Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 56 of 117
Found at i:12606163 original size:21 final size:21
Alignment explanation
Indices: 12606139--12606189 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
12606129 TAGACATATA
*
12606139 TTATTTTAATATAATAAATTT
1 TTATTTTAATATAAAAAATTT
*
12606160 TTATTTTAATTTAAAAAATTT
1 TTATTTTAATATAAAAAATTT
*
12606181 ATATTTTAA
1 TTATTTTAA
12606190 ACTCAATAGG
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTTTAATATAAAAAATTT
Found at i:12606411 original size:19 final size:19
Alignment explanation
Indices: 12606369--12606411 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
12606359 AATCCTGTTT
** *
12606369 ATTTTTTTTCCTTTCATCA
1 ATTTTTTTTAATTTCATAA
*
12606388 TTTTTTTTTAATTTCATAA
1 ATTTTTTTTAATTTCATAA
12606407 ATTTT
1 ATTTT
12606412 GCAAAAAATA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTTTTAATTTCATAA
Found at i:12607210 original size:33 final size:33
Alignment explanation
Indices: 12607173--12607238 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
12607163 TTTTTTTTTT
*
12607173 TTGCTATCATCTCTCTTTCTTATAAAAGAAAAA
1 TTGCTATCATCTCTCTTTCCTATAAAAGAAAAA
* * * * *
12607206 TTGCTCTCATTTGTCTTTCCTGTAAAATAAAAA
1 TTGCTATCATCTCTCTTTCCTATAAAAGAAAAA
12607239 AGGAAAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (33 bp):
TTGCTATCATCTCTCTTTCCTATAAAAGAAAAA
Found at i:12619971 original size:2 final size:2
Alignment explanation
Indices: 12619964--12619998 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12619954 TCCAATCATA
* *
12619964 AT AT AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12619999 ATTGTTGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:12631123 original size:12 final size:12
Alignment explanation
Indices: 12631106--12631130 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12631096 AAACAAAATT
12631106 AAATAAATATAA
1 AAATAAATATAA
12631118 AAATAAATATAA
1 AAATAAATATAA
12631130 A
1 A
12631131 TGCTGACCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATATAA
Found at i:12637167 original size:17 final size:17
Alignment explanation
Indices: 12637109--12637168 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
12637099 GCATATTCAT
12637109 TTATTAATTTAAAGTTTA
1 TTATTAATTTAAA-TTTA
* *
12637127 TTTTTTAATTCAAATTTA
1 -TTATTAATTTAAATTTA
** *
12637145 AAATTAATTTTAATTTA
1 TTATTAATTTAAATTTA
12637162 TTATTAA
1 TTATTAA
12637169 AAAATTAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 17 0.53
18 4 0.12
19 11 0.34
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATTAATTTAAATTTA
Found at i:12637231 original size:34 final size:34
Alignment explanation
Indices: 12637166--12637231 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
12637156 AATTTATTAT
**
12637166 TAAAAAATTAAATTAATAAATAAATTTTAACTCA
1 TAAAAAATTAAATTAATAAATAAATCATAACTCA
12637200 TAAAAAA-TAAATTAAAATAAA-AAATCATAACT
1 TAAAAAATTAAATT--AATAAATAAATCATAACT
12637232 AAAACACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.21
34 16 0.57
35 6 0.21
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (34 bp):
TAAAAAATTAAATTAATAAATAAATCATAACTCA
Found at i:12638255 original size:21 final size:21
Alignment explanation
Indices: 12638207--12638288 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
12638197 GAGTCATAAC
* *
12638207 TATGATACAATGACTCATTAT
1 TATGGTACAGTGACTCATTAT
12638228 TATGGTACAGTGACTCATTAT
1 TATGGTACAGTGACTCATTAT
* * *
12638249 TAGGGTACAGTAACTCATCACT
1 TATGGTACAGTGACTCATTA-T
*
12638271 TATGGTACGGTGACTCAT
1 TATGGTACAGTGACTCAT
12638289 CACTATGACT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 36 0.69
22 16 0.31
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (21 bp):
TATGGTACAGTGACTCATTAT
Found at i:12640665 original size:19 final size:19
Alignment explanation
Indices: 12640625--12640665 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12640615 ATATAAAAGT
* *
12640625 AAATCAAAATAAAATCAAA
1 AAATAAAAATAAAATAAAA
12640644 AAATAAAAATAAAATAAAA
1 AAATAAAAATAAAATAAAA
12640663 AAA
1 AAA
12640666 CTTGCGATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATAAAAATAAAATAAAA
Found at i:12640876 original size:20 final size:20
Alignment explanation
Indices: 12640853--12640913 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
12640843 AAAAAACCTA
12640853 AAAATTCAACCAAAAATTGG
1 AAAATTCAACCAAAAATTGG
* * ** *
12640873 AAAACTC-ATC-AAACCT-A
1 AAAATTCAACCAAAAATTGG
12640890 AAAATTCAACCAAAAATTGG
1 AAAATTCAACCAAAAATTGG
12640910 AAAA
1 AAAA
12640914 CTCATCAATT
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
17 6 0.21
18 6 0.21
19 6 0.21
20 10 0.36
ACGTcount: A:0.57, C:0.18, G:0.07, T:0.18
Consensus pattern (20 bp):
AAAATTCAACCAAAAATTGG
Found at i:12640887 original size:37 final size:37
Alignment explanation
Indices: 12640846--12640921 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
12640836 CTTTTTAAAA
12640846 AAACCTAAAAATTCAACCAAAAATTGGAAAACTCATC
1 AAACCTAAAAATTCAACCAAAAATTGGAAAACTCATC
12640883 AAACCTAAAAATTCAACCAAAAATTGGAAAACTCATC
1 AAACCTAAAAATTCAACCAAAAATTGGAAAACTCATC
12640920 AA
1 AA
12640922 TTTCTAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.18
Consensus pattern (37 bp):
AAACCTAAAAATTCAACCAAAAATTGGAAAACTCATC
Found at i:12640952 original size:38 final size:37
Alignment explanation
Indices: 12640846--12640945 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
12640836 CTTTTTAAAA
*
12640846 AAACCTAAAAATTCAACCAAAAATTGGAAAACTCATC
1 AAACCTAAAAAGTCAACCAAAAATTGGAAAACTCATC
*
12640883 AAACCTAAAAATTCAACCAAAAATTGGAAAACTCATC
1 AAACCTAAAAAGTCAACCAAAAATTGGAAAACTCATC
**
12640920 AATTTCTAGAAAAGTC-ACCAAAAATT
1 AA-ACCTA-AAAAGTCAACCAAAAATT
12640946 CAAAAACAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
37 39 0.67
38 13 0.22
39 6 0.10
ACGTcount: A:0.53, C:0.20, G:0.06, T:0.21
Consensus pattern (37 bp):
AAACCTAAAAAGTCAACCAAAAATTGGAAAACTCATC
Found at i:12642794 original size:12 final size:12
Alignment explanation
Indices: 12642777--12642805 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12642767 CAATAAAATA
12642777 AAAAAAAAATTC
1 AAAAAAAAATTC
12642789 AAAAAAAAATTC
1 AAAAAAAAATTC
12642801 AAAAA
1 AAAAA
12642806 TATAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:12642811 original size:33 final size:33
Alignment explanation
Indices: 12642735--12642811 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
12642725 TTGCTTAGTA
* *
12642735 AAAAAATAAAAAAATAAATGAATAATAAAAGTC
1 AAAAAATAAAAAAATAAATCAATAAAAAAAGTC
*
12642768 AATAAAATAAAAAAA-AAATTCAA-AAAAAAATTC
1 AA-AAAATAAAAAAATAAA-TCAATAAAAAAAGTC
12642801 AAAAATATAAA
1 AAAAA-ATAAA
12642812 GTAAGTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 3 0.08
33 20 0.53
34 15 0.39
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.18
Consensus pattern (33 bp):
AAAAAATAAAAAAATAAATCAATAAAAAAAGTC
Found at i:12643111 original size:13 final size:13
Alignment explanation
Indices: 12643095--12643119 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12643085 AAAAACTCAT
12643095 CAAAAAATTCAAC
1 CAAAAAATTCAAC
12643108 CAAAAAATTCAA
1 CAAAAAATTCAA
12643120 AGATTCATCC
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:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (13 bp):
CAAAAAATTCAAC
Found at i:12643621 original size:3 final size:3
Alignment explanation
Indices: 12643600--12643798 Score: 140
Period size: 3 Copynumber: 69.3 Consensus size: 3
12643590 AATGAAACAA
12643600 AAT AA- AAT AAAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
12643646 AAT AAT -AT AAC CAT AAT AAT AA- AAT -AT AA- CAT AAT -AT AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
12643689 -AT ACT AAT -AT ACT ATAT ATAT TAT ACT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
12643734 AAT -AT AAT GAT AAT -AT AAT AAC AAT -AT AAT -AT GACAC AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -A-AT AAT AAT
12643776 AAT AAT AAT AAT AA- AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
12643799 TGATACTATA
Statistics
Matches: 155, Mismatches: 22, Indels: 38
0.72 0.10 0.18
Matches are distributed among these distances:
2 28 0.18
3 113 0.73
4 13 0.08
5 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12646326 original size:68 final size:68
Alignment explanation
Indices: 12646217--12646353 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
12646207 TTCCCTGAAG
12646217 TAGTAAACAAGACCAGATATTGAGGTAGGTTTAAGGTAACCTTATAGAATATTTAGTTTTGCAAA
1 TAGTAAACAAGACCAGATATTGAGGTAGGTTTAAGGTAACCTTATAGAATATTTAGTTTTGCAAA
12646282 TTT
66 TTT
* *
12646285 TAGTAAACAAGACCAGATATTGAGGTAGGTTTAAGGTAACCTTGTAGAATATTTGGTTTTGCAAA
1 TAGTAAACAAGACCAGATATTGAGGTAGGTTTAAGGTAACCTTATAGAATATTTAGTTTTGCAAA
12646350 TTT
66 TTT
12646353 T
1 T
12646354 TTTAATACTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (68 bp):
TAGTAAACAAGACCAGATATTGAGGTAGGTTTAAGGTAACCTTATAGAATATTTAGTTTTGCAAA
TTT
Found at i:12653929 original size:196 final size:196
Alignment explanation
Indices: 12653591--12653981 Score: 685
Period size: 196 Copynumber: 2.0 Consensus size: 196
12653581 AGAAATTAAA
12653591 GAGATTTCAATGAAAATGAATCTTTGACATACTAAAACATAGTTAAATGGGATTAAAACTAGAAA
1 GAGATTTCAATGAAAATGAATCTTTGACATACTAAAACATAGTTAAATGGGATTAAAACTAGAAA
*
12653656 AAAAATCATTAAATGATAGAGATATTCTAGTTTTTACCTATAATAGTTATCAGTTTCAAACAAAG
66 AAAAATCATTAAATAATAGAGATATTCTAGTTTTTACCTATAATAGTTATCAGTTTCAAACAAAG
* *
12653721 AATATTTTAGTTTGAGGGTAAAGGAATTT-GAAATGGTTAAAACTGAAATTCAACTAGCAATTAC
131 AATATCTTAGTTTGAGGGTAAAGGAATTTAG-AATGGTTAAAACTAAAATTCAACTAGCAATTAC
12653785 AT
195 AT
*
