387 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
50805340 AGGATTATAC
* *
50805350 TTCATTATTCTATTTTAAT
1 TTCAGTATTCTATTTGAAT
50805369 TTCAGTATTC-ATTTGAAT
1 TTCAGTATTCTATTTGAAT
50805387 T
1 T
50805388 AAAATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (19 bp):
TTCAGTATTCTATTTGAAT
Found at i:50805479 original size:29 final size:29
Alignment explanation
Indices: 50805413--50805483 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
50805403 TTTAAATGAT
* *
50805413 ATATATTTTTATAATTTTTAAAAGATTAA
1 ATATATTTTTATAATTTTAAAAAGATAAA
*
50805442 ATCAAATTTTTATAATTTTAAAAAG-TAAA
1 AT-ATATTTTTATAATTTTAAAAAGATAAA
50805471 AGTATATTTTTAT
1 A-TATATTTTTAT
50805484 CTTTACTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.42
30 21 0.58
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (29 bp):
ATATATTTTTATAATTTTAAAAAGATAAA
Found at i:50806776 original size:43 final size:43
Alignment explanation
Indices: 50806728--50806814 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
50806718 AGCCAAGTAC
*
50806728 ATAAACATCACTTGTAATACAACCTTACAGCTTGCTACTTTAT
1 ATAAACATCACTTGTAATACAACCTTACAGCTTCCTACTTTAT
50806771 ATAAACATCACTTGTAATACAACCTTACAGCTTCCTACTTTAT
1 ATAAACATCACTTGTAATACAACCTTACAGCTTCCTACTTTAT
50806814 A
1 A
50806815 ATCTTAAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (43 bp):
ATAAACATCACTTGTAATACAACCTTACAGCTTCCTACTTTAT
Found at i:50810252 original size:19 final size:19
Alignment explanation
Indices: 50810228--50810264 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50810218 TTAAAATCTA
50810228 AAAATACAAAAAAATTATT
1 AAAATACAAAAAAATTATT
* *
50810247 AAAATATAAAGAAATTAT
1 AAAATACAAAAAAATTAT
50810265 AACTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAATACAAAAAAATTATT
Found at i:50819735 original size:31 final size:29
Alignment explanation
Indices: 50819680--50819750 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
50819670 AAAGTTTGAA
*
50819680 TTAATTTTAAATTCATTTTTAAATTTATC
1 TTAAATTTAAATTCATTTTTAAATTTATC
* *
50819709 TTAAATTTAAATTTACTTATTTAAATTTATT
1 TTAAATTTAAATTCA-TT-TTTAAATTTATC
50819740 TTAAATTTAAA
1 TTAAATTTAAA
50819751 CTTAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 13 0.35
30 2 0.05
31 22 0.59
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATTTAAATTCATTTTTAAATTTATC
Found at i:50819747 original size:11 final size:11
Alignment explanation
Indices: 50819678--50819748 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
50819668 TTAAAGTTTG
*
50819678 AATTAATTTTA
1 AATTTATTTTA
*
50819689 AATTCATTTTTA
1 AATTTA-TTTTA
*
50819701 AATTTATCTTA
1 AATTTATTTTA
*
50819712 AATTTAAATTT-
1 AATTT-ATTTTA
*
50819723 -ACTTA-TTTA
1 AATTTATTTTA
50819732 AATTTATTTTA
1 AATTTATTTTA
50819743 AATTTA
1 AATTTA
50819749 AACTTAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 3 0.06
9 1 0.02
10 7 0.15
11 24 0.50
12 13 0.27
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:50819759 original size:17 final size:17
Alignment explanation
Indices: 50819727--50819761 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
50819717 AAATTTACTT
* *
50819727 ATTTAAATTTATTTTAA
1 ATTTAAACTTAATTTAA
50819744 ATTTAAACTTAATTTAA
1 ATTTAAACTTAATTTAA
50819761 A
1 A
50819762 ATAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAACTTAATTTAA
Found at i:50819842 original size:28 final size:27
Alignment explanation
Indices: 50819800--50819862 Score: 117
Period size: 28 Copynumber: 2.3 Consensus size: 27
50819790 CAATGTCCAT
50819800 TTACAAAAGCCCAAATTAAAGGCCCGA
1 TTACAAAAGCCCAAATTAAAGGCCCGA
50819827 TTACAAGAAGCCCAAATTAAAGGCCCGA
1 TTACAA-AAGCCCAAATTAAAGGCCCGA
50819855 TTACAAAA
1 TTACAAAA
50819863 AACCCAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 8 0.23
28 27 0.77
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (27 bp):
TTACAAAAGCCCAAATTAAAGGCCCGA
Found at i:50820460 original size:16 final size:16
Alignment explanation
Indices: 50820439--50820469 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50820429 TAAAAATATT
50820439 ATTAATAATCATAATA
1 ATTAATAATCATAATA
*
50820455 ATTAATAATTATAAT
1 ATTAATAATCATAAT
50820470 TAATATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAATAATCATAATA
Found at i:50820462 original size:7 final size:7
Alignment explanation
Indices: 50820439--50820508 Score: 67
Period size: 7 Copynumber: 10.3 Consensus size: 7
50820429 TAAAAATATT
50820439 ATTAATA
1 ATTAATA
50820446 ATCATAATA
1 AT--TAATA
50820455 ATTAATA
1 ATTAATA
50820462 ATT-ATA
1 ATTAATA
50820468 ATTAAT-
1 ATTAATA
* *
50820474 ATTTATG
1 ATTAATA
50820481 ATT-ATA
1 ATTAATA
*
50820487 GTTAAT-
