Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000886.1 Hibiscus syriacus cultivar Beakdansim tig00001731_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: 974096
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 4 of 4
Found at i:770188 original size:7 final size:7
Alignment explanation
Indices: 770149--770176 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
770139 ATTATCTTAA
770149 TATTATT
1 TATTATT
770156 TATTATT
1 TATTATT
770163 TATTATT
1 TATTATT
770170 TATTATT
1 TATTATT
770177 CATTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTATT
Found at i:771532 original size:6 final size:6
Alignment explanation
Indices: 771516--771550 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
771506 TGAATCGAGT
771516 TTTTAAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
771551 TGCAATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:786895 original size:21 final size:22
Alignment explanation
Indices: 786869--786920 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
786859 AGGGAATTGA
786869 TCCCCCCATG-AGGGAACCGAT
1 TCCCCCCATGAAGGGAACCGAT
** *
786890 TCCCCCTTTGAAAGGGAATCGAT
1 TCCCCCCATG-AAGGGAACCGAT
786913 TCCCCCCA
1 TCCCCCCA
786921 CAGGGGAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 8 0.33
23 16 0.67
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.19
Consensus pattern (22 bp):
TCCCCCCATGAAGGGAACCGAT
Found at i:791145 original size:85 final size:85
Alignment explanation
Indices: 790986--791456 Score: 683
Period size: 85 Copynumber: 5.5 Consensus size: 85
790976 ACAGAGGAAG
* * *
790986 TTTACAACATAGCTCAAGGCGAGAAGGACTATCTGTCAACAAAAAACCTTCGAGTTCGATTACAT
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-GAAAACCTTCGAGTTCGATTACAT
*
791051 TCAGTTCAAGGGCATATCAAA
65 TCAGCTCAAGGGCATATCAAA
** * * *
791072 TTTGTAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAATGAAAACCTTCGATTTCGATTACATT
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAACCTTCGAGTTCGATTACATT
791137 CAGCTCAAGGGCATATCAAA
66 CAGCTCAAGGGCATATCAAA
* *
791157 TTTACAGCATAGCTCAAGGCGAGAAGGTCTATCTGTCAACGAAAACCTTCGAGTTTGATTACATT
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAACCTTCGAGTTCGATTACATT
*
791222 CAGCTCAAGGGCATATCTAA
66 CAGCTCAAGGGCATATCAAA
* * *
791242 TTTACAGCATATCTCAAGGCTAGAAGGGCTATTTGTCAACGAAAACCTTCGAGTTCGATTACATT
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAACCTTCGAGTTCGATTACATT
*
791307 AAGCTCAAGGGCATATCAAA
66 CAGCTCAAGGGCATATCAAA
* ** * * *
791327 TTTACAACATAGCTCAAGGTAAGAAGGGCTATATGTCAAC-AAAGACCTTTGAGTTCGATTCCAT
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAA-ACCTTCGAGTTCGATTACAT
791391 TCAGCTCAAGGGCATATCAAA
65 TCAGCTCAAGGGCATATCAAA
* * * *
791412 TTTACAACATAGCTCTAGACGAGAAGGGCTATCTGTCAACAAAAA
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAA
791457 ACTGTCAAGT
Statistics
Matches: 346, Mismatches: 37, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
84 3 0.01
85 306 0.88
86 37 0.11
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (85 bp):
TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAACCTTCGAGTTCGATTACATT
CAGCTCAAGGGCATATCAAA
Found at i:792339 original size:35 final size:37
Alignment explanation
Indices: 792110--792360 Score: 264
Period size: 38 Copynumber: 6.8 Consensus size: 37
792100 TTAAAATCGA
***
792110 TTTTTGAAAATATATAT--TATATAG-TTTTGAAAACG
1 TTTTTGAAAATATATATAATATATAGTTTTTG-AATTT
* * * **
792145 GTTTTCAAATATATATATATTATATAG-TTTTGTTTTT
1 TTTTTGAAA-ATATATATAATATATAGTTTTTGAATTT
792182 TTTTTGAAAACATATATATAATATATAGTTTTTGAATTTT
1 TTTTTG-AAA-ATATATATAATATATAGTTTTTGAA-TTT
***
792222 TTTTTGAAAATATATATAATATATAGTTTTTGAAAAC
1 TTTTTGAAAATATATATAATATATAGTTTTTGAATTT
*
792259 ATTTTGAAAATATATATAATATATAGTTTTTGAATTT
1 TTTTTGAAAATATATATAATATATAGTTTTTGAATTT
*
792296 TTTTTG-AAA-ATGTAT-ATATATAGTTTTTGAATTTT
1 TTTTTGAAAATATATATAATATATAGTTTTTGAA-TTT
* *
792331 TTTTTGAAAATGTATATAATATGTAGTTTT
1 TTTTTGAAAATATATATAATATATAGTTTT
792361 GAAAATATAT
Statistics
Matches: 181, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
34 16 0.09
35 21 0.12
36 14 0.08
37 46 0.25
38 67 0.37
39 8 0.04
40 9 0.05
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAATTT
Found at i:792380 original size:23 final size:24
Alignment explanation
Indices: 792332--792383 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
792322 TTGAATTTTT
*
792332 TTTTGAAAATGTATATAATATGTAG
1 TTTTGAAAA-GTATATAATATATAG
*
792357 TTTTGAAAA-TATATATTATATAG
1 TTTTGAAAAGTATATAATATATAG
792380 TTTT
1 TTTT
792384 AAAGCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.64
25 9 0.36
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
TTTTGAAAAGTATATAATATATAG
Found at i:792447 original size:39 final size:39
Alignment explanation
Indices: 792365--792465 Score: 132
Period size: 39 Copynumber: 2.6 Consensus size: 39
792355 AGTTTTGAAA
* * * *
792365 ATATATATTATATAGTTTTAAAGCAATTTTTGAATATAT
1 ATATATATTATATAGTTTTAAAACAATTTTTGAAAAAAC
*
792404 ATATATATTATATGATTTTTAAAACAATTTTT-AAAAAAC
1 ATATATATTATAT-AGTTTTAAAACAATTTTTGAAAAAAC
*
792443 ATATATAATATATAGTTTTAAAA
1 ATATATATTATATAGTTTTAAAA
792466 ATGATTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 9 0.17
39 29 0.54
40 16 0.30
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (39 bp):
ATATATATTATATAGTTTTAAAACAATTTTTGAAAAAAC
Found at i:792544 original size:26 final size:26
Alignment explanation
Indices: 792492--792544 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
792482 TATATTAATA
*
792492 TTTTTTTAATTTTCTAATTTTTATTT
1 TTTTTTTAATTTTCTAATTTTCATTT
* * * *
792518 TTTTTTTTATTTTTTCATTTTCGTTT
1 TTTTTTTAATTTTCTAATTTTCATTT
792544 T
1 T
792545 AGGTCCAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (26 bp):
TTTTTTTAATTTTCTAATTTTCATTT
Found at i:794940 original size:26 final size:27
Alignment explanation
Indices: 794888--794943 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
794878 ATTTATGAAA
* *
794888 TTATGAGTCGAGTCAAAAAATTAAATT
1 TTATGAATCGAGACAAAAAATTAAATT
* *
794915 TTATGAATCGAGACAAAAATTTAATTT
1 TTATGAATCGAGACAAAAAATTAAATT
794942 TT
1 TT
794944 CAAATCGAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (27 bp):
TTATGAATCGAGACAAAAAATTAAATT
Found at i:794949 original size:26 final size:26
Alignment explanation
Indices: 794903--794952 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
794893 AGTCGAGTCA
*
794903 AAAAATTAAATTTTATGAATCGAGAC
1 AAAAATTAAATTTTATAAATCGAGAC
*
794929 AAAAATTTAATTTT-TCAAATCGAG
1 AAAAATTAAATTTTAT-AAATCGAG
794953 TATCAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (26 bp):
AAAAATTAAATTTTATAAATCGAGAC