12653787 GAGATTTCAATGAAAATGAATCTTTGACATACTAAAACATAGTTAAATGGGATTAAGACTAGAAA
1 GAGATTTCAATGAAAATGAATCTTTGACATACTAAAACATAGTTAAATGGGATTAAAACTAGAAA
*
12653852 AAAAATCATTAAATAATGGAGATATTCTAGTTTTTACCTATAATAGTTATCAGTTTCAAACAAAG
66 AAAAATCATTAAATAATAGAGATATTCTAGTTTTTACCTATAATAGTTATCAGTTTCAAACAAAG
* * * *
12653917 AATATCTTAGTTTGAGTGTAAAGGGATTTAGAGTGGTTGAAACTAAAATTCAACTAGCAATTACA
131 AATATCTTAGTTTGAGGGTAAAGGAATTTAGAATGGTTAAAACTAAAATTCAACTAGCAATTACA
12653982 CGGAACAAAG
Statistics
Matches: 185, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
196 184 0.99
197 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (196 bp):
GAGATTTCAATGAAAATGAATCTTTGACATACTAAAACATAGTTAAATGGGATTAAAACTAGAAA
AAAAATCATTAAATAATAGAGATATTCTAGTTTTTACCTATAATAGTTATCAGTTTCAAACAAAG
AATATCTTAGTTTGAGGGTAAAGGAATTTAGAATGGTTAAAACTAAAATTCAACTAGCAATTACA
T
Found at i:12655711 original size:117 final size:117
Alignment explanation
Indices: 12655505--12655719 Score: 326
Period size: 117 Copynumber: 1.8 Consensus size: 117
12655495 ACTTTAAAAT
* * * *
12655505 TCAATCTCTATAAATAGATATTTTTATGGGTTCATTTGACATATTCAAAATTTCATATTTTTCCT
1 TCAATCTCTATAAATAAATATTTTTATGGGTTAATTTGACATATTAAAAATTTCAGATTTTTCCT
*
12655570 CTGTTTTCTCCTATTCTTTCATAAATAAAAGTTAAATTTGGTAGGTTTAGAG
66 CTGTTTTCTACTATTCTTTCATAAATAAAAGTTAAATTTGGTAGGTTTAGAG
*
12655622 TCAATCTCTATAAATAAATATTTTTGTGGGTTAATTTGACATATTAAAAAATTT-AGATTTTT-C
1 TCAATCTCTATAAATAAATATTTTTATGGGTTAATTTGACATATT-AAAAATTTCAGATTTTTCC
* *
12655685 TTTTTTTTCTTACTATTCTTTCATAAATAAAAGTT
65 TCTGTTTTC-TACTATTCTTTCATAAATAAAAGTT
12655720 GATTTCTTTG
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
116 8 0.09
117 73 0.83
118 7 0.08
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (117 bp):
TCAATCTCTATAAATAAATATTTTTATGGGTTAATTTGACATATTAAAAATTTCAGATTTTTCCT
CTGTTTTCTACTATTCTTTCATAAATAAAAGTTAAATTTGGTAGGTTTAGAG
Found at i:12664163 original size:70 final size:69
Alignment explanation
Indices: 12664089--12664284 Score: 197
Period size: 70 Copynumber: 2.8 Consensus size: 69
12664079 AAACTATAAA
12664089 ATTTTT-TCATAA-TAAAGAATTATTAAAATATAATTTCAATATCAATTACGTTTTTTATCTTAA
1 ATTTTTAT-ATAATTAAAGAATT-TTAAAATATAATTTCAATATCAATTACGTTTTTTAT-TTAA
12664152 AAACA-TG
63 AAA-AGTG
* *
12664159 ATTTTTATAGAAATTATAA-AATTTTGAAAATATAATTTCAATATCCATTACG-TTTTTATTTAA
1 ATTTTTATA-TAATTA-AAGAATTTT-AAAATATAATTTCAATATCAATTACGTTTTTTATTTAA
12664222 AAAATGTG
63 AAAA-GTG
* * * * *
12664230 ATTTTTGT-TGAATTATAGAATTCTAAAAATATAATTTCAATATCTATTATGTTTT
1 ATTTTTATAT-AATTAAAGAATT-TTAAAATATAATTTCAATATCAATTACGTTTT
12664285 CTTTAAAATA
Statistics
Matches: 107, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
69 2 0.02
70 47 0.44
71 25 0.23
72 31 0.29
73 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (69 bp):
ATTTTTATATAATTAAAGAATTTTAAAATATAATTTCAATATCAATTACGTTTTTTATTTAAAAA
AGTG
Found at i:12664197 original size:72 final size:71
Alignment explanation
Indices: 12664113--12664435 Score: 252
Period size: 72 Copynumber: 4.6 Consensus size: 71
12664103 AAGAATTATT
* * *
12664113 AAAATATAATTTCAATATCAATTACGTTTTTTATCTTAAAAACATGATTTTTATAGAAATTATAA
1 AAAATATAATTTCAATATCAATTAC-TTTTTTATCTTAAAAACATGATCTTTATTGAAACTATAA
12664178 AATTTTG
65 AATTTTG
* * * * *
12664185 AAAATATAATTTCAATATCCATTACGTTTTTAT-TTAAAAA-ATGTGATTTTTGTTG-AATTATA
1 AAAATATAATTTCAATATCAATTACTTTTTTATCTTAAAAACA--TGATCTTTATTGAAACTATA
* * *
12664247 GAATTCTA
64 AAATTTTG
* * * *
12664255 AAAATATAATTTCAATATCTATTA-TGTTTTCT-TTAAAATAC--GATCTTTATTGAAACTATAT
1 AAAATATAATTTCAATATCAATTACTTTTTTATCTTAAAA-ACATGATCTTTATTGAAACTATAA
12664316 AATTTTG
65 AATTTTG
*** * * * *
12664323 AAAATATAGCATCAATATCCACTATA-TTTTGTTATCTT-AAAACGTAATCCTTATTGAAACTAT
1 AAAATATAATTTCAATAT-CAAT-TACTTTT-TTATCTTAAAAACATGATCTTTATTGAAACTAT
**
12664386 AAAATAATG
63 AAAATTTTG
* * * *
12664395 AAAATATACTTTCAAAATCACTAAAC-TTTTTATCTTAAAAA
1 AAAATATAATTTCAATATCAAT-TACTTTTTTATCTTAAAAA
12664436 TGTTGTTCTC
Statistics
Matches: 204, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
67 9 0.04
68 26 0.13
69 14 0.07
70 57 0.28
71 36 0.18
72 62 0.30
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (71 bp):
AAAATATAATTTCAATATCAATTACTTTTTTATCTTAAAAACATGATCTTTATTGAAACTATAAA
ATTTTG
Found at i:12665606 original size:13 final size:12
Alignment explanation
Indices: 12665587--12665616 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
12665577 TATATTTTTT
12665587 AAAAAACAAAAA
1 AAAAAACAAAAA
12665599 ATAAAAACAAAAA
1 A-AAAAACAAAAA
12665612 AAAAA
1 AAAAA
12665617 TTTCTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.03
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:12667349 original size:2 final size:2
Alignment explanation
Indices: 12667342--12667380 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12667332 TATAATAAAA
12667342 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12667381 ATTATTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12672203 original size:20 final size:20
Alignment explanation
Indices: 12672174--12672211 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12672164 TATTAGATTG
*
12672174 TTGTTGTGTTTGATGTTGAA
1 TTGTTATGTTTGATGTTGAA
12672194 TTGTTATGTTTGATGTTG
1 TTGTTATGTTTGATGTTG
12672212 GATTATTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (20 bp):
TTGTTATGTTTGATGTTGAA
Found at i:12672219 original size:23 final size:22
Alignment explanation
Indices: 12672169--12672220 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
12672159 TTCTGTATTA
* *
12672169 GATTGTTGTTGTGTTTGATGTT
1 GATTATTGTTATGTTTGATGTT
12672191 GA--ATTGTTATGTTTGATGTT
1 GATTATTGTTATGTTTGATGTT
12672211 GGATTATTGT
1 -GATTATTGT
12672221 GGGCTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 16 0.64
21 2 0.08
22 2 0.08
23 5 0.20
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (22 bp):
GATTATTGTTATGTTTGATGTT
Found at i:12672966 original size:20 final size:20
Alignment explanation
Indices: 12672906--12672951 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
12672896 CAATTTGAAG
*
12672906 ATTTAAAAATGCACAAATAA
1 ATTTAAAAATTCACAAATAA
12672926 ATTTAAAAATTCACAAATAA
1 ATTTAAAAATTCACAAATAA
12672946 ATTTAA
1 ATTTAA
12672952 TGATTTGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (20 bp):
ATTTAAAAATTCACAAATAA
Found at i:12673044 original size:18 final size:18
Alignment explanation
Indices: 12673023--12673085 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
12673013 AAAATTTACA
12673023 AAAAGTTCCAAGATTCAT
1 AAAAGTTCCAAGATTCAT
**
12673041 AAAAAAGTT-CAATGATTCGC
1 --AAAAGTTCCAA-GATTCAT
**
12673061 AAAAAATCCAAGATTCAT
1 AAAAGTTCCAAGATTCAT
12673079 AAAAGTT
1 AAAAGTT
12673086 TAAAGATTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 15 0.45
19 6 0.18
20 12 0.36
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.25
Consensus pattern (18 bp):
AAAAGTTCCAAGATTCAT
Found at i:12673045 original size:20 final size:20
Alignment explanation
Indices: 12673022--12673082 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
12673012 AAAAATTTAC
12673022 AAAAAGTTCCAAGATTCATA
1 AAAAAGTTCCAAGATTCATA
**
12673042 AAAAAGTT-CAATGATTCGCA
1 AAAAAGTTCCAA-GATTCATA
12673062 AAAAA--TCCAAGATTCATA
1 AAAAAGTTCCAAGATTCATA
12673080 AAA
1 AAA
12673083 GTTTAAAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
20 19 0.54
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.23
Consensus pattern (20 bp):
AAAAAGTTCCAAGATTCATA
Found at i:12673091 original size:18 final size:18
Alignment explanation
Indices: 12673070--12673165 Score: 61
Period size: 18 Copynumber: 5.4 Consensus size: 18
12673060 CAAAAAATCC
12673070 AAGATTCATAAAAGTTTA
1 AAGATTCATAAAAGTTTA
*** * *
12673088 AAGATTTGCAAGAGTTCA
1 AAGATTCATAAAAGTTTA
*
12673106 AAGGTTCATAAGAA-TTTA
1 AAGATTCATAA-AAGTTTA
* ** *
12673124 GAGATTTGTAAAAGTCTA
1 AAGATTCATAAAAGTTTA
* *
12673142 ATGATTCACAAAAG-TTA
1 AAGATTCATAAAAGTTTA
12673159 AAGATTC
1 AAGATTC
12673166 GTAGGAGTTG
Statistics
Matches: 53, Mismatches: 23, Indels: 5
0.65 0.28 0.06
Matches are distributed among these distances:
17 10 0.19
18 42 0.79
19 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (18 bp):
AAGATTCATAAAAGTTTA
Found at i:12673114 original size:36 final size:35
Alignment explanation
Indices: 12673070--12673217 Score: 115
Period size: 36 Copynumber: 4.3 Consensus size: 35
12673060 CAAAAAATCC
12673070 AAGATTCATAAAAGTTTAAAGATTTGCAAGAGTTCA
1 AAGATTCATAAAA-TTTAAAGATTTGCAAGAGTTCA
* * * *
12673106 AAGGTTCATAAGAATTTAGAGATTTGTAAAAG-TCTA
1 AAGATTCATAA-AATTTAAAGATTTGCAAGAGTTC-A
* * * * * * *
12673142 ATGATTCACAAAAGTTAAAGATTCGTAGGAGTT-G
1 AAGATTCATAAAATTTAAAGATTTGCAAGAGTTCA
* **
12673176 AAGATTCATAAGATTTAAA-ATTTGCAAG-GTTTG
1 AAGATTCATAAAATTTAAAGATTTGCAAGAGTTCA
12673209 AAGATTCAT
1 AAGATTCAT
12673218 GACAGTTGGA
Statistics
Matches: 88, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
32 3 0.03
33 16 0.18
34 15 0.17
35 17 0.19
36 35 0.40
37 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.32
Consensus pattern (35 bp):
AAGATTCATAAAATTTAAAGATTTGCAAGAGTTCA
Found at i:12673299 original size:8 final size:8
Alignment explanation
Indices: 12673286--12673350 Score: 58
Period size: 8 Copynumber: 7.8 Consensus size: 8
12673276 GAATATTTGC
12673286 AAGATTTA
1 AAGATTTA
*
12673294 AAGATTCAA
1 AAGATT-TA
*
12673303 AAAATTTA
1 AAGATTTA
*
12673311 AAGATTCA
1 AAGATTTA
12673319 CAAGATTTA
1 -AAGATTTA
*
12673328 AAGATTCAA
1 AAGATT-TA
*
12673337 AAGAGTTA
1 AAGATTTA
12673345 AAGATT
1 AAGATT
12673351 CGCCAAATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
8 25 0.57
9 19 0.43
