Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 69 of 198
Found at i:21485774 original size:33 final size:33
Alignment explanation
Indices: 21485733--21485802 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
21485723 ATAATAAAAT
* * *
21485733 ATATTTAAATAATTTAATATAATGGTACATAAA
1 ATATTTAAATAATTTAACACAATGATACATAAA
21485766 ATATTTAAATAATTTAACACAATGATACATAAA
1 ATATTTAAATAATTTAACACAATGATACATAAA
21485799 ATAT
1 ATAT
21485803 AAAGTAATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (33 bp):
ATATTTAAATAATTTAACACAATGATACATAAA
Found at i:21487581 original size:20 final size:17
Alignment explanation
Indices: 21487537--21487586 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 17
21487527 TGGTATTCTC
21487537 AGAAAATATAATTTATTT
1 AGAAAATA-AATTTATTT
21487555 AGAAAATAGAATTTATACTT
1 AGAAAATA-AATTTAT--TT
*
21487575 GGAAAATAAATT
1 AGAAAATAAATT
21487587 CTCATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 15 0.54
19 4 0.14
20 9 0.32
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (17 bp):
AGAAAATAAATTTATTT
Found at i:21487964 original size:16 final size:16
Alignment explanation
Indices: 21487943--21487976 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
21487933 TTATTTTTAA
*
21487943 CTAATTAACTAATTTT
1 CTAATTAAATAATTTT
21487959 CTAATTAAATAATTTT
1 CTAATTAAATAATTTT
21487975 CT
1 CT
21487977 CATCTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (16 bp):
CTAATTAAATAATTTT
Found at i:21488306 original size:19 final size:19
Alignment explanation
Indices: 21488282--21488319 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21488272 GAGCTAGCGA
21488282 AGGGACCGATTGGACATAT
1 AGGGACCGATTGGACATAT
21488301 AGGGACCGATTGGACATAT
1 AGGGACCGATTGGACATAT
21488320 GTGATTACAG
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:0.32, C:0.16, G:0.32, T:0.21
Consensus pattern (19 bp):
AGGGACCGATTGGACATAT
Found at i:21489996 original size:25 final size:25
Alignment explanation
Indices: 21489942--21490011 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
21489932 AGACTCACCA
* * *
21489942 CAGCTCGTATGAGCTTACTGGTTTG
1 CAGCTCGTAGGAGCTTACCGATTTG
*
21489967 TAGCTCGTAGGAGCTTACCGATATT-
1 CAGCTCGTAGGAGCTTACCGAT-TTG
*
21489992 CAGCTCGGAGGAGCTTACCG
1 CAGCTCGTAGGAGCTTACCG
21490012 TTTATCGCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (25 bp):
CAGCTCGTAGGAGCTTACCGATTTG
Found at i:21492945 original size:16 final size:17
Alignment explanation
Indices: 21492924--21492955 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
21492914 AATTAGGTTG
21492924 AGAAAATT-ATTTAATT
1 AGAAAATTAATTTAATT
21492940 AGAAAATTAATTTAAT
1 AGAAAATTAATTTAAT
21492956 AAATCATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
AGAAAATTAATTTAATT
Found at i:21495705 original size:5 final size:5
Alignment explanation
Indices: 21495690--21495730 Score: 73
Period size: 5 Copynumber: 8.0 Consensus size: 5
21495680 TTGAAGTATG
21495690 TATTGA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATT-A TATTA TATTA TATTA TATTA TATTA TATTA TATTA
21495731 GAAGATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 31 0.89
6 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:21499027 original size:56 final size:56
Alignment explanation
Indices: 21498877--21499015 Score: 217
Period size: 56 Copynumber: 2.5 Consensus size: 56
21498867 ATTATGTTAA
**
21498877 GATATTATTATGATATATTATCTTTTAGCAATTTGATTCATAATGGGAGATTATAG
1 GATATTATTATGGGATATTATCTTTTAGCAATTTGATTCATAATGGGAGATTATAG
* * *
21498933 GATATTATAATGGGATATTAT-TTCTTAGCAATTTGATTCTTAATGGGATATTATAG
1 GATATTATTATGGGATATTATCTT-TTAGCAATTTGATTCATAATGGGAGATTATAG
21498989 GATATTATTATGGGATATTATCTTTTA
1 GATATTATTATGGGATATTATCTTTTA
21499016 ATAGTTTGAT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
55 2 0.03
56 71 0.95
57 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (56 bp):
GATATTATTATGGGATATTATCTTTTAGCAATTTGATTCATAATGGGAGATTATAG
Found at i:21504200 original size:50 final size:50
Alignment explanation
Indices: 21504119--21504290 Score: 211
Period size: 50 Copynumber: 3.4 Consensus size: 50
21504109 CATTTGGGTA
*
21504119 AAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGAT
* * *
21504169 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCTTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGAT
* * * * * *
21504219 GAGAGGCCCCGCT-TAAGACCATGTCTAGGACATGGCATGGGGACCGATAT
1 AAGAGGTCCC-ATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGAT
* **
21504269 GAGAACTCCCATGTAAGACCAT
1 AAGAGGTCCCATGTAAGACCAT
21504291 ATTTGGGATA
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.01
50 102 0.98
51 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGAT
Found at i:21504310 original size:100 final size:100
Alignment explanation
Indices: 21504132--21504311 Score: 252
Period size: 100 Copynumber: 1.8 Consensus size: 100
21504122 AGGTCCCATG
* * ** *
21504132 TAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATAAGAGGTCCCATGTAAGACCATGTATGG
1 TAAGACCATGTCTAGGACATGGCATGGGCACCGAGATAAGAACTCCCATGTAAGACCATATATGG
* *
21504197 GACATGGCTTTGGCACCGAGATGAGAGGCCCCGCT
66 GACATGACATTGGCACCGAGATGAGAGGCCCCGCT
* * * *
21504232 TAAGACCATGTCTAGGACATGGCATGGGGACCGATATGAGAACTCCCATGTAAGACCATATTTGG
1 TAAGACCATGTCTAGGACATGGCATGGGCACCGAGATAAGAACTCCCATGTAAGACCATATATGG
*
21504297 GATATGACATTGGCA
66 GACATGACATTGGCA
21504312 GTACAGGAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 68 1.00
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (100 bp):
TAAGACCATGTCTAGGACATGGCATGGGCACCGAGATAAGAACTCCCATGTAAGACCATATATGG
GACATGACATTGGCACCGAGATGAGAGGCCCCGCT
Found at i:21505024 original size:13 final size:13
Alignment explanation
Indices: 21505008--21505073 Score: 96
Period size: 13 Copynumber: 5.1 Consensus size: 13
21504998 TTTAAACCAA
21505008 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
21505021 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* * *
21505034 GCTTTTCCATAGC
1 ACTTTTCAAAAGC
21505047 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
21505060 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
21505073 A
1 A
21505074 ATGAAGAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:21505288 original size:16 final size:16
Alignment explanation
Indices: 21505267--21505297 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21505257 TTTATTTAAG
21505267 CAAGTAAGTAAGTAAA
1 CAAGTAAGTAAGTAAA
*
21505283 CAAGTAAGTGAGTAA
1 CAAGTAAGTAAGTAA
21505298 GTAAAGAATA
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:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (16 bp):
CAAGTAAGTAAGTAAA
Found at i:21506540 original size:13 final size:13
Alignment explanation
Indices: 21506522--21506562 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
21506512 GGTGTTACAC
*
21506522 ACACGAGCGTGTG
1 ACACGACCGTGTG
21506535 ACACGACCGTGTG
1 ACACGACCGTGTG
21506548 ACACGACCGTGTG
1 ACACGACCGTGTG
21506561 AC
1 AC
21506563 CCTACTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.15
Consensus pattern (13 bp):
ACACGACCGTGTG
Found at i:21506865 original size:9 final size:9
Alignment explanation
Indices: 21506851--21506935 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
21506841 CTTGGTTAAA
21506851 AATTAACCG
1 AATTAACCG
21506860 AATTAACCG
1 AATTAACCG
21506869 AATTAACCG
1 AATTAACCG
* * *
21506878 GATTAATCA
1 AATTAACCG
21506887 AATTAACCG
1 AATTAACCG
* *
21506896 GATTACCCG
1 AATTAACCG
21506905 AATTAACCG
1 AATTAACCG
*
21506914 AATTACCCG
1 AATTAACCG
*
21506923 AATTAACTG
1 AATTAACCG
21506932 AATT
1 AATT
21506936 GAATCACTAC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 63 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:21507003 original size:20 final size:20
Alignment explanation
Indices: 21506955--21507004 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
21506945 CATAATTAAA
21506955 TTATTTTTAGACTTTTAAACT
1 TTATTTTTAGA-TTTTAAACT
* *
21506976 TTAGTTTTAG-TTTTAGAATT
1 TTATTTTTAGATTTTA-AACT
21506996 TTATTTTTA
1 TTATTTTTA
21507005 TTTATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 9 0.36
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.62
Consensus pattern (20 bp):
TTATTTTTAGATTTTAAACT
Found at i:21507015 original size:20 final size:19
Alignment explanation
Indices: 21506967--21507015 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
