Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 51 of 91
Found at i:17866849 original size:39 final size:39
Alignment explanation
Indices: 17866747--17866857 Score: 129
Period size: 39 Copynumber: 2.9 Consensus size: 39
17866737 AACTTAGCTT
* * *
17866747 ATGTGCACTCCCACACCGCACATAG-TTA-AT-ATCTTC
1 ATGTGCACTCCCACACCGCACATGGCATATATCATCATC
* * *
17866783 ATGTGCACTCCAACACCACACAAGGCATATATCATCATC
1 ATGTGCACTCCCACACCGCACATGGCATATATCATCATC
* *
17866822 ATGTGCTCTCCCACACTGCACATGGCATATATCATC
1 ATGTGCACTCCCACACCGCACATGGCATATATCATC
17866858 GACTTGTGCT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
36 21 0.34
37 2 0.03
38 2 0.03
39 36 0.59
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.25
Consensus pattern (39 bp):
ATGTGCACTCCCACACCGCACATGGCATATATCATCATC
Found at i:17866882 original size:39 final size:39
Alignment explanation
Indices: 17866781--17866875 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
17866771 GTTAATATCT
* * **
17866781 TCATGTGCACTCCAACACCACACAAGGCATATATCATCA
1 TCATGTGCTCTCCCACACTGCACAAGGCATATATCATCA
*
17866820 TCATGTGCTCTCCCACACTGCACATGGCATATATCATCGA
1 TCATGTGCTCTCCCACACTGCACAAGGCATATATCATC-A
* *
17866860 -CTTGTGCTCTTCCACA
1 TCATGTGCTCTCCCACA
17866876 TCGCACACTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 47 0.98
40 1 0.02
ACGTcount: A:0.27, C:0.34, G:0.13, T:0.26
Consensus pattern (39 bp):
TCATGTGCTCTCCCACACTGCACAAGGCATATATCATCA
Found at i:17867429 original size:20 final size:20
Alignment explanation
Indices: 17867387--17867429 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
17867377 AACAAGAAGA
* **
17867387 AGAAGTTGTTGGAAGTGAGG
1 AGAAGGTGTTGGAAGAAAGG
*
17867407 AGAAGGTGTTGGAAGAAATG
1 AGAAGGTGTTGGAAGAAAGG
17867427 AGA
1 AGA
17867430 TATTTATCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.42, T:0.21
Consensus pattern (20 bp):
AGAAGGTGTTGGAAGAAAGG
Found at i:17868882 original size:10 final size:10
Alignment explanation
Indices: 17868867--17868893 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
17868857 CTCGATCATA
17868867 TTTTTTTTAT
1 TTTTTTTTAT
17868877 TTTTTTTTAT
1 TTTTTTTTAT
17868887 TTTTTTT
1 TTTTTTT
17868894 GGCTATTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:17870572 original size:37 final size:37
Alignment explanation
Indices: 17870525--17870606 Score: 164
Period size: 37 Copynumber: 2.2 Consensus size: 37
17870515 AATGCAATAT
17870525 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
17870562 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
17870599 CATCATCA
1 CATCATCA
17870607 CACAACATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.26, C:0.38, G:0.10, T:0.27
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:17870715 original size:2 final size:2
Alignment explanation
Indices: 17870708--17870758 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
17870698 NNNNNNNNNN
17870708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17870750 TA TA TA TA T
1 TA TA TA TA T
17870759 CAACATAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17871415 original size:20 final size:20
Alignment explanation
Indices: 17871392--17871431 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17871382 AGAAAAACAA
*
17871392 GAAGTTGCTGGAAAAATGAG
1 GAAGCTGCTGGAAAAATGAG
*
17871412 GAAGCTGCTGGAGAAATGAG
1 GAAGCTGCTGGAAAAATGAG
17871432 ATATGTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.38, T:0.17
Consensus pattern (20 bp):
GAAGCTGCTGGAAAAATGAG
Found at i:17882787 original size:40 final size:38
Alignment explanation
Indices: 17882695--17882790 Score: 122
Period size: 38 Copynumber: 2.5 Consensus size: 38
17882685 ATACTGCCCG
* *
17882695 TGTGCACGATGTGGGGGAATGTACACGATGGCATTATC
1 TGTGCACGATGTGGGGGAATGTACACGATGACATTATA
* *
17882733 TGTGCACAATGTGGGGGGATGTACACGATGAC-TCTAGCTA
1 TGTGCACGATGTGGGGGAATGTACACGATGACAT-TA--TA
17882773 TGTGCACGATGTGGGGGA
1 TGTGCACGATGTGGGGGA
17882791 GGGCACATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 1 0.02
38 31 0.63
40 17 0.35
ACGTcount: A:0.23, C:0.16, G:0.36, T:0.25
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGAATGTACACGATGACATTATA
Found at i:17882819 original size:56 final size:55
Alignment explanation
Indices: 17882755--17882913 Score: 198
Period size: 56 Copynumber: 2.9 Consensus size: 55
17882745 GGGGGGATGT
*
17882755 ACACGATGACTCTAGCTATGTGCACGATGT-GGGGGAGGGCACATGAGCTAGGTGAG
1 ACACGATGACTC-AGCTATGTGCACGATGTGGGGGGA-TGCACATGAGCTAGGTGAG
* *
17882811 ACACGATGACTCCGGCTATGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAG
1 ACACGATGACT-CAGCTATGTGCACGATGTGGGGGGATGCACATGAGCTAGGTGAG
*** *
17882867 ATGGGATG--TCATGCTATGTGCACAATGTGGGGGGATGCACATGAGCT
1 ACACGATGACTCA-GCTATGTGCACGATGTGGGGGGATGCACATGAGCT
17882914 GGATGGGATG
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
53 1 0.01
54 35 0.38
56 49 0.53
57 7 0.08
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (55 bp):
ACACGATGACTCAGCTATGTGCACGATGTGGGGGGATGCACATGAGCTAGGTGAG
Found at i:17884483 original size:20 final size:20
Alignment explanation
Indices: 17884458--17884497 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17884448 CTATAAATAT
*
17884458 CTCATTTCTCCAGCAGCTTC
1 CTCATTTCTCCAGCAACTTC
*
17884478 CTCATTTTTCCAGCAACTTC
1 CTCATTTCTCCAGCAACTTC
17884498 TTGTTCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.38, G:0.07, T:0.38
Consensus pattern (20 bp):
CTCATTTCTCCAGCAACTTC
Found at i:17885346 original size:17 final size:19
Alignment explanation
Indices: 17885305--17885346 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
17885295 ATATATATAT
17885305 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
17885326 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
17885343 ATGA
1 ATGA
17885347 TATTGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:17885382 original size:37 final size:37
Alignment explanation
Indices: 17885341--17885459 Score: 177
Period size: 37 Copynumber: 3.2 Consensus size: 37
17885331 TAATGTTGTG
*
17885341 TGATGATATTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
* *
17885378 TGATGATGTT-AGAGTGTGAGAGTAAGGAGTGCACACA
1 TGATGATGTTGA-AGTGTGCGAGTAGGGAGTGCACACA
* *
17885415 TGATGATGTTGAAGTGTGCGAGTTGGGAGTGTACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
17885452 TGATGATG
1 TGATGATG
17885460 ATATTGCATT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
36 1 0.01
37 71 0.97
38 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.36, T:0.27
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:17894827 original size:35 final size:35
Alignment explanation
Indices: 17894735--17894839 Score: 156
Period size: 35 Copynumber: 3.0 Consensus size: 35
17894725 ACTCAGCTCG
* ***
17894735 TGTGTACTCCCTACACGCACAAGGCAATATCATCA
1 TGTGCACTCCCTACACGCACATTTCAATATCATCA
17894770 TGTGCACTCCCTACACGCACATTTCAATATCATCA
1 TGTGCACTCCCTACACGCACATTTCAATATCATCA
* *
17894805 TGTGCACTCCCTATACGTACATTTCAATATCATCA
1 TGTGCACTCCCTACACGCACATTTCAATATCATCA
17894840 CACTCATTCC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.30, C:0.31, G:0.10, T:0.29
Consensus pattern (35 bp):
TGTGCACTCCCTACACGCACATTTCAATATCATCA
Found at i:17908832 original size:20 final size:21
Alignment explanation
Indices: 17908804--17908852 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
17908794 GAAGTAAGAA
* *
17908804 AAAAAAAAGGAAAGGAAAA-G
1 AAAAAAAAGAAAAGAAAAATG
*
17908824 AAAACAAAGAAAAGAAAAATG
1 AAAAAAAAGAAAAGAAAAATG
*
17908845 AAAGAAAA
1 AAAAAAAA
17908853 TTGAATATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGAAAAGAAAAATG
Found at i:17908835 original size:19 final size:17
Alignment explanation
Indices: 17908799--17908842 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
17908789 AGAAAGAAGT
*
17908799 AAGAAAAAAAAAAGGAA
1 AAGAAAAAAAAAAAGAA
*
17908816 AGGAAAAGAAAACAAAGAA
1 AAGAAAA-AAAA-AAAGAA
17908835 AAGAAAAA
1 AAGAAAAA
17908843 TGAAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 6 0.27
18 5 0.23
19 11 0.50
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAAGAA
Found at i:17910386 original size:20 final size:21
Alignment explanation
Indices: 17910355--17910393 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17910345 CCTTTAAGCT
*
17910355 TTTCTCTTCCTTTTTCTTTTC
1 TTTCTCTTCCTTCTTCTTTTC
17910376 TTTCT-TTCCTTCTTCTTT
1 TTTCTCTTCCTTCTTCTTT
17910394 CTTCTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTCTCTTCCTTCTTCTTTTC
Found at i:17913717 original size:19 final size:19
Alignment explanation
Indices: 17913690--17913727 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17913680 CCATTTAACT
17913690 TATTAGAGTATAATTTGAG
1 TATTAGAGTATAATTTGAG
*
17913709 TATTGGAGTATAATTTGAG
1 TATTAGAGTATAATTTGAG
17913728 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATAATTTGAG
Found at i:17913934 original size:28 final size:30
Alignment explanation
Indices: 17913893--17913952 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
17913883 GGCTATGGGC
* *
17913893 AATTTTTCAGTTTT-T-GGGGTAAAAATGT
1 AATTTTTCACTTTTATAGGGGCAAAAATGT
* *
17913921 AATTTTTGACTTTTATAGGGGCAAAAGTGT
1 AATTTTTCACTTTTATAGGGGCAAAAATGT
17913951 AA
1 AA
17913953 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
29 1 0.04
30 13 0.50
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.42
Consensus pattern (30 bp):
AATTTTTCACTTTTATAGGGGCAAAAATGT
Found at i:17916561 original size:15 final size:15
Alignment explanation
Indices: 17916522--17916562 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
