Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397282.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_25.0, 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: 1368273
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 33278 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:817127 original size:80 final size:80
Alignment explanation
Indices: 817011--817209 Score: 209
Period size: 80 Copynumber: 2.5 Consensus size: 80
817001 ATATTTCAGT
** * ** * * * * * *
817011 ACATACATCTCATGGCATGTATTTCATAATAACATAAATCGTTCACAGGCTTAGCCTACATTGTA
1 ACATACATCTCATGGCATACATGTCATAATCTCATAAATCATCCACAGACTCAGCCCACAGTGTA
*
817076 CATGATATGCTCAAC
66 CATGACATGCTCAAC
* * * * *
817091 ACATACAACTCATGGCATACATGTCATAATCTCATAACTCATCCATATACTCAGCCCATAGTGTA
1 ACATACATCTCATGGCATACATGTCATAATCTCATAAATCATCCACAGACTCAGCCCACAGTGTA
*
817156 CATGACATTCTCAAC
66 CATGACATGCTCAAC
* * *
817171 ACATATATCTTATGGCATACATGTTATAATCTCATAAAT
1 ACATACATCTCATGGCATACATGTCATAATCTCATAAAT
817210 GGAACTCATG
Statistics
Matches: 96, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
80 96 1.00
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (80 bp):
ACATACATCTCATGGCATACATGTCATAATCTCATAAATCATCCACAGACTCAGCCCACAGTGTA
CATGACATGCTCAAC
Found at i:820887 original size:2 final size:2
Alignment explanation
Indices: 820882--820912 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
820872 AAATAAATAA
*
820882 AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
820913 TTGAAAAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:821456 original size:7 final size:7
Alignment explanation
Indices: 821444--821468 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
821434 ACAAACAAAA
821444 CAAATCC
1 CAAATCC
821451 CAAATCC
1 CAAATCC
821458 CAAATCC
1 CAAATCC
821465 CAAA
1 CAAA
821469 AAAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (7 bp):
CAAATCC
Found at i:826779 original size:31 final size:33
Alignment explanation
Indices: 826744--826810 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 33
826734 ATGGTAAAAG
826744 TATAAAGACAATT-T-TAACTTTGATTAAT-TTT
1 TATAAAGACAATTATATAA-TTTGATTAATATTT
** *
826775 TATAATTACAATTATATAATTTTATTAATATTT
1 TATAAAGACAATTATATAATTTGATTAATATTT
826808 TAT
1 TAT
826811 TATTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 11 0.37
32 10 0.33
33 9 0.30
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (33 bp):
TATAAAGACAATTATATAATTTGATTAATATTT
Found at i:828379 original size:11 final size:12
Alignment explanation
Indices: 828360--828395 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
828350 CTGTTAGTGG
828360 CCATAGCCATCA
1 CCATAGCCATCA
*
828372 CC-TAGCCATCG
1 CCATAGCCATCA
828383 CCATAGCCATCA
1 CCATAGCCATCA
828395 C
1 C
828396 TTGTCCATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.28, C:0.44, G:0.11, T:0.17
Consensus pattern (12 bp):
CCATAGCCATCA
Found at i:828408 original size:23 final size:23
Alignment explanation
Indices: 828357--828415 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
828347 CACCTGTTAG
828357 TGGCCATAGCCATCACCTAGCCA
1 TGGCCATAGCCATCACCTAGCCA
* *
828380 TCGCCATAGCCATCA-CTTGTCCA
1 TGGCCATAGCCATCACCTAG-CCA
*
828403 TGGCCATGGCCAT
1 TGGCCATAGCCAT
828416 TGACAAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (23 bp):
TGGCCATAGCCATCACCTAGCCA
Found at i:830316 original size:92 final size:92
Alignment explanation
Indices: 830164--830333 Score: 243
Period size: 92 Copynumber: 1.8 Consensus size: 92
830154 AGTTTAGATT
* * *
830164 TTCTATAATAGTTTGCTAAGACCAATCAAAATCACCATGGATGCTACAACTGGAGGTGCACCTTT
1 TTCTATAATAGTTTCCTAAGACCAATCAAAATCACCATGGATGCTACAACTAGAGATGCACCTTT
830229 GAGTAAATCCATTTATTAGTTTAAACA
66 GAGTAAATCCATTTATTAGTTTAAACA
* ** * * *
830256 TTCTATACTAGTTTCCTGGGACCAATTAAAA-CTACCATTGATGCTACAACTAGAGATGCACTTT
1 TTCTATAATAGTTTCCTAAGACCAATCAAAATC-ACCATGGATGCTACAACTAGAGATGCACCTT
830320 TGAGTAAATCCATT
65 TGAGTAAATCCATT
830334 GATCAGGCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
91 1 0.01
92 67 0.99
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (92 bp):
TTCTATAATAGTTTCCTAAGACCAATCAAAATCACCATGGATGCTACAACTAGAGATGCACCTTT
GAGTAAATCCATTTATTAGTTTAAACA
Found at i:833225 original size:19 final size:19
Alignment explanation
Indices: 833203--833247 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
833193 ACGATGAAAA
*
833203 AAAAAAAG-AGAAAATGTTG
1 AAAAAAAGTACAAAA-GTTG
*
833222 AAAAAAAGTTCAAAAGTTG
1 AAAAAAAGTACAAAAGTTG
833241 AAAAAAA
1 AAAAAAA
833248 AAGTGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.67, C:0.02, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAAAAAGTACAAAAGTTG
Found at i:835433 original size:16 final size:15
Alignment explanation
Indices: 835414--835445 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
835404 TAATTTTAAT
835414 AATATTAAATAATTTA
1 AATATTAAA-AATTTA
835430 AATATTAAAAATTTA
1 AATATTAAAAATTTA
835445 A
1 A
835446 GTTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATTAAAAATTTA
Found at i:835513 original size:20 final size:20
Alignment explanation
Indices: 835427--835515 Score: 57
Period size: 20 Copynumber: 4.8 Consensus size: 20
835417 ATTAAATAAT
* *
835427 TTAAATATTAAAAATTTAAG
1 TTAAATATTAATATTTTAAG
*
835447 TTAAA-A--AAT-TTTTAAA
1 TTAAATATTAATATTTTAAG
*
835463 TT-AATATGAATATTTTTAA-
1 TTAAATATTAATA-TTTTAAG
* * *
835482 AT-ATTTTTAATATTTTAAG
1 TTAAATATTAATATTTTAAG
835501 TTAAATATTAATATT
1 TTAAATATTAATATT
835516 CATCAATTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
15 2 0.04
16 8 0.15
17 2 0.04
18 9 0.17
19 10 0.19
20 21 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TTAAATATTAATATTTTAAG
Found at i:852512 original size:55 final size:54
Alignment explanation
Indices: 852426--852538 Score: 122
Period size: 55 Copynumber: 2.1 Consensus size: 54
852416 TTAGTAAAGG
* * *
852426 AATTTTCCTTGGAAATGCATTATCGATAGAAAATTCTGTCAAAAATTTCCAACGA
1 AATTTTCCTTGGAAATGCATTATCAAAAGAAAATTC-ATCAAAAATTTCCAACGA
* * * *
852481 AATTTTCCATTGG-AATGCATT-TCCAAAAGAAATTTCATCAGAAATTTCTAACGG
1 AATTTTCC-TTGGAAATGCATTAT-CAAAAGAAAATTCATCAAAAATTTCCAACGA
852535 AATT
1 AATT
852539 CCATGAGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
54 19 0.39
55 26 0.53
56 4 0.08
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (54 bp):
AATTTTCCTTGGAAATGCATTATCAAAAGAAAATTCATCAAAAATTTCCAACGA
Found at i:852717 original size:24 final size:23
Alignment explanation
Indices: 852690--852741 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
852680 ATTCCGTTAA
*
852690 AAATTTATGACAGAATCTCGTTGG
1 AAATTTATGACAGAAT-TCATTGG
* **
852714 AAATTTTTGATTGAATTCATTGG
1 AAATTTATGACAGAATTCATTGG
852737 AAATT
1 AAATT
852742 CTTTTCCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (23 bp):
AAATTTATGACAGAATTCATTGG
Found at i:855725 original size:15 final size:16
Alignment explanation
Indices: 855705--855735 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
855695 CATATTTTGT
855705 TTACATTTAT-ACATA
1 TTACATTTATAACATA
855720 TTACATTTATAACATA
1 TTACATTTATAACATA
855736 GTATACAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
TTACATTTATAACATA
Found at i:858307 original size:18 final size:17
Alignment explanation
Indices: 858261--858310 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
858251 AAATATAACT
* *
858261 TAAAATATTAAATAAAA
1 TAAAAAATTAAAAAAAA
858278 TAAAAACA-TAAAAATAAA
1 TAAAAA-ATTAAAAA-AAA
858296 TAAAAAATTAAAAAA
1 TAAAAAATTAAAAAA
858311 GTGGAGCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
TAAAAAATTAAAAAAAA
Found at i:859156 original size:51 final size:51
Alignment explanation
Indices: 859080--859379 Score: 309
Period size: 51 Copynumber: 5.9 Consensus size: 51
859070 GCAAGGTGCT
* * * * *
859080 AGCAGGGGTGCACAGCATAGGCCCC-TGGGCAAGCCAGCACGACAAGATACC
1 AGCAGGGGCGCACAGCACA-GCCCCTTGGGCGAGCCAGCCCGACAGGATACC
* *
859131 AGCAGGGGCGCACAGCACAGGCCCC-TGGGCGAGCCAGCCCTACAGGATGCC
1 AGCAGGGGCGCACAGCACA-GCCCCTTGGGCGAGCCAGCCCGACAGGATACC
* * ** ** *
859182 AGCAGGGGCGCACAGCACAGCCCCTTAGGCGAGCCTGCCCGGTAGGGGACT
1 AGCAGGGGCGCACAGCACAGCCCCTTGGGCGAGCCAGCCCGACAGGATACC
* * * * ** **
859233 AGCAAGGGCGCACAGCATAGCCCCTTAGGCGAGCCTGCCCGGTAGGGGACC
1 AGCAGGGGCGCACAGCACAGCCCCTTGGGCGAGCCAGCCCGACAGGATACC
* * *
859284 AGCAGGGGCGCACAGCACAGCCCCTTGGGCGAGCCAGCCCGACATGATGCT
1 AGCAGGGGCGCACAGCACAGCCCCTTGGGCGAGCCAGCCCGACAGGATACC
* *
859335 AGCAGGGGCGCACAACACAAGCCCC-TGGGCGAGCCAGCCCTACAG
1 AGCAGGGGCGCACAGCAC-AGCCCCTTGGGCGAGCCAGCCCGACAG
859380 AAAGCCAGGC
Statistics
Matches: 214, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
50 5 0.02
51 203 0.95
52 6 0.03
ACGTcount: A:0.23, C:0.35, G:0.34, T:0.08
Consensus pattern (51 bp):
AGCAGGGGCGCACAGCACAGCCCCTTGGGCGAGCCAGCCCGACAGGATACC
Found at i:859783 original size:71 final size:71
Alignment explanation
Indices: 859586--859783 Score: 188
Period size: 71 Copynumber: 2.8 Consensus size: 71
859576 GGAGCACGGT
* * * * *** *
859586 ACGCAGG-TCTGGGGCCCGTCGGCCCAACAGGGGTGCGCGGCACACAGGATGGCATTGCATGGGT