21506957 ATTTTTAGAC
*
21506967 TTTTAAACTTTAGTTTTAG
1 TTTTAAATTTTAGTTTTAG
* *
21506986 TTTTAGAATTTTATTTTTAT
1 TTTTA-AATTTTAGTTTTAG
21507006 TTATTAAATT
1 TT-TTAAATT
21507016 ATTTGTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 17 0.68
21 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (19 bp):
TTTTAAATTTTAGTTTTAG
Found at i:21508938 original size:25 final size:25
Alignment explanation
Indices: 21508908--21509005 Score: 65
Period size: 25 Copynumber: 4.0 Consensus size: 25
21508898 GCCCTTTCTC
*
21508908 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCATGA
* * * **
21508933 GAGCCATGTAAC-GAGAAGATTATCC
1 GAGCCATATAACAG-GAAGCTCATGA
* * ** *
21508958 GGGCTATATAATGGGAAGCTCATAA
1 GAGCCATATAACAGGAAGCTCATGA
*
21508983 GAGCCATAT-TCAGGAAGCTCATG
1 GAGCCATATAACAGGAAGCTCATG
21509006 CGAACCAATA
Statistics
Matches: 52, Mismatches: 19, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
24 11 0.21
25 40 0.77
26 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATGA
Found at i:21509138 original size:26 final size:26
Alignment explanation
Indices: 21509101--21509150 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
21509091 GGAAGCTTTG
21509101 AAGAGCTATTAATCTG-GAAGCTCACA
1 AAGAGCTATTAATC-GAGAAGCTCACA
21509127 AAGAGCCT-TTAATCGAGAAGCTCA
1 AAGAG-CTATTAATCGAGAAGCTCA
21509151 TGAAAAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.05
26 19 0.86
27 2 0.09
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
AAGAGCTATTAATCGAGAAGCTCACA
Found at i:21509159 original size:26 final size:26
Alignment explanation
Indices: 21509109--21509183 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
21509099 TGAAGAGCTA
*
21509109 TTAATCTG-GAAGCTCACAAAGAGCC-T
1 TTAATC-GAGAAGCTCATAAA-AGCCAT
21509135 TTAATCGAGAAGCTCATGAAAAGCCAT
1 TTAATCGAGAAGCTCAT-AAAAGCCAT
* *
21509162 ATAAT-GAGACGCTCATAAAAGC
1 TTAATCGAGAAGCTCATAAAAGC
21509184 TGCGGAGTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 7 0.16
26 28 0.65
27 8 0.19
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (26 bp):
TTAATCGAGAAGCTCATAAAAGCCAT
Found at i:21509706 original size:42 final size:42
Alignment explanation
Indices: 21509647--21509730 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
21509637 CAATCCAATT
21509647 CACATTGTAAGGCCCAAATTTAGCCCAGGCCCGTACCAAATA
1 CACATTGTAAGGCCCAAATTTAGCCCAGGCCCGTACCAAATA
21509689 CACATTGTAAGGCCCAAATTTAGCCCAGGCCCGTACCAAATA
1 CACATTGTAAGGCCCAAATTTAGCCCAGGCCCGTACCAAATA
21509731 AACCAAACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (42 bp):
CACATTGTAAGGCCCAAATTTAGCCCAGGCCCGTACCAAATA
Found at i:21510195 original size:20 final size:20
Alignment explanation
Indices: 21510172--21510211 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21510162 TTCGATTTAG
**
21510172 TATTTTATTGTATCTTTTTT
1 TATTTTATTAAATCTTTTTT
*
21510192 TATTTTTTTAAATCTTTTTT
1 TATTTTATTAAATCTTTTTT
21510212 CTTCTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (20 bp):
TATTTTATTAAATCTTTTTT
Found at i:21510965 original size:3 final size:3
Alignment explanation
Indices: 21510957--21511020 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
21510947 ATGTTTGATG
* * * *
21510957 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA ATA TT- TTC GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21511004 TTTA TTA TTA TT- TTA TT
1 -TTA TTA TTA TTA TTA TT
21511021 TACTTACTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:21515840 original size:13 final size:13
Alignment explanation
Indices: 21515819--21515856 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
21515809 AGAGGGGTGT
21515819 TAGGATATTATTA
1 TAGGATATTATTA
21515832 T-GAGATATTATTA
1 TAG-GATATTATTA
21515845 TAGGATATTATT
1 TAGGATATTATT
21515857 TCTTAGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 21 0.91
14 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (13 bp):
TAGGATATTATTA
Found at i:21515911 original size:56 final size:56
Alignment explanation
Indices: 21515827--21515932 Score: 169
Period size: 56 Copynumber: 1.9 Consensus size: 56
21515817 GTTAGGATAT
*
21515827 TATTATGAGATATTATTATAGGATATTAT-TTCTTAGCAATTTGATTCCTAGTGAGA
1 TATTATGAGATATTATTATAGAATATTATCTT-TTAGCAATTTGATTCCTAGTGAGA
* *
21515883 TATTATGTGATATTATTATATAATATTATCTTTTAGCAATTTGATTCCTA
1 TATTATGAGATATTATTATAGAATATTATCTTTTAGCAATTTGATTCCTA
21515933 CTTAACTACT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
56 44 0.96
57 2 0.04
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (56 bp):
TATTATGAGATATTATTATAGAATATTATCTTTTAGCAATTTGATTCCTAGTGAGA
Found at i:21515959 original size:56 final size:57
Alignment explanation
Indices: 21515849--21515967 Score: 129
Period size: 56 Copynumber: 2.1 Consensus size: 57
21515839 TTATTATAGG
* * *
21515849 ATATTATTTCTTAGCAATTTGATTCCTAGTGAGATATTATGTGATATTATTATATA-
1 ATATTATTTCTTAGCAATTTGATTCCTACTGAGATACTATGTGATAATATTATATAT
*
21515905 ATATTATCTT-TTAGCAATTTGATTCCTACTTA-ACTACTACTGT-ATAGATATATATATAT
1 ATATTAT-TTCTTAGCAATTTGATTCCTACTGAGA-TACTA-TGTGATA-ATAT-TATATAT
21515964 ATAT
1 ATAT
21515968 ATACCTTTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
55 1 0.02
56 34 0.64
57 8 0.15
58 6 0.11
59 4 0.08
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (57 bp):
ATATTATTTCTTAGCAATTTGATTCCTACTGAGATACTATGTGATAATATTATATAT
Found at i:21517583 original size:9 final size:9
Alignment explanation
Indices: 21517569--21517671 Score: 136
Period size: 9 Copynumber: 11.4 Consensus size: 9
21517559 TTTGGTTAAA
21517569 AATTAACCG
1 AATTAACCG
21517578 AATTAACCG
1 AATTAACCG
*
21517587 AATTAACCA
1 AATTAACCG
*
21517596 AATTACCCG
1 AATTAACCG
21517605 AATTAACCG
1 AATTAACCG
21517614 AATT-ACCTG
1 AATTAACC-G
*
21517623 AATTACCCG
1 AATTAACCG
21517632 AATTAACCG
1 AATTAACCG
*
21517641 AATTACCCG
1 AATTAACCG
*
21517650 AATTAACCA
1 AATTAACCG
*
21517659 AATTAACCA
1 AATTAACCG
21517668 AATT
1 AATT
21517672 GAATCACTAC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
8 3 0.04
9 78 0.94
10 2 0.02
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:21517818 original size:18 final size:18
Alignment explanation
Indices: 21517778--21517821 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21517768 TAATTTTATG
**
21517778 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
21517796 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
21517814 CTTGGGTT
1 ATTGGGTT
21517822 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:21518217 original size:18 final size:17
Alignment explanation
Indices: 21518193--21518239 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
21518183 AATTAAACTT
*
21518193 TTTTAAAAATTAAAAAT
1 TTTTAAAAATTAAAAAA
*
21518210 TGTTTAAAAAATAAAAAAA
1 T-TTT-AAAAATTAAAAAA
21518229 TTTTAAAAATT
1 TTTTAAAAATT
21518240 TTAAAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TTTTAAAAATTAAAAAA
Found at i:21518227 original size:27 final size:25
Alignment explanation
Indices: 21518197--21518259 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
21518187 AAACTTTTTT
21518197 AAAAATTAAAAATTGTTTAAAAA-ATAA
1 AAAAATTAAAAA-T-TTTAAAAATAT-A
*
21518224 AAAAATTTTAAAAATTTTAAAAGTATA
1 AAAAA--TTAAAAATTTTAAAAATATA
21518251 AAAAATTAA
1 AAAAATTAA
21518260 CAATGCCGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
25 4 0.12
27 18 0.56
28 3 0.09
29 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (25 bp):
AAAAATTAAAAATTTTAAAAATATA
Found at i:21518245 original size:18 final size:18
Alignment explanation
Indices: 21518192--21518245 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
21518182 CAATTAAACT
21518192 TTTTTAAAAA-TTAAAAA
1 TTTTTAAAAATTTAAAAA
* *
21518209 TTGTTTAAAAAATAAAAAA
1 TT-TTTAAAAATTTAAAAA
*
21518228 ATTTTAAAAATTTTAAAA
1 TTTTTAAAAA-TTTAAAA
21518246 GTATAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 16 0.53
19 12 0.40
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
TTTTTAAAAATTTAAAAA
Found at i:21518391 original size:29 final size:28
Alignment explanation
Indices: 21518348--21518412 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
21518338 TTTTTTAATA
* *
21518348 AAAATTTATAATTTTTATAAT-TTTTTT
1 AAAATTTATAATTTTTAAAATAATTTTT
*
21518375 ATAAATTTATGATTTTTTAAAATAATTTTT
1 A-AAATTTAT-AATTTTTAAAATAATTTTT
21518405 AAAATTTA
1 AAAATTTA
21518413 AAAGGCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 8 0.25
