Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019768.1 Corchorus olitorius cultivar O-4 contig19801, 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: 93121
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:721 original size:30 final size:30
Alignment explanation
Indices: 685--743 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
675 AAGCTGCATT
685 TGATCAATGATTTGATCAAATTTGTGGAAA
1 TGATCAATGATTTGATCAAATTTGTGGAAA
715 TGATCAATGATTTGATCAAATTTGTGGAA
1 TGATCAATGATTTGATCAAATTTGTGGAA
744 CTCATCCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (30 bp):
TGATCAATGATTTGATCAAATTTGTGGAAA
Found at i:9326 original size:19 final size:18
Alignment explanation
Indices: 9293--9328 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9283 TGAAAATAAT
9293 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
9311 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
9329 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:13555 original size:210 final size:210
Alignment explanation
Indices: 13189--13615 Score: 775
Period size: 210 Copynumber: 2.0 Consensus size: 210
13179 AATACAGAAA
13189 TAAA-AGTTTGTGCATAGGTGCAGTTAGGTGCTCCCGTGAATAGATCACATATCATCCCAAACTC
1 TAAATAGTTTGTGCATAGGTGCAGTTAGGTGCTCCCGTGAATAGATCACATATCATCCCAAACTC
13253 AATGATTCATCATGTAGTTCTTTCACCCCCAGCTTTGAATATATTTCAGCTATTTTTTGGTTCAA
66 AATGATTCATCATGTAGTTCTTTCACCCCCAGCTTTGAATATATTTCAGCTATTTTTTGGTTCAA
* * * *
13318 CTGCAACATAGAAATACAATCAAATGTAAGTAATTTTCTATAATAAAACTATGCCATGTTTAATT
131 CTACAACATAGAAATACAATCAAATGTAAGTAATTGTATATAATAAAACTATGCCATGTTTAAAT
13383 AACATGTCTGCAATG
196 AACATGTCTGCAATG
*
13398 TAAATAGTTTGTGCATAGGTGCAGTTAGGTGTTCCCGTGAATAGATCACATATCATCCCAAACTC
1 TAAATAGTTTGTGCATAGGTGCAGTTAGGTGCTCCCGTGAATAGATCACATATCATCCCAAACTC
* *
13463 AATGATTCATCGTGTTGTTCTTTCACCCCCAGCTTTGAATATATTTCAGCTATTTTTTGGTTCAA
66 AATGATTCATCATGTAGTTCTTTCACCCCCAGCTTTGAATATATTTCAGCTATTTTTTGGTTCAA
13528 CTACAACATAGAAATACAATCAAATGTAAGTAATTGTATATAATAAAACTATGCCATGTTTAAAT
131 CTACAACATAGAAATACAATCAAATGTAAGTAATTGTATATAATAAAACTATGCCATGTTTAAAT
*
13593 AACTTGTCTGCAATG
196 AACATGTCTGCAATG
13608 TAAATAGT
1 TAAATAGT
13616 ATACAAATCA
Statistics
Matches: 209, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
209 4 0.02
210 205 0.98
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (210 bp):
TAAATAGTTTGTGCATAGGTGCAGTTAGGTGCTCCCGTGAATAGATCACATATCATCCCAAACTC
AATGATTCATCATGTAGTTCTTTCACCCCCAGCTTTGAATATATTTCAGCTATTTTTTGGTTCAA
CTACAACATAGAAATACAATCAAATGTAAGTAATTGTATATAATAAAACTATGCCATGTTTAAAT
AACATGTCTGCAATG
Found at i:15995 original size:99 final size:100
Alignment explanation
Indices: 15810--16007 Score: 256
Period size: 99 Copynumber: 2.0 Consensus size: 100
15800 TATGAGCCTA
*
15810 AAAAATGTTCAAAATAAAAAATTCCAGCAGGTTAATGTTTTTTTACACTTCACTATGCAAAAATA
1 AAAAATGTTCAAAATAAAAAATTCCAGCAGGTTAA-GTATTTTTACACTTCACTATGCAAAAATA
* *
15875 AGCATTACAGCACATTAACATGTTGTTAAAAGTCCT
65 AGCATTACAACACATTAACATGTTATTAAAAGTCCT
* * * *
15911 AAAAATGTTTCAAAAT-AAAATTTCTAGCATGTTAA-TATTTTTATACTTCACTATGCAAAAATA
1 AAAAATG-TTCAAAATAAAAAATTCCAGCAGGTTAAGTATTTTTACACTTCACTATGCAAAAATA
* * * * *
15974 TGCATTCCAACATATTGACATGTTATTAGAAGTC
65 AGCATTACAACACATTAACATGTTATTAAAAGTC
16008 ATATGAAATT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
99 53 0.63
101 23 0.27
102 8 0.10
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (100 bp):
AAAAATGTTCAAAATAAAAAATTCCAGCAGGTTAAGTATTTTTACACTTCACTATGCAAAAATAA
GCATTACAACACATTAACATGTTATTAAAAGTCCT
Found at i:17842 original size:20 final size:20
Alignment explanation
Indices: 17817--17860 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
17807 TTCATCAATT
17817 ATTAA-TTCTAATAATTCATA
1 ATTAATTTC-AATAATTCATA
17837 ATTAATTTCAATAATTCATA
1 ATTAATTTCAATAATTCATA
17857 ATTA
1 ATTA
17861 GAACACATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAATTTCAATAATTCATA
Found at i:17898 original size:25 final size:24
Alignment explanation
Indices: 17870--17930 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 24
17860 AGAACACATG
17870 ATTAATAAAATAATCAAAAATCATA
1 ATTAA-AAAATAATCAAAAATCATA
*
17895 ATTAACAAAAATAATCAAAAATCGTA
1 ATT-A-AAAAATAATCAAAAATCATA
17921 A-TAAAAAATA
1 ATTAAAAAATA
17931 CATGATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 7 0.21
24 1 0.03
25 4 0.12
26 20 0.61
27 1 0.03
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.25
Consensus pattern (24 bp):
ATTAAAAAATAATCAAAAATCATA
Found at i:19633 original size:335 final size:328
Alignment explanation
Indices: 18603--19763 Score: 1263
Period size: 335 Copynumber: 3.5 Consensus size: 328
18593 ATACCTTACA
* * * ** *
