Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007962.1 Hibiscus syriacus cultivar Beakdansim tig00110391_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: 1774241
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1074214 original size:2 final size:2
Alignment explanation
Indices: 1074207--1074302 Score: 67
Period size: 2 Copynumber: 48.0 Consensus size: 2
1074197 AAAGTACAAG
* *
1074207 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA GT- TT TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
1074250 TA AA GTA TA TA TA CA TA TA TA -A TA -A TA TA AA GTA TA -A GTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
1074290 TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA
1074303 AAAAGTATAA
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
1 5 0.07
2 65 0.87
3 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1074333 original size:22 final size:21
Alignment explanation
Indices: 1074273--1074607 Score: 170
Period size: 22 Copynumber: 15.6 Consensus size: 21
1074263 CATATATAAT
*
1074273 AATATAAAGTATAAGTATATTATA
1 AATATAAAGTAT-A-TA-AGTATA
* * *
1074297 TATATAAA-AAGTATAATTATA
1 AATATAAAGTA-TATAAGTATA
*
1074318 AAGACTAAAGTATATAAGTATA
1 AATA-TAAAGTATATAAGTATA
* *
1074340 TAATATAAAATATATAAGCATTA
1 -AATATAAAGTATATAAGTA-TA
*
1074363 AATATAAAGTATATAACTATA
1 AATATAAAGTATATAAGTATA
*
1074384 TAACTAT--A-TATA-AACTATA
1 -AA-TATAAAGTATATAAGTATA
1074403 AACTATAAAGTGTATATATA-TATA
1 AA-TATAAA--GTATATA-AGTATA
*
1074427 TATATATAAAGTTTTAGTGTAAAGTAT-
1 -A-ATATAAAG---TA-TAT-AAGTATA
1074454 -ATATAACA-TATAATAA-TATA
1 AATATAA-AGTAT-ATAAGTATA
1074474 AAT-TATAAGTATAT-A-TATA
1 AATATA-AAGTATATAAGTATA
*
1074493 TAATATAAAG--TACAAGTATA
1 -AATATAAAGTATATAAGTATA
*
1074513 TAATATAAAGTATACAAGTATTA
1 -AATATAAAGTATATAAGTA-TA
*
1074536 AATATAAAGTATATAAATAT-
1 AATATAAAGTATATAAGTATA
1074556 AATATAAAGTATATAAGTATTA
1 AATATAAAGTATATAAGTA-TA
1074578 AATAT-AAGTATA-AA-TA-A
1 AATATAAAGTATATAAGTATA
1074595 AATATAAAGTATA
1 AATATAAAGTATA
1074608 AGTATATAAG
Statistics
Matches: 255, Mismatches: 18, Indels: 82
0.72 0.05 0.23
Matches are distributed among these distances:
17 6 0.02
18 15 0.06
19 18 0.07
20 53 0.21
21 31 0.12
22 76 0.30
23 18 0.07
24 19 0.07
25 9 0.04
26 3 0.01
27 3 0.01
28 4 0.02
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (21 bp):
AATATAAAGTATATAAGTATA
Found at i:1074395 original size:18 final size:18
Alignment explanation
Indices: 1074372--1074409 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1074362 AAATATAAAG
1074372 TATAT-AACTATATAACTA
1 TATATAAACTATA-AACTA
1074390 TATATAAACTATAAACTA
1 TATATAAACTATAAACTA
1074408 TA
1 TA
1074410 AAGTGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
TATATAAACTATAAACTA
Found at i:1074475 original size:26 final size:26
Alignment explanation
Indices: 1074446--1074629 Score: 77
Period size: 26 Copynumber: 7.1 Consensus size: 26
1074436 AGTTTTAGTG
1074446 TAAAGTATATA-TAACATATA-ATAATA
1 TAAAGTATA-AGT-ACATATATATAATA
* *
1074472 TAAATTATAAGTATATATATATAATA
1 TAAAGTATAAGTACATATATATAATA
* *
1074498 TAAAGTACAAGTATATA-ATATAAAGTA
1 TAAAGTATAAGTACATATATAT-AA-TA
* *
1074525 TACAAGTAT---TAAATATAAAGT-ATA
1 TA-AAGTATAAGTACATATATA-TAATA
* *
1074549 TAAA-TATAA-TATAAAGTATATAAGTA
1 TAAAGTATAAGTACATA-TATATAA-TA
* *
1074575 TTAAA-TATAAGT--ATAAATAAAATA
1 -TAAAGTATAAGTACATATATATAATA
*
1074599 TAAAGTATAAGTATATAAGTATATATATA
1 TAAAGTATAAGTACAT-A-TATATA-ATA
1074628 TA
1 TA
1074630 TATATATATA
Statistics
Matches: 123, Mismatches: 15, Indels: 37
0.70 0.09 0.21
Matches are distributed among these distances:
22 3 0.02
23 6 0.05
24 18 0.15
25 26 0.21
26 40 0.33
27 15 0.12
28 10 0.08
29 5 0.04
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (26 bp):
TAAAGTATAAGTACATATATATAATA
Found at i:1074512 original size:20 final size:20
Alignment explanation
Indices: 1074480--1074621 Score: 127
Period size: 20 Copynumber: 7.0 Consensus size: 20
1074470 TATAAATTAT
1074480 AAGTATATA-TATATAATATA
1 AAGTATA-AGTATATAATATA
*
1074500 AAGTACAAGTATATAATATA
1 AAGTATAAGTATATAATATA
1074520 AAGTATACAAGTAT-TAAATATA
1 AAGTAT--AAGTATAT-AATATA
*
1074542 AAGTATATA-AATATAATATA
1 AAGTATA-AGTATATAATATA
1074562 AAGTATATAAGTAT-TAA-ATA
1 AAG--TATAAGTATATAATATA
*
1074582 TAAGTATAA--ATAAAATATA
1 -AAGTATAAGTATATAATATA
1074601 AAGTATAAGTATATAAGTATA
1 AAGTATAAGTATATAA-TATA
1074622 TATATATATA
Statistics
Matches: 101, Mismatches: 6, Indels: 29
0.74 0.04 0.21
Matches are distributed among these distances:
17 2 0.02
18 10 0.10
19 9 0.09
20 42 0.42
21 14 0.14
22 24 0.24
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.34
Consensus pattern (20 bp):
AAGTATAAGTATATAATATA
Found at i:1074551 original size:195 final size:192
Alignment explanation
Indices: 1074217--1074629 Score: 543
Period size: 195 Copynumber: 2.1 Consensus size: 192
1074207 TATATATATA
*
1074217 TATATATATATATATATATATAAAGTTTTAGTATAAAGTATATATACATATATAATAATATAAAG
1 TATATATATATATATATATATAAAGTTTTAGTATAAAGTATATATACACATATAATAATATAAAG
* * *
1074282 TATAAGTATATTATATATATAAAAAGTATAATTATAAAGACTAAAGTATATAAGTATATAATATA
66 TATAAGTATATTATATATATAAAAAGTACAAGTATAAAGACTAAAGTATACAAGTATATAATATA
*
1074347 AAATATATAAGCAT-TAAATATAAAGTATATAACTATATAACTAT-A-TATAAACTATAAACTAT
131 AAATATATAA--ATAT-AATATAAAGTATATAACTAT-TAAATATAAGTATAAA-TA-AAA-TAT
1074409 AAAG
189 AAAG
* * *
1074413 TGTATATATATATATATATATAAAGTTTTAGTGTAAAGTATATATA-ACATATAATAATATAAAT
1 TATATATATATATATATATATAAAGTTTTAGTATAAAGTATATATACACATATAATAATATAAAG
* *
1074477 TATAAGTATA-TATATATAATATAAAGTACAAGTATATAATA-TAAAGTATACAAGTAT-TAAAT
66 TATAAGTATATTATATAT-ATAAAAAGTACAAGTATA-AAGACTAAAGTATACAAGTATAT-AAT
* *
1074539 ATAAAGTATATAAATATAATATAAAGTATATAAGTATTAAATATAAGTATAAATAAAATATAAAG
128 ATAAAATATATAAATATAATATAAAGTATATAACTATTAAATATAAGTATAAATAAAATATAAAG
1074604 TATAAGTATATAAGTATATATATATA
1 TAT-A-TATAT-A-TATATATATATA
1074630 TATATATATA
Statistics
Matches: 194, Mismatches: 13, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
191 9 0.05
192 10 0.05
193 29 0.15
194 16 0.08
195 83 0.43
196 47 0.24
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (192 bp):
TATATATATATATATATATATAAAGTTTTAGTATAAAGTATATATACACATATAATAATATAAAG
TATAAGTATATTATATATATAAAAAGTACAAGTATAAAGACTAAAGTATACAAGTATATAATATA
AAATATATAAATATAATATAAAGTATATAACTATTAAATATAAGTATAAATAAAATATAAAG
Found at i:1074599 original size:39 final size:41
Alignment explanation
Indices: 1074514--1074607 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 41
1074504 ACAAGTATAT
*
1074514 AATATAAAGTATACAAGTATTAAATATAAAGTATATAAATAT
1 AATATAAAGTATACAAGTATTAAATATAAAG-ATATAAATAA
*
1074556 AATATAAAGTATATAAGTATTAAATAT-AAG-TATAAATAA
1 AATATAAAGTATACAAGTATTAAATATAAAGATATAAATAA
1074595 AATATAAAGTATA
1 AATATAAAGTATA
1074608 AGTATATAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 21 0.42
41 3 0.06
42 26 0.52
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (41 bp):
AATATAAAGTATACAAGTATTAAATATAAAGATATAAATAA
Found at i:1074623 original size:2 final size:2
Alignment explanation
Indices: 1074618--1074877 Score: 124
Period size: 2 Copynumber: 132.0 Consensus size: 2
1074608 AGTATATAAG
*
1074618 TA TA TA TA TA TA TA TA TA TA TA TA CA CT- TA TA TA -A 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
*
1074659 TA CT- TA TA TA TA TA TA TA TA TA TA TA TA TA CT- TA TA TA CTT
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
* * * * *
1074700 TA GT- TT TA TA -A T- TA TA CTT TA TA TA CTT TA TA TT TA -A TT
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA
* * *
1074739 TA TA T- TA TA TA TA TA TA T- TA TA CTT TT TA TA T- TT TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* *
1074779 TA TA T- TT TA TA TA T- TA CT- TA TA CT- TA TA T- TA TA TGC T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA T-A TA
* * *
1074816 TA TA TA CTT TA GTC TT 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
*
1074860 TA TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1074878 ACTTATACTT
Statistics
Matches: 201, Mismatches: 25, Indels: 64
0.69 0.09 0.22
Matches are distributed among these distances:
1 18 0.09
2 170 0.85
3 13 0.06
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1074625 original size:10 final size:9
Alignment explanation
Indices: 1074610--1074688 Score: 76
Period size: 10 Copynumber: 8.7 Consensus size: 9
1074600 AAAGTATAAG
1074610 TATATAAGTA
1 TATATAA-TA
1074620 TATAT-ATA
1 TATATAATA
1074628 TATAT-ATA
1 TATATAATA
1074636 TATATACACT-
1 TATATA-A-TA
1074646 TATATAATA
1 TATATAATA
*
1074655 TATATACT-
1 TATATAATA
1074663 TATATATATA
1 TATATA-ATA
1074673 TATATATATA
1 TATATA-ATA
1074683 TATATA
1 TATATA
1074689 CTTATATACT
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
8 22 0.36
9 10 0.16
10 28 0.46
11 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (9 bp):
TATATAATA
Found at i:1074891 original size:20 final size:21
Alignment explanation
Indices: 1074624--1074915 Score: 103
Period size: 20 Copynumber: 14.2 Consensus size: 21
1074614 TAAGTATATA
*
1074624 TATATATATATA-TATATACACT
1 TATATATATATACT-TATAC-TT
1074646 TATATA-ATATA--TATAC-T
1 TATATATATATACTTATACTT
*
1074663 TATATATATATA-TATATA-TA
1 TATATATATATACT-TATACTT
*
1074683 TATATACTTATATACTT-TAGTTT
1 TATATA--TATATACTTATA-CTT
1074706 TATA-AT-TATACTTTATATACTT
1 TATATATATATAC--T-TATACTT
*
1074728 TATAT-T-TA-ATTTATA--T
1 TATATATATATACTTATACTT
1074744 TATATATATATA-TTATACTT
1 TATATATATATACTTATACTT
* *
1074764 TTTATAT-TTTACTTATA-TAT
1 TATATATATATACTTATACT-T
*
1074784 TTTATATAT-TACTTATAC-T
1 TATATATATATACTTATACTT
*
1074803 TATAT-TATATGCTTATATACTT
1 TATATATATATAC-T-TATACTT
* * *
1074825 TAGTCTTTATATA-TATATA-TA
1 TA-TATATATATACT-TATACTT
**
1074846 TATATATATATA-TATATA-AA
1 TATATATATATACT-TATACTT
1074866 TATATATATATAACTTATACTT
1 TATATATATAT-ACTTATACTT
* *
1074888 TATATTTTATATATGTATATACTT
1 TATA-TATATATA-CT-TATACTT
1074912 TATA
1 TATA
1074916 CTAAAACTAT
Statistics
Matches: 217, Mismatches: 18, Indels: 68
0.72 0.06 0.22
Matches are distributed among these distances:
16 6 0.03
17 8 0.04
18 19 0.09
19 23 0.11
20 66 0.30
21 23 0.11
22 39 0.18
23 17 0.08
24 16 0.07
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (21 bp):
TATATATATATACTTATACTT
Found at i:1075020 original size:9 final size:9
Alignment explanation
Indices: 1075008--1075032 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1074998 TTATACTTTA
1075008 TATATAAAC
1 TATATAAAC
1075017 TATATAAAC
1 TATATAAAC
1075026 TATATAA
1 TATATAA
1075033 TTTATACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (9 bp):
TATATAAAC
Found at i:1075111 original size:21 final size:22
Alignment explanation
Indices: 1075065--1075118 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
1075055 TATAATTATA
*
1075065 CATA-ATAATTAAATATAAGCT
1 CATATATATTTAAATATAAGCT
*
1075086 C-TATATATTTAAATATAA-TT
1 CATATATATTTAAATATAAGCT
1075106 CATATATAATTTA
1 CATATAT-ATTTA
1075119 CATTTAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 19 0.68