17916512 GATCAAAGAA
*
17916522 TTTGGTTTTAAAGCT
1 TTTGATTTTAAAGCT
* *
17916537 TTGGAGTTTAAAGCT
1 TTTGATTTTAAAGCT
17916552 TTTGATTTTAA
1 TTTGATTTTAA
17916563 TATTGTTTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.51
Consensus pattern (15 bp):
TTTGATTTTAAAGCT
Found at i:17927202 original size:35 final size:35
Alignment explanation
Indices: 17927131--17927250 Score: 107
Period size: 35 Copynumber: 3.3 Consensus size: 35
17927121 ATGTTAGGTG
* *
17927131 TAACCTTTACAACATGCCTTTTGTAGGATCAAGCA
1 TAACCTTTACAACATGCCTTTTGCAAGATCAAGCA
* * *
17927166 TAACCTTTACAGCATGCCTTTTGCAAGATTAGGCA
1 TAACCTTTACAACATGCCTTTTGCAAGATCAAGCA
* * *
17927201 TAA-CTTCTATCAAGACATTGCCTTTTTCATGTTCAAGCA
1 TAACCTT-TA-C-A-ACA-TGCCTTTTGCAAGATCAAGCA
*
17927240 CAACCTTTACA
1 TAACCTTTACA
17927251 CAAGATGCAG
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
34 3 0.04
35 35 0.52
36 1 0.01
37 2 0.03
38 3 0.04
39 20 0.30
40 3 0.04
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (35 bp):
TAACCTTTACAACATGCCTTTTGCAAGATCAAGCA
Found at i:17932807 original size:20 final size:20
Alignment explanation
Indices: 17932765--17932808 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
17932755 AATTGGATGC
* *
17932765 ATATTTGAGGATATATATAT
1 ATATATGAGGATATAAATAT
17932785 ATATATGAGGATATCAAAT-T
1 ATATATGAGGATAT-AAATAT
17932805 ATAT
1 ATAT
17932809 GAGTTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (20 bp):
ATATATGAGGATATAAATAT
Found at i:17934137 original size:29 final size:29
Alignment explanation
Indices: 17934055--17934184 Score: 129
Period size: 29 Copynumber: 4.4 Consensus size: 29
17934045 TCTTGTCCGT
17934055 AATTAAGACAAAA-ATTATTTTATCTTGTCTA
1 AATTAAGACAAAACA-TA-TTT-TCTTGTCTA
* ** * *
17934086 AATTTGAGAC-AATTATGTATTCTTGTCTA
1 AA-TTAAGACAAAACATATTTTCTTGTCTA
*
17934115 GATTAAGACAAAACATATTTTCTTGTCTA
1 AATTAAGACAAAACATATTTTCTTGTCTA
* * *
17934144 AATTAAGACCAAACATGTTTTCTTATCTA
1 AATTAAGACAAAACATATTTTCTTGTCTA
17934173 AATTAAGACAAA
1 AATTAAGACAAA
17934185 CATGTTAAAG
Statistics
Matches: 81, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
28 6 0.07
29 61 0.75
30 2 0.02
31 5 0.06
32 7 0.09
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
AATTAAGACAAAACATATTTTCTTGTCTA
Found at i:17934167 original size:58 final size:60
Alignment explanation
Indices: 17934055--17934184 Score: 160
Period size: 58 Copynumber: 2.2 Consensus size: 60
17934045 TCTTGTCCGT
* ** *
17934055 AATTAAGACAAAAATTATTTTATCTTGTCTAAATTTGAGACAATTATGTATTCTTGTCTA
1 AATTAAGACAAAAATTATTTTATCTTGTCTAAATTTAAGACAAACATGTATTCTTATCTA
* *
17934115 GATTAAGACAAAACA-TA-TTT-TCTTGTCTAAA-TTAAGACCAAACATGTTTTCTTATCTA
1 AATTAAGACAAAA-ATTATTTTATCTTGTCTAAATTTAAGA-CAAACATGTATTCTTATCTA
17934173 AATTAAGACAAA
1 AATTAAGACAAA
17934185 CATGTTAAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
57 5 0.08
58 38 0.62
59 3 0.05
60 14 0.23
61 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (60 bp):
AATTAAGACAAAAATTATTTTATCTTGTCTAAATTTAAGACAAACATGTATTCTTATCTA
Found at i:17935917 original size:32 final size:33
Alignment explanation
Indices: 17935881--17936027 Score: 149
Period size: 35 Copynumber: 4.4 Consensus size: 33
17935871 TTTACCGAGA
17935881 TCAACCAAAACC-CAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTCAAAGTGGTTTTTCAAAGGC
* *
17935913 TCAACCACAACCTTTCACAA-TGGTTTTTC-ACGGAC
1 TCAACCAAAACC--TCA-AAGTGGTTTTTCAAAGG-C
17935948 TCAACCAAAACC-CAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTCAAAGTGGTTTTTCAAAGGC
* * ** *
17935980 TCAACCACAACCTACAACAATGGTTTTTCACGGGA
1 TCAACCAAAACCT-CAA-AGTGGTTTTTCAAAGGC
17936015 TCAACCAAAACCT
1 TCAACCAAAACCT
17936028 AAAAACTAAC
Statistics
Matches: 95, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
31 2 0.02
32 34 0.36
33 3 0.03
34 6 0.06
35 48 0.51
36 2 0.02
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (33 bp):
TCAACCAAAACCTCAAAGTGGTTTTTCAAAGGC
Found at i:17935928 original size:67 final size:66
Alignment explanation
Indices: 17935854--17936026 Score: 278
Period size: 67 Copynumber: 2.6 Consensus size: 66
17935844 GCTTAGCCAA
17935854 AACCTTTCACAATGGTTTTT-ACCGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CG-GATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
17935918 CAC
64 CAC
17935921 AACCTTTCACAATGGTTTTTCACGGACTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGA-TCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
17935986 AC
65 AC
*
17935988 AACC-TACAACAATGGTTTTTCACGGGATCAACCAAAACC
1 AACCTTTC-ACAATGGTTTTTCAC-GGATCAACCAAAACC
17936027 TAAAAACTAA
Statistics
Matches: 101, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
66 4 0.04
67 93 0.92
68 4 0.04
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (66 bp):
AACCTTTCACAATGGTTTTTCACGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCA
C
Found at i:17936028 original size:35 final size:34
Alignment explanation
Indices: 17935862--17936027 Score: 148
Period size: 35 Copynumber: 4.9 Consensus size: 34
17935852 AAAACCTTTC
*
17935862 ACAATGGTTTTT-ACCGAGATCAACCAAAACC-CA
1 ACAATGGTTTTTCACAG-GATCAACCAAAACCTCA
* * * *
17935895 A-AGTGGTTTTTCAAAGGCTCAACCACAACCTTTC-
1 ACAATGGTTTTTCACAGGATCAACCAAAACC--TCA
17935929 ACAATGGTTTTTCAC-GGACTCAACCAAAACC-CA
1 ACAATGGTTTTTCACAGGA-TCAACCAAAACCTCA
* * * *
17935962 A-AGTGGTTTTTCAAAGGCTCAACCACAACCTACA
1 ACAATGGTTTTTCACAGGATCAACCAAAACCT-CA
*
17935996 ACAATGGTTTTTCACGGGATCAACCAAAACCT
1 ACAATGGTTTTTCACAGGATCAACCAAAACCT
17936028 AAAAACTAAC
Statistics
Matches: 104, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
32 44 0.42
33 6 0.06
34 6 0.06
35 48 0.46
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (34 bp):
ACAATGGTTTTTCACAGGATCAACCAAAACCTCA
Found at i:17936502 original size:73 final size:74
Alignment explanation
Indices: 17936418--17936611 Score: 220
Period size: 73 Copynumber: 2.6 Consensus size: 74
17936408 ACAGAATGAT
* *
17936418 CTTAGTTGACTAACTTCGCTCTTAGTCGACTAAGTTGTCTCTGTCTTCTG-A-TCCTAG-TTTTT
1 CTTAGTCGACTAACTTCGTTCTTAGTCGACTAAGTTGTCTCTGTCTT-TGAAGT-CTAGATTTTT
*
17936480 GGTAGT-GAGCA
64 GGCAGTAG-GCA
* * *
17936491 CTTAGTCGACTAACTTCTTTCTTAGTCGATTAAGTTGTTTCTGT-TTTGAAGTCTAGATTTTTGG
1 CTTAGTCGACTAACTTCGTTCTTAGTCGACTAAGTTGTCTCTGTCTTTGAAGTCTAGATTTTTGG
*
17936555 CAGTAGGCT
66 CAGTAGGCA
* * *
17936564 CTTAGTCGACTAACTTAGTTCTTGGTCAACTAAGTCT-TCTCTGTCTTT
1 CTTAGTCGACTAACTTCGTTCTTAGTCGACTAAGT-TGTCTCTGTCTTT
17936612 TAATGCTCTT
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
71 2 0.02
72 7 0.07
73 88 0.86
74 5 0.05
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (74 bp):
CTTAGTCGACTAACTTCGTTCTTAGTCGACTAAGTTGTCTCTGTCTTTGAAGTCTAGATTTTTGG
CAGTAGGCA
Found at i:17940030 original size:35 final size:35
Alignment explanation
Indices: 17939991--17940070 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
17939981 TTAATTGTTT
* **
17939991 AATTTAATCAATTAGGCCCAATGACTTAATTAAAC
1 AATTTAATCAATTAAGCCCAACAACTTAATTAAAC
*
17940026 AATTTAATTAATTAAGCCCAACAACTTAATTAAAC
1 AATTTAATCAATTAAGCCCAACAACTTAATTAAAC
17940061 AATTTTAATC
1 AA-TTTAATC
17940071 TAGTACTTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 33 0.85
36 6 0.15
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (35 bp):
AATTTAATCAATTAAGCCCAACAACTTAATTAAAC
Found at i:17942039 original size:38 final size:39
Alignment explanation
Indices: 17941953--17942055 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 39
17941943 ACCCGGCTCA
*
17941953 TGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAGG-ACCATCG
* * *
17941993 TGTGCATCCCCCCACATCATGCACA-ATCAGTG-CCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAG-GACCATCG
17942031 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
17942056 CAGGCACTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
38 29 0.52
39 3 0.05
40 24 0.43
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACATAGCAGGACCATCG
Found at i:17947162 original size:21 final size:22
Alignment explanation
Indices: 17947138--17947178 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
17947128 AGTTTGTTAG
*
17947138 ATTTAATTTTGCTT-TTTAATA
1 ATTTAAATTTGCTTATTTAATA
*
17947159 ATTTAAATTTGGTTATTTAA
1 ATTTAAATTTGCTTATTTAA
17947179 ATAAGATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTTAAATTTGCTTATTTAATA
Found at i:17949444 original size:39 final size:40
Alignment explanation
Indices: 17949400--17949525 Score: 113
Period size: 37 Copynumber: 3.1 Consensus size: 40
17949390 GGGAGTGTGG
17949400 ATGATGAG-ATTGCCTATGTGCGCGATGTGGGGGGAGCAC
1 ATGATGAGAATTGCCTATGTGCGCGATGTGGGGGGAGCAC
* * *
17949439 ATGATG-GCATTAG--T-TGTGCACGATGTGGGGGTGCA-CATG
1 ATGATGAGAATT-GCCTATGTGCGCGATGTGGGGG-G-AGCA-C
17949478 ATGATGATGATATATGCC-ATGTGCGCGATGTGGGGGGAGCAC
1 ATGATGA-GA-AT-TGCCTATGTGCGCGATGTGGGGGGAGCAC
17949520 ATGATG
1 ATGATG
17949526 GCATTAGTTG
Statistics
Matches: 69, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
37 16 0.23
38 5 0.07
39 16 0.23
40 1 0.01
41 1 0.01
42 10 0.14
43 4 0.06
44 16 0.23
ACGTcount: A:0.22, C:0.13, G:0.39, T:0.25
Consensus pattern (40 bp):
ATGATGAGAATTGCCTATGTGCGCGATGTGGGGGGAGCAC
Found at i:17949476 original size:36 final size:37
Alignment explanation
Indices: 17949416--17949549 Score: 137
Period size: 36 Copynumber: 3.5 Consensus size: 37
17949406 AGATTGCCTA
17949416 TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
1 TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
* * * *
17949453 TGTGCACGATGT-GGGGGTGCACATGATGATGATGATATATGCCA
1 TGTGCGCGATGTGGGGGGAGCACATGATG--G--CAT-TA-G--T