18603 TCATCTAACCAAATCTTAGCAACATTGGATTTAAGAATTTGTTTTTACGAGTATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATCAGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
18668 TTCAATTTAATTAGAAATTAATTTAGAAAAAAATAAGAAATACGATATTAAAAGCGTAAAAAGCC
66 TTCAATTTAATTAGAAATTAATTTAG-AAAAAATAAGAAA-ACGATATTAAAA-CGTAAAAA-CC
18733 CTCCAATATTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAGAAA
127 CTCCAATATTTTTGGCGTTGAATTATATATTTTT-TGAGTATTTTAGCCAAAAATTGAGGAGAAA
*
18798 T-TATTCGTATCAAAGTTTTGCAAAATTTTAGCCG-AA-----AT--CAAACCATCACGGTTTTT
191 TATATTCGTATC-AATTTTTGC-AAATTTTAGCCGAAATCGTGATAACAAACCATCACGG-TTTT
* * * * * *
18854 TGGCTAAAAACGAAATAAGGGGACCCTGCTCAATTTTGCAAGATTTTTTGCTCCAAGACCACTTG
253 TGACTAAAAACGAATTACGGGGACCCAGCTCAATTTTGCATGAATTTTTGCTCCAAGACCACTTG
18919 AAATATCTATAT
318 -AATATCTATAT
* * *
18931 TCATCTAATCAAATCTCAGCCACATCAGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATCAGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
* * *
18996 TTCAATTTAATTAGAAATTAATTT-G---GAA-AAGAAAACAATATTAGAAACGGCAAAAACCCT
66 TTCAATTTAATTAGAAATTAATTTAGAAAAAATAAGAAAACGATATTA-AAAC-GTAAAAACCCT
* * * * * * * *
19056 TCAATCTTTTTTGCGATGAATTATATACTCTTTTGAATA-TTTAGGCAAAAATTGA-G-CAAATA
129 CCAATATTTTTGGCGTTGAATTATATA-TTTTTTGAGTATTTTAGCCAAAAATTGAGGAGAAATA
* * ** * * * * *
19118 TCTACCGGGTCAATTTTTACAAAGTTTTAGCCTAAATCGTG-TAA-TAATCATCACAGTTTTT-A
193 TAT-TCGTATCAATTTTTGCAAA-TTTTAGCCGAAATCGTGATAACAAACCATCACGGTTTTTGA
* ** * * * * * *
19180 GCTAAAAAAGCGTT-CTGAGGCCCCAGATCAGTTTTACATG-ATTTTTGCCGCCAAGACTC-CTT
256 -CTAAAAACGAATTAC-GGGGACCCAGCTCAATTTTGCATGAATTTTTG-CTCCAAGAC-CACTT
*
19242 GAGATATCCATAT
317 GA-ATATCTATAT
* * ** *
19255 TCATCTAATCAAACCTCAACCACATTGGATTTAAGAATTTGTTTTTACGAGTATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATCAGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
19320 TTCAATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGTAAAAAGCCC
66 TTCAATTTAATTAGAAATTAATTTAGAAAAAATAAGAAA-ACGATATTAAAA-CGTAAAAA-CCC
19385 TCCAATATTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAGAAAT
128 TCCAATATTTTTGGCGTTGAATTATATATTTTT-TGAGTATTTTAGCCAAAAATTGAGGAGAAAT
*
19450 AT-TTCGTATCAATTTTTGCGAAATTTTAGCCGAAATCGTGCATTAACAAACCATCATGGTTTTT
192 ATATTCGTATCAATTTTTGC-AAATTTTAGCCGAAATCGTG-A-TAACAAACCATCACGGTTTTT
* *
19514 GACTAAAAACGAATTACGGGGACCCGGCTCAATTTTGCATGAATTTTTGCTCCGAGACCACTTGA
254 GACTAAAAACGAATTACGGGGACCCAGCTCAATTTTGCATGAATTTTTGCTCCAAGACCACTTGA
*
19579 ATTATCTATAC
319 A-TATCTATAT
* * *
19590 TCATCTAATCAAATCTCAGCCACATCAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTT
1 TCATCTAATCAAATCTCAGCCACATCAGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * * *
19655 TTCGATTTAATTAGAAATTAATTTGGAAAATATAGGAAAACGATATTGGAAACGTCAAAAAACCT
66 TTCAATTTAATTAGAAATTAATTTAGAAAAAATAAGAAAACGATATT-AAAACGT-AAAAACCCT
* * * * *
19720 TCAATCTTTTTGGCGTTGACTTGTATAATTTTTTGAGCATTTTA
129 CCAATATTTTTGGCGTTGAATTATAT-ATTTTTTGAGTATTTTA
19764 AGTGGGTCCT
Statistics
Matches: 683, Mismatches: 106, Indels: 82
0.78 0.12 0.09
Matches are distributed among these distances:
318 7 0.01
319 18 0.03
320 21 0.03
321 41 0.06
322 19 0.03
323 9 0.01
324 134 0.20
325 11 0.02
327 1 0.00
328 82 0.12
329 19 0.03
330 41 0.06
331 43 0.06
332 5 0.01
333 6 0.01
334 51 0.07
335 166 0.24
336 9 0.01
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (328 bp):
TCATCTAATCAAATCTCAGCCACATCAGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
TTCAATTTAATTAGAAATTAATTTAGAAAAAATAAGAAAACGATATTAAAACGTAAAAACCCTCC
AATATTTTTGGCGTTGAATTATATATTTTTTGAGTATTTTAGCCAAAAATTGAGGAGAAATATAT
TCGTATCAATTTTTGCAAATTTTAGCCGAAATCGTGATAACAAACCATCACGGTTTTTGACTAAA
AACGAATTACGGGGACCCAGCTCAATTTTGCATGAATTTTTGCTCCAAGACCACTTGAATATCTA
TAT
Found at i:23608 original size:29 final size:29
Alignment explanation
Indices: 23570--23625 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
23560 TAAAATTTTT
*
23570 CTTTTATTTC-TTTTATTTTCTTTTTCCCC
1 CTTTTATTTCTTTTTA-ATTCTTTTTCCCC
*
23599 CTTTTTTTTCTTTTTAATTCTTTTTCC
1 CTTTTATTTCTTTTTAATTCTTTTTCC
23626 TTCTCTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (29 bp):
CTTTTATTTCTTTTTAATTCTTTTTCCCC
Found at i:23621 original size:19 final size:19
Alignment explanation
Indices: 23565--23623 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
23555 TATTCTAAAA
*
23565 TTTTTC-TTTTATTTCTTT
1 TTTTTCTTTTTAATTCTTT
****
23583 TATTTTCTTTTTCCCCCTTT
1 T-TTTTCTTTTTAATTCTTT
23603 TTTTTCTTTTTAATTCTTT
1 TTTTTCTTTTTAATTCTTT
23622 TT
1 TT
23624 CCTTCTCTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
18 1 0.03
19 21 0.68
20 9 0.29
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTCTTTTTAATTCTTT
Found at i:23762 original size:15 final size:15
Alignment explanation