22 5 0.18
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
CATATATATTTAAATATAAGCT
Found at i:1075133 original size:20 final size:21
Alignment explanation
Indices: 1075108--1075161 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
1075098 ATATAATTCA
1075108 TATATAATTTACATT-TAAAC
1 TATATAATTTACATTATAAAC
*
1075128 TATATAATTTATATTAATAAAC
1 TATATAATTTACATT-ATAAAC
*
1075150 TATATAGTTTAC
1 TATATAATTTAC
1075162 GTATAGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 14 0.48
22 15 0.52
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (21 bp):
TATATAATTTACATTATAAAC
Found at i:1075186 original size:2 final size:2
Alignment explanation
Indices: 1075179--1075219 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
1075169 TCAATAGTTC
*
1075179 AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1075218 AT
1 AT
1075220 TTTGGCTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:1075216 original size:17 final size:19
Alignment explanation
Indices: 1075186--1075222 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1075176 TTCATATATA
1075186 TATATATATATATATATTT
1 TATATATATATATATATTT
1075205 TATAT-TAT-TATATATTT
1 TATATATATATATATATTT
1075222 T
1 T
1075223 GGCTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATATATATATATATTT
Found at i:1080386 original size:20 final size:20
Alignment explanation
Indices: 1080352--1080399 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1080342 AACGAGTTTC
*
1080352 TTTTG-AAAGCAAAATTG-GA
1 TTTTGAAAAGCAAAA-TGAAA
*
1080371 TTTTGAAAATCAAAATGAAA
1 TTTTGAAAAGCAAAATGAAA
1080391 TTTTGAAAA
1 TTTTGAAAA
1080400 CGGATTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATGAAA
Found at i:1085461 original size:82 final size:82
Alignment explanation
Indices: 1085366--1085724 Score: 450
Period size: 82 Copynumber: 4.4 Consensus size: 82
1085356 CCAAATAATG
* * * * * *
1085366 GTGGTGCATTATCATCTTCTGCAAATTTTCAAAGATCATTTAATGCATAATTTGATCAAATTTTT
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTTT
**
1085431 AGAAAACATGTGAAATA
66 AGAAAACGGGTGAAATA
* * ** * * *
1085448 GTGGTGCATTATCATATTCTGTAACTTTTCTGACGTCATTCAATGCATTATTTAAACAACTTTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTTT
1085513 AGAAAACGGGTGAAATA
66 AGAAAACGGGTGAAATA
* ** * * * *
1085530 GTAGTGTGTTATTATCTTCTGGAACTTTTCAAAGGTTATTCAATGTATAATTTAAACAACTTTTT
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTTT
1085595 AGAAAACGGGTGAAATA
66 AGAAAACGGGTGAAATA
* *
1085612 GTGTTGCATTATCATCTTCTGCAACTTTTCAAAGGTTATTCAATGCATAATTTAAACAACTTTTT
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTTT
* *
1085677 AGACAATGGGTGAAATA
66 AGAAAACGGGTGAAATA
* *
1085694 GTGGTGTC-TTATCATATTCAGCAACTTTTCA
1 GTGGTG-CATTATCATCTTCTGCAACTTTTCA
1085725 GTGATGATCA
Statistics
Matches: 236, Mismatches: 40, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
82 235 1.00
83 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (82 bp):
GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTTT
AGAAAACGGGTGAAATA
Found at i:1087055 original size:19 final size:19
Alignment explanation
Indices: 1087006--1087105 Score: 87
Period size: 19 Copynumber: 5.3 Consensus size: 19
1086996 ACTTTCACAT
*
1087006 TTCATAATTTATTTTCTA-A
1 TTCATAACTTATTTTC-AGA
* * * * *
1087025 ATCAAAATTTATTTCCATA
1 TTCATAACTTATTTTCAGA
1087044 TTCATAACTTATTTTCAGA
1 TTCATAACTTATTTTCAGA
* * *
1087063 CTCATTACTTA-CTTCAGA
1 TTCATAACTTATTTTCAGA
*
1087081 TTCATAACTTATTTTCAAA
1 TTCATAACTTATTTTCAGA
1087100 TTCATA
1 TTCATA
1087106 GCCCAATGTA
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
18 16 0.25
19 48 0.75
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (19 bp):
TTCATAACTTATTTTCAGA
Found at i:1087080 original size:18 final size:18
Alignment explanation
Indices: 1087045--1087091 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1087035 ATTTCCATAT
*
1087045 TCATAACTTATTTTCAGAC
1 TCATAACTTA-CTTCAGAC
* *
1087064 TCATTACTTACTTCAGAT
1 TCATAACTTACTTCAGAC
1087082 TCATAACTTA
1 TCATAACTTA
1087092 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (18 bp):
TCATAACTTACTTCAGAC
Found at i:1088668 original size:13 final size:13
Alignment explanation
Indices: 1088650--1088679 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1088640 TGACTTTGAC
*
1088650 TGACCGTTAACTT
1 TGACCGTAAACTT
1088663 TGACCGTAAACTT
1 TGACCGTAAACTT
1088676 TGAC
1 TGAC
1088680 AAAAAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (13 bp):
TGACCGTAAACTT
Found at i:1089821 original size:26 final size:26
Alignment explanation
Indices: 1089792--1089843 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1089782 AAGCAACCCA
1089792 TTTTTCTAATGACTTAAAATAAGTGG
1 TTTTTCTAATGACTTAAAATAAGTGG
1089818 TTTTTCTAATGACTTAAAATAAGTGG
1 TTTTTCTAATGACTTAAAATAAGTGG
1089844 ATATCTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (26 bp):
TTTTTCTAATGACTTAAAATAAGTGG
Found at i:1090255 original size:16 final size:17
Alignment explanation
Indices: 1090228--1090259 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1090218 GATATCCTGA
1090228 TAAATCAACATGAATCT
1 TAAATCAACATGAATCT
1090245 TAAAT-AACATGAATC
1 TAAATCAACATGAATC
1090260 ATCGTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (17 bp):
TAAATCAACATGAATCT
Found at i:1094455 original size:30 final size:29
Alignment explanation
Indices: 1094421--1094492 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1094411 TAAAATTACA
* *
1094421 ATTTTAGTCCCTAAACTTTTCCAAAGTTCC
1 ATTTTAGTCACTAAAC-TTTCAAAAGTTCC
* * *
1094451 ATTTTAGTTACTTAACTTTCAAAATTTCC
1 ATTTTAGTCACTAAACTTTCAAAAGTTCC
*
1094480 ATTTTGGTCACTA
1 ATTTTAGTCACTA
1094493 TTCGAAATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (29 bp):
ATTTTAGTCACTAAACTTTCAAAAGTTCC
Found at i:1094480 original size:29 final size:30
Alignment explanation
Indices: 1094402--1094491 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
1094392 GGGCCGGATT
* * * *
1094402 TTAACTTTTTAAAATTACAATTTTAGTCCC
1 TTAACTTTTCAAAATTTCCATTTTAGTCAC
* * * *
1094432 TAAACTTTTCCAAAGTTCCATTTTAGTTAC
1 TTAACTTTTCAAAATTTCCATTTTAGTCAC
*
1094462 TTAAC-TTTCAAAATTTCCATTTTGGTCAC
1 TTAACTTTTCAAAATTTCCATTTTAGTCAC
1094491 T
1 T
1094492 ATTCGAAATT
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 21 0.45
30 26 0.55
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (30 bp):
TTAACTTTTCAAAATTTCCATTTTAGTCAC
Found at i:1105717 original size:15 final size:14
Alignment explanation
Indices: 1105698--1105923 Score: 89
Period size: 15 Copynumber: 14.5 Consensus size: 14
1105688 GGGAAAAAAT
1105698 AAAAATAAAATAAA
1 AAAAATAAAATAAA
*
1105712 ACAAAACAAAATCAAGAGA
1 A-AAAATAAAAT--A-A-A
1105731 AAAAAGTAAAATAAA
1 AAAAA-TAAAATAAA
1105746 AAAAGATAAAA-AAA
1 AAAA-ATAAAATAAA
* *
1105760 ATAAATAAAACAAA
1 AAAAATAAAATAAA
*
1105774 GAAAATTAAAATAATA
1 -AAAAATAAAATAA-A
*
1105790 AAAAAGAAAATATTAA
1 AAAAATAAAATA--AA
* *
1105806 ATCAAATAAAA-AAC
1 A-AAAATAAAATAAA
* *
1105820 AAAAACAAAAAAACA
1 AAAAATAAAATAA-A
1105835 ATATAAATAATAATAATA
1 A-A-AAATAA-AATAA-A
1105853 ATAAATATAAAATAAGAA
1 A-AAA-ATAAAAT-A-AA
*
1105871 AAAAACTAATATATATA
1 AAAAA-TAA-A-ATAAA
* *
1105888 TAAAATAAAA-AAT
1 AAAAATAAAATAAA
1105901 AAAAATAAAGATAAA
1 AAAAATAAA-ATAAA
1105916 TAAAAATA
1 -AAAAATA
1105924 TATAAATAAC
Statistics
Matches: 162, Mismatches: 23, Indels: 52
0.68 0.10 0.22
Matches are distributed among these distances:
13 22 0.14
14 16 0.10
15 43 0.27
16 18 0.11
17 31 0.19
18 22 0.14
19 10 0.06
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (14 bp):
AAAAATAAAATAAA
Found at i:1105751 original size:23 final size:21
Alignment explanation
Indices: 1105693--1105817 Score: 65
Period size: 23 Copynumber: 5.6 Consensus size: 21
1105683 AAAAAGGGAA
* *
1105693 AAAATAAAAATAAA-ATAAAAC
1 AAAATAAAAA-AAAGAAAAAAT
* *
1105714 AAAACAAAATCAAGAGAAAAAAGT
1 AAAATAAAA--AAAAGAAAAAA-T
* *
1105738 AAAATAAAAAAAGATAAAAAAA
1 AAAATAAAAAAA-AGAAAAAAT
* *
1105760 ATAAATAAAACAAAG-AAAATT
1 A-AAATAAAAAAAAGAAAAAAT
*
1105781 AAAATAATAAAAAAGAAAATAT
1 AAAATAA-AAAAAAGAAAAAAT
*
1105803 TAAATCAAATAAAAA
1 AAAAT-AAA-AAAAA
1105818 ACAAAAACAA
Statistics
Matches: 78, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
20 6 0.08
21 19 0.24
22 15 0.19
23 30 0.38
24 8 0.10
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAATAAAAAAAAGAAAAAAT
Found at i:1105758 original size:9 final size:9
Alignment explanation
Indices: 1105676--1105794 Score: 62
Period size: 9 Copynumber: 12.4 Consensus size: 9
1105666 GACTATTCTT
1105676 AAAAAATAA
1 AAAAAATAA
1105685 AAAGGGAAA-AA
1 AAA---AAATAA
1105696 ATAAAAATAA
1 A-AAAAATAA
*
1105706 AATAAAACAA
1 AA-AAAATAA
1105716 AACAAAATCAA
1 AA-AAAAT-AA
*
1105727 GAGAAAA-AA
1 -AAAAAATAA
**
1105736 GTAAAATAA
1 AAAAAATAA
1105745 AAAAAGATAA
1 AAAAA-ATAA
1105755 AAAAAATAA
1 AAAAAATAA
* *
1105764 ATAAAACAA
1 AAAAAATAA
* *
1105773 AGAAAATTA
1 AAAAAATAA
*
1105782 AAATAATAA
1 AAAAAATAA
1105791 AAAA
1 AAAA
1105795 GAAAATATTA
Statistics
Matches: 83, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
8 4 0.05
9 40 0.48
10 24 0.29
11 9 0.11
12 6 0.07
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1105856 original size:42 final size:41
Alignment explanation
Indices: 1105810--1105905 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 41
1105800 TATTAAATCA
1105810 AATAAAA-AACAAAAACAAAAAAAC-AATATAAATAATAATAAT
1 AATAAAATAA-AAAAACAAAAAAACTAATATAAAT-ATAA-AAT
* * *
1105852 AATAAATATAAAATAAGAAAAAAACTAATATATATATAAAAT
1 AATAAA-ATAAAAAAACAAAAAAACTAATATAAATATAAAAT
1105894 AA-AAAATAAAAA
1 AATAAAATAAAAA
1105906 TAAAGATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
40 6 0.13
41 3 0.06
42 11 0.23
43 17 0.36
44 10 0.21
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (41 bp):
AATAAAATAAAAAAACAAAAAAACTAATATAAATATAAAAT
Found at i:1105881 original size:35 final size:32
Alignment explanation
Indices: 1105845--1105905 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1105835 ATATAAATAA
1105845 TAATA-ATA-ATAAATATAAAATAAGAAAAAAAC
1 TAATATATATATAAA-ATAAAA-AAGAAAAAAAC
*
1105877 TAATATATATATAAAATAAAAAATAAAAA
1 TAATATATATATAAAATAAAAAAGAAAAA
1105906 TAAAGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 12 0.46
33 9 0.35
34 5 0.19
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (32 bp):
TAATATATATATAAAATAAAAAAGAAAAAAAC
Found at i:1105914 original size:24 final size:24
Alignment explanation
Indices: 1105731--1105932 Score: 88
Period size: 24 Copynumber: 8.3 Consensus size: 24
1105721 AATCAAGAGA
*
1105731 AAAAAGTAAA-ATAAAA-AAAGATAAA
1 AAAAA-TAAATATAAAATAAA-A-AAT
1105756 AAAAATAAATA-AAACA-AAGAAAAT
1 AAAAATAAATATAAA-ATAA-AAAAT
* *
1105780 TAAAAT-AATA-AAAA-AGAAAAT
1 AAAAATAAATATAAAATAAAAAAT
* *
1105801 ATTAAATCAAATA-AAAA-ACAAAAAC
1 A-AAAAT-AAATATAAAATA-AAAAAT
* *
1105826 AAAAAAACAATAT-AAAT-AATAAT
1 AAAAATA-AATATAAAATAAAAAAT
*
1105849 AATAATAAATATAAAATAAGAAAA-
1 AAAAATAAATATAAAATAA-AAAAT
1105873 AAACTAATATATATATAAAATAAAAAAT