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (8 bp):
AAGATTTA
Found at i:12673346 original size:51 final size:51
Alignment explanation
Indices: 12673286--12673459 Score: 152
Period size: 51 Copynumber: 3.4 Consensus size: 51
12673276 GAATATTTGC
* *
12673286 AAGATTTAAAGATTCAAAAAATTTAAAGATTCACAAGATTTAAAGATTCAA
1 AAGAGTTAAAGATTCACAAAATTTAAAGATTCACAAGATTTAAAGATTCAA
* * * * * ***
12673337 AAGAGTTAAAGATTCGCCAAATTTGAATATTCACAAGATTTAAAAATTTGT
1 AAGAGTTAAAGATTCACAAAATTTAAAGATTCACAAGATTTAAAGATTCAA
* * * * * ** * * *
12673388 AAGAGTTGAATATTCATAAGAGTTAAAGATTCGTAAAAGTTAAAGATTCGTA
1 AAGAGTTAAAGATTCACAAAATTTAAAGATTCACAAGATTTAAAGATTC-AA
12673440 AA-AGTTAAAGATTCACAAAA
1 AAGAGTTAAAGATTCACAAAA
12673460 GTTGAAAATT
Statistics
Matches: 91, Mismatches: 31, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
51 89 0.98
52 2 0.02
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (51 bp):
AAGAGTTAAAGATTCACAAAATTTAAAGATTCACAAGATTTAAAGATTCAA
Found at i:12673377 original size:17 final size:17
Alignment explanation
Indices: 12673285--12673457 Score: 114
Period size: 17 Copynumber: 10.2 Consensus size: 17
12673275 TGAATATTTG
12673285 CAAGATTTAAAGATTCA
1 CAAGATTTAAAGATTCA
* *
12673302 AAAAATTTAAAGATTCA
1 CAAGATTTAAAGATTCA
12673319 CAAGATTTAAAGATTCA
1 CAAGATTTAAAGATTCA
* * *
12673336 AAAGAGTTAAAGATTCGC
1 CAAGATTTAAAGATTC-A
* *
12673354 CAA-ATTTGAATATTCA
1 CAAGATTTAAAGATTCA
* **
12673370 CAAGATTTAAAAATTTG
1 CAAGATTTAAAGATTCA
* * * *
12673387 TAAGAGTTGAATATTCA
1 CAAGATTTAAAGATTCA
* * *
12673404 TAAGAGTTAAAGATTCG
1 CAAGATTTAAAGATTCA
* * * *
12673421 TAAAAGTTAAAGATTCG
1 CAAGATTTAAAGATTCA
* * *
12673438 TAAAAGTTAAAGATTCA
1 CAAGATTTAAAGATTCA
12673455 CAA
1 CAA
12673458 AAGTTGAAAA
Statistics
Matches: 126, Mismatches: 28, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
16 3 0.02
17 121 0.96
18 2 0.02
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (17 bp):
CAAGATTTAAAGATTCA
Found at i:12673460 original size:34 final size:34
Alignment explanation
Indices: 12673023--12673462 Score: 139
Period size: 34 Copynumber: 12.7 Consensus size: 34
12673013 AAAATTTACA
* *
12673023 AAAAGTTCCAAGATTCATAAAAAAGTTCAATGATTCGC
1 AAAAGTT-AAAGATTCAT--AAAAGTT-AAAGATTCGC
* ** *
12673061 AAAAAATCCAAGATTCATAAAAGTTTAAAGATTTGC
1 -AAAAGTTAAAGATTCATAAAAG-TTAAAGATTCGC
* * * * * *
12673097 AAGAGTTCAAAGGTTCATAAGAATTTAGAGATTTGT
1 AAAAGTT-AAAGATTCATAA-AAGTTAAAGATTCGC
* * *
12673133 AAAAGTCTAATGATTCACAAAAGTTAAAGATTCGT
1 AAAAGT-TAAAGATTCATAAAAGTTAAAGATTCGC
** * * * *
12673168 AGGAGTTGAAGATTCATAAGATTTAAA-ATTTGC
1 AAAAGTTAAAGATTCATAAAAGTTAAAGATTCGC
* * * * **
12673201 -AAGGTTTGAAGATTCATGACAGTTGGAGATTCGC
1 AAAAG-TTAAAGATTCATAAAAGTTAAAGATTCGC
* * * * * *
12673235 AAAAGTTTAAGATTCGTAATAGTAAAAAATTTGC
1 AAAAGTTAAAGATTCATAAAAGTTAAAGATTCGC
* * * *** * * **
12673269 AAGAGTTGAATATTTGCAAGATTTAAAGATTCAA
1 AAAAGTTAAAGATTCATAAAAGTTAAAGATTCGC
* * * * *
12673303 AAAATTTAAAGATTCACAAGATTTAAAGATTC-A
1 AAAAGTTAAAGATTCATAAAAGTTAAAGATTCGC
*** * * * *
12673336 AAAGAGTTAAAGATTCGCCAAATTTGAATATTCAC
1 AAA-AGTTAAAGATTCATAAAAGTTAAAGATTCGC
* * * ** * * * **
12673371 AAGATTTAAAAATTTGTAAGAGTTGAATATTCAT
1 AAAAGTTAAAGATTCATAAAAGTTAAAGATTCGC
* * *
12673405 AAGAGTTAAAGATTCGTAAAAGTTAAAGATTCGT
1 AAAAGTTAAAGATTCATAAAAGTTAAAGATTCGC
*
12673439 AAAAGTTAAAGATTCACAAAAGTT
1 AAAAGTTAAAGATTCATAAAAGTT
12673463 GAAAATTTGC
Statistics
Matches: 301, Mismatches: 91, Indels: 23
0.73 0.22 0.06
Matches are distributed among these distances:
32 1 0.00
33 25 0.08
34 183 0.61
35 25 0.08
36 47 0.16
37 5 0.02
38 10 0.03
39 5 0.02
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (34 bp):
AAAAGTTAAAGATTCATAAAAGTTAAAGATTCGC
Found at i:12674179 original size:17 final size:17
Alignment explanation
Indices: 12674157--12674189 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12674147 TCATATTGAA
*
12674157 TTTTTCTTTTTCCTTTG
1 TTTTTCGTTTTCCTTTG
12674174 TTTTTCGTTTTCCTTT
1 TTTTTCGTTTTCCTTT
12674190 CATTTTTTCA
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:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTCGTTTTCCTTTG
Found at i:12674232 original size:16 final size:16
Alignment explanation
Indices: 12674187--12674234 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
12674177 TTCGTTTTCC
12674187 TTTCATTTTTTCATATCT
1 TTTCATTTTTT-AT-TCT
12674205 TTTC-TTTTTTATTCT
1 TTTCATTTTTTATTCT
*
12674220 TTTCATTTCTTATTC
1 TTTCATTTTTTATTC
12674235 ACTTCATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 7 0.25
16 11 0.39
17 6 0.21
18 4 0.14
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCATTTTTTATTCT
Found at i:12678001 original size:109 final size:108
Alignment explanation
Indices: 12677864--12678072 Score: 262
Period size: 109 Copynumber: 1.9 Consensus size: 108
12677854 ATTTTTCACA
* * * *
12677864 ATTTAAGGAAAAATTGATATTTCAACTTTTTCCTAAATATTTACTTAAATTTTAT-TTTTAA-AA
1 ATTTAAGGAAAAATTAATATTTCAACTTTTTCCTAAAT-TTTAC-AAAAATTTATGTTTCAAGAA
* *
12677927 AATTTTGATATTTCAACT-TTTGTCTTAATTTTCAAAATATTTTTC
64 AATATTCATATTTCAACTCTTT-TCTTAATTTTCAAAATATTTTTC
* * * * *
12677972 ATTTCAAGGAAAGATTAATATTTTAACTTTTTTCTTAATTTTTCAAAAATTTATGTTTCAAGAAA
1 ATTT-AAGGAAAAATTAATATTTCAACTTTTTCCTAAATTTTACAAAAATTTATGTTTCAAGAAA
12678037 ATATTCATATTTCAACTCTTTTCTTAATTTTCAAAA
65 ATATTCATATTTCAACTCTTTTCTTAATTTTCAAAA
12678073 CAAATTTATT
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
107 8 0.09
108 13 0.15
109 62 0.72
110 3 0.03
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (108 bp):
ATTTAAGGAAAAATTAATATTTCAACTTTTTCCTAAATTTTACAAAAATTTATGTTTCAAGAAAA
TATTCATATTTCAACTCTTTTCTTAATTTTCAAAATATTTTTC
Found at i:12678059 original size:54 final size:54
Alignment explanation
Indices: 12677871--12678072 Score: 175
Period size: 54 Copynumber: 3.7 Consensus size: 54
12677861 ACAATTTAAG
* * * *
12677871 GAAAA-ATTGATATTTCAACTTTTTCCTAAATATTTACTTAAAT-TTTAT--TTTTAA
1 GAAAATATTAATATTTCAACTTTTT-CTTAAT-TTT-C-AAAATATTTATCATTTCAA
* * *
12677925 -AAAATTTTGATATTTCAACTTTTGTCTTAATTTTCAAAATATTTTTCATTTCAA
1 GAAAATATTAATATTTCAACTTTT-TCTTAATTTTCAAAATATTTATCATTTCAA
* * * *
12677979 GGAAAGATTAATATTTTAACTTTTTTCTTAATTTTTCAAAA-ATTTAT-GTTTCAA
1 GAAAATATTAATATTTCAAC-TTTTTCTTAA-TTTTCAAAATATTTATCATTTCAA
*
12678033 GAAAATATTCATATTTCAACTCTTTTCTTAATTTTCAAAA
1 GAAAATATTAATATTTCAACT-TTTTCTTAATTTTCAAAA
12678073 CAAATTTATT
Statistics
Matches: 123, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
51 4 0.03
52 5 0.04
53 17 0.14
54 58 0.47
55 26 0.21
56 13 0.11
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (54 bp):
GAAAATATTAATATTTCAACTTTTTCTTAATTTTCAAAATATTTATCATTTCAA
Found at i:12678141 original size:4 final size:4
Alignment explanation
Indices: 12678132--12678156 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12678122 AATCCACATA
12678132 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
12678157 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:12681774 original size:33 final size:34
Alignment explanation
Indices: 12681714--12681779 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
12681704 GTATTTTTTA
*
12681714 AACTTACTATATATGAAAATTTGGTAAGTTATAT
1 AACTTACTAGATATGAAAATTTGGTAAGTTATAT
**
12681748 AACTTACTAGATATG-TTATTTGGTAAGTTATA
1 AACTTACTAGATATGAAAATTTGGTAAGTTATA
12681780 AAATTTACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (34 bp):
AACTTACTAGATATGAAAATTTGGTAAGTTATAT
Found at i:12683452 original size:23 final size:23
Alignment explanation
Indices: 12683433--12683479 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12683423 TTGTGTTATC
12683433 TGATAATTGCTAATTATGTTGCT
1 TGATAATTGCTAATTATGTTGCT
* *
12683456 TGATGATTGCTAATTGTGTTGCT
1 TGATAATTGCTAATTATGTTGCT
12683479 T
1 T
12683480 CTCGTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.49
Consensus pattern (23 bp):
TGATAATTGCTAATTATGTTGCT
Found at i:12696986 original size:16 final size:16
Alignment explanation
Indices: 12696961--12696997 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
12696951 GGTTACGAAT
12696961 ATGG-TGACAGTTGTA
1 ATGGATGACAGTTGTA
12696976 ATGGATGACAGTTGTA
1 ATGGATGACAGTTGTA
12696992 ATGGAT
1 ATGGAT
12696998 CTAGACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.32
Consensus pattern (16 bp):
ATGGATGACAGTTGTA
Found at i:12698261 original size:36 final size:31
Alignment explanation
Indices: 12698190--12698254 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 31
12698180 AAATCATTTT
12698190 ATTTTTTATTATATAATAAATTAATAAATAA
1 ATTTTTTATTATATAATAAATTAATAAATAA
* *
12698221 ATTTTATTATTATATAGTAAACTAATAAATAA
1 ATTTT-TTATTATATAATAAATTAATAAATAA
12698253 AT
1 AT
12698255 AAATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 5 0.16
32 26 0.84
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (31 bp):
ATTTTTTATTATATAATAAATTAATAAATAA
Found at i:12700190 original size:16 final size:15
Alignment explanation
Indices: 12700169--12700199 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
12700159 GTTTGTAAGT
12700169 TTTGCTTTGCCTTTTA
1 TTTGCTTT-CCTTTTA
12700185 TTTGCTTTCCTTTTA
1 TTTGCTTTCCTTTTA
12700200 ATGTTATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.06, C:0.19, G:0.10, T:0.65
Consensus pattern (15 bp):
TTTGCTTTCCTTTTA
Found at i:12703553 original size:6 final size:6
Alignment explanation
Indices: 12703544--12703572 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12703534 ATAATAATTA
12703544 TTATTG TTATTG TTATTG TTATTG TTATT
1 TTATTG TTATTG TTATTG TTATTG TTATT
12703573 ACTATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
TTATTG
