Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008310.1 Hibiscus syriacus cultivar Beakdansim tig00111000_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: 3887810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 15
Found at i:1002259 original size:5 final size:5
Alignment explanation
Indices: 1002246--1002540 Score: 66
Period size: 5 Copynumber: 60.6 Consensus size: 5
1002236 AAATGTAATG
* *
1002246 AAAAT -AAAT AAAAT AAAA- AATAA- AAAA- ACAAAT GAAAT -AAAT AAGAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT A-AAAT AAAAT AAAAT AAAAT
* *
1002293 AAGAT -AAAG AAAAT -AAA- AAAAT AAAGAT -AAAT AAAA- AGTAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT A--AAAT
* * *
1002336 AAAAT AAAGAT -ACAG AAAAT AAAAT AAAAT -AAAT AAAA- ATAAA- GAAAT
1 AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT
* * * *
1002384 AAAA- ATAAAG AAAAT AATAAT AATAT -ACAT ATAAT -AAAT -AAAT -AAAT
1 AAAAT A-AAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * **
1002431 AAAA- ACAGGAAT AAAGT AAAA- ATAAA- GAAAT AAAAT AAATAT AAAGG
1 AAAAT A-A--AAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAA-AT AAAAT
* **
1002478 AAATAA AAAAT AAGGT AAAGAT AAAA- AAGAAT AAAA- AGAAA- AAAA-
1 AAA-AT AAAAT AAAAT AAA-AT AAAAT AA-AAT AAAAT A-AAAT AAAAT
* *
1002523 AAAAA AAAAA AAAAT AAA
1 AAAAT AAAAT AAAAT AAA
1002541 GAATATATAT
Statistics
Matches: 223, Mismatches: 31, Indels: 72
0.68 0.10 0.22
Matches are distributed among these distances:
4 63 0.28
5 128 0.57
6 27 0.12
7 4 0.02
8 1 0.00
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:1002336 original size:11 final size:10
Alignment explanation
Indices: 1002247--1002540 Score: 81
Period size: 10 Copynumber: 29.3 Consensus size: 10
1002237 AATGTAATGA
*
1002247 AAATAAATA-
1 AAATAAAAAT
1002256 AAATAAAAA-
1 AAATAAAAAT
*
1002265 ATAA-AAAAAC
1 A-AATAAAAAT
*
1002275 AAAT-GAAAT
1 AAATAAAAAT
*
1002284 AAAT-AAGAT
1 AAATAAAAAT
*
1002293 AAGATAAAGA-
1 AA-ATAAAAAT
1002303 AAAT-AAAA-
1 AAATAAAAAT
*
1002311 AAATAAAGAT
1 AAATAAAAAT
1002321 AAATAAAAAGT
1 AAATAAAAA-T
1002332 AAAT-AAAAT
1 AAATAAAAAT
1002341 AAAGATACAGAAAAT
1 -AA-AT--A-AAAAT
1002356 AAA-ATAAAAT
1 AAATA-AAAAT
1002366 AAATAAAAAT
1 AAATAAAAAT
*
1002376 AAAGAAATAA-
1 AAATAAA-AAT
*
1002386 AAATAAAGA-
1 AAATAAAAAT
*
1002395 AAATAATAAT
1 AAATAAAAAT
1002405 AATATACATATAAT
1 AA-ATA-A-A-AAT
1002419 AAAT--AAAT
1 AAATAAAAAT
*
1002427 AAATAAAAAC
1 AAATAAAAAT
*
1002437 AGGAAT-AAAGT
1 A--AATAAAAAT
*
1002448 AAA-AATAAAG
1 AAATAA-AAAT
1002458 AAAT-AAAAT
1 AAATAAAAAT
**
1002467 AAATATAAAGG
1 AAATA-AAAAT
1002478 AAATAAAAAAT
1 AAAT-AAAAAT
* *
1002489 AAGGTAAAGAT
1 AA-ATAAAAAT
1002500 AAA-AAAGAAT
1 AAATAAA-AAT
1002510 AAA-AAGAAA-
1 AAATAA-AAAT
*
1002519 AAA-AAAAAA
1 AAATAAAAAT
*
1002528 AAAAAAAAAT
1 AAATAAAAAT
1002538 AAA
1 AAA
1002541 GAATATATAT
Statistics
Matches: 219, Mismatches: 30, Indels: 71
0.68 0.09 0.22
Matches are distributed among these distances:
8 17 0.08
9 64 0.29
10 76 0.35
11 41 0.19
12 6 0.03
13 3 0.01
14 7 0.03
15 5 0.02
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.16
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1002338 original size:29 final size:27
Alignment explanation
Indices: 1002247--1002487 Score: 87
Period size: 29 Copynumber: 8.4 Consensus size: 27
1002237 AATGTAATGA
**
1002247 AAATAAATAAAAT-AAAAAATAAAAAAAC
1 AAATAAA-AAAATAAAAAAAT-AAAAAGT
* * * * * *
1002275 AAATGAAATAAATAAGATAAGATAAAGA
1 AAAT-AAAAAAATAAAAAAATAAAAAGT
1002303 AAATAAAAAAATAAAGATAAATAAAAAGT
1 AAATAAAAAAATAAA-A-AAATAAAAAGT
*
1002332 AAATAAAATAAAGATACAGAAAAT-AAAA-T
1 AAAT-AAA-AAA-ATA-AAAAAATAAAAAGT
*
1002361 AAAATAAATAAAAATAAAGAAATAAAAA-T
1 -AAAT-AA-AAAAATAAAAAAATAAAAAGT
* * * *
1002390 AAAGAAAATAATAATAATATACATATAA-T
1 AAATAAAAAAATAAAAAAATA-A-A-AAGT
* **
1002419 AAATAAATAAATAAAAACAGGAATAAAGT
1 AAATAAAAAAATAAAAA-AATAA-AAAGT
* * *
1002448 AAAAATAAAGAAATAAAATAAATATAAAGG
1 --AAATAAAAAAATAAAA-AAATAAAAAGT
1002478 AAATAAAAAA
1 AAATAAAAAA
1002488 TAAGGTAAAG
Statistics
Matches: 160, Mismatches: 34, Indels: 38
0.69 0.15 0.16
Matches are distributed among these distances:
26 11 0.07
27 12 0.08
28 37 0.23
29 47 0.29
30 22 0.14
31 25 0.16
32 5 0.03
33 1 0.01
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.18
Consensus pattern (27 bp):
AAATAAAAAAATAAAAAAATAAAAAGT
Found at i:1002374 original size:63 final size:61
Alignment explanation
Indices: 1002303--1002485 Score: 180
Period size: 63 Copynumber: 2.9 Consensus size: 61
1002293 AAGATAAAGA
*
1002303 AAATAAAAAAATAAAGATAAATAA-AAAGTAAATAAAATAAAGATACAGAAAATAAAATAAAAT
1 AAATAAAAAAATAAAGATAAA-AATAAAG-AAATAAAATAAATATACAGAAAATAAAAT-AAAT
* *
1002366 AAAT--AAAAATAAAGAAATAAAAATAAAGAAAATAATAAT-AATATACATATAAT-AAATAAAT
1 AAATAAAAAAATAAAG--ATAAAAATAAAG-AAATAA-AATAAATATACAGAAAATAAAATAAAT
* *
1002427 AAATAAAAACAGGAATAAAG-TAAAAATAAAGAAATAAAATAAATATAAAGGAAATAAAA
1 AAAT-AAAA-A--AATAAAGATAAAAATAAAGAAATAAAATAAATATACAGAAAATAAAA
1002486 AATAAGGTAA
Statistics
Matches: 100, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
61 18 0.18
62 9 0.09
63 46 0.46
64 19 0.19
65 1 0.01
67 7 0.07
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.19
Consensus pattern (61 bp):
AAATAAAAAAATAAAGATAAAAATAAAGAAATAAAATAAATATACAGAAAATAAAATAAAT
Found at i:1002496 original size:27 final size:28
Alignment explanation
Indices: 1002450--1002502 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1002440 AATAAAGTAA
*
1002450 AAATAAAGAAATAAAATAAATATAAAGG
1 AAATAAAGAAATAAAATAAAGATAAAGG
**
1002478 AAATAAA-AAATAAGGTAAAGATAAA
1 AAATAAAGAAATAAAATAAAGATAAA
1002503 AAAGAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (28 bp):
AAATAAAGAAATAAAATAAAGATAAAGG
Found at i:1002513 original size:9 final size:9
Alignment explanation
Indices: 1002494--1002543 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
1002484 AAAATAAGGT
*
1002494 AAAGATAAA
1 AAAGAAAAA
*
1002503 AAAGAATAA
1 AAAGAAAAA
1002512 AAAGAAAAA
1 AAAGAAAAA
1002521 AAA-AAAAA
1 AAAGAAAAA
1002529 AAA-AAAAA
1 AAAGAAAAA
1002537 TAAAGAA
1 -AAAGAA
1002544 TATATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
8 13 0.36
9 21 0.58
10 2 0.06
ACGTcount: A:0.86, C:0.00, G:0.08, T:0.06
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:1002625 original size:15 final size:15
Alignment explanation
Indices: 1002605--1002634 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1002595 AGAAAATAGG
1002605 AACAAAAAAATAAAA
1 AACAAAAAAATAAAA
*
1002620 AACAAATAAATAAAA
1 AACAAAAAAATAAAA
1002635 TGAATAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (15 bp):
AACAAAAAAATAAAA
Found at i:1006013 original size:16 final size:17
Alignment explanation
Indices: 1005989--1006021 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1005979 ATTTATAGCA
1005989 TATAGTATAT-ATGTAT
1 TATAGTATATAATGTAT
*
1006005 TATATTATATAATGTAT
1 TATAGTATATAATGTAT
1006022 ACTAACAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
TATAGTATATAATGTAT
Found at i:1007314 original size:2 final size:2
Alignment explanation
Indices: 1007307--1007331 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1007297 ACTTTTATTT
1007307 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1007332 TATCTCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1017833 original size:12 final size:13
Alignment explanation
Indices: 1017816--1017847 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1017806 TAAGTCGAAG
1017816 AAGAAAAAG-AAA
1 AAGAAAAAGAAAA
1017828 AAG-AAAAGAAAA
1 AAGAAAAAGAAAA
1017840 AAGAAAAA
1 AAGAAAAA
1017848 ACATTTAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 9 0.50
13 4 0.22
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:1018900 original size:60 final size:62
Alignment explanation
Indices: 1018741--1018905 Score: 192
Period size: 65 Copynumber: 2.6 Consensus size: 62
1018731 TTTACAAAAG
* ** *
1018741 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTTAAAGTCAATTTGGTGGAACTTACTTAAG
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGGAA--TAC-TAAC
* * *
1018806 ATTGGATTTCAATTTCACGATGAAGGATATCCAACTCAAAACCAATTTGGT-GAA-AC-AATC
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGGAATACTAA-C
* *
1018866 CTTGGATTTCAACTTCATAACGAAGGATATCCAACTCAAA
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
1018906 GCTCAACATC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.02
60 35 0.40
61 2 0.02
64 3 0.03
65 45 0.52
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (62 bp):
ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGGAATACTAAC
Found at i:1021115 original size:65 final size:64
Alignment explanation
Indices: 1021039--1021194 Score: 215
Period size: 65 Copynumber: 2.4 Consensus size: 64
1021029 TCACTCCATT
* *
1021039 TCGAATGCATTTAGTGTACCGATGCACA-AGCCATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTAGTGTACCGATGCACAGA-CCATGCATCGATGCACTCCTGAAT-CTTTGAAAC
1021103 A
64 A
* * **
1021104 TCGAATACATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTTTGAAACA
1 TCGAATGCATTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATCTTTGAAACA
* *
1021168 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTAGTGTACCGATGCAC
1021195 CCCTAGTGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 32 0.40
65 47 0.59
66 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (64 bp):
TCGAATGCATTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATCTTTGAAACA
Found at i:1024285 original size:22 final size:22
Alignment explanation
Indices: 1024236--1024286 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1024226 TGGTAGATGG
*
1024236 CTATTCTAGATATACTTGGGTT
1 CTATTTTAGATATACTTGGGTT
1024258 CTATTTTAGATATACTTGGGTT
1 CTATTTTAGATATACTTGGGTT
1024280 CTATTTT
1 CTATTTT
1024287 TAAGTACTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.51
Consensus pattern (22 bp):
CTATTTTAGATATACTTGGGTT
Found at i:1026968 original size:23 final size:22
Alignment explanation
Indices: 1026937--1027010 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