1 AAA--AATA-A-ATATAAAATAAAAAAT
*
1105901 AAAAATAAAGAT-AAATAAAAATAT
1 AAAAATAAATATAAAATAAAAA-AT
*
1105925 ATAAATAA
1 AAAAATAA
1105933 CATTATGTAA
Statistics
Matches: 141, Mismatches: 17, Indels: 39
0.72 0.09 0.20
Matches are distributed among these distances:
21 5 0.04
22 11 0.08
23 30 0.21
24 48 0.34
25 19 0.13
26 9 0.06
27 5 0.04
28 14 0.10
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (24 bp):
AAAAATAAATATAAAATAAAAAAT
Found at i:1105924 original size:42 final size:42
Alignment explanation
Indices: 1105826--1105932 Score: 121
Period size: 42 Copynumber: 2.5 Consensus size: 42
1105816 AAACAAAAAC
* *
1105826 AAAAAAACAATATAAATAATAATAATAATAAATATAAAATAAG
1 AAAAAAACAATATATAT-ATAATAATAAAAAATATAAAATAAG
1105869 AAAAAAACTAATATATATATAA-AATAAAAAATA-AAAATAAAG
1 AAAAAAAC-AATATATATATAATAATAAAAAATATAAAAT-AAG
*
1105911 ATAAATAAA-AATATATAAATAA
1 A-AAA-AAACAATATATATATAA
1105933 CATTATGTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
41 5 0.09
42 26 0.46
43 15 0.26
44 11 0.19
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (42 bp):
AAAAAAACAATATATATATAATAATAAAAAATATAAAATAAG
Found at i:1105928 original size:10 final size:10
Alignment explanation
Indices: 1105738--1105929 Score: 57
Period size: 10 Copynumber: 19.2 Consensus size: 10
1105728 AGAAAAAAGT
1105738 AAAATAAA-A
1 AAAATAAATA
1105747 AAAGATAAA-A
1 AAA-ATAAATA
1105757 AAAATAAAT-
1 AAAATAAATA
* *
1105766 AAAACAAAGA
1 AAAATAAATA
*
1105776 AAATTAAAATA
1 AAAAT-AAATA
*
1105787 ATAAA-AAAGA
1 A-AAATAAATA
1105797 AAATATTAAAT-
1 AAA-A-TAAATA
*
1105808 CAAATAAA-A
1 AAAATAAATA
*
1105817 AACAA-AAACA
1 AA-AATAAATA
*
1105827 AAAAAACAATA
1 AAAATA-AATA
*
1105838 TAAATAATAATA
1 AAAAT-A-AATA
*
1105850 ATAATAAATA
1 AAAATAAATA
*
1105860 TAAAAT-AAGA
1 -AAAATAAATA
*
1105870 AAAA-AACT-
1 AAAATAAATA
* *
1105878 AATATATATA
1 AAAATAAATA
1105888 TAAAATAAA-A
1 -AAAATAAATA
1105898 AATAA-AAATA
1 AA-AATAAATA
*
1105908 AAGATAAATA
1 AAAATAAATA
*
1105918 AAAATATATA
1 AAAATAAATA
1105928 AA
1 AA
1105930 TAACATTATG
Statistics
Matches: 133, Mismatches: 28, Indels: 43
0.65 0.14 0.21
Matches are distributed among these distances:
8 3 0.02
9 40 0.30
10 53 0.40
11 24 0.18
12 13 0.10
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (10 bp):
AAAATAAATA
Found at i:1107113 original size:15 final size:15
Alignment explanation
Indices: 1107093--1107123 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1107083 CCTAACTGAT
*
1107093 TCGGGTTTGGACCGG
1 TCGGGTCTGGACCGG
1107108 TCGGGTCTGGACCGG
1 TCGGGTCTGGACCGG
1107123 T
1 T
1107124 TTAGGTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.23, G:0.45, T:0.26
Consensus pattern (15 bp):
TCGGGTCTGGACCGG
Found at i:1110413 original size:21 final size:21
Alignment explanation
Indices: 1110371--1110413 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1110361 TTTCTGGGTT
* * *
1110371 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1110392 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1110413 A
1 A
1110414 TGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1110474 original size:67 final size:68
Alignment explanation
Indices: 1110393--1110544 Score: 243
Period size: 67 Copynumber: 2.2 Consensus size: 68
1110383 ACCCATTCAA
* * *
1110393 GGGGAACCGATACCCCCTCAATGAATATGAATTTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
1110457 AGG
66 AGG
*
1110460 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
*
1110525 GGG
66 AGG
*
1110528 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1110545 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 55 0.71
68 23 0.29
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
AGG
Found at i:1111213 original size:149 final size:149
Alignment explanation
Indices: 1111020--1111323 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
1111010 GGGTAGAGGG
* *
1111020 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
1111085 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1111150 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1111169 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1111234 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1111299 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1111318 TCTACG
1 TCTACG
1111324 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1111346 original size:23 final size:23
Alignment explanation
Indices: 1111302--1111346 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1111292 ATCATTATAT
*
1111302 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1111325 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1111347 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1117444 original size:21 final size:21
Alignment explanation
Indices: 1117402--1117444 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1117392 TTTCTGGGTT
* * *
1117402 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1117423 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1117444 A
1 A
1117445 TGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1117505 original size:67 final size:67
Alignment explanation
Indices: 1117424--1117574 Score: 230
Period size: 67 Copynumber: 2.3 Consensus size: 67
1117414 ACCCATTCAA
* * *
1117424 GGGGAACCGATACCCCCTCAATGAATATGAATTTCCAAAATGCTAGAGGGGAATCGATACCCCAA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAAAATGCTAGAGGGGAACCGATACCCCAA
1117489 GG
66 GG
* * * *
1117491 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATTCTAGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAAAATGCTAGAGGGGAACCGATACCCCAA
1117556 GG
66 GG
*
1117558 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1117575 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 76 1.00
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAAAATGCTAGAGGGGAACCGATACCCCAA
GG
Found at i:1117563 original size:20 final size:20
Alignment explanation
Indices: 1117538--1117575 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1117528 GAATTCTAGA
1117538 GGGGAACCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
1117558 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1117576 TGAGAAAAAA
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:0.24, C:0.37, G:0.32, T:0.08
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:1118372 original size:23 final size:23
Alignment explanation
Indices: 1118328--1118372 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1118318 ATCATTATAT
*
1118328 GGCACTACGGTACAATTCTACGG
1 GGCACTACGGTACAATTATACGG
* * *
1118351 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTACAATTATACG
1118373 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGG
Found at i:1128372 original size:10 final size:10
Alignment explanation
Indices: 1128357--1128381 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1128347 GATCTTTCTC
1128357 TAGTTTTGTA
1 TAGTTTTGTA
1128367 TAGTTTTGTA
1 TAGTTTTGTA
1128377 TAGTT
1 TAGTT
1128382 CTTCACGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (10 bp):
TAGTTTTGTA
Found at i:1128817 original size:67 final size:67
Alignment explanation
Indices: 1128740--1128874 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
1128730 TCTGATATTT
1128740 TCAAATACCGTGTCACTATATATATAGATTTTTTAAATAAATACAATATATTTTATACCAATCTA
1 TCAAATACCGTGTCACTATATATATAGATTTTTTAAATAAATACAATATATTTTATACCAATCTA
1128805 AC
66 AC
1128807 TCAAATACCGTGTCACTATATATATAGATTTTTTAAATAAATACAATATATTTTATACCAATCTA
1 TCAAATACCGTGTCACTATATATATAGATTTTTTAAATAAATACAATATATTTTATACCAATCTA
1128872 AC
66 AC
1128874 T
1 T
1128875 TAGGTTCAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.39
Consensus pattern (67 bp):
TCAAATACCGTGTCACTATATATATAGATTTTTTAAATAAATACAATATATTTTATACCAATCTA
AC
Found at i:1129534 original size:3 final size:3
Alignment explanation
Indices: 1129528--1129601 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
1129518 TTTTTATCCA
*
1129528 TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1129576 TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1129602 AATATATATT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1129539 original size:9 final size:9
Alignment explanation
Indices: 1129527--1129613 Score: 84
Period size: 9 Copynumber: 9.1 Consensus size: 9
1129517 TTTTTTATCC
1129527 ATATTATTA
1 ATATTATTA
1129536 ATATTATTA
1 ATATTATTA
*
1129545 TTATTATTA
1 ATATTATTA
*
1129554 TTATTATTA
1 ATATTATTA
*
1129563 TTATTATTA
1 ATATTATTA
*
1129572 TTATTATTA
1 ATATTATTA
1129581 TCATTATTATTA
1 --A-TATTATTA
*
1129593 TTATTATTAA
1 ATATTATT-A
1129603 ATATATATTA
1 ATAT-TATTA
1129613 A
1 A
1129614 ATATATATAA
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
9 51 0.74
10 6 0.09
11 4 0.06
12 8 0.12
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (9 bp):
ATATTATTA
Found at i:1129613 original size:11 final size:11
Alignment explanation
Indices: 1129597--1129626 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1129587 TTATTATTAT
1129597 TATTAAATATA
1 TATTAAATATA
1129608 TATTAAATATA
1 TATTAAATATA
1129619 TA-TAAATA
1 TATTAAATA
1129627 ATTAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1130922 original size:23 final size:20
Alignment explanation
Indices: 1130892--1130944 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 20
1130882 ATTTTTAAAT
*
1130892 TTTATTTTACTATAATTTATTCA
1 TTTATTTTACTAT--GTT-TTCA
1130915 TTTATTTTA-TATGTTTTCA
1 TTTATTTTACTATGTTTTCA
1130934 TTTATTTTACT
1 TTTATTTTACT
1130945 GCTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 13 0.46
20 3 0.11
22 3 0.11
23 9 0.32
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTATTTTACTATGTTTTCA
Found at i:1142373 original size:6 final size:6
Alignment explanation
Indices: 1142359--1142428 Score: 56
Period size: 6 Copynumber: 11.5 Consensus size: 6
1142349 TGAAGAAAAG
* *
1142359 AAAGAA AAAGGA AAAG-G AAA-AA AAAGAA AAAGAAA AAAGAAAA AAAGAGA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA AAAG--AA AAAGA-A
*
1142409 AAA-AA ACAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAA
1142429 AGGGGGGTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
5 9 0.17
6 27 0.51
7 10 0.19
8 7 0.13
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:1142374 original size:16 final size:15
Alignment explanation
Indices: 1142353--1142429 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 15
1142343 TATGCTTGAA
1142353 GAAAAGAAAGAAAAAG
1 GAAAAGAAA-AAAAAG
1142369 GAAAAGGAAAAAAAAG
1 GAAAA-GAAAAAAAAG
* *
1142385 AAAAAGAAAAAAGAAA
1 GAAAAGAAAAAA-AAG
*
1142401 AAAAGAGAAAAAAACAG
1 GAAA-AGAAAAAAA-AG
*
1142418 AAAAAGAAAAAA
1 GAAAAGAAAAAA
1142430 GGGGGGTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
15 7 0.13
16 30 0.56
17 17 0.31
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (15 bp):
GAAAAGAAAAAAAAG
Found at i:1142378 original size:22 final size:22
Alignment explanation
Indices: 1142351--1142412 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