29 17 0.53
30 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
AAAATTTATAATTTTTAAAATAATTTTT
Found at i:21520984 original size:13 final size:13
Alignment explanation
Indices: 21520968--21521002 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
21520958 TTTAAACAAA
*
21520968 TTAATTAACTTAT
1 TTAATTAACTAAT
21520981 TTAATTAACTAAT
1 TTAATTAACTAAT
*
21520994 TTAACTAAC
1 TTAATTAAC
21521003 AGCAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:21522349 original size:12 final size:13
Alignment explanation
Indices: 21522289--21522351 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
21522279 AACTATGAAC
21522289 TTTTCTTCTTCTTT
1 TTTTCTTCTTC-TT
21522303 TTTTCTT-TT-TT
1 TTTTCTTCTTCTT
* **
21522314 TTTTAATTCTGAATT
1 TTTT-CTTCT-TCTT
21522329 TTTTCTTCTTCTT
1 TTTTCTTCTTCTT
21522342 TTTT-TTCTTC
1 TTTTCTTCTTC
21522352 AATACTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
11 6 0.15
12 8 0.20
13 9 0.22
14 11 0.28
15 6 0.15
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTCTTCTTCTT
Found at i:21527660 original size:41 final size:39
Alignment explanation
Indices: 21527603--21527755 Score: 164
Period size: 41 Copynumber: 3.8 Consensus size: 39
21527593 ACCTTTTGGG
*
21527603 GCTTTAGCGGCATTTTTTCAAAAGCGCCGCTAATGCTCTA
1 GCTTTAGCGGCATTTTTTAAAAAGCGCCGCTAATGCTC-A
*
21527643 GCTTTTAGCGGCA-TTTTTAATAAAGCGTCGCTAATGCTCA
1 GC-TTTAGCGGCATTTTTTAA-AAAGCGCCGCTAATGCTCA
* **
21527683 GACCTTTAGCGGCGTTTTCGAAAAAGCGCCGCTAATGCTCA
1 G--CTTTAGCGGCATTTTTTAAAAAGCGCCGCTAATGCTCA
** *
21527724 GGGCTTTAGCGGCGCTTTTCAAAAAGCGCCGC
1 --GCTTTAGCGGCATTTTTTAAAAAGCGCCGC
21527756 AAAAACATTT
Statistics
Matches: 97, Mismatches: 9, Indels: 13
0.82 0.08 0.11
Matches are distributed among these distances:
40 10 0.10
41 80 0.82
42 6 0.06
43 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (39 bp):
GCTTTAGCGGCATTTTTTAAAAAGCGCCGCTAATGCTCA
Found at i:21528581 original size:7 final size:7
Alignment explanation
Indices: 21528569--21528611 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
21528559 ATTGTAAAAG
21528569 AGGGGTT
1 AGGGGTT
21528576 AGGGGTT
1 AGGGGTT
*
21528583 AAGGGTT
1 AGGGGTT
*
21528590 AGAGGTT
1 AGGGGTT
21528597 AGGGGTT
1 AGGGGTT
21528604 AGGGGTT
1 AGGGGTT
21528611 A
1 A
21528612 CGAGTTTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.21, C:0.00, G:0.51, T:0.28
Consensus pattern (7 bp):
AGGGGTT
Found at i:21532354 original size:41 final size:41
Alignment explanation
Indices: 21532294--21532423 Score: 131
Period size: 41 Copynumber: 3.1 Consensus size: 41
21532284 AACATTTTTT
* *
21532294 TAAAAGTCATGTTTTTAGTGGCGTTTGTCA-AAAAGCGCCGC
1 TAAAAGTCATCTTTATAGTGGCGTTTGT-AGAAAAGCGCCGC
21532335 TAAAAGTCATCTTTATAGTGGCGTTTGTAGGAAAAGCGCCGC
1 TAAAAGTCATCTTTATAGTGGCGTTTGTA-GAAAAGCGCCGC
* * * *
21532377 TAAAGGTCTTGGTCTTT-T-GCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAAGTC---ATCTTTATAGTGGCGTTTGT-AGAAAAGCGCCGC
21532420 TAAA
1 TAAA
21532424 GGTCTTGGTC
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
40 1 0.01
41 26 0.34
42 18 0.23
43 26 0.34
44 1 0.01
45 5 0.06
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (41 bp):
TAAAAGTCATCTTTATAGTGGCGTTTGTAGAAAAGCGCCGC
Found at i:21532412 original size:43 final size:43
Alignment explanation
Indices: 21532307--21532446 Score: 171
Period size: 43 Copynumber: 3.3 Consensus size: 43
21532297 AAGTCATGTT
* * * *
21532307 TTTAGTGGCGTTTGTCA--AAAAGCGCCGCTAAAAGTCAT-CT-
1 TTTAGCGGCGTTTGT-AGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
21532347 TTATAGTGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TT-TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
21532391 TTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCTTGGTC
21532434 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
21532447 TTTCCGGCTC
Statistics
Matches: 88, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
40 3 0.03
41 13 0.15
42 19 0.22
43 51 0.58
44 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:21532748 original size:20 final size:20
Alignment explanation
Indices: 21532723--21532875 Score: 98
Period size: 20 Copynumber: 7.6 Consensus size: 20
21532713 ATACCAATAA
21532723 TTCTAAAGATTTATCAAAAT
1 TTCTAAAGATTTATCAAAAT
** *
21532743 TTCTAAACCTTTA-CCAAAT
1 TTCTAAAGATTTATCAAAAT
* *
21532762 TCTCT-AAG-GTTATACAAATTT
1 T-TCTAAAGATTTAT-CAAA-AT
* * *
21532783 TTTTAAGGATTTATCAAAACA
1 TTCTAAAGATTTATCAAAA-T
* *
21532804 TT-TAAAAATTTACCAAAAT
1 TTCTAAAGATTTATCAAAAT
*
21532823 TTCTAAAGATTTTACCAAAAT
1 TTCTAAAGA-TTTATCAAAAT
* * *
21532844 TTCTAAGGATTTAACAATAT
1 TTCTAAAGATTTATCAAAAT
*
21532864 TTCTAAACATTT
1 TTCTAAAGATTT
21532876 TCTTAATGTT
Statistics
Matches: 102, Mismatches: 22, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
18 3 0.03
19 10 0.10
20 56 0.55
21 29 0.28
22 4 0.04
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (20 bp):
TTCTAAAGATTTATCAAAAT
Found at i:21532838 original size:21 final size:21
Alignment explanation
Indices: 21532812--21532876 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
21532802 CATTTAAAAA
21532812 TTTACCAAAATTTCTAAAGAT
1 TTTACCAAAATTTCTAAAGAT
*
21532833 TTTACCAAAATTTCTAAGGA-
1 TTTACCAAAATTTCTAAAGAT
* * *
21532853 TTTAACAATATTTCTAAACAT
1 TTTACCAAAATTTCTAAAGAT
21532874 TTT
1 TTT
21532877 CTTAATGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (21 bp):
TTTACCAAAATTTCTAAAGAT
Found at i:21536476 original size:20 final size:20
Alignment explanation
Indices: 21536453--21536516 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
21536443 AGGGGCACAA
*
21536453 AAGTGCATTCAGGGGTACCG
1 AAGTGCAATCAGGGGTACCG
* * * *
21536473 AAGTACAAACATGGGCA-CG
1 AAGTGCAATCAGGGGTACCG
*
21536492 TAAGTGCAATCAGGGATACCG
1 -AAGTGCAATCAGGGGTACCG
21536513 AAGT
1 AAGT
21536517 ACAAACATGG
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (20 bp):
AAGTGCAATCAGGGGTACCG
Found at i:21536531 original size:40 final size:40
Alignment explanation
Indices: 21536434--21536535 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 40
21536424 GAGTTACTGG
* * ** * *
21536434 AGTATAAACAGGGGCACAAAAGTGCATTCAGGGGTACCGA
1 AGTACAAACATGGGCACGTAAGTGCAATCAGGGATACCGA
21536474 AGTACAAACATGGGCACGTAAGTGCAATCAGGGATACCGA
1 AGTACAAACATGGGCACGTAAGTGCAATCAGGGATACCGA
21536514 AGTACAAACATGGGCACGTAAG
1 AGTACAAACATGGGCACGTAAG
21536536 GTAATCATCA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.15
Consensus pattern (40 bp):
AGTACAAACATGGGCACGTAAGTGCAATCAGGGATACCGA
Found at i:21546317 original size:40 final size:40
Alignment explanation
Indices: 21546273--21546451 Score: 187
Period size: 40 Copynumber: 4.5 Consensus size: 40
21546263 GTATAAATAA
* * * * *
21546273 GGGCATGAAAGTGCATTCAAGGGTACTAAAGTACAGATAG
1 GGGCATGTAAGTGCAATCAAGGGTACCAAAGTACAAACAG
* * * *
21546313 GGGCATGTATGTGCATTTAGGGGTACCAAAGTACAAACAG
1 GGGCATGTAAGTGCAATCAAGGGTACCAAAGTACAAACAG
* ** * *
21546353 TGGCACATAAGTGCAATCAAGGGTACCGAAGTACAAACAA
1 GGGCATGTAAGTGCAATCAAGGGTACCAAAGTACAAACAG
* * * * *
21546393 GCGCACGTAAGTGCAATCAGGGGTACCGAAGTACAGACAG
1 GGGCATGTAAGTGCAATCAAGGGTACCAAAGTACAAACAG
21546433 GGGCATGTAAGTGCAATCA
1 GGGCATGTAAGTGCAATCA
21546452 TCAATAATTA
Statistics
Matches: 115, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (40 bp):
GGGCATGTAAGTGCAATCAAGGGTACCAAAGTACAAACAG
Found at i:21546393 original size:20 final size:20
Alignment explanation
Indices: 21546333--21546427 Score: 59
Period size: 20 Copynumber: 4.8 Consensus size: 20
21546323 GTGCATTTAG
*
21546333 GGGTACCAAAGTACAAAC-A
1 GGGTACCGAAGTACAAACAA
* ** * *
21546352 GTGGCACATAAGTGCAATCAA
1 G-GGTACCGAAGTACAAACAA
21546373 GGGTACCGAAGTACAAACAA
1 GGGTACCGAAGTACAAACAA
* * * * *
21546393 GCGCA-CGTAAGTGCAATCAG
1 GGGTACCG-AAGTACAAACAA
21546413 GGGTACCGAAGTACA
1 GGGTACCGAAGTACA
21546428 GACAGGGGCA
Statistics
Matches: 54, Mismatches: 18, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
19 3 0.06
20 47 0.87
21 4 0.07
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (20 bp):
GGGTACCGAAGTACAAACAA
Found at i:21552994 original size:20 final size:20
Alignment explanation
Indices: 21552953--21552993 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
21552943 AAAGTTTTAT
21552953 AATTTTTTGTATAACCTTAA
1 AATTTTTTGTATAACCTTAA
*
21552973 AATTTTTTGTA-AATCTTAA
1 AATTTTTTGTATAACCTTAA
21552992 AA
1 AA