1 ATTAATA
50820493 ATTAATA
1 ATTAATA
50820500 ATTAATA
1 ATTAATA
50820507 AT
1 AT
50820509 ATTAAAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
6 20 0.38
7 26 0.49
9 7 0.13
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (7 bp):
ATTAATA
Found at i:50820468 original size:13 final size:13
Alignment explanation
Indices: 50820452--50820508 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
50820442 AATAATCATA
50820452 ATAATTAATAATT
1 ATAATTAATAATT
*
50820465 ATAATTAATATTT
1 ATAATTAATAATT
* *
50820478 ATGATT-ATAGTT
1 ATAATTAATAATT
50820490 A-ATATTAATAATT
1 ATA-ATTAATAATT
50820503 AATAAT
1 -ATAAT
50820509 ATTAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 9 0.26
13 22 0.63
14 3 0.09
15 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (13 bp):
ATAATTAATAATT
Found at i:50820503 original size:19 final size:19
Alignment explanation
Indices: 50820438--50820508 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
50820428 ATAAAAATAT
*
50820438 TATTAATAATCATAA-T-A
1 TATTAATAATTATAATTAA
50820455 -ATTAATAATTATAATTAA
1 TATTAATAATTATAATTAA
* * *
50820473 TATTTATGATTATAGTTAA
1 TATTAATAATTATAATTAA
50820492 TATTAATAATTAATAAT
1 TATTAATAATT-ATAAT
50820509 ATTAAAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 13 0.30
17 1 0.02
18 1 0.02
19 24 0.56
20 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTAATAATTATAATTAA
Found at i:50821661 original size:30 final size:30
Alignment explanation
Indices: 50821627--50821982 Score: 367
Period size: 30 Copynumber: 11.9 Consensus size: 30
50821617 AATCGTCCAG
* *
50821627 AAATTACATTTCGACCCCAAAACTTTTTGA
1 AAATTACATTTTGACCCCAAAACTTTTTCA
* * *
50821657 AAATTATATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTTCA
* *
50821687 AAATTACATTTCGACCCCAAAACTTTCT-A
1 AAATTACATTTTGACCCCAAAACTTTTTCA
* * *
50821716 AAATTTATATTTTGACCCCAAAACTTTCTAA
1 AAA-TTACATTTTGACCCCAAAACTTTTTCA
* *
50821747 AAATTACATTTTAACCCCTAAA-TTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTT-CA
* *
50821777 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTTCA
* * ** *
50821807 AATTTACACTTTGACCCTTAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTTCA
* * *
50821837 AAATTATATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTTCA
* * * * *
50821867 AAATTATATTTCGACCTCAAAACTTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTTTCA
*
50821897 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTTCA
*
50821927 AAATTACATTTTGACTCCAAAAC-TTTTCTA
1 AAATTACATTTTGACCCCAAAACTTTTTC-A
* * * *
50821957 AAATTATACTTTAACCCCGAAACTTT
1 AAATTACATTTTGACCCCAAAACTTT
50821983 CAAAAATTAT
Statistics
Matches: 271, Mismatches: 49, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
29 12 0.04
30 249 0.92
31 10 0.04
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTTCA
Found at i:50821793 original size:90 final size:90
Alignment explanation
Indices: 50821627--50822010 Score: 458
Period size: 90 Copynumber: 4.3 Consensus size: 90
50821617 AATCGTCCAG
* ** *
50821627 AAATTACATTTCGACCCCAAAACTTTTTGAAAATTATATTTTGACCCTAAAACTTTTCCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATT
*
50821692 ACATTTCGACCCCAAAACTTTCTAA
66 ATATTTCGACCCCAAAACTTTCTAA
* * * * *
50821717 AATTTATATTTTGACCCCAAAAC-TTTCTAAAAATTACATTTTAACCCCT-AAATTTTTCCAAAA
1 AAATTACATTTTGACCCCAAAACTTTTC-CAAAATTACATTTTGA-CCCTAAAACTTTTCCAAAA
* *
50821780 TTATATTTTGACCCCAAAACTTT-TCCA
64 TTATATTTCGACCCCAAAACTTTCT-AA
* * ** *
50821807 AATTTACACTTTGACCCTTAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATT
*
50821872 ATATTTCGACCTCAAAACTTTCTAA
66 ATATTTCGACCCCAAAACTTTCTAA
*
50821897 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACTCC-AAAACTTTTCTAAAAT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGAC-CCTAAAACTTTTCCAAAAT
* *
50821961 TATACTTT-AACCCCGAAACTTTC-AA
65 TATA-TTTCGACCCCAAAACTTTCTAA
* *
50821986 AAATTATTATTTT-ACCCCCAAACTT
1 AAATTA-CATTTTGACCCCAAAACTT
50822011 CCCTAAATCC
Statistics
Matches: 252, Mismatches: 33, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
89 27 0.11
90 211 0.84
91 14 0.06
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (90 bp):
AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATT
ATATTTCGACCCCAAAACTTTCTAA
Found at i:50821998 original size:60 final size:60
Alignment explanation
Indices: 50821622--50822010 Score: 457
Period size: 60 Copynumber: 6.5 Consensus size: 60
50821612 CCCTAAATCG
* *
50821622 TCCAGAAATTACATTTCGACCCCAAAACTTTT-TGAAAATTATATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTTTCT-AAAATTATATTTTGACCCCAAAACTTT
*