Found at i:801921 original size:27 final size:28
Alignment explanation
Indices: 801891--801944 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
801881 TATAATATAT
801891 TCATTTTACACTTCAAGGGT-ATTTTGG
1 TCATTTTACACTTCAAGGGTAATTTTGG
*
801918 TCATTTTACATTTCAAGGGTAATTTTG
1 TCATTTTACACTTCAAGGGTAATTTTG
801945 TGTTTTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (28 bp):
TCATTTTACACTTCAAGGGTAATTTTGG
Found at i:802550 original size:19 final size:19
Alignment explanation
Indices: 802526--802566 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
802516 TGGTCAGACC
* *
802526 AGTCAATGGGTCAGGTCAA
1 AGTCAACGGGTCAAGTCAA
802545 AGTCAACGGGTCAAGTCAA
1 AGTCAACGGGTCAAGTCAA
802564 AGT
1 AGT
802567 TAAATTGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (19 bp):
AGTCAACGGGTCAAGTCAA
Found at i:805949 original size:27 final size:27
Alignment explanation
Indices: 805900--805951 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
805890 AATATAGCCA
* *
805900 TTTTACACTTCAAGGGCATTTTTGTCC
1 TTTTACACTTCAAGGGAAATTTTGTCC
*
805927 TTTTACACTTCAGGGGAAATTTTGT
1 TTTTACACTTCAAGGGAAATTTTGT
805952 GTTTACATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.44
Consensus pattern (27 bp):
TTTTACACTTCAAGGGAAATTTTGTCC
Found at i:807467 original size:2 final size:2
Alignment explanation
Indices: 807460--807484 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
807450 AGACACAAAC
807460 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
807485 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:809593 original size:2 final size:2
Alignment explanation
Indices: 809586--809614 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
809576 AATTCGTACA
809586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
809615 AACACATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:810776 original size:29 final size:29
Alignment explanation
Indices: 810721--810778 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
810711 ATTTGTCCTA
* *
810721 TAACTTTTTAAAATTACCAAATAGGTCCC
1 TAACTTTTAAAAATTACAAAATAGGTCCC
*
810750 TAACTTTTAAAAAATTATAAAAT-GGTCCC
1 TAACTTTT-AAAAATTACAAAATAGGTCCC
810779 AATATTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (29 bp):
TAACTTTTAAAAATTACAAAATAGGTCCC
Found at i:821635 original size:18 final size:18
Alignment explanation
Indices: 821605--821654 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 18
821595 GAAAAACATT
821605 ATATTTTTAATTAAAAATA
1 ATATTTTT-ATTAAAAATA
*
821624 ATATTTTTATT---ATTA
1 ATATTTTTATTAAAAATA
821639 ATATTTTT-TTAAAAAT
1 ATATTTTTATTAAAAAT
821655 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
17 2 0.08
18 3 0.12
19 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTTTTATTAAAAATA
Found at i:829731 original size:19 final size:18
Alignment explanation
Indices: 829707--829763 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
829697 CTAGATTTAG
829707 AACTTATTTCCAAATTCAT
1 AACTTATTT-CAAATTCAT
* *
829726 AACTTATTTTTATATTCAT
1 AACTTA-TTTCAAATTCAT
*
829745 ATCTTAATTTCAAATTCAT
1 AACTT-ATTTCAAATTCAT
829764 GACCCATTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 27 0.87
20 4 0.13
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (18 bp):
AACTTATTTCAAATTCAT
Found at i:832517 original size:29 final size:31
Alignment explanation
Indices: 832470--832533 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
832460 ATAATTTTGG
* *
832470 TTAGTGACCAAAATGTAAA-TTTTG-AAAGT
1 TTAGTGACCAAAATATAAAGTTTGGAAAAGT
*
832499 TTAGTGACCAAAGTATAAAGTTTGGAAAAGT
1 TTAGTGACCAAAATATAAAGTTTGGAAAAGT
832530 TTAG
1 TTAG
832534 AGACGAGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 17 0.57
30 4 0.13
31 9 0.30
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (31 bp):
TTAGTGACCAAAATATAAAGTTTGGAAAAGT
Found at i:851858 original size:20 final size:20
Alignment explanation
Indices: 851833--851884 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
851823 TTTTGGTGCA
851833 GAGGGAATCGATACCCTCAT
1 GAGGGAATCGATACCCTCAT
*
851853 GAGGGAACCGATACCCTCAT
1 GAGGGAATCGATACCCTCAT
851873 GAGGGAATCGAT
1 GAGGGAATCGAT
851885 TCCCCCTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (20 bp):
GAGGGAATCGATACCCTCAT
Found at i:851926 original size:19 final size:19
Alignment explanation
Indices: 851875--851937 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
851865 ACCCTCATGA
851875 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCC--T--AG
* *
851898 GGAAACCGATTCCCCCTAG
1 GGGAATCGATTCCCCCTAG
*
851917 GGGAATCGATACCCCCT-G
1 GGGAATCGATTCCCCCTAG
851935 GGG
1 GGG
851938 TTCTGGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.11
19 16 0.46
21 1 0.03
23 14 0.40
ACGTcount: A:0.22, C:0.30, G:0.29, T:0.19
Consensus pattern (19 bp):
GGGAATCGATTCCCCCTAG
Found at i:855576 original size:17 final size:17
Alignment explanation
Indices: 855556--855651 Score: 59
Period size: 17 Copynumber: 5.2 Consensus size: 17
855546 TTATATATAG
855556 TATATAATAATATAAAC
1 TATATAATAATATAAAC
855573 TATATAATTTATATTAATAAAC
1 TATATAA--TA-A-T-ATAAAC
* * * *
855595 TATATAGTTTTATATATAG
1 TATATA--ATAATATAAAC
* *
855614 TTTATATTAATATAAAC
1 TATATAATAATATAAAC
855631 TATATAATAAATATAAA-
1 TATATAAT-AATATAAAC
855648 TATA
1 TATA
855652 AACTATATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
17 25 0.41
18 8 0.13
19 11 0.18
20 2 0.03
21 2 0.03
22 13 0.21
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
TATATAATAATATAAAC
Found at i:855585 original size:24 final size:22
Alignment explanation
Indices: 855549--855600 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
855539 CCAAAGTTTA
*
855549 TATATAGTATATAATAATATAAAC
1 TATATAATATAT-ATAA-ATAAAC
* *
855573 TATATAATTTATATTAATAAAC
1 TATATAATATATATAAATAAAC
855595 TATATA
1 TATATA
855601 GTTTTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.48
23 3 0.12
24 10 0.40
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
TATATAATATATATAAATAAAC
Found at i:855592 original size:22 final size:23
Alignment explanation
Indices: 855567--855609 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
855557 ATATAATAAT
855567 ATAAACTATATA-ATTTATATTA
1 ATAAACTATATAGATTTATATTA
*
855589 ATAAACTATATAGTTTTATAT
1 ATAAACTATATAGATTTATAT
855610 ATAGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAAACTATATAGATTTATATTA
Found at i:855644 original size:24 final size:25
Alignment explanation
Indices: 855616--855693 Score: 95
Period size: 24 Copynumber: 3.0 Consensus size: 25
855606 ATATATAGTT
855616 TATATTAATATAAACTATATAATAA
1 TATATTAATATAAACTATATAATAA
*
855641 -ATATAAATATAAACTATATAATAA
