Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 92 of 216
Found at i:28448739 original size:11 final size:12
Alignment explanation
Indices: 28448698--28448745 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
28448688 TAAAAATTAA
28448698 AAAAAGTATTTT
1 AAAAAGTATTTT
**
28448710 -AAAA--ATTAA
1 AAAAAGTATTTT
28448719 AAAAAGTATTTT
1 AAAAAGTATTTT
28448731 AAAAA-TATTTT
1 AAAAAGTATTTT
28448742 AAAA
1 AAAA
28448746 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
9 3 0.10
10 4 0.14
11 14 0.48
12 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (12 bp):
AAAAAGTATTTT
Found at i:28448751 original size:17 final size:17
Alignment explanation
Indices: 28448729--28448775 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
28448719 AAAAAGTATT
*
28448729 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
28448746 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
28448763 ATAAATATATTTA
1 TTAAAAATATTTA
28448776 TTATATAGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:28454956 original size:11 final size:12
Alignment explanation
Indices: 28454940--28454968 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
28454930 GTTTTATATA
28454940 TTTAACATGT-T
1 TTTAACATGTGT
28454951 TTTAACATGTGT
1 TTTAACATGTGT
28454963 TTTAAC
1 TTTAAC
28454969 CTTTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (12 bp):
TTTAACATGTGT
Found at i:28462113 original size:6 final size:6
Alignment explanation
Indices: 28462102--28462132 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
28462092 AGCTACTCCC
28462102 TATCTT TATCTT TATCTT TATCTT TATCTT T
1 TATCTT TATCTT TATCTT TATCTT TATCTT T
28462133 TTCTCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TATCTT
Found at i:28462157 original size:6 final size:6
Alignment explanation
Indices: 28462104--28462168 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
28462094 CTACTCCCTA
* * * * *
28462104 TCTTTA TCTTTA TCTTTA TCTTTA TCTTTT TCTCTTT TATTCTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCT-TTT TCTT-TT TCTTTT
*
28462154 TC-TTT TCTTCT TCTT
1 TCTTTT TCTTTT TCTT
28462169 ACTAATACTA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
5 5 0.10
6 37 0.71
7 10 0.19
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (6 bp):
TCTTTT
Found at i:28475088 original size:230 final size:223
Alignment explanation
Indices: 28474661--28475139 Score: 536
Period size: 230 Copynumber: 2.1 Consensus size: 223
28474651 AAAAGAAATA
* * * *
28474661 TGACAAGTGAAACTATA-TATATGGTACATATATATTTAATGTGTGAATGATTTTTGTGGATCAC
1 TGACAAGTGAAACTATATTATATGGCACATATATATTTAATGTATAAATGATTTTTATGGATCAC
*
28474725 ATTAAATGCAATGTTTTATTGTAAAAACGAAAAAAAAACGTTTTATTCCTCAAAATGTTTGAATA
66 ATTAAATGCAAAGTTTTATTGTAAAAACG-AAAAAAAACGTTTTATTCCTCAAAATGTTTGAATA
* *** * *
28474790 TATATAGGCAACAATTATAATAATAATAAAAATCCCTTTGGATATCATTCGCTTAATTTTTGTAT
130 TATATA-GCAACAATTATAATAATAAAAAAAATCCCTTCCAATATCATTCCCTTAATTTTTCTAT
28474855 ATTAAAAATTATGTGGCAAACTTCAATGTT
194 ATTAAAAATTATGTGGCAAACTTCAATGTT
* * * * * *
28474885 TGACAAATGAAACTATATTTATATGGCATATGTATATTTAATTTATAAATGTTTTTTATGGGTCA
1 TGACAAGTGAAACTATA-TTATATGGCACATATATATTTAATGTATAAATGATTTTTATGGATCA
* * * * *
28474950 CATTAAGTGCAAAGTTTTCA-TGTAAAAATG-GAAAAAATGTTTTATTCCTCGAAATGTTTGAAT
65 CATTAAATGCAAAGTTTT-ATTGTAAAAACGAAAAAAAACGTTTTATTCCTCAAAATGTTTGAAT
*
28475013 ATTATATA-CAA-TATTATGACAGTAATTATTAAAAAAAAATCCCTTCCAATATCATTCCCTTAA
129 A-TATATAGCAACAATTAT-A-A-T-A--A-T-AAAAAAAATCCCTTCCAATATCATTCCCTTAA
* * * *
28475076 TTTTTCTATATTAAAATTTATGTGGTAAGCTTCGATGTT
185 TTTTTCTATATTAAAAATTATGTGGCAAACTTCAATGTT
* *
28475115 TGACAAGTGGAATTATATCTATATG
1 TGACAAGTGAAACTATAT-TATATG
28475140 ATATAAGTGC
Statistics
Matches: 212, Mismatches: 30, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
222 5 0.02
223 4 0.02
224 48 0.23
225 7 0.03
226 63 0.30
227 1 0.00
228 1 0.00
229 2 0.01
230 81 0.38
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (223 bp):
TGACAAGTGAAACTATATTATATGGCACATATATATTTAATGTATAAATGATTTTTATGGATCAC
ATTAAATGCAAAGTTTTATTGTAAAAACGAAAAAAAACGTTTTATTCCTCAAAATGTTTGAATAT
ATATAGCAACAATTATAATAATAAAAAAAATCCCTTCCAATATCATTCCCTTAATTTTTCTATAT
TAAAAATTATGTGGCAAACTTCAATGTT
Found at i:28475402 original size:21 final size:20
Alignment explanation
Indices: 28475348--28475402 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
28475338 AATAAACACC
*
28475348 AAAAATTTATTTTAAAAATA
1 AAAAATATATTTTAAAAATA
* *
28475368 AAAAA-AGCATTTTAAAATTA
1 AAAAATA-TATTTTAAAAATA
28475388 AAAAATATATATTTA
1 AAAAATATAT-TTTA
28475403 TTATATATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATATATTTTAAAAATA
Found at i:28476185 original size:20 final size:21
Alignment explanation
Indices: 28476160--28476214 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
28476150 TTATTTTTAA
28476160 AAATATTTTTATAAAAAT-AT
1 AAATATTTTTATAAAAATAAT
**
28476180 AAATATTAATA-AAAAATAAT
1 AAATATTTTTATAAAAATAAT
*
28476200 ATATATTTTTTATAA
1 AAATA-TTTTTATAA
28476215 TTTTAATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 6 0.22
20 15 0.56
21 4 0.15
22 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATATTTTTATAAAAATAAT
Found at i:28476266 original size:16 final size:15
Alignment explanation
Indices: 28476210--28476266 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
28476200 ATATATTTTT
28476210 TATAAT-TTTAATT-
1 TATAATATTTAATTA
28476223 TAT-ATATTTAA-TA
1 TATAATATTTAATTA
**
28476236 TATAATTATACAATTA
1 TATAA-TATTTAATTA
28476252 TATAGATATTTAATT
1 TATA-ATATTTAATT
28476267 TTATTTTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.09
13 11 0.32
14 1 0.03
15 5 0.15
16 13 0.38
17 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
TATAATATTTAATTA
Found at i:28476315 original size:6 final size:6
Alignment explanation
Indices: 28476304--28476350 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
28476294 ATTTAATAAT
* *
28476304 ATATTA ATATTA ATATTA ATATTA AAATAA ATA-TA ATATTA TATATT
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA -ATATT
28476351 TTAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 4 0.11
6 26 0.74
7 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATATTA
Found at i:28476315 original size:26 final size:26
Alignment explanation
Indices: 28476278--28476356 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 26
28476268 TATTTTATCA
* *
28476278 ATATTAAAATTATACAATTTAATAAT
1 ATATTAATATTATATAATTTAATAAT
28476304 ATATTAATATTAATATTAATATTAA-AAT
1 ATATTAATATT-ATA-TAAT-TTAATAAT
* *
28476332 AAATATAATATTATATATTTTAATA
1 ATAT-TAATATTATATAATTTAATA
28476357 TTTTTATTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
26 14 0.32
27 7 0.16
28 12 0.27
29 11 0.25
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTAATATTATATAATTTAATAAT
Found at i:28487269 original size:52 final size:53
Alignment explanation
Indices: 28487192--28487375 Score: 169
Period size: 52 Copynumber: 3.3 Consensus size: 53
28487182 CTATTTCAAA
* * *
28487192 AATAATATTATT-CTAATATATTTAATATTAAATTAAATTTAATACTTATCTT
1 AATAATATTATTATTAATATATTTAATATTAAATTTAATTTAATATTTATCTT
* * *
28487244 AATAATATT-TTATTAAT-TATCTTAATATTAGATTTAACTTAATGTTTATCTTGT
1 AATAATATTATTATTAATATAT-TTAATATTAAATTTAATTTAATATTTATC-T-T
*
28487298 AGATAAATATTCAATTAATTTAATAATATTTAATATTAAATTTAATCTAATATTTATCTT
1 A-AT-AATATT--ATT-A-TTAAT-ATATTTAATATTAAATTTAATTTAATATTTATCTT
*
28487358 GATAAGTATTA-TATTAAT
1 AATAA-TATTATTATTAAT
28487376 TTAATATTAA
Statistics
Matches: 107, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
51 5 0.05
52 37 0.35
53 1 0.01
54 7 0.07
55 3 0.03
56 7 0.07
57 1 0.01
58 2 0.02
59 8 0.07
60 2 0.02
61 6 0.06
62 25 0.23
63 3 0.03
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (53 bp):
AATAATATTATTATTAATATATTTAATATTAAATTTAATTTAATATTTATCTT
Found at i:28487335 original size:62 final size:59
Alignment explanation
Indices: 28487265--28487381 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 59
28487255 ATTAATTATC
* *
28487265 TTAATATTAGATTTAA-CTTAATGTTTATCTTGTAGATAAATATTCA-ATTAATTTAATAATAT
1 TTAATATTAAATTTAATC-TAATATTTATC-T-T-GATAAATATT-ATATTAATTTAATAATAT
*
28487327 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
28487382 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
58 1 0.02
59 21 0.42
60 1 0.02
61 1 0.02
62 25 0.50
63 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAATAT
Found at i:28487520 original size:26 final size:22
Alignment explanation
Indices: 28487491--28487538 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 22
28487481 AGTTGTAGAC
28487491 AGAAAATTCTCTGAAGAGATTATTTT
1 AGAAAATT-TCT--AGAGA-TATTTT
28487517 AGAAAATTTCTAGAGATATTTT
1 AGAAAATTTCTAGAGATATTTT
28487539 TTATTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 3 0.14
26 8 0.36
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (22 bp):
AGAAAATTTCTAGAGATATTTT
Found at i:28492440 original size:32 final size:32