50821683 TCCAAAATTACATTTCGACCCCAAAAC-TTTCTAAAATTTATATTTTGACCCCAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCTAAAA-TTATATTTTGACCCCAAAACTTT
* * * * *
50821742 TCTAAAAATTACATTTTAACCCCTAAATTTTTCCAAAATTATATTTTGACCCCAAAACTTT
1 TC-CAAAATTACATTTTGACCCCAAAACTTTTCTAAAATTATATTTTGACCCCAAAACTTT
* * ** * *
50821803 TCCAAATTTACACTTTGACCCTTAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCTAAAATTATATTTTGACCCCAAAACTTT
* * * *
50821863 TCCAAAATTATATTTCGACCTCAAAAC-TTTCTAAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCT-AAAATTATATTTTGACCCCAAAACTTT
* * * *
50821923 TCCAAAATTACATTTTGACTCCAAAACTTTTCTAAAATTATACTTTAACCCCGAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCTAAAATTATATTTTGACCCCAAAACTTT
* * *
50821982 TCAAAAATTATTATTTT-ACCCCCAAACTT
1 TCCAAAATTA-CATTTTGACCCCAAAACTT
50822011 CCCTAAATCC
Statistics
Matches: 284, Mismatches: 36, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
59 36 0.13
60 227 0.80
61 21 0.07
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (60 bp):
TCCAAAATTACATTTTGACCCCAAAACTTTTCTAAAATTATATTTTGACCCCAAAACTTT
Found at i:50822046 original size:59 final size:58
Alignment explanation
Indices: 50821983--50822178 Score: 162
Period size: 59 Copynumber: 3.4 Consensus size: 58
50821973 CCGAAACTTT
* * *
50821983 CAAAAATTATTATTTTACCCCCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACTATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * * * * * * * ** * **
50822042 CAAAACTTACTGTTTTGCCTCCGAACTTTCCAAAATTTCA-TGTTGACCTTGTTTTTGC
1 CAAAAATTACTATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * * *
50822100 CAAAATTTACCATTTTATTCCCCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACTATTTTA-CCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
*
50822158 CAAAAATTACAATTTTACCCC
1 CAAAAATTACTATTTTACCCC
50822179 TAAAACCCAA
Statistics
Matches: 99, Mismatches: 36, Indels: 6
0.70 0.26 0.04
Matches are distributed among these distances:
57 3 0.03
58 46 0.46
59 50 0.51
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.37
Consensus pattern (58 bp):
CAAAAATTACTATTTTACCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
Found at i:50826352 original size:21 final size:19
Alignment explanation
Indices: 50826320--50826359 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
50826310 TGCAGATATA
*
50826320 AGGTGTTGAAGGTGTATTTT
1 AGGTGTTAAAGGTGT-TTTT
50826340 AGGTAGTTAAAGGTGTTTTT
1 AGGT-GTTAAAGGTGTTTTT
50826360 CAAAGGGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.45
Consensus pattern (19 bp):
AGGTGTTAAAGGTGTTTTT
Found at i:50828682 original size:23 final size:23
Alignment explanation
Indices: 50828647--50828692 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
50828637 TAATCGAGTG
* *
50828647 AAATTATTCATGTTAAATTAAAA
1 AAATTAATAATGTTAAATTAAAA
50828670 AAATTAATAATGTTAAATTAAAA
1 AAATTAATAATGTTAAATTAAAA
50828693 TTTTGTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (23 bp):
AAATTAATAATGTTAAATTAAAA
Found at i:50828930 original size:26 final size:27
Alignment explanation
Indices: 50828896--50828965 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
50828886 TTTTAAAAAA
*
50828896 TTTATAATTTTTTTAAAAATACA-AAT
1 TTTAAAATTTTTTTAAAAATACAGAAT
* * * **
50828922 TTTAGAATTTTTATAAATATTTAGAAT
1 TTTAAAATTTTTTTAAAAATACAGAAT
50828949 TTTAAAATTATTTTTAA
1 TTTAAAATT-TTTTTAA
50828966 TTTTTAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
26 18 0.51
27 11 0.31
28 6 0.17
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (27 bp):
TTTAAAATTTTTTTAAAAATACAGAAT
Found at i:50828970 original size:19 final size:19
Alignment explanation
Indices: 50828920--50828984 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 19
50828910 AAAAATACAA
50828920 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTA-AAATT
*
50828940 ATTTAGAA-TTTTAAAATT
1 ATTTTGAATTTTTAAAATT
*
50828958 ATTTTTAATTTTTAAAATTT
1 ATTTTGAATTTTTAAAA-TT
50828978 ATTTTGA
1 ATTTTGA
50828985 TTCTTTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 11 0.29
20 12 0.32
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:50837696 original size:59 final size:60
Alignment explanation
Indices: 50837591--50837753 Score: 172
Period size: 62 Copynumber: 2.7 Consensus size: 60
50837581 ATTTTTTTTT
* * * *
50837591 TAATTTGGTATATAAA-TTTTTT-GACCCAATTTGATATCTAAACTTGACA-CATTTTCC
1 TAATTTGGTACATAAATTTTTTTAGATCCAATTTGGTACCTAAACTTGACATCATTTTCC
* * **
50837648 TAATTTGGTACCTAAATTTTTTTAGATCCAATTTGGTACCTGAACTTGACATTTTTTTTCC
1 TAATTTGGTACATAAATTTTTTTAGATCCAATTTGGTACCTAAACTTGACA-TCATTTTCC
* * *
50837709 TAATTTGGCACTTAATCTTTTTTTAGAAT-CAATTTGGTACCTAAA
1 TAATTTGGTACATAA-ATTTTTTTAG-ATCCAATTTGGTACCTAAA