Found at i:12703578 original size:18 final size:18
Alignment explanation
Indices: 12703544--12703578 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12703534 ATAATAATTA
**
12703544 TTATTGTTATTGTTATTG
1 TTATTGTTATTACTATTG
12703562 TTATTGTTATTACTATT
1 TTATTGTTATTACTATT
12703579 ATTAATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (18 bp):
TTATTGTTATTACTATTG
Found at i:12707985 original size:13 final size:13
Alignment explanation
Indices: 12707967--12707996 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
12707957 TTTTTTTATC
12707967 CCTATCGTCGCCA
1 CCTATCGTCGCCA
12707980 CCTATCGTCGCCA
1 CCTATCGTCGCCA
12707993 CCTA
1 CCTA
12707997 CCTTCAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.13, T:0.23
Consensus pattern (13 bp):
CCTATCGTCGCCA
Found at i:12708395 original size:80 final size:80
Alignment explanation
Indices: 12708216--12708464 Score: 374
Period size: 80 Copynumber: 3.1 Consensus size: 80
12708206 CTTAAATATT
* * * * * *
12708216 ATGGTTTGCTAAACCTTGTTGTCTAATATTGTGTTGCTGAATGGTATTGTATGATATT-GGGGGT
1 ATGGTTTGCTGAACCTTGTTGTTTGATATTGTTTTGTTGAATGGTATTGTATGATATTGGGGGGC
12708280 TGAATCATATGCTGA
66 TGAATCATATGCTGA
*
12708295 ATGGTTTGCTGAACCTTGTTGTTTGATATTGTTTTGTTGAATGGTATTCTATGATATTGGGGGGC
1 ATGGTTTGCTGAACCTTGTTGTTTGATATTGTTTTGTTGAATGGTATTGTATGATATTGGGGGGC
12708360 TGAATCATATGCTGA
66 TGAATCATATGCTGA
* * *
12708375 ATGGTTTGCTGAACCTTGTTGTTTGATATTATTTTTTTGAATGATATTGTATGATATTGGGGGGC
1 ATGGTTTGCTGAACCTTGTTGTTTGATATTGTTTTGTTGAATGGTATTGTATGATATTGGGGGGC
** *
12708440 TGAATTGTATGTTGA
66 TGAATCATATGCTGA
12708455 ATGGTTTGCT
1 ATGGTTTGCT
12708465 AAAATTTGTT
Statistics
Matches: 155, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 52 0.34
80 103 0.66
ACGTcount: A:0.21, C:0.08, G:0.27, T:0.45
Consensus pattern (80 bp):
ATGGTTTGCTGAACCTTGTTGTTTGATATTGTTTTGTTGAATGGTATTGTATGATATTGGGGGGC
TGAATCATATGCTGA
Found at i:12714488 original size:49 final size:49
Alignment explanation
Indices: 12714337--12714861 Score: 509
Period size: 49 Copynumber: 10.7 Consensus size: 49
12714327 GTGAAGAAAT
* *
12714337 CATAGTCAAGTAACTTTAAAAATCTTTCTTTTTGAAAAAGCGCTCCTATAAA
1 CATAGGCAAGTAACTTTAAAAATCTTTC--TTTG-AAAAGTGCTCCTATAAA
* * * * * *
12714389 AATAAGCAAATAACTTTAAAATAT-TTCTTTTTGAAAAAGTG-TCTTGTAAA
1 CATAGGCAAGTAACTTTAAAA-ATCTT-TCTTTG-AAAAGTGCTCCTATAAA
* * *
12714439 CATAGGCAAGTGACTTTAAAAATCTTTCTATGAAAAGTGCTTCTATAAA
1 CATAGGCAAGTAACTTTAAAAATCTTTCTTTGAAAAGTGCTCCTATAAA
* *
12714488 CATAGGCAAGTGACTTTAAAAATCTCTCTTTG-AAA--------ATAAA
1 CATAGGCAAGTAACTTTAAAAATCTTTCTTTGAAAAGTGCTCCTATAAA
* * *
12714528 CATAGGCAAGTGACTTTAAGAATCTTTCTTTAAAAAGTGCTCCTATAAA
1 CATAGGCAAGTAACTTTAAAAATCTTTCTTTGAAAAGTGCTCCTATAAA
* * * * *
12714577 CATAGACAAGTGACTTTAAGAATCTTTTTTTGAAAAGTGTTCCTATAAA
1 CATAGGCAAGTAACTTTAAAAATCTTTCTTTGAAAAGTGCTCCTATAAA
* * *
12714626 TATAGGCAAGTAA-TTCTAAAAATCTTTCTTTCAAAAATGCTCCTATAAA
1 CATAGGCAAGTAACTT-TAAAAATCTTTCTTTGAAAAGTGCTCCTATAAA
* ** *
12714675 CATAGGTAAGTAACTTTTGAAATCTTTTATTTGAAAAGTGCTCCTATAAA
1 CATAGGCAAGTAACTTTAAAAATC-TTTCTTTGAAAAGTGCTCCTATAAA
* * * *
12714725 CATAGGCAAGTGACTTTTAAAGTCTTTCTTTGAAAAGTGCTCTTATAAA
1 CATAGGCAAGTAACTTTAAAAATCTTTCTTTGAAAAGTGCTCCTATAAA
* * * * * *
12714774 TATAGGTAAGTAACTTAAAAAAAAAATCTCTATTTGAAAATTGCTCCTATAAA
1 CATAGGCAAGTAACTT----TAAAAATCTTTCTTTGAAAAGTGCTCCTATAAA
12714827 CATAGGCAAGTAAC-TTAAAAATCTTTCTTTGAAAA
1 CATAGGCAAGTAACTTTAAAAATCTTTCTTTGAAAA
12714862 ATTTTTGAAA
Statistics
Matches: 391, Mismatches: 62, Indels: 44
0.79 0.12 0.09
Matches are distributed among these distances:
40 34 0.09
41 3 0.01
48 29 0.07
49 183 0.47
50 70 0.18
51 11 0.03
52 20 0.05
53 41 0.10
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (49 bp):
CATAGGCAAGTAACTTTAAAAATCTTTCTTTGAAAAGTGCTCCTATAAA
Found at i:12714538 original size:40 final size:40
Alignment explanation
Indices: 12714483--12714563 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
12714473 AAGTGCTTCT
*
12714483 ATAAACATAGGCAAGTGACTTTAAAAATCTCTCTTTGAAA
1 ATAAACATAGGCAAGTGACTTTAAAAATCTCTCTTTAAAA
* *
12714523 ATAAACATAGGCAAGTGACTTTAAGAATCTTTCTTTAAAA
1 ATAAACATAGGCAAGTGACTTTAAAAATCTCTCTTTAAAA
12714563 A
1 A
12714564 GTGCTCCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (40 bp):
ATAAACATAGGCAAGTGACTTTAAAAATCTCTCTTTAAAA
Found at i:12714587 original size:89 final size:89
Alignment explanation
Indices: 12714435--12714612 Score: 284
Period size: 89 Copynumber: 2.0 Consensus size: 89
12714425 AAGTGTCTTG
* * *
12714435 TAAACATAGGCAAGTGACTTTAAAAATCTTTCTATGAAAAGTGCTTCTATAAACATAGGCAAGTG
1 TAAACATAGGCAAGTGACTTTAAAAATCTTTCTATAAAAAGTGCTCCTATAAACATAGACAAGTG
12714500 ACTTTAAAAATCTCTCTTTGAAAA
66 ACTTTAAAAATCTCTCTTTGAAAA
* *
12714524 TAAACATAGGCAAGTGACTTTAAGAATCTTTCTTTAAAAAGTGCTCCTATAAACATAGACAAGTG
1 TAAACATAGGCAAGTGACTTTAAAAATCTTTCTATAAAAAGTGCTCCTATAAACATAGACAAGTG
* * *
12714589 ACTTTAAGAATCTTTTTTTGAAAA
66 ACTTTAAAAATCTCTCTTTGAAAA
12714613 GTGTTCCTAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (89 bp):
TAAACATAGGCAAGTGACTTTAAAAATCTTTCTATAAAAAGTGCTCCTATAAACATAGACAAGTG
ACTTTAAAAATCTCTCTTTGAAAA
Found at i:12714751 original size:99 final size:98
Alignment explanation
Indices: 12714523--12714863 Score: 393
Period size: 99 Copynumber: 3.4 Consensus size: 98
12714513 CTCTTTGAAA
* **
12714523 ATAAACATAGGCAAGTGACTTTAAGAATCTTTCTTT-AAAAAGTGCTCCTATAAACATAGACAAG
1 ATAAACATAGGCAAGTGAC-TTAAAAATCTTTCTTTGAAAAA-TGCTCCTATAAACATAGGTAAG
* *
12714587 TGAC-TTTAAGAATCTTTT-TTTGAAAAGTGTTCCT
64 TAACTTTTAA-AATCTTTTATTTGAAAAGTGCTCCT
* * * *
12714621 ATAAATATAGGCAAGTAATTCTAAAAATCTTTCTTTCAAAAATGCTCCTATAAACATAGGTAAGT
1 ATAAACATAGGCAAGTGACT-TAAAAATCTTTCTTTGAAAAATGCTCCTATAAACATAGGTAAGT
*
12714686 AACTTTTGAAATCTTTTATTTGAAAAGTGCTCCT
65 AACTTTTAAAATCTTTTATTTGAAAAGTGCTCCT
* * * * *
12714720 ATAAACATAGGCAAGTGACTTTTAAAGTCTTTCTTTGAAAAGTGCTCTTATAAATATAGGTAAGT
1 ATAAACATAGGCAAGTGAC-TTAAAAATCTTTCTTTGAAAAATGCTCCTATAAACATAGGTAAGT
** * *
12714785 AACTTAAAAAAAAAATC-TCTATTTGAAAATTGCTCCT
65 AACTT----TTAAAATCTTTTATTTGAAAAGTGCTCCT
*
12714822 ATAAACATAGGCAAGTAACTTAAAAATCTTTCTTTGAAAAAT
1 ATAAACATAGGCAAGTGACTTAAAAATCTTTCTTTGAAAAAT
12714864 TTTTGAAAGT
Statistics
Matches: 207, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
97 1 0.00
98 61 0.29
99 83 0.40
100 1 0.00
101 20 0.10
102 36 0.17
103 5 0.02
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (98 bp):
ATAAACATAGGCAAGTGACTTAAAAATCTTTCTTTGAAAAATGCTCCTATAAACATAGGTAAGTA
ACTTTTAAAATCTTTTATTTGAAAAGTGCTCCT
Found at i:12714795 original size:148 final size:148
Alignment explanation
Indices: 12714523--12714842 Score: 412
Period size: 148 Copynumber: 2.1 Consensus size: 148
12714513 CTCTTTGAAA
* *
12714523 ATAAACATAGGCAAGTGAC-TTTAAGAATCTTTCTTTAAAAAGTGCTCCTATAAACATAGACAAG
1 ATAAACATAGGCAAGTAACTTTTAAGAATCTTTATTTAAAAAGTGCTCCTATAAACATAGACAAG
* * ** *
12714587 TGACTTTAAGAATCTTTTTTTGAAAAGTGTTCCTATAAATATAGGCAAGTAATTCTAAAAATCTT
66 TGACTTTAAGAATCTTTCTTTGAAAAGTGCTCCTATAAATATAGGCAAGTAATTAAAAAAATCTC
*
12714652 TCTTTCAAAAATGCTCCT
131 TATTTCAAAAATGCTCCT
* * * *
12714670 ATAAACATAGGTAAGTAACTTTTGA-AATCTTTTATTTGAAAAGTGCTCCTATAAACATAGGCAA
1 ATAAACATAGGCAAGTAACTTTTAAGAATC-TTTATTTAAAAAGTGCTCCTATAAACATAGACAA
* * *
12714734 GTGACTTTTAA-AGTCTTTCTTTGAAAAGTGCTCTTATAAATATAGGTAAGTAACTTAAAAAAAA
65 GTGAC-TTTAAGAATCTTTCTTTGAAAAGTGCTCCTATAAATATAGGCAAGTAA-TT---AAAAA
* *
12714798 AATCTCTATTTGAAAATTGCTCCT
125 AATCTCTATTTCAAAAATGCTCCT
12714822 ATAAACATAGGCAAGTAACTT
1 ATAAACATAGGCAAGTAACTT
12714843 AAAAATCTTT
Statistics
Matches: 148, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
147 21 0.14
148 77 0.52
149 7 0.05
152 43 0.29
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (148 bp):
ATAAACATAGGCAAGTAACTTTTAAGAATCTTTATTTAAAAAGTGCTCCTATAAACATAGACAAG
TGACTTTAAGAATCTTTCTTTGAAAAGTGCTCCTATAAATATAGGCAAGTAATTAAAAAAATCTC
TATTTCAAAAATGCTCCT
Found at i:12714908 original size:26 final size:25
Alignment explanation
Indices: 12714853--12714913 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
12714843 AAAAATCTTT
* *
12714853 CTTTGAAAAATTTTTGAAAGTTTGA
1 CTTTGAAAAAGTTTTGAAAGTTTCA
*
12714878 TTTTGAAAAAGTTTT-AAAGTGTCTCA
1 CTTTGAAAAAGTTTTGAAAGT-T-TCA
12714904 CTTTGAAAAA
1 CTTTGAAAAA
12714914 TTAGGTTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 5 0.17
25 14 0.47
26 11 0.37
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (25 bp):
CTTTGAAAAAGTTTTGAAAGTTTCA
Found at i:12715545 original size:14 final size:14
Alignment explanation
Indices: 12715528--12715570 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
12715518 TTCATTTTTC
12715528 CCATTCATTTCATT
1 CCATTCATTTCATT
12715542 CCATTCATTTCATT
1 CCATTCATTTCATT
12715556 CCATTTC-TTTCATT
1 CCA-TTCATTTCATT
12715570 C
1 C
12715571 ATTTTCACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 25 0.89
15 3 0.11
ACGTcount: A:0.19, C:0.30, G:0.00, T:0.51
Consensus pattern (14 bp):
CCATTCATTTCATT
Found at i:12716260 original size:20 final size:20
Alignment explanation
Indices: 12716235--12716277 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12716225 TTCTTTTCTA
* *
12716235 TTTTCTTTTTTTTTTCTTTT
1 TTTTCTTTTCTTTTACTTTT
12716255 TTTTCTTTTCTTTTACTTTT
1 TTTTCTTTTCTTTTACTTTT
12716275 TTT
1 TTT
12716278 GTTTGTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTCTTTTCTTTTACTTTT
Found at i:12716262 original size:32 final size:33
Alignment explanation
Indices: 12716217--12716291 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
12716207 AACTTGGATC
* *
12716217 CTTCTTTATTCTTTTCTATTTTCTTTTTTT-TTT
1 CTTCTTTTTTCTTTTCT-TTTACTTTTTTTGTTT