1 ACGCAGGCTC-GGGGCCCGCCGGCCCAGCAGGGGTACGCGGCACGCAGGATGGCACAACATGGGG
859650 ACGCGGC
65 ACGCGGC
* * * *
859657 ACGCAGGCTCGAGGCCCGCCTGCCCAGTAGGGGTGA-GCGGCACGCAGG-GGCGCACAACATGGG
1 ACGCAGGCTCGGGGCCCGCCGGCCCAGCAGGGGT-ACGCGGCACGCAGGATG-GCACAACATGGG
859720 CGA-GCGGC
64 -GACGCGGC
** * *
859728 ACTTAGGCTCGGGGCCTGCCGGCCCAGCAGGGGTACGCGGCACGCTGGATGGCACA
1 ACGCAGGCTCGGGGCCCGCCGGCCCAGCAGGGGTACGCGGCACGCAGGATGGCACA
859784 GCAGGGCCGA
Statistics
Matches: 101, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
70 2 0.02
71 95 0.94
72 4 0.04
ACGTcount: A:0.17, C:0.31, G:0.41, T:0.11
Consensus pattern (71 bp):
ACGCAGGCTCGGGGCCCGCCGGCCCAGCAGGGGTACGCGGCACGCAGGATGGCACAACATGGGGA
CGCGGC
Found at i:859999 original size:15 final size:15
Alignment explanation
Indices: 859979--860016 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
859969 TTTCCCTTCT
859979 AAATATTTTGGAGGG
1 AAATATTTTGGAGGG
859994 AAATATTTTGGAGGG
1 AAATATTTTGGAGGG
860009 AAATATTT
1 AAATATTT
860017 AAGAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (15 bp):
AAATATTTTGGAGGG
Found at i:860768 original size:14 final size:14
Alignment explanation
Indices: 860738--860772 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
860728 TATATTTAAT
*
860738 TATATATATCTACA
1 TATATATATATACA
*
860752 TATATATATATAGA
1 TATATATATATACA
860766 TATATAT
1 TATATAT
860773 TCTTTGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (14 bp):
TATATATATATACA
Found at i:864838 original size:17 final size:18
Alignment explanation
Indices: 864816--864849 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
864806 TCGACGTGAT
864816 CGAATTAATT-GATTAAC
1 CGAATTAATTCGATTAAC
*
864833 CGAATTAGTTCGATTAA
1 CGAATTAATTCGATTAA
864850 TTCGATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (18 bp):
CGAATTAATTCGATTAAC
Found at i:865270 original size:7 final size:7
Alignment explanation
Indices: 865258--865284 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
865248 TGTTTAAGAT
865258 TTTAATA
1 TTTAATA
865265 TTTAATA
1 TTTAATA
865272 TTTAATA
1 TTTAATA
865279 TTTAAT
1 TTTAAT
865285 TCGGTATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAATA
Found at i:867916 original size:27 final size:26
Alignment explanation
Indices: 867867--867921 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
867857 AAAGCTTACA
867867 AAGCTTACATGACACAACGTTTTATAT
1 AAGCTTACATGACACAACGTTTTA-AT
* * * *
867894 AAGCTTACTTGGCACAGCTTTTTAAT
1 AAGCTTACATGACACAACGTTTTAAT
867920 AA
1 AA
867922 ATTTGATTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (26 bp):
AAGCTTACATGACACAACGTTTTAAT
Found at i:869945 original size:23 final size:23
Alignment explanation
Indices: 869876--870039 Score: 202
Period size: 23 Copynumber: 7.1 Consensus size: 23
869866 TTTTCAAGAG
* * *
869876 TCACGAACTTGGACTTTGTCTTGA
1 TCACGAACTTCGCCGTTG-CTTGA
** * * *
869900 TCACGAGTTTCACCGTCGTTTGA
1 TCACGAACTTCGCCGTTGCTTGA
*
869923 TCACGAACTTCGCTGTTGCTTGA
1 TCACGAACTTCGCCGTTGCTTGA
*
869946 TTACGAACTTCGCCGTTGCTTGA
1 TCACGAACTTCGCCGTTGCTTGA
*
869969 TCACGAACTTCGCCGCTGCTTGA
1 TCACGAACTTCGCCGTTGCTTGA
*
869992 TCACGAACTTCGCTGTTGCTTGA
1 TCACGAACTTCGCCGTTGCTTGA
*
870015 TCACAAACTTCGCCGTTGCTTGA
1 TCACGAACTTCGCCGTTGCTTGA
870038 TC
1 TC
870040 TTCACCCCAG
Statistics
Matches: 118, Mismatches: 22, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
23 107 0.91
24 11 0.09
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (23 bp):
TCACGAACTTCGCCGTTGCTTGA
Found at i:870108 original size:18 final size:18
Alignment explanation
Indices: 870077--870119 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
870067 TGATCTCTGA
870077 AATGCTT-TCAATCTTCG
1 AATGCTTCTCAATCTTCG
*
870094 AATGCTTCTCTATCTTCG
1 AATGCTTCTCAATCTTCG
870112 AATGCTTC
1 AATGCTTC
870120 CGAATGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.42
Consensus pattern (18 bp):
AATGCTTCTCAATCTTCG
Found at i:870562 original size:79 final size:80
Alignment explanation
Indices: 870352--870679 Score: 477
Period size: 80 Copynumber: 4.1 Consensus size: 80
870342 AATTTGATTT
* * * * *
870352 TTATCTCTAAATTAATATA-A-TTA-TTAGAGATAATTTAAATGACCAATAACTAA-ATTTTAAT
1 TTATCTCTAAA-TAATTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATA-TTTGAT
* *
870413 TGGTCAAAAATATGAAGA
64 TGGTC-AAAATATAAATA
* * * * *
870431 TTATCTCCAAATTATTTGGATTTATTTAGAGATAATTTGGATGACCAATAGCTAATATTTGATTG
1 TTATCTCTAAATAATTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATATTTGATTG
870496 GTCAAAATATAAATA
66 GTCAAAATATAAATA
870511 TTATCTCTAAATAATTTAGATTTA-TTAGAGATAAATTGAATGACCAATAGCTAATATTTGATTG
1 TTATCTCTAAATAATTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATATTTGATTG
870575 GTCAAAATATAAATA
66 GTCAAAATATAAATA
870590 TTATCTCTAAATAATTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATATTTGATTG
1 TTATCTCTAAATAATTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATATTTGATTG
*
870655 GTCAAAATATGAATA
66 GTCAAAATATAAATA
870670 TTATCTCTAA
1 TTATCTCTAA
870680 TTTATTTTGA
Statistics
Matches: 228, Mismatches: 16, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
78 4 0.02
79 88 0.39
80 98 0.43
81 37 0.16
82 1 0.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (80 bp):
TTATCTCTAAATAATTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATATTTGATTG
GTCAAAATATAAATA
Found at i:870641 original size:159 final size:159
Alignment explanation
Indices: 870352--870679 Score: 491
Period size: 159 Copynumber: 2.1 Consensus size: 159
870342 AATTTGATTT
*
870352 TTATCTCTAAATTAATATAATTATTAGAGATAATTTAAATGACCAATAACTAAATTTTAATTGGT
1 TTATCTCTAAATTAATATAATTATTAGAGATAAATTAAATGACCAATAACTAAATTTTAATTGGT
* * * * *
870417 CAAAAATATGAAGATTATCTCCAAATTATTTGGATTTATTTAGAGATAATTTGGATGACCAATAG
66 CAAAAATATAAAGATTATCTCCAAATAATTTAGATTTATTTAGAGATAAATTGAATGACCAATAG
870482 CTAATATTTGATTGGTCAAAATATAAATA
131 CTAATATTTGATTGGTCAAAATATAAATA
* * * *
870511 TTATCTCTAAA-TAATTTAGATTTATTAGAGATAAATTGAATGACCAATAGCT-AATATTTGATT
1 TTATCTCTAAATTAATATA-A-TTATTAGAGATAAATTAAATGACCAATAACTAAAT-TTTAATT
* *
870574 GGTC-AAAATATAAATATTATCTCTAAATAATTTAGATTTATTTAGAGATAAATTGAATGACCAA
63 GGTCAAAAATATAAAGATTATCTCCAAATAATTTAGATTTATTTAGAGATAAATTGAATGACCAA
*
870638 TAGCTAATATTTGATTGGTCAAAATATGAATA
128 TAGCTAATATTTGATTGGTCAAAATATAAATA
870670 TTATCTCTAA
1 TTATCTCTAA
870680 TTTATTTTGA
Statistics
Matches: 153, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
158 6 0.04
159 109 0.71
160 38 0.25
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (159 bp):
TTATCTCTAAATTAATATAATTATTAGAGATAAATTAAATGACCAATAACTAAATTTTAATTGGT
CAAAAATATAAAGATTATCTCCAAATAATTTAGATTTATTTAGAGATAAATTGAATGACCAATAG
CTAATATTTGATTGGTCAAAATATAAATA
Found at i:874127 original size:60 final size:60
Alignment explanation
Indices: 874063--874194 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 60
874053 TGGGCTTTAG
** *
874063 GTCCCCTTTTACCCACTTGTGGAAACAAG-GTATGCCACCTAATACGAATCGAGGCTTCAA
1 GTCCCCTTTTACCCACTTGTGGAAAC-AGCCCACGCCACCTAATACGAATCGAGGCTTCAA
* ** * * * ** *
874123 GTCCCCCTTTACTTACTTGTGGCAACTGCCCACGCCATCTAATGTGAATCGGGGCTTCAA
1 GTCCCCTTTTACCCACTTGTGGAAACAGCCCACGCCACCTAATACGAATCGAGGCTTCAA
874183 GTCCCCTTTTAC
1 GTCCCCTTTTAC
874195 AATCACATAT
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
59 1 0.02
60 57 0.98
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (60 bp):
GTCCCCTTTTACCCACTTGTGGAAACAGCCCACGCCACCTAATACGAATCGAGGCTTCAA
Found at i:875022 original size:2 final size:2
Alignment explanation
Indices: 875015--875040 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
875005 CAAACTTCAA
875015 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
875041 CAACTCAATA
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:878102 original size:14 final size:15
Alignment explanation
Indices: 878079--878111 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
878069 CTTGTTTAGC
878079 TTAT-ACTCTACT-T
1 TTATAACTCTACTCT
878092 TTATAACTCTACTCT
1 TTATAACTCTACTCT
878107 TTATA
1 TTATA
878112 CTTTAACTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 8 0.44
15 6 0.33
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATAACTCTACTCT
Found at i:893428 original size:2 final size:2
Alignment explanation
Indices: 893404--893441 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
893394 TCTTTGGCTG
* *
893404 TC TC T- TC TC TT TC TC TA TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
893442 AAACACTGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:896990 original size:8 final size:8
Alignment explanation
Indices: 896977--897007 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
896967 CTCATCCTCT
896977 CTCTCTCC
1 CTCTCTCC
896985 CTCTCTCC
1 CTCTCTCC
*
896993 CTCTCTCA
1 CTCTCTCC
897001 CTCTCTC
1 CTCTCTC
897008 ATTGTATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.58, G:0.00, T:0.39
Consensus pattern (8 bp):
CTCTCTCC
Found at i:899340 original size:26 final size:26
Alignment explanation