50837754 TTTATTAAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 14 0.16
58 6 0.07
59 23 0.26
61 19 0.22
62 24 0.27
63 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.45
Consensus pattern (60 bp):
TAATTTGGTACATAAATTTTTTTAGATCCAATTTGGTACCTAAACTTGACATCATTTTCC
Found at i:50837730 original size:61 final size:60
Alignment explanation
Indices: 50837561--50837753 Score: 182
Period size: 58 Copynumber: 3.2 Consensus size: 60
50837551 TTAATATAAC
** * * * *
50837561 ATTTGGTATTTAAATTTGACATTTTTTTT-TTAATTTGGTA-TATAAATTTTTT-GACCCA
1 ATTTGGTACCTAAACTTGACATTTTTTTTCCTAATTTGGTACT-TAATTTTTTTAGATCCA
* * ** *
50837619 ATTTGATATCTAAACTTGACA--CATTTTCCTAATTTGGTACCTAAATTTTTTTAGATCCA
1 ATTTGGTACCTAAACTTGACATTTTTTTTCCTAATTTGGTA-CTTAATTTTTTTAGATCCA
* *
50837678 ATTTGGTACCTGAACTTGACATTTTTTTTCCTAATTTGGCACTTAATCTTTTTTTAGAAT-CA
1 ATTTGGTACCTAAACTTGACATTTTTTTTCCTAATTTGGTACTTAA--TTTTTTTAG-ATCCA
50837740 ATTTGGTACCTAAA
1 ATTTGGTACCTAAA
50837754 TTTATTAAAT
Statistics
Matches: 109, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
56 4 0.04
57 10 0.09
58 26 0.24
59 24 0.22
60 4 0.04
61 15 0.14
62 24 0.22
63 2 0.02
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (60 bp):
ATTTGGTACCTAAACTTGACATTTTTTTTCCTAATTTGGTACTTAATTTTTTTAGATCCA
Found at i:50838757 original size:3 final size:3
Alignment explanation
Indices: 50838749--50838773 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
50838739 TACCATCATT
50838749 ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC A
50838774 TTATCATCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:50842677 original size:18 final size:18
Alignment explanation
Indices: 50842644--50842680 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
50842634 AATAAAACAT
*
50842644 TAAAAATTCATAAAAAAA
1 TAAAAATACATAAAAAAA
*
50842662 TAAAAATACATTAAAAAA
1 TAAAAATACATAAAAAAA
50842680 T
1 T
50842681 TTAATTCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAAATACATAAAAAAA
Found at i:50846228 original size:16 final size:17
Alignment explanation
Indices: 50846209--50846242 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
50846199 ATATTGTTTA
50846209 TATTTTATAATA-TTTT
1 TATTTTATAATACTTTT
*
50846225 TATTTTTTAATACTTTT
1 TATTTTATAATACTTTT
50846242 T
1 T
50846243 GTAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTATAATACTTTT
Found at i:50846252 original size:21 final size:22
Alignment explanation
Indices: 50846225--50846272 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
50846215 ATAATATTTT
* * *
50846225 TATTTTTTAATACTTTTTGTAA
1 TATTTTTAAATAATTTTTATAA
50846247 -ATTTTTAAATAATTTTTATAA
1 TATTTTTAAATAATTTTTATAA
50846268 TATTT
1 TATTT
50846273 GTATTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTTTTAAATAATTTTTATAA
Found at i:50848784 original size:12 final size:12
Alignment explanation
Indices: 50848767--50848792 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
50848757 GTCGAAGTAT
50848767 AACAACATTATA
1 AACAACATTATA
50848779 AACAACATTATA
1 AACAACATTATA
50848791 AA
1 AA
50848793 ACAAGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (12 bp):
AACAACATTATA
Found at i:50849428 original size:2 final size:2
Alignment explanation
Indices: 50849421--50849462 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
50849411 TGTATCCTCA
50849421 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
50849463 CCCCTCACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:50850680 original size:24 final size:24
Alignment explanation
Indices: 50850627--50850680 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
50850617 AATATAATGA
* * *
50850627 TAAAAATATATATTTTTTATTTTT
1 TAAAAATATATAATTTATATTTTC
50850651 TAAAAA-ATTATAATTTATATTTCTC
1 TAAAAATA-TATAATTTATATTT-TC
50850676 TAAAA
1 TAAAA
50850681 TAAATTCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 18 0.72
25 6 0.24
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAAAATATATAATTTATATTTTC
Found at i:50853620 original size:22 final size:22
Alignment explanation
Indices: 50853595--50853653 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
50853585 CTTTTCTGCG
*
50853595 TTTTCAATTTCTTCTTT-CTTT
1 TTTTTAATTTCTTCTTTCCTTT
* **
50853616 TTTTTACTCCCTT-TTTCCTTTT
1 TTTTTAATTTCTTCTTTCC-TTT
50853638 TTTTTAATTTCTTCTT
1 TTTTTAATTTCTTCTT
50853654 AAGTTCTAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
20 3 0.11
21 10 0.36
22 13 0.46
23 2 0.07
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTAATTTCTTCTTTCCTTT
Found at i:50857520 original size:62 final size:61
Alignment explanation
Indices: 50857395--50857543 Score: 196