21552994 AAAATGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (20 bp):
AATTTTTTGTATAACCTTAA
Found at i:21558041 original size:16 final size:16
Alignment explanation
Indices: 21558020--21558054 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
21558010 TTTGTATCTT
21558020 ATGGTACTTGCACTTA
1 ATGGTACTTGCACTTA
*
21558036 ATGGTACTTTCACTTA
1 ATGGTACTTGCACTTA
21558052 ATG
1 ATG
21558055 AGGGTAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (16 bp):
ATGGTACTTGCACTTA
Found at i:21560356 original size:33 final size:33
Alignment explanation
Indices: 21560318--21560384 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
21560308 AACCAATAAG
21560318 TAAGGAGGAAAACCTATGTTCTTTCTAGTGCTA
1 TAAGGAGGAAAACCTATGTTCTTTCTAGTGCTA
21560351 TAAGGAGGAAAACCTATGTTCTTTCTAGTGCTA
1 TAAGGAGGAAAACCTATGTTCTTTCTAGTGCTA
21560384 T
1 T
21560385 CACACCCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (33 bp):
TAAGGAGGAAAACCTATGTTCTTTCTAGTGCTA
Found at i:21561239 original size:17 final size:17
Alignment explanation
Indices: 21561217--21561249 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21561207 CACTAACATT
*
21561217 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
21561234 AAAATGCAATGACAAT
1 AAAATGCAATGACAAT
21561250 GTGTACTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:21581419 original size:25 final size:27
Alignment explanation
Indices: 21581391--21581457 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 27
21581381 AAAATTGGTA
21581391 AGACATTTTCCATTCT-TCTCT-A-AGC
1 AGACATTTTCCATTCTCT-TCTAACAGC
**
21581416 AGACATTTTCTGTTCTCTTCTAAGCAGC
1 AGACATTTTCCATTCTCTTCTAA-CAGC
21581444 AGACATTTTCCATT
1 AGACATTTTCCATT
21581458 TCTCAAAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 17 0.50
26 2 0.06
28 15 0.44
ACGTcount: A:0.24, C:0.25, G:0.10, T:0.40
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAACAGC
Found at i:21583799 original size:15 final size:16
Alignment explanation
Indices: 21583774--21583806 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
21583764 ATTTTTCAAC
21583774 TTTCAATGCTTTCATT
1 TTTCAATGCTTTCATT
21583790 TTTC-ATGCTTTCATT
1 TTTCAATGCTTTCATT
21583805 TT
1 TT
21583807 AAGTGGTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTCAATGCTTTCATT
Found at i:21585338 original size:35 final size:36
Alignment explanation
Indices: 21585290--21585358 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
21585280 ATTTGTTAGA
21585290 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
21585326 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
21585359 ATGGTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Found at i:21586417 original size:71 final size:72
Alignment explanation
Indices: 21586298--21586440 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 72
21586288 TTGATACATT
*
21586298 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
21586363 TTGGATA
66 TTGGATA
*
21586370 TATGTGGTGTAATATTATGCAC-TAGACAATGTTGTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
21586434 TTGGATA
66 TTGGATA
21586441 ATATTATTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 47 0.68
72 22 0.32
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (72 bp):
TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
TTGGATA
Found at i:21586650 original size:14 final size:14
Alignment explanation
Indices: 21586631--21586658 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21586621 ACAATTTATT
21586631 AATATATATTAATA
1 AATATATATTAATA
21586645 AATATATATTAATA
1 AATATATATTAATA
21586659 TATGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:21586716 original size:32 final size:33
Alignment explanation
Indices: 21586680--21586764 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
21586670 AACTTTTCCG
* * *
21586680 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
21586712 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
21586744 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
21586765 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:21586763 original size:14 final size:15
Alignment explanation
Indices: 21586741--21586817 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
21586731 TTACCAAACA
21586741 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
21586755 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
21586770 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
21586790 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
21586804 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
21586818 ACTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:21586782 original size:20 final size:20
Alignment explanation
Indices: 21586757--21586796 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21586747 AATATTTTCC
*
21586757 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
21586777 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
21586797 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:21586802 original size:34 final size:35
Alignment explanation
Indices: 21586745--21586811 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
21586735 CAAACACCAG
*
21586745 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
21586780 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
21586812 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:21586818 original size:14 final size:14
Alignment explanation
Indices: 21586780--21586819 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
21586770 ACAGAAAAGT
*
21586780 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
21586794 AAATCATTTTACGG
1 AAAACATTTTACAG
21586808 AAAACATTTTAC
1 AAAACATTTTAC
21586820 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:21588764 original size:25 final size:25
Alignment explanation
Indices: 21588730--21588799 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
21588720 ACGAGACTTA
* *
21588730 AATTTCTCACACGAGTTGTGAATGT
1 AATTTCTCACACGAGCTGTGAATAT
21588755 AATTTCTCACACGAGCTGTGAATAT
1 AATTTCTCACACGAGCTGTGAATAT
*
21588780 AATTTCTCACATGAGCTGTG
1 AATTTCTCACACGAGCTGTG
21588800 GAGAATCCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (25 bp):
AATTTCTCACACGAGCTGTGAATAT
Found at i:21601188 original size:21 final size:21
Alignment explanation
Indices: 21601158--21601199 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
21601148 TGTCATTCTA
21601158 GACAACCACATCTACGTCTCT
1 GACAACCACATCTACGTCTCT
*
21601179 GACAATCACATCTACGTCTCT
1 GACAACCACATCTACGTCTCT
21601200 ATCTTCTGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.36, G:0.10, T:0.26
Consensus pattern (21 bp):
GACAACCACATCTACGTCTCT
Found at i:21606733 original size:19 final size:19
Alignment explanation
Indices: 21606708--21606754 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
21606698 GTCCAAAAAC
* *
21606708 ATACCAAAATTTTTAATTT
1 ATACCAAAATTTCTAACTT
*
21606727 TTACCAAAATTTCTAACTT
1 ATACCAAAATTTCTAACTT
21606746 ATACCAAAA
1 ATACCAAAA
21606755 CTAAAAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (19 bp):
ATACCAAAATTTCTAACTT
Found at i:21608600 original size:15 final size:17
Alignment explanation
Indices: 21608582--21608614 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
21608572 ATCCTTTTCT
21608582 TCTTTTTT-TTTT-TTA
1 TCTTTTTTATTTTCTTA
21608597 TCTTTTTTATTTTCTTA
1 TCTTTTTTATTTTCTTA
21608614 T
1 T
21608615 TTGTTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (17 bp):
TCTTTTTTATTTTCTTA
Found at i:21613805 original size:23 final size:25
Alignment explanation
Indices: 21613761--21613807 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 25
21613751 AAATATGTAG
21613761 TTTAATATATTTATTTTTAAATAAT
1 TTTAATATATTTATTTTTAAATAAT
21613786 TTTAAT-TATTTA-TTTTAAATAA
1 TTTAATATATTTATTTTTAAATAA
21613808 AAGTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 10 0.45
24 6 0.27
25 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTAATATATTTATTTTTAAATAAT
Found at i:21615232 original size:17 final size:19
Alignment explanation
Indices: 21615210--21615246 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
21615200 AAAAAAAAAC
21615210 AAAGGA-AC-AAATAATAA
1 AAAGGACACAAAATAATAA
21615227 AAAGGATCACAAAATAATAA
1 AAAGGA-CACAAAATAATAA
21615247 TGAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.68, C:0.08, G:0.11, T:0.14
Consensus pattern (19 bp):