Indices: 899311--899360 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
899301 GTAACCGGCT
899311 AGTGGAATTAGATAGATATGCACCCG
1 AGTGGAATTAGATAGATATGCACCCG
*
899337 AGTGGAATTAGCTAGATATGCACC
1 AGTGGAATTAGATAGATATGCACC
899361 TGAATCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (26 bp):
AGTGGAATTAGATAGATATGCACCCG
Found at i:907946 original size:3 final size:3
Alignment explanation
Indices: 907934--907969 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
907924 TATTCTAGAC
*
907934 TAA T-A TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
907970 GGAAACTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:932577 original size:18 final size:18
Alignment explanation
Indices: 932554--932588 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
932544 CTATCTTTCA
*
932554 AAATTGTTCAAATCATTT
1 AAATTGCTCAAATCATTT
*
932572 AAATTGCTCCAATCATT
1 AAATTGCTCAAATCATT
932589 GCATTCAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATTGCTCAAATCATTT
Found at i:935992 original size:23 final size:23
Alignment explanation
Indices: 935966--936012 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
935956 TGGGATTGTT
935966 AATTGGCCTAAGAATTAATTCTC
1 AATTGGCCTAAGAATTAATTCTC
935989 AATTGGCCTAAGAATTAATTCTC
1 AATTGGCCTAAGAATTAATTCTC
936012 A
1 A
936013 CACTTGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (23 bp):
AATTGGCCTAAGAATTAATTCTC
Found at i:936812 original size:18 final size:17
Alignment explanation
Indices: 936785--936818 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
936775 ATATATTGCA
936785 TAATGATACTTCTACAC
1 TAATGATACTTCTACAC
*
936802 TAATAGATACTTGTACA
1 TAAT-GATACTTCTACA
936819 TTCCTTGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (17 bp):
TAATGATACTTCTACAC
Found at i:938630 original size:35 final size:35
Alignment explanation
Indices: 938524--938637 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 35
938514 TTGTTGAATA
**
938524 GTTTCACTTGATCTCATGAAACTGCTATTGTAAGG
1 GTTTCACTTGATCTCATGAAAAAGCTATTGTAAGG
* * *
938559 ATGTCACTTGATCTCTTGAAAAAGCTATTGTAAGG
1 GTTTCACTTGATCTCATGAAAAAGCTATTGTAAGG
*
938594 GTTTCACTTGATCTCATGAAAAAGCTATTGTGAGG
1 GTTTCACTTGATCTCATGAAAAAGCTATTGTAAGG
938629 GTTTCACTT
1 GTTTCACTT
938638 TACCCCATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (35 bp):
GTTTCACTTGATCTCATGAAAAAGCTATTGTAAGG
Found at i:947782 original size:28 final size:28
Alignment explanation
Indices: 947751--947862 Score: 125
Period size: 28 Copynumber: 4.0 Consensus size: 28
947741 TATTACACGT
947751 CATGTTGAAAAATGTAGTTGTTACATAC
1 CATGTTGAAAAATGTAGTTGTTACATAC
* * * * **
947779 CATGTTTAAGATTTTAGTTGTTACATGT
1 CATGTTGAAAAATGTAGTTGTTACATAC
* **
947807 CATGTTTAAAAATGTAGTTGTTACACGC
1 CATGTTGAAAAATGTAGTTGTTACATAC
* *
947835 CATGTTGAAAAATTTAGTTATTACATAC
1 CATGTTGAAAAATGTAGTTGTTACATAC
947863 TACGATGAAA
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (28 bp):
CATGTTGAAAAATGTAGTTGTTACATAC
Found at i:947809 original size:56 final size:56
Alignment explanation
Indices: 947741--947860 Score: 168
Period size: 56 Copynumber: 2.1 Consensus size: 56
947731 CAAGATGTAG
* * * * *
947741 TATTACACGTCATGTTGAAAAATGTAGTTGTTACATACCATGTTTAAGATTTTAGT
1 TATTACATGTCATGTTGAAAAATGTAGTTGTTACACACCATGTTGAAAAATTTAGT
* * *
947797 TGTTACATGTCATGTTTAAAAATGTAGTTGTTACACGCCATGTTGAAAAATTTAGT
1 TATTACATGTCATGTTGAAAAATGTAGTTGTTACACACCATGTTGAAAAATTTAGT
947853 TATTACAT
1 TATTACAT
947861 ACTACGATGA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (56 bp):
TATTACATGTCATGTTGAAAAATGTAGTTGTTACACACCATGTTGAAAAATTTAGT
Found at i:947874 original size:56 final size:56
Alignment explanation
Indices: 947756--947874 Score: 132
Period size: 56 Copynumber: 2.1 Consensus size: 56
947746 CACGTCATGT
* * * * * * * *
947756 TGAAAAATGTAGTTGTTACATACCATGTTTAAGATTTTAGTTGTTACATGTCATGT
1 TGAAAAATGTAGTTGTTACACACCATGTTGAAAAATTTAGTTATTACATCTCACGA
* *
947812 TTAAAAATGTAGTTGTTACACGCCATGTTGAAAAATTTAGTTATTACATACT-ACGA
1 TGAAAAATGTAGTTGTTACACACCATGTTGAAAAATTTAGTTATTACAT-CTCACGA
947868 TGAAAAA
1 TGAAAAA
947875 GTTATTATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
56 50 0.98
57 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (56 bp):
TGAAAAATGTAGTTGTTACACACCATGTTGAAAAATTTAGTTATTACATCTCACGA
Found at i:954452 original size:21 final size:22
Alignment explanation
Indices: 954423--954466 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
954413 TAAGTGTTAA
954423 TTTAAGTTA-TTTTAGTTAAAT
1 TTTAAGTTATTTTTAGTTAAAT
* *
954444 TTTAGGTTATTTTTATTTAAAT
1 TTTAAGTTATTTTTAGTTAAAT
954466 T
1 T
954467 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTTAGTTAAAT
Found at i:955132 original size:12 final size:12
Alignment explanation
Indices: 955117--955164 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
955107 AGAGATTTTT
955117 GAGGCAGCAAGA
1 GAGGCAGCAAGA
955129 GAGGCAGCAAGA
1 GAGGCAGCAAGA
955141 GAGGCAGCAA-A
1 GAGGCAGCAAGA
955152 GGAGGCAGCAAGA
1 -GAGGCAGCAAGA
955165 AACTATTCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:957540 original size:2 final size:2
Alignment explanation
Indices: 957533--957566 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
957523 TTTCTTGCAT
957533 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
957567 CTGAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:957981 original size:23 final size:23
Alignment explanation
Indices: 957965--958010 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
957955 TAATCTTTTA
957965 TGGTATAAGTCCATAATCATCCT
1 TGGTATAAGTCCATAATCATCCT
*
957988 TGGTCTAAGTCCATAATCATCCT
1 TGGTATAAGTCCATAATCATCCT
958011 CAAGCTTTAT
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:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (23 bp):
TGGTATAAGTCCATAATCATCCT
Found at i:958659 original size:41 final size:40
Alignment explanation
Indices: 958583--958675 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 40
958573 AGAGAAAAAA
958583 AGAAAAGAAGAACAGTCCATCACCAAAGAGCAAGG-AGGA-
1 AGAAAA-AAGAACAGTCCATCACCAAAGAGCAAGGAAGGAG
* * *
958622 AGCAAAAAGAATAGTCCATCACCATAGAGCAATAAGGAAGGAG
1 AGAAAAAAGAACAGTCCATCACCAAAGAGC---AAGGAAGGAG
958665 AGAAAAAAGAA
1 AGAAAAAAGAA
958676 AACGAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
38 22 0.49
39 5 0.11
41 4 0.09
42 4 0.09
43 10 0.22
ACGTcount: A:0.54, C:0.15, G:0.24, T:0.08
Consensus pattern (40 bp):
AGAAAAAAGAACAGTCCATCACCAAAGAGCAAGGAAGGAG
Found at i:959149 original size:21 final size:21
Alignment explanation
Indices: 959123--959162 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
959113 AATATAAAAA
959123 TATTATATTATT-TTTTAATGT
1 TATTAT-TTATTATTTTAATGT
959144 TATTATTTATTATTTTAAT
1 TATTATTTATTATTTTAAT
959163 TACTTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TATTATTTATTATTTTAATGT
Found at i:959381 original size:15 final size:15
Alignment explanation
Indices: 959363--959396 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
959353 ATATTCTTAG
959363 CAATCACATTCCCAA
1 CAATCACATTCCCAA
*
959378 CAATCACATTCTCAA
1 CAATCACATTCCCAA
959393 CAAT
1 CAAT
959397 ATACCAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (15 bp):
CAATCACATTCCCAA
Found at i:959840 original size:77 final size:77
Alignment explanation
Indices: 959759--959922 Score: 224
Period size: 77 Copynumber: 2.1 Consensus size: 77
959749 ATGATTTCAC
* * *
959759 AAATTAAAATGATATTCTTAATTTTACGAATTTCCTTT-AAAGTAGGAAACAATTTCTTATTCTT
1 AAATTAAAATGATATCCTTAATTTTAAGAATTACCTTTAAAAG-AGGAAACAATTTCTTATTCTT
959823 TATGAATCACTC-A
65 TATGAATCAC-CAA
** * *
959836 AAATTAAAATTCTATCCTTAATTTTAAGAATTACTTTTAAAAGAGGAAACAATTTCTTTTTCTTT
1 AAATTAAAATGATATCCTTAATTTTAAGAATTACCTTTAAAAGAGGAAACAATTTCTTATTCTTT
*
959901 ATGGATCACCAA
66 ATGAATCACCAA
959913 AAATTAAAAT
1 AAATTAAAAT
959923 AGATGGCATT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
76 1 0.01
77 72 0.94
78 4 0.05
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (77 bp):
AAATTAAAATGATATCCTTAATTTTAAGAATTACCTTTAAAAGAGGAAACAATTTCTTATTCTTT
ATGAATCACCAA
Found at i:963152 original size:21 final size:20
Alignment explanation
Indices: 963128--963172 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
963118 TTCAAGTAAT
963128 TTAAAATAAAATAACTTAAAA
1 TTAAAATAAAATAA-TTAAAA
** *
963149 TTAAGGTAAAATAATTTAAA
1 TTAAAATAAAATAATTAAAA
963169 TTAA
1 TTAA
963173 CCACTTAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
TTAAAATAAAATAATTAAAA
Found at i:966178 original size:22 final size:22
Alignment explanation
Indices: 966152--966313 Score: 135
Period size: 22 Copynumber: 7.4 Consensus size: 22
966142 AGTTTTGGTG
* *
966152 GTTTTTAGGCATTGTGTAACTG
1 GTTTTTAGGCATTGCGTAACTA
* * * *
966174 GTTTTGAGGTATTGTGTGACTA
1 GTTTTTAGGCATTGCGTAACTA
* *
966196 GTGTTTAGGCATTGCGTTACTA
1 GTTTTTAGGCATTGCGTAACTA
* * * * *
966218 ATTATTAGGCATTACATGACTA
1 GTTTTTAGGCATTGCGTAACTA
* *
966240 GTTTTTAAGTATTGCGTAACTA
1 GTTTTTAGGCATTGCGTAACTA
* *
966262 GTTTTTAGGCATTACGTTACTA
1 GTTTTTAGGCATTGCGTAACTA
* * *