12716250 CTT-TTTTTTCTTTTCTTTTACTTTTTTTGTTT
1 CTTCTTTTTTCTTTTCTTTTACTTTTTTTGTTT
*
12716282 GTTCTTTTTT
1 CTTCTTTTTT
12716292 TTTATTTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 11 0.30
32 17 0.46
33 9 0.24
ACGTcount: A:0.04, C:0.13, G:0.03, T:0.80
Consensus pattern (33 bp):
CTTCTTTTTTCTTTTCTTTTACTTTTTTTGTTT
Found at i:12727940 original size:8 final size:8
Alignment explanation
Indices: 12727895--12727985 Score: 56
Period size: 7 Copynumber: 12.5 Consensus size: 8
12727885 AGTTTTAAAG
12727895 TTTAGGG-
1 TTTAGGGT
*
12727902 TTGAGGGT
1 TTTAGGGT
*
12727910 TTTAGTGT
1 TTTAGGGT
*
12727918 TTT-GAGT
1 TTTAGGGT
*
12727925 TTTTGGGT
1 TTTAGGGT
12727933 TTTAGGGT
1 TTTAGGGT
*
12727941 TTGA-GG-
1 TTTAGGGT
12727947 TTT-GGGT
1 TTTAGGGT
12727954 TTTAGGG-
1 TTTAGGGT
* *
12727961 CTT-GGGG
1 TTTAGGGT
12727968 TTT-GGGT
1 TTTAGGGT
12727975 TTTA-GGT
1 TTTAGGGT
12727982 TTTA
1 TTTA
12727986 AGTTTTTGGT
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
6 7 0.11
7 34 0.52
8 25 0.38
ACGTcount: A:0.10, C:0.01, G:0.38, T:0.51
Consensus pattern (8 bp):
TTTAGGGT
Found at i:12727952 original size:21 final size:21
Alignment explanation
Indices: 12727906--12728006 Score: 96
Period size: 21 Copynumber: 4.8 Consensus size: 21
12727896 TTAGGGTTGA
* *
12727906 GGGTTTTAGTGTTTTGAGTTTTT
1 GGGTTTTAG-GGTTTGAG-GTTT
12727929 GGGTTTTAGGGTTTGAGGTTT
1 GGGTTTTAGGGTTTGAGGTTT
* *
12727950 GGGTTTTAGGGCTTGGGGTTT
1 GGGTTTTAGGGTTTGAGGTTT
* * *
12727971 GGGTTTTAGGTTTTAAGTTTT
1 GGGTTTTAGGGTTTGAGGTTT
* *
12727992 TGGTATTA-GGTTTGA
1 GGGTTTTAGGGTTTGA
12728007 TGTATAGGGT
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 5 0.08
21 44 0.68
22 7 0.11
23 9 0.14
ACGTcount: A:0.11, C:0.01, G:0.37, T:0.51
Consensus pattern (21 bp):
GGGTTTTAGGGTTTGAGGTTT
Found at i:12727985 original size:7 final size:7
Alignment explanation
Indices: 12727907--12728004 Score: 54
Period size: 7 Copynumber: 13.7 Consensus size: 7
12727897 TAGGGTTGAG
12727907 GGTTTTA
1 GGTTTTA
12727914 GTGTTTTGA
1 G-GTTTT-A
* *
12727923 GTTTTTG
1 GGTTTTA
12727930 GGTTTTA
1 GGTTTTA
*
12727937 GGGTTTGA
1 -GGTTTTA
*
12727945 GG-TTTG
1 GGTTTTA
12727951 GGTTTTA
1 GGTTTTA
** *
12727958 GGGCTTG
1 GGTTTTA
* *
12727965 GGGTTTG
1 GGTTTTA
12727972 GGTTTTA
1 GGTTTTA
12727979 GGTTTTA
1 GGTTTTA
* *
12727986 AGTTTTT
1 GGTTTTA
*
12727993 GGTATTA
1 GGTTTTA
12728000 GGTTT
1 GGTTT
12728005 GATGTATAGG
Statistics
Matches: 67, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
6 4 0.06
7 46 0.69
8 15 0.22
9 2 0.03
ACGTcount: A:0.10, C:0.01, G:0.36, T:0.53
Consensus pattern (7 bp):
GGTTTTA
Found at i:12728090 original size:16 final size:16
Alignment explanation
Indices: 12728069--12728102 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12728059 TCTTAGGGAA
12728069 TTGGAG-TTCATAGGAT
1 TTGGAGTTTCAT-GGAT
12728085 TTGGAGTTTCATGGAT
1 TTGGAGTTTCATGGAT
12728101 TT
1 TT
12728103 CTGGTTGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.21, C:0.06, G:0.29, T:0.44
Consensus pattern (16 bp):
TTGGAGTTTCATGGAT
Found at i:12730548 original size:43 final size:44
Alignment explanation
Indices: 12730501--12730595 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
12730491 CTCTCATTAT
* *
12730501 AGGCTCAATAA-TTTT-AGAATATTTAAAAAGCTATTCTTATCAG
1 AGGCTCAACAAGTTTTGAAAAT-TTTAAAAAGCTATTCTTATCAG
* * * *
12730544 AGGCTAAACAAGTTTTGAAAATTTTAAAAGGCTTTTTTTATCAG
1 AGGCTCAACAAGTTTTGAAAATTTTAAAAAGCTATTCTTATCAG
12730588 AGGCTCAA
1 AGGCTCAA
12730596 AAACTTCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 9 0.21
44 30 0.70
45 4 0.09
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (44 bp):
AGGCTCAACAAGTTTTGAAAATTTTAAAAAGCTATTCTTATCAG
Found at i:12730614 original size:44 final size:44
Alignment explanation
Indices: 12730521--12730617 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
12730511 ATTTTAGAAT
* * *
12730521 ATTTAAAAAGCTATTCTTATCAGAGGCTAAACAAGTTTTGAAAA
1 ATTTAAAAAGCTATTCTTATCAGAGGCTAAACAACTTCTAAAAA
* * * *
12730565 TTTTAAAAGGCTTTTTTTATCAGAGGCTCAAA-AACTTCTAAAAA
1 ATTTAAAAAGCTATTCTTATCAGAGGCT-AAACAACTTCTAAAAA
12730609 ATTTAAAAA
1 ATTTAAAAA
12730618 ACTTCTCTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
44 40 0.93
45 3 0.07
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (44 bp):
ATTTAAAAAGCTATTCTTATCAGAGGCTAAACAACTTCTAAAAA
Found at i:12730677 original size:44 final size:43
Alignment explanation
Indices: 12730629--12731297 Score: 248
Period size: 43 Copynumber: 15.5 Consensus size: 43
12730619 CTTCTCTAAA
*
12730629 CAAAGGTTCAACAACTTTTGAAAAATATAAAAGGCTCATCTCAT
1 CAAAGGTTCAATAAC-TTTGAAAAATATAAAAGGCTCATCTCAT
* * * *
12730673 CAAAGGCTAT-AA-AACTTT-AAAATTTTGAAAA-ACTCTTCTCAT
1 CAAAGG-T-TCAATAACTTTGAAAAATAT-AAAAGGCTCATCTCAT
* * * * * *
12730715 CAGAGGCTT-GATGACTTTGAAAAAT-TAAAAGGTTCCTCTCTT
1 CAAAGG-TTCAATAACTTTGAAAAATATAAAAGGCTCATCTCAT
* * *
12730757 CAGAGGTT--ATGAAACTTTTGAAAAAAATAAAAGGCATC-TCTTAT
1 CAAAGGTTCAAT--AAC-TTTGAAAAATATAAAAGGC-TCATCTCAT
* * * *
12730801 CAAAGATTCAATAACTTTAAAAAATATAAAAGGATAATCTCAT
1 CAAAGGTTCAATAACTTTGAAAAATATAAAAGGCTCATCTCAT
* ** *
12730844 -AAGAGGCTT-AGTAACTTTGAAAAATATAAAAGATTC-TCTTAT
1 CAA-AGG-TTCAATAACTTTGAAAAATATAAAAGGCTCATCTCAT
* * * * * *
12730886 CAGAA-GCTCAATGATTTTAAAAAATTATAAAAGGCTTATTTCAT
1 CA-AAGGTTCAATAACTTTGAAAAA-TATAAAAGGCTCATCTCAT
* * * * * *
12730930 TAAAGGCTCAAAAAC-TAG-AAAATATAAAAGACTCCTCTCAT
1 CAAAGGTTCAATAACTTTGAAAAATATAAAAGGCTCATCTCAT
** * * *
12730971 CTAACACATT-GA-AACTTTGAAAAATATAAAAGGCTCCTCTTAT
1 C-AA-AGGTTCAATAACTTTGAAAAATATAAAAGGCTCATCTCAT
* * *** * * *
12731014 TAAAGGCTCACCGACTTTAAAAAATTATAAAAGACTCATCCCAT
1 CAAAGGTTCAATAACTTTGAAAAA-TATAAAAGGCTCATCTCAT
* * ** * * *
12731058 CAAAGACTT-AATAACTTTGAGAAATATAAAAAACCCCTC-CAC
1 CAAAG-GTTCAATAACTTTGAAAAATATAAAAGGCTCATCTCAT
* * * * *
12731100 CAAAGGCGTT-TA-AACTTTAAAAAATTATAAATGACTCATCTTAT
1 CAAA-G-GTTCAATAACTTTGAAAAA-TATAAAAGGCTCATCTCAT
* *** * * * *
12731144 CATATAATCAATAACTTTAAAAAATTATAAAAGACTCTTCTTAT
1 CAAAGGTTCAATAACTTTGAAAAA-TATAAAAGGCTCATCTCAT
* * * *
12731188 CAAAGGTTCAACAACTTT-AAAAATTTTAAAAAGCTCTTCTCAT
1 CAAAGGTTCAATAACTTTGAAAAA-TATAAAAGGCTCATCTCAT
* ** * * *
12731231 CAGAGGCCCAACAACTTTAAAAAATTATAAAAAGCTCATCTCAT
1 CAAAGGTTCAATAACTTTGAAAAA-TATAAAAGGCTCATCTCAT
* * * *
12731275 CAAAAGCTCAACAATTTTGAAAA
1 CAAAGGTTCAATAACTTTGAAAA
12731298 TTTTAAAAAG
Statistics
Matches: 469, Mismatches: 120, Indels: 72
0.71 0.18 0.11
Matches are distributed among these distances:
40 2 0.00
41 29 0.06
42 91 0.19
43 177 0.38
44 161 0.34
45 6 0.01
46 3 0.01
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (43 bp):
CAAAGGTTCAATAACTTTGAAAAATATAAAAGGCTCATCTCAT
Found at i:12731225 original size:43 final size:43
Alignment explanation
Indices: 12731151--12731309 Score: 185
Period size: 44 Copynumber: 3.7 Consensus size: 43
12731141 TATCATATAA
* * * *
12731151 TCAATAACTTTAAAAA-ATTATAAAAGACTCTTCTTATCAAAGGT
1 TCAACAACTTTAAAAATTTTA-AAAAG-CTCTTCTCATCAAAGGC
*
12731195 TCAACAACTTTAAAAATTTTAAAAAGCTCTTCTCATCAGAGGC
1 TCAACAACTTTAAAAATTTTAAAAAGCTCTTCTCATCAAAGGC
* * * *
12731238 CCAACAACTTTAAAAAATTATAAAAAGCTCATCTCATCAAAAGC
1 TCAACAACTTT-AAAAATTTTAAAAAGCTCTTCTCATCAAAGGC
* *
12731282 TCAACAATTTTGAAAATTTTAAAAAGCT
1 TCAACAACTTTAAAAATTTTAAAAAGCT
12731310 TTTTAACTAA
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
43 39 0.39
44 57 0.58
45 3 0.03
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (43 bp):
TCAACAACTTTAAAAATTTTAAAAAGCTCTTCTCATCAAAGGC
Found at i:12732481 original size:14 final size:15
Alignment explanation
Indices: 12732462--12732516 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
12732452 AAGTCTTCCT
12732462 TTTTTC-TCATTTCA
1 TTTTTCATCATTTCA
12732476 TTTTTCATC-TTTCA
1 TTTTTCATCATTTCA
**
12732490 TTTTT--TTTTTCTCA
1 TTTTTCATCATT-TCA
12732504 TTTTTCATCATTT
1 TTTTTCATCATTT
12732517 TTCTTTCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 24 0.73
15 3 0.09
16 3 0.09
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTCATCATTTCA
Found at i:12732504 original size:21 final size:19
Alignment explanation
Indices: 12732476--12732546 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 19
12732466 TCTCATTTCA
12732476 TTTTTCATCTTTCATTTTTT
1 TTTTTCAT-TTTCATTTTTT
*
12732496 TTTTCTCATTTTTCATCATTTT
1 TTTT-TCA-TTTTCAT-TTTTT
*
12732518 TCTTTCATTTATCATTTTTGT
1 TTTTTCATTT-TCATTTTT-T
12732539 TTTATTCA
1 TTT-TTCA
12732547 CTACAACCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 10 0.24
21 19 0.46
22 12 0.29
ACGTcount: A:0.14, C:0.15, G:0.01, T:0.69
Consensus pattern (19 bp):
TTTTTCATTTTCATTTTTT
Found at i:12736716 original size:3 final size:3
Alignment explanation
Indices: 12736708--12736733 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12736698 TAGAATACAC
12736708 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
12736734 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12737971 original size:18 final size:17
Alignment explanation
Indices: 12737948--12737981 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12737938 CCGTATTCTA
12737948 TTCAATGTCAAATAAGAT
1 TTCAATGTCAAA-AAGAT
*
12737966 TTCAATTTCAAAAAGA
1 TTCAATGTCAAAAAGA
12737982 ATTCTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (17 bp):
TTCAATGTCAAAAAGAT
Found at i:12739788 original size:25 final size:24
Alignment explanation
Indices: 12739757--12739805 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
12739747 TAGTTATATT
12739757 TAAATTATTTATTTATTTAATATAG
1 TAAATTATTTATTTATTT-ATATAG
12739782 TAAATTATTTATTTATTTATATAG