Period size: 61 Copynumber: 2.5 Consensus size: 61
50857385 TTAATATAAT
* * *
50857395 ATTTGGTATTTGAACTTGACAC--TTTTTTTTAATTTAATACTTAAACTTTTTTTGACCCA
1 ATTTGATATTTGAACTTGATACTTTTTTTTTTAATTTAATACTTAAACTTTTTTTGAACCA
* *
50857454 ATTTGATATTTGAACTTGATACTTTTTTTTTTAATTTTATACTTAAACTTTTTTTGGAATCA
1 ATTTGATATTTGAACTTGATACTTTTTTTTTTAATTTAATACTTAAACTTTTTTT-GAACCA
* * *
50857516 ATTTGATACTTGAATTTGGTA-TTTTTTT
1 ATTTGATATTTGAACTTGATACTTTTTTT
50857544 CCTAATTTGG
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
59 20 0.25
61 37 0.47
62 22 0.28
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.55
Consensus pattern (61 bp):
ATTTGATATTTGAACTTGATACTTTTTTTTTTAATTTAATACTTAAACTTTTTTTGAACCA
Found at i:50857868 original size:31 final size:29
Alignment explanation
Indices: 50857790--50857924 Score: 73
Period size: 31 Copynumber: 4.6 Consensus size: 29
50857780 GGACCCAGAA
* *
50857790 AAGTTTAAGCATCAACTTAAAAAAAGTGTC
1 AAGTTT-AGTATCAAATTAAAAAAAGTGTC
* *
50857820 AAATCTAGGTA-CTAAATTAGAAAAAAGTGTC
1 AAGTTTA-GTATC-AAATTA-AAAAAAGTGTC
* **
50857851 AAGTTTGAGTATCAAATTGGACCAAA--G--
1 AAGTTT-AGTATCAAATT-AAAAAAAGTGTC
*
50857878 AAATTTAGGTATCAAATTAAAAAAAGTGTC
1 AAGTTTA-GTATCAAATTAAAAAAAGTGTC
* *
50857908 AAATTTAAGTACCAAAT
1 AAGTTT-AGTATCAAAT
50857925 ATTATATTAA
Statistics
Matches: 79, Mismatches: 14, Indels: 24
0.68 0.12 0.21
Matches are distributed among these distances:
26 5 0.06
27 15 0.19
28 1 0.01
29 3 0.04
30 25 0.32
31 28 0.35
32 2 0.03
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.27
Consensus pattern (29 bp):
AAGTTTAGTATCAAATTAAAAAAAGTGTC
Found at i:50857901 original size:89 final size:89
Alignment explanation
Indices: 50857739--50857924 Score: 250
Period size: 88 Copynumber: 2.1 Consensus size: 89
50857729 AAAAAATTAA
* *
50857739 GTACCAAATTAGAAAAAAGAGTCAGGTTCAAGTATCAAATTGGACCCAGAAAAGTTTAAGCATCA
1 GTACCAAATTAGAAAAAAGAGTCAAGTTCAAGTATCAAATTGGACCCAGAAAAATTTAAGCATCA
*
50857804 ACTTAAAAAAAGTGTCAAATCTAG
66 AATTAAAAAAAGTGTCAAATCTAG
* * ** * *
50857828 GTACTAAATTAGAAAAAAGTGTCAAGTTTGAGTATCAAATTGGA-CCA-AAGAAATTTAGGTATC
1 GTACCAAATTAGAAAAAAGAGTCAAGTTCAAGTATCAAATTGGACCCAGAA-AAATTTAAGCATC
* *
50857891 AAATTAAAAAAAGTGTCAAATTTAA
65 AAATTAAAAAAAGTGTCAAATCTAG
50857916 GTACCAAAT
1 GTACCAAAT
50857925 ATTATATTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
87 2 0.02
88 43 0.51
89 39 0.46
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (89 bp):
GTACCAAATTAGAAAAAAGAGTCAAGTTCAAGTATCAAATTGGACCCAGAAAAATTTAAGCATCA
AATTAAAAAAAGTGTCAAATCTAG
Found at i:50873399 original size:58 final size:58
Alignment explanation
Indices: 50873337--50873480 Score: 163
Period size: 59 Copynumber: 2.5 Consensus size: 58
50873327 TATGGATATC
50873337 CGGGGGCAAAATGGTAATTTTGGTAAAATCGAGGTTAAAA-ATGGAATTTTAA-AG-GTTT
1 CGGGGGCAAAATGGTAATTTTGGTAAAATCGAGGTTAAAATA-GG-A-TTTAAGAGAGTTT
* * * *
50873395 CGGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAATAGGATTTAAGAGATTTTT
1 CGGGGGCAAAATGGT-AATTTTGGTAAAATCGAGGTTAAAATAGGATTTAAGAGA-GTTT
*
50873455 CGGGGTCAAAAT-GTAATTTTGG-AAAA
1 CGGGGGCAAAATGGTAATTTTGGTAAAA
50873481 GTTTTGGGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
57 8 0.11
58 25 0.34
59 27 0.36
60 14 0.19
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.31
Consensus pattern (58 bp):
CGGGGGCAAAATGGTAATTTTGGTAAAATCGAGGTTAAAATAGGATTTAAGAGAGTTT
Found at i:50874172 original size:22 final size:22
Alignment explanation
Indices: 50874147--50874198 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
50874137 CCGTCAGTGC
50874147 CACGCGCCGTTGCTCCTCCGTT
1 CACGCGCCGTTGCTCCTCCGTT
50874169 CACGCGCCGTTGCTCCTCCGTT
1 CACGCGCCGTTGCTCCTCCGTT
50874191 CACGCGCC
1 CACGCGCC
50874199 TCCGATCAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.06, C:0.48, G:0.23, T:0.23
Consensus pattern (22 bp):
CACGCGCCGTTGCTCCTCCGTT
Found at i:50874569 original size:15 final size:16
Alignment explanation
Indices: 50874537--50874571 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
50874527 TATACTTTAT
50874537 TTAAAAATATTAATTA
1 TTAAAAATATTAATTA
*
50874553 TTAAAGATATT-ATTA
1 TTAAAAATATTAATTA
50874568 TTAA
1 TTAA
50874572 TGCTAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TTAAAAATATTAATTA
Found at i:50875235 original size:6 final size:6
Alignment explanation
Indices: 50875208--50875280 Score: 62
Period size: 6 Copynumber: 12.2 Consensus size: 6
50875198 ATGTTTATTG
* * * *
50875208 TTTAAA TTTTAA TTTTAA TTTAAA TTTAAA -GTAAA TTTAAGTA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA
50875257 TTTAAGA --TAAA TTTAAA TTTAAA T
