Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008904.1 Hibiscus syriacus cultivar Beakdansim tig00112184_pilon, 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: 372056
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 3
Found at i:131366 original size:19 final size:19
Alignment explanation
Indices: 131233--131374 Score: 94
Period size: 19 Copynumber: 8.1 Consensus size: 19
131223 TCTTTTGGTT
*
131233 GAAATGAAAAT--CAACGA
1 GAAATGAAAATCGCAACGC
*
131250 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
131270 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
131287 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
131303 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
131320 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
131336 GAAATG-AAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
131354 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
131373 GA
1 GA
131375 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
14 17 0.18
15 2 0.02
16 4 0.04
17 6 0.06
18 27 0.28
19 34 0.35
20 7 0.07
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:131403 original size:19 final size:19
Alignment explanation
Indices: 131370--131414 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
131360 AAAATCGCAA
*
131370 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
131389 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
131408 TGCGATT
1 TGCGATT
131415 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:131965 original size:20 final size:19
Alignment explanation
Indices: 131939--131992 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
131929 GGCGCTATGT
131939 AAATCGCGTTGCGAAAGTC
1 AAATCGCGTTGCGAAAGTC
131958 AGAATCGCGTTGCGAAAGTC
1 A-AATCGCGTTGCGAAAGTC
*
131978 AATATCTCGTTGCGA
1 AA-ATCGCGTTGCGA
131993 TTTTGTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (19 bp):
AAATCGCGTTGCGAAAGTC
Found at i:134922 original size:47 final size:47
Alignment explanation
Indices: 134849--134939 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 47
134839 ATAATATGAT
* * *
134849 AATTTGAAAGTGATTATAAAATAAAGATAATTAATATTTTATTTTCA
1 AATTTGAAAGTGATTATAAAATAAAGACAATCAATATTTCATTTTCA
**
134896 AATTTG-AAGTGATTATAAGCTAAAAGACAATCAATATTTCATTT
1 AATTTGAAAGTGATTATAAAAT-AAAGACAATCAATATTTCATTT
134940 CCGAAACTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
46 13 0.34
47 25 0.66
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (47 bp):
AATTTGAAAGTGATTATAAAATAAAGACAATCAATATTTCATTTTCA
Found at i:140407 original size:23 final size:23
Alignment explanation
Indices: 140360--140407 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
140350 AATAACATAT
* * **
140360 TAGGTAGTGTTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
140383 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
140406 TA
1 TA
140408 TGCATTTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:141665 original size:184 final size:182
Alignment explanation
Indices: 141169--141722 Score: 743
Period size: 182 Copynumber: 3.0 Consensus size: 182
141159 GTATTTACTA
*
141169 ATTTTTTTAAAGTATCGACACTTTATAGGCACTATAACTTCTTCTCTTTTAAATTCTAAAAGTGT
1 ATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGT
* * ** * *
141234 CGATACTTTTATTAAAGTATCGACACTTTCAACATATACAATAGTT-CTTTATCGGTTTTGTCAT
66 CGATACTTATATTAAATTATCGACACTTTCAACATATACGGTA-TTGCTTTACCGGTTTTTTCAT
* *
141298 TTTGAGACCGGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATAC
130 TTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATAC
** * * * *
141351 ATTTTCATAAAGTATCAACACTTTTTAGACGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGT
1 ATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGT
* * * ** * *
141416 TGATACTTATATTAAATTAGCGACACTTTCAACATATCCGGTAGAGCTTTACCAGATTTTTCATT
66 CGATACTTATATTAAATTATCGACACTTTCAACATATACGGTATTGCTTTACCGGTTTTTTCATT
* *
141481 TTGGGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATAT
131 TTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATAC
* * *
141533 ATTTTTTTAAAGTATCGACACTTTATAGGCGTTATAAATTATTCTCTCTTTTAAATTCTAAAAGT
1 ATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTT-CT-TCTCTTTTAAATTCTAAAAGT
* * *
141598 GTCGATAGTTATATTAAATTATCGACACTTTCAACATATTCGGTATTGTTTTACCGGTTTTTTCA
64 GTCGATACTTATATTAAATTATCGACACTTTCAACATATACGGTATTGCTTTACCGGTTTTTTCA
* * * * *
141663 TTTCGAGACCGATTTTATCATATTTTTACCTGTAATATT-TCTATAGAGCGATAC
129 TTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGT-TATAGATCGATAC
141717 ATTTTT
1 ATTTTT
141723 CATTTGTATC
Statistics
Matches: 319, Mismatches: 49, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
182 190 0.60
183 2 0.01
184 127 0.40
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (182 bp):
ATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGT
CGATACTTATATTAAATTATCGACACTTTCAACATATACGGTATTGCTTTACCGGTTTTTTCATT
TTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATAC
Found at i:156678 original size:9 final size:9
Alignment explanation
Indices: 156657--156733 Score: 58
Period size: 9 Copynumber: 8.9 Consensus size: 9
156647 AAAAGATAAT
156657 AAAATGAAA-
1 AAAAT-AAAG
*
156666 AAAATAAAT
1 AAAATAAAG
156675 AAAAT-AAG
1 AAAATAAAG
156683 CAAAAT---G
1 -AAAATAAAG
156690 AAAATAAAG
1 AAAATAAAG
*
156699 AAACAGAAAG
1 AAA-ATAAAG
*
156709 AAAATAGA-
1 AAAATAAAG
156717 AAAATAAAG
1 AAAATAAAG
156726 AAAATAAA
1 AAAATAAA
156734 TAAGAAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
6 5 0.09
7 1 0.02
8 12 0.21
9 30 0.54
10 8 0.14
ACGTcount: A:0.75, C:0.03, G:0.10, T:0.12
Consensus pattern (9 bp):
AAAATAAAG
Found at i:156742 original size:22 final size:22
Alignment explanation
Indices: 156709--156760 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
156699 AAACAGAAAG
156709 AAAAT-AGAAAAATAAAGAAA-A
1 AAAATAAGAAAAATAAA-AAATA
*
156730 TAAATAAGAAAAATAAAAAATA
1 AAAATAAGAAAAATAAAAAATA
156752 AAAATAAGA
1 AAAATAAGA
156761 CAATAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (22 bp):
AAAATAAGAAAAATAAAAAATA
Found at i:156772 original size:30 final size:30
Alignment explanation
Indices: 156676--156771 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 30
156666 AAAATAAATA
*
156676 AAATAAGCAAAAT-G-AAAATAAAGAAACAG
1 AAATAAGAAAAATAGAAAAATAAAGAAA-AG
*
156705 --A-AAG-AAAATAGAAAAATAAAGAAAAT
1 AAATAAGAAAAATAGAAAAATAAAGAAAAG
156731 AAATAAGAAAAATA-AAAAATAAA-AATAAG
1 AAATAAGAAAAATAGAAAAATAAAGAA-AAG
156760 ACAAT-AGAAAAA
1 A-AATAAGAAAAA
156772 AATTTAATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
25 5 0.09
26 5 0.09
27 13 0.23
28 3 0.05
29 22 0.39
30 9 0.16
ACGTcount: A:0.75, C:0.03, G:0.10, T:0.11
Consensus pattern (30 bp):
AAATAAGAAAAATAGAAAAATAAAGAAAAG
Found at i:156948 original size:36 final size:36
Alignment explanation
Indices: 156883--156963 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 36
156873 AAGATAATGT
156883 TATATATAAAGGTAAAAAAAACTAAAAAAACTA-AAAA
1 TATATATAAAGGTAAAAAAAAC-AAAAAAA-TAGAAAA
*
156920 TATAATATAATA-GTAAAAAAAAC-CAAAAATAGAAAA
1 TAT-ATATAA-AGGTAAAAAAAACAAAAAAATAGAAAA
156956 TATATATA
1 TATATATA
156964 CAATTATAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
35 7 0.17
36 12 0.30
37 3 0.08
38 17 0.43
39 1 0.03
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (36 bp):
TATATATAAAGGTAAAAAAAACAAAAAAATAGAAAA
Found at i:157083 original size:32 final size:33
Alignment explanation
Indices: 157015--157095 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 33
157005 AAAAATAATT
** *
157015 AATATATATATATTAATAGTAGGTATACAAATAA
1 AATATATATATAAAAATAGTA-GTATACAAACAA
157049 AATATATATATAAAAATACGTA-TATAC-AACAA
1 AATATATATATAAAAATA-GTAGTATACAAACAA
157081 AATA-ATAATATAAAA
1 AATATAT-ATATAAAA
157096 TAATAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 2 0.05
32 16 0.38
33 5 0.12
34 16 0.38
35 3 0.07
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (33 bp):
AATATATATATAAAAATAGTAGTATACAAACAA
Found at i:162506 original size:157 final size:154
Alignment explanation
Indices: 162222--162532 Score: 579
Period size: 157 Copynumber: 2.0 Consensus size: 154
162212 CCTCTTCTCA
162222 TAGTGACTGGGCTGAAAACCGAGCCGAACTGATCTAACTTCATATAGGAAGGATTGGATTAATTA
1 TAGTGACTGGGCTGAAAACCGAGCCGAACTGATCTAACTTCATATAGGAAGGATTGGATTAATTA
162287 TTCCTTGTAGAAATTTCCTAAACCCTCTTTCAGTTTTGGCACATCGGCCCAGGGTTTGCTTGATC
66 TTCCTTGTAGAAATTTCCTAAACCCTCTTTCAGTTTTGGCACATCGGCCCAGGGTTTGCTTGATC
162352 TCTATATCTTGGTGTA-TTAGAGAGT
131 TC--TATCTTGGTGTATTTAGAGAGT
162377 TAGTGACTGGGCTGAAAACCGAGCCCGAACTGATCTAACTTCAATATAGGAAGGATTGGATTAAT
1 TAGTGACTGGGCTGAAAACCGAG-CCGAACTGATCTAACTTC-ATATAGGAAGGATTGGATTAAT
162442 TATTCCTTGTAGAAATTTCCTAAACCCTCTTTCAGTTTTGGCACATCGGCCCAGGGTTTGCTTGA
64 TATTCCTTGTAGAAATTTCCTAAACCCTCTTTCAGTTTTGGCACATCGGCCCAGGGTTTGCTTGA
162507 TCTCTATCTTGGTGTATTTAGAGAGT
129 TCTCTATCTTGGTGTATTTAGAGAGT
162533 CAAGGTTTAT
Statistics
Matches: 153, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
155 35 0.23
156 27 0.18
157 91 0.59
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (154 bp):
TAGTGACTGGGCTGAAAACCGAGCCGAACTGATCTAACTTCATATAGGAAGGATTGGATTAATTA
TTCCTTGTAGAAATTTCCTAAACCCTCTTTCAGTTTTGGCACATCGGCCCAGGGTTTGCTTGATC
TCTATCTTGGTGTATTTAGAGAGT
Found at i:168638 original size:17 final size:17
Alignment explanation
Indices: 168616--168662 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
168606 AATAAAGAAG
*
168616 ATAAAATTAAAGAG-TGA
1 ATAAAATTAAAAAGAT-A
*
168633 ATAAAACTAAAAAGATA
1 ATAAAATTAAAAAGATA
*
168650 ATAAAATGAAAAA
1 ATAAAATTAAAAA
168663 AAAGTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 24 0.96
18 1 0.04
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (17 bp):
ATAAAATTAAAAAGATA
Found at i:168743 original size:27 final size:26
Alignment explanation
Indices: 168647--168806 Score: 94
Period size: 27 Copynumber: 6.0 Consensus size: 26
168637 AACTAAAAAG
*
168647 ATAATAAAATGAAAAA-AAAGTAAATAAA
1 ATAA-AAAAT-AAAAATAAAGAAAAT-AA
* *
168675 ATAAGCAAAATGAAAATAAAGAAACAGAA