966284 ATTTTTAAGCATTACGTAACTA
1 GTTTTTAGGCATTGCGTAACTA
*
966306 ATTTTTAG
1 GTTTTTAG
966314 ATATTACATA
Statistics
Matches: 110, Mismatches: 30, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 110 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.44
Consensus pattern (22 bp):
GTTTTTAGGCATTGCGTAACTA
Found at i:966238 original size:44 final size:44
Alignment explanation
Indices: 966190--966330 Score: 158
Period size: 44 Copynumber: 3.2 Consensus size: 44
966180 AGGTATTGTG
* * * *
966190 TGACTAGTGTTTAGGCATTGCGTTACTAATTATTAGGCATTACA
1 TGACTAGTTTTTAAGCATTGCGTAACTAATTTTTAGGCATTACA
* * *
966234 TGACTAGTTTTTAAGTATTGCGTAACTAGTTTTTAGGCATTACG
1 TGACTAGTTTTTAAGCATTGCGTAACTAATTTTTAGGCATTACA
* * * **
966278 TTACTAATTTTTAAGCATTACGTAACTAATTTTTAGATATTACA
1 TGACTAGTTTTTAAGCATTGCGTAACTAATTTTTAGGCATTACA
966322 T-AGCTAGTT
1 TGA-CTAGTT
966331 GATATGACGT
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 1 0.01
44 79 0.99
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (44 bp):
TGACTAGTTTTTAAGCATTGCGTAACTAATTTTTAGGCATTACA
Found at i:966311 original size:66 final size:66
Alignment explanation
Indices: 966182--966312 Score: 181
Period size: 66 Copynumber: 2.0 Consensus size: 66
966172 TGGTTTTGAG
* * * * * *
966182 GTATTGTGTGACTAGTGTTTAGGCATTGCGTTACTAATTATTAGGCATTACATGACTAGTTTTTA
1 GTATTGCGTAACTAGTGTTTAGGCATTACGTTACTAATTATTAAGCATTACATAACTAATTTTTA
966247 A
66 A
* * *
966248 GTATTGCGTAACTAGTTTTTAGGCATTACGTTACTAATTTTTAAGCATTACGTAACTAATTTTTA
1 GTATTGCGTAACTAGTGTTTAGGCATTACGTTACTAATTATTAAGCATTACATAACTAATTTTTA
966313 GATATTACAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (66 bp):
GTATTGCGTAACTAGTGTTTAGGCATTACGTTACTAATTATTAAGCATTACATAACTAATTTTTA
A
Found at i:966329 original size:66 final size:66
Alignment explanation
Indices: 966192--966330 Score: 172
Period size: 66 Copynumber: 2.1 Consensus size: 66
966182 GTATTGTGTG
* * * * * * *
966192 ACTAGTGTTTAGGCATTGCGTTACTAATTATTAGGCATTACATGACTAGTTTTTAAGTATTGCGT
1 ACTAGTTTTTAGGCATTACGTTACTAATTATTAAGCATTACATAACTAATTTTTAAGTATTACAT
966257 A
66 A
* *
966258 ACTAGTTTTTAGGCATTACGTTACTAATTTTTAAGCATTACGTAACTAATTTTT-AGATATTACA
1 ACTAGTTTTTAGGCATTACGTTACTAATTATTAAGCATTACATAACTAATTTTTAAG-TATTACA
966322 TA
65 TA
*
966324 GCTAGTT
1 ACTAGTT
966331 GATATGACGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
65 2 0.03
66 60 0.97
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.42
Consensus pattern (66 bp):
ACTAGTTTTTAGGCATTACGTTACTAATTATTAAGCATTACATAACTAATTTTTAAGTATTACAT
A
Found at i:966377 original size:16 final size:16
Alignment explanation
Indices: 966356--966397 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
966346 GACTGGTTGA
966356 TAGGCATTGCGTGACT
1 TAGGCATTGCGTGACT
966372 TAGGCATTGCGTGACT
1 TAGGCATTGCGTGACT
966388 TAGGCATTGC
1 TAGGCATTGC
966398 TTAAAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (16 bp):
TAGGCATTGCGTGACT
Found at i:966450 original size:22 final size:22
Alignment explanation
Indices: 966399--966474 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
966389 AGGCATTGCT
966399 TAAAAA-TCAGTCACGTAATGTC
1 TAAAAACT-AGTCACGTAATGTC
966421 T-AAAACTAGTCACGTAATGTC
1 TAAAAACTAGTCACGTAATGTC
* **
966442 TAAAAACTAGTCTCGTAATACC
1 TAAAAACTAGTCACGTAATGTC
966464 TAAAAACTAGT
1 TAAAAACTAGT
966475 GACACAATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
21 19 0.39
22 30 0.61
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (22 bp):
TAAAAACTAGTCACGTAATGTC
Found at i:966907 original size:28 final size:29
Alignment explanation
Indices: 966860--966915 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
966850 GATTAAAAAT
966860 AATTAAATTATAATGAAGGA-TATTTTTG
1 AATTAAATTATAATGAAGGATTATTTTTG
966888 AATTAAATT-T-ATGAGGAGGATTATTTTT
1 AATTAAATTATAATGA--AGGATTATTTTT
966916 CACAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 4 0.16
27 1 0.04
28 13 0.52
29 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (29 bp):
AATTAAATTATAATGAAGGATTATTTTTG
Found at i:967280 original size:16 final size:15
Alignment explanation
Indices: 967237--967294 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
967227 TTCCCCATCC
*
967237 ATTTCCCTCTAAAA-
1 ATTTCCCTCCAAAAG
* *
967251 TTTTCCCTCCAAAGG
1 ATTTCCCTCCAAAAG
967266 ATTTCCCTCCAAAAG
1 ATTTCCCTCCAAAAG
*
967281 ATTTTCCTCCAAAA
1 ATTTCCCTCCAAAA
967295 CCATTTGGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 11 0.30
15 26 0.70
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (15 bp):
ATTTCCCTCCAAAAG
Found at i:967300 original size:16 final size:15
Alignment explanation
Indices: 967236--967300 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
967226 GTTCCCCATC
*
967236 CATTTCCCTCTAAAA
1 CATTTCCCTCCAAAA
* *
967251 -TTTTCCCTCCAAAG
1 CATTTCCCTCCAAAA
*
967265 GATTTCCCTCCAAAA
1 CATTTCCCTCCAAAA
* *
967280 GATTTTCCTCCAAAA
1 CATTTCCCTCCAAAA
967295 CCATTT
1 -CATTT
967301 GGGAGGGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 11 0.27
15 26 0.63
16 4 0.10
ACGTcount: A:0.29, C:0.32, G:0.05, T:0.34
Consensus pattern (15 bp):
CATTTCCCTCCAAAA
Found at i:967378 original size:27 final size:27
Alignment explanation
Indices: 967348--967400 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
967338 GGGAAATCCC
967348 TACATGGGTCTTGGTGGGCTGGCACCA
1 TACATGGGTCTTGGTGGGCTGGCACCA
967375 TACATGGGTCTTGGTGGGCTGGCACC
1 TACATGGGTCTTGGTGGGCTGGCACC
967401 CTCTTGGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.13, C:0.23, G:0.38, T:0.26
Consensus pattern (27 bp):
TACATGGGTCTTGGTGGGCTGGCACCA
Found at i:967447 original size:14 final size:14
Alignment explanation
Indices: 967428--967456 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
967418 GGGTCTGGGC
967428 TGTGGCCCGTGACA
1 TGTGGCCCGTGACA
967442 TGTGGCCCGTGACA
1 TGTGGCCCGTGACA
967456 T
1 T
967457 AATGCTACGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.28, G:0.34, T:0.24
Consensus pattern (14 bp):
TGTGGCCCGTGACA
Found at i:970752 original size:76 final size:77
Alignment explanation
Indices: 970675--970977 Score: 275
Period size: 80 Copynumber: 3.9 Consensus size: 77
970665 AATATAATTA
* *
970675 TTAGAGATAATTTAAATGACCAATAATTAA-ATTTTAATT-GTCAAAATATAAGATTATCTCCAA
1 TTAGAGATAAATTAAATGACCAATAATTAATA-TTTGATTGGTCAAAATATAA-ATTATCT-CAA
*
970738 AT-ATTTGGATTTAT
63 ATAATTTAGATTTAT
** *
970752 TTAGAG-TAAATTGGATGA-C-A-AATCTAATATTTGATTGGTCAAAATATAAATATTATCTCTA
1 TTAGAGATAAATTAAATGACCAATAAT-TAATATTTGATTGGTCAAAATAT-AA-ATTATCTCAA
970813 ATAATTTAGATTTAT
63 ATAATTTAGATTTAT
* * **
970828 TTAGAGATAAATGATATGACCAATAGCTAATATTTGATTGGTCAAAATATAAATTATTATCTCTA
1 TTAGAGATAAATTAAATGACCAATAATTAATATTTGATTGGTCAAAATAT-AA--ATTATCTC-A
970893 AATAATTTAGAATTTAT
62 AATAATTTAG-ATTTAT
* * ** *
970910 TTAGAG-TAAATT-GATGAACAATAGCTAATATTTGATTGGTCAAAATGA-ATATTATCTCTAAA
1 TTAGAGATAAATTAAATGACCAATAATTAATATTTGATTGGTCAAAAT-ATAAATTATCTC-AAA
*
970972 TTATTT
64 TAATTT
970978 TGAGAGTAAA
Statistics
Matches: 195, Mismatches: 18, Indels: 26
0.82 0.08 0.11
Matches are distributed among these distances:
73 3 0.02
74 10 0.05
75 16 0.08
76 35 0.18
77 32 0.16
78 1 0.01
79 28 0.14
80 42 0.22
81 16 0.08
82 12 0.06
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (77 bp):
TTAGAGATAAATTAAATGACCAATAATTAATATTTGATTGGTCAAAATATAAATTATCTCAAATA
ATTTAGATTTAT
Found at i:970943 original size:80 final size:78
Alignment explanation
Indices: 970714--970977 Score: 355
Period size: 80 Copynumber: 3.4 Consensus size: 78
970704 AATTTTAATT
* * * *
970714 GTCAAAATAT-AAGATTATCTCCAAAT-ATTTGGATTTATTTAGAGTAAATTGGATG-ACAA-AT
1 GTCAAAATATAAATATTATCTCTAAATAATTTAGATTTATTTAGAGTAAATT-GATGAACAATAG
970775 CTAATATTTGATTG
65 CTAATATTTGATTG
*
970789 GTCAAAATATAAATATTATCTCT-AATAATTTAGATTTATTTAGAGATAAA-TGATATGACCAAT
1 GTCAAAATATAAATATTATCTCTAAATAATTTAGATTTATTTAGAG-TAAATTG--ATGAACAAT
970852 AGCTAATATTTGATTG
63 AGCTAATATTTGATTG
970868 GTCAAAATATAAATTATTATCTCTAAATAATTTAGAATTTATTTAGAGTAAATTGATGAACAATA
1 GTCAAAATATAAA-TATTATCTCTAAATAATTTAG-ATTTATTTAGAGTAAATTGATGAACAATA
970933 GCTAATATTTGATTG
64 GCTAATATTTGATTG
* *
970948 GTC-AAA-ATGAATATTATCTCTAAATTATTT
1 GTCAAAATATAAATATTATCTCTAAATAATTT
970978 TGAGAGTAAA
Statistics
Matches: 170, Mismatches: 8, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
75 14 0.08
76 28 0.16
77 25 0.15
78 7 0.04
79 31 0.18
80 37 0.22
81 14 0.08
82 14 0.08
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.40
Consensus pattern (78 bp):
GTCAAAATATAAATATTATCTCTAAATAATTTAGATTTATTTAGAGTAAATTGATGAACAATAGC
TAATATTTGATTG
Found at i:971326 original size:16 final size:16
Alignment explanation
Indices: 971307--971354 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
971297 TAACTTTAGA
971307 AGAAGTATATTGCAAT
1 AGAAGTATATTGCAAT
* **
971323 AGAATTATAATTTTAA-
1 AGAAGTAT-ATTGCAAT
971339 AGAAGTATATTGCAAT
1 AGAAGTATATTGCAAT
971355 TGGTATGCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
15 5 0.21
16 14 0.58
17 5 0.21
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (16 bp):