1026927 GACAGTATAC
1026937 CGATGCATCCCTTGAATGTGCAT
1 CGATGCAT-CCTTGAATGTGCAT
* * *
1026960 CGATACAT-CATGAA-GATGCAC
1 CGATGCATCCTTGAATG-TGCAT
*
1026981 CGATGTATTCCTTGAATGTGCAT
1 CGATGCA-TCCTTGAATGTGCAT
1027004 CGATGCA
1 CGATGCA
1027011 CACTGCTGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
20 1 0.03
21 14 0.36
22 1 0.03
23 22 0.56
24 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (22 bp):
CGATGCATCCTTGAATGTGCAT
Found at i:1028971 original size:22 final size:22
Alignment explanation
Indices: 1028936--1028983 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1028926 TTGATATGTT
*
1028936 TTTGGATTGTTTGAATTTGATG
1 TTTGGATTGTTTGAATTGGATG
1028958 ATTTGGA-TGTTTGAATTGGATG
1 -TTTGGATTGTTTGAATTGGATG
1028980 TTTG
1 TTTG
1028984 AACTTAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (22 bp):
TTTGGATTGTTTGAATTGGATG
Found at i:1028978 original size:13 final size:13
Alignment explanation
Indices: 1028960--1028985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1028950 ATTTGATGAT
1028960 TTGGATGTTTGAA
1 TTGGATGTTTGAA
1028973 TTGGATGTTTGAA
1 TTGGATGTTTGAA
1028986 CTTAAATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
TTGGATGTTTGAA
Found at i:1029812 original size:64 final size:65
Alignment explanation
Indices: 1029658--1029813 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
1029648 GCACTCCATT
* * *
1029658 TCGAATGCATTTAGTGTACCGATGCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACA
1 TCGAATGCATTTAGTGTACCGATGCACAAGCCATGCATCGATGAACTCCTGAATACTTTGAAACA
* * **
1029723 TCGAATGCATTTTGTGTACTGATGCAC-AGACCATGCATCGATGAACTCCTGGCT-CTTTGAAAC
1 TCGAATGCATTTAGTGTACCGATGCACAAG-CCATGCATCGATGAACTCCTGAATACTTTGAAAC
1029786 A
65 A
* * *
1029787 TCGAATGTAATTAGTGTACCAATGCAC
1 TCGAATGCATTTAGTGTACCGATGCAC
1029814 CCCTAGTGTA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 33 0.42
65 45 0.58
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
TCGAATGCATTTAGTGTACCGATGCACAAGCCATGCATCGATGAACTCCTGAATACTTTGAAACA
Found at i:1030831 original size:18 final size:18
Alignment explanation
Indices: 1030810--1030871 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
1030800 TTTATTTATT
1030810 TTATTTAATTTAATTCTA
1 TTATTTAATTTAATTCTA
* *
1030828 TTATTTTATTTTATTCTA
1 TTATTTAATTTAATTCTA
* * *
1030846 TTTTTTAGTTTTTAATTTTA
1 TTATTTA--ATTTAATTCTA
1030866 TTATTT
1 TTATTT
1030872 TTTATAATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 21 0.62
20 13 0.38
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (18 bp):
TTATTTAATTTAATTCTA
Found at i:1030834 original size:38 final size:38
Alignment explanation
Indices: 1030790--1030876 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
1030780 GTTTATGCTT
1030790 TTATTTTTTATTTATT-TATTTTATTTA-ATTTAATTCTA
1 TTATTTTTTATTTATTCTA-TTT-TTTAGATTTAATTCTA
* * *
1030828 TTATTTTAT-TTTATTCTATTTTTTAGTTTTTAATTTTA
1 TTATTTTTTATTTATTCTATTTTTTAG-ATTTAATTCTA
1030866 TTATTTTTTAT
1 TTATTTTTTAT
1030877 AATTTTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.10
37 9 0.22
38 27 0.66
39 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (38 bp):
TTATTTTTTATTTATTCTATTTTTTAGATTTAATTCTA
Found at i:1030847 original size:10 final size:9
Alignment explanation
Indices: 1030796--1030893 Score: 50
Period size: 8 Copynumber: 11.1 Consensus size: 9
1030786 GCTTTTATTT
1030796 TTTA-TTTA
1 TTTATTTTA
1030804 TTTATTTTA
1 TTTATTTTA
*
1030813 TTTAATTTAA
1 TTT-ATTTTA
*
1030823 TTCTATTAT-
1 TT-TATTTTA
1030832 TTTATTTTA
1 TTTATTTTA
1030841 TTCTA-TTT-
1 TT-TATTTTA
*
1030849 TTTAGTTT-
1 TTTATTTTA
*
1030857 TTAATTTTA
1 TTTATTTTA
1030866 -TTATTTT-
1 TTTATTTTA
1030873 TTATAATTTTA
1 TT-T-ATTTTA
1030884 TATT-TTTTA
1 T-TTATTTTA
1030893 T
1 T
1030894 CATCATTATT
Statistics
Matches: 71, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
7 2 0.03
8 27 0.38
9 21 0.30
10 17 0.24
11 3 0.04
12 1 0.01
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1030857 original size:23 final size:21
Alignment explanation
Indices: 1030808--1030876 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 21
1030798 TATTTATTTA
* *
1030808 TTTTATTTAATTTAATTCTATTA
1 TTTTATTTTATTT-ATT-TTTTA
1030831 TTTTATTTTATTCTATTTTTTA
1 TTTTATTTTATT-TATTTTTTA
1030853 GTTTTTAATTTTA-TTATTTTTTA
1 --TTTT-ATTTTATTTATTTTTTA
1030876 T
1 T
1030877 AATTTTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 1 0.03
22 4 0.10
23 23 0.57
24 6 0.15
25 6 0.15
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.72
Consensus pattern (21 bp):
TTTTATTTTATTTATTTTTTA
Found at i:1030882 original size:25 final size:24
Alignment explanation
Indices: 1030791--1030893 Score: 68
Period size: 25 Copynumber: 4.0 Consensus size: 24
1030781 TTTATGCTTT
*
1030791 TATTTTTTATTTATTTATTTTATT-
1 TATTTTTTAATT-TTTATTTTATTA
* *
1030815 TAATTTAATTCTATTATTTTATTTTATTC
1 T-ATTT--TT-TAAT-TTTTATTTTATTA
*
1030844 TATTTTTTAGTTTTTAATTTTATTA
1 TATTTTTTAATTTTT-ATTTTATTA
1030869 T-TTTTTATAATTTTATATTTT-TTA
1 TATTTTT-TAATTTT-TATTTTATTA
1030893 T
1 T
1030894 CATCATTATT
Statistics
Matches: 67, Mismatches: 3, Indels: 18
0.76 0.03 0.20
Matches are distributed among these distances:
24 14 0.21
25 27 0.40
26 3 0.04
27 2 0.03
28 19 0.28
29 2 0.03
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (24 bp):
TATTTTTTAATTTTTATTTTATTA
Found at i:1030887 original size:17 final size:18
Alignment explanation
Indices: 1030854--1030893 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
1030844 TATTTTTTAG
1030854 TTTT-TAATTTTATTATT
1 TTTTATAATTTTATTATT
1030871 TTTTATAATTTTA-TATT
1 TTTTATAATTTTATTATT
1030888 TTTTAT
1 TTTTAT
1030894 CATCATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATAATTTTATTATT
Found at i:1038447 original size:44 final size:44
Alignment explanation
Indices: 1038323--1038588 Score: 315
Period size: 44 Copynumber: 6.0 Consensus size: 44
1038313 AAACCAGGAG
* * *
1038323 TGGCACCTTTCTGCCAA-AATACACCGTTATGCATTTAAGTTTCATTTG
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCA--T---TTTCATTTA
*
1038371 TGGCACCTTTCTGCCAA-AATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1038414 TAGCACATTTCTGCTAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1038458 TGACACATTTTTGCCAATAATGTACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1038502 TGGTACATTTCTGCCGATAATGCAACGTTATGCATTTT--TTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* **
1038544 TGGCACCTTTCTGCCAATAATGCAATGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1038588 T
1 T
1038589 TCATTCATTT
Statistics
Matches: 193, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
42 38 0.20
43 22 0.11
44 100 0.52
46 1 0.01
48 32 0.17
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:1039450 original size:23 final size:23
Alignment explanation
Indices: 1039404--1039464 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1039394 AGCTCGTATC
*
1039404 ATTGCACCGAAGTG-CACGTAGA
1 ATTGCACCGTAGTGCCACGTAGA
*
1039426 ATTGCACCGTAGTGCCGCGTAGA
1 ATTGCACCGTAGTGCCACGTAGA
*
1039449 ATTGCATCGTAGTGCC
1 ATTGCACCGTAGTGCC
1039465 TTATAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 13 0.37
23 22 0.63
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (23 bp):
ATTGCACCGTAGTGCCACGTAGA
Found at i:1046375 original size:44 final size:44
Alignment explanation
Indices: 1046309--1046565 Score: 363
Period size: 44 Copynumber: 5.9 Consensus size: 44
1046299 GGTGGCACCT
* *
1046309 TTTCTGCCAA-AATGCATCGTTATGCATTTTCATTTATGGCACC
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
* * * *
1046352 TCTCTACCAATAATGTACTGTTATGCATTTTCATTTATGGCACA
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
* * * *
1046396 TTTCTCCCAATAATGCACCATTATGCATTTTCATTTACGGCACC
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
*
1046440 TTTCTGCCAATAATGCACCGTTAAGCATTTTCATTTATGGCACA
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
* * * *
1046484 TTTCTGCCAAAAATGCACCGTTATGCATTTTCATTTATAGTACT
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
*
1046528 TTTTTGCCAATAATGCACCGTTATGCATTTTCATTTAT
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
1046566 TCATTCATTT
Statistics
Matches: 188, Mismatches: 25, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
43 8 0.04
44 180 0.96
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (44 bp):
TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
Found at i:1047007 original size:44 final size:42
Alignment explanation
Indices: 1046937--1047078 Score: 194
Period size: 44 Copynumber: 3.2 Consensus size: 42
1046927 TGCATTTAAG
* * *
1046937 TTTCATTTGTGGCACCTTTCTACCAATAATGCATCGTTATGCAT
1 TTTCATTTATGGCA-CATTCTGCCAATAATGCA-CGTTATGCAT
1046981 TTTCATTTATGGCATCATTCTGCCAATAATGCACCGTTATGCAT
1 TTTCATTTATGGCA-CATTCTGCCAATAATGCA-CGTTATGCAT
*
1047025 TTTCATTTATGGCACATTTCTGCCAATAATGCACTATTATGCAT
1 TTTCATTTATGGCACA-TTCTGCCAATAATGCAC-GTTATGCAT
1047069 TTTCATTTAT
1 TTTCATTTAT
1047079 ACATTCATTT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
43 3 0.03
44 87 0.97
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (42 bp):
TTTCATTTATGGCACATTCTGCCAATAATGCACGTTATGCAT
Found at i:1057595 original size:10 final size:10
Alignment explanation
Indices: 1057575--1057622 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 10
1057565 ACATAAAATA
1057575 TTATAAT-TT
1 TTATAATATT
1057584 TTATAATATT
1 TTATAATATT
1057594 TTATATTATATTTT
1 TTATA--ATA--TT
1057608 TTATAATATT
1 TTATAATATT
1057618 TTATA
1 TTATA
1057623 TTACACTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 7 0.21
10 14 0.41
12 6 0.18
14 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATAATATT
Found at i:1057599 original size:24 final size:24
Alignment explanation
Indices: 1057572--1057625 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1057562 CCAACATAAA
1057572 ATATTATAATTTTTATAATATTTT
1 ATATTATAATTTTTATAATATTTT
*
1057596 ATATTATATTTTTTATAATATTTT
1 ATATTATAATTTTTATAATATTTT
1057620 ATATTA
1 ATATTA