1 TTTAA-A TTTAAA TTTAAA TTTAAA T
50875281 CAATTTAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
4 1 0.02
5 7 0.13
6 41 0.75
7 1 0.02
8 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:50875235 original size:11 final size:11
Alignment explanation
Indices: 50875215--50875290 Score: 55
Period size: 11 Copynumber: 6.6 Consensus size: 11
50875205 TTGTTTAAAT
*
50875215 TTTAATTTTAA
1 TTTAAATTTAA
50875226 TTTAAATTTAA
1 TTTAAATTTAA
**
50875237 AGTAAATTTAA
1 TTTAAATTTAA
50875248 GTAATTAAATTTAA
1 -T--TTAAATTTAA
**
50875262 GATAAATTTAAA
1 TTTAAATTT-AA
*
50875274 TTTAAA-TCAA
1 TTTAAATTTAA
50875284 TTTAAAT
1 TTTAAAT
50875291 CCAAATTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
10 8 0.16
11 27 0.54
12 6 0.12
14 9 0.18
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:50875285 original size:16 final size:15
Alignment explanation
Indices: 50875239--50875290 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
50875229 AAATTTAAAG
*
50875239 TAAATTTAAGTAA-T
1 TAAATTTAAATAATT
50875253 TAAATTTAAGATAAATT
1 TAAATTTAA-AT-AATT
50875270 TAAATTTAAATCAATT
1 TAAATTTAAAT-AATT
50875286 TAAAT
1 TAAAT
50875291 CCAAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 13 0.39
17 10 0.30
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (15 bp):
TAAATTTAAATAATT
Found at i:50875779 original size:31 final size:31
Alignment explanation
Indices: 50875744--50875920 Score: 102
Period size: 32 Copynumber: 5.3 Consensus size: 31
50875734 TTATCCACTC
50875744 TACTTCAATTCCGAGGGGATGACGTTGCTCT
1 TACTTCAATTCCGAGGGGATGACGTTGCTCT
* ** * * *
50875775 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACT
1 TACTTCAA-TTCCGAGGGGATGAC--G-T-TGCTCT
* *
50875811 CTACTTCAATTTCAAGGGGATGACGTTGCTCT
1 -TACTTCAATTCCGAGGGGATGACGTTGCTCT
* ** * * *
50875843 TACTTCAATTTCAGAGATGAAGACATGTTATCCACT
1 TACTTCAA-TTCCGAGGGGATGAC--G-T-TGCTCT
* *
50875879 CTACTTCAATTTCAAGGGGATGACGTTGCTCT
1 -TACTTCAATTCCGAGGGGATGACGTTGCTCT
50875911 TACTTCAATT
1 TACTTCAATT
50875921 TTAGAGATGA
Statistics
Matches: 104, Mismatches: 30, Indels: 24
0.66 0.19 0.15
Matches are distributed among these distances:
31 26 0.25
32 28 0.27
33 2 0.02
34 4 0.04
35 2 0.02
36 26 0.25
37 16 0.15
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (31 bp):
TACTTCAATTCCGAGGGGATGACGTTGCTCT
Found at i:50875799 original size:68 final size:68
Alignment explanation
Indices: 50875712--50876183 Score: 836
Period size: 68 Copynumber: 6.9 Consensus size: 68
50875702 CTTATTTCAA
* * * *
50875712 CAATTTCAAAGATAAAGACGTGTTATCCACTCTACTTCAATTCCGAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
50875777 CTT
66 CTT
50875780 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
50875845 CTT
66 CTT
*
50875848 CAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
50875913 CTT
66 CTT
* *
50875916 CAATTTTAGAGATGAAGACGTGTTATCCACTCTATTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
50875981 CTT
66 CTT
*
50875984 CAATTTCAGAGATGAAGACGTGTTATCCACTCTATTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
50876049 CTT
66 CTT
* **
50876052 CAATTTCAGAGATGAAGACATGTTATCCACTCTGTTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
50876117 CTT
66 CTT
*
50876120 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTT
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTT
50876184 GTTTGGTTTG
Statistics
Matches: 389, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 389 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (68 bp):
CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
CTT
Found at i:50876091 original size:37 final size:36
Alignment explanation
Indices: 50875712--50876173 Score: 291
Period size: 37 Copynumber: 13.4 Consensus size: 36
50875702 CTTATTTCAA
* *
50875712 CAATTTCAAAGATAAAGACGTGTTATCCACTCTACTT
1 CAATTTCAGAGATGAAGAC-TGTTATCCACTCTACTT
* ** * * *
50875749 CAA-TTCCGAGGGGATGAC-G-T-TGCTCT-TACTT
1 CAATTTCAGAGATGAAGACTGTTATCCACTCTACTT
50875780 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTT
1 CAATTTCAGAGATGAAGAC-TGTTATCCACTCTACTT
** * * *
50875817 CAATTTCA-AGGGGATGAC-G-T-TGCTCT-TACTT
1 CAATTTCAGAGATGAAGACTGTTATCCACTCTACTT
50875848 CAATTTCAGAGATGAAGACATGTTATCCACTCTACTT
1 CAATTTCAGAGATGAAGAC-TGTTATCCACTCTACTT
** * * *
50875885 CAATTTCA-AGGGGATGAC-G-T-TGCTCT-TACTT
1 CAATTTCAGAGATGAAGACTGTTATCCACTCTACTT
* *
50875916 CAATTTTAGAGATGAAGACGTGTTATCCACTCTATTT
1 CAATTTCAGAGATGAAGAC-TGTTATCCACTCTACTT
** * * *
50875953 CAATTTCA-AGGGGATGAC-G-T-TGCTCT-TACTT
1 CAATTTCAGAGATGAAGACTGTTATCCACTCTACTT
*
50875984 CAATTTCAGAGATGAAGACGTGTTATCCACTCTATTT
1 CAATTTCAGAGATGAAGAC-TGTTATCCACTCTACTT