AGAAGTATATTGCAAT
Found at i:971345 original size:32 final size:33
Alignment explanation
Indices: 971292--971354 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
971282 TAGGTAAGAA
971292 AATTATAACTTTAGAAGAAGTATATTGCAATAG
1 AATTATAACTTTAGAAGAAGTATATTGCAATAG
*
971325 AATTATAATTTTA-AAGAAGTATATTGCAAT
1 AATTATAACTTTAGAAGAAGTATATTGCAAT
971355 TGGTATGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.37
Consensus pattern (33 bp):
AATTATAACTTTAGAAGAAGTATATTGCAATAG
Found at i:972011 original size:2 final size:2
Alignment explanation
Indices: 972004--972029 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
971994 TGTAAGAAAA
972004 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
972030 CCTACAAGCC
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:972272 original size:36 final size:35
Alignment explanation
Indices: 972221--972515 Score: 177
Period size: 36 Copynumber: 7.9 Consensus size: 35
972211 ACGTGATTTG
*
972221 TTATCCTCGGAGGGTGCTCTTTATAATAGCACTTA
1 TTATCCTTGGAGGGTGCTCTTTATAATAGCACTTA
* *
972256 TTAATCCTTGGGGGGTGCTCTTTAAAATAGCACACAATTTA
1 TT-ATCCTTGGAGGGTGCTCTTTATAATAG--CAC---TTA
* ** * *
972297 TTATCCTCGGATAGTACT-TTTATAATAGCAACTTG
1 TTATCCTTGGAGGGTGCTCTTTATAATAGC-ACTTA
* * *
972332 TTGATCTTTGG-GAGTGCTC-TTATACTAGCACACGATTCA
1 TT-ATCCTTGGAGGGTGCTCTTTATAATAG--CAC--TT-A
** * *
972371 TTATCCTTGGAAAAGTGCTCTTTGTAATAGCACTTG
1 TTATCCTTGG-AGGGTGCTCTTTATAATAGCACTTA
*
972407 TTGATCCTT-GAGAGGTGCTCTTTATACTAGCACACGATTCA
1 TT-ATCCTTGGAG-GGTGCTCTTTATAATAG--CAC--TT-A
* *
972448 TTATCCTTGGAGGGTGTTCTTTATAATAGCACTTG
1 TTATCCTTGGAGGGTGCTCTTTATAATAGCACTTA
*
972483 TTGATCCTTGG-GAGGTGCTCTTTATATTAGCAC
1 TT-ATCCTTGGAG-GGTGCTCTTTATAATAGCAC
972516 ATAATTTAGA
Statistics
Matches: 202, Mismatches: 31, Indels: 53
0.71 0.11 0.19
Matches are distributed among these distances:
35 23 0.11
36 77 0.38
37 10 0.05
38 20 0.10
39 14 0.07
40 41 0.20
41 17 0.08
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (35 bp):
TTATCCTTGGAGGGTGCTCTTTATAATAGCACTTA
Found at i:972285 original size:76 final size:76
Alignment explanation
Indices: 972193--972516 Score: 384
Period size: 76 Copynumber: 4.3 Consensus size: 76
972183 AAATTAAGGT
* ** ** * *
972193 GGTGCTCTTTACAATAGCACGTGATTTGTTATCCTCGGAGGGTGCTCTTTATAATAGCACTTATT
1 GGTGCTCTTTATAATAGCACACGATTCATTATCCTCGGAGAGTGCTCTTTATAATAGCACTTGTT
* *
972258 AATCCTTGGGG
66 GATCCTTGGGA
* * * * *
972269 GGTGCTCTTTAAAATAGCACACAATTTATTATCCTCGGATAGTACT-TTTATAATAGCAACTTGT
1 GGTGCTCTTTATAATAGCACACGATTCATTATCCTCGGAGAGTGCTCTTTATAATAGC-ACTTGT
*
972333 TGATCTTTGGGA
65 TGATCCTTGGGA
* * * *
972345 -GTGCTC-TTATACTAGCACACGATTCATTATCCTTGGAAAAGTGCTCTTTGTAATAGCACTTGT
1 GGTGCTCTTTATAATAGCACACGATTCATTATCCTCGG-AGAGTGCTCTTTATAATAGCACTTGT
*
972408 TGATCCTTGAGA
65 TGATCCTTGGGA
* * * *
972420 GGTGCTCTTTATACTAGCACACGATTCATTATCCTTGGAGGGTGTTCTTTATAATAGCACTTGTT
1 GGTGCTCTTTATAATAGCACACGATTCATTATCCTCGGAGAGTGCTCTTTATAATAGCACTTGTT
972485 GATCCTTGGGA
66 GATCCTTGGGA
*
972496 GGTGCTCTTTATATTAGCACA
1 GGTGCTCTTTATAATAGCACA
972517 TAATTTAGAA
Statistics
Matches: 215, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
74 25 0.12
75 39 0.18
76 121 0.56
77 30 0.14
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (76 bp):
GGTGCTCTTTATAATAGCACACGATTCATTATCCTCGGAGAGTGCTCTTTATAATAGCACTTGTT
GATCCTTGGGA
Found at i:972414 original size:151 final size:153
Alignment explanation
Indices: 972234--972516 Score: 392
Period size: 151 Copynumber: 1.9 Consensus size: 153
972224 TCCTCGGAGG
* * *
972234 GTGCTCTTTATAATAGCACTTATTAATCCTTGGGGGGTGCTCTTTAAAATAGCACACAATTTATT
1 GTGCTCTTTATAATAGCACTTATTAATCCTTGAGAGGTGCTCTTTAAAATAGCACACAATTCATT
* *
972299 ATCCTCGGATAGTACT-TTTATAATAGCAACTTGTTGATCTTTGGGA-GTGCTC-TTATACTAGC
66 ATCCTCGGAGAGTACTCTTTATAATAGC-ACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGC
972361 ACACGATTCATTATCCTTGGAAAA
130 ACACGATTCATTATCCTTGGAAAA
* * * * * *
972385 GTGCTCTTTGTAATAGCACTTGTTGATCCTTGAGAGGTGCTCTTTATACTAGCACACGATTCATT
1 GTGCTCTTTATAATAGCACTTATTAATCCTTGAGAGGTGCTCTTTAAAATAGCACACAATTCATT
* * ** *
972450 ATCCTTGGAGGGTGTTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATATTAGCA
66 ATCCTCGGAGAGTACTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCA
972515 CA
131 CA
972517 TAATTTAGAA
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
151 84 0.74
152 17 0.15
153 12 0.11
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (153 bp):
GTGCTCTTTATAATAGCACTTATTAATCCTTGAGAGGTGCTCTTTAAAATAGCACACAATTCATT
ATCCTCGGAGAGTACTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCA
CACGATTCATTATCCTTGGAAAA
Found at i:983166 original size:24 final size:24
Alignment explanation
Indices: 983139--983211 Score: 105
Period size: 23 Copynumber: 3.1 Consensus size: 24
983129 TCACCCTCGC
983139 CTTGATCACGAACTTCGCCTGTTG
1 CTTGATCACGAACTTCGCCTGTTG
*
983163 CTTGATCACGAACCTCGCC-GTTG
1 CTTGATCACGAACTTCGCCTGTTG
* *
983186 CTTTATCACGAACTT-TCCTGTTG
1 CTTGATCACGAACTTCGCCTGTTG
983209 CTT
1 CTT
983212 TATCTTCACC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 2 0.05
23 24 0.55
24 18 0.41
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.36
Consensus pattern (24 bp):
CTTGATCACGAACTTCGCCTGTTG
Found at i:983279 original size:18 final size:18
Alignment explanation
Indices: 983253--983295 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
983243 TAATCTCTGA
983253 AATGC-TCTCAATCTTCG
1 AATGCTTCTCAATCTTCG
* *
983270 AATGCTTCTCTATCTTTG
1 AATGCTTCTCAATCTTCG
983288 AATGCTTC
1 AATGCTTC
983296 CGAATGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.42
Consensus pattern (18 bp):
AATGCTTCTCAATCTTCG
Found at i:986338 original size:2 final size:2
Alignment explanation
Indices: 986331--986355 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
986321 TTGCGTACTT
986331 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
986356 TAAATTATTA
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:989142 original size:20 final size:21
Alignment explanation
Indices: 989117--989158 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
989107 CTCTTAAAGT
989117 AATTTAA-AAAAATAACTTAA
1 AATTTAACAAAAATAACTTAA
*
989137 AATTTAACTAAAATAACTTAA
1 AATTTAACAAAAATAACTTAA
989158 A
1 A
989159 GTAATCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTTAACAAAAATAACTTAA
Found at i:1001528 original size:53 final size:53
Alignment explanation
Indices: 1001464--1001572 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
1001454 GCTTCGGTGG
*
1001464 AAAGGTTAAGATTATGGGAAGAAAAAACTGAGAGTTTCGAAACTACAAACGAT
1 AAAGGTTAAGATTATGGGAAGAAAAAACTGAGAGTTTCAAAACTACAAACGAT
*
1001517 AAAGGTTAAGATTATGGGAAGAAAAAACTGAGAGTTTCAAAACTGCAAACGAT
1 AAAGGTTAAGATTATGGGAAGAAAAAACTGAGAGTTTCAAAACTACAAACGAT
1001570 AAA
1 AAA
1001573 TATGTATGCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.49, C:0.09, G:0.22, T:0.20
Consensus pattern (53 bp):
AAAGGTTAAGATTATGGGAAGAAAAAACTGAGAGTTTCAAAACTACAAACGAT
Found at i:1002795 original size:43 final size:43
Alignment explanation
Indices: 1002729--1002813 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
1002719 TACATTATCG
* **
1002729 ATTAGAAAAAATAAACATGGTTACAAACTTAAGTGTCAACACT
1 ATTAGAAAAAATAAAAAAAGTTACAAACTTAAGTGTCAACACT
* *
1002772 ATTAGGAAAAATAAAAAAAGTTACAAACTTAGGTGTCAACAC
1 ATTAGAAAAAATAAAAAAAGTTACAAACTTAAGTGTCAACAC
1002814 CATTCCCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.24
Consensus pattern (43 bp):
ATTAGAAAAAATAAAAAAAGTTACAAACTTAAGTGTCAACACT
Found at i:1005702 original size:25 final size:25
Alignment explanation
Indices: 1005676--1005853 Score: 151
Period size: 25 Copynumber: 7.1 Consensus size: 25
1005666 AAGGTAATGC
*
1005676 AATGCCATACAGATAA-AATTCACGC
1 AATGCCATACAGATAACAA-TCACGT
*
1005701 AATGCCATATAGATAACAATCACGT
1 AATGCCATACAGATAACAATCACGT
* **
1005726 AATGCCATACATATAACACCCACGT
1 AATGCCATACAGATAACAATCACGT
* *
1005751 AATGCCATACAAATAACAATCACAT
1 AATGCCATACAGATAACAATCACGT
* * **
1005776 AATGCCATACATATAACACTCACAC
1 AATGCCATACAGATAACAATCACGT
* ** * * * *
1005801 ACTTTCATACAAATAATAGTCATGT
1 AATGCCATACAGATAACAATCACGT
* * *
1005826 AATGCCTTATAGATAACAATCATGT
1 AATGCCATACAGATAACAATCACGT
1005851 AAT
1 AAT
1005854 AACCTATATA
Statistics
Matches: 122, Mismatches: 30, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
25 120 0.98
26 2 0.02
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (25 bp):
AATGCCATACAGATAACAATCACGT
Found at i:1005861 original size:25 final size:25
Alignment explanation
Indices: 1005820--1005874 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1005810 CAAATAATAG
*
1005820 TCATGTAATGCCTTATAGATAACAA
1 TCATGTAATACCTTATAGATAACAA
* *
1005845 TCATGTAATAACC-TATATATAACAG
1 TCATGTAAT-ACCTTATAGATAACAA
1005870 TCATG
1 TCATG
1005875 CAATGCCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (25 bp):
TCATGTAATACCTTATAGATAACAA
Found at i:1008934 original size:16 final size:17
Alignment explanation