1 ATAA--AAAATAAAAATAAAGAAA-ATAA
* * *
168704 ACAAAATAGAAAAATAAAGAAAATAA
1 ATAAAAAATAAAAATAAAGAAAATAA
* * *
168730 ATAACAAAGT-AAAATAAATAAGAAAAA
1 ATAA-AAAATAAAAATAAAGAA-AATAA
* *
168757 ATAAAAAATAAAAATAAAGACAAGAGA
1 ATAAAAAATAAAAATAAAGAAAATA-A
* *
168784 A-AAAAAAT-GAAATAAATAAAATA
1 ATAAAAAATAAAAATAAAGAAAATA
168807 TAGGCAAATC
Statistics
Matches: 102, Mismatches: 23, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
25 11 0.11
26 30 0.29
27 36 0.35
28 8 0.08
29 16 0.16
30 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (26 bp):
ATAAAAAATAAAAATAAAGAAAATAA
Found at i:168772 original size:53 final size:55
Alignment explanation
Indices: 168641--168776 Score: 136
Period size: 53 Copynumber: 2.5 Consensus size: 55
168631 GAATAAAACT
* *
168641 AAAAAGATAATAAAATGAAAAA-AAAGTAAATAAAATAAGCAAAATGAAAATAAAGA
1 AAAAAAATAA-AAAAT-AAAAATAAAGAAAATAAAATAAGCAAAATGAAAATAAAGA
* * * * * *
168697 AACAGAAACAAAATAGAAAAATAAAGAAAAT-AAATAA-CAAAGT-AAAATAAATA
1 AA-AAAAATAAAAAATAAAAATAAAGAAAATAAAATAAGCAAAATGAAAATAAAGA
168750 AGAAAAAATAAAAAATAAAAATAAAGA
1 A-AAAAAATAAAAAATAAAAATAAAGA
168777 CAAGAGAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
53 30 0.46
54 6 0.09
55 11 0.17
56 13 0.20
57 5 0.08
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.13
Consensus pattern (55 bp):
AAAAAAATAAAAAATAAAAATAAAGAAAATAAAATAAGCAAAATGAAAATAAAGA
Found at i:168804 original size:17 final size:17
Alignment explanation
Indices: 168724--168804 Score: 51
Period size: 17 Copynumber: 4.7 Consensus size: 17
168714 AAAATAAAGA
* * *
168724 AAATAAATAACAAAGTA
1 AAATAAATAAAAAAATG
168741 AAATAAATAAGAAAAAAT-
1 AAATAAAT-A-AAAAAATG
*
168759 AAA-AAATAAAAATAAAG
1 AAATAAATAAAAA-AATG
* *
168776 ACAAGAGA-AAAAAAATG
1 A-AATAAATAAAAAAATG
168793 AAATAAATAAAA
1 AAATAAATAAAA
168805 TATAGGCAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
15 4 0.08
16 7 0.14
17 21 0.42
18 11 0.22
19 7 0.14
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (17 bp):
AAATAAATAAAAAAATG
Found at i:168943 original size:26 final size:28
Alignment explanation
Indices: 168897--168953 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
168887 AAAATAATGT
*
168897 ATATATATATATAGGT-AAAAACTAAAA
1 ATATATATATATAGGTAAAAAACCAAAA
168924 ATATA-ATATATA-GTAAAAAAACCAAAA
1 ATATATATATATAGGT-AAAAAACCAAAA
168951 ATA
1 ATA
168954 GAAAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 2 0.07
26 7 0.26
27 18 0.67
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (28 bp):
ATATATATATATAGGTAAAAAACCAAAA
Found at i:169080 original size:19 final size:17
Alignment explanation
Indices: 169058--169110 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
169048 AAATAAAAAA
169058 ATATATAAAAAATACATAT
1 ATATATAAAAAATA-A-AT
*
169077 ATATATAGCAAAATAAAT
1 ATATATA-AAAAATAAAT
169095 A-ATATAAAATAATAAA
1 ATATATAAAA-AATAAA
169111 AATAACAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 2 0.07
17 11 0.37
18 3 0.10
19 8 0.27
20 6 0.20
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (17 bp):
ATATATAAAAAATAAAT
Found at i:171510 original size:18 final size:19
Alignment explanation
Indices: 171474--171510 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
171464 CACGGAATGT
171474 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
171494 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
171511 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:172165 original size:18 final size:19
Alignment explanation
Indices: 172127--172168 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
172117 TGGTTCACGA
*
172127 AATATAAGATTACCAGTGGG
1 AATAAAAGATTACCAG-GGG
172147 AATAAAAGATTACCA-GGG
1 AATAAAAGATTACCAGGGG
172165 AATA
1 AATA
172169 GGATTACTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (19 bp):
AATAAAAGATTACCAGGGG
Found at i:174498 original size:11 final size:11
Alignment explanation
Indices: 174484--174508 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
174474 AAAAGGTAAT
174484 AAAAACAAATG
1 AAAAACAAATG
174495 AAAAACAAATG
1 AAAAACAAATG
174506 AAA
1 AAA
174509 TAAAGAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAACAAATG
Found at i:174592 original size:27 final size:26
Alignment explanation
Indices: 174533--174650 Score: 94
Period size: 27 Copynumber: 4.3 Consensus size: 26
174523 TTAAAGAGTG
* *
174533 AATAAAGCTAAAAAGATAATAAAATG-AA
1 AATAAAG-AAAAAAAATAA-AAAA-GAAA
* *
174561 AATAAAGAAACAAAAACAAAATAGAAA
1 AATAAAGAAA-AAAAATAAAAAAGAAA
* *
174588 AATAAAGAAAATAAATAAACAAAGTAA
1 AATAAAGAAAAAAAATAAA-AAAGAAA
* *
174615 AATAAATAAGAAAAAAATAAAAAATAAA
1 AATAAA-GA-AAAAAAATAAAAAAGAAA
174643 AATAAAGA
1 AATAAAGA
174651 CAAGAGAAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
26 8 0.11
27 29 0.40
28 25 0.35
29 10 0.14
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (26 bp):
AATAAAGAAAAAAAATAAAAAAGAAA
Found at i:174627 original size:40 final size:36
Alignment explanation
Indices: 174553--174642 Score: 94
Period size: 36 Copynumber: 2.4 Consensus size: 36
174543 AAAAGATAAT
*
174553 AAAAT-GAAAATAAAGAAACAAAAACAAAATAGAAA
1 AAAATAGAAAATAAAGAAACAAAAAAAAAATAGAAA
*
174588 AATAA-AGAAAATAAATAAACAAAGTAAAATAAATAAGAAA
1 AA-AATAGAAAATAAAGAAACAAA--AAAA-AAAT-AGAAA
*
174628 AAAATAAAAAATAAA
1 AAAATAGAAAATAAA
174643 AATAAAGACA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
35 2 0.04
36 18 0.40
38 3 0.07
39 6 0.13
40 16 0.36
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (36 bp):
AAAATAGAAAATAAAGAAACAAAAAAAAAATAGAAA
Found at i:174633 original size:15 final size:13
Alignment explanation
Indices: 174559--174648 Score: 63
Period size: 13 Copynumber: 6.6 Consensus size: 13
174549 TAATAAAATG
*
174559 AAAATAAAGAAACA
1 AAAATAAA-AAAAA
* * *
174573 AAAACAAAATAGA
1 AAAATAAAAAAAA
*
174586 AAAATAAAGAAAA
1 AAAATAAAAAAAA
* **
174599 TAAATAAACAAAGT
1 AAAATAAA-AAAAA
174613 AAAATAAATAAGAAA
1 AAAATAAA-AA-AAA
*
174628 AAAATAAAAAATA
1 AAAATAAAAAAAA
174641 AAAATAAA
1 AAAATAAA
174649 GACAAGAGAA
Statistics
Matches: 58, Mismatches: 16, Indels: 5
0.73 0.20 0.06
Matches are distributed among these distances:
13 29 0.50
14 20 0.34
15 9 0.16
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAATAAAAAAAA
Found at i:174812 original size:31 final size:32
Alignment explanation
Indices: 174777--174852 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
174767 GATAATGTAT
*
174777 ATATATATATATAGGT-AAAAAACTAAAAATA-
1 ATATATATATATA-GTAAAAAAACCAAAAATAG
174808 ATATA-ATATAATAGTAAAAAAACCAAAAATAG
1 ATATATATAT-ATAGTAAAAAAACCAAAAATAG
* *
174840 AAAAATATATATA
1 ATATATATATATA
174853 AGATATAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 6 0.16
31 22 0.58
32 6 0.16
33 4 0.11
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.26
Consensus pattern (32 bp):
ATATATATATATAGTAAAAAAACCAAAAATAG
Found at i:180856 original size:15 final size:16
Alignment explanation
Indices: 180828--180859 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
180818 AAAATCTTTC
180828 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
180844 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
180859 T
1 T
180860 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:181633 original size:16 final size:16
Alignment explanation
Indices: 181609--181642 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
181599 TATCGCCGAC
*
181609 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
181625 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
181641 CG
1 CG
181643 TGAATAGTAA
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:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:182328 original size:18 final size:19
Alignment explanation
Indices: 182288--182331 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
182278 TTTGGTTCAC
* *
182288 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTACCAG-G
182308 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
182326 GGAATA
1 GGAATA
182332 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:182512 original size:37 final size:37
Alignment explanation
Indices: 182478--182547 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
182468 TACAAATTGT
182478 AAAAT-TTTATAT-ATTTTCTTTAAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTAAAAAAATTAAATTC
* * *
182514 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAAATTAAA
182548 AATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 4 0.14
37 20 0.69
38 5 0.17
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATAATTTTTTTAAAAAAATTAAATTC
Found at i:182897 original size:19 final size:19
Alignment explanation
Indices: 182873--182936 Score: 128
Period size: 19 Copynumber: 3.4 Consensus size: 19
182863 GCCAACCAAA
182873 CATGGGAATGTGGGATTCC
1 CATGGGAATGTGGGATTCC
182892 CATGGGAATGTGGGATTCC
1 CATGGGAATGTGGGATTCC
182911 CATGGGAATGTGGGATTCC
1 CATGGGAATGTGGGATTCC
182930 CATGGGA
1 CATGGGA
182937 TGAGAATCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.25
Consensus pattern (19 bp):
CATGGGAATGTGGGATTCC
Found at i:187495 original size:60 final size:60
Alignment explanation
Indices: 187369--187483 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
187359 GTCATGTGAC
* * ** ** *
187369 CATTTTATAACTTTTAATAGTCGGGAGACTCAACAAAGTAACGTCATATAATTAGAGAAT
1 CATTTTTTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCATATAATAAGAGAAT
* *
187429 CATTTTTTAACTTTTAATAGTCGAGAGACTCATCAAAACAACACCCTATAATAAG
1 CATTTTTTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCATATAATAAG
187484 GGGATTATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (60 bp):
CATTTTTTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCATATAATAAGAGAAT
Found at i:188489 original size:23 final size:24
Alignment explanation
Indices: 188463--188516 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
188453 ATCTACTTGG
* *
188463 ATTTTATGTTCA-GTTTATTTTAA
1 ATTTTATGTTAACGTTTATGTTAA
*
188486 ATTTTA-GTTAACTTTTATGTTAA
1 ATTTTATGTTAACGTTTATGTTAA
188509 A-TTTATGT
1 ATTTTATGT