1142341 ATTATGCTTG
* *
1142351 AAGAAAAGAAAGAAAAAGGAAA
1 AAGAAAAAAAAGAAAAAGAAAA
*
1142373 AGGAAAAAAAAGAAAAAGAAAA
1 AAGAAAAAAAAGAAAAAGAAAA
1142395 AAGAAAAAAAGAGAAAAA
1 AAGAAAAAAA-AGAAAAA
1142413 AACAGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 28 0.80
23 7 0.20
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAAAGAAAAAGAAAA
Found at i:1142380 original size:7 final size:7
Alignment explanation
Indices: 1142359--1142430 Score: 55
Period size: 7 Copynumber: 10.6 Consensus size: 7
1142349 TGAAGAAAAG
1142359 AAAGAAA
1 AAAGAAA
*
1142366 AAGGAAA
1 AAAGAAA
1142373 AGGAA-AAA
1 A--AAGAAA
1142381 AAAG-AA
1 AAAGAAA
1142387 AAAGAAA
1 AAAGAAA
1142394 AAAGAAA
1 AAAGAAA
*
1142401 AAA-AGAG
1 AAAGA-AA
1142408 AAA-AAA
1 AAAGAAA
*
1142414 ACAG-AA
1 AAAGAAA
1142420 AAAGAAA
1 AAAGAAA
1142427 AAAG
1 AAAG
1142431 GGGGGTTAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
6 17 0.33
7 30 0.58
8 4 0.08
9 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:1142419 original size:10 final size:9
Alignment explanation
Indices: 1142354--1142422 Score: 52
Period size: 10 Copynumber: 7.1 Consensus size: 9
1142344 ATGCTTGAAG
1142354 AAAAGAAAGA
1 AAAAGAAA-A
1142364 AAAAGGAAAA
1 AAAA-GAAAA
1142374 GGAAAA-AAAA
1 --AAAAGAAAA
*
1142384 GAAAA-AGAA
1 -AAAAGAAAA
1142393 AAAAGAAAA
1 AAAAGAAAA
1142402 AAAGAGAAAA
1 AAA-AGAAAA
1142412 AAACAGAAAA
1 AAA-AGAAAA
1142422 A
1 A
1142423 GAAAAAAGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
8 4 0.08
9 14 0.27
10 25 0.49
11 4 0.08
12 4 0.08
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:1142420 original size:33 final size:31
Alignment explanation
Indices: 1142370--1142430 Score: 104
Period size: 33 Copynumber: 1.9 Consensus size: 31
1142360 AAGAAAAAGG
1142370 AAAAGGAAAAAAAAGAAAAAGAAAAAAGAAA
1 AAAAGGAAAAAAAAGAAAAAGAAAAAAGAAA
1142401 AAAAGAGAAAAAAACAGAAAAAGAAAAAAG
1 AAAAG-GAAAAAAA-AGAAAAAGAAAAAAG
1142431 GGGGGTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 5 0.18
32 8 0.29
33 15 0.54
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (31 bp):
AAAAGGAAAAAAAAGAAAAAGAAAAAAGAAA
Found at i:1142768 original size:16 final size:16
Alignment explanation
Indices: 1142742--1142786 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1142732 TTTGAATACA
*
1142742 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
1142759 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
1142774 ATTCAATTTATTT
1 ATTCAATTTATTT
1142787 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:1143722 original size:83 final size:83
Alignment explanation
Indices: 1143526--1144329 Score: 1253
Period size: 83 Copynumber: 9.7 Consensus size: 83
1143516 CATTAACTGA
* *
1143526 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCAGGTTGGACAG
1 AAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
*
1143590 AA-CAATCATTGAATTTAG
65 AACCAATCATTGAATTTGG
* ** *
1143608 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTAATCTTTGAGTTATTTGATCTGGTTGGACAG
1 AAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
*
1143672 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTGG
* *
1143691 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTT-TAGCAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAG
1143755 AACCAATCATTGAATTTGG
65 AACCAATCATTGAATTTGG
* *
1143774 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1143838 AACCAATCATTGAATTTGG
65 AACCAATCATTGAATTTGG
1143857 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
*
1143922 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTGG
* * *
1143940 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAGCAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAG
*
1144004 AACCAATCATTGAATTGGG
65 AACCAATCATTGAATTTGG
* *
1144023 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
*
1144088 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTGG
* *
1144106 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-TAGCAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAG
*
1144170 AACCAATCATTGAATTGGG
65 AACCAATCATTGAATTTGG
* * *
1144189 AAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1144254 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
* *
1144272 AAGATGAATGTGTTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1144330 TGGTAAGAAC
Statistics
Matches: 666, Mismatches: 46, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
82 69 0.10
83 592 0.89
84 5 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACCAATCATTGAATTTGG
Found at i:1145174 original size:112 final size:112
Alignment explanation
Indices: 1144976--1146591 Score: 2240
Period size: 112 Copynumber: 14.0 Consensus size: 112
1144966 CAAAGATTTC
* * *
1144976 GAATTCACCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
1145041 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
1145089 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1145154 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
* *
1145201 GAATTCATCATTTGATGGATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1145266 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
1145313 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * ** *
1145378 AGAAAGAAGAAGTTCATAATAAGAAAGAACTTGTTCAAATTTTTGCAT
66 AGGAAGAAGAAGTTCATAATGAG-AAGAATTTGTTCAACCTTTTGCCT
** *
1145426 -AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAG
1 GAATTC-AT--C--AA-TTGATGGATT---AT----CTTTTCCAGAG-AAGTTCATAATGAGAAG
1145490 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
52 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
1145551 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1145616 A-GAAG-AGAAGTTCATAATGAGAAGAA-TTGTTCAACC-TTTGCCT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
1145659 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * * *
1145724 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCAT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
** *
1145771 -AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAG
1 GAATTC-AT--C--AA-TTGATGGATT---AT----CTTTTCCAGAG-AAGTTCATAATGAGAAG
1145835 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
52 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
*
1145896 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAAATCATCTGAAGA
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1145961 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
* *
1146008 GAATTCATCATTTGATGGATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * * *
1146073 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCAT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
** *
1146120 -AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAG
1 GAATTC-AT--C--AA-TTGATGGATT---AT----CTTTTCCAGAG-AAGTTCATAATGAGAAG
1146184 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
52 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
*
1146245 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAATTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * * *
1146310 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCAT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
** *
1146357 -AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAG
1 GAATTC-AT--C--AA-TTGATGGATT---AT----CTTTTCCAGAG-AAGTTCATAATGAGAAG
1146421 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
52 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
1146482 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
1146547 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1146592 ATAATTCTAT
Statistics
Matches: 1354, Mismatches: 84, Indels: 131
0.86 0.05 0.08
Matches are distributed among these distances:
108 73 0.05
109 13 0.01
110 41 0.03
111 28 0.02
112 646 0.48
113 97 0.07
114 3 0.00
115 1 0.00
116 5 0.00
117 30 0.02
118 7 0.01
120 34 0.03
121 10 0.01
123 4 0.00
124 33 0.02
125 257 0.19
126 72 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT
Found at i:1145905 original size:237 final size:230
Alignment explanation
Indices: 1144999--1146664 Score: 2340
Period size: 237 Copynumber: 7.2 Consensus size: 230
1144989 GATGGATCAT
1144999 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
1145064 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTC
66 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATAGATGGATTATCTTTTCCAGAGAAGTTC
* * * *
1145129 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCT
131 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
* *** * *
1145194 TTTGCCTGAATTC-AT-C--ATTTGATGGA-TCAT-
196 TTTGCAT-AATTCTATACAAAGGAGATAGATTAATC
1145224 CTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
1145288 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTC
66 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATAGATGGATTATCTTTTCCAGAGAAGTTC
*
1145353 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAAGAACTTGTTCAAAT
131 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAG-AAGAACTTGTTCAACT
1145418 TTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGC
195 TTTTGCATAATTCTAT-ACA-AAGGAGATAGATTA--AT---C
1145461 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
1145526 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTC
66 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATAGATGGATTATCTTTTCCAGAGAAGTTC
* *
1145591 ATAATGAGAAGAACTCATCTGAAGAAG-AAG-AGAAGTTCATAATGAGAAGAA-TTGTTCAAC-C
131 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
* ** *
1145652 TTTGCCTGAATTC-AT-C-AA-TTGATGGATT-AT-
196 TTTGCAT-AATTCTATACAAAGGAGATAGATTAATC
* *
1145682 CTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * *
1145746 GAAGAACTTGTTCAACTTTTTGCAT-AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTT
66 GAAGAATTTGTTCAACCTTTTGCCTGAATTC-AT--C--AA-TAGATGGATT---AT----CTTT
* *
1145810 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
118 TCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAG
* * * ** *
1145875 AATTTGTTCAACCTTTTGCCTGAATTC-AT-C-AA-TTGATGGATT-AT-
182 AACTTGTTCAACTTTTTGCAT-AATTCTATACAAAGGAGATAGATTAATC
*
1145919 CTTTTCCAGAG-AAGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * *
1145983 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCATTTGATGGATCATCTTTTCCAGAGAAGTTC
66 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATAGATGGATTATCTTTTCCAGAGAAGTTC
1146048 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
131 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
1146113 TTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGC
196 TTTGCATAATTCTAT-ACA-AAGGAGATAGATTA--AT---C
1146155 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *
1146220 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTATCTTTTCCAGAGAAATTC
66 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATAGATGGATTATCTTTTCCAGAGAAGTTC
1146285 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
131 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