17949497 TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
1 TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
*
17949534 TGTGC-CGATGTAGGGG
1 TGTGCGCGATGTGGGGG
17949550 TGCACACAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
36 25 0.32
37 16 0.20
38 1 0.01
39 1 0.01
40 4 0.05
41 4 0.05
42 1 0.01
43 1 0.01
44 11 0.14
45 15 0.19
ACGTcount: A:0.20, C:0.13, G:0.41, T:0.25
Consensus pattern (37 bp):
TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
Found at i:17949500 original size:81 final size:80
Alignment explanation
Indices: 17949399--17949555 Score: 271
Period size: 81 Copynumber: 1.9 Consensus size: 80
17949389 TGGGAGTGTG
17949399 GATGATGAGATTGCCTATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTGTGCACGATG
1 GATGATGAGATTGCCTATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTGTGC-CGATG
*
17949464 TGGGGGTGCACATGAT
65 TAGGGGTGCACATGAT
*
17949480 GATGATGATATATGCC-ATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTGTGCCGATG
1 GATGATGAGAT-TGCCTATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTGTGCCGATG
17949544 TAGGGGTGCACA
65 TAGGGGTGCACA
17949556 CAATGACTCC
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
80 16 0.22
81 53 0.73
82 4 0.05
ACGTcount: A:0.22, C:0.14, G:0.39, T:0.25
Consensus pattern (80 bp):
GATGATGAGATTGCCTATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTGTGCCGATGT
AGGGGTGCACATGAT
Found at i:17956473 original size:20 final size:20
Alignment explanation
Indices: 17956448--17956489 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
17956438 GGAAAAGAAG
17956448 AGAGGAAGCCACGGTGGTGA
1 AGAGGAAGCCACGGTGGTGA
*
17956468 AGAGGAAGCCATGGTGGTGA
1 AGAGGAAGCCACGGTGGTGA
17956488 AG
1 AG
17956490 GGAGTGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.12, G:0.45, T:0.12
Consensus pattern (20 bp):
AGAGGAAGCCACGGTGGTGA
Found at i:17956964 original size:19 final size:19
Alignment explanation
Indices: 17956940--17956977 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17956930 AAGTAATATC
17956940 CCACTATTATGAGGTGAGT
1 CCACTATTATGAGGTGAGT
17956959 CCACTATTATGAGGTGAGT
1 CCACTATTATGAGGTGAGT
17956978 AGGGGGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (19 bp):
CCACTATTATGAGGTGAGT
Found at i:17959476 original size:73 final size:74
Alignment explanation
Indices: 17959365--17959542 Score: 191
Period size: 73 Copynumber: 2.4 Consensus size: 74
17959355 TTCTTCGTTG
* * * * *
17959365 ATCACTTCGGTGCCATGTGGGATTTGAACCT-TCACCAGTTG-TTTCGATAGAAGTGTGATTTGA
1 ATCACTTCAGTGCCATGTGTGATTTGAACCTCTCACCAGTTGCTTT-GACACAAGCGTGATTTGA
*
17959428 ACCTCCACTA
65 ACCTCCACCA
* * * * * *
17959438 GTTACTTCAGTACCATGTGTGATTAGAACCTCT-GCCAGTTGCTTTGGCACAAGCGTGATTTGAA
1 ATCACTTCAGTGCCATGTGTGATTTGAACCTCTCACCAGTTGCTTTGACACAAGCGTGATTTGAA
*
17959502 CCTCTACCA
66 CCTCCACCA
* *
17959511 ATCACTTCAATGCCATGCGTGATTTGAACCTC
1 ATCACTTCAGTGCCATGTGTGATTTGAACCTC
17959543 CATTAGTCAC
Statistics
Matches: 84, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
73 80 0.95
74 4 0.05
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (74 bp):
ATCACTTCAGTGCCATGTGTGATTTGAACCTCTCACCAGTTGCTTTGACACAAGCGTGATTTGAA
CCTCCACCA
Found at i:17959592 original size:37 final size:37
Alignment explanation
Indices: 17959551--17959622 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
17959541 TCCATTAGTC
* * *
17959551 ACTTTGATGCTGTGCAGGATTTGACTCTCCACCAACT
1 ACTTTAATGCTGAGAAGGATTTGACTCTCCACCAACT
*
17959588 ACTTTAATGCTGAGAATGATTTGACTCTCCACCAA
1 ACTTTAATGCTGAGAAGGATTTGACTCTCCACCAA
17959623 TTGCTTCGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (37 bp):
ACTTTAATGCTGAGAAGGATTTGACTCTCCACCAACT
Found at i:17977123 original size:20 final size:20
Alignment explanation
Indices: 17977088--17977129 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
17977078 TAATTTAAAG
17977088 TAAAATAACATTAAATTTAAC
1 TAAAATAACATTAAA-TTAAC
*
17977109 TAAAATGAC-TTAAATTAAC
1 TAAAATAACATTAAATTAAC
17977128 TA
1 TA
17977130 CTCAACATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 5 0.25
21 8 0.40
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAATAACATTAAATTAAC
Found at i:17982142 original size:72 final size:72
Alignment explanation
Indices: 17982060--17982196 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 72
17982050 AAGGACTTTG
** ** *
17982060 AAGCCTATCTATTGATAGATAGCCAC-AATCTATTGATAGATGATGTCGTTTTCACAAAAATAAA
1 AAGCCTATCTATCAATAGATAGCC-CTAATCTAACGATAGATGATGCCGTTTTCACAAAAATAAA
17982124 AGGGGTAA
65 AGGGGTAA
17982132 AAGCCTATCTATCAATAGATAGCCCTAATCTAACGATAGATGATGCCGTTTTCACAAAAATAAAA
1 AAGCCTATCTATCAATAGATAGCCCTAATCTAACGATAGATGATGCCGTTTTCACAAAAATAAAA
17982197 TGGATAAATG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 1 0.02
72 58 0.98
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (72 bp):
AAGCCTATCTATCAATAGATAGCCCTAATCTAACGATAGATGATGCCGTTTTCACAAAAATAAAA
GGGGTAA
Found at i:17984130 original size:21 final size:19
Alignment explanation
Indices: 17984097--17984138 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
17984087 ACATGTTAAG
17984097 TAGTTAATTTATGTTATTT
1 TAGTTAATTTATGTTATTT
17984116 TAGTTATATTTTATGTTATTT
1 TAGTTA-A-TTTATGTTATTT
17984137 TA
1 TA
17984139 TTTTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (19 bp):
TAGTTAATTTATGTTATTT
Found at i:18007985 original size:20 final size:21
Alignment explanation
Indices: 18007962--18008008 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
18007952 CTTCTAAACC
18007962 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCTCAATAAG
* *
18007982 TCAAATTATACTCTTAATAAG
1 TCAAATCATACTCTCAATAAG
18008003 TCAAAT
1 TCAAAT
18008009 GGAGTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (21 bp):
TCAAATCATACTCTCAATAAG
Found at i:18009847 original size:19 final size:19
Alignment explanation
Indices: 18009823--18009869 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
18009813 GGCTGACTTT
18009823 TCATTAAAACAATATTAAA
1 TCATTAAAACAATATTAAA
*
18009842 TCATTAAAATAATATTAAA
1 TCATTAAAACAATATTAAA
18009861 TCATTAAAA
1 TCATTAAAA
18009870 AGTGCCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (19 bp):
TCATTAAAACAATATTAAA
Found at i:18012982 original size:43 final size:42
Alignment explanation
Indices: 18012763--18012988 Score: 138
Period size: 43 Copynumber: 5.3 Consensus size: 42
18012753 ATTAAGCAAT
* * * * * *
18012763 ATCAAGGATATCATCTATTATGCTTGGAACCATAGTACCT-TAG
1 ATCAAGGATATCAGC-ATTATGTTTGGAATCGTAGCA-CTACAG
* * * *
18012806 ATCAAGGATATCAAGCATTAGGCTTGGAAGCCTAGCACTACAG
1 ATCAAGGATATC-AGCATTATGTTTGGAATCGTAGCACTACAG
* * * * *
18012849 ATCAAGGATATTAAGCATAATGATTT-GAATTGTATCACTATAG
1 ATCAAGGATA-TCAGCATTATG-TTTGGAATCGTAGCACTACAG
* * *
18012892 ATCAAGGATATCAAGCATTACGTTTGGTA-CGATAACACCCTAC--
1 ATCAAGGATATC-AGCATTATGTTTGGAATCG-TAGCA--CTACAG
* *
18012935 ATCAAGGATATCATCTATTATGTTTGGAATTGTAGCACTACAG
1 ATCAAGGATATCAGC-ATTATGTTTGGAATCGTAGCACTACAG
*
18012978 ATCAAAGATAT
1 ATCAAGGATAT
18012989 TTAGTAGAAA
Statistics
Matches: 142, Mismatches: 28, Indels: 26
0.72 0.14 0.13
Matches are distributed among these distances:
41 4 0.03
42 9 0.06
43 120 0.85
44 6 0.04
45 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (42 bp):
ATCAAGGATATCAGCATTATGTTTGGAATCGTAGCACTACAG
Found at i:18017132 original size:19 final size:19
Alignment explanation
Indices: 18017108--18017146 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
18017098 CTATAAAATA
*
18017108 TCTTGAATTTCTAGCAGCT
1 TCTTGAATTTCCAGCAGCT
18017127 TCTTGAATTTCCAGCAGCT
1 TCTTGAATTTCCAGCAGCT
18017146 T
1 T
18017147 GTCTTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (19 bp):
TCTTGAATTTCCAGCAGCT
Found at i:18018006 original size:43 final size:43
Alignment explanation
Indices: 18017938--18018062 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 43
18017928 TATTGACTCG
* **
18017938 GCTATGTACGAGTAGGGAGTGCGCATAAGCTGAG-GATGACCTG
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCTG-GTGATGACCCA
* * * *
18017981 GTTATGTGCGAGTAGGGAGTACGCATAACCCGGTGATGACCCA
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCA
* *
18018024 GCCATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGA
18018063 TGATGATGGG
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.21
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCA
Found at i:18018389 original size:21 final size:21
Alignment explanation
Indices: 18018363--18018408 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
18018353 CAGAACTGGT
* * *
18018363 TCTCGCTGCAGTGATAATGAA
1 TCTCGCTACAGTGAAAAAGAA
18018384 TCTCGCTACAGTGAAAAAGAA
1 TCTCGCTACAGTGAAAAAGAA
18018405 TCTC
1 TCTC
18018409 ATTGCAGCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (21 bp):
TCTCGCTACAGTGAAAAAGAA
Found at i:18029550 original size:13 final size:13
Alignment explanation
Indices: 18029529--18029567 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
18029519 ATTTTCCAAC
18029529 GAAATATTTCGTTG
1 GAAA-ATTTCGTTG
18029543 GAAAATTTCGTTG
1 GAAAATTTCGTTG
18029556 GAAAATTTCGTT
1 GAAAATTTCGTT
18029568 TGTAATANNN
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41
Consensus pattern (13 bp):
GAAAATTTCGTTG
Found at i:18038270 original size:411 final size:410
Alignment explanation
Indices: 18037508--18038328 Score: 1399
Period size: 411 Copynumber: 2.0 Consensus size: 410
18037498 TCTCGGAACC
* * *
18037508 AAATTGAAATTTAGCACTGCTTTTCACCCATAGACGGATGGTCAGTTAGAGAGGACTATCCAGAC
1 AAATTGAAATTTAGCACTGCTTTTCACCCACAGACGGATGGTCAGTCAGAAAGGACTATCCAGAC
*