** * * *
50876021 CAATTTCA-AGGGGATGAC-G-T-TGCTCT-TACTT
1 CAATTTCAGAGATGAAGACTGTTATCCACTCTACTT
**
50876052 CAATTTCAGAGATGAAGACATGTTATCCACTCTGTTT
1 CAATTTCAGAGATGAAGAC-TGTTATCCACTCTACTT
** * * *
50876089 CAATTTCA-AGGGGATGAC-G-T-TGCTCT-TACTT
1 CAATTTCAGAGATGAAGACTGTTATCCACTCTACTT
50876120 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTT
1 CAATTTCAGAGATGAAGAC-TGTTATCCACTCTACTT
50876157 CAATTTCAAGAGGATGA
1 CAATTTC-AGA-GATGA
50876174 CGTTGCTCTT
Statistics
Matches: 313, Mismatches: 74, Indels: 74
0.68 0.16 0.16
Matches are distributed among these distances:
31 68 0.22
32 70 0.22
33 6 0.02
34 12 0.04
35 6 0.02
36 68 0.22
37 75 0.24
38 3 0.01
39 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (36 bp):
CAATTTCAGAGATGAAGACTGTTATCCACTCTACTT
Found at i:50892669 original size:30 final size:30
Alignment explanation
Indices: 50892624--50892736 Score: 181
Period size: 30 Copynumber: 3.7 Consensus size: 30
50892614 TTAAGAGATT
* *
50892624 TTTTCGGGGTCAAAATGTAATTTTGGAAAAG
1 TTTT-GGGGTTAAAATATAATTTTGGAAAAG
*
50892655 TTTTGGGGTTAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTTAAAATATAATTTTGGAAAAG
50892685 TTTTGGGGTTAAAATATAATTTTGGAAAAG
1 TTTTGGGGTTAAAATATAATTTTGGAAAAG
*
50892715 TTTTTGGGTTAAAATATAATTT
1 TTTTGGGGTTAAAATATAATTT
50892737 CTAGATTGTT
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 75 0.95
31 4 0.05
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.42
Consensus pattern (30 bp):
TTTTGGGGTTAAAATATAATTTTGGAAAAG
Found at i:50893769 original size:15 final size:16
Alignment explanation
Indices: 50893737--50893771 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
50893727 TATACTTTAT
50893737 TTAAAAATATTAATTA
1 TTAAAAATATTAATTA
*
50893753 TTAAAGATATT-ATTA
1 TTAAAAATATTAATTA
50893768 TTAA
1 TTAA
50893772 TGCTAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TTAAAAATATTAATTA
Found at i:50894441 original size:6 final size:6
Alignment explanation
Indices: 50894408--50894486 Score: 67
Period size: 6 Copynumber: 13.2 Consensus size: 6
50894398 ATGTTTATTG
* *
50894408 TTTAAA TTTTAA TTTTAA TTTAAA TTTAAA TTT--A TCTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA--A
*
50894457 CTTAAA TTTAAGA --TAAA TTTAAA TTTAAA T
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA T
50894487 CAATTTAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
4 3 0.05
5 5 0.08
6 45 0.74
7 3 0.05
8 5 0.08
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:50894441 original size:17 final size:16
Alignment explanation
Indices: 50894408--50894496 Score: 83
Period size: 17 Copynumber: 5.4 Consensus size: 16
50894398 ATGTTTATTG
*
50894408 TTTAAATTTTAATTTTAA
1 TTTAAA-TTTAA-ATTAA
*
50894426 TTTAAATTTAAATTTA
1 TTTAAATTTAAATTAA
50894442 TCTTAAATTT-AATT-A
1 T-TTAAATTTAAATTAA
* *
50894457 CTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATTAA
*
50894474 TTTAAATTTAAATCAA
1 TTTAAATTTAAATTAA
50894490 TTTAAAT
1 TTTAAAT
50894497 CCAAGTTAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
14 8 0.13
15 2 0.03
16 21 0.34
17 24 0.39
18 6 0.10
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (16 bp):
TTTAAATTTAAATTAA
Found at i:50896559 original size:28 final size:28
Alignment explanation
Indices: 50896523--50896576 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
50896513 ATAAAAAAAT
*
50896523 AAAATCCAAAACACAAATAAAGTCCACA
1 AAAACCCAAAACACAAATAAAGTCCACA
50896551 AAAACCCAAAACACAAATAAAGTCCA
1 AAAACCCAAAACACAAATAAAGTCCA
50896577 TATTTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.61, C:0.26, G:0.04, T:0.09
Consensus pattern (28 bp):
AAAACCCAAAACACAAATAAAGTCCACA
Found at i:50896727 original size:22 final size:22
Alignment explanation
Indices: 50896701--50896745 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
50896691 AGATCAACAC
50896701 AAATA-AAATCACATACATATCA
1 AAATATAAATCACA-ACATATCA
* *
50896723 AAATATCAATCTCAACATATCA
1 AAATATAAATCACAACATATCA
50896745 A
1 A
50896746 TCACCATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATATAAATCACAACATATCA
Found at i:50896974 original size:50 final size:50
Alignment explanation
Indices: 50896918--50897084 Score: 235
Period size: 50 Copynumber: 3.3 Consensus size: 50
50896908 GCTATCACTA
* * *
50896918 ATTTGCAGATAAACTATCACTGATAACTCTTTGTGGATAAGCCACCATTG
1 ATTTACAGATAAACTGTCACTGATAACACTTTGTGGATAAGCCACCATTG
* * * * * *
50896968 ACTTGCAGATAAACTGCCACTAATAACACTTTGTGGACAAGCCACCATTA
1 ATTTACAGATAAACTGTCACTGATAACACTTTGTGGATAAGCCACCATTG
* *
50897018 ATTTACAAATAAACTGTCACTGATAACACTTTGTGGATAAGCCACCACTG
1 ATTTACAGATAAACTGTCACTGATAACACTTTGTGGATAAGCCACCATTG