Alignment explanation
Indices: 28492399--28492463 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
28492389 GTTAAGTTAG
*
28492399 TTAATATTGTAGCTAA-GTTGTATTTATATTTC
1 TTAATATTGTAGCTAAGGTT-TATTTACATTTC
28492431 TTAATATTGTAGCTAAGGTTTATTTACATTTC
1 TTAATATTGTAGCTAAGGTTTATTTACATTTC
28492463 T
1 T
28492464 AGTCCCTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.90
33 3 0.10
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (32 bp):
TTAATATTGTAGCTAAGGTTTATTTACATTTC
Found at i:28494355 original size:18 final size:18
Alignment explanation
Indices: 28494332--28494368 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28494322 TTTTTATGTG
* *
28494332 TGTTTATTTTTGTTTTTA
1 TGTTTATTTGTGTGTTTA
28494350 TGTTTATTTGTGTGTTTA
1 TGTTTATTTGTGTGTTTA
28494368 T
1 T
28494369 TTTTTTATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.16, T:0.73
Consensus pattern (18 bp):
TGTTTATTTGTGTGTTTA
Found at i:28494455 original size:41 final size:42
Alignment explanation
Indices: 28494394--28494477 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 42
28494384 CAAAAAAAAA
* *
28494394 TCAAAAATTCCAAAAATATTT-TTCGTTTTTATTTTTAATTTT
1 TCAAAAATTCCAAAAATATTTCTT-GCTTTCATTTTTAATTTT
28494436 TCAAAAA-TCCAAAAATATTTCTTGCTTTCATTTTTAATTTT
1 TCAAAAATTCCAAAAATATTTCTTGCTTTCATTTTTAATTTT
28494477 T
1 T
28494478 GTTATTGCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
41 30 0.77
42 9 0.23
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (42 bp):
TCAAAAATTCCAAAAATATTTCTTGCTTTCATTTTTAATTTT
Found at i:28505923 original size:19 final size:21
Alignment explanation
Indices: 28505878--28505923 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
28505868 ACGAAAAACC
28505878 AAATTAA-ATTAAATTAATCA
1 AAATTAACATTAAATTAATCA
28505898 AAA-TAACA-TAAATTAAT-A
1 AAATTAACATTAAATTAATCA
28505916 AAATTAAC
1 AAATTAAC
28505924 TAAGACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.17
19 16 0.67
20 4 0.17
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTAACATTAAATTAATCA
Found at i:28507333 original size:10 final size:10
Alignment explanation
Indices: 28507315--28507345 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28507305 TTACCTAAAA
*
28507315 TCAAACCATT
1 TCAATCCATT
28507325 TCAATCCATT
1 TCAATCCATT
28507335 TCAATCCATT
1 TCAATCCATT
28507345 T
1 T
28507346 TATGCATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
TCAATCCATT
Found at i:28510293 original size:9 final size:10
Alignment explanation
Indices: 28510273--28510300 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
28510263 GAAAGTAATT
28510273 AAAAATTAAA
1 AAAAATTAAA
28510283 AAAAATTAAA
1 AAAAATTAAA
28510293 AAAAATTA
1 AAAAATTA
28510301 TGTAACCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:28513250 original size:8 final size:8
Alignment explanation
Indices: 28513239--28513269 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
28513229 TAAATAATGA
28513239 AAATAAAC
1 AAATAAAC
28513247 AAATAAAC
1 AAATAAAC
28513255 AAATAAAC
1 AAATAAAC
28513263 AAATAAA
1 AAATAAA
28513270 ATAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATAAAC
Found at i:28514397 original size:78 final size:77
Alignment explanation
Indices: 28514268--28514419 Score: 277
Period size: 78 Copynumber: 2.0 Consensus size: 77
28514258 ATATAAGGCT
28514268 CGTGTTAGCCTATTGGGTCATAACACCTACGAAATGTGTTAAAAACACTTATTTTTATTAATTTT
1 CGTGTTAGCCTATTGGGTCATAACACCTACGAAATGTGTTAAAAACACTTATTTTTATTAA-TTT
28514333 CTATCCTAAGTCC
65 CTATCCTAAGTCC
* *
28514346 CGTGTTAGCCTATTGGGTCATAACACTTATGAAATGTGTTAAAAACACTTATTTTTATTAATTTC
1 CGTGTTAGCCTATTGGGTCATAACACCTACGAAATGTGTTAAAAACACTTATTTTTATTAATTTC
28514411 TATCCTAAG
66 TATCCTAAG
28514420 GCCTAATTAC
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 13 0.18
78 59 0.82
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (77 bp):
CGTGTTAGCCTATTGGGTCATAACACCTACGAAATGTGTTAAAAACACTTATTTTTATTAATTTC
TATCCTAAGTCC
Found at i:28535547 original size:40 final size:40
Alignment explanation
Indices: 28535503--28535650 Score: 145
Period size: 40 Copynumber: 3.7 Consensus size: 40
28535493 ATTTGCAATA
* *
28535503 AGGGGTATTGAAGTACAAATAGGGGGACGTATGTGTAATC
1 AGGGGTATCGAAGTACAAATAGGGGCACGTATGTGTAATC
* * * * **
28535543 AGGGGTATCGAAGTACAAGTAGGGTCACATATGTGCAGCC
1 AGGGGTATCGAAGTACAAATAGGGGCACGTATGTGTAATC
* * * * *
28535583 AAGGGTATCGAAGTTCAAATAAGGGCACGCATGTGCT-ATA
1 AGGGGTATCGAAGTACAAATAGGGGCACGTATGTG-TAATC
* *
28535623 AGGGGTACCGAAGTACAAACAGGGGCAC
1 AGGGGTATCGAAGTACAAATAGGGGCAC
28535651 ATTTGTACAA
Statistics
Matches: 83, Mismatches: 24, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.20
Consensus pattern (40 bp):
AGGGGTATCGAAGTACAAATAGGGGCACGTATGTGTAATC
Found at i:28535652 original size:80 final size:80
Alignment explanation
Indices: 28535505--28535652 Score: 190
Period size: 80 Copynumber: 1.9 Consensus size: 80
28535495 TTGCAATAAG
* * * * * * ** *
28535505 GGGTATTGAAGTACAAATAGGGGGACGTATGTGTAATCAGGGGTATCGAAGTACAAGTAGGGTCA
1 GGGTATCGAAGTACAAATAAGGGCACGCATGTGTAATAAGGGGTACCGAAGTACAAACAGGGGCA
28535570 CATATGTGCAGCCAA
66 CATATGTGCAGCCAA
*
28535585 GGGTATCGAAGTTCAAATAAGGGCACGCATGTGCT-ATAAGGGGTACCGAAGTACAAACAGGGGC
1 GGGTATCGAAGTACAAATAAGGGCACGCATGTG-TAATAAGGGGTACCGAAGTACAAACAGGGGC
28535649 ACAT
65 ACAT
28535653 TTGTACAATC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 56 0.98
81 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.20
Consensus pattern (80 bp):
GGGTATCGAAGTACAAATAAGGGCACGCATGTGTAATAAGGGGTACCGAAGTACAAACAGGGGCA
CATATGTGCAGCCAA
Found at i:28543280 original size:70 final size:72
Alignment explanation
Indices: 28543166--28543316 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
28543156 GGGGAATCAT
* *
28543166 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
28543230 GATATCG
66 GATATCG
***
28543237 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
28543301 GATATCG
66 GATATCG
28543308 CACTTAGCA
1 CACTTAGCA
28543317 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:28543347 original size:103 final size:103
Alignment explanation
Indices: 28543236--28543457 Score: 374
Period size: 103 Copynumber: 2.2 Consensus size: 103
28543226 AATGGATATC
28543236 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
28543301 GAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
28543339 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
28543404 GATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
28543442 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
28543458 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 111 0.99
104 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:28543359 original size:26 final size:26
Alignment explanation
Indices: 28543329--28543379 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
28543319 ACCAATGAAC
*
28543329 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
28543355 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
28543380 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:28543818 original size:29 final size:29
Alignment explanation
Indices: 28543785--28543848 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
28543775 TAATCCACCA
28543785 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
28543814 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
28543844 CCCAA
1 CCCAA
28543849 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:28543822 original size:30 final size:30
Alignment explanation
Indices: 28543792--28543848 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28543782 CCACCCAACT
28543792 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
28543821 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
28543849 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:28550830 original size:70 final size:72
Alignment explanation
Indices: 28550716--28550866 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
28550706 GGGGAATCAT
* *
28550716 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
28550780 GATATCG
66 GATATCG
***
28550787 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
28550851 GATATCG
66 GATATCG
28550858 CACTTAGCA
1 CACTTAGCA
28550867 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:28550970 original size:104 final size:103
Alignment explanation
Indices: 28550786--28551008 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
28550776 AATGGATATC
28550786 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
28550851 GATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
28550889 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
28550954 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
65 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
28550993 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
28551009 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 17 0.15