18037573 CTTGGAGGATCTGTTACGGGCTTGTGTCATTGACTTTATTGGGAGTTGGGACAGACATTTGCCAT
66 CTTGGAGGATATGTTACGGGCTTGTGTCATTGACTTTATTGGGAGTTGGGACAGACATTTGCCAT
* * * * * * *
18037638 TGGTGGAGTTCGCGTATAATAACAGTTTTCAGTCTAGTATTGGGATGGCACCATACGAGGCTTTG
131 TGGTGGAATTCGCGTACAACAACAGCTTTCAGTCTAGCATTGGGATGGCACCATACGAAGCTTTA
* *** *
18037703 TATGGAAGGAAGTGCCAAACTTTGCTCTGTTGGAATGAAGTAGGTGAAAGGAAGTTAGTGAGTGT
196 TATGGAAGGAAATGCCAAACTCCACTCTGTTGGAATGAAGTAGGTGAAAGAAAGTTAGTGAGTGT
18037768 GGAATTGATCGAGCTAACTAATGACAAGATCAAGGTTATACGAGAGAGGCTAAAGGTAGCCCAGG
261 GGAATTGATCGAGCTAACTAATGACAAGATCAAGGTTATACGAGAGAGGCTAAAGGTAGCCCAGG
18037833 ATAGGCAGAAGAGCTATGCAGATAAACGGAGAAAAGACTTGGAGTTTGAGATCGATGATAAAGTT
326 ATAGGCAGAAGAGCTATGCAGATAAACGGAGAAAAGACTTGGAGTTTGAGATCGATGATAAAGTT
18037898 TTTCTTAAGGTTTCTCCTTG
391 TTTCTTAAGGTTTCTCCTTG
18037918 NAAATTGAAATTTAGCACTGCTTTTCACCCACAGACGGATGGTCAGTCAGAAAGGACTATCCAGA
1 -AAATTGAAATTTAGCACTGCTTTTCACCCACAGACGGATGGTCAGTCAGAAAGGACTATCCAGA
18037983 CCTTGGAGGATATGTTACGGGCTTGTGTCATTGACTTTATTGGGAGTTGGGACAGACATTTGCCA
65 CCTTGGAGGATATGTTACGGGCTTGTGTCATTGACTTTATTGGGAGTTGGGACAGACATTTGCCA
* * * *
18038048 TTGGTGGAATTTGCTTACAACAATAGCTTTCAGTCTAGCATTGGTATGGCACCATACGAAGCTTT
130 TTGGTGGAATTCGCGTACAACAACAGCTTTCAGTCTAGCATTGGGATGGCACCATACGAAGCTTT
* ** * * *
18038113 ATATGGAAGGAAATGTCGTACTCCACTTTGTTGGGATGAAGTGGGTGAAAGAAAGTTAGTGAGTG
195 ATATGGAAGGAAATGCCAAACTCCACTCTGTTGGAATGAAGTAGGTGAAAGAAAGTTAGTGAGTG
18038178 TGGAATTGATCGAGCTAACTAATGACAAGATCAAGGTTATACGAGAGAGGCTAAAGGTAGCCCAG
260 TGGAATTGATCGAGCTAACTAATGACAAGATCAAGGTTATACGAGAGAGGCTAAAGGTAGCCCAG
18038243 GATAGGCAGAAGAGCTATGCAGATAAACGGAGAAAAGACTTGGAGTTTGAGATCGATGATAAAGT
325 GATAGGCAGAAGAGCTATGCAGATAAACGGAGAAAAGACTTGGAGTTTGAGATCGATGATAAAGT
18038308 TTTTCTTAAGGTTTCTCCTTG
390 TTTTCTTAAGGTTTCTCCTTG
18038329 GAAAGGTAAT
Statistics
Matches: 384, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
411 384 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (410 bp):
AAATTGAAATTTAGCACTGCTTTTCACCCACAGACGGATGGTCAGTCAGAAAGGACTATCCAGAC
CTTGGAGGATATGTTACGGGCTTGTGTCATTGACTTTATTGGGAGTTGGGACAGACATTTGCCAT
TGGTGGAATTCGCGTACAACAACAGCTTTCAGTCTAGCATTGGGATGGCACCATACGAAGCTTTA
TATGGAAGGAAATGCCAAACTCCACTCTGTTGGAATGAAGTAGGTGAAAGAAAGTTAGTGAGTGT
GGAATTGATCGAGCTAACTAATGACAAGATCAAGGTTATACGAGAGAGGCTAAAGGTAGCCCAGG
ATAGGCAGAAGAGCTATGCAGATAAACGGAGAAAAGACTTGGAGTTTGAGATCGATGATAAAGTT
TTTCTTAAGGTTTCTCCTTG
Found at i:18038591 original size:30 final size:30
Alignment explanation
Indices: 18038555--18038614 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
18038545 CATTTTCCAC
18038555 GTCTCCATGCTTAAGAAATATGTACCAGAT
1 GTCTCCATGCTTAAGAAATATGTACCAGAT
*
18038585 GTCTCCATGCTTAAGAAATATGTACTAGAT
1 GTCTCCATGCTTAAGAAATATGTACCAGAT
18038615 CCCTCTCACG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (30 bp):
GTCTCCATGCTTAAGAAATATGTACCAGAT
Found at i:18046846 original size:19 final size:18
Alignment explanation
Indices: 18046804--18046846 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
18046794 GGGTGAGAAA
18046804 AATATTTTAAAATAAAAC
1 AATATTTTAAAATAAAAC
* * *
18046822 ATTATTTTATGAATAAAAT
1 AATATTTTA-AAATAAAAC
18046841 AATATT
1 AATATT
18046847 AATATTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTTTAAAATAAAAC
Found at i:18047824 original size:34 final size:34
Alignment explanation
Indices: 18047760--18047845 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
18047750 GAAAGGAACT
18047760 GATTTTTGAGAGAAGAAAGGGAGGCCTTGTGCTATC
1 GATTTTTGAGAG--GAAAGGGAGGCCTTGTGCTATC
* *
18047796 GATTTTTGAGAGGAAAGAGG-GGCTTTGTGCTGTC
1 GATTTTTGAGAGGAAAG-GGAGGCCTTGTGCTATC
*
18047830 AATTTTTGAGAGGAAA
1 GATTTTTGAGAGGAAA
18047846 AAAGGCCTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
34 32 0.70
35 2 0.04
36 12 0.26
ACGTcount: A:0.28, C:0.08, G:0.34, T:0.30
Consensus pattern (34 bp):
GATTTTTGAGAGGAAAGGGAGGCCTTGTGCTATC
Found at i:18047869 original size:34 final size:33
Alignment explanation
Indices: 18047781--18047884 Score: 95
Period size: 34 Copynumber: 3.1 Consensus size: 33
18047771 GAAGAAAGGG
* *
18047781 AGGCC-TTGTGCTATCGATTTTTGAGAGGAAAGA
1 AGGCCTTTGTGCT-GCGATTTTTGAGAGGAAAAA
* * *
18047814 GGGGCTTTGTGCTGTCAATTTTTGAGAGGAAAAA
1 AGGCCTTTGTGCTG-CGATTTTTGAGAGGAAAAA
*
18047848 AGGCCTTGTGTTGCTG-GATTTTTGGGAAGGAAAAA
1 AGGCCTT-TG-TGCTGCGATTTTTGAG-AGGAAAAA
18047883 AG
1 AG
18047885 AAGAAGCTGG
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
33 3 0.05
34 37 0.65
35 12 0.21
36 5 0.09
ACGTcount: A:0.27, C:0.10, G:0.33, T:0.31
Consensus pattern (33 bp):
AGGCCTTTGTGCTGCGATTTTTGAGAGGAAAAA
Found at i:18048074 original size:27 final size:28
Alignment explanation
Indices: 18048044--18048107 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
18048034 AAAAAAACAT
18048044 AATAATAATAAA-AATATAAAATAAATA
1 AATAATAATAAAGAATATAAAATAAATA
* * * *
18048071 AATAA-AGTAAAGTATATAATATATATA
1 AATAATAATAAAGAATATAAAATAAATA
*
18048098 TATAATAATA
1 AATAATAATA
18048108 TATATTAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 5 0.17
27 21 0.72
28 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (28 bp):
AATAATAATAAAGAATATAAAATAAATA
Found at i:18048455 original size:154 final size:154
Alignment explanation
Indices: 18048160--18048460 Score: 559
Period size: 154 Copynumber: 2.0 Consensus size: 154
18048150 GGAACACTGT
18048160 GGTGGTAGGCCAAAGAAAAATAACAAATGGTCGGTATGAGGGAATAGCTAGATACGTTTACGAAT
1 GGTGGTAGGCCAAAGAAAAATAACAAATGGTCGGTATGAGGGAATAGCTAGATACGTTTACGAAT
* * *
18048225 TAAATAGCGATGTAGCGTCCCGCTATTGTGAGATGAGTAGGGGTTGTCCATTTTAAAATTTTCGT
66 TAAATAGCGACGTAACATCCCGCTATTGTGAGATGAGTAGGGGTTGTCCATTTTAAAATTTTCGT
18048290 AAATATATATATGTATTTTATTTA
131 AAATATATATATGTATTTTATTTA
18048314 NGGTGGTAGGCCAAAGAAAAATAACAAATGGTCGGTATGAGGGAATAGCTAGATACGTTTACGAA
1 -GGTGGTAGGCCAAAGAAAAATAACAAATGGTCGGTATGAGGGAATAGCTAGATACGTTTACGAA
18048379 TT-AATAGCGACGTAACATCCCGCTATTGTGAGATGAGTAGGGGTTGTCCATTTTAAAATTTTCG
65 TTAAATAGCGACGTAACATCCCGCTATTGTGAGATGAGTAGGGGTTGTCCATTTTAAAATTTTCG
18048443 TAAATATATATATGTATT
130 TAAATATATATATGTATT
18048461 ATTTATTTTA
Statistics
Matches: 143, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
154 77 0.54
155 66 0.46
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (154 bp):
GGTGGTAGGCCAAAGAAAAATAACAAATGGTCGGTATGAGGGAATAGCTAGATACGTTTACGAAT
TAAATAGCGACGTAACATCCCGCTATTGTGAGATGAGTAGGGGTTGTCCATTTTAAAATTTTCGT
AAATATATATATGTATTTTATTTA
Found at i:18060145 original size:35 final size:35
Alignment explanation
Indices: 18060034--18060162 Score: 120
Period size: 34 Copynumber: 3.7 Consensus size: 35
18060024 GAAAGGAACT
* * *
18060034 GATTTTTGAGAGAAGAAAGGGAGGCCTTGTGCTGTC
1 GATTTTTGAGAG-GGAAAGAGAGGCCTTGTGCTGTG
* * *
18060070 AATTTTTGAGA-GGAAAGAGGGGCTTTGTGCTGTCG
1 GATTTTTGAGAGGGAAAGAGAGGCCTTGTGCTGT-G
*
18060105 G-TTTTTGAGAGGGAAA-AGAGGCCTTGTGTTGATG
1 GATTTTTGAGAGGGAAAGAGAGGCCTTGTGCTG-TG
* *
18060139 GATTTTTGGGAAGGAAAAGAGAGG
1 GATTTTTGAG-AGGGAAAGAGAGG
18060163 AAGCTGGGCT
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
34 41 0.55
35 13 0.17
36 16 0.21
37 5 0.07
ACGTcount: A:0.26, C:0.07, G:0.38, T:0.29
Consensus pattern (35 bp):
GATTTTTGAGAGGGAAAGAGAGGCCTTGTGCTGTG
Found at i:18060375 original size:5 final size:5
Alignment explanation
Indices: 18060325--18060372 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
18060315 ACATAATAGT
*
18060325 AATAA AATAAA AATAA TAA-AA ATATAA AATAA AATAA AATAA AGTAA
1 AATAA AAT-AA AATAA -AATAA A-ATAA AATAA AATAA AATAA AATAA
18060372 A
1 A
18060373 GTATATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
4 1 0.03
5 27 0.71
6 10 0.26
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:18067762 original size:21 final size:20
Alignment explanation
Indices: 18067732--18067770 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
18067722 GGTTTTTCTC
18067732 TTTTCTTCTT-TTCCTCTCTA
1 TTTTCTTCTTGTT-CTCTCTA
18067752 TTTTCTCTCTTGTTCTCTC
1 TTTTCT-TCTTGTTCTCTC
18067771 CTTATGGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 9 0.53
22 2 0.12
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTCTTCTTGTTCTCTCTA
Found at i:18077843 original size:23 final size:23
Alignment explanation
Indices: 18077803--18077846 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
18077793 TATTAATATG
* *
18077803 TTTTATATGTAAGCTTATAGTAA
1 TTTTATATATAAGATTATAGTAA
*
18077826 TTTTATATATATGATTATAGT
1 TTTTATATATAAGATTATAGT
18077847 TATTAGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (23 bp):
TTTTATATATAAGATTATAGTAA
Found at i:18079783 original size:13 final size:13
Alignment explanation
Indices: 18079765--18079789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18079755 TTTCAGAAAA
18079765 TTTATAAAATCAT
1 TTTATAAAATCAT
18079778 TTTATAAAATCA
1 TTTATAAAATCA
18079790 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:18084929 original size:30 final size:28
Alignment explanation
Indices: 18084877--18084936 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 28
18084867 GTCTATGGGC
*
18084877 AATTTTTCAGTTTTTGGGGTAAAAATGT
1 AATTTTTCACTTTTTGGGGTAAAAATGT
* *
18084905 AATTTTTGACTTTTATGAGGGTAAAAGTGT
1 AATTTTTCACTTTT-TG-GGGTAAAAATGT
18084935 AA
1 AA
18084937 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 2 0.07
30 13 0.48
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (28 bp):
AATTTTTCACTTTTTGGGGTAAAAATGT
Found at i:18086096 original size:16 final size:16
Alignment explanation
Indices: 18086075--18086109 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18086065 ATAAAATATT