1 TAAATTATTTATTTATTTATATAG
12739806 AGTGTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TAAATTATTTATTTATTTATATAG
Found at i:12740381 original size:88 final size:91
Alignment explanation
Indices: 12740289--12740533 Score: 226
Period size: 88 Copynumber: 2.8 Consensus size: 91
12740279 ATATTATCCT
* ** *
12740289 TTTTTTATTTTAAAAACATGGTTTTTATTGAAA-T-TATAGAATTTTGACAAA-T-AA-TTTTTT
1 TTTTTTATCTTAAAAACATAATTTTTATTGAAAGTGTA-AAAATTTTGA-AAATTAAATTTTTTT
*
12740349 TCATAATATATTTTTAACAAGAATTATG
64 TCATAATATATTTTTAACAAGAACTATG
** *
12740377 TTTTTTATCTTAAAAATGTAATTTTTGTTGAAAGTGTAAAAATTTTGAAAATTAAATTTTTTTTC
1 TTTTTTATCTTAAAAACATAATTTTTATTGAAAGTGTAAAAATTTTGAAAATTAAATTTTTTTTC
* * *
12740442 TTAATATATTTTTATCAAGGACTATG
66 ATAATATATTTTTAACAAGAACTATG
* * * * * * *
12740468 -TTCTTATCTTAAAAATATAA--CTTGTTGAAA--GTATAAATTTCGAAAATTTAA-TTTTTTT-
1 TTTTTTATCTTAAAAACATAATTTTTATTGAAAGTGTAAAAATTTTGAAAATTAAATTTTTTTTC
12740526 ATAATATA
66 ATAATATA
12740534 GCTTTAATAA
Statistics
Matches: 134, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
84 7 0.05
85 7 0.05
86 18 0.13
88 39 0.29
89 11 0.08
90 22 0.16
91 30 0.22
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (91 bp):
TTTTTTATCTTAAAAACATAATTTTTATTGAAAGTGTAAAAATTTTGAAAATTAAATTTTTTTTC
ATAATATATTTTTAACAAGAACTATG
Found at i:12740813 original size:15 final size:15
Alignment explanation
Indices: 12740775--12740828 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
12740765 TAAAAACTAG
12740775 AATTTGTTGAAAATATA
1 AATTT-TTGAAAA-ATA
*
12740792 AAATTTTGAAAAATA
1 AATTTTTGAAAAATA
** *
12740807 AATTTTTTCATAATA
1 AATTTTTGAAAAATA
12740822 AATTTTT
1 AATTTTT
12740829 AACAAAAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 21 0.66
16 7 0.22
17 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (15 bp):
AATTTTTGAAAAATA
Found at i:12741310 original size:91 final size:90
Alignment explanation
Indices: 12741165--12741462 Score: 265
Period size: 91 Copynumber: 3.3 Consensus size: 90
12741155 GAAATTATAG
* * * * * *
12741165 AATTTTGACAAATAAATTTTTTAATAATATATTTTTA-ATAAAAGTTACATTTTTTATCTTAAAA
1 AATTTTAAAAAATAAATTTTTTCATAATATATTTTTACA-AAGA-CTA-AGTTTTTATCTTAAAA
*
12741229 ATACAATATTTGTTGTTGAAAGTAT-AG
63 ATACAATATTTGTTGTTGAAAGTATAAA
*
12741256 AATTTTAAAAAATAAAATTTTTTCATAATATATTTTTCACAAAGACTAAGTTTTTATCTAAAAAA
1 AATTTTAAAAAAT-AAATTTTTTCATAATATATTTTT-ACAAAGACTAAGTTTTTATCTTAAAAA
*
12741321 TGCAAGT-TTTGTTG--G-AAGTATAAA
64 TACAA-TATTTGTTGTTGAAAGTATAAA
* * *
12741345 AATCTTGAAAAATAAAAGTTTTTTTCATAATATATTTTTAGCAAGGACTAAGTTTTTTATCTTAA
1 AATTTTAAAAAAT-AAA--TTTTTTCATAATATATTTTTA-CAAAGACTAAG-TTTTTATCTTAA
* ** *
12741410 AAACAC-A-AGGT-TTGTTGAAAGT-TCAA
61 AAATACAATATTTGTTGTTGAAAGTATAAA
* *
12741436 AATTTCAAAAAATAAATTTTTTTATAA
1 AATTTTAAAAAATAAATTTTTTCATAA
12741463 AATAATTTCA
Statistics
Matches: 172, Mismatches: 22, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
88 16 0.09
89 20 0.12
90 5 0.03
91 82 0.48
92 44 0.26
93 4 0.02
94 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (90 bp):
AATTTTAAAAAATAAATTTTTTCATAATATATTTTTACAAAGACTAAGTTTTTATCTTAAAAATA
CAATATTTGTTGTTGAAAGTATAAA
Found at i:12743087 original size:14 final size:14
Alignment explanation
Indices: 12743068--12743098 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12743058 CATGTCAGTT
12743068 CCAATTTCTAGGTA
1 CCAATTTCTAGGTA
12743082 CCAATTTCTAGGTA
1 CCAATTTCTAGGTA
12743096 CCA
1 CCA
12743099 GATAAGCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (14 bp):
CCAATTTCTAGGTA
Found at i:12747199 original size:5 final size:6
Alignment explanation
Indices: 12747176--12747206 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
12747166 TGTCTTATAT
12747176 TAAAAA TTAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA -TAAAAA TAAAAA TAAAAA TAAAAA
12747207 ATGATGTGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:12747518 original size:24 final size:23
Alignment explanation
Indices: 12747449--12747526 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
12747439 TATTACATCG
* *
12747449 TAATTAAATTAT-AATTATTAA-A
1 TAATTAAATAATAAATTA-AAATA
*
12747471 TAATTAATTAATAAATTAAAATA
1 TAATTAAATAATAAATTAAAATA
* *
12747494 TAATTAAATAATCAAATTCATATA
1 TAATTAAATAAT-AAATTAAAATA
*
12747518 TAATAAAAT
1 TAATTAAAT
12747527 TTGAATCTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 12 0.26
23 17 0.37
24 17 0.37
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
TAATTAAATAATAAATTAAAATA
Found at i:12753020 original size:15 final size:15
Alignment explanation
Indices: 12752996--12753029 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12752986 CTGATGAAGG
* *
12752996 TGCTATTACTACTGT
1 TGCTACTACTAATGT
12753011 TGCTACTACTAATGT
1 TGCTACTACTAATGT
12753026 TGCT
1 TGCT
12753030 GACACCTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (15 bp):
TGCTACTACTAATGT
Found at i:12769408 original size:17 final size:18
Alignment explanation
Indices: 12769386--12769424 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12769376 ACATATGTAC
12769386 TTATAA-ATTAA-ATTTAT
1 TTATAACATTAATATTT-T
12769403 TTATAACATTAATATTTT
1 TTATAACATTAATATTTT
12769421 TTAT
1 TTAT
12769425 TTTTTATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 10 0.50
19 4 0.20
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATAACATTAATATTTT
Found at i:12770287 original size:309 final size:309
Alignment explanation
Indices: 12769728--12770353 Score: 1189
Period size: 309 Copynumber: 2.0 Consensus size: 309
12769718 GTGATGAAAT
12769728 CATCTCAAATTAGAATATTTAAGGAAAAATTACACGTAAAAATTAAAGAGATATCCTTTCTTAAA
1 CATCTCAAATTAGAATATTTAAGGAAAAATTACACGTAAAAATTAAAGAGATATCCTTTCTTAAA
12769793 TGGAAAAGCATATAGTTTTAACAGGTGATCTATTCAATCTTGTAAGAAAAATATTTGAGATTGAG
66 TGGAAAAGCATATAGTTTTAACAGGTGATCTATTCAATCTTGTAAGAAAAATATTTGAGATTGAG
* *
12769858 ATGAAAGATTTACTGTTAGTTGCAAAAGTAATTTTGTAGATGACTAAATGCCCAACTAAATTAGT
131 ATGAAAGATTTACTGTCAGTTGCAAAAGTAATTTTGTAGATGACTAAATGCCCAACGAAATTAGT
*
12769923 TTGATAATTAATGTAATTAAGGTTATGAACTTTTTAAAAAGAAAATATCAACCATAATGAAAAAT
196 TTGACAATTAATGTAATTAAGGTTATGAACTTTTTAAAAAGAAAATATCAACCATAATGAAAAAT
*
12769988 ATGGATTCTGAATTTAGTAATAAATGAATAAAATAAATTAAGTGATCAA
261 ATGGATTCTGAATTTAGTAATAAATGAATAAAATAAATTAAGTGACCAA
*
12770037 CATCTCAAATTAGAATATTTAAGGAAAAATTACACGTAAAAATTAAAGAGATATTCTTTCTTAAA
1 CATCTCAAATTAGAATATTTAAGGAAAAATTACACGTAAAAATTAAAGAGATATCCTTTCTTAAA
*
12770102 TGGAAAAGCATATAGTTTTAACAGGTGATCTGTTCAATCTTGTAAGAAAAATATTTGAGATTGAG
66 TGGAAAAGCATATAGTTTTAACAGGTGATCTATTCAATCTTGTAAGAAAAATATTTGAGATTGAG
12770167 ATGAAAGATTTACTGTCAGTTGCAAAAGTAATTTTGTAGATGACTAAATGCCCAACGAAATTAGT
131 ATGAAAGATTTACTGTCAGTTGCAAAAGTAATTTTGTAGATGACTAAATGCCCAACGAAATTAGT
*
12770232 TTGACAATTATTGTAATTAAGGTTATGAACTTTTTAAAAAGAAAATATCAACCATAATGAAAAAT
196 TTGACAATTAATGTAATTAAGGTTATGAACTTTTTAAAAAGAAAATATCAACCATAATGAAAAAT
12770297 ATGGATTCTGAATTTAGTAATAAATGAATAAAATAAATTAAGTGACCAA
261 ATGGATTCTGAATTTAGTAATAAATGAATAAAATAAATTAAGTGACCAA
12770346 CATCTCAA
1 CATCTCAA
12770354 CATACCTCAT
Statistics
Matches: 310, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
309 310 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (309 bp):
CATCTCAAATTAGAATATTTAAGGAAAAATTACACGTAAAAATTAAAGAGATATCCTTTCTTAAA
TGGAAAAGCATATAGTTTTAACAGGTGATCTATTCAATCTTGTAAGAAAAATATTTGAGATTGAG
ATGAAAGATTTACTGTCAGTTGCAAAAGTAATTTTGTAGATGACTAAATGCCCAACGAAATTAGT
TTGACAATTAATGTAATTAAGGTTATGAACTTTTTAAAAAGAAAATATCAACCATAATGAAAAAT
ATGGATTCTGAATTTAGTAATAAATGAATAAAATAAATTAAGTGACCAA
Found at i:12770959 original size:3 final size:3
Alignment explanation
Indices: 12770951--12771030 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
12770941 AGATTTTTTG
12770951 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12770999 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12771031 GTCAAAGCTC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12771695 original size:25 final size:25
Alignment explanation
Indices: 12771665--12771730 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
12771655 TTAATATAAC
*
12771665 TATTAAAATATTAAAAATTGTCTAT
1 TATTAAAATATTAAAAATTATCTAT
*
12771690 TATTAAAGTATATT-AAAATTATTTAT
1 TATTAAA--ATATTAAAAATTATCTAT
*
12771716 TATTTAAATTATTAA
1 TA-TTAAAATATTAA
12771731 TATTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 11 0.32
26 13 0.38
27 10 0.29
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (25 bp):
TATTAAAATATTAAAAATTATCTAT
Found at i:12771719 original size:16 final size:15
Alignment explanation
Indices: 12771699--12771738 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
12771689 TTATTAAAGT
12771699 ATATTAAAATTATTTA
1 ATATTAAAATTA-TTA
* *
12771715 TTATTTAAATTATTA
1 ATATTAAAATTATTA
12771730 ATATTAAAA
1 ATATTAAAA
12771739 AATAATTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTAAAATTATTA
Found at i:12771722 original size:27 final size:25
Alignment explanation
Indices: 12771665--12771735 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
12771655 TTAATATAAC
*
12771665 TATTAAA-ATATTAAAAATTGTCTAT
1 TATTAAATATATT-AAAATTATCTAT
*
12771690 TATTAAAGTATATTAAAATTATTTAT
1 TATTAAA-TATATTAAAATTATCTAT
*
12771716 TATTTAAAT-TATTAATATTA
1 TA-TTAAATATATTAAAATTA
12771736 AAAAATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 17 0.43
26 13 0.32
27 10 0.25
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (25 bp):
TATTAAATATATTAAAATTATCTAT
Found at i:12772005 original size:22 final size:21
Alignment explanation
Indices: 12771980--12772020 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12771970 AAATATTACA