104 94 0.84
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:28551370 original size:29 final size:29
Alignment explanation
Indices: 28551337--28551400 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
28551327 TAATCCACCA
28551337 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
28551366 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
28551396 CCCAA
1 CCCAA
28551401 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:28551374 original size:30 final size:30
Alignment explanation
Indices: 28551344--28551400 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28551334 CCACCCAACT
28551344 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
28551373 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
28551401 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:28559843 original size:27 final size:28
Alignment explanation
Indices: 28559813--28559895 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 28
28559803 GGCATAACGG
28559813 TCATTTTACCCCAT-GGGGGTATTTCGA
1 TCATTTTACCCCATCGGGGGTATTTCGA
*
28559840 TCATTTT-CCCCTTCGGGGGGTATTTCGA
1 TCATTTTACCCCATC-GGGGGTATTTCGA
* * * *
28559868 TAATTTTA-CCCTTCGAGGGCATTTCGA
1 TCATTTTACCCCATCGGGGGTATTTCGA
28559895 T
1 T
28559896 AGTTTAACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.10
27 19 0.39
28 25 0.51
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.39
Consensus pattern (28 bp):
TCATTTTACCCCATCGGGGGTATTTCGA
Found at i:28559866 original size:28 final size:27
Alignment explanation
Indices: 28559827--28559896 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 27
28559817 TTTACCCCAT
* *
28559827 GGGGGTATTTCGATCATTTTCCCCTTC
1 GGGGGTATTTCGATAATTTTACCCTTC
28559854 GGGGGGTATTTCGATAATTTTACCCTTC
1 -GGGGGTATTTCGATAATTTTACCCTTC
* *
28559882 GAGGGCATTTCGATA
1 GGGGGTATTTCGATA
28559897 GTTTAACAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 13 0.34
28 25 0.66
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (27 bp):
GGGGGTATTTCGATAATTTTACCCTTC
Found at i:28566056 original size:24 final size:24
Alignment explanation
Indices: 28566029--28566078 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
28566019 ATTTGTGAAA
**
28566029 TTGTT-AATTTTGAATTCTGTTTTT
1 TTGTTAAATTTT-AATTCCATTTTT
28566053 TTGTTAAATTTTAATTCCATTTTT
1 TTGTTAAATTTTAATTCCATTTTT
28566077 TT
1 TT
28566079 CTGTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.66
Consensus pattern (24 bp):
TTGTTAAATTTTAATTCCATTTTT
Found at i:28567803 original size:16 final size:17
Alignment explanation
Indices: 28567776--28567810 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28567766 AGAGAGTTGA
28567776 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
28567793 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
28567809 GA
1 GA
28567811 TTGAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:28577672 original size:16 final size:17
Alignment explanation
Indices: 28577645--28577679 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28577635 AAAGAGTTGA
28577645 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
28577662 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
28577678 GA
1 GA
28577680 TTTAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:28602459 original size:12 final size:12
Alignment explanation
Indices: 28602442--28602466 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28602432 TTACGTTTTA
28602442 AAATTTAAAATT
1 AAATTTAAAATT
28602454 AAATTTAAAATT
1 AAATTTAAAATT
28602466 A
1 A
28602467 CCTCTGTTTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTTAAAATT
Found at i:28614827 original size:19 final size:20
Alignment explanation
Indices: 28614779--28614831 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
28614769 ACAAAAAAAA
28614779 AAAGATTCAAAATAATTTTC
1 AAAGATTCAAAATAATTTTC
*
28614799 AAAAATTCAAAATAATTTT-
1 AAAGATTCAAAATAATTTTC
*
28614818 TAAGATTCAAAATA
1 AAAGATTCAAAATA
28614832 TTTATAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAGATTCAAAATAATTTTC
Found at i:28615113 original size:23 final size:23
Alignment explanation
Indices: 28615069--28615114 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28615059 TATTGTAAGC
* ***
28615069 TTTTAATTTGACATGCTTAATTT
1 TTTTAATTTAACATGAAAAATTT
28615092 TTTTAATTTAACATGAAAAATTT
1 TTTTAATTTAACATGAAAAATTT
28615115 CACTCGATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTTAATTTAACATGAAAAATTT
Found at i:28615392 original size:57 final size:56
Alignment explanation
Indices: 28615287--28615401 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 56
28615277 TAATGATTAT
* * *
28615287 AAGTCATCGTTATAGGGCAACCCAAGTAGTAGAATGAACAGTATTGACAGATAGAA
1 AAGTCATCATTATAGGGCAACCCAAGTAGTAGAATGAACAGTACTGACAAATAGAA
* * * * *
28615343 AAGTCATCATTGTAGGGCAATCCGAGGTGGTAGAATGACCAGTACTGACAAATAGAA
1 AAGTCATCATTATAGGGCAA-CCCAAGTAGTAGAATGAACAGTACTGACAAATAGAA
28615400 AA
1 AA
28615402 AGCCATTGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
56 18 0.36
57 32 0.64
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (56 bp):
AAGTCATCATTATAGGGCAACCCAAGTAGTAGAATGAACAGTACTGACAAATAGAA
Found at i:28617632 original size:10 final size:10
Alignment explanation
Indices: 28617614--28617643 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
28617604 TAACATAAAA
28617614 AAAACTAAATT
1 AAAA-TAAATT
28617625 AAAATAAATT
1 AAAATAAATT
28617635 AAAATAAAT
1 AAAATAAAT
28617644 AAACATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATAAATT
Found at i:28629562 original size:30 final size:30
Alignment explanation
Indices: 28629526--28629595 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
28629516 CTATATTTTA
*
28629526 GTGGCACACGACTGTGCCACTAACCCGTAC
1 GTGGCACACGACTGTGCCACTAACCCATAC
* * *
28629556 GTGGCACATGGCTGTGCCACTAACCCATGC
1 GTGGCACACGACTGTGCCACTAACCCATAC
28629586 GTGGCACACG
1 GTGGCACACG
28629596 GTTGTGTGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.21, C:0.34, G:0.27, T:0.17
Consensus pattern (30 bp):
GTGGCACACGACTGTGCCACTAACCCATAC
Found at i:28632027 original size:22 final size:22
Alignment explanation
Indices: 28631997--28632039 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28631987 ATTGTTAATA
*
28631997 ATAATATTATTGTTATTATTAT
1 ATAACATTATTGTTATTATTAT
*
28632019 ATAACATTATTTTTATTATTA
1 ATAACATTATTGTTATTATTA
28632040 AACCAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
ATAACATTATTGTTATTATTAT
Found at i:28637042 original size:41 final size:40
Alignment explanation
Indices: 28636997--28637229 Score: 277
Period size: 41 Copynumber: 5.6 Consensus size: 40
28636987 GTTACATGAT
* *
28636997 GGAATCAGCACTTAGCAACCACCTTATAATTAATGATACGG
1 GGAATCAGCACATAGCAACC-CCTTATAATCAATGATACGG
* * * *
28637038 GGAATCAGCACATAGTAACCCCTTTCACAAACAAGGATACGG
1 GGAATCAGCACATAGCAACCCC-TT-ATAATCAATGATACGG
* * *
28637080 TGGAATCAGCACTTAGCAACCATCTTATAATCAATGATATGG
1 -GGAATCAGCACATAGCAACC-CCTTATAATCAATGATACGG
* *
28637122 GGAATCAGCACATAGCAACCCCTTTCAGAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCC-TT-ATAATCAATGATACGG
*
28637164 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGG
1 -GGAATCAGCACATAGCAACC-CCTTATAATCAATGATACGG
28637206 GGAATCAGCACATAGCAACCCCTT
1 GGAATCAGCACATAGCAACCCCTT
28637230 TCATTCAAAG
Statistics
Matches: 162, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
40 7 0.04
41 60 0.37
42 51 0.31
43 41 0.25
44 3 0.02
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (40 bp):
GGAATCAGCACATAGCAACCCCTTATAATCAATGATACGG
Found at i:28637142 original size:84 final size:84
Alignment explanation
Indices: 28636996--28637232 Score: 420
Period size: 84 Copynumber: 2.8 Consensus size: 84
28636986 CGTTACATGA
* *
28636996 TGGAATCAGCACTTAGCAACCACCTTATAATTAATGATACGGGGAATCAGCACATAGTAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
28637061 TTCACAAACAAGGATACGG
66 TTCACAAACAAGGATACGG
* *
28637080 TGGAATCAGCACTTAGCAACCATCTTATAATCAATGATATGGGGAATCAGCACATAGCAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
* *
28637145 TTCAGAATCAAGGATACGG
66 TTCACAAACAAGGATACGG
28637164 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
28637229 TTCA
66 TTCA
28637233 TTCAAAGAAT
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 145 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (84 bp):
TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
TTCACAAACAAGGATACGG
Found at i:28639254 original size:19 final size:19
Alignment explanation
Indices: 28639228--28639302 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 19
28639218 ATATGGTATC
28639228 TAAA-TATATAGATGGTTG
1 TAAACTATATAGATGGTTG
28639246 TAAAC--TATAG-TGGTTG
1 TAAACTATATAGATGGTTG
* * *
28639262 CAAGC-A-AT--ATGGTATC
1 TAAACTATATAGATGGT-TG
28639278 TAAA-TATATAGATGGTTG
1 TAAACTATATAGATGGTTG
28639296 TAAACTA
1 TAAACTA
28639303 GTTATGTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 17