1057626 CACTCATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATATTATAATTTTTATAATATTTT
Found at i:1057606 original size:12 final size:12
Alignment explanation
Indices: 1057572--1057625 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
1057562 CCAACATAAA
1057572 ATATTATAATTTT
1 ATATTAT-ATTTT
*
1057585 -TATAATATTTT
1 ATATTATATTTT
1057596 ATATTATATTTT
1 ATATTATATTTT
* *
1057608 TTATAATATTTT
1 ATATTATATTTT
1057620 ATATTA
1 ATATTA
1057626 CACTCATTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 5 0.15
12 29 0.85
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:1071819 original size:12 final size:12
Alignment explanation
Indices: 1071802--1071826 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1071792 TTCTCTTCCC
1071802 CGTTCATCTCCT
1 CGTTCATCTCCT
1071814 CGTTCATCTCCT
1 CGTTCATCTCCT
1071826 C
1 C
1071827 CGACTGTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.08, T:0.40
Consensus pattern (12 bp):
CGTTCATCTCCT
Found at i:1076971 original size:12 final size:12
Alignment explanation
Indices: 1076954--1076978 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1076944 CCTAGATCAC
1076954 TGTTTCCCCAAT
1 TGTTTCCCCAAT
1076966 TGTTTCCCCAAT
1 TGTTTCCCCAAT
1076978 T
1 T
1076979 TCTTCTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTCCCCAAT
Found at i:1077007 original size:12 final size:12
Alignment explanation
Indices: 1076990--1077018 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1076980 CTTCTTCTCT
1076990 TCCTCGTTCATC
1 TCCTCGTTCATC
1077002 TCCTCGTTCATC
1 TCCTCGTTCATC
1077014 TCCTC
1 TCCTC
1077019 TGACTGTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.45, G:0.07, T:0.41
Consensus pattern (12 bp):
TCCTCGTTCATC
Found at i:1078400 original size:49 final size:49
Alignment explanation
Indices: 1078346--1078446 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
1078336 TCATTAGCTA
1078346 TTTAGGACTTTTAGAACTCTTCTCTTATAAAAAGAAGGCTTCATTCAAC
1 TTTAGGACTTTTAGAACTCTTCTCTTATAAAAAGAAGGCTTCATTCAAC
1078395 TTTAGGACTTTTAGAACTCTTCTCTTATAAAAAGAAGGCTTCATTCAAC
1 TTTAGGACTTTTAGAACTCTTCTCTTATAAAAAGAAGGCTTCATTCAAC
1078444 TTT
1 TTT
1078447 GTAAATACAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (49 bp):
TTTAGGACTTTTAGAACTCTTCTCTTATAAAAAGAAGGCTTCATTCAAC
Found at i:1083235 original size:21 final size:21
Alignment explanation
Indices: 1083209--1083268 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
1083199 AGAATATGGA
*
1083209 GTATTGGTATTGCCTAAGGGG
1 GTATTGGTACTGCCTAAGGGG
1083230 GTATTGGTACTGCCTAA-GGG
1 GTATTGGTACTGCCTAAGGGG
*
1083250 GTATTGGTACTGCATAAGG
1 GTATTGGTACTGCCTAAGG
1083269 CAGTATCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.22, C:0.12, G:0.35, T:0.32
Consensus pattern (21 bp):
GTATTGGTACTGCCTAAGGGG
Found at i:1083872 original size:21 final size:21
Alignment explanation
Indices: 1083846--1083891 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1083836 ATAATAATAA
* *
1083846 TAATAATTTATTTTTTATTTT
1 TAATAATATATTTTTTATATT
1083867 TAATAATATATTTTTTATATT
1 TAATAATATATTTTTTATATT
1083888 TAAT
1 TAAT
1083892 TTTCTGAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TAATAATATATTTTTTATATT
Found at i:1083889 original size:27 final size:24
Alignment explanation
Indices: 1083843--1083894 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 24
1083833 AAAATAATAA
*
1083843 TAATAATAATTTATTTTTTATTTT
1 TAATAATAATTTATTTTTTAATTT
*
1083867 TAATAATATATTTTTTATATTTAATTT
1 TAATAATA-ATTTATT-T-TTTAATTT
1083894 T
1 T
1083895 CTGAGCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
25 6 0.26
26 1 0.04
27 8 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TAATAATAATTTATTTTTTAATTT
Found at i:1095007 original size:191 final size:184
Alignment explanation
Indices: 1094667--1095010 Score: 476
Period size: 191 Copynumber: 1.8 Consensus size: 184
1094657 TTTGAAATAT
* *
1094667 TCAAAAGATAAAACTCCTTTTATCATTCAAACTTAAATAGATATTATTTTAATTTAACAAAAATA
1 TCAAAAGATAAAACTCCTTTTATCATTCAAACTTAAACAAATATTATTTTAATTTAACAAAAATA
* * * * * *
1094732 TATAATTATCTTTAATATTCAAAGTTAAAATGGTAACAAATACCTTTTTAAGTTGAAATATTCAA
66 TATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATACATTTTTAAATTGAAATATTAAA
1094797 AGAGTAATTATCCTACTAATATTCAAATTAAATAATATATTTAATTTACAATGG
131 AGAGTAATTATCCTACTAATATTCAAATTAAATAATATATTTAATTTACAATGG
*
1094851 TCAAAAGAT-AAACTCCTTTTA-CTATTTAAACTTAAACAAATATTATTTTAATTTGAAATATAC
1 TCAAAAGATAAAACTCCTTTTATC-ATTCAAACTTAAACAAATATTATTTTAA-TT----TA-AC
*
1094914 AAAAATATATAATTATCTTTTAATATTTAAAATTAAAAAAGATAACAAATACATTTTTAAATTGA
59 AAAAATATATAATTATC-TTTAATATTCAAAATT-AAAAAGATAACAAATACATTTTTAAATTGA
** *
1094979 CTTATTAAAAGAGTAATTATCTTACTAATATT
122 AATATTAAAAGAGTAATTATCCTACTAATATT
1095011 TAGGGGGCGT
Statistics
Matches: 138, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
182 1 0.01
183 37 0.27
184 11 0.08
188 2 0.01
189 19 0.14
190 14 0.10
191 54 0.39
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (184 bp):
TCAAAAGATAAAACTCCTTTTATCATTCAAACTTAAACAAATATTATTTTAATTTAACAAAAATA
TATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATACATTTTTAAATTGAAATATTAAA
AGAGTAATTATCCTACTAATATTCAAATTAAATAATATATTTAATTTACAATGG
Found at i:1095627 original size:16 final size:16
Alignment explanation
Indices: 1095608--1095640 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1095598 CAGTAATCAC
1095608 ATTCCCTGATAATCTT
1 ATTCCCTGATAATCTT
1095624 ATTCCCTGATAATCTT
1 ATTCCCTGATAATCTT
1095640 A
1 A
1095641 CATTCCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTCCCTGATAATCTT
Found at i:1099502 original size:62 final size:62
Alignment explanation
Indices: 1099389--1099508 Score: 147
Period size: 62 Copynumber: 1.9 Consensus size: 62
1099379 CAGATAATAA
* * *
1099389 TATTTTTTTAATTTAAAATATTCAAAAGATAAATCTCCTTTTATCATTCAAACTTAAATATG
1 TATTATTTTAATTTAAAATATACAAAAGATAAATCTCCTTTAATCATTCAAACTTAAATATG
* *
1099451 TATTATTTTAA-TTAAAATATACAAAAGTATATAAT-TAGCTTTAAT-ATTCAAAGTTAAA
1 TATTATTTTAATTTAAAATATACAAAAG-ATA-AATCT-CCTTTAATCATTCAAACTTAAA
1099509 AAGGTGATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 15 0.30
62 26 0.52
63 9 0.18
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (62 bp):
TATTATTTTAATTTAAAATATACAAAAGATAAATCTCCTTTAATCATTCAAACTTAAATATG
Found at i:1100396 original size:21 final size:22
Alignment explanation
Indices: 1100367--1100417 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
1100357 CTTGAAACTT
1100367 TTTCGAGTTGAGT-AAAAAAAA
1 TTTCGAGTTGAGTCAAAAAAAA
*
1100388 TTTCTAGTTGAGTCAAAAAAAA
1 TTTCGAGTTGAGTCAAAAAAAA
1100410 -TTCGAGTT
1 TTTCGAGTT
1100418 ATTTGAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (22 bp):
TTTCGAGTTGAGTCAAAAAAAA
Found at i:1101135 original size:162 final size:161
Alignment explanation
Indices: 1100895--1101190 Score: 486
Period size: 163 Copynumber: 1.8 Consensus size: 161
1100885 CAAATTTGAT
* *
1100895 AAAAGCGGACTTAAAATAAAGGTGAATTCAAGAAATAAGAAAATTAAAAAAAATTGAGGGACTAA
1 AAAAGCGAACTTAAAATAAAGATGAATTCAAGAAATAAGAAAATTAAAAAAAATTGAGGGACTAA
* * *
1100960 ATTGAAAAAT-AAAAGTTTGTTATCAAAAAGAGGAATTGAAAGTACATATGTATTCTATGATGGT
66 ATTGAAAAATAAAAAATTTGTTATCAAAAAGAGAAATTGAAAGTACATATGTATTCTATGATGAT
1101024 TTAGGAACATGTGGATCAAATTTGGTAAAAA
131 TTAGGAACATGTGGATCAAATTTGGTAAAAA
* *
1101055 AAAAGACGAACTTAAAATAAATGATGAATTGAAGAAATAAGAAAATTATAAAAAATTGAGGGACT
1 AAAAG-CGAACTTAAAATAAA-GATGAATTCAAGAAATAAGAAAATTAAAAAAAATTGAGGGACT
* *
1101120 AAATTGAAAAATAAAAAATTTGTTATCAAAAAGATAAATTGAAAGTACATATGTATTTTATGATG
64 AAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGAAATTGAAAGTACATATGTATTCTATGATG
1101185 ATTTAG
129 ATTTAG
1101191 CAGCACGTGG
Statistics
Matches: 124, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
160 5 0.04
161 14 0.11
162 52 0.42
163 53 0.43
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (161 bp):
AAAAGCGAACTTAAAATAAAGATGAATTCAAGAAATAAGAAAATTAAAAAAAATTGAGGGACTAA
ATTGAAAAATAAAAAATTTGTTATCAAAAAGAGAAATTGAAAGTACATATGTATTCTATGATGAT
TTAGGAACATGTGGATCAAATTTGGTAAAAA
Found at i:1102429 original size:31 final size:31
Alignment explanation
Indices: 1102357--1102422 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1102347 GTTATGTCGA
*
1102357 GGACCATATTGCAAACAGACTAACTGTTGGG
1 GGACCATATTGCAAACAGACTAAATGTTGGG
*
1102388 GGACCATATTGCAAA-AGGATTAAATGTTGGG
1 GGACCATATTGCAAACA-GACTAAATGTTGGG
1102419 GGAC
1 GGAC
1102423 TGTATTGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (31 bp):
GGACCATATTGCAAACAGACTAAATGTTGGG
Found at i:1107571 original size:134 final size:134
Alignment explanation
Indices: 1107331--1107572 Score: 344
Period size: 134 Copynumber: 1.8 Consensus size: 134
1107321 AACTAAGTTC
* * * ** * *
1107331 CGAAATGGTAATTCACAAATTCATTATGAATTTCATGGATGCACACATAGTGCCGAGAGTACATA
1 CGAAATAGTAATTCACAAACTCATTATAAATACCATGGATGCACACATAGTGCCGAAAGTACACA
1107396 TAGTACTGATACGAAAAATGCAACATATGCATTAAACAAAATCAATAACTTTTATACATAATTGT
66 TAGTACTGATACGAAAAATGCAACATATGCATTAAACAAAATCAATAACTTTTATACATAATTGT
1107461 ATGT
131 ATGT
* *
1107465 CGAAATAGTAATTCACGAACTCATTATAAATACCATGGTTGCACATC-TAGTGCCGAAAGTACAC
1 CGAAATAGTAATTCACAAACTCATTATAAATACCATGGATGCACA-CATAGTGCCGAAAGTACAC
* * *
1107529 ATAGTGCTGATACG-AAAATGCACCATTATGCATTACACAAAATC
65 ATAGTACTGATACGAAAAATGCAACA-TATGCATTAAACAAAATC
1107573 GATCGATAAC
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
133 10 0.11
134 83 0.88
135 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (134 bp):
CGAAATAGTAATTCACAAACTCATTATAAATACCATGGATGCACACATAGTGCCGAAAGTACACA
TAGTACTGATACGAAAAATGCAACATATGCATTAAACAAAATCAATAACTTTTATACATAATTGT
ATGT
Found at i:1109623 original size:74 final size:75
Alignment explanation
Indices: 1109545--1109707 Score: 220
Period size: 74 Copynumber: 2.2 Consensus size: 75
1109535 ACCTCTAAGG
* ** * *
1109545 GGGTATCGGTACCCATTGGGCATTCTGTTTTTGTCGGAGCCAAAATTAGCATACGGGTATTGG-T
1 GGGTATCGGTACCCATTGGGCATTATGTTTTCCTCAGAGCCAAAATTAGCATACGGGTATCGGAT
1109609 ACCCTATGAA
66 ACCCTATGAA
* * *
1109619 GGGTATCGGTACCCATTTGGCATTATGTTTTCCTCAGAGCCAAAATTGGCATAGGGGTATCGGTA