188517 ATGAAATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (24 bp):
ATTTTATGTTAACGTTTATGTTAA
Found at i:188507 original size:12 final size:12
Alignment explanation
Indices: 188463--188516 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 12
188453 ATCTACTTGG
*
188463 ATTTTATGTT-C
1 ATTTTATGTTAA
* *
188474 AGTTTATTTTAA
1 ATTTTATGTTAA
188486 ATTTTA-GTTAA
1 ATTTTATGTTAA
*
188497 CTTTTATGTTAA
1 ATTTTATGTTAA
188509 A-TTTATGT
1 ATTTTATGT
188517 ATGAAATCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
11 24 0.71
12 10 0.29
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (12 bp):
ATTTTATGTTAA
Found at i:189771 original size:15 final size:15
Alignment explanation
Indices: 189759--189788 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
189749 TATATTATAT
189759 TATGTATTATTATTA
1 TATGTATTATTATTA
*
189774 TATTTATTATTATTA
1 TATGTATTATTATTA
189789 ATAGAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TATGTATTATTATTA
Found at i:189774 original size:18 final size:18
Alignment explanation
Indices: 189751--189788 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
189741 AAAAAATATA
189751 TATTATA-TTATGTATTAT
1 TATTATATTTAT-TATTAT
189769 TATTATATTTATTATTAT
1 TATTATATTTATTATTAT
189787 TA
1 TA
189789 ATAGAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTATATTTATTATTAT
Found at i:189780 original size:12 final size:13
Alignment explanation
Indices: 189747--189786 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
189737 GATTAAAAAA
189747 TATATATTA-TAT
1 TATATATTATTAT
*
189759 TATGTATTATTAT
1 TATATATTATTAT
189772 TATAT-TTATTAT
1 TATATATTATTAT
189784 TAT
1 TAT
189787 TAATAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TATATATTATTAT
Found at i:189798 original size:18 final size:19
Alignment explanation
Indices: 189757--189798 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
189747 TATATATTAT
* *
189757 ATTATGTATTATTATTATA
1 ATTATGTATTATTAATAGA
*
189776 TTTAT-TATTATTAATAGA
1 ATTATGTATTATTAATAGA
189794 ATTAT
1 ATTAT
189799 AATACATGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTATGTATTATTAATAGA
Found at i:191710 original size:30 final size:28
Alignment explanation
Indices: 191628--191711 Score: 69
Period size: 30 Copynumber: 2.9 Consensus size: 28
191618 CATTTTGGAC
* * *
191628 TTTTAAATTTCAGTTTGTGATATTTGGT
1 TTTTAAATTTCTGTTTGTGCTATTTGCT
* * * * *
191656 CTTCAAATTTTCTATTTTTACTATTCTAGCT
1 TTTTAAA-TTTCTGTTTGTGCTATT-T-GCT
191687 TTTTAAATTTCTGTTTGTGCTATTT
1 TTTTAAATTTCTGTTTGTGCTATTT
191712 TAATCCTTTA
Statistics
Matches: 40, Mismatches: 13, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
28 5 0.12
29 13 0.32
30 15 0.38
31 7 0.17
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (28 bp):
TTTTAAATTTCTGTTTGTGCTATTTGCT
Found at i:191722 original size:30 final size:30
Alignment explanation
Indices: 191688--191771 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 30
191678 ATTCTAGCTT
*
191688 TTTAAATTTCTGTTTGT-GCTATTTTAATCC
1 TTTAAATTTCTGTTT-TCGCTATTTTAATAC
* *
191718 TTT-AATTTCTATTTTCGTTATTTTAATAC
1 TTTAAATTTCTGTTTTCGCTATTTTAATAC
* **
191747 -TTAAAGTTTTTGTTTTATCTATTTT
1 TTTAAA-TTTCTGTTTTCGCTATTTT
191772 GGTCTTTATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.07
29 23 0.53
30 17 0.40
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (30 bp):
TTTAAATTTCTGTTTTCGCTATTTTAATAC
Found at i:196498 original size:2 final size:2
Alignment explanation
Indices: 196486--196531 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
196476 TCATTTATCC
*
196486 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
196528 AT AT
1 AT AT
196532 CCTTTGTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:196765 original size:11 final size:11
Alignment explanation
Indices: 196749--196801 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
196739 AAGCAAGGAT
196749 AATAAAGAGAA
1 AATAAAGAGAA
196760 AATAAAGAGAA
1 AATAAAGAGAA
*
196771 AA-AACAAAGAA
1 AATAA-AGAGAA
*
196782 AA-AAAAAGAAA
1 AATAAAGAG-AA
196793 AATAAAGAG
1 AATAAAGAG
196802 CTAAAAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
10 6 0.16
11 26 0.70
12 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (11 bp):
AATAAAGAGAA
Found at i:196839 original size:16 final size:16
Alignment explanation
Indices: 196769--196854 Score: 66
Period size: 16 Copynumber: 5.1 Consensus size: 16
196759 AAATAAAGAG
196769 AAAAAACAAAGAAAAA
1 AAAAAACAAAGAAAAA
*
196785 AAAAGAA-AAATAAAGAGCTA
1 AAAA-AACAAAGAAA-A---A
***
196805 AAAAAACAAAGAGTGA
1 AAAAAACAAAGAAAAA
196821 AAAAAACAAAGAAAAA
1 AAAAAACAAAGAAAAA
* *
196837 AAAAAAAAAATAAAAA
1 AAAAAACAAAGAAAAA
196853 AA
1 AA
196855 TAAAGATAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
16 40 0.74
17 3 0.06
19 2 0.04
20 9 0.17
ACGTcount: A:0.81, C:0.05, G:0.09, T:0.05
Consensus pattern (16 bp):
AAAAAACAAAGAAAAA
Found at i:197530 original size:32 final size:32
Alignment explanation
Indices: 197494--197577 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
197484 TAAGAAGGCT
*
197494 AAACCATTGACCAAAACCAACCTGAGACATTC
1 AAACCATTGACCAAAAACAACCTGAGACATTC
197526 AAACCATTGACCAAAAACAACCTGAGACATTC
1 AAACCATTGACCAAAAACAACCTGAGACATTC
*
197558 AAACCATTGACCAAACACAA
1 AAACCATTGACCAAAAACAA
197578 TAACCTGAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.48, C:0.30, G:0.08, T:0.14
Consensus pattern (32 bp):
AAACCATTGACCAAAAACAACCTGAGACATTC
Found at i:198014 original size:33 final size:32
Alignment explanation
Indices: 197916--198033 Score: 191
Period size: 32 Copynumber: 3.7 Consensus size: 32
197906 AAGCAATAGA
*
197916 GGGCATCTTTGGAAATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
197948 GGGCATATTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
197980 GGGCGTCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
*
198013 GGGCATCTTTAGAGATTCAAC
1 GGGCATCTTTGGAGATTCAAC
198034 GTCCTGAAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 52 0.66
33 27 0.34
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:198183 original size:34 final size:34
Alignment explanation
Indices: 198140--198261 Score: 174
Period size: 34 Copynumber: 3.6 Consensus size: 34
198130 AGATTTTTTT
*
198140 TGTCTCACTTGAGATAATTTCTCAAAATAAATTC
1 TGTCTCACTTGAGACAATTTCTCAAAATAAATTC
198174 TGTCTCACTTGAGACAATTTCTCAAAATAAATT-
1 TGTCTCACTTGAGACAATTTCTCAAAATAAATTC
* *
198207 TCGTCTCGCTTGAGACAATTTCTCAAAACAAATTC
1 T-GTCTCACTTGAGACAATTTCTCAAAATAAATTC
* * *
198242 CGTCTCGCTTGAGATAATTT
1 TGTCTCACTTGAGACAATTT
198262 TTCTCTGAGA
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
33 1 0.01
34 80 0.99
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (34 bp):
TGTCTCACTTGAGACAATTTCTCAAAATAAATTC
Found at i:198586 original size:40 final size:40
Alignment explanation
Indices: 198533--199075 Score: 897
Period size: 40 Copynumber: 13.6 Consensus size: 40
198523 ACATGTTTTA
198533 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
198573 TTAAAACATAAGATTTTATCTCACTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
*
198613 TTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
198653 ATGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
198693 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
*
198733 TTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
198773 ATGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* * *
198813 TTGAAACATAAGATTTTATATCACTCAAGATTGATTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
*
198853 TTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTG-TTTTTCC
*
198894 TTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
198934 TTGAAACAGAAGATTTTATCTCATTCAAGATTTTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
198974 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* ***
199014 TTGAAACATAAGATTTTATCTTGTTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
*
199054 TTGAAACAAAAGATTTTATCTC
1 TTGAAACAGAAGATTTTATCTC
199076 GCTGAGATAG
Statistics
Matches: 470, Mismatches: 32, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
40 431 0.92
41 39 0.08
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (40 bp):
TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
Found at i:198705 original size:23 final size:23
Alignment explanation
Indices: 198679--198747 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
198669 TATCTCATTC
198679 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* * **
198702 AAGA-T-TTTAT-C-T--CACTC
1 AAGATTGTTTTTCCTTGAAACAG
198719 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
198742 AAGATT
1 AAGATT
198748 TTATCTCGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 6 0.19
18 1 0.03
19 5 0.16
20 2 0.06
21 5 0.16
22 1 0.03
23 12 0.38
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:199026 original size:23 final size:22
Alignment explanation
Indices: 199000--199068 Score: 58
Period size: 23 Copynumber: 3.3 Consensus size: 22
198990 TATCTCACTC
199000 AAGATTGTTTTTCCTTGAAACA
1 AAGATTGTTTTTCCTTGAAACA
* **
199022 TAAGA-T-TTTAT-CTTG-TTC-
1 -AAGATTGTTTTTCCTTGAAACA
199040 AAGATTGTTTTTCCTTGAAACAA
1 AAGATTGTTTTTCCTTGAAAC-A
199063 AAGATT
1 AAGATT
199069 TTATCTCGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 5 0.15
20 8 0.24
21 5 0.15
22 1 0.03
23 10 0.29
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (22 bp):
AAGATTGTTTTTCCTTGAAACA
Found at i:199226 original size:43 final size:43
Alignment explanation
Indices: 199130--199341 Score: 290
Period size: 43 Copynumber: 5.0 Consensus size: 43
199120 CCTGCTTTTC
* *
199130 AGGGGTTTCTTGAAGAAAAGCTTGAAGGACCATC--GATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
*
199171 AGGGGTTTCTTGATGATAAGCTTGAAGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* *
199214 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCATGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* *
199257 ATGGG-TTCTTTGATGACAAGCTTG-AGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGACAAGCTTGAAG-GACCATCGTGATATGT