1 TATATTAATATAAACTATATAATAA
*
855665 TTTATATGTTATATAAACTATATATATAA
1 --TATAT-TAATATAAACTATATA-ATAA
855694 CCTATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
24 23 0.51
27 4 0.09
28 14 0.31
29 4 0.09
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (25 bp):
TATATTAATATAAACTATATAATAA
Found at i:855656 original size:60 final size:58
Alignment explanation
Indices: 855545--855660 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
855535 AGGGCCAAAG
** *
855545 TTTATATATAGTATATAATAATATAAACTATATAATTTATATTAATAAACTATATAGT
1 TTTATATATAGTATATAATAATATAAACTATATAATAAATATAAATAAACTATATAGT
* *
855603 TTTATATATAGTTTATATTAATATAAACTATATAATAAATATAAATATAAACTATATA
1 TTTATATATAGTATATAATAATATAAACTATATAATAAATAT-AA-ATAAACTATATA
855661 ATAATTTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 38 0.75
59 1 0.02
60 12 0.24
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (58 bp):
TTTATATATAGTATATAATAATATAAACTATATAATAAATATAAATAAACTATATAGT
Found at i:855664 original size:12 final size:12
Alignment explanation
Indices: 855625--855664 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
855615 TTATATTAAT
855625 ATAAACTATATA
1 ATAAACTATATA
*
855637 ATAAA-TATAAA
1 ATAAACTATATA
855648 TATAAACTATATA
1 -ATAAACTATATA
855661 ATAA
1 ATAA
855665 TTTATATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 5 0.21
12 14 0.58
13 5 0.21
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAAACTATATA
Found at i:855671 original size:60 final size:58
Alignment explanation
Indices: 855546--855680 Score: 157
Period size: 58 Copynumber: 2.3 Consensus size: 58
855536 GGGCCAAAGT
* ** * * *
855546 TTATATATAGTATATAATAATATAAACTATATAATTTATATTAATAAACTATATAGTT
1 TTATATATAGTTTATAATAATATAAACTATATAATAAATATAAATAAACTATATAATA
*
855604 TTATATATAGTTTATATTAATATAAACTATATAATAAATATAAATATAAACTATATAATAA
1 TTATATATAGTTTATAATAATATAAACTATATAATAAATAT-AA-ATAAACTATATAAT-A
855665 TT-TATAT-GTTATATAA
1 TTATATATAGTT-TATAA
855681 ACTATATATA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
58 37 0.57
59 4 0.06
60 22 0.34
61 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (58 bp):
TTATATATAGTTTATAATAATATAAACTATATAATAAATATAAATAAACTATATAATA
Found at i:856786 original size:25 final size:27
Alignment explanation
Indices: 856733--856786 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
856723 AAACTATTCC
* *
856733 TTTGCATTATTAATAATGTTTTATCTAA
1 TTTGCATTATAAATAA-GTTTTATATAA
856761 TTTGCATT-TAAATAA-TTTTATATAA
1 TTTGCATTATAAATAAGTTTTATATAA
856786 T
1 T
856787 AGGTCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
27 6 0.25
28 8 0.33
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (27 bp):
TTTGCATTATAAATAAGTTTTATATAA
Found at i:856981 original size:16 final size:16
Alignment explanation
Indices: 856962--857016 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
856952 CAGATCATTT
*
856962 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
856978 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
* *
856994 ACAAGTTAGGTTGAAA
1 ACAGGTCAGGTTGAAA
857010 ACAGGTC
1 ACAGGTC
857017 GGGTAATACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:864044 original size:20 final size:19
Alignment explanation
Indices: 864021--864115 Score: 113
Period size: 20 Copynumber: 5.0 Consensus size: 19
864011 GAGGGATTAT
864021 CAGTGGTCCTTCGGGACAA
1 CAGTGGTCCTTCGGGACAA
864040 GCAGTGGTCCTTCGGGAC-A
1 -CAGTGGTCCTTCGGGACAA
* * *
864059 TAGTGGTTCTTCGGAACAA
1 CAGTGGTCCTTCGGGACAA
*
864078 TCAGTGGTCATTCGGGAC-A
1 -CAGTGGTCCTTCGGGACAA
*
864097 TAGTGGTCCTTCGGGACAA
1 CAGTGGTCCTTCGGGACAA
864116 ATATTCAGTG
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
18 29 0.46
19 4 0.06
20 30 0.48
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.25
Consensus pattern (19 bp):
CAGTGGTCCTTCGGGACAA
Found at i:864065 original size:18 final size:18
Alignment explanation
Indices: 864022--864114 Score: 114
Period size: 18 Copynumber: 4.9 Consensus size: 18
864012 AGGGATTATC
*
864022 AGTGGTCCTTCGGGACAAGC
1 AGTGGTCCTTCGGGAC-A-T
864042 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
864060 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
864079 CAGTGGTCATTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
864098 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
864115 AATATTCAGT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
18 30 0.47
19 5 0.08
20 29 0.45
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:864083 original size:38 final size:38
Alignment explanation
Indices: 864022--864115 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
864012 AGGGATTATC
*
864022 AGTGGTCCTTCGGGACAAGCAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAAGCAGTGGTCATTCGGGACAT
* * *
864060 AGTGGTTCTTCGGAACAATCAGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGGGACAAGCAGTGGTCATTCGGGACAT
864098 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAA
864116 ATATTCAGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACAAGCAGTGGTCATTCGGGACAT
Found at i:864487 original size:4 final size:4
Alignment explanation
Indices: 864480--864514 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
864470 TGAGAATGAC
864480 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AGTGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-TGT AT
864515 TTGTTACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:867003 original size:20 final size:20
Alignment explanation
Indices: 866978--867026 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
866968 CTGGGGACAA
866978 TATCGATACCACAAGGTTAG
1 TATCGATACCACAAGGTTAG
866998 TATCGATACCACAAGGTTAG
1 TATCGATACCACAAGGTTAG
867018 TATCGATAC
1 TATCGATAC
867027 TGGCAGGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (20 bp):
TATCGATACCACAAGGTTAG
Found at i:881608 original size:24 final size:24
Alignment explanation
Indices: 881581--881628 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
881571 AAGTAGAGTT
* *
881581 TTTATCGATTGACCATGTTTAGTG
1 TTTATCGATCGACAATGTTTAGTG
*
881605 TTTATCGATCGATAATGTTTAGTG
1 TTTATCGATCGACAATGTTTAGTG
881629 CATTCGTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (24 bp):
TTTATCGATCGACAATGTTTAGTG
Found at i:881675 original size:25 final size:25
Alignment explanation
Indices: 881622--881685 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
881612 ATCGATAATG
*
881622 TTTAGTGCATTCG-TGCACTCCAGT
1 TTTAGTGCATTTGTTGCACTCCAGT
* * *
881646 ATTAGTGCATTTGTTGCCCTCCTGT
1 TTTAGTGCATTTGTTGCACTCCAGT
*
881671 TTTAGTACA-TTGTTG
1 TTTAGTGCATTTGTTG
881686 AATATTTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 17 0.52