AAAGGACACAAAATAATAA
Found at i:21620243 original size:17 final size:18
Alignment explanation
Indices: 21620207--21620254 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
21620197 CCACATCAGC
21620207 AAATGAATTTAAACTTAAA
1 AAAT-AATTTAAACTTAAA
21620226 AAATAATTTAAA-TTAAA
1 AAATAATTTAAACTTAAA
21620243 AAA-ACATTTAAA
1 AAATA-ATTTAAA
21620255 ACCCCTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 15 0.54
18 8 0.29
19 4 0.14
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATAATTTAAACTTAAA
Found at i:21620897 original size:114 final size:113
Alignment explanation
Indices: 21620736--21620941 Score: 326
Period size: 114 Copynumber: 1.8 Consensus size: 113
21620726 TAGTCACTGT
*
21620736 ATATTTAGCTGATTTGTTATAGGGTTCATAAGAAATTGTGTGATTTTTTTATTTTTTTTAATTGG
1 ATATTTAGCCGATTTGTTATAGGGTTCATAAGAAATTGTGTGATTTTTTTA-TTTTTTTAATTGG
*
21620801 ATAATAATGAAACATTTCTTTCTCATGCATGAAATGTATTTGGGTAAGC
65 ATAATAATGAAACATTTCTTTCCCATGCATGAAATGTATTTGGGTAAGC
*
21620850 ATATTTAGCCGATTTGTTTTAGGGTTCATAAGAAATTAG-G-GATTTTTTTTATTTTTTTAATTG
1 ATATTTAGCCGATTTGTTATAGGGTTCATAAGAAATT-GTGTGA-TTTTTTTATTTTTTTAATTG
* *
21620913 GATATTGATGAAACATTTCTTTCCCATGC
64 GATAATAATGAAACATTTCTTTCCCATGC
21620942 GTAAATATTA
Statistics
Matches: 85, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
113 40 0.47
114 44 0.52
115 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (113 bp):
ATATTTAGCCGATTTGTTATAGGGTTCATAAGAAATTGTGTGATTTTTTTATTTTTTTAATTGGA
TAATAATGAAACATTTCTTTCCCATGCATGAAATGTATTTGGGTAAGC
Found at i:21622437 original size:82 final size:82
Alignment explanation
Indices: 21622326--21622496 Score: 263
Period size: 82 Copynumber: 2.1 Consensus size: 82
21622316 ATTTCAAAAA
* *
21622326 AAAAAAAAAACAAAATATGTTATACTAACAAAATGATC-CTATAGCAATAAGATGTTAACCAACC
1 AAAAAATAAACAAAATATATTATACTAACAAAATGATCTC-ATAGCAATAAGATGTTAACCAACC
*
21622390 ATTTCAACAAATCATTTC
65 ATTTCAACAAAACATTTC
* * *
21622408 AAAAAATAAACAAAATATATTATGCTAACAAAATGATCTCATAGTAGTAAGATGTTAACCAACCA
1 AAAAAATAAACAAAATATATTATACTAACAAAATGATCTCATAGCAATAAGATGTTAACCAACCA
21622473 TTTCAACAAAACATTTC
66 TTTCAACAAAACATTTC
*
21622490 AACAAAT
1 AAAAAAT
21622497 CATTTCAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 80 0.99
83 1 0.01
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.26
Consensus pattern (82 bp):
AAAAAATAAACAAAATATATTATACTAACAAAATGATCTCATAGCAATAAGATGTTAACCAACCA
TTTCAACAAAACATTTC
Found at i:21622489 original size:13 final size:13
Alignment explanation
Indices: 21622471--21622510 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
21622461 GTTAACCAAC
21622471 CATTTCAACAAAA
1 CATTTCAACAAAA
*
21622484 CATTTCAACAAAT
1 CATTTCAACAAAA
21622497 CATTTCAA-AAAA
1 CATTTCAACAAAA
21622509 CA
1 CA
21622511 AACAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (13 bp):
CATTTCAACAAAA
Found at i:21622901 original size:140 final size:140
Alignment explanation
Indices: 21622642--21622904 Score: 402
Period size: 140 Copynumber: 1.9 Consensus size: 140
21622632 GACTGAAAAC
* * *
21622642 AAAAATTAGAACCCCAAATTAGATTTAAATAATTTGGAATTGACATTAAAAAGTGTTTACGATAT
1 AAAAATCAGAACCCCAAATTAGATTAAAATAATTTGGAATTGACATTAAAAAGTGTATACGATAT
* * * *
21622707 ACCTGTGATCCAATTGTGTTAGGCTGAATGCATGGTGTTTTGTTGTTCTTTTTTTGGCTTCCAGA
66 ACCTGTGATCCAATTGTATTAGGCTGAATGCATGGTATTATGTTGTTCTATTTTTGGCTTCCAGA
21622772 CTAAAACCAA
131 CTAAAACCAA
* *
21622782 AAAAATCAGAACCCCAAATTAGATTAAAATATTTTTGAATTGACATTAAAATAGTGTATACGATA
1 AAAAATCAGAACCCCAAATTAGATTAAAATAATTTGGAATTGACATTAAAA-AGTGTATACGATA
* *
21622847 TACCTGTGATCCAGTTTGTATTAGGCTGAATGCATGGTATTATGTTGTTAT-TTTTTGG
65 TACCTGTGATCCA-ATTGTATTAGGCTGAATGCATGGTATTATGTTGTTCTATTTTTGG
21622905 GTATCTAGTT
Statistics
Matches: 111, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
140 47 0.42
141 32 0.29
142 32 0.29
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (140 bp):
AAAAATCAGAACCCCAAATTAGATTAAAATAATTTGGAATTGACATTAAAAAGTGTATACGATAT
ACCTGTGATCCAATTGTATTAGGCTGAATGCATGGTATTATGTTGTTCTATTTTTGGCTTCCAGA
CTAAAACCAA
Found at i:21625160 original size:54 final size:54
Alignment explanation
Indices: 21625078--21625186 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
21625068 CCACTTCCCT
* *
21625078 AACCCTCTCCTCATCACATCCATCACTCTCACCACCTTCACTGACAGCAACATC
1 AACCCTCTCCTCACCACATCCATCACTCTCACCACCTTCACTGACAACAACATC
* *
21625132 AACCCTCTCTTCACCACCTCCATCACTCTCACCACCTTCACTGACAACAACATC
1 AACCCTCTCCTCACCACATCCATCACTCTCACCACCTTCACTGACAACAACATC
21625186 A
1 A
21625187 TCACCCTCCC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.28, C:0.47, G:0.03, T:0.22
Consensus pattern (54 bp):
AACCCTCTCCTCACCACATCCATCACTCTCACCACCTTCACTGACAACAACATC
Found at i:21627765 original size:9 final size:9
Alignment explanation
Indices: 21627743--21627778 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
21627733 TGGTTAGTCG
21627743 TTAACTTGTT
1 TTAA-TTGTT
*
21627753 TTAATTTTT
1 TTAATTGTT
21627762 TTAATTGTT
1 TTAATTGTT
21627771 TTAATTGT
1 TTAATTGT
21627779 GGGTAAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.67
Consensus pattern (9 bp):
TTAATTGTT
Found at i:21629235 original size:43 final size:43
Alignment explanation
Indices: 21629153--21629238 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
21629143 CATGGGTTTA
* * * *
21629153 TATGTATGTTTTTATGGAACTCCTATTTTATATGTTTAGTATG
1 TATGTATGCTTTTATGGAACTCCAATCTTATATGATTAGTATG
*
21629196 TATGTATGCTTTTATGGAGCTTCCAATCTTATAT-ATTAGTATG
1 TATGTATGCTTTTATGGAAC-TCCAATCTTATATGATTAGTATG
21629239 CGATGATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 26 0.70
44 11 0.30
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.50
Consensus pattern (43 bp):
TATGTATGCTTTTATGGAACTCCAATCTTATATGATTAGTATG
Found at i:21632320 original size:28 final size:27
Alignment explanation
Indices: 21632276--21632329 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
21632266 GAGTTTGCAC
* * *
21632276 TTTTTTTTTAATGTGGTAGTTGTATTA
1 TTTTTTTTCAATATGGTACTTGTATTA
21632303 TTTTTTGTTCAATATGGTACTTGTATT
1 TTTTTT-TTCAATATGGTACTTGTATT
21632330 TGACAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.19, C:0.04, G:0.17, T:0.61
Consensus pattern (27 bp):
TTTTTTTTCAATATGGTACTTGTATTA
Found at i:21637467 original size:14 final size:14
Alignment explanation
Indices: 21637448--21637475 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21637438 ACCAATAAGT
21637448 GCATCAGTAAATGG
1 GCATCAGTAAATGG
21637462 GCATCAGTAAATGG
1 GCATCAGTAAATGG
21637476 TATGAGTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (14 bp):
GCATCAGTAAATGG
Found at i:21638149 original size:21 final size:21
Alignment explanation
Indices: 21638125--21638165 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21638115 ACCTTTTCTA
**
21638125 AAGTTAAAAGTCAAAACCATT
1 AAGTTAAAAGGAAAAACCATT
21638146 AAGTTAAAAGGAAAAACCAT
1 AAGTTAAAAGGAAAAACCAT
21638166 AATATTGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGAAAAACCATT
Found at i:21639119 original size:13 final size:13
Alignment explanation
Indices: 21639101--21639127 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21639091 TCTGACTTAG
21639101 TTCCTTAAGTTAC
1 TTCCTTAAGTTAC
21639114 TTCCTTAAGTTAC
1 TTCCTTAAGTTAC
21639127 T
1 T
21639128 ATAAAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (13 bp):
TTCCTTAAGTTAC
Found at i:21645481 original size:13 final size:14
Alignment explanation
Indices: 21645455--21645484 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
21645445 GATGTAAGCT
21645455 AAGGAATAAGAGGA
1 AAGGAATAAGAGGA
21645469 AAGGAAT-AGAGGA
1 AAGGAATAAGAGGA
21645482 AAG
1 AAG
21645485 AAAACTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
AAGGAATAAGAGGA
Found at i:21664109 original size:15 final size:15
Alignment explanation
Indices: 21664089--21664118 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21664079 AGAACTTATG
21664089 TAACACCCCTTACTC
1 TAACACCCCTTACTC
21664104 TAACACCCCTTACTC
1 TAACACCCCTTACTC
21664119 AGGCCCGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.47, G:0.00, T:0.27
Consensus pattern (15 bp):
TAACACCCCTTACTC
Found at i:21665523 original size:50 final size:50
Alignment explanation
Indices: 21665409--21665657 Score: 320
Period size: 50 Copynumber: 4.8 Consensus size: 50
21665399 GATAATAACT
* * **
21665409 TGCCAAAGCCATGTCCCATACATGGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