12771980 AAATAAAAAATAAAATCAATAG
1 AAATAAAAAAT-AAATCAATAG
* *
12772002 AAATAATAACTAAATCAAT
1 AAATAAAAAATAAATCAAT
12772021 TCCTATAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (21 bp):
AAATAAAAAATAAATCAATAG
Found at i:12772018 original size:21 final size:22
Alignment explanation
Indices: 12771992--12772043 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
12771982 ATAAAAAATA
*
12771992 AAATCAATAGAAATAAT-AACT
1 AAATCAATACAAATAATCAACT
* **
12772013 AAATCAATTCCTATAATCAACT
1 AAATCAATACAAATAATCAACT
12772035 AAATCAATA
1 AAATCAATA
12772044 TATAATATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (22 bp):
AAATCAATACAAATAATCAACT
Found at i:12776481 original size:21 final size:22
Alignment explanation
Indices: 12776455--12776505 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
12776445 TAAAAAATAC
*
12776455 AATCAATAGAAATAA-TAACTA
1 AATCAATACAAATAATTAACTA
* **
12776476 AATCAATTCTTATAATTAACTA
1 AATCAATACAAATAATTAACTA
12776498 AATCAATA
1 AATCAATA
12776506 TCTAATATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (22 bp):
AATCAATACAAATAATTAACTA
Found at i:12782513 original size:13 final size:13
Alignment explanation
Indices: 12782495--12782524 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12782485 TCTCAGTGTT
12782495 AAAAAGCAAAAAA
1 AAAAAGCAAAAAA
*
12782508 AAAAAGTAAAAAA
1 AAAAAGCAAAAAA
12782521 AAAA
1 AAAA
12782525 TGTACACCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.87, C:0.03, G:0.07, T:0.03
Consensus pattern (13 bp):
AAAAAGCAAAAAA
Found at i:12785513 original size:22 final size:22
Alignment explanation
Indices: 12785488--12785531 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12785478 AATAAGACAT
*
12785488 AATTTATTAATTAATAGTGTAA
1 AATTTATTAATTAATAATGTAA
12785510 AATTTATTAATTAATAATGTAA
1 AATTTATTAATTAATAATGTAA
12785532 TATGTGCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (22 bp):
AATTTATTAATTAATAATGTAA
Found at i:12787062 original size:3 final size:3
Alignment explanation
Indices: 12787054--12787082 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12787044 TGCTCGTTTA
12787054 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12787083 AATCTCAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12788809 original size:28 final size:28
Alignment explanation
Indices: 12788778--12788839 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
12788768 AATCAGAAAT
*
12788778 GAATATCCAAAAATTCTTAAAGCTTATC
1 GAATATCCAAAAATTCTTAAAACTTATC
** *
12788806 GAATATCTGAGAATTCTTAAAACTTATC
1 GAATATCCAAAAATTCTTAAAACTTATC
*
12788834 GGATAT
1 GAATAT
12788840 ATATTTTCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (28 bp):
GAATATCCAAAAATTCTTAAAACTTATC
Found at i:12789915 original size:23 final size:23
Alignment explanation
Indices: 12789878--12789921 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12789868 ATGAAAATAG
*
12789878 TAAAAGTAATTATTTATTAATTT
1 TAAAAGTAATGATTTATTAATTT
* *
12789901 TAAAAGTTATGATTTTTTAAT
1 TAAAAGTAATGATTTATTAAT
12789922 AATAACTTTT
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (23 bp):
TAAAAGTAATGATTTATTAATTT
Found at i:12790358 original size:16 final size:16
Alignment explanation
Indices: 12790337--12790367 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12790327 AATTTTAGAT
12790337 ACCATTTATATTTTAA
1 ACCATTTATATTTTAA
12790353 ACCATTTATATTTTA
1 ACCATTTATATTTTA
12790368 TCTTACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (16 bp):
ACCATTTATATTTTAA
Found at i:12793314 original size:36 final size:37
Alignment explanation
Indices: 12793267--12793337 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
12793257 AAATCTAAAT
12793267 AAATAAAAAATATA-AAAAATCA-ACAAATAAAAAACC
1 AAATAAAAAATATATAAAAAT-ATACAAATAAAAAACC
*
12793303 AAATAAAAAATATATAAAAATATATAAATAAAAAA
1 AAATAAAAAATATATAAAAATATACAAATAAAAAA
12793338 TATAATAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (37 bp):
AAATAAAAAATATATAAAAATATACAAATAAAAAACC
Found at i:12793344 original size:12 final size:12
Alignment explanation
Indices: 12793263--12793374 Score: 72
Period size: 12 Copynumber: 9.2 Consensus size: 12
12793253 ATGAAAATCT
12793263 AAATA-AATAAA
1 AAATATAATAAA
12793274 AAATATAA-AAA
1 AAATATAATAAA
*
12793285 ATCAACA-AATAAA
1 A--AATATAATAAA
*
12793298 AAACCA-AATAAA
1 AAA-TATAATAAA
12793310 AAATAT-ATAAA
1 AAATATAATAAA
12793321 AATATATAAATAAA
1 AA-ATAT-AATAAA
**
12793335 AAATATAATAGT
1 AAATATAATAAA
*
12793347 ATATATAATAATA
1 AAATATAATAA-A
*
12793360 ACATAGTAATAAA
1 AAATA-TAATAAA
12793373 AA
1 AA
12793375 TAATTAATAA
Statistics
Matches: 81, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
11 19 0.23
12 32 0.40
13 17 0.21
14 13 0.16
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (12 bp):
AAATATAATAAA
Found at i:12793873 original size:25 final size:25
Alignment explanation
Indices: 12793847--12793904 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
12793837 GATGTGAGAG
12793847 AAGAAACAAACGATAGCACTAAAAGA
1 AAGAAA-AAACGATAGCACTAAAAGA
* * *
12793873 AAGAGAAATCGATAGCACTAAAAAAA
1 AAGAAAAAACGATAGCACT-AAAAGA
12793899 AAGAAA
1 AAGAAA
12793905 TTGGCAACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.64, C:0.12, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAAAACGATAGCACTAAAAGA
Found at i:12795365 original size:38 final size:38
Alignment explanation
Indices: 12795322--12795412 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
12795312 AAAGAGGTTC
* * * *
12795322 GTAAAACCCTAAAACGAAATCCTAAGTTGAAACCCTAAA
1 GTAAAACCTTAAAACAAAACCCTAA-ATGAAACCCTAAA
12795361 -TAAAACCTTAAAACAAAACCCTAAATGAAACCCTAAA
1 GTAAAACCTTAAAACAAAACCCTAAATGAAACCCTAAA
*
12795398 GCAAAACCTTAAAAC
1 GTAAAACCTTAAAAC
12795413 CCTGAGTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 12 0.26
38 34 0.74
ACGTcount: A:0.53, C:0.24, G:0.07, T:0.16
Consensus pattern (38 bp):
GTAAAACCTTAAAACAAAACCCTAAATGAAACCCTAAA
Found at i:12795372 original size:12 final size:12
Alignment explanation
Indices: 12795351--12795410 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
12795341 TCCTAAGTTG
*
12795351 AAACCCTAAATA
1 AAACCCTAAACA
*
12795363 AAACCTTAAAACA
1 AAACCCT-AAACA
**
12795376 AAACCCTAAATG
1 AAACCCTAAACA
12795388 AAACCCTAAAGCA
1 AAACCCTAAA-CA
*
12795401 AAACCTTAAA
1 AAACCCTAAA
12795411 ACCCTGAGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
12 19 0.50
13 19 0.50
ACGTcount: A:0.57, C:0.25, G:0.03, T:0.15
Consensus pattern (12 bp):
AAACCCTAAACA
Found at i:12795378 original size:13 final size:13
Alignment explanation
Indices: 12795351--12795412 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
12795341 TCCTAAGTTG
*
12795351 AAACCCT-AAATA
1 AAACCCTAAAACA
*
12795363 AAACCTTAAAACA
1 AAACCCTAAAACA
**
12795376 AAACCCT-AAATG
1 AAACCCTAAAACA
*
12795388 AAACCCTAAAGCA
1 AAACCCTAAAACA
*
12795401 AAACCTTAAAAC
1 AAACCCTAAAAC
12795413 CCTGAGTGAA
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
12 16 0.42
13 22 0.58
ACGTcount: A:0.56, C:0.26, G:0.03, T:0.15
Consensus pattern (13 bp):
AAACCCTAAAACA
Found at i:12795385 original size:25 final size:25
Alignment explanation
Indices: 12795351--12795410 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
12795341 TCCTAAGTTG
*
12795351 AAACCCTAAATAAAACCTTAAAACA
1 AAACCCTAAATAAAACCCTAAAACA
* *
12795376 AAACCCTAAATGAAACCCTAAAGCA
1 AAACCCTAAATAAAACCCTAAAACA
*
12795401 AAACCTTAAA
1 AAACCCTAAA
12795411 ACCCTGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.57, C:0.25, G:0.03, T:0.15
Consensus pattern (25 bp):
AAACCCTAAATAAAACCCTAAAACA
Found at i:12795463 original size:12 final size:12
Alignment explanation
Indices: 12795448--12795487 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
12795438 CCCTAAATCT
*
12795448 TAAATGAAATCC
1 TAAATGAAACCC
*
12795460 TAAATTAAAACCC
1 TAAA-TGAAACCC
12795473 TAAATGAAACCC
1 TAAATGAAACCC
12795485 TAA
1 TAA
12795488 GTTAAAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.53, C:0.20, G:0.05, T:0.23
Consensus pattern (12 bp):
TAAATGAAACCC
Found at i:12795476 original size:13 final size:13
Alignment explanation
Indices: 12795458--12795497 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
12795448 TAAATGAAAT
12795458 CCTAAATTAAAAC
1 CCTAAATTAAAAC
*
12795471 CCTAAA-TGAAAC
1 CCTAAATTAAAAC
*
12795483 CCTAAGTTAAAAC
1 CCTAAATTAAAAC
12795496 CC
1 CC
12795498 GAAACTCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.47, C:0.28, G:0.05, T:0.20
Consensus pattern (13 bp):
CCTAAATTAAAAC
Found at i:12795477 original size:25 final size:25
Alignment explanation
Indices: 12795448--12795497 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12795438 CCCTAAATCT
*
12795448 TAAATGAAATCCTAAATTAAAACCC
1 TAAATGAAACCCTAAATTAAAACCC
*
12795473 TAAATGAAACCCTAAGTTAAAACCC
1 TAAATGAAACCCTAAATTAAAACCC
12795498 GAAACTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (25 bp):
TAAATGAAACCCTAAATTAAAACCC
Found at i:12795768 original size:17 final size:16
Alignment explanation
Indices: 12795741--12795782 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
12795731 TTATATTTTA
*
12795741 AAATAAAAATAAGATT
1 AAATAAAAATAAAATT
12795757 AAATAAAGAATAAAATT
1 AAATAAA-AATAAAATT
12795774 AAA-AAAAAT
1 AAATAAAAAT
12795783 TTAAATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 11 0.46
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (16 bp):
AAATAAAAATAAAATT
Found at i:12797375 original size:16 final size:17
Alignment explanation
Indices: 12797346--12797408 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 17
12797336 CTGAGCTGAC