0.65 0.09 0.26
Matches are distributed among these distances:
15 4 0.10
16 15 0.36
17 7 0.17
18 9 0.21
19 7 0.17
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.35
Consensus pattern (19 bp):
TAAACTATATAGATGGTTG
Found at i:28639260 original size:50 final size:50
Alignment explanation
Indices: 28639201--28639302 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
28639191 AGTAATGGTG
28639201 TATAGTGGTTGCAAGCAATATGGTATCTAAATATATAGATGGTTGTAAAC
1 TATAGTGGTTGCAAGCAATATGGTATCTAAATATATAGATGGTTGTAAAC
28639251 TATAGTGGTTGCAAGCAATATGGTATCTAAATATATAGATGGTTGTAAAC
1 TATAGTGGTTGCAAGCAATATGGTATCTAAATATATAGATGGTTGTAAAC
28639301 TA
1 TA
28639303 GTTATGTTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (50 bp):
TATAGTGGTTGCAAGCAATATGGTATCTAAATATATAGATGGTTGTAAAC
Found at i:28639745 original size:27 final size:27
Alignment explanation
Indices: 28639715--28639787 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
28639705 GTATATGTAG
*
28639715 GAAGTCCATCAGGACTATCTAACATGA
1 GAAGTCCATCAGGAATATCTAACATGA
* * *
28639742 GAAGTCCGTCAAGAGTATCTAACATGA
1 GAAGTCCATCAGGAATATCTAACATGA
*
28639769 AAAGTCCATCAGGAATATC
1 GAAGTCCATCAGGAATATC
28639788 ATGTGGAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (27 bp):
GAAGTCCATCAGGAATATCTAACATGA
Found at i:28643273 original size:206 final size:205
Alignment explanation
Indices: 28642910--28643418 Score: 686
Period size: 206 Copynumber: 2.5 Consensus size: 205
28642900 CTTGGTTATT
* * * * * *
28642910 AAAGTGTATGGCAGGTTTGGATTTTTCCAAAGTTATGGTTTGTCATATGCATAC-ATATAGCCTT
1 AAAGTGAATTGCAGGTTTGGATTTTTCTAAAGTTATTGTTTGCCATGTGCATACTA-ATAGCCTT
* * * * *
28642974 AGGAAATAGACAAATAAGTTCCTA--TT-TGACAAATCAATTTTTATTGAATTATTTGAAACTGT
65 AGGAAAAAGACAAATCAGTTCCTATTTTATGACTAATCAATCTTTATTGAATTATTCGAAACTGT
* *
28643036 GTCTGTCATTGAATTTTTCAAATACGATTCAAAACATTTTTCAAATGTTGATCCAAATATGATCA
130 GTATGTCATTGAATTATTCAAATACGATTCAAAACATTTTTCAAATGTTGATCCAAATATGATCA
28643101 TTGTTTGTATC
195 TTGTTTGTATC
* * * *
28643112 AAAGTGAATTGTAGGTTTGGATTTTTCTAAAGGTATTGTCTGCCATGTGCATACTAATATCCTTA
1 AAAGTGAATTGCAGGTTTGGATTTTTCTAAAGTTATTGTTTGCCATGTGCATACTAATAGCCTTA
* * * *
28643177 GGAAAGAGACAAATCAGTTCTTATTTTTATGACTTATCAGTCTTTATTGAATTATTCGAATA-TG
66 GGAAAAAGACAAATCAGTTCCTA-TTTTATGACTAATCAATCTTTATTGAATTATTCGAA-ACTG
* * * *
28643241 TGTATGTCATTGAATTATTCAAATATGATTCAAAACCTTTTTTAAATGTTGATTCAAATATGATC
129 TGTATGTCATTGAATTATTCAAATACGATTCAAAACATTTTTCAAATGTTGATCCAAATATGATC
28643306 ATTGTTTGTATC
194 ATTGTTTGTATC
* * *
28643318 AAATTGAATTGCAGGTTTGGATTTTTATAAAGTTATTGTTTGCCATGTGCCTACTAATAGCCTTA
1 AAAGTGAATTGCAGGTTTGGATTTTTCTAAAGTTATTGTTTGCCATGTGCATACTAATAGCCTTA
*
28643383 GGAAAAAGACAAATCAATTCCTATCTTTATGACTAA
66 GGAAAAAGACAAATCAGTTCCTAT-TTTATGACTAA
28643419 CAGTATCAAA
Statistics
Matches: 265, Mismatches: 35, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
202 73 0.28
203 1 0.00
205 3 0.01
206 187 0.71
207 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (205 bp):
AAAGTGAATTGCAGGTTTGGATTTTTCTAAAGTTATTGTTTGCCATGTGCATACTAATAGCCTTA
GGAAAAAGACAAATCAGTTCCTATTTTATGACTAATCAATCTTTATTGAATTATTCGAAACTGTG
TATGTCATTGAATTATTCAAATACGATTCAAAACATTTTTCAAATGTTGATCCAAATATGATCAT
TGTTTGTATC
Found at i:28643454 original size:11 final size:11
Alignment explanation
Indices: 28643438--28643480 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
28643428 AGGTCCTTTG
28643438 GATTCAAATAT
1 GATTCAAATAT
28643449 GATTCAAATAT
1 GATTCAAATAT
* *
28643460 CATTTAAATAT
1 GATTCAAATAT
*
28643471 GAATCAAATA
1 GATTCAAATA
28643481 CGACAAATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (11 bp):
GATTCAAATAT
Found at i:28647967 original size:53 final size:53
Alignment explanation
Indices: 28647895--28647999 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
28647885 TTTTTGGGCT
* * * *
28647895 TATTGTGTAAATTTTCCTATTACTACTACTGATTTATTAACTTAAGCAGATTA
1 TATTGTGTAAATTTACCTATTACTACTACTGATGTATAAACTTAAACAGATTA
* * * *
28647948 TATTTTGTAAATTTACCTATTATTGCTACTGATGTCTAAACTTAAACAGATT
1 TATTGTGTAAATTTACCTATTACTACTACTGATGTATAAACTTAAACAGATT
28648000 GTTACTGTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (53 bp):
TATTGTGTAAATTTACCTATTACTACTACTGATGTATAAACTTAAACAGATTA
Found at i:28652778 original size:7 final size:7
Alignment explanation
Indices: 28652766--28652799 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
28652756 ATGCTACTAT
28652766 TGATATA
1 TGATATA
28652773 TGATATA
1 TGATATA
28652780 TGATATA
1 TGATATA
28652787 T-ATATA
1 TGATATA
28652793 T-ATATA
1 TGATATA
28652799 T
1 T
28652800 AGAGAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (7 bp):
TGATATA
Found at i:28661886 original size:38 final size:38
Alignment explanation
Indices: 28661828--28661902 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
28661818 ATCTCAACCA
* *
28661828 CTAGATTCTGATTCTATCAAATTGTAACCGTTTAAAAG
1 CTAGATTCTAATTCTATCAAATCGTAACCGTTTAAAAG
* *
28661866 CTAGATTCTAATTTTTTCAAATCGTAACCGTTTAAAA
1 CTAGATTCTAATTCTATCAAATCGTAACCGTTTAAAA
28661903 ATATATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (38 bp):
CTAGATTCTAATTCTATCAAATCGTAACCGTTTAAAAG
Found at i:28662523 original size:86 final size:86
Alignment explanation
Indices: 28662367--28662528 Score: 195
Period size: 86 Copynumber: 1.9 Consensus size: 86
28662357 TTAAATTCGA
* * * *
28662367 TGAATTCATCAAGTTGGTCTCAATAGGACCAACTAAACTCTGTATATGAACTCATTAAGAGTAAT
1 TGAATTCATCAAGTTGGTCTCAATAGGACCAACCAAACTCTGGATATAAACTCACTAAGAGTAAT
28662432 AAACTCAACCTCATATGTTAG
66 AAACTCAACCTCATATGTTAG
* * *
28662453 TGAATTCATCAAGATT-GTCTCAATAGGACCACCCAAA-TCTTGGGATATAAATTGACTAAGAGT
1 TGAATTCATCAAG-TTGGTCTCAATAGGACCAACCAAACTC-T-GGATATAAACTCACTAAGAGT
* *
28662516 GA-GAACTCAACCT
63 AATAAACTCAACCT
28662529 TATGCATGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
85 2 0.03
86 43 0.67
87 19 0.30
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (86 bp):
TGAATTCATCAAGTTGGTCTCAATAGGACCAACCAAACTCTGGATATAAACTCACTAAGAGTAAT
AAACTCAACCTCATATGTTAG
Found at i:28663964 original size:26 final size:26
Alignment explanation
Indices: 28663928--28664053 Score: 130
Period size: 26 Copynumber: 4.8 Consensus size: 26
28663918 TCCGTTCATA
28663928 GTCCTTCGACCAACTCAAACTCAAGG
1 GTCCTTCGACCAACTCAAACTCAAGG
**
28663954 GTCCTTCGACCAACTCAAACTTTAGG
1 GTCCTTCGACCAACTCAAACTCAAGG
* * * * * *
28663980 CTTCTTCGACCCACTAAAACTCGAGT
1 GTCCTTCGACCAACTCAAACTCAAGG
* *
28664006 ATCC-TCTGACCAACTCAAACTTAAGG
1 GTCCTTC-GACCAACTCAAACTCAAGG
28664032 GTCC-TCTGACCAACTCAAACTC
1 GTCCTTC-GACCAACTCAAACTC
28664054 CTAAGGCCTT
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
25 2 0.02
26 79 0.98
ACGTcount: A:0.29, C:0.34, G:0.13, T:0.24
Consensus pattern (26 bp):
GTCCTTCGACCAACTCAAACTCAAGG
Found at i:28664052 original size:52 final size:52
Alignment explanation
Indices: 28663929--28664053 Score: 146
Period size: 52 Copynumber: 2.4 Consensus size: 52
28663919 CCGTTCATAG
* *
28663929 TCCTTCGACCAACTCAAACTCAAGGGTCCTTCGACCAACTCAAACTTTAGGC
1 TCCTTCGACCAACTCAAACTCAAGGATCCTTCGACCAACTCAAACTTAAGGC
* * * * * *
28663981 TTCTTCGACCCACTAAAACTCGAGTATCC-TCTGACCAACTCAAACTTAAGGG
1 TCCTTCGACCAACTCAAACTCAAGGATCCTTC-GACCAACTCAAACTTAAGGC
28664033 TCC-TCTGACCAACTCAAACTC
1 TCCTTC-GACCAACTCAAACTC
28664054 CTAAGGCCTT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
51 4 0.07
52 56 0.93
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.24
Consensus pattern (52 bp):
TCCTTCGACCAACTCAAACTCAAGGATCCTTCGACCAACTCAAACTTAAGGC
Found at i:28666202 original size:16 final size:17
Alignment explanation
Indices: 28666172--28666203 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28666162 TTCTAAGAAG
28666172 CACTTTTGAGACAAAAA
1 CACTTTTGAGACAAAAA
28666189 CACTTTTG-GACAAAA
1 CACTTTTGAGACAAAA
28666204 GAATTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (17 bp):
CACTTTTGAGACAAAAA
Found at i:28668620 original size:25 final size:24
Alignment explanation
Indices: 28668581--28668653 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
28668571 CTCTCAAGCA
**
28668581 CTATAACGGAAAGCTCACAAAGAGC
1 CTATAACGGGTAGCTC-CAAAGAGC
*
28668606 CTATAACGGGTAGCTTCAAAGAG-
1 CTATAACGGGTAGCTCCAAAGAGC
* *
28668629 CAATTAACGGGTAGCTCCGAAGAGC
1 CTA-TAACGGGTAGCTCCAAAGAGC
28668654 AATTAACGGC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 2 0.05
24 25 0.62
25 13 0.32
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (24 bp):
CTATAACGGGTAGCTCCAAAGAGC
Found at i:28668636 original size:24 final size:24
Alignment explanation
Indices: 28668592--28668662 Score: 90
Period size: 24 Copynumber: 2.9 Consensus size: 24
28668582 TATAACGGAA
*
28668592 AGCTCACAAAGAGC-CTATAACGGGT
1 AGCTC-CAAAGAGCAAT-TAACGGGT
*
28668617 AGCTTCAAAGAGCAATTAACGGGT
1 AGCTCCAAAGAGCAATTAACGGGT
*
28668641 AGCTCCGAAGAGCAATTAACGG
1 AGCTCCAAAGAGCAATTAACGG
28668663 CAACACCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
24 36 0.88