Indices: 1008904--1008936 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1008894 TTCTTCTTTT
1008904 TATTTATATTATTTAAC
1 TATTTATATTATTTAAC
1008921 TATTTATA-TATTTAAC
1 TATTTATATTATTTAAC
1008937 CATTGTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTATATTATTTAAC
Found at i:1010656 original size:15 final size:16
Alignment explanation
Indices: 1010625--1010669 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
1010615 TTTTATTTTG
1010625 TATTAACTTTATAAAAAT
1 TATTAAC-TTAT-AAAAT
1010643 TA-TAACTTATAAAAT
1 TATTAACTTATAAAAT
1010658 TATTAA-TTATAA
1 TATTAACTTATAA
1010670 TAAATATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 13 0.50
16 7 0.27
17 4 0.15
18 2 0.08
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
TATTAACTTATAAAAT
Found at i:1023483 original size:6 final size:6
Alignment explanation
Indices: 1023472--1023505 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1023462 GAGTGCTATT
*
1023472 GCCAAA GCCAAA GCCAAA GCCAAA GCCAGA GCCA
1 GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GCCA
1023506 TTGGGGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.35, G:0.21, T:0.00
Consensus pattern (6 bp):
GCCAAA
Found at i:1031723 original size:217 final size:217
Alignment explanation
Indices: 1031330--1031752 Score: 648
Period size: 217 Copynumber: 1.9 Consensus size: 217
1031320 CTGTAAGCAC
* *
1031330 ACAAAGTCATAAGGCATGGGACTCCACTCTACCTCTAGTCAAATCAACGTTCAAAATTCATCCCT
1 ACAAAGTCATAAGGCATGGGACTCCACTCAACCTCAAGTCAAATCAACGTTCAAAATTCATCCCT
* * *
1031395 TAGATGGAACACATATCCAAAAATCATGCCATTGTGCTTATGACATTCCATACGTCTACATCAAA
66 TAGATGGAACACATACCCAAAAATCAGGCCATTGTGCTTATGACATTCCATACGTCCACATCAAA
** * * *
1031460 TCATATTCAAATTTAATGAGCTTTAGTCATCTCGAAGCTCAATATGATTTTAAGTGCTTTCAAAT
131 TCATATTCAAATTTAACAAGCTTCAGTCATCTCGAAGCTCAATATGATTCTAAGTGCCTTCAAAT
*
1031525 CTTTAAGGCATGATCTAGGCAT
196 CTCTAAGGCATGATCTAGGCAT
* * **
1031547 ACAAAGTCATAAGGGATGGGACTCCACTCAACCTCAAGTCAAATCAATGTTCGGAATTCATCCCT
1 ACAAAGTCATAAGGCATGGGACTCCACTCAACCTCAAGTCAAATCAACGTTCAAAATTCATCCCT
* *
1031612 TAGATGGAACACATACCCACAAATCAGGCCATTGTGCTTATGACATTCCATATGTCCACATCAAA
66 TAGATGGAACACATACCCAAAAATCAGGCCATTGTGCTTATGACATTCCATACGTCCACATCAAA
** * * *
1031677 TCATATTTGAATTTAACAAGCTTCAGTCATTTCTAAGCTTAATATGATTCTAAGTGCCTTCAAAT
131 TCATATTCAAATTTAACAAGCTTCAGTCATCTCGAAGCTCAATATGATTCTAAGTGCCTTCAAAT
1031742 CTCTAAGGCAT
196 CTCTAAGGCAT
1031753 CATCAAACAA
Statistics
Matches: 184, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
217 184 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (217 bp):
ACAAAGTCATAAGGCATGGGACTCCACTCAACCTCAAGTCAAATCAACGTTCAAAATTCATCCCT
TAGATGGAACACATACCCAAAAATCAGGCCATTGTGCTTATGACATTCCATACGTCCACATCAAA
TCATATTCAAATTTAACAAGCTTCAGTCATCTCGAAGCTCAATATGATTCTAAGTGCCTTCAAAT
CTCTAAGGCATGATCTAGGCAT
Found at i:1032528 original size:18 final size:19
Alignment explanation
Indices: 1032505--1032541 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1032495 AGTATTTATT
1032505 TCCTAGC-TTTCAAAAATA
1 TCCTAGCTTTTCAAAAATA
1032523 TCCTAGCTTTTCAAAAATA
1 TCCTAGCTTTTCAAAAATA
1032542 ACCAAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (19 bp):
TCCTAGCTTTTCAAAAATA
Found at i:1036866 original size:34 final size:35
Alignment explanation
Indices: 1036796--1036885 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 35
1036786 TAAAGCATTA
** *
1036796 AACCC-TAACAACACTTTTTCATAGGAACATGCAG
1 AACCCTTAACAATGCTTTTTCATAGGAACAAGCAG
* * *
1036830 AACCCTTAATAATG-TTTTTCATAGGACCAAGTAG
1 AACCCTTAACAATGCTTTTTCATAGGAACAAGCAG
**
1036864 AACTTTTAACAATGCTTTTTCA
1 AACCCTTAACAATGCTTTTTCA
1036886 CGGGAGTAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
34 33 0.73
35 12 0.27
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (35 bp):
AACCCTTAACAATGCTTTTTCATAGGAACAAGCAG
Found at i:1041157 original size:12 final size:12
Alignment explanation
Indices: 1041140--1041174 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1041130 CTAGATGAAG
1041140 CAAAATCATGTT
1 CAAAATCATGTT
*
1041152 CAAAATTCATATT
1 CAAAA-TCATGTT
1041165 CAAAATCATG
1 CAAAATCATG
1041175 GGTGAGCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (12 bp):
CAAAATCATGTT
Found at i:1047357 original size:22 final size:22
Alignment explanation
Indices: 1047332--1047377 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1047322 TGGAGTATGA
* *
1047332 CTCGAAACAAAAATATTGACAC
1 CTCGAAAAAAAAAGATTGACAC
1047354 CTCGAAAAAAAAAGATTGACAC
1 CTCGAAAAAAAAAGATTGACAC
1047376 CT
1 CT
1047378 ATTGGATGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (22 bp):
CTCGAAAAAAAAAGATTGACAC
Found at i:1054329 original size:34 final size:35
Alignment explanation
Indices: 1054291--1054364 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
1054281 TGTAATGTTG
* * *
1054291 TTTAAGTTACTGTTT-AGTTGTTTGTTTTTAGA-TA
1 TTTAAGTTACTATTTGAGATATTTGTTTTT-GATTA
*
1054325 TTTAAGTTGCTATTTGAGATATTTGTTTTTGATTA
1 TTTAAGTTACTATTTGAGATATTTGTTTTTGATTA
1054360 TTTAA
1 TTTAA
1054365 ATTTAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 15 0.44
35 19 0.56
ACGTcount: A:0.23, C:0.03, G:0.16, T:0.58
Consensus pattern (35 bp):
TTTAAGTTACTATTTGAGATATTTGTTTTTGATTA
Found at i:1065682 original size:58 final size:58
Alignment explanation
Indices: 1065616--1065728 Score: 183
Period size: 58 Copynumber: 1.9 Consensus size: 58
1065606 TTGTGGTTCC
*
1065616 TATTTTATTGTTAGTGGTAGTTTTTC-ATTTCAAGTTGTTGAAGGTTGTGTCTCCACCT
1 TATTTTATTGTTAGTGGTA-TTTTTCAATTTCAAGTTATTGAAGGTTGTGTCTCCACCT
* *
1065674 TATTTTATTGTTAGTGGTATTTTTCAATTTCATGTTATTGGAGGTTGTGTCTCCA
1 TATTTTATTGTTAGTGGTATTTTTCAATTTCAAGTTATTGAAGGTTGTGTCTCCA
1065729 ACTTTCCACT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
57 6 0.12
58 45 0.88
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (58 bp):
TATTTTATTGTTAGTGGTATTTTTCAATTTCAAGTTATTGAAGGTTGTGTCTCCACCT
Found at i:1066626 original size:19 final size:20
Alignment explanation
Indices: 1066602--1066643 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1066592 AGGCACTCTC
1066602 ACTCAAGCAC-AAAAATTGA
1 ACTCAAGCACAAAAAATTGA
1066621 ACTCAAGCACAAAAAATTGA
1 ACTCAAGCACAAAAAATTGA
1066641 ACT
1 ACT
1066644 TTATATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (20 bp):
ACTCAAGCACAAAAAATTGA
Found at i:1075270 original size:16 final size:15
Alignment explanation
Indices: 1075248--1075283 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
1075238 AAAAAGGATT
1075248 CTAGTCATGCCAGTA
1 CTAGTCATGCCAGTA
1075263 CATAGTCATGCCAGTA
1 C-TAGTCATGCCAGTA
1075279 CTAGT
1 CTAGT
1075284 TCAGTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (15 bp):
CTAGTCATGCCAGTA
Found at i:1080518 original size:30 final size:31
Alignment explanation
Indices: 1080453--1080520 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
1080443 GTGTCTGGTT
* *
1080453 TAAATTAAATAAAAATATATAATATAAAAAT
1 TAAATTGAATAAAAATATATAATATAAAAAC
1080484 TAAATTGAAT-AAAATAGTA-AA-ATAAGAAAC
1 TAAATTGAATAAAAATA-TATAATATAA-AAAC
1080514 TAAATTG
1 TAAATTG
1080521 TACAAAGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 4 0.12
30 18 0.55
31 11 0.33
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.29
Consensus pattern (31 bp):
TAAATTGAATAAAAATATATAATATAAAAAC
Found at i:1081477 original size:60 final size:60
Alignment explanation
Indices: 1081384--1081505 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
1081374 TGGATATTGT
* *
1081384 ACAAGGACTATACTTTTACTTAATTTTTGTTCTAGCAAAGCTTACAAGCCTTTTGAAAGG
1 ACAAGGACCATACTTTTACTTAATTTTTGTTCTAGCAAAGCTTACAAGCCTCTTGAAAGG
* * * *
1081444 ACAAGGACCATCCTTTTACTTTATTTTTGTTCTAGTAAAGGTTACAAGCCTCTTGAAAGG
1 ACAAGGACCATACTTTTACTTAATTTTTGTTCTAGCAAAGCTTACAAGCCTCTTGAAAGG
1081504 AC
1 AC
1081506 TAGGTGATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (60 bp):
ACAAGGACCATACTTTTACTTAATTTTTGTTCTAGCAAAGCTTACAAGCCTCTTGAAAGG
Found at i:1084930 original size:61 final size:61
Alignment explanation
Indices: 1084825--1085007 Score: 255
Period size: 61 Copynumber: 3.0 Consensus size: 61
1084815 ATATTTGATT
*
1084825 GAAAAAGGGGGACCTGAAGCCCCGATTTATATT-GCGTGGCGTGGGCAGTTCCCACGAGTAG
1 GAAAAAGGGGGACCTGAAGCCCCAATTTATATTAG-GTGGCGTGGGCAGTTCCCACGAGTAG
* * * *
1084886 GAAAAAAGGGGACCTAAAGCCCCAATTCATATTAGGTGGTGTGGGCAGTTCCCACGAGTAG
1 GAAAAAGGGGGACCTGAAGCCCCAATTTATATTAGGTGGCGTGGGCAGTTCCCACGAGTAG
* * *
1084947 G-TAAAGGGGGACCTGAAGCCCCAATTTATA-TATGGTGGCATGGGCAATTCCCACGAGTAG
1 GAAAAAGGGGGACCTGAAGCCCCAATTTATATTA-GGTGGCGTGGGCAGTTCCCACGAGTAG
1085007 G
1 G
1085008 TGATGGTGTC
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
59 2 0.02
60 50 0.46
61 55 0.51
62 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (61 bp):
GAAAAAGGGGGACCTGAAGCCCCAATTTATATTAGGTGGCGTGGGCAGTTCCCACGAGTAG
Found at i:1092401 original size:21 final size:21
Alignment explanation
Indices: 1092375--1092427 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1092365 CGTTCATGCA
1092375 ATTCATGACAAAGACTGATAC
1 ATTCATGACAAAGACTGATAC
* * *
1092396 ATTCATAACAAAGACTTATGC