Indices: 23726--23770 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
23716 AAACGGCCTA
*
23726 TTTCTCTTTCTTTTT-
1 TTTC-CTTTTTTTTTC
23741 TTT-CTTTTTTTTTC
1 TTTCCTTTTTTTTTC
23755 TTTCCTTTTTTTTTC
1 TTTCCTTTTTTTTTC
23770 T
1 T
23771 GTTTGGCTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 9 0.33
14 3 0.11
15 15 0.56
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCCTTTTTTTTTC
Found at i:29817 original size:36 final size:36
Alignment explanation
Indices: 29770--29847 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
29760 CATAAGAAAA
** *
29770 GCCCAAATACATAATTAAGTTGGCTTAACTCTATTG
1 GCCCAAATACATAATTAAGTTGGCCCAACTCTACTG
*
29806 GCCCAAATACATAATTAAGTTGGCCCAACTTTACTG
1 GCCCAAATACATAATTAAGTTGGCCCAACTCTACTG
29842 GCCCAA
1 GCCCAA
29848 TACTACCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.28
Consensus pattern (36 bp):
GCCCAAATACATAATTAAGTTGGCCCAACTCTACTG
Found at i:30003 original size:13 final size:13
Alignment explanation
Indices: 29985--30070 Score: 67
Period size: 13 Copynumber: 7.1 Consensus size: 13
29975 GGGAGAAATC
29985 AAGTTCTTCATCA
1 AAGTTCTTCATCA
*
29998 AAGTTCTTCAAC-
1 AAGTTCTTCATCA
* *
30010 AAG-TCTCCA-CC
1 AAGTTCTTCATCA
*
30021 AAGTTATTCATCA
1 AAGTTCTTCATCA
*
30034 AAGTTCTTCAAC-
1 AAGTTCTTCATCA
*
30046 AAGTT-TTCA-CC
1 AAGTTCTTCATCA
*
30057 CAGTTCTTCATCA
1 AAGTTCTTCATCA
30070 A
1 A
30071 GCTCTCCACC
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
10 2 0.04
11 16 0.28
12 16 0.28
13 23 0.40
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (13 bp):
AAGTTCTTCATCA
Found at i:30025 original size:36 final size:36
Alignment explanation
Indices: 29984--30070 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
29974 AGGGAGAAAT
29984 CAAGTTCTTCATCAAAGTTCTTCAACAAGTCTCCAC
1 CAAGTTCTTCATCAAAGTTCTTCAACAAGTCTCCAC
* * *
30020 CAAGTTATTCATCAAAGTTCTTCAACAAGTTTTCAC
1 CAAGTTCTTCATCAAAGTTCTTCAACAAGTCTCCAC
*
30056 CCAGTTCTTCATCAA
1 CAAGTTCTTCATCAA
30071 GCTCTCCACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (36 bp):
CAAGTTCTTCATCAAAGTTCTTCAACAAGTCTCCAC
Found at i:37972 original size:52 final size:52
Alignment explanation
Indices: 37894--37995 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 52
37884 TAAAAAAAAT
* *
37894 GCCTGCTAAGTTGAAAACCCCATTGGGGTGGCTTAGGCAAAAGTTAAGGCAA
1 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCCTAGGCAAAAGTTAAGGCAA
* *
37946 GCCTGCTAGGTTGAAAACCCCATTGGGGCGGCCTAGGCAAAATTTAAGGC
1 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCCTAGGCAAAAGTTAAGGC
37996 TTAAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (52 bp):
GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCCTAGGCAAAAGTTAAGGCAA
Found at i:41659 original size:45 final size:45
Alignment explanation
Indices: 41591--41863 Score: 429
Period size: 45 Copynumber: 6.0 Consensus size: 45
41581 GAGAAAGTCG
* *
41591 AAGAGGCCGATGCAGAGGTAGAGGGCGATGAAAATCAACCCCGCC
1 AAGAGTCCGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCC
* *
41636 AAGAGTCCGATGCAGAGGCAGAGGGCGATGAAAATCAACCCCGCC
1 AAGAGTCCGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCC
* * *
41681 AAGAGCCCGTTGCAGAGGTAGAGGGCGATAAAAAATCAACCCTGCC
1 AAGAGTCCGATGCAGAGGTAGAGGGCGAT-AAAAATCAACCCCGCC
* *
41727 AAGAGTTCGATGCAGAGGTAGAGTGCGATAAAAATCAACCCCGCC
1 AAGAGTCCGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCC
* *
41772 AAGAGTCCGATGTAGAGGTAGAGGGCGATGAAAATCAACCCCGCC
1 AAGAGTCCGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCC
*
41817 AAGAGTCCGATGCAGAGGTAGAGGGGGATAAAAATCAACCCCGCC
1 AAGAGTCCGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCC
41862 AA
1 AA
41864 AAAAGCCGTA
Statistics
Matches: 208, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 169 0.81
46 39 0.19
ACGTcount: A:0.35, C:0.23, G:0.30, T:0.12
Consensus pattern (45 bp):
AAGAGTCCGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCC
Found at i:41835 original size:136 final size:135
Alignment explanation
Indices: 41598--41863 Score: 451
Period size: 136 Copynumber: 2.0 Consensus size: 135
41588 TCGAAGAGGC
*
41598 CGATGCAGAGGTAGAGGGCGATGAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGCAGAGGGCG
1 CGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGCAGAGGGCG
* *
41663 ATGAAAATCAACCCCGCCAAGAGCCCGTTGCAGAGGTAGAGGGCGATAAAAAATCAACCCTGCCA
66 ATGAAAATCAACCCCGCCAAGAGCCCGATGCAGAGGTAGAGGGCGAT-AAAAATCAACCCCGCCA
41728 AGAGTT
130 AGAGTT
* * *
41734 CGATGCAGAGGTAGAGTGCGATAAAAATCAACCCCGCCAAGAGTCCGATGTAGAGGTAGAGGGCG
1 CGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGCAGAGGGCG
* *
41799 ATGAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGTAGAGGGGGATAAAAATCAACCCCGCCAA
66 ATGAAAATCAACCCCGCCAAGAGCCCGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCCAA
41864 AAAAGCCGTA
Statistics
Matches: 122, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
135 17 0.14
136 105 0.86
ACGTcount: A:0.35, C:0.24, G:0.30, T:0.12
Consensus pattern (135 bp):
CGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGCAGAGGGCG
ATGAAAATCAACCCCGCCAAGAGCCCGATGCAGAGGTAGAGGGCGATAAAAATCAACCCCGCCAA
GAGTT
Found at i:42050 original size:39 final size:40
Alignment explanation
Indices: 41989--42064 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
41979 ACCTCGTTGC
*
41989 CGCTAGAAGGTTTCTTCGGGACACGATTGGGA-CCATTGG
1 CGCTAGAAGGTTTCTTCGGGACACGATTAGGAGCCATTGG
* *
42028 CGCTTGAAGGTTTCTTCTGGACACGATTAGGAGCCAT
1 CGCTAGAAGGTTTCTTCGGGACACGATTAGGAGCCAT
42065 GATAGTGGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 29 0.88
40 4 0.12
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (40 bp):
CGCTAGAAGGTTTCTTCGGGACACGATTAGGAGCCATTGG
Found at i:43936 original size:36 final size:36
Alignment explanation
Indices: 43862--43939 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
43852 CATAAGAAAA
* ** *
43862 GCCCAAATACATAATTAAGTTGGCTTAACTCTATTG
1 GCCCAAATACATAATTAAGTTGACCCAACTCTACTG
*
43898 GCCCAAATACATAATTAAGTTGACCCAACTTTACTG
1 GCCCAAATACATAATTAAGTTGACCCAACTCTACTG
43934 GCCCAA
1 GCCCAA
43940 TACTACCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (36 bp):
GCCCAAATACATAATTAAGTTGACCCAACTCTACTG
Found at i:44095 original size:13 final size:13
Alignment explanation
Indices: 44077--44135 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
44067 GGGAAAAATC
44077 AAGTTCTTCATCA
1 AAGTTCTTCATCA
*
44090 AAGTTCTTCAAC-
1 AAGTTCTTCATCA
* *
44102 AAG-TCTCCA-CC
1 AAGTTCTTCATCA
*
44113 AAGTTATTCATCA
1 AAGTTCTTCATCA
44126 AAGTTCTTCA
1 AAGTTCTTCA
44136 ACAAGTTATC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 1 0.03
11 8 0.22
12 7 0.19
13 21 0.57
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.34
Consensus pattern (13 bp):
AAGTTCTTCATCA
Found at i:44117 original size:36 final size:36
Alignment explanation
Indices: 44076--44167 Score: 134
Period size: 36 Copynumber: 2.6 Consensus size: 36
44066 AGGGAAAAAT
44076 CAAGTTCTTCATCAAAGTTCTTCAACAAGTCT-CCAC
1 CAAGTTCTTCATCAAAGTTCTTCAACAAGT-TACCAC
* *
44112 CAAGTTATTCATCAAAGTTCTTCAACAAGTTATCAC
1 CAAGTTCTTCATCAAAGTTCTTCAACAAGTTACCAC
*
44148 CCAGTTCTTCATC-AAGTTCT
1 CAAGTTCTTCATCAAAGTTCT
44168 CCACCAATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
35 8 0.16
36 43 0.84
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (36 bp):
CAAGTTCTTCATCAAAGTTCTTCAACAAGTTACCAC
Found at i:49187 original size:18 final size:18
Alignment explanation
Indices: 49166--49200 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
49156 TGGATATGTT
49166 TTATTCTTTTTCTTTATC
1 TTATTCTTTTTCTTTATC
49184 TTATTCTTTTTCTTTAT
1 TTATTCTTTTTCTTTAT
49201 TTTCTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTCTTTTTCTTTATC
Found at i:53822 original size:31 final size:31
Alignment explanation
Indices: 53779--53849 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
53769 AAATGGAACT
* *
53779 TTAGGGACTGATTTGAGCTGATTTTACAAGG
1 TTAGGGACTGATTTGAGCCGATTTTACAACG
*
53810 TTAGGGATTGATTTGAGCCGATTTTACAACG
1 TTAGGGACTGATTTGAGCCGATTTTACAACG
53841 TTAGGGACT
1 TTAGGGACT
53850 TAATTAACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.35
Consensus pattern (31 bp):
TTAGGGACTGATTTGAGCCGATTTTACAACG
Found at i:61529 original size:25 final size:25
Alignment explanation
Indices: 61495--61544 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
61485 ACAAACAATC
*
61495 TTGAACACTCTCGCTCGGTCTCTAT
1 TTGAACACTCTCGCTCGCTCTCTAT
*
61520 TTGAGCACTCTCGCTCGCTCTCTAT
1 TTGAACACTCTCGCTCGCTCTCTAT
61545 AAACCAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.16, T:0.36
Consensus pattern (25 bp):
TTGAACACTCTCGCTCGCTCTCTAT
Found at i:64013 original size:27 final size:27
Alignment explanation
Indices: 63980--64043 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
63970 TTTCGGTATC
** *
63980 TTACAATTTTGACTTGTTGGGACAATT
1 TTACAATTTTGACTACTTGCGACAATT
* *
64007 TTGCAATTTTGAGTACTTGCGACAATT
1 TTACAATTTTGACTACTTGCGACAATT
64034 TTACAATTTT
1 TTACAATTTT
64044 CAGTTGCTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (27 bp):
TTACAATTTTGACTACTTGCGACAATT
Found at i:64054 original size:27 final size:27
Alignment explanation
Indices: 63980--64054 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
63970 TTTCGGTATC
* * *
63980 TTACAATTTTGACTTGTTGGGACAATT
1 TTACAATTTTGAGTTGCTGCGACAATT
* *
64007 TTGCAATTTTGAG-TACTTGCGACAATT
1 TTACAATTTTGAGTTGC-TGCGACAATT
*
64034 TTACAATTTTCAGTTGCTGCG
1 TTACAATTTTGAGTTGCTGCG
64055 GCATCCTTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 1 0.03