25 16 0.48
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (25 bp):
TTTAGTGCATTTGTTGCACTCCAGT
Found at i:882614 original size:23 final size:23
Alignment explanation
Indices: 882588--882639 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
882578 GTAAGTAGAT
*
882588 GAGTAGGAGGTTCAAGAATAAGC
1 GAGTAGGAGGTTCAAGAATAAGA
882611 GAGTAGGAGGTTCAAGAATAAGA
1 GAGTAGGAGGTTCAAGAATAAGA
882634 GAGTAG
1 GAGTAG
882640 TGATGGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.06, G:0.37, T:0.17
Consensus pattern (23 bp):
GAGTAGGAGGTTCAAGAATAAGA
Found at i:887942 original size:24 final size:24
Alignment explanation
Indices: 887915--887969 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
887905 GCATACGAGC
*
887915 ACTCCTGTACTAGTACATTTGGGT
1 ACTCCTGTACTAGTACATTCGGGT
* ** *
887939 ACTCCTATGTTAGTACATTCGTGT
1 ACTCCTGTACTAGTACATTCGGGT
887963 ACTCCTG
1 ACTCCTG
887970 GAACTATATG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (24 bp):
ACTCCTGTACTAGTACATTCGGGT
Found at i:891987 original size:31 final size:31
Alignment explanation
Indices: 891952--892026 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
891942 AACATCCAAA
891952 TGACCAAAACTTAATAAAACCG-TAACATAAG
1 TGACCAAAACTTAATAAAA-CGATAACATAAG
* **
891983 TGACCAAAACTTAATAAAATGATAATGTAAG
1 TGACCAAAACTTAATAAAACGATAACATAAG
892014 TGACCAAAACTTA
1 TGACCAAAACTTA
892027 TGTTTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 1 0.03
31 39 0.98
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.23
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAACGATAACATAAG
Found at i:900916 original size:54 final size:54
Alignment explanation
Indices: 900859--901179 Score: 376
Period size: 54 Copynumber: 5.9 Consensus size: 54
900849 GCCGATATAA
* * * * * *
900859 TCATTCATAAACTCATTATGAATTTTGTGGTTTGTACACTTAATATCGGTACGA
1 TCATTCATAAACTCATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATACGG
* * *
900913 TCATTTATAAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACGG
1 TCATTCATAAACTCATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATACGG
* * *
900967 TCTTTCATAAACTCATTATAAATTCTGTGGGTTGCACACTTAGTG-CTGATACGG
1 TCATTCATAAACTCATTATGAATTTTGTGGGTTGCACACTTAGTGTC-GATACGG
* * * * *
901021 TCGTTCATAAACTCATTATGAATTCTATGGGCTGCACACTTAGTGTCGATATGG
1 TCATTCATAAACTCATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATACGG
* * * * * *
901075 TCGTTCATAAACTCATTATGAATTTCGTGGATTGCACACTTAGTGCCAATACAG
1 TCATTCATAAACTCATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATACGG
** *
901129 T-AGTTCATAAACTCATTATGAATTCCGTGGGTTGCATACTTAGTGTCGATA
1 TCA-TTCATAAACTCATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATA
901180 GTAGACATAG
Statistics
Matches: 230, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
53 1 0.00
54 228 0.99
55 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (54 bp):
TCATTCATAAACTCATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATACGG
Found at i:901087 original size:162 final size:162
Alignment explanation
Indices: 900818--901179 Score: 447
Period size: 162 Copynumber: 2.2 Consensus size: 162
900808 GTTTCCATAA
* * * *
900818 CATTATAAGTTCTTTGAGG-TGCACACGTAGTGCCGATATAATCATTCATAAACTCATTATGAAT
1 CATTATAAATTCTGTG-GGTTGCACACTTAGTGCCGATACAATCATTCATAAACTCATTATGAAT
* * ** * * * *
900882 TTTGTGGTTTGTACACTTAATATCGGTACGATCATTTATAAACTCATTATGAATTTCGTGGGTTG
65 TCTATGGGCTGCACACTTAATATCGATACGATCATTCATAAACTCATTATGAATTTCGTGGATTG
* * **
900947 CACACTTAGTGCCGATACGGTCTTTCATAAACT
130 CACACTTAGTGCCAATACAGTAGTTCATAAACT
* ** *
900980 CATTATAAATTCTGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCATAAACTCATTATGAATT
1 CATTATAAATTCTGTGGGTTGCACACTTAGTGCCGATACAATCATTCATAAACTCATTATGAATT
* * * * *
901045 CTATGGGCTGCACACTTAGTGTCGATATGGTCGTTCATAAACTCATTATGAATTTCGTGGATTGC
66 CTATGGGCTGCACACTTAATATCGATACGATCATTCATAAACTCATTATGAATTTCGTGGATTGC
901110 ACACTTAGTGCCAATACAGTAGTTCATAAACT
131 ACACTTAGTGCCAATACAGTAGTTCATAAACT
* * * *
901142 CATTATGAATTCCGTGGGTTGCATACTTAGTGTCGATA
1 CATTATAAATTCTGTGGGTTGCACACTTAGTGCCGATA
901180 GTAGACATAG
Statistics
Matches: 169, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
161 2 0.01
162 167 0.99
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (162 bp):
CATTATAAATTCTGTGGGTTGCACACTTAGTGCCGATACAATCATTCATAAACTCATTATGAATT
CTATGGGCTGCACACTTAATATCGATACGATCATTCATAAACTCATTATGAATTTCGTGGATTGC
ACACTTAGTGCCAATACAGTAGTTCATAAACT
Found at i:905044 original size:20 final size:21
Alignment explanation
Indices: 905021--905073 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
905011 CAAAGAACCG
905021 AAAAACATGCCA-AAAAGCAT
1 AAAAACATGCCATAAAAGCAT
* *
905041 AAAAACATGTCATAAAGGCAT
1 AAAAACATGCCATAAAAGCAT
905062 ATGAAAACATGC
1 A--AAAACATGC
905074 AACACATGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
23 8 0.30
ACGTcount: A:0.55, C:0.17, G:0.13, T:0.15
Consensus pattern (21 bp):
AAAAACATGCCATAAAAGCAT
Found at i:906766 original size:17 final size:17
Alignment explanation
Indices: 906744--906787 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
906734 GAGGACTTAG
*
906744 GAATTAATAATAAAAAT-
1 GAATTAA-AAGAAAAATA
906761 GAATTAAAAGAAAAATA
1 GAATTAAAAGAAAAATA
906778 GAATTTAAAA
1 GAA-TTAAAA
906788 AAATTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 10 0.42
18 6 0.25
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (17 bp):
GAATTAAAAGAAAAATA
Found at i:908712 original size:2 final size:2
Alignment explanation
Indices: 908701--908741 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
908691 TAAAGGAAAT
908701 TA TA -A 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
908742 AAGTTGAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:910761 original size:233 final size:233
Alignment explanation
Indices: 910354--911973 Score: 2123
Period size: 233 Copynumber: 7.0 Consensus size: 233
910344 TAAAAAAATG
** *
910354 AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATCAAAATTTTTGAAAAGTGAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * * *
910419 AACTAGTACACTATTTCTAAAATTTATAAGTCTTTCGGGCCATTAGTAAGTCTTTCAAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * *
910484 GCTTAAATCCTTCAGGTCATATATAAGTCTTTCGAGCAAGATGATAAGTACTTCGGGCCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
** * * *
910549 AAGTTCTTCGGGCGGGATGTTTTCACAT-TCTCTTAAAA
196 AAGACCTTTGGGCAGGATGTTTTCACATGTCTC-TCAAA
*
910587 AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGCTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* *
910652 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTATTTCGAGCAAGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * **
910717 GCTTAAATCATTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCATTTAGGCCATCC--
131 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
* * * *
910780 ---A--TTCGGGCAAGATGTTTTCACATGTCTATCGAA
196 AAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAA
* ** * * *
910813 ATATGAGAAATATTTCTCGTTTAAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * *
910878 ACCTAGTAAAATATTTCCAAAA-TTATAAGTCATTCGGGCCATCAGTAAGTCTTCCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* *
910942 GCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
*
911007 AAGACCTTTGGGTAGGATGTTTTCACATGTCTCTCAAA
196 AAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAA
* * *
911045 AAATGAGAAAGGTTTCTCATTCAAATCTATG--ATTTGAATTTTTTGAAAAGTAAGAAAGGTTTC
1 AAATGAGAAAGGTTTCTCATTTAAAT-T-TGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTC
* * * * * *
911108 TTACCTAGTAAATTATTTCCAAAATATATAAGTCCTTCAGACCATCAATAAGTCTTTCGAGCAAG
64 TTACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* *
911173 ATGCTTAAATCCTTCGGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCC
129 ATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
*
911238 ATAAGACCTTTGGGAAGGATGTTTTCACATGTCTCTCAAA
194 ATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAA
* * * * *
911278 AAATGAGAAAGTTTTCTCGTTAAAATTTGAAAATTGAAATTTTTTAGAAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * *
911343 ACCTAGTAAACTTTTTCCAAAATTTATAAGTCCTTTGGGCCATCAGTACGTCTTTCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * *
911408 GTTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGAGCCATGCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
* * * * * * *
911473 AAGACCTTTGGACAAGATATTTTTACATATCTATCGAA
196 AAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAA
* ** * * * * *
911511 ATATGAGAATTGTTTCTCATTTAAATCTGAAAATTAAAATTTTTTGAAAGGTGAGAAAAGTTTCT
1 AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAA-TTTTTGAAAAGTAAGAAAGGTTTCT
* * * * * *
911576 TACCTACTAAACTATTT-CAAAAATTATAAATCCTTTGGGCTATCAATAAGTCTTTCGAGCATGA
65 TACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * *
911640 TGCTTAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCTTCGAGCCATCCA
130 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
* *
911705 TAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCGAA
195 TAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAA
* * ** * * *
911744 AAATGAGAAAGGTTTCTCATTCAAATCTGTGATTTGAAATTATTGAAAAGTAAGAAAGGTTTCTC
1 AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
** ** *
911809 ACCTAGTAAACTATTTCC-AAATTATATAAGTATTTTAGGCCATCTGTAAGTCTTTCGAGCATGA
66 ACCTAGTAAACTATTTCCAAAATT-TATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* *
911873 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATTATAAGTCCTTTGGGCCATCCA
130 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
* * *
911938 TAAGAACTTTGGGCATGATGTTTTCACAGGTCTCTC
195 TAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTC
911974 TTTTTCAAGA
Statistics
Matches: 1205, Mismatches: 166, Indels: 32
0.86 0.12 0.02
Matches are distributed among these distances:
225 94 0.08
226 102 0.08
227 3 0.00
230 1 0.00
231 2 0.00
232 141 0.12
233 825 0.68
234 37 0.03
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (233 bp):
AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
AAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCAAA
Found at i:911668 original size:42 final size:41
Alignment explanation
Indices: 911622--911702 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 41
911612 GGGCTATCAA
* * * *
911622 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATCTG
1 TAAGTCTTTCGAGAAAGATG-ATAAATCCTTCGAGCCATCTG
*
911664 TAAGTCTTTCGAGAAAGATGATAAGTCCTTCGAGCCATC
1 TAAGTCTTTCGAGAAAGATGATAAATCCTTCGAGCCATC
911703 CATAAGACCT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 16 0.47
42 18 0.53
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (41 bp):
TAAGTCTTTCGAGAAAGATGATAAATCCTTCGAGCCATCTG
Found at i:911861 original size:699 final size:691
Alignment explanation
Indices: 910354--911973 Score: 2341
Period size: 699 Copynumber: 2.3 Consensus size: 691
910344 TAAAAAAATG
* * ** * ** *
910354 AAATGAGAAAGGTTTCTCATTTAAATTTGAAAATCAAAATTTTTGAAAAGTGAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTCAAATCTGTGATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * *
910419 AACTAGTACACTATTTCTAAAATT-TATAAGTCTTTCGGGCCAT-TAGTAAGTCTTTCAAGCATG
66 ACCTAGTAAACTATTTC-CAAATTATATAAGTCTTTCAGGCCATCT-GTAAGTCTTTCGAGCATG
* * * * *
910482 ATGCTTAAATCCTTCAGGTCATATATAAGTCTTTCGAGCAAGATGATAAGTACTTCGGGCCATCC
129 ATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCC
** * * * *
910547 ATAAGTTCTTCGGGCGGGATGTTTTCACAT-TCTCTTAAAAAAATGAGAAAGGTTTCTCATTTAA
194 ATAAGAACTTTGGGCAGGATGTTTTCACATGTCTC-TCAAAAAATGAGAAAGGTTTCTCATTAAA
910611 ATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGCTTCTTACCTAGTAAACTATTTCCAAAATT
258 ATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGCTTCTTACCTAGTAAACTATTTCCAAAATT
910676 TATAAGTCCTTCGGGCCATCAGTAAGTATTTCGAGCAAGATGCTTAAATCATTCGGGTCATCTGT
323 TATAAGTCCTTCGGGCCATCAGTAAGTATTTCGAGCAAGATGCTTAAATCATTCGGGTCATCTGT
* * * *
910741 AAGTCTTTCAAGCAAGATGATAAGTCATTTAGGCCATCCATTCGGGCAAGATGTTTTCACATGTC
388 AAGTCTTTCAAGCAAGATGATAAGTCATTGAGGCCATCCATTCGGACAAGATATTTTCACATATC
* * *
910806 TATCGAAATATGAGAAATATTTCTCGTTTAAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAG
453 TATCGAAATATGAGAAATATTTCTCATTTAAATCTGAAAATTAAAATTTTTTAAAAGTAAGAAAA
* * * *
910871 GTTTCTTACCTAGTAAAATATTTCCAAAATTATAAGTCATTCGGGCCATCAGTAAGTCTTCCGAG
518 GTTTCTTACCTACTAAAATATTTCAAAAATTATAAATCATTCGGGCCATCAATAAGTCTTCCGAG
*
910936 CATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCC
583 CATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCTTCGAGCC
* *
911001 ATCCATAAGACCTTTGGGTAGGATGTTTTCACATGTCTCTCAAA
648 ATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAA
* *
911045 AAATGAGAAAGGTTTCTCATTCAAATCTATGATTTGAATTTTTTGAAAAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTCAAATCTGTGATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * * * ** *
911110 ACCTAGTAAATTATTTCCAAAATATATAAGTCCTTCAGACCATCAATAAGTCTTTCGAGCAAGAT
66 ACCTAGTAAACTATTTCCAAATTATATAAGTCTTTCAGGCCATCTGTAAGTCTTTCGAGCATGAT
*
911175 GCTTAAATCCTTCGGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCAT
* * * *
911240 AAGACCTTTGGGAAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAGTTTTCTCGTTAAAATT
196 AAGAACTTTGGGCAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAGGTTTCTCATTAAAATT
* * * *
911305 TGAAAATTGAAATTTTTTAGAAGTAAGAAAGGTTTCTTACCTAGTAAACTTTTTCCAAAATTTAT
261 TGAAAATTGAAATTTTTGAAAAGTAAGAAAGGCTTCTTACCTAGTAAACTATTTCCAAAATTTAT
* * * * * *
911370 AAGTCCTTTGGGCCATCAGTACGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAG
326 AAGTCCTTCGGGCCATCAGTAAGTATTTCGAGCAAGATGCTTAAATCATTCGGGTCATCTGTAAG
* * * *
911435 TCTTTCGAGCAAGATGATAAGTCATTCGA-GCCATGCATAAGACCTTTGGACAAGATATTTTTAC
391 TCTTTCAAGCAAGATGATAAGTCATT-GAGGCCAT-C------CATTCGGACAAGATATTTTCAC
* * * *
911499 ATATCTATCGAAATATGAGAATTGTTTCTCATTTAAATCTGAAAATTAAAATTTTTTGAAAGGTG
448 ATATCTATCGAAATATGAGAAATATTTCTCATTTAAATCTGAAAATTAAAATTTTTT-AAAAGTA
* * * *
911564 AGAAAAGTTTCTTACCTACTAAACTATTTCAAAAATTATAAATCCTTTGGGCTATCAATAAGTCT
512 AGAAAAGTTTCTTACCTACTAAAATATTTCAAAAATTATAAATCATTCGGGCCATCAATAAGTCT
*
911629 TTCGAGCATGATGCTTAAATCCTTC-GAGTCATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCT
577 TCCGAGCATGATGCTTAAATCCTTCAG-GTCATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCT
*
911693 TCGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCGAA
641 TCGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAA
* *
911744 AAATGAGAAAGGTTTCTCATTCAAATCTGTGATTTGAAATTATTGAAAAGTAAGAAAGGTTTCTC
1 AAATGAGAAAGGTTTCTCATTCAAATCTGTGATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* *
911809 ACCTAGTAAACTATTTCCAAATTATATAAGTATTTTAGGCCATCTGTAAGTCTTTCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAATTATATAAGTCTTTCAGGCCATCTGTAAGTCTTTCGAGCATGAT
*
911874 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATTATAAGTCCTTTGGGCCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCAT
* *
911939 AAGAACTTTGGGCATGATGTTTTCACAGGTCTCTC
196 AAGAACTTTGGGCAGGATGTTTTCACATGTCTCTC
911974 TTTTTCAAGA
Statistics
Matches: 822, Mismatches: 94, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
690 4 0.00
691 362 0.44
692 6 0.01
698 70 0.09
699 380 0.46
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (691 bp):
AAATGAGAAAGGTTTCTCATTCAAATCTGTGATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
ACCTAGTAAACTATTTCCAAATTATATAAGTCTTTCAGGCCATCTGTAAGTCTTTCGAGCATGAT
GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCAT
AAGAACTTTGGGCAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAGGTTTCTCATTAAAATT
TGAAAATTGAAATTTTTGAAAAGTAAGAAAGGCTTCTTACCTAGTAAACTATTTCCAAAATTTAT
AAGTCCTTCGGGCCATCAGTAAGTATTTCGAGCAAGATGCTTAAATCATTCGGGTCATCTGTAAG
TCTTTCAAGCAAGATGATAAGTCATTGAGGCCATCCATTCGGACAAGATATTTTCACATATCTAT
CGAAATATGAGAAATATTTCTCATTTAAATCTGAAAATTAAAATTTTTTAAAAGTAAGAAAAGTT
TCTTACCTACTAAAATATTTCAAAAATTATAAATCATTCGGGCCATCAATAAGTCTTCCGAGCAT
GATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCTTCGAGCCATC
CATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAA
Found at i:912055 original size:42 final size:42
Alignment explanation
Indices: 911981--912096 Score: 124
Period size: 42 Copynumber: 2.8 Consensus size: 42
911971 CTCTTTTTCA
* * * * *
911981 AGATTTGATTTTCCCTGAGTGACAGCGGAACAAGTCTTCCCC
1 AGATATGATATTCCTTGAGTGAAAGCGGAACAAGTATTCCCC
* * *
912023 AGATCTGATATTCCTTGAGTGAAAGTGGAACAAGTATTCCTC
1 AGATATGATATTCCTTGAGTGAAAGCGGAACAAGTATTCCCC
* * * *
912065 ATATATGATATTACTTGAGTGATAGCAGAACA
1 AGATATGATATTCCTTGAGTGAAAGCGGAACA
912097 TATCCCTTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (42 bp):
AGATATGATATTCCTTGAGTGAAAGCGGAACAAGTATTCCCC
Found at i:914188 original size:130 final size:130
Alignment explanation
Indices: 914051--914347 Score: 332
Period size: 130 Copynumber: 2.3 Consensus size: 130
914041 GCATAAGGGG
* * * * *
914051 TCATTTATTCTCGACTCGAAATAATTTGATATTGTCGTTTTCT-CTCGAATTAATATCGATTTTT
1 TCATTTATTCTCGA-TCGAAATAATTAGATATTATCATTTT-TACTCGAATCAATATCGAATTTT
* * *
914115 TAGACAG-AATATTAATATCTCTTTATTTCAATTGG-GTAATAAATGACTATTTTAATGCACGAA
64 AAGA-AGAAATAGTAATATCTCTTTATTTCAATTGGAGTAATAAACGACTATTTTAATGCACGAA
914178 ATG-
128 A-GA
* * * * * * * *
914181 TCGTTTATTCTCGATTGAAAATCATTAGATGTTATTATTTTTACTTGAATCGATATTGAATTTTA
1 TCATTTATTCTCGATCG-AAATAATTAGATATTATCATTTTTACTCGAATCAATATCGAATTTTA
* *
914246 AGATGAAATAGTAATATCTCTTTATTTCAATTGGAGTAATAAACGACTGTTTTAATGCACGAAAG
65 AGAAGAAATAGTAATATCTCTTTATTTCAATTGGAGTAATAAACGACTATTTTAATGCACGAAAG
914311 A
130 A
* *
914312 TCATTTATTCTCTATTGGAAATAATTAGATATTATC
1 TCATTTATTCTCGA-TCGAAATAATTAGATATTATC
914348 TTTCTCACTC
Statistics
Matches: 137, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
129 4 0.03
130 77 0.56
131 54 0.39
132 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (130 bp):
TCATTTATTCTCGATCGAAATAATTAGATATTATCATTTTTACTCGAATCAATATCGAATTTTAA
GAAGAAATAGTAATATCTCTTTATTTCAATTGGAGTAATAAACGACTATTTTAATGCACGAAAGA
Found at i:918647 original size:3 final size:3
Alignment explanation
Indices: 918634--918674 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
918624 TCTCGTTAAC
*
918634 ATT ATT A-T ATT ATT ATT ATT -TT AGTT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
918675 TTACAAACTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:918663 original size:15 final size:14
Alignment explanation
Indices: 918634--918670 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
918624 TCTCGTTAAC
*
918634 ATTATTATATTATT
1 ATTATTTTATTATT
918648 ATTATTTTAGTTATT
1 ATTATTTTA-TTATT
918663 ATTATTTT
1 ATTATTTT
918671 TATTTTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
ATTATTTTATTATT
Found at i:918855 original size:30 final size:30
Alignment explanation
Indices: 918812--918870 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
918802 TAGCATCAAA
*
918812 CGTCACCGTCGCCAGAGTGGAGATCCTAGT
1 CGTCACCGCCGCCAGAGTGGAGATCCTAGT
*
918842 CGTCGCCGCCGCCAGAGTGGAGATCCTAG
1 CGTCACCGCCGCCAGAGTGGAGATCCTAG
918871 CTGTCGACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.17
Consensus pattern (30 bp):
CGTCACCGCCGCCAGAGTGGAGATCCTAGT
Found at i:919155 original size:23 final size:23
Alignment explanation
Indices: 919127--919180 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
919117 TTTGGTGAAG
919127 AAGAAAAAACAACAAAAACAAAA
1 AAGAAAAAACAACAAAAACAAAA
* *
919150 AGGAAAAAACAACAAAAAGAAAA
1 AAGAAAAAACAACAAAAACAAAA
919173 AAGAAAAA
1 AAGAAAAA
919181 TAGAGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (23 bp):
AAGAAAAAACAACAAAAACAAAA
Found at i:919163 original size:17 final size:16
Alignment explanation
Indices: 919143--919174 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
919133 AAACAACAAA
919143 AACAAAAAGGAAAAAAC
1 AACAAAAA-GAAAAAAC
919160 AACAAAAAGAAAAAA
1 AACAAAAAGAAAAAA
919175 GAAAAATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (16 bp):
AACAAAAAGAAAAAAC
Found at i:925382 original size:25 final size:23