21665460 TGCCCATGCCATGTCCTAGACATGGTCTTATA-GGGAACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGG-ACCTCTCATCTCGG
*
21665510 TGCCAACGACATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
21665560 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
21665615 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
21665658 TTACCCAAAT
Statistics
Matches: 175, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
50 97 0.55
51 31 0.18
53 5 0.03
55 2 0.01
56 40 0.23
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:21666045 original size:29 final size:31
Alignment explanation
Indices: 21665995--21666052 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
21665985 CCTCGACTCT
*
21665995 AACTTTTTCAAAATTACGA-TTTTGCCCCTA
1 AACTTTTGCAAAATTACGATTTTTGCCCCTA
* *
21666025 AACTTTTGCATAATTA-TATTTTTGCCCC
1 AACTTTTGCAAAATTACGATTTTTGCCCC
21666053 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (31 bp):
AACTTTTGCAAAATTACGATTTTTGCCCCTA
Found at i:21685383 original size:25 final size:25
Alignment explanation
Indices: 21685355--21685436 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
21685345 GTTCTGACCC
21685355 ACAGCTCGTGAGAGCATACCGATTT
1 ACAGCTCGTGAGAGCATACCGATTT
* *
21685380 ACAGCTGGTGAGGGCATACCGATTT
1 ACAGCTCGTGAGAGCATACCGATTT
* * *
21685405 ACAGCTCGAGTA-AACATACCGATTC
1 ACAGCTCGTG-AGAGCATACCGATTT
21685430 ACAGCTC
1 ACAGCTC
21685437 TATGAGCATA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
25 48 0.98
26 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACCGATTT
Found at i:21686595 original size:12 final size:12
Alignment explanation
Indices: 21686578--21686607 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21686568 TCAGGCTATT
21686578 ACACGGCCTAGC
1 ACACGGCCTAGC
*
21686590 ACACGGCCTGGC
1 ACACGGCCTAGC
21686602 ACACGG
1 ACACGG
21686608 GCGTGCGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:21694529 original size:18 final size:18
Alignment explanation
Indices: 21694506--21694543 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
21694496 TTTCCATGTG
21694506 TAACATTTTATTTAAGGT
1 TAACATTTTATTTAAGGT
*
21694524 TAACATTTTATTTAGGGT
1 TAACATTTTATTTAAGGT
21694542 TA
1 TA
21694544 GGGTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (18 bp):
TAACATTTTATTTAAGGT
Found at i:21694634 original size:17 final size:17
Alignment explanation
Indices: 21694612--21694693 Score: 91
Period size: 16 Copynumber: 4.9 Consensus size: 17
21694602 GTTTTTATAT
21694612 ATTTTTTATAATTTTTA
1 ATTTTTTATAATTTTTA
*
21694629 ATTTTTTAT-A-TATTA
1 ATTTTTTATAATTTTTA
21694644 ATTTTTTTATAATTTTTA
1 A-TTTTTTATAATTTTTA
**
21694662 A-TTTTTATATATAATT-
1 ATTTTTTATA-ATTTTTA
21694678 ATTTTTTATAATTTTT
1 ATTTTTTATAATTTTT
21694694 TGAGATGTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
15 5 0.09
16 22 0.41
17 22 0.41
18 5 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTTATAATTTTTA
Found at i:21694667 original size:32 final size:34
Alignment explanation
Indices: 21694611--21694693 Score: 136
Period size: 33 Copynumber: 2.5 Consensus size: 34
21694601 TGTTTTTATA
21694611 TATTTTTTATAATTTTTAATTTTTTATATATTAA-
1 TATTTTTTATAATTTTTAATTTTTTATATA-TAAT
21694645 T-TTTTTTATAATTTTTAA-TTTTTATATATAAT
1 TATTTTTTATAATTTTTAATTTTTTATATATAAT
21694677 TATTTTTTATAATTTTT
1 TATTTTTTATAATTTTT
21694694 TGAGATGTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
31 3 0.06
32 11 0.23
33 32 0.68
34 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (34 bp):
TATTTTTTATAATTTTTAATTTTTTATATATAAT
Found at i:21697033 original size:16 final size:16
Alignment explanation
Indices: 21697012--21697066 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
21697002 TTGAAAATGA
* *
21697012 ATGCATGCATTCCTGG
1 ATGCATGCATGCATGG
*
21697028 ATGCATGGATGCATGG
1 ATGCATGCATGCATGG
* *
21697044 ATGCATGGATGCATGT
1 ATGCATGCATGCATGG
21697060 ATGCATG
1 ATGCATG
21697067 TATGTATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (16 bp):
ATGCATGCATGCATGG
Found at i:21697038 original size:8 final size:8
Alignment explanation
Indices: 21697025--21697066 Score: 75
Period size: 8 Copynumber: 5.2 Consensus size: 8
21697015 CATGCATTCC
21697025 TGGATGCA
1 TGGATGCA
21697033 TGGATGCA
1 TGGATGCA
21697041 TGGATGCA
1 TGGATGCA
21697049 TGGATGCA
1 TGGATGCA
*
21697057 TGTATGCA
1 TGGATGCA
21697065 TG
1 TG
21697067 TATGTATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.29
Consensus pattern (8 bp):
TGGATGCA
Found at i:21697073 original size:4 final size:4
Alignment explanation
Indices: 21697056--21697165 Score: 211
Period size: 4 Copynumber: 27.5 Consensus size: 4
21697046 GCATGGATGC
*
21697056 ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
21697104 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
21697152 ATGT ATGT ATGT AT
1 ATGT ATGT ATGT AT
21697166 TTGAAGTCTT
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 104 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:21698651 original size:33 final size:33
Alignment explanation
Indices: 21698609--21698673 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
21698599 AAAATATTTT
21698609 AAATATTTTAATATAATTAAATATAAAAATAAA
1 AAATATTTTAATATAATTAAATATAAAAATAAA
* *
21698642 AAATCTTTTAATATAATTTAATATAAAAATAA
1 AAATATTTTAATATAATTAAATATAAAAATAA
21698674 TTATATTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (33 bp):
AAATATTTTAATATAATTAAATATAAAAATAAA
Found at i:21706244 original size:34 final size:35
Alignment explanation
Indices: 21706189--21706255 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
21706179 CAAACACCAA
* *
21706189 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGGAAATCATTTTACAGAAAAGT
*
21706224 AAAACATTTTCC-GGAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGGAAATCATTTTACAGAAAA
21706256 TATTTTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGGAAATCATTTTACAGAAAAGT
Found at i:21706647 original size:9 final size:9
Alignment explanation
Indices: 21706633--21706776 Score: 57
Period size: 9 Copynumber: 15.7 Consensus size: 9
21706623 ATAAAGTGCA
21706633 AAAAATTAT
1 AAAAATTAT
*
21706642 AAAAATGATT
1 AAAAATTA-T
* *
21706652 ATAAATGA-
1 AAAAATTAT
21706660 AGAAAATTAT
1 A-AAAATTAT
*
21706670 ATAAATTAT
1 AAAAATTAT
21706679 -AAAATTAT
1 AAAAATTAT
*
21706687 TAAAATTGCA-
1 AAAAATT--AT
*
21706697 AAAAAGTATT
1 AAAAATTA-T
21706707 AAAAATTTAT
1 AAAAA-TTAT
* * *
21706717 TAAAATAAC
1 AAAAATTAT
21706726 AAAATATTAT
1 AAAA-ATTAT
*
21706736 ATAAATTAT
1 AAAAATTAT
*
21706745 GAAAA--AT
1 AAAAATTAT
21706752 AAAAA-TAT
1 AAAAATTAT
*
21706760 GAAAAATATTT
1 -AAAAAT-TAT
21706771 AAAAAT
1 AAAAAT
21706777 GTAGACAATT
Statistics
Matches: 101, Mismatches: 20, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
7 6 0.06
8 11 0.11
9 43 0.43
10 36 0.36
11 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:21706697 original size:64 final size:64
Alignment explanation
Indices: 21706629--21706777 Score: 157
Period size: 65 Copynumber: 2.3 Consensus size: 64
21706619 ATATATAAAG
* *
21706629 TGCAAAAAATTATAAAAATGATTATAAATGAA-GAAA-ATTATATAAATTAT-AAAATTATTAAA
1 TGCAAAAAATTATAAAAATGATTA-AAAT-AACAAAATATTATATAAATTATGAAAA--ATAAAA
21706691 AT-
62 ATA
* *
21706693 TGCAAAAAAGTATTAAAAATTTATTAAAATAACAAAATATTATATAAATTATGAAAAATAAAAAT
1 TGCAAAAAATTA-TAAAAA-TGATTAAAATAACAAAATATTATATAAATTATGAAAAATAAAAAT
21706758 A
64 A
21706759 TG-AAAAATATT-TAAAAATG
1 TGCAAAAA-ATTATAAAAATG
21706778 TAGACAATTA
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
63 1 0.01
64 19 0.26
65 25 0.35
66 23 0.32
67 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (64 bp):
TGCAAAAAATTATAAAAATGATTAAAATAACAAAATATTATATAAATTATGAAAAATAAAAATA
Found at i:21707093 original size:19 final size:20
Alignment explanation
Indices: 21707057--21707094 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21707047 TTCTTATAAT
21707057 TTTGTTTCATATATTTTTAA
1 TTTGTTTCATATATTTTTAA
*
21707077 TTTGTTTTATA-ATTTTTA
1 TTTGTTTCATATATTTTTA
21707095 TGCTTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTGTTTCATATATTTTTAA
Found at i:21707242 original size:32 final size:33
Alignment explanation
Indices: 21707201--21707278 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 33
21707191 AAATCATATC
*
21707201 TTTTTATAATTACATAA-TTTTTAAATTTTT-TA
1 TTTTAATAATT-CATAATTTTTTAAATTTTTATA
* *