1146350 TTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGC
196 TTTGCATAATTCTAT-ACA-AAGGAGATAGATTA--AT---C
1146392 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
1146457 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTC
66 GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATAGATGGATTATCTTTTCCAGAGAAGTTC
1146522 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
131 ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
1146587 TTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATC
196 TTTGCATAATTCTAT-ACA-AAGGAGATAGATTA--ATC
* **
1146626 AGCCTTTATAGAGAAAGTTCATAATGAGAAGAACTCATC
1 --CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
1146665 AAGAGCTTAT
Statistics
Matches: 1336, Mismatches: 54, Indels: 91
0.90 0.04 0.06
Matches are distributed among these distances:
219 5 0.00
220 75 0.06
221 11 0.01
222 1 0.00
223 5 0.00
224 246 0.18
225 53 0.04
226 1 0.00
227 1 0.00
228 11 0.01
229 11 0.01
230 6 0.00
231 2 0.00
232 19 0.01
233 44 0.03
234 17 0.01
235 27 0.02
236 69 0.05
237 582 0.44
238 150 0.11
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (230 bp):
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATAGATGGATTATCTTTTCCAGAGAAGTTC
ATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
TTTGCATAATTCTATACAAAGGAGATAGATTAATC
Found at i:1146194 original size:349 final size:349
Alignment explanation
Indices: 1144976--1146591 Score: 2497
Period size: 349 Copynumber: 4.7 Consensus size: 349
1144966 CAAAGATTTC
* *
1144976 GAATTCACCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCAATTGATGGATCATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
1145041 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTC-AT--C--AA-
65 AAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCAT-AATTCTATCACAGAAG
** *
1145100 TTGATGGATT---AT----CTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
129 GAGATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
1145157 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCATTTGATGGATC
194 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATT
1145222 ATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
259 ATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1145287 AGAAGAATTTGTTCAACCTTTTGCCT
324 AGAAGAATTTGTTCAACCTTTTGCCT
*
1145313 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
1145378 AGAAAGAAGAAGTTCATAATAAGAAAGAACTTGTTCAAATTTTTGCATAATTCTATCACAGAAGG
66 AGAAAGAAGAAGTTCATAATAAG-AAGAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGG
1145443 AGATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
130 AGATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1145508 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTA
195 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTA
1145573 TCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAG-AGAAGTTCATAATGA
260 TCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1145636 GAAGAA-TTGTTCAACC-TTTGCCT
325 GAAGAATTTGTTCAACCTTTTGCCT
*
1145659 GAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1145724 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGA
66 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGA
1145789 GATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
131 GATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1145854 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTAT
196 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTAT
*
1145919 CTTTTCCAGAGAAGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
261 CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1145984 AAGAATTTGTTCAACCTTTTGCCT
326 AAGAATTTGTTCAACCTTTTGCCT
*
1146008 GAATTCATCATTTGATGGATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATTCATCAATTGATGGATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1146073 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGA
66 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGA
1146138 GATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
131 GATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1146203 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTAT
196 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTAT
* * *
1146268 CTTTTCCAGAGAAATTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAG
261 CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * *
1146333 AAGAACTTGTTCAACTTTTTGCAT
326 AAGAATTTGTTCAACCTTTTGCCT
* * *
1146357 -AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAG
1 GAATTC-AT--C------A-ATTGA-T-GGATCA-TCTTTTCCAGAG-AAGTTCATAATGAGAAG
* * * * *
1146421 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAAT
52 AACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCAT-AAT
** *
1146486 TC-AT--C--AA-TTGATGGATT---AT----CTTTTCCAGAG-AAGTTCATAATGAGAAGAACT
116 TCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
* * * *
1146537 CATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
181 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1146592 ATAATTCTAT
Statistics
Matches: 1204, Mismatches: 41, Indels: 56
0.93 0.03 0.04
Matches are distributed among these distances:
336 57 0.05
337 53 0.04
339 1 0.00
341 2 0.00
342 7 0.01
345 215 0.18
346 99 0.08
347 31 0.03
348 36 0.03
349 436 0.36
350 153 0.13
351 1 0.00
354 2 0.00
357 8 0.01
358 5 0.00
359 1 0.00
360 6 0.00
361 11 0.01
362 75 0.06
363 5 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (349 bp):
GAATTCATCAATTGATGGATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGA
GATAGATTAGCATCAGCCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAATTGATGGATTAT
CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTTTGCCT
Found at i:1146914 original size:3 final size:3
Alignment explanation
Indices: 1146908--1146994 Score: 147
Period size: 3 Copynumber: 28.7 Consensus size: 3
1146898 TTTTTATCCA
*
1146908 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1146954 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1146995 AATATATATT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 76 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1147006 original size:11 final size:11
Alignment explanation
Indices: 1146990--1147019 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1146980 TTATTATTAT
1146990 TATTAAATATA
1 TATTAAATATA
1147001 TATTAAATATA
1 TATTAAATATA
1147012 TA-TAAATA
1 TATTAAATA
1147020 ATTAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1153104 original size:30 final size:30
Alignment explanation
Indices: 1153013--1153111 Score: 103
Period size: 30 Copynumber: 3.2 Consensus size: 30
1153003 ATTAATTTTT
*
1153013 TTTTAATTTAAATTTTAAGGTCTAAATTGAAA
1 TTTTAA-TTAAATTTT-GGGTCTAAATTGAAA
* * *
1153045 -TTTAATTATAATTATGGGACTAAAATGAAA
1 TTTTAATTA-AATTTTGGGTCTAAATTGAAA
1153075 TTTTAA-TAAATTTTGGGTCTAAATTTGAAA
1 TTTTAATTAAATTTTGGGTCTAAA-TTGAAA
1153105 GTTTTAA
1 -TTTTAA
1153112 ATTTAGAGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
29 13 0.23
30 22 0.39
31 21 0.38
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.44
Consensus pattern (30 bp):
TTTTAATTAAATTTTGGGTCTAAATTGAAA
Found at i:1153817 original size:19 final size:20
Alignment explanation
Indices: 1153779--1153817 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1153769 ACCGTTGACC
1153779 ATCGCTGTTGACTATTAACT
1 ATCGCTGTTGACTATTAACT
*
1153799 ATCGTTGTTGACT-TTAACT
1 ATCGCTGTTGACTATTAACT
1153818 GTTGATCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (20 bp):
ATCGCTGTTGACTATTAACT
Found at i:1164231 original size:3 final size:3
Alignment explanation
Indices: 1164223--1164254 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1164213 CAATTTACCC
1164223 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1164255 GGGTAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1168419 original size:2 final size:2
Alignment explanation
Indices: 1168412--1168441 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1168402 ATTAGAATCA
*
1168412 AT AT AT AT AC 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
1168442 CTCAATTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1171994 original size:18 final size:18
Alignment explanation
Indices: 1171973--1172008 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1171963 CCAGAGAATT
* *
1171973 CGAACTCGAACCTGAAAC
1 CGAACCCGAACCGGAAAC
1171991 CGAACCCGAACCGGAAAC
1 CGAACCCGAACCGGAAAC
1172009 GTTTGATGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.36, G:0.19, T:0.06
Consensus pattern (18 bp):
CGAACCCGAACCGGAAAC
Found at i:1177496 original size:20 final size:20
Alignment explanation
Indices: 1177471--1177520 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1177461 CAAAACTAAG
*
1177471 AAAAAATTCAAAACCCATAA
1 AAAAAACTCAAAACCCATAA
1177491 AAAAAACTCAAAACCCATAA
1 AAAAAACTCAAAACCCATAA
1177511 AAAAAACTCA
1 AAAAAACTCA
1177521 CTGATTCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.66, C:0.22, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAAAACTCAAAACCCATAA
Found at i:1179393 original size:13 final size:13
Alignment explanation
Indices: 1179375--1179403 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1179365 ATGGATTATA
1179375 GTCGTTGGAACTC
1 GTCGTTGGAACTC
1179388 GTCGTTGGAACTC
1 GTCGTTGGAACTC
1179401 GTC
1 GTC
1179404 CTGTGGGCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.24, G:0.31, T:0.31
Consensus pattern (13 bp):
GTCGTTGGAACTC
Found at i:1181378 original size:145 final size:145
Alignment explanation
Indices: 1181110--1181498 Score: 519
Period size: 145 Copynumber: 2.7 Consensus size: 145
1181100 CCCAAAAATG
** * * * *
1181110 TCAAAACGGACCATTAATATTACAGGATGCCATACAATGGCAACAACTTTTCAATGCCCCATCAA
1 TCAAAACGGGTCATTAATAATGCAGGATGCCAAAAAAT-GCAACAACTTTTCAATGCCCCATCAA
* * **
1181175 TCATCTTCAGCAACTTTTCAGTGAAATGTCATCTCTAATAATGCATCATGCCTGAAAATGTCAAA
65 TCATCTTCAGCAACTTTTTAGTGAAATGTCATCTCTAATAATGCACCATGCCCAAAAATGTCAAA
1181240 A-ACCATTAATACTCT
130 AGACCATTAATACTCT
* * * * * **
1181255 TTAGAACGGGTCATTAATAATGCAGGATGCCAGAAAATGCCAACAATTTTTCATTATCCCATCAA
1 TCAAAACGGGTCATTAATAATGCAGGATGCCAAAAAATG-CAACAACTTTTCAATGCCCCATCAA
* *
1181320 TCATCTTCAGTAAATTTTTAGTGAAATGTCATCTCTAATAATGCACCATGCCCAAAAATGTCAAA
65 TCATCTTCAGCAACTTTTTAGTGAAATGTCATCTCTAATAATGCACCATGCCCAAAAATGTCAAA
*
1181385 ATGGGCCATTAATACTCT
130 A--GACCATTAATACTCT
* *
1181403 TCAAAACGGGTCATTAATAATGCAAGATGCCAAAAAATGCAAGCAACTTTTCAGTGCCCCATCAA
1 TCAAAACGGGTCATTAATAATGCAGGATGCCAAAAAATGCAA-CAACTTTTCAATGCCCCATCAA
*
1181468 TCTTCTTCAGCAACTTTTTAGTGAAATGTCA
65 TCATCTTCAGCAACTTTTTAGTGAAATGTCA
1181499 AGTCATTTCT
Statistics
Matches: 209, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
144 1 0.00
145 111 0.53
147 3 0.01
148 94 0.45
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (145 bp):
TCAAAACGGGTCATTAATAATGCAGGATGCCAAAAAATGCAACAACTTTTCAATGCCCCATCAAT
CATCTTCAGCAACTTTTTAGTGAAATGTCATCTCTAATAATGCACCATGCCCAAAAATGTCAAAA
GACCATTAATACTCT
Found at i:1190132 original size:3 final size:3