25 5 0.12
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (24 bp):
AGCTCCAAAGAGCAATTAACGGGT
Found at i:28668738 original size:26 final size:26
Alignment explanation
Indices: 28668704--28668769 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
28668694 AAGCGAGCAC
* *
28668704 TAACAGGAAGCTCACAAAGAGCC-TT
1 TAACGGGAAGCTCACAAAGAGCCATA
*
28668729 TAATCGGGAAGCTCACGAAGAGCCATA
1 TAA-CGGGAAGCTCACAAAGAGCCATA
*
28668756 TAACGGGACGCTCA
1 TAACGGGAAGCTCA
28668770 TAAGAGTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.09
26 28 0.80
27 4 0.11
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (26 bp):
TAACGGGAAGCTCACAAAGAGCCATA
Found at i:28673855 original size:41 final size:41
Alignment explanation
Indices: 28673804--28673986 Score: 156
Period size: 41 Copynumber: 4.5 Consensus size: 41
28673794 TTTAAACAGA
* **
28673804 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCAG
1 TTCACCGGCACTT-AGCCTGATAGGCTTATAGCCTAATTCAG
* * *
28673845 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGATAGGCTTATAGCCTAATTCAG
* * * * *
28673886 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGATAGGCTTATAG-CCTAATTCAG
* * * * * * *
28673927 TTCACTGGCATTTAGCCTGCTAGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGATAGGCTTATAG-CCTAATTCAG
28673968 TTCACCGGCACTTAGCCTG
1 TTCACCGGCACTTAGCCTG
28673987 CTAGATGTAT
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 123 0.98
42 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGATAGGCTTATAGCCTAATTCAG
Found at i:28674013 original size:41 final size:41
Alignment explanation
Indices: 28673839--28674000 Score: 236
Period size: 41 Copynumber: 4.0 Consensus size: 41
28673829 TTATAGTTTA
* * * *
28673839 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTGTAG-CCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCC-G
*
28673880 ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
* *
28673921 ATTCAATTCACTGGCATTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
28673962 ATTCAATTCACCGGCACTTAGCCTGCTAGATGTATAGTC
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTC
28674001 TGAATAATTT
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
41 109 0.98
42 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (41 bp):
ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
Found at i:28683119 original size:15 final size:15
Alignment explanation
Indices: 28683099--28683132 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
28683089 GGTGATGTCA
28683099 TAATCTAAAAAATAT
1 TAATCTAAAAAATAT
28683114 TAATCTAAAAAATAT
1 TAATCTAAAAAATAT
28683129 TAAT
1 TAAT
28683133 AATCAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATCTAAAAAATAT
Found at i:28684409 original size:24 final size:24
Alignment explanation
Indices: 28684381--28684427 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
28684371 AGCAAGCCCA
* *
28684381 GAAAAAAGAAAAAGAAAGAAAAAG
1 GAAAAAAGAAAAACAAAAAAAAAG
*
28684405 GAAAAAAGGAAAACAAAAAAAAA
1 GAAAAAAGAAAAACAAAAAAAAA
28684428 ACAAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (24 bp):
GAAAAAAGAAAAACAAAAAAAAAG
Found at i:28684433 original size:24 final size:24
Alignment explanation
Indices: 28684382--28684435 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
28684372 GCAAGCCCAG
* * **
28684382 AAAAAAGAAAAAGAAAGAAAAAGG
1 AAAAAAGAAAAACAAAAAAAAAAC
*
28684406 AAAAAAGGAAAACAAAAAAAAAAC
1 AAAAAAGAAAAACAAAAAAAAAAC
28684430 AAAAAA
1 AAAAAA
28684436 AAAGGTACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (24 bp):
AAAAAAGAAAAACAAAAAAAAAAC
Found at i:28684445 original size:14 final size:11
Alignment explanation
Indices: 28684414--28684438 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28684404 GGAAAAAAGG
28684414 AAAACAAAAAA
1 AAAACAAAAAA
28684425 AAAACAAAAAA
1 AAAACAAAAAA
28684436 AAA
1 AAA
28684439 GGTACAAGAG
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:28691471 original size:9 final size:9
Alignment explanation
Indices: 28691454--28691490 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28691444 TGAGTTTTCG
28691454 AATTCGAAT
1 AATTCGAAT
*
28691463 AACTCGAAT
1 AATTCGAAT
28691472 AATTCGAAT
1 AATTCGAAT
28691481 AATTCGAAT
1 AATTCGAAT
28691490 A
1 A
28691491 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28691573 original size:30 final size:31
Alignment explanation
Indices: 28691539--28691599 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
28691529 GAACTTTTTT
* *
28691539 ACTTTTCCCTCAAAACTTTTACCCCT-TCCC
1 ACTTTCCCCCCAAAACTTTTACCCCTCTCCC
*
28691569 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCCAAAACTTTTACCCCTCTCCC
28691600 CTCCCAATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACCCCTCTCCC
Found at i:28691738 original size:30 final size:31
Alignment explanation
Indices: 28691704--28691764 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
28691694 AAATCTTTTA
28691704 TTTTCCCCCAAAATTTTTACTCCC-TCCCAT
1 TTTTCCCCCAAAATTTTTACTCCCTTCCCAT
* * *
28691734 TTTTCTCCTAAAATTTTTATTCCCTTCCCAT
1 TTTTCCCCCAAAATTTTTACTCCCTTCCCAT
28691765 CCCACCTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTTCCCCCAAAATTTTTACTCCCTTCCCAT
Found at i:28691888 original size:21 final size:21
Alignment explanation
Indices: 28691859--28691898 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
28691849 TCCCTCAAAC
28691859 TTTTATTCCCCAAAACTTTTTA
1 TTTTATT-CCCAAAACTTTTTA
*
28691881 TTTT-TTCCCTAAACTTTT
1 TTTTATTCCCAAAACTTTT
28691899 ACTTCCTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATTCCCAAAACTTTTTA
Found at i:28700883 original size:24 final size:24
Alignment explanation
Indices: 28700856--28700910 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
28700846 AAATCCAATT
*
28700856 CTAATCAATGTCAAATATATTATG
1 CTAATAAATGTCAAATATATTATG
* **
28700880 CTAATAAATGTTAAATATATTACA
1 CTAATAAATGTCAAATATATTATG
28700904 CTAATAA
1 CTAATAA
28700911 GTACTAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.36
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATG
Found at i:28700918 original size:24 final size:24
Alignment explanation
Indices: 28700868--28700919 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
28700858 AATCAATGTC
** **
28700868 AAATATATTATGCTAATAAATGTT
1 AAATATATTACACTAATAAATACT
*
28700892 AAATATATTACACTAATAAGTACT
1 AAATATATTACACTAATAAATACT
28700916 AAAT
1 AAAT
28700920 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTACACTAATAAATACT
Found at i:28705068 original size:20 final size:20
Alignment explanation
Indices: 28705043--28705082 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28705033 CGTAAAATGA
*
28705043 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
28705063 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
28705083 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:28705072 original size:34 final size:35
Alignment explanation
Indices: 28705028--28705094 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28705018 TAGTAAAATA
*
28705028 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
28705062 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
28705095 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:28705814 original size:111 final size:113
Alignment explanation
Indices: 28705618--28705841 Score: 398
Period size: 111 Copynumber: 2.0 Consensus size: 113
28705608 TGATGAAGTA
* * *
28705618 TTGTTGTCTAAGAGAGAGAGAGTAGTGATATATGTATACCATATGAACATACAGTACTTTTTCTA
1 TTGTTGTCTAAGAGAGAGAGAGTAGTCATATATGTATACCATATAAACATACACTACTTTTTCTA
*
28705683 AATTTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 AATGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
28705731 TTGTTGTCT-A-AGAGAGAGAGTAGTCATATATGTATACCATATAAACATACACTACTTTTTCTA
1 TTGTTGTCTAAGAGAGAGAGAGTAGTCATATATGTATACCATATAAACATACACTACTTTTTCTA
28705794 AATGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 AATGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
28705842 CATGGTATTG
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
111 97 0.91
112 1 0.01
113 9 0.08
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (113 bp):
TTGTTGTCTAAGAGAGAGAGAGTAGTCATATATGTATACCATATAAACATACACTACTTTTTCTA
AATGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
Found at i:28708382 original size:14 final size:15
Alignment explanation
Indices: 28708363--28708391 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28708353 TGCCGAAAAA
28708363 TTCAGAAAA-CAATT
1 TTCAGAAAACCAATT
28708377 TTCAGAAAACCAATT
1 TTCAGAAAACCAATT
28708392 CCCATAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (15 bp):
TTCAGAAAACCAATT
Found at i:28710539 original size:56 final size:56
Alignment explanation
Indices: 28710453--28710572 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
28710443 ACAAGGGATG
28710453 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
28710509 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