*
18086075 ATGTTTTCTAATTAAA
1 ATGTTTTCTAATAAAA
*
18086091 ATGTTTTTTAATAAAA
1 ATGTTTTCTAATAAAA
18086107 ATG
1 ATG
18086110 AGATTTATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (16 bp):
ATGTTTTCTAATAAAA
Found at i:18088802 original size:13 final size:13
Alignment explanation
Indices: 18088784--18088808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18088774 GGAGAAATTG
18088784 TGATTTTATAAAA
1 TGATTTTATAAAA
18088797 TGATTTTATAAA
1 TGATTTTATAAA
18088809 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:18090427 original size:26 final size:26
Alignment explanation
Indices: 18090391--18090446 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
18090381 ATAATATGGT
18090391 ATGCAACTTATCTGACTACCGCTTAA
1 ATGCAACTTATCTGACTACCGCTTAA
18090417 ATGCAACTTATCTGACTACCGCTTAA
1 ATGCAACTTATCTGACTACCGCTTAA
18090443 ATGC
1 ATGC
18090447 GGANCAGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (26 bp):
ATGCAACTTATCTGACTACCGCTTAA
Found at i:18090595 original size:200 final size:199
Alignment explanation
Indices: 18090252--18090649 Score: 778
Period size: 200 Copynumber: 2.0 Consensus size: 199
18090242 TCCTAATCCT
*
18090252 AGTCTCCAAGCACAATTTCTGTACTTTTACCAATGTAATTTACTCACCACCTATCCACAATGTAC
1 AGTCTCCAAGCACAATCTCTGTACTTTTACCAATGTAATTTACTCACCACCTATCCACAATGTAC
18090317 AATACATAATTCACCACATCAATACTTGACCATTATAAAATCAATTCAGGCTCGGTGTATATGAA
66 AATACATAATTCACCACATCAATACTTGACCATTATAAAATCAATTCAGGCTCGGTGTATATGAA
18090382 TAATATGGTATGCAACTTATCTGACTACCGCTTAAATGCAACTTATCTGACTACCGCTTAAATGC
131 TAATATGGTATGCAACTTATCTGACTACCGCTTAAATGCAACTTATCTGACTACCGCTTAAATGC
18090447 GGANC
196 GGA-C
18090452 AGTCTCCAAGCACAATCTCTGTACTTTTACCAATGTAATTTACTCACCACCTATCCACAATGTAC
1 AGTCTCCAAGCACAATCTCTGTACTTTTACCAATGTAATTTACTCACCACCTATCCACAATGTAC
18090517 AATACATAATTCACCACATCAATACTTGACCATTATAAAATCAATTCAGGCTCGGTGTATATGAA
66 AATACATAATTCACCACATCAATACTTGACCATTATAAAATCAATTCAGGCTCGGTGTATATGAA
18090582 TAATATGGTATGCAACTTATCTGACTACCGCTTAAATGCAACTTATCTGACTACCGCTTAAATGC
131 TAATATGGTATGCAACTTATCTGACTACCGCTTAAATGCAACTTATCTGACTACCGCTTAAATGC
18090647 GGA
196 GGA
18090650 GCTGACCTAA
Statistics
Matches: 197, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 197 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (199 bp):
AGTCTCCAAGCACAATCTCTGTACTTTTACCAATGTAATTTACTCACCACCTATCCACAATGTAC
AATACATAATTCACCACATCAATACTTGACCATTATAAAATCAATTCAGGCTCGGTGTATATGAA
TAATATGGTATGCAACTTATCTGACTACCGCTTAAATGCAACTTATCTGACTACCGCTTAAATGC
GGAC
Found at i:18090627 original size:26 final size:26
Alignment explanation
Indices: 18090591--18090646 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
18090581 ATAATATGGT
18090591 ATGCAACTTATCTGACTACCGCTTAA
1 ATGCAACTTATCTGACTACCGCTTAA
18090617 ATGCAACTTATCTGACTACCGCTTAA
1 ATGCAACTTATCTGACTACCGCTTAA
18090643 ATGC
1 ATGC
18090647 GGAGCTGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (26 bp):
ATGCAACTTATCTGACTACCGCTTAA
Found at i:18091593 original size:19 final size:19
Alignment explanation
Indices: 18091569--18091606 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18091559 ACTTCTAAAC
*
18091569 CTCAAATCATACTTCAATA
1 CTCAAATCATACTCCAATA
18091588 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
18091607 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:18092775 original size:172 final size:172
Alignment explanation
Indices: 18092492--18092814 Score: 508
Period size: 172 Copynumber: 1.9 Consensus size: 172
18092482 TCCTTTCATT
* *
18092492 TTTTTCTTTCCCTTTCTCTCTCTAGTCGCAGCCACCCTCTCACTTCTCTCTAAACTTTTTCCTCC
1 TTTTTCTTTCCCTTTCTCTCTCTAGTCGCAGCCACCCTCCCACTTCTCTCTAAACTTTTCCCTCC
*
18092557 GTCGACCGCTTTCTCCTTCTCTCTCACCTTCCCCTCCATAGGTGGCTTGAAGCTCGGTCACCCAA
66 GTCGACCGCTTTCTCCTTCTCTCTCACCTTCCCCTCCACAGGTGGCTTGAAGCTCGGTCACCC-A
18092622 AACCCTAAATATCTCTTCCCTCTGCCAACAATCCCTCCCTTCA
130 AACCCTAAATATCTCTTCCCTCTGCCAACAATCCCTCCCTTCA
*
18092665 TTTTTCTTTCCCTTTCTCTCTCTAGTCGCGGCCA-CCTCCCACTTCTCTCTAAACTTTTCCCTCC
1 TTTTTCTTTCCCTTTCTCTCTCTAGTCGCAGCCACCCTCCCACTTCTCTCTAAACTTTTCCCTCC
* ** * * *
18092729 GTTGGTCGCTTTCTCCTTTTCTCT-ATCC-TCCCCTGCCACCGGTGGCTTGAAGCTCTGTCACCC
66 GTCGACCGCTTTCTCCTTCTCTCTCA-CCTTCCCCT-CCACAGGTGGCTTGAAGCTCGGTCACCC
18092792 AAACCCTAAATATCTCTTCCCTC
129 AAACCCTAAATATCTCTTCCCTC
18092815 CACTGACAAT
Statistics
Matches: 138, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
171 30 0.22
172 75 0.54
173 33 0.24
ACGTcount: A:0.14, C:0.41, G:0.10, T:0.36
Consensus pattern (172 bp):
TTTTTCTTTCCCTTTCTCTCTCTAGTCGCAGCCACCCTCCCACTTCTCTCTAAACTTTTCCCTCC
GTCGACCGCTTTCTCCTTCTCTCTCACCTTCCCCTCCACAGGTGGCTTGAAGCTCGGTCACCCAA
ACCCTAAATATCTCTTCCCTCTGCCAACAATCCCTCCCTTCA
Found at i:18092961 original size:10 final size:10
Alignment explanation
Indices: 18092946--18092993 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
18092936 CCCTTTAGTT
18092946 TTTTATTTAA
1 TTTTATTTAA
*
18092956 TTTTA-TTAT
1 TTTTATTTAA
*
18092965 TTTTAATTAA
1 TTTTATTTAA
*
18092975 TTTTGTTTAA
1 TTTTATTTAA
18092985 TTTTCATTT
1 TTTT-ATTT
18092994 TTATTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 8 0.26
10 20 0.65
11 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:18092983 original size:29 final size:30
Alignment explanation
Indices: 18092946--18093037 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 30
18092936 CCCTTTAGTT
*
18092946 TTTTATTTAATTTTATTATTT-TTAATTAA
1 TTTTGTTTAATTTTATTATTTATTAATTAA
18092975 TTTTGTTTAATTTTCATT-TTTATTATATT-A
1 TTTTGTTTAATTTT-ATTATTTATTA-ATTAA
* *
18093005 -TTTGATT-ATTTTATTTATTTATTGATTAA
1 TTTTGTTTAATTTTA-TTATTTATTAATTAA
18093034 TTTT
1 TTTT
18093038 TATTATATAC
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
27 1 0.02
28 10 0.19
29 29 0.55
30 10 0.19
31 3 0.06
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (30 bp):
TTTTGTTTAATTTTATTATTTATTAATTAA
Found at i:18093016 original size:21 final size:23
Alignment explanation
Indices: 18092990--18093045 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 23
18092980 TTTAATTTTC
18092990 ATTTTTATTATA-TTATTTGATT-
1 ATTTTTATTATATTTA-TTGATTA
18093012 A-TTTTATT-TATTTATTGATTA
1 ATTTTTATTATATTTATTGATTA
18093033 ATTTTTATTATAT
1 ATTTTTATTATAT
18093046 ACATTTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 8 0.27
21 11 0.37
22 8 0.27
23 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (23 bp):
ATTTTTATTATATTTATTGATTA
Found at i:18093676 original size:33 final size:33
Alignment explanation
Indices: 18093633--18093698 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
18093623 AAGAAGTTGA
18093633 CTACCATTTTCTTCA-TGTTTAGCAACAAGATTG
1 CTACCATTTTCTT-AGTGTTTAGCAACAAGATTG
* *
18093666 CTACCGTTTTCTTAGTGTTTAGCAACAATATTG
1 CTACCATTTTCTTAGTGTTTAGCAACAAGATTG
18093699 AAAGATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (33 bp):
CTACCATTTTCTTAGTGTTTAGCAACAAGATTG
Found at i:18095168 original size:580 final size:575
Alignment explanation
Indices: 18094072--18095220 Score: 1874
Period size: 580 Copynumber: 2.0 Consensus size: 575
18094062 CTATGCCTTC
*
18094072 AAACGTTATCAGTCTCACAATTGCATTGGAAGAGAAAGTAGAAAATCTTTCAGAAAACTTGGGTA
1 AAACGTTACCAGTCTCACAATTGCATTGGAAGAGAAAGTAGAAAATCTTTCAGAAAACTTGGGTA
*
18094137 AGATACGTGATGAATTACGTGGAGAAATACATGAAGAAATTAAAAATGCAATGACGGAAAGCATG
66 AGATACGTGATGAATTACGTGGAGAAATACATGAAGAAATTAAAAATACAATGACGGAAAGCATG
* ** *
18094202 AGTGAATTTATGACACGTATGAAAACCATGATCATGACTAATGCACTTTCAAAACAAGAAATGCA
131 AATGAATTTATGACACACATGAAAACCATGATCATGACTAATGCACTTTCAAAAAAAGAAATGCA
* *
18094267 GGACCTTCAAGCTAACATCTGCACAAGTAAGATCACATTTCATGATATGATGTCAATGTTTCACT
196 GGACCTTCAAGCTAAAATCTGCACAAGTAAGAACACATTTCATGATATGATGTCAATGTTTCACT
* * *
18094332 GCTGCACTGAGATACTTTTTAGTATAGCTGTTTAATAACAATTTTAGCTTTATAATCATATGTGT
261 ACTACACTGAGATACTTTTTAGTATAGCTGTTTAATAACAATTTTAGATTTATAATCATATGTGT
*
18094397 TGAACTTTTCTTAGATATTGTGTGTTAGGGTAATTTTGAATTGTATGAGTTTCACTTTGAATTTC
326 TGAACTTTTCTTAGATATTGTGTGTTAGGGTAATTTTGAATTGTATGAATTTCACTTTGAATTTC
18094462 GGTTTTTAATATTTGTTTCTTTTATATAATATGAAATTCAAATGTCGATGTGAATGGATATTTTA
391 GGTTTTTAATATTTGTTTCTTTTATATAATATGAAATTCAAATGTCGATGTGAATGGATATTTTA
18094527 TTATCGAAATGGAAATTTGTATTTTTTTTTGGGAAAGCAATTTTTGGTAATTTTTTTGAAAATTG
456 TTATCGAAATGGAAATTTGTATTTTTTTTTGGGAAAGCAATTTTTGGTAATTTTTTTGAAAATTG
* * * *
18094592 GTAATCTAGTAAAATAAATTTTCGTTGGAAAAGCATTTCCAAC-AAAAANTCAACTT
521 GTAATCTAGTAAAAT-AATTTCCATTGAAAAAACATTTCCAACGAAAAA-TCAACTT
* * *
18094648 AAACGTTACCAGTCTCGCAATTGCATTGGAAGAGAAAGTAGAAAATCTTTCTGAAAATTTGGGTA
1 AAACGTTACCAGTCTCACAATTGCATTGGAAGAGAAAGTAGAAAATCTTTCAGAAAACTTGGGTA
* *
18094713 AGATACGTGATGAATTACGTGGAGAAATACATGAAGAAATTAAAAATACAATGGCGGAAATCATG
66 AGATACGTGATGAATTACGTGGAGAAATACATGAAGAAATTAAAAATACAATGACGGAAAGCATG
* * *
18094778 AATGAATTTATGGCACACATGGAAACCATGATCATGAGTAATGCACTTTCAAAATAAAGAAATGC
131 AATGAATTTATGACACACATGAAAACCATGATCATGACTAATGCACTTTCAAAA-AAAGAAATGC
* *
18094843 AGGACCTTCAAGCTAAAATCTTG-ACAAGTAAGAACACAACATTTCATGATATGATGTCTATTTT
195 AGGACCTTCAAGCTAAAATC-TGCACAAGTAAG-A-AC-ACATTTCATGATATGATGTCAATGTT
* * *
18094907 TCACTACTACACTTAGATACTTTTTAGTATAGCTGTTTCATAACACA-TTTAGATTTATATTCAT
256 TCACTACTACACTGAGATACTTTTTAGTATAGCTGTTTAATAACA-ATTTTAGATTTATAATCAT
* * * *
18094971 ATGTGTTTAA-TTTTTTTAGATATTGTGTGTTTAGGGTAATTTTTAATTGTATGAATTTGACTTT
320 ATGTGTTGAACTTTTCTTAGATATTGTGTG-TTAGGGTAATTTTGAATTGTATGAATTTCACTTT
*
18095035 GAATTTTGGTTTTTAATATTTGTTTCTTTTATATAATATGAAATTCAAATGTCGATGTGAATGGA
384 GAATTTCGGTTTTTAATATTTGTTTCTTTTATATAATATGAAATTCAAATGTCGATGTGAATGGA