Alignment explanation
Indices: 1190126--1190158 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1190116 AATTTTTTTC
*
1190126 ATT ATT A-T ATT ATT ATC ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1190159 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1191610 original size:17 final size:17
Alignment explanation
Indices: 1191589--1191635 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1191579 TTTTTAAATA
1191589 AATAAATATTTTACTTT
1 AATAAATATTTTACTTT
* *
1191606 TATAAATTATATT-CTTT
1 AATAAA-TATTTTACTTT
1191623 AATAAATATTTTA
1 AATAAATATTTTA
1191636 TTAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 5 0.21
17 14 0.58
18 5 0.21
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (17 bp):
AATAAATATTTTACTTT
Found at i:1196800 original size:2 final size:2
Alignment explanation
Indices: 1196793--1196828 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1196783 TTATCCTTTA
1196793 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
1196829 CCTTTGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1197154 original size:22 final size:21
Alignment explanation
Indices: 1197123--1197185 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 21
1197113 CTCATCCAGC
1197123 AAAAAAAAAAGAAGAATGAAA-
1 AAAAAAAAAAGAA-AATGAAAT
*
1197144 AAAGAAAAAAAGAAAAAGAAAT
1 AAA-AAAAAAAGAAAATGAAAT
*
1197166 AAAAAAAAAGGAAAAATGAA
1 AAAAAAAAAAG-AAAATGAA
1197186 TCAAGATGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 16 0.44
22 20 0.56
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAAGAAAATGAAAT
Found at i:1197159 original size:14 final size:13
Alignment explanation
Indices: 1197123--1197181 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 13
1197113 CTCATCCAGC
1197123 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
**
1197136 GAATGAAAAAAGAA
1 -AAAAAAAAAAGAA
1197150 AAAAAGAAAAAGAA
1 AAAAA-AAAAAGAA
1197164 ATAAAAAAAAAGGAA
1 A-AAAAAAAAA-GAA
1197179 AAA
1 AAA
1197182 TGAATCAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 3 0.08
14 27 0.71
15 8 0.21
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:1197162 original size:25 final size:26
Alignment explanation
Indices: 1197123--1197172 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1197113 CTCATCCAGC
*
1197123 AAAAAAAAAAGAAG-AATGAAAAAAG
1 AAAAAAAAAAGAAGAAATAAAAAAAG
1197148 AAAAAAAGAAA-AAGAAATAAAAAAA
1 AAAAAAA-AAAGAAGAAATAAAAAAA
1197173 AAGGAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (26 bp):
AAAAAAAAAAGAAGAAATAAAAAAAG
Found at i:1199609 original size:114 final size:114
Alignment explanation
Indices: 1199406--1199631 Score: 346
Period size: 114 Copynumber: 2.0 Consensus size: 114
1199396 AAGTGTCATG
* * *
1199406 TTCTCGTAGTAGAAATAAGGAGGCCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
1199471 TAATTTGATATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
66 TAATTAGATAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
1199520 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
** * *
1199585 TGGTTCAG-TAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 TAATT-AGATAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
1199632 CTGCCTGATC
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 100 0.99
115 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TAATTAGATAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
Found at i:1202145 original size:22 final size:22
Alignment explanation
Indices: 1202119--1202195 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
1202109 ATCTACACTC
1202119 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1202141 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1202163 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1202185 TTCAAAGATGA
1 TTCAAAGATGA
1202196 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1202970 original size:76 final size:76
Alignment explanation
Indices: 1202871--1203741 Score: 1535
Period size: 76 Copynumber: 11.5 Consensus size: 76
1202861 CTATTTCCCA
1202871 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1202936 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1202947 CATTTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTCTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1203012 AGCCTTAGGGT
66 AGCCTTAGGGT
1203023 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1203088 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1203099 CACCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTCTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1203164 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1203175 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTCTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1203240 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1203251 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1203316 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1203327 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1203392 AGCCTTAGGGT
66 AGCCTTAGGGT
**
1203403 CATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1203468 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1203479 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1203544 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1203555 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1203620 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1203631 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1203696 AACCTTCGGGT
66 AGCCTTAGGGT
* * * * *
1203707 CGTCTATAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAA
1203742 CATTTACATC
Statistics
Matches: 766, Mismatches: 29, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 766 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1203867 original size:3 final size:3
Alignment explanation
Indices: 1203861--1203904 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
1203851 AATTTTTTTC
1203861 ATT ATT ATT ATT ATT ATT ATT A-T ATT A-T ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1203905 AATAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1205135 original size:27 final size:28
Alignment explanation
Indices: 1205093--1205157 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
1205083 ATTACTAGTT
*
1205093 TTTTTATTTATAGTTTTA-ATTTCATTA
1 TTTTTAATTATAGTTTTATATTTCATTA
* *
1205120 TTTTTAATTATTGTTTTATATTTTATTA
1 TTTTTAATTATAGTTTTATATTTCATTA
*
1205148 TTATT-ATTAT
1 TTTTTAATTAT
1205158 GTATAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTAATTATAGTTTTATATTTCATTA
Found at i:1205391 original size:15 final size:15
Alignment explanation
Indices: 1205345--1205400 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
1205335 TAAATAAATA
1205345 AATATTTTACTTTTA-T
1 AATA-TTTA-TTTTATT
1205361 AA-ATTATATTTT-TT
1 AATATT-TATTTTATT
1205375 AATATTTATTTTATT
1 AATATTTATTTTATT
1205390 AATATTTATTT
1 AATATTTATTT
1205401 ATTTTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
14 15 0.42
15 19 0.53
16 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
AATATTTATTTTATT
Found at i:1205411 original size:18 final size:19
Alignment explanation
Indices: 1205377--1205413 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1205367 TATTTTTTAA
1205377 TATTTATTTTATTAATATT
1 TATTTATTTTATTAATATT
1205396 TATTTATTTT-TTAATATT
1 TATTTATTTTATTAATATT
1205414 GAAGGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTATTTTATTAATATT
Found at i:1207354 original size:2 final size:2
Alignment explanation
Indices: 1207271--1207339 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
1207261 TTTCTTTAAC
1207271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1207312 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
1207340 CTTATAAGAA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1208165 original size:2 final size:2
Alignment explanation
Indices: 1208158--1208252 Score: 167
Period size: 2 Copynumber: 48.0 Consensus size: 2
1208148 TCGTTTAATA
1208158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1208199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
1208240 AT AT AT AT CAT AT
1 AT AT AT AT -AT AT
1208253 TCCTTGAGGT
Statistics
Matches: 90, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.02
2 86 0.96
3 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1211129 original size:18 final size:18
Alignment explanation
Indices: 1211106--1211143 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1211096 GTTTCGAAGT
1211106 AAAGTATTCCAGTTTCTG
1 AAAGTATTCCAGTTTCTG
1211124 AAAGTATTCCAGTTTCTG
1 AAAGTATTCCAGTTTCTG
1211142 AA
1 AA
1211144 TCCTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (18 bp):
AAAGTATTCCAGTTTCTG
Found at i:1218776 original size:221 final size:223
Alignment explanation
Indices: 1218393--1218837 Score: 876
Period size: 221 Copynumber: 2.0 Consensus size: 223
1218383 TATATACATC
1218393 ATTACAGATATATTTGTATACACCCGTTTTTGTCCAGATTTTTTTTTATTCTATTATTATTATTA
1 ATTACAGATATATTTGTATACACCCGTTTTTGTCCAGATTTTTTTTTATTCTATTATTATTATTA
1218458 TTATTATTAAATTATTACAAATTTACATCTTTTGTAGACTCAACCAGTGACCCAATTACGAAACC
66 TTATTATTAAATTATTACAAATTTACATCTTTTGTAGACTCAACCAGTGACCCAATTACGAAACC
1218523 CAGAAGCCAGCTGAAGCTACTCAACAACCCAGGTTCCGCCTCA-GATTCGACCC-CCTCAGGCCC
131 CAGAAGCCAGCTGAAGCTACTCAACAACCCAGGTTCCGCCTCAGGATTCGACCCGCCTCAGGCCC
1218586 ATTAGATAACCCAATAGATTAGGGTTTT
196 ATTAGATAACCCAATAGATTAGGGTTTT
1218614 ATTACAGATATATTTGTATACACCCGTTTTTGTCCAGATTTTTTTTTATTCTATTATTATTATTA
1 ATTACAGATATATTTGTATACACCCGTTTTTGTCCAGATTTTTTTTTATTCTATTATTATTATTA
1218679 TTATTATTAAATTATTACAAATTTACATCTTTTGTAGACTCAACCAGTGACCCAATTACGAAACC
66 TTATTATTAAATTATTACAAATTTACATCTTTTGTAGACTCAACCAGTGACCCAATTACGAAACC
1218744 CAGAAGCCAGCTGAAGCTACTCAACAACCCAGGTTCCGCCTCAGGATTCGACCCGCCTCAGGCCC
131 CAGAAGCCAGCTGAAGCTACTCAACAACCCAGGTTCCGCCTCAGGATTCGACCCGCCTCAGGCCC
1218809 ATTAGATAACCCAATAGATTAGGGTTTT
196 ATTAGATAACCCAATAGATTAGGGTTTT
1218837 A
1 A
1218838 CCCTTTTGCT
Statistics
Matches: 222, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
221 173 0.78
222 10 0.05
223 39 0.18
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (223 bp):
ATTACAGATATATTTGTATACACCCGTTTTTGTCCAGATTTTTTTTTATTCTATTATTATTATTA
TTATTATTAAATTATTACAAATTTACATCTTTTGTAGACTCAACCAGTGACCCAATTACGAAACC
CAGAAGCCAGCTGAAGCTACTCAACAACCCAGGTTCCGCCTCAGGATTCGACCCGCCTCAGGCCC
ATTAGATAACCCAATAGATTAGGGTTTT
Found at i:1221196 original size:24 final size:24
Alignment explanation
Indices: 1221164--1221210 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1221154 CTCATATAAA
*
1221164 ATGCACCGAAGTGCCACGTAGAAC
1 ATGCACCGAAGTGCCACATAGAAC
1221188 ATGCACCGAAGTGCCACATAGAA
1 ATGCACCGAAGTGCCACATAGAA
1221211 TGTCCCGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.13
Consensus pattern (24 bp):
ATGCACCGAAGTGCCACATAGAAC
Found at i:1221236 original size:21 final size:21
Alignment explanation
Indices: 1221193--1221352 Score: 87