Alignment explanation
Indices: 925340--925393 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
925330 AAGTTTATTA
*
925340 TTTTAATTTTTTATTTAT-ATAT
1 TTTTAATTTTTTAGTTATAATAT
925362 TTGTTAATATTTGTTAGTTATAATAT
1 TT-TTAAT-TTT-TTAGTTATAATAT
925388 TTTTAA
1 TTTTAA
925394 GTGTTATTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 2 0.07
23 5 0.19
24 3 0.11
25 11 0.41
26 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTTAATTTTTTAGTTATAATAT
Found at i:925675 original size:15 final size:15
Alignment explanation
Indices: 925655--925697 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
925645 TTTTTATCTT
925655 TTAAAATTATTTTTC
1 TTAAAATTATTTTTC
925670 TTAAAATTATTTTTC
1 TTAAAATTATTTTTC
925685 TTAAAATTATTTT
1 TTAAAATTATTTT
925698 AAAAGGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAAAATTATTTTTC
Found at i:949218 original size:89 final size:89
Alignment explanation
Indices: 949067--949272 Score: 308
Period size: 89 Copynumber: 2.3 Consensus size: 89
949057 AGATTTTACA
* * * *
949067 AGTCTGATATCCACAGAAA-AGTAGTGGAACATATTCTTTTCACCACATATTTGGTCTTCCTGGC
1 AGTCTGATCTCCAC-GAAAGAGTAGTGGAACAAATTCTTTTCACCACAAATTTGGACTTCCTGGC
*
949131 AAAGCAGCGAATAAAATCAACCTCG
65 AAAACAGCGAATAAAATCAACCTCG
*
949156 AGTCTGATCTCCACGAAAGAGTAGTGGAATAAATTCTTTTCACCACAAATTTGGACTTCCTGGCA
1 AGTCTGATCTCCACGAAAGAGTAGTGGAACAAATTCTTTTCACCACAAATTTGGACTTCCTGGCA
* *
949221 AAACATCGAATCAAATCAACCTCG
66 AAACAGCGAATAAAATCAACCTCG
949245 AGTCAT-ATCTCCACGAAAGAGTAGTGGA
1 AGTC-TGATCTCCACGAAAGAGTAGTGGA
949273 CCAGATTATT
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
88 4 0.04
89 102 0.95
90 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (89 bp):
AGTCTGATCTCCACGAAAGAGTAGTGGAACAAATTCTTTTCACCACAAATTTGGACTTCCTGGCA
AAACAGCGAATAAAATCAACCTCG
Found at i:949482 original size:73 final size:72
Alignment explanation
Indices: 949315--949584 Score: 312
Period size: 73 Copynumber: 3.7 Consensus size: 72
949305 CTAGAAAAGC
* * * * *
949315 AGTGAATCAAATCAATCTTAGTCTTCACAGAAGAGTAGTGAAGCAAATCAATCTTA-GCCTTCAC
1 AGTGAAGCAAATCAATCATAGCCTTCACAGAAGAGTAGTGAAACAAATCAAT-TTATTCCTTCAC
*
949379 AGAATAGT
65 AGAAGAGT
* * * *
949387 AGTGTAGCAAAGCAATCATAGCCTTCACAGAAGAGTAGTGAAGCAAATCAATTATATTCATTCAC
1 AGTGAAGCAAATCAATCATAGCCTTCACAGAAGAGTAGTGAAACAAATCAATT-TATTCCTTCAC
*
949452 ATAAGAGT
65 AGAAGAGT
* * *
949460 AGTGAAGCAAACCAATCATAGCCTTCACAGAAGAGTAGTGAAACAAAT-ATTTTCTTATCCTTCA
1 AGTGAAGCAAATCAATCATAGCCTTCACAGAAGAGTAGTGAAACAAATCAATTT-AT-TCCTTCA
*
949524 TAGAAGAGT
64 CAGAAGAGT
* *
949533 AGTGAAGCATATCAATCA-AGCCTTCACAAAAAAGAGTAGTGAAACAAATCAA
1 AGTGAAGCAAATCAATCATAGCCTTCAC--AGAAGAGTAGTGAAACAAATCAA
949585 GATCAAATCT
Statistics
Matches: 170, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
71 2 0.01
72 62 0.36
73 86 0.51
74 19 0.11
75 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (72 bp):
AGTGAAGCAAATCAATCATAGCCTTCACAGAAGAGTAGTGAAACAAATCAATTTATTCCTTCACA
GAAGAGT
Found at i:949568 original size:37 final size:36
Alignment explanation
Indices: 949315--949584 Score: 301
Period size: 36 Copynumber: 7.4 Consensus size: 36
949305 CTAGAAAAGC
* * *
949315 AGTGAATCAAATCAATCTTAGTCTTCACAGAAGAGT
1 AGTGAAGCAAATCAATCATAGCCTTCACAGAAGAGT
* *
949351 AGTGAAGCAAATCAATCTTAGCCTTCACAGAATAGT
1 AGTGAAGCAAATCAATCATAGCCTTCACAGAAGAGT
* *
949387 AGTGTAGCAAAGCAATCATAGCCTTCACAGAAGAGT
1 AGTGAAGCAAATCAATCATAGCCTTCACAGAAGAGT
* * * *
949423 AGTGAAGCAAATCAATTATATTCATTCACATAAGAGT
1 AGTGAAGCAAATCAATCATA-GCCTTCACAGAAGAGT
*
949460 AGTGAAGCAAACCAATCATAGCCTTCACAGAAGAGT
1 AGTGAAGCAAATCAATCATAGCCTTCACAGAAGAGT
* * * * *
949496 AGTGAAACAAAT-ATTTTCTTATCCTTCATAGAAGAGT
1 AGTGAAGCAAATCA--ATCATAGCCTTCACAGAAGAGT
* *
949533 AGTGAAGCATATCAATCA-AGCCTTCACAAAAAAGAGT
1 AGTGAAGCAAATCAATCATAGCCTTCAC--AGAAGAGT
*
949570 AGTGAAACAAATCAA
1 AGTGAAGCAAATCAA
949585 GATCAAATCT
Statistics
Matches: 195, Mismatches: 33, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
35 8 0.04
36 107 0.55
37 79 0.41
38 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (36 bp):
AGTGAAGCAAATCAATCATAGCCTTCACAGAAGAGT
Found at i:955321 original size:178 final size:177
Alignment explanation
Indices: 955035--955367 Score: 420
Period size: 178 Copynumber: 1.9 Consensus size: 177
955025 TCTTAATGCT
* * * *
955035 TAAGTCCTTCAGGCCATCAGTAAGTATTTCGAGCATTATGCTTAAATCCTTTGGGTCATATATAA
1 TAAGTCCTTCAGGCCATCAGTAAGTATTTCGAACATGATGATTAAATCCTTCGGGTCATATATAA
* * * * * *
955100 GTCTTTCGAGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTTCGGGCAGGATGTTGTCAC
66 GTCTTTCAAGCAAGATGACAAGTCATTCAGCCCATCCATAAGACCATCAGACAGGATGTTGTCAC
955165 ATGATTTTCGAAAAATGAGAAAACAATTTTCAAAGTTTTTTTTATTAG
131 ATGATTTTCGAAAAATGA-AAAACAATTTTCAAAGTTTTTTTTATTAG
* * * *
955213 TAAGTCCTTC-GTGCTATTAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTCATTTATA
1 TAAGTCCTTCAG-GCCATCAGTAAGTATTTCGAACATGATGATTAAATCCTTCGGGTCATATATA
** * * *
955277 A-TCATTTCAAGCAAGATGACAAGTTC-TTCAGCCCATTTATAAGACCATCAGACATGATTTTTT
65 AGTC-TTTCAAGCAAGATGACAAG-TCATTCAGCCCATCCATAAGACCATCAGACAGGATGTTGT
* *
955340 TACATGATTTTCGAAAATTGAAAAACAA
128 CACATGATTTTCGAAAAATGAAAAACAA
955368 ATTCTAAAGT
Statistics
Matches: 131, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
177 10 0.08
178 119 0.91
179 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (177 bp):
TAAGTCCTTCAGGCCATCAGTAAGTATTTCGAACATGATGATTAAATCCTTCGGGTCATATATAA
GTCTTTCAAGCAAGATGACAAGTCATTCAGCCCATCCATAAGACCATCAGACAGGATGTTGTCAC
ATGATTTTCGAAAAATGAAAAACAATTTTCAAAGTTTTTTTTATTAG
Found at i:956009 original size:238 final size:238
Alignment explanation
Indices: 955209--956101 Score: 1139
Period size: 240 Copynumber: 3.7 Consensus size: 238
955199 GTTTTTTTTA
* * * *
955209 TTAGTAAGTCCTTCGTGCTATTAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTCATTT
1 TTAGTAAGTCCATCGTGCCATCAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTCATCT
* * * * * * * *
955274 ATAATCATTTCAAGCAAGATGACAAGTTCTTCAGCCCATTTATAAGACCATCAGACATGATTTTT
66 ATAAGCCTTTCGAGCAAGATGATAAGTCCTTCAGCCCATTTATAAGACCTTCGGACATGATGTTT
* * * * * * *
955339 TTACATGATTTTCGAAAATTGAAAAACAAATTCTAAAGTTTCTCATTTAAATTTTTTTTCT-AAA
131 TCACATGATTTTCAAAAAATGAAAAACAATTTCCAAAGTTTCTTATTTAAA--TCTTTTCTGAAA
* *
955403 AATGAAATTTTTTAAAAGTAAGAAAATGATTTCCAAAGTTTCTTAC
194 ATTG-AATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTAC
* * *
955449 TTAGTAAGT-CATGCGTTCCATCAGTAAGTCTTTCGAATATGATGATTAAATCCTTCGAGTCATC
1 TTAGTAAGTCCAT-CGTGCCATCAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTCATC
* *
955513 TATAAGCCTTTTGAGTAAGATGATAAGTCCTTCAGCCCATTTATAAGACCTTCGGACATGATGTT