28710565 ATGGGCAA
1 ATGGGCAA
28710573 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:28712077 original size:47 final size:47
Alignment explanation
Indices: 28712030--28712377 Score: 504
Period size: 47 Copynumber: 7.4 Consensus size: 47
28712020 AATGTTAAAG
* *
28712030 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-A
1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
28712076 GTGTATATATATGTGATAAGGCCGAATAGCCAATGTGATGAATGTGAACA
1 -TG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* *
28712126 TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* *
28712173 TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* *
28712220 TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* *
28712267 TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-A
1 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* *
28712313 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAA-G
1 -TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACA
*
28712361 TGTATAAATGTGATAAG
1 TGTATATATGTGATAAG
28712378 TCCCGAAGGG
Statistics
Matches: 273, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
46 1 0.00
47 226 0.83
48 3 0.01
49 42 0.15
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
Found at i:28712255 original size:22 final size:22
Alignment explanation
Indices: 28712228--28712349 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
28712218 CATGTGTATG
28712228 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
28712250 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
28712275 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
28712297 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
28712322 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
28712344 TGTGAT
1 TGTGAT
28712350 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:28724018 original size:79 final size:81
Alignment explanation
Indices: 28723878--28724062 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 81
28723868 TTGAATGATG
*
28723878 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28723942 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * *
28723957 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCAGG-TTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCC-GGACTAAGAT-CCGAAGGC
*
28724018 ATTTGTGCGAGTTACTATA
63 ATTTGTGCGAGATACTATA
* *
28724037 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28724063 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
78 1 0.01
79 56 0.61
80 35 0.38
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:28724076 original size:40 final size:40
Alignment explanation
Indices: 28723879--28724062 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
28723869 TGAATGATGT
* * * *
28723879 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28723919 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
28723959 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
28723997 TCCAGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28724038 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28724063 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28724084 original size:79 final size:79
Alignment explanation
Indices: 28723931--28724095 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
28723921 GGACTAAGAT
* **
28723931 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28723996 ATCCAGGTTAAGTC
66 ATCCAGGTTAAATC
* *
28724010 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28724073 TATATCC-GGTTAAATT
63 TAAATCCAGGTTAAATC
28724089 CCGAAGG
1 CCGAAGG
28724096 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCAGGTTAAATC
Found at i:28754389 original size:39 final size:40
Alignment explanation
Indices: 28754312--28754458 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
28754302 TAGCTCCTCG
* * *
28754312 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
28754352 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
28754391 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
28754431 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
28754459 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:28754469 original size:80 final size:80
Alignment explanation
Indices: 28754358--28754538 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
28754348 CTCATTCAAT
* * *
28754358 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
28754421 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
28754437 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
28754501 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
28754518 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
28754539 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:28754498 original size:40 final size:40
Alignment explanation
Indices: 28754355--28754538 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
28754345 TAACTCATTC
* *
28754355 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
28754395 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
28754435 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
28754475 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
28754516 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28754539 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:28759182 original size:34 final size:34
Alignment explanation
Indices: 28759142--28759242 Score: 105
Period size: 34 Copynumber: 3.0 Consensus size: 34
28759132 TTTATATGTG
28759142 AACTGTGTTAATGTGTGGACCGTGTAAATATGCA
1 AACTGTGTTAATGTGTGGACCGTGTAAATATGCA
* ** * ** ** *
28759176 AGCTGTGACAATGTGCGTG-TTGTGTTTATAAGCA
1 AACTGTGTTAATGTGTG-GACCGTGTAAATATGCA
28759210 AACTGTGTTAATGTGTGGACCGTGTAAATATGC
1 AACTGTGTTAATGTGTGGACCGTGTAAATATGC
28759243 GACATATGAC
Statistics
Matches: 47, Mismatches: 18, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
33 1 0.02
34 45 0.96
35 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (34 bp):
AACTGTGTTAATGTGTGGACCGTGTAAATATGCA
Found at i:28759202 original size:68 final size:68
Alignment explanation
Indices: 28759128--28759259 Score: 203
Period size: 68 Copynumber: 1.9 Consensus size: 68
28759118 TATACATATA
* ** *
28759128 TGTGTTTATATGTGAACTGTGTTAATGTGTGGACCGTGTAAATATGCAAGC-TGTGACAATGTGC
1 TGTGTTTATAAGCAAACTGTGTTAATGTGTGGACCGTGTAAATATGCAA-CATATGACAATGTGC
28759192 GTGT
65 GTGT
*
28759196 TGTGTTTATAAGCAAACTGTGTTAATGTGTGGACCGTGTAAATATGCGACATATGACAATGTGC
1 TGTGTTTATAAGCAAACTGTGTTAATGTGTGGACCGTGTAAATATGCAACATATGACAATGTGC
28759260 TGGCTATGTC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 1 0.02
68 57 0.98
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (68 bp):
TGTGTTTATAAGCAAACTGTGTTAATGTGTGGACCGTGTAAATATGCAACATATGACAATGTGCG
TGT
Found at i:28759387 original size:17 final size:17
Alignment explanation
Indices: 28759365--28759466 Score: 78
Period size: 17 Copynumber: 6.0 Consensus size: 17
28759355 GTGTGAGTTG
*
28759365 TGTTTATATGCTAGCTA
1 TGTTTATATGCGAGCTA
* *
28759382 TGTTTATATGCGAGTTG
1 TGTTTATATGCGAGCTA
** * * *
28759399 TGCATATATGCAAGTTG
1 TGTTTATATGCGAGCTA
*
28759416 TGTTTACATGCGAGCTA
1 TGTTTATATGCGAGCTA
** * *
28759433 TGTTTATATATGAGTTG
1 TGTTTATATGCGAGCTA
*
28759450 TGTTTATACGCGAGCTA
1 TGTTTATATGCGAGCTA
28759467 GCTTTGTCAA
Statistics
Matches: 63, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 63 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.42
Consensus pattern (17 bp):
TGTTTATATGCGAGCTA
Found at i:28759397 original size:34 final size:34
Alignment explanation
Indices: 28759359--28759441 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
28759349 GACAATGTGT
* *
28759359 GAGTTGTGTTTATATGCTAGCTATGTTTATATGC
1 GAGTTGTGTTTATATGCAAGCTATGTTTACATGC
** * *
28759393 GAGTTGTGCATATATGCAAGTTGTGTTTACATGC
1 GAGTTGTGTTTATATGCAAGCTATGTTTACATGC
* *
28759427 GAGCTATGTTTATAT
1 GAGTTGTGTTTATAT
28759442 ATGAGTTGTG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.43
Consensus pattern (34 bp):
GAGTTGTGTTTATATGCAAGCTATGTTTACATGC
Found at i:28763216 original size:50 final size:50
Alignment explanation
Indices: 28763137--28763320 Score: 217
Period size: 50 Copynumber: 3.7 Consensus size: 50
28763127 TTTCCTGTAC
* * * * ** * *
28763137 TGCCAATGTCATATCCCAGATATGTTCTTACATGGGAGTTCTTATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** *
28763187 TGTCC-ATGCCATGTCCCAGACATAGTCTTACGGGGGACCTCTCATCTCGT
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
28763237 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGTACCTCTCCTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
28763287 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
28763321 CCAATGCCAT
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 2 0.02
50 108 0.96
51 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:28763323 original size:32 final size:32
Alignment explanation