21707233 TTTTAATAATTCTTAATTTTTTAAGTTTTTAGTA
1 TTTTAATAATTCATAATTTTTTAAATTTTTA-TA
21707267 TTTTATATAATT
1 TTTTA-ATAATT
21707279 TTTAGTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 4 0.10
32 22 0.56
34 7 0.18
35 6 0.15
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (33 bp):
TTTTAATAATTCATAATTTTTTAAATTTTTATA
Found at i:21707290 original size:27 final size:27
Alignment explanation
Indices: 21707250--21707307 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
21707240 AATTCTTAAT
21707250 TTTTTAAGTTTTTAGTA-TTTTATATAA
1 TTTTTAAGTTTTTA-TATTTTTATATAA
*
21707277 TTTTT-AGTTATTTATATTTTTTTATAA
1 TTTTTAAGTT-TTTATATTTTTATATAA
21707304 TTTT
1 TTTT
21707308 CTATATCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTTTAAGTTTTTATATTTTTATATAA
Found at i:21707297 original size:35 final size:34
Alignment explanation
Indices: 21707201--21707290 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 34
21707191 AAATCATATC
* * *
21707201 TTTTTATAATTACATAATT-TTTAAATTTTT--TA
1 TTTTAATAATT-CTTAATTATTTAAGTTTTTAGTA
*
21707233 TTTTAATAATTCTTAATTTTTTAAGTTTTTAGTA
1 TTTTAATAATTCTTAATTATTTAAGTTTTTAGTA
* *
21707267 TTTTATATAATTTTTAGTTATTTA
1 TTTTA-ATAATTCTTAATTATTTA
21707291 TATTTTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
31 6 0.12
32 20 0.42
34 7 0.15
35 15 0.31
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.63
Consensus pattern (34 bp):
TTTTAATAATTCTTAATTATTTAAGTTTTTAGTA
Found at i:21707299 original size:19 final size:19
Alignment explanation
Indices: 21707231--21707293 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
21707221 TTAAATTTTT
*
21707231 TATTTTA-ATAATTCTTA-
1 TATTTTATATAATTTTTAG
21707248 -ATTTT-T-TAAGTTTTTAG
1 TATTTTATATAA-TTTTTAG
21707265 TATTTTATATAATTTTTAG
1 TATTTTATATAATTTTTAG
21707284 T-TATTTATAT
1 TAT-TTTATAT
21707294 TTTTTTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
15 3 0.08
16 10 0.26
18 6 0.16
19 16 0.42
20 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (19 bp):
TATTTTATATAATTTTTAG
Found at i:21707318 original size:20 final size:20
Alignment explanation
Indices: 21707289--21707327 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21707279 TTTAGTTATT
*
21707289 TATATTTTTTTATAATTTTC
1 TATATCTTTTTATAATTTTC
21707309 TATATCTTTTTATAATTTT
1 TATATCTTTTTATAATTTT
21707328 TTTACTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TATATCTTTTTATAATTTTC
Found at i:21707328 original size:10 final size:10
Alignment explanation
Indices: 21707287--21707329 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
21707277 TTTTTAGTTA
*
21707287 TTTATATTTT
1 TTTATAATTT
21707297 TTTATAATTT
1 TTTATAATTT
*
21707307 TCTAT-ATCTT
1 TTTATAAT-TT
21707317 TTTATAATTT
1 TTTATAATTT
21707327 TTT
1 TTT
21707330 TACTTTTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 2 0.07
10 24 0.86
11 2 0.07
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATAATTT
Found at i:21709641 original size:22 final size:21
Alignment explanation
Indices: 21709598--21709642 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
21709588 GTATAATGAG
*
21709598 AATTTTTAAAAATTTATGGAA
1 AATTTTTAAAAATTTATAGAA
21709619 AATTTTCTAAAAATTTCA-AGAA
1 AATTTT-TAAAAATTT-ATAGAA
21709641 AA
1 AA
21709643 AAAATCATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 14 0.67
23 1 0.05
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (21 bp):
AATTTTTAAAAATTTATAGAA
Found at i:21711893 original size:8 final size:8
Alignment explanation
Indices: 21711882--21711906 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21711872 TATATTTACC
21711882 TTTTAAAA
1 TTTTAAAA
21711890 TTTTAAAA
1 TTTTAAAA
21711898 TTTTAAAA
1 TTTTAAAA
21711906 T
1 T
21711907 ATTTTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:21713074 original size:6 final size:6
Alignment explanation
Indices: 21713058--21713096 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
21713048 TCTTACTTTA
*
21713058 CCCATTC CCCATC CCCATC CCCATC CCCATC CCCGTC CC
1 CCCA-TC CCCATC CCCATC CCCATC CCCATC CCCATC CC
21713097 TCCTCATCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.13, C:0.67, G:0.03, T:0.18
Consensus pattern (6 bp):
CCCATC
Found at i:21716306 original size:23 final size:24
Alignment explanation
Indices: 21716270--21716316 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
21716260 AATAAAATTC
* *
21716270 TTCTCTTAATAATAA-ATTTTTAT
1 TTCTCTTAACAATAAGAGTTTTAT
*
21716293 TTCTCTTTACAATAAGAGTTTTAT
1 TTCTCTTAACAATAAGAGTTTTAT
21716317 ATATTGAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (24 bp):
TTCTCTTAACAATAAGAGTTTTAT
Found at i:21717565 original size:25 final size:27
Alignment explanation
Indices: 21717506--21717557 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
21717496 CATGAATTTG
*
21717506 ATAAAAATAGAAAATAAATATTATATT
1 ATAAAAATAGAAAATAAATAATATATT
21717533 ATAAAAAT-GAAAATAAA-AATATATT
1 ATAAAAATAGAAAATAAATAATATATT
21717558 TTCAAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.29
26 9 0.38
27 8 0.33
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (27 bp):
ATAAAAATAGAAAATAAATAATATATT
Found at i:21722448 original size:38 final size:37
Alignment explanation
Indices: 21722397--21722488 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 37
21722387 CTCCAAAAAT
21722397 AATATTATTTTAATAG-ATTTAATATTAGA-TT-ATATTA
1 AATATTATTTTAATAGTATTT--TATTA-ATTTAATATTA
21722434 AATACTTATTTTAATAGTATTTTATTAATTTAATATTA
1 AATA-TTATTTTAATAGTATTTTATTAATTTAATATTA
21722472 AAGTGATTATTTTAATA
1 AA-T-ATTATTTTAATA
21722489 TTAAATTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
36 1 0.02
37 11 0.22
38 20 0.41
39 16 0.33
40 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (37 bp):
AATATTATTTTAATAGTATTTTATTAATTTAATATTA
Found at i:21723431 original size:22 final size:20
Alignment explanation
Indices: 21723398--21723440 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
21723388 AACAACTATG
21723398 AAACTAAATAAAACCATAAA
1 AAACTAAATAAAACCATAAA
*
21723418 AAACATAAACTAAAACCCTAAA
1 AAAC-TAAA-TAAAACCATAAA
21723440 A
1 A
21723441 CTATAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 4 0.20
22 12 0.60
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.14
Consensus pattern (20 bp):
AAACTAAATAAAACCATAAA
Found at i:21723482 original size:17 final size:17
Alignment explanation
Indices: 21723430--21723483 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
21723420 ACATAAACTA
*
21723430 AAACCCTAAAACTATAG
1 AAACCCTAAAACTAAAG
** *
21723447 AAAAACTAAAAGATGAAAG
1 AAACCCTAAAA-CT-AAAG
21723466 AAACCCTAAAACTAAAG
1 AAACCCTAAAACTAAAG
21723483 A
1 A
21723484 GCTCTTTAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
17 14 0.50
18 2 0.07
19 12 0.43
ACGTcount: A:0.61, C:0.17, G:0.09, T:0.13
Consensus pattern (17 bp):
AAACCCTAAAACTAAAG
Found at i:21726401 original size:14 final size:14
Alignment explanation
Indices: 21726384--21726418 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
21726374 GCTTGATTAA
21726384 ATATGTGTTACATG
1 ATATGTGTTACATG
*
21726398 ATATATGTTACATG
1 ATATGTGTTACATG
21726412 AGTATGT
1 A-TATGT
21726419 AAATGCTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (14 bp):
ATATGTGTTACATG
Found at i:21728777 original size:25 final size:25
Alignment explanation
Indices: 21728716--21728813 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 25
21728706 TCAATACCTG
* * * *
21728716 GCTCTCATGAGGTTCCCGATATTCG
1 GCTCACATGAGCTTCCCGATATACA
* *
21728741 GCTCGCAAGAGCTTCCCGATATACA
1 GCTCACATGAGCTTCCCGATATACA
* *
21728766 GCTCATATGAGCTTTCCG-T-TACTTA
1 GCTCACATGAGCTTCCCGATATAC--A
*
21728791 GCTCACATGAGCTTCCCGTTATA
1 GCTCACATGAGCTTCCCGATATA
21728814 TGGCTCGGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
23 3 0.05
24 1 0.02
25 51 0.88
26 1 0.02
27 2 0.03
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (25 bp):
GCTCACATGAGCTTCCCGATATACA
Found at i:21730565 original size:26 final size:26
Alignment explanation
Indices: 21730536--21730588 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
21730526 AACCAACCCT
21730536 TACCGATTGTCTAACCGCAATATAGG
1 TACCGATTGTCTAACCGCAATATAGG
**
21730562 TACCGATTGTCTAACCGTGATATAGG
1 TACCGATTGTCTAACCGCAATATAGG
21730588 T
1 T
21730589 TTTCACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (26 bp):
TACCGATTGTCTAACCGCAATATAGG
Found at i:21731575 original size:21 final size:21