65 TATAAGCCTTTCGAGCAAGATGATAAGTCCTTCAGCCCATTTATAAGACCTTCGGACATGATGTT
** * * *
955578 TTCACATGAATTTT-GGAAAATGAGAAAACAATTTCCAAAGTTTATGATTTAAAATCTTTTATGA
130 TTCACATG-ATTTTCAAAAAATGA-AAAACAATTTCCAAAGTTTCTTATTT-AAATCTTTTCTGA
* *
955642 AAATGGAATTTTTAAAAAGTAAGAAAATGATTTCCAAAGTTTCTTAC
192 AAATTGAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTAC
* * * * *
955689 CTAGTAAGTCCTTCATACCATCAGTAAGTCTTTCGAACATGATGATTAAATCTTTCGGGTCATCT
1 TTAGTAAGTCCATCGTGCCATCAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTCATCT
* * *
955754 ATAAGCCTTTCGAGCAAGATGATAAGTCCTTTAGCCCATTTATAAGACCTTCGGGCAGGATGTTT
66 ATAAGCCTTTCGAGCAAGATGATAAGTCCTTCAGCCCATTTATAAGACCTTCGGACATGATGTTT
955819 TCACATGATTTTCAAAAAATGAGAAAACAATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAA
131 TCACATGATTTTCAAAAAATGA-AAAACAATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAA
* * *
955884 TTG-ATTTTTGAAAAGTAAGAAAATGATTTGCAAAGTTTATTTC
195 TTGAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTAC
* * * **
955927 TTAGCAAGTCCATCGGGCCATCAGTAAGTCTTTTGAGTATGATGATTAAATCCTTCGGGTCATCT
1 TTAGTAAGTCCATCGTGCCATCAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTCATCT
** * ** * *
955992 ATAAGCCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGACTTTCGG-TATGATGTTT
66 ATAAGCCTTTCGAGCAAGATGATAAGTCCTTCAGCCCATTTATAAGACCTTCGGACATGATGTTT
* ** *
956056 TCACATGATTTTAAAAAAATGAAAAAGTATTTCCAAAGCTTCTTAT
131 TCACATGATTTTCAAAAAATGAAAAACAATTTCCAAAGTTTCTTAT
956102 CTATTATTTT
Statistics
Matches: 574, Mismatches: 72, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
236 21 0.04
237 29 0.05
238 140 0.24
239 24 0.04
240 323 0.56
241 34 0.06
242 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (238 bp):
TTAGTAAGTCCATCGTGCCATCAGTAAGTCTTTCGAACATGATGATTAAATCCTTCGGGTCATCT
ATAAGCCTTTCGAGCAAGATGATAAGTCCTTCAGCCCATTTATAAGACCTTCGGACATGATGTTT
TCACATGATTTTCAAAAAATGAAAAACAATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAAT
TGAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTAC
Found at i:956037 original size:41 final size:42
Alignment explanation
Indices: 955932--956044 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
955922 ATTTCTTAGC
* * * * *
955932 AAGTCCATCGGGCCAT-CAGTAAGTCTTTTGAGTATGATGATT
1 AAGTCCTTCGGGCCATCCA-TAAGACTTTCGAGCAAGATGATT
* * * *
955974 AAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGA-T
1 AAGTCCTTCGGGCCATCCATAAGACTTTCGAGCAAGATGATT
*
956015 AAGTCCTTTGGGCCATCCATAAGACTTTCG
1 AAGTCCTTCGGGCCATCCATAAGACTTTCG
956045 GTATGATGTT
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 26 0.46
42 30 0.53
43 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
AAGTCCTTCGGGCCATCCATAAGACTTTCGAGCAAGATGATT
Found at i:956774 original size:131 final size:129
Alignment explanation
Indices: 956392--956859 Score: 575
Period size: 130 Copynumber: 3.6 Consensus size: 129
956382 CATGAAGAAC
* * * * *
956392 AGTGGAATGAATCAATGTTTCCAGATCTGATATACCTAAAGAGCAGCGGAACATATCCCTTTTTT
1 AGTGGAATGAATCAATGTTTCCAGATCTGATCTACCTGAAGAGCAGCGGAGCAGATCCCTTTTTC
*
956457 AGATTTGATCTTACCTGAGGAGTAGTGGAACAAATCTACCTTGATTTAATATTCCCTGAAAAAGT
66 AGATTTGATCTTCCCTGAGGAGTAGTGGAACAAATCTACCTTGATTTAATATTCCCT-AAAAAGT
* * ** *
956522 AGTGGAATGAACCAATGTTTCCAGATCTAATCTA-CTGAAGAGCAGTAGAGTAGATCCCCTTTTT
1 AGTGGAATGAATCAATGTTTCCAGATCTGATCTACCTGAAGAGCAGCGGAGCAGAT-CCCTTTTT
* * *
956586 CAGATTCGATCTTCCCTAAGAAGTAGTGGAACAAATCTACCTTGATTTAATATTCCCTAAAAAGT
65 CAGATTTGATCTTCCCTGAGGAGTAGTGGAACAAATCTACCTTGATTTAATATTCCCTAAAAAGT
* * *
956651 AGTGGAATGAATCAACT-TTTCCAGATCTGATCTACCTGAATAGAAGTGGAGCAGATCCTCTTTT
1 AGTGGAATGAATCAA-TGTTTCCAGATCTGATCTACCTGAAGAGCAGCGGAGCAGATCC-CTTTT
* * * * * *
956715 TCTAGATTTGATCTTCCCTGAGGAGCAGTTGAACAAGTCTTCCTTGATTCAATCTTCCCTAAAGA
64 TC-AGATTTGATCTTCCCTGAGGAGTAGTGGAACAAATCTACCTTGATTTAATATTCCCTAAA-A
*
956780 A-C
127 AGT
* * * * *
956782 AGTGGAGTGAATCAATGTGTCCCGATCTGATCTAACCTGAAGAGTAGCGGAGCAAATCCC-TTTT
1 AGTGGAATGAATCAATGTTTCCAGATCTGATCT-ACCTGAAGAGCAGCGGAGCAGATCCCTTTTT
*
956846 CAGATTTTATCTTC
65 CAGATTTGATCTTC
956860 AAGAATCTCT
Statistics
Matches: 292, Mismatches: 38, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
129 66 0.23
130 123 0.42
131 80 0.27
132 23 0.08
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (129 bp):
AGTGGAATGAATCAATGTTTCCAGATCTGATCTACCTGAAGAGCAGCGGAGCAGATCCCTTTTTC
AGATTTGATCTTCCCTGAGGAGTAGTGGAACAAATCTACCTTGATTTAATATTCCCTAAAAAGT
Found at i:957080 original size:23 final size:22
Alignment explanation
Indices: 957044--957086 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
957034 CTCGTTAACA
957044 TTGTTATATTATTATTATTTAG
1 TTGTTATATTATTATTATTTAG
957066 TTGTTATTATTATTATTATTT
1 TTGTTA-TATTATTATTATTT
957087 TACAAACCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
TTGTTATATTATTATTATTTAG
Found at i:966824 original size:40 final size:40
Alignment explanation
Indices: 966769--966894 Score: 243
Period size: 40 Copynumber: 3.1 Consensus size: 40
966759 TGTGCAACCT
966769 TCGACTCGCTAGTAGGGACAATAACCTTTAACCCACTGAC
1 TCGACTCGCTAGTAGGGACAATAACCTTTAACCCACTGAC
*
966809 TCGACTCGCTAGTAGGGACAATAACCTTTTACCCACTGAC
1 TCGACTCGCTAGTAGGGACAATAACCTTTAACCCACTGAC
966849 TCGACTCGCTAGTAGGGACAATAACCTTTAACCCACTGAC
1 TCGACTCGCTAGTAGGGACAATAACCTTTAACCCACTGAC
966889 TCGACT
1 TCGACT
966895 TGCTCTCCAT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (40 bp):
TCGACTCGCTAGTAGGGACAATAACCTTTAACCCACTGAC
Found at i:970225 original size:15 final size:15
Alignment explanation
Indices: 970205--970300 Score: 156
Period size: 15 Copynumber: 6.4 Consensus size: 15
970195 AAGGTTTCTA
970205 GAGGTGCCTATTGTT
1 GAGGTGCCTATTGTT
*
970220 GAGGTGTCTATTGTT
1 GAGGTGCCTATTGTT
* *
970235 AAGGTGTCTATTGTT
1 GAGGTGCCTATTGTT
970250 GAGGTGCCTATTGTT
1 GAGGTGCCTATTGTT
*
970265 GAGGTGTCTATTGTT
1 GAGGTGCCTATTGTT
970280 GAGGTGCCTATTGTT
1 GAGGTGCCTATTGTT
970295 GAGGTG
1 GAGGTG
970301 TCTTGCATTA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 75 1.00
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.42
Consensus pattern (15 bp):
GAGGTGCCTATTGTT
Found at i:970256 original size:45 final size:45
Alignment explanation
Indices: 970205--970300 Score: 174
Period size: 45 Copynumber: 2.1 Consensus size: 45
970195 AAGGTTTCTA
*
970205 GAGGTGCCTATTGTTGAGGTGTCTATTGTTAAGGTGTCTATTGTT
1 GAGGTGCCTATTGTTGAGGTGTCTATTGTTAAGGTGCCTATTGTT
*
970250 GAGGTGCCTATTGTTGAGGTGTCTATTGTTGAGGTGCCTATTGTT
1 GAGGTGCCTATTGTTGAGGTGTCTATTGTTAAGGTGCCTATTGTT
970295 GAGGTG
1 GAGGTG
970301 TCTTGCATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.42
Consensus pattern (45 bp):
GAGGTGCCTATTGTTGAGGTGTCTATTGTTAAGGTGCCTATTGTT
Done.