*
199300 AGGGGTTTCTTGATGACAAG-TTTAAGGGACCATCGTGATATG
1 AGGGGTTTCTTGATGACAAGCTTGAA-GGACCATCGTGATATG
199342 CAGTGATTCC
Statistics
Matches: 152, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
41 32 0.21
42 6 0.04
43 110 0.72
44 4 0.03
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (43 bp):
AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
Found at i:199517 original size:90 final size:91
Alignment explanation
Indices: 199362--199575 Score: 385
Period size: 90 Copynumber: 2.4 Consensus size: 91
199352 TTGGTGACAA
* * *
199362 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
1 TAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTCTAAGTCCTTCAGGCCATCCATAAGACCTTCA
199427 GTGCAAGATGTTTTCAAATGAGATTT
66 GTGCAAGATGTTTTCAAATGAGATTT
199453 T-AGAAACTAAGCCTTCGGGGGTTTCTTGATTTCTAAGTCCTTCAGGCCATCCATAAGACCTTCA
1 TAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTCTAAGTCCTTCAGGCCATCCATAAGACCTTCA
*
199517 GTGCATGATGTTTTCAAATGAGATTT
66 GTGCAAGATGTTTTCAAATGAGATTT
199543 TAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
1 TAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
199576 TTAAATCATT
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
90 86 0.73
91 32 0.27
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (91 bp):
TAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTCTAAGTCCTTCAGGCCATCCATAAGACCTTCA
GTGCAAGATGTTTTCAAATGAGATTT
Found at i:199852 original size:15 final size:15
Alignment explanation
Indices: 199840--199869 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
199830 TATATTATAT
199840 TATGTATTATTATTA
1 TATGTATTATTATTA
*
199855 TATTTATTATTATTA
1 TATGTATTATTATTA
199870 ATAGAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TATGTATTATTATTA
Found at i:199855 original size:18 final size:18
Alignment explanation
Indices: 199832--199869 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
199822 AAAAAATATA
199832 TATTATA-TTATGTATTAT
1 TATTATATTTAT-TATTAT
199850 TATTATATTTATTATTAT
1 TATTATATTTATTATTAT
199868 TA
1 TA
199870 ATAGAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTATATTTATTATTAT
Found at i:199861 original size:12 final size:13
Alignment explanation
Indices: 199828--199867 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
199818 GATTAAAAAA
199828 TATATATTA-TAT
1 TATATATTATTAT
*
199840 TATGTATTATTAT
1 TATATATTATTAT
199853 TATAT-TTATTAT
1 TATATATTATTAT
199865 TAT
1 TAT
199868 TAATAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TATATATTATTAT
Found at i:199879 original size:18 final size:19
Alignment explanation
Indices: 199838--199880 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
199828 TATATATTAT
* *
199838 ATTATGTATTATTATTATA
1 ATTATGTATTATTAATAGA
*
199857 TTTAT-TATTATTAATAGA
1 ATTATGTATTATTAATAGA
199875 ATTATG
1 ATTATG
199881 ATACATGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
ATTATGTATTATTAATAGA
Found at i:201756 original size:59 final size:59
Alignment explanation
Indices: 201693--201806 Score: 131
Period size: 59 Copynumber: 1.9 Consensus size: 59
201683 TATTTTAGGA
* * * *
201693 TTTAAA-GTTCATGTTTTTGCCATTTTGGTCTTTTAAATTTCAGTTTGTGATATTTGGTC
1 TTTAAATGTTC-TATTTTTACCATTCTAGTCTTTTAAATTTCAGTTTGTGATATTTGGTC
* * * * *
201752 TTTAAATTTTCTATTTTTACTATTCTAGTTTTTTAAATTTCTGTTTGTGCTATTT
1 TTTAAATGTTCTATTTTTACCATTCTAGTCTTTTAAATTTCAGTTTGTGATATTT
201807 TAATCCTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
59 42 0.93
60 3 0.07
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.59
Consensus pattern (59 bp):
TTTAAATGTTCTATTTTTACCATTCTAGTCTTTTAAATTTCAGTTTGTGATATTTGGTC
Found at i:201805 original size:30 final size:28
Alignment explanation
Indices: 201693--201806 Score: 84
Period size: 30 Copynumber: 3.9 Consensus size: 28
201683 TATTTTAGGA
* * *
201693 TTTAAAGTTCATGTTTTTGCCATTTTGGTCT
1 TTTAAATTTC-TGTTTGTGCTA-TTTGGT-T
* * *
201724 TTTAAATTTCAGTTTGTGATATTTGGTC
1 TTTAAATTTCTGTTTGTGCTATTTGGTT
* * * *
201752 TTTAAATTTTCTATTTTTACTATTCTAGTTT
1 TTTAAA-TTTCTGTTTGTGCTATT-T-GGTT
201783 TTTAAATTTCTGTTTGTGCTATTT
1 TTTAAATTTCTGTTTGTGCTATTT
201807 TAATCCTTTA
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
28 6 0.09
29 19 0.30
30 22 0.34
31 17 0.27
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.59
Consensus pattern (28 bp):
TTTAAATTTCTGTTTGTGCTATTTGGTT
Found at i:201817 original size:30 final size:30
Alignment explanation
Indices: 201783--201858 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
201773 ATTCTAGTTT
*
201783 TTTAAATTTCTGTTTGT-GCTATTTTAATCC
1 TTTAAATTTCTGTTT-TCGCTATTTTAATAC
* * *
201813 TTTAATTTTCTATTTTCGTTATTTTAATAC
1 TTTAAATTTCTGTTTTCGCTATTTTAATAC
*
201843 -TTAAAGTTTTTGTTTT
1 TTTAAA-TTTCTGTTTT
201859 TATCTATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.62
Consensus pattern (30 bp):
TTTAAATTTCTGTTTTCGCTATTTTAATAC
Found at i:202168 original size:16 final size:16
Alignment explanation
Indices: 202128--202168 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
202118 AACACATACC
202128 AATT-TTTTTTCTTAA
1 AATTGTTTTTTCTTAA
* *
202143 AAATGATTTTTCTTAA
1 AATTGTTTTTTCTTAA
202159 AATTGTTTTT
1 AATTGTTTTT
202169 AAAAGACGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (16 bp):
AATTGTTTTTTCTTAA
Found at i:203838 original size:16 final size:16
Alignment explanation
Indices: 203812--203851 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
203802 CAATTTCACG
203812 CTTTT-TTTCTTGTTT
1 CTTTTCTTTCTTGTTT
*
203827 CTTTTCTTTCTTTTTT
1 CTTTTCTTTCTTGTTT
*
203843 CCTTTCTTT
1 CTTTTCTTT
203852 TTTCTTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (16 bp):
CTTTTCTTTCTTGTTT
Found at i:203866 original size:12 final size:11
Alignment explanation
Indices: 203814--203858 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
203804 ATTTCACGCT
203814 TTTTTTCTTGT-
1 TTTTTTCTT-TC
203825 TTCTTTTCTTTC
1 TT-TTTTCTTTC
203837 TTTTTTCCTTTC
1 TTTTTT-CTTTC
203849 TTTTTTCTTT
1 TTTTTTCTTT
203859 GATTTTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:204473 original size:18 final size:18
Alignment explanation
Indices: 204450--204484 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
204440 ATTTCCAAGG
204450 TATTA-TTTACTTATTTTT
1 TATTATTTTACTT-TTTTT
204468 TATTATTTTACTTTTTT
1 TATTATTTTACTTTTTT
204485 AACTTTCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTATTTTACTTTTTTT
Found at i:207567 original size:14 final size:15
Alignment explanation
Indices: 207548--207584 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
207538 CCTTATTGCA
*
207548 TTTGCATCTCGTA-T
1 TTTGCATCTCCTATT
207562 TTTGCA-CTCCTATT
1 TTTGCATCTCCTATT
207576 TTTGCATCT
1 TTTGCATCT
207585 TTGCATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.14, C:0.24, G:0.11, T:0.51
Consensus pattern (15 bp):
TTTGCATCTCCTATT
Found at i:209949 original size:36 final size:36
Alignment explanation
Indices: 209896--211157 Score: 329
Period size: 39 Copynumber: 33.1 Consensus size: 36
209886 TTAATACAAG
* *
209896 AAGATTTATCTCTCTTGAGATTGTTTTTCTTAAAAC
1 AAGATTTATCTCGCTTGAGATAGTTTTTCTTAAAAC
* * * *
209932 AAGATTTGTCTCGCTTGAGACAGTTTCTACTTGAAACAAG
1 AAGATTTATCTCGCTTGAGATAGTTT-TTCTT--AA-AAC
* * * * *
209972 AAGATTCATTTCACTTAAGATTGTTTTTCTTAAAAC
1 AAGATTTATCTCGCTTGAGATAGTTTTTCTTAAAAC
* ** *
210008 AAGATTCATCTCGCTTGAGATAGTTTTTTGACTCGAAAT
1 AAGATTTATCTCGCTTGAGATAG-TTTTT--CTTAAAAC
* * ** * * *
210047 AAGACATTTCATTTCACTACAGATTGTATTTCTTAAACC
1 AAG--ATTT-ATCTCGCTTGAGATAGTTTTTCTTAAAAC
* ** *
210086 AAGATTCATCTCG-TGTGAGATAGTTTCACTTGAAATAG
1 AAGATTTATCTCGCT-TGAGATAGTTTTTCTT-AAA-AC
* *
210124 AAGATTTATCTCACTTGAGATTA-TTTGTCTTAAAAC
1 AAGATTTATCTCGCTTGAGA-TAGTTTTTCTTAAAAC
* ** * *
210160 TAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* * * * ** * *
210198 AAGATTTTATCTTGCGTGAAAGAGTTTCACTCGAAACAA
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* ** * *
210237 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
** * ** * *
210276 AAGATTTTATCTCATTTGAGATTGTTTCACTCGAAACAA
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
** * *
210315 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAA
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
** * *
210354 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAA
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
** *
210393 AAGATTTTATCTCGCTTGAGATAGTTTAACTCAAAAC
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCTTAAAAC
** * *
210430 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 --AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* * * *
210471 AAGATTCATCTCACTTGAG--A-TTATT-TTAAAAA
1 AAGATTTATCTCGCTTGAGATAGTTTTTCTTAAAAC
** * ** * *
210503 AAGATTTTATCTTACTTGAGATTGTTTCACTCGAAACAA
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* * ** * *
210542 AAGATTTTTATCTCGCTTAAGATTGTTTCACTCGAAACAT
1 AAGA--TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* * *
210582 AAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAATAG
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* ** * *
210621 AAGATTTTATCT-GTCTTGAGATTGTTTCACTCGAAACAA
1 AAGA-TTTATCTCG-CTTGAGATAGTTTTTCT-TAAA-AC
** * *
210660 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* * ** *
210699 AAGATTTTATCTCGGTTGAGATAGTTTCACTCGAAAAAA
1 AAGA-TTTATCTCGCTTGAGATAGTTT--TTCTTAAAAC
* ** *
210738 AAGATTTTATCTAGCTTGAGATAGTTTAACTCAAAAC
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCTTAAAAC
** * *
210775 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 --AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* * *
210816 AAGATTCATCTCACTTGAG--A-TTGTT-TTAAAAC
1 AAGATTTATCTCGCTTGAGATAGTTTTTCTTAAAAC
* * ** * *
210848 AAGATTTTATCTCGGTTGAGATTGTTTCACTCGAAACAG
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
** *
210887 AAGATTTTTATCTCGCTTGAGATAGTTTCACTCAAAAC
1 AAGA--TTTATCTCGCTTGAGATAGTTTTTCTTAAAAC
* * ** * *
210925 AGAAGATTTTATCTCACATGAGATAGTTTCACTCAAAATAG
1 --AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* * * *