18095100 TATTTTATTATCGAAATGGAAATTTGTATTTTTTTTTGGGAAAGCAATTTTTGGTAATTTTTTTG
449 TATTTTATTATCGAAATGGAAATTTGTATTTTTTTTTGGGAAAGCAATTTTTGGTAATTTTTTTG
*
18095165 AAAATTGGTAATCTAGTAAAATAATTTCCATTGAAAAAACATTTCCCACGAAAAAT
514 AAAATTGGTAATCTAGTAAAATAATTTCCATTGAAAAAACATTTCCAACGAAAAAT
18095221 ACAGTTGCAA
Statistics
Matches: 530, Mismatches: 35, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
576 171 0.32
577 37 0.07
578 3 0.01
579 42 0.08
580 276 0.52
581 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (575 bp):
AAACGTTACCAGTCTCACAATTGCATTGGAAGAGAAAGTAGAAAATCTTTCAGAAAACTTGGGTA
AGATACGTGATGAATTACGTGGAGAAATACATGAAGAAATTAAAAATACAATGACGGAAAGCATG
AATGAATTTATGACACACATGAAAACCATGATCATGACTAATGCACTTTCAAAAAAAGAAATGCA
GGACCTTCAAGCTAAAATCTGCACAAGTAAGAACACATTTCATGATATGATGTCAATGTTTCACT
ACTACACTGAGATACTTTTTAGTATAGCTGTTTAATAACAATTTTAGATTTATAATCATATGTGT
TGAACTTTTCTTAGATATTGTGTGTTAGGGTAATTTTGAATTGTATGAATTTCACTTTGAATTTC
GGTTTTTAATATTTGTTTCTTTTATATAATATGAAATTCAAATGTCGATGTGAATGGATATTTTA
TTATCGAAATGGAAATTTGTATTTTTTTTTGGGAAAGCAATTTTTGGTAATTTTTTTGAAAATTG
GTAATCTAGTAAAATAATTTCCATTGAAAAAACATTTCCAACGAAAAATCAACTT
Found at i:18095290 original size:15 final size:14
Alignment explanation
Indices: 18095269--18095302 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
18095259 TTGGAAATGC
*
18095269 TTTTCCAATAGAAT
1 TTTTCCAACAGAAT
18095283 TGTTTCCAACAGAAT
1 T-TTTCCAACAGAAT
18095298 TTTTC
1 TTTTC
18095303 GTTGGAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (14 bp):
TTTTCCAACAGAAT
Found at i:18097280 original size:19 final size:19
Alignment explanation
Indices: 18097251--18097294 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
18097241 TATTACAAAT
18097251 AAATAAAATAAT-AATAATAA
1 AAAT-AAATAATAAAT-ATAA
18097271 AAATAAATAATAAATATAA
1 AAATAAATAATAAATATAA
18097290 AAATA
1 AAATA
18097295 CCATGATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATAAATAATAAATATAA
Found at i:18097505 original size:13 final size:13
Alignment explanation
Indices: 18097487--18097551 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
18097477 GAAGTTATTC
*
18097487 AATAAAAATAACA
1 AATAAAAATAATA
*
18097500 AATAAATAACAATA
1 AATAAA-AATAATA
*
18097514 GATAAGAAA-AA-A
1 AATAA-AAATAATA
*
18097526 GGATAAAAATAATA
1 -AATAAAAATAATA
18097540 AATAAAAATAAT
1 AATAAAAATAAT
18097552 TCAAATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 4 0.09
13 26 0.60
14 12 0.28
15 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.18
Consensus pattern (13 bp):
AATAAAAATAATA
Found at i:18097871 original size:11 final size:11
Alignment explanation
Indices: 18097836--18097874 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
18097826 TAATATAATA
18097836 ATAAAA-ATAT
1 ATAAAATATAT
* *
18097846 AAAAAATATAA
1 ATAAAATATAT
18097857 ATAAAATATAT
1 ATAAAATATAT
18097868 ATAAAAT
1 ATAAAAT
18097875 TTTTGTCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAATATAT
Found at i:18097990 original size:20 final size:19
Alignment explanation
Indices: 18097965--18098047 Score: 66
Period size: 20 Copynumber: 4.4 Consensus size: 19
18097955 AATGTAAAGT
18097965 ATAAAAAATAACAATTAGA-A
1 ATAAAAAATAA-AATTA-ATA
* * *
18097985 ATAAAATAGAAAATATGATA
1 ATAAAAAATAAAAT-TAATA
18098005 ATAAAAAATAAAA-TAA-A
1 ATAAAAAATAAAATTAATA
*
18098022 AT-GAAAATAATAATTAATA
1 ATAAAAAATAA-AATTAATA
18098041 ATAAAAA
1 ATAAAAA
18098048 TAGACAATTG
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
16 7 0.14
17 5 0.10
18 5 0.10
19 7 0.14
20 25 0.51
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (19 bp):
ATAAAAAATAAAATTAATA
Found at i:18101597 original size:16 final size:17
Alignment explanation
Indices: 18101578--18101625 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
18101568 AAAAAATGGC
18101578 AAACAAATGAAT-ATAG
1 AAACAAATGAATCATAG
** *
18101594 AAACCCATGAATCATTG
1 AAACAAATGAATCATAG
*
18101611 AAACAAATAAATCAT
1 AAACAAATGAATCAT
18101626 TTACGATAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (17 bp):
AAACAAATGAATCATAG
Found at i:18103314 original size:21 final size:22
Alignment explanation
Indices: 18103281--18103323 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
18103271 TAATATTACC
*
18103281 TTTTTTTTATTTC-CATTTTTA
1 TTTTTGTTATTTCACATTTTTA
*
18103302 TTTTTGTTCTTTCAACATTTTT
1 TTTTTGTTATTTC-ACATTTTT
18103324 CAGAGACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTTGTTATTTCACATTTTTA
Found at i:18107853 original size:2 final size:2
Alignment explanation
Indices: 18107800--18107844 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18107790 TATCATGTTG
18107800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18107842 AT A
1 AT A
18107845 CGAATATATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18107944 original size:42 final size:42
Alignment explanation
Indices: 18107898--18108017 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 42
18107888 TTGACCGGCT
* * *
18107898 ATGTGCGAGTGGGAGTGTGCATAAGCCGATGCTGACC-AGACG
1 ATGTGCTAGTGGGAGTGTGCATAAGCCGATGATGACCTAG-CC
* **
18107940 ATGTGTTAGTGGGAGTACGCATAAGCCGATGATGACCTAGCC
1 ATGTGCTAGTGGGAGTGTGCATAAGCCGATGATGACCTAGCC
* *
18107982 ATGTGCTAGTGGG-GAGTGCATATGAGCTGATGATGA
1 ATGTGCTAGTGGGAGTGTGCATA--AGCCGATGATGA
18108018 TGGGAGGGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
41 6 0.09
42 45 0.70
43 13 0.20
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.23
Consensus pattern (42 bp):
ATGTGCTAGTGGGAGTGTGCATAAGCCGATGATGACCTAGCC
Found at i:18108418 original size:21 final size:21
Alignment explanation
Indices: 18108392--18108432 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
18108382 TTGCCACTTT
18108392 AATCTCGCTGCAGCGAGAAAG
1 AATCTCGCTGCAGCGAGAAAG
*
18108413 AATCTCGTTGCAGCGAGAAA
1 AATCTCGCTGCAGCGAGAAA
18108433 CTTTCTGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (21 bp):
AATCTCGCTGCAGCGAGAAAG
Found at i:18110167 original size:35 final size:35
Alignment explanation
Indices: 18110128--18110269 Score: 207
Period size: 35 Copynumber: 4.1 Consensus size: 35
18110118 GTGTGGATAG
18110128 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
* *
18110163 TGATGTTGATGTGTGCGAGTAGGGATTGCGCA--A
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
*
18110196 TGATGTTGATGTGTACGAGTAGGGAGTGCACACGA
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
* * * *
18110231 TGATGTTGAAGTGTGCAAGCAGGGAGTGCACAAGA
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
18110266 TGAT
1 TGAT
18110270 ATTGCCTTGT
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
33 30 0.32
35 65 0.68
ACGTcount: A:0.25, C:0.11, G:0.38, T:0.26
Consensus pattern (35 bp):
TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
Found at i:18110205 original size:68 final size:68
Alignment explanation
Indices: 18110128--18110255 Score: 220
Period size: 68 Copynumber: 1.9 Consensus size: 68
18110118 GTGTGGATAG
* * * *
18110128 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGATGATGTTGATGTGTGCGAGTAGGGATTGCG
1 TGATGTTGATGTGTACGAGTAGGGAGTGCACACGATGATGTTGAAGTGTGCAAGCAGGGATTGCG
18110193 CAA
66 CAA
18110196 TGATGTTGATGTGTACGAGTAGGGAGTGCACACGATGATGTTGAAGTGTGCAAGCAGGGA
1 TGATGTTGATGTGTACGAGTAGGGAGTGCACACGATGATGTTGAAGTGTGCAAGCAGGGA
18110256 GTGCACAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.24, C:0.10, G:0.39, T:0.27
Consensus pattern (68 bp):
TGATGTTGATGTGTACGAGTAGGGAGTGCACACGATGATGTTGAAGTGTGCAAGCAGGGATTGCG
CAA
Found at i:18119415 original size:16 final size:16
Alignment explanation
Indices: 18119391--18119421 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18119381 ATAGACCTAA
*
18119391 GGTATAAATGAATGAT
1 GGTAAAAATGAATGAT
18119407 GGTAAAAATGAATGA
1 GGTAAAAATGAATGA
18119422 AAAAGATAGA
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:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (16 bp):
GGTAAAAATGAATGAT
Found at i:18120191 original size:35 final size:35
Alignment explanation
Indices: 18120152--18120253 Score: 168
Period size: 35 Copynumber: 2.9 Consensus size: 35
18120142 GTGTGGATAG
* *
18120152 TGATGTTGATGTGTGTGACTAGGGAGTGCACACGA
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
*
18120187 TGATGTTGATGTGTGCGAGTTGGGAGTGCACACGA
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
*
18120222 TGATGTTGAAGTGTGCGAGTAGGGAGTGCACA
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACA
18120254 TTGGCTGAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.23, C:0.11, G:0.39, T:0.27
Consensus pattern (35 bp):
TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
Found at i:18126698 original size:49 final size:49
Alignment explanation
Indices: 18126636--18126777 Score: 200
Period size: 49 Copynumber: 2.9 Consensus size: 49
18126626 ATTACATTAG
* * *
18126636 CTTATGCGCACTCCCTACTCACACATAGTCGGGTCATCATCATCATCGA
1 CTTATGCTCACTCCCTACTCGCACATAGCCGGGTCATCATCATCATCGA
*
18126685 CTTATGCTTACTCCCTACTCGCACATAGCCGGGTCATCATCATCATCGA
1 CTTATGCTCACTCCCTACTCGCACATAGCCGGGTCATCATCATCATCGA
*
18126734 CTTATG-TGCACTCCTTACTCGCAC-TAGCCGGGTCAAT-ATCATCA
1 CTTATGCT-CACTCCCTACTCGCACATAGCCGGGTC-ATCATCATCA
18126778 CACAACATTA
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
48 18 0.21
49 67 0.79
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (49 bp):
CTTATGCTCACTCCCTACTCGCACATAGCCGGGTCATCATCATCATCGA
Found at i:18134449 original size:10 final size:10
Alignment explanation
Indices: 18134434--18134459 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18134424 CGTAATCCAT
18134434 CAAGCCCAAG
1 CAAGCCCAAG
18134444 CAAGCCCAAG
1 CAAGCCCAAG