1 GGGTATCGGTACCCATTGGGCATTATGTTTTCCTCAGAGCCAAAATTAGCATACGGGTATCGG-A
* *
1109684 TACCTTATGAG
65 TACCCTATGAA
1109695 GGGTATCGGTACC
1 GGGTATCGGTACC
1109708 TCCCTATTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
74 55 0.71
76 22 0.29
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (75 bp):
GGGTATCGGTACCCATTGGGCATTATGTTTTCCTCAGAGCCAAAATTAGCATACGGGTATCGGAT
ACCCTATGAA
Found at i:1112009 original size:21 final size:20
Alignment explanation
Indices: 1111938--1112035 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 20
1111928 AACCTGACAG
* *
1111938 GGGGTATCGGTACCCTT-ATA
1 GGGGTATCGATACACTTGA-A
*
1111958 GGGGTATCGATACACATTAAAA
1 GGGGTATCGATACAC-TT-GAA
*
1111980 GATGGTATCGATACACGTTGAA
1 G-GGGTATCGATACAC-TTGAA
*
1112002 GGGGTATCGATAC-CTAGCAA
1 GGGGTATCGATACACTTG-AA
1112022 GGGGGTATCGATAC
1 -GGGGTATCGATAC
1112036 CTGGTGCACA
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
19 2 0.03
20 16 0.25
21 26 0.40
22 5 0.08
23 16 0.25
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (20 bp):
GGGGTATCGATACACTTGAA
Found at i:1117924 original size:71 final size:73
Alignment explanation
Indices: 1117779--1117956 Score: 247
Period size: 71 Copynumber: 2.4 Consensus size: 73
1117769 GTTAAATGAC
*
1117779 TAGGGGTATCGGTACCTCTAAG-GGGGTATCGGTACCTATTGGGCATTATGTTTTTCTCGGAGCC
1 TAGGGGTATCGGTACC-CTATGAGGGGTATCGG-ACCTATTGGGCATTATGTTTTTCTCGGAGCC
1117843 AAAATTGGCA
64 AAAATTGGCA
* *
1117853 TAGGGGTATCGGTACCCTATGAGGGGTATCGG-CC-ATTTGGCATT-TTTTTTTCCTCGGAGCCA
1 TAGGGGTATCGGTACCCTATGAGGGGTATCGGACCTATTGGGCATTATGTTTTT-CTCGGAGCCA
1117915 AAATTGGCA
65 AAATTGGCA
*
1117924 TAGGGGTATCGGTACACCCTATGAGGGGCATCG
1 TAGGGGTATCGGT--ACCCTATGAGGGGTATCG
1117957 ATACCTCCCT
Statistics
Matches: 96, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
70 6 0.06
71 41 0.43
72 2 0.02
73 21 0.22
74 26 0.27
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (73 bp):
TAGGGGTATCGGTACCCTATGAGGGGTATCGGACCTATTGGGCATTATGTTTTTCTCGGAGCCAA
AATTGGCA
Found at i:1118259 original size:8 final size:8
Alignment explanation
Indices: 1118246--1118274 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1118236 AGTTTAAGCT
1118246 TTTTCCCA
1 TTTTCCCA
1118254 TTTTCCCA
1 TTTTCCCA
1118262 TTTTCCCA
1 TTTTCCCA
1118270 TTTTC
1 TTTTC
1118275 AACCTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.34, G:0.00, T:0.55
Consensus pattern (8 bp):
TTTTCCCA
Found at i:1127972 original size:5 final size:5
Alignment explanation
Indices: 1127947--1128013 Score: 71
Period size: 5 Copynumber: 12.8 Consensus size: 5
1127937 AAGACAACCC
* * *
1127947 ATTTT ATTTT CCAATTT ATTTA ATTTT ATTTA ATTTT AATTTT ATTTT
1 ATTTT ATTTT --ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT
*
1127995 ATTTT ATTTC ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTT
1128014 CATTACATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
5 42 0.82
6 5 0.10
7 4 0.08
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.70
Consensus pattern (5 bp):
ATTTT
Found at i:1127976 original size:10 final size:10
Alignment explanation
Indices: 1127961--1128034 Score: 66
Period size: 10 Copynumber: 7.7 Consensus size: 10
1127951 TATTTTCCAA
1127961 TTTATTTAAT
1 TTTATTTAAT
1127971 TTTATTTAA-
1 TTTATTTAAT
1127980 --T-TTTAAT
1 TTTATTTAAT
*
1127987 TTTATTTTAT
1 TTTATTTAAT
*
1127997 TTTATTTCAT
1 TTTATTTAAT
*
1128007 TTTATTTCAT
1 TTTATTTAAT
**
1128017 TACATATTAAT
1 TTTAT-TTAAT
1128028 TTTATTT
1 TTTATTT
1128035 TTCTTTGAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
6 5 0.10
7 1 0.02
9 1 0.02
10 38 0.73
11 7 0.13
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATTTAAT
Found at i:1127984 original size:16 final size:16
Alignment explanation
Indices: 1127961--1128013 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1127951 TATTTTCCAA
1127961 TTTA-TTTAATTTTAT
1 TTTATTTTAATTTTAT
*
1127976 TTAATTTTAATTTTAT
1 TTTATTTTAATTTTAT
*
1127992 TTTATTTT-ATTTCAT
1 TTTATTTTAATTTTAT
1128007 TTTATTT
1 TTTATTT
1128014 CATTACATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 16 0.47
16 18 0.53
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTTAATTTTAT
Found at i:1127990 original size:26 final size:26
Alignment explanation
Indices: 1127961--1128010 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1127951 TATTTTCCAA
1127961 TTTATTTAATTTTATTTAATTTTAAT
1 TTTATTTAATTTTATTTAATTTTAAT
* *
1127987 TTTATTTTATTTTATTTCATTTTA
1 TTTATTTAATTTTATTTAATTTTA
1128011 TTTCATTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTATTTAATTTTATTTAATTTTAAT
Found at i:1131140 original size:9 final size:9
Alignment explanation
Indices: 1131126--1131177 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
1131116 GAATAACAAC
*
1131126 AGAAAATAT
1 AGAAAAAAT
1131135 AGAAAAAAT
1 AGAAAAAAT
1131144 AGAAAAAATTT
1 AGAAAAAA--T
* *
1131155 AAAAAAAAA
1 AGAAAAAAT
*
1131164 AGAAAAAAA
1 AGAAAAAAT
1131173 AGAAA
1 AGAAA
1131178 TTGGTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 29 0.78
11 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (9 bp):
AGAAAAAAT
Found at i:1132767 original size:23 final size:22
Alignment explanation
Indices: 1132741--1132790 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
1132731 TAGCTCGTAG
1132741 AAATGCACCGAAGTGTCGCATA-A
1 AAATGCACCGAAGTG-C-CATATA
*
1132764 AAATGCACCGAGGTGCCATATA
1 AAATGCACCGAAGTGCCATATA
1132786 AAATG
1 AAATG
1132791 TCCATAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
23 14 0.56
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (22 bp):
AAATGCACCGAAGTGCCATATA
Found at i:1132873 original size:21 final size:21
Alignment explanation
Indices: 1132835--1132910 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
1132825 TATATACATA
* *
1132835 TTCCCAAGGACCAAATATGTG
1 TTCCAAAGGACCAAATATATG
**
1132856 -TCTCAAAGGACCGTATATATG
1 TTC-CAAAGGACCAAATATATG
** *
1132877 TTCCAAAGGATTACATATATG
1 TTCCAAAGGACCAAATATATG
* *
1132898 TCCCGAAGGACCA
1 TTCCAAAGGACCA
1132911 CGTAGAACCC
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (21 bp):
TTCCAAAGGACCAAATATATG
Found at i:1133751 original size:20 final size:20
Alignment explanation
Indices: 1133726--1133775 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1133716 GATACCCTCA
1133726 GTATCGATACTGCTCCTTTG
1 GTATCGATACTGCTCCTTTG
1133746 GTATCGATACTGCTCCTTTG
1 GTATCGATACTGCTCCTTTG
1133766 GTATCGATAC
1 GTATCGATAC
1133776 CCCTTGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (20 bp):
GTATCGATACTGCTCCTTTG
Found at i:1136357 original size:55 final size:55
Alignment explanation
Indices: 1136224--1136493 Score: 348
Period size: 55 Copynumber: 4.9 Consensus size: 55
1136214 TTTATTAAGA
* * ** *
1136224 TGCACACGTAGTGTC-TATACGG-TAGTTCATCAACTCATGATGAATTTTGTGG-GT
1 TGCACACATAGTG-CATGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATT
* * * *
1136278 TGCACACATTGTACATGTATGGTTATTCGTCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
*
1136333 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * * *
1136388 TGTATACATAGTGCCTGTACGATTATTCATCAACTCATGATAAATTCTGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
*
1136443 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTG
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTG
1136494 AAATGCACAC
Statistics
Matches: 186, Mismatches: 27, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 39 0.21
55 146 0.78
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (55 bp):
TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:1136525 original size:54 final size:54
Alignment explanation
Indices: 1136249--1136563 Score: 284
Period size: 55 Copynumber: 5.8 Consensus size: 54
1136239 TATACGGTAG
** * * *
1136249 TTCATCAACTCATGATGAATTTTGTGG-GTTGCACACAT--TGTACATGTATGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGT-C--GTACGATTA
* *
1136303 TTCGTCAACTCATGATGAATTCCGTGGATTTGCACACATAGTG-CATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTC--GTACGATTA
* * * *
1136358 TTCATCAACTCATGATGAATTTCGTGGATTTGTATACATAGTGCCTGTACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTC-GTACGATTA
* * * *
1136413 TTCATCAACTCATGATAAATTCTGTGGATTTGCACACATAGTGCTTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTG-TCGTACGATTA
** * *
1136468 TTCATCAACTCATGATGAATTCCGT-GAAATGCACACTTAGTGTCGAAACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCG-TACGATTA
* * * * *
1136522 TTCATCCACAT-AGGATGAATTCCGTAGA-ATGCACACTTAGTG
1 TTCATCAAC-TCATGATGAATTCCGTGGATTTGCACACATAGTG
1136564 CCTATTTGGT
Statistics
Matches: 225, Mismatches: 28, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.01
54 79 0.35
55 141 0.63
56 1 0.00
57 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (54 bp):
TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCGTACGATTA
Found at i:1136916 original size:20 final size:20
Alignment explanation
Indices: 1136891--1136933 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1136881 GGCTCCTCAA
1136891 TATCGAT-ACCCATACTATGG
1 TATCGATCA-CCATACTATGG
1136911 TATCGATCTACCATACTATGG
1 TATCGATC-ACCATACTATGG
1136932 TA
1 TA
1136934 CCGCTACTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 13 0.62
22 1 0.05
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCGATCACCATACTATGG
Found at i:1139073 original size:21 final size:21
Alignment explanation
Indices: 1139044--1139083 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1139034 TCTTTTTACA
*
1139044 CTAATCCCTAAACATTAAACC
1 CTAAGCCCTAAACATTAAACC
*
1139065 CTAAGCCCTAAACCTTAAA
1 CTAAGCCCTAAACATTAAA
1139084 TCTTAACCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.03, T:0.23
Consensus pattern (21 bp):
CTAAGCCCTAAACATTAAACC
Found at i:1140679 original size:13 final size:13
Alignment explanation
Indices: 1140661--1140685 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1140651 TGGAAAGATC
1140661 ATTTTTATAATAA
1 ATTTTTATAATAA
1140674 ATTTTTATAATA
1 ATTTTTATAATA
1140686 TTCGATTTAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTTATAATAA
Found at i:1142518 original size:2 final size:2