27 35 0.92
28 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (27 bp):
TTACAATTTTGAGTTGCTGCGACAATT
Found at i:64143 original size:27 final size:27
Alignment explanation
Indices: 64083--64170 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
64073 GACACTTGTG
64083 GTAATTTTGGCTAGTTGCAGGG---TTTT
1 GTAATTTTGGCTAGTTG--GGGCAATTTT
64109 GTAATTTTGGCTAGTTGGGGCAATTTT
1 GTAATTTTGGCTAGTTGGGGCAATTTT
* **
64136 GTAATTTTGAGC-ACTTGCAGCAATTTT
1 GTAATTTTG-GCTAGTTGGGGCAATTTT
*
64163 GCAATTTT
1 GTAATTTT
64171 TGGGTTGCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
24 3 0.06
26 17 0.31
27 32 0.59
28 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.25, T:0.44
Consensus pattern (27 bp):
GTAATTTTGGCTAGTTGGGGCAATTTT
Found at i:64278 original size:93 final size:92
Alignment explanation
Indices: 64111--64294 Score: 214
Period size: 93 Copynumber: 2.0 Consensus size: 92
64101 AGGGTTTTGT
* *
64111 AATTTTGGCTAGTTGGGGCAATTTTGTAATTTTGAGCACTTGCAGCAATTTTGCAATTTTTGGGT
1 AATTTTGGCTAGTTGGGGCAATTTTGTAATTTTGAGCACTTGCAGCAATTTGGCAATTTTTGGGC
64176 TGCTACGGC-ATCTTTGACTAGTTGTGGC
66 TGCTACGGCAAT-TTTG-CTAGTTGTGGC
** * * * *
64204 AATTTTGGCTAGTTGCGGG-GTTTTTGTAATTTTG-GCTAGTTGCGGGAATTGTGGTAA-TTTTG
1 AATTTTGGCTAGTTG-GGGCAATTTTGTAATTTTGAGC-ACTTGCAGCAATT-TGGCAATTTTTG
*
64266 GGCTGCTGCGGCAATTTTGCTAGTTGTGG
63 GGCTGCTACGGCAATTTTGCTAGTTGTGG
64295 GGCTTGTATA
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
92 12 0.15
93 57 0.73
94 9 0.12
ACGTcount: A:0.17, C:0.12, G:0.30, T:0.41
Consensus pattern (92 bp):
AATTTTGGCTAGTTGGGGCAATTTTGTAATTTTGAGCACTTGCAGCAATTTGGCAATTTTTGGGC
TGCTACGGCAATTTTGCTAGTTGTGGC
Found at i:64631 original size:29 final size:28
Alignment explanation
Indices: 64575--64643 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 28
64565 ATTTCCATTA
*
64575 TCATTAATTA-CTTGGTGCGACATCTCT
1 TCATTACTTAGCTTGGTGCGACATCTCT
* * *
64602 TCATTGCTTAGCTTGGCTGCGGCATTTCT
1 TCATTACTTAGCTTGG-TGCGACATCTCT
64631 TCATTACTTAGCT
1 TCATTACTTAGCT
64644 GCAGCATCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 8 0.23
28 5 0.14
29 22 0.63
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (28 bp):
TCATTACTTAGCTTGGTGCGACATCTCT
Found at i:65131 original size:27 final size:27
Alignment explanation
Indices: 65092--65145 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
65082 TGACTTTGAA
65092 AGTTGGTACTATGGCCACAGCTCCCGC
1 AGTTGGTACTATGGCCACAGCTCCCGC
* * *
65119 AGTTGGTAGTATGGCTACGGCTCCCGC
1 AGTTGGTACTATGGCCACAGCTCCCGC
65146 CGCAATTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.24
Consensus pattern (27 bp):
AGTTGGTACTATGGCCACAGCTCCCGC
Found at i:65319 original size:37 final size:37
Alignment explanation
Indices: 65251--65384 Score: 106
Period size: 37 Copynumber: 3.5 Consensus size: 37
65241 GCCGTAGCTC
* * *
65251 CCGCGATTGGGACTTATGCCATGGCGGCTTATGGCTT
1 CCGCGGTTGGGACTTATGCCATAGCGACTTATGGCTT
* * *
65288 CCGCAGTTGGGACTTATGTCGTAGCGACTTATACTGTAGCTT
1 CCGCGGTTGGGACTTATGCCATAGCGAC-T-TA-TG--GCTT
* * * * * *
65330 TCGTGGTAGGGACTTATGCCATGGCGTCTTATGGCTC
1 CCGCGGTTGGGACTTATGCCATAGCGACTTATGGCTT
*
65367 CCGCGGTTGGGACCTATG
1 CCGCGGTTGGGACTTATG
65385 TCGTAGCTCT
Statistics
Matches: 73, Mismatches: 19, Indels: 10
0.72 0.19 0.10
Matches are distributed among these distances:
37 39 0.53
38 1 0.01
39 4 0.05
40 4 0.05
41 1 0.01
42 24 0.33
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (37 bp):
CCGCGGTTGGGACTTATGCCATAGCGACTTATGGCTT
Found at i:65663 original size:50 final size:50
Alignment explanation
Indices: 65601--66056 Score: 563
Period size: 50 Copynumber: 9.1 Consensus size: 50
65591 TACGCAAAAA
* * *
65601 ATCTCATGCCTTATGCCATAGACTTATGATGCCATAATTTTTGACGCCGT
1 ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCCGC
* *
65651 ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAAGGTTTGACACCGC
1 ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCCGC
* * * * * * *
65701 ATCTCATGCCTTATGTCGTAGGCTTGTGATACCGTAACGTTTGACGCCGC
1 ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCCGC
* * ** *
65751 ATCTCATGCCTTATGCCATAGACTTCTTATGTCATAACATTTGACACCGC
1 ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCCGC
* * *
65801 ATCTCATGCCTTATGCCATAGACTTATTATGCCATAATGTTTGGCGCCGC
1 ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCCGC
* *
65851 ATCTCATTCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCAGC
1 ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCCGC
* * *** ** *
65901 ATCTCATGCCTTATGCCACAGACTTATGATGTTGTAATGTTTGATTCCAC
1 ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCCGC
* * *
65951 ATCTTATGCCTTATGCCATAG-GTTGCTGATGCCATAATGTTTGACGCTGC
1 ATCTCATGCCTTATGCCATAGACTT-CTGATGCCATAATGTTTGACGCCGC