18134454 CAAGCC
1 CAAGCC
18134460 TATTAATCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.42, G:0.19, T:0.00
Consensus pattern (10 bp):
CAAGCCCAAG
Found at i:18135793 original size:43 final size:43
Alignment explanation
Indices: 18135719--18135837 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
18135709 TCACCAGCTC
* * * *
18135719 ATGCGCATTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCATC-CTCGGCTT
*
18135762 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCCTCGGCTT
** *
18135805 ATGCATACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCA
18135838 ATATAATTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 65 0.98
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCCTCGGCTT
Found at i:18171461 original size:19 final size:19
Alignment explanation
Indices: 18171430--18171478 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
18171420 TTTCCTTCCA
* *
18171430 CTTTCTCCTTTCTTTGTTTT
1 CTTTCT-CTTTCTCTATTTT
18171450 CTTTCTCTTTCTCTATTTT
1 CTTTCTCTTTCTCTATTTT
*
18171469 CTTTTTCTTT
1 CTTTCTCTTT
18171479 TTTTCTTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (19 bp):
CTTTCTCTTTCTCTATTTT
Found at i:18173002 original size:9 final size:8
Alignment explanation
Indices: 18172977--18173039 Score: 58
Period size: 9 Copynumber: 7.8 Consensus size: 8
18172967 TCTATTATTG
18172977 TTTATTATT
1 TTTATT-TT
*
18172986 TATATTTT
1 TTTATTTT
*
18172994 TCTATTTT
1 TTTATTTT
18173002 TTTA-TTT
1 TTTATTTT
*
18173009 TTTA-GTT
1 TTTATTTT
18173016 TTTATTTT
1 TTTATTTT
18173024 ATTTATTTT
1 -TTTATTTT
18173033 TATTATT
1 T-TTATT
18173040 ATGATAACCT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
7 13 0.28
8 15 0.33
9 18 0.39
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTATTTT
Found at i:18173017 original size:14 final size:14
Alignment explanation
Indices: 18172971--18173036 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 14
18172961 CAAATTTCTA
18172971 TTATTGTTTA-TTAT
1 TTATT-TTTATTTAT
*
18172985 TTATATTTT-TCTA-
1 TTAT-TTTTATTTAT
18172998 TT-TTTTTATTT-T
1 TTATTTTTATTTAT
18173010 TTAGTTTTTATTTTAT
1 TTA-TTTTTA-TTTAT
18173026 TTATTTTTATT
1 TTATTTTTATT
18173037 ATTATGATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
11 4 0.10
12 5 0.12
13 2 0.05
14 17 0.40
15 10 0.24
16 4 0.10
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (14 bp):
TTATTTTTATTTAT
Found at i:18173020 original size:32 final size:32
Alignment explanation
Indices: 18172964--18173039 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
18172954 TTGTTTTCAA
*
18172964 ATTTCTATTATTGTTTATTATTTATATTT-TTCT
1 ATTTTTATTATTGTTTATTATTTAT-TTTATT-T
*
18172997 ATTTTT-TTATTTTTTAGTT-TTTATTTTATTT
1 ATTTTTATTATTGTTTA-TTATTTATTTTATTT
18173028 ATTTTTATTATT
1 ATTTTTATTATT
18173040 ATGATAACCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 10 0.26
32 21 0.55
33 7 0.18
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (32 bp):
ATTTTTATTATTGTTTATTATTTATTTTATTT
Found at i:18173021 original size:22 final size:25
Alignment explanation
Indices: 18172965--18173035 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 25
18172955 TGTTTTCAAA
* *
18172965 TTTCTATTATTGTTTATTATTTATATT
1 TTTCTATT-TTATTTATT-TTTATAGT
18172992 TTTCTATTTT-TTTATTTTT-TAGT
1 TTTCTATTTTATTTATTTTTATAGT
18173015 TTT-TATTTTATTTATTTTTAT
1 TTTCTATTTTATTTATTTTTAT
18173036 TATTATGATA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 6 0.15
23 15 0.37
24 4 0.10
25 6 0.15
26 2 0.05
27 8 0.20
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (25 bp):
TTTCTATTTTATTTATTTTTATAGT
Found at i:18173041 original size:16 final size:16
Alignment explanation
Indices: 18172964--18173041 Score: 72
Period size: 16 Copynumber: 4.9 Consensus size: 16
18172954 TTGTTTTCAA
* *
18172964 ATTTCTATTATTGTTT
1 ATTTTTATTATTATTT
*
18172980 ATTATTTA-TATTTTTCT
1 ATT-TTTATTATTATT-T
*
18172997 ATTTTT-TTATTTTTT
1 ATTTTTATTATTATTT
18173012 AGTTTTTATT-TTATTT
1 A-TTTTTATTATTATTT
18173028 ATTTTTATTATTAT
1 ATTTTTATTATTAT
18173042 GATAACCTCG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
15 10 0.19
16 34 0.64
17 9 0.17
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
ATTTTTATTATTATTT
Found at i:18173325 original size:23 final size:21
Alignment explanation
Indices: 18173283--18173329 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
18173273 TTAAGTACTA
*
18173283 AGCTTGAAAACTAGAATATGCG
1 AGCTTGAAAAATAGAATATG-G
18173305 AGCTTGTAAAAATA-AAGTATGG
1 AGCTTG-AAAAATAGAA-TATGG
18173327 AGC
1 AGC
18173330 AAGTAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (21 bp):
AGCTTGAAAAATAGAATATGG
Found at i:18175258 original size:29 final size:28
Alignment explanation
Indices: 18175212--18175266 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
18175202 ACAACCTCTT
*
18175212 TACCTTTTTCAAAGAGGTATACCTTTTC
1 TACCTTTTTCAAAGAGGTATAACTTTTC
**
18175240 TACCTTTTTCTATCGAGGTATAACTTT
1 TACCTTTTTC-AAAGAGGTATAACTTT
18175267 ACAATAGTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (28 bp):
TACCTTTTTCAAAGAGGTATAACTTTTC
Found at i:18177029 original size:12 final size:12
Alignment explanation
Indices: 18177012--18177048 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
18177002 ATGTCGTGCT
18177012 ATTTTTTAACTC
1 ATTTTTTAACTC
*
18177024 ATTTTTCAACTC
1 ATTTTTTAACTC
18177036 A--TTTTAACTC
1 ATTTTTTAACTC
18177046 ATT
1 ATT
18177049 CTAACCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTTTTAACTC
Found at i:18177044 original size:10 final size:10
Alignment explanation
Indices: 18177015--18177053 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
18177005 TCGTGCTATT
18177015 TTTTAACTCA
1 TTTTAACTCA
18177025 TTTTTCAACTCA
1 -TTTT-AACTCA
18177037 TTTTAACTCA
1 TTTTAACTCA
*
18177047 TTCTAAC
1 TTTTAAC
18177054 CCCCTGCACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 12 0.46
11 8 0.31
12 6 0.23
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTTAACTCA
Found at i:18177368 original size:35 final size:36
Alignment explanation
Indices: 18177290--18177371 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
18177280 TCTCACTAGC
* *
18177290 TCATGTGCACTTCCACACCGCACATAGCTAGAATCA
1 TCATGTGCACTCCCACACCGCACAAAGCTAGAATCA
*
18177326 TCCTGTGCACTCCCACACCGCA-AAAGGC-A-ATATCA
1 TCATGTGCACTCCCACACCGCACAAA-GCTAGA-ATCA
18177361 TCATGTGCACT
1 TCATGTGCACT
18177372 ATCACCTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 1 0.03
35 17 0.43
36 22 0.55
ACGTcount: A:0.29, C:0.34, G:0.15, T:0.22
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACAAAGCTAGAATCA
Found at i:18177449 original size:52 final size:52
Alignment explanation
Indices: 18177381--18177535 Score: 240
Period size: 52 Copynumber: 3.0 Consensus size: 52
18177371 TATCACCTTG
* *
18177381 CACATGGCGTATATCATTAGTGTGTGCACTCACATAGCACACCACTATCACA
1 CACATGGCATATATCATCAGTGTGTGCACTCACATAGCACACCACTATCACA
* *
18177433 CATATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACA
1 CACATGGCATATATCATCAGTGTGTGCACTCACATAGCACACCACTATCACA
* *
18177485 CACATGGCATTTATCATCAGTGTGTGCACTCTCACTA-CACACCACTATCAC
1 CACATGGCATATATCATCAGTGTGTGCACTCACA-TAGCACACCACTATCAC
18177536 CATCATGTGC
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
52 93 0.99
53 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (52 bp):
CACATGGCATATATCATCAGTGTGTGCACTCACATAGCACACCACTATCACA
Found at i:18180722 original size:14 final size:15
Alignment explanation
Indices: 18180687--18180726 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
18180677 GGAAGGAGTA
**
18180687 AGAAAAGAAAAGGAG
1 AGAAAAGAAAACAAG
18180702 AGAAAAGAAAACAAG
1 AGAAAAGAAAACAAG
18180717 -GAAAAGAAAA
1 AGAAAAGAAAA
18180727 TGAAACTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAACAAG
Found at i:18183885 original size:37 final size:37
Alignment explanation
Indices: 18183838--18183956 Score: 204
Period size: 37 Copynumber: 3.2 Consensus size: 37
18183828 AATGCAATAT
*
18183838 CATCATCATGTGTGCACTCCCTACTCACACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
*
18183875 CATCATCATGTGTGCACTCCCTACTCGCACAC-TCTAT
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTC-AA
18183912 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
18183949 CATCATCA
1 CATCATCA
18183957 CACGACATTA
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
36 2 0.03
37 73 0.95
38 2 0.03
ACGTcount: A:0.25, C:0.38, G:0.09, T:0.28
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:18187977 original size:72 final size:73
Alignment explanation
Indices: 18187886--18188083 Score: 285
Period size: 72 Copynumber: 2.7 Consensus size: 73
18187876 GTATTGAAAA
* *
18187886 ACAGAACCGACTTAGTCGACCAAGATGTGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTA-G
1 ACAGAACCAACTTAGTCGACCAAGAAGTGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTACG
*
18187950 A-CTTCAAG
66 AGC-ACAAG
* *
18187958 ACAGAACCAACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATGCTCTCTGCCAGAATCTACG
1 ACAGAACCAACTTAGTCGACCAAGAAGTGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTACG
*
18188023 AGCAGAAG
66 AGCACAAG
**
18188031 ACAGAACCAACTTAGTCGACCAAGAAGAAAGTTAGTCGACTAAGA-GCTCTCTG
1 ACAGAACCAACTTAGTCGACCAAGAAGTGAGTTAGTCGACTAA-ATGCTCTCTG
18188084 TCTGCAATTT
Statistics
Matches: 114, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
72 59 0.52
73 53 0.46
74 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (73 bp):
ACAGAACCAACTTAGTCGACCAAGAAGTGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTACG
AGCACAAG