Alignment explanation
Indices: 1142506--1142539 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1142496 TCGAAACGCG
*
1142506 CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1142540 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:1142544 original size:2 final size:2
Alignment explanation
Indices: 1142539--1142564 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1142529 ACACACACAC
1142539 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
1142565 TGTAAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1144375 original size:30 final size:30
Alignment explanation
Indices: 1144339--1144435 Score: 133
Period size: 30 Copynumber: 3.2 Consensus size: 30
1144329 TATTAGATAA
1144339 AAATGAATGATACATGCTATGAAATGAATT
1 AAATGAATGATACATGCTATGAAATGAATT
* *
1144369 AAATGAATGATACATGCTATGAAATAAATG
1 AAATGAATGATACATGCTATGAAATGAATT
* * *
1144399 AAGTGAATAAAACATGCTATGAAATGAA-T
1 AAATGAATGATACATGCTATGAAATGAATT
1144428 AAAGTGAA
1 AAA-TGAA
1144436 AGGTAAAGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 56 0.97
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.26
Consensus pattern (30 bp):
AAATGAATGATACATGCTATGAAATGAATT
Found at i:1146373 original size:6 final size:7
Alignment explanation
Indices: 1146353--1146389 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
1146343 CTCATCTATT
1146353 AGAAAAA
1 AGAAAAA
1146360 AGAAAAAA
1 AG-AAAAA
1146368 AGAAAAA
1 AGAAAAA
1146375 AGAAAAA
1 AGAAAAA
1146382 AGAAAAA
1 AGAAAAA
1146389 A
1 A
1146390 TATGCAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:1146373 original size:15 final size:15
Alignment explanation
Indices: 1146353--1146425 Score: 69
Period size: 15 Copynumber: 4.8 Consensus size: 15
1146343 CTCATCTATT
1146353 AGAAAAAAGAAAAAA
1 AGAAAAAAGAAAAAA
1146368 AGAAAAAAG-AAAAA
1 AGAAAAAAGAAAAAA
* **
1146382 AGAAAAAATATGCAAA
1 AGAAAAAAGA-AAAAA
*
1146398 AG-AAAAGGAAAAAGA
1 AGAAAAAAGAAAAA-A
1146413 AGAATAAAAGAAA
1 AGAA-AAAAGAAA
1146426 TTGAATCAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
14 15 0.33
15 17 0.38
16 6 0.13
17 7 0.16
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.04
Consensus pattern (15 bp):
AGAAAAAAGAAAAAA
Found at i:1146381 original size:22 final size:22
Alignment explanation
Indices: 1146353--1146425 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 22
1146343 CTCATCTATT
1146353 AGAAAAAAGAAAAAAAGAAAAA
1 AGAAAAAAGAAAAAAAGAAAAA
*
1146375 AGAAAAAAGAAAAAATATG-CAAA
1 AGAAAAAAGAAAAAA-A-GAAAAA
*
1146398 AG-AAAAGGAAAAAGAAGAATAAA
1 AGAAAAAAGAAAAA-AAGAA-AAA
1146421 AGAAA
1 AGAAA
1146426 TTGAATCAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
21 1 0.02
22 26 0.62
23 12 0.29
24 3 0.07
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.04
Consensus pattern (22 bp):
AGAAAAAAGAAAAAAAGAAAAA
Found at i:1149103 original size:73 final size:73
Alignment explanation
Indices: 1148983--1149646 Score: 1012
Period size: 73 Copynumber: 9.1 Consensus size: 73
1148973 CAACATTTTC
*
1148983 AAAACAAAGATTTGTCTCGCTT-AGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATA
1 AAAAC-AAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATA
1149047 GTTTTTCTT
65 GTTTTTCTT
* * * *
1149056 AAAACAAGATTTGTCTTGCTTGAGACAGTTTCACTCGAAATATAAATTTATCTCACTCGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATAG
1149121 TTTTTCTT
66 TTTTTCTT
* *
1149129 AAAACAAGATTTGTGTCGCTTGAGACAGTTTCACTCGAAATAGAAATTTATCTCACTTGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATAG
1149194 TTTTTCTT
66 TTTTTCTT
*
1149202 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATAG
1149267 TTTTTCTT
66 TTTTTCTT
***** *
1149275 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAA-TTTTTTTTATCTCACTCGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATAG
1149339 TTTTTCTT
66 TTTTTCTT
** ** * *
1149347 TTAACAAGATTTGTCTTACTTTAGACAGTTTCACTCGAAACAGAAATTTATCTAACTTGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATAG
1149412 TTTTTCTT
66 TTTTTCTT
* * *
1149420 AAAACAATATTTGTATCGCTTGAGACAGTTTCACTCGAAACA-AAATTTTATCTCACTTGAGATT
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAA-TTTATCTCACTTGAGATA
1149484 GTTTTTCTT
65 GTTTTTCTT
* * **
1149493 AAAACAAGATTTGTCTCGCTTGAGATAGTTTCACTCGAAACAGAAATTTATCTCACTTGATATTT
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATAG
1149558 TTTTTCTT
66 TTTTTCTT
** *
1149566 AAAACAAGAGATGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATTG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATAG
1149631 TTTTTCTT
66 TTTTTCTT
1149639 -AAACAAGA
1 AAAACAAGA
1149647 GATTGTTTTT
Statistics
Matches: 541, Mismatches: 46, Indels: 9
0.91 0.08 0.02
Matches are distributed among these distances:
72 88 0.16
73 450 0.83
74 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (73 bp):
AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATAG
TTTTTCTT
Found at i:1149513 original size:291 final size:292
Alignment explanation
Indices: 1148983--1149646 Score: 1048
Period size: 291 Copynumber: 2.3 Consensus size: 292
1148973 CAACATTTTC
1148983 AAAACAAAGATTTGTCTCGCTT-AGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATA
1 AAAAC-AAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATA
* * * *
1149047 GTTTTTCTTAAAACAAGATTTGTCTTGCTTGAGACAGTTTCACTCGAAATATAAATTTATCTCAC
65 GTTTTTCTTAAAACAAGATTTGTCTTACTTGAGACAGTTTCACTCGAAACAGAAATTTATCTAAC
* *
1149112 TCGAGATAGTTTTTCTTAAAACAAGATTTGTGTCGCTTGAGACAGTTTCACTCGAAATAGAAATT
130 TCGAGATAGTTTTTCTTAAAACAAGATTTGTATCGCTTGAGACAGTTTCACTCGAAACAGAAATT
1149177 TATCTCACTTGAGATAGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAA
195 TATCTCACTTGAGATAGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAA
1149242 CAGAAATTTATCTCACTCGAGATAGTTTTTCTT
260 CAGAAATTTATCTCACTCGAGATAGTTTTTCTT
*****
1149275 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAA-TTTTTTTTATCTCACTCGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
** *
1149339 TTTTTCTTTTAACAAGATTTGTCTTACTTTAGACAGTTTCACTCGAAACAGAAATTTATCTAACT
66 TTTTTCTTAAAACAAGATTTGTCTTACTTGAGACAGTTTCACTCGAAACAGAAATTTATCTAACT
* *
1149404 TGAGATAGTTTTTCTTAAAACAATATTTGTATCGCTTGAGACAGTTTCACTCGAAACA-AAATTT
131 CGAGATAGTTTTTCTTAAAACAAGATTTGTATCGCTTGAGACAGTTTCACTCGAAACAGAAA-TT
* *
1149468 TATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGATAGTTTCACTCGAAA
195 TATCTCACTTGAGATAGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAA
* * **
1149533 CAGAAATTTATCTCACTTGATATTTTTTTTCTT
260 CAGAAATTTATCTCACTCGAGATAGTTTTTCTT
** * *
1149566 AAAACAAGAGATGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTTGAGATTG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
1149631 TTTTTCTT-AAACAAGA
66 TTTTTCTTAAAACAAGA
1149647 GATTGTTTTT
Statistics
Matches: 337, Mismatches: 32, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
290 3 0.01
291 286 0.85
292 48 0.14
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (292 bp):
AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
TTTTTCTTAAAACAAGATTTGTCTTACTTGAGACAGTTTCACTCGAAACAGAAATTTATCTAACT
CGAGATAGTTTTTCTTAAAACAAGATTTGTATCGCTTGAGACAGTTTCACTCGAAACAGAAATTT
ATCTCACTTGAGATAGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAAC
AGAAATTTATCTCACTCGAGATAGTTTTTCTT
Found at i:1149672 original size:20 final size:21
Alignment explanation
Indices: 1149624--1149667 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1149614 TATCTCACTT
1149624 GAGATTGTTTTTCTTAAACAA
1 GAGATTGTTTTTCTTAAACAA
1149645 GAGATTGTTTTTCTTAAACAA
1 GAGATTGTTTTTCTTAAACAA
1149666 GA
1 GA
1149668 TTTGTCTCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (21 bp):
GAGATTGTTTTTCTTAAACAA
Found at i:1149691 original size:93 final size:95
Alignment explanation
Indices: 1149558--1149744 Score: 236
Period size: 93 Copynumber: 2.0 Consensus size: 95
1149548 CTTGATATTT
*
1149558 TTTTTCTTAAAACAAGAGATGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAA-TTTATCTCAC
1 TTTTTCTTAAAACAAGAGATGTCTCGCTTGAGACAATTTCACTCGAAACAGAAATTTTATCTCAC
* * *
1149622 TTGAGATTGTTTTTCTTAAA-CAAGAGATTG
66 TCGAGATAGTTTTTCTCAAAGCAA-AGATTG
** * * ** * *
1149652 TTTTTCTT-AAACAAGATTTGTCTCGCTTGAGATAATTTCACTCGCAGTAGAAATTTTATTTCGC
1 TTTTTCTTAAAACAAGAGATGTCTCGCTTGAGACAATTTCACTCGAAACAGAAATTTTATCTCAC
1149716 TCGAGATAGTTTTTCTCAAAGCAAAGATT
66 TCGAGATAGTTTTTCTCAAAGCAAAGATT
1149745 TGTCTCGCTT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
93 38 0.48
94 38 0.48
95 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (95 bp):
TTTTTCTTAAAACAAGAGATGTCTCGCTTGAGACAATTTCACTCGAAACAGAAATTTTATCTCAC
TCGAGATAGTTTTTCTCAAAGCAAAGATTG
Found at i:1150413 original size:139 final size:137
Alignment explanation
Indices: 1150160--1150473 Score: 411
Period size: 139 Copynumber: 2.3 Consensus size: 137
1150150 AGATCAGTAG
* * * *
1150160 CAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGATAAGAAGTTCATAA
1 CAACATTTCCAATGGAGAATTCATAATGAGAAGAACTCATCCAATGAGGGAAAAGAAGTTCATAA
* * *
1150225 TGAAAAGAACTTGTTCAACCTTAGTTCGATTCATCGCATATGGAGTTGAATCAACGACACCTAAC
66 TGAAAAGAACTTGTTAAACCTTAGTTCGATTCATCACATATGGAGTTGAATC-A-GAAACCTAAC
*
1150290 TCGAGGGAT
129 TCGAGGCAT
* * * *
1150299 CACCATTTCCATTGGAGAATTCATAATGAGAAGAACTCATCCGATGGGGGAAAAGAAGTTCATAA
1 CAACATTTCCAATGGAGAATTCATAATGAGAAGAACTCATCCAATGAGGGAAAAGAAGTTCATAA
*
1150364 T-AAGAAGAACTTGTTAAACCTTA-TCTCGATTCATCACATATGGAGTTGAATCAGAAACCTCAC
66 TGAA-AAGAACTTGTTAAACCTTAGT-TCGATTCATCACATATGGAGTTGAATCAGAAACCTAAC
1150427 TCGAGGCAT
129 TCGAGGCAT
*
1150436 CAACA-TTCTCAAAGGA-ATAGTTCATAATGAGAAGAACT
1 CAACATTTC-CAATGGAGA-A-TTCATAATGAGAAGAACT
1150474 TGTTCAACCT
Statistics
Matches: 155, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
136 4 0.03
137 26 0.17
138 22 0.14
139 103 0.66
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (137 bp):
CAACATTTCCAATGGAGAATTCATAATGAGAAGAACTCATCCAATGAGGGAAAAGAAGTTCATAA
TGAAAAGAACTTGTTAAACCTTAGTTCGATTCATCACATATGGAGTTGAATCAGAAACCTAACTC
GAGGCAT
Found at i:1151919 original size:33 final size:33
Alignment explanation