50897068 ATTTACAGATAAACTGT
1 ATTTACAGATAAACTGT
50897085 TACTTACTTC
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 101 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (50 bp):
ATTTACAGATAAACTGTCACTGATAACACTTTGTGGATAAGCCACCATTG
Found at i:50897021 original size:100 final size:100
Alignment explanation
Indices: 50896897--50897083 Score: 284
Period size: 100 Copynumber: 1.9 Consensus size: 100
50896887 CGAAACACCA
* * * * *
50896897 TTTGTGGACAAGCTATCACTAATTTGCAGATAAACTATCACTGATAACTCTTTGTGGATAAGCCA
1 TTTGTGGACAAGCCACCACTAATTTACAAATAAACTATCACTGATAACACTTTGTGGATAAGCCA
* *
50896962 CCATTGACTTGCAGATAAACTGCCACTAATAACAC
66 CCACTGACTTACAGATAAACTGCCACTAATAACAC
* *
50896997 TTTGTGGACAAGCCACCATTAATTTACAAATAAACTGTCACTGATAACACTTTGTGGATAAGCCA
1 TTTGTGGACAAGCCACCACTAATTTACAAATAAACTATCACTGATAACACTTTGTGGATAAGCCA
*
50897062 CCACTGATTTACAGATAAACTG
66 CCACTGACTTACAGATAAACTG
50897084 TTACTTACTT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 77 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (100 bp):
TTTGTGGACAAGCCACCACTAATTTACAAATAAACTATCACTGATAACACTTTGTGGATAAGCCA
CCACTGACTTACAGATAAACTGCCACTAATAACAC
Found at i:50902957 original size:34 final size:36
Alignment explanation
Indices: 50902916--50902986 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 36
50902906 CAATTACGTG
*
50902916 TTTTTTTTTTTTT-A-AATTTCAATTACGTGTTTCC
1 TTTTTTTTTTTTTAAGAAATTCAATTACGTGTTTCC
50902950 TTTTTTTTTTTTTAAAGAAATTCAATTACGTGTTTCC
1 TTTTTTTTTTTTT-AAGAAATTCAATTACGTGTTTCC
50902987 ATAACCACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 13 0.39
36 1 0.03
37 19 0.58
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (36 bp):
TTTTTTTTTTTTTAAGAAATTCAATTACGTGTTTCC
Found at i:50903247 original size:26 final size:26
Alignment explanation
Indices: 50903218--50903275 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
50903208 CTATAATTCG
* *
50903218 ATTTAACAATCAATTTTACAAAATAT
1 ATTTAACAATAAAATTTACAAAATAT
***
50903244 ATTTTTTAATAAAATTTACAAAATAT
1 ATTTAACAATAAAATTTACAAAATAT
*
50903270 AATTAA
1 ATTTAA
50903276 TTTCACTCAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTTAACAATAAAATTTACAAAATAT
Found at i:50903900 original size:19 final size:19
Alignment explanation
Indices: 50903876--50903915 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
50903866 GAATACTATC
50903876 TATTTTATATTTTAATAAT
1 TATTTTATATTTTAATAAT
* *
50903895 TATTTTTTATTTTCATAAT
1 TATTTTATATTTTAATAAT
50903914 TA
1 TA
50903916 ATTAGACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTATATTTTAATAAT
Found at i:50905335 original size:20 final size:20
Alignment explanation
Indices: 50905310--50905351 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
50905300 AATATCATAA
50905310 AACTTTCATACACAATTATT
1 AACTTTCATACACAATTATT
50905330 AACTTTCATACACAATTATT
1 AACTTTCATACACAATTATT
50905350 AA
1 AA
50905352 AAATAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (20 bp):
AACTTTCATACACAATTATT
Found at i:50912038 original size:28 final size:28
Alignment explanation
Indices: 50912007--50912067 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
50911997 TTTTTATATT
* *
50912007 TTATTATAAATGTTTTATTTTATTTTT-A
1 TTATTATAAAT-TTTTAATATATTTTTCA
* *
50912035 TTATTTTTAATTTTTAATATATTTTTCA
1 TTATTATAAATTTTTAATATATTTTTCA
50912063 TTATT
1 TTATT
50912068 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (28 bp):
TTATTATAAATTTTTAATATATTTTTCA
Found at i:50912039 original size:41 final size:39
Alignment explanation
Indices: 50911993--50912077 Score: 102
Period size: 39 Copynumber: 2.1 Consensus size: 39
50911983 TAGTTGTTTC
*
50911993 ATTATTTTTATATTTTATTATAAATGTTTT-ATT-TTATTTTT
1 ATTATTTTTA-ATTTT-TAATAAAT-TTTTCATTATT-TTTTT
*
50912034 ATTATTTTTAATTTTTAATATATTTTTCATTATTTTTTT
1 ATTATTTTTAATTTTTAATAAATTTTTCATTATTTTTTT
50912073 ATTAT
1 ATTAT
50912078 AAATGTCTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
38 4 0.10
39 19 0.47
40 7 0.17
41 10 0.25
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (39 bp):
ATTATTTTTAATTTTTAATAAATTTTTCATTATTTTTTT
Found at i:50912040 original size:9 final size:9
Alignment explanation
Indices: 50912026--50912075 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
50912016 ATGTTTTATT
50912026 TTATTTTTA
1 TTATTTTTA
50912035 TTATTTTTA
1 TTATTTTTA
50912044 --ATTTTTAA
1 TTATTTTT-A
50912052 TATATTTTTCA
1 T-TATTTTT-A
50912063 TTATTTTT-
1 TTATTTTTA
50912071 TTATT
1 TTATT
50912076 ATAAATGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
7 6 0.17
8 6 0.17
9 9 0.25
10 7 0.19
11 8 0.22
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTTA
Done.