* *
12797346 TTTATGTATCTTTA-TT
1 TTTATTTATTTTTACTT
12797362 TTTATTTATTTTTACTT
1 TTTATTTATTTTTACTT
*
12797379 TTT-TTTCATTTTATTCTAT
1 TTTATTT-ATTTT-TACT-T
12797398 TTTATTTATTT
1 TTTATTTATTT
12797409 AACCATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 15 0.38
17 10 0.26
18 3 0.08
19 8 0.21
20 3 0.08
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTATTTATTTTTACTT
Found at i:12799113 original size:8 final size:7
Alignment explanation
Indices: 12799077--12799109 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
12799067 ATATTTCATA
12799077 TTTTTAT
1 TTTTTAT
12799084 TTTTTAT
1 TTTTTAT
12799091 TTTTTAT
1 TTTTTAT
12799098 TTTTTAT
1 TTTTTAT
12799105 TTTTT
1 TTTTT
12799110 TATTCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:12799130 original size:22 final size:22
Alignment explanation
Indices: 12799083--12799132 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
12799073 CATATTTTTA
* * *
12799083 TTTTTTATTTTTTATTTTTTAT
1 TTTTTTATTCTTTACTTTGTAT
12799105 TTTTTTATTCTTT-CTTTGTAT
1 TTTTTTATTCTTTACTTTGTAT
12799126 CTTTTTT
1 -TTTTTT
12799133 TACCAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.10, C:0.06, G:0.02, T:0.82
Consensus pattern (22 bp):
TTTTTTATTCTTTACTTTGTAT
Found at i:12800115 original size:25 final size:24
Alignment explanation
Indices: 12800065--12800122 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
12800055 AAATAAATAT
*
12800065 AAAATATAAAAAATCAACAAATAA
1 AAAATATAAAAAATCAACAAACAA
*
12800089 AAAATATATAAAAAT-ATATAAACAA
1 AAAATATA-AAAAATCA-ACAAACAA
12800114 AAAATATAA
1 AAAATATAA
12800123 TAGTATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (24 bp):
AAAATATAAAAAATCAACAAACAA
Found at i:12802097 original size:12 final size:12
Alignment explanation
Indices: 12802080--12802128 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
12802070 AATACTAAGC
12802080 TAAAACCCTAAA
1 TAAAACCCTAAA
*
12802092 TAAAACCTTAAAA
1 TAAAACCCT-AAA
* *
12802105 CAAAACCTTAAA
1 TAAAACCCTAAA
*
12802117 TGAAACCCTAAA
1 TAAAACCCTAAA
12802129 GCGAAACCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 20 0.65
13 11 0.35
ACGTcount: A:0.57, C:0.22, G:0.02, T:0.18
Consensus pattern (12 bp):
TAAAACCCTAAA
Found at i:12802109 original size:25 final size:25
Alignment explanation
Indices: 12802081--12802141 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
12802071 ATACTAAGCT
*
12802081 AAAACCCTAAATAAAACCTTAAAAC
1 AAAACCCTAAATAAAACCCTAAAAC
* * *
12802106 AAAACCTTAAATGAAACCCTAAAGC
1 AAAACCCTAAATAAAACCCTAAAAC
*
12802131 GAAACCCTAAA
1 AAAACCCTAAA
12802142 ACCCTAAGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.56, C:0.25, G:0.05, T:0.15
Consensus pattern (25 bp):
AAAACCCTAAATAAAACCCTAAAAC
Found at i:12802183 original size:14 final size:14
Alignment explanation
Indices: 12802166--12802199 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12802156 TTGAAACCTG
*
12802166 AAACCTTAAAATTA
1 AAACCCTAAAATTA
*
12802180 AAACCCTAAAGTTA
1 AAACCCTAAAATTA
12802194 AAACCC
1 AAACCC
12802200 GAAACTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.24, G:0.03, T:0.21
Consensus pattern (14 bp):
AAACCCTAAAATTA
Found at i:12804070 original size:19 final size:19
Alignment explanation
Indices: 12804042--12804091 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
12804032 TTTATTTTTA
12804042 TTTATTTTTACTTTTTT-CAT
1 TTTA-TTTTA-TTTTTTACAT
*
12804062 TTTATTTTATTTTTTATAT
1 TTTATTTTATTTTTTACAT
12804081 TTTA-TTTATTT
1 TTTATTTTATTT
12804092 AACTATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 13 0.46
19 11 0.39
20 4 0.14
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTATTTTATTTTTTACAT
Found at i:12804100 original size:17 final size:15
Alignment explanation
Indices: 12804030--12804107 Score: 83
Period size: 14 Copynumber: 5.3 Consensus size: 15
12804020 ACTTTATGTA
12804030 TATTTAT-TTTTATT
1 TATTTATATTTTATT
*
12804044 TATTTTTACTTTT-TT
1 TATTTATA-TTTTATT
*
12804059 CATTT-TATTTTATT
1 TATTTATATTTTATT
12804073 T-TTTATATTTTATT
1 TATTTATATTTTATT
12804087 TATTTAACTATTTTATT
1 TATTT-A-TATTTTATT
12804104 TATT
1 TATT
12804108 ATTTATTCAT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
13 7 0.13
14 20 0.37
15 9 0.17
16 5 0.09
17 13 0.24
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTATATTTTATT
Found at i:12804121 original size:24 final size:24
Alignment explanation
Indices: 12804073--12804122 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12804063 TTATTTTATT
*
12804073 TTTTATATTTTATTTATTTAACTA
1 TTTTATATTTTATTTATTCAACTA
*
12804097 TTTTAT-TTATTATTTATTCATCTA
1 TTTTATATT-TTATTTATTCAACTA
12804121 TT
1 TT
12804123 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTATATTTTATTTATTCAACTA
Found at i:12815766 original size:66 final size:66
Alignment explanation
Indices: 12815693--12816001 Score: 210
Period size: 66 Copynumber: 4.7 Consensus size: 66
12815683 TTTTTTGCCA
* * * *
12815693 TGGCTTGGTCCAGGTCATTTTATTTTTTTAACCTATGATTTAATCTCGATCACTCATTTTCGATC
1 TGGCTTGGTCCAGGTCATTTTATTTTTTTAACATATGATTCAATCTCGATCACTCATCTTCGACC
12815758 T
66 T
* * ** * * * * * * * **
12815759 TAGCTTGGTCTAGACCATTTTA-TTTTTCAAAATCACGGTTTAATCTCTG-TCATTCATTTTTTA
1 TGGCTTGGTCCAGGTCATTTTATTTTTTTAACAT-ATGATTCAATCTC-GATCACTCATCTTCGA
12815822 CCT
64 CCT
* * * * * ** * **
12815825 TGGCTCGATCCAAGTTATTTTAATTTTTTAATTTGTGATTCAAT-TTTAGTCACTCATCTTCGAC
1 TGGCTTGGTCCAGGTCATTTTATTTTTTTAACATATGATTCAATCTCGA-TCACTCATCTTCGAC
12815889 CT
65 CT
*** * * * *
12815891 TGGCTCAATCCAGGTCATTTTATTTTTTTGACATATGATTCAATCACGGTCACCCATCTTCGACC
1 TGGCTTGGTCCAGGTCATTTTATTTTTTTAACATATGATTCAATCTCGATCACTCATCTTCGACC
12815956 T
66 T
* * * * * *
12815957 TGGCTTAGTCTAGGTCATTTCATTTTTTTGACCTACGATTCAATC
1 TGGCTTGGTCCAGGTCATTTTATTTTTTTAACATATGATTCAATC
12816002 GCAATTACTC
Statistics
Matches: 184, Mismatches: 53, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
65 9 0.05
66 166 0.90
67 9 0.05
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.45
Consensus pattern (66 bp):
TGGCTTGGTCCAGGTCATTTTATTTTTTTAACATATGATTCAATCTCGATCACTCATCTTCGACC
T
Found at i:12817392 original size:17 final size:17
Alignment explanation
Indices: 12817334--12817410 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 17
12817324 TTTAGGTATT
12817334 TTTATTTTTAT-TTATT-
1 TTTATTTTTATATT-TTA
12817350 TTTACTTGTTT-TCATTTTA
1 TTTA-TT-TTTAT-ATTTTA
12817369 TTCTATTTTTATATTTTA
1 TT-TATTTTTATATTTTA
*
12817387 TTTA-TTTGACTATTTTA
1 TTTATTTTTA-TATTTTA
12817404 TTTATTT
1 TTTATTT
12817411 ATTTATTATT
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
16 8 0.16
17 16 0.31
18 18 0.35
19 7 0.14
20 2 0.04
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTATTTTTATATTTTA
Found at i:12817417 original size:17 final size:17
Alignment explanation
Indices: 12817363--12817417 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
12817353 ACTTGTTTTC
12817363 ATTTTATTCTATTT-TTAT
1 ATTTTATT-TATTTATT-T
*
12817381 ATTTTATTTATTTGA-CT
1 ATTTTATTTATTT-ATTT
12817398 ATTTTATTTATTTATTT
1 ATTTTATTTATTTATTT
12817415 ATT
1 ATT
12817418 ATTTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 1 0.03
17 23 0.72
18 8 0.25
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (17 bp):
ATTTTATTTATTTATTT
Found at i:12817424 original size:17 final size:17
Alignment explanation
Indices: 12817330--12817424 Score: 56
Period size: 16 Copynumber: 5.5 Consensus size: 17
12817320 TGAATTTAGG
12817330 TATTTTTA-TT-TTTATT
1 TATTTTTATTTATTTA-T
* *
12817346 TATTTTTACTTGTTT-T
1 TATTTTTATTTATTTAT
*
12817362 CA-TTTTATTCTATTT-T
1 TATTTTTATT-TATTTAT
12817378 TATATTTTATTTATTTGACT
1 TAT-TTTTATTTATTT-A-T
*
12817398 ATTTTATTTATTTATTTAT
1 -TATT-TTTATTTATTTAT
12817417 TATTTTTA
1 TATTTTTA
12817425 AAAAATATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
15 6 0.10
16 16 0.25
17 11 0.17
18 13 0.21
19 1 0.02
20 3 0.05
21 13 0.21
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (17 bp):
TATTTTTATTTATTTAT
Found at i:12828296 original size:35 final size:35
Alignment explanation
Indices: 12828257--12828325 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
12828247 CTGAAATACA
12828257 TATAAACTTTGGTTTAAAAAAATAAAATATAAAAT
1 TATAAACTTTGGTTTAAAAAAATAAAATATAAAAT
* *
12828292 TATAAACTTTGGTTTGAAAAAATAAAGTATAAAA
1 TATAAACTTTGGTTTAAAAAAATAAAATATAAAA
12828326 AAAATAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (35 bp):
TATAAACTTTGGTTTAAAAAAATAAAATATAAAAT
Found at i:12828333 original size:36 final size:35
Alignment explanation
Indices: 12828258--12828333 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
12828248 TGAAATACAT
**
12828258 ATAAACTTTGGTTTAAAAAAATAAAATATAAAATT
1 ATAAACTTTGGTTTAAAAAAATAAAATATAAAAAA
* *
12828293 ATAAACTTTGGTTTGAAAAAATAAAGTATAAAAAAA
1 ATAAACTTTGGTTTAAAAAAATAAAATAT-AAAAAA
12828329 ATAAA
1 ATAAA
12828334 GAAACTCAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 27 0.75
36 9 0.25
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (35 bp):
ATAAACTTTGGTTTAAAAAAATAAAATATAAAAAA
Found at i:12829443 original size:19 final size:18
Alignment explanation
Indices: 12829387--12829444 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 18
12829377 GAAAATTTTG
*
12829387 AAAAAAATAAGAGAAAAG
1 AAAAAAATAAGAGAAAAA
* **
12829405 AAAAAAAGAA-A-AAAGG
1 AAAAAAATAAGAGAAAAA
12829421 AAAAAAATAAGAGAAAAA
1 AAAAAAATAAGAGAAAAA
12829439 TAAAAA
1 -AAAAA
12829445 GAGGATTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 13 0.41
17 2 0.06
18 12 0.38
19 5 0.16
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAAATAAGAGAAAAA
Done.