* * * *
66001 ATCTCATGCCTTATGCCACAGACTTTTGATGTCATAATGTTTGACACCGC
1 ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCCGC
66051 ATCTCA
1 ATCTCA
66057 CTTGGTTGTT
Statistics
Matches: 342, Mismatches: 62, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
49 2 0.01
50 338 0.99
51 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (50 bp):
ATCTCATGCCTTATGCCATAGACTTCTGATGCCATAATGTTTGACGCCGC
Found at i:69622 original size:16 final size:16
Alignment explanation
Indices: 69601--69632 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
69591 CCAATTGGCA
69601 TATAAAGAACACTAAT
1 TATAAAGAACACTAAT
69617 TATAAAGAACACTAAT
1 TATAAAGAACACTAAT
69633 AGTGTGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.25
Consensus pattern (16 bp):
TATAAAGAACACTAAT
Found at i:82237 original size:22 final size:22
Alignment explanation
Indices: 82212--82304 Score: 64
Period size: 22 Copynumber: 4.2 Consensus size: 22
82202 CCTTATAAAC
82212 TTTTGATAACATTCCTATGAAA
1 TTTTGATAACATTCCTATGAAA
* *
82234 TTTTGATAACGA-TACTATGCAA
1 TTTTGATAAC-ATTCCTATGAAA
* * * * *
82256 TTTCGAAAACCTTCCAATCAAA
1 TTTTGATAACATTCCTATGAAA
** *
82278 TTTCAAGAAC-TTCCCTATGAAA
1 TTTTGATAACATT-CCTATGAAA
82300 TTTTG
1 TTTTG
82305 TTAATCACCC
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
21 2 0.04
22 50 0.94
23 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (22 bp):
TTTTGATAACATTCCTATGAAA
Found at i:82654 original size:17 final size:17
Alignment explanation
Indices: 82627--82675 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
82617 TGTAATTTTT
*
82627 GATCACCGGTGATCTT-
1 GATCACTGGTGATCTTA
82643 GCATCACTGGTGATCTTA
1 G-ATCACTGGTGATCTTA
*
82661 GATCACTAGTGATCT
1 GATCACTGGTGATCT
82676 GGGGGGTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 1 0.03
17 27 0.93
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (17 bp):
GATCACTGGTGATCTTA
Found at i:82792 original size:23 final size:23
Alignment explanation
Indices: 82766--82845 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
82756 CCTCGGTATG
82766 AAATTTTGATAAACATTCATATA
1 AAATTTTGATAAACATTCATATA
* * *
82789 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACATTCATATA
* * *
82812 AAATTTTGAT-AACTTTCTTATG
1 AAATTTTGATAAACATTCATATA
82834 AAATTTTGATAA
1 AAATTTTGATAA
82846 TCACAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
22 18 0.37
23 31 0.63
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAACATTCATATA
Found at i:82915 original size:22 final size:22
Alignment explanation
Indices: 82722--82926 Score: 111
Period size: 22 Copynumber: 9.5 Consensus size: 22
82712 ACACTATGAA
**
82722 AAATTTTGATAATCA-AACTATG
1 AAATTTTGATAA-CATCCCTATG
* * * **
82744 AAATTGTAATAACCTCGGTATG
1 AAATTTTGATAACATCCCTATG
* * *
82766 AAATTTTGATAAACATTCATATA
1 AAATTTTGAT-AACATCCCTATG
* *
82789 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACATCCCTATG
* * *
82812 AAATTTTGATAACTTTCTTATG
1 AAATTTTGATAACATCCCTATG
*
82834 AAATTTTGAT-A-AT--C-A-C
1 AAATTTTGATAACATCCCTATG
*
82850 AAATTTTGATAACGTCCCTATG
1 AAATTTTGATAACATCCCTATG
* * **
82872 -ATTTTTCGATAACTTCATTATG
1 AAATTTT-GATAACATCCCTATG
*
82894 AAATTTTGTTAACATCCCTATG
1 AAATTTTGATAACATCCCTATG
*
82916 GAATTTTGATA
1 AAATTTTGATA
82927 TAAAATTTTG
Statistics
Matches: 137, Mismatches: 36, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
16 10 0.07
17 2 0.01
18 1 0.01
20 2 0.01
21 8 0.06
22 72 0.53
23 42 0.31
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACATCCCTATG
Found at i:82971 original size:22 final size:22
Alignment explanation
Indices: 82946--83024 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
82936 GAAAACTAAA
82946 CTATGAAATTTTGATATCCTCT
1 CTATGAAATTTTGATATCCTCT
*
82968 CTATGAAATTTTGATAATCC-CC
1 CTATGAAATTTTGAT-ATCCTCT
* * *
82990 CTTTGAAATTTTAATAACCT-T
1 CTATGAAATTTTGATATCCTCT
*
83011 CATACGAAATTTTG
1 C-TATGAAATTTTG
83025 GTAATCACAC
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.09
22 38 0.83
23 4 0.09
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATATCCTCT
Found at i:83120 original size:22 final size:21
Alignment explanation
Indices: 83095--83153 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
83085 TAATAACATT
83095 ATGAAATTTCGATAACCT-TCCA
1 ATGAAATTT-GATAACCTCT-CA
* *
83117 ATGAAATGTTGCTAACCTCTCT
1 ATGAAAT-TTGATAACCTCTCA
83139 ATGAAATTTTGATAA
1 ATGAAA-TTTGATAA
83154 TCATACTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (21 bp):
ATGAAATTTGATAACCTCTCA
Found at i:83165 original size:44 final size:42
Alignment explanation
Indices: 83094--83198 Score: 104
Period size: 44 Copynumber: 2.5 Consensus size: 42
83084 ATAATAACAT
* * * * **