Indices: 28763287--28763352 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
28763277 CTCCTCTCGG
* *
28763287 TGCCAATGCCATGTCCCAGACATGGTCTTACA
1 TGCCAATGCCATATCCCAGACATGGTATTACA
28763319 TGCCAATGCCATATCCCAGACATGGTATTACA
1 TGCCAATGCCATATCCCAGACATGGTATTACA
28763351 TG
1 TG
28763353 GGATCTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (32 bp):
TGCCAATGCCATATCCCAGACATGGTATTACA
Found at i:28769090 original size:24 final size:25
Alignment explanation
Indices: 28769039--28769090 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
28769029 TGCTGGACCG
* *
28769039 ATATTTTTCTATGAAAGTAGACTTA
1 ATATTTTTCAATGAAAGTAGACTCA
28769064 ATATTTTTCAATGAAAGTAGA-TCA
1 ATATTTTTCAATGAAAGTAGACTCA
28769088 ATA
1 ATA
28769091 AGCTTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (25 bp):
ATATTTTTCAATGAAAGTAGACTCA
Found at i:28769950 original size:50 final size:50
Alignment explanation
Indices: 28769825--28770122 Score: 269
Period size: 50 Copynumber: 5.9 Consensus size: 50
28769815 TACTAATAAC
* * ** * *
28769825 ATGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTTTCCTAT--
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * * **
28769873 ACTGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCG
1 A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * * *
28769924 GTGCCCATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATATCG
* * ** * *
28769974 GTGCCAATGCCATGTCCCATACATGGTCTTACATGAAACCTCTCGTCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * *
28770024 ATGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTTATAATCTCATTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---G
* *
28770080 ATGCCAATGCCATGTCCCAGACATGGTATTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28770123 TTACCCAAAT
Statistics
Matches: 202, Mismatches: 37, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 119 0.59
51 1 0.00
53 2 0.01
56 40 0.20
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
Found at i:28785215 original size:12 final size:12
Alignment explanation
Indices: 28785198--28785222 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28785188 TCCTGAAGTG
28785198 ACAAATAAATAA
1 ACAAATAAATAA
28785210 ACAAATAAATAA
1 ACAAATAAATAA
28785222 A
1 A
28785223 AGAAACTTGG
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:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
ACAAATAAATAA
Found at i:28787436 original size:35 final size:35
Alignment explanation
Indices: 28787397--28787467 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
28787387 GGATTAAAAG
28787397 AAAGGAAATATTTCCATTGATATCATTAATCATTC
1 AAAGGAAATATTTCCATTGATATCATTAATCATTC
28787432 AAAGGAAATATTTCCATTGATATCATTAATCATTC
1 AAAGGAAATATTTCCATTGATATCATTAATCATTC
28787467 A
1 A
28787468 GCCATTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (35 bp):
AAAGGAAATATTTCCATTGATATCATTAATCATTC
Found at i:28795830 original size:7 final size:7
Alignment explanation
Indices: 28795819--28795864 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
28795809 TGGATTGGAT
28795819 GAGAGTG
1 GAGAGTG
*
28795826 AAGAGTG
1 GAGAGTG
28795833 GAGAGTG
1 GAGAGTG
28795840 GAGAGTG
1 GAGAGTG
28795847 GAGAGTG
1 GAGAGTG
28795854 GAGAGTG
1 GAGAGTG
28795861 GAGA
1 GAGA
28795865 CAATTGCCCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.54, T:0.13
Consensus pattern (7 bp):
GAGAGTG
Found at i:28796500 original size:36 final size:37
Alignment explanation
Indices: 28796460--28796531 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
28796450 CTTTTAACTT
*
28796460 TCCTTTT-TTTCTTTA-TTTTTC-ATTTTCTTCTATTTC
1 TCCTTTTGTTT-TTTAGTTTTTCTATGTT-TTCTATTTC
28796496 TCCTTTTGTTTTTTAGTTTTTCTATGTTTTCTATTT
1 TCCTTTTGTTTTTTAGTTTTTCTATGTTTTCTATTT
28796532 GTGGACTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 11 0.34
37 17 0.53
38 4 0.12
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.72
Consensus pattern (37 bp):
TCCTTTTGTTTTTTAGTTTTTCTATGTTTTCTATTTC
Found at i:28797017 original size:15 final size:16
Alignment explanation
Indices: 28796997--28797026 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28796987 AAGTTTTTTT
28796997 TTATTTTTTA-ATAAC
1 TTATTTTTTATATAAC
28797012 TTATTTTTTATATAA
1 TTATTTTTTATATAA
28797027 AAAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTTTTTATATAAC
Found at i:28797224 original size:131 final size:134
Alignment explanation
Indices: 28797050--28797297 Score: 380
Period size: 131 Copynumber: 1.9 Consensus size: 134
28797040 TGTAATTATA
* *
28797050 TAATGAAAATATTTTATATATATATTATTATATTAAATATATTTTATCTTTTAAAAACATC-ACT
1 TAATGAAAATATATTATATATATATCATTATATTAAATATATTTTAT-TTTTAAAAACATCAACT
* * *
28797114 TATTTTTTATAT-TTTTCTTTATATAT-AATTTTTTATGTAAAATATTT-TTTTCACTTACATTG
65 AATTTTTTATATATATT-TTTATATATAAATTTTATATGTAAAATATTTATTTTCACTTACATTG
28797176 TGGATG
129 TGGATG
* *
28797182 TAATGAAAATATATTGT-TATATATCATTATGTTAAATATATTTTATTTTTAAAAACATCAACTA
1 TAATGAAAATATATTATATATATATCATTATATTAAATATATTTTATTTTTAAAAACATCAACTA
28797246 ATTTTTTATATATATTTTTATATATAAATTTTATATGTAAAATATTTATTTT
66 ATTTTTTATATATATTTTTATATATAAATTTTATATGTAAAATATTTATTTT
28797298 TTCATATACA
Statistics
Matches: 105, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
130 13 0.12
131 50 0.48
132 38 0.36
133 4 0.04
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.54
Consensus pattern (134 bp):
TAATGAAAATATATTATATATATATCATTATATTAAATATATTTTATTTTTAAAAACATCAACTA
ATTTTTTATATATATTTTTATATATAAATTTTATATGTAAAATATTTATTTTCACTTACATTGTG
GATG
Found at i:28797269 original size:14 final size:13
Alignment explanation
Indices: 28797248--28797281 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
28797238 ATCAACTAAT
28797248 TTTTTATATAT-A
1 TTTTTATATATAA
28797260 TTTTTATATATAA
1 TTTTTATATATAA
*
28797273 ATTTTATAT
1 TTTTTATAT
28797282 GTAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTATATATAA
Found at i:28797286 original size:13 final size:13
Alignment explanation
Indices: 28797249--28797286 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
28797239 TCAACTAATT
*
28797249 TTTTATATAT-AT
1 TTTTATATATAAA
28797261 TTTTATATATAAA
1 TTTTATATATAAA
*
28797274 TTTTATATGTAAA
1 TTTTATATATAAA
28797287 ATATTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TTTTATATATAAA
Found at i:28797342 original size:131 final size:129
Alignment explanation
Indices: 28797076--28797346 Score: 304
Period size: 131 Copynumber: 2.1 Consensus size: 129
28797066 TATATATATT
* *
28797076 ATTATATTAAATATATTTTATCTTTTAAAAACATCACTTATTTTTTATATTTTTCTTTATATATA
1 ATTAT-TTAAATATATTTTATCTTTTAAAAACATCACTAATTTTTTATATTATTCTTTATATATA
* * * ** * *
28797141 ATTTTTTATGTAAAATATTTTTTTCACTTACATTGTGGATGTAATGAAAATATATTGTTATATAT
65 ATTTTATATGTAAAATATTTTTTTCACTTACATTATGGA-GTAATGAAAATATACTAATATAAAA
*
28797206 C
129 A
28797207 ATTATGTTAAATATATTTTAT-TTTTAAAAACATCAACTAATTTTTTATATATATT-TTTATATA
1 ATTAT-TTAAATATATTTTATCTTTTAAAAACATC-ACTAATTTTTTATAT-TATTCTTTATATA
28797270 TAAATTTTATATGTAAAATATTTATTTTTTCA-TATACATTATGGA-T-ATGATAAAT-T-CTAA
63 T-AATTTTATATGTAAAATA--T-TTTTTTCACT-TACATTATGGAGTAATGA-AAATATACTAA
28797330 TATAAAAA
122 TATAAAAA
28797338 ATTATTTAA
1 ATTATTTAA
28797347 TCATTTCAAA
Statistics
Matches: 121, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
130 17 0.14
131 54 0.45
132 25 0.21
133 5 0.04
134 2 0.02
135 18 0.15
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (129 bp):
ATTATTTAAATATATTTTATCTTTTAAAAACATCACTAATTTTTTATATTATTCTTTATATATAA
TTTTATATGTAAAATATTTTTTTCACTTACATTATGGAGTAATGAAAATATACTAATATAAAAA
Found at i:28801106 original size:26 final size:26
Alignment explanation
Indices: 28801073--28801125 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28801063 AAAAGTTGGG
28801073 GTAATTGTGTAAATTTGAAAAATTAA
1 GTAATTGTGTAAATTTGAAAAATTAA
28801099 GTAATTGTGTAAATTTGAAAAATTAA
1 GTAATTGTGTAAATTTGAAAAATTAA
28801125 G
1 G
28801126 GGGTATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (26 bp):
GTAATTGTGTAAATTTGAAAAATTAA
Found at i:28801573 original size:21 final size:21
Alignment explanation
Indices: 28801549--28801597 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28801539 ACGAGCTTTT
28801549 GTTTAACTCATATGAGTTTCC
1 GTTTAACTCATATGAGTTTCC
* * * *
28801570 GTTTAGCTCTTTTGAGTTTCT
1 GTTTAACTCATATGAGTTTCC
28801591 GTTTAAC
1 GTTTAAC
28801598 CCTTCTGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.49
Consensus pattern (21 bp):
GTTTAACTCATATGAGTTTCC
Found at i:28801594 original size:42 final size:42
Alignment explanation
Indices: 28801523--28801623 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
28801513 TCGTGTTTAC
* *
28801523 TTTCCGTTTAGCTCTCACGAGCTTTTGTTTAACTCATATGAG
1 TTTCCGTTTAGCTCTTACGAGCTTTTGTTTAACCCATATGAG
** * * *
28801565 TTTCCGTTTAGCTCTTTTGAG-TTTCTGTTTAACCCTTCTGGG
1 TTTCCGTTTAGCTCTTACGAGCTTT-TGTTTAACCCATATGAG
*
28801607 TTTCCGTTCAGCTCTTA
1 TTTCCGTTTAGCTCTTA