Alignment explanation
Indices: 21731548--21731598 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
21731538 TGAGCCTAGG
*
21731548 CCGTGTGGCTTAGAAACATGA
1 CCGTGTGGCTCAGAAACATGA
*
21731569 CTGTGTGGCTCAGAAACATGA
1 CCGTGTGGCTCAGAAACATGA
21731590 CCGTGTGGC
1 CCGTGTGGC
21731599 CAAACCGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.24
Consensus pattern (21 bp):
CCGTGTGGCTCAGAAACATGA
Found at i:21733394 original size:16 final size:16
Alignment explanation
Indices: 21733364--21733406 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
21733354 GAATTTACAA
**
21733364 CTTAAACATTTAAATC
1 CTTAAACATCAAAATC
21733380 CTTAAACATCAAAATC
1 CTTAAACATCAAAATC
* *
21733396 ATTAAAAATCA
1 CTTAAACATCA
21733407 GTTTACAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (16 bp):
CTTAAACATCAAAATC
Found at i:21747753 original size:31 final size:31
Alignment explanation
Indices: 21747714--21747789 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
21747704 GTTACAACTG
**
21747714 GTCACTGAACTATTTGAAAGTTTTCATTTAA
1 GTCACTGAACTATTCAAAAGTTTTCATTTAA
* * *
21747745 GTTACTGAACTATTCAAAAGTTTTTATTTAT
1 GTCACTGAACTATTCAAAAGTTTTCATTTAA
*
21747776 GTCACTGAGCTATT
1 GTCACTGAACTATT
21747790 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAGTTTTCATTTAA
Found at i:21759966 original size:16 final size:16
Alignment explanation
Indices: 21759945--21760010 Score: 123
Period size: 16 Copynumber: 4.1 Consensus size: 16
21759935 TGGTTCGCTC
21759945 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
*
21759961 TATTGGATTAGAAGTG
1 TATTGGATTAGAGGTG
21759977 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
21759993 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
21760009 TA
1 TA
21760011 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TATTGGATTAGAGGTG
Found at i:21780145 original size:22 final size:20
Alignment explanation
Indices: 21780115--21780154 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21780105 ATCGGTTTAT
*
21780115 AAAAAAATCTTTATAAAAACA
1 AAAAAAATCCTTA-AAAAACA
21780136 AAAAGAAATCCTTAAAAAA
1 AAAA-AAATCCTTAAAAAA
21780155 TTCGAGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.68, C:0.10, G:0.03, T:0.20
Consensus pattern (20 bp):
AAAAAAATCCTTAAAAAACA
Found at i:21797791 original size:40 final size:40
Alignment explanation
Indices: 21797736--21797837 Score: 141
Period size: 40 Copynumber: 2.5 Consensus size: 40
21797726 TGGCATCAGT
* *
21797736 GGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGC
1 GGCGCTTCTTGAAAAACGCCGCTATAGATCGACCATTAGC
*
21797776 GGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGC
1 GGCGCTTCTTGAAAAACGCCGCTATAGATCGACCATTAGC
* * * *
21797816 GGCGGTTGTTTAAAAATGCCGC
1 GGCGCTTCTTGAAAAACGCCGC
21797838 AAAAGATTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
GGCGCTTCTTGAAAAACGCCGCTATAGATCGACCATTAGC
Found at i:21797803 original size:154 final size:153
Alignment explanation
Indices: 21797598--21798087 Score: 567
Period size: 154 Copynumber: 3.2 Consensus size: 153
21797588 TAACAAACGC
* * * * * * *
21797598 CGCCGCTATAGATTGAGCATTAGCGGCGCTTTTTGAGAAATGCCACTATAGGTTGAACATTAGCG
1 CGCCGCTATAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
* *
21797663 GCGCTT-TCTGAAAATCGCCGCAAAAAAATTAAGCACAACACGTGGTTTTATGTTGAGCTTTAGT
66 GCGCTTGT-TGAAAATCGCCGCAAAAAAATTAAGCACAACACGTCGTTTTATATTGAGCTTTAGT
*
21797727 GGCATCAGTGGCGCTTTTTGAAAAA
130 GGCATTAGTGGCGCTTTTTG-AAAA
21797752 CGCCGCTATAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
1 CGCCGCTATAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
* * * ** * *
21797817 GCGGTTGTTTAAAAAT-GCCGC-AAAAGATTAAGCACAACTTGTCGTTCTATTTTGAGCTTTAGT
66 GCGCTTG-TTGAAAATCGCCGCAAAAAAATTAAGCACAACACGTCGTTTTATATTGAGCTTTAGT
* * *
21797880 GACATTAGTGACAC-TTTTGTAAAA
130 GGCATTAGTGGCGCTTTTTG-AAAA
* * * * * *
21797904 TGCCGTTACAGATCGAGCATTAGCGGTGCTTCTTGAAAAACGTCGCTATAGGTCGGCCATTAGCG
1 CGCCGCTATAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
* * *
21797969 GCGCTTGTTGAAAAAC-CCTGCAAAAAATTTAAGCACAACGCCGTCGTTTTATATTGAGCTTTTA
66 GCGCTTGTTGAAAATCGCC-GCAAAAAAATTAAGCACAAC-ACGTCGTTTTATATTGAGC-TTTA
** *
21798033 GTGGCATTAACGGTGCTTTGTTGAAAA
128 GTGGCATTAGTGGCGCTTT-TTGAAAA
* *
21798060 CGCTGATATAGATCGAGCATTAGCGGCG
1 CGCCGCTATAGATCGAGCATTAGCGGCG
21798088 TTTTTCCTAA
Statistics
Matches: 281, Mismatches: 46, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
151 8 0.03
152 76 0.27
153 61 0.22
154 83 0.30
155 20 0.07
156 30 0.11
157 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (153 bp):
CGCCGCTATAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
GCGCTTGTTGAAAATCGCCGCAAAAAAATTAAGCACAACACGTCGTTTTATATTGAGCTTTAGTG
GCATTAGTGGCGCTTTTTGAAAA
Found at i:21797938 original size:152 final size:153
Alignment explanation
Indices: 21797598--21798087 Score: 529
Period size: 152 Copynumber: 3.2 Consensus size: 153
21797588 TAACAAACGC
* * * * * * * *
21797598 CGCCGCTATAGATTGAGCATTAGCGGCGCTTTTTGAGAAATGCCACTATAGGTTGAACATTAGCG
1 CGCCGCTACAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
* * * *
21797663 GCGCTT-TCTGAAAATCGCCGCAAAAAAATTAAGCACAACACGTGGTTTTATGTTGAGCTTTAGT
66 GCGCTTGTTTAAAAAT-GCCGC-AAAAAATTAAGCACAACACGTCGTTTTATATTGAGCTTTAGT
* * *
21797727 GGCATCAGTGGCGCTTTTTGAAAAA
129 GGCATTAGTGACACTTTTTGAAAAA
*
21797752 CGCCGCTATAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
1 CGCCGCTACAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
* * ** * * *
21797817 GCGGTTGTTTAAAAATGCCGCAAAAGATTAAGCACAACTTGTCGTTCTATTTTGAGCTTTAGTGA
66 GCGCTTGTTTAAAAATGCCGCAAAAAATTAAGCACAACACGTCGTTTTATATTGAGCTTTAGTGG
*
21797882 CATTAGTGACAC-TTTTGTAAAA
131 CATTAGTGACACTTTTTGAAAAA
* * * * *
21797904 TGCCGTTACAGATCGAGCATTAGCGGTGCTTCTTGAAAAACGTCGCTATAGGTCGGCCATTAGCG
1 CGCCGCTACAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
* * *
21797969 GCGCTTGTTGAAAAA-CCCTGCAAAAAATTTAAGCACAACGCCGTCGTTTTATATTGAGCTTTTA
66 GCGCTTGTTTAAAAATGCC-GCAAAAAA-TTAAGCACAAC-ACGTCGTTTTATATTGAGC-TTTA
** ***
21798033 GTGGCATTAACGGTGCTTTGTTG-AAAA
127 GTGGCATTAGTGACACTTT-TTGAAAAA
* * *
21798060 CGCTGATATAGATCGAGCATTAGCGGCG
1 CGCCGCTACAGATCGAGCATTAGCGGCG
21798088 TTTTTCCTAA
Statistics
Matches: 283, Mismatches: 46, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
151 2 0.01
152 88 0.31
153 57 0.20
154 83 0.29
155 21 0.07
156 29 0.10
157 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (153 bp):
CGCCGCTACAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTATAGGTCGACCATTAGCG
GCGCTTGTTTAAAAATGCCGCAAAAAATTAAGCACAACACGTCGTTTTATATTGAGCTTTAGTGG
CATTAGTGACACTTTTTGAAAAA
Found at i:21798527 original size:20 final size:21
Alignment explanation
Indices: 21798494--21798554 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
21798484 GTTAAGAGTT
*
21798494 TAGTGTTTACGATTTAGGGTG
1 TAGTGTTTATGATTTAGGGTG
* *
21798515 TAG-GTTTATGATTTAGTGTT
1 TAGTGTTTATGATTTAGGGTG
*
21798535 TAGTGTTTATGGTTTAGGGT
1 TAGTGTTTATGATTTAGGGT
21798555 TTTAAGGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.49
Consensus pattern (21 bp):
TAGTGTTTATGATTTAGGGTG
Found at i:21798543 original size:14 final size:13
Alignment explanation
Indices: 21798491--21798566 Score: 55
Period size: 14 Copynumber: 5.5 Consensus size: 13
21798481 AATGTTAAGA
21798491 GTTTAGTGTTTACG
1 GTTTAGTGTTTA-G
* * *
21798505 ATTTAGGGTGTAG
1 GTTTAGTGTTTAG
21798518 GTTTA-TGATTTAG
1 GTTTAGTG-TTTAG
21798531 TGTTTAGTGTTTATG
1 -GTTTAGTGTTTA-G
*
21798546 GTTTAGGGTTTTAAG
1 GTTTAGTG-TTT-AG
21798561 GTTTAG
1 GTTTAG
21798567 AGGTTAATAG
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
12 1 0.02
13 9 0.18
14 25 0.51
15 13 0.27
16 1 0.02
ACGTcount: A:0.18, C:0.01, G:0.30, T:0.50
Consensus pattern (13 bp):
GTTTAGTGTTTAG
Found at i:21798563 original size:15 final size:15
Alignment explanation
Indices: 21798540--21798615 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
21798530 GTGTTTAGTG
*
21798540 TTTATGGTTTAGGGT
1 TTTAAGGTTTAGGGT
21798555 TTTAAGGTTTAGAGG-
1 TTTAAGGTTTAG-GGT
*
21798570 -TTAATAGTTTAGGG-
1 TTTAA-GGTTTAGGGT
* *
21798584 TTTAGGGTTTAAGGT
1 TTTAAGGTTTAGGGT
*
21798599 TTTAAGGTTTATGGT
1 TTTAAGGTTTAGGGT
21798614 TT
1 TT
21798616 AGCTAAAAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
14 13 0.26
15 35 0.70
16 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (15 bp):
TTTAAGGTTTAGGGT
Done.