210966 AAAATTTTATCTCGCTTGAGATAGTTTTACTCGAAACAT
1 AAGA-TTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* ** * *
211005 AAGATTT-TATCGCTTGAGATAGTTTCACTCGAAACAT
1 AAGATTTATCTCGCTTGAGATAGTTTTTCT-TAAA-AC
* ** *
211042 AATATTTTATCTCGCTTGCA-ATAGTTTCACTCAAAAC
1 AAGA-TTTATCTCGCTTG-AGATAGTTTTTCTTAAAAC
** *
211079 ATAAGATTTTATCTCGCTTGAGATAGTTTCAC-AAGAAAC
1 --AAGA-TTTATCTCGCTTGAGATAGTTTTTCTTA-AAAC
* * *
211118 AAAAGATTTATCTCACTTGATATTGTTTTTCTTAAAAC
1 --AAGATTTATCTCGCTTGAGATAGTTTTTCTTAAAAC
211156 AA
1 AA
211158 ACTATGCCTC
Statistics
Matches: 994, Mismatches: 173, Indels: 118
0.77 0.13 0.09
Matches are distributed among these distances:
32 10 0.01
33 31 0.03
34 2 0.00
35 7 0.01
36 89 0.09
37 63 0.06
38 98 0.10
39 572 0.58
40 99 0.10
41 12 0.01
42 11 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (36 bp):
AAGATTTATCTCGCTTGAGATAGTTTTTCTTAAAAC
Found at i:210089 original size:78 final size:77
Alignment explanation
Indices: 209891--210203 Score: 322
Period size: 74 Copynumber: 4.1 Consensus size: 77
209881 CTTATTTAAT
* * * * ** *
209891 ACAAGAAGATTTATCTCTCTTGAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAG-
1 ACAAGAAGATTCATTTCACTTAAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGT
*
209955 TTTCTACTTGAA
66 TTTCTACTCGAA
209967 ACAAGAAGATTCATTTCACTTAAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGT
1 ACAAGAAGATTCATTTCACTTAAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGT
*
210032 TTTTTGACTCGAA
66 TTTCT-ACTCGAA
* * * *
210045 ATAAGACA-TTTCATTTCAC-TACAGATTGTATTTCTTAAACCAAGATTCATCTCG-TGTGAGAT
1 ACAAGA-AGATTCATTTCACTTA-AGATTGTTTTTCTTAAAACAAGATTCATCTCGCT-TGAGAT
*
210107 AG-TTTC-ACTTGAA
63 AGTTTTCTACTCGAA
* * * * * * * *
210120 A-TAGAAGATTTATCTCACTTGAGATTATTTGTCTTAAAACTAGATTTATCTCGCTTGAGATAG-
1 ACAAGAAGATTCATTTCACTTAAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGT
210183 TTTC-ACTCGAA
66 TTTCTACTCGAA
210194 AC-AGAAGATT
1 ACAAGAAGATT
210204 TTATCTTGCG
Statistics
Matches: 201, Mismatches: 27, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
73 1 0.00
74 64 0.32
75 9 0.04
76 57 0.28
77 10 0.05
78 59 0.29
79 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (77 bp):
ACAAGAAGATTCATTTCACTTAAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGT
TTTCTACTCGAA
Found at i:210264 original size:78 final size:78
Alignment explanation
Indices: 210093--211137 Score: 1260
Period size: 78 Copynumber: 13.6 Consensus size: 78
210083 ACCAAGATTC
* * * **
210093 ATCTCG-TGTGAGATAGTTTCACTTGAAATAGAAGA-TTTATCTCACTTGAGATTA-TTTGTCT-
1 ATCTCGCT-TGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGA-TAGTTTCACTC
* **
210154 TAAA-ACTAGA-TTT
64 GAAACAGAAGATTTT
* * * *
210167 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTTGCGTGAAAGAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
210232 AACAAAAGATTTT
66 AACAGAAGATTTT
* ** *
210245 ATCTCGCTTGAGATTGTTTCACTCGAAACAGAAGATTTTATCTCATTTGAGATTGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
210310 AACAAAAGATTTT
66 AACAGAAGATTTT
* *
210323 ATCTCGCTTGAGATAGTTTCACTCGAAATAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
210388 AACAAAAGATTTT
66 AACAGAAGATTTT
* *
210401 ATCTCGCTTGAGATAGTTTAACTCAAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
210466 AACAGAAGA-TTC
66 AACAGAAGATTTT
* * ** *
210478 ATCTCACTTGAGATTA-TTT---T--AAA-AAAAGATTTTATCTTACTTGAGATTGTTTCACTCG
1 ATCTCGCTTGAGA-TAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
*
210536 AAACAAAAGATTTTT
65 AAACAGAAGA-TTTT
* * * *
210551 ATCTCGCTTAAGATTGTTTCACTCGAAACATAAGATTTTATCTCGCTTGAGATAGTTTTACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
210616 AATAGAAGATTTT
66 AACAGAAGATTTT
* *
210629 ATCT-GTCTTGAGATTGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
1 ATCTCG-CTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
210693 AAACAGAAGATTTT
65 AAACAGAAGATTTT
* * * * * *
210707 ATCTCGGTTGAGATAGTTTCACTCGAAAAAAAAGATTTTATCTAGCTTGAGATAGTTTAACTCAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
210772 AACAGAAGATTTT
66 AACAGAAGATTTT
* * *
210785 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTCATCTCACTTGAGATTGTTT---T--A
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
210844 AA-ACAAGATTTT
66 AACAGAAGATTTT
* * *
210856 ATCTCGGTTGAGATTGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTCA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTTATCTCGCTTGAGATAGTTTCACTCG
210921 AAACAGAAGATTTT
65 AAACAGAAGATTTT
* * * * * *
210935 ATCTCACATGAGATAGTTTCACTCAAAATAGAAAATTTTATCTCGCTTGAGATAGTTTTACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
211000 AACATAAGATTTT
66 AACAGAAGATTTT
* * *
211013 A--TCGCTTGAGATAGTTTCACTCGAAACATAATATTTTATCTCGCTTGCA-ATAGTTTCACTCA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTG-AGATAGTTTCACTCG
*
211075 AAACATAAGATTTT
65 AAACAGAAGATTTT
** * *
211089 ATCTCGCTTGAGATAGTTTCACAAGAAACAAAAGA-TTTATCTCACTTGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGA
211138 TATTGTTTTT
Statistics
Matches: 846, Mismatches: 96, Indels: 56
0.85 0.10 0.06
Matches are distributed among these distances:
71 82 0.10
72 7 0.01
73 35 0.04
74 34 0.04
75 18 0.02
76 72 0.09
77 53 0.06
78 469 0.55
79 76 0.09
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (78 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
AACAGAAGATTTT
Found at i:210584 original size:22 final size:22
Alignment explanation
Indices: 210521--210587 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
210511 ATCTTACTTG
*
210521 AGATTGTTTCACTCGAAACAAA
1 AGATTGTTTCACTCGAAACATA
*
210543 AGATT-TTT-ATCTCG---CTTA
1 AGATTGTTTCA-CTCGAAACATA
210561 AGATTGTTTCACTCGAAACATA
1 AGATTGTTTCACTCGAAACATA
210583 AGATT
1 AGATT
210588 TTATCTCGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
18 7 0.19
19 7 0.19
20 2 0.06
21 7 0.19
22 13 0.36
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
AGATTGTTTCACTCGAAACATA
Found at i:210626 original size:345 final size:344
Alignment explanation
Indices: 210093--211137 Score: 1534
Period size: 345 Copynumber: 3.0 Consensus size: 344
210083 ACCAAGATTC
* * *
210093 ATCTCG-TGTGAGATAGTTTCACTTGAAATAGAAGATTTATCTCACTTGAGATTATTTGTCTTAA
1 ATCTCGCT-TGAGATAGTTTCACTCGAAACAGAAGATTCATCTCACTTGAGATTA--T-T-TTAA
* * * *
210157 AACTAGA-TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTTATCTTGCGTGAAAG
61 AACAAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAGAAGATTTTTATCTCGC-T-TAAG
* *
210220 A-GTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAGAAGATTTT
124 ATGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTT
*
210284 ATCTCATTTGAGATTGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
189 ATCTCGTTTGAGATTGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
210349 AATAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGA
254 AACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGA
210414 TAGTTTAACTCAAAACAGAAGATTTT
319 TAGTTTAACTCAAAACAGAAGATTTT
*
210440 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTCATCTCACTTGAGATTATTTTAAAAAAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTCATCTCACTTGAGATTATTTTAAAACAA
** *
210505 GATTTTATCTTACTTGAGATTGTTTCACTCGAAACAAAAGATTTTTATCTCGCTTAAGATTGTTT
66 GATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTAAGA-TGTTT
* *
210570 CACTCGAAACATAAGATTTTATCTCGCTTGAGATAGTTTTACTCGAAATAGAAGATTTTATCT-G
130 CACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCG
*
210634 TCTTGAGATTGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
195 T-TTGAGATTGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAA
* * *
210699 AAGATTTTATCTCGGTTGAGATAGTTTCACTCGAAAAAAAAGATTTTATCTAGCTTGAGATAGTT
259 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTT
210764 TAACTCAAAACAGAAGATTTT
324 TAACTCAAAACAGAAGATTTT
*
210785 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTCATCTCACTTGAGATTGTTTTAAAACAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTCATCTCACTTGAGATTATTTTAAAACAA
* *
210850 GATTTTATCTCGGTTGAGATTGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTT
66 GATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTAAGAT-GTTT
* * * * * *
210915 CACTCAAAACAGAAGATTTTATCTCACATGAGATAGTTTCACTCAAAATAGAAAATTTTATCTCG
130 CACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCG
* * * * *
210980 CTTGAGATAGTTTTACTCGAAACATAAGATTTTA--TCGCTTGAGATAGTTTCACTCGAAACATA
195 TTTGAGATTGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAA
* * *
211043 ATATTTTATCTCGCTTGCA-ATAGTTTCACTCAAAACATAAGATTTTATCTCGCTTGAGATAGTT
260 AGATTTTATCTCGCTTG-AGATAGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTT
* * *
211107 TCAC-AAGAAACAAAAGA-TTT
324 TAACTCA-AAACAGAAGATTTT
*
211127 ATCTCACTTGA
1 ATCTCGCTTGA
211138 TATTGTTTTT
Statistics
Matches: 638, Mismatches: 50, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
342 14 0.02
343 109 0.17
344 39 0.06
345 425 0.67
346 1 0.00
347 49 0.08
348 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (344 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTCATCTCACTTGAGATTATTTTAAAACAA
GATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTAAGATGTTTC
ACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCGT
TTGAGATTGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAA
GATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTA
ACTCAAAACAGAAGATTTT
Found at i:211236 original size:59 final size:59
Alignment explanation
Indices: 211161--211599 Score: 515
Period size: 59 Copynumber: 7.4 Consensus size: 59
211151 AAAACAAACT
* * * * **
211161 ATGCCTCGCTTGAGGGATCAACATTTTATTTGCTCGATTCATAATGCTTCGAATCAGCA
1 ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTTGATTCACAACACTTCGAATCAGCA
*
211220 ACGCCTCACTTGAGGGATCAACA-TTTCTTTTGCTTGATTCACAACACTTCGAATCAGCA
1 ATGCCTCACTTGAGGGATCAACATTTTC-TTTGCTTGATTCACAACACTTCGAATCAGCA
* * *
211279 ATGCCTCACTTGAGGGATCAACATTTCCTTTGCTTGATTCA-AACCACTTCGAATTAGTA
1 ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTTGATTCACAA-CACTTCGAATCAGCA
* * * * *