28801624 ATAGCTTCTA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 3 0.06
42 46 0.94
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.47
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTTACGAGCTTTTGTTTAACCCATATGAG
Found at i:28801641 original size:42 final size:42
Alignment explanation
Indices: 28801564--28801679 Score: 99
Period size: 42 Copynumber: 2.8 Consensus size: 42
28801554 ACTCATATGA
* * * * *
28801564 GTTTCCGTTTAGCTCTTTTGAGTTTCTGTTTAACCCTTCTGG
1 GTTTCCGTTCAGCTCTTATGAGCTTCTATTCAACCCTTCTGG
* **
28801606 GTTTCCGTTCAGCTCTTAAT-AGCTTCTATTCAACCCTTATAC
1 GTTTCCGTTCAGCTCTT-ATGAGCTTCTATTCAACCCTTCTGG
** ** *
28801648 GTTTTTGTTTGGCTCTTATGAGCTTCTGTTCA
1 GTTTCCGTTCAGCTCTTATGAGCTTCTATTCA
28801680 GCCTTCGGGC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 2 0.03
42 56 0.95
43 1 0.02
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.47
Consensus pattern (42 bp):
GTTTCCGTTCAGCTCTTATGAGCTTCTATTCAACCCTTCTGG
Found at i:28803498 original size:50 final size:50
Alignment explanation
Indices: 28803388--28803585 Score: 191
Period size: 50 Copynumber: 3.8 Consensus size: 50
28803378 ATTTGGGTAA
* * * *
28803388 AGAGATCCCATGTAAGACTATGTCTGGGACATGACATTGGCATCATTGAGATCAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGAT--T
**
28803443 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATT
1 -AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATT
* * * * *
28803494 AGAGGTTCCC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGG-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATT
** * *
28803544 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28803586 GTACAAGAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
49 4 0.03
50 68 0.57
51 5 0.04
53 5 0.04
55 1 0.01
56 37 0.31
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATT
Found at i:28803905 original size:17 final size:17
Alignment explanation
Indices: 28803883--28803920 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
28803873 AATATTGAAA
28803883 AATCCACTTTAAGTCAG
1 AATCCACTTTAAGTCAG
28803900 AATCCACTTTAAGTCAG
1 AATCCACTTTAAGTCAG
28803917 AATC
1 AATC
28803921 AATATTAATC
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:0.37, C:0.24, G:0.11, T:0.29
Consensus pattern (17 bp):
AATCCACTTTAAGTCAG
Found at i:28803928 original size:17 final size:16
Alignment explanation
Indices: 28803890--28803937 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
28803880 AAAAATCCAC
*
28803890 TTTAAGTCAGAATCCAC
1 TTTAAGTCAGAAT-CAA
28803907 TTTAAGTCAGAATCAA
1 TTTAAGTCAGAATCAA
*
28803923 TATTAA-TCAAAATCA
1 T-TTAAGTCAGAATCA
28803938 TAAATCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (16 bp):
TTTAAGTCAGAATCAA
Found at i:28805625 original size:50 final size:51
Alignment explanation
Indices: 28805555--28805688 Score: 191
Period size: 50 Copynumber: 2.6 Consensus size: 51
28805545 ACTTTTATCA
* *
28805555 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* *
28805604 TTACGGTTCACGTAGTAGCCTTTACATAGTACTACACACGTGACCAAAGCTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* *
28805656 TTCGGTACACATAGTAGCCTTCACTTAGTACTA
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTA
28805689 GCCTTTACAC
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
49 2 0.03
50 38 0.51
51 30 0.41
52 4 0.05
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (51 bp):
TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
Found at i:28805696 original size:68 final size:68
Alignment explanation
Indices: 28805619--28805756 Score: 249
Period size: 68 Copynumber: 2.0 Consensus size: 68
28805609 GTTCACGTAG
* *
28805619 TAGCCTTTACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAG
1 TAGCCTTTACACAGTACTACACACGTGACCAAAGCTTGTCGGTACACATAGTAGCCTTCACTTAG
28805684 TAC
66 TAC
*
28805687 TAGCCTTTACACAGTACTACACACGTGACCAAAGCTTGTCGGTACACATTGTAGCCTTCACTTAG
1 TAGCCTTTACACAGTACTACACACGTGACCAAAGCTTGTCGGTACACATAGTAGCCTTCACTTAG
28805752 TAC
66 TAC
28805755 TA
1 TA
28805757 CACATGTGAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (68 bp):
TAGCCTTTACACAGTACTACACACGTGACCAAAGCTTGTCGGTACACATAGTAGCCTTCACTTAG
TAC
Found at i:28805790 original size:119 final size:117
Alignment explanation
Indices: 28805561--28805807 Score: 266
Period size: 119 Copynumber: 2.1 Consensus size: 117
28805551 ATCATTCGAT
* * * * * *
28805561 ACAC-GTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTAGCCT
1 ACACAGTACTAGCCTTCACACAGTACTACACACGTGACCAAGTTGTACGGTACACATAGTAGCCT
* *
28805625 TTACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTC
66 TCACATAGTACTACACACGTGACCAAA-CTTTTCGATACACATAGTAGCCTTC
** * *
28805678 ACTTAGTACTAGCCTTTACACAGTACTACACACGTGACCAAAGCTTGT-CGGTACACATTGTAGC
1 ACACAGTACTAGCCTTCACACAGTACTACACACGTGACC-AAG-TTGTACGGTACACATAGTAGC
* * * * **
28805742 CTTCACTTAGTACTACACATGTGACCATTA-TTTATCGATTCATGTAGTAGCCTTC
64 CTTCACATAGTACTACACACGTGACCA-AACTTT-TCGATACACATAGTAGCCTTC
28805797 ACACAGTACTA
1 ACACAGTACTA
28805808 CACATGTGTT
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
117 2 0.02
118 33 0.31
119 66 0.63
120 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (117 bp):
ACACAGTACTAGCCTTCACACAGTACTACACACGTGACCAAGTTGTACGGTACACATAGTAGCCT
TCACATAGTACTACACACGTGACCAAACTTTTCGATACACATAGTAGCCTTC
Found at i:28813159 original size:50 final size:50
Alignment explanation
Indices: 28812985--28813231 Score: 241
Period size: 49 Copynumber: 4.9 Consensus size: 50
28812975 TGATAATAAC
* * * *
28812985 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGT-TTCTAG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * ** *
28813032 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * **
28813084 GTGCC-ATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
28813133 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATGATCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---G
* * *
28813189 ATGCCAATGTCATGTCCCAGGCATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28813232 TTACCCAAAT
Statistics
Matches: 165, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
48 1 0.01
49 74 0.45
50 40 0.24
51 2 0.01
52 3 0.02
53 5 0.03
56 40 0.24
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:28822106 original size:19 final size:19
Alignment explanation
Indices: 28822082--28822122 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
28822072 TATTTTAAAG
28822082 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
28822101 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
28822120 TTA
1 TTA
28822123 GAATAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:28823141 original size:49 final size:47
Alignment explanation
Indices: 28823078--28823203 Score: 150
Period size: 46 Copynumber: 2.7 Consensus size: 47
28823068 AATTATAAAA
*
28823078 TCAAATAATTATTTCAAATATCACAATTATTTTTACATGTGAAATATT
1 TCAAAAAATTATTTCAAATATCA-AATTATTTTTACATGTGAAATATT
** *
28823126 TCAAAAAAATTATTTCAAATAT--TTTTATTTTTATATGTGAAATATT
1 TC-AAAAAATTATTTCAAATATCAAATTATTTTTACATGTGAAATATT
* *
28823172 TCAAATAATTAATTCAAATATCAATATT-TTTT
1 TCAAAAAATTATTTCAAATATCAA-ATTATTTT
28823204 CACCTGCATT
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
45 17 0.26
46 23 0.35
47 4 0.06
48 4 0.06
49 18 0.27
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (47 bp):
TCAAAAAATTATTTCAAATATCAAATTATTTTTACATGTGAAATATT
Found at i:28823200 original size:45 final size:45
Alignment explanation
Indices: 28823078--28823202 Score: 160
Period size: 45 Copynumber: 2.7 Consensus size: 45
28823068 AATTATAAAA
28823078 TCAAATAATTATTTCAAATATCACAATTATTTTTACATGTGAAATATT
1 TCAAATAATTATTTCAAATAT--CAA-TATTTTTACATGTGAAATATT
* *** *
28823126 TCAAAAAAATTATTTCAAATATTTTTATTTTTATATGTGAAATATT
1 TC-AAATAATTATTTCAAATATCAATATTTTTACATGTGAAATATT
*
28823172 TCAAATAATTAATTCAAATATCAATATTTTT
1 TCAAATAATTATTTCAAATATCAATATTTTT
28823203 TCACCTGCAT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
45 24 0.36
46 22 0.33
48 2 0.03
49 18 0.27
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.46
Consensus pattern (45 bp):
TCAAATAATTATTTCAAATATCAATATTTTTACATGTGAAATATT
Found at i:28827395 original size:13 final size:13
Alignment explanation
Indices: 28827377--28827401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28827367 AAATCTGTTT
28827377 TGAGTGCTGCTCA
1 TGAGTGCTGCTCA
28827390 TGAGTGCTGCTC
1 TGAGTGCTGCTC
28827402 TTGTTAAGGC
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:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (13 bp):
TGAGTGCTGCTCA
Found at i:28829098 original size:17 final size:18
Alignment explanation
Indices: 28829078--28829111 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28829068 ATTATTAAGA
*
28829078 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAAATATAT
28829095 ATTTTAATTAAAATATA
1 ATTTTAATTAAAATATA
28829112 AATCCAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAATTAAAATATAT
Done.