1 ATTCATGACAAAGACTGATAC
*
1092417 ATTTATGACAA
1 ATTCATGACAA
1092428 GGATTGATGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (21 bp):
ATTCATGACAAAGACTGATAC
Found at i:1094978 original size:25 final size:25
Alignment explanation
Indices: 1094950--1095009 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
1094940 GTGGTCATAA
* * *
1094950 CCATGTATATCAACTCGTGGCCTAG
1 CCATGTATATCAACCCATGACCTAG
*
1094975 CCATGTATATCAACCCATGACCTTG
1 CCATGTATATCAACCCATGACCTAG
1095000 CCATGTATAT
1 CCATGTATAT
1095010 ACCATAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (25 bp):
CCATGTATATCAACCCATGACCTAG
Found at i:1097143 original size:25 final size:25
Alignment explanation
Indices: 1097112--1097166 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1097102 TCATGACTTG
*
1097112 ATCTTGATCATGAACTATACTTGAT
1 ATCTTGATCACGAACTATACTTGAT
*
1097137 ATCTTGATCACGAACTATATTTGAT
1 ATCTTGATCACGAACTATACTTGAT
1097162 ATCTT
1 ATCTT
1097167 TGTTTGAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (25 bp):
ATCTTGATCACGAACTATACTTGAT
Found at i:1097191 original size:48 final size:47
Alignment explanation
Indices: 1097139--1097240 Score: 168
Period size: 48 Copynumber: 2.1 Consensus size: 47
1097129 TACTTGATAT
* *
1097139 CTTGATCACGAACTATATTTGATATCTTTGTTTGAAGGGTCTTCACGA
1 CTTGATCACGAACTATATTTGATATCTTCGTTTCAAGGGTCTTCA-GA
*
1097187 CTTGATCACGAACTATATTTGATATCTTCGTTTCATGGGTCTTCAGA
1 CTTGATCACGAACTATATTTGATATCTTCGTTTCAAGGGTCTTCAGA
1097234 CTTGATC
1 CTTGATC
1097241 TCGATCACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
47 9 0.18
48 42 0.82
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (47 bp):
CTTGATCACGAACTATATTTGATATCTTCGTTTCAAGGGTCTTCAGA
Found at i:1097281 original size:76 final size:77
Alignment explanation
Indices: 1097195--1097338 Score: 202
Period size: 76 Copynumber: 1.9 Consensus size: 77
1097185 GACTTGATCA
* * *
1097195 CGAACTATATTTGATATCTTCG-TTTCATGGGTCTTCA-GACTTGATCTCGATCACAAACTATAC
1 CGAACTATATTTGATATCTTCGCTTT-AAGGGTCTTCACAACTTGATCTAGATCACAAACTATAC
1097258 TTGACCTTTATCG
65 TTGACCTTTATCG
* * * *
1097271 CGAACTATATTTGATATCTTTGCTTTAAGGGTCTTCACAACTTGGTCTAGATCACGAACTATATT
1 CGAACTATATTTGATATCTTCGCTTTAAGGGTCTTCACAACTTGATCTAGATCACAAACTATACT
1097336 TGA
66 TGA
1097339 TATCTTGATC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
76 31 0.53
77 28 0.47
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (77 bp):
CGAACTATATTTGATATCTTCGCTTTAAGGGTCTTCACAACTTGATCTAGATCACAAACTATACT
TGACCTTTATCG
Found at i:1097301 original size:124 final size:126
Alignment explanation
Indices: 1097058--1097344 Score: 366
Period size: 124 Copynumber: 2.2 Consensus size: 126
1097048 GCAACTTAAT
* * *
1097058 CTTGATCACGAACTATATATTTGATATCTTTGCTTTAAGGGTCTTCATGACTTGATCTTGATCAT
1 CTTGATCACGAAC--TATATTTGATATCTTCGCTTTAAGGGTCTTCATGACTTGATCTCGATCAC
* * *
1097123 GAACTATACTTGATATCTTGATCACGAACTATATTTGATATCTTTGTTTGAAGGGTCTTCACGA
64 AAACTATACTTGA-ACCTTGATCACGAACTATATTTGATATCTTTGTTTGAAGGGTCTTCACAA
*
1097187 CTTGATCACGAACTATATTTGATATCTTCG-TTTCATGGGTCTTCA-GACTTGATCTCGATCACA
1 CTTGATCACGAACTATATTTGATATCTTCGCTTT-AAGGGTCTTCATGACTTGATCTCGATCACA
* *
1097250 AACTATACTTG-ACCTTTATCGCGAACTATATTTGATATCTTTGCTTT-AAGGGTCTTCACAA
65 AACTATACTTGAACCTTGATCACGAACTATATTTGATATCTTTG-TTTGAAGGGTCTTCACAA
1097311 CTTGGTCTAGATCACGAACTATATTTGATATCTT
1 C----T-T-GATCACGAACTATATTTGATATCTT
1097345 GATCATGACC
Statistics
Matches: 141, Mismatches: 9, Indels: 15
0.85 0.05 0.09
Matches are distributed among these distances:
124 43 0.30
125 3 0.02
126 29 0.21
127 26 0.18
128 1 0.01
129 14 0.10
130 25 0.18
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (126 bp):
CTTGATCACGAACTATATTTGATATCTTCGCTTTAAGGGTCTTCATGACTTGATCTCGATCACAA
ACTATACTTGAACCTTGATCACGAACTATATTTGATATCTTTGTTTGAAGGGTCTTCACAA
Found at i:1097366 original size:25 final size:25
Alignment explanation
Indices: 1097338--1097491 Score: 128
Period size: 25 Copynumber: 5.8 Consensus size: 25
1097328 ACTATATTTG
*
1097338 ATATCTTGATCATGACCTTCGTTTA
1 ATATCTTGATCATGAACTTCGTTTA
* *
1097363 ATATCTTGATCATGAACTTTGCTTA
1 ATATCTTGATCATGAACTTCGTTTA
* *
1097388 ATATCTTGATTATGAACTTCATTGTTGCTTG
1 ATATCTTGATCATGAACTTC---G-T--TTA
** *
1097419 ATATCTTGATCATGAACTTCACTTG
1 ATATCTTGATCATGAACTTCGTTTA
*
1097444 ATATCTTGATCACGAACTTCGTTACTA
1 ATATCTTGATCATGAACTTCGTT--TA
* *
1097471 GATATCTTGATTACGAACTTC
1 -ATATCTTGATCATGAACTTC
1097492 ACTTGGTATC
Statistics
Matches: 105, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
25 63 0.60
27 1 0.01
28 20 0.19
31 21 0.20
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (25 bp):
ATATCTTGATCATGAACTTCGTTTA
Found at i:1097423 original size:31 final size:31
Alignment explanation
Indices: 1097360--1097439 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
1097350 TGACCTTCGT
1097360 TTAATATCTTGATCATGAA---C--T-TTGC
1 TTAATATCTTGATCATGAACTTCATTGTTGC
*
1097385 TTAATATCTTGATTATGAACTTCATTGTTGC
1 TTAATATCTTGATCATGAACTTCATTGTTGC
*
1097416 TTGATATCTTGATCATGAACTTCA
1 TTAATATCTTGATCATGAACTTCA
1097440 CTTGATATCT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 18 0.39
28 1 0.02
30 1 0.02
31 26 0.57
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (31 bp):
TTAATATCTTGATCATGAACTTCATTGTTGC
Found at i:1097432 original size:81 final size:83
Alignment explanation
Indices: 1097335--1097492 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 83
1097325 CGAACTATAT
* ** * *
1097335 TTGATATCTTGATCATGACCTTCGTTTAATATCTTGATCATGAACTTTGCT-TA-ATATCTTGAT
1 TTGATATCTTGATCATGAACTTCACTTAATATCTTGATCACGAACTTCGCTATAGATATCTTGAT
*
1097398 TATGAACTTCATTGTTGC
66 TACGAACTTCATTGTTGC
* *
1097416 TTGATATCTTGATCATGAACTTCACTTGATATCTTGATCACGAACTTCGTTACTAGATATCTTGA
1 TTGATATCTTGATCATGAACTTCACTTAATATCTTGATCACGAACTTCGCTA-TAGATATCTTGA
1097481 TTACGAACTTCA
65 TTACGAACTTCA
1097493 CTTGGTATCT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 44 0.67
83 2 0.03
84 20 0.30
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (83 bp):
TTGATATCTTGATCATGAACTTCACTTAATATCTTGATCACGAACTTCGCTATAGATATCTTGAT
TACGAACTTCATTGTTGC
Found at i:1099395 original size:29 final size:29
Alignment explanation
Indices: 1099363--1099456 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
1099353 GAAAAGATAC
*
1099363 AAGAGAAGAAGTTGTATGTGAACAAGTAT
1 AAGAGAAGAAGTTGTATGTGAACAAGAAT
* ** * * *
1099392 AAGAGAAGAAATTGTACATGAATAGGAAC
1 AAGAGAAGAAGTTGTATGTGAACAAGAAT
* * *
1099421 AAGAGAATAAGGTGTATGTGAACAAGCAT
1 AAGAGAAGAAGTTGTATGTGAACAAGAAT
*
1099450 ATGAGAA
1 AAGAGAA
1099457 CAAGATAAGA
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.48, C:0.05, G:0.27, T:0.20
Consensus pattern (29 bp):
AAGAGAAGAAGTTGTATGTGAACAAGAAT
Found at i:1099738 original size:35 final size:35
Alignment explanation
Indices: 1099699--1099813 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
1099689 CTGCTTATTA
* * *
1099699 TAGTTGTTCTGCATTAAA-TAGTACTTCACTTGCTC
1 TAGTTGTTCTACA-TAAAGTAGCACTTCACTTGTTC
* *
1099734 TAGTTGTTCTACGTAAAGTAGCGCATT-ACTTGTTC
1 TAGTTGTTCTACATAAAGTAGCAC-TTCACTTGTTC
* *
1099769 TAGTTGTTCTACATAAAGTAGCACTTCACTTATTT
1 TAGTTGTTCTACATAAAGTAGCACTTCACTTGTTC
1099804 TAGTTGTTCT
1 TAGTTGTTCT
1099814 TTGTACAACT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
34 6 0.09
35 60 0.88
36 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.43
Consensus pattern (35 bp):
TAGTTGTTCTACATAAAGTAGCACTTCACTTGTTC
Found at i:1104315 original size:5 final size:6
Alignment explanation
Indices: 1104300--1104330 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1104290 TTTTGATCGT
*
1104300 TTTTTC TTTTTC TTTTTC TTTTTC TTCTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T
1104331 CAGGCGAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:1108171 original size:39 final size:39
Alignment explanation
Indices: 1108087--1108170 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
1108077 TATATTGTGT
1108087 ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAGA
1 ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAGA
1108126 ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAG-
1 ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAGA
1108164 ACAAAAA
1 ACAAAAA
1108171 AACATGTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 7 0.16
39 38 0.84
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36
Consensus pattern (39 bp):
ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAGA
Found at i:1108191 original size:29 final size:28
Alignment explanation
Indices: 1108143--1108280 Score: 141
Period size: 29 Copynumber: 4.8 Consensus size: 28
1108133 TGACAGCTTT
*
1108143 AACATGTTTGTTTTAATTTAGACAAAAA
1 AACATGTTTGTCTTAATTTAGACAAAAA
* * *
1108171 AACATGTTTGGTATTCATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAAAA
*
1108200 AATATGTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAA-AAA
* * * * *
1108230 AATATTTTTTATCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAAAA
*