83094 TATGAAATTTCGATAACCTTCCAATGAAATGTTGCTAACCTCTC-
1 TATGAAATTTTGATAATCATACAATGAAAT-TT-AAAACCTC-CA
*
83138 TATGAAATTTTGATAATCATACTATGAAATTTAAAACCTCCA
1 TATGAAATTTTGATAATCATACAATGAAATTTAAAACCTCCA
*
83180 TATGAAATTTTAATAATCA
1 TATGAAATTTTGATAATCA
83199 CAATATAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 24 0.46
43 2 0.04
44 25 0.48
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (42 bp):
TATGAAATTTTGATAATCATACAATGAAATTTAAAACCTCCA
Found at i:83324 original size:22 final size:22
Alignment explanation
Indices: 83250--83324 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
83240 AACCTCGTTT
*
83250 TAAAATTTTGATAACTTTTCTA
1 TAAAATTTTGATAACCTTTCTA
* * **
83272 TTAACTTTTGATAACCACAT-TA
1 TAAAATTTTGATAACC-TTTCTA
*
83294 T-GAATTTTGATAACCTTTCTA
1 TAAAATTTTGATAACCTTTCTA
83315 TAAAATTTTG
1 TAAAATTTTG
83325 GTGATCTGAT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
22 23 0.57
23 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (22 bp):
TAAAATTTTGATAACCTTTCTA
Found at i:83360 original size:22 final size:21
Alignment explanation
Indices: 83253--83364 Score: 66
Period size: 22 Copynumber: 5.0 Consensus size: 21
83243 CTCGTTTTAA
** *
83253 AATTTTGATAACTTTTCTATT
1 AATTTTGATAACTACTCTATG
*
83274 AACTTTTGATAACCACAT-TATG
1 AA-TTTTGATAACTAC-TCTATG
* *
83296 AATTTTGATAACCT-TTCTATAA
1 AATTTTGATAA-CTACTCTAT-G
* *
83318 AATTTTGGTGATCTGATCTCTATG
1 AATTTTGAT-AACT-A-CTCTATG
83342 AATTTTTGATAACTACTCTATG
1 AA-TTTTGATAACTACTCTATG
83364 A
1 A
83365 GTTTGATTGC
Statistics
Matches: 68, Mismatches: 13, Indels: 19
0.68 0.13 0.19
Matches are distributed among these distances:
20 1 0.01
21 14 0.21
22 34 0.50
23 3 0.04
24 5 0.07
25 11 0.16
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (21 bp):
AATTTTGATAACTACTCTATG
Found at i:83593 original size:65 final size:66
Alignment explanation
Indices: 83431--83622 Score: 181
Period size: 65 Copynumber: 2.9 Consensus size: 66
83421 TAACATTACT
* * * * * * * *
83431 ATGAAATTTTGGTAACCACACTATGAAATCTTTGATAACCTCCTTATAAAATTTAGATAACCACA
1 ATGAAATTCTGATAACCTCGCTATGAAAT-TTTGATAACCTCCATATGAAATTTTGATAAACACA
*
83496 CT
65 CA
* *
83498 ATGAAATTCTGATAACCTCGCTGTGGAATTTTGATAACCTCC-TATGAAATTTTGATAAACACAC
1 ATGAAATTCTGATAACCTCGCTATGAAATTTTGATAACCTCCATATGAAATTTTGATAAACACAC
83562 A
66 A
* * * * *
83563 ATGAAATTTTTATAACTTTC-CTATAAAATTTTAATAACCTAATCCATATGAAATTTTGAT
1 ATGAAATTCTGATAAC-CTCGCTATGAAATTTTGATAACC---TCCATATGAAATTTTGAT
83623 GACAACACTG
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
65 48 0.47
66 15 0.15
67 23 0.22
68 3 0.03
69 14 0.14
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (66 bp):
ATGAAATTCTGATAACCTCGCTATGAAATTTTGATAACCTCCATATGAAATTTTGATAAACACAC
A
Found at i:83652 original size:22 final size:22
Alignment explanation
Indices: 83428--83661 Score: 179
Period size: 22 Copynumber: 10.5 Consensus size: 22
83418 TTCTAACATT
*
83428 ACTATGAAATTTTGGTAACCAC
1 ACTATGAAATTTTGATAACCAC
*
83450 ACTATGAAATCTTTGATAACCTC
1 ACTATGAAAT-TTTGATAACCAC
* *
83473 -CTTATAAAATTTAGATAACCAC
1 AC-TATGAAATTTTGATAACCAC
* *
83495 ACTATGAAATTCTGATAACCTC
1 ACTATGAAATTTTGATAACCAC
* * * *
83517 GCTGTGGAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCAC
*
83539 -CTATGAAATTTTGATAAACAC
1 ACTATGAAATTTTGATAACCAC
* * **
83560 ACAATGAAATTTTTATAACTTTC
1 ACTATGAAATTTTGATAAC-CAC
* *
83583 -CTATAAAATTTTAATAACCTA-
1 ACTATGAAATTTTGATAACC-AC
* *
83604 ATCCATATGAAATTTTGATGACAAC
1 A--C-TATGAAATTTTGATAACCAC
* *
83629 ACTGTGAAATTTTGATAATCAC
1 ACTATGAAATTTTGATAACCAC
*
83651 ACTATAAAATT
1 ACTATGAAATT
83662 GGTAACCACA
Statistics
Matches: 164, Mismatches: 37, Indels: 22
0.74 0.17 0.10
Matches are distributed among these distances:
21 17 0.10
22 110 0.67
23 20 0.12
24 2 0.01
25 15 0.09
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCAC
Found at i:85719 original size:21 final size:21
Alignment explanation
Indices: 85693--85761 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
85683 AGCTTAAGGG
85693 TTCAAAATAGGGTTCTTGAGT
1 TTCAAAATAGGGTTCTTGAGT
* *
85714 TTCAAATTAGGGTTCTTGATTT
1 TTCAAAATAGGGTTCTTGA-GT
85736 TTCAAAATTAGGGTTCTTGAGT
1 TTCAAAA-TAGGGTTCTTGAGT
85758 TTCA
1 TTCA
85762 TCTTCAATCG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 18 0.43
22 12 0.29
23 12 0.29
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.43
Consensus pattern (21 bp):
TTCAAAATAGGGTTCTTGAGT
Found at i:85747 original size:23 final size:22
Alignment explanation
Indices: 85693--85761 Score: 106
Period size: 23 Copynumber: 3.2 Consensus size: 22
85683 AGCTTAAGGG
85693 TTCAAAA-TAGGGTTCTTGAGT
1 TTCAAAATTAGGGTTCTTGAGT
*
85714 TTC-AAATTAGGGTTCTTGATTT
1 TTCAAAATTAGGGTTCTTGA-GT
85736 TTCAAAATTAGGGTTCTTGAGT