Indices: 1151854--1151933 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 33
1151844 ATTTTGGGCA
1151854 TTATATTTTGATATCTATTATTTTAGTTCTTTACT
1 TTATATTTT-A-ATCTATTATTTTAGTTCTTTACT
*
1151889 TTATATTTTAATCTTTTATTTTA-TTCCTTTACT
1 TTATATTTTAATCTATTATTTTAGTT-CTTTACT
1151922 TTATATTTTAAT
1 TTATATTTTAAT
1151934 TTATGTCATT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
32 2 0.05
33 31 0.72
34 1 0.02
35 9 0.21
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.65
Consensus pattern (33 bp):
TTATATTTTAATCTATTATTTTAGTTCTTTACT
Found at i:1151935 original size:26 final size:25
Alignment explanation
Indices: 1151902--1151960 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
1151892 TATTTTAATC
*
1151902 TTTTATTTTAT-TCCTTTACTTTATA
1 TTTTA-TTTATGTCATTTACTTTATA
*
1151927 TTTTAATTTATGTCATTTACTTTTTA
1 TTTT-ATTTATGTCATTTACTTTATA
1151953 -TTTATTTA
1 TTTTATTTA
1151961 ATTTCATCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 5 0.17
25 12 0.40
26 13 0.43
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (25 bp):
TTTTATTTATGTCATTTACTTTATA
Found at i:1153650 original size:33 final size:28
Alignment explanation
Indices: 1153583--1153650 Score: 73
Period size: 33 Copynumber: 2.2 Consensus size: 28
1153573 GTTAGAATCT
1153583 TTAATTTAAATTAAATATTTTTTCTCGA
1 TTAATTTAAATTAAATATTTTTTCTCGA
* *
1153611 TAAATTTAAATATAAGAATATTTTTTATCTTGA
1 TTAATTTAAAT-T-A-AATA-TTTTT-TCTCGA
1153644 TTAATTT
1 TTAATTT
1153651 TAAAAATGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 10 0.31
29 1 0.03
30 1 0.03
31 4 0.12
32 5 0.16
33 11 0.34
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (28 bp):
TTAATTTAAATTAAATATTTTTTCTCGA
Found at i:1156110 original size:30 final size:30
Alignment explanation
Indices: 1156074--1156130 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1156064 CAACCCTCTC
* * *
1156074 CGGTAATTTTCCCGATATATCACCGGTGAT
1 CGGTAATATTACCGATATAACACCGGTGAT
*
1156104 CGGTAATATTACCGATCTAACACCGGT
1 CGGTAATATTACCGATATAACACCGGT
1156131 CAGACTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (30 bp):
CGGTAATATTACCGATATAACACCGGTGAT
Found at i:1156293 original size:50 final size:51
Alignment explanation
Indices: 1156168--1156296 Score: 134
Period size: 52 Copynumber: 2.5 Consensus size: 51
1156158 TTAGAAGTAA
* * * ** * *
1156168 AGCGCGCCCCCTGCACCACGTTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCCTGCAACGCGCTATACGATGAGCTGGCGCCACATGAGGTAT
* * *
1156219 AGCGCCCCCCCCTGCAATGCGCTATACGGTGAGCTGGCGCCACAT-AGGTAT
1 AGCG-CGCCCCCTGCAACGCGCTATACGATGAGCTGGCGCCACATGAGGTAT
* *
1156270 AGCGCGGCCCCTGCAGCGCGCTATACG
1 AGCGCGCCCCCTGCAACGCGCTATACG
1156297 CCACGTAGGG
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
50 19 0.30
51 13 0.21
52 31 0.49
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (51 bp):
AGCGCGCCCCCTGCAACGCGCTATACGATGAGCTGGCGCCACATGAGGTAT
Found at i:1156425 original size:51 final size:49
Alignment explanation
Indices: 1156308--1156430 Score: 185
Period size: 49 Copynumber: 2.5 Consensus size: 49
1156298 CACGTAGGGG
**
1156308 TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCTAATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCCTAATAATTTTA
*
1156357 TATAGCGCGGGGTAGGTACCGCGAC-ATACCTTTACTCCTGATATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCG-CTATACCTTTACTCCT-A-ATAATTTTA
1156408 TATAGCGCGGGGCAGGTACCGCG
1 TATAGCGCGGGGCAGGTACCGCG
1156431 TTTTGTATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
49 34 0.51
50 2 0.03
51 31 0.46
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (49 bp):
TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCCTAATAATTTTA
Found at i:1162258 original size:110 final size:111
Alignment explanation
Indices: 1162064--1162284 Score: 363
Period size: 110 Copynumber: 2.0 Consensus size: 111
1162054 ATTACAAAAA
* * * *
1162064 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
1162129 AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTAGAGATAT
*
1162175 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
* *
1162239 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTAGAGATAT
1162285 ATGATTTCCA
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 69 0.68
111 33 0.32
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTAGAGATAT
Found at i:1162422 original size:12 final size:10
Alignment explanation
Indices: 1162408--1162448 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1162398 ACCTTAAAAA
*
1162408 GAGAGTATTT
1 GAGAGAATTT
1162418 GAGAGAAATTT
1 GAGAG-AATTT
1162429 -AGAGAATTT
1 GAGAGAATTT
1162438 GAGAGAATTT
1 GAGAGAATTT
1162448 G
1 G
1162449 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1162626 original size:50 final size:51
Alignment explanation
Indices: 1162572--1162679 Score: 119
Period size: 51 Copynumber: 2.1 Consensus size: 51
1162562 TAGCGCACTT
* **
1162572 CAGGGGCCACGATATA-CCCACGTGGTGCCAGCTCACCGTATAGCGCGGTA
1 CAGGGGCCACGATATACCCCACGTGGCGCCAAATCACCGTATAGCGCGGTA
* * * * * * *
1162622 CAGGGGGCGCGCTATACCCCACGTGGCGCTAAATTATCGTATAGCGCGGTG
1 CAGGGGCCACGATATACCCCACGTGGCGCCAAATCACCGTATAGCGCGGTA
1162673 CAGGGGC
1 CAGGGGC
1162680 GCGCTTTACT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
50 13 0.28
51 33 0.72
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (51 bp):
CAGGGGCCACGATATACCCCACGTGGCGCCAAATCACCGTATAGCGCGGTA
Found at i:1174468 original size:117 final size:118
Alignment explanation
Indices: 1174248--1174469 Score: 254
Period size: 117 Copynumber: 1.9 Consensus size: 118
1174238 CTTTCAAATC
* * *
1174248 AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGAGTT
1 AAAATTTTCTTTTTCAATACTTTCAAATTTCAGTTTTGAAAGCTCTAAATCATTCTTCAACAGTT
* *
1174313 TATTTTGATTTTCAAAATCCATTTTTGTTTCTAGAAGAAGTTTGTTTAATTTG
66 TATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * * *
1174366 AAAA-TTTCTTTTTCAA-AGTTTTCATATTTTAGTTTTGAAAGCTCTAACTCATTTTTCAACA-T
1 AAAATTTTCTTTTTCAATA-CTTTCAAATTTCAGTTTTGAAAGCTCTAAATCATTCTTCAACAGT
* * * **
1174428 TTCATTTTGTTTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
65 TT-ATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
1174470 ATCATTTTTA
Statistics
Matches: 86, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
116 4 0.05
117 74 0.86
118 8 0.09
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (118 bp):
AAAATTTTCTTTTTCAATACTTTCAAATTTCAGTTTTGAAAGCTCTAAATCATTCTTCAACAGTT
TATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:1175931 original size:65 final size:65
Alignment explanation
Indices: 1175791--1175950 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
1175781 TGCACTAAGA
* *
1175791 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGACGCATGGCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCAGAGTGCATCGACGCATGGCTT
* * *
1175855 GTGTATCGATGCATAAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCAGAGTGCATCGACGCATGGCT
1175918 AT
65 -T
*
1175920 GTGCATTGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
1175951 CAATTTATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 28 0.33
65 55 0.64
66 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCAGAGTGCATCGACGCATGGCTT
Found at i:1175989 original size:65 final size:64
Alignment explanation
Indices: 1175791--1175998 Score: 196
Period size: 65 Copynumber: 3.2 Consensus size: 64
1175781 TGCACTAAGA
* * * *
1175791 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA--AATAGCCA-GAGTGCATCGACGCATGGC
1 GTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATA-CAATGAGTGCATCGATGCATGG-
1175853 TT
63 TT
* * *
1175855 GTGTATCGATGCATAAAATGCATTCGATGTT---TTCATAAAACCCTGAGTGCATCGATGCATGG
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTTATACAA---TGAGTGCATCGATGCATGG
1175917 TAT
63 T-T
* *
1175920 GTGCATTGATGCATAAAATGCATTCGATGTTCAATTTATTCAATG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTTATACAATGAGTGCATCGATGCATGG-TT
*
1175984 GGTGCATCGGTGCAT
1 -GTGCATCGATGCAT
1175999 CACTTTGAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
61 1 0.01
62 3 0.03
63 2 0.02
64 45 0.38
65 62 0.52
68 6 0.05
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTCAATTTATACAATGAGTGCATCGATGCATGGTT
Found at i:1177357 original size:59 final size:57
Alignment explanation
Indices: 1177294--1177410 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 57
1177284 CATCTCTTCG
* *
1177294 AGAAAATTTTCCAAAACAAGTAGTAGTTTCACAAAACTATACAAAACAAAATCTTCACA
1 AGAAAATGTTCCAAAACAAGTAGTAGTTTAACAAAACTATA-AAAA-AAAATCTTCACA
* * * *
1177353 AGAAAATGTTCCAAAACAAGTAGTGGTTTAACAACACTCTAATAAAAAATCTTCACA
1 AGAAAATGTTCCAAAACAAGTAGTAGTTTAACAAAACTATAAAAAAAAATCTTCACA
1177410 A
1 A
1177411 TATTTTACAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 13 0.25
58 3 0.06
59 36 0.69
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (57 bp):
AGAAAATGTTCCAAAACAAGTAGTAGTTTAACAAAACTATAAAAAAAAATCTTCACA
Found at i:1180138 original size:2 final size:2
Alignment explanation
Indices: 1180131--1180204 Score: 102
Period size: 2 Copynumber: 39.0 Consensus size: 2
1180121 GTTAAAATAC
* *
1180131 AT AT AT AT AT AT AT AT AT -T CT A- AA AT AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1180169 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
1180205 TAAAACCATA
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
1 4 0.06
2 62 0.94
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1180963 original size:43 final size:44
Alignment explanation
Indices: 1180862--1181019 Score: 178
Period size: 43 Copynumber: 3.6 Consensus size: 44
1180852 CGCTACTGAG
* * * *
1180862 TTAAGCCAAGTGAAATGATTCTTTAGACGACTCTCATTCGCGGGT
1 TTAAGCCAAGTGAAATGATTCTTTAGATGACT-TCCTTCACAGGT
* * * *
1180907 TTAAGCCAGGTG-AAGGATTCTTTGGATGGCTTCCTTCACAGGT
1 TTAAGCCAAGTGAAATGATTCTTTAGATGACTTCCTTCACAGGT
* * *
1180950 TTAAGCCAAGTGAAATG-TT-TTCAGATGACTTCCTTTCTCTGGT
1 TTAAGCCAAGTGAAATGATTCTTTAGATGACTTCC-TTCACAGGT
1180993 TTAAGCCAAGTGAAATGATTCTTTAGA
1 TTAAGCCAAGTGAAATGATTCTTTAGA
1181020 CGAATTACCT
Statistics
Matches: 93, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