211338 ATGTCTCACTTGAGGGATCAACATTTCCTTTGCTTGATTAACAATACTTCGAATTAGCA
1 ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTTGATTCACAACACTTCGAATCAGCA
* * * *
211397 ATACCTCACTTGAGGGATCAATA-TTTCTTTTGCTCGATTCACAACACTTCGAATCAGTA
1 ATGCCTCACTTGAGGGATCAACATTTTC-TTTGCTTGATTCACAACACTTCGAATCAGCA
* * * * *
211456 ATACCTCACTCGAGGGATCAATATTTCCTTTGCTTGATTCACAACACTTCGAATCAGTA
1 ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTTGATTCACAACACTTCGAATCAGCA
* * * * * * *
211515 ATGCCTCATTTGAGGGATCAATATTTTCTTTTCTCGATTTATAACACTTCGAATCAGCG
1 ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTTGATTCACAACACTTCGAATCAGCA
* * * *
211574 ACGTCTCACTCGAGGGACCAACATTT
1 ATGCCTCACTTGAGGGATCAACATTT
211600 CCAATGGAAA
Statistics
Matches: 331, Mismatches: 43, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
58 8 0.02
59 315 0.95
60 8 0.02
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (59 bp):
ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTTGATTCACAACACTTCGAATCAGCA
Found at i:211370 original size:118 final size:118
Alignment explanation
Indices: 211161--211601 Score: 569
Period size: 118 Copynumber: 3.7 Consensus size: 118
211151 AAAACAAACT
* ** **
211161 ATGCCTCGCTTGAGGGATCAACATTTTATTTGCTCGATTCATAATGCTTCGAATCAGCAACGCCT
1 ATGCCTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCATAACACTTCGAATCAGCAACGCCT
* *
211226 CACTTGAGGGATCAACATTTCTTTTGCTTGATTCACAACACTTCGAATCAGCA
66 CACTCGAGGGATCAACATTTCCTTTGCTTGATTCACAACACTTCGAATCAGCA
* * * * *
211279 ATGCCTCACTTGAGGGATCAACATTTCCTTTGCTTGATTCA-AACCACTTCGAATTAGTAATGTC
1 ATGCCTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCATAA-CACTTCGAATCAGCAACGCC
* * * *
211343 TCACTTGAGGGATCAACATTTCCTTTGCTTGATTAACAATACTTCGAATTAGCA
65 TCACTCGAGGGATCAACATTTCCTTTGCTTGATTCACAACACTTCGAATCAGCA
* * * * * **
211397 ATACCTCACTTGAGGGATCAATATTTCTTTTGCTCGATTCACAACACTTCGAATCAGTAATACCT
1 ATGCCTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCATAACACTTCGAATCAGCAACGCCT
* *
211462 CACTCGAGGGATCAATATTTCCTTTGCTTGATTCACAACACTTCGAATCAGTA
66 CACTCGAGGGATCAACATTTCCTTTGCTTGATTCACAACACTTCGAATCAGCA
* * * * * * *
211515 ATGCCTCATTTGAGGGATCAATATTTTCTTTTCTCGATTTATAACACTTCGAATCAGCGACGTCT
1 ATGCCTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCATAACACTTCGAATCAGCAACGCCT
*
211580 CACTCGAGGGACCAACATTTCC
66 CACTCGAGGGATCAACATTTCC
211602 AATGGAAAGA
Statistics
Matches: 280, Mismatches: 41, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
117 2 0.01
118 276 0.99
119 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (118 bp):
ATGCCTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCATAACACTTCGAATCAGCAACGCCT
CACTCGAGGGATCAACATTTCCTTTGCTTGATTCACAACACTTCGAATCAGCA
Found at i:211465 original size:177 final size:177
Alignment explanation
Indices: 211161--211600 Score: 612
Period size: 177 Copynumber: 2.5 Consensus size: 177
211151 AAAACAAACT
* * * * *
211161 ATGCCTCGCTTGAGGGATCAACATTTTATTTGCTCGATTCATAATGCTTCGAATCAGCAACGCCT
1 ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTCGATTAATAATACTTCGAATCAGCAACACCT
* * *
211226 CACTTGAGGGATCAACATTTCTTTTGCTTGATTCACAACACTTCGAATCAGCAATGCCTCACTTG
66 CACTTGAGGGATCAACATTTCTTTTGCTCGATTCACAACACTTCGAATCAGCAATACCTCACTCG
*
211291 AGGGATCAACATTTCCTTTGCTTGATTCA-AACCACTTCGAATTAGTA
131 AGGGATCAACATTTCCTTTGCTTGATTCACAA-CACTTCGAATCAGTA
* * * * * *
211338 ATGTCTCACTTGAGGGATCAACATTTCCTTTGCTTGATTAACAATACTTCGAATTAGCAATACCT
1 ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTCGATTAATAATACTTCGAATCAGCAACACCT
* *
211403 CACTTGAGGGATCAATATTTCTTTTGCTCGATTCACAACACTTCGAATCAGTAATACCTCACTCG
66 CACTTGAGGGATCAACATTTCTTTTGCTCGATTCACAACACTTCGAATCAGCAATACCTCACTCG
*
211468 AGGGATCAATATTTCCTTTGCTTGATTCACAACACTTCGAATCAGTA
131 AGGGATCAACATTTCCTTTGCTTGATTCACAACACTTCGAATCAGTA
* * * * * * **
211515 ATGCCTCATTTGAGGGATCAATATTTTCTTTTCTCGATTTATAACACTTCGAATCAGCGACGTCT
1 ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTCGATTAATAATACTTCGAATCAGCAACACCT
* *
211580 CACTCGAGGGACCAACATTTC
66 CACTTGAGGGATCAACATTTC
211601 CAATGGAAAG
Statistics
Matches: 227, Mismatches: 35, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
177 225 0.99
178 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (177 bp):
ATGCCTCACTTGAGGGATCAACATTTTCTTTGCTCGATTAATAATACTTCGAATCAGCAACACCT
CACTTGAGGGATCAACATTTCTTTTGCTCGATTCACAACACTTCGAATCAGCAATACCTCACTCG
AGGGATCAACATTTCCTTTGCTTGATTCACAACACTTCGAATCAGTA
Found at i:212751 original size:15 final size:15
Alignment explanation
Indices: 212731--212760 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
212721 TATCTTTTTT
212731 TAAAAAAAGAAAAAA
1 TAAAAAAAGAAAAAA
212746 TAAAAAAAGAAAAAA
1 TAAAAAAAGAAAAAA
212761 GTTGTATTTA
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:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (15 bp):
TAAAAAAAGAAAAAA
Found at i:213233 original size:34 final size:35
Alignment explanation
Indices: 213195--213260 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
213185 TTTTTCCCTT
213195 TATTTT-TTAGTACTTTAAT-TTTAGTA-CTTTTATA
1 TATTTTATTAGT-CTTTAATATTT-GTATCTTTTATA
*
213229 TATTTTATTTGTCTTTAATATTTGTATCTTTT
1 TATTTTATTAGTCTTTAATATTTGTATCTTTT
213261 TATTGCCCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (35 bp):
TATTTTATTAGTCTTTAATATTTGTATCTTTTATA
Found at i:215228 original size:21 final size:21
Alignment explanation
Indices: 215176--215234 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 21
215166 CATATGAAAG
* *
215176 CATCTTGCCCAAAGGACTTAT
1 CATCTTGCTCGAAGGACTTAT
** *
215197 -AGATGGCTCGAAGGACTTAT
1 CATCTTGCTCGAAGGACTTAT
*
215217 CATCTTGCTCGAAAGACT
1 CATCTTGCTCGAAGGACT
215235 GACAGATGAC
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (21 bp):
CATCTTGCTCGAAGGACTTAT
Found at i:215330 original size:258 final size:257
Alignment explanation
Indices: 214870--215422 Score: 851
Period size: 258 Copynumber: 2.1 Consensus size: 257
214860 ATTTTTCAAA
** * *
214870 AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAAGTTTCTTGCCCAAGGGTC
1 AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAAGCATCTTGCCCAAAGGAC
* * *
214935 TTATAGATGGCCTGAAGGACTTATCATCTTGCTCGAAAAACTGATAGATGGCATGAAGATTTAAT
66 TTATAGATGGCCTGAAGGACTTATCATCTTGCTCGAAAAACTGACAGATGCCATAAAGATTTAAT
* * * * *
215000 CATCGTGCTTGAAAGACTTACTGATGGCTCAAAGGTCTTACCAATTTTGGAAATAGTTTATTAGG
131 CATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
* *
215065 CAAGAAACTTTAGAAATCGCTTTCTTACTTTTCAAAAAATTCATTTTCTAAAAATACTAAATG
196 CAAGAAACTTTAGAAATCACTTTCTTACTTTTCAAAAAATTCATCTTCT-AAAATACTAAATG
215128 AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAAGCATCTTGCCCAAAGGAC
1 AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAAGCATCTTGCCCAAAGGAC
*
215193 TTATAGATGG-CTCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCA-AAAGATTT
66 TTATAGATGGCCT-GAAGGACTTATCATCTTGCTCGAAAAACTGACAGATG--CCATAAAGATTT
* *
215256 AATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-CAATTTTGGAATTAGTTTACT
128 AATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACT
* * * **
215320 ATGTAAGAAACTTTTGAAATCACTTTCTTACTTTTCAAAATCTTCATCTTCTAAAATACTAAATG
193 AGGCAAGAAACTTTAGAAATCACTTTCTTACTTTTCAAAAAATTCATCTTCTAAAATACTAAATG
215385 AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTAT
1 AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTAT
215423 ATAAAAACAA
Statistics
Matches: 270, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
257 53 0.20
258 170 0.63
259 45 0.17
260 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (257 bp):
AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAAGCATCTTGCCCAAAGGAC
TTATAGATGGCCTGAAGGACTTATCATCTTGCTCGAAAAACTGACAGATGCCATAAAGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
CAAGAAACTTTAGAAATCACTTTCTTACTTTTCAAAAAATTCATCTTCTAAAATACTAAATG
Found at i:217467 original size:15 final size:15
Alignment explanation
Indices: 217444--217484 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
217434 ACTTGATATG
*
217444 TTCTCTTTCTTCTTC
1 TTCTTTTTCTTCTTC
217459 TTCTTTTTCTTC-TC
1 TTCTTTTTCTTCTTC
217473 TT-TTTTT-TTCTT
1 TTCTTTTTCTTCTT
217485 TTTTATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 3 0.12
13 6 0.25
14 4 0.17
15 11 0.46
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTTTCTTCTTC
Found at i:217468 original size:12 final size:12
Alignment explanation
Indices: 217447--217487 Score: 52
Period size: 10 Copynumber: 3.6 Consensus size: 12
217437 TGATATGTTC
217447 TCTTTCTTCTTCT
1 TCTTT-TTCTTCT
217460 TCTTTTTCTTC-
1 TCTTTTTCTTCT
217471 TCTTTTT-TT-T
1 TCTTTTTCTTCT
217481 TCTTTTT
1 TCTTTTT
217488 TATTGTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 6 0.22
13 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TCTTTTTCTTCT
Found at i:228906 original size:21 final size:21
Alignment explanation
Indices: 228880--228960 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
228870 CAGAACCCCA
*
228880 GGGGGGTATCGATTCCCCTAT
1 GGGGGGAATCGATTCCCCTAT
* *
228901 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-T-AT
* *
228924 AGGGGGAATCGGTT-CCCTCA-
1 GGGGGGAATCGATTCCCCT-AT
*
228944 GGGGGGGATCGATTCCC
1 GGGGGGAATCGATTCCC
228961 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 11 0.22
21 21 0.42
22 4 0.08
23 14 0.28
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTAT
Found at i:232814 original size:22 final size:21
Alignment explanation
Indices: 232772--232811 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
232762 GAGTTTGTTT
*
232772 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
232793 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
232812 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:251162 original size:2 final size:2
Alignment explanation
Indices: 251155--251194 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
251145 AATACAATTA
251155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
251195 TATTTATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252792 original size:18 final size:17