Period size: 21 Copynumber: 7.5 Consensus size: 21
1221183 AGAACATGCA
*
1221193 CCGAAGTG-CCACATAGAATGTC
1 CCGAAG-GACCACATA-TATGTC
*
1221215 CCGAAGGATCACATATATGTC
1 CCGAAGGACCACATATATGTC
* *
1221236 CCGAAAGACCACATAGAATTGTC
1 CCGAAGGACCACATA-TA-TGTC
* * *
1221259 CC-ATATGACCACAAATATGTT
1 CCGA-AGGACCACATATATGTC
*
1221280 CCAAAGGACCAACCATATA--TC
1 CCGAAGGACC-A-CATATATGTC
* * *
1221301 CCGAATGATCACATATAAGTTC
1 CCGAAGGACCACATATATG-TC
* * *
1221323 CC-AGGGATCATATATATGTC
1 CCGAAGGACCACATATATGTC
1221343 CCGAAGGACC
1 CCGAAGGACC
1221353 GTGTAGAACC
Statistics
Matches: 106, Mismatches: 21, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
19 6 0.06
20 5 0.05
21 54 0.51
22 21 0.20
23 20 0.19
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
CCGAAGGACCACATATATGTC
Found at i:1227727 original size:24 final size:22
Alignment explanation
Indices: 1227691--1227757 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
1227681 AGAATATACA
1227691 CCAAAGTG-CCATATAGAATGTC
1 CCAAAG-GACCATATAGAATGTC
* * * *
1227713 CCGAAGGATCACATA-TATGTC
1 CCAAAGGACCATATAGAATGTC
1227734 CCAAAGGACCATATAGAATTGTC
1 CCAAAGGACCATATAGAA-TGTC
1227757 C
1 C
1227758 GTAGAACCAC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 18 0.53
22 11 0.32
23 5 0.15
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (22 bp):
CCAAAGGACCATATAGAATGTC
Found at i:1227734 original size:21 final size:21
Alignment explanation
Indices: 1227708--1227845 Score: 82
Period size: 21 Copynumber: 6.5 Consensus size: 21
1227698 GCCATATAGA
*
1227708 ATGTCCCGAAGGATCACATAT
1 ATGTCCCGAAGGACCACATAT
* * *
1227729 ATGTCCCAAAGGACCATATAGA
1 ATGTCCCGAAGGACCACATA-T
* *
1227751 ATTGT-CCGTAGAACCACATAT
1 A-TGTCCCGAAGGACCACATAT
* * * *
1227772 ATGTTCCAAAGGACCAAACAT
1 ATGTCCCGAAGGACCACATAT
* *
1227793 ATATCCCGAAGGATCACATAT
1 ATGTCCCGAAGGACCACATAT
* * * * *
1227814 AAGTACTC-AGGGATCATATAT
1 ATGT-CCCGAAGGACCACATAT
1227835 ATGTCCCGAAG
1 ATGTCCCGAAG
1227846 AACCGTGTAG
Statistics
Matches: 84, Mismatches: 28, Indels: 10
0.69 0.23 0.08
Matches are distributed among these distances:
20 5 0.06
21 62 0.74
22 14 0.17
23 3 0.04
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATAT
Found at i:1227747 original size:43 final size:43
Alignment explanation
Indices: 1227691--1227814 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 43
1227681 AGAATATACA
1227691 CCAAAGTG-CCATATAGAATGTCCCGAAGGATCACATATATGTC
1 CCAAAG-GACCATATAGAATGTCCCGAAGGATCACATATATGTC
* * * *
1227734 CCAAAGGACCATATAGAATTGT-CCGTAGAACCACATATATGTT
1 CCAAAGGACCATATAGAA-TGTCCCGAAGGATCACATATATGTC
* *
1227777 CCAAAGGACCA-A-ACATATATCCCGAAGGATCACATATA
1 CCAAAGGACCATATAGA-ATGTCCCGAAGGATCACATATA
1227815 AGTACTCAGG
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
41 4 0.06
42 17 0.25
43 44 0.65
44 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (43 bp):
CCAAAGGACCATATAGAATGTCCCGAAGGATCACATATATGTC
Found at i:1233785 original size:13 final size:13
Alignment explanation
Indices: 1233763--1233805 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1233753 TCCTAATGGG
1233763 CAAT-TTTGAAAA
1 CAATGTTTGAAAA
**
1233775 CTTTGTTTGAAAA
1 CAATGTTTGAAAA
1233788 CAATGTTTGAAAA
1 CAATGTTTGAAAA
1233801 TCAAT
1 -CAAT
1233806 ATGTAGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 2 0.08
13 19 0.76
14 4 0.16
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:1234301 original size:23 final size:23
Alignment explanation
Indices: 1234274--1234324 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1234264 ACCCTCATGA
1234274 GGGTATCAGTACCCATTCAAAGG
1 GGGTATCAGTACCCATTCAAAGG
*
1234297 GGGTATCGGTACCCATTCAAAGG
1 GGGTATCAGTACCCATTCAAAGG
1234320 GGGTA
1 GGGTA
1234325 CCGATACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (23 bp):
GGGTATCAGTACCCATTCAAAGG
Found at i:1234332 original size:23 final size:23
Alignment explanation
Indices: 1234283--1234332 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1234273 AGGGTATCAG
* *
1234283 TACCCATTCAAAGGGGGTATCGG
1 TACCCATTCAAAGGGGGTACCGA
1234306 TACCCATTCAAAGGGGGTACCGA
1 TACCCATTCAAAGGGGGTACCGA
1234329 TACC
1 TACC
1234333 TAGCGCACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TACCCATTCAAAGGGGGTACCGA
Found at i:1237882 original size:20 final size:21
Alignment explanation
Indices: 1237851--1237890 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1237841 GAAGTTTTAA
*
1237851 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTTCTCTTGAT
1237872 GATCATC-ATTTTCTCTTGA
1 GATCATCAATTTTCTCTTGA
1237891 AAGTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (21 bp):
GATCATCAATTTTCTCTTGAT
Found at i:1239739 original size:20 final size:21
Alignment explanation
Indices: 1239702--1239744 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1239692 ATCAACATTT
*
1239702 TTGCATTTGCATTTGCA-TCA
1 TTGCATTTGCATTGGCATTCA
1239722 TTGCATTCTGCA-TGGCATTCA
1 TTGCATT-TGCATTGGCATTCA
1239743 TT
1 TT
1239745 CAAACATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (21 bp):
TTGCATTTGCATTGGCATTCA
Found at i:1241389 original size:22 final size:22
Alignment explanation
Indices: 1241322--1241389 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
1241312 ATTCGAGGGC
*
1241322 TTCATAGGTCCTTCGAGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
* *
1241343 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACAAA
1241365 TTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
1241387 TTC
1 TTC
1241390 CATATGCCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 17 0.41
22 24 0.59
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:1247556 original size:67 final size:68
Alignment explanation
Indices: 1247457--1247583 Score: 186
Period size: 67 Copynumber: 1.9 Consensus size: 68
1247447 CCATTCAACA
* *
1247457 GGTACTGATACCCTCTCAAACGAAAAGAATTACATAATGTAATAAGGGTACCGATACCCCCACAG
1 GGTACCGATACCCTCTCAAACGAAAAGAATTACAGAATGTAATAAGGGTACCGATACCCCCACAG
1247522 TAG
66 TAG
* **
1247525 GGTACCGATACCCTC-CTAAACG-GAAGAATTACAGAATGTCGTAAGGGTACCGATACCCC
1 GGTACCGATACCCTCTC-AAACGAAAAGAATTACAGAATGTAATAAGGGTACCGATACCCC
1247584 AAGAGGTGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
67 34 0.64
68 19 0.36
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (68 bp):
GGTACCGATACCCTCTCAAACGAAAAGAATTACAGAATGTAATAAGGGTACCGATACCCCCACAG
TAG
Found at i:1248174 original size:21 final size:22
Alignment explanation
Indices: 1248148--1248207 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
1248138 GTCGAGGGTT
1248148 TCATAGGTCATTCGGGACA-AC
1 TCATAGGTCATTCGGGACATAC
*
1248169 TCATAGGTCATTCGGGACATAT
1 TCATAGGTCATTCGGGACATAC
* *
1248191 TCACAGGTCCTTCGGGA
1 TCATAGGTCATTCGGGA
1248208 TAAATTCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (22 bp):
TCATAGGTCATTCGGGACATAC
Found at i:1248214 original size:22 final size:21
Alignment explanation
Indices: 1248147--1248214 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
1248137 AGTCGAGGGT
*
1248147 TTCATAGGTCATTCGGGACAA
1 TTCATAGGTCATTCGGGAAAA
* *
1248168 CTCATAGGTCATTCGGGACATA
1 TTCATAGGTCATTCGGGA-AAA
* *
1248190 TTCACAGGTCCTTCGGGATAAA
1 TTCATAGGTCATTCGGGA-AAA
1248212 TTC
1 TTC
1248215 CATATGCCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 17 0.45
22 21 0.55
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
TTCATAGGTCATTCGGGAAAA
Found at i:1250636 original size:17 final size:16
Alignment explanation
Indices: 1250616--1250662 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
1250606 AAGATCACAT
1250616 CAAAGCAAAGAAAAAAG
1 CAAAG-AAAGAAAAAAG
*
1250633 CAAAGAAAGAAAAAAAA
1 CAAAGAAAG-AAAAAAG
1250650 CAAAGAAA-AAAAA
1 CAAAGAAAGAAAAA
1250663 GATGATATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 5 0.18
16 4 0.14
17 19 0.68
ACGTcount: A:0.79, C:0.09, G:0.13, T:0.00
Consensus pattern (16 bp):
CAAAGAAAGAAAAAAG
Found at i:1250656 original size:13 final size:13
Alignment explanation
Indices: 1250638--1250662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1250628 AAAAGCAAAG
1250638 AAAGAAAAAAAAC
1 AAAGAAAAAAAAC
1250651 AAAGAAAAAAAA
1 AAAGAAAAAAAA
1250663 GATGATATGA
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:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAC
Found at i:1251541 original size:22 final size:21
Alignment explanation
Indices: 1251516--1251578 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
1251506 AAAGGGTAAT
1251516 ATTTTCAAACTTTTGATTAAAC
1 ATTTTCAAACTTTTGATT-AAC
* * *
1251538 ATTTTTCAACATCCTTTTAATTGAT
1 A-TTTTCAA-A--CTTTTGATTAAC
1251563 ATTTTCAAACTTTTGA
1 ATTTTCAAACTTTTGA
1251579 AAATAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
21 6 0.18
22 1 0.03
23 8 0.24
24 8 0.24
25 2 0.06
26 8 0.24
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTTCAAACTTTTGATTAAC
Found at i:1251944 original size:36 final size:36
Alignment explanation
Indices: 1251877--1251983 Score: 126
Period size: 36 Copynumber: 2.9 Consensus size: 36
1251867 AAAAAAAAAT
* **
1251877 TCTCGCTTGAGAC-AGTTTTCTAAAAACAAATTTTG
1 TCTCGCTTGAGACAATTTTTCTAAAAACAAATTTCA
* *
1251912 TCTCGCTTGAGACAATTTTTCTCAAAATAAATTTCA
1 TCTCGCTTGAGACAATTTTTCTAAAAACAAATTTCA
*
1251948 TCTCGCTTGAGACATTTTTTCTTTAAAACACAAATT
1 TCTCGCTTGAGACAATTTTTC--TAAAA-ACAAATT
1251984 ATGAAGTTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 13 0.22
36 37 0.62
38 4 0.07
39 6 0.10
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (36 bp):
TCTCGCTTGAGACAATTTTTCTAAAAACAAATTTCA
Found at i:1252058 original size:36 final size:36
Alignment explanation
Indices: 1251991--1252078 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 36
1251981 ATTATGAAGT
* * *
1251991 TGTTTCACTAGAAACAAAATTTATAATCTTTGAGTC
1 TGTTTCTCTTGAAACAAAATTTATAATCTTTGAGAC
* *
1252027 TGTTTCTCTTGAAACAAATTTTAT-CTCCTTTGAGAC
1 TGTTTCTCTTGAAACAAAATTTATAAT-CTTTGAGAC
*
1252063 AGTTTCT-TGTGAAACA
1 TGTTTCTCT-TGAAACA
1252079 CCAATCTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
35 2 0.05
36 42 0.95
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (36 bp):
TGTTTCTCTTGAAACAAAATTTATAATCTTTGAGAC
Found at i:1252169 original size:29 final size:29
Alignment explanation
Indices: 1252131--1252238 Score: 83
Period size: 29 Copynumber: 3.5 Consensus size: 29
1252121 CCTTGAGGCA
*
1252131 GTTTCTCTTGAAATATTATCTTTGAGATC
1 GTTTCCCTTGAAATATTATCTTTGAGATC
* *
1252160 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGA-C
1 GTTTCCCTTG--A--AA-TAT-TATCT-TTGAGATC
* * *
1252195 AGTTTCTCTTGAAACATTATATTTGAGATC
1 -GTTTCCCTTGAAATATTATCTTTGAGATC
1252225 GTTTCCCTTGAAAT
1 GTTTCCCTTGAAAT
1252239 GAATTTTTCT
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
29 27 0.45
30 4 0.07
31 2 0.03
32 2 0.03
33 2 0.03
34 3 0.05
35 5 0.08
36 15 0.25
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (29 bp):
GTTTCCCTTGAAATATTATCTTTGAGATC
Found at i:1252198 original size:65 final size:65
Alignment explanation
Indices: 1252013--1252336 Score: 352
Period size: 65 Copynumber: 5.0 Consensus size: 65