1 TTCAAAATTAGGGTTCTTGAGT
85758 TTCA
1 TTCA
85762 TCTTCAATCG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 3 0.07
21 15 0.35
22 9 0.21
23 16 0.37
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.43
Consensus pattern (22 bp):
TTCAAAATTAGGGTTCTTGAGT
Found at i:90418 original size:44 final size:43
Alignment explanation
Indices: 90281--90446 Score: 188
Period size: 43 Copynumber: 3.8 Consensus size: 43
90271 GTTTGGTAAT
* * * * ***
90281 CAAAATTTCATAATAAGATTATTAAAATTTCATCCGAAGGTTA
1 CAAAATTTCATAAGAAGGTTATCAAAATTTCATACTCCGGTTA
* *
90324 TCAAAAATTTCATAAGGAGGTTATCAAAATTTCATAGTCCGGTTA
1 -C-AAAATTTCATAAGAAGGTTATCAAAATTTCATACTCCGGTTA
* * * *
90369 CAAAATTTTATAAGAAGGTTATAAAAAATTCATACTCTGGTTA
1 CAAAATTTCATAAGAAGGTTATCAAAATTTCATACTCCGGTTA
90412 CCAAAATTTCATAAGAAGGTTATCAAAATTTCATA
1 -CAAAATTTCATAAGAAGGTTATCAAAATTTCATA
90447 GAGTGCTTAT
Statistics
Matches: 102, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
43 36 0.35
44 33 0.32
45 33 0.32
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (43 bp):
CAAAATTTCATAAGAAGGTTATCAAAATTTCATACTCCGGTTA
Found at i:90456 original size:22 final size:22
Alignment explanation
Indices: 90279--90463 Score: 162
Period size: 22 Copynumber: 8.4 Consensus size: 22
90269 TTGTTTGGTA
* *
90279 ATCAAAATTTCATAATAAGATT
1 ATCAAAATTTCATAAGAAGGTT
* **
90301 ATTAAAATTTCATCCGAAGGTT
1 ATCAAAATTTCATAAGAAGGTT
*
90323 ATCAAAAATTTCATAAGGAGGTT
1 ATC-AAAATTTCATAAGAAGGTT
**
90346 ATCAAAATTTCAT-AGTCCGGTT
1 ATCAAAATTTCATAAG-AAGGTT
*
90368 A-CAAAATTTTATAAGAAGGTT
1 ATCAAAATTTCATAAGAAGGTT
* * ****
90389 ATAAAAAATTCATACTCTGGTT
1 ATCAAAATTTCATAAGAAGGTT
*
90411 ACCAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAAGAAGGTT
90433 ATCAAAATTTCAT-AG-AGTGCTT
1 ATCAAAATTTCATAAGAAG-G-TT
90455 ATCAAAATT
1 ATCAAAATT
90464 GTAGGGATTA
Statistics
Matches: 128, Mismatches: 29, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.02
21 20 0.16
22 87 0.68
23 19 0.15
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAAGAAGGTT
Found at i:90461 original size:44 final size:44
Alignment explanation
Indices: 90274--90463 Score: 195
Period size: 44 Copynumber: 4.3 Consensus size: 44
90264 TGTCTTTGTT
* * * * *
90274 TGGTAATCAAAATTTCATAATAAGATTATTAAAATTTCATCCGA-
1 TGGTTATCAAAATTTCATAAGAAGGTTATCAAAATTTCAT-AGAC
* * *
90318 AGGTTATCAAAAATTTCATAAGGAGGTTATCAAAATTTCATAGTC
1 TGGTTATC-AAAATTTCATAAGAAGGTTATCAAAATTTCATAGAC
* * * * **
90363 CGGTTA-CAAAATTTTATAAGAAGGTTATAAAAAATTCATACTC
1 TGGTTATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGAC
* *
90406 TGGTTACCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGAG
1 TGGTTATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGAC
*
90450 TGCTTATCAAAATT
1 TGGTTATCAAAATT
90464 GTAGGGATTA
Statistics
Matches: 120, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
43 36 0.30
44 51 0.43
45 33 0.28
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (44 bp):
TGGTTATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGAC
Found at i:90571 original size:22 final size:22
Alignment explanation
Indices: 90533--90625 Score: 98
Period size: 22 Copynumber: 4.2 Consensus size: 22
90523 AAGATTTTGA
* * *
90533 TTATTAAAATTTCATAGTGTGG
1 TTATCAAATTTTCATAGTGAGG
* *
90555 TTATCAAATTTTTATAGAGAGG
1 TTATCAAATTTTCATAGTGAGG
*
90577 TTATCGAAA-TTTCATAATGAGG
1 TTATC-AAATTTTCATAGTGAGG
* *
90599 TTATCAAATTTTCAGAGTGTGG
1 TTATCAAATTTTCATAGTGAGG
90621 TTATC
1 TTATC
90626 GATATTTCTA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
21 3 0.05
22 52 0.90
23 3 0.05
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (22 bp):
TTATCAAATTTTCATAGTGAGG
Found at i:90602 original size:44 final size:44
Alignment explanation
Indices: 90539--90633 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 44
90529 TTGATTATTA
* * * *
90539 AAATTTCATAGTGTGGTTATCAAATTTTTATAGAGAGGTTATCG
1 AAATTTCATAATGAGGTTATCAAATTTTCAGAGAGAGGTTATCG
* *
90583 AAATTTCATAATGAGGTTATCAAATTTTCAGAGTGTGGTTATCG
1 AAATTTCATAATGAGGTTATCAAATTTTCAGAGAGAGGTTATCG
*
90627 ATATTTC
1 AAATTTC
90634 TATGTTGGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (44 bp):
AAATTTCATAATGAGGTTATCAAATTTTCAGAGAGAGGTTATCG
Found at i:90633 original size:22 final size:22
Alignment explanation
Indices: 90573--90633 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
90563 TTTTTATAGA
*
90573 GAGGTTATCGAAATTTCATAAT
1 GAGGTTATCGAAATTTCAGAAT
*
90595 GAGGTTATC-AAATTTTCAGAGT
1 GAGGTTATCGAAA-TTTCAGAAT
* *
90617 GTGGTTATCGATATTTC
1 GAGGTTATCGAAATTTC
90634 TATGTTGGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.09
22 28 0.85
23 2 0.06
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (22 bp):
GAGGTTATCGAAATTTCAGAAT
Done.