Alignment explanation
Indices: 252766--252826 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
252756 GGGTCTGTAT
*
252766 AAATAAAAATAAAAACTA
1 AAATTAAAATAAAAA-TA
*
252784 AAATTAAAATTAAAA-A
1 AAATTAAAATAAAAATA
* *
252800 AAATTAAAATAATAAGTT
1 AAATTAAAATAA-AAATA
252818 AAATTAAAA
1 AAATTAAAA
252827 ATCCGGATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 12 0.33
17 2 0.06
18 22 0.61
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AAATTAAAATAAAAATA
Found at i:257648 original size:2 final size:2
Alignment explanation
Indices: 257643--257681 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
257633 AAACGAATTA
257643 AT AT AT AT AT AT AT AT AT AT 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 AT AT A
257682 ATAGTATAAG
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:269161 original size:23 final size:23
Alignment explanation
Indices: 269117--269176 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
269107 GAACACCTAC
* *
269117 GCGAACATATAAAAGAATATATTT
1 GCGAACAT-TAAATGAACATATTT
*
269141 GCGTACATTAAATGAACATATTT
1 GCGAACATTAAATGAACATATTT
*
269164 GCGAACAATAAAT
1 GCGAACATTAAAT
269177 AAACGAACAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 24 0.77
24 7 0.23
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (23 bp):
GCGAACATTAAATGAACATATTT
Found at i:270660 original size:2 final size:2
Alignment explanation
Indices: 270653--270684 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
270643 TTCAAGTGAC
270653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
270685 GGCAAACCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:272639 original size:16 final size:16
Alignment explanation
Indices: 272618--272648 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
272608 TTTTGTATTT
272618 TTAAAGAAATAAAAAA
1 TTAAAGAAATAAAAAA
*
272634 TTAAAGTAATAAAAA
1 TTAAAGAAATAAAAA
272649 TATATTAAGT
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:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
TTAAAGAAATAAAAAA
Found at i:283153 original size:19 final size:19
Alignment explanation
Indices: 283129--283165 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
283119 ATGACCAACA
*
283129 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
283148 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
283166 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:283256 original size:21 final size:21
Alignment explanation
Indices: 283210--283263 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
283200 GATTTTTACT
*
283210 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
283231 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
283252 ATCGCAATGCGA
1 ATCGCATTGCGA
283264 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:283914 original size:19 final size:18
Alignment explanation
Indices: 283892--283950 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
283882 AAAATCGCAA
283892 TGCGATTTTAGTTTCGCGT
1 TGCGATTTTA-TTTCGCGT
*
283911 TGCGA---T-TTTCTCGT
1 TGCGATTTTATTTCGCGT
283925 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-ATTTCGCGT
283944 TGCGATT
1 TGCGATT
283951 ATCTCGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 12 0.36
16 1 0.03
17 1 0.03
19 19 0.58
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:283925 original size:14 final size:14
Alignment explanation
Indices: 283903--283963 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 14
283893 GCGATTTTAG
*
283903 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
283917 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
283931 TTTCATTTCGCGTTGCGAT
1 TTTC---T--CGTTGCGAT
*
283950 TATCTCGTTGCGAT
1 TTTCTCGTTGCGAT
283964 AGTCATTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 26 0.65
16 1 0.03
17 1 0.03
19 12 0.30
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:283940 original size:33 final size:34
Alignment explanation
Indices: 283892--283987 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
283882 AAAATCGCAA
283892 TGCGATTTT-AGTTTCGCGTTGCGATTTTCTCGT
1 TGCGATTTTCAGTTTCGCGTTGCGATTTTCTCGT
*
283925 TGCGATTTTCA-TTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCAGTTTCGCGTTGCGATTTTCTCGT
** * *
283958 TGCGATAGTCATTTTCGTGTTGCGATTTTC
1 TGCGATTTTCAGTTTCGCGTTGCGATTTTC
283988 ATTTTCGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
33 39 0.70
34 17 0.30
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (34 bp):
TGCGATTTTCAGTTTCGCGTTGCGATTTTCTCGT
Found at i:283981 original size:20 final size:20
Alignment explanation
Indices: 283956--284003 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
283946 CGATTATCTC
283956 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
283976 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
*
283996 ATTGCGAT
1 GTTGCGAT
284004 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.48
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:284004 original size:20 final size:20
Alignment explanation
Indices: 283966--284006 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
283956 GTTGCGATAG
*
283966 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTATTGCGATTT
283986 TCATTTTCGTATTGCGATTT
1 TCATTTTCGTATTGCGATTT
284006 T
1 T
284007 AAGTTTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTATTGCGATTT
Found at i:284013 original size:20 final size:20
Alignment explanation
Indices: 283970--284013 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
283960 CGATAGTCAT
* * *
283970 TTTCGTGTTGCGATTTTCAT
1 TTTCGTATTGCGATTTTAAG
283990 TTTCGTATTGCGATTTTAAG
1 TTTCGTATTGCGATTTTAAG
284010 TTTC
1 TTTC
284014 ATAAACTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTATTGCGATTTTAAG
Found at i:285893 original size:20 final size:20
Alignment explanation
Indices: 285870--285938 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
285860 GAAACTTAAA
285870 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
285890 ATCGCAACGTGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
285910 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
285930 ATCGCAACG
1 ATCGCAACG
285939 GGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:285980 original size:33 final size:34
Alignment explanation
Indices: 285930--286005 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
285920 GAATTTGACT
*
285930 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
* *
285963 ATCGCAACGTGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
285997 ATCGCAACG
1 ATCGCAACG
286006 CGAATTTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
Found at i:285995 original size:20 final size:20
Alignment explanation
Indices: 285972--286009 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
285962 AATCGCAACG
*
285972 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
285992 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
286010 TTTAGTTTCG
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:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:286027 original size:19 final size:19
Alignment explanation
Indices: 286005--286047 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
285995 AAATCGCAAC
*
286005 GCGA-ATTTAGTTTCGCGTT
1 GCGATATTTA-TTTCGCATT
*
286024 GCGATTTTTATTTCGCATT
1 GCGATATTTATTTCGCATT
286043 GCGAT
1 GCGAT
286048 TATCCCGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (19 bp):
GCGATATTTATTTCGCATT
Found at i:286048 original size:19 final size:20
Alignment explanation
Indices: 286010--286048 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
286000 GCAACGCGAA
*
286010 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
286030 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
286049 ATCCCGTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:286115 original size:20 final size:20
Alignment explanation
Indices: 286057--286117 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
286047 TTATCCCGTA
**
286057 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCATTTTCGCGTT
*
286077 GCGATAGTCATTTCCGCGTT
1 GCGATAGTCATTTTCGCGTT
*
286097 GCGATAGTCATTTTTGCGTT
1 GCGATAGTCATTTTCGCGTT
286117 G
1 G
286118 TGATTTTAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
GCGATAGTCATTTTCGCGTT
Found at i:286685 original size:42 final size:42
Alignment explanation
Indices: 286621--286732 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 42
286611 CTGTCATCGT
* * *
286621 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * * **
286663 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCTCCTGTCATCGT
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * * *
286705 TGAAAAGGTCCCTCCCACCATTCAAGAG
1 TCAAGAGGCCCCTCCCACCGTTCAAGAG
286733 CCCGATTCAC
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:286687 original size:21 final size:21
Alignment explanation
Indices: 286618--286732 Score: 79
Period size: 21 Copynumber: 5.5 Consensus size: 21
286608 CACCTGTCAT
* * *
286618 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCCCCTCCCAC
**
286639 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGCCCCTCCCA-C
* *
286661 C-CTCAAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
* ** *
286681 CGTTCAAGAGGCTCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* * *
286702 CGTTGAAAAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
*
286723 CATTCAAGAG
1 CGTTCAAGAG
286733 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 25, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
20 2 0.03
21 64 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:287536 original size:20 final size:20
Alignment explanation
Indices: 287511--287625 Score: 158
Period size: 20 Copynumber: 5.8 Consensus size: 20
287501 ATTGTCTGAT
287511 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
287531 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
287551 TTGCGATAATCAAATTCGTG
1 TTGCGATAGTCAAATTCGCG
*
287571 TTGCGATAGTCAAATTCGTG
1 TTGCGATAGTCAAATTCGCG