1252003 AACAAAATTT
*
1252013 ATAATCTTTGAG-TCTGTTTCTCTTGAAACAAATTTTATCTC-CTTTGAGACAGTTTCT-TGTGA
1 ATAATCTTTGAGATC-GTTTCCCTTGAAACAAATTTTATCTCTC-TTGAGACAGTTTCTCT-TGA
1252075 AAC
63 AAC
* * * * * * * *
1252078 ACCAATCTTTGTGTTTGTTT-TCTTGGAAACAAAGTTTTGTCTCCCTTGAGGCAGTTTCTCTTGA
1 A-TAATCTTTGAGATCGTTTCCCTT-GAAACAAA-TTTTATCTCTCTTGAGACAGTTTCTCTTGA
*
1252142 AAT
63 AAC
* * *
1252145 ATTATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 ATAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAAC
* * ** *
1252210 ATTATATTTGAGATCGTTTCCCTTGAAATGAATTTT-TCTCTCTTGAGACAGCTTCTCTTGAAAC
1 ATAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAAC
* ** * *
1252274 ATAATCTTTGAGTTTTTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATAGTTTTTCTTGAA
1 ATAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAA
1252337 GCAAATCCCT
Statistics
Matches: 222, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
64 56 0.25
65 92 0.41
66 41 0.18
67 31 0.14
68 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (65 bp):
ATAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAAC
Found at i:1252298 original size:129 final size:132
Alignment explanation
Indices: 1252013--1252336 Score: 372
Period size: 129 Copynumber: 2.5 Consensus size: 132
1252003 AACAAAATTT
* *
1252013 ATAATCTTTGAGTCTGTTTCTCTTGAAACAAATTTTATCTC-CTTTGAGACAGTTTCT-TGTGAA
1 ATAATCTTTGAGTTTGTTTCCCTTGAAACAAATTTTATCTCTC-TTGAGACAGTTTCTCT-TGAA
* * * * * * *
1252076 ACACCAATCTTTGTGTTTGTTTTCTTGGAAACAAAGTTTTGTCTCCCTTGAGGCAGTTTCTCTTG
64 ACACCAATATTTGAGATCGTTTCCTTGGAAACAAAGTTTTGTCTCCCTTGAGACAGCTTCTCTTG
*
1252141 AAAT
129 AAAC
* * * * *
1252145 ATTATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 ATAATCTTTGAGTTTGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAAC
** ** *
1252210 A-TTATATTTGAGATCGTTTCCCTT-GAAATGAA-TTTT-TCTCTCTTGAGACAGCTTCTCTTGA
66 ACCAATATTTGAGATCGTTT-CCTTGGAAACAAAGTTTTGTCTCCCTTGAGACAGCTTCTCTTGA
1252271 AAC
130 AAC
* * *
1252274 ATAATCTTTGAGTTTTTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATAGTTTTTCTTGAA
1 ATAATCTTTGAGTTTGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAA
1252337 GCAAATCCCT
Statistics
Matches: 161, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
129 79 0.49
130 4 0.02
131 18 0.11
132 58 0.36
133 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (132 bp):
ATAATCTTTGAGTTTGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAAC
ACCAATATTTGAGATCGTTTCCTTGGAAACAAAGTTTTGTCTCCCTTGAGACAGCTTCTCTTGAA
AC
Found at i:1252588 original size:131 final size:131
Alignment explanation
Indices: 1252341--1252826 Score: 460
Period size: 131 Copynumber: 3.7 Consensus size: 131
1252331 CTTGAAGCAA
* * * * * *
1252341 ATCCCTAAAGATTGTCAGCCATCTTCATGACGTAGGAACCGTGTCATCCACCGACCAGATCTCAT
1 ATCCCTAAAGATGGTCAGTCATCCTCATCACGTAGGAACCGTATCATCCACCGACCAGATCTCCT
** * *
1252406 CATCACTTAGGAGCCGCGTCAACCTTAGATAACTAGTCGTCCTCATCACGTAGGAACCATATTTT
66 CATCACTTAGGAGCCATGTCAACCCTAGATAACTAGTCGTCCTCATCACGTAGGAACCATATTAT
1252471 C
131 C
* * * * *
1252472 ATCCTTAAATATGGTCAGTCATCCTCATCACGTAGGAACTGTATCATCCCCCAACCAGATCTCCT
1 ATCCCTAAAGATGGTCAGTCATCCTCATCACGTAGGAACCGTATCATCCACCGACCAGATCTCCT
* * * * * * * *
1252537 CATCACGTAAGAGCCATGTCACCCCTATATAACTAGCCGTCCTCATTACGTAGGAGCCATGTTAT
66 CATCACTTAGGAGCCATGTCAACCCTAGATAACTAGTCGTCCTCATCACGTAGGAACCATATTAT
1252602 C
131 C
* * * * * *
1252603 ATCCCTAAAGATGGCCAATTATCCTCATCACGTAGGAACCGTATTATCCTCCGACCAGATTTCCT
1 ATCCCTAAAGATGGTCAGTCATCCTCATCACGTAGGAACCGTATCATCCACCGACCAGATCTCCT
* * ** *
1252668 CATCACTTAGGAG-CAGTGTCAGCCCTAGATAA-TCAGTCGTCCTCATCGCGTATAAACCATGTT
66 CATCACTTAGGAGCCA-TGTCAACCCTAGATAACT-AGTCGTCCTCATCACGTAGGAACCATATT
1252731 ATCACC
129 AT---C
* * * * ** * * * * *
1252737 ATCCCTAAAGATTG-CATGGT-GTGCTCATCACCTAGGAATTGTGTCAGCCACTGACCATACCTC
1 ATCCCTAAAGATGGTCA--GTCATCCTCATCACGTAGGAACCGTATCATCCACCGACCAGATCTC
*
1252800 CTCATCACGTAGGAGCCATGTC-ACCCT
64 CTCATCACTTAGGAGCCATGTCAACCCT
1252827 TATACGACCA
Statistics
Matches: 287, Mismatches: 60, Indels: 14
0.80 0.17 0.04
Matches are distributed among these distances:
130 3 0.01
131 213 0.74
133 6 0.02
134 62 0.22
135 3 0.01
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (131 bp):
ATCCCTAAAGATGGTCAGTCATCCTCATCACGTAGGAACCGTATCATCCACCGACCAGATCTCCT
CATCACTTAGGAGCCATGTCAACCCTAGATAACTAGTCGTCCTCATCACGTAGGAACCATATTAT
C
Found at i:1256433 original size:2 final size:2
Alignment explanation
Indices: 1256426--1256467 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1256416 TCCTTAGTTT
1256426 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1256468 AGCCGAGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1256491 original size:14 final size:14
Alignment explanation
Indices: 1256472--1256508 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1256462 TCTCTCAGCC
1256472 GAGTAAAAGGAGCA
1 GAGTAAAAGGAGCA
1256486 GAGTAAAAGGAGCA
1 GAGTAAAAGGAGCA
*
1256500 GAGCAAAAG
1 GAGTAAAAG
1256509 TCAATACACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.35, T:0.05
Consensus pattern (14 bp):
GAGTAAAAGGAGCA
Found at i:1263752 original size:36 final size:36
Alignment explanation
Indices: 1263705--1263796 Score: 166
Period size: 36 Copynumber: 2.6 Consensus size: 36
1263695 CTCAATTATC
*
1263705 ATAAGCCAAAATTATTTCATATATGAATGTTAATAG
1 ATAAGCCAAAATTATTCCATATATGAATGTTAATAG
1263741 ATAAGCCAAAATTATTCCATATATGAATGTTAATAG
1 ATAAGCCAAAATTATTCCATATATGAATGTTAATAG
*
1263777 ATAAGCCAAAAATATTCCAT
1 ATAAGCCAAAATTATTCCAT
1263797 GAATGTTCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.33
Consensus pattern (36 bp):
ATAAGCCAAAATTATTCCATATATGAATGTTAATAG
Found at i:1267090 original size:13 final size:13
Alignment explanation
Indices: 1267072--1267098 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1267062 TCTACTTAGG
1267072 TTGATAGAAGGAA
1 TTGATAGAAGGAA
1267085 TTGATAGAAGGAA
1 TTGATAGAAGGAA
1267098 T
1 T
1267099 AATTTGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (13 bp):
TTGATAGAAGGAA
Found at i:1268066 original size:66 final size:66
Alignment explanation
Indices: 1267988--1268138 Score: 266
Period size: 66 Copynumber: 2.3 Consensus size: 66
1267978 AGCAACTTTC
* **
1267988 AATAATACCCTCACGTTTCTCAATTTTACGATTAAAAGTTATAATATGATCATTTGACTATTCAT
1 AATAATAACCTCACGTTTCTCAATTTTACGATTAAAAGTTATAATATGATCACCTGACTATTCAT
1268053 T
66 T
1268054 AATAATAACCTCACGTTTCTCAATTTTACGATTAAAAGTTATAATATGATCACCTGACTATTCAT
1 AATAATAACCTCACGTTTCTCAATTTTACGATTAAAAGTTATAATATGATCACCTGACTATTCAT
1268119 T
66 T
*
1268120 AATAATATCCTCACGTTTC
1 AATAATAACCTCACGTTTC
1268139 ATAATCGAGT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 81 1.00
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (66 bp):
AATAATAACCTCACGTTTCTCAATTTTACGATTAAAAGTTATAATATGATCACCTGACTATTCAT
T
Found at i:1269070 original size:18 final size:19
Alignment explanation
Indices: 1269036--1269075 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1269026 CTTTACCCTA
1269036 TTTTAAATTAGTTTTTAAAT
1 TTTTAAATTAGTTTTT-AAT
1269056 TTTTAAA-TA-TTTTTAAT
1 TTTTAAATTAGTTTTTAAT
1269073 TTT
1 TTT
1269076 ATTCTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 2 0.10
20 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTAGTTTTTAAT
Found at i:1269981 original size:21 final size:21
Alignment explanation
Indices: 1269955--1270172 Score: 252
Period size: 21 Copynumber: 10.5 Consensus size: 21
1269945 GTTTCCAGAT
* *
1269955 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTCGACTA
1269976 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1269997 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1270018 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
1270038 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
1270059 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1270080 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
1270101 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1270122 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
1270142 TCGCAACGCAAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
1270163 TCGCAATGCG
1 TCGCAATGCG
1270173 GACCACGACC
Statistics
Matches: 169, Mismatches: 17, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
20 32 0.19
21 137 0.81
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1270135 original size:104 final size:104
Alignment explanation
Indices: 1269955--1270172 Score: 357
Period size: 104 Copynumber: 2.1 Consensus size: 104
1269945 GTTTCCAGAT
* * * *
1269955 TCGCAACGCGAACTTTGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATC
1 TCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACTATC
* *
1270020 GCAATGCGAATATGTAAATCGCAATGCGATA-GTCGACTA
66 GCAATGCGAATATGTAAATCGCAACGC-AAACGTCGACTA
1270059 TCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACTATC
1 TCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACTATC
*
1270124 GCAATGCGAATATGTAAATCGCAACGCAAACTTCGACTA
66 GCAATGCGAATATGTAAATCGCAACGCAAACGTCGACTA
1270163 TCGCAATGCG
1 TCGCAATGCG
1270173 GACCACGACC
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 2 0.02
104 104 0.98
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (104 bp):
TCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACTATC
GCAATGCGAATATGTAAATCGCAACGCAAACGTCGACTA
Found at i:1270184 original size:6 final size:6
Alignment explanation
Indices: 1270173--1270210 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
1270163 TCGCAATGCG
1270173 GACCAC GACCAC GACCAC GACCAC GACC-C GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1270211 CGAGACGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1270723 original size:6 final size:6
Alignment explanation
Indices: 1270712--1270756 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1270702 TCTCGTCTCG
1270712 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1270757 AATGGTAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1273551 original size:31 final size:31
Alignment explanation
Indices: 1273499--1273559 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1273489 TAAATCGTAA
*
1273499 TATATATATAACGATATTTTTTTCATTAAAT
1 TATATATATAACGAGATTTTTTTCATTAAAT
1273530 TATATCATATAACGAGA-TTTTTTCATTAAA
1 TATAT-ATATAACGAGATTTTTTTCATTAAA
1273560 ACTATACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (31 bp):
TATATATATAACGAGATTTTTTTCATTAAAT
Found at i:1274846 original size:38 final size:38
Alignment explanation
Indices: 1274781--1274868 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
1274771 TTTATTTTGT
* *
1274781 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGAGTTGAG
1 TCGGGTCGGGTTTTTTTAAGTGTAATATTCGAGTCGAG
* *
1274818 TCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTAATATTCGAGTCGAG
*
1274856 TCGGATCGGGTTT
1 TCGGGTCGGGTTT
1274869 GGGTTTAGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 10 0.22
38 35 0.78
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTAATATTCGAGTCGAG
Done.