42 11 0.12
43 46 0.49
44 20 0.22
45 16 0.17
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (44 bp):
TTAAGCCAAGTGAAATGATTCTTTAGATGACTTCCTTCACAGGT
Found at i:1187342 original size:17 final size:17
Alignment explanation
Indices: 1187309--1187351 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1187299 AGAGGAGAAG
1187309 AAAGAAAGAGAAGGAATA
1 AAAG-AAGAGAAGGAATA
*
1187327 AAAGAAGATGAA-GAATG
1 AAAGAAGA-GAAGGAATA
1187344 AAAGAAGA
1 AAAGAAGA
1187352 AACATTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (17 bp):
AAAGAAGAGAAGGAATA
Found at i:1187440 original size:69 final size:71
Alignment explanation
Indices: 1187358--1187498 Score: 214
Period size: 73 Copynumber: 2.0 Consensus size: 71
1187348 AAGAAACATT
* *
1187358 TTGCTCTTCCATAAACCCCACGTCTAT-AAG-AAGAATCCCCACAAATTAACCATGCTTTTCCCA
1 TTGCTCTTCCATAAACCCCACGTCTATAAAGAAAGAATCCCCAAAAATCAACCATGCTTTTCCCA
1187421 AATGGG
66 AATGGG
* *
1187427 TTGCTCTTCCATAAACCCCATGTCTATAAGAAGAAAGAATCCCCAAAAATCAGCCATGCTTTTCC
1 TTGCTCTTCCATAAACCCCACGTCTAT-A-AAGAAAGAATCCCCAAAAATCAACCATGCTTTTCC
1187492 CAAATGG
64 CAAATGG
1187499 ATAAATCGCA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
69 26 0.41
72 3 0.05
73 35 0.55
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (71 bp):
TTGCTCTTCCATAAACCCCACGTCTATAAAGAAAGAATCCCCAAAAATCAACCATGCTTTTCCCA
AATGGG
Found at i:1189704 original size:2 final size:2
Alignment explanation
Indices: 1189697--1189726 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1189687 CATTCTTCAA
1189697 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
1189727 TAAATATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1190845 original size:58 final size:58
Alignment explanation
Indices: 1190752--1190869 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
1190742 TTTTAATCTC
*
1190752 AATCATTTCCTTATAGTTTATTCTTTGTTAGACCTTTATTAATAATTTCTAGCACCTT
1 AATCATTTCCTTATAGTTTATTCTTTGTTACACCTTTATTAATAATTTCTAGCACCTT
1190810 AATCATTTCCTTATAGTTTATTCTTTGTTACACCTTTATTAATAATTTCTAGCACCTT
1 AATCATTTCCTTATAGTTTATTCTTTGTTACACCTTTATTAATAATTTCTAGCACCTT
1190868 AA
1 AA
1190870 CTTACCAATC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (58 bp):
AATCATTTCCTTATAGTTTATTCTTTGTTACACCTTTATTAATAATTTCTAGCACCTT
Found at i:1191771 original size:22 final size:21
Alignment explanation
Indices: 1191743--1191863 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 21
1191733 ATGAATTTCT
*
1191743 TTAGCACTGGTACGAAAGTGCA
1 TTAGCACTGATAC-AAAGTGCA
*
1191765 TTAGCACTAATACATAAGTGCA
1 TTAGCACTGATACA-AAGTGCA
*
1191787 TTAGCATTGATACGGAAA-TGCA
1 TTAGCACTGATAC--AAAGTGCA
* * *
1191809 TCAACATTGATACAGAAGTGCA
1 TTAGCACTGATACA-AAGTGCA
* * *
1191831 TTATCACTGATACTAAATTGCC
1 TTAGCACTGATAC-AAAGTGCA
*
1191853 TTAGCATTGAT
1 TTAGCACTGAT
1191864 CGAAATATAT
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 72 0.90
23 3 0.04
24 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (21 bp):
TTAGCACTGATACAAAGTGCA
Found at i:1193990 original size:17 final size:19
Alignment explanation
Indices: 1193955--1193994 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
1193945 GAAGAAATAA
1193955 AGAGAATGAAGAAGAAAGG
1 AGAGAATGAAGAAGAAAGG
1193974 AGAGAATATGAAGAAGGAAAG
1 AGAG-A-ATGAAGAA-GAAAG
1193995 AAGAACCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 1 0.06
21 8 0.44
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.07
Consensus pattern (19 bp):
AGAGAATGAAGAAGAAAGG
Found at i:1196024 original size:20 final size:21
Alignment explanation
Indices: 1196001--1196040 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1195991 TTTATCATTA
1196001 TTTAAATTTTT-AAATTAAAT
1 TTTAAATTTTTAAAATTAAAT
*
1196021 TTTATATTTTTAAAATTAAA
1 TTTAAATTTTTAAAATTAAA
1196041 CTATTTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAATTTTTAAAATTAAAT
Found at i:1196298 original size:2 final size:2
Alignment explanation
Indices: 1196293--1196328 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1196283 AATACCACAT
1196293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1196329 ATGTTATAAG
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):
TA
Found at i:1196561 original size:33 final size:33
Alignment explanation
Indices: 1196519--1196584 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1196509 TCCGATTTGC
1196519 CCAAATGCCATCTTCAGTTCAATATATTTTCTA
1 CCAAATGCCATCTTCAGTTCAATATATTTTCTA
*
1196552 CCAAATGCCATCTTCAGTTTAATATATTTTCTA
1 CCAAATGCCATCTTCAGTTCAATATATTTTCTA
1196585 TTTAAAATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (33 bp):
CCAAATGCCATCTTCAGTTCAATATATTTTCTA
Found at i:1197176 original size:29 final size:29
Alignment explanation
Indices: 1197134--1197189 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1197124 CTATGCACCG
1197134 GATAATTTTATGCAGGGATGGACAAAGCA
1 GATAATTTTATGCAGGGATGGACAAAGCA
* *
1197163 GATAATTTTATGCAGTGATGGATAAAG
1 GATAATTTTATGCAGGGATGGACAAAG
1197190 GAAACGGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (29 bp):
GATAATTTTATGCAGGGATGGACAAAGCA
Found at i:1199679 original size:12 final size:13
Alignment explanation
Indices: 1199662--1199706 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 13
1199652 ATGATTAATG
1199662 GAAATAAA-AAAT
1 GAAATAAAGAAAT
1199674 GAAATAAAGAAAT
1 GAAATAAAGAAAT
*
1199687 GAAAGAATAAGAAAT
1 GAAA-TA-AAGAAAT
1199702 GAAAT
1 GAAAT
1199707 GGATAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 8 0.29
13 8 0.29
14 1 0.04
15 11 0.39
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:1200277 original size:19 final size:21
Alignment explanation
Indices: 1200234--1200285 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1200224 GAAACCCCTT
1200234 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
1200255 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
1200274 TGAAGATACATG
1 TGAAAATACATG
1200286 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:1202481 original size:36 final size:36
Alignment explanation
Indices: 1202440--1202508 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1202430 CTTCAAAATG
*
1202440 CTTTTCTTCATTTGAATTTTCCTCTAAACGTTCAAA
1 CTTTTCTTCATTTGAATTTTCCTCCAAACGTTCAAA
*
1202476 CTTTTCTTCATTTGAATTTTCCTCCAAATGTTC
1 CTTTTCTTCATTTGAATTTTCCTCCAAACGTTC
1202509 TCCTTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.22, C:0.23, G:0.06, T:0.49
Consensus pattern (36 bp):
CTTTTCTTCATTTGAATTTTCCTCCAAACGTTCAAA
Found at i:1203376 original size:19 final size:18
Alignment explanation
Indices: 1203346--1203383 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1203336 AAGGTAATGA
*
1203346 AAATGATGAAAGCAAAGG
1 AAATGATGAAAGAAAAGG
1203364 AAATGATGAAAAGAAAAGG
1 AAATGATG-AAAGAAAAGG
1203383 A
1 A
1203384 TGAAGATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.61, C:0.03, G:0.26, T:0.11
Consensus pattern (18 bp):
AAATGATGAAAGAAAAGG
Found at i:1203812 original size:15 final size:14
Alignment explanation
Indices: 1203775--1203817 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
1203765 TGATTAATGG
1203775 AAATAAGAAATGAA
1 AAATAAGAAATGAA
*
1203789 ATA-AAGAAATGAA
1 AAATAAGAAATGAA
1203802 AGAATAAGAAATGAA
1 A-AATAAGAAATGAA
1203817 A
1 A
1203818 TGGATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 11 0.44
14 3 0.12
15 11 0.44
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (14 bp):
AAATAAGAAATGAA
Found at i:1205541 original size:24 final size:24
Alignment explanation
Indices: 1205514--1205585 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
1205504 AAACGGAGAT
*
1205514 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
1205538 ATCATATATTAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
1205562 ATCAGAAACCAGAACAAAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
1205586 GAAATGTATC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1208057 original size:18 final size:18
Alignment explanation
Indices: 1208036--1208073 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1208026 GGTCAACGGA
* *
1208036 TCGGGTCAATGGGTCGGG
1 TCGGGTCAACGGGTCAGG
1208054 TCGGGTCAACGGGTCAGG
1 TCGGGTCAACGGGTCAGG
1208072 TC
1 TC
1208074 TGGTTGTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.21, G:0.45, T:0.21
Consensus pattern (18 bp):
TCGGGTCAACGGGTCAGG
Found at i:1208073 original size:13 final size:13
Alignment explanation
Indices: 1208013--1208055 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
1208003 GCCGGTCAAC
1208013 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1208026 GGTCAACGGATCG
1 GGTCAACGGGTCG
*
1208039 GGTCAATGGGTCG
1 GGTCAACGGGTCG
1208052 GGTC
1 GGTC
1208056 GGGTCAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1212043 original size:122 final size:122
Alignment explanation
Indices: 1211817--1212135 Score: 365
Period size: 122 Copynumber: 2.6 Consensus size: 122
1211807 TTATATTTTG
* * * * * * *
1211817 AGATAAATTATTTGTTGAATATGACAATGATCCTTCTCATTGAGAAAATCGGGTCAATCTGGAAA
1 AGATGAATTATTTGTTGAAGATGACGATGATCTTTCTCGTTGAGGAAATCGGGTCAATCTAGAAA
* * * *
1211882 TAATTTTGTGTTGAAGACGGCTCTTCTCATCCGTGTTGAAGAGATCTGG-TCACTTTC
66 TAATTTGGTGTTGAAGACGACTCTGCTCATCCATGTTGAAGAGATCTGGTTCA-TTTC
* ** *
1211939 AGATGAATTATTTGTTGAAGATGACGCTCCTCTTTCTCGTTGAGGAAATTGGGTCAATCTAGAAA
1 AGATGAATTATTTGTTGAAGATGACGATGATCTTTCTCGTTGAGGAAATCGGGTCAATCTAGAAA
* ** * *
1212004 TAATTTGGTGTTGAAGACGACTCTGCTTATTTATTTTGAAGAGATCTGGTTGATTTC
66 TAATTTGGTGTTGAAGACGACTCTGCTCATCCATGTTGAAGAGATCTGGTTCATTTC
* * * *
1212061 AGATGAATTGA-TTGTTGAAGATGATGATGTTCCTTTGT-GTTGAGGAAATCGGGTAAATCTAGA
1 AGATGAATT-ATTTGTTGAAGATGACGATGAT-CTTTCTCGTTGAGGAAATCGGGTCAATCTAGA
*
1212124 GATAATTTGGTG
64 AATAATTTGGTG
1212136 ACAACACAAT
Statistics
Matches: 166, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
122 158 0.95
123 8 0.05
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.37
Consensus pattern (122 bp):
AGATGAATTATTTGTTGAAGATGACGATGATCTTTCTCGTTGAGGAAATCGGGTCAATCTAGAAA
TAATTTGGTGTTGAAGACGACTCTGCTCATCCATGTTGAAGAGATCTGGTTCATTTC