Found at i:18200403 original size:40 final size:38
Alignment explanation
Indices: 18200350--18200442 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
18200340 TCATGTGCAT
* *
18200350 CCCACATCGTGCACATAGCTGGTGCCATCGTGTGCATCCC
1 CCCACATCGTGCACA-A-CTAGTGCCATCGTGTACATCCC
* *
18200390 CCCACATCATGCACAATTAGTGCCATCGTGTACATCCC
1 CCCACATCGTGCACAACTAGTGCCATCGTGTACATCCC
18200428 CCCACATCGTGCACA
1 CCCACATCGTGCACA
18200443 CGGGCACTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 33 0.69
39 1 0.02
40 14 0.29
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.22
Consensus pattern (38 bp):
CCCACATCGTGCACAACTAGTGCCATCGTGTACATCCC
Found at i:18201377 original size:19 final size:19
Alignment explanation
Indices: 18201329--18201378 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
18201319 TGGAAGAAGA
* *
18201329 AGAAGGAGAAGAAGCTGCT
1 AGAAAGAGAAGAAACTGCT
**
18201348 AGAAATTGAAGAAACTGCT
1 AGAAAGAGAAGAAACTGCT
*
18201367 TGAAAGAGAAGA
1 AGAAAGAGAAGA
18201379 TATTTATAGC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.30, T:0.14
Consensus pattern (19 bp):
AGAAAGAGAAGAAACTGCT
Found at i:18218258 original size:36 final size:36
Alignment explanation
Indices: 18218199--18218306 Score: 118
Period size: 35 Copynumber: 3.0 Consensus size: 36
18218189 TCTCACCAAC
*
18218199 TCATGTGCACTTCCACA-CTGCACATA-GCTAGA-ATCA
1 TCATGTGCACTCCCACATC-GCACATAGGC-A-ATATCA
*
18218235 TCCTGTGCACTCCCACATCGCACA-AGGCAATATCA
1 TCATGTGCACTCCCACATCGCACATAGGCAATATCA
*
18218270 TCATGTGCACTCCCACCTCGCACAT-GGCATATATCA
1 TCATGTGCACTCCCACATCGCACATAGGCA-ATATCA
18218306 T
1 T
18218307 TAGTGTGTGC
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
34 1 0.02
35 32 0.51
36 29 0.46
37 1 0.02
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (36 bp):
TCATGTGCACTCCCACATCGCACATAGGCAATATCA
Found at i:18218371 original size:52 final size:52
Alignment explanation
Indices: 18218288--18218391 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
18218278 ACTCCCACCT
* * *
18218288 CGCACATGGCATATATCATTAGTGTGTGCACTCACACAGCACACCACTATCA
1 CGCACAGGGCATATATCATTAGTGTGCGCACTCACACAACACACCACTATCA
*
18218340 CGCACAGGGCATATATCATTAGTGTGCGCACTCACACAACACACCATTATCA
1 CGCACAGGGCATATATCATTAGTGTGCGCACTCACACAACACACCACTATCA
18218392 TCGTCAAGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (52 bp):
CGCACAGGGCATATATCATTAGTGTGCGCACTCACACAACACACCACTATCA
Found at i:18219542 original size:370 final size:374
Alignment explanation
Indices: 18218854--18219601 Score: 1351
Period size: 370 Copynumber: 2.0 Consensus size: 374
18218844 CAAACCCATT
*
18218854 AAACTAATTATTCAAGTTTAAAGTTTCTTTACCTTGGTGCTTGAAGGTATAAAGATCAACCAAAC
1 AAACTAATTATTCAAGCTTAAAGTTTCTTTACCTTGGTGCTTGAAGGTATAAAGATCAACCAAAC
18218919 CTAGCAAATTTCAAGGAAAGAAATTTTGCAGAAACTTAGAAAATAAAGTCTAAAAATTACAAACC
66 CTAGCAAATTTCAAGGAAAGAAATTTTGCAGAAACTTAGAAAATAAAGTCTAAAAATTACAAACC
*
18218984 CATAAATTCAAAAATTCAATGGTTGAAAATATATACCTTTTAGCCTTAAAAATGAAGATTTGAAG
131 CATAAATTCAAAAATTCAATGGTTGAAAATATATACCTTTTAGCCTTAAAAATGAAAATTTGAAG
* *
18219049 CCAAAAATCCAAGTGTTGTTGAAAGTGGAGTAGAAATAGAAAATAAAAGAAAGGAAGAGAGATTT
196 CCAAAAACCCAAGTGTTGTTGAAAGTGGAGTAGAAATAGAAAATAAAAGAAAAGAAGAGAGATTT
* *
18219114 TTCTTTCTCTCTCCTAGGGTTTAGATGTGCTGAAAATTGGGGTTAGAAGCTACAGGTTTGATGCC
261 TTCTTTCTCTCACCTAGGGTTTAGATGTGCTGAAAATTAGGGTTAGAAGCTACAGGTTTGATGCC
* *
18219179 CAAGAAGTTAAGAGAA-GAAGGAGTAAGAAAAGAAAAGGAAAG-AAAGA
326 AAAGAAGTTAAGAGAAGGAAAGAGTAAGAAAAGAAAAGGAAAGAAAAGA
*
18219226 AAACNAATTATTCAAGCTTAAAGTTTCTTTACCTTGGTGCTTGAAGGTATAAAGATCAACCAAAC
1 AAACTAATTATTCAAGCTTAAAGTTTCTTTACCTTGGTGCTTGAAGGTATAAAGATCAACCAAAC
18219291 CTAGCAAATTTCAAGGAAAGAAATTTTGCAGAAACTTAGAAAATAAAGTCTAAAAATTACAAA-C
66 CTAGCAAATTTCAAGGAAAGAAATTTTGCAGAAACTTAGAAAATAAAGTCTAAAAATTACAAACC
18219355 CATAAATTCAAAAATTCAA-GGTTGAAAATATATACCTTTTAGCCTTAAAAATGAAAATTTGAAG
131 CATAAATTCAAAAATTCAATGGTTGAAAATATATACCTTTTAGCCTTAAAAATGAAAATTTGAAG
18219419 CCAAAAACCCAAGTGTTGTTGAAAGTGGAGTAGAAATAGAAAATAAAAGAAAAGAAGAGAGATTT
196 CCAAAAACCCAAGTGTTGTTGAAAGTGGAGTAGAAATAGAAAATAAAAGAAAAGAAGAGAGATTT
* * *
18219484 TTCTTTCTCTCACCTAGGGTTTCGTTGTGCTGAAAATTAGGGTTAGAAGCTACAGGTTTGGTGCC
261 TTCTTTCTCTCACCTAGGGTTTAGATGTGCTGAAAATTAGGGTTAGAAGCTACAGGTTTGATGCC
*
18219549 AAAGAAGTTAGGAGAAGGAAAGAGTAAGAAAAGAAAAGGAAAGAAAAGA
326 AAAGAAGTTAAGAGAAGGAAAGAGTAAGAAAAGAAAAGGAAAGAAAAGA
18219598 AAAC
1 AAAC
18219602 AAGGAAAAGA
Statistics
Matches: 361, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
370 181 0.50
371 45 0.12
372 135 0.37
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (374 bp):
AAACTAATTATTCAAGCTTAAAGTTTCTTTACCTTGGTGCTTGAAGGTATAAAGATCAACCAAAC
CTAGCAAATTTCAAGGAAAGAAATTTTGCAGAAACTTAGAAAATAAAGTCTAAAAATTACAAACC
CATAAATTCAAAAATTCAATGGTTGAAAATATATACCTTTTAGCCTTAAAAATGAAAATTTGAAG
CCAAAAACCCAAGTGTTGTTGAAAGTGGAGTAGAAATAGAAAATAAAAGAAAAGAAGAGAGATTT
TTCTTTCTCTCACCTAGGGTTTAGATGTGCTGAAAATTAGGGTTAGAAGCTACAGGTTTGATGCC
AAAGAAGTTAAGAGAAGGAAAGAGTAAGAAAAGAAAAGGAAAGAAAAGA
Found at i:18219584 original size:5 final size:5
Alignment explanation
Indices: 18219574--18219620 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
18219564 AGGAAAGAGT
* * *
18219574 AAGAA AAGAA AAGGA AAGAA AAGAA AA-CA AGGAA AAGAA AATGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA-GAA AA
18219621 TCTTGATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
4 2 0.06
5 27 0.79
6 5 0.15
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:18219610 original size:14 final size:15
Alignment explanation
Indices: 18219574--18219614 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
18219564 AGGAAAGAGT
*
18219574 AAGAAAAGAAAAGGA
1 AAGAAAAGAAAAGCA
18219589 AAGAAAAGAAAA-CA
1 AAGAAAAGAAAAGCA
*
18219603 AGGAAAAGAAAA
1 AAGAAAAGAAAA
18219615 TGAAAATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAAGCA
Found at i:18219612 original size:19 final size:19
Alignment explanation
Indices: 18219584--18219620 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
18219574 AAGAAAAGAA
18219584 AAGGAAAGAAAA-GAAAAC
1 AAGGAAAGAAAATGAAAAC
18219602 AAGGAAAAGAAAATGAAAA
1 AAGG-AAAGAAAATGAAAA
18219621 TCTTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.73, C:0.03, G:0.22, T:0.03
Consensus pattern (19 bp):
AAGGAAAGAAAATGAAAAC
Found at i:18229367 original size:14 final size:15
Alignment explanation
Indices: 18229341--18229369 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18229331 TTATTGTCAT
18229341 AAGCCATTAAATTTA
1 AAGCCATTAAATTTA
18229356 AAGCCA-TAAATTTA
1 AAGCCATTAAATTTA
18229370 CAACACAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (15 bp):
AAGCCATTAAATTTA
Found at i:18229451 original size:13 final size:13
Alignment explanation
Indices: 18229433--18229457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18229423 TTTCAGAAAA
18229433 TTTATAAAATCAT
1 TTTATAAAATCAT
18229446 TTTATAAAATCA
1 TTTATAAAATCA
18229458 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:18234665 original size:5 final size:5
Alignment explanation
Indices: 18234660--18234699 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
18234650 CTATTCTACC
*
18234660 TAACC TAACT TAACT TAAC- TAACT TAACT TAACT TAACT T
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT T
18234700 GGGCCACGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.38
Consensus pattern (5 bp):
TAACT
Found at i:18234683 original size:14 final size:14
Alignment explanation
Indices: 18234664--18234699 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
18234654 TCTACCTAAC
18234664 CTAACTTAACTTAA
1 CTAACTTAACTTAA
18234678 CTAACTTAACTTAA
1 CTAACTTAACTTAA
18234692 CTTAACTT
1 C-TAACTT
18234700 GGGCCACGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (14 bp):
CTAACTTAACTTAA
Found at i:18234687 original size:19 final size:19
Alignment explanation
Indices: 18234659--18234698 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
18234649 TCTATTCTAC
18234659 CTAACCTAACTTAACTTAA
1 CTAACCTAACTTAACTTAA
*
18234678 CTAACTTAACTTAACTTAA
1 CTAACCTAACTTAACTTAA
18234697 CT
1 CT
18234699 TGGGCCACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (19 bp):
CTAACCTAACTTAACTTAA
Found at i:18234754 original size:15 final size:14
Alignment explanation
Indices: 18234734--18234779 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
18234724 TTCTTAAAAC
18234734 AACTTTAAAATCAGA
1 AACTTTAAAATCA-A
18234749 AACTTTAAAATCCAA
1 AACTTTAAAAT-CAA
*
18234764 AGCTTTAAAATCAA
1 AACTTTAAAATCAA
18234778 AA
1 AA
18234780 TCTCTAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 22 0.79
16 2 0.07
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (14 bp):
AACTTTAAAATCAA
Found at i:18241743 original size:19 final size:19
Alignment explanation
Indices: 18241706--18241743 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18241696 CCATTTAACT
* *
18241706 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATCTGAG
18241725 TATTGGAGTATAATCTGAG
1 TATTGGAGTATAATCTGAG
18241744 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (19 bp):
TATTGGAGTATAATCTGAG
Found at i:18241950 original size:28 final size:29
Alignment explanation
Indices: 18241909--18241968 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
18241899 GTCTATGGGC
* *
18241909 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
*
18241937 AATTTTTCACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
18241967 AA
1 AA
18241969 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
30 14 0.52
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Done.