1108259 AACATGTTTGTCTCAATTTAGA
1 AACATGTTTGTCTTAATTTAGA
1108281 TAAGATAAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
28 31 0.34
29 35 0.39
30 12 0.13
31 12 0.13
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAAAA
Found at i:1108259 original size:59 final size:58
Alignment explanation
Indices: 1108143--1108305 Score: 195
Period size: 59 Copynumber: 2.8 Consensus size: 58
1108133 TGACAGCTTT
* * * ** * * *
1108143 AACATGTTTGTTTTAATTTAGACAA-AAAAACATGTTTGGTATTCATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
*
1108200 AATATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
* *
1108259 AACATGTTTGTCTCAATTTAGATAAGATAAAATA-TTTTTATCTTAAT
1 AACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTTATCTTAAT
1108306 TAAAGATAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 17 0.19
58 26 0.29
59 48 0.53
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
Found at i:1108871 original size:13 final size:13
Alignment explanation
Indices: 1108853--1108880 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1108843 GAAGAATAAG
1108853 TGCTAAACTTGTT
1 TGCTAAACTTGTT
1108866 TGCTAAACTTGTT
1 TGCTAAACTTGTT
1108879 TG
1 TG
1108881 ATCGAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.46
Consensus pattern (13 bp):
TGCTAAACTTGTT
Found at i:1112119 original size:29 final size:29
Alignment explanation
Indices: 1112073--1112166 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
1112063 GAAAAGGTGC
* *
1112073 AAGAGAAGAAGCTATACGTTAACAAGTAT
1 AAGAGAAGAAGCTGTACGTGAACAAGTAT
** * * *
1112102 AAGAGAAGAAATTGTACGTGAATAGGTAC
1 AAGAGAAGAAGCTGTACGTGAACAAGTAT
* * *
1112131 AAAAGAAGAAGGTGTATGTGAACAAGTAT
1 AAGAGAAGAAGCTGTACGTGAACAAGTAT
*
1112160 ACGAGAA
1 AAGAGAA
1112167 CAAGATAAGA
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.48, C:0.07, G:0.26, T:0.19
Consensus pattern (29 bp):
AAGAGAAGAAGCTGTACGTGAACAAGTAT
Found at i:1112377 original size:18 final size:18
Alignment explanation
Indices: 1112334--1112377 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1112324 TCATTTAAGT
* **
1112334 GAAGTAGTTATTCTATTT
1 GAAGTAGTTATTCCATAC
*
1112352 GAAATAGTTATTCCATAC
1 GAAGTAGTTATTCCATAC
1112370 GAAGTAGT
1 GAAGTAGT
1112378 ACTTTACTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (18 bp):
GAAGTAGTTATTCCATAC
Found at i:1112445 original size:35 final size:35
Alignment explanation
Indices: 1112374--1112446 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
1112364 CCATACGAAG
* * *** *
1112374 TAGTACTTTACTTATTTTAGTTGTTTTGCATTAAA
1 TAGTACTTCACTTATTTTAGCTGTTACACATGAAA
1112409 TAGTACTTCACTTATTTTAGCTGTTACACATGAAA
1 TAGTACTTCACTTATTTTAGCTGTTACACATGAAA
1112444 TAG
1 TAG
1112447 CGCATCATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (35 bp):
TAGTACTTCACTTATTTTAGCTGTTACACATGAAA
Found at i:1115572 original size:2 final size:2
Alignment explanation
Indices: 1115565--1115594 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1115555 GAGGGGTTAT
1115565 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
1115595 CACATATTAT
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):
TA
Found at i:1119502 original size:52 final size:52
Alignment explanation
Indices: 1119445--1119575 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 52
1119435 AATATAGTGT
* *
1119445 ATAACATCATGTGCATAG-GCTGTAATAAGCCACAACATCATGTGCAT-AGCGT
1 ATAACATCATGTGCATAGTG-TGTAACAAGCCACAACATCATGTGCATGA-CGC
* * * * * *
1119497 GTAACATCATTTGCATTGTGTGTAACACGCCATAACATTATGTGCATGACGC
1 ATAACATCATGTGCATAGTGTGTAACAAGCCACAACATCATGTGCATGACGC
*
1119549 ATAACATCATGTGCATGGTGTGTAACA
1 ATAACATCATGTGCATAGTGTGTAACA
1119576 TCATGTGCAC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
52 64 0.97
53 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (52 bp):
ATAACATCATGTGCATAGTGTGTAACAAGCCACAACATCATGTGCATGACGC
Found at i:1119504 original size:21 final size:21
Alignment explanation
Indices: 1119478--1119523 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1119468 AATAAGCCAC
1119478 AACATCATGTGCATAGCGTGT
1 AACATCATGTGCATAGCGTGT
* * *
1119499 AACATCATTTGCATTGTGTGT
1 AACATCATGTGCATAGCGTGT
1119520 AACA
1 AACA
1119524 CGCCATAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (21 bp):
AACATCATGTGCATAGCGTGT
Found at i:1119742 original size:21 final size:21
Alignment explanation
Indices: 1119702--1119746 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1119692 CACATCACAT
*
1119702 CATCATGTGCATGGCATGTAA
1 CATCATGTGCATAGCATGTAA
**
1119723 CATCATGTGCATAGTGTGTAA
1 CATCATGTGCATAGCATGTAA
1119744 CAT
1 CAT
1119747 GTCAAAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (21 bp):
CATCATGTGCATAGCATGTAA
Found at i:1119756 original size:31 final size:31
Alignment explanation
Indices: 1119721--1119807 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
1119711 CATGGCATGT
1119721 AACATCATGTGCATAGTGTGTAACATGTCAA
1 AACATCATGTGCATAGTGTGTAACATGTCAA
* * * *
1119752 AACATTATGTGCATAGTTTGTAACACGTCAC
1 AACATCATGTGCATAGTGTGTAACATGTCAA
* * *
1119783 ATCATC-TGTGCATGGAGTGTAACAT
1 AACATCATGTGCATAGTGTGTAACAT
1119808 CATGTGCATA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
30 15 0.33
31 31 0.67
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (31 bp):
AACATCATGTGCATAGTGTGTAACATGTCAA
Found at i:1119774 original size:52 final size:52
Alignment explanation
Indices: 1119659--1119776 Score: 119
Period size: 52 Copynumber: 2.3 Consensus size: 52
1119649 CACCTTTCAA
* * * * * *
1119659 CATAGTGTATAACATCAGGTGCATAGTTTGTTACACATCACATCATCATGTG
1 CATAGTATGTAACATCAGGTGCATAGTGTGTAACACATCAAAACATCATGTG
* * * ** *
1119711 CATGGCATGTAACATCATGTGCATAGTGTGTAACATGTCAAAACATTATGTG
1 CATAGTATGTAACATCAGGTGCATAGTGTGTAACACATCAAAACATCATGTG
*
1119763 CATAGTTTGTAACA
1 CATAGTATGTAACA
1119777 CGTCACATCA
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (52 bp):
CATAGTATGTAACATCAGGTGCATAGTGTGTAACACATCAAAACATCATGTG
Found at i:1119817 original size:51 final size:52
Alignment explanation
Indices: 1119752--1119877 Score: 166
Period size: 51 Copynumber: 2.4 Consensus size: 52
1119742 AACATGTCAA
* * * *
1119752 AACATTATGTGCATAGTTTGTAACACGTCACATCATC-TGTGCATGGA-GTGT
1 AACATCATGTGCATAGTGTGTAACACGTCAAAACATCATGTGCAT-GACGTGT
* *
1119803 AACATCATGTGCATAGTGTATAACACTTCAAAACATCATGTGCATGACGTGT
1 AACATCATGTGCATAGTGTGTAACACGTCAAAACATCATGTGCATGACGTGT
*
1119855 AATATCATGTGCATAGTGTGTAA
1 AACATCATGTGCATAGTGTGTAA
1119878 TATCATGTGC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
51 33 0.51
52 32 0.49
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (52 bp):
AACATCATGTGCATAGTGTGTAACACGTCAAAACATCATGTGCATGACGTGT
Found at i:1119818 original size:82 final size:83
Alignment explanation
Indices: 1119669--1119847 Score: 274
Period size: 82 Copynumber: 2.2 Consensus size: 83
1119659 CATAGTGTAT
* *
1119669 AACATCAGGTGCATAGTTTGTTACACATCACATCATCATGTGCATGGCATGTAACATCATGTGCA
1 AACATCATGTGCATAGTTTGTAACACATCACATCATCATGTGCATGGCATGTAACATCATGTGCA
*
1119734 TAGTGTGTAACA-TGTCAA
66 TAGTGTATAACACT-TCAA
* *
1119752 AACATTATGTGCATAGTTTGTAACACGTCACATCATC-TGTGCATGG-AGTGTAACATCATGTGC
1 AACATCATGTGCATAGTTTGTAACACATCACATCATCATGTGCATGGCA-TGTAACATCATGTGC
1119815 ATAGTGTATAACACTTCAA
65 ATAGTGTATAACACTTCAA
1119834 AACATCATGTGCAT
1 AACATCATGTGCAT
1119848 GACGTGTAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
81 1 0.01
82 53 0.60
83 34 0.39
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (83 bp):
AACATCATGTGCATAGTTTGTAACACATCACATCATCATGTGCATGGCATGTAACATCATGTGCA
TAGTGTATAACACTTCAA
Found at i:1119822 original size:19 final size:19
Alignment explanation
Indices: 1119785--1119822 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1119775 CACGTCACAT
1119785 CATCTGTGCATGGAGTGTAA
1 CATCTGTGCAT-GAGTGTAA
1119805 CATCATGTGCAT-AGTGTA
1 CATC-TGTGCATGAGTGTA
1119823 TAACACTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (19 bp):
CATCTGTGCATGAGTGTAA
Found at i:1119826 original size:21 final size:20
Alignment explanation
Indices: 1119785--1119827 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1119775 CACGTCACAT
* *
1119785 CATCTGTGCATGGAGTGTAA
1 CATCTGTGCATAGAGTATAA
*
1119805 CATCATGTGCATAGTGTATAA
1 CATC-TGTGCATAGAGTATAA
1119826 CA
1 CA
1119828 CTTCAAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (20 bp):
CATCTGTGCATAGAGTATAA
Found at i:1119863 original size:21 final size:22
Alignment explanation
Indices: 1119837--1119930 Score: 117
Period size: 21 Copynumber: 4.5 Consensus size: 22
1119827 ACTTCAAAAC
*
1119837 ATCATGTGCATGACGTGTAA-T
1 ATCATGTGCATGATGTGTAACT
1119858 ATCATGTGCAT-AGTGTGTAA-T
1 ATCATGTGCATGA-TGTGTAACT
*
1119879 ATCATGTGCATGGTGTGTAACT
1 ATCATGTGCATGATGTGTAACT
*
1119901 -TCATGTGCATGGTGTGTAACT
1 ATCATGTGCATGATGTGTAACT
1119922 -TCATGTGCA
1 ATCATGTGCA
1119931 CTTGATATAA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
20 1 0.01
21 66 0.97
22 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (22 bp):
ATCATGTGCATGATGTGTAACT
Done.