Found at i:1212666 original size:220 final size:220
Alignment explanation
Indices: 1211976--1212864 Score: 1004
Period size: 220 Copynumber: 4.1 Consensus size: 220
1211966 TCCTCTTTCT
* ** * * * * * * *** *
1211976 CGTTGAGGAAATTGGGTCAATCTAGAAATAATTTGGTGTTGAAGACGACTCTGCTTATTTATTTT
1 CGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTGAAAATGACACTGCTCATCCGTGTT
* * * * * * *
1212041 GAAGAGATCTGGTTGA-TTTCAGATGAATTGATTGTTGAAGATGATGATGTTCCTT-TGTGTTGA
66 GAAGAGATATGG-TCATTTTCAGGTAAATTGTTTGCTGAAGATGACGATGTTCCTTCT-TGTTGA
* * * * *
1212104 GGAAATCGGGTAAATCTAGAGATAATTTGGTGACAACACAATCCCTTCACGTTGAGGAAGTCTGA
129 GGAAATCGGGTCAATCTAGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGA
*
1212169 TTATCTGAGGATGACACTGCTCCTTCG
194 TTATCTGAGGATGACAATGCTCCTTCG
* * *
1212196 CGTTGAGGAGATCAGGTCAATCTGGAGATAATTTGATGTTGAAAATGACACTACTCATCTGTGTT
1 CGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTGAAAATGACACTGCTCATCCGTGTT
*
1212261 GAAGAGATCTGGTCATTTTCAGGTAAATTGTTTTGCTGAAGATGACG-TCGTTCCTTCTTGTTGA
66 GAAGAGATATGGTCATTTTCAGGTAAATTG-TTTGCTGAAGATGACGAT-GTTCCTTCTTGTTGA
* * * * * * * * * *
1212325 GGAAATTGTGTCAATCT-G-GA-GA--TGGTGGCAAAATGGTTCCTTCGCGTTGAGGAAGTCTGA
129 GGAAATCGGGTCAATCTAGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGA
* * * * *
1212385 TTATATAAGGACGACAATTCTTCTTCG
194 TTATCTGAGGATGACAATGCTCCTTCG
* * * * * * *
1212412 CTTTGAGGAGATCGGGTTAATCTAGAGATAATTTGTTGTTGAGAATGACATTGCTCATCCATGTT
1 CGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTGAAAATGACACTGCTCATCCGTGTT
* *
1212477 GAAGAGATATGGTCATTTTCAAGTAAATTGTTTGCTGGAGATGACGATGTTCCTTCTTGTTGAGG
66 GAAGAGATATGGTCATTTTCAGGTAAATTGTTTGCTGAAGATGACGATGTTCCTTCTTGTTGAGG
* * *
1212542 AAATCGGGTCAATGTAGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGAAAGTCTGTTT
131 AAATCGGGTCAATCTAGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGATT
* *
1212607 ATCTGAGGATGACACTGCTCCTTCA
196 ATCTGAGGATGACAATGCTCCTTCG
* * * *
1212632 TGTTGAGGAGATCAGATCAATCTAGAGATAATTTGATGTTAAAAATGGCACTGCTCATCCGTGTT
1 CGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTGAAAATGACACTGCTCATCCGTGTT
* * ** *
1212697 AAATAGATATGGTTGTTTTCAGGTAAATTTTTTGCTGAAGATGAC-ATTGTTCCTTCTTGTTGAG
66 GAAGAGATATGGTCATTTTCAGGTAAATTGTTTGCTGAAGATGACGA-TGTTCCTTCTTGTTGAG
* * * *
1212761 GAAATTGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGCATTGAGGAAGTCTGAT
130 GAAATCGGGTCAATCTAGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGAT
* *
1212826 TGTCTGAGGATGACAATGCTCATTCG
195 TATCTGAGGATGACAATGCTCCTTCG
1212852 CGTTGAGGAGATC
1 CGTTGAGGAGATC
1212865 TAGTCATAGT
Statistics
Matches: 558, Mismatches: 100, Indels: 22
0.82 0.15 0.03
Matches are distributed among these distances:
215 44 0.08
216 137 0.25
217 2 0.00
218 2 0.00
219 5 0.01
220 327 0.59
221 40 0.07
222 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (220 bp):
CGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTGAAAATGACACTGCTCATCCGTGTT
GAAGAGATATGGTCATTTTCAGGTAAATTGTTTGCTGAAGATGACGATGTTCCTTCTTGTTGAGG
AAATCGGGTCAATCTAGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGATT
ATCTGAGGATGACAATGCTCCTTCG
Found at i:1213198 original size:103 final size:103
Alignment explanation
Indices: 1213027--1213256 Score: 295
Period size: 103 Copynumber: 2.3 Consensus size: 103
1213017 GGTGAGATAA
*
1213027 AATTTTGTTTCAAGTGAAA-TATTT-CAAAATTTTAGTTTCAAGGGAAAACTATCTCAAGCGAGA
1 AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTTAGTTTCAAGGGAAAACTATCTCAAGCGAGA
* *
1213090 CGAAATTGGTTTTTAAGAAAATAATCAT-AGGCGAGATC
66 CGAAATTAGTTTTTAAGAAAACAATC-TCAGGCGAGATC
* ** * ** *
1213128 AATTTTGTTTCAAGTTAAACAATTTCCAATTTTTTTGTTTTGAGGGAAAACTATCTCAAGTGAGA
1 AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTTAGTTTCAAGGGAAAACTATCTCAAGCGAGA
* * ** *
1213193 TGAAATTAGTTTTTAGGAAAACAATCTCAGTTGATATC
66 CGAAATTAGTTTTTAAGAAAACAATCTCAGGCGAGATC
1213231 AATTTTGTTTCAAGTGAAACAATTTC
1 AATTTTGTTTCAAGTGAAACAATTTC
1213257 AAACTTTGCA
Statistics
Matches: 110, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
101 18 0.16
102 5 0.05
103 87 0.79
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (103 bp):
AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTTAGTTTCAAGGGAAAACTATCTCAAGCGAGA
CGAAATTAGTTTTTAAGAAAACAATCTCAGGCGAGATC
Found at i:1219521 original size:2 final size:2
Alignment explanation
Indices: 1219514--1219563 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1219504 TCAATAGTTT
1219514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1219556 TA TA -A TA T
1 TA TA TA TA T
1219564 GATCATTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1222284 original size:35 final size:36
Alignment explanation
Indices: 1222238--1222333 Score: 126
Period size: 35 Copynumber: 2.8 Consensus size: 36
1222228 GGCATTCATG
* *
1222238 GAGTATCGATACCTGGAGGGT-AGTATCGATACCAC
1 GAGTATCGATACCTAGAAGGTCAGTATCGATACCAC
* *
1222273 GAGTATCGATA-CTATAAGGTCAGTATTGATACCAC
1 GAGTATCGATACCTAGAAGGTCAGTATCGATACCAC
*
1222308 GAGTATCGATA-CTATAAGGTCAGTAT
1 GAGTATCGATACCTAGAAGGTCAGTAT
1222334 TGATTCCAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
34 6 0.11
35 50 0.89
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (36 bp):
GAGTATCGATACCTAGAAGGTCAGTATCGATACCAC
Found at i:1222303 original size:20 final size:20
Alignment explanation
Indices: 1222274--1222333 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1222264 CGATACCACG
1222274 AGTATCGATACTATAAGGTC
1 AGTATCGATACTATAAGGTC
* * *
1222294 AGTATTGATAC---CACG--
1 AGTATCGATACTATAAGGTC
1222309 AGTATCGATACTATAAGGTC
1 AGTATCGATACTATAAGGTC
1222329 AGTAT
1 AGTAT
1222334 TGATTCCAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
15 10 0.34
17 2 0.07
18 2 0.07
20 15 0.52
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTATAAGGTC
Found at i:1222334 original size:35 final size:35
Alignment explanation
Indices: 1222259--1222337 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
1222249 CCTGGAGGGT
*
1222259 AGTATCGATACCACGAGTATCGATACTATAAGGTC
1 AGTATTGATACCACGAGTATCGATACTATAAGGTC
1222294 AGTATTGATACCACGAGTATCGATACTATAAGGTC
1 AGTATTGATACCACGAGTATCGATACTATAAGGTC
1222329 AGTATTGAT
1 AGTATTGAT
1222338 TCCAATTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (35 bp):
AGTATTGATACCACGAGTATCGATACTATAAGGTC
Found at i:1222581 original size:53 final size:54
Alignment explanation
Indices: 1222460--1222625 Score: 271
Period size: 54 Copynumber: 3.1 Consensus size: 54
1222450 ATCTTTCTTT
* *
1222460 TATCATAAGAAATTAAGGATTGAATTATAATACTTGGAATATATGATTGTGTAGA
1 TATC-TAAGAAATTAAGGATCGAATTATAATACTTGGAATGTATGATTGTGTAGA
*
1222515 TATCTAAGAAATTAATGATCGAATTATAATACTTGGAA-GTATGATTGTGTAGA
1 TATCTAAGAAATTAAGGATCGAATTATAATACTTGGAATGTATGATTGTGTAGA
* *
1222568 TATCTAAGAAATTAAGGATCAAATTATAATGCTTGGAATGTATGATTGTGTAGA
1 TATCTAAGAAATTAAGGATCGAATTATAATACTTGGAATGTATGATTGTGTAGA
1222622 TATC
1 TATC
1222626 GAGCACAAGC
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
53 49 0.47
54 51 0.49
55 4 0.04
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (54 bp):
TATCTAAGAAATTAAGGATCGAATTATAATACTTGGAATGTATGATTGTGTAGA
Found at i:1223133 original size:22 final size:22
Alignment explanation
Indices: 1223105--1223149 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1223095 AGTCGAGGGT
*
1223105 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGAGACATA
1223127 TACATAGGTCCTTCGAGACATA
1 TACATAGGTCCTTCGAGACATA
1223149 T
1 T
1223150 TTCACATGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (22 bp):
TACATAGGTCCTTCGAGACATA
Found at i:1226979 original size:23 final size:23
Alignment explanation
Indices: 1226953--1227001 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
1226943 ATCAACAAAG
*
1226953 AAATTG-AAGCACTCAAAAGAATA
1 AAATTGCAAGAACTCAAAAGAA-A
1226976 AAATTGCAAGAACTCAAAAGAAA
1 AAATTGCAAGAACTCAAAAGAAA
1226999 AAA
1 AAA
1227002 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.14
Consensus pattern (23 bp):
AAATTGCAAGAACTCAAAAGAAA
Found at i:1227006 original size:5 final size:5
Alignment explanation
Indices: 1226998--1227031 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
1226988 CTCAAAAGAA
*
1226998 AAAAG AAAAA AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1227032 TTGAAGCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1231184 original size:25 final size:25
Alignment explanation
Indices: 1231146--1231194 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1231136 ACAAAGTAAG
1231146 TCGTCAGAAGATTACTGACGGAAAT
1 TCGTCAGAAGATTACTGACGGAAAT
* *
1231171 TCGTCAGTATATTACTGACGGAAA
1 TCGTCAGAAGATTACTGACGGAAA
1231195 AATTAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (25 bp):
TCGTCAGAAGATTACTGACGGAAAT
Found at i:1232179 original size:31 final size:31
Alignment explanation
Indices: 1232144--1232204 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1232134 TAGGTGAATC
*
1232144 TGTCAGAAATTTGTGACAGATCCACATATTT
1 TGTCACAAATTTGTGACAGATCCACATATTT
** *
1232175 TGTCACAAATTTGTGATGGGTCCACATATT
1 TGTCACAAATTTGTGACAGATCCACATATT
1232205 CCATCACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (31 bp):
TGTCACAAATTTGTGACAGATCCACATATTT
Found at i:1232212 original size:31 final size:31
Alignment explanation
Indices: 1232150--1232217 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1232140 AATCTGTCAG
***
1232150 AAATTTGTGACAGATCCACATATTTTGTCAC
1 AAATTTGTGACAGATCCACATATTCCATCAC
** *
1232181 AAATTTGTGATGGGTCCACATATTCCATCAC
1 AAATTTGTGACAGATCCACATATTCCATCAC
1232212 AAATTT
1 AAATTT
1232218 AAAAAATTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (31 bp):
AAATTTGTGACAGATCCACATATTCCATCAC
Found at i:1233242 original size:23 final size:23
Alignment explanation
Indices: 1233215--1233260 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1233205 ATTCAACAAA
1233215 ACATCAGATAATATTAAAAAACT
1 ACATCAGATAATATTAAAAAACT
*
1233238 ACATCATATAATATTAAAAAACT
1 ACATCAGATAATATTAAAAAACT
1233261 TGAAGTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
ACATCAGATAATATTAAAAAACT
Done.