* *
287591 TTGTGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCG
* *
287611 CTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
287626 GAATGTGTAA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:287604 original size:60 final size:60
Alignment explanation
Indices: 287511--287625 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
287501 ATTGTCTGAT
**
287511 TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATAATCAAATTCGTG
1 TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCACTGCGATAATCAAATTCGTG
* * * *
287571 TTGCGATAGTCAAATTCGTGTTGTGATAGTCAAATTCGCACTGCGATATTCAAAT
1 TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCACTGCGATAATCAAAT
287626 GAATGTGTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (60 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCACTGCGATAATCAAATTCGTG
Found at i:287819 original size:18 final size:18
Alignment explanation
Indices: 287796--287830 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
287786 AAGCCGGTTG
*
287796 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
287814 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
287831 GTCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:290113 original size:24 final size:24
Alignment explanation
Indices: 290079--290134 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
290069 CTGAAACATC
*
290079 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
290103 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
290127 ATCAAAAT
1 ATCAAAAT
290135 TTCGAATACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:290809 original size:17 final size:17
Alignment explanation
Indices: 290787--290824 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
290777 CGGATGGGGA
290787 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
290804 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
290821 AGGA
1 AGGA
290825 ACGGATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:290833 original size:22 final size:20
Alignment explanation
Indices: 290784--290834 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
290774 TGCCGGATGG
290784 GGAAGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
290804 ---AGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
290821 AGGAACGGATGTCG
1 -GGAA-GGATGTCG
290835 CCGGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 17 0.65
21 1 0.04
22 8 0.31
ACGTcount: A:0.25, C:0.08, G:0.39, T:0.27
Consensus pattern (20 bp):
GGAAGGATGTCGTTGGATAT
Found at i:291078 original size:20 final size:19
Alignment explanation
Indices: 291055--291100 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
291045 GGAAACTGAT
* *
291055 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
291075 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
291094 TTGCGAT
1 TTGCGAT
291101 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:291090 original size:19 final size:19
Alignment explanation
Indices: 291066--291102 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
291056 TGCGATACTG
*
291066 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
291085 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
291103 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:292550 original size:2 final size:2
Alignment explanation
Indices: 292543--292569 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
292533 TTTCCTTTAT
292543 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
292570 GTCATTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:297737 original size:17 final size:18
Alignment explanation
Indices: 297701--297744 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
297691 GAATCAAAAG
*
297701 AAAAATAATGATATAATAT
1 AAAAATAA-GATAAAATAT
297720 AAAAATAA-ATAAAATAT
1 AAAAATAAGATAAAATAT
297737 AAGAAATA
1 AA-AAATA
297745 CCAACAATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 5 0.22
19 8 0.35
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAAATAAGATAAAATAT
Found at i:298717 original size:21 final size:21
Alignment explanation
Indices: 298691--298730 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
298681 ACATGGCTTT
298691 CCATGCATGGCCAGGGGGAAG
1 CCATGCATGGCCAGGGGGAAG
* *
298712 CCATGCGTGGCCGGGGGGA
1 CCATGCATGGCCAGGGGGA
298731 GGAGTCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.47, T:0.10
Consensus pattern (21 bp):
CCATGCATGGCCAGGGGGAAG
Found at i:303754 original size:2 final size:2
Alignment explanation
Indices: 303747--303813 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
303737 TCAGTTTTAT
303747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
303789 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
303814 TCTGGGTATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:305255 original size:19 final size:19
Alignment explanation
Indices: 305228--305269 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
305218 TGCTCTCCCG
*
305228 TCCCTAAAATAAATCCCCA
1 TCCCCAAAATAAATCCCCA
* *
305247 TCCCCAAAATGAATCCCCG
1 TCCCCAAAATAAATCCCCA
305266 TCCC
1 TCCC
305270 TGCCCCGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.43, G:0.05, T:0.19
Consensus pattern (19 bp):
TCCCCAAAATAAATCCCCA
Found at i:305717 original size:2 final size:2
Alignment explanation
Indices: 305710--305750 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
305700 TTAATATAAA
305710 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
305751 CATTATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:308740 original size:21 final size:21
Alignment explanation
Indices: 308684--308843 Score: 106
Period size: 21 Copynumber: 7.9 Consensus size: 21
308674 GATTCTGACT
* * *
308684 ATCGCATTGCG-ATTTTCCTA
1 ATCGCAATGCGAATTTACGTA
*
308704 ATTCGCATTGCG-ATTTACGTA
1 A-TCGCAATGCGAATTTACGTA
** *
308725 ATCGCAATGCGAATTTGGGAA
1 ATCGCAATGCGAATTTACGTA
308746 ATCGCAATGCGAA--TACGTAA
1 ATCGCAATGCGAATTTACGT-A
* *
308766 ATCGCAATGCGAA-TTAGGAAA
1 ATCGCAATGCGAATTTACG-TA
*
308787 ATCGCAATGTGAA--TACGTAA
1 ATCGCAATGCGAATTTACGT-A
*
308807 ATCGCAATGCGAATCTGAC-T-
1 ATCGCAATGCGAAT-TTACGTA
308827 ATCGCAATGCG-ATTTAC
1 ATCGCAATGCGAATTTAC
308844 ATAGCGCCAT
Statistics
Matches: 114, Mismatches: 17, Indels: 20
0.75 0.11 0.13
Matches are distributed among these distances:
18 3 0.03
19 4 0.04
20 51 0.45
21 53 0.46
22 1 0.01
23 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (21 bp):
ATCGCAATGCGAATTTACGTA
Found at i:308751 original size:41 final size:41
Alignment explanation
Indices: 308719--308820 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
308709 CATTGCGATT
* *
308719 TACGT-AATCGCAATGCGAATTTGGGAAATCGCAATGCGAA
1 TACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAA
*
308759 TACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGTGAA
1 TACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAA
308800 TACGTAAATCGCAATGCGAAT
1 TACGTAAATCGCAATGCGAAT
308821 CTGACTATCG
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
40 5 0.09
41 53 0.91
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (41 bp):
TACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAA
Found at i:309429 original size:33 final size:33
Alignment explanation
Indices: 309371--309463 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
309361 TGAGAATGAA
* ** *
309371 AATCGCAATGCGGAAATGACTATCGCAACGAGCG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
*
309405 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
309438 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
309464 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 42 0.81
34 10 0.19
ACGTcount: A:0.42, C:0.25, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:309500 original size:14 final size:14
Alignment explanation
Indices: 309481--309569 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
309471 TTTCATTTCG
309481 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
309495 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
309514 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
309528 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
309547 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
309561 CGTTGCGAT
1 CGTTGCGAT
309570 AGTCATTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 29 0.48
16 6 0.10
17 6 0.10
19 20 0.33
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:309506 original size:33 final size:33
Alignment explanation
Indices: 309464--309618 Score: 229
Period size: 33 Copynumber: 4.5 Consensus size: 33
309454 CAAAATCGCA
309464 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
309497 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
309530 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
309563 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTATCTCG
1 TTGCGATTTTCATTT-CGCGTTGCGA--TTC----TCTCG
309603 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
309619 AACCAAAAGA
Statistics
Matches: 111, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
33 79 0.71
34 10 0.09
36 3 0.03
39 1 0.01
40 18 0.16
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:311498 original size:94 final size:93
Alignment explanation
Indices: 311311--311593 Score: 448
Period size: 94 Copynumber: 3.1 Consensus size: 93
311301 TAGATTGCTT
* *
311311 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
311372 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
311401 AGTAAATTTATTCGGTTGCTGCTAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
311466 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
311495 AGTAAATTTGTTCCGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
311560 ATTTGTCTTTGTTTTATCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
311588 AGTAAA
1 AGTAAA
311594 GCAATCCATT
Statistics
Matches: 179, Mismatches: 9, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
90 34 0.19
92 3 0.02
93 29 0.16
94 